############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/genoset_1.48.0.tar.gz && rm -rf genoset.buildbin-libdir && mkdir genoset.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genoset.buildbin-libdir genoset_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL genoset_1.48.0.zip && rm genoset_1.48.0.tar.gz genoset_1.48.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 108k 100 108k 0 0 566k 0 --:--:-- --:--:-- --:--:-- 569k install for i386 * installing *source* package 'genoset' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bounds.c -o bounds.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rangeSummaries.c -o rangeSummaries.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o genoset.dll tmp.def bounds.o init.o rangeSummaries.o utils.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/genoset.buildbin-libdir/00LOCK-genoset/00new/genoset/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'genoset' finding HTML links ... done GenoSet-class html finding level-2 HTML links ... done RleDataFrame-class html RleDataFrame-views html baf2mbaf html boundingIndices html boundingIndicesByChr html bounds2Rle html calcGC html calcGC2 html chr-methods html chrIndices-methods html chrInfo-methods html chrNames-methods html chrOrder html chrPartitioning html cn2lr-methods html do_rledf_range_summary html do_rledf_views html fixSegNAs html gcCorrect html genoPlot-methods html genoPos-methods html genome html genomeAxis html genomicranges-methods html genoset-dataset html genoset-methods html genoset-package html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/genoset.buildbin-libdir/00LOCK-genoset/00new/genoset/help/genoset.html genoset-subset html isGenomeOrder html lr2cn html modeCenter html numCallable html pos-methods html rangeSampleMeans html rangeSegMeanLength-methods html rbindDataframe html readGenoSet html runCBS html segPairTable-methods html segTable-methods html segs2Granges html segs2Rle html segs2RleDataFrame html toGenomeOrder html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: Package 'genoset' is deprecated and will be removed from Bioconductor version 3.14 ** testing if installed package can be loaded from final location Warning: Package 'genoset' is deprecated and will be removed from Bioconductor version 3.14 ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'genoset' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bounds.c -o bounds.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rangeSummaries.c -o rangeSummaries.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o genoset.dll tmp.def bounds.o init.o rangeSummaries.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/genoset.buildbin-libdir/genoset/libs/x64 ** testing if installed package can be loaded Warning: Package 'genoset' is deprecated and will be removed from Bioconductor version 3.14 * MD5 sums packaged installation of 'genoset' as genoset_1.48.0.zip * DONE (genoset) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'genoset' successfully unpacked and MD5 sums checked