[Bioperl-l] Problems with Bioperl-ext package on WinVista?

[Mark A. Jensen]

[OOps. Sorry about that. The compiler ideas still apply however.]
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Jonny Dalzell" <jdalzell03 at qub.ac.uk>
Cc: <Bioperl-l at lists.open-bio.org>
Sent: Tuesday, August 11, 2009 7:44 PM
Subject: Re: [Bioperl-l] Problems with Bioperl-ext package on WinVista?


> Bio::Tools::Hmm doesn't use HMMER, it uses a C-based extension in  bioperl-ext 
> that generates HMM's (XS-based bindings I think).  I have  managed to compile 
> it successfully on Ubuntu and Mac OS X, but  WinVista is a whole different 
> bag-o-worms altogether (untested AFAIK).
>
> For the record, I do not recommend using it; I'm unsure about it's 
> maintenance status, so it may be released separately.  It would be  best to 
> use something better supported, such as the HMMER wrapper in  bioperl-run and 
> the hmmer parsers in bioperl-core.  We may also have  wrappers for similar 
> code available in biolib at some future point.
>
> chris
>
> On Aug 11, 2009, at 1:52 PM, Jonny Dalzell wrote:
>
>>
>> Hi,
>>
>> I'm as sure as I can be.  I look in the HHMER folder and it contains
>> "Domain.pm", "Results.pm", and "Set.pm".  I thought perhaps it was  something
>> to do with @INC, but I put
>> "use lib "strawberry/per/lib C:/strawberry/perl/site/lib/Bio/ Tools/";" at
>> the top of my script, which definately encompasses the directory it  should
>> be in, and I still get...
>>
>> "Can't locate Bio/Tools/HMM.pm in @INC (@INC contains: strawberry/ per/lib
>> C:/strawberry/perl/site/lib/
>> Bio/Tools/ C:/strawberry/perl/lib C:/strawberry/perl/site/lib .) at  HMM.txt
>> line 5.
>> BEGIN failed--compilation aborted at HMM.txt line 5."
>>
>> I'm out of ideas.
>>
>> Jonny
>> -- 
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>> http://www.nabble.com/Problems-with-Bioperl-ext-package-on-WinVista--tp24919498p24923606.html
>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>
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