############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf SAGx.buildbin-libdir && mkdir SAGx.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SAGx_1.66.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SAGx.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SAGx.buildbin-libdir SAGx_1.66.0.tar.gz' >>>>>>> * installing *source* package ‘SAGx’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c minigsea.c -o minigsea.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c newboot.c -o newboot.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c samrocNboot.c -o samrocNboot.o clang -mmacosx-version-min=10.13 -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-3.13-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 Warning: Package 'SAGx' is deprecated and will be removed from Bioconductor version 3.14 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: Package 'SAGx' is deprecated and will be removed from Bioconductor version 3.14 ** 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/4.1/Resources/lib/libgcc_s.1.dylib" "SAGx.buildbin-libdir/SAGx/libs/SAGx.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "SAGx.buildbin-libdir/SAGx/libs/SAGx.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "SAGx.buildbin-libdir/SAGx/libs/SAGx.so"