[Bioc-devel] Help with creating first Bioconductor package

Martin Morgan mtmorgan at fredhutch.org
Sat Nov 15 21:39:16 CET 2014

On 11/15/2014 12:04 PM, January Weiner wrote:
> Dear Martin,
> thanks for your description, just a question
>> mkdir -p ~/src/R-devel
>> cd ~/src/R-devel
>> svn co https://svn.r-project.org/R/trunk
>> tools/rsync-recommended
> I think this should be
> trunk/tools/rsync-recommended
>> mkdir -p ~/bin/R-devel
>> cd ~/bin/R-devel
>> ~/src/R-devel/configure && make -j
> and
> ~/src/R-devel/trunk/configure  && make -j
> (etc.)
> am I right?

yes; for the record I guess my recipe is more like

mkdir -p ~/src
cd ~/src
svn co https://svn.r-project.org/R/trunk R-devel

which creates ~/src/R-devel without the intervening /trunk. Sorry for the 
imprecision, but your understanding seems to be correct.

>> so that you can say Rdev when you want to use R-devel. Always use biocLite()
>> to install packages, from CRAN or Bioc, and you're fine. Do the same for the
>> current release branch with the svn url
>> https://svn.r-project.org/R/branches/R-3-1-branch.
> Why should I do that? I thought R-3-1-branch should be generally the
> stable release -- the one that I is conveniently installed and
> distributed using my regular package manager, without me having to
> worry about it. You have confused me.

R-3-1-branch gets updated with changes that will make it to the 'next' release 
in the R-3.1 series, so for instance changes made now will appear in 3.1.2 when 
that is released.

Whether it's important as a Bioc developer to track the R-3-1-branch or not is a 
little involved.

Based on past experience, my guess is that R 3.1.2 will be a final 'bug fix' 
release shortly before the release of R 3.2.0. This means that users of the 
current Bioc 3.0 release will expect Bioc 3.0 packages to work with R 3.1.2, and 
that the responsible developer will check that that is the case. On the other 
hand, since the changes are in the 3.1 series one would expect the 3.1.2 changes 
to consist of bug fixes, rather than new features or changed functionality that 
breaks code that works with R-3.1.1 or R-3.1.0 (I don't believe there is any 
formal statement to this effect from R-core). Also, relatively few Bioc users 
will switch to 3.1.2, but will instead move more or less immediately to R 3.2.0 
(and to what will become Bioc 3.1), which (again based on past experience) will 
be released more-or-less at the same time as R 3.1.2.

Looking forward to the next development cycle and assuming R and Bioc releases 
follow the pattern that they have in the recent past, Bioc 3.2 and 3.3 will both 
be based on the R-3.2 series. Bioc 3.2 and Bioc 'devel' at the time of the Bioc 
3.2 release will be built against the R-3-2-branch, with R-devel more-or-less 
irrelevant from a Bioc perspective. R-devel will again become relevant after 
Bioc 3.3 is released.

Presumably that's enough confusion for one email; sorry about that.


> Kind regards,
> j.

Computational Biology / Fred Hutchinson Cancer Research Center
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