Your message dated Wed, 14 Dec 2022 21:19:12 +0000
with message-id <e1p5z9k-00azyz...@fasolo.debian.org>
and subject line Bug#1021675: fixed in ariba 2.14.6+ds-4
has caused the Debian Bug report #1021675,
regarding ariba: autopkgtest regression and ftbfs with samtools 1.16
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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--
1021675: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1021675
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: ariba
Version: 2.14.6+ds-3
Severity: serious
Tags: ftbfs upstream help
Justification: fails to build from source (but built successfully in the past)
Greetings,
Following the upgrade of htslib, samtools and bcftools from
versions 1.13 to 1.16, ariba hits autopkgtest regressions which
are preventing migration of python-pysam to testing. The test
failures are also present during the build time test suite,
causing the package to fail to build from source.
I attempted to begin wrapping up a patch fixing/working around
the problem which looks to be caused by the migration of mpileup
functionalities from samtools to bcftools, but the test suite
then chokes on non-matching command output, for which I don't
know whether the new results are sound and simply need
adjustments, or if errors could have been left over. Temporary
patch is below for reference, but is not sufficient on his own
to fix the failure:
-------8<--------------8<--------------8<--------------8<-------
--- a/ariba/samtools_variants.py
+++ b/ariba/samtools_variants.py
@@ -1,6 +1,7 @@
import os
import sys
import pysam
+import pysam.bcftools
import pyfastaq
import vcfcall_ariba
@@ -36,13 +37,11 @@
tmp_vcf = self.vcf_file + '.tmp'
with open(tmp_vcf, 'w') as f:
- print(pysam.mpileup(
+ print(pysam.bcftools.mpileup(
'-t', 'INFO/AD,INFO/ADF,INFO/ADR',
'-L', '99999999',
'-A',
'-f', self.ref_fa,
- '-u',
- '-v',
self.bam,
), end='', file=f)
-------8<--------------8<--------------8<--------------8<-------
I already provided upstream with my findings on their issue
tracker[1] in a related entry, but I don't know for sure how
much active they are these days. This note in debbugs is mostly
to document the issue for Med team members before they spend too
much time debugging this issue in parallel (and also seeking
help if possible).
[1]: https://github.com/sanger-pathogens/ariba/issues/327
Have a nice day, :)
Étienne.
-- System Information:
Debian Release: bookworm/sid
APT prefers unstable
APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.19.0-2-amd64 (SMP w/12 CPU threads; PREEMPT)
Locale: LANG=C.UTF-8, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
--
Étienne Mollier <emoll...@emlwks999.eu>
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/5, please excuse my verbosity.
On air: Gazpacho - Valerie's Friend
signature.asc
Description: PGP signature
--- End Message ---
--- Begin Message ---
Source: ariba
Source-Version: 2.14.6+ds-4
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
ariba, 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 1021...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated ariba 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: SHA512
Format: 1.8
Date: Wed, 14 Dec 2022 21:34:16 +0100
Source: ariba
Architecture: source
Version: 2.14.6+ds-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1021675 1022508
Changes:
ariba (2.14.6+ds-4) unstable; urgency=medium
.
[ Andreas Tille ]
* Team upload.
* Fix watch file
* Standards-Version: 4.6.1 (routine-update)
* Add salsa-ci file (routine-update)
.
[ Étienne Mollier ]
* mpileup-1.16.patch: add; fix mpileup calls since htslib 1.16.
(Closes: #1021675, #1022508)
* skip-cluster-test.patch: add; skip due to mismatched output.
* adjust-bowtie2-test.patch: skip some bowtie2 tests needing refresh.
* d/control: don't built for python3.11 until pysam supports it.
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