[Bioperl-l] perl 5.10 released

Dave Messina David.Messina at sbc.su.se
Wed Dec 19 18:42:14 EST 2007

Hi Chris and everyone,

With most of the optional dependencies installed, I'm seeing  
essentially the same test failures, including the CODE ref thingy.  
I've noted this on the new Wiki page you created.

According to Data::Dumper's documentation,
Data::Dumper cheats with CODE references. If a code reference is  
encountered in the structure being processed (and if you haven't set  
theDeparse flag), an anonymous subroutine that contains the string  
'"DUMMY"' will be inserted in its place, and a warning will be printed  
if Purity is set. You can eval the result, but bear in mind that the  
anonymous sub that gets created is just a placeholder. Someday, perl  
will have a switch to cache-on-demand the string representation of a  
compiled piece of code, I hope. If you have prior knowledge of all the  
code refs that your data structures are likely to have, you can use  
the Seen method to pre-seed the internal reference table and make the  
dumped output point to them, instead. See EXAMPLES above.

So it's not BioPerl per se, but we can probably work around it.

>>> - Bio::Ontology::SimpleGOEngine::GraphAdaptor throws an exception
>>>> because Graph::Directed isn't installed.
>>> Odd, that should be caught out before tests are run.  Needs to be
>>> fixed, but one would think this would fail as well under 5.8.
>> Yep, and in a minute here I'll test it under 5.8.

Strangely, the Ontology tests properly get skipped under 5.8.


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