############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf BicARE.buildbin-libdir && mkdir BicARE.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BicARE_1.61.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BicARE.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BicARE.buildbin-libdir BicARE_1.61.0.tar.gz' >>>>>>> * installing *source* package ‘BicARE’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BicARE.c -o BicARE.o BicARE.c:439:12: warning: unused variable 'invk' [-Wunused-variable] double invk = 1/(double)*k; ^ 1 warning generated. 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 BicARE.so BicARE.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc/meat/BicARE.buildbin-libdir/00LOCK-BicARE/00new/BicARE/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 (BicARE) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR BicARE.buildbin-libdir/BicARE/libs/BicARE.so >>>>>>> >>>>>>> Paths before fix: BicARE.buildbin-libdir/BicARE/libs/BicARE.so: BicARE.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "BicARE.buildbin-libdir/BicARE/libs/BicARE.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "BicARE.buildbin-libdir/BicARE/libs/BicARE.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "BicARE.buildbin-libdir/BicARE/libs/BicARE.so" >>>>>>> Paths after fix: BicARE.buildbin-libdir/BicARE/libs/BicARE.so: BicARE.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)