GNU bug report logs - #77357
[PATCH 0/1] Remove freebayes

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: guix-patches <at> gnu.org
Cc: rekado <at> elephly.net, Andreas Enge <andreas <at> enge.fr>
Subject: [PATCH 0/1] Remove freebayes
Date: Sat, 29 Mar 2025 10:52:45 +0100

I noticed that the package does not build when updating parallel.
It should be possible to somehow repair it, but apparently nobody has
noticed that the package does not build any more for almost two years:
   https://ci.guix.gnu.org/build/9529724/details
   first failure:
   https://ci.guix.gnu.org/build/1171985/details
So if there is no interest in it, there is maybe no point in spending
time on it.

I would suggest to remove it on or after April 29.

Andreas Enge (1):
  gnu: Remove freebayes.

 gnu/packages/bioinformatics.scm | 82 ---------------------------------
 1 file changed, 82 deletions(-)


base-commit: 67f4a2feadbb6cc04a61b5a3bc7b8f4bace2a0bb
-- 
2.49.0

Message #8 received at 77357 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: 77357 <at> debbugs.gnu.org
Cc: rekado <at> elephly.net
Subject: Re: [PATCH 0/1] Remove freebayes
Date: Sat, 29 Mar 2025 11:01:43 +0100

I made a mistake in submitting the patch series; the (trivial) patch is
in #77358, which I have closed; we can continue the discussion here.

Andreas

Message #11 received at 77357 <at> debbugs.gnu.org (full text, mbox):

From: Sebastian Dümcke <code <at> sam-d.com>
To: 77357 <at> debbugs.gnu.org
Subject: Re: [PATCH 0/1] Remove freebayes
Date: Sun, 30 Mar 2025 18:12:01 +0200

Dear Andreas,

I know I have a manifest somewhere depending on freebayes. However, I am 
unsure when was the last time I ran it. And even then I could use 
time-machine to get a working version of freebayes running. So removing 
it is not a big deal. However, it seems that upstream is aware of the 
failing test suite [1]. Unfortubnately building --with-latest=freebayes 
did not immediately lead me to success.

Perhaps what should be discussed is the potential overlap (at leat 
conceptually) between the guix channel bioinformatic tools (as found in 
bioinformatics.scm) and the many more tools in the guix-science channel. 
Would it make sense to move all these packages over to the guix-science 
channel?

Best
Sebastian

[1]: https://github.com/freebayes/freebayes/issues/786

Message #14 received at 77357 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Andreas Enge <andreas <at> enge.fr>
Cc: 77357 <at> debbugs.gnu.org
Subject: Re: [PATCH 0/1] Remove freebayes
Date: Wed, 02 Apr 2025 09:54:01 +0200

I have previously brought this up with upstream in an attempt to 
fix this, but I haven't yet been successful in fixing it.

-- 
Ricardo

Message #17 received at 77357 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: Sebastian Dümcke <code <at> sam-d.com>,
 77357 <at> debbugs.gnu.org
Subject: Re: [PATCH 0/1] Remove freebayes
Date: Wed, 2 Apr 2025 10:45:11 +0200

Hello,

cc-ing all discussion participants, as unfortunately debbugs does not do so.
If I understand Sebastian correctly, then freebayes works, just the test
suite does not? In that case, we could also just disable the tests with a
pointer to the upstream issue. But then it would be nice if someone could
first confirm that the package itself works :)

Concerning guix-science, its description on codeberg says
   This GNU Guix channel provides recent versions of scientific software,
   which cannot be included upstream.

This clearly is not the case of freebayes, which already is included :)

Andreas

Message #20 received at 77357 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: Sebastian Dümcke <code <at> sam-d.com>,
 77357 <at> debbugs.gnu.org
Subject: Re: [PATCH 0/1] Remove freebayes
Date: Wed, 2 Apr 2025 11:05:08 +0200

Ricardo sent a bug upstream about a year ago:
   https://github.com/freebayes/freebayes/issues/825

Pjotrp mentions vcflib, which is a package with only freebayes as
dependency in Guix. We are at version 1.0.9 of February 2023, and there
is a 1.0.12 from November 2024. But the package recipe is quite the
nightmare...

Andreas

Message #23 received at 77357 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Andreas Enge <andreas <at> enge.fr>
Cc: Sebastian Dümcke <code <at> sam-d.com>, 77357 <at> debbugs.gnu.org
Subject: Re: [PATCH 0/1] Remove freebayes
Date: Thu, 03 Apr 2025 17:09:13 +0200

Andreas Enge <andreas <at> enge.fr> writes:

> Ricardo sent a bug upstream about a year ago:
>    https://github.com/freebayes/freebayes/issues/825
>
> Pjotrp mentions vcflib, which is a package with only freebayes 
> as
> dependency in Guix. We are at version 1.0.9 of February 2023, 
> and there
> is a 1.0.12 from November 2024. But the package recipe is quite 
> the
> nightmare...

I have locally updated vcflib to 1.0.12 and managed to build the 
latest version of freebayes.
It was not fun.

I'll push this once I've cleaned up my unrelated WIP for ITK.

-- 
Ricardo

Message #26 received at 77357 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: Sebastian Dümcke <code <at> sam-d.com>,
 77357 <at> debbugs.gnu.org
Subject: Re: [PATCH 0/1] Remove freebayes
Date: Thu, 3 Apr 2025 17:15:19 +0200

Am Thu, Apr 03, 2025 at 05:09:13PM +0200 schrieb Ricardo Wurmus:
> I have locally updated vcflib to 1.0.12 and managed to build the latest
> version of freebayes.
> It was not fun.

I imagine, congratulations!

Andreas

Message #29 received at 77357 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Andreas Enge <andreas <at> enge.fr>
Cc: Sebastian Dümcke <code <at> sam-d.com>, 77357 <at> debbugs.gnu.org
Subject: Re: [PATCH 0/1] Remove freebayes
Date: Thu, 03 Apr 2025 23:25:16 +0200

Andreas Enge <andreas <at> enge.fr> writes:

> Am Thu, Apr 03, 2025 at 05:09:13PM +0200 schrieb Ricardo Wurmus:
>> I have locally updated vcflib to 1.0.12 and managed to build 
>> the latest
>> version of freebayes.
>> It was not fun.

Pushed with commit efaa20d2d86bc4f10dfc45a25fca50a0dad6e917.
Can we close this issue?

-- 
Ricardo

Message #34 received at 77357-done <at> debbugs.gnu.org (full text, mbox):

From: Arun Isaac <arunisaac <at> systemreboot.net>
To: 77357-done <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>, Andreas Enge <andreas <at> enge.fr>,
 Sebastian Dümcke <code <at> sam-d.com>
Subject: Re: [PATCH 0/1] Remove freebayes
Date: Fri, 04 Apr 2025 01:41:34 +0100

Hi all,

Thank you all for your hard work. I use freebayes in my research, and I
can confirm that it actually works and produces scientifically
meaningful results.

Regards,
Arun

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