[R] Dependency-aware scripting tools for R

[Ben Bolker]

Sean Davis <sdavis2 <at> mail.nih.gov> writes:

> 
> There are numerous tools like scons, make, ruffus, ant, rake, etc.
> that can be used to build complex pipelines based on task
> dependencies.  These tools are written in a variety of languages, but
> I have not seen such a thing for R.  Is anyone aware of a package
> available?  The goal is to be able to develop robust bioinformatic
> pipelines driven by scripts written in R.

  This might (?) be better for r-devel (although it's a bit of a toss-up).
Most of the activity I've seen along these lines in the R community has used
make ... it's a tradeoff between (1) re-inventing (and polishing) the wheel
for the n^th time and (2) getting rid of another dependency. (In contrast
to the use of (e.g.) configure and make, consider the pipeline used for
installing R itself and constructing and testing packages -- this has moved
from a dependence on Perl to being completely self-contained.)

  Bottom line: I think you could do the scripting in R, but IMO it
probably makes the most sense to leave the dependency management to make.