[Bioc-devel] Bug tracker for Bioconductor?

Nicolas Delhomme nicolas.delhomme at umu.se
Tue May 20 16:33:21 CEST 2014

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.



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]]
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