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 âas > posted on the some mailing list of your choosing but you donât have to let > us know what it is.â > > I hope I am sort of funny. > > Sort of. > > So, to answer your question âdo we really need...â, Iâd 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 donât 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 > >> UmeÃ¥ 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 - UmeÃ¥ universitet > >> UmeÃ¥ 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]]
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