############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Bioc.gff.buildbin-libdir && mkdir Bioc.gff.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Bioc.gff_0.99.17.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Bioc.gff.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Bioc.gff.buildbin-libdir Bioc.gff_0.99.17.tar.gz' >>>>>>> * installing *source* package ‘Bioc.gff’ ... ** this is package ‘Bioc.gff’ version ‘0.99.17’ ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.1.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_Bioc_gff.c -o R_init_Bioc_gff.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c readGFF.c -o readGFF.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o Bioc.gff.so R_init_Bioc_gff.o S4Vectors_stubs.o XVector_stubs.o readGFF.o utils.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Users/biocbuild/bbs-3.22-bioc/meat/Bioc.gff.buildbin-libdir/00LOCK-Bioc.gff/00new/Bioc.gff/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 (Bioc.gff) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR Bioc.gff.buildbin-libdir/Bioc.gff/libs/Bioc.gff.so >>>>>>> >>>>>>> Paths before fix: Bioc.gff.buildbin-libdir/Bioc.gff/libs/Bioc.gff.so: Bioc.gff.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "Bioc.gff.buildbin-libdir/Bioc.gff/libs/Bioc.gff.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "Bioc.gff.buildbin-libdir/Bioc.gff/libs/Bioc.gff.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "Bioc.gff.buildbin-libdir/Bioc.gff/libs/Bioc.gff.so" >>>>>>> Paths after fix: Bioc.gff.buildbin-libdir/Bioc.gff/libs/Bioc.gff.so: Bioc.gff.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)