STAN 2.1.3 Benedikt Zacher
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/STAN | Last Changed Rev: 117964 / Revision: 121152 | Last Changed Date: 2016-05-30 02:58:47 -0700 (Mon, 30 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | | |
moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | [ OK ] | |
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### Running command:
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### rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh STAN_2.1.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R STAN.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=STAN.buildbin-libdir STAN_2.1.3.tar.gz'
>>>>>>>
* installing *source* package ‘STAN’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c Bernoulli.cpp -o Bernoulli.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c EmissionFactory.cpp -o EmissionFactory.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c EmissionFunction.cpp -o EmissionFunction.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c HMM.cpp -o HMM.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c InitialProbability.cpp -o InitialProbability.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c JointlyIndependent.cpp -o JointlyIndependent.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c MemoryAllocation.cpp -o MemoryAllocation.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c Multinomial.cpp -o Multinomial.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c MultivariateGaussian.cpp -o MultivariateGaussian.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c NegativeBinomial.cpp -o NegativeBinomial.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c Poisson.cpp -o Poisson.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c PoissonLogNormal.cpp -o PoissonLogNormal.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c RAccessUtils.cpp -o RAccessUtils.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c RWrapper.cpp -o RWrapper.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c TransitionMatrix.cpp -o TransitionMatrix.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -w -D_RDLL_ -fPIC -Wall -mtune=core2 -g -O2 -c matUtils.cpp -o matUtils.o
clang++ -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 STAN.so Bernoulli.o EmissionFactory.o EmissionFunction.o HMM.o InitialProbability.o JointlyIndependent.o MemoryAllocation.o Multinomial.o MultivariateGaussian.o NegativeBinomial.o ParamContainerEmissions.o Poisson.o PoissonLogNormal.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/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-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/3.3/Resources/lib/libgcc_s.1.dylib" "STAN.buildbin-libdir/STAN/libs//STAN.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "STAN.buildbin-libdir/STAN/libs//STAN.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/lib/libreadline.dylib" "STAN.buildbin-libdir/STAN/libs//STAN.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "STAN.buildbin-libdir/STAN/libs//STAN.so"