[Bioperl-l] misleading error messages...

[Jason Stajich]

On Tue, 6 May 2003, Alok Saldanha wrote:

> Hello,
>
> I have installed additional external packages, such as IO::String,
> after installing bioperl, and it's lead to confusing error messages.
> For instance,
>
> perl -e 'use IO::String'
>
> runs fine, but I'm still getting stuff like:
>
> perl test1.pl
> Your system does not have IO::String installed so the DB retrieval
> method is not available at /Library/Perl/Bio/Perl.pm line 466
>          Bio::Perl::get_sequence('swissprot', 'ROA1_HUMAN') called at
> test1.pl line 6
>

So the error message is misleading in the tutorial.  You should see
warnings about a whole lot more modules when you run perl Makefile.PL as
is described in the README/INSTALL.

You in fact have not installed HTTP::Request::Common as the msg below
states.  I am submitting as a bug at http://bugzilla.bioperl.org so that
Peter or someone will fix the tutorial docs.


>
> This is untrue; I think it might actually be failing do to the lack of
> LWP stuff, for instance:
>
> perl -e 'use Bio::DB::SwissProt'
> Can't locate HTTP/Request/Common.pm in @INC (@INC contains:
> /System/Library/Perl/darwin /System/Library/Perl /Library/Perl/darwin
> /Library/Perl /Library/Perl /Network/Library/Perl/darwin
> /Network/Library/Perl /Network/Library/Perl .) at
> /Library/Perl/Bio/DB/SwissProt.pm line 106.
> BEGIN failed--compilation aborted at /Library/Perl/Bio/DB/SwissProt.pm
> line 106.
> Compilation failed in require at -e line 1.
> BEGIN failed--compilation aborted at -e line 1.
>
>
> 	-Alok
>
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>

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