[Bioc-devel] Bug tracker for Bioconductor?
Cook, Malcolm
MEC at stowers.org
Tue May 27 17:25:45 CEST 2014
>> 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....
>>
>
>I don't really have anything constructive to add to the thread.
Actually your history lesson is valuable to the discussion. Thanks!
Honestly, I really don't have a great problem with things as they stand. I get plenty of attention to _my_ questions/observations in a timely and informative manner....
I do think that the BioC project hosting a tracking system might eliminate a hurdle for some developers, but the trade-off is hard for me to assess.
Cheers,
Malcolm
>
> From a project perspective it would be great to have a centralized bug tracking
>facility; there are many bugs, they are poorly tracked even by the most diligent
>of us, and it would benefit users and developers alike to have a convenient way
>to view our laundry.
>
>Most off-the-shelf bug tracking systems are not designed to work under the
>'federated' (I guess that's not the right technical description) model of
>Bioconductor where there are a large number of individual projects, so
>implementing a workable solution requires quite a lot of effort and / or ongoing
>management. As we've seen with the rise of github and its use by even key
>contributors to the project, it is very difficult to impose a central system on
>our developers, even for such a key aspect as code management. Users are
>similarly very difficult beasts to train, so their structured participation
>would be inconsistent. While on the one hand bug tracking might seem like a
>no-brainer for an experienced developer, it adds another hurdle (along with
>mastering version control, the R package system, vignettes, ...) to potentially
>discourage more novice developers who nonetheless are making valuable
>contributions to the project.
>
>In response to the earlier thread, the developers in Seattle did use an
>Atlassian / Jira based internal bug tracking system and pursued it for about a
>year, with the goal being to make it available generally if it seemed like it
>would 'fly'. There was varied enthusiasm and participation within the group.
>Perhaps I was less diligent than others; I found that my bugs were either
>addressed before they got into the tracker, or entered the tracker as a place to
>die. The bugs would die because they weren't of high enough importance or
>clearly enough articulated to act on when they arose, and with the passage of
>time their perceived importance and relevance declined. There were some
>individual successes, where tracking a bug helped to coordinate input from
>different people and to collate insights and proposed solutions into a focused
>discussion, and where the bug tracker served as a kind of long-term memory bank
>for issues that did eventually get addressed. Use of the tracker declined with
>time, presenting an increasingly inaccurate representation of activity in the
>project.
>
>Martin
>
>
>> In any case,
>>
>> +1,
>>
>> Malcolm
>>
>> >-----Original Message-----
>> >From: 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
>> >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>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
>> >> Email: 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> 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 mailing list
>> >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>
>> >>
>> >
>> > [[alternative HTML version deleted]]
>>
>
>
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