Xiuwen Zheng
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SeqArray |
| Branch: RELEASE_3_8 |
| Last Commit: 585cb72 |
| Last Changed Date: 2019-03-10 01:42:10 -0400 (Sun, 10 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:22:44 -0400 (Sat, 13 Apr 2019).
| Package 1416/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SeqArray 1.22.6 Xiuwen Zheng
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SeqArray |
| Version: 1.22.6 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/SeqArray_1.22.6.tar.gz && rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SeqArray.buildbin-libdir SeqArray_1.22.6.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL SeqArray_1.22.6.zip && rm SeqArray_1.22.6.tar.gz SeqArray_1.22.6.zip |
| StartedAt: 2019-04-12 19:48:39 -0400 (Fri, 12 Apr 2019) |
| EndedAt: 2019-04-12 19:50:16 -0400 (Fri, 12 Apr 2019) |
| EllapsedTime: 96.7 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/SeqArray_1.22.6.tar.gz && rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SeqArray.buildbin-libdir SeqArray_1.22.6.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL SeqArray_1.22.6.zip && rm SeqArray_1.22.6.tar.gz SeqArray_1.22.6.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1912k 100 1912k 0 0 28.3M 0 --:--:-- --:--:-- --:--:-- 30.1M
install for i386
* installing *source* package 'SeqArray' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvToGDS.cpp -o ConvToGDS.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c FileMerge.cpp -o FileMerge.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c GetData.cpp -o GetData.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Index.cpp -o Index.o
Index.cpp: In member function 'SeqArray::TSelection::TSampStruct* SeqArray::TSelection::GetStructSample()':
Index.cpp:658:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (num_samp*numPloidy != num)
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c LinkSNPRelate.cpp -o LinkSNPRelate.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Methods.cpp -o Methods.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_SeqArray.c -o R_SeqArray.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ReadBySample.cpp -o ReadBySample.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ReadByVariant.cpp -o ReadByVariant.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c SeqArray.cpp -o SeqArray.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pkg_test.cpp -o pkg_test.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c samtools_ext.c -o samtools_ext.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c vectorization.c -o vectorization.o
C:/Rtools/mingw_32/bin/g++ -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 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˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/SeqArray.buildbin-libdir/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
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
seqSNP2GDS html
seqSetFilter html
seqSetFilterCond html
seqStorageOption html
seqSummary html
seqSystem html
seqTranspose html
seqVCF2GDS html
seqVCF_Header html
seqVCF_SampID html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'SeqArray' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvToGDS.cpp -o ConvToGDS.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c FileMerge.cpp -o FileMerge.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c GetData.cpp -o GetData.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Index.cpp -o Index.o
Index.cpp: In member function 'SeqArray::TSelection::TSampStruct* SeqArray::TSelection::GetStructSample()':
Index.cpp:658:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (num_samp*numPloidy != num)
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c LinkSNPRelate.cpp -o LinkSNPRelate.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Methods.cpp -o Methods.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_SeqArray.c -o R_SeqArray.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ReadBySample.cpp -o ReadBySample.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ReadByVariant.cpp -o ReadByVariant.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c SeqArray.cpp -o SeqArray.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pkg_test.cpp -o pkg_test.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c samtools_ext.c -o samtools_ext.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c vectorization.c -o vectorization.o
C:/Rtools/mingw_64/bin/g++ -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 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˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/SeqArray.buildbin-libdir/SeqArray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SeqArray' as SeqArray_1.22.6.zip
* DONE (SeqArray)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'SeqArray' successfully unpacked and MD5 sums checked
In R CMD INSTALL