Merge master into staging-next

2021-11-02 00:01:32 +00:00 · 2021-11-02 00:01:32 +00:00 · d27dd6653e
commit d27dd6653e
parent 107b7f5d39 550dab224a
51 changed files with 2118 additions and 1323 deletions
--- a/maintainers/maintainer-list.nix
+++ b/maintainers/maintainer-list.nix
@ -11263,6 +11263,17 @@
    githubId = 1141680;
    name = "Thane Gill";
  };
+  thblt = {
+    name = "Thibault Polge";
+    email = "thibault@thb.lt";
+    matrix = "@thbltp:matrix.org";
+    github = "thblt";
+    githubId = 2453136;
+    keys = [{
+      longkeyid = "rsa4096/0x63A44817A52EAB7B";
+      fingerprint = "D2A2 F0A1 E7A8 5E6F B711  DEE5 63A4 4817 A52E AB7B";
+    }];
+  };
  TheBrainScrambler = {
    email = "esthromeris@riseup.net";
    github = "TheBrainScrambler";
--- a/nixos/doc/manual/from_md/release-notes/rl-2111.section.xml
+++ b/nixos/doc/manual/from_md/release-notes/rl-2111.section.xml
@ -1515,6 +1515,23 @@ Superuser created successfully.
          option.
        </para>
      </listitem>
+      <listitem>
+        <para>
+          The
+          <link xlink:href="options.html#opt-services.smokeping.host">services.smokeping.host</link>
+          option was added and defaulted to
+          <literal>localhost</literal>. Before,
+          <literal>smokeping</literal> listened to all interfaces by
+          default. NixOS defaults generally aim to provide
+          non-Internet-exposed defaults for databases and internal
+          monitoring tools, see e.g.
+          <link xlink:href="https://github.com/NixOS/nixpkgs/issues/100192">#100192</link>.
+          Further, the systemd service for <literal>smokeping</literal>
+          got reworked defaults for increased operational stability, see
+          <link xlink:href="https://github.com/NixOS/nixpkgs/pull/144127">PR
+          #144127</link> for details.
+        </para>
+      </listitem>
      <listitem>
        <para>
          The
--- a/nixos/doc/manual/release-notes/rl-2111.section.md
+++ b/nixos/doc/manual/release-notes/rl-2111.section.md
@ -445,6 +445,8 @@ In addition to numerous new and upgraded packages, this release has the followin

 - The [networking.wireless.iwd](options.html#opt-networking.wireless.iwd.enable) module has a new [networking.wireless.iwd.settings](options.html#opt-networking.wireless.iwd.settings) option.

+- The [services.smokeping.host](options.html#opt-services.smokeping.host) option was added and defaulted to `localhost`. Before, `smokeping` listened to all interfaces by default. NixOS defaults generally aim to provide non-Internet-exposed defaults for databases and internal monitoring tools, see e.g. [#100192](https://github.com/NixOS/nixpkgs/issues/100192). Further, the systemd service for `smokeping` got reworked defaults for increased operational stability, see [PR #144127](https://github.com/NixOS/nixpkgs/pull/144127) for details.
+
 - The [services.syncoid.enable](options.html#opt-services.syncoid.enable) module now properly drops ZFS permissions after usage. Before it delegated permissions to whole pools instead of datasets and didn't clean up after execution. You can manually look this up for your pools by running `zfs allow your-pool-name` and use `zfs unallow syncoid your-pool-name` to clean this up.

 - Zfs: `latestCompatibleLinuxPackages` is now exported on the zfs package. One can use `boot.kernelPackages = config.boot.zfs.package.latestCompatibleLinuxPackages;` to always track the latest compatible kernel with a given version of zfs.
--- a/nixos/modules/programs/neovim.nix
+++ b/nixos/modules/programs/neovim.nix
@ -139,7 +139,7 @@ in {
    environment.systemPackages = [
      cfg.finalPackage
    ];
-    environment.variables = { EDITOR = mkOverride 900 "nvim"; };
+    environment.variables.EDITOR = mkIf cfg.defaultEditor (mkOverride 900 "nvim");

    programs.neovim.finalPackage = pkgs.wrapNeovim cfg.package {
      inherit (cfg) viAlias vimAlias;
--- a/nixos/modules/services/networking/smokeping.nix
+++ b/nixos/modules/services/networking/smokeping.nix
@ -131,10 +131,15 @@ in
      };
      imgUrl = mkOption {
        type = types.str;
-        default = "http://${cfg.hostName}:${toString cfg.port}/cache";
-        defaultText = literalExpression ''"http://''${hostName}:''${toString port}/cache"'';
+        default = "cache";
+        defaultText = literalExpression ''"cache"'';
        example = "https://somewhere.example.com/cache";
-        description = "Base url for images generated in the cgi.";
+        description = ''
+          Base url for images generated in the cgi.
+
+          The default is a relative URL to ensure it works also when e.g. forwarding
+          the GUI port via SSH.
+        '';
      };
      linkStyle = mkOption {
        type = types.enum ["original" "absolute" "relative"];
@ -167,6 +172,17 @@ in
        defaultText = literalExpression "pkgs.smokeping";
        description = "Specify a custom smokeping package";
      };
+      host = mkOption {
+        type = types.nullOr types.str;
+        default = "localhost";
+        example = "192.0.2.1"; # rfc5737 example IP for documentation
+        description = ''
+          Host/IP to bind to for the web server.
+
+          Setting it to <literal>null</literal> skips passing the -h option to thttpd,
+          which makes it bind to all interfaces.
+        '';
+      };
      port = mkOption {
        type = types.int;
        default = 8081;
@ -297,10 +313,11 @@ in
    };
    users.groups.${cfg.user} = {};
    systemd.services.smokeping = {
-      wantedBy = [ "multi-user.target"];
+      requiredBy = [ "multi-user.target"];
      serviceConfig = {
        User = cfg.user;
        Restart = "on-failure";
+        ExecStart = "${cfg.package}/bin/smokeping --config=${configPath} --nodaemon";
      };
      preStart = ''
        mkdir -m 0755 -p ${smokepingHome}/cache ${smokepingHome}/data
@ -311,18 +328,29 @@ in
        ${cfg.package}/bin/smokeping --check --config=${configPath}
        ${cfg.package}/bin/smokeping --static --config=${configPath}
      '';
-      script = "${cfg.package}/bin/smokeping --config=${configPath} --nodaemon";
    };
    systemd.services.thttpd = mkIf cfg.webService {
-      wantedBy = [ "multi-user.target"];
+      requiredBy = [ "multi-user.target"];
      requires = [ "smokeping.service"];
-      partOf = [ "smokeping.service"];
      path = with pkgs; [ bash rrdtool smokeping thttpd ];
-      script = ''thttpd -u ${cfg.user} -c "**.fcgi" -d ${smokepingHome} -p ${builtins.toString cfg.port} -D -nos'';
-      serviceConfig.Restart = "always";
+      serviceConfig = {
+        Restart = "always";
+        ExecStart = lib.concatStringsSep " " (lib.concatLists [
+          [ "${pkgs.thttpd}/bin/thttpd" ]
+          [ "-u ${cfg.user}" ]
+          [ ''-c "**.fcgi"'' ]
+          [ "-d ${smokepingHome}" ]
+          (lib.optional (cfg.host != null) "-h ${cfg.host}")
+          [ "-p ${builtins.toString cfg.port}" ]
+          [ "-D -nos" ]
+        ]);
+      };
    };
  };

-  meta.maintainers = with lib.maintainers; [ erictapen ];
+  meta.maintainers = with lib.maintainers; [
+    erictapen
+    nh2
+  ];
 }

--- a/nixos/modules/services/x11/desktop-managers/plasma5.nix
+++ b/nixos/modules/services/x11/desktop-managers/plasma5.nix
@ -14,10 +14,6 @@ let

  ini = pkgs.formats.ini { };

-  pulseaudio = config.hardware.pulseaudio;
-  pactl = "${getBin pulseaudio.package}/bin/pactl";
-  sed = "${getBin pkgs.gnused}/bin/sed";
-
  gtkrc2 = writeText "gtkrc-2.0" ''
    # Default GTK+ 2 config for NixOS Plasma 5
    include "/run/current-system/sw/share/themes/Breeze/gtk-2.0/gtkrc"
@ -80,7 +76,7 @@ let
    # Qt from doing this wackiness in the first place.
    trolltech_conf="''${XDG_CONFIG_HOME}/Trolltech.conf"
    if [ -e "$trolltech_conf" ]; then
-        ${sed} -i "$trolltech_conf" -e '/nix\\store\|nix\/store/ d'
+      ${getBin pkgs.gnused}/bin/sed -i "$trolltech_conf" -e '/nix\\store\|nix\/store/ d'
    fi

    # Remove the kbuildsyscoca5 cache. It will be regenerated
@ -101,43 +97,36 @@ let
    XDG_CONFIG_HOME=''${XDG_CONFIG_HOME:-$HOME/.config}
  '';

-  startplasma =
-    ''
-      ${set_XDG_CONFIG_HOME}
-      mkdir -p "''${XDG_CONFIG_HOME}"
+  startplasma = ''
+    ${set_XDG_CONFIG_HOME}
+    mkdir -p "''${XDG_CONFIG_HOME}"
+  '' + optionalString config.hardware.pulseaudio.enable ''
+    # Load PulseAudio module for routing support.
+    # See also: http://colin.guthr.ie/2009/10/so-how-does-the-kde-pulseaudio-support-work-anyway/
+      ${getBin config.hardware.pulseaudio.package}/bin/pactl load-module module-device-manager "do_routing=1"
+  '' + ''
+    ${activationScript}

-    ''
-    + optionalString pulseaudio.enable ''
-      # Load PulseAudio module for routing support.
-      # See also: http://colin.guthr.ie/2009/10/so-how-does-the-kde-pulseaudio-support-work-anyway/
-        ${pactl} load-module module-device-manager "do_routing=1"
-
-    ''
-    + ''
-      ${activationScript}
-
-      # Create default configurations if Plasma has never been started.
-      kdeglobals="''${XDG_CONFIG_HOME}/kdeglobals"
-      if ! [ -f "$kdeglobals" ]
-      then
-          kcminputrc="''${XDG_CONFIG_HOME}/kcminputrc"
-          if ! [ -f "$kcminputrc" ]; then
-              cat ${kcminputrc} >"$kcminputrc"
-          fi
-
-          gtkrc2="$HOME/.gtkrc-2.0"
-          if ! [ -f "$gtkrc2" ]; then
-              cat ${gtkrc2} >"$gtkrc2"
-          fi
-
-          gtk3_settings="''${XDG_CONFIG_HOME}/gtk-3.0/settings.ini"
-          if ! [ -f "$gtk3_settings" ]; then
-              mkdir -p "$(dirname "$gtk3_settings")"
-              cat ${gtk3_settings} >"$gtk3_settings"
-          fi
+    # Create default configurations if Plasma has never been started.
+    kdeglobals="''${XDG_CONFIG_HOME}/kdeglobals"
+    if ! [ -f "$kdeglobals" ]; then
+      kcminputrc="''${XDG_CONFIG_HOME}/kcminputrc"
+      if ! [ -f "$kcminputrc" ]; then
+          cat ${kcminputrc} >"$kcminputrc"
      fi

-    '';
+      gtkrc2="$HOME/.gtkrc-2.0"
+      if ! [ -f "$gtkrc2" ]; then
+          cat ${gtkrc2} >"$gtkrc2"
+      fi
+
+      gtk3_settings="''${XDG_CONFIG_HOME}/gtk-3.0/settings.ini"
+      if ! [ -f "$gtk3_settings" ]; then
+          mkdir -p "$(dirname "$gtk3_settings")"
+          cat ${gtk3_settings} >"$gtk3_settings"
+      fi
+    fi
+  '';

 in

@ -202,27 +191,24 @@ in
      services.xserver.displayManager.sessionPackages = [ pkgs.libsForQt5.plasma5.plasma-workspace ];

      security.wrappers = {
-        kcheckpass =
-          {
-            setuid = true;
-            owner = "root";
-            group = "root";
-            source = "${getBin libsForQt5.kscreenlocker}/libexec/kcheckpass";
-          };
-        start_kdeinit =
-          {
-            setuid = true;
-            owner = "root";
-            group = "root";
-            source = "${getBin libsForQt5.kinit}/libexec/kf5/start_kdeinit";
-          };
-        kwin_wayland =
-          {
-            owner = "root";
-            group = "root";
-            capabilities = "cap_sys_nice+ep";
-            source = "${getBin plasma5.kwin}/bin/kwin_wayland";
-          };
+        kcheckpass = {
+          setuid = true;
+          owner = "root";
+          group = "root";
+          source = "${getBin libsForQt5.kscreenlocker}/libexec/kcheckpass";
+        };
+        start_kdeinit = {
+          setuid = true;
+          owner = "root";
+          group = "root";
+          source = "${getBin libsForQt5.kinit}/libexec/kf5/start_kdeinit";
+        };
+        kwin_wayland = {
+          owner = "root";
+          group = "root";
+          capabilities = "cap_sys_nice+ep";
+          source = "${getBin plasma5.kwin}/bin/kwin_wayland";
+        };
      };

      # DDC support
@ -372,9 +358,12 @@ in
      programs.ssh.askPassword = mkDefault "${plasma5.ksshaskpass.out}/bin/ksshaskpass";

      # Enable helpful DBus services.
+      services.accounts-daemon.enable = true;
+      # when changing an account picture the accounts-daemon reads a temporary file containing the image which systemsettings5 may place under /tmp
+      systemd.services.accounts-daemon.serviceConfig.PrivateTmp = false;
      services.udisks2.enable = true;
      services.upower.enable = config.powerManagement.enable;
-      services.system-config-printer.enable = (mkIf config.services.printing.enable (mkDefault true));
+      services.system-config-printer.enable = mkIf config.services.printing.enable (mkDefault true);
      services.xserver.libinput.enable = mkDefault true;

      # Extra UDEV rules used by Solid
@ -427,5 +416,4 @@ in
      nixpkgs.config.firefox.enablePlasmaBrowserIntegration = true;
    })
  ];
-
 }
--- a/nixos/tests/all-tests.nix
+++ b/nixos/tests/all-tests.nix
@ -418,7 +418,6 @@ in
  sonarr = handleTest ./sonarr.nix {};
  spacecookie = handleTest ./spacecookie.nix {};
  spark = handleTestOn ["x86_64-linux"] ./spark {};
-  spike = handleTest ./spike.nix {};
  sslh = handleTest ./sslh.nix {};
  sssd = handleTestOn ["x86_64-linux"] ./sssd.nix {};
  sssd-ldap = handleTestOn ["x86_64-linux"] ./sssd-ldap.nix {};
--- a/nixos/tests/spike.nix
+++ b/nixos/tests/spike.nix
@ -1,22 +0,0 @@
-import ./make-test-python.nix ({ pkgs, ... }:
-
-let
-  riscvPkgs = import ../.. { crossSystem = pkgs.lib.systems.examples.riscv64-embedded; };
-in
-{
-  name = "spike";
-  meta = with pkgs.lib.maintainers; { maintainers = [ blitz ]; };
-
-  machine = { pkgs, lib, ... }: {
-    environment.systemPackages = [ pkgs.spike riscvPkgs.riscv-pk riscvPkgs.hello ];
-  };
-
-  # Run the RISC-V hello applications using the proxy kernel on the
-  # Spike emulator and see whether we get the expected output.
-  testScript =
-    ''
-      machine.wait_for_unit("multi-user.target")
-      output = machine.succeed("spike -m64 $(which pk) $(which hello)")
-      assert "Hello, world!" in output
-    '';
-})
--- a/pkgs/applications/misc/auto-multiple-choice/default.nix
+++ b/pkgs/applications/misc/auto-multiple-choice/default.nix
@ -0,0 +1,163 @@
+{ lib
+, stdenv
+, fetchurl
+, perlPackages
+, makeWrapper
+, wrapGAppsHook
+, cairo
+, dblatex
+, gnumake
+, gobject-introspection
+, graphicsmagick
+, gsettings-desktop-schemas
+, gtk3
+, libnotify
+, librsvg
+, libxslt
+, netpbm
+, opencv
+, pango
+, perl
+, pkg-config
+, poppler
+, auto-multiple-choice
+}:
+stdenv.mkDerivation rec {
+  pname = "auto-multiple-choice";
+  version = "1.5.1";
+  src = fetchurl {
+    url = "https://download.auto-multiple-choice.net/${pname}_${version}_precomp.tar.gz";
+    sha256 = "71831122f7b43245d3289617064e0b561817c0130ee1773c1b957841b28b854c";
+  };
+  tlType = "run";
+
+  # There's only the Makefile
+  dontConfigure = true;
+
+  makeFlags = [
+    "PERLPATH=${perl}/bin/perl"
+    # We *need* to pass DESTDIR, as the Makefile ignores PREFIX.
+    "DESTDIR=$(out)"
+    # Relative paths.
+    "BINDIR=/bin"
+    "PERLDIR=/share/perl5"
+    "MODSDIR=/lib/"
+    "TEXDIR=/tex/latex/" # what texlive.combine expects
+    "TEXDOCDIR=/share/doc/texmf/" # TODO where to put this?
+    "MAN1DIR=/share/man/man1"
+    "DESKTOPDIR=/share/applications"
+    "METAINFODIR=/share/metainfo"
+    "ICONSDIR=/share/auto-multiple-choice/icons"
+    "APPICONDIR=/share/icons/hicolor"
+    "LOCALEDIR=/share/locale"
+    "MODELSDIR=/share/auto-multiple-choice/models"
+    "DOCDIR=/share/doc/auto-multiple-choice"
+    "SHARED_MIMEINFO_DIR=/share/mime/packages"
+    "LANG_GTKSOURCEVIEW_DIR=/share/gtksourceview-4/language-specs"
+    # Pretend to be redhat so `install` doesn't try to chown/chgrp.
+    "SYSTEM_TYPE=rpm"
+  ];
+
+  preFixup = ''
+    makeWrapperArgs+=("''${gappsWrapperArgs[@]}")
+  '';
+
+  postFixup = ''
+    wrapProgram $out/bin/auto-multiple-choice \
+    ''${makeWrapperArgs[@]} \
+    --prefix PERL5LIB : "${with perlPackages; makePerlPath [
+      ArchiveZip
+      DBDSQLite
+      Cairo
+      CairoGObject
+      DBI
+      Glib
+      GlibObjectIntrospection
+      Gtk3
+      LocaleGettext
+      PerlMagick
+      TextCSV
+      XMLParser
+      XMLSimple
+      XMLWriter
+    ]}:"$out/share/perl5 \
+    --prefix XDG_DATA_DIRS : "$out/share" \
+    --set TEXINPUTS ":.:$out/share/texmf/tex/latex/AMC"
+  '';
+
+  nativeBuildInputs = [
+    pkg-config
+    makeWrapper
+    wrapGAppsHook
+  ];
+
+  buildInputs = [
+    cairo
+    cairo.dev
+    dblatex
+    gnumake
+    gobject-introspection
+    graphicsmagick
+    gsettings-desktop-schemas
+    gtk3
+    libnotify
+    librsvg
+    libxslt
+    netpbm
+    opencv
+    pango
+    poppler
+  ] ++ (with perlPackages; [
+    perl
+    ArchiveZip
+    Cairo
+    CairoGObject
+    DBDSQLite
+    DBI
+    Glib
+    GlibObjectIntrospection
+    Gtk3
+    LocaleGettext
+    PerlMagick
+    TextCSV
+    XMLParser
+    XMLSimple
+    XMLWriter
+  ]);
+
+  meta = with lib; {
+    description = "Create and manage multiple choice questionnaires with automated marking.";
+    longDescription = ''
+      Create, manage and mark multiple-choice questionnaires.
+      auto-multiple-choice features automated or manual formatting with
+      LaTeX, shuffling of questions and answers and automated marking using
+      Optical Mark Recognition.
+
+      Questionnaires can be created using either a very simple text syntax,
+      AMC-TXT, or LaTeX. In the latter case, your TeXLive installation must
+      be combined with this package.  This can be done in configuration.nix
+      as follows:
+
+      <screen>
+      …
+      environment.systemPackages = with pkgs; [
+        auto-multiple-choice
+        (texlive.combine {
+          inherit (pkgs.texlive) scheme-full;
+          extra =
+            {
+              pkgs = [ auto-multiple-choice ];
+            };
+        })
+      ];
+      </screen>
+
+      For usage instructions, see documentation at the project's homepage.
+    '';
+    homepage = "https://www.auto-multiple-choice.net/";
+    changelog = "https://gitlab.com/jojo_boulix/auto-multiple-choice/-/blob/master/ChangeLog";
+    license = licenses.gpl2Plus;
+    maintainers = [ maintainers.thblt ];
+    platforms = platforms.all;
+  };
+}
--- a/pkgs/applications/misc/dbeaver/default.nix
+++ b/pkgs/applications/misc/dbeaver/default.nix
@ -18,13 +18,13 @@

 stdenv.mkDerivation rec {
  pname = "dbeaver";
-  version = "21.2.3"; # When updating also update fetchedMavenDeps.sha256
+  version = "21.2.4"; # When updating also update fetchedMavenDeps.sha256

  src = fetchFromGitHub {
    owner = "dbeaver";
    repo = "dbeaver";
    rev = version;
-    sha256 = "0xu/uMMloCUuhKs392kn6qJzlobDNuvwlHGdS/gGAB8=";
+    sha256 = "BPcTj2YIGyP3g4qrQlDp13lziJwSUt0Zn00CayDku9g=";
  };

  fetchedMavenDeps = stdenv.mkDerivation {
--- a/pkgs/applications/misc/markmind/default.nix
+++ b/pkgs/applications/misc/markmind/default.nix
@ -0,0 +1,48 @@
+{ lib, stdenv, fetchurl, appimageTools, makeWrapper, electron }:
+
+stdenv.mkDerivation rec {
+  pname = "markmind";
+  version = "1.3.1";
+
+  src = fetchurl {
+    url = "https://github.com/MarkMindCkm/Mark-Mind/releases/download/v${version}/Mark.Mind-${version}.AppImage";
+    sha256 = "sha256-iOJ0IOIzleA69rv94Qd35rMbHc+XSi8OPatf2V6sYrI=";
+  };
+
+  appimageContents = appimageTools.extractType2 {
+    name = "markmind-${version}";
+    inherit src;
+  };
+
+  dontUnpack = true;
+  dontConfigure = true;
+  dontBuild = true;
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/bin $out/share/markmind $out/share/applications
+    cp -a ${appimageContents}/{locales,resources} $out/share/markmind
+    cp -a ${appimageContents}/mind.desktop $out/share/applications/markmind.desktop
+    cp -a ${appimageContents}/usr/share/icons $out/share
+    substituteInPlace $out/share/applications/markmind.desktop \
+      --replace 'Exec=AppRun' 'Exec=markmind'
+
+    runHook postInstall
+  '';
+
+  postFixup = ''
+    makeWrapper ${electron}/bin/electron $out/bin/markmind \
+      --add-flags $out/share/markmind/resources/app.asar
+  '';
+
+  meta = with lib; {
+    description = "Mind map and outliner editor";
+    homepage = "https://github.com/MarkMindCkm/Mark-Mind";
+    license = licenses.mit;
+    maintainers = with maintainers; [ wolfangaukang ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
--- a/pkgs/applications/misc/slides/default.nix
+++ b/pkgs/applications/misc/slides/default.nix
@ -7,13 +7,13 @@

 buildGoModule rec {
  pname = "slides";
-  version = "0.6.2";
+  version = "0.7.2";

  src = fetchFromGitHub {
    owner = "maaslalani";
    repo = "slides";
    rev = "v${version}";
-    sha256 = "sha256-D2ex9/XN5JMKwn+g1cB77UMquYW9NdTzhCCvVtTOBfU=";
+    sha256 = "02zdgn0pnjqharvmn9rww45yrja8dzww64s3fryxx4pm8g5km9nf";
  };

  checkInputs = [
@ -21,7 +21,7 @@ buildGoModule rec {
    go
  ];

-  vendorSha256 = "sha256-pI5/1LJVP/ZH64Dy2rUoOXM21oqJ8KA0/L8ClGRb5UY=";
+  vendorSha256 = "06vb5xnss6ibgbsny6cadphfkzw8z3np5qgn3hp2wpf3hxgcnnvs";

  ldflags = [
    "-s"
--- a/pkgs/applications/misc/whalebird/default.nix
+++ b/pkgs/applications/misc/whalebird/default.nix
@ -0,0 +1,61 @@
+{ lib, stdenv, fetchurl, dpkg, autoPatchelfHook, makeWrapper, electron
+, nodePackages, alsa-lib, gtk3, libxshmfence, mesa, nss }:
+
+stdenv.mkDerivation rec {
+  pname = "whalebird";
+  version = "4.4.5";
+
+  src = fetchurl {
+    url = "https://github.com/h3poteto/whalebird-desktop/releases/download/${version}/Whalebird-${version}-linux-x64.deb";
+    sha256 = "sha256-CIlj9Sc/hj2UMgQzfHA3iQYO6EPqcndqkNUCBecHq+E=";
+  };
+
+  nativeBuildInputs = [
+    dpkg
+    autoPatchelfHook
+    makeWrapper
+    nodePackages.asar
+  ];
+
+  buildInputs = [ alsa-lib gtk3 libxshmfence mesa nss ];
+
+  dontConfigure = true;
+
+  unpackPhase = ''
+    dpkg-deb -x ${src} ./
+  '';
+
+  buildPhase = ''
+    runHook preBuild
+
+    # Necessary steps to find the tray icon
+    asar extract opt/Whalebird/resources/app.asar "$TMP/work"
+    substituteInPlace $TMP/work/dist/electron/main.js \
+      --replace "Mo,\"tray_icon.png\"" "\"$out/opt/Whalebird/resources/build/icons/tray_icon.png\""
+    asar pack --unpack='{*.node,*.ftz,rect-overlay}' "$TMP/work" opt/Whalebird/resources/app.asar
+
+    runHook postBuild
+  '';
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir $out
+    mv usr/share opt $out
+
+    substituteInPlace $out/share/applications/whalebird.desktop \
+      --replace '/opt/Whalebird' $out/bin
+    makeWrapper ${electron}/bin/electron $out/bin/whalebird \
+      --add-flags $out/opt/Whalebird/resources/app.asar
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Electron based Mastodon, Pleroma and Misskey client for Windows, Mac and Linux";
+    homepage = "https://whalebird.social";
+    license = licenses.mit;
+    maintainers = with maintainers; [ wolfangaukang ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
--- a/pkgs/applications/networking/instant-messengers/telegram/tdesktop/default.nix
+++ b/pkgs/applications/networking/instant-messengers/telegram/tdesktop/default.nix
@ -29,6 +29,7 @@
 , webkitgtk
 , jemalloc
 , rnnoise
+, abseil-cpp
  # Transitive dependencies:
 , util-linuxMinimal
 , pcre
@ -57,7 +58,11 @@
 # - https://github.com/void-linux/void-packages/blob/master/srcpkgs/telegram-desktop/template

 let
-  tg_owt = callPackage ./tg_owt.nix { };
+  tg_owt = callPackage ./tg_owt.nix {
+    abseil-cpp = abseil-cpp.override {
+      cxxStandard = "17";
+    };
+  };
 in
 mkDerivation rec {
  pname = "telegram-desktop";
--- a/pkgs/applications/networking/instant-messengers/threema-desktop/default.nix
+++ b/pkgs/applications/networking/instant-messengers/threema-desktop/default.nix
@ -0,0 +1,54 @@
+{ lib, stdenv, fetchurl, dpkg, autoPatchelfHook, makeWrapper, electron
+, alsa-lib, glibc, gtk3, libxshmfence, mesa, nss }:
+
+stdenv.mkDerivation rec {
+  pname = "threema-desktop";
+  version = "1.0.3";
+
+  src = fetchurl {
+    # As Threema only offers a Latest Release url, the plan is to upload each
+    # new release url to web.archive.org until their Github releases page gets populated.
+    url = "https://web.archive.org/web/20211027194646/https://releases.threema.ch/web-electron/v1/release/Threema-Latest.deb";
+    sha256 = "sha256-qiFv52nnyfHxCWTePmyxW/MgzFy3EUxmW6n+UIkw7tk=";
+  };
+
+  nativeBuildInputs = [
+    dpkg
+    autoPatchelfHook
+    makeWrapper
+  ];
+
+  buildInputs = [ alsa-lib glibc gtk3 libxshmfence mesa nss ];
+
+  dontBuild = true;
+  dontConfigure = true;
+
+  unpackPhase = ''
+    # Can't unpack with the common dpkg-deb -x method
+    dpkg --fsys-tarfile $src | tar --extract
+  '';
+
+  installPhase = ''
+    runHook preInstall
+
+    # This will cause confusion, not needed
+    rm -r usr/bin
+    mv usr $out
+
+    runHook postInstall
+  '';
+
+  postFixup = ''
+    mv $out/share/applications/threema.desktop $out/share/applications/threema-desktop.desktop
+    makeWrapper ${electron}/bin/electron $out/bin/threema \
+      --add-flags $out/lib/threema/resources/app.asar
+  '';
+
+  meta = with lib; {
+    description = "Desktop client for Threema, a privacy-focused end-to-end encrypted mobile messenger";
+    homepage = "https://threema.ch";
+    license = licenses.agpl3Only;
+    maintainers = with maintainers; [ wolfangaukang ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
--- a/pkgs/applications/science/logic/lean/default.nix
+++ b/pkgs/applications/science/logic/lean/default.nix
@ -2,7 +2,7 @@

 stdenv.mkDerivation rec {
  pname = "lean";
-  version = "3.33.0";
+  version = "3.35.0";

  src = fetchFromGitHub {
    owner  = "leanprover-community";
@ -11,8 +11,8 @@ stdenv.mkDerivation rec {
    # from. this is then used to check whether an olean file should be
    # rebuilt. don't use a tag as rev because this will get replaced into
    # src/githash.h.in in preConfigure.
-    rev    = "a0fb1e8c7ac81dfd2e80ad0de08f4e57ee853d82";
-    sha256 = "03xz3c3dzjhvjzpa8811cgzzqzw8fpajmspykavmb259i391w0y7";
+    rev    = "a68d251bfc57341d8f1f6d8c6e548a0b08ff3b92";
+    sha256 = "0f91kvd4z7rsjyagfx56y1vxmf4wjds7bnz6yh3sd4xx770z58d4";
  };

  nativeBuildInputs = [ cmake ];
--- a/pkgs/applications/science/logic/why3/default.nix
+++ b/pkgs/applications/science/logic/why3/default.nix
@ -23,7 +23,7 @@ stdenv.mkDerivation rec {
    # S-expression output for why3pp
    ppx_deriving ppx_sexp_conv
    # Coq Support
-    coqPackages.coq coqPackages.flocq ocamlPackages.camlp5
+    coqPackages.coq coqPackages.flocq
  ];

  propagatedBuildInputs = with ocamlPackages; [ camlzip num re sexplib ];
--- a/pkgs/applications/video/kodi-packages/jellyfin/default.nix
+++ b/pkgs/applications/video/kodi-packages/jellyfin/default.nix
@ -5,13 +5,13 @@ in
 buildKodiAddon rec {
  pname = "jellyfin";
  namespace = "plugin.video.jellyfin";
-  version = "0.7.4";
+  version = "0.7.7";

  src = fetchFromGitHub {
    owner = "jellyfin";
    repo = "jellyfin-kodi";
    rev = "v${version}";
-    sha256 = "1ykgz1l2gmpdlsp3fbm31q8757879i9dd13svslqykvxadg69x03";
+    sha256 = "06glhnpayldficvvhlkbxg7zizl2wqms66fnc3p63nm3y7mqa9dd";
  };

  nativeBuildInputs = [
--- a/pkgs/applications/video/vdr/default.nix
+++ b/pkgs/applications/video/vdr/default.nix
@ -5,12 +5,12 @@
 }: stdenv.mkDerivation rec {

  pname = "vdr";
-  version = "2.4.7";
+  version = "2.5.6";

  src = fetchgit {
    url = "git://git.tvdr.de/vdr.git";
    rev = version;
-    sha256 = "sha256-hDJ/DemWuLddDvXGqxkSTIqATlWUjolcP7ojjhK2CDk=";
+    sha256 = "sha256-hgP8EIGwEPj30fijZzcujnvutG+acU4qqqvgY6FB/z4=";
  };

  enableParallelBuilding = true;
--- a/pkgs/applications/video/vdr/plugins.nix
+++ b/pkgs/applications/video/vdr/plugins.nix
@ -130,12 +130,12 @@ in {

  epgsearch = stdenv.mkDerivation rec {
    pname = "vdr-epgsearch";
-    version = "20191202";
+    version = "2.4.1";

    src = fetchgit {
      url = "git://projects.vdr-developer.org/vdr-plugin-epgsearch.git";
-      sha256 = "18kskwnnscr4rb4yzfikw1la318zjgraf340cl7n9z77chi2gi8m";
-      rev = "602d66c55964998ce25c6c57b302949a9517f149";
+      sha256 = "sha256-UlbPCkUFN0Gyxjw9xq2STFTDZRVcPPNjadSQd4o2o9U=";
+      rev = "v${version}";
    };

    postPatch = ''
--- a/pkgs/applications/virtualization/spike/default.nix
+++ b/pkgs/applications/virtualization/spike/default.nix
@ -1,4 +1,4 @@
-{ lib, stdenv, fetchgit, dtc, nixosTests, fetchpatch }:
+{ lib, stdenv, fetchgit, dtc, fetchpatch }:

 stdenv.mkDerivation rec {
  pname = "spike";
@ -28,9 +28,20 @@ stdenv.mkDerivation rec {

  doCheck = true;

-  passthru.tests = {
-    can-run-hello-world = nixosTests.spike;
-  };
+  # To test whether spike is working, we run the RISC-V hello applications using the RISC-V proxy
+  # kernel on the Spike emulator and see whether we get the expected output.
+  doInstallCheck = true;
+  installCheckPhase =
+    let
+      riscvPkgs = import ../../../.. { crossSystem = lib.systems.examples.riscv64-embedded; };
+    in
+    ''
+      runHook preInstallCheck
+
+      $out/bin/spike -m64 ${riscvPkgs.riscv-pk}/bin/pk ${riscvPkgs.hello}/bin/hello | grep -Fq "Hello, world"
+
+      runHook postInstallCheck
+    '';

  meta = with lib; {
    description = "A RISC-V ISA Simulator";
--- a/pkgs/applications/window-managers/river/default.nix
+++ b/pkgs/applications/window-managers/river/default.nix
@ -19,13 +19,13 @@

 stdenv.mkDerivation rec {
  pname = "river";
-  version = "unstable-2021-09-30";
+  version = "unstable-2021-11-01";

  src = fetchFromGitHub {
    owner = "ifreund";
    repo = pname;
-    rev = "e6bb373240bc08668c8e6e14996a3f8765941158";
-    sha256 = "sha256-dYruRpsud2XYrVY2f4f2dkRRSh1oU9rn2GRwAkJqW3A=";
+    rev = "363fd3f6a466004eec157a40e51684e56992b857";
+    sha256 = "sha256-RzReUo1p2z4UQaO5n6PKQlEv0vTBGg+1Wq1UIYii0Mo=";
    fetchSubmodules = true;
  };

--- a/pkgs/data/themes/kwin-decorations/sierra-breeze-enhanced/default.nix
+++ b/pkgs/data/themes/kwin-decorations/sierra-breeze-enhanced/default.nix
@ -0,0 +1,38 @@
+{ stdenv
+, fetchFromGitHub
+, cmake
+, extra-cmake-modules
+, wrapQtAppsHook
+, kwin
+, lib
+}:
+
+stdenv.mkDerivation rec {
+  pname = "sierra-breeze-enhanced";
+  version = "1.0.3";
+
+  src = fetchFromGitHub {
+    owner = "kupiqu";
+    repo = "SierraBreezeEnhanced";
+    rev = "V${version}";
+    sha256 = "0kqbfn1jqsbii3hqcqlb93x8cg8dyh5mf66i9r237w41knks5mnw";
+  };
+
+  nativeBuildInputs = [ cmake extra-cmake-modules wrapQtAppsHook ];
+  buildInputs = [ kwin ];
+
+  cmakeFlags = [
+    "-DCMAKE_INSTALL_PREFIX=$out"
+    "-DCMAKE_BUILD_TYPE=Release"
+    "-DBUILD_TESTING=OFF"
+    "-DKDE_INSTALL_USE_QT_SYS_PATHS=ON"
+  ];
+
+  meta = with lib; {
+    description = "OSX-like window decoration for KDE Plasma written in C++";
+    homepage = "https://github.com/kupiqu/SierraBreezeEnhanced";
+    changelog = "https://github.com/kupiqu/SierraBreezeEnhanced/releases/tag/V${version}";
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ flexagoon ];
+  };
+}
--- a/pkgs/development/compilers/rust/make-rust-platform.nix
+++ b/pkgs/development/compilers/rust/make-rust-platform.nix
@ -1,6 +1,6 @@
-{ buildPackages, callPackage }:
+{ buildPackages, callPackage, stdenv }@prev:

-{ rustc, cargo, ... }:
+{ rustc, cargo, stdenv ? prev.stdenv, ... }:

 rec {
  rust = {
@ -14,22 +14,22 @@ rec {

  buildRustPackage = callPackage ../../../build-support/rust {
    git = buildPackages.gitMinimal;
-    inherit cargoBuildHook cargoCheckHook cargoInstallHook cargoSetupHook
+    inherit stdenv cargoBuildHook cargoCheckHook cargoInstallHook cargoSetupHook
      fetchCargoTarball importCargoLock rustc;
  };

  importCargoLock = buildPackages.callPackage ../../../build-support/rust/import-cargo-lock.nix {};

  rustcSrc = callPackage ./rust-src.nix {
-    inherit rustc;
+    inherit stdenv rustc;
  };

  rustLibSrc = callPackage ./rust-lib-src.nix {
-    inherit rustc;
+    inherit stdenv rustc;
  };

  # Hooks
  inherit (callPackage ../../../build-support/rust/hooks {
-    inherit cargo rustc;
+    inherit stdenv cargo rustc;
  }) cargoBuildHook cargoCheckHook cargoInstallHook cargoSetupHook maturinBuildHook;
 }
--- a/pkgs/development/libraries/abseil-cpp/default.nix
+++ b/pkgs/development/libraries/abseil-cpp/default.nix
@ -1,4 +1,11 @@
-{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, static ? stdenv.hostPlatform.isStatic }:
+{ lib
+, stdenv
+, fetchFromGitHub
+, fetchpatch
+, cmake
+, static ? stdenv.hostPlatform.isStatic
+, cxxStandard ? null
+}:

 stdenv.mkDerivation rec {
  pname = "abseil-cpp";
@ -21,8 +28,9 @@ stdenv.mkDerivation rec {
  ];

  cmakeFlags = [
-    "-DCMAKE_CXX_STANDARD=17"
    "-DBUILD_SHARED_LIBS=${if static then "OFF" else "ON"}"
+  ] ++ lib.optionals (cxxStandard != null) [
+    "-DCMAKE_CXX_STANDARD=${cxxStandard}"
  ];

  nativeBuildInputs = [ cmake ];
--- a/pkgs/development/libraries/accountsservice/default.nix
+++ b/pkgs/development/libraries/accountsservice/default.nix
@ -1,4 +1,5 @@
-{ lib, stdenv
+{ lib
+, stdenv
 , fetchurl
 , fetchpatch
 , substituteAll
@ -89,6 +90,6 @@ stdenv.mkDerivation rec {
    homepage = "https://www.freedesktop.org/wiki/Software/AccountsService";
    license = licenses.gpl3;
    maintainers = with maintainers; [ pSub ];
-    platforms = with platforms; linux;
+    platforms = platforms.linux;
  };
 }
--- a/pkgs/development/libraries/accountsservice/fix-paths.patch
+++ b/pkgs/development/libraries/accountsservice/fix-paths.patch
@ -29,7 +29,7 @@ index 9f57af5..e65289d 100644
                          name);
 
 -                argv[0] = "/usr/sbin/usermod";
-+                argv[0] = "@shadown@/bin/usermod";
+                argv[0] = "@shadow@/bin/usermod";
                 argv[1] = "-c";
                 argv[2] = name;
                 argv[3] = "--";
--- a/pkgs/development/libraries/bash/bash-preexec/default.nix
+++ b/pkgs/development/libraries/bash/bash-preexec/default.nix
@ -21,6 +21,10 @@ in stdenvNoCC.mkDerivation {
  patchPhase = ''
    # Needed since the tests expect that HISTCONTROL is set.
    sed -i '/setup()/a HISTCONTROL=""' test/bash-preexec.bats
+
+    # Skip tests failing with Bats 1.5.0.
+    # See https://github.com/rcaloras/bash-preexec/issues/121
+    sed -i '/^@test.*IFS/,/^}/d' test/bash-preexec.bats
  '';

  checkPhase = ''
--- a/pkgs/development/libraries/grpc/default.nix
+++ b/pkgs/development/libraries/grpc/default.nix
@ -57,14 +57,13 @@ stdenv.mkDerivation rec {
    "-DgRPC_ABSL_PROVIDER=package"
    "-DBUILD_SHARED_LIBS=ON"
    "-DCMAKE_SKIP_BUILD_RPATH=OFF"
+  ] ++ lib.optionals (stdenv.hostPlatform != stdenv.buildPlatform) [
+    "-D_gRPC_PROTOBUF_PROTOC_EXECUTABLE=${buildPackages.protobuf}/bin/protoc"
+  ] ++ lib.optionals ((stdenv.hostPlatform.useLLVM or false) && lib.versionOlder stdenv.cc.cc.version "11.0") [
    # Needs to be compiled with -std=c++11 for clang < 11. Interestingly this is
    # only an issue with the useLLVM stdenv, not the darwin stdenv…
    # https://github.com/grpc/grpc/issues/26473#issuecomment-860885484
-    (if (stdenv.hostPlatform.useLLVM or false) && lib.versionOlder stdenv.cc.cc.version "11.0"
-     then "-DCMAKE_CXX_STANDARD=11"
-     else "-DCMAKE_CXX_STANDARD=17")
-  ] ++ lib.optionals (stdenv.hostPlatform != stdenv.buildPlatform) [
-    "-D_gRPC_PROTOBUF_PROTOC_EXECUTABLE=${buildPackages.protobuf}/bin/protoc"
+    "-DCMAKE_CXX_STANDARD=11"
  ];

  # CMake creates a build directory by default, this conflicts with the
--- a/pkgs/development/python-modules/azure-mgmt-eventhub/default.nix
+++ b/pkgs/development/python-modules/azure-mgmt-eventhub/default.nix
@ -11,12 +11,12 @@

 buildPythonPackage rec {
  pname = "azure-mgmt-eventhub";
-  version = "9.1.0";
+  version = "10.0.0";

  src = fetchPypi {
    inherit pname version;
    extension = "zip";
-    sha256 = "0ba9f10e1e8d03247a316e777d6f27fabf268d596dda2af56ac079fcdf5e7afe";
+    sha256 = "0856574ef4b73bbbc62834051061e2081400aba7e3715e10ef5181d639e86a0b";
  };

  propagatedBuildInputs = [
--- a/pkgs/development/python-modules/google-cloud-appengine-logging/default.nix
+++ b/pkgs/development/python-modules/google-cloud-appengine-logging/default.nix
@ -12,11 +12,11 @@

 buildPythonPackage rec {
  pname = "google-cloud-appengine-logging";
-  version = "1.0.0";
+  version = "1.1.0";

  src = fetchPypi {
    inherit pname version;
-    sha256 = "f10760c7df7052e63a79547b36fb439ab8a0f72fe28ff8356a0755c45ab75412";
+    sha256 = "91fe9b0833f6e1a46293dcc0e483716372c9ff4a95ebe51276c5f0092cb9defd";
  };

  propagatedBuildInputs = [
--- a/pkgs/development/python-modules/pex/default.nix
+++ b/pkgs/development/python-modules/pex/default.nix
@ -6,12 +6,12 @@

 buildPythonPackage rec {
  pname = "pex";
-  version = "2.1.53";
+  version = "2.1.54";
  format = "setuptools";

  src = fetchPypi {
    inherit pname version;
-    sha256 = "802cd39468b4bf27ff23d9911f76a6c66689cc906e12b9102aeace6491a8d084";
+    sha256 = "5878d97e4b6df920cb7b4a45254501746945193289c934c707e36107594c0982";
  };

  nativeBuildInputs = [
--- a/pkgs/development/python-modules/pyclip/default.nix
+++ b/pkgs/development/python-modules/pyclip/default.nix
@ -0,0 +1,40 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, buildPythonPackage
+, pytest
+, xclip
+, xvfb-run
+}:
+
+buildPythonPackage rec {
+  pname = "pyclip";
+  version = "0.5.4";
+
+  src = fetchFromGitHub {
+    owner = "spyoungtech";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "19ff9cgnfx03mbmy5zpbdi986ppx38a5jf97vkqnic4g5sd1qyrn";
+  };
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace docs/README.md README.md
+  '';
+
+  checkInputs = [ pytest ] ++ lib.optionals stdenv.isLinux [ xclip xvfb-run ];
+
+  checkPhase = ''
+    runHook preCheck
+    ${lib.optionalString stdenv.isLinux "xvfb-run -s '-screen 0 800x600x24'"} pytest tests
+    runHook postCheck
+  '';
+
+  meta = with lib; {
+    description = "Cross-platform clipboard utilities supporting both binary and text data";
+    homepage = "https://github.com/spyoungtech/pyclip";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ mcaju ];
+  };
+}
--- a/pkgs/development/r-modules/bioc-experiment-packages.nix
+++ b/pkgs/development/r-modules/bioc-experiment-packages.nix
@ -259,7 +259,7 @@ in with self; {
  curatedBladderData = derive2 { name="curatedBladderData"; version="1.28.0"; sha256="1f66avn99wxsyy1jkiljgcir8vy9wg266blmdsh0wrjlk0cb2jmx"; depends=[affy]; };
  curatedBreastData = derive2 { name="curatedBreastData"; version="2.20.0"; sha256="1gick1qkwgjgw76m99g9lxljnh2mrlawq9789h8kfp48cpdzs99b"; depends=[Biobase BiocStyle ggplot2 impute XML]; };
  curatedCRCData = derive2 { name="curatedCRCData"; version="2.24.0"; sha256="1pzlw72an1flqz0lr52diqslkxgpcrfgzzw99llilmpr40nwdb4z"; depends=[BiocGenerics nlme]; };
-  curatedMetagenomicData = derive2 { name="curatedMetagenomicData"; version="3.0.6"; sha256="0iiqxwq14hslalk529da459zyaq763iwl8yygancgcmhv2vhb6jk"; depends=[AnnotationHub dplyr ExperimentHub magrittr purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect TreeSummarizedExperiment]; };
+  curatedMetagenomicData = derive2 { name="curatedMetagenomicData"; version="3.0.10"; sha256="15v8dirzjlyb1bp2r82yvhax9vgnxyamfps7042sncvzmxlyjnp8"; depends=[AnnotationHub dplyr ExperimentHub magrittr purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect TreeSummarizedExperiment]; };
  curatedOvarianData = derive2 { name="curatedOvarianData"; version="1.30.0"; sha256="1qfhwkbr884g1xgrp8d2d20d9b2c1v5pvv3kf49lypxcd7m5njzg"; depends=[affy BiocGenerics]; };
  curatedTCGAData = derive2 { name="curatedTCGAData"; version="1.14.0"; sha256="0fr368619d75jwqjn4mrcc3dagd7hnk8xpm4y3arrn15g92wflzh"; depends=[AnnotationHub ExperimentHub HDF5Array MultiAssayExperiment S4Vectors SummarizedExperiment]; };
  davidTiling = derive2 { name="davidTiling"; version="1.32.0"; sha256="0yjd5myq67hgjrpxw4n1kpplsgndw43jg97ghvb1jpxfshhajs0x"; depends=[Biobase GO_db tilingArray]; };
@ -267,7 +267,7 @@ in with self; {
  derfinderData = derive2 { name="derfinderData"; version="2.10.0"; sha256="1xmc6b2634iff34mw08bxxgasq9s3p3yl6b4s492pcrj4jj21x25"; depends=[]; };
  diffloopdata = derive2 { name="diffloopdata"; version="1.20.0"; sha256="03z6m4fvf69bgqzijyn7ccagqq7kcjb1056nqc303n5l2pp0ms1b"; depends=[]; };
  diggitdata = derive2 { name="diggitdata"; version="1.24.0"; sha256="0hj7nw306pdy5nwbv5bhl8yrgh09f5jp263l8jiw8fha3vhygsqk"; depends=[Biobase viper]; };
-  dorothea = derive2 { name="dorothea"; version="1.4.1"; sha256="0qhsvb88hv6rvz731rn8hjm4dkba9l575anb5vkh5lzzc088qy61"; depends=[bcellViper dplyr magrittr viper]; };
+  dorothea = derive2 { name="dorothea"; version="1.4.2"; sha256="0r0ax28rqa0grp0vlq7dfsrl048lhhzxjmaapwm4asnqqv0rl13q"; depends=[bcellViper dplyr magrittr viper]; };
  dressCheck = derive2 { name="dressCheck"; version="0.30.0"; sha256="0vd0gaqgry2vwfh4pnqzr341dlr723w0ivlq9da85066lcyqjlmg"; depends=[Biobase]; };
  dyebiasexamples = derive2 { name="dyebiasexamples"; version="1.32.0"; sha256="0bmc53rma0mmyvj0wmzbvwdyjlzqh1wvl1225xmfqzcri8681g27"; depends=[GEOquery marray]; };
  ecoliLeucine = derive2 { name="ecoliLeucine"; version="1.32.0"; sha256="0lkqkwnfn14s41hz9yvzr4ic9rmv005dljhf237rgprmjy72p2ij"; depends=[affy ecolicdf]; };
@ -374,7 +374,7 @@ in with self; {
  seqCNA_annot = derive2 { name="seqCNA.annot"; version="1.28.0"; sha256="112766y3fknrnmnv13nxzgyspw1l331x4vk2i3dfab0hg1khjr2c"; depends=[]; };
  seqc = derive2 { name="seqc"; version="1.26.0"; sha256="0vm726y6m67jc2kqqkav1j1a1irs6qz43pg4dmr6kdpslj1yyy2m"; depends=[Biobase]; };
  serumStimulation = derive2 { name="serumStimulation"; version="1.28.0"; sha256="0cf70km8virxjpz93rfvvfnzykqxvrlzgacfrksf07izj90dp6s8"; depends=[]; };
-  sesameData = derive2 { name="sesameData"; version="1.10.0"; sha256="11i5mkwl5gjy7rdbrnqvinfgxba7pqvh6jrzmvgld31sjdzz8s4x"; depends=[AnnotationHub curl ExperimentHub rmarkdown]; };
+  sesameData = derive2 { name="sesameData"; version="1.10.1"; sha256="0h4d2mbaizxqacc52xc4yd5x7p6ywsskaf1y2x8dznrijszmxi2i"; depends=[AnnotationHub curl ExperimentHub rmarkdown]; };
  seventyGeneData = derive2 { name="seventyGeneData"; version="1.28.0"; sha256="1jyb6lj71dhc00fka4913zxxkd6cqmd39r4khx1bhpi7nnvf7qcf"; depends=[]; };
  shinyMethylData = derive2 { name="shinyMethylData"; version="1.12.0"; sha256="0q9m7ywsdqk02bnadxf2g975zy8sddw8yrjrr0rcl730jhznw5ph"; depends=[]; };
  signatureSearchData = derive2 { name="signatureSearchData"; version="1.6.0"; sha256="12s2mp4lkr47gwspqnllrkmzldr99dqqjxrqrcjl2xmzn93fry72"; depends=[affy Biobase dplyr ExperimentHub limma magrittr R_utils rhdf5 signatureSearch]; };
--- a/pkgs/development/r-modules/bioc-packages.nix
+++ b/pkgs/development/r-modules/bioc-packages.nix
@ -50,8 +50,8 @@ in with self; {
  AneuFinder = derive2 { name="AneuFinder"; version="1.20.0"; sha256="0m6wphlriq7y21ih1p2kzml5jzcic79jc52kkk59dkjj8j88yllk"; depends=[AneuFinderData bamsignals BiocGenerics Biostrings cowplot DNAcopy doParallel ecp foreach GenomeInfoDb GenomicAlignments GenomicRanges ggdendro ggplot2 ggrepel IRanges mclust ReorderCluster reshape2 Rsamtools S4Vectors]; };
  AnnotationDbi = derive2 { name="AnnotationDbi"; version="1.54.1"; sha256="0fcammls431pgmp47r85k0zh3bz42bajbqdmafd31kpqncc1ijal"; depends=[Biobase BiocGenerics DBI IRanges KEGGREST RSQLite S4Vectors]; };
  AnnotationFilter = derive2 { name="AnnotationFilter"; version="1.16.0"; sha256="0799jja6v7l3jsi26wbjalkr5lriaxid05xb5g36iq93myhaj0sa"; depends=[GenomicRanges lazyeval]; };
-  AnnotationForge = derive2 { name="AnnotationForge"; version="1.34.0"; sha256="1by3diy0y4809k97cw97mp4j177gn1dzhqil8myij1r7b8sk7hax"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; };
-  AnnotationHub = derive2 { name="AnnotationHub"; version="3.0.1"; sha256="12i8lafy1z97gs4knqi7r5l1hd7dr6j8a23qj4fkdpqsdpyz21z7"; depends=[AnnotationDbi BiocFileCache BiocGenerics BiocManager BiocVersion curl dplyr httr interactiveDisplayBase rappdirs RSQLite S4Vectors yaml]; };
+  AnnotationForge = derive2 { name="AnnotationForge"; version="1.34.1"; sha256="0g75b2adak87raw0vn20fjh5980y7svknh8ih1sn4fwryglp4ggg"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; };
+  AnnotationHub = derive2 { name="AnnotationHub"; version="3.0.2"; sha256="09drr13qqdj7b711axmlxv2gkaw17cvkhl0g2rh7w0b2vx13fg7y"; depends=[AnnotationDbi BiocFileCache BiocGenerics BiocManager BiocVersion curl dplyr httr interactiveDisplayBase rappdirs RSQLite S4Vectors yaml]; };
  AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.22.0"; sha256="0jnh3d8v00xxnqcfmzhha75fai9cr1lrjm153i1cy2z9mi31rzr1"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocCheck BiocGenerics BiocManager biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges jsonlite OrganismDbi RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; };
  ArrayExpress = derive2 { name="ArrayExpress"; version="1.52.0"; sha256="0ivmy1zfxagk29ss8vjl2nj6mjsab9l6ddmpji7s3ay4fqmppji5"; depends=[Biobase limma oligo XML]; };
  ArrayExpressHTS = derive2 { name="ArrayExpressHTS"; version="1.42.0"; sha256="1v6ifl5vz2d4kxhbqp7fj3lwi6jffk0ngjy3kpqbj0la5wjpy93n"; depends=[Biobase BiocGenerics biomaRt Biostrings bitops edgeR GenomicRanges Hmisc IRanges R2HTML RColorBrewer Rhtslib rJava Rsamtools sampling sendmailR ShortRead snow svMisc XML]; };
@ -223,7 +223,7 @@ in with self; {
  ConsensusClusterPlus = derive2 { name="ConsensusClusterPlus"; version="1.56.0"; sha256="163nr50nyvwrsajmm0cgxp70pqk61mgw0k7ams694hcb42162j8b"; depends=[ALL Biobase cluster]; };
  CopyNumberPlots = derive2 { name="CopyNumberPlots"; version="1.8.0"; sha256="0gza6a06jf161r88f4sm4l51qpb94x05wapy0750w76pv148blq9"; depends=[cn_mops GenomeInfoDb GenomicRanges IRanges karyoploteR regioneR rhdf5 Rsamtools SummarizedExperiment VariantAnnotation]; };
  CopywriteR = derive2 { name="CopywriteR"; version="2.24.0"; sha256="0pacs714d9b1fdz68pp9ca0x77d376s19lxb82np4l9fgx0rgkxp"; depends=[BiocParallel chipseq CopyhelpeR data_table DNAcopy futile_logger GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges matrixStats Rsamtools S4Vectors]; };
-  CoreGx = derive2 { name="CoreGx"; version="1.4.1"; sha256="10d85v3c3sf0h8ap49hz9lp81cmim1zx89svw95dpsa3ndi9rcs8"; depends=[Biobase BiocGenerics BiocParallel crayon data_table glue lsa MatrixGenerics MultiAssayExperiment piano rlang S4Vectors SummarizedExperiment]; };
+  CoreGx = derive2 { name="CoreGx"; version="1.4.2"; sha256="1xn4fj6djyg5w8yg7170wfj0mllazmdxhwng013zfg1qynpxx20f"; depends=[Biobase BiocGenerics BiocParallel crayon data_table glue lsa MatrixGenerics MultiAssayExperiment piano rlang S4Vectors SummarizedExperiment]; };
  Cormotif = derive2 { name="Cormotif"; version="1.38.0"; sha256="0mkbj09rdxvcf4dmj5ri2099rs5k5391pdiw8kgj79framjjzmdg"; depends=[affy limma]; };
  CountClust = derive2 { name="CountClust"; version="1.20.0"; sha256="0prnv10zib8m21n5iv8gjkin09j9kj96aidjaylgpzc3a7f74286"; depends=[cowplot flexmix ggplot2 gtools limma maptpx picante plyr reshape2 slam SQUAREM]; };
  CoverageView = derive2 { name="CoverageView"; version="1.30.0"; sha256="1xhirbjdw09cqm4xvysxqicvqjbahavwvs7shg4cb05gwyd2ha8g"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors]; };
@ -262,7 +262,7 @@ in with self; {
  DNABarcodes = derive2 { name="DNABarcodes"; version="1.22.0"; sha256="1wiqmzjcb7flp7ldcgbx91asxxrmm1rg9pcfljniab9xcsldhksp"; depends=[BH Matrix Rcpp]; };
  DNAcopy = derive2 { name="DNAcopy"; version="1.66.0"; sha256="0mgq814f6c2271d2lxg763bsnv3ma4ari5xa4x1rbksv8yvcjc4d"; depends=[]; };
  DNAshapeR = derive2 { name="DNAshapeR"; version="1.20.0"; sha256="09271m79llrs48h8723qsvl4aigjwaif6is0mkdk2dpqi80aza3k"; depends=[Biostrings fields GenomicRanges Rcpp]; };
-  DOSE = derive2 { name="DOSE"; version="3.18.2"; sha256="0kp6j42mpxrpd02cjrzqmrx3rvvpi90xiy4gc5km6ny3vxbhlaqw"; depends=[AnnotationDbi BiocParallel DO_db fgsea ggplot2 GOSemSim qvalue reshape2]; };
+  DOSE = derive2 { name="DOSE"; version="3.18.3"; sha256="09blmrgzxaknn263zf3zqc5yx27wjwznsr8lqsm118k4wpfxj504"; depends=[AnnotationDbi BiocParallel DO_db fgsea ggplot2 GOSemSim qvalue reshape2]; };
  DRIMSeq = derive2 { name="DRIMSeq"; version="1.20.0"; sha256="1rswd4lks4v6nfkkiqn2spicjpwsbi2sg8wz44bhf2idxc5mlad4"; depends=[BiocGenerics BiocParallel edgeR GenomicRanges ggplot2 IRanges limma MASS reshape2 S4Vectors]; };
  DSS = derive2 { name="DSS"; version="2.40.0"; sha256="094z7n8m4mygvxpl7vlh8ls4aggrxcmsc0wh8khnz61sfsv2q15l"; depends=[Biobase BiocParallel bsseq DelayedArray]; };
  DTA = derive2 { name="DTA"; version="2.38.0"; sha256="10fnqvip3sxxpxq6y9565gkrzk2gr4269l5xcdph4awrjlq6pshz"; depends=[LSD scatterplot3d]; };
@ -301,7 +301,7 @@ in with self; {
  EGSEA = derive2 { name="EGSEA"; version="1.20.0"; sha256="0wxql39p42craa9z209l9pxr3kqb99kq7y9cwwvkdhp5q2bsfsrj"; depends=[AnnotationDbi Biobase DT edgeR EGSEAdata gage ggplot2 Glimma globaltest gplots GSVA HTMLUtils htmlwidgets hwriter limma metap org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db PADOG pathview plotly RColorBrewer safe stringi topGO]; };
  ELMER = derive2 { name="ELMER"; version="2.16.0"; sha256="07yl4xcymk4km5zglj9hcgdb0hjjrnr374yp6r59j8cz76smym92"; depends=[biomaRt circlize ComplexHeatmap DelayedArray doParallel downloader dplyr ELMER_data GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggpubr ggrepel gridExtra Gviz IRanges lattice magrittr Matrix MultiAssayExperiment plotly plyr progress purrr readr reshape reshape2 rmarkdown rtracklayer rvest S4Vectors scales stringr SummarizedExperiment TCGAbiolinks tibble tidyr xml2]; };
  EMDomics = derive2 { name="EMDomics"; version="2.22.0"; sha256="0m11n9wj6rh5x0fzih8s661h0dziss907bwbc9hnmsjkabvvl39s"; depends=[BiocParallel CDFt emdist ggplot2 matrixStats preprocessCore]; };
-  ENmix = derive2 { name="ENmix"; version="1.28.5"; sha256="1gf2xxz9991644x8c4nv3fs6g321zqk9c0j6v1bx47j5jyfi5iy1"; depends=[AnnotationHub Biobase doParallel dynamicTreeCut ExperimentHub foreach genefilter geneplotter gplots gtools illuminaio impute IRanges irr matrixStats minfi preprocessCore quadprog RPMM S4Vectors SummarizedExperiment]; };
+  ENmix = derive2 { name="ENmix"; version="1.28.8"; sha256="0fhknqi4mfzg3fzy8krvhcrd2a18wsqdf4b257d5rc3hzj26rvqb"; depends=[AnnotationHub Biobase doParallel dynamicTreeCut ExperimentHub foreach genefilter geneplotter gplots gtools illuminaio impute IRanges irr matrixStats minfi preprocessCore quadprog RPMM S4Vectors SummarizedExperiment]; };
  ERSSA = derive2 { name="ERSSA"; version="1.10.0"; sha256="0ph4bscydwn1a9w91b3ab1lj31kn7ddi9wfm6bhdv949pb4p48xn"; depends=[BiocParallel DESeq2 edgeR ggplot2 plyr RColorBrewer]; };
  EWCE = derive2 { name="EWCE"; version="1.0.1"; sha256="0dyzvkqi0dzrjhs50p1d9kcyyin4vvjjrdjjh7mxwpr4kirxghdh"; depends=[AnnotationHub biomaRt cowplot ewceData ExperimentHub future ggdendro ggplot2 gridExtra HGNChelper limma Matrix reshape2 RNOmni scales stringr SummarizedExperiment]; };
  EmpiricalBrownsMethod = derive2 { name="EmpiricalBrownsMethod"; version="1.20.0"; sha256="1zaz8h2mzh0fnfq9h3yvhnj2mpafd36vwlfa5c92piddrrk9g9q8"; depends=[]; };
@ -454,7 +454,7 @@ in with self; {
  HilbertVis = derive2 { name="HilbertVis"; version="1.50.0"; sha256="1fiycg4zkkgb5jynxv6jglc9x3skr9s4xf9aisywgkv2rv4hhk13"; depends=[lattice]; };
  HilbertVisGUI = derive2 { name="HilbertVisGUI"; version="1.50.0"; sha256="1685p65kf827ynbcxfb6dsp5bn7xjgwvrcp8q958jir84ma1glzf"; depends=[HilbertVis]; };
  HubPub = derive2 { name="HubPub"; version="1.0.0"; sha256="00hrhhdahp5dccxad1i7q1wgn4fbdrw01jpa2vdx13f2dqzhwvls"; depends=[available aws_s3 BiocManager biocthis dplyr fs usethis]; };
-  HumanTranscriptomeCompendium = derive2 { name="HumanTranscriptomeCompendium"; version="1.8.1"; sha256="1wwhcm1v30mdgwixfnn9lrbwc6v61z3zkh71vfkc6gbrh588xl8h"; depends=[S4Vectors shiny ssrch SummarizedExperiment]; };
+  HumanTranscriptomeCompendium = derive2 { name="HumanTranscriptomeCompendium"; version="1.8.3"; sha256="1bbdqiw8bmnac9r1jk1jamj4ilakn1rnqy9n77p4565yaa9ij9dp"; depends=[S4Vectors shiny ssrch SummarizedExperiment]; };
  HybridMTest = derive2 { name="HybridMTest"; version="1.36.0"; sha256="1xfri7da9wp38292b29l9rw6rabafv119baj7a4q238vfp6jjp9h"; depends=[Biobase fdrtool MASS survival]; };
  IHW = derive2 { name="IHW"; version="1.20.0"; sha256="0b393a8ayzbnrgkk562w1dj7avacpb3wc7yq7awiki24wi5g2lfw"; depends=[BiocGenerics fdrtool lpsymphony slam]; };
  ILoReg = derive2 { name="ILoReg"; version="1.2.0"; sha256="1fxfv7p3bjaam49pria2p9ggq0qnmzx2kjlsp2z53anvnp8dw9zb"; depends=[aricode cluster cowplot dendextend DescTools doRNG doSNOW dplyr fastcluster foreach ggplot2 LiblineaR Matrix parallelDist pheatmap plyr reshape2 RSpectra Rtsne S4Vectors scales SingleCellExperiment SparseM SummarizedExperiment umap]; };
@ -485,17 +485,18 @@ in with self; {
  InterMineR = derive2 { name="InterMineR"; version="1.14.1"; sha256="1p7dvn2s2xq39zxxbmqma0i2ha0nj9bl65awp2h5b0yrqx12ia0v"; depends=[Biostrings GenomicRanges httr igraph IRanges RCurl RJSONIO S4Vectors sqldf SummarizedExperiment XML xml2]; };
  InteractionSet = derive2 { name="InteractionSet"; version="1.20.0"; sha256="034xidjmn67n1471fnpdmz7gjm6p05cj8sp9nssc3gxdzn54a6xb"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges Matrix Rcpp S4Vectors SummarizedExperiment]; };
  InteractiveComplexHeatmap = derive2 { name="InteractiveComplexHeatmap"; version="1.0.0"; sha256="0i6n49vac0pzimx82hk4ssfc21hml68j5is3czl4m40sn541s4gv"; depends=[clisymbols ComplexHeatmap digest GetoptLong htmltools IRanges jsonlite kableExtra RColorBrewer S4Vectors shiny svglite]; };
+  IntramiRExploreR = derive2 { name="IntramiRExploreR"; version="1.14.1"; sha256="16f1q9gbb1zd71ygmwikh9ns9392x8mf1srf0zkfn0ikcr7i6vb6"; depends=[FGNet igraph knitr]; };
  IsoCorrectoR = derive2 { name="IsoCorrectoR"; version="1.10.0"; sha256="05vqn4y2qrvgap8fl7cqc5qmg4aqc09bn0n6n527h1zsjkvam7w8"; depends=[dplyr magrittr pracma quadprog readr readxl stringr tibble WriteXLS]; };
  IsoCorrectoRGUI = derive2 { name="IsoCorrectoRGUI"; version="1.8.0"; sha256="1xqqfvbwnfg45ajkk55138px3plsdjgmzdd6rnj5lq7pbykxlf1m"; depends=[IsoCorrectoR readxl tcltk2]; };
  IsoGeneGUI = derive2 { name="IsoGeneGUI"; version="2.28.0"; sha256="0vnlja5r982m38vayy4njgybpy6da17vvi959qvwlrfglkk29l77"; depends=[Biobase ff geneplotter goric Iso IsoGene jpeg multtest ORCME ORIClust orQA RColorBrewer Rcpp relimp tkrplot xlsx]; };
-  IsoformSwitchAnalyzeR = derive2 { name="IsoformSwitchAnalyzeR"; version="1.14.0"; sha256="0m6y227jyd0009cphrm2g06j9m9js5n02akdan5k31v2migz0bm1"; depends=[Biobase BiocGenerics Biostrings BSgenome DBI DEXSeq dplyr DRIMSeq edgeR futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges limma magrittr plyr RColorBrewer RCurl readr reshape2 rtracklayer stringr tibble tximeta tximport VennDiagram XVector]; };
+  IsoformSwitchAnalyzeR = derive2 { name="IsoformSwitchAnalyzeR"; version="1.14.1"; sha256="0zfwhaz5p0ivyjd06nm16vfwywnzani5plh8jyj3fp6h9qjsgzd4"; depends=[Biobase BiocGenerics Biostrings BSgenome DBI DEXSeq dplyr DRIMSeq edgeR futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges limma magrittr plyr RColorBrewer RCurl readr reshape2 rtracklayer stringr tibble tximeta tximport VennDiagram XVector]; };
  KBoost = derive2 { name="KBoost"; version="1.0.0"; sha256="15x0n45v5qjb4qgp4hdw0cvwc49fwgpn4j41qhixn6c3dbyn0588"; depends=[]; };
  KCsmart = derive2 { name="KCsmart"; version="2.50.0"; sha256="0fz7pn7z9yyvi9k5va4imjr2bk62jf6gvyymm0jcmw1dlca3g6i7"; depends=[BiocGenerics KernSmooth multtest siggenes]; };
  KEGGREST = derive2 { name="KEGGREST"; version="1.32.0"; sha256="15313d20v3ziyn52fhc6fbzcy1kxjkdx18124bxhdfd14f4aypcd"; depends=[Biostrings httr png]; };
  KEGGgraph = derive2 { name="KEGGgraph"; version="1.52.0"; sha256="0zxdph5hzr3kzj2g1mjqpiviwa189a5sq4bw7wiry6r79fdnklqs"; depends=[graph RCurl Rgraphviz XML]; };
  KEGGlincs = derive2 { name="KEGGlincs"; version="1.18.0"; sha256="1k1b1d0nzp3psk1qx5mcz6l8had1ymfdnm1xn0rmwzgny5mzcma0"; depends=[AnnotationDbi gtools hgu133a_db httr igraph KEGGgraph KEGGREST KOdata org_Hs_eg_db plyr RJSONIO XML]; };
  KinSwingR = derive2 { name="KinSwingR"; version="1.10.0"; sha256="0zj16im3j2kvgi84mgpk0x8kqp8l831zkqcvjn27y73dvniiycby"; depends=[BiocParallel data_table sqldf]; };
-  KnowSeq = derive2 { name="KnowSeq"; version="1.6.1"; sha256="146715xrgdc45m0qbr07kn91glf37vqicbryaqng7n788m2d0nsb"; depends=[caret cqn e1071 edgeR ggplot2 gridExtra Hmisc httr jsonlite kernlab limma praznik R_utils randomForest reshape2 rlist rmarkdown stringr sva XML]; };
+  KnowSeq = derive2 { name="KnowSeq"; version="1.6.3"; sha256="1wsbs97n27iwhxh0fjxsfqz25p6rn2rh6r4cibnmvm18vkm54hvp"; depends=[caret cqn e1071 edgeR ggplot2 gridExtra Hmisc httr jsonlite kernlab limma praznik R_utils randomForest reshape2 rlist rmarkdown stringr sva XML]; };
  LACE = derive2 { name="LACE"; version="1.4.0"; sha256="1v4nsm4bx6kmsx6ivwn18zki4h9yri4mpigaqpwi1flfbfgm9wa5"; depends=[data_tree igraph RColorBrewer Rfast SummarizedExperiment]; };
  LBE = derive2 { name="LBE"; version="1.60.0"; sha256="0fd8qihzy7v7zzn1kky3ja7k3n4mav3myi2bkdrlw7nhrxsx1hys"; depends=[]; };
  LEA = derive2 { name="LEA"; version="3.4.0"; sha256="10pbaq5lmc1w1jpplvxxmpqjmf6c0k9hxd8l8c209ldwsxnhjn6a"; depends=[]; };
@ -547,7 +548,7 @@ in with self; {
  MLSeq = derive2 { name="MLSeq"; version="2.10.0"; sha256="0yww4w66rjbk3gbj86wd07i2z6ic4vjcxy7cacrvbvwkjbdxkzb4"; depends=[Biobase caret DESeq2 edgeR foreach ggplot2 limma plyr sSeq SummarizedExperiment xtable]; };
  MMAPPR2 = derive2 { name="MMAPPR2"; version="1.6.0"; sha256="0dgsszfv3pgmbnns5pxaixkfni5k4c995247cfvkmz5gbwrlfh1g"; depends=[Biobase BiocGenerics BiocParallel data_table dplyr ensemblVEP GenomeInfoDb GenomicRanges gmapR IRanges magrittr Rsamtools S4Vectors stringr tidyr VariantAnnotation VariantTools]; };
  MMDiff2 = derive2 { name="MMDiff2"; version="1.20.0"; sha256="1k7zgn9m7plfqqjsw6rlwcf28cysp3xg05krz8qii066plms291f"; depends=[Biobase Biostrings BSgenome GenomicRanges ggplot2 locfit RColorBrewer Rsamtools S4Vectors shiny]; };
-  MMUPHin = derive2 { name="MMUPHin"; version="1.6.1"; sha256="0p2szcbk2rrxzg2j43fw7rv9n32flwwk399yma9mqi0jrsh9wqsk"; depends=[cowplot dplyr fpc ggplot2 igraph Maaslin2 metafor tidyr]; };
+  MMUPHin = derive2 { name="MMUPHin"; version="1.6.2"; sha256="1hagg3fyyr6wzy02rcpd5rmniah78q5ndh1w7l4pc4mrmbfs4srn"; depends=[cowplot dplyr fpc ggplot2 igraph Maaslin2 metafor tidyr]; };
  MODA = derive2 { name="MODA"; version="1.18.0"; sha256="02yzc9sg2yqbr05zxw2mqd2fizy0r0fh0g6wszljzcabbadwxbcn"; depends=[AMOUNTAIN cluster dynamicTreeCut igraph RColorBrewer WGCNA]; };
  MOFA2 = derive2 { name="MOFA2"; version="1.2.2"; sha256="1hx1bgcyjcs5kan13dg2i4a43m3p0981cqdxizrz1j43xf6h26ln"; depends=[basilisk corrplot cowplot DelayedArray dplyr forcats ggplot2 ggrepel HDF5Array magrittr pheatmap RColorBrewer reshape2 reticulate rhdf5 Rtsne stringi tidyr uwot]; };
  MOGAMUN = derive2 { name="MOGAMUN"; version="1.2.1"; sha256="1x0v7ha2a3ldqiwxyn9l9z2frbshpn04k5zy8rxhbk447b0hca5z"; depends=[BiocParallel igraph RCy3 RUnit stringr]; };
@ -565,7 +566,7 @@ in with self; {
  MSstats = derive2 { name="MSstats"; version="4.0.1"; sha256="1x5cxz4i65fv055ksj6jsiaj60px457hqkhp58rhvaf8cg9gvf8c"; depends=[checkmate data_table ggplot2 ggrepel gplots limma lme4 marray MASS MSstatsConvert preprocessCore Rcpp RcppArmadillo survival]; };
  MSstatsConvert = derive2 { name="MSstatsConvert"; version="1.2.2"; sha256="1mwxlbv7jb61in0zsrsy09prhgv54nh5wkj3zcs89lgvc813jgpm"; depends=[checkmate data_table log4r stringi]; };
  MSstatsLOBD = derive2 { name="MSstatsLOBD"; version="1.0.0"; sha256="09mlgcvj7a30c6rryr1zx7743gxpwcz7xyxcvfgd4ci492i3s670"; depends=[ggplot2 minpack_lm Rcpp]; };
-  MSstatsPTM = derive2 { name="MSstatsPTM"; version="1.2.3"; sha256="11na5g9k12c68br23bn23ibbnaa4h98vx50hyh3q740cz6vphffz"; depends=[Biostrings checkmate data_table dplyr ggplot2 ggrepel gridExtra MSstats MSstatsConvert MSstatsTMT Rcpp stringr]; };
+  MSstatsPTM = derive2 { name="MSstatsPTM"; version="1.2.4"; sha256="11byb6hiahsn33k2myav7g66fx9514idxpr7vzf6v49jiz53b9qc"; depends=[Biostrings checkmate data_table dplyr ggplot2 ggrepel gridExtra MSstats MSstatsConvert MSstatsTMT Rcpp stringr]; };
  MSstatsQC = derive2 { name="MSstatsQC"; version="2.10.0"; sha256="0z62xy689qbbwak6j1kqhagm0z8k9m7c8sdns59mc0xz1s6valh8"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics]; };
  MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.12.0"; sha256="0jr8x1fv648kky5w6438hdj9w151a7mbb4z28nds60k44bvk521v"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly shiny]; };
  MSstatsSampleSize = derive2 { name="MSstatsSampleSize"; version="1.6.0"; sha256="0cyddrm3wj28apik58wnm698gwbz5d8q5b7w4x1mp2qsp7af6c7y"; depends=[BiocParallel caret ggplot2 gridExtra MSstats reshape2]; };
@ -605,7 +606,7 @@ in with self; {
  MiChip = derive2 { name="MiChip"; version="1.46.0"; sha256="10i7bq9qcwvhy7mh47zk9105837p68zd7cidl9pss6l6h03rszfm"; depends=[Biobase]; };
  MiPP = derive2 { name="MiPP"; version="1.64.0"; sha256="0g8vlbcwy7djfpgg3483hw65a6g472z7h329vqsrfk782i4wzglr"; depends=[Biobase e1071 MASS]; };
  MiRaGE = derive2 { name="MiRaGE"; version="1.34.0"; sha256="19y8kyirm0pzvv6p3dsnn9zws189anw5a2h2aiivgh6y6jis8g57"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager S4Vectors]; };
-  MicrobiotaProcess = derive2 { name="MicrobiotaProcess"; version="1.4.3"; sha256="0rbzsacz3sqpwslq9fvfa1mxa7n00bp8jf4z4i767q0d6xhy9v7v"; depends=[ape Biostrings coin dplyr foreach ggplot2 ggrepel ggsignif ggstar ggtree magrittr MASS patchwork rlang SummarizedExperiment tibble tidyr tidyselect tidytree treeio vegan zoo]; };
+  MicrobiotaProcess = derive2 { name="MicrobiotaProcess"; version="1.4.4"; sha256="0r8z2vjj32zblzhk2dyx2na3z35fzxf3lgrnb97vz4l5navgmghp"; depends=[ape Biostrings coin dplyr foreach ggplot2 ggrepel ggsignif ggstar ggtree magrittr MASS patchwork rlang SummarizedExperiment tibble tidyr tidyselect tidytree treeio vegan zoo]; };
  MineICA = derive2 { name="MineICA"; version="1.32.0"; sha256="1cpy8fpfff0k0s4qxmis6351nk1v507a2jszg3hhw3aacbpm7gqp"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt cluster colorspace fastICA foreach fpc ggplot2 GOstats graph gtools Hmisc igraph JADE lumi lumiHumanAll_db marray mclust plyr RColorBrewer Rgraphviz scales xtable]; };
  MinimumDistance = derive2 { name="MinimumDistance"; version="1.36.0"; sha256="0jp2icr0z56d3phickr3dhgkmiapfl7z93mipzc7ll139m3ayzj8"; depends=[Biobase BiocGenerics data_table DNAcopy ff foreach GenomeInfoDb GenomicRanges IRanges lattice MatrixGenerics matrixStats oligoClasses S4Vectors SummarizedExperiment VanillaICE]; };
  ModCon = derive2 { name="ModCon"; version="1.0.0"; sha256="1qd1545w6jgpd4xnqwbhv10yzn70lc3hslqr56gg30mc7p8qbkh8"; depends=[data_table]; };
@ -619,7 +620,7 @@ in with self; {
  Mulcom = derive2 { name="Mulcom"; version="1.42.0"; sha256="0law2r7hf22jm8029s8yw1b03dmh3grpnjsp7gkavrmp5355rm9m"; depends=[Biobase fields]; };
  MultiAssayExperiment = derive2 { name="MultiAssayExperiment"; version="1.18.0"; sha256="0l0arf3q1f6zy6pdgsy3h5n523sg1hlilv7lj7snr5814idgdj51"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors SummarizedExperiment tidyr]; };
  MultiBaC = derive2 { name="MultiBaC"; version="1.2.0"; sha256="0c6vah8396vklwk8sqg3rapifaz0f527w5jw2ddpz2nmmnigy2b8"; depends=[ggplot2 Matrix MultiAssayExperiment ropls]; };
-  MultiDataSet = derive2 { name="MultiDataSet"; version="1.20.0"; sha256="1hyk40xgmy50rqxwdvc64d3pgz5vsg8vmlj5cp5m0n5m0adxcdfj"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggrepel IRanges limma qqman S4Vectors SummarizedExperiment]; };
+  MultiDataSet = derive2 { name="MultiDataSet"; version="1.20.2"; sha256="06wcncz10jm54g0m9yk2314lg8x666p5r4zhi57sp2p50cj1lvnz"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggrepel IRanges limma qqman S4Vectors SummarizedExperiment]; };
  MultiMed = derive2 { name="MultiMed"; version="2.14.0"; sha256="1s23gf8vvi76k4z7qvw3zvfjqs0w5rg3lijfs8b4z23nphadv4gg"; depends=[]; };
  MungeSumstats = derive2 { name="MungeSumstats"; version="1.0.1"; sha256="1l9j0b3j6n4fi5c657h958kz88fzlcq5r7vfx9xhpy5y9di319k7"; depends=[Biostrings BSgenome data_table GenomicRanges]; };
  MutationalPatterns = derive2 { name="MutationalPatterns"; version="3.2.0"; sha256="0433i4xbz8hrfaj8fxgzps3x8dqrl5vgwzg7qmp4cy5sb1lw5wvs"; depends=[BiocGenerics Biostrings BSgenome cowplot dplyr GenomeInfoDb GenomicRanges ggalluvial ggdendro ggplot2 IRanges magrittr NMF pracma purrr S4Vectors stringr tibble tidyr VariantAnnotation]; };
@ -649,7 +650,7 @@ in with self; {
  OMICsPCA = derive2 { name="OMICsPCA"; version="1.10.0"; sha256="1r26pj3rlk211581ddyfga1ghja11x4jy60kdwqzl74gnrjh8nvb"; depends=[cluster clValid corrplot cowplot data_table factoextra FactoMineR fpc GenomeInfoDb ggplot2 HelloRanges IRanges kableExtra magick MASS MultiAssayExperiment NbClust OMICsPCAdata pdftools PerformanceAnalytics reshape2 rgl rmarkdown rtracklayer tidyr]; };
  OPWeight = derive2 { name="OPWeight"; version="1.14.0"; sha256="1d3bp3l77335idc3yd9dz1zadby05w46bws835ga7vc824rd08p5"; depends=[MASS qvalue tibble]; };
  ORFhunteR = derive2 { name="ORFhunteR"; version="1.0.0"; sha256="0y4xpzma0lz8qaqr538spwahyis753l6nvdqm4cmynvahkxdqxdj"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg38 data_table Peptides randomForest Rcpp rtracklayer stringr xfun]; };
-  ORFik = derive2 { name="ORFik"; version="1.12.11"; sha256="0ylwhk4ahgwqp7l301nyvg73snsc2r72kkxjb3c90pi1cdn4kap3"; depends=[AnnotationDbi BiocGenerics BiocParallel biomartr Biostrings BSgenome cowplot data_table DESeq2 fst GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra httr IRanges R_utils Rcpp Rsamtools rtracklayer S4Vectors SummarizedExperiment xml2]; };
+  ORFik = derive2 { name="ORFik"; version="1.12.13"; sha256="0bg6bxrjj8y8464k5238h3rp2cqld6gxhcgc698bip483wl9kbbx"; depends=[AnnotationDbi BiocGenerics BiocParallel biomartr Biostrings BSgenome cowplot data_table DESeq2 fst GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra httr IRanges R_utils Rcpp Rsamtools rtracklayer S4Vectors SummarizedExperiment xml2]; };
  OSAT = derive2 { name="OSAT"; version="1.40.0"; sha256="1carfhb447z696mxb48b99mqr1lh7zr3gkyq7myajbxjym6a51kf"; depends=[]; };
  OTUbase = derive2 { name="OTUbase"; version="1.42.0"; sha256="1yg376iab78blb8qv4d5hq2mb7va4ir3vp8jrl7a8dqcqvgjm8w0"; depends=[Biobase Biostrings IRanges S4Vectors ShortRead vegan]; };
  OUTRIDER = derive2 { name="OUTRIDER"; version="1.10.0"; sha256="1vvc2w9c31z67khy85i1r8jjhpbkb0vcxwax2lr84rp314b09021"; depends=[BBmisc BiocGenerics BiocParallel data_table DESeq2 generics GenomicFeatures GenomicRanges ggplot2 heatmaply IRanges matrixStats pcaMethods pheatmap plotly plyr PRROC RColorBrewer Rcpp RcppArmadillo reshape2 S4Vectors scales SummarizedExperiment]; };
@ -657,7 +658,7 @@ in with self; {
  OmaDB = derive2 { name="OmaDB"; version="2.8.0"; sha256="0h7df541pr46ayc2gvv3c49lhmgksimghid71qw5xxn122zgp8sa"; depends=[ape Biostrings GenomicRanges httr IRanges jsonlite plyr topGO]; };
  OmicCircos = derive2 { name="OmicCircos"; version="1.30.0"; sha256="1agdy155nk7a4v53whw1fvljsb8gnhvypgjd5w43c41dshhhpc6w"; depends=[GenomicRanges]; };
  OmicsLonDA = derive2 { name="OmicsLonDA"; version="1.8.0"; sha256="1fj7jrczn9rjriw3dbnmsh25bzh7ng9pi8rcdy664xwkm8n840gc"; depends=[BiocGenerics BiocParallel ggplot2 gss plyr pracma SummarizedExperiment zoo]; };
-  Omixer = derive2 { name="Omixer"; version="1.2.3"; sha256="07cadrp5dsm4xx6gnnvxprb3fv9s3yhm7syr8p72yzl01b05b5d0"; depends=[dplyr forcats ggplot2 gridExtra magrittr RColorBrewer readr stringr tibble tidyselect]; };
+  Omixer = derive2 { name="Omixer"; version="1.2.4"; sha256="1bkyr50nq6vjp2xpyi1915xa93y1ih54m1p2dsjvcnjvd52zfngp"; depends=[dplyr forcats ggplot2 gridExtra magrittr RColorBrewer readr stringr tibble tidyselect]; };
  OmnipathR = derive2 { name="OmnipathR"; version="3.0.4"; sha256="0rbq3h3cp5dgpy5ifmbnfm6z8w4jv45wjzyl1f4qacgrbyf2l30a"; depends=[checkmate curl digest dplyr httr igraph jsonlite later logger magrittr progress purrr rappdirs readr readxl rlang stringr tibble tidyr tidyselect xml2 yaml]; };
  OncoScore = derive2 { name="OncoScore"; version="1.20.0"; sha256="1765pvqikvckgzajjsa5f0y5fiwyvi3syxafawl765bph83n9f99"; depends=[biomaRt]; };
  OncoSimulR = derive2 { name="OncoSimulR"; version="3.0.0"; sha256="1nsyqs4ai6nrsydi8cw7cxalf7pjzfdafdqx6ga91gyfbj4pv55k"; depends=[car data_table dplyr ggplot2 ggrepel graph gtools igraph RColorBrewer Rcpp Rgraphviz smatr stringr]; };
@ -704,7 +705,7 @@ in with self; {
  PhosR = derive2 { name="PhosR"; version="1.2.0"; sha256="1fravmg690is1lqp2afzg22ywycx0p2sqp6hw97s51phyw5f82vn"; depends=[BiocGenerics circlize dendextend dplyr e1071 GGally ggdendro ggplot2 ggpubr ggtext igraph limma network pcaMethods pheatmap preprocessCore RColorBrewer reshape2 rlang ruv S4Vectors SummarizedExperiment tidyr]; };
  PhyloProfile = derive2 { name="PhyloProfile"; version="1.6.6"; sha256="0jabsrjzlgw38mm0qmwfa7zygpl9fir3gyn0r75dyvrbz7z3psc2"; depends=[ape BiocStyle bioDist Biostrings colourpicker data_table DT energy ExperimentHub ggplot2 gridExtra OmaDB pbapply plyr RColorBrewer RCurl shiny shinyBS shinyjs xml2 zoo]; };
  Pi = derive2 { name="Pi"; version="2.4.0"; sha256="1k0i2jw216k6vbjda4d500whzhdagssci1030ywh5d9fg6z9zm37"; depends=[BiocGenerics caret dnet dplyr GenomeInfoDb GenomicRanges ggnetwork ggplot2 ggrepel glmnet igraph IRanges lattice MASS Matrix osfr plot3D purrr randomForest RCircos readr ROCR scales supraHex tibble tidyr]; };
-  Pigengene = derive2 { name="Pigengene"; version="1.18.0"; sha256="173x4kwgg7f11c4s6jq1rcwcml4b5kcd3wvxxczzdbd58h4ayb4j"; depends=[BiocStyle bnlearn C50 dplyr gdata GO_db graph impute MASS matrixStats partykit pheatmap preprocessCore Rgraphviz WGCNA]; };
+  Pigengene = derive2 { name="Pigengene"; version="1.18.10"; sha256="1khkx7p11k11bays33zbv34mppgp02yxhhsg48kjvq9zg7rqq52a"; depends=[BiocStyle bnlearn C50 dplyr gdata GO_db graph impute MASS matrixStats partykit pheatmap preprocessCore Rgraphviz WGCNA]; };
  PloGO2 = derive2 { name="PloGO2"; version="1.4.0"; sha256="13ilmsy24j3p9f3addz1i9fwscra47rgq4j7ndz46d1h2rd3rdvy"; depends=[GO_db GOstats httr lattice openxlsx xtable]; };
  PoDCall = derive2 { name="PoDCall"; version="1.0.0"; sha256="1sblbxwpqvznm51addm0rrbzimybqb9amawg53v94802cmk5c6jd"; depends=[diptest DT ggplot2 gridExtra LaplacesDemon mclust purrr readr rlist shiny shinyjs]; };
  PoTRA = derive2 { name="PoTRA"; version="1.8.2"; sha256="1wxirc82xn634xzp3z9h4g3hnn6l8x81ayvhhrwplja2fc5kbh7a"; depends=[BiocGenerics graph graphite igraph org_Hs_eg_db]; };
@ -805,7 +806,7 @@ in with self; {
  ReactomeGraph4R = derive2 { name="ReactomeGraph4R"; version="1.0.0"; sha256="19vgz9kxnvf959hpxwmgv0s6g52qg7aa4glsn40s17mrsbmprgvg"; depends=[data_table doParallel foreach getPass jsonlite magrittr neo4r purrr ReactomeContentService4R rlang]; };
  ReactomePA = derive2 { name="ReactomePA"; version="1.36.0"; sha256="1293z89ai766c559axgr7mz5x4564gyl9xqzf6s8s0aj1xb35gqf"; depends=[AnnotationDbi DOSE enrichplot ggplot2 ggraph graphite igraph reactome_db]; };
  ReadqPCR = derive2 { name="ReadqPCR"; version="1.38.0"; sha256="0a5paks4q210h3261p59mc19pbwq3znkn7mirsvcpv9y6ha7jfzj"; depends=[Biobase]; };
-  RedeR = derive2 { name="RedeR"; version="1.40.4"; sha256="1cyn76dhmnkca03bfk0w2hj8jly6kz8iwg9qi7kwgqs6rcamh4sn"; depends=[igraph]; };
+  RedeR = derive2 { name="RedeR"; version="1.40.5"; sha256="1jamcdh70f0mq99ydlxry080r0jsxh798b8bpij1r4jq5px94wbp"; depends=[igraph]; };
  RefPlus = derive2 { name="RefPlus"; version="1.62.0"; sha256="0j9xia747rhbxz7vx20cvb3bsqpz6y4q1mh7m9nas0x3dfrzcci9"; depends=[affy affyPLM Biobase preprocessCore]; };
  RegEnrich = derive2 { name="RegEnrich"; version="1.2.0"; sha256="1n6sgvbmbknp20i732w5xv2a882ri1xli7h3n4wcsl95614aszl5"; depends=[BiocParallel BiocSet DESeq2 DOSE dplyr fgsea ggplot2 limma magrittr randomForest reshape2 S4Vectors SummarizedExperiment tibble WGCNA]; };
  RepViz = derive2 { name="RepViz"; version="1.8.0"; sha256="0jpa9h59q1rjqxx4g6gsk4v33zf9k2xb1cggp4hpgyy7n9cqph0h"; depends=[biomaRt GenomicRanges IRanges Rsamtools S4Vectors]; };
@ -834,7 +835,7 @@ in with self; {
  Rsubread = derive2 { name="Rsubread"; version="2.6.4"; sha256="043m4512q73x6q529hqfgrap0fq5anvny4va085nafia06b805pi"; depends=[Matrix]; };
  Rtpca = derive2 { name="Rtpca"; version="1.2.0"; sha256="0z8q7iyk3f38sn928fan96lwy2xkhx5bzhq184sbn8v3hadhhxyd"; depends=[Biobase dplyr fdrtool ggplot2 pROC tibble tidyr]; };
  Rtreemix = derive2 { name="Rtreemix"; version="1.54.0"; sha256="0rkvkdwyivlvx32azmfwfv1pg1c879mil3h9wz7pwlmxg5ick3yi"; depends=[Biobase graph Hmisc]; };
-  S4Vectors = derive2 { name="S4Vectors"; version="0.30.0"; sha256="0v5vxmg0a27ivgymmzfl595rcb1m3dz27r2wzbk1j97rlpwy1p4q"; depends=[BiocGenerics]; };
+  S4Vectors = derive2 { name="S4Vectors"; version="0.30.2"; sha256="0n13j8fkiy8b071wvwwh3ip9cvq22f74hb1msx91mdab2xl47zxs"; depends=[BiocGenerics]; };
  SAIGEgds = derive2 { name="SAIGEgds"; version="1.6.0"; sha256="0liacxqmalsmg4siafvbas177n6q53rzf2j9hhxv25gp97kld85s"; depends=[gdsfmt Rcpp RcppArmadillo RcppParallel SeqArray SPAtest]; };
  SANTA = derive2 { name="SANTA"; version="2.28.0"; sha256="0nncii7zwgrw8l4njiw63x3ml6qfm53sa29ldrlipaynmv1cwdzh"; depends=[igraph Matrix]; };
  SBGNview = derive2 { name="SBGNview"; version="1.6.0"; sha256="0b44b5ll7ydq6a15543glcwpw4kyvrbfjzwh99v0s8mnpxjfqrfn"; depends=[AnnotationDbi bookdown httr igraph KEGGREST knitr pathview Rdpack rmarkdown rsvg SBGNview_data SummarizedExperiment xml2]; };
@ -913,7 +914,7 @@ in with self; {
  SpatialDecon = derive2 { name="SpatialDecon"; version="1.2.0"; sha256="0sdlz4ikddvghs3r1dbdqkhgl6351rgawy799kam6x0pkcsf2chr"; depends=[logNormReg]; };
  SpatialExperiment = derive2 { name="SpatialExperiment"; version="1.2.1"; sha256="1dx8s4mx95ibwsdfy3mb3xkavng7qwfrjwv3hbf4abxy8vyg2zl5"; depends=[BiocFileCache BiocGenerics DropletUtils magick rjson S4Vectors SingleCellExperiment SummarizedExperiment]; };
  SpeCond = derive2 { name="SpeCond"; version="1.46.0"; sha256="1si7xmmhcklq00cpzsf1w4sg1w6bxp1yk16l25h1znhmpwby65x9"; depends=[Biobase fields hwriter mclust RColorBrewer]; };
-  Spectra = derive2 { name="Spectra"; version="1.2.0"; sha256="0fqhih567zdv8rv54zz2ly68xv8k1n0wb923xdm3i6550h41cj3r"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; };
+  Spectra = derive2 { name="Spectra"; version="1.2.2"; sha256="0781iq76mbz99rf28nvzv3rc9iv9h71sc7r7yjgyfprxas3a0yrs"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; };
  SpectralTAD = derive2 { name="SpectralTAD"; version="1.8.0"; sha256="1bi7r0qid9xa0zzyh32hgi8fyw184dfc7lksrls4ngvy6282sc27"; depends=[BiocParallel cluster dplyr GenomicRanges HiCcompare magrittr Matrix PRIMME]; };
  SpidermiR = derive2 { name="SpidermiR"; version="1.22.1"; sha256="0019ax9m1bnmg78hczkxi9zb2i9iqxlgmanwaxffrfj31r2qr2kr"; depends=[AnnotationDbi gdata ggplot2 gplots gridExtra httr igraph lattice latticeExtra MAGeCKFlute miRNAtap miRNAtap_db networkD3 org_Hs_eg_db TCGAbiolinks visNetwork]; };
  SplicingFactory = derive2 { name="SplicingFactory"; version="1.0.3"; sha256="0nlhpnkvcc8h9sgdhlsfsf8yz232cyfwyayqhj5c6ix4y7r1rvxm"; depends=[SummarizedExperiment]; };
@ -925,7 +926,7 @@ in with self; {
  SubCellBarCode = derive2 { name="SubCellBarCode"; version="1.8.0"; sha256="03wccycmj4krvknwk12jkp8mg6c4adk454akfybgydkydws0vh2y"; depends=[AnnotationDbi caret e1071 ggplot2 ggrepel gridExtra networkD3 org_Hs_eg_db Rtsne scatterplot3d]; };
  SummarizedBenchmark = derive2 { name="SummarizedBenchmark"; version="2.10.0"; sha256="1s629qqaqs8yr20k99ahq1fk0jr8ka60s1qpvzy80wmha7khzaix"; depends=[BiocGenerics BiocParallel crayon digest dplyr ggplot2 mclust rlang S4Vectors sessioninfo stringr SummarizedExperiment tibble tidyr UpSetR]; };
  SummarizedExperiment = derive2 { name="SummarizedExperiment"; version="1.22.0"; sha256="16np5ik6jgbi68mhlib6yskywwbaa50mlr7m3sh1hqk889whfn1g"; depends=[Biobase BiocGenerics DelayedArray GenomeInfoDb GenomicRanges IRanges Matrix MatrixGenerics S4Vectors]; };
-  Summix = derive2 { name="Summix"; version="1.0.2"; sha256="1ypbzhz6cqlfqn5lm7s5wj2xnylw16n44hvp2dyx5w63bxsnaxl3"; depends=[nloptr]; };
+  Summix = derive2 { name="Summix"; version="1.0.3"; sha256="1yvcf4mkz9hclx52zhiz9gzrvspkasc6rayyhw5x7x9c0fxdh6y8"; depends=[nloptr]; };
  Sushi = derive2 { name="Sushi"; version="1.30.0"; sha256="1m5l0nflhcynb3gz7b8qzvknb0s6xhds8z1yl3mbv8ic9qn2knv4"; depends=[biomaRt zoo]; };
  SwathXtend = derive2 { name="SwathXtend"; version="2.14.0"; sha256="08j4d2yyxvf8zch5paai5pr48b6g6yzh67500gv8w2pmx8mnwaml"; depends=[e1071 lattice openxlsx VennDiagram]; };
  SwimR = derive2 { name="SwimR"; version="1.29.0"; sha256="0n58x3i4k3icvhg8z60zlhpszv8bb9pain07nl9rszyvmpi71vg2"; depends=[gplots R2HTML signal]; };
@ -933,9 +934,9 @@ in with self; {
  SynMut = derive2 { name="SynMut"; version="1.8.0"; sha256="09fszipz9nfhxhzyq27ng9xlip9gn29hs70gblr0ssz3g6bi7mni"; depends=[BiocGenerics Biostrings seqinr stringr]; };
  TADCompare = derive2 { name="TADCompare"; version="1.2.0"; sha256="1w7pw16kzh4wgzk97d83sysggbabarvcvjvq3z66pxf8p647fxy4"; depends=[cluster cowplot dplyr ggplot2 ggpubr HiCcompare magrittr Matrix PRIMME RColorBrewer reshape2 tidyr]; };
  TAPseq = derive2 { name="TAPseq"; version="1.4.0"; sha256="1smv992954wr26ljycram7mlf9yjx38mmcma7agqiqyfqafn7dci"; depends=[BiocGenerics BiocParallel Biostrings BSgenome dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges S4Vectors tidyr]; };
-  TBSignatureProfiler = derive2 { name="TBSignatureProfiler"; version="1.4.1"; sha256="1bhn7wl8851snwklr18kxkzkismjhyzhpp1va3g5zp1726hq3gbc"; depends=[ASSIGN BiocGenerics BiocParallel ComplexHeatmap DESeq2 DT edgeR gdata ggplot2 GSVA magrittr RColorBrewer reshape2 rlang ROCit S4Vectors singscore SummarizedExperiment]; };
+  TBSignatureProfiler = derive2 { name="TBSignatureProfiler"; version="1.4.11"; sha256="173pgd4rv1ry81kg1fpc0bllryx5zgg7xfpj06plwv5lx31v0nb0"; depends=[ASSIGN BiocGenerics BiocParallel ComplexHeatmap DESeq2 DT edgeR gdata ggplot2 GSVA magrittr RColorBrewer reshape2 rlang ROCit S4Vectors singscore SummarizedExperiment]; };
  TCC = derive2 { name="TCC"; version="1.32.0"; sha256="0im8gc5v28d4a5mrn4905x0kr0427x6qnr6nyawyrf6pcy13ffwd"; depends=[baySeq DESeq2 edgeR ROC]; };
-  TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.20.0"; sha256="01jzvhyr4z09yfz5jnjwi9r7h9sqkbfr7jgdkbj8qn3q5yd721h0"; depends=[biomaRt data_table downloader dplyr GenomicRanges ggplot2 httr IRanges jsonlite knitr plyr purrr R_utils readr rvest S4Vectors stringr SummarizedExperiment TCGAbiolinksGUI_data tibble tidyr XML xml2]; };
+  TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.20.1"; sha256="0c6has5ch3q526f6h84s7g2a7mga4slga4i758lm0vpnzx2fj1v2"; depends=[biomaRt data_table downloader dplyr GenomicRanges ggplot2 httr IRanges jsonlite knitr plyr purrr R_utils readr rvest S4Vectors stringr SummarizedExperiment TCGAbiolinksGUI_data tibble tidyr XML xml2]; };
  TCGAbiolinksGUI = derive2 { name="TCGAbiolinksGUI"; version="1.18.0"; sha256="0prsrzrzhf5w6nipjvwlc61c0za8xg8xiqfc5igqlhz3hxlw7c29"; depends=[caret clusterProfiler colourpicker data_table downloader DT ELMER ggplot2 ggrepel maftools pathview plotly readr sesame shiny shinyBS shinydashboard shinyFiles shinyjs stringr SummarizedExperiment TCGAbiolinks TCGAbiolinksGUI_data]; };
  TCGAutils = derive2 { name="TCGAutils"; version="1.12.0"; sha256="00xbby4kzifkxm7aff9vha80kfbb311yj3fk3b4xvgmvpg9pwhiq"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; };
  TCseq = derive2 { name="TCseq"; version="1.16.0"; sha256="0qjac5cg7gzdrx44v50l7yz15k36lf5qvp5p4r58n1vc3b8y23yn"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; };
@ -1100,8 +1101,8 @@ in with self; {
  bridge = derive2 { name="bridge"; version="1.56.0"; sha256="1d6621kd5x7b9s6l7clbs3vf17aljhxgpj7m8ji0j2swidii7m0x"; depends=[rama]; };
  bsseq = derive2 { name="bsseq"; version="1.28.0"; sha256="1xpv85hr681kkkilsnasndkszwmzbzq11y0lff4na2ilsm7sqmmi"; depends=[beachmat Biobase BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats GenomeInfoDb GenomicRanges gtools HDF5Array IRanges limma locfit permute R_utils Rcpp rhdf5 S4Vectors scales SummarizedExperiment]; };
  bumphunter = derive2 { name="bumphunter"; version="1.34.0"; sha256="0wi38vwfi8qr10x4xifhylxx7vfc6fqvqs649iq7lf0y7islwq2v"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; };
-  cBioPortalData = derive2 { name="cBioPortalData"; version="2.4.8"; sha256="1f5iz7hdxp0zr088d2vg3wwvd7na6g9s6p0fywzwjc51s4cxagsr"; depends=[AnVIL BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges MultiAssayExperiment RaggedExperiment readr RTCGAToolbox S4Vectors SummarizedExperiment TCGAutils tibble tidyr]; };
-  cTRAP = derive2 { name="cTRAP"; version="1.10.0"; sha256="1p8z5vvmny7h76rsd8pfwinxx34q8hvacm35gbr3sgyyi3y618dx"; depends=[binr biomaRt cowplot data_table dplyr DT fastmatch fgsea ggplot2 ggrepel highcharter httr limma pbapply R_utils readxl reshape2 rhdf5 scales shiny tibble]; };
+  cBioPortalData = derive2 { name="cBioPortalData"; version="2.4.10"; sha256="1yfyfnlnhn8ryzyqbl51lqvsgcf84kqpibn9r24i0hd78y5jbhkm"; depends=[AnVIL BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges MultiAssayExperiment RaggedExperiment readr RTCGAToolbox S4Vectors SummarizedExperiment TCGAutils tibble tidyr]; };
+  cTRAP = derive2 { name="cTRAP"; version="1.10.1"; sha256="0bj1zqdkbv9dww6y8z82bkzirlaqxcsq1x0vm3pbm0ssp48118w0"; depends=[binr biomaRt cowplot data_table dplyr DT fastmatch fgsea ggplot2 ggrepel highcharter httr limma pbapply R_utils readxl reshape2 rhdf5 scales shiny tibble]; };
  caOmicsV = derive2 { name="caOmicsV"; version="1.22.0"; sha256="1h43ml0alpcyafafn8rbm784gr0xpy00942vghqyf3i3y1zq0522"; depends=[bc3net igraph]; };
  calm = derive2 { name="calm"; version="1.6.0"; sha256="1k25dn8xvnpqhlzzmhjqzcpx3i7mc2avxgd8mwr116jwg4fwk077"; depends=[mgcv]; };
  canceR = derive2 { name="canceR"; version="1.26.0"; sha256="170v9ln5p399vzh6l4xl28yfbi93kj65m0pb4980mrzpb8199xkp"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; };
@ -1143,7 +1144,7 @@ in with self; {
  cliqueMS = derive2 { name="cliqueMS"; version="1.6.0"; sha256="0ian0lqjp6p4lxmxnqk5l5kw2j3h2lff3widz5cfqr71421fn92q"; depends=[BH igraph matrixStats MSnbase qlcMatrix Rcpp RcppArmadillo xcms]; };
  clonotypeR = derive2 { name="clonotypeR"; version="1.30.0"; sha256="1siisyqsczjgqp0rm7r9n4j2r52h1g4yi8p7j33w7k8kw4ay03jm"; depends=[]; };
  clst = derive2 { name="clst"; version="1.40.0"; sha256="1lqj36567bahb58naygqhpf09lid0whqma6rilvzg68l6px06nz4"; depends=[lattice ROC]; };
-  clstutils = derive2 { name="clstutils"; version="1.40.0"; sha256="0hg9cibl5bqwr6rkflzk1syvb2ixngbzbkhj8am3rw7akcp7g90z"; depends=[ape clst lattice rjson RSQLite]; };
+  clstutils = derive2 { name="clstutils"; version="1.40.1"; sha256="0z03ciq2gyrziwg4bmsbf9f0kwrl9h64wnvpnx81f5xzjbwlqzsh"; depends=[ape clst lattice rjson RSQLite]; };
  clustComp = derive2 { name="clustComp"; version="1.20.0"; sha256="18kq0s9cv4b5dy28cg104simyykka6gx9bfb1nhgz4z6ljb65ccn"; depends=[sm]; };
  clusterExperiment = derive2 { name="clusterExperiment"; version="2.12.0"; sha256="1fhmayciwn1m124b4dcs3gzbghgk9f7a7qmjnvvxc958cywcwkx5"; depends=[ape BiocGenerics BiocSingular cluster DelayedArray edgeR HDF5Array howmany kernlab limma locfdr Matrix matrixStats mbkmeans NMF phylobase pracma RColorBrewer Rcpp S4Vectors scales SingleCellExperiment stringr SummarizedExperiment zinbwave]; };
  clusterProfiler = derive2 { name="clusterProfiler"; version="4.0.5"; sha256="1dccrl2ffhgmv3iqlmpln7z86ahpf0j9ma194fnknsgi3cd9rhrl"; depends=[AnnotationDbi DOSE downloader dplyr enrichplot GO_db GOSemSim magrittr plyr qvalue rlang tidyr yulab_utils]; };
@ -1234,7 +1235,7 @@ in with self; {
  dir_expiry = derive2 { name="dir.expiry"; version="1.0.0"; sha256="05mk7iwzay1xrgvssbz7nyl5d1n03syalbk18lmjmbx05dy0cjik"; depends=[filelock]; };
  discordant = derive2 { name="discordant"; version="1.16.0"; sha256="17an31wai4nk5jxip9h8k4jv20wpd97c1jzcy8bcyfkz4w5yywwv"; depends=[Biobase biwt gtools MASS]; };
  distinct = derive2 { name="distinct"; version="1.4.1"; sha256="0yi3l990fk21ilrfkipdgzqvr9kl3a67xsad10f929gw0zpplxy7"; depends=[doParallel doRNG foreach ggplot2 limma Matrix Rcpp RcppArmadillo scater SingleCellExperiment SummarizedExperiment]; };
-  dittoSeq = derive2 { name="dittoSeq"; version="1.4.2"; sha256="1wyn7p7k1rasjxhi4sfgn0ddxhikp21svkglaxy41w30b3b1b9cb"; depends=[colorspace cowplot ggplot2 ggrepel ggridges gridExtra pheatmap reshape2 S4Vectors SingleCellExperiment SummarizedExperiment]; };
+  dittoSeq = derive2 { name="dittoSeq"; version="1.4.4"; sha256="05i1amfpy3vzvhxv3dn66rhcw09c8ip499pnj7swglvyxfmlfw8p"; depends=[colorspace cowplot ggplot2 ggrepel ggridges gridExtra pheatmap reshape2 S4Vectors SingleCellExperiment SummarizedExperiment]; };
  divergence = derive2 { name="divergence"; version="1.8.0"; sha256="1lg7bz9pqsnn8h69fh30xmsynp47dg407kifdfq0kq6rxj38gwrf"; depends=[SummarizedExperiment]; };
  dks = derive2 { name="dks"; version="1.38.0"; sha256="134jqcd9b0yg8in77g8wjvb8wqm5w4vfqh93hp05w95pjxks7d57"; depends=[cubature]; };
  dmrseq = derive2 { name="dmrseq"; version="1.12.0"; sha256="1jbbjifjsnk9261wqmdwkbzj1w52g6vaanpk4w816ri0fap587m4"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; };
@ -1255,14 +1256,14 @@ in with self; {
  eiR = derive2 { name="eiR"; version="1.32.0"; sha256="1gz78xw3cwbb03s02gr5lzghnvx19afxw3ylk0ijm4qhfqbw7m0c"; depends=[BiocGenerics ChemmineR DBI digest RcppAnnoy RCurl RUnit snow snowfall]; };
  eisaR = derive2 { name="eisaR"; version="1.4.0"; sha256="198x3h2r4hicad2dz892z8rknn3jwk4qskl3m7a6pqf5swqhsg5c"; depends=[BiocGenerics edgeR GenomicRanges IRanges limma S4Vectors SummarizedExperiment]; };
  enrichTF = derive2 { name="enrichTF"; version="1.8.0"; sha256="0kbrhd98pdx0xd6zninipmly2i4zax5vwldw0mmxp6ipbgwcv54y"; depends=[BiocGenerics BSgenome clusterProfiler GenomeInfoDb GenomicRanges ggplot2 ggpubr heatmap3 IRanges JASPAR2018 magrittr motifmatchr pipeFrame R_utils rmarkdown rtracklayer S4Vectors TFBSTools]; };
-  enrichplot = derive2 { name="enrichplot"; version="1.12.2"; sha256="194sfmcnjfi3fvvfpljg1f80f44vvvxiij336b8z1dgzki6bqa3r"; depends=[cowplot DOSE ggplot2 ggraph ggtree GOSemSim igraph magrittr plyr purrr RColorBrewer reshape2 scatterpie shadowtext]; };
+  enrichplot = derive2 { name="enrichplot"; version="1.12.3"; sha256="0a4v7ymy9jn66iw093jngzszkvr2mfzzlxp0h6nnvlbnbvqqzgm3"; depends=[cowplot DOSE ggplot2 ggraph ggtree GOSemSim igraph magrittr plyr purrr RColorBrewer reshape2 scatterpie shadowtext]; };
  ensemblVEP = derive2 { name="ensemblVEP"; version="1.34.0"; sha256="0zg5g7hvi965mbxxqkxli1pbk88yz9a3bfgmdjawh5blfznmyqw5"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; };
  ensembldb = derive2 { name="ensembldb"; version="2.16.4"; sha256="15yllkxr6sj5pfvkvv285nk3q5374nzq1iz8ywmnrq910k3xagd8"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; };
  epiNEM = derive2 { name="epiNEM"; version="1.16.0"; sha256="0dw998b5mgf20wzwgvq4xv6sw47jv96wa266ldg6z9m8s4cl0mr2"; depends=[BoolNet e1071 graph gtools igraph latex2exp lattice latticeExtra minet mnem pcalg RColorBrewer]; };
  epialleleR = derive2 { name="epialleleR"; version="1.0.0"; sha256="114ymmcxhpj4nqrgk3962mc6skb580hpchqsci6kq81h2lq0yl6v"; depends=[BH BiocGenerics data_table GenomeInfoDb GenomicRanges Rcpp Rsamtools stringi SummarizedExperiment VariantAnnotation]; };
  epidecodeR = derive2 { name="epidecodeR"; version="1.0.2"; sha256="08h6pdnyamxn6m1ps7abl2wkjj1m58gjm0718zpj6452yrrjaa6g"; depends=[dplyr EnvStats GenomicRanges ggplot2 ggpubr IRanges rstatix rtracklayer]; };
  epigenomix = derive2 { name="epigenomix"; version="1.32.0"; sha256="08hdlrz9i6xkb076nvv8gz0i6hjfklrlyln9d7fzhnfi5vpmyyn8"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; };
-  epigraHMM = derive2 { name="epigraHMM"; version="1.0.4"; sha256="1wmdcprgz11jfkw0ybygpv7rfhs0dsmmq42g72pyska0hl81mw6j"; depends=[bamsignals csaw data_table GenomeInfoDb GenomicRanges ggplot2 ggpubr GreyListChIP IRanges limma magrittr MASS Matrix pheatmap Rcpp RcppArmadillo rhdf5 Rhdf5lib Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; };
+  epigraHMM = derive2 { name="epigraHMM"; version="1.0.8"; sha256="1s2k123hczf32v22vq8qhm84mmryvsmbabgpylm1azgwz6fybc1h"; depends=[bamsignals csaw data_table GenomeInfoDb GenomicRanges ggplot2 ggpubr GreyListChIP IRanges limma magrittr MASS Matrix pheatmap Rcpp RcppArmadillo rhdf5 Rhdf5lib Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; };
  epihet = derive2 { name="epihet"; version="1.8.0"; sha256="02xnmxwhm0l2m8mxnfgv1d8mlmyy1pjlspglq88pnbyr0kr0zcyy"; depends=[data_table doParallel EntropyExplorer foreach GenomicRanges ggplot2 igraph IRanges pheatmap qvalue ReactomePA Rtsne S4Vectors WGCNA]; };
  epivizr = derive2 { name="epivizr"; version="2.22.0"; sha256="08qk680pn89whc5vbnrq6ras51sygccnqnlixvyijxid0gbzfp8h"; depends=[bumphunter epivizrData epivizrServer GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
  epivizrChart = derive2 { name="epivizrChart"; version="1.14.0"; sha256="19gighqj05cbn7jj9mfqxi578al4ig2562gcsfh1l7cskvkvv85s"; depends=[BiocGenerics epivizrData epivizrServer htmltools rjson]; };
@ -1282,7 +1283,7 @@ in with self; {
  fCI = derive2 { name="fCI"; version="1.22.0"; sha256="0hp6r8ihwrwgp26sbx8awvrwilsqipjsgi6331gjzl6nypd3zcjx"; depends=[FNN gtools psych rgl VennDiagram zoo]; };
  fabia = derive2 { name="fabia"; version="2.38.0"; sha256="1v68835z39hsd34vaa07n2kwhrps6mdppxhhbz637lab2pr4h13r"; depends=[Biobase]; };
  factDesign = derive2 { name="factDesign"; version="1.68.0"; sha256="0qavr5kmg8jlr6gqr31hf371zyzs3fpxvbz5bmla2mwx1c66ih2r"; depends=[Biobase]; };
-  famat = derive2 { name="famat"; version="1.1.1"; sha256="1sby916vs12vwvnjf6ap0cgb5fmmkzg8j3ldiibfgrm17x8x4gmm"; depends=[clusterProfiler dplyr DT GO_db gprofiler2 KEGGREST magrittr MPINet ontologyIndex org_Hs_eg_db plotly reactome_db rWikiPathways shiny shinyBS shinydashboard stringr tidyr]; };
+  famat = derive2 { name="famat"; version="1.2.1"; sha256="15mvmabimr6ch5m8z2xr4hgxwxmzlha4vmm81635nl764wcya13l"; depends=[clusterProfiler dplyr DT GO_db gprofiler2 KEGGREST magrittr MPINet ontologyIndex org_Hs_eg_db plotly reactome_db rWikiPathways shiny shinyBS shinydashboard stringr tidyr]; };
  farms = derive2 { name="farms"; version="1.44.0"; sha256="1zrkdg64kljyi8kvdicimlzmanjyn365lfncyndv4zlqj1majpf9"; depends=[affy Biobase MASS]; };
  fastLiquidAssociation = derive2 { name="fastLiquidAssociation"; version="1.28.0"; sha256="0hznf9408ppqqp5ykwjn36dcvn2wjd4101fqab49zba7hwycf6vs"; depends=[doParallel Hmisc impute LiquidAssociation preprocessCore WGCNA]; };
  fastseg = derive2 { name="fastseg"; version="1.38.0"; sha256="006v7qs707xmnr35b7rw135pyvacrmhv55a3c53birkpsrjgkps0"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors]; };
@ -1350,7 +1351,7 @@ in with self; {
  geneRecommender = derive2 { name="geneRecommender"; version="1.64.0"; sha256="0rbnb09l3nyci962hl5i8m4fsiy97nngyg3ficlk4pihsx0bwwz8"; depends=[Biobase]; };
  geneRxCluster = derive2 { name="geneRxCluster"; version="1.28.0"; sha256="0vqwbp8b74a33dhbdkisn8nhvprxsi9pqgw92f0s7j367313qljz"; depends=[GenomicRanges IRanges]; };
  geneXtendeR = derive2 { name="geneXtendeR"; version="1.18.0"; sha256="1gqpcibv9mscxna1h8kkl7shw4gvs2z0jrrg18hrjx918pq6wifb"; depends=[AnnotationDbi BiocStyle data_table dplyr GO_db networkD3 org_Rn_eg_db RColorBrewer rtracklayer SnowballC tm wordcloud]; };
-  genefilter = derive2 { name="genefilter"; version="1.74.0"; sha256="0dy9pmlb0pc9b4ks5fb9zgnmhc9f2mkqmsdlb7f5z88xmj68y4qk"; depends=[annotate AnnotationDbi Biobase BiocGenerics survival]; };
+  genefilter = derive2 { name="genefilter"; version="1.74.1"; sha256="0lsh6akhqm1fadxr7066rcx5y7rnd020icx2cq0bfpymz6ajzsvx"; depends=[annotate AnnotationDbi Biobase BiocGenerics survival]; };
  genefu = derive2 { name="genefu"; version="2.24.2"; sha256="06nak5izjacr9708d134m6y7fnnhy7pylgjl843zdz9cqw5qnjch"; depends=[AIMS amap biomaRt iC10 impute limma mclust survcomp]; };
  geneplast = derive2 { name="geneplast"; version="1.18.0"; sha256="1lfwj7xhkk8gi1arr5mf38s44gb6j450ai5ir83y5m7mw6s0vphb"; depends=[ape data_table igraph snow]; };
  geneplotter = derive2 { name="geneplotter"; version="1.70.0"; sha256="1d085lfa3yif5wkys1fb0zzgg0cqwd1y18vasgqqdr6rva075d4z"; depends=[annotate AnnotationDbi Biobase BiocGenerics lattice RColorBrewer]; };
@ -1426,7 +1427,7 @@ in with self; {
  iasva = derive2 { name="iasva"; version="1.10.0"; sha256="1i2jnyaayqwdz5sfa9lbbw7vjwk55cp30caiy4x09b0dsb5pxxdn"; depends=[BiocParallel cluster irlba SummarizedExperiment]; };
  ibh = derive2 { name="ibh"; version="1.40.0"; sha256="13gbgi1wymx36khnvhrr47q7laxhg6kxmcc8vmlfsv804ckcy4mx"; depends=[simpIntLists]; };
  icetea = derive2 { name="icetea"; version="1.10.0"; sha256="1yrbgwrwilgm15v0aqw160xid52qb7ggd0k0qc44bjgrn0xs7iqf"; depends=[BiocGenerics BiocParallel Biostrings csaw DESeq2 edgeR GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges limma Rsamtools rtracklayer S4Vectors ShortRead SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm6_ensGene VariantAnnotation]; };
-  ideal = derive2 { name="ideal"; version="1.16.0"; sha256="1m636ippzyb8ccbbcazp1sifsld4glwavzx3ljl632p1438l1w8m"; depends=[AnnotationDbi base64enc BiocParallel DESeq2 dplyr DT GenomicRanges ggplot2 ggrepel GO_db goseq GOstats gplots heatmaply IHW IRanges knitr limma pcaExplorer pheatmap plotly rentrez rintrojs rmarkdown S4Vectors shiny shinyAce shinyBS shinydashboard stringr SummarizedExperiment topGO UpSetR]; };
+  ideal = derive2 { name="ideal"; version="1.16.1"; sha256="0kag3l6bh0507c01ca7avgh7a55580fr189wgwfippiqhb2n8hj1"; depends=[AnnotationDbi base64enc BiocParallel DESeq2 dplyr DT GenomicRanges ggplot2 ggrepel GO_db goseq GOstats gplots heatmaply IHW IRanges knitr limma pcaExplorer pheatmap plotly rentrez rintrojs rmarkdown S4Vectors shiny shinyAce shinyBS shinydashboard stringr SummarizedExperiment topGO UpSetR]; };
  idiogram = derive2 { name="idiogram"; version="1.68.0"; sha256="08py2vllkqsarzgbk3r0jnd2dw18f71d1gb9qbbjrkac4i1f6rpk"; depends=[annotate Biobase plotrix]; };
  idpr = derive2 { name="idpr"; version="1.2.0"; sha256="17xvmwc0kpc74az89zp17qrd24ghnd11a76hb037pfyda285l067"; depends=[Biostrings dplyr ggplot2 jsonlite magrittr plyr rlang]; };
  idr2d = derive2 { name="idr2d"; version="1.6.0"; sha256="1yp0s9qbwdh34m6xxly4nf5j1f7n8cpxwqibwwb18wlklq8i4g22"; depends=[dplyr futile_logger GenomeInfoDb GenomicRanges ggplot2 idr IRanges magrittr reticulate scales stringr]; };
@ -1526,7 +1527,7 @@ in with self; {
  methylMnM = derive2 { name="methylMnM"; version="1.30.0"; sha256="1av81b9s7dz7aa9g6pa13l5lyxn8frgb6shfq2if1sqsksfpmwmz"; depends=[edgeR statmod]; };
  methylPipe = derive2 { name="methylPipe"; version="1.26.0"; sha256="1q1bybxqal9ny04s71fwwyj29536glpcss5x7zbmj20kd1ll35dm"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicRanges gplots Gviz IRanges marray Rsamtools S4Vectors SummarizedExperiment]; };
  methylSig = derive2 { name="methylSig"; version="1.4.0"; sha256="1phkc09vxyydn0qqy0r5j31lxcym0rznjwdqd8sh1diy0w7g23bf"; depends=[bsseq DelayedArray DelayedMatrixStats DSS GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
-  methylscaper = derive2 { name="methylscaper"; version="1.0.0"; sha256="1a3hgfg4sybkn6ga9widfvrr8qw9r27k3r06g52rafbkvhanydkx"; depends=[BiocParallel Biostrings data_table Rfast seqinr seriation shiny shinyFiles shinyjs SummarizedExperiment]; };
+  methylscaper = derive2 { name="methylscaper"; version="1.0.1"; sha256="0ryasmnr3d75hl7iwwgkzf5an24jwds501y6zpx6nqdq3fs0k2a7"; depends=[BiocParallel Biostrings data_table Rfast seqinr seriation shiny shinyFiles shinyjs SummarizedExperiment]; };
  methylumi = derive2 { name="methylumi"; version="2.38.0"; sha256="1941rc524ssx8gwhmwk40mgfrhddfs6hgldvs7bi22r29gm4y7qj"; depends=[annotate AnnotationDbi Biobase BiocGenerics FDb_InfiniumMethylation_hg19 genefilter GenomeInfoDb GenomicRanges ggplot2 illuminaio IRanges lattice matrixStats minfi reshape2 S4Vectors scales SummarizedExperiment]; };
  mfa = derive2 { name="mfa"; version="1.14.0"; sha256="18z88rhps3a7fa5za5y76dxnk95sawgyi33wcsq4zpx000gc9a01"; depends=[Biobase coda dplyr ggmcmc ggplot2 magrittr MCMCglmm MCMCpack Rcpp tibble]; };
  mgsa = derive2 { name="mgsa"; version="1.40.0"; sha256="15qs1fkakkk904243ym03zin54y49d3x0hc1skj82ly5dydp30k2"; depends=[gplots]; };
@ -1564,7 +1565,7 @@ in with self; {
  mogsa = derive2 { name="mogsa"; version="1.26.0"; sha256="197s2kc1dd2y33w32w4pvhwav37mmgn6rvin4r2l0xy98mvjzkj5"; depends=[Biobase BiocGenerics cluster corpcor genefilter gplots graphite GSEABase svd]; };
  monocle = derive2 { name="monocle"; version="2.20.0"; sha256="05j1vc51f39xalggdq27y7218gkr3zq7fh7jhzsb4jj7fpn837ry"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree densityClust dplyr fastICA ggplot2 HSMMSingleCell igraph irlba limma MASS Matrix matrixStats pheatmap plyr proxy qlcMatrix RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; };
  mosaics = derive2 { name="mosaics"; version="2.30.0"; sha256="14jdgiy8wi5psglsq0z6svkn7r3dn5sil5prs2w32csl3w14g7c5"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges lattice MASS Rcpp Rsamtools S4Vectors]; };
-  motifStack = derive2 { name="motifStack"; version="1.36.0"; sha256="0yn348kmw7v46iym913ncx4yh5nxzmba8bdys52s12ldgjja53gp"; depends=[ade4 Biostrings ggplot2 htmlwidgets XML]; };
+  motifStack = derive2 { name="motifStack"; version="1.36.1"; sha256="140xclzgn5z64v5nm4kvj0qwvqb7ix91bbmimsfc6k1p0l8lwsvv"; depends=[ade4 Biostrings ggplot2 htmlwidgets XML]; };
  motifbreakR = derive2 { name="motifbreakR"; version="2.6.1"; sha256="1n6v8a7c27aswmbrlcwcpghf27aplkc6nn923imglc3c0sh2lkrz"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges grImport Gviz IRanges matrixStats MotifDb motifStack rtracklayer S4Vectors stringr SummarizedExperiment TFMPvalue VariantAnnotation]; };
  motifcounter = derive2 { name="motifcounter"; version="1.16.0"; sha256="1w2d68iaibz1gh0f1mlqb4grwv1i89v0vn11050w5pbqv2jbz9vr"; depends=[Biostrings]; };
  motifmatchr = derive2 { name="motifmatchr"; version="1.14.0"; sha256="1vif3dp4lv4jz1pxsq0ig791ir8q65jmrlqmkyfxpfxfj5alqnbm"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment TFBSTools]; };
@ -1709,9 +1710,9 @@ in with self; {
  progeny = derive2 { name="progeny"; version="1.14.0"; sha256="10vpjvl4wps857xiy8rpzr82jzdfbc5rgwh3ir3my26lfws4hfz8"; depends=[Biobase dplyr ggplot2 ggrepel gridExtra tidyr]; };
  projectR = derive2 { name="projectR"; version="1.8.0"; sha256="0c7vi6x8jdwpl6pcih1r9kdwrjjjf7swyx124c2w2fq2f115qp07"; depends=[cluster CoGAPS dplyr ggalluvial ggplot2 limma NMF RColorBrewer reshape2 ROCR scales viridis]; };
  proteinProfiles = derive2 { name="proteinProfiles"; version="1.32.0"; sha256="1rkl5v7marwxs7069hhsvp69inlpvbklpgzn58yfsk47d7ljrhhr"; depends=[]; };
-  psichomics = derive2 { name="psichomics"; version="1.18.5"; sha256="1a7mmjy7p05xcjdnq6xvs334xmjcfxjhha5xjvnabkpnsy55qv03"; depends=[AnnotationDbi AnnotationHub BiocFileCache cluster colourpicker data_table digest dplyr DT edgeR fastICA fastmatch ggplot2 ggrepel highcharter htmltools httr jsonlite limma pairsD3 plyr R_utils Rcpp recount reshape2 Rfast shiny shinyBS shinyjs stringr SummarizedExperiment survival XML xtable]; };
+  psichomics = derive2 { name="psichomics"; version="1.18.6"; sha256="0pny5y04xqk9gn1mwaly6ml1i69jmz7d9yl0vzflflhnvbr4lm11"; depends=[AnnotationDbi AnnotationHub BiocFileCache cluster colourpicker data_table digest dplyr DT edgeR fastICA fastmatch ggplot2 ggrepel highcharter htmltools httr jsonlite limma pairsD3 plyr purrr R_utils Rcpp recount reshape2 Rfast shiny shinyBS shinyjs stringr SummarizedExperiment survival XML xtable]; };
  psygenet2r = derive2 { name="psygenet2r"; version="1.24.0"; sha256="185z387cdipac0sljgfx3xc39sv4p7f26amaw5lfnf822ibmhf5d"; depends=[BgeeDB Biobase biomaRt ggplot2 GO_db igraph labeling RCurl reshape2 stringr topGO]; };
-  ptairMS = derive2 { name="ptairMS"; version="1.0.0"; sha256="1kpa6j6qwikjgfjkvkg8klq8yqwkqwkb9l7mribp1ijvpwak0w39"; depends=[Biobase bit64 chron data_table doParallel DT enviPat foreach ggplot2 ggpubr gridExtra Hmisc minpack_lm MSnbase plotly Rcpp rhdf5 rlang scales shiny signal]; };
+  ptairMS = derive2 { name="ptairMS"; version="1.0.1"; sha256="1ss1dwbdls977l2hjjvfl4cjyd9f822wh0bjyg4dhq33mypr7sfj"; depends=[Biobase bit64 chron data_table doParallel DT enviPat foreach ggplot2 ggpubr gridExtra Hmisc minpack_lm MSnbase plotly Rcpp rhdf5 rlang scales shiny shinyscreenshot signal]; };
  pulsedSilac = derive2 { name="pulsedSilac"; version="1.6.0"; sha256="1vvcrd38v1x602z72hxvbb66xg1r6p2a1izmkivdifkzy0i5m1vl"; depends=[cowplot ggplot2 ggridges MuMIn R_utils robustbase S4Vectors SummarizedExperiment taRifx UpSetR]; };
  puma = derive2 { name="puma"; version="3.34.0"; sha256="0bqc37bj2hmwjiri5x2x0pahhvz1zaqaphandv6v3zjrabgv60dm"; depends=[affy affyio Biobase mclust oligo oligoClasses]; };
  pvac = derive2 { name="pvac"; version="1.40.0"; sha256="1qdi6m2xdk751xkdxbm9wk16x5r2j8diggr7h4x953wwgc9wfi3m"; depends=[affy Biobase]; };
@ -1756,9 +1757,9 @@ in with self; {
  receptLoss = derive2 { name="receptLoss"; version="1.4.0"; sha256="17fpvpz73f6h650sbfvnvvcmabxxzjg134msfidff35n63j7jkkn"; depends=[dplyr ggplot2 magrittr SummarizedExperiment tidyr]; };
  reconsi = derive2 { name="reconsi"; version="1.4.0"; sha256="0bpfxhbgrxf84qxzz7w4spxm91m34n8ghigf1l78hdsin98x8zy0"; depends=[ggplot2 KernSmooth matrixStats phyloseq reshape2]; };
  recount = derive2 { name="recount"; version="1.18.1"; sha256="0lkanj072r7vz95cp90chrb3kfgkkvsd8bvvizvw4rasfljbb01d"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; };
-  recount3 = derive2 { name="recount3"; version="1.2.5"; sha256="12wzryyw46hbd0yimrdnh72j01rih444wdczc2482h3k3c78hkjc"; depends=[BiocFileCache data_table GenomicRanges Matrix R_utils RCurl rtracklayer S4Vectors sessioninfo SummarizedExperiment]; };
-  recountmethylation = derive2 { name="recountmethylation"; version="1.2.0"; sha256="1hljsx0q1c64ghdagfz217klkd43vn6wxx9cfm7aydxgj1qz98h5"; depends=[BiocFileCache HDF5Array minfi R_utils RCurl rhdf5 S4Vectors]; };
-  recoup = derive2 { name="recoup"; version="1.20.0"; sha256="1h2s7h5nhkcjxy4j9w95ydp3iaiqb0bp08fkxx5v5nf7fjvjnyxl"; depends=[BiocGenerics biomaRt Biostrings circlize ComplexHeatmap GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 httr IRanges Rsamtools RSQLite rtracklayer S4Vectors stringr]; };
+  recount3 = derive2 { name="recount3"; version="1.2.6"; sha256="0j0syvl3yzd8q8yba9s3r109m255qrs7zy6abhypmq1ds842gvpr"; depends=[BiocFileCache data_table GenomicRanges Matrix R_utils RCurl rtracklayer S4Vectors sessioninfo SummarizedExperiment]; };
+  recountmethylation = derive2 { name="recountmethylation"; version="1.2.3"; sha256="0k5hnc0ywppdyr8y8y90p5iidrm3mwsc2c1ihjb4v3cgf3w9nby3"; depends=[BiocFileCache HDF5Array minfi R_utils RCurl rhdf5 S4Vectors]; };
+  recoup = derive2 { name="recoup"; version="1.20.1"; sha256="1sspqlqlm4ifxr74yp3621qhnyh3x989nzvxgah142lf0p3ch77m"; depends=[BiocGenerics biomaRt Biostrings circlize ComplexHeatmap GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 httr IRanges Rsamtools RSQLite rtracklayer S4Vectors stringr]; };
  regionReport = derive2 { name="regionReport"; version="1.26.0"; sha256="044hwavvi4mp6j6sxjsdm88dbzxjg4p18qw4y0bp2zsj9swf8ffc"; depends=[BiocStyle DEFormats derfinder DESeq2 GenomeInfoDb GenomicRanges knitr knitrBootstrap RefManageR rmarkdown S4Vectors SummarizedExperiment]; };
  regioneR = derive2 { name="regioneR"; version="1.24.0"; sha256="0xzzaz3cl6pyxfsg0d931v8k15wbd05s5mnsb7igxldc5qqg3nsl"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; };
  regsplice = derive2 { name="regsplice"; version="1.18.0"; sha256="0vnq82xhj9401j17zb0p40ls6aqwng7ganllkblkh744bqlqrbd6"; depends=[edgeR glmnet limma pbapply S4Vectors SummarizedExperiment]; };
@ -1836,7 +1837,7 @@ in with self; {
  selectKSigs = derive2 { name="selectKSigs"; version="1.4.0"; sha256="04g0hrcc0kqlkj3f31yd9fxq216r5jknvbfn1x2153s0v11i7ys9"; depends=[gtools HiLDA magrittr Rcpp]; };
  semisup = derive2 { name="semisup"; version="1.16.0"; sha256="19cvnbshk6qyxb001m2nrzlnc5v1n3lcpr79bka0lavmsi1wqa62"; depends=[VGAM]; };
  seq2pathway = derive2 { name="seq2pathway"; version="1.24.0"; sha256="1wa1aqczdjw03q77j923xwk32ljlqawnwl6z1vddmz731fk1ddpz"; depends=[biomaRt GenomicRanges GSA nnet seq2pathway_data WGCNA]; };
-  seqCAT = derive2 { name="seqCAT"; version="1.14.0"; sha256="18ammsypfxqdrdz0h9i1s9hkdn0m42v4vszaqp4jvnhzw306mnv3"; depends=[dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges rlang rtracklayer S4Vectors scales SummarizedExperiment tidyr VariantAnnotation]; };
+  seqCAT = derive2 { name="seqCAT"; version="1.14.1"; sha256="0jqam3msr64w1frmh5wgiqx1msnl1f3cj2ycs5ks1mszga89w3d3"; depends=[dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges rlang rtracklayer S4Vectors scales SummarizedExperiment tidyr VariantAnnotation]; };
  seqCNA = derive2 { name="seqCNA"; version="1.38.0"; sha256="07n21a6ini41yalhab049xi7ibx7nbp7pjyvpngqjjjnfy8z6l2k"; depends=[adehabitatLT doSNOW GLAD seqCNA_annot]; };
  seqLogo = derive2 { name="seqLogo"; version="1.58.0"; sha256="1253sj1hc6bbrff0iv5xa3v9znqvisll0fy6fdjka9c778fn4mcp"; depends=[]; };
  seqPattern = derive2 { name="seqPattern"; version="1.24.0"; sha256="0h74z84zyvfzclsm0g13b95hirn99185wc6lp53jkzah9yyi59ay"; depends=[Biostrings GenomicRanges IRanges KernSmooth plotrix]; };
@ -1844,7 +1845,7 @@ in with self; {
  seqbias = derive2 { name="seqbias"; version="1.40.0"; sha256="06w43plv4x1pafybq633n7adqp9yj3bvaaamq7vylmkfbcx3nl8k"; depends=[Biostrings GenomicRanges Rhtslib]; };
  seqcombo = derive2 { name="seqcombo"; version="1.14.1"; sha256="1cbp56nh5gz92napg82vh8gs3vlrj92xqggf5j6v30hw1hd7q7lp"; depends=[Biostrings cowplot dplyr ggplot2 igraph magrittr yulab_utils]; };
  seqsetvis = derive2 { name="seqsetvis"; version="1.12.0"; sha256="1gviian0xykia1xh42w5r202nlm03hpkfgnc4yabalmv4zmwndh8"; depends=[data_table eulerr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 ggplotify IRanges limma pbapply pbmcapply png RColorBrewer Rsamtools rtracklayer S4Vectors UpSetR]; };
-  sesame = derive2 { name="sesame"; version="1.10.4"; sha256="0cw6mlw1ckpc2xrwmdwvcirysk58klb5x6x9lwh93qsa2ij8m0bk"; depends=[BiocParallel DNAcopy GenomicRanges ggplot2 illuminaio IRanges KernSmooth MASS matrixStats preprocessCore randomForest S4Vectors sesameData stringr SummarizedExperiment tibble wheatmap]; };
+  sesame = derive2 { name="sesame"; version="1.10.5"; sha256="1y20lc9g31j9cqd11v2dd8lwx0476cgiwfzdka7y6qwlkqi9jwdw"; depends=[BiocParallel DNAcopy GenomicRanges ggplot2 illuminaio IRanges KernSmooth MASS matrixStats preprocessCore randomForest S4Vectors sesameData stringr SummarizedExperiment tibble wheatmap]; };
  sevenC = derive2 { name="sevenC"; version="1.12.0"; sha256="0gwvjf1zmkr6j9id1wm5f2abnrm9anby8xbcr17fbkchzas0kw03"; depends=[BiocGenerics boot data_table GenomeInfoDb GenomicRanges InteractionSet IRanges purrr readr rtracklayer S4Vectors]; };
  sevenbridges = derive2 { name="sevenbridges"; version="1.22.0"; sha256="1pa1hhfvnsdkgyv6qh7bg3fzbvcmccr7km877vgqhlpgfir10ig2"; depends=[curl data_table docopt httr jsonlite objectProperties S4Vectors stringr uuid yaml]; };
  shinyMethyl = derive2 { name="shinyMethyl"; version="1.28.0"; sha256="0b5i9anjz02k98zam29hixhrxbak0ghfbv00jj4041cbs42dkaja"; depends=[BiocGenerics IlluminaHumanMethylation450kmanifest matrixStats minfi RColorBrewer shiny]; };
@ -1854,14 +1855,14 @@ in with self; {
  siggenes = derive2 { name="siggenes"; version="1.66.0"; sha256="0lva0f255fcpy625frvij4n14q7nw4jcx8n2hlkxid4mgkfqwlhf"; depends=[Biobase multtest scrime]; };
  sights = derive2 { name="sights"; version="1.18.0"; sha256="0dzmikqfxypbhq5zax4yfr2m0bal79raq7ggrg8m2crqda6020i6"; depends=[ggplot2 lattice MASS qvalue reshape2]; };
  signatureSearch = derive2 { name="signatureSearch"; version="1.6.3"; sha256="1c63a9l5rlvjn6v7cxk136kvng4rbmvlg5jdzz0zsi48vipwhm4f"; depends=[AnnotationDbi BiocGenerics BiocParallel clusterProfiler data_table DelayedArray DOSE dplyr ExperimentHub fastmatch fgsea ggplot2 GSEABase HDF5Array magrittr Matrix qvalue Rcpp reactome_db readr reshape2 rhdf5 RSQLite scales SummarizedExperiment visNetwork]; };
-  signeR = derive2 { name="signeR"; version="1.18.0"; sha256="0bn9h6q90ihlm9027shl74lwzc9niw1yb7fmcxxs42nv65sqv4hs"; depends=[BiocGenerics Biostrings class GenomeInfoDb GenomicRanges IRanges nloptr NMF PMCMR Rcpp RcppArmadillo VariantAnnotation]; };
+  signeR = derive2 { name="signeR"; version="1.18.1"; sha256="18arsfdnmjqv9g70j2d1kw2k2dlk55sy7r0jq9hwf545q7sn5fwi"; depends=[BiocGenerics Biostrings class GenomeInfoDb GenomicRanges IRanges nloptr NMF PMCMRplus Rcpp RcppArmadillo VariantAnnotation]; };
  sigsquared = derive2 { name="sigsquared"; version="1.24.0"; sha256="0awb5k9k459jnmb3rr08407w95r65ip50kgqffpdn9qqrjdimgva"; depends=[Biobase survival]; };
  similaRpeak = derive2 { name="similaRpeak"; version="1.24.0"; sha256="1hhzzidva3z9z1mj5j75mhgns8j7nhn0gnhjdpwmz25c0hc5n5l1"; depends=[R6]; };
  simplifyEnrichment = derive2 { name="simplifyEnrichment"; version="1.2.0"; sha256="0rqa414kvyjjmj4932zk39rqa14z13b57rkrxdrf16jmq2r437vh"; depends=[AnnotationDbi BiocGenerics circlize clue cluster ComplexHeatmap digest GetoptLong GO_db GOSemSim Matrix org_Hs_eg_db proxyC slam tm]; };
  sincell = derive2 { name="sincell"; version="1.24.0"; sha256="140xcarald9pdfp45y84317wzx2cicq4sh3zyn3i563chhi2xqir"; depends=[cluster entropy fastICA fields ggplot2 igraph MASS proxy Rcpp reshape2 Rtsne scatterplot3d statmod TSP]; };
  singleCellTK = derive2 { name="singleCellTK"; version="2.2.0"; sha256="1qdf57mj0hx30zzci0hhvahhqcx2mbq3g7q4vc4mggsxxm0j0r4l"; depends=[AnnotationDbi ape batchelor Biobase BiocParallel celda celldex circlize cluster colorspace colourpicker ComplexHeatmap cowplot data_table DelayedArray DelayedMatrixStats DESeq2 dplyr DropletUtils DT enrichR ExperimentHub fields fishpond ggplot2 ggplotify ggrepel ggtree gridExtra GSEABase GSVA GSVAdata igraph KernSmooth limma magrittr MAST Matrix matrixStats metap msigdbr multtest plotly R_utils RColorBrewer reshape2 reticulate rmarkdown ROCR Rtsne S4Vectors scater scDblFinder scds scMerge scran scRNAseq Seurat shiny shinyalert shinycssloaders shinyjs SingleCellExperiment SingleR SummarizedExperiment sva TENxPBMCData tximport uwot withr yaml zinbwave]; };
  singscore = derive2 { name="singscore"; version="1.12.0"; sha256="16d452s6527xwxsfbfqxjnyn8ifx4lfqfrfkv516w1rs28qnpri3"; depends=[Biobase BiocParallel edgeR ggplot2 ggrepel GSEABase magrittr matrixStats plotly plyr RColorBrewer reshape reshape2 S4Vectors SummarizedExperiment tidyr]; };
-  sitadela = derive2 { name="sitadela"; version="1.0.0"; sha256="1hwvy7n0m930llh4j44yk1cp7pkwyx8999w5zdsxvwal7h44mggi"; depends=[Biobase BiocGenerics biomaRt Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rsamtools RSQLite rtracklayer S4Vectors]; };
+  sitadela = derive2 { name="sitadela"; version="1.0.1"; sha256="0zslaw3yvavypc7lkwcz6nxcwhgp86f9gcjjv0hn43zhxwzbyal7"; depends=[Biobase BiocGenerics biomaRt Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rsamtools RSQLite rtracklayer S4Vectors]; };
  sitePath = derive2 { name="sitePath"; version="1.8.4"; sha256="10syb7nrl83psy1lz06jpy96j1h4mgc8hrrhhikqcb4zqd7x14js"; depends=[ape aplot ggplot2 ggrepel ggtree gridExtra RColorBrewer Rcpp seqinr tidytree]; };
  sizepower = derive2 { name="sizepower"; version="1.62.0"; sha256="1025yfziv9znd278xz7cq8c17nhf5kwrf82nxx2s9pf0zhnh18sp"; depends=[]; };
  skewr = derive2 { name="skewr"; version="1.24.0"; sha256="194bhbv2y90wzqdb4axqq4qg6cihjbz3nvnkfpb82mbh8cai1l0f"; depends=[IlluminaHumanMethylation450kmanifest methylumi minfi mixsmsn RColorBrewer S4Vectors wateRmelon]; };
@ -1910,7 +1911,7 @@ in with self; {
  swfdr = derive2 { name="swfdr"; version="1.18.0"; sha256="0mqc28s0kw87d93m8z9xkh81s8j6y18ggkdgx48iil5adw8rfs00"; depends=[]; };
  switchBox = derive2 { name="switchBox"; version="1.28.0"; sha256="10zriwb306rd9lnw8vxqgwx4cj40j8dv9z4dx7ba3b78rrhj67kz"; depends=[gplots pROC]; };
  switchde = derive2 { name="switchde"; version="1.18.0"; sha256="1rq2ccw1byz87g6425h1wfmzn4crl0jfn56d4ns7gxsw32jj4258"; depends=[dplyr ggplot2 SingleCellExperiment SummarizedExperiment]; };
-  synergyfinder = derive2 { name="synergyfinder"; version="3.0.13"; sha256="1md6ah2yv79n1h7jd21nfjrs41gan3n430sw64qwranngrqd6sy5"; depends=[dplyr drc furrr future ggforce ggplot2 ggrepel gstat kriging lattice magrittr metR mice nleqslv pbapply plotly purrr reshape2 sp SpatialExtremes stringr tidyr tidyverse vegan]; };
+  synergyfinder = derive2 { name="synergyfinder"; version="3.0.14"; sha256="01n26iqrn4ngx8xkzml5ahzgg3c4s9q05c6gi4lm40x30d57gk1i"; depends=[dplyr drc furrr future ggforce ggplot2 ggrepel gstat kriging lattice magrittr metR mice nleqslv pbapply plotly purrr reshape2 sp SpatialExtremes stringr tidyr tidyverse vegan]; };
  synlet = derive2 { name="synlet"; version="1.22.0"; sha256="197j5dw8ginr7rhiv8fwcixm5bf9gbbjnzqkvgjm3wd8803fhx5k"; depends=[doBy dplyr ggplot2 magrittr RankProd RColorBrewer reshape2]; };
  systemPipeR = derive2 { name="systemPipeR"; version="1.26.3"; sha256="01l35l5zj87qkarrbal9la6kshk3j7k8hy3iimv3gdnnz4axmvs7"; depends=[annotate assertthat batchtools Biostrings crayon DESeq2 DOT edgeR GenomicFeatures GenomicRanges ggplot2 GO_db GOstats IRanges limma magrittr pheatmap rjson Rsamtools rsvg S4Vectors ShortRead stringr SummarizedExperiment testthat VariantAnnotation yaml]; };
  systemPipeShiny = derive2 { name="systemPipeShiny"; version="1.2.0"; sha256="1s4ammnfs70x6apz1r83qaj9p9f5ppiv1z3n76jc71bd7gab1lym"; depends=[assertthat bsplus crayon dplyr drawer DT ggplot2 glue htmltools magrittr openssl plotly R6 rlang RSQLite rstudioapi shiny shinyAce shinydashboard shinydashboardPlus shinyFiles shinyjqui shinyjs shinytoastr shinyWidgets spsComps spsUtil stringr styler tibble vroom yaml]; };
@ -1943,7 +1944,7 @@ in with self; {
  transcriptR = derive2 { name="transcriptR"; version="1.20.0"; sha256="0xl88fk8i4pnbd7hw4v48awdgr5il1fgml0x7dqb00rgcmjbk5yr"; depends=[BiocGenerics caret chipseq e1071 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges pROC reshape2 Rsamtools rtracklayer S4Vectors]; };
  transcriptogramer = derive2 { name="transcriptogramer"; version="1.14.0"; sha256="18sks1p27qs7vfvs37vdaidj6r7pbwg5479lyv1pycvwgrz1sxwv"; depends=[biomaRt data_table doSNOW foreach ggplot2 igraph limma progress RedeR snow tidyr topGO]; };
  transite = derive2 { name="transite"; version="1.10.0"; sha256="1x8qf28m2hqx0b968wdffy1gm1kffvv08hzm2yy2z7z0kxfj8mm0"; depends=[BiocGenerics Biostrings dplyr GenomicRanges ggplot2 ggseqlogo gridExtra Rcpp scales TFMPvalue]; };
-  transomics2cytoscape = derive2 { name="transomics2cytoscape"; version="1.2.1"; sha256="1v88a5pfgnkda396f92svrky8ikawg1cq53447k4hc0g3p5cg5px"; depends=[dplyr KEGGREST RCy3]; };
+  transomics2cytoscape = derive2 { name="transomics2cytoscape"; version="1.2.2"; sha256="19rpc3s0b1fmslr6jzfij61wipg49820hy63079ns7j0ldxj8zvp"; depends=[dplyr KEGGREST RCy3]; };
  traseR = derive2 { name="traseR"; version="1.22.0"; sha256="197gy5a8zb1mxjhjvpxlpgna9qq1cwlqhd0pjq69vbzjhvhrr643"; depends=[BSgenome_Hsapiens_UCSC_hg19 GenomicRanges IRanges]; };
  treeio = derive2 { name="treeio"; version="1.16.2"; sha256="1y60yvg1rl21cab9xrkns0209pg44mwr90qj099dvk97wsjkx67g"; depends=[ape dplyr jsonlite magrittr rlang tibble tidytree]; };
  treekoR = derive2 { name="treekoR"; version="1.0.0"; sha256="09b7mjf6zaq1gnm9yvd5178v1i137cxlp3bzqgzsll0ipgxrf1av"; depends=[ape data_table dplyr ggiraph ggplot2 ggtree hopach magrittr patchwork SingleCellExperiment tidyr]; };
--- a/pkgs/development/r-modules/cran-packages.nix
+++ b/pkgs/development/r-modules/cran-packages.nix
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@ -278,7 +278,7 @@ let
    audio = [ pkgs.portaudio ];
    BayesSAE = [ pkgs.gsl ];
    BayesVarSel = [ pkgs.gsl ];
-    BayesXsrc = with pkgs; [ readline.dev ncurses ];
+    BayesXsrc = with pkgs; [ readline.dev ncurses gsl ];
    bigGP = [ pkgs.mpi ];
    bio3d = [ pkgs.zlib ];
    BiocCheck = [ pkgs.which ];
@ -422,6 +422,33 @@ let
    VariantAnnotation = with pkgs; [ zlib.dev curl.dev ];
    snpStats = [ pkgs.zlib.dev ];
    hdf5r = [ pkgs.hdf5.dev ];
+    httpgd = with pkgs; [ cairo.dev ];
+    SymTS = [ pkgs.gsl ];
+    VBLPCM = [ pkgs.gsl ];
+    dynr = [ pkgs.gsl ];
+    mixlink = [ pkgs.gsl ];
+    ridge = [ pkgs.gsl ];
+    smam = [ pkgs.gsl ];
+    rnetcarto = [ pkgs.gsl ];
+    rGEDI = [ pkgs.gsl ];
+    mmpca = [ pkgs.gsl ];
+    monoreg = [ pkgs.gsl ];
+    mvst = [ pkgs.gsl ];
+    mixture = [ pkgs.gsl ];
+    jSDM = [ pkgs.gsl ];
+    immunoClust = [ pkgs.gsl ];
+    hSDM = [ pkgs.gsl ];
+    flowPeaks = [ pkgs.gsl ];
+    fRLR = [ pkgs.gsl ];
+    eaf = [ pkgs.gsl ];
+    diseq = [ pkgs.gsl ];
+    cit = [ pkgs.gsl ];
+    abn = [ pkgs.gsl ];
+    SimInf = [ pkgs.gsl ];
+    RJMCMCNucleosomes = [ pkgs.gsl ];
+    RDieHarder = [ pkgs.gsl ];
+    QF = [ pkgs.gsl ];
+    PICS = [ pkgs.gsl ];
  };

  packagesWithBuildInputs = {
@ -515,6 +542,35 @@ let
    DirichletMultinomial = with pkgs; [ gsl ];
    DiffBind = with pkgs; [ zlib.dev ];
    CNEr = with pkgs; [ zlib ];
+    GMMAT = with pkgs; [ zlib.dev bzip2.dev ];
+    HiCDCPlus = [ pkgs.zlib.dev ];
+    PopGenome = [ pkgs.zlib.dev ];
+    QuasR = [ pkgs.zlib.dev ];
+    Rbowtie2 = [ pkgs.zlib.dev ];
+    Rmmquant = [ pkgs.zlib.dev ];
+    SICtools = with pkgs; [ zlib.dev ncurses.dev ];
+    Signac = [ pkgs.zlib.dev ];
+    TransView = [ pkgs.zlib.dev ];
+    bigsnpr = [ pkgs.zlib.dev ];
+    divest = [ pkgs.zlib.dev ];
+    hipread = [ pkgs.zlib.dev ];
+    jackalope = with pkgs; [ zlib.dev xz.dev ];
+    largeList = [ pkgs.zlib.dev ];
+    mappoly = [ pkgs.zlib.dev ];
+    matchingMarkets = [ pkgs.zlib.dev ];
+    methylKit = [ pkgs.zlib.dev ];
+    ndjson = [ pkgs.zlib.dev ];
+    podkat = [ pkgs.zlib.dev ];
+    qrqc = [ pkgs.zlib.dev ];
+    rJPSGCS = [ pkgs.zlib.dev ];
+    rhdf5filters = [ pkgs.zlib.dev ];
+    rtk = [ pkgs.zlib.dev ];
+    scPipe = [ pkgs.zlib.dev ];
+    seqTools = [ pkgs.zlib.dev ];
+    seqbias = [ pkgs.zlib.dev ];
+    sparkwarc = [ pkgs.zlib.dev ];
+    RoBMA = [ pkgs.jags ];
+    rGEDI = with pkgs; [ libgeotiff.dev libaec zlib.dev hdf5.dev ];
  };

  packagesRequiringX = [
@ -726,6 +782,28 @@ let
    "stepR"
    "styler"
    "TreeTools"
+    "ACNE"
+    "APAlyzer"
+    "EstMix"
+    "PECA"
+    "Quartet"
+    "ShinyQuickStarter"
+    "TIN"
+    "TotalCopheneticIndex"
+    "TreeDist"
+    "biocthis"
+    "calmate"
+    "fgga"
+    "fulltext"
+    "immuneSIM"
+    "mastif"
+    "shinymeta"
+    "shinyobjects"
+    "wppi"
+    "pins"
+    "CoTiMA"
+    "TBRDist"
+    "Rogue"
  ];

  packagesToSkipCheck = [
@ -741,6 +819,31 @@ let
    "NetLogoR"
    "proj4"
    "x13binary"
+
+    # Impure network access during build
+    "waddR"
+
+    # ExperimentHub dependents, require net access during build
+    "DuoClustering2018"
+    "FieldEffectCrc"
+    "GenomicDistributionsData"
+    "HDCytoData"
+    "HMP16SData"
+    "PANTHER_db"
+    "RNAmodR_Data"
+    "SCATEData"
+    "SingleMoleculeFootprintingData"
+    "TabulaMurisData"
+    "benchmarkfdrData2019"
+    "bodymapRat"
+    "clustifyrdatahub"
+    "depmap"
+    "emtdata"
+    "metaboliteIDmapping"
+    "msigdb"
+    "muscData"
+    "org_Mxanthus_db"
+    "scpdata"
  ];

  otherOverrides = old: new: {
@ -803,10 +906,6 @@ let
      patchPhase = "patchShebangs configure";
    });

-    BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: {
-      patches = [ ./patches/BayesXsrc.patch ];
-    });
-
    Rhdf5lib = old.Rhdf5lib.overrideDerivation (attrs: {
      patches = [ ./patches/Rhdf5lib.patch ];
    });
@ -1076,6 +1175,13 @@ let
          'dest_file <- file.path("~/.cache/", "h2o.jar")'
      '';
    });
+
+    SICtools = old.SICtools.overrideDerivation (attrs: {
+      preConfigure = ''
+        substituteInPlace src/Makefile --replace "-lcurses" "-lncurses"
+      '';
+    });
+
  };
 in
  self
--- a/pkgs/development/r-modules/patches/BayesXsrc.patch
+++ b/pkgs/development/r-modules/patches/BayesXsrc.patch
@ -1,55 +0,0 @@
-diff -ru -x '*~' BayesXsrc_org/MD5 BayesXsrc/MD5
--- BayesXsrc_org/MD5	2013-11-22 21:59:01.000000000 +0900
-+++ BayesXsrc/MD5	2014-10-14 22:50:46.040754675 +0900
-@@ -4,7 +4,7 @@
- cba21fc7e2d39608d0241d8cedc4fd43 *R/run.bayesx.R
- 112cb3aff0f8f0cd60bb146b14df1fcf *inst/CITATION
- cf04425475f03ee67c06efcebbd8d476 *man/run.bayesx.Rd
-1f73de4dba1228cdaa8d5435d1c1656b *src/Makefile
-+658152ec0b336198a2654385bb27666d *src/Makefile
- 2971212d003d1d647110264fb471e63b *src/Makefile.win
- e0fd1515e0d2f8553d4034c3f7544fc5 *src/bayesxsrc/adaptiv/fullcond_adaptiv.cpp
- 08cd954d541c3c0d635bbbd61cd05d15 *src/bayesxsrc/adaptiv/fullcond_adaptiv.h
-@@ -320,7 +320,7 @@
- 465ac930657299f89a0a164232dc15d2 *src/dev-Makefile
- d9aafe726622cd8c46bab760fef0d813 *src/dev-Makefile.win
- 50413e579bc999d49037293a612190c0 *src/install.libs.R
-1f73de4dba1228cdaa8d5435d1c1656b *src/rel-Makefile
-+658152ec0b336198a2654385bb27666d *src/rel-Makefile
- 2971212d003d1d647110264fb471e63b *src/rel-Makefile.win
- 4d675785837670b6a9b2b3405812a910 *tests/data.raw
- 1d3777462fcefa39559aa645305a65f2 *tests/mcmc.R
-diff -ru -x '*~' BayesXsrc_org/src/Makefile BayesXsrc/src/Makefile
--- BayesXsrc_org/src/Makefile	2013-11-22 21:49:16.000000000 +0900
-+++ BayesXsrc/src/Makefile	2014-10-14 22:47:15.458766001 +0900
-@@ -137,11 +137,11 @@
- 	${PSPLINES_OBJS}\
- 	${STRUCTADD_OBJS}\
- 	bayesxsrc/main.o\
-       	bayesxsrc/samson/multgaussian.o\
-+	bayesxsrc/samson/multgaussian.o\
- 	bayesxsrc/adaptiv/fullcond_adaptiv.o\
- 	bayesxsrc/alex/mixture.o
- 
-LDFLAGS  += -L${R_HOME}/lib -lreadline -lcurses
-+LDFLAGS  += -L${R_HOME}/lib -lreadline -lncurses
- CPPFLAGS +=  -Ibayesxsrc/. -I"bayesxsrc/bib"  -I"bayesxsrc/alex"  -I"bayesxsrc/adaptiv"  -I"bayesxsrc/andrea"  -I"bayesxsrc/dag"  -I"bayesxsrc/graph"  -I"bayesxsrc/mcmc"  -I"bayesxsrc/psplines"  -I"bayesxsrc/samson"  -I"bayesxsrc/leyre"  -I"bayesxsrc/structadd"
- CPPFLAGS += -D__BUILDING_GNU -D__BUILDING_LINUX -DTEMPL_INCL_DEF -D_MSC_VER2 -DNO_TEMPLATE_FRIENDS -DINCLUDE_REML -DINCLUDE_MCMC
- # CXXFLAGS += -O3 -ansi
-diff -ru -x '*~' BayesXsrc_org/src/rel-Makefile BayesXsrc/src/rel-Makefile
--- BayesXsrc_org/src/rel-Makefile	2013-10-08 21:28:09.000000000 +0900
-+++ BayesXsrc/src/rel-Makefile	2014-10-14 22:47:04.601766431 +0900
-@@ -137,11 +137,11 @@
- 	${PSPLINES_OBJS}\
- 	${STRUCTADD_OBJS}\
- 	bayesxsrc/main.o\
-       	bayesxsrc/samson/multgaussian.o\
-+	bayesxsrc/samson/multgaussian.o\
- 	bayesxsrc/adaptiv/fullcond_adaptiv.o\
- 	bayesxsrc/alex/mixture.o
- 
-LDFLAGS  += -L${R_HOME}/lib -lreadline -lcurses
-+LDFLAGS  += -L${R_HOME}/lib -lreadline -lncurses
- CPPFLAGS +=  -Ibayesxsrc/. -I"bayesxsrc/bib"  -I"bayesxsrc/alex"  -I"bayesxsrc/adaptiv"  -I"bayesxsrc/andrea"  -I"bayesxsrc/dag"  -I"bayesxsrc/graph"  -I"bayesxsrc/mcmc"  -I"bayesxsrc/psplines"  -I"bayesxsrc/samson"  -I"bayesxsrc/leyre"  -I"bayesxsrc/structadd"
- CPPFLAGS += -D__BUILDING_GNU -D__BUILDING_LINUX -DTEMPL_INCL_DEF -D_MSC_VER2 -DNO_TEMPLATE_FRIENDS -DINCLUDE_REML -DINCLUDE_MCMC
- # CXXFLAGS += -O3 -ansi
--- a/pkgs/development/tools/misc/nxpmicro-mfgtools/default.nix
+++ b/pkgs/development/tools/misc/nxpmicro-mfgtools/default.nix
@ -3,6 +3,7 @@
 , cmake
 , pkg-config
 , bzip2
+, installShellFiles
 , libusb1
 , libzip
 , openssl
@ -10,16 +11,16 @@

 stdenv.mkDerivation rec {
  pname = "nxpmicro-mfgtools";
-  version = "1.4.72";
+  version = "1.4.165";

  src = fetchFromGitHub {
    owner = "NXPmicro";
    repo = "mfgtools";
    rev = "uuu_${version}";
-    sha256 = "1s3wlz4yb2p8by5p66vr0z72n84mxkrmda63x9yr6pinqinsyrvv";
+    sha256 = "0k309lp27d4k6x4qq0badbk8i47xsc6f3fffz73650iyfs4hcniw";
  };

-  nativeBuildInputs = [ cmake pkg-config ];
+  nativeBuildInputs = [ cmake pkg-config installShellFiles ];

  buildInputs = [ bzip2 libusb1 libzip openssl ];

@ -31,6 +32,8 @@ stdenv.mkDerivation rec {
    $out/bin/uuu -udev > udev-rules 2>stderr.txt
    rules_file="$(cat stderr.txt|grep '1: put above udev run into'|sed 's|^.*/||')"
    install -D udev-rules "$out/lib/udev/rules.d/$rules_file"
+    installShellCompletion --cmd uuu \
+      --bash ../snap/local/bash-completion/universal-update-utility
  '';

  meta = with lib; {
@ -48,7 +51,7 @@ stdenv.mkDerivation rec {
    '';
    homepage = "https://github.com/NXPmicro/mfgtools";
    license = licenses.bsd3;
-    maintainers = [ maintainers.bmilanov ];
+    maintainers = with maintainers; [ bmilanov jraygauthier ];
    platforms = platforms.all;
  };
 }
--- a/pkgs/development/tools/open-policy-agent/default.nix
+++ b/pkgs/development/tools/open-policy-agent/default.nix
@ -1,26 +1,67 @@
-{ lib, buildGoModule, fetchFromGitHub }:
+{ lib
+, buildGoModule
+, fetchFromGitHub
+, installShellFiles
+
+, enableWasmEval ? false
+}:

 buildGoModule rec {
  pname = "open-policy-agent";
-  version = "0.32.1";
+  version = "0.33.1";

  src = fetchFromGitHub {
    owner = "open-policy-agent";
    repo = "opa";
    rev = "v${version}";
-    sha256 = "sha256-pd0bOE0cSi+93B0U46KpeC7AHgsV3oBJcT/wg8XED5Y=";
+    sha256 = "sha256-n0VuzYlgn9IGiaxzDeuVjMqFbDwTe3UjExk7BT2DNZc=";
  };
  vendorSha256 = null;

+  nativeBuildInputs = [ installShellFiles ];
+
  subPackages = [ "." ];

  ldflags = [ "-s" "-w" "-X github.com/open-policy-agent/opa/version.Version=${version}" ];

+  tags = lib.optional enableWasmEval (
+    builtins.trace
+      ("Warning: enableWasmEval breaks reproducability, "
+        + "ensure you need wasm evaluation. "
+        + "`opa build` does not need this feature.")
+      "opa_wasm");
+
+  preCheck = ''
+    # Feed in all but the e2e tests for testing
+    # This is because subPackages above limits what is built to just what we
+    # want but also limits the tests
+    getGoDirs() {
+      go list ./... | grep -v e2e
+    }
+
+    # Remove test case that fails on < go1.17
+    rm test/cases/testdata/cryptox509parsecertificates/test-cryptox509parsecertificates-0123.yaml
+  '';
+
+  postInstall = ''
+    installShellCompletion --cmd opa \
+      --bash <($out/bin/opa completion bash) \
+      --fish <($out/bin/opa completion fish) \
+      --zsh <($out/bin/opa completion zsh)
+  '';
+
  doInstallCheck = true;
  installCheckPhase = ''
    runHook preInstallCheck
+
    $out/bin/opa --help
    $out/bin/opa version | grep "Version: ${version}"
+
+    ${lib.optionalString enableWasmEval ''
+      # If wasm is enabled verify it works
+      $out/bin/opa eval -t wasm 'trace("hello from wasm")'
+    ''}
+
    runHook postInstallCheck
  '';

--- a/pkgs/development/tools/protoc-gen-twirp_php/default.nix
+++ b/pkgs/development/tools/protoc-gen-twirp_php/default.nix
@ -2,16 +2,16 @@

 buildGoModule rec {
  pname = "protoc-gen-twirp_php";
-  version = "0.7.5";
+  version = "0.8.0";

  # fetchFromGitHub currently not possible, because go.mod and go.sum are export-ignored
  src = fetchgit {
    url = "https://github.com/twirphp/twirp.git";
    rev = "v${version}";
-    sha256 = "sha256-pHGGZaMBggBUu2CZCxWrZ592K5V93vPI2sZnFkqku2k=";
+    sha256 = "sha256-TaHfyYoWsA/g5xZFxIMNwE1w6Dd9Cq5bp1gpQudYLs0=";
  };

-  vendorSha256 = "sha256-p7t+2QgPkcTmsK+jKcPCPDCchNup9F326yKc6JbJHOE=";
+  vendorSha256 = "sha256-z3Yp+Yy03g2DAvWUZXaOxQWONjnYUl69eTpYIDPhsqc=";

  subPackages = [ "protoc-gen-twirp_php" ];

--- a/pkgs/development/tools/tabnine/default.nix
+++ b/pkgs/development/tools/tabnine/default.nix
@ -1,18 +1,29 @@
 { stdenv, lib, fetchurl, unzip }:
 let
-  platform =
-    if stdenv.hostPlatform.system == "x86_64-linux" then {
+  supportedPlatforms = {
+    "x86_64-linux" = {
      name = "x86_64-unknown-linux-musl";
-      sha256 = "sha256-+jxjHE2/6IGptMlKXGebHcaIVokOP76ut325EbkdaA0=";
-    } else if stdenv.hostPlatform.system == "x86_64-darwin" then {
+      sha256 = "sha256-On+Sokm2+BV3JbIwK8oPO6882FOWBlgSaAp3VAyR+RM=";
+    };
+    "x86_64-darwin" = {
      name = "x86_64-apple-darwin";
-      sha256 = "sha256-87Hy1akNrZWQbKutkv4CToTyMcxRc7Y24o1+vI4pev8=";
-    } else throw "Not supported on ${stdenv.hostPlatform.system}";
+      sha256 = "sha256-4YCm42mVcsEvY4I5MWrnbfgUIU7KUIrEirvjN8ISIr0=";
+    };
+    "aarch64-darwin" = {
+      name = "aarch64-apple-darwin";
+      sha256 = "sha256-HN4o5bGX389eAR7ea5EY1JlId8q4lSPGJ4cZo9c2aP4=";
+    };
+  };
+  platform =
+    if (builtins.hasAttr stdenv.hostPlatform.system supportedPlatforms) then
+      builtins.getAttr (stdenv.hostPlatform.system) supportedPlatforms
+    else
+      throw "Not supported on ${stdenv.hostPlatform.system}";
 in
 stdenv.mkDerivation rec {
  pname = "tabnine";
  # You can check the latest version with `curl -sS https://update.tabnine.com/bundles/version`
-  version = "3.6.8";
+  version = "3.7.25";

  src = fetchurl {
    url = "https://update.tabnine.com/bundles/${version}/${platform.name}/TabNine.zip";
@ -42,7 +53,7 @@ stdenv.mkDerivation rec {
    homepage = "https://tabnine.com";
    description = "Smart Compose for code that uses deep learning to help you write code faster";
    license = licenses.unfree;
-    platforms = [ "x86_64-darwin" "x86_64-linux" ];
+    platforms = [ "x86_64-darwin" "aarch64-darwin" "x86_64-linux" ];
    maintainers = with maintainers; [ lovesegfault ];
  };
 }
--- a/pkgs/os-specific/linux/hd-idle/default.nix
+++ b/pkgs/os-specific/linux/hd-idle/default.nix
@ -1,25 +1,28 @@
-{ lib, stdenv, fetchurl }:
+{ lib, buildGoModule, fetchFromGitHub, installShellFiles }:

-stdenv.mkDerivation rec {
+buildGoModule rec {
  pname = "hd-idle";
-  version = "1.05";
+  version = "1.16";

-  src = fetchurl {
-    url = "mirror://sourceforge/project/hd-idle/hd-idle-${version}.tgz";
-    sha256 = "031sm996s0rhy3z91b9xvyimsj2yd2fhsww2al2hxda5s5wzxzjf";
+  src = fetchFromGitHub {
+    owner = "adelolmo";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "sha256-LZcMwF/BhHiWWXMcrzbk8GyvwXdA3B2olmbOBxQwV5g=";
  };

-  prePatch = ''
-    substituteInPlace Makefile \
-      --replace "-g root -o root" ""
-  '';
+  vendorSha256 = null;

-  installFlags = [ "TARGET_DIR=$(out)" ];
+  nativeBuildInputs = [ installShellFiles ];
+
+  postInstall = ''
+    installManPage debian/hd-idle.8
+  '';

  meta = with lib; {
    description = "Spins down external disks after a period of idle time";
-    homepage = "http://hd-idle.sourceforge.net/";
-    license = licenses.gpl2Plus;
+    homepage = "https://github.com/adelolmo/hd-idle";
+    license = licenses.gpl3Plus;
    platforms = platforms.linux;
    maintainers = [ maintainers.rycee ];
  };
--- a/pkgs/servers/monitoring/zabbix/versions.nix
+++ b/pkgs/servers/monitoring/zabbix/versions.nix
@ -1,11 +1,11 @@
 generic: {
  v50 = generic {
-    version = "5.0.15";
-    sha256 = "1q9xwixzdj3w9qmarpp8xbkjphsz4m185br8g6i9f96676hrw5ww";
+    version = "5.0.17";
+    sha256 = "11ppax0l0m8lzd1872g4l0jhng8bkkq3577kc364fmfxnsvkc60k";
  };

  v40 = generic {
-    version = "4.0.33";
-    sha256 = "05pdqiql6xv1l7cn2piydsfjiaw6np0rbl1n5wg7bc7r4ikiyp4v";
+    version = "4.0.35";
+    sha256 = "0qq49658b22xxsjlmldjqwssri16s1y3c0wj3a5hzs8sk5qclcr5";
  };
 }
--- a/pkgs/tools/misc/etcher/default.nix
+++ b/pkgs/tools/misc/etcher/default.nix
@ -9,15 +9,19 @@
 }:

 let
+  inherit (stdenv.hostPlatform) system;
+
+  throwSystem = throw "Unsupported system: ${stdenv.hostPlatform.system}";
+
  sha256 = {
-    "x86_64-linux" = "sha256-Tasynkzyy8UIalQn6qhIuPWDflf4pL76D2czgEijrPw=";
-    "i686-linux" = "0z6y45sz086njpywg7f0jn6n02qynb1qbi889g2kcgwbfjvmcpm1";
-  }."${stdenv.system}";
+    "x86_64-linux" = "sha256-n8i4ZqjugeUfXpTzVgIwVomfPk6HvPEbTZLe/jFgwFg=";
+    "i686-linux" = "sha256-lLGfhW6el2ZOcaykH1kTjGldXo7/0q5O8QnslnDlWAQ=";
+  }."${system}" or throwSystem;

  arch = {
    "x86_64-linux" = "amd64";
    "i686-linux" = "i386";
-  }."${stdenv.system}";
+  }."${system}" or throwSystem;

  electron = electron_12;

@ -25,7 +29,7 @@ in

 stdenv.mkDerivation rec {
  pname = "etcher";
-  version = "1.5.122";
+  version = "1.6.0";

  src = fetchurl {
    url = "https://github.com/balena-io/etcher/releases/download/v${version}/balena-etcher-electron_${version}_${arch}.deb";
--- a/pkgs/tools/misc/fclones/default.nix
+++ b/pkgs/tools/misc/fclones/default.nix
@ -8,16 +8,16 @@

 rustPlatform.buildRustPackage rec {
  pname = "fclones";
-  version = "0.17.0";
+  version = "0.17.1";

  src = fetchFromGitHub {
    owner = "pkolaczk";
    repo = pname;
    rev = "v${version}";
-    sha256 = "sha256-JygW1Ri9BA4Qssu6MlQCCjnAok9OD2pcGdavOyHxbIo=";
+    sha256 = "0d5an35fnz9rdr2ssm952zpzn4jynpvbfyidnqcmp0lclr60c2ir";
  };

-  cargoSha256 = "sha256-sDHsj0qxKW5JJCI9H0WytgugtEmLaLU2EIgCcXdfQH0=";
+  cargoSha256 = "sha256-CtQ4grQqgMUYzPDw2Qankl8jmqwwCrawNCmaY97JPkQ=";

  buildInputs = lib.optionals stdenv.isDarwin [
    AppKit
--- a/pkgs/tools/security/buttercup-desktop/default.nix
+++ b/pkgs/tools/security/buttercup-desktop/default.nix
@ -0,0 +1,33 @@
+{ lib, fetchurl, appimageTools }:
+
+let
+  pname = "buttercup-desktop";
+  version = "2.13.0";
+  name = "${pname}-${version}";
+  src = fetchurl {
+    url = "https://github.com/buttercup/buttercup-desktop/releases/download/v${version}/Buttercup-linux-x86_64.AppImage";
+    sha256 = "sha256-JXXJZyd/fp2463WyxIB+pKcNzGUFfCouPE6iTx2lhME=";
+  };
+  appimageContents = appimageTools.extractType2 { inherit name src; };
+
+in appimageTools.wrapType2 {
+  inherit name src;
+
+  extraPkgs = pkgs: (appimageTools.defaultFhsEnvArgs.multiPkgs pkgs) ++ [ pkgs.libsecret ];
+
+  extraInstallCommands = ''
+    mv $out/bin/${name} $out/bin/buttercup-desktop
+    install -m 444 -D ${appimageContents}/buttercup.desktop -t $out/share/applications
+    substituteInPlace $out/share/applications/buttercup.desktop \
+      --replace 'Exec=AppRun' 'Exec=buttercup-desktop'
+    cp -r ${appimageContents}/usr/share/icons $out/share
+  '';
+
+  meta = with lib; {
+    description = "Cross-Platform Passwords & Secrets Vault";
+    homepage = "https://buttercup.pw";
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ wolfangaukang ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
--- a/pkgs/tools/security/pinentry/default.nix
+++ b/pkgs/tools/security/pinentry/default.nix
@ -43,11 +43,11 @@ in

 pinentryMkDerivation rec {
  pname = "pinentry";
-  version = "1.1.0";
+  version = "1.2.0";

  src = fetchurl {
    url = "mirror://gnupg/pinentry/${pname}-${version}.tar.bz2";
-    sha256 = "0w35ypl960pczg5kp6km3dyr000m1hf0vpwwlh72jjkjza36c1v8";
+    sha256 = "sha256-EAcgRaPgQ9BYH5HNVnb8rH/+6VehZjat7apPWDphZHA=";
  };

  nativeBuildInputs = [ pkg-config autoreconfHook ]
--- a/pkgs/tools/system/datefudge/default.nix
+++ b/pkgs/tools/system/datefudge/default.nix
@ -1,4 +1,4 @@
-{ lib, stdenv, fetchgit, fetchpatch }:
+{ stdenv, lib, fetchgit, fetchpatch, makeWrapper, coreutils }:

 stdenv.mkDerivation rec {
  pname = "datefudge";
@ -10,6 +10,10 @@ stdenv.mkDerivation rec {
    sha256 = "1nh433yx4y4djp0bs6aawqbwk7miq7fsbs9wpjlyh2k9dvil2lrm";
  };

+  nativeBuildInputs = [ makeWrapper ];
+
+  buildInputs = [ coreutils ];
+
  postPatch = ''
    substituteInPlace Makefile \
     --replace "/usr" "/" \
@ -20,7 +24,10 @@ stdenv.mkDerivation rec {

  installFlags = [ "DESTDIR=$(out)" ];

-  postInstall = "chmod +x $out/lib/datefudge/datefudge.so";
+  postInstall = ''
+    chmod +x $out/lib/datefudge/datefudge.so
+    wrapProgram $out/bin/datefudge --prefix PATH : ${coreutils}/bin
+  '';

  meta = with lib; {
    description = "Fake the system date";
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@ -2123,6 +2123,8 @@ with pkgs;

  butane = callPackage ../development/tools/butane { };

+  buttercup-desktop = callPackage ../tools/security/buttercup-desktop { };
+
  charles = charles4;
  inherit (callPackage ../applications/networking/charles {})
    charles3
@ -5050,7 +5052,11 @@ with pkgs;

  fcitx5-chinese-addons = libsForQt5.callPackage ../tools/inputmethods/fcitx5/fcitx5-chinese-addons.nix { };

-  fcitx5-mozc = libsForQt5.callPackage ../tools/inputmethods/fcitx5/fcitx5-mozc.nix { };
+  fcitx5-mozc = libsForQt5.callPackage ../tools/inputmethods/fcitx5/fcitx5-mozc.nix {
+    abseil-cpp = abseil-cpp.override {
+      cxxStandard = "17";
+    };
+  };

  fcitx5-configtool = libsForQt5.callPackage ../tools/inputmethods/fcitx5/fcitx5-configtool.nix { };

@ -9901,6 +9907,8 @@ with pkgs;

  thinkpad-scripts = python3.pkgs.callPackage ../tools/misc/thinkpad-scripts { };

+  threema-desktop = callPackage ../applications/networking/instant-messengers/threema-desktop { };
+
  tidy-viewer = callPackage ../tools/text/tidy-viewer { };

  tiled = libsForQt5.callPackage ../applications/editors/tiled { };
@ -23385,6 +23393,8 @@ with pkgs;

  shades-of-gray-theme = callPackage ../data/themes/shades-of-gray { };

+  sierra-breeze-enhanced = libsForQt5.callPackage ../data/themes/kwin-decorations/sierra-breeze-enhanced { };
+
  sjasmplus = callPackage ../development/compilers/sjasmplus { };

  skeu = callPackage ../data/themes/skeu { };
@ -23825,6 +23835,8 @@ with pkgs;

  audio-recorder = callPackage ../applications/audio/audio-recorder { };

+  auto-multiple-choice = callPackage ../applications/misc/auto-multiple-choice { };
+
  autokey = callPackage ../applications/office/autokey { };

  autotalent = callPackage ../applications/audio/autotalent { };
@ -26393,6 +26405,10 @@ with pkgs;

  markets = callPackage ../applications/misc/markets { };

+  markmind = callPackage ../applications/misc/markmind {
+    electron = electron_9;
+  };
+
  marp = callPackage ../applications/office/marp { };

  magnetico = callPackage ../applications/networking/p2p/magnetico { };
@ -28822,6 +28838,10 @@ with pkgs;

  weston = callPackage ../applications/window-managers/weston { pipewire = pipewire_0_2; };

+  whalebird = callPackage ../applications/misc/whalebird {
+    electron = electron_12;
+  };
+
  wio = callPackage ../applications/window-managers/wio { };

  whitebox-tools = callPackage ../applications/gis/whitebox-tools {
@ -31175,7 +31195,12 @@ with pkgs;

  or-tools = callPackage ../development/libraries/science/math/or-tools {
    python = python3;
-    abseil-cpp = abseil-cpp.override { static = true; };
+    # or-tools builds with -std=c++17, so abseil-cpp must
+    # also be built that way
+    abseil-cpp = abseil-cpp.override {
+      static = true;
+      cxxStandard = "17";
+    };
  };

  rubiks = callPackage ../development/libraries/science/math/rubiks { };
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@ -6184,6 +6184,8 @@ in {

  pyclimacell = callPackage ../development/python-modules/pyclimacell { };

+  pyclip = callPackage ../development/python-modules/pyclip { };
+
  pyclipper = callPackage ../development/python-modules/pyclipper { };

  pycm = callPackage ../development/python-modules/pycm { };