[Bioperl-l] strange error after changing to RC1.5

Daniel Lang daniel.lang at biologie.uni-freiburg.de
Fri Mar 11 05:06:19 EST 2005

Hash: SHA1

Hi Allen,

When I add the line to all Bio::Annotation::*, we run into various other
errors, e.g. :
Can't call method "primary_key" on an undefined value at
line 1325.!

What are these overloaded methods for?
Who/What is calling ->ne()?

I´ve tried using the latest cvs version with the Annotation classes from
december: This error is gone but then all SeqFeature tag_values are
stringified memory addresses:

~                     )"
~                     /clone="Bio::Annotation::SimpleValue=HASH(0x76883d14)"




~                     /note="Bio::Annotation::SimpleValue=HASH(0x76883da4)"

To make it even more complicated, I´ve dumped both seq objects (the one
all with classes from dec´04 and the bioperl-live with only the
Annotation classes from dec´04) there is no diff!?
The Seq, SeqI, RichSeq SeqFeature::Generic objects didn´t change since

- -Daniel

Allen Day wrote:
| I'm unable to test the code in PersistentObject.pm as I don't have biosql
| set up, but you might try adding this to Reference.pm
|   use overload 'ne' => sub { "$_[0]" ne "$_[1]" }
| Please let me know if this fixes your error and I'll add this 'ne'
| overload to all the Bio::Annotation::* classes on HEAD.
| -Allen
| On Wed, 9 Mar 2005, Daniel Lang wrote:
|>I´m retrieving seq objects from a local biosql db (using the latest cvs
|>verion of bioperl-db) and e.g. writing them with SeqIO. After changing
|>from a cvs version ~ 12/04 to RC1.5 or latest cvs version, I get the
|>following error:
|>Operation `ne': no method found,!!left argument in overloaded package
|>Bio::Annotation::Reference,!!right argument has no overloaded magic at
|>line 534, <GEN1> line 1.!
|>The module PersistentObject.pm hasn´t changed and in Reference.pm there
|>is only this change:
|>diff bioperl-live-Dec04/Bio/Annotation/Reference.pm
|>< # $Id: Reference.pm,v 1.21 2004/08/19 20:13:32 lapp Exp $
|> > # $Id: Reference.pm,v 1.22 2005/02/02 22:13:22 allenday Exp $
|>< # use overload '""' => \&as_text;
|> > use overload '""' => sub { $_[0]->title || ''};
|> > use overload 'eq' => sub { "$_[0]" eq "$_[1]" };
|>I´ve reversed this, but no positive result - the error remains...
|>Any hints?
|>Thanks in advance,
|>Bioperl-l mailing list
|>Bioperl-l at portal.open-bio.org

Version: GnuPG v1.2.5 (MingW32)
Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org


More information about the Bioperl-l mailing list