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BioC 3.4: BUILD BIN report for STAN on morelia

This page was generated on 2016-09-21 03:53:29 -0700 (Wed, 21 Sep 2016).

Package 1166/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: STAN
Version: 2.1.3
Command: 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
StartedAt: 2016-09-20 15:35:34 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 15:36:00 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 25.8 seconds
RetCode: 0
Status:  OK 
PackageFile: STAN_2.1.3.tgz
PackageFileSize: 915.3 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   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
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> 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"