[Bioperl-l] Fail to run a script in Bio::DB::GenBank's document

Chirag Matkar chiragmatkarbioinfo at gmail.com
Mon Oct 24 12:38:24 EDT 2011


Tao,

You can install URI::Escape through CPAN.

On Mon, Oct 24, 2011 at 6:37 PM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> As might be implied by the error, you do not have URI::Escape installed,
> which is a dependency of Bio::DB::GenBank.
>
> chris
>
> On Oct 24, 2011, at 6:37 AM, Tao Zhu wrote:
>
> > Here is a script copied totally from documents for module
> Bio::DB::GenBank,
> >
> >
> > use Bio::DB::GenBank;
> > my $gb = Bio::DB::GenBank->new();
> > my $seq_obj = $gb->get_Seq_by_acc('J00522');
> >
> > When I try to run it, it failed. The message appear like this:
> >> Can't locate URI/Escape.pm in @INC (@INC contains:
> /home/zhut/bin/PerlModule
> /home/zhut/localperl/lib/site_perl/5.12.3/x86_64-linux
> /home/zhut/localperl/lib/site_perl/5.12.3
> /home/zhut/localperl/lib/5.12.3/x86_64-linux /home/zhut/localperl/lib/5.12.3
> .) at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100.
> >> BEGIN failed--compilation aborted at
> /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100.
> >> Compilation failed in require at
> /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91.
> >> BEGIN failed--compilation aborted at
> /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91.
> >> Compilation failed in require at (eval 2) line 2.
> >>      ...propagated at /home/zhut/localperl/lib/5.12.3/base.pm line 94.
> >> BEGIN failed--compilation aborted at
> /home/zhut/bin/PerlModule/Bio/DB/GenBank.pm line 171.
> >> Compilation failed in require at perlprogram_2.pl line 5.
> >> BEGIN failed--compilation aborted at perlprogram_2.pl line 5.
> >
> > I've never see such error before, how does this come?
> >
> > --
> > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> > 100875, China
> > Email: tzhu at mail.bnu.edu.cn
> >
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>
>
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-- 
Regards,
Chirag


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