R: Difference between revisions
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If you with to use `nix-shell` to generate an on-the-fly environment with some R packages, the command is similar: | If you with to use `nix-shell` to generate an on-the-fly environment with some R packages, the command is similar: | ||
<syntaxhighlight lang=" | <syntaxhighlight lang="console"> | ||
nix-shell --packages 'rWrapper.override{packages = [ rPackages.ggplot2 ];}' | $ nix-shell --packages 'rWrapper.override{packages = [ rPackages.ggplot2 ];}' | ||
</syntaxhighlight> | </syntaxhighlight> | ||
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You will need to obtain the `rev` and `sha256` for the package on github [https://search.nixos.org/packages?show=nix-prefetch-git&type=packages&query=nix-prefetch-git which can be found by using the `nix-prefetch-git` command line tool.] For the above example, running <code>nix-prefetch-git https://github.com/rstudio/rmarkdown</code> from a terminal will generate the information. You may need to manually specify other R-package/system dependencies for the specific package in the `propagatedBuildInputs`. This information can be found in the `DESCRIPTION` file of the R-package source directory. | You will need to obtain the `rev` and `sha256` for the package on github [https://search.nixos.org/packages?show=nix-prefetch-git&type=packages&query=nix-prefetch-git which can be found by using the `nix-prefetch-git` command line tool.] For the above example, running <code>nix-prefetch-git https://github.com/rstudio/rmarkdown</code> from a terminal will generate the information. You may need to manually specify other R-package/system dependencies for the specific package in the `propagatedBuildInputs`. This information can be found in the `DESCRIPTION` file of the R-package source directory. | ||
== Install an R package from source == | |||
If you need a specific version of a package or find one that is not available in Nixpkgs, you can use `rPackages.buildRPackage` to build from source. The example below builds S4Arrays from BioConductor.<syntaxhighlight lang="nix"> | |||
let | |||
pkgs = import <nixpkgs> { }; | |||
customPackage = pkgs.rPackages.buildRPackage { | |||
name = "S4Arrays"; | |||
src = pkgs.fetchurl { | |||
url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/S4Arrays_1.8.1.tar.gz"; | |||
hash = "sha256-8f2oA0xgwI6CucXbMU1yJC4W6tiVMcDAk8D3Ur3zxw8="; | |||
}; | |||
buildInputs = with pkgs.rPackages; [ | |||
pkgs.R | |||
Matrix | |||
abind | |||
BiocGenerics | |||
S4Vectors | |||
IRanges | |||
crayon | |||
]; | |||
}; | |||
in | |||
pkgs.mkShell { | |||
packages = with pkgs.rPackages; [ | |||
pkgs.R | |||
Matrix | |||
abind | |||
BiocGenerics | |||
S4Vectors | |||
IRanges | |||
crayon | |||
customPackage # the package we built from source. | |||
]; | |||
} | |||
</syntaxhighlight> | |||
== A note on knitr == | == A note on knitr == | ||
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To knit a .Rmd file to a pdf (or .Rnw), you need to have included in your envronment <code> pkgs.texlive.combined.scheme-full</code>as well as <code> pandoc </code> or it will fail to knit. None of the other texlive packages contain the proper "frame" package. Note there are likely other workarounds but this requires the least effort. | To knit a .Rmd file to a pdf (or .Rnw), you need to have included in your envronment <code> pkgs.texlive.combined.scheme-full</code>as well as <code> pandoc </code> or it will fail to knit. None of the other texlive packages contain the proper "frame" package. Note there are likely other workarounds but this requires the least effort. | ||
If <code>R</code> is included (using wrapper) but <code>pandoc</code> is not wanted in the user environment, one can expose it just for the R with | |||
<syntaxhighlight lang="nix"> | |||
(rWrapper.override{ | |||
packages = with rPackages; [ | |||
markdown | |||
# other plugins go also here | |||
]; | |||
}).overrideAttrs (old: { | |||
buildInputs = (old.buildInputs or []) ++ [ | |||
pkgs.pandoc | |||
]; | |||
}); | |||
</syntaxhighlight> | |||
== Other Editors == | == Other Editors == | ||
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When the R package "officer" has been installed from the Nix package manager, "save_as_docx" does not work: | When the R package "officer" has been installed from the Nix package manager, "save_as_docx" does not work: | ||
<pre> | |||
Error in write_xml.xml_document(private$doc, file = private$filename) : | Error in write_xml.xml_document(private$doc, file = private$filename) : | ||
Error closing file | Error closing file | ||
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2: In write_xml.xml_document(private$doc, file = private$filename) : | 2: In write_xml.xml_document(private$doc, file = private$filename) : | ||
Permission denie [1501] | Permission denie [1501] | ||
</pre> | |||
However officer does work if installed using the conventional install.packages() which can be enabled as discussed in | However officer does work if installed using the conventional install.packages() which can be enabled as discussed in | ||