NetPathMiner 1.6.0
Ahmed Mohamed
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/NetPathMiner | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | [ OK ] | |
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### Running command:
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### rm -rf NetPathMiner.buildbin-libdir && mkdir NetPathMiner.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh NetPathMiner_1.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R NetPathMiner.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=NetPathMiner.buildbin-libdir NetPathMiner_1.6.0.tar.gz'
>>>>>>>
* installing *source* package ‘NetPathMiner’ ...
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
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... yes
untarring boost include tree...
libSBML found, finding configuration...
pkg-config tool found
libsbml.pc found. Using pkg-config to extract it.
Package /usr/local/lib/pkgconfig/libsbml.pc.bak was not found in the pkg-config search path.
Perhaps you should add the directory containing `/usr/local/lib/pkgconfig/libsbml.pc.bak.pc'
to the PKG_CONFIG_PATH environment variable
No package '/usr/local/lib/pkgconfig/libsbml.pc.bak' found
Package /usr/local/lib/pkgconfig/libsbml.pc.bak was not found in the pkg-config search path.
Perhaps you should add the directory containing `/usr/local/lib/pkgconfig/libsbml.pc.bak.pc'
to the PKG_CONFIG_PATH environment variable
No package '/usr/local/lib/pkgconfig/libsbml.pc.bak' found
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I . -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DHAVE_XML -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -DHAVE_SBML -fPIC -Wall -mtune=core2 -g -O2 -c PathRanker.cpp -o PathRanker.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c handlesegfault.c -o handlesegfault.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c hme3m.c -o hme3m.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c init.c -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I . -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DHAVE_XML -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -DHAVE_SBML -fPIC -Wall -mtune=core2 -g -O2 -c kgml_interface.cpp -o kgml_interface.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I . -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DHAVE_XML -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -DHAVE_SBML -fPIC -Wall -mtune=core2 -g -O2 -c methods.cpp -o methods.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I . -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DHAVE_XML -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -DHAVE_SBML -fPIC -Wall -mtune=core2 -g -O2 -c pathScope.cpp -o pathScope.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I . -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DHAVE_XML -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -DHAVE_SBML -fPIC -Wall -mtune=core2 -g -O2 -c sbml_interface.cpp -o sbml_interface.o
clang++ -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 -lsbml -lxml2 -lxml2 -lsbml -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/NetPathMiner.buildbin-libdir/NetPathMiner/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* 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/3.2/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/3.2/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/3.2/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/3.2/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/3.2/Resources/lib/libquadmath.0.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs//NetPathMiner.so"