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r-modules: Updated definitions of CRAN and Bioc packages. #108268
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The last snapshot was 4 months ago (2020-08-19). I also found that I needed newer definitions when I was trying to fix the R arrow package. This update required a couple of manual changes: 1. Removing a few deleted packages from default.nix 2. Renaming the "assert" package to "r_assert" in generate-r-packages.R because "assert" is a keyword in Nix
darwin patch diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 387a5d0bb63..7cdb5f72658 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -379,6 +379,7 @@ let
rmutil = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
robustbase = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
SparseM = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
+ hexbin = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
svKomodo = [ pkgs.which ];
nat = [ pkgs.which ];
nat_templatebrains = [ pkgs.which ]; |
This is a semi-automatic executed nixpkgs-review which does not build all packages (e.g. lumo, tensorflow or pytorch) Result of 1 package failed to build and are new build failure:
5 packages built:
|
`data.table` had a `postInstall` step to rename `data.table.so` to `datatable.so`, but after the package bump the file was already called `datatable.so` and `mv` command would fail.
I added @SuperSandro2000's Darwin patch and also fixed a bug with the
but after the package bump, I only caught the problem with Also, for context, I'm doing this bump now because I'm trying to fix the R Arrow package (#81761). I got a fix for that running locally, but found that I needed to bump the R packages so that the R Arrow package has the same version as the C++ Arrow library in Nixpkgs. But it also seems good to have more up to date package definitions anyway. |
I don't know anything like this. If ofborg evals everything it is usually fine. |
Result of 2 packages built:
|
This is a semi-automatic executed nixpkgs-review which does not build all packages (e.g. lumo, tensorflow or pytorch) Result of 4 packages built:
|
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Test builds are running at https://hydra.nixos.org/jobset/nixpkgs/r-updates ...
Thank you very much for your efforts, everyone! |
Updated the R package definitions.
This involved two manual code changes:
I followed the steps in the R manual section, testing the result with
nix-build test-evaluation.nix --dry-run
.Motivation for this change
R package set was last updated >4 months ago (2020-08-19).
Things done
sandbox
innix.conf
on non-NixOS linux)nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
./result/bin/
)nix path-info -S
before and after)