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author | Alyssa Ross <hi@alyssa.is> | 2019-01-07 02:18:36 +0000 |
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committer | Alyssa Ross <hi@alyssa.is> | 2019-01-07 02:18:47 +0000 |
commit | 36f56d99fa0a0765c9f1de4a5f17a9b05830c3f2 (patch) | |
tree | b3faaf573407b32aa645237a4d16b82778a39a92 /nixpkgs/doc/languages-frameworks/r.section.md | |
parent | 4e31070265257dc67d120c27e0f75c2344fdfa9a (diff) | |
parent | abf060725d7614bd3b9f96764262dfbc2f9c2199 (diff) | |
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Add 'nixpkgs/' from commit 'abf060725d7614bd3b9f96764262dfbc2f9c2199'
git-subtree-dir: nixpkgs git-subtree-mainline: 4e31070265257dc67d120c27e0f75c2344fdfa9a git-subtree-split: abf060725d7614bd3b9f96764262dfbc2f9c2199
Diffstat (limited to 'nixpkgs/doc/languages-frameworks/r.section.md')
-rw-r--r-- | nixpkgs/doc/languages-frameworks/r.section.md | 120 |
1 files changed, 120 insertions, 0 deletions
diff --git a/nixpkgs/doc/languages-frameworks/r.section.md b/nixpkgs/doc/languages-frameworks/r.section.md new file mode 100644 index 000000000000..c8f02bd14780 --- /dev/null +++ b/nixpkgs/doc/languages-frameworks/r.section.md @@ -0,0 +1,120 @@ +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: + +```nix +{ + 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: +```nix +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 uses a standard set of packages and ignores any custom R +environments or installed packages you may have. To create a custom +environment, see `rstudioWrapper`, which functions similarly to +`rWrapper`: + +```nix +{ + packageOverrides = super: let self = super.pkgs; in + { + + rstudioEnv = super.rstudioWrapper.override { + packages = with self.rPackages; [ + dplyr + ggplot2 + reshape2 + ]; + }; + }; +} +``` + +Then like above, `nix-env -f "<nixpkgs>" -iA rstudioEnv` will install +this into your user profile. + +Alternatively, you can create a self-contained `shell.nix` without the need to +modify any configuration files: + +```nix +{ pkgs ? import <nixpkgs> {} +}: + +pkgs.rstudioWrapper.override { + packages = with pkgs.rPackages; [ dplyr ggplot2 reshape2 ]; +} + +``` + +Executing `nix-shell` will then drop you into an environment equivalent to the +one above. If you need additional packages just add them to the list and +re-enter the shell. + +## Updating the package set + +```bash +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 + +```bash +nix-build test-evaluation.nix --dry-run +``` + +If this exits fine, the expression is ok. If not, you have to edit `default.nix` |