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 < 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 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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