Package: GeneticsPed

Version: 1.45.0

Command: rm -rf GeneticsPed.buildbin-libdir && mkdir GeneticsPed.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GeneticsPed_1.45.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GeneticsPed.buildbin-libdir

StartedAt: 2019-04-09 05:25:51 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:27:09 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 77.3 seconds

RetCode: 0

Status:  OK

PackageFile: GeneticsPed_1.45.0.tgz

PackageFileSize: 655.1 KiB

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### Running command:
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###   rm -rf GeneticsPed.buildbin-libdir && mkdir GeneticsPed.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GeneticsPed_1.45.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GeneticsPed.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GeneticsPed.buildbin-libdir GeneticsPed_1.45.0.tar.gz'
>>>>>>> 

* installing *source* package ‘GeneticsPed’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ainverse.cc -o ainverse.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c eibd.cc -o eibd.o
gfortran   -fPIC  -g -O2  -c ggmatmult.f -o ggmatmult.o
gfortran   -fPIC  -g -O2  -c gpi.f -o gpi.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c inbreed.cc -o inbreed.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c inverseAdditive.cc -o inverseAdditive.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c meuwissen.cc -o meuwissen.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pedSort.cc -o pedSort.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pedtemplate.cc -o pedtemplate.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c register.cc -o register.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c sargolzaei.c -o sargolzaei.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c sortped.cc -o sortped.o
clang++ -std=gnu++11 -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 GeneticsPed.so ainverse.o eibd.o ggmatmult.o gpi.o inbreed.o inverseAdditive.o meuwissen.o pedSort.o pedtemplate.o register.o sargolzaei.o sortped.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/GeneticsPed.buildbin-libdir/GeneticsPed/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 (GeneticsPed)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs//GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs//GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs//GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs//GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs//GeneticsPed.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs//GeneticsPed.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs//GeneticsPed.so"