Package: SAGx

Version: 1.61.0

Command: rm -rf SAGx.buildbin-libdir && mkdir SAGx.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SAGx_1.61.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SAGx.buildbin-libdir

StartedAt: 2020-01-16 11:44:45 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 11:45:07 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 21.1 seconds

RetCode: 0

Status:  OK

PackageFile: SAGx_1.61.0.tgz

PackageFileSize: 546.3 KiB

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### Running command:
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###   rm -rf SAGx.buildbin-libdir && mkdir SAGx.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SAGx_1.61.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SAGx.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SAGx.buildbin-libdir SAGx_1.61.0.tar.gz'
>>>>>>> 

* installing *source* package ‘SAGx’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c minigsea.c -o minigsea.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c newboot.c -o newboot.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c samrocNboot.c -o samrocNboot.o
clang -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 SAGx.so minigsea.o newboot.o samrocNboot.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/SAGx.buildbin-libdir/00LOCK-SAGx/00new/SAGx/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 (SAGx)


>>>>>>> 
>>>>>>> FIXING LINKS FOR SAGx.buildbin-libdir/SAGx/libs//SAGx.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "SAGx.buildbin-libdir/SAGx/libs//SAGx.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "SAGx.buildbin-libdir/SAGx/libs//SAGx.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.5.2.dylib" "SAGx.buildbin-libdir/SAGx/libs//SAGx.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.dylib" "SAGx.buildbin-libdir/SAGx/libs//SAGx.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "SAGx.buildbin-libdir/SAGx/libs//SAGx.so"