Package: GOSim

Version: 1.22.0

Command: rm -rf GOSim.buildbin-libdir && mkdir GOSim.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GOSim_1.22.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GOSim.buildbin-libdir

StartedAt: 2019-10-16 08:42:31 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 08:43:17 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 46.0 seconds

RetCode: 0

Status:  OK

PackageFile: GOSim_1.22.0.tgz

PackageFileSize: 518.1 KiB

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### Running command:
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###   rm -rf GOSim.buildbin-libdir && mkdir GOSim.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GOSim_1.22.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GOSim.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GOSim.buildbin-libdir GOSim_1.22.0.tar.gz'
>>>>>>> 

* installing *source* package ‘GOSim’ ...
** 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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "require(Rcpp); Rcpp:::CxxFlags()"` -fPIC  -Wall -g -O2  -c OAWrapper.cpp -o OAWrapper.o
Loading required package: Rcpp
In file included from OAWrapper.cpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
    inline void warning(const std::string& message) {        // #nocov start
                                                    ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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 hungarian2.c -o hungarian2.o
Loading required package: Rcpp
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 GOSim.so OAWrapper.o hungarian2.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Loading required package: Rcpp
installing to /Users/biocbuild/bbs-3.9-bioc/meat/GOSim.buildbin-libdir/00LOCK-GOSim/00new/GOSim/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 (GOSim)


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