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bioperl / Bio-DB-NCBIHelper

BioPerl modules for accessing data from NCBI
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Use of uninitialized value $Bio::DB::NCBIHelper::HOSTBASE in concatenation (.) or string at /usr/share/perl5/Bio/DB/Query/GenBank.pm line 103. #1

Closed jmartinsjrbr closed 5 years ago

jmartinsjrbr commented 9 years ago

We have update our bioperl version to 1.6923. Now, when we ran the local version of Guidance, an dna sequence multiple alignment software (http://guidance.tau.ac.il/), we get the following error:

"Use of uninitialized value $Bio::DB::NCBIHelper::HOSTBASE in concatenation (.) or string at /usr/share/perl5/Bio/DB/Query/GenBank.pm line 103." "Use of uninitialized value $Bio::DB::NCBIHelper::HOSTBASE in concatenation (.) or string at /usr/share/perl5/Bio/DB/Query/GenBank.pm line 104."

Could provide any help?

Best regards, Joaquim

cjfields commented 9 years ago

@jmartinsjrbr sorry no idea, but my guess is there is a conflict with the code expected in the Guidance code and the newer version. W/o access to the source code we can't help much.

cjfields commented 8 years ago

@jmartinsjrbr can you test this against the latest v1.7.0 release? I anticipate the upcoming NCBI changes will affect your code.

cjfields commented 7 years ago

@jmartinsjrbr just a note, NCBI has updated their access to require HTTPS, it's very possible any remote access would break unless you update to the latest bioperl release.

jmartinsjrbr commented 7 years ago

Thank you! I will try those tips you suggested. Best regards

cjfields commented 5 years ago

@jmartinsjrbr closing ticket out, assuming this is fixed. Feel free to reopen if this isn't addressed.

carandraug commented 5 years ago

For what is worth, this was "fixed" with bioperl/bioperl-live@adebb794f1479a4f86106713ba5912ba