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BioC 2.14: BUILD BIN report for ChemmineR on petty

This page was generated on 2014-10-08 08:58:29 -0700 (Wed, 08 Oct 2014).

Package 138/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineR 2.16.9
ChemmineR Team
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/ChemmineR
Last Changed Rev: 93217 / Revision: 95116
Last Changed Date: 2014-08-06 10:10:09 -0700 (Wed, 06 Aug 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK [ OK ]
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: ChemmineR
Version: 2.16.9
Command: rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineR_2.16.9.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ChemmineR.buildbin-libdir
StartedAt: 2014-10-08 01:17:06 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:17:28 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 22.3 seconds
RetCode: 0
Status:  OK 
PackageFile: ChemmineR_2.16.9.tgz
PackageFileSize: 1.67 MiB

Command output

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###
### Running command:
###
###   rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineR_2.16.9.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ChemmineR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ChemmineR.buildbin-libdir ChemmineR_2.16.9.tar.gz'
>>>>>>> 

* installing *source* package ‘ChemmineR’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c DisjointSets.cpp -o DisjointSets.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c cluster.cc -o cluster.o
cluster.cc: In function ‘int nbr_intersect(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&)’:
cluster.cc:118: warning: comparison between signed and unsigned integer expressions
cluster.cc:118: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘int contains(int, std::vector<int, std::allocator<int> >&)’:
cluster.cc:131: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘DisjointSets cluster(int, int, int, int)’:
cluster.cc:267: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘void loadNNMatrix(int, int, int, SEXPREC*)’:
cluster.cc:284: warning: comparison between signed and unsigned integer expressions
cluster.cc:298: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘void loadNNList(int, int, SEXPREC*)’:
cluster.cc:314: warning: comparison between signed and unsigned integer expressions
cluster.cc:332: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘SEXPREC* jarvis_patrick(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
cluster.cc:390: warning: comparison between signed and unsigned integer expressions
cluster.cc: At global scope:
cluster.cc:49: warning: ‘void prepare_neighbors(const char*, int, int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c desc.cc -o desc.o
desc.cc: In function ‘SEXPREC* genAPDescriptor(SEXPREC*)’:
desc.cc:249: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c formats.cc -o formats.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c molecule.cc -o molecule.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c r_wrap.cc -o r_wrap.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c script.cc -o script.o
desc.h:39: warning: ‘elements’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c similarity.cc -o similarity.o
desc.h:39: warning: ‘elements’ defined but not used
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o desc.o formats.o molecule.o r_wrap.o script.o similarity.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/ChemmineR.buildbin-libdir/ChemmineR/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘as.vector’ from package ‘base’ in package ‘ChemmineR’
Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘ChemmineR’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘ChemmineR’
Creating a generic function for ‘print’ from package ‘base’ in package ‘ChemmineR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChemmineR)


>>>>>>> 
>>>>>>> FIXING LINKS FOR ChemmineR.buildbin-libdir/ChemmineR/libs//ChemmineR.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgcc_s.1.dylib" "ChemmineR.buildbin-libdir/ChemmineR/libs//ChemmineR.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.2.dylib" "ChemmineR.buildbin-libdir/ChemmineR/libs//ChemmineR.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.5.2.dylib" "ChemmineR.buildbin-libdir/ChemmineR/libs//ChemmineR.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "ChemmineR.buildbin-libdir/ChemmineR/libs//ChemmineR.so"