Question: BioPerl: Use of uninitialized value $Bio::DB::NCBIHelper::HOSTBASE
0
gravatar for tino_s3004
4.1 years ago by
tino_s30040
European Union
tino_s30040 wrote:

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 • 1.2k views
ADD COMMENTlink modified 4.1 years ago by RamRS21k • written 4.1 years ago by tino_s30040

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

ADD REPLYlink written 4.1 years ago by SES8.2k

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

​use Bio::DB::GenBank;
ADD REPLYlink written 4.0 years ago by tino_s30040

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

ADD REPLYlink written 4.0 years ago by SES8.2k
0
gravatar for RamRS
4.1 years ago by
RamRS21k
Houston, TX
RamRS21k wrote:

$BIO is wrong. Use just BIO

ADD COMMENTlink written 4.1 years ago by RamRS21k

What $BIO are you referring to? 

ADD REPLYlink written 4.0 years ago by tino_s30040

I thought you were using $BIO instead of BIO. Please ignore it.

ADD REPLYlink written 4.0 years ago by RamRS21k
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