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Bug#1024170: mcl breaks roary autopkgtest: different output
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Paul Gevers
Nov 15, 2022, 3:31:25 PM11/15/22
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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: debi...@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
Control: found -1 mcl/1:22-282+ds-1
Control: found -1 roary/3.13.0+dfsg-1
Severity: serious
Tags: sid bookworm
User: debi...@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
Nilesh Patra
Nov 16, 2022, 7:10:04 AM11/16/22
to
On Wed, Nov 16, 2022 at 11:25:02AM +0100, Andreas Tille wrote:
mcl has stopped vendoring mxcdeblast since your last upload[1] but it was doing so earlier.
> 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.
$ debdiff mcl_14-137+ds-9.dsc mcl_22-282+ds-1.dsc 2>/dev/null | wc -l
51040
That's quite a lot of lines. Something definitely changed.
[1]: https://packages.debian.org/sid/amd64/mcl/filelist
--
Best,
Nilesh
> 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
The error is here ^^^
> > 2022/11/15 09:16:56 Cannot find the mcxdeblast executable, please ensure its
> > in your PATH
mcl has stopped vendoring mxcdeblast since your last upload[1] but it was doing so earlier.
> 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.
$ debdiff mcl_14-137+ds-9.dsc mcl_22-282+ds-1.dsc 2>/dev/null | wc -l
51040
That's quite a lot of lines. Something definitely changed.
[1]: https://packages.debian.org/sid/amd64/mcl/filelist
--
Best,
Nilesh
Andreas Tille
Nov 16, 2022, 8:10:03 AM11/16/22
to
Control: tags -1 pending
Am Wed, Nov 16, 2022 at 05:35:12PM +0530 schrieb Nilesh Patra:
> > $ debdiff mcl_14-137+ds-9.dsc mcl_22-282+ds-1.dsc 2>/dev/null | wc -l
> > 51040
> >
> > That's quite a lot of lines. Something definitely changed.
>
> And I found out what that is.
>
> $ git checkout debian/1%14-137+ds-9
> Note: switching to 'debian/1%14-137+ds-9'.
> $ $ find . -name mcxdeblast
> ./src/alien/oxygen/src/mcxdeblast
>
> $ git checkout master
> $ find . -name mcxdeblast
> [... no output ...]
>
> Upstream changed the code and stopped vendoring mcxdeblast
You are perfectly right. I stupidly checked against the version in
testing in my local test.
I'll re-add the according script to the mcl package and when doing
so roary test passes.
Thanks for opening my eyes
Andreas.
--
http://fam-tille.de
Am Wed, Nov 16, 2022 at 05:35:12PM +0530 schrieb Nilesh Patra:
> > $ debdiff mcl_14-137+ds-9.dsc mcl_22-282+ds-1.dsc 2>/dev/null | wc -l
> > 51040
> >
> > That's quite a lot of lines. Something definitely changed.
>
>
> $ git checkout debian/1%14-137+ds-9
> Note: switching to 'debian/1%14-137+ds-9'.
> $ $ find . -name mcxdeblast
> ./src/alien/oxygen/src/mcxdeblast
>
> $ git checkout master
> $ find . -name mcxdeblast
> [... no output ...]
>
> Upstream changed the code and stopped vendoring mcxdeblast
You are perfectly right. I stupidly checked against the version in
testing in my local test.
I'll re-add the according script to the mcl package and when doing
so roary test passes.
Thanks for opening my eyes
Andreas.
--
http://fam-tille.de
Nilesh Patra
Nov 16, 2022, 8:30:04 AM11/16/22
to
--
Best,
Nilesh
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