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

[Andreas Tille]

Hi,

Am Tue, Nov 15, 2022 at 09:16:53PM +0100 schrieb Paul Gevers:
> 2022/11/15 09:16:56 Cannot find the mcxdeblast executable, please ensure its
> in your PATH

This is strange.  I've changed some unrelated things inside the
autopkgtest in git.  This resolves the issue above and the expected
files are created.

It turns out that the call

$ roary -f out *.gff
Use of uninitialized value in require at /usr/lib/x86_64-linux-gnu/perl5/5.36/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

Use of uninitialized value in require at /usr/lib/x86_64-linux-gnu/perl5/5.36/Encode.pm line 70.


results in a non-zero return code which makes the test fail despite
the calculated results seem to be correct.  Sascha (or anyone else)
would you mind checking this?

Kind regards
   Andreas.

-- 
http://fam-tille.de