[Bioperl-l] perl 5.10 released

Chris Fields cjfields at uiuc.edu
Wed Dec 19 20:41:51 EST 2007

On Dec 19, 2007, at 5:42 PM, Dave Messina wrote:

> 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.

May be something in Module::Build or Build.PL that needs tweaking.

It looks like EntrezGene parsing is broken for now using perl 5.10;  
the 'pseudohash' warnings with perl 5.8 were indicating something was  
amiss but we could never place it.  Any fixes will have to wait until  
after svn migration.  Not sure what's going on with the others fails  
just yet.

>>>> - 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.
> Dave

May be worth looking into.  Have you added it to the wiki?


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