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bioperl/Bio-EUtilities
test errors: choice/seq contains no opening bracket

Greetings, A couple of days ago, we noticed in Debian sid that the test suite of Bio::EUtilities begun to fail with multiple occurrences of the following error affecting different tests: choice/seq contains ...
  • emollier
  • 3
  • Opened 
    on Jan 21
  • #16

bioperl/Bio-EUtilities
Printing an error should stringify structures included in the error message

I m using Bio::DB::EUtilities to fetch linked assemblies for some input nuccore accessions. Occasionally, the server responds with an error instead of a history. The result is a warning like this printed ...
  • yzhernand
  • Opened 
    on Oct 16, 2020
  • #15

bioperl/Bio-EUtilities
api key value causes issue son programs if empty

entrez requests require an email for a few years. However, in practice it works fine without email. Similarly, entrez now requires an API key but in practice it works fine if it s omitted. The difference ...
  • carandraug
  • 6
  • Opened 
    on Mar 9, 2020
  • #14

bioperl/Bio-EUtilities
Bio::Tools:EUtilities Looks like a typo

I m trying to use Bio::Tools::EUtilities and I am getting an error: Can t locate object method warn via package self (perhaps you forgot to load self ?) at /usr/local/share/perl/5.26.1/Bio/Tools/EUtilities.pm ...
  • wgallin
  • 2
  • Opened 
    on Feb 23, 2020
  • #13

bioperl/Bio-EUtilities
api_key support

Does this repo support the new api_key parameter?
Feature Request
  • pcantalupo
  • 6
  • Opened 
    on Nov 2, 2017
  • #9

bioperl/Bio-EUtilities
Requirements

Hi there, Could someone point me in the direction of the requirements of this interface? What version of perl does it require, what are any other dependencies? Cheers! Katherine
  • katbeaulieu
  • 5
  • Opened 
    on Apr 21, 2017
  • #8

bioperl/Bio-EUtilities
no Bio::EUtilities module actually exists

Despite the distribution name, Bio::EUtilities, there is not actually a Bio::EUtilities module. While this is not a requirement, I am faced with people that find that confusing. I guess this could also ...
  • carandraug
  • 1
  • Opened 
    on Feb 3, 2017
  • #7

bioperl/Bio-EUtilities
testsuite requires internet connection

Several of the test units in t/ require internet connection. This happens because the xml parsers download the dtd from the ncbi servers to validate the xml files. See debian bug #852004 for details. ...
  • carandraug
  • Opened 
    on Jan 26, 2017
  • #6

bioperl/Bio-EUtilities
Difference between protein_pubmed_refseq, protein_pubmed, and protein_pubmed_weighted?

Hey, I would like to ask what the difference is between protein_pubmed_refseq, protein_pubmed, and protein_pubmed_weighted? Best, Nils
  • nilsrudqvist
  • 1
  • Opened 
    on Aug 14, 2016
  • #5

bioperl/Bio-EUtilities
Change base URLs for NCBI services to use https instead of http

To improve end user security and privacy, and by Federal government mandate OMB memo M-08-023, NCBI will be moving all web services to HTTPS-only by September 30, 2016. Looking over the biojava source ...
  • elucify
  • 2
  • Opened 
    on Jul 15, 2016
  • #4
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