STAN.install - Githubissues

Yikun commented 1 year ago
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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL STAN
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘STAN’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c Bernoulli.cpp -o Bernoulli.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c EmissionFactory.cpp -o EmissionFactory.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c EmissionFunction.cpp -o EmissionFunction.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c HMM.cpp -o HMM.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c InitialProbability.cpp -o InitialProbability.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c JointlyIndependent.cpp -o JointlyIndependent.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c MemoryAllocation.cpp -o MemoryAllocation.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c Multinomial.cpp -o Multinomial.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c MultivariateGaussian.cpp -o MultivariateGaussian.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c NegativeBinomial.cpp -o NegativeBinomial.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c Poisson.cpp -o Poisson.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c PoissonLogNormal.cpp -o PoissonLogNormal.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c RAccessUtils.cpp -o RAccessUtils.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c RWrapper.cpp -o RWrapper.o
RWrapper.cpp: In function ‘EmissionFunction** RGETEMISSION(SEXP, int, SEXP, int*, const char*, double***, int*, int, SEXP, int*, int*, int*)’:
RWrapper.cpp:350:16: warning: ‘HMMEmissionFunctions’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  350 |         return HMMEmissionFunctions;
      |                ^~~~~~~~~~~~~~~~~~~~
RWrapper.cpp: In function ‘SEXPREC* prepareEmission(const char*, SEXP, SEXP, EmissionFunction**, int)’:
RWrapper.cpp:1157:16: warning: ‘sexpemissionParam’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1157 |         return sexpemissionParam;
      |                ^~~~~~~~~~~~~~~~~
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c TransitionMatrix.cpp -o TransitionMatrix.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c matUtils.cpp -o matUtils.o
matUtils.cpp: In function ‘double matrixDet(double**, int)’:
matUtils.cpp:118:20: error: too few arguments to function ‘void dspev_(const char*, const char*, const int*, double*, double*, double*, const int*, double*, int*, size_t, size_t)’
  118 |     F77_NAME(dspev)("V", "U", &myN, myAP, myW, myZ, &myldz, myWork, &myInfo) ;
      |                    ^
In file included from /home/biocbuild/bbs-3.17-bioc/R/include/R.h:78,
                 from matUtils.h:6,
                 from matUtils.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:1050:10: note: declared here
 1050 | F77_NAME(dspev)(const char* jobz, const char* uplo, const int* n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:1050:1: note: in expansion of macro ‘F77_NAME’
 1050 | F77_NAME(dspev)(const char* jobz, const char* uplo, const int* n,
      | ^~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: matUtils.o] Error 1
ERROR: compilation failed for package ‘STAN’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/STAN’
martin-g commented 1 year ago
Fails the same on x86_64: https://bioconductor.org/checkResults/3.17/bioc-LATEST/STAN/nebbiolo1-install.html
martin-g commented 1 year ago
I wasn't able to find a Github repo for this package. Maintainer: Rafael Campos-Martin <campos at mpipz.mpg.de> Since the problem also happens on x86_64 I will not bother the maintainer for now.
martin-g commented 11 months ago
The STAN package has been deprecated in 3.17 and removed in 3.18
Yikun / BBS

STAN.install #25
