Package: RSeqAn

Version: 1.4.0

Command: rm -rf RSeqAn.buildbin-libdir && mkdir RSeqAn.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RSeqAn_1.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R RSeqAn.buildbin-libdir

StartedAt: 2019-10-16 09:19:47 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 09:20:13 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 25.6 seconds

RetCode: 0

Status:  OK

PackageFile: RSeqAn_1.4.0.tgz

PackageFileSize: 1.669 MiB

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### Running command:
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###   rm -rf RSeqAn.buildbin-libdir && mkdir RSeqAn.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RSeqAn_1.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R RSeqAn.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=RSeqAn.buildbin-libdir RSeqAn_1.4.0.tar.gz'
>>>>>>> 

* installing *source* package ‘RSeqAn’ ...
** using staged installation
** libs
clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c charstring.cpp -o charstring.o
clang++ -std=gnu++14 -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 RSeqAn.so RcppExports.o charstring.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/RSeqAn.buildbin-libdir/00LOCK-RSeqAn/00new/RSeqAn/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 (RSeqAn)


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