[Bioperl-l] throwing in the towel

[Hilmar Lapp]

Ewan Birney wrote:
> >
> > b) Index.t is failing on Bio::Index::AbstractSeq fetch.  I can't find a
> > reason for this other than something to do with file handles or the DBM
> > stuff.  It fails on a retrieve though and since it works on UNIX I am
> > inclined to think that the DBM implementation is not quite up to snuff on
> > NT?
> >
> 
> This happens to me on badly-set up UNIX boxes.

Right. This was exactly the problem Peter, a colleague of mine,
was having. After re-installing his machine it worked fine. The
phenomenon we saw there was that the index file was created with
extensions .pag and .dir, i.e., indexing worked. However it
couldn't reopen the index, due to the extensions. Consequently,
retrieve failed.

> 
> > c) GDB.t doesn't seem to be very happy.  Again I cannot seem to trace the
> > problem, I attempted to make the module fairly generic, but I see that
> > didn't actually work either.  I'm fine with dropping it from the release
> > or at least disabling the tests if we cannot fix it.  I'd rather it not
> > hold up the release though.
> 
> Let's go with a test-disable here. Hilmar - thoughts?
> 

Disable test and disclaim usability under Perl 5.004 (did it
trouble under 5.6.x, too? Under 5.005 it's working just
perfectly.). We'll have to figure out the real reason after the
release (and the final fix will be part of a 0.7.x bugfix
release).

It's probably helpful if one of you submits a good report to the
bug tracker.

	Hilmar
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Hilmar Lapp                              email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
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