Re: [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

2024-03-22 Thread Ivan Krylov via R-package-devel 
В Thu, 21 Mar 2024 18:32:59 +
Annaig De-Walsche  пишет:

> If ever I condition the use of OpenMD directives, users will indeed
> be capable of installing the package, but they wont access to a
> performant version of the code, as it necessitates the use of OpenMD.
> Is there a method to explicitly express that the use of OpenMD is
> highly encouraged?

I think the most practical method would be to produce a
packageStartupMessage() from the .onAttach function of your package if
you detect that the package has been compiled without OpenMP support:
https://cran.r-project.org/doc/manuals/R-exts.html#Load-hooks

> In practical, how to know from R code if OpenMP is present or not?

Your C code will have to detect it and provide this information to the
R code. WRE 1.6.4 says:

>> [C]heck carefully that you have followed the advice in the
>> subsection on OpenMP support [WRE 1.2.1.1]. In particular, any use
>> of OpenMP in C/C++ code will need to use
>> 
>>  #ifdef _OPENMP
>>  # include 
>>  #endif



Similarly, any time you use #pragma omp ... or call
omp_set_num_threads(), it needs to be wrapped in #ifdef _OPENMP ...
#endif.

Additionally, it is important to make sure that during tests and
examples, your OpenMP code doesn't use more than two threads:
https://cran.r-project.org/web/packages/policies.html
This is in place because CRAN checks are run in parallel, and a package
that tries to helpfully use all of the processor cores would interfere
with other packages being checked at the same time.

>   [[alternative HTML version deleted]]

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-- 
Très cordialement,
Ivan

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Re: [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

2024-03-21 Thread Annaig De-Walsche 
Dear Dirk,


Thank you for your help !


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,
| Anna�g De Walsche
| Quantitative Genetics and Evolution unit of INRAE
| Gif-sur-Yvette, France
|

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

In fact, I obtain this error message when I am running the 
rhub::check_for_cran() function. Here is the complete message: 
https://builder.r-hub.io/status/original/qch_2.0.2.tar.gz-4a652faedad6484c9dcd1f44db057f72

| 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.

Thank you for the clarification. If ever I condition the use of OpenMD 
directives, users will indeed be capable of installing the package, but they 
wont access to a performant version of the code, as it necessitates the use of 
OpenMD. Is there a method to explicitly express that the use of OpenMD is 
highly encouraged?

| g++ -fsanitize=undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++11 
-shared -L/usr/local/lib/R/lib

Re: [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

2024-03-21 Thread Dirk Eddelbuettel 


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