[Bioperl-l] SOS----for BioPerl Installing

Jason Stajich jason at cgt.duhs.duke.edu
Tue Aug 3 07:54:36 EDT 2004

So.... are you using OS X or OS 9?

You need to install IO::String, URI, HTML::Parser, and LWP if you want to
use the remote access capabilities.

You can also use the cpan interface which will automatically install
dependancies for you.

perl -MCPAN -e shell

On OS X you can also use fink to install Bioperl which will also install
the necessary dependancies.

On Tue, 3 Aug 2004, Alex Zhang wrote:

> Dear friends,
> Hi! I faced some problems when installing BioPerl on Macintosh.
> I am using James D. Tisdall's Masterhing Perl for Bioinformatics and
> following the installation instructions.
> When running a test program, which is
> ************************
> use Bio::Perl;
> $seq_object = get_sequence('swissprot',"R0A1_HUMAN");
> write_sequence(">roa1.fasta",'fasta',$seq_object);
> ************************
> it displayed that "Your systems does not have one of LWP,
> HTTP::Request::Common,IO::String installed so the DB retrieval method is
> not available.
> Full error message is:
>   No such file or directory
>     Bio::Perl::get_sequence('swissprot','ROA1-HUMAN') called at Bo11.pl
> line 3".
> Then I downloaded libwww-perl-5.64 and installed it. But two errors
> appeared. One was: "Checking for URI...........failed" and the other one
> was "Checking for HTML::Parser..failed". Then I downloaded the URI and
> HTML::Parser modules from CPAN and run the test program again. But the
> program still bothered me.
> So I wish I could get suggestions from you!
> Thanks,
>   Alex
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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