[Bioperl-l] Bio::SeqIO::staden::read make test error

Michael Stubbington Michael.Stubbington at hpa.org.uk
Wed Apr 15 03:43:39 EDT 2009

Thanks a lot for your help.

I finally solved the problem with a combination of:

1) Checking out the latest bioperl-ext from svn.
2) A fresh install of an earlier version of io_lib (8.12)
3) Changing <config.h> to "config.h" in os.h

Everything seems to be working now.

Best wishes,


-----Original Message-----
From: Chris Fields [mailto:cjfields at illinois.edu] 
Sent: 14 April 2009 16:20
To: Roy Chaudhuri
Cc: Michael Stubbington; bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Bio::SeqIO::staden::read make test error

For ABI files you'll need an older version of io_lib that supports ABI  
or the io_lib that comes with the full staden package.  Recent  
versions of io_lib don't have ABI support built-in anymore.


On Apr 14, 2009, at 9:54 AM, Roy Chaudhuri wrote:

> Hi Mike.
> I did get that problem solved in the end, thanks to lots of help  
> from Aaron Mackey. Looking at the bioperl-l archives it seems like  
> we stopped cc-ing the mailing list at some point. The last archived  
> message in the thread
> ) had the correct solution - the code change was incorporated into  
> the bioperl-ext CVS, and is in the latest version that you can get  
> from SVN (see http://www.bioperl.org/wiki/Ext_package). If that  
> doesn't solve the problem you must be experiencing a different issue.
> You should also bear in mind the message Chris Fields sent to the  
> list a few days ago, and have a look at using BioLib instead:
>> Just to note, we're not actively supporting much of the bioperl- 
>> ext  code, in favor of the BioLib initiative:
>> http://biolib.open-bio.org/wiki/Main_Page
>> If you do use bioperl-ext I suggest only using the latest code  
>> from  svn (and that in combination with bioperl-live).
> >
>> chris
> Hope this helps.
> Roy.
> Michael Stubbington wrote:
>> Dear Dr. Chaudhuri,
>> I am currently trying to write a bioperl script that parses .abi  
>> sequence files. I am having exactly the same problem as you did when
>> you posted this enquiry to the bioperl mailing list
>> . I was wondering if you ever solved the problem and, if so, can  
>> you remember
>> what you did? I'd be very grateful for any help you can provide. I
>> can't find this problem mentioned anywhere else online.
>> Thank you for your time.
>> Mike
> --
> Dr. Roy Chaudhuri
> Department of Veterinary Medicine
> University of Cambridge, U.K.
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> Bioperl-l at lists.open-bio.org
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