6ecc641d08
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.
3.2 KiB
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