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BUILD BIN report for NetPathMiner on merida2

This page was generated on 2019-04-09 13:29:41 -0400 (Tue, 09 Apr 2019).

Package 1076/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NetPathMiner 1.19.5
Ahmed Mohamed
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/NetPathMiner
Branch: master
Last Commit: 666f2f7
Last Changed Date: 2019-04-02 17:32:19 -0400 (Tue, 02 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]

Summary

Package: NetPathMiner
Version: 1.19.5
Command: rm -rf NetPathMiner.buildbin-libdir && mkdir NetPathMiner.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh NetPathMiner_1.19.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R NetPathMiner.buildbin-libdir
StartedAt: 2019-04-09 05:59:37 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:00:46 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 68.6 seconds
RetCode: 0
Status:  OK 
PackageFile: NetPathMiner_1.19.5.tgz
PackageFileSize: 2.662 MiB

Command output

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### Running command:
###
###   rm -rf NetPathMiner.buildbin-libdir && mkdir NetPathMiner.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh NetPathMiner_1.19.5.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_1.19.5.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
Couldn't find libsbml.pc. Searching for libsbml in candidate directories.
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   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include/ -fPIC  -Wall -g -O2  -c PathRanker.cpp -o PathRanker.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c handlesegfault.c -o handlesegfault.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hme3m.c -o hme3m.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -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   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include/ -fPIC  -Wall -g -O2  -c kgml_interface.cpp -o kgml_interface.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include/ -fPIC  -Wall -g -O2  -c methods.cpp -o methods.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include/ -fPIC  -Wall -g -O2  -c pathScope.cpp -o pathScope.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include/ -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 -lsbml -lxml2 -lxml2 -lz -lpthread -licucore -lm -lsbml -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-3.9-bioc/meat/NetPathMiner.buildbin-libdir/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
* 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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/Resources/lib/libquadmath.0.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs//NetPathMiner.so"