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This queue is for tickets about the bioperl CPAN distribution.

Report information
The Basics
Id:
92064
Status:
open
Priority:
Low/Low
Queue:
bioperl
People
Owner:
Nobody in particular
Requestors:
CHORNY [...] cpan.org
tsibley [...] cpan.org
Cc:
AdminCc:
BugTracker
Severity:
Normal
Broken in:
1.6.923
Fixed in:
(no value)

History
Sat Jan 11 17:50:17 2014 CHORNY [...] cpan.org - Ticket created
Subject: Bio::SeqIO is not indexed correctly

"install Bio::SeqIO" installs CJFIELDS/BioPerl-1.6.922.tar.gz because in 1.6.923 Bio::SeqIO does not have a version. -- Alexandr Ciornii, http://chorny.net
Sat Jan 11 18:46:08 2014 cjfields [...] uiuc.edu - Correspondence added
From: cjfields@uiuc.edu

On Sat Jan 11 17:50:17 2014, CHORNY wrote:
Show quoted text
> "install Bio::SeqIO" installs CJFIELDS/BioPerl-1.6.922.tar.gz because > in 1.6.923 Bio::SeqIO does not have a version.
This was due to some changes in the CPAN indexer that have broken how versions are passed on to all the classes via Bio::Root::Version. This will likely not be fixed until we release v 1.7.
Sat Jan 11 18:46:08 2014 The RT System itself - Status changed from 'new' to 'open'
Tue Apr 22 17:38:58 2014 tsibley [...] cpan.org - Requestor tsibley [...] cpan.org added
Tue Apr 22 17:39:32 2014 tsibley [...] cpan.org - Subject changed from 'Bio::SeqIO is not indexed correctly' to 'BioPerl release 1.6.923 is not indexed correctly'
Tue Apr 22 17:47:30 2014 tsibley [...] cpan.org - Correspondence added

On Sat Jan 11 15:46:08 2014, cjfields wrote:
Show quoted text
> On Sat Jan 11 17:50:17 2014, CHORNY wrote:
> > "install Bio::SeqIO" installs CJFIELDS/BioPerl-1.6.922.tar.gz because > > in 1.6.923 Bio::SeqIO does not have a version.
> > This was due to some changes in the CPAN indexer that have broken how > versions are passed on to all the classes via Bio::Root::Version. > This will likely not be fixed until we release v 1.7.
Is there a timeline for the 1.7 release? This issue was also discussed independently at https://github.com/andk/pause/issues/75, with excerpts from the indexing errors. Can you try forcing a re-index of CJFIELDS/BioPerl-1.006923.tar.gz on PAUSE to see if newer PAUSE code handles it better? I'm not sure what changed in PAUSE with regard to version parsing, but a re-index may help.
Tue Apr 22 17:58:07 2014 tsibley [...] cpan.org - Correspondence added

Another option to fix this pre-1.7 would be to use a META.yml or META.json-driven index on PAUSE by including a "provides" section that lists packages and there versions. This avoids the need to adjust versioning the code itself. Information on provides: https://metacpan.org/pod/CPAN::Meta::Spec#provides
Wed Jul 08 00:34:34 2015 SREZIC [...] cpan.org - Correspondence added

On 2014-01-11 17:50:17, CHORNY wrote:
Show quoted text
> "install Bio::SeqIO" installs CJFIELDS/BioPerl-1.6.922.tar.gz because > in 1.6.923 Bio::SeqIO does not have a version.
1.6.924 also seems to have index problems: cpan[3]> m BioPerl Module id = BioPerl CPAN_USERID CJFIELDS (Christopher Fields <cjfields@bioperl.org>) CPAN_VERSION undef CPAN_FILE C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz UPLOAD_DATE 2013-12-18 INST_FILE (not installed) -> which is not the latest available BioPerl (JFIELDS/BioPerl-1.6.924.tar.gz)
Wed Jul 08 00:36:56 2015 SREZIC [...] cpan.org - Correspondence added

On 2015-07-08 00:34:34, SREZIC wrote:
Show quoted text
> On 2014-01-11 17:50:17, CHORNY wrote:
> > "install Bio::SeqIO" installs CJFIELDS/BioPerl-1.6.922.tar.gz because > > in 1.6.923 Bio::SeqIO does not have a version.
> > > 1.6.924 also seems to have index problems: > > cpan[3]> m BioPerl > Module id = BioPerl > CPAN_USERID CJFIELDS (Christopher Fields <cjfields@bioperl.org>) > CPAN_VERSION undef > CPAN_FILE C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz > UPLOAD_DATE 2013-12-18 > INST_FILE (not installed) > > -> which is not the latest available BioPerl (JFIELDS/BioPerl- > 1.6.924.tar.gz)
Oops, this should read CJFIELDS/BioPerl-1.6.924.tar.gz
Thu Jul 07 14:39:32 2016 cjfields [...] uiuc.edu - Correspondence added

We're still seeing some odd issues with versioning, in particular with CPAN vs cpanm vs MetaCPAN reporting different versions. We'll see if we can sort out the problem with newer 1.7x RCs On Tue Jul 07 23:36:56 2015, SREZIC wrote:
Show quoted text
> On 2015-07-08 00:34:34, SREZIC wrote:
> > On 2014-01-11 17:50:17, CHORNY wrote:
> > > "install Bio::SeqIO" installs CJFIELDS/BioPerl-1.6.922.tar.gz because > > > in 1.6.923 Bio::SeqIO does not have a version.
> > > > > > 1.6.924 also seems to have index problems: > > > > cpan[3]> m BioPerl > > Module id = BioPerl > > CPAN_USERID CJFIELDS (Christopher Fields <cjfields@bioperl.org>) > > CPAN_VERSION undef > > CPAN_FILE C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz > > UPLOAD_DATE 2013-12-18 > > INST_FILE (not installed) > > > > -> which is not the latest available BioPerl (JFIELDS/BioPerl- > > 1.6.924.tar.gz)
> > Oops, this should read CJFIELDS/BioPerl-1.6.924.tar.gz >
Thu Sep 15 23:11:41 2016 cjfields [...] uiuc.edu - Correspondence added

On Thu Jul 07 13:39:32 2016, cjfields wrote:
Show quoted text
> We're still seeing some odd issues with versioning, in particular with > CPAN vs cpanm vs MetaCPAN reporting different versions. We'll see if > we can sort out the problem with newer 1.7x RCs > > On Tue Jul 07 23:36:56 2015, SREZIC wrote:
> > On 2015-07-08 00:34:34, SREZIC wrote:
> > > On 2014-01-11 17:50:17, CHORNY wrote:
> > > > "install Bio::SeqIO" installs CJFIELDS/BioPerl-1.6.922.tar.gz > > > > because > > > > in 1.6.923 Bio::SeqIO does not have a version.
> > > > > > > > > 1.6.924 also seems to have index problems: > > > > > > cpan[3]> m BioPerl > > > Module id = BioPerl > > > CPAN_USERID CJFIELDS (Christopher Fields > > > <cjfields@bioperl.org>) > > > CPAN_VERSION undef > > > CPAN_FILE C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz > > > UPLOAD_DATE 2013-12-18 > > > INST_FILE (not installed) > > > > > > -> which is not the latest available BioPerl (JFIELDS/BioPerl- > > > 1.6.924.tar.gz)
> > > > Oops, this should read CJFIELDS/BioPerl-1.6.924.tar.gz > >
Looking at the last release on search.cpan.org it seems to have indexed all modules except those not inheriting Bio::Root::Version. We'll see if the issue persists after the 1.7.0 release, if so I will add explicit numbers to the next point release. http://search.cpan.org/~cjfields/BioPerl-1.6.924/

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