R updates (#523821)

After fixing the registration bug I determined that the module was way
too verbose and did not need to provide all of the options provided in
the application. I've stopped explicitly declaring all options that
aren't needed to make a basic version of the module function. The
assertions have also been updated to mirror this fact and will alert a
user when the specific required options are unset. A new documnetation
file was also added as this module, like other mautrix modules, is quite
complex and may need more explaining.

nixos/doc/manual/redirects.json

@@ -65,6 +65,42 @@
   "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

@@ -0,0 +1,156 @@
+# 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

@@ -5,15 +5,59 @@
   ...
 }:
 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 = {
@@ -23,238 +67,14 @@ in
       package = lib.mkPackageOption pkgs "mautrix-discord" { };
 
       settings = lib.mkOption {
-        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 = { };
+        apply = lib.recursiveUpdate settingsDefault;
+        type = format.type;
+        default = settingsDefault;
         example = lib.literalExpression ''
           {
             homeserver = {
               address = "http://localhost:8008";
-              domain = "public-domain.tld";
-            };
-
-            appservice.public = {
-              prefix = "/public";
-              external = "https://public-appservice-address/public";
+              domain = "example.com";
             };
 
             bridge.permissions = {
@@ -265,8 +85,12 @@ 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.
         '';
       };
 
@@ -282,12 +106,9 @@ in
 
       dataDir = lib.mkOption {
         type = lib.types.path;
-        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.
-        '';
+        default = defaultDataDir;
+        defaultText = defaultDataDir;
+        description = "Directory to store the bridge's data.";
       };
 
       # 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
@@ -295,92 +116,31 @@ in
         type = lib.types.nullOr lib.types.path;
         default = null;
         description = ''
-          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 = "$MAUTRIX_DISCORD_APPSERVICE_AS_TOKEN"`
-          and then specify `MAUTRIX_DISCORD_APPSERVICE_AS_TOKEN="{token}"` in the environment file.
-          This value will get substituted into the configuration file as a token.
+          File containing environment variables for secret substitution.
+          Variables in the config like `$VARIABLE` will be replaced.
         '';
       };
 
-      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.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.
-        '';
+          cfg.settings.homeserver.address or "" != "" && cfg.settings.homeserver.domain or "" != "";
+        message = "services.mautrix-discord.settings.homeserver.{address,domain} must 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 ];
@@ -392,7 +152,9 @@ in
 
     systemd.services = {
       matrix-synapse = lib.mkIf cfg.registerToSynapse {
-        serviceConfig.SupplementaryGroups = [ "mautrix-discord-registration" ];
+        serviceConfig.SupplementaryGroups = [
+          "mautrix-discord"
+        ];
         # Make synapse depend on the registration service when auto-registering
         wants = [ "mautrix-discord-registration.service" ];
         after = [ "mautrix-discord-registration.service" ];
@@ -471,15 +233,18 @@ 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 = 27;
+          UMask = "027";
 
           User = "mautrix-discord";
           Group = "mautrix-discord";
@@ -501,8 +266,8 @@ in
         description = "Mautrix-Discord, a Matrix-Discord puppeting/relaybot bridge";
 
         wantedBy = [ "multi-user.target" ];
-        wants = [ "network-online.target" ] ++ cfg.serviceDependencies;
-        after = [ "network-online.target" ] ++ cfg.serviceDependencies;
+        wants = [ "network-online.target" ] ++ serviceDependencies;
+        after = [ "network-online.target" ] ++ serviceDependencies;
         path = [
           pkgs.lottieconverter
           pkgs.ffmpeg-headless
@@ -536,6 +301,8 @@ in
           ProtectHostname = true;
           ProtectClock = true;
 
+          UMask = "027";
+
           SystemCallArchitectures = "native";
           SystemCallErrorNumber = "EPERM";
           SystemCallFilter = "@system-service";
@@ -546,10 +313,12 @@ in
       };
     };
 
-    meta = {
-      maintainers = with lib.maintainers; [
-        mistyttm
-      ];
-    };
+  };
+
+  meta = {
+    maintainers = with lib.maintainers; [
+      mistyttm
+    ];
+    doc = ./mautrix-discord.md;
   };
 }

nixos/tests/matrix/mautrix-discord.nix

@@ -1,4 +1,4 @@
-{ pkgs, lib, ... }:
+{ pkgs, ... }:
 let
   homeserverUrl = "http://homeserver:8008";
 in
@@ -53,6 +53,7 @@ in
 
             appservice = {
               address = "http://homeserver:8009";
+              hostname = "0.0.0.0";
               port = 8009;
               id = "discord";
               bot = {
@@ -60,8 +61,6 @@ 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";
@@ -75,6 +74,17 @@ in
                 "*" = "relay";
               };
             };
+
+            logging = {
+              min_level = "info";
+              writers = [
+                {
+                  type = "stdout";
+                  format = "pretty-colored";
+                  time_format = " ";
+                }
+              ];
+            };
           };
         };
 
@@ -157,6 +167,57 @@ 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 = "4.5.3";
+  version = "4.6.0";
 
   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-qlwe1Ck8cnGsUT1lRnA1asDopq1eQr4BQ2XREVC1uPI=";
+      hash = "sha256-uNybRUNmDHtZa4eTjfUyOUNQNgl2Un00QijuDtEuRew=";
     };
 
   outputs = [

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

@@ -10,11 +10,14 @@
   oniguruma,
   openssl,
   zlib,
+  versionCheckHook,
 }:
 rustPlatform.buildRustPackage (finalAttrs: {
   pname = "forgejo-cli";
   version = "0.5.0";
 
+  __structuredAttrs = true;
+
   src = fetchFromCodeberg {
     owner = "forgejo-contrib";
     repo = "forgejo-cli";
@@ -49,6 +52,10 @@ 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 = "2025.12.21.1";
+  version = "2026.05.30.1";
 
   src = fetchFromGitHub {
     owner = "phpactor";
     repo = "phpactor";
     tag = finalAttrs.version;
-    hash = "sha256-9hkYU/Mhxl49tIZa3Vyj3kXftNIgZXUlH1T6/4obM7I=";
+    hash = "sha256-Harrs0SM00MVBicMfvs3bcLQf/PSTp6k7hcEExGELWE=";
   };
 
-  vendorHash = "sha256-XsybPL391WGHztWPaZAN1l2hWQMQ0tklZ9yjkKjGzsI=";
+  vendorHash = "sha256-PztP3qN6LL+1UshNyuJof0WT9Dg5MfXwfQr57kBG9hM=";
 
   nativeBuildInputs = [ installShellFiles ];
 

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

@@ -7,15 +7,15 @@
 
 buildNpmPackage rec {
   pname = "zwave-js-ui";
-  version = "11.19.0";
+  version = "11.19.1";
 
   src = fetchFromGitHub {
     owner = "zwave-js";
     repo = "zwave-js-ui";
     tag = "v${version}";
-    hash = "sha256-hn5Y5ADAybwSK5hv3J7qlyjPztD6QRB4oq9JTuLg9Vk=";
+    hash = "sha256-9dqvQxlk+DdYcpCgoLR8EqtgwJwMA4Dvtwc8n1K8Cic=";
   };
-  npmDepsHash = "sha256-hHalQUYj2T6AnxU0/EcbobY5UxgwvaS2NAy95FASTCk=";
+  npmDepsHash = "sha256-dED08xcbgO3zfNRP9iNuTcL+73HnfBnwDrPCGY4TZBQ=";
 
   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 = "0.15.13";
+  version = "0.15.14";
   pyproject = true;
   __structuredAttrs = true;
 
@@ -22,7 +22,7 @@ buildPythonPackage (finalAttrs: {
     owner = "uriyyo";
     repo = "fastapi-pagination";
     tag = finalAttrs.version;
-    hash = "sha256-c+bXtc4MQdd+UlsBHtVL6F2lBu46yry9OTKsMbu1Mhw=";
+    hash = "sha256-W3SgSne3GgRl2W6l3NWUguvzxigLCVgMLiT/fMIWSAE=";
   };
 
   build-system = [

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

@@ -2,6 +2,7 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+  symlinkJoin,
 
   # build-system
   setuptools,
@@ -30,6 +31,7 @@
   joblib,
   # jsonpath-python,
   nltk,
+  nltk-data,
   olefile,
   orderly-set,
   python-dateutil,
@@ -118,6 +120,18 @@
 }:
 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";
@@ -133,6 +147,11 @@ 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
@@ -257,10 +276,14 @@ buildPythonPackage rec {
     ];
   };
 
-  pythonImportsCheck = [ "unstructured" ];
+  pythonImportsCheck = [
+    "unstructured"
+    # exercises the bundled NLTK corpora lookup, so the build catches an attempted download
+    "unstructured.nlp.tokenize"
+  ];
 
-  # test try to download punkt from nltk
-  # figure out how to make it available to enable the tests
+  # 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.
   doCheck = false;
 
   nativeCheckInputs = [

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

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

pkgs/development/r-modules/default.nix

@@ -765,7 +765,9 @@ let
     ];
     RGtk2 = [ pkgs.gtk2.dev ];
     rhdf5 = [ pkgs.zlib ];
-    Rhdf5lib = with pkgs; [ zlib.dev ];
+    Rhdf5lib = with pkgs; [
+      cmake
+    ];
     Rhpc = with pkgs; [
       zlib
       bzip2.dev
@@ -821,7 +823,10 @@ let
     rpanel = [ pkgs.tclPackages.bwidget ];
     Rpoppler = [ pkgs.poppler ];
     RPostgreSQL = with pkgs; [ libpq.pg_config ];
-    RProtoBuf = [ pkgs.protobuf ];
+    RProtoBuf = with pkgs; [
+      protobuf
+      abseil-cpp.dev
+    ];
     rsamplr = with pkgs; [
       cargo
       rustc
@@ -865,6 +870,10 @@ let
       cargo
       rustc
     ];
+    tinyimg = with pkgs; [
+      cargo
+      rustc
+    ];
     caugi = with pkgs; [
       cargo
       rustc
@@ -966,6 +975,7 @@ let
       fontconfig.dev
       freetype.dev
     ];
+    rlas = [ pkgs.pkg-config ];
     TAQMNGR = [ pkgs.zlib.dev ];
     TDA = [ pkgs.gmp ];
     tesseract = with pkgs; [
@@ -1227,10 +1237,16 @@ 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
@@ -1251,6 +1267,10 @@ let
       fftw.dev
       pkg-config
     ];
+    Rhdf5lib = with pkgs; [
+      curl
+      zlib.dev
+    ];
     GRAB = [ pkgs.zlib.dev ];
     jqr = [ pkgs.jq.out ];
     kza = [ pkgs.pkg-config ];
@@ -1541,7 +1561,13 @@ let
     redux = [ pkgs.hiredis ];
     RmecabKo = [ pkgs.mecab ];
     markets = [ pkgs.gsl ];
-    rlas = [ pkgs.boost ];
+    rlas = with pkgs; [
+      boost
+      gdal
+      proj
+      sqlite
+      geos
+    ];
     bgx = [ pkgs.boost ];
     PoissonBinomial = [ pkgs.fftw.dev ];
     poisbinom = [ pkgs.fftw.dev ];
@@ -1947,6 +1973,10 @@ let
       postPatch = "patchShebangs configure";
     });
 
+    fixest = old.fixest.overrideAttrs (attrs: {
+      postPatch = "patchShebangs configure";
+    });
+
     arcgisplaces = old.arcgisplaces.overrideAttrs (attrs: {
       postPatch = "patchShebangs configure";
     });
@@ -1979,6 +2009,10 @@ 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";
@@ -2440,6 +2474,10 @@ 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/
@@ -2948,7 +2986,10 @@ let
     );
 
     lpsymphony = old.lpsymphony.overrideAttrs (attrs: {
-      preConfigure = ''
+      postPatch = ''
+        substituteInPlace configure \
+          --replace-fail '--libs SYMPHONY' '--libs symphony' \
+          --replace-fail '--cflags SYMPHONY' '--cflags symphony'
         patchShebangs configure
       '';
     });
@@ -3108,7 +3149,13 @@ let
 
     Rhdf5lib =
       let
-        hdf5 = pkgs.hdf5_1_10;
+        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
+          '';
+        });
       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 97becd7..803ca39 100644
+index 2af2b3e..21ddc00 100644
 --- a/R/zzz.R
 +++ b/R/zzz.R
-@@ -20,7 +20,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+@@ -22,7 +22,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
  
    path <- Sys.getenv(
      x = "RHDF5LIB_RPATH",
@@ -10,70 +10,48 @@ index 97becd7..803ca39 100644
 +    unset = ""
    )
  
-   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',
+   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', 
                                        patharch, winlibs)
                              }, {
 -                              sprintf('"%s/libhdf5.a"%s%s', 
-+                              sprintf('-lhdf5',
-                                       patharch, .getSzipLoc(patharch), .getDynamicLinks())
++                              sprintf('-lhdf5', 
+                                       patharch, .getSzipLoc(patharch), .getDynamicLinks(patharch))
                              }
                       )
-@@ -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',
+@@ -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', 
                                        patharch, winlibs)
                              }, {
 -                              sprintf('"%s/libhdf5_cpp.a" "%s/libhdf5.a"%s%s',
 +                              sprintf('-lhdf5_cpp -lhdf5',
-                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
+                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks(patharch))
                              }
                       )
-@@ -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',
+@@ -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', 
                                        patharch, winlibs)
                              }, {
 -                              sprintf('"%s/libhdf5_hl.a" "%s/libhdf5.a"%s%s', 
-+                              sprintf('-lhdf5_hl -lhdf5',
-                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
++                              sprintf('-lhdf5_hl -lhdf5', 
+                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks(patharch))
                              }
                       )
-@@ -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',
+@@ -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', 
                                        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, .getSzipLoc(patharch), .getDynamicLinks(patharch))
                              }
                       )
-@@ -124,6 +124,7 @@ getHdf5Version <- function() {
- #'
+@@ -113,6 +113,7 @@ getHdf5Version <- function() {
+ #' @noRd
  #' @keywords internal
- .getDynamicLinks <- function() {
+ .getDynamicLinks <- function(path) {
 +  return("")
-   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}"
+   settings_file <- file.path(path, "libhdf5.settings")
+   libhdf5_settings <- readLines(settings_file)
+   libstr <- grep("Extra libraries", x = libhdf5_settings, fixed = TRUE, value = TRUE) |> 

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

@@ -9,39 +9,3 @@ 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";
+  version = "8.4.8.6";
 
   src = fetchFromGitHub {
     owner = "postgres-plr";
     repo = "plr";
     tag = "REL${lib.replaceString "." "_" finalAttrs.version}";
-    hash = "sha256-FLL61HsZ6WaWBP9NqrJjhMFSVyVBIpVO0wv+kXMuAaU=";
+    hash = "sha256-SBLv9GsyYmYdxrWmGiMIiFRGl5FA+j2RcSmKz9pMv2E=";
   };
 
   nativeBuildInputs = [ pkg-config ];