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BioC 3.2: BUILD BIN report for STAN on perceval

This page was generated on 2015-10-27 17:36:29 -0400 (Tue, 27 Oct 2015).

Package 1021/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STAN 1.4.0
Benedikt Zacher
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/STAN
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  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: STAN
Version: 1.4.0
Command: rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh STAN_1.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R STAN.buildbin-libdir
StartedAt: 2015-10-27 12:47:16 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 12:47:54 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 38.2 seconds
RetCode: 0
Status:  OK 
PackageFile: STAN_1.4.0.tgz
PackageFileSize: 914.5 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh STAN_1.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R STAN.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=STAN.buildbin-libdir STAN_1.4.0.tar.gz'
>>>>>>> 

* installing *source* package ‘STAN’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -w -D_RDLL_   -fPIC  -mtune=core2 -g -O2 -Wall  -c Bernoulli.cpp -o Bernoulli.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -w -D_RDLL_   -fPIC  -mtune=core2 -g -O2 -Wall  -c EmissionFactory.cpp -o EmissionFactory.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -w -D_RDLL_   -fPIC  -mtune=core2 -g -O2 -Wall  -c EmissionFunction.cpp -o EmissionFunction.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -w -D_RDLL_   -fPIC  -mtune=core2 -g -O2 -Wall  -c HMM.cpp -o HMM.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -w -D_RDLL_   -fPIC  -mtune=core2 -g -O2 -Wall  -c InitialProbability.cpp -o InitialProbability.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -w -D_RDLL_   -fPIC  -mtune=core2 -g -O2 -Wall  -c JointlyIndependent.cpp -o JointlyIndependent.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -w -D_RDLL_   -fPIC  -mtune=core2 -g -O2 -Wall  -c MemoryAllocation.cpp -o MemoryAllocation.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -w -D_RDLL_   -fPIC  -mtune=core2 -g -O2 -Wall  -c MultivariateGaussian.cpp -o MultivariateGaussian.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -w -D_RDLL_   -fPIC  -mtune=core2 -g -O2 -Wall  -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -w -D_RDLL_   -fPIC  -mtune=core2 -g -O2 -Wall  -c RAccessUtils.cpp -o RAccessUtils.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -w -D_RDLL_   -fPIC  -mtune=core2 -g -O2 -Wall  -c RWrapper.cpp -o RWrapper.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -w -D_RDLL_   -fPIC  -mtune=core2 -g -O2 -Wall  -c TransitionMatrix.cpp -o TransitionMatrix.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -w -D_RDLL_   -fPIC  -mtune=core2 -g -O2 -Wall  -c matUtils.cpp -o matUtils.o
llvm-g++-4.2 -arch x86_64 -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 STAN.so Bernoulli.o EmissionFactory.o EmissionFunction.o HMM.o InitialProbability.o JointlyIndependent.o MemoryAllocation.o MultivariateGaussian.o ParamContainerEmissions.o RAccessUtils.o RWrapper.o TransitionMatrix.o matUtils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/STAN.buildbin-libdir/STAN/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 (STAN)


>>>>>>> 
>>>>>>> FIXING LINKS FOR STAN.buildbin-libdir/STAN/libs//STAN.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" "STAN.buildbin-libdir/STAN/libs//STAN.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.2.dylib" "STAN.buildbin-libdir/STAN/libs//STAN.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" "STAN.buildbin-libdir/STAN/libs//STAN.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "STAN.buildbin-libdir/STAN/libs//STAN.so"