R : Copyright 2005, The R Foundation for Statistical Computing Version 2.1.1 (2005-06-20), ISBN 3-900051-07-0 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 a HTML browser interface to help. Type 'q()' to quit R. > invisible(options(echo = TRUE)) > > > > options(repos = "http://lib.stat.cmu.edu/R/CRAN/") > update.packages(ask=F) trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/acepack_1.3-2.2.tar.gz' Content type 'application/x-gzip' length 18596 bytes opened URL ================================================== downloaded 18Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/aster_0.3.tar.gz' Content type 'application/x-gzip' length 211125 bytes opened URL ================================================== downloaded 206Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/BradleyTerry_0.8-5.tar.gz' Content type 'application/x-gzip' length 125488 bytes opened URL ================================================== downloaded 122Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/brlr_0.8-2.tar.gz' Content type 'application/x-gzip' length 8202 bytes opened URL ================================================== downloaded 8202 bytes trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/caTools_1.2.tar.gz' Content type 'application/x-gzip' length 49896 bytes opened URL ================================================== downloaded 48Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/clac_0.1-2.tar.gz' Content type 'application/x-gzip' length 120316 bytes opened URL ================================================== downloaded 117Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/clim.pact_2.2-0.tar.gz' Content type 'application/x-gzip' length 5436941 bytes opened URL ================================================== downloaded 5309Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/combinat_0.0-6.tar.gz' Content type 'application/x-gzip' length 7677 bytes opened URL ================================================== downloaded 7677 bytes trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/cyclones_1.1-5.tar.gz' Content type 'application/x-gzip' length 2786072 bytes opened URL ================================================== downloaded 2720Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/DAAG_0.58.tar.gz' Content type 'application/x-gzip' length 260245 bytes opened URL ================================================== downloaded 254Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/dblcens_1.1.3.tar.gz' Content type 'application/x-gzip' length 15992 bytes opened URL ================================================== downloaded 15Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/fortunes_1.1-2.tar.gz' Content type 'application/x-gzip' length 25269 bytes opened URL ================================================== downloaded 24Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/gregmisc_2.0.8.tar.gz' Content type 'application/x-gzip' length 901 bytes opened URL ================================================== downloaded 901 bytes trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/glmmML_0.26-3.tar.gz' Content type 'application/x-gzip' length 24733 bytes opened URL ================================================== downloaded 24Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/gRbase_0.1.23.tar.gz' Content type 'application/x-gzip' length 35156 bytes opened URL ================================================== downloaded 34Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/irr_0.6.tar.gz' Content type 'application/x-gzip' length 13812 bytes opened URL ================================================== downloaded 13Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/kernlab_0.6-2.tar.gz' Content type 'application/x-gzip' length 1163831 bytes opened URL ================================================== downloaded 1136Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/lattice_0.12-3.tar.gz' Content type 'application/x-gzip' length 209825 bytes opened URL ================================================== downloaded 204Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/limma_2.0.4.tar.gz' Content type 'application/x-gzip' length 661138 bytes opened URL ================================================== downloaded 645Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/locfdr_1.0-3.tar.gz' Content type 'application/x-gzip' length 150135 bytes opened URL ================================================== downloaded 146Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/MarkedPointProcess_0.1.5.tar.gz' Content type 'application/x-gzip' length 470711 bytes opened URL ================================================== downloaded 459Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/MatchIt_1.0-2.tar.gz' Content type 'application/x-gzip' length 37917 bytes opened URL ================================================== downloaded 37Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/Matrix_0.98-3.tar.gz' Content type 'application/x-gzip' length 626712 bytes opened URL ================================================== downloaded 612Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/mgcv_1.3-5.tar.gz' Content type 'application/x-gzip' length 243952 bytes opened URL ================================================== downloaded 238Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/NADA_1.2-2.tar.gz' Content type 'application/x-gzip' length 42573 bytes opened URL ================================================== downloaded 41Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/outliers_0.12.tar.gz' Content type 'application/x-gzip' length 14570 bytes opened URL ================================================== downloaded 14Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/prabclus_2.0-1.tar.gz' Content type 'application/x-gzip' length 49408 bytes opened URL ================================================== downloaded 48Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/R2WinBUGS_1.0-0.tar.gz' Content type 'application/x-gzip' length 1099661 bytes opened URL ================================================== downloaded 1073Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/RandomFields_1.3.1.tar.gz' Content type 'application/x-gzip' length 317282 bytes opened URL ================================================== downloaded 309Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/ref_0.91.tar.gz' Content type 'application/x-gzip' length 24831 bytes opened URL ================================================== downloaded 24Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/RGraphics_1.0-4.tar.gz' Content type 'application/x-gzip' length 118601 bytes opened URL ================================================== downloaded 115Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/SoPhy_1.0.19.tar.gz' Content type 'application/x-gzip' length 2459503 bytes opened URL ================================================== downloaded 2401Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/SwissAir_1.0.5.tar.gz' Content type 'application/x-gzip' length 788766 bytes opened URL ================================================== downloaded 770Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/waveslim_1.5.tar.gz' Content type 'application/x-gzip' length 562897 bytes opened URL ================================================== downloaded 549Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/XML_0.97-8.tar.gz' Content type 'application/x-gzip' length 557863 bytes opened URL ================================================== downloaded 544Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/Zelig_2.3-2.tar.gz' Content type 'application/x-gzip' length 296317 bytes opened URL ================================================== downloaded 289Kb * Installing *source* package 'acepack' ... ** libs gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c ace.f -o ace.o gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c avas.f -o avas.o gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c rlsmo.f -o rlsmo.o gcc -shared -L/usr/local/lib -o acepack.so ace.o avas.o rlsmo.o -lgfortran -lm -lgcc_s -L/usr/lib/R/lib -lR ** R ** help >>> Building/Updating help pages for package 'acepack' Formats: text html latex example ace text html latex example avas text html latex example ** building package indices ... * DONE (acepack) * Installing *source* package 'aster' ... ** libs gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c astchk.c -o astchk.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c astcond.c -o astcond.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c astderiv2.c -o astderiv2.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c astderiv3.c -o astderiv3.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c astderiv4.c -o astderiv4.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c astderiv.c -o astderiv.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c astfam.c -o astfam.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c astfish.c -o astfish.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c astsim.c -o astsim.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c asttrans2.c -o asttrans2.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c asttrans5.c -o asttrans5.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c asttrans6.c -o asttrans6.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c asttrans7.c -o asttrans7.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c asttrans8.c -o asttrans8.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c asttrans9.c -o asttrans9.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c asttrans.c -o asttrans.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c astunco.c -o astunco.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c init.c -o init.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c matops.c -o matops.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c raster.c -o raster.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c vatops.c -o vatops.o gcc -shared -L/usr/local/lib -o aster.so astchk.o astcond.o astderiv2.o astderiv3.o astderiv4.o astderiv.o astfam.o astfish.o astsim.o asttrans2.o asttrans5.o asttrans6.o asttrans7.o asttrans8.o asttrans9.o asttrans.o astunco.o init.o matops.o raster.o vatops.o -L/usr/lib/R/lib -lR ** R ** data ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'aster' Formats: text html latex example anova.aster text html latex example aster text html latex example echinacea text html latex example families text html latex example mlogl text html latex predict.aster text html latex example raster text html latex example rnzp text html latex example summary.aster text html latex ** building package indices ... * DONE (aster) * Installing *source* package 'brlr' ... ** R ** data ** help >>> Building/Updating help pages for package 'brlr' Formats: text html latex example brlr text html latex example lizards text html latex example ** building package indices ... * DONE (brlr) * Installing *source* package 'caTools' ... ** libs g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c GifTools.cc -o GifTools.o GifTools.cc: In member function 'void BitPacker::SubmitCode(short int, short int)': GifTools.cc:142: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result GifTools.cc: In member function 'void BitPacker::WriteFlush()': GifTools.cc:161: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result GifTools.cc: In function 'int imwriteGif(char*, uchar*, int, int, int, int, int*, bool, int, int, char*)': GifTools.cc:451: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result GifTools.cc:490: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result GifTools.cc:501: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c rawfunc.c -o rawfunc.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c runfunc.c -o runfunc.o g++ -shared -L/usr/local/lib -o caTools.so GifTools.o rawfunc.o runfunc.o -L/usr/lib/R/lib -lR ** R ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'caTools' Formats: text html latex example ENVI text html latex example GIF text html latex example LogitBoost text html latex example base64 text html latex example bin2raw text html latex example colAUC text html latex example combs text html latex example predict.LogitBoost text html latex example runfunc text html latex example sample.split text html latex example sum.exact text html latex example trapz text html latex example ** building package indices ... * DONE (caTools) * Installing *source* package 'clac' ... ** libs gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c CLAC1.f -o CLAC1.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c CLAC_buildtree.c -o CLAC_buildtree.o CLAC_buildtree.c: In function 'hclust_inside': CLAC_buildtree.c:128: warning: incompatible implicit declaration of built-in function 'malloc' CLAC_buildtree.c: In function 'clacarray': CLAC_buildtree.c:220: warning: incompatible implicit declaration of built-in function 'malloc' gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c CLAC_selectnode.c -o CLAC_selectnode.o CLAC_selectnode.c: In function 'subtree': CLAC_selectnode.c:23: warning: incompatible implicit declaration of built-in function 'malloc' CLAC_selectnode.c: In function 'selectclust': CLAC_selectnode.c:103: warning: incompatible implicit declaration of built-in function 'malloc' CLAC_selectnode.c: In function 'selectleaf': CLAC_selectnode.c:166: warning: incompatible implicit declaration of built-in function 'malloc' gcc -shared -L/usr/local/lib -o clac.so CLAC1.o CLAC_buildtree.o CLAC_selectnode.o -lgfortran -lm -lgcc_s -L/usr/lib/R/lib -lR ** R ** data ** help >>> Building/Updating help pages for package 'clac' Formats: text html latex example BACarray text html latex clac.Excel text html latex clac.PlotAllArray.R text html latex example clac.PlotConsensus.R text html latex example clac.PlotSingleArray.R text html latex example clac.preparenormal.R text html latex example clac.tumorarray.R text html latex example ** building package indices ... * DONE (clac) * Installing *source* package 'clim.pact' ... ** R ** data ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'clim.pact' Formats: text html latex example CCA text html latex example COn0E65N text html latex example DNMI.t2m text html latex example DS text html latex example EOF text html latex example EOF2field text html latex example MVR text html latex example POP text html latex example SSA text html latex example addClim text html latex example addland text html latex example addland_data text html latex example adjust.eof text html latex example anomaly.field text html latex example anomaly.station text html latex example avail.elem text html latex example bergen.dm_data text html latex example bergen.t2m_data text html latex example caldat text html latex example catFields text html latex example cdfcont text html latex example cdfextract text html latex example composite.field text html latex example corEOF text html latex example corField text html latex example datestr2num text html latex example delta text html latex example dist2norm text html latex example distAB text html latex example ds2station text html latex example eof.c_data text html latex example eof.dc_data text html latex example eof.dmc_data text html latex example eof.mc_data text html latex example eof.slp_data text html latex example getdnmi text html latex example getecsn text html latex example getgiss text html latex example getnacd text html latex example getnordklim text html latex example grd.box.ts text html latex example helsinki.t2_data text html latex example instring text html latex example julday text html latex example km2lat text html latex example km2lon text html latex example koebenhavn.t2m_data text html latex example lagStation text html latex example lower.case text html latex example map text html latex example map.eof text html latex example mapField text html latex example meanField text html latex example mergeEOF text html latex example mergeStation text html latex example mixFields text html latex example mod text html latex example newFig text html latex example num2str text html latex example objDS text html latex example oslo.dm_data text html latex example oslo.t2m_data text html latex example patternIndex text html latex example plot.station text html latex example plotDS text html latex example plotDSobj text html latex example plotEOF text html latex example plotField text html latex example plumePlot text html latex example r2cdf text html latex example retrieve.nc text html latex example reverse text html latex example rotate text html latex example satellite text html latex example station.obj text html latex example station.obj.dm text html latex example stationmap text html latex example stockholm.t2m_data text html latex example strip text html latex example tromsoe.t2m_data text html latex example upper.case text html latex example what.data text html latex example ** building package indices ... * DONE (clim.pact) * Installing *source* package 'combinat' ... ** R ** help >>> Building/Updating help pages for package 'combinat' Formats: text html latex example combn text html latex example dmnom text html latex example hcube text html latex example nsimplex text html latex example permn text html latex example rmultinomial text html latex example x2u text html latex example xsimplex text html latex example ** building package indices ... * DONE (combinat) * Installing *source* package 'DAAG' ... ** R ** data ** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'DAAG' Formats: text html latex example ACF1 text html latex example Cars93.summary text html latex example Lottario text html latex example Manitoba.lakes text html latex example ais text html latex allbacks text html latex example anesthetic text html latex example ant111b text html latex appletaste text html latex example austpop text html latex example bestset.noise text html latex example bomsoi text html latex example bounce text html latex carprice text html latex example cfseal text html latex example cities text html latex example component.residual text html latex example cuckoos text html latex example cv.binary text html latex example cv.lm text html latex example dewpoint text html latex example elastic1 text html latex example elastic2 text html latex example elasticband text html latex example fossilfuel text html latex example frogs text html latex example fruitohms text html latex example geophones text html latex example head.injury text html latex hills text html latex example houseprices text html latex example humanpower text html latex example ironslag text html latex example jobs text html latex example kiwishade text html latex example leafshape text html latex leafshape17 text html latex example leaftemp text html latex example leaftemp.all text html latex litters text html latex example logisticsim text html latex example measles text html latex mifem text html latex example mignonette text html latex example milk text html latex example modelcars text html latex example monica text html latex example moths text html latex example nsw74psid1 text html latex example nsw74psid3 text html latex example nsw74psidA text html latex example onesamp text html latex example onet.permutation text html latex example oneway.plot text html latex example orings text html latex example overlap.density text html latex example ozone text html latex example pair65 text html latex example panel.corr text html latex example panelplot text html latex example pause text html latex poissonsim text html latex example possum text html latex example possumsites text html latex example powerplot text html latex example primates text html latex example qreference text html latex example races2000 text html latex example rainforest text html latex example rareplants text html latex example rice text html latex example roller text html latex example science text html latex example seedrates text html latex example show.colors text html latex example simulate.linear text html latex example socsupport text html latex example softbacks text html latex example spam7 text html latex example sugar text html latex example tinting text html latex example toupper.initial text html latex example toycars text html latex example two65 text html latex example twot.permutation text html latex example vif text html latex example vince111b text html latex vlt text html latex example wages1833 text html latex example ** building package indices ... * DONE (DAAG) * Installing *source* package 'dblcens' ... ** libs gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c d011ch.c -o d011ch.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c ma.c -o ma.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c urnew010.c -o urnew010.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c wur.c -o wur.o gcc -shared -L/usr/local/lib -o dblcens.so d011ch.o ma.o urnew010.o wur.o -L/usr/lib/R/lib -lR ** R ** help >>> Building/Updating help pages for package 'dblcens' Formats: text html latex example d011 text html latex example d011ch text html latex example ** building package indices ... * DONE (dblcens) * Installing *source* package 'fortunes' ... ** R ** inst ** help >>> Building/Updating help pages for package 'fortunes' Formats: text html latex example fortunes text html latex example ** building package indices ... * DONE (fortunes) * Installing *source* package 'gregmisc' ... No man pages found in package 'gregmisc' ** building package indices ... * DONE (gregmisc) * Installing *source* package 'glmmML' ... ** libs gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c bfun.c -o bfun.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c c2f.c -o c2f.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c fun.c -o fun.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c GB_zeroin.c -o GB_zeroin.o gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c ghq.f -o ghq.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c glmmb0.c -o glmmb0.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c glmmboot.c -o glmmboot.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c glmmml.c -o glmmml.o gcc -shared -L/usr/local/lib -o glmmML.so bfun.o c2f.o fun.o GB_zeroin.o ghq.o glmmb0.o glmmboot.o glmmml.o -lblas -lgfortran -lm -lgcc_s -L/usr/lib/R/lib -lR ** R ** help >>> Building/Updating help pages for package 'glmmML' Formats: text html latex example glmmML text html latex example glmmML.fit text html latex example glmmboot text html latex example print.glmmML text html latex example print.glmmboot text html latex summary.glmmML text html latex example summary.glmmboot text html latex example ** building package indices ... * DONE (glmmML) * Installing *source* package 'gRbase' ... ** R ** data ** demo ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'gRbase' Formats: text html latex example cadcomplete text html latex example carcass text html latex dietox text html latex example gModel text html latex example gRbase-internal text html latex gRbase text html latex gRfit text html latex example gmData text html latex hllm text html latex example mathmark text html latex example rats text html latex reinis text html latex validVarTypes text html latex example ** building package indices ... * DONE (gRbase) * Installing *source* package 'irr' ... ** R ** data ** help >>> Building/Updating help pages for package 'irr' Formats: text html latex example agree text html latex example anxiety text html latex example diagnoses text html latex example finn text html latex example icc text html latex example iota text html latex example kappa2 text html latex example kappam.fleiss text html latex example kappam.light text html latex example kendall text html latex example maxwell text html latex example meancor text html latex example meanrho text html latex example print.icclist text html latex example print.irrlist text html latex example robinson text html latex example video text html latex example ** building package indices ... * DONE (irr) * Installing *source* package 'kernlab' ... ** libs gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dbreakpt.c -o dbreakpt.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dcauchy.c -o dcauchy.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dgpnrm.c -o dgpnrm.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dgpstep.c -o dgpstep.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dprecond.c -o dprecond.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dprsrch.c -o dprsrch.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dspcg.c -o dspcg.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dtron.c -o dtron.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dtrpcg.c -o dtrpcg.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dtrqsol.c -o dtrqsol.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c misc.c -o misc.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c solvebqp.c -o solvebqp.o g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c svm.cpp -o svm.o g++ -shared -L/usr/local/lib -o kernlab.so dbreakpt.o dcauchy.o dgpnrm.o dgpstep.o dprecond.o dprsrch.o dspcg.o dtron.o dtrpcg.o dtrqsol.o misc.o solvebqp.o svm.o -lblas -lgfortran -lm -lgcc_s -L/usr/lib/R/lib -lRlapack -L/usr/lib/R/lib -lR ** R ** data ** inst ** save image Creating a new generic function for 'predict' in 'kernlab' Creating a new generic function for 'plot' in 'kernlab' ** help >>> Building/Updating help pages for package 'kernlab' Formats: text html latex example chol.reduce text html latex example couple text html latex example dots text html latex example gausspr-class text html latex example gausspr text html latex example inc.chol-class text html latex example income text html latex inlearn text html latex example ipop-class text html latex example ipop text html latex example kcca-class text html latex example kcca text html latex example kernel-class text html latex example kernelMatrix text html latex example kfa-class text html latex example kfa text html latex example kha-class text html latex example kha text html latex example kkmeans text html latex example kpca-class text html latex example kpca text html latex example ksvm-class text html latex example ksvm text html latex example musk text html latex example onlearn-class text html latex example onlearn text html latex example plot text html latex example predict.ksvm text html latex example promotergene text html latex example ranking-class text html latex example ranking text html latex example rvm-class text html latex example rvm text html latex example sigest text html latex example spam text html latex specc-class text html latex example specc text html latex example spirals text html latex example ticdata text html latex ** building package indices ... * DONE (kernlab) * Installing *source* package 'lattice' ... ** libs gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c threeDplot.c -o threeDplot.o gcc -shared -L/usr/local/lib -o lattice.so threeDplot.o -L/usr/lib/R/lib -lR ** R ** data ** moving datasets to lazyload DB ** demo ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'lattice' Formats: text html latex example Lattice text html latex Rows text html latex banking text html latex barchart.table text html latex example barley text html latex example cloud text html latex example draw.colorkey text html latex draw.key text html latex environmental text html latex example ethanol text html latex example histogram text html latex example interaction text html latex example lattice.options text html latex example latticeParseFormula text html latex levelplot text html latex example llines text html latex lset text html latex example make.groups text html latex example melanoma text html latex example oneway text html latex panel.axis text html latex panel.barchart text html latex panel.bwplot text html latex panel.cloud text html latex panel.densityplot text html latex panel.dotplot text html latex panel.functions text html latex panel.histogram text html latex panel.levelplot text html latex panel.pairs text html latex panel.parallel text html latex panel.qqmath text html latex panel.qqmathline text html latex panel.stripplot text html latex panel.superpose text html latex panel.violin text html latex example panel.xyplot text html latex prepanel.functions text html latex print.trellis text html latex example qq text html latex example qqmath text html latex example rfs text html latex example shingles text html latex example simpleKey text html latex singer text html latex example splom text html latex example strip.default text html latex example tmd text html latex example trellis.device text html latex trellis.object text html latex trellis.par.get text html latex example update.trellis text html latex example utilities.3d text html latex xyplot text html latex example ** building package indices ... * DONE (lattice) * Installing *source* package 'limma' ... ** R ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'limma' Formats: text html latex example 01Introduction text html latex 02classes text html latex 03reading text html latex 04Background text html latex 05Normalization text html latex 06linearmodels text html latex 07SingleChannel text html latex 08Tests text html latex 09Diagnostics text html latex 10Other text html latex LargeDataObject text html latex example PrintLayout text html latex example TestResults text html latex example anova-method text html latex arrayWeights text html latex example arrayWeightsQuick text html latex example asdataframe text html latex asmalist text html latex asmatrix text html latex auROC text html latex example backgroundcorrect text html latex example blockDiag text html latex example bwss text html latex bwss.matrix text html latex cbind text html latex example changelog text html latex channel2M text html latex example classifytests text html latex example contrasts.fit text html latex example controlStatus text html latex example convest text html latex example decideTests text html latex dim text html latex example dimnames text html latex dupcor text html latex example ebayes text html latex example exprset2 text html latex fitfdist text html latex geneSetTest text html latex example getSpacing text html latex example getlayout text html latex example gls.series text html latex example gridspotrc text html latex heatdiagram text html latex example helpMethods text html latex example imageplot text html latex example imageplot3by2 text html latex intraspotCorrelation text html latex example isfullrank text html latex example isnumeric text html latex example kooperberg text html latex example limmaUsersGuide text html latex example lm.series text html latex example lmFit text html latex lmscFit text html latex example loessfit text html latex example m.spot text html latex ma3x3 text html latex example makeContrasts text html latex example makeunique text html latex example malist text html latex marraylm text html latex matvec text html latex example mdplot text html latex merge text html latex example modelMatrix text html latex example modifyWeights text html latex example mrlm text html latex example normalizeRobustSpline text html latex example normalizeWithinArrays text html latex example normalizebetweenarrays text html latex example normalizeprintorder text html latex example normalizequantiles text html latex normalizescale text html latex example normexp text html latex normexpfit text html latex example normexpsignal text html latex plotDensities text html latex example plotma text html latex example plotma3by2 text html latex plotprinttiploess text html latex poolvar text html latex example printHead text html latex printorder text html latex example protectMetachar text html latex example qqt text html latex example qualwt text html latex example read.maimages text html latex example read.matrix text html latex read.series text html latex readGPRHeader text html latex readImaGeneHeader text html latex readSpotTypes text html latex readTargets text html latex readgal text html latex example removeext text html latex example rg.genepix text html latex rg.quantarray text html latex rg.series.spot text html latex rg.spot text html latex rglist text html latex splitName text html latex example squeezeVar text html latex example subsetting text html latex example summary text html latex targetsA2C text html latex example tmixture text html latex toptable text html latex example trigammainverse text html latex example trimWhiteSpace text html latex example uniquegenelist text html latex example unwrapdups text html latex example venn text html latex example volcanoplot text html latex weightedmedian text html latex writefit text html latex zscore text html latex example ** building package indices ... * DONE (limma) * Installing *source* package 'locfdr' ... ** R ** data ** inst ** help >>> Building/Updating help pages for package 'locfdr' Formats: text html latex example hivdata text html latex lfdrsim text html latex locfdr text html latex example ** building package indices ... * DONE (locfdr) * Installing *source* package 'MatchIt' ... ** R ** data ** demo ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'MatchIt' Formats: text html latex example diagnose text html latex distance text html latex exactmatch text html latex help.matchit text html latex incomedata text html latex lalonde text html latex match.data text html latex matchdef text html latex matchit text html latex neyman text html latex plot.matchit text html latex print.matchit text html latex subclassify text html latex summary.matchit text html latex summary.neyman text html latex ** building package indices ... * DONE (MatchIt) * Installing *source* package 'mgcv' ... ** libs gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c gcv.c -o gcv.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c magic.c -o magic.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mat.c -o mat.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c matrix.c -o matrix.o matrix.c: In function 'dumpmat': matrix.c:246: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result matrix.c: In function 'readmat': matrix.c:257: warning: ignoring return value of 'fread', declared with attribute warn_unused_result matrix.c:258: warning: ignoring return value of 'fread', declared with attribute warn_unused_result matrix.c:261: warning: ignoring return value of 'fread', declared with attribute warn_unused_result matrix.c: In function 'gettextmatrix': matrix.c:1972: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mgcv.c -o mgcv.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c qp.c -o qp.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c tprs.c -o tprs.o gcc -shared -L/usr/local/lib -o mgcv.so gcv.o magic.o mat.o matrix.o mgcv.o qp.o tprs.o -L/usr/lib/R/lib -lRlapack -lblas -lgfortran -lm -lgcc_s -L/usr/lib/R/lib -lR ** R ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'mgcv' Formats: text html latex example Predict.matrix text html latex example anova.gam text html latex example exclude.too.far text html latex example extract.lme.cov text html latex example fix.family.link text html latex fixDependence text html latex example formXtViX text html latex formula.gam text html latex full.score text html latex gam text html latex example gam.check text html latex example gam.control text html latex gam.convergence text html latex gam.fit text html latex gam.fit2 text html latex gam.method text html latex gam.models text html latex example gam.neg.bin text html latex example gam.outer text html latex gam.selection text html latex example gam.setup text html latex gam.side text html latex example gam2objective text html latex gamObject text html latex gamm text html latex example gamm.setup text html latex get.var text html latex example influence.gam text html latex initial.sp text html latex interpret.gam text html latex logLik.gam text html latex magic text html latex example magic.post.proc text html latex mgcv text html latex example mgcv.control text html latex mono.con text html latex example mroot text html latex new.name text html latex example notExp text html latex example notExp2 text html latex example null.space.dimension text html latex example pcls text html latex example pdIdnot text html latex example pdTens text html latex example place.knots text html latex example plot.gam text html latex example predict.gam text html latex example print.gam text html latex residuals.gam text html latex s text html latex example smooth.construct text html latex example smoothCon text html latex step.gam text html latex example summary.gam text html latex example te text html latex example tensor.prod.model.matrix text html latex example uniquecombs text html latex example vcov.gam text html latex example vis.gam text html latex example ** building package indices ... * DONE (mgcv) * Installing *source* package 'NADA' ... ** R ** data ** help >>> Building/Updating help pages for package 'NADA' Formats: text html latex example Ag text html latex Arsenic text html latex AsExample text html latex Atra text html latex AtraAlt text html latex Atrazine text html latex Bloodlead text html latex Cadmium text html latex Cen text html latex example ChlfmCA text html latex CuZn text html latex CuZnAlt text html latex DFe text html latex DOC text html latex Golden text html latex Hatchery text html latex HgFish text html latex MDCu text html latex NADA-internal text html latex NADA.As text html latex Oahu text html latex Recon text html latex Roach text html latex SedPb text html latex Silver text html latex TCE text html latex TCEReg text html latex Tbl1one text html latex Thames text html latex cendiff-methods text html latex cendiff text html latex example cenfit-class text html latex example cenfit-methods text html latex example cenfit text html latex example flip-methods text html latex hc.ppoints text html latex example lines-methods text html latex mean-methods text html latex median-methods text html latex pct.censored text html latex example plot-methods text html latex predict-methods text html latex print-methods text html latex quantile-methods text html latex example ros-class text html latex example ros-methods text html latex ros text html latex example sd-methods text html latex splitQual text html latex example summary-methods text html latex ** building package indices ... * DONE (NADA) * Installing *source* package 'outliers' ... ** R ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'outliers' Formats: text html latex example chisq.out.test text html latex example cochran.test text html latex example dixon.test text html latex example grubbs.test text html latex example outlier text html latex example qcochran text html latex example qdixon text html latex qgrubbs text html latex qtable text html latex rm.outlier text html latex example scores text html latex example ** building package indices ... * DONE (outliers) * Installing *source* package 'prabclus' ... ** R ** data ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'prabclus' Formats: text html latex example NNclean text html latex example autoconst text html latex example cluspop.nb text html latex example comp.test text html latex example concomp text html latex example conregmat text html latex example distratio text html latex example geco text html latex example geo2neighbor text html latex example homogen.test text html latex example hprabclust text html latex example incmatrix text html latex example jaccard text html latex example kulczynski text html latex example kykladspecreg text html latex example lcomponent text html latex example nb text html latex example nbtest text html latex example nn text html latex example piecewiselin text html latex example pop.sim text html latex example prabclust text html latex example prabinit text html latex example prabtest text html latex example qkulczynski text html latex example randpop.nb text html latex example summary.prabtest text html latex example waterdist text html latex example ** building package indices ... * DONE (prabclus) * Installing *source* package 'R2WinBUGS' ... ** R ** data ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'R2WinBUGS' Formats: text html latex example attach.all text html latex example bugs text html latex example bugs.data text html latex bugs.inits text html latex bugs.plot text html latex bugs.run text html latex bugs.script text html latex bugs.sims text html latex bugs.update.settings text html latex decode.parameter.name text html latex monitor text html latex plot.bugs text html latex print.bugs text html latex read.bugs text html latex schools text html latex write.datafile text html latex ** building package indices ... * DONE (R2WinBUGS) * Installing *source* package 'RandomFields' ... ** libs g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c addownfctns.cc -o addownfctns.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c auxiliary.cc -o auxiliary.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c avltr.cc -o avltr.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c D.H.cc -o D.H.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c extremes.cc -o extremes.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c Hyperfcts.cc -o Hyperfcts.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c modelling.cc -o modelling.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c MPP.cc -o MPP.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c MPPFcts.cc -o MPPFcts.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c RFcircembed.cc -o RFcircembed.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c RFCovFcts.cc -o RFCovFcts.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c RFdirect.cc -o RFdirect.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c RFempvario.cc -o RFempvario.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c RFgetNset.cc -o RFgetNset.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c RFhyperplan.cc -o RFhyperplan.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c RFinitNerror.cc -o RFinitNerror.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c RFnugget.cc -o RFnugget.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c RFother.cc -o RFother.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c RFsimu.cc -o RFsimu.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c RFspectral.cc -o RFspectral.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c RFtbm.cc -o RFtbm.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c win_linux_aux.cc -o win_linux_aux.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c Xempvario.cc -o Xempvario.o g++ -I/usr/lib/R/include -I/usr/local/include -g -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c xx.cc -o xx.o g++ -shared -L/usr/local/lib -o RandomFields.so addownfctns.o auxiliary.o avltr.o D.H.o extremes.o Hyperfcts.o modelling.o MPP.o MPPFcts.o RFcircembed.o RFCovFcts.o RFdirect.o RFempvario.o RFgetNset.o RFhyperplan.o RFinitNerror.o RFnugget.o RFother.o RFsimu.o RFspectral.o RFtbm.o win_linux_aux.o Xempvario.o xx.o -L/usr/lib/R/lib -lR ** R ** data ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'RandomFields' Formats: text html latex example CheckAndComplete text html latex example CondSimu text html latex example CovarianceFct text html latex example Dev text html latex example EmpiricalVariogram text html latex example GaussRF text html latex example GetPracticalRange text html latex example GetRegisterInfo text html latex example Kriging text html latex example Locator text html latex example MaxStableRF text html latex example RFMethods text html latex example RFparameters text html latex example RandomFields text html latex Readline text html latex example Registers text html latex example ShowModels text html latex example SimulateRF text html latex auxiliary.fcts text html latex example eval.parameters text html latex example fileexists text html latex fitvario text html latex example fractal text html latex getactions text html latex example hostname text html latex hurst text html latex parameter.range text html latex example parampositions text html latex example regression text html latex sleep text html latex soil text html latex example useraction text html latex example userinput text html latex ** building package indices ... * DONE (RandomFields) * Installing *source* package 'ref' ... ** R ** exec ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'ref' Formats: text html latex example HanoiTower text html latex example as.ref text html latex example deref text html latex example is.ref text html latex example optimal.index text html latex example ref text html latex example refdata text html latex example regression.test.refdata text html latex example sleep.wrapper text html latex ** building package indices ... * DONE (ref) * Installing *source* package 'SwissAir' ... ** data ** help >>> Building/Updating help pages for package 'SwissAir' Formats: text html latex example AirQual text html latex example ** building package indices ... * DONE (SwissAir) tar: Read 9728 bytes from - * Installing *source* package 'waveslim' ... ** libs gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c bell-p-w.f -o bell-p-w.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dwt2.c -o dwt2.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dwt3.c -o dwt3.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dwt.c -o dwt.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c hosking.c -o hosking.o gcc -shared -L/usr/local/lib -o waveslim.so bell-p-w.o dwt2.o dwt3.o dwt.o hosking.o -lgfortran -lm -lgcc_s -L/usr/lib/R/lib -lR ** R ** data ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'waveslim' Formats: text html latex example Andel text html latex Dualtree text html latex example Farras text html latex Selesnick text html latex Thresholding text html latex ar1 text html latex bandpass text html latex barbara text html latex basis text html latex example blocks text html latex brick.wall text html latex convolve2D text html latex cpi text html latex dau text html latex denoise.dwt.2d text html latex example doppler text html latex dpss.taper text html latex dualfilt1 text html latex dwpt.2d text html latex dwpt text html latex example dwpt.boot text html latex dwpt.sim text html latex example dwt.2d text html latex example dwt.3d text html latex dwt text html latex example exchange text html latex fb text html latex example fdp.mle text html latex example find.adaptive.basis text html latex heavisine text html latex hilbert text html latex hilbert.filter text html latex hosking.sim text html latex example hwt.analysis text html latex ibm text html latex japan text html latex jumpsine text html latex kobe text html latex linchirp text html latex mexm text html latex modwt.2d text html latex example modwt.3d text html latex modwt text html latex example mra.2d text html latex example mra.3d text html latex mra text html latex example mult.loc text html latex my.acf text html latex example nile text html latex ortho.basis text html latex example phase.shift text html latex phase.shift.hilbert text html latex plot.dwt.2d text html latex qmf text html latex example rotcumvar text html latex sdf text html latex example shift.2d text html latex example sine.taper text html latex spin.covariance text html latex example spp.mle text html latex spp.var text html latex squared.gain text html latex example stack.plot text html latex testing.hov text html latex tourism text html latex unemploy text html latex up.sample text html latex wave.filter text html latex wave.variance text html latex example wavelet.filter text html latex example wpt.test text html latex example xbox text html latex ** building package indices ... * DONE (waveslim) * Installing *source* package 'XML' ... checking for gcc... gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for xml2-config... /usr/bin/xml2-config Located parser file -I/usr/include/libxml2/parser.h Checking for 1.8: -I/usr/include/libxml2 Using libxml2.* checking for gzopen in -lz... yes checking for xmlParseFile in -lxml2... yes checking for xmlHashSize in -lxml2... yes Using built-in xmlHashSize Checking DTD parsing (presence of externalSubset)... checking for xmlHashSize in -lxml2... yes Found xmlHashSize checking for xmlDocDumpFormatMemoryEnc in -lxml2... yes checking libxml/xmlversion.h usability... yes checking libxml/xmlversion.h presence... yes checking for libxml/xmlversion.h... yes Expat: FALSE Checking for return type of xmlHashScan element routine. No return value for xmlHashScan **************************************** Configuration information: Libxml settings libxml include directory: -I/usr/include/libxml2 libxml library directory: -L/usr/lib -lxml2 -lz -lpthread -lm -lz -lxml2 libxml 2: -DLIBXML2=1 Compilation flags: -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 Link flags: -L/usr/lib -lxml2 -lz -lpthread -lm -lz -lxml2 **************************************** configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/supports.R config.status: creating inst/scripts/RSXML.csh config.status: creating inst/scripts/RSXML.bsh ** libs gcc -I/usr/lib/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c DocParse.c -o DocParse.o DocParse.c: In function 'RS_XML_ParseTree': DocParse.c:122: warning: pointer targets in passing argument 1 of 'htmlParseDoc' differ in signedness DocParse.c:124: warning: pointer targets in passing argument 1 of 'xmlStrdup' differ in signedness DocParse.c:124: warning: pointer targets in assignment differ in signedness DocParse.c: In function 'RS_XML_convertXMLDoc': DocParse.c:261: warning: pointer targets in assignment differ in signedness DocParse.c: In function 'processNamespaceDefinitions': DocParse.c:317: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness DocParse.c: In function 'RS_XML_createXMLNode': DocParse.c:348: warning: pointer targets in initialization differ in signedness DocParse.c:356: warning: pointer targets in passing argument 1 of 'trim' differ in signedness DocParse.c:392: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness DocParse.c:412: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness DocParse.c: In function 'convertNode': DocParse.c:453: warning: pointer targets in assignment differ in signedness DocParse.c: In function 'RS_XML_createNameSpaceIdentifier': DocParse.c:544: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness DocParse.c:547: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness DocParse.c:566: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness DocParse.c: In function 'RS_XML_createNodeChildren': DocParse.c:669: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness DocParse.c: In function 'RS_XML_AttributeList': DocParse.c:743: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness DocParse.c:754: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness DocParse.c: In function 'RS_XML_xmlNodeName': DocParse.c:881: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness DocParse.c: In function 'RS_XML_xmlNodeNamespace': DocParse.c:899: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness DocParse.c:900: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness gcc -I/usr/lib/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c EventParse.c -o EventParse.o gcc -I/usr/lib/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c ExpatParse.c -o ExpatParse.o gcc -I/usr/lib/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c HTMLParse.c -o HTMLParse.o HTMLParse.c: In function 'RS_XML_HtmlParseTree': HTMLParse.c:55: warning: pointer targets in passing argument 1 of 'htmlParseDoc' differ in signedness HTMLParse.c:57: warning: pointer targets in passing argument 1 of 'xmlStrdup' differ in signedness HTMLParse.c:57: warning: pointer targets in assignment differ in signedness gcc -I/usr/lib/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c RSDTD.c -o RSDTD.o RSDTD.c: In function 'RS_XML_getDTD': RSDTD.c:130: warning: pointer targets in passing argument 2 of 'xmlCreateIntSubset' differ in signedness RSDTD.c:139: warning: pointer targets in passing argument 2 of 'ctxt->sax->internalSubset' differ in signedness RSDTD.c:139: warning: pointer targets in passing argument 3 of 'ctxt->sax->internalSubset' differ in signedness RSDTD.c:139: warning: pointer targets in passing argument 4 of 'ctxt->sax->internalSubset' differ in signedness RSDTD.c:143: warning: pointer targets in passing argument 2 of 'ctxt->sax->externalSubset' differ in signedness RSDTD.c:143: warning: pointer targets in passing argument 3 of 'ctxt->sax->externalSubset' differ in signedness RSDTD.c:143: warning: pointer targets in passing argument 4 of 'ctxt->sax->externalSubset' differ in signedness RSDTD.c: In function 'RS_xmlElementTableConverter': RSDTD.c:313: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness RSDTD.c: In function 'RS_xmlEntityTableConverter': RSDTD.c:387: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness RSDTD.c: In function 'RS_XML_createDTDEntity': RSDTD.c:422: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness RSDTD.c:433: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness RSDTD.c:437: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness RSDTD.c: In function 'RS_XML_createDTDElement': RSDTD.c:479: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness RSDTD.c: In function 'RS_XML_createDTDElementContents': RSDTD.c:566: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness RSDTD.c: In function 'RS_XML_createDTDElementAttributes': RSDTD.c:666: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness RSDTD.c: In function 'RS_XML_createDTDAttribute': RSDTD.c:715: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness RSDTD.c:729: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness RSDTD.c: In function 'RS_XML_AttributeEnumerationList': RSDTD.c:767: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness gcc -I/usr/lib/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c RUtils.c -o RUtils.o gcc -I/usr/lib/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c Utils.c -o Utils.o gcc -I/usr/lib/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c XMLEventParse.c -o XMLEventParse.o XMLEventParse.c: In function 'RS_XML_libXMLEventParse': XMLEventParse.c:200: warning: pointer targets in passing argument 1 of 'xmlCreateDocParserCtxt' differ in signedness XMLEventParse.c: In function 'RS_XML_cdataBlockHandler': XMLEventParse.c:302: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness gcc -I/usr/lib/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c XMLTree.c -o XMLTree.o XMLTree.c: In function 'R_xmlNewComment': XMLTree.c:56: warning: pointer targets in passing argument 1 of 'xmlNewComment' differ in signedness XMLTree.c: In function 'R_newXMLTextNode': XMLTree.c:65: warning: pointer targets in passing argument 1 of 'xmlNewText' differ in signedness XMLTree.c: In function 'R_newXMLCDataNode': XMLTree.c:81: warning: pointer targets in passing argument 2 of 'xmlNewCDataBlock' differ in signedness XMLTree.c: In function 'R_newXMLPINode': XMLTree.c:96: warning: pointer targets in passing argument 1 of 'xmlNewPI' differ in signedness XMLTree.c:96: warning: pointer targets in passing argument 2 of 'xmlNewPI' differ in signedness XMLTree.c: In function 'R_newXMLNode': XMLTree.c:117: warning: pointer targets in passing argument 3 of 'xmlNewDocNode' differ in signedness XMLTree.c:124: warning: pointer targets in passing argument 2 of 'xmlSetProp' differ in signedness XMLTree.c:124: warning: pointer targets in passing argument 3 of 'xmlSetProp' differ in signedness XMLTree.c: In function 'R_newXMLDoc': XMLTree.c:186: warning: pointer targets in passing argument 1 of 'xmlNewDoc' differ in signedness XMLTree.c: In function 'R_newXMLDtd': XMLTree.c:202: warning: pointer targets in passing argument 2 of 'xmlNewDtd' differ in signedness XMLTree.c:202: warning: pointer targets in passing argument 3 of 'xmlNewDtd' differ in signedness XMLTree.c:202: warning: pointer targets in passing argument 4 of 'xmlNewDtd' differ in signedness XMLTree.c: In function 'R_xmlNewNs': XMLTree.c:228: warning: pointer targets in passing argument 2 of 'xmlNewNs' differ in signedness XMLTree.c:228: warning: pointer targets in passing argument 3 of 'xmlNewNs' differ in signedness XMLTree.c: In function 'R_saveXMLDOM': XMLTree.c:300: warning: pointer targets in passing argument 2 of 'xmlNewDtd' differ in signedness XMLTree.c:300: warning: pointer targets in passing argument 3 of 'xmlNewDtd' differ in signedness XMLTree.c:300: warning: pointer targets in passing argument 4 of 'xmlNewDtd' differ in signedness XMLTree.c:348: warning: pointer targets in passing argument 1 of 'Rf_mkChar' differ in signedness gcc -shared -L/usr/local/lib -o XML.so DocParse.o EventParse.o ExpatParse.o HTMLParse.o RSDTD.o RUtils.o Utils.o XMLEventParse.o XMLTree.o -L/usr/lib -lxml2 -lz -lpthread -lm -lz -lxml2 -L/usr/lib/R/lib -lR ** R ** inst ** save image ** help >>> Building/Updating help pages for package 'XML' Formats: text html latex example AssignXMLNode text html latex example Doctype-class text html latex example Doctype text html latex example SAXMethods text html latex example SAXState-class text html latex example XMLNode-class text html latex example append.XMLNode text html latex example asXMLNode text html latex example dtdElement text html latex example dtdElementValidEntry text html latex example dtdIsAttribute text html latex example dtdValidElement text html latex example genericSAXHandlers text html latex example length.XMLNode text html latex example libxmlVersion text html latex example names.XMLNode text html latex example newXMLDoc text html latex example parseDTD text html latex example print text html latex example saveXML text html latex example supportsExpat text html latex example toString text html latex example xmlApply text html latex example xmlAttributeType text html latex example xmlAttrs text html latex example xmlChildren text html latex example xmlContainsEntity text html latex example xmlDOMApply text html latex example xmlElementsByTagName text html latex example xmlEventHandler text html latex example xmlEventParse text html latex example xmlGetAttr text html latex example xmlHandler text html latex example xmlName text html latex example xmlNamespace text html latex example xmlNode text html latex example xmlOutput text html latex example xmlParent text html latex example xmlRoot text html latex example xmlSize text html latex example xmlSubset text html latex example xmlTree text html latex example xmlTreeParse text html latex example xmlValue text html latex example ** building package indices ... * DONE (XML) * Installing *source* package 'Zelig' ... ** R ** data ** demo ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'Zelig' Formats: text html latex example MatchIt.url text html latex Zelig text html latex Zelig.url text html latex coalition text html latex dims text html latex example gsource text html latex example help.zelig text html latex hoff text html latex house text html latex immigration text html latex macro text html latex match.data text html latex mexico text html latex mid text html latex plot.ci text html latex plot.zelig text html latex repl text html latex rocplot text html latex example sanction text html latex setx text html latex sim text html latex summary.zelig text html latex ternarypoints text html latex turnout text html latex user.prompt text html latex example ** building package indices ... * DONE (Zelig) * Installing *source* package 'BradleyTerry' ... ** R ** data ** inst ** help >>> Building/Updating help pages for package 'BradleyTerry' Formats: text html latex example BTabilities text html latex example BTm text html latex example BTresiduals text html latex example baseball text html latex example citations text html latex example ** building package indices ... * DONE (BradleyTerry) * Installing *source* package 'cyclones' ... ** R ** data ** preparing package for lazy loading Error in library(ncdf) : there is no package called 'ncdf' Execution halted ERROR: lazy loading failed for package 'cyclones' ** Removing '/usr/lib/R/library/cyclones' ** Restoring previous '/usr/lib/R/library/cyclones' * Installing *source* package 'MarkedPointProcess' ... ** libs g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c auxiliary.cc -o auxiliary.o g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c MPPanalyse.cc -o MPPanalyse.o g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c MPPbasics.cc -o MPPbasics.o g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c MPPsimu.cc -o MPPsimu.o g++ -shared -L/usr/local/lib -o MarkedPointProcess.so auxiliary.o MPPanalyse.o MPPbasics.o MPPsimu.o -L/usr/lib/R/lib -lR ** R ** data ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'MarkedPointProcess' Formats: text html latex example BITOEK text html latex example MarkedPointProcess text html latex get.mpp.names text html latex mpp.characteristics text html latex example rfm.test text html latex example simulate.mpp text html latex example splitmodel text html latex example srd text html latex example ** building package indices ... * DONE (MarkedPointProcess) * Installing *source* package 'Matrix' ... ** libs gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c HBMM.c -o HBMM.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c Metis_utils.c -o Metis_utils.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c R_ldl.c -o R_ldl.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dgBCMatrix.c -o dgBCMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c init.c -o init.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c lmer.c -o lmer.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c Mutils.c -o Mutils.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dense.c -o dense.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dCholCMatrix.c -o dCholCMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dgCMatrix.c -o dgCMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dgTMatrix.c -o dgTMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dgeMatrix.c -o dgeMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dpoMatrix.c -o dpoMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dppMatrix.c -o dppMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dsCMatrix.c -o dsCMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dsTMatrix.c -o dsTMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dsyMatrix.c -o dsyMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dspMatrix.c -o dspMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dtCMatrix.c -o dtCMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dtTMatrix.c -o dtTMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dtrMatrix.c -o dtrMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c dtpMatrix.c -o dtpMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c factorizations.c -o factorizations.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c iohb.c -o iohb.o iohb.c: In function 'readHB_header': iohb.c:336: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:339: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result iohb.c:344: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:354: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:366: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:375: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result iohb.c:384: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c: In function 'readHB_mat_double': iohb.c:456: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:479: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:507: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c: In function 'readHB_aux_double': iohb.c:657: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:668: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:675: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:695: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:723: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c: In function 'readHB_mat_char': iohb.c:1008: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:1031: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:1059: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c: In function 'readHB_aux_char': iohb.c:1221: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:1232: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:1242: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:1260: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result iohb.c:1291: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c lCholCMatrix.c -o lCholCMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c lgCMatrix.c -o lgCMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c lgTMatrix.c -o lgTMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c lsCMatrix.c -o lsCMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c ltCMatrix.c -o ltCMatrix.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mmio.c -o mmio.o gcc -I/usr/lib/R/include -I/usr/local/include -I./Metis -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c triplet_to_col.c -o triplet_to_col.o touch Metis.stamp make[1]: Entering directory `/tmp/R.INSTALL.Y11317/Matrix/src/Metis' gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c coarsen.c -o coarsen.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c fm.c -o fm.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c initpart.c -o initpart.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c match.c -o match.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c ccgraph.c -o ccgraph.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c memory.c -o memory.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c pmetis.c -o pmetis.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c pqueue.c -o pqueue.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c refine.c -o refine.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c util.c -o util.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c timing.c -o timing.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c debug.c -o debug.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c bucketsort.c -o bucketsort.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c graph.c -o graph.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c stat.c -o stat.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c kmetis.c -o kmetis.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c kwayrefine.c -o kwayrefine.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c kwayfm.c -o kwayfm.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c balance.c -o balance.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c ometis.c -o ometis.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c srefine.c -o srefine.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c sfm.c -o sfm.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c separator.c -o separator.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mincover.c -o mincover.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mmd.c -o mmd.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mesh.c -o mesh.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c meshpart.c -o meshpart.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c frename.c -o frename.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c fortran.c -o fortran.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c myqsort.c -o myqsort.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c compress.c -o compress.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c parmetis.c -o parmetis.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c estmem.c -o estmem.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mpmetis.c -o mpmetis.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mcoarsen.c -o mcoarsen.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mmatch.c -o mmatch.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c minitpart.c -o minitpart.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mbalance.c -o mbalance.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mrefine.c -o mrefine.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mutil.c -o mutil.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mfm.c -o mfm.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mkmetis.c -o mkmetis.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mkwayrefine.c -o mkwayrefine.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mkwayfmh.c -o mkwayfmh.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mrefine2.c -o mrefine2.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c minitpart2.c -o minitpart2.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mbalance2.c -o mbalance2.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mfm2.c -o mfm2.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c kvmetis.c -o kvmetis.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c kwayvolrefine.c -o kwayvolrefine.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c kwayvolfm.c -o kwayvolfm.o gcc -I/usr/lib/R/include -I/usr/local/include -I. -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c subdomains.c -o subdomains.o ar -rucs ../Metis.a coarsen.o fm.o initpart.o match.o ccgraph.o memory.o pmetis.o pqueue.o refine.o util.o timing.o debug.o bucketsort.o graph.o stat.o kmetis.o kwayrefine.o kwayfm.o balance.o ometis.o srefine.o sfm.o separator.o mincover.o mmd.o mesh.o meshpart.o frename.o fortran.o myqsort.o compress.o parmetis.o estmem.o mpmetis.o mcoarsen.o mmatch.o minitpart.o mbalance.o mrefine.o mutil.o mfm.o mkmetis.o mkwayrefine.o mkwayfmh.o mrefine2.o minitpart2.o mbalance2.o mfm2.o kvmetis.o kwayvolrefine.o kwayvolfm.o subdomains.o make[1]: Leaving directory `/tmp/R.INSTALL.Y11317/Matrix/src/Metis' gcc -shared -L/usr/local/lib -o Matrix.so HBMM.o Metis_utils.o R_ldl.o dgBCMatrix.o init.o lmer.o Mutils.o dense.o dCholCMatrix.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsTMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o iohb.o lCholCMatrix.o lgCMatrix.o lgTMatrix.o lsCMatrix.o ltCMatrix.o mmio.o triplet_to_col.o Metis.a -L/usr/lib/R/lib -lRlapack -lblas -L/usr/lib/R/lib -lR ** R ** data ** moving datasets to lazyload DB ** inst ** preparing package for lazy loading Creating a new generic function for 'as.matrix' in 'Matrix' Creating a new generic function for 'unname' in 'Matrix' Creating a new generic function for 'crossprod' in 'Matrix' Creating a new generic function for 'solve' in 'Matrix' Creating a new generic function for 't' in 'Matrix' Creating a new generic function for 'diag' in 'Matrix' Creating a new generic function for 'determinant' in 'Matrix' Creating a new generic function for 'image' in 'Matrix' Creating a new generic function for 'kronecker' in 'Matrix' Creating a new generic function for 'colSums' in 'Matrix' Creating a new generic function for 'colMeans' in 'Matrix' Creating a new generic function for 'rowSums' in 'Matrix' Creating a new generic function for 'rowMeans' in 'Matrix' Creating a new generic function for 'chol' in 'Matrix' Creating a new generic function for 'summary' in 'Matrix' Creating a new generic function for 'logLik' in 'Matrix' Creating a new generic function for 'anova' in 'Matrix' Creating a new generic function for 'update' in 'Matrix' Creating a new generic function for 'confint' in 'Matrix' Creating a new generic function for 'deviance' in 'Matrix' Creating a new generic function for 'formula' in 'Matrix' Creating a new generic function for 'vcov' in 'Matrix' Creating a new generic function for 'fitted' in 'Matrix' Creating a new generic function for 'residuals' in 'Matrix' Creating a new generic function for 'resid' in 'Matrix' Creating a new generic function for 'coef' in 'Matrix' Creating a new generic function for 'plot' in 'Matrix' Creating a new generic function for 'with' in 'Matrix' Creating a new generic function for 'terms' in 'Matrix' ** help >>> Building/Updating help pages for package 'Matrix' Formats: text html latex example BIC text html latex Cholesky-class text html latex example Hilbert text html latex example LU-class text html latex example Matrix-class text html latex Matrix text html latex example Schur text html latex example VarCorr-class text html latex VarCorr text html latex example Xtrct-methods text html latex example bCrosstab text html latex example corrmatrix-class text html latex example dCholCMatrix-class text html latex example dMatrix-class text html latex ddenseMatrix-class text html latex example dgBCMatrix-class text html latex dgCMatrix-class text html latex example dgRMatrix-class text html latex dgTMatrix-class text html latex example dgeMatrix-class text html latex dpoMatrix-class text html latex example dsCMatrix-class text html latex dsparseMatrix-class text html latex example dsyMatrix-class text html latex example dtCMatrix-class text html latex dtpMatrix-class text html latex example dtrMatrix-class text html latex example expand text html latex example expm text html latex example externalFormats text html latex example facmul text html latex example fixef text html latex example lmer-class text html latex lmer text html latex example lsparseMatrix-classes text html latex lu text html latex example mcmcsamp text html latex example mm text html latex example norm text html latex example pMatrix-class text html latex example pdmatrix-class text html latex ranef text html latex example rcond text html latex example sleepstudy text html latex example sparseMatrix-class text html latex example tcrossprod text html latex example unpack text html latex example writeHB text html latex example y text html latex example ** building package indices ... * DONE (Matrix) * Installing *source* package 'RGraphics' ... ** R ** data ** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'RGraphics' Formats: text html latex example faceA text html latex figures text html latex grid.imageFun text html latex grid.imageGrob text html latex grid.ozFun text html latex imageGrob text html latex ocean text html latex ozGrob text html latex ozImage text html latex ozKey text html latex ozTemp text html latex plot.newclass text html latex ribbonLegend text html latex roundRect text html latex splitString text html latex splitTextGrob text html latex volcanoRoads text html latex ** building package indices ... * DONE (RGraphics) * Installing *source* package 'SoPhy' ... ** libs gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c analytic.f -o analytic.o g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c auxiliary.cc -o auxiliary.o g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c horizon.cc -o horizon.o gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c INPUT2.f -o INPUT2.o In file INPUT2.f:382 if(n-k) 12,15,13 1 Warning: Obsolete: arithmetic IF statement at (1) In file INPUT2.f:448 IF (Num-e) 11,14,12 1 Warning: Obsolete: arithmetic IF statement at (1) gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c MATERIAL2.f -o MATERIAL2.o gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c ORTHOFEM.f -o ORTHOFEM.o gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c OUTPUT2.f -o OUTPUT2.o gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c PCK.f -o PCK.o g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c read.tiff2rgb.cc -o read.tiff2rgb.o gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c SINK2.f -o SINK2.o gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c SOLUTE2.f -o SOLUTE2.o gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c SWMS_2D.f -o SWMS_2D.o gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c TIME2.f -o TIME2.o gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c WATFLOW2.f -o WATFLOW2.o g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c win_linux_aux.cc -o win_linux_aux.o g++ -shared -L/usr/local/lib -o SoPhy.so analytic.o auxiliary.o horizon.o INPUT2.o MATERIAL2.o ORTHOFEM.o OUTPUT2.o PCK.o read.tiff2rgb.o SINK2.o SOLUTE2.o SWMS_2D.o TIME2.o WATFLOW2.o win_linux_aux.o -lgfortran -lm -lgcc_s -ltiff -lgfortran -lm -lgcc_s -L/usr/lib/R/lib -lR ** R ** data ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'SoPhy' Formats: text html latex example CDE text html latex example SoPhy text html latex analyse.profile text html latex example calculate.horizons text html latex example create.roots text html latex example create.stones text html latex example create.waterflow text html latex example draw.horizons text html latex example flowpattern text html latex example modify.horizons text html latex example my.legend text html latex example pareto text html latex plotFlow text html latex example plotRF text html latex example plotRGB text html latex example plotWater text html latex example quader text html latex example read.picture text html latex example read.swms2d.table text html latex example risk.index text html latex example sh text html latex example simulate.horizons text html latex example swms2d text html latex example tracers text html latex example write.picture text html latex xswms2d text html latex example ** building package indices ... * DONE (SoPhy) The downloaded packages are in /tmp/Rtmpv32038/downloaded_packages Warning message: installation of package 'cyclones' had non-zero exit status in: install.packages(update[, "Package"], instlib, contriburl = contriburl, > x <- packageStatus(repositories="http://cran.r-project.org/src/contrib") > st <- x$avai["Status"] > install.packages(rownames(st)[which(st$Status=="not installed")], dependencies=T) dependency 'RDCOMClient' is not available trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/BRugs_0.2-3.tar.gz' Content type 'application/x-gzip' length 7916520 bytes opened URL ================================================== downloaded 7730Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/DEoptim_1.0-6.tar.gz' Content type 'application/x-gzip' length 11646 bytes opened URL ================================================== downloaded 11Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/gap_1.0-3.tar.gz' Content type 'application/x-gzip' length 477551 bytes opened URL ================================================== downloaded 466Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/gnomeGUI_2.1.0-1.tar.gz' Content type 'application/x-gzip' length 76192 bytes opened URL ================================================== downloaded 74Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/grouped_0.1-0.tar.gz' Content type 'application/x-gzip' length 20651 bytes opened URL ================================================== downloaded 20Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/hapsim_0.1.tar.gz' Content type 'application/x-gzip' length 8122 bytes opened URL ================================================== downloaded 8122 bytes trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/iid.test_0.5.tar.gz' Content type 'application/x-gzip' length 64067 bytes opened URL ================================================== downloaded 62Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/mblm_0.1.tar.gz' Content type 'application/x-gzip' length 4425 bytes opened URL ================================================== downloaded 4425 bytes trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/mimR_1.2.6.tar.gz' Content type 'application/x-gzip' length 342654 bytes opened URL ================================================== downloaded 334Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/moments_0.1.tar.gz' Content type 'application/x-gzip' length 3649 bytes opened URL ================================================== downloaded 3649 bytes trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/ncdf_1.4.tar.gz' Content type 'application/x-gzip' length 67182 bytes opened URL ================================================== downloaded 65Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/powerpkg_1.2.tar.gz' Content type 'application/x-gzip' length 6319 bytes opened URL ================================================== downloaded 6319 bytes trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/rcdd_0.6-3.tar.gz' Content type 'application/x-gzip' length 237879 bytes opened URL ================================================== downloaded 232Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/reshape_0.4.tar.gz' Content type 'application/x-gzip' length 11154 bytes opened URL ================================================== downloaded 10Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/rgdal_0.2-7.tar.gz' Content type 'application/x-gzip' length 41601 bytes opened URL ================================================== downloaded 40Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/Rmpi_0.4-9.tar.gz' Content type 'application/x-gzip' length 62799 bytes opened URL ================================================== downloaded 61Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/RMySQL_0.5-5.tar.gz' Content type 'application/x-gzip' length 280328 bytes opened URL ================================================== downloaded 273Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/RNetCDF_1.1-3.tar.gz' Content type 'application/x-gzip' length 50504 bytes opened URL ================================================== downloaded 49Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/RODBC_1.1-4.tar.gz' Content type 'application/x-gzip' length 69049 bytes opened URL ================================================== downloaded 67Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/ROracle_0.5-5.tar.gz' Content type 'application/x-gzip' length 141483 bytes opened URL ================================================== downloaded 138Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/RQuantLib_0.1.13.tar.gz' Content type 'application/x-gzip' length 39727 bytes opened URL ================================================== downloaded 38Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/RScaLAPACK_0.4.0.tar.gz' Content type 'application/x-gzip' length 751567 bytes opened URL ================================================== downloaded 733Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/rsprng_0.3-1.tar.gz' Content type 'application/x-gzip' length 35033 bytes opened URL ================================================== downloaded 34Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/RWinEdt_1.7-3.tar.gz' Content type 'application/x-gzip' length 325188 bytes opened URL ================================================== downloaded 317Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/simex_1.0.tar.gz' Content type 'application/x-gzip' length 16963 bytes opened URL ================================================== downloaded 16Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/taskPR_0.2.7.tar.gz' Content type 'application/x-gzip' length 61834 bytes opened URL ================================================== downloaded 60Kb * Installing *source* package 'BRugs' ... Package 'BRugs' currently only works under Windows.\nIt is supposed to work under Linux in future releases. ERROR: configuration failed for package 'BRugs' * Installing *source* package 'DEoptim' ... ** R ** help >>> Building/Updating help pages for package 'DEoptim' Formats: text html latex example DEoptim text html latex example ** building package indices ... * DONE (DEoptim) tar: Read 3072 bytes from - * Installing *source* package 'gap' ... ** libs gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c 2k.c -o 2k.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c 2ld.c -o 2ld.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c cline.c -o cline.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c gc.c -o gc.o gc.c: In function 'xehm': gc.c:1498: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result gc.c:1507: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result gc.c:1537: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result gc.c:1548: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c gcontrol.c -o gcontrol.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c gif.c -o gif.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c hap.c -o hap.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c hwe.hardy.c -o hwe.hardy.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c kin.morgan.c -o kin.morgan.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c makeped.c -o makeped.o makeped.c: In function 'read_pedigree': makeped.c:165: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result makeped.c: In function 'read_person': makeped.c:179: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result makeped.c: In function 'getind': makeped.c:264: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result makeped.c: In function 'getindpa': makeped.c:344: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result makeped.c: In function 'readped': makeped.c:467: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result makeped.c:489: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result makeped.c:500: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result makeped.c: In function 'save_loops': makeped.c:615: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result makeped.c:621: warning: ignoring return value of 'gets', declared with attribute warn_unused_result makeped.c: In function 'file_loops': makeped.c:821: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result makeped.c:822: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result makeped.c: In function 'save_probands': makeped.c:1058: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result makeped.c:1064: warning: ignoring return value of 'gets', declared with attribute warn_unused_result makeped.c: In function 'file_probands': makeped.c:1190: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result makeped.c:1191: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result makeped.c: In function 'get_probands': makeped.c:1422: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c mia.c -o mia.o mia.c: In function 'mia': mia.c:56: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result mia.c:98: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result mia.c:110: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result mia.c:119: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result mia.c:199: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result mia.c:201: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result mia.c:244: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result mia.c:247: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result mia.c:261: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result mia.c:265: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c muvar.c -o muvar.o gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c pfc.f -o pfc.o gfortran -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c pfc.sim.f -o pfc.sim.o gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c pgc.c -o pgc.o pgc.c: In function 'getloci': pgc.c:194: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result pgc.c:195: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result pgc.c:201: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result pgc.c:204: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result pgc.c:205: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result pgc.c:206: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result pgc.c:209: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result pgc.c: In function 'getdat': pgc.c:302: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result pgc.c:307: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result pgc.c: In function 'getlocim': pgc.c:434: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result pgc.c:435: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result pgc.c:441: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result pgc.c:444: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result pgc.c:445: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result pgc.c:446: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result pgc.c:449: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result pgc.c: In function 'getdatm': pgc.c:539: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result pgc.c:546: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result pgc.c: In function 'noid': pgc.c:777: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result pgc.c:784: warning: ignoring return value of 'sscanf', declared with attribute warn_unused_result gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c whscore.c -o whscore.o gcc -shared -L/usr/local/lib -o gap.so 2k.o 2ld.o cline.o gc.o gcontrol.o gif.o hap.o hwe.hardy.o kin.morgan.o makeped.o mia.o muvar.o pfc.o pfc.sim.o pgc.o whscore.o -lgfortran -lm -lgcc_s -L/usr/lib/R/lib -lR ** R ** data ** moving datasets to lazyload DB ** demo ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'gap' Formats: text html latex example aldh2 text html latex apoeapoc text html latex bt text html latex example cf text html latex chow.test text html latex example crohn text html latex fa text html latex fbsize text html latex example fsnps text html latex gap-internal text html latex gc.em text html latex example gcontrol text html latex example gcp text html latex example genecounting text html latex example gif text html latex example hap text html latex example hap.em text html latex example hap.score text html latex example hla text html latex htr text html latex example hwe text html latex example hwe.hardy text html latex example kbyl text html latex example kin.morgan text html latex example makeped text html latex example mao text html latex mia text html latex example mtdt text html latex example muvar text html latex example nep499 text html latex pbsize text html latex example pedtodot text html latex example pfc text html latex example pfc.sim text html latex example pgc text html latex example plot.hap.score text html latex example print.hap.score text html latex example s2k text html latex example snca text html latex tbyt text html latex example whscore text html latex example ** building package indices ... * DONE (gap) * Installing *source* package 'pathmix' ... ** libs gfortran -xf77-cpp-input -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c almini.f -o almini.o gfortran -xf77-cpp-input -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c almize.f -o almize.o gfortran -xf77-cpp-input -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c almtest.f -o almtest.o gfortran -xf77-cpp-input -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c cpyfil.f -o cpyfil.o gfortran -xf77-cpp-input -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c defalt3a.f -o defalt3a.o gfortran -xf77-cpp-input -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c defalt3b.f -o defalt3b.o gfortran -xf77-cpp-input -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c eval.f -o eval.o gfortran -xf77-cpp-input -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c files.f -o files.o gfortran -xf77-cpp-input -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c fmcard.f -o fmcard.o gfortran -xf77-cpp-input -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c fun3a.f -o fun3a.o gfortran -xf77-cpp-input -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c fun3b.f -o fun3b.o In file fun3b.f:33 + sigma /(mxfmsz*mxfmsz)*0./, nold /ngroup*-99/ 1 Error: Syntax error in DATA statement at (1) make: *** [fun3b.o] Error 1 ERROR: compilation failed for package 'pathmix' ** Removing '/usr/lib/R/library/gap' ** Removing '/usr/lib/R/library/pathmix' ** Removing '/usr/lib/R/library/pointer' * Installing *Frontend* package 'gnomeGUI' ... Using R Installation in R_HOME=/usr/lib/R checking for sed... /bin/sed checking for a BSD-compatible install... /usr/bin/install -c checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking whether we can compute C Make dependencies... yes, using gcc -MM checking for gnome-config... no checking for gnomeConf.sh file in /usr/local/lib... not found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h making command-grep.d from command-grep.c command-grep.c:2:19: error: gnome.h: No such file or directory command-grep.c:3:25: error: glade/glade.h: No such file or directory In file included from terminal.h:26, from command-grep.c:6: gtkconsole.h:37:21: error: gdk/gdk.h: No such file or directory gtkconsole.h:38:25: error: gtk/gtktext.h: No such file or directory gtkconsole.h:39:27: error: gtk/gtksignal.h: No such file or directory making gdkrotated.d from gdkrotated.c In file included from gdkrotated.c:21: gdkrotated.h:21:21: error: gdk/gdk.h: No such file or directory making gnome-find-dialog.d from gnome-find-dialog.c In file included from gnome-find-dialog.c:29: gnome-find-dialog.h:25:37: error: libgnomeui/gnome-dialog.h: No such file or directory gnome-find-dialog.c:37:21: error: gtk/gtk.h: No such file or directory gnome-find-dialog.c:38:36: error: libgnomeui/gnome-stock.h: No such file or directory gnome-find-dialog.c:39:37: error: libgnomeui/gnome-uidefs.h: No such file or directory making gtkconsole.d from gtkconsole.c gtkconsole.c:29:28: error: gdk/gdkkeysyms.h: No such file or directory In file included from gtkconsole.c:38: gtkconsole.h:37:21: error: gdk/gdk.h: No such file or directory gtkconsole.h:38:25: error: gtk/gtktext.h: No such file or directory gtkconsole.h:39:27: error: gtk/gtksignal.h: No such file or directory making savehistory.d from savehistory.c In file included from savehistory.c:22: gtkconsole.h:37:21: error: gdk/gdk.h: No such file or directory gtkconsole.h:38:25: error: gtk/gtktext.h: No such file or directory gtkconsole.h:39:27: error: gtk/gtksignal.h: No such file or directory In file included from savehistory.c:23: terminal.h:24:19: error: gnome.h: No such file or directory making system-choosefile.d from system-choosefile.c In file included from system-choosefile.c:23: terminal.h:24:19: error: gnome.h: No such file or directory In file included from terminal.h:26, from system-choosefile.c:23: gtkconsole.h:37:21: error: gdk/gdk.h: No such file or directory gtkconsole.h:38:25: error: gtk/gtktext.h: No such file or directory gtkconsole.h:39:27: error: gtk/gtksignal.h: No such file or directory making system-console.d from system-console.c In file included from system-console.c:23: terminal.h:24:19: error: gnome.h: No such file or directory In file included from terminal.h:26, from system-console.c:23: gtkconsole.h:37:21: error: gdk/gdk.h: No such file or directory gtkconsole.h:38:25: error: gtk/gtktext.h: No such file or directory gtkconsole.h:39:27: error: gtk/gtksignal.h: No such file or directory making system-showfiles.d from system-showfiles.c In file included from system-showfiles.c:33: terminal.h:24:19: error: gnome.h: No such file or directory In file included from terminal.h:26, from system-showfiles.c:33: gtkconsole.h:37:21: error: gdk/gdk.h: No such file or directory gtkconsole.h:38:25: error: gtk/gtktext.h: No such file or directory gtkconsole.h:39:27: error: gtk/gtksignal.h: No such file or directory making system.d from system.c system.c:28:19: error: gnome.h: No such file or directory system.c:29:25: error: glade/glade.h: No such file or directory system.c:30:31: error: libgnome/libgnome.h: No such file or directory In file included from system.c:50: gtkconsole.h:37:21: error: gdk/gdk.h: No such file or directory gtkconsole.h:38:25: error: gtk/gtktext.h: No such file or directory gtkconsole.h:39:27: error: gtk/gtksignal.h: No such file or directory making terminal-find.d from terminal-find.c In file included from terminal-find.c:25: gnome-find-dialog.h:25:37: error: libgnomeui/gnome-dialog.h: No such file or directory In file included from terminal-find.c:26: terminal.h:24:19: error: gnome.h: No such file or directory In file included from terminal.h:26, from terminal-find.c:26: gtkconsole.h:37:21: error: gdk/gdk.h: No such file or directory gtkconsole.h:38:25: error: gtk/gtktext.h: No such file or directory gtkconsole.h:39:27: error: gtk/gtksignal.h: No such file or directory making terminal-functions.d from terminal-functions.c In file included from terminal-functions.c:24: terminal.h:24:19: error: gnome.h: No such file or directory In file included from terminal.h:26, from terminal-functions.c:24: gtkconsole.h:37:21: error: gdk/gdk.h: No such file or directory gtkconsole.h:38:25: error: gtk/gtktext.h: No such file or directory gtkconsole.h:39:27: error: gtk/gtksignal.h: No such file or directory making terminal-menu.d from terminal-menu.c In file included from terminal-menu.c:30: terminal.h:24:19: error: gnome.h: No such file or directory In file included from terminal.h:26, from terminal-menu.c:30: gtkconsole.h:37:21: error: gdk/gdk.h: No such file or directory gtkconsole.h:38:25: error: gtk/gtktext.h: No such file or directory gtkconsole.h:39:27: error: gtk/gtksignal.h: No such file or directory In file included from terminal-menu.c:33: terminal-menu.h:1:21: error: gtk/gtk.h: No such file or directory making terminal-prefs.d from terminal-prefs.c In file included from terminal-prefs.c:27: terminal-prefs.h:21:19: error: gnome.h: No such file or directory In file included from terminal.h:26, from terminal-prefs.c:28: gtkconsole.h:37:21: error: gdk/gdk.h: No such file or directory gtkconsole.h:38:25: error: gtk/gtktext.h: No such file or directory gtkconsole.h:39:27: error: gtk/gtksignal.h: No such file or directory terminal-prefs.c:30:25: error: glade/glade.h: No such file or directory terminal-prefs.c:31:18: error: glib.h: No such file or directory making terminal-toolbar.d from terminal-toolbar.c In file included from terminal-toolbar.c:21: terminal.h:24:19: error: gnome.h: No such file or directory In file included from terminal.h:26, from terminal-toolbar.c:21: gtkconsole.h:37:21: error: gdk/gdk.h: No such file or directory gtkconsole.h:38:25: error: gtk/gtktext.h: No such file or directory gtkconsole.h:39:27: error: gtk/gtksignal.h: No such file or directory In file included from terminal-toolbar.c:22: terminal-toolbar.h:22:21: error: gtk/gtk.h: No such file or directory making terminal.d from terminal.c In file included from terminal.c:22: terminal.h:24:19: error: gnome.h: No such file or directory In file included from terminal.h:26, from terminal.c:22: gtkconsole.h:37:21: error: gdk/gdk.h: No such file or directory gtkconsole.h:38:25: error: gtk/gtktext.h: No such file or directory gtkconsole.h:39:27: error: gtk/gtksignal.h: No such file or directory In file included from terminal.c:27: terminal-toolbar.h:22:21: error: gtk/gtk.h: No such file or directory make[1]: Entering directory `/tmp/R.INSTALL.g13775/gnomeGUI' make[1]: `Makedeps' is up to date. make[1]: Leaving directory `/tmp/R.INSTALL.g13775/gnomeGUI' make[1]: Entering directory `/tmp/R.INSTALL.g13775/gnomeGUI' gcc -I. -I/usr/lib/R/include -DHAVE_CONFIG_H -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c command-grep.c -o command-grep.o command-grep.c:2:19: error: gnome.h: No such file or directory command-grep.c:3:25: error: glade/glade.h: No such file or directory In file included from command-grep.c:5: command-grep.h:1: error: syntax error before '*' token In file included from terminal.h:26, from command-grep.c:6: gtkconsole.h:37:21: error: gdk/gdk.h: No such file or directory gtkconsole.h:38:25: error: gtk/gtktext.h: No such file or directory gtkconsole.h:39:27: error: gtk/gtksignal.h: No such file or directory In file included from terminal.h:26, from command-grep.c:6: gtkconsole.h:61: error: syntax error before 'GtkText' gtkconsole.h:61: warning: no semicolon at end of struct or union gtkconsole.h:63: warning: data definition has no type or storage class gtkconsole.h:64: error: syntax error before 'history_index' gtkconsole.h:64: warning: data definition has no type or storage class gtkconsole.h:65: error: syntax error before '*' token gtkconsole.h:65: warning: data definition has no type or storage class gtkconsole.h:66: error: syntax error before 'history_num_items' gtkconsole.h:66: warning: data definition has no type or storage class gtkconsole.h:68: error: syntax error before 'input_color' gtkconsole.h:68: warning: data definition has no type or storage class gtkconsole.h:69: error: syntax error before 'output_color' gtkconsole.h:69: warning: data definition has no type or storage class gtkconsole.h:70: error: syntax error before 'bg_color' gtkconsole.h:70: warning: data definition has no type or storage class gtkconsole.h:72: error: syntax error before 'input_enabled' gtkconsole.h:72: warning: data definition has no type or storage class gtkconsole.h:73: error: syntax error before 'input_start_index' gtkconsole.h:73: warning: data definition has no type or storage class gtkconsole.h:74: error: syntax error before 'line_available' gtkconsole.h:74: warning: data definition has no type or storage class gtkconsole.h:76: error: syntax error before 'buffer_type' gtkconsole.h:76: warning: data definition has no type or storage class gtkconsole.h:77: error: syntax error before 'buffer_index' gtkconsole.h:77: warning: data definition has no type or storage class gtkconsole.h:78: error: syntax error before 'out_buf' gtkconsole.h:78: warning: data definition has no type or storage class gtkconsole.h:81: error: syntax error before '*' token gtkconsole.h:81: warning: data definition has no type or storage class gtkconsole.h:82: error: syntax error before '}' token gtkconsole.h:86: error: syntax error before 'GtkTextClass' gtkconsole.h:86: warning: no semicolon at end of struct or union gtkconsole.h:91: error: syntax error before 'gpointer' gtkconsole.h:94: error: syntax error before '}' token gtkconsole.h:97: error: syntax error before 'gtk_console_get_type' gtkconsole.h:97: warning: data definition has no type or storage class gtkconsole.h:98: error: syntax error before '*' token gtkconsole.h:98: error: syntax error before '*' token gtkconsole.h:98: warning: data definition has no type or storage class gtkconsole.h:103: error: syntax error before 'gchar' gtkconsole.h:107: error: syntax error before 'gchar' gtkconsole.h:114: error: syntax error before 'gchar' gtkconsole.h:119: error: syntax error before 'gtk_console_save_history' gtkconsole.h:119: error: syntax error before 'gchar' gtkconsole.h:120: warning: data definition has no type or storage class gtkconsole.h:121: error: syntax error before 'gtk_console_restore_history' gtkconsole.h:121: error: syntax error before 'gchar' gtkconsole.h:122: warning: data definition has no type or storage class gtkconsole.h:125: error: syntax error before 'gtk_console_get_input_start_index' gtkconsole.h:125: warning: data definition has no type or storage class gtkconsole.h:126: error: syntax error before 'gtk_console_get_line_available' gtkconsole.h:126: warning: data definition has no type or storage class gtkconsole.h:127: error: syntax error before 'gtk_console_get_input_enabled' gtkconsole.h:127: warning: data definition has no type or storage class In file included from command-grep.c:6: terminal.h:41: error: syntax error before '*' token terminal.h:41: warning: data definition has no type or storage class terminal.h:42: error: syntax error before '*' token terminal.h:42: warning: data definition has no type or storage class terminal.h:43: error: syntax error before '*' token terminal.h:43: warning: data definition has no type or storage class terminal.h:45: error: syntax error before '*' token terminal.h:45: warning: data definition has no type or storage class In file included from command-grep.c:7: terminal-functions.h:7: error: syntax error before '*' token terminal-functions.h:8: error: syntax error before '*' token terminal-functions.h:9: error: syntax error before '*' token terminal-functions.h:16: error: syntax error before '*' token terminal-functions.h:18: error: syntax error before '*' token terminal-functions.h:20: error: syntax error before '*' token command-grep.c:9: error: syntax error before '*' token command-grep.c: In function 'commands_grep_cb': command-grep.c:11: error: 'GladeXML' undeclared (first use in this function) command-grep.c:11: error: (Each undeclared identifier is reported only once command-grep.c:11: error: for each function it appears in.) command-grep.c:11: error: 'grep_xml' undeclared (first use in this function) command-grep.c:12: error: 'GtkWidget' undeclared (first use in this function) command-grep.c:12: error: 'grep_dialog' undeclared (first use in this function) command-grep.c:12: error: 'grep_pattern_entry' undeclared (first use in this function) command-grep.c:12: error: 'grep_object_entry' undeclared (first use in this function) command-grep.c:13: error: 'grep_case_cb' undeclared (first use in this function) command-grep.c:13: error: 'grep_extended_cb' undeclared (first use in this function) command-grep.c:13: error: 'grep_value_cb' undeclared (first use in this function) command-grep.c:14: error: 'gint' undeclared (first use in this function) command-grep.c:14: error: syntax error before 'button' command-grep.c:15: error: 'gchar' undeclared (first use in this function) command-grep.c:15: error: 'pattern' undeclared (first use in this function) command-grep.c:15: error: 'object' undeclared (first use in this function) command-grep.c:33: error: 'button' undeclared (first use in this function) make[1]: *** [command-grep.o] Error 1 make[1]: Leaving directory `/tmp/R.INSTALL.g13775/gnomeGUI' make: *** [R] Error 2 ERROR: make failed for package 'gnomeGUI' * Installing *source* package 'grouped' ... ** R ** data ** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'grouped' Formats: text html latex example Sdata text html latex example Seeds text html latex example anova.grouped text html latex example equispaced text html latex example grouped text html latex example plot.grouped text html latex example power.grouped text html latex example residuals.grouped text html latex example rounding text html latex example summary.grouped text html latex example summary.resid.grouped text html latex example ** building package indices ... * DONE (grouped) * Installing *source* package 'hapsim' ... ** libs gcc -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -c hapsim.c -o hapsim.o gcc -shared -L/usr/local/lib -o hapsim.so hapsim.o -L/usr/lib/R/lib -lR ** R ** data ** help >>> Building/Updating help pages for package 'hapsim' Formats: text html latex example ACEdata text html latex allelefreqs text html latex example checkpd text html latex cor2dprime text html latex cortocov text html latex example covtocor text html latex example divlocus text html latex example haplodata text html latex example haplosim text html latex example ldplot text html latex example makepd text html latex mergemats text html latex mse text html latex sumsqscale text html latex example ** building package indices ... * DONE (hapsim) * Installing *source* package 'iid.test' ... ** R ** data ** help >>> Building/Updating help pages for package 'iid.test' Formats: text html latex example daily.station.records text html latex example iid.test text html latex example n.records text html latex example obs text html latex example test.iid.test text html latex example ** building package indices ... * DONE (iid.test) * Installing *source* package 'mblm' ... ** R ** help >>> Building/Updating help pages for package 'mblm' Formats: text html latex example confint.mblm text html latex example mblm text html latex example summary.mblm text html latex example ** building package indices ... * DONE (mblm) * Installing *source* package 'mimR' ... Package 'mimR' can only be installed/used under Windows. ERROR: configuration failed for package 'mimR' * Installing *source* package 'moments' ... ** R ** help >>> Building/Updating help pages for package 'moments' Formats: text html latex example agostino.test text html latex example anscombe.test text html latex example bonett.test text html latex example geary text html latex example kurtosis text html latex example moment text html latex example skewness text html latex example ** building package indices ... * DONE (moments) * Installing *source* package 'ncdf' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking /usr/local/include/netcdf.h usability... no checking /usr/local/include/netcdf.h presence... no checking for /usr/local/include/netcdf.h... no checking /usr/include/netcdf.h usability... no checking /usr/include/netcdf.h presence... no checking for /usr/include/netcdf.h... no checking /root/include/netcdf.h usability... no checking /root/include/netcdf.h presence... no checking for /root/include/netcdf.h... no checking /root/src/netcdf/netcdf.h usability... no checking /root/src/netcdf/netcdf.h presence... no checking for /root/src/netcdf/netcdf.h... no checking /root/src/netcdf/netcdf-3.4/netcdf.h usability... no checking /root/src/netcdf/netcdf-3.4/netcdf.h presence... no checking for /root/src/netcdf/netcdf-3.4/netcdf.h... no checking /root/src/netcdf/netcdf-3.4/src/libsrc/netcdf.h usability... no checking /root/src/netcdf/netcdf-3.4/src/libsrc/netcdf.h presence... no checking for /root/src/netcdf/netcdf-3.4/src/libsrc/netcdf.h... no checking /sw/include/netcdf.h usability... no checking /sw/include/netcdf.h presence... no checking for /sw/include/netcdf.h... no Fatal error: I cannot find the directory that holds the netcdf include file netcdf.h! You can specify it as follows: ./configure --with-netcdf_incdir=directory_with_file_netcdf.h *** Special note for R CMD INSTALL users: ********************************* The syntax for specifying multiple --configure-args does not seem to be well documented in R. If you have installed the netcdf include and library directories in some non-standard location, you can specify BOTH these during the R CMD INSTALL process using the following syntax: R CMD INSTALL --configure-args="-with-netcdf_incdir=/path/to/netcdf/incdir -with-netcdf_libdir=/path/to/netcdf/libdir" ncdf_1.1.tar.gz where you should, of course, specify your own netcdf include and library directories, and the actual package name. *************************************************************************** ERROR: configuration failed for package 'ncdf' * Installing *source* package 'powerpkg' ... ** R ** help >>> Building/Updating help pages for package 'powerpkg' Formats: text html latex example fnfam text html latex example fx text html latex example nsibs text html latex example ntdt text html latex example ntdt.q text html latex example plotDom text html latex example plotNsibs text html latex example plotNtdt text html latex example ptb text html latex example ptdt text html latex example ** building package indices ... * DONE (powerpkg) * Installing *source* package 'rcdd' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking for __gmpz_init in -lgmp... yes checking for dd_DDMatrix2Poly2 in -lcddgmp... no configure: error: cddgmp not found or built with C++, see README ERROR: configuration failed for package 'rcdd' * Installing *source* package 'reshape' ... ** R ** data ** help >>> Building/Updating help pages for package 'reshape' Formats: text html latex example as.data.frame.reshape_matrix text html latex example as.matrix.reshape_df text html latex example check_formula text html latex example clean.vars text html latex example condense text html latex example deshape.check text html latex example deshape text html latex example expand.grid.df text html latex example expand text html latex example margin.vars text html latex example merge_all text html latex example merge_recurse text html latex example print.reshape_df text html latex example print.reshape_matrix text html latex example rbind.fill text html latex example reshape text html latex example reshape1 text html latex example reshape_parse_formula text html latex example tips text html latex ** building package indices ... * DONE (reshape) * Installing *source* package 'rgdal' ... ./configure: line 1111: gdal-config: command not found I was unable to find the gdal-config script distributed with GDAL. If you have not installed the GDAL libraries, you can download the source from http://www.remotesensing.org/gdal/ If you have installed the GDAL libraries, then make sure that gdal-config is in your path. Try typing gdal-config at a shell prompt and see if it runs. If not, find it and add its path to your shell path. ERROR: configuration failed for package 'rgdal' * Installing *source* package 'Rmpi' ... Try to find mpi.h ... checking for gcc... gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes Try to find libmpi ... checking for main in -lmpi... no libmpi not found. exiting... ERROR: configuration failed for package 'Rmpi' * Installing *source* package 'RMySQL' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for compress in -lz... yes checking for getopt_long in -lc... yes checking for mysql_init in -lmysqlclient... no checking for mysql.h... no checking for mysql_init in -lmysqlclient... no checking for mysql_init in -lmysqlclient... no checking for mysql_init in -lmysqlclient... no checking for mysql_init in -lmysqlclient... no checking for mysql_init in -lmysqlclient... no checking for /usr/local/include/mysql/mysql.h... no checking for /usr/include/mysql/mysql.h... no checking for /usr/local/mysql/include/mysql/mysql.h... no checking for /opt/include/mysql/mysql.h... no checking for /include/mysql/mysql.h... no Configuration error: could not find the MySQL installation include and/or library directories. Manually specify the location of the MySQL libraries and the header files and re-run R CMD INSTALL. INSTRUCTIONS: 1. Define and export the 2 shell variables PKG_CPPFLAGS and PKG_LIBS to include the directory for header files (*.h) and libraries, for example (using Bourne shell syntax): export PKG_CPPFLAGS="-I" export PKG_LIBS="-L -lmysqlclient" Re-run the R INSTALL command: R CMD INSTALL RMySQL_.tar.gz 2. Alternatively, you may pass the configure arguments --with-mysql-dir= (distribution directory) or --with-mysql-inc= (where MySQL header files reside) --with-mysql-lib= (where MySQL libraries reside) in the call to R INSTALL --configure-args='...' R CMD INSTALL --configure-args='--with-mysql-dir=DIR' RMySQL_.tar.gz ERROR: configuration failed for package 'RMySQL' * Installing *source* package 'RNetCDF' ... checking for gcc... gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for executable suffix... checking for object suffix... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for main in -lnetcdf... no configure: error: netcdf library not found ERROR: configuration failed for package 'RNetCDF' * Installing *source* package 'RODBC' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking sql.h usability... no checking sql.h presence... no checking for sql.h... no checking sqlext.h usability... no checking sqlext.h presence... no checking for sqlext.h... no configure: error: "ODBC headers sql.h and sqlext.h not found" ERROR: configuration failed for package 'RODBC' * Installing *source* package 'ROracle' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E ROracle configuration error: You must set the shell variable ORACLE_HOME to the directory where Oracle resides and re-run R CMD INSTALL e.g., (using Bourne shell syntax): export ORACLE_HOME=/opt/oracle R CMD INSTALL ROracle ERROR: configuration failed for package 'ROracle' * Installing *source* package 'RQuantLib' ... checking for g++... g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking for quantlib-config... no Your installation does not appear to have QuantLib installed as the quantlib-config utility script could not be found. Please make sure that QuantLib is installed before building RQuantLib. ERROR: configuration failed for package 'RQuantLib' * Installing *source* package 'RScaLAPACK' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking for library containing openpty... -lutil checking for library containing pow... -lm checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes checking for pthread_atfork in -lpthread... yes checking for MPI_Comm_spawn... no checking for MPI_Comm_spawn in -lmpi... no checking for lam_rtrstore in -llam... yes checking for MPI_Comm_spawn_multiple in -lmpi... yes checking for mpi_comm_create__ in -llamf77mpi... no Error! liblamf77mpi is required (part of lam installation). ERROR: configuration failed for package 'RScaLAPACK' * Installing *source* package 'rsprng' ... checking for gcc... gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed Try to find sprng.h ... checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking sprng.h usability... no checking sprng.h presence... no checking for sprng.h... no Cannot find sprng 2.0 header file. ERROR: configuration failed for package 'rsprng' * Installing *source* package 'RWinEdt' ... Package 'RWinEdt' can only be installed/used under Windows. ERROR: configuration failed for package 'RWinEdt' * Installing *source* package 'simex' ... ** R ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'simex' Formats: text html latex example check.mc.matrix text html latex example construct.s text html latex example diag.block text html latex example extract.covmat text html latex example fit.nls text html latex mcsimex text html latex example misclass text html latex example overview text html latex plot.SIMEX text html latex example predict.MCSIMEX text html latex predict.SIMEX text html latex print.SIMEX text html latex refit text html latex example simex text html latex example summary.MCSIMEX text html latex example summary.SIMEX text html latex example ** building package indices ... * DONE (simex) * Installing *source* package 'taskPR' ... creating cache ./config.cache checking for gcc... gcc checking whether the C compiler (gcc ) works... yes checking whether the C compiler (gcc ) is a cross-compiler... no checking whether we are using GNU C... yes checking whether gcc accepts -g... yes checking how to run the C preprocessor... gcc -E checking for mpi.h... yes checking for pthread_detach in -lpthread... yes checking for MPI_Comm_spawn... no checking for MPI_Comm_spawn in -lmpi... no checking for lam_rtrstore in -llam... no Error! liblam is required (mpich won't work). ERROR: configuration failed for package 'taskPR' The downloaded packages are in /tmp/Rtmpv32038/downloaded_packages There were 17 warnings (use warnings() to see them) > > proc.time() [1] 17.61 3.15 5063.55 403.86 45.38 >