############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/crlmm_1.52.0.tar.gz && rm -rf crlmm.buildbin-libdir && mkdir crlmm.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=crlmm.buildbin-libdir crlmm_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL crlmm_1.52.0.zip && rm crlmm_1.52.0.tar.gz crlmm_1.52.0.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 12 3494k 12 433k 0 0 604k 0 0:00:05 --:--:-- 0:00:05 604k 52 3494k 52 1823k 0 0 1061k 0 0:00:03 0:00:01 0:00:02 1061k 100 3494k 100 3494k 0 0 1414k 0 0:00:02 0:00:02 --:--:-- 1414k install for i386 * installing *source* package 'crlmm' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gtypeCaller.c -o gtypeCaller.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-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 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -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 crlmm.dll tmp.def gtypeCaller.o init.o trimmed.o utils.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/crlmm.buildbin-libdir/00LOCK-crlmm/00new/crlmm/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' ** help *** installing help indices converting help for package 'crlmm' finding HTML links ... done ABpanel html AssayData-methods html finding level-2 HTML links ... done CNSet-methods html ListClassConstructors html PredictionRegion-class html batchStatisticAccessors html calculateRBaf html celfile-utils html cnSetExample html cnrmaAffy html constructAffyCNSet html constructInf html copynumberAccessors html crlmm-package html crlmm html crlmmCopynumber html genotype.Illumina html genotype html genotypeAffy html genotypeInf html genotypes html plotSNPs html posteriorProbability html predictionRegion html preprocessInf html readGenCallOutput html readIdatFiles html snprma html snprmaAffy html validCdfNames html xyplot html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' ** testing if installed package can be loaded from final location No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'crlmm' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gtypeCaller.c -o gtypeCaller.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-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 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -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 crlmm.dll tmp.def gtypeCaller.o init.o trimmed.o utils.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/crlmm.buildbin-libdir/crlmm/libs/x64 ** testing if installed package can be loaded No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' * MD5 sums packaged installation of 'crlmm' as crlmm_1.52.0.zip * DONE (crlmm) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'crlmm' successfully unpacked and MD5 sums checked