Package: SAIGEgds

Version: 1.0.2

Command: rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SAIGEgds_1.0.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SAIGEgds.buildbin-libdir

StartedAt: 2020-04-15 08:39:36 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 08:40:29 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 52.6 seconds

RetCode: 0

Status:  OK

PackageFile: SAIGEgds_1.0.2.tgz

PackageFileSize: 1.922 MiB

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### Running command:
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###   rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SAIGEgds_1.0.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SAIGEgds.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SAIGEgds.buildbin-libdir SAIGEgds_1.0.2.tar.gz'
>>>>>>> 

* installing *source* package ‘SAIGEgds’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c SPATest.cpp -o SPATest.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c saige_fitnull.cpp -o saige_fitnull.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c saige_main.cpp -o saige_main.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c vectorization.cpp -o vectorization.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 SAIGEgds.so SPATest.o saige_fitnull.o saige_main.o vectorization.o -lm -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-3.10-bioc/meat/SAIGEgds.buildbin-libdir/00LOCK-SAIGEgds/00new/SAIGEgds/libs
** R
** 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 (SAIGEgds)


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