BioPerl: Use of uninitialized value $Bio::DB::NCBIHelper::HOSTBASE
0
0
Entering edit mode
9.1 years ago
tino_s3004 • 0

Hi,

I'm new to both Perl and especially to BioPerl so bear with me.

It was a struggle to install BioPerl on Windows to begin with and now I got this error just by trying to run: use Bio::DB::GenBank;

Use of uninitialized value $Bio::DB::NCBIHelper::HOSTBASE in concatenation (.) or string at C:/Strawberry/perl/site/lib/Bio/DB/Query/GenBank.pm line 103.
Use of uninitialized value $Bio::DB::NCBIHelper::HOSTBASE in concatenation (.) or string at C:/Strawberry/perl/site/lib/Bio/DB/Query/GenBank.pm line 104.

line 103: use constant EPOST       => $Bio::DB::NCBIHelper::HOSTBASE.'/entrez/eutils/epost.fcgi';
line 104: use constant ESEARCH     => $Bio::DB::NCBIHelper::HOSTBASE.'/entrez/eutils/esearch.fcgi';

However if I try to print $Bio::DB::NCBIHelper::HOSTBASE it prints the correct hostbase (http://eutils.ncbi.nlm.nih.gov), meaning that it is in fact not uninitialized right?

bioperl perl • 2.4k views
ADD COMMENT
0
Entering edit mode

Please show a small piece of code that generates the error.

ADD REPLY
0
Entering edit mode

Well there is not much to show. Like I said the error occurs just by running the line:

​use Bio::DB::GenBank;
ADD REPLY
0
Entering edit mode

I can't reproduce that, could you please show us the version of bioperl you are using.

ADD REPLY

Login before adding your answer.

Traffic: 2117 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6