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BUILD BIN report for STAN on merida2

This page was generated on 2019-04-09 13:30:06 -0400 (Tue, 09 Apr 2019).

Package 1560/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STAN 2.11.0
Rafael Campos-Martin
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/STAN
Branch: master
Last Commit: 123b152
Last Changed Date: 2018-11-30 12:12:22 -0400 (Fri, 30 Nov 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS [ OK ]

Summary

Package: STAN
Version: 2.11.0
Command: rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh STAN_2.11.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R STAN.buildbin-libdir
StartedAt: 2019-04-09 06:35:26 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:36:41 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 75.1 seconds
RetCode: 0
Status:  OK 
PackageFile: STAN_2.11.0.tgz
PackageFileSize: 1.302 MiB

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_2.11.0.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_2.11.0.tar.gz'
>>>>>>> 

* installing *source* package ‘STAN’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c Bernoulli.cpp -o Bernoulli.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c EmissionFactory.cpp -o EmissionFactory.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c EmissionFunction.cpp -o EmissionFunction.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c HMM.cpp -o HMM.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c InitialProbability.cpp -o InitialProbability.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c JointlyIndependent.cpp -o JointlyIndependent.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c MemoryAllocation.cpp -o MemoryAllocation.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c Multinomial.cpp -o Multinomial.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c MultivariateGaussian.cpp -o MultivariateGaussian.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c NegativeBinomial.cpp -o NegativeBinomial.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c Poisson.cpp -o Poisson.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c PoissonLogNormal.cpp -o PoissonLogNormal.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c RAccessUtils.cpp -o RAccessUtils.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c RWrapper.cpp -o RWrapper.o
RWrapper.cpp:343:17: warning: variable 'HMMEmissionFunctions' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if(strcmp(type,poissonlognormal) == 0)
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RWrapper.cpp:350:16: note: uninitialized use occurs here
        return HMMEmissionFunctions;
               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RWrapper.cpp:343:14: note: remove the 'if' if its condition is always true
        else if(strcmp(type,poissonlognormal) == 0)
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RWrapper.cpp:311:48: note: initialize the variable 'HMMEmissionFunctions' to silence this warning
        EmissionFunction **HMMEmissionFunctions;
                                               ^
                                                = nullptr
RWrapper.cpp:1140:21: warning: variable 'sexpemissionParam' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
            else if(strcmp(type, multinomial) == 0)
                    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RWrapper.cpp:1157:16: note: uninitialized use occurs here
        return sexpemissionParam;
               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RWrapper.cpp:1140:18: note: remove the 'if' if its condition is always true
            else if(strcmp(type, multinomial) == 0)
                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RWrapper.cpp:1123:31: note: initialize the variable 'sexpemissionParam' to silence this warning
        SEXP sexpemissionParam;
                              ^
                               = nullptr
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c TransitionMatrix.cpp -o TransitionMatrix.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c matUtils.cpp -o matUtils.o
matUtils.cpp:114:10: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    for (register int i = 0 ; i < myN ; i++)
         ^˜˜˜˜˜˜˜˜
matUtils.cpp:115:14: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
        for (register int j = i ; j < myldz ; j++)
             ^˜˜˜˜˜˜˜˜
matUtils.cpp:125:10: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    for (register int i = 0 ; i < myNCol ; i++)
         ^˜˜˜˜˜˜˜˜
3 warnings generated.
clang++ -std=gnu++11 -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/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-3.9-bioc/meat/STAN.buildbin-libdir/STAN/libs
** R
** data
** inst
** byte-compile and prepare 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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/Resources/lib/libquadmath.0.dylib" "STAN.buildbin-libdir/STAN/libs//STAN.so"