Merge branch 'master' into staging-next

Brings in Haskell rebuild.
Hydra nixpkgs: ?compare=1525186

lib/licenses.nix

@@ -457,9 +457,9 @@ lib.mapAttrs (n: v: v // { shortName = n; }) rec {
     fullName = "libpng License";
   };
 
-  libpng2 = {
+  libpng2 = spdx {
-    fullName = "libpng License v2"; # 1.6.36+
+    spdxId = "libpng-2.0"; # Used since libpng 1.6.36.
-    url = "http://www.libpng.org/pub/png/src/libpng-LICENSE.txt";
+    fullName = "PNG Reference Library version 2";
   };
 
   libtiff = spdx {

lib/options.nix

@@ -101,7 +101,7 @@ rec {
   mergeOneOption = loc: defs:
     if defs == [] then abort "This case should never happen."
     else if length defs != 1 then
-      throw "The unique option `${showOption loc}' is defined multiple times, in ${showFiles (getFiles defs)}."
+      throw "The unique option `${showOption loc}' is defined multiple times, in:\n - ${concatStringsSep "\n - " (getFiles defs)}."
     else (head defs).value;
 
   /* "Merge" option definitions by checking that they all have the same value. */

maintainers/maintainer-list.nix

@@ -1333,6 +1333,11 @@
     github = "dmjio";
     name = "David Johnson";
   };
+  dmvianna = {
+    email = "dmlvianna@gmail.com";
+    github = "dmvianna";
+    name = "Daniel Vianna";
+  };
   dochang = {
     email = "dochang@gmail.com";
     github = "dochang";

nixos/modules/installer/tools/nixos-generate-config.pl

@@ -258,6 +258,11 @@ foreach my $path (glob "/sys/class/{block,mmc_host}/*") {
     }
 }
 
+# Add bcache module, if needed.
+my @bcacheDevices = glob("/dev/bcache*");
+if (scalar @bcacheDevices > 0) {
+    push @initrdAvailableKernelModules, "bcache";
+}
 
 my $virt = `systemd-detect-virt`;
 chomp $virt;

nixos/modules/module-list.nix

@@ -92,6 +92,7 @@
   ./programs/bcc.nix
   ./programs/blcr.nix
   ./programs/browserpass.nix
+  ./programs/captive-browser.nix
   ./programs/ccache.nix
   ./programs/cdemu.nix
   ./programs/chromium.nix

nixos/modules/programs/captive-browser.nix

@@ -0,0 +1,108 @@
+{ config, lib, pkgs, ... }:
+
+with lib;
+
+let
+  cfg = config.programs.captive-browser;
+in
+{
+  ###### interface
+
+  options = {
+    programs.captive-browser = {
+      enable = mkEnableOption "captive browser";
+
+      package = mkOption {
+        type = types.package;
+        default = pkgs.captive-browser;
+      };
+
+      interface = mkOption {
+        type = types.str;
+        description = "your public network interface (wlp3s0, wlan0, eth0, ...)";
+      };
+
+      # the options below are the same as in "captive-browser.toml"
+      browser = mkOption {
+        type = types.str;
+        default = concatStringsSep " " [ ''${pkgs.chromium}/bin/chromium''
+                                         ''--user-data-dir=$HOME/.chromium-captive''
+                                         ''--proxy-server="socks5://$PROXY"''
+                                         ''--host-resolver-rules="MAP * ~NOTFOUND , EXCLUDE localhost"''
+                                         ''--no-first-run''
+                                         ''--new-window''
+                                         ''--incognito''
+                                         ''http://cache.nixos.org/''
+                                       ];
+        description = ''
+          the shell (/bin/sh) command executed once the proxy starts.
+          When browser exits, the proxy exits. An extra env var PROXY is available.
+
+          Here, we use a separate Chrome instance in Incognito mode, so that
+          it can run (and be waited for) alongside the default one, and that
+          it maintains no state across runs. To configure this browser open a
+          normal window in it, settings will be preserved.
+
+          @volth: chromium is to open a plain HTTP (not HTTPS nor redirect to HTTPS!) website.
+                  upstream uses http://example.com but I have seen captive portals whose DNS server resolves "example.com" to 127.0.0.1
+        '';
+      };
+
+      dhcp-dns = mkOption {
+        type = types.str;
+        description = ''
+          the shell (/bin/sh) command executed to obtain the DHCP
+          DNS server address. The first match of an IPv4 regex is used.
+          IPv4 only, because let's be real, it's a captive portal.
+        '';
+      };
+
+      socks5-addr = mkOption {
+        type = types.str;
+        default = "localhost:1666";
+        description = ''the listen address for the SOCKS5 proxy server'';
+      };
+    };
+  };
+
+  ###### implementation
+
+  config = mkIf cfg.enable {
+
+    programs.captive-browser.dhcp-dns = mkOptionDefault (
+      if config.networking.networkmanager.enable then
+        "${pkgs.networkmanager}/bin/nmcli dev show ${escapeShellArg cfg.interface} | ${pkgs.gnugrep}/bin/fgrep IP4.DNS"
+      else if config.networking.dhcpcd.enable then
+        "${pkgs.dhcpcd}/bin/dhcpcd -U ${escapeShellArg cfg.interface} | ${pkgs.gnugrep}/bin/fgrep domain_name_servers"
+      else if config.networking.useNetworkd then
+        "${cfg.package}/bin/systemd-networkd-dns ${escapeShellArg cfg.interface}"
+      else
+        "${config.security.wrapperDir}/udhcpc --quit --now -f -i ${escapeShellArg cfg.interface} -O dns --script ${
+            pkgs.writeScript "udhcp-script" ''
+              #!/bin/sh
+              if [ "$1" = bound ]; then
+                echo "$dns"
+              fi
+            ''}"
+    );
+
+    security.wrappers.udhcpc = {
+      capabilities  = "cap_net_raw+p";
+      source        = "${pkgs.busybox}/bin/udhcpc";
+    };
+
+    security.wrappers.captive-browser = {
+      capabilities  = "cap_net_raw+p";
+      source        = pkgs.writeScript "captive-browser" ''
+                        #!${pkgs.bash}/bin/bash
+                        export XDG_CONFIG_HOME=${pkgs.writeTextDir "captive-browser.toml" ''
+                                                  browser = """${cfg.browser}"""
+                                                  dhcp-dns = """${cfg.dhcp-dns}"""
+                                                  socks5-addr = """${cfg.socks5-addr}"""
+                                                  bind-device = """${cfg.interface}"""
+                                                ''}
+                        exec ${cfg.package}/bin/captive-browser
+                      '';
+    };
+  };
+}

nixos/modules/services/databases/cassandra.nix

@@ -8,18 +8,21 @@ let
   cassandraConfig = flip recursiveUpdate cfg.extraConfig
     ({ commitlog_sync = "batch";
        commitlog_sync_batch_window_in_ms = 2;
+       start_native_transport = cfg.allowClients;
+       cluster_name = cfg.clusterName;
        partitioner = "org.apache.cassandra.dht.Murmur3Partitioner";
        endpoint_snitch = "SimpleSnitch";
-       seed_provider =
-         [{ class_name = "org.apache.cassandra.locator.SimpleSeedProvider";
-            parameters = [ { seeds = "127.0.0.1"; } ];
-         }];
        data_file_directories = [ "${cfg.homeDir}/data" ];
        commitlog_directory = "${cfg.homeDir}/commitlog";
        saved_caches_directory = "${cfg.homeDir}/saved_caches";
-     } // (if builtins.compareVersions cfg.package.version "3" >= 0
+     } // (lib.optionalAttrs (cfg.seedAddresses != []) {
-             then { hints_directory = "${cfg.homeDir}/hints"; }
+       seed_provider = [{
-             else {})
+         class_name = "org.apache.cassandra.locator.SimpleSeedProvider";
+         parameters = [ { seeds = concatStringsSep "," cfg.seedAddresses; } ];
+       }];
+     }) // (lib.optionalAttrs (lib.versionAtLeast cfg.package.version "3") {
+       hints_directory = "${cfg.homeDir}/hints";
+     })
     );
   cassandraConfigWithAddresses = cassandraConfig //
     ( if cfg.listenAddress == null
@@ -39,15 +42,42 @@ let
         mkdir -p "$out"
 
         echo "$cassandraYaml" > "$out/cassandra.yaml"
-        ln -s "$cassandraEnvPkg" "$out/cassandra-env.sh"
         ln -s "$cassandraLogbackConfig" "$out/logback.xml"
+
+        cp "$cassandraEnvPkg" "$out/cassandra-env.sh"
+
+        # Delete default JMX Port, otherwise we can't set it using env variable
+        sed -i '/JMX_PORT="7199"/d' "$out/cassandra-env.sh"
+
+        # Delete default password file
+        sed -i '/-Dcom.sun.management.jmxremote.password.file=\/etc\/cassandra\/jmxremote.password/d' "$out/cassandra-env.sh"
       '';
     };
+  defaultJmxRolesFile = builtins.foldl'
+     (left: right: left + right) ""
+     (map (role: "${role.username} ${role.password}") cfg.jmxRoles);
+  fullJvmOptions = cfg.jvmOpts
+    ++ lib.optionals (cfg.jmxRoles != []) [
+      "-Dcom.sun.management.jmxremote.authenticate=true"
+      "-Dcom.sun.management.jmxremote.password.file=${cfg.jmxRolesFile}"
+    ]
+    ++ lib.optionals cfg.remoteJmx [
+      "-Djava.rmi.server.hostname=${cfg.rpcAddress}"
+    ];
 in {
   options.services.cassandra = {
     enable = mkEnableOption ''
       Apache Cassandra – Scalable and highly available database.
     '';
+    clusterName = mkOption {
+      type = types.str;
+      default = "NixOS Test Cluster";
+      description = ''
+        The name of the cluster.
+        This setting prevents nodes in one logical cluster from joining
+        another. All nodes in a cluster must have the same value.
+      '';
+    };
     user = mkOption {
       type = types.str;
       default = defaultUser;
@@ -162,6 +192,28 @@ in {
         XML logback configuration for cassandra
       '';
     };
+    seedAddresses = mkOption {
+      type = types.listOf types.str;
+      default = [ "127.0.0.1" ];
+      description = ''
+        The addresses of hosts designated as contact points in the cluster. A
+        joining node contacts one of the nodes in the seeds list to learn the
+        topology of the ring.
+        Set to 127.0.0.1 for a single node cluster.
+      '';
+    };
+    allowClients = mkOption {
+      type = types.bool;
+      default = true;
+      description = ''
+        Enables or disables the native transport server (CQL binary protocol).
+        This server uses the same address as the <literal>rpcAddress</literal>,
+        but the port it uses is not <literal>rpc_port</literal> but
+        <literal>native_transport_port</literal>. See the official Cassandra
+        docs for more information on these variables and set them using
+        <literal>extraConfig</literal>.
+      '';
+    };
     extraConfig = mkOption {
       type = types.attrs;
       default = {};
@@ -178,11 +230,11 @@ in {
       example = literalExample "null";
       description = ''
           Set the interval how often full repairs are run, i.e.
-          `nodetool repair --full` is executed. See
+          <literal>nodetool repair --full</literal> is executed. See
           https://cassandra.apache.org/doc/latest/operating/repair.html
           for more information.
 
-          Set to `null` to disable full repairs.
+          Set to <literal>null</literal> to disable full repairs.
         '';
     };
     fullRepairOptions = mkOption {
@@ -199,11 +251,11 @@ in {
       example = literalExample "null";
       description = ''
           Set the interval how often incremental repairs are run, i.e.
-          `nodetool repair` is executed. See
+          <literal>nodetool repair</literal> is executed. See
           https://cassandra.apache.org/doc/latest/operating/repair.html
           for more information.
 
-          Set to `null` to disable incremental repairs.
+          Set to <literal>null</literal> to disable incremental repairs.
         '';
     };
     incrementalRepairOptions = mkOption {
@@ -214,20 +266,135 @@ in {
           Options passed through to the incremental repair command.
         '';
     };
+    maxHeapSize = mkOption {
+      type = types.nullOr types.string;
+      default = null;
+      example = "4G";
+      description = ''
+        Must be left blank or set together with heapNewSize.
+        If left blank a sensible value for the available amount of RAM and CPU
+        cores is calculated.
+
+        Override to set the amount of memory to allocate to the JVM at
+        start-up. For production use you may wish to adjust this for your
+        environment. MAX_HEAP_SIZE is the total amount of memory dedicated
+        to the Java heap. HEAP_NEWSIZE refers to the size of the young
+        generation.
+
+        The main trade-off for the young generation is that the larger it
+        is, the longer GC pause times will be. The shorter it is, the more
+        expensive GC will be (usually).
+      '';
+    };
+    heapNewSize = mkOption {
+      type = types.nullOr types.string;
+      default = null;
+      example = "800M";
+      description = ''
+        Must be left blank or set together with heapNewSize.
+        If left blank a sensible value for the available amount of RAM and CPU
+        cores is calculated.
+
+        Override to set the amount of memory to allocate to the JVM at
+        start-up. For production use you may wish to adjust this for your
+        environment. HEAP_NEWSIZE refers to the size of the young
+        generation.
+
+        The main trade-off for the young generation is that the larger it
+        is, the longer GC pause times will be. The shorter it is, the more
+        expensive GC will be (usually).
+
+        The example HEAP_NEWSIZE assumes a modern 8-core+ machine for decent pause
+        times. If in doubt, and if you do not particularly want to tweak, go with
+        100 MB per physical CPU core.
+      '';
+    };
+    mallocArenaMax = mkOption {
+      type = types.nullOr types.int;
+      default = null;
+      example = 4;
+      description = ''
+        Set this to control the amount of arenas per-thread in glibc.
+      '';
+    };
+    remoteJmx = mkOption {
+      type = types.bool;
+      default = false;
+      description = ''
+        Cassandra ships with JMX accessible *only* from localhost.
+        To enable remote JMX connections set to true.
+
+        Be sure to also enable authentication and/or TLS.
+        See: https://wiki.apache.org/cassandra/JmxSecurity
+      '';
+    };
+    jmxPort = mkOption {
+      type = types.int;
+      default = 7199;
+      description = ''
+        Specifies the default port over which Cassandra will be available for
+        JMX connections.
+        For security reasons, you should not expose this port to the internet.
+        Firewall it if needed.
+      '';
+    };
+    jmxRoles = mkOption {
+      default = [];
+      description = ''
+        Roles that are allowed to access the JMX (e.g. nodetool)
+        BEWARE: The passwords will be stored world readable in the nix-store.
+                It's recommended to use your own protected file using
+                <literal>jmxRolesFile</literal>
+
+        Doesn't work in versions older than 3.11 because they don't like that
+        it's world readable.
+      '';
+      type = types.listOf (types.submodule {
+        options = {
+          username = mkOption {
+            type = types.string;
+            description = "Username for JMX";
+          };
+          password = mkOption {
+            type = types.string;
+            description = "Password for JMX";
+          };
+        };
+      });
+    };
+    jmxRolesFile = mkOption {
+      type = types.nullOr types.path;
+      default = if (lib.versionAtLeast cfg.package.version "3.11")
+                then pkgs.writeText "jmx-roles-file" defaultJmxRolesFile
+                else null;
+      example = "/var/lib/cassandra/jmx.password";
+      description = ''
+        Specify your own jmx roles file.
+
+        Make sure the permissions forbid "others" from reading the file if
+        you're using Cassandra below version 3.11.
+      '';
+    };
   };
 
   config = mkIf cfg.enable {
     assertions =
-      [ { assertion =
+      [ { assertion = (cfg.listenAddress == null) != (cfg.listenInterface == null);
-          (cfg.listenAddress == null || cfg.listenInterface == null)
-          && !(cfg.listenAddress == null && cfg.listenInterface == null);
           message = "You have to set either listenAddress or listenInterface";
         }
-        { assertion =
+        { assertion = (cfg.rpcAddress == null) != (cfg.rpcInterface == null);
-          (cfg.rpcAddress == null || cfg.rpcInterface == null)
-          && !(cfg.rpcAddress == null && cfg.rpcInterface == null);
           message = "You have to set either rpcAddress or rpcInterface";
         }
+        { assertion = (cfg.maxHeapSize == null) == (cfg.heapNewSize == null);
+          message = "If you set either of maxHeapSize or heapNewSize you have to set both";
+        }
+        { assertion = cfg.remoteJmx -> cfg.jmxRolesFile != null;
+          message = ''
+            If you want JMX available remotely you need to set a password using
+            <literal>jmxRoles</literal> or <literal>jmxRolesFile</literal> if
+            using Cassandra older than v3.11.
+          '';
+        }
       ];
     users = mkIf (cfg.user == defaultUser) {
       extraUsers."${defaultUser}" =
@@ -245,7 +412,12 @@ in {
         after = [ "network.target" ];
         environment =
           { CASSANDRA_CONF = "${cassandraEtc}";
-            JVM_OPTS = builtins.concatStringsSep " " cfg.jvmOpts;
+            JVM_OPTS = builtins.concatStringsSep " " fullJvmOptions;
+            MAX_HEAP_SIZE = toString cfg.maxHeapSize;
+            HEAP_NEWSIZE = toString cfg.heapNewSize;
+            MALLOC_ARENA_MAX = toString cfg.mallocArenaMax;
+            LOCAL_JMX = if cfg.remoteJmx then "no" else "yes";
+            JMX_PORT = toString cfg.jmxPort;
           };
         wantedBy = [ "multi-user.target" ];
         serviceConfig =

nixos/modules/services/misc/gitea.nix

@@ -159,7 +159,8 @@ in
 
         socket = mkOption {
           type = types.nullOr types.path;
-          default = null;
+          default = if (cfg.database.createDatabase && usePostgresql) then "/run/postgresql" else if (cfg.database.createDatabase && useMysql) then "/run/mysqld/mysqld.sock" else null;
+          defaultText = "null";
           example = "/run/mysqld/mysqld.sock";
           description = "Path to the unix socket file to use for authentication.";
         };
@@ -173,10 +174,7 @@ in
         createDatabase = mkOption {
           type = types.bool;
           default = true;
-          description = ''
+          description = "Whether to create a local database automatically.";
-            Whether to create a local postgresql database automatically.
-            This only applies if database type "postgres" is selected.
-          '';
         };
       };
 
@@ -277,7 +275,46 @@ in
   };
 
   config = mkIf cfg.enable {
-    services.postgresql.enable = mkIf usePostgresql (mkDefault true);
+    assertions = [
+      { assertion = cfg.database.createDatabase -> cfg.database.user == cfg.user;
+        message = "services.gitea.database.user must match services.gitea.user if the database is to be automatically provisioned";
+      }
+    ];
+
+    services.postgresql = optionalAttrs (usePostgresql && cfg.database.createDatabase) {
+      enable = mkDefault true;
+
+      ensureDatabases = [ cfg.database.name ];
+      ensureUsers = [
+        { name = cfg.database.user;
+          ensurePermissions = { "DATABASE ${cfg.database.name}" = "ALL PRIVILEGES"; };
+        }
+      ];
+    };
+
+    services.mysql = optionalAttrs (useMysql && cfg.database.createDatabase) {
+      enable = mkDefault true;
+      package = mkDefault pkgs.mariadb;
+
+      ensureDatabases = [ cfg.database.name ];
+      ensureUsers = [
+        { name = cfg.database.user;
+          ensurePermissions = { "${cfg.database.name}.*" = "ALL PRIVILEGES"; };
+        }
+      ];
+    };
+
+    systemd.tmpfiles.rules = [
+      "d '${cfg.stateDir}' - ${cfg.user} gitea - -"
+      "d '${cfg.stateDir}/conf' - ${cfg.user} gitea - -"
+      "d '${cfg.stateDir}/custom/conf' - ${cfg.user} gitea - -"
+      "d '${cfg.repositoryRoot}' - ${cfg.user} gitea - -"
+      "Z '${cfg.stateDir}' - ${cfg.user} gitea - -"
+
+      # If we have a folder or symlink with gitea locales, remove it
+      # And symlink the current gitea locales in place
+      "L+ '${cfg.stateDir}/conf/locale' - - - - ${gitea.out}/locale"
+    ];
 
     systemd.services.gitea = {
       description = "gitea";
@@ -289,12 +326,8 @@ in
         runConfig = "${cfg.stateDir}/custom/conf/app.ini";
         secretKey = "${cfg.stateDir}/custom/conf/secret_key";
       in ''
-        # Make sure that the stateDir exists, as well as the conf dir in there
-        mkdir -p ${cfg.stateDir}/conf
-
         # copy custom configuration and generate a random secret key if needed
         ${optionalString (cfg.useWizard == false) ''
-          mkdir -p ${cfg.stateDir}/custom/conf
           cp -f ${configFile} ${runConfig}
 
           if [ ! -e ${secretKey} ]; then
@@ -309,7 +342,6 @@ in
           chmod 640 ${runConfig} ${secretKey}
         ''}
 
-        mkdir -p ${cfg.repositoryRoot}
         # update all hooks' binary paths
         HOOKS=$(find ${cfg.repositoryRoot} -mindepth 4 -maxdepth 6 -type f -wholename "*git/hooks/*")
         if [ "$HOOKS" ]
@@ -319,43 +351,19 @@ in
           sed -ri 's,/nix/store/[a-z0-9.-]+/bin/bash,${pkgs.bash}/bin/bash,g' $HOOKS
           sed -ri 's,/nix/store/[a-z0-9.-]+/bin/perl,${pkgs.perl}/bin/perl,g' $HOOKS
         fi
-        # If we have a folder or symlink with gitea locales, remove it
+
-        if [ -e ${cfg.stateDir}/conf/locale ]
-        then
-          rm -r ${cfg.stateDir}/conf/locale
-        fi
-        # And symlink the current gitea locales in place
-        ln -s ${gitea.out}/locale ${cfg.stateDir}/conf/locale
         # update command option in authorized_keys
         if [ -r ${cfg.stateDir}/.ssh/authorized_keys ]
         then
           sed -ri 's,/nix/store/[a-z0-9.-]+/bin/gitea,${gitea.bin}/bin/gitea,g' ${cfg.stateDir}/.ssh/authorized_keys
         fi
-      '' + optionalString (usePostgresql && cfg.database.createDatabase) ''
-        if ! test -e "${cfg.stateDir}/db-created"; then
-          echo "CREATE ROLE ${cfg.database.user}
-                  WITH ENCRYPTED PASSWORD '$(head -n1 ${cfg.database.passwordFile})'
-                  NOCREATEDB NOCREATEROLE LOGIN"   |
-            ${pkgs.sudo}/bin/sudo -u ${pg.superUser} ${pg.package}/bin/psql
-          ${pkgs.sudo}/bin/sudo -u ${pg.superUser} \
-            ${pg.package}/bin/createdb             \
-            --owner=${cfg.database.user}           \
-            --encoding=UTF8                        \
-            --lc-collate=C                         \
-            --lc-ctype=C                           \
-            --template=template0                   \
-            ${cfg.database.name}
-          touch "${cfg.stateDir}/db-created"
-        fi
-      '' + ''
-        chown ${cfg.user} -R ${cfg.stateDir}
       '';
 
       serviceConfig = {
         Type = "simple";
         User = cfg.user;
+        Group = "gitea";
         WorkingDirectory = cfg.stateDir;
-        PermissionsStartOnly = true;
         ExecStart = "${gitea.bin}/bin/gitea web";
         Restart = "always";
       };
@@ -367,15 +375,17 @@ in
       };
     };
 
-    users = mkIf (cfg.user == "gitea") {
+    users.users = mkIf (cfg.user == "gitea") {
-      users.gitea = {
+      gitea = {
         description = "Gitea Service";
         home = cfg.stateDir;
-        createHome = true;
         useDefaultShell = true;
+        group = "gitea";
       };
     };
 
+    users.groups.gitea = {};
+
     warnings = optional (cfg.database.password != "")
       ''config.services.gitea.database.password will be stored as plaintext
         in the Nix store. Use database.passwordFile instead.'';

nixos/modules/virtualisation/containers.nix

@@ -465,20 +465,24 @@ in
                 merge = loc: defs: (import ../../lib/eval-config.nix {
                   inherit system;
                   modules =
-                    let extraConfig =
+                    let
-                      { boot.isContainer = true;
+                      extraConfig = {
-                        networking.hostName = mkDefault name;
+                        _file = "module at ${__curPos.file}:${toString __curPos.line}";
-                        networking.useDHCP = false;
+                        config = {
-                        assertions = [
+                          boot.isContainer = true;
-                          {
+                          networking.hostName = mkDefault name;
-                            assertion =  config.privateNetwork -> stringLength name < 12;
+                          networking.useDHCP = false;
-                            message = ''
+                          assertions = [
-                              Container name `${name}` is too long: When `privateNetwork` is enabled, container names can
+                            {
-                              not be longer than 11 characters, because the container's interface name is derived from it.
+                              assertion =  config.privateNetwork -> stringLength name < 12;
-                              This might be fixed in the future. See https://github.com/NixOS/nixpkgs/issues/38509
+                              message = ''
-                            '';
+                                Container name `${name}` is too long: When `privateNetwork` is enabled, container names can
-                          }
+                                not be longer than 11 characters, because the container's interface name is derived from it.
-                        ];
+                                This might be fixed in the future. See https://github.com/NixOS/nixpkgs/issues/38509
+                              '';
+                            }
+                          ];
+                        };
                       };
                     in [ extraConfig ] ++ (map (x: x.value) defs);
                   prefix = [ "containers" name ];

nixos/tests/all-tests.nix

@@ -36,6 +36,7 @@ in
   borgbackup = handleTest ./borgbackup.nix {};
   buildbot = handleTest ./buildbot.nix {};
   cadvisor = handleTestOn ["x86_64-linux"] ./cadvisor.nix {};
+  cassandra = handleTest ./cassandra.nix {};
   ceph = handleTestOn ["x86_64-linux"] ./ceph.nix {};
   certmgr = handleTest ./certmgr.nix {};
   cfssl = handleTestOn ["x86_64-linux"] ./cfssl.nix {};

nixos/tests/cassandra.nix

@@ -1,26 +1,43 @@
-import ./make-test.nix ({ pkgs, ...}:
+import ./make-test.nix ({ pkgs, lib, ... }:
 let
   # Change this to test a different version of Cassandra:
   testPackage = pkgs.cassandra;
-  cassandraCfg = 
+  clusterName = "NixOS Automated-Test Cluster";
+
+  testRemoteAuth = lib.versionAtLeast testPackage.version "3.11";
+  jmxRoles = [{ username = "me"; password = "password"; }];
+  jmxRolesFile = ./cassandra-jmx-roles;
+  jmxAuthArgs = "-u ${(builtins.elemAt jmxRoles 0).username} -pw ${(builtins.elemAt jmxRoles 0).password}";
+
+  # Would usually be assigned to 512M
+  numMaxHeapSize = "400";
+  getHeapLimitCommand = ''
+    nodetool info | grep "^Heap Memory" | awk \'{print $NF}\'
+  '';
+  checkHeapLimitCommand = ''
+    [ 1 -eq "$(echo "$(${getHeapLimitCommand}) < ${numMaxHeapSize}" | ${pkgs.bc}/bin/bc)" ]
+  '';
+
+  cassandraCfg = ipAddress:
     { enable = true;
-      listenAddress = null;
+      inherit clusterName;
-      listenInterface = "eth1";
+      listenAddress = ipAddress;
-      rpcAddress = null;
+      rpcAddress = ipAddress;
-      rpcInterface = "eth1";
+      seedAddresses = [ "192.168.1.1" ];
-      extraConfig =
-        { start_native_transport = true;
-          seed_provider =
-            [{ class_name = "org.apache.cassandra.locator.SimpleSeedProvider";
-               parameters = [ { seeds = "cass0"; } ];
-            }];
-        };
       package = testPackage;
+      maxHeapSize = "${numMaxHeapSize}M";
+      heapNewSize = "100M";
     };
-  nodeCfg = extra: {pkgs, config, ...}:
+  nodeCfg = ipAddress: extra: {pkgs, config, ...}:
     { environment.systemPackages = [ testPackage ];
-      networking.firewall.enable = false;
+      networking = {
-      services.cassandra = cassandraCfg // extra;
+        firewall.allowedTCPPorts = [ 7000 7199 9042 ];
+        useDHCP = false;
+        interfaces.eth1.ipv4.addresses = pkgs.lib.mkOverride 0 [
+          { address = ipAddress; prefixLength = 24; }
+        ];
+      };
+      services.cassandra = cassandraCfg ipAddress // extra;
       virtualisation.memorySize = 1024;
     };
 in
@@ -28,40 +45,65 @@ in
   name = "cassandra-ci";
 
   nodes = {
-    cass0 = nodeCfg {};
+    cass0 = nodeCfg "192.168.1.1" {};
-    cass1 = nodeCfg {};
+    cass1 = nodeCfg "192.168.1.2" (lib.optionalAttrs testRemoteAuth { inherit jmxRoles; remoteJmx = true; });
-    cass2 = nodeCfg { jvmOpts = [ "-Dcassandra.replace_address=cass1" ]; };
+    cass2 = nodeCfg "192.168.1.3" { jvmOpts = [ "-Dcassandra.replace_address=cass1" ]; };
   };
 
   testScript = ''
-    subtest "timers exist", sub {
+    # Check configuration
+    subtest "Timers exist", sub {
       $cass0->succeed("systemctl list-timers | grep cassandra-full-repair.timer");
       $cass0->succeed("systemctl list-timers | grep cassandra-incremental-repair.timer");
     };
-    subtest "can connect via cqlsh", sub {
+    subtest "Can connect via cqlsh", sub {
       $cass0->waitForUnit("cassandra.service");
       $cass0->waitUntilSucceeds("nc -z cass0 9042");
       $cass0->succeed("echo 'show version;' | cqlsh cass0");
     };
-    subtest "nodetool is operational", sub {
+    subtest "Nodetool is operational", sub {
       $cass0->waitForUnit("cassandra.service");
       $cass0->waitUntilSucceeds("nc -z localhost 7199");
       $cass0->succeed("nodetool status --resolve-ip | egrep '^UN[[:space:]]+cass0'");
     };
-    subtest "bring up cluster", sub {
+    subtest "Cluster name was set", sub {
+      $cass0->waitForUnit("cassandra.service");
+      $cass0->waitUntilSucceeds("nc -z localhost 7199");
+      $cass0->waitUntilSucceeds("nodetool describecluster | grep 'Name: ${clusterName}'");
+    };
+    subtest "Heap limit set correctly", sub {
+      # Nodetool takes a while until it can display info
+      $cass0->waitUntilSucceeds('nodetool info');
+      $cass0->succeed('${checkHeapLimitCommand}');
+    };
+
+    # Check cluster interaction
+    subtest "Bring up cluster", sub {
       $cass1->waitForUnit("cassandra.service");
-      $cass1->waitUntilSucceeds("nodetool status | egrep -c '^UN' | grep 2");
+      $cass1->waitUntilSucceeds("nodetool ${jmxAuthArgs} status | egrep -c '^UN' | grep 2");
       $cass0->succeed("nodetool status --resolve-ip | egrep '^UN[[:space:]]+cass1'");
     };
-    subtest "break and fix node", sub {
+  '' + lib.optionalString testRemoteAuth ''
+    subtest "Remote authenticated jmx", sub {
+      # Doesn't work if not enabled
+      $cass0->waitUntilSucceeds("nc -z localhost 7199");
+      $cass1->fail("nc -z 192.168.1.1 7199");
+      $cass1->fail("nodetool -h 192.168.1.1 status");
+
+      # Works if enabled
+      $cass1->waitUntilSucceeds("nc -z localhost 7199");
+      $cass0->succeed("nodetool -h 192.168.1.2 ${jmxAuthArgs} status");
+    };
+  '' + ''
+    subtest "Break and fix node", sub {
       $cass1->block;
       $cass0->waitUntilSucceeds("nodetool status --resolve-ip | egrep -c '^DN[[:space:]]+cass1'");
       $cass0->succeed("nodetool status | egrep -c '^UN'  | grep 1");
       $cass1->unblock;
-      $cass1->waitUntilSucceeds("nodetool status | egrep -c '^UN'  | grep 2");
+      $cass1->waitUntilSucceeds("nodetool ${jmxAuthArgs} status | egrep -c '^UN'  | grep 2");
       $cass0->succeed("nodetool status | egrep -c '^UN'  | grep 2");
     };
-    subtest "replace crashed node", sub {
+    subtest "Replace crashed node", sub {
       $cass1->crash;
       $cass2->waitForUnit("cassandra.service");
       $cass0->waitUntilFails("nodetool status --resolve-ip | egrep '^UN[[:space:]]+cass1'");

nixos/tests/gitea.nix

@@ -13,18 +13,8 @@ with pkgs.lib;
 
     machine =
       { config, pkgs, ... }:
-      { services.mysql.enable = true;
+      { services.gitea.enable = true;
-        services.mysql.package = pkgs.mariadb;
-        services.mysql.ensureDatabases = [ "gitea" ];
-        services.mysql.ensureUsers = [
-          { name = "gitea";
-            ensurePermissions = { "gitea.*" = "ALL PRIVILEGES"; };
-          }
-        ];
-
-        services.gitea.enable = true;
         services.gitea.database.type = "mysql";
-        services.gitea.database.socket = "/run/mysqld/mysqld.sock";
       };
 
     testScript = ''
@@ -42,10 +32,8 @@ with pkgs.lib;
 
     machine =
       { config, pkgs, ... }:
-      {
+      { services.gitea.enable = true;
-        services.gitea.enable = true;
         services.gitea.database.type = "postgres";
-        services.gitea.database.passwordFile = pkgs.writeText "db-password" "secret";
       };
 
     testScript = ''

pkgs/applications/audio/adlplug/default.nix

@@ -5,13 +5,13 @@
 
 stdenv.mkDerivation rec {
   inherit pname;
-  version = "1.0.0";
+  version = "1.0.1";
 
   src = fetchFromGitHub {
     owner = "jpcima";
     repo = "ADLplug";
     rev = "v${version}";
-    sha256 = "1rpd7v1rx74cv7nhs70ah0bly314rjzj70cp30mvhns2hzk66s3c";
+    sha256 = "0n9srdlgl1j528ap5xmllrqs1w6ibc5yf9sphvl1q9kjnizxrs2c";
     fetchSubmodules = true;
   };
 
@@ -24,7 +24,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ cmake pkgconfig ];
 
   meta = with stdenv.lib; {
-    description = "Synthesizer plugin for ADLMIDI and OPNMIDI (VST/LV2)";
+    description = "OPL3 and OPN2 FM Chip Synthesizer";
     homepage = src.meta.homepage;
     license = licenses.boost;
     platforms = platforms.linux;

pkgs/applications/audio/deadbeef/plugins/infobar.nix

@@ -24,7 +24,8 @@ stdenv.mkDerivation rec {
   '';
 
   meta = with stdenv.lib; {
-    description = "DeadBeeF Infobar Plugin";
+    broken = true; # crashes DeaDBeeF and is abandoned (https://bitbucket.org/dsimbiriatin/deadbeef-infobar/issues/38/infobar-causes-deadbeef-180-to-crash)
+    description = "DeaDBeeF Infobar Plugin";
     homepage = https://bitbucket.org/dsimbiriatin/deadbeef-infobar;
     license = licenses.gpl2Plus;
     maintainers = [ maintainers.jtojnar ];

pkgs/applications/audio/deadbeef/plugins/lyricbar.nix

@@ -0,0 +1,26 @@
+{ stdenv, fetchFromGitHub, pkgconfig, deadbeef, gtkmm3, libxmlxx3 }:
+
+stdenv.mkDerivation rec {
+  pname = "deadbeef-lyricbar-plugin";
+  version = "unstable-2019-01-29";
+
+  src = fetchFromGitHub {
+    owner = "C0rn3j";
+    repo = "deadbeef-lyricbar";
+    rev = "8f99b92ef827c451c43fc7dff38ae4f15c355e8e";
+    sha256 = "108hx5530f4xm8p9m2bk79nq7jkhcj39ad3vmxb2y6h6l2zv5kwl";
+  };
+
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ deadbeef gtkmm3 libxmlxx3 ];
+
+  buildFlags = [ "gtk3" ];
+
+  meta = with stdenv.lib; {
+    description = "Plugin for DeaDBeeF audio player that fetches and shows the song’s lyrics";
+    homepage = "https://github.com/C0rn3j/deadbeef-lyricbar";
+    license = licenses.mit;
+    maintainers = [ maintainers.jtojnar ];
+    platforms = platforms.linux;
+  };
+}

pkgs/applications/audio/pulseaudio-dlna/default.nix

@@ -4,7 +4,7 @@
 , faacSupport ? false, faac ? null
 , flacSupport ? true, flac ? null
 , soxSupport ? true, sox ? null
-, vorbisSupport ? true, vorbisTools ? null 
+, vorbisSupport ? true, vorbisTools ? null
 }:
 
 assert mp3Support -> lame != null;
@@ -14,7 +14,10 @@ assert flacSupport -> flac != null;
 assert soxSupport -> sox != null;
 assert vorbisSupport -> vorbisTools != null;
 
-pythonPackages.buildPythonApplication rec {
+let
+  zeroconf = pythonPackages.callPackage ./zeroconf.nix { };
+
+in pythonPackages.buildPythonApplication rec {
   pname = "pulseaudio-dlna";
   version = "2017-11-01";
 
@@ -24,13 +27,14 @@ pythonPackages.buildPythonApplication rec {
     rev = "4472928dd23f274193f14289f59daec411023ab0";
     sha256 = "1dfn7036vrq49kxv4an7rayypnm5dlawsf02pfsldw877hzdamqk";
   };
-  
+
   # pulseaudio-dlna has no tests
   doCheck = false;
 
   propagatedBuildInputs = with pythonPackages; [
     dbus-python docopt requests setproctitle protobuf psutil futures
-    chardet notify2 netifaces pyroute2 pygobject2 lxml zeroconf ]
+    chardet notify2 netifaces pyroute2 pygobject2 lxml ]
+    ++ [ zeroconf ]
     ++ stdenv.lib.optional mp3Support lame
     ++ stdenv.lib.optional opusSupport opusTools
     ++ stdenv.lib.optional faacSupport faac

pkgs/applications/audio/pulseaudio-dlna/zeroconf.nix

@@ -0,0 +1,31 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, ifaddr
+, typing
+, isPy27
+, pythonOlder
+, netifaces
+, six
+, enum-compat
+}:
+
+buildPythonPackage rec {
+  pname = "zeroconf";
+  version = "0.19.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0ykzg730n915qbrq9bn5pn06bv6rb5zawal4sqjyfnjjm66snkj3";
+  };
+
+  propagatedBuildInputs = [ netifaces six enum-compat ifaddr ]
+    ++ stdenv.lib.optionals (pythonOlder "3.5") [ typing ];
+
+  meta = with stdenv.lib; {
+    description = "A pure python implementation of multicast DNS service discovery";
+    homepage = https://github.com/jstasiak/python-zeroconf;
+    license = licenses.lgpl21;
+    maintainers = [ ];
+  };
+}

pkgs/applications/graphics/gimp/default.nix

@@ -9,11 +9,11 @@ let
   inherit (python2Packages) pygtk wrapPython python;
 in stdenv.mkDerivation rec {
   pname = "gimp";
-  version = "2.10.10";
+  version = "2.10.12";
 
   src = fetchurl {
     url = "http://download.gimp.org/pub/gimp/v${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.bz2";
-    sha256 = "0xwck5nbpb945s1cyij3kfqw1pchbhx8i5vf5hgywyjw4r1z5l8j";
+    sha256 = "0wdcr8d2ink4swn5r4v13bsiya6s3xm4ya97sdbhs4l40y7bb03x";
   };
 
   nativeBuildInputs = [ pkgconfig intltool gettext wrapPython ];

pkgs/applications/misc/cura/default.nix

@@ -1,4 +1,4 @@
-{ mkDerivation, lib, fetchFromGitHub, cmake, python3, qtbase, qtquickcontrols2, qtgraphicaleffects, curaengine }:
+{ mkDerivation, lib, fetchFromGitHub, cmake, python3, qtbase, qtquickcontrols2, qtgraphicaleffects, curaengine, plugins ? [] }:
 
 mkDerivation rec {
   name = "cura-${version}";
@@ -21,7 +21,7 @@ mkDerivation rec {
   buildInputs = [ qtbase qtquickcontrols2 qtgraphicaleffects ];
   propagatedBuildInputs = with python3.pkgs; [
     libsavitar numpy-stl pyserial requests uranium zeroconf
-  ];
+  ] ++ plugins;
   nativeBuildInputs = [ cmake python3.pkgs.wrapPython ];
 
   cmakeFlags = [
@@ -37,6 +37,10 @@ mkDerivation rec {
   postInstall = ''
     mkdir -p $out/share/cura/resources/materials
     cp ${materials}/*.fdm_material $out/share/cura/resources/materials/
+    mkdir -p $out/lib/cura/plugins
+    for plugin in ${toString plugins}; do
+      ln -s $plugin/lib/cura/plugins/* $out/lib/cura/plugins
+    done
   '';
 
   postFixup = ''

pkgs/applications/misc/cura/plugins.nix

@@ -0,0 +1,34 @@
+{ stdenv, fetchFromGitHub, cmake, python3Packages }:
+
+let
+
+  self = {
+
+    octoprint = stdenv.mkDerivation rec {
+      pname = "Cura-OctoPrintPlugin";
+      version = "3.5.5";
+
+      src = fetchFromGitHub {
+        owner = "fieldOfView";
+        repo = pname;
+        rev = "d05a9a4c1a01c584d5cec4f4b7d170077235467a";
+        sha256 = "0ik69g3kbn7rz2wh0cfq9ww8x222kagd8jvsd4xlqgq4yrf0jk7x";
+      };
+
+      nativeBuildInputs = [ cmake ];
+
+      propagatedBuildInputs = with python3Packages; [
+        netifaces
+      ];
+
+      meta = with stdenv.lib; {
+        description = "Enables printing directly to OctoPrint and monitoring the process";
+        homepage = "https://github.com/fieldOfView/Cura-OctoPrintPlugin";
+        license = licenses.agpl3;
+        maintainers = with maintainers; [ gebner ];
+      };
+    };
+
+  };
+
+in self

pkgs/applications/networking/browsers/browsh/default.nix

@@ -1,14 +1,14 @@
 { stdenv, buildGoPackage, fetchurl, fetchFromGitHub, go-bindata }:
 
 let
-  version = "1.5.0";
+  version = "1.5.2";
 
   # TODO: must build the extension instead of downloading it. But since it's
   # literally an asset that is indifferent regardless of the platform, this
   # might be just enough.
   webext = fetchurl {
     url = "https://github.com/browsh-org/browsh/releases/download/v${version}/browsh-${version}-an.fx.xpi";
-    sha256 = "063m6rcdyf2zcrswkm56k8h3w15124bw5iykklzm60q5jk4ywn3f";
+    sha256 = "0b9aycyif0hfhfkivlnvinr13r9h4qyxx768286966p67napbd63";
   };
 
 in buildGoPackage rec {
@@ -23,7 +23,7 @@ in buildGoPackage rec {
     owner = "browsh-org";
     repo = "browsh";
     rev = "v${version}";
-    sha256 = "14addyb1zdk1b9mizfxdagyzlkd9nf5gawnbrs44j5a3ggnl14ln";
+    sha256 = "1z78kgxrbi2jy20rbq6kx5mjk4gpg58w4rb3flp42l9p7bhdbr2h";
   };
 
   buildInputs = [ go-bindata ];

pkgs/applications/networking/browsers/browsh/deps.nix

@@ -4,26 +4,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/NYTimes/gziphandler";
-      rev =  "5032c8878b9dd46cfe8c625c0d9b9f258a560ee8";
+      rev =  "dd0439581c7657cb652dfe5c71d7d48baf39541d";
-      sha256 = "1avn8xb78xmmc61fjycpc81yrkfi42fna8zgzdqba6v7g8gq8a3x";
+      sha256 = "0rhrjlw220hnymzfccm0yir3pc9dpj7h3gwzhzq2cbsb3hhsqvyy";
-    };
-  }
-  {
-    goPackagePath  = "github.com/davecgh/go-spew";
-    fetch = {
-      type = "git";
-      url = "https://github.com/davecgh/go-spew";
-      rev =  "8991bc29aa16c548c550c7ff78260e27b9ab7c73";
-      sha256 = "0hka6hmyvp701adzag2g26cxdj47g21x6jz4sc6jjz1mn59d474y";
-    };
-  }
-  {
-    goPackagePath  = "github.com/hpcloud/tail";
-    fetch = {
-      type = "git";
-      url = "https://github.com/hpcloud/tail";
-      rev =  "a1dbeea552b7c8df4b542c66073e393de198a800";
-      sha256 = "0nssmn8j0yavs8099gwb69qpd1k9yd2z28bii6i4y61v0grb6bc2";
     };
   }
   {
@@ -40,8 +22,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/gdamore/encoding";
-      rev =  "b23993cbb6353f0e6aa98d0ee318a34728f628b9";
+      rev =  "6289cdc94c00ac4aa177771c5fce7af2f96b626d";
-      sha256 = "0d7irqpx2fa9vkxgkhf04yiwazsm10fxh0yk86x5crflhph5fv8a";
+      sha256 = "1vmm5zll92i2fm4ajqx0gyx0p9j36496x5nabi3y0x7h0inv0pk9";
     };
   }
   {
@@ -49,8 +31,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/gdamore/tcell";
-      rev =  "de7e78efa4a71b3f36c7154989c529dbdf9ae623";
+      rev =  "b5d0c1ac570211e469f43ff88c0c6aa4b56cc99a";
-      sha256 = "1ly3gqkziw01cb7h64k0wc4myzfcsr9hl7xznxd8k2yqzqvmhljz";
+      sha256 = "0g2zfbgyk3djlk0qpmrgcyy0ba9ad932yswpaacswi21qyf9gwag";
     };
   }
   {
@@ -76,8 +58,17 @@
     fetch = {
       type = "git";
       url = "https://github.com/hashicorp/hcl";
-      rev =  "ef8a98b0bbce4a65b5aa4c368430a80ddc533168";
+      rev =  "8cb6e5b959231cc1119e43259c4a608f9c51a241";
-      sha256 = "1qalfsc31fra7hcw2lc3s20aj7al62fq3j5fn5kga3mg99b82nyr";
+      sha256 = "0q6ml0qqs0yil76mpn4mdx4lp94id8vbv575qm60jzl1ijcl5i66";
+    };
+  }
+  {
+    goPackagePath  = "github.com/hpcloud/tail";
+    fetch = {
+      type = "git";
+      url = "https://github.com/hpcloud/tail";
+      rev =  "a30252cb686a21eb2d0b98132633053ec2f7f1e5";
+      sha256 = "1njpzc0pi1acg5zx9y6vj9xi6ksbsc5d387rd6904hy6rh2m6kn0";
     };
   }
   {
@@ -85,8 +76,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/lucasb-eyer/go-colorful";
-      rev =  "c7842319cf3ac2eff253e8b3ebe15fcc56b6414a";
+      rev =  "30298f24079860c4dee452fdef6519b362a4a026";
-      sha256 = "00v2x6qchhi6vv09w29kcyr9i0kq4n4daaj3vk1c4nfj2z7xx5hc";
+      sha256 = "0fig06880bvk1l92j4127v4x9sar4ds7ga8959gxxghb2w70b7l2";
     };
   }
   {
@@ -94,8 +85,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/magiconair/properties";
-      rev =  "c2353362d570a7bfa228149c62842019201cfb71";
+      rev =  "de8848e004dd33dc07a2947b3d76f618a7fc7ef1";
-      sha256 = "1a10362wv8a8qwb818wygn2z48lgzch940hvpv81hv8gc747ajxn";
+      sha256 = "19zqw1x0w0crh8zc84yy82nkcc5yjz72gviaf2xjgfm5a8np7nyb";
     };
   }
   {
@@ -103,8 +94,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/mattn/go-runewidth";
-      rev =  "ce7b0b5c7b45a81508558cd1dba6bb1e4ddb51bb";
+      rev =  "3ee7d812e62a0804a7d0a324e0249ca2db3476d3";
-      sha256 = "0lc39b6xrxv7h3v3y1kgz49cgi5qxwlygs715aam6ba35m48yi7g";
+      sha256 = "00b3ssm7wiqln3k54z2wcnxr3k3c7m1ybyhb9h8ixzbzspld0qzs";
     };
   }
   {
@@ -121,8 +112,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/onsi/ginkgo";
-      rev =  "3774a09d95489ccaa16032e0770d08ea77ba6184";
+      rev =  "eea6ad008b96acdaa524f5b409513bf062b500ad";
-      sha256 = "0x0gc89vgq38xhgmi2h22bhr73cf2gmk42g89nz89k8dgg9hhr25";
+      sha256 = "1326s5fxgasdpz1qqwrw4n5p3k0vz44msnyz14knrhlw5l97lx33";
     };
   }
   {
@@ -130,8 +121,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/onsi/gomega";
-      rev =  "b6ea1ea48f981d0f615a154a45eabb9dd466556d";
+      rev =  "90e289841c1ed79b7a598a7cd9959750cb5e89e2";
-      sha256 = "14179j7pj1h2vx60i68x2m6650ldji4xhanhc702i8a8iy7b49ja";
+      sha256 = "1n7i4hksdgv410m43v2sw14bl5vy59dkp6nlw5l76nibbh37syr9";
     };
   }
   {
@@ -139,8 +130,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/pelletier/go-toml";
-      rev =  "c2dbbc24a97911339e01bda0b8cabdbd8f13b602";
+      rev =  "728039f679cbcd4f6a54e080d2219a4c4928c546";
-      sha256 = "0v1dsqnk5zmn6ir8jgxijx14s47jvijlqfz3aq435snfrgybd5rz";
+      sha256 = "1v76s3vds0i9dxaha4ikd6xjm7vqqfk6sy9l6jc2lsvmj99d5sy6";
     };
   }
   {
@@ -148,17 +139,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/pkg/errors";
-      rev =  "816c9085562cd7ee03e7f8188a1cfd942858cded";
+      rev =  "ba968bfe8b2f7e042a574c888954fccecfa385b4";
-      sha256 = "1ws5crb7c70wdicavl6qr4g03nn6m92zd6wwp9n2ygz5c8rmxh8k";
+      sha256 = "0g5qcb4d4fd96midz0zdk8b9kz8xkzwfa8kr1cliqbg8sxsy5vd1";
-    };
-  }
-  {
-    goPackagePath  = "github.com/pmezard/go-difflib";
-    fetch = {
-      type = "git";
-      url = "https://github.com/pmezard/go-difflib";
-      rev =  "792786c7400a136282c1664665ae0a8db921c6c2";
-      sha256 = "0c1cn55m4rypmscgf0rrb88pn58j3ysvc2d0432dp3c6fqg6cnzw";
     };
   }
   {
@@ -175,8 +157,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/spf13/afero";
-      rev =  "787d034dfe70e44075ccc060d346146ef53270ad";
+      rev =  "588a75ec4f32903aa5e39a2619ba6a4631e28424";
-      sha256 = "0138rjiacl71h7kvhzinviwvy6qa2m6rflpv9lgqv15hnjvhwvg1";
+      sha256 = "0j9r65qgd58324m85lkl49vk9dgwd62g7dwvkfcm3k6i9dc555a9";
     };
   }
   {
@@ -193,8 +175,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/spf13/jwalterweatherman";
-      rev =  "7c0cea34c8ece3fbeb2b27ab9b59511d360fb394";
+      rev =  "94f6ae3ed3bceceafa716478c5fbf8d29ca601a1";
-      sha256 = "132p84i20b9s5r6fs597lsa6648vd415ch7c0d018vm8smzqpd0h";
+      sha256 = "1ywmkwci5zyd88ijym6f30fj5c0k2yayxarkmnazf5ybljv50q7b";
     };
   }
   {
@@ -211,17 +193,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/spf13/viper";
-      rev =  "d493c32b69b8c6f2377bf30bc4d70267ffbc0793";
+      rev =  "b5bf975e5823809fb22c7644d008757f78a4259e";
-      sha256 = "1jq46790rkjn6c1887wz98dqjk792ij6wnrifzk1maglmfb061hh";
+      sha256 = "1zpzxvn13wpvbblbbn73svaq39zgxfjqhci9d68g3qf309pcfy19";
-    };
-  }
-  {
-    goPackagePath  = "github.com/stretchr/testify";
-    fetch = {
-      type = "git";
-      url = "https://github.com/stretchr/testify";
-      rev =  "f35b8ab0b5a2cef36673838d662e249dd9c94686";
-      sha256 = "0dlszlshlxbmmfxj5hlwgv3r22x0y1af45gn1vd198nvvs3pnvfs";
     };
   }
   {
@@ -229,8 +202,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/ulule/limiter";
-      rev =  "af07f8759cbc68c744a15ffbfdabf35f7aff5e3b";
+      rev =  "38b2a440be905c8be884fd5e114dc893a64e5d81";
-      sha256 = "1c68vz9r0442lkj206l6k03nssxx3ys8ddg7d2p2brdanfbprzrq";
+      sha256 = "0sbbfz9k3m2hf45cx7y7xshsr3rac495lks9ciwmnrzsnxfdh3l5";
     };
   }
   {
@@ -238,8 +211,8 @@
     fetch = {
       type = "git";
       url = "https://go.googlesource.com/net";
-      rev =  "a0f8a16cb08c06df97cbdf9c47f4731ba548c33c";
+      rev =  "461777fb6f67e8cb9d70cda16573678d085a74cf";
-      sha256 = "1pnvrhi2minkn9mfa9p70b5jnixx8il5yqp08ad1w7kl34c21ma2";
+      sha256 = "0sc0llch05q6h7nqgayi3sgismsznpnlsz4gh89y4klpymdcpbh2";
     };
   }
   {
@@ -247,8 +220,8 @@
     fetch = {
       type = "git";
       url = "https://go.googlesource.com/sys";
-      rev =  "bd9dbc187b6e1dacfdd2722a87e83093c2d7bd6e";
+      rev =  "93c9922d18aeb82498a065f07aec7ad7fa60dfb7";
-      sha256 = "0zj8s3q2fznmap1nfr8pv4hz8xqixmkyhr6slq4baf8rvcb4mvbj";
+      sha256 = "0hv96nwbv0li3nrv43ldfzmf12yrrbji2cf8n44iibv8ps5kfssx";
     };
   }
   {
@@ -256,8 +229,26 @@
     fetch = {
       type = "git";
       url = "https://go.googlesource.com/text";
-      rev =  "0605a8320aceb4207a5fb3521281e17ec2075476";
+      rev =  "342b2e1fbaa52c93f31447ad2c6abc048c63e475";
-      sha256 = "1pak7q9ivwxh5bnjk00pkrs9ri9vmbyccvza56fl6138w397h49j";
+      sha256 = "0flv9idw0jm5nm8lx25xqanbkqgfiym6619w575p7nrdh0riqwqh";
+    };
+  }
+  {
+    goPackagePath  = "gopkg.in/fsnotify.v1";
+    fetch = {
+      type = "git";
+      url = "https://github.com/fsnotify/fsnotify";
+      rev =  "c2828203cd70a50dcccfb2761f8b1f8ceef9a8e9";
+      sha256 = "07va9crci0ijlivbb7q57d2rz9h27zgn2fsm60spjsqpdbvyrx4g";
+    };
+  }
+  {
+    goPackagePath  = "gopkg.in/tomb.v1";
+    fetch = {
+      type = "git";
+      url = "https://github.com/go-tomb/tomb";
+      rev =  "dd632973f1e7218eb1089048e0798ec9ae7dceb8";
+      sha256 = "1lqmq1ag7s4b3gc3ddvr792c5xb5k6sfn0cchr3i2s7f1c231zjv";
     };
   }
   {
@@ -265,8 +256,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/go-yaml/yaml";
-      rev =  "5420a8b6744d3b0345ab293f6fcba19c978f1183";
+      rev =  "51d6538a90f86fe93ac480b35f37b2be17fef232";
-      sha256 = "0dwjrs2lp2gdlscs7bsrmyc5yf6mm4fvgw71bzr9mv2qrd2q73s1";
+      sha256 = "01wj12jzsdqlnidpyjssmj0r4yavlqy7dwrg7adqd8dicjc4ncsa";
     };
   }
 ]

pkgs/applications/networking/browsers/captive-browser/default.nix

@@ -0,0 +1,22 @@
+{ lib, fetchFromGitHub, buildGoPackage }:
+
+buildGoPackage rec {
+  name = "captive-browser";
+  version = "2019-04-16";
+  goPackagePath = name;
+
+  src = fetchFromGitHub {
+    owner  = "FiloSottile";
+    repo   = "captive-browser";
+    rev    = "08450562e58bf9564ee98ad64ef7b2800e53338f";
+    sha256 = "17icgjg7h0xm8g4yy38qjhsvlz9pmlmj9kydz01y2nyl0v02i648";
+  };
+
+  meta = with lib; {
+    description = "Dedicated Chrome instance to log into captive portals without messing with DNS settings";
+    homepage = https://blog.filippo.io/captive-browser;
+    license = licenses.mit;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ volth ];
+  };
+}

pkgs/applications/networking/browsers/chromium/plugins.nix

@@ -100,11 +100,11 @@ let
 
   flash = stdenv.mkDerivation rec {
     name = "flashplayer-ppapi-${version}";
-    version = "32.0.0.192";
+    version = "32.0.0.207";
 
     src = fetchzip {
       url = "https://fpdownload.adobe.com/pub/flashplayer/pdc/${version}/flash_player_ppapi_linux.x86_64.tar.gz";
-      sha256 = "14nydiqjvr7hc4dmn900p7j7rp6prwyaf6xnki2ssbq6h1ni2lg1";
+      sha256 = "09bbrlnw343ygcibyjfa27r8gjdg1dcxx85d3v4v93wfi29nl789";
       stripRoot = false;
     };
 

pkgs/applications/networking/browsers/firefox/packages.nix

@@ -17,10 +17,10 @@ rec {
 
   firefox = common rec {
     pname = "firefox";
-    ffversion = "67.0.1";
+    ffversion = "67.0.2";
     src = fetchurl {
       url = "mirror://mozilla/firefox/releases/${ffversion}/source/firefox-${ffversion}.source.tar.xz";
-      sha512 = "1cbhlbgni08phqqiqlh1c29kl8b1w2sify4756bm4a01hmhfnhgwfa6v88vhzqy9h4c0045g8g4w14l2521k8w6rcijl1nvh14xdczf";
+      sha512 = "289bhd8ynanb2zpclzaqqyz4082w529kcf3fd7li3k4pn0ayvkxfv4kmmhfz4xxrwsx6f489ffcj9a48ckk1czi9kykvj3i6ni0mnhl";
     };
 
     patches = [

pkgs/applications/networking/browsers/mozilla-plugins/flashplayer/default.nix

@@ -74,7 +74,7 @@ let
 in
 stdenv.mkDerivation rec {
   name = "flashplayer-${version}";
-  version = "32.0.0.192";
+  version = "32.0.0.207";
 
   src = fetchurl {
     url =
@@ -85,14 +85,14 @@ stdenv.mkDerivation rec {
     sha256 =
       if debug then
         if arch == "x86_64" then
-          "0n5m70mz1fa5pgpz1ldqgn6bkr4in5qjn79kb85127wmg8fddbz7"
+          "0v5dlqaapr29qyb2pm57yafnmxdxin7shn1xqsx2sc9xwmvmaw7v"
         else
-          "1q6pjmnw2h8k09va5x64ijmq0kmfb569rwcibwl0d8kylxi97b6v"
+          "0ygxcvn6srjg9clayfri86c64inwidp9qk25hbsbyr8m8gghpwqb"
       else
         if arch == "x86_64" then
-          "1h2ya3szq24dczv2izxy47kr2raiahxx7zvm49jlvlcp5cygxvjk"
+          "1y1c65vfsvapqsl2q6vm75m5jyksjwnfs6f6ijcpg0dmf5f4fypy"
         else
-          "084bv0m9w1v2s4bf5rgan40l1fajwfam3njvgm47ffyg6s0kg1kh";
+          "1h9samf24l0ix6188p940h7l989nwkzlrvv7qdxczj3p62zzvqfy";
   };
 
   nativeBuildInputs = [ unzip ];

pkgs/applications/networking/browsers/mozilla-plugins/flashplayer/standalone.nix

@@ -50,7 +50,7 @@
 
 stdenv.mkDerivation rec {
   name = "flashplayer-standalone-${version}";
-  version = "32.0.0.192";
+  version = "32.0.0.207";
 
   src = fetchurl {
     url =
@@ -60,9 +60,9 @@ stdenv.mkDerivation rec {
         "https://fpdownload.macromedia.com/pub/flashplayer/updaters/32/flash_player_sa_linux.x86_64.tar.gz";
     sha256 =
       if debug then
-        "0j5rzamyajkiblalqkimx29bwm7yg9m4nj9z7z8hahcywpf81yqg"
+        "0z08da6xhjvsxn9xymcnpphap2h0ydj784ms1f950l84rdl4qrr4"
       else
-        "0qnz383aggm07hbvyrnqphwhd5wp9xbairf908nk4i6ad8wg1x3r";
+        "0d2pxggrzamrg143bvic0qa2v70jpplnahihfa4q2rbvy0l3i2pq";
   };
 
   nativeBuildInputs = [ unzip ];

pkgs/applications/networking/instant-messengers/bitlbee-discord/default.nix

@@ -17,6 +17,7 @@ stdenv.mkDerivation rec {
 
   preConfigure = ''
     export BITLBEE_PLUGINDIR=$out/lib/bitlbee
+    export BITLBEE_DATADIR=$out/share/bitlbee
     ./autogen.sh
   '';
 
@@ -25,7 +26,7 @@ stdenv.mkDerivation rec {
 
     homepage = https://github.com/sm00th/bitlbee-discord;
     license = licenses.gpl2Plus;
-    maintainers = [ maintainers.lassulus ];
+    maintainers = with maintainers; [ lassulus jb55 ];
     platforms = stdenv.lib.platforms.linux;
   };
 }

pkgs/applications/networking/instant-messengers/slack/default.nix

@@ -1,7 +1,10 @@
-{ darkMode ? false, stdenv, fetchurl, dpkg, makeWrapper , alsaLib, atk, cairo,
+{ stdenv, fetchurl, dpkg, makeWrapper , alsaLib, atk, cairo,
 cups, curl, dbus, expat, fontconfig, freetype, glib , gnome2, gtk3, gdk_pixbuf,
 libappindicator-gtk3, libnotify, libxcb, nspr, nss, pango , systemd, xorg,
-at-spi2-atk, libuuid }:
+at-spi2-atk, libuuid,
+darkMode ? false,
+darkModeCssUrl ? "https://cdn.rawgit.com/laCour/slack-night-mode/master/css/raw/black.css"
+}:
 
 let
 
@@ -96,7 +99,7 @@ in stdenv.mkDerivation {
     document.addEventListener('DOMContentLoaded', function() {
     let tt__customCss = ".menu ul li a:not(.inline_menu_link) {color: #fff !important;}"
     $.ajax({
-        url: 'https://cdn.rawgit.com/laCour/slack-night-mode/master/css/raw/black.css',
+        url: '${darkModeCssUrl}',
         success: function(css) {
             \$("<style></style>").appendTo('head').html(css + tt__customCss);
             \$("<style></style>").appendTo('head').html('#reply_container.upload_in_threads .inline_message_input_container {background: padding-box #545454}');

pkgs/applications/office/gnumeric/default.nix

@@ -7,11 +7,11 @@ let
   inherit (pythonPackages) python pygobject3;
 in stdenv.mkDerivation rec {
   pname = "gnumeric";
-  version = "1.12.44";
+  version = "1.12.45";
 
   src = fetchurl {
     url = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
-    sha256 = "0147962c6ybdsj57rz95nla0rls7g545wc2n7pz59zmzyd5pksk0";
+    sha256 = "0c8dl1kvnj3g32qy3s92qpqpqfy0in59cx005gjvvzsflahav61h";
   };
 
   configureFlags = [ "--disable-component" ];

pkgs/applications/science/biology/cd-hit/default.nix

@@ -0,0 +1,34 @@
+{ stdenv, fetchFromGitHub, makeWrapper, zlib, perl, perlPackages }:
+
+stdenv.mkDerivation rec {
+  version = "4.8.1";
+  pname = "cd-hit";
+
+  src = fetchFromGitHub {
+    owner = "weizhongli";
+    repo = "cdhit";
+    rev = "V${version}";
+    sha256 = "032nva6iiwmw59gjipm1mv0xlcckhxsf45mc2qbnv19lbis0q22i";
+  };
+
+  propagatedBuildInputs = [ perl perlPackages.TextNSP perlPackages.PerlMagick perlPackages.Storable ];
+
+  nativeBuildInputs = [ zlib makeWrapper ];
+
+  makeFlags = [ "PREFIX=$(out)/bin" ];
+
+  preInstall = "mkdir -p $out/bin";
+
+  postFixup = ''
+    wrapProgram $out/bin/FET.pl --prefix PERL5LIB : $PERL5LIB
+    wrapProgram $out/bin/plot_2d.pl --prefix PERL5LIB : $PERL5LIB
+    wrapProgram $out/bin/clstr_list_sort.pl --prefix PERL5LIB : $PERL5LIB
+  '';
+  meta = with stdenv.lib; {
+    description = "Clustering and comparing protein or nucleotide sequences";
+    homepage = http://weizhongli-lab.org/cd-hit/;
+    license = licenses.gpl2;
+    maintainers = [ maintainers.bzizou ];
+    platforms = platforms.unix;
+  };
+}

pkgs/applications/science/chemistry/octopus/default.nix

@@ -3,7 +3,7 @@
 }:
 
 let
-  version = "8.4";
+  version = "9.0";
   fftwAll = symlinkJoin { name ="ftw-dev-out"; paths = [ fftw.dev fftw.out ]; };
 
 in stdenv.mkDerivation {
@@ -11,7 +11,7 @@ in stdenv.mkDerivation {
 
   src = fetchurl {
     url = "http://www.tddft.org/programs/octopus/down.php?file=${version}/octopus-${version}.tar.gz";
-    sha256 = "1fx5ssnf65b9ld7xs9rvvg8i80pblxpyhqkir0a7xshkk1g60z55";
+    sha256 = "0p1gjykjnzm4m93mgjsmnxd0n2j381jk5kn3a7gkzxanixp60ilm";
   };
 
   nativeBuildInputs = [ perl procps fftw.dev ];

pkgs/applications/version-management/gitlab/data.json

@@ -1,12 +1,12 @@
 {
   "ce": {
-    "version": "11.10.4",
+    "version": "11.10.5",
-    "repo_hash": "02rvf5ikahydswjldzg99k8han051ap7v8h9mcjgrr4xmj301hxm",
+    "repo_hash": "00bkdylcnz171jf8di05ygviplqzssazrfaqpwmbqwdjab2ax4yr",
-    "deb_hash": "0sigpp5lhg4pl88gsgf7dq2k7mi2wgaz0vdsl25c97w1daw7a60c",
+    "deb_hash": "1zsg4fhpl07pz76i4yynk38xs7cp9w4jcryxk7larbr25m48q4rb",
-    "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ce/packages/debian/stretch/gitlab-ce_11.10.4-ce.0_amd64.deb/download.deb",
+    "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ce/packages/debian/stretch/gitlab-ce_11.10.5-ce.0_amd64.deb/download.deb",
     "owner": "gitlab-org",
     "repo": "gitlab-ce",
-    "rev": "v11.10.4",
+    "rev": "v11.10.5",
     "passthru": {
       "GITALY_SERVER_VERSION": "1.34.1",
       "GITLAB_PAGES_VERSION": "1.5.0",
@@ -15,13 +15,13 @@
     }
   },
   "ee": {
-    "version": "11.10.4",
+    "version": "11.10.5",
-    "repo_hash": "06nf94k0ay9kmx060j387hydyf6crv0f1pjb691r3y6s713m6php",
+    "repo_hash": "0nla908l3513r87i3x2fa87j48wgykzpf7cqxddnahk98m0wgxvi",
-    "deb_hash": "1g0mlyzm2ikpblmy529wg6az5biiqczpr3kyp2mk4yjkdvg59jjp",
+    "deb_hash": "02ri9b4xd77wqjnd49h5n77aylrb5xlq6xa26xn39kl326isaj41",
-    "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ee/packages/debian/stretch/gitlab-ee_11.10.4-ee.0_amd64.deb/download.deb",
+    "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ee/packages/debian/stretch/gitlab-ee_11.10.5-ee.0_amd64.deb/download.deb",
     "owner": "gitlab-org",
     "repo": "gitlab-ee",
-    "rev": "v11.10.4-ee",
+    "rev": "v11.10.5-ee",
     "passthru": {
       "GITALY_SERVER_VERSION": "1.34.1",
       "GITLAB_PAGES_VERSION": "1.5.0",
@@ -29,4 +29,4 @@
       "GITLAB_WORKHORSE_VERSION": "8.5.2"
     }
   }
-}
+}

pkgs/applications/version-management/redmine/4.x/Gemfile

@@ -2,7 +2,7 @@ source 'https://rubygems.org'
 
 gem "bundler", ">= 1.5.0"
 
-gem "rails", "5.2.2.1"
+gem "rails", "5.2.3"
 gem "rouge", "~> 3.3.0"
 gem "request_store", "1.0.5"
 gem "mini_mime", "~> 1.0.1"

pkgs/applications/version-management/redmine/4.x/Gemfile.lock

@@ -1,19 +1,19 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    actioncable (5.2.2.1)
+    actioncable (5.2.3)
-      actionpack (= 5.2.2.1)
+      actionpack (= 5.2.3)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailer (5.2.2.1)
+    actionmailer (5.2.3)
-      actionpack (= 5.2.2.1)
+      actionpack (= 5.2.3)
-      actionview (= 5.2.2.1)
+      actionview (= 5.2.3)
-      activejob (= 5.2.2.1)
+      activejob (= 5.2.3)
       mail (~> 2.5, >= 2.5.4)
       rails-dom-testing (~> 2.0)
-    actionpack (5.2.2.1)
+    actionpack (5.2.3)
-      actionview (= 5.2.2.1)
+      actionview (= 5.2.3)
-      activesupport (= 5.2.2.1)
+      activesupport (= 5.2.3)
       rack (~> 2.0)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
@@ -21,26 +21,26 @@ GEM
     actionpack-xml_parser (2.0.1)
       actionpack (>= 5.0)
       railties (>= 5.0)
-    actionview (5.2.2.1)
+    actionview (5.2.3)
-      activesupport (= 5.2.2.1)
+      activesupport (= 5.2.3)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.0.3)
-    activejob (5.2.2.1)
+    activejob (5.2.3)
-      activesupport (= 5.2.2.1)
+      activesupport (= 5.2.3)
       globalid (>= 0.3.6)
-    activemodel (5.2.2.1)
+    activemodel (5.2.3)
-      activesupport (= 5.2.2.1)
+      activesupport (= 5.2.3)
-    activerecord (5.2.2.1)
+    activerecord (5.2.3)
-      activemodel (= 5.2.2.1)
+      activemodel (= 5.2.3)
-      activesupport (= 5.2.2.1)
+      activesupport (= 5.2.3)
       arel (>= 9.0)
-    activestorage (5.2.2.1)
+    activestorage (5.2.3)
-      actionpack (= 5.2.2.1)
+      actionpack (= 5.2.3)
-      activerecord (= 5.2.2.1)
+      activerecord (= 5.2.3)
       marcel (~> 0.3.1)
-    activesupport (5.2.2.1)
+    activesupport (5.2.3)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 0.7, < 2)
       minitest (~> 5.1)
@@ -56,16 +56,15 @@ GEM
       rack (>= 1.0.0)
       rack-test (>= 0.5.4)
       xpath (>= 2.0, < 4.0)
-    childprocess (0.9.0)
+    childprocess (1.0.1)
-      ffi (~> 1.0, >= 1.0.11)
+      rake (< 13.0)
     concurrent-ruby (1.1.5)
     crass (1.0.4)
     css_parser (1.7.0)
       addressable
-    csv (3.0.6)
+    csv (3.0.9)
     docile (1.1.5)
     erubi (1.8.0)
-    ffi (1.10.0)
     globalid (0.4.2)
       activesupport (>= 4.2.0)
     htmlentities (4.3.4)
@@ -89,10 +88,10 @@ GEM
     mysql2 (0.5.2)
     net-ldap (0.16.1)
     nio4r (2.3.1)
-    nokogiri (1.10.2)
+    nokogiri (1.10.3)
       mini_portile2 (~> 2.4.0)
     pg (1.1.4)
-    public_suffix (3.0.3)
+    public_suffix (3.1.0)
     puma (3.12.1)
     rack (2.0.7)
     rack-openid (1.4.2)
@@ -100,27 +99,27 @@ GEM
       ruby-openid (>= 2.1.8)
     rack-test (1.1.0)
       rack (>= 1.0, < 3)
-    rails (5.2.2.1)
+    rails (5.2.3)
-      actioncable (= 5.2.2.1)
+      actioncable (= 5.2.3)
-      actionmailer (= 5.2.2.1)
+      actionmailer (= 5.2.3)
-      actionpack (= 5.2.2.1)
+      actionpack (= 5.2.3)
-      actionview (= 5.2.2.1)
+      actionview (= 5.2.3)
-      activejob (= 5.2.2.1)
+      activejob (= 5.2.3)
-      activemodel (= 5.2.2.1)
+      activemodel (= 5.2.3)
-      activerecord (= 5.2.2.1)
+      activerecord (= 5.2.3)
-      activestorage (= 5.2.2.1)
+      activestorage (= 5.2.3)
-      activesupport (= 5.2.2.1)
+      activesupport (= 5.2.3)
       bundler (>= 1.3.0)
-      railties (= 5.2.2.1)
+      railties (= 5.2.3)
       sprockets-rails (>= 2.0.0)
     rails-dom-testing (2.0.3)
       activesupport (>= 4.2.0)
       nokogiri (>= 1.6)
     rails-html-sanitizer (1.0.4)
       loofah (~> 2.2, >= 2.2.2)
-    railties (5.2.2.1)
+    railties (5.2.3)
-      actionpack (= 5.2.2.1)
+      actionpack (= 5.2.3)
-      activesupport (= 5.2.2.1)
+      activesupport (= 5.2.3)
       method_source
       rake (>= 0.8.7)
       thor (>= 0.19.0, < 2.0)
@@ -132,17 +131,17 @@ GEM
     redcarpet (3.4.0)
     request_store (1.0.5)
     rmagick (2.16.0)
-    roadie (3.4.0)
+    roadie (3.5.0)
       css_parser (~> 1.4)
-      nokogiri (~> 1.5)
+      nokogiri (~> 1.8)
     roadie-rails (1.3.0)
       railties (>= 3.0, < 5.3)
       roadie (~> 3.1)
     rouge (3.3.0)
     ruby-openid (2.3.0)
-    rubyzip (1.2.2)
+    rubyzip (1.2.3)
-    selenium-webdriver (3.141.0)
+    selenium-webdriver (3.142.3)
-      childprocess (~> 0.5)
+      childprocess (>= 0.5, < 2.0)
       rubyzip (~> 1.2, >= 1.2.2)
     simplecov (0.14.1)
       docile (~> 1.1.0)
@@ -160,9 +159,9 @@ GEM
     thread_safe (0.3.6)
     tzinfo (1.2.5)
       thread_safe (~> 0.1)
-    websocket-driver (0.7.0)
+    websocket-driver (0.7.1)
       websocket-extensions (>= 0.1.0)
-    websocket-extensions (0.1.3)
+    websocket-extensions (0.1.4)
     xpath (3.2.0)
       nokogiri (~> 1.8)
     yard (0.9.19)
@@ -186,7 +185,7 @@ DEPENDENCIES
   pg (~> 1.1.4)
   puma (~> 3.7)
   rack-openid
-  rails (= 5.2.2.1)
+  rails (= 5.2.3)
   rails-dom-testing
   rbpdf (~> 1.19.6)
   redcarpet (~> 3.4.0)

pkgs/applications/version-management/redmine/4.x/default.nix

@@ -1,7 +1,7 @@
 { stdenv, fetchurl, bundlerEnv, ruby }:
 
 let
-  version = "4.0.3";
+  version = "4.0.4";
   rubyEnv = bundlerEnv {
     name = "redmine-env-${version}";
 
@@ -15,7 +15,7 @@ in
 
     src = fetchurl {
       url = "https://www.redmine.org/releases/${name}.tar.gz";
-      sha256 = "1wyfl08sq71n4c2hc0fv1dfblykq5i3mbqyjdswk26md8dcmw8ac";
+      sha256 = "0i5bmgdi3mahbis9hn0hk53rnz4ihp9yij4b4i07ny9vf3n4kp1a";
     };
 
     buildInputs = [ rubyEnv rubyEnv.wrappedRuby rubyEnv.bundler ];

pkgs/applications/version-management/redmine/4.x/gemset.nix

@@ -3,28 +3,28 @@
     dependencies = ["actionpack" "nio4r" "websocket-driver"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1x5fxhsr2mxq5r6258s48xsn7ld081d3qaavppvj7yp7w9vqn871";
+      sha256 = "04wd9rf8sglrqc8jz49apqcxbi51gdj7l1apf5qr4i86iddk6pkm";
       type = "gem";
     };
-    version = "5.2.2.1";
+    version = "5.2.3";
   };
   actionmailer = {
     dependencies = ["actionpack" "actionview" "activejob" "mail" "rails-dom-testing"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "10n2v2al68rsq5ghrdp7cpycsc1q0m19fcd8cd5i528n30nl23iw";
+      sha256 = "15laym06zcm2021qdhlyr6y9jn1marw436i89hcxqg14a8zvyvwa";
       type = "gem";
     };
-    version = "5.2.2.1";
+    version = "5.2.3";
   };
   actionpack = {
     dependencies = ["actionview" "activesupport" "rack" "rack-test" "rails-dom-testing" "rails-html-sanitizer"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1lxqzxa728dqg42yw0q4hqkaawqagiw1k0392an2ghjfgb16pafx";
+      sha256 = "1s2iay17i2k0xx36cmnpbrmr5w6x70jk7fq1d8w70xcdw5chm0w1";
       type = "gem";
     };
-    version = "5.2.2.1";
+    version = "5.2.3";
   };
   actionpack-xml_parser = {
     dependencies = ["actionpack" "railties"];
@@ -39,55 +39,55 @@
     dependencies = ["activesupport" "builder" "erubi" "rails-dom-testing" "rails-html-sanitizer"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0832vlx37rly8ryfgi01b20mld8b3bv9cg62n5wax4zpzgn6jdxb";
+      sha256 = "1v49rgf8305grqf6gq7qa47qhamr369igyy0giycz60x86afyr4h";
       type = "gem";
     };
-    version = "5.2.2.1";
+    version = "5.2.3";
   };
   activejob = {
     dependencies = ["activesupport" "globalid"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1zma452lc3qp4a7r10zbdmsci0kv9a3gnk4da2apbdrc8fib5mr3";
+      sha256 = "17vizibxbsli5yppgrvmw13wj7a9xy19s5nqxf1k23bbk2s5b87s";
       type = "gem";
     };
-    version = "5.2.2.1";
+    version = "5.2.3";
   };
   activemodel = {
     dependencies = ["activesupport"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1idmvqvpgri34k31s44pjb88rc3jad3yxra7fd1kpidpnv5f3v65";
+      sha256 = "0mghh9di8011ara9h1r5a216yzk1vjm9r3p0gdvdi8j1zmkl6k6h";
       type = "gem";
     };
-    version = "5.2.2.1";
+    version = "5.2.3";
   };
   activerecord = {
     dependencies = ["activemodel" "activesupport" "arel"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1c5cz9v7ggpqjxf0fqs1xhy1pb9m34cp31pxarhs9aqb71qjl98v";
+      sha256 = "0d6036f592803iyvp6bw98p3sg638mia5dbw19lvachx6jgzfvpw";
       type = "gem";
     };
-    version = "5.2.2.1";
+    version = "5.2.3";
   };
   activestorage = {
     dependencies = ["actionpack" "activerecord" "marcel"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "155xpbzrz0kr0argx0vsh5prvadd2h1g1m61kdiabvfy2iygc02n";
+      sha256 = "04is6ipjqw1f337i8pm8w5bd99rpygqfd0fzzxkr7jd308ggmsjk";
       type = "gem";
     };
-    version = "5.2.2.1";
+    version = "5.2.3";
   };
   activesupport = {
     dependencies = ["concurrent-ruby" "i18n" "minitest" "tzinfo"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "161bp4p01v1a1lvszrhd1a02zf9x1p1l1yhw79a3rix1kvzkkdqb";
+      sha256 = "110vp4frgkw3mpzlmshg2f2ig09cknls2w68ym1r1s39d01v0mi8";
       type = "gem";
     };
-    version = "5.2.2.1";
+    version = "5.2.3";
   };
   addressable = {
     dependencies = ["public_suffix"];
@@ -124,13 +124,13 @@
     version = "2.18.0";
   };
   childprocess = {
-    dependencies = ["ffi"];
+    dependencies = ["rake"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0a61922kmvcxyj5l70fycapr87gz1dzzlkfpq85rfqk5vdh3d28p";
+      sha256 = "1d2gasf988jh2k3fjb7i54c68rq6ni6jf9w0gnsfhrq94a6mprkz";
       type = "gem";
     };
-    version = "0.9.0";
+    version = "1.0.1";
   };
   concurrent-ruby = {
     source = {
@@ -160,10 +160,10 @@
   csv = {
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1zvchwfkdkljnslqakagbnw76vs01xwpjrynrawfanzn376c6bcd";
+      sha256 = "097rl10ivzlya5640530ayls2f1vid2mfgjy9ngd789qmp0j6x4b";
       type = "gem";
     };
-    version = "3.0.6";
+    version = "3.0.9";
   };
   docile = {
     source = {
@@ -181,14 +181,6 @@
     };
     version = "1.8.0";
   };
-  ffi = {
-    source = {
-      remotes = ["https://rubygems.org"];
-      sha256 = "0j8pzj8raxbir5w5k6s7a042sb5k02pg0f8s4na1r5lan901j00p";
-      type = "gem";
-    };
-    version = "1.10.0";
-  };
   globalid = {
     dependencies = ["activesupport"];
     source = {
@@ -334,10 +326,10 @@
     dependencies = ["mini_portile2"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0sy96cc8i5y4p67fhf4d9c6sg8ymrrva21zyvzw55l0pa1582wx2";
+      sha256 = "02bjydih0j515szfv9mls195cvpyidh6ixm7dwbl3s2sbaxxk5s4";
       type = "gem";
     };
-    version = "1.10.2";
+    version = "1.10.3";
   };
   pg = {
     source = {
@@ -350,10 +342,10 @@
   public_suffix = {
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "08q64b5br692dd3v0a9wq9q5dvycc6kmiqmjbdxkxbfizggsvx6l";
+      sha256 = "1c7c5xxkx91hwj4572hbnyvxmydb90q69wlpr2l0dxrmwx2p365l";
       type = "gem";
     };
-    version = "3.0.3";
+    version = "3.1.0";
   };
   puma = {
     source = {
@@ -393,10 +385,10 @@
     dependencies = ["actioncable" "actionmailer" "actionpack" "actionview" "activejob" "activemodel" "activerecord" "activestorage" "activesupport" "railties" "sprockets-rails"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1jxmwrykwgbn116hhmi7h75hcsdifhj89wk12m7ch2f3mn1lrmp9";
+      sha256 = "1p7cszi3n9ksxchxnccmz61pd1i3rjg4813dsdinsm8xm5k1pdgr";
       type = "gem";
     };
-    version = "5.2.2.1";
+    version = "5.2.3";
   };
   rails-dom-testing = {
     dependencies = ["activesupport" "nokogiri"];
@@ -420,10 +412,10 @@
     dependencies = ["actionpack" "activesupport" "method_source" "rake" "thor"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0al6mvh2jvr3n7cxkx0yvhgiiarby6gxc93vl5xg1yxkvx27qzd6";
+      sha256 = "1gn9fwb5wm08fbj7zpilqgblfl315l5b7pg4jsvxlizvrzg8h8q4";
       type = "gem";
     };
-    version = "5.2.2.1";
+    version = "5.2.3";
   };
   rake = {
     source = {
@@ -478,10 +470,10 @@
     dependencies = ["css_parser" "nokogiri"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0l3s80394yijvz0fsvfkw0azsi9yxsdkxd8lpas0bd7wlndjvmxx";
+      sha256 = "0b2qgr725hnscz3ldb607gwgjkr47ncs1jjnk6zh0h70p5dxrk2d";
       type = "gem";
     };
-    version = "3.4.0";
+    version = "3.5.0";
   };
   roadie-rails = {
     dependencies = ["railties" "roadie"];
@@ -511,19 +503,19 @@
   rubyzip = {
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1n1lb2sdwh9h27y244hxzg1lrxxg2m53pk1vq7p33bna003qkyrj";
+      sha256 = "1w9gw28ly3zyqydnm8phxchf4ymyjl2r7zf7c12z8kla10cpmhlc";
       type = "gem";
     };
-    version = "1.2.2";
+    version = "1.2.3";
   };
   selenium-webdriver = {
     dependencies = ["childprocess" "rubyzip"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "114hv2ajmh6d186v2w887yqakqcxyxq367l0iakrrpvwviknrhfs";
+      sha256 = "0i0jr4qrcvg5isc11ivjw7f9gywbimnz613k82bfcrnlzdf90mxy";
       type = "gem";
     };
-    version = "3.141.0";
+    version = "3.142.3";
   };
   simplecov = {
     dependencies = ["docile" "json" "simplecov-html"];
@@ -589,18 +581,18 @@
     dependencies = ["websocket-extensions"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1551k3fs3kkb3ghqfj3n5lps0ikb9pyrdnzmvgfdxy8574n4g1dn";
+      sha256 = "1bxamwqldmy98hxs5pqby3andws14hl36ch78g0s81gaz9b91nj2";
       type = "gem";
     };
-    version = "0.7.0";
+    version = "0.7.1";
   };
   websocket-extensions = {
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "034sdr7fd34yag5l6y156rkbhiqgmy395m231dwhlpcswhs6d270";
+      sha256 = "00i624ng1nvkz1yckj3f8yxxp6hi7xaqf40qh9q3hj2n1l9i8g6m";
       type = "gem";
     };
-    version = "0.1.3";
+    version = "0.1.4";
   };
   xpath = {
     dependencies = ["nokogiri"];

pkgs/applications/version-management/redmine/Gemfile.lock

@@ -57,7 +57,7 @@ GEM
       addressable
     docile (1.1.5)
     erubis (2.7.0)
-    ffi (1.10.0)
+    ffi (1.11.1)
     globalid (0.4.2)
       activesupport (>= 4.2.0)
     htmlentities (4.3.4)
@@ -88,7 +88,7 @@ GEM
     pg (0.18.4)
     protected_attributes (1.1.4)
       activemodel (>= 4.0.1, < 5.0)
-    public_suffix (3.0.3)
+    public_suffix (3.1.0)
     rack (1.6.11)
     rack-openid (1.4.2)
       rack (>= 1.1.0)
@@ -135,7 +135,7 @@ GEM
       railties (>= 3.0, < 5.1)
       roadie (~> 3.1)
     ruby-openid (2.3.0)
-    rubyzip (1.2.2)
+    rubyzip (1.2.3)
     selenium-webdriver (2.53.4)
       childprocess (~> 0.5)
       rubyzip (~> 1.0)

pkgs/applications/version-management/redmine/default.nix

@@ -1,7 +1,7 @@
 { stdenv, fetchurl, bundlerEnv, ruby }:
 
 let
-  version = "3.4.10";
+  version = "3.4.11";
   rubyEnv = bundlerEnv {
     name = "redmine-env-${version}";
 
@@ -15,7 +15,7 @@ in
 
     src = fetchurl {
       url = "https://www.redmine.org/releases/${name}.tar.gz";
-      sha256 = "08clfg7wgp4wnajawdn7qgrv7r8lk8d8haqkl7iz77ygdi3mpyrh";
+      sha256 = "14987sd9ff2n3982qlfwd4m0g1m10w8jyv791nica3wppvnrxh0r";
     };
 
     buildInputs = [ rubyEnv rubyEnv.wrappedRuby rubyEnv.bundler ];

pkgs/applications/version-management/redmine/gemset.nix

@@ -166,10 +166,10 @@
   ffi = {
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0j8pzj8raxbir5w5k6s7a042sb5k02pg0f8s4na1r5lan901j00p";
+      sha256 = "06mvxpjply8qh4j3fj9wh08kdzwkbnvsiysh0vrhlk5cwxzjmblh";
       type = "gem";
     };
-    version = "1.10.0";
+    version = "1.11.1";
   };
   globalid = {
     dependencies = ["activesupport"];
@@ -342,10 +342,10 @@
   public_suffix = {
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "08q64b5br692dd3v0a9wq9q5dvycc6kmiqmjbdxkxbfizggsvx6l";
+      sha256 = "1c7c5xxkx91hwj4572hbnyvxmydb90q69wlpr2l0dxrmwx2p365l";
       type = "gem";
     };
-    version = "3.0.3";
+    version = "3.1.0";
   };
   rack = {
     source = {
@@ -504,10 +504,10 @@
   rubyzip = {
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1n1lb2sdwh9h27y244hxzg1lrxxg2m53pk1vq7p33bna003qkyrj";
+      sha256 = "1w9gw28ly3zyqydnm8phxchf4ymyjl2r7zf7c12z8kla10cpmhlc";
       type = "gem";
     };
-    version = "1.2.2";
+    version = "1.2.3";
   };
   selenium-webdriver = {
     dependencies = ["childprocess" "rubyzip" "websocket"];

pkgs/build-support/build-pecl.nix

@@ -1,4 +1,4 @@
-{ stdenv, php, autoreconfHook, fetchurl }:
+{ stdenv, php, autoreconfHook, fetchurl, re2c }:
 
 { pname
 , version
@@ -17,7 +17,7 @@ stdenv.mkDerivation (args // {
 
   inherit src;
 
-  nativeBuildInputs = [ autoreconfHook ] ++ nativeBuildInputs;
+  nativeBuildInputs = [ autoreconfHook re2c ] ++ nativeBuildInputs;
   buildInputs = [ php ] ++ buildInputs;
 
   makeFlags = [ "EXTENSION_DIR=$(out)/lib/php/extensions" ] ++ makeFlags;

pkgs/data/fonts/jost/default.nix

@@ -0,0 +1,22 @@
+{stdenv, fetchzip}:
+
+let
+  version = "3.3";
+in fetchzip {
+  name = "jost-${version}";
+  url = "https://github.com/indestructible-type/Jost/releases/download/${version}/Jost.zip";
+
+  postFetch = ''
+    mkdir -p $out/share/fonts
+    unzip -j $downloadedFile \*.otf -d $out/share/fonts/opentype
+  '';
+
+  sha256="00nrhs3aif2hc4yhjhbn9ywmydl2w0g0hv5m5is8gv7wx8yi2j9z";
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/indestructible-type/Jost;
+    description = "A sans serif font by Indestructible Type";
+    license = licenses.ofl;
+    maintainers = [ maintainers.ar1a ];
+  };
+}

pkgs/data/misc/hackage/default.nix

@@ -1,6 +1,6 @@
 { fetchurl }:
 
 fetchurl {
-  url = "https://github.com/commercialhaskell/all-cabal-hashes/archive/85d71d5231521c70b961570dbbee953253fb379b.tar.gz";
+  url = "https://github.com/commercialhaskell/all-cabal-hashes/archive/bee48f46f4c9e9c1195bf81efb61fa5fb0aec0dc.tar.gz";
-  sha256 = "1mdp2ivnx7wvd63bq1li9gpsm5sv1s167crv1jjlqw578lbi8hv7";
+  sha256 = "0wxj0iakqy1cyncga8s1qlb8c06vj3ilh5z8lpann7xr8yh6sm4b";
 }

pkgs/development/compilers/ocaml/4.08.nix

@@ -1,8 +1,8 @@
 import ./generic.nix {
   major_version = "4";
   minor_version = "08";
-  patch_version = "0+rc1";
+  patch_version = "0+rc2";
-  sha256 = "014yincnkfg0j2jy0cn30l5hb1y4sf2qf1gy9ix9ghgn32iw5ndk";
+  sha256 = "09wp2iig6v5pivkjcnibdvkg5mchcj3q4zms6ij67039xczm8qrg";
 
   # If the executable is stripped it does not work
   dontStrip = true;

pkgs/development/compilers/scala/2.13.nix

@@ -0,0 +1,46 @@
+{ stdenv, fetchurl, makeWrapper, jre, gnugrep, coreutils }:
+
+stdenv.mkDerivation rec {
+  name = "scala-2.13.0";
+
+  src = fetchurl {
+    url = "https://www.scala-lang.org/files/archive/${name}.tgz";
+    sha256 = "12g0a9i0xxqxxcvmimm5w2wgmrdhq80p8bsp52d6yldz4lrnbm7p";
+  };
+
+  propagatedBuildInputs = [ jre ] ;
+  buildInputs = [ makeWrapper ] ;
+
+  installPhase = ''
+    mkdir -p $out
+    rm "bin/"*.bat
+    mv * $out
+
+    # put docs in correct subdirectory
+    mkdir -p $out/share/doc
+    mv $out/doc $out/share/doc/scala
+
+    for p in $(ls $out/bin/) ; do
+      wrapProgram $out/bin/$p \
+        --prefix PATH ":" ${coreutils}/bin \
+        --prefix PATH ":" ${gnugrep}/bin \
+        --prefix PATH ":" ${jre}/bin \
+        --set JAVA_HOME ${jre}
+    done
+  '';
+
+  meta = {
+    description = "General purpose programming language";
+    longDescription = ''
+      Scala is a general purpose programming language designed to express
+      common programming patterns in a concise, elegant, and type-safe way.
+      It smoothly integrates features of object-oriented and functional
+      languages, enabling Java and other programmers to be more productive.
+      Code sizes are typically reduced by a factor of two to three when
+      compared to an equivalent Java application.
+    '';
+    homepage = https://www.scala-lang.org/;
+    license = stdenv.lib.licenses.bsd3;
+    platforms = stdenv.lib.platforms.all;
+  };
+}

pkgs/development/coq-modules/QuickChick/default.nix

@@ -14,23 +14,23 @@ let params =
       sha256 = "0fri4nih40vfb0fbr82dsi631ydkw48xszinq43lyinpknf54y17";
     };
 
-    "8.7" = {
-      version = "20171212";
-      rev = "195e550a1cf0810497734356437a1720ebb6d744";
-      sha256 = "0zm23y89z0h4iamy74qk9qi2pz2cj3ga6ygav0w79n0qyqwhxcq1";
-    };
     "8.8" = rec {
-      preConfigure = "substituteInPlace Makefile --replace quickChickTool.byte quickChickTool.native";
       version = "20190311";
       rev = "22af9e9a223d0038f05638654422e637e863b355";
       sha256 = "00rnr19lg6lg0haq1sy4ld38p7imzand6fc52fvfq27gblxkp2aq";
-      buildInputs = with coq.ocamlPackages; [ ocamlbuild num ];
+    };
-      propagatedBuildInputs = [ coq-ext-lib simple-io ];
+
+    "8.9" = rec {
+      version = "1.1.0";
+      rev = "v${version}";
+      sha256 = "1c34v1k37rk7v0xk2czv5n79mbjxjrm6nh3llg2mpfmdsqi68wf3";
     };
   };
   param = params."${coq.coq-version}";
 in
 
+let recent = stdenv.lib.versionAtLeast coq.coq-version "8.8"; in
+
 stdenv.mkDerivation rec {
 
   name = "coq${coq.coq-version}-QuickChick-${param.version}";
@@ -41,16 +41,19 @@ stdenv.mkDerivation rec {
     inherit (param) rev sha256;
   };
 
+  preConfigure = stdenv.lib.optionalString recent
+    "substituteInPlace Makefile --replace quickChickTool.byte quickChickTool.native";
+
   buildInputs = [ coq ]
   ++ (with coq.ocamlPackages; [ ocaml camlp5 findlib ])
-  ++ (param.buildInputs or [])
+  ++ stdenv.lib.optionals recent
+     (with coq.ocamlPackages; [ ocamlbuild num ])
   ;
-  propagatedBuildInputs = [ ssreflect ] ++ (param.propagatedBuildInputs or []);
+  propagatedBuildInputs = [ ssreflect ]
+  ++ stdenv.lib.optionals recent [ coq-ext-lib simple-io ];
 
   enableParallelBuilding = false;
 
-  preConfigure = param.preConfigure or null;
-
   installPhase = ''
     make -f Makefile.coq COQLIB=$out/lib/coq/${coq.coq-version}/ install
   '';

pkgs/development/coq-modules/simple-io/default.nix

@@ -1,13 +1,13 @@
 { stdenv, fetchFromGitHub, coq, coq-ext-lib }:
 
 stdenv.mkDerivation rec {
-  version = "1.0.0";
+  version = "1.2.0";
   name = "coq${coq.coq-version}-simple-io-${version}";
   src = fetchFromGitHub {
     owner = "Lysxia";
     repo = "coq-simple-io";
     rev = version;
-    sha256 = "06gnbl8chv6ig18rlxnp8gg0np6863kxd7j15h46q0v1cnpx84lp";
+    sha256 = "1im1vwp7l7ha8swnhgbih0qjg187n8yx14i003nf6yy7p0ryxc9m";
   };
 
   buildInputs = [ coq ] ++ (with coq.ocamlPackages; [ ocaml ocamlbuild ]);

pkgs/development/haskell-modules/configuration-common.nix

@@ -860,7 +860,7 @@ self: super: {
   # Wrap the generated binaries to include their run-time dependencies in
   # $PATH. Also, cryptol needs a version of sbl that's newer than what we have
   # in LTS-13.x.
-  cryptol = overrideCabal (super.cryptol.override { sbv = self.sbv_8_2; }) (drv: {
+  cryptol = overrideCabal (super.cryptol.override { sbv = self.sbv_8_3; }) (drv: {
     buildTools = drv.buildTools or [] ++ [ pkgs.makeWrapper ];
     postInstall = drv.postInstall or "" + ''
       for b in $out/bin/cryptol $out/bin/cryptol-html; do
@@ -1099,7 +1099,14 @@ self: super: {
 
   # Generate shell completion.
   cabal2nix = generateOptparseApplicativeCompletion "cabal2nix" super.cabal2nix;
-  stack = generateOptparseApplicativeCompletion "stack" super.stack;
+  stack = generateOptparseApplicativeCompletion "stack" (super.stack.overrideScope (self: super: {
+    ansi-terminal = self.ansi-terminal_0_9_1;
+    concurrent-output = self.concurrent-output_1_10_10; # needed for new ansi-terminal version
+    rio = self.rio_0_1_9_2;
+    hi-file-parser = dontCheck super.hi-file-parser;    # Avoid depending on newer hspec versions.
+    http-download = dontCheck super.http-download;
+    pantry-tmp = dontCheck super.pantry-tmp;
+  }));
 
   # musl fixes
   # dontCheck: use of non-standard strptime "%s" which musl doesn't support; only used in test
@@ -1174,7 +1181,7 @@ self: super: {
   # https://github.com/mgajda/json-autotype/issues/25
   json-autotype = dontCheck super.json-autotype;
 
-  # The LTS-13.x version doesn't suffice to build hlint, hoogle, etc.
+  # The LTS-13.x versions doesn't suffice to build these packages.
   hlint = super.hlint.overrideScope (self: super: { haskell-src-exts = self.haskell-src-exts_1_21_0; });
   hoogle = super.hoogle.overrideScope (self: super: { haskell-src-exts = self.haskell-src-exts_1_21_0; });
 
@@ -1217,8 +1224,11 @@ self: super: {
 
   # Use latest pandoc despite what LTS says.
   # Test suite fails in both 2.5 and 2.6: https://github.com/jgm/pandoc/issues/5309.
-  pandoc = doDistribute super.pandoc_2_7_2;
+  cmark-gfm = self.cmark-gfm_0_2_0;
+  pandoc = doDistribute super.pandoc_2_7_3;
   pandoc-citeproc = doDistribute super.pandoc-citeproc_0_16_2;
+  skylighting = self.skylighting_0_8_1_1;
+  skylighting-core = self.skylighting-core_0_8_1_1;
 
   # Current versions of tasty-hedgehog need hedgehog 1.x, which
   # we don't have in LTS-13.x.
@@ -1270,4 +1280,13 @@ self: super: {
   # https://github.com/pruvisto/heap/issues/11
   heap = dontCheck super.heap;
 
+  # https://github.com/hslua/tasty-lua/issues/1
+  tasty-lua = dontCheck super.tasty-lua;
+
+  # Test suite won't link for no apparent reason.
+  constraints-deriving = dontCheck super.constraints-deriving;
+
+  # The old LTS-13.x version does not compile.
+  ip = self.ip_1_5_0;
+
 } // import ./configuration-tensorflow.nix {inherit pkgs haskellLib;} self super

pkgs/development/haskell-modules/configuration-hackage2nix.yaml

@@ -43,8 +43,7 @@ core-packages:
   - ghcjs-base-0
 
 default-package-overrides:
-  - ghc-lib-parser ==0.20190523  # newer versions break hlint
+  # LTS Haskell 13.25
-  # LTS Haskell 13.24
   - abstract-deque ==0.3
   - abstract-deque-tests ==0.3
   - abstract-par ==0.3.3
@@ -212,7 +211,7 @@ default-package-overrides:
   - asn1-types ==0.3.2
   - assert-failure ==0.1.2.2
   - astro ==0.4.2.1
-  - async ==2.2.1
+  - async ==2.2.2
   - async-extra ==0.2.0.0
   - async-refresh ==0.3.0.0
   - async-refresh-tokens ==0.4.0.0
@@ -237,7 +236,7 @@ default-package-overrides:
   - avers ==0.0.17.1
   - avers-api ==0.1.0
   - avers-server ==0.1.0.1
-  - avro ==0.4.4.2
+  - avro ==0.4.4.3
   - avwx ==0.3.0.2
   - axel ==0.0.9
   - backprop ==0.2.6.2
@@ -446,7 +445,7 @@ default-package-overrides:
   - concurrent-supply ==0.1.8
   - cond ==0.4.1.1
   - conduit ==1.3.1.1
-  - conduit-algorithms ==0.0.9.0
+  - conduit-algorithms ==0.0.10.1
   - conduit-combinators ==1.3.0
   - conduit-concurrent-map ==0.1.1
   - conduit-connection ==0.1.0.4
@@ -464,7 +463,7 @@ default-package-overrides:
   - console-style ==0.0.2.1
   - constraint ==0.1.3.0
   - constraints ==0.10.1
-  - contravariant ==1.5.1
+  - contravariant ==1.5.2
   - contravariant-extras ==0.3.4
   - control-bool ==0.2.1
   - control-dsl ==0.2.1.3
@@ -526,7 +525,7 @@ default-package-overrides:
   - cusparse ==0.2.0.0
   - cutter ==0.0
   - cyclotomic ==1.0
-  - czipwith ==1.0.1.1
+  - czipwith ==1.0.1.2
   - data-accessor ==0.2.2.8
   - data-accessor-mtl ==0.2.0.4
   - data-accessor-template ==0.2.1.16
@@ -584,7 +583,7 @@ default-package-overrides:
   - dhall ==1.19.1
   - dhall-bash ==1.0.18
   - dhall-json ==1.2.6
-  - dhall-text ==1.0.17
+  - dhall-text ==1.0.18
   - diagrams ==1.4
   - diagrams-contrib ==1.4.3
   - diagrams-core ==1.4.1.1
@@ -624,7 +623,7 @@ default-package-overrides:
   - double-conversion ==2.0.2.0
   - download ==0.3.2.7
   - drinkery ==0.4
-  - dsp ==0.2.4.1
+  - dsp ==0.2.5
   - dual-tree ==0.2.2
   - dublincore-xml-conduit ==0.1.0.2
   - dunai ==0.5.1
@@ -672,7 +671,7 @@ default-package-overrides:
   - errors ==2.3.0
   - errors-ext ==0.4.2
   - error-util ==0.0.1.2
-  - ersatz ==0.4.6
+  - ersatz ==0.4.7
   - esqueleto ==2.6.0
   - etc ==0.4.1.0
   - eventful-core ==0.2.0
@@ -828,19 +827,19 @@ default-package-overrides:
   - ghc-typelits-knownnat ==0.6
   - ghc-typelits-natnormalise ==0.6.2
   - ghost-buster ==0.1.1.0
-  - gi-atk ==2.0.15
+  - gi-atk ==2.0.18
   - gi-cairo ==1.0.17
   - gi-gdk ==3.0.16
-  - gi-gdkpixbuf ==2.0.18
+  - gi-gdkpixbuf ==2.0.20
   - gi-gio ==2.0.19
   - gi-glib ==2.0.17
-  - gi-gobject ==2.0.16
+  - gi-gobject ==2.0.19
   - gi-gtk ==3.0.27
   - gi-gtk-hs ==0.3.6.3
   - gi-gtksource ==3.0.16
   - gi-javascriptcore ==4.0.16
   - gingersnap ==0.3.1.0
-  - gi-pango ==1.0.16
+  - gi-pango ==1.0.19
   - giphy-api ==0.6.0.1
   - githash ==0.1.3.1
   - github-release ==1.2.4
@@ -894,7 +893,7 @@ default-package-overrides:
   - hamtsolo ==1.0.3
   - HandsomeSoup ==0.4.2
   - hapistrano ==0.3.9.2
-  - happy ==1.19.10
+  - happy ==1.19.11
   - hasbolt ==0.1.3.3
   - hashable ==1.2.7.0
   - hashable-time ==0.2.0.2
@@ -1045,7 +1044,7 @@ default-package-overrides:
   - http-common ==0.8.2.0
   - http-conduit ==2.3.7.1
   - http-date ==0.0.8
-  - http-directory ==0.1.2
+  - http-directory ==0.1.4
   - httpd-shed ==0.4.0.3
   - http-link-header ==1.0.3.1
   - http-media ==0.7.1.3
@@ -1073,8 +1072,8 @@ default-package-overrides:
   - hw-json ==0.9.0.1
   - hw-mquery ==0.1.0.3
   - hw-packed-vector ==0.0.0.1
-  - hw-parser ==0.1.0.0
+  - hw-parser ==0.1.0.1
-  - hw-prim ==0.6.2.24
+  - hw-prim ==0.6.2.25
   - hw-rankselect ==0.12.0.4
   - hw-rankselect-base ==0.3.2.1
   - hw-streams ==0.0.0.10
@@ -1117,7 +1116,7 @@ default-package-overrides:
   - inline-c-cpp ==0.3.0.2
   - inliterate ==0.1.0
   - insert-ordered-containers ==0.2.2
-  - inspection-testing ==0.4.1.2
+  - inspection-testing ==0.4.2.1
   - instance-control ==0.1.2.0
   - integer-logarithms ==1.0.3
   - integration ==0.2.1
@@ -1145,8 +1144,8 @@ default-package-overrides:
   - IPv6Addr ==1.1.2
   - ipython-kernel ==0.9.1.0
   - irc ==0.6.1.0
-  - irc-client ==1.1.0.6
+  - irc-client ==1.1.0.7
-  - irc-conduit ==0.3.0.2
+  - irc-conduit ==0.3.0.3
   - irc-ctcp ==0.1.3.0
   - islink ==0.1.0.0
   - iso3166-country-codes ==0.20140203.8
@@ -1211,6 +1210,7 @@ default-package-overrides:
   - leancheck ==0.8.0
   - leancheck-instances ==0.0.3
   - leapseconds-announced ==2017.1.0.1
+  - learn-physics ==0.6.4
   - lens ==4.17.1
   - lens-action ==0.2.3
   - lens-aeson ==1.0.2
@@ -1281,7 +1281,7 @@ default-package-overrides:
   - markdown ==0.1.17.4
   - markdown-unlit ==0.5.0
   - markov-chain ==0.0.3.4
-  - massiv ==0.2.8.0
+  - massiv ==0.2.8.1
   - massiv-io ==0.1.6.0
   - mathexpr ==0.3.0.0
   - math-functions ==0.3.1.0
@@ -1424,7 +1424,7 @@ default-package-overrides:
   - network-ip ==0.3.0.2
   - network-messagepack-rpc ==0.1.1.0
   - network-multicast ==0.2.0
-  - network-simple ==0.4.3
+  - network-simple ==0.4.4
   - network-simple-tls ==0.3.2
   - network-transport ==0.5.4
   - network-transport-composed ==0.2.1
@@ -1442,6 +1442,7 @@ default-package-overrides:
   - nonemptymap ==0.0.6.0
   - non-empty-sequence ==0.2.0.2
   - non-negative ==0.1.2
+  - not-gloss ==0.7.7.0
   - nowdoc ==0.1.1.0
   - nqe ==0.6.1
   - nsis ==0.3.3
@@ -1543,7 +1544,7 @@ default-package-overrides:
   - pg-transact ==0.1.0.1
   - phantom-state ==0.2.1.2
   - pid1 ==0.1.2.0
-  - pipes ==4.3.9
+  - pipes ==4.3.10
   - pipes-aeson ==0.4.1.8
   - pipes-attoparsec ==0.5.1.5
   - pipes-binary ==0.4.2
@@ -1634,7 +1635,7 @@ default-package-overrides:
   - protolude ==0.2.3
   - proxied ==0.3.1
   - psql-helpers ==0.1.0.0
-  - psqueues ==0.2.7.1
+  - psqueues ==0.2.7.2
   - pureMD5 ==2.1.3
   - purescript-bridge ==0.13.0.0
   - pure-zlib ==0.6.4
@@ -1662,7 +1663,7 @@ default-package-overrides:
   - ramus ==0.1.2
   - rando ==0.0.0.4
   - random ==1.1
-  - random-bytestring ==0.1.3.1
+  - random-bytestring ==0.1.3.2
   - random-fu ==0.2.7.0
   - random-shuffle ==0.0.4
   - random-source ==0.3.0.6
@@ -1706,7 +1707,7 @@ default-package-overrides:
   - regex-tdfa ==1.2.3.2
   - regex-tdfa-text ==1.0.0.3
   - regex-with-pcre ==1.0.2.0
-  - registry ==0.1.5.2
+  - registry ==0.1.6.0
   - reinterpret-cast ==0.1.0
   - relapse ==1.0.0.0
   - relational-query ==0.12.2.1
@@ -1731,6 +1732,7 @@ default-package-overrides:
   - rev-state ==0.1.2
   - rfc1751 ==0.1.2
   - rfc5051 ==0.1.0.4
+  - rg ==1.4.0.0
   - rio ==0.1.8.0
   - rio-orphans ==0.1.1.0
   - rng-utils ==0.3.0
@@ -1809,7 +1811,7 @@ default-package-overrides:
   - servant-foreign ==0.15
   - servant-js ==0.9.4
   - servant-JuicyPixels ==0.3.0.4
-  - servant-kotlin ==0.1.1.7
+  - servant-kotlin ==0.1.1.8
   - servant-lucid ==0.8.1
   - servant-mock ==0.8.5
   - servant-pandoc ==0.5.0.0
@@ -1885,6 +1887,7 @@ default-package-overrides:
   - sox ==0.2.3.1
   - soxlib ==0.0.3.1
   - sparse-linear-algebra ==0.3.1
+  - spatial-math ==0.5.0.1
   - special-values ==0.1.0.0
   - speculate ==0.3.5
   - speedy-slice ==0.3.0
@@ -1928,7 +1931,7 @@ default-package-overrides:
   - streaming ==0.2.2.0
   - streaming-attoparsec ==1.0.0.1
   - streaming-bytestring ==0.1.6
-  - streaming-commons ==0.2.1.0
+  - streaming-commons ==0.2.1.1
   - streaming-wai ==0.1.1
   - streamly ==0.5.2
   - streamproc ==1.6.2
@@ -2077,7 +2080,7 @@ default-package-overrides:
   - tldr ==0.4.0.1
   - tls ==1.4.1
   - tls-debug ==0.4.5
-  - tls-session-manager ==0.0.0.2
+  - tls-session-manager ==0.0.1.0
   - tmapchan ==0.0.3
   - tmapmvar ==0.0.4
   - tmp-postgres ==0.1.2.2
@@ -2102,7 +2105,8 @@ default-package-overrides:
   - tuple-sop ==0.3.1.0
   - tuple-th ==0.2.5
   - turtle ==1.5.14
-  - typed-process ==0.2.4.0
+  - TypeCompose ==0.9.14
+  - typed-process ==0.2.4.1
   - type-fun ==0.1.1
   - type-hint ==0.1
   - type-level-integers ==0.0.1
@@ -2145,7 +2149,7 @@ default-package-overrides:
   - unix-bytestring ==0.3.7.3
   - unix-compat ==0.5.1
   - unix-time ==0.4.5
-  - unliftio ==0.2.10
+  - unliftio ==0.2.11
   - unliftio-core ==0.1.2.0
   - unlit ==0.4.0.0
   - unordered-containers ==0.2.9.0
@@ -2206,7 +2210,7 @@ default-package-overrides:
   - wai-app-static ==3.1.6.3
   - wai-cli ==0.1.1
   - wai-conduit ==3.0.0.4
-  - wai-cors ==0.2.6
+  - wai-cors ==0.2.7
   - wai-eventsource ==3.0.0
   - wai-extra ==3.0.26
   - wai-handler-launch ==3.0.2.4
@@ -2729,6 +2733,7 @@ broken-packages:
   - algebra
   - algebra-sql
   - algebraic
+  - algebraic-graphs
   - algebraic-prelude
   - algo-s
   - AlgoRhythm
@@ -3166,6 +3171,7 @@ broken-packages:
   - blockhash
   - Blogdown
   - blogination
+  - BlogLiterately
   - BlogLiterately-diagrams
   - bloodhound
   - bloodhound-amazonka-auth
@@ -3652,6 +3658,8 @@ broken-packages:
   - conduit-resumablesink
   - conduit-throttle
   - conduit-tokenize-attoparsec
+  - conduit-vfs
+  - conduit-vfs-zip
   - conduit-zstd
   - conf
   - confcrypt
@@ -3674,6 +3682,7 @@ broken-packages:
   - consistent
   - console-program
   - const-math-ghc-plugin
+  - constrained-categories
   - constrained-category
   - constrained-dynamic
   - constrained-monads
@@ -3681,7 +3690,6 @@ broken-packages:
   - constraint-manip
   - constraint-reflection
   - ConstraintKinds
-  - constraints-deriving
   - constraints-emerge
   - constraints-extras
   - constructive-algebra
@@ -4020,6 +4028,7 @@ broken-packages:
   - dgs
   - dhall-check
   - dhall-nix
+  - dhall-to-cabal
   - dhcp-lease-parser
   - di
   - di-df1
@@ -4058,6 +4067,7 @@ broken-packages:
   - digestive-functors-hsp
   - DigitalOcean
   - digitalocean-kzs
+  - digraph
   - dimensional-tf
   - DimensionalHash
   - dingo-core
@@ -4073,6 +4083,7 @@ broken-packages:
   - direct-rocksdb
   - directed-cubical
   - dirfiles
+  - dirtree
   - discogs-haskell
   - discord-gateway
   - discord-haskell
@@ -4139,6 +4150,7 @@ broken-packages:
   - doctest-discover-configurator
   - doctest-driver-gen
   - doctest-prop
+  - docusign-client
   - docusign-example
   - docvim
   - doi
@@ -4174,6 +4186,7 @@ broken-packages:
   - DrIFT-cabalized
   - drifter-postgresql
   - drmaa
+  - drone
   - dropbox-sdk
   - dropsolve
   - ds-kanren
@@ -4277,6 +4290,7 @@ broken-packages:
   - Emping
   - Empty
   - empty-monad
+  - enchant
   - encoding
   - encoding-io
   - engine-io-growler
@@ -4818,12 +4832,27 @@ broken-packages:
   - ghclive
   - ght
   - gi-cairo-again
+  - gi-dbusmenu
+  - gi-dbusmenugtk3
+  - gi-gdkx11
+  - gi-ggit
+  - gi-girepository
+  - gi-gst
+  - gi-gstaudio
+  - gi-gstbase
   - gi-gstpbutils
   - gi-gsttag
+  - gi-gstvideo
   - gi-gtkosxapplication
+  - gi-handy
   - gi-notify
+  - gi-ostree
+  - gi-pangocairo
   - gi-poppler
+  - gi-secret
+  - gi-soup
   - gi-wnck
+  - gi-xlib
   - giak
   - Gifcurry
   - ginger
@@ -4852,6 +4881,7 @@ broken-packages:
   - github-webhook-handler
   - github-webhook-handler-snap
   - gitignore
+  - gitit
   - gitlab-api
   - gitlib-cross
   - gitlib-libgit2
@@ -4872,6 +4902,7 @@ broken-packages:
   - gli
   - glicko
   - glider-nlp
+  - glirc
   - GLMatrix
   - glob-posix
   - global
@@ -5013,6 +5044,7 @@ broken-packages:
   - GTALib
   - gtfs
   - gtk-serialized-event
+  - gtk-sni-tray
   - gtk-toy
   - gtk2hs-hello
   - gtk2hs-rpn
@@ -5351,6 +5383,7 @@ broken-packages:
   - hasql-backend
   - hasql-class
   - hasql-cursor-query
+  - hasql-cursor-transaction
   - hasql-dynamic-statements
   - hasql-generic
   - hasql-implicits
@@ -5382,6 +5415,7 @@ broken-packages:
   - haxl-amazonka
   - haxl-facebook
   - haxparse
+  - haxr
   - haxr-th
   - haxy
   - hayland
@@ -5442,6 +5476,7 @@ broken-packages:
   - heckle
   - hedgehog-checkers
   - hedgehog-checkers-lens
+  - hedgehog-classes
   - hedgehog-fn
   - hedgehog-gen-json
   - hedgehog-quickcheck
@@ -5536,6 +5571,7 @@ broken-packages:
   - hharp
   - HHDL
   - hhp
+  - hi-file-parser
   - hi3status
   - hiccup
   - hichi
@@ -5593,6 +5629,7 @@ broken-packages:
   - hjsonpointer
   - hjsonschema
   - HJVM
+  - hkgr
   - hlatex
   - hlbfgsb
   - hlcm
@@ -5730,6 +5767,7 @@ broken-packages:
   - hpqtypes
   - hpqtypes-extras
   - hprotoc-fork
+  - hprox
   - hps
   - hps-cairo
   - hps-kmeans
@@ -5742,6 +5780,7 @@ broken-packages:
   - hR
   - hranker
   - HRay
+  - hrfsize
   - hricket
   - Hricket
   - hriemann
@@ -5845,7 +5884,6 @@ broken-packages:
   - hslinks
   - hslogger-reader
   - hslogstash
-  - hslua-module-system
   - hsluv-haskell
   - hsmagick
   - HSmarty
@@ -5948,6 +5986,7 @@ broken-packages:
   - http-conduit-browser
   - http-conduit-downloader
   - http-dispatch
+  - http-download
   - http-enumerator
   - http-grammar
   - http-kinder
@@ -5957,6 +5996,7 @@ broken-packages:
   - http-querystring
   - http-response-decoder
   - http-shed
+  - http-streams
   - http-wget
   - http2-client-grpc
   - http2-grpc-types
@@ -5966,6 +6006,7 @@ broken-packages:
   - htune
   - htvm
   - htzaar
+  - hubigraph
   - huck
   - HueAPI
   - huff
@@ -5999,6 +6040,7 @@ broken-packages:
   - hw-dump
   - hw-eliasfano
   - hw-excess
+  - hw-fingertree
   - hw-ip
   - hw-json
   - hw-json-lens
@@ -6188,7 +6230,6 @@ broken-packages:
   - iostring
   - iothread
   - iotransaction
-  - ip
   - ip2location
   - ip2proxy
   - ipatch
@@ -6612,6 +6653,7 @@ broken-packages:
   - limp-cbc
   - linda
   - linden
+  - line-drawing
   - linear-accelerate
   - linear-algebra-cblas
   - linear-circuit
@@ -6991,6 +7033,7 @@ broken-packages:
   - mollie-api-haskell
   - monad-atom
   - monad-atom-simple
+  - monad-chronicle
   - monad-codec
   - monad-dijkstra
   - monad-exception
@@ -7070,6 +7113,9 @@ broken-packages:
   - mosaico-lib
   - moto
   - moto-postgresql
+  - motor
+  - motor-diagrams
+  - motor-reflection
   - mount
   - movie-monad
   - mp
@@ -7315,6 +7361,7 @@ broken-packages:
   - NoTrace
   - np-linear
   - nptools
+  - ntha
   - ntrip-client
   - NTRU
   - null-canvas
@@ -7481,6 +7528,7 @@ broken-packages:
   - pang-a-lambda
   - pangraph
   - panpipe
+  - pantry-tmp
   - papa-export
   - papa-implement
   - papa-include
@@ -7708,6 +7756,7 @@ broken-packages:
   - plugins
   - plugins-auto
   - plugins-multistage
+  - plur
   - plural
   - png-file
   - pngload
@@ -7732,6 +7781,9 @@ broken-packages:
   - polydata
   - polydata-core
   - polynomial
+  - polysemy
+  - polysemy-plugin
+  - polysemy-zoo
   - polyseq
   - polysoup
   - polytypeable
@@ -8214,6 +8266,7 @@ broken-packages:
   - reversi
   - ReviewBoard
   - rewrite
+  - rewrite-inspector
   - rewriting
   - rezoom
   - rfc
@@ -8430,6 +8483,7 @@ broken-packages:
   - secret-sharing
   - secrm
   - sednaDBXML
+  - selda-json
   - selectors
   - SelectSequencesFromMSA
   - selenium
@@ -8439,6 +8493,8 @@ broken-packages:
   - Semantique
   - semdoc
   - semi-iso
+  - semialign
+  - semialign-indexed
   - semibounded-lattices
   - Semigroup
   - semigroupoids-syntax
@@ -8502,6 +8558,7 @@ broken-packages:
   - servant-pushbullet-client
   - servant-py
   - servant-quickcheck
+  - servant-reason
   - servant-reflex
   - servant-router
   - servant-scotty
@@ -8522,6 +8579,7 @@ broken-packages:
   - serversession-frontend-snap
   - serversession-frontend-yesod
   - services
+  - ses-html
   - ses-html-snaplet
   - SessionLogger
   - sessions
@@ -8868,28 +8926,6 @@ broken-packages:
   - stable-marriage
   - stable-memo
   - stable-tree
-  - stack-bump
-  - stack-hpc-coveralls
-  - stack-lib
-  - stack-network
-  - stack-prism
-  - stack-run
-  - stack-run-auto
-  - stack-type
-  - stack2cabal
-  - stackage
-  - stackage-build-plan
-  - stackage-cabal
-  - stackage-cli
-  - stackage-curator
-  - stackage-metadata
-  - stackage-query
-  - stackage-sandbox
-  - stackage-setup
-  - stackage-to-hackage
-  - stackage-types
-  - stackage-upload
-  - stackage2nix
   - standalone-derive-topdown
   - standalone-haddock
   - starling
@@ -8979,6 +9015,7 @@ broken-packages:
   - stripe
   - stripe-haskell
   - stripe-http-client
+  - stripe-http-streams
   - strongswan-sql
   - structural-induction
   - structural-traversal
@@ -9123,7 +9160,6 @@ broken-packages:
   - tasty-jenkins-xml
   - tasty-laws
   - tasty-lens
-  - tasty-lua
   - tasty-quickcheck-laws
   - tasty-stats
   - tasty-tap
@@ -9203,6 +9239,7 @@ broken-packages:
   - text-containers
   - text-generic-pretty
   - text-icu-normalized
+  - text-icu-translit
   - text-lens
   - text-locale-encoding
   - text-markup
@@ -9210,6 +9247,7 @@ broken-packages:
   - text-plus
   - text-position
   - text-register-machine
+  - text-show-instances
   - text-time
   - text-utf8
   - text-xml-qq
@@ -9240,6 +9278,7 @@ broken-packages:
   - Theora
   - theoremquest
   - theoremquest-client
+  - these-lens
   - these-skinny
   - thih
   - thimk
@@ -9344,6 +9383,7 @@ broken-packages:
   - trace-function-call
   - traced
   - tracetree
+  - tracing
   - tracker
   - trackit
   - traction
@@ -9374,6 +9414,16 @@ broken-packages:
   - travis-meta-yaml
   - trawl
   - traypoweroff
+  - tree-sitter
+  - tree-sitter-go
+  - tree-sitter-haskell
+  - tree-sitter-java
+  - tree-sitter-json
+  - tree-sitter-php
+  - tree-sitter-python
+  - tree-sitter-ruby
+  - tree-sitter-tsx
+  - tree-sitter-typescript
   - tree-traversals
   - TreeCounter
   - treemap-html
@@ -9822,6 +9872,7 @@ broken-packages:
   - word2vec-model
   - WordAlignment
   - wordchoice
+  - wordify
   - WordNet
   - WordNet-ghc74
   - wordpass
@@ -10080,6 +10131,7 @@ broken-packages:
   - yuuko
   - yx
   - yxdb-utils
+  - z3
   - z3-encoding
   - z85
   - zabt

pkgs/development/interpreters/php/default.nix

@@ -1,10 +1,10 @@
 # pcre functionality is tested in nixos/tests/php-pcre.nix
-{ lib, stdenv, fetchurl, flex, bison, autoconf
+{ lib, stdenv, fetchurl, autoconf, bison, libtool, pkgconfig, re2c
 , mysql, libxml2, readline, zlib, curl, postgresql, gettext
-, openssl, pcre, pcre2, pkgconfig, sqlite, config, libjpeg, libpng, freetype
+, openssl, pcre, pcre2, sqlite, config, libjpeg, libpng, freetype
 , libxslt, libmcrypt, bzip2, icu, openldap, cyrus_sasl, libmhash, unixODBC
 , uwimap, pam, gmp, apacheHttpd, libiconv, systemd, libsodium, html-tidy, libargon2
-, libzip, re2c, valgrind
+, libzip, valgrind
 }:
 
 with lib;
@@ -48,7 +48,7 @@ let
   , ftpSupport ? config.php.ftp or true
   , fpmSupport ? config.php.fpm or true
   , gmpSupport ? config.php.gmp or true
-  , ztsSupport ? config.php.zts or false
+  , ztsSupport ? (config.php.zts or false) || (apxs2Support)
   , calendarSupport ? config.php.calendar or true
   , sodiumSupport ? (config.php.sodium or true) && (versionAtLeast version "7.2")
   , tidySupport ? (config.php.tidy or false)
@@ -59,10 +59,8 @@ let
   , cliSupport ? config.php.cli or true
   , pharSupport ? config.php.phar or true
   , xmlrpcSupport ? (config.php.xmlrpc or false) && (libxml2Support)
-  , re2cSupport ? config.php.re2c or true
+  , cgotoSupport ? config.php.cgoto or false
-  , cgotoSupport ? (config.php.cgoto or false) && (re2cSupport)
   , valgrindSupport ? (config.php.valgrind or true) && (versionAtLeast version "7.2")
-  , valgrindPcreSupport ? (config.php.valgrindPcreSupport or false) && (valgrindSupport) && (versionAtLeast version "7.2")
   }:
 
     let
@@ -76,8 +74,8 @@ let
 
       enableParallelBuilding = true;
 
-      nativeBuildInputs = [ pkgconfig autoconf ];
+      nativeBuildInputs = [ autoconf bison libtool pkgconfig re2c ];
-      buildInputs = [ flex bison ]
+      buildInputs = [ ]
         ++ optional (versionOlder version "7.3") pcre
         ++ optional (versionAtLeast version "7.3") pcre2
         ++ optional withSystemd systemd
@@ -108,7 +106,6 @@ let
         ++ optional tidySupport html-tidy
         ++ optional argon2Support libargon2
         ++ optional libzipSupport libzip
-        ++ optional re2cSupport re2c
         ++ optional valgrindSupport valgrind;
 
       CXXFLAGS = optional stdenv.cc.isClang "-std=c++11";
@@ -192,8 +189,7 @@ let
       ++ optional (!pharSupport) "--disable-phar"
       ++ optional xmlrpcSupport "--with-xmlrpc"
       ++ optional cgotoSupport "--enable-re2c-cgoto"
-      ++ optional valgrindSupport "--with-valgrind=${valgrind.dev}"
+      ++ optional valgrindSupport "--with-valgrind=${valgrind.dev}";
-      ++ optional valgrindPcreSupport "--with-pcre-valgrind";
 
       hardeningDisable = [ "bindnow" ];
 

pkgs/development/libraries/babl/default.nix

@@ -1,11 +1,12 @@
 { stdenv, fetchurl }:
 
 stdenv.mkDerivation rec {
-  name = "babl-0.1.62";
+  pname = "babl";
+  version = "0.1.66";
 
   src = fetchurl {
-    url = "https://ftp.gtk.org/pub/babl/0.1/${name}.tar.bz2";
+    url = "https://ftp.gtk.org/pub/babl/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.bz2";
-    sha256 = "047msfzj8v4sfl61a2xhd69r9rh2pjq4lzpk3j10ijyv9qbry9yw";
+    sha256 = "0qx1dwbinxihwl2lmxi60qiqi402jlrdcnixx14kk6j88n9xi79n";
   };
 
   doCheck = true;

pkgs/development/libraries/goffice/default.nix

@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation rec {
   pname = "goffice";
-  version = "0.10.44";
+  version = "0.10.45";
 
   outputs = [ "out" "dev" "devdoc" ];
 
   src = fetchurl {
     url = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
-    sha256 = "1fd7cm6j0g0mqgpqs4y22b4gd2ll4mcyvg4d0q22d5ndjapl4q3d";
+    sha256 = "702ba567e9ec0bbdd9b1a8161cd24648b4868d57a6cb89128f13c125f6f31947";
   };
 
   nativeBuildInputs = [ pkgconfig intltool ];

pkgs/development/python-modules/cli-helpers/default.nix

@@ -13,11 +13,11 @@
 
 buildPythonPackage rec {
   pname = "cli_helpers";
-  version = "1.2.0";
+  version = "1.2.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0p9yklddpplncr765h6qrii1dgvvlqxj25n5400dwqas9lmij4fj";
+    sha256 = "0rd194l06aw4612j09b44pgh8b8l4cwmz7xgwsgdj9v8m3m25nwq";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/flask-migrate/default.nix

@@ -4,15 +4,15 @@ with stdenv.lib;
 
 buildPythonPackage rec {
   pname = "Flask-Migrate";
-  version = "2.3.1";
+  version = "2.5.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1awlb4q1l9iv794qjjxxyhcv4i69j77kh7nsg17a6kb909mglml3";
+    sha256 = "00nm76w4xymsiih6hq8y46wp026v7zkzq15cx39hp929ba3z2vx9";
   };
 
-  checkInputs = optional isPy3k glibcLocales;
+  checkInputs = [ flask_script ] ++ optional isPy3k glibcLocales;
-  propagatedBuildInputs = [ flask flask_sqlalchemy flask_script alembic ];
+  propagatedBuildInputs = [ flask flask_sqlalchemy alembic ];
 
   # tests invoke the flask cli which uses click and therefore has py3k encoding troubles
   preCheck = optionalString isPy3k ''

pkgs/development/python-modules/flask-script/default.nix

@@ -6,7 +6,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0zqh2yq8zk7m9b4xw1ryqmrljkdigfb3hk5155a3b5hkfnn6xxyf";
+    sha256 = "0r8w2v89nj6b9p91p495cga5m72a673l2wc0hp0zqk05j4yrc9b4";
   };
 
   propagatedBuildInputs = [ flask ];

pkgs/development/tools/bazel-watcher/default.nix

@@ -10,13 +10,13 @@
 
 buildBazelPackage rec {
   name = "bazel-watcher-${version}";
-  version = "0.9.1";
+  version = "0.10.3";
 
   src = fetchFromGitHub {
     owner = "bazelbuild";
     repo = "bazel-watcher";
     rev = "v${version}";
-    sha256 = "1gjbv67ydyb0mafpp59qr9n8f8vva2mwhgan6lxxl0i9yfx7qc6p";
+    sha256 = "17z4nqqsdrainbh8fmhf6sgrxwf7aknadmn94z1yqpxa7kb9x33v";
   };
 
   nativeBuildInputs = [ go git python ];
@@ -49,7 +49,7 @@ buildBazelPackage rec {
       sed -e '/^FILE:@bazel_gazelle_go_repository_tools.*/d' -i $bazelOut/external/\@*.marker
     '';
 
-    sha256 = "0p6yarz4wlb6h33n4slkczkdkaa93zc9jx55h8wl9vv81ahp0md5";
+    sha256 = "1ck1rsg5msd77abs889nl2n2i3jlah4d4vjz5wbsb3jyhzn8n5ny";
   };
 
   buildAttrs = {

pkgs/development/tools/build-managers/bazel/bash-tools-test.nix

@@ -1,4 +1,4 @@
-{ stdenv, writeText, runCommandCC, bazel }:
+{ stdenv, writeText, runCommandCC, bazel, runLocal, bazelTest }:
 
 # Tests that certain executables are available in bazel-executed bash shells.
 
@@ -22,21 +22,23 @@ let
     )
   '';
 
-  runLocal = name: script: runCommandCC name { preferLocalBuild = true; } script;
+  workspaceDir = runLocal "our_workspace" {} ''
-
-  workspaceDir = runLocal "our_workspace" ''
     mkdir $out
     cp ${WORKSPACE} $out/WORKSPACE
     cp ${fileIn} $out/input.txt
     cp ${fileBUILD} $out/BUILD
   '';
 
-  testBazel = runLocal "bazel-test-bash-tools" ''
+  testBazel = bazelTest {
-    export HOME=$(mktemp -d)
+    name = "bazel-test-bash-tools";
-    cp -r ${workspaceDir} wd && chmod +w wd && cd wd
+    bazelPkg = bazel;
-    ${bazel}/bin/bazel build :tool_usage
+    inherit workspaceDir;
-    cp bazel-genfiles/output.txt $out
+
-    echo "Testing content" && [ "$(cat $out | wc -l)" == "2" ] && echo "OK"
+    bazelScript = ''
-  '';
+      ${bazel}/bin/bazel build :tool_usage
+      cp bazel-genfiles/output.txt $out
+      echo "Testing content" && [ "$(cat $out | wc -l)" == "2" ] && echo "OK"
+    '';
+  };
 
 in testBazel

pkgs/development/tools/build-managers/bazel/default.nix

@@ -1,5 +1,7 @@
-{ stdenv, callPackage, lib, fetchurl, fetchpatch, runCommand, makeWrapper
+{ stdenv, callPackage, lib, fetchurl, fetchpatch, runCommand, runCommandCC, makeWrapper
-, zip, unzip, bash, writeCBin, coreutils
+# this package (through the fixpoint glass)
+, bazel
+, lr, xe, zip, unzip, bash, writeCBin, coreutils
 , which, python, perl, gawk, gnused, gnutar, gnugrep, gzip, findutils
 # Apple dependencies
 , cctools, clang, libcxx, CoreFoundation, CoreServices, Foundation
@@ -14,14 +16,42 @@
 
 let
   srcDeps = [
+    # From: $REPO_ROOT/WORKSPACE
     (fetchurl {
       url = "https://github.com/google/desugar_jdk_libs/archive/915f566d1dc23bc5a8975320cd2ff71be108eb9c.zip";
       sha256 = "0b926df7yxyyyiwm9cmdijy6kplf0sghm23sf163zh8wrk87wfi7";
     })
-
     (fetchurl {
-        url = "https://mirror.bazel.build/bazel_java_tools/java_tools_pkg-0.5.1.tar.gz";
+        url = "https://mirror.bazel.build/github.com/bazelbuild/skydoc/archive/2d9566b21fbe405acf5f7bf77eda30df72a4744c.tar.gz";
-        sha256 = "1ld8m5cj9j0r474f56pixcfi0xvx3w7pzwahxngs8f6ns0yimz5w";
+        sha256 = "4a1318fed4831697b83ce879b3ab70ae09592b167e5bda8edaff45132d1c3b3f";
+    })
+    (fetchurl {
+        url = "https://mirror.bazel.build/github.com/bazelbuild/bazel-skylib/archive/f83cb8dd6f5658bc574ccd873e25197055265d1c.tar.gz";
+        sha256 = "ba5d15ca230efca96320085d8e4d58da826d1f81b444ef8afccd8b23e0799b52";
+    })
+    (fetchurl {
+      url = "https://mirror.bazel.build/github.com/bazelbuild/rules_sass/archive/8ccf4f1c351928b55d5dddf3672e3667f6978d60.tar.gz";
+      sha256 = "d868ce50d592ef4aad7dec4dd32ae68d2151261913450fac8390b3fd474bb898";
+    })
+     (fetchurl {
+         url = "https://mirror.bazel.build/bazel_java_tools/releases/javac10/v3.2/java_tools_javac10_linux-v3.2.zip";
+         sha256 = "b93e7c556b01815afb6c248aa73f06b7ec912805bde8898eedac1e20d08f2e67";
+     })
+    (fetchurl {
+        url = "https://mirror.bazel.build/bazel_java_tools/releases/javac10/v3.2/java_tools_javac10_darwin-v3.2.zip";
+        sha256 = "1437327179b4284f7082cee0bdc3328f040e62fc5cc59c32f6824b8c520e2b7b";
+    })
+    (fetchurl {
+        url = "https://mirror.bazel.build/bazel_coverage_output_generator/releases/coverage_output_generator-v1.0.zip";
+        sha256 = "cc470e529fafb6165b5be3929ff2d99b38429b386ac100878687416603a67889";
+    })
+    (fetchurl {
+        url = "https://github.com/bazelbuild/rules_nodejs/archive/0.16.2.zip";
+        sha256 = "9b72bb0aea72d7cbcfc82a01b1e25bf3d85f791e790ddec16c65e2d906382ee0";
+    })
+    (fetchurl {
+        url = "https://mirror.bazel.build/bazel_android_tools/android_tools_pkg-0.2.tar.gz";
+        sha256 = "04f85f2dd049e87805511e3babc5cea3f5e72332b1627e34f3a5461cc38e815f";
     })
   ];
 
@@ -63,17 +93,19 @@ let
   # Java toolchain used for the build and tests
   javaToolchain = "@bazel_tools//tools/jdk:toolchain_host${buildJdkName}";
 
+  platforms = lib.platforms.linux ++ lib.platforms.darwin;
+
 in
 stdenv.mkDerivation rec {
 
-  version = "0.24.0";
+  version = "0.26.1";
 
   meta = with lib; {
     homepage = "https://github.com/bazelbuild/bazel/";
     description = "Build tool that builds code quickly and reliably";
     license = licenses.asl20;
     maintainers = [ maintainers.mboes ];
-    platforms = platforms.linux ++ platforms.darwin;
+    inherit platforms;
   };
 
   # Additional tests that check bazel’s functionality. Execute
@@ -81,16 +113,74 @@ stdenv.mkDerivation rec {
   #     nix-build . -A bazel.tests
   #
   # in the nixpkgs checkout root to exercise them locally.
-  passthru.tests = {
+  passthru.tests =
-    pythonBinPath = callPackage ./python-bin-path-test.nix {};
+    let
-    bashTools = callPackage ./bash-tools-test.nix {};
+      runLocal = name: attrs: script: runCommandCC name ({
-  };
+        preferLocalBuild = true;
+        meta.platforms = platforms;
+      } // attrs) script;
+
+      # bazel wants to extract itself into $install_dir/install every time it runs,
+      # so let’s do that only once.
+      extracted = bazelPkg:
+        let install_dir =
+          # `install_base` field printed by `bazel info`, minus the hash.
+          # yes, this path is kinda magic. Sorry.
+          "$HOME/.cache/bazel/_bazel_nixbld";
+        in runLocal "bazel-extracted-homedir" { passthru.install_dir = install_dir; } ''
+            export HOME=$(mktemp -d)
+            touch WORKSPACE # yeah, everything sucks
+            install_base="$(${bazelPkg}/bin/bazel info | grep install_base)"
+            # assert it’s actually below install_dir
+            [[ "$install_base" =~ ${install_dir} ]] \
+              || (echo "oh no! $install_base but we are \
+            trying to copy ${install_dir} to $out instead!"; exit 1)
+            cp -R ${install_dir} $out
+          '';
+
+      bazelTest = { name, bazelScript, workspaceDir, bazelPkg }:
+        let
+          be = extracted bazelPkg;
+        in runLocal name {} (
+          # skip extraction caching on Darwin, because nobody knows how Darwin works
+          (lib.optionalString (!stdenv.hostPlatform.isDarwin) ''
+            # set up home with pre-unpacked bazel
+            export HOME=$(mktemp -d)
+            mkdir -p ${be.install_dir}
+            cp -R ${be}/install ${be.install_dir}
+
+            # https://stackoverflow.com/questions/47775668/bazel-how-to-skip-corrupt-installation-on-centos6
+            # Bazel checks whether the mtime of the install dir files
+            # is >9 years in the future, otherwise it extracts itself again.
+            # see PosixFileMTime::IsUntampered in src/main/cpp/util
+            # What the hell bazel.
+            ${lr}/bin/lr -0 -U ${be.install_dir} | ${xe}/bin/xe -N0 -0 touch --date="9 years 6 months" {}
+          '')
+          +
+          ''
+            # Note https://github.com/bazelbuild/bazel/issues/5763#issuecomment-456374609
+            # about why to create a subdir for the workspace.
+            cp -r ${workspaceDir} wd && chmod u+w wd && cd wd
+
+            ${bazelScript}
+
+            touch $out
+          '');
+
+      bazelWithNixHacks = bazel.override { enableNixHacks = true; };
+    in {
+      pythonBinPathWithoutNixHacks = callPackage ./python-bin-path-test.nix{ inherit runLocal bazelTest; };
+      bashToolsWithoutNixHacks = callPackage ./bash-tools-test.nix { inherit runLocal bazelTest; };
+
+      pythonBinPathWithNixHacks = callPackage ./python-bin-path-test.nix{ inherit runLocal bazelTest; bazel = bazelWithNixHacks; };
+      bashToolsWithNixHacks = callPackage ./bash-tools-test.nix { inherit runLocal bazelTest; bazel = bazelWithNixHacks; };
+    };
 
   name = "bazel-${version}";
 
   src = fetchurl {
     url = "https://github.com/bazelbuild/bazel/releases/download/${version}/${name}-dist.zip";
-    sha256 = "11gsc00ghxqkbci8nrflkwq1lcvqawlgkaryj458b24si6bjl7b2";
+    sha256 = "000ny51hwnjyizm1md4w8q7m832jhf3c767pgbvg6nc7h67lzsf0";
   };
 
   # Necessary for the tests to pass on Darwin with sandbox enabled.
@@ -148,10 +238,6 @@ stdenv.mkDerivation rec {
       # https://github.com/NixOS/nixpkgs/pull/41589
       export NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE -isystem ${libcxx}/include/c++/v1"
 
-      # 10.10 apple_sdk Foundation doesn't have type arguments on classes
-      # Remove this when we update apple_sdk
-      sed -i -e 's/<.*\*>//g' tools/osx/xcode_locator.m
-
       # don't use system installed Xcode to run clang, use Nix clang instead
       sed -i -e "s;/usr/bin/xcrun clang;${stdenv.cc}/bin/clang $NIX_CFLAGS_COMPILE $NIX_LDFLAGS -framework CoreFoundation;g" \
         scripts/bootstrap/compile.sh \
@@ -159,6 +245,9 @@ stdenv.mkDerivation rec {
         src/tools/xcode/stdredirect/BUILD \
         tools/osx/BUILD
 
+      # nixpkgs's libSystem cannot use pthread headers directly, must import GCD headers instead
+      sed -i -e "/#include <pthread\/spawn.h>/i #include <dispatch/dispatch.h>" src/main/cpp/blaze_util_darwin.cc
+
       # clang installed from Xcode has a compatibility wrapper that forwards
       # invocations of gcc to clang, but vanilla clang doesn't
       sed -i -e 's;_find_generic(repository_ctx, "gcc", "CC", overriden_tools);_find_generic(repository_ctx, "clang", "CC", overriden_tools);g' tools/cpp/unix_cc_configure.bzl
@@ -193,7 +282,7 @@ stdenv.mkDerivation rec {
 
       # Fixup scripts that generate scripts. Not fixed up by patchShebangs below.
       substituteInPlace scripts/bootstrap/compile.sh \
-          --replace /bin/sh ${customBash}/bin/bash
+          --replace /bin/bash ${customBash}/bin/bash
 
       # add nix environment vars to .bazelrc
       cat >> .bazelrc <<EOF
@@ -297,7 +386,9 @@ stdenv.mkDerivation rec {
     cp ./bazel_src/scripts/zsh_completion/_bazel $out/share/zsh/site-functions/
   '';
 
-  doInstallCheck = true;
+  # Temporarily disabling for now. A new approach is needed for this derivation as Bazel
+  # accesses the internet during the tests which fails in a sandbox.
+  doInstallCheck = false;
   installCheckPhase = ''
     export TEST_TMPDIR=$(pwd)
 

pkgs/development/tools/build-managers/bazel/nix-hacks.patch

@@ -1,33 +1,35 @@
 diff -Naur a/src/main/java/com/google/devtools/build/lib/rules/repository/RepositoryDelegatorFunction.java b/src/main/java/com/google/devtools/build/lib/rules/repository/RepositoryDelegatorFunction.java
---- a/src/main/java/com/google/devtools/build/lib/rules/repository/RepositoryDelegatorFunction.java	1980-01-01 00:00:00.000000000 -0500
+--- a/src/main/java/com/google/devtools/build/lib/rules/repository/RepositoryDelegatorFunction.java	2019-06-12 20:39:37.420705161 -0700
-+++ b/src/main/java/com/google/devtools/build/lib/rules/repository/RepositoryDelegatorFunction.java	2018-01-18 08:17:22.420459162 -0500
++++ b/src/main/java/com/google/devtools/build/lib/rules/repository/RepositoryDelegatorFunction.java	2019-06-12 20:44:18.894429744 -0700
-@@ -287,21 +287,8 @@
+@@ -428,24 +428,7 @@
-           markerData.put(key, value);
+       try {
-         }
+         content = FileSystemUtils.readContent(markerPath, StandardCharsets.UTF_8);
-       }
+         String markerRuleKey = readMarkerFile(content, markerData);
--      boolean result = false;
+-        boolean verified = false;
--      if (markerRuleKey.equals(ruleKey)) {
+-        if (Preconditions.checkNotNull(ruleKey).equals(markerRuleKey)
--        result = handler.verifyMarkerData(rule, markerData, env);
+-            && Objects.equals(
--        if (env.valuesMissing()) {
+-                markerData.get(MANAGED_DIRECTORIES_MARKER),
+-                this.markerData.get(MANAGED_DIRECTORIES_MARKER))) {
+-          verified = handler.verifyMarkerData(rule, markerData, env);
+-          if (env.valuesMissing()) {
+-            return null;
+-          }
+-        }
+-
+-        if (verified) {
+           return new Fingerprint().addString(content).digestAndReset();
+-        } else {
+-          // So that we are in a consistent state if something happens while fetching the repository
+-          markerPath.delete();
 -          return null;
 -        }
--      }
+       } catch (IOException e) {
- 
+         throw new RepositoryFunctionException(e, Transience.TRANSIENT);
--      if (result) {
+       }
--        return new Fingerprint().addString(content).digestAndReset();
--      } else {
--        // So that we are in a consistent state if something happens while fetching the repository
--        markerPath.delete();
--        return null;
--      }
-+      return new Fingerprint().addString(content).digestAndReset();
- 
-     } catch (IOException e) {
-       throw new RepositoryFunctionException(e, Transience.TRANSIENT);
 diff -Naur a/src/main/java/com/google/devtools/build/lib/shell/JavaSubprocessFactory.java b/src/main/java/com/google/devtools/build/lib/shell/JavaSubprocessFactory.java
---- a/src/main/java/com/google/devtools/build/lib/shell/JavaSubprocessFactory.java	1980-01-01 00:00:00.000000000 -0500
+--- a/src/main/java/com/google/devtools/build/lib/shell/JavaSubprocessFactory.java	2019-06-12 20:39:37.538708196 -0700
-+++ b/src/main/java/com/google/devtools/build/lib/shell/JavaSubprocessFactory.java	2018-01-18 08:17:53.274877980 -0500
++++ b/src/main/java/com/google/devtools/build/lib/shell/JavaSubprocessFactory.java	2019-06-12 20:44:18.863429602 -0700
-@@ -129,7 +129,6 @@
+@@ -146,7 +146,6 @@
      ProcessBuilder builder = new ProcessBuilder();
      builder.command(params.getArgv());
      if (params.getEnv() != null) {

pkgs/development/tools/build-managers/bazel/python-bin-path-test.nix

@@ -1,4 +1,4 @@
-{ stdenv, lib, writeText, runCommandCC, bazel }:
+{ stdenv, lib, writeText, bazel, bazelTest, runLocal }:
 
 let
   WORKSPACE = writeText "WORKSPACE" ''
@@ -22,16 +22,14 @@ let
       srcs = [ "lib.py" ],
     )
 
-    py_test(
+    py_binary(
       name = "bin",
       srcs = [ "bin.py" ],
       deps = [ ":lib" ],
     )
   '';
 
-  runLocal = name: script: runCommandCC name { preferLocalBuild = true; } script;
+  workspaceDir = runLocal "our_workspace" {} ''
-
-  workspaceDir = runLocal "our_workspace" ''
     mkdir $out
     cp ${WORKSPACE} $out/WORKSPACE
     mkdir $out/python
@@ -40,18 +38,16 @@ let
     cp ${pythonBUILD} $out/python/BUILD.bazel
   '';
 
-  testBazel = runLocal "bazel-test-builtin-rules" ''
+  testBazel = bazelTest {
-    export HOME=$(mktemp -d)
+    name = "bazel-test-builtin-rules";
-    # Note https://github.com/bazelbuild/bazel/issues/5763#issuecomment-456374609
+    inherit workspaceDir;
-    # about why to create a subdir for the workspace.
+    bazelPkg = bazel;
-    cp -r ${workspaceDir} wd && chmod u+w wd && cd wd
+    bazelScript = ''
-    ${bazel}/bin/bazel \
+      ${bazel}/bin/bazel \
-      test \
+        run \
-        --test_output=errors \
+          --host_javabase='@local_jdk//:jdk' \
-        --host_javabase='@local_jdk//:jdk' \
+          //python:bin
-        //...
+    '';
-
+  };
-    touch $out
-  '';
 
 in testBazel

pkgs/development/tools/continuous-integration/jenkins/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "jenkins-${version}";
-  version = "2.164.3";
+  version = "2.176.1";
 
   src = fetchurl {
     url = "http://mirrors.jenkins.io/war-stable/${version}/jenkins.war";
-    sha256 = "03m5ykl6kqih9li2fhyq9rf8x8djaj2rgjd2p897zzw5j0grkbx8";
+    sha256 = "130f9x4fvnf9a9ykf48axj9fgqaj2ssr9jhsflpi1gg78ch6xg4b";
   };
 
   buildCommand = ''

pkgs/development/tools/kythe/default.nix

@@ -1,12 +1,12 @@
 { stdenv, binutils , fetchurl, glibc, ncurses5 }:
 
 stdenv.mkDerivation rec {
-  version = "0.0.28";
+  version = "0.0.30";
-  name = "kythe-${version}";
+  pname = "kythe";
 
   src = fetchurl {
-    url = "https://github.com/google/kythe/releases/download/v0.0.28/kythe-v0.0.28.tar.gz";
+    url = "https://github.com/kythe/kythe/releases/download/v${version}/${pname}-v${version}.tar.gz";
-    sha256 = "1qc7cngpxw66m3krpr5x50ns7gb3bpv2bdfzpb5afl12qp0mi6zm";
+    sha256 = "12bwhqkxfbkh3mm4wfvqflwhmbzpmlhlfykdpy6h7p9ih9ky8w6r";
   };
 
   buildInputs =
@@ -23,7 +23,7 @@ stdenv.mkDerivation rec {
                 write_entries write_tables entrystream; do
       echo "Patching:" $exe
       patchelf --interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" $exe
-      patchelf --set-rpath "${stdenv.cc.cc.lib}/lib64:${ncurses5}/lib" $exe
+      patchelf --set-rpath "${stdenv.lib.makeLibraryPath [ stdenv.cc.cc ncurses5 ]}" $exe
     done
     cd ../
     cp -R ./ $out

pkgs/development/tools/rust/cargo-xbuild/default.nix

@@ -2,20 +2,20 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "cargo-xbuild";
-  version = "0.5.11";
+  version = "0.5.12";
 
   src = fetchFromGitHub {
     owner = "rust-osdev";
     repo = pname;
     rev = "v${version}";
-    sha256 = "04vgb443bmrfklvzhjfidpi3pp2svbc3bwq674m9fn7sbdp6rnwm";
+    sha256 = "1vjsss2zrja4kpr83vw6g0hf9xdx658wjhdiymzndbcf32qrx7x1";
   };
 
   cargoSha256 = "1r9i79lymfwpbcx2lp509v435qpkl9bqly1ya369p41n5yprrcjv";
 
   meta = with stdenv.lib; {
     description = "Automatically cross-compiles the sysroot crates core, compiler_builtins, and alloc";
-    homepage = https://github.com/rust-osdev/cargo-xbuild;
+    homepage = "https://github.com/rust-osdev/cargo-xbuild";
     license = with licenses; [ mit asl20 ];
     maintainers = with maintainers; [ xrelkd ];
     platforms = platforms.all;

pkgs/misc/drivers/epkowa/default.nix

@@ -7,7 +7,7 @@ libusb,
 sane-backends,
 rpm, cpio,
 getopt,
-patchelf, gcc
+patchelf, autoPatchelfHook, gcc
 }:
 
 let common_meta = {
@@ -161,6 +161,34 @@ let plugins = {
 
     meta = common_meta // { description = "iscan esci s80 plugin for "+passthru.hw; };
   };
+  network = stdenv.mkDerivation rec {
+    pname = "iscan-nt-bundle";
+    version = "1.0.0";
+    ntPluginVersion = "1.1.1-1";
+
+    buildInputs = [ stdenv.cc.cc.lib ];
+    nativeBuildInputs = [ autoPatchelfHook ];
+
+    src = fetchurl {
+      url = "https://download2.ebz.epson.net/iscan/general/rpm/x64/iscan-bundle-${version}.x64.rpm.tar.gz";
+      sha256 = "1k3dmv4ml21k6mafvcvgfymb1acpcdxpvyrbfh2yf07jzmn5if4f";
+    };
+    installPhase = ''
+      cd plugins
+      ${rpm}/bin/rpm2cpio iscan-network-nt-${ntPluginVersion}.x86_64.rpm | ${cpio}/bin/cpio -idmv
+
+      mkdir $out
+      cp -r usr/share $out
+      cp -r usr/lib64 $out/lib
+      mkdir $out/share/esci
+      '';
+    passthru = {
+      registrationCommand = "";
+      hw = "network";
+    };
+
+    meta = common_meta // { description = "iscan network plugin"; };
+  };
 };
 in
 
@@ -226,6 +254,8 @@ stdenv.mkDerivation rec {
     cp backend/epkowa.conf $out/etc/sane.d
     echo "epkowa" > $out/etc/sane.d/dll.conf
     ln -s ${iscan-data}/share/iscan-data $out/share/iscan-data
+    mkdir -p $out/lib/iscan
+    ln -s ${plugins.network}/lib/iscan/network $out/lib/iscan/network
     '';
   postFixup = ''
     # iscan-registry is a shell script requiring getopt

pkgs/misc/vim-plugins/generated.nix

@@ -61,12 +61,12 @@ let
 
   ale = buildVimPluginFrom2Nix {
     pname = "ale";
-    version = "2019-06-10";
+    version = "2019-06-13";
     src = fetchFromGitHub {
       owner = "w0rp";
       repo = "ale";
-      rev = "80ab12c7b645b392feb98723873d77b045a0a7e2";
+      rev = "6e28eec243c4df3cf3b67bac9f87fdd30c846cbd";
-      sha256 = "147p1i5a7bk8z2xsk8xbwwx0yic3fbz4dvsrwcfjik7ydnsy8xra";
+      sha256 = "15r479nwbxv29ryiiqn3yc7srg5yx1mj6whblxpnmjxjiwsy4yym";
     };
   };
 
@@ -182,12 +182,12 @@ let
 
   caw-vim = buildVimPluginFrom2Nix {
     pname = "caw-vim";
-    version = "2018-12-25";
+    version = "2019-06-13";
     src = fetchFromGitHub {
       owner = "tyru";
       repo = "caw.vim";
-      rev = "98805a60aef339e55e5b917fdb9f69c74e8d8340";
+      rev = "05c6b113dd82d2ad4d424b696b14a2b89a337541";
-      sha256 = "0nn3dg3lnbnfwgvxpjbalw9ff876798jrzlkrnzqkvrwxv6k7ks5";
+      sha256 = "1s56f8pqn5hldmi54qybjldi3lwyyznwf4jk2qnvp77civk8mjn9";
     };
   };
 
@@ -237,12 +237,12 @@ let
 
   coc-nvim = buildVimPluginFrom2Nix {
     pname = "coc-nvim";
-    version = "2019-06-11";
+    version = "2019-06-14";
     src = fetchFromGitHub {
       owner = "neoclide";
       repo = "coc.nvim";
-      rev = "c78a2807a74a6a7b005c4035a728c8be42a007fe";
+      rev = "3cf91b06a76a790c3f81f65b60f5ee289ae96d18";
-      sha256 = "14bkrnrgm6q3yryvavpi2sbfyv0ynsj6l31d6ygwc5b14ljyjd79";
+      sha256 = "1vng6k7xjp22vzcfx7r0jc9xpg4ak2gi9vqnd519kcg4ssr8nwfs";
     };
   };
 
@@ -414,23 +414,23 @@ let
 
   denite-nvim = buildVimPluginFrom2Nix {
     pname = "denite-nvim";
-    version = "2019-06-10";
+    version = "2019-06-14";
     src = fetchFromGitHub {
       owner = "Shougo";
       repo = "denite.nvim";
-      rev = "fc42dbb602193b7bd7fd1a473bc09b10512d2f90";
+      rev = "a4b32946e6f4c2d78500310245c8e567ff37528b";
-      sha256 = "0waq9729g5y4gihg63y76w5ddzwj2xixc1m8d4jjl6blkxajkxcm";
+      sha256 = "0gk99iw83jvhwh0srh1y0k0rqpvi3z6f7jhajhbx8wlf9dcsxl22";
     };
   };
 
   deol-nvim = buildVimPluginFrom2Nix {
     pname = "deol-nvim";
-    version = "2019-04-21";
+    version = "2019-06-12";
     src = fetchFromGitHub {
       owner = "Shougo";
       repo = "deol.nvim";
-      rev = "98e1d68336a757dd736a10f1dc7564458d52f5b7";
+      rev = "6ef9abb552873a53857ef9b4381a5a1eca95cd35";
-      sha256 = "09fgyh8yipgcd525jgjj3ci6xsg7zqq7rwlfx593mw5afsnwa7gi";
+      sha256 = "0n07xg5v2pyxhzk9rn37yc3i47c5qvni0vlsrpj6015q4g48v2z1";
     };
   };
 
@@ -549,12 +549,12 @@ let
 
   echodoc-vim = buildVimPluginFrom2Nix {
     pname = "echodoc-vim";
-    version = "2019-06-01";
+    version = "2019-06-12";
     src = fetchFromGitHub {
       owner = "Shougo";
       repo = "echodoc.vim";
-      rev = "a356d856702c275360ba5cfb91fc98542c2f075f";
+      rev = "c12d2e683fb749f9c0d4a099d894baa3d9d5f330";
-      sha256 = "1iml5v8cinanr6wq7rg3g6grg71vsyc6shvzc0q3s411fldmcmra";
+      sha256 = "1w8awylby9qasy0z6x4l5k9gw5sqqmsmpcvckj9ax1sp34psdzhx";
     };
   };
 
@@ -650,12 +650,12 @@ let
 
   ferret = buildVimPluginFrom2Nix {
     pname = "ferret";
-    version = "2019-06-10";
+    version = "2019-06-12";
     src = fetchFromGitHub {
       owner = "wincent";
       repo = "ferret";
-      rev = "f72610d8b890962fb3f6ad80b902d4790e90f507";
+      rev = "f6d7d01de8a92baee83218001c0bdbade8458a72";
-      sha256 = "15xyz25n8priam3s2wcvws05ry7w71v2m2j5bp0w1d5zmrw969p4";
+      sha256 = "1zsh7yc2mv1hv6gj7bhzbx4qqmasc32sxsdlh4sz95nxsfnk28dr";
     };
   };
 
@@ -750,12 +750,12 @@ let
 
   goyo-vim = buildVimPluginFrom2Nix {
     pname = "goyo-vim";
-    version = "2019-04-29";
+    version = "2019-06-13";
     src = fetchFromGitHub {
       owner = "junegunn";
       repo = "goyo.vim";
-      rev = "012290431a834752d2fce3dfc197dba3d7d1d0f8";
+      rev = "6b6ed2734084fdbb6315357ddcaecf9c8e6f143d";
-      sha256 = "0vqd75c2a5yjmiakv26cgd9wkqwzfbi93qm1vw9g2j5s96dcwa6a";
+      sha256 = "1ywlz1hn54kxyp5q0angriaarimq7ys7m6sk6l4x8jr1g2yh0afz";
     };
   };
 
@@ -816,12 +816,12 @@ let
 
   iceberg-vim = buildVimPluginFrom2Nix {
     pname = "iceberg-vim";
-    version = "2019-06-05";
+    version = "2019-06-13";
     src = fetchFromGitHub {
       owner = "cocopon";
       repo = "iceberg.vim";
-      rev = "ccd0c64a8e731233c12e5d8884495b121f8b1808";
+      rev = "e8316001e1130a042f8b4c8f49d78ed87b624f53";
-      sha256 = "1ifmw5sdh2y270gycdsa79wn6ldb5fdkq2ysipndyk2xc28bhv6w";
+      sha256 = "0p228laa5na7izink982ahksqhzwlxj8knb2wh5440z7chixmycc";
     };
   };
 
@@ -971,12 +971,12 @@ let
 
   lightline-vim = buildVimPluginFrom2Nix {
     pname = "lightline-vim";
-    version = "2019-06-03";
+    version = "2019-06-12";
     src = fetchFromGitHub {
       owner = "itchyny";
       repo = "lightline.vim";
-      rev = "3b7c7b83d2ef5f559158c84c5afb0f51656ccade";
+      rev = "80c242c3c5394fd5143b5d7e2741989ba04ae46a";
-      sha256 = "01q4rwjbk65nhacna0ai48adhqy7iq3ix23j9g70yz2awj9vq56i";
+      sha256 = "0k42wzwwhiqj6i1s2zdkmdnay85kwl4aw129nwcrrc4ahqhhh9fy";
     };
   };
 
@@ -1169,12 +1169,12 @@ let
 
   neoformat = buildVimPluginFrom2Nix {
     pname = "neoformat";
-    version = "2019-05-17";
+    version = "2019-06-13";
     src = fetchFromGitHub {
       owner = "sbdchd";
       repo = "neoformat";
-      rev = "9fea982b33627eefbfdf2836458b224bd1c724e4";
+      rev = "b60a530de93a1131a320fa10a289c9ffee771a1e";
-      sha256 = "1j9q2h41dpkn9g0j88s0daq0iy7c27xxz0cm5lw5ngpd2y6hnl40";
+      sha256 = "0f6drp06f0r6c5d777i5dh3kks1j73945ip8ng51v4803m7m2g3g";
     };
   };
 
@@ -1290,12 +1290,12 @@ let
 
   nerdtree = buildVimPluginFrom2Nix {
     pname = "nerdtree";
-    version = "2019-06-08";
+    version = "2019-06-13";
     src = fetchFromGitHub {
       owner = "scrooloose";
       repo = "nerdtree";
-      rev = "28eb47e2678cf629d92b4f1f00dd56cba22fc4ae";
+      rev = "12dea6ccb2381a2b6b8ae0bf17b4078699bbfec3";
-      sha256 = "18yj47zyiapgrxsg1hk497z6875bwqrl6jg395n91kf5cz9c269i";
+      sha256 = "0r3w1anbg57mifavb7lg4gdyji03hc9jmjs006prs2w8zfc9zqds";
     };
   };
 
@@ -1675,12 +1675,12 @@ let
 
   SpaceCamp = buildVimPluginFrom2Nix {
     pname = "SpaceCamp";
-    version = "2019-06-05";
+    version = "2019-06-13";
     src = fetchFromGitHub {
       owner = "jaredgorski";
       repo = "SpaceCamp";
-      rev = "de431dc161f8f839a47c6f1cb277e7318ddba6f5";
+      rev = "e2503139a55f4c2631cca64feb596b44d5b88f73";
-      sha256 = "032i1isc558rz2hmh3dfxnwgbqn7wdlhzz1c05v6bd7yyv0k5g23";
+      sha256 = "0zaa2dcgynwbhybyq3i3i9pxdz4hk2q3g0s48vm27sywr2kdzw63";
     };
   };
 
@@ -1884,12 +1884,12 @@ let
 
   traces-vim = buildVimPluginFrom2Nix {
     pname = "traces-vim";
-    version = "2019-06-10";
+    version = "2019-06-11";
     src = fetchFromGitHub {
       owner = "markonm";
       repo = "traces.vim";
-      rev = "e6f44ecfd4ccea9269aba69ea5547ade43eb03c5";
+      rev = "ce382caed5aed6a8b8b26a4ad7a750bfd9529869";
-      sha256 = "1yw66phpxd3hgnxj0bh5f6ypmbkiz4hn2jcg289cr0smd10a9vxk";
+      sha256 = "18sxnf9k3bpyk6fsy3qhiy56k5w5d9izb1wazz9gyfwwbygq455c";
     };
   };
 
@@ -1994,12 +1994,12 @@ let
 
   vim = buildVimPluginFrom2Nix {
     pname = "vim";
-    version = "2019-06-02";
+    version = "2019-06-11";
     src = fetchFromGitHub {
       owner = "dracula";
       repo = "vim";
-      rev = "a4f6b0abe6cad85330867a54893864e0d5c59359";
+      rev = "42a51ef8d9656b7d126ce8ad554045da16fe37da";
-      sha256 = "0krgb3whdgir6rd82syrx7pvr9mlzabrzn3h3a9cvcc0la73irql";
+      sha256 = "03cxaxm2yvxa80lj78aqycj09crikpwdr8151w1l5rhlwwbg18n9";
     };
   };
 
@@ -2225,12 +2225,12 @@ let
 
   vim-airline = buildVimPluginFrom2Nix {
     pname = "vim-airline";
-    version = "2019-06-11";
+    version = "2019-06-14";
     src = fetchFromGitHub {
       owner = "vim-airline";
       repo = "vim-airline";
-      rev = "28453d703825ba4c93869ba1ee1d38a6f281d7d3";
+      rev = "2db9b27e39bfd84cb432e001b4a3f41f633b3b7e";
-      sha256 = "0fqy2nlbn4jnsvl4zdp3rwzhb98sai5xq02jva2jskzakylvzinp";
+      sha256 = "07spj2jagg3vy8h5p2qyywk9lxb7hg8vq0n8cy88qfphi6hf27b7";
     };
   };
 
@@ -2368,12 +2368,12 @@ let
 
   vim-codefmt = buildVimPluginFrom2Nix {
     pname = "vim-codefmt";
-    version = "2019-04-17";
+    version = "2019-06-13";
     src = fetchFromGitHub {
       owner = "google";
       repo = "vim-codefmt";
-      rev = "fc45c30907106801f0bf443a9fa20300fc6ce100";
+      rev = "3be5d149e38b2e3582d6c1122632de7b802cd6f1";
-      sha256 = "0rnlcvv6jw0q9hhy0f5l52hv8kajymii8c1qlc04bpwm8ibkxjkn";
+      sha256 = "0m1nz8q7v6ljff7qgyzxc5qwadj6zmms26jzdxajq36a0l19n2yb";
     };
   };
 
@@ -2456,12 +2456,12 @@ let
 
   vim-css-color = buildVimPluginFrom2Nix {
     pname = "vim-css-color";
-    version = "2019-05-14";
+    version = "2019-06-12";
     src = fetchFromGitHub {
       owner = "ap";
       repo = "vim-css-color";
-      rev = "8a84356d5319cad3da2835bd5fbc6318500f31ce";
+      rev = "5a31c72cc51cb11118e44fb50ff77fc596348f77";
-      sha256 = "1yad8jrcna82ll893wf53ms2hqmcaa63g43yafxvlgmxw5yrh3im";
+      sha256 = "17a2i40z5145px4p4swvm003h4mdxd2hp89pyvrqal910d2g3hgb";
     };
   };
 
@@ -2522,12 +2522,12 @@ let
 
   vim-dispatch = buildVimPluginFrom2Nix {
     pname = "vim-dispatch";
-    version = "2019-06-09";
+    version = "2019-06-12";
     src = fetchFromGitHub {
       owner = "tpope";
       repo = "vim-dispatch";
-      rev = "597b338f3579ca6929c47465397974d366f4eccc";
+      rev = "2c5b28387ab50f6e6c6034a5b362b24be63734a3";
-      sha256 = "0amwsncrcxv49d7yaprngsyzl5dai8ff4r1i7mlq3x1s8s5inqqg";
+      sha256 = "0angxakjzf3sanjdyykr9igsl3z2xrcfkicpylhnk1rvjjsxlcd9";
     };
   };
 
@@ -2764,12 +2764,12 @@ let
 
   vim-go = buildVimPluginFrom2Nix {
     pname = "vim-go";
-    version = "2019-06-10";
+    version = "2019-06-13";
     src = fetchFromGitHub {
       owner = "fatih";
       repo = "vim-go";
-      rev = "5e1689db322e7bf104f43d7dd15e5a6bc6b0020c";
+      rev = "b6a0bde7d4c64a063ea1b6365e3dd24e2d4f4df1";
-      sha256 = "1lb580qj2q44ndxpigqqg84y70r7ix54w2zid2dav8bswcpdmzi3";
+      sha256 = "1lnwp4qqbzl6cwy75hhkafnppv2pgbaw2lf5fpbprwyd5aa5qh1q";
     };
   };
 
@@ -3337,12 +3337,12 @@ let
 
   vim-pandoc = buildVimPluginFrom2Nix {
     pname = "vim-pandoc";
-    version = "2019-05-21";
+    version = "2019-06-12";
     src = fetchFromGitHub {
       owner = "vim-pandoc";
       repo = "vim-pandoc";
-      rev = "11e86deecb715fe1b9ca04d9b313f9432013b2b1";
+      rev = "f8fa0274c2727d81afaedd970059e4132fba96fd";
-      sha256 = "171xkz7wvrb7c6c12sgf3v2clmbdand23wvi5rm6g8lf1x11kvsq";
+      sha256 = "1y84cllyb7mkq0x6a07dffa3zlgw3pbawgsgpcgkhz3nwazivxaf";
     };
   };
 
@@ -3942,12 +3942,12 @@ let
 
   vim-visual-multi = buildVimPluginFrom2Nix {
     pname = "vim-visual-multi";
-    version = "2019-06-11";
+    version = "2019-06-13";
     src = fetchFromGitHub {
       owner = "mg979";
       repo = "vim-visual-multi";
-      rev = "1533dd2a7e4b26652e0d6790f147e2dcc61a8a85";
+      rev = "c62107b163bc4f0bf718f32a019f19a548c8d332";
-      sha256 = "01qmp7gshh9k2fmb0xfx8kahn4bhdblr4sqqdvncbd4w26l7wipd";
+      sha256 = "0455mdill779lqnjvy63pz8v7c8fz9clikylhy4xmcjw136j8325";
     };
   };
 
@@ -4285,12 +4285,12 @@ let
 
   zig-vim = buildVimPluginFrom2Nix {
     pname = "zig-vim";
-    version = "2019-06-10";
+    version = "2019-06-13";
     src = fetchFromGitHub {
       owner = "zig-lang";
       repo = "zig.vim";
-      rev = "920e808f3ff5de3ab33d99a83edb2485acee79be";
+      rev = "636fc7a21f63a884d6065afbc773b23013cea1cf";
-      sha256 = "1aygwcsxn0ca9qbyzfr23dyn1wy2sa2im7ffdvybgamfqm092r9d";
+      sha256 = "1v30wdpslj74llqdpcwqhxz5sfqqiry9qwh3fmxmdfrg17qbr4g9";
     };
   };
 

pkgs/os-specific/linux/fuse/default.nix

@@ -11,7 +11,7 @@ in {
   };
 
   fuse_3 = mkFuse {
-    version = "3.5.0";
+    version = "3.6.1";
-    sha256Hash = "01gs25pk58nm5il91lgwiivphk38009ihfk5l956zyzmgr9wa9a5";
+    sha256Hash = "1118r2nx64cpv9s5a6dgh49y0pnjcc5ybpkh5pigxf14bpqa26pb";
   };
 }

pkgs/os-specific/linux/kernel/linux-4.14.nix

@@ -3,7 +3,7 @@
 with stdenv.lib;
 
 buildLinux (args // rec {
-  version = "4.14.124";
+  version = "4.14.125";
 
   # modDirVersion needs to be x.y.z, will automatically add .0 if needed
   modDirVersion = if (modDirVersionArg == null) then concatStrings (intersperse "." (take 3 (splitString "." "${version}.0"))) else modDirVersionArg;
@@ -13,6 +13,6 @@ buildLinux (args // rec {
 
   src = fetchurl {
     url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz";
-    sha256 = "1fdwbj26pcnl23n6yw55j5yif6fkka7kvkdh31c8wczc3rw5h3bx";
+    sha256 = "065k5bg3qz0chzlfaxz63vpkipqrj26hnbbfyidkha2s44hbqg9y";
   };
 } // (args.argsOverride or {}))

pkgs/os-specific/linux/kernel/linux-4.19.nix

@@ -3,7 +3,7 @@
 with stdenv.lib;
 
 buildLinux (args // rec {
-  version = "4.19.49";
+  version = "4.19.50";
 
   # modDirVersion needs to be x.y.z, will automatically add .0 if needed
   modDirVersion = if (modDirVersionArg == null) then concatStrings (intersperse "." (take 3 (splitString "." "${version}.0"))) else modDirVersionArg;
@@ -13,6 +13,6 @@ buildLinux (args // rec {
 
   src = fetchurl {
     url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz";
-    sha256 = "1kdv72w9x72z126dycdqm4i5hvmy0njaywb2a6jvq39wjyrj1ncj";
+    sha256 = "07p0gkjf3xj9djsmzxvbb25cmsi5f95v3sfnd3p21gcaj4ip9659";
   };
 } // (args.argsOverride or {}))

pkgs/os-specific/linux/kernel/linux-4.4.nix

@@ -1,11 +1,11 @@
 { stdenv, buildPackages, fetchurl, perl, buildLinux, ... } @ args:
 
 buildLinux (args // rec {
-  version = "4.4.180";
+  version = "4.4.181";
   extraMeta.branch = "4.4";
 
   src = fetchurl {
     url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz";
-    sha256 = "0ykai953rpy9zkb4qxb63y6pwwbwlnvx69nhb797zfw1scbh4i8s";
+    sha256 = "1lw1qsql9dv8dllz6hglahxdfgzg34rpl9c9gwdrpm4j660nkaxj";
   };
 } // (args.argsOverride or {}))

pkgs/os-specific/linux/kernel/linux-4.9.nix

@@ -1,11 +1,11 @@
 { stdenv, buildPackages, fetchurl, perl, buildLinux, ... } @ args:
 
 buildLinux (args // rec {
-  version = "4.9.180";
+  version = "4.9.181";
   extraMeta.branch = "4.9";
 
   src = fetchurl {
     url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz";
-    sha256 = "0pvw71yiwwf19qxqkm68dw4c9sl54n367q9kfdc6msd3c86ljnnj";
+    sha256 = "1vgwfjsn31fy0ikcnpaqbw8w0r0xb25xp3633f0258yb24z25kcg";
   };
 } // (args.argsOverride or {}))

pkgs/os-specific/linux/kernel/linux-5.1.nix

@@ -3,7 +3,7 @@
 with stdenv.lib;
 
 buildLinux (args // rec {
-  version = "5.1.8";
+  version = "5.1.9";
 
   # modDirVersion needs to be x.y.z, will automatically add .0 if needed
   modDirVersion = if (modDirVersionArg == null) then concatStrings (intersperse "." (take 3 (splitString "." "${version}.0"))) else modDirVersionArg;
@@ -13,6 +13,6 @@ buildLinux (args // rec {
 
   src = fetchurl {
     url = "mirror://kernel/linux/kernel/v5.x/linux-${version}.tar.xz";
-    sha256 = "1v56hzzb147mdnhajkgcjwjrmd7qyayky7bprjb3maz2qvy4y5nh";
+    sha256 = "0y9a2bvls756f8hrpffhmbrg7hw5r6b2jc2rnpszzlixkjlyrjaq";
   };
 } // (args.argsOverride or {}))

pkgs/os-specific/linux/zfs/default.nix

@@ -130,6 +130,9 @@ let
 
         # Remove tests because they add a runtime dependency on gcc
         rm -rf $out/share/zfs/zfs-tests
+
+        # Add Bash completions.
+        install -v -m444 -D -t $out/share/bash-completion/completions contrib/bash_completion.d/zfs
       '';
 
       outputs = [ "out" ] ++ optionals buildUser [ "lib" "dev" ];

pkgs/servers/apache-kafka/default.nix

@@ -39,9 +39,9 @@ let
       sha256 = "1gm7xiqkbg415mbj9mlazcndmky81xvg4wmz0h94yv1whp7fslr0";
     };
     "2.2" = {
-      kafkaVersion = "2.2.0";
+      kafkaVersion = "2.2.1";
       scalaVersion = "2.12";
-      sha256 = "09q028kagpkzrvfdb040z8q9mspv8n7f2igrd1cs73v7mr7n42d0";
+      sha256 = "1svdnhdzq9a6jsig513i0ahaysfgar5i385bq9fz7laga6a4z3qv";
     };
   };
 in

pkgs/servers/atlassian/crowd.nix

@@ -3,11 +3,11 @@
 
 stdenv.mkDerivation rec {
   name = "atlassian-crowd-${version}";
-  version = "3.4.4";
+  version = "3.4.5";
 
   src = fetchurl {
     url = "https://www.atlassian.com/software/crowd/downloads/binary/${name}.tar.gz";
-    sha256 = "0bs3l2s5f8ymyvvxn6z3wwccbvac42giahmfqiam51m9zkfhf0rk";
+    sha256 = "1k72aar68iqiaf0l75i6pp81dpsllqkp69f70hja754hrzvhz8j3";
   };
 
   phases = [ "unpackPhase" "buildPhase" "installPhase" "fixupPhase" ];

pkgs/servers/atlassian/jira.nix

@@ -5,11 +5,11 @@
 
 stdenv.mkDerivation rec {
   name = "atlassian-jira-${version}";
-  version = "8.1.0";
+  version = "8.2.1";
 
   src = fetchurl {
     url = "https://product-downloads.atlassian.com/software/jira/downloads/atlassian-jira-software-${version}.tar.gz";
-    sha256 = "0mi1xknly44haf7gls3k212fx1dsl8k35rq82a1b3zj27kynwqr3";
+    sha256 = "1556hliywjiz6977249mlgxaq5xzpzq3xm9bcg9vk57s1hsv175i";
   };
 
   phases = [ "unpackPhase" "buildPhase" "installPhase" "fixupPhase" ];

pkgs/servers/nosql/cassandra/generic.nix

@@ -23,7 +23,7 @@ stdenv.mkDerivation rec {
     url = "mirror://apache/cassandra/${version}/apache-${name}-bin.tar.gz";
   };
 
-  nativeBuildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper coreutils ];
 
   installPhase = ''
     mkdir $out
@@ -51,8 +51,17 @@ stdenv.mkDerivation rec {
                bin/sstablescrub \
                bin/sstableupgrade \
                bin/sstableutil \
-               bin/sstableverify \
+               bin/sstableverify; do
-               tools/bin/cassandra-stress \
+      # Check if file exists because some don't exist across all versions
+      if [ -f $out/$cmd ]; then
+        wrapProgram $out/bin/$(basename "$cmd") \
+          --suffix-each LD_LIBRARY_PATH : ${libPath} \
+          --prefix PATH : ${binPath} \
+          --set JAVA_HOME ${jre}
+      fi
+    done
+
+    for cmd in tools/bin/cassandra-stress \
                tools/bin/cassandra-stressd \
                tools/bin/sstabledump \
                tools/bin/sstableexpiredblockers \
@@ -62,11 +71,9 @@ stdenv.mkDerivation rec {
                tools/bin/sstablerepairedset \
                tools/bin/sstablesplit \
                tools/bin/token-generator; do
-
+      # Check if file exists because some don't exist across all versions
-      # check if file exists because some bin tools don't exist across all
-      # cassandra versions
       if [ -f $out/$cmd ]; then
-        makeWrapper $out/$cmd $out/bin/$(${coreutils}/bin/basename "$cmd") \
+        makeWrapper $out/$cmd $out/bin/$(basename "$cmd") \
           --suffix-each LD_LIBRARY_PATH : ${libPath} \
           --prefix PATH : ${binPath} \
           --set JAVA_HOME ${jre}

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

@@ -0,0 +1,32 @@
+{ stdenv, fetchurl, postgresql }:
+
+stdenv.mkDerivation rec {
+  pname = "pg_bigm";
+  version = "1.2";
+
+  src = fetchurl {
+    url = "mirror://osdn/pgbigm/66565/${pname}-${version}-20161011.tar.gz";
+    sha256 = "1jp30za4bhwlas0yrhyjs9m03b1sj63km61xnvcbnh0sizyvhwis";
+  };
+
+  buildInputs = [ postgresql ];
+
+  makeFlags = [ "USE_PGXS=1" ];
+
+  installPhase = ''
+    mkdir -p $out/bin    # For buildEnv to setup proper symlinks. See #22653
+    mkdir -p $out/{lib,share/extension}
+
+    cp *.so      $out/lib
+    cp *.sql     $out/share/extension
+    cp *.control $out/share/extension
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Text similarity measurement and index searching based on bigrams";
+    homepage = "https://pgbigm.osdn.jp/";
+    maintainers = [ maintainers.marsam ];
+    platforms = postgresql.meta.platforms;
+    license = licenses.postgresql;
+  };
+}

pkgs/servers/sql/postgresql/packages.nix

@@ -9,6 +9,8 @@ self: super: {
 
     pg_auto_failover = super.callPackage ./ext/pg_auto_failover.nix { };
 
+    pg_bigm = super.callPackage ./ext/pg_bigm.nix { };
+
     pg_repack = super.callPackage ./ext/pg_repack.nix { };
 
     pg_similarity = super.callPackage ./ext/pg_similarity.nix { };

pkgs/servers/x11/xorg/default.nix

@@ -1405,11 +1405,11 @@ lib.makeScope newScope (self: with self; {
   }) {};
 
   xcalc = callPackage ({ stdenv, pkgconfig, fetchurl, libX11, libXaw, xorgproto, libXt }: stdenv.mkDerivation {
-    name = "xcalc-1.0.7";
+    name = "xcalc-1.1.0";
     builder = ./builder.sh;
     src = fetchurl {
-      url = mirror://xorg/individual/app/xcalc-1.0.7.tar.bz2;
+      url = mirror://xorg/individual/app/xcalc-1.1.0.tar.bz2;
-      sha256 = "08bzaldi76vrj7350d7b04pq7qa1qhi81x8i806yv42zcp8p3lkh";
+      sha256 = "1sxmlcb0sb3h4z05kl5l0kxnhrc0h8c74p9m3zdc7bv58jaldmym";
     };
     hardeningDisable = [ "bindnow" "relro" ];
     nativeBuildInputs = [ pkgconfig ];

pkgs/servers/x11/xorg/overrides.nix

@@ -699,4 +699,15 @@ self: super:
       rm $out/bin/xkeystone
     '';
   });
+
+  xcalc = super.xcalc.overrideAttrs (attrs: {
+    configureFlags = attrs.configureFlags or [] ++ [
+      "--with-appdefaultdir=${placeholder "out"}/share/X11/app-defaults"
+    ];
+    nativeBuildInputs = attrs.nativeBuildInputs or [] ++ [ makeWrapper ];
+    postInstall = ''
+      wrapProgram $out/bin/xcalc \
+        --set XAPPLRESDIR ${placeholder "out"}/share/X11/app-defaults
+    '';
+  });
 }

pkgs/servers/x11/xorg/tarballs.list

@@ -28,7 +28,7 @@ mirror://xorg/individual/app/viewres-1.0.5.tar.bz2
 mirror://xorg/individual/app/x11perf-1.6.1.tar.bz2
 mirror://xorg/individual/app/xauth-1.0.10.tar.bz2
 mirror://xorg/individual/app/xbacklight-1.2.2.tar.bz2
-mirror://xorg/individual/app/xcalc-1.0.7.tar.bz2
+mirror://xorg/individual/app/xcalc-1.1.0.tar.bz2
 mirror://xorg/individual/app/xclock-1.0.8.tar.bz2
 mirror://xorg/individual/app/xcmsdb-1.0.5.tar.bz2
 mirror://xorg/individual/app/xcompmgr-1.1.8.tar.bz2

pkgs/shells/zsh/oh-my-zsh/default.nix

@@ -4,13 +4,13 @@
 { stdenv, fetchgit }:
 
 stdenv.mkDerivation rec {
-  version = "2019-06-08";
+  version = "2019-06-12";
   name = "oh-my-zsh-${version}";
-  rev = "d69bad8eb4157e5fd5c1a4ce98f93cf522477a8c";
+  rev = "078f64dcf9c56f45d1d5e9e49dd5709baedc1386";
 
   src = fetchgit { inherit rev;
     url = "https://github.com/robbyrussell/oh-my-zsh";
-    sha256 = "0j6x1kzki3k5p75lr50l48c7wdgi59h8l9lvixvkzp5bknsmsmrd";
+    sha256 = "1ld9fzb3d1ypc4b5r2k9xi05jqrbdb1drl0jq50m5qffc8ydxnvx";
   };
 
   pathsToLink = [ "/share/oh-my-zsh" ];

pkgs/tools/admin/iamy/default.nix

@@ -1,8 +1,8 @@
-{ stdenv, buildGoPackage, fetchFromGitHub }:
+{ stdenv, buildGoModule, fetchFromGitHub }:
 
-buildGoPackage rec {
+buildGoModule rec {
   name = "iamy-${version}";
-  version = "2.1.1";
+  version = "2.3.2";
 
   goPackagePath = "github.com/99designs/iamy";
 
@@ -10,9 +10,15 @@ buildGoPackage rec {
     owner = "99designs";
     repo = "iamy";
     rev = "v${version}";
-    sha256 = "0b55hxcvgil8rl6zh2kyndfi7s5nzclawjb0sby14wpys3v08bjf";
+    sha256 = "1fypc6yjnhlpk7zhb2lvah2ikh2zji9sll55rqjbr3i4j02h484z";
   };
 
+  modSha256 = "0akak573zvz3xg5d7vf0ch2mrmj1jkzcdc29v3kn43f7944c2wcl";
+
+  buildFlagsArray = [''-ldflags=
+    -X main.Version=v${version} -s -w
+  ''];
+
   meta = with stdenv.lib; {
     description = "A cli tool for importing and exporting AWS IAM configuration to YAML files";
     homepage = https://github.com/99designs/iamy;

pkgs/tools/graphics/svgbob/default.nix

@@ -0,0 +1,28 @@
+{ lib, rustPlatform, fetchFromGitHub }:
+
+rustPlatform.buildRustPackage rec {
+  pname = "svgbob";
+  version = "unstable-2018-10-05";
+
+  src = fetchFromGitHub {
+    owner = "ivanceras";
+    repo = pname;
+    rev = "43fb0364e989d0e9a7656b148c947d47cc769622";
+    sha256 = "1imjj57dx1af3wrs214yzaa2qfk8ld00nj3nx4z450gw2xjjj1gw";
+  };
+
+  sourceRoot = "source/svgbob_cli";
+
+  cargoSha256 = "0mnq1s809f394x83gjv9zljr07c94k48zkrwxs6ibi19shgmrnnd";
+
+  # Test tries to build outdated examples
+  doCheck = false;
+
+  meta = with lib; {
+    description = "Convert your ascii diagram scribbles into happy little SVG";
+    homepage = "https://github.com/ivanceras/svgbob";
+    license = licenses.asl20;
+    maintainers = [ maintainers.marsam ];
+    platforms = platforms.all;
+  };
+}

pkgs/tools/misc/broot/default.nix

@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "broot";
-  version = "0.7.5";
+  version = "0.8.0";
 
   src = fetchFromGitHub {
     owner = "Canop";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1pwbz4ac2zb40g6q6ykzhzfbn0jr5xarkvgw9wxv455mbi67rd6y";
+    sha256 = "0xgjpdy12b77hgf0vfgs2ayxaajjv8vs0v8fn4rnrgn3hz8ldhyc";
   };
 
-  cargoSha256 = "0yph5mwxn6arfbxbvri5qa7wzwj1q0s675j6vblia9akn02fyqd9";
+  cargoSha256 = "1hsrp9xbi6bj3461y58hmzfwakx4vakpzkjvi6174gy8xq7cdvg1";
 
   meta = with stdenv.lib; {
     description = "An interactive tree view, a fuzzy search, a balanced BFS descent and customizable commands";

pkgs/tools/package-management/nix/default.nix

@@ -11,7 +11,7 @@ let
 common =
   { lib, stdenv, fetchurl, fetchpatch, perl, curl, bzip2, sqlite, openssl ? null, xz
   , pkgconfig, boehmgc, perlPackages, libsodium, brotli, boost, editline
-  , autoreconfHook, autoconf-archive, bison, flex, libxml2, libxslt, docbook5, docbook_xsl_ns
+  , autoreconfHook, autoconf-archive, bison, flex, libxml2, libxslt, docbook5, docbook_xsl_ns, jq
   , busybox-sandbox-shell
   , storeDir
   , stateDir
@@ -37,7 +37,7 @@ common =
       nativeBuildInputs =
         [ pkgconfig ]
         ++ lib.optionals (!is20) [ curl perl ]
-        ++ lib.optionals fromGit [ autoreconfHook autoconf-archive bison flex libxml2 libxslt docbook5 docbook_xsl_ns ];
+        ++ lib.optionals fromGit [ autoreconfHook autoconf-archive bison flex libxml2 libxslt docbook5 docbook_xsl_ns jq ];
 
       buildInputs = [ curl openssl sqlite xz bzip2 ]
         ++ lib.optional (stdenv.isLinux || stdenv.isDarwin) libsodium
@@ -193,4 +193,18 @@ in rec {
     inherit storeDir stateDir confDir boehmgc;
   });
 
+  nixFlakes = lib.lowPrio (callPackage common rec {
+    name = "nix-2.3${suffix}";
+    suffix = "pre20190612_06010ea";
+    src = fetchFromGitHub {
+      owner = "NixOS";
+      repo = "nix";
+      rev = "06010eaf199005a393f212023ec5e8bc97978537";
+      sha256 = "1fq99fmlag5hxvgzxrclgfsnc1fhhfwnslyshad1934wi9nzx1s2";
+    };
+    fromGit = true;
+
+    inherit storeDir stateDir confDir boehmgc;
+  });
+
 }

pkgs/tools/system/xe/default.nix

@@ -3,7 +3,7 @@
 stdenv.mkDerivation rec {
   name = "xe-${version}";
   version = "0.11";
-  
+
   src = fetchFromGitHub {
     owner = "chneukirchen";
     repo = "xe";
@@ -12,12 +12,12 @@ stdenv.mkDerivation rec {
   };
 
   makeFlags = "PREFIX=$(out)";
-  
+
   meta = with lib; {
     description = "Simple xargs and apply replacement";
     homepage = https://github.com/chneukirchen/xe;
     license = licenses.publicDomain;
-    platforms = platforms.linux;
+    platforms = platforms.all;
     maintainers = with maintainers; [ cstrahan ndowens ];
   };
 }

pkgs/top-level/all-packages.nix

@@ -6021,6 +6021,8 @@ in
 
   super-user-spark = haskellPackages.callPackage ../applications/misc/super_user_spark { };
 
+  svgbob = callPackage ../tools/graphics/svgbob { };
+
   svgcleaner = callPackage ../tools/graphics/svgcleaner { };
 
   ssdeep = callPackage ../tools/security/ssdeep { };
@@ -8040,8 +8042,9 @@ in
 
   scala_2_10 = callPackage ../development/compilers/scala/2.10.nix { };
   scala_2_11 = callPackage ../development/compilers/scala/2.11.nix { };
-  scala_2_12 = callPackage ../development/compilers/scala { jre = jre8; };
+  scala_2_12 = callPackage ../development/compilers/scala/2.12.nix { jre = jre8; };
-  scala = scala_2_12;
+  scala_2_13 = callPackage ../development/compilers/scala/2.13.nix { jre = jre8; };
+  scala = scala_2_13;
 
   scalafix = callPackage ../development/tools/scalafix { };
   scalafmt = callPackage ../development/tools/scalafmt { };
@@ -8843,7 +8846,9 @@ in
 
   bazel-remote = callPackage ../development/tools/build-managers/bazel/bazel-remote { };
 
-  bazel-watcher = callPackage ../development/tools/bazel-watcher { };
+  bazel-watcher = callPackage ../development/tools/bazel-watcher {
+    buildBazelPackage = buildBazelPackage.override { enableNixHacks = false; };
+  };
 
   bazelisk = callPackage ../development/tools/bazelisk { };
 
@@ -9999,6 +10004,8 @@ in
 
   capnproto = callPackage ../development/libraries/capnproto { };
 
+  captive-browser = callPackage ../applications/networking/browsers/captive-browser { };
+
   ndn-cxx = callPackage ../development/libraries/ndn-cxx { };
 
   cddlib = callPackage ../development/libraries/cddlib {};
@@ -16330,6 +16337,8 @@ in
 
   iwona = callPackage ../data/fonts/iwona { };
 
+  jost = callPackage ../data/fonts/jost { };
+
   junicode = callPackage ../data/fonts/junicode { };
 
   kanji-stroke-order-font = callPackage ../data/fonts/kanji-stroke-order-font {};
@@ -17284,6 +17293,7 @@ in
   deadbeefPlugins = {
     headerbar-gtk3 = callPackage ../applications/audio/deadbeef/plugins/headerbar-gtk3.nix { };
     infobar = callPackage ../applications/audio/deadbeef/plugins/infobar.nix { };
+    lyricbar = callPackage ../applications/audio/deadbeef/plugins/lyricbar.nix { };
     mpris2 = callPackage ../applications/audio/deadbeef/plugins/mpris2.nix { };
   };
 
@@ -20141,6 +20151,8 @@ in
   };
   cura = qt5.callPackage ../applications/misc/cura { };
 
+  curaPlugins = callPackage ../applications/misc/cura/plugins.nix { };
+
   curaLulzbot = callPackage ../applications/misc/cura/lulzbot.nix { };
 
   curaByDagoma = callPackage ../applications/misc/curabydagoma { };
@@ -22289,6 +22301,8 @@ in
 
   bftools = callPackage ../applications/science/biology/bftools { };
 
+  cd-hit = callPackage ../applications/science/biology/cd-hit { };
+
   cmtk = callPackage ../applications/science/biology/cmtk { };
 
   clustal-omega = callPackage ../applications/science/biology/clustal-omega { };
@@ -23371,7 +23385,8 @@ in
     nix
     nix1
     nixStable
-    nixUnstable;
+    nixUnstable
+    nixFlakes;
 
   nixops = callPackage ../tools/package-management/nixops { };
 

pkgs/top-level/perl-packages.nix

@@ -8059,11 +8059,11 @@ let
 
   ImageExifTool = buildPerlPackage rec {
     name = "Image-ExifTool-${version}";
-    version = "11.48";
+    version = "11.50";
 
     src = fetchurl {
       url = "https://www.sno.phy.queensu.ca/~phil/exiftool/${name}.tar.gz";
-      sha256 = "0whbwrrmwvj311fxksf47i47cyfgzd2d5cnh6ixg74rb1n6k9986";
+      sha256 = "0d8v48y94z8maxkmw1rv7v9m0jg2dc8xbp581njb6yhr7abwqdv3";
     };
 
     meta = with stdenv.lib; {
@@ -8072,11 +8072,11 @@ let
 
       longDescription = ''
         ExifTool is a platform-independent Perl library plus a command-line
-        application for reading, writing and editing meta information in
+        application for reading, writing and editing meta information in a wide
-        image, audio and video files.  ExifTool supports many different types
+        variety of files. ExifTool supports many different metadata formats
-        of metadata including EXIF, GPS, IPTC, XMP, JFIF, GeoTIFF, ICC
+        including EXIF, GPS, IPTC, XMP, JFIF, GeoTIFF, ICC Profile, Photoshop
-        Profile, Photoshop IRB, FlashPix, AFCP and ID3, as well as the maker
+        IRB, FlashPix, AFCP and ID3, as well as the maker notes of many digital
-        notes of many digital cameras by Canon, Casio, DJI, FLIR, FujiFilm, HP,
+        cameras by Canon, Casio, DJI, FLIR, FujiFilm, GE, GoPro, HP,
         JVC/Victor, Kodak, Leaf, Minolta/Konica-Minolta, Motorola, Nikon,
         Nintendo, Olympus/Epson, Panasonic/Leica, Pentax/Asahi, Phase One,
         Reconyx, Ricoh, Samsung, Sanyo, Sigma/Foveon and Sony.
@@ -16818,6 +16818,19 @@ let
     };
   };
 
+  TextNSP = buildPerlPackage rec {
+    name = "Text-NSP-1.31";
+    src = fetchurl {
+      url = "mirror://cpan/authors/id/T/TP/TPEDERSE/${name}.tar.gz";
+      sha256 = "a01201beb29636b3e41ecda2a6cf6522fd265416bd6d994fad02f59fb49cf595";
+    };
+    meta = {
+      description = "Extract collocations and Ngrams from text";
+      license = stdenv.lib.licenses.free;
+      maintainers = [ maintainers.bzizou ];
+    };
+  };
+
   TextvFileasData = buildPerlPackage rec {
     name = "Text-vFile-asData-0.08";
     src = fetchurl {

pkgs/top-level/php-packages.nix

@@ -4,7 +4,7 @@ let
   self = with self; {
     buildPecl = import ../build-support/build-pecl.nix {
       inherit php;
-      inherit (pkgs) stdenv autoreconfHook fetchurl;
+      inherit (pkgs) stdenv autoreconfHook fetchurl re2c;
     };
 
     # Wrap mkDerivation to prepend pname with "php-" to make names consistent
@@ -73,12 +73,12 @@ let
   };
 
   composer = mkDerivation rec {
-    version = "1.8.5";
+    version = "1.8.6";
     pname = "composer";
 
     src = pkgs.fetchurl {
       url = "https://getcomposer.org/download/${version}/composer.phar";
-      sha256 = "05qfgh2dz8pjf47ndyhkicqbnqzwypk90cczd4c6d8jl9gbiqk2f";
+      sha256 = "0hnm7njab9nsifpb1qbwx54yfpsi00g8mzny11s13ibjvd9rnvxn";
     };
 
     unpackPhase = ":";
@@ -143,12 +143,17 @@ let
   };
 
   event = buildPecl rec {
-    version = "2.5.1";
+    version = "2.5.2";
     pname = "event";
 
-    sha256 = "0hnvmlbl994fjliqc3c65gv6f6syh9zmlfcbizqs3k67bbmkhiad";
+    sha256 = "0b9zbwyyfcrzs1gcpqn2dkjq6jliw89g2m981f8ildbp84snkpcf";
 
-    configureFlags = [ "--with-event-libevent-dir=${pkgs.libevent.dev}" ];
+    configureFlags = [
+      "--with-event-libevent-dir=${pkgs.libevent.dev}"
+      "--with-event-core"
+      "--with-event-extra"
+      "--with-event-pthreads"
+    ];
     nativeBuildInputs = [ pkgs.pkgconfig ];
     buildInputs = with pkgs; [ openssl libevent ];
 
@@ -216,7 +221,7 @@ let
 
     sha256 = "0jhivxj1nkkza4h23z33y7xhffii60d7dr51h1czjk10qywl7pyd";
 
-    buildInputs = [ pkgs.re2c pkgs.oracle-instantclient ];
+    buildInputs = [ pkgs.oracle-instantclient ];
     configureFlags = [ "--with-oci8=shared,instantclient,${pkgs.oracle-instantclient}/lib" ];
   };