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BioC 3.3: INSTALL report for SeqArray on moscato2

This page was generated on 2016-10-13 12:51:22 -0700 (Thu, 13 Oct 2016).

Package 1052/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqArray 1.12.9
Xiuwen Zheng
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/SeqArray
Last Changed Rev: 121528 / Revision: 122332
Last Changed Date: 2016-09-29 01:10:38 -0700 (Thu, 29 Sep 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] ERROR  skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SeqArray
Version: 1.12.9
Command: rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/SeqArray_1.12.9.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=SeqArray.buildbin-libdir --merge-multiarch SeqArray_1.12.9.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL SeqArray_1.12.9.zip && rm SeqArray_1.12.9.tar.gz SeqArray_1.12.9.zip
StartedAt: 2016-10-12 19:16:31 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 19:20:33 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 242.5 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/SeqArray_1.12.9.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=SeqArray.buildbin-libdir --merge-multiarch SeqArray_1.12.9.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL SeqArray_1.12.9.zip  && rm SeqArray_1.12.9.tar.gz SeqArray_1.12.9.zip
###
##############################################################################
##############################################################################




install for i386

* installing *source* package 'SeqArray' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c ConvToGDS.cpp -o ConvToGDS.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c FileMerge.cpp -o FileMerge.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c GetData.cpp -o GetData.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c Index.cpp -o Index.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c LinkSNPRelate.cpp -o LinkSNPRelate.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c Methods.cpp -o Methods.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_SeqArray.c -o R_SeqArray.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c ReadBySample.cpp -o ReadBySample.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c ReadByVariant.cpp -o ReadByVariant.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c SeqArray.cpp -o SeqArray.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c pkg_test.cpp -o pkg_test.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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 vectorization.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/SeqArray.buildbin-libdir/SeqArray/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'SeqArray' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c ConvToGDS.cpp -o ConvToGDS.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c FileMerge.cpp -o FileMerge.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c GetData.cpp -o GetData.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c Index.cpp -o Index.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c LinkSNPRelate.cpp -o LinkSNPRelate.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c Methods.cpp -o Methods.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_SeqArray.c -o R_SeqArray.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c ReadBySample.cpp -o ReadBySample.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c ReadByVariant.cpp -o ReadByVariant.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c SeqArray.cpp -o SeqArray.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c pkg_test.cpp -o pkg_test.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.3-bioc/R/library/gdsfmt/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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 vectorization.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/SeqArray.buildbin-libdir/SeqArray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SeqArray' as SeqArray_1.12.9.zip
* DONE (SeqArray)
* installing to library 'E:/biocbld/bbs-3.3-bioc/R/library'
package 'SeqArray' successfully unpacked and MD5 sums checked