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This page was generated on 2023-04-20 12:50:36 -0400 (Thu, 20 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-04-19 r84288) -- "Unsuffered Consequences" 3941
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INSTALL results for STAN on nebbiolo2


To the developers/maintainers of the STAN package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/STAN.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 2012/2223HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STAN 2.27.1  (landing page)
Rafael Campos-Martin
Snapshot Date: 2023-04-19 23:55:56 -0400 (Wed, 19 Apr 2023)
git_url: https://git.bioconductor.org/packages/STAN
git_branch: devel
git_last_commit: d204c36
git_last_commit_date: 2023-04-10 10:51:45 -0400 (Mon, 10 Apr 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  ERROR    ERROR  skipped

Summary

Package: STAN
Version: 2.27.1
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL STAN
StartedAt: 2023-04-20 03:43:34 -0400 (Thu, 20 Apr 2023)
EndedAt: 2023-04-20 03:43:43 -0400 (Thu, 20 Apr 2023)
EllapsedTime: 8.6 seconds
RetCode: 1
Status:   ERROR  

Command output

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###
### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL STAN
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c Bernoulli.cpp -o Bernoulli.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c EmissionFactory.cpp -o EmissionFactory.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c EmissionFunction.cpp -o EmissionFunction.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c HMM.cpp -o HMM.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c InitialProbability.cpp -o InitialProbability.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c JointlyIndependent.cpp -o JointlyIndependent.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c MemoryAllocation.cpp -o MemoryAllocation.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c Multinomial.cpp -o Multinomial.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c MultivariateGaussian.cpp -o MultivariateGaussian.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c NegativeBinomial.cpp -o NegativeBinomial.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c Poisson.cpp -o Poisson.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c PoissonLogNormal.cpp -o PoissonLogNormal.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c RAccessUtils.cpp -o RAccessUtils.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-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++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c TransitionMatrix.cpp -o TransitionMatrix.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-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:114:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  114 |     for (register int i = 0 ; i < myN ; i++)
      |                       ^
matUtils.cpp:115:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  115 |         for (register int j = i ; j < myldz ; j++)
      |                           ^
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-3.18-bioc/R/include/R.h:78,
                 from matUtils.h:6,
                 from matUtils.cpp:2:
/home/biocbuild/bbs-3.18-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-3.18-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-3.18-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,
      | ^~~~~~~~
matUtils.cpp:125:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  125 |     for (register int i = 0 ; i < myNCol ; i++)
      |                       ^
make: *** [/home/biocbuild/bbs-3.18-bioc/R/etc/Makeconf:198: matUtils.o] Error 1
ERROR: compilation failed for package ‘STAN’
* removing ‘/home/biocbuild/bbs-3.18-bioc/R/site-library/STAN’