Merge master into staging-next

nixos/doc/manual/redirects.json

@@ -65,42 +65,6 @@
   "module-services-keycloak-unix-socket": [
     "index.html#module-services-keycloak-unix-socket"
   ],
-  "module-services-mautrix-discord": [
-    "index.html#module-services-mautrix-discord"
-  ],
-  "module-services-mautrix-discord-advanced": [
-    "index.html#module-services-mautrix-discord-advanced"
-  ],
-  "module-services-mautrix-discord-authentication": [
-    "index.html#module-services-mautrix-discord-authentication"
-  ],
-  "module-services-mautrix-discord-backfill": [
-    "index.html#module-services-mautrix-discord-backfill"
-  ],
-  "module-services-mautrix-discord-basic-example": [
-    "index.html#module-services-mautrix-discord-basic-example"
-  ],
-  "module-services-mautrix-discord-basic-usage": [
-    "index.html#module-services-mautrix-discord-basic-usage"
-  ],
-  "module-services-mautrix-discord-double-puppet": [
-    "index.html#module-services-mautrix-discord-double-puppet"
-  ],
-  "module-services-mautrix-discord-encryption": [
-    "index.html#module-services-mautrix-discord-encryption"
-  ],
-  "module-services-mautrix-discord-server-defaults": [
-    "index.html#module-services-mautrix-discord-server-defaults"
-  ],
-  "module-services-mautrix-discord-setup": [
-    "index.html#module-services-mautrix-discord-setup"
-  ],
-  "module-services-mautrix-discord-synapse": [
-    "index.html#module-services-mautrix-discord-synapse"
-  ],
-  "module-services-mautrix-discord-troubleshooting": [
-    "index.html#module-services-mautrix-discord-troubleshooting"
-  ],
   "module-services-tandoor-recipes-migrating-media-option-move": [
     "index.html#module-services-tandoor-recipes-migrating-media-option-move",
     "index.html#module-services-tandoor-recipes-migrating-media-option-1"

nixos/modules/services/matrix/mautrix-discord.md

@@ -1,156 +0,0 @@
-# Mautrix-Discord {#module-services-mautrix-discord}
-
-*Source:* {file}`modules/services/matrix/mautrix-discord`
-
-*Upstream documentation:* <https://docs.mau.fi/bridges/go/discord/index.html>
-
-[Mautrix-Discord](https://github.com/mautrix/discord) is a Matrix-Discord bridge.
-
-## Basic Usage {#module-services-mautrix-discord-basic-usage}
-
-The common setup is to enable the bridge, point it at your homeserver, and set the permissions you want to allow:
-
-1. Set `services.mautrix-discord.enable` to `true`.
-2. Set `services.mautrix-discord.settings.homeserver.address` and `services.mautrix-discord.settings.homeserver.domain`.
-3. Override `services.mautrix-discord.settings.bridge.permissions` if the default relay permissions do not fit your deployment.
-
-The module provides sensible defaults for the appservice listener, registration tokens, and relay permissions.
-
-### Basic Example {#module-services-mautrix-discord-basic-example}
-
-```nix
-{
-  services.mautrix-discord = {
-    enable = true;
-    registerToSynapse = true;
-    settings = {
-      homeserver = {
-        address = "http://localhost:8008";
-        domain = "example.com";
-      };
-      bridge.permissions = {
-        "example.com" = "user";
-        "@admin:example.com" = "admin";
-      };
-    };
-  };
-}
-```
-
-### Server Defaults {#module-services-mautrix-discord-server-defaults}
-
-By default, the bridge listens on `http://localhost:29334` and generates its appservice tokens automatically.
-
-## Authentication {#module-services-mautrix-discord-authentication}
-
-If you want to store the bridge database outside the default SQLite file, set `settings.appservice.database` to use PostgreSQL instead of SQLite:
-
-```nix
-{
-  services.mautrix-discord.settings.appservice.database = {
-    type = "postgres";
-    uri = "postgresql:///mautrix-discord?host=/run/postgresql";
-  };
-}
-```
-
-If the connection needs a password, combine it with `services.mautrix-discord.environmentFile`:
-
-```nix
-{
-  services.mautrix-discord = {
-    environmentFile = "/run/secrets/mautrix-discord-env";
-    settings.appservice.database.uri = "postgresql://mautrix:$DB_PASSWORD@localhost/mautrix-discord";
-  };
-}
-```
-
-Use `services.mautrix-discord.environmentFile` for any secret you do not want in the Nix store.
-This includes database passwords, shared secrets, and similar values.
-
-Example:
-
-```nix
-{
-  services.mautrix-discord = {
-    environmentFile = "/run/secrets/mautrix-discord-env";
-    settings.bridge.login_shared_secret_map = {
-      "example.com" = "$SHARED_SECRET";
-    };
-  };
-}
-```
-
-## Bridge Setup {#module-services-mautrix-discord-setup}
-
-After the service starts, open a chat with `@discordbot:example.com`, send `login`, and follow the instructions to link your Discord account.
-
-For more detail, see the [Mautrix-Discord documentation](https://docs.mau.fi/bridges/go/discord/index.html).
-
-## Advanced Configuration {#module-services-mautrix-discord-advanced}
-
-The upstream default configuration is available at [example-config.yaml](https://github.com/mautrix/discord/blob/main/example-config.yaml). To print the generated default configuration from the package, run:
-
-```bash
-nix-shell -p mautrix-discord --run "mautrix-discord -e"
-```
-
-### Encryption {#module-services-mautrix-discord-encryption}
-
-```nix
-{
-  services.mautrix-discord.settings.bridge.encryption = {
-    allow = true;
-    default = true;
-    require = false;
-  };
-}
-```
-
-Encryption needs additional bridge-side setup. See the [bridge encryption documentation](https://docs.mau.fi/bridges/general/end-to-bridge-encryption.html) for details.
-
-### Backfill {#module-services-mautrix-discord-backfill}
-
-```nix
-{
-  services.mautrix-discord.settings.bridge.backfill.forward_limits.initial = {
-    dm = 50;
-    channel = 50;
-    thread = 50;
-  };
-}
-```
-
-### Double Puppeting {#module-services-mautrix-discord-double-puppet}
-
-```nix
-{
-  services.mautrix-discord = {
-    environmentFile = "/run/secrets/mautrix-discord-env";
-    settings.bridge.login_shared_secret_map = {
-      "example.com" = "$SHARED_SECRET";
-    };
-  };
-}
-```
-where  `/run/secrets/mautrix-discord-env` contains
-```
-SHARED_SECRET=aProtectedSecret
-```
-
-## Synapse Integration {#module-services-mautrix-discord-synapse}
-
-When `services.mautrix-discord.registerToSynapse` is `true`, the bridge writes its registration file automatically and Synapse picks it up.
-
-If Synapse is enabled, this option defaults to `true`.
-
-## Troubleshooting {#module-services-mautrix-discord-troubleshooting}
-
-- View logs with `journalctl -u mautrix-discord.service -f`.
-- Check `systemctl status mautrix-discord` if the bridge does not start.
-- Verify the homeserver can reach the configured appservice address.
-- Ensure the registration file exists and Synapse can read it.
-
-For more help, see the
-[Mautrix-Discord documentation](https://docs.mau.fi/bridges/go/discord/index.html)
-or the support room at [#discord:maunium.net](https://matrix.to/#/#discord:maunium.net).

nixos/modules/services/matrix/mautrix-discord.nix

@@ -5,59 +5,15 @@
   ...
 }:
 let
-  defaultDataDir = "/var/lib/mautrix-discord";
   cfg = config.services.mautrix-discord;
   dataDir = cfg.dataDir;
   format = pkgs.formats.yaml { };
-  serviceDependencies = [
-    "mautrix-discord-registration.service"
-  ]
-  ++ (lib.lists.optional config.services.matrix-synapse.enable config.services.matrix-synapse.serviceUnit)
-  ++ (lib.lists.optional config.services.matrix-conduit.enable "matrix-conduit.service")
-  ++ (lib.lists.optional config.services.dendrite.enable "dendrite.service");
 
   registrationFile = "${dataDir}/discord-registration.yaml";
 
   settingsFile = "${dataDir}/config.yaml";
   settingsFileUnformatted = format.generate "discord-config-unsubstituted.yaml" cfg.settings;
   default_token = "This value is generated when generating the registration";
-  settingsDefault = {
-    homeserver = {
-      address = "";
-      domain = "";
-    };
-
-    appservice = {
-      address = "http://localhost:29334";
-      hostname = "0.0.0.0";
-      port = 29334;
-      database = {
-        type = "sqlite3";
-        uri = "file:${defaultDataDir}/mautrix-discord.db?_txlock=immediate";
-      };
-      id = "discord";
-      bot = {
-        username = "discordbot";
-        displayname = "Discord bridge bot";
-        avatar = "mxc://maunium.net/nIdEykemnwdisvHbpxflpDlC";
-      };
-      as_token = default_token;
-      hs_token = default_token;
-    };
-
-    bridge.permissions."*" = "relay";
-
-    logging = {
-      min_level = "info";
-      writers = [
-        {
-          type = "stdout";
-          format = "pretty-colored";
-          time_format = " ";
-        }
-      ];
-    };
-  };
 in
 {
   options = {
@@ -67,14 +23,238 @@ in
       package = lib.mkPackageOption pkgs "mautrix-discord" { };
 
       settings = lib.mkOption {
-        apply = lib.recursiveUpdate settingsDefault;
-        type = format.type;
-        default = settingsDefault;
+        type = lib.types.submodule {
+          freeformType = format.type;
+
+          config = {
+            _module.args = { inherit cfg lib; };
+          };
+
+          options = {
+            homeserver = lib.mkOption {
+              type = lib.types.attrs;
+              default = {
+                software = "standard";
+                status_endpoint = null;
+                message_send_checkpoint_endpoint = null;
+                async_media = false;
+                websocket = false;
+                ping_interval_seconds = 0;
+              };
+              description = ''
+                fullDataDiration.
+                                See [example-config.yaml](https://github.com/mautrix/discord/blob/main/example-config.yaml)
+                                for more information.
+              '';
+            };
+
+            appservice = lib.mkOption {
+              type = lib.types.attrs;
+              default = {
+                address = "http://localhost:29334";
+                hostname = "0.0.0.0";
+                port = 29334;
+                database = {
+                  type = "sqlite3";
+                  uri = "file:/var/lib/mautrix-discord/mautrix-discord.db?_txlock=immediate";
+                  max_open_conns = 20;
+                  max_idle_conns = 2;
+                  max_conn_idle_time = null;
+                  max_conn_lifetime = null;
+                };
+                id = "discord";
+                bot = {
+                  username = "discordbot";
+                  displayname = "Discord bridge bot";
+                  avatar = "mxc://maunium.net/nIdEykemnwdisvHbpxflpDlC";
+                };
+                ephemeral_events = true;
+                async_transactions = false;
+                as_token = "This value is generated when generating the registration";
+                hs_token = "This value is generated when generating the registration";
+              };
+              defaultText = lib.literalExpression ''
+                {
+                  address = "http://localhost:29334";
+                  hostname = "0.0.0.0";
+                  port = 29334;
+                  database = {
+                    type = "sqlite3";
+                    uri = "file:''${config.services.mautrix-discord.dataDir}/mautrix-discord.db?_txlock=immediate";
+                    max_open_conns = 20;
+                    max_idle_conns = 2;
+                    max_conn_idle_time = null;
+                    max_conn_lifetime = null;
+                  };
+                  id = "discord";
+                  bot = {
+                    username = "discordbot";
+                    displayname = "Discord bridge bot";
+                    avatar = "mxc://maunium.net/nIdEykemnwdisvHbpxflpDlC";
+                  };
+                  ephemeral_events = true;
+                  async_transactions = false;
+                  as_token = "This value is generated when generating the registration";
+                  hs_token = "This value is generated when generating the registration";
+                }
+              '';
+              description = ''
+                Appservice configuration.
+                See [example-config.yaml](https://github.com/mautrix/discord/blob/main/example-config.yaml)
+                for more information.
+              '';
+            };
+
+            bridge = lib.mkOption {
+              type = lib.types.attrs;
+              default = {
+                username_template = "discord_{{.}}";
+                displayname_template = "{{if .Webhook}}Webhook{{else}}{{or .GlobalName .Username}}{{if .Bot}} (bot){{end}}{{end}}";
+                channel_name_template = "{{if or (eq .Type 3) (eq .Type 4)}}{{.Name}}{{else}}#{{.Name}}{{end}}";
+                guild_name_template = "{{.Name}}";
+                private_chat_portal_meta = "default";
+                public_address = null;
+                avatar_proxy_key = "generate";
+                portal_message_buffer = 128;
+                startup_private_channel_create_limit = 5;
+                delivery_receipts = false;
+                message_status_events = false;
+                message_error_notices = true;
+                restricted_rooms = true;
+                autojoin_thread_on_open = true;
+                embed_fields_as_tables = true;
+                mute_channels_on_create = false;
+                sync_direct_chat_list = false;
+                resend_bridge_info = false;
+                custom_emoji_reactions = true;
+                delete_portal_on_channel_delete = false;
+                delete_guild_on_leave = true;
+                federate_rooms = true;
+                prefix_webhook_messages = true;
+                enable_webhook_avatars = false;
+                use_discord_cdn_upload = true;
+                #proxy =
+                cache_media = "unencrypted";
+                direct_media = {
+                  enabled = false;
+                  #server_name = "discord-media.example.com";
+                  #well_known_response =
+                  allow_proxy = true;
+                  server_key = "generate";
+                };
+                animated_sticker = {
+                  target = "webp";
+                  args = {
+                    width = 320;
+                    height = 320;
+                    fps = 25;
+                  };
+                };
+                double_puppet_server_map = {
+                  #"example.com" = "https://example.com";
+                };
+                double_puppet_allow_discovery = false;
+                login_shared_secret_map = {
+                  #"example.com" = "foobar";
+                };
+                command_prefix = "!discord";
+                management_room_text = {
+                  welcome = "Hello, I'm a Discord bridge bot.";
+                  welcome_connected = "Use `help` for help.";
+                  welcome_unconnected = "Use `help` for help or `login` to log in.";
+                  additional_help = "";
+                };
+                backfill = {
+                  forward_limits = {
+                    initial = {
+                      dm = 0;
+                      channel = 0;
+                      thread = 0;
+                    };
+                    missed = {
+                      dm = 0;
+                      channel = 0;
+                      thread = 0;
+                    };
+                    max_guild_members = -1;
+                  };
+                };
+                encryption = {
+                  allow = false;
+                  default = false;
+                  appservice = false;
+                  msc4190 = false;
+                  require = false;
+                  allow_key_sharing = false;
+                  plaintext_mentions = false;
+                  delete_keys = {
+                    delete_outbound_on_ack = false;
+                    dont_store_outbound = false;
+                    ratchet_on_decrypt = false;
+                    delete_fully_used_on_decrypt = false;
+                    delete_prev_on_new_session = false;
+                    delete_on_device_delete = false;
+                    periodically_delete_expired = false;
+                    delete_outdated_inbound = false;
+                  };
+                  verification_levels = {
+                    receive = "unverified";
+                    send = "unverified";
+                    share = "cross-signed-tofu";
+                  };
+                  rotation = {
+                    enable_custom = false;
+                    milliseconds = 604800000;
+                    messages = 100;
+                    disable_device_change_key_rotation = false;
+                  };
+                };
+                provisioning = {
+                  prefix = "/_matrix/provision";
+                  shared_secret = "generate";
+                  debug_endpoints = false;
+                };
+                permissions = {
+                  "*" = "relay";
+                  #"example.com" = "user";
+                  #"@admin:example.com": "admin";
+                };
+              };
+              description = ''
+                Bridge configuration.
+                See [example-config.yaml](https://github.com/mautrix/discord/blob/main/example-config.yaml)
+                for more information.
+              '';
+            };
+            logging = lib.mkOption {
+              type = lib.types.attrs;
+              default = {
+                min_level = "info";
+                writers = lib.singleton {
+                  type = "stdout";
+                  format = "pretty-colored";
+                  time_format = " ";
+                };
+              };
+              description = ''
+                Logging configuration.
+                See [example-config.yaml](https://github.com/mautrix/discord/blob/main/example-config.yaml)
+                for more information.
+              '';
+            };
+          };
+        };
+        default = { };
         example = lib.literalExpression ''
           {
             homeserver = {
               address = "http://localhost:8008";
-              domain = "example.com";
+              domain = "public-domain.tld";
+            };
+
+            appservice.public = {
+              prefix = "/public";
+              external = "https://public-appservice-address/public";
             };
 
             bridge.permissions = {
@@ -85,12 +265,8 @@ in
         '';
         description = ''
           {file}`config.yaml` configuration as a Nix attribute set.
-
           Configuration options should match those described in
           [example-config.yaml](https://github.com/mautrix/discord/blob/main/example-config.yaml).
-
-          Secret tokens should be specified using {option}`environmentFile`
-          instead of this world-readable attribute set.
         '';
       };
 
@@ -106,9 +282,12 @@ in
 
       dataDir = lib.mkOption {
         type = lib.types.path;
-        default = defaultDataDir;
-        defaultText = defaultDataDir;
-        description = "Directory to store the bridge's data.";
+        default = "/var/lib/mautrix-discord";
+        defaultText = "/var/lib/mautrix-discord";
+        description = ''
+          Directory to store the bridge's configuration and database files.
+          This directory will be created if it does not exist.
+        '';
       };
 
       # TODO: Get upstream to add an environment File option. Refer to https://github.com/NixOS/nixpkgs/pull/404871#issuecomment-2895663652 and https://github.com/mautrix/discord/issues/187
@@ -116,31 +295,92 @@ in
         type = lib.types.nullOr lib.types.path;
         default = null;
         description = ''
-          File containing environment variables for secret substitution.
-          Variables in the config like `$VARIABLE` will be replaced.
+          File containing environment variables to substitute when copying the configuration
+          out of Nix store to the `services.mautrix-discord.dataDir`.
+          Can be used for storing the secrets without making them available in the Nix store.
+          For example, you can set `services.mautrix-discord.settings.appservice.as_token = "$MAUTRIX_DISCORD_APPSERVICE_AS_TOKEN"`
+          and then specify `MAUTRIX_DISCORD_APPSERVICE_AS_TOKEN="{token}"` in the environment file.
+          This value will get substituted into the configuration file as a token.
         '';
       };
 
+      serviceUnit = lib.mkOption {
+        type = lib.types.str;
+        readOnly = true;
+        default = "mautrix-discord.service";
+        description = ''
+          The systemd unit (a service or a target) for other services to depend on if they
+          need to be started after matrix-synapse.
+          This option is useful as the actual parent unit for all matrix-synapse processes
+          changes when configuring workers.
+        '';
+      };
+
+      registrationServiceUnit = lib.mkOption {
+        type = lib.types.str;
+        readOnly = true;
+        default = "mautrix-discord-registration.service";
+        description = ''
+          The registration service that generates the registration file.
+          Systemd unit (a service or a target) for other services to depend on if they
+          need to be started after mautrix-discord registration service.
+          This option is useful as the actual parent unit for all matrix-synapse processes
+          changes when configuring workers.
+        '';
+      };
+
+      serviceDependencies = lib.mkOption {
+        type = lib.types.listOf lib.types.str;
+        default = [
+          cfg.registrationServiceUnit
+        ]
+        ++ (lib.lists.optional config.services.matrix-synapse.enable config.services.matrix-synapse.serviceUnit)
+        ++ (lib.lists.optional config.services.matrix-conduit.enable "matrix-conduit.service")
+        ++ (lib.lists.optional config.services.dendrite.enable "dendrite.service");
+
+        defaultText = ''
+          [ cfg.registrationServiceUnit ] ++
+          (lib.lists.optional config.services.matrix-synapse.enable config.services.matrix-synapse.serviceUnit) ++
+          (lib.lists.optional config.services.matrix-conduit.enable "matrix-conduit.service") ++
+          (lib.lists.optional config.services.dendrite.enable "dendrite.service");
+        '';
+        description = ''
+          List of Systemd services to require and wait for when starting the application service.
+        '';
+      };
     };
   };
   config = lib.mkIf cfg.enable {
-
     assertions = [
       {
         assertion =
-          cfg.settings.homeserver.address or "" != "" && cfg.settings.homeserver.domain or "" != "";
-        message = "services.mautrix-discord.settings.homeserver.{address,domain} must be set.";
+          cfg.settings.homeserver.domain or "" != "" && cfg.settings.homeserver.address or "" != "";
+        message = ''
+          The options with information about the homeserver:
+          `services.mautrix-discord.settings.homeserver.domain` and
+          `services.mautrix-discord.settings.homeserver.address` have to be set.
+        '';
+      }
+      {
+        assertion = cfg.settings.bridge.permissions or { } != { };
+        message = ''
+          The option `services.mautrix-discord.settings.bridge.permissions` has to be set.
+        '';
       }
     ];
 
     users.users.mautrix-discord = {
       isSystemUser = true;
       group = "mautrix-discord";
+      extraGroups = [ "mautrix-discord-registration" ];
       home = dataDir;
       description = "Mautrix-Discord bridge user";
     };
 
     users.groups.mautrix-discord = { };
+    users.groups.mautrix-discord-registration = {
+      members = lib.lists.optional config.services.matrix-synapse.enable "matrix-synapse";
+    };
 
     services.matrix-synapse = lib.mkIf cfg.registerToSynapse {
       settings.app_service_config_files = [ registrationFile ];
@@ -152,9 +392,7 @@ in
 
     systemd.services = {
       matrix-synapse = lib.mkIf cfg.registerToSynapse {
-        serviceConfig.SupplementaryGroups = [
-          "mautrix-discord"
-        ];
+        serviceConfig.SupplementaryGroups = [ "mautrix-discord-registration" ];
         # Make synapse depend on the registration service when auto-registering
         wants = [ "mautrix-discord-registration.service" ];
         after = [ "mautrix-discord-registration.service" ];
@@ -233,18 +471,15 @@ in
             '${settingsFile}' '${registrationFile}' > '${registrationFile}.tmp'
           mv '${registrationFile}.tmp' '${registrationFile}'
 
-          # Application services should not be rate limited by default.
-          yq -Y '.rate_limited = false' '${registrationFile}' > '${registrationFile}.tmp'
-          mv '${registrationFile}.tmp' '${registrationFile}'
-
           umask $old_umask
+          chown :mautrix-discord-registration '${registrationFile}'
           chmod 640 '${registrationFile}'
         '';
 
         serviceConfig = {
           Type = "oneshot";
           RemainAfterExit = true;
-          UMask = "027";
+          UMask = 27;
 
           User = "mautrix-discord";
           Group = "mautrix-discord";
@@ -266,8 +501,8 @@ in
         description = "Mautrix-Discord, a Matrix-Discord puppeting/relaybot bridge";
 
         wantedBy = [ "multi-user.target" ];
-        wants = [ "network-online.target" ] ++ serviceDependencies;
-        after = [ "network-online.target" ] ++ serviceDependencies;
+        wants = [ "network-online.target" ] ++ cfg.serviceDependencies;
+        after = [ "network-online.target" ] ++ cfg.serviceDependencies;
         path = [
           pkgs.lottieconverter
           pkgs.ffmpeg-headless
@@ -301,8 +536,6 @@ in
           ProtectHostname = true;
           ProtectClock = true;
 
-          UMask = "027";
-
           SystemCallArchitectures = "native";
           SystemCallErrorNumber = "EPERM";
           SystemCallFilter = "@system-service";
@@ -313,12 +546,10 @@ in
       };
     };
 
-  };
-
-  meta = {
-    maintainers = with lib.maintainers; [
-      mistyttm
-    ];
-    doc = ./mautrix-discord.md;
+    meta = {
+      maintainers = with lib.maintainers; [
+        mistyttm
+      ];
+    };
   };
 }

nixos/tests/matrix/mautrix-discord.nix

@@ -1,4 +1,4 @@
-{ pkgs, ... }:
+{ pkgs, lib, ... }:
 let
   homeserverUrl = "http://homeserver:8008";
 in
@@ -53,7 +53,6 @@ in
 
             appservice = {
               address = "http://homeserver:8009";
-              hostname = "0.0.0.0";
               port = 8009;
               id = "discord";
               bot = {
@@ -61,6 +60,8 @@ in
                 displayname = "Discord bridge bot";
                 avatar = "mxc://maunium.net/nIdEykemnwdisvHbpxflpDlC";
               };
+              # Don't override as_token/hs_token - let them use the default placeholder
+              # which will trigger automatic generation
 
               database = {
                 type = "sqlite3";
@@ -74,17 +75,6 @@ in
                 "*" = "relay";
               };
             };
-
-            logging = {
-              min_level = "info";
-              writers = [
-                {
-                  type = "stdout";
-                  format = "pretty-colored";
-                  time_format = " ";
-                }
-              ];
-            };
           };
         };
 
@@ -167,57 +157,6 @@ in
     with subtest("verify registration file was created"):
         homeserver.wait_until_succeeds("test -f /var/lib/mautrix-discord/discord-registration.yaml")
 
-        # Verify the module wrote the expected bridge configuration.
-        config_homeserver_address = homeserver.succeed("yq -r '.homeserver.address' /var/lib/mautrix-discord/config.yaml").strip()
-        config_homeserver_domain = homeserver.succeed("yq -r '.homeserver.domain' /var/lib/mautrix-discord/config.yaml").strip()
-        config_appservice_address = homeserver.succeed("yq -r '.appservice.address' /var/lib/mautrix-discord/config.yaml").strip()
-        config_appservice_hostname = homeserver.succeed("yq -r '.appservice.hostname' /var/lib/mautrix-discord/config.yaml").strip()
-        config_appservice_port = homeserver.succeed("yq -r '.appservice.port' /var/lib/mautrix-discord/config.yaml").strip()
-        config_appservice_id = homeserver.succeed("yq -r '.appservice.id' /var/lib/mautrix-discord/config.yaml").strip()
-        config_bot_username = homeserver.succeed("yq -r '.appservice.bot.username' /var/lib/mautrix-discord/config.yaml").strip()
-        config_bot_displayname = homeserver.succeed("yq -r '.appservice.bot.displayname' /var/lib/mautrix-discord/config.yaml").strip()
-        config_bot_avatar = homeserver.succeed("yq -r '.appservice.bot.avatar' /var/lib/mautrix-discord/config.yaml").strip()
-        config_database_type = homeserver.succeed("yq -r '.appservice.database.type' /var/lib/mautrix-discord/config.yaml").strip()
-        config_database_uri = homeserver.succeed("yq -r '.appservice.database.uri' /var/lib/mautrix-discord/config.yaml").strip()
-        config_permission = homeserver.succeed("yq -r '.bridge.permissions[\"*\"]' /var/lib/mautrix-discord/config.yaml").strip()
-        config_logging_min_level = homeserver.succeed("yq -r '.logging.min_level' /var/lib/mautrix-discord/config.yaml").strip()
-        config_logging_writer_type = homeserver.succeed("yq -r '.logging.writers[0].type' /var/lib/mautrix-discord/config.yaml").strip()
-        config_logging_writer_format = homeserver.succeed("yq -r '.logging.writers[0].format' /var/lib/mautrix-discord/config.yaml").strip()
-        reg_rate_limited = homeserver.succeed("yq -r '.rate_limited' /var/lib/mautrix-discord/discord-registration.yaml").strip()
-
-        assert config_homeserver_address == "http://homeserver:8008", \
-          f"Unexpected homeserver address: {config_homeserver_address}"
-        assert config_homeserver_domain == "homeserver", \
-          f"Unexpected homeserver domain: {config_homeserver_domain}"
-        assert config_appservice_address == "http://homeserver:8009", \
-          f"Unexpected appservice address: {config_appservice_address}"
-        assert config_appservice_hostname == "0.0.0.0", \
-          f"Unexpected appservice hostname: {config_appservice_hostname}"
-        assert config_appservice_port == "8009", \
-          f"Unexpected appservice port: {config_appservice_port}"
-        assert config_appservice_id == "discord", \
-          f"Unexpected appservice id: {config_appservice_id}"
-        assert config_bot_username == "discordbot", \
-          f"Unexpected bot username: {config_bot_username}"
-        assert config_bot_displayname == "Discord bridge bot", \
-          f"Unexpected bot displayname: {config_bot_displayname}"
-        assert config_bot_avatar == "mxc://maunium.net/nIdEykemnwdisvHbpxflpDlC", \
-          f"Unexpected bot avatar: {config_bot_avatar}"
-        assert config_database_type == "sqlite3-fk-wal", \
-          f"Unexpected database type: {config_database_type}"
-        assert config_database_uri == "file:/var/lib/mautrix-discord/mautrix-discord.db?_txlock=immediate", \
-          f"Unexpected database uri: {config_database_uri}"
-        assert config_permission == "relay", \
-          f"Unexpected default permission mapping: {config_permission}"
-        assert config_logging_min_level == "info", \
-          f"Unexpected logging min_level: {config_logging_min_level}"
-        assert config_logging_writer_type == "stdout", \
-          f"Unexpected logging writer type: {config_logging_writer_type}"
-        assert config_logging_writer_format == "pretty-colored", \
-          f"Unexpected logging writer format: {config_logging_writer_format}"
-        assert reg_rate_limited == "false", \
-          f"Registration file should disable rate limiting by default, got: {reg_rate_limited}"
-
         # Verify tokens were generated and are not default values
         config_as_token = homeserver.succeed("yq -r '.appservice.as_token' /var/lib/mautrix-discord/config.yaml").strip()
         config_hs_token = homeserver.succeed("yq -r '.appservice.hs_token' /var/lib/mautrix-discord/config.yaml").strip()

pkgs/applications/science/math/R/default.nix

@@ -45,7 +45,7 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "R";
-  version = "4.6.0";
+  version = "4.5.3";
 
   src =
     let
@@ -53,7 +53,7 @@ stdenv.mkDerivation (finalAttrs: {
     in
     fetchurl {
       url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz";
-      hash = "sha256-uNybRUNmDHtZa4eTjfUyOUNQNgl2Un00QijuDtEuRew=";
+      hash = "sha256-qlwe1Ck8cnGsUT1lRnA1asDopq1eQr4BQ2XREVC1uPI=";
     };
 
   outputs = [

pkgs/by-name/fo/forgejo-cli/package.nix

@@ -10,14 +10,11 @@
   oniguruma,
   openssl,
   zlib,
-  versionCheckHook,
 }:
 rustPlatform.buildRustPackage (finalAttrs: {
   pname = "forgejo-cli";
   version = "0.5.0";
 
-  __structuredAttrs = true;
-
   src = fetchFromCodeberg {
     owner = "forgejo-contrib";
     repo = "forgejo-cli";
@@ -52,10 +49,6 @@ rustPlatform.buildRustPackage (finalAttrs: {
       --zsh <($out/bin/fj completion zsh)
   '';
 
-  nativeInstallCheckInputs = [ versionCheckHook ];
-  versionCheckProgramArg = "version";
-  doInstallCheck = true;
-
   meta = {
     description = "CLI application for interacting with Forgejo";
     homepage = "https://codeberg.org/forgejo-contrib/forgejo-cli";

pkgs/by-name/ph/phpactor/package.nix

@@ -7,16 +7,16 @@
 }:
 php.buildComposerProject2 (finalAttrs: {
   pname = "phpactor";
-  version = "2026.05.30.1";
+  version = "2025.12.21.1";
 
   src = fetchFromGitHub {
     owner = "phpactor";
     repo = "phpactor";
     tag = finalAttrs.version;
-    hash = "sha256-Harrs0SM00MVBicMfvs3bcLQf/PSTp6k7hcEExGELWE=";
+    hash = "sha256-9hkYU/Mhxl49tIZa3Vyj3kXftNIgZXUlH1T6/4obM7I=";
   };
 
-  vendorHash = "sha256-PztP3qN6LL+1UshNyuJof0WT9Dg5MfXwfQr57kBG9hM=";
+  vendorHash = "sha256-XsybPL391WGHztWPaZAN1l2hWQMQ0tklZ9yjkKjGzsI=";
 
   nativeBuildInputs = [ installShellFiles ];
 

pkgs/by-name/zw/zwave-js-ui/package.nix

@@ -7,15 +7,15 @@
 
 buildNpmPackage rec {
   pname = "zwave-js-ui";
-  version = "11.19.1";
+  version = "11.19.0";
 
   src = fetchFromGitHub {
     owner = "zwave-js";
     repo = "zwave-js-ui";
     tag = "v${version}";
-    hash = "sha256-9dqvQxlk+DdYcpCgoLR8EqtgwJwMA4Dvtwc8n1K8Cic=";
+    hash = "sha256-hn5Y5ADAybwSK5hv3J7qlyjPztD6QRB4oq9JTuLg9Vk=";
   };
-  npmDepsHash = "sha256-dED08xcbgO3zfNRP9iNuTcL+73HnfBnwDrPCGY4TZBQ=";
+  npmDepsHash = "sha256-hHalQUYj2T6AnxU0/EcbobY5UxgwvaS2NAy95FASTCk=";
 
   passthru.tests.zwave-js-ui = nixosTests.zwave-js-ui;
 

pkgs/development/python-modules/fastapi-pagination/default.nix

@@ -14,7 +14,7 @@
 
 buildPythonPackage (finalAttrs: {
   pname = "fastapi-pagination";
-  version = "0.15.14";
+  version = "0.15.13";
   pyproject = true;
   __structuredAttrs = true;
 
@@ -22,7 +22,7 @@ buildPythonPackage (finalAttrs: {
     owner = "uriyyo";
     repo = "fastapi-pagination";
     tag = finalAttrs.version;
-    hash = "sha256-W3SgSne3GgRl2W6l3NWUguvzxigLCVgMLiT/fMIWSAE=";
+    hash = "sha256-c+bXtc4MQdd+UlsBHtVL6F2lBu46yry9OTKsMbu1Mhw=";
   };
 
   build-system = [

pkgs/development/python-modules/unstructured/default.nix

@@ -2,7 +2,6 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
-  symlinkJoin,
 
   # build-system
   setuptools,
@@ -31,7 +30,6 @@
   joblib,
   # jsonpath-python,
   nltk,
-  nltk-data,
   olefile,
   orderly-set,
   python-dateutil,
@@ -120,18 +118,6 @@
 }:
 let
   version = "0.18.31";
-
-  # unstructured downloads these NLTK corpora at import time unless they are already on
-  # nltk.data.path, which fails in offline or read-only builds. Bundle them and register
-  # the directory in postPatch. It must be named "nltk_data": unstructured's resolver
-  # uses paths ending in "nltk_data" as-is and appends "/nltk_data" to any others.
-  nltkData = symlinkJoin {
-    name = "nltk_data";
-    paths = with nltk-data; [
-      averaged-perceptron-tagger-eng
-      punkt-tab
-    ];
-  };
 in
 buildPythonPackage rec {
   pname = "unstructured";
@@ -147,11 +133,6 @@ buildPythonPackage rec {
 
   build-system = [ setuptools ];
 
-  postPatch = ''
-    substituteInPlace unstructured/nlp/tokenize.py \
-      --replace-fail 'import nltk' 'import nltk; nltk.data.path.append("${nltkData}")'
-  '';
-
   dependencies = [
     # Base dependencies
     anyio
@@ -276,14 +257,10 @@ buildPythonPackage rec {
     ];
   };
 
-  pythonImportsCheck = [
-    "unstructured"
-    # exercises the bundled NLTK corpora lookup, so the build catches an attempted download
-    "unstructured.nlp.tokenize"
-  ];
+  pythonImportsCheck = [ "unstructured" ];
 
-  # the import-time NLTK download is handled via nltkData above, but the test suite has
-  # further offline/data requirements that are not yet verified, so keep it disabled.
+  # test try to download punkt from nltk
+  # figure out how to make it available to enable the tests
   doCheck = false;
 
   nativeCheckInputs = [

pkgs/development/r-modules/bioc-annotation-packages.json

@@ -1,6 +1,6 @@
 {
   "extraArgs": {
-    "biocVersion": "3.23"
+    "biocVersion": "3.22"
   },
   "packages": {
     "AHCytoBands": {
@@ -737,8 +737,8 @@
     },
     "BioMartGOGeneSets": {
       "name": "BioMartGOGeneSets",
-      "version": "0.99.12",
-      "sha256": "11x00v18vd5ppm9asg120dmhmqamzsacy64v3kmmxfn7rhxl25b2",
+      "version": "0.99.11",
+      "sha256": "1ack8v1q0zg15gs816n9f4pwrzrpsv4va6j0r8847pw0pvavwpiq",
       "depends": ["GenomicRanges", "S4Vectors"]
     },
     "CENTREannotation": {
@@ -749,8 +749,8 @@
     },
     "CTCF": {
       "name": "CTCF",
-      "version": "0.99.14",
-      "sha256": "06nyz5758mq04hzvc7bl0ld2d173zabs9xyhva01y92b19yy8nfp",
+      "version": "0.99.13",
+      "sha256": "097w2rad5fxyg2dkghz6ws93q1l7hlc6f9dnw1n30gs2bdv5hbyb",
       "depends": []
     },
     "ChemmineDrugs": {
@@ -887,14 +887,14 @@
     },
     "GO_db": {
       "name": "GO.db",
-      "version": "3.23.1",
-      "sha256": "0ays2n3jivigpr7m3y3rba8gjyqr7g3qxdslppww0z0zzm4m808z",
+      "version": "3.22.0",
+      "sha256": "1liyl1ic2d08an0h6yxllggkv9n8vyp1bfjwvqzk5ana17lzmimf",
       "depends": ["AnnotationDbi"]
     },
     "GeneSummary": {
       "name": "GeneSummary",
-      "version": "0.99.7",
-      "sha256": "0pl843r230cgq0nh5pwp19zz823dwdv789kfcgdhylijx3h2ymfk",
+      "version": "0.99.6",
+      "sha256": "0h6afrjb00afrcw6mwslxp7cmwfzp4qfxh0aa4f41kfjd3cymmp5",
       "depends": []
     },
     "GenomeInfoDbData": {
@@ -1241,8 +1241,8 @@
     },
     "Orthology_eg_db": {
       "name": "Orthology.eg.db",
-      "version": "3.23.0",
-      "sha256": "0640jwylw67cw8sylmyfcqm8cak5i2bx9k925bwm0bjmayxl8yw3",
+      "version": "3.22.0",
+      "sha256": "14wng7izmr7wx3yimjlvmk87vf1z3z0n88y2nghn8a2iqci1rl3s",
       "depends": ["AnnotationDbi"]
     },
     "PANTHER_db": {
@@ -1673,8 +1673,8 @@
     },
     "UniProtKeywords": {
       "name": "UniProtKeywords",
-      "version": "0.99.8",
-      "sha256": "1mhbhar70acwgjmlfkfrqc2hskqvbgsaf9xlzv8ph66x6gvbyqb7",
+      "version": "0.99.7",
+      "sha256": "10id2lk2mbccay7p44pk58zhkiqc58x237qr76plivgpcc8xhjzq",
       "depends": []
     },
     "XtraSNPlocs_Hsapiens_dbSNP144_GRCh37": {
@@ -2093,8 +2093,8 @@
     },
     "excluderanges": {
       "name": "excluderanges",
-      "version": "0.99.11",
-      "sha256": "1czr9hr84hzwa7fyzm51425nphy0b9h5yfvgkij5v8qgq565w02a",
+      "version": "0.99.10",
+      "sha256": "0j9njpnbh731ffimr1sbvix3wsivnh9nwxg6sbrpwp8gl0pnl7r0",
       "depends": ["GenomicRanges"]
     },
     "fitCons_UCSC_hg19": {
@@ -2513,8 +2513,8 @@
     },
     "hpAnnot": {
       "name": "hpAnnot",
-      "version": "1.1.3",
-      "sha256": "0gnir407flzzkkljxf2brqrw2kaycl8azi0wc5yn1fhl7x5zidq1",
+      "version": "1.1.1",
+      "sha256": "0bkfcj9igi7ylhf3arszqnqzaxsxvfv2gn2smzx6ymzq5a8sc0yg",
       "depends": ["AnnotationHub"]
     },
     "hs25kresogen_db": {
@@ -3749,20 +3749,20 @@
     },
     "org_Hs_eg_db": {
       "name": "org.Hs.eg.db",
-      "version": "3.23.1",
-      "sha256": "1zlwsk1hq40xi8xd7wc974jp8gky6x7icc9788ch77glbik201j7",
+      "version": "3.22.0",
+      "sha256": "0bia1ppxnyjpw4p3rk19q1l8rrcraccpz4w69f3ja0q0im0xrgfi",
       "depends": ["AnnotationDbi"]
     },
     "org_Mm_eg_db": {
       "name": "org.Mm.eg.db",
-      "version": "3.23.0",
-      "sha256": "0i252737v6wk0im41gnksz4qkzf286kwgfq60yqc1mfva77m8yjh",
+      "version": "3.22.0",
+      "sha256": "16liabdbkfqzhna3rw1zgf777r3xm8knrbvy0181c2nsn2jkxsv3",
       "depends": ["AnnotationDbi"]
     },
     "org_Mmu_eg_db": {
       "name": "org.Mmu.eg.db",
-      "version": "3.23.0",
-      "sha256": "08l4bckvn42yjgpkcmq87c1c2z4g8cfjc9jm5ibb84v5ffjw92ij",
+      "version": "3.22.0",
+      "sha256": "0ga0c9635pkigmr0l9vazh3qdpyxki1y8l7mbgcp1y8sfkyjn33c",
       "depends": ["AnnotationDbi"]
     },
     "org_Mxanthus_db": {
@@ -3779,14 +3779,14 @@
     },
     "org_Pt_eg_db": {
       "name": "org.Pt.eg.db",
-      "version": "3.23.0",
-      "sha256": "1hfvrv2n9gc0h4s6ql4lv8q8qjf75c4y5p2hlplhphzi38j54vhl",
+      "version": "3.22.0",
+      "sha256": "1i67vccx3a6zak34nwdhrbhm7hkjz9qbai9jvwrlql6z8xc6n6q0",
       "depends": ["AnnotationDbi"]
     },
     "org_Rn_eg_db": {
       "name": "org.Rn.eg.db",
-      "version": "3.23.0",
-      "sha256": "1j1gs8bk1a247shhs5z41s4pk6hw4ssy7405fv5q16m5ilpwgc1g",
+      "version": "3.22.0",
+      "sha256": "0vqpmbivxd1yvapa5gz9mrxlk6ivrzak55dw2sfjm8sl308rmaj4",
       "depends": ["AnnotationDbi"]
     },
     "org_Sc_sgd_db": {
@@ -3797,14 +3797,14 @@
     },
     "org_Ss_eg_db": {
       "name": "org.Ss.eg.db",
-      "version": "3.23.0",
-      "sha256": "0ijn7dfh485lww1d9bp8j40fcjr1lx8vdnlq6ydwq3ni4bifkzqp",
+      "version": "3.22.0",
+      "sha256": "03qlbkvxfmdgpl8dwx72msd9asx12izvq2vmidqfyipyr7r79cbm",
       "depends": ["AnnotationDbi"]
     },
     "org_Xl_eg_db": {
       "name": "org.Xl.eg.db",
-      "version": "3.23.0",
-      "sha256": "1w856a5hkp9a5g41nd69xwvzaf1nmq7zqjsn7w5p1i2zsxv1i1k1",
+      "version": "3.22.0",
+      "sha256": "1h8jvdzhpp9d4zaaczhmg6hk32p77l63v3095ln58rhy9m18pg0f",
       "depends": ["AnnotationDbi"]
     },
     "paeg1acdf": {
@@ -5111,8 +5111,8 @@
     },
     "reactome_db": {
       "name": "reactome.db",
-      "version": "1.96.0",
-      "sha256": "0b43ri3clg6ynp197vy24936n762k0f43v9m51g1lar2w4qc2zhb",
+      "version": "1.95.0",
+      "sha256": "1b87byr45cmqa7jyd5fw3askmrzfhdljjp2d7jcmm88baf45mfg6",
       "depends": ["AnnotationDbi"]
     },
     "rgu34a_db": {

pkgs/development/r-modules/default.nix

@@ -765,9 +765,7 @@ let
     ];
     RGtk2 = [ pkgs.gtk2.dev ];
     rhdf5 = [ pkgs.zlib ];
-    Rhdf5lib = with pkgs; [
-      cmake
-    ];
+    Rhdf5lib = with pkgs; [ zlib.dev ];
     Rhpc = with pkgs; [
       zlib
       bzip2.dev
@@ -823,10 +821,7 @@ let
     rpanel = [ pkgs.tclPackages.bwidget ];
     Rpoppler = [ pkgs.poppler ];
     RPostgreSQL = with pkgs; [ libpq.pg_config ];
-    RProtoBuf = with pkgs; [
-      protobuf
-      abseil-cpp.dev
-    ];
+    RProtoBuf = [ pkgs.protobuf ];
     rsamplr = with pkgs; [
       cargo
       rustc
@@ -870,10 +865,6 @@ let
       cargo
       rustc
     ];
-    tinyimg = with pkgs; [
-      cargo
-      rustc
-    ];
     caugi = with pkgs; [
       cargo
       rustc
@@ -975,7 +966,6 @@ let
       fontconfig.dev
       freetype.dev
     ];
-    rlas = [ pkgs.pkg-config ];
     TAQMNGR = [ pkgs.zlib.dev ];
     TDA = [ pkgs.gmp ];
     tesseract = with pkgs; [
@@ -1237,16 +1227,10 @@ let
       xz.dev
       zlib.dev
     ];
-    fs = [ pkgs.libuv ];
     pgenlibr = [ pkgs.zlib.dev ];
     fftw = [ pkgs.pkg-config ];
     gdtools = [ pkgs.pkg-config ];
     archive = [ pkgs.libarchive ];
-    lpsymphony = with pkgs; [
-      symphony
-      cgl
-      clp
-    ];
     gdalcubes = with pkgs; [
       proj.dev
       gdal
@@ -1267,10 +1251,6 @@ let
       fftw.dev
       pkg-config
     ];
-    Rhdf5lib = with pkgs; [
-      curl
-      zlib.dev
-    ];
     GRAB = [ pkgs.zlib.dev ];
     jqr = [ pkgs.jq.out ];
     kza = [ pkgs.pkg-config ];
@@ -1561,13 +1541,7 @@ let
     redux = [ pkgs.hiredis ];
     RmecabKo = [ pkgs.mecab ];
     markets = [ pkgs.gsl ];
-    rlas = with pkgs; [
-      boost
-      gdal
-      proj
-      sqlite
-      geos
-    ];
+    rlas = [ pkgs.boost ];
     bgx = [ pkgs.boost ];
     PoissonBinomial = [ pkgs.fftw.dev ];
     poisbinom = [ pkgs.fftw.dev ];
@@ -1973,10 +1947,6 @@ let
       postPatch = "patchShebangs configure";
     });
 
-    fixest = old.fixest.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     arcgisplaces = old.arcgisplaces.overrideAttrs (attrs: {
       postPatch = "patchShebangs configure";
     });
@@ -2009,10 +1979,6 @@ let
       postPatch = "patchShebangs configure";
     });
 
-    ramr = old.ramr.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     roxigraph = old.roxigraph.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         LIBCLANG_PATH = "${lib.getLib pkgs.libclang}/lib";
@@ -2474,10 +2440,6 @@ let
       '';
     });
 
-    RProtoBuf = old.RProtoBuf.overrideAttrs (attrs: {
-      configureFlags = [ "ac_cv_prog_cxx_cxx11=" ];
-    });
-
     JavaGD = old.JavaGD.overrideAttrs (attrs: {
       preConfigure = ''
         export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
@@ -2986,10 +2948,7 @@ let
     );
 
     lpsymphony = old.lpsymphony.overrideAttrs (attrs: {
-      postPatch = ''
-        substituteInPlace configure \
-          --replace-fail '--libs SYMPHONY' '--libs symphony' \
-          --replace-fail '--cflags SYMPHONY' '--cflags symphony'
+      preConfigure = ''
         patchShebangs configure
       '';
     });
@@ -3149,13 +3108,7 @@ let
 
     Rhdf5lib =
       let
-        hdf5 = pkgs.hdf5.overrideAttrs (attrs: {
-          cmakeFlags = attrs.cmakeFlags ++ [ "-DHDF5_ENABLE_ROS3_VFD:BOOL=TRUE" ];
-          buildInputs = attrs.buildInputs ++ [ pkgs.curl.dev ];
-          postInstall = attrs.postInstall or "" + ''
-            cp src/libhdf5.settings $dev/lib
-          '';
-        });
+        hdf5 = pkgs.hdf5_1_10;
       in
       old.Rhdf5lib.overrideAttrs (attrs: {
         propagatedBuildInputs = attrs.propagatedBuildInputs ++ [

pkgs/development/r-modules/patches/Rhdf5lib.patch

@@ -1,8 +1,8 @@
 diff --git a/R/zzz.R b/R/zzz.R
-index 2af2b3e..21ddc00 100644
+index 97becd7..803ca39 100644
 --- a/R/zzz.R
 +++ b/R/zzz.R
-@@ -22,7 +22,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+@@ -20,7 +20,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
  
    path <- Sys.getenv(
      x = "RHDF5LIB_RPATH",
@@ -10,48 +10,70 @@ index 2af2b3e..21ddc00 100644
 +    unset = ""
    )
  
-   sysname <- Sys.info()['sysname']
-@@ -47,7 +47,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
-                               sprintf('-L%s -lhdf5 %s', 
+   if (nzchar(.Platform$r_arch)) {
+@@ -59,7 +59,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5 %s',
                                        patharch, winlibs)
                              }, {
 -                              sprintf('"%s/libhdf5.a"%s%s', 
-+                              sprintf('-lhdf5', 
-                                       patharch, .getSzipLoc(patharch), .getDynamicLinks(patharch))
++                              sprintf('-lhdf5',
+                                       patharch, .getSzipLoc(patharch), .getDynamicLinks())
                              }
                       )
-@@ -58,7 +58,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
-                               sprintf('-L%s -lhdf5_cpp -lhdf5 %s', 
+@@ -70,7 +70,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5_cpp -lhdf5 %s',
                                        patharch, winlibs)
                              }, {
 -                              sprintf('"%s/libhdf5_cpp.a" "%s/libhdf5.a"%s%s',
 +                              sprintf('-lhdf5_cpp -lhdf5',
-                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks(patharch))
+                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
                              }
                       )
-@@ -69,7 +69,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
-                               sprintf('-L%s -lhdf5_hl -lhdf5 %s', 
+@@ -81,7 +81,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5_hl -lhdf5 %s',
                                        patharch, winlibs)
                              }, {
 -                              sprintf('"%s/libhdf5_hl.a" "%s/libhdf5.a"%s%s', 
-+                              sprintf('-lhdf5_hl -lhdf5', 
-                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks(patharch))
++                              sprintf('-lhdf5_hl -lhdf5',
+                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
                              }
                       )
-@@ -80,7 +80,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
-                               sprintf('-L%s -lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5 %s', 
+@@ -92,7 +92,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5 %s',
                                        patharch, winlibs)
                              }, {
 -                              sprintf('"%s/libhdf5_hl_cpp.a" "%s/libhdf5_hl.a" "%s/libhdf5_cpp.a" "%s/libhdf5.a"%s%s',
 +                              sprintf('-lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5',
-                                       patharch, patharch, patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks(patharch))
+                                       patharch, patharch, patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
                              }
                       )
-@@ -113,6 +113,7 @@ getHdf5Version <- function() {
- #' @noRd
+@@ -124,6 +124,7 @@ getHdf5Version <- function() {
+ #'
  #' @keywords internal
- .getDynamicLinks <- function(path) {
+ .getDynamicLinks <- function() {
 +  return("")
-   settings_file <- file.path(path, "libhdf5.settings")
-   libhdf5_settings <- readLines(settings_file)
-   libstr <- grep("Extra libraries", x = libhdf5_settings, fixed = TRUE, value = TRUE) |> 
+   sysname <- Sys.info()['sysname']
+   if(sysname == "Windows") {
+     links <- "-lz"
+diff --git a/src/Makevars.in b/src/Makevars.in
+index addb6a0..590784a 100644
+--- a/src/Makevars.in
++++ b/src/Makevars.in
+@@ -18,7 +18,7 @@ USER_LIB_DIR = ${R_PACKAGE_DIR}/lib${R_ARCH}/
+ 
+ PKG_CPPFLAGS = -I${USER_INCLUDE_DIR} ${ZLIB_INCLUDE}
+ PKG_CFLAGS = ${ZLIB_LIB}
+-PKG_LIBS = "${USER_LIB_DIR}libhdf5.a" @SZIP_LIB@ -lz
++PKG_LIBS = -lhdf5 -lsz
+ 
+ 
+ 
+@@ -26,7 +26,7 @@ all: $(SHLIB)
+ 
+ $(SHLIB): Rhdf5lib.o
+ 
+-Rhdf5lib.o: copy-hdf5 @COPY_SZIP@
++Rhdf5lib.o:
+ 
+ copy-szip: copy-hdf5
+ 	cp hdf5/libaec-1.0.4/build/szip/lib/libsz.a "${USER_LIB_DIR}"

pkgs/development/r-modules/patches/rhdf5.patch

@@ -9,3 +9,39 @@ index 713b44c..704ac17 100644
  
  #PKG_CFLAGS = -Wall
  
+diff --git a/src/h5testLock.c b/src/h5testLock.c
+index b326444..5d58b4a 100644
+--- a/src/h5testLock.c
++++ b/src/h5testLock.c
+@@ -8,16 +8,16 @@ SEXP _h5fileLock(SEXP _file_name) {
+   int lk = -1;
+ 
+   /* create the temporary file */
+-  fd = HDopen(file_name, O_RDWR | O_CREAT | O_TRUNC, 0666);
++  fd = open(file_name, O_RDWR | O_CREAT | O_TRUNC, 0666);
+ 
+   /* try to lock file */
+-  lk = HDflock(fd, LOCK_EX | LOCK_NB);
++  lk = flock(fd, LOCK_EX | LOCK_NB);
+   
+   /* unlock so we can remove */
+-  HDflock(fd, LOCK_UN);
++  flock(fd, LOCK_UN);
+   
+   /* close */
+-  HDclose(fd);
++  close(fd);
+   
+   /* return value of lock attempt */
+   PROTECT(Rval = allocVector(INTSXP, 1));
+diff --git a/src/h5testLock.h b/src/h5testLock.h
+index 2c1c5e4..25914ff 100644
+--- a/src/h5testLock.h
++++ b/src/h5testLock.h
+@@ -1,5 +1,5 @@
+ #include <fcntl.h>
++#include <unistd.h>
+ #include "myhdf5.h"
+-#include <H5private.h>
+ 
+ SEXP _h5fileLock();

pkgs/servers/sql/postgresql/ext/plr.nix

@@ -13,13 +13,13 @@
 
 postgresqlBuildExtension (finalAttrs: {
   pname = "plr";
-  version = "8.4.8.6";
+  version = "8.4.8";
 
   src = fetchFromGitHub {
     owner = "postgres-plr";
     repo = "plr";
     tag = "REL${lib.replaceString "." "_" finalAttrs.version}";
-    hash = "sha256-SBLv9GsyYmYdxrWmGiMIiFRGl5FA+j2RcSmKz9pMv2E=";
+    hash = "sha256-FLL61HsZ6WaWBP9NqrJjhMFSVyVBIpVO0wv+kXMuAaU=";
   };
 
   nativeBuildInputs = [ pkg-config ];