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BioC 3.2: BUILD BIN report for SNPRelate on perceval

This page was generated on 2015-10-27 17:36:36 -0400 (Tue, 27 Oct 2015).

Package 994/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPRelate 1.4.0
Xiuwen Zheng
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/SNPRelate
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SNPRelate
Version: 1.4.0
Command: rm -rf SNPRelate.buildbin-libdir && mkdir SNPRelate.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SNPRelate_1.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SNPRelate.buildbin-libdir
StartedAt: 2015-10-27 12:44:22 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 12:44:59 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 36.9 seconds
RetCode: 0
Status:  OK 
PackageFile: SNPRelate_1.4.0.tgz
PackageFileSize: 3.283 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SNPRelate.buildbin-libdir && mkdir SNPRelate.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SNPRelate_1.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SNPRelate.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SNPRelate.buildbin-libdir SNPRelate_1.4.0.tar.gz'
>>>>>>> 

* installing *source* package ‘SNPRelate’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ConvToGDS.cpp -o ConvToGDS.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_SNPRelate.c -o R_SNPRelate.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c SNPRelate.cpp -o SNPRelate.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c dGenGWAS.cpp -o dGenGWAS.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c dVect.cpp -o dVect.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genFst.cpp -o genFst.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genHWE.cpp -o genHWE.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genIBD.cpp -o genIBD.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genIBS.cpp -o genIBS.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genKING.cpp -o genKING.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genLD.cpp -o genLD.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genPCA.cpp -o genPCA.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genRec.cpp -o genRec.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genSlideWin.cpp -o genSlideWin.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o SNPRelate.so ConvToGDS.o R_SNPRelate.o SNPRelate.o dGenGWAS.o dVect.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genRec.o genSlideWin.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/SNPRelate.buildbin-libdir/SNPRelate/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SNPRelate)


>>>>>>> 
>>>>>>> FIXING LINKS FOR SNPRelate.buildbin-libdir/SNPRelate/libs//SNPRelate.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgcc_s.1.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs//SNPRelate.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.2.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs//SNPRelate.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs//SNPRelate.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs//SNPRelate.so"