Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:30:06 -0400 (Tue, 09 Apr 2019).
Package 1560/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
STAN 2.11.0 Rafael Campos-Martin
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | [ OK ] |
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 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> 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"