############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/maftools_2.8.05.tar.gz && rm -rf maftools.buildbin-libdir && mkdir maftools.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=maftools.buildbin-libdir maftools_2.8.05.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL maftools_2.8.05.zip && rm maftools_2.8.05.tar.gz maftools_2.8.05.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 19 6612k 19 1312k 0 0 1862k 0 0:00:03 --:--:-- 0:00:03 1862k 66 6612k 66 4428k 0 0 2608k 0 0:00:02 0:00:01 0:00:01 2607k 100 6612k 100 6612k 0 0 2922k 0 0:00:02 0:00:02 --:--:-- 2923k install for i386 * installing *source* package 'maftools' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ntcounts.c -o ntcounts.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c somaticfreq.c -o somaticfreq.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o maftools.dll tmp.def ntcounts.o somaticfreq.o C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -Lc:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -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/maftools.buildbin-libdir/00LOCK-maftools/00new/maftools/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'maftools' finding HTML links ... done GISTIC-class html MAF-class html MAF html OncogenicPathways html PlotOncogenicPathways html annovarToMaf html bamreadcounts html cancerhotspots html clinicalEnrichment html coBarplot html coOncoplot html compareSignatures html drugInteractions html estimateSignatures html extractSignatures html filterMaf html forestPlot html genesToBarcodes html genotypeMatrix html getClinicalData html getCytobandSummary html getFields html getGeneSummary html getSampleSummary html gisticBubblePlot html gisticChromPlot html gisticOncoPlot html icgcSimpleMutationToMAF html inferHeterogeneity html lollipopPlot html lollipopPlot2 html maf2mae html mafCompare html mafSummary html mafSurvGroup html mafSurvival html mafbarplot html math.score html merge_mafs html mutCountMatrix html oncodrive html oncoplot html oncostrip html pfamDomains html plotApobecDiff html plotCBSsegments html plotClusters html plotCophenetic html plotEnrichmentResults html plotOncodrive html plotProtein html plotSignatures html plotTiTv html plotVaf html plotmafSummary html prepareMutSig html rainfallPlot html read.maf html readGistic html setMaf html signatureEnrichment html somaticInteractions html subsetMaf html finding level-2 HTML links ... done survGroup html tcgaAvailable html tcgaCompare html tcgaDriverBP html tcgaLoad html titv html tmb html trinucleotideMatrix html vafCompare html write.GisticSummary html write.mafSummary 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 'maftools' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ntcounts.c -o ntcounts.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c somaticfreq.c -o somaticfreq.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o maftools.dll tmp.def ntcounts.o somaticfreq.o C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -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/maftools.buildbin-libdir/maftools/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'maftools' as maftools_2.8.05.zip * DONE (maftools) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'maftools' successfully unpacked and MD5 sums checked