BioC 3.6: BUILD BIN report for STAN on veracruz1

Package: STAN

Version: 1.0.0

Command: rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh STAN_1.0.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R STAN.buildbin-libdir

StartedAt: 2017-08-17 11:28:08 -0400 (Thu, 17 Aug 2017)

EndedAt: 2017-08-17 11:28:31 -0400 (Thu, 17 Aug 2017)

EllapsedTime: 22.9 seconds

RetCode: 0

Status:  OK

PackageFile: STAN_1.0.0.tgz

PackageFileSize: 940.7 KiB

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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_1.0.0.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_1.0.0.tar.gz'
>>>>>>> 

* installing *source* package ‘STAN’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -w -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c Bernoulli.cpp -o Bernoulli.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -w -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c EmissionFactory.cpp -o EmissionFactory.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -w -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c EmissionFunction.cpp -o EmissionFunction.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -w -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c HMM.cpp -o HMM.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -w -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c InitialProbability.cpp -o InitialProbability.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -w -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c JointlyIndependent.cpp -o JointlyIndependent.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -w -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c MemoryAllocation.cpp -o MemoryAllocation.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -w -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c MultivariateGaussian.cpp -o MultivariateGaussian.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -w -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -w -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c RAccessUtils.cpp -o RAccessUtils.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -w -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c RWrapper.cpp -o RWrapper.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -w -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c TransitionMatrix.cpp -o TransitionMatrix.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -w -D_RDLL_ -fopenmp  -fPIC  -Wall -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 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/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-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"
install_name_tool -change "/usr/local/gfortran/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/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "STAN.buildbin-libdir/STAN/libs//STAN.so"