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This queue is for tickets about the bioperl CPAN distribution.

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The Basics
Id: 105292
Status: resolved
Priority: 0/
Queue: bioperl
People
Owner: birney [...] sanger.ac.uk
Requestors: explorer [...] joaquinferrero.com
Cc:
AdminCc:
Bug Information
Severity: Critical
Broken in: 1.6.924
Fixed in: (no value)

History Show all quoted text
  Wed Jun 17 09:23:38 2015 explorer [...] joaquinferrero.com - Ticket created
Subject: CGI.pm, new dependency for BioPerl with Perl v5.22
BioPerl fail with v5.22.0 because CGI.pm is not included. http://www.cpantesters.org/cpan/report/64f6cdbe-090a-11e5-beb0-ee69f292232d ------------------------------------------------------------------------------- # Failed test 'use Bio::DB::Query::HIVQuery;' # at t/RemoteDB/HIV/HIVQuery.t line 12. # Tried to use 'Bio::DB::Query::HIVQuery'. # Error: Can't locate CGI.pm in @INC (you may need to install the CGI module) (@INC contains: /tmp/loop_over_bdir-23446-ksHUr3/BioPerl-1.6.924-G1Nfqd/blib/lib /tmp/loop_over_bdir-23446-ksHUr3/BioPerl-1.6.924-G1Nfqd/blib/arch /tmp/loop_over_bdir-23446-ksHUr3/BioPerl-1.6.924-G1Nfqd /home/sand/src/perl/repoperls/installed-perls/perl/v5.22.0/8005/lib/site_perl/5.22.0/x86_64-linux-thread-multi /home/sand/src/perl/repoperls/installed-perls/perl/v5.22.0/8005/lib/site_perl/5.22.0 /home/sand/src/perl/repoperls/installed-perls/perl/v5.22.0/8005/lib/5.22.0/x86_64-linux-thread-multi /home/sand/src/perl/repoperls/installed-perls/perl/v5.22.0/8005/lib/5.22.0 .) at /tmp/loop_over_bdir-23446-ksHUr3/BioPerl-1.6.924-G1Nfqd/blib/lib/Bio/DB/Query/HIVQuery.pm line 212. # BEGIN failed--compilation aborted at /tmp/loop_over_bdir-23446-ksHUr3/BioPerl-1.6.924-G1Nfqd/blib/lib/Bio/DB/Query/HIVQuery.pm line 212. # Compilation failed in require at t/RemoteDB/HIV/HIVQuery.t line 12. # BEGIN failed--compilation aborted at t/RemoteDB/HIV/HIVQuery.t line 12. Can't locate object method "new" via package "Bio::DB::Query::HIVQuery" at t/RemoteDB/HIV/HIVQuery.t line 21. -------------------------------------------------------------------------------
  Mon Jul 11 00:06:36 2016 cjfields [...] uiuc.edu - Correspondence added
Was added as a recommended module for the next release; tests are skipped if the module isn't installed. On Wed Jun 17 08:23:38 2015, explorer@joaquinferrero.com wrote: Show quoted text
> BioPerl fail with v5.22.0 because CGI.pm is not included. > > http://www.cpantesters.org/cpan/report/64f6cdbe-090a-11e5-beb0- > ee69f292232d > ------------------------------------------------------------------------------- > # Failed test 'use Bio::DB::Query::HIVQuery;' > # at t/RemoteDB/HIV/HIVQuery.t line 12. > # Tried to use 'Bio::DB::Query::HIVQuery'. > # Error: Can't locate CGI.pm in @INC (you may need to install the > CGI module) (@INC contains: /tmp/loop_over_bdir-23446-ksHUr3/BioPerl- > 1.6.924-G1Nfqd/blib/lib /tmp/loop_over_bdir-23446-ksHUr3/BioPerl- > 1.6.924-G1Nfqd/blib/arch /tmp/loop_over_bdir-23446-ksHUr3/BioPerl- > 1.6.924-G1Nfqd /home/sand/src/perl/repoperls/installed- > perls/perl/v5.22.0/8005/lib/site_perl/5.22.0/x86_64-linux-thread-multi > /home/sand/src/perl/repoperls/installed- > perls/perl/v5.22.0/8005/lib/site_perl/5.22.0 > /home/sand/src/perl/repoperls/installed- > perls/perl/v5.22.0/8005/lib/5.22.0/x86_64-linux-thread-multi > /home/sand/src/perl/repoperls/installed- > perls/perl/v5.22.0/8005/lib/5.22.0 .) at /tmp/loop_over_bdir-23446- > ksHUr3/BioPerl-1.6.924-G1Nfqd/blib/lib/Bio/DB/Query/HIVQuery.pm line > 212. > # BEGIN failed--compilation aborted at /tmp/loop_over_bdir-23446- > ksHUr3/BioPerl-1.6.924-G1Nfqd/blib/lib/Bio/DB/Query/HIVQuery.pm line > 212. > # Compilation failed in require at t/RemoteDB/HIV/HIVQuery.t line 12. > # BEGIN failed--compilation aborted at t/RemoteDB/HIV/HIVQuery.t line > 12. > Can't locate object method "new" via package > "Bio::DB::Query::HIVQuery" at t/RemoteDB/HIV/HIVQuery.t line 21. > -------------------------------------------------------------------------------
  Mon Jul 11 00:06:36 2016 The RT System itself - Status changed from 'new' to 'open'
  Mon Jul 11 00:06:37 2016 cjfields [...] uiuc.edu - Status changed from 'open' to 'resolved'