Re: [rb-general] Paper preprint: Reproducible genomics analysis pipelines with GNU Guix

[Ricardo Wurmus <rekado@elephly.net>]

Ludovic Courtès <ludovic.courtes@inria.fr> writes:

> Perhaps we could add to Autoconf-Archive (if it doesn’t have such things
> already) macros to deal with the R and Python stuff you had to deal
> with?  And then publish a simple template that people could use as a
> starting point.

I submitted my macros for R packages (and they have been accepted), but
I actually don’t really like them because they are not as useful as it
may seem.  While they do check for R packages in the environment at
configure time, nothing is done to record the environment necessary to
access these packages.

That’s a general problem for software that depends on search path
environment variables.  I can’t just record the location of each
individual R package that was detected and use that to set up the
environment at runtime.  The R packages have other runtime dependencies
that would also need to be recorded.

It’s not ideal.

--
Ricardo