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BioC 3.2: BUILD BIN report for groHMM on perceval

This page was generated on 2015-11-10 14:49:16 -0800 (Tue, 10 Nov 2015).

Package 468/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
groHMM 1.4.0
Anusha Nagari, W. Lee Kraus
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/groHMM
Last Changed Rev: 109589 / Revision: 110496
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 UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: groHMM
Version: 1.4.0
Command: rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh groHMM_1.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R groHMM.buildbin-libdir
StartedAt: 2015-11-10 11:22:31 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 11:22:56 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 24.3 seconds
RetCode: 0
Status:  OK 
PackageFile: groHMM_1.4.0.tgz
PackageFileSize: 4.141 MiB

Command output

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###
### Running command:
###
###   rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh groHMM_1.4.0.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_1.4.0.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-3.2-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/3.2/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/3.2/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/3.2/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/3.2/Resources/lib/libreadline.dylib" "groHMM.buildbin-libdir/groHMM/libs//groHMM.so"