[Bioperl-l] bioperl-ext package installation error

Chris Fields cjfields at illinois.edu
Sat Nov 20 04:50:17 UTC 2010


You need to install the bioperl-ext module Bio::SeqIO::staden::read, which uses XS bindings to io_lib, but there's a bit of a caveat: we're not really maintaining that code anymore.  Saying that, it does work using io_lib version 1.12.2 (my local version). 

Here's the code, please make sure to note the README (specifically, the version of io_lib you will need and the problems you may run into):



On Nov 19, 2010, at 2:03 PM, Alan Twaddle wrote:

> Hello all,
>     I am trying to write a simple script to parse an ABI file into usable
> data which requires the staden io_lib of which I installed. However, am
> receiving an error message when trying to run my script that says the
> following:
> ------------- EXCEPTION: Bio::Root::SystemException -------------
> MSG: Bio::SeqIO::staden::read is not available; make sure the bioperl-ext
> package has been installed successfully!
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
> STACK: Bio::SeqIO::abi::_initialize /usr/local/share/perl/5.10.1/Bio/SeqIO/
> abi.pm:100
> STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:360
> STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:390
> STACK: AB1_parser.pl:10
> I didn't receive any error messages when installing the staden package so
> I'm assuming that there's some path specified in some file that is pointing
> to the wrong place. I don't know if this is the case but if you have any
> suggestions about how to fix this I would greatly appreciate it! Thank you
> very much!
> -- 
> Alan Twaddle, B.S.
> MUC class of 2010
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> Bioperl-l at lists.open-bio.org
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