Bug #118107 for Bio-Tools-Primer3Redux: Module compilation fails (missing Bio::Tools::Run::WrapperBase)

Tue Sep 27 16:00:52 2016 SREZIC [...] cpan.org - Ticket created

Subject:

Module compilation fails (missing Bio::Tools::Run::WrapperBase)

My smoker machines started to report the following failure while running the test suite: ... Base class package "Bio::Tools::Run::WrapperBase" is empty. (Perhaps you need to 'use' the module which defines that package first, or make that module available in @INC (@INC contains: lib /tmpfs/.cpan-build-cpansand/2016092718/Bio-Tools-Primer3Redux-0.09-0/blib/lib /tmpfs/.cpan-build-cpansand/2016092718/Bio-Tools-Primer3Redux-0.09-0/blib/arch /opt/perl-5.25.5/lib/site_perl/5.25.5/x86_64-linux /opt/perl-5.25.5/lib/site_perl/5.25.5 /opt/perl-5.25.5/lib/5.25.5/x86_64-linux /opt/perl-5.25.5/lib/5.25.5 .). at lib/Bio/Tools/Run/Primer3Redux.pm line 20. BEGIN failed--compilation aborted at lib/Bio/Tools/Run/Primer3Redux.pm line 20. Compilation failed in require at -e line 1. # Failed test 'Bio::Tools::Run::Primer3Redux loaded ok' # at t/00-compile.t line 48. # '' # doesn't match '(?^s:^\s*Bio::Tools::Run::Primer3Redux ok)' # Looks like you failed 1 test of 5. t/00-compile.t .......... Dubious, test returned 1 (wstat 256, 0x100) Failed 1/5 subtests ... It seems that Bio::Tools::Run::WrapperBase was removed from BioPerl-1.007000

Tue Sep 27 16:14:33 2016 cjfields [...] uiuc.edu - Correspondence added

On Tue Sep 27 15:00:52 2016, SREZIC wrote: Show quoted text

> My smoker machines started to report the following failure while > running the test suite: > > ... > Base class package "Bio::Tools::Run::WrapperBase" is empty. > (Perhaps you need to 'use' the module which defines that package > first, > or make that module available in @INC (@INC contains: lib > /tmpfs/.cpan-build-cpansand/2016092718/Bio-Tools-Primer3Redux-0.09- > 0/blib/lib /tmpfs/.cpan-build-cpansand/2016092718/Bio-Tools- > Primer3Redux-0.09-0/blib/arch /opt/perl- > 5.25.5/lib/site_perl/5.25.5/x86_64-linux /opt/perl- > 5.25.5/lib/site_perl/5.25.5 /opt/perl-5.25.5/lib/5.25.5/x86_64-linux > /opt/perl-5.25.5/lib/5.25.5 .). > at lib/Bio/Tools/Run/Primer3Redux.pm line 20. > BEGIN failed--compilation aborted at lib/Bio/Tools/Run/Primer3Redux.pm > line 20. > Compilation failed in require at -e line 1. > > # Failed test 'Bio::Tools::Run::Primer3Redux loaded ok' > # at t/00-compile.t line 48. > # '' > # doesn't match '(?^s:^\s*Bio::Tools::Run::Primer3Redux ok)' > # Looks like you failed 1 test of 5. > t/00-compile.t .......... > Dubious, test returned 1 (wstat 256, 0x100) > Failed 1/5 subtests > ... > > > It seems that Bio::Tools::Run::WrapperBase was removed from BioPerl- > 1.007000

Yes, I believe it was moved into bioperl-run. We need to work on a new release of that code, but one quick workaround would be to add this specific dependency to the Bio::Tools::Run::Primer3Redux distribution (it probably req. Bio::Root::Root). I'll try adding that in, which should pull in the older bioperl release (1.6.924) for now, until the newer bioperl-run is out.

Tue Sep 27 16:14:34 2016 The RT System itself - Status changed from 'new' to 'open'

Tue Sep 27 16:17:55 2016 cjfields [...] uiuc.edu - Correspondence added

On Tue Sep 27 15:00:52 2016, SREZIC wrote: Show quoted text

> My smoker machines started to report the following failure while > running the test suite: > > ... > Base class package "Bio::Tools::Run::WrapperBase" is empty. > (Perhaps you need to 'use' the module which defines that package > first, > or make that module available in @INC (@INC contains: lib > /tmpfs/.cpan-build-cpansand/2016092718/Bio-Tools-Primer3Redux-0.09- > 0/blib/lib /tmpfs/.cpan-build-cpansand/2016092718/Bio-Tools- > Primer3Redux-0.09-0/blib/arch /opt/perl- > 5.25.5/lib/site_perl/5.25.5/x86_64-linux /opt/perl- > 5.25.5/lib/site_perl/5.25.5 /opt/perl-5.25.5/lib/5.25.5/x86_64-linux > /opt/perl-5.25.5/lib/5.25.5 .). > at lib/Bio/Tools/Run/Primer3Redux.pm line 20. > BEGIN failed--compilation aborted at lib/Bio/Tools/Run/Primer3Redux.pm > line 20. > Compilation failed in require at -e line 1. > > # Failed test 'Bio::Tools::Run::Primer3Redux loaded ok' > # at t/00-compile.t line 48. > # '' > # doesn't match '(?^s:^\s*Bio::Tools::Run::Primer3Redux ok)' > # Looks like you failed 1 test of 5. > t/00-compile.t .......... > Dubious, test returned 1 (wstat 256, 0x100) > Failed 1/5 subtests > ... > > > It seems that Bio::Tools::Run::WrapperBase was removed from BioPerl- > 1.007000

One thing I forgot; is there a way to detect downstream failures from smoke tests for missing dists like this (or a way for us to do this on our own)? We really would like to make sure any bioperl reverse dependencies are going to be vetted for these issues prior to future releases, since we anticipate moving or reorganizing more code in the long run.

Tue Sep 27 17:07:52 2016 SREZIC [...] cpan.org - Correspondence added

On 2016-09-27 16:17:55, cjfields wrote: Show quoted text

> On Tue Sep 27 15:00:52 2016, SREZIC wrote:

> > My smoker machines started to report the following failure while > > running the test suite: > > > > ... > > Base class package "Bio::Tools::Run::WrapperBase" is empty. > > (Perhaps you need to 'use' the module which defines that package > > first, > > or make that module available in @INC (@INC contains: lib > > /tmpfs/.cpan-build-cpansand/2016092718/Bio-Tools-Primer3Redux-0.09- > > 0/blib/lib /tmpfs/.cpan-build-cpansand/2016092718/Bio-Tools- > > Primer3Redux-0.09-0/blib/arch /opt/perl- > > 5.25.5/lib/site_perl/5.25.5/x86_64-linux /opt/perl- > > 5.25.5/lib/site_perl/5.25.5 /opt/perl-5.25.5/lib/5.25.5/x86_64-linux > > /opt/perl-5.25.5/lib/5.25.5 .). > > at lib/Bio/Tools/Run/Primer3Redux.pm line 20. > > BEGIN failed--compilation aborted at > > lib/Bio/Tools/Run/Primer3Redux.pm > > line 20. > > Compilation failed in require at -e line 1. > > > > # Failed test 'Bio::Tools::Run::Primer3Redux loaded ok' > > # at t/00-compile.t line 48. > > # '' > > # doesn't match '(?^s:^\s*Bio::Tools::Run::Primer3Redux ok)' > > # Looks like you failed 1 test of 5. > > t/00-compile.t .......... > > Dubious, test returned 1 (wstat 256, 0x100) > > Failed 1/5 subtests > > ... > > > > > > It seems that Bio::Tools::Run::WrapperBase was removed from BioPerl- > > 1.007000

> > One thing I forgot; is there a way to detect downstream failures from > smoke tests for missing dists like this (or a way for us to do this on > our own)?

A possible approach to do it on your own: - compile the same perl into two different locations - configure CPAN::Reporter for these perls to use different .cpanreporter directories (and maybe to not sent any reports to the central testers database, but keep them only on the local disk) - install the stable and devel versions of the primary module (here: bioperl) into the two perls - determine the reverse dependencies (e.g. using api.metacpan.org or deps.cpantesters.org) - run the test suites for the revdeps on both perls and accumulate the test reports & results - and finally do a diff between the results There are a lot of details to make this process smooth (e.g.: make sure there's no interactivity while running the tests; handle hanging tests automatically; recognize random test results; filter out known problems ...). Maybe it's easier to just ask on the cpan-testers-discuss mailing list, people there can do this for you. Regards, Slaven