To support the decentralized model, it would be nice to have a standard way
of directing users to the right bug tracker. Perhaps this could be
specified as a URL in the DESCRIPTION and the Bioc package page could link
to it.


On Fri, May 23, 2014 at 12:42 PM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> I want to remind some posters in this thread that most Bioconductor
> packages are being developed by non-overlapping sets of people and that it
> is therefore not clear at all that a common bug tracker across the project
> is necessary (says the person who has definitely "lost" bugs reported per
> email).
>
> For example, with the new github bridge I am intending to use github as a
> devel repository for my packages because I get 1) pull requests (aka bug
> fixes and feature enhancements) and 2) bug tracking.  But this workflow may
> not work well for everyone.
>
> In general, for every bug reported on the email list I get quite a few
> more private emails.  But the flip side is that the number of bugs reported
> for me packages is much smaller than the number of bugs reported across all
> bioc packages,
>
> Best,
> Kasper
>
>
> On Fri, May 23, 2014 at 3:35 PM, Cook, Malcolm <MEC@stowers.org> wrote:
>
>> Michael,
>>
>> Well, BioC has many suggestions and requirements for how packages are to
>> be constructed, documented, and deployed.
>>
>> http://www.bioconductor.org/developers/package-guidelines/
>>
>> The only thing about bugs is: Response to bug reports and questions from
>> users regarding your package as posted on the bioconductor mailing list.
>>
>> I think this is minimalistic.
>>
>> In a similar vein as your suggestion, though, this might read instead “as
>> posted on the some mailing list of your choosing but you don’t have to let
>> us know what it is.”
>>
>> I hope I am sort of funny.
>>
>> Sort of.
>>
>> So, to answer your question “do we really need...”, I’d vote
>>
>> +2
>>
>> !Malcolm
>>
>>
>> From: Michael Lawrence [mailto:lawrence.michael@gene.com]
>> Sent: Friday, May 23, 2014 1:31 PM
>> To: Cook, Malcolm
>> Cc: Keith Hughitt; Nicolas Delhomme; Martin Morgan;
>> bioc-devel@r-project.org
>> Subject: Re: [Bioc-devel] Bug tracker for Bioconductor?
>>
>> Do we really need a centralized bug-tracker or would it be best to leave
>> that to the individual packages, e.g., using the github tracker via the
>> github-svn-bridge? Many are probably already doing that.
>> Michael
>>
>>
>> On Fri, May 23, 2014 at 11:16 AM, Cook, Malcolm <MEC@stowers.org<mailto:
>> MEC@stowers.org>> wrote:
>> Martin,
>>
>> I'm sure you're watching this thread.....
>>
>> Can we take it as some "feedback from other developers" that you
>> requested way back in
>> https://stat.ethz.ch/pipermail/bioc-devel/2011-October/002854.html when
>> I wished for similar....
>>
>> In any case,
>>
>> +1,
>>
>> Malcolm
>>
>>  >-----Original Message-----
>>  >From: bioc-devel-bounces@r-project.org<mailto:
>> bioc-devel-bounces@r-project.org> [mailto:
>> bioc-devel-bounces@r-project.org<mailto:bioc-devel-bounces@r-project.org>]
>> On Behalf Of Keith Hughitt
>>  >Sent: Friday, May 23, 2014 12:53 PM
>>  >To: Nicolas Delhomme
>>  >Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
>>  >Subject: Re: [Bioc-devel] Bug tracker for Bioconductor?
>>  >
>>  >Hi Nico,
>>  >
>>  >It's a shame that the effort did not gain more traction in 2004. I
>> wonder
>>  >if things would look differently now as the community has grown
>>  >significantly larger?
>>  >
>>  >It does seem like there are a relatively small number of bug-related
>>  >questions on the mailing lists. I wonder though if this could be in part
>>  >because some people may be hesitant to ask their questions on such a
>> large
>>  >list, and instead end up either forgoing the question or contacting the
>>  >software authors directly?
>>  >
>>  >Also, even if there is only a trickle of bug and feature-request related
>>  >posts to the mailing list across time, without any way to keep track of
>> how
>>  >many of those issues are open/unresolved, it's hard to gauge whether the
>>  >project really is low-maintenance, or if there are actually a large
>> number
>>  >of issues that have just been unanswered or forgotten.
>>  >
>>  >There would definitely be a burden associated with setting up a more
>>  >sophisticated system for dealing with bugs. I am just not convinced that
>>  >the burden would be too great, or that it is not worth taking on :)
>>  >
>>  >Cheers,
>>  >Keith
>>  >
>>  >
>>  >On Tue, May 20, 2014 at 10:33 AM, Nicolas Delhomme
>>  ><nicolas.delhomme@umu.se<mailto:nicolas.delhomme@umu.se>>wrote:
>>
>>  >
>>  >> Hej Keith!
>>  >>
>>  >> I agree that this would be useful. For having been very close to the
>> 2004
>>  >> attempt - a then colleague of mine set up a solution similar to what
>> you
>>  >> describe - I can tell you that the main reason for it dying out was
>> that
>>  >> despite advertising it, it never got widely used. I don’t know what
>> the
>>  >> reasons for that really were, but from experience I know that many
>> fellow
>>  >> bioinformaticians find such tools more time-consuming than  handling
>> bug
>>  >> tracking through emails. And after all very few packages require
>> frequent
>>  >> support, as can be devised from questions to the mailing list, so I do
>>  >> understand their point.
>>  >>
>>  >> Cheers,
>>  >>
>>  >> Nico
>>  >>
>>  >> ---------------------------------------------------------------
>>  >> Nicolas Delhomme
>>  >>
>>  >> The Street Lab
>>  >> Department of Plant Physiology
>>  >> Umeå Plant Science Center
>>  >>
>>  >> Tel: +46 90 786 5478<tel:%2B46%2090%20786%205478>
>>  >> Email: nicolas.delhomme@plantphys.umu.se<mailto:
>> nicolas.delhomme@plantphys.umu.se>
>>
>>  >> SLU - Umeå universitet
>>  >> Umeå S-901 87 Sweden
>>  >> ---------------------------------------------------------------
>>  >>
>>  >> On 20 May 2014, at 15:04, Keith Hughitt <keith.hughitt@gmail.com
>> <mailto:keith.hughitt@gmail.com>> wrote:
>>  >>
>>  >> > Hello all,
>>  >> >
>>  >> > I was wondering if there had been any progress towards adopting a
>> bug
>>  >> > tracking system for Bioconductor?
>>  >> >
>>  >> > It has been discussed at least a couple times in the past, e.g.:
>>  >> >
>>  >> >    -
>> https://stat.ethz.ch/pipermail/bioc-devel/2011-October/002844.html
>>  >> >    -
>> https://stat.ethz.ch/pipermail/bioc-devel/2004-October/000040.html
>>  >> >
>>  >> > But as far as I can tell, no such system has been set up and the
>> current
>>  >> > approach is to report issues to the mailing list.
>>  >> >
>>  >> > The main reasons I see for adopting such a system would be:
>>  >> >
>>  >> > 1. Centralized location for reporting and tracking bugs and feature
>>  >> > requests; this also makes it more straight-forward to see if anyone
>> else
>>  >> > has already reported a specific issue.
>>  >> >
>>  >> > 2. Ability to associate a given issue with specific a project
>>  >> >
>>  >> > 3. Ability to assign priorities to various issues and assign
>> developers
>>  >> to
>>  >> > work on them.
>>  >> >
>>  >> > 4. Easy to track changes made to a given release.
>>  >> >
>>  >> > 5. Separate usage and development discussion (mailing list) for
>>  >> > issue-related discussion.
>>  >> >
>>  >> > Something like trac <http://trac.edgewall.org/> would be
>> sufficient to
>>  >> > cover all of the above issues, although something with closer
>> integration
>>  >> > to the codebase such as Github <https://github.com/> or
>>  >> > Bitbucket<https://bitbucket.org/>might provide some additional
>>  >> > benefits. Of course, migrating to a separate
>>  >> > VCS not a trivial matter and would itself merit a separate
>> discussion.
>>  >> >
>>  >> > A couple examples of issue trackers working well for R projects:
>>  >> >
>>  >> >    https://github.com/hadley/ggplot2/issues
>>  >> >    https://github.com/yihui/knitr
>>  >> >
>>  >> > Thank you all for your excellent work on Bioconductor! It is a
>> really
>>  >> > amazing resource.
>>  >> >
>>  >> > Regards,
>>  >> > Keith
>>  >> >
>>  >> >       [[alternative HTML version deleted]]
>>  >> >
>>  >> > _______________________________________________
>>  >> > Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing
>> list
>>
>>  >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>  >>
>>  >>
>>  >
>>  >      [[alternative HTML version deleted]]
>>
>> _______________________________________________
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>>
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>>
>>
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>>
>>
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>

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