Back to Multiple platform build/check report for BioC 3.17:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2023-10-16 11:36:42 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 2018/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STAN 2.28.0  (landing page)
Rafael Campos-Martin
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/STAN
git_branch: RELEASE_3_17
git_last_commit: 606ff05
git_last_commit_date: 2023-04-25 10:33:29 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  ERROR    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
merida1macOS 12.6.4 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

BUILD results for STAN on palomino3


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.
- 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.

raw results

Summary

Package: STAN
Version: 2.28.0
Command: chmod a+r STAN -R && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data STAN
StartedAt: 2023-10-15 22:41:09 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 22:41:25 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 16.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r STAN -R && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data STAN
###
##############################################################################
##############################################################################


* 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: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Bernoulli.cpp -o Bernoulli.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c EmissionFactory.cpp -o EmissionFactory.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c EmissionFunction.cpp -o EmissionFunction.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c HMM.cpp -o HMM.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c InitialProbability.cpp -o InitialProbability.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c JointlyIndependent.cpp -o JointlyIndependent.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MemoryAllocation.cpp -o MemoryAllocation.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Multinomial.cpp -o Multinomial.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MultivariateGaussian.cpp -o MultivariateGaussian.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c NegativeBinomial.cpp -o NegativeBinomial.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Poisson.cpp -o Poisson.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PoissonLogNormal.cpp -o PoissonLogNormal.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RAccessUtils.cpp -o RAccessUtils.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 [-Wmaybe-uninitialized]
  350 |         return HMMEmissionFunctions;
      |                ^~~~~~~~~~~~~~~~~~~~
RWrapper.cpp:311:28: note: 'HMMEmissionFunctions' was declared here
  311 |         EmissionFunction **HMMEmissionFunctions;
      |                            ^~~~~~~~~~~~~~~~~~~~
RWrapper.cpp: In function 'SEXPREC* prepareEmission(const char*, SEXP, SEXP, EmissionFunction**, int)':
RWrapper.cpp:1157:16: warning: 'sexpemissionParam' may be used uninitialized [-Wmaybe-uninitialized]
 1157 |         return sexpemissionParam;
      |                ^~~~~~~~~~~~~~~~~
RWrapper.cpp:1123:14: note: 'sexpemissionParam' was declared here
 1123 |         SEXP sexpemissionParam;
      |              ^~~~~~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c TransitionMatrix.cpp -o TransitionMatrix.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 F:/biocbuild/bbs-3.17-bioc/R/include/R.h:78,
                 from matUtils.h:6,
                 from matUtils.cpp:2:
F:/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,
      |          ^~~~~
F:/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 ## _
      |                         ^
F:/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,
      | ^~~~~~~~
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: *** [F:/biocbuild/bbs-3.17-bioc/R/etc/x64/Makeconf:272: matUtils.o] Error 1
ERROR: compilation failed for package 'STAN'
* removing 'F:/biocbuild/bbs-3.17-bioc/tmpdir/Rtmp4euqaE/Rinst354025d7640f/STAN'
      -----------------------------------
ERROR: package installation failed