[Bioperl-l] Reference to a staden module under Bio::SeqIO.pm

[Chris Fields]

This seems to be a problem with PerlApp and eval{}; judging by a quick  
Google search this isn't the only module affected.  The line in  
question is wrapped in an eval{} to check for the availability of  
Bio::SeqIO::staden::read (but not die on it).

BTW, the eval was moved into the relevant plugin modules post-1.5.2,  
so the eval{} is checked when the module is loaded dynamically (i.e.  
when a format requiring it is passed in).  It was causing other issues  
with ActivePerl installations and was redundant, so it was removed.

http://bugzilla.open-bio.org/show_bug.cgi?id=2295

chris

On Aug 3, 2008, at 2:10 PM, Dave Messina wrote:

> Hi Kevin,
>
> The staden module is a oddball one, to be sure.
>
> A search on the BioPerl website turns up this FAQ entry:
> http://www.bioperl.org/wiki/FAQ#bioperl-ext_won.27t_compile_the_staden_IO_lib_part_-_what_do_I_do.3F
>
> Also the Windows install page
> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
>
> says:
>
>> Some external programs such as Staden <http://www.bioperl.org/wiki/Staden 
>> > and
>> the EMBOSS <http://www.bioperl.org/wiki/EMBOSS> suite of programs  
>> can only
>> be installed on Windows by using Cygwin <http://www.cygwin.com/>  
>> and its gcc
>> C compiler <http://gcc.gnu.org/> (see Bioperl in Cygwin, below)
>>
>
>
> In any case, the staden module (and associated external libraries)  
> is used
> only if you are trying to read the scf, abi, alf, pln, exp, ctf, or  
> ztr
> binary formats. So your edit shouldn't cause you any problems  
> otherwise.
>
> Dave
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign