GNU bug report logs - #44613
[PATCH] Fix build for bedtools

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Roel Janssen <roel <at> gnu.org>
Subject: bug#44613: closed (Re: [bug#44613] [PATCH] Fix build for bedtools)
Date: Fri, 13 Nov 2020 14:02:02 +0000

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Your bug report

#44613: [PATCH] Fix build for bedtools

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 44613 <at> debbugs.gnu.org.

-- 
44613: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=44613
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Roel Janssen <roel <at> gnu.org>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: 44613-done <at> debbugs.gnu.org
Subject: Re: [bug#44613] [PATCH] Fix build for bedtools
Date: Fri, 13 Nov 2020 15:00:57 +0100

Hi Simon,

On Fri, 2020-11-13 at 14:34 +0100, zimoun wrote:
> Hi Roel,
> 
> On Fri, 13 Nov 2020 at 13:55, Roel Janssen <roel <at> gnu.org> wrote:
> 
> > I also tried removing the bundled htslib for bedtools, but didn't
> > go
> > this route for two reasons:
> > - The bundled htslib for bedtools seems "slightly modified" (I
> > didn't
> > investigate further)
> > - Replacing the references to libhts.a with $(pkg-config htslib --
> > cflags --libs) produced various linker errors. So I stopped right
> > there.
> > 
> > I'm sure more tools will likely have failed because of the htslib
> > upgrade (sorry about this!), so having htslib-1.9 around for some
> > time
> > may be a good fallback for now.
> 
> Thank for your explanations.
> 
> 
> > Just to double-check: Is it OK to push the proposed patches?
> 
> I have not tried them but they LGTM.
> 

Thanks for the quick review. I pushed the patches in
c3232fcc7785abc1057a0d4b5b1832f1e39c9c1b,
da4a38edad52f7bb5a8d41465d09f3f0197fd0b7, and
3ede804f6d4c38ff0b9a5705544a8c35f6827ff1.

Kind regards,
Roel Janssen

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From: Roel Janssen <roel <at> gnu.org>
To: guix-patches <at> gnu.org
Subject: [PATCH] Fix build for bedtools
Date: Fri, 13 Nov 2020 12:01:04 +0100

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Dear Guix,

By updating samtools to 1.11, I introduced a build failure for
bedtools. More precisely, the tests for intersect break in precisely
this way:
https://github.com/arq5x/bedtools2/issues/814

With the following patches, I'd like to add samtools-1.9, htslib-1.9
(samtools depends on that) to fix this problem with bedtools.

Alternatively we could add a patch to disable the failing bedtools
tests.  I manually inspected the test results, and seem to match
perfectly (indicating that there's no problem with bedtools).

Kind regards,
Roel Janssen

[0003-gnu-bedtools-Use-samtools-1.9.patch (text/x-patch, attachment)]

[0002-gnu-Add-samtools-1.9.patch (text/x-patch, attachment)]

[0001-gnu-Add-htslib-1.9.patch (text/x-patch, attachment)]

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