############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf NetPathMiner.buildbin-libdir && mkdir NetPathMiner.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh NetPathMiner_1.34.2.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_1.34.2.tar.gz' >>>>>>> * installing *source* package ‘NetPathMiner’ ... ** using staged installation removing boost headers... 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 -mmacosx-version-min=10.13 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 -mmacosx-version-min=10.13 accepts -g... yes checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -E checking for xmlParseFile in -lxml2... yes checking for readSBML in -lsbml... no untarring boost include tree... SBML not found. libXML2 found checking for xml2-config... /usr/bin/xml2-config configure: creating ./config.status config.status: creating src/Makevars ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I . -I/usr/local/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -Wall -g -O2 -c PathRanker.cpp -o PathRanker.o In file included from PathRanker.cpp:25: /usr/local/include/boost/pending/relaxed_heap.hpp:14:1: warning: This header is deprecated. Use the standard heap functions instead. [-W#pragma-messages] BOOST_HEADER_DEPRECATED("the standard heap functions") ^ /usr/local/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED' # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :26:2: note: expanded from here message("This header is deprecated. Use " "the standard heap functions" " instead.") ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c handlesegfault.c -o handlesegfault.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c hme3m.c -o hme3m.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I . -I/usr/local/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -Wall -g -O2 -c kgml_interface.cpp -o kgml_interface.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I . -I/usr/local/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -Wall -g -O2 -c methods.cpp -o methods.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I . -I/usr/local/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -Wall -g -O2 -c pathScope.cpp -o pathScope.o In file included from pathScope.cpp:30: /usr/local/include/boost/pending/relaxed_heap.hpp:14:1: warning: This header is deprecated. Use the standard heap functions instead. [-W#pragma-messages] BOOST_HEADER_DEPRECATED("the standard heap functions") ^ /usr/local/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED' # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :30:2: note: expanded from here message("This header is deprecated. Use " "the standard heap functions" " instead.") ^ 1 warning generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I . -I/usr/local/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -Wall -g -O2 -c sbml_interface.cpp -o sbml_interface.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 NetPathMiner.so PathRanker.o handlesegfault.o hme3m.o init.o kgml_interface.o methods.o pathScope.o sbml_interface.o -lxml2 -L/Library/Developer/CommandLineTools/SDKs/MacOSX.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/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (10.14) than being linked (10.13) ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (10.14) than being linked (10.13) installing to /Users/biocbuild/bbs-3.16-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 LINKS FOR NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so >>>>>>> install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/lib/libquadmath.0.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so" install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so" install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so"