[R-pkg-devel] Request for assistance: error in installing on Debian (undefined symbol: omp_get_num_procs) and note in checking the HTML versions (no command 'tidy' found, package 'V8' unavailable)

[Annaig De-Walsche]

Dear R-package-devel Community,

I hope this email finds you well. I am reaching out to seek assistance regarding package development in R.

Specifically, I am currently developing an R package for querying composite hypotheses using Rccp. While my package can be installed correctly on my local computer (Windows), I have encountered some issues installing on Debian Linux, R-devel, GCC ASAN/UBSAN. The corresponding error message is below. I have no problems installing on Fedora Linux, R-devel, clang, gfortran or Ubuntu Linux 20.04.1 LTS, R-release, GCC. You will find attached my package.
Additionally, I obtained some notes checking the HTML versions of the manual on all platforms that say:

Skipping checking HTML validation: no command 'tidy' found
Skipping checking math rendering: package 'V8' unavailable

I have searched through the available documentation and resources, but I still need help understanding the error and note messages. Hence, I am turning to this community, hoping that some of you have encountered similar issues.

Thank you very much for considering my request. I would be grateful if anyone could provide me with some help.

Best regards,
Annaïg De Walsche
Quantitative Genetics and Evolution unit of INRAE
Gif-sur-Yvette, France


Installing package into ‘/home/docker/R’
(as ‘lib’ is unspecified)
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
* installing *source* package ‘qch’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Debian 13.2.0-7) 13.2.0’
using C++11
g++ -fsanitize=undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I'/home/docker/R/Rcpp/include' -I'/home/docker/R/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native  -c RcppExports.cpp -o RcppExports.o
g++ -fsanitize=undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I'/home/docker/R/Rcpp/include' -I'/home/docker/R/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native  -c updatePrior_rcpp.cpp -o updatePrior_rcpp.o
updatePrior_rcpp.cpp:55: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   55 |    #pragma omp parallel num_threads(threads_nb)
      |
updatePrior_rcpp.cpp:65: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
   65 |      #pragma omp for
      |
updatePrior_rcpp.cpp:92: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
   92 |      #pragma omp critical
      |
updatePrior_rcpp.cpp:178: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  178 |   #pragma omp parallel num_threads(threads_nb)
      |
updatePrior_rcpp.cpp:190: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
  190 |     #pragma omp for
      |
updatePrior_rcpp.cpp:289: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  289 | #pragma omp parallel num_threads(threads_nb)
      |
updatePrior_rcpp.cpp:301: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
  301 | #pragma omp for
      |
updatePrior_rcpp.cpp:341: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  341 | #pragma omp critical
      |
updatePrior_rcpp.cpp:409: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  409 | #pragma omp parallel num_threads(threads_nb)
      |
updatePrior_rcpp.cpp:423: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
  423 | #pragma omp for
      |
updatePrior_rcpp.cpp:527: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  527 | #pragma omp parallel num_threads(threads_nb)
      |
updatePrior_rcpp.cpp:539: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
  539 | #pragma omp for
      |
updatePrior_rcpp.cpp:580: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  580 | #pragma omp critical
      |
g++ -fsanitize=undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o qch.so RcppExports.o updatePrior_rcpp.o -L/usr/local/lib/R/lib -lRlapack -L/usr/local/lib/R/lib -lRblas -lgfortran -lm -lubsan -lquadmath -L/usr/local/lib/R/lib -lR
installing to /home/docker/R/00LOCK-qch/00new/qch/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Note: wrong number of arguments to '!='
Note: wrong number of arguments to '<'
Note: wrong number of arguments to '>'
** help
*** installing help indices
** building package indices
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
** testing if installed package can be loaded from temporary location
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Error: package or namespace load failed for ‘qch’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/docker/R/00LOCK-qch/00new/qch/libs/qch.so':
  /home/docker/R/00LOCK-qch/00new/qch/libs/qch.so: undefined symbol: omp_get_num_procs
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/docker/R/qch’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpKcHSZQ/file1371d2b1944/qch_2.0.2.tar.gz’ had non-zero exit status
>
>
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
> library(qch)
Error in library(qch) : there is no package called ‘qch’
Execution halted
Build step 'Execute shell' marked build as failure
Pinging https://builder.r-hub.io/build/FAILURE/qch_2.0.2.tar.gz-4a652faedad6484c9dcd1f44db057f72/2024-03-20T19:25:45Z
{"status":"ok"}
Finished: FAILURE


-------------- next part --------------
A non-text attachment was scrubbed...
Name: qch_2.0.2.tar.gz
Type: application/x-gzip
Size: 339847 bytes
Desc: qch_2.0.2.tar.gz
URL: <https://stat.ethz.ch/pipermail/r-package-devel/attachments/20240321/4ecf2c1d/attachment.bin>