Your message dated Wed, 16 Sep 2020 07:18:26 +0000 with message-id <e1kirhy-000bek...@fasolo.debian.org> and subject line Bug#970340: fixed in rna-star 2.7.5c+dfsg-3 has caused the Debian Bug report #970340, regarding rna-star: autopkgtest regression: --genomeSAindexNbases 8 is too large for the genome size=99940 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.) -- 970340: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=970340 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: rna-star Version: 2.7.5c+dfsg-1 X-Debbugs-CC: debian...@lists.debian.org Severity: serious User: debian...@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of rna-star the autopkgtest of rna-star fails in testing when that autopkgtest is run with the binary packages of rna-star from unstable. It passes when run with only packages from testing. In tabular form: pass fail rna-star from testing 2.7.5c+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 to testing [1]. Can you please investigate the situation and fix it? 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=rna-star https://ci.debian.net/data/autopkgtest/testing/amd64/r/rna-star/7008363/log.gz autopkgtest [20:08:01]: test command1: [----------------------- Sep 13 20:08:01 ..... started STAR run Sep 13 20:08:01 ... starting to generate Genome files Sep 13 20:08:01 ..... processing annotations GTF !!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 Sep 13 20:08:01 ... starting to sort Suffix Array. This may take a long time... Sep 13 20:08:01 ... sorting Suffix Array chunks and saving them to disk... Sep 13 20:08:01 ... loading chunks from disk, packing SA... Sep 13 20:08:01 ... finished generating suffix array Sep 13 20:08:01 ... generating Suffix Array index Sep 13 20:08:01 ... completed Suffix Array index Sep 13 20:08:01 ... writing Genome to disk ... Sep 13 20:08:01 ... writing Suffix Array to disk ... Sep 13 20:08:01 ... writing SAindex to disk Sep 13 20:08:01 ..... finished successfully Sep 13 20:08:01 ..... started STAR run Sep 13 20:08:01 ..... loading genome Sep 13 20:08:01 ..... started mapping Sep 13 20:08:02 ..... finished mapping Sep 13 20:08:02 ..... finished successfully autopkgtest [20:08:02]: test command1: -----------------------] autopkgtest [20:08:02]: test command1: - - - - - - - - - - results - - - - - - - - - - command1 FAIL stderr: !!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7
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--- Begin Message ---Source: rna-star Source-Version: 2.7.5c+dfsg-3 Done: Sascha Steinbiss <sa...@debian.org> We believe that the bug you reported is fixed in the latest version of rna-star, 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 970...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Sascha Steinbiss <sa...@debian.org> (supplier of updated rna-star 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: Wed, 16 Sep 2020 08:56:26 +0200 Source: rna-star Architecture: source Version: 2.7.5c+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Closes: 970340 Changes: rna-star (2.7.5c+dfsg-3) unstable; urgency=medium . * Source upload to enable testing migration. * Confirmed autopkgtest fixed. Closes: #970340 Checksums-Sha1: 962c6d2f9298f9fd84f722a3d4c4e6afde0180de 2148 rna-star_2.7.5c+dfsg-3.dsc 2f2f64fbd28b435599888c3624e9b4adc79014c3 375820 rna-star_2.7.5c+dfsg-3.debian.tar.xz f7c3e1ce885dccd1bb72d737525b53145709ec75 6774 rna-star_2.7.5c+dfsg-3_amd64.buildinfo Checksums-Sha256: 0d6075e333460fb131d748ef9bf4b0e38f51b581dbed3bd428621c44c9b28ef0 2148 rna-star_2.7.5c+dfsg-3.dsc bef237b2c6b5908545721af954fbfca6197e31d246c257541c1246315c2f30cc 375820 rna-star_2.7.5c+dfsg-3.debian.tar.xz d51d5022725cf01257e1c30c0efa340fa2c40b1da58784790f0f60159adf5aef 6774 rna-star_2.7.5c+dfsg-3_amd64.buildinfo Files: 34731aed649f62ed655dfa50593cfff3 2148 science optional rna-star_2.7.5c+dfsg-3.dsc 0da12be6d010c7789d0e034ad2cb191e 375820 science optional rna-star_2.7.5c+dfsg-3.debian.tar.xz feb42066919dfa48e422b7cf965470f2 6774 science optional rna-star_2.7.5c+dfsg-3_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAl9huFAACgkQ6NN64vCf SHKU0A//d1+zduYu7ZIvxbIwO8Kv9A5P3y+z88dp7OYxVk8s9k45+kYzDg0D6EOQ 5qlhXDpXyve6rImToy9IkRu2LeD/cMEOemTwf4888mMRnjHg2HpRrQ9z2vjn+1Hj cGCMykxmWBP6izdnpQN2UMAq92IbfDbfYMqbpc8siVcNtOcnv8QET34rHTKC0JkC 8kk54MZRETiyp5WcjpHXUCykPyKYG6qRyXpGWDmvOl0EgMSLhXbJPO0tY38FBMOq pzM8mdlk3+66hC6rppxiJmvY+LBa6jyncWx7+JG1RwfuQdVpcjkKeYk2p3egxl6m eb34e9wyS+wCRpNJB7h7iNHttFD5UbMcZVkJ9kwgLrHKa/lku9tomEE+SEx9Pq3+ MVwa2EKyLIP29TQ0KQCd6z/2dJfRFWedtjSQKVO5LQhQM0RREapfxjm5o7ZUujE4 4pKX1oQffjizA8keGqt1x864XbEsBYOFAB9mQO+W0+RX5aKed0vV/6ZrPuTvaBwA 8q/aFgMiM19yIsPy/emM/mriSKr/L7dm04UxFzoZi46IwjHAF8MGpDRD1lk12/k2 zRwTo6XHXAOhcXkMH63ZDdBzgRq5oEfJq/xpZz7nuCp2NbLnd0NUYyZj8OegOvFL 51sbS7ssxqpz/33OaTND22O51FOGR4J/VGErrZoP3dg6RxkBUq0= =aQoz -----END PGP SIGNATURE-----
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