We are still using Pandoc’s Markdown parser, which differs from CommonMark spec slightly.

Notably:
- Line breaks in lists behave differently.
- Admonitions do not support the simpler syntax https://github.com/jgm/commonmark-hs/issues/75
- The auto_identifiers uses a different algorithm – I made the previous ones explicit.
- Languages (classes) of code blocks cannot contain whitespace so we have to use “pycon” alias instead of Python “console” as GitHub’s linguist

While at it, I also fixed the following issues:
- ShellSesssion was used
- Removed some pointless docbook tags.

2021-06-07 06:34:59 +02:00

3.2 KiB

Raw Blame History

R

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:

with import <nixpkgs> {};
{
  myProject = stdenv.mkDerivation {
    name = "myProject";
    version = "1";
    src = if 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:

{
    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:

{ 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

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

Rscript generate-r-packages.R bioc-annotation > bioc-annotation-packages.nix.new
mv bioc-annotation-packages.nix.new bioc-annotation-packages.nix

Rscript generate-r-packages.R bioc-experiment > bioc-experiment-packages.nix.new
mv bioc-experiment-packages.nix.new bioc-experiment-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

3.2 KiB Raw Blame History

R

Installation

RStudio

Updating the package set

Testing if the Nix-expression could be evaluated

3.2 KiB

Raw Blame History