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BioC 3.5: BUILD BIN report for STAN on toluca2

This page was generated on 2017-04-23 14:38:47 -0400 (Sun, 23 Apr 2017).

Package 1271/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STAN 2.3.0
Benedikt Zacher
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/STAN
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS [ OK ]
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: STAN
Version: 2.3.0
Command: rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh STAN_2.3.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R STAN.buildbin-libdir
StartedAt: 2017-04-23 12:47:28 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 12:47:58 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 30.1 seconds
RetCode: 0
Status:  OK 
PackageFile: STAN_2.3.0.tgz
PackageFileSize: 975.2 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh STAN_2.3.0.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_2.3.0.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-3.5-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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/Resources/lib/libquadmath.0.dylib" "STAN.buildbin-libdir/STAN/libs//STAN.so"