Your message dated Wed, 16 Nov 2022 12:50:44 +0000
with message-id <[email protected]>
and subject line Bug#1024170: fixed in mcl 1:22-282+ds-2
has caused the Debian Bug report #1024170,
regarding mcl breaks roary autopkgtest: different output
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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--
1024170: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024170
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: mcl, roary
Control: found -1 mcl/1:22-282+ds-1
Control: found -1 roary/3.13.0+dfsg-1
Severity: serious
Tags: sid bookworm
User: [email protected]
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of mcl the autopkgtest of roary fails in testing
when that autopkgtest is run with the binary packages of mcl from
unstable. It passes when run with only packages from testing. In tabular
form:
pass fail
mcl from testing 1:22-282+ds-1
roary from testing 3.13.0+dfsg-1
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of mcl to testing
[1]. Due to the nature of this issue, I filed this bug report against
both packages. Can you please investigate the situation and reassign the
bug to the right package?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://qa.debian.org/excuses.php?package=mcl
https://ci.debian.net/data/autopkgtest/testing/amd64/r/roary/28320848/log.gz
Use of uninitialized value in require at
/usr/share/perl5/HTTP/Headers.pm line 302.
Use of uninitialized value in require at
/usr/lib/x86_64-linux-gnu/perl/5.36/Encode.pm line 70.
Please cite Roary if you use any of the results it produces:
Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong,
Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush,
Jacqueline A. Keane, Julian Parkhill,
"Roary: Rapid large-scale prokaryote pan genome analysis",
Bioinformatics, 2015 Nov 15;31(22):3691-3693
doi: http://doi.org/10.1093/bioinformatics/btv421
Pubmed: 26198102
2022/11/15 09:16:56 Cannot find the mcxdeblast executable, please ensure
its in your PATH
2,6c2,6
< out/_blast_results
< out/_clustered
< out/_clustered.clstr
< out/_combined_files
< out/_combined_files.groups
---
out/accessory.header.embl
out/accessory.tab
out/accessory_binary_genes.fa
out/accessory_binary_genes.fa.newick
out/accessory_graph.dot
7a8,18
out/clustered_proteins
out/core_accessory.header.embl
out/core_accessory.tab
out/core_accessory_graph.dot
out/gene_presence_absence.Rtab
out/gene_presence_absence.csv
out/number_of_conserved_genes.Rtab
out/number_of_genes_in_pan_genome.Rtab
out/number_of_new_genes.Rtab
out/number_of_unique_genes.Rtab
out/summary_statistics.txt
autopkgtest [09:16:57]: test test-installed
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: mcl
Source-Version: 1:22-282+ds-2
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
mcl, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <[email protected]> (supplier of updated mcl 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 16 Nov 2022 17:51:43 +0530
Source: mcl
Architecture: source
Version: 1:22-282+ds-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 1024170
Changes:
mcl (1:22-282+ds-2) unstable; urgency=medium
.
* Team Upload.
* Re-vendor mcxdeblast back (Closes: #1024170)
Checksums-Sha1:
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8bcc507f287f9880ddc4c4ae54e8ce124e831b48 384548 mcl_22-282+ds-2.debian.tar.xz
696c1a49b932be3d29efdb03d8025c91fe97b840 5729 mcl_22-282+ds-2_amd64.buildinfo
Checksums-Sha256:
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mcl_22-282+ds-2.dsc
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mcl_22-282+ds-2.debian.tar.xz
7af070a12c22c41ff5a8a68d57b8ab05fd4e8acdfb9ab179e3db2bc3653490a0 5729
mcl_22-282+ds-2_amd64.buildinfo
Files:
4120aff7e0727e6bda541a7eff08fb67 1462 math optional mcl_22-282+ds-2.dsc
e03fd5f9b3a17e41a225d7dd9a52637f 384548 math optional
mcl_22-282+ds-2.debian.tar.xz
d1550ff95dd899e9b7576253f633fe80 5729 math optional
mcl_22-282+ds-2_amd64.buildinfo
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--- End Message ---
