Yea, but I was thinking a formal field for the bug tracker (like IssueTracker), for the sake of clarity. The package page could somehow highlight it to keep people from missing it. And maybe even an automated way from within R to browse to the tracker URL.
On Fri, May 23, 2014 at 12:58 PM, Dan Tenenbaum <dtene...@fhcrc.org> wrote: > > > ----- 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 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]] > > > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > [[alternative HTML version deleted]]
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