On 05/23/2014 11:16 AM, Cook, Malcolm 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....
I don't really have anything constructive to add to the thread.
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-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
>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>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.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> 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 mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>
> [[alternative HTML version deleted]]
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
