Solved, but remaining issue with r-bioc-tximport (Was: List of all packages in BioConductor transition dependency level 1 failing due issue with either RUnit or testthat)
Hi,
thanks to several hints I was able to nearly solve all issues.
On Thu, Sep 02, 2021 at 01:12:29PM +0200, Andreas Tille wrote:
>
> The packages in question are mentioned as Test-Depends and I have no
> idea why these are not found.
It was solved by accorcing debian/tests/autopkgtest-pkg-r.conf featuring
the needed extra_depends.
> The transition is effectively blocked by these issues and any ideas are
> really welcome.
The last blocker is
https://salsa.debian.org/r-pkg-team/r-bioc-tximport/-/jobs/1902367
...
> skip_if_not_installed("tximportData")
Error: Reason: tximportData cannot be loaded
Execution halted
...
Dylan, in debian/tests/autopkgtest-pkg-r.hook I removed all tests in
need of r-bioc-tximportdata (which is in new now - an error will be
triggered once it gets accepted, thus we get a "signal" to remove that
means). I wonder whether your patch[1] should be changed to simply
remove the line
library(tximportData)
and be done. If you have a better solution please apply this and feel
free to upload.
Kind regards and thanks to all who gave useful hints
Andreas.
[1] https://salsa.debian.org/r-pkg-team/r-bioc-tximport/-/blob/master/debian/patches/Fix_autopkgtest.patch
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