Package: SMAP

Version: 1.48.0

Command: rm -rf SMAP.buildbin-libdir && mkdir SMAP.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SMAP_1.48.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SMAP.buildbin-libdir

StartedAt: 2019-10-16 09:27:12 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 09:27:33 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 21.0 seconds

RetCode: 0

Status:  OK

PackageFile: SMAP_1.48.0.tgz

PackageFileSize: 1.332 MiB

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### Running command:
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###   rm -rf SMAP.buildbin-libdir && mkdir SMAP.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SMAP_1.48.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SMAP.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SMAP.buildbin-libdir SMAP_1.48.0.tar.gz'
>>>>>>> 

* installing *source* package ‘SMAP’ ...
** 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 gradient.c -o gradient.o
gradient.c:247:10: warning: unused variable 'tmp' [-Wunused-variable]
                double tmp;
                       ^
1 warning generated.
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 init.c -o init.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 overlap.c -o overlap.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 prob.c -o prob.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 viterbi.c -o viterbi.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 SMAP.so gradient.o init.o overlap.o prob.o viterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/SMAP.buildbin-libdir/00LOCK-SMAP/00new/SMAP/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 (SMAP)


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