Your message dated Mon, 29 Jun 2020 11:35:51 +0000 with message-id <e1jps4l-0007wy...@fasolo.debian.org> and subject line Bug#963774: fixed in mcl 1:14-137+ds-8 has caused the Debian Bug report #963774, regarding mcl breaks roary autopkgtest: Cannot find the mcxdeblast executable, please ensure its in your PATH to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 963774: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=963774 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---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: -----------------------]
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---Source: mcl Source-Version: 1:14-137+ds-8 Done: Shayan Doust <he...@shayandoust.me> We believe that the bug you reported is fixed in the latest version of mcl, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 963...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Shayan Doust <he...@shayandoust.me> (supplier of updated mcl package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 29 Jun 2020 10:54:16 +0100 Source: mcl Architecture: source Version: 1:14-137+ds-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Shayan Doust <he...@shayandoust.me> Closes: 963774 Changes: mcl (1:14-137+ds-8) unstable; urgency=medium . * Add myself as an uploader * Modify patch to fix missing scripts' installation (Closes: #963774) Checksums-Sha1: 59b17a96226d0346fc500ce2156caf189850470b 2201 mcl_14-137+ds-8.dsc 647d89163d49fe8f889bc2092b85eb8980708808 384452 mcl_14-137+ds-8.debian.tar.xz 5e24e5a928b03ebda9884328f74d2a85997228fa 7662 mcl_14-137+ds-8_amd64.buildinfo Checksums-Sha256: ed50936b712786ceaa127894ce0c42781f429d0c8584714d0f739d5d2f7a4c65 2201 mcl_14-137+ds-8.dsc 7e08811b74f56ec2823465afd3ad62f08d8df6753c6cce6ecba9a27825e2e3cc 384452 mcl_14-137+ds-8.debian.tar.xz 87a3581767d11de9277a29ebb19e71ecc96b2a50ad670638bb68271ab71ce725 7662 mcl_14-137+ds-8_amd64.buildinfo Files: badb012fd27e443cb5ad0ce7b9448271 2201 math optional mcl_14-137+ds-8.dsc cb4f10c11524faed8324edcef64569d5 384452 math optional mcl_14-137+ds-8.debian.tar.xz fb939364354b2e32d060f1f7f6d8dbc3 7662 math optional mcl_14-137+ds-8_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl75zzERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtG12BAAm7TE/s2ntCMddyLIFPVCzCUUMlTWq7+U +NF2GkIZxufAqqAp0NUgDBpbcGvouFM0v9hQY0FWhG2RTbgQqzpbtQ/HhIJ7CcV2 R2VaJqXg2Ueytf9qp3xjcgDaBUXE6XWjSrwDpzYlR3KFRFiQPU8T/8qqqDTwqwjO xOCPWYF6Pwxxx1iWqlKFihcRR7wn3ZgCdCONjMEiIZMBFHIr2bRJ3AbsTdo/6OJG syOb7JavvZ8hR5NQAWHIPAF10dcr8maojjIpbMJwsZUBpMjl4cLXn3Yz4K1p3v3T hhO1+Whz0W3jQrq7yOzrQGONgvfeCVWAS23/bpGyxn9RCDtQ1//UgyomO75n29j7 e/wVbs9DeEFEhTHLbrmY0/IkuxeLgpos/mUDvUMbRrpx2YqgDp6QJkZFomoyRVXw 5qab/iVY4FPdVCERbaXRkut/dQ3shhFpDKBBL2dbDqDfaU4IpnxdLUYt4H2hrEOu QE4hJL4kmORfMU3TCsoV9/JHvHD9FatOQa2YEhYSs2QtzeHCj8y/lSBUIWxxvpso QkkMskqMnBJTjx9NTaDNh1firy1bTcxeIN4U11AMkY7rYqik6Ey8lM0w1R/SU7ym PlwaoI634WfWaNz8i4Fd3I08lxjhm8cPTL0N+2Bthz2NOhOj0ouxIWYdI4fT8Fxm yYOiJKz+Ulk= =VDGo -----END PGP SIGNATURE-----
--- End Message ---
