[Bioc-devel] Bug tracker for Bioconductor?
Dan Tenenbaum
dtenenba at fhcrc.org
Fri May 23 21:58:55 CEST 2014
----- Original Message -----
> From: "Michael Lawrence" <lawrence.michael at gene.com>
> To: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> Cc: "Michael Lawrence" <lawrence.michael at gene.com>, bioc-devel at r-project.org
> Sent: Friday, May 23, 2014 12:48:55 PM
> Subject: Re: [Bioc-devel] Bug tracker for Bioconductor?
>
> 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.
Already done; see for example the ACME package landing page:
http://www.bioconductor.org/packages/release/bioc/html/ACME.html
The URL is a clickable link. This could be the link to the github issue tracker. Note that you can have multiple URLs in the URL field, I believe comma separated. See also
http://www.bioconductor.org/developers/how-to/git-svn/#advertise
Dan
>
>
> On Fri, May 23, 2014 at 12:42 PM, Kasper Daniel Hansen <
> kasperdanielhansen at 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 at 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 at gene.com]
> >> Sent: Friday, May 23, 2014 1:31 PM
> >> To: Cook, Malcolm
> >> Cc: Keith Hughitt; Nicolas Delhomme; Martin Morgan;
> >> bioc-devel at 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 at stowers.org<mailto:
> >> MEC at 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 at r-project.org<mailto:
> >> bioc-devel-bounces at r-project.org> [mailto:
> >> bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>]
> >> On Behalf Of Keith Hughitt
> >> >Sent: Friday, May 23, 2014 12:53 PM
> >> >To: Nicolas Delhomme
> >> >Cc: bioc-devel at r-project.org<mailto:bioc-devel at 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 at umu.se<mailto:nicolas.delhomme at 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 at plantphys.umu.se<mailto:
> >> nicolas.delhomme at plantphys.umu.se>
> >>
> >> >> SLU - Umeå universitet
> >> >> Umeå S-901 87 Sweden
> >> >> ---------------------------------------------------------------
> >> >>
> >> >> On 20 May 2014, at 15:04, Keith Hughitt
> >> >> <keith.hughitt at gmail.com
> >> <mailto:keith.hughitt at 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 at r-project.org<mailto:Bioc-devel at r-project.org>
> >> >> > mailing
> >> list
> >>
> >> >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >>
> >> >>
> >> >
> >> > [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing
> >> list
> >>
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >>
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> >>
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >>
> >
>
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