############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/genomation_1.26.0.tar.gz && rm -rf genomation.buildbin-libdir && mkdir genomation.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genomation.buildbin-libdir genomation_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL genomation_1.26.0.zip && rm genomation_1.26.0.tar.gz genomation_1.26.0.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 21 4098k 21 868k 0 0 1051k 0 0:00:03 --:--:-- 0:00:03 1051k 66 4098k 66 2719k 0 0 1507k 0 0:00:02 0:00:01 0:00:01 1507k 100 4098k 100 4098k 0 0 1740k 0 0:00:02 0:00:02 --:--:-- 1741k install for i386 * installing *source* package 'genomation' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c binSum.cpp -o binSum.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o genomation.dll tmp.def RcppExports.o binSum.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/genomation.buildbin-libdir/00LOCK-genomation/00new/genomation/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' ** help *** installing help indices converting help for package 'genomation' finding HTML links ... done AnnotationByFeature-class html AnnotationByGeneParts-class html AnnotationByGeneParts-methods html Max_c html Mean_c html Median_c html Min_c html Ops-ScoreMatrix-ScoreMatrix-method html Ops-ScoreMatrixList-ScoreMatrixList-method html Ops-ScoreMatrixList-numeric-method html Ops-numeric-ScoreMatrixList-method html RandomEnrichment-class html ScoreMatrix-class html ScoreMatrix-methods html ScoreMatrixBin-methods html ScoreMatrixList-class html ScoreMatrixList-methods html Sum_c html annotatGrWithGeneParts html annotateWithFeature-methods html annotateWithFeatureFlank-methods html annotateWithFeatures-methods html annotateWithGeneParts-methods html finding level-2 HTML links ... done bed12ToExons html bed12ToIntrons html binMatrix-methods html binMax html binMean html binMedian html binMin html binSum html binner html c.ScoreMatrix html c.ScoreMatrixList html cage html calculateOverlapSignificance-methods html checkBedValidity html checkClass html compressedAndUrl2temp html constrainRanges html convertBed2Exons-methods html convertBed2Introns-methods html convertBedDf-methods html cpgi html detectUCSCheader html distance2NearestFeature html enrichmentMatrix-ScoreMatrix-method html enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method html enrichmentMatrix-ScoreMatrixList-method html file.ext html findFeatureComb-methods html galpTo2Ranges html genes html getColors html getFeatsWithTargetsStats-methods html getFlanks-methods html getMembers-methods html getRandomEnrichment-methods html getTargetAnnotationStats-methods html gffToGRanges html heatMatrix html heatMeta html heatTargetAnnotation-methods html intersectScoreMatrixList-methods html listSliceMax html listSliceMean html listSliceMedian html listSliceMin html listSliceSum html multiHeatMatrix html orderBy-methods html patternMatrix-methods html plotMeta html plotTargetAnnotation-methods html promoters html randomizeFeature-methods html read.zip html readBam html readBed html readBigWig html readBroadPeak html readFeatureFlank-methods html readGeneric html readNarrowPeak html readTableFast html readTranscriptFeatures-methods html scaleScoreMatrix-methods html scaleScoreMatrixList html show-methods html sub-ScoreMatrix-ANY-ANY-ANY-method html sub-ScoreMatrixList-ANY-ANY-ANY-method html target.type html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' ** testing if installed package can be loaded from final location Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'genomation' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c binSum.cpp -o binSum.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o genomation.dll tmp.def RcppExports.o binSum.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/genomation.buildbin-libdir/genomation/libs/x64 ** testing if installed package can be loaded Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' * MD5 sums packaged installation of 'genomation' as genomation_1.26.0.zip * DONE (genomation) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'genomation' successfully unpacked and MD5 sums checked