Re: Heads up: bioperl release candidate

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Re: Heads up: bioperl release candidate

Christopher Fields
Hi Andreas,

> On Jul 7, 2016, at 10:57 AM, Andreas Tille <[hidden email]> wrote:
>
> Hi Michael,
>
> On Thu, Jul 07, 2016 at 10:20:18AM -0400, Michael Crusoe wrote:
>> Hello from the Bioinformatics Open Source Conference codefest.
>>
>> I'm sitting here with Hilmar Lapp & Christopher Fields who are working on a
>> new release of bioperl.
>>
>> If someone would like to try updating the Debian package with the release
>> candidate and testing it that would be useful:
>>
>> https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007000_003.tar.gz
>
> I personally do not feel able to do real testing.  However, it would be
> great if the release would include the quilt patches we are currently
> applying.
>
> Kind regards
>
>       Andreas.
>
> --
> http://fam-tille.de

I’m mainly putting out little fires with errors from CPAN Tester reports, but Michael has pointed the patches out and these are going in now (you may see some pings coming in from commits).

chris
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Re: Heads up: bioperl release candidate

Christopher Fields

> On Jul 11, 2016, at 8:13 AM, Charles Plessy <[hidden email]> wrote:
>
> Le Thu, Jul 07, 2016 at 10:20:18AM -0400, Michael Crusoe a écrit :
>>
>> If someone would like to try updating the Debian package with the release
>> candidate and testing it that would be useful:
>>
>> https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007000_003.tar.gz
>
> Hi Michael and everybody,
>
> I tested the packaging of /BioPerl-1.007000_004.tar.gz, and it went fine.  Some
> regression tests could not be run as not all the optional modules and software
> were installed on my laptop.
>
> Our automated test did not report anything significant.  Here is a copy of the
> typos it found.
>
> I: bioperl: spelling-error-in-manpage usr/share/man/man1/bp_biogetseq.1p.gz retrives retrieves
> I: bioperl: spelling-error-in-manpage usr/share/man/man1/bp_extract_feature_seq.1p.gz specifed specified
> I: bioperl: spelling-error-in-manpage usr/share/man/man1/bp_hivq.1p.gz retreive retrieve
> I: bioperl: spelling-error-in-manpage ... use --no-tag-display-limit to see all (or pipe to a file/program)
> W: bioperl: manpage-has-bad-whatis-entry usr/share/man/man1/bp_netinstall.1p.gz
> W: bioperl: manpage-has-bad-whatis-entry usr/share/man/man1/bp_search2gff.1p.gz
> W: bioperl: manpage-has-bad-whatis-entry usr/share/man/man1/bp_seqcut.1p.gz
> I: libbio-perl-perl: spelling-error-in-manpage usr/share/man/man3/Bio::Align::AlignI.3pm.gz wont won't
> I: libbio-perl-perl: spelling-error-in-manpage usr/share/man/man3/Bio::AnalysisI.3pm.gz refrence reference
> I: libbio-perl-perl: spelling-error-in-manpage usr/share/man/man3/Bio::AnalysisI.3pm.gz folowing following
> I: libbio-perl-perl: spelling-error-in-manpage ... use --no-tag-display-limit to see all (or pipe to a file/program)
> W: libbio-perl-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Bio::Index::Stockholm.3pm.gz
> W: libbio-perl-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Bio::OntologyIO::Handlers::BaseSAXHandler.3pm.gz
> W: libbio-perl-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Bio::OntologyIO::obo.3pm.gz
> W: libbio-perl-perl: manpage-has-bad-whatis-entry ... use --no-tag-display-limit to see all (or pipe to a file/program)
> W: libbio-perl-perl: manpage-has-errors-from-man usr/share/man/man3/Bio::SeqIO::bsml.3pm.gz 361: warning [p 4, 0.2i]: can't break line
>
> Have a nice day,
>
> Charles
>
> --
> Charles Plessy
> Debian Med packaging team,
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan

Thanks Charles!  I’ll link to this as a bug report for doc fixes.

chris
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