Back to Multiple platform build/check report for BioC 3.6
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

INSTALL report for SeqArray on tokay1

This page was generated on 2018-04-12 13:22:38 -0400 (Thu, 12 Apr 2018).

Package 1271/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqArray 1.18.2
Xiuwen Zheng
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/SeqArray
Branch: RELEASE_3_6
Last Commit: 89baf03
Last Changed Date: 2017-12-22 21:47:56 -0400 (Fri, 22 Dec 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SeqArray
Version: 1.18.2
Command: rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/SeqArray_1.18.2.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=SeqArray.buildbin-libdir --merge-multiarch SeqArray_1.18.2.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL SeqArray_1.18.2.zip && rm SeqArray_1.18.2.tar.gz SeqArray_1.18.2.zip
StartedAt: 2018-04-11 18:42:03 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 18:43:51 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 108.7 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir  && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/SeqArray_1.18.2.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=SeqArray.buildbin-libdir --merge-multiarch SeqArray_1.18.2.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL SeqArray_1.18.2.zip  && rm SeqArray_1.18.2.tar.gz SeqArray_1.18.2.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
100 1896k  100 1896k    0     0  3636k      0 --:--:-- --:--:-- --:--:-- 3661k

install for i386

* installing *source* package 'SeqArray' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c ConvToGDS.cpp -o ConvToGDS.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c FileMerge.cpp -o FileMerge.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c GetData.cpp -o GetData.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c Index.cpp -o Index.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c LinkSNPRelate.cpp -o LinkSNPRelate.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c Methods.cpp -o Methods.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c ReadBySample.cpp -o ReadBySample.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c ReadByVariant.cpp -o ReadByVariant.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c SeqArray.cpp -o SeqArray.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/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 vectorization.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-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  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSMfzfj/R.INSTALL175c375277b2/SeqArray/man/SeqVarGDSClass-class.Rd:52: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSMfzfj/R.INSTALL175c375277b2/SeqArray/man/SeqVarGDSClass-class.Rd:56: missing file link 'DNAStringSetList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSMfzfj/R.INSTALL175c375277b2/SeqArray/man/SeqVarGDSClass-class.Rd:72: missing file link 'DataFrameList'
    seqAlleleFreq                           html  
    seqApply                                html  
    finding level-2 HTML links ... done

    seqAsVCF                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSMfzfj/R.INSTALL175c375277b2/SeqArray/man/seqAsVCF.Rd:29: missing file link 'CollapsedVCF'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSMfzfj/R.INSTALL175c375277b2/SeqArray/man/seqAsVCF.Rd:34: missing file link 'VCF'
    seqBED2GDS                              html  
    seqBlockApply                           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  
    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˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c ConvToGDS.cpp -o ConvToGDS.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c FileMerge.cpp -o FileMerge.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c GetData.cpp -o GetData.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c Index.cpp -o Index.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c LinkSNPRelate.cpp -o LinkSNPRelate.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c Methods.cpp -o Methods.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c ReadBySample.cpp -o ReadBySample.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c ReadByVariant.cpp -o ReadByVariant.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c SeqArray.cpp -o SeqArray.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include"   -I"C:/local323/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 vectorization.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/SeqArray.buildbin-libdir/SeqArray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SeqArray' as SeqArray_1.18.2.zip
* DONE (SeqArray)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'SeqArray' successfully unpacked and MD5 sums checked
In R CMD INSTALL