[Bioc-devel] Distinction between release and devel package websites

Martin Morgan mtmorgan at fhcrc.org
Wed Jul 23 03:27:23 CEST 2014

On 07/22/2014 06:17 PM, Vincent Carey wrote:
> On Tue, Jul 22, 2014 at 7:10 PM, Andrzej OleÅ› <andrzej.oles at gmail.com>
> wrote:
>> Hi Dan, Michael, Julian,
>> Thank's for keeping the links to the tarballs!
>> I don't argue that mixing release and devel is a good idea in general.
>> Rather, that for some users this might be the best compromise between
>> the following two objectives:
>> 1. a stable working environment
>> 2. the possibility to use or just quickly check a specific new feature
>> available in the devel version of package X
> IMHO this is the road to ruin.
>> Switching entirely to devel is quite often a no-no for them because of
>> the unstable nature of the devel branch. And maintaining both release
> I personally have never done the homework required to have
> both branches on hand with convenient updating.  It is
> surely feasible and I would imagine a number of folks reading this have
> done it for themselves.  It is probably not trivial to do it portably but a
> doc
> with suggestions for key platforms would be a nice contribution.  I used
> to have Rrel and Rdev scripts that made it work and that is easily worked
> out but it is not very elegant and transitioning to new releases of R is
> laborious.

FWIW one approach _is_ (well ok, sufficiently obscure to be not) documented at


but it is commented out so only appears in the source version of the page; 
apparently it was more confusing than helpful, and the approach changes 
depending on whether Bioc devel is on R devel or not.


>> and devel only adds to their frustration. As a developer I would like
>> to have the freedom to advise people on using the latest devel version
>> of my package regardless of whether they are running release or devel
>> if I think that this is safe for them, which is typically the case for
>> many upstream packages without (many) reverse dependencies. I don't
>> see the point of unnecessary obstructing this approach and I'm not
>> sure I understand why there is such an outrage about mixing release
>> and devel. In contrary, quite often this can be much safer than
> Depends on your definition of safety.  I think that we have gained much
> from the clean separation, in terms of user support effort and freedom to
> experiment in devel.  "Experts" can do what they like and deal with the
> consequences themselves, but the general approach to the user community
> should be principled and it should be: 1) in general, use release branch and
> report bugs and see that they are fixed in a timely way; if they are not,
> let
> the core know -- 2) if you expect help, do all package installations via
> biocLite() --
> 3) we like seeing mileage on the devel branch and encourage its use for
> novel features, but it needs to be used with the appropriate version of R
> and the
> devel package set.
>> switching between BioC branches. I personally do not want to find
>> myself in a position when I advice a user to switch to BioC devel
>> because of some new function from my package he/she would like to give
> This is an engineering commitment to a stable release branch.  No new
> features,
> only bug fixes.  We have benefited from this immensely.
>> a try only to learn that this broke his/hers scripts (due to the
>> changes in some other packages).
>> To sum up, I believe that mixing release and devel might be beneficial
>> in some specific cases similar to the above described one and it's
>> important that the infrastructure allows leveraging this approach,
>> e.g. by providing direct access to devel tarballs.
>> Cheers,
>> Andrzej
>> On Tue, Jul 22, 2014 at 11:12 PM, Julian Gehring <julian.gehring at embl.de>
>> wrote:
>>> Hi Andzrej,
>>> thank you, I see your point but I'm afraid I must disagree with you.
>>> I've had this situation numerous times that I have added/fixed
>>> something in the devel branch of a package and had to advice the users
>>> to use this latest version. Needless to say, they were typically using
>>> the release branch, and it was a relatively painless procedure for
>>> them to pick the tarball from the devel landing page and proceed with
>>> manual installation. Of course, this could be also achieved by
>>> installing from the svn, however, this is not very welcome from the
>>> user's perspective.
>>> I'm not sure I understand to need to mix devel and release.  If there is
>> a
>>> bug in the release branch, it should be also patched there.  And if users
>>> need the features of the devel branch, they would have to switch to devel
>>> anyway.
>>> Best
>>> Julian
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

More information about the Bioc-devel mailing list