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

Jendoubi Bedhiafi, Takoua t@jendoub|14 @end|ng |rom |mper|@|@@c@uk
Mon Aug 24 23:08:59 CEST 2020

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'
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"
> ## 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:

Any ideas on how this can be solved are welcome.

Thanks in advance,

Dr. Takoua Jendoubi
Statistics section | Department of Mathematics |
Imperial College London | Room 533 |
South Kensington Campus | London |
SW7 2AZ |

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