groHMM 1.0.2
Minho Chae, W. Lee Kraus
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/groHMM | | Last Changed Rev: 96298 / Revision: 102249 | | Last Changed Date: 2014-10-31 12:24:01 -0700 (Fri, 31 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | [ OK ] |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK |
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### Running command:
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### rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh groHMM_1.0.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R groHMM.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=groHMM.buildbin-libdir groHMM_1.0.2.tar.gz'
>>>>>>>
* installing *source* package ‘groHMM’ ...
It is recommended to use ‘given’ instead of ‘middle’.
It is recommended to use ‘given’ instead of ‘middle’.
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c AnnotateProbes.c -o AnnotateProbes.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c DecayAlgorithm.c -o DecayAlgorithm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c MLEfit.c -o MLEfit.o
hmmHeader.h:282: warning: ‘MargainalizeSumLogProbOver’ defined but not used
hmmHeader.h:301: warning: ‘expSum’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c RegisterRRoutines.c -o RegisterRRoutines.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c Windowing.c -o Windowing.o
Windowing.c: In function ‘WindowAnalysis’:
Windowing.c:147: warning: unused variable ‘II’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c hmmEM.c -o hmmEM.o
UsefulValues.h:39: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used
hmmHeader.h:282: warning: ‘MargainalizeSumLogProbOver’ defined but not used
hmmHeader.h:301: warning: ‘expSum’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c hmmFwBw.c -o hmmFwBw.o
UsefulValues.h:39: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used
hmmHeader.h:282: warning: ‘MargainalizeSumLogProbOver’ defined but not used
hmmHeader.h:301: warning: ‘expSum’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c: In function ‘SStatsNormExp’:
hmmMiscFunctions.c:385: warning: unused variable ‘wi’
hmmMiscFunctions.c: In function ‘UpdateNormExp’:
hmmMiscFunctions.c:418: warning: unused variable ‘epsilon’
hmmMiscFunctions.c: At top level:
UsefulValues.h:39: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c hmmViterbi.c -o hmmViterbi.o
UsefulValues.h:39: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used
hmmHeader.h:282: warning: ‘MargainalizeSumLogProbOver’ defined but not used
hmmHeader.h:301: warning: ‘expSum’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -L/usr/local/lib -o groHMM.so AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/groHMM.buildbin-libdir/groHMM/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (groHMM)
>>>>>>>
>>>>>>> FIXING LINKS FOR groHMM.buildbin-libdir/groHMM/libs//groHMM.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" "groHMM.buildbin-libdir/groHMM/libs//groHMM.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.2.dylib" "groHMM.buildbin-libdir/groHMM/libs//groHMM.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" "groHMM.buildbin-libdir/groHMM/libs//groHMM.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "groHMM.buildbin-libdir/groHMM/libs//groHMM.so"