Hello Andreas, That's very strange. I will see if I can reproduce this from
what you've said and find a solution to it tomorrow. Kind regards, Shayan Doust
-------- Original message --------From: Andreas Tille <ti...@debian.org> Date:
27/06/2020 07:11 (GMT+00:00) To: Paul Gevers <elb...@debian.org>,
963...@bugs.debian.org, Shayan Doust <he...@shayandoust.me> Subject: Re:
Bug#963774: mcl breaks roary autopkgtest: Cannot find the
mcxdeblast executable, please ensure its in your PATH Hi Shayan,it seems make
is not traversing src/alien/oxygen to install the saidtool (and the other one
mclblastline) as well as its manpages. Icreated the debdiff with the version
in testing:$ debdiff mcl_1%3a14-137+ds-4_amd64.deb
mcl_1%3a14-137+ds-7_amd64.deb [The following lists of changes regard files as
different if they havedifferent names, permissions or owners.]Files in first
.deb but not in second--------------------------------------rw-r--r--
root/root /usr/share/man/man1/mclblastline.1.gz-rw-r--r-- root/root
/usr/share/man/man1/mcxdeblast.1.gz-rwxr-xr-x root/root
/usr/bin/mclblastline-rwxr-xr-x root/root /usr/bin/mcxdeblastControl files:
lines which differ (wdiff
format)------------------------------------------------Depends: libc6 (>=
[-2.14)-] {+2.29)+}Homepage: [-http://micans.org/mcl/-]
{+https://micans.org/mcl/+}Installed-Size: [-3986-] {+4509+}Version:
[-1:14-137+ds-4-] {+1:14-137+ds-7+}I admit I don't understand why make does not
do anything in/build/mcl-14-137+ds/src/alien# makemake[1]: Entering directory
'/build/mcl-14-137+ds/src/alien'make[1]: Nothing to be done for
'all-am'.make[1]: Leaving directory '/build/mcl-14-137+ds/src/alien'If I do in
the pbuilder chroot cd src/alien/oxygen/doc && makethe manpages will be build
and cd src/alien/oxygen/src && make installdoes an installation to
/usr/local/bin.So the way to re-add the missing files manually seems to be
clear. ButI wonder why this was not needed in version 1:14-137+ds-4. Since
youworked intensely on the mcl package recently you might have an idea fora
more straightforward fix.Kind regards Andreas.On Fri, Jun 26, 2020 at
08:48:01PM +0200, Paul Gevers wrote:> 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...@lists.debian.org> User:
debian...@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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