Bug#970340: [Debian-med-packaging] Bug#970340: rna-star: autopkgtest regression: --genomeSAindexNbases 8 is too large for the genome size=99940
Dear Sascha, On Tue, Sep 15, 2020 at 04:32:02PM +0200, Sascha Steinbiss wrote: > > I can confirm that that was the issue. I have pushed a fix to git and > will make an upload later if there are no objections. No objections for fixing a bug at all. ;-) Thanks a lot Andreas. -- http://fam-tille.de
Bug#970340: [Debian-med-packaging] Bug#970340: rna-star: autopkgtest regression: --genomeSAindexNbases 8 is too large for the genome size=99940
Hi all, >> you once wrote that test. Do you have any idea how to fix it? > > Since this is just a warning, it might be sufficient to simply add > > Restrictions: allow-stderr > > That would make sure that printing a warning to stderr does not cause > the test to fail. I will test this later and fix it if that was the problem. I can confirm that that was the issue. I have pushed a fix to git and will make an upload later if there are no objections. Best regards Sascha
Bug#970340: rna-star: autopkgtest regression: --genomeSAindexNbases 8 is too large for the genome size=99940
Hi all, > you once wrote that test. Do you have any idea how to fix it? Since this is just a warning, it might be sufficient to simply add Restrictions: allow-stderr That would make sure that printing a warning to stderr does not cause the test to fail. I will test this later and fix it if that was the problem. Cheers Sascha
Bug#970340: rna-star: autopkgtest regression: --genomeSAindexNbases 8 is too large for the genome size=99940
Hi Sascha, you once wrote that test. Do you have any idea how to fix it? Steffen, you know that package. Any idea what to do? Kind regards Andreas. On Mon, Sep 14, 2020 at 10:15:12PM +0200, Paul Gevers wrote: > 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: > >passfail > rna-star from testing2.7.5c+dfsg-1 > all others from testingfrom 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 > > ___ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de
Bug#970340: rna-star: autopkgtest regression: --genomeSAindexNbases 8 is too large for the genome size=99940
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: passfail rna-star from testing2.7.5c+dfsg-1 all others from testingfrom 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
