Hi Maintainer

The autopkgtests of r-bioc-deseq2 regressed in testing sometime after
2021-09-07 11:35:05 UTC [1].

E: Package 'r-bioc-tximportdata' has no installation candidate
pkg-r-autopkgtest    FAIL badpkg
blame: r-bioc-deseq2

I suspect this is due to #961138.

Regards
Graham


[1] https://ci.debian.net/packages/r/r-bioc-deseq2/testing/amd64/

We believe that the bug you reported is fixed in the latest version of
r-bioc-deseq2, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 994443@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated r-bioc-deseq2 package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Sun, 26 Sep 2021 20:58:45 +0200
Source: r-bioc-deseq2
Architecture: source
Version: 1.32.0+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 994443
Changes:
 r-bioc-deseq2 (1.32.0+dfsg-2) unstable; urgency=medium
 .
   [ Nilesh Patra ]
   * d/t/autopkgtest-pkg-r.conf: Add r-bioc-tximportdata
     Closes: #994443
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r-bioc-deseq2's autopkgtests started to again pass in testing on
2021-09-29, once r-bioc-tximportdata migrated.
However, the autopkgtests in stable continue to fail [1].

I think you are doing something wrong if a change in a package in
unstable affects a package in testing and stable.


[1] https://ci.debian.net/packages/r/r-bioc-deseq2/stable/amd64/

On Thu, 21 Oct 2021 15:15:52 +0200 Graham Inggs <ginggs@debian.org> wrote:
 > Control: reopen -1
 >
 > r-bioc-deseq2's autopkgtests started to again pass in testing on
 > 2021-09-29, once r-bioc-tximportdata migrated.
 > However, the autopkgtests in stable continue to fail [1].

Correct, because the package r-bioc-tximportdata does not exist in stable.

control: fixed -1 1.32.0+dfsg-3

Hi Graham,

I think this has got nothing to do with our changes in unstable -- I'd be very surprised if so,
since essentially atleast stable is disconnected, unless some other package has been on-purpose updated there.
As I can see, tests in stable were always failing[1]
This is due to missing dep, see Michael's mail below.

So I'm marking this bug as fixed in the latest version to avoid autoremoval. Hope that is okay.

[1]: https://ci.debian.net/packages/r/r-bioc-deseq2/stable/amd64/

Nilesh

Hi Nilesh

What changed in unstable, was that r-bioc-tximportdata was accepted on
2021-09-10, causing r-bioc-deseq2's autopkgtests to fail in testing
and stable.

They were passing in testing up until 2021-09-07, so they would have
been passing in stable on the day of the bullseye release.

Removing r-bioc-deseq2 from testing will not solve this bug.
Reassigning this bug to r-bioc-tximportdata and removing
r-bioc-tximportdata from testing will not help either, as only
removing r-bioc-tximportdata from unstable will make r-bioc-deseq2's
autopkgtests pass again.  I suggest reassigning this bug to dh-r,
where this behaviour in pkg-r-autopkgtest can at least be disabled for
now, until a proper solution for #961138 can be found.

Regards
Graham

control: reassign -1 dh-r
control: severity -1 important
control: retitle -1 pkg-r-autopkgtest: please use the same number of packages as release, and not base it on apt lists

Hi Graham,

Done.

Thanks, Nilesh

Maybe this is a duplicate of https://bugs.debian.org/961138 which is
fixed now in Testing.

Thank you,
Jeremy Bícha

Hi Jeremy

My understanding is #961138 was for the changes in autodep8 and that
there are still changes that need to be made in dh-r.

There is a merge request against dhr- mentioned in #961138 [1].

Regards
Graham


[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=961138#77