############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SeqArray_1.34.0.tar.gz && rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SeqArray.buildbin-libdir SeqArray_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SeqArray_1.34.0.zip && rm SeqArray_1.34.0.tar.gz SeqArray_1.34.0.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 0 1930k 0 15987 0 0 118k 0 0:00:16 --:--:-- 0:00:16 119k 47 1930k 47 923k 0 0 815k 0 0:00:02 0:00:01 0:00:01 815k 100 1930k 100 1930k 0 0 1115k 0 0:00:01 0:00:01 --:--:-- 1115k install for i386 * installing *source* package 'SeqArray' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConvToGDS.cpp -o ConvToGDS.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FileMerge.cpp -o FileMerge.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GetData.cpp -o GetData.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Index.cpp -o Index.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LinkSNPRelate.cpp -o LinkSNPRelate.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Methods.cpp -o Methods.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_SeqArray.c -o R_SeqArray.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadBySample.cpp -o ReadBySample.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadByUnit.cpp -o ReadByUnit.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadByVariant.cpp -o ReadByVariant.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SeqArray.cpp -o SeqArray.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pkg_test.cpp -o pkg_test.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c samtools_ext.c -o samtools_ext.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vectorization.c -o vectorization.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SeqArray.dll tmp.def ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByUnit.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.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/SeqArray.buildbin-libdir/00LOCK-SeqArray/00new/SeqArray/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'SeqArray' finding HTML links ... done KG_P1_SampData html SeqArray-package html SeqVarGDSClass-class html finding level-2 HTML links ... done seqAddValue html seqAlleleFreq html seqApply html seqAsVCF html seqBED2GDS html seqBlockApply html seqCheck html seqClose html seqDelete html seqDigest html seqExampleFileName html seqExport html seqGDS2SNP html seqGDS2VCF html seqGetData html seqGetFilter html seqMerge html seqMissing html seqNewVarData html seqNumAllele html seqOpen html seqOptimize html seqParallel html seqParallelSetup html seqRecompress html seqResetVariantID html seqSNP2GDS html seqSetFilter html seqSetFilterCond html seqStorageOption html seqSummary html seqSystem html seqTranspose html seqUnitApply html seqUnitFilterCond html seqUnitSlidingWindows html seqVCF2GDS html seqVCF_Header html seqVCF_SampID 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 'SeqArray' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConvToGDS.cpp -o ConvToGDS.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FileMerge.cpp -o FileMerge.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GetData.cpp -o GetData.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Index.cpp -o Index.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LinkSNPRelate.cpp -o LinkSNPRelate.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Methods.cpp -o Methods.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_SeqArray.c -o R_SeqArray.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadBySample.cpp -o ReadBySample.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadByUnit.cpp -o ReadByUnit.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadByVariant.cpp -o ReadByVariant.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SeqArray.cpp -o SeqArray.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pkg_test.cpp -o pkg_test.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c samtools_ext.c -o samtools_ext.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vectorization.c -o vectorization.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SeqArray.dll tmp.def ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByUnit.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.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/SeqArray.buildbin-libdir/SeqArray/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'SeqArray' as SeqArray_1.34.0.zip * DONE (SeqArray) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'SeqArray' successfully unpacked and MD5 sums checked