[Debian-med-packaging] Bug#880347: bug squashing target: Probably bowtie 1.2.1.1 issue (Was: Bug#880347: bioperl-run: FTBFS: Test failures)

[Andreas Tille]

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.

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