Commit Graph

1535 Commits

Author SHA1 Message Date
Justin Bedo
9dcccd3de1 rPackages.fru: fix build 2026-02-19 16:25:52 +11:00
Justin Bedo
c622b74833 rPackages.RPesto: fix build 2026-02-19 16:25:52 +11:00
Justin Bedo
66680e2869 rPackages.b32: fix build 2026-02-19 16:25:51 +11:00
Justin Bedő
3af4d5a294 rPackages.roxigraph: fix build (#491889) 2026-02-19 13:48:55 +11:00
Justin Bedő
b190f46290 rPackages.caugi: fix build (#491879) 2026-02-19 13:48:01 +11:00
Justin Bedő
7e71cdb9fa rPackages.trajeR: fix build (#457912) 2026-02-19 13:00:35 +11:00
László Kupcsik
df1c93cc0c rPackages.roxigraph: fix build 2026-02-18 23:31:50 +01:00
László Kupcsik
4bf605a455 rPackages.caugi: fix build 2026-02-18 22:54:55 +01:00
Justin Bedő
0d0e392784 rPackages.fwtraits: fix build (#491413) 2026-02-18 11:40:31 +11:00
Justin Bedő
60a2bd2d5e rPackages.enderecobr: fix build (#491415) 2026-02-18 11:18:51 +11:00
Justin Bedő
7164259280 rPackages.TreeDist: 2.11.1 -> 2.12.0 (#491411) 2026-02-18 11:18:30 +11:00
Justin Bedő
d9acbdca4a rPackages.yaml12: fix build (#491402) 2026-02-18 11:17:54 +11:00
Bruno Rodrigues
5a9c53e281 rPackages.enderecobr: fix build 2026-02-17 15:54:08 +01:00
Bruno Rodrigues
dbd801decf rPackages.fwtraits: fix build 2026-02-17 15:44:03 +01:00
Bruno Rodrigues
36aeb2b385 rPackages.TreeDist: 2.11.1 -> 2.12.0 2026-02-17 15:38:32 +01:00
Bruno Rodrigues
8df41d9da3 rPackages.ready4: fix build 2026-02-17 15:23:28 +01:00
Bruno Rodrigues
107a348c7a rPackages.yaml12: fix build 2026-02-17 15:18:56 +01:00
László Kupcsik
3631a12e5e rPackages.XYomics: add missing dep 2026-02-17 00:27:55 +01:00
László Kupcsik
5f2682497b rPackages.harbinger: fix build 2026-02-16 10:03:00 +11:00
Justin Bedő
fd7da040ff rPackages.msigdbr: update hash (#490515) 2026-02-16 09:10:32 +11:00
Justin Bedő
19790b55de rPackages.SAIGEgds: fix build (#490501) 2026-02-16 09:10:06 +11:00
László Kupcsik
851f316bd5 rPackages.msigdbr: update hash 2026-02-14 22:48:58 +01:00
László Kupcsik
4b1a847a22 rPackages.SAIGEgds: fix build 2026-02-14 21:40:29 +01:00
László Kupcsik
83dc019473 rPackages.pqsfinder: add missing dep 2026-02-14 21:27:56 +01:00
Justin Bedo
9deca009e6 rPackages: CRAN and BioC update 2026-02-13 16:29:01 +11:00
K900
15a6983bd3 Merge remote-tracking branch 'origin/master' into staging-next 2026-02-11 21:30:26 +03:00
quantenzitrone
8cef967e96 commons-{bcel,bsf,compress,daemon,fileupload,io,lang,logging,math}: rename from commons{Bcel,Bsf,Compress,Daemon,FileUpload,Io,Lang,Logging,Math}
The upstream repo names are the same as the new package names.
The old package names are probably relicts from when nix didn't
properly support dashes in identifiers.
2026-02-10 16:50:48 +01:00
Antoine du Hamel
7459fe949f nodejs: make nodejs_* depend on nodejs-slim_* 2026-02-03 23:54:16 +01:00
quantenzitrone
7d8132a92c treewide: remove references to the xorg namespace in pkgs (automated)
this creates some eval errors that will be fixed in the next commit

done with the following script:

```fish
\#!/usr/bin/env fish

set packagesjson (nix eval --impure --json --expr '
let
  lib = import ./lib;
in
import pkgs/servers/x11/xorg/default.nix (lib.mapAttrs (
  name: _:
  if name == "lib" then
    lib
  else if name == "config" then
    { allowAliases = false; }
  else
    name
) (__functionArgs (import pkgs/servers/x11/xorg/default.nix))) { }
' | jq)

set one (grep '^    [A-Za-z0-9_-]*$' pkgs/servers/x11/xorg/default.nix | string trim | string replace -r '$' Z | sort | string sub -e -1)
set two (grep '^  [A-Za-z0-9_-]* = [A-Za-z0-9_-]*;$' pkgs/servers/x11/xorg/default.nix | cut -d= -f1 | string trim | string replace -r '$' Z | sort | string sub -e -1)

for arg in $one $two
    set oname $arg
    set nname (echo $packagesjson | jq -r .$oname)

    if test $nname = null
        echo (set_color red)warn:(set_color normal) unknown package xorg.$oname >&2
        continue
    end

    echo $oname "->" $nname

    # replace basic xorg.$name references
    for file in (rg -F "xorg.$oname" --files-with-matches pkgs)
        # special cases
        sd -F "$oname = xorg.$oname;" "$nname = $nname;" $file

        # replace
        sd -F "xorg.$oname" "$nname" $file

        # fixup function arguments

        # prevent duplicate function args
        if grep -E " ($oname|$nname),\$" $file >/dev/null
            continue
        end

        if grep 'xorg\..' $file >/dev/null # case1: there is more so we can't just remove the function arg

            if grep ' xorg,$' $file >/dev/null
                sd ' xorg,$' " xorg,
                $nname," $file

            else if grep ' xorg ? .*,$' $file >/dev/null
                sd 'xorg( ? .*),$' "xorg\$1,
                $nname," $file

            else
                sd -F 'xorg,' "$nname,
                xorg," $file
            end

        else # case there is no more xorg..* so we can just replace the function arg
            sd 'xorg(| ? .*),.*$' "$nname," $file
        end
    end
end

nix fmt
```
2026-01-25 22:28:09 +01:00
TomaSajt
7a5f8418de rPackages.V8: fix build by pinning nodejs to nodejs_22 2026-01-17 04:01:19 +01:00
Bruno Rodrigues
16998dd60c rstudio: fix loading of project-specific .Rprofile 2026-01-15 16:24:07 +01:00
jopejoe1
4aa7e6a971 rPackages: seperate pname and version
Co-authored-by: TomaSajt <62384384+TomaSajt@users.noreply.github.com>
2026-01-13 19:11:15 +01:00
Justin Bedő
284add3b99 rPackages.RBioFormats: fix build and revdeps properly (#472944) 2026-01-07 23:51:50 +00:00
Aleksana
82de48822d rPackages.rvisidata: fix runtime failure (#473407) 2025-12-31 16:22:56 +00:00
László Kupcsik
6772a554bb rPackages.RBioFormats: vendor BioFormats from nixpkgs 2025-12-31 10:38:29 -05:00
László Kupcsik
7adc846037 rPackages.rvisidata: fix runtime failure
Point the package to the vd binary
2025-12-22 15:27:42 -05:00
K900
3fb88224bc Merge remote-tracking branch 'origin/staging-next' into staging 2025-12-02 09:10:32 +03:00
Sandro Jäckel
aa22853984 R: add man output 2025-11-18 23:40:21 +01:00
László Kupcsik
ad0a163378 rPackages.iscream: fix build and optimize
- Add missing build inputs
 - Compile htslib with libdeflate
 - Remove superfluous Rhtslib dependency
2025-11-17 09:38:27 +11:00
Justin Bedő
828432505b rPackages.rsamplr: add cargo and rust (#457923) 2025-11-17 09:20:51 +11:00
László Kupcsik
be4de6bbc8 rPackages.trajeR: fix build 2025-11-15 12:19:34 +01:00
László Kupcsik
ec118fcead rPackages.rsamplr: add cargo and rust 2025-11-15 12:17:20 +01:00
László Kupcsik
ba1746619d rPackages.blosc: add missing dep 2025-11-14 21:49:57 +01:00
Justin Bedő
da4fc2743b rPackages.DEploid: add missing dep (#460477) 2025-11-12 23:34:13 +11:00
Justin Bedő
8e88708455 rPackages.EHRmuse: add missing dep (#460131) 2025-11-12 23:32:57 +11:00
Justin Bedő
340f20ad8c rPackages.GeoFIS: add missing deps (#460124) 2025-11-12 23:31:16 +11:00
Justin Bedő
23b4c6fd1a rPackages.ironseed: fix build (#460120) 2025-11-12 23:29:17 +11:00
Justin Bedő
cfa4a68226 rPackages.SLmetrics: add missing dep (#460115) 2025-11-12 23:27:22 +11:00
Justin Bedő
7cc00dc085 rPackages.milorGWAS: add missing dep (#460110) 2025-11-12 23:26:07 +11:00
Justin Bedő
c467b79471 rPackages.registr: add missing dep (#459870) 2025-11-12 23:23:37 +11:00