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Bug#1011265: marked as done (Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15])

Your message dated Thu, 18 Dec 2025 09:52:39 +0100
with message-id <a44ac0dc-a766-41eb-add7-bec2daeeb70b@debian.org>
and subject line Re: Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]
has caused the Debian Bug report #1011265,
regarding Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]
to be marked as done.

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1011265: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1011265
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--- Begin Message --- 
Package: release.debian.org
User: release.debian.org@packages.debian.org
Usertag: britney

Hi,

On 11-05-2022 12:34, Graham Inggs wrote:

Yes, please go ahead.

Tracker is at:
https://release.debian.org/transitions/html/r-api-bioc-3.15.html
There's three package still waiting for an upload, r-bioc-progeny, r-bioc-monocle and r-bioc-scater. When is the ETA for those?
Apart from these missing uploads, there's a bunch of autopkgtest regressions blocking the migration of the set [1]. I have a hunch that quite some regressions are caused by missing *versioned* (test) dependencies that cause incompatible sets to be tested. Thinking more about it that could very well be a bug in our migration software failing to properly handle the Provides which glues this all together and which is uniquely provided by r-bioc-biocgenerics. Remember that our migration software tries to determine the minimal (source based) set (deducted from real package relations, i.e. Depends, Conflicts and Breaks) that needs to come from unstable to be tested in testing. You can see which source packages it deducted from the third line of each autopkgtest log. E.g. [2] has: 
--pin-packages=unstable=src:r-bioc-megadepth,src:r-bioc-biocgenerics

And than later:
The following packages have unmet dependencies:
 r-bioc-rtracklayer : Depends: r-api-bioc-3.14
Depends: r-bioc-rsamtools (>= 1.31.2) but it is not going to be installed Depends: r-bioc-genomicalignments (>= 1.15.6) but it is not going to be installed
I'll see if some manual addition pinning helps, but checking the status in unstable may also be a good way to see what the status is. In the mean time, this mail is also a bug report against britney, if the manual pinning helps, we'll need to see how to improve it. 

Paul

[1] https://people.debian.org/~elbrus/ci/regressions.html
[2] https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-bioc-megadepth/21776746/log.gz

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--- Begin Message --- 
Hi,

On 5/19/22 09:40, Paul Gevers wrote:
Thinking more about it that could very well be a bug in our migration software failing to properly handle the Provides which glues this all together and which is uniquely provided by r-bioc-biocgenerics. 


I just deployed a fix for this. It became commit 5541ec3.

Paul

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