[R-pkg-devel] help in identifying a segfault (rhub)

[Gábor Csárdi]

Is this reproducible on R-hub? Do you see it with the other R-devel
containers as well?

Some things to try:

Try running address sanitizer on your package to see if it can find
any memory errors. You can do this on R-hub as well, if you cannot do
it on your machine.

Try downloading the https://hub.docker.com/r/rhub/fedora-clang-devel
Docker container and reproduce this locally.

Gabor

On Mon, Aug 24, 2020 at 10:09 PM Jendoubi Bedhiafi, Takoua
<t.jendoubi14 using imperial.ac.uk> wrote:
>
> Hi all,
>
> I am reaching out to seeking help in debugging my package.
> The package has been already on CRAN for some time, updated twice. Also, I have been checking the package regularly on rhub, since my last submission to CRAN, with no errors.
>
> However, recently last checks on rhub end with a segmentation fault for the following platform:
> Platform:       Fedora Linux, R-devel, clang, gfortran
>
> From the error log below it seems that the error happens after running the examples:
>
>
> * checking examples with --run-donttest ...sh: line 1: 10229 Segmentation fault      (core dumped) LANGUAGE=en _R_CHECK_INTERNALS2_=1 R_LIBS=/tmp/RtmpBr5Iyu/RLIBS_264b50c09c34 R_ENVIRON_USER='' R_LIBS_USER='' R_LIBS_SITE='no_such_dir' '/opt/R-devel/lib64/R/bin/R' --vanilla --encoding=UTF-8 > 'iCARH-Ex.Rout' 2>&1 < 'iCARH-Ex.R'
>  ERROR
> Running examples in ‘iCARH-Ex.R’ failed
> The error most likely occurred in:
>
> > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> > ### Name: iCARH.getPathwaysMat
> > ### Title: Builds pathways adjacency matrices
> > ### Aliases: iCARH.getPathwaysMat
> >
> > ### ** Examples
> >
> > keggid = list("C08363")
> > iCARH.getPathwaysMat(keggid, "rno")
> [1] "no result"
> NULL
> > ## No test:
> > keggid = list("Unk1", "C00350","Unk2",c("C08363", "C00712"))
> > iCARH.getPathwaysMat(keggid, "rno")
> named list()
> > ## End(No test)
> >
> >
> >
> >
> > base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> > base::cat("iCARH.getPathwaysMat", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> > cleanEx()
>
>  *** caught segfault ***
> address 0xffffffffffffff96, cause 'memory not mapped'
> An irrecoverable exception occurred. R is aborting now ...
>
>
>  The full log link is below:
> https://builder.r-hub.io/status/original/iCARH_2.0.2.1.tar.gz-5af530549db347e2827b37d9e8b00231
>
> Any ideas on how this can be solved are welcome.
>
> Thanks in advance,
> Bw,
>
> Dr. Takoua Jendoubi
> Statistics section | Department of Mathematics |
> Imperial College London | Room 533 |
> South Kensington Campus | London |
> SW7 2AZ |
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel