[Bioperl-l] throwing in the towel

[Ewan Birney]

On Thu, 1 Mar 2001, Hilmar Lapp wrote:

> 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).

Ok. I am currently debugging this ;) It might come out in the next 10
minutes.


The problem is - Jason would understand this if he was awake - we are not
getting into $state ==2 in the parsing the GDB file. I suspect something
is up either in the LWP that comes with 5.0004 and/or interaction between
LWP and the perl internals. 


I am going to give this another 10 mins of sweat. 


I hate event driven parsers that have to be stateful. Yuk.

(in fact, I hate parsers completely)




> 
> It's probably helpful if one of you submits a good report to the
> bug tracker.
> 
> 	Hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                              email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
> -----------------------------------------------------------------
> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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