Ahmed Mohamed
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/NetPathMiner |
| Branch: master |
| Last Commit: df342e5 |
| Last Changed Date: 2019-10-29 13:37:30 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:38:59 -0500 (Thu, 16 Jan 2020).
| Package 1144/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| NetPathMiner 1.23.0 Ahmed Mohamed
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | [ OK ] | |
| Package: NetPathMiner |
| Version: 1.23.0 |
| Command: rm -rf NetPathMiner.buildbin-libdir && mkdir NetPathMiner.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh NetPathMiner_1.23.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R NetPathMiner.buildbin-libdir |
| StartedAt: 2020-01-16 11:24:02 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 11:24:44 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 42.5 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: NetPathMiner_1.23.0.tgz |
| PackageFileSize: 2.621 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf NetPathMiner.buildbin-libdir && mkdir NetPathMiner.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh NetPathMiner_1.23.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R NetPathMiner.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=NetPathMiner.buildbin-libdir NetPathMiner_1.23.0.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 deprecated checking for gcc... clang 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 accepts -g... yes checking for clang option to accept ISO C89... none needed checking how to run the C preprocessor... clang -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I . -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -fPIC -Wall -g -O2 -c PathRanker.cpp -o PathRanker.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c handlesegfault.c -o handlesegfault.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c hme3m.c -o hme3m.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I . -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -fPIC -Wall -g -O2 -c kgml_interface.cpp -o kgml_interface.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I . -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -fPIC -Wall -g -O2 -c methods.cpp -o methods.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I . -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -fPIC -Wall -g -O2 -c pathScope.cpp -o pathScope.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I . -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -fPIC -Wall -g -O2 -c sbml_interface.cpp -o sbml_interface.o clang++ -std=gnu++11 -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 -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-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.11-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/4.0/Resources/lib/libgcc_s.1.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs//NetPathMiner.so" install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs//NetPathMiner.so" install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.5.2.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs//NetPathMiner.so" install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs//NetPathMiner.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs//NetPathMiner.so" install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs//NetPathMiner.so" install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs//NetPathMiner.so"