From 5309818bf744a166a236ee2f829c154975cf6bcc Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Sun, 26 Sep 2021 07:29:58 +1000 Subject: [PATCH] doc: clarify location of rPackages overrides Detail the location of rPackage overrides and how broken builds should be addressed. --- doc/languages-frameworks/r.section.md | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/doc/languages-frameworks/r.section.md b/doc/languages-frameworks/r.section.md index 6b64e264b669..ad0fb10987c9 100644 --- a/doc/languages-frameworks/r.section.md +++ b/doc/languages-frameworks/r.section.md @@ -96,6 +96,11 @@ re-enter the shell. ## Updating the package set {#updating-the-package-set} +There is a script and associated environment for regenerating the package +sets and synchronising the rPackages tree to the current CRAN and matching +BIOC release. These scripts are found in the `pkgs/development/r-modules` +directory and executed as follows: + ```bash nix-shell generate-shell.nix @@ -112,4 +117,11 @@ 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 ` reads `-packages.nix`, therefor the renaming. +`generate-r-packages.R ` reads `-packages.nix`, therefore +the renaming. + +Some packages require overrides to specify external dependencies or other +patches and special requirements. These overrides are specified in the +`pkgs/development/r-modules/default.nix` file. As the `*-packages.nix` +contents are automatically generated it should not be edited and broken +builds should be addressed using overrides.