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This queue is for tickets about the Bio-LITE-Taxonomy-NCBI-Gi2taxid CPAN distribution.

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The Basics
Id: 91576
Status: patched
Priority: 0/
Queue: Bio-LITE-Taxonomy-NCBI-Gi2taxid
People
Owner: MOTIF [...] cpan.org
Requestors: dana.price [...] gmail.com
Cc:
AdminCc:
Bug Information
Severity: (no value)
Broken in: (no value)
Fixed in: (no value)

History Show all quoted text
  Sun Dec 22 00:00:46 2013 dana.price [...] gmail.com - Ticket created
Subject: substr outside of string in new_dict
Date: Sun, 22 Dec 2013 00:00:30 -0500
To: bug-Bio-LITE-Taxonomy-NCBI-Gi2taxid [...] rt.cpan.org
From: Dana Price <dana.price [...] gmail.com>
For the last several months/releases of the NCBI taxonomy, when trying to construct a binary database I've been getting the following error: substr outside of string at /usr/local/share/perl/5.10.0/Bio/LITE/Taxonomy/NCBI/Gi2taxid.pm line 202 This happens near the end of the .dmp file, I believe, as I can take the first several million lines and the script will complete just fine. the code is lifted straight from the doc: use Bio::LITE::Taxonomy::NCBI::Gi2taxid<https://metacpan.org/module/Bio::LITE::Taxonomy::NCBI::Gi2taxid> qw/new_dict/; new_dict (in => "gi_taxid_prot.dmp", out => "gi_taxid_prot.bin"); Thanks, Dana
  Mon Dec 23 06:31:01 2013 MOTIF [...] cpan.org - Correspondence added
This should be fixed in v0.10 Now the creation of the bin file is slower, but safer and with very low memory footprint. Let me know if this version solves the issue and if you find any other problem. M; El Dom Dic 22 00:00:46 2013, dana.price@gmail.com escribió: Show quoted text
> For the last several months/releases of the NCBI taxonomy, when trying > to > construct a binary database I've been getting the following error: > > substr outside of string at > /usr/local/share/perl/5.10.0/Bio/LITE/Taxonomy/NCBI/Gi2taxid.pm line > 202 > > This happens near the end of the .dmp file, I believe, as I can take > the > first several million lines and the script will complete just fine. > > the code is lifted straight from the doc: > > use > Bio::LITE::Taxonomy::NCBI::Gi2taxid<https://metacpan.org/module/Bio::LITE::Taxonomy::NCBI::Gi2taxid> > qw/new_dict/; > > new_dict (in => "gi_taxid_prot.dmp", > out => "gi_taxid_prot.bin"); > > Thanks, > Dana
  Mon Dec 23 06:31:01 2013 The RT System itself - Status changed from 'new' to 'open'
  Mon Dec 23 06:31:02 2013 MOTIF [...] cpan.org - Status changed from 'open' to 'patched'
  Mon Dec 23 06:31:02 2013 MOTIF [...] cpan.org - Taken