[Debian-med-packaging] Bug#1024170: mcl breaks roary autopkgtest: different output

[Paul Gevers]

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: debian-ci at lists.debian.org
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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: OpenPGP_signature
Type: application/pgp-signature
Size: 495 bytes
Desc: OpenPGP digital signature
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20221115/e46cf374/attachment.sig>