[Bioperl-l] IO::String missing

[Jason Stajich]

Everything that isn't in the Bio:: namespace is in CPAN -
www.cpan.org

>From the INSTALL document:
 - External modules: Bioperl uses functionality provided in other
   Perl modules.  Some of these are included in the standard perl
   install and some need to be obtained from the CPAN (www.cpan.org)
   site.  The list of external modules is included at the bottom of
   the INSTALL document and in the bptutorial.pl tutorial.  The
   Bioperl Bundle (Bundle::BioPerl) available through CPAN can make
   this process even easier.  Simply install the bundle in your CPAN
   shell and all necessary modules will be installed.


On Wed, 5 Feb 2003, nkuipers wrote:

> Hello,
>
> I just downloaded the 1.2 distro.  I am not root, therefore I used perl
> MakeFile.PL LIB=/home/nkuipers/lib.  A number of warnings were thrown during
> make test, most having to do with the absence of IO::String (a few others
> regarding certain XML parsers and SOAP are of no concern to me).
>
> A test script that contains only:
>
> use lib "/home/nkuipers/lib";
> use Bio::Index::Blast;
>
> throws the warning:
>
> "Can't locate IO/String.pm in @INC (@INC contains...) at
> /home/nkuipers/lib/Bio/Index/Blast.pm line 87.
>
> Line 87 is "use IO::String;".
>
> In browsing the CPAN bioperl1.2 namespace and www.bioperl.org I could not find
> an IO::String module to install manually before installing bioperl1.2.  Could
> someone please tell me where I am being stupid?  Thanks.
>
> I am on Red Hat 8.0 using Perl 5.8.0.
>
> Cheers,
>
> Nathanael Kuipers
> ---
> Bioinformatics Technician
> Center for Biomedical Research,
> Dept. of Biology, University of Victoria
> Victoria BC, Canada
>
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> Bioperl-l at bioperl.org
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu