[Bioperl-l] misleading error messages...

[Alok Saldanha]

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


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