.. | ||
patches | ||
bioc-annotation-packages.nix | ||
bioc-experiment-packages.nix | ||
bioc-packages.nix | ||
cran-packages.nix | ||
default.nix | ||
generate-r-packages.R | ||
generate-shell.nix | ||
generic-builder.nix | ||
README.md | ||
test-evaluation.nix | ||
wrapper.nix |
R packages
Installation
Define an environment for R that contains all the libraries that you'd like to use by adding the following snippet to your $HOME/.config/nixpkgs/config.nix file:
{
packageOverrides = super: let self = super.pkgs; in
{
rEnv = super.rWrapper.override {
packages = with self.rPackages; [
devtools
ggplot2
reshape2
yaml
optparse
];
};
};
}
Then you can use nix-env -f "<nixpkgs>" -iA rEnv
to install it into your user
profile. The set of available libraries can be discovered by running the
command nix-env -f "<nixpkgs>" -qaP -A rPackages
. The first column from that
output is the name that has to be passed to rWrapper in the code snipped above.
However, if you'd like to add a file to your project source to make the
environment available for other contributors, you can create a default.nix
file like so:
let
pkgs = import <nixpkgs> {};
stdenv = pkgs.stdenv;
in with pkgs; {
myProject = stdenv.mkDerivation {
name = "myProject";
version = "1";
src = if pkgs.lib.inNixShell then null else nix;
buildInputs = with rPackages; [
R
ggplot2
knitr
];
};
}
and then run nix-shell .
to be dropped into a shell with those packages
available.
RStudio
RStudio by default will not use the libraries installed like above.
You must override its R version with your custom R environment, and
set useRPackages
to true
, like below:
{
packageOverrides = super: let self = super.pkgs; in
{
rEnv = super.rWrapper.override {
packages = with self.rPackages; [
devtools
ggplot2
reshape2
yaml
optparse
];
};
rstudioEnv = super.rstudio.override {
R = rEnv;
useRPackages = true;
};
};
}
Then like above, nix-env -f "<nixpkgs>" -iA rstudioEnv
will install
this into your user profile.
Updating the package set
nix-shell generate-shell.nix
Rscript generate-r-packages.R cran > cran-packages.nix.new
mv cran-packages.nix.new cran-packages.nix
Rscript generate-r-packages.R bioc > bioc-packages.nix.new
mv bioc-packages.nix.new bioc-packages.nix
generate-r-packages.R <repo>
reads <repo>-packages.nix
, therefor the renaming.
Testing if the Nix-expression could be evaluated
nix-build test-evaluation.nix --dry-run
If this exits fine, the expression is ok. If not, you have to edit default.nix