Xiuwen Zheng
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/SeqArray |
| Branch: RELEASE_3_12 |
| Last Commit: 6a9e919 |
| Last Changed Date: 2020-10-27 10:49:50 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:33:33 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the SeqArray package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1675/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SeqArray 1.30.0 (landing page) Xiuwen Zheng
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SeqArray |
| Version: 1.30.0 |
| Command: C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SeqArray_1.30.0.tar.gz && rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SeqArray.buildbin-libdir SeqArray_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SeqArray_1.30.0.zip && rm SeqArray_1.30.0.tar.gz SeqArray_1.30.0.zip |
| StartedAt: 2021-05-05 17:04:19 -0400 (Wed, 05 May 2021) |
| EndedAt: 2021-05-05 17:05:38 -0400 (Wed, 05 May 2021) |
| EllapsedTime: 79.1 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SeqArray_1.30.0.tar.gz && rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SeqArray.buildbin-libdir SeqArray_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SeqArray_1.30.0.zip && rm SeqArray_1.30.0.tar.gz SeqArray_1.30.0.zip
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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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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
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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/SeqArray.buildbin-libdir/SeqArray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SeqArray' as SeqArray_1.30.0.zip
* DONE (SeqArray)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'SeqArray' successfully unpacked and MD5 sums checked