Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:22 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the SeqArray package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SeqArray.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1731/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SeqArray 1.32.0 (landing page) Xiuwen Zheng
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: SeqArray |
Version: 1.32.0 |
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/SeqArray_1.32.0.tar.gz && rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SeqArray.buildbin-libdir SeqArray_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SeqArray_1.32.0.zip && rm SeqArray_1.32.0.tar.gz SeqArray_1.32.0.zip |
StartedAt: 2021-10-14 07:44:31 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 07:49:02 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 271.5 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/SeqArray_1.32.0.tar.gz && rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SeqArray.buildbin-libdir SeqArray_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SeqArray_1.32.0.zip && rm SeqArray_1.32.0.tar.gz SeqArray_1.32.0.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 5 1932k 5 99685 0 0 505k 0 0:00:03 --:--:-- 0:00:03 504k 100 1932k 100 1932k 0 0 4566k 0 --:--:-- --:--:-- --:--:-- 4568k 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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/SeqArray.buildbin-libdir/SeqArray/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'SeqArray' as SeqArray_1.32.0.zip * DONE (SeqArray) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'SeqArray' successfully unpacked and MD5 sums checked