[Rcpp-devel] Something strange with the package check and calls to C abort

[Dirk Eddelbuettel]

On 29 October 2022 at 20:41, Juan Domingo Esteve wrote:
|   I am new to this list and I am using Rcpp for my first large and serious package, so

No worries. "By construction" we all were at that point at some point in the past.

| I apologize if probably this is a naive question, but I have browsed the web and looked
| at the stored mail messages of this list from the beginning of this year without finding
| an answer.
| 
|   My package passed the checks and I was about to try uploading to CRAN but this morning
| I have updated all R packages (including Rcpp and devtools) and now the package fails the
| check because of two warnings. These are
| 
| Found ‘abort’, possibly from ‘abort’ (C)
|        Objects: ‘RcppExports.o’, ‘fullmatrix.o’, ‘jmatrix.o’,
|          ‘matgetcols.o’, ‘matgetdiag.o’, ‘matgetrows.o’, ‘matmetadata.o’,
|          ‘matwrite.o’, ‘memhelper.o’, ‘sparsematrix.o’,
|          ‘symmetricmatrix.o’, ‘teststop.o’
|      Found ‘printf’, possibly from ‘printf’ (C)
|        Objects: ‘RcppExports.o’, ‘fullmatrix.o’, ‘jmatrix.o’,
|          ‘matgetcols.o’, ‘matgetdiag.o’, ‘matgetrows.o’, ‘matmetadata.o’,
|          ‘matwrite.o’, ‘memhelper.o’, ‘sparsematrix.o’,
|          ‘symmetricmatrix.o’, ‘teststop.o’
| 
| I don't call abort, exit or any similar C library function and all my
| interaction are through Rcpp::Rcout, Rcpp::Rcerr, Rcpp::warning and
| Rcpp::stop.
| 
| After some checks, I have found that this happens when I use
| Rcpp::warning and Rcpp::stop. Indeed, with a code like this in testtstop.cpp
| 
| #include <Rcpp.h>
| 
| void test()
| {
|   Rcpp::Rcout << "This is the standard output\n";
|   Rcpp::Rcerr << "This is the standard error\n";
|   Rcpp::warning("This is a warning\n");
|   Rcpp::stop("This should stop the program.\n");
|   return;
| }
| 
| the object teststop.o disappears from the list of those which annoy
| devtools:check when I comment the lines with Rcpp::warning and Rcpp::stop.

Simplify.  Only use devtools::check() when you are positively sure you know
what it is doing. If in doubt rely only on R CMD build + R CMD check.

A package containing (only) that file above should NOT warn. If it does,
something else is wrong.

Also, using such a minimal package is very good practice. Isolating errors is
the key to debugging.
 
| As a last resort, I have tried to download the sources of the Rcpp
| package itself and compile/check in the same way, to convince myself
| that the failure might be there. And indeed, I have got this:
| 
| W  checking compiled code ...
|     File ‘Rcpp/libs/Rcpp.so’:
|       Found ‘abort’, possibly from ‘abort’ (C)
|         Objects: ‘attributes.o’, ‘module.o’
|       Found ‘printf’, possibly from ‘printf’ (C)
|         Objects: ‘attributes.o’, ‘module.o’
| 
|     Compiled code should not call entry points which might terminate R nor
|     write to stdout/stderr instead of to the console, nor use Fortran I/O
|     nor system RNGs.

Well now if we look at the (official !!) page

   https://cran.r-project.org/web/checks/check_results_Rcpp.html

we see no such warnings. Nor do I here. So you have to be a bot more
forthcoming in how you created those.

| An abort function is effectively called from file inst/include/Rcpp/r_cast.h
| at lines 75 and 129.
| 
| Might this be the cause of the check failure?

No.

| I know that this seems more a problem from devtools:check than from Rcpp, but
| it is much more likely that I am totally misunderstanding the question, since

Yes.

| this would prevent any package done with Rcpp to be uploaded to CRAN and many
| people would have already noticed.
| 
|   So again, I reiterate my apologies and if you are so kind to point me to
| appropriate documentation to solve the issue, I would be very grateful.

Start with simpler, more self contained examples. Use the tested and
prescribed tools (neither 'Writing R Extensions' by R Core nor our
documentation mentions or suggests devtools as far as I know).

Minimal examples *are* helpful. When I needed to be sure I (re-)created UBSAN
or ASAN errors I created the sanitizers package with known *true positives*
ensure I could validate my test case.

Here you will see that simple use of

   std::cout
   std::cerr
   print
   abort
   exit

are all sufficient to create this error. And guess what: you will not find
them in the Rcpp sources.

Good luck, and keep probing. It is worth it.

Cheers, Dirk

|   Sincerely
| 
|    Juan
| -- 
| ________________________________________________________________
| Juan Domingo Esteve
| Dept. of Informatics, School of Engineering
| University of Valencia
| Avda. de la Universidad, s/n.
|          46100-Burjasot (Valencia)
|             SPAIN
| 
| Telephone:      +34-963543572
| Fax:            +34-963543550
| email:  Juan.Domingo at uv.es
| ________________________________________________________________
| _______________________________________________
| Rcpp-devel mailing list
| Rcpp-devel at lists.r-forge.r-project.org
| https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
-- 
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org