[Nix-dev] Using R with Bioconductor

[Jeffrey David Johnson]

Nope just that really, but it could use a little more explanation: when
downloading the new packages I found them to be unreliable. That is
each time some of the curl calls would fail but it would be different
ones. I think that might have to do with my heavily refactored
generate-r-packages.R, or with my university internet. It works slower
but more reliably from my laptop off campus. Best guess is that
either I triggered some kind of limit on concurrent or daily downloads
from bioconductor.statistik.tu-dortmund.de, or I was downloading faster
than my hard drive could write (such a first world problem!). I
partially fixed it by running the script repeatedly.

I'd also like to write something short in the manual/wiki.
Embarassingly I haven't figured out how to write/build my own R
packages using buildRPackage yet though. It never came up because my
current project is a mess of R + python + bash code glued together with
makefiles. But any of the pre-hashed R packages can be installed or used
in a shell like you'd expect:

with import <nixpkgs> {};
stdenv.mkDerivation {
  buildInputs = with rPackages; [ package1 package2 ... ];
}

Jeff

On Thu, 18 Jun 2015 14:04:41 +0200
Rok Garbas <rok at garbas.si> wrote:

> Quoting Jeffrey David Johnson (2015-06-18 06:20:57)
> > Wonderful, thanks for pushing it forward! I did some more on it but
> > then got sidetracked by grad school and kind of dropped the ball. There
> > is one more thing though...
> > 
> > After splitting CRAN and BIOC packages up, I discovered that
> > many of the BIOC ones require other Annotation or Experiment data
> > packages. So I added those too. They're hosted on the same bioconductor
> > servers but under different subdirectories. I added them as separate
> > files because it was easier with my existing code, but hoped to
> > integrate them into the same BIOC file and update the broken packages
> > list before doing a pull request. Then I didn't get around to it.
> > 
> > This is a working implementation (just missing the updated broken
> > list) that shows the new subdirectories in default.nix around line 50:
> > 
> > https://github.com/jefdaj/nixpkgs/tree/master/pkgs/development/r-modules
> > 
> > Any chance that could make it into the release too?
> > Jeff
> > 
> 
> Hi Jeffrey,
> 
> This really looks nice, I would love to see this in 15.06.
> 
> I see 3 TODO items here [1] I we want to remove them. Is there anythigs left on
> you todo list?
> 
> And maybe R language should get a short section in the manual [2] since there
> is no mention of language support of R. Instructions how to update the manual
> are here [3].
> 
> 
> 
> [1] https://github.com/NixOS/nixpkgs/compare/master...jefdaj:master#diff-789598f937b7fe2f8e737d7e3f4e206dR3
> [2] http://nixos.org/nixpkgs/manual/#chap-language-support
> [3] https://nixos.org/wiki/Contributing_to_Nix_documentation
> 
> 
> 
> --
> Rok Garbas - http://www.garbas.si