Your message dated Mon, 04 Jan 2021 12:33:25 +0000
with message-id <e1kwp37-000iu1...@fasolo.debian.org>
and subject line Bug#978679: fixed in bedtools 2.29.2+dfsg-5
has caused the Debian Bug report #978679,
regarding bedtools: autpkgtest failures
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
978679: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=978679
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: bedtools
Version: 2.29.2+dfsg-4
Severity: serious
The autopkgtests for bedtools are failing on all tested architectures
(though they are "not a regression" on i386 and armhf). When I look at
the amd64 failure logs, the failures all seem to be missing "../htsutil"
Testing bedtools bamtobed:
test-bamtobed.sh: line 22: ../htsutil: No such file or directory
Testing bedtools bamtofastq:
test-bamtofastq.sh: line 17: ../htsutil: No such file or directory
Testing bedtools bedtobam:
bedtobam.t1...test-bedtobam.sh: line 23: ../htsutil: No such file or
directory
Testing bedtools coverage:
test-coverage.sh: line 22: ../htsutil: No such file or directory
Testing bedtools genomecov:
test-genomecov.sh: line 22: ../htsutil: No such file or directory
Testing bedtools intersect:
intersect.t01...ok
intersect.t02...ok
intersect.t03...ok
intersect.t04...ok
intersect.t05...ok
intersect.t06...ok
intersect.t07...ok
intersect.t08...ok
intersect.t09...ok
intersect.t10...ok
intersect.t11...ok
intersect.t12...ok
intersect.t13...ok
intersect.t14...ok
intersect.t15...ok
intersect.t16...ok
test-intersect.sh: line 200: ../htsutil: No such file or directory
Testing bedtools multicov:
test-multicov.sh: line 17: ../htsutil: No such file or directory
--- End Message ---
--- Begin Message ---
Source: bedtools
Source-Version: 2.29.2+dfsg-5
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
bedtools, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 978...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated bedtools package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Mon, 04 Jan 2021 13:01:58 +0100
Source: bedtools
Architecture: source
Version: 2.29.2+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 978679
Changes:
bedtools (2.29.2+dfsg-5) unstable; urgency=medium
.
* Delete standard debian/gbp.conf
* Revert deletion of test binary htsutil since it is needed to replace
samtools that's not working any more for this purpose
* Move htsutil tool to bedtools package
Closes: #978679
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