R version 2.9.2 (2009-08-24) Copyright (C) 2009 The R Foundation for Statistical Computing 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. 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. - MKL libraries for acclerated math installed: see help (setMKLthreads) - ParallelR packages installed: see help (package='foreach') Type 'revo()' to visit www.revolution-computing.com for the latest REvolution R news, 'forum()' for the community forum, or 'readme()' for release notes. > png(filename="install.r%02d.png") > > ## install the basic bioconductor packages > source( "http://bioconductor.org/biocLite.R") > biocLite() Using R version 2.9.2, biocinstall version 2.4.13. Installing Bioconductor version 2.4 packages: [1] "affy" "affydata" "affyPLM" "annaffy" "annotate" [6] "Biobase" "biomaRt" "Biostrings" "DynDoc" "gcrma" [11] "genefilter" "geneplotter" "hgu95av2.db" "limma" "marray" [16] "multtest" "vsn" "xtable" "affyQCReport" Please wait... 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 sed... /bin/sed checking for pkg-config... /usr/bin/pkg-config checking for xml2-config... no Cannot find xml2-config checking for curl-config... no Cannot find curl-config make[1]: Entering directory `/tmp/Rtmpwv7bAI/R.INSTALL327b23c6/Biobase/src' gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c Rinit.c -o Rinit.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c anyMissing.c -o anyMissing.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c envir.c -o envir.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c matchpt.c -o matchpt.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c rowMedians.c -o rowMedians.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c sublist_extract.c -o sublist_extract.o gcc -std=gnu99 -shared -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/usr/lib/R/lib -lR make[1]: Leaving directory `/tmp/Rtmpwv7bAI/R.INSTALL327b23c6/Biobase/src' >>> Building/Updating help pages for package 'Biobase' Formats: text html latex example Aggregate text html latex example Biobase-package text html latex ScalarObject-class text html latex example abstract text html latex addVig2Menu text html latex example annotatedDataFrameFrom-methods text html latex annotation text html latex anyMissing text html latex example assayData text html latex biocReposList text html latex example cache text html latex example channel text html latex example channelNames text html latex example class.AnnotatedDataFrame text html latex example class.AssayData text html latex class.ExpressionSet text html latex example class.MIAME text html latex class.MultiSet text html latex example class.NChannelSet text html latex example class.SnpSet text html latex class.Versioned text html latex example class.VersionedBiobase text html latex example class.Versions text html latex example class.VersionsNull text html latex example class.aggregator text html latex class.characterORmiame text html latex class.container text html latex example class.eSet text html latex example classVersion text html latex example combine text html latex example contents text html latex example copyEnv text html latex example copySubstitute text html latex example createPackage text html latex example data.aaMap text html latex example data.geneData text html latex example data.reporter text html latex example data.sample.ExpressionSet text html latex example data.sample.MultiSet text html latex example defunct text html latex description text html latex dims text html latex dumpPackTxt text html latex example esApply text html latex example exprs text html latex featureData text html latex featureNames text html latex getPkgVigs text html latex example internals text html latex isCurrent text html latex example isUnique text html latex example isVersioned text html latex example lcSuffix text html latex example listLen text html latex example makeDataPackage text html latex example matchpt text html latex example multiassign text html latex example note text html latex example notes text html latex openPDF text html latex example openVignette text html latex example package.version text html latex example phenoData text html latex read.AnnotatedDataFrame text html latex example read.MIAME text html latex example readExpressionSet text html latex example reverseSplit text html latex example rowMedians text html latex example rowQ text html latex example selectChannels text html latex example selectSome text html latex example storageMode text html latex strbreak text html latex example subListExtract text html latex example testBioCConnection text html latex example updateObject text html latex example updateOldESet text html latex example userQuery text html latex validMsg text html latex example >>> Building/Updating help pages for package 'DynDoc' Formats: text html latex example DynDoc-class text html latex SweaveOptions-class text html latex Vignette-class text html latex chunkList-class text html latex example codeChunk-class text html latex example getPkgVigList text html latex example getVignette text html latex getVignetteCode text html latex getVignetteHeader text html latex tangleToR text html latex example vignetteCode-class text html latex >>> Building/Updating help pages for package 'hgu95av2.db' Formats: text html latex example hgu95av2ACCNUM text html latex example hgu95av2ALIAS2PROBE text html latex example hgu95av2BASE text html latex example hgu95av2CHR text html latex example hgu95av2CHRLENGTHS text html latex example hgu95av2CHRLOC text html latex example hgu95av2ENSEMBL text html latex example hgu95av2ENTREZID text html latex example hgu95av2ENZYME text html latex example hgu95av2ENZYME2PROBE text html latex example hgu95av2GENENAME text html latex example hgu95av2GO text html latex example hgu95av2GO2ALLPROBES text html latex example hgu95av2GO2PROBE text html latex example hgu95av2MAP text html latex example hgu95av2MAPCOUNTS text html latex example hgu95av2OMIM text html latex example hgu95av2ORGANISM text html latex example hgu95av2PATH text html latex example hgu95av2PATH2PROBE text html latex example hgu95av2PFAM text html latex example hgu95av2PMID text html latex example hgu95av2PMID2PROBE text html latex example hgu95av2PROSITE text html latex example hgu95av2REFSEQ text html latex example hgu95av2SYMBOL text html latex example hgu95av2UNIGENE text html latex example hgu95av2UNIPROT text html latex example hgu95av2_dbconn text html latex example make[1]: Entering directory `/tmp/RtmpcthjgL/R.INSTALL327b23c6/limma/src' gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c normexp.c -o normexp.o gcc -std=gnu99 -shared -o limma.so normexp.o -L/usr/lib/R/lib -lR make[1]: Leaving directory `/tmp/RtmpcthjgL/R.INSTALL327b23c6/limma/src' >>> 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 EList text html latex LargeDataObject text html latex example PrintLayout text html latex example TestResults text html latex example alias2Symbol text html latex example anova-method text html latex arrayWeights text html latex example arrayWeightsQuick text html latex example asMatrixWeights text html latex example asdataframe text html latex asmalist text html latex asmatrix text html latex auROC text html latex example avedups text html latex avereps text html latex 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 exprsMA text html latex fitfdist text html latex fitted.MArrayLM text html latex geneSetTest text html latex example getEAWP text html latex getSpacing text html latex example getlayout text html latex example gls.series text html latex 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 lmFit text html latex example lmscFit text html latex example loessfit text html latex example ma3x3 text html latex example makeContrasts text html latex example makeunique text html latex example malist text html latex marraylm text html latex mdplot text html latex merge text html latex example mergeScansRG text html latex example modelMatrix text html latex example modifyWeights text html latex example mrlm text html latex normalizeMedianAbsValues 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 normexpfit text html latex example normexpsignal text html latex example plotDensities text html latex example plotFB text html latex plotMDS text html latex example plotSA text html latex plotlines text html latex 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 printtipWeights text html latex example protectMetachar text html latex example qqt text html latex example qualwt text html latex example read.columns text html latex read.maimages text html latex example readGPRHeader text html latex readImaGeneHeader text html latex example readSpotTypes text html latex readTargets text html latex readgal text html latex example removeBatchEffect text html latex removeext text html latex example residuals.MArrayLM text html latex rglist text html latex roast text html latex example romer text html latex example selectmodel text html latex example squeezeVar text html latex example strsplit2 text html latex example subsetting text html latex example summary text html latex symbols2indices 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 example weightedmedian text html latex example writefit text html latex zscore text html latex example >>> Building/Updating help pages for package 'xtable' Formats: text html latex example print.xtable text html latex string text html latex table.attributes text html latex tli text html latex xtable text html latex example creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for main in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes updating cache ./config.cache creating ./config.status creating src/Makevars make[1]: Entering directory `/tmp/RtmpjxRbha/R.INSTALL327b23c6/affy/src' gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1 -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c chipbackground.c -o chipbackground.o gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1 -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c getall_locations.c -o getall_locations.o gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1 -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c mas5calls.c -o mas5calls.o gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1 -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c rma2.c -o rma2.o gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1 -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c rma_common.c -o rma_common.o gcc -std=gnu99 -shared -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -L/usr/lib/R/lib -lR make[1]: Leaving directory `/tmp/RtmpjxRbha/R.INSTALL327b23c6/affy/src' >>> Building/Updating help pages for package 'affy' Formats: text html latex example AffyBatch-class text html latex example AffyRNAdeg text html latex example MAplot text html latex example ProbeSet-class text html latex example ProgressBarText-class text html latex example SpikeIn text html latex affy-options text html latex example affy.scalevalue.exprSet text html latex barplot.ProbeSet text html latex example bg.adjust text html latex bgc text html latex example cdfFromBioC text html latex cdfenv.example text html latex cleancdfname text html latex example debug.affy123 text html latex expresso text html latex example expressoWidget text html latex example fit.li.wong text html latex example generateExprSet-methods text html latex example generateExprVal-methods text html latex example generateExprVal.method.avgdiff text html latex example generateExprVal.method.playerout text html latex hlog text html latex justrma text html latex list.celfiles text html latex example loess.normalize text html latex maffy.normalise text html latex example maffy.subset text html latex example mas5 text html latex example mas5calls text html latex example merge.AffyBatch text html latex multiloess text html latex mva.pairs text html latex example normalize-methods text html latex example normalize text html latex normalize.constant text html latex normalize.contrast text html latex normalize.invariantset text html latex normalize.loess text html latex example normalize.qspline text html latex normalize.quantiles text html latex normalize.quantiles.robust text html latex pairs.AffyBatch text html latex plot.ProbeSet text html latex example plot.density text html latex example plotLocation text html latex example pmcorrect text html latex example ppsetApply text html latex example probeMatch-methods text html latex probeNames-methods text html latex read.affybatch text html latex example read.probematrix text html latex rma text html latex example setAffyOptions text html latex example simplemultiLoess text html latex summary text html latex tukey.biweight text html latex whatcdf text html latex xy2indices text html latex example >>> Building/Updating help pages for package 'annaffy' Formats: text html latex example aaf.character text html latex aaf.goterm text html latex aaf.handler text html latex aaf.integer text html latex aaf.raw text html latex aafChromLoc-class text html latex aafChromLoc text html latex example aafChromosome-class text html latex aafChromosome text html latex example aafCytoband-class text html latex aafCytoband text html latex example aafDescription-class text html latex aafDescription text html latex example aafExpr text html latex aafGO-class text html latex aafGO text html latex example aafGOItem-class text html latex aafGenBank-class text html latex aafGenBank text html latex example aafIntensity-class text html latex aafList-class text html latex aafLocusLink-class text html latex aafLocusLink text html latex example aafPathway-class text html latex aafPathway text html latex example aafPathwayItem-class text html latex aafProbe-class text html latex aafProbe text html latex example aafPubMed-class text html latex aafPubMed text html latex example aafSearchGO text html latex aafSearchText text html latex example aafSigned-class text html latex aafSymbol-class text html latex aafSymbol text html latex example aafTable-class text html latex aafTable text html latex aafTableAnn text html latex aafTableFrame text html latex aafTableInt text html latex aafUniGene-class text html latex aafUniGene text html latex example chkPkgs text html latex getCSS-methods text html latex getHTML-methods text html latex getTD-methods text html latex getText-methods text html latex getURL-methods text html latex is.annpkg text html latex example selectorWidget text html latex >>> Building/Updating help pages for package 'annotate' Formats: text html latex example ACCNUMStats text html latex example GO2heatmap text html latex example GOmnplot text html latex example HTMLPage-class text html latex example LL2homology text html latex example PMIDAmat text html latex example PWAmat text html latex example UniGeneQuery text html latex example accessionToUID text html latex example annPkgName text html latex example aqListGOIDs text html latex example buildChromLocation text html latex example buildPubMedAbst text html latex example chrCats text html latex example chromLocation-class text html latex example compatibleVersions text html latex example dropECode text html latex example entrezGeneByID text html latex example entrezGeneQuery text html latex example filterGOByOntology text html latex example findNeighbors text html latex example genbank text html latex example genelocator text html latex example getAnnMap text html latex example getEvidence text html latex example getGOTerm text html latex example getOntology text html latex example getPMInfo text html latex example getSYMBOL text html latex example getSeq4Acc text html latex example getTDRows text html latex hasGOannote text html latex example hgByChroms text html latex example hgCLengths text html latex example hgu95AProbLocs text html latex hgu95Achroloc text html latex example hgu95Achrom text html latex example hgu95All text html latex example hgu95Asym text html latex example homoData-class text html latex example htmlpage text html latex example isValidkey text html latex example makeAnchor text html latex example mapOrgs text html latex neighborGeneFinder text html latex example p2LL text html latex example pm.abstGrep text html latex example pm.getabst text html latex example pm.titles text html latex example pmAbst2HTML text html latex example pmid2MIAME text html latex example pmidQuery text html latex example probesByLL text html latex example pubMedAbst-class text html latex example pubmed text html latex example readGEOAnn text html latex example serializeEnv text html latex example setRepository text html latex example updateSymbolsToValidKeys text html latex example usedChromGenes text html latex example make[1]: Entering directory `/tmp/RtmpDs9Inl/R.INSTALL327b23c6/Biostrings/src' gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c BAB_class.c -o BAB_class.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c Dups_utils.c -o Dups_utils.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c MIndex_utils.c -o MIndex_utils.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c RoSeq_utils.c -o RoSeq_utils.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c SparseList_utils.c -o SparseList_utils.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c XStringSet_class.c -o XStringSet_class.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c XString_class.c -o XString_class.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c align_needwunsQS.c -o align_needwunsQS.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c align_utils.c -o align_utils.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c char_translate.c -o char_translate.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c copy_seq.c -o copy_seq.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c fasta_io.c -o fasta_io.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c find_palindromes.c -o find_palindromes.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c inject_code.c -o inject_code.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c letter_frequency.c -o letter_frequency.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c match_BOC.c -o match_BOC.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c match_BOC2.c -o match_BOC2.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c match_PWM.c -o match_PWM.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c match_pattern.c -o match_pattern.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c match_pattern_at.c -o match_pattern_at.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c match_pattern_indels.c -o match_pattern_indels.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c match_pdict.c -o match_pdict.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c match_pdict_ACtree.c -o match_pdict_ACtree.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c match_pdict_Twobit.c -o match_pdict_Twobit.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c match_reporting.c -o match_reporting.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c matchprobes.c -o matchprobes.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c pmatchPattern.c -o pmatchPattern.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c replace_letter_at.c -o replace_letter_at.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c strutils.c -o strutils.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c utils.c -o utils.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/IRanges/include" -fpic -g -O2 -c xscat.c -o xscat.o gcc -std=gnu99 -shared -o Biostrings.so BAB_class.o Dups_utils.o IRanges_stubs.o MIndex_utils.o PreprocessedTB_class.o R_init_Biostrings.o RoSeq_utils.o SparseList_utils.o XStringSet_class.o XString_class.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o char_translate.o copy_seq.o fasta_io.o find_palindromes.o inject_code.o letter_frequency.o match_BOC.o match_BOC2.o match_PWM.o match_pattern.o match_pattern_at.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree.o match_pdict_ACtree2.o match_pdict_Twobit.o match_reporting.o matchprobes.o pmatchPattern.o replace_letter_at.o strutils.o utils.o xscat.o -L/usr/lib/R/lib -lR make[1]: Leaving directory `/tmp/RtmpDs9Inl/R.INSTALL327b23c6/Biostrings/src' >>> Building/Updating help pages for package 'Biostrings' Formats: text html latex example AAString-class text html latex example AMINO_ACID_CODE text html latex example AlignedXStringSet-class text html latex example BOC_SubjectString-class text html latex Biostrings-internals text html latex DNAString-class text html latex example GENETIC_CODE text html latex example IUPAC_CODE_MAP text html latex example InDel-class text html latex MIndex-class text html latex example MaskedXString-class text html latex example PDict-class text html latex example PairwiseAlignedXStringSet-class text html latex example QualityScaledXStringSet-class text html latex example RNAString-class text html latex example XString-class text html latex example XStringPartialMatches-class text html latex XStringQuality-class text html latex example XStringSet-class text html latex example XStringSet-io text html latex example XStringViews-class text html latex example XStringViews-constructors text html latex example align-utils text html latex example basecontent text html latex example chartr text html latex example complementSeq text html latex example findPalindromes text html latex example gregexpr2 text html latex example injectHardMask text html latex example letter text html latex example letterFrequency text html latex example longestConsecutive text html latex example maskMotif text html latex example match-utils text html latex example matchLRPatterns text html latex example matchPDict-exact text html latex example matchPDict-inexact text html latex example matchPWM text html latex example matchPattern text html latex example matchProbePair text html latex example matchprobes text html latex example needwunsQS text html latex example nucleotideFrequency text html latex example pairwiseAlignment text html latex example phiX174Phage text html latex example pid text html latex example pmatchPattern text html latex readFASTA text html latex example replaceLetterAt text html latex example reverse text html latex example reverseSeq text html latex example stringDist text html latex example subXString text html latex substitution_matrices text html latex example toComplex text html latex example translate text html latex example trimLRPatterns text html latex example xscat text html latex example yeastSEQCHR1 text html latex example >>> Building/Updating help pages for package 'marray' Formats: text html latex example boxplot text html latex example bracketMethods text html latex cbind text html latex checkTargetInfo text html latex example coerce-methods text html latex dim text html latex example findID text html latex example htmlPage text html latex example image text html latex example ma2D text html latex example maBoxplot text html latex example maColorBar text html latex example maCompCoord text html latex example maCompInd text html latex example maCompLayout text html latex example maCompNormA text html latex example maCompPlate text html latex example maCoord2Ind text html latex example maDefaultPar text html latex example maDotsDefaults text html latex example maDotsMatch text html latex example maGenControls text html latex example maGeneTable text html latex example maImage text html latex example maImage.func text html latex example maInd2Coord text html latex example maLegendLines text html latex example maLoess text html latex example maLoessLines text html latex example maMAD text html latex example maMed text html latex example maNA text html latex maNorm text html latex example maNorm2D text html latex example maNormLoess text html latex example maNormMAD text html latex example maNormMain text html latex example maNormMed text html latex example maNormScale text html latex example maNum2Logic text html latex example maPalette text html latex example maPlot text html latex example maPlot.func text html latex example maSelectGnames text html latex example maText text html latex example maTop text html latex example maTwoSamples text html latex mapGeneInfo text html latex example marray-internal text html latex marrayInfo-class text html latex example marrayLayout-class text html latex example marrayNorm-class text html latex example marrayRaw-class text html latex example opVersionID text html latex example plotMA text html latex example print-methods text html latex read.Galfile text html latex example read.marrayInfo text html latex example read.marrayLayout text html latex example read.marrayRaw text html latex example rm.na text html latex example showLargeObject text html latex stat.confband.text text html latex example stat.gnames text html latex example swirl text html latex write.list text html latex example write.marray text html latex example write.xls text html latex example make[1]: Entering directory `/tmp/Rtmp1Im1VZ/R.INSTALL327b23c6/multtest/src' gcc -std=gnu99 -I/usr/share/R/include -DUSEDOUBLE -fpic -g -O2 -c Rpack.c -o Rpack.o gcc -std=gnu99 -I/usr/share/R/include -DUSEDOUBLE -fpic -g -O2 -c VScount.c -o VScount.o gcc -std=gnu99 -I/usr/share/R/include -DUSEDOUBLE -fpic -g -O2 -c block_sampling_fixed.c -o block_sampling_fixed.o gcc -std=gnu99 -I/usr/share/R/include -DUSEDOUBLE -fpic -g -O2 -c bootloop.c -o bootloop.o gcc -std=gnu99 -I/usr/share/R/include -DUSEDOUBLE -fpic -g -O2 -c mt.c -o mt.o gcc -std=gnu99 -I/usr/share/R/include -DUSEDOUBLE -fpic -g -O2 -c pairt_sampling.c -o pairt_sampling.o gcc -std=gnu99 -I/usr/share/R/include -DUSEDOUBLE -fpic -g -O2 -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o gcc -std=gnu99 -I/usr/share/R/include -DUSEDOUBLE -fpic -g -O2 -c random.c -o random.o gcc -std=gnu99 -I/usr/share/R/include -DUSEDOUBLE -fpic -g -O2 -c sampling.c -o sampling.o gcc -std=gnu99 -I/usr/share/R/include -DUSEDOUBLE -fpic -g -O2 -c sampling_fixed.c -o sampling_fixed.o gcc -std=gnu99 -I/usr/share/R/include -DUSEDOUBLE -fpic -g -O2 -c stat_func.c -o stat_func.o gcc -std=gnu99 -I/usr/share/R/include -DUSEDOUBLE -fpic -g -O2 -c stat_order.c -o stat_order.o gcc -std=gnu99 -shared -o multtest.so Rpack.o VScount.o block_sampling_fixed.o bootloop.o mt.o pairt_sampling.o pairt_sampling_fixed.o random.o sampling.o sampling_fixed.o stat_func.o stat_order.o -lm -L/usr/lib/R/lib -lR make[1]: Leaving directory `/tmp/Rtmp1Im1VZ/R.INSTALL327b23c6/multtest/src' >>> Building/Updating help pages for package 'multtest' Formats: text html latex example EBMTP-class text html latex example EBMTP text html latex example Hsets text html latex example MTP-class text html latex example MTP-methods text html latex MTP text html latex example boot.null text html latex example corr.null text html latex example fwer2gfwer text html latex example get.index text html latex example golub text html latex meanX text html latex example mt.internal text html latex mt.maxT text html latex example mt.plot text html latex example mt.rawp2adjp text html latex example mt.reject text html latex example mt.sample.teststat text html latex example mt.teststat text html latex example ss.maxT text html latex example wapply text html latex example >>> Building/Updating help pages for package 'affydata' Formats: text html latex example Dilution text html latex make[1]: Entering directory `/tmp/RtmpygDeYY/R.INSTALL327b23c6/gcrma/src' gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c baseProfile.c -o baseProfile.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c computeAffinities.c -o computeAffinities.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c postmean.c -o postmean.o gcc -std=gnu99 -shared -o gcrma.so baseProfile.o computeAffinities.o postmean.o -L/usr/lib/R/lib -lR make[1]: Leaving directory `/tmp/RtmpygDeYY/R.INSTALL327b23c6/gcrma/src' >>> Building/Updating help pages for package 'gcrma' Formats: text html latex example affinity.spline.coefs text html latex bg.adjust.affinities text html latex bg.adjust.gcrma text html latex example bg.parameters.ns text html latex compute.affinities text html latex fast.bkg text html latex gcrma text html latex example gcrma.engine text html latex gcrma.engine2 text html latex getCDF text html latex justGCRMA text html latex make[1]: Entering directory `/tmp/RtmpN4SEB1/R.INSTALL327b23c6/genefilter/src' g++ -I/usr/share/R/include -fpic -g -O2 -c half_range_mode.cpp -o half_range_mode.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c nd.c -o nd.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c pAUC.c -o pAUC.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c rowPAUCs.c -o rowPAUCs.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c rowttests.c -o rowttests.o gfortran -fpic -g -O2 -c ttest.f -o ttest.o g++ -shared -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -lgfortran -lm -L/usr/lib/R/lib -lR make[1]: Leaving directory `/tmp/RtmpN4SEB1/R.INSTALL327b23c6/genefilter/src' >>> Building/Updating help pages for package 'genefilter' Formats: text html latex example Anova text html latex example allNA text html latex example coxfilter text html latex example cv text html latex example dist2 text html latex example eSetFilter text html latex example filterfun text html latex example findLargest text html latex example gapFilter text html latex example genefilter text html latex example genefinder text html latex example genescale text html latex example half.range.mode text html latex example kOverA text html latex example maxA text html latex example nsFilter text html latex example pOverA text html latex example rowFtests text html latex example rowROC-class text html latex example rowSds text html latex example rowpAUCs text html latex example shorth text html latex example tdata text html latex example ttest text html latex example >>> Building/Updating help pages for package 'geneplotter' Formats: text html latex example GetColor text html latex example Makesense text html latex example alongChrom text html latex example amplicon.plot text html latex example cColor text html latex example cPlot text html latex example cScale text html latex example classes text html latex eset133a text html latex example groupedHeatmap text html latex example histStack text html latex example imageMap text html latex example make.chromOrd text html latex example multiecdf text html latex example openHtmlPage text html latex example plotChr text html latex example plotExpressionGraph text html latex example savepng text html latex example make[1]: Entering directory `/tmp/RtmpCP0NLq/R.INSTALL327b23c6/vsn/src' gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c vsn.c -o vsn.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c vsn2.c -o vsn2.o gcc -std=gnu99 -shared -o vsn.so init.o vsn.o vsn2.o -L/usr/lib/R/lib -lR make[1]: Leaving directory `/tmp/RtmpCP0NLq/R.INSTALL327b23c6/vsn/src' >>> Building/Updating help pages for package 'vsn' Formats: text html latex example class.vsn text html latex example class.vsnInput text html latex getIntensityMatrix text html latex example justvsn text html latex example kidney text html latex example lymphoma text html latex example meanSdPlot text html latex example normalize.AffyBatch.vsn text html latex example sagmbSimulateData text html latex example scalingFactorTransformation text html latex example vsn-package text html latex vsn text html latex example vsn2 text html latex example vsn2trsf text html latex example vsnLikelihood text html latex example vsnPlotPar text html latex example vsnh text html latex example make[1]: Entering directory `/tmp/RtmpIjtp3r/R.INSTALL327b23c6/affyPLM/src' gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c LESN.c -o LESN.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c PLM_avg_log.c -o PLM_avg_log.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c PLM_biweight.c -o PLM_biweight.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c PLM_log_avg.c -o PLM_log_avg.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c PLM_medianPM.c -o PLM_medianPM.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c PLM_median_logPM.c -o PLM_median_logPM.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c PLM_medianpolish.c -o PLM_medianpolish.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c PLM_modelmatrix.c -o PLM_modelmatrix.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c SCAB.c -o SCAB.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c chipbackground.c -o chipbackground.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c common_types.c -o common_types.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c do_PLMrlm.c -o do_PLMrlm.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c do_PLMrma.c -o do_PLMrma.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c do_PLMthreestep.c -o do_PLMthreestep.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c idealmismatch.c -o idealmismatch.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c lm_threestep.c -o lm_threestep.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c matrix_functions.c -o matrix_functions.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c nthLargestPM.c -o nthLargestPM.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c preprocess.c -o preprocess.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c psi_fns.c -o psi_fns.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c qnorm_probeset.c -o qnorm_probeset.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c read_rmaexpress.c -o read_rmaexpress.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c rlm_PLM.c -o rlm_PLM.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c rlm_threestep.c -o rlm_threestep.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c rma_PLM.c -o rma_PLM.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c rma_common.c -o rma_common.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c scaling.c -o scaling.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c threestep.c -o threestep.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c threestep_PLM.c -o threestep_PLM.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c threestep_common.c -o threestep_common.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c threestep_summary.c -o threestep_summary.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c threestep_summary_methods.c -o threestep_summary_methods.o gcc -std=gnu99 -I/usr/share/R/include -I"/home/phillord/R/i486-pc-linux-gnu-library/2.9/preprocessCore/include" -fpic -g -O2 -c transfns.c -o transfns.o gcc -std=gnu99 -shared -o affyPLM.so LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o -lgfortran -lm -llapack -lblas -lz -L/usr/lib/R/lib -lR make[1]: Leaving directory `/tmp/RtmpIjtp3r/R.INSTALL327b23c6/affyPLM/src' >>> Building/Updating help pages for package 'affyPLM' Formats: text html latex example MAplot text html latex PLMset-class text html latex PLMset2exprSet text html latex example ReadRMAExpress text html latex affyPLM-internal text html latex bg.correct.LESN text html latex example fitPLM text html latex example normalize.exprSet text html latex example normalize.quantiles.probeset text html latex normalize.scaling text html latex example preprocess text html latex example pseudo text html latex rmaPLM text html latex example threestep text html latex example threestepPLM text html latex example >>> Building/Updating help pages for package 'affyQCReport' Formats: text html latex example QCReport text html latex example affyQAReport text html latex example borderQC1 text html latex example borderQC2 text html latex example correlationPlot text html latex example signalDist text html latex example titlePage text html latex example The downloaded packages are in ‘/tmp/RtmpB3Sk50/downloaded_packages’ > biocLite('soybeanprobe') Using R version 2.9.2, biocinstall version 2.4.13. Installing Bioconductor version 2.4 packages: [1] "soybeanprobe" Please wait... >>> Building/Updating help pages for package 'soybeanprobe' Formats: text html latex example soybeanprobe text html latex example The downloaded packages are in ‘/tmp/RtmpB3Sk50/downloaded_packages’ > > > ## ensure installation before carrying on. > > > warnings() Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'XML' had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'RCurl' had non-zero exit status 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'biomaRt' had non-zero exit status >