| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:13 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 | ||||
| Package 2018/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rafael Campos-Martin
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | ERROR | ERROR | skipped | skipped | ||||||||
|
To the developers/maintainers of the STAN package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: STAN |
| Version: 2.28.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data STAN |
| StartedAt: 2023-10-16 22:15:27 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 22:15:48 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 20.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data STAN
###
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* checking for file ‘STAN/DESCRIPTION’ ... OK
* preparing ‘STAN’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘STAN’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
for (register int i = 0 ; i < myN ; i++)
^~~~~~~~~
matUtils.cpp:115:14: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
for (register int j = i ; j < myldz ; j++)
^~~~~~~~~
matUtils.cpp:118:5: error: no matching function for call to 'dspev_'
F77_NAME(dspev)("V", "U", &myN, myAP, myW, myZ, &myldz, myWork, &myInfo) ;
^~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:81:24: note: expanded from macro 'F77_NAME'
#define F77_NAME(x) F77_CALL(x)
^~~~~~~~~~~
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:77:22: note: expanded from macro 'F77_CALL'
# define F77_CALL(x) x ## _
^~~~~~
<scratch space>:184:1: note: expanded from here
dspev_
^~~~~~
/Library/Frameworks/R.framework/Resources/include/R_ext/Lapack.h:1050:1: note: candidate function not viable: requires 11 arguments, but 9 were provided
F77_NAME(dspev)(const char* jobz, const char* uplo, const int* n,
^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:81:24: note: expanded from macro 'F77_NAME'
#define F77_NAME(x) F77_CALL(x)
^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:77:22: note: expanded from macro 'F77_CALL'
# define F77_CALL(x) x ## _
^
<scratch space>:324:1: note: expanded from here
dspev_
^
matUtils.cpp:125:10: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
for (register int i = 0 ; i < myNCol ; i++)
^~~~~~~~~
4 errors generated.
make: *** [matUtils.o] Error 1
ERROR: compilation failed for package ‘STAN’
* removing ‘/private/tmp/Rtmpq87dVd/Rinsta2a446a8411c/STAN’
-----------------------------------
ERROR: package installation failed