Package: BioQC

Version: 1.12.0

Command: rm -rf BioQC.buildbin-libdir && mkdir BioQC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BioQC_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R BioQC.buildbin-libdir

StartedAt: 2019-10-01 08:03:54 -0400 (Tue, 01 Oct 2019)

EndedAt: 2019-10-01 08:04:25 -0400 (Tue, 01 Oct 2019)

EllapsedTime: 30.6 seconds

RetCode: 0

Status:  OK

PackageFile: BioQC_1.12.0.tgz

PackageFileSize: 322.4 KiB

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### Running command:
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###   rm -rf BioQC.buildbin-libdir && mkdir BioQC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BioQC_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R BioQC.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BioQC.buildbin-libdir BioQC_1.12.0.tar.gz'
>>>>>>> 

* installing *source* package ‘BioQC’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'`  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c gini.c -o gini.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'`  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c init.c -o init.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'`  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c read_gmt.cpp -o read_gmt.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'`  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c stat_rank.c -o stat_rank.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'`  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c wmw_test.c -o wmw_test.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 BioQC.so gini.o init.o read_gmt.o stat_rank.o wmw_test.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/BioQC.buildbin-libdir/00LOCK-BioQC/00new/BioQC/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: /private/tmp/RtmpcEL8EV/R.INSTALLef0917f6a647/BioQC/man/IndexList.Rd:6: All text must be in a section
Warning: /private/tmp/RtmpcEL8EV/R.INSTALLef0917f6a647/BioQC/man/IndexList.Rd:7: All text must be in a section
Warning: /private/tmp/RtmpcEL8EV/R.INSTALLef0917f6a647/BioQC/man/IndexList.Rd:9: All text must be in a section
*** 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 (BioQC)


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