############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf NetPathMiner.buildbin-libdir && mkdir NetPathMiner.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh NetPathMiner_1.42.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R NetPathMiner.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=NetPathMiner.buildbin-libdir NetPathMiner_1.42.0.tar.gz' >>>>>>> * installing *source* package ‘NetPathMiner’ ... ** using staged installation restoring Makevars.in file... mv: _Makevars.in_: No such file or directory rm: Makevars: No such file or directory removing compiled code... rm: *.o: No such file or directory 'config' variable 'CPP' is defunct checking for gcc... clang -arch x86_64 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether clang -arch x86_64 accepts -g... yes checking for clang -arch x86_64 option to accept ISO C89... none needed checking how to run the C preprocessor... clang -arch x86_64 -E checking for xmlParseFile in -lxml2... yes checking for readSBML in -lsbml... no SBML not found. libXML2 found checking for xml2-config... /usr/bin/xml2-config configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ 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 -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c handlesegfault.c -o handlesegfault.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hme3m.c -o hme3m.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c kgml_interface.cpp -o kgml_interface.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c methods.cpp -o methods.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sbml_interface.cpp -o sbml_interface.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o NetPathMiner.so handlesegfault.o hme3m.o init.o kgml_interface.o methods.o sbml_interface.o -lxml2 -L/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/NetPathMiner.buildbin-libdir/00LOCK-NetPathMiner/00new/NetPathMiner/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 (NetPathMiner) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so >>>>>>> >>>>>>> Paths before fix: NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so: NetPathMiner.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 66.1.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.1) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) >>>>>>> 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" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.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" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.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" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so" install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so" install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so" >>>>>>> Paths after fix: NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so: NetPathMiner.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 66.1.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.1) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)