[Debian-med-packaging] Bug#963774: mcl breaks roary autopkgtest: Cannot find the mcxdeblast executable, please ensure its in your PATH

[Paul Gevers]

Source: mcl, roary
Control: found -1 mcl/1:14-137+ds-7
Control: found -1 roary/3.13.0+dfsg-1
Severity: serious
Tags: sid bullseye
X-Debbugs-CC: debian-ci at lists.debian.org
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    1:14-137+ds-7
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/6058047/log.gz

autopkgtest [18:20:38]: test test-installed: [-----------------------
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/5.30/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

2020/06/25 18:20:41 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 [18:20:41]: test test-installed: -----------------------]

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