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Subject: |
[PATCH] Fix build for bedtools |
Date: |
Fri, 13 Nov 2020 12:01:04 +0100 |
User-agent: |
Evolution 3.38.1 (3.38.1-1.fc33) |
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
Description: Text Data
0002-gnu-Add-samtools-1.9.patch
Description: Text Data
0001-gnu-Add-htslib-1.9.patch
Description: Text Data
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--- Begin Message ---
Subject: |
Re: [bug#44613] [PATCH] Fix build for bedtools |
Date: |
Fri, 13 Nov 2020 15:00:57 +0100 |
User-agent: |
Evolution 3.38.1 (3.38.1-1.fc33) |
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@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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