Rafael Campos-Martin
| Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/STAN |
| git_branch: RELEASE_3_16 |
| git_last_commit: a982cef |
| git_last_commit_date: 2023-01-19 11:18:47 -0400 (Thu, 19 Jan 2023) |
| Back to Mac ARM64 build report for BioC 3.16 |
|
This page was generated on 2023-04-19 11:01:58 -0400 (Wed, 19 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson | macOS 13.0 Ventura | arm64 | 4.2.2 (2022-10-31) -- "Innocent and Trusting" | 4256 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the STAN package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1970/2183 | Hostname | OS / Arch | INSTALL | BUILD | BUILD BIN | ||||||||
| STAN 2.26.2 (landing page) Rafael Campos-Martin
| kjohnson | macOS 13.0 Ventura / arm64 | OK | OK | OK | | |||||||
| Package: STAN |
| Version: 2.26.2 |
| Command: rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh STAN_2.26.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R STAN.buildbin-libdir |
| StartedAt: 2023-04-18 19:55:34 -0400 (Tue, 18 Apr 2023) |
| EndedAt: 2023-04-18 19:58:12 -0400 (Tue, 18 Apr 2023) |
| EllapsedTime: 157.9 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: STAN_2.26.2.tgz |
| PackageFileSize: 1.434 MiB |
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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_2.26.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R STAN.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=STAN.buildbin-libdir STAN_2.26.2.tar.gz'
>>>>>>>
* installing *source* package ‘STAN’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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
HMM.cpp:967:12: warning: variable 'allT' set but not used [-Wunused-but-set-variable]
double allT = 0;
^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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++ -arch arm64 -std=gnu++14 -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-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/STAN.buildbin-libdir/00LOCK-STAN/00new/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 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)
>>>>>>>
>>>>>>> FIXING LINKS FOR STAN.buildbin-libdir/STAN/libs/STAN.so
>>>>>>>
install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "STAN.buildbin-libdir/STAN/libs/STAN.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "STAN.buildbin-libdir/STAN/libs/STAN.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "STAN.buildbin-libdir/STAN/libs/STAN.so"
install_name_tool -change "/opt/R/arm64/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "STAN.buildbin-libdir/STAN/libs/STAN.so"
install_name_tool -change "/opt/R/arm64/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "STAN.buildbin-libdir/STAN/libs/STAN.so"