Package: girafe

Version: 1.35.0

Command: rm -rf girafe.buildbin-libdir && mkdir girafe.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh girafe_1.35.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R girafe.buildbin-libdir

StartedAt: 2019-04-09 07:07:58 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 07:08:54 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 56.0 seconds

RetCode: 0

Status:  OK

PackageFile: girafe_1.35.0.tgz

PackageFileSize: 2.098 MiB

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf girafe.buildbin-libdir && mkdir girafe.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh girafe_1.35.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R girafe.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=girafe.buildbin-libdir girafe_1.35.0.tar.gz'
>>>>>>> 

* installing *source* package ‘girafe’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c coverage.cpp -o coverage.o
coverage.cpp:2:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c girafe_init.c -o girafe_init.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 girafe.so coverage.o girafe_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/girafe.buildbin-libdir/00LOCK-girafe/00new/girafe/libs
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘IRanges’ for request: ‘sort’ when loading ‘girafe’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘girafe’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘IRanges’ for request: ‘sort’ when loading ‘girafe’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘IRanges’ for request: ‘sort’ when loading ‘girafe’
** testing if installed package keeps a record of temporary installation path
* DONE (girafe)


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