[Bioperl-l] tests failing, please help

[Heikki Lehvaslaiho]

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

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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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