############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Biobase_2.54.0.tar.gz && rm -rf Biobase.buildbin-libdir && mkdir Biobase.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Biobase.buildbin-libdir Biobase_2.54.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Biobase_2.54.0.zip && rm Biobase_2.54.0.tar.gz Biobase_2.54.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 47 1152k 47 546k 0 0 734k 0 0:00:01 --:--:-- 0:00:01 735k 100 1152k 100 1152k 0 0 968k 0 0:00:01 0:00:01 --:--:-- 969k install for i386 * installing *source* package 'Biobase' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c anyMissing.c -o anyMissing.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c envir.c -o envir.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matchpt.c -o matchpt.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rowMedians.c -o rowMedians.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sublist_extract.c -o sublist_extract.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o Biobase.dll tmp.def Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/Biobase.buildbin-libdir/00LOCK-Biobase/00new/Biobase/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'Biobase' finding HTML links ... done Aggregate html Biobase-package html ScalarObject-class html abstract html addVig2Menu html annotatedDataFrameFrom-methods html anyMissing html assayData html cache html channel html channelNames html class.AnnotatedDataFrame html finding level-2 HTML links ... done class.AssayData html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/Biobase.buildbin-libdir/00LOCK-Biobase/00new/Biobase/help/AssayData.html class.ExpressionSet html class.MIAME html class.MIAxE html class.MultiSet html class.NChannelSet html class.SnpSet html class.Versioned html class.VersionedBiobase html class.Versions html class.VersionsNull html class.aggregator html class.characterORmiame html class.container html class.eSet html classVersion html contents html copyEnv html copySubstitute html createPackage html data.aaMap html data.geneData html data.reporter html data.sample.ExpressionSet html data.sample.MultiSet html defunct html description html dumpPackTxt html esApply html exprs html featureData html featureNames html getPkgVigs html internals html isCurrent html isUnique html isVersioned html lcSuffix html listLen html makeDataPackage html matchpt html multiassign html note html notes html openPDF html openVignette html package.version html phenoData html protocolData html read.AnnotatedDataFrame html read.MIAME html readExpressionSet html reverseSplit html rowMedians html rowQ html selectChannels html selectSome html snpCall html storageMode html strbreak html subListExtract html testBioCConnection html updateObjectTo html updateOldESet html userQuery html validMsg 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 install for x64 * installing *source* package 'Biobase' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c anyMissing.c -o anyMissing.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c envir.c -o envir.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matchpt.c -o matchpt.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rowMedians.c -o rowMedians.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sublist_extract.c -o sublist_extract.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o Biobase.dll tmp.def Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/Biobase.buildbin-libdir/Biobase/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'Biobase' as Biobase_2.54.0.zip * DONE (Biobase) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'Biobase' successfully unpacked and MD5 sums checked