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

Andreas Tille tille at debian.org
Sat Jun 27 07:11:04 BST 2020


Hi Shayan,

it seems make is not traversing src/alien/oxygen to install the said
tool (and the other one mclblastline) as well as its manpages.  I
created 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 have
different 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/mcxdeblast

Control 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# make
make[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 && make

the manpages will be build and

   cd src/alien/oxygen/src && make install

does an installation to /usr/local/bin.

So the way to re-add the missing files manually seems to be clear.  But
I wonder why this was not needed in version 1:14-137+ds-4.  Since you
worked intensely on the mcl package recently you might have an idea for
a 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-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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