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.
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--
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
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- 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
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