Back to Build/check report for BioC 3.13 on Apple's new arm64 arch |
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This page was generated on 2021-01-31 03:53:37 -0500 (Sun, 31 Jan 2021).
These are experimental builds on Apple's new arm64 arch. See here for more information. |
To the developers/maintainers of the STAN package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1762/1938 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
STAN 2.19.0 Rafael Campos-Martin
| taxco | macOS 11.0.1 Big Sur / arm64 | OK | NA | NA | |||||||||
Package: STAN |
Version: 2.19.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL STAN |
StartedAt: 2021-01-30 18:50:30 -0500 (Sat, 30 Jan 2021) |
EndedAt: 2021-01-30 18:52:26 -0500 (Sat, 30 Jan 2021) |
EllapsedTime: 115.9 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL STAN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library’ * installing *source* package ‘STAN’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c Bernoulli.cpp -o Bernoulli.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c EmissionFactory.cpp -o EmissionFactory.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c EmissionFunction.cpp -o EmissionFunction.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c HMM.cpp -o HMM.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c InitialProbability.cpp -o InitialProbability.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c JointlyIndependent.cpp -o JointlyIndependent.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c MemoryAllocation.cpp -o MemoryAllocation.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c Multinomial.cpp -o Multinomial.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c MultivariateGaussian.cpp -o MultivariateGaussian.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c NegativeBinomial.cpp -o NegativeBinomial.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c Poisson.cpp -o Poisson.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c PoissonLogNormal.cpp -o PoissonLogNormal.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c RAccessUtils.cpp -o RAccessUtils.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -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/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c TransitionMatrix.cpp -o TransitionMatrix.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D_RDLL_ -fPIC -falign-functions=64 -Wall -g -O2 -c matUtils.cpp -o matUtils.o matUtils.cpp:114:10: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-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++17 [-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++17 [-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/opt/R/arm64/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/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/00LOCK-STAN/00new/STAN/libs ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (STAN)