[Bioperl-l] tests failing, please help

[Brian Osborne]

Heikki et al.

>The remaining problems are:

>* Registry tests failing
>   -- but we knew that already

I would like a bit of help with this, I'd like to know if the behavior I see
with Cygwin is the same elsewhere. Could someone please do the following?

Comment out the END line in Registry.t and run the test twice.

When I do this the first run fails and the second succeeds. All the END line
is doing is cleaning up the Flat databases that the test creates. To me it
appears as if I make a Flat database and then call the Registry in the same
script I'll see an error, but if the databases already exist and I call the
Registry everything, at least as tested in Registry.t, is fine.

Can you someone try this?

Thanks again,

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Heikki
Lehvaslaiho
Sent: Thursday, November 13, 2003 9:26 AM
To: Bioperl
Subject: [Bioperl-l] tests failing, please help


I've now gone through all warnings and failures in the bioperl-live test
suite. I was running a brand new perl 5.8.2. Some of the errors I saw
are due to perl not talking to a right CPAN module.

The most serious and widespread problems were caused by
Bio::LocatableSeq::trunc() not handling sequences with strand=-1
correctly (my code!). In the process of fixing it, I've touched start()
and end(), too. You can now initialise a LocatableSeq with sequence only
and start() and and end() will return correct values.

The remaining problems are:

* Registry tests failing
   -- but we knew that already

* EncodedSeq needs fixing,
  -- this might be related to LocatableSeq or not
  -- Aaron?

* t/SeqFeature.t hangs on $feat->gff_string() call
  -- pressing return releases it
& GFF.t has IO handle problems
  -- these two might be related
  -- Lincoln?

If some other tests fail for you, especially due to my "fixes", let me
know.

        -Heikki

--
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________

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