[Bioc-devel] Bug tracker for Bioconductor?

Keith Hughitt keith.hughitt at gmail.com
Sun Jun 8 15:37:54 CEST 2014

I agree that trying to incorporate all bioconductor projects into a
single bug tracker could be messy. Although Github could handle this
(e.g. using project-specific issue labels), it might still become

Instead, perhaps it would be best just to spend some time to draft
some "suggested" conventions for dealing with issues, and follow those
conventions for the core package.

Then, similar to CRAN, a "issues" link could be included on each
bioconductor project page to direct people to the relevant issue
tracker, if one has been setup.

This would make it very straight-forward for users to find where to
report bugs and feature-requests for any given project. By keeping
things as "guidelines" or "suggestions", people can still choose not
to maintain a dedicated issue tracker if they are really opposed to
it, or to choose an alternative bug tracking system aside from the
recommended one if they have a strong preference -- the link will
still be in the same place though so the user can at least find it
just as easily.

Finally, once some conventions have been agreed on, the pages on the
(1) setting up an issue tracker and (2) reporting a a bug or feature
request could be fleshed out a bit more to make it very easy for both
users and devs to orient themselves. For the devs, this could include
instructions for setting up the recommended issue tracker, and how to
populate the relevant field on the bioconductor project. For the
users, this could include a more detailed description of where to
report bugs, what information to include, etc.

Keith<div class="gmail_extra"><br><br><div class="gmail_quote">On Tue,
May 27, 2014 at 11:25 AM, Cook, Malcolm <span dir="ltr"><<a
href="mailto:MEC at stowers.org"
target="_blank">MEC at stowers.org</a>></span> wrote:<br><blockquote
class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex"><div class="">>> Martin,<br>
 >> I'm sure you're watching this thread.....<br>
 >> Can we take it as some "feedback from other developers"
that you requested way back in <a
 >devel/2011-October/002854.<wbr>html when I wished for similar....<br>
 >I don't really have anything constructive to add to the thread.<br>
</div>Actually your history lesson is valuable to the discussion.
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....<br>
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.<br>
<div class="HOEnZb"><div class="h5"><br>
 > From a project perspective it would be great to have a
centralized bug tracking<br>
 >facility; there are many bugs, they are poorly tracked even
by the most diligent<br>
 >of us, and it would benefit users and developers alike to
have a convenient way<br>
 >to view our laundry.<br>
 >Most off-the-shelf bug tracking systems are not designed to
work under the<br>
 >'federated' (I guess that's not the right technical
description) model of<br>
 >Bioconductor where there are a large number of individual
projects, so<br>
 >implementing a workable solution requires quite a lot of
effort and / or ongoing<br>
 >management. As we've seen with the rise of github and its
use by even key<br>
 >contributors to the project, it is very difficult to impose
a central system on<br>
 >our developers, even for such a key aspect as code
management. Users are<br>
 >similarly very difficult beasts to train, so their
structured participation<br>
 >would be inconsistent. While on the one hand bug tracking
might seem like a<br>
 >no-brainer for an experienced developer, it adds another
hurdle (along with<br>
 >mastering version control, the R package system, vignettes,
...) to potentially<br>
 >discourage more novice developers who nonetheless are making
 >contributions to the project.<br>
 >In response to the earlier thread, the developers in Seattle
did use an<br>
 >Atlassian / Jira based internal bug tracking system and
pursued it for about a<br>
 >year, with the goal being to make it available generally if
it seemed like it<br>
 >would 'fly'. There was varied enthusiasm and participation
within the group.<br>
 >Perhaps I was less diligent than others; I found that my
bugs were either<br>
 >addressed before they got into the tracker, or entered the
tracker as a place to<br>
 >die. The bugs would die because they weren't of high enough
importance or<br>
 >clearly enough articulated to act on when they arose, and
with the passage of<br>
 >time their perceived importance and relevance declined.
There were some<br>
 >individual successes, where tracking a bug helped to
coordinate input from<br>
 >different people and to collate insights and proposed
solutions into a focused<br>
 >discussion, and where the bug tracker served as a kind of
long-term memory bank<br>
 >for issues that did eventually get addressed. Use of the
tracker declined with<br>
 >time, presenting an increasingly inaccurate representation
of activity in the<br>
 >> In any case,<br>
 >> +1,<br>
 >> Malcolm<br>
 >>   >-----Original Message-----<br>
 >>   >From: <a
href="mailto:bioc-devel-bounces at r-project.org">bioc-devel-bounces at r-project.<wbr>org</a>
[mailto:<a href="mailto:bioc-devel-bounces at r-project.org">bioc-devel-bounces at r-<wbr>project.org</a>]
On Behalf Of Keith Hughitt<br>
 >>   >Sent: Friday, May 23, 2014 12:53 PM<br>
 >>   >To: Nicolas Delhomme<br>
 >>   >Cc: <a
href="mailto:bioc-devel at r-project.org">bioc-devel at r-project.org</a><br>
 >>   >Subject: Re: [Bioc-devel] Bug tracker for
 >>   ><br>
 >>   >Hi Nico,<br>
 >>   ><br>
 >>   >It's a shame that the effort did not gain
more traction in 2004. I wonder<br>
 >>   >if things would look differently now as the
community has grown<br>
 >>   >significantly larger?<br>
 >>   ><br>
 >>   >It does seem like there are a relatively
small number of bug-related<br>
 >>   >questions on the mailing lists. I wonder
though if this could be in part<br>
 >>   >because some people may be hesitant to ask
their questions on such a large<br>
 >>   >list, and instead end up either forgoing the
question or contacting the<br>
 >>   >software authors directly?<br>
 >>   ><br>
 >>   >Also, even if there is only a trickle of bug
and feature-request related<br>
 >>   >posts to the mailing list across time,
without any way to keep track of how<br>
 >>   >many of those issues are open/unresolved,
it's hard to gauge whether the<br>
 >>   >project really is low-maintenance, or if
there are actually a large number<br>
 >>   >of issues that have just been unanswered or
 >>   ><br>
 >>   >There would definitely be a burden
associated with setting up a more<br>
 >>   >sophisticated system for dealing with bugs.
I am just not convinced that<br>
 >>   >the burden would be too great, or that it is
not worth taking on :)<br>
 >>   ><br>
 >>   >Cheers,<br>
 >>   >Keith<br>
 >>   ><br>
 >>   ><br>
 >>   >On Tue, May 20, 2014 at 10:33 AM, Nicolas Delhomme<br>
 >>   ><<a
href="mailto:nicolas.delhomme at umu.se">nicolas.delhomme at umu.se</a>><wbr>wrote:<br>
 >>   ><br>
 >>   >> Hej Keith!<br>
 >>   >><br>
 >>   >> I agree that this would be useful. For
having been very close to the 2004<br>
 >>   >> attempt - a then colleague of mine set
up a solution similar to what you<br>
 >>   >> describe - I can tell you that the main
reason for it dying out was that<br>
 >>   >> despite advertising it, it never got
widely used. I don’t know what the<br>
 >>   >> reasons for that really were, but from
experience I know that many fellow<br>
 >>   >> bioinformaticians find such tools more
time-consuming than  handling bug<br>
 >>   >> tracking through emails. And after all
very few packages require frequent<br>
 >>   >> support, as can be devised from
questions to the mailing list, so I do<br>
 >>   >> understand their point.<br>
 >>   >><br>
 >>   >> Cheers,<br>
 >>   >><br>
 >>   >> Nico<br>
 >>   >><br>
 >>   >>
 >>   >> Nicolas Delhomme<br>
 >>   >><br>
 >>   >> The Street Lab<br>
 >>   >> Department of Plant Physiology<br>
 >>   >> Umeå Plant Science Center<br>
 >>   >><br>
 >>   >> Tel: <a
href="tel:%2B46%2090%20786%205478" value="+46907865478">+46 90 786
 >>   >> Email: <a
href="mailto:nicolas.delhomme at plantphys.umu.se">nicolas.delhomme at plantphys.<wbr>umu.se</a><br>
 >>   >> SLU - Umeå universitet<br>
 >>   >> Umeå S-901 87 Sweden<br>
 >>   >>
 >>   >><br>
 >>   >> On 20 May 2014, at 15:04, Keith Hughitt
<<a href="mailto:keith.hughitt at gmail.com">keith.hughitt at gmail.com</a>>
 >>   >><br>
 >>   >> > Hello all,<br>
 >>   >> ><br>
 >>   >> > I was wondering if there had been
any progress towards adopting a bug<br>
 >>   >> > tracking system for Bioconductor?<br>
 >>   >> ><br>
 >>   >> > It has been discussed at least a
couple times in the past, e.g.:<br>
 >>   >> ><br>
 >>   >> >    - <a
 >>   >> >    - <a
 >>   >> ><br>
 >>   >> > But as far as I can tell, no such
system has been set up and the current<br>
 >>   >> > approach is to report issues to
the mailing list.<br>
 >>   >> ><br>
 >>   >> > The main reasons I see for
adopting such a system would be:<br>
 >>   >> ><br>
 >>   >> > 1. Centralized location for
reporting and tracking bugs and feature<br>
 >>   >> > requests; this also makes it more
straight-forward to see if anyone else<br>
 >>   >> > has already reported a specific issue.<br>
 >>   >> ><br>
 >>   >> > 2. Ability to associate a given
issue with specific a project<br>
 >>   >> ><br>
 >>   >> > 3. Ability to assign priorities to
various issues and assign developers<br>
 >>   >> to<br>
 >>   >> > work on them.<br>
 >>   >> ><br>
 >>   >> > 4. Easy to track changes made to a
given release.<br>
 >>   >> ><br>
 >>   >> > 5. Separate usage and development
discussion (mailing list) for<br>
 >>   >> > issue-related discussion.<br>
 >>   >> ><br>
 >>   >> > Something like trac <<a
target="_blank">http://trac.edgewall.org/</a>> would be sufficient
 >>   >> > cover all of the above issues,
although something with closer integration<br>
 >>   >> > to the codebase such as Github
<<a href="https://github.com/"
target="_blank">https://github.com/</a>> or<br>
 >>   >> > Bitbucket<<a
target="_blank">https://bitbucket.<wbr>org/</a>>might provide some
 >>   >> > benefits. Of course, migrating to
a separate<br>
 >>   >> > VCS not a trivial matter and would
itself merit a separate discussion.<br>
 >>   >> ><br>
 >>   >> > A couple examples of issue
trackers working well for R projects:<br>
 >>   >> ><br>
 >>   >> >    <a
 >>   >> >    <a
 >>   >> ><br>
 >>   >> > Thank you all for your excellent
work on Bioconductor! It is a really<br>
 >>   >> > amazing resource.<br>
 >>   >> ><br>
 >>   >> > Regards,<br>
 >>   >> > Keith<br>
 >>   >> ><br>
 >>   >> >       [[alternative
HTML version deleted]]<br>
 >>   >> ><br>
 >>   >> >
 >>   >> > <a
href="mailto:Bioc-devel at r-project.org">Bioc-devel at r-project.org</a>
mailing list<br>
 >>   >> > <a
 >>   >><br>
 >>   >><br>
 >>   ><br>
 >>   > [[alternative HTML version deleted]]<br>
 >Computational Biology / Fred Hutchinson Cancer Research Center<br>
 >1100 Fairview Ave. N.<br>
 >PO Box 19024 Seattle, WA 98109<br>
 >Location: Arnold Building M1 B861<br>
 >Phone: <a href="tel:%28206%29%20667-2793"
value="+12066672793">(206) 667-2793</a><br>

More information about the Bioc-devel mailing list