[Debian-med-packaging] Bug#970340: rna-star: autopkgtest regression: --genomeSAindexNbases 8 is too large for the genome size=99940

[Paul Gevers]

Source: rna-star
Version: 2.7.5c+dfsg-1
X-Debbugs-CC: debian-ci at lists.debian.org
Severity: serious
User: debian-ci at 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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