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Re: How to sneak in Test-Depends like r-cran-testthat into automated testing for BioC packages





On Wed, 1 Sep, 2021, 5:51 pm Andreas Tille, <tille@debian.org> wrote:
On Wed, Sep 01, 2021 at 05:20:44PM +0530, Nilesh Patra wrote:
> https://sources.debian.org/src/r-bioc-gsva/1.38.2+ds-3/debian/tests/autopkgtest-pkg-r.conf/
>
> Simply add a d/tests/autopkgtest-pkg-r.conf

Tried this in

   https://salsa.debian.org/r-pkg-team/r-bioc-tximport/-/commit/fed58c3d64f8a80f18b01d91617c7584be2c2324

but failed.

We have the salsa CI results, and it's clear that testthat is getting loaded now as opposed to the last CI.

https://salsa.debian.org/r-pkg-team/r-bioc-tximport/-/jobs/1897039

The new error fails because it does not have tximportData.
Fixing this should be straightforward as well, provided we have it in the archive.
Can you do this?

If you are getting the same error locally, then your likely need to update your schroot, and install the latest versions of autodep8 and autopkgtest packages.

And that said, the autopkgtests do not even install dependencies for me in the chroot, because some dependency of this package hasn't been built with bioc api 3.13 and that looks legit to me.
I'm a bit surprised that both salsa CI and your build environment are able to satisfy deps.
Either the images at both are not the latest, or the error is sitting in front of my screen not very sure.

Nilesh



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