GNU bug report logs - #47821
[PATCH] Update htslib, bcftools, samtools, bedtools

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From: Efraim Flashner <efraim <at> flashner.co.il>
To: Roel Janssen <roel <at> gnu.org>
Cc: 47821 <at> debbugs.gnu.org
Subject: [bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools
Date: Thu, 29 Apr 2021 09:43:35 +0300

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On Wed, Apr 28, 2021 at 04:05:09PM +0200, Roel Janssen wrote:
> On Tue, 2021-04-27 at 10:32 +0300, Efraim Flashner wrote:
> > On Fri, Apr 16, 2021 at 11:55:39AM +0200, Roel Janssen wrote:
> > > Hi Guix,
> > > 
> > > The following patches update htslib, bcftools, samtools, and
> > > bedtools.
> > > I've succesfully built bedtools with the latest samtools instead of
> > > the
> > > 1.9 version.
> > 
> > These look good and are ready for merging. Can you take a look at
> > python-pybedtools? There's a new version out which I hope builds with
> > the newer version of bedtools.
> > 
> > Thanks.
> > 
> 
> I looked at python-pybedtools and came up with the following patch.
> The test phase is still not entirely happy because it ends with:
> 
> ---
> ================ 497 passed, 3 xfailed, 426 warnings in 25.49s
> =================
> Error in atexit._run_exitfuncs:
> Traceback (most recent call last):
>   File "/gnu/store/rz42ba0my9vrgbkjpkzr2drmnjk5ah50-python-
> 3.8.2/lib/python3.8/shutil.py", line 704, in rmtree
>     orig_st = os.lstat(path)
> ---
> 
> I attached the patch that I have that at least builds the newer version
> of python-pybedtools.  I don't know how to further test it.
> 
> Can I in the meantime already push the patches for updating htslib,
> bcftools, samtools and bedtools?
> 

Yeah, those patches LGTM.


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Efraim Flashner   <efraim <at> flashner.co.il>   אפרים פלשנר
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