----- Original Message ----- > From: "Michael Lawrence" <lawrence.mich...@gene.com> > To: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com> > Cc: "Michael Lawrence" <lawrence.mich...@gene.com>, bioc-devel@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 < > kasperdanielhan...@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 <m...@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.mich...@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 > >> <m...@stowers.org<mailto: > >> m...@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-boun...@r-project.org<mailto: > >> bioc-devel-boun...@r-project.org> [mailto: > >> bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@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.delho...@umu.se<mailto:nicolas.delho...@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.delho...@plantphys.umu.se<mailto: > >> nicolas.delho...@plantphys.umu.se> > >> > >> >> SLU - Umeå universitet > >> >> Umeå S-901 87 Sweden > >> >> --------------------------------------------------------------- > >> >> > >> >> On 20 May 2014, at 15:04, Keith Hughitt > >> >> <keith.hugh...@gmail.com > >> <mailto:keith.hugh...@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]] > >> > >> _______________________________________________ > >> 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]] > >> > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > >> > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
