On Mon, 2013-08-12 at 12:41 +0100, Peter Cock wrote:
> On Mon, Aug 12, 2013 at 12:27 PM, Bjoern Gruening
> <bjoern.gruen...@gmail.com> wrote:
> > Hi,
> >
> >> Hi Bjoern & Greg,
> >>
> >> The Biopython package looks OK on the test tool shed,
> >> http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
> >>
> >> This includes the lines:
> >>
> >>     <package name="numpy" version="1.7.1">
> >>         <repository changeset_revision="ad6ebe2c75ef"
> >> name="package_numpy_1_7" owner="bgruening"
> >> prior_installation_required="True"
> >> toolshed="http://testtoolshed.g2.bx.psu.edu"; />
> >>     </package>
> >>     <package name="matplotlib" version="1.2.1">
> >>         <repository changeset_revision="c888aa8ed318"
> >> name="package_matplotlib_1_2" owner="bgruening"
> >> prior_installation_required="True"
> >> toolshed="http://testtoolshed.g2.bx.psu.edu"; />
> >>     </package>
> >>
> >> Note that we plan to update those dependencies to point
> >> at the IUC account, not Bjoern's personal account.
> >>
> >> However, on the main Tool Shed something is broken with the
> >> dependencies lacking relevant revisions:
> >> http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
> >>
> >>     <package name="numpy" version="1.7.1">
> >>         <repository name="package_numpy_1_7" owner="bgruening"
> >> prior_installation_required="True"
> >> toolshed="http://toolshed.g2.bx.psu.edu"; />
> >>     </package>
> >>     <package name="matplotlib" version="1.2.1">
> >>         <repository name="package_matplotlib_1_2" owner="bgruening"
> >> prior_installation_required="True"
> >> toolshed="http://toolshed.g2.bx.psu.edu"; />
> >>     </package>
> >
> > Upps ... :(
> >
> >> My guess is the revisions failed because there is no such
> >> repository on the main Tool Shed (they do exist under the
> >> new IUC user through, while on the Test Tool Shed they
> >> exist under both usernames for now).
> >>
> >> Bjoern, do you remember if this was a manual upload to
> >> the Main Tool Shed, or done via the migration script?
> >
> > It was done manually.
> >
> >> Greg, if this was uploaded manually, the reference to
> >> non-existent repositories should have shown up as an
> >> error. If this was migrated, was there no error message?
> >>
> >> Bjoern, are you happy to update both the test & main
> >> repositories to point at the IUC packages now? Or
> >> should I do that myself?
> >
> > Done! Hope it works now.
> >
> > Thanks for pointing that out!
> > Bjoern
> 
> Great - that seems to have solve the Biopython issue,
> although I'm curious if there is a glitch in the Tool Shed
> failing to issue a warning in a case like this?

Yes, a waning would be really great. I totally missed it :(

> Thanks,
> 
> Peter


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