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

[Dylan Aïssi]

Hi,

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.

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?

Best,
Dylan

[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