[Nix-dev] Using R with Bioconductor

[Jeffrey David Johnson]

OK, turns out it's not so bad! We can skip biocLite and install packages
directly, same as from CRAN. Draft changes here:

https://github.com/NixOS/nixpkgs/compare/master...jefdaj:bioc-pullreq

Opinions? I considered splitting off a separate
bioc-modules folder, but then I noticed the majority of "broken" R
packages are just missing Bioconductor dependencies and decided the two
aren't really separate. Plus it would be a lot of duplicated code, some
of which I don't understand well enough to maintain.

There might be conflicts between the Bioconductor and CRAN release
schedules. I think a unified set of packages could require holding back
from upgrading to the latest CRAN releases on occasion, so if that's a
big problem maybe we do need two sets of packages (current CRAN,
previous CRAN + current Bioconductor). Anyone familiar enough with
Bioconductor to say for sure? Should I go ahead and make a pull
request?

I've attached the bash script I made to list remaining dependencies.
After I ran it I had to go through and manually correct some things it
doesn't pick up, like packages that exist but are known not to build.

Jeff

On Sun, 8 Mar 2015 12:00:27 -0700
Jeffrey David Johnson <jefdaj at gmail.com> wrote:

> Do any of you guys/gals use R and Bioconductor?
> 
> The only page I can find related to setting it up is <https://nixos.org/wiki/R>.
> Bioconductor is a whole additional ecosystem on top of R/CRAN,
> with its own installer. You normally use it like:
> 
>     source("http://bioconductor.org/biocLite.R")
>     biocLite("PackageName")
> 
> They explain why at <http://bioconductor.org/install/#why-biocLite>.
> How hard would it be to package that using Nix?
> Thanks
> Jeff
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