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.jendoub...@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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
