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

Fields, Christopher J cjfields at illinois.edu
Mon Oct 24 09:07:56 EDT 2011


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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