############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL limma ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'limma' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c init.c -o init.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c normexp.c -o normexp.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c weighted_lowess.c -o weighted_lowess.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o limma.dll tmp.def init.o normexp.o weighted_lowess.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-limma/00new/limma/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'limma' finding HTML links ... done 01Introduction html 02classes html 03reading html 04Background html 05Normalization html 06linearmodels html 07SingleChannel html 08Tests html 09Diagnostics html 10GeneSetTests html 11RNAseq html EList html LargeDataObject html PrintLayout html TestResults html alias2Symbol html anova-method html arrayWeights html arrayWeightsQuick html asMatrixWeights html asdataframe html asmalist html asmatrix html auROC html avearrays html avedups html avereps html backgroundcorrect html barcodeplot html beadCountWeights html blockDiag html bwss html bwss.matrix html camera html cbind html changelog html channel2M html chooseLowessSpan html classifytestsF html contrastAsCoef html contrasts.fit html controlStatus html coolmap html cumOverlap html decideTests html detectionPValue html diffSplice html dim html dimnames html dupcor html ebayes html exprsMA html fitGammaIntercept html fitfdist html fitmixture html fitted.MArrayLM html genas html geneSetTest html getEAWP html getSpacing html getlayout html gls.series html goana html gridspotrc html head html heatdiagram html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-limma/00new/limma/help/heatDiagram.html helpMethods html ids2indices html imageplot html imageplot3by2 html intraspotCorrelation html isfullrank html isnumeric html kooperberg html limmaUsersGuide html lm.series html lmFit html lmscFit html loessfit html logcosh html logsumexp html ma3x3 html makeContrasts html makeunique html malist html marraylm html mdplot html merge html mergeScansRG html modelMatrix html modifyWeights html mrlm html nec html normalizeCyclicLoess html normalizeMedianAbsValues html normalizeRobustSpline html normalizeVSN html normalizeWithinArrays html normalizebetweenarrays html normalizeprintorder html normalizequantiles html normexpfit html normexpfitcontrol html normexpfitdetectionp html normexpsignal html plotDensities html plotExonJunc html plotExons html plotFB html plotMD html plotMDS html plotRLDF html plotSA html plotSplice html plotWithHighlights html plotlines html plotma html plotma3by2 html plotprinttiploess html poolvar html predFCm html printHead html printorder html printtipWeights html propTrueNull html propexpr html protectMetachar html qqt html qualwt html rankSumTestwithCorrelation html read.columns html read.idat html read.ilmn html read.ilmn.targets html read.maimages html readGPRHeader html readImaGeneHeader html readSampleInfoFromGEO html readSpotTypes html readTargets html readgal html removeBatchEffect html removeext html residuals.MArrayLM html rglist html roast html romer html selectmodel html squeezeVar html strsplit2 html subsetting html summary html targetsA2C html tmixture html topGO html topRomer html topSplice html toptable html tricubeMovingAverage html trigammainverse html trimWhiteSpace html uniquegenelist html unwrapdups html venn html volcanoplot html voom html voomWithQualityWeights html vooma html weightedLowess html weightedmedian html writefit html wsva html zscore html zscoreT html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (limma) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'DynDoc' is missing or broken done