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: [email protected] 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.gzUse 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
OpenPGP_signature
Description: OpenPGP digital signature
