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BioC 3.5: BUILD BIN report for SeqArray on toluca2

This page was generated on 2017-04-23 14:37:12 -0400 (Sun, 23 Apr 2017).

Package 1195/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqArray 1.15.6
Xiuwen Zheng
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SeqArray
Last Changed Rev: 128808 / Revision: 129046
Last Changed Date: 2017-04-17 22:21:24 -0400 (Mon, 17 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK [ OK ]
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SeqArray
Version: 1.15.6
Command: rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SeqArray_1.15.6.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SeqArray.buildbin-libdir
StartedAt: 2017-04-23 12:43:33 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 12:44:10 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 37.4 seconds
RetCode: 0
Status:  OK 
PackageFile: SeqArray_1.15.6.tgz
PackageFileSize: 4.116 MiB

Command output

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###
### Running command:
###
###   rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SeqArray_1.15.6.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SeqArray.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SeqArray.buildbin-libdir SeqArray_1.15.6.tar.gz'
>>>>>>> 

* installing *source* package ‘SeqArray’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ConvToGDS.cpp -o ConvToGDS.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c FileMerge.cpp -o FileMerge.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c GetData.cpp -o GetData.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c Index.cpp -o Index.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c LinkSNPRelate.cpp -o LinkSNPRelate.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c Methods.cpp -o Methods.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c R_SeqArray.c -o R_SeqArray.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ReadBySample.cpp -o ReadBySample.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ReadByVariant.cpp -o ReadByVariant.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c SeqArray.cpp -o SeqArray.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c pkg_test.cpp -o pkg_test.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c vectorization.c -o vectorization.o
clang++ -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 -o SeqArray.so 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/SeqArray.buildbin-libdir/SeqArray/libs
** 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
* DONE (SeqArray)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.so"