[Bioperl-l] Test overhaul complete

Nathan S. Haigh n.haigh at sheffield.ac.uk
Wed Jun 27 15:16:40 EDT 2007


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Chris Fields wrote:
> 
> On Jun 27, 2007, at 1:44 PM, Nathan S. Haigh wrote:
> 
>> Sendu Bala wrote:
>>> ...
>>> Bio::SeqIO::entrezgene is still generating 'Pseudo-hashes are
>>> deprecated' warnings.
>>
>> Ah, that reminds me!
>>
>> I recently tried to do an install of the cvs head (a week or two ago) on
>> a clean installation of Debian 4.0 (etch). During the installation, of
>> dependencies, Bio::ASN1::EntrezGene threw an error as it depends on
>> Bioperl. I seem to remember this circular dependency cropping up before
>> - am I correct - and can you remind me how this was "fixed"?
>>
>> Cheers
>> Nath
> 
> Wonder if Mingyi Liu would allow Bio::ASN1::EntrezGene to become part of
> Bioperl (and he could be come a dev).  That would solve it.
> 
> chris

Just to put the feelers out to see what people think.

It seems (to me at least) that Bioperl modules could/should? be released
as individual modules and that "bioperl" would really constitute a
"bundle" of all these modules - in terms of CPAN anyway. Am I correct in
this thinking? The Bio::ASN1::EntrezGene could simply require a
particular module rather than the whole of bioperl - might get out of
the circular dependency theoretically!?

I'm not suggesting moving in this direction, but just wondered what
others thought about this concept?

Nath
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