On 12/16/16, 5:11 AM, "Bioperl-l on behalf of Carnë Draug" <[email protected] on behalf of [email protected]> wrote:
>On 16 December 2016 at 10:02, Andreas Tille <[email protected]> wrote: >> Hi, >> >> when trying to run Bioperl-run unit tests while BioPerl 1.7.1 is >> installed (on a Debian system with the current Debian package in >> unstable) I get lots of errors of type >> >> Can't locate Bio/Tools/Run/WrapperBase.pm in @INC (you may need to >> install the Bio::Tools::Run::WrapperBase module) >> >> When checking BioPerl 1.6.x hat a file Bio/Tools/Run/WrapperBase.pm >> which was removed in BioPerl 1.7.x and thus lots of tests are failing. >> >> Kind regards >> >> Andreas. > >That module (Bio::Tools::Run::WrapperBase) is now part of bioperl-run [1]. >Unfortunately, it seems that there has been no new release of bioperl-run >since that change. > >I am not sure what's the plan for bioperl to make a new release of >bioperl-run (adding bioperl mailing list to CC) but can Debian patch >bioperl-run to include those files like upstream has done for the >next release? > >Carnë > >[1] >https://github.com/bioperl/bioperl-run/commit/acd57a7d14112c5fd2cd979005b072efdaf57679 It may be easier to simply make a new bioperl-run release that includes the module. I can probably do that this weekend. We had a similar issue with Bio-Graphics (which uses another removed module, Bio::Coordinate::Pair). That has a separate set of problems associated with version numbering that need to be dealt with. chris >
