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The Basics
Id: 116721
Status: resolved
Priority: 0/
Queue: bioperl-run

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Owner: Nobody in particular
Requestors: SREZIC [...] cpan.org
Cc:
AdminCc:

Bug Information
Severity: (no value)
Broken in: 1.006900
Fixed in: (no value)



Subject: Hash randomization (?) issue in tests
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Some tests fail, probably only on perls >= 5.18, due to hash randomization. For example: # Failed test 'translate params' # at t/Bowtie.t line 111. # got: '-v 4 -S --solexa-quals -y' # expected: '-v 4 --solexa-quals -y -S' # Required executable for Bio::Tools::Run::Bowtie is not present # Looks like you failed 1 test of 73. t/Bowtie.t .................... Dubious, test returned 1 (wstat 256, 0x100) Failed 1/73 subtests (less 40 skipped subtests: 32 okay) # Failed test 'translate params' # at t/Maq.t line 73. # got: 'assemble -r 0.005 -m 4 -s' # expected: 'assemble -m 4 -r 0.005 -s' # Required executable for Bio::Tools::Run::Maq is not present # Looks like you failed 1 test of 51. t/Maq.t ....................... Dubious, test returned 1 (wstat 256, 0x100) Failed 1/51 subtests (less 27 skipped subtests: 23 okay)
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This is not appearing for me using recent perl versions (5.24, 5.26), but it's possible this may have been directly addressed within Test::More and is_deeply(). On Thu Aug 04 16:10:58 2016, SREZIC wrote: Show quoted text
> Some tests fail, probably only on perls >= 5.18, due to hash > randomization. For example: > > # Failed test 'translate params' > # at t/Bowtie.t line 111. > # got: '-v 4 -S --solexa-quals -y' > # expected: '-v 4 --solexa-quals -y -S' > # Required executable for Bio::Tools::Run::Bowtie is not present > # Looks like you failed 1 test of 73. > t/Bowtie.t .................... > Dubious, test returned 1 (wstat 256, 0x100) > Failed 1/73 subtests > (less 40 skipped subtests: 32 okay) > > > # Failed test 'translate params' > # at t/Maq.t line 73. > # got: 'assemble -r 0.005 -m 4 -s' > # expected: 'assemble -m 4 -r 0.005 -s' > # Required executable for Bio::Tools::Run::Maq is not present > # Looks like you failed 1 test of 51. > t/Maq.t ....................... > Dubious, test returned 1 (wstat 256, 0x100) > Failed 1/51 subtests > (less 27 skipped subtests: 23 okay)
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I don't see this problem in BioPerl-Run-1.007002 anymore, so will mark this issue as resolved. On 2017-09-16 12:03:45, cjfields wrote: Show quoted text
> This is not appearing for me using recent perl versions (5.24, 5.26), > but it's possible this may have been directly addressed within > Test::More and is_deeply(). > > On Thu Aug 04 16:10:58 2016, SREZIC wrote:
> > Some tests fail, probably only on perls >= 5.18, due to hash > > randomization. For example: > > > > # Failed test 'translate params' > > # at t/Bowtie.t line 111. > > # got: '-v 4 -S --solexa-quals -y' > > # expected: '-v 4 --solexa-quals -y -S' > > # Required executable for Bio::Tools::Run::Bowtie is not present > > # Looks like you failed 1 test of 73. > > t/Bowtie.t .................... > > Dubious, test returned 1 (wstat 256, 0x100) > > Failed 1/73 subtests > > (less 40 skipped subtests: 32 okay) > > > > > > # Failed test 'translate params' > > # at t/Maq.t line 73. > > # got: 'assemble -r 0.005 -m 4 -s' > > # expected: 'assemble -m 4 -r 0.005 -s' > > # Required executable for Bio::Tools::Run::Maq is not present > > # Looks like you failed 1 test of 51. > > t/Maq.t ....................... > > Dubious, test returned 1 (wstat 256, 0x100) > > Failed 1/51 subtests > > (less 27 skipped subtests: 23 okay)


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