[R-pkg-team] Bug#947004: S4Vectors Segmentation fault after r-base-core update (Was: Bug#947004: Tests segfaults (since the r-base-core update?))

[Andreas Tille]

On Sat, Jan 11, 2020 at 10:12:48AM +0100, Dylan Aïssi wrote:
> Le ven. 10 janv. 2020 à 00:30, Pages, Herve <hpages at fredhutch.org> a écrit :
> > Based on the traceback the error happens during evaluation of the 1st
> > argument ('target') passed to checkEqualsNumeric(), that is, during
> > evaluation of 'runmed(y, 7)'. Since this involves base R code only
> > (runmed() is implemented in the stats package) I would say that it's not
> > immediately obvious that the problem is in my court.
> 
> Thanks Hervé for this.

+1
 
> I just updated how to run Debian autopkgtests [1-2] by replacing:
> 
> > LC_ALL=C R --no-save <<EOT
> > require("S4Vectors")
> > S4Vectors:::.test()
> > EOT
> 
> with
> 
> > LC_ALL=C.UTF-8 R --no-save -e 'BiocGenerics:::testPackage("S4Vectors")'
> 
> which seems to be the recommended way to run tests for bioconductor
> packages. And now, there is no segfault anymore for S4vectors but
> IRanges is still crashing. Should we upload these fixes into
> Debian/unstable?

Thanks for the fix - IMHO it makes sense to upload in any way if we
are doing something differently than it should be done.  Would you
mind checking other BioConductor packages as well?

Kind regards and thanks for your investigation

      Andreas.
 
> [1] https://salsa.debian.org/r-pkg-team/r-bioc-s4vectors/commit/51b8ca2571dac1685e748679568edf4463cbfd59
> [2] https://salsa.debian.org/r-pkg-team/r-bioc-iranges/commit/06a76a22fa236f919fc0038c5c01aec35ec2ecda
> [3] https://bioconductor.org/developers/how-to/unitTesting-guidelines/#RUnitConventions

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