Centos 6.3 64 bit

I just noticed my external disk for Centos was in 32 bit, and maybe we are safe to use 64.

Installed a fresh Centos 6.3 and then tried to make a journal to summarize the updates/hassles. IN the process, I generated 5 files of text output from the terminal, which I catted together. I see now that's too huge, but for records, it is uploaded to https://pj.freefaculty.org/scraps/install-eshell-all.txt

Still I wonder. No attachments allowed with blog posts?  I can't figure that out!  Aha! treat it as media!  install-eshell-all

I installed everything needed to develop rpm packages, and as I went, I was uploading results to


I dumped the SRPMS and the RPMS that same folder. Eventually, I will cycle back and sort it out, maybe build an RPM repository.

1) configure .rpmmacros in pauljohn32, create LinuxDownloads/redhat

%_topdir /home/pauljohn32/LinuxDownloads/redhat

%_unpackaged_files_terminate_build      0

%_missing_doc_files_terminate_build     0

2) Tried to build emacs 24, found missing packages. See file "install-shell.txt" for install of many packages and the EPEL repository.

installed emacs 24.2, and uploaded to https://pj.freefaculty.org/EL/6/x86_64

3) The system updater asked to update a lot of packages. OK!

4) Edit sshd to make X11forwarding ON by default

5) yum installs:

yum install xfig transfig xfig2ps blt tcl-devel tk-devel inkscape lyx texmacs

yum -y install R-devel
yum -y install R

yum -y install R-car R-lmtest R-multcomp R-mvtnorm R-systemfit R-zoo

yum -y install filezilla

yum -y install yumex

8). Put "pauljohn32" in the wheel group, edit /etc/sudoers to enable wheel

7). Ach. Lyx is version 1.6.  Build 2.0.3 and install.

build/install tex-simplecv first.

build requires;

fontpackages-devel is needed by lyx-2.0.3-1.el6.x86_64
enchant-devel is needed by lyx-2.0.3-1.el6.x86_64
hunspell-devel is needed by lyx-2.0.3-1.el6.x86_64
qt4-devel is needed by lyx-2.0.3-1.el6.x86_64

Finally, built LyX-2.0.3 RPM, uploaded that.

8) Can't find ESS package for EL6. WTF??

Build emacs-ess, install, test, upload

9) install my init.el on system.

10) swarm

install hdf5-devel, gcc, gcc-objc, gperf

11) openbugs: cant compile because of this error:

make[1]: Entering directory
gcc -o OpenBUGSCli OpenBUGSCli.c -L ../lib -Wl,-rpath,\$ORIGIN/../lib -m32
/usr/bin/ld: skipping incompatible
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/libgcc_s.so when searching for -lgcc_s
/usr/bin/ld: skipping incompatible
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/libgcc_s.so when searching for -lgcc_s
/usr/bin/ld: cannot find -lgcc_s
collect2: ld returned 1 exit status
make[1]: *** [OpenBUGSCli] Error 1
make[1]: Leaving directory
make: *** [all-recursive] Error 1
error: Bad exit status from /var/tmp/rpm-tmp.mELKHJ (%prep)
uild & upload

$ sudo yum install libgcc-4.4.6-4.el6.i686

$ rpmbuild -ba openbugs-3.2.2.spec

$ sudo rpm -ivh openbugs-3.2.2-2.x86_64.rpm


12: To image disk to other devices, some changes were necessary for some laptops.

First, because I am frustrated with SELinux, turn that off. edit /etc/selinux/config and disable it. Restart.

Then use e2label to set the disk partitions with labeled "usbhome", "usbroot", "usbroot".  This cannot be done with the swap partition, it is necessary to turn off the swap (swapoff -a), then run mkswap -L usbswap /dev/sda3, then turn swap back on.  After that,  the UUID notations from /boot/grub/grub.conf are replaced by LABEL statements.

Similar change is required in /etc/fstab

13. Realized JAGS (Just another Gibbs Sampler) could be compiled and run.  Grabbed the SRPM from http://download.opensuse.org/repositories/home:/cornell_vrdc/CentOS_CentOS-6/src/

and rebuilt and uploaded it. Could have just used the RPM they provided, but decided to rebuild so that the build process would help me notice more development packages that need to be installed.

14. Check /usr/lib/R/etc/Renviron. Not improvements in setup, now there is a place to install packages without getting in the way of RPM installs. Lets use the first one here.


$ sudo mkdir -p /usr/local/lib/R/site-library

$ sudo R

> install.packages("rjags", lib="/usr/local/lib/R/site-library", dep=TRUE)

While I am at it, I might as well install more R packages.  Get the script


Make some updates. Will change name to version -02 and leave in /usr/local/bin. Will be executable Rscript.

Along the way to do that, I noticed /usr/local/bin was empty and did not show in the PATH.  Will have to reboot to log out and log in to see if it notices the file there. Probably need to enter /etc/profile to fix it.

While testing, I ran R-labSelectInstall-02.R inside R, line by line, for testing.

Running just the first bit:

update.packages(ask=F, checkBuilt=T, dep=T)

launches a massive package rebuild that will probably expose more missing RPM devel packages. Continuing through the script R-labSelectInstall-02.R, these packages are installed in /usr/local/lib/R/site-library:

abind                  gWidgets              RArcInfo
actuar                 gWidgetsRGtk2         raster
ada                    gWidgetstcltk         rattle
ade4                   hdf5                  rbenchmark
ade4TkGUI              hexbin                Rcmdr
adehabitat             HSAUR                 Rcpp
AGD                    HyperbolicDist        RcppArmadillo
akima                  igraph                Rcsdp
amap                   igraph0               R.devices
Amelia                 igraphdata            relations
anchors                ineq                  relevent
aod                    influence.ME          relimp
ape                    inline                reshape
aplpack                iplots                reshape2
arules                 ipred                 rgenoud
arulesViz              isa2                  Rglpk
bayesm                 Iso                   RGtk2
bayesmix               ISwR                  rjags
bestglm                iterators             rJava
betareg                itertools             RJSONIO
biclust                JavaGD                rlecuyer
bitops                 JGR                   rmeta
BMA                    Kendall               R.methodsS3
brew                   kernlab               rms
BRugs                  labeling              ROCR
cairoDevice            languageR             R.oo
CarbonEL               lars                  rpanel
caTools                lasso2                rpart.plot
cba                    latentnet             rrcov
CircStats              latticist             R.rsp
clue                   lava                  RSQLite
clv                    lavaan                RSvgDevice
cmprsk                 lmec                  RSVGTipsDevice
cocorresp              lmeSplines            Rsymphony
coda                   lmm                   RUnit
colorspace             locfit                R.utils
combinat               logspline             SASmixed
corpcor                lokern                scales
cslogistic             longitudinal          scapeMCMC
cubature               longitudinalData      scatterplot3d
DBI                    longmemo              segmented
deldir                 longRPart             SemiPar
descr                  lpSolve               seriation
Devore5                mapproj               setRNG
Devore6                maps                  sets
diagram                maptools              sfsmisc
dichromat              mcgibbsit             shape
digest                 mclust                shapefiles
diptest                mcmc                  shapes
DistributionUtils      MCMCglmm              SkewHyperbolic
dlm                    MCMCpack              slam
doBy                   MCPAN                 sm
dse                    mda                   smoothSurv
e1071                  memisc                sn
earth                  memoise               sna
Ecdat                  MEMSS                 snow
ecodist                mice                  snowFT
effects                micEcon               sp
eha                    misc3d                spam
eiPack                 miscTools             spatialCovariance
ElemStatLearn          mitools               spatialkernel
ellipse                mix                   spatstat
ergm                   mlbench               spdep
ergm.userterms         mnormt                splancs
evaluate               MNP                   stabledist
faraway                msm                   StatDataML
fBasics                mstate                statmod
fdrtool                munsell               statnet
ffmanova               network               stepwise
fields                 networkDynamic        stringr
fImport                norm                  subselect
flexclust              np                    survBayes
flexmix                numDeriv              tcltk2
foreach                nws                   tclust
forecast               odfWeave              TeachingDemos
forward                orthopolynom          tensorA
fpc                    pan                   testthat
fracdiff               party                 tfplot
gam                    PBSmapping            tframe
gamlss                 pcaPP                 tkrplot
gamlss.data            permute               tree
gamlss.dist            pixmap                trimcluster
gamm4                  playwith              tripack
gclus                  plotmo                trust
gdata                  plotrix               TSP
gee                    plyr                  tweedie
geepack                pmml                  urca
GeneralizedHyperbolic  png                   UsingR
geoR                   polspline             VarianceGamma
geoRglm                polycor               vcd
ggplot2                polynom               vegan
glmmAK                 prabclus              verification
glmmBUGS               prim                  VGAM
glmmML                 prodlim               VIM
gmodels                proto                 waveslim
gof                    proxy                 WDI
googleVis              pscl                  weightedKmeans
GPArotation            pspline               wnominate
gpclib                 psych                 XLConnect
gplots                 qgraph                XLConnectJars
gregmisc               R2HTML                XML
gridBase               R2WinBUGS             Zelig
gsl                    RandomFields          zipfR
gtable                 randomSurvivalForest
gtools                 RANN

And these ones failed to build, I'll check why later. The first set is obvious, they just need to be removed from my wish list, while the latter ones fail because required devel software is not installed. Since I'm not using those now, I'll probably ignore them.

1: packages ‘Design’, ‘amer’, ‘DCluster’, ‘ZIGP’, ‘impute’ are not available (for R version 2.15.1)
2: In install.packages(desiredPackages[!alreadyHave], dependencies = c("Imports",  :
installation of package ‘Rmpi’ had non-zero exit status
3: In install.packages(desiredPackages[!alreadyHave], dependencies = c("Imports",  :
installation of package ‘rsprng’ had non-zero exit status
4: In install.packages(desiredPackages[!alreadyHave], dependencies = c("Imports",  :
installation of package ‘ncdf’ had non-zero exit status
5: In install.packages(desiredPackages[!alreadyHave], dependencies = c("Imports",  :
installation of package ‘ncdf4’ had non-zero exit status
6: In install.packages(desiredPackages[!alreadyHave], dependencies = c("Imports",  :
installation of package ‘fftw’ had non-zero exit status
7: In install.packages(desiredPackages[!alreadyHave], dependencies = c("Imports",  :
installation of package ‘RODBC’ had non-zero exit status
8: In install.packages(desiredPackages[!alreadyHave], dependencies = c("Imports",  :
installation of package ‘rgdal’ had non-zero exit status
9: In install.packages(desiredPackages[!alreadyHave], dependencies = c("Imports",  :
installation of package ‘rggobi’ had non-zero exit status
10: In install.packages(desiredPackages[!alreadyHave], dependencies = c("Imports",  :
installation of package ‘rgeos’ had non-zero exit status

I'm still having some trouble getting R-labSelectInstall-02.R to run from the command line using Rscript, I want to add it as a weekly cron job when it is fixed.

Installed ggobi and ggobi-devel so that rggobi does install

14. Tested yum groups, noticed I'd be getting some potentially useful packages

$ sudo yum groupinstall  "Desktop Platform Development"


Installing : libXp-1.0.0-15.1.el6.x86_64                                 1/11
Installing : libXp-devel-1.0.0-15.1.el6.x86_64                           2/11
Installing : openmotif-2.3.3-4.el6.x86_64                                3/11
Installing : mesa-libGLw-6.5.1-10.el6.x86_64                             4/11
Installing : libmng-devel-1.0.10-4.1.el6.x86_64                          5/11
Installing : libXmu-devel-1.0.5-1.el6.x86_64                             6/11
Installing : openmotif-devel-2.3.3-4.el6.x86_64                          7/11
Installing : mesa-libGLw-devel-6.5.1-10.el6.x86_64                       8/11
Installing : qt3-devel-3.3.8b-30.el6.x86_64                              9/11
Installing : libXtst-devel-                        10/11
Installing : xorg-x11-docs-1.3-6.1.el6.noarch                           11/11
Verifying  : libXmu-devel-1.0.5-1.el6.x86_64                             1/11
Verifying  : libXp-devel-1.0.0-15.1.el6.x86_64                           2/11
Verifying  : xorg-x11-docs-1.3-6.1.el6.noarch                            3/11
Verifying  : openmotif-devel-2.3.3-4.el6.x86_64                          4/11
Verifying  : openmotif-2.3.3-4.el6.x86_64                                5/11
Verifying  : libmng-devel-1.0.10-4.1.el6.x86_64                          6/11
Verifying  : mesa-libGLw-6.5.1-10.el6.x86_64                             7/11
Verifying  : mesa-libGLw-devel-6.5.1-10.el6.x86_64                       8/11
Verifying  : libXp-1.0.0-15.1.el6.x86_64                                 9/11
Verifying  : libXtst-devel-                        10/11
Verifying  : qt3-devel-3.3.8b-30.el6.x86_64                             11/11

libXtst-devel.x86_64 0: mesa-libGLw-devel.x86_64 0:6.5.1-10.el6
qt3-devel.x86_64 0:3.3.8b-30.el6      xorg-x11-docs.noarch 0:1.3-6.1.el6

Dependency Installed:
libXmu-devel.x86_64 0:1.0.5-1.el6      libXp.x86_64 0:1.0.0-15.1.el6
libXp-devel.x86_64 0:1.0.0-15.1.el6    libmng-devel.x86_64 0:1.0.10-4.1.el6
mesa-libGLw.x86_64 0:6.5.1-10.el6      openmotif.x86_64 0:2.3.3-4.el6
openmotif-devel.x86_64 0:2.3.3-4.el6


15. yum install sshfs ntfs-3g ntfsprogs

Put user in fuse group. Wish that were for all users to make it automatic!

Install flashplayer RPM from adobe.com


About pauljohn

Paul E. Johnson is a Professor of Political Science at the University of Kansas. He is an avid Linux User, an adequate system administrator and C programmer, and humility is one of his greatest strengths.
This entry was posted in Linux. Bookmark the permalink.