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BioC 3.1: INSTALL report for SeqArray on moscato2

This page was generated on 2015-10-09 09:30:15 -0700 (Fri, 09 Oct 2015).

Package 887/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqArray 1.8.0
Xiuwen Zheng
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/SeqArray
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
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 ] OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SeqArray
Version: 1.8.0
Command: C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.1/bioc/src/contrib/SeqArray_1.8.0.tar.gz && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch SeqArray_1.8.0.tar.gz && rm SeqArray_1.8.0.tar.gz
StartedAt: 2015-10-08 19:01:13 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 19:02:30 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 77.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.1/bioc/src/contrib/SeqArray_1.8.0.tar.gz && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch SeqArray_1.8.0.tar.gz && rm SeqArray_1.8.0.tar.gz
###
##############################################################################
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install for i386

* installing to library 'E:/biocbld/bbs-3.1-bioc/R/library'
* installing *source* package 'SeqArray' ...
** libs
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.1-bioc/R/library/gdsfmt/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.1-bioc/R/library/gdsfmt/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
ConvVCF2GDS.cpp: In function 'SEXPREC* sqa_Parse_VCF4(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
ConvVCF2GDS.cpp:854:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.1-bioc/R/library/gdsfmt/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_SeqArray.c -o R_SeqArray.o
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.1-bioc/R/library/gdsfmt/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c ReadByVariant.cpp -o ReadByVariant.o
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.1-bioc/R/library/gdsfmt/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c SeqArray.cpp -o SeqArray.o
g++ -m32 -shared -s -static-libgcc -o SeqArray.dll tmp.def ConvGDS2VCF.o ConvVCF2GDS.o R_SeqArray.o ReadByVariant.o SeqArray.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/R/library/SeqArray/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
   'SeqArrayTutorial.Rnw' 
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing to library 'E:/biocbld/bbs-3.1-bioc/R/library'
* installing *source* package 'SeqArray' ...
** libs
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.1-bioc/R/library/gdsfmt/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.1-bioc/R/library/gdsfmt/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
ConvVCF2GDS.cpp: In function 'SEXPREC* sqa_Parse_VCF4(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
ConvVCF2GDS.cpp:854:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.1-bioc/R/library/gdsfmt/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_SeqArray.c -o R_SeqArray.o
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.1-bioc/R/library/gdsfmt/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c ReadByVariant.cpp -o ReadByVariant.o
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I. -DUSING_R   -I"E:/biocbld/bbs-3.1-bioc/R/library/gdsfmt/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c SeqArray.cpp -o SeqArray.o
g++ -m64 -shared -s -static-libgcc -o SeqArray.dll tmp.def ConvGDS2VCF.o ConvVCF2GDS.o R_SeqArray.o ReadByVariant.o SeqArray.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/R/library/SeqArray/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* DONE (SeqArray)