############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/oligo_1.56.0.tar.gz && rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=oligo.buildbin-libdir oligo_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL oligo_1.56.0.zip && rm oligo_1.56.0.tar.gz oligo_1.56.0.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 6 14.9M 6 992k 0 0 1561k 0 0:00:09 --:--:-- 0:00:09 1560k 23 14.9M 23 3643k 0 0 2230k 0 0:00:06 0:00:01 0:00:05 2230k 37 14.9M 37 5663k 0 0 2144k 0 0:00:07 0:00:02 0:00:05 2145k 54 14.9M 54 8313k 0 0 2285k 0 0:00:06 0:00:03 0:00:03 2285k 77 14.9M 77 11.6M 0 0 2566k 0 0:00:05 0:00:04 0:00:01 2565k 100 14.9M 100 14.9M 0 0 2836k 0 0:00:05 0:00:05 --:--:-- 3007k install for i386 * installing *source* package 'oligo' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DABG.c -o DABG.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ParserGzXYS.c -o ParserGzXYS.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ParserXYS.c -o ParserXYS.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c baseProfile.c -o baseProfile.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c basecontent.c -o basecontent.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chipbackground.c -o chipbackground.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mas5calls.c -o mas5calls.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma2.c -o rma2.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma_common.c -o rma_common.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c trimmed.c -o trimmed.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o oligo.dll tmp.def DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -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/oligo.buildbin-libdir/00LOCK-oligo/00new/oligo/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading Note: in method for 'pm<-' with signature 'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"': expanding the signature to include omitted arguments in definition: subset = "missing", target = "missing" Note: in method for 'mm<-' with signature 'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"': expanding the signature to include omitted arguments in definition: subset = "missing", target = "missing" ** help *** installing help indices converting help for package 'oligo' finding HTML links ... done Index-methods html IntensityMatrix-methods html MAplot-methods html Sequences-methods html basecontent html basicPLM html basicRMA html boxplot html chromosome html colors html coordinates html crlmm html fitProbeLevelModel html getAffinitySplineCoefficients html getBaseProfile html getContainer html getCrlmmSummaries html getNetAffx html getNgsColorsInfo html getPlatformDesign html getProbeInfo html hist html image html justSNPRMA html list.xysfiles html oligo-package html oligoDefunct html oligoPLM-class html paCalls html plotM-methods html pmAllele html pmFragmentLength html pmPosition html pmStrand html preprocessTools html probeNames html read.celfiles html read.xysfiles html readSummaries html rma-methods html runDate html sequenceDesignMatrix html snprma 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 'oligo' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DABG.c -o DABG.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ParserGzXYS.c -o ParserGzXYS.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ParserXYS.c -o ParserXYS.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c baseProfile.c -o baseProfile.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c basecontent.c -o basecontent.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chipbackground.c -o chipbackground.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mas5calls.c -o mas5calls.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma2.c -o rma2.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma_common.c -o rma_common.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c trimmed.c -o trimmed.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o oligo.dll tmp.def DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -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/oligo.buildbin-libdir/oligo/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'oligo' as oligo_1.56.0.zip * DONE (oligo) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'oligo' successfully unpacked and MD5 sums checked