Bug#880347: bug squashing target: Probably bowtie 1.2.1.1 issue (Was: Bug#880347: bioperl-run: FTBFS: Test failures)
Hi Alex, On Thu, Dec 07, 2017 at 06:12:05PM +0100, Alex Mestiashvili wrote: > > That's a trivial one, s/reads processed: 1000/reads processed: 2000/ > I'll take care. Cool! Thanks a lot. BTW, there are *lots* if easy ones - just in case this will keep motivation of all team members higher. ;-) Kind regards Andreas. -- http://fam-tille.de
Bug#880347: bug squashing target: Probably bowtie 1.2.1.1 issue (Was: Bug#880347: bioperl-run: FTBFS: Test failures)
> ... > # Failed test 'bowtie success' > # at t/Bowtie.t line 188. > # '# reads processed: 2000 > # # reads with at least one reported alignment: 2000 (100.00%) > # # reads that failed to align: 0 (0.00%) > # Reported 1000 paired-end alignments to 1 output stream(s) > # ' > # doesn't match '(?^:reads processed: 1000)' > > # Failed test 'bowtie success' > # at t/Bowtie.t line 195. > # '# reads processed: 2000 > # # reads with at least one reported alignment: 2000 (100.00%) > # # reads that failed to align: 0 (0.00%) > # Reported 1000 paired-end alignments to 1 output stream(s) > # ' > # doesn't match '(?^:reads processed: 1000)' > # Looks like you failed 2 tests of 61. > t/Bowtie.t . > ... > > > I suspect that some change between bowtie 1.2.0 and bowtie 1.2.1.1 is > responsible for the issue in bioperl-run. I wonder whether tracking > down this issue sounds interesting for somebody who knows (and uses) > bowtie a bit. > > Kind regards > >Andreas. > Hi Andreas, That's a trivial one, s/reads processed: 1000/reads processed: 2000/ I'll take care. Best regards, Alex
Bug#880347: bug squashing target: Probably bowtie 1.2.1.1 issue (Was: Bug#880347: bioperl-run: FTBFS: Test failures)
Hi, this bug report has a time correlation to the upload of the new version of bowtie (1.2.1.1): On Mon, Oct 30, 2017 at 09:08:15PM +0100, Lucas Nussbaum wrote: > Source: bioperl-run > Version: 1.7.2-1 > Severity: serious > ... > > Relevant part (hopefully): > > ok 9 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not > > present > > ok 10 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not > > present > > ok 11 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not > > present > > ok 12 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not > > present > > ok > > > > Test Summary Report > > --- > > t/Bowtie.t (Wstat: 512 Tests: 61 Failed: 2) > > Failed tests: 43, 45 > > Non-zero exit status: 2 > > Files=72, Tests=1690, 156 wallclock secs ( 0.24 usr 0.07 sys + 133.72 cusr > > 6.41 csys = 140.44 CPU) > > Result: FAIL > > Failed 1/72 test programs. 2/1690 subtests failed. > > dh_auto_test: perl Build test --verbose 1 returned exit code 255 > > debian/rules:32: recipe for target 'override_dh_auto_test' failed Earlier in the log: ... # Failed test 'bowtie success' # at t/Bowtie.t line 188. # '# reads processed: 2000 # # reads with at least one reported alignment: 2000 (100.00%) # # reads that failed to align: 0 (0.00%) # Reported 1000 paired-end alignments to 1 output stream(s) # ' # doesn't match '(?^:reads processed: 1000)' # Failed test 'bowtie success' # at t/Bowtie.t line 195. # '# reads processed: 2000 # # reads with at least one reported alignment: 2000 (100.00%) # # reads that failed to align: 0 (0.00%) # Reported 1000 paired-end alignments to 1 output stream(s) # ' # doesn't match '(?^:reads processed: 1000)' # Looks like you failed 2 tests of 61. t/Bowtie.t . ... I suspect that some change between bowtie 1.2.0 and bowtie 1.2.1.1 is responsible for the issue in bioperl-run. I wonder whether tracking down this issue sounds interesting for somebody who knows (and uses) bowtie a bit. Kind regards Andreas. -- http://fam-tille.de
Bug#880347: bioperl-run: FTBFS: Test failures
Source: bioperl-run Version: 1.7.2-1 Severity: serious Tags: buster sid User: debian...@lists.debian.org Usertags: qa-ftbfs-20171030 qa-ftbfs Justification: FTBFS on amd64 Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > ok 9 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present > ok 10 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not > present > ok 11 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not > present > ok 12 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not > present > ok > > Test Summary Report > --- > t/Bowtie.t (Wstat: 512 Tests: 61 Failed: 2) > Failed tests: 43, 45 > Non-zero exit status: 2 > Files=72, Tests=1690, 156 wallclock secs ( 0.24 usr 0.07 sys + 133.72 cusr > 6.41 csys = 140.44 CPU) > Result: FAIL > Failed 1/72 test programs. 2/1690 subtests failed. > dh_auto_test: perl Build test --verbose 1 returned exit code 255 > debian/rules:32: recipe for target 'override_dh_auto_test' failed The full build log is available from: http://aws-logs.debian.net/2017/10/30/bioperl-run_1.7.2-1_unstable.log A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! About the archive rebuild: The rebuild was done on EC2 VM instances from Amazon Web Services, using a clean, minimal and up-to-date chroot. Every failed build was retried once to eliminate random failures.
