Dear Dirk:
Thank you very much for your extremely quick response.
I have cheked with R CMD build + R CMD check, as you suggested,
and I have found the error.
The call to abort is still present with R CMD check but, when I
copy the code in another machine which I have not yet updated, it
works perfectly.
The check generates file symbols.rds that, when loaded with
S<-loadRDS("symbols.rds") shows the complete table, and certainly,
symbol abort is present only in the second machine.
My guess is that this may be related with the _default_ compilation
flags (I haven't altered myself), which are different between both
machines. Since it seems a quite specific and obscure problem, I will
try to isolate with a minimal package, as you suggest, and I will post
a summary including all details and compilation/linking flags, since it
might help others with the same problem (if anyone else).
Again, thank you very much for your time.
Sincerely
Juan
El 29/10/22 a las 20:58, Dirk Eddelbuettel escribió:
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://urldefense.com/v3/__https://cran.r-project.org/web/checks/check_results_Rcpp.html__;!!D9dNQwwGXtA!U8voohz5lb9Mvawf6PO0kKpLjrSsFH5HIpTOnCYaEkk5sEeKpsyaRk0HznuPjkWWoF4Cw6MIh1_g$
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.domi...@uv.es
| ________________________________________________________________
| _______________________________________________
| Rcpp-devel mailing list
| Rcpp-devel@lists.r-forge.r-project.org
|
https://urldefense.com/v3/__https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel__;!!D9dNQwwGXtA!U8voohz5lb9Mvawf6PO0kKpLjrSsFH5HIpTOnCYaEkk5sEeKpsyaRk0HznuPjkWWoF4Cww_Q9-9j$
--
________________________________________________________________
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.domi...@uv.es
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