[pauljohn@localhost ~]$ wget http://dl.fedoraproject.org/pub/epel/6/SRPMS/R-3.0.1-2.el6.src.rpm bash: wget: command not found... [pauljohn@localhost ~]$ sudo yum install wget [sudo] password for pauljohn: Loaded plugins: langpacks, presto, refresh-packagekit updates/metalink | 20 kB 00:00 updates | 4.6 kB 00:00 updates/primary_db | 6.8 MB 00:01 updates/group_gz | 446 kB 00:00 Resolving Dependencies --> Running transaction check ---> Package wget.i686 0:1.13.4-7.fc17 will be installed --> Finished Dependency Resolution Dependencies Resolved ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: wget i686 1.13.4-7.fc17 updates 499 k Transaction Summary ================================================================================ Install 1 Package Total download size: 499 k Installed size: 1.8 M Is this ok [y/N]: y Downloading Packages: wget-1.13.4-7.fc17.i686.rpm | 499 kB 00:00 Running Transaction Check Running Transaction Test Transaction Test Succeeded Running Transaction Installing : wget-1.13.4-7.fc17.i686 1/1 Verifying : wget-1.13.4-7.fc17.i686 1/1 Installed: wget.i686 0:1.13.4-7.fc17 Complete! [pauljohn@localhost ~]$ wget http://dl.fedoraproject.org/pub/epel/6/SRPMS/R-3.0.1-2.el6.src.rpm --2013-08-06 17:17:48-- http://dl.fedoraproject.org/pub/epel/6/SRPMS/R-3.0.1-2.el6.src.rpm Resolving dl.fedoraproject.org (dl.fedoraproject.org)... 209.132.181.27, 209.132.181.23, 209.132.181.24, ... Connecting to dl.fedoraproject.org (dl.fedoraproject.org)|209.132.181.27|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 25530350 (24M) [application/x-rpm] Saving to: `R-3.0.1-2.el6.src.rpm' 100%[======================================>] 25,530,350 607K/s in 45s 2013-08-06 17:18:33 (554 KB/s) - `R-3.0.1-2.el6.src.rpm' saved [25530350/25530350] [pauljohn@localhost ~]$ rpm -ivh R-3.0.1-2.el6.src.rpm warning: R-3.0.1-2.el6.src.rpm: Header V3 RSA/SHA256 Signature, key ID 0608b895: NOKEY 1:R warning: user mockbuild does not exist - using root warning: group mockbuild does not exist - using root ########################################### [100%] warning: user mockbuild does not exist - using root warning: group mockbuild does not exist - using root warning: user mockbuild does not exist - using root warning: group mockbuild does not exist - using root warning: user mockbuild does not exist - using root warning: group mockbuild does not exist - using root [pauljohn@localhost ~]$ cd LinuxDownloads/redhat/SPECS/ [pauljohn@localhost SPECS]$ ls build2.txt R.spec swarm-nojdk-2.4.1.spec-64 build.txt swarm-build-OK-fedora17i696.txt openbugs-3.2.2.spec swarm-nojdk-2.4.1.spec [pauljohn@localhost SPECS]$ rpmbuild -ba R.spec error: Failed build dependencies: libjpeg-devel is needed by R-3.0.1-2.fc17.i386 readline-devel is needed by R-3.0.1-2.fc17.i386 ncurses-devel is needed by R-3.0.1-2.fc17.i386 blas >= 3.0 is needed by R-3.0.1-2.fc17.i386 java-1.5.0-gcj is needed by R-3.0.1-2.fc17.i386 lapack-devel is needed by R-3.0.1-2.fc17.i386 libSM-devel is needed by R-3.0.1-2.fc17.i386 libICE-devel is needed by R-3.0.1-2.fc17.i386 libXt-devel is needed by R-3.0.1-2.fc17.i386 libXmu-devel is needed by R-3.0.1-2.fc17.i386 cairo-devel is needed by R-3.0.1-2.fc17.i386 libtiff-devel is needed by R-3.0.1-2.fc17.i386 pango-devel is needed by R-3.0.1-2.fc17.i386 xz-devel is needed by R-3.0.1-2.fc17.i386 libicu-devel is needed by R-3.0.1-2.fc17.i386 /snip/ went to terminal several times to run yum because eshell hates sudo. Welcome to the Emacs shell ~/LinuxDownloads/redhat/SPECS $ yum install libICE-devel Loaded plugins: langpacks, presto, refresh-packagekit You need to be root to perform this command. ~/LinuxDownloads/redhat/SPECS $ sudo yum install libICE-devel Loaded plugins: langpacks, presto, refresh-packagekit Resolving Dependencies --> Running transaction check ---> Package libICE-devel.i686 0:1.0.8-1.fc17 will be installed --> Finished Dependency Resolution Dependencies Resolved ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: libICE-devel i686 1.0.8-1.fc17 fedora 48 k Transaction Summary ================================================================================ Install 1 Package Total download size: 48 k Installed size: 262 k Is this ok [y/N]: Exiting on user Command Your transaction was saved, rerun it with: yum load-transaction /tmp/yum_save_tx.2013-08-06.22-22.Q_ihsa.yumtx ~/LinuxDownloads/redhat/SPECS $ sudo yum install libXt-devel libXmu-devel cairo-devel libtiff-devel Loaded plugins: langpacks, presto, refresh-packagekit Resolving Dependencies --> Running transaction check ---> Package cairo-devel.i686 0:1.10.2-7.fc17 will be installed --> Processing Dependency: pkgconfig(pixman-1) >= 0.18.4 for package: cairo-devel-1.10.2-7.fc17.i686 --> Processing Dependency: pixman-devel >= 0.18.4 for package: cairo-devel-1.10.2-7.fc17.i686 --> Processing Dependency: pkgconfig(gobject-2.0) for package: cairo-devel-1.10.2-7.fc17.i686 --> Processing Dependency: pkgconfig(glib-2.0) for package: cairo-devel-1.10.2-7.fc17.i686 ---> Package libXmu-devel.i686 0:1.1.0-3.fc17 will be installed --> Processing Dependency: pkgconfig(xext) for package: libXmu-devel-1.1.0-3.fc17.i686 --> Processing Dependency: libXext-devel for package: libXmu-devel-1.1.0-3.fc17.i686 ---> Package libXt-devel.i686 0:1.1.2-2.fc17 will be installed --> Processing Dependency: pkgconfig(sm) for package: libXt-devel-1.1.2-2.fc17.i686 --> Processing Dependency: pkgconfig(ice) for package: libXt-devel-1.1.2-2.fc17.i686 ---> Package libtiff-devel.i686 0:3.9.7-2.fc17 will be installed --> Processing Dependency: libtiff = 3.9.7-2.fc17 for package: libtiff-devel-3.9.7-2.fc17.i686 --> Running transaction check ---> Package glib2-devel.i686 0:2.32.4-2.fc17 will be installed --> Processing Dependency: glib2 = 2.32.4-2.fc17 for package: glib2-devel-2.32.4-2.fc17.i686 ---> Package libICE-devel.i686 0:1.0.8-1.fc17 will be installed ---> Package libSM-devel.i686 0:1.2.1-1.fc17 will be installed ---> Package libXext-devel.i686 0:1.3.1-1.fc17 will be installed ---> Package libtiff.i686 0:3.9.5-3.fc17 will be updated ---> Package libtiff.i686 0:3.9.7-2.fc17 will be an update ---> Package pixman-devel.i686 0:0.28.0-1.fc17 will be installed --> Processing Dependency: pixman = 0.28.0-1.fc17 for package: pixman-devel-0.28.0-1.fc17.i686 --> Running transaction check ---> Package glib2.i686 0:2.32.1-1.fc17 will be updated ---> Package glib2.i686 0:2.32.4-2.fc17 will be an update ---> Package pixman.i686 0:0.24.4-2.fc17 will be updated ---> Package pixman.i686 0:0.28.0-1.fc17 will be an update --> Finished Dependency Resolution Dependencies Resolved ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: cairo-devel i686 1.10.2-7.fc17 fedora 579 k libXmu-devel i686 1.1.0-3.fc17 fedora 38 k libXt-devel i686 1.1.2-2.fc17 fedora 473 k libtiff-devel i686 3.9.7-2.fc17 updates 447 k Installing for dependencies: glib2-devel i686 2.32.4-2.fc17 updates 1.8 M libICE-devel i686 1.0.8-1.fc17 fedora 48 k libSM-devel i686 1.2.1-1.fc17 fedora 12 k libXext-devel i686 1.3.1-1.fc17 fedora 73 k pixman-devel i686 0.28.0-1.fc17 updates 18 k Updating for dependencies: glib2 i686 2.32.4-2.fc17 updates 1.9 M libtiff i686 3.9.7-2.fc17 updates 138 k pixman i686 0.28.0-1.fc17 updates 221 k Transaction Summary ================================================================================ Install 4 Packages (+5 Dependent packages) Upgrade ( 3 Dependent packages) Total download size: 5.8 M Is this ok [y/N]: Exiting on user Command Your transaction was saved, rerun it with: yum load-transaction /tmp/yum_save_tx.2013-08-06.22-23.lnTDcn.yumtx ~/LinuxDownloads/redhat/SPECS $ sudo yum -y install libXt-devel libXmu-devel cairo-devel libtiff-devel Loaded plugins: langpacks, presto, refresh-packagekit Resolving Dependencies --> Running transaction check ---> Package cairo-devel.i686 0:1.10.2-7.fc17 will be installed --> Processing Dependency: pkgconfig(pixman-1) >= 0.18.4 for package: cairo-devel-1.10.2-7.fc17.i686 --> Processing Dependency: pixman-devel >= 0.18.4 for package: cairo-devel-1.10.2-7.fc17.i686 --> Processing Dependency: pkgconfig(gobject-2.0) for package: cairo-devel-1.10.2-7.fc17.i686 --> Processing Dependency: pkgconfig(glib-2.0) for package: cairo-devel-1.10.2-7.fc17.i686 ---> Package libXmu-devel.i686 0:1.1.0-3.fc17 will be installed --> Processing Dependency: pkgconfig(xext) for package: libXmu-devel-1.1.0-3.fc17.i686 --> Processing Dependency: libXext-devel for package: libXmu-devel-1.1.0-3.fc17.i686 ---> Package libXt-devel.i686 0:1.1.2-2.fc17 will be installed --> Processing Dependency: pkgconfig(sm) for package: libXt-devel-1.1.2-2.fc17.i686 --> Processing Dependency: pkgconfig(ice) for package: libXt-devel-1.1.2-2.fc17.i686 ---> Package libtiff-devel.i686 0:3.9.7-2.fc17 will be installed --> Processing Dependency: libtiff = 3.9.7-2.fc17 for package: libtiff-devel-3.9.7-2.fc17.i686 --> Running transaction check ---> Package glib2-devel.i686 0:2.32.4-2.fc17 will be installed --> Processing Dependency: glib2 = 2.32.4-2.fc17 for package: glib2-devel-2.32.4-2.fc17.i686 ---> Package libICE-devel.i686 0:1.0.8-1.fc17 will be installed ---> Package libSM-devel.i686 0:1.2.1-1.fc17 will be installed ---> Package libXext-devel.i686 0:1.3.1-1.fc17 will be installed ---> Package libtiff.i686 0:3.9.5-3.fc17 will be updated ---> Package libtiff.i686 0:3.9.7-2.fc17 will be an update ---> Package pixman-devel.i686 0:0.28.0-1.fc17 will be installed --> Processing Dependency: pixman = 0.28.0-1.fc17 for package: pixman-devel-0.28.0-1.fc17.i686 --> Running transaction check ---> Package glib2.i686 0:2.32.1-1.fc17 will be updated ---> Package glib2.i686 0:2.32.4-2.fc17 will be an update ---> Package pixman.i686 0:0.24.4-2.fc17 will be updated ---> Package pixman.i686 0:0.28.0-1.fc17 will be an update --> Finished Dependency Resolution Dependencies Resolved ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: cairo-devel i686 1.10.2-7.fc17 fedora 579 k libXmu-devel i686 1.1.0-3.fc17 fedora 38 k libXt-devel i686 1.1.2-2.fc17 fedora 473 k libtiff-devel i686 3.9.7-2.fc17 updates 447 k Installing for dependencies: glib2-devel i686 2.32.4-2.fc17 updates 1.8 M libICE-devel i686 1.0.8-1.fc17 fedora 48 k libSM-devel i686 1.2.1-1.fc17 fedora 12 k libXext-devel i686 1.3.1-1.fc17 fedora 73 k pixman-devel i686 0.28.0-1.fc17 updates 18 k Updating for dependencies: glib2 i686 2.32.4-2.fc17 updates 1.9 M libtiff i686 3.9.7-2.fc17 updates 138 k pixman i686 0.28.0-1.fc17 updates 221 k Transaction Summary ================================================================================ Install 4 Packages (+5 Dependent packages) Upgrade ( 3 Dependent packages) Total download size: 5.8 M Downloading Packages: Setting up and reading Presto delta metadata updates/prestodelta | 1.3 MB 00:00 Processing delta metadata Download delta size: 499 k (1/3): glib2-2.32.1-1.fc17_2.32.4-2.fc17.i686.drpm | 285 kB 00:00 (2/3): libtiff-3.9.5-3.fc17_3.9.7-2.fc17.i686.drpm | 40 kB 00:00 (3/3): pixman-0.24.4-2.fc17_0.28.0-1.fc17.i686.drpm | 174 kB 00:00 Finishing rebuild of rpms, from deltarpms | 2.3 MB 00:03 Presto reduced the update size by 79% (from 2.3 M to 499 k). (1/9): cairo-devel-1.10.2-7.fc17.i686.rpm | 579 kB 00:00 (2/9): glib2-devel-2.32.4-2.fc17.i686.rpm | 1.8 MB 00:00 (3/9): libICE-devel-1.0.8-1.fc17.i686.rpm | 48 kB 00:00 (4/9): libSM-devel-1.2.1-1.fc17.i686.rpm | 12 kB 00:00 (5/9): libXext-devel-1.3.1-1.fc17.i686.rpm | 73 kB 00:00 (6/9): libXmu-devel-1.1.0-3.fc17.i686.rpm | 38 kB 00:00 (7/9): libXt-devel-1.1.2-2.fc17.i686.rpm | 473 kB 00:00 (8/9): libtiff-devel-3.9.7-2.fc17.i686.rpm | 447 kB 00:00 (9/9): pixman-devel-0.28.0-1.fc17.i686.rpm | 18 kB 00:00 -------------------------------------------------------------------------------- Total 1.4 MB/s | 3.5 MB 00:02 Running Transaction Check Running Transaction Test Transaction Test Succeeded Running Transaction Installing : libICE-devel-1.0.8-1.fc17.i686 1/15 Installing : libSM-devel-1.2.1-1.fc17.i686 2/15 Installing : libXt-devel-1.1.2-2.fc17.i686 3/15 Installing : libXext-devel-1.3.1-1.fc17.i686 4/15 Updating : libtiff-3.9.7-2.fc17.i686 5/15 Updating : pixman-0.28.0-1.fc17.i686 6/15 Installing : pixman-devel-0.28.0-1.fc17.i686 7/15 Updating : glib2-2.32.4-2.fc17.i686 8/15 Installing : libtiff-devel-3.9.7-2.fc17.i686 9/15 Installing : libXmu-devel-1.1.0-3.fc17.i686 10/15 Installing : glib2-devel-2.32.4-2.fc17.i686 11/15 Installing : cairo-devel-1.10.2-7.fc17.i686 12/15 Cleanup : libtiff-3.9.5-3.fc17.i686 13/15 Cleanup : pixman-0.24.4-2.fc17.i686 14/15 Cleanup : glib2-2.32.1-1.fc17.i686 15/15 Verifying : libXt-devel-1.1.2-2.fc17.i686 1/15 Verifying : cairo-devel-1.10.2-7.fc17.i686 2/15 Verifying : libXmu-devel-1.1.0-3.fc17.i686 3/15 Verifying : libtiff-devel-3.9.7-2.fc17.i686 4/15 Verifying : pixman-devel-0.28.0-1.fc17.i686 5/15 Verifying : glib2-devel-2.32.4-2.fc17.i686 6/15 Verifying : libSM-devel-1.2.1-1.fc17.i686 7/15 Verifying : glib2-2.32.4-2.fc17.i686 8/15 Verifying : pixman-0.28.0-1.fc17.i686 9/15 Verifying : libICE-devel-1.0.8-1.fc17.i686 10/15 Verifying : libXext-devel-1.3.1-1.fc17.i686 11/15 Verifying : libtiff-3.9.7-2.fc17.i686 12/15 Verifying : libtiff-3.9.5-3.fc17.i686 13/15 Verifying : pixman-0.24.4-2.fc17.i686 14/15 Verifying : glib2-2.32.1-1.fc17.i686 15/15 Installed: cairo-devel.i686 0:1.10.2-7.fc17 libXmu-devel.i686 0:1.1.0-3.fc17 libXt-devel.i686 0:1.1.2-2.fc17 libtiff-devel.i686 0:3.9.7-2.fc17 Dependency Installed: glib2-devel.i686 0:2.32.4-2.fc17 libICE-devel.i686 0:1.0.8-1.fc17 libSM-devel.i686 0:1.2.1-1.fc17 libXext-devel.i686 0:1.3.1-1.fc17 pixman-devel.i686 0:0.28.0-1.fc17 Dependency Updated: glib2.i686 0:2.32.4-2.fc17 libtiff.i686 0:3.9.7-2.fc17 pixman.i686 0:0.28.0-1.fc17 Complete! ~/LinuxDownloads/redhat/SPECS $ sudo yum -y install libXt-devel libXmu-devel cairo-devel libtiff-devel Loaded plugins: langpacks, presto, refresh-packagekit Package libXt-devel-1.1.2-2.fc17.i686 already installed and latest version Package libXmu-devel-1.1.0-3.fc17.i686 already installed and latest version Package cairo-devel-1.10.2-7.fc17.i686 already installed and latest version Package libtiff-devel-3.9.7-2.fc17.i686 already installed and latest version Nothing to do ~/LinuxDownloads/redhat/SPECS $ rpmbuild -ba R.spec error: Failed build dependencies: libjpeg-devel is needed by R-3.0.1-2.fc17.i386 readline-devel is needed by R-3.0.1-2.fc17.i386 ncurses-devel is needed by R-3.0.1-2.fc17.i386 blas >= 3.0 is needed by R-3.0.1-2.fc17.i386 java-1.5.0-gcj is needed by R-3.0.1-2.fc17.i386 lapack-devel is needed by R-3.0.1-2.fc17.i386 pango-devel is needed by R-3.0.1-2.fc17.i386 xz-devel is needed by R-3.0.1-2.fc17.i386 libicu-devel is needed by R-3.0.1-2.fc17.i386 ~/LinuxDownloads/redhat/SPECS $ sudo yum -y install ncurses-devel blas java lapack-devel pango-devel xz-devel libicu-devel Loaded plugins: langpacks, presto, refresh-packagekit Resolving Dependencies --> Running transaction check ---> Package blas.i686 0:3.4.2-2.fc17 will be installed ---> Package java-1.7.0-openjdk.i686 1:1.7.0.25-2.3.12.1.fc17 will be installed --> Processing Dependency: jpackage-utils >= 1.7.3-1jpp.2 for package: 1:java-1.7.0-openjdk-1.7.0.25-2.3.12.1.fc17.i686 --> Processing Dependency: xorg-x11-fonts-Type1 for package: 1:java-1.7.0-openjdk-1.7.0.25-2.3.12.1.fc17.i686 --> Processing Dependency: tzdata-java for package: 1:java-1.7.0-openjdk-1.7.0.25-2.3.12.1.fc17.i686 --> Processing Dependency: rhino for package: 1:java-1.7.0-openjdk-1.7.0.25-2.3.12.1.fc17.i686 ---> Package lapack-devel.i686 0:3.4.2-2.fc17 will be installed --> Processing Dependency: lapack(x86-32) = 3.4.2-2.fc17 for package: lapack-devel-3.4.2-2.fc17.i686 --> Processing Dependency: blas-devel(x86-32) = 3.4.2-2.fc17 for package: lapack-devel-3.4.2-2.fc17.i686 --> Processing Dependency: liblapacke.so.3 for package: lapack-devel-3.4.2-2.fc17.i686 --> Processing Dependency: liblapack.so.3 for package: lapack-devel-3.4.2-2.fc17.i686 ---> Package libicu-devel.i686 0:4.8.1.1-5.fc17 will be installed --> Processing Dependency: libicu = 4.8.1.1-5.fc17 for package: libicu-devel-4.8.1.1-5.fc17.i686 ---> Package ncurses-devel.i686 0:5.9-11.20130511.fc17 will be installed --> Processing Dependency: ncurses-libs(x86-32) = 5.9-11.20130511.fc17 for package: ncurses-devel-5.9-11.20130511.fc17.i686 --> Processing Dependency: libncurses++w.so.5 for package: ncurses-devel-5.9-11.20130511.fc17.i686 --> Processing Dependency: libncurses++.so.5 for package: ncurses-devel-5.9-11.20130511.fc17.i686 ---> Package pango-devel.i686 0:1.30.0-1.fc17 will be installed ---> Package xz-devel.i686 0:5.1.2-1alpha.fc17 will be installed --> Processing Dependency: xz-libs = 5.1.2-1alpha.fc17 for package: xz-devel-5.1.2-1alpha.fc17.i686 --> Running transaction check ---> Package blas-devel.i686 0:3.4.2-2.fc17 will be installed ---> Package jpackage-utils.i686 0:1.7.5-18.2.fc17 will be installed ---> Package lapack.i686 0:3.4.2-2.fc17 will be installed ---> Package libicu.i686 0:4.8.1.1-2.fc17 will be updated ---> Package libicu.i686 0:4.8.1.1-5.fc17 will be an update ---> Package ncurses-libs.i686 0:5.9-4.20120204.fc17 will be updated --> Processing Dependency: ncurses-libs = 5.9-4.20120204.fc17 for package: ncurses-5.9-4.20120204.fc17.i686 ---> Package ncurses-libs.i686 0:5.9-11.20130511.fc17 will be an update --> Processing Dependency: ncurses-base = 5.9-11.20130511.fc17 for package: ncurses-libs-5.9-11.20130511.fc17.i686 ---> Package rhino.noarch 0:1.7R3-4.fc17 will be installed --> Processing Dependency: jline for package: rhino-1.7R3-4.fc17.noarch ---> Package tzdata-java.noarch 0:2013c-1.fc17 will be installed ---> Package xorg-x11-fonts-Type1.noarch 0:7.5-5.fc17 will be installed --> Processing Dependency: ttmkfdir for package: xorg-x11-fonts-Type1-7.5-5.fc17.noarch --> Processing Dependency: ttmkfdir for package: xorg-x11-fonts-Type1-7.5-5.fc17.noarch ---> Package xz-libs.i686 0:5.1.1-2alpha.fc17 will be updated --> Processing Dependency: xz-libs = 5.1.1-2alpha.fc17 for package: xz-5.1.1-2alpha.fc17.i686 ---> Package xz-libs.i686 0:5.1.2-1alpha.fc17 will be an update --> Running transaction check ---> Package jline.noarch 0:1.0-1.fc17 will be installed ---> Package ncurses.i686 0:5.9-4.20120204.fc17 will be updated ---> Package ncurses.i686 0:5.9-11.20130511.fc17 will be an update ---> Package ncurses-base.i686 0:5.9-4.20120204.fc17 will be updated ---> Package ncurses-base.noarch 0:5.9-11.20130511.fc17 will be an update ---> Package ttmkfdir.i686 0:3.0.9-35.fc17 will be installed ---> Package xz.i686 0:5.1.1-2alpha.fc17 will be updated ---> Package xz.i686 0:5.1.2-1alpha.fc17 will be an update --> Finished Dependency Resolution Dependencies Resolved ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: blas i686 3.4.2-2.fc17 updates 372 k java-1.7.0-openjdk i686 1:1.7.0.25-2.3.12.1.fc17 updates 26 M lapack-devel i686 3.4.2-2.fc17 updates 70 k libicu-devel i686 4.8.1.1-5.fc17 updates 671 k ncurses-devel i686 5.9-11.20130511.fc17 updates 713 k pango-devel i686 1.30.0-1.fc17 fedora 297 k xz-devel i686 5.1.2-1alpha.fc17 updates 43 k Installing for dependencies: blas-devel i686 3.4.2-2.fc17 updates 11 k jline noarch 1.0-1.fc17 fedora 69 k jpackage-utils i686 1.7.5-18.2.fc17 updates 75 k lapack i686 3.4.2-2.fc17 updates 5.2 M rhino noarch 1.7R3-4.fc17 fedora 981 k ttmkfdir i686 3.0.9-35.fc17 fedora 41 k tzdata-java noarch 2013c-1.fc17 updates 157 k xorg-x11-fonts-Type1 noarch 7.5-5.fc17 fedora 521 k Updating for dependencies: libicu i686 4.8.1.1-5.fc17 updates 5.3 M ncurses i686 5.9-11.20130511.fc17 updates 295 k ncurses-base noarch 5.9-11.20130511.fc17 updates 68 k ncurses-libs i686 5.9-11.20130511.fc17 updates 286 k xz i686 5.1.2-1alpha.fc17 updates 197 k xz-libs i686 5.1.2-1alpha.fc17 updates 104 k Transaction Summary ================================================================================ Install 7 Packages (+8 Dependent packages) Upgrade ( 6 Dependent packages) Total download size: 42 M Downloading Packages: Setting up and reading Presto delta metadata Processing delta metadata Download delta size: 967 k (1/5): libicu-4.8.1.1-2.fc17_4.8.1.1-5.fc17.i686.drpm | 438 kB 00:00 (2/5): ncurses-5.9-4.20120204.fc17_5.9-11.20130511.fc17. | 272 kB 00:00 (3/5): ncurses-libs-5.9-4.20120204.fc17_5.9-11.20130511. | 156 kB 00:00 (4/5): xz-5.1.1-2alpha.fc17_5.1.2-1alpha.fc17.i686.drpm | 77 kB 00:00 (5/5): xz-libs-5.1.1-2alpha.fc17_5.1.2-1alpha.fc17.i686. | 24 kB 00:00 Finishing rebuild of rpms, from deltarpms | 6.1 MB 00:05 Presto reduced the update size by 85% (from 6.1 M to 967 k). Package(s) data still to download: 68 k (1/16): blas-3.4.2-2.fc17.i686.rpm | 372 kB 00:00 (2/16): blas-devel-3.4.2-2.fc17.i686.rpm | 11 kB 00:00 (3/16): java-1.7.0-openjdk-1.7.0.25-2.3.12.1.fc17.i686.r | 26 MB 00:04 (4/16): jline-1.0-1.fc17.noarch.rpm | 69 kB 00:00 (5/16): jpackage-utils-1.7.5-18.2.fc17.i686.rpm | 75 kB 00:00 (6/16): lapack-3.4.2-2.fc17.i686.rpm | 5.2 MB 00:00 (7/16): lapack-devel-3.4.2-2.fc17.i686.rpm | 70 kB 00:00 (8/16): libicu-devel-4.8.1.1-5.fc17.i686.rpm | 671 kB 00:00 (9/16): ncurses-base-5.9-11.20130511.fc17.noarch.rpm | 68 kB 00:00 (10/16): ncurses-devel-5.9-11.20130511.fc17.i686.rpm | 713 kB 00:00 (11/16): pango-devel-1.30.0-1.fc17.i686.rpm | 297 kB 00:00 (12/16): rhino-1.7R3-4.fc17.noarch.rpm | 981 kB 00:00 (13/16): ttmkfdir-3.0.9-35.fc17.i686.rpm | 41 kB 00:00 (14/16): tzdata-java-2013c-1.fc17.noarch.rpm | 157 kB 00:00 (15/16): xorg-x11-fonts-Type1-7.5-5.fc17.noarch.rpm | 521 kB 00:00 (16/16): xz-devel-5.1.2-1alpha.fc17.i686.rpm | 43 kB 00:00 -------------------------------------------------------------------------------- Total 3.8 MB/s | 36 MB 00:09 Running Transaction Check Running Transaction Test Transaction Test Succeeded Running Transaction Installing : jpackage-utils-1.7.5-18.2.fc17.i686 1/27 Installing : jline-1.0-1.fc17.noarch 2/27 Installing : rhino-1.7R3-4.fc17.noarch 3/27 Installing : tzdata-java-2013c-1.fc17.noarch 4/27 Updating : ncurses-base-5.9-11.20130511.fc17.noarch 5/27 Installing : pango-devel-1.30.0-1.fc17.i686 6/27 Updating : ncurses-libs-5.9-11.20130511.fc17.i686 7/27 Updating : xz-libs-5.1.2-1alpha.fc17.i686 8/27 Installing : blas-3.4.2-2.fc17.i686 9/27 Installing : blas-devel-3.4.2-2.fc17.i686 10/27 Installing : lapack-3.4.2-2.fc17.i686 11/27 Installing : ttmkfdir-3.0.9-35.fc17.i686 12/27 Installing : xorg-x11-fonts-Type1-7.5-5.fc17.noarch 13/27 Updating : libicu-4.8.1.1-5.fc17.i686 14/27 Installing : lapack-devel-3.4.2-2.fc17.i686 15/27 Installing : xz-devel-5.1.2-1alpha.fc17.i686 16/27 Installing : ncurses-devel-5.9-11.20130511.fc17.i686 17/27 Installing : libicu-devel-4.8.1.1-5.fc17.i686 18/27 Installing : 1:java-1.7.0-openjdk-1.7.0.25-2.3.12.1.fc17.i686 19/27 Updating : xz-5.1.2-1alpha.fc17.i686 20/27 Updating : ncurses-5.9-11.20130511.fc17.i686 21/27 Cleanup : ncurses-5.9-4.20120204.fc17.i686 22/27 Cleanup : ncurses-libs-5.9-4.20120204.fc17.i686 23/27 Cleanup : xz-5.1.1-2alpha.fc17.i686 24/27 Cleanup : xz-libs-5.1.1-2alpha.fc17.i686 25/27 Cleanup : ncurses-base-5.9-4.20120204.fc17.i686 26/27 Cleanup : libicu-4.8.1.1-2.fc17.i686 27/27 Verifying : jline-1.0-1.fc17.noarch 1/27 Verifying : 1:java-1.7.0-openjdk-1.7.0.25-2.3.12.1.fc17.i686 2/27 Verifying : ncurses-base-5.9-11.20130511.fc17.noarch 3/27 Verifying : ncurses-libs-5.9-11.20130511.fc17.i686 4/27 Verifying : pango-devel-1.30.0-1.fc17.i686 5/27 Verifying : ncurses-devel-5.9-11.20130511.fc17.i686 6/27 Verifying : blas-3.4.2-2.fc17.i686 7/27 Verifying : libicu-4.8.1.1-5.fc17.i686 8/27 Verifying : tzdata-java-2013c-1.fc17.noarch 9/27 Verifying : xz-devel-5.1.2-1alpha.fc17.i686 10/27 Verifying : rhino-1.7R3-4.fc17.noarch 11/27 Verifying : lapack-3.4.2-2.fc17.i686 12/27 Verifying : lapack-devel-3.4.2-2.fc17.i686 13/27 Verifying : xz-5.1.2-1alpha.fc17.i686 14/27 Verifying : jpackage-utils-1.7.5-18.2.fc17.i686 15/27 Verifying : ttmkfdir-3.0.9-35.fc17.i686 16/27 Verifying : xz-libs-5.1.2-1alpha.fc17.i686 17/27 Verifying : xorg-x11-fonts-Type1-7.5-5.fc17.noarch 18/27 Verifying : ncurses-5.9-11.20130511.fc17.i686 19/27 Verifying : libicu-devel-4.8.1.1-5.fc17.i686 20/27 Verifying : blas-devel-3.4.2-2.fc17.i686 21/27 Verifying : xz-libs-5.1.1-2alpha.fc17.i686 22/27 Verifying : libicu-4.8.1.1-2.fc17.i686 23/27 Verifying : ncurses-5.9-4.20120204.fc17.i686 24/27 Verifying : ncurses-base-5.9-4.20120204.fc17.i686 25/27 Verifying : xz-5.1.1-2alpha.fc17.i686 26/27 Verifying : ncurses-libs-5.9-4.20120204.fc17.i686 27/27 Installed: blas.i686 0:3.4.2-2.fc17 java-1.7.0-openjdk.i686 1:1.7.0.25-2.3.12.1.fc17 lapack-devel.i686 0:3.4.2-2.fc17 libicu-devel.i686 0:4.8.1.1-5.fc17 ncurses-devel.i686 0:5.9-11.20130511.fc17 pango-devel.i686 0:1.30.0-1.fc17 xz-devel.i686 0:5.1.2-1alpha.fc17 Dependency Installed: blas-devel.i686 0:3.4.2-2.fc17 jline.noarch 0:1.0-1.fc17 jpackage-utils.i686 0:1.7.5-18.2.fc17 lapack.i686 0:3.4.2-2.fc17 rhino.noarch 0:1.7R3-4.fc17 ttmkfdir.i686 0:3.0.9-35.fc17 tzdata-java.noarch 0:2013c-1.fc17 xorg-x11-fonts-Type1.noarch 0:7.5-5.fc17 Dependency Updated: libicu.i686 0:4.8.1.1-5.fc17 ncurses.i686 0:5.9-11.20130511.fc17 ncurses-base.noarch 0:5.9-11.20130511.fc17 ncurses-libs.i686 0:5.9-11.20130511.fc17 xz.i686 0:5.1.2-1alpha.fc17 xz-libs.i686 0:5.1.2-1alpha.fc17 Complete! ~/LinuxDownloads/redhat/SPECS $ rpmbuild -ba R.spec error: Failed build dependencies: libjpeg-devel is needed by R-3.0.1-2.fc17.i386 readline-devel is needed by R-3.0.1-2.fc17.i386 java-1.5.0-gcj is needed by R-3.0.1-2.fc17.i386 ~/LinuxDownloads/redhat/SPECS $ sudo yum -y install libjpeg-devel readline-devel java-1.5.0-gcj ~/LinuxDownloads/redhat/SPECS $ rpmbuild -ba R.spec error: Failed build dependencies: libjpeg-devel is needed by R-3.0.1-2.fc17.i386 readline-devel is needed by R-3.0.1-2.fc17.i386 java-1.5.0-gcj is needed by R-3.0.1-2.fc17.i386 ~/LinuxDownloads/redhat/SPECS $ rpmbuild -ba R.spec Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.EX7bMk + umask 022 + cd /home/pauljohn/LinuxDownloads/redhat/BUILD + cd /home/pauljohn/LinuxDownloads/redhat/BUILD + rm -rf R-3.0.1 + /usr/bin/tar -xf - + /usr/bin/gzip -dc /home/pauljohn/LinuxDownloads/redhat/SOURCES/R-3.0.1.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd R-3.0.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + cat + chmod +x /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/R-prov + cat + chmod +x /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/R-req + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.FVz2vH + umask 022 + cd /home/pauljohn/LinuxDownloads/redhat/BUILD + cd R-3.0.1 + echo 'R_LIBS_SITE=${R_LIBS_SITE-'\''/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib/R/library:/usr/share/R/library'\''}' + export R_PDFVIEWER=/usr/bin/xdg-open + R_PDFVIEWER=/usr/bin/xdg-open + export R_PRINTCMD=lpr + R_PRINTCMD=lpr + export R_BROWSER=/usr/bin/xdg-open + R_BROWSER=/usr/bin/xdg-open + case "i386" in + export 'CC=gcc -m32' + CC='gcc -m32' + export 'CXX=g++ -m32' + CXX='g++ -m32' + export 'F77=gfortran -m32' + F77='gfortran -m32' + export 'FC=gfortran -m32' + FC='gfortran -m32' + export 'FCFLAGS=-O2 -g -march=i386 -mtune=i686' + FCFLAGS='-O2 -g -march=i386 -mtune=i686' + grep -A30 'R is now' - + CFLAGS='-O2 -g -march=i386 -mtune=i686' + export CFLAGS + CXXFLAGS='-O2 -g -march=i386 -mtune=i686' + export CXXFLAGS + FFLAGS='-O2 -g -march=i386 -mtune=i686' + export FFLAGS + ./configure --host=i686-pc-linux-gnu --build=i686-pc-linux-gnu --program-prefix= --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-system-zlib --with-system-bzlib --with-system-pcre --with-lapack --with-tcl-config=/usr/lib/tclConfig.sh --with-tk-config=/usr/lib/tkConfig.sh --enable-R-shlib --enable-prebuilt-html rdocdir=/usr/share/doc/R-3.0.1 rincludedir=/usr/include/R rsharedir=/usr/share/R + make make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/m4' make[1]: Nothing to be done for `R'. make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/m4' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/tools' make[1]: Nothing to be done for `R'. make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/tools' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/html' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/html' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' make[2]: Nothing to be done for `R'. make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/etc' make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/etc' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/share' make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/share' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/scripts' creating src/scripts/R.fe make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/scripts' mkdir -p -- ../../bin make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/scripts' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/scripts' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include' mkdir -p -- ../../include make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include/R_ext' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/blas' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/blas' gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c blas.f -o blas.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c cmplxblas.f -o cmplxblas.o gcc -m32 -std=gnu99 -shared -fopenmp -L/usr/local/lib -o libRblas.so blas.o cmplxblas.o -lgfortran -lm -lquadmath # xerbla.o make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/blas' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/blas' mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/blas' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/blas' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/tre' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/tre' making regcomp.d from regcomp.c making regerror.d from regerror.c making regexec.d from regexec.c making tre-ast.d from tre-ast.c making tre-compile.d from tre-compile.c making tre-match-approx.d from tre-match-approx.c making tre-match-backtrack.d from tre-match-backtrack.c making tre-match-parallel.d from tre-match-parallel.c making tre-mem.d from tre-mem.c making tre-parse.d from tre-parse.c making tre-stack.d from tre-stack.c making xmalloc.d from xmalloc.c make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/tre' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/tre' gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c regcomp.c -o regcomp.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c regerror.c -o regerror.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c regexec.c -o regexec.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-ast.c -o tre-ast.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-compile.c -o tre-compile.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-mem.c -o tre-mem.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-parse.c -o tre-parse.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-stack.c -o tre-stack.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c xmalloc.c -o xmalloc.o rm -f libtre.a ar cr libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o xmalloc.o ranlib libtre.a make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/tre' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/tre' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/appl' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/appl' making integrate.d from integrate.c making interv.d from interv.c making maxcol.d from maxcol.c making optim.d from optim.c making pretty.d from pretty.c making uncmin.d from uncmin.c make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/appl' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/appl' gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c integrate.c -o integrate.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c interv.c -o interv.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c maxcol.c -o maxcol.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c optim.c -o optim.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pretty.c -o pretty.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c uncmin.c -o uncmin.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dchdc.f -o dchdc.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dpbfa.f -o dpbfa.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dpbsl.f -o dpbsl.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dpoco.f -o dpoco.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dpodi.f -o dpodi.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dpofa.f -o dpofa.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dposl.f -o dposl.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dqrdc.f -o dqrdc.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dqrdc2.f -o dqrdc2.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dqrls.f -o dqrls.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dqrsl.f -o dqrsl.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dqrutl.f -o dqrutl.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dsvdc.f -o dsvdc.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dtrco.f -o dtrco.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dtrsl.f -o dtrsl.o rm -f libappl.a ar cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o ranlib libappl.a make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/appl' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/appl' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath' making mlutils.d from mlutils.c making d1mach.d from d1mach.c making i1mach.d from i1mach.c making fmax2.d from fmax2.c making fmin2.d from fmin2.c making fprec.d from fprec.c making fround.d from fround.c making ftrunc.d from ftrunc.c making sign.d from sign.c making fsign.d from fsign.c making imax2.d from imax2.c making imin2.d from imin2.c making chebyshev.d from chebyshev.c making log1p.d from log1p.c making expm1.d from expm1.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making dnbinom.d from dnbinom.c making pnbinom.d from pnbinom.c making qnbinom.d from qnbinom.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath' gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c mlutils.c -o mlutils.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c d1mach.c -o d1mach.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c i1mach.c -o i1mach.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c fmax2.c -o fmax2.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c fmin2.c -o fmin2.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c fprec.c -o fprec.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c fround.c -o fround.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c ftrunc.c -o ftrunc.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sign.c -o sign.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c fsign.c -o fsign.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c imax2.c -o imax2.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c imin2.c -o imin2.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c chebyshev.c -o chebyshev.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c log1p.c -o log1p.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c expm1.c -o expm1.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c lgammacor.c -o lgammacor.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c gammalims.c -o gammalims.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c stirlerr.c -o stirlerr.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bd0.c -o bd0.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c gamma.c -o gamma.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c lgamma.c -o lgamma.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c gamma_cody.c -o gamma_cody.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c beta.c -o beta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c lbeta.c -o lbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c polygamma.c -o polygamma.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bessel_i.c -o bessel_i.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bessel_j.c -o bessel_j.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bessel_k.c -o bessel_k.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bessel_y.c -o bessel_y.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c choose.c -o choose.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c snorm.c -o snorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sexp.c -o sexp.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dgamma.c -o dgamma.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pgamma.c -o pgamma.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qgamma.c -o qgamma.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rgamma.c -o rgamma.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dbeta.c -o dbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pbeta.c -o pbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qbeta.c -o qbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rbeta.c -o rbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dunif.c -o dunif.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c punif.c -o punif.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qunif.c -o qunif.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c runif.c -o runif.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnorm.c -o dnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnorm.c -o pnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnorm.c -o qnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rnorm.c -o rnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dlnorm.c -o dlnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c plnorm.c -o plnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qlnorm.c -o qlnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rlnorm.c -o rlnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c df.c -o df.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pf.c -o pf.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qf.c -o qf.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rf.c -o rf.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnf.c -o dnf.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dt.c -o dt.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pt.c -o pt.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qt.c -o qt.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rt.c -o rt.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnt.c -o dnt.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dchisq.c -o dchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pchisq.c -o pchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qchisq.c -o qchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rchisq.c -o rchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rnchisq.c -o rnchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dbinom.c -o dbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pbinom.c -o pbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qbinom.c -o qbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rbinom.c -o rbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rmultinom.c -o rmultinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dcauchy.c -o dcauchy.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pcauchy.c -o pcauchy.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qcauchy.c -o qcauchy.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rcauchy.c -o rcauchy.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dexp.c -o dexp.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pexp.c -o pexp.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qexp.c -o qexp.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rexp.c -o rexp.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dgeom.c -o dgeom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pgeom.c -o pgeom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qgeom.c -o qgeom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rgeom.c -o rgeom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dhyper.c -o dhyper.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c phyper.c -o phyper.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qhyper.c -o qhyper.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rhyper.c -o rhyper.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnbinom.c -o dnbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnbinom.c -o pnbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnbinom.c -o qnbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rnbinom.c -o rnbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dpois.c -o dpois.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c ppois.c -o ppois.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qpois.c -o qpois.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rpois.c -o rpois.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dweibull.c -o dweibull.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pweibull.c -o pweibull.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qweibull.c -o qweibull.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rweibull.c -o rweibull.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dlogis.c -o dlogis.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c plogis.c -o plogis.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qlogis.c -o qlogis.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rlogis.c -o rlogis.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnchisq.c -o dnchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnchisq.c -o pnchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnchisq.c -o qnchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnbeta.c -o dnbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnbeta.c -o pnbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnbeta.c -o qnbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnf.c -o pnf.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnt.c -o pnt.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnf.c -o qnf.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnt.c -o qnt.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c ptukey.c -o ptukey.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qtukey.c -o qtukey.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c toms708.c -o toms708.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c wilcox.c -o wilcox.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c signrank.c -o signrank.o rm -rf libnmath.a ar cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o expm1.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o ranlib libnmath.a make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' config.status: creating src/unix/Makefile make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' making Rembedded.d from Rembedded.c making dynload.d from dynload.c making system.d from system.c making sys-unix.d from sys-unix.c making sys-std.d from sys-std.c making X11.d from X11.c make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c Rembedded.c -o Rembedded.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dynload.c -o dynload.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c system.c -o system.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sys-unix.c -o sys-unix.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sys-std.c -o sys-std.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c X11.c -o X11.o rm -rf libunix.a ar cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o ranlib libunix.a make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -DR_HOME='"/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1"' -o Rscript \ ./Rscript.c make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' config.status: creating src/main/Makefile make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' making CommandLineArgs.d from CommandLineArgs.c making Rdynload.d from Rdynload.c making Renviron.d from Renviron.c making RNG.d from RNG.c making agrep.d from agrep.c making apply.d from apply.c making arithmetic.d from arithmetic.c making array.d from array.c making attrib.d from attrib.c making bind.d from bind.c making builtin.d from builtin.c making character.d from character.c making coerce.d from coerce.c making colors.d from colors.c making complex.d from complex.c making connections.d from connections.c making context.d from context.c making cum.d from cum.c making dcf.d from dcf.c making datetime.d from datetime.c making debug.d from debug.c making deparse.d from deparse.c making devices.d from devices.c making dotcode.d from dotcode.c making dounzip.d from dounzip.c making dstruct.d from dstruct.c making duplicate.d from duplicate.c making edit.d from edit.c making engine.d from engine.c making envir.d from envir.c making errors.d from errors.c making eval.d from eval.c making format.d from format.c making gevents.d from gevents.c making gram.d from gram.c making gram-ex.d from gram-ex.c making graphics.d from graphics.c making grep.d from grep.c making identical.d from identical.c making inlined.d from inlined.c making inspect.d from inspect.c making internet.d from internet.c making iosupport.d from iosupport.c making lapack.d from lapack.c making list.d from list.c making localecharset.d from localecharset.c making logic.d from logic.c making main.d from main.c making mapply.d from mapply.c making match.d from match.c making memory.d from memory.c making names.d from names.c making objects.d from objects.c making options.d from options.c making paste.d from paste.c making platform.d from platform.c making plot.d from plot.c making plot3d.d from plot3d.c making plotmath.d from plotmath.c making print.d from print.c making printarray.d from printarray.c making printvector.d from printvector.c making printutils.d from printutils.c making qsort.d from qsort.c making random.d from random.c making raw.d from raw.c making registration.d from registration.c making relop.d from relop.c making rlocale.d from rlocale.c making saveload.d from saveload.c making scan.d from scan.c making seq.d from seq.c making serialize.d from serialize.c making sort.d from sort.c making source.d from source.c making split.d from split.c making sprintf.d from sprintf.c making startup.d from startup.c making subassign.d from subassign.c making subscript.d from subscript.c making subset.d from subset.c making summary.d from summary.c making sysutils.d from sysutils.c making unique.d from unique.c making util.d from util.c making version.d from version.c making vfonts.d from vfonts.c making Rmain.d from Rmain.c making alloca.d from alloca.c making mkdtemp.d from mkdtemp.c making strdup.d from strdup.c making strncasecmp.d from strncasecmp.c make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c CommandLineArgs.c -o CommandLineArgs.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c Rdynload.c -o Rdynload.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c Renviron.c -o Renviron.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c RNG.c -o RNG.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c agrep.c -o agrep.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c apply.c -o apply.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c arithmetic.c -o arithmetic.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c array.c -o array.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c attrib.c -o attrib.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bind.c -o bind.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c builtin.c -o builtin.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c character.c -o character.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c coerce.c -o coerce.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c colors.c -o colors.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c complex.c -o complex.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c connections.c -o connections.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c context.c -o context.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c cum.c -o cum.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dcf.c -o dcf.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c datetime.c -o datetime.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c debug.c -o debug.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c deparse.c -o deparse.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c devices.c -o devices.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dotcode.c -o dotcode.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dounzip.c -o dounzip.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dstruct.c -o dstruct.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c duplicate.c -o duplicate.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c edit.c -o edit.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c engine.c -o engine.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c envir.c -o envir.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c errors.c -o errors.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c eval.c -o eval.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c format.c -o format.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c gevents.c -o gevents.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c gram.c -o gram.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c gram-ex.c -o gram-ex.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c graphics.c -o graphics.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c grep.c -o grep.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c identical.c -o identical.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c inlined.c -o inlined.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c inspect.c -o inspect.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c internet.c -o internet.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c iosupport.c -o iosupport.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c lapack.c -o lapack.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c list.c -o list.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c localecharset.c -o localecharset.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c logic.c -o logic.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c main.c -o main.o main.c: In function 'dummy_ii': main.c:1548:5: warning: function returns address of local variable [enabled by default] gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c mapply.c -o mapply.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c match.c -o match.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c memory.c -o memory.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c names.c -o names.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c objects.c -o objects.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c options.c -o options.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c paste.c -o paste.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c platform.c -o platform.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c plot.c -o plot.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c plot3d.c -o plot3d.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c plotmath.c -o plotmath.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c print.c -o print.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c printarray.c -o printarray.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c printvector.c -o printvector.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c printutils.c -o printutils.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qsort.c -o qsort.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c random.c -o random.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c raw.c -o raw.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c registration.c -o registration.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c relop.c -o relop.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rlocale.c -o rlocale.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c saveload.c -o saveload.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c scan.c -o scan.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c seq.c -o seq.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c serialize.c -o serialize.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sort.c -o sort.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c source.c -o source.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c split.c -o split.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sprintf.c -o sprintf.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c startup.c -o startup.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c subassign.c -o subassign.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c subscript.c -o subscript.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c subset.c -o subset.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c summary.c -o summary.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sysutils.c -o sysutils.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c unique.c -o unique.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c util.c -o util.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c version.c -o version.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c vfonts.c -o vfonts.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c xxxpr.f -o xxxpr.o gcc -m32 -std=gnu99 -shared -fopenmp -L/usr/local/lib -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a -L../../lib -lRblas -lgfortran -lm -lquadmath -lreadline -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/bin/exec make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c Rmain.c -o Rmain.o gcc -m32 -std=gnu99 -Wl,--export-dynamic -fopenmp -L/usr/local/lib -o R.bin Rmain.o -L../../lib -lR -lRblas make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' making Rhttpd.d from Rhttpd.c making Rsock.d from Rsock.c making internet.d from internet.c making nanoftp.d from nanoftp.c making nanohttp.d from nanohttp.c making sock.d from sock.c making sockconn.d from sockconn.c make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c Rsock.c -o Rsock.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c internet.c -o internet.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c nanoftp.c -o nanoftp.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c nanohttp.c -o nanohttp.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c sock.c -o sock.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c sockconn.c -o sockconn.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o internet.so Rhttpd.o Rsock.o internet.o nanoftp.o nanohttp.o sock.o sockconn.o -L../../../lib -lR make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/modules make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' making Lapack.d from Lapack.c make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -ffloat-store -c dlamch.f -o dlamch.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dlapack.f -o dlapack.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c cmplx.f -o cmplx.o gcc -m32 -std=gnu99 -shared -fopenmp -L/usr/local/lib -o libRlapack.so dlamch.o dlapack.o cmplx.o -L../../../lib -lRblas -lgfortran -lm -lquadmath make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c Lapack.c -o Lapack.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o lapack.so Lapack.o -L../../../lib -lR -L../../../lib -lRlapack -L../../../lib -lRblas -lgfortran -lm -lquadmath make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib/libRlapack.so is unchanged make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' making g_alab_her.d from g_alab_her.c making g_cntrlify.d from g_cntrlify.c making g_fontdb.d from g_fontdb.c making g_her_glyph.d from g_her_glyph.c make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c g_alab_her.c -o g_alab_her.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c g_cntrlify.c -o g_cntrlify.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c g_fontdb.c -o g_fontdb.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c g_her_glyph.c -o g_her_glyph.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o vfonts.so g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o -L../../../lib -lR -lm make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' making devX11.d from devX11.c making rotated.d from rotated.c making rbitmap.d from rbitmap.c make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c devX11.c -o devX11.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rotated.c -o rotated.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rbitmap.c -o rbitmap.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o R_X11.so devX11.o rotated.o rbitmap.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -lX11 -lX11 -lXt -lXmu -ltiff -ljpeg -lpng -lz -L../../../lib -lR -lm gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dataentry.c -o dataentry.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -lX11 -lX11 -lXt -lXmu -L../../../lib -lR -lm make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' mkdir -p -- ../../library make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/profile' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/translations' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/translations' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/translations' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/base' building package 'base' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/base' mkdir -p -- ../../../library/base/demo make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/base' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/base' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools' mkdir -p -- ../../../library/tools/R make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools' make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools/src' making text.d from text.c making init.d from init.c making Rmd5.d from Rmd5.c making md5.d from md5.c making signals.d from signals.c making install.d from install.c making getfmts.d from getfmts.c making http.d from http.c making gramLatex.d from gramLatex.c making gramRd.d from gramRd.c gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c text.c -o text.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c Rmd5.c -o Rmd5.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c md5.c -o md5.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c signals.c -o signals.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c install.c -o install.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c getfmts.c -o getfmts.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c http.c -o http.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c gramLatex.c -o gramLatex.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c gramRd.c -o gramRd.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools/src' make[6]: `Makedeps' is up to date. make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools/src' make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools/src' make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools/src' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/compiler' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/compiler' byte-compiling package 'compiler' Error: package 'compiler' was built before R 3.0.0: please re-install it Execution halted make[4]: *** [../../../library/compiler/R/compiler.rdb] Error 1 make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/compiler' make[3]: *** [all] Error 2 make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/compiler' make[2]: *** [R] Error 1 make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src' make: *** [R] Error 1 error: Bad exit status from /var/tmp/rpm-tmp.FVz2vH (%build) RPM build errors: Bad exit status from /var/tmp/rpm-tmp.FVz2vH (%build) ~/LinuxDownloads/redhat/SPECS $ R R version 2.15.0 (2012-03-30) Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i386-redhat-linux-gnu (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > q() Save workspace image? [y/n/c]: n ~/LinuxDownloads/redhat/SPECS $ rpm -e R error: can't create transaction lock on /var/lib/rpm/.rpm.lock (Permission denied) ~/LinuxDownloads/redhat/SPECS $ sudo rpm -e R ~/LinuxDownloads/redhat/SPECS $ R R version 2.15.0 (2012-03-30) Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i386-redhat-linux-gnu (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > q() Save workspace image? [y/n/c]: n ~/LinuxDownloads/redhat/SPECS $ rpmbuild -ba R.spec Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.eQubzc + umask 022 + cd /home/pauljohn/LinuxDownloads/redhat/BUILD + cd /home/pauljohn/LinuxDownloads/redhat/BUILD + rm -rf R-3.0.1 + /usr/bin/tar -xf - + /usr/bin/gzip -dc /home/pauljohn/LinuxDownloads/redhat/SOURCES/R-3.0.1.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd R-3.0.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + cat + chmod +x /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/R-prov + cat + chmod +x /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/R-req + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.aKdm3f + umask 022 + cd /home/pauljohn/LinuxDownloads/redhat/BUILD + cd R-3.0.1 + echo 'R_LIBS_SITE=${R_LIBS_SITE-'\''/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib/R/library:/usr/share/R/library'\''}' + export R_PDFVIEWER=/usr/bin/xdg-open + R_PDFVIEWER=/usr/bin/xdg-open + export R_PRINTCMD=lpr + R_PRINTCMD=lpr + export R_BROWSER=/usr/bin/xdg-open + R_BROWSER=/usr/bin/xdg-open + case "i386" in + export 'CC=gcc -m32' + CC='gcc -m32' + export 'CXX=g++ -m32' + CXX='g++ -m32' + export 'F77=gfortran -m32' + F77='gfortran -m32' + export 'FC=gfortran -m32' + FC='gfortran -m32' + export 'FCFLAGS=-O2 -g -march=i386 -mtune=i686' + FCFLAGS='-O2 -g -march=i386 -mtune=i686' + grep -A30 'R is now' - + CFLAGS='-O2 -g -march=i386 -mtune=i686' + export CFLAGS + CXXFLAGS='-O2 -g -march=i386 -mtune=i686' + export CXXFLAGS + FFLAGS='-O2 -g -march=i386 -mtune=i686' + export FFLAGS + ./configure --host=i686-pc-linux-gnu --build=i686-pc-linux-gnu --program-prefix= --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-system-zlib --with-system-bzlib --with-system-pcre --with-lapack --with-tcl-config=/usr/lib/tclConfig.sh --with-tk-config=/usr/lib/tkConfig.sh --enable-R-shlib --enable-prebuilt-html rdocdir=/usr/share/doc/R-3.0.1 rincludedir=/usr/include/R rsharedir=/usr/share/R + make make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/m4' make[1]: Nothing to be done for `R'. make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/m4' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/tools' make[1]: Nothing to be done for `R'. make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/tools' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/html' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/html' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' make[2]: Nothing to be done for `R'. make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/etc' make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/etc' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/share' make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/share' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/scripts' creating src/scripts/R.fe make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/scripts' mkdir -p -- ../../bin make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/scripts' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/scripts' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include' mkdir -p -- ../../include make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include/R_ext' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/blas' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/blas' gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c blas.f -o blas.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c cmplxblas.f -o cmplxblas.o gcc -m32 -std=gnu99 -shared -fopenmp -L/usr/local/lib -o libRblas.so blas.o cmplxblas.o -lgfortran -lm -lquadmath # xerbla.o make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/blas' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/blas' mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/blas' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/blas' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/tre' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/tre' making regcomp.d from regcomp.c making regerror.d from regerror.c making regexec.d from regexec.c making tre-ast.d from tre-ast.c making tre-compile.d from tre-compile.c making tre-match-approx.d from tre-match-approx.c making tre-match-backtrack.d from tre-match-backtrack.c making tre-match-parallel.d from tre-match-parallel.c making tre-mem.d from tre-mem.c making tre-parse.d from tre-parse.c making tre-stack.d from tre-stack.c making xmalloc.d from xmalloc.c make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/tre' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/tre' gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c regcomp.c -o regcomp.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c regerror.c -o regerror.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c regexec.c -o regexec.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-ast.c -o tre-ast.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-compile.c -o tre-compile.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-mem.c -o tre-mem.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-parse.c -o tre-parse.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c tre-stack.c -o tre-stack.o gcc -m32 -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c xmalloc.c -o xmalloc.o rm -f libtre.a ar cr libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o xmalloc.o ranlib libtre.a make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/tre' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/tre' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/appl' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/appl' making integrate.d from integrate.c making interv.d from interv.c making maxcol.d from maxcol.c making optim.d from optim.c making pretty.d from pretty.c making uncmin.d from uncmin.c make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/appl' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/appl' gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c integrate.c -o integrate.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c interv.c -o interv.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c maxcol.c -o maxcol.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c optim.c -o optim.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pretty.c -o pretty.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c uncmin.c -o uncmin.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dchdc.f -o dchdc.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dpbfa.f -o dpbfa.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dpbsl.f -o dpbsl.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dpoco.f -o dpoco.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dpodi.f -o dpodi.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dpofa.f -o dpofa.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dposl.f -o dposl.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dqrdc.f -o dqrdc.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dqrdc2.f -o dqrdc2.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dqrls.f -o dqrls.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dqrsl.f -o dqrsl.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dqrutl.f -o dqrutl.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dsvdc.f -o dsvdc.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dtrco.f -o dtrco.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dtrsl.f -o dtrsl.o rm -f libappl.a ar cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o ranlib libappl.a make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/appl' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/appl' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath' making mlutils.d from mlutils.c making d1mach.d from d1mach.c making i1mach.d from i1mach.c making fmax2.d from fmax2.c making fmin2.d from fmin2.c making fprec.d from fprec.c making fround.d from fround.c making ftrunc.d from ftrunc.c making sign.d from sign.c making fsign.d from fsign.c making imax2.d from imax2.c making imin2.d from imin2.c making chebyshev.d from chebyshev.c making log1p.d from log1p.c making expm1.d from expm1.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making dnbinom.d from dnbinom.c making pnbinom.d from pnbinom.c making qnbinom.d from qnbinom.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath' gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c mlutils.c -o mlutils.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c d1mach.c -o d1mach.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c i1mach.c -o i1mach.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c fmax2.c -o fmax2.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c fmin2.c -o fmin2.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c fprec.c -o fprec.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c fround.c -o fround.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c ftrunc.c -o ftrunc.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sign.c -o sign.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c fsign.c -o fsign.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c imax2.c -o imax2.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c imin2.c -o imin2.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c chebyshev.c -o chebyshev.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c log1p.c -o log1p.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c expm1.c -o expm1.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c lgammacor.c -o lgammacor.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c gammalims.c -o gammalims.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c stirlerr.c -o stirlerr.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bd0.c -o bd0.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c gamma.c -o gamma.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c lgamma.c -o lgamma.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c gamma_cody.c -o gamma_cody.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c beta.c -o beta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c lbeta.c -o lbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c polygamma.c -o polygamma.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bessel_i.c -o bessel_i.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bessel_j.c -o bessel_j.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bessel_k.c -o bessel_k.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bessel_y.c -o bessel_y.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c choose.c -o choose.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c snorm.c -o snorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sexp.c -o sexp.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dgamma.c -o dgamma.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pgamma.c -o pgamma.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qgamma.c -o qgamma.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rgamma.c -o rgamma.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dbeta.c -o dbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pbeta.c -o pbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qbeta.c -o qbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rbeta.c -o rbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dunif.c -o dunif.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c punif.c -o punif.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qunif.c -o qunif.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c runif.c -o runif.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnorm.c -o dnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnorm.c -o pnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnorm.c -o qnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rnorm.c -o rnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dlnorm.c -o dlnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c plnorm.c -o plnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qlnorm.c -o qlnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rlnorm.c -o rlnorm.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c df.c -o df.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pf.c -o pf.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qf.c -o qf.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rf.c -o rf.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnf.c -o dnf.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dt.c -o dt.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pt.c -o pt.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qt.c -o qt.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rt.c -o rt.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnt.c -o dnt.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dchisq.c -o dchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pchisq.c -o pchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qchisq.c -o qchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rchisq.c -o rchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rnchisq.c -o rnchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dbinom.c -o dbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pbinom.c -o pbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qbinom.c -o qbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rbinom.c -o rbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rmultinom.c -o rmultinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dcauchy.c -o dcauchy.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pcauchy.c -o pcauchy.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qcauchy.c -o qcauchy.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rcauchy.c -o rcauchy.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dexp.c -o dexp.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pexp.c -o pexp.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qexp.c -o qexp.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rexp.c -o rexp.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dgeom.c -o dgeom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pgeom.c -o pgeom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qgeom.c -o qgeom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rgeom.c -o rgeom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dhyper.c -o dhyper.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c phyper.c -o phyper.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qhyper.c -o qhyper.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rhyper.c -o rhyper.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnbinom.c -o dnbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnbinom.c -o pnbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnbinom.c -o qnbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rnbinom.c -o rnbinom.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dpois.c -o dpois.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c ppois.c -o ppois.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qpois.c -o qpois.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rpois.c -o rpois.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dweibull.c -o dweibull.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pweibull.c -o pweibull.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qweibull.c -o qweibull.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rweibull.c -o rweibull.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dlogis.c -o dlogis.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c plogis.c -o plogis.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qlogis.c -o qlogis.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rlogis.c -o rlogis.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnchisq.c -o dnchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnchisq.c -o pnchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnchisq.c -o qnchisq.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnbeta.c -o dnbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnbeta.c -o pnbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnbeta.c -o qnbeta.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnf.c -o pnf.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnt.c -o pnt.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnf.c -o qnf.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnt.c -o qnt.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c ptukey.c -o ptukey.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qtukey.c -o qtukey.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c toms708.c -o toms708.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c wilcox.c -o wilcox.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c signrank.c -o signrank.o rm -rf libnmath.a ar cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o expm1.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o ranlib libnmath.a make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' config.status: creating src/unix/Makefile make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' making Rembedded.d from Rembedded.c making dynload.d from dynload.c making system.d from system.c making sys-unix.d from sys-unix.c making sys-std.d from sys-std.c making X11.d from X11.c make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c Rembedded.c -o Rembedded.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dynload.c -o dynload.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c system.c -o system.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sys-unix.c -o sys-unix.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sys-std.c -o sys-std.o gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c X11.c -o X11.o rm -rf libunix.a ar cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o ranlib libunix.a make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -DR_HOME='"/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1"' -o Rscript \ ./Rscript.c make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' config.status: creating src/main/Makefile make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' making CommandLineArgs.d from CommandLineArgs.c making Rdynload.d from Rdynload.c making Renviron.d from Renviron.c making RNG.d from RNG.c making agrep.d from agrep.c making apply.d from apply.c making arithmetic.d from arithmetic.c making array.d from array.c making attrib.d from attrib.c making bind.d from bind.c making builtin.d from builtin.c making character.d from character.c making coerce.d from coerce.c making colors.d from colors.c making complex.d from complex.c making connections.d from connections.c making context.d from context.c making cum.d from cum.c making dcf.d from dcf.c making datetime.d from datetime.c making debug.d from debug.c making deparse.d from deparse.c making devices.d from devices.c making dotcode.d from dotcode.c making dounzip.d from dounzip.c making dstruct.d from dstruct.c making duplicate.d from duplicate.c making edit.d from edit.c making engine.d from engine.c making envir.d from envir.c making errors.d from errors.c making eval.d from eval.c making format.d from format.c making gevents.d from gevents.c making gram.d from gram.c making gram-ex.d from gram-ex.c making graphics.d from graphics.c making grep.d from grep.c making identical.d from identical.c making inlined.d from inlined.c making inspect.d from inspect.c making internet.d from internet.c making iosupport.d from iosupport.c making lapack.d from lapack.c making list.d from list.c making localecharset.d from localecharset.c making logic.d from logic.c making main.d from main.c making mapply.d from mapply.c making match.d from match.c making memory.d from memory.c making names.d from names.c making objects.d from objects.c making options.d from options.c making paste.d from paste.c making platform.d from platform.c making plot.d from plot.c making plot3d.d from plot3d.c making plotmath.d from plotmath.c making print.d from print.c making printarray.d from printarray.c making printvector.d from printvector.c making printutils.d from printutils.c making qsort.d from qsort.c making random.d from random.c making raw.d from raw.c making registration.d from registration.c making relop.d from relop.c making rlocale.d from rlocale.c making saveload.d from saveload.c making scan.d from scan.c making seq.d from seq.c making serialize.d from serialize.c making sort.d from sort.c making source.d from source.c making split.d from split.c making sprintf.d from sprintf.c making startup.d from startup.c making subassign.d from subassign.c making subscript.d from subscript.c making subset.d from subset.c making summary.d from summary.c making sysutils.d from sysutils.c making unique.d from unique.c making util.d from util.c making version.d from version.c making vfonts.d from vfonts.c making Rmain.d from Rmain.c making alloca.d from alloca.c making mkdtemp.d from mkdtemp.c making strdup.d from strdup.c making strncasecmp.d from strncasecmp.c make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c CommandLineArgs.c -o CommandLineArgs.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c Rdynload.c -o Rdynload.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c Renviron.c -o Renviron.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c RNG.c -o RNG.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c agrep.c -o agrep.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c apply.c -o apply.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c arithmetic.c -o arithmetic.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c array.c -o array.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c attrib.c -o attrib.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bind.c -o bind.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c builtin.c -o builtin.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c character.c -o character.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c coerce.c -o coerce.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c colors.c -o colors.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c complex.c -o complex.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c connections.c -o connections.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c context.c -o context.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c cum.c -o cum.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dcf.c -o dcf.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c datetime.c -o datetime.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c debug.c -o debug.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c deparse.c -o deparse.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c devices.c -o devices.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dotcode.c -o dotcode.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dounzip.c -o dounzip.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dstruct.c -o dstruct.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c duplicate.c -o duplicate.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c edit.c -o edit.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c engine.c -o engine.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c envir.c -o envir.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c errors.c -o errors.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c eval.c -o eval.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c format.c -o format.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c gevents.c -o gevents.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c gram.c -o gram.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c gram-ex.c -o gram-ex.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c graphics.c -o graphics.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c grep.c -o grep.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c identical.c -o identical.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c inlined.c -o inlined.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c inspect.c -o inspect.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c internet.c -o internet.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c iosupport.c -o iosupport.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c lapack.c -o lapack.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c list.c -o list.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c localecharset.c -o localecharset.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c logic.c -o logic.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c main.c -o main.o main.c: In function 'dummy_ii': main.c:1548:5: warning: function returns address of local variable [enabled by default] gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c mapply.c -o mapply.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c match.c -o match.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c memory.c -o memory.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c names.c -o names.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c objects.c -o objects.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c options.c -o options.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c paste.c -o paste.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c platform.c -o platform.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c plot.c -o plot.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c plot3d.c -o plot3d.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c plotmath.c -o plotmath.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c print.c -o print.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c printarray.c -o printarray.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c printvector.c -o printvector.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c printutils.c -o printutils.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qsort.c -o qsort.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c random.c -o random.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c raw.c -o raw.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c registration.c -o registration.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c relop.c -o relop.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rlocale.c -o rlocale.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c saveload.c -o saveload.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c scan.c -o scan.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c seq.c -o seq.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c serialize.c -o serialize.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sort.c -o sort.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c source.c -o source.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c split.c -o split.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sprintf.c -o sprintf.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c startup.c -o startup.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c subassign.c -o subassign.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c subscript.c -o subscript.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c subset.c -o subset.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c summary.c -o summary.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sysutils.c -o sysutils.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c unique.c -o unique.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c util.c -o util.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c version.c -o version.o gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c vfonts.c -o vfonts.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c xxxpr.f -o xxxpr.o gcc -m32 -std=gnu99 -shared -fopenmp -L/usr/local/lib -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a -L../../lib -lRblas -lgfortran -lm -lquadmath -lreadline -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/bin/exec make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' gcc -m32 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c Rmain.c -o Rmain.o gcc -m32 -std=gnu99 -Wl,--export-dynamic -fopenmp -L/usr/local/lib -o R.bin Rmain.o -L../../lib -lR -lRblas make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' making Rhttpd.d from Rhttpd.c making Rsock.d from Rsock.c making internet.d from internet.c making nanoftp.d from nanoftp.c making nanohttp.d from nanohttp.c making sock.d from sock.c making sockconn.d from sockconn.c make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c Rsock.c -o Rsock.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c internet.c -o internet.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c nanoftp.c -o nanoftp.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c nanohttp.c -o nanohttp.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c sock.c -o sock.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -fvisibility=hidden -c sockconn.c -o sockconn.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o internet.so Rhttpd.o Rsock.o internet.o nanoftp.o nanohttp.o sock.o sockconn.o -L../../../lib -lR make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/modules make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' making Lapack.d from Lapack.c make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -ffloat-store -c dlamch.f -o dlamch.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dlapack.f -o dlapack.o gfortran -m32 -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c cmplx.f -o cmplx.o gcc -m32 -std=gnu99 -shared -fopenmp -L/usr/local/lib -o libRlapack.so dlamch.o dlapack.o cmplx.o -L../../../lib -lRblas -lgfortran -lm -lquadmath make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c Lapack.c -o Lapack.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o lapack.so Lapack.o -L../../../lib -lR -L../../../lib -lRlapack -L../../../lib -lRblas -lgfortran -lm -lquadmath make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib/libRlapack.so is unchanged make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' making g_alab_her.d from g_alab_her.c making g_cntrlify.d from g_cntrlify.c making g_fontdb.d from g_fontdb.c making g_her_glyph.d from g_her_glyph.c make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c g_alab_her.c -o g_alab_her.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c g_cntrlify.c -o g_cntrlify.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c g_fontdb.c -o g_fontdb.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c g_her_glyph.c -o g_her_glyph.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o vfonts.so g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o -L../../../lib -lR -lm make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' making devX11.d from devX11.c making rotated.d from rotated.c making rbitmap.d from rbitmap.c make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c devX11.c -o devX11.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rotated.c -o rotated.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rbitmap.c -o rbitmap.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o R_X11.so devX11.o rotated.o rbitmap.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -lX11 -lX11 -lXt -lXmu -ltiff -ljpeg -lpng -lz -L../../../lib -lR -lm gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dataentry.c -o dataentry.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -lX11 -lX11 -lXt -lXmu -L../../../lib -lR -lm make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' mkdir -p -- ../../library make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/profile' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/translations' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/translations' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/translations' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/base' building package 'base' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/base' mkdir -p -- ../../../library/base/demo make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/base' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/base' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools' mkdir -p -- ../../../library/tools/R make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools' make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools/src' making text.d from text.c making init.d from init.c making Rmd5.d from Rmd5.c making md5.d from md5.c making signals.d from signals.c making install.d from install.c making getfmts.d from getfmts.c making http.d from http.c making gramLatex.d from gramLatex.c making gramRd.d from gramRd.c gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c text.c -o text.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c Rmd5.c -o Rmd5.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c md5.c -o md5.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c signals.c -o signals.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c install.c -o install.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c getfmts.c -o getfmts.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c http.c -o http.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c gramLatex.c -o gramLatex.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c gramRd.c -o gramRd.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools/src' make[6]: `Makedeps' is up to date. make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools/src' make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools/src' make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools/src' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/compiler' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/compiler' byte-compiling package 'compiler' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/compiler' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/compiler' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/base' byte-compiling package 'base' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/base' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools' byte-compiling package 'tools' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/utils' mkdir -p -- ../../../library/utils/R mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/utils' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/utils' make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/utils/src' making init.d from init.c making io.d from io.c making size.d from size.c making sock.d from sock.c making stubs.d from stubs.c making utils.d from utils.c gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c io.c -o io.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c size.c -o size.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c sock.c -o sock.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c stubs.c -o stubs.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c utils.c -o utils.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/utils/src' make[6]: `Makedeps' is up to date. make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/utils/src' make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/utils/src' make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/utils/src' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/utils' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/utils' byte-compiling package 'utils' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/utils' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/utils' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices' mkdir -p -- ../../../library/grDevices/R mkdir -p -- ../../../library/grDevices/afm mkdir -p -- ../../../library/grDevices/enc mkdir -p -- ../../../library/grDevices/icc make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices' make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices/src' making axis_scales.d from axis_scales.c making chull.d from chull.c making devices.d from devices.c making init.d from init.c making stubs.d from stubs.c making colors.d from colors.c making devCairo.d from devCairo.c making devPicTeX.d from devPicTeX.c making devPS.d from devPS.c making devQuartz.d from devQuartz.c gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c axis_scales.c -o axis_scales.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c chull.c -o chull.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c devices.c -o devices.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c stubs.c -o stubs.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c colors.c -o colors.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c devCairo.c -o devCairo.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c devPicTeX.c -o devPicTeX.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c devPS.c -o devPS.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c devQuartz.c -o devQuartz.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices/src' make[6]: `Makedeps' is up to date. make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices/src' make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[7]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c make[8]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices/src/cairo' make[8]: `Makedeps' is up to date. make[8]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices/src/cairo' make[8]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices/src/cairo' make[9]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices/src/cairo' gcc -m32 -std=gnu99 -I. -I../../../../../src/include -I../../../../../src/include -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I../../../../../src/modules/X11 -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c cairoBM.c -o cairoBM.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -ltiff -ljpeg -lpng -lz -L../../../../../lib -lR -lm make[9]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices/src/cairo' make[8]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices/src/cairo' make[7]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices/src/cairo' make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices/src' make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices/src' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices' byte-compiling package 'grDevices' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grDevices' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/graphics' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/graphics' make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/graphics/src' making init.d from init.c making base.d from base.c making graphics.d from graphics.c making par.d from par.c making plot.d from plot.c making plot3d.d from plot3d.c making stem.d from stem.c gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c base.c -o base.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c graphics.c -o graphics.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c par.c -o par.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c plot.c -o plot.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c plot3d.c -o plot3d.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c stem.c -o stem.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/graphics/src' make[6]: `Makedeps' is up to date. make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/graphics/src' make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/graphics/src' make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/graphics/src' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/graphics' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/graphics' byte-compiling package 'graphics' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/graphics' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/graphics' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats' mkdir -p -- ../../../library/stats/R make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats' make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats/src' making init.d from init.c making kmeans.d from kmeans.c making ansari.d from ansari.c making bandwidths.d from bandwidths.c making chisqsim.d from chisqsim.c making d2x2xk.d from d2x2xk.c making fexact.d from fexact.c making kendall.d from kendall.c making ks.d from ks.c making line.d from line.c making smooth.d from smooth.c making prho.d from prho.c making swilk.d from swilk.c making ksmooth.d from ksmooth.c making loessc.d from loessc.c making monoSpl.d from monoSpl.c making isoreg.d from isoreg.c making Srunmed.d from Srunmed.c making dblcen.d from dblcen.c making distance.d from distance.c making hclust-utils.d from hclust-utils.c making nls.d from nls.c making rWishart.d from rWishart.c making HoltWinters.d from HoltWinters.c making PPsum.d from PPsum.c making arima.d from arima.c making burg.d from burg.c making filter.d from filter.c making mAR.d from mAR.c making pacf.d from pacf.c making starma.d from starma.c making port.d from port.c making family.d from family.c making sbart.d from sbart.c making approx.d from approx.c making loglin.d from loglin.c making lowess.d from lowess.c making massdist.d from massdist.c making splines.d from splines.c making lm.d from lm.c making complete_cases.d from complete_cases.c making cov.d from cov.c making deriv.d from deriv.c making fft.d from fft.c making fourier.d from fourier.c making model.d from model.c making optim.d from optim.c making optimize.d from optimize.c making integrate.d from integrate.c making random.d from random.c making distn.d from distn.c making zeroin.d from zeroin.c making rcont.d from rcont.c making influence.d from influence.c gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c kmeans.c -o kmeans.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c ansari.c -o ansari.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c bandwidths.c -o bandwidths.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c chisqsim.c -o chisqsim.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c d2x2xk.c -o d2x2xk.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c fexact.c -o fexact.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c kendall.c -o kendall.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c ks.c -o ks.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c line.c -o line.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c smooth.c -o smooth.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c prho.c -o prho.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c swilk.c -o swilk.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c ksmooth.c -o ksmooth.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c loessc.c -o loessc.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c monoSpl.c -o monoSpl.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c isoreg.c -o isoreg.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c Srunmed.c -o Srunmed.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c dblcen.c -o dblcen.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c distance.c -o distance.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c hclust-utils.c -o hclust-utils.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c nls.c -o nls.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c rWishart.c -o rWishart.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c HoltWinters.c -o HoltWinters.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c PPsum.c -o PPsum.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c arima.c -o arima.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c burg.c -o burg.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c filter.c -o filter.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c mAR.c -o mAR.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c pacf.c -o pacf.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c starma.c -o starma.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c port.c -o port.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c family.c -o family.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c sbart.c -o sbart.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c approx.c -o approx.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c loglin.c -o loglin.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c lowess.c -o lowess.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c massdist.c -o massdist.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c splines.c -o splines.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c lm.c -o lm.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c complete_cases.c -o complete_cases.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c cov.c -o cov.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c deriv.c -o deriv.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c fft.c -o fft.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c fourier.c -o fourier.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c model.c -o model.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c optim.c -o optim.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c optimize.c -o optimize.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c integrate.c -o integrate.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c random.c -o random.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c distn.c -o distn.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c zeroin.c -o zeroin.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c rcont.c -o rcont.o gcc -m32 -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c influence.c -o influence.o gfortran -m32 -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c bsplvd.f -o bsplvd.o gfortran -m32 -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c bvalue.f -o bvalue.o gfortran -m32 -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c bvalus.f -o bvalus.o gfortran -m32 -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c loessf.f -o loessf.o gfortran -m32 -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c ppr.f -o ppr.o gfortran -m32 -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c qsbart.f -o qsbart.o gfortran -m32 -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c sgram.f -o sgram.o gfortran -m32 -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c sinerp.f -o sinerp.o gfortran -m32 -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c sslvrg.f -o sslvrg.o gfortran -m32 -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c stxwx.f -o stxwx.o gfortran -m32 -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c hclust.f -o hclust.o gfortran -m32 -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c kmns.f -o kmns.o gfortran -m32 -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c eureka.f -o eureka.o gfortran -m32 -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c stl.f -o stl.o gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -ffloat-store -c portsrc.f -o portsrc.o gfortran -m32 -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c lminfl.f -o lminfl.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -fopenmp -L../../../../lib -lRlapack -L../../../../lib -lRblas -lgfortran -lm -lquadmath -L../../../../lib -lR make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats/src' make[6]: `Makedeps' is up to date. make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats/src' make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats/src' make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats/src' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats' byte-compiling package 'stats' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/datasets' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/datasets' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/methods' mkdir -p -- ../../../library/methods/R make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/methods' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/methods' make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/methods/src' making do_substitute_direct.d from do_substitute_direct.c making init.d from init.c making methods_list_dispatch.d from methods_list_dispatch.c making slot.d from slot.c making class_support.d from class_support.c making tests.d from tests.c making utils.d from utils.c gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c do_substitute_direct.c -o do_substitute_direct.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c methods_list_dispatch.c -o methods_list_dispatch.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c slot.c -o slot.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c class_support.c -o class_support.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c tests.c -o tests.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c utils.c -o utils.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/methods/src' make[6]: `Makedeps' is up to date. make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/methods/src' make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/methods/src' make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/methods/src' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/methods' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/methods' byte-compiling 'methods' initializing class and method definitions ... done make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/methods' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/methods' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grid' mkdir -p -- ../../../library/grid/R make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grid' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grid' make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grid/src' making gpar.d from gpar.c making grid.d from grid.c making just.d from just.c making layout.d from layout.c making matrix.d from matrix.c making register.d from register.c making state.d from state.c making unit.d from unit.c making util.d from util.c making viewport.d from viewport.c gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c gpar.c -o gpar.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c grid.c -o grid.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c just.c -o just.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c layout.c -o layout.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c matrix.c -o matrix.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c register.c -o register.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c state.c -o state.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c unit.c -o unit.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c util.c -o util.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c viewport.c -o viewport.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grid/src' make[6]: `Makedeps' is up to date. make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grid/src' make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grid/src' make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grid/src' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grid' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grid' byte-compiling package 'grid' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grid' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/grid' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/splines' mkdir -p -- ../../../library/splines/R make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/splines' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/splines' make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/splines/src' making splines.d from splines.c gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c splines.c -o splines.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o splines.so splines.o -L../../../../lib -lR make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/splines/src' make[6]: `Makedeps' is up to date. make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/splines/src' make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/splines/src' mkdir -p -- ../../../../library/splines/libs make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/splines/src' make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/splines/src' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/splines' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/splines' byte-compiling package 'splines' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/splines' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/splines' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats4' building package 'stats4' mkdir -p -- ../../../library/stats4 make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats4' mkdir -p -- ../../../library/stats4/R make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats4' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats4' byte-compiling package 'stats4' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats4' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/stats4' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tcltk' building package 'tcltk' mkdir -p -- ../../../library/tcltk/R make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tcltk' mkdir -p -- ../../../library/tcltk/exec make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tcltk' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tcltk/src' making init.d from init.c making tcltk.d from tcltk.c making tcltk_unix.d from tcltk_unix.c gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I/usr/include -I/usr/include -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I/usr/include -I/usr/include -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c tcltk.c -o tcltk.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I/usr/include -I/usr/include -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c tcltk_unix.c -o tcltk_unix.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib -ltcl8.5 -L/usr/lib -ltk8.5 -lX11 -lm -L../../../../lib -lR make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tcltk/src' make[5]: `Makedeps' is up to date. make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tcltk/src' make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tcltk/src' mkdir -p -- ../../../../library/tcltk/libs make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tcltk/src' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tcltk/src' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tcltk' byte-compiling package 'tcltk' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tcltk' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tcltk' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/parallel' building package 'parallel' mkdir -p -- ../../../library/parallel mkdir -p -- ../../../library/parallel/doc make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/parallel' mkdir -p -- ../../../library/parallel/R make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/parallel' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/parallel' make[5]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/parallel/src' making init.d from init.c making rngstream.d from rngstream.c making fork.d from fork.c gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c rngstream.c -o rngstream.o gcc -m32 -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c fork.c -o fork.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/parallel/src' make[6]: `Makedeps' is up to date. make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/parallel/src' make[6]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/parallel/src' mkdir -p -- ../../../../library/parallel/libs make[6]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/parallel/src' make[5]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/parallel/src' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/parallel' make[4]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/parallel' byte-compiling package 'parallel' make[4]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/parallel' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/parallel' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/base' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/base' installing parsed NAMESPACE files make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/tests' make[1]: Nothing to be done for `R'. make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/tests' you should 'make docs' now ... make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc' creating NEWS creating NEWS.pdf make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' creating doc/manual/R-FAQ.html creating doc/manual/version.texi creating doc/manual/R-admin.html creating doc/manual/R-data.html creating doc/manual/R-exts.html creating doc/manual/R-intro.html creating doc/manual/R-ints.html creating doc/manual/R-lang.html make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/html' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/html' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' installing parsed Rd make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' building/updating package metadata ... make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' writing package indices make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' building all R object docs converting help for package 'base' Arithmetic html AsIs html Bessel html CallExternal html Colon html Comparison html Constants html Control html Cstack_info html DateTimeClasses html Dates html Defunct html Deprecated html Encoding html EnvVar html Extract html Extract.data.frame html Extract.factor html Extremes html Foreign-internal html Foreign html Hyperbolic html ISOdatetime html Internal html InternalMethods html Last.value html Log html Logic html LongVectors html MathFun html Memory-limits html Memory html NA html NULL html NumericConstants html Ops.Date html Paren html Platform html Primitive html Quotes html Random-user html Random html RdUtils html Recall html Reserved html Rhome html Round html Special html Startup html Syntax html Sys.getenv html Sys.getpid html Sys.glob html Sys.info html Sys.localeconv html Sys.readlink html Sys.setFileTime html Sys.setenv html Sys.sleep html Sys.time html Sys.which html Trig html UseMethod html Vectorize html Version html abbreviate html agrep html all html all.equal html allnames html any html aperm html append html apply html args html array html as.Date html as.POSIXlt html Rd warning: /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/base/man/as.POSIXlt.Rd:127: missing file link 'format.POSIXlt' as.data.frame html as.environment html as.function html assign html assignOps html attach html attr html attributes html autoload html backsolve html base-defunct html base-deprecated html base-internal html base-package html basename html bincode html bindenv html bitwise html body html bquote html browser html browserText html builtins html by html c html call html callCC html capabilities html cat html cbind html char.expand html character html charmatch html chartr html chol html chol2inv html class html col html colSums html colnames html commandArgs html comment html complex html conditions html conflicts html connections html contributors html copyright html crossprod html cumsum html cut.POSIXt html cut html data.class html data.frame html data.matrix html dataframeHelpers html date html dcf html debug html delayedAssign html deparse html deparseOpts html det html detach html dev html diag html diff html difftime html dim html dimnames html do.call html double html dput html drop html droplevels html dump html duplicated html dynload html eapply html eigen html encodeString html environment html eval html exists html expand.grid html expression html factor html file.access html file.choose html file.info html file.path html file.show html files html files2 html find.package html findInterval html force html formals html format html format.info html format.pval html formatDL html formatc html function html funprog html gc html gc.time html gctorture html get html getCallingDLL html getDLLRegisteredRoutines html getLoadedDLLs html getNativeSymbolInfo html gettext html getwd html gl html grep html grepRaw html groupGeneric html gzcon html hexmode html iconv html icuSetCollate html identical html identity html ifelse html integer html interaction html interactive html invisible html is.finite html is.function html is.language html is.object html is.recursive html is.single html is.unsorted html isR html isS4 html isSymmetric html jitter html kappa html kronecker html l10n_info html labels html lapply html lazyload html length html levels html libPaths html library html library.dynam html license html list html list.files html list2env html load html locales html logical html lower.tri html ls html make.names html make.unique html mapply html margin.table html mat.or.vec html match html match.arg html match.call html match.fun html matmult html matrix html maxCol html mean html memCompress html memory.profile html merge html message html missing html mode html name html names html nargs html nchar html nlevels html noquote html norm html normalizePath html notyet html nrow html ns-dblcolon html ns-hooks html ns-internal html ns-load html ns-reflect html ns-topenv html numeric html numeric_version html octmode html on.exit html options html order html outer html parse html paste html path.expand html pmatch html polyroot html pos.to.env html pretty html print html Rd warning: /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/base/man/print.Rd:81: missing file link '.print.via.format' print.dataframe html print.default html prmatrix html proc.time html prod html prop.table html pushBack html qr html qraux html quit html range html rank html rapply html raw html rawConnection html rawConversion html readBin html readChar html readLines html readRDS html readRenviron html readline html reg.finalizer html regex html regmatches html rep html replace html rev html rle html rm html round.POSIXt html row html row.names html rowsum html sQuote html sample html save html scale html scan html search html seek html seq.Date html seq.POSIXt html seq html sequence html serialize html setTimeLimit html sets html shQuote html showConnections html sign html sink html slice.index html slotOp html socketSelect html solve html sort html source html split html sprintf html srcfile html standardGeneric html stop html stopifnot html strptime html strsplit html strtoi html strtrim html structure html strwrap html subset html substitute html substr html sum html summary html svd html sweep html switch html sys.parent html sys.source html system html system.file html system.time html system2 html t html table html tabulate html tapply html taskCallback html taskCallbackManager html taskCallbackNames html tempfile html textconnections html tilde html timezones html toString html trace html traceback html tracemem html transform html try html typeof html unique html unlink html unlist html unname html userhooks html utf8Conversion html vector html warning html warnings html weekday.POSIXt html which html which.min html with html withVisible html write html writeLines html xtfrm html zMachine html zScript html zapsmall html zpackages html zutils html Signals html converting help for package 'tools' HTMLheader html HTMLlinks html QC html Rd2HTML html Rd2txt_options html RdTextFilter html Rdiff html Rdindex html Rdutils html SweaveTeXFilter html add_datalist html bibstyle html buildVignettes html charsets html checkFF html checkMD5sums html checkPoFiles html checkRd html checkRdaFiles html checkTnF html checkVignettes html check_packages_in_dir html Rd warning: /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/tools/man/check_packages_in_dir.Rd:89: missing file link 'parLapply' codoc html compactPDF html delimMatch html dependsOnPkgs html encoded html fileutils html getDepList html installFoundDepends html makeLazyLoading html make_translations_pkg html md5sum html package.dependencies html package_dependencies html parseLatex html parse_Rd html print.via.format html pskill html psnice html read.00Index html readNEWS html showNonASCII html startDynamicHelp html testInstalledPackage html texi2dvi html toHTML html toRd html tools-defunct html tools-deprecated html tools-package html undoc html update_pkg_po html vignetteDepends html vignetteEngine html writePACKAGES html xgettext html converting help for package 'utils' INSTALL html PkgUtils html Question html REMOVE html RShowDoc html RSiteSearch html Rprof html Rprofmem html Rscript html Rtangle html RweaveLatex html SHLIB html Sweave html SweaveSyntConv html SweaveUtils html URLencode html View html adist html alarm html apropos html aregexec html aspell-utils html aspell html available.packages html bibentry html browseEnv html browseURL html browseVignettes html bug.report html capture.output html chooseBioCmirror html chooseCRANmirror html citEntry html citation html cite html close.socket html combn html compareVersion html contrib.url html count.fields html create.post html data html dataentry html debugger html demo html download.file html download.packages html edit html edit.data.frame html example html file.edit html filetest html findLineNum html fix html flush.console html format html getAnywhere html getFromNamespace html getParseData html getS3method html glob2rx html globalVariables html head html help html help.request html help.search html help.start html install.packages html installed.packages html localeToCharset html ls_str html maintainer html make.packages.html html make.socket html menu html methods html mirrorAdmin html modifyList html news html object.size html package.skeleton html packageDescription html packageName html packageStatus html page html person html process.events html prompt html promptData html promptPackage html rcompgen html read.DIF html read.fortran html read.fwf html read.socket html read.table html recover html relist html remove.packages html removeSource html roman html rtags html savehistory html select.list html sessionInfo html setRepositories html sourceutils html stack html str html summaryRprof html tar html toLatex html txtProgressBar html type.convert html untar html unzip html update.packages html url.show html utils-defunct html utils-deprecated html utils-package html vignette html write.table html zip html BATCH html COMPILE html LINK html RHOME html memory.size html nsl html converting help for package 'grDevices' Devices html Hershey html Japanese html Type1Font html adjustcolor html as.graphicsAnnot html as.raster html axisTicks html boxplot.stats html cairo html check.options html chull html cm html col2rgb html colorRamp html colors html contourLines html convertColor html densCols html dev html dev.capabilities html dev.capture html dev.flush html dev.interactive html dev.size html dev2 html dev2bitmap html devAskNewPage html embedFonts html extendrange html getGraphicsEvent html grDevices-defunct html grDevices-package html gray html gray.colors html hcl html hsv html make.rgb html n2mfrow html nclass html palette html palettes html pdf html pdf.options html pictex html plotmath html postscript html postscriptFonts html pretty.Date html ps.options html recordGraphics html recordplot html rgb html rgb2hsv html trans3d html xfig html xy.coords html xyTable html xyz.coords html png html quartz html quartzFonts html savePlot html x11 html x11Fonts html converting help for package 'graphics' abline html arrows html assocplot html axTicks html axis.POSIXct html axis html barplot html box html boxplot html boxplot.matrix html bxp html cdplot html clip html contour html convertXY html coplot html curve html dotchart html filled.contour html fourfoldplot html frame html graphics-defunct html graphics-package html grid html hist.POSIXt html hist html identify html image html layout html legend html lines html locator html matplot html mosaicplot html mtext html pairs html panel.smooth html par html persp html pie html plot html plot.dataframe html plot.default html plot.design html plot.factor html plot.formula html plot.table html plot.window html plot.xy html plothistogram html points html polygon html polypath html rasterImage html rect html rug html screen html segments html smoothScatter html spineplot html stars html stem html stripchart html strwidth html sunflowerplot html symbols html text html title html units html xspline html zAxis html converting help for package 'stats' AIC html ARMAacf html ARMAtoMA html Beta html Binomial html Cauchy html Chisquare html Distributions html Exponential html Fdist html GammaDist html Geometric html HoltWinters html Hypergeometric html IQR html KalmanLike html Logistic html Lognormal html Multinom html NLSstAsymptotic html NLSstClosestX html NLSstLfAsymptote html NLSstRtAsymptote html NegBinomial html Normal html Poisson html SSD html SSasymp html SSasympOff html SSasympOrig html SSbiexp html SSfol html SSfpl html SSgompertz html SSlogis html SSmicmen html SSweibull html SignRank html StructTS html TDist html Tukey html TukeyHSD html Uniform html Weibull html Wilcoxon html acf html acf2AR html add1 html addmargins html aggregate html alias html anova html anova.glm html anova.lm html anova.mlm html ansari.test html aov html approxfun html ar html ar.ols html arima html arima.sim html arima0 html as.hclust html asOneSidedFormula html ave html bandwidth html bartlett.test html binom.test html biplot html biplot.princomp html birthday html box.test html cancor html case.names html checkMFClasses html chisq.test html cmdscale html coef html complete.cases html confint html constrOptim html contrast html contrasts html convolve html cophenetic html cor html cor.test html cov.wt html cpgram html cutree html decompose html delete.response html dendrapply html dendrogram html density html deriv html deviance html df.residual html diffinv html dist html dummy.coef html ecdf html eff.aovlist html effects html embed html expand.model.frame html extractAIC html factanal html factor.scope html family html fft html filter html fisher.test html fitted.values html fivenum html fligner.test html formula html formula.nls html friedman.test html ftable html ftable.formula html getInitial html glm html glm.control html glm.summaries html hclust html heatmap html identify.hclust html influence.measures html integrate html interaction.plot html is.empty html isoreg html kernapply html kernel html kmeans html kruskal.test html ks.test html ksmooth html lag html lag.plot html line html lm html lm.influence html lm.summaries html lmfit html loadings html loess html loess.control html logLik html loglin html lowess html ls.diag html ls.print html lsfit html mad html mahalanobis html make.link html makepredictcall html manova html mantelhaen.test html mauchly.test html mcnemar.test html median html medpolish html model.extract html model.frame html model.matrix html model.tables html monthplot html mood.test html na.action html na.contiguous html na.fail html nafns html naprint html nextn html nlm html nlminb html nls html nls.control html nobs html numericDeriv html offset html oneway.test html optim html optimize html order.dendrogram html p.adjust html pairwise.prop.test html pairwise.t.test html pairwise.table html pairwise.wilcox.test html plot.HoltWinters html plot.acf html plot.density html plot.isoreg html plot.lm html plot.ppr html plot.profile.nls html plot.spec html plot.stepfun html plot.ts html poisson.test html poly html power html power.anova.test html power.prop.test html power.t.test html pp.test html ppoints html ppr html prcomp html predict.HoltWinters html predict html predict.arima html predict.glm html predict.lm html predict.loess html predict.nls html predict.smooth.spline html preplot html princomp html print.power.htest html print.ts html printCoefmat html profile html profile.nls html proj html prop.test html prop.trend.test html qqnorm html quade.test html quantile html r2dtable html rWishart html read.ftable html rect.hclust html relevel html reorder.dendrogram html reorder.factor html replications html reshape html residuals html runmed html scatter.smooth html screeplot html sd html se.contrast html selfStart html setNames html shapiro.test html simulate html smooth html smooth.spline html smoothEnds html sortedXyData html spec.ar html spec.pgram html spec.taper html spectrum html splinefun html start html stat.anova html stats-defunct html stats-deprecated html stats-package html step html stepfun html stl html stlmethods html summary.aov html summary.glm html summary.lm html summary.manova html summary.nls html summary.princomp html supsmu html symnum html t.test html termplot html terms html terms.formula html terms.object html time html toeplitz html ts-methods html ts html ts.plot html ts.union html tsSmooth html tsdiag html tsp html uniroot html update html update.formula html var.test html varimax html vcov html weighted.mean html weighted.residuals html weights html wilcox.test html window html xtabs html zC html converting help for package 'datasets' AirPassengers html BJsales html BOD html ChickWeight html DNase html EuStockMarkets html Formaldehyde html HairEyeColor html Harman23.cor html Harman74.cor html Indometh html InsectSprays html JohnsonJohnson html LakeHuron html LifeCycleSavings html Loblolly html Nile html Orange html OrchardSprays html PlantGrowth html Puromycin html Theoph html Titanic html ToothGrowth html UCBAdmissions html UKDriverDeaths html UKLungDeaths html UKgas html USAccDeaths html USArrests html USJudgeRatings html USPersonalExpenditure html VADeaths html WWWusage html WorldPhones html ability.cov html airmiles html airquality html anscombe html attenu html attitude html austres html beavers html cars html chickwts html co2 html crimtab html datasets-package html discoveries html esoph html euro html eurodist html faithful html freeny html infert html iris html islands html lh html longley html lynx html morley html mtcars html nhtemp html nottem html occupationalStatus html precip html presidents html pressure html quakes html randu html rivers html rock html sleep html stackloss html state html sunspot.month html sunspot.year html sunspots html swiss html treering html trees html uspop html volcano html warpbreaks html women html zCO2 html converting help for package 'methods' BasicClasses html Classes html Documentation html EmptyMethodsList-class html EnvironmentClass html GenericFunctions html LanguageClasses html LinearMethodsList-class html MethodDefinition-class html MethodSupport html MethodWithNext-class html Methods html MethodsList-class html MethodsList html NextMethod html ObjectsWithPackage-class html RClassUtils html RMethodUtils html S3Part html S4groupGeneric html SClassExtension-class html StructureClasses html TraceClasses html as html callGeneric html canCoerce html cbind2 html className html classRepresentation-class html classesToAM html dotsMethods html evalSource html findClass html findMethods html fixPrevious html genericFunction-class html getClass html getMethod html getPackageName html hasArg html implicitGeneric html inheritedSlotNames html initialize-methods html is html isSealedMethod html languageEl html localRefClass html method.skeleton html methodUtilities html methods-defunct html methods-deprecated html methods-package html new html nonStructure-class html promptClass html promptMethods html refClass html representation html selectSuperClasses html setClass html setClassUnion html setGeneric html setLoadActions html setMethod html setOldClass html setSClass html show html showMethods html signature-class html slot html stdRefClass html substituteDirect html testInheritedMethods html validObject html zBasicFunsList html converting help for package 'grid' Grid html absolute.size html arrow html calcStringMetric html convertNative html current.viewport html dataViewport html drawDetails html editDetails html gEdit html gPath html getNames html gpar html grid-internal html grid-package html grid.DLapply html grid.add html grid.arrows html grid.bezier html grid.cap html grid.circle html grid.clip html grid.collection html grid.convert html grid.copy html grid.curve html grid.delay html grid.display.list html grid.draw html grid.edit html grid.force html grid.frame html grid.function html grid.get html grid.grab html grid.grill html grid.grob html grid.layout html grid.lines html grid.locator html grid.ls html grid.move.to html grid.newpage html grid.null html grid.pack html grid.path html grid.place html grid.plot.and.legend html grid.points html grid.polygon html grid.pretty html grid.raster html grid.record html grid.rect html grid.refresh html grid.remove html grid.reorder html grid.roundrect html grid.segments html grid.set html grid.show.layout html grid.show.viewport html grid.text html grid.xaxis html grid.xspline html grid.yaxis html grobName html grobWidth html grobX html makeContent html plotViewport html pop.viewport html push.viewport html showGrob html showViewport html stringWidth html unit html unit.c html unit.length html unit.pmin html unit.rep html valid.just html validDetails html viewport html viewports html vpPath html widthDetails html xDetails html xsplinePoints html converting help for package 'splines' asVector html backSpline html bs html interpSpline html ns html periodicSpline html polySpline html predict.bSpline html predict.bs html splineDesign html finding level-2 HTML links ... done Rd warning: /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/splines/man/splineDesign.Rd:39: missing link 'sparseMatrix-class' splineKnots html splineOrder html splines-package html xyVector html converting help for package 'stats4' coef-methods html confint-methods html logLik-methods html mle-class html mle html plot-methods html profile-methods html profile.mle-class html show-methods html stats4-package html summary-methods html summary.mle-class html update-methods html vcov-methods html converting help for package 'tcltk' TclInterface html TkCommands html TkWidgetcmds html TkWidgets html tclServiceMode html tcltk-defunct html tcltk-package html tkProgressBar html tkStartGUI html tk_choose.dir html tk_choose.files html tk_messageBox html tk_select.list html tkpager html converting help for package 'compiler' compile html converting help for package 'parallel' RngStream html clusterApply html detectCores html makeCluster html parallel-package html splitIndices html children html mcaffinity html mcfork html mclapply html mcparallel html pvec html make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/Recommended' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/Recommended' begin installing recommended package MASS * installing *source* package 'MASS' ... ** package 'MASS' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/tmp/Rtmp5nUici/R.INSTALL78c613577475/MASS/src' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c MASS.c -o MASS.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c lqs.c -o lqs.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o MASS.so MASS.o lqs.o -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lR make[3]: Leaving directory `/tmp/Rtmp5nUici/R.INSTALL78c613577475/MASS/src' installing to /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/library/MASS/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'MASS' finding HTML links ... done Aids2 html Animals html Boston html Cars93 html Cushings html DDT html GAGurine html Insurance html MASS-internal html Melanoma html Null html OME html Pima.tr html Rabbit html Rubber html SP500 html Sitka html Sitka89 html Skye html Traffic html UScereal html UScrime html VA html abbey html accdeaths html addterm html anorexia html anova.negbin html area html bacteria html bandwidth.nrd html bcv html beav1 html beav2 html biopsy html birthwt html boxcox html cabbages html caith html cats html cement html chem html con2tr html confint html contr.sdif html coop html corresp html cov.rob html cov.trob html cpus html crabs html deaths html denumerate html dose.p html drivers html dropterm html eagles html epil html eqscplot html farms html fgl html fitdistr html forbes html fractions html galaxies html gamma.dispersion html gamma.shape.glm html gehan html genotype html geyser html gilgais html ginv html glm.convert html glm.nb html glmmPQL html hills html hist.scott html housing html huber html hubers html immer html isoMDS html kde2d html lda html ldahist html leuk html lm.gls html lm.ridge html loglm html loglm1 html logtrans html lqs html mammals html mca html mcycle html menarche html michelson html minn38 html motors html muscle html mvrnorm html negative.binomial html newcomb html nlschools html npk html npr1 html oats html painters html pairs.lda html parcoord html petrol html phones html plot.lda html plot.mca html plot.profile html polr html predict.glmmPQL html predict.lda html predict.lqs html predict.mca html predict.qda html profile.glm html qda html quine html rational html renumerate html rlm html rms.curv html rnegbin html road html rotifer html sammon html ships html shoes html shrimp html shuttle html snails html stdres html steam html stepAIC html stormer html studres html summary.loglm html summary.negbin html summary.rlm html survey html synth.tr html theta.md html topo html truehist html ucv html waders html whiteside html width.SJ html write.matrix html wtloss html ** building package indices ** testing if installed package can be loaded * DONE (MASS) Making 'packages.html' ... done begin installing recommended package lattice * installing *source* package 'lattice' ... ** package 'lattice' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/tmp/RtmpkkM9Ra/R.INSTALL78e23930ea7c/lattice/src' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c threeDplot.c -o threeDplot.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o lattice.so init.o threeDplot.o -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lR make[3]: Leaving directory `/tmp/RtmpkkM9Ra/R.INSTALL78e23930ea7c/lattice/src' installing to /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/library/lattice/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'lattice' finding HTML links ... done Lattice html Rows html axis.default html banking html barchart.table html barley html cloud html draw.colorkey html draw.key html environmental html ethanol html histogram html interaction html lattice.options html latticeParseFormula html level.colors html levelplot html llines html lset html make.groups html melanoma html oneway html packet.panel.default html panel.axis html panel.barchart html panel.bwplot html panel.cloud html panel.densityplot html panel.dotplot html panel.functions html panel.histogram html panel.levelplot html panel.loess html panel.number html panel.pairs html panel.parallel html panel.qqmath html panel.qqmathline html panel.smoothScatter html panel.spline html panel.stripplot html panel.superpose html panel.violin html panel.xyplot html prepanel.default html prepanel.functions html print.trellis html qq html qqmath html rfs html shingles html simpleKey html simpleTheme html singer html splom html strip.default html tmd html trellis.device html trellis.object html trellis.par.get html update.trellis html utilities.3d html xyplot html xyplot.ts html ** building package indices ** testing if installed package can be loaded * DONE (lattice) Making 'packages.html' ... done begin installing recommended package Matrix * installing *source* package 'Matrix' ... ** package 'Matrix' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c CHMfactor.c -o CHMfactor.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c Csparse.c -o Csparse.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c TMatrix_as.c -o TMatrix_as.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c Tsparse.c -o Tsparse.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c Mutils.c -o Mutils.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c chm_common.c -o chm_common.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c cs.c -o cs.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c cs_utils.c -o cs_utils.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c dense.c -o dense.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c dgCMatrix.c -o dgCMatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c dgTMatrix.c -o dgTMatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c dgeMatrix.c -o dgeMatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c dpoMatrix.c -o dpoMatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c dppMatrix.c -o dppMatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c dsCMatrix.c -o dsCMatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c dsyMatrix.c -o dsyMatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c dspMatrix.c -o dspMatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c dtCMatrix.c -o dtCMatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c dtTMatrix.c -o dtTMatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c dtrMatrix.c -o dtrMatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c dtpMatrix.c -o dtpMatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c factorizations.c -o factorizations.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ldense.c -o ldense.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c lgCMatrix.c -o lgCMatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c sparseQR.c -o sparseQR.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c abIndex.c -o abIndex.o make[4]: Entering directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/CHOLMOD' ( cd Lib ; make clean ) make[5]: Entering directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/CHOLMOD/Lib' make[5]: Leaving directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/CHOLMOD/Lib' make[4]: Leaving directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/CHOLMOD' make[4]: Entering directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/COLAMD' ( cd Source ; make clean ) make[5]: Entering directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/COLAMD/Source' make[5]: Leaving directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/COLAMD/Source' make[4]: Leaving directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/COLAMD' make[4]: Entering directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/AMD' ( cd Source ; make clean ) make[5]: Entering directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/AMD/Source' make[5]: Leaving directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/AMD/Source' make[4]: Leaving directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/AMD' make[4]: Entering directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/SuiteSparse_config' make[4]: Leaving directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/SuiteSparse_config' make[4]: Entering directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/CHOLMOD' ( cd Lib ; make ) make[5]: Entering directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/CHOLMOD/Lib' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Core/cholmod_aat.c -o cholmod_aat.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Core/cholmod_add.c -o cholmod_add.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Core/cholmod_band.c -o cholmod_band.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Core/cholmod_common.c -o cholmod_common.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Core/cholmod_complex.c -o cholmod_complex.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Core/cholmod_copy.c -o cholmod_copy.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Core/cholmod_dense.c -o cholmod_dense.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Core/cholmod_error.c -o cholmod_error.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Core/cholmod_factor.c -o cholmod_factor.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Core/cholmod_memory.c -o cholmod_memory.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Core/cholmod_sparse.c -o cholmod_sparse.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Core/cholmod_transpose.c -o cholmod_transpose.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Core/cholmod_triplet.c -o cholmod_triplet.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Check/cholmod_check.c -o cholmod_check.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Check/cholmod_read.c -o cholmod_read.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Check/cholmod_write.c -o cholmod_write.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Modify/cholmod_updown.c -o cholmod_updown.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Core/cholmod_aat.c -o cholmod_l_aat.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Core/cholmod_add.c -o cholmod_l_add.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Core/cholmod_band.c -o cholmod_l_band.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Core/cholmod_common.c -o cholmod_l_common.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Core/cholmod_complex.c -o cholmod_l_complex.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Core/cholmod_copy.c -o cholmod_l_copy.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Core/cholmod_dense.c -o cholmod_l_dense.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Core/cholmod_error.c -o cholmod_l_error.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Core/cholmod_factor.c -o cholmod_l_factor.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Core/cholmod_memory.c -o cholmod_l_memory.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Core/cholmod_sparse.c -o cholmod_l_sparse.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Core/cholmod_transpose.c -o cholmod_l_transpose.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Core/cholmod_triplet.c -o cholmod_l_triplet.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Check/cholmod_check.c -o cholmod_l_check.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Check/cholmod_read.c -o cholmod_l_read.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Check/cholmod_write.c -o cholmod_l_write.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Modify/cholmod_updown.c -o cholmod_l_updown.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -DDLONG -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o make[5]: Leaving directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/CHOLMOD/Lib' make[4]: Leaving directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/CHOLMOD' make[4]: Entering directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/COLAMD' ( cd Source ; make lib ) make[5]: Entering directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/COLAMD/Source' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c colamd_global.c -o colamd_global.o colamd_global.c:22:44: warning: initialization from incompatible pointer type [enabled by default] gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c colamd.c -o colamd.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDLONG -c colamd.c -o colamd_l.o ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o make[5]: Leaving directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/COLAMD/Source' make[4]: Leaving directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/COLAMD' make[4]: Entering directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/AMD' ( cd Source ; make lib ) make[5]: Entering directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/AMD/Source' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDINT -c amd_1.c -o amd_i_1.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDLONG -c amd_1.c -o amd_l_1.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDINT -c amd_2.c -o amd_i_2.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDLONG -c amd_2.c -o amd_l_2.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDINT -c amd_order.c -o amd_i_order.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDLONG -c amd_order.c -o amd_l_order.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDINT -c amd_control.c -o amd_i_control.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDLONG -c amd_control.c -o amd_l_control.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDINT -c amd_info.c -o amd_i_info.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDLONG -c amd_info.c -o amd_l_info.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDINT -c amd_global.c -o amd_i_global.o amd_global.c:81:41: warning: initialization from incompatible pointer type [enabled by default] gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -I../Include -DDLONG -c amd_global.c -o amd_l_global.o amd_global.c:81:41: warning: initialization from incompatible pointer type [enabled by default] ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o amd_i_global.o amd_l_global.o make[5]: Leaving directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/AMD/Source' make[4]: Leaving directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/AMD' make[4]: Entering directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/SuiteSparse_config' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -DNTIMER -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c SuiteSparse_config.c -o SuiteSparse_config.o ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o make[4]: Leaving directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src/SuiteSparse_config' gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lRlapack -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lRblas -lgfortran -lm -lquadmath -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lR make[3]: Leaving directory `/tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/src' installing to /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/library/Matrix/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'image' from package 'graphics' in package 'Matrix' Creating a generic function for 'solve' from package 'base' in package 'Matrix' Creating a generic function for 'chol2inv' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix' Creating a generic function for 'determinant' from package 'base' in package 'Matrix' Creating a generic function for 'update' from package 'stats' in package 'Matrix' Creating a generic function for 't' from package 'base' in package 'Matrix' Creating a generic function for 'diag' from package 'base' in package 'Matrix' Creating a generic function for 'as.matrix' from package 'base' in package 'Matrix' Creating a generic function for 'as.array' from package 'base' in package 'Matrix' Creating a generic function for 'head' from package 'utils' in package 'Matrix' Creating a generic function for 'tail' from package 'utils' in package 'Matrix' Creating a generic function for 'drop' from package 'base' in package 'Matrix' Creating a generic function for 'as.vector' from package 'base' in package 'Matrix' Creating a generic function for 'mean' from package 'base' in package 'Matrix' Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix' Creating a generic function for 'isSymmetric' from package 'base' in package 'Matrix' Creating a generic function for 'unname' from package 'base' in package 'Matrix' Creating a generic function for 'chol' from package 'base' in package 'Matrix' Creating a generic function for 'norm' from package 'base' in package 'Matrix' Creating a generic function for 'rcond' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'rcond' from package 'base' in package 'Matrix' Creating a generic function for 'all.equal' from package 'base' in package 'Matrix' Creating a generic function for 'diff' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc" Creating a generic function for 'colSums' from package 'base' in package 'Matrix' Creating a generic function for 'colMeans' from package 'base' in package 'Matrix' Creating a generic function for 'rowSums' from package 'base' in package 'Matrix' Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix' in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix' Creating a generic function for 'qr' from package 'base' in package 'Matrix' Creating a generic function for 'diag<-' from package 'base' in package 'Matrix' Creating a generic function for 'crossprod' from package 'base' in package 'Matrix' Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix' Creating a generic function for 'print' from package 'base' in package 'Matrix' Creating a generic function for 'summary' from package 'base' in package 'Matrix' Creating a generic function for 'which' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM" in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph" in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph" in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL" in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL" Creating a generic function for 'format' from package 'base' in package 'Matrix' Creating a generic function for 'qr.R' from package 'base' in package 'Matrix' Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix' Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix' Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix' Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix' ** help *** installing help indices converting help for package 'Matrix' finding HTML links ... done BunchKaufman-methods html CAex html CHMfactor-class html Cholesky-class html Cholesky html CsparseMatrix-class html Diagonal html Hilbert html KNex html LU-class html Matrix-class html Matrix html MatrixFactorization-class html RsparseMatrix-class html Schur-class html Schur html SparseM-conv html Subassign-methods html TsparseMatrix-class html USCounties html Xtrct-methods html abIndex-class html Rd warning: /tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/man/abIndex-class.Rd:81: missing file link 'Ops' abIseq html all-methods html all.equal-methods html atomicVector-class html band html bandSparse html bdiag html cBind html chol html chol2inv-methods html colSums html compMatrix-class html condest html dMatrix-class html ddenseMatrix-class html ddiMatrix-class html denseMatrix-class html dgCMatrix-class html dgRMatrix-class html dgTMatrix-class html dgeMatrix-class html diagU2N html diagonalMatrix-class html dpoMatrix-class html drop0 html dsCMatrix-class html dsRMatrix-class html dsparseMatrix-class html dsyMatrix-class html dtCMatrix-class html dtRMatrix-class-def html dtpMatrix-class html dtrMatrix-class html expand html expm html externalFormats html facmul html forceSymmetric html formatSparseM html generalMatrix-class html image-methods html Rd warning: /tmp/RtmpUi6fpw/R.INSTALL78fe1040072c/Matrix/man/image-methods.Rd:45: missing file link 'panel.levelplot.raster' index-class html invPerm html is.na-methods html is.null.DN html isSymmetric-methods html kronecker-methods html ldenseMatrix-class html ldiMatrix-class html lgeMatrix-class html lsparseMatrix-classes html lsyMatrix-class html ltrMatrix-class html lu html nMatrix-class html ndenseMatrix-class html nearPD html ngeMatrix-class html nnzero html norm html nsparseMatrix-classes html nsyMatrix-class html ntrMatrix-class html number-class html pMatrix-class html printSpMatrix html qr-methods html rankMatrix html rcond html rep2abI html replValue-class html rleDiff-class html spMatrix html sparse.model.matrix html sparseLU-class html sparseMatrix-class html sparseMatrix html sparseQR-class html sparseVector-class html sparseVector html symmetricMatrix-class html symmpart html tcrossprod html triangularMatrix-class html unpack html unused-classes html updown html ** building package indices Loading required package: Matrix ** installing vignettes 'Comparisons.Rnw' 'Design-issues.Rnw' 'Intro2Matrix.Rnw' 'Introduction.Rnw' 'sparseModels.Rnw' ** testing if installed package can be loaded * DONE (Matrix) Making 'packages.html' ... done begin installing recommended package nlme * installing *source* package 'nlme' ... ** libs make[3]: Entering directory `/tmp/Rtmpq3wcmg/R.INSTALL7af86d33fa56/nlme/src' gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c chol.f -o chol.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c corStruct.c -o corStruct.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c gnls.c -o gnls.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c matrix.c -o matrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c nlOptimizer.c -o nlOptimizer.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c nlme.c -o nlme.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c nlmefit.c -o nlmefit.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c nls.c -o nls.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -march=i386 -mtune=i686 -c pdMat.c -o pdMat.o gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c rs.f -o rs.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o nls.o pdMat.o rs.o -lgfortran -lm -lquadmath -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lR make[3]: Leaving directory `/tmp/Rtmpq3wcmg/R.INSTALL7af86d33fa56/nlme/src' installing to /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/library/nlme/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'nlme' finding HTML links ... done ACF html ACF.gls html ACF.lme html Alfalfa html Assay html BodyWeight html Cefamandole html Coef html Covariate html Covariate.varFunc html Dialyzer html Dim html Dim.corSpatial html Dim.corStruct html Dim.pdMat html Earthquake html Extract.pdMat html Fatigue html Gasoline html Glucose html Glucose2 html Gun html IGF html Initialize html Initialize.corStruct html Initialize.glsStruct html Initialize.lmeStruct html Initialize.reStruct html Initialize.varFunc html LDEsysMat html Machines html MathAchSchool html MathAchieve html Matrix html Matrix.pdMat html Matrix.reStruct html Meat html Milk html Muscle html Names html Names.formula html Names.pdBlocked html Names.pdMat html Names.reStruct html Nitrendipene html Oats html Orthodont html Ovary html Oxboys html Oxide html PBG html Phenobarb html Pixel html Quinidine html Rail html RatPupWeight html Relaxin html Remifentanil html Soybean html Spruce html Tetracycline1 html Tetracycline2 html VarCorr html Variogram html Variogram.corExp html Variogram.corGaus html Variogram.corLin html Variogram.corRatio html Variogram.corSpatial html Variogram.corSpher html Variogram.default html Variogram.gls html Variogram.lme html Wafer html Wheat html Wheat2 html allCoef html anova.gls html anova.lme html as.matrix.corStruct html as.matrix.pdMat html as.matrix.reStruct html asOneFormula html asTable html augPred html balancedGrouped html bdf html coef.corStruct html coef.gnls html coef.lmList html coef.lme html coef.modelStruct html coef.pdMat html coef.reStruct html coef.varFunc html collapse html collapse.groupedData html compareFits html comparePred html corAR1 html corARMA html corCAR1 html corClasses html corCompSymm html corExp html corFactor html corFactor.corStruct html corGaus html corLin html corMatrix html corMatrix.corStruct html corMatrix.pdMat html corMatrix.reStruct html corNatural html corRatio html corSpatial html corSpher html corSymm html ergoStool html fdHess html fitted.glsStruct html fitted.gnlsStruct html fitted.lmList html fitted.lme html fitted.lmeStruct html fitted.nlmeStruct html fixed.effects html fixef.lmList html formula.pdBlocked html formula.pdMat html formula.reStruct html gapply html getCovariate html getCovariate.corStruct html getCovariate.data.frame html getCovariate.varFunc html getCovariateFormula html getData html getData.gls html getData.lmList html getData.lme html getGroups html getGroups.corStruct html getGroups.data.frame html getGroups.gls html getGroups.lmList html getGroups.lme html getGroups.varFunc html getGroupsFormula html getResponse html getResponseFormula html getVarCov html gls html glsControl html glsObject html glsStruct html gnls html gnlsControl html gnlsObject html gnlsStruct html groupedData html gsummary html intervals html intervals.gls html intervals.lmList html intervals.lme html isBalanced html isInitialized html lmList html lmList.groupedData html lme html lme.groupedData html lme.lmList html lmeControl html lmeObject html lmeScale html lmeStruct html logDet html logDet.corStruct html logDet.pdMat html logDet.reStruct html logLik.corStruct html logLik.glsStruct html logLik.gnls html logLik.gnlsStruct html logLik.lmList html logLik.lme html logLik.lmeStruct html logLik.reStruct html logLik.varFunc html model.matrix.reStruct html needUpdate html needUpdate.modelStruct html nlme html nlme.nlsList html nlmeControl html nlmeObject html nlmeStruct html nlsList html nlsList.selfStart html pairs.compareFits html pairs.lmList html pairs.lme html pdBlocked html pdClasses html pdCompSymm html pdConstruct html pdConstruct.pdBlocked html pdDiag html pdFactor html pdFactor.reStruct html pdIdent html pdLogChol html pdMat html pdMatrix html pdMatrix.reStruct html pdNatural html pdSymm html phenoModel html plot.ACF html plot.Variogram html plot.augPred html plot.compareFits html plot.gls html plot.intervals.lmList html plot.lmList html plot.lme html plot.nffGroupedData html plot.nfnGroupedData html plot.nmGroupedData html plot.ranef.lmList html plot.ranef.lme html pooledSD html predict.gls html predict.gnls html predict.lmList html predict.lme html predict.nlme html print.summary.pdMat html print.varFunc html qqnorm.gls html qqnorm.lme html quinModel html random.effects html ranef.lmList html ranef.lme html reStruct html recalc html recalc.corStruct html recalc.modelStruct html recalc.reStruct html recalc.varFunc html residuals.gls html residuals.glsStruct html residuals.gnlsStruct html residuals.lmList html residuals.lme html residuals.lmeStruct html residuals.nlmeStruct html simulate.lme html solve.pdMat html solve.reStruct html splitFormula html summary.corStruct html summary.gls html summary.lmList html summary.lme html summary.modelStruct html summary.nlsList html summary.pdMat html summary.varFunc html update.modelStruct html update.varFunc html varClasses html varComb html varConstPower html varExp html varFixed html varFunc html varIdent html varPower html varWeights html varWeights.glsStruct html varWeights.lmeStruct html ** building package indices ** testing if installed package can be loaded * DONE (nlme) Making 'packages.html' ... done begin installing recommended package survival * installing *source* package 'survival' ... ** package 'survival' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/tmp/RtmpIvlLZB/R.INSTALL7b3012d1b321/survival/src' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c agexact.c -o agexact.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c agfit3.c -o agfit3.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c agfit5.c -o agfit5.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c agmart.c -o agmart.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c agmart2.c -o agmart2.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c agscore.c -o agscore.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c agsurv3.c -o agsurv3.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c agsurv4.c -o agsurv4.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c agsurv5.c -o agsurv5.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c chinv2.c -o chinv2.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c chinv3.c -o chinv3.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c cholesky2.c -o cholesky2.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c cholesky3.c -o cholesky3.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c chsolve2.c -o chsolve2.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c chsolve3.c -o chsolve3.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c concordance1.c -o concordance1.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c cox_Rcallback.c -o cox_Rcallback.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c coxcount1.c -o coxcount1.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c coxdetail.c -o coxdetail.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c coxexact.c -o coxexact.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c coxfit2.c -o coxfit2.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c coxfit5.c -o coxfit5.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c coxfit6.c -o coxfit6.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c coxmart.c -o coxmart.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c coxmart2.c -o coxmart2.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c coxph_wtest.c -o coxph_wtest.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c coxsafe.c -o coxsafe.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c coxscho.c -o coxscho.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c coxscore.c -o coxscore.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c dmatrix.c -o dmatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c doloop.c -o doloop.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c msurv.c -o msurv.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c pyears1.c -o pyears1.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c pyears2.c -o pyears2.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c pyears3b.c -o pyears3b.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c pystep.c -o pystep.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c survConcordance.c -o survConcordance.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c survdiff2.c -o survdiff2.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c survfit4.c -o survfit4.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c survfitci.c -o survfitci.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c survpenal.c -o survpenal.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c survreg6.c -o survreg6.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c survreg7.c -o survreg7.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c survregc1.c -o survregc1.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c survregc2.c -o survregc2.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o survival.so agexact.o agfit3.o agfit5.o agmart.o agmart2.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o chsolve2.o chsolve3.o concordance1.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit2.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore.o dmatrix.o doloop.o init.o msurv.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lR make[3]: Leaving directory `/tmp/RtmpIvlLZB/R.INSTALL7b3012d1b321/survival/src' installing to /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/library/survival/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'survival' finding HTML links ... done Surv html aareg html aml html anova.coxph html attrassign html basehaz html bladder html cch html cgd html clogit html cluster html colon html cox.zph html coxph html coxph.control html coxph.detail html coxph.object html dsurvreg html frailty html heart html is.ratetable html kidney html lines.survfit html logan html lung html mgus html model.frame.coxph html model.matrix.coxph html nwtco html ovarian html pbc html pbcseq html plot.aareg html plot.cox.zph html plot.survfit html predict.coxph html predict.survreg html print.aareg html print.summary.coxph html print.summary.survexp html print.summary.survfit html print.survfit html pspline html pyears html quantile.survfit html ratetable html ratetableDate html rats html rats2 html residuals.coxph html residuals.survreg html ridge html stanford2 html strata html summary.aareg html summary.coxph html summary.survexp html summary.survfit html survConcordance html survSplit html survdiff html survexp html survexp.fit html survexp.us html survfit html survfit.coxph html survfit.formula html survfit.object html survfitcoxph.fit html survival-internal html survobrien html survreg html survreg.control html survreg.distributions html survreg.object html survregDtest html tcut html tobin html tt html untangle.specials html uspop2 html veteran html ** building package indices ** installing vignettes 'timedep.Rnw' ** testing if installed package can be loaded * DONE (survival) Making 'packages.html' ... done begin installing recommended package boot * installing *source* package 'boot' ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'boot' finding HTML links ... done EEF.profile html Imp.Estimates html abc.ci html acme html aids html aircondit html amis html aml html beaver html bigcity html boot-practicals html boot html boot.array html boot.ci html brambles html breslow html calcium html cane html capability html catsM html cav html cd4 html cd4.nested html censboot html channing html claridge html cloth html co.transfer html coal html control html corr html cum3 html cv.glm html darwin html dogs html downs.bc html ducks html empinf html envelope html exp.tilt html fir html freq.array html frets html glm.diag html glm.diag.plots html gravity html hirose html imp.weights html inv.logit html islay html jack.after.boot html k3.linear html linear.approx html lines.saddle.distn html logit html manaus html melanoma html motor html neuro html nitrofen html nodal html norm.ci html nuclear html paulsen html plot.boot html poisons html polar html print.boot html print.bootci html print.saddle.distn html print.simplex html remission html saddle html saddle.distn html saddle.distn.object html salinity html simplex html simplex.object html smooth.f html sunspot html survival html tau html tilt.boot html tsboot html tuna html urine html var.linear html wool html ** building package indices ** testing if installed package can be loaded * DONE (boot) Making 'packages.html' ... done begin installing recommended package cluster * installing *source* package 'cluster' ... ** package 'cluster' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/tmp/RtmpMRLdiV/R.INSTALL7be121f42ba9/cluster/src' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c clara.c -o clara.o gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c daisy.f -o daisy.o gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c dysta.f -o dysta.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c fanny.c -o fanny.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c mona.f -o mona.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c pam.c -o pam.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c sildist.c -o sildist.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c spannel.c -o spannel.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c twins.c -o twins.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -lquadmath -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lR make[3]: Leaving directory `/tmp/RtmpMRLdiV/R.INSTALL7be121f42ba9/cluster/src' installing to /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/library/cluster/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'cluster' finding HTML links ... done agnes html agnes.object html agriculture html animals html bannerplot html chorSub html clara html clara.object html clusGap html clusplot.default html Rd warning: /tmp/RtmpMRLdiV/R.INSTALL7be121f42ba9/cluster/man/clusplot.default.Rd:208: missing file link 'cov.mve' clusplot.partition html cluster-internal html coef.hclust html daisy html diana html dissimilarity.object html ellipsoidhull html Rd warning: /tmp/RtmpMRLdiV/R.INSTALL7be121f42ba9/cluster/man/ellipsoidhull.Rd:36: missing file link 'cov.mve' Rd warning: /tmp/RtmpMRLdiV/R.INSTALL7be121f42ba9/cluster/man/ellipsoidhull.Rd:86: missing file link 'cov.mve' fanny html fanny.object html flower html lower.to.upper.tri.inds html mona html mona.object html pam html pam.object html partition.object html plantTraits html plot.agnes html Rd warning: /tmp/RtmpMRLdiV/R.INSTALL7be121f42ba9/cluster/man/plot.agnes.Rd:73: missing file link 'plot.dendrogram' plot.diana html plot.mona html plot.partition html pltree html pltree.twins html pluton html predict.ellipsoid html print.agnes html print.clara html print.diana html print.dissimilarity html Rd warning: /tmp/RtmpMRLdiV/R.INSTALL7be121f42ba9/cluster/man/print.dissimilarity.Rd:27: missing file link 'print.dist' print.fanny html print.mona html print.pam html ruspini html silhouette html sizeDiss html summary.agnes html summary.clara html summary.diana html summary.mona html summary.pam html twins.object html volume.ellipsoid html votes.repub html xclara html ** building package indices ** testing if installed package can be loaded * DONE (cluster) Making 'packages.html' ... done begin installing recommended package codetools * installing *source* package 'codetools' ... ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'codetools' finding HTML links ... done checkUsage html codetools html findGlobals html showTree html ** building package indices ** testing if installed package can be loaded * DONE (codetools) Making 'packages.html' ... done begin installing recommended package foreign * installing *source* package 'foreign' ... ** package 'foreign' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/tmp/RtmpabYCWO/R.INSTALL7c2749988da0/foreign/src' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c R_systat.c -o R_systat.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c Rdbfread.c -o Rdbfread.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c Rdbfwrite.c -o Rdbfwrite.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c SASxport.c -o SASxport.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c avl.c -o avl.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c dbfopen.c -o dbfopen.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c file-handle.c -o file-handle.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c format.c -o format.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c minitab.c -o minitab.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c pfm-read.c -o pfm-read.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c sfm-read.c -o sfm-read.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c spss.c -o spss.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c stataread.c -o stataread.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lR make[3]: Leaving directory `/tmp/RtmpabYCWO/R.INSTALL7c2749988da0/foreign/src' installing to /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/library/foreign/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'foreign' finding HTML links ... done lookup.xport html read.S html read.arff html read.dbf html read.dta html read.epiinfo html read.mtp html read.octave html read.spss html read.ssd html read.systat html read.xport html write.arff html write.dbf html write.dta html write.foreign html ** building package indices ** testing if installed package can be loaded * DONE (foreign) Making 'packages.html' ... done begin installing recommended package KernSmooth * installing *source* package 'KernSmooth' ... ** package 'KernSmooth' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/tmp/RtmpVzl2S4/R.INSTALL7c673e1ae0d6/KernSmooth/src' gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c blkest.f -o blkest.o gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c cp.f -o cp.o gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c dgedi.f -o dgedi.o gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c dgefa.f -o dgefa.o gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c dgesl.f -o dgesl.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c linbin.f -o linbin.o gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c linbin2D.f -o linbin2D.o gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c locpoly.f -o locpoly.o gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c rlbin.f -o rlbin.o gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c sdiag.f -o sdiag.o gfortran -m32 -fpic -O2 -g -march=i386 -mtune=i686 -c sstdiag.f -o sstdiag.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lR make[3]: Leaving directory `/tmp/RtmpVzl2S4/R.INSTALL7c673e1ae0d6/KernSmooth/src' installing to /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/library/KernSmooth/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'KernSmooth' finding HTML links ... done bkde html bkde2D html bkfe html dpih html dpik html dpill html locpoly html ** building package indices ** testing if installed package can be loaded * DONE (KernSmooth) Making 'packages.html' ... done begin installing recommended package rpart * installing *source* package 'rpart' ... ** libs make[3]: Entering directory `/tmp/RtmpMYS124/R.INSTALL7ca14997100/rpart/src' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c anova.c -o anova.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c anovapred.c -o anovapred.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c branch.c -o branch.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c bsplit.c -o bsplit.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c choose_surg.c -o choose_surg.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c fix_cp.c -o fix_cp.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c free_tree.c -o free_tree.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c gini.c -o gini.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c graycode.c -o graycode.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c insert_split.c -o insert_split.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c make_cp_list.c -o make_cp_list.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c make_cp_table.c -o make_cp_table.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c mysort.c -o mysort.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c nodesplit.c -o nodesplit.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c partition.c -o partition.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c poisson.c -o poisson.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c pred_rpart.c -o pred_rpart.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c print_tree.c -o print_tree.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c rpart.c -o rpart.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c rpart_callback.c -o rpart_callback.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c rpartexp.c -o rpartexp.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c rpartexp2.c -o rpartexp2.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c rpcountup.c -o rpcountup.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c rpmatrix.c -o rpmatrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c rundown.c -o rundown.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c rundown2.c -o rundown2.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c surrogate.c -o surrogate.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c usersplit.c -o usersplit.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c xpred.c -o xpred.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c xval.c -o xval.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lR make[3]: Leaving directory `/tmp/RtmpMYS124/R.INSTALL7ca14997100/rpart/src' installing to /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/library/rpart/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'rpart' finding HTML links ... done car.test.frame html car90 html cu.summary html kyphosis html labels.rpart html meanvar.rpart html na.rpart html path.rpart html plot.rpart html plotcp html post.rpart html predict.rpart html print.rpart html printcp html prune.rpart html residuals.rpart html rpart-internal html rpart html rpart.control html rpart.exp html rpart.object html rsq.rpart html snip.rpart html solder html stagec html summary.rpart html text.rpart html xpred.rpart html ** building package indices ** installing vignettes 'longintro.Rnw' 'usercode.Rnw' ** testing if installed package can be loaded * DONE (rpart) Making 'packages.html' ... done begin installing recommended package class * installing *source* package 'class' ... ** package 'class' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/tmp/RtmpLzZZVV/R.INSTALL7d143b889176/class/src' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c class.c -o class.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o class.so class.o -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lR make[3]: Leaving directory `/tmp/RtmpLzZZVV/R.INSTALL7d143b889176/class/src' installing to /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/library/class/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'class' finding HTML links ... done SOM html batchSOM html condense html knn html knn.cv html knn1 html lvq1 html lvq2 html lvq3 html lvqinit html lvqtest html multiedit html olvq1 html reduce.nn html somgrid html ** building package indices ** testing if installed package can be loaded * DONE (class) Making 'packages.html' ... done begin installing recommended package nnet * installing *source* package 'nnet' ... ** package 'nnet' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/tmp/RtmplH2Jim/R.INSTALL7d2d7f36d583/nnet/src' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c nnet.c -o nnet.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o nnet.so nnet.o -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lR make[3]: Leaving directory `/tmp/RtmplH2Jim/R.INSTALL7d2d7f36d583/nnet/src' installing to /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/library/nnet/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'nnet' finding HTML links ... done class.ind html multinom html nnet.Hess html nnet html predict.nnet html which.is.max html ** building package indices ** testing if installed package can be loaded * DONE (nnet) Making 'packages.html' ... done begin installing recommended package spatial * installing *source* package 'spatial' ... ** libs make[3]: Entering directory `/tmp/RtmpEZQzlh/R.INSTALL7d462d417035/spatial/src' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c krc.c -o krc.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c pps.c -o pps.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o spatial.so init.o krc.o pps.o -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lR make[3]: Leaving directory `/tmp/RtmpEZQzlh/R.INSTALL7d462d417035/spatial/src' installing to /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/library/spatial/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'spatial' finding HTML links ... done Kaver html Kenvl html Kfn html Psim html SSI html Strauss html anova.trls html correlogram html expcov html ppgetregion html ppinit html pplik html ppregion html predict.trls html prmat html semat html surf.gls html surf.ls html trls.influence html trmat html variogram html ** building package indices ** testing if installed package can be loaded * DONE (spatial) Making 'packages.html' ... done begin installing recommended package mgcv * installing *source* package 'mgcv' ... ** libs make[3]: Entering directory `/tmp/Rtmp0YjoVB/R.INSTALL7d654368eea4/mgcv/src' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c gdi.c -o gdi.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c init.c -o init.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c magic.c -o magic.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c mat.c -o mat.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c matrix.c -o matrix.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c mgcv.c -o mgcv.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c misc.c -o misc.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c qp.c -o qp.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c soap.c -o soap.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c sparse-smooth.c -o sparse-smooth.o gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c tprs.c -o tprs.o gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o mgcv.so gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o qp.o soap.o sparse-smooth.o tprs.o -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lRlapack -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lRblas -lgfortran -lm -lquadmath -L/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/lib -lR make[3]: Leaving directory `/tmp/Rtmp0YjoVB/R.INSTALL7d654368eea4/mgcv/src' installing to /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/library/mgcv/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'mgcv' finding HTML links ... done Predict.matrix html Predict.matrix.cr.smooth html Predict.matrix.soap.film html Tweedie html anova.gam html bam html Rd warning: /tmp/Rtmp0YjoVB/R.INSTALL7d654368eea4/mgcv/man/bam.Rd:13: missing file link 'parallel' Rd warning: /tmp/Rtmp0YjoVB/R.INSTALL7d654368eea4/mgcv/man/bam.Rd:115: missing file link 'parLapply' Rd warning: /tmp/Rtmp0YjoVB/R.INSTALL7d654368eea4/mgcv/man/bam.Rd:155: missing file link 'makeForkCluster' bam.update html cSplineDes html choose.k html columb html concurvity html exclude.too.far html extract.lme.cov html fix.family.link html fixDependence html formXtViX html formula.gam html fs.test html full.score html gam html gam.check html gam.control html gam.convergence html gam.fit html gam.fit3 html gam.models html gam.outer html gam.selection html gam.side html gam.vcomp html gam2objective html gamObject html gamSim html gamm html get.var html in.out html inSide html influence.gam html initial.sp html interpret.gam html ldTweedie html linear.functional.terms html logLik.gam html ls.size html magic html magic.post.proc html mgcv-FAQ html mgcv-package html model.matrix.gam html mono.con html mroot html negbin html new.name html notExp html notExp2 html null.space.dimension html pcls html pdIdnot html pdTens html pen.edf html place.knots html plot.gam html polys.plot html predict.bam html Rd warning: /tmp/Rtmp0YjoVB/R.INSTALL7d654368eea4/mgcv/man/predict.bam.Rd:71: missing file link 'parLapply' predict.gam html print.gam html qq.gam html rTweedie html random.effects html residuals.gam html rig html s html slanczos html smooth.construct html smooth.construct.ad.smooth.spec html smooth.construct.cr.smooth.spec html smooth.construct.ds.smooth.spec html smooth.construct.fs.smooth.spec html smooth.construct.mrf.smooth.spec html smooth.construct.ps.smooth.spec html smooth.construct.re.smooth.spec html smooth.construct.so.smooth.spec html smooth.construct.sos.smooth.spec html smooth.construct.tensor.smooth.spec html smooth.construct.tp.smooth.spec html smooth.terms html smoothCon html sp.vcov html spasm.construct html step.gam html summary.gam html t2 html te html tensor.prod.model.matrix html uniquecombs html vcov.gam html vis.gam html ** building package indices ** testing if installed package can be loaded * DONE (mgcv) Making 'packages.html' ... done make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/Recommended' make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library/Recommended' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' building/updating vignettes for package 'grid' ... building/updating vignettes for package 'parallel' ... building/updating vignettes for package 'utils' ... make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1' configuring Java ... Java interpreter : /usr/bin/java Java version : 1.7.0_25 Java home path : /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.25/jre Java compiler : not present Java headers gen.: Java archive tool: trying to compile and link a JNI progam detected JNI cpp flags : detected JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -ljvm make[2]: Entering directory `/tmp/RJRECONF.sroyfq' gcc -m32 -std=gnu99 -I/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -march=i386 -mtune=i686 -c conftest.c -o conftest.o conftest.c:1:17: fatal error: jni.h: No such file or directory compilation terminated. make[2]: *** [conftest.o] Error 1 make[2]: Leaving directory `/tmp/RJRECONF.sroyfq' Unable to compile a JNI program Java library path: JNI cpp flags : JNI linker flags : Updating Java configuration in /home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1 Done. make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1' + cd src/nmath/standalone + make (cd ../../include; make Rmath.h) make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include' make[1]: `Rmath.h' is up to date. make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include' Copying source files make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath/standalone' making mlutils.d from mlutils.c making d1mach.d from d1mach.c making i1mach.d from i1mach.c making fmax2.d from fmax2.c making fmin2.d from fmin2.c making fprec.d from fprec.c making fround.d from fround.c making ftrunc.d from ftrunc.c making sign.d from sign.c making fsign.d from fsign.c making imax2.d from imax2.c making imin2.d from imin2.c making chebyshev.d from chebyshev.c making log1p.d from log1p.c making expm1.d from expm1.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making dnbinom.d from dnbinom.c making pnbinom.d from pnbinom.c making qnbinom.d from qnbinom.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c making std_unif.d from std_unif.c make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath/standalone' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath/standalone' gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c mlutils.c -o mlutils.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c d1mach.c -o d1mach.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c i1mach.c -o i1mach.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c fmax2.c -o fmax2.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c fmin2.c -o fmin2.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c fprec.c -o fprec.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c fround.c -o fround.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c ftrunc.c -o ftrunc.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c sign.c -o sign.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c fsign.c -o fsign.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c imax2.c -o imax2.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c imin2.c -o imin2.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c chebyshev.c -o chebyshev.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c log1p.c -o log1p.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c expm1.c -o expm1.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c lgammacor.c -o lgammacor.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c gammalims.c -o gammalims.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c stirlerr.c -o stirlerr.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c bd0.c -o bd0.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c gamma.c -o gamma.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c lgamma.c -o lgamma.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c gamma_cody.c -o gamma_cody.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c beta.c -o beta.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c lbeta.c -o lbeta.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c polygamma.c -o polygamma.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c bessel_i.c -o bessel_i.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c bessel_j.c -o bessel_j.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c bessel_k.c -o bessel_k.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c bessel_y.c -o bessel_y.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c choose.c -o choose.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c snorm.c -o snorm.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c sexp.c -o sexp.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dgamma.c -o dgamma.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pgamma.c -o pgamma.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qgamma.c -o qgamma.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rgamma.c -o rgamma.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dbeta.c -o dbeta.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pbeta.c -o pbeta.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qbeta.c -o qbeta.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rbeta.c -o rbeta.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dunif.c -o dunif.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c punif.c -o punif.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qunif.c -o qunif.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c runif.c -o runif.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dnorm.c -o dnorm.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pnorm.c -o pnorm.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qnorm.c -o qnorm.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rnorm.c -o rnorm.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dlnorm.c -o dlnorm.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c plnorm.c -o plnorm.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qlnorm.c -o qlnorm.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rlnorm.c -o rlnorm.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c df.c -o df.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pf.c -o pf.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qf.c -o qf.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rf.c -o rf.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dnf.c -o dnf.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dt.c -o dt.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pt.c -o pt.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qt.c -o qt.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rt.c -o rt.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dnt.c -o dnt.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dchisq.c -o dchisq.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pchisq.c -o pchisq.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qchisq.c -o qchisq.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rchisq.c -o rchisq.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rnchisq.c -o rnchisq.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dbinom.c -o dbinom.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pbinom.c -o pbinom.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qbinom.c -o qbinom.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rbinom.c -o rbinom.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rmultinom.c -o rmultinom.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dcauchy.c -o dcauchy.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pcauchy.c -o pcauchy.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qcauchy.c -o qcauchy.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rcauchy.c -o rcauchy.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dexp.c -o dexp.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pexp.c -o pexp.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qexp.c -o qexp.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rexp.c -o rexp.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dgeom.c -o dgeom.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pgeom.c -o pgeom.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qgeom.c -o qgeom.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rgeom.c -o rgeom.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dhyper.c -o dhyper.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c phyper.c -o phyper.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qhyper.c -o qhyper.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rhyper.c -o rhyper.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dnbinom.c -o dnbinom.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pnbinom.c -o pnbinom.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qnbinom.c -o qnbinom.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rnbinom.c -o rnbinom.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dpois.c -o dpois.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c ppois.c -o ppois.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qpois.c -o qpois.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rpois.c -o rpois.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dweibull.c -o dweibull.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pweibull.c -o pweibull.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qweibull.c -o qweibull.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rweibull.c -o rweibull.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dlogis.c -o dlogis.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c plogis.c -o plogis.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qlogis.c -o qlogis.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c rlogis.c -o rlogis.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dnchisq.c -o dnchisq.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pnchisq.c -o pnchisq.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qnchisq.c -o qnchisq.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c dnbeta.c -o dnbeta.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pnbeta.c -o pnbeta.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qnbeta.c -o qnbeta.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pnf.c -o pnf.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c pnt.c -o pnt.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qnf.c -o qnf.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qnt.c -o qnt.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c ptukey.c -o ptukey.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c qtukey.c -o qtukey.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c toms708.c -o toms708.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c wilcox.c -o wilcox.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c signrank.c -o signrank.o gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -march=i386 -mtune=i686 -c std_unif.c -o std_unif.o ar cr libRmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o expm1.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o std_unif.o ranlib libRmath.a make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath/standalone' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath/standalone' gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c mlutils.c -o mlutils.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c d1mach.c -o d1mach.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c i1mach.c -o i1mach.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c fmax2.c -o fmax2.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c fmin2.c -o fmin2.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c fprec.c -o fprec.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c fround.c -o fround.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c ftrunc.c -o ftrunc.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sign.c -o sign.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c fsign.c -o fsign.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c imax2.c -o imax2.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c imin2.c -o imin2.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c chebyshev.c -o chebyshev.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c log1p.c -o log1p.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c expm1.c -o expm1.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c lgammacor.c -o lgammacor.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c gammalims.c -o gammalims.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c stirlerr.c -o stirlerr.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bd0.c -o bd0.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c gamma.c -o gamma.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c lgamma.c -o lgamma.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c gamma_cody.c -o gamma_cody.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c beta.c -o beta.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c lbeta.c -o lbeta.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c polygamma.c -o polygamma.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bessel_i.c -o bessel_i.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bessel_j.c -o bessel_j.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bessel_k.c -o bessel_k.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c bessel_y.c -o bessel_y.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c choose.c -o choose.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c snorm.c -o snorm.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c sexp.c -o sexp.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dgamma.c -o dgamma.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pgamma.c -o pgamma.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qgamma.c -o qgamma.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rgamma.c -o rgamma.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dbeta.c -o dbeta.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pbeta.c -o pbeta.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qbeta.c -o qbeta.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rbeta.c -o rbeta.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dunif.c -o dunif.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c punif.c -o punif.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qunif.c -o qunif.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c runif.c -o runif.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnorm.c -o dnorm.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnorm.c -o pnorm.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnorm.c -o qnorm.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rnorm.c -o rnorm.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dlnorm.c -o dlnorm.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c plnorm.c -o plnorm.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qlnorm.c -o qlnorm.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rlnorm.c -o rlnorm.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c df.c -o df.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pf.c -o pf.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qf.c -o qf.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rf.c -o rf.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnf.c -o dnf.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dt.c -o dt.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pt.c -o pt.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qt.c -o qt.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rt.c -o rt.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnt.c -o dnt.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dchisq.c -o dchisq.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pchisq.c -o pchisq.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qchisq.c -o qchisq.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rchisq.c -o rchisq.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rnchisq.c -o rnchisq.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dbinom.c -o dbinom.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pbinom.c -o pbinom.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qbinom.c -o qbinom.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rbinom.c -o rbinom.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rmultinom.c -o rmultinom.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dcauchy.c -o dcauchy.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pcauchy.c -o pcauchy.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qcauchy.c -o qcauchy.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rcauchy.c -o rcauchy.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dexp.c -o dexp.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pexp.c -o pexp.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qexp.c -o qexp.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rexp.c -o rexp.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dgeom.c -o dgeom.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pgeom.c -o pgeom.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qgeom.c -o qgeom.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rgeom.c -o rgeom.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dhyper.c -o dhyper.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c phyper.c -o phyper.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qhyper.c -o qhyper.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rhyper.c -o rhyper.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnbinom.c -o dnbinom.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnbinom.c -o pnbinom.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnbinom.c -o qnbinom.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rnbinom.c -o rnbinom.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dpois.c -o dpois.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c ppois.c -o ppois.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qpois.c -o qpois.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rpois.c -o rpois.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dweibull.c -o dweibull.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pweibull.c -o pweibull.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qweibull.c -o qweibull.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rweibull.c -o rweibull.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dlogis.c -o dlogis.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c plogis.c -o plogis.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qlogis.c -o qlogis.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c rlogis.c -o rlogis.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnchisq.c -o dnchisq.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnchisq.c -o pnchisq.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnchisq.c -o qnchisq.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c dnbeta.c -o dnbeta.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnbeta.c -o pnbeta.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnbeta.c -o qnbeta.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnf.c -o pnf.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c pnt.c -o pnt.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnf.c -o qnf.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qnt.c -o qnt.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c ptukey.c -o ptukey.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c qtukey.c -o qtukey.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c toms708.c -o toms708.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c wilcox.c -o wilcox.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c signrank.c -o signrank.lo gcc -m32 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -c std_unif.c -o std_unif.lo gcc -m32 -std=gnu99 -shared -fopenmp -L/usr/local/lib -o libRmath.so mlutils.lo d1mach.lo i1mach.lo fmax2.lo fmin2.lo fprec.lo fround.lo ftrunc.lo sign.lo fsign.lo imax2.lo imin2.lo chebyshev.lo log1p.lo expm1.lo lgammacor.lo gammalims.lo stirlerr.lo bd0.lo gamma.lo lgamma.lo gamma_cody.lo beta.lo lbeta.lo polygamma.lo bessel_i.lo bessel_j.lo bessel_k.lo bessel_y.lo choose.lo snorm.lo sexp.lo dgamma.lo pgamma.lo qgamma.lo rgamma.lo dbeta.lo pbeta.lo qbeta.lo rbeta.lo dunif.lo punif.lo qunif.lo runif.lo dnorm.lo pnorm.lo qnorm.lo rnorm.lo dlnorm.lo plnorm.lo qlnorm.lo rlnorm.lo df.lo pf.lo qf.lo rf.lo dnf.lo dt.lo pt.lo qt.lo rt.lo dnt.lo dchisq.lo pchisq.lo qchisq.lo rchisq.lo rnchisq.lo dbinom.lo pbinom.lo qbinom.lo rbinom.lo rmultinom.lo dcauchy.lo pcauchy.lo qcauchy.lo rcauchy.lo dexp.lo pexp.lo qexp.lo rexp.lo dgeom.lo pgeom.lo qgeom.lo rgeom.lo dhyper.lo phyper.lo qhyper.lo rhyper.lo dnbinom.lo pnbinom.lo qnbinom.lo rnbinom.lo dpois.lo ppois.lo qpois.lo rpois.lo dweibull.lo pweibull.lo qweibull.lo rweibull.lo dlogis.lo plogis.lo qlogis.lo rlogis.lo dnchisq.lo pnchisq.lo qnchisq.lo dnbeta.lo pnbeta.lo qnbeta.lo pnf.lo pnt.lo qnf.lo qnt.lo ptukey.lo qtukey.lo toms708.lo wilcox.lo signrank.lo std_unif.lo -lm make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath/standalone' + make pdf make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' creating doc/manual/version.tex collecting LaTeX docs for package 'base' ... 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This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) %&-line parsing enabled. entering extended mode (./fullrefman.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, arabic, basque, bulgarian, coptic, welsh, czech, slovak, german, ng erman, danish, esperanto, spanish, catalan, galician, estonian, farsi, finnish, french, greek, monogreek, ancientgreek, croatian, hungarian, interlingua, ibyc us, indonesian, icelandic, italian, latin, mongolian, dutch, norsk, polish, por tuguese, pinyin, romanian, russian, slovenian, uppersorbian, serbian, swedish, turkish, ukenglish, ukrainian, loaded. 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Underfull \hbox (badness 10000) in paragraph at lines 137--145 \T1/ptm/m/n/10 It equals \T1/fi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 137--145 \T1/fi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/fi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 148--155 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [5] [6] Underfull \hbox (badness 1178) in paragraph at lines 291--295 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/fi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [7] [8] Underfull \hbox (badness 3977) in paragraph at lines 372--375 []\T1/ptm/m/n/10 logical: should \T1/fi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [9] Underfull \hbox (badness 2556) in paragraph at lines 498--504 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/fi4/m/n/10 insertions\T1/ptm/m/n/10 ', [10] [11] [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1062--1065 []\T1/ptm/m/n/10 If the calls to \T1/fi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/fi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] Underfull \hbox (badness 10000) in paragraph at lines 1263--1269 []\T1/fi4/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/fi4/m/n/10 x mod y \T1/ptm/m /n/10 and \T1/fi4/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I t is guar-an-teed that Underfull \hbox (badness 3323) in paragraph at lines 1263--1269 \T1/fi4/m/n/10 x == (x %% y) + y * ( x %/% y ) \T1/ptm/m/n/10 (up to round-in g er-ror) un-less \T1/fi4/m/n/10 y == 0 \T1/ptm/m/n/10 where the [22] [23] [24] [25] [26] [27] [28] [29] [30] Underfull \hbox (badness 10000) in paragraph at lines 1943--1945 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] Underfull \hbox (badness 10000) in paragraph at lines 3370--3372 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [52] [53] [54] [55] [56] [57] [58] [59] Underfull \hbox (badness 2970) in paragraph at lines 3949--3955 []\T1/ptm/m/n/10 is there sup-port the [][]\T1/fi4/m/n/10 svg[][][]\T1/ptm/m/n/ 10 , [][]\T1/fi4/m/n/10 cairo_pdf[][][] \T1/ptm/m/n/10 and [][]\T1/fi4/m/n/10 c airo_ps[][][] \T1/ptm/m/n/10 de-vices, and for [60] [61] [62] [63] [64] [65] [66] [67] Underfull \hbox (badness 2521) in paragraph at lines 4505--4507 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [68] [69] Underfull \hbox (badness 1337) in paragraph at lines 4649--4655 \T1/ptm/m/n/10 LA-PACK re-quires LA-PACK >= 3.2 and was added in \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.2. The value of \T1/fi4/m/n/10 tol \T1/ptm/m/n/10 is [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] Underfull \hbox (badness 2096) in paragraph at lines 5719--5732 []\T1/ptm/m/n/10 New restarts for \T1/fi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [86] [87] [88] [89] Underfull \hbox (badness 10000) in paragraph at lines 6042--6045 []\T1/ptm/m/n/10 A note on `\T1/fi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [90] [91] [92] Underfull \hbox (badness 2790) in paragraph at lines 6257--6264 []\T1/fi4/m/n/10 file \T1/ptm/m/n/10 can be used with \T1/fi4/m/n/10 descriptio n = "clipboard" \T1/ptm/m/n/10 in mode \T1/fi4/m/n/10 "r" \T1/ptm/m/n/10 only. This reads Underfull \hbox (badness 3471) in paragraph at lines 6257--6264 \T1/ptm/m/n/10 the X11 pri-mary se-lec-tion (see [][]$\T1/fi4/m/n/10 http : / / standards . freedesktop . org / clipboards-[]spec / [93] [94] Underfull \vbox (badness 10000) has occurred while \output is active [95] [96] [97] [98] [99] [100] [101] Underfull \hbox (badness 4595) in paragraph at lines 6859--6862 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [102] Underfull \hbox (badness 2351) in paragraph at lines 6916--6919 [][][]\T1/fi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/fi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/fi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [103] [104] [105] Underfull \hbox (badness 10000) in paragraph at lines 7161--7172 []\T1/fi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing [106] Underfull \hbox (badness 4479) in paragraph at lines 7232--7241 [][][]\T1/fi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), Underfull \hbox (badness 2469) in paragraph at lines 7232--7241 [][]\T1/fi4/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods, [][]\T1/fi4/m/n/10 Math.data.frame[][][] \T1/ptm/m/n/10 etc, about \T1/ptm/m/i t/10 Group \T1/ptm/m/n/10 meth-ods for [107] [108] [109] [110] [111] [112] Underfull \hbox (badness 10000) in paragraph at lines 7640--7652 \T1/fi4/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n /10 may give \T1/fi4/m/n/10 NA\T1/ptm/m/n/10 , and hence Underfull \hbox (badness 6220) in paragraph at lines 7640--7652 \T1/fi4/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz = "UTC") \T1/ptm/m/n/10 wi ll give \T1/fi4/m/n/10 "1969-12-31 23:59:00"\T1/ptm/m/n/10 . [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] Underfull \hbox (badness 1394) in paragraph at lines 8766--8771 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/fi4/m/n/10 difftime \T1/ptm/m/n/10 with [129] [130] [131] [132] [133] [134] Underfull \hbox (badness 10000) in paragraph at lines 9210--9214 [][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / IEEE _ 754-[]198 5$[][]\T1/ptm/m/n/10 , [][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wi ki / IEEE _ [135] [136] [137] [138] [139] [140] Underfull \hbox (badness 2150) in paragraph at lines 9593--9596 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 9607--9615 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for [141] Underfull \hbox (badness 5622) in paragraph at lines 9648--9654 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/fi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 4569) in paragraph at lines 10677--10681 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 10677--10681 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [156] [157] [158] [159] [160] [161] [162] Underfull \hbox (badness 2698) in paragraph at lines 11219--11228 []\T1/ptm/m/n/10 Both \T1/fi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/fi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 11219--11228 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] Underfull \hbox (badness 2253) in paragraph at lines 12166--12168 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [177] Underfull \hbox (badness 1565) in paragraph at lines 12227--12231 [][][]\T1/fi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/fi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and Underfull \hbox (badness 10000) in paragraph at lines 12270--12272 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/fi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/fi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [178] [179] Underfull \hbox (badness 1292) in paragraph at lines 12333--12341 \T1/ptm/m/n/10 ing spe-cial pager names be-ing in-ter-cepted by lower-level cod e (such as \T1/fi4/m/n/10 "internal" \T1/ptm/m/n/10 and [180] Underfull \hbox (badness 1466) in paragraph at lines 12401--12404 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ fi4/m/n/10 file.copy \T1/ptm/m/n/10 and [181] Underfull \hbox (badness 10000) in paragraph at lines 12507--12511 [][][]\T1/fi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/fi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ fi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 12518--12521 [][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / Hard _ link$[][] \T1/ptm/m/n/10 and [][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / [182] [183] [184] Underfull \hbox (badness 3965) in paragraph at lines 12765--12769 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] Underfull \hbox (badness 4429) in paragraph at lines 13469--13472 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/fi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [196] Underfull \hbox (badness 10000) in paragraph at lines 13555--13557 []\T1/ptm/m/n/10 If you set \T1/fi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/fi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 13561--13565 []\T1/fi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so Underfull \hbox (badness 1052) in paragraph at lines 13561--13565 \T1/fi4/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "fg") \T1/ptm/m/n/10 gives \T1/fi4/m/n/10 c("6.1", " 13")\T1/ptm/m/n/10 . If you [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] Underfull \hbox (badness 1092) in paragraph at lines 14313--14318 [][]\T1/fi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [208] [209] [210] Underfull \hbox (badness 6741) in paragraph at lines 14561--14565 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/fi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/fi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [211] [212] [213] [214] [215] Underfull \hbox (badness 1867) in paragraph at lines 14859--14866 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [216] [217] [218] Underfull \vbox (badness 10000) has occurred while \output is active [219] [220] Underfull \hbox (badness 3679) in paragraph at lines 15235--15237 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/fi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [221] [222] [223] [224] [225] [226] Underfull \hbox (badness 1478) in paragraph at lines 15703--15706 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] Underfull \hbox (badness 1442) in paragraph at lines 16379--16381 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/fi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [237] Underfull \hbox (badness 2452) in paragraph at lines 16471--16487 [][][]\T1/fi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/fi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] Underfull \hbox (badness 4739) in paragraph at lines 17116--17118 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [248] [249] [250] [251] [252] [253] Underfull \hbox (badness 1077) in paragraph at lines 17514--17519 \T1/ptm/m/n/10 trix or, if \T1/fi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/fi4/m/n/10 simplify2array()\T1/ptm /m/n/10 . [254] [255] [256] [257] [258] [259] [260] Underfull \hbox (badness 10000) in paragraph at lines 17992--17996 []\T1/ptm/m/n/10 By de-fault \T1/fi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/fi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 17992--17996 \T1/ptm/m/n/10 `\T1/fi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/fi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/fi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/fi4/m/n/10 /library\T1/ptm/m/n/10 ' [261] [262] Underfull \hbox (badness 1014) in paragraph at lines 18145--18150 []\T1/ptm/m/n/10 Normally \T1/fi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/fi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/fi4/m/n/10 FALSE \T1/ptm/m/n/10 if [263] [264] [265] [266] [267] [268] [269] [270] [271] [272] Underfull \hbox (badness 1264) in paragraph at lines 18853--18858 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [273] [274] [275] [276] [277] [278] Underfull \hbox (badness 4954) in paragraph at lines 19277--19283 []\T1/fi4/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment to be of log-i-cal type. For [][]\T1/fi4/m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 10000) in paragraph at lines 19277--19283 \T1/ptm/m/n/10 this uses the [][]\T1/fi4/m/n/10 levels[][][] \T1/ptm/m/n/10 (la -bels). Like [][]\T1/fi4/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri butes in-clud-ing Underfull \hbox (badness 10000) in paragraph at lines 19277--19283 \T1/ptm/m/n/10 names. Char-ac-ter strings \T1/fi4/m/n/10 c("T", "TRUE", "True", "true") \T1/ptm/m/n/10 are re-garded as true, [279] [280] [281] [282] [283] Underfull \hbox (badness 10000) in paragraph at lines 19584--19586 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/fi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] Underfull \hbox (badness 1655) in paragraph at lines 20567--20573 [][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / Data _ compressi on$[][] \T1/ptm/m/n/10 for back-ground on data com-pres-sion, [298] [299] [300] Underfull \hbox (badness 1484) in paragraph at lines 20728--20736 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been [301] [302] [303] [304] Underfull \hbox (badness 2790) in paragraph at lines 20995--20998 []\T1/fi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 20995--20998 \T1/fi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [305] [306] [307] [308] [309] [310] Underfull \hbox (badness 10000) in paragraph at lines 21434--21437 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 21434--21437 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] Underfull \hbox (badness 1199) in paragraph at lines 22481--22487 []\T1/ptm/m/n/10 The de-fault method for \T1/fi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/fi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/fi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 22481--22487 \T1/ptm/m/n/10 ([][]type[][][] \T1/fi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/fi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/fi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [327] [328] [329] [330] [331] [332] [333] Underfull \hbox (badness 1038) in paragraph at lines 23014--23023 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 10000) in paragraph at lines 23014--23023 \T1/fi4/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats", "methods")\T1/ptm/m/n/10 . Underfull \hbox (badness 1881) in paragraph at lines 23024--23027 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 23043--23045 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [334] Underfull \hbox (badness 10000) in paragraph at lines 23107--23116 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/fi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2600) in paragraph at lines 23107--23116 \T1/ptm/m/n/10 `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/fi4/m/n/10 /bin/pager\T1/pt m/m/n/10 ', which se-lects a pager via the \T1/fi4/m/n/10 PAGER \T1/ptm/m/n/10 en-vi-ron-ment vari-able Underfull \hbox (badness 2142) in paragraph at lines 23117--23123 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/fi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 23130--23135 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/fi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 23140--23149 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [335] [336] [337] Underfull \hbox (badness 10000) in paragraph at lines 23381--23387 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/fi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 23381--23387 \T1/ptm/m/n/10 e.g. the de-fault `\T1/fi4/m/n/10 "http://www.bioconductor.org"\ T1/ptm/m/n/10 ' or the Eu-ro-pean mir- Underfull \hbox (badness 10000) in paragraph at lines 23381--23387 \T1/ptm/m/n/10 ror `\T1/fi4/m/n/10 "http://bioconductor.statistik.tu-dortmund.d e"\T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 23393--23396 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/fi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/fi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 23418--23420 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 7203) in paragraph at lines 23446--23449 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/fi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/fi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3128) in paragraph at lines 23456--23462 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/fi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der the CRAN OS X build) Underfull \hbox (badness 1881) in paragraph at lines 23456--23462 \T1/ptm/m/n/10 and \T1/fi4/m/n/10 "mac.binary."\T1/ptm/m/n/10 . Win-dows uses \ T1/fi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/fi4/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and [338] Underfull \hbox (badness 10000) in paragraph at lines 23464--23471 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/fi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 23464--23471 \T1/fi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 23464--23471 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 10000) in paragraph at lines 23464--23471 \T1/fi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [339] [340] [341] [342] Underfull \hbox (badness 10000) in paragraph at lines 23765--23769 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/fi4/m/n/10 X \T1/ptm/m/n /10 and \T1/fi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/fi4/m/n/10 A \T1/ptm/ m/n/10 with di-men- Underfull \hbox (badness 10000) in paragraph at lines 23765--23769 \T1/ptm/m/n/10 sion \T1/fi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e- ment \T1/fi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [343] [344] [345] [346] Underfull \hbox (badness 1748) in paragraph at lines 24064--24068 \T1/ptm/m/n/10 seem un-de-sir-able, e.g., when past-ing two char-ac-ter vec-tor s, or very de-sir-able, e.g. in [347] [348] [349] [350] [351] [352] [353] [354] Underfull \hbox (badness 2726) in paragraph at lines 24563--24566 []\T1/ptm/m/n/10 character string (or \T1/fi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/fi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [355] [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] Underfull \hbox (badness 1052) in paragraph at lines 25368--25373 []\T1/fi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [367] [368] [369] [370] [371] Underfull \hbox (badness 1097) in paragraph at lines 25757--25765 []\T1/ptm/m/n/10 The seed, \T1/fi4/m/n/10 .Random.seed[-1] == r[1:3] \T1/ptm/m/ n/10 is an in-te-ger vec-tor of length [372] [373] [374] [375] Underfull \hbox (badness 1533) in paragraph at lines 26073--26076 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [376] [377] [378] [379] [380] [381] [382] [383] [384] [385] [386] [387] [388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399] Underfull \hbox (badness 6188) in paragraph at lines 27726--27728 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/fi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [400] [401] [402] [403] [404] [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] Underfull \hbox (badness 10000) in paragraph at lines 28925--28928 []\T1/fi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., Underfull \hbox (badness 3229) in paragraph at lines 28925--28928 \T1/fi4/m/n/10 save(list = ls(all = TRUE), file = ".RData")\T1/ptm/m/n/10 . It is also what hap-pens with [418] [419] [420] Underfull \hbox (badness 2302) in paragraph at lines 29125--29132 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 29125--29132 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 2698) in paragraph at lines 29125--29132 \T1/ptm/m/n/10 val-ues. In the case \T1/fi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, but Underfull \hbox (badness 4805) in paragraph at lines 29125--29132 \T1/ptm/m/n/10 in gen-eral it is not. (To scale by the stan-dard de-vi-a-tions with-out cen-ter-ing, use [421] [422] Underfull \hbox (badness 2261) in paragraph at lines 29278--29283 []\T1/ptm/m/n/10 If \T1/fi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 29305--29311 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 4001) in paragraph at lines 29305--29311 \T1/ptm/m/n/10 `\T1/fi4/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o c-tal and hex-adec-i-mal rep-re-sen-ta- [423] Underfull \hbox (badness 10000) in paragraph at lines 29378--29383 []\T1/ptm/m/n/10 Note that since \T1/fi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by Underfull \hbox (badness 1701) in paragraph at lines 29378--29383 \T1/fi4/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10 will give an empty fi-nal line if [424] [425] [426] [427] [428] Underfull \hbox (badness 6188) in paragraph at lines 29712--29715 []\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence \T1/fi4/m/ n/10 1, 2, ..., length(along.with)\T1/ptm/m/n/10 . [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] Underfull \vbox (badness 10000) has occurred while \output is active [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] Underfull \hbox (badness 1072) in paragraph at lines 32120--32124 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 32125--32129 []\T1/ptm/m/n/10 The command-line op-tion `\T1/fi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/fi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/fi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 32153--32159 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/fi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 32153--32159 \T1/ptm/m/n/10 and `\T1/fi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, e.g. Underfull \hbox (badness 3343) in paragraph at lines 32162--32169 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 32162--32169 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment Underfull \hbox (badness 1917) in paragraph at lines 32162--32169 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/fi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [464] [465] [466] [467] [468] Underfull \hbox (badness 10000) in paragraph at lines 32452--32458 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/fi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487] [488] [489] Underfull \hbox (badness 1248) in paragraph at lines 33821--33831 []\T1/ptm/m/n/10 If \T1/fi4/m/n/10 EXPR \T1/ptm/m/n/10 eval-u-ates to a char-ac -ter string then that string is matched (ex-actly)to the names Underfull \hbox (badness 1902) in paragraph at lines 33821--33831 \T1/ptm/m/n/10 of the el-e-ments in \T1/fi4/m/n/10 ...\T1/ptm/m/n/10 . If there is a match then that el-e-ment is eval-u-ated un-less it Underfull \hbox (badness 2772) in paragraph at lines 33821--33831 \T1/ptm/m/n/10 is miss-ing, in which case the next non-missing el-e-ment is eva l-u-ated, so for ex-am-ple [490] [491] Underfull \hbox (badness 4416) in paragraph at lines 34006--34008 []\T1/ptm/m/n/10 Argument \T1/fi4/m/n/10 names \T1/ptm/m/n/10 was in-tro-duced in \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.13.0 to avoid need-ing the com-mon use of [492] [493] Underfull \hbox (badness 3333) in paragraph at lines 34099--34104 []\T1/ptm/m/n/10 If a file-name starts with \T1/fi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [494] [495] [496] [497] [498] [499] [500] [501] [502] Underfull \hbox (badness 1472) in paragraph at lines 34706--34709 []\T1/ptm/m/n/10 logical. If \T1/fi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [503] [504] [505] [506] [507] [508] [509] [510] Underfull \hbox (badness 4217) in paragraph at lines 35222--35225 []\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/fi 4/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies [511] [512] Underfull \hbox (badness 2671) in paragraph at lines 35356--35359 []\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/fi4/m/n/10 ...\T1/pt m/m/n/10 . If set to \T1/fi4/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies [513] [514] [515] [516] [517] Underfull \hbox (badness 10000) in paragraph at lines 35754--35757 [][][]\T1/fi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$http : / / developer . r-[]project . org / [518] [519] Underfull \hbox (badness 10000) in paragraph at lines 35875--35879 [][][]\T1/fi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/fi4/m/n/10 http : / / developer . [520] Underfull \hbox (badness 10000) in paragraph at lines 35937--35941 [][][]\T1/fi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/fi4/m/n/10 http : / / developer . [521] [522] [523] [524] [525] [526] [527] [528] [529] Underfull \hbox (badness 10000) in paragraph at lines 36558--36560 []\T1/ptm/m/n/10 Using [][]\T1/fi4/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal l-ing [530] [531] [532] [533] [534] [535] [536] Underfull \hbox (badness 1990) in paragraph at lines 37062--37070 []\T1/fi4/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e r-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 4846) in paragraph at lines 37062--37070 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/fi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [537] [538] [539] [540] Underfull \hbox (badness 1515) in paragraph at lines 37331--37336 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0 [541] [542] [543] Underfull \hbox (badness 1917) in paragraph at lines 37554--37561 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/fi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [544] [545] [546] [547] [548] [549] [550] [551] Underfull \hbox (badness 3668) in paragraph at lines 38120--38122 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [552] [553] Underfull \hbox (badness 2401) in paragraph at lines 38220--38224 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/fi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [554] [555] Underfull \hbox (badness 10000) in paragraph at lines 38396--38401 []\T1/ptm/m/n/10 If \T1/fi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/fi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/fi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/fi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is Underfull \hbox (badness 1454) in paragraph at lines 38396--38401 \T1/fi4/m/n/10 arrayInd(which(x), dim(x), dimnames(x))\T1/ptm/m/n/10 , namely a ma-trix whose rows each are the [556] [557] [558] [559] [560] [561] [562] Underfull \hbox (badness 10000) in paragraph at lines 38815--38820 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/fi4/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 38815--38820 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to Underfull \hbox (badness 1102) in paragraph at lines 38815--38820 \T1/fi4/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10 , so \T1/fi4/m/n/10 NA \T1/ptm/m/n/10 val-ues are given rank \T1/fi4/m/n/10 NA [563] Underfull \hbox (badness 5417) in paragraph at lines 38905--38909 []\T1/fi4/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [564] Underfull \hbox (badness 10000) in paragraph at lines 38966--38970 []\T1/fi4/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard ' reg-exps, in-clud-ing el-e-ments named [565]) (./compiler-pkg.tex [566] Chapter 2. [567] [568] [569]) (./datasets-pkg.tex [570] Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] Overfull \hbox (1.81013pt too wide) in paragraph at lines 691--694 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [582] [583] Overfull \hbox (1.81013pt too wide) in paragraph at lines 824--827 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [584] [585] [586] [587] Overfull \hbox (1.81013pt too wide) in paragraph at lines 1130--1133 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] Overfull \hbox (1.81013pt too wide) in paragraph at lines 1702--1705 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [598] [599] [600] [601] [602] [603] [604] Overfull \hbox (1.81013pt too wide) in paragraph at lines 2124--2127 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [605] [606] [607] [608] [609] [610] [611] Overfull \hbox (1.81013pt too wide) in paragraph at lines 2601--2604 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [612] Overfull \vbox (13.87083pt too high) has occurred while \output is active [613] Underfull \vbox (badness 1721) has occurred while \output is active [614] [615] Overfull \vbox (12.25539pt too high) has occurred while \output is active [616] [617] Overfull \vbox (17.12102pt too high) has occurred while \output is active [618] [619] [620] [621] [622] [623] [624] [625] [626] Overfull \hbox (1.81013pt too wide) in paragraph at lines 3573--3576 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [627] [628] [629] [630] Underfull \hbox (badness 1325) in paragraph at lines 3809--3812 []\T1/ptm/m/n/10 For back-ground on Bristle-cone pines and Methuse-lah Walk, se e [][]$\T1/fi4/m/n/10 http : / / www . sonic . net / [631] [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] [642] [643]) (./grDevices-pkg.tex [644] Chapter 4. [645] [646] [647] [648] Underfull \hbox (badness 1484) in paragraph at lines 274--278 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/fi4/m/n/10 c(mi, ma, n.)\T1/p tm/m/n/10 , with iden-ti-cal mean-ing to [649] [650] [651] [652] [653] [654] [655] [656] [657] [658] [659] [660] Underfull \hbox (badness 5175) in paragraph at lines 1041--1043 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [661] [662] [663] Underfull \hbox (badness 1852) in paragraph at lines 1234--1237 []\T1/fi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [664] [665] [666] Underfull \hbox (badness 1490) in paragraph at lines 1436--1441 \T1/ptm/m/n/10 by [][]\T1/fi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/fi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/fi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "yes" \T1/ptm/m/n/10 and [667] Underfull \hbox (badness 2698) in paragraph at lines 1490--1493 []\T1/fi4/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [668] Underfull \hbox (badness 10000) in paragraph at lines 1559--1563 []\T1/ptm/m/n/10 logical; if \T1/fi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/fi4/m/n/10 TRUE \T1/ptm/m/n/10 when Underfull \hbox (badness 6332) in paragraph at lines 1559--1563 [][]\T1/fi4/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/fi 4/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is among the [669] [670] [671] [672] Underfull \hbox (badness 1033) in paragraph at lines 1842--1855 \T1/fi4/m/n/10 "pgnm"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "pgnmraw"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "pnm"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "pnmraw"\T1/ptm/m/n/10 , \T 1/fi4/m/n/10 "ppm"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "ppmraw"\T1/ptm/m/n/10 , \T1/ fi4/m/n/10 "pkm"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "pkmraw"\T1/ptm/m/n/10 , \T1/fi 4/m/n/10 "tiffcrle"\T1/ptm/m/n/10 , Underfull \hbox (badness 3758) in paragraph at lines 1842--1855 \T1/fi4/m/n/10 "tiffg3"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "tiffg32d"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "tifflzw"\T1/ptm/m/n/ 10 , \T1/fi4/m/n/10 "tiffpack"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "tiff12nc"\T1/ptm /m/n/10 , \T1/fi4/m/n/10 "tiff24nc"\T1/ptm/m/n/10 , Underfull \hbox (badness 3128) in paragraph at lines 1842--1855 \T1/fi4/m/n/10 "tiff32nc" "psmono"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "psgray"\T1/p tm/m/n/10 , \T1/fi4/m/n/10 "psrgb"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "bit"\T1/ptm/ m/n/10 , \T1/fi4/m/n/10 "bitrgb"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "bitcmyk"\T1/pt m/m/n/10 , \T1/fi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , Underfull \hbox (badness 1546) in paragraph at lines 1842--1855 \T1/fi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "pngalpha"\T1/ptm/m/n/1 0 , \T1/fi4/m/n/10 "png16"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "png256"\T1/ptm/m/n/1 0 , \T1/fi4/m/n/10 "png16m"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "png48"\T1/ptm/m/n/1 0 , \T1/fi4/m/n/10 "jpeg"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "jpeggray"\T1/ptm/m/n/ 10 , [673] [674] Underfull \hbox (badness 10000) in paragraph at lines 1951--1953 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [675] [676] Underfull \hbox (badness 6758) in paragraph at lines 2103--2106 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [677] [678] [679] [680] [681] [682] [683] [684] Underfull \hbox (badness 10000) in paragraph at lines 2606--2607 Underfull \vbox (badness 10000) has occurred while \output is active [685] [686] [687] [688] [689] [690] Underfull \hbox (badness 1755) in paragraph at lines 3044--3046 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/fi4/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [691] [692] [693] [694] [695] Underfull \hbox (badness 7851) in paragraph at lines 3365--3368 []\T1/ptm/m/n/10 For use with \T1/fi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3379--3381 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/fi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [696] [697] Underfull \hbox (badness 1173) in paragraph at lines 3495--3505 []\T1/ptm/m/n/10 The \T1/fi4/m/n/10 paper \T1/ptm/m/n/10 ar-gu-ment sets the `\ T1/fi4/m/n/10 /MediaBox\T1/ptm/m/n/10 ' en-try in the file, which de-faults to \T1/fi4/m/n/10 width \T1/ptm/m/n/10 by [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] Underfull \hbox (badness 1067) in paragraph at lines 4196--4203 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [708] [709] [710] Underfull \hbox (badness 1789) in paragraph at lines 4418--4420 []\T1/ptm/m/n/10 title string to em-bed as the \T1/fi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [711] Underfull \hbox (badness 1377) in paragraph at lines 4468--4473 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues Underfull \hbox (badness 2671) in paragraph at lines 4495--4503 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/fi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as [712] Underfull \hbox (badness 1418) in paragraph at lines 4544--4551 \T1/ptm/m/n/10 it is one of \T1/fi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/fi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ fi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4552--4561 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4552--4561 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4562--4564 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [713] Underfull \hbox (badness 1057) in paragraph at lines 4673--4678 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/fi4/m/n/10 "rgb"\T1/ptm/m/n/10 ) (which is RGB+gray) and [714] Underfull \hbox (badness 7344) in paragraph at lines 4733--4735 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso [715] [716] Underfull \hbox (badness 2035) in paragraph at lines 4857--4866 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 4857--4866 \T1/ptm/m/n/10 vided: \T1/fi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/fi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/fi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 4857--4866 \T1/fi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/fi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/fi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/fi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [717] Underfull \hbox (badness 6775) in paragraph at lines 4924--4932 \T1/ptm/m/n/10 can be found at [][]$\T1/fi4/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Underfull \hbox (badness 3000) in paragraph at lines 4924--4932 \T1/ptm/m/n/10 Lunde's CJKV re-sources are at [][]$\T1/fi4/m/n/10 ftp : / / ftp . oreilly . com / pub / examples / nutshell / cjkv / Underfull \hbox (badness 7344) in paragraph at lines 4943--4945 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso [718] [719] Underfull \hbox (badness 1546) in paragraph at lines 5063--5071 []\T1/ptm/m/n/10 arguments \T1/fi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/fi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/fi4/m/n/10 title\T1/ptm/m/n/10 , \T1/fi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/fi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/fi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/fi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/fi4/m/n/10 width\T1/ptm/m/ n/10 , [720] Underfull \hbox (badness 1648) in paragraph at lines 5140--5144 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [721] [722] [723] [724] [725] [726] [727] Underfull \hbox (badness 10000) in paragraph at lines 5558--5561 []\T1/fi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [728] Underfull \vbox (badness 10000) has occurred while \output is active [729] [730] [731] [732] [733] Underfull \hbox (badness 1189) in paragraph at lines 5954--5956 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [734] Underfull \hbox (badness 10000) in paragraph at lines 6052--6054 []\T1/fi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [735] [736] [737] [738] Underfull \hbox (badness 3780) in paragraph at lines 6343--6349 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/fi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [739] [740] [741] Underfull \hbox (badness 2680) in paragraph at lines 6539--6541 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/fi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [742] [743] [744]) (./graphics-pkg.tex Chapter 5. [745] [746] Underfull \hbox (badness 2856) in paragraph at lines 177--180 []\T1/ptm/m/n/10 For each \T1/fi4/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b e-tween the point \T1/fi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the point [747] [748] [749] [750] [751] Underfull \hbox (badness 4492) in paragraph at lines 465--471 []\T1/ptm/m/n/10 When \T1/fi4/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [752] [753] [754] Underfull \hbox (badness 10000) in paragraph at lines 690--697 []\T1/fi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/fi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [755] [756] [757] Underfull \hbox (badness 1389) in paragraph at lines 856--859 []\T1/ptm/m/n/10 logical. If \T1/fi4/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic h di-vide ad-ja-cent (non-stacked!) bars [758] Underfull \vbox (badness 10000) has occurred while \output is active [759] [760] [761] [762] [763] Underfull \hbox (badness 4634) in paragraph at lines 1253--1256 [][][]\T1/fi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/fi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] Underfull \hbox (badness 1009) in paragraph at lines 2286--2293 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] Underfull \vbox (badness 10000) has occurred while \output is active [801] [802] [803] [804] Underfull \hbox (badness 1867) in paragraph at lines 3911--3915 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [805] [806] [807] [808] [809] [810] [811] Underfull \hbox (badness 1924) in paragraph at lines 4362--4367 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 2529) in paragraph at lines 4391--4394 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used: see [812] [813] [814] [815] [816] Underfull \hbox (badness 10000) in paragraph at lines 4735--4741 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/fi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4735--4741 \T1/fi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/fi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that Underfull \hbox (badness 1072) in paragraph at lines 4735--4741 \T1/fi4/m/n/10 c([][]strwidth[][][](ch), [][]strheight[][][](ch)) \T1/ptm/m/n/1 0 for a given string \T1/fi4/m/n/10 ch \T1/ptm/m/n/10 is usu-ally much more pre - [817] [818] Underfull \hbox (badness 10000) in paragraph at lines 4865--4868 [819 ] Underfull \hbox (badness 10000) in paragraph at lines 4926--4928 [820 ] [821] Underfull \hbox (badness 10000) in paragraph at lines 5115--5117 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/fi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [822] Underfull \vbox (badness 10000) has occurred while \output is active [823] [824] Underfull \hbox (badness 4156) in paragraph at lines 5271--5274 []\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/fi4/m/n/10 z \T1/ptm /m/n/10 co-or-di-nates. Of-ten used with [825] [826] [827] [828] [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] [839] [840] [841] [842] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6520--6521 [][] [843 ] [844] Underfull \vbox (badness 10000) has occurred while \output is active [845] Overfull \hbox (9.78088pt too wide) in paragraph at lines 6679--6679 []\T1/fi4/m/n/9 TestChars(font = 5) # Euro might be at 160 (0+10*16). Mac OS has apple at 240 (0+15*16).[] [846] [847] [848] [849] [850] [851] [852] [853] Underfull \hbox (badness 1048) in paragraph at lines 7227--7232 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [854] [855] Underfull \hbox (badness 1540) in paragraph at lines 7343--7346 []\T1/ptm/m/n/10 For each \T1/fi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/fi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [856] [857] [858] [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] Underfull \hbox (badness 2050) in paragraph at lines 8155--8159 []\T1/ptm/m/n/10 For \T1/fi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/fi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [869] [870] [871] [872] [873] (/usr/share/texmf/tex/latex/inconsolata/ts1fi4.fd ) [874] Underfull \hbox (badness 6691) in paragraph at lines 8555--8558 []\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex- pan-sion) Underfull \hbox (badness 2799) in paragraph at lines 8558--8560 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font and size \T1/fi4/m/n/10 par ("font.sub") \T1/ptm/m/n/10 and color [875]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8640 \HeaderA{units}{Graphical Units}{units} [876] [877] [878] [879]) (./grid-pkg.tex [880] Chapter 6. [881] [882] [883] [884] [885] [886] Underfull \hbox (badness 2680) in paragraph at lines 405--408 []\T1/ptm/m/n/10 Note that \T1/fi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /fi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [887] [888] [889] [890] [891] [892] [893] [894] [895] Underfull \hbox (badness 4279) in paragraph at lines 945--954 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/fi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/fi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/fi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [896] [897] [898] Underfull \hbox (badness 2781) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 Both func-tions cre-ate an ar-rows grob (a graph-i-cal ob-ject de-scrib-ing ar-rows), but only [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948] Underfull \hbox (badness 1067) in paragraph at lines 4359--4362 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [949] [950] [951] [952] Underfull \hbox (badness 7256) in paragraph at lines 4598--4600 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] Underfull \hbox (badness 2096) in paragraph at lines 5805--5811 \T1/ptm/m/n/10 pos-si-ble to add and sub-tract unit ob-jects (e.g., \T1/fi4/m/n /10 unit(1, "npc") - unit(1, "inches")\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 5805--5811 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [971] [972] [973] [974] [975] [976] [977] Underfull \hbox (badness 7649) in paragraph at lines 6267--6270 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like [978] [979] [980] [981] [982]) (./methods-pkg.tex Chapter 7. [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] Underfull \hbox (badness 2237) in paragraph at lines 1432--1434 []\T1/ptm/m/n/10 The class \T1/fi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/fi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/fi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] Underfull \hbox (badness 1590) in paragraph at lines 1979--1986 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/fi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests Underfull \hbox (badness 10000) in paragraph at lines 2028--2033 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/fi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 2028--2033 \T1/ptm/m/n/10 file name is passed to \T1/fi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/fi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] Underfull \hbox (badness 10000) in paragraph at lines 2628--2631 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/fi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/fi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1017] [1018] Underfull \hbox (badness 1132) in paragraph at lines 2768--2772 []\T1/ptm/m/n/10 In \T1/fi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/fi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/fi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in Underfull \hbox (badness 1033) in paragraph at lines 2800--2805 \T1/ptm/m/n/10 In ad-di-tion, \T1/fi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/fi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1019] [1020] [1021] [1022] [1023] [1024] [1025] Underfull \hbox (badness 1102) in paragraph at lines 3308--3310 []\T1/fi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1026] [1027] [1028] [1029] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\T1/ptm/m/n/10 The \T1/fi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3645--3654 []\T1/ptm/m/n/10 The [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] Underfull \hbox (badness 1436) in paragraph at lines 4550--4553 []\T1/ptm/m/n/10 The class \T1/fi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/fi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4579--4585 []\T1/ptm/m/n/10 class [][]\T1/fi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4579--4585 \T1/fi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/fi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1043] [1044] [1045] [1046] [1047] [1048] [1049] Underfull \vbox (badness 10000) has occurred while \output is active [1050] [1051] Underfull \hbox (badness 1092) in paragraph at lines 5251--5258 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 5251--5258 \T1/ptm/m/n/10 if se-lect-ing class \T1/fi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/fi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and Underfull \hbox (badness 4036) in paragraph at lines 5299--5302 []\T1/ptm/m/n/10 Object of class \T1/fi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1052] [1053] [1054] [1055] [1056] Underfull \hbox (badness 1087) in paragraph at lines 5619--5624 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1057] [1058] [1059] Underfull \hbox (badness 2221) in paragraph at lines 5845--5850 []\T1/ptm/m/n/10 Two op-tional method names are in-ter-preted spe-cially, \T1/f i4/m/n/10 initialize \T1/ptm/m/n/10 and [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069]pdfTeX war ning (ext4): destination with the same identifier (name{Rfn.S4}) has been alrea dy used, duplicate ignored \relax l.6701 \aliasA{S4}{S3Part}{S4} [1070] [1071] [1072]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.6977 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.6979 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.6980 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.6982 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.6983 \aliasA{Summary}{S4groupGeneric}{Summary} [1073] Underfull \hbox (badness 2050) in paragraph at lines 7044--7048 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1074] [1075] [1076] Underfull \hbox (badness 1286) in paragraph at lines 7227--7229 []\T1/ptm/m/n/10 for \T1/fi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/fi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] Underfull \vbox (badness 10000) has occurred while \output is active [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] Underfull \hbox (badness 2894) in paragraph at lines 9560--9564 []\T1/ptm/m/n/10 Chambers, John M. (2009) \T1/ptm/m/it/10 Class In-her-i-tance in R [][]$\T1/fi4/m/n/10 http : / / stat . stanford . edu / ~jmc4 / [1107] Underfull \hbox (badness 1852) in paragraph at lines 9639--9643 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., [1108] [1109] [1110]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 15--17 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/fi4 /m/n/10 "L'Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[][][]: see [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] Underfull \hbox (badness 3386) in paragraph at lines 1221--1224 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/fi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1128] [1129] [1130]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/fi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143]) (./stats-pkg.tex [1144] Chapter 10. [1145] [1146] [1147] [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] Underfull \hbox (badness 1412) in paragraph at lines 832--834 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/fi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/fi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1157] [1158] [1159] [1160] [1161] [1162] [1163] [1164] Underfull \hbox (badness 2503) in paragraph at lines 1320--1323 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1165] [1166] Underfull \hbox (badness 10000) in paragraph at lines 1499--1503 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] Underfull \hbox (badness 3965) in paragraph at lines 2150--2152 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1177] [1178] [1179] [1180] [1181] Underfull \hbox (badness 3965) in paragraph at lines 2479--2481 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 2503) in paragraph at lines 3255--3258 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] Underfull \hbox (badness 3989) in paragraph at lines 4477--4484 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] Underfull \hbox (badness 2932) in paragraph at lines 5092--5094 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/fi4/m/n/10 x \T1/ptm/m/n/10 and \T1/fi4/m/n/10 y \T1/ptm/m/n/10 is given by [1221] [1222] [1223] Underfull \hbox (badness 1603) in paragraph at lines 5299--5304 []\T1/fi4/m/n/10 var \T1/ptm/m/n/10 is just an-other in-ter-face to \T1/fi4/m/n /10 cov\T1/ptm/m/n/10 , where \T1/fi4/m/n/10 na.rm \T1/ptm/m/n/10 is used to de -ter-mine the de-fault for Underfull \hbox (badness 1472) in paragraph at lines 5299--5304 \T1/fi4/m/n/10 use \T1/ptm/m/n/10 when that is un-spec-i-fied. If \T1/fi4/m/n/1 0 na.rm \T1/ptm/m/n/10 is \T1/fi4/m/n/10 TRUE \T1/ptm/m/n/10 then the com-plete ob-ser-va-tions (rows) Underfull \hbox (badness 3108) in paragraph at lines 5299--5304 \T1/ptm/m/n/10 are used (\T1/fi4/m/n/10 use = "na.or.complete"\T1/ptm/m/n/10 ) to com-pute the vari-ance. Oth-er-wise, by de-fault Underfull \hbox (badness 1142) in paragraph at lines 5333--5345 \T1/ptm/m/n/10 For \T1/fi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1224] [1225] Underfull \hbox (badness 2503) in paragraph at lines 5472--5476 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1226] Underfull \hbox (badness 1168) in paragraph at lines 5533--5538 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] Underfull \hbox (badness 8132) in paragraph at lines 5976--5981 \T1/ptm/m/n/10 then \T1/fi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/fi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1235] [1236] [1237] Underfull \hbox (badness 7081) in paragraph at lines 6231--6234 []\T1/ptm/m/n/10 Objects of class \T1/fi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/fi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6235--6237 []\T1/fi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/fi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1238] [1239] [1240] [1241] [1242] Underfull \vbox (badness 10000) has occurred while \output is active [1243] [1244] [1245] [1246] [1247] [1248] [1249] Underfull \hbox (badness 10000) in paragraph at lines 7035--7038 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/fi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1250] [1251] Underfull \hbox (badness 10000) in paragraph at lines 7172--7175 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/fi4/m/n/10 ht tp : / / cran . r-[]project . org / web / views / [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] Underfull \hbox (badness 2626) in paragraph at lines 8625--8628 []\T1/ptm/m/n/10 Either \T1/fi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/fi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1274] [1275] Underfull \hbox (badness 2503) in paragraph at lines 8725--8729 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1276] [1277] [1278] [1279] [1280] Overfull \hbox (11.88992pt too wide) in paragraph at lines 9059--9061 []\T1/ptm/m/n/10 the char-ac-ter string \T1/fi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] Underfull \hbox (badness 1019) in paragraph at lines 9725--9728 []\T1/ptm/m/n/10 See also [][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [][]$\T1/fi4/m/n/ 10 http : / / dlmf . [1290] [1291] [1292] [1293] Underfull \hbox (badness 4518) in paragraph at lines 9986--9991 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1294] [1295] [1296] [1297] [1298] Underfull \hbox (badness 2142) in paragraph at lines 10327--10330 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10346--10349 []\T1/ptm/m/n/10 When \T1/fi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/fi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1299] Underfull \hbox (badness 1708) in paragraph at lines 10408--10411 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1300] [1301] [1302] [1303] [1304] Underfull \hbox (badness 1694) in paragraph at lines 10772--10775 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 10791--10800 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1305] [1306] [1307] [1308] [1309] [1310] [1311]pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.hat}) has been already used, duplicate i gnored \relax l.11238 \aliasA{hat}{influence.measures}{hat} [1312] [1313] Underfull \hbox (badness 1484) in paragraph at lines 11362--11364 []\T1/ptm/m/n/10 The func-tion \T1/fi4/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 4441) in paragraph at lines 11909--11911 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] Underfull \hbox (badness 4518) in paragraph at lines 12869--12874 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] Underfull \hbox (badness 4518) in paragraph at lines 13487--13492 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] Overfull \hbox (5.6622pt too wide) in paragraph at lines 14053--14055 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/fi4/m/n/10 -plnorm(t, r, lower = FALSE, l og = TRUE)\T1/ptm/m/n/10 . [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] Underfull \hbox (badness 2503) in paragraph at lines 14682--14686 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1364] [1365] Underfull \vbox (badness 10000) has occurred while \output is active [1366] [1367] [1368] [1369] [1370] [1371] Underfull \hbox (badness 3009) in paragraph at lines 15190--15196 []\T1/fi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/fi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/fi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] Underfull \hbox (badness 2359) in paragraph at lines 16811--16813 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1396] Underfull \vbox (badness 10000) has occurred while \output is active [1397] Underfull \vbox (badness 10000) has occurred while \output is active [1398] [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] Underfull \hbox (badness 1377) in paragraph at lines 17713--17718 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 17718--17721 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 2343) in paragraph at lines 17731--17735 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 2080) in paragraph at lines 17731--17735 \T1/ptm/m/n/10 the value by a fac-tor of \T1/fi4/m/n/10 reltol * (abs(val) + re ltol) \T1/ptm/m/n/10 at a step. De-faults to [1410] Underfull \hbox (badness 2662) in paragraph at lines 17739--17743 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/fi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/fi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/fi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1411] [1412] Underfull \vbox (badness 10000) has occurred while \output is active [1413] [1414] [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 1337) in paragraph at lines 18355--18358 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] Underfull \hbox (badness 5563) in paragraph at lines 19082--19084 []\T1/ptm/m/n/10 logical. If \T1/fi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19085--19088 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1432] [1433] [1434] [1435] [1436] Underfull \hbox (badness 1675) in paragraph at lines 19372--19375 []\T1/ptm/m/n/10 Setting \T1/fi4/m/n/10 lower.tail = FALSE \T1/ptm/m/n/10 al-lo ws to get much more pre-cise re-sults when the de-fault, [1437] Underfull \hbox (badness 2503) in paragraph at lines 19457--19460 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 19484--19486 []\T1/ptm/m/n/10 the char-ac-ter string \T1/fi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] Underfull \hbox (badness 10000) in paragraph at lines 20454--20460 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/fi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/fi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] Underfull \hbox (badness 2111) in paragraph at lines 21422--21427 []\T1/ptm/m/n/10 Utility func-tion to be used in higher-level [][]\T1/fi4/m/n/1 0 print[][][] \T1/ptm/m/n/10 meth-ods, such as [][]\T1/fi4/m/n/10 print.summary .lm[][][]\T1/ptm/m/n/10 , [1469] [1470] [1471] [1472] [1473] Underfull \hbox (badness 1337) in paragraph at lines 21761--21767 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] Underfull \hbox (badness 10000) in paragraph at lines 22554--22557 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 1675) in paragraph at lines 22554--22557 \T1/fi4/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if al-ready [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] Underfull \hbox (badness 10000) in paragraph at lines 23130--23133 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/fi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1494] Underfull \hbox (badness 3690) in paragraph at lines 23181--23185 [][][]\T1/fi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from Underfull \hbox (badness 1062) in paragraph at lines 23181--23185 \T1/fi4/m/n/10 runmed(*, endrule = "median")\T1/ptm/m/n/10 . [][]\T1/fi4/m/n/10 smooth[][][] \T1/ptm/m/n/10 uses run-ning me-di-ans of 3 for its com-pound [1495] [1496] [1497] [1498] Underfull \hbox (badness 7667) in paragraph at lines 23447--23449 []\T1/ptm/m/n/10 a nu-meric vec-tor or an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-je ct which is co-ercible to one by [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] Underfull \vbox (badness 10000) has occurred while \output is active [1525] Underfull \hbox (badness 3514) in paragraph at lines 25197--25202 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1526] Underfull \hbox (badness 3514) in paragraph at lines 25259--25264 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1527] Underfull \hbox (badness 3514) in paragraph at lines 25316--25321 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1528] Underfull \hbox (badness 3514) in paragraph at lines 25377--25383 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1529] [1530] [1531] Underfull \hbox (badness 3514) in paragraph at lines 25572--25577 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1532] Underfull \hbox (badness 3514) in paragraph at lines 25628--25633 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1533] Underfull \hbox (badness 3514) in paragraph at lines 25685--25690 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1534] Underfull \hbox (badness 3514) in paragraph at lines 25740--25745 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1535] Underfull \hbox (badness 6691) in paragraph at lines 25809--25814 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1536] [1537] [1538] [1539] [1540] [1541] [1542] Underfull \hbox (badness 10000) in paragraph at lines 26279--26282 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 26279--26282 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/fi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] Underfull \hbox (badness 5431) in paragraph at lines 26885--26887 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/f i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1553] [1554] [1555] Underfull \hbox (badness 5431) in paragraph at lines 27095--27098 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/f i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1556] [1557] [1558] [1559] [1560] Underfull \hbox (badness 1337) in paragraph at lines 27406--27410 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1561] [1562] Underfull \hbox (badness 10000) in paragraph at lines 27523--27526 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/fi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1563] [1564] [1565] Underfull \hbox (badness 1616) in paragraph at lines 27706--27709 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] Underfull \hbox (badness 1337) in paragraph at lines 29085--29089 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] Underfull \hbox (badness 1337) in paragraph at lines 29569--29573 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1595] Underfull \hbox (badness 5161) in paragraph at lines 29662--29664 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1596] [1597] [1598] [1599] [1600] Underfull \hbox (badness 10000) in paragraph at lines 30026--30031 []\T1/ptm/m/n/10 There is a \T1/fi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/fi4/m/n/10 table \T1/ptm/m/n/10 or Underfull \hbox (badness 3209) in paragraph at lines 30026--30031 \T1/fi4/m/n/10 xtabs(*, sparse = FALSE)\T1/ptm/m/n/10 , which gives ba-sic in-f or-ma-tion and per-forms a chi-squared [1601] [1602] [1603]) (./stats4-pkg.tex [1604] Chapter 11. [1605] [1606] [1607] [1608] [1609] [1610]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1611] [1612] [1613]) (./tcltk-pkg.tex [1614] Chapter 12. [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \vbox (badness 10000) has occurred while \output is active [1622] Underfull \hbox (badness 1546) in paragraph at lines 649--656 []\T1/fi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing any Tk or Tcl com-mand by sim-ply run-ning [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] Underfull \hbox (badness 3375) in paragraph at lines 1391--1394 [][][]\T1/fi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the OS X GUI), [][]\T1/fi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh ose [1634]) (./tools-pkg.tex Chapter 13. [1635] LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined (Font) using `T1/fi4/m/n' instead on input line 72. [1636] Underfull \hbox (badness 1308) in paragraph at lines 173--186 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 types Underfull \hbox (badness 4967) in paragraph at lines 173--186 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/fi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 173--186 \T1/fi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/fi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/fi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/fi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 173--186 \T1/fi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/fi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/fi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/fi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1637] [1638] [1639] Underfull \hbox (badness 2080) in paragraph at lines 333--338 \T1/ptm/m/n/10 ac-ters. It is sorted by Uni-code point and within a point al-ph a-bet-i-cally on the glyph Underfull \hbox (badness 2644) in paragraph at lines 333--338 \T1/ptm/m/n/10 (there can be more than one name for a Uni-code point). The data are in the file [1640] [1641] [1642] [1643] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1644] [1645] [1646] [1647] Underfull \hbox (badness 1635) in paragraph at lines 851--853 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1648] Underfull \hbox (badness 4441) in paragraph at lines 925--933 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- Underfull \hbox (badness 1014) in paragraph at lines 945--947 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies [1649] Underfull \hbox (badness 10000) in paragraph at lines 968--971 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 968--971 \T1/fi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/f i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1650] [1651] Underfull \hbox (badness 10000) in paragraph at lines 1096--1098 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1652] [1653] Underfull \hbox (badness 7981) in paragraph at lines 1263--1267 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1263--1267 \T1/fi4/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . Underfull \hbox (badness 1082) in paragraph at lines 1269--1271 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/fi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1654] [1655] [1656] [1657] Underfull \hbox (badness 5726) in paragraph at lines 1532--1537 []\T1/ptm/m/n/10 If \T1/fi4/m/n/10 reduce \T1/ptm/m/n/10 is \T1/fi4/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/fi4/m/n/10 De pendsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 1532--1537 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1658] [1659] [1660] [1661] [1662] Underfull \hbox (badness 7981) in paragraph at lines 1848--1854 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1848--1854 \T1/fi4/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1663] [1664] [1665] [1666] LaTeX Font Warning: Font shape `T1/fi4/m/sl' undefined (Font) using `T1/fi4/m/n' instead on input line 2102. [1667] [1668] [1669] Underfull \hbox (badness 1424) in paragraph at lines 2338--2340 []\T1/fi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1670] [1671] [1672] [1673] [1674] [1675] [1676] Underfull \hbox (badness 1675) in paragraph at lines 2852--2854 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing how the news en-tries shoul d be \T1/ptm/m/it/10 chopped\T1/ptm/m/n/10 ; [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] Underfull \hbox (badness 1838) in paragraph at lines 3427--3433 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/fi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/fi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 3427--3433 \T1/ptm/m/n/10 `\T1/fi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1686] Underfull \hbox (badness 5726) in paragraph at lines 3507--3512 []\T1/ptm/m/n/10 If \T1/fi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/fi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/fi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 3507--3512 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1687] [1688] Underfull \hbox (badness 1688) in paragraph at lines 3645--3657 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/fi4/m/sl/10 PACKAGES\T1/ptm/m/n/10 ' and [1689] [1690] [1691] [1692]) (./utils-pkg.tex Chapter 14. Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/fi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1693] [1694] [1695] Underfull \hbox (badness 1454) in paragraph at lines 198--201 []\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive , \T1/fi4/m/sl/10 TRUE \T1/ptm/m/n/10 by de- Underfull \hbox (badness 1540) in paragraph at lines 214--217 []\T1/fi4/m/sl/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for the same task as \T1/fi4/m/sl/10 apropos\T1/ptm/m/n/10 . How-ever, by de-fault [1696] [1697] [1698] [1699] [1700] Underfull \hbox (badness 10000) in paragraph at lines 539--545 []\T1/ptm/m/n/10 Functions \T1/fi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/fi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 539--545 \T1/fi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/fi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1701] [1702] Underfull \hbox (badness 5847) in paragraph at lines 650--656 []\T1/ptm/m/n/10 Argument \T1/fi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 650--656 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/fi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as Underfull \hbox (badness 3861) in paragraph at lines 715--720 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/fi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/fi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] Underfull \hbox (badness 1371) in paragraph at lines 1288--1290 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/fi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/fi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1712] [1713] [1714] [1715] Underfull \hbox (badness 2057) in paragraph at lines 1560--1562 []\T1/ptm/m/n/10 None for \T1/fi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1716] [1717] Underfull \hbox (badness 5189) in paragraph at lines 1745--1747 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1718] [1719] [1720] Underfull \hbox (badness 1661) in paragraph at lines 1960--1967 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/fi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- [1721] Underfull \hbox (badness 1990) in paragraph at lines 1972--1975 []\T1/ptm/m/n/10 a [][]\T1/fi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/fi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/fi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1722] [1723] [1724] [1725] [1726] Overfull \hbox (6.10922pt too wide) in paragraph at lines 2363--2366 []\T1/ptm/m/n/10 files end-ing `\T1/fi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/fi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/fi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";")\T1/ptm/m/n/10 , [1727] [1728] [1729] [1730] [1731] [1732] [1733] [1734] Underfull \hbox (badness 1430) in paragraph at lines 2936--2942 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/fi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 2837) in paragraph at lines 2936--2942 \T1/fi4/m/sl/10 internet.info \T1/ptm/m/n/10 op-tion. The de-tails de-pend on t he plat-form and scheme, but set-ting [1735] Underfull \hbox (badness 1231) in paragraph at lines 2980--2986 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1736] [1737] [1738] [1739] [1740] [1741] Underfull \hbox (badness 1210) in paragraph at lines 3360--3367 []\T1/ptm/m/n/10 logical or ex-pres-sion; if not \T1/fi4/m/sl/10 FALSE\T1/ptm/m /n/10 , the ran-dom num-ber gen-er-a-tor state [1742] [1743] [1744] [1745] [1746]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.3743 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.3743 ...mat Unordered and Ordered Lists}{format} [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] Underfull \hbox (badness 1371) in paragraph at lines 4648--4650 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/fi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/fi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1761] [1762] Underfull \hbox (badness 1502) in paragraph at lines 4737--4742 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 4737--4742 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1763] [1764] Underfull \hbox (badness 10000) in paragraph at lines 4901--4910 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1765] [1766] Underfull \hbox (badness 3118) in paragraph at lines 5017--5019 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [1767] Underfull \hbox (badness 2057) in paragraph at lines 5099--5105 \T1/ptm/m/n/10 can be source archives or bi-nary pack-age archive files (as cre -ated by Underfull \hbox (badness 1348) in paragraph at lines 5145--5150 []\T1/ptm/m/n/10 logical in-di-cat-ing to also in-stall unin-stalled pack-ages which these pack- Underfull \hbox (badness 3884) in paragraph at lines 5145--5150 \T1/ptm/m/n/10 ages de-pend on/link to/import/suggest (and so on re-cur-sively) . Not Underfull \hbox (badness 3657) in paragraph at lines 5145--5150 \T1/ptm/m/n/10 used if \T1/fi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be a char-ac-ter vec-tor, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 5158--5165 []\T1/fi4/m/sl/10 TRUE \T1/ptm/m/n/10 means (as from \T1/phv/m/n/10 R \T1/ptm/m /n/10 2.15.0) to use Underfull \hbox (badness 10000) in paragraph at lines 5158--5165 \T1/fi4/m/sl/10 c("Depends", "Imports", "LinkingTo", "Suggests") \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 pkgs \T1/ptm/m/n/10 and Underfull \hbox (badness 2103) in paragraph at lines 5158--5165 \T1/fi4/m/sl/10 c("Depends", "Imports", "LinkingTo") \T1/ptm/m/n/10 for added d e-pen-den-cies: this [1768] Underfull \hbox (badness 10000) in paragraph at lines 5200--5203 []\T1/ptm/m/n/10 (not used on Win-dows) anal-o-gous to \T1/fi4/m/sl/10 configur e.args \T1/ptm/m/n/10 for flag Underfull \hbox (badness 10000) in paragraph at lines 5226--5229 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 5226--5229 \T1/ptm/m/n/10 passed to \T1/fi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou rce pack-age in-stall. E.g., [1769] [1770] Underfull \hbox (badness 10000) in paragraph at lines 5356--5361 [][][]\T1/fi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] [1787] Underfull \hbox (badness 10000) in paragraph at lines 6480--6482 []\T1/fi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 6485--6490 []\T1/ptm/m/n/10 If a `\T1/fi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [1788] [1789] [1790] Underfull \hbox (badness 10000) in paragraph at lines 6642--6645 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 6642--6645 [][]\T1/fi4/m/sl/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/fi4/m/sl/1 0 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els [1791] [1792] [1793] [1794] [1795] Underfull \hbox (badness 1789) in paragraph at lines 7023--7025 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] Underfull \hbox (badness 1097) in paragraph at lines 7822--7825 []\T1/ptm/m/n/10 The name \T1/fi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [1807] [1808] Underfull \hbox (badness 3000) in paragraph at lines 7950--7955 [][][]\T1/fi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/fi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [1809] [1810] [1811] [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 2134) in paragraph at lines 8512--8517 [][][]\T1/fi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/fi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [1817] [1818] [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] Underfull \hbox (badness 10000) in paragraph at lines 9455--9457 [][][]$\T1/fi4/m/sl/10 http : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/fi4/m/sl/10 http : / / www . gnu . org / software / emacs / [1831] [1832] [1833] Underfull \hbox (badness 10000) in paragraph at lines 9633--9637 []\T1/ptm/m/n/10 The de-fault for \T1/fi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 9664--9670 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [1834] Underfull \hbox (badness 2096) in paragraph at lines 9778--9781 []\T1/ptm/m/n/10 logical (\T1/fi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 9782--9785 []\T1/ptm/m/n/10 logical (\T1/fi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [1835] Underfull \hbox (badness 1009) in paragraph at lines 9849--9860 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [1836] [1837] [1838] [1839] [1840] Underfull \hbox (badness 2635) in paragraph at lines 10150--10153 []\T1/ptm/m/n/10 Repository `\T1/fi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [1841] [1842] [1843] [1844] [1845] Underfull \hbox (badness 5970) in paragraph at lines 10514--10517 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 3449) in paragraph at lines 10525--10534 []\T1/ptm/m/n/10 string in-di-cat-ing if the \T1/fi4/m/sl/10 width \T1/ptm/m/n/ 10 ar-gu-ment's spec-i-fi-ca-tion should be fol- Underfull \hbox (badness 7379) in paragraph at lines 10525--10534 \T1/ptm/m/n/10 lowed strictly, one of the val-ues \T1/fi4/m/sl/10 c("no", "cut" , "wrap")\T1/ptm/m/n/10 . De- Underfull \hbox (badness 1824) in paragraph at lines 10525--10534 \T1/ptm/m/n/10 faults to the \T1/fi4/m/sl/10 strict.width \T1/ptm/m/n/10 com-po -nent of op-tion \T1/fi4/m/sl/10 "str" \T1/ptm/m/n/10 (see [][]\T1/fi4/m/sl/10 options[][][]\T1/ptm/m/n/10 ) Underfull \hbox (badness 3769) in paragraph at lines 10525--10534 \T1/ptm/m/n/10 which de-faults to \T1/fi4/m/sl/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons; \T1/fi4/m/sl/10 "wrap" \T1/ptm/m/n/10 uses [1846] [1847] [1848] Underfull \hbox (badness 10000) in paragraph at lines 10693--10695 []\T1/ptm/m/n/10 Options other than \T1/fi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [1849] [1850] Underfull \hbox (badness 2213) in paragraph at lines 10847--10854 []\T1/ptm/m/n/10 If \T1/fi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, Underfull \hbox (badness 1688) in paragraph at lines 10847--10854 \T1/ptm/m/n/10 and se-lected if their \T1/fi4/m/sl/10 extension \T1/ptm/m/n/10 com-po-nent matches (as a reg-exp) the file name. Ob- [1851] [1852] [1853] Underfull \hbox (badness 10000) in paragraph at lines 11088--11091 [][][]$\T1/fi4/m/sl/10 http : / / en . wikipedia . org / wiki / Tar _ (file _ f ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/fi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 11088--11091 \T1/fi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [1854] [1855] [1856] [1857] [1858] [1859] [1860] [1861] Underfull \hbox (badness 10000) in paragraph at lines 11593--11595 []\T1/ptm/m/n/10 Arguments such as \T1/fi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/fi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 1052) in paragraph at lines 11596--11598 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 11626--11631 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined Underfull \hbox (badness 10000) in paragraph at lines 11626--11631 \T1/ptm/m/n/10 see [][]\T1/fi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/fi4/m/sl/10 available = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 6961) in paragraph at lines 11626--11631 \T1/fi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by de- [1862] Underfull \hbox (badness 10000) in paragraph at lines 11655--11658 [][][]\T1/fi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [1863] Underfull \hbox (badness 10000) in paragraph at lines 11733--11738 []\T1/ptm/m/n/10 Characters in a URL other than the En-glish al-phanu-meric cha r-ac-ters and [1864] [1865] [1866] [1867] Underfull \hbox (badness 1454) in paragraph at lines 11960--11964 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [1868] Underfull \hbox (badness 10000) in paragraph at lines 12030--12032 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion e.g. [1869] [1870] [1871]) [1872] [1873] [1874] (./KernSmooth-pkg.tex Chapter 15. [1875] [1876] [1877] [1878] [1879] [1880] [1881] [1882] [1883] [1884]) (./MASS-pkg.tex Chapter 16. [1885] [1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901] [1902] [1903] [1904] [1905] [1906] Underfull \hbox (badness 7256) in paragraph at lines 1601--1603 []\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo r [1907] [1908] [1909] [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917] [1918] [1919] [1920] [1921] Underfull \hbox (badness 7944) in paragraph at lines 2691--2694 []\T1/ptm/m/n/10 further ar-gu-ments for \T1/fi4/m/sl/10 plot \T1/ptm/m/n/10 an d graph-i-cal pa-ram-e-ters. Note that [1922] [1923] [1924] Underfull \hbox (badness 2384) in paragraph at lines 2861--2866 []\T1/ptm/m/n/10 Distributions \T1/fi4/m/sl/10 "beta"\T1/ptm/m/n/10 , \T1/fi4/m /sl/10 "cauchy"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "chi-squared"\T1/ptm/m/n/10 , \ T1/fi4/m/sl/10 "exponential"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "f"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2861--2866 \T1/fi4/m/sl/10 "gamma"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "geometric"\T1/ptm/m/n/ 10 , \T1/fi4/m/sl/10 "log-normal"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "lognormal"\T 1/ptm/m/n/10 , \T1/fi4/m/sl/10 "logistic"\T1/ptm/m/n/10 , Underfull \hbox (badness 2293) in paragraph at lines 2861--2866 \T1/fi4/m/sl/10 "negative binomial"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "normal"\T1 /ptm/m/n/10 , \T1/fi4/m/sl/10 "Poisson"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "t" \T1 /ptm/m/n/10 and \T1/fi4/m/sl/10 "weibull" \T1/ptm/m/n/10 are [1925] [1926] Underfull \hbox (badness 4686) in paragraph at lines 3029--3031 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds Underfull \hbox (badness 2591) in paragraph at lines 3043--3047 []\T1/ptm/m/n/10 where \T1/fi4/m/sl/10 p1\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 p2\T1 /ptm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/fi4/m /sl/10 cycles \T1/ptm/m/n/10 terms or when a [1927] [1928] [1929] Underfull \hbox (badness 10000) in paragraph at lines 3231--3233 []\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/fi4/m/sl/10 Gamma \T1/ptm/m/n/ 10 fam-ily or \T1/fi4/m/sl/10 quasi \T1/ptm/m/n/10 fam-ily with [1930] [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] Underfull \hbox (badness 10000) in paragraph at lines 4800--4803 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm Underfull \hbox (badness 1173) in paragraph at lines 4800--4803 \T1/fi4/m/sl/10 response ~ predictors\T1/ptm/m/n/10 . See the doc-u-men-ta-tion of \T1/fi4/m/sl/10 formula \T1/ptm/m/n/10 for other [1952] Underfull \hbox (badness 10000) in paragraph at lines 4878--4881 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm Underfull \hbox (badness 1173) in paragraph at lines 4878--4881 \T1/fi4/m/sl/10 response ~ predictors\T1/ptm/m/n/10 . See the doc-u-men-ta-tion of \T1/fi4/m/sl/10 formula \T1/ptm/m/n/10 for other [1953] [1954] [1955] [1956] [1957] [1958] Underfull \hbox (badness 1975) in paragraph at lines 5355--5357 []\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in the case of [1959] [1960] [1961] [1962] [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970] [1971] [1972] [1973] [1974] Underfull \vbox (badness 10000) has occurred while \output is active [1975] [1976] [1977] [1978] [1979] [1980] [1981] [1982] Underfull \hbox (badness 10000) in paragraph at lines 7103--7110 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm Underfull \hbox (badness 1540) in paragraph at lines 7103--7110 \T1/fi4/m/sl/10 response ~ predictors\T1/ptm/m/n/10 . The re-sponse should be a fac-tor (prefer-ably [1983] [1984] [1985] [1986] Underfull \hbox (badness 6775) in paragraph at lines 7341--7344 \T1/ptm/m/n/10 only the first \T1/fi4/m/sl/10 dimen \T1/ptm/m/n/10 dis-crim-i-n ant com-po-nents are used (ex-cept for [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] Underfull \hbox (badness 4686) in paragraph at lines 7974--7976 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [1995] Underfull \hbox (badness 2591) in paragraph at lines 7990--7994 []\T1/ptm/m/n/10 where \T1/fi4/m/sl/10 p1\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 p2\T1 /ptm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/fi4/m /sl/10 cycles \T1/ptm/m/n/10 terms or when a [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014] Underfull \hbox (badness 1259) in paragraph at lines 9376--9378 []\T1/ptm/m/n/10 if \T1/fi4/m/sl/10 TRUE \T1/ptm/m/n/10 re-turn ob-served and e x-pected fre-quen-cies in the re-sult. Us-ing [2015] [2016] [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032]) (./Matrix-pkg.tex Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 42--45 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 42--45 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2033] Underfull \hbox (badness 1769) in paragraph at lines 96--99 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2034] [2035] [2036] [2037] Underfull \hbox (badness 5119) in paragraph at lines 502--506 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class [2038] [2039] Underfull \hbox (badness 2418) in paragraph at lines 589--592 []\T1/ptm/m/n/10 The value of \T1/fi4/m/sl/10 bdiag() \T1/ptm/m/n/10 in-heris f rom class [][]\T1/fi4/m/sl/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , whereas \T1/f i4/m/sl/10 .bdiag() \T1/ptm/m/n/10 re-turns a [2040] [2041] Underfull \hbox (badness 10000) in paragraph at lines 731--734 []\T1/ptm/m/n/10 In some ver-sions of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , [][]\T1/ fi4/m/sl/10 eigen[][][](CAex) \T1/ptm/m/n/10 fell into an in-fi-nite loop (wher eas [2042] [2043] [2044] Underfull \hbox (badness 10000) in paragraph at lines 997--999 []\T1/fi4/m/sl/10 signature(a = "CHMfactor", b = "numeric") \T1/ptm/m/n/10 call the above [2045]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho l}) has been already used, duplicate ignored \relax l.1072 ...composition - 'Matrix' S4 Generic}{chol} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic ate ignored \relax l.1072 ...composition - 'Matrix' S4 Generic}{chol} [2046pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha s been already used, duplicate ignored \endgroup \set@typeset@protect l.1140 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.ch ol,lsCMatrix.Rdash.method}) has been already used, duplicate ignored \endgroup \set@typeset@protect l.1140 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.ch ol,nsCMatrix.Rdash.method}) has been already used, duplicate ignored \endgroup \set@typeset@protect l.1140 ] [2047] Underfull \hbox (badness 2277) in paragraph at lines 1286--1289 []\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer -ent types of ma-tri-ces. Use [2048] Underfull \hbox (badness 5741) in paragraph at lines 1322--1326 []\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/fi4/m/sl/10 CHMfactor[][][] \T1/p tm/m/n/10 and [][]\T1/fi4/m/sl/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion [][]\T1/fi4/m/sl/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra [2049] Underfull \hbox (badness 10000) in paragraph at lines 1416--1423 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/fi4/m/sl/10 n ew("Cholesky", ...) \T1/ptm/m/n/10 or [2050] Underfull \hbox (badness 1097) in paragraph at lines 1445--1448 []\T1/ptm/m/n/10 Class \T1/fi4/m/sl/10 "MatrixFactorization" \T1/ptm/m/n/10 and \T1/fi4/m/sl/10 "dtrMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/fi4/m/sl/10 " dgeMatrix"\T1/ptm/m/n/10 , by class Underfull \hbox (badness 1783) in paragraph at lines 1451--1455 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend [2051]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col Sums}) has been already used, duplicate ignored \relax l.1508 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup licate ignored \relax l.1508 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl icate ignored \relax l.1509 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i gnored \relax l.1530 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig nored \relax l.1541 \aliasA{rowSums}{colSums}{rowSums} [2052] [2053] [2054] [2055] Overfull \hbox (19.92062pt too wide) in paragraph at lines 1843--1844 []\T1/fi4/m/sl/10 signature(x = "CsparseMatrix", i = "index", j = "missing", va lue = "replValue")\T1/ptm/m/n/10 : Overfull \hbox (9.92062pt too wide) in paragraph at lines 1844--1845 []\T1/fi4/m/sl/10 signature(x = "CsparseMatrix", i = "index", j = "index", valu e = "replValue")\T1/ptm/m/n/10 : Overfull \hbox (19.92062pt too wide) in paragraph at lines 1845--1846 []\T1/fi4/m/sl/10 signature(x = "CsparseMatrix", i = "missing", j = "index", va lue = "replValue")\T1/ptm/m/n/10 : [2056] Underfull \hbox (badness 4543) in paragraph at lines 1963--1965 []\T1/ptm/m/n/10 Use [][]\T1/fi4/m/sl/10 showMethods[][][](class = "ddenseMatri x", where = "package:Matrix") \T1/ptm/m/n/10 for an [2057] [2058] Underfull \hbox (badness 10000) in paragraph at lines 2085--2087 []\T1/ptm/m/n/10 Use [][]\T1/fi4/m/sl/10 showMethods[][][](class = "denseMatrix ", where = "package:Matrix") \T1/ptm/m/n/10 for an [2059] Underfull \hbox (badness 10000) in paragraph at lines 2179--2181 []\T1/fi4/m/sl/10 signature(x = "dgCMatrix", y = "missing") \T1/ptm/m/n/10 re-t urns \T1/fi4/m/sl/10 t(x) %*% x \T1/ptm/m/n/10 as an [2060] [2061] [2062] Underfull \hbox (badness 10000) in paragraph at lines 2474--2476 []\T1/fi4/m/sl/10 signature(x = "dgTMatrix", y = "missing") \T1/ptm/m/n/10 re-t urns \T1/fi4/m/sl/10 t(x) %*% x \T1/ptm/m/n/10 as an [2063] Underfull \hbox (badness 6842) in paragraph at lines 2563--2566 []\T1/fi4/m/sl/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T 1/fi4/m/sl/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/fi4/m/sl/10 ldiMatrix[] [][] \T1/ptm/m/n/10 (with ``su-per-class'' [2064] [2065] Underfull \hbox (badness 10000) in paragraph at lines 2882--2884 []\T1/fi4/m/sl/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equi v-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2066] [2067] [2068] Underfull \hbox (badness 10000) in paragraph at lines 3142--3144 [][][]\T1/fi4/m/sl/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pr efer-able to (and more ef-fi-cient than) [2069] [2070] [2071] Underfull \hbox (badness 10000) in paragraph at lines 3432--3435 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/fi4/m/sl/10 n ew("dsCMatrix", ...) \T1/ptm/m/n/10 or [2072] [2073] [2074] [2075] [2076] Underfull \hbox (badness 2318) in paragraph at lines 3882--3886 []\T1/ptm/m/n/10 Class \T1/fi4/m/sl/10 "dgCMatrix"\T1/ptm/m/n/10 , di-rectly. C lass \T1/fi4/m/sl/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/fi 4/m/sl/10 "dMatrix"\T1/ptm/m/n/10 , [2077] [2078] [2079] [2080] Underfull \hbox (badness 10000) in paragraph at lines 4194--4199 []\T1/fi4/m/sl/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and o ther sig-na-tures (use Underfull \hbox (badness 4254) in paragraph at lines 4194--4199 \T1/fi4/m/sl/10 showMethods("%*%", class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mul-ti-pli-ca-tion. Mul-ti-pli-ca-tion [2081] [2082] Underfull \hbox (badness 10000) in paragraph at lines 4313--4318 []\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite Tay-lor se-ries Underfull \hbox (badness 1067) in paragraph at lines 4313--4318 \T1/fi4/m/sl/10 expm(A) = I + A + A^2/2! + A^3/3! + ... \T1/ptm/m/n/10 (al-thou gh this is def-i-nitely not the way to [2083] [2084] Overfull \hbox (5.28088pt too wide) in paragraph at lines 4447--4447 [] \T1/fi4/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/ Boeing/msc00726.tar.gz"))))[] Overfull \hbox (50.28088pt too wide) in paragraph at lines 4450--4450 [] \T1/fi4/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] [2085] [2086] [2087] Underfull \hbox (badness 1931) in paragraph at lines 4675--4677 []\T1/ptm/m/n/10 a string spec-i-fy-ing how the \T1/fi4/m/sl/10 zero.print \T1/ ptm/m/n/10 codes should be aligned, see [2088] [2089] [2090] Underfull \hbox (badness 5862) in paragraph at lines 4881--4884 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ]\T1/fi4/m/sl/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use [2091] Underfull \hbox (badness 2846) in paragraph at lines 4973--4975 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/fi4/m/sl/10 p \T1/ptm/m/n/10 con- tains val-ues \T1/fi4/m/sl/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault, [2092] [2093] [2094] [2095] [2096] Underfull \hbox (badness 10000) in paragraph at lines 5339--5342 []\T1/fi4/m/sl/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2097] Underfull \hbox (badness 2478) in paragraph at lines 5451--5456 []\T1/ptm/m/n/10 Class \T1/fi4/m/sl/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly . Class \T1/fi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/fi4/m/sl/10 "lde nseMatrix"\T1/ptm/m/n/10 . Class [2098] Underfull \hbox (badness 10000) in paragraph at lines 5459--5462 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); use, e.g., [2099] Underfull \hbox (badness 10000) in paragraph at lines 5644--5647 []\T1/fi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2100] Underfull \hbox (badness 10000) in paragraph at lines 5742--5745 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2101] Underfull \hbox (badness 10000) in paragraph at lines 5817--5820 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2102] Underfull \hbox (badness 2050) in paragraph at lines 5887--5890 []\T1/fi4/m/sl/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth -ods for dif-fer-ent types of ma-tri-ces. Use [2103] [2104] [2105] Underfull \hbox (badness 6268) in paragraph at lines 6082--6085 []\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math- e-mat-i-cally''), Underfull \hbox (badness 6268) in paragraph at lines 6106--6110 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/fi4/m/sl/10 matrix[][][]\T1/ptm/m/n/1 0 . How-ever, [2106]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6212 \aliasA{det}{Matrix-class}{det} [2107] Underfull \hbox (badness 3547) in paragraph at lines 6318--6321 []\T1/fi4/m/sl/10 signature(object = "Matrix")\T1/ptm/m/n/10 : draws an [][]\T1 /fi4/m/sl/10 image[][][] \T1/ptm/m/n/10 of the ma-trix en-tries, us-ing Underfull \hbox (badness 10000) in paragraph at lines 6323--6326 [2108] Underfull \hbox (badness 1430) in paragraph at lines 6447--6452 []\T1/ptm/m/n/10 classes in-her-it-ing from \T1/fi4/m/sl/10 "MatrixFactorizatio n"\T1/ptm/m/n/10 , such as [][]\T1/fi4/m/sl/10 LU[][][]\T1/ptm/m/n/10 , [][]\T1 /fi4/m/sl/10 Cholesky[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 CHMfactor[][][] \T1/ptm/m/n/10 , and [2109] Underfull \hbox (badness 10000) in paragraph at lines 6516--6519 []\T1/fi4/m/sl/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2110] Underfull \hbox (badness 10000) in paragraph at lines 6568--6570 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/fi4/m/sl/10 X <- (X + t(X))/2 \T1 /ptm/m/n/10 should be done, af-ter [2111] [2112] [2113] Underfull \hbox (badness 2478) in paragraph at lines 6747--6752 []\T1/ptm/m/n/10 Class \T1/fi4/m/sl/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly . Class \T1/fi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/fi4/m/sl/10 "nde nseMatrix"\T1/ptm/m/n/10 . Class Underfull \hbox (badness 10000) in paragraph at lines 6755--6758 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); use, e.g., [2114] [2115] Underfull \hbox (badness 5924) in paragraph at lines 6941--6943 []\T1/ptm/m/n/10 fast sim-ple meth-ods pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm}) ha s been already used, duplicate ignored \relax l.6979 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.6979 \HeaderA{norm}{Matrix Norms}{norm} [2116] [2117] Underfull \hbox (badness 10000) in paragraph at lines 7234--7237 []\T1/fi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2118] Underfull \hbox (badness 10000) in paragraph at lines 7324--7327 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2119] Underfull \hbox (badness 10000) in paragraph at lines 7400--7403 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2120] [2121] Underfull \hbox (badness 10000) in paragraph at lines 7519--7521 []\T1/fi4/m/sl/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and oth er sig-na-tures (use Underfull \hbox (badness 3118) in paragraph at lines 7524--7527 []\T1/fi4/m/sl/10 signature(from = "numeric", to = "pMatrix")\T1/ptm/m/n/10 : a user con-ve-nience, to al-low Underfull \hbox (badness 10000) in paragraph at lines 7527--7534 []\T1/fi4/m/sl/10 signature(from = "pMatrix", to = "matrix")\T1/ptm/m/n/10 : co -er-cion to a tra-di-tional Underfull \hbox (badness 3417) in paragraph at lines 7552--7554 []\T1/ptm/m/n/10 The in-verse of the typ-i-cal \T1/fi4/m/sl/10 "pMatrix" \T1/pt m/m/n/10 con-struc-tor, \T1/fi4/m/sl/10 P <- as(ip, "pMatrix") \T1/ptm/m/n/10 i s sim-ply [2122] [2123] [2124]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}) has been already used, duplicate ignored \relax l.7731 \aliasA{qr}{qr-methods}{qr} Underfull \hbox (badness 5119) in paragraph at lines 7773--7776 []\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma- trix with [2125] Underfull \hbox (badness 3333) in paragraph at lines 7829--7834 []\T1/ptm/m/n/10 nonnegative num-ber spec-i-fy-ing a tol-er-ance for ``prac-ti- cally zero'' with Underfull \hbox (badness 6125) in paragraph at lines 7829--7834 \T1/ptm/m/n/10 spe-cific mean-ing de-pend-ing on \T1/fi4/m/sl/10 method\T1/ptm/ m/n/10 ; by de-fault, \T1/fi4/m/sl/10 max(dim(x)) * [2126]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rco nd}) has been already used, duplicate ignored \relax l.7895 ... the Reciprocal Condition Number}{rcond} [2127] [2128] [2129] [2130] [2131] [2132] [2133] [2134] [2135] [2136] [2137] [2138] [2139] [2140] Underfull \hbox (badness 4441) in paragraph at lines 8935--8943 []\T1/fi4/m/sl/10 signature(from = "factor", to = "sparseMatrix")\T1/ptm/m/n/10 : Co-er-cion of a fac-tor to Underfull \hbox (badness 1112) in paragraph at lines 8935--8943 \T1/fi4/m/sl/10 "sparseMatrix" \T1/ptm/m/n/10 pro-duces the ma-trix of in-di-ca -tor \T1/ptm/b/n/10 rows \T1/ptm/m/n/10 stored as an ob-ject of class Underfull \hbox (badness 10000) in paragraph at lines 8961--8965 [][][]\T1/fi4/m/sl/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, such as [][]\T1/fi4/m/sl/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or [2141]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr. Q}) has been already used, duplicate ignored \relax l.8996 \aliasA{qr.Q}{sparseQR-class}{qr.Q} Underfull \hbox (badness 1303) in paragraph at lines 9022--9031 []\T1/ptm/m/n/10 The de-com-po-si-tion is of the form \T1/fi4/m/sl/10 A[p+1,] = = Q %*% R\T1/ptm/m/n/10 , if the \T1/fi4/m/sl/10 q \T1/ptm/m/n/10 slot is of le ngth 0 or [2142] [2143]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.toeplitz}) has been already used, duplicate ignored \relax l.9268 ...{toeplitz}{sparseVector-class}{toeplitz} [2144] Underfull \hbox (badness 10000) in paragraph at lines 9353--9356 []\T1/fi4/m/sl/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/fi4/ m/sl/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2145] Underfull \hbox (badness 10000) in paragraph at lines 9380--9382 [][][]\T1/fi4/m/sl/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-stru c-tion of sparse vec-tors (apart from [2146] Underfull \hbox (badness 4699) in paragraph at lines 9483--9489 [][][]\T1/fi4/m/sl/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more usual con-struc-tor of such ma-tri-ces; sim-i-larly, [2147] [2148] Underfull \hbox (badness 2057) in paragraph at lines 9637--9639 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2149]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcr ossprod}) has been already used, duplicate ignored \relax l.9663 ...{Cross-product of transpose}{tcrossprod} [2150] [2151] Underfull \hbox (badness 1831) in paragraph at lines 9877--9883 []\T1/ptm/m/n/10 For con-ve-nience, meth-ods for some op-er-a-tions such as \T1 /fi4/m/sl/10 %*% \T1/ptm/m/n/10 and \T1/fi4/m/sl/10 crossprod \T1/ptm/m/n/10 ar e de-fined [2152] [2153] [2154] [2155] Overfull \hbox (63.78088pt too wide) in paragraph at lines 10133--10133 []\T1/fi4/m/n/9 system.time(MJ <- sapply(rho, function(x) determinant(IM - x * USCounties, logarithm = TRUE)$modulus))[] [2156] Underfull \hbox (badness 6910) in paragraph at lines 10308--10310 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2157] [2158]) (./boot-pkg.tex Chapter 18. [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167] Overfull \hbox (3.25928pt too wide) in paragraph at lines 641--647 []\T1/ptm/m/n/10 logical, only al-lowed to be \T1/fi4/m/sl/10 TRUE \T1/ptm/m/n/ 10 for \T1/fi4/m/sl/10 sim = "ordinary", stype = "i", n = 0 [2168] Underfull \hbox (badness 1097) in paragraph at lines 786--794 []\T1/ptm/m/n/10 For most of the \T1/fi4/m/sl/10 boot \T1/ptm/m/n/10 meth-ods t he re-sam-pling is done in the mas-ter pro-cess, but not if Underfull \hbox (badness 6173) in paragraph at lines 795--805 []\T1/ptm/m/n/10 Where random-number gen-er-a-tion is done in the worker pro-ce sses, the de-fault be- Underfull \hbox (badness 1728) in paragraph at lines 795--805 \T1/ptm/m/n/10 haviour is that each worker chooses a sep-a-rate seed, non-repro ducibly. How-ever, with [2169] Underfull \hbox (badness 1881) in paragraph at lines 817--819 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. [2170] Underfull \vbox (badness 10000) has occurred while \output is active [2171] [2172] Underfull \hbox (badness 10000) in paragraph at lines 1057--1061 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1057--1061 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues Underfull \hbox (badness 5592) in paragraph at lines 1057--1061 \T1/fi4/m/sl/10 c("norm","basic", "stud", "perc", "bca") \T1/ptm/m/n/10 or sim- ply \T1/fi4/m/sl/10 "all" \T1/ptm/m/n/10 which [2173] Underfull \hbox (badness 2150) in paragraph at lines 1094--1100 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2174] [2175] [2176] [2177] Underfull \hbox (badness 1571) in paragraph at lines 1434--1436 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2178] [2179] [2180] [2181] [2182] [2183] Underfull \hbox (badness 1005) in paragraph at lines 1788--1795 []\T1/ptm/m/n/10 The sim-u-la-tion type. Pos-si-ble types are \T1/fi4/m/sl/10 " ordinary" \T1/ptm/m/n/10 (case re-sam-pling), [2184] [2185] Underfull \vbox (badness 10000) has occurred while \output is active [2186] [2187] Underfull \hbox (badness 7379) in paragraph at lines 2072--2074 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2188] [2189] [2190] Underfull \hbox (badness 1565) in paragraph at lines 2326--2331 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set [2191] Underfull \hbox (badness 1881) in paragraph at lines 2420--2422 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. [2192] [2193] Underfull \hbox (badness 2970) in paragraph at lines 2524--2528 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/fi4/m/s l/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/fi4/m/sl/10 n \T1/ptm/m/n/10 is t he sam-ple Underfull \hbox (badness 2310) in paragraph at lines 2524--2528 \T1/ptm/m/n/10 size, if \T1/fi4/m/sl/10 unbiased \T1/ptm/m/n/10 is \T1/fi4/m/sl /10 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/fi4/m/sl/10 1/n \T1/ptm/m/n /10 is used. This is mul-ti-plied by [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] Underfull \hbox (badness 10000) in paragraph at lines 4178--4180 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2218] [2219] [2220] Underfull \hbox (badness 2393) in paragraph at lines 4377--4380 []\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with fre-quency vec-tor \T1/fi4/m/sl/10 f \T1/ptm/m/n/10 is given by [2221] [2222] [2223] [2224] [2225] [2226] [2227] [2228] Underfull \hbox (badness 3000) in paragraph at lines 4947--4950 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2229] [2230] [2231] [2232] Underfull \hbox (badness 2293) in paragraph at lines 5226--5229 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5226--5229 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243] Underfull \hbox (badness 4954) in paragraph at lines 6007--6010 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/fi4/m/sl/10 "sa ddle.distn"\T1/ptm/m/n/10 . See the help file for [2244] [2245] [2246] [2247] [2248] [2249] [2250] [2251] [2252] Underfull \hbox (badness 1596) in paragraph at lines 6728--6732 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2253] [2254] [2255] [2256] [2257] [2258] [2259] [2260] [2261] [2262]) (./class-pkg.tex Chapter 19. [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] Underfull \hbox (badness 10000) in paragraph at lines 608--610 []\T1/ptm/m/n/10 the size of the code-book. De-faults to Underfull \hbox (badness 3977) in paragraph at lines 608--610 \T1/fi4/m/sl/10 min(round(0.4*ng*(ng-1 + p/2),0), n) \T1/ptm/m/n/10 where \T1/f i4/m/sl/10 ng \T1/ptm/m/n/10 is the num-ber of [2271] [2272] [2273] [2274] [2275] [2276] [2277] [2278]) (./cluster-pkg.tex Chapter 20. [2279] Underfull \hbox (badness 1231) in paragraph at lines 59--66 \T1/ptm/m/n/10 which uses (a con-stant ver-sion of) the Lance-Williams for-mula and the [2280] [2281] [2282] [2283] [2284] [2285] [2286] Underfull \hbox (badness 4144) in paragraph at lines 587--590 []\T1/ptm/m/n/10 Setting this to \T1/fi4/m/sl/10 FALSE \T1/ptm/m/n/10 saves mem -ory (and hence time), but dis-ables [2287] [2288] [2289] Underfull \hbox (badness 10000) in paragraph at lines 754--756 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2290] Underfull \hbox (badness 10000) in paragraph at lines 841--843 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is [2291] [2292] [2293] Underfull \hbox (badness 6110) in paragraph at lines 1019--1023 []\T1/ptm/m/n/10 when \T1/fi4/m/sl/10 x \T1/ptm/m/n/10 does not have a \T1/fi4/ m/sl/10 diss \T1/ptm/m/n/10 nor a \T1/fi4/m/sl/10 data \T1/ptm/m/n/10 com-po-ne nt, e.g., for [2294] [2295] [2296] [2297] [2298] Underfull \hbox (badness 2503) in paragraph at lines 1397--1400 []\T1/ptm/m/n/10 an ob-ject of class \T1/fi4/m/sl/10 "hclust" \T1/ptm/m/n/10 or \T1/fi4/m/sl/10 "twins"\T1/ptm/m/n/10 , i.e., typ-i-cally the re-sult of [2299] [2300] [2301] [2302] [2303] [2304] [2305] [2306] Underfull \hbox (badness 10000) in paragraph at lines 1964--1966 []\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as Underfull \hbox (badness 10000) in paragraph at lines 1988--1994 [][][]\T1/fi4/m/sl/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [][]\T1/fi4/m/sl/10 predict[][][] \T1/ptm/m/n/10 method for \T1/fi4/m/sl/10 ell ipsoid \T1/ptm/m/n/10 ob-jects. [2307] [2308] [2309] [2310] Underfull \hbox (badness 6675) in paragraph at lines 2220--2222 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see [2311] [2312] [2313] [2314] [2315] Underfull \hbox (badness 1014) in paragraph at lines 2584--2594 \T1/ptm/m/n/10 on the re-sult \T1/fi4/m/sl/10 pr <- pam(..)\T1/ptm/m/n/10 , or di-rectly its com-po-nent \T1/fi4/m/sl/10 pr$silinfo$avg.width\T1/ptm/m/n/10 , see also Underfull \hbox (badness 1616) in paragraph at lines 2624--2629 []\T1/ptm/m/n/10 The de-fault \T1/fi4/m/sl/10 FALSE \T1/ptm/m/n/10 (or in-te-ge r \T1/fi4/m/sl/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al -go-rithm, whereas [2316] Underfull \hbox (badness 2980) in paragraph at lines 2662--2666 [][][]\T1/fi4/m/sl/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-enc es; [][]\T1/fi4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 cl ara[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 daisy[][][]\T1/ptm/m/n/10 , [][]\ T1/fi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [2317] [2318] [2319] [2320] [2321] Underfull \hbox (badness 1142) in paragraph at lines 3000--3003 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/fi4/m/sl/10 par[][][]\T1/ ptm/m/n/10 ) may also be sup-plied and are passed to [2322] [2323] Underfull \hbox (badness 1142) in paragraph at lines 3119--3122 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/fi4/m/sl/10 par[][][]\T1/ ptm/m/n/10 ) may also be sup-plied and are passed to [2324] [2325] [2326] Underfull \hbox (badness 2582) in paragraph at lines 3342--3347 [][][]\T1/fi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/1 0 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 clusplot.default [][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/fi 4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 clara[][][]\T1/p tm/m/n/10 , [2327] Underfull \hbox (badness 10000) in paragraph at lines 3428--3433 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/fi 4/m/sl/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 4378) in paragraph at lines 3428--3433 \T1/ptm/m/n/10 which dis-patches to [][]\T1/fi4/m/sl/10 plot.hclust[][][](..)\T 1/ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider [2328] [2329] [2330] [2331] [2332] Underfull \hbox (badness 10000) in paragraph at lines 3718--3720 []\T1/ptm/m/n/10 a \T1/fi4/m/sl/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T 1/fi4/m/sl/10 summary.dissimilarity \T1/ptm/m/n/10 one for [2333] [2334] [2335] [2336] Underfull \hbox (badness 4108) in paragraph at lines 3942--3947 []\T1/ptm/m/n/10 arguments passed [][]\T1/fi4/m/sl/10 barplot[][][]()\T1/ptm/m/ n/10 ; note that the de-fault used to be \T1/fi4/m/sl/10 col Underfull \hbox (badness 1062) in paragraph at lines 3997--3999 []\T1/ptm/m/n/10 numeric (rank 1) ar-ray of clus-ter-wise \T1/ptm/m/it/10 means \T1/ptm/m/n/10 of sil-hou-ette widths where [2337] Underfull \hbox (badness 1383) in paragraph at lines 4019--4024 []\T1/ptm/m/n/10 While \T1/fi4/m/sl/10 silhouette() \T1/ptm/m/n/10 is \T1/ptm/m /it/10 in-trin-sic \T1/ptm/m/n/10 to the [][]\T1/fi4/m/sl/10 partition[][][] \T 1/ptm/m/n/10 clus-ter-ings, and hence has a (triv-ial) [2338] [2339] [2340] [2341] [2342] [2343] [2344] [2345]) (./codetools-pkg.tex [2346] Chapter 21. [2347] [2348] [2349] [2350] [2351]) (./foreign-pkg.tex [2352] Chapter 22. Underfull \hbox (badness 1331) in paragraph at lines 33--37 \T1/ptm/m/n/10 (XPORT) For-mat'' avail-able as [][]$\T1/fi4/m/sl/10 http : / / ftp . sas . com / techsup / download / technote / ts140 . [2353] [2354] [2355] [2356] [2357] [2358] [2359] [2360] [2361] [2362] [2363] Underfull \hbox (badness 10000) in paragraph at lines 704--705 [2364] Underfull \hbox (badness 1642) in paragraph at lines 759--763 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Set in SAS [2365] [2366] [2367] [2368] [2369] Underfull \hbox (badness 10000) in paragraph at lines 1115--1121 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/fi4/m/sl/10 foreign :::writeForeignStata\T1/ptm/m/n/10 , [2370] [2371]) (./lattice-pkg.tex [2372] Chapter 23. [2373] [2374] [2375] [2376] [2377] [2378] Underfull \hbox (badness 10000) in paragraph at lines 480--485 []\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/fi4/m/sl/10 scales \T1/ptm/m/n/10 in this case may be [2379] [2380] [2381] [2382] [2383] [2384] [2385] [2386] [2387] [2388] Underfull \hbox (badness 1062) in paragraph at lines 1398--1402 \T1/ptm/m/n/10 no-ta-tion for the x and y axes re-spec-tively. See doc-u-men-ta -tion for [2389] [2390] [2391] Underfull \hbox (badness 1803) in paragraph at lines 1566--1583 [][][]\T1/fi4/m/sl/10 Lattice[][][] \T1/ptm/m/n/10 for an overview of the pack- age, as well as [][]\T1/fi4/m/sl/10 barchart.table[][][]\T1/ptm/m/n/10 , [][]\T 1/fi4/m/sl/10 print.trellis[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][]\T1/fi4/m/sl/10 panel.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 p anel.superpose[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 panel.loess[][][]\T1/p tm/m/n/10 , [][]\T1/fi4/m/sl/10 panel.average[][][]\T1/ptm/m/n/10 , [][]\T1/fi4 /m/sl/10 strip.default[][][]\T1/ptm/m/n/10 , [2392] [2393] Underfull \hbox (badness 3009) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/fi4/m/sl/10 xyplot[][ ][]\T1/ptm/m/n/10 , which may pass them on to Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to [2394] [2395] [2396] [2397] [2398] Underfull \hbox (badness 10000) in paragraph at lines 2086--2093 []\T1/ptm/m/n/10 For the \T1/fi4/m/sl/10 formula \T1/ptm/m/n/10 method, \T1/fi4 /m/sl/10 x \T1/ptm/m/n/10 can be a for-mula of the form Underfull \hbox (badness 1173) in paragraph at lines 2086--2093 \T1/fi4/m/sl/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togr ams or ker-nel den-sity es-ti- [2399] [2400] [2401] [2402] Underfull \hbox (badness 7064) in paragraph at lines 2360--2364 []\T1/ptm/m/n/10 For the \T1/fi4/m/sl/10 "formula" \T1/ptm/m/n/10 method, \T1/f i4/m/sl/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2403] [2404] Underfull \hbox (badness 7064) in paragraph at lines 2545--2552 []\T1/ptm/m/n/10 For the \T1/fi4/m/sl/10 "formula" \T1/ptm/m/n/10 method, \T1/f i4/m/sl/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2405] [2406] [2407] Underfull \hbox (badness 10000) in paragraph at lines 2759--2764 []\T1/ptm/m/n/10 for the \T1/fi4/m/sl/10 formula \T1/ptm/m/n/10 method, a for-m ula of the form \T1/fi4/m/sl/10 z ~ x * y [2408] Underfull \hbox (badness 2781) in paragraph at lines 2846--2848 []\T1/ptm/m/n/10 A color ramp spec-i-fi-ca-tion, as in the \T1/fi4/m/sl/10 col. regions \T1/ptm/m/n/10 ar-gu-ment in [2409] Underfull \hbox (badness 2486) in paragraph at lines 2957--2961 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2410] [2411] [2412] Underfull \hbox (badness 10000) in paragraph at lines 3108--3116 []\T1/ptm/m/n/10 For the \T1/fi4/m/sl/10 "formula" \T1/ptm/m/n/10 meth-ods, a f or-mula of the form \T1/fi4/m/sl/10 z ~ x [2413] [2414] [2415] [2416]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \relax l.3429 \aliasA{parallel}{B\_08\_splom}{parallel} [2417] [2418] [2419] [2420] [2421] [2422] [2423] Underfull \hbox (badness 2277) in paragraph at lines 3920--3924 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings by Underfull \hbox (badness 10000) in paragraph at lines 3920--3924 \T1/ptm/m/n/10 spec-i-fy-ing \T1/fi4/m/sl/10 lattice.options(default.theme = "c ol.whitebg")\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3920--3924 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2424] [2425] Underfull \hbox (badness 1173) in paragraph at lines 4059--4063 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4086--4088 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when [2426] [2427] [2428] Underfull \hbox (badness 3492) in paragraph at lines 4282--4292 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/fi4/m/sl/10 col \T1/ptm/m/n/10 is used for com-po-nents \T1/fi4/m/sl/10 "plot.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4307--4310 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/fi4/m/sl/10 plo t.symbol\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 plot.polygon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4310--4312 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/fi4/m/sl/10 p lot.polygon \T1/ptm/m/n/10 and [2429] [2430] [2431] [2432] [2433] [2434] [2435] [2436] [2437] [2438] Underfull \hbox (badness 6157) in paragraph at lines 5033--5036 []\T1/fi4/m/sl/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles via rect-an-gles. \T1/fi4/m/sl/10 print.shingle \T1/ptm/m/n/10 and [2439] [2440] [2441] [2442] [2443] [2444] Underfull \hbox (badness 10000) in paragraph at lines 5484--5487 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 5592) in paragraph at lines 5484--5487 \T1/fi4/m/sl/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the le ft of pan-els us-ing [2445] [2446] [2447] [2448] [2449] Underfull \hbox (badness 4805) in paragraph at lines 5844--5848 []\T1/ptm/m/n/10 logical, whether the view-port be-ing as-signed fo-cus should be high- Underfull \hbox (badness 10000) in paragraph at lines 5855--5862 []\T1/ptm/m/n/10 For \T1/fi4/m/sl/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-t ra pa-ram-e-ters are passed on to Underfull \hbox (badness 1226) in paragraph at lines 5855--5862 \T1/fi4/m/sl/10 panel.identify\T1/ptm/m/n/10 . For \T1/fi4/m/sl/10 panel.identi fy\T1/ptm/m/n/10 , ex-tra ar-gu-ments are treated as Underfull \hbox (badness 2418) in paragraph at lines 5855--5862 \T1/ptm/m/n/10 graph-i-cal pa-ram-e-ters and are used for la-belling. For \T1/f i4/m/sl/10 trellis.focus Underfull \hbox (badness 10000) in paragraph at lines 5855--5862 \T1/ptm/m/n/10 and \T1/fi4/m/sl/10 trellis.switchFocus\T1/ptm/m/n/10 , these ar e used (in com-bi-na-tion with Underfull \hbox (badness 1259) in paragraph at lines 5855--5862 [][]\T1/fi4/m/sl/10 lattice.options[][][]\T1/ptm/m/n/10 ) for high-light-ing th e cho-sen view-port if so re-quested. [2450] [2451] [2452] [2453] Underfull \hbox (badness 4242) in paragraph at lines 6155--6160 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- Underfull \hbox (badness 2529) in paragraph at lines 6155--6160 \T1/ptm/m/n/10 ter \T1/fi4/m/sl/10 plot.polygon \T1/ptm/m/n/10 is used if there is no group-ing vari-able, oth-er-wise [2454] [2455] Underfull \hbox (badness 2310) in paragraph at lines 6271--6276 []\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/fi4/m/sl/10 x \T1/ptm/m/n/ 10 for ev-ery level of \T1/fi4/m/sl/10 y \T1/ptm/m/n/10 (or the other way round if [2456] [2457] [2458] [2459] [2460] [2461] [2462] [2463] [2464] [2465] [2466] [2467] [2468] [2469] [2470] Underfull \hbox (badness 2012) in paragraph at lines 7323--7326 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2471] [2472] Underfull \hbox (badness 3333) in paragraph at lines 7495--7497 []\T1/ptm/m/n/10 default colours are ob-tained from \T1/fi4/m/sl/10 plot.symbol \T1/ptm/m/n/10 and \T1/fi4/m/sl/10 plot.line \T1/ptm/m/n/10 us-ing [2473] [2474] [2475] [2476] [2477] [2478] Underfull \hbox (badness 1436) in paragraph at lines 7905--7911 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for Underfull \hbox (badness 1661) in paragraph at lines 7905--7911 \T1/fi4/m/sl/10 panel.abline \T1/ptm/m/n/10 should be taken from the ``ref-er-e nce.line'' pa-ram-e-ter set- Underfull \hbox (badness 1231) in paragraph at lines 7905--7911 \T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti ngs. The [2479] [2480] [2481] [2482] [2483] [2484] [2485] [2486] Underfull \hbox (badness 10000) in paragraph at lines 8463--8466 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/fi4/m/sl/10 panel.superp ose \T1/ptm/m/n/10 from [2487] Underfull \hbox (badness 1092) in paragraph at lines 8509--8511 []\T1/ptm/m/n/10 Deepayan Sarkar \T1/fi4/m/sl/10 \T1/ptm/m/n/10 (\T1/fi4/m/sl/10 panel.superpose.2 \T1/ptm/m/n/10 orig-i-nally con- [2488] [2489] Underfull \hbox (badness 3895) in paragraph at lines 8670--8673 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/fi4/m/sl/10 type \T 1/ptm/m/n/10 has a dif-fer-ent mean-ing in [2490] Underfull \hbox (badness 1515) in paragraph at lines 8746--8750 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2491] Underfull \hbox (badness 6316) in paragraph at lines 8852--8857 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2492] Underfull \hbox (badness 5908) in paragraph at lines 8869--8872 []\T1/ptm/m/n/10 list, sim-i-lar to those pro-duced by \T1/fi4/m/sl/10 xscale.c omponents.default \T1/ptm/m/n/10 and [2493] [2494] [2495] [2496] Overfull \hbox (36.94879pt too wide) in paragraph at lines 9157--9161 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/fi4 /m/sl/10 left, right, left.name, right.name, condition Overfull \hbox (29.63074pt too wide) in paragraph at lines 9157--9161 \T1/ptm/m/n/10 for 2-D, and \T1/fi4/m/sl/10 left, right.x, right.y, left.nam e, right.x.name, right.y.name, condition [2497] [2498] [2499] [2500] [2501] [2502] [2503] Underfull \hbox (badness 1442) in paragraph at lines 9613--9617 []\T1/ptm/m/n/10 Factor with lev-els \T1/fi4/m/sl/10 "Svansota"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "No. 462"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Manchuria"\T1/ptm/m /n/10 , \T1/fi4/m/sl/10 "No. 475"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Velvet"\T1/p tm/m/n/10 , Underfull \hbox (badness 2573) in paragraph at lines 9618--9621 []\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/fi4/m/sl/10 "Grand Rapids"\T1/ptm/m /n/10 , \T1/fi4/m/sl/10 "Duluth"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "University Fa rm"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Morris"\T1/ptm/m/n/10 , [2504] [2505] [2506]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9842 \aliasA{melanoma}{H\_melanoma}{melanoma} [2507] [2508] [2509] [2510]) (./mgcv-pkg.tex Chapter 24. [2511] [2512] Underfull \hbox (badness 1052) in paragraph at lines 149--151 []\T1/ptm/m/n/10 selects ex-act test statis-tic to use for sin-gle smooth term p-values. See [2513] [2514] Underfull \hbox (badness 1142) in paragraph at lines 281--285 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 303--308 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2515] Underfull \hbox (badness 2626) in paragraph at lines 353--356 []\T1/ptm/m/n/10 If all smooths are P-splines and all ten-sor prod-ucts are of the form [2516] [2517] [2518] [2519] [2520] Underfull \hbox (badness 1158) in paragraph at lines 613--615 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2521] [2522] [2523] [2524] [2525] [2526] [2527] [2528] [2529] [2530] [2531] [2532] [2533] [2534] [2535] [2536] Underfull \hbox (badness 1142) in paragraph at lines 1642--1646 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2537] Underfull \hbox (badness 1043) in paragraph at lines 1665--1669 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2538] [2539] [2540] [2541] [2542] Underfull \vbox (badness 10000) has occurred while \output is active [2543] Underfull \vbox (badness 10000) has occurred while \output is active [2544] Underfull \vbox (badness 10000) has occurred while \output is active [2545] [2546] [2547] [2548] [2549] [2550] [2551] [2552] [2553] [2554] [2555] [2556] Underfull \hbox (badness 10000) in paragraph at lines 2921--2925 []\T1/ptm/m/n/10 Random ef-fects can be added to \T1/fi4/m/sl/10 gam \T1/ptm/m/ n/10 mod-els us-ing \T1/fi4/m/sl/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see [2557] [2558] Underfull \vbox (badness 10000) has occurred while \output is active [2559] [2560] [2561] [2562] [2563] [2564] [2565] [2566] [2567] Underfull \hbox (badness 1142) in paragraph at lines 3649--3653 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2568] [2569] Underfull \hbox (badness 1231) in paragraph at lines 3741--3743 []\T1/fi4/m/sl/10 gamm \T1/ptm/m/n/10 per-forms poorly with bi-nary data, since it uses PQL. It is bet-ter to use \T1/fi4/m/sl/10 gam \T1/ptm/m/n/10 with [2570] [2571] Underfull \vbox (badness 10000) has occurred while \output is active [2572] [2573] [2574] [2575] [2576] [2577] [2578] [2579] [2580] [2581] [2582] Underfull \hbox (badness 6001) in paragraph at lines 4632--4634 []\T1/ptm/m/n/10 Simon N. Wood \T1/fi4/m/sl/10 \T1/p tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's [2583] [2584] [2585] Underfull \vbox (badness 10000) has occurred while \output is active [2586] [2587] [2588] [2589] [2590] [2591] [2592] [2593] [2594] [2595] [2596] [2597] [2598] [2599] Underfull \hbox (badness 6001) in paragraph at lines 5671--5673 []\T1/ptm/m/n/10 Simon N. Wood \T1/fi4/m/sl/10 \T1/p tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's [2600] Underfull \vbox (badness 10000) has occurred while \output is active [2601] [2602] [2603] [2604] [2605] [2606] [2607] [2608] Underfull \vbox (badness 10000) has occurred while \output is active [2609] Underfull \hbox (badness 1038) in paragraph at lines 6304--6307 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/fi4/m/sl/10 Dim. pdIndot\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 coef.pdIdnot\T1/ptm/m/n/10 , \T1/fi4/m/ sl/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6304--6307 \T1/fi4/m/sl/10 logDet.pdIdnot\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 pdConstruct.pdId not\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/fi4/m/ sl/10 pdMatrix.pdIdnot\T1/ptm/m/n/10 , [2610] Underfull \hbox (badness 10000) in paragraph at lines 6360--6363 []\T1/ptm/m/n/10 These func-tions (\T1/fi4/m/sl/10 pdTens\T1/ptm/m/n/10 , \T1/f i4/m/sl/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 pdFactor.pdTens\T 1/ptm/m/n/10 , \T1/fi4/m/sl/10 pdMatrix.pdTens\T1/ptm/m/n/10 , [2611] [2612] [2613] [2614] [2615] [2616] [2617] [2618] [2619] Overfull \hbox (29.78088pt too wide) in paragraph at lines 6927--6927 [] \T1/fi4/m/sl/10 block.size=50000,newdata.guaranteed=FALSE,na.action= na.pass,cluster=NULL,...)[] [2620] Underfull \hbox (badness 1852) in paragraph at lines 6996--6999 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/fi4/m/sl/10 termplot[] [][]\T1/ptm/m/n/10 , if \T1/fi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at- tribute \T1/fi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and [2621] [2622] Underfull \hbox (badness 1852) in paragraph at lines 7142--7145 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/fi4/m/sl/10 termplot[] [][]\T1/ptm/m/n/10 , if \T1/fi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at- tribute \T1/fi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and [2623] [2624] Underfull \vbox (badness 10000) has occurred while \output is active [2625] [2626] Underfull \hbox (badness 1205) in paragraph at lines 7350--7352 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 7350--7352 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 7356--7361 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2627] Underfull \hbox (badness 1205) in paragraph at lines 7437--7439 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 7437--7439 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2628] [2629] [2630] Underfull \hbox (badness 1253) in paragraph at lines 7636--7638 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [2631] [2632] [2633] [2634] [2635] [2636] [2637] [2638] [2639] [2640] [2641] Underfull \hbox (badness 1975) in paragraph at lines 8297--8302 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2642] [2643] Underfull \hbox (badness 1762) in paragraph at lines 8386--8398 \T1/ptm/m/n/10 plate re-gres-sion splines: see [][]\T1/fi4/m/sl/10 tprs[][][]\T 1/ptm/m/n/10 ); \T1/fi4/m/sl/10 ts.smooth.spec \T1/ptm/m/n/10 (thin plate re-gr es-sion splines with [2644] [2645] [2646] Underfull \hbox (badness 7667) in paragraph at lines 8596--8602 [][][]\T1/fi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like [2647] Underfull \hbox (badness 10000) in paragraph at lines 8637--8638 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2648] [2649] Underfull \hbox (badness 10000) in paragraph at lines 8763--8765 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2650] [2651] Underfull \hbox (badness 10000) in paragraph at lines 8890--8891 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2652] [2653] Underfull \hbox (badness 1436) in paragraph at lines 9024--9029 \T1/ptm/m/n/10 nest-ing of the smooth within the fac-tor. Note how-ever that: i ) \T1/fi4/m/sl/10 gamm \T1/ptm/m/n/10 only al-lows one [2654] [2655] [2656] [2657] [2658] [2659] [2660] [2661] Underfull \hbox (badness 10000) in paragraph at lines 9459--9465 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a [2662] [2663] [2664] Underfull \vbox (badness 10000) has occurred while \output is active [2665] Underfull \vbox (badness 10000) has occurred while \output is active [2666] Overfull \hbox (9.78088pt too wide) in paragraph at lines 9755--9755 []\T1/fi4/m/n/9 b <- gam(z~s(x,y,k=c(30,15),bs="so",xt=list(bnd=bnd,nmax=nmax) ),knots=knots,method="REML")[] Overfull \hbox (5.28088pt too wide) in paragraph at lines 9761--9761 [] \T1/fi4/m/n/9 s(x,y,k=c(30,15),bs="sw",xt=list(bnd=bnd,nmax=nmax)) ,knots=knots,method="REML")[] Underfull \hbox (badness 10000) in paragraph at lines 9801--9802 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2667] [2668] [2669] [2670] Underfull \hbox (badness 3895) in paragraph at lines 9992--9997 [][][]\T1/fi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 10037--10039 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2671] [2672] [2673] [2674] Underfull \hbox (badness 1371) in paragraph at lines 10211--10217 []\T1/fi4/m/sl/10 bs="ad" \T1/ptm/m/n/10 Uni-vari-ate and bi-vari-ate adap-tive smooths are avail-able (see Underfull \hbox (badness 10000) in paragraph at lines 10251--10255 [][][]\T1/fi4/m/sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 te[][][]\T1/p tm/m/n/10 , [][]\T1/fi4/m/sl/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/ fi4/m/sl/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 cubic.regre ssion.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/fi4/m/sl/10 p.spline[][][]\T1/ptm/m/n /10 , [][]\T1/fi4/m/sl/10 mrf[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10251--10255 \T1/ptm/m/n/10 code[][]soap[][][], code[][]Spherical.Spline[][][], [][]\T1/fi4/ m/sl/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 user.defined. smooth[][][]\T1/ptm/m/n/10 , [2675] Underfull \hbox (badness 2326) in paragraph at lines 10318--10325 []\T1/ptm/m/n/10 These wrap-per func-tions ex-ist to al-low smooths spec-i-fied us-ing [][]\T1/fi4/m/sl/10 smooth.construct[][][] \T1/ptm/m/n/10 and [2676] Underfull \hbox (badness 2158) in paragraph at lines 10375--10375 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [2677] [2678] [2679] [2680] [2681] [2682] [2683] [2684] [2685] [2686] [2687] [2688] [2689] [2690] [2691] [2692] [2693] Underfull \hbox (badness 6001) in paragraph at lines 11473--11475 []\T1/ptm/m/n/10 Simon N. Wood \T1/fi4/m/sl/10 \T1/p tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's [2694] [2695] [2696] [2697] Underfull \hbox (badness 1796) in paragraph at lines 11697--11700 []\T1/ptm/m/n/10 other op-tions to pass on to [][]\T1/fi4/m/sl/10 persp[][][]\T 1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 image[][][] \T1/ptm/m/n/10 or [][]\T1/fi4/m/ sl/10 contour[][][]\T1/ptm/m/n/10 . In par-tic-u-lar [2698] [2699] [2700]) (./nlme-pkg.tex Chapter 25. [2701] [2702] [2703] [2704] [2705] [2706] [2707] [2708] [2709] [2710] [2711] [2712] [2713] [2714] [2715] [2716] [2717] [2718] [2719] [2720] [2721] [2722] [2723] [2724] [2725] [2726] [2727] [2728] [2729] [2730] Underfull \hbox (badness 2875) in paragraph at lines 1996--2002 []\T1/ptm/m/n/10 an op-tional log-i-cal value or one-sided for-mula, in-di-cat- ing a co-vari-ate Underfull \hbox (badness 1466) in paragraph at lines 1996--2002 \T1/ptm/m/n/10 that is in-ner to the \T1/fi4/m/sl/10 displayLevel \T1/ptm/m/n/1 0 group-ing fac-tor. If equal to \T1/fi4/m/sl/10 TRUE\T1/ptm/m/n/10 , [2731] [2732] [2733] [2734] Underfull \hbox (badness 10000) in paragraph at lines 2257--2263 [][][]\T1/fi4/m/sl/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 corARMA [][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][ ]\T1/fi4/m/sl/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Initi alize.corStruct[][][]\T1/ptm/m/n/10 , [2735] [2736] [2737] [2738] [2739] [2740] [2741] [2742] [2743] [2744] [2745] [2746] [2747] [2748] [2749] [2750] [2751] [2752] [2753] [2754] [2755] [2756] [2757] [2758] [2759] [2760] [2761] [2762] [2763] [2764] [2765] [2766] [2767] Underfull \hbox (badness 1067) in paragraph at lines 4410--4415 \T1/ptm/m/n/10 ma-trix), \T1/fi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues ), and \T1/fi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to [2768] [2769] [2770] [2771] [2772] [2773] [2774] [2775] [2776] [2777] [2778] [2779] Underfull \hbox (badness 10000) in paragraph at lines 5156--5160 [][][]\T1/fi4/m/sl/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/ m/sl/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 getCo variate.varFunc[][][]\T1/ptm/m/n/10 , [2780] [2781] [2782] [2783] [2784] [2785] [2786] Underfull \hbox (badness 10000) in paragraph at lines 5588--5591 [][][]\T1/fi4/m/sl/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/1 0 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 getGroups.gls[ ][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 getGroups.lmList[][][]\T1/ptm/m/n/10 , [2787] [2788] [2789] [2790] [2791] [2792] [2793] Underfull \hbox (badness 10000) in paragraph at lines 5969--5974 [][][]\T1/fi4/m/sl/10 getGroupsFormula.gls[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/ sl/10 getGroupsFormula.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 getGrou psFormula.lme[][][]\T1/ptm/m/n/10 , [2794] [2795] [2796] [2797] Underfull \hbox (badness 1490) in paragraph at lines 6239--6250 [][][]\T1/fi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 glsC ontrol[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 glsObject[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 plot. gls[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 predict.gls[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 qqnorm.gls[][][]\T1/ptm/m/n/10 , [2798] Underfull \hbox (badness 10000) in paragraph at lines 6310--6312 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [2799] [2800] [2801] [2802] [2803] [2804] Underfull \hbox (badness 10000) in paragraph at lines 6728--6730 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [2805] [2806] [2807] [2808] [2809] Underfull \hbox (badness 10000) in paragraph at lines 7001--7008 [][][]\T1/fi4/m/sl/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 gapply[ ][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T 1/fi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 plot.nffGroupedData [][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 plot.nfnGroupedData[][][]\T1/ptm/m/n /10 , [2810] [2811] [2812] Underfull \hbox (badness 10000) in paragraph at lines 7263--7268 [][][]\T1/fi4/m/sl/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/ sl/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Initialize .glsStruct[][][]\T1/ptm/m/n/10 , [2813] [2814] [2815] [2816] [2817] [2818] [2819] [2820] [2821] [2822] [2823] [2824] Underfull \hbox (badness 1642) in paragraph at lines 8042--8064 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [2825] [2826] Underfull \hbox (badness 1642) in paragraph at lines 8213--8235 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [2827] [2828] [2829] [2830] [2831] Underfull \hbox (badness 10000) in paragraph at lines 8523--8525 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [2832] [2833] [2834] [2835] [2836] Underfull \hbox (badness 10000) in paragraph at lines 8826--8833 [][][]\T1/fi4/m/sl/10 lm[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 lme.lmList[] [][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 plot.lmList[][][]\T1/ptm/m/n/10 , [][] \T1/fi4/m/sl/10 pooledSD[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 predict.lmLi st[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 residuals.lmList[][][]\T1/ptm/m/n/ 10 , [2837] [2838] [2839] [2840] [2841] [2842] [2843] [2844] Underfull \hbox (badness 10000) in paragraph at lines 9351--9358 [][][]\T1/fi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/fi4/m/sl/10 gls[][][]\T1 /ptm/m/n/10 , [][]\T1/fi4/m/sl/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T 1/fi4/m/sl/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 logLik .lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 logLik.lmList[][][]\T1/ptm /m/n/10 , [2845] [2846] [2847] [2848] [2849]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9713 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9713 ...rA{Matrix}{Assign Matrix Values}{Matrix} [2850] [2851] [2852] [2853] [2854] [2855] [2856] [2857] [2858] [2859] [2860] [2861] Underfull \hbox (badness 1596) in paragraph at lines 10489--10515 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [2862] [2863] Underfull \hbox (badness 1490) in paragraph at lines 10627--10633 [][][]\T1/fi4/m/sl/10 nlmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 nlm e.nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 nlmeObject[][][]\T1/ptm/m/n /10 , [][]\T1/fi4/m/sl/10 nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 nlm eStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 reStruct[][][]\T1/ptm/m/n/10 , [2864] [2865] [2866] [2867] Underfull \hbox (badness 10000) in paragraph at lines 10865--10867 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [2868] [2869] [2870] [2871] [2872] [2873] [2874] [2875] [2876] [2877] [2878] [2879] [2880] [2881] [2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890] [2891] [2892] [2893] [2894] [2895] [2896] [2897] [2898] [2899] [2900] [2901] [2902] [2903] [2904] [2905] [2906] [2907] [2908] [2909] Underfull \hbox (badness 1286) in paragraph at lines 13722--13729 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/fi4/m/sl /10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/fi4/m/sl/10 inner \T1/ptm/m/n/10 or [2910] [2911] [2912] [2913] [2914] [2915] [2916] [2917] Underfull \hbox (badness 1215) in paragraph at lines 14250--14252 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. 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De-fault de-pends on the method func-tion: \T1/fi4/m/sl/1 0 "Blocked" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17119--17128 \T1/fi4/m/sl/10 pdBlocked\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Compound Symmetry" \ T1/ptm/m/n/10 for \T1/fi4/m/sl/10 pdCompSymm\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "D iagonal" Underfull \hbox (badness 10000) in paragraph at lines 17119--17128 \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 pdDiag\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Mult iple of an Identity" \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 pdIdent\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17119--17128 \T1/fi4/m/sl/10 "General Positive-Definite, Natural Parametrization" \T1/ptm/m/ n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17119--17128 \T1/fi4/m/sl/10 pdNatural\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "General Positive-Def inite" \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 pdSymm\T1/ptm/m/n/10 , and [2961] Underfull \hbox (badness 10000) in paragraph at lines 17183--17191 \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 varComb\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Con stant plus power of covariate" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17183--17191 \T1/fi4/m/sl/10 varConstPower\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Exponential of v ariance covariate" \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 varExp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17183--17191 \T1/fi4/m/sl/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 varIdent\T1/ptm/m/n/10 , [2962] [2963] [2964] [2965] [2966] [2967] [2968] [2969] [2970] [2971] [2972] [2973] Underfull \hbox (badness 10000) in paragraph at lines 17959--17969 [][][]\T1/fi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/1 0 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.corLin[ ][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.corRatio[][][]\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 17959--17969 [][]\T1/fi4/m/sl/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl /10 Variogram.corSpher[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.defa ult[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.gls[][][]\T1/ptm/m/n/10 , [2974] [2975] [2976] [2977] [2978] Underfull \hbox (badness 5036) in paragraph at lines 18283--18292 [][][]\T1/fi4/m/sl/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Vari ogram[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.default[][][]\T1/ptm/ m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/fi4 /m/sl/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [2979] [2980] [2981] [2982] [2983] [2984] [2985] [2986] [2987] [2988] [2989] [2990] [2991]) (./nnet-pkg.tex [2992] Chapter 26. [2993] Underfull \hbox (badness 10000) in paragraph at lines 78--87 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2994] [2995] [2996] [2997] [2998] [2999] [3000]) (./rpart-pkg.tex Chapter 27. [3001] [3002] [3003] [3004] [3005] Underfull \hbox (badness 2556) in paragraph at lines 349--353 \T1/ptm/m/n/10 im-plies \T1/fi4/m/sl/10 minlength = 0L\T1/ptm/m/n/10 , \T1/fi4/ m/sl/10 pretty = NULL \T1/ptm/m/n/10 im-plies \T1/fi4/m/sl/10 minlength = 1L\T1 /ptm/m/n/10 , and [3006] [3007] [3008] [3009] [3010] [3011] [3012] [3013] [3014] [3015] [3016] Underfull \hbox (badness 3219) in paragraph at lines 1113--1116 []\T1/ptm/m/n/10 For re-gres-sion or \T1/fi4/m/sl/10 anova \T1/ptm/m/n/10 trees all three resid-ual def-i-ni-tions re-duce to [3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027] [3028] [3029]) (./spatial-pkg.tex [3030] Chapter 28. [3031] [3032] [3033] [3034] [3035] [3036] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047] [3048] [3049]) (./survival-pkg.tex [3050] Chapter 29. [3051] [3052] [3053]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.212 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica te ignored \relax l.212 ... Myelogenous Leukemia survival data}{aml} [3054] [3055] [3056] [3057] Underfull \vbox (badness 10000) has occurred while \output is active [3058] [3059] [3060] [3061] [3062] [3063]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.colon}) has been already used, duplicate ignored \relax l.902 ...herapy for Stage B/C colon cancer}{colon} [3064] [3065] [3066] [3067] [3068] [3069] [3070] [3071] [3072] [3073] Overfull \hbox (139.78088pt too wide) in paragraph at lines 1671--1671 []\T1/fi4/m/sl/10 frailty.gamma(x, sparse = (nclass > 5), theta, df, eps = 1e- 05, method = c("em","aic", "df", "fixed"), ...)[] Overfull \hbox (94.78088pt too wide) in paragraph at lines 1672--1672 []\T1/fi4/m/sl/10 frailty.gaussian(x, sparse = (nclass > 5), theta, df, method =c("reml","aic", "df", "fixed"), ...)[] Overfull \hbox (134.78088pt too wide) in paragraph at lines 1673--1673 []\T1/fi4/m/sl/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, tdf = 5,method = c("aic", "df", "fixed"), ...)[] [3074] [3075] [3076] [3077] Underfull \vbox (badness 2012) has occurred while \output is active [3078] Underfull \hbox (badness 1389) in paragraph at lines 1966--1968 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3079] [3080] [3081] [3082] [3083] [3084] [3085] Underfull \vbox (badness 10000) has occurred while \output is active [3086] [3087] [3088] [3089] [3090] [3091] [3092] [3093] [3094] [3095] [3096] [3097] Underfull \hbox (badness 5274) in paragraph at lines 3190--3192 []\T1/ptm/m/n/10 an ob-ject of class \T1/fi4/m/sl/10 "summary.survfit"\T1/ptm/m /n/10 , which is the re-sult of the [3098] [3099] [3100] [3101] Underfull \hbox (badness 1540) in paragraph at lines 3535--3538 []\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per -son years if [3102] [3103] [3104] [3105] [3106] [3107] [3108] [3109] Underfull \hbox (badness 1281) in paragraph at lines 4085--4090 []\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/fi4/m/sl/10 "response "\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "deviance"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "d fbeta"\T1/ptm/m/n/10 , [3110] [3111] [3112] [3113] [3114] [3115] [3116] [3117] [3118] [3119] [3120] [3121] Underfull \hbox (badness 10000) in paragraph at lines 4938--4947 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3122] [3123] [3124] Underfull \hbox (badness 4686) in paragraph at lines 5100--5102 []\T1/ptm/m/n/10 numeric value to scale the re-sults. 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Transcript written on fullrefman.log. This is makeindex, version 2.14 [02-Oct-2002] (kpathsea + Thai support). Scanning input file fullrefman.idx.........................done (21390 entries accepted, 60 rejected). Sorting entries...............................................................................................................................................................................................................................................done (353784 comparisons). Generating output file fullrefman.ind........................done (11006 lines written, 101 warnings). Output written in fullrefman.ind. Transcript written in fullrefman.ilg. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) %&-line parsing enabled. entering extended mode (./fullrefman.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, arabic, basque, bulgarian, coptic, welsh, czech, slovak, german, ng erman, danish, esperanto, spanish, catalan, galician, estonian, farsi, finnish, french, greek, monogreek, ancientgreek, croatian, hungarian, interlingua, ibyc us, indonesian, icelandic, italian, latin, mongolian, dutch, norsk, polish, por tuguese, pinyin, romanian, russian, slovenian, uppersorbian, serbian, swedish, turkish, ukenglish, ukrainian, loaded. 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[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46]) [47] [48] [1] [2] (./base-pkg.tex Chapter 1. Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [3] [4] Underfull \hbox (badness 10000) in paragraph at lines 137--145 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/fi4/bx/n/10 x \T 1/ptm/m/n/10 such that \T1/fi4/bx/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 137--145 \T1/ptm/m/n/10 It equals \T1/fi4/bx/n/10 double.base ^ double.neg.ulp.digits \T 1/ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 137--145 \T1/fi4/bx/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/fi4/bx/n/10 double.round ing \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 148--155 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [5] [6] Underfull \hbox (badness 1178) in paragraph at lines 291--295 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/fi4/bx/n /10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [7] [8] Underfull \hbox (badness 3977) in paragraph at lines 372--375 []\T1/ptm/m/n/10 logical: should \T1/fi4/bx/n/10 minlength \T1/ptm/m/n/10 be ob -served strictly? Note that set-ting [9] Underfull \hbox (badness 2556) in paragraph at lines 498--504 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/fi4/bx/n/10 insertions\T1/ptm/m/n/10 ', [10] [11] [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1062--1065 []\T1/ptm/m/n/10 If the calls to \T1/fi4/bx/n/10 FUN \T1/ptm/m/n/10 re-turn vec -tors of dif-fer-ent lengths, \T1/fi4/bx/n/10 apply \T1/ptm/m/n/10 re-turns a l ist of length [19] [20] [21] Underfull \hbox (badness 10000) in paragraph at lines 1263--1269 []\T1/fi4/bx/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/fi4/bx/n/10 x mod y \T1/ptm /m/n/10 and \T1/fi4/bx/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion . It is guar-an-teed that Underfull \hbox (badness 3323) in paragraph at lines 1263--1269 \T1/fi4/bx/n/10 x == (x %% y) + y * ( x %/% y ) \T1/ptm/m/n/10 (up to round-i ng er-ror) un-less \T1/fi4/bx/n/10 y == 0 \T1/ptm/m/n/10 where the [22] [23] [24] [25] [26] [27] [28] [29] [30] Underfull \hbox (badness 10000) in paragraph at lines 1943--1945 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] Underfull \hbox (badness 10000) in paragraph at lines 3370--3372 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [52] [53] [54] [55] [56] [57] [58] [59] Underfull \hbox (badness 2970) in paragraph at lines 3949--3955 []\T1/ptm/m/n/10 is there sup-port the [][]\T1/fi4/bx/n/10 svg[][][]\T1/ptm/m/n /10 , [][]\T1/fi4/bx/n/10 cairo_pdf[][][] \T1/ptm/m/n/10 and [][]\T1/fi4/bx/n/1 0 cairo_ps[][][] \T1/ptm/m/n/10 de-vices, and for [60] [61] [62] [63] [64] [65] [66] [67] Underfull \hbox (badness 2521) in paragraph at lines 4505--4507 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [68] [69] Underfull \hbox (badness 1337) in paragraph at lines 4649--4655 \T1/ptm/m/n/10 LA-PACK re-quires LA-PACK >= 3.2 and was added in \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.2. The value of \T1/fi4/bx/n/10 tol \T1/ptm/m/n/10 is [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] Underfull \hbox (badness 2096) in paragraph at lines 5719--5732 []\T1/ptm/m/n/10 New restarts for \T1/fi4/bx/n/10 withRestarts \T1/ptm/m/n/10 c an be spec-i-fied in sev-eral ways. The sim-plest is in [86] [87] [88] [89] Underfull \hbox (badness 10000) in paragraph at lines 6042--6045 []\T1/ptm/m/n/10 A note on `\T1/fi4/bx/n/10 file://\T1/ptm/m/n/10 ' URLs. The m ost gen-eral form (from RFC1738) is [90] [91] [92] Underfull \hbox (badness 2790) in paragraph at lines 6257--6264 []\T1/fi4/bx/n/10 file \T1/ptm/m/n/10 can be used with \T1/fi4/bx/n/10 descript ion = "clipboard" \T1/ptm/m/n/10 in mode \T1/fi4/bx/n/10 "r" \T1/ptm/m/n/10 onl y. This reads Underfull \hbox (badness 3471) in paragraph at lines 6257--6264 \T1/ptm/m/n/10 the X11 pri-mary se-lec-tion (see [][]$\T1/fi4/bx/n/10 http : / / standards . freedesktop . org / clipboards-[]spec / [93] [94] Underfull \vbox (badness 10000) has occurred while \output is active [95] [96] [97] [98] [99] [100] [101] Underfull \hbox (badness 4595) in paragraph at lines 6859--6862 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [102] Underfull \hbox (badness 2351) in paragraph at lines 6916--6919 [][][]\T1/fi4/bx/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac- cord-ing to a group fac-tor; [][]\T1/fi4/bx/n/10 factor[][][]\T1/ptm/m/n/10 , [ ][]\T1/fi4/bx/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 table[][] []\T1/ptm/m/n/10 , [103] [104] [105] Underfull \hbox (badness 10000) in paragraph at lines 7161--7172 []\T1/fi4/bx/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments t o a data frame by call-ing [106] Underfull \hbox (badness 4479) in paragraph at lines 7232--7241 [][][]\T1/fi4/bx/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 plot.data.fra me[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 print.data.frame[][][]\T1/ptm/m/n/ 10 , [][]\T1/fi4/bx/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 na mes[][][] \T1/ptm/m/n/10 (for the col-umn names), Underfull \hbox (badness 2469) in paragraph at lines 7232--7241 [][]\T1/fi4/bx/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods , [][]\T1/fi4/bx/n/10 Math.data.frame[][][] \T1/ptm/m/n/10 etc, about \T1/ptm/m /it/10 Group \T1/ptm/m/n/10 meth-ods for [107] [108] [109] [110] [111] [112] Underfull \hbox (badness 10000) in paragraph at lines 7640--7652 \T1/fi4/bx/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/ n/10 may give \T1/fi4/bx/n/10 NA\T1/ptm/m/n/10 , and hence Underfull \hbox (badness 6220) in paragraph at lines 7640--7652 \T1/fi4/bx/n/10 as.POSIXct("1969-12-31 23:59:59", tz = "UTC") \T1/ptm/m/n/10 w ill give \T1/fi4/bx/n/10 "1969-12-31 23:59:00"\T1/ptm/m/n/10 . [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] Underfull \hbox (badness 1394) in paragraph at lines 8766--8771 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/fi4/bx/n/10 difftime \T1/ptm/m/n/10 with [129] [130] [131] [132] [133] [134] Underfull \hbox (badness 10000) in paragraph at lines 9210--9214 [][][]$\T1/fi4/bx/n/10 http : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/fi4/bx/n/10 http : / / en . wikipedia . org / wiki / IEEE _ [135] [136] [137] [138] [139] [140] Underfull \hbox (badness 2150) in paragraph at lines 9593--9596 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 9607--9615 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for [141] Underfull \hbox (badness 5622) in paragraph at lines 9648--9654 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/fi4/bx/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 4569) in paragraph at lines 10677--10681 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 10677--10681 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [156] [157] [158] [159] [160] [161] [162] Underfull \hbox (badness 2698) in paragraph at lines 11219--11228 []\T1/ptm/m/n/10 Both \T1/fi4/bx/n/10 $ \T1/ptm/m/n/10 and \T1/fi4/bx/n/10 [[ \ T1/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are al-lowed Underfull \hbox (badness 4341) in paragraph at lines 11219--11228 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] Underfull \hbox (badness 2253) in paragraph at lines 12166--12168 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [177] Underfull \hbox (badness 1565) in paragraph at lines 12227--12231 [][][]\T1/fi4/bx/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-b olic links, [][]\T1/fi4/bx/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 file.access[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 list.files[][][]\T1/ptm/ m/n/10 , and Underfull \hbox (badness 10000) in paragraph at lines 12270--12272 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/fi4/b x/n/10 PATH \T1/ptm/m/n/10 and \T1/fi4/bx/n/10 R_LIBS \T1/ptm/m/n/10 with [178] [179] Underfull \hbox (badness 1292) in paragraph at lines 12333--12341 \T1/ptm/m/n/10 ing spe-cial pager names be-ing in-ter-cepted by lower-level cod e (such as \T1/fi4/bx/n/10 "internal" \T1/ptm/m/n/10 and [180] Underfull \hbox (badness 1466) in paragraph at lines 12401--12404 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ fi4/bx/n/10 file.copy \T1/ptm/m/n/10 and [181] Underfull \hbox (badness 10000) in paragraph at lines 12507--12511 [][][]\T1/fi4/bx/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 file. access[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 file.path[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 list. files[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 unlink[][][]\T1/ptm/m/n/10 , [] []\T1/fi4/bx/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 12518--12521 [][][]$\T1/fi4/bx/n/10 http : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/fi4/bx/n/10 http : / / en . wikipedia . org / wik i / [182] [183] [184] Underfull \hbox (badness 3965) in paragraph at lines 12765--12769 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] Underfull \hbox (badness 4429) in paragraph at lines 13469--13472 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/fi4/bx/n/10 complex[][][] \T1/ptm/m/n/10 only for [196] Underfull \hbox (badness 10000) in paragraph at lines 13555--13557 []\T1/ptm/m/n/10 If you set \T1/fi4/bx/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/fi4/bx/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 13561--13565 []\T1/fi4/bx/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num- bers on the dec-i-mal point, so Underfull \hbox (badness 1052) in paragraph at lines 13561--13565 \T1/fi4/bx/n/10 formatC(c(6.11, 13.1), digits = 2, format = "fg") \T1/ptm/m/n/1 0 gives \T1/fi4/bx/n/10 c("6.1", " 13")\T1/ptm/m/n/10 . If you [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] Underfull \hbox (badness 1092) in paragraph at lines 14313--14318 [][]\T1/fi4/bx/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter the DLL has been loaded us-ing [208] [209] [210] Underfull \hbox (badness 6741) in paragraph at lines 14561--14565 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/fi4/bx/n/10 CRoutine\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 CallRoutine\T1/ptm/m/n/ 10 , [211] [212] [213] [214] [215] Underfull \hbox (badness 1867) in paragraph at lines 14859--14866 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [216] [217] [218] Underfull \vbox (badness 10000) has occurred while \output is active [219] [220] Underfull \hbox (badness 3679) in paragraph at lines 15235--15237 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/fi4/bx/n/10 htt p : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [221] [222] [223] [224] [225] [226] Underfull \hbox (badness 1478) in paragraph at lines 15703--15706 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] Underfull \hbox (badness 1442) in paragraph at lines 16379--16381 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/fi4/bx/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [237] Underfull \hbox (badness 2452) in paragraph at lines 16471--16487 [][][]\T1/fi4/bx/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 as .complex[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 as.double[][][]\T1/ptm/m/n/1 0 , [][]\T1/fi4/bx/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 as .logical[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 as.vector[][][]\T1/ptm/m/n/10 , [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] Underfull \hbox (badness 4739) in paragraph at lines 17116--17118 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [248] [249] [250] [251] [252] [253] Underfull \hbox (badness 1077) in paragraph at lines 17514--17519 \T1/ptm/m/n/10 trix or, if \T1/fi4/bx/n/10 simplify = "array"\T1/ptm/m/n/10 , a n ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/fi4/bx/n/10 simplify2array()\T1/p tm/m/n/10 . [254] [255] [256] [257] [258] [259] [260] Underfull \hbox (badness 10000) in paragraph at lines 17992--17996 []\T1/ptm/m/n/10 By de-fault \T1/fi4/bx/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, a nd \T1/fi4/bx/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 17992--17996 \T1/ptm/m/n/10 `\T1/fi4/bx/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/fi4/bx/ n/10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or ` \T1/fi4/bx/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/fi4/bx/n/10 /library\T1/ptm/m/ n/10 ' [261] [262] Underfull \hbox (badness 1014) in paragraph at lines 18145--18150 []\T1/ptm/m/n/10 Normally \T1/fi4/bx/n/10 library \T1/ptm/m/n/10 re-turns (in-v is-i-bly) the list of at-tached pack-ages, but \T1/fi4/bx/n/10 TRUE \T1/ptm/m/n /10 or \T1/fi4/bx/n/10 FALSE \T1/ptm/m/n/10 if [263] [264] [265] [266] [267] [268] [269] [270] [271] [272] Underfull \hbox (badness 1264) in paragraph at lines 18853--18858 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [273] [274] [275] [276] [277] [278] Underfull \hbox (badness 4954) in paragraph at lines 19277--19283 []\T1/fi4/bx/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment to be of log-i-cal type. For [][]\T1/fi4/bx/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 10000) in paragraph at lines 19277--19283 \T1/ptm/m/n/10 this uses the [][]\T1/fi4/bx/n/10 levels[][][] \T1/ptm/m/n/10 (l a-bels). Like [][]\T1/fi4/bx/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-t ributes in-clud-ing Underfull \hbox (badness 10000) in paragraph at lines 19277--19283 \T1/ptm/m/n/10 names. Char-ac-ter strings \T1/fi4/bx/n/10 c("T", "TRUE", "True" , "true") \T1/ptm/m/n/10 are re-garded as true, [279] [280] [281] [282] [283] Underfull \hbox (badness 10000) in paragraph at lines 19584--19586 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/fi4/bx/n/10 make.unique \T1/ptm/m/ n/10 has the prop-erty that [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] Underfull \hbox (badness 1655) in paragraph at lines 20567--20573 [][][]$\T1/fi4/bx/n/10 http : / / en . wikipedia . org / wiki / Data _ compress ion$[][] \T1/ptm/m/n/10 for back-ground on data com-pres-sion, [298] [299] [300] Underfull \hbox (badness 1484) in paragraph at lines 20728--20736 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been [301] [302] [303] [304] Underfull \hbox (badness 2790) in paragraph at lines 20995--20998 []\T1/fi4/bx/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes- sages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 20995--20998 \T1/fi4/bx/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still mes-sages, so can be sup-pressed by [305] [306] [307] [308] [309] [310] Underfull \hbox (badness 10000) in paragraph at lines 21434--21437 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 21434--21437 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] Underfull \hbox (badness 1199) in paragraph at lines 22481--22487 []\T1/ptm/m/n/10 The de-fault method for \T1/fi4/bx/n/10 is.numeric \T1/ptm/m/n /10 re-turns \T1/fi4/bx/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mo de[][][] \T1/fi4/bx/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 22481--22487 \T1/ptm/m/n/10 ([][]type[][][] \T1/fi4/bx/n/10 "double" \T1/ptm/m/n/10 or type \T1/fi4/bx/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/fi4/bx/n/1 0 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, [327] [328] [329] [330] [331] [332] [333] Underfull \hbox (badness 1038) in paragraph at lines 23014--23023 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 10000) in paragraph at lines 23014--23023 \T1/fi4/bx/n/10 c("datasets", "utils", "grDevices", "graphics", "stats", "methods")\T1/ptm/m/n/10 . Underfull \hbox (badness 1881) in paragraph at lines 23024--23027 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 23043--23045 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [334] Underfull \hbox (badness 10000) in paragraph at lines 23107--23116 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/fi4/b x/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2600) in paragraph at lines 23107--23116 \T1/ptm/m/n/10 `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/fi4/bx/n/10 /bin/pager\T1/p tm/m/n/10 ', which se-lects a pager via the \T1/fi4/bx/n/10 PAGER \T1/ptm/m/n/1 0 en-vi-ron-ment vari-able Underfull \hbox (badness 2142) in paragraph at lines 23117--23123 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/fi4/bx/n/10 postsc ript[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 23130--23135 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/fi4/bx/n/10 postscript[][][] \T1/ ptm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 23140--23149 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [335] [336] [337] Underfull \hbox (badness 10000) in paragraph at lines 23381--23387 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/fi4/bx /n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 23381--23387 \T1/ptm/m/n/10 e.g. the de-fault `\T1/fi4/bx/n/10 "http://www.bioconductor.org" \T1/ptm/m/n/10 ' or the Eu-ro-pean mir- Underfull \hbox (badness 10000) in paragraph at lines 23381--23387 \T1/ptm/m/n/10 ror `\T1/fi4/bx/n/10 "http://bioconductor.statistik.tu-dortmund. de"\T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 23393--23396 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/fi4/bx/n/10 create.post[] [][] \T1/ptm/m/n/10 (and hence[][]\T1/fi4/bx/n/10 bug.report[][][] \T1/ptm/m/n/ 10 and Underfull \hbox (badness 2689) in paragraph at lines 23418--23420 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 7203) in paragraph at lines 23446--23449 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/fi4/bx/n/10 create.po st[][][] \T1/ptm/m/n/10 and hence [][]\T1/fi4/bx/n/10 bug.report[][][] \T1/ptm/ m/n/10 and Underfull \hbox (badness 3128) in paragraph at lines 23456--23462 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/fi4/bx/n/10 "source" \T1/ptm/m/n/10 ( the de-fault ex-cept un-der the CRAN OS X build) Underfull \hbox (badness 1881) in paragraph at lines 23456--23462 \T1/ptm/m/n/10 and \T1/fi4/bx/n/10 "mac.binary."\T1/ptm/m/n/10 . Win-dows uses \T1/fi4/bx/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/fi4/bx/n/10 "mac.binary.leopa rd" \T1/ptm/m/n/10 and [338] Underfull \hbox (badness 10000) in paragraph at lines 23464--23471 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/fi4/bx/n/10 upd ate.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 23464--23471 \T1/fi4/bx/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util- i-ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 23464--23471 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 10000) in paragraph at lines 23464--23471 \T1/fi4/bx/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.c ran"; [339] [340] [341] [342] Underfull \hbox (badness 10000) in paragraph at lines 23765--23769 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/fi4/bx/n/10 X \T1/ptm/m/ n/10 and \T1/fi4/bx/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/fi4/bx/n/10 A \T1/p tm/m/n/10 with di-men- Underfull \hbox (badness 10000) in paragraph at lines 23765--23769 \T1/ptm/m/n/10 sion \T1/fi4/bx/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e -ment \T1/fi4/bx/n/10 A[c(arrayindex.x, arrayindex.y)] [343] [344] [345] [346] Underfull \hbox (badness 1748) in paragraph at lines 24064--24068 \T1/ptm/m/n/10 seem un-de-sir-able, e.g., when past-ing two char-ac-ter vec-tor s, or very de-sir-able, e.g. in [347] [348] [349] [350] [351] [352] [353] [354] Underfull \hbox (badness 2726) in paragraph at lines 24563--24566 []\T1/ptm/m/n/10 character string (or \T1/fi4/bx/n/10 NULL\T1/ptm/m/n/10 ) in-d i-cat-ing [][]\T1/fi4/bx/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-pu t, see [355] [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] Underfull \hbox (badness 1052) in paragraph at lines 25368--25373 []\T1/fi4/bx/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/ 10 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vid ed [367] [368] [369] [370] [371] Underfull \hbox (badness 1097) in paragraph at lines 25757--25765 []\T1/ptm/m/n/10 The seed, \T1/fi4/bx/n/10 .Random.seed[-1] == r[1:3] \T1/ptm/m /n/10 is an in-te-ger vec-tor of length [372] [373] [374] [375] Underfull \hbox (badness 1533) in paragraph at lines 26073--26076 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [376] [377] [378] [379] [380] [381] [382] [383] [384] [385] [386] [387] [388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399] Underfull \hbox (badness 6188) in paragraph at lines 27726--27728 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/fi4/bx/n/10 http : / / pubs . opengroup . org / onlinepubs / 9699919799 / [400] [401] [402] [403] [404] [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] Underfull \hbox (badness 10000) in paragraph at lines 28925--28928 []\T1/fi4/bx/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my cur-rent workspace', i.e., Underfull \hbox (badness 3229) in paragraph at lines 28925--28928 \T1/fi4/bx/n/10 save(list = ls(all = TRUE), file = ".RData")\T1/ptm/m/n/10 . It is also what hap-pens with [418] [419] [420] Underfull \hbox (badness 2302) in paragraph at lines 29125--29132 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 29125--29132 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 2698) in paragraph at lines 29125--29132 \T1/ptm/m/n/10 val-ues. In the case \T1/fi4/bx/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, but Underfull \hbox (badness 4805) in paragraph at lines 29125--29132 \T1/ptm/m/n/10 in gen-eral it is not. (To scale by the stan-dard de-vi-a-tions with-out cen-ter-ing, use [421] [422] Underfull \hbox (badness 2261) in paragraph at lines 29278--29283 []\T1/ptm/m/n/10 If \T1/fi4/bx/n/10 strip.white \T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 29305--29311 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 4001) in paragraph at lines 29305--29311 \T1/ptm/m/n/10 `\T1/fi4/bx/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta- [423] Underfull \hbox (badness 10000) in paragraph at lines 29378--29383 []\T1/ptm/m/n/10 Note that since \T1/fi4/bx/n/10 sep \T1/ptm/m/n/10 is a sep-a- ra-tor and not a ter-mi-na-tor, read-ing a file by Underfull \hbox (badness 1701) in paragraph at lines 29378--29383 \T1/fi4/bx/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/1 0 will give an empty fi-nal line if [424] [425] [426] [427] [428] Underfull \hbox (badness 6188) in paragraph at lines 29712--29715 []\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence \T1/fi4/bx /n/10 1, 2, ..., length(along.with)\T1/ptm/m/n/10 . [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] Underfull \vbox (badness 10000) has occurred while \output is active [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] Underfull \hbox (badness 1072) in paragraph at lines 32120--32124 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 32125--32129 []\T1/ptm/m/n/10 The command-line op-tion `\T1/fi4/bx/n/10 --vanilla\T1/ptm/m/n /10 ' im-plies `\T1/fi4/bx/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/fi4/bx/n/1 0 --no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 32153--32159 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/fi4/bx/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 32153--32159 \T1/ptm/m/n/10 and `\T1/fi4/bx/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked fo r first in architecture-specific di-rec-to-ries, e.g. Underfull \hbox (badness 3343) in paragraph at lines 32162--32169 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 32162--32169 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment Underfull \hbox (badness 1917) in paragraph at lines 32162--32169 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/fi4/bx /n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [464] [465] [466] [467] [468] Underfull \hbox (badness 10000) in paragraph at lines 32452--32458 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/fi4/bx/n/10 for mat \T1/ptm/m/n/10 meth-ods is [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487] [488] [489] Underfull \hbox (badness 1248) in paragraph at lines 33821--33831 []\T1/ptm/m/n/10 If \T1/fi4/bx/n/10 EXPR \T1/ptm/m/n/10 eval-u-ates to a char-a c-ter string then that string is matched (ex-actly)to the names Underfull \hbox (badness 1902) in paragraph at lines 33821--33831 \T1/ptm/m/n/10 of the el-e-ments in \T1/fi4/bx/n/10 ...\T1/ptm/m/n/10 . If ther e is a match then that el-e-ment is eval-u-ated un-less it Underfull \hbox (badness 2772) in paragraph at lines 33821--33831 \T1/ptm/m/n/10 is miss-ing, in which case the next non-missing el-e-ment is eva l-u-ated, so for ex-am-ple [490] [491] Underfull \hbox (badness 4416) in paragraph at lines 34006--34008 []\T1/ptm/m/n/10 Argument \T1/fi4/bx/n/10 names \T1/ptm/m/n/10 was in-tro-duced in \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.13.0 to avoid need-ing the com-mon use of [492] [493] Underfull \hbox (badness 3333) in paragraph at lines 34099--34104 []\T1/ptm/m/n/10 If a file-name starts with \T1/fi4/bx/n/10 . \T1/ptm/m/n/10 th is may need to be matched ex-plic-itly: for ex-am-ple [494] [495] [496] [497] [498] [499] [500] [501] [502] Underfull \hbox (badness 1472) in paragraph at lines 34706--34709 []\T1/ptm/m/n/10 logical. If \T1/fi4/bx/n/10 TRUE\T1/ptm/m/n/10 , func-tions ke ep their source in-clud-ing com-ments, see [503] [504] [505] [506] [507] [508] [509] [510] Underfull \hbox (badness 4217) in paragraph at lines 35222--35225 []\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/fi 4/bx/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies [511] [512] Underfull \hbox (badness 2671) in paragraph at lines 35356--35359 []\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/fi4/bx/n/10 ...\T1/p tm/m/n/10 . If set to \T1/fi4/bx/n/10 NULL\T1/ptm/m/n/10 , it im-plies [513] [514] [515] [516] [517] Underfull \hbox (badness 10000) in paragraph at lines 35754--35757 [][][]\T1/fi4/bx/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [][]$http : / / developer . r-[]project . org / [518] [519] Underfull \hbox (badness 10000) in paragraph at lines 35875--35879 [][][]\T1/fi4/bx/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 removeTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 getTaskCallbackNa mes[][][]\T1/ptm/m/n/10 \ [][]$\T1/fi4/bx/n/10 http : / / developer . [520] Underfull \hbox (badness 10000) in paragraph at lines 35937--35941 [][][]\T1/fi4/bx/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 removeTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 taskCallbackManag er[][][]\T1/ptm/m/n/10 \ [][]$\T1/fi4/bx/n/10 http : / / developer . [521] [522] [523] [524] [525] [526] [527] [528] [529] Underfull \hbox (badness 10000) in paragraph at lines 36558--36560 []\T1/ptm/m/n/10 Using [][]\T1/fi4/bx/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 ( from pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, ca ll-ing [530] [531] [532] [533] [534] [535] [536] Underfull \hbox (badness 1990) in paragraph at lines 37062--37070 []\T1/fi4/bx/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 4846) in paragraph at lines 37062--37070 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/fi4/bx/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [537] [538] [539] [540] Underfull \hbox (badness 1515) in paragraph at lines 37331--37336 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0 [541] [542] [543] Underfull \hbox (badness 1917) in paragraph at lines 37554--37561 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/fi4/bx/n/10 UseMethod("fun") \T1 /ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [544] [545] [546] [547] [548] [549] [550] [551] Underfull \hbox (badness 3668) in paragraph at lines 38120--38122 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [552] [553] Underfull \hbox (badness 2401) in paragraph at lines 38220--38224 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/fi4/bx/n/10 options[][][]("wa rn") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [554] [555] Underfull \hbox (badness 10000) in paragraph at lines 38396--38401 []\T1/ptm/m/n/10 If \T1/fi4/bx/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/fi4/ bx/n/10 x \T1/ptm/m/n/10 is an [][]\T1/fi4/bx/n/10 array[][][] \T1/ptm/m/n/10 ( has a [][]\T1/fi4/bx/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is Underfull \hbox (badness 1454) in paragraph at lines 38396--38401 \T1/fi4/bx/n/10 arrayInd(which(x), dim(x), dimnames(x))\T1/ptm/m/n/10 , namely a ma-trix whose rows each are the [556] [557] [558] [559] [560] [561] [562] Underfull \hbox (badness 10000) in paragraph at lines 38815--38820 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/fi4/bx/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 38815--38820 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to Underfull \hbox (badness 1102) in paragraph at lines 38815--38820 \T1/fi4/bx/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10 , so \T1/fi4/bx/n/10 NA \T1/ptm/m/n/10 val-ues are given rank \T1/fi4/bx/n/10 NA [563] Underfull \hbox (badness 5417) in paragraph at lines 38905--38909 []\T1/fi4/bx/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rent ly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [564] Underfull \hbox (badness 10000) in paragraph at lines 38966--38970 []\T1/fi4/bx/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dar d' reg-exps, in-clud-ing el-e-ments named [565]) (./compiler-pkg.tex [566] Chapter 2. [567] [568] [569]) (./datasets-pkg.tex [570] Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] Overfull \hbox (1.81013pt too wide) in paragraph at lines 691--694 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("nfnGroupedData", "nfGro upedData", "groupedData", "data.frame") [582] [583] Overfull \hbox (1.81013pt too wide) in paragraph at lines 824--827 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("nfnGroupedData", "nfGro upedData", "groupedData", "data.frame") [584] [585] [586] [587] Overfull \hbox (1.81013pt too wide) in paragraph at lines 1130--1133 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("nfnGroupedData", "nfGro upedData", "groupedData", "data.frame") [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] Overfull \hbox (1.81013pt too wide) in paragraph at lines 1702--1705 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("nfnGroupedData", "nfGro upedData", "groupedData", "data.frame") [598] [599] [600] [601] [602] [603] [604] Overfull \hbox (1.81013pt too wide) in paragraph at lines 2124--2127 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("nfnGroupedData", "nfGro upedData", "groupedData", "data.frame") [605] [606] [607] [608] [609] [610] [611] Overfull \hbox (1.81013pt too wide) in paragraph at lines 2601--2604 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("nfnGroupedData", "nfGro upedData", "groupedData", "data.frame") [612] Overfull \vbox (13.87083pt too high) has occurred while \output is active [613] Underfull \vbox (badness 1721) has occurred while \output is active [614] [615] Overfull \vbox (12.25539pt too high) has occurred while \output is active [616] [617] Overfull \vbox (17.12102pt too high) has occurred while \output is active [618] [619] [620] [621] [622] [623] [624] [625] [626] Overfull \hbox (1.81013pt too wide) in paragraph at lines 3573--3576 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("nfnGroupedData", "nfGro upedData", "groupedData", "data.frame") [627] [628] [629] [630] Underfull \hbox (badness 1325) in paragraph at lines 3809--3812 []\T1/ptm/m/n/10 For back-ground on Bristle-cone pines and Methuse-lah Walk, se e [][]$\T1/fi4/bx/n/10 http : / / www . sonic . net / [631] [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] [642] [643]) (./grDevices-pkg.tex [644] Chapter 4. [645] [646] [647] [648] Underfull \hbox (badness 1484) in paragraph at lines 274--278 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/fi4/bx/n/10 c(mi, ma, n.)\T1/ ptm/m/n/10 , with iden-ti-cal mean-ing to [649] [650] [651] [652] [653] [654] [655] [656] [657] [658] [659] [660] Underfull \hbox (badness 5175) in paragraph at lines 1041--1043 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [661] [662] [663] Underfull \hbox (badness 1852) in paragraph at lines 1234--1237 []\T1/fi4/bx/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col -ors that will be used in plot-ting, call-ing [664] [665] [666] Underfull \hbox (badness 1490) in paragraph at lines 1436--1441 \T1/ptm/m/n/10 by [][]\T1/fi4/bx/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][] \T1/fi4/bx/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/fi4/bx /n/10 "no"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "yes" \T1/ptm/m/n/10 and [667] Underfull \hbox (badness 2698) in paragraph at lines 1490--1493 []\T1/fi4/bx/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture , oth-er-wise a ma-trix of color names (for [668] Underfull \hbox (badness 10000) in paragraph at lines 1559--1563 []\T1/ptm/m/n/10 logical; if \T1/fi4/bx/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/fi4/bx/n/10 TRUE \T1/ptm/m/n/10 when Underfull \hbox (badness 6332) in paragraph at lines 1559--1563 [][]\T1/fi4/bx/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/f i4/bx/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is among the [669] [670] [671] [672] Underfull \hbox (badness 1033) in paragraph at lines 1842--1855 \T1/fi4/bx/n/10 "pgnm"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "pgnmraw"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "pnm"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "pnmraw"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "ppm"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "ppmraw"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "pkm"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "pkmraw"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "tiffcrle"\T1/ptm/m/n/10 , Underfull \hbox (badness 3758) in paragraph at lines 1842--1855 \T1/fi4/bx/n/10 "tiffg3"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "tiffg32d"\T1/ptm/m/n/ 10 , \T1/fi4/bx/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "tifflzw"\T1/ptm/ m/n/10 , \T1/fi4/bx/n/10 "tiffpack"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "tiff12nc"\ T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "tiff24nc"\T1/ptm/m/n/10 , Underfull \hbox (badness 3128) in paragraph at lines 1842--1855 \T1/fi4/bx/n/10 "tiff32nc" "psmono"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "psgray"\T1 /ptm/m/n/10 , \T1/fi4/bx/n/10 "psrgb"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "bit"\T1/ ptm/m/n/10 , \T1/fi4/bx/n/10 "bitrgb"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "bitcmyk" \T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "pngmono"\T1/ptm/m/n/10 , Underfull \hbox (badness 1546) in paragraph at lines 1842--1855 \T1/fi4/bx/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "pngalpha"\T1/ptm/m/n /10 , \T1/fi4/bx/n/10 "png16"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "png256"\T1/ptm/m /n/10 , \T1/fi4/bx/n/10 "png16m"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "png48"\T1/ptm /m/n/10 , \T1/fi4/bx/n/10 "jpeg"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "jpeggray"\T1/ ptm/m/n/10 , [673] [674] Underfull \hbox (badness 10000) in paragraph at lines 1951--1953 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [675] [676] Underfull \hbox (badness 6758) in paragraph at lines 2103--2106 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [677] [678] [679] [680] [681] [682] [683] [684] Underfull \hbox (badness 10000) in paragraph at lines 2606--2607 Underfull \vbox (badness 10000) has occurred while \output is active [685] [686] [687] [688] [689] [690] Underfull \hbox (badness 1755) in paragraph at lines 3044--3046 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/fi4/bx/n/10 nr, nc \T1/ptm/ m/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [691] [692] [693] [694] [695] Underfull \hbox (badness 7851) in paragraph at lines 3365--3368 []\T1/ptm/m/n/10 For use with \T1/fi4/bx/n/10 onefile = FALSE \T1/ptm/m/n/10 gi ve a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3379--3381 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/fi4/bx/n/10 /Title\T1/ptm/m /n/10 ' field in the file. De-faults to [696] [697] Underfull \hbox (badness 1173) in paragraph at lines 3495--3505 []\T1/ptm/m/n/10 The \T1/fi4/bx/n/10 paper \T1/ptm/m/n/10 ar-gu-ment sets the ` \T1/fi4/bx/n/10 /MediaBox\T1/ptm/m/n/10 ' en-try in the file, which de-faults t o \T1/fi4/bx/n/10 width \T1/ptm/m/n/10 by [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] Underfull \hbox (badness 1067) in paragraph at lines 4196--4203 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [708] [709] [710] Underfull \hbox (badness 1789) in paragraph at lines 4418--4420 []\T1/ptm/m/n/10 title string to em-bed as the \T1/fi4/bx/n/10 Title \T1/ptm/m/ n/10 com-ment in the file. De-faults to [711] Underfull \hbox (badness 1377) in paragraph at lines 4468--4473 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues Underfull \hbox (badness 2671) in paragraph at lines 4495--4503 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/fi4/ bx/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as [712] Underfull \hbox (badness 1418) in paragraph at lines 4544--4551 \T1/ptm/m/n/10 it is one of \T1/fi4/bx/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/fi 4/bx/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "Courier"\T1/ptm/m/n/10 , \ T1/fi4/bx/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "Helvetica-Narrow"\T 1/ptm/m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4552--4561 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4552--4561 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4562--4564 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [713] Underfull \hbox (badness 1057) in paragraph at lines 4673--4678 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/fi4/bx/n/10 "rgb"\T1/ptm/m/n/10 ) (which is RGB+gray) and [714] Underfull \hbox (badness 7344) in paragraph at lines 4733--4735 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso [715] [716] Underfull \hbox (badness 2035) in paragraph at lines 4857--4866 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 4857--4866 \T1/ptm/m/n/10 vided: \T1/fi4/bx/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/fi4/bx/n /10 "Bookman"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "Courier"\T1/ptm/m/n/10 , \T1/fi4 /bx/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "Helvetica-Narrow"\T1/ptm/ m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4857--4866 \T1/fi4/bx/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "Palatin o" \T1/ptm/m/n/10 and \T1/fi4/bx/n/10 "Times"\T1/ptm/m/n/10 ; \T1/fi4/bx/n/10 " URWGothic"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "URWBookman"\T1/ptm/m/n/10 , [717] Underfull \hbox (badness 6775) in paragraph at lines 4924--4932 \T1/ptm/m/n/10 can be found at [][]$\T1/fi4/bx/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Underfull \hbox (badness 3000) in paragraph at lines 4924--4932 \T1/ptm/m/n/10 Lunde's CJKV re-sources are at [][]$\T1/fi4/bx/n/10 ftp : / / ft p . oreilly . com / pub / examples / nutshell / cjkv / Underfull \hbox (badness 7344) in paragraph at lines 4943--4945 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso [718] [719] Underfull \hbox (badness 1546) in paragraph at lines 5063--5071 []\T1/ptm/m/n/10 arguments \T1/fi4/bx/n/10 onefile\T1/ptm/m/n/10 , \T1/fi4/bx/n /10 family\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 title\T1/ptm/m/n/10 , \T1/fi4/bx/n/1 0 fonts\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 encoding\T1/ptm/m/n/10 , \T1/fi4/bx/n/1 0 bg\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 fg\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 width\T 1/ptm/m/n/10 , [720] Underfull \hbox (badness 1648) in paragraph at lines 5140--5144 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [721] [722] [723] [724] [725] [726] [727] Underfull \hbox (badness 10000) in paragraph at lines 5558--5561 []\T1/fi4/bx/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (re d/green/blue) into HSV space [728] Underfull \vbox (badness 10000) has occurred while \output is active [729] [730] [731] [732] [733] Underfull \hbox (badness 1189) in paragraph at lines 5954--5956 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [734] Underfull \hbox (badness 10000) in paragraph at lines 6052--6054 []\T1/fi4/bx/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [735] [736] [737] [738] Underfull \hbox (badness 3780) in paragraph at lines 6343--6349 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/fi4/bx/n/ 10 "AvantGarde"\T1/ptm/m/n/10 , [739] [740] [741] Underfull \hbox (badness 2680) in paragraph at lines 6539--6541 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/fi4/bx/n/10 number[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [742] [743] [744]) (./graphics-pkg.tex Chapter 5. [745] [746] Underfull \hbox (badness 2856) in paragraph at lines 177--180 []\T1/ptm/m/n/10 For each \T1/fi4/bx/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn be-tween the point \T1/fi4/bx/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the poi nt [747] [748] [749] [750] [751] Underfull \hbox (badness 4492) in paragraph at lines 465--471 []\T1/ptm/m/n/10 When \T1/fi4/bx/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mar k lo-ca-tions are com-puted in-ter-nally (the same way [752] [753] [754] Underfull \hbox (badness 10000) in paragraph at lines 690--697 []\T1/fi4/bx/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/ ptm/m/n/10 in-ter-face to the C func-tion \T1/fi4/bx/n/10 CreateAtVector() \T1/ ptm/m/n/10 in [755] [756] [757] Underfull \hbox (badness 1389) in paragraph at lines 856--859 []\T1/ptm/m/n/10 logical. If \T1/fi4/bx/n/10 TRUE\T1/ptm/m/n/10 , the lines whi ch di-vide ad-ja-cent (non-stacked!) bars [758] Underfull \vbox (badness 10000) has occurred while \output is active [759] [760] [761] [762] [763] Underfull \hbox (badness 4634) in paragraph at lines 1253--1256 [][][]\T1/fi4/bx/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/fi4/bx/n/10 boxplot.formula[][][]\T1/ptm/m /n/10 , [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] Underfull \hbox (badness 1009) in paragraph at lines 2286--2293 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] Underfull \vbox (badness 10000) has occurred while \output is active [801] [802] [803] [804] Underfull \hbox (badness 1867) in paragraph at lines 3911--3915 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [805] [806] [807] [808] [809] [810] [811] Underfull \hbox (badness 1924) in paragraph at lines 4362--4367 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 2529) in paragraph at lines 4391--4394 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used: see [812] [813] [814] [815] [816] Underfull \hbox (badness 10000) in paragraph at lines 4735--4741 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/fi4/bx/ n/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4735--4741 \T1/fi4/bx/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/fi4/bx/n/10 par("cin")/par("pi n") \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that Underfull \hbox (badness 1072) in paragraph at lines 4735--4741 \T1/fi4/bx/n/10 c([][]strwidth[][][](ch), [][]strheight[][][](ch)) \T1/ptm/m/n/ 10 for a given string \T1/fi4/bx/n/10 ch \T1/ptm/m/n/10 is usu-ally much more p re- [817] [818] Underfull \hbox (badness 10000) in paragraph at lines 4865--4868 [819 ] Underfull \hbox (badness 10000) in paragraph at lines 4926--4928 [820 ] [821] Underfull \hbox (badness 10000) in paragraph at lines 5115--5117 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/fi4/bx/n/10 lty = 2:6\T1/ptm/m/n/10 ) cor-re-spond to [822] Underfull \vbox (badness 10000) has occurred while \output is active [823] [824] Underfull \hbox (badness 4156) in paragraph at lines 5271--5274 []\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/fi4/bx/n/10 z \T1/pt m/m/n/10 co-or-di-nates. Of-ten used with [825] [826] [827] [828] [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] [839] [840] [841] [842] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6520--6521 [][] [843 ] [844] Underfull \vbox (badness 10000) has occurred while \output is active [845] Overfull \hbox (9.78088pt too wide) in paragraph at lines 6679--6679 []\T1/fi4/m/n/9 TestChars(font = 5) # Euro might be at 160 (0+10*16). Mac OS has apple at 240 (0+15*16).[] [846] [847] [848] [849] [850] [851] [852] [853] Underfull \hbox (badness 1048) in paragraph at lines 7227--7232 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [854] [855] Underfull \hbox (badness 1540) in paragraph at lines 7343--7346 []\T1/ptm/m/n/10 For each \T1/fi4/bx/n/10 i\T1/ptm/m/n/10 , a line seg-ment is drawn be-tween the point \T1/fi4/bx/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the point [856] [857] [858] [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] Underfull \hbox (badness 2050) in paragraph at lines 8155--8159 []\T1/ptm/m/n/10 For \T1/fi4/bx/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/fi4/bx/n/10 pch\T1/ptm/m/n/10 ) is dra wn. For [869] [870] [871] [872] [873] (/usr/share/texmf/tex/latex/inconsolata/ts1fi4.fd ) [874] Underfull \hbox (badness 6691) in paragraph at lines 8555--8558 []\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex- pan-sion) Underfull \hbox (badness 2799) in paragraph at lines 8558--8560 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font and size \T1/fi4/bx/n/10 pa r("font.sub") \T1/ptm/m/n/10 and color [875]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8640 \HeaderA{units}{Graphical Units}{units} [876] [877] [878] [879]) (./grid-pkg.tex [880] Chapter 6. [881] [882] [883] [884] [885] [886] Underfull \hbox (badness 2680) in paragraph at lines 405--408 []\T1/ptm/m/n/10 Note that \T1/fi4/bx/n/10 preDrawDetails \T1/ptm/m/n/10 and \T 1/fi4/bx/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-t ion of [887] [888] [889] [890] [891] [892] [893] [894] [895] Underfull \hbox (badness 4279) in paragraph at lines 945--954 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/fi4/bx/n/10 pushViewport[][][]\T1/ptm/ m/n/10 , [][]\T1/fi4/bx/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n /10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 seekViewport[][][]\T 1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/fi4 /bx/n/10 unit[][][]\T1/ptm/m/n/10 , [896] [897] [898] Underfull \hbox (badness 2781) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 Both func-tions cre-ate an ar-rows grob (a graph-i-cal ob-ject de-scrib-ing ar-rows), but only [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948] Underfull \hbox (badness 1067) in paragraph at lines 4359--4362 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [949] [950] [951] [952] Underfull \hbox (badness 7256) in paragraph at lines 4598--4600 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] Underfull \hbox (badness 2096) in paragraph at lines 5805--5811 \T1/ptm/m/n/10 pos-si-ble to add and sub-tract unit ob-jects (e.g., \T1/fi4/bx/ n/10 unit(1, "npc") - unit(1, "inches")\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 5805--5811 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [971] [972] [973] [974] [975] [976] [977] Underfull \hbox (badness 7649) in paragraph at lines 6267--6270 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like [978] [979] [980] [981] [982]) (./methods-pkg.tex Chapter 7. [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] Underfull \hbox (badness 2237) in paragraph at lines 1432--1434 []\T1/ptm/m/n/10 The class \T1/fi4/bx/n/10 "className" \T1/ptm/m/n/10 ex-tends \T1/fi4/bx/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/fi4/bx/n/10 "pack age"\T1/ptm/m/n/10 , also of class [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] Underfull \hbox (badness 1590) in paragraph at lines 1979--1986 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/fi4/bx/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests Underfull \hbox (badness 10000) in paragraph at lines 2028--2033 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/fi4/bx/n/10 insertSource \T1/ptm/m/n/10 can be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 2028--2033 \T1/ptm/m/n/10 file name is passed to \T1/fi4/bx/n/10 insertSource \T1/ptm/m/n/ 10 it calls \T1/fi4/bx/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] Underfull \hbox (badness 10000) in paragraph at lines 2628--2631 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/fi4/bx/n/10 setGeneric[][][] \T1/ ptm/m/n/10 and [][]\T1/fi4/bx/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate ob-jects of class [1017] [1018] Underfull \hbox (badness 1132) in paragraph at lines 2768--2772 []\T1/ptm/m/n/10 In \T1/fi4/bx/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/fi4/bx/n /10 TRUE\T1/ptm/m/n/10 , the \T1/fi4/bx/n/10 package \T1/ptm/m/n/10 slot of the re-turned re-sult is in Underfull \hbox (badness 1033) in paragraph at lines 2800--2805 \T1/ptm/m/n/10 In ad-di-tion, \T1/fi4/bx/n/10 removeGeneric \T1/ptm/m/n/10 re-m oves the func-tion it-self; \T1/fi4/bx/n/10 removeMethods \T1/ptm/m/n/10 re-sto res the [1019] [1020] [1021] [1022] [1023] [1024] [1025] Underfull \hbox (badness 1102) in paragraph at lines 3308--3310 []\T1/fi4/bx/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string n ame of the pack-age (with-out the ex-tra-ne-ous [1026] [1027] [1028] [1029] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\T1/ptm/m/n/10 The \T1/fi4/bx/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3645--3654 []\T1/ptm/m/n/10 The [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] Underfull \hbox (badness 1436) in paragraph at lines 4550--4553 []\T1/ptm/m/n/10 The class \T1/fi4/bx/n/10 "SealedMethodDefinition" \T1/ptm/m/n /10 is cre-ated by a call to [][]\T1/fi4/bx/n/10 setMethod[][][] \T1/ptm/m/n/10 with ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4579--4585 []\T1/ptm/m/n/10 class [][]\T1/fi4/bx/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4579--4585 \T1/fi4/bx/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\ T1/fi4/bx/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1043] [1044] [1045] [1046] [1047] [1048] [1049] Underfull \vbox (badness 10000) has occurred while \output is active [1050] [1051] Underfull \hbox (badness 1092) in paragraph at lines 5251--5258 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 5251--5258 \T1/ptm/m/n/10 if se-lect-ing class \T1/fi4/bx/n/10 "track" \T1/ptm/m/n/10 for \T1/fi4/bx/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other me th-ods list and Underfull \hbox (badness 4036) in paragraph at lines 5299--5302 []\T1/ptm/m/n/10 Object of class \T1/fi4/bx/n/10 "PossibleMethod" \T1/ptm/m/n/1 0 the method to use in re-sponse to a [1052] [1053] [1054] [1055] [1056] Underfull \hbox (badness 1087) in paragraph at lines 5619--5624 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1057] [1058] [1059] Underfull \hbox (badness 2221) in paragraph at lines 5845--5850 []\T1/ptm/m/n/10 Two op-tional method names are in-ter-preted spe-cially, \T1/f i4/bx/n/10 initialize \T1/ptm/m/n/10 and [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069]pdfTeX war ning (ext4): destination with the same identifier (name{Rfn.S4}) has been alrea dy used, duplicate ignored \relax l.6701 \aliasA{S4}{S3Part}{S4} [1070] [1071] [1072]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.6977 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.6979 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.6980 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.6982 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.6983 \aliasA{Summary}{S4groupGeneric}{Summary} [1073] Underfull \hbox (badness 2050) in paragraph at lines 7044--7048 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1074] [1075] [1076] Underfull \hbox (badness 1286) in paragraph at lines 7227--7229 []\T1/ptm/m/n/10 for \T1/fi4/bx/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/fi4/bx/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-c ally [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] Underfull \vbox (badness 10000) has occurred while \output is active [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] Underfull \hbox (badness 2894) in paragraph at lines 9560--9564 []\T1/ptm/m/n/10 Chambers, John M. (2009) \T1/ptm/m/it/10 Class In-her-i-tance in R [][]$\T1/fi4/bx/n/10 http : / / stat . stanford . edu / ~jmc4 / [1107] Underfull \hbox (badness 1852) in paragraph at lines 9639--9643 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., [1108] [1109] [1110]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 15--17 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/fi4 /bx/n/10 "L'Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[][][]: see [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] Underfull \hbox (badness 3386) in paragraph at lines 1221--1224 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/fi4/bx/n/10 . Random.seed \T1/ptm/m/n/10 when the [1128] [1129] [1130]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/fi4/bx/n/10 \T1/ptm /m/n/10 and William N. Ven-ables [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143]) (./stats-pkg.tex [1144] Chapter 10. [1145] [1146] [1147] [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] Underfull \hbox (badness 1412) in paragraph at lines 832--834 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/fi4/bx/n/10 lm \T1/ptm/m/n/10 or \T1/fi4/bx/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1157] [1158] [1159] [1160] [1161] [1162] [1163] [1164] Underfull \hbox (badness 2503) in paragraph at lines 1320--1323 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/bx/n/10 "two.sided"\T1/ptm/m/n/10 , [1165] [1166] Underfull \hbox (badness 10000) in paragraph at lines 1499--1503 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("aov", "lm") \T1/ptm/m/n /10 or for mul-ti-ple re-sponses of class [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] Underfull \hbox (badness 3965) in paragraph at lines 2150--2152 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1177] [1178] [1179] [1180] [1181] Underfull \hbox (badness 3965) in paragraph at lines 2479--2481 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 2503) in paragraph at lines 3255--3258 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/bx/n/10 "two.sided"\T1/ptm/m/n/10 , [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] Underfull \hbox (badness 3989) in paragraph at lines 4477--4484 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] Underfull \hbox (badness 2932) in paragraph at lines 5092--5094 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/fi4/bx/n/10 x \T1/ptm/m/n/10 and \T1/fi4/bx/n/10 y \T1/ptm/m/n/10 i s given by [1221] [1222] [1223] Underfull \hbox (badness 1603) in paragraph at lines 5299--5304 []\T1/fi4/bx/n/10 var \T1/ptm/m/n/10 is just an-other in-ter-face to \T1/fi4/bx /n/10 cov\T1/ptm/m/n/10 , where \T1/fi4/bx/n/10 na.rm \T1/ptm/m/n/10 is used to de-ter-mine the de-fault for Underfull \hbox (badness 1472) in paragraph at lines 5299--5304 \T1/fi4/bx/n/10 use \T1/ptm/m/n/10 when that is un-spec-i-fied. If \T1/fi4/bx/n /10 na.rm \T1/ptm/m/n/10 is \T1/fi4/bx/n/10 TRUE \T1/ptm/m/n/10 then the com-pl ete ob-ser-va-tions (rows) Underfull \hbox (badness 3108) in paragraph at lines 5299--5304 \T1/ptm/m/n/10 are used (\T1/fi4/bx/n/10 use = "na.or.complete"\T1/ptm/m/n/10 ) to com-pute the vari-ance. Oth-er-wise, by de-fault Underfull \hbox (badness 1142) in paragraph at lines 5333--5345 \T1/ptm/m/n/10 For \T1/fi4/bx/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method i s un-usual but avail-able for the sake of com-plete-ness. [1224] [1225] Underfull \hbox (badness 2503) in paragraph at lines 5472--5476 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/bx/n/10 "two.sided"\T1/ptm/m/n/10 , [1226] Underfull \hbox (badness 1168) in paragraph at lines 5533--5538 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] Underfull \hbox (badness 8132) in paragraph at lines 5976--5981 \T1/ptm/m/n/10 then \T1/fi4/bx/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the s ame graph struc-ture as \T1/fi4/bx/n/10 x \T1/ptm/m/n/10 and for each node, [1235] [1236] [1237] Underfull \hbox (badness 7081) in paragraph at lines 6231--6234 []\T1/ptm/m/n/10 Objects of class \T1/fi4/bx/n/10 "hclust" \T1/ptm/m/n/10 can b e con-verted to class \T1/fi4/bx/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6235--6237 []\T1/fi4/bx/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gr am \T1/fi4/bx/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1238] [1239] [1240] [1241] [1242] Underfull \vbox (badness 10000) has occurred while \output is active [1243] [1244] [1245] [1246] [1247] [1248] [1249] Underfull \hbox (badness 10000) in paragraph at lines 7035--7038 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/fi4/bx/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1250] [1251] Underfull \hbox (badness 10000) in paragraph at lines 7172--7175 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/fi4/bx/n/10 h ttp : / / cran . r-[]project . org / web / views / [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] Underfull \hbox (badness 2626) in paragraph at lines 8625--8628 []\T1/ptm/m/n/10 Either \T1/fi4/bx/n/10 "convolution" \T1/ptm/m/n/10 or \T1/fi4 /bx/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1274] [1275] Underfull \hbox (badness 2503) in paragraph at lines 8725--8729 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/bx/n/10 "two.sided"\T1/ptm/m/n/10 , [1276] [1277] [1278] [1279] [1280] Overfull \hbox (11.88992pt too wide) in paragraph at lines 9059--9061 []\T1/ptm/m/n/10 the char-ac-ter string \T1/fi4/bx/n/10 "Fligner-Killeen test o f homogeneity of variances"\T1/ptm/m/n/10 . [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] Underfull \hbox (badness 1019) in paragraph at lines 9725--9728 []\T1/ptm/m/n/10 See also [][]$\T1/fi4/bx/n/10 http : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [][]$\T1/fi4/bx/ n/10 http : / / dlmf . [1290] [1291] [1292] [1293] Underfull \hbox (badness 4518) in paragraph at lines 9986--9991 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1294] [1295] [1296] [1297] [1298] Underfull \hbox (badness 2142) in paragraph at lines 10327--10330 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10346--10349 []\T1/ptm/m/n/10 When \T1/fi4/bx/n/10 trace \T1/ptm/m/n/10 is true, calls to [] []\T1/fi4/bx/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS i t-er-a-tion. Hence, [1299] Underfull \hbox (badness 1708) in paragraph at lines 10408--10411 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1300] [1301] [1302] [1303] [1304] Underfull \hbox (badness 1694) in paragraph at lines 10772--10775 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 10791--10800 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1305] [1306] [1307] [1308] [1309] [1310] [1311]pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.hat}) has been already used, duplicate i gnored \relax l.11238 \aliasA{hat}{influence.measures}{hat} [1312] [1313] Underfull \hbox (badness 1484) in paragraph at lines 11362--11364 []\T1/ptm/m/n/10 The func-tion \T1/fi4/bx/n/10 hat() \T1/ptm/m/n/10 ex-ists mai nly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 4441) in paragraph at lines 11909--11911 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] Underfull \hbox (badness 4518) in paragraph at lines 12869--12874 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] Underfull \hbox (badness 4518) in paragraph at lines 13487--13492 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] Overfull \hbox (5.6622pt too wide) in paragraph at lines 14053--14055 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/fi4/bx/n/10 -plnorm(t, r, lower = FALSE, log = TRUE)\T1/ptm/m/n/10 . [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] Underfull \hbox (badness 2503) in paragraph at lines 14682--14686 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/bx/n/10 "two.sided"\T1/ptm/m/n/10 , [1364] [1365] Underfull \vbox (badness 10000) has occurred while \output is active [1366] [1367] [1368] [1369] [1370] [1371] Underfull \hbox (badness 3009) in paragraph at lines 15190--15196 []\T1/fi4/bx/n/10 model.offset \T1/ptm/m/n/10 and \T1/fi4/bx/n/10 model.respons e \T1/ptm/m/n/10 are equiv-a-lent to \T1/fi4/bx/n/10 model.extract(, "offset") \T1/ptm/m/n/10 and [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] Underfull \hbox (badness 2359) in paragraph at lines 16811--16813 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1396] Underfull \vbox (badness 10000) has occurred while \output is active [1397] Underfull \vbox (badness 10000) has occurred while \output is active [1398] [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] Underfull \hbox (badness 1377) in paragraph at lines 17713--17718 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 17718--17721 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 2343) in paragraph at lines 17731--17735 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 2080) in paragraph at lines 17731--17735 \T1/ptm/m/n/10 the value by a fac-tor of \T1/fi4/bx/n/10 reltol * (abs(val) + r eltol) \T1/ptm/m/n/10 at a step. De-faults to [1410] Underfull \hbox (badness 2662) in paragraph at lines 17739--17743 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/fi4/bx/n/10 "BFGS"\T1/p tm/m/n/10 , \T1/fi4/bx/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/fi4/bx/n/10 "SANN " \T1/ptm/m/n/10 meth-ods if [1411] [1412] Underfull \vbox (badness 10000) has occurred while \output is active [1413] [1414] [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 1337) in paragraph at lines 18355--18358 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] Underfull \hbox (badness 5563) in paragraph at lines 19082--19084 []\T1/ptm/m/n/10 logical. If \T1/fi4/bx/n/10 TRUE\T1/ptm/m/n/10 , add to al-rea dy ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19085--19088 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1432] [1433] [1434] [1435] [1436] Underfull \hbox (badness 1675) in paragraph at lines 19372--19375 []\T1/ptm/m/n/10 Setting \T1/fi4/bx/n/10 lower.tail = FALSE \T1/ptm/m/n/10 al-l ows to get much more pre-cise re-sults when the de-fault, [1437] Underfull \hbox (badness 2503) in paragraph at lines 19457--19460 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/bx/n/10 "two.sided"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 19484--19486 []\T1/ptm/m/n/10 the char-ac-ter string \T1/fi4/bx/n/10 "Exact Poisson test" \T 1/ptm/m/n/10 or [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] Underfull \hbox (badness 10000) in paragraph at lines 20454--20460 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/fi4/bx/n/10 predict.ar[] [][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [] []\T1/fi4/bx/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] Underfull \hbox (badness 2111) in paragraph at lines 21422--21427 []\T1/ptm/m/n/10 Utility func-tion to be used in higher-level [][]\T1/fi4/bx/n/ 10 print[][][] \T1/ptm/m/n/10 meth-ods, such as [][]\T1/fi4/bx/n/10 print.summa ry.lm[][][]\T1/ptm/m/n/10 , [1469] [1470] [1471] [1472] [1473] Underfull \hbox (badness 1337) in paragraph at lines 21761--21767 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] Underfull \hbox (badness 10000) in paragraph at lines 22554--22557 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 1675) in paragraph at lines 22554--22557 \T1/fi4/bx/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied fo r ef-fi-ciency if al-ready [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] Underfull \hbox (badness 10000) in paragraph at lines 23130--23133 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/fi4/bx/n/10 y = ru nmed(x, k) \T1/ptm/m/n/10 sim-ply has [1494] Underfull \hbox (badness 3690) in paragraph at lines 23181--23185 [][][]\T1/fi4/bx/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey' s end point rule and is called by de-fault from Underfull \hbox (badness 1062) in paragraph at lines 23181--23185 \T1/fi4/bx/n/10 runmed(*, endrule = "median")\T1/ptm/m/n/10 . [][]\T1/fi4/bx/n/ 10 smooth[][][] \T1/ptm/m/n/10 uses run-ning me-di-ans of 3 for its com-pound [1495] [1496] [1497] [1498] Underfull \hbox (badness 7667) in paragraph at lines 23447--23449 []\T1/ptm/m/n/10 a nu-meric vec-tor or an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-je ct which is co-ercible to one by [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] Underfull \vbox (badness 10000) has occurred while \output is active [1525] Underfull \hbox (badness 3514) in paragraph at lines 25197--25202 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1526] Underfull \hbox (badness 3514) in paragraph at lines 25259--25264 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1527] Underfull \hbox (badness 3514) in paragraph at lines 25316--25321 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1528] Underfull \hbox (badness 3514) in paragraph at lines 25377--25383 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1529] [1530] [1531] Underfull \hbox (badness 3514) in paragraph at lines 25572--25577 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1532] Underfull \hbox (badness 3514) in paragraph at lines 25628--25633 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1533] Underfull \hbox (badness 3514) in paragraph at lines 25685--25690 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1534] Underfull \hbox (badness 3514) in paragraph at lines 25740--25745 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1535] Underfull \hbox (badness 6691) in paragraph at lines 25809--25814 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 x\T1/ ptm/m/n/10 . It is the value of the ex-pres-sion [1536] [1537] [1538] [1539] [1540] [1541] [1542] Underfull \hbox (badness 10000) in paragraph at lines 26279--26282 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 26279--26282 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/fi4/bx/n/10 NULL\T1/ptm/m /n/10 , the de-fault, [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] Underfull \hbox (badness 5431) in paragraph at lines 26885--26887 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/f i4/bx/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1553] [1554] [1555] Underfull \hbox (badness 5431) in paragraph at lines 27095--27098 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/f i4/bx/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1556] [1557] [1558] [1559] [1560] Underfull \hbox (badness 1337) in paragraph at lines 27406--27410 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1561] [1562] Underfull \hbox (badness 10000) in paragraph at lines 27523--27526 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/fi4/bx/n/10 rt()\T1/ptm/m/n/10 , only for [1563] [1564] [1565] Underfull \hbox (badness 1616) in paragraph at lines 27706--27709 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] Underfull \hbox (badness 1337) in paragraph at lines 29085--29089 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] Underfull \hbox (badness 1337) in paragraph at lines 29569--29573 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1595] Underfull \hbox (badness 5161) in paragraph at lines 29662--29664 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1596] [1597] [1598] [1599] [1600] Underfull \hbox (badness 10000) in paragraph at lines 30026--30031 []\T1/ptm/m/n/10 There is a \T1/fi4/bx/n/10 summary \T1/ptm/m/n/10 method for c on-tin-gency ta-ble ob-jects cre-ated by \T1/fi4/bx/n/10 table \T1/ptm/m/n/10 o r Underfull \hbox (badness 3209) in paragraph at lines 30026--30031 \T1/fi4/bx/n/10 xtabs(*, sparse = FALSE)\T1/ptm/m/n/10 , which gives ba-sic in- for-ma-tion and per-forms a chi-squared [1601] [1602] [1603]) (./stats4-pkg.tex [1604] Chapter 11. [1605] [1606] [1607] [1608] [1609] [1610]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1611] [1612] [1613]) (./tcltk-pkg.tex [1614] Chapter 12. [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \vbox (badness 10000) has occurred while \output is active [1622] Underfull \hbox (badness 1546) in paragraph at lines 649--656 []\T1/fi4/bx/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-in g any Tk or Tcl com-mand by sim-ply run-ning [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] Underfull \hbox (badness 3375) in paragraph at lines 1391--1394 [][][]\T1/fi4/bx/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the OS X GUI), [][]\T1/fi4/bx/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1634]) (./tools-pkg.tex Chapter 13. [1635] LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined (Font) using `T1/fi4/m/n' instead on input line 72. [1636] Underfull \hbox (badness 1308) in paragraph at lines 173--186 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 types Underfull \hbox (badness 4967) in paragraph at lines 173--186 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/fi4/bx/n/10 bib entry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 173--186 \T1/fi4/bx/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 formatInProc eedings\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 formatManual\T1/ptm/m/n/10 , \T1/fi4/bx /n/10 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 173--186 \T1/fi4/bx/n/10 formatMisc\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 formatPhdthesis\T1/p tm/m/n/10 , \T1/fi4/bx/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 f ormatTechreport \T1/ptm/m/n/10 and [1637] [1638] [1639] Underfull \hbox (badness 2080) in paragraph at lines 333--338 \T1/ptm/m/n/10 ac-ters. It is sorted by Uni-code point and within a point al-ph a-bet-i-cally on the glyph Underfull \hbox (badness 2644) in paragraph at lines 333--338 \T1/ptm/m/n/10 (there can be more than one name for a Uni-code point). The data are in the file [1640] [1641] [1642] [1643] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1644] [1645] [1646] [1647] Underfull \hbox (badness 1635) in paragraph at lines 851--853 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1648] Underfull \hbox (badness 4441) in paragraph at lines 925--933 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- Underfull \hbox (badness 1014) in paragraph at lines 945--947 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies [1649] Underfull \hbox (badness 10000) in paragraph at lines 968--971 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 968--971 \T1/fi4/bx/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/ fi4/bx/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1650] [1651] Underfull \hbox (badness 10000) in paragraph at lines 1096--1098 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1652] [1653] Underfull \hbox (badness 7981) in paragraph at lines 1263--1267 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1263--1267 \T1/fi4/bx/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1 /ptm/m/n/10 . Underfull \hbox (badness 1082) in paragraph at lines 1269--1271 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/fi4/bx/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1654] [1655] [1656] [1657] Underfull \hbox (badness 5726) in paragraph at lines 1532--1537 []\T1/ptm/m/n/10 If \T1/fi4/bx/n/10 reduce \T1/ptm/m/n/10 is \T1/fi4/bx/n/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/fi4/bx/n/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 1532--1537 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1658] [1659] [1660] [1661] [1662] Underfull \hbox (badness 7981) in paragraph at lines 1848--1854 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1848--1854 \T1/fi4/bx/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1 /ptm/m/n/10 . [1663] [1664] [1665] [1666] LaTeX Font Warning: Font shape `T1/fi4/m/sl' undefined (Font) using `T1/fi4/m/n' instead on input line 2102. [1667] [1668] [1669] Underfull \hbox (badness 1424) in paragraph at lines 2338--2340 []\T1/fi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1670] [1671] [1672] [1673] [1674] [1675] [1676] Underfull \hbox (badness 1675) in paragraph at lines 2852--2854 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing how the news en-tries shoul d be \T1/ptm/m/it/10 chopped\T1/ptm/m/n/10 ; [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] Underfull \hbox (badness 1838) in paragraph at lines 3427--3433 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/fi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/fi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 3427--3433 \T1/ptm/m/n/10 `\T1/fi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1686] Underfull \hbox (badness 5726) in paragraph at lines 3507--3512 []\T1/ptm/m/n/10 If \T1/fi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/fi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/fi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 3507--3512 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1687] [1688] Underfull \hbox (badness 1688) in paragraph at lines 3645--3657 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/fi4/m/sl/10 PACKAGES\T1/ptm/m/n/10 ' and [1689] [1690] [1691] [1692]) (./utils-pkg.tex Chapter 14. Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/fi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1693] [1694] [1695] Underfull \hbox (badness 1454) in paragraph at lines 198--201 []\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive , \T1/fi4/m/sl/10 TRUE \T1/ptm/m/n/10 by de- Underfull \hbox (badness 1540) in paragraph at lines 214--217 []\T1/fi4/m/sl/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for the same task as \T1/fi4/m/sl/10 apropos\T1/ptm/m/n/10 . How-ever, by de-fault [1696] [1697] [1698] [1699] [1700] Underfull \hbox (badness 10000) in paragraph at lines 539--545 []\T1/ptm/m/n/10 Functions \T1/fi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/fi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 539--545 \T1/fi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/fi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1701] [1702] Underfull \hbox (badness 5847) in paragraph at lines 650--656 []\T1/ptm/m/n/10 Argument \T1/fi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 650--656 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/fi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as Underfull \hbox (badness 3861) in paragraph at lines 715--720 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/fi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/fi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] Underfull \hbox (badness 1371) in paragraph at lines 1288--1290 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/fi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/fi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1712] [1713] [1714] [1715] Underfull \hbox (badness 2057) in paragraph at lines 1560--1562 []\T1/ptm/m/n/10 None for \T1/fi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1716] [1717] Underfull \hbox (badness 5189) in paragraph at lines 1745--1747 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1718] [1719] [1720] Underfull \hbox (badness 1661) in paragraph at lines 1960--1967 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/fi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- [1721] Underfull \hbox (badness 1990) in paragraph at lines 1972--1975 []\T1/ptm/m/n/10 a [][]\T1/fi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/fi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/fi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1722] [1723] [1724] [1725] [1726] Overfull \hbox (6.10922pt too wide) in paragraph at lines 2363--2366 []\T1/ptm/m/n/10 files end-ing `\T1/fi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/fi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/fi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";")\T1/ptm/m/n/10 , [1727] [1728] [1729] [1730] [1731] [1732] [1733] [1734] Underfull \hbox (badness 1430) in paragraph at lines 2936--2942 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/fi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 2837) in paragraph at lines 2936--2942 \T1/fi4/m/sl/10 internet.info \T1/ptm/m/n/10 op-tion. The de-tails de-pend on t he plat-form and scheme, but set-ting [1735] Underfull \hbox (badness 1231) in paragraph at lines 2980--2986 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1736] [1737] [1738] [1739] [1740] [1741] Underfull \hbox (badness 1210) in paragraph at lines 3360--3367 []\T1/ptm/m/n/10 logical or ex-pres-sion; if not \T1/fi4/m/sl/10 FALSE\T1/ptm/m /n/10 , the ran-dom num-ber gen-er-a-tor state [1742] [1743] [1744] [1745] [1746]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.3743 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.3743 ...mat Unordered and Ordered Lists}{format} [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] Underfull \hbox (badness 1371) in paragraph at lines 4648--4650 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/fi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/fi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1761] [1762] Underfull \hbox (badness 1502) in paragraph at lines 4737--4742 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 4737--4742 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1763] [1764] Underfull \hbox (badness 10000) in paragraph at lines 4901--4910 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1765] [1766] Underfull \hbox (badness 3118) in paragraph at lines 5017--5019 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [1767] Underfull \hbox (badness 2057) in paragraph at lines 5099--5105 \T1/ptm/m/n/10 can be source archives or bi-nary pack-age archive files (as cre -ated by Underfull \hbox (badness 1348) in paragraph at lines 5145--5150 []\T1/ptm/m/n/10 logical in-di-cat-ing to also in-stall unin-stalled pack-ages which these pack- Underfull \hbox (badness 3884) in paragraph at lines 5145--5150 \T1/ptm/m/n/10 ages de-pend on/link to/import/suggest (and so on re-cur-sively) . Not Underfull \hbox (badness 3657) in paragraph at lines 5145--5150 \T1/ptm/m/n/10 used if \T1/fi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be a char-ac-ter vec-tor, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 5158--5165 []\T1/fi4/m/sl/10 TRUE \T1/ptm/m/n/10 means (as from \T1/phv/m/n/10 R \T1/ptm/m /n/10 2.15.0) to use Underfull \hbox (badness 10000) in paragraph at lines 5158--5165 \T1/fi4/m/sl/10 c("Depends", "Imports", "LinkingTo", "Suggests") \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 pkgs \T1/ptm/m/n/10 and Underfull \hbox (badness 2103) in paragraph at lines 5158--5165 \T1/fi4/m/sl/10 c("Depends", "Imports", "LinkingTo") \T1/ptm/m/n/10 for added d e-pen-den-cies: this [1768] Underfull \hbox (badness 10000) in paragraph at lines 5200--5203 []\T1/ptm/m/n/10 (not used on Win-dows) anal-o-gous to \T1/fi4/m/sl/10 configur e.args \T1/ptm/m/n/10 for flag Underfull \hbox (badness 10000) in paragraph at lines 5226--5229 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 5226--5229 \T1/ptm/m/n/10 passed to \T1/fi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou rce pack-age in-stall. E.g., [1769] [1770] Underfull \hbox (badness 10000) in paragraph at lines 5356--5361 [][][]\T1/fi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] [1787] Underfull \hbox (badness 10000) in paragraph at lines 6480--6482 []\T1/fi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 6485--6490 []\T1/ptm/m/n/10 If a `\T1/fi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [1788] [1789] [1790] Underfull \hbox (badness 10000) in paragraph at lines 6642--6645 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 6642--6645 [][]\T1/fi4/m/sl/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/fi4/m/sl/1 0 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els [1791] [1792] [1793] [1794] [1795] Underfull \hbox (badness 1789) in paragraph at lines 7023--7025 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] Underfull \hbox (badness 1097) in paragraph at lines 7822--7825 []\T1/ptm/m/n/10 The name \T1/fi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [1807] [1808] Underfull \hbox (badness 3000) in paragraph at lines 7950--7955 [][][]\T1/fi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/fi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [1809] [1810] [1811] [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 2134) in paragraph at lines 8512--8517 [][][]\T1/fi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/fi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [1817] [1818] [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] Underfull \hbox (badness 10000) in paragraph at lines 9455--9457 [][][]$\T1/fi4/m/sl/10 http : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/fi4/m/sl/10 http : / / www . gnu . org / software / emacs / [1831] [1832] [1833] Underfull \hbox (badness 10000) in paragraph at lines 9633--9637 []\T1/ptm/m/n/10 The de-fault for \T1/fi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 9664--9670 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [1834] Underfull \hbox (badness 2096) in paragraph at lines 9778--9781 []\T1/ptm/m/n/10 logical (\T1/fi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 9782--9785 []\T1/ptm/m/n/10 logical (\T1/fi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [1835] Underfull \hbox (badness 1009) in paragraph at lines 9849--9860 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [1836] [1837] [1838] [1839] [1840] Underfull \hbox (badness 2635) in paragraph at lines 10150--10153 []\T1/ptm/m/n/10 Repository `\T1/fi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [1841] [1842] [1843] [1844] [1845] Underfull \hbox (badness 5970) in paragraph at lines 10514--10517 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 3449) in paragraph at lines 10525--10534 []\T1/ptm/m/n/10 string in-di-cat-ing if the \T1/fi4/m/sl/10 width \T1/ptm/m/n/ 10 ar-gu-ment's spec-i-fi-ca-tion should be fol- Underfull \hbox (badness 7379) in paragraph at lines 10525--10534 \T1/ptm/m/n/10 lowed strictly, one of the val-ues \T1/fi4/m/sl/10 c("no", "cut" , "wrap")\T1/ptm/m/n/10 . De- Underfull \hbox (badness 1824) in paragraph at lines 10525--10534 \T1/ptm/m/n/10 faults to the \T1/fi4/m/sl/10 strict.width \T1/ptm/m/n/10 com-po -nent of op-tion \T1/fi4/m/sl/10 "str" \T1/ptm/m/n/10 (see [][]\T1/fi4/m/sl/10 options[][][]\T1/ptm/m/n/10 ) Underfull \hbox (badness 3769) in paragraph at lines 10525--10534 \T1/ptm/m/n/10 which de-faults to \T1/fi4/m/sl/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons; \T1/fi4/m/sl/10 "wrap" \T1/ptm/m/n/10 uses [1846] [1847] [1848] Underfull \hbox (badness 10000) in paragraph at lines 10693--10695 []\T1/ptm/m/n/10 Options other than \T1/fi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [1849] [1850] Underfull \hbox (badness 2213) in paragraph at lines 10847--10854 []\T1/ptm/m/n/10 If \T1/fi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, Underfull \hbox (badness 1688) in paragraph at lines 10847--10854 \T1/ptm/m/n/10 and se-lected if their \T1/fi4/m/sl/10 extension \T1/ptm/m/n/10 com-po-nent matches (as a reg-exp) the file name. Ob- [1851] [1852] [1853] Underfull \hbox (badness 10000) in paragraph at lines 11088--11091 [][][]$\T1/fi4/m/sl/10 http : / / en . wikipedia . org / wiki / Tar _ (file _ f ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/fi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 11088--11091 \T1/fi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [1854] [1855] [1856] [1857] [1858] [1859] [1860] [1861] Underfull \hbox (badness 10000) in paragraph at lines 11593--11595 []\T1/ptm/m/n/10 Arguments such as \T1/fi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/fi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 1052) in paragraph at lines 11596--11598 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 11626--11631 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined Underfull \hbox (badness 10000) in paragraph at lines 11626--11631 \T1/ptm/m/n/10 see [][]\T1/fi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/fi4/m/sl/10 available = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 6961) in paragraph at lines 11626--11631 \T1/fi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by de- [1862] Underfull \hbox (badness 10000) in paragraph at lines 11655--11658 [][][]\T1/fi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [1863] Underfull \hbox (badness 10000) in paragraph at lines 11733--11738 []\T1/ptm/m/n/10 Characters in a URL other than the En-glish al-phanu-meric cha r-ac-ters and [1864] [1865] [1866] [1867] Underfull \hbox (badness 1454) in paragraph at lines 11960--11964 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [1868] Underfull \hbox (badness 10000) in paragraph at lines 12030--12032 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion e.g. [1869] [1870] [1871]) [1872] [1873] [1874] (./KernSmooth-pkg.tex Chapter 15. [1875] [1876] [1877] [1878] [1879] [1880] [1881] [1882] [1883] [1884]) (./MASS-pkg.tex Chapter 16. [1885] [1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901] [1902] [1903] [1904] [1905] [1906] Underfull \hbox (badness 7256) in paragraph at lines 1601--1603 []\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo r [1907] [1908] [1909] [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917] [1918] [1919] [1920] [1921] Underfull \hbox (badness 7944) in paragraph at lines 2691--2694 []\T1/ptm/m/n/10 further ar-gu-ments for \T1/fi4/m/sl/10 plot \T1/ptm/m/n/10 an d graph-i-cal pa-ram-e-ters. Note that [1922] [1923] [1924] Underfull \hbox (badness 2384) in paragraph at lines 2861--2866 []\T1/ptm/m/n/10 Distributions \T1/fi4/m/sl/10 "beta"\T1/ptm/m/n/10 , \T1/fi4/m /sl/10 "cauchy"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "chi-squared"\T1/ptm/m/n/10 , \ T1/fi4/m/sl/10 "exponential"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "f"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2861--2866 \T1/fi4/m/sl/10 "gamma"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "geometric"\T1/ptm/m/n/ 10 , \T1/fi4/m/sl/10 "log-normal"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "lognormal"\T 1/ptm/m/n/10 , \T1/fi4/m/sl/10 "logistic"\T1/ptm/m/n/10 , Underfull \hbox (badness 2293) in paragraph at lines 2861--2866 \T1/fi4/m/sl/10 "negative binomial"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "normal"\T1 /ptm/m/n/10 , \T1/fi4/m/sl/10 "Poisson"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "t" \T1 /ptm/m/n/10 and \T1/fi4/m/sl/10 "weibull" \T1/ptm/m/n/10 are [1925] [1926] Underfull \hbox (badness 4686) in paragraph at lines 3029--3031 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds Underfull \hbox (badness 2591) in paragraph at lines 3043--3047 []\T1/ptm/m/n/10 where \T1/fi4/m/sl/10 p1\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 p2\T1 /ptm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/fi4/m /sl/10 cycles \T1/ptm/m/n/10 terms or when a [1927] [1928] [1929] Underfull \hbox (badness 10000) in paragraph at lines 3231--3233 []\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/fi4/m/sl/10 Gamma \T1/ptm/m/n/ 10 fam-ily or \T1/fi4/m/sl/10 quasi \T1/ptm/m/n/10 fam-ily with [1930] [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] Underfull \hbox (badness 10000) in paragraph at lines 4800--4803 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm Underfull \hbox (badness 1173) in paragraph at lines 4800--4803 \T1/fi4/m/sl/10 response ~ predictors\T1/ptm/m/n/10 . See the doc-u-men-ta-tion of \T1/fi4/m/sl/10 formula \T1/ptm/m/n/10 for other [1952] Underfull \hbox (badness 10000) in paragraph at lines 4878--4881 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm Underfull \hbox (badness 1173) in paragraph at lines 4878--4881 \T1/fi4/m/sl/10 response ~ predictors\T1/ptm/m/n/10 . See the doc-u-men-ta-tion of \T1/fi4/m/sl/10 formula \T1/ptm/m/n/10 for other [1953] [1954] [1955] [1956] [1957] [1958] Underfull \hbox (badness 1975) in paragraph at lines 5355--5357 []\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in the case of [1959] [1960] [1961] [1962] [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970] [1971] [1972] [1973] [1974] Underfull \vbox (badness 10000) has occurred while \output is active [1975] [1976] [1977] [1978] [1979] [1980] [1981] [1982] Underfull \hbox (badness 10000) in paragraph at lines 7103--7110 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm Underfull \hbox (badness 1540) in paragraph at lines 7103--7110 \T1/fi4/m/sl/10 response ~ predictors\T1/ptm/m/n/10 . The re-sponse should be a fac-tor (prefer-ably [1983] [1984] [1985] [1986] Underfull \hbox (badness 6775) in paragraph at lines 7341--7344 \T1/ptm/m/n/10 only the first \T1/fi4/m/sl/10 dimen \T1/ptm/m/n/10 dis-crim-i-n ant com-po-nents are used (ex-cept for [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] Underfull \hbox (badness 4686) in paragraph at lines 7974--7976 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [1995] Underfull \hbox (badness 2591) in paragraph at lines 7990--7994 []\T1/ptm/m/n/10 where \T1/fi4/m/sl/10 p1\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 p2\T1 /ptm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/fi4/m /sl/10 cycles \T1/ptm/m/n/10 terms or when a [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014] Underfull \hbox (badness 1259) in paragraph at lines 9376--9378 []\T1/ptm/m/n/10 if \T1/fi4/m/sl/10 TRUE \T1/ptm/m/n/10 re-turn ob-served and e x-pected fre-quen-cies in the re-sult. Us-ing [2015] [2016] [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032]) (./Matrix-pkg.tex Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 42--45 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 42--45 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2033] Underfull \hbox (badness 1769) in paragraph at lines 96--99 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2034] [2035] [2036] [2037] Underfull \hbox (badness 5119) in paragraph at lines 502--506 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class [2038] [2039] Underfull \hbox (badness 2418) in paragraph at lines 589--592 []\T1/ptm/m/n/10 The value of \T1/fi4/m/sl/10 bdiag() \T1/ptm/m/n/10 in-heris f rom class [][]\T1/fi4/m/sl/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , whereas \T1/f i4/m/sl/10 .bdiag() \T1/ptm/m/n/10 re-turns a [2040] [2041] Underfull \hbox (badness 10000) in paragraph at lines 731--734 []\T1/ptm/m/n/10 In some ver-sions of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , [][]\T1/ fi4/m/sl/10 eigen[][][](CAex) \T1/ptm/m/n/10 fell into an in-fi-nite loop (wher eas [2042] [2043] [2044] Underfull \hbox (badness 10000) in paragraph at lines 997--999 []\T1/fi4/m/sl/10 signature(a = "CHMfactor", b = "numeric") \T1/ptm/m/n/10 call the above [2045]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho l}) has been already used, duplicate ignored \relax l.1072 ...composition - 'Matrix' S4 Generic}{chol} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic ate ignored \relax l.1072 ...composition - 'Matrix' S4 Generic}{chol} [2046pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha s been already used, duplicate ignored \endgroup \set@typeset@protect l.1140 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.ch ol,lsCMatrix.Rdash.method}) has been already used, duplicate ignored \endgroup \set@typeset@protect l.1140 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.ch ol,nsCMatrix.Rdash.method}) has been already used, duplicate ignored \endgroup \set@typeset@protect l.1140 ] [2047] Underfull \hbox (badness 2277) in paragraph at lines 1286--1289 []\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer -ent types of ma-tri-ces. Use [2048] Underfull \hbox (badness 5741) in paragraph at lines 1322--1326 []\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/fi4/m/sl/10 CHMfactor[][][] \T1/p tm/m/n/10 and [][]\T1/fi4/m/sl/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion [][]\T1/fi4/m/sl/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra [2049] Underfull \hbox (badness 10000) in paragraph at lines 1416--1423 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/fi4/m/sl/10 n ew("Cholesky", ...) \T1/ptm/m/n/10 or [2050] Underfull \hbox (badness 1097) in paragraph at lines 1445--1448 []\T1/ptm/m/n/10 Class \T1/fi4/m/sl/10 "MatrixFactorization" \T1/ptm/m/n/10 and \T1/fi4/m/sl/10 "dtrMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/fi4/m/sl/10 " dgeMatrix"\T1/ptm/m/n/10 , by class Underfull \hbox (badness 1783) in paragraph at lines 1451--1455 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend [2051]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col Sums}) has been already used, duplicate ignored \relax l.1508 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup licate ignored \relax l.1508 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl icate ignored \relax l.1509 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i gnored \relax l.1530 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig nored \relax l.1541 \aliasA{rowSums}{colSums}{rowSums} [2052] [2053] [2054] [2055] Overfull \hbox (19.92062pt too wide) in paragraph at lines 1843--1844 []\T1/fi4/m/sl/10 signature(x = "CsparseMatrix", i = "index", j = "missing", va lue = "replValue")\T1/ptm/m/n/10 : Overfull \hbox (9.92062pt too wide) in paragraph at lines 1844--1845 []\T1/fi4/m/sl/10 signature(x = "CsparseMatrix", i = "index", j = "index", valu e = "replValue")\T1/ptm/m/n/10 : Overfull \hbox (19.92062pt too wide) in paragraph at lines 1845--1846 []\T1/fi4/m/sl/10 signature(x = "CsparseMatrix", i = "missing", j = "index", va lue = "replValue")\T1/ptm/m/n/10 : [2056] Underfull \hbox (badness 4543) in paragraph at lines 1963--1965 []\T1/ptm/m/n/10 Use [][]\T1/fi4/m/sl/10 showMethods[][][](class = "ddenseMatri x", where = "package:Matrix") \T1/ptm/m/n/10 for an [2057] [2058] Underfull \hbox (badness 10000) in paragraph at lines 2085--2087 []\T1/ptm/m/n/10 Use [][]\T1/fi4/m/sl/10 showMethods[][][](class = "denseMatrix ", where = "package:Matrix") \T1/ptm/m/n/10 for an [2059] Underfull \hbox (badness 10000) in paragraph at lines 2179--2181 []\T1/fi4/m/sl/10 signature(x = "dgCMatrix", y = "missing") \T1/ptm/m/n/10 re-t urns \T1/fi4/m/sl/10 t(x) %*% x \T1/ptm/m/n/10 as an [2060] [2061] [2062] Underfull \hbox (badness 10000) in paragraph at lines 2474--2476 []\T1/fi4/m/sl/10 signature(x = "dgTMatrix", y = "missing") \T1/ptm/m/n/10 re-t urns \T1/fi4/m/sl/10 t(x) %*% x \T1/ptm/m/n/10 as an [2063] Underfull \hbox (badness 6842) in paragraph at lines 2563--2566 []\T1/fi4/m/sl/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T 1/fi4/m/sl/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/fi4/m/sl/10 ldiMatrix[] [][] \T1/ptm/m/n/10 (with ``su-per-class'' [2064] [2065] Underfull \hbox (badness 10000) in paragraph at lines 2882--2884 []\T1/fi4/m/sl/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equi v-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2066] [2067] [2068] Underfull \hbox (badness 10000) in paragraph at lines 3142--3144 [][][]\T1/fi4/m/sl/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pr efer-able to (and more ef-fi-cient than) [2069] [2070] [2071] Underfull \hbox (badness 10000) in paragraph at lines 3432--3435 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/fi4/m/sl/10 n ew("dsCMatrix", ...) \T1/ptm/m/n/10 or [2072] [2073] [2074] [2075] [2076] Underfull \hbox (badness 2318) in paragraph at lines 3882--3886 []\T1/ptm/m/n/10 Class \T1/fi4/m/sl/10 "dgCMatrix"\T1/ptm/m/n/10 , di-rectly. C lass \T1/fi4/m/sl/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/fi 4/m/sl/10 "dMatrix"\T1/ptm/m/n/10 , [2077] [2078] [2079] [2080] Underfull \hbox (badness 10000) in paragraph at lines 4194--4199 []\T1/fi4/m/sl/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and o ther sig-na-tures (use Underfull \hbox (badness 4254) in paragraph at lines 4194--4199 \T1/fi4/m/sl/10 showMethods("%*%", class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mul-ti-pli-ca-tion. Mul-ti-pli-ca-tion [2081] [2082] Underfull \hbox (badness 10000) in paragraph at lines 4313--4318 []\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite Tay-lor se-ries Underfull \hbox (badness 1067) in paragraph at lines 4313--4318 \T1/fi4/m/sl/10 expm(A) = I + A + A^2/2! + A^3/3! + ... \T1/ptm/m/n/10 (al-thou gh this is def-i-nitely not the way to [2083] [2084] Overfull \hbox (5.28088pt too wide) in paragraph at lines 4447--4447 [] \T1/fi4/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/ Boeing/msc00726.tar.gz"))))[] Overfull \hbox (50.28088pt too wide) in paragraph at lines 4450--4450 [] \T1/fi4/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] [2085] [2086] [2087] Underfull \hbox (badness 1931) in paragraph at lines 4675--4677 []\T1/ptm/m/n/10 a string spec-i-fy-ing how the \T1/fi4/m/sl/10 zero.print \T1/ ptm/m/n/10 codes should be aligned, see [2088] [2089] [2090] Underfull \hbox (badness 5862) in paragraph at lines 4881--4884 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ]\T1/fi4/m/sl/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use [2091] Underfull \hbox (badness 2846) in paragraph at lines 4973--4975 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/fi4/m/sl/10 p \T1/ptm/m/n/10 con- tains val-ues \T1/fi4/m/sl/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault, [2092] [2093] [2094] [2095] [2096] Underfull \hbox (badness 10000) in paragraph at lines 5339--5342 []\T1/fi4/m/sl/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2097] Underfull \hbox (badness 2478) in paragraph at lines 5451--5456 []\T1/ptm/m/n/10 Class \T1/fi4/m/sl/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly . Class \T1/fi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/fi4/m/sl/10 "lde nseMatrix"\T1/ptm/m/n/10 . Class [2098] Underfull \hbox (badness 10000) in paragraph at lines 5459--5462 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); use, e.g., [2099] Underfull \hbox (badness 10000) in paragraph at lines 5644--5647 []\T1/fi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2100] Underfull \hbox (badness 10000) in paragraph at lines 5742--5745 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2101] Underfull \hbox (badness 10000) in paragraph at lines 5817--5820 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2102] Underfull \hbox (badness 2050) in paragraph at lines 5887--5890 []\T1/fi4/m/sl/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth -ods for dif-fer-ent types of ma-tri-ces. Use [2103] [2104] [2105] Underfull \hbox (badness 6268) in paragraph at lines 6082--6085 []\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math- e-mat-i-cally''), Underfull \hbox (badness 6268) in paragraph at lines 6106--6110 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/fi4/m/sl/10 matrix[][][]\T1/ptm/m/n/1 0 . How-ever, [2106]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6212 \aliasA{det}{Matrix-class}{det} [2107] Underfull \hbox (badness 3547) in paragraph at lines 6318--6321 []\T1/fi4/m/sl/10 signature(object = "Matrix")\T1/ptm/m/n/10 : draws an [][]\T1 /fi4/m/sl/10 image[][][] \T1/ptm/m/n/10 of the ma-trix en-tries, us-ing Underfull \hbox (badness 10000) in paragraph at lines 6323--6326 [2108] Underfull \hbox (badness 1430) in paragraph at lines 6447--6452 []\T1/ptm/m/n/10 classes in-her-it-ing from \T1/fi4/m/sl/10 "MatrixFactorizatio n"\T1/ptm/m/n/10 , such as [][]\T1/fi4/m/sl/10 LU[][][]\T1/ptm/m/n/10 , [][]\T1 /fi4/m/sl/10 Cholesky[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 CHMfactor[][][] \T1/ptm/m/n/10 , and [2109] Underfull \hbox (badness 10000) in paragraph at lines 6516--6519 []\T1/fi4/m/sl/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2110] Underfull \hbox (badness 10000) in paragraph at lines 6568--6570 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/fi4/m/sl/10 X <- (X + t(X))/2 \T1 /ptm/m/n/10 should be done, af-ter [2111] [2112] [2113] Underfull \hbox (badness 2478) in paragraph at lines 6747--6752 []\T1/ptm/m/n/10 Class \T1/fi4/m/sl/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly . Class \T1/fi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/fi4/m/sl/10 "nde nseMatrix"\T1/ptm/m/n/10 . Class Underfull \hbox (badness 10000) in paragraph at lines 6755--6758 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); use, e.g., [2114] [2115] Underfull \hbox (badness 5924) in paragraph at lines 6941--6943 []\T1/ptm/m/n/10 fast sim-ple meth-ods pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm}) ha s been already used, duplicate ignored \relax l.6979 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.6979 \HeaderA{norm}{Matrix Norms}{norm} [2116] [2117] Underfull \hbox (badness 10000) in paragraph at lines 7234--7237 []\T1/fi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2118] Underfull \hbox (badness 10000) in paragraph at lines 7324--7327 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2119] Underfull \hbox (badness 10000) in paragraph at lines 7400--7403 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2120] [2121] Underfull \hbox (badness 10000) in paragraph at lines 7519--7521 []\T1/fi4/m/sl/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and oth er sig-na-tures (use Underfull \hbox (badness 3118) in paragraph at lines 7524--7527 []\T1/fi4/m/sl/10 signature(from = "numeric", to = "pMatrix")\T1/ptm/m/n/10 : a user con-ve-nience, to al-low Underfull \hbox (badness 10000) in paragraph at lines 7527--7534 []\T1/fi4/m/sl/10 signature(from = "pMatrix", to = "matrix")\T1/ptm/m/n/10 : co -er-cion to a tra-di-tional Underfull \hbox (badness 3417) in paragraph at lines 7552--7554 []\T1/ptm/m/n/10 The in-verse of the typ-i-cal \T1/fi4/m/sl/10 "pMatrix" \T1/pt m/m/n/10 con-struc-tor, \T1/fi4/m/sl/10 P <- as(ip, "pMatrix") \T1/ptm/m/n/10 i s sim-ply [2122] [2123] [2124]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}) has been already used, duplicate ignored \relax l.7731 \aliasA{qr}{qr-methods}{qr} Underfull \hbox (badness 5119) in paragraph at lines 7773--7776 []\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma- trix with [2125] Underfull \hbox (badness 3333) in paragraph at lines 7829--7834 []\T1/ptm/m/n/10 nonnegative num-ber spec-i-fy-ing a tol-er-ance for ``prac-ti- cally zero'' with Underfull \hbox (badness 6125) in paragraph at lines 7829--7834 \T1/ptm/m/n/10 spe-cific mean-ing de-pend-ing on \T1/fi4/m/sl/10 method\T1/ptm/ m/n/10 ; by de-fault, \T1/fi4/m/sl/10 max(dim(x)) * [2126]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rco nd}) has been already used, duplicate ignored \relax l.7895 ... the Reciprocal Condition Number}{rcond} [2127] [2128] [2129] [2130] [2131] [2132] [2133] [2134] [2135] [2136] [2137] [2138] [2139] [2140] Underfull \hbox (badness 4441) in paragraph at lines 8935--8943 []\T1/fi4/m/sl/10 signature(from = "factor", to = "sparseMatrix")\T1/ptm/m/n/10 : Co-er-cion of a fac-tor to Underfull \hbox (badness 1112) in paragraph at lines 8935--8943 \T1/fi4/m/sl/10 "sparseMatrix" \T1/ptm/m/n/10 pro-duces the ma-trix of in-di-ca -tor \T1/ptm/b/n/10 rows \T1/ptm/m/n/10 stored as an ob-ject of class Underfull \hbox (badness 10000) in paragraph at lines 8961--8965 [][][]\T1/fi4/m/sl/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, such as [][]\T1/fi4/m/sl/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or [2141]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr. Q}) has been already used, duplicate ignored \relax l.8996 \aliasA{qr.Q}{sparseQR-class}{qr.Q} Underfull \hbox (badness 1303) in paragraph at lines 9022--9031 []\T1/ptm/m/n/10 The de-com-po-si-tion is of the form \T1/fi4/m/sl/10 A[p+1,] = = Q %*% R\T1/ptm/m/n/10 , if the \T1/fi4/m/sl/10 q \T1/ptm/m/n/10 slot is of le ngth 0 or [2142] [2143]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.toeplitz}) has been already used, duplicate ignored \relax l.9268 ...{toeplitz}{sparseVector-class}{toeplitz} [2144] Underfull \hbox (badness 10000) in paragraph at lines 9353--9356 []\T1/fi4/m/sl/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/fi4/ m/sl/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2145] Underfull \hbox (badness 10000) in paragraph at lines 9380--9382 [][][]\T1/fi4/m/sl/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-stru c-tion of sparse vec-tors (apart from [2146] Underfull \hbox (badness 4699) in paragraph at lines 9483--9489 [][][]\T1/fi4/m/sl/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more usual con-struc-tor of such ma-tri-ces; sim-i-larly, [2147] [2148] Underfull \hbox (badness 2057) in paragraph at lines 9637--9639 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2149]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcr ossprod}) has been already used, duplicate ignored \relax l.9663 ...{Cross-product of transpose}{tcrossprod} [2150] [2151] Underfull \hbox (badness 1831) in paragraph at lines 9877--9883 []\T1/ptm/m/n/10 For con-ve-nience, meth-ods for some op-er-a-tions such as \T1 /fi4/m/sl/10 %*% \T1/ptm/m/n/10 and \T1/fi4/m/sl/10 crossprod \T1/ptm/m/n/10 ar e de-fined [2152] [2153] [2154] [2155] Overfull \hbox (63.78088pt too wide) in paragraph at lines 10133--10133 []\T1/fi4/m/n/9 system.time(MJ <- sapply(rho, function(x) determinant(IM - x * USCounties, logarithm = TRUE)$modulus))[] [2156] Underfull \hbox (badness 6910) in paragraph at lines 10308--10310 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2157] [2158]) (./boot-pkg.tex Chapter 18. [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167] Overfull \hbox (3.25928pt too wide) in paragraph at lines 641--647 []\T1/ptm/m/n/10 logical, only al-lowed to be \T1/fi4/m/sl/10 TRUE \T1/ptm/m/n/ 10 for \T1/fi4/m/sl/10 sim = "ordinary", stype = "i", n = 0 [2168] Underfull \hbox (badness 1097) in paragraph at lines 786--794 []\T1/ptm/m/n/10 For most of the \T1/fi4/m/sl/10 boot \T1/ptm/m/n/10 meth-ods t he re-sam-pling is done in the mas-ter pro-cess, but not if Underfull \hbox (badness 6173) in paragraph at lines 795--805 []\T1/ptm/m/n/10 Where random-number gen-er-a-tion is done in the worker pro-ce sses, the de-fault be- Underfull \hbox (badness 1728) in paragraph at lines 795--805 \T1/ptm/m/n/10 haviour is that each worker chooses a sep-a-rate seed, non-repro ducibly. How-ever, with [2169] Underfull \hbox (badness 1881) in paragraph at lines 817--819 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. [2170] Underfull \vbox (badness 10000) has occurred while \output is active [2171] [2172] Underfull \hbox (badness 10000) in paragraph at lines 1057--1061 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1057--1061 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues Underfull \hbox (badness 5592) in paragraph at lines 1057--1061 \T1/fi4/m/sl/10 c("norm","basic", "stud", "perc", "bca") \T1/ptm/m/n/10 or sim- ply \T1/fi4/m/sl/10 "all" \T1/ptm/m/n/10 which [2173] Underfull \hbox (badness 2150) in paragraph at lines 1094--1100 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2174] [2175] [2176] [2177] Underfull \hbox (badness 1571) in paragraph at lines 1434--1436 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2178] [2179] [2180] [2181] [2182] [2183] Underfull \hbox (badness 1005) in paragraph at lines 1788--1795 []\T1/ptm/m/n/10 The sim-u-la-tion type. Pos-si-ble types are \T1/fi4/m/sl/10 " ordinary" \T1/ptm/m/n/10 (case re-sam-pling), [2184] [2185] Underfull \vbox (badness 10000) has occurred while \output is active [2186] [2187] Underfull \hbox (badness 7379) in paragraph at lines 2072--2074 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2188] [2189] [2190] Underfull \hbox (badness 1565) in paragraph at lines 2326--2331 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set [2191] Underfull \hbox (badness 1881) in paragraph at lines 2420--2422 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. [2192] [2193] Underfull \hbox (badness 2970) in paragraph at lines 2524--2528 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/fi4/m/s l/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/fi4/m/sl/10 n \T1/ptm/m/n/10 is t he sam-ple Underfull \hbox (badness 2310) in paragraph at lines 2524--2528 \T1/ptm/m/n/10 size, if \T1/fi4/m/sl/10 unbiased \T1/ptm/m/n/10 is \T1/fi4/m/sl /10 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/fi4/m/sl/10 1/n \T1/ptm/m/n /10 is used. This is mul-ti-plied by [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] Underfull \hbox (badness 10000) in paragraph at lines 4178--4180 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2218] [2219] [2220] Underfull \hbox (badness 2393) in paragraph at lines 4377--4380 []\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with fre-quency vec-tor \T1/fi4/m/sl/10 f \T1/ptm/m/n/10 is given by [2221] [2222] [2223] [2224] [2225] [2226] [2227] [2228] Underfull \hbox (badness 3000) in paragraph at lines 4947--4950 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2229] [2230] [2231] [2232] Underfull \hbox (badness 2293) in paragraph at lines 5226--5229 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5226--5229 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243] Underfull \hbox (badness 4954) in paragraph at lines 6007--6010 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/fi4/m/sl/10 "sa ddle.distn"\T1/ptm/m/n/10 . See the help file for [2244] [2245] [2246] [2247] [2248] [2249] [2250] [2251] [2252] Underfull \hbox (badness 1596) in paragraph at lines 6728--6732 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2253] [2254] [2255] [2256] [2257] [2258] [2259] [2260] [2261] [2262]) (./class-pkg.tex Chapter 19. [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] Underfull \hbox (badness 10000) in paragraph at lines 608--610 []\T1/ptm/m/n/10 the size of the code-book. De-faults to Underfull \hbox (badness 3977) in paragraph at lines 608--610 \T1/fi4/m/sl/10 min(round(0.4*ng*(ng-1 + p/2),0), n) \T1/ptm/m/n/10 where \T1/f i4/m/sl/10 ng \T1/ptm/m/n/10 is the num-ber of [2271] [2272] [2273] [2274] [2275] [2276] [2277] [2278]) (./cluster-pkg.tex Chapter 20. [2279] Underfull \hbox (badness 1231) in paragraph at lines 59--66 \T1/ptm/m/n/10 which uses (a con-stant ver-sion of) the Lance-Williams for-mula and the [2280] [2281] [2282] [2283] [2284] [2285] [2286] Underfull \hbox (badness 4144) in paragraph at lines 587--590 []\T1/ptm/m/n/10 Setting this to \T1/fi4/m/sl/10 FALSE \T1/ptm/m/n/10 saves mem -ory (and hence time), but dis-ables [2287] [2288] [2289] Underfull \hbox (badness 10000) in paragraph at lines 754--756 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2290] Underfull \hbox (badness 10000) in paragraph at lines 841--843 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is [2291] [2292] [2293] Underfull \hbox (badness 6110) in paragraph at lines 1019--1023 []\T1/ptm/m/n/10 when \T1/fi4/m/sl/10 x \T1/ptm/m/n/10 does not have a \T1/fi4/ m/sl/10 diss \T1/ptm/m/n/10 nor a \T1/fi4/m/sl/10 data \T1/ptm/m/n/10 com-po-ne nt, e.g., for [2294] [2295] [2296] [2297] [2298] Underfull \hbox (badness 2503) in paragraph at lines 1397--1400 []\T1/ptm/m/n/10 an ob-ject of class \T1/fi4/m/sl/10 "hclust" \T1/ptm/m/n/10 or \T1/fi4/m/sl/10 "twins"\T1/ptm/m/n/10 , i.e., typ-i-cally the re-sult of [2299] [2300] [2301] [2302] [2303] [2304] [2305] [2306] Underfull \hbox (badness 10000) in paragraph at lines 1964--1966 []\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as Underfull \hbox (badness 10000) in paragraph at lines 1988--1994 [][][]\T1/fi4/m/sl/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [][]\T1/fi4/m/sl/10 predict[][][] \T1/ptm/m/n/10 method for \T1/fi4/m/sl/10 ell ipsoid \T1/ptm/m/n/10 ob-jects. [2307] [2308] [2309] [2310] Underfull \hbox (badness 6675) in paragraph at lines 2220--2222 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see [2311] [2312] [2313] [2314] [2315] Underfull \hbox (badness 1014) in paragraph at lines 2584--2594 \T1/ptm/m/n/10 on the re-sult \T1/fi4/m/sl/10 pr <- pam(..)\T1/ptm/m/n/10 , or di-rectly its com-po-nent \T1/fi4/m/sl/10 pr$silinfo$avg.width\T1/ptm/m/n/10 , see also Underfull \hbox (badness 1616) in paragraph at lines 2624--2629 []\T1/ptm/m/n/10 The de-fault \T1/fi4/m/sl/10 FALSE \T1/ptm/m/n/10 (or in-te-ge r \T1/fi4/m/sl/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al -go-rithm, whereas [2316] Underfull \hbox (badness 2980) in paragraph at lines 2662--2666 [][][]\T1/fi4/m/sl/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-enc es; [][]\T1/fi4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 cl ara[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 daisy[][][]\T1/ptm/m/n/10 , [][]\ T1/fi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [2317] [2318] [2319] [2320] [2321] Underfull \hbox (badness 1142) in paragraph at lines 3000--3003 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/fi4/m/sl/10 par[][][]\T1/ ptm/m/n/10 ) may also be sup-plied and are passed to [2322] [2323] Underfull \hbox (badness 1142) in paragraph at lines 3119--3122 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/fi4/m/sl/10 par[][][]\T1/ ptm/m/n/10 ) may also be sup-plied and are passed to [2324] [2325] [2326] Underfull \hbox (badness 2582) in paragraph at lines 3342--3347 [][][]\T1/fi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/1 0 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 clusplot.default [][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/fi 4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 clara[][][]\T1/p tm/m/n/10 , [2327] Underfull \hbox (badness 10000) in paragraph at lines 3428--3433 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/fi 4/m/sl/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 4378) in paragraph at lines 3428--3433 \T1/ptm/m/n/10 which dis-patches to [][]\T1/fi4/m/sl/10 plot.hclust[][][](..)\T 1/ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider [2328] [2329] [2330] [2331] [2332] Underfull \hbox (badness 10000) in paragraph at lines 3718--3720 []\T1/ptm/m/n/10 a \T1/fi4/m/sl/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T 1/fi4/m/sl/10 summary.dissimilarity \T1/ptm/m/n/10 one for [2333] [2334] [2335] [2336] Underfull \hbox (badness 4108) in paragraph at lines 3942--3947 []\T1/ptm/m/n/10 arguments passed [][]\T1/fi4/m/sl/10 barplot[][][]()\T1/ptm/m/ n/10 ; note that the de-fault used to be \T1/fi4/m/sl/10 col Underfull \hbox (badness 1062) in paragraph at lines 3997--3999 []\T1/ptm/m/n/10 numeric (rank 1) ar-ray of clus-ter-wise \T1/ptm/m/it/10 means \T1/ptm/m/n/10 of sil-hou-ette widths where [2337] Underfull \hbox (badness 1383) in paragraph at lines 4019--4024 []\T1/ptm/m/n/10 While \T1/fi4/m/sl/10 silhouette() \T1/ptm/m/n/10 is \T1/ptm/m /it/10 in-trin-sic \T1/ptm/m/n/10 to the [][]\T1/fi4/m/sl/10 partition[][][] \T 1/ptm/m/n/10 clus-ter-ings, and hence has a (triv-ial) [2338] [2339] [2340] [2341] [2342] [2343] [2344] [2345]) (./codetools-pkg.tex [2346] Chapter 21. [2347] [2348] [2349] [2350] [2351]) (./foreign-pkg.tex [2352] Chapter 22. Underfull \hbox (badness 1331) in paragraph at lines 33--37 \T1/ptm/m/n/10 (XPORT) For-mat'' avail-able as [][]$\T1/fi4/m/sl/10 http : / / ftp . sas . com / techsup / download / technote / ts140 . [2353] [2354] [2355] [2356] [2357] [2358] [2359] [2360] [2361] [2362] [2363] Underfull \hbox (badness 10000) in paragraph at lines 704--705 [2364] Underfull \hbox (badness 1642) in paragraph at lines 759--763 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Set in SAS [2365] [2366] [2367] [2368] [2369] Underfull \hbox (badness 10000) in paragraph at lines 1115--1121 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/fi4/m/sl/10 foreign :::writeForeignStata\T1/ptm/m/n/10 , [2370] [2371]) (./lattice-pkg.tex [2372] Chapter 23. [2373] [2374] [2375] [2376] [2377] [2378] Underfull \hbox (badness 10000) in paragraph at lines 480--485 []\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/fi4/m/sl/10 scales \T1/ptm/m/n/10 in this case may be [2379] [2380] [2381] [2382] [2383] [2384] [2385] [2386] [2387] [2388] Underfull \hbox (badness 1062) in paragraph at lines 1398--1402 \T1/ptm/m/n/10 no-ta-tion for the x and y axes re-spec-tively. See doc-u-men-ta -tion for [2389] [2390] [2391] Underfull \hbox (badness 1803) in paragraph at lines 1566--1583 [][][]\T1/fi4/m/sl/10 Lattice[][][] \T1/ptm/m/n/10 for an overview of the pack- age, as well as [][]\T1/fi4/m/sl/10 barchart.table[][][]\T1/ptm/m/n/10 , [][]\T 1/fi4/m/sl/10 print.trellis[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][]\T1/fi4/m/sl/10 panel.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 p anel.superpose[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 panel.loess[][][]\T1/p tm/m/n/10 , [][]\T1/fi4/m/sl/10 panel.average[][][]\T1/ptm/m/n/10 , [][]\T1/fi4 /m/sl/10 strip.default[][][]\T1/ptm/m/n/10 , [2392] [2393] Underfull \hbox (badness 3009) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/fi4/m/sl/10 xyplot[][ ][]\T1/ptm/m/n/10 , which may pass them on to Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to [2394] [2395] [2396] [2397] [2398] Underfull \hbox (badness 10000) in paragraph at lines 2086--2093 []\T1/ptm/m/n/10 For the \T1/fi4/m/sl/10 formula \T1/ptm/m/n/10 method, \T1/fi4 /m/sl/10 x \T1/ptm/m/n/10 can be a for-mula of the form Underfull \hbox (badness 1173) in paragraph at lines 2086--2093 \T1/fi4/m/sl/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togr ams or ker-nel den-sity es-ti- [2399] [2400] [2401] [2402] Underfull \hbox (badness 7064) in paragraph at lines 2360--2364 []\T1/ptm/m/n/10 For the \T1/fi4/m/sl/10 "formula" \T1/ptm/m/n/10 method, \T1/f i4/m/sl/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2403] [2404] Underfull \hbox (badness 7064) in paragraph at lines 2545--2552 []\T1/ptm/m/n/10 For the \T1/fi4/m/sl/10 "formula" \T1/ptm/m/n/10 method, \T1/f i4/m/sl/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2405] [2406] [2407] Underfull \hbox (badness 10000) in paragraph at lines 2759--2764 []\T1/ptm/m/n/10 for the \T1/fi4/m/sl/10 formula \T1/ptm/m/n/10 method, a for-m ula of the form \T1/fi4/m/sl/10 z ~ x * y [2408] Underfull \hbox (badness 2781) in paragraph at lines 2846--2848 []\T1/ptm/m/n/10 A color ramp spec-i-fi-ca-tion, as in the \T1/fi4/m/sl/10 col. regions \T1/ptm/m/n/10 ar-gu-ment in [2409] Underfull \hbox (badness 2486) in paragraph at lines 2957--2961 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2410] [2411] [2412] Underfull \hbox (badness 10000) in paragraph at lines 3108--3116 []\T1/ptm/m/n/10 For the \T1/fi4/m/sl/10 "formula" \T1/ptm/m/n/10 meth-ods, a f or-mula of the form \T1/fi4/m/sl/10 z ~ x [2413] [2414] [2415] [2416]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \relax l.3429 \aliasA{parallel}{B\_08\_splom}{parallel} [2417] [2418] [2419] [2420] [2421] [2422] [2423] Underfull \hbox (badness 2277) in paragraph at lines 3920--3924 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings by Underfull \hbox (badness 10000) in paragraph at lines 3920--3924 \T1/ptm/m/n/10 spec-i-fy-ing \T1/fi4/m/sl/10 lattice.options(default.theme = "c ol.whitebg")\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3920--3924 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2424] [2425] Underfull \hbox (badness 1173) in paragraph at lines 4059--4063 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4086--4088 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when [2426] [2427] [2428] Underfull \hbox (badness 3492) in paragraph at lines 4282--4292 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/fi4/m/sl/10 col \T1/ptm/m/n/10 is used for com-po-nents \T1/fi4/m/sl/10 "plot.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4307--4310 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/fi4/m/sl/10 plo t.symbol\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 plot.polygon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4310--4312 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/fi4/m/sl/10 p lot.polygon \T1/ptm/m/n/10 and [2429] [2430] [2431] [2432] [2433] [2434] [2435] [2436] [2437] [2438] Underfull \hbox (badness 6157) in paragraph at lines 5033--5036 []\T1/fi4/m/sl/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles via rect-an-gles. \T1/fi4/m/sl/10 print.shingle \T1/ptm/m/n/10 and [2439] [2440] [2441] [2442] [2443] [2444] Underfull \hbox (badness 10000) in paragraph at lines 5484--5487 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 5592) in paragraph at lines 5484--5487 \T1/fi4/m/sl/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the le ft of pan-els us-ing [2445] [2446] [2447] [2448] [2449] Underfull \hbox (badness 4805) in paragraph at lines 5844--5848 []\T1/ptm/m/n/10 logical, whether the view-port be-ing as-signed fo-cus should be high- Underfull \hbox (badness 10000) in paragraph at lines 5855--5862 []\T1/ptm/m/n/10 For \T1/fi4/m/sl/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-t ra pa-ram-e-ters are passed on to Underfull \hbox (badness 1226) in paragraph at lines 5855--5862 \T1/fi4/m/sl/10 panel.identify\T1/ptm/m/n/10 . For \T1/fi4/m/sl/10 panel.identi fy\T1/ptm/m/n/10 , ex-tra ar-gu-ments are treated as Underfull \hbox (badness 2418) in paragraph at lines 5855--5862 \T1/ptm/m/n/10 graph-i-cal pa-ram-e-ters and are used for la-belling. For \T1/f i4/m/sl/10 trellis.focus Underfull \hbox (badness 10000) in paragraph at lines 5855--5862 \T1/ptm/m/n/10 and \T1/fi4/m/sl/10 trellis.switchFocus\T1/ptm/m/n/10 , these ar e used (in com-bi-na-tion with Underfull \hbox (badness 1259) in paragraph at lines 5855--5862 [][]\T1/fi4/m/sl/10 lattice.options[][][]\T1/ptm/m/n/10 ) for high-light-ing th e cho-sen view-port if so re-quested. [2450] [2451] [2452] [2453] Underfull \hbox (badness 4242) in paragraph at lines 6155--6160 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- Underfull \hbox (badness 2529) in paragraph at lines 6155--6160 \T1/ptm/m/n/10 ter \T1/fi4/m/sl/10 plot.polygon \T1/ptm/m/n/10 is used if there is no group-ing vari-able, oth-er-wise [2454] [2455] Underfull \hbox (badness 2310) in paragraph at lines 6271--6276 []\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/fi4/m/sl/10 x \T1/ptm/m/n/ 10 for ev-ery level of \T1/fi4/m/sl/10 y \T1/ptm/m/n/10 (or the other way round if [2456] [2457] [2458] [2459] [2460] [2461] [2462] [2463] [2464] [2465] [2466] [2467] [2468] [2469] [2470] Underfull \hbox (badness 2012) in paragraph at lines 7323--7326 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2471] [2472] Underfull \hbox (badness 3333) in paragraph at lines 7495--7497 []\T1/ptm/m/n/10 default colours are ob-tained from \T1/fi4/m/sl/10 plot.symbol \T1/ptm/m/n/10 and \T1/fi4/m/sl/10 plot.line \T1/ptm/m/n/10 us-ing [2473] [2474] [2475] [2476] [2477] [2478] Underfull \hbox (badness 1436) in paragraph at lines 7905--7911 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for Underfull \hbox (badness 1661) in paragraph at lines 7905--7911 \T1/fi4/m/sl/10 panel.abline \T1/ptm/m/n/10 should be taken from the ``ref-er-e nce.line'' pa-ram-e-ter set- Underfull \hbox (badness 1231) in paragraph at lines 7905--7911 \T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti ngs. The [2479] [2480] [2481] [2482] [2483] [2484] [2485] [2486] Underfull \hbox (badness 10000) in paragraph at lines 8463--8466 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/fi4/m/sl/10 panel.superp ose \T1/ptm/m/n/10 from [2487] Underfull \hbox (badness 1092) in paragraph at lines 8509--8511 []\T1/ptm/m/n/10 Deepayan Sarkar \T1/fi4/m/sl/10 \T1/ptm/m/n/10 (\T1/fi4/m/sl/10 panel.superpose.2 \T1/ptm/m/n/10 orig-i-nally con- [2488] [2489] Underfull \hbox (badness 3895) in paragraph at lines 8670--8673 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/fi4/m/sl/10 type \T 1/ptm/m/n/10 has a dif-fer-ent mean-ing in [2490] Underfull \hbox (badness 1515) in paragraph at lines 8746--8750 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2491] Underfull \hbox (badness 6316) in paragraph at lines 8852--8857 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2492] Underfull \hbox (badness 5908) in paragraph at lines 8869--8872 []\T1/ptm/m/n/10 list, sim-i-lar to those pro-duced by \T1/fi4/m/sl/10 xscale.c omponents.default \T1/ptm/m/n/10 and [2493] [2494] [2495] [2496] Overfull \hbox (36.94879pt too wide) in paragraph at lines 9157--9161 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/fi4 /m/sl/10 left, right, left.name, right.name, condition Overfull \hbox (29.63074pt too wide) in paragraph at lines 9157--9161 \T1/ptm/m/n/10 for 2-D, and \T1/fi4/m/sl/10 left, right.x, right.y, left.nam e, right.x.name, right.y.name, condition [2497] [2498] [2499] [2500] [2501] [2502] [2503] Underfull \hbox (badness 1442) in paragraph at lines 9613--9617 []\T1/ptm/m/n/10 Factor with lev-els \T1/fi4/m/sl/10 "Svansota"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "No. 462"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Manchuria"\T1/ptm/m /n/10 , \T1/fi4/m/sl/10 "No. 475"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Velvet"\T1/p tm/m/n/10 , Underfull \hbox (badness 2573) in paragraph at lines 9618--9621 []\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/fi4/m/sl/10 "Grand Rapids"\T1/ptm/m /n/10 , \T1/fi4/m/sl/10 "Duluth"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "University Fa rm"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Morris"\T1/ptm/m/n/10 , [2504] [2505] [2506]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9842 \aliasA{melanoma}{H\_melanoma}{melanoma} [2507] [2508] [2509] [2510]) (./mgcv-pkg.tex Chapter 24. [2511] [2512] Underfull \hbox (badness 1052) in paragraph at lines 149--151 []\T1/ptm/m/n/10 selects ex-act test statis-tic to use for sin-gle smooth term p-values. See [2513] [2514] Underfull \hbox (badness 1142) in paragraph at lines 281--285 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 303--308 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2515] Underfull \hbox (badness 2626) in paragraph at lines 353--356 []\T1/ptm/m/n/10 If all smooths are P-splines and all ten-sor prod-ucts are of the form [2516] [2517] [2518] [2519] [2520] Underfull \hbox (badness 1158) in paragraph at lines 613--615 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2521] [2522] [2523] [2524] [2525] [2526] [2527] [2528] [2529] [2530] [2531] [2532] [2533] [2534] [2535] [2536] Underfull \hbox (badness 1142) in paragraph at lines 1642--1646 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2537] Underfull \hbox (badness 1043) in paragraph at lines 1665--1669 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2538] [2539] [2540] [2541] [2542] Underfull \vbox (badness 10000) has occurred while \output is active [2543] Underfull \vbox (badness 10000) has occurred while \output is active [2544] Underfull \vbox (badness 10000) has occurred while \output is active [2545] [2546] [2547] [2548] [2549] [2550] [2551] [2552] [2553] [2554] [2555] [2556] Underfull \hbox (badness 10000) in paragraph at lines 2921--2925 []\T1/ptm/m/n/10 Random ef-fects can be added to \T1/fi4/m/sl/10 gam \T1/ptm/m/ n/10 mod-els us-ing \T1/fi4/m/sl/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see [2557] [2558] Underfull \vbox (badness 10000) has occurred while \output is active [2559] [2560] [2561] [2562] [2563] [2564] [2565] [2566] [2567] Underfull \hbox (badness 1142) in paragraph at lines 3649--3653 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2568] [2569] Underfull \hbox (badness 1231) in paragraph at lines 3741--3743 []\T1/fi4/m/sl/10 gamm \T1/ptm/m/n/10 per-forms poorly with bi-nary data, since it uses PQL. It is bet-ter to use \T1/fi4/m/sl/10 gam \T1/ptm/m/n/10 with [2570] [2571] Underfull \vbox (badness 10000) has occurred while \output is active [2572] [2573] [2574] [2575] [2576] [2577] [2578] [2579] [2580] [2581] [2582] Underfull \hbox (badness 6001) in paragraph at lines 4632--4634 []\T1/ptm/m/n/10 Simon N. Wood \T1/fi4/m/sl/10 \T1/p tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's [2583] [2584] [2585] Underfull \vbox (badness 10000) has occurred while \output is active [2586] [2587] [2588] [2589] [2590] [2591] [2592] [2593] [2594] [2595] [2596] [2597] [2598] [2599] Underfull \hbox (badness 6001) in paragraph at lines 5671--5673 []\T1/ptm/m/n/10 Simon N. Wood \T1/fi4/m/sl/10 \T1/p tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's [2600] Underfull \vbox (badness 10000) has occurred while \output is active [2601] [2602] [2603] [2604] [2605] [2606] [2607] [2608] Underfull \vbox (badness 10000) has occurred while \output is active [2609] Underfull \hbox (badness 1038) in paragraph at lines 6304--6307 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/fi4/m/sl/10 Dim. pdIndot\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 coef.pdIdnot\T1/ptm/m/n/10 , \T1/fi4/m/ sl/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6304--6307 \T1/fi4/m/sl/10 logDet.pdIdnot\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 pdConstruct.pdId not\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/fi4/m/ sl/10 pdMatrix.pdIdnot\T1/ptm/m/n/10 , [2610] Underfull \hbox (badness 10000) in paragraph at lines 6360--6363 []\T1/ptm/m/n/10 These func-tions (\T1/fi4/m/sl/10 pdTens\T1/ptm/m/n/10 , \T1/f i4/m/sl/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 pdFactor.pdTens\T 1/ptm/m/n/10 , \T1/fi4/m/sl/10 pdMatrix.pdTens\T1/ptm/m/n/10 , [2611] [2612] [2613] [2614] [2615] [2616] [2617] [2618] [2619] Overfull \hbox (29.78088pt too wide) in paragraph at lines 6927--6927 [] \T1/fi4/m/sl/10 block.size=50000,newdata.guaranteed=FALSE,na.action= na.pass,cluster=NULL,...)[] [2620] Underfull \hbox (badness 1852) in paragraph at lines 6996--6999 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/fi4/m/sl/10 termplot[] [][]\T1/ptm/m/n/10 , if \T1/fi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at- tribute \T1/fi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and [2621] [2622] Underfull \hbox (badness 1852) in paragraph at lines 7142--7145 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/fi4/m/sl/10 termplot[] [][]\T1/ptm/m/n/10 , if \T1/fi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at- tribute \T1/fi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and [2623] [2624] Underfull \vbox (badness 10000) has occurred while \output is active [2625] [2626] Underfull \hbox (badness 1205) in paragraph at lines 7350--7352 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 7350--7352 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 7356--7361 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2627] Underfull \hbox (badness 1205) in paragraph at lines 7437--7439 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 7437--7439 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2628] [2629] [2630] Underfull \hbox (badness 1253) in paragraph at lines 7636--7638 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [2631] [2632] [2633] [2634] [2635] [2636] [2637] [2638] [2639] [2640] [2641] Underfull \hbox (badness 1975) in paragraph at lines 8297--8302 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2642] [2643] Underfull \hbox (badness 1762) in paragraph at lines 8386--8398 \T1/ptm/m/n/10 plate re-gres-sion splines: see [][]\T1/fi4/m/sl/10 tprs[][][]\T 1/ptm/m/n/10 ); \T1/fi4/m/sl/10 ts.smooth.spec \T1/ptm/m/n/10 (thin plate re-gr es-sion splines with [2644] [2645] [2646] Underfull \hbox (badness 7667) in paragraph at lines 8596--8602 [][][]\T1/fi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like [2647] Underfull \hbox (badness 10000) in paragraph at lines 8637--8638 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2648] [2649] Underfull \hbox (badness 10000) in paragraph at lines 8763--8765 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2650] [2651] Underfull \hbox (badness 10000) in paragraph at lines 8890--8891 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2652] [2653] Underfull \hbox (badness 1436) in paragraph at lines 9024--9029 \T1/ptm/m/n/10 nest-ing of the smooth within the fac-tor. Note how-ever that: i ) \T1/fi4/m/sl/10 gamm \T1/ptm/m/n/10 only al-lows one [2654] [2655] [2656] [2657] [2658] [2659] [2660] [2661] Underfull \hbox (badness 10000) in paragraph at lines 9459--9465 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a [2662] [2663] [2664] Underfull \vbox (badness 10000) has occurred while \output is active [2665] Underfull \vbox (badness 10000) has occurred while \output is active [2666] Overfull \hbox (9.78088pt too wide) in paragraph at lines 9755--9755 []\T1/fi4/m/n/9 b <- gam(z~s(x,y,k=c(30,15),bs="so",xt=list(bnd=bnd,nmax=nmax) ),knots=knots,method="REML")[] Overfull \hbox (5.28088pt too wide) in paragraph at lines 9761--9761 [] \T1/fi4/m/n/9 s(x,y,k=c(30,15),bs="sw",xt=list(bnd=bnd,nmax=nmax)) ,knots=knots,method="REML")[] Underfull \hbox (badness 10000) in paragraph at lines 9801--9802 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2667] [2668] [2669] [2670] Underfull \hbox (badness 3895) in paragraph at lines 9992--9997 [][][]\T1/fi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 10037--10039 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2671] [2672] [2673] [2674] Underfull \hbox (badness 1371) in paragraph at lines 10211--10217 []\T1/fi4/m/sl/10 bs="ad" \T1/ptm/m/n/10 Uni-vari-ate and bi-vari-ate adap-tive smooths are avail-able (see Underfull \hbox (badness 10000) in paragraph at lines 10251--10255 [][][]\T1/fi4/m/sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 te[][][]\T1/p tm/m/n/10 , [][]\T1/fi4/m/sl/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/ fi4/m/sl/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 cubic.regre ssion.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/fi4/m/sl/10 p.spline[][][]\T1/ptm/m/n /10 , [][]\T1/fi4/m/sl/10 mrf[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10251--10255 \T1/ptm/m/n/10 code[][]soap[][][], code[][]Spherical.Spline[][][], [][]\T1/fi4/ m/sl/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 user.defined. smooth[][][]\T1/ptm/m/n/10 , [2675] Underfull \hbox (badness 2326) in paragraph at lines 10318--10325 []\T1/ptm/m/n/10 These wrap-per func-tions ex-ist to al-low smooths spec-i-fied us-ing [][]\T1/fi4/m/sl/10 smooth.construct[][][] \T1/ptm/m/n/10 and [2676] Underfull \hbox (badness 2158) in paragraph at lines 10375--10375 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [2677] [2678] [2679] [2680] [2681] [2682] [2683] [2684] [2685] [2686] [2687] [2688] [2689] [2690] [2691] [2692] [2693] Underfull \hbox (badness 6001) in paragraph at lines 11473--11475 []\T1/ptm/m/n/10 Simon N. Wood \T1/fi4/m/sl/10 \T1/p tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's [2694] [2695] [2696] [2697] Underfull \hbox (badness 1796) in paragraph at lines 11697--11700 []\T1/ptm/m/n/10 other op-tions to pass on to [][]\T1/fi4/m/sl/10 persp[][][]\T 1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 image[][][] \T1/ptm/m/n/10 or [][]\T1/fi4/m/ sl/10 contour[][][]\T1/ptm/m/n/10 . In par-tic-u-lar [2698] [2699] [2700]) (./nlme-pkg.tex Chapter 25. [2701] [2702] [2703] [2704] [2705] [2706] [2707] [2708] [2709] [2710] [2711] [2712] [2713] [2714] [2715] [2716] [2717] [2718] [2719] [2720] [2721] [2722] [2723] [2724] [2725] [2726] [2727] [2728] [2729] [2730] Underfull \hbox (badness 2875) in paragraph at lines 1996--2002 []\T1/ptm/m/n/10 an op-tional log-i-cal value or one-sided for-mula, in-di-cat- ing a co-vari-ate Underfull \hbox (badness 1466) in paragraph at lines 1996--2002 \T1/ptm/m/n/10 that is in-ner to the \T1/fi4/m/sl/10 displayLevel \T1/ptm/m/n/1 0 group-ing fac-tor. If equal to \T1/fi4/m/sl/10 TRUE\T1/ptm/m/n/10 , [2731] [2732] [2733] [2734] Underfull \hbox (badness 10000) in paragraph at lines 2257--2263 [][][]\T1/fi4/m/sl/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 corARMA [][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][ ]\T1/fi4/m/sl/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Initi alize.corStruct[][][]\T1/ptm/m/n/10 , [2735] [2736] [2737] [2738] [2739] [2740] [2741] [2742] [2743] [2744] [2745] [2746] [2747] [2748] [2749] [2750] [2751] [2752] [2753] [2754] [2755] [2756] [2757] [2758] [2759] [2760] [2761] [2762] [2763] [2764] [2765] [2766] [2767] Underfull \hbox (badness 1067) in paragraph at lines 4410--4415 \T1/ptm/m/n/10 ma-trix), \T1/fi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues ), and \T1/fi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to [2768] [2769] [2770] [2771] [2772] [2773] [2774] [2775] [2776] [2777] [2778] [2779] Underfull \hbox (badness 10000) in paragraph at lines 5156--5160 [][][]\T1/fi4/m/sl/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/ m/sl/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 getCo variate.varFunc[][][]\T1/ptm/m/n/10 , [2780] [2781] [2782] [2783] [2784] [2785] [2786] Underfull \hbox (badness 10000) in paragraph at lines 5588--5591 [][][]\T1/fi4/m/sl/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/1 0 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 getGroups.gls[ ][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 getGroups.lmList[][][]\T1/ptm/m/n/10 , [2787] [2788] [2789] [2790] [2791] [2792] [2793] Underfull \hbox (badness 10000) in paragraph at lines 5969--5974 [][][]\T1/fi4/m/sl/10 getGroupsFormula.gls[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/ sl/10 getGroupsFormula.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 getGrou psFormula.lme[][][]\T1/ptm/m/n/10 , [2794] [2795] [2796] [2797] Underfull \hbox (badness 1490) in paragraph at lines 6239--6250 [][][]\T1/fi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 glsC ontrol[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 glsObject[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 plot. gls[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 predict.gls[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 qqnorm.gls[][][]\T1/ptm/m/n/10 , [2798] Underfull \hbox (badness 10000) in paragraph at lines 6310--6312 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [2799] [2800] [2801] [2802] [2803] [2804] Underfull \hbox (badness 10000) in paragraph at lines 6728--6730 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [2805] [2806] [2807] [2808] [2809] Underfull \hbox (badness 10000) in paragraph at lines 7001--7008 [][][]\T1/fi4/m/sl/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 gapply[ ][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T 1/fi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 plot.nffGroupedData [][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 plot.nfnGroupedData[][][]\T1/ptm/m/n /10 , [2810] [2811] [2812] Underfull \hbox (badness 10000) in paragraph at lines 7263--7268 [][][]\T1/fi4/m/sl/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/ sl/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Initialize .glsStruct[][][]\T1/ptm/m/n/10 , [2813] [2814] [2815] [2816] [2817] [2818] [2819] [2820] [2821] [2822] [2823] [2824] Underfull \hbox (badness 1642) in paragraph at lines 8042--8064 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [2825] [2826] Underfull \hbox (badness 1642) in paragraph at lines 8213--8235 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [2827] [2828] [2829] [2830] [2831] Underfull \hbox (badness 10000) in paragraph at lines 8523--8525 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [2832] [2833] [2834] [2835] [2836] Underfull \hbox (badness 10000) in paragraph at lines 8826--8833 [][][]\T1/fi4/m/sl/10 lm[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 lme.lmList[] [][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 plot.lmList[][][]\T1/ptm/m/n/10 , [][] \T1/fi4/m/sl/10 pooledSD[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 predict.lmLi st[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 residuals.lmList[][][]\T1/ptm/m/n/ 10 , [2837] [2838] [2839] [2840] [2841] [2842] [2843] [2844] Underfull \hbox (badness 10000) in paragraph at lines 9351--9358 [][][]\T1/fi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/fi4/m/sl/10 gls[][][]\T1 /ptm/m/n/10 , [][]\T1/fi4/m/sl/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T 1/fi4/m/sl/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 logLik .lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 logLik.lmList[][][]\T1/ptm /m/n/10 , [2845] [2846] [2847] [2848] [2849]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9713 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9713 ...rA{Matrix}{Assign Matrix Values}{Matrix} [2850] [2851] [2852] [2853] [2854] [2855] [2856] [2857] [2858] [2859] [2860] [2861] Underfull \hbox (badness 1596) in paragraph at lines 10489--10515 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [2862] [2863] Underfull \hbox (badness 1490) in paragraph at lines 10627--10633 [][][]\T1/fi4/m/sl/10 nlmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 nlm e.nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 nlmeObject[][][]\T1/ptm/m/n /10 , [][]\T1/fi4/m/sl/10 nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 nlm eStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 reStruct[][][]\T1/ptm/m/n/10 , [2864] [2865] [2866] [2867] Underfull \hbox (badness 10000) in paragraph at lines 10865--10867 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [2868] [2869] [2870] [2871] [2872] [2873] [2874] [2875] [2876] [2877] [2878] [2879] [2880] [2881] [2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890] [2891] [2892] [2893] [2894] [2895] [2896] [2897] [2898] [2899] [2900] [2901] [2902] [2903] [2904] [2905] [2906] [2907] [2908] [2909] Underfull \hbox (badness 1286) in paragraph at lines 13722--13729 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/fi4/m/sl /10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/fi4/m/sl/10 inner \T1/ptm/m/n/10 or [2910] [2911] [2912] [2913] [2914] [2915] [2916] [2917] Underfull \hbox (badness 1215) in paragraph at lines 14250--14252 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [2918] [2919] [2920] [2921] [2922] [2923] [2924] [2925] [2926] [2927] [2928] [2929] [2930]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.random.effects}) has been already used, duplicate ignored \relax l.15131 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15131 ...Extract Random Effects}{random.effects} [2931] [2932] [2933] [2934] [2935] [2936] [2937] [2938] [2939] [2940] [2941] Underfull \hbox (badness 1067) in paragraph at lines 15842--15847 \T1/ptm/m/n/10 ma-trix), \T1/fi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues ), and \T1/fi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to [2942] [2943] [2944] [2945] Underfull \hbox (badness 1448) in paragraph at lines 16081--16090 \T1/ptm/m/n/10 Op-tions in-clude \T1/fi4/m/sl/10 "response" \T1/ptm/m/n/10 for the "raw" resid-u-als (ob-served - fit-ted), [2946] [2947] Underfull \hbox (badness 10000) in paragraph at lines 16209--16227 []\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form [2948] [2949] [2950] [2951] [2952] [2953] [2954] [2955] [2956] Underfull \hbox (badness 1728) in paragraph at lines 16786--16789 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [2957] [2958] [2959] [2960] Underfull \hbox (badness 10000) in paragraph at lines 17119--17128 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the \T 1/fi4/m/sl/10 pdMat Underfull \hbox (badness 6725) in paragraph at lines 17119--17128 \T1/ptm/m/n/10 class. De-fault de-pends on the method func-tion: \T1/fi4/m/sl/1 0 "Blocked" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17119--17128 \T1/fi4/m/sl/10 pdBlocked\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Compound Symmetry" \ T1/ptm/m/n/10 for \T1/fi4/m/sl/10 pdCompSymm\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "D iagonal" Underfull \hbox (badness 10000) in paragraph at lines 17119--17128 \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 pdDiag\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Mult iple of an Identity" \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 pdIdent\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17119--17128 \T1/fi4/m/sl/10 "General Positive-Definite, Natural Parametrization" \T1/ptm/m/ n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17119--17128 \T1/fi4/m/sl/10 pdNatural\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "General Positive-Def inite" \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 pdSymm\T1/ptm/m/n/10 , and [2961] Underfull \hbox (badness 10000) in paragraph at lines 17183--17191 \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 varComb\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Con stant plus power of covariate" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17183--17191 \T1/fi4/m/sl/10 varConstPower\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Exponential of v ariance covariate" \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 varExp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17183--17191 \T1/fi4/m/sl/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 varIdent\T1/ptm/m/n/10 , [2962] [2963] [2964] [2965] [2966] [2967] [2968] [2969] [2970] [2971] [2972] [2973] Underfull \hbox (badness 10000) in paragraph at lines 17959--17969 [][][]\T1/fi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/1 0 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.corLin[ ][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.corRatio[][][]\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 17959--17969 [][]\T1/fi4/m/sl/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl /10 Variogram.corSpher[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.defa ult[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.gls[][][]\T1/ptm/m/n/10 , [2974] [2975] [2976] [2977] [2978] Underfull \hbox (badness 5036) in paragraph at lines 18283--18292 [][][]\T1/fi4/m/sl/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Vari ogram[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.default[][][]\T1/ptm/ m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/fi4 /m/sl/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [2979] [2980] [2981] [2982] [2983] [2984] [2985] [2986] [2987] [2988] [2989] [2990] [2991]) (./nnet-pkg.tex [2992] Chapter 26. [2993] Underfull \hbox (badness 10000) in paragraph at lines 78--87 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2994] [2995] [2996] [2997] [2998] [2999] [3000]) (./rpart-pkg.tex Chapter 27. [3001] [3002] [3003] [3004] [3005] Underfull \hbox (badness 2556) in paragraph at lines 349--353 \T1/ptm/m/n/10 im-plies \T1/fi4/m/sl/10 minlength = 0L\T1/ptm/m/n/10 , \T1/fi4/ m/sl/10 pretty = NULL \T1/ptm/m/n/10 im-plies \T1/fi4/m/sl/10 minlength = 1L\T1 /ptm/m/n/10 , and [3006] [3007] [3008] [3009] [3010] [3011] [3012] [3013] [3014] [3015] [3016] Underfull \hbox (badness 3219) in paragraph at lines 1113--1116 []\T1/ptm/m/n/10 For re-gres-sion or \T1/fi4/m/sl/10 anova \T1/ptm/m/n/10 trees all three resid-ual def-i-ni-tions re-duce to [3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027] [3028] [3029]) (./spatial-pkg.tex [3030] Chapter 28. [3031] [3032] [3033] [3034] [3035] [3036] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047] [3048] [3049]) (./survival-pkg.tex [3050] Chapter 29. [3051] [3052] [3053]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.212 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica te ignored \relax l.212 ... Myelogenous Leukemia survival data}{aml} [3054] [3055] [3056] [3057] Underfull \vbox (badness 10000) has occurred while \output is active [3058] [3059] [3060] [3061] [3062] [3063]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.colon}) has been already used, duplicate ignored \relax l.902 ...herapy for Stage B/C colon cancer}{colon} [3064] [3065] [3066] [3067] [3068] [3069] [3070] [3071] [3072] [3073] Overfull \hbox (139.78088pt too wide) in paragraph at lines 1671--1671 []\T1/fi4/m/sl/10 frailty.gamma(x, sparse = (nclass > 5), theta, df, eps = 1e- 05, method = c("em","aic", "df", "fixed"), ...)[] Overfull \hbox (94.78088pt too wide) in paragraph at lines 1672--1672 []\T1/fi4/m/sl/10 frailty.gaussian(x, sparse = (nclass > 5), theta, df, method =c("reml","aic", "df", "fixed"), ...)[] Overfull \hbox (134.78088pt too wide) in paragraph at lines 1673--1673 []\T1/fi4/m/sl/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, tdf = 5,method = c("aic", "df", "fixed"), ...)[] [3074] [3075] [3076] [3077] Underfull \vbox (badness 2012) has occurred while \output is active [3078] Underfull \hbox (badness 1389) in paragraph at lines 1966--1968 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3079] [3080] [3081] [3082] [3083] [3084] [3085] Underfull \vbox (badness 10000) has occurred while \output is active [3086] [3087] [3088] [3089] [3090] [3091] [3092] [3093] [3094] [3095] [3096] [3097] Underfull \hbox (badness 5274) in paragraph at lines 3190--3192 []\T1/ptm/m/n/10 an ob-ject of class \T1/fi4/m/sl/10 "summary.survfit"\T1/ptm/m /n/10 , which is the re-sult of the [3098] [3099] [3100] [3101] Underfull \hbox (badness 1540) in paragraph at lines 3535--3538 []\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per -son years if [3102] [3103] [3104] [3105] [3106] [3107] [3108] [3109] Underfull \hbox (badness 1281) in paragraph at lines 4085--4090 []\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/fi4/m/sl/10 "response "\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "deviance"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "d fbeta"\T1/ptm/m/n/10 , [3110] [3111] [3112] [3113] [3114] [3115] [3116] [3117] [3118] [3119] [3120] [3121] Underfull \hbox (badness 10000) in paragraph at lines 4938--4947 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3122] [3123] [3124] Underfull \hbox (badness 4686) in paragraph at lines 5100--5102 []\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/fi4/m/sl/10 rateta ble \T1/ptm/m/n/10 is in units/day, [3125] [3126] [3127] Underfull \hbox (badness 10000) in paragraph at lines 5342--5346 [][][]\T1/fi4/m/sl/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 survfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 survfit.object[][][]\T 1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 print.survfit[][][]\T1/ptm/m/n/10 , [][]\T1/ fi4/m/sl/10 plot.survfit[][][]\T1/ptm/m/n/10 , [3128] [3129] [3130] [3131] [3132] [3133] [3134] [3135] [3136] Underfull \hbox (badness 1354) in paragraph at lines 6038--6042 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. 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at lines 5218--5219 []\T1/fi4/m/it/10 Compare,lsparseMatrix,lsparseMatrix-method Underfull \vbox (badness 1348) has occurred while \output is active [3211] Overfull \hbox (40.8567pt too wide) in paragraph at lines 5226--5227 []\T1/fi4/m/it/10 Compare,triangularMatrix,diagonalMatrix-method [3212] Underfull \vbox (badness 1226) has occurred while \output is active [3213] Overfull \hbox (30.8567pt too wide) in paragraph at lines 5394--5395 []\T1/fi4/m/it/10 crossprod,CsparseMatrix,CsparseMatrix-method Overfull \hbox (25.8567pt too wide) in paragraph at lines 5395--5396 []\T1/fi4/m/it/10 crossprod,CsparseMatrix,ddenseMatrix-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 5396--5397 []\T1/fi4/m/it/10 crossprod,CsparseMatrix,diagonalMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 5398--5399 []\T1/fi4/m/it/10 crossprod,CsparseMatrix,missing-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 5399--5400 []\T1/fi4/m/it/10 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[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46]) [47] [48] [1] [2] (./base-pkg.tex Chapter 1. Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [3] [4] Underfull \hbox (badness 10000) in paragraph at lines 137--145 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/fi4/bx/n/10 x \T 1/ptm/m/n/10 such that \T1/fi4/bx/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 137--145 \T1/ptm/m/n/10 It equals \T1/fi4/bx/n/10 double.base ^ double.neg.ulp.digits \T 1/ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 137--145 \T1/fi4/bx/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/fi4/bx/n/10 double.round ing \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 148--155 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [5] [6] Underfull \hbox (badness 1178) in paragraph at lines 291--295 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/fi4/bx/n /10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [7] [8] Underfull \hbox (badness 3977) in paragraph at lines 372--375 []\T1/ptm/m/n/10 logical: should \T1/fi4/bx/n/10 minlength \T1/ptm/m/n/10 be ob -served strictly? Note that set-ting [9] Underfull \hbox (badness 2556) in paragraph at lines 498--504 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/fi4/bx/n/10 insertions\T1/ptm/m/n/10 ', [10] [11] [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1062--1065 []\T1/ptm/m/n/10 If the calls to \T1/fi4/bx/n/10 FUN \T1/ptm/m/n/10 re-turn vec -tors of dif-fer-ent lengths, \T1/fi4/bx/n/10 apply \T1/ptm/m/n/10 re-turns a l ist of length [19] [20] [21] Underfull \hbox (badness 10000) in paragraph at lines 1263--1269 []\T1/fi4/bx/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/fi4/bx/n/10 x mod y \T1/ptm /m/n/10 and \T1/fi4/bx/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion . It is guar-an-teed that Underfull \hbox (badness 3323) in paragraph at lines 1263--1269 \T1/fi4/bx/n/10 x == (x %% y) + y * ( x %/% y ) \T1/ptm/m/n/10 (up to round-i ng er-ror) un-less \T1/fi4/bx/n/10 y == 0 \T1/ptm/m/n/10 where the [22] [23] [24] [25] [26] [27] [28] [29] [30] Underfull \hbox (badness 10000) in paragraph at lines 1943--1945 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] Underfull \hbox (badness 10000) in paragraph at lines 3370--3372 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [52] [53] [54] [55] [56] [57] [58] [59] Underfull \hbox (badness 2970) in paragraph at lines 3949--3955 []\T1/ptm/m/n/10 is there sup-port the [][]\T1/fi4/bx/n/10 svg[][][]\T1/ptm/m/n /10 , [][]\T1/fi4/bx/n/10 cairo_pdf[][][] \T1/ptm/m/n/10 and [][]\T1/fi4/bx/n/1 0 cairo_ps[][][] \T1/ptm/m/n/10 de-vices, and for [60] [61] [62] [63] [64] [65] [66] [67] Underfull \hbox (badness 2521) in paragraph at lines 4505--4507 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [68] [69] Underfull \hbox (badness 1337) in paragraph at lines 4649--4655 \T1/ptm/m/n/10 LA-PACK re-quires LA-PACK >= 3.2 and was added in \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.2. The value of \T1/fi4/bx/n/10 tol \T1/ptm/m/n/10 is [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] Underfull \hbox (badness 2096) in paragraph at lines 5719--5732 []\T1/ptm/m/n/10 New restarts for \T1/fi4/bx/n/10 withRestarts \T1/ptm/m/n/10 c an be spec-i-fied in sev-eral ways. The sim-plest is in [86] [87] [88] [89] Underfull \hbox (badness 10000) in paragraph at lines 6042--6045 []\T1/ptm/m/n/10 A note on `\T1/fi4/bx/n/10 file://\T1/ptm/m/n/10 ' URLs. The m ost gen-eral form (from RFC1738) is [90] [91] [92] Underfull \hbox (badness 2790) in paragraph at lines 6257--6264 []\T1/fi4/bx/n/10 file \T1/ptm/m/n/10 can be used with \T1/fi4/bx/n/10 descript ion = "clipboard" \T1/ptm/m/n/10 in mode \T1/fi4/bx/n/10 "r" \T1/ptm/m/n/10 onl y. This reads Underfull \hbox (badness 3471) in paragraph at lines 6257--6264 \T1/ptm/m/n/10 the X11 pri-mary se-lec-tion (see [][]$\T1/fi4/bx/n/10 http : / / standards . freedesktop . org / clipboards-[]spec / [93] [94] Underfull \vbox (badness 10000) has occurred while \output is active [95] [96] [97] [98] [99] [100] [101] Underfull \hbox (badness 4595) in paragraph at lines 6859--6862 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [102] Underfull \hbox (badness 2351) in paragraph at lines 6916--6919 [][][]\T1/fi4/bx/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac- cord-ing to a group fac-tor; [][]\T1/fi4/bx/n/10 factor[][][]\T1/ptm/m/n/10 , [ ][]\T1/fi4/bx/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 table[][] []\T1/ptm/m/n/10 , [103] [104] [105] Underfull \hbox (badness 10000) in paragraph at lines 7161--7172 []\T1/fi4/bx/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments t o a data frame by call-ing [106] Underfull \hbox (badness 4479) in paragraph at lines 7232--7241 [][][]\T1/fi4/bx/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 plot.data.fra me[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 print.data.frame[][][]\T1/ptm/m/n/ 10 , [][]\T1/fi4/bx/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 na mes[][][] \T1/ptm/m/n/10 (for the col-umn names), Underfull \hbox (badness 2469) in paragraph at lines 7232--7241 [][]\T1/fi4/bx/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods , [][]\T1/fi4/bx/n/10 Math.data.frame[][][] \T1/ptm/m/n/10 etc, about \T1/ptm/m /it/10 Group \T1/ptm/m/n/10 meth-ods for [107] [108] [109] [110] [111] [112] Underfull \hbox (badness 10000) in paragraph at lines 7640--7652 \T1/fi4/bx/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/ n/10 may give \T1/fi4/bx/n/10 NA\T1/ptm/m/n/10 , and hence Underfull \hbox (badness 6220) in paragraph at lines 7640--7652 \T1/fi4/bx/n/10 as.POSIXct("1969-12-31 23:59:59", tz = "UTC") \T1/ptm/m/n/10 w ill give \T1/fi4/bx/n/10 "1969-12-31 23:59:00"\T1/ptm/m/n/10 . [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] Underfull \hbox (badness 1394) in paragraph at lines 8766--8771 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/fi4/bx/n/10 difftime \T1/ptm/m/n/10 with [129] [130] [131] [132] [133] [134] Underfull \hbox (badness 10000) in paragraph at lines 9210--9214 [][][]$\T1/fi4/bx/n/10 http : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/fi4/bx/n/10 http : / / en . wikipedia . org / wiki / IEEE _ [135] [136] [137] [138] [139] [140] Underfull \hbox (badness 2150) in paragraph at lines 9593--9596 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 9607--9615 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for [141] Underfull \hbox (badness 5622) in paragraph at lines 9648--9654 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/fi4/bx/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 4569) in paragraph at lines 10677--10681 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 10677--10681 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [156] [157] [158] [159] [160] [161] [162] Underfull \hbox (badness 2698) in paragraph at lines 11219--11228 []\T1/ptm/m/n/10 Both \T1/fi4/bx/n/10 $ \T1/ptm/m/n/10 and \T1/fi4/bx/n/10 [[ \ T1/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are al-lowed Underfull \hbox (badness 4341) in paragraph at lines 11219--11228 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] Underfull \hbox (badness 2253) in paragraph at lines 12166--12168 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [177] Underfull \hbox (badness 1565) in paragraph at lines 12227--12231 [][][]\T1/fi4/bx/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-b olic links, [][]\T1/fi4/bx/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 file.access[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 list.files[][][]\T1/ptm/ m/n/10 , and Underfull \hbox (badness 10000) in paragraph at lines 12270--12272 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/fi4/b x/n/10 PATH \T1/ptm/m/n/10 and \T1/fi4/bx/n/10 R_LIBS \T1/ptm/m/n/10 with [178] [179] Underfull \hbox (badness 1292) in paragraph at lines 12333--12341 \T1/ptm/m/n/10 ing spe-cial pager names be-ing in-ter-cepted by lower-level cod e (such as \T1/fi4/bx/n/10 "internal" \T1/ptm/m/n/10 and [180] Underfull \hbox (badness 1466) in paragraph at lines 12401--12404 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ fi4/bx/n/10 file.copy \T1/ptm/m/n/10 and [181] Underfull \hbox (badness 10000) in paragraph at lines 12507--12511 [][][]\T1/fi4/bx/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 file. access[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 file.path[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 list. files[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 unlink[][][]\T1/ptm/m/n/10 , [] []\T1/fi4/bx/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 12518--12521 [][][]$\T1/fi4/bx/n/10 http : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/fi4/bx/n/10 http : / / en . wikipedia . org / wik i / [182] [183] [184] Underfull \hbox (badness 3965) in paragraph at lines 12765--12769 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] Underfull \hbox (badness 4429) in paragraph at lines 13469--13472 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/fi4/bx/n/10 complex[][][] \T1/ptm/m/n/10 only for [196] Underfull \hbox (badness 10000) in paragraph at lines 13555--13557 []\T1/ptm/m/n/10 If you set \T1/fi4/bx/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/fi4/bx/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 13561--13565 []\T1/fi4/bx/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num- bers on the dec-i-mal point, so Underfull \hbox (badness 1052) in paragraph at lines 13561--13565 \T1/fi4/bx/n/10 formatC(c(6.11, 13.1), digits = 2, format = "fg") \T1/ptm/m/n/1 0 gives \T1/fi4/bx/n/10 c("6.1", " 13")\T1/ptm/m/n/10 . If you [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] Underfull \hbox (badness 1092) in paragraph at lines 14313--14318 [][]\T1/fi4/bx/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter the DLL has been loaded us-ing [208] [209] [210] Underfull \hbox (badness 6741) in paragraph at lines 14561--14565 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/fi4/bx/n/10 CRoutine\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 CallRoutine\T1/ptm/m/n/ 10 , [211] [212] [213] [214] [215] Underfull \hbox (badness 1867) in paragraph at lines 14859--14866 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [216] [217] [218] Underfull \vbox (badness 10000) has occurred while \output is active [219] [220] Underfull \hbox (badness 3679) in paragraph at lines 15235--15237 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/fi4/bx/n/10 htt p : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [221] [222] [223] [224] [225] [226] Underfull \hbox (badness 1478) in paragraph at lines 15703--15706 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] Underfull \hbox (badness 1442) in paragraph at lines 16379--16381 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/fi4/bx/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [237] Underfull \hbox (badness 2452) in paragraph at lines 16471--16487 [][][]\T1/fi4/bx/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 as .complex[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 as.double[][][]\T1/ptm/m/n/1 0 , [][]\T1/fi4/bx/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 as .logical[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 as.vector[][][]\T1/ptm/m/n/10 , [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] Underfull \hbox (badness 4739) in paragraph at lines 17116--17118 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [248] [249] [250] [251] [252] [253] Underfull \hbox (badness 1077) in paragraph at lines 17514--17519 \T1/ptm/m/n/10 trix or, if \T1/fi4/bx/n/10 simplify = "array"\T1/ptm/m/n/10 , a n ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/fi4/bx/n/10 simplify2array()\T1/p tm/m/n/10 . [254] [255] [256] [257] [258] [259] [260] Underfull \hbox (badness 10000) in paragraph at lines 17992--17996 []\T1/ptm/m/n/10 By de-fault \T1/fi4/bx/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, a nd \T1/fi4/bx/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 17992--17996 \T1/ptm/m/n/10 `\T1/fi4/bx/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/fi4/bx/ n/10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or ` \T1/fi4/bx/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/fi4/bx/n/10 /library\T1/ptm/m/ n/10 ' [261] [262] Underfull \hbox (badness 1014) in paragraph at lines 18145--18150 []\T1/ptm/m/n/10 Normally \T1/fi4/bx/n/10 library \T1/ptm/m/n/10 re-turns (in-v is-i-bly) the list of at-tached pack-ages, but \T1/fi4/bx/n/10 TRUE \T1/ptm/m/n /10 or \T1/fi4/bx/n/10 FALSE \T1/ptm/m/n/10 if [263] [264] [265] [266] [267] [268] [269] [270] [271] [272] Underfull \hbox (badness 1264) in paragraph at lines 18853--18858 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [273] [274] [275] [276] [277] [278] Underfull \hbox (badness 4954) in paragraph at lines 19277--19283 []\T1/fi4/bx/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment to be of log-i-cal type. For [][]\T1/fi4/bx/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 10000) in paragraph at lines 19277--19283 \T1/ptm/m/n/10 this uses the [][]\T1/fi4/bx/n/10 levels[][][] \T1/ptm/m/n/10 (l a-bels). Like [][]\T1/fi4/bx/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-t ributes in-clud-ing Underfull \hbox (badness 10000) in paragraph at lines 19277--19283 \T1/ptm/m/n/10 names. Char-ac-ter strings \T1/fi4/bx/n/10 c("T", "TRUE", "True" , "true") \T1/ptm/m/n/10 are re-garded as true, [279] [280] [281] [282] [283] Underfull \hbox (badness 10000) in paragraph at lines 19584--19586 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/fi4/bx/n/10 make.unique \T1/ptm/m/ n/10 has the prop-erty that [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] Underfull \hbox (badness 1655) in paragraph at lines 20567--20573 [][][]$\T1/fi4/bx/n/10 http : / / en . wikipedia . org / wiki / Data _ compress ion$[][] \T1/ptm/m/n/10 for back-ground on data com-pres-sion, [298] [299] [300] Underfull \hbox (badness 1484) in paragraph at lines 20728--20736 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been [301] [302] [303] [304] Underfull \hbox (badness 2790) in paragraph at lines 20995--20998 []\T1/fi4/bx/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes- sages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 20995--20998 \T1/fi4/bx/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still mes-sages, so can be sup-pressed by [305] [306] [307] [308] [309] [310] Underfull \hbox (badness 10000) in paragraph at lines 21434--21437 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 21434--21437 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] Underfull \hbox (badness 1199) in paragraph at lines 22481--22487 []\T1/ptm/m/n/10 The de-fault method for \T1/fi4/bx/n/10 is.numeric \T1/ptm/m/n /10 re-turns \T1/fi4/bx/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mo de[][][] \T1/fi4/bx/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 22481--22487 \T1/ptm/m/n/10 ([][]type[][][] \T1/fi4/bx/n/10 "double" \T1/ptm/m/n/10 or type \T1/fi4/bx/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/fi4/bx/n/1 0 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, [327] [328] [329] [330] [331] [332] [333] Underfull \hbox (badness 1038) in paragraph at lines 23014--23023 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 10000) in paragraph at lines 23014--23023 \T1/fi4/bx/n/10 c("datasets", "utils", "grDevices", "graphics", "stats", "methods")\T1/ptm/m/n/10 . Underfull \hbox (badness 1881) in paragraph at lines 23024--23027 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 23043--23045 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [334] Underfull \hbox (badness 10000) in paragraph at lines 23107--23116 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/fi4/b x/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2600) in paragraph at lines 23107--23116 \T1/ptm/m/n/10 `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/fi4/bx/n/10 /bin/pager\T1/p tm/m/n/10 ', which se-lects a pager via the \T1/fi4/bx/n/10 PAGER \T1/ptm/m/n/1 0 en-vi-ron-ment vari-able Underfull \hbox (badness 2142) in paragraph at lines 23117--23123 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/fi4/bx/n/10 postsc ript[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 23130--23135 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/fi4/bx/n/10 postscript[][][] \T1/ ptm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 23140--23149 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [335] [336] [337] Underfull \hbox (badness 10000) in paragraph at lines 23381--23387 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/fi4/bx /n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 23381--23387 \T1/ptm/m/n/10 e.g. the de-fault `\T1/fi4/bx/n/10 "http://www.bioconductor.org" \T1/ptm/m/n/10 ' or the Eu-ro-pean mir- Underfull \hbox (badness 10000) in paragraph at lines 23381--23387 \T1/ptm/m/n/10 ror `\T1/fi4/bx/n/10 "http://bioconductor.statistik.tu-dortmund. de"\T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 23393--23396 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/fi4/bx/n/10 create.post[] [][] \T1/ptm/m/n/10 (and hence[][]\T1/fi4/bx/n/10 bug.report[][][] \T1/ptm/m/n/ 10 and Underfull \hbox (badness 2689) in paragraph at lines 23418--23420 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 7203) in paragraph at lines 23446--23449 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/fi4/bx/n/10 create.po st[][][] \T1/ptm/m/n/10 and hence [][]\T1/fi4/bx/n/10 bug.report[][][] \T1/ptm/ m/n/10 and Underfull \hbox (badness 3128) in paragraph at lines 23456--23462 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/fi4/bx/n/10 "source" \T1/ptm/m/n/10 ( the de-fault ex-cept un-der the CRAN OS X build) Underfull \hbox (badness 1881) in paragraph at lines 23456--23462 \T1/ptm/m/n/10 and \T1/fi4/bx/n/10 "mac.binary."\T1/ptm/m/n/10 . Win-dows uses \T1/fi4/bx/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/fi4/bx/n/10 "mac.binary.leopa rd" \T1/ptm/m/n/10 and [338] Underfull \hbox (badness 10000) in paragraph at lines 23464--23471 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/fi4/bx/n/10 upd ate.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 23464--23471 \T1/fi4/bx/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util- i-ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 23464--23471 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 10000) in paragraph at lines 23464--23471 \T1/fi4/bx/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.c ran"; [339] [340] [341] [342] Underfull \hbox (badness 10000) in paragraph at lines 23765--23769 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/fi4/bx/n/10 X \T1/ptm/m/ n/10 and \T1/fi4/bx/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/fi4/bx/n/10 A \T1/p tm/m/n/10 with di-men- Underfull \hbox (badness 10000) in paragraph at lines 23765--23769 \T1/ptm/m/n/10 sion \T1/fi4/bx/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e -ment \T1/fi4/bx/n/10 A[c(arrayindex.x, arrayindex.y)] [343] [344] [345] [346] Underfull \hbox (badness 1748) in paragraph at lines 24064--24068 \T1/ptm/m/n/10 seem un-de-sir-able, e.g., when past-ing two char-ac-ter vec-tor s, or very de-sir-able, e.g. in [347] [348] [349] [350] [351] [352] [353] [354] Underfull \hbox (badness 2726) in paragraph at lines 24563--24566 []\T1/ptm/m/n/10 character string (or \T1/fi4/bx/n/10 NULL\T1/ptm/m/n/10 ) in-d i-cat-ing [][]\T1/fi4/bx/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-pu t, see [355] [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] Underfull \hbox (badness 1052) in paragraph at lines 25368--25373 []\T1/fi4/bx/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/ 10 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vid ed [367] [368] [369] [370] [371] Underfull \hbox (badness 1097) in paragraph at lines 25757--25765 []\T1/ptm/m/n/10 The seed, \T1/fi4/bx/n/10 .Random.seed[-1] == r[1:3] \T1/ptm/m /n/10 is an in-te-ger vec-tor of length [372] [373] [374] [375] Underfull \hbox (badness 1533) in paragraph at lines 26073--26076 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [376] [377] [378] [379] [380] [381] [382] [383] [384] [385] [386] [387] [388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399] Underfull \hbox (badness 6188) in paragraph at lines 27726--27728 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/fi4/bx/n/10 http : / / pubs . opengroup . org / onlinepubs / 9699919799 / [400] [401] [402] [403] [404] [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] Underfull \hbox (badness 10000) in paragraph at lines 28925--28928 []\T1/fi4/bx/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my cur-rent workspace', i.e., Underfull \hbox (badness 3229) in paragraph at lines 28925--28928 \T1/fi4/bx/n/10 save(list = ls(all = TRUE), file = ".RData")\T1/ptm/m/n/10 . It is also what hap-pens with [418] [419] [420] Underfull \hbox (badness 2302) in paragraph at lines 29125--29132 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 29125--29132 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 2698) in paragraph at lines 29125--29132 \T1/ptm/m/n/10 val-ues. In the case \T1/fi4/bx/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, but Underfull \hbox (badness 4805) in paragraph at lines 29125--29132 \T1/ptm/m/n/10 in gen-eral it is not. (To scale by the stan-dard de-vi-a-tions with-out cen-ter-ing, use [421] [422] Underfull \hbox (badness 2261) in paragraph at lines 29278--29283 []\T1/ptm/m/n/10 If \T1/fi4/bx/n/10 strip.white \T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 29305--29311 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 4001) in paragraph at lines 29305--29311 \T1/ptm/m/n/10 `\T1/fi4/bx/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta- [423] Underfull \hbox (badness 10000) in paragraph at lines 29378--29383 []\T1/ptm/m/n/10 Note that since \T1/fi4/bx/n/10 sep \T1/ptm/m/n/10 is a sep-a- ra-tor and not a ter-mi-na-tor, read-ing a file by Underfull \hbox (badness 1701) in paragraph at lines 29378--29383 \T1/fi4/bx/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/1 0 will give an empty fi-nal line if [424] [425] [426] [427] [428] Underfull \hbox (badness 6188) in paragraph at lines 29712--29715 []\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence \T1/fi4/bx /n/10 1, 2, ..., length(along.with)\T1/ptm/m/n/10 . [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] Underfull \vbox (badness 10000) has occurred while \output is active [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] Underfull \hbox (badness 1072) in paragraph at lines 32120--32124 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 32125--32129 []\T1/ptm/m/n/10 The command-line op-tion `\T1/fi4/bx/n/10 --vanilla\T1/ptm/m/n /10 ' im-plies `\T1/fi4/bx/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/fi4/bx/n/1 0 --no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 32153--32159 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/fi4/bx/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 32153--32159 \T1/ptm/m/n/10 and `\T1/fi4/bx/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked fo r first in architecture-specific di-rec-to-ries, e.g. Underfull \hbox (badness 3343) in paragraph at lines 32162--32169 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 32162--32169 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment Underfull \hbox (badness 1917) in paragraph at lines 32162--32169 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/fi4/bx /n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [464] [465] [466] [467] [468] Underfull \hbox (badness 10000) in paragraph at lines 32452--32458 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/fi4/bx/n/10 for mat \T1/ptm/m/n/10 meth-ods is [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487] [488] [489] Underfull \hbox (badness 1248) in paragraph at lines 33821--33831 []\T1/ptm/m/n/10 If \T1/fi4/bx/n/10 EXPR \T1/ptm/m/n/10 eval-u-ates to a char-a c-ter string then that string is matched (ex-actly)to the names Underfull \hbox (badness 1902) in paragraph at lines 33821--33831 \T1/ptm/m/n/10 of the el-e-ments in \T1/fi4/bx/n/10 ...\T1/ptm/m/n/10 . If ther e is a match then that el-e-ment is eval-u-ated un-less it Underfull \hbox (badness 2772) in paragraph at lines 33821--33831 \T1/ptm/m/n/10 is miss-ing, in which case the next non-missing el-e-ment is eva l-u-ated, so for ex-am-ple [490] [491] Underfull \hbox (badness 4416) in paragraph at lines 34006--34008 []\T1/ptm/m/n/10 Argument \T1/fi4/bx/n/10 names \T1/ptm/m/n/10 was in-tro-duced in \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.13.0 to avoid need-ing the com-mon use of [492] [493] Underfull \hbox (badness 3333) in paragraph at lines 34099--34104 []\T1/ptm/m/n/10 If a file-name starts with \T1/fi4/bx/n/10 . \T1/ptm/m/n/10 th is may need to be matched ex-plic-itly: for ex-am-ple [494] [495] [496] [497] [498] [499] [500] [501] [502] Underfull \hbox (badness 1472) in paragraph at lines 34706--34709 []\T1/ptm/m/n/10 logical. If \T1/fi4/bx/n/10 TRUE\T1/ptm/m/n/10 , func-tions ke ep their source in-clud-ing com-ments, see [503] [504] [505] [506] [507] [508] [509] [510] Underfull \hbox (badness 4217) in paragraph at lines 35222--35225 []\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/fi 4/bx/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies [511] [512] Underfull \hbox (badness 2671) in paragraph at lines 35356--35359 []\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/fi4/bx/n/10 ...\T1/p tm/m/n/10 . If set to \T1/fi4/bx/n/10 NULL\T1/ptm/m/n/10 , it im-plies [513] [514] [515] [516] [517] Underfull \hbox (badness 10000) in paragraph at lines 35754--35757 [][][]\T1/fi4/bx/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [][]$http : / / developer . r-[]project . org / [518] [519] Underfull \hbox (badness 10000) in paragraph at lines 35875--35879 [][][]\T1/fi4/bx/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 removeTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 getTaskCallbackNa mes[][][]\T1/ptm/m/n/10 \ [][]$\T1/fi4/bx/n/10 http : / / developer . [520] Underfull \hbox (badness 10000) in paragraph at lines 35937--35941 [][][]\T1/fi4/bx/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 removeTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 taskCallbackManag er[][][]\T1/ptm/m/n/10 \ [][]$\T1/fi4/bx/n/10 http : / / developer . [521] [522] [523] [524] [525] [526] [527] [528] [529] Underfull \hbox (badness 10000) in paragraph at lines 36558--36560 []\T1/ptm/m/n/10 Using [][]\T1/fi4/bx/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 ( from pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, ca ll-ing [530] [531] [532] [533] [534] [535] [536] Underfull \hbox (badness 1990) in paragraph at lines 37062--37070 []\T1/fi4/bx/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 4846) in paragraph at lines 37062--37070 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/fi4/bx/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [537] [538] [539] [540] Underfull \hbox (badness 1515) in paragraph at lines 37331--37336 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0 [541] [542] [543] Underfull \hbox (badness 1917) in paragraph at lines 37554--37561 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/fi4/bx/n/10 UseMethod("fun") \T1 /ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [544] [545] [546] [547] [548] [549] [550] [551] Underfull \hbox (badness 3668) in paragraph at lines 38120--38122 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [552] [553] Underfull \hbox (badness 2401) in paragraph at lines 38220--38224 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/fi4/bx/n/10 options[][][]("wa rn") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [554] [555] Underfull \hbox (badness 10000) in paragraph at lines 38396--38401 []\T1/ptm/m/n/10 If \T1/fi4/bx/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/fi4/ bx/n/10 x \T1/ptm/m/n/10 is an [][]\T1/fi4/bx/n/10 array[][][] \T1/ptm/m/n/10 ( has a [][]\T1/fi4/bx/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is Underfull \hbox (badness 1454) in paragraph at lines 38396--38401 \T1/fi4/bx/n/10 arrayInd(which(x), dim(x), dimnames(x))\T1/ptm/m/n/10 , namely a ma-trix whose rows each are the [556] [557] [558] [559] [560] [561] [562] Underfull \hbox (badness 10000) in paragraph at lines 38815--38820 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/fi4/bx/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 38815--38820 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to Underfull \hbox (badness 1102) in paragraph at lines 38815--38820 \T1/fi4/bx/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10 , so \T1/fi4/bx/n/10 NA \T1/ptm/m/n/10 val-ues are given rank \T1/fi4/bx/n/10 NA [563] Underfull \hbox (badness 5417) in paragraph at lines 38905--38909 []\T1/fi4/bx/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rent ly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [564] Underfull \hbox (badness 10000) in paragraph at lines 38966--38970 []\T1/fi4/bx/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dar d' reg-exps, in-clud-ing el-e-ments named [565]) (./compiler-pkg.tex [566] Chapter 2. [567] [568] [569]) (./datasets-pkg.tex [570] Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] Overfull \hbox (1.81013pt too wide) in paragraph at lines 691--694 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("nfnGroupedData", "nfGro upedData", "groupedData", "data.frame") [582] [583] Overfull \hbox (1.81013pt too wide) in paragraph at lines 824--827 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("nfnGroupedData", "nfGro upedData", "groupedData", "data.frame") [584] [585] [586] [587] Overfull \hbox (1.81013pt too wide) in paragraph at lines 1130--1133 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("nfnGroupedData", "nfGro upedData", "groupedData", "data.frame") [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] Overfull \hbox (1.81013pt too wide) in paragraph at lines 1702--1705 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("nfnGroupedData", "nfGro upedData", "groupedData", "data.frame") [598] [599] [600] [601] [602] [603] [604] Overfull \hbox (1.81013pt too wide) in paragraph at lines 2124--2127 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("nfnGroupedData", "nfGro upedData", "groupedData", "data.frame") [605] [606] [607] [608] [609] [610] [611] Overfull \hbox (1.81013pt too wide) in paragraph at lines 2601--2604 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("nfnGroupedData", "nfGro upedData", "groupedData", "data.frame") [612] Overfull \vbox (13.87083pt too high) has occurred while \output is active [613] Underfull \vbox (badness 1721) has occurred while \output is active [614] [615] Overfull \vbox (12.25539pt too high) has occurred while \output is active [616] [617] Overfull \vbox (17.12102pt too high) has occurred while \output is active [618] [619] [620] [621] [622] [623] [624] [625] [626] Overfull \hbox (1.81013pt too wide) in paragraph at lines 3573--3576 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("nfnGroupedData", "nfGro upedData", "groupedData", "data.frame") [627] [628] [629] [630] Underfull \hbox (badness 1325) in paragraph at lines 3809--3812 []\T1/ptm/m/n/10 For back-ground on Bristle-cone pines and Methuse-lah Walk, se e [][]$\T1/fi4/bx/n/10 http : / / www . sonic . net / [631] [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] [642] [643]) (./grDevices-pkg.tex [644] Chapter 4. [645] [646] [647] [648] Underfull \hbox (badness 1484) in paragraph at lines 274--278 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/fi4/bx/n/10 c(mi, ma, n.)\T1/ ptm/m/n/10 , with iden-ti-cal mean-ing to [649] [650] [651] [652] [653] [654] [655] [656] [657] [658] [659] [660] Underfull \hbox (badness 5175) in paragraph at lines 1041--1043 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [661] [662] [663] Underfull \hbox (badness 1852) in paragraph at lines 1234--1237 []\T1/fi4/bx/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col -ors that will be used in plot-ting, call-ing [664] [665] [666] Underfull \hbox (badness 1490) in paragraph at lines 1436--1441 \T1/ptm/m/n/10 by [][]\T1/fi4/bx/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][] \T1/fi4/bx/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/fi4/bx /n/10 "no"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "yes" \T1/ptm/m/n/10 and [667] Underfull \hbox (badness 2698) in paragraph at lines 1490--1493 []\T1/fi4/bx/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture , oth-er-wise a ma-trix of color names (for [668] Underfull \hbox (badness 10000) in paragraph at lines 1559--1563 []\T1/ptm/m/n/10 logical; if \T1/fi4/bx/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/fi4/bx/n/10 TRUE \T1/ptm/m/n/10 when Underfull \hbox (badness 6332) in paragraph at lines 1559--1563 [][]\T1/fi4/bx/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/f i4/bx/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is among the [669] [670] [671] [672] Underfull \hbox (badness 1033) in paragraph at lines 1842--1855 \T1/fi4/bx/n/10 "pgnm"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "pgnmraw"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "pnm"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "pnmraw"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "ppm"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "ppmraw"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "pkm"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "pkmraw"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "tiffcrle"\T1/ptm/m/n/10 , Underfull \hbox (badness 3758) in paragraph at lines 1842--1855 \T1/fi4/bx/n/10 "tiffg3"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "tiffg32d"\T1/ptm/m/n/ 10 , \T1/fi4/bx/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "tifflzw"\T1/ptm/ m/n/10 , \T1/fi4/bx/n/10 "tiffpack"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "tiff12nc"\ T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "tiff24nc"\T1/ptm/m/n/10 , Underfull \hbox (badness 3128) in paragraph at lines 1842--1855 \T1/fi4/bx/n/10 "tiff32nc" "psmono"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "psgray"\T1 /ptm/m/n/10 , \T1/fi4/bx/n/10 "psrgb"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "bit"\T1/ ptm/m/n/10 , \T1/fi4/bx/n/10 "bitrgb"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "bitcmyk" \T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "pngmono"\T1/ptm/m/n/10 , Underfull \hbox (badness 1546) in paragraph at lines 1842--1855 \T1/fi4/bx/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "pngalpha"\T1/ptm/m/n /10 , \T1/fi4/bx/n/10 "png16"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "png256"\T1/ptm/m /n/10 , \T1/fi4/bx/n/10 "png16m"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "png48"\T1/ptm /m/n/10 , \T1/fi4/bx/n/10 "jpeg"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "jpeggray"\T1/ ptm/m/n/10 , [673] [674] Underfull \hbox (badness 10000) in paragraph at lines 1951--1953 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [675] [676] Underfull \hbox (badness 6758) in paragraph at lines 2103--2106 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [677] [678] [679] [680] [681] [682] [683] [684] Underfull \hbox (badness 10000) in paragraph at lines 2606--2607 Underfull \vbox (badness 10000) has occurred while \output is active [685] [686] [687] [688] [689] [690] Underfull \hbox (badness 1755) in paragraph at lines 3044--3046 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/fi4/bx/n/10 nr, nc \T1/ptm/ m/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [691] [692] [693] [694] [695] Underfull \hbox (badness 7851) in paragraph at lines 3365--3368 []\T1/ptm/m/n/10 For use with \T1/fi4/bx/n/10 onefile = FALSE \T1/ptm/m/n/10 gi ve a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3379--3381 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/fi4/bx/n/10 /Title\T1/ptm/m /n/10 ' field in the file. De-faults to [696] [697] Underfull \hbox (badness 1173) in paragraph at lines 3495--3505 []\T1/ptm/m/n/10 The \T1/fi4/bx/n/10 paper \T1/ptm/m/n/10 ar-gu-ment sets the ` \T1/fi4/bx/n/10 /MediaBox\T1/ptm/m/n/10 ' en-try in the file, which de-faults t o \T1/fi4/bx/n/10 width \T1/ptm/m/n/10 by [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] Underfull \hbox (badness 1067) in paragraph at lines 4196--4203 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [708] [709] [710] Underfull \hbox (badness 1789) in paragraph at lines 4418--4420 []\T1/ptm/m/n/10 title string to em-bed as the \T1/fi4/bx/n/10 Title \T1/ptm/m/ n/10 com-ment in the file. De-faults to [711] Underfull \hbox (badness 1377) in paragraph at lines 4468--4473 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues Underfull \hbox (badness 2671) in paragraph at lines 4495--4503 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/fi4/ bx/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as [712] Underfull \hbox (badness 1418) in paragraph at lines 4544--4551 \T1/ptm/m/n/10 it is one of \T1/fi4/bx/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/fi 4/bx/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "Courier"\T1/ptm/m/n/10 , \ T1/fi4/bx/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "Helvetica-Narrow"\T 1/ptm/m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4552--4561 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4552--4561 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4562--4564 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [713] Underfull \hbox (badness 1057) in paragraph at lines 4673--4678 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/fi4/bx/n/10 "rgb"\T1/ptm/m/n/10 ) (which is RGB+gray) and [714] Underfull \hbox (badness 7344) in paragraph at lines 4733--4735 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso [715] [716] Underfull \hbox (badness 2035) in paragraph at lines 4857--4866 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 4857--4866 \T1/ptm/m/n/10 vided: \T1/fi4/bx/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/fi4/bx/n /10 "Bookman"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "Courier"\T1/ptm/m/n/10 , \T1/fi4 /bx/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "Helvetica-Narrow"\T1/ptm/ m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4857--4866 \T1/fi4/bx/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "Palatin o" \T1/ptm/m/n/10 and \T1/fi4/bx/n/10 "Times"\T1/ptm/m/n/10 ; \T1/fi4/bx/n/10 " URWGothic"\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 "URWBookman"\T1/ptm/m/n/10 , [717] Underfull \hbox (badness 6775) in paragraph at lines 4924--4932 \T1/ptm/m/n/10 can be found at [][]$\T1/fi4/bx/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Underfull \hbox (badness 3000) in paragraph at lines 4924--4932 \T1/ptm/m/n/10 Lunde's CJKV re-sources are at [][]$\T1/fi4/bx/n/10 ftp : / / ft p . oreilly . com / pub / examples / nutshell / cjkv / Underfull \hbox (badness 7344) in paragraph at lines 4943--4945 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso [718] [719] Underfull \hbox (badness 1546) in paragraph at lines 5063--5071 []\T1/ptm/m/n/10 arguments \T1/fi4/bx/n/10 onefile\T1/ptm/m/n/10 , \T1/fi4/bx/n /10 family\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 title\T1/ptm/m/n/10 , \T1/fi4/bx/n/1 0 fonts\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 encoding\T1/ptm/m/n/10 , \T1/fi4/bx/n/1 0 bg\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 fg\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 width\T 1/ptm/m/n/10 , [720] Underfull \hbox (badness 1648) in paragraph at lines 5140--5144 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [721] [722] [723] [724] [725] [726] [727] Underfull \hbox (badness 10000) in paragraph at lines 5558--5561 []\T1/fi4/bx/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (re d/green/blue) into HSV space [728] Underfull \vbox (badness 10000) has occurred while \output is active [729] [730] [731] [732] [733] Underfull \hbox (badness 1189) in paragraph at lines 5954--5956 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [734] Underfull \hbox (badness 10000) in paragraph at lines 6052--6054 []\T1/fi4/bx/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [735] [736] [737] [738] Underfull \hbox (badness 3780) in paragraph at lines 6343--6349 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/fi4/bx/n/ 10 "AvantGarde"\T1/ptm/m/n/10 , [739] [740] [741] Underfull \hbox (badness 2680) in paragraph at lines 6539--6541 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/fi4/bx/n/10 number[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [742] [743] [744]) (./graphics-pkg.tex Chapter 5. [745] [746] Underfull \hbox (badness 2856) in paragraph at lines 177--180 []\T1/ptm/m/n/10 For each \T1/fi4/bx/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn be-tween the point \T1/fi4/bx/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the poi nt [747] [748] [749] [750] [751] Underfull \hbox (badness 4492) in paragraph at lines 465--471 []\T1/ptm/m/n/10 When \T1/fi4/bx/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mar k lo-ca-tions are com-puted in-ter-nally (the same way [752] [753] [754] Underfull \hbox (badness 10000) in paragraph at lines 690--697 []\T1/fi4/bx/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/ ptm/m/n/10 in-ter-face to the C func-tion \T1/fi4/bx/n/10 CreateAtVector() \T1/ ptm/m/n/10 in [755] [756] [757] Underfull \hbox (badness 1389) in paragraph at lines 856--859 []\T1/ptm/m/n/10 logical. If \T1/fi4/bx/n/10 TRUE\T1/ptm/m/n/10 , the lines whi ch di-vide ad-ja-cent (non-stacked!) bars [758] Underfull \vbox (badness 10000) has occurred while \output is active [759] [760] [761] [762] [763] Underfull \hbox (badness 4634) in paragraph at lines 1253--1256 [][][]\T1/fi4/bx/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/fi4/bx/n/10 boxplot.formula[][][]\T1/ptm/m /n/10 , [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] Underfull \hbox (badness 1009) in paragraph at lines 2286--2293 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] Underfull \vbox (badness 10000) has occurred while \output is active [801] [802] [803] [804] Underfull \hbox (badness 1867) in paragraph at lines 3911--3915 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [805] [806] [807] [808] [809] [810] [811] Underfull \hbox (badness 1924) in paragraph at lines 4362--4367 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 2529) in paragraph at lines 4391--4394 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used: see [812] [813] [814] [815] [816] Underfull \hbox (badness 10000) in paragraph at lines 4735--4741 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/fi4/bx/ n/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4735--4741 \T1/fi4/bx/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/fi4/bx/n/10 par("cin")/par("pi n") \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that Underfull \hbox (badness 1072) in paragraph at lines 4735--4741 \T1/fi4/bx/n/10 c([][]strwidth[][][](ch), [][]strheight[][][](ch)) \T1/ptm/m/n/ 10 for a given string \T1/fi4/bx/n/10 ch \T1/ptm/m/n/10 is usu-ally much more p re- [817] [818] Underfull \hbox (badness 10000) in paragraph at lines 4865--4868 [819 ] Underfull \hbox (badness 10000) in paragraph at lines 4926--4928 [820 ] [821] Underfull \hbox (badness 10000) in paragraph at lines 5115--5117 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/fi4/bx/n/10 lty = 2:6\T1/ptm/m/n/10 ) cor-re-spond to [822] Underfull \vbox (badness 10000) has occurred while \output is active [823] [824] Underfull \hbox (badness 4156) in paragraph at lines 5271--5274 []\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/fi4/bx/n/10 z \T1/pt m/m/n/10 co-or-di-nates. Of-ten used with [825] [826] [827] [828] [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] [839] [840] [841] [842] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6520--6521 [][] [843 ] [844] Underfull \vbox (badness 10000) has occurred while \output is active [845] Overfull \hbox (9.78088pt too wide) in paragraph at lines 6679--6679 []\T1/fi4/m/n/9 TestChars(font = 5) # Euro might be at 160 (0+10*16). Mac OS has apple at 240 (0+15*16).[] [846] [847] [848] [849] [850] [851] [852] [853] Underfull \hbox (badness 1048) in paragraph at lines 7227--7232 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [854] [855] Underfull \hbox (badness 1540) in paragraph at lines 7343--7346 []\T1/ptm/m/n/10 For each \T1/fi4/bx/n/10 i\T1/ptm/m/n/10 , a line seg-ment is drawn be-tween the point \T1/fi4/bx/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the point [856] [857] [858] [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] Underfull \hbox (badness 2050) in paragraph at lines 8155--8159 []\T1/ptm/m/n/10 For \T1/fi4/bx/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/fi4/bx/n/10 pch\T1/ptm/m/n/10 ) is dra wn. For [869] [870] [871] [872] [873] (/usr/share/texmf/tex/latex/inconsolata/ts1fi4.fd ) [874] Underfull \hbox (badness 6691) in paragraph at lines 8555--8558 []\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex- pan-sion) Underfull \hbox (badness 2799) in paragraph at lines 8558--8560 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font and size \T1/fi4/bx/n/10 pa r("font.sub") \T1/ptm/m/n/10 and color [875]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8640 \HeaderA{units}{Graphical Units}{units} [876] [877] [878] [879]) (./grid-pkg.tex [880] Chapter 6. [881] [882] [883] [884] [885] [886] Underfull \hbox (badness 2680) in paragraph at lines 405--408 []\T1/ptm/m/n/10 Note that \T1/fi4/bx/n/10 preDrawDetails \T1/ptm/m/n/10 and \T 1/fi4/bx/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-t ion of [887] [888] [889] [890] [891] [892] [893] [894] [895] Underfull \hbox (badness 4279) in paragraph at lines 945--954 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/fi4/bx/n/10 pushViewport[][][]\T1/ptm/ m/n/10 , [][]\T1/fi4/bx/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n /10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 seekViewport[][][]\T 1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/fi4 /bx/n/10 unit[][][]\T1/ptm/m/n/10 , [896] [897] [898] Underfull \hbox (badness 2781) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 Both func-tions cre-ate an ar-rows grob (a graph-i-cal ob-ject de-scrib-ing ar-rows), but only [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948] Underfull \hbox (badness 1067) in paragraph at lines 4359--4362 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [949] [950] [951] [952] Underfull \hbox (badness 7256) in paragraph at lines 4598--4600 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] Underfull \hbox (badness 2096) in paragraph at lines 5805--5811 \T1/ptm/m/n/10 pos-si-ble to add and sub-tract unit ob-jects (e.g., \T1/fi4/bx/ n/10 unit(1, "npc") - unit(1, "inches")\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 5805--5811 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [971] [972] [973] [974] [975] [976] [977] Underfull \hbox (badness 7649) in paragraph at lines 6267--6270 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like [978] [979] [980] [981] [982]) (./methods-pkg.tex Chapter 7. [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] Underfull \hbox (badness 2237) in paragraph at lines 1432--1434 []\T1/ptm/m/n/10 The class \T1/fi4/bx/n/10 "className" \T1/ptm/m/n/10 ex-tends \T1/fi4/bx/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/fi4/bx/n/10 "pack age"\T1/ptm/m/n/10 , also of class [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] Underfull \hbox (badness 1590) in paragraph at lines 1979--1986 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/fi4/bx/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests Underfull \hbox (badness 10000) in paragraph at lines 2028--2033 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/fi4/bx/n/10 insertSource \T1/ptm/m/n/10 can be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 2028--2033 \T1/ptm/m/n/10 file name is passed to \T1/fi4/bx/n/10 insertSource \T1/ptm/m/n/ 10 it calls \T1/fi4/bx/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] Underfull \hbox (badness 10000) in paragraph at lines 2628--2631 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/fi4/bx/n/10 setGeneric[][][] \T1/ ptm/m/n/10 and [][]\T1/fi4/bx/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate ob-jects of class [1017] [1018] Underfull \hbox (badness 1132) in paragraph at lines 2768--2772 []\T1/ptm/m/n/10 In \T1/fi4/bx/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/fi4/bx/n /10 TRUE\T1/ptm/m/n/10 , the \T1/fi4/bx/n/10 package \T1/ptm/m/n/10 slot of the re-turned re-sult is in Underfull \hbox (badness 1033) in paragraph at lines 2800--2805 \T1/ptm/m/n/10 In ad-di-tion, \T1/fi4/bx/n/10 removeGeneric \T1/ptm/m/n/10 re-m oves the func-tion it-self; \T1/fi4/bx/n/10 removeMethods \T1/ptm/m/n/10 re-sto res the [1019] [1020] [1021] [1022] [1023] [1024] [1025] Underfull \hbox (badness 1102) in paragraph at lines 3308--3310 []\T1/fi4/bx/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string n ame of the pack-age (with-out the ex-tra-ne-ous [1026] [1027] [1028] [1029] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\T1/ptm/m/n/10 The \T1/fi4/bx/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3645--3654 []\T1/ptm/m/n/10 The [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] Underfull \hbox (badness 1436) in paragraph at lines 4550--4553 []\T1/ptm/m/n/10 The class \T1/fi4/bx/n/10 "SealedMethodDefinition" \T1/ptm/m/n /10 is cre-ated by a call to [][]\T1/fi4/bx/n/10 setMethod[][][] \T1/ptm/m/n/10 with ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4579--4585 []\T1/ptm/m/n/10 class [][]\T1/fi4/bx/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4579--4585 \T1/fi4/bx/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\ T1/fi4/bx/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1043] [1044] [1045] [1046] [1047] [1048] [1049] Underfull \vbox (badness 10000) has occurred while \output is active [1050] [1051] Underfull \hbox (badness 1092) in paragraph at lines 5251--5258 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 5251--5258 \T1/ptm/m/n/10 if se-lect-ing class \T1/fi4/bx/n/10 "track" \T1/ptm/m/n/10 for \T1/fi4/bx/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other me th-ods list and Underfull \hbox (badness 4036) in paragraph at lines 5299--5302 []\T1/ptm/m/n/10 Object of class \T1/fi4/bx/n/10 "PossibleMethod" \T1/ptm/m/n/1 0 the method to use in re-sponse to a [1052] [1053] [1054] [1055] [1056] Underfull \hbox (badness 1087) in paragraph at lines 5619--5624 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1057] [1058] [1059] Underfull \hbox (badness 2221) in paragraph at lines 5845--5850 []\T1/ptm/m/n/10 Two op-tional method names are in-ter-preted spe-cially, \T1/f i4/bx/n/10 initialize \T1/ptm/m/n/10 and [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069]pdfTeX war ning (ext4): destination with the same identifier (name{Rfn.S4}) has been alrea dy used, duplicate ignored \relax l.6701 \aliasA{S4}{S3Part}{S4} [1070] [1071] [1072]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.6977 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.6979 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.6980 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.6982 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.6983 \aliasA{Summary}{S4groupGeneric}{Summary} [1073] Underfull \hbox (badness 2050) in paragraph at lines 7044--7048 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1074] [1075] [1076] Underfull \hbox (badness 1286) in paragraph at lines 7227--7229 []\T1/ptm/m/n/10 for \T1/fi4/bx/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/fi4/bx/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-c ally [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] Underfull \vbox (badness 10000) has occurred while \output is active [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] Underfull \hbox (badness 2894) in paragraph at lines 9560--9564 []\T1/ptm/m/n/10 Chambers, John M. (2009) \T1/ptm/m/it/10 Class In-her-i-tance in R [][]$\T1/fi4/bx/n/10 http : / / stat . stanford . edu / ~jmc4 / [1107] Underfull \hbox (badness 1852) in paragraph at lines 9639--9643 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., [1108] [1109] [1110]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 15--17 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/fi4 /bx/n/10 "L'Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[][][]: see [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] Underfull \hbox (badness 3386) in paragraph at lines 1221--1224 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/fi4/bx/n/10 . Random.seed \T1/ptm/m/n/10 when the [1128] [1129] [1130]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/fi4/bx/n/10 \T1/ptm /m/n/10 and William N. Ven-ables [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143]) (./stats-pkg.tex [1144] Chapter 10. [1145] [1146] [1147] [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] Underfull \hbox (badness 1412) in paragraph at lines 832--834 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/fi4/bx/n/10 lm \T1/ptm/m/n/10 or \T1/fi4/bx/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1157] [1158] [1159] [1160] [1161] [1162] [1163] [1164] Underfull \hbox (badness 2503) in paragraph at lines 1320--1323 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/bx/n/10 "two.sided"\T1/ptm/m/n/10 , [1165] [1166] Underfull \hbox (badness 10000) in paragraph at lines 1499--1503 []\T1/ptm/m/n/10 An ob-ject of class \T1/fi4/bx/n/10 c("aov", "lm") \T1/ptm/m/n /10 or for mul-ti-ple re-sponses of class [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] Underfull \hbox (badness 3965) in paragraph at lines 2150--2152 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1177] [1178] [1179] [1180] [1181] Underfull \hbox (badness 3965) in paragraph at lines 2479--2481 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 2503) in paragraph at lines 3255--3258 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/bx/n/10 "two.sided"\T1/ptm/m/n/10 , [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] Underfull \hbox (badness 3989) in paragraph at lines 4477--4484 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] Underfull \hbox (badness 2932) in paragraph at lines 5092--5094 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/fi4/bx/n/10 x \T1/ptm/m/n/10 and \T1/fi4/bx/n/10 y \T1/ptm/m/n/10 i s given by [1221] [1222] [1223] Underfull \hbox (badness 1603) in paragraph at lines 5299--5304 []\T1/fi4/bx/n/10 var \T1/ptm/m/n/10 is just an-other in-ter-face to \T1/fi4/bx /n/10 cov\T1/ptm/m/n/10 , where \T1/fi4/bx/n/10 na.rm \T1/ptm/m/n/10 is used to de-ter-mine the de-fault for Underfull \hbox (badness 1472) in paragraph at lines 5299--5304 \T1/fi4/bx/n/10 use \T1/ptm/m/n/10 when that is un-spec-i-fied. If \T1/fi4/bx/n /10 na.rm \T1/ptm/m/n/10 is \T1/fi4/bx/n/10 TRUE \T1/ptm/m/n/10 then the com-pl ete ob-ser-va-tions (rows) Underfull \hbox (badness 3108) in paragraph at lines 5299--5304 \T1/ptm/m/n/10 are used (\T1/fi4/bx/n/10 use = "na.or.complete"\T1/ptm/m/n/10 ) to com-pute the vari-ance. Oth-er-wise, by de-fault Underfull \hbox (badness 1142) in paragraph at lines 5333--5345 \T1/ptm/m/n/10 For \T1/fi4/bx/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method i s un-usual but avail-able for the sake of com-plete-ness. [1224] [1225] Underfull \hbox (badness 2503) in paragraph at lines 5472--5476 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/bx/n/10 "two.sided"\T1/ptm/m/n/10 , [1226] Underfull \hbox (badness 1168) in paragraph at lines 5533--5538 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] Underfull \hbox (badness 8132) in paragraph at lines 5976--5981 \T1/ptm/m/n/10 then \T1/fi4/bx/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the s ame graph struc-ture as \T1/fi4/bx/n/10 x \T1/ptm/m/n/10 and for each node, [1235] [1236] [1237] Underfull \hbox (badness 7081) in paragraph at lines 6231--6234 []\T1/ptm/m/n/10 Objects of class \T1/fi4/bx/n/10 "hclust" \T1/ptm/m/n/10 can b e con-verted to class \T1/fi4/bx/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6235--6237 []\T1/fi4/bx/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gr am \T1/fi4/bx/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1238] [1239] [1240] [1241] [1242] Underfull \vbox (badness 10000) has occurred while \output is active [1243] [1244] [1245] [1246] [1247] [1248] [1249] Underfull \hbox (badness 10000) in paragraph at lines 7035--7038 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/fi4/bx/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1250] [1251] Underfull \hbox (badness 10000) in paragraph at lines 7172--7175 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/fi4/bx/n/10 h ttp : / / cran . r-[]project . org / web / views / [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] Underfull \hbox (badness 2626) in paragraph at lines 8625--8628 []\T1/ptm/m/n/10 Either \T1/fi4/bx/n/10 "convolution" \T1/ptm/m/n/10 or \T1/fi4 /bx/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1274] [1275] Underfull \hbox (badness 2503) in paragraph at lines 8725--8729 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/bx/n/10 "two.sided"\T1/ptm/m/n/10 , [1276] [1277] [1278] [1279] [1280] Overfull \hbox (11.88992pt too wide) in paragraph at lines 9059--9061 []\T1/ptm/m/n/10 the char-ac-ter string \T1/fi4/bx/n/10 "Fligner-Killeen test o f homogeneity of variances"\T1/ptm/m/n/10 . [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] Underfull \hbox (badness 1019) in paragraph at lines 9725--9728 []\T1/ptm/m/n/10 See also [][]$\T1/fi4/bx/n/10 http : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [][]$\T1/fi4/bx/ n/10 http : / / dlmf . [1290] [1291] [1292] [1293] Underfull \hbox (badness 4518) in paragraph at lines 9986--9991 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1294] [1295] [1296] [1297] [1298] Underfull \hbox (badness 2142) in paragraph at lines 10327--10330 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10346--10349 []\T1/ptm/m/n/10 When \T1/fi4/bx/n/10 trace \T1/ptm/m/n/10 is true, calls to [] []\T1/fi4/bx/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS i t-er-a-tion. Hence, [1299] Underfull \hbox (badness 1708) in paragraph at lines 10408--10411 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1300] [1301] [1302] [1303] [1304] Underfull \hbox (badness 1694) in paragraph at lines 10772--10775 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 10791--10800 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1305] [1306] [1307] [1308] [1309] [1310] [1311]pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.hat}) has been already used, duplicate i gnored \relax l.11238 \aliasA{hat}{influence.measures}{hat} [1312] [1313] Underfull \hbox (badness 1484) in paragraph at lines 11362--11364 []\T1/ptm/m/n/10 The func-tion \T1/fi4/bx/n/10 hat() \T1/ptm/m/n/10 ex-ists mai nly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 4441) in paragraph at lines 11909--11911 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] Underfull \hbox (badness 4518) in paragraph at lines 12869--12874 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] Underfull \hbox (badness 4518) in paragraph at lines 13487--13492 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] Overfull \hbox (5.6622pt too wide) in paragraph at lines 14053--14055 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/fi4/bx/n/10 -plnorm(t, r, lower = FALSE, log = TRUE)\T1/ptm/m/n/10 . [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] Underfull \hbox (badness 2503) in paragraph at lines 14682--14686 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/bx/n/10 "two.sided"\T1/ptm/m/n/10 , [1364] [1365] Underfull \vbox (badness 10000) has occurred while \output is active [1366] [1367] [1368] [1369] [1370] [1371] Underfull \hbox (badness 3009) in paragraph at lines 15190--15196 []\T1/fi4/bx/n/10 model.offset \T1/ptm/m/n/10 and \T1/fi4/bx/n/10 model.respons e \T1/ptm/m/n/10 are equiv-a-lent to \T1/fi4/bx/n/10 model.extract(, "offset") \T1/ptm/m/n/10 and [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] Underfull \hbox (badness 2359) in paragraph at lines 16811--16813 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1396] Underfull \vbox (badness 10000) has occurred while \output is active [1397] Underfull \vbox (badness 10000) has occurred while \output is active [1398] [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] Underfull \hbox (badness 1377) in paragraph at lines 17713--17718 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 17718--17721 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 2343) in paragraph at lines 17731--17735 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 2080) in paragraph at lines 17731--17735 \T1/ptm/m/n/10 the value by a fac-tor of \T1/fi4/bx/n/10 reltol * (abs(val) + r eltol) \T1/ptm/m/n/10 at a step. De-faults to [1410] Underfull \hbox (badness 2662) in paragraph at lines 17739--17743 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/fi4/bx/n/10 "BFGS"\T1/p tm/m/n/10 , \T1/fi4/bx/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/fi4/bx/n/10 "SANN " \T1/ptm/m/n/10 meth-ods if [1411] [1412] Underfull \vbox (badness 10000) has occurred while \output is active [1413] [1414] [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 1337) in paragraph at lines 18355--18358 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] Underfull \hbox (badness 5563) in paragraph at lines 19082--19084 []\T1/ptm/m/n/10 logical. If \T1/fi4/bx/n/10 TRUE\T1/ptm/m/n/10 , add to al-rea dy ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19085--19088 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1432] [1433] [1434] [1435] [1436] Underfull \hbox (badness 1675) in paragraph at lines 19372--19375 []\T1/ptm/m/n/10 Setting \T1/fi4/bx/n/10 lower.tail = FALSE \T1/ptm/m/n/10 al-l ows to get much more pre-cise re-sults when the de-fault, [1437] Underfull \hbox (badness 2503) in paragraph at lines 19457--19460 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/fi4/bx/n/10 "two.sided"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 19484--19486 []\T1/ptm/m/n/10 the char-ac-ter string \T1/fi4/bx/n/10 "Exact Poisson test" \T 1/ptm/m/n/10 or [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] Underfull \hbox (badness 10000) in paragraph at lines 20454--20460 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/fi4/bx/n/10 predict.ar[] [][]\T1/ptm/m/n/10 , [][]\T1/fi4/bx/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [] []\T1/fi4/bx/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] Underfull \hbox (badness 2111) in paragraph at lines 21422--21427 []\T1/ptm/m/n/10 Utility func-tion to be used in higher-level [][]\T1/fi4/bx/n/ 10 print[][][] \T1/ptm/m/n/10 meth-ods, such as [][]\T1/fi4/bx/n/10 print.summa ry.lm[][][]\T1/ptm/m/n/10 , [1469] [1470] [1471] [1472] [1473] Underfull \hbox (badness 1337) in paragraph at lines 21761--21767 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] Underfull \hbox (badness 10000) in paragraph at lines 22554--22557 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 1675) in paragraph at lines 22554--22557 \T1/fi4/bx/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied fo r ef-fi-ciency if al-ready [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] Underfull \hbox (badness 10000) in paragraph at lines 23130--23133 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/fi4/bx/n/10 y = ru nmed(x, k) \T1/ptm/m/n/10 sim-ply has [1494] Underfull \hbox (badness 3690) in paragraph at lines 23181--23185 [][][]\T1/fi4/bx/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey' s end point rule and is called by de-fault from Underfull \hbox (badness 1062) in paragraph at lines 23181--23185 \T1/fi4/bx/n/10 runmed(*, endrule = "median")\T1/ptm/m/n/10 . [][]\T1/fi4/bx/n/ 10 smooth[][][] \T1/ptm/m/n/10 uses run-ning me-di-ans of 3 for its com-pound [1495] [1496] [1497] [1498] Underfull \hbox (badness 7667) in paragraph at lines 23447--23449 []\T1/ptm/m/n/10 a nu-meric vec-tor or an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-je ct which is co-ercible to one by [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] Underfull \vbox (badness 10000) has occurred while \output is active [1525] Underfull \hbox (badness 3514) in paragraph at lines 25197--25202 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1526] Underfull \hbox (badness 3514) in paragraph at lines 25259--25264 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1527] Underfull \hbox (badness 3514) in paragraph at lines 25316--25321 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1528] Underfull \hbox (badness 3514) in paragraph at lines 25377--25383 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1529] [1530] [1531] Underfull \hbox (badness 3514) in paragraph at lines 25572--25577 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1532] Underfull \hbox (badness 3514) in paragraph at lines 25628--25633 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1533] Underfull \hbox (badness 3514) in paragraph at lines 25685--25690 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1534] Underfull \hbox (badness 3514) in paragraph at lines 25740--25745 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 input \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1535] Underfull \hbox (badness 6691) in paragraph at lines 25809--25814 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/fi4/bx/n/10 x\T1/ ptm/m/n/10 . It is the value of the ex-pres-sion [1536] [1537] [1538] [1539] [1540] [1541] [1542] Underfull \hbox (badness 10000) in paragraph at lines 26279--26282 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 26279--26282 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/fi4/bx/n/10 NULL\T1/ptm/m /n/10 , the de-fault, [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] Underfull \hbox (badness 5431) in paragraph at lines 26885--26887 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/f i4/bx/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1553] [1554] [1555] Underfull \hbox (badness 5431) in paragraph at lines 27095--27098 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/f i4/bx/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1556] [1557] [1558] [1559] [1560] Underfull \hbox (badness 1337) in paragraph at lines 27406--27410 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1561] [1562] Underfull \hbox (badness 10000) in paragraph at lines 27523--27526 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/fi4/bx/n/10 rt()\T1/ptm/m/n/10 , only for [1563] [1564] [1565] Underfull \hbox (badness 1616) in paragraph at lines 27706--27709 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] Underfull \hbox (badness 1337) in paragraph at lines 29085--29089 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] Underfull \hbox (badness 1337) in paragraph at lines 29569--29573 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1595] Underfull \hbox (badness 5161) in paragraph at lines 29662--29664 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1596] [1597] [1598] [1599] [1600] Underfull \hbox (badness 10000) in paragraph at lines 30026--30031 []\T1/ptm/m/n/10 There is a \T1/fi4/bx/n/10 summary \T1/ptm/m/n/10 method for c on-tin-gency ta-ble ob-jects cre-ated by \T1/fi4/bx/n/10 table \T1/ptm/m/n/10 o r Underfull \hbox (badness 3209) in paragraph at lines 30026--30031 \T1/fi4/bx/n/10 xtabs(*, sparse = FALSE)\T1/ptm/m/n/10 , which gives ba-sic in- for-ma-tion and per-forms a chi-squared [1601] [1602] [1603]) (./stats4-pkg.tex [1604] Chapter 11. [1605] [1606] [1607] [1608] [1609] [1610]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1611] [1612] [1613]) (./tcltk-pkg.tex [1614] Chapter 12. [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \vbox (badness 10000) has occurred while \output is active [1622] Underfull \hbox (badness 1546) in paragraph at lines 649--656 []\T1/fi4/bx/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-in g any Tk or Tcl com-mand by sim-ply run-ning [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] Underfull \hbox (badness 3375) in paragraph at lines 1391--1394 [][][]\T1/fi4/bx/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the OS X GUI), [][]\T1/fi4/bx/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1634]) (./tools-pkg.tex Chapter 13. [1635] LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined (Font) using `T1/fi4/m/n' instead on input line 72. [1636] Underfull \hbox (badness 1308) in paragraph at lines 173--186 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 types Underfull \hbox (badness 4967) in paragraph at lines 173--186 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/fi4/bx/n/10 bib entry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 173--186 \T1/fi4/bx/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 formatInProc eedings\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 formatManual\T1/ptm/m/n/10 , \T1/fi4/bx /n/10 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 173--186 \T1/fi4/bx/n/10 formatMisc\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 formatPhdthesis\T1/p tm/m/n/10 , \T1/fi4/bx/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/fi4/bx/n/10 f ormatTechreport \T1/ptm/m/n/10 and [1637] [1638] [1639] Underfull \hbox (badness 2080) in paragraph at lines 333--338 \T1/ptm/m/n/10 ac-ters. It is sorted by Uni-code point and within a point al-ph a-bet-i-cally on the glyph Underfull \hbox (badness 2644) in paragraph at lines 333--338 \T1/ptm/m/n/10 (there can be more than one name for a Uni-code point). The data are in the file [1640] [1641] [1642] [1643] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1644] [1645] [1646] [1647] Underfull \hbox (badness 1635) in paragraph at lines 851--853 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1648] Underfull \hbox (badness 4441) in paragraph at lines 925--933 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- Underfull \hbox (badness 1014) in paragraph at lines 945--947 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies [1649] Underfull \hbox (badness 10000) in paragraph at lines 968--971 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 968--971 \T1/fi4/bx/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/ fi4/bx/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1650] [1651] Underfull \hbox (badness 10000) in paragraph at lines 1096--1098 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1652] [1653] Underfull \hbox (badness 7981) in paragraph at lines 1263--1267 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1263--1267 \T1/fi4/bx/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1 /ptm/m/n/10 . Underfull \hbox (badness 1082) in paragraph at lines 1269--1271 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/fi4/bx/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1654] [1655] [1656] [1657] Underfull \hbox (badness 5726) in paragraph at lines 1532--1537 []\T1/ptm/m/n/10 If \T1/fi4/bx/n/10 reduce \T1/ptm/m/n/10 is \T1/fi4/bx/n/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/fi4/bx/n/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 1532--1537 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1658] [1659] [1660] [1661] [1662] Underfull \hbox (badness 7981) in paragraph at lines 1848--1854 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1848--1854 \T1/fi4/bx/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1 /ptm/m/n/10 . [1663] [1664] [1665] [1666] LaTeX Font Warning: Font shape `T1/fi4/m/sl' undefined (Font) using `T1/fi4/m/n' instead on input line 2102. [1667] [1668] [1669] Underfull \hbox (badness 1424) in paragraph at lines 2338--2340 []\T1/fi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1670] [1671] [1672] [1673] [1674] [1675] [1676] Underfull \hbox (badness 1675) in paragraph at lines 2852--2854 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing how the news en-tries shoul d be \T1/ptm/m/it/10 chopped\T1/ptm/m/n/10 ; [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] Underfull \hbox (badness 1838) in paragraph at lines 3427--3433 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/fi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/fi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 3427--3433 \T1/ptm/m/n/10 `\T1/fi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1686] Underfull \hbox (badness 5726) in paragraph at lines 3507--3512 []\T1/ptm/m/n/10 If \T1/fi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/fi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/fi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 3507--3512 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1687] [1688] Underfull \hbox (badness 1688) in paragraph at lines 3645--3657 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/fi4/m/sl/10 PACKAGES\T1/ptm/m/n/10 ' and [1689] [1690] [1691] [1692]) (./utils-pkg.tex Chapter 14. Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/fi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1693] [1694] [1695] Underfull \hbox (badness 1454) in paragraph at lines 198--201 []\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive , \T1/fi4/m/sl/10 TRUE \T1/ptm/m/n/10 by de- Underfull \hbox (badness 1540) in paragraph at lines 214--217 []\T1/fi4/m/sl/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for the same task as \T1/fi4/m/sl/10 apropos\T1/ptm/m/n/10 . How-ever, by de-fault [1696] [1697] [1698] [1699] [1700] Underfull \hbox (badness 10000) in paragraph at lines 539--545 []\T1/ptm/m/n/10 Functions \T1/fi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/fi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 539--545 \T1/fi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/fi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1701] [1702] Underfull \hbox (badness 5847) in paragraph at lines 650--656 []\T1/ptm/m/n/10 Argument \T1/fi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 650--656 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/fi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as Underfull \hbox (badness 3861) in paragraph at lines 715--720 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/fi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/fi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] Underfull \hbox (badness 1371) in paragraph at lines 1288--1290 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/fi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/fi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1712] [1713] [1714] [1715] Underfull \hbox (badness 2057) in paragraph at lines 1560--1562 []\T1/ptm/m/n/10 None for \T1/fi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1716] [1717] Underfull \hbox (badness 5189) in paragraph at lines 1745--1747 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1718] [1719] [1720] Underfull \hbox (badness 1661) in paragraph at lines 1960--1967 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/fi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- [1721] Underfull \hbox (badness 1990) in paragraph at lines 1972--1975 []\T1/ptm/m/n/10 a [][]\T1/fi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/fi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/fi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1722] [1723] [1724] [1725] [1726] Overfull \hbox (6.10922pt too wide) in paragraph at lines 2363--2366 []\T1/ptm/m/n/10 files end-ing `\T1/fi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/fi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/fi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";")\T1/ptm/m/n/10 , [1727] [1728] [1729] [1730] [1731] [1732] [1733] [1734] Underfull \hbox (badness 1430) in paragraph at lines 2936--2942 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/fi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 2837) in paragraph at lines 2936--2942 \T1/fi4/m/sl/10 internet.info \T1/ptm/m/n/10 op-tion. The de-tails de-pend on t he plat-form and scheme, but set-ting [1735] Underfull \hbox (badness 1231) in paragraph at lines 2980--2986 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1736] [1737] [1738] [1739] [1740] [1741] Underfull \hbox (badness 1210) in paragraph at lines 3360--3367 []\T1/ptm/m/n/10 logical or ex-pres-sion; if not \T1/fi4/m/sl/10 FALSE\T1/ptm/m /n/10 , the ran-dom num-ber gen-er-a-tor state [1742] [1743] [1744] [1745] [1746]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.3743 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.3743 ...mat Unordered and Ordered Lists}{format} [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] Underfull \hbox (badness 1371) in paragraph at lines 4648--4650 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/fi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/fi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1761] [1762] Underfull \hbox (badness 1502) in paragraph at lines 4737--4742 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 4737--4742 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1763] [1764] Underfull \hbox (badness 10000) in paragraph at lines 4901--4910 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1765] [1766] Underfull \hbox (badness 3118) in paragraph at lines 5017--5019 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [1767] Underfull \hbox (badness 2057) in paragraph at lines 5099--5105 \T1/ptm/m/n/10 can be source archives or bi-nary pack-age archive files (as cre -ated by Underfull \hbox (badness 1348) in paragraph at lines 5145--5150 []\T1/ptm/m/n/10 logical in-di-cat-ing to also in-stall unin-stalled pack-ages which these pack- Underfull \hbox (badness 3884) in paragraph at lines 5145--5150 \T1/ptm/m/n/10 ages de-pend on/link to/import/suggest (and so on re-cur-sively) . Not Underfull \hbox (badness 3657) in paragraph at lines 5145--5150 \T1/ptm/m/n/10 used if \T1/fi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be a char-ac-ter vec-tor, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 5158--5165 []\T1/fi4/m/sl/10 TRUE \T1/ptm/m/n/10 means (as from \T1/phv/m/n/10 R \T1/ptm/m /n/10 2.15.0) to use Underfull \hbox (badness 10000) in paragraph at lines 5158--5165 \T1/fi4/m/sl/10 c("Depends", "Imports", "LinkingTo", "Suggests") \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 pkgs \T1/ptm/m/n/10 and Underfull \hbox (badness 2103) in paragraph at lines 5158--5165 \T1/fi4/m/sl/10 c("Depends", "Imports", "LinkingTo") \T1/ptm/m/n/10 for added d e-pen-den-cies: this [1768] Underfull \hbox (badness 10000) in paragraph at lines 5200--5203 []\T1/ptm/m/n/10 (not used on Win-dows) anal-o-gous to \T1/fi4/m/sl/10 configur e.args \T1/ptm/m/n/10 for flag Underfull \hbox (badness 10000) in paragraph at lines 5226--5229 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 5226--5229 \T1/ptm/m/n/10 passed to \T1/fi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou rce pack-age in-stall. E.g., [1769] [1770] Underfull \hbox (badness 10000) in paragraph at lines 5356--5361 [][][]\T1/fi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] [1787] Underfull \hbox (badness 10000) in paragraph at lines 6480--6482 []\T1/fi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 6485--6490 []\T1/ptm/m/n/10 If a `\T1/fi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [1788] [1789] [1790] Underfull \hbox (badness 10000) in paragraph at lines 6642--6645 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 6642--6645 [][]\T1/fi4/m/sl/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/fi4/m/sl/1 0 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els [1791] [1792] [1793] [1794] [1795] Underfull \hbox (badness 1789) in paragraph at lines 7023--7025 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] Underfull \hbox (badness 1097) in paragraph at lines 7822--7825 []\T1/ptm/m/n/10 The name \T1/fi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [1807] [1808] Underfull \hbox (badness 3000) in paragraph at lines 7950--7955 [][][]\T1/fi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/fi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [1809] [1810] [1811] [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 2134) in paragraph at lines 8512--8517 [][][]\T1/fi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/fi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [1817] [1818] [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] Underfull \hbox (badness 10000) in paragraph at lines 9455--9457 [][][]$\T1/fi4/m/sl/10 http : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/fi4/m/sl/10 http : / / www . gnu . org / software / emacs / [1831] [1832] [1833] Underfull \hbox (badness 10000) in paragraph at lines 9633--9637 []\T1/ptm/m/n/10 The de-fault for \T1/fi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 9664--9670 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [1834] Underfull \hbox (badness 2096) in paragraph at lines 9778--9781 []\T1/ptm/m/n/10 logical (\T1/fi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 9782--9785 []\T1/ptm/m/n/10 logical (\T1/fi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [1835] Underfull \hbox (badness 1009) in paragraph at lines 9849--9860 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [1836] [1837] [1838] [1839] [1840] Underfull \hbox (badness 2635) in paragraph at lines 10150--10153 []\T1/ptm/m/n/10 Repository `\T1/fi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [1841] [1842] [1843] [1844] [1845] Underfull \hbox (badness 5970) in paragraph at lines 10514--10517 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 3449) in paragraph at lines 10525--10534 []\T1/ptm/m/n/10 string in-di-cat-ing if the \T1/fi4/m/sl/10 width \T1/ptm/m/n/ 10 ar-gu-ment's spec-i-fi-ca-tion should be fol- Underfull \hbox (badness 7379) in paragraph at lines 10525--10534 \T1/ptm/m/n/10 lowed strictly, one of the val-ues \T1/fi4/m/sl/10 c("no", "cut" , "wrap")\T1/ptm/m/n/10 . De- Underfull \hbox (badness 1824) in paragraph at lines 10525--10534 \T1/ptm/m/n/10 faults to the \T1/fi4/m/sl/10 strict.width \T1/ptm/m/n/10 com-po -nent of op-tion \T1/fi4/m/sl/10 "str" \T1/ptm/m/n/10 (see [][]\T1/fi4/m/sl/10 options[][][]\T1/ptm/m/n/10 ) Underfull \hbox (badness 3769) in paragraph at lines 10525--10534 \T1/ptm/m/n/10 which de-faults to \T1/fi4/m/sl/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons; \T1/fi4/m/sl/10 "wrap" \T1/ptm/m/n/10 uses [1846] [1847] [1848] Underfull \hbox (badness 10000) in paragraph at lines 10693--10695 []\T1/ptm/m/n/10 Options other than \T1/fi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [1849] [1850] Underfull \hbox (badness 2213) in paragraph at lines 10847--10854 []\T1/ptm/m/n/10 If \T1/fi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, Underfull \hbox (badness 1688) in paragraph at lines 10847--10854 \T1/ptm/m/n/10 and se-lected if their \T1/fi4/m/sl/10 extension \T1/ptm/m/n/10 com-po-nent matches (as a reg-exp) the file name. Ob- [1851] [1852] [1853] Underfull \hbox (badness 10000) in paragraph at lines 11088--11091 [][][]$\T1/fi4/m/sl/10 http : / / en . wikipedia . org / wiki / Tar _ (file _ f ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/fi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 11088--11091 \T1/fi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [1854] [1855] [1856] [1857] [1858] [1859] [1860] [1861] Underfull \hbox (badness 10000) in paragraph at lines 11593--11595 []\T1/ptm/m/n/10 Arguments such as \T1/fi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/fi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 1052) in paragraph at lines 11596--11598 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 11626--11631 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined Underfull \hbox (badness 10000) in paragraph at lines 11626--11631 \T1/ptm/m/n/10 see [][]\T1/fi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/fi4/m/sl/10 available = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 6961) in paragraph at lines 11626--11631 \T1/fi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by de- [1862] Underfull \hbox (badness 10000) in paragraph at lines 11655--11658 [][][]\T1/fi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [1863] Underfull \hbox (badness 10000) in paragraph at lines 11733--11738 []\T1/ptm/m/n/10 Characters in a URL other than the En-glish al-phanu-meric cha r-ac-ters and [1864] [1865] [1866] [1867] Underfull \hbox (badness 1454) in paragraph at lines 11960--11964 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [1868] Underfull \hbox (badness 10000) in paragraph at lines 12030--12032 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion e.g. [1869] [1870] [1871]) [1872] [1873] [1874] (./KernSmooth-pkg.tex Chapter 15. [1875] [1876] [1877] [1878] [1879] [1880] [1881] [1882] [1883] [1884]) (./MASS-pkg.tex Chapter 16. [1885] [1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901] [1902] [1903] [1904] [1905] [1906] Underfull \hbox (badness 7256) in paragraph at lines 1601--1603 []\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo r [1907] [1908] [1909] [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917] [1918] [1919] [1920] [1921] Underfull \hbox (badness 7944) in paragraph at lines 2691--2694 []\T1/ptm/m/n/10 further ar-gu-ments for \T1/fi4/m/sl/10 plot \T1/ptm/m/n/10 an d graph-i-cal pa-ram-e-ters. Note that [1922] [1923] [1924] Underfull \hbox (badness 2384) in paragraph at lines 2861--2866 []\T1/ptm/m/n/10 Distributions \T1/fi4/m/sl/10 "beta"\T1/ptm/m/n/10 , \T1/fi4/m /sl/10 "cauchy"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "chi-squared"\T1/ptm/m/n/10 , \ T1/fi4/m/sl/10 "exponential"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "f"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2861--2866 \T1/fi4/m/sl/10 "gamma"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "geometric"\T1/ptm/m/n/ 10 , \T1/fi4/m/sl/10 "log-normal"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "lognormal"\T 1/ptm/m/n/10 , \T1/fi4/m/sl/10 "logistic"\T1/ptm/m/n/10 , Underfull \hbox (badness 2293) in paragraph at lines 2861--2866 \T1/fi4/m/sl/10 "negative binomial"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "normal"\T1 /ptm/m/n/10 , \T1/fi4/m/sl/10 "Poisson"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "t" \T1 /ptm/m/n/10 and \T1/fi4/m/sl/10 "weibull" \T1/ptm/m/n/10 are [1925] [1926] Underfull \hbox (badness 4686) in paragraph at lines 3029--3031 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds Underfull \hbox (badness 2591) in paragraph at lines 3043--3047 []\T1/ptm/m/n/10 where \T1/fi4/m/sl/10 p1\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 p2\T1 /ptm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/fi4/m /sl/10 cycles \T1/ptm/m/n/10 terms or when a [1927] [1928] [1929] Underfull \hbox (badness 10000) in paragraph at lines 3231--3233 []\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/fi4/m/sl/10 Gamma \T1/ptm/m/n/ 10 fam-ily or \T1/fi4/m/sl/10 quasi \T1/ptm/m/n/10 fam-ily with [1930] [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] Underfull \hbox (badness 10000) in paragraph at lines 4800--4803 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm Underfull \hbox (badness 1173) in paragraph at lines 4800--4803 \T1/fi4/m/sl/10 response ~ predictors\T1/ptm/m/n/10 . See the doc-u-men-ta-tion of \T1/fi4/m/sl/10 formula \T1/ptm/m/n/10 for other [1952] Underfull \hbox (badness 10000) in paragraph at lines 4878--4881 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm Underfull \hbox (badness 1173) in paragraph at lines 4878--4881 \T1/fi4/m/sl/10 response ~ predictors\T1/ptm/m/n/10 . See the doc-u-men-ta-tion of \T1/fi4/m/sl/10 formula \T1/ptm/m/n/10 for other [1953] [1954] [1955] [1956] [1957] [1958] Underfull \hbox (badness 1975) in paragraph at lines 5355--5357 []\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in the case of [1959] [1960] [1961] [1962] [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970] [1971] [1972] [1973] [1974] Underfull \vbox (badness 10000) has occurred while \output is active [1975] [1976] [1977] [1978] [1979] [1980] [1981] [1982] Underfull \hbox (badness 10000) in paragraph at lines 7103--7110 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm Underfull \hbox (badness 1540) in paragraph at lines 7103--7110 \T1/fi4/m/sl/10 response ~ predictors\T1/ptm/m/n/10 . The re-sponse should be a fac-tor (prefer-ably [1983] [1984] [1985] [1986] Underfull \hbox (badness 6775) in paragraph at lines 7341--7344 \T1/ptm/m/n/10 only the first \T1/fi4/m/sl/10 dimen \T1/ptm/m/n/10 dis-crim-i-n ant com-po-nents are used (ex-cept for [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] Underfull \hbox (badness 4686) in paragraph at lines 7974--7976 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [1995] Underfull \hbox (badness 2591) in paragraph at lines 7990--7994 []\T1/ptm/m/n/10 where \T1/fi4/m/sl/10 p1\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 p2\T1 /ptm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/fi4/m /sl/10 cycles \T1/ptm/m/n/10 terms or when a [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014] Underfull \hbox (badness 1259) in paragraph at lines 9376--9378 []\T1/ptm/m/n/10 if \T1/fi4/m/sl/10 TRUE \T1/ptm/m/n/10 re-turn ob-served and e x-pected fre-quen-cies in the re-sult. Us-ing [2015] [2016] [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032]) (./Matrix-pkg.tex Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 42--45 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 42--45 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2033] Underfull \hbox (badness 1769) in paragraph at lines 96--99 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2034] [2035] [2036] [2037] Underfull \hbox (badness 5119) in paragraph at lines 502--506 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class [2038] [2039] Underfull \hbox (badness 2418) in paragraph at lines 589--592 []\T1/ptm/m/n/10 The value of \T1/fi4/m/sl/10 bdiag() \T1/ptm/m/n/10 in-heris f rom class [][]\T1/fi4/m/sl/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , whereas \T1/f i4/m/sl/10 .bdiag() \T1/ptm/m/n/10 re-turns a [2040] [2041] Underfull \hbox (badness 10000) in paragraph at lines 731--734 []\T1/ptm/m/n/10 In some ver-sions of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , [][]\T1/ fi4/m/sl/10 eigen[][][](CAex) \T1/ptm/m/n/10 fell into an in-fi-nite loop (wher eas [2042] [2043] [2044] Underfull \hbox (badness 10000) in paragraph at lines 997--999 []\T1/fi4/m/sl/10 signature(a = "CHMfactor", b = "numeric") \T1/ptm/m/n/10 call the above [2045]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho l}) has been already used, duplicate ignored \relax l.1072 ...composition - 'Matrix' S4 Generic}{chol} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic ate ignored \relax l.1072 ...composition - 'Matrix' S4 Generic}{chol} [2046pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha s been already used, duplicate ignored \endgroup \set@typeset@protect l.1140 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.ch ol,lsCMatrix.Rdash.method}) has been already used, duplicate ignored \endgroup \set@typeset@protect l.1140 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.ch ol,nsCMatrix.Rdash.method}) has been already used, duplicate ignored \endgroup \set@typeset@protect l.1140 ] [2047] Underfull \hbox (badness 2277) in paragraph at lines 1286--1289 []\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer -ent types of ma-tri-ces. Use [2048] Underfull \hbox (badness 5741) in paragraph at lines 1322--1326 []\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/fi4/m/sl/10 CHMfactor[][][] \T1/p tm/m/n/10 and [][]\T1/fi4/m/sl/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion [][]\T1/fi4/m/sl/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra [2049] Underfull \hbox (badness 10000) in paragraph at lines 1416--1423 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/fi4/m/sl/10 n ew("Cholesky", ...) \T1/ptm/m/n/10 or [2050] Underfull \hbox (badness 1097) in paragraph at lines 1445--1448 []\T1/ptm/m/n/10 Class \T1/fi4/m/sl/10 "MatrixFactorization" \T1/ptm/m/n/10 and \T1/fi4/m/sl/10 "dtrMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/fi4/m/sl/10 " dgeMatrix"\T1/ptm/m/n/10 , by class Underfull \hbox (badness 1783) in paragraph at lines 1451--1455 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend [2051]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col Sums}) has been already used, duplicate ignored \relax l.1508 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup licate ignored \relax l.1508 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl icate ignored \relax l.1509 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i gnored \relax l.1530 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig nored \relax l.1541 \aliasA{rowSums}{colSums}{rowSums} [2052] [2053] [2054] [2055] Overfull \hbox (19.92062pt too wide) in paragraph at lines 1843--1844 []\T1/fi4/m/sl/10 signature(x = "CsparseMatrix", i = "index", j = "missing", va lue = "replValue")\T1/ptm/m/n/10 : Overfull \hbox (9.92062pt too wide) in paragraph at lines 1844--1845 []\T1/fi4/m/sl/10 signature(x = "CsparseMatrix", i = "index", j = "index", valu e = "replValue")\T1/ptm/m/n/10 : Overfull \hbox (19.92062pt too wide) in paragraph at lines 1845--1846 []\T1/fi4/m/sl/10 signature(x = "CsparseMatrix", i = "missing", j = "index", va lue = "replValue")\T1/ptm/m/n/10 : [2056] Underfull \hbox (badness 4543) in paragraph at lines 1963--1965 []\T1/ptm/m/n/10 Use [][]\T1/fi4/m/sl/10 showMethods[][][](class = "ddenseMatri x", where = "package:Matrix") \T1/ptm/m/n/10 for an [2057] [2058] Underfull \hbox (badness 10000) in paragraph at lines 2085--2087 []\T1/ptm/m/n/10 Use [][]\T1/fi4/m/sl/10 showMethods[][][](class = "denseMatrix ", where = "package:Matrix") \T1/ptm/m/n/10 for an [2059] Underfull \hbox (badness 10000) in paragraph at lines 2179--2181 []\T1/fi4/m/sl/10 signature(x = "dgCMatrix", y = "missing") \T1/ptm/m/n/10 re-t urns \T1/fi4/m/sl/10 t(x) %*% x \T1/ptm/m/n/10 as an [2060] [2061] [2062] Underfull \hbox (badness 10000) in paragraph at lines 2474--2476 []\T1/fi4/m/sl/10 signature(x = "dgTMatrix", y = "missing") \T1/ptm/m/n/10 re-t urns \T1/fi4/m/sl/10 t(x) %*% x \T1/ptm/m/n/10 as an [2063] Underfull \hbox (badness 6842) in paragraph at lines 2563--2566 []\T1/fi4/m/sl/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T 1/fi4/m/sl/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/fi4/m/sl/10 ldiMatrix[] [][] \T1/ptm/m/n/10 (with ``su-per-class'' [2064] [2065] Underfull \hbox (badness 10000) in paragraph at lines 2882--2884 []\T1/fi4/m/sl/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equi v-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2066] [2067] [2068] Underfull \hbox (badness 10000) in paragraph at lines 3142--3144 [][][]\T1/fi4/m/sl/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pr efer-able to (and more ef-fi-cient than) [2069] [2070] [2071] Underfull \hbox (badness 10000) in paragraph at lines 3432--3435 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/fi4/m/sl/10 n ew("dsCMatrix", ...) \T1/ptm/m/n/10 or [2072] [2073] [2074] [2075] [2076] Underfull \hbox (badness 2318) in paragraph at lines 3882--3886 []\T1/ptm/m/n/10 Class \T1/fi4/m/sl/10 "dgCMatrix"\T1/ptm/m/n/10 , di-rectly. C lass \T1/fi4/m/sl/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/fi 4/m/sl/10 "dMatrix"\T1/ptm/m/n/10 , [2077] [2078] [2079] [2080] Underfull \hbox (badness 10000) in paragraph at lines 4194--4199 []\T1/fi4/m/sl/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and o ther sig-na-tures (use Underfull \hbox (badness 4254) in paragraph at lines 4194--4199 \T1/fi4/m/sl/10 showMethods("%*%", class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mul-ti-pli-ca-tion. Mul-ti-pli-ca-tion [2081] [2082] Underfull \hbox (badness 10000) in paragraph at lines 4313--4318 []\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite Tay-lor se-ries Underfull \hbox (badness 1067) in paragraph at lines 4313--4318 \T1/fi4/m/sl/10 expm(A) = I + A + A^2/2! + A^3/3! + ... \T1/ptm/m/n/10 (al-thou gh this is def-i-nitely not the way to [2083] [2084] Overfull \hbox (5.28088pt too wide) in paragraph at lines 4447--4447 [] \T1/fi4/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/ Boeing/msc00726.tar.gz"))))[] Overfull \hbox (50.28088pt too wide) in paragraph at lines 4450--4450 [] \T1/fi4/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] [2085] [2086] [2087] Underfull \hbox (badness 1931) in paragraph at lines 4675--4677 []\T1/ptm/m/n/10 a string spec-i-fy-ing how the \T1/fi4/m/sl/10 zero.print \T1/ ptm/m/n/10 codes should be aligned, see [2088] [2089] [2090] Underfull \hbox (badness 5862) in paragraph at lines 4881--4884 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ]\T1/fi4/m/sl/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use [2091] Underfull \hbox (badness 2846) in paragraph at lines 4973--4975 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/fi4/m/sl/10 p \T1/ptm/m/n/10 con- tains val-ues \T1/fi4/m/sl/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault, [2092] [2093] [2094] [2095] [2096] Underfull \hbox (badness 10000) in paragraph at lines 5339--5342 []\T1/fi4/m/sl/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2097] Underfull \hbox (badness 2478) in paragraph at lines 5451--5456 []\T1/ptm/m/n/10 Class \T1/fi4/m/sl/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly . Class \T1/fi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/fi4/m/sl/10 "lde nseMatrix"\T1/ptm/m/n/10 . Class [2098] Underfull \hbox (badness 10000) in paragraph at lines 5459--5462 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); use, e.g., [2099] Underfull \hbox (badness 10000) in paragraph at lines 5644--5647 []\T1/fi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2100] Underfull \hbox (badness 10000) in paragraph at lines 5742--5745 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2101] Underfull \hbox (badness 10000) in paragraph at lines 5817--5820 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2102] Underfull \hbox (badness 2050) in paragraph at lines 5887--5890 []\T1/fi4/m/sl/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth -ods for dif-fer-ent types of ma-tri-ces. Use [2103] [2104] [2105] Underfull \hbox (badness 6268) in paragraph at lines 6082--6085 []\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math- e-mat-i-cally''), Underfull \hbox (badness 6268) in paragraph at lines 6106--6110 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/fi4/m/sl/10 matrix[][][]\T1/ptm/m/n/1 0 . How-ever, [2106]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6212 \aliasA{det}{Matrix-class}{det} [2107] Underfull \hbox (badness 3547) in paragraph at lines 6318--6321 []\T1/fi4/m/sl/10 signature(object = "Matrix")\T1/ptm/m/n/10 : draws an [][]\T1 /fi4/m/sl/10 image[][][] \T1/ptm/m/n/10 of the ma-trix en-tries, us-ing Underfull \hbox (badness 10000) in paragraph at lines 6323--6326 [2108] Underfull \hbox (badness 1430) in paragraph at lines 6447--6452 []\T1/ptm/m/n/10 classes in-her-it-ing from \T1/fi4/m/sl/10 "MatrixFactorizatio n"\T1/ptm/m/n/10 , such as [][]\T1/fi4/m/sl/10 LU[][][]\T1/ptm/m/n/10 , [][]\T1 /fi4/m/sl/10 Cholesky[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 CHMfactor[][][] \T1/ptm/m/n/10 , and [2109] Underfull \hbox (badness 10000) in paragraph at lines 6516--6519 []\T1/fi4/m/sl/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2110] Underfull \hbox (badness 10000) in paragraph at lines 6568--6570 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/fi4/m/sl/10 X <- (X + t(X))/2 \T1 /ptm/m/n/10 should be done, af-ter [2111] [2112] [2113] Underfull \hbox (badness 2478) in paragraph at lines 6747--6752 []\T1/ptm/m/n/10 Class \T1/fi4/m/sl/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly . Class \T1/fi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/fi4/m/sl/10 "nde nseMatrix"\T1/ptm/m/n/10 . Class Underfull \hbox (badness 10000) in paragraph at lines 6755--6758 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); use, e.g., [2114] [2115] Underfull \hbox (badness 5924) in paragraph at lines 6941--6943 []\T1/ptm/m/n/10 fast sim-ple meth-ods pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm}) ha s been already used, duplicate ignored \relax l.6979 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.6979 \HeaderA{norm}{Matrix Norms}{norm} [2116] [2117] Underfull \hbox (badness 10000) in paragraph at lines 7234--7237 []\T1/fi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2118] Underfull \hbox (badness 10000) in paragraph at lines 7324--7327 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2119] Underfull \hbox (badness 10000) in paragraph at lines 7400--7403 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/fi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/fi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2120] [2121] Underfull \hbox (badness 10000) in paragraph at lines 7519--7521 []\T1/fi4/m/sl/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and oth er sig-na-tures (use Underfull \hbox (badness 3118) in paragraph at lines 7524--7527 []\T1/fi4/m/sl/10 signature(from = "numeric", to = "pMatrix")\T1/ptm/m/n/10 : a user con-ve-nience, to al-low Underfull \hbox (badness 10000) in paragraph at lines 7527--7534 []\T1/fi4/m/sl/10 signature(from = "pMatrix", to = "matrix")\T1/ptm/m/n/10 : co -er-cion to a tra-di-tional Underfull \hbox (badness 3417) in paragraph at lines 7552--7554 []\T1/ptm/m/n/10 The in-verse of the typ-i-cal \T1/fi4/m/sl/10 "pMatrix" \T1/pt m/m/n/10 con-struc-tor, \T1/fi4/m/sl/10 P <- as(ip, "pMatrix") \T1/ptm/m/n/10 i s sim-ply [2122] [2123] [2124]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}) has been already used, duplicate ignored \relax l.7731 \aliasA{qr}{qr-methods}{qr} Underfull \hbox (badness 5119) in paragraph at lines 7773--7776 []\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma- trix with [2125] Underfull \hbox (badness 3333) in paragraph at lines 7829--7834 []\T1/ptm/m/n/10 nonnegative num-ber spec-i-fy-ing a tol-er-ance for ``prac-ti- cally zero'' with Underfull \hbox (badness 6125) in paragraph at lines 7829--7834 \T1/ptm/m/n/10 spe-cific mean-ing de-pend-ing on \T1/fi4/m/sl/10 method\T1/ptm/ m/n/10 ; by de-fault, \T1/fi4/m/sl/10 max(dim(x)) * [2126]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rco nd}) has been already used, duplicate ignored \relax l.7895 ... the Reciprocal Condition Number}{rcond} [2127] [2128] [2129] [2130] [2131] [2132] [2133] [2134] [2135] [2136] [2137] [2138] [2139] [2140] Underfull \hbox (badness 4441) in paragraph at lines 8935--8943 []\T1/fi4/m/sl/10 signature(from = "factor", to = "sparseMatrix")\T1/ptm/m/n/10 : Co-er-cion of a fac-tor to Underfull \hbox (badness 1112) in paragraph at lines 8935--8943 \T1/fi4/m/sl/10 "sparseMatrix" \T1/ptm/m/n/10 pro-duces the ma-trix of in-di-ca -tor \T1/ptm/b/n/10 rows \T1/ptm/m/n/10 stored as an ob-ject of class Underfull \hbox (badness 10000) in paragraph at lines 8961--8965 [][][]\T1/fi4/m/sl/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, such as [][]\T1/fi4/m/sl/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or [2141]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr. Q}) has been already used, duplicate ignored \relax l.8996 \aliasA{qr.Q}{sparseQR-class}{qr.Q} Underfull \hbox (badness 1303) in paragraph at lines 9022--9031 []\T1/ptm/m/n/10 The de-com-po-si-tion is of the form \T1/fi4/m/sl/10 A[p+1,] = = Q %*% R\T1/ptm/m/n/10 , if the \T1/fi4/m/sl/10 q \T1/ptm/m/n/10 slot is of le ngth 0 or [2142] [2143]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.toeplitz}) has been already used, duplicate ignored \relax l.9268 ...{toeplitz}{sparseVector-class}{toeplitz} [2144] Underfull \hbox (badness 10000) in paragraph at lines 9353--9356 []\T1/fi4/m/sl/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/fi4/ m/sl/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2145] Underfull \hbox (badness 10000) in paragraph at lines 9380--9382 [][][]\T1/fi4/m/sl/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-stru c-tion of sparse vec-tors (apart from [2146] Underfull \hbox (badness 4699) in paragraph at lines 9483--9489 [][][]\T1/fi4/m/sl/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more usual con-struc-tor of such ma-tri-ces; sim-i-larly, [2147] [2148] Underfull \hbox (badness 2057) in paragraph at lines 9637--9639 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2149]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcr ossprod}) has been already used, duplicate ignored \relax l.9663 ...{Cross-product of transpose}{tcrossprod} [2150] [2151] Underfull \hbox (badness 1831) in paragraph at lines 9877--9883 []\T1/ptm/m/n/10 For con-ve-nience, meth-ods for some op-er-a-tions such as \T1 /fi4/m/sl/10 %*% \T1/ptm/m/n/10 and \T1/fi4/m/sl/10 crossprod \T1/ptm/m/n/10 ar e de-fined [2152] [2153] [2154] [2155] Overfull \hbox (63.78088pt too wide) in paragraph at lines 10133--10133 []\T1/fi4/m/n/9 system.time(MJ <- sapply(rho, function(x) determinant(IM - x * USCounties, logarithm = TRUE)$modulus))[] [2156] Underfull \hbox (badness 6910) in paragraph at lines 10308--10310 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2157] [2158]) (./boot-pkg.tex Chapter 18. [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167] Overfull \hbox (3.25928pt too wide) in paragraph at lines 641--647 []\T1/ptm/m/n/10 logical, only al-lowed to be \T1/fi4/m/sl/10 TRUE \T1/ptm/m/n/ 10 for \T1/fi4/m/sl/10 sim = "ordinary", stype = "i", n = 0 [2168] Underfull \hbox (badness 1097) in paragraph at lines 786--794 []\T1/ptm/m/n/10 For most of the \T1/fi4/m/sl/10 boot \T1/ptm/m/n/10 meth-ods t he re-sam-pling is done in the mas-ter pro-cess, but not if Underfull \hbox (badness 6173) in paragraph at lines 795--805 []\T1/ptm/m/n/10 Where random-number gen-er-a-tion is done in the worker pro-ce sses, the de-fault be- Underfull \hbox (badness 1728) in paragraph at lines 795--805 \T1/ptm/m/n/10 haviour is that each worker chooses a sep-a-rate seed, non-repro ducibly. How-ever, with [2169] Underfull \hbox (badness 1881) in paragraph at lines 817--819 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. [2170] Underfull \vbox (badness 10000) has occurred while \output is active [2171] [2172] Underfull \hbox (badness 10000) in paragraph at lines 1057--1061 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1057--1061 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues Underfull \hbox (badness 5592) in paragraph at lines 1057--1061 \T1/fi4/m/sl/10 c("norm","basic", "stud", "perc", "bca") \T1/ptm/m/n/10 or sim- ply \T1/fi4/m/sl/10 "all" \T1/ptm/m/n/10 which [2173] Underfull \hbox (badness 2150) in paragraph at lines 1094--1100 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2174] [2175] [2176] [2177] Underfull \hbox (badness 1571) in paragraph at lines 1434--1436 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2178] [2179] [2180] [2181] [2182] [2183] Underfull \hbox (badness 1005) in paragraph at lines 1788--1795 []\T1/ptm/m/n/10 The sim-u-la-tion type. Pos-si-ble types are \T1/fi4/m/sl/10 " ordinary" \T1/ptm/m/n/10 (case re-sam-pling), [2184] [2185] Underfull \vbox (badness 10000) has occurred while \output is active [2186] [2187] Underfull \hbox (badness 7379) in paragraph at lines 2072--2074 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2188] [2189] [2190] Underfull \hbox (badness 1565) in paragraph at lines 2326--2331 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set [2191] Underfull \hbox (badness 1881) in paragraph at lines 2420--2422 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. [2192] [2193] Underfull \hbox (badness 2970) in paragraph at lines 2524--2528 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/fi4/m/s l/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/fi4/m/sl/10 n \T1/ptm/m/n/10 is t he sam-ple Underfull \hbox (badness 2310) in paragraph at lines 2524--2528 \T1/ptm/m/n/10 size, if \T1/fi4/m/sl/10 unbiased \T1/ptm/m/n/10 is \T1/fi4/m/sl /10 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/fi4/m/sl/10 1/n \T1/ptm/m/n /10 is used. This is mul-ti-plied by [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] Underfull \hbox (badness 10000) in paragraph at lines 4178--4180 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2218] [2219] [2220] Underfull \hbox (badness 2393) in paragraph at lines 4377--4380 []\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with fre-quency vec-tor \T1/fi4/m/sl/10 f \T1/ptm/m/n/10 is given by [2221] [2222] [2223] [2224] [2225] [2226] [2227] [2228] Underfull \hbox (badness 3000) in paragraph at lines 4947--4950 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2229] [2230] [2231] [2232] Underfull \hbox (badness 2293) in paragraph at lines 5226--5229 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5226--5229 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243] Underfull \hbox (badness 4954) in paragraph at lines 6007--6010 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/fi4/m/sl/10 "sa ddle.distn"\T1/ptm/m/n/10 . See the help file for [2244] [2245] [2246] [2247] [2248] [2249] [2250] [2251] [2252] Underfull \hbox (badness 1596) in paragraph at lines 6728--6732 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2253] [2254] [2255] [2256] [2257] [2258] [2259] [2260] [2261] [2262]) (./class-pkg.tex Chapter 19. [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] Underfull \hbox (badness 10000) in paragraph at lines 608--610 []\T1/ptm/m/n/10 the size of the code-book. De-faults to Underfull \hbox (badness 3977) in paragraph at lines 608--610 \T1/fi4/m/sl/10 min(round(0.4*ng*(ng-1 + p/2),0), n) \T1/ptm/m/n/10 where \T1/f i4/m/sl/10 ng \T1/ptm/m/n/10 is the num-ber of [2271] [2272] [2273] [2274] [2275] [2276] [2277] [2278]) (./cluster-pkg.tex Chapter 20. [2279] Underfull \hbox (badness 1231) in paragraph at lines 59--66 \T1/ptm/m/n/10 which uses (a con-stant ver-sion of) the Lance-Williams for-mula and the [2280] [2281] [2282] [2283] [2284] [2285] [2286] Underfull \hbox (badness 4144) in paragraph at lines 587--590 []\T1/ptm/m/n/10 Setting this to \T1/fi4/m/sl/10 FALSE \T1/ptm/m/n/10 saves mem -ory (and hence time), but dis-ables [2287] [2288] [2289] Underfull \hbox (badness 10000) in paragraph at lines 754--756 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2290] Underfull \hbox (badness 10000) in paragraph at lines 841--843 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is [2291] [2292] [2293] Underfull \hbox (badness 6110) in paragraph at lines 1019--1023 []\T1/ptm/m/n/10 when \T1/fi4/m/sl/10 x \T1/ptm/m/n/10 does not have a \T1/fi4/ m/sl/10 diss \T1/ptm/m/n/10 nor a \T1/fi4/m/sl/10 data \T1/ptm/m/n/10 com-po-ne nt, e.g., for [2294] [2295] [2296] [2297] [2298] Underfull \hbox (badness 2503) in paragraph at lines 1397--1400 []\T1/ptm/m/n/10 an ob-ject of class \T1/fi4/m/sl/10 "hclust" \T1/ptm/m/n/10 or \T1/fi4/m/sl/10 "twins"\T1/ptm/m/n/10 , i.e., typ-i-cally the re-sult of [2299] [2300] [2301] [2302] [2303] [2304] [2305] [2306] Underfull \hbox (badness 10000) in paragraph at lines 1964--1966 []\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as Underfull \hbox (badness 10000) in paragraph at lines 1988--1994 [][][]\T1/fi4/m/sl/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [][]\T1/fi4/m/sl/10 predict[][][] \T1/ptm/m/n/10 method for \T1/fi4/m/sl/10 ell ipsoid \T1/ptm/m/n/10 ob-jects. [2307] [2308] [2309] [2310] Underfull \hbox (badness 6675) in paragraph at lines 2220--2222 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see [2311] [2312] [2313] [2314] [2315] Underfull \hbox (badness 1014) in paragraph at lines 2584--2594 \T1/ptm/m/n/10 on the re-sult \T1/fi4/m/sl/10 pr <- pam(..)\T1/ptm/m/n/10 , or di-rectly its com-po-nent \T1/fi4/m/sl/10 pr$silinfo$avg.width\T1/ptm/m/n/10 , see also Underfull \hbox (badness 1616) in paragraph at lines 2624--2629 []\T1/ptm/m/n/10 The de-fault \T1/fi4/m/sl/10 FALSE \T1/ptm/m/n/10 (or in-te-ge r \T1/fi4/m/sl/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al -go-rithm, whereas [2316] Underfull \hbox (badness 2980) in paragraph at lines 2662--2666 [][][]\T1/fi4/m/sl/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-enc es; [][]\T1/fi4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 cl ara[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 daisy[][][]\T1/ptm/m/n/10 , [][]\ T1/fi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [2317] [2318] [2319] [2320] [2321] Underfull \hbox (badness 1142) in paragraph at lines 3000--3003 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/fi4/m/sl/10 par[][][]\T1/ ptm/m/n/10 ) may also be sup-plied and are passed to [2322] [2323] Underfull \hbox (badness 1142) in paragraph at lines 3119--3122 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/fi4/m/sl/10 par[][][]\T1/ ptm/m/n/10 ) may also be sup-plied and are passed to [2324] [2325] [2326] Underfull \hbox (badness 2582) in paragraph at lines 3342--3347 [][][]\T1/fi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/1 0 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 clusplot.default [][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/fi 4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 clara[][][]\T1/p tm/m/n/10 , [2327] Underfull \hbox (badness 10000) in paragraph at lines 3428--3433 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/fi 4/m/sl/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 4378) in paragraph at lines 3428--3433 \T1/ptm/m/n/10 which dis-patches to [][]\T1/fi4/m/sl/10 plot.hclust[][][](..)\T 1/ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider [2328] [2329] [2330] [2331] [2332] Underfull \hbox (badness 10000) in paragraph at lines 3718--3720 []\T1/ptm/m/n/10 a \T1/fi4/m/sl/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T 1/fi4/m/sl/10 summary.dissimilarity \T1/ptm/m/n/10 one for [2333] [2334] [2335] [2336] Underfull \hbox (badness 4108) in paragraph at lines 3942--3947 []\T1/ptm/m/n/10 arguments passed [][]\T1/fi4/m/sl/10 barplot[][][]()\T1/ptm/m/ n/10 ; note that the de-fault used to be \T1/fi4/m/sl/10 col Underfull \hbox (badness 1062) in paragraph at lines 3997--3999 []\T1/ptm/m/n/10 numeric (rank 1) ar-ray of clus-ter-wise \T1/ptm/m/it/10 means \T1/ptm/m/n/10 of sil-hou-ette widths where [2337] Underfull \hbox (badness 1383) in paragraph at lines 4019--4024 []\T1/ptm/m/n/10 While \T1/fi4/m/sl/10 silhouette() \T1/ptm/m/n/10 is \T1/ptm/m /it/10 in-trin-sic \T1/ptm/m/n/10 to the [][]\T1/fi4/m/sl/10 partition[][][] \T 1/ptm/m/n/10 clus-ter-ings, and hence has a (triv-ial) [2338] [2339] [2340] [2341] [2342] [2343] [2344] [2345]) (./codetools-pkg.tex [2346] Chapter 21. [2347] [2348] [2349] [2350] [2351]) (./foreign-pkg.tex [2352] Chapter 22. Underfull \hbox (badness 1331) in paragraph at lines 33--37 \T1/ptm/m/n/10 (XPORT) For-mat'' avail-able as [][]$\T1/fi4/m/sl/10 http : / / ftp . sas . com / techsup / download / technote / ts140 . [2353] [2354] [2355] [2356] [2357] [2358] [2359] [2360] [2361] [2362] [2363] Underfull \hbox (badness 10000) in paragraph at lines 704--705 [2364] Underfull \hbox (badness 1642) in paragraph at lines 759--763 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Set in SAS [2365] [2366] [2367] [2368] [2369] Underfull \hbox (badness 10000) in paragraph at lines 1115--1121 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/fi4/m/sl/10 foreign :::writeForeignStata\T1/ptm/m/n/10 , [2370] [2371]) (./lattice-pkg.tex [2372] Chapter 23. [2373] [2374] [2375] [2376] [2377] [2378] Underfull \hbox (badness 10000) in paragraph at lines 480--485 []\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/fi4/m/sl/10 scales \T1/ptm/m/n/10 in this case may be [2379] [2380] [2381] [2382] [2383] [2384] [2385] [2386] [2387] [2388] Underfull \hbox (badness 1062) in paragraph at lines 1398--1402 \T1/ptm/m/n/10 no-ta-tion for the x and y axes re-spec-tively. See doc-u-men-ta -tion for [2389] [2390] [2391] Underfull \hbox (badness 1803) in paragraph at lines 1566--1583 [][][]\T1/fi4/m/sl/10 Lattice[][][] \T1/ptm/m/n/10 for an overview of the pack- age, as well as [][]\T1/fi4/m/sl/10 barchart.table[][][]\T1/ptm/m/n/10 , [][]\T 1/fi4/m/sl/10 print.trellis[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][]\T1/fi4/m/sl/10 panel.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 p anel.superpose[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 panel.loess[][][]\T1/p tm/m/n/10 , [][]\T1/fi4/m/sl/10 panel.average[][][]\T1/ptm/m/n/10 , [][]\T1/fi4 /m/sl/10 strip.default[][][]\T1/ptm/m/n/10 , [2392] [2393] Underfull \hbox (badness 3009) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/fi4/m/sl/10 xyplot[][ ][]\T1/ptm/m/n/10 , which may pass them on to Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to [2394] [2395] [2396] [2397] [2398] Underfull \hbox (badness 10000) in paragraph at lines 2086--2093 []\T1/ptm/m/n/10 For the \T1/fi4/m/sl/10 formula \T1/ptm/m/n/10 method, \T1/fi4 /m/sl/10 x \T1/ptm/m/n/10 can be a for-mula of the form Underfull \hbox (badness 1173) in paragraph at lines 2086--2093 \T1/fi4/m/sl/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togr ams or ker-nel den-sity es-ti- [2399] [2400] [2401] [2402] Underfull \hbox (badness 7064) in paragraph at lines 2360--2364 []\T1/ptm/m/n/10 For the \T1/fi4/m/sl/10 "formula" \T1/ptm/m/n/10 method, \T1/f i4/m/sl/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2403] [2404] Underfull \hbox (badness 7064) in paragraph at lines 2545--2552 []\T1/ptm/m/n/10 For the \T1/fi4/m/sl/10 "formula" \T1/ptm/m/n/10 method, \T1/f i4/m/sl/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2405] [2406] [2407] Underfull \hbox (badness 10000) in paragraph at lines 2759--2764 []\T1/ptm/m/n/10 for the \T1/fi4/m/sl/10 formula \T1/ptm/m/n/10 method, a for-m ula of the form \T1/fi4/m/sl/10 z ~ x * y [2408] Underfull \hbox (badness 2781) in paragraph at lines 2846--2848 []\T1/ptm/m/n/10 A color ramp spec-i-fi-ca-tion, as in the \T1/fi4/m/sl/10 col. regions \T1/ptm/m/n/10 ar-gu-ment in [2409] Underfull \hbox (badness 2486) in paragraph at lines 2957--2961 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2410] [2411] [2412] Underfull \hbox (badness 10000) in paragraph at lines 3108--3116 []\T1/ptm/m/n/10 For the \T1/fi4/m/sl/10 "formula" \T1/ptm/m/n/10 meth-ods, a f or-mula of the form \T1/fi4/m/sl/10 z ~ x [2413] [2414] [2415] [2416]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \relax l.3429 \aliasA{parallel}{B\_08\_splom}{parallel} [2417] [2418] [2419] [2420] [2421] [2422] [2423] Underfull \hbox (badness 2277) in paragraph at lines 3920--3924 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings by Underfull \hbox (badness 10000) in paragraph at lines 3920--3924 \T1/ptm/m/n/10 spec-i-fy-ing \T1/fi4/m/sl/10 lattice.options(default.theme = "c ol.whitebg")\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3920--3924 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2424] [2425] Underfull \hbox (badness 1173) in paragraph at lines 4059--4063 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4086--4088 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when [2426] [2427] [2428] Underfull \hbox (badness 3492) in paragraph at lines 4282--4292 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/fi4/m/sl/10 col \T1/ptm/m/n/10 is used for com-po-nents \T1/fi4/m/sl/10 "plot.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4307--4310 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/fi4/m/sl/10 plo t.symbol\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 plot.polygon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4310--4312 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/fi4/m/sl/10 p lot.polygon \T1/ptm/m/n/10 and [2429] [2430] [2431] [2432] [2433] [2434] [2435] [2436] [2437] [2438] Underfull \hbox (badness 6157) in paragraph at lines 5033--5036 []\T1/fi4/m/sl/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles via rect-an-gles. \T1/fi4/m/sl/10 print.shingle \T1/ptm/m/n/10 and [2439] [2440] [2441] [2442] [2443] [2444] Underfull \hbox (badness 10000) in paragraph at lines 5484--5487 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 5592) in paragraph at lines 5484--5487 \T1/fi4/m/sl/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the le ft of pan-els us-ing [2445] [2446] [2447] [2448] [2449] Underfull \hbox (badness 4805) in paragraph at lines 5844--5848 []\T1/ptm/m/n/10 logical, whether the view-port be-ing as-signed fo-cus should be high- Underfull \hbox (badness 10000) in paragraph at lines 5855--5862 []\T1/ptm/m/n/10 For \T1/fi4/m/sl/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-t ra pa-ram-e-ters are passed on to Underfull \hbox (badness 1226) in paragraph at lines 5855--5862 \T1/fi4/m/sl/10 panel.identify\T1/ptm/m/n/10 . For \T1/fi4/m/sl/10 panel.identi fy\T1/ptm/m/n/10 , ex-tra ar-gu-ments are treated as Underfull \hbox (badness 2418) in paragraph at lines 5855--5862 \T1/ptm/m/n/10 graph-i-cal pa-ram-e-ters and are used for la-belling. For \T1/f i4/m/sl/10 trellis.focus Underfull \hbox (badness 10000) in paragraph at lines 5855--5862 \T1/ptm/m/n/10 and \T1/fi4/m/sl/10 trellis.switchFocus\T1/ptm/m/n/10 , these ar e used (in com-bi-na-tion with Underfull \hbox (badness 1259) in paragraph at lines 5855--5862 [][]\T1/fi4/m/sl/10 lattice.options[][][]\T1/ptm/m/n/10 ) for high-light-ing th e cho-sen view-port if so re-quested. [2450] [2451] [2452] [2453] Underfull \hbox (badness 4242) in paragraph at lines 6155--6160 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- Underfull \hbox (badness 2529) in paragraph at lines 6155--6160 \T1/ptm/m/n/10 ter \T1/fi4/m/sl/10 plot.polygon \T1/ptm/m/n/10 is used if there is no group-ing vari-able, oth-er-wise [2454] [2455] Underfull \hbox (badness 2310) in paragraph at lines 6271--6276 []\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/fi4/m/sl/10 x \T1/ptm/m/n/ 10 for ev-ery level of \T1/fi4/m/sl/10 y \T1/ptm/m/n/10 (or the other way round if [2456] [2457] [2458] [2459] [2460] [2461] [2462] [2463] [2464] [2465] [2466] [2467] [2468] [2469] [2470] Underfull \hbox (badness 2012) in paragraph at lines 7323--7326 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2471] [2472] Underfull \hbox (badness 3333) in paragraph at lines 7495--7497 []\T1/ptm/m/n/10 default colours are ob-tained from \T1/fi4/m/sl/10 plot.symbol \T1/ptm/m/n/10 and \T1/fi4/m/sl/10 plot.line \T1/ptm/m/n/10 us-ing [2473] [2474] [2475] [2476] [2477] [2478] Underfull \hbox (badness 1436) in paragraph at lines 7905--7911 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for Underfull \hbox (badness 1661) in paragraph at lines 7905--7911 \T1/fi4/m/sl/10 panel.abline \T1/ptm/m/n/10 should be taken from the ``ref-er-e nce.line'' pa-ram-e-ter set- Underfull \hbox (badness 1231) in paragraph at lines 7905--7911 \T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti ngs. The [2479] [2480] [2481] [2482] [2483] [2484] [2485] [2486] Underfull \hbox (badness 10000) in paragraph at lines 8463--8466 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/fi4/m/sl/10 panel.superp ose \T1/ptm/m/n/10 from [2487] Underfull \hbox (badness 1092) in paragraph at lines 8509--8511 []\T1/ptm/m/n/10 Deepayan Sarkar \T1/fi4/m/sl/10 \T1/ptm/m/n/10 (\T1/fi4/m/sl/10 panel.superpose.2 \T1/ptm/m/n/10 orig-i-nally con- [2488] [2489] Underfull \hbox (badness 3895) in paragraph at lines 8670--8673 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/fi4/m/sl/10 type \T 1/ptm/m/n/10 has a dif-fer-ent mean-ing in [2490] Underfull \hbox (badness 1515) in paragraph at lines 8746--8750 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2491] Underfull \hbox (badness 6316) in paragraph at lines 8852--8857 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2492] Underfull \hbox (badness 5908) in paragraph at lines 8869--8872 []\T1/ptm/m/n/10 list, sim-i-lar to those pro-duced by \T1/fi4/m/sl/10 xscale.c omponents.default \T1/ptm/m/n/10 and [2493] [2494] [2495] [2496] Overfull \hbox (36.94879pt too wide) in paragraph at lines 9157--9161 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/fi4 /m/sl/10 left, right, left.name, right.name, condition Overfull \hbox (29.63074pt too wide) in paragraph at lines 9157--9161 \T1/ptm/m/n/10 for 2-D, and \T1/fi4/m/sl/10 left, right.x, right.y, left.nam e, right.x.name, right.y.name, condition [2497] [2498] [2499] [2500] [2501] [2502] [2503] Underfull \hbox (badness 1442) in paragraph at lines 9613--9617 []\T1/ptm/m/n/10 Factor with lev-els \T1/fi4/m/sl/10 "Svansota"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "No. 462"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Manchuria"\T1/ptm/m /n/10 , \T1/fi4/m/sl/10 "No. 475"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Velvet"\T1/p tm/m/n/10 , Underfull \hbox (badness 2573) in paragraph at lines 9618--9621 []\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/fi4/m/sl/10 "Grand Rapids"\T1/ptm/m /n/10 , \T1/fi4/m/sl/10 "Duluth"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "University Fa rm"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Morris"\T1/ptm/m/n/10 , [2504] [2505] [2506]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9842 \aliasA{melanoma}{H\_melanoma}{melanoma} [2507] [2508] [2509] [2510]) (./mgcv-pkg.tex Chapter 24. [2511] [2512] Underfull \hbox (badness 1052) in paragraph at lines 149--151 []\T1/ptm/m/n/10 selects ex-act test statis-tic to use for sin-gle smooth term p-values. See [2513] [2514] Underfull \hbox (badness 1142) in paragraph at lines 281--285 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 303--308 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2515] Underfull \hbox (badness 2626) in paragraph at lines 353--356 []\T1/ptm/m/n/10 If all smooths are P-splines and all ten-sor prod-ucts are of the form [2516] [2517] [2518] [2519] [2520] Underfull \hbox (badness 1158) in paragraph at lines 613--615 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2521] [2522] [2523] [2524] [2525] [2526] [2527] [2528] [2529] [2530] [2531] [2532] [2533] [2534] [2535] [2536] Underfull \hbox (badness 1142) in paragraph at lines 1642--1646 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2537] Underfull \hbox (badness 1043) in paragraph at lines 1665--1669 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2538] [2539] [2540] [2541] [2542] Underfull \vbox (badness 10000) has occurred while \output is active [2543] Underfull \vbox (badness 10000) has occurred while \output is active [2544] Underfull \vbox (badness 10000) has occurred while \output is active [2545] [2546] [2547] [2548] [2549] [2550] [2551] [2552] [2553] [2554] [2555] [2556] Underfull \hbox (badness 10000) in paragraph at lines 2921--2925 []\T1/ptm/m/n/10 Random ef-fects can be added to \T1/fi4/m/sl/10 gam \T1/ptm/m/ n/10 mod-els us-ing \T1/fi4/m/sl/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see [2557] [2558] Underfull \vbox (badness 10000) has occurred while \output is active [2559] [2560] [2561] [2562] [2563] [2564] [2565] [2566] [2567] Underfull \hbox (badness 1142) in paragraph at lines 3649--3653 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2568] [2569] Underfull \hbox (badness 1231) in paragraph at lines 3741--3743 []\T1/fi4/m/sl/10 gamm \T1/ptm/m/n/10 per-forms poorly with bi-nary data, since it uses PQL. It is bet-ter to use \T1/fi4/m/sl/10 gam \T1/ptm/m/n/10 with [2570] [2571] Underfull \vbox (badness 10000) has occurred while \output is active [2572] [2573] [2574] [2575] [2576] [2577] [2578] [2579] [2580] [2581] [2582] Underfull \hbox (badness 6001) in paragraph at lines 4632--4634 []\T1/ptm/m/n/10 Simon N. Wood \T1/fi4/m/sl/10 \T1/p tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's [2583] [2584] [2585] Underfull \vbox (badness 10000) has occurred while \output is active [2586] [2587] [2588] [2589] [2590] [2591] [2592] [2593] [2594] [2595] [2596] [2597] [2598] [2599] Underfull \hbox (badness 6001) in paragraph at lines 5671--5673 []\T1/ptm/m/n/10 Simon N. Wood \T1/fi4/m/sl/10 \T1/p tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's [2600] Underfull \vbox (badness 10000) has occurred while \output is active [2601] [2602] [2603] [2604] [2605] [2606] [2607] [2608] Underfull \vbox (badness 10000) has occurred while \output is active [2609] Underfull \hbox (badness 1038) in paragraph at lines 6304--6307 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/fi4/m/sl/10 Dim. pdIndot\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 coef.pdIdnot\T1/ptm/m/n/10 , \T1/fi4/m/ sl/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6304--6307 \T1/fi4/m/sl/10 logDet.pdIdnot\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 pdConstruct.pdId not\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/fi4/m/ sl/10 pdMatrix.pdIdnot\T1/ptm/m/n/10 , [2610] Underfull \hbox (badness 10000) in paragraph at lines 6360--6363 []\T1/ptm/m/n/10 These func-tions (\T1/fi4/m/sl/10 pdTens\T1/ptm/m/n/10 , \T1/f i4/m/sl/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 pdFactor.pdTens\T 1/ptm/m/n/10 , \T1/fi4/m/sl/10 pdMatrix.pdTens\T1/ptm/m/n/10 , [2611] [2612] [2613] [2614] [2615] [2616] [2617] [2618] [2619] Overfull \hbox (29.78088pt too wide) in paragraph at lines 6927--6927 [] \T1/fi4/m/sl/10 block.size=50000,newdata.guaranteed=FALSE,na.action= na.pass,cluster=NULL,...)[] [2620] Underfull \hbox (badness 1852) in paragraph at lines 6996--6999 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/fi4/m/sl/10 termplot[] [][]\T1/ptm/m/n/10 , if \T1/fi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at- tribute \T1/fi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and [2621] [2622] Underfull \hbox (badness 1852) in paragraph at lines 7142--7145 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/fi4/m/sl/10 termplot[] [][]\T1/ptm/m/n/10 , if \T1/fi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at- tribute \T1/fi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and [2623] [2624] Underfull \vbox (badness 10000) has occurred while \output is active [2625] [2626] Underfull \hbox (badness 1205) in paragraph at lines 7350--7352 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 7350--7352 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 7356--7361 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2627] Underfull \hbox (badness 1205) in paragraph at lines 7437--7439 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 7437--7439 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2628] [2629] [2630] Underfull \hbox (badness 1253) in paragraph at lines 7636--7638 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [2631] [2632] [2633] [2634] [2635] [2636] [2637] [2638] [2639] [2640] [2641] Underfull \hbox (badness 1975) in paragraph at lines 8297--8302 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2642] [2643] Underfull \hbox (badness 1762) in paragraph at lines 8386--8398 \T1/ptm/m/n/10 plate re-gres-sion splines: see [][]\T1/fi4/m/sl/10 tprs[][][]\T 1/ptm/m/n/10 ); \T1/fi4/m/sl/10 ts.smooth.spec \T1/ptm/m/n/10 (thin plate re-gr es-sion splines with [2644] [2645] [2646] Underfull \hbox (badness 7667) in paragraph at lines 8596--8602 [][][]\T1/fi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like [2647] Underfull \hbox (badness 10000) in paragraph at lines 8637--8638 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2648] [2649] Underfull \hbox (badness 10000) in paragraph at lines 8763--8765 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2650] [2651] Underfull \hbox (badness 10000) in paragraph at lines 8890--8891 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2652] [2653] Underfull \hbox (badness 1436) in paragraph at lines 9024--9029 \T1/ptm/m/n/10 nest-ing of the smooth within the fac-tor. Note how-ever that: i ) \T1/fi4/m/sl/10 gamm \T1/ptm/m/n/10 only al-lows one [2654] [2655] [2656] [2657] [2658] [2659] [2660] [2661] Underfull \hbox (badness 10000) in paragraph at lines 9459--9465 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a [2662] [2663] [2664] Underfull \vbox (badness 10000) has occurred while \output is active [2665] Underfull \vbox (badness 10000) has occurred while \output is active [2666] Overfull \hbox (9.78088pt too wide) in paragraph at lines 9755--9755 []\T1/fi4/m/n/9 b <- gam(z~s(x,y,k=c(30,15),bs="so",xt=list(bnd=bnd,nmax=nmax) ),knots=knots,method="REML")[] Overfull \hbox (5.28088pt too wide) in paragraph at lines 9761--9761 [] \T1/fi4/m/n/9 s(x,y,k=c(30,15),bs="sw",xt=list(bnd=bnd,nmax=nmax)) ,knots=knots,method="REML")[] Underfull \hbox (badness 10000) in paragraph at lines 9801--9802 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2667] [2668] [2669] [2670] Underfull \hbox (badness 3895) in paragraph at lines 9992--9997 [][][]\T1/fi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 10037--10039 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2671] [2672] [2673] [2674] Underfull \hbox (badness 1371) in paragraph at lines 10211--10217 []\T1/fi4/m/sl/10 bs="ad" \T1/ptm/m/n/10 Uni-vari-ate and bi-vari-ate adap-tive smooths are avail-able (see Underfull \hbox (badness 10000) in paragraph at lines 10251--10255 [][][]\T1/fi4/m/sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 te[][][]\T1/p tm/m/n/10 , [][]\T1/fi4/m/sl/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/ fi4/m/sl/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 cubic.regre ssion.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/fi4/m/sl/10 p.spline[][][]\T1/ptm/m/n /10 , [][]\T1/fi4/m/sl/10 mrf[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10251--10255 \T1/ptm/m/n/10 code[][]soap[][][], code[][]Spherical.Spline[][][], [][]\T1/fi4/ m/sl/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 user.defined. smooth[][][]\T1/ptm/m/n/10 , [2675] Underfull \hbox (badness 2326) in paragraph at lines 10318--10325 []\T1/ptm/m/n/10 These wrap-per func-tions ex-ist to al-low smooths spec-i-fied us-ing [][]\T1/fi4/m/sl/10 smooth.construct[][][] \T1/ptm/m/n/10 and [2676] Underfull \hbox (badness 2158) in paragraph at lines 10375--10375 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [2677] [2678] [2679] [2680] [2681] [2682] [2683] [2684] [2685] [2686] [2687] [2688] [2689] [2690] [2691] [2692] [2693] Underfull \hbox (badness 6001) in paragraph at lines 11473--11475 []\T1/ptm/m/n/10 Simon N. Wood \T1/fi4/m/sl/10 \T1/p tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's [2694] [2695] [2696] [2697] Underfull \hbox (badness 1796) in paragraph at lines 11697--11700 []\T1/ptm/m/n/10 other op-tions to pass on to [][]\T1/fi4/m/sl/10 persp[][][]\T 1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 image[][][] \T1/ptm/m/n/10 or [][]\T1/fi4/m/ sl/10 contour[][][]\T1/ptm/m/n/10 . In par-tic-u-lar [2698] [2699] [2700]) (./nlme-pkg.tex Chapter 25. [2701] [2702] [2703] [2704] [2705] [2706] [2707] [2708] [2709] [2710] [2711] [2712] [2713] [2714] [2715] [2716] [2717] [2718] [2719] [2720] [2721] [2722] [2723] [2724] [2725] [2726] [2727] [2728] [2729] [2730] Underfull \hbox (badness 2875) in paragraph at lines 1996--2002 []\T1/ptm/m/n/10 an op-tional log-i-cal value or one-sided for-mula, in-di-cat- ing a co-vari-ate Underfull \hbox (badness 1466) in paragraph at lines 1996--2002 \T1/ptm/m/n/10 that is in-ner to the \T1/fi4/m/sl/10 displayLevel \T1/ptm/m/n/1 0 group-ing fac-tor. If equal to \T1/fi4/m/sl/10 TRUE\T1/ptm/m/n/10 , [2731] [2732] [2733] [2734] Underfull \hbox (badness 10000) in paragraph at lines 2257--2263 [][][]\T1/fi4/m/sl/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 corARMA [][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][ ]\T1/fi4/m/sl/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Initi alize.corStruct[][][]\T1/ptm/m/n/10 , [2735] [2736] [2737] [2738] [2739] [2740] [2741] [2742] [2743] [2744] [2745] [2746] [2747] [2748] [2749] [2750] [2751] [2752] [2753] [2754] [2755] [2756] [2757] [2758] [2759] [2760] [2761] [2762] [2763] [2764] [2765] [2766] [2767] Underfull \hbox (badness 1067) in paragraph at lines 4410--4415 \T1/ptm/m/n/10 ma-trix), \T1/fi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues ), and \T1/fi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to [2768] [2769] [2770] [2771] [2772] [2773] [2774] [2775] [2776] [2777] [2778] [2779] Underfull \hbox (badness 10000) in paragraph at lines 5156--5160 [][][]\T1/fi4/m/sl/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/ m/sl/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 getCo variate.varFunc[][][]\T1/ptm/m/n/10 , [2780] [2781] [2782] [2783] [2784] [2785] [2786] Underfull \hbox (badness 10000) in paragraph at lines 5588--5591 [][][]\T1/fi4/m/sl/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/1 0 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 getGroups.gls[ ][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 getGroups.lmList[][][]\T1/ptm/m/n/10 , [2787] [2788] [2789] [2790] [2791] [2792] [2793] Underfull \hbox (badness 10000) in paragraph at lines 5969--5974 [][][]\T1/fi4/m/sl/10 getGroupsFormula.gls[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/ sl/10 getGroupsFormula.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 getGrou psFormula.lme[][][]\T1/ptm/m/n/10 , [2794] [2795] [2796] [2797] Underfull \hbox (badness 1490) in paragraph at lines 6239--6250 [][][]\T1/fi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 glsC ontrol[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 glsObject[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 plot. gls[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 predict.gls[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 qqnorm.gls[][][]\T1/ptm/m/n/10 , [2798] Underfull \hbox (badness 10000) in paragraph at lines 6310--6312 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [2799] [2800] [2801] [2802] [2803] [2804] Underfull \hbox (badness 10000) in paragraph at lines 6728--6730 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [2805] [2806] [2807] [2808] [2809] Underfull \hbox (badness 10000) in paragraph at lines 7001--7008 [][][]\T1/fi4/m/sl/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 gapply[ ][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T 1/fi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 plot.nffGroupedData [][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 plot.nfnGroupedData[][][]\T1/ptm/m/n /10 , [2810] [2811] [2812] Underfull \hbox (badness 10000) in paragraph at lines 7263--7268 [][][]\T1/fi4/m/sl/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/ sl/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Initialize .glsStruct[][][]\T1/ptm/m/n/10 , [2813] [2814] [2815] [2816] [2817] [2818] [2819] [2820] [2821] [2822] [2823] [2824] Underfull \hbox (badness 1642) in paragraph at lines 8042--8064 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [2825] [2826] Underfull \hbox (badness 1642) in paragraph at lines 8213--8235 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [2827] [2828] [2829] [2830] [2831] Underfull \hbox (badness 10000) in paragraph at lines 8523--8525 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [2832] [2833] [2834] [2835] [2836] Underfull \hbox (badness 10000) in paragraph at lines 8826--8833 [][][]\T1/fi4/m/sl/10 lm[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 lme.lmList[] [][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 plot.lmList[][][]\T1/ptm/m/n/10 , [][] \T1/fi4/m/sl/10 pooledSD[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 predict.lmLi st[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 residuals.lmList[][][]\T1/ptm/m/n/ 10 , [2837] [2838] [2839] [2840] [2841] [2842] [2843] [2844] Underfull \hbox (badness 10000) in paragraph at lines 9351--9358 [][][]\T1/fi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/fi4/m/sl/10 gls[][][]\T1 /ptm/m/n/10 , [][]\T1/fi4/m/sl/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T 1/fi4/m/sl/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 logLik .lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 logLik.lmList[][][]\T1/ptm /m/n/10 , [2845] [2846] [2847] [2848] [2849]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9713 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9713 ...rA{Matrix}{Assign Matrix Values}{Matrix} [2850] [2851] [2852] [2853] [2854] [2855] [2856] [2857] [2858] [2859] [2860] [2861] Underfull \hbox (badness 1596) in paragraph at lines 10489--10515 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [2862] [2863] Underfull \hbox (badness 1490) in paragraph at lines 10627--10633 [][][]\T1/fi4/m/sl/10 nlmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 nlm e.nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 nlmeObject[][][]\T1/ptm/m/n /10 , [][]\T1/fi4/m/sl/10 nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 nlm eStruct[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 reStruct[][][]\T1/ptm/m/n/10 , [2864] [2865] [2866] [2867] Underfull \hbox (badness 10000) in paragraph at lines 10865--10867 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [2868] [2869] [2870] [2871] [2872] [2873] [2874] [2875] [2876] [2877] [2878] [2879] [2880] [2881] [2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890] [2891] [2892] [2893] [2894] [2895] [2896] [2897] [2898] [2899] [2900] [2901] [2902] [2903] [2904] [2905] [2906] [2907] [2908] [2909] Underfull \hbox (badness 1286) in paragraph at lines 13722--13729 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/fi4/m/sl /10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/fi4/m/sl/10 inner \T1/ptm/m/n/10 or [2910] [2911] [2912] [2913] [2914] [2915] [2916] [2917] Underfull \hbox (badness 1215) in paragraph at lines 14250--14252 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [2918] [2919] [2920] [2921] [2922] [2923] [2924] [2925] [2926] [2927] [2928] [2929] [2930]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.random.effects}) has been already used, duplicate ignored \relax l.15131 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15131 ...Extract Random Effects}{random.effects} [2931] [2932] [2933] [2934] [2935] [2936] [2937] [2938] [2939] [2940] [2941] Underfull \hbox (badness 1067) in paragraph at lines 15842--15847 \T1/ptm/m/n/10 ma-trix), \T1/fi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues ), and \T1/fi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to [2942] [2943] [2944] [2945] Underfull \hbox (badness 1448) in paragraph at lines 16081--16090 \T1/ptm/m/n/10 Op-tions in-clude \T1/fi4/m/sl/10 "response" \T1/ptm/m/n/10 for the "raw" resid-u-als (ob-served - fit-ted), [2946] [2947] Underfull \hbox (badness 10000) in paragraph at lines 16209--16227 []\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form [2948] [2949] [2950] [2951] [2952] [2953] [2954] [2955] [2956] Underfull \hbox (badness 1728) in paragraph at lines 16786--16789 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [2957] [2958] [2959] [2960] Underfull \hbox (badness 10000) in paragraph at lines 17119--17128 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the \T 1/fi4/m/sl/10 pdMat Underfull \hbox (badness 6725) in paragraph at lines 17119--17128 \T1/ptm/m/n/10 class. De-fault de-pends on the method func-tion: \T1/fi4/m/sl/1 0 "Blocked" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17119--17128 \T1/fi4/m/sl/10 pdBlocked\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Compound Symmetry" \ T1/ptm/m/n/10 for \T1/fi4/m/sl/10 pdCompSymm\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "D iagonal" Underfull \hbox (badness 10000) in paragraph at lines 17119--17128 \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 pdDiag\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Mult iple of an Identity" \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 pdIdent\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17119--17128 \T1/fi4/m/sl/10 "General Positive-Definite, Natural Parametrization" \T1/ptm/m/ n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17119--17128 \T1/fi4/m/sl/10 pdNatural\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "General Positive-Def inite" \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 pdSymm\T1/ptm/m/n/10 , and [2961] Underfull \hbox (badness 10000) in paragraph at lines 17183--17191 \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 varComb\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Con stant plus power of covariate" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17183--17191 \T1/fi4/m/sl/10 varConstPower\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "Exponential of v ariance covariate" \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 varExp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17183--17191 \T1/fi4/m/sl/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for \T1/fi4/m/sl/10 varIdent\T1/ptm/m/n/10 , [2962] [2963] [2964] [2965] [2966] [2967] [2968] [2969] [2970] [2971] [2972] [2973] Underfull \hbox (badness 10000) in paragraph at lines 17959--17969 [][][]\T1/fi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/1 0 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.corLin[ ][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.corRatio[][][]\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 17959--17969 [][]\T1/fi4/m/sl/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl /10 Variogram.corSpher[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.defa ult[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.gls[][][]\T1/ptm/m/n/10 , [2974] [2975] [2976] [2977] [2978] Underfull \hbox (badness 5036) in paragraph at lines 18283--18292 [][][]\T1/fi4/m/sl/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Vari ogram[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.default[][][]\T1/ptm/ m/n/10 , [][]\T1/fi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/fi4 /m/sl/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [2979] [2980] [2981] [2982] [2983] [2984] [2985] [2986] [2987] [2988] [2989] [2990] [2991]) (./nnet-pkg.tex [2992] Chapter 26. [2993] Underfull \hbox (badness 10000) in paragraph at lines 78--87 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2994] [2995] [2996] [2997] [2998] [2999] [3000]) (./rpart-pkg.tex Chapter 27. [3001] [3002] [3003] [3004] [3005] Underfull \hbox (badness 2556) in paragraph at lines 349--353 \T1/ptm/m/n/10 im-plies \T1/fi4/m/sl/10 minlength = 0L\T1/ptm/m/n/10 , \T1/fi4/ m/sl/10 pretty = NULL \T1/ptm/m/n/10 im-plies \T1/fi4/m/sl/10 minlength = 1L\T1 /ptm/m/n/10 , and [3006] [3007] [3008] [3009] [3010] [3011] [3012] [3013] [3014] [3015] [3016] Underfull \hbox (badness 3219) in paragraph at lines 1113--1116 []\T1/ptm/m/n/10 For re-gres-sion or \T1/fi4/m/sl/10 anova \T1/ptm/m/n/10 trees all three resid-ual def-i-ni-tions re-duce to [3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027] [3028] [3029]) (./spatial-pkg.tex [3030] Chapter 28. [3031] [3032] [3033] [3034] [3035] [3036] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047] [3048] [3049]) (./survival-pkg.tex [3050] Chapter 29. [3051] [3052] [3053]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.212 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica te ignored \relax l.212 ... Myelogenous Leukemia survival data}{aml} [3054] [3055] [3056] [3057] Underfull \vbox (badness 10000) has occurred while \output is active [3058] [3059] [3060] [3061] [3062] [3063]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.colon}) has been already used, duplicate ignored \relax l.902 ...herapy for Stage B/C colon cancer}{colon} [3064] [3065] [3066] [3067] [3068] [3069] [3070] [3071] [3072] [3073] Overfull \hbox (139.78088pt too wide) in paragraph at lines 1671--1671 []\T1/fi4/m/sl/10 frailty.gamma(x, sparse = (nclass > 5), theta, df, eps = 1e- 05, method = c("em","aic", "df", "fixed"), ...)[] Overfull \hbox (94.78088pt too wide) in paragraph at lines 1672--1672 []\T1/fi4/m/sl/10 frailty.gaussian(x, sparse = (nclass > 5), theta, df, method =c("reml","aic", "df", "fixed"), ...)[] Overfull \hbox (134.78088pt too wide) in paragraph at lines 1673--1673 []\T1/fi4/m/sl/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, tdf = 5,method = c("aic", "df", "fixed"), ...)[] [3074] [3075] [3076] [3077] Underfull \vbox (badness 2012) has occurred while \output is active [3078] Underfull \hbox (badness 1389) in paragraph at lines 1966--1968 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3079] [3080] [3081] [3082] [3083] [3084] [3085] Underfull \vbox (badness 10000) has occurred while \output is active [3086] [3087] [3088] [3089] [3090] [3091] [3092] [3093] [3094] [3095] [3096] [3097] Underfull \hbox (badness 5274) in paragraph at lines 3190--3192 []\T1/ptm/m/n/10 an ob-ject of class \T1/fi4/m/sl/10 "summary.survfit"\T1/ptm/m /n/10 , which is the re-sult of the [3098] [3099] [3100] [3101] Underfull \hbox (badness 1540) in paragraph at lines 3535--3538 []\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per -son years if [3102] [3103] [3104] [3105] [3106] [3107] [3108] [3109] Underfull \hbox (badness 1281) in paragraph at lines 4085--4090 []\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/fi4/m/sl/10 "response "\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "deviance"\T1/ptm/m/n/10 , \T1/fi4/m/sl/10 "d fbeta"\T1/ptm/m/n/10 , [3110] [3111] [3112] [3113] [3114] [3115] [3116] [3117] [3118] [3119] [3120] [3121] Underfull \hbox (badness 10000) in paragraph at lines 4938--4947 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3122] [3123] [3124] Underfull \hbox (badness 4686) in paragraph at lines 5100--5102 []\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/fi4/m/sl/10 rateta ble \T1/ptm/m/n/10 is in units/day, [3125] [3126] [3127] Underfull \hbox (badness 10000) in paragraph at lines 5342--5346 [][][]\T1/fi4/m/sl/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 survfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 survfit.object[][][]\T 1/ptm/m/n/10 , [][]\T1/fi4/m/sl/10 print.survfit[][][]\T1/ptm/m/n/10 , [][]\T1/ fi4/m/sl/10 plot.survfit[][][]\T1/ptm/m/n/10 , [3128] [3129] [3130] [3131] [3132] [3133] [3134] [3135] [3136] Underfull \hbox (badness 1354) in paragraph at lines 6038--6042 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. 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at lines 5218--5219 []\T1/fi4/m/it/10 Compare,lsparseMatrix,lsparseMatrix-method Underfull \vbox (badness 1348) has occurred while \output is active [3211] Overfull \hbox (40.8567pt too wide) in paragraph at lines 5226--5227 []\T1/fi4/m/it/10 Compare,triangularMatrix,diagonalMatrix-method [3212] Underfull \vbox (badness 1226) has occurred while \output is active [3213] Overfull \hbox (30.8567pt too wide) in paragraph at lines 5394--5395 []\T1/fi4/m/it/10 crossprod,CsparseMatrix,CsparseMatrix-method Overfull \hbox (25.8567pt too wide) in paragraph at lines 5395--5396 []\T1/fi4/m/it/10 crossprod,CsparseMatrix,ddenseMatrix-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 5396--5397 []\T1/fi4/m/it/10 crossprod,CsparseMatrix,diagonalMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 5398--5399 []\T1/fi4/m/it/10 crossprod,CsparseMatrix,missing-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 5399--5400 []\T1/fi4/m/it/10 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Transcript written on fullrefman.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-FAQ.t2d/pdf/xt r/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/usr/share/texmf/fonts/map/pdftex/ updmap/pdftex.map}] [-1] Chapter 1 Cross reference values unknown; you must run TeX again. Chapter 2 [1] [2] [3] [4] [5] Underfull \hbox (badness 3158) in paragraph at lines 552--565 []@textrm Debian pack-ages, main-tained by Dirk Ed-del-buet-tel, have long been part of Underfull \hbox (badness 10000) in paragraph at lines 580--582 []@textrm See [][]@texttt http://CRAN.R-project.org/bin/linux/suse/README.html[ ][][] @textrm for in-for-ma-tion [6] Underfull \hbox (badness 10000) in paragraph at lines 663--666 []@textrm John M. Cham-bers (2008), ``Soft-ware for Data Anal-y-sis: Pro- Underfull \hbox (badness 8132) in paragraph at lines 663--666 @textrm gram-ming with R''. Springer, New York, ISBN 978-0-387-75935-7, Underfull \hbox (badness 10000) in paragraph at lines 671--674 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 671--674 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 2846) in paragraph at lines 690--693 []@textrm William N. Ven-ables and Brian D. Rip-ley (2002), ``Mod-ern Ap-plied Underfull \hbox (badness 10000) in paragraph at lines 690--693 @textrm Statis-tics with S'' (4th edi-tion). Springer, ISBN 0-387-95457-0, [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] Overfull \hbox (5.53629pt too wide) in paragraph at lines 1586--1589 []@textrm See also [][]@texttt http://en.wikipedia.org/wiki/R_programming_langu age#Commercialized_ Chapter 4 [18] [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] Underfull \hbox (badness 4217) in paragraph at lines 3299--3310 @texttt doku.php?id=tips:graphics-base:2yaxes[][][] @textrm for more in-for-ma- tion, in-clud-ing strong [40] [41] Chapter 8 [42] Chapter 9 [43] [44] Chapter 10 [45] [46] [47] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (49 pages, 337407 bytes). Transcript written on R-FAQ.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-FAQ.t2d/pdf/xt r/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-FAQ.aux) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/usr/share/texmf/fonts/map/pdftex/ updmap/pdftex.map}] (./R-FAQ.toc [-1] [-2]) [-3] (./R-FAQ.toc) (./R-FAQ.toc) Chapter 1 Chapter 2 [1] [2] [3] [4] [5] Underfull \hbox (badness 3158) in paragraph at lines 552--565 []@textrm Debian pack-ages, main-tained by Dirk Ed-del-buet-tel, have long been part of Underfull \hbox (badness 10000) in paragraph at lines 580--582 []@textrm See [][]@texttt http://CRAN.R-project.org/bin/linux/suse/README.html[ ][][] @textrm for in-for-ma-tion [6] Underfull \hbox (badness 10000) in paragraph at lines 663--666 []@textrm John M. Cham-bers (2008), ``Soft-ware for Data Anal-y-sis: Pro- Underfull \hbox (badness 8132) in paragraph at lines 663--666 @textrm gram-ming with R''. Springer, New York, ISBN 978-0-387-75935-7, Underfull \hbox (badness 10000) in paragraph at lines 671--674 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 671--674 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 2846) in paragraph at lines 690--693 []@textrm William N. Ven-ables and Brian D. Rip-ley (2002), ``Mod-ern Ap-plied Underfull \hbox (badness 10000) in paragraph at lines 690--693 @textrm Statis-tics with S'' (4th edi-tion). Springer, ISBN 0-387-95457-0, [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] Overfull \hbox (5.53629pt too wide) in paragraph at lines 1586--1589 []@textrm See also [][]@texttt http://en.wikipedia.org/wiki/R_programming_langu age#Commercialized_ Chapter 4 [18] [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] Underfull \hbox (badness 4217) in paragraph at lines 3299--3310 @texttt doku.php?id=tips:graphics-base:2yaxes[][][] @textrm for more in-for-ma- tion, in-clud-ing strong [40] [41] Chapter 8 [42] Chapter 9 [43] [44] Chapter 10 [45] [46] [47] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (51 pages, 388841 bytes). Transcript written on R-FAQ.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-FAQ.t2d/pdf/xt r/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-FAQ.aux) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/usr/share/texmf/fonts/map/pdftex/ updmap/pdftex.map}] (./R-FAQ.toc [-1] [-2]) [-3] (./R-FAQ.toc) (./R-FAQ.toc) Chapter 1 Chapter 2 [1] [2] [3] [4] [5] Underfull \hbox (badness 3158) in paragraph at lines 552--565 []@textrm Debian pack-ages, main-tained by Dirk Ed-del-buet-tel, have long been part of Underfull \hbox (badness 10000) in paragraph at lines 580--582 []@textrm See [][]@texttt http://CRAN.R-project.org/bin/linux/suse/README.html[ ][][] @textrm for in-for-ma-tion [6] Underfull \hbox (badness 10000) in paragraph at lines 663--666 []@textrm John M. Cham-bers (2008), ``Soft-ware for Data Anal-y-sis: Pro- Underfull \hbox (badness 8132) in paragraph at lines 663--666 @textrm gram-ming with R''. Springer, New York, ISBN 978-0-387-75935-7, Underfull \hbox (badness 10000) in paragraph at lines 671--674 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 671--674 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 2846) in paragraph at lines 690--693 []@textrm William N. Ven-ables and Brian D. Rip-ley (2002), ``Mod-ern Ap-plied Underfull \hbox (badness 10000) in paragraph at lines 690--693 @textrm Statis-tics with S'' (4th edi-tion). Springer, ISBN 0-387-95457-0, [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] Overfull \hbox (5.53629pt too wide) in paragraph at lines 1586--1589 []@textrm See also [][]@texttt http://en.wikipedia.org/wiki/R_programming_langu age#Commercialized_ Chapter 4 [18] [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] Underfull \hbox (badness 4217) in paragraph at lines 3299--3310 @texttt doku.php?id=tips:graphics-base:2yaxes[][][] @textrm for more in-for-ma- tion, in-clud-ing strong [40] [41] Chapter 8 [42] Chapter 9 [43] [44] Chapter 10 [45] [46] [47] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (51 pages, 388841 bytes). Transcript written on R-FAQ.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-admin.t2d/pdf/ xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Underfull \hbox (badness 4303) in paragraph at lines 188--194 @textrm to check out `@texttt r-devel[]@textrm '[] into di-rec-tory @textsl pat h @textrm (which will be cre-ated if nec-es-sary). Underfull \hbox (badness 2181) in paragraph at lines 188--194 @textrm The al-pha, beta and RC ver-sions of an up-com-ing @textsl x.y.0 @textr m re-lease are avail-able from [1] Chapter 2 [2] Cross reference values unknown; you must run TeX again. [3] [4] [5] [6] [7] Underfull \hbox (badness 2932) in paragraph at lines 770--780 []@textrm When sub-architectures are used the ver-sion of @texttt Rscript[] @te xtrm in e.g. `@texttt /usr/bin[]@textrm '[] will Underfull \hbox (badness 6775) in paragraph at lines 770--780 @textrm be the last in-stalled, but architecture-specific ver-sions will be ava il-able in e.g. [8] Underfull \hbox (badness 10000) in paragraph at lines 862--868 []@textrm One that may be use-ful when work-ing on R it-self is the op-tion Underfull \hbox (badness 10000) in paragraph at lines 862--868 @textrm `@texttt --disable-byte-compiled-packages[]@textrm '[], which en-sures that the base and rec-om- Chapter 3 [9] [10] Underfull \hbox (badness 7685) in paragraph at lines 1040--1044 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [11] Underfull \hbox (badness 10000) in paragraph at lines 1076--1083 []@textrm You need @texttt libpng[]@textrm , @texttt jpeg[] @textrm and @textt t libtiff[] @textrm sources (avail-able, e.g., from Underfull \hbox (badness 5460) in paragraph at lines 1076--1083 [][]@texttt http://www.libpng.org/[][][]@textrm , [][]@texttt http://www.ijg.o rg[][][] @textrm and [][]@texttt http://download.osgeo.org/ [12] Underfull \hbox (badness 10000) in paragraph at lines 1178--1182 []@textrm Running @texttt make[] @textrm in `@textttsl R_HOME@texttt /src/gnuwi n32/bitmap[]@textrm '[] or @texttt make bitmapdll[] @textrm in Underfull \hbox (badness 10000) in paragraph at lines 1178--1182 @textrm `@textttsl R_HOME@texttt /src/gnuwin32[]@textrm '[] should build `@text tt Rbitmap.dll[]@textrm '[] and in-stall it un-der Overfull \hbox (7.78543pt too wide) in paragraph at lines 1194--1200 @textrm built by Si-mon Ur-banek at [][]@texttt http://www.rforge.net/Cairo/fil es/cairo-current-win.tar.gz[][][]@textrm . [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] Chapter 6 [19] [20] [21] [22] [23] Underfull \hbox (badness 4467) in paragraph at lines 2017--2022 @textrm independent `@texttt configure.win[]@textrm '[], or if `@texttt --forc e-biarch[]@textrm '[] or a field in the [24] [25] Chapter 7 [26] [27] [28] Chapter 8 [29] Chapter 9 [30] [31] [32] Appendix A [33] [34] Underfull \hbox (badness 10000) in paragraph at lines 2923--2925 [][][]@smallrm also known as @smalltt ttf-mscorefonts-installer[] @smallrm in t he De-bian/Ubuntu world: see also Underfull \hbox (badness 3396) in paragraph at lines 2920--2938 @textrm avail-able at [][]@texttt https://fedorahosted.org/liberation-fonts/[][ ][]@textrm ,$[]$ which cover the Latin, [35] Underfull \hbox (badness 10000) in paragraph at lines 2988--2994 []@textrm The @texttt bitmap[] @textrm and @texttt dev2bitmap[] @textrm de-vice s and also @texttt embedFonts()[] @textrm use ghost-script [36] [37] [38] Underfull \hbox (badness 10000) in paragraph at lines 3273--3280 []@textrm For In-tel pro-ces-sors$[]$ un-der Linux, there is In-tel's Math Ker- nel Li-brary Underfull \hbox (badness 3428) in paragraph at lines 3273--3280 @textrm ([][]@texttt http://www.intel.com/software/products/mkl/[][][]@textrm ) . You are strongly en-cour-aged to [39] [40] [41] Appendix B [42] [43] [44] [45] [46] Appendix C [47] Underfull \hbox (badness 5504) in paragraph at lines 3967--3971 []@textrm C macros to se-lect par-tic-u-lar plat-forms can be tricky to track d own (there Underfull \hbox (badness 6961) in paragraph at lines 3967--3971 @textrm is a fair amount of mis-in-for-ma-tion on the Web). The Wiki (cur-rentl y) at Underfull \hbox (badness 10000) in paragraph at lines 3967--3971 [][]@texttt http://sourceforge.net/p/predef/wiki/Home/[][][] @textrm can be hel p-ful. The R sources [48] [49] [50] [51] Underfull \hbox (badness 2057) in paragraph at lines 4313--4321 @textrm (`Xcode') but nowa-days need to be in-stalled sep-a-rately. They can be down-loaded Underfull \hbox (badness 10000) in paragraph at lines 4313--4321 @textrm from [][]@texttt http://developer.apple.com/devcenter/mac/[][][] @textr m (you will need to reg-is- Underfull \hbox (badness 2512) in paragraph at lines 4313--4321 @textrm ter there) or if you have a re-cent Xcode in-stalled (from the App Stor e or from [52] [53] Overfull \hbox (18.36986pt too wide) in paragraph at lines 4483--4487 @textrm rently Java 7 from [][]@texttt http://www.oracle.com/technetwork/java/j avase/downloads/index.html[][][]@textrm ); Overfull \hbox (22.06111pt too wide) in paragraph at lines 4511--4511 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/1.6.0_43-b01-447.jdk/Con tents/Home[] [54] Overfull \hbox (154.06339pt too wide) in paragraph at lines 4572--4573 []@textrm See also the `@texttt INSTALL[]@textrm '[] file in the check-out or d i-rectly at [][]@texttt https://svn.r-project.org/R-packages/trunk/Mac-GUI/INST ALL[][][]@textrm . [55] Underfull \hbox (badness 10000) in paragraph at lines 4708--4711 []@textrm You can tar-get spe-cific Sparc ar-chi-tec-tures for (slightly) highe r per-for-mance: [56] [57] [58] Underfull \hbox (badness 2111) in paragraph at lines 4944--4949 []@textrm The re-cent WU test-ing was done us-ing com-pil-ers from both the @re ducedrm GNU @textrm Com-piler [59] [60] Underfull \hbox (badness 4492) in paragraph at lines 5136--5145 @textrm PACK code to avoid com-pu-ta-tions en-tirely in extended-precision reg- is-ters, so file Appendix D [61] [62] Underfull \hbox (badness 5302) in paragraph at lines 5334--5337 []@textrm You may need to set the en-vi-ron-ment vari-able @texttt CYGWIN[] @te xtrm to a value in-clud-ing [63] (Function and variable index) [64] (Concept index) [65] (Environment variable index) [66] [67] ) (see the transcript file for additional information) Output written on R-admin.pdf (70 pages, 408881 bytes). Transcript written on R-admin.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-admin.t2d/pdf/ xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-admin.aux) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-admin.toc [-1] [-2]) [-3] (./R-admin.toc) (./R-admin.toc) Chapter 1 Underfull \hbox (badness 4303) in paragraph at lines 188--194 @textrm to check out `@texttt r-devel[]@textrm '[] into di-rec-tory @textsl pat h @textrm (which will be cre-ated if nec-es-sary). Underfull \hbox (badness 2181) in paragraph at lines 188--194 @textrm The al-pha, beta and RC ver-sions of an up-com-ing @textsl x.y.0 @textr m re-lease are avail-able from [1] Chapter 2 [2] [3] [4] [5] [6] [7] Underfull \hbox (badness 2932) in paragraph at lines 770--780 []@textrm When sub-architectures are used the ver-sion of @texttt Rscript[] @te xtrm in e.g. `@texttt /usr/bin[]@textrm '[] will Underfull \hbox (badness 6775) in paragraph at lines 770--780 @textrm be the last in-stalled, but architecture-specific ver-sions will be ava il-able in e.g. [8] Underfull \hbox (badness 10000) in paragraph at lines 862--868 []@textrm One that may be use-ful when work-ing on R it-self is the op-tion Underfull \hbox (badness 10000) in paragraph at lines 862--868 @textrm `@texttt --disable-byte-compiled-packages[]@textrm '[], which en-sures that the base and rec-om- Chapter 3 [9] [10] Underfull \hbox (badness 7685) in paragraph at lines 1040--1044 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [11] Underfull \hbox (badness 10000) in paragraph at lines 1076--1083 []@textrm You need @texttt libpng[]@textrm , @texttt jpeg[] @textrm and @textt t libtiff[] @textrm sources (avail-able, e.g., from Underfull \hbox (badness 5460) in paragraph at lines 1076--1083 [][]@texttt http://www.libpng.org/[][][]@textrm , [][]@texttt http://www.ijg.o rg[][][] @textrm and [][]@texttt http://download.osgeo.org/ [12] Underfull \hbox (badness 10000) in paragraph at lines 1178--1182 []@textrm Running @texttt make[] @textrm in `@textttsl R_HOME@texttt /src/gnuwi n32/bitmap[]@textrm '[] or @texttt make bitmapdll[] @textrm in Underfull \hbox (badness 10000) in paragraph at lines 1178--1182 @textrm `@textttsl R_HOME@texttt /src/gnuwin32[]@textrm '[] should build `@text tt Rbitmap.dll[]@textrm '[] and in-stall it un-der Overfull \hbox (7.78543pt too wide) in paragraph at lines 1194--1200 @textrm built by Si-mon Ur-banek at [][]@texttt http://www.rforge.net/Cairo/fil es/cairo-current-win.tar.gz[][][]@textrm . [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] Chapter 6 [19] [20] [21] [22] [23] Underfull \hbox (badness 4467) in paragraph at lines 2017--2022 @textrm independent `@texttt configure.win[]@textrm '[], or if `@texttt --forc e-biarch[]@textrm '[] or a field in the [24] [25] Chapter 7 [26] [27] [28] Chapter 8 [29] Chapter 9 [30] [31] [32] Appendix A [33] [34] Underfull \hbox (badness 10000) in paragraph at lines 2923--2925 [][][]@smallrm also known as @smalltt ttf-mscorefonts-installer[] @smallrm in t he De-bian/Ubuntu world: see also Underfull \hbox (badness 3396) in paragraph at lines 2920--2938 @textrm avail-able at [][]@texttt https://fedorahosted.org/liberation-fonts/[][ ][]@textrm ,$[]$ which cover the Latin, [35] Underfull \hbox (badness 10000) in paragraph at lines 2988--2994 []@textrm The @texttt bitmap[] @textrm and @texttt dev2bitmap[] @textrm de-vice s and also @texttt embedFonts()[] @textrm use ghost-script [36] [37] [38] Underfull \hbox (badness 10000) in paragraph at lines 3273--3280 []@textrm For In-tel pro-ces-sors$[]$ un-der Linux, there is In-tel's Math Ker- nel Li-brary Underfull \hbox (badness 3428) in paragraph at lines 3273--3280 @textrm ([][]@texttt http://www.intel.com/software/products/mkl/[][][]@textrm ) . You are strongly en-cour-aged to [39] [40] [41] Appendix B [42] [43] [44] [45] [46] Appendix C [47] Underfull \hbox (badness 5504) in paragraph at lines 3967--3971 []@textrm C macros to se-lect par-tic-u-lar plat-forms can be tricky to track d own (there Underfull \hbox (badness 6961) in paragraph at lines 3967--3971 @textrm is a fair amount of mis-in-for-ma-tion on the Web). The Wiki (cur-rentl y) at Underfull \hbox (badness 10000) in paragraph at lines 3967--3971 [][]@texttt http://sourceforge.net/p/predef/wiki/Home/[][][] @textrm can be hel p-ful. The R sources [48] [49] [50] [51] Underfull \hbox (badness 2057) in paragraph at lines 4313--4321 @textrm (`Xcode') but nowa-days need to be in-stalled sep-a-rately. They can be down-loaded Underfull \hbox (badness 10000) in paragraph at lines 4313--4321 @textrm from [][]@texttt http://developer.apple.com/devcenter/mac/[][][] @textr m (you will need to reg-is- Underfull \hbox (badness 2512) in paragraph at lines 4313--4321 @textrm ter there) or if you have a re-cent Xcode in-stalled (from the App Stor e or from [52] [53] Overfull \hbox (18.36986pt too wide) in paragraph at lines 4483--4487 @textrm rently Java 7 from [][]@texttt http://www.oracle.com/technetwork/java/j avase/downloads/index.html[][][]@textrm ); Overfull \hbox (22.06111pt too wide) in paragraph at lines 4511--4511 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/1.6.0_43-b01-447.jdk/Con tents/Home[] [54] Overfull \hbox (154.06339pt too wide) in paragraph at lines 4572--4573 []@textrm See also the `@texttt INSTALL[]@textrm '[] file in the check-out or d i-rectly at [][]@texttt https://svn.r-project.org/R-packages/trunk/Mac-GUI/INST ALL[][][]@textrm . [55] Underfull \hbox (badness 10000) in paragraph at lines 4708--4711 []@textrm You can tar-get spe-cific Sparc ar-chi-tec-tures for (slightly) highe r per-for-mance: [56] [57] [58] Underfull \hbox (badness 2111) in paragraph at lines 4944--4949 []@textrm The re-cent WU test-ing was done us-ing com-pil-ers from both the @re ducedrm GNU @textrm Com-piler [59] [60] Underfull \hbox (badness 4492) in paragraph at lines 5136--5145 @textrm PACK code to avoid com-pu-ta-tions en-tirely in extended-precision reg- is-ters, so file Appendix D [61] [62] Underfull \hbox (badness 5302) in paragraph at lines 5334--5337 []@textrm You may need to set the en-vi-ron-ment vari-able @texttt CYGWIN[] @te xtrm to a value in-clud-ing [63] (Function and variable index) [64] (./R-admin.vrs) (Concept index) [65] (./R-admin.cps) (Environment variable index) [66] (./R-admin.ens) [67] ) (see the transcript file for additional information) Output written on R-admin.pdf (72 pages, 492554 bytes). Transcript written on R-admin.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-admin.t2d/pdf/ xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-admin.aux) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-admin.toc [-1] [-2]) [-3] (./R-admin.toc) (./R-admin.toc) Chapter 1 Underfull \hbox (badness 4303) in paragraph at lines 188--194 @textrm to check out `@texttt r-devel[]@textrm '[] into di-rec-tory @textsl pat h @textrm (which will be cre-ated if nec-es-sary). Underfull \hbox (badness 2181) in paragraph at lines 188--194 @textrm The al-pha, beta and RC ver-sions of an up-com-ing @textsl x.y.0 @textr m re-lease are avail-able from [1] Chapter 2 [2] [3] [4] [5] [6] [7] Underfull \hbox (badness 2932) in paragraph at lines 770--780 []@textrm When sub-architectures are used the ver-sion of @texttt Rscript[] @te xtrm in e.g. `@texttt /usr/bin[]@textrm '[] will Underfull \hbox (badness 6775) in paragraph at lines 770--780 @textrm be the last in-stalled, but architecture-specific ver-sions will be ava il-able in e.g. [8] Underfull \hbox (badness 10000) in paragraph at lines 862--868 []@textrm One that may be use-ful when work-ing on R it-self is the op-tion Underfull \hbox (badness 10000) in paragraph at lines 862--868 @textrm `@texttt --disable-byte-compiled-packages[]@textrm '[], which en-sures that the base and rec-om- Chapter 3 [9] [10] Underfull \hbox (badness 7685) in paragraph at lines 1040--1044 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [11] Underfull \hbox (badness 10000) in paragraph at lines 1076--1083 []@textrm You need @texttt libpng[]@textrm , @texttt jpeg[] @textrm and @textt t libtiff[] @textrm sources (avail-able, e.g., from Underfull \hbox (badness 5460) in paragraph at lines 1076--1083 [][]@texttt http://www.libpng.org/[][][]@textrm , [][]@texttt http://www.ijg.o rg[][][] @textrm and [][]@texttt http://download.osgeo.org/ [12] Underfull \hbox (badness 10000) in paragraph at lines 1178--1182 []@textrm Running @texttt make[] @textrm in `@textttsl R_HOME@texttt /src/gnuwi n32/bitmap[]@textrm '[] or @texttt make bitmapdll[] @textrm in Underfull \hbox (badness 10000) in paragraph at lines 1178--1182 @textrm `@textttsl R_HOME@texttt /src/gnuwin32[]@textrm '[] should build `@text tt Rbitmap.dll[]@textrm '[] and in-stall it un-der Overfull \hbox (7.78543pt too wide) in paragraph at lines 1194--1200 @textrm built by Si-mon Ur-banek at [][]@texttt http://www.rforge.net/Cairo/fil es/cairo-current-win.tar.gz[][][]@textrm . [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] Chapter 6 [19] [20] [21] [22] [23] Underfull \hbox (badness 4467) in paragraph at lines 2017--2022 @textrm independent `@texttt configure.win[]@textrm '[], or if `@texttt --forc e-biarch[]@textrm '[] or a field in the [24] [25] Chapter 7 [26] [27] [28] Chapter 8 [29] Chapter 9 [30] [31] [32] Appendix A [33] [34] Underfull \hbox (badness 10000) in paragraph at lines 2923--2925 [][][]@smallrm also known as @smalltt ttf-mscorefonts-installer[] @smallrm in t he De-bian/Ubuntu world: see also Underfull \hbox (badness 3396) in paragraph at lines 2920--2938 @textrm avail-able at [][]@texttt https://fedorahosted.org/liberation-fonts/[][ ][]@textrm ,$[]$ which cover the Latin, [35] Underfull \hbox (badness 10000) in paragraph at lines 2988--2994 []@textrm The @texttt bitmap[] @textrm and @texttt dev2bitmap[] @textrm de-vice s and also @texttt embedFonts()[] @textrm use ghost-script [36] [37] [38] Underfull \hbox (badness 10000) in paragraph at lines 3273--3280 []@textrm For In-tel pro-ces-sors$[]$ un-der Linux, there is In-tel's Math Ker- nel Li-brary Underfull \hbox (badness 3428) in paragraph at lines 3273--3280 @textrm ([][]@texttt http://www.intel.com/software/products/mkl/[][][]@textrm ) . You are strongly en-cour-aged to [39] [40] [41] Appendix B [42] [43] [44] [45] [46] Appendix C [47] Underfull \hbox (badness 5504) in paragraph at lines 3967--3971 []@textrm C macros to se-lect par-tic-u-lar plat-forms can be tricky to track d own (there Underfull \hbox (badness 6961) in paragraph at lines 3967--3971 @textrm is a fair amount of mis-in-for-ma-tion on the Web). The Wiki (cur-rentl y) at Underfull \hbox (badness 10000) in paragraph at lines 3967--3971 [][]@texttt http://sourceforge.net/p/predef/wiki/Home/[][][] @textrm can be hel p-ful. The R sources [48] [49] [50] [51] Underfull \hbox (badness 2057) in paragraph at lines 4313--4321 @textrm (`Xcode') but nowa-days need to be in-stalled sep-a-rately. They can be down-loaded Underfull \hbox (badness 10000) in paragraph at lines 4313--4321 @textrm from [][]@texttt http://developer.apple.com/devcenter/mac/[][][] @textr m (you will need to reg-is- Underfull \hbox (badness 2512) in paragraph at lines 4313--4321 @textrm ter there) or if you have a re-cent Xcode in-stalled (from the App Stor e or from [52] [53] Overfull \hbox (18.36986pt too wide) in paragraph at lines 4483--4487 @textrm rently Java 7 from [][]@texttt http://www.oracle.com/technetwork/java/j avase/downloads/index.html[][][]@textrm ); Overfull \hbox (22.06111pt too wide) in paragraph at lines 4511--4511 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/1.6.0_43-b01-447.jdk/Con tents/Home[] [54] Overfull \hbox (154.06339pt too wide) in paragraph at lines 4572--4573 []@textrm See also the `@texttt INSTALL[]@textrm '[] file in the check-out or d i-rectly at [][]@texttt https://svn.r-project.org/R-packages/trunk/Mac-GUI/INST ALL[][][]@textrm . [55] Underfull \hbox (badness 10000) in paragraph at lines 4708--4711 []@textrm You can tar-get spe-cific Sparc ar-chi-tec-tures for (slightly) highe r per-for-mance: [56] [57] [58] Underfull \hbox (badness 2111) in paragraph at lines 4944--4949 []@textrm The re-cent WU test-ing was done us-ing com-pil-ers from both the @re ducedrm GNU @textrm Com-piler [59] [60] Underfull \hbox (badness 4492) in paragraph at lines 5136--5145 @textrm PACK code to avoid com-pu-ta-tions en-tirely in extended-precision reg- is-ters, so file Appendix D [61] [62] Underfull \hbox (badness 5302) in paragraph at lines 5334--5337 []@textrm You may need to set the en-vi-ron-ment vari-able @texttt CYGWIN[] @te xtrm to a value in-clud-ing [63] (Function and variable index) [64] (./R-admin.vrs) (Concept index) [65] (./R-admin.cps) (Environment variable index) [66] (./R-admin.ens) [67] ) (see the transcript file for additional information) Output written on R-admin.pdf (72 pages, 492554 bytes). Transcript written on R-admin.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-data.t2d/pdf/x tr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Overfull \hbox (8.53186pt too wide) in paragraph at lines 97--97 [][]@textbf dataframes2xls[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 108--108 [][]@textbf RPostgreSQL[][]| Overfull \hbox (2.49414pt too wide) in paragraph at lines 115--115 [][]@textbf xlsReadWrite[][]| Chapter 1 [1] Cross reference values unknown; you must run TeX again. Underfull \hbox (badness 7558) in paragraph at lines 199--201 [][][]@smallrm Currently not avail-able from that repos-i-tory but as a source pack-age for down-load from [2] [3] [4] Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Underfull \hbox (badness 2088) in paragraph at lines 1103--1111 []@textrm Octave is a nu-mer-i-cal lin-ear al-ge-bra sys-tem ([][]@texttt http: //www.octave.org[][][]@textrm ), and func-tion Chapter 4 [13] Underfull \hbox (badness 3058) in paragraph at lines 1195--1201 @textrm data-bases and even text files (pos-si-bly com-pressed). Open Data-base Con-nec-tiv-ity [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 1354--1358 []@textrm Package [][]@textbf RMongo[][] @textrm pro-vides an R in-ter-face to a Java client for `Mon-goDB' Underfull \hbox (badness 10000) in paragraph at lines 1354--1358 @textrm ([][]@texttt http://en.wikipedia.org/wiki/MongoDB[][][]@textrm ) data-b ases, which are queried us-ing [16] Underfull \hbox (badness 3690) in paragraph at lines 1415--1419 []@textrm These are con-ve-nient in-ter-faces to read/write/test/delete ta-bles in the data-base. [17] Underfull \hbox (badness 2529) in paragraph at lines 1492--1496 @texttt access.php[][][]@textrm ) drivers pro-vide ODBC in-ter-faces to Ac-cess data-bases (in-clud-ing Ac-cess [18] Chapter 5 [19] Underfull \hbox (badness 10000) in paragraph at lines 1752--1758 []@textrm Packages [][]@textbf hdf5[][]@textrm , [][]@textbf h5r[][]@textrm , B io-con-duc-tor's @textbf rhdf5@textrm , [][]@textbf RNetCDF[][]@textrm , [][]@t extbf ncdf[][] @textrm and [][]@textbf ncdf4[][] @textrm on Underfull \hbox (badness 10000) in paragraph at lines 1752--1758 @reducedrm CRAN @textrm pro-vide in-ter-faces to @reducedrm NASA@textrm 's HDF5 (Hi-er-ar-chi-cal Data For-mat, see Underfull \hbox (badness 10000) in paragraph at lines 1752--1758 [][]@texttt http://hdf.ncsa.uiuc.edu/HDF5/[][][]@textrm ) and to UCAR's netCDF data files (net-work Underfull \hbox (badness 2111) in paragraph at lines 1778--1788 @textrm been adopted for the 'Xbase' fam-ily of data-bases, cov-er-ing dBase, C lip-per, Fox-Pro Chapter 6 [20] Chapter 7 [21] [22] [23] Underfull \hbox (badness 2150) in paragraph at lines 2088--2092 []@textrm A sum-mary of all the con-nec-tions cur-rently opened by the user can be found by [24] Chapter 8 [25] Underfull \hbox (badness 3815) in paragraph at lines 2234--2236 []@textrm The ear-lier low-level in-ter-face is given by func-tions @texttt mak e.socket[]@textrm , @texttt read.socket[]@textrm , Chapter 9 [26] Underfull \hbox (badness 2012) in paragraph at lines 2307--2316 []@textrm If you do not have Ex-cel, many other pro-grams are able to read such spread- Underfull \hbox (badness 7326) in paragraph at lines 2307--2316 @textrm sheets and ex-port in a text for-mat on both Win-dows and Unix, for ex- am- Underfull \hbox (badness 10000) in paragraph at lines 2307--2316 @textrm ple Gnu-meric ([][]@texttt http://www.gnome.org/projects/gnumeric/[][][ ]@textrm ) and OpenOf-fice Appendix A [27] Overfull \hbox (44.1188pt too wide) in paragraph at lines 2398--2401 @textrm B. D. Rip-ley (2001) Con-nec-tions. @texttt \@textit R News@textrm , @t extbf 1/1@textrm , 16--7. @texttt \[][]http://www.r-project.org/doc/Rnews/Rnews _ (Function and variable index) [28] (Concept index) [29] [30] ) (see the transcript file for additional information) Output written on R-data.pdf (33 pages, 241180 bytes). Transcript written on R-data.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-data.t2d/pdf/x tr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-data.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-data.toc [-1]) [-2] (./R-data.toc) (./R-data.toc) (Acknowledgements) Overfull \hbox (8.53186pt too wide) in paragraph at lines 97--97 [][]@textbf dataframes2xls[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 108--108 [][]@textbf RPostgreSQL[][]| Overfull \hbox (2.49414pt too wide) in paragraph at lines 115--115 [][]@textbf xlsReadWrite[][]| Chapter 1 [1] Underfull \hbox (badness 7558) in paragraph at lines 199--201 [][][]@smallrm Currently not avail-able from that repos-i-tory but as a source pack-age for down-load from [2] [3] [4] Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Underfull \hbox (badness 2088) in paragraph at lines 1103--1111 []@textrm Octave is a nu-mer-i-cal lin-ear al-ge-bra sys-tem ([][]@texttt http: //www.octave.org[][][]@textrm ), and func-tion Chapter 4 [13] Underfull \hbox (badness 3058) in paragraph at lines 1195--1201 @textrm data-bases and even text files (pos-si-bly com-pressed). Open Data-base Con-nec-tiv-ity [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 1354--1358 []@textrm Package [][]@textbf RMongo[][] @textrm pro-vides an R in-ter-face to a Java client for `Mon-goDB' Underfull \hbox (badness 10000) in paragraph at lines 1354--1358 @textrm ([][]@texttt http://en.wikipedia.org/wiki/MongoDB[][][]@textrm ) data-b ases, which are queried us-ing [16] Underfull \hbox (badness 3690) in paragraph at lines 1415--1419 []@textrm These are con-ve-nient in-ter-faces to read/write/test/delete ta-bles in the data-base. [17] Underfull \hbox (badness 2529) in paragraph at lines 1492--1496 @texttt access.php[][][]@textrm ) drivers pro-vide ODBC in-ter-faces to Ac-cess data-bases (in-clud-ing Ac-cess [18] Chapter 5 [19] Underfull \hbox (badness 10000) in paragraph at lines 1752--1758 []@textrm Packages [][]@textbf hdf5[][]@textrm , [][]@textbf h5r[][]@textrm , B io-con-duc-tor's @textbf rhdf5@textrm , [][]@textbf RNetCDF[][]@textrm , [][]@t extbf ncdf[][] @textrm and [][]@textbf ncdf4[][] @textrm on Underfull \hbox (badness 10000) in paragraph at lines 1752--1758 @reducedrm CRAN @textrm pro-vide in-ter-faces to @reducedrm NASA@textrm 's HDF5 (Hi-er-ar-chi-cal Data For-mat, see Underfull \hbox (badness 10000) in paragraph at lines 1752--1758 [][]@texttt http://hdf.ncsa.uiuc.edu/HDF5/[][][]@textrm ) and to UCAR's netCDF data files (net-work Underfull \hbox (badness 2111) in paragraph at lines 1778--1788 @textrm been adopted for the 'Xbase' fam-ily of data-bases, cov-er-ing dBase, C lip-per, Fox-Pro Chapter 6 [20] Chapter 7 [21] [22] [23] Underfull \hbox (badness 2150) in paragraph at lines 2088--2092 []@textrm A sum-mary of all the con-nec-tions cur-rently opened by the user can be found by [24] Chapter 8 [25] Underfull \hbox (badness 3815) in paragraph at lines 2234--2236 []@textrm The ear-lier low-level in-ter-face is given by func-tions @texttt mak e.socket[]@textrm , @texttt read.socket[]@textrm , Chapter 9 [26] Underfull \hbox (badness 2012) in paragraph at lines 2307--2316 []@textrm If you do not have Ex-cel, many other pro-grams are able to read such spread- Underfull \hbox (badness 7326) in paragraph at lines 2307--2316 @textrm sheets and ex-port in a text for-mat on both Win-dows and Unix, for ex- am- Underfull \hbox (badness 10000) in paragraph at lines 2307--2316 @textrm ple Gnu-meric ([][]@texttt http://www.gnome.org/projects/gnumeric/[][][ ]@textrm ) and OpenOf-fice Appendix A [27] Overfull \hbox (44.1188pt too wide) in paragraph at lines 2398--2401 @textrm B. D. Rip-ley (2001) Con-nec-tions. @texttt \@textit R News@textrm , @t extbf 1/1@textrm , 16--7. @texttt \[][]http://www.r-project.org/doc/Rnews/Rnews _ (Function and variable index) [28] (./R-data.vrs [29]) (Concept index) [30] (./R-data.cps) [31] ) (see the transcript file for additional information) Output written on R-data.pdf (35 pages, 308829 bytes). Transcript written on R-data.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-data.t2d/pdf/x tr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-data.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-data.toc [-1]) [-2] (./R-data.toc) (./R-data.toc) (Acknowledgements) Overfull \hbox (8.53186pt too wide) in paragraph at lines 97--97 [][]@textbf dataframes2xls[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 108--108 [][]@textbf RPostgreSQL[][]| Overfull \hbox (2.49414pt too wide) in paragraph at lines 115--115 [][]@textbf xlsReadWrite[][]| Chapter 1 [1] Underfull \hbox (badness 7558) in paragraph at lines 199--201 [][][]@smallrm Currently not avail-able from that repos-i-tory but as a source pack-age for down-load from [2] [3] [4] Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Underfull \hbox (badness 2088) in paragraph at lines 1103--1111 []@textrm Octave is a nu-mer-i-cal lin-ear al-ge-bra sys-tem ([][]@texttt http: //www.octave.org[][][]@textrm ), and func-tion Chapter 4 [13] Underfull \hbox (badness 3058) in paragraph at lines 1195--1201 @textrm data-bases and even text files (pos-si-bly com-pressed). Open Data-base Con-nec-tiv-ity [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 1354--1358 []@textrm Package [][]@textbf RMongo[][] @textrm pro-vides an R in-ter-face to a Java client for `Mon-goDB' Underfull \hbox (badness 10000) in paragraph at lines 1354--1358 @textrm ([][]@texttt http://en.wikipedia.org/wiki/MongoDB[][][]@textrm ) data-b ases, which are queried us-ing [16] Underfull \hbox (badness 3690) in paragraph at lines 1415--1419 []@textrm These are con-ve-nient in-ter-faces to read/write/test/delete ta-bles in the data-base. [17] Underfull \hbox (badness 2529) in paragraph at lines 1492--1496 @texttt access.php[][][]@textrm ) drivers pro-vide ODBC in-ter-faces to Ac-cess data-bases (in-clud-ing Ac-cess [18] Chapter 5 [19] Underfull \hbox (badness 10000) in paragraph at lines 1752--1758 []@textrm Packages [][]@textbf hdf5[][]@textrm , [][]@textbf h5r[][]@textrm , B io-con-duc-tor's @textbf rhdf5@textrm , [][]@textbf RNetCDF[][]@textrm , [][]@t extbf ncdf[][] @textrm and [][]@textbf ncdf4[][] @textrm on Underfull \hbox (badness 10000) in paragraph at lines 1752--1758 @reducedrm CRAN @textrm pro-vide in-ter-faces to @reducedrm NASA@textrm 's HDF5 (Hi-er-ar-chi-cal Data For-mat, see Underfull \hbox (badness 10000) in paragraph at lines 1752--1758 [][]@texttt http://hdf.ncsa.uiuc.edu/HDF5/[][][]@textrm ) and to UCAR's netCDF data files (net-work Underfull \hbox (badness 2111) in paragraph at lines 1778--1788 @textrm been adopted for the 'Xbase' fam-ily of data-bases, cov-er-ing dBase, C lip-per, Fox-Pro Chapter 6 [20] Chapter 7 [21] [22] [23] Underfull \hbox (badness 2150) in paragraph at lines 2088--2092 []@textrm A sum-mary of all the con-nec-tions cur-rently opened by the user can be found by [24] Chapter 8 [25] Underfull \hbox (badness 3815) in paragraph at lines 2234--2236 []@textrm The ear-lier low-level in-ter-face is given by func-tions @texttt mak e.socket[]@textrm , @texttt read.socket[]@textrm , Chapter 9 [26] Underfull \hbox (badness 2012) in paragraph at lines 2307--2316 []@textrm If you do not have Ex-cel, many other pro-grams are able to read such spread- Underfull \hbox (badness 7326) in paragraph at lines 2307--2316 @textrm sheets and ex-port in a text for-mat on both Win-dows and Unix, for ex- am- Underfull \hbox (badness 10000) in paragraph at lines 2307--2316 @textrm ple Gnu-meric ([][]@texttt http://www.gnome.org/projects/gnumeric/[][][ ]@textrm ) and OpenOf-fice Appendix A [27] Overfull \hbox (44.1188pt too wide) in paragraph at lines 2398--2401 @textrm B. D. Rip-ley (2001) Con-nec-tions. @texttt \@textit R News@textrm , @t extbf 1/1@textrm , 16--7. @texttt \[][]http://www.r-project.org/doc/Rnews/Rnews _ (Function and variable index) [28] (./R-data.vrs [29]) (Concept index) [30] (./R-data.cps) [31] ) (see the transcript file for additional information) Output written on R-data.pdf (35 pages, 308827 bytes). Transcript written on R-data.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-data.t2d/pdf/x tr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-data.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-data.toc [-1]) [-2] (./R-data.toc) (./R-data.toc) (Acknowledgements) Overfull \hbox (8.53186pt too wide) in paragraph at lines 97--97 [][]@textbf dataframes2xls[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 108--108 [][]@textbf RPostgreSQL[][]| Overfull \hbox (2.49414pt too wide) in paragraph at lines 115--115 [][]@textbf xlsReadWrite[][]| Chapter 1 [1] Underfull \hbox (badness 7558) in paragraph at lines 199--201 [][][]@smallrm Currently not avail-able from that repos-i-tory but as a source pack-age for down-load from [2] [3] [4] Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Underfull \hbox (badness 2088) in paragraph at lines 1103--1111 []@textrm Octave is a nu-mer-i-cal lin-ear al-ge-bra sys-tem ([][]@texttt http: //www.octave.org[][][]@textrm ), and func-tion Chapter 4 [13] Underfull \hbox (badness 3058) in paragraph at lines 1195--1201 @textrm data-bases and even text files (pos-si-bly com-pressed). Open Data-base Con-nec-tiv-ity [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 1354--1358 []@textrm Package [][]@textbf RMongo[][] @textrm pro-vides an R in-ter-face to a Java client for `Mon-goDB' Underfull \hbox (badness 10000) in paragraph at lines 1354--1358 @textrm ([][]@texttt http://en.wikipedia.org/wiki/MongoDB[][][]@textrm ) data-b ases, which are queried us-ing [16] Underfull \hbox (badness 3690) in paragraph at lines 1415--1419 []@textrm These are con-ve-nient in-ter-faces to read/write/test/delete ta-bles in the data-base. [17] Underfull \hbox (badness 2529) in paragraph at lines 1492--1496 @texttt access.php[][][]@textrm ) drivers pro-vide ODBC in-ter-faces to Ac-cess data-bases (in-clud-ing Ac-cess [18] Chapter 5 [19] Underfull \hbox (badness 10000) in paragraph at lines 1752--1758 []@textrm Packages [][]@textbf hdf5[][]@textrm , [][]@textbf h5r[][]@textrm , B io-con-duc-tor's @textbf rhdf5@textrm , [][]@textbf RNetCDF[][]@textrm , [][]@t extbf ncdf[][] @textrm and [][]@textbf ncdf4[][] @textrm on Underfull \hbox (badness 10000) in paragraph at lines 1752--1758 @reducedrm CRAN @textrm pro-vide in-ter-faces to @reducedrm NASA@textrm 's HDF5 (Hi-er-ar-chi-cal Data For-mat, see Underfull \hbox (badness 10000) in paragraph at lines 1752--1758 [][]@texttt http://hdf.ncsa.uiuc.edu/HDF5/[][][]@textrm ) and to UCAR's netCDF data files (net-work Underfull \hbox (badness 2111) in paragraph at lines 1778--1788 @textrm been adopted for the 'Xbase' fam-ily of data-bases, cov-er-ing dBase, C lip-per, Fox-Pro Chapter 6 [20] Chapter 7 [21] [22] [23] Underfull \hbox (badness 2150) in paragraph at lines 2088--2092 []@textrm A sum-mary of all the con-nec-tions cur-rently opened by the user can be found by [24] Chapter 8 [25] Underfull \hbox (badness 3815) in paragraph at lines 2234--2236 []@textrm The ear-lier low-level in-ter-face is given by func-tions @texttt mak e.socket[]@textrm , @texttt read.socket[]@textrm , Chapter 9 [26] Underfull \hbox (badness 2012) in paragraph at lines 2307--2316 []@textrm If you do not have Ex-cel, many other pro-grams are able to read such spread- Underfull \hbox (badness 7326) in paragraph at lines 2307--2316 @textrm sheets and ex-port in a text for-mat on both Win-dows and Unix, for ex- am- Underfull \hbox (badness 10000) in paragraph at lines 2307--2316 @textrm ple Gnu-meric ([][]@texttt http://www.gnome.org/projects/gnumeric/[][][ ]@textrm ) and OpenOf-fice Appendix A [27] Overfull \hbox (44.1188pt too wide) in paragraph at lines 2398--2401 @textrm B. D. Rip-ley (2001) Con-nec-tions. @texttt \@textit R News@textrm , @t extbf 1/1@textrm , 16--7. @texttt \[][]http://www.r-project.org/doc/Rnews/Rnews _ (Function and variable index) [28] (./R-data.vrs [29]) (Concept index) [30] (./R-data.cps) [31] ) (see the transcript file for additional information) Output written on R-data.pdf (35 pages, 308827 bytes). Transcript written on R-data.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-exts.t2d/pdf/x tr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Chapter 1 [1] Cross reference values unknown; you must run TeX again. [2] Underfull \hbox (badness 4660) in paragraph at lines 275--278 []@textrm For the con-ven-tions for files `@texttt NEWS[]@textrm '[] and `@text tt ChangeLog[]@textrm '[] in the @reducedrm GNU @textrm project see [3] [4] [5] [6] [7] Underfull \hbox (badness 5847) in paragraph at lines 690--701 @textrm of Eco-nomic Lit-er-a-ture Clas-si-fi-ca-tion Sys-tem, [][]@texttt http ://www.aeaweb.org/journal/jel_ Underfull \hbox (badness 5231) in paragraph at lines 690--701 @textrm of the Amer-i-can Math-e-mat-i-cal So-ci-ety, [][]@texttt http://www.am s.org/msc/[][][]@textrm ). The sub-ject [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] Underfull \hbox (badness 10000) in paragraph at lines 1742--1744 [][][][][]@smalltt http://www.openmp.org/[][][]@smallrm , [][]@smalltt http://e n.wikipedia.org/wiki/OpenMP[][][]@smallrm , [][]@smalltt https://computing.llnl .gov/ [20] Overfull \hbox (46.15797pt too wide) in paragraph at lines 1880--1880 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 1882--1882 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [21] [22] [23] [24] [25] [26] [27] [28] Underfull \hbox (badness 2809) in paragraph at lines 2485--2491 @textrm (or set the en-vi-ron-ment vari-able @texttt _R_BUILD_KEEP_EMPTY_DIRS_[ ] @textrm to `@texttt TRUE[]@textrm '[], or have a [29] [30] Underfull \hbox (badness 4556) in paragraph at lines 2710--2718 @textrm Others you may see are @texttt \VignettePackage[] @textrm (cur-rently i g-nored), @texttt \VignetteDepends[] Underfull \hbox (badness 2617) in paragraph at lines 2710--2718 @textrm pack-age in-stal-la-tion time to cre-ate the saved data frame `@texttt Meta/vignette.rds[]@textrm '[], but Underfull \hbox (badness 3579) in paragraph at lines 2710--2718 @textrm The @texttt \VignetteEngine[] @textrm state-ment is de-scribed in [][]$ @textsy h$@textrm un-de-fined$@textsy i$ @textrm [Non-Sweave vi-gnettes], [31] [32] Overfull \hbox (70.02316pt too wide) in paragraph at lines 2870--2872 []@textrm Current sub-mis-sion in-struc-tions are linked from [][]@texttt http: //CRAN.R-project.org/banner.shtml#submitting[][][]@textrm . [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] Chapter 2 [47] [48] [49] [50] [51] [52] [53] [54] Underfull \hbox (badness 2707) in paragraph at lines 4847--4853 []@textrm Packages may have an over-view help page with an @texttt \alias[] @te xtttsl pkg-name@texttt -package[]@textrm , e.g. Underfull \hbox (badness 3635) in paragraph at lines 4854--4860 []@textrm Skeletons of doc-u-men-ta-tion for a pack-age can be gen-er-ated us-i ng the func-tion [55] [56] [57] [58] [59] Underfull \hbox (badness 10000) in paragraph at lines 5232--5239 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and Underfull \hbox (badness 3919) in paragraph at lines 5232--5239 @texttt \figure{@textttsl filename@texttt }{@textttsl alternate text@texttt }[] @textrm . This will in-clude a copy of the fig-ure in [60] [61] Underfull \hbox (badness 10000) in paragraph at lines 5409--5415 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text @textrm part of [62] [63] [64] Overfull \hbox (3.59178pt too wide) in paragraph at lines 5678--5681 []@textrm Another is the Eclipse IDE with the Stat-ET plu-gin ([][]@texttt http ://www.walware.de/goto/statet[][][]@textrm ), Underfull \hbox (badness 3029) in paragraph at lines 5685--5687 []@textrm Some R front-ends pro-vide edit-ing sup-port for `@texttt .Rd[]@textr m '[] files, for ex-am-ple RStu-dio Chapter 3 [65] [66] [67] [68] Underfull \hbox (badness 2443) in paragraph at lines 6037--6040 []@textrm Data frames are slower than ma-tri-ces and this is an ex-am-ple of wh y. Us-ing Underfull \hbox (badness 10000) in paragraph at lines 6060--6065 []@textrm Options in-clude us-ing @texttt sprof[] @textrm for a shared ob-ject, and @texttt oprofile[] @textrm (see Underfull \hbox (badness 4927) in paragraph at lines 6060--6065 [][]@texttt http://oprofile.sourceforge.net/[][][]@textrm ) and @texttt perf[] @textrm (see [][]@texttt https://perf.wiki.kernel.org/ [69] [70] Overfull \hbox (310.88272pt too wide) in paragraph at lines 6153--6158 [][]@texttt https://developer.apple.com/library/mac/#documentation/DeveloperToo ls/Conceptual/InstrumentsUserGuide/Introduction/Introduction.html[][][]@textrm ). Chapter 4 [71] [72] [73] [74] [75] Underfull \hbox (badness 10000) in paragraph at lines 6534--6543 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [76] [77] Underfull \hbox (badness 10000) in paragraph at lines 6742--6746 []@texttt valgrind[] @textrm is good at spot-ting the use of unini-tial-ized va l-ues: use op-tion [78] Overfull \hbox (50.80455pt too wide) in paragraph at lines 6835--6835 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [79] [80] [81] [82] Chapter 5 [83] [84] [85] [86] [87] [88] [89] [90] Underfull \hbox (badness 10000) in paragraph at lines 7871--7882 @textrm file `@texttt README.packages[]@textrm '[] and [][]@texttt http://www.s tats.uwo.ca/faculty/murdoch/software/ [91] [92] [93] Overfull \hbox (16.31242pt too wide) in paragraph at lines 8110--8110 []@texttt PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="pa ckB"))' \[] [94] Overfull \hbox (37.99364pt too wide) in paragraph at lines 8159--8159 []@texttt PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="pa ckB"))' \[] [95] [96] [97] [98] [99] [100] [101] [102] Underfull \hbox (badness 2781) in paragraph at lines 8885--8887 [][][]@smallrm You can as-sign a @smallit copy @smallrm of the ob-ject in the e n-vi-ron-ment frame @smalltt rho[] @smallrm us-ing @smalltt defineVar(symbol, [103] Underfull \hbox (badness 10000) in paragraph at lines 8967--8969 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] Overfull \hbox (22.06111pt too wide) in paragraph at lines 9995--9995 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [117] Chapter 6 [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] Underfull \hbox (badness 10000) in paragraph at lines 11145--11149 @texttt <- order(x, y, na.last, decreasing)[] @textrm cor-re-sponds to @texttt R_orderVector(indx, n, [129] [130] [131] Underfull \hbox (badness 2689) in paragraph at lines 11450--11456 []@textrm The vis-i-bil-ity mech-a-nism is not avail-able on Win-dows, but ther e is an equally [132] [133] Underfull \hbox (badness 10000) in paragraph at lines 11579--11587 []@textrm The graph-ics sys-tems are ex-posed in head-ers `@texttt R_ext/Graphi csEngine.h[]@textrm '[], Underfull \hbox (badness 3240) in paragraph at lines 11579--11587 @textrm `@texttt R_ext/GraphicsDevice.h[]@textrm '[] (which it in-cludes) and ` @texttt R_ext/QuartzDevice.h[]@textrm '[]. Fa-cil-i- Chapter 7 [134] [135] Chapter 8 [136] [137] [138] Overfull \hbox (33.55849pt too wide) in paragraph at lines 11986--11986 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [139] [140] [141] Underfull \hbox (badness 10000) in paragraph at lines 12229--12236 @texttt internet/nanoftp.c[]@textrm '[], `@texttt src/modules/internet/nanohtt p.c[]@textrm '[] and `@texttt src/modules/ [142] [143] Underfull \hbox (badness 10000) in paragraph at lines 12349--12358 []@textrm There is a (D)COM server called @texttt StatConnector[] @textrm writ -ten by Thomas Underfull \hbox (badness 10000) in paragraph at lines 12349--12358 @textrm Baier avail-able via [][]@texttt http://CRAN.R-project.org/other-softw are.html[][][] @textrm or [144] [145] Underfull \hbox (badness 6284) in paragraph at lines 12495--12502 @textrm may be avail-able from the Win-dows Reg-istry: it will be in @texttt H KEY_LOCAL_ Underfull \hbox (badness 10000) in paragraph at lines 12495--12502 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and Underfull \hbox (badness 3769) in paragraph at lines 12495--12502 @texttt HKEY_CURRENT_USER\Software\R-core\R\InstallPath[] @textrm oth-er-wise, if se-lected dur-ing [146] (Function and variable index) [147] (Concept index) [148] [149] ) (see the transcript file for additional information) Output written on R-exts.pdf (152 pages, 758222 bytes). Transcript written on R-exts.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-exts.t2d/pdf/x tr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-exts.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-exts.toc [-1] [-2] [-3]) [-4] (./R-exts.toc) (./R-exts.toc) (Acknowledgements) Chapter 1 [1] [2] Underfull \hbox (badness 4660) in paragraph at lines 275--278 []@textrm For the con-ven-tions for files `@texttt NEWS[]@textrm '[] and `@text tt ChangeLog[]@textrm '[] in the @reducedrm GNU @textrm project see [3] [4] [5] [6] [7] Underfull \hbox (badness 5847) in paragraph at lines 690--701 @textrm of Eco-nomic Lit-er-a-ture Clas-si-fi-ca-tion Sys-tem, [][]@texttt http ://www.aeaweb.org/journal/jel_ Underfull \hbox (badness 5231) in paragraph at lines 690--701 @textrm of the Amer-i-can Math-e-mat-i-cal So-ci-ety, [][]@texttt http://www.am s.org/msc/[][][]@textrm ). The sub-ject [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] Underfull \hbox (badness 10000) in paragraph at lines 1742--1744 [][][][][]@smalltt http://www.openmp.org/[][][]@smallrm , [][]@smalltt http://e n.wikipedia.org/wiki/OpenMP[][][]@smallrm , [][]@smalltt https://computing.llnl .gov/ [20] Overfull \hbox (46.15797pt too wide) in paragraph at lines 1880--1880 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 1882--1882 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [21] [22] [23] [24] [25] [26] [27] Underfull \hbox (badness 2809) in paragraph at lines 2485--2491 @textrm (or set the en-vi-ron-ment vari-able @texttt _R_BUILD_KEEP_EMPTY_DIRS_[ ] @textrm to `@texttt TRUE[]@textrm '[], or have a [28] [29] [30] Underfull \hbox (badness 4556) in paragraph at lines 2710--2718 @textrm Others you may see are @texttt \VignettePackage[] @textrm (cur-rently i g-nored), @texttt \VignetteDepends[] [31] [32] Overfull \hbox (70.02316pt too wide) in paragraph at lines 2870--2872 []@textrm Current sub-mis-sion in-struc-tions are linked from [][]@texttt http: //CRAN.R-project.org/banner.shtml#submitting[][][]@textrm . [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] Chapter 2 [47] [48] [49] [50] [51] [52] [53] Underfull \hbox (badness 2707) in paragraph at lines 4847--4853 []@textrm Packages may have an over-view help page with an @texttt \alias[] @te xtttsl pkg-name@texttt -package[]@textrm , e.g. Underfull \hbox (badness 3635) in paragraph at lines 4854--4860 []@textrm Skeletons of doc-u-men-ta-tion for a pack-age can be gen-er-ated us-i ng the func-tion [54] [55] [56] [57] [58] Underfull \hbox (badness 10000) in paragraph at lines 5232--5239 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and Underfull \hbox (badness 3919) in paragraph at lines 5232--5239 @texttt \figure{@textttsl filename@texttt }{@textttsl alternate text@texttt }[] @textrm . This will in-clude a copy of the fig-ure in [59] [60] Underfull \hbox (badness 10000) in paragraph at lines 5409--5415 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text @textrm part of [61] [62] [63] Overfull \hbox (3.59178pt too wide) in paragraph at lines 5678--5681 []@textrm Another is the Eclipse IDE with the Stat-ET plu-gin ([][]@texttt http ://www.walware.de/goto/statet[][][]@textrm ), Underfull \hbox (badness 3029) in paragraph at lines 5685--5687 []@textrm Some R front-ends pro-vide edit-ing sup-port for `@texttt .Rd[]@textr m '[] files, for ex-am-ple RStu-dio Chapter 3 [64] [65] [66] [67] Underfull \hbox (badness 2443) in paragraph at lines 6037--6040 []@textrm Data frames are slower than ma-tri-ces and this is an ex-am-ple of wh y. Us-ing Underfull \hbox (badness 10000) in paragraph at lines 6060--6065 []@textrm Options in-clude us-ing @texttt sprof[] @textrm for a shared ob-ject, and @texttt oprofile[] @textrm (see Underfull \hbox (badness 4927) in paragraph at lines 6060--6065 [][]@texttt http://oprofile.sourceforge.net/[][][]@textrm ) and @texttt perf[] @textrm (see [][]@texttt https://perf.wiki.kernel.org/ [68] [69] Overfull \hbox (310.88272pt too wide) in paragraph at lines 6153--6158 [][]@texttt https://developer.apple.com/library/mac/#documentation/DeveloperToo ls/Conceptual/InstrumentsUserGuide/Introduction/Introduction.html[][][]@textrm ). Chapter 4 [70] [71] [72] [73] [74] Underfull \hbox (badness 10000) in paragraph at lines 6534--6543 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [75] [76] Underfull \hbox (badness 10000) in paragraph at lines 6742--6746 []@texttt valgrind[] @textrm is good at spot-ting the use of unini-tial-ized va l-ues: use op-tion [77] Overfull \hbox (50.80455pt too wide) in paragraph at lines 6835--6835 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [78] [79] [80] [81] Chapter 5 [82] [83] [84] [85] [86] [87] [88] [89] Underfull \hbox (badness 10000) in paragraph at lines 7871--7882 @textrm file `@texttt README.packages[]@textrm '[] and [][]@texttt http://www.s tats.uwo.ca/faculty/murdoch/software/ [90] [91] [92] Overfull \hbox (16.31242pt too wide) in paragraph at lines 8110--8110 []@texttt PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="pa ckB"))' \[] [93] Overfull \hbox (37.99364pt too wide) in paragraph at lines 8159--8159 []@texttt PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="pa ckB"))' \[] [94] [95] [96] [97] [98] [99] [100] [101] Underfull \hbox (badness 2781) in paragraph at lines 8885--8887 [][][]@smallrm You can as-sign a @smallit copy @smallrm of the ob-ject in the e n-vi-ron-ment frame @smalltt rho[] @smallrm us-ing @smalltt defineVar(symbol, [102] Underfull \hbox (badness 10000) in paragraph at lines 8967--8969 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] Overfull \hbox (22.06111pt too wide) in paragraph at lines 9995--9995 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [116] Chapter 6 [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] Underfull \hbox (badness 10000) in paragraph at lines 11145--11149 @texttt <- order(x, y, na.last, decreasing)[] @textrm cor-re-sponds to @texttt R_orderVector(indx, n, [128] [129] [130] Underfull \hbox (badness 2689) in paragraph at lines 11450--11456 []@textrm The vis-i-bil-ity mech-a-nism is not avail-able on Win-dows, but ther e is an equally [131] [132] Underfull \hbox (badness 10000) in paragraph at lines 11579--11587 []@textrm The graph-ics sys-tems are ex-posed in head-ers `@texttt R_ext/Graphi csEngine.h[]@textrm '[], Underfull \hbox (badness 3240) in paragraph at lines 11579--11587 @textrm `@texttt R_ext/GraphicsDevice.h[]@textrm '[] (which it in-cludes) and ` @texttt R_ext/QuartzDevice.h[]@textrm '[]. Fa-cil-i- Chapter 7 [133] [134] Chapter 8 [135] [136] [137] Overfull \hbox (33.55849pt too wide) in paragraph at lines 11986--11986 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [138] [139] [140] Underfull \hbox (badness 10000) in paragraph at lines 12229--12236 @texttt internet/nanoftp.c[]@textrm '[], `@texttt src/modules/internet/nanohtt p.c[]@textrm '[] and `@texttt src/modules/ [141] [142] Underfull \hbox (badness 10000) in paragraph at lines 12349--12358 []@textrm There is a (D)COM server called @texttt StatConnector[] @textrm writ -ten by Thomas Underfull \hbox (badness 10000) in paragraph at lines 12349--12358 @textrm Baier avail-able via [][]@texttt http://CRAN.R-project.org/other-softw are.html[][][] @textrm or [143] [144] Underfull \hbox (badness 6284) in paragraph at lines 12495--12502 @textrm may be avail-able from the Win-dows Reg-istry: it will be in @texttt H KEY_LOCAL_ Underfull \hbox (badness 10000) in paragraph at lines 12495--12502 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and Underfull \hbox (badness 3769) in paragraph at lines 12495--12502 @texttt HKEY_CURRENT_USER\Software\R-core\R\InstallPath[] @textrm oth-er-wise, if se-lected dur-ing [145] (Function and variable index) [146] (./R-exts.vrs [147] [148]) (Concept index) [149] (./R-exts.cps [150]) [151] ) (see the transcript file for additional information) Output written on R-exts.pdf (157 pages, 925258 bytes). Transcript written on R-exts.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-exts.t2d/pdf/x tr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-exts.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-exts.toc [-1] [-2] [-3]) [-4] (./R-exts.toc) (./R-exts.toc) (Acknowledgements) Chapter 1 [1] [2] Underfull \hbox (badness 4660) in paragraph at lines 275--278 []@textrm For the con-ven-tions for files `@texttt NEWS[]@textrm '[] and `@text tt ChangeLog[]@textrm '[] in the @reducedrm GNU @textrm project see [3] [4] [5] [6] [7] Underfull \hbox (badness 5847) in paragraph at lines 690--701 @textrm of Eco-nomic Lit-er-a-ture Clas-si-fi-ca-tion Sys-tem, [][]@texttt http ://www.aeaweb.org/journal/jel_ Underfull \hbox (badness 5231) in paragraph at lines 690--701 @textrm of the Amer-i-can Math-e-mat-i-cal So-ci-ety, [][]@texttt http://www.am s.org/msc/[][][]@textrm ). The sub-ject [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] Underfull \hbox (badness 10000) in paragraph at lines 1742--1744 [][][][][]@smalltt http://www.openmp.org/[][][]@smallrm , [][]@smalltt http://e n.wikipedia.org/wiki/OpenMP[][][]@smallrm , [][]@smalltt https://computing.llnl .gov/ [20] Overfull \hbox (46.15797pt too wide) in paragraph at lines 1880--1880 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 1882--1882 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [21] [22] [23] [24] [25] [26] [27] Underfull \hbox (badness 2809) in paragraph at lines 2485--2491 @textrm (or set the en-vi-ron-ment vari-able @texttt _R_BUILD_KEEP_EMPTY_DIRS_[ ] @textrm to `@texttt TRUE[]@textrm '[], or have a [28] [29] [30] Underfull \hbox (badness 4556) in paragraph at lines 2710--2718 @textrm Others you may see are @texttt \VignettePackage[] @textrm (cur-rently i g-nored), @texttt \VignetteDepends[] [31] [32] Overfull \hbox (70.02316pt too wide) in paragraph at lines 2870--2872 []@textrm Current sub-mis-sion in-struc-tions are linked from [][]@texttt http: //CRAN.R-project.org/banner.shtml#submitting[][][]@textrm . [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] Chapter 2 [47] [48] [49] [50] [51] [52] [53] Underfull \hbox (badness 2707) in paragraph at lines 4847--4853 []@textrm Packages may have an over-view help page with an @texttt \alias[] @te xtttsl pkg-name@texttt -package[]@textrm , e.g. Underfull \hbox (badness 3635) in paragraph at lines 4854--4860 []@textrm Skeletons of doc-u-men-ta-tion for a pack-age can be gen-er-ated us-i ng the func-tion [54] [55] [56] [57] [58] Underfull \hbox (badness 10000) in paragraph at lines 5232--5239 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and Underfull \hbox (badness 3919) in paragraph at lines 5232--5239 @texttt \figure{@textttsl filename@texttt }{@textttsl alternate text@texttt }[] @textrm . This will in-clude a copy of the fig-ure in [59] [60] Underfull \hbox (badness 10000) in paragraph at lines 5409--5415 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text @textrm part of [61] [62] [63] Overfull \hbox (3.59178pt too wide) in paragraph at lines 5678--5681 []@textrm Another is the Eclipse IDE with the Stat-ET plu-gin ([][]@texttt http ://www.walware.de/goto/statet[][][]@textrm ), Underfull \hbox (badness 3029) in paragraph at lines 5685--5687 []@textrm Some R front-ends pro-vide edit-ing sup-port for `@texttt .Rd[]@textr m '[] files, for ex-am-ple RStu-dio Chapter 3 [64] [65] [66] [67] Underfull \hbox (badness 2443) in paragraph at lines 6037--6040 []@textrm Data frames are slower than ma-tri-ces and this is an ex-am-ple of wh y. Us-ing Underfull \hbox (badness 10000) in paragraph at lines 6060--6065 []@textrm Options in-clude us-ing @texttt sprof[] @textrm for a shared ob-ject, and @texttt oprofile[] @textrm (see Underfull \hbox (badness 4927) in paragraph at lines 6060--6065 [][]@texttt http://oprofile.sourceforge.net/[][][]@textrm ) and @texttt perf[] @textrm (see [][]@texttt https://perf.wiki.kernel.org/ [68] [69] Overfull \hbox (310.88272pt too wide) in paragraph at lines 6153--6158 [][]@texttt https://developer.apple.com/library/mac/#documentation/DeveloperToo ls/Conceptual/InstrumentsUserGuide/Introduction/Introduction.html[][][]@textrm ). Chapter 4 [70] [71] [72] [73] [74] Underfull \hbox (badness 10000) in paragraph at lines 6534--6543 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [75] [76] Underfull \hbox (badness 10000) in paragraph at lines 6742--6746 []@texttt valgrind[] @textrm is good at spot-ting the use of unini-tial-ized va l-ues: use op-tion [77] Overfull \hbox (50.80455pt too wide) in paragraph at lines 6835--6835 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [78] [79] [80] [81] Chapter 5 [82] [83] [84] [85] [86] [87] [88] [89] Underfull \hbox (badness 10000) in paragraph at lines 7871--7882 @textrm file `@texttt README.packages[]@textrm '[] and [][]@texttt http://www.s tats.uwo.ca/faculty/murdoch/software/ [90] [91] [92] Overfull \hbox (16.31242pt too wide) in paragraph at lines 8110--8110 []@texttt PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="pa ckB"))' \[] [93] Overfull \hbox (37.99364pt too wide) in paragraph at lines 8159--8159 []@texttt PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="pa ckB"))' \[] [94] [95] [96] [97] [98] [99] [100] [101] Underfull \hbox (badness 2781) in paragraph at lines 8885--8887 [][][]@smallrm You can as-sign a @smallit copy @smallrm of the ob-ject in the e n-vi-ron-ment frame @smalltt rho[] @smallrm us-ing @smalltt defineVar(symbol, [102] Underfull \hbox (badness 10000) in paragraph at lines 8967--8969 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] Overfull \hbox (22.06111pt too wide) in paragraph at lines 9995--9995 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [116] Chapter 6 [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] Underfull \hbox (badness 10000) in paragraph at lines 11145--11149 @texttt <- order(x, y, na.last, decreasing)[] @textrm cor-re-sponds to @texttt R_orderVector(indx, n, [128] [129] [130] Underfull \hbox (badness 2689) in paragraph at lines 11450--11456 []@textrm The vis-i-bil-ity mech-a-nism is not avail-able on Win-dows, but ther e is an equally [131] [132] Underfull \hbox (badness 10000) in paragraph at lines 11579--11587 []@textrm The graph-ics sys-tems are ex-posed in head-ers `@texttt R_ext/Graphi csEngine.h[]@textrm '[], Underfull \hbox (badness 3240) in paragraph at lines 11579--11587 @textrm `@texttt R_ext/GraphicsDevice.h[]@textrm '[] (which it in-cludes) and ` @texttt R_ext/QuartzDevice.h[]@textrm '[]. Fa-cil-i- Chapter 7 [133] [134] Chapter 8 [135] [136] [137] Overfull \hbox (33.55849pt too wide) in paragraph at lines 11986--11986 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [138] [139] [140] Underfull \hbox (badness 10000) in paragraph at lines 12229--12236 @texttt internet/nanoftp.c[]@textrm '[], `@texttt src/modules/internet/nanohtt p.c[]@textrm '[] and `@texttt src/modules/ [141] [142] Underfull \hbox (badness 10000) in paragraph at lines 12349--12358 []@textrm There is a (D)COM server called @texttt StatConnector[] @textrm writ -ten by Thomas Underfull \hbox (badness 10000) in paragraph at lines 12349--12358 @textrm Baier avail-able via [][]@texttt http://CRAN.R-project.org/other-softw are.html[][][] @textrm or [143] [144] Underfull \hbox (badness 6284) in paragraph at lines 12495--12502 @textrm may be avail-able from the Win-dows Reg-istry: it will be in @texttt H KEY_LOCAL_ Underfull \hbox (badness 10000) in paragraph at lines 12495--12502 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and Underfull \hbox (badness 3769) in paragraph at lines 12495--12502 @texttt HKEY_CURRENT_USER\Software\R-core\R\InstallPath[] @textrm oth-er-wise, if se-lected dur-ing [145] (Function and variable index) [146] (./R-exts.vrs [147] [148]) (Concept index) [149] (./R-exts.cps [150]) [151] ) (see the transcript file for additional information) Output written on R-exts.pdf (157 pages, 925250 bytes). Transcript written on R-exts.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-exts.t2d/pdf/x tr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-exts.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-exts.toc [-1] [-2] [-3]) [-4] (./R-exts.toc) (./R-exts.toc) (Acknowledgements) Chapter 1 [1] [2] Underfull \hbox (badness 4660) in paragraph at lines 275--278 []@textrm For the con-ven-tions for files `@texttt NEWS[]@textrm '[] and `@text tt ChangeLog[]@textrm '[] in the @reducedrm GNU @textrm project see [3] [4] [5] [6] [7] Underfull \hbox (badness 5847) in paragraph at lines 690--701 @textrm of Eco-nomic Lit-er-a-ture Clas-si-fi-ca-tion Sys-tem, [][]@texttt http ://www.aeaweb.org/journal/jel_ Underfull \hbox (badness 5231) in paragraph at lines 690--701 @textrm of the Amer-i-can Math-e-mat-i-cal So-ci-ety, [][]@texttt http://www.am s.org/msc/[][][]@textrm ). The sub-ject [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] Underfull \hbox (badness 10000) in paragraph at lines 1742--1744 [][][][][]@smalltt http://www.openmp.org/[][][]@smallrm , [][]@smalltt http://e n.wikipedia.org/wiki/OpenMP[][][]@smallrm , [][]@smalltt https://computing.llnl .gov/ [20] Overfull \hbox (46.15797pt too wide) in paragraph at lines 1880--1880 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 1882--1882 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [21] [22] [23] [24] [25] [26] [27] Underfull \hbox (badness 2809) in paragraph at lines 2485--2491 @textrm (or set the en-vi-ron-ment vari-able @texttt _R_BUILD_KEEP_EMPTY_DIRS_[ ] @textrm to `@texttt TRUE[]@textrm '[], or have a [28] [29] [30] Underfull \hbox (badness 4556) in paragraph at lines 2710--2718 @textrm Others you may see are @texttt \VignettePackage[] @textrm (cur-rently i g-nored), @texttt \VignetteDepends[] [31] [32] Overfull \hbox (70.02316pt too wide) in paragraph at lines 2870--2872 []@textrm Current sub-mis-sion in-struc-tions are linked from [][]@texttt http: //CRAN.R-project.org/banner.shtml#submitting[][][]@textrm . [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] Chapter 2 [47] [48] [49] [50] [51] [52] [53] Underfull \hbox (badness 2707) in paragraph at lines 4847--4853 []@textrm Packages may have an over-view help page with an @texttt \alias[] @te xtttsl pkg-name@texttt -package[]@textrm , e.g. Underfull \hbox (badness 3635) in paragraph at lines 4854--4860 []@textrm Skeletons of doc-u-men-ta-tion for a pack-age can be gen-er-ated us-i ng the func-tion [54] [55] [56] [57] [58] Underfull \hbox (badness 10000) in paragraph at lines 5232--5239 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and Underfull \hbox (badness 3919) in paragraph at lines 5232--5239 @texttt \figure{@textttsl filename@texttt }{@textttsl alternate text@texttt }[] @textrm . This will in-clude a copy of the fig-ure in [59] [60] Underfull \hbox (badness 10000) in paragraph at lines 5409--5415 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text @textrm part of [61] [62] [63] Overfull \hbox (3.59178pt too wide) in paragraph at lines 5678--5681 []@textrm Another is the Eclipse IDE with the Stat-ET plu-gin ([][]@texttt http ://www.walware.de/goto/statet[][][]@textrm ), Underfull \hbox (badness 3029) in paragraph at lines 5685--5687 []@textrm Some R front-ends pro-vide edit-ing sup-port for `@texttt .Rd[]@textr m '[] files, for ex-am-ple RStu-dio Chapter 3 [64] [65] [66] [67] Underfull \hbox (badness 2443) in paragraph at lines 6037--6040 []@textrm Data frames are slower than ma-tri-ces and this is an ex-am-ple of wh y. Us-ing Underfull \hbox (badness 10000) in paragraph at lines 6060--6065 []@textrm Options in-clude us-ing @texttt sprof[] @textrm for a shared ob-ject, and @texttt oprofile[] @textrm (see Underfull \hbox (badness 4927) in paragraph at lines 6060--6065 [][]@texttt http://oprofile.sourceforge.net/[][][]@textrm ) and @texttt perf[] @textrm (see [][]@texttt https://perf.wiki.kernel.org/ [68] [69] Overfull \hbox (310.88272pt too wide) in paragraph at lines 6153--6158 [][]@texttt https://developer.apple.com/library/mac/#documentation/DeveloperToo ls/Conceptual/InstrumentsUserGuide/Introduction/Introduction.html[][][]@textrm ). Chapter 4 [70] [71] [72] [73] [74] Underfull \hbox (badness 10000) in paragraph at lines 6534--6543 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [75] [76] Underfull \hbox (badness 10000) in paragraph at lines 6742--6746 []@texttt valgrind[] @textrm is good at spot-ting the use of unini-tial-ized va l-ues: use op-tion [77] Overfull \hbox (50.80455pt too wide) in paragraph at lines 6835--6835 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [78] [79] [80] [81] Chapter 5 [82] [83] [84] [85] [86] [87] [88] [89] Underfull \hbox (badness 10000) in paragraph at lines 7871--7882 @textrm file `@texttt README.packages[]@textrm '[] and [][]@texttt http://www.s tats.uwo.ca/faculty/murdoch/software/ [90] [91] [92] Overfull \hbox (16.31242pt too wide) in paragraph at lines 8110--8110 []@texttt PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="pa ckB"))' \[] [93] Overfull \hbox (37.99364pt too wide) in paragraph at lines 8159--8159 []@texttt PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="pa ckB"))' \[] [94] [95] [96] [97] [98] [99] [100] [101] Underfull \hbox (badness 2781) in paragraph at lines 8885--8887 [][][]@smallrm You can as-sign a @smallit copy @smallrm of the ob-ject in the e n-vi-ron-ment frame @smalltt rho[] @smallrm us-ing @smalltt defineVar(symbol, [102] Underfull \hbox (badness 10000) in paragraph at lines 8967--8969 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] Overfull \hbox (22.06111pt too wide) in paragraph at lines 9995--9995 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [116] Chapter 6 [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] Underfull \hbox (badness 10000) in paragraph at lines 11145--11149 @texttt <- order(x, y, na.last, decreasing)[] @textrm cor-re-sponds to @texttt R_orderVector(indx, n, [128] [129] [130] Underfull \hbox (badness 2689) in paragraph at lines 11450--11456 []@textrm The vis-i-bil-ity mech-a-nism is not avail-able on Win-dows, but ther e is an equally [131] [132] Underfull \hbox (badness 10000) in paragraph at lines 11579--11587 []@textrm The graph-ics sys-tems are ex-posed in head-ers `@texttt R_ext/Graphi csEngine.h[]@textrm '[], Underfull \hbox (badness 3240) in paragraph at lines 11579--11587 @textrm `@texttt R_ext/GraphicsDevice.h[]@textrm '[] (which it in-cludes) and ` @texttt R_ext/QuartzDevice.h[]@textrm '[]. Fa-cil-i- Chapter 7 [133] [134] Chapter 8 [135] [136] [137] Overfull \hbox (33.55849pt too wide) in paragraph at lines 11986--11986 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [138] [139] [140] Underfull \hbox (badness 10000) in paragraph at lines 12229--12236 @texttt internet/nanoftp.c[]@textrm '[], `@texttt src/modules/internet/nanohtt p.c[]@textrm '[] and `@texttt src/modules/ [141] [142] Underfull \hbox (badness 10000) in paragraph at lines 12349--12358 []@textrm There is a (D)COM server called @texttt StatConnector[] @textrm writ -ten by Thomas Underfull \hbox (badness 10000) in paragraph at lines 12349--12358 @textrm Baier avail-able via [][]@texttt http://CRAN.R-project.org/other-softw are.html[][][] @textrm or [143] [144] Underfull \hbox (badness 6284) in paragraph at lines 12495--12502 @textrm may be avail-able from the Win-dows Reg-istry: it will be in @texttt H KEY_LOCAL_ Underfull \hbox (badness 10000) in paragraph at lines 12495--12502 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and Underfull \hbox (badness 3769) in paragraph at lines 12495--12502 @texttt HKEY_CURRENT_USER\Software\R-core\R\InstallPath[] @textrm oth-er-wise, if se-lected dur-ing [145] (Function and variable index) [146] (./R-exts.vrs [147] [148]) (Concept index) [149] (./R-exts.cps [150]) [151] ) (see the transcript file for additional information) Output written on R-exts.pdf (157 pages, 925250 bytes). Transcript written on R-exts.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-intro.t2d/pdf/ xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] <./i mages/hist.pdf> [34] <./images/ecdf.pdf> <./images/QQ.pdf> [35] [36] <./images/ ice.pdf> [37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45] [46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] <./image s/fig11.pdf> [71] <./images/fig12.pdf> [72] [73] [74] [75] Underfull \hbox (badness 10000) in paragraph at lines 6411--6414 @textrm and these can be ac-cessed from R via the pack-age [][]@textbf rggobi[] []@textrm , de-scribed at Chapter 13 [76] [77] Appendix A [78] [79] [80] [81] Appendix B [82] Underfull \hbox (badness 2635) in paragraph at lines 6837--6843 @textrm `@texttt --no-site-file[]@textrm '[] was given. The name of this file is taken from the value Underfull \hbox (badness 2158) in paragraph at lines 6837--6843 @textrm of the @texttt R_PROFILE[] @textrm en-vi-ron-ment vari-able. If that v ari-able is un-set, the de-fault [83] [84] [85] Underfull \hbox (badness 4752) in paragraph at lines 7103--7115 []@textrm In ad-di-tion, you can use op-tions `@texttt --arch=[]@textrm '[], `@ texttt --no-environ[]@textrm '[], `@texttt --no-init-file[]@textrm '[], [86] [87] [88] Appendix C [89] [90] Appendix D [91] Appendix E [92] Appendix F [93] [94] ) (see the transcript file for additional information)< /usr/share/texmf/fonts/type1/bluesky/cm/cmtt9.pfb> Output written on R-intro.pdf (97 pages, 514724 bytes). Transcript written on R-intro.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-intro.t2d/pdf/ xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-intro.aux) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-intro.toc [-1] [-2] [-3]) [-4] (./R-intro.toc) (./R-intro.toc) (Preface) Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] <./images/hist.pdf> [34] <./images/ecdf.pdf> <./images/QQ.p df> [35] [36] <./images/ice.pdf> [37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45] [46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] <./images/fig11.pdf> [71] <./images/fig12.pdf> [72] [73] [74] [75] Underfull \hbox (badness 10000) in paragraph at lines 6411--6414 @textrm and these can be ac-cessed from R via the pack-age [][]@textbf rggobi[] []@textrm , de-scribed at Chapter 13 [76] [77] Appendix A [78] [79] [80] Appendix B [81] [82] Underfull \hbox (badness 2635) in paragraph at lines 6837--6843 @textrm `@texttt --no-site-file[]@textrm '[] was given. The name of this file is taken from the value Underfull \hbox (badness 2158) in paragraph at lines 6837--6843 @textrm of the @texttt R_PROFILE[] @textrm en-vi-ron-ment vari-able. If that v ari-able is un-set, the de-fault [83] [84] [85] Underfull \hbox (badness 4752) in paragraph at lines 7103--7115 []@textrm In ad-di-tion, you can use op-tions `@texttt --arch=[]@textrm '[], `@ texttt --no-environ[]@textrm '[], `@texttt --no-init-file[]@textrm '[], [86] [87] [88] Appendix C [89] [90] Appendix D [91] (./R-intro.vrs [92] [93]) Appendix E [94] (./R-intro.cps [95]) Appendix F [96] [97] ) (see the transcript file for additional information) Output written on R-intro.pdf (103 pages, 654071 bytes). Transcript written on R-intro.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-intro.t2d/pdf/ xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-intro.aux) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-intro.toc [-1] [-2] [-3]) [-4] (./R-intro.toc) (./R-intro.toc) (Preface) Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] <./images/hist.pdf> [34] <./images/ecdf.pdf> <./images/QQ.p df> [35] [36] <./images/ice.pdf> [37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45] [46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] <./images/fig11.pdf> [71] <./images/fig12.pdf> [72] [73] [74] [75] Underfull \hbox (badness 10000) in paragraph at lines 6411--6414 @textrm and these can be ac-cessed from R via the pack-age [][]@textbf rggobi[] []@textrm , de-scribed at Chapter 13 [76] [77] Appendix A [78] [79] [80] Appendix B [81] [82] Underfull \hbox (badness 2635) in paragraph at lines 6837--6843 @textrm `@texttt --no-site-file[]@textrm '[] was given. The name of this file is taken from the value Underfull \hbox (badness 2158) in paragraph at lines 6837--6843 @textrm of the @texttt R_PROFILE[] @textrm en-vi-ron-ment vari-able. If that v ari-able is un-set, the de-fault [83] [84] [85] Underfull \hbox (badness 4752) in paragraph at lines 7103--7115 []@textrm In ad-di-tion, you can use op-tions `@texttt --arch=[]@textrm '[], `@ texttt --no-environ[]@textrm '[], `@texttt --no-init-file[]@textrm '[], [86] [87] [88] Appendix C [89] [90] Appendix D [91] (./R-intro.vrs [92] [93]) Appendix E [94] (./R-intro.cps [95]) Appendix F [96] [97] ) (see the transcript file for additional information) Output written on R-intro.pdf (103 pages, 654071 bytes). Transcript written on R-intro.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-ints.t2d/pdf/x tr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 2 [21] [22] [23] [24] [25] Chapter 3 [26] [27] Chapter 4 [28] [29] Chapter 5 [30] Chapter 6 [31] Underfull \hbox (badness 10000) in paragraph at lines 2694--2697 @texttt ~paul/R/basegraph.html[][][] @textrm and [][]@texttt http://www.stat.au ckland.ac.nz/~paul/R/ [32] [33] [34] [35] [36] Underfull \hbox (badness 4467) in paragraph at lines 3190--3194 []@textrm The in-ter-pre-ta-tion of the line tex-ture (@texttt par("lty"[]@text rm ) is de-scribed in the header [37] [38] [39] [40] Underfull \hbox (badness 6428) in paragraph at lines 3494--3498 []@textrm The base sys-tem state is con-tained in @texttt baseSystemState[] @te xtrm struc-ture de-fined in [41] Chapter 7 [42] Underfull \hbox (badness 10000) in paragraph at lines 3606--3615 []@texttt R.app[] @textrm re-lies on `@texttt libR.dylib[]@textrm '[] be-ing in a spe-cific place, and hence on R Underfull \hbox (badness 10000) in paragraph at lines 3606--3615 @textrm hav-ing been built and in-stalled as a Mac OS X `frame-work'. Specif-i- cally, Underfull \hbox (badness 10000) in paragraph at lines 3606--3615 @textrm it uses `@texttt /Library/Frameworks/R.framework/R[]@textrm '[]. This i s a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3606--3615 @textrm as frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re-solves to Underfull \hbox (badness 10000) in paragraph at lines 3606--3615 @textrm `@texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib /libR.dylib[]@textrm '[], [43] Chapter 8 [44] [45] [46] [47] [48] Chapter 9 [49] [50] Chapter 10 [51] Chapter 11 [52] Chapter 12 [53] [54] (Function and variable index) [55] (Concept index) [56] [57] ) (see the transcript file for additional information) Output written on R-ints.pdf (60 pages, 336918 bytes). Transcript written on R-ints.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-ints.t2d/pdf/x tr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-ints.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-ints.toc [-1]) [-2] (./R-ints.toc) (./R-ints.toc) Chapter 1 [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 2 [21] [22] [23] [24] [25] Chapter 3 [26] [27] Chapter 4 [28] [29] Chapter 5 [30] Chapter 6 [31] Underfull \hbox (badness 10000) in paragraph at lines 2694--2697 @texttt ~paul/R/basegraph.html[][][] @textrm and [][]@texttt http://www.stat.au ckland.ac.nz/~paul/R/ [32] [33] [34] [35] [36] Underfull \hbox (badness 4467) in paragraph at lines 3190--3194 []@textrm The in-ter-pre-ta-tion of the line tex-ture (@texttt par("lty"[]@text rm ) is de-scribed in the header [37] [38] [39] [40] Underfull \hbox (badness 6428) in paragraph at lines 3494--3498 []@textrm The base sys-tem state is con-tained in @texttt baseSystemState[] @te xtrm struc-ture de-fined in [41] Chapter 7 [42] Underfull \hbox (badness 10000) in paragraph at lines 3606--3615 []@texttt R.app[] @textrm re-lies on `@texttt libR.dylib[]@textrm '[] be-ing in a spe-cific place, and hence on R Underfull \hbox (badness 10000) in paragraph at lines 3606--3615 @textrm hav-ing been built and in-stalled as a Mac OS X `frame-work'. Specif-i- cally, Underfull \hbox (badness 10000) in paragraph at lines 3606--3615 @textrm it uses `@texttt /Library/Frameworks/R.framework/R[]@textrm '[]. This i s a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3606--3615 @textrm as frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re-solves to Underfull \hbox (badness 10000) in paragraph at lines 3606--3615 @textrm `@texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib /libR.dylib[]@textrm '[], [43] Chapter 8 [44] [45] [46] [47] [48] Chapter 9 [49] [50] Chapter 10 [51] Chapter 11 [52] Chapter 12 [53] [54] (Function and variable index) [55] (./R-ints.vrs [56]) (Concept index) [57] (./R-ints.cps) [58] ) (see the transcript file for additional information) Output written on R-ints.pdf (62 pages, 417501 bytes). Transcript written on R-ints.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-ints.t2d/pdf/x tr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-ints.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-ints.toc [-1]) [-2] (./R-ints.toc) (./R-ints.toc) Chapter 1 [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 2 [21] [22] [23] [24] [25] Chapter 3 [26] [27] Chapter 4 [28] [29] Chapter 5 [30] Chapter 6 [31] Underfull \hbox (badness 10000) in paragraph at lines 2694--2697 @texttt ~paul/R/basegraph.html[][][] @textrm and [][]@texttt http://www.stat.au ckland.ac.nz/~paul/R/ [32] [33] [34] [35] [36] Underfull \hbox (badness 4467) in paragraph at lines 3190--3194 []@textrm The in-ter-pre-ta-tion of the line tex-ture (@texttt par("lty"[]@text rm ) is de-scribed in the header [37] [38] [39] [40] Underfull \hbox (badness 6428) in paragraph at lines 3494--3498 []@textrm The base sys-tem state is con-tained in @texttt baseSystemState[] @te xtrm struc-ture de-fined in [41] Chapter 7 [42] Underfull \hbox (badness 10000) in paragraph at lines 3606--3615 []@texttt R.app[] @textrm re-lies on `@texttt libR.dylib[]@textrm '[] be-ing in a spe-cific place, and hence on R Underfull \hbox (badness 10000) in paragraph at lines 3606--3615 @textrm hav-ing been built and in-stalled as a Mac OS X `frame-work'. Specif-i- cally, Underfull \hbox (badness 10000) in paragraph at lines 3606--3615 @textrm it uses `@texttt /Library/Frameworks/R.framework/R[]@textrm '[]. This i s a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3606--3615 @textrm as frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re-solves to Underfull \hbox (badness 10000) in paragraph at lines 3606--3615 @textrm `@texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib /libR.dylib[]@textrm '[], [43] Chapter 8 [44] [45] [46] [47] [48] Chapter 9 [49] [50] Chapter 10 [51] Chapter 11 [52] Chapter 12 [53] [54] (Function and variable index) [55] (./R-ints.vrs [56]) (Concept index) [57] (./R-ints.cps) [58] ) (see the transcript file for additional information) Output written on R-ints.pdf (62 pages, 417501 bytes). Transcript written on R-ints.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-lang.t2d/pdf/x tr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Chapter 2 [1] [2] Cross reference values unknown; you must run TeX again. Overfull \hbox (8.41086pt too wide) in paragraph at lines 300--301 @textbf storage.mode| [3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27] [28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7 [39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 4355--4357 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] [47] [48] [49] [50] (Function and Variable Index) [51] (Concept Index) [52] Appendix A [53] [54] ) (see the transcript file for additional information) Output written on R-lang.pdf (57 pages, 291391 bytes). Transcript written on R-lang.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-lang.t2d/pdf/x tr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-lang.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-lang.toc [-1] [-2]) [-3] (./R-lang.toc) (./R-lang.toc) Chapter 1 Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 300--301 @textbf storage.mode| [3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27] [28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7 [39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 4355--4357 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] [47] [48] [49] [50] (Function and Variable Index) [51] (./R-lang.vrs [52]) (Concept Index) [53] (./R-lang.cps) Appendix A [54] [55] ) (see the transcript file for additional information) Output written on R-lang.pdf (60 pages, 409337 bytes). Transcript written on R-lang.log. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual/R-lang.t2d/pdf/x tr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-lang.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-lang.toc [-1] [-2]) [-3] (./R-lang.toc) (./R-lang.toc) Chapter 1 Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 300--301 @textbf storage.mode| [3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27] [28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7 [39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 4355--4357 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] [47] [48] [49] [50] (Function and Variable Index) [51] (./R-lang.vrs [52]) (Concept Index) [53] (./R-lang.cps) Appendix A [54] [55] ) (see the transcript file for additional information) Output written on R-lang.pdf (60 pages, 409337 bytes). Transcript written on R-lang.log. make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc' + make info make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' /usr/bin/makeinfo --enable-encoding -D UseExternalXrefs -I. R-FAQ.texi /usr/bin/makeinfo --enable-encoding -D UseExternalXrefs -I. R-admin.texi /usr/bin/makeinfo --enable-encoding -D UseExternalXrefs -I. R-data.texi /usr/bin/makeinfo --enable-encoding -D UseExternalXrefs -I. R-exts.texi /usr/bin/makeinfo --enable-encoding -D UseExternalXrefs -I. R-intro.texi /usr/bin/makeinfo --enable-encoding -D UseExternalXrefs -I. R-ints.texi /usr/bin/makeinfo --enable-encoding -D UseExternalXrefs -I. R-lang.texi make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc' + for i in doc/manual/R-intro.info doc/manual/R-FAQ.info doc/FAQ doc/manual/R-admin.info doc/manual/R-exts.info-1 + iconv -f iso-8859-1 -t utf-8 -o doc/manual/R-intro.info.utf8 doc/manual/R-intro.info + mv doc/manual/R-intro.info.utf8 doc/manual/R-intro.info + for i in doc/manual/R-intro.info doc/manual/R-FAQ.info doc/FAQ doc/manual/R-admin.info doc/manual/R-exts.info-1 + iconv -f iso-8859-1 -t utf-8 -o doc/manual/R-FAQ.info.utf8 doc/manual/R-FAQ.info + mv doc/manual/R-FAQ.info.utf8 doc/manual/R-FAQ.info + for i in doc/manual/R-intro.info doc/manual/R-FAQ.info doc/FAQ doc/manual/R-admin.info doc/manual/R-exts.info-1 + iconv -f iso-8859-1 -t utf-8 -o doc/FAQ.utf8 doc/FAQ + mv doc/FAQ.utf8 doc/FAQ + for i in doc/manual/R-intro.info doc/manual/R-FAQ.info doc/FAQ doc/manual/R-admin.info doc/manual/R-exts.info-1 + iconv -f iso-8859-1 -t utf-8 -o doc/manual/R-admin.info.utf8 doc/manual/R-admin.info + mv doc/manual/R-admin.info.utf8 doc/manual/R-admin.info + for i in doc/manual/R-intro.info doc/manual/R-FAQ.info doc/FAQ doc/manual/R-admin.info doc/manual/R-exts.info-1 + iconv -f iso-8859-1 -t utf-8 -o doc/manual/R-exts.info-1.utf8 doc/manual/R-exts.info-1 + mv doc/manual/R-exts.info-1.utf8 doc/manual/R-exts.info-1 + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.twzlyD + umask 022 + cd /home/pauljohn/LinuxDownloads/redhat/BUILD + cd R-3.0.1 + make DESTDIR=/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386 install install-info mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/m4' make[1]: Nothing to be done for `install'. make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/m4' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/tools' make[1]: Nothing to be done for `install'. make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/tools' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc' installing doc ... mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/doc/R-3.0.1 mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/man/man1 make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/html' installing doc/html ... mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/doc/R-3.0.1/html make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/html' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' installing doc/manual ... mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/doc/R-3.0.1/manual make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/etc' mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/etc installing etc ... make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/etc' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/share' installing share ... mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/R mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/R/R mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/R/dictionaries mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/R/encodings mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/R/java mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/R/licenses mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/R/make mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/R/sh mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/R/texmf mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/R/texmf/bibtex/bib mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/R/texmf/bibtex/bst mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/R/texmf/tex/latex make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/share' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/scripts' mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/bin mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/bin make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/scripts' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include' mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/include/R make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include/R_ext' mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/include/R/R_ext make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include/R_ext' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/blas' mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/lib make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/blas' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/bzip2' make[3]: Nothing to be done for `install'. make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/bzip2' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/pcre' make[3]: Nothing to be done for `install'. make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/pcre' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/tre' make[3]: Nothing to be done for `install'. make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/tre' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/xdr' make[3]: Nothing to be done for `install'. make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/xdr' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/xz' make[3]: Nothing to be done for `install'. make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/xz' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/zlib' make[3]: Nothing to be done for `install'. make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/zlib' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/intl' make[3]: Nothing to be done for `install'. make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra/intl' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/extra' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/appl' make[2]: Nothing to be done for `install'. make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/appl' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath' make[2]: Nothing to be done for `install'. make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/nmath' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' gcc -m32 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -march=i386 -mtune=i686 -DR_HOME='"/usr/lib/R"' -o Rscript \ ./Rscript.c mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/pkgconfig make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/unix' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/bin/exec make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/main' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/modules make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/internet' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/lapack' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/vfonts' make[3]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' make[3]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules/X11' make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/modules' make[2]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library installing packages ... building HTML index ... make[2]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/library' make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/tests' make[1]: Nothing to be done for `install'. make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/tests' make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' mkdir -p -- /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/info /usr/bin/install -c -m 644 "./dir" "/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/info" installing R info pages ... updating '/usr/share/info/dir' ... make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' + make DESTDIR=/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386 install-pdf make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' installing R manuals in PDF format ... make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/doc/manual' + rm -f /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/info/dir + rm -f /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/info/dir.old + install -p CAPABILITIES /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/doc/R-3.0.1 + cd src/nmath/standalone + make install DESTDIR=/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386 make[1]: Entering directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include' make[1]: `Rmath.h' is up to date. make[1]: Leaving directory `/home/pauljohn/LinuxDownloads/redhat/BUILD/R-3.0.1/src/include' + mkdir -p /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/etc/ld.so.conf.d + echo /usr/lib/R/lib + mkdir -p /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/R/library + mkdir -p /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/etc/rpm/ + install -m0644 /home/pauljohn/LinuxDownloads/redhat/SOURCES/macros.R /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/etc/rpm/ + mkdir -p /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/rpm/ + install -m0755 /home/pauljohn/LinuxDownloads/redhat/SOURCES/R-make-search-index.sh /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/rpm/ + touch -r NEWS /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/doc/R-3.0.1/CAPABILITIES + touch -r NEWS doc/manual/R-FAQ.pdf doc/manual/R-admin.pdf doc/manual/R-data.pdf doc/manual/R-exts.pdf doc/manual/R-intro.pdf doc/manual/R-ints.pdf doc/manual/R-lang.pdf doc/manual/fullrefman.pdf + touch -r NEWS /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/bin/R + sed -i 's|\..\/\..|/usr/lib/R|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/doc/R-3.0.1/html/packages.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/KernSmooth/html/00Index.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/KernSmooth/html/bkde.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/KernSmooth/html/bkde2D.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/KernSmooth/html/bkfe.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/KernSmooth/html/dpih.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/KernSmooth/html/dpik.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/KernSmooth/html/dpill.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/KernSmooth/html/locpoly.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/00Index.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/Aids2.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/Animals.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/Boston.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/Cars93.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/Cushings.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/DDT.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/GAGurine.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/Insurance.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/MASS-internal.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/Melanoma.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/Null.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/OME.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/Pima.tr.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/Rabbit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/Rubber.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/SP500.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/Sitka.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/Sitka89.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/Skye.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/Traffic.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/UScereal.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/UScrime.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/VA.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/abbey.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/accdeaths.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/addterm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/anorexia.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/anova.negbin.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/area.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/bacteria.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/bandwidth.nrd.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/bcv.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/beav1.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/beav2.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/biopsy.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/birthwt.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/boxcox.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/cabbages.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/caith.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/cats.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/cement.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/chem.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/con2tr.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/confint.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/contr.sdif.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/coop.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/corresp.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/cov.rob.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/cov.trob.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/cpus.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/crabs.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/deaths.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/denumerate.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/dose.p.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/drivers.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/dropterm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/eagles.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/epil.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/eqscplot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/farms.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/fgl.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/fitdistr.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/forbes.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/fractions.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/galaxies.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/gamma.dispersion.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/gamma.shape.glm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/gehan.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/genotype.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/geyser.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/gilgais.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/ginv.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/glm.convert.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/glm.nb.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/glmmPQL.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/hills.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/hist.scott.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/housing.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/huber.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/hubers.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/immer.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/isoMDS.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/kde2d.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/lda.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/ldahist.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/leuk.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/lm.gls.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/lm.ridge.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/loglm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/loglm1.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/logtrans.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/lqs.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/mammals.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/mca.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/mcycle.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/menarche.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/michelson.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/minn38.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/motors.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/muscle.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/mvrnorm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/negative.binomial.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/newcomb.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/nlschools.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/npk.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/npr1.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/oats.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/painters.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/pairs.lda.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/parcoord.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/petrol.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/phones.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/plot.lda.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/plot.mca.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/plot.profile.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/polr.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/predict.glmmPQL.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/predict.lda.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/predict.lqs.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/predict.mca.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/predict.qda.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/profile.glm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/qda.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/quine.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/rational.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/renumerate.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/rlm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/rms.curv.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/rnegbin.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/road.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/rotifer.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/sammon.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/ships.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/shoes.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/shrimp.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/shuttle.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/snails.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/MASS/html/stdres.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/Sys.sleep.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/Sys.time.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/Sys.which.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/Trig.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/UseMethod.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/Vectorize.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/Version.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/abbreviate.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/agrep.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/all.equal.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/all.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/allnames.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/any.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/aperm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/append.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/apply.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/args.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/array.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/as.Date.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/as.POSIXlt.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/as.data.frame.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/as.environment.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/as.function.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/assign.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/assignOps.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/attach.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/attr.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/attributes.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/autoload.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/backsolve.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/base-defunct.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/base-deprecated.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/base-internal.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/base-package.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/basename.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/bincode.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/bindenv.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/bitwise.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/body.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/bquote.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/browser.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/browserText.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/builtins.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/by.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/c.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/call.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/callCC.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/capabilities.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/cat.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/cbind.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/char.expand.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/character.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/charmatch.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/chartr.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/chol.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/chol2inv.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/class.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/col.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/colSums.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/colnames.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/commandArgs.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/comment.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/complex.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/conditions.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/conflicts.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/connections.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/contributors.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/copyright.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/crossprod.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/cumsum.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/cut.POSIXt.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/cut.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/data.class.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/data.frame.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/data.matrix.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/dataframeHelpers.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/date.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/dcf.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/debug.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/delayedAssign.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/deparse.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/deparseOpts.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/det.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/detach.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/dev.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/diag.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/diff.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/difftime.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/dim.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/dimnames.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/do.call.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/double.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/dput.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/drop.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/droplevels.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/dump.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/duplicated.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/dynload.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/eapply.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/eigen.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/encodeString.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/environment.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/eval.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/exists.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/expand.grid.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/expression.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/factor.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/file.access.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/file.choose.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/file.info.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/file.path.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/file.show.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/files.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/files2.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/find.package.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/findInterval.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/force.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/formals.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/format.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/format.info.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/format.pval.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/formatDL.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/formatc.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/function.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/funprog.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/gc.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/gc.time.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/gctorture.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/get.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/getCallingDLL.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/getDLLRegisteredRoutines.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/getLoadedDLLs.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/getNativeSymbolInfo.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/gettext.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/getwd.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/gl.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/grep.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/grepRaw.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/groupGeneric.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/gzcon.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/hexmode.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/iconv.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/icuSetCollate.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/identical.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/identity.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/ifelse.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/integer.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/interaction.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/interactive.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/invisible.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/is.finite.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/is.function.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/is.language.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/is.object.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/is.recursive.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/is.single.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/is.unsorted.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/isR.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/isS4.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/isSymmetric.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/jitter.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/kappa.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/kronecker.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/l10n_info.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/labels.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/lapply.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/lazyload.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/length.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/levels.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/libPaths.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/library.dynam.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/library.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/license.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/list.files.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/list.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/list2env.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/load.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/locales.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/logical.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/lower.tri.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/ls.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/make.names.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/make.unique.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/mapply.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/margin.table.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/mat.or.vec.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/match.arg.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/match.call.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/match.fun.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/match.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/matmult.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/matrix.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/maxCol.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/mean.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/memCompress.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/memory.profile.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/merge.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/message.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/missing.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/mode.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/name.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/names.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/nargs.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/nchar.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/nlevels.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/noquote.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/norm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/normalizePath.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/notyet.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/nrow.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/ns-dblcolon.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/ns-hooks.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/ns-internal.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/ns-load.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/ns-reflect.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/ns-topenv.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/numeric.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/numeric_version.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/octmode.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/on.exit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/options.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/order.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/outer.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/parse.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/paste.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/path.expand.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/pmatch.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/polyroot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/pos.to.env.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/pretty.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/print.dataframe.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/print.default.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/print.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/prmatrix.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/proc.time.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/prod.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/prop.table.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/pushBack.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/qr.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/qraux.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/quit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/range.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/rank.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/rapply.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/raw.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/rawConnection.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/rawConversion.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/readBin.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/readChar.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/readLines.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/readRDS.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/readRenviron.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/readline.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/reg.finalizer.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/regex.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/regmatches.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/rep.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/replace.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/rev.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/rle.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/rm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/round.POSIXt.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/row.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/row.names.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/rowsum.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/sQuote.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/sample.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/save.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/scale.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/scan.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/search.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/seek.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/seq.Date.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/seq.POSIXt.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/seq.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/sequence.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/serialize.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/setTimeLimit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/sets.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/shQuote.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/showConnections.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/sign.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/sink.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/slice.index.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/slotOp.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/socketSelect.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/solve.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/sort.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/source.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/split.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/sprintf.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/srcfile.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/standardGeneric.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/stop.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/stopifnot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/strptime.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/strsplit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/strtoi.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/strtrim.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/structure.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/strwrap.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/subset.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/substitute.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/substr.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/sum.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/summary.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/svd.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/sweep.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/switch.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/sys.parent.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/sys.source.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/system.file.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/system.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/system.time.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/system2.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/t.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/table.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/tabulate.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/tapply.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/taskCallback.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/taskCallbackManager.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/taskCallbackNames.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/tempfile.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/textconnections.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/tilde.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/timezones.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/toString.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/trace.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/traceback.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/tracemem.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/transform.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/try.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/typeof.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/unique.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/unlink.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/unlist.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/unname.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/userhooks.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/utf8Conversion.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/vector.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/warning.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/warnings.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/weekday.POSIXt.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/which.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/which.min.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/with.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/withVisible.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/write.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/writeLines.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/xtfrm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/zMachine.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/zScript.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/zapsmall.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/zpackages.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/base/html/zutils.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/00Index.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/EEF.profile.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/Imp.Estimates.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/abc.ci.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/acme.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/aids.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/aircondit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/amis.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/aml.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/beaver.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/bigcity.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/boot-practicals.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/boot.array.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/boot.ci.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/boot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/brambles.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/breslow.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/calcium.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/cane.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/capability.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/catsM.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/cav.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/cd4.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/cd4.nested.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/censboot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/channing.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/claridge.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/cloth.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/co.transfer.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/coal.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/control.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/corr.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/cum3.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/cv.glm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/darwin.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/dogs.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/downs.bc.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/ducks.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/empinf.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/envelope.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/exp.tilt.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/fir.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/freq.array.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/frets.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/glm.diag.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/glm.diag.plots.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/gravity.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/hirose.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/imp.weights.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/inv.logit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/islay.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/jack.after.boot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/k3.linear.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/linear.approx.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/lines.saddle.distn.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/logit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/manaus.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/melanoma.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/motor.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/neuro.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/nitrofen.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/nodal.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/norm.ci.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/nuclear.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/paulsen.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/plot.boot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/poisons.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/polar.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/print.boot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/print.bootci.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/print.saddle.distn.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/print.simplex.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/remission.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/saddle.distn.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/saddle.distn.object.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/saddle.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/salinity.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/simplex.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/simplex.object.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/smooth.f.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/sunspot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/survival.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/tau.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/tilt.boot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/tsboot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/tuna.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/urine.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/var.linear.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/boot/html/wool.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/00Index.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/SOM.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/batchSOM.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/condense.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/knn.cv.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/knn.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/knn1.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/lvq1.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/lvq2.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/lvq3.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/lvqinit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/lvqtest.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/multiedit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/olvq1.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/reduce.nn.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/class/html/somgrid.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/00Index.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/agnes.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/agnes.object.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/agriculture.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/animals.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/bannerplot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/chorSub.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/clara.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/clara.object.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/clusGap.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/clusplot.default.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/clusplot.partition.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/cluster-internal.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/coef.hclust.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/daisy.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/diana.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/dissimilarity.object.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/ellipsoidhull.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/fanny.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/fanny.object.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/flower.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/lower.to.upper.tri.inds.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/mona.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/mona.object.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/pam.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/pam.object.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/partition.object.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/plantTraits.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/plot.agnes.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/plot.diana.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/plot.mona.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/plot.partition.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/pltree.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/pltree.twins.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/pluton.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/predict.ellipsoid.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/print.agnes.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/print.clara.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/print.diana.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/print.dissimilarity.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/print.fanny.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/print.mona.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/print.pam.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/ruspini.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/silhouette.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/sizeDiss.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/summary.agnes.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/summary.clara.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/summary.diana.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/summary.mona.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/summary.pam.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/twins.object.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/volume.ellipsoid.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/votes.repub.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/cluster/html/xclara.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/codetools/html/00Index.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/codetools/html/checkUsage.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/codetools/html/codetools.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/codetools/html/findGlobals.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/codetools/html/showTree.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/compiler/html/00Index.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/compiler/html/compile.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/00Index.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/AirPassengers.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/BJsales.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/BOD.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/ChickWeight.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/DNase.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/EuStockMarkets.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/Formaldehyde.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/HairEyeColor.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/Harman23.cor.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/Harman74.cor.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/Indometh.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/InsectSprays.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/JohnsonJohnson.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/LakeHuron.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/LifeCycleSavings.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/Loblolly.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/Nile.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/Orange.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/OrchardSprays.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/PlantGrowth.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/Puromycin.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/Theoph.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/Titanic.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/ToothGrowth.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/UCBAdmissions.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/UKDriverDeaths.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/UKLungDeaths.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/UKgas.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/USAccDeaths.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/USArrests.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/USJudgeRatings.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/USPersonalExpenditure.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/VADeaths.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/WWWusage.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/WorldPhones.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/ability.cov.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/airmiles.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/airquality.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/anscombe.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/attenu.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/attitude.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/austres.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/beavers.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/cars.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/chickwts.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/co2.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/crimtab.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/datasets-package.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/discoveries.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/esoph.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/euro.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/eurodist.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/faithful.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/freeny.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/infert.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/iris.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/islands.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/lh.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/longley.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/lynx.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/quakes.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/randu.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/rivers.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/rock.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/trees.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/uspop.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/volcano.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/warpbreaks.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/women.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/datasets/html/zCO2.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/00Index.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/lookup.xport.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/read.S.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/read.arff.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/read.dbf.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/read.dta.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/read.epiinfo.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/read.mtp.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/read.octave.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/read.spss.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/read.ssd.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/read.systat.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/read.xport.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/write.arff.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/write.dbf.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/write.dta.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/foreign/html/write.foreign.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/00Index.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/Devices.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/Hershey.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/Japanese.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/Type1Font.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/adjustcolor.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/as.graphicsAnnot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/as.raster.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/axisTicks.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/boxplot.stats.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/cairo.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/check.options.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/chull.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/cm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/col2rgb.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/colorRamp.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/colors.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/contourLines.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/convertColor.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/densCols.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grDevices/html/dev.capabilities.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grid/html/grobName.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grid/html/grobWidth.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grid/html/grobX.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/grid/html/makeContent.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/interaction.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/lattice.options.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/latticeParseFormula.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/level.colors.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/melanoma.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/oneway.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/packet.panel.default.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/panel.axis.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/panel.dotplot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/panel.functions.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/panel.histogram.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/panel.levelplot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/panel.loess.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/panel.number.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/panel.pairs.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/panel.parallel.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/panel.qqmath.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/panel.qqmathline.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/panel.smoothScatter.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/lattice/html/panel.spline.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/mgcv/html/formXtViX.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/mgcv/html/formula.gam.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/mgcv/html/fs.test.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/mgcv/html/full.score.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/nlme/html/getResponse.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/nlme/html/getResponseFormula.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/nlme/html/getVarCov.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/nlme/html/gls.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/nlme/html/glsControl.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/nlme/html/glsObject.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/nlme/html/glsStruct.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/nlme/html/gnls.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/nlme/html/lmList.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/nlme/html/lme.groupedData.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/nlme/html/lme.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/nlme/html/lme.lmList.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/getInitial.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/glm.control.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/glm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/glm.summaries.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/kernapply.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/kernel.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/kmeans.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/kruskal.test.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/ks.test.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/ksmooth.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/lag.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/lag.plot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/line.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/lm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/lm.influence.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/lm.summaries.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/lmfit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/loadings.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/loess.control.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/loess.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/logLik.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/loglin.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/lowess.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/ls.diag.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/make.link.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/makepredictcall.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/manova.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/mantelhaen.test.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/model.extract.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/model.frame.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/model.matrix.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/model.tables.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/monthplot.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/mood.test.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/na.action.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/na.contiguous.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/nlm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/nlminb.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/nls.control.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/nls.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/nobs.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/numericDeriv.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/offset.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats/html/oneway.test.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats4/html/logLik-methods.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats4/html/mle-class.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats4/html/mle.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats4/html/plot-methods.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats4/html/profile-methods.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats4/html/profile.mle-class.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats4/html/show-methods.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats4/html/stats4-package.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats4/html/summary-methods.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats4/html/summary.mle-class.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats4/html/update-methods.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/stats4/html/vcov-methods.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/anova.coxph.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/attrassign.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/basehaz.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/bladder.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/colon.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/cox.zph.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/coxph.control.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/coxph.detail.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/logan.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/lung.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/mgus.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/model.frame.coxph.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/predict.coxph.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/predict.survreg.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/print.aareg.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/print.summary.coxph.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/print.summary.survexp.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/print.summary.survfit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/print.survfit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/pspline.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/pyears.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/quantile.survfit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/ratetable.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/ratetableDate.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/rats.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/rats2.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/residuals.coxph.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/residuals.survreg.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/ridge.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/stanford2.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/strata.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/summary.aareg.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/summary.coxph.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/summary.survexp.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/summary.survfit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/survival/html/survConcordance.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' 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/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/check_packages_in_dir.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/codoc.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/compactPDF.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/delimMatch.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/dependsOnPkgs.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/encoded.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/fileutils.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/getDepList.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/installFoundDepends.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/makeLazyLoading.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/make_translations_pkg.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/md5sum.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/package.dependencies.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/package_dependencies.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/parseLatex.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/parse_Rd.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/print.via.format.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/pskill.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/psnice.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/read.00Index.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/readNEWS.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/showNonASCII.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/startDynamicHelp.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/testInstalledPackage.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/texi2dvi.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/toHTML.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/toRd.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/tools-defunct.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/tools-deprecated.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/tools-package.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/undoc.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/update_pkg_po.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/vignetteDepends.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/vignetteEngine.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/writePACKAGES.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/tools/html/xgettext.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/00Index.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/BATCH.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/COMPILE.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/INSTALL.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/LINK.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/PkgUtils.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/Question.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/REMOVE.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/RHOME.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/RShowDoc.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/RSiteSearch.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/Rprof.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/Rprofmem.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/Rscript.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/Rtangle.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/RweaveLatex.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/SHLIB.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/Sweave.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/SweaveSyntConv.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/SweaveUtils.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/URLencode.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/View.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/adist.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/alarm.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/apropos.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/aregexec.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/aspell-utils.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/aspell.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/available.packages.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/bibentry.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/browseEnv.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/browseURL.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/browseVignettes.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/bug.report.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/capture.output.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/chooseBioCmirror.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/chooseCRANmirror.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/citEntry.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/citation.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/cite.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/close.socket.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/combn.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/compareVersion.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/contrib.url.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/count.fields.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/create.post.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/data.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/dataentry.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/debugger.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/demo.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/download.file.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/download.packages.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/edit.data.frame.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/edit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/example.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/file.edit.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/filetest.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/findLineNum.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/fix.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/flush.console.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/format.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/getAnywhere.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/getFromNamespace.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/getParseData.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/getS3method.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/glob2rx.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/globalVariables.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/head.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/help.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/help.request.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/help.search.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/help.start.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/install.packages.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/installed.packages.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/localeToCharset.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/ls_str.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/maintainer.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/make.packages.html.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/make.socket.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/memory.size.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/menu.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/methods.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/mirrorAdmin.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/modifyList.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/news.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/nsl.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/object.size.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/package.skeleton.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/packageDescription.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/packageName.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/packageStatus.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/page.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/person.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/process.events.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/prompt.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/promptData.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/promptPackage.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/rcompgen.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/read.DIF.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/read.fortran.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/read.fwf.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/read.socket.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/read.table.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/recover.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/relist.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/remove.packages.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/removeSource.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/roman.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/rtags.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/savehistory.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/select.list.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/sessionInfo.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/setRepositories.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/sourceutils.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/stack.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/str.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/summaryRprof.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/tar.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/toLatex.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/txtProgressBar.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/type.convert.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/untar.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/unzip.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/update.packages.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/url.show.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/utils-defunct.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/utils-deprecated.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/utils-package.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/vignette.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/write.table.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.0.1|g' /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/utils/html/zip.html + chmod +x /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/R/sh/echo.sh + chmod -x /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R/library/mgcv/CITATION /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/doc/R-3.0.1/CAPABILITIES + pushd /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R ~/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/lib/R ~/LinuxDownloads/redhat/BUILD/R-3.0.1 + ln -s ../../include/R include + popd ~/LinuxDownloads/redhat/BUILD/R-3.0.1 + mkdir -p /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/texmf/tex/latex + pushd /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/texmf/tex/latex ~/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/texmf/tex/latex ~/LinuxDownloads/redhat/BUILD/R-3.0.1 + ln -s ../../../R/texmf/tex/latex R + popd ~/LinuxDownloads/redhat/BUILD/R-3.0.1 + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump Processing files: R-3.0.1-2.fc17.i386 Processing files: R-core-3.0.1-2.fc17.i386 Provides: KernSmooth.so MASS.so Matrix.so R-KernSmooth = 2.23.10 R-MASS = 7.3.26 R-Matrix = 1.0.12 R-base = 3.0.1 R-boot = 1.3.9 R-class = 7.3.7 R-cluster = 1.14.4 R-codetools = 0.2.8 R-datasets = 3.0.1 R-foreign = 0.8.53 R-grDevices = 3.0.1 R-graphics = 3.0.1 R-grid = 3.0.1 R-lattice = 0.20.15 R-methods = 3.0.1 R-mgcv = 1.7.22 R-nlme = 3.1.109 R-nnet = 7.3.6 R-parallel = 3.0.1 R-rpart = 4.1.1 R-spatial = 7.3.6 R-splines = 3.0.1 R-stats = 3.0.1 R-stats4 = 3.0.1 R-survival = 2.37.4 R-tcltk = 3.0.1 R-tools = 3.0.1 R-utils = 3.0.1 R_X11.so R_de.so cairo.so class.so cluster.so foreign.so grDevices.so graphics.so grid.so internet.so lapack.so lattice.so libR.so libRblas.so libRlapack.so methods.so mgcv.so nlme.so nnet.so parallel.so rpart.so spatial.so splines.so stats.so survival.so tcltk.so tools.so utils.so vfonts.so Requires(interp): /bin/sh /bin/sh /bin/sh /bin/sh Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires(post): /bin/sh Requires(preun): /bin/sh Requires(postun): /bin/sh Requires: /bin/bash /bin/sh ld-linux.so.2 ld-linux.so.2(GLIBC_2.1) libICE.so.6 libR.so libRblas.so libRlapack.so libSM.so.6 libX11.so.6 libXmu.so.6 libXt.so.6 libbz2.so.1 libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.2) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.6) libc.so.6(GLIBC_2.7) libcairo.so.2 libdl.so.2 libdl.so.2(GLIBC_2.0) libdl.so.2(GLIBC_2.1) libgfortran.so.3 libgfortran.so.3(GFORTRAN_1.0) libglib-2.0.so.0 libgobject-2.0.so.0 libgomp.so.1 libgomp.so.1(GOMP_1.0) libgomp.so.1(OMP_1.0) libicui18n.so.48 libicuuc.so.48 libjpeg.so.62 libjpeg.so.62(LIBJPEG_6.2) liblzma.so.5 liblzma.so.5(XZ_5.0) libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libpango-1.0.so.0 libpangocairo-1.0.so.0 libpcre.so.0 libpng15.so.15 libpng15.so.15(PNG15_0) libpthread.so.0 libpthread.so.0(GLIBC_2.0) libpthread.so.0(GLIBC_2.2) libquadmath.so.0 libreadline.so.6 librt.so.1 librt.so.1(GLIBC_2.2) libtcl8.5.so libtiff.so.3 libtk8.5.so libz.so.1 rtld(GNU_HASH) Obsoletes: R-Matrix < 0.999375-7 Processing files: R-core-devel-3.0.1-2.fc17.i386 Provides: R-Matrix-devel = 1.0.12 pkgconfig(libR) = 3.0.1 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/pkg-config Obsoletes: R-Matrix-devel < 0.999375-7 Processing files: R-devel-3.0.1-2.fc17.i386 Processing files: R-java-3.0.1-2.fc17.i386 Processing files: R-java-devel-3.0.1-2.fc17.i386 Processing files: libRmath-3.0.1-2.fc17.i386 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.SlD664 + umask 022 + cd /home/pauljohn/LinuxDownloads/redhat/BUILD + cd R-3.0.1 + DOCDIR=/home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/doc/libRmath-3.0.1 + export DOCDIR + /usr/bin/mkdir -p /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/doc/libRmath-3.0.1 + cp -pr doc/COPYING /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386/usr/share/doc/libRmath-3.0.1 + exit 0 Provides: libRmath.so Requires(interp): /sbin/ldconfig /sbin/ldconfig Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires(post): /sbin/ldconfig Requires(postun): /sbin/ldconfig Requires: libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1.3) libgomp.so.1 libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libpthread.so.0 libpthread.so.0(GLIBC_2.0) rtld(GNU_HASH) Processing files: libRmath-devel-3.0.1-2.fc17.i386 Provides: pkgconfig(libRmath) = 3.0.1 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/pkg-config Processing files: libRmath-static-3.0.1-2.fc17.i386 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386 Wrote: /home/pauljohn/LinuxDownloads/redhat/SRPMS/R-3.0.1-2.fc17.src.rpm Wrote: /home/pauljohn/LinuxDownloads/redhat/RPMS/i386/R-3.0.1-2.fc17.i386.rpm Wrote: /home/pauljohn/LinuxDownloads/redhat/RPMS/i386/R-core-3.0.1-2.fc17.i386.rpm Wrote: /home/pauljohn/LinuxDownloads/redhat/RPMS/i386/R-core-devel-3.0.1-2.fc17.i386.rpm Wrote: /home/pauljohn/LinuxDownloads/redhat/RPMS/i386/R-devel-3.0.1-2.fc17.i386.rpm Wrote: /home/pauljohn/LinuxDownloads/redhat/RPMS/i386/R-java-3.0.1-2.fc17.i386.rpm Wrote: /home/pauljohn/LinuxDownloads/redhat/RPMS/i386/R-java-devel-3.0.1-2.fc17.i386.rpm Wrote: /home/pauljohn/LinuxDownloads/redhat/RPMS/i386/libRmath-3.0.1-2.fc17.i386.rpm Wrote: /home/pauljohn/LinuxDownloads/redhat/RPMS/i386/libRmath-devel-3.0.1-2.fc17.i386.rpm Wrote: /home/pauljohn/LinuxDownloads/redhat/RPMS/i386/libRmath-static-3.0.1-2.fc17.i386.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.KnbE5J + umask 022 + cd /home/pauljohn/LinuxDownloads/redhat/BUILD + cd R-3.0.1 + rm -rf /home/pauljohn/LinuxDownloads/redhat/BUILDROOT/R-3.0.1-2.fc17.i386 + exit 0 ~/LinuxDownloads/redhat/SPECS $