############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf affy.buildbin-libdir && mkdir affy.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affy.buildbin-libdir affy_1.70.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'affy' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** 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 -DHAVE_ZLIB -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 -DHAVE_ZLIB -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 getall_locations.c -o getall_locations.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 -DHAVE_ZLIB -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 -DHAVE_ZLIB -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 -DHAVE_ZLIB -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 -shared -s -static-libgcc -o affy.dll tmp.def chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -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/affy.buildbin-libdir/00LOCK-affy/00new/affy/libs/i386 ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'affy' finding HTML links ... done AffyBatch-class html finding level-2 HTML links ... done AffyRNAdeg html MAplot html ProbeSet-class html ProgressBarText-class html SpikeIn html affy-deprecated html affy-options html affy.scalevalue.exprSet html barplot.ProbeSet html bg.adjust html bgc html cdfFromBioC html cdfenv.example html cleancdfname html debug.affy123 html expresso html expressoWidget html fit.li.wong html generateExprSet-methods html generateExprVal-methods html generateExprVal.method.avgdiff html generateExprVal.method.playerout html hlog html justrma html list.celfiles html maffy.subset html mas5 html mas5calls html merge.AffyBatch html mva.pairs html normalize-methods html normalize.constant html normalize.contrast html normalize.invariantset html normalize.loess html normalize.qspline html normalize.quantiles html normalize.quantiles.robust html pairs.AffyBatch html plot.ProbeSet html plot.density html plotLocation html pmcorrect html ppsetApply html probeMatch-methods html probeNames-methods html read.affybatch html read.probematrix html rma html setAffyOptions html summary html tukey.biweight html whatcdf html xy2indices 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 'affy' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** 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 -DHAVE_ZLIB -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 -DHAVE_ZLIB -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 getall_locations.c -o getall_locations.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 -DHAVE_ZLIB -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 -DHAVE_ZLIB -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 -DHAVE_ZLIB -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 -shared -s -static-libgcc -o affy.dll tmp.def chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -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/affy.buildbin-libdir/affy/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'affy' as affy_1.70.0.zip * DONE (affy)