[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)

Dirk Eddelbuettel edd @end|ng |rom deb|@n@org
Thu Mar 21 18:00:53 CET 2024 

Salut Annaig,

On 21 March 2024 at 09:26, Annaig De-Walsche wrote:
| 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. 

My preferred typo. The package is actually called Rcpp (pp as in plus-plus).
 
| 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
| 

Could you share with us which actual Docker container you started?

| 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
|       |

You seem to be using a number of OpenMP directives. That is good and
performant. But OpenMP cannot be assumed as given; some OSs more or less skip
it alltogether, some platforms or compilers may not have it. I ran into the
same issue earlier trying to test something with clang on Linux, it would not
find the OpenMP library gcc happily finds. I moved on in that (local) use case.

In short you probably want to condition your use.

| 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

Related. You query a helper function from OpenMP. You could consider to make this
conditional and just return 1L (i.e. single-threaded) when there is no OpenMP.

In short, this seems to be caused by your package not coping with a more
restricted environment.

Amicalement,  Dirk

| 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
| 
| x[DELETED ATTACHMENT qch_2.0.2.tar.gz, application/x-gzip]
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-- 
dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org

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