Package: sigPathway

Version: 1.52.0

Command: rm -rf sigPathway.buildbin-libdir && mkdir sigPathway.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sigPathway_1.52.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R sigPathway.buildbin-libdir

StartedAt: 2019-10-16 09:26:01 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 09:26:12 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 11.5 seconds

RetCode: 0

Status:  OK

PackageFile: sigPathway_1.52.0.tgz

PackageFileSize: 707.5 KiB

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### Running command:
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###   rm -rf sigPathway.buildbin-libdir && mkdir sigPathway.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sigPathway_1.52.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R sigPathway.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=sigPathway.buildbin-libdir sigPathway_1.52.0.tar.gz'
>>>>>>> 

* installing *source* package ‘sigPathway’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c calc_gene_set_internal.c -o calc_gene_set_internal.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c calc_gene_set_stat.c -o calc_gene_set_stat.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c calc_probe_stat.c -o calc_probe_stat.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c calc_weights.c -o calc_weights.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c matrix_fn.c -o matrix_fn.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c permute.c -o permute.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c shuffle.c -o shuffle.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c sigPathway.c -o sigPathway.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 sigPathway.so calc_gene_set_internal.o calc_gene_set_stat.o calc_probe_stat.o calc_weights.o matrix_fn.o permute.o shuffle.o sigPathway.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -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/sigPathway.buildbin-libdir/00LOCK-sigPathway/00new/sigPathway/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sigPathway)


>>>>>>> 
>>>>>>> FIXING LINKS FOR sigPathway.buildbin-libdir/sigPathway/libs//sigPathway.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" "sigPathway.buildbin-libdir/sigPathway/libs//sigPathway.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "sigPathway.buildbin-libdir/sigPathway/libs//sigPathway.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" "sigPathway.buildbin-libdir/sigPathway/libs//sigPathway.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "sigPathway.buildbin-libdir/sigPathway/libs//sigPathway.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "sigPathway.buildbin-libdir/sigPathway/libs//sigPathway.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "sigPathway.buildbin-libdir/sigPathway/libs//sigPathway.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "sigPathway.buildbin-libdir/sigPathway/libs//sigPathway.so"