Merge master into haskell-updates

.github/CODEOWNERS

@@ -41,7 +41,8 @@
 /pkgs/build-support/cc-wrapper                   @Ericson2314
 /pkgs/build-support/bintools-wrapper             @Ericson2314
 /pkgs/build-support/setup-hooks                  @Ericson2314
-/pkgs/build-support/setup-hooks/auto-patchelf.sh @aszlig
+/pkgs/build-support/setup-hooks/auto-patchelf.sh @layus
+/pkgs/build-support/setup-hooks/auto-patchelf.py @layus
 
 # Nixpkgs build-support
 /pkgs/build-support/writers @lassulus @Profpatsch

nixos/doc/manual/from_md/release-notes/rl-2205.section.xml

@@ -1043,6 +1043,14 @@
           <literal>admin</literal> and <literal>password</literal>.
         </para>
       </listitem>
+      <listitem>
+        <para>
+          The <literal>taskserver</literal> module no longer implicitly
+          opens ports in the firewall configuration. This is now
+          controlled through the option
+          <literal>services.taskserver.openFirewall</literal>.
+        </para>
+      </listitem>
       <listitem>
         <para>
           The <literal>autorestic</literal> package has been upgraded
@@ -1263,6 +1271,15 @@
           <literal>true</literal>.
         </para>
       </listitem>
+      <listitem>
+        <para>
+          <literal>services.github-runner</literal> has been hardened.
+          Notably address families and system calls have been
+          restricted, which may adversely affect some kinds of testing,
+          e.g. using <literal>AF_BLUETOOTH</literal> to test bluetooth
+          devices.
+        </para>
+      </listitem>
       <listitem>
         <para>
           The terraform 0.12 compatibility has been removed and the
@@ -2141,6 +2158,12 @@
           <link xlink:href="https://github.com/uber/pam-ussh">pam-ussh</link>.
         </para>
       </listitem>
+      <listitem>
+        <para>
+          The <literal>vscode-extensions.ionide.ionide-fsharp</literal>
+          package has been updated to 6.0.0 and now requires .NET 6.0.
+        </para>
+      </listitem>
       <listitem>
         <para>
           The <literal>zrepl</literal> package has been updated from

nixos/doc/manual/release-notes/rl-2205.section.md

@@ -443,6 +443,10 @@ In addition to numerous new and upgraded packages, this release has the followin
 
 - `services.miniflux.adminCredentialFiles` is now required, instead of defaulting to `admin` and `password`.
 
+- The `taskserver` module no longer implicitly opens ports in the firewall
+  configuration. This is now controlled through the option
+  `services.taskserver.openFirewall`.
+
 - The `autorestic` package has been upgraded from 1.3.0 to 1.5.0 which introduces breaking changes in config file, check [their migration guide](https://autorestic.vercel.app/migration/1.4_1.5) for more details.
 
 - For `pkgs.python3.pkgs.ipython`, its direct dependency `pkgs.python3.pkgs.matplotlib-inline`
@@ -498,6 +502,10 @@ In addition to numerous new and upgraded packages, this release has the followin
 
 - The Tor SOCKS proxy is now actually disabled if `services.tor.client.enable` is set to `false` (the default). If you are using this functionality but didn't change the setting or set it to `false`, you now need to set it to `true`.
 
+- `services.github-runner` has been hardened.  Notably address families and
+  system calls have been restricted, which may adversely affect some kinds of
+  testing, e.g. using `AF_BLUETOOTH` to test bluetooth devices.
+
 - The terraform 0.12 compatibility has been removed and the `terraform.withPlugins` and `terraform-providers.mkProvider` implementations simplified. Providers now need to be stored under
 `$out/libexec/terraform-providers/<registry>/<owner>/<name>/<version>/<os>_<arch>/terraform-provider-<name>_v<version>` (which mkProvider does).
 
@@ -770,6 +778,8 @@ In addition to numerous new and upgraded packages, this release has the followin
 
 - `security.pam.ussh` has been added, which allows authorizing PAM sessions based on SSH _certificates_ held within an SSH agent, using [pam-ussh](https://github.com/uber/pam-ussh).
 
+- The `vscode-extensions.ionide.ionide-fsharp` package has been updated to 6.0.0 and now requires .NET 6.0.
+
 - The `zrepl` package has been updated from 0.4.0 to 0.5:
 
   - The RPC protocol version was bumped; all zrepl daemons in a setup must be updated and restarted before replication can resume.

nixos/modules/hardware/video/amdgpu-pro.nix

@@ -51,9 +51,10 @@ in
       (isYes "KALLSYMS_ALL")
     ];
 
-    boot.initrd.extraUdevRulesCommands = ''
+    boot.initrd.extraUdevRulesCommands = mkIf (!config.boot.initrd.systemd.enable) ''
       cp -v ${package}/etc/udev/rules.d/*.rules $out/
     '';
+    boot.initrd.services.udev.packages = [ package ];
 
     environment.systemPackages =
       [ package.vulkan ] ++

nixos/modules/services/continuous-integration/github-runner.nix

@@ -299,6 +299,16 @@ in
         RestrictRealtime = true;
         RestrictSUIDSGID = true;
         UMask = "0066";
+        ProtectProc = "invisible";
+        ProcSubset = "pid";
+        SystemCallFilter = [
+          "~@debug"
+          "~@mount"
+          "~@privileged"
+          "~@cpu-emulation"
+          "~@obsolete"
+        ];
+        RestrictAddressFamilies = [ "AF_INET" "AF_INET6" "AF_UNIX" "AF_NETLINK" ];
 
         # Needs network access
         PrivateNetwork = false;

nixos/modules/services/mail/mailman.nix

@@ -318,7 +318,9 @@ in {
     systemd.services = {
       mailman = {
         description = "GNU Mailman Master Process";
-        after = [ "network.target" ];
+        before = lib.optional cfg.enablePostfix "postfix.service";
+        after = [ "network.target" ]
+          ++ lib.optional cfg.enablePostfix "postfix-setup.service";
         restartTriggers = [ config.environment.etc."mailman.cfg".source ];
         wantedBy = [ "multi-user.target" ];
         serviceConfig = {

nixos/modules/services/mail/postfix.nix

@@ -723,23 +723,10 @@ in
         { ${setgidGroup}.gid = config.ids.gids.postdrop;
         };
 
-      systemd.services.postfix =
-        { description = "Postfix mail server";
-
-          wantedBy = [ "multi-user.target" ];
-          after = [ "network.target" ];
-          path = [ pkgs.postfix ];
-
-          serviceConfig = {
-            Type = "forking";
-            Restart = "always";
-            PIDFile = "/var/lib/postfix/queue/pid/master.pid";
-            ExecStart = "${pkgs.postfix}/bin/postfix start";
-            ExecStop = "${pkgs.postfix}/bin/postfix stop";
-            ExecReload = "${pkgs.postfix}/bin/postfix reload";
-          };
-
-          preStart = ''
+      systemd.services.postfix-setup =
+        { description = "Setup for Postfix mail server";
+          serviceConfig.Type = "oneshot";
+          script = ''
             # Backwards compatibility
             if [ ! -d /var/lib/postfix ] && [ -d /var/postfix ]; then
               mkdir -p /var/lib
@@ -777,6 +764,24 @@ in
           '';
         };
 
+      systemd.services.postfix =
+        { description = "Postfix mail server";
+
+          wantedBy = [ "multi-user.target" ];
+          after = [ "network.target" "postfix-setup.service" ];
+          requires = [ "postfix-setup.service" ];
+          path = [ pkgs.postfix ];
+
+          serviceConfig = {
+            Type = "forking";
+            Restart = "always";
+            PIDFile = "/var/lib/postfix/queue/pid/master.pid";
+            ExecStart = "${pkgs.postfix}/bin/postfix start";
+            ExecStop = "${pkgs.postfix}/bin/postfix stop";
+            ExecReload = "${pkgs.postfix}/bin/postfix reload";
+          };
+        };
+
       services.postfix.config = (mapAttrs (_: v: mkDefault v) {
         compatibility_level  = pkgs.postfix.version;
         mail_owner           = cfg.user;

nixos/modules/services/misc/taskserver/default.nix

@@ -106,7 +106,7 @@ let
 
   certtool = "${pkgs.gnutls.bin}/bin/certtool";
 
-  nixos-taskserver = with pkgs.python2.pkgs; buildPythonApplication {
+  nixos-taskserver = with pkgs.python3.pkgs; buildPythonApplication {
     name = "nixos-taskserver";
 
     src = pkgs.runCommand "nixos-taskserver-src" { preferLocalBuild = true; } ''
@@ -277,10 +277,6 @@ in {
         example = "::";
         description = ''
           The address (IPv4, IPv6 or DNS) to listen on.
-
-          If the value is something else than <literal>localhost</literal> the
-          port defined by <option>listenPort</option> is automatically added to
-          <option>networking.firewall.allowedTCPPorts</option>.
         '';
       };
 
@@ -292,6 +288,14 @@ in {
         '';
       };
 
+      openFirewall = mkOption {
+        type = types.bool;
+        default = false;
+        description = ''
+          Whether to open the firewall for the specified Taskserver port.
+        '';
+      };
+
       fqdn = mkOption {
         type = types.str;
         default = "localhost";
@@ -560,7 +564,7 @@ in {
         '';
       };
     })
-    (mkIf (cfg.enable && cfg.listenHost != "localhost") {
+    (mkIf (cfg.enable && cfg.openFirewall) {
       networking.firewall.allowedTCPPorts = [ cfg.listenPort ];
     })
   ];

nixos/modules/services/misc/taskserver/helper-tool.py

@@ -90,7 +90,7 @@ def certtool_cmd(*args, **kwargs):
     """
     return subprocess.check_output(
         [CERTTOOL_COMMAND] + list(args),
-        preexec_fn=lambda: os.umask(0077),
+        preexec_fn=lambda: os.umask(0o077),
         stderr=subprocess.STDOUT,
         **kwargs
     )
@@ -164,7 +164,7 @@ def generate_key(org, user):
     pubcert = os.path.join(basedir, "public.cert")
 
     try:
-        os.makedirs(basedir, mode=0700)
+        os.makedirs(basedir, mode=0o700)
 
         certtool_cmd("-p", "--bits", CERT_BITS, "--outfile", privkey)
 
@@ -301,7 +301,7 @@ class Organisation(object):
             return None
         if name not in self.users.keys():
             output = taskd_cmd("add", "user", self.name, name,
-                               capture_stdout=True)
+                               capture_stdout=True, encoding='utf-8')
             key = RE_USERKEY.search(output)
             if key is None:
                 msg = "Unable to find key while creating user {}."
@@ -412,9 +412,9 @@ class Manager(object):
         if org is not None:
             if self.ignore_imperative and is_imperative(name):
                 return
-            for user in org.users.keys():
+            for user in list(org.users.keys()):
                 org.del_user(user)
-            for group in org.groups.keys():
+            for group in list(org.groups.keys()):
                 org.del_group(group)
             taskd_cmd("remove", "org", name)
             del self._lazy_orgs[name]

nixos/modules/services/networking/bird.nix

@@ -68,8 +68,7 @@ in
     systemd.services.bird2 = {
       description = "BIRD Internet Routing Daemon";
       wantedBy = [ "multi-user.target" ];
-      reloadIfChanged = true;
-      restartTriggers = [ config.environment.etc."bird/bird2.conf".source ];
+      reloadTriggers = [ config.environment.etc."bird/bird2.conf".source ];
       serviceConfig = {
         Type = "forking";
         Restart = "on-failure";

nixos/tests/taskserver.nix

@@ -63,6 +63,7 @@ in {
     server = {
       services.taskserver.enable = true;
       services.taskserver.listenHost = "::";
+      services.taskserver.openFirewall = true;
       services.taskserver.fqdn = "server";
       services.taskserver.organisations = {
         testOrganisation.users = [ "alice" "foo" ];

pkgs/applications/audio/osdlyrics/default.nix

@@ -0,0 +1,87 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+
+, autoreconfHook
+, pkg-config
+, intltool
+
+, glib
+, gtk2
+, dbus-glib
+, libappindicator-gtk2
+, libnotify
+, python3
+, runtimeShell
+}:
+
+stdenv.mkDerivation rec {
+  pname = "osdlyrics";
+  version = "0.5.10";
+
+  src = fetchFromGitHub {
+    owner = "osdlyrics";
+    repo = "osdlyrics";
+    rev = version;
+    sha256 = "sha256-x9gIT1JkfPIc4RmmQJLv9rOG2WqAftoTK5uiRlS65zU=";
+  };
+
+  nativeBuildInputs = [
+    autoreconfHook
+    pkg-config
+    intltool
+  ];
+
+  buildInputs = [
+    glib
+    gtk2
+    dbus-glib
+    libappindicator-gtk2
+    libnotify
+    python3.pkgs.wrapPython
+    (python3.withPackages (pp: with pp; [
+      chardet
+      dbus-python
+      future
+      pycurl
+      pygobject3
+    ]))
+  ];
+
+  postFixup = ''
+    extractExecLine() {
+      serviceFile=$1
+      program=$2
+
+      execLine=$(grep --only-matching --perl-regexp 'Exec=\K(.+)' "$serviceFile")
+      echo "#!${runtimeShell}" > "$program"
+      echo "exec $execLine" >> "$program"
+      chmod +x "$program"
+
+      substituteInPlace "$serviceFile" \
+        --replace "Exec=$execLine" "Exec=$program"
+    }
+
+    # Extract the exec line into a separate program so that it can be wrapped.
+    mkdir -p "$out/libexec/osdlyrics/"
+    for svcFile in "$out/share/dbus-1/services"/*; do
+      svc=$(basename "$svcFile" ".service")
+      if grep "python" "$svcFile"; then
+        extractExecLine "$svcFile" "$out/libexec/osdlyrics/$svc"
+      fi
+    done
+
+    for p in "$out/bin/osdlyrics-create-lyricsource" "$out/bin/osdlyrics-daemon" "$out/libexec/osdlyrics"/*; do
+      wrapProgram "$p" \
+        --prefix PYTHONPATH : "$out/${python3.sitePackages}"
+    done
+  '';
+
+  meta = with lib; {
+    description = "Standalone lyrics fetcher/displayer";
+    homepage = "https://github.com/osdlyrics/osdlyrics";
+    license = licenses.gpl3Plus;
+    maintainers = with maintainers; [ jtojnar ];
+    platforms = platforms.linux;
+  };
+}

pkgs/applications/editors/cudatext/default.nix

@@ -38,13 +38,13 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "cudatext";
-  version = "1.161.0";
+  version = "1.162.0";
 
   src = fetchFromGitHub {
     owner = "Alexey-T";
     repo = "CudaText";
     rev = version;
-    sha256 = "sha256-FxeJpKc++fDHdYuYmjL6qY/rilA++ljcB/9U54+/+P0=";
+    sha256 = "sha256-lAH0HXtzWs1iFVzM/tvnBT1s1Mt0AGs4TqdtFu1NeMw=";
   };
 
   postPatch = ''

pkgs/applications/editors/cudatext/deps.json

@@ -1,23 +1,23 @@
 {
   "EncConv": {
     "owner": "Alexey-T",
-    "rev": "2022.03.02",
-    "sha256": "sha256-fBN6Ix5CqhzMbNrWGn6nw6+JRDmEfqe6o8JGHERkiPE="
+    "rev": "2022.04.18",
+    "sha256": "sha256-UV07a9qNzd0JQWCq/eD0K9fA7kxAKj5OP7dOpECo8xw="
   },
   "ATBinHex-Lazarus": {
     "owner": "Alexey-T",
-    "rev": "2021.11.17",
-    "sha256": "sha256-wdYH0sISFNx42zt07gLn9ANxcyrq3WrbRhWfTFgPQWw="
+    "rev": "2022.04.16",
+    "sha256": "sha256-7ye73KSpoPvvxBNwBC3uloufFE+448RDyNScumk1ViE="
   },
   "ATFlatControls": {
     "owner": "Alexey-T",
-    "rev": "2022.03.17",
-    "sha256": "sha256-zpirFZcqIT53tZhgxQGdwVB6pA98SQLr1o3f+Lhq2QY="
+    "rev": "2022.04.18",
+    "sha256": "sha256-Bp/pkbTPLiVaDSstzTaNjKb+msPw8Tuny75n/aYBpUc="
   },
   "ATSynEdit": {
     "owner": "Alexey-T",
-    "rev": "2022.04.11",
-    "sha256": "sha256-CoNjxQSQJhtVvvO9fJBGmfjbWhwZJ31Jk0YcISKqKiU="
+    "rev": "2022.04.18",
+    "sha256": "sha256-tvFESbamCt7A6Xv8WGh0dKzr9neelYMM7guySOunfvk="
   },
   "ATSynEdit_Cmp": {
     "owner": "Alexey-T",
@@ -26,8 +26,8 @@
   },
   "EControl": {
     "owner": "Alexey-T",
-    "rev": "2022.04.11.1",
-    "sha256": "sha256-QwxnP7zY5AaMBqe2qH2l8lrfD6JQ+RNY5sucwL+o1Ts="
+    "rev": "2022.04.18",
+    "sha256": "sha256-Wp+/f/z2H/WANq9u8mRDn0BaeyFWiPpLrW0YqyT+ezw="
   },
   "ATSynEdit_Ex": {
     "owner": "Alexey-T",

pkgs/applications/editors/jupyter-kernels/octave/kernel.nix

@@ -4,20 +4,18 @@ with python3Packages;
 
 buildPythonPackage rec {
   pname = "octave-kernel";
-  version = "0.32.0";
+  version = "0.34.2";
 
   src = fetchPypi {
     pname = "octave_kernel";
     inherit version;
-    sha256 = "0dfbxfcf3bz4jswnpkibnjwlkgy0y4j563nrhaqxv3nfa65bksif";
+    sha256 = "sha256-5ki2lekfK7frPsmPBIzYQOfANCUY9x+F2ZRAQSdPTxo=";
   };
 
   propagatedBuildInputs = [ metakernel ipykernel ];
 
-  # Tests require jupyter_kernel_test to run, but it hasn't seen a
-  # release since 2017 and seems slightly abandoned.
-  # Doing fetchPypi on it doesn't work, even though it exists here:
-  # https://pypi.org/project/jupyter_kernel_test/.
+  # Tests fail because the kernel appears to be halting or failing to launch
+  # There appears to be a similar problem with metakernel's tests
   doCheck = false;
 
   meta = with lib; {

pkgs/applications/editors/mle/default.nix

@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, termbox, pcre, uthash, lua5_3 }:
+{ lib, stdenv, fetchFromGitHub, termbox, pcre, uthash, lua5_3, makeWrapper, installShellFiles }:
 
 stdenv.mkDerivation rec {
   pname = "mle";
@@ -18,12 +18,22 @@ stdenv.mkDerivation rec {
     patchShebangs tests/*
   '';
 
+  nativeBuildInputs = [ makeWrapper installShellFiles ];
+
   buildInputs = [ termbox pcre uthash lua5_3 ];
 
   doCheck = true;
 
   installFlags = [ "prefix=${placeholder "out"}" ];
 
+  postInstall = ''
+    installManPage mle.1
+  '';
+
+  postFixup = lib.optionalString stdenv.isDarwin ''
+    wrapProgram $out/bin/mle --prefix DYLD_LIBRARY_PATH : ${termbox}/lib
+  '';
+
   meta = with lib; {
     description = "Small, flexible terminal-based text editor";
     homepage = "https://github.com/adsr/mle";

pkgs/applications/editors/vscode/extensions/default.nix

@@ -1123,8 +1123,8 @@ let
         mktplcRef = {
           name = "Ionide-fsharp";
           publisher = "Ionide";
-          version = "5.10.1";
-          sha256 = "sha256-LkWWgyh4khPyUgekVeO8ZzPK+1gTrS8d9Yz6/kHomr8=";
+          version = "6.0.1";
+          sha256 = "sha256-1W1qKnjmyK80np+J6S/nku3QJGypxYnuE0BPw8Onzas=";
         };
         meta = with lib; {
           changelog = "https://marketplace.visualstudio.com/items/Ionide.Ionide-fsharp/changelog";

pkgs/applications/graphics/inkscape/default.nix

@@ -48,6 +48,7 @@ let
       lxml
       pillow
       scour
+      pyserial
     ]);
 in
 stdenv.mkDerivation rec {

pkgs/applications/misc/bottles/default.nix

@@ -21,20 +21,22 @@ in
 python3Packages.buildPythonApplication rec {
   pname = "bottles";
   version = "2022.4.14-trento-1";
-  sha256 = "16cb01fhxa64f8fadwpr0mawfmchig6xlbx20mz4q9yh5fnagywj";
-  # Note: Update via pkgs/applications/misc/bottles/update.py
-  # mostly copypasted from pkgs/applications/networking/instant-messengers/telegram/tdesktop/update.py
 
   src = fetchFromGitHub {
     owner = "bottlesdevs";
     repo = pname;
     rev = version;
-    inherit sha256;
+    sha256 = "16cb01fhxa64f8fadwpr0mawfmchig6xlbx20mz4q9yh5fnagywj";
   };
 
   postPatch = ''
     chmod +x build-aux/meson/postinstall.py
     patchShebangs build-aux/meson/postinstall.py
+
+    substituteInPlace src/backend/wine/winecommand.py \
+      --replace \
+        'self.__get_runner()' \
+        '(lambda r: (f"${steam-run}/bin/steam-run {r}", r)[r == "wine" or r == "wine64"])(self.__get_runner())'
   '';
 
   nativeBuildInputs = [
@@ -89,22 +91,10 @@ python3Packages.buildPythonApplication rec {
   strictDeps = false; # broken with gobject-introspection setup hook, see https://github.com/NixOS/nixpkgs/issues/56943
   dontWrapGApps = true; # prevent double wrapping
 
-  preConfigure = ''
-    patchShebangs build-aux/meson/postinstall.py
-    substituteInPlace src/backend/wine/winecommand.py \
-      --replace \
-        'self.__get_runner()' \
-        '(lambda r: (f"${steam-run}/bin/steam-run {r}", r)[r == "wine" or r == "wine64"])(self.__get_runner())'
-  '';
-
   preFixup = ''
     makeWrapperArgs+=("''${gappsWrapperArgs[@]}")
   '';
 
-  passthru = {
-    updateScript = ./update.py;
-  };
-
   meta = with lib; {
     description = "An easy-to-use wineprefix manager";
     homepage = "https://usebottles.com/";

pkgs/applications/misc/bottles/update.py

@@ -1,65 +0,0 @@
-#! /usr/bin/env nix-shell
-#! nix-shell -i python3 -p python3 nix nix-prefetch-git
-
-import fileinput
-import json
-import os
-import re
-import subprocess
-
-from datetime import datetime
-from urllib.request import urlopen, Request
-
-
-DIR = os.path.dirname(os.path.abspath(__file__))
-HEADERS = {'Accept': 'application/vnd.github.v3+json'}
-
-
-def github_api_request(endpoint):
-    base_url = 'https://api.github.com/'
-    request = Request(base_url + endpoint, headers=HEADERS)
-    with urlopen(request) as http_response:
-        return json.loads(http_response.read().decode('utf-8'))
-
-
-def get_commit_date(repo, sha):
-    url = f'https://api.github.com/repos/{repo}/commits/{sha}'
-    request = Request(url, headers=HEADERS)
-    with urlopen(request) as http_response:
-        commit = json.loads(http_response.read().decode())
-        date = commit['commit']['committer']['date'].rstrip('Z')
-        date = datetime.fromisoformat(date).date().isoformat()
-        return 'unstable-' + date
-
-
-def nix_prefetch_git(url, rev):
-    """Prefetches the requested Git revision (incl. submodules) of the given repository URL."""
-    print(f'nix-prefetch-git {url} {rev}')
-    out = subprocess.check_output(['nix-prefetch-git', '--quiet', '--url', url, '--rev', rev, '--fetch-submodules'])
-    return json.loads(out)['sha256']
-
-
-def nix_prefetch_url(url, unpack=False):
-    """Prefetches the content of the given URL."""
-    print(f'nix-prefetch-url {url}')
-    options = ['--type', 'sha256']
-    if unpack:
-        options += ['--unpack']
-    out = subprocess.check_output(['nix-prefetch-url'] + options + [url])
-    return out.decode('utf-8').rstrip()
-
-
-def update_file(relpath, version, sha256):
-    file_path = os.path.join(DIR, relpath)
-    with fileinput.FileInput(file_path, inplace=True) as f:
-        for line in f:
-            result = line
-            result = re.sub(r'^  version = ".+";', f'  version = "{version}";', result)
-            result = re.sub(r'^  sha256 = ".+";', f'  sha256 = "{sha256}";', result)
-            print(result, end='')
-
-
-if __name__ == "__main__":
-    bottles_version = github_api_request('repos/bottlesdevs/Bottles/releases/latest')['tag_name']
-    bottles_hash = nix_prefetch_git('https://github.com/bottlesdevs/Bottles.git', bottles_version)
-    update_file('default.nix', bottles_version, bottles_hash)

pkgs/applications/misc/copyq/default.nix

@@ -17,13 +17,13 @@
 
 mkDerivation rec {
   pname = "CopyQ";
-  version = "6.0.1";
+  version = "6.1.0";
 
   src = fetchFromGitHub {
     owner = "hluk";
     repo = "CopyQ";
     rev = "v${version}";
-    sha256 = "sha256-edrRgnjbszqJLbGLE4anCJSGApymvK0O+2ks5jWe8aw=";
+    sha256 = "sha256-2BWyLVxH50G+S/Hp8E5hWG64DcIamtZPGm0nSMwEhY4=";
   };
 
   nativeBuildInputs = [

pkgs/applications/misc/debian-goodies/default.nix

@@ -0,0 +1,70 @@
+{ lib
+, stdenv
+, fetchFromGitLab
+, curl
+, dialog
+, installShellFiles
+, perl
+, python3
+}:
+
+stdenv.mkDerivation rec {
+  pname = "debian-goodies";
+  version = "0.87";
+
+  src = fetchFromGitLab {
+    domain = "salsa.debian.org";
+    owner = "debian";
+    repo = "debian-goodies";
+    rev = "debian/${version}";
+    sha256 = "sha256-7O2AY7tWYiOIy4ImFBxWu6S+ljc3VmqS/j4KyEzVVIA=";
+  };
+
+  postPatch = ''
+    substituteInPlace debmany/debmany \
+      --replace "/usr/bin/dialog" "${dialog}/bin/dialog" \
+      --replace "/usr/bin/whiptail" "${python3.pkgs.snack}/bin/whiptail"
+
+    substituteInPlace dman \
+      --replace "curl" "${curl}/bin/curl"
+  '';
+
+  nativeBuildInputs = [
+    installShellFiles
+  ];
+
+  buildInputs = [
+    perl
+    python3
+  ];
+
+  installPhase = ''
+    runHook preInstall
+
+    # see https://salsa.debian.org/debian/debian-goodies/-/blob/master/debian/install
+    for bin in checkrestart dgrep dglob debget dpigs debman dman popbugs which-pkg-broke which-pkg-broke-build dhomepage debmany/debmany check-enhancements find-dbgsym-packages; do
+      install -Dm755 $bin -t $out/bin
+    done
+
+    install -Dm644 find-dbgsym-packages-templates/* -t $out/share/debian-goodies/find-dbgsym-packages-templates/
+
+    installShellCompletion --bash \
+      debmany/bash_completion/debmany \
+      debian/bash-completion
+
+    installManPage \
+      *.1 \
+      debmany/man/*.1 \
+      *.8
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Small toolbox-style utilities for Debian systems";
+    homepage = "https://salsa.debian.org/debian/debian-goodies";
+    license = licenses.gpl2Plus;
+    platforms = platforms.unix;
+    maintainers = with maintainers; [ SuperSandro2000 ];
+  };
+}

pkgs/applications/misc/hello/default.nix

@@ -3,7 +3,7 @@
 , fetchurl
 , nixos
 , testVersion
-, testEqualDerivation
+, testers
 , hello
 }:
 
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
     version = testVersion { package = hello; };
 
     invariant-under-noXlibs =
-      testEqualDerivation
+      testers.testEqualDerivation
         "hello must not be rebuilt when environment.noXlibs is set."
         hello
         (nixos { environment.noXlibs = true; }).pkgs.hello;

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

@@ -61,6 +61,13 @@ let
     url = "https://chromium.googlesource.com/chromium/tools/build/+/e77882e0dde52c2ccf33c5570929b75b4a2a2522/recipes/recipe_modules/chromium/resources/clang-format?format=TEXT";
     sha256 = "0ic3hn65dimgfhakli1cyf9j3cxcqsf1qib706ihfhmlzxf7256l";
   };
+  # https://webrtc-review.googlesource.com/c/src/+/255601
+  webrtcWaylandScreenshareCoredumpFix = fetchurl {
+    # PipeWire capturer: check existence of cursor metadata
+    name = "webrtc-wayland-screenshare-coredump-fix.patch";
+    url = "https://webrtc-review.googlesource.com/changes/src~255601/revisions/2/patch?download";
+    hash = "sha256-PHGwEoYhMa+ZL2ner10FwdGUWUxsVr+HWuZOAEugYDY=";
+  };
 
   # The additional attributes for creating derivations based on the chromium
   # source tree.
@@ -162,7 +169,9 @@ let
       ./patches/widevine-79.patch
     ];
 
-    postPatch = ''
+    postPatch = optionalString (versionRange "100" "101") ''
+      base64 --decode ${webrtcWaylandScreenshareCoredumpFix} | patch -p1 -d third_party/webrtc
+    '' + ''
       # remove unused third-party
       for lib in ${toString gnSystemLibraries}; do
         if [ -d "third_party/$lib" ]; then

pkgs/applications/networking/cluster/fluxcd/default.nix

@@ -1,9 +1,9 @@
 { lib, buildGoModule, fetchFromGitHub, fetchzip, installShellFiles }:
 
 let
-  version = "0.28.5";
-  sha256 = "11k8sb8pjhrg8ar256rfdw736cg32m6n8xcfhyqc3r4pkj3ksli8";
-  manifestsSha256 = "1gjya8xcmx065ywx7bc2xdsp3qj2y47b7l1dlr4y0hzp19pclmcw";
+  version = "0.29.1";
+  sha256 = "0sqavlylkbcgk9yfblh85rfi3lxv23rlcrq8cw1ikn832gncg7dk";
+  manifestsSha256 = "1ph0qbjc1l3h5n0myza3dw71x30iva34nx6f7vfiy8fpapcf1qbi";
 
   manifests = fetchzip {
     url =
@@ -23,7 +23,7 @@ in buildGoModule rec {
     inherit sha256;
   };
 
-  vendorSha256 = "sha256-kxI2sOaY66XLIRMT1l3VLQh1XR4nvvsYvsdZbVLxbHM=";
+  vendorSha256 = "sha256-v208yuWWPzLxrbkgXikE2PiFv9NXNEG4K1zrLHyaleI=";
 
   postUnpack = ''
     cp -r ${manifests} source/cmd/flux/manifests

pkgs/applications/networking/cluster/terraform/default.nix

@@ -192,9 +192,9 @@ rec {
   };
 
   terraform_1 = mkTerraform {
-    version = "1.1.8";
-    sha256 = "sha256-U3RuLnDQD1EbPZG/wPuVMbSKmR3EqspkoK0Ky8aZb7k=";
-    vendorSha256 = "sha256-Jy9o0O80OjagrHG25CSPblI49zKx0N8pwvEotk9qm3s=";
+    version = "1.1.9";
+    sha256 = "sha256-6dyP3Y5cK+/qLoC2QPZW3QNgqOeVXegC06Pa7pSv1iE=";
+    vendorSha256 = "sha256-YI/KeoOIxgCAS3Q6SXaW8my0PyFD+pyksshQEAknsz4=";
     patches = [ ./provider-path-0_15.patch ];
     passthru = { inherit plugins; };
   };

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

@@ -3,10 +3,10 @@
 mkFranzDerivation rec {
   pname = "franz";
   name = "Franz";
-  version = "5.6.1";
+  version = "5.9.2";
   src = fetchurl {
     url = "https://github.com/meetfranz/franz/releases/download/v${version}/franz_${version}_amd64.deb";
-    sha256 = "1gn0n1hr6z2gsdnpxysyq6sm8y7cjr9jafhsam8ffw0bq74kph7p";
+    sha256 = "sha256-W/60g5CbSUZcNASjdbiS7DNv9375GiesEG60QLLAh1g=";
   };
   meta = with lib; {
     description = "A free messaging app that combines chat & messaging services into one application";

pkgs/applications/science/logic/isabelle/default.nix

@@ -1,7 +1,33 @@
-{ lib, stdenv, fetchurl, coreutils, nettools, java, scala, polyml, z3, veriT, vampire, eprover-ho, naproche, rlwrap, perl, makeDesktopItem, isabelle-components, isabelle, symlinkJoin }:
+{ lib, stdenv, fetchurl, coreutils, nettools, java, scala, polyml, z3, veriT, vampire, eprover-ho, naproche, rlwrap, perl, makeDesktopItem, isabelle-components, isabelle, symlinkJoin, fetchhg }:
 # nettools needed for hostname
 
-stdenv.mkDerivation rec {
+let
+  sha1 = stdenv.mkDerivation {
+    pname = "isabelle-sha1";
+    version = "2021-1";
+
+    src = fetchhg {
+      url = "https://isabelle.sketis.net/repos/sha1";
+      rev = "e0239faa6f42";
+      sha256 = "sha256-4sxHzU/ixMAkSo67FiE6/ZqWJq9Nb9OMNhMoXH2bEy4=";
+    };
+
+    buildPhase = (if stdenv.isDarwin then ''
+      LDFLAGS="-dynamic -undefined dynamic_lookup -lSystem"
+    '' else ''
+      LDFLAGS="-fPIC -shared"
+    '') + ''
+      CFLAGS="-fPIC -I."
+      $CC $CFLAGS -c sha1.c -o sha1.o
+      $LD $LDFLAGS sha1.o -o libsha1.so
+    '';
+
+    installPhase = ''
+      mkdir -p $out/lib
+      cp libsha1.so $out/lib/
+    '';
+  };
+in stdenv.mkDerivation rec {
   pname = "isabelle";
   version = "2021-1";
 
@@ -82,6 +108,9 @@ stdenv.mkDerivation rec {
       --replace 'cmd.add("/usr/bin/env");' "" \
       --replace 'cmd.add("bash");' "cmd.add(\"$SHELL\");"
 
+    substituteInPlace src/Pure/General/sha1.ML \
+      --replace '"$ML_HOME/" ^ (if ML_System.platform_is_windows then "sha1.dll" else "libsha1.so")' '"${sha1}/lib/libsha1.so"'
+
     rm -r heaps
   '' + (if ! stdenv.isLinux then "" else ''
     arch=${if stdenv.hostPlatform.system == "x86_64-linux" then "x86_64-linux" else "x86-linux"}

pkgs/applications/science/logic/naproche/default.nix

@@ -2,13 +2,13 @@
 
 with haskellPackages; mkDerivation {
   pname = "Naproche-SAD";
-  version = "0.1.0.0";
+  version = "2022-04-19";
 
   src = fetchFromGitHub {
     owner = "naproche";
     repo = "naproche";
-    rev = "d39cea85ace04d5b3775fde9972a33886799bfe6";
-    sha256 = "1zqrldmxkzbyg9bssrbwb00zic29904igcipaz1m9al0456yjnkf";
+    rev = "2514c04e715395b7a839e11b63046eafb9c6a1da";
+    sha256 = "1bdgyk4fk65xi7n778rbgddpg4zhggj8wjslxbizrzi81my9a3vm";
   };
 
   isExecutable = true;

pkgs/applications/virtualization/qemu/allow-virtfs-on-darwin.patch

@@ -1,77 +0,0 @@
-From 4ca09b7cd1d42eb6b1587fed74cd4d684e31bfbe Mon Sep 17 00:00:00 2001
-From: Keno Fischer <keno@juliacomputing.com>
-Date: Sun, 27 Feb 2022 17:35:22 -0500
-Subject: [PATCH] 9p: darwin: meson: Allow VirtFS on Darwin
-
-To allow VirtFS on darwin, we need to check that pthread_fchdir_np is
-available, which has only been available since macOS 10.12.
-
-Additionally, virtfs_proxy_helper is disabled on Darwin. This patch
-series does not currently provide an implementation of the proxy-helper,
-but this functionality could be implemented later on.
-
-Signed-off-by: Keno Fischer <keno@juliacomputing.com>
-[Michael Roitzsch: - Rebase for NixOS]
-Signed-off-by: Michael Roitzsch <reactorcontrol@icloud.com>
-[Will Cohen: - Rebase to master]
-Signed-off-by: Will Cohen <wwcohen@gmail.com>
-Reviewed-by: Paolo Bonzini <pbonzini@redhat.com>
-[Will Cohen: - Add check for pthread_fchdir_np to virtfs
-             - Add comments to patch commit
-             - Note that virtfs_proxy_helper does not work
-               on macOS
-             - Fully adjust meson virtfs error note to specify
-               macOS
-             - Rebase to master]
-Signed-off-by: Will Cohen <wwcohen@gmail.com>
-Message-Id: <20220227223522.91937-12-wwcohen@gmail.com>
-Signed-off-by: Christian Schoenebeck <qemu_oss@crudebyte.com>
-Acked-by: Christian Schoenebeck <qemu_oss@crudebyte.com>
----
- fsdev/meson.build |  1 +
- meson.build       | 17 +++++++++++------
- 2 files changed, 12 insertions(+), 6 deletions(-)
-
-diff --git a/fsdev/meson.build b/fsdev/meson.build
-index adf57cc43e..b632b66348 100644
---- a/fsdev/meson.build
-+++ b/fsdev/meson.build
-@@ -7,6 +7,7 @@ fsdev_ss.add(when: ['CONFIG_FSDEV_9P'], if_true: files(
-   'qemu-fsdev.c',
- ), if_false: files('qemu-fsdev-dummy.c'))
- softmmu_ss.add_all(when: 'CONFIG_LINUX', if_true: fsdev_ss)
-+softmmu_ss.add_all(when: 'CONFIG_DARWIN', if_true: fsdev_ss)
- 
- if have_virtfs_proxy_helper
-   executable('virtfs-proxy-helper',
-diff --git a/meson.build b/meson.build
-index 2265fa409a..6d73c02903 100644
---- a/meson.build
-+++ b/meson.build
-@@ -1383,12 +1383,17 @@ endif
- have_host_block_device = (targetos != 'darwin' or
-     cc.has_header('IOKit/storage/IOMedia.h'))
- 
--have_virtfs = (targetos == 'linux' and
--    have_system and
--    libattr.found() and
--    libcap_ng.found())
--
--have_virtfs_proxy_helper = have_virtfs and have_tools
-+have_virtfs = get_option('virtfs') \
-+    .require(targetos == 'linux' or targetos == 'darwin',
-+             error_message: 'virtio-9p (virtfs) requires Linux or macOS') \
-+    .require(targetos == 'linux' or cc.has_function('pthread_fchdir_np'),
-+             error_message: 'virtio-9p (virtfs) on macOS requires the presence of pthread_fchdir_np') \
-+    .require(targetos == 'darwin' or (libattr.found() and libcap_ng.found()),
-+             error_message: 'virtio-9p (virtfs) on Linux requires libcap-ng-devel and libattr-devel') \
-+    .disable_auto_if(not have_tools and not have_system) \
-+    .allowed()
-+
-+have_virtfs_proxy_helper = targetos != 'darwin' and have_virtfs and have_tools
- 
- if get_option('virtfs').enabled()
-   if not have_virtfs
--- 
-2.35.1
-

pkgs/applications/virtualization/qemu/default.nix

@@ -4,6 +4,7 @@
 , makeWrapper, runtimeShell, removeReferencesTo
 , attr, libcap, libcap_ng, socat
 , CoreServices, Cocoa, Hypervisor, rez, setfile
+, guestAgentSupport ? with stdenv.hostPlatform; isLinux || isSunOS || isWindows
 , numaSupport ? stdenv.isLinux && !stdenv.isAarch32, numactl
 , seccompSupport ? stdenv.isLinux, libseccomp
 , alsaSupport ? lib.hasSuffix "linux" stdenv.hostPlatform.system && !nixosTestRunner
@@ -40,11 +41,11 @@ stdenv.mkDerivation rec {
     + lib.optionalString xenSupport "-xen"
     + lib.optionalString hostCpuOnly "-host-cpu-only"
     + lib.optionalString nixosTestRunner "-for-vm-tests";
-  version = "6.2.0";
+  version = "7.0.0";
 
   src = fetchurl {
     url= "https://download.qemu.org/qemu-${version}.tar.xz";
-    sha256 = "0iavlsy9hin8k38230j8lfmyipx3965zljls1dp34mmc8n75vqb8";
+    sha256 = "sha256-9rN1x5UfcoQCeYsLqrsthkeMpT1Eztvvq74cRr9G+Dk=";
   };
 
   depsBuildBuild = [ buildPackages.stdenv.cc ];
@@ -82,80 +83,26 @@ stdenv.mkDerivation rec {
 
   dontUseMesonConfigure = true; # meson's configurePhase isn't compatible with qemu build
 
-  outputs = [ "out" "ga" ];
+  outputs = [ "out" ] ++ lib.optional guestAgentSupport "ga";
   # On aarch64-linux we would shoot over the Hydra's 2G output limit.
   separateDebugInfo = !(stdenv.isAarch64 && stdenv.isLinux);
 
   patches = [
     ./fix-qemu-ga.patch
-    # MTP Devices were broken in QEMU 6.1.0, this patch fixes that.
-     (fetchpatch {
-       url = "https://gitlab.com/qemu-project/qemu/-/commit/9d30c78c7d3b994825cbe63fa277279ae3ef4248.patch";
-       sha256 = "sha256-AChB9HMEShrM+2UW2aOT9+MqlAm568sG3HxHK3nDC/M=";
-     })
-    # Cocoa clipboard support only works on macOS 10.14+
-    (fetchpatch {
-      url = "https://gitlab.com/qemu-project/qemu/-/commit/7e3e20d89129614f4a7b2451fe321cc6ccca3b76.diff";
-      sha256 = "09xz06g57wxbacic617pq9c0qb7nly42gif0raplldn5lw964xl2";
-      revert = true;
-    })
-    # 9p-darwin for 7.0 backported to 6.2.0
-    #
-    # Can generally be removed when updating derivation to 7.0. Nine of the
-    # patches can be drawn directly from QEMU upstream, but the second commit
-    # and the eleventh commit had to be modified when rebasing back to 6.2.0.
-    (fetchpatch {
-      url = "https://gitlab.com/qemu-project/qemu/-/commit/e0bd743bb2dd4985791d4de880446bdbb4e04fed.patch";
-      sha256 = "sha256-c6QYL3zig47fJwm6rqkqGp3E1PakVTaihvXDRebbBlQ=";
-    })
-    ./rename-9p-util.patch
-    (fetchpatch {
-      url = "https://gitlab.com/qemu-project/qemu/-/commit/f41db099c71151291c269bf48ad006de9cbd9ca6.patch";
-      sha256 = "sha256-70/rrhZw+02JJbJ3CoW8B1GbdM4Lwb2WkUdwstYAoIQ=";
-    })
-    (fetchpatch {
-      url = "https://gitlab.com/qemu-project/qemu/-/commit/6b3b279bd670c6a2fa23c9049820c814f0e2c846.patch";
-      sha256 = "sha256-7WqklSvLirEuxTXTIMQDQhWpXnwMseJ1RumT+faq/Y8=";
-    })
-    (fetchpatch {
-      url = "https://gitlab.com/qemu-project/qemu/-/commit/67a71e3b71a2834d028031a92e76eb9444e423c6.patch";
-      sha256 = "sha256-COFm/SwfJSoSl9YDpL6ceAE8CcE4mGhsGxw1HMuL++o=";
-    })
-    (fetchpatch {
-      url = "https://gitlab.com/qemu-project/qemu/-/commit/38d7fd68b0c8775b5253ab84367419621aa032e6.patch";
-      sha256 = "sha256-iwGIzq9FWW6zpbDg/IKrp5OZpK9cgQqTRWWq8WBIHRQ=";
-    })
-    (fetchpatch {
-      url = "https://gitlab.com/qemu-project/qemu/-/commit/57b3910bc3513ab515296692daafd1c546f3c115.patch";
-      sha256 = "sha256-ybl9+umZAcQKHYL7NkGJQC0W7bccTagA9KQiFaR2LYA=";
-    })
-    (fetchpatch {
-      url = "https://gitlab.com/qemu-project/qemu/-/commit/b5989326f558faedd2511f29459112cced2ca8f5.patch";
-      sha256 = "sha256-s+O9eCgj2Ev+INjL9LY9MJBdISIdZLslI3lue2DICGM=";
-    })
-    (fetchpatch {
-      url = "https://gitlab.com/qemu-project/qemu/-/commit/029ed1bd9defa33a80bb40cdcd003699299af8db.patch";
-      sha256 = "sha256-mGqcRWcEibDJdhTRrN7ZWrMuCfUWW8vWiFj7sb2/RYo=";
-    })
-    (fetchpatch {
-      url = "https://gitlab.com/qemu-project/qemu/-/commit/d3671fd972cd185a6923433aa4802f54d8b62112.patch";
-      sha256 = "sha256-GUh5o7mbFTm/dm6CqcGdoMlC+YrV8RlcEwu/mxrfTzo=";
-    })
-    # The next two commits are to make Linux v5.17 work on aarch64-darwin. These are included in QEMU v7.
-    (fetchpatch {
-      url = "https://gitlab.com/qemu-project/qemu/-/commit/ad99f64f1cfff7c5e7af0e697523d9b7e45423b6.patch";
-      sha256 = "sha256-e6WtfQIPEiXhWucd5ab7UIoccbWEAv3bwksn4hR85CY=";
-    })
-    (fetchpatch {
-      url = "https://gitlab.com/qemu-project/qemu/-/commit/7f6c295cdfeaa229c360cac9a36e4e595aa902ae.patch";
-      sha256 = "sha256-mORtgfU1CYQFKO5UrXgM9cJyZxeF2bz8iAoq0UlFQeY=";
-    })
-    ./allow-virtfs-on-darwin.patch
+
     # QEMU upstream does not demand compatibility to pre-10.13, so 9p-darwin
     # support on nix requires utimensat fallback. The patch adding this fallback
     # set was removed during the process of upstreaming this functionality, and
     # will still be needed in nix until the macOS SDK reaches 10.13+.
     ./provide-fallback-for-utimensat.patch
+    # Cocoa clipboard support only works on macOS 10.14+
+    ./revert-ui-cocoa-add-clipboard-support.patch
+    # Standard about panel requires AppKit and macOS 10.13+
+    (fetchpatch {
+      url = "https://gitlab.com/qemu-project/qemu/-/commit/99eb313ddbbcf73c1adcdadceba1423b691c6d05.diff";
+      sha256 = "sha256-gTRf9XENAfbFB3asYCXnw4OV4Af6VE1W56K2xpYDhgM=";
+      revert = true;
+    })
   ]
     ++ lib.optional nixosTestRunner ./force-uid0-on-9p.patch;
 
@@ -194,7 +141,6 @@ stdenv.mkDerivation rec {
     "--disable-strip" # We'll strip ourselves after separating debug info.
     "--enable-docs"
     "--enable-tools"
-    "--enable-guest-agent"
     "--localstatedir=/var"
     "--sysconfdir=/etc"
     # Always use our Meson, not the bundled version, which doesn't
@@ -202,6 +148,7 @@ stdenv.mkDerivation rec {
     "--meson=meson"
     "--cross-prefix=${stdenv.cc.targetPrefix}"
     "--cpu=${stdenv.hostPlatform.uname.processor}"
+    (lib.enableFeature guestAgentSupport "guest-agent")
   ] ++ lib.optional numaSupport "--enable-numa"
     ++ lib.optional seccompSupport "--enable-seccomp"
     ++ lib.optional smartcardSupport "--enable-smartcard"
@@ -233,7 +180,7 @@ stdenv.mkDerivation rec {
   postFixup = ''
     # the .desktop is both invalid and pointless
     rm -f $out/share/applications/qemu.desktop
-
+  '' + lib.optionalString guestAgentSupport ''
     # move qemu-ga (guest agent) to separate output
     mkdir -p $ga/bin
     mv $out/bin/qemu-ga $ga/bin/

pkgs/applications/virtualization/qemu/provide-fallback-for-utimensat.patch

@@ -1,4 +1,4 @@
-From 70328c307001f4bb75d30d93c5bba3c3cd790c88 Mon Sep 17 00:00:00 2001
+From 747a741772cde6bb340eb8bdb493390280de8d16 Mon Sep 17 00:00:00 2001
 From: Keno Fischer <keno@juliacomputing.com>
 Date: Sat, 16 Jun 2018 20:56:54 -0400
 Subject: [PATCH] 9p: darwin: Provide fallback impl for utimensat
@@ -160,7 +160,7 @@ index db451b0784..320697f347 100644
 +    return utimensat(dirfd, filename, times, AT_SYMLINK_NOFOLLOW);
 +}
 diff --git a/hw/9pfs/9p-util.h b/hw/9pfs/9p-util.h
-index 1f74d37558..a4b002d1b5 100644
+index 97e681e167..fd50d6243a 100644
 --- a/hw/9pfs/9p-util.h
 +++ b/hw/9pfs/9p-util.h
 @@ -36,6 +36,12 @@ static inline int qemu_lsetxattr(const char *path, const char *name,
@@ -176,14 +176,14 @@ index 1f74d37558..a4b002d1b5 100644
  static inline void close_preserve_errno(int fd)
  {
      int serrno = errno;
-@@ -96,6 +102,8 @@ ssize_t flistxattrat_nofollow(int dirfd, const char *filename,
+@@ -98,6 +104,8 @@ ssize_t flistxattrat_nofollow(int dirfd, const char *filename,
                                char *list, size_t size);
  ssize_t fremovexattrat_nofollow(int dirfd, const char *filename,
                                  const char *name);
 +int utimensat_nofollow(int dirfd, const char *filename,
 +                       const struct timespec times[2]);
  
- /**
+ /*
   * Darwin has d_seekoff, which appears to function similarly to d_off.
 -- 
 2.35.1

pkgs/applications/virtualization/qemu/rename-9p-util.patch

@@ -1,54 +0,0 @@
-From 011b121d7f84c8974f03a81582cf1107249245bb Mon Sep 17 00:00:00 2001
-From: Keno Fischer <keno@juliacomputing.com>
-Date: Sun, 27 Feb 2022 17:35:13 -0500
-Subject: [PATCH] 9p: Rename 9p-util -> 9p-util-linux
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-The current file only has the Linux versions of these functions.
-Rename the file accordingly and update the Makefile to only build
-it on Linux. A Darwin version of these will follow later in the
-series.
-
-Signed-off-by: Keno Fischer <keno@juliacomputing.com>
-[Michael Roitzsch: - Rebase for NixOS]
-Signed-off-by: Michael Roitzsch <reactorcontrol@icloud.com>
-Signed-off-by: Will Cohen <wwcohen@gmail.com>
-Reviewed-by: Greg Kurz <groug@kaod.org>
-Reviewed-by: Philippe Mathieu-Daudé <f4bug@amsat.org>
-Message-Id: <20220227223522.91937-3-wwcohen@gmail.com>
-Signed-off-by: Christian Schoenebeck <qemu_oss@crudebyte.com>
----
- hw/9pfs/{9p-util.c => 9p-util-linux.c} | 0
- hw/9pfs/meson.build                    | 2 +-
- 2 files changed, 1 insertion(+), 1 deletion(-)
- rename hw/9pfs/{9p-util.c => 9p-util-linux.c} (100%)
-
-diff --git a/hw/9pfs/9p-util.c b/hw/9pfs/9p-util-linux.c
-similarity index 100%
-rename from hw/9pfs/9p-util.c
-rename to hw/9pfs/9p-util-linux.c
-diff --git a/hw/9pfs/meson.build b/hw/9pfs/meson.build
-index 99be5d9119..1b28e70040 100644
---- a/hw/9pfs/meson.build
-+++ b/hw/9pfs/meson.build
-@@ -4,7 +4,6 @@ fs_ss.add(files(
-   '9p-posix-acl.c',
-   '9p-proxy.c',
-   '9p-synth.c',
--  '9p-util.c',
-   '9p-xattr-user.c',
-   '9p-xattr.c',
-   '9p.c',
-@@ -14,6 +13,7 @@ fs_ss.add(files(
-   'coth.c',
-   'coxattr.c',
- ))
-+fs_ss.add(when: 'CONFIG_LINUX', if_true: files('9p-util-linux.c'))
- fs_ss.add(when: 'CONFIG_XEN', if_true: files('xen-9p-backend.c'))
- softmmu_ss.add_all(when: 'CONFIG_FSDEV_9P', if_true: fs_ss)
- 
--- 
-2.35.1
-

pkgs/applications/virtualization/qemu/revert-ui-cocoa-add-clipboard-support.patch

@@ -0,0 +1,208 @@
+From 19b0952b36b6b5c4bd2665cc0bd4e55a85f81b55 Mon Sep 17 00:00:00 2001
+From: Will Cohen <willcohen@users.noreply.github.com>
+Date: Tue, 29 Mar 2022 14:00:56 -0400
+Subject: [PATCH] Revert "ui/cocoa: Add clipboard support"
+
+This reverts commit 7e3e20d89129614f4a7b2451fe321cc6ccca3b76.
+---
+ include/ui/clipboard.h |   2 +-
+ ui/clipboard.c         |   2 +-
+ ui/cocoa.m             | 121 -----------------------------------------
+ 3 files changed, 2 insertions(+), 123 deletions(-)
+
+diff --git a/include/ui/clipboard.h b/include/ui/clipboard.h
+index ce76aa451f..c4e1dc4ff4 100644
+--- a/include/ui/clipboard.h
++++ b/include/ui/clipboard.h
+@@ -269,7 +269,7 @@ void qemu_clipboard_set_data(QemuClipboardPeer *peer,
+                              QemuClipboardInfo *info,
+                              QemuClipboardType type,
+                              uint32_t size,
+-                             const void *data,
++                             void *data,
+                              bool update);
+ 
+ G_DEFINE_AUTOPTR_CLEANUP_FUNC(QemuClipboardInfo, qemu_clipboard_info_unref)
+diff --git a/ui/clipboard.c b/ui/clipboard.c
+index 9079ef829b..6b9ed59e1b 100644
+--- a/ui/clipboard.c
++++ b/ui/clipboard.c
+@@ -140,7 +140,7 @@ void qemu_clipboard_set_data(QemuClipboardPeer *peer,
+                              QemuClipboardInfo *info,
+                              QemuClipboardType type,
+                              uint32_t size,
+-                             const void *data,
++                             void *data,
+                              bool update)
+ {
+     if (!info ||
+diff --git a/ui/cocoa.m b/ui/cocoa.m
+index c4e5468f9e..cd3bdf0cec 100644
+--- a/ui/cocoa.m
++++ b/ui/cocoa.m
+@@ -28,7 +28,6 @@
+ #include <crt_externs.h>
+ 
+ #include "qemu-common.h"
+-#include "ui/clipboard.h"
+ #include "ui/console.h"
+ #include "ui/input.h"
+ #include "ui/kbd-state.h"
+@@ -107,10 +106,6 @@ static void cocoa_switch(DisplayChangeListener *dcl,
+ static QemuSemaphore app_started_sem;
+ static bool allow_events;
+ 
+-static NSInteger cbchangecount = -1;
+-static QemuClipboardInfo *cbinfo;
+-static QemuEvent cbevent;
+-
+ // Utility functions to run specified code block with iothread lock held
+ typedef void (^CodeBlock)(void);
+ typedef bool (^BoolCodeBlock)(void);
+@@ -1805,105 +1800,6 @@ static void addRemovableDevicesMenuItems(void)
+     qapi_free_BlockInfoList(pointerToFree);
+ }
+ 
+-@interface QemuCocoaPasteboardTypeOwner : NSObject<NSPasteboardTypeOwner>
+-@end
+-
+-@implementation QemuCocoaPasteboardTypeOwner
+-
+-- (void)pasteboard:(NSPasteboard *)sender provideDataForType:(NSPasteboardType)type
+-{
+-    if (type != NSPasteboardTypeString) {
+-        return;
+-    }
+-
+-    with_iothread_lock(^{
+-        QemuClipboardInfo *info = qemu_clipboard_info_ref(cbinfo);
+-        qemu_event_reset(&cbevent);
+-        qemu_clipboard_request(info, QEMU_CLIPBOARD_TYPE_TEXT);
+-
+-        while (info == cbinfo &&
+-               info->types[QEMU_CLIPBOARD_TYPE_TEXT].available &&
+-               info->types[QEMU_CLIPBOARD_TYPE_TEXT].data == NULL) {
+-            qemu_mutex_unlock_iothread();
+-            qemu_event_wait(&cbevent);
+-            qemu_mutex_lock_iothread();
+-        }
+-
+-        if (info == cbinfo) {
+-            NSData *data = [[NSData alloc] initWithBytes:info->types[QEMU_CLIPBOARD_TYPE_TEXT].data
+-                                           length:info->types[QEMU_CLIPBOARD_TYPE_TEXT].size];
+-            [sender setData:data forType:NSPasteboardTypeString];
+-            [data release];
+-        }
+-
+-        qemu_clipboard_info_unref(info);
+-    });
+-}
+-
+-@end
+-
+-static QemuCocoaPasteboardTypeOwner *cbowner;
+-
+-static void cocoa_clipboard_notify(Notifier *notifier, void *data);
+-static void cocoa_clipboard_request(QemuClipboardInfo *info,
+-                                    QemuClipboardType type);
+-
+-static QemuClipboardPeer cbpeer = {
+-    .name = "cocoa",
+-    .notifier = { .notify = cocoa_clipboard_notify },
+-    .request = cocoa_clipboard_request
+-};
+-
+-static void cocoa_clipboard_update_info(QemuClipboardInfo *info)
+-{
+-    if (info->owner == &cbpeer || info->selection != QEMU_CLIPBOARD_SELECTION_CLIPBOARD) {
+-        return;
+-    }
+-
+-    if (info != cbinfo) {
+-        NSAutoreleasePool * pool = [[NSAutoreleasePool alloc] init];
+-        qemu_clipboard_info_unref(cbinfo);
+-        cbinfo = qemu_clipboard_info_ref(info);
+-        cbchangecount = [[NSPasteboard generalPasteboard] declareTypes:@[NSPasteboardTypeString] owner:cbowner];
+-        [pool release];
+-    }
+-
+-    qemu_event_set(&cbevent);
+-}
+-
+-static void cocoa_clipboard_notify(Notifier *notifier, void *data)
+-{
+-    QemuClipboardNotify *notify = data;
+-
+-    switch (notify->type) {
+-    case QEMU_CLIPBOARD_UPDATE_INFO:
+-        cocoa_clipboard_update_info(notify->info);
+-        return;
+-    case QEMU_CLIPBOARD_RESET_SERIAL:
+-        /* ignore */
+-        return;
+-    }
+-}
+-
+-static void cocoa_clipboard_request(QemuClipboardInfo *info,
+-                                    QemuClipboardType type)
+-{
+-    NSData *text;
+-
+-    switch (type) {
+-    case QEMU_CLIPBOARD_TYPE_TEXT:
+-        text = [[NSPasteboard generalPasteboard] dataForType:NSPasteboardTypeString];
+-        if (text) {
+-            qemu_clipboard_set_data(&cbpeer, info, type,
+-                                    [text length], [text bytes], true);
+-            [text release];
+-        }
+-        break;
+-    default:
+-        break;
+-    }
+-}
+-
+ /*
+  * The startup process for the OSX/Cocoa UI is complicated, because
+  * OSX insists that the UI runs on the initial main thread, and so we
+@@ -1938,7 +1834,6 @@ static void cocoa_clipboard_request(QemuClipboardInfo *info,
+     COCOA_DEBUG("Second thread: calling qemu_main()\n");
+     status = qemu_main(gArgc, gArgv, *_NSGetEnviron());
+     COCOA_DEBUG("Second thread: qemu_main() returned, exiting\n");
+-    [cbowner release];
+     exit(status);
+ }
+ 
+@@ -2054,18 +1949,6 @@ static void cocoa_refresh(DisplayChangeListener *dcl)
+             [cocoaView setAbsoluteEnabled:YES];
+         });
+     }
+-
+-    if (cbchangecount != [[NSPasteboard generalPasteboard] changeCount]) {
+-        qemu_clipboard_info_unref(cbinfo);
+-        cbinfo = qemu_clipboard_info_new(&cbpeer, QEMU_CLIPBOARD_SELECTION_CLIPBOARD);
+-        if ([[NSPasteboard generalPasteboard] availableTypeFromArray:@[NSPasteboardTypeString]]) {
+-            cbinfo->types[QEMU_CLIPBOARD_TYPE_TEXT].available = true;
+-        }
+-        qemu_clipboard_update(cbinfo);
+-        cbchangecount = [[NSPasteboard generalPasteboard] changeCount];
+-        qemu_event_set(&cbevent);
+-    }
+-
+     [pool release];
+ }
+ 
+@@ -2105,10 +1988,6 @@ static void cocoa_display_init(DisplayState *ds, DisplayOptions *opts)
+ 
+     // register vga output callbacks
+     register_displaychangelistener(&dcl);
+-
+-    qemu_event_init(&cbevent, false);
+-    cbowner = [[QemuCocoaPasteboardTypeOwner alloc] init];
+-    qemu_clipboard_peer_register(&cbpeer);
+ }
+ 
+ static QemuDisplay qemu_display_cocoa = {
+-- 
+2.35.1
+

pkgs/applications/virtualization/virtualbox/guest-additions/default.nix

@@ -5,13 +5,9 @@ let
   version = virtualbox.version;
   xserverVListFunc = builtins.elemAt (lib.splitVersion xorg.xorgserver.version);
 
-  # Forced to 1.18 in <nixpkgs/nixos/modules/services/x11/xserver.nix>
-  # as it even fails to build otherwise.  Still, override this even here,
-  # in case someone does just a standalone build
-  # (not via videoDrivers = ["vboxvideo"]).
-  # It's likely to work again in some future update.
-  xserverABI = let abi = xserverVListFunc 0 + xserverVListFunc 1;
-    in if abi == "119" || abi == "120" then "118" else abi;
+  # Forced to 1.18; vboxvideo doesn't seem to provide any newer ABI,
+  # and nixpkgs doesn't support older ABIs anymore.
+  xserverABI = "118";
 
   # Specifies how to patch binaries to make sure that libraries loaded using
   # dlopen are found. We grep binaries for specific library names and patch

pkgs/build-support/emacs/wrapper.nix

@@ -144,6 +144,7 @@ runCommand
           find $pkg -name "*-autoloads.el" \
               -exec echo \(load \"{}\" \'noerror \'nomessage\) \; >> $siteAutoloads
         done
+        echo "(provide 'nix-generated-autoload)" >> $siteAutoloads
 
         siteStart="$out/share/emacs/site-lisp/site-start.el"
         siteStartByteCompiled="$siteStart"c
@@ -196,12 +197,18 @@ runCommand
     # Wrap emacs and friends so they find our site-start.el before the original.
     for prog in $emacs/bin/*; do # */
       local progname=$(basename "$prog")
+      local autoloadExpression=""
       rm -f "$out/bin/$progname"
+      if [[ $progname == emacs ]]; then
+        # progs other than "emacs" do not understand the `-l` switches
+        autoloadExpression="-l cl-loaddefs -l nix-generated-autoload"
+      fi
 
       substitute ${./wrapper.sh} $out/bin/$progname \
         --subst-var-by bash ${emacs.stdenv.shell} \
         --subst-var-by wrapperSiteLisp "$deps/share/emacs/site-lisp" \
         --subst-var-by wrapperSiteLispNative "$deps/share/emacs/native-lisp:" \
+        --subst-var autoloadExpression \
         --subst-var prog
       chmod +x $out/bin/$progname
     done

pkgs/build-support/emacs/wrapper.sh

@@ -44,4 +44,4 @@ export emacsWithPackages_siteLisp=@wrapperSiteLisp@
 export EMACSNATIVELOADPATH="${newNativeLoadPath[*]}"
 export emacsWithPackages_siteLispNative=@wrapperSiteLispNative@
 
-exec @prog@ -l cl-loaddefs -l nix-generated-autoload "$@"
+exec @prog@ @autoloadExpression@ "$@"

pkgs/build-support/fetchgit/default.nix

@@ -27,6 +27,7 @@ in
 , # Impure env vars (https://nixos.org/nix/manual/#sec-advanced-attributes)
   # needed for netrcPhase
   netrcImpureEnvVars ? []
+, meta ? {}
 }:
 
 /* NOTE:
@@ -90,5 +91,5 @@ stdenvNoCC.mkDerivation {
     "GIT_PROXY_COMMAND" "NIX_GIT_SSL_CAINFO" "SOCKS_SERVER"
   ];
 
-  inherit preferLocalBuild;
+  inherit preferLocalBuild meta;
 }

pkgs/build-support/fetchurl/default.nix

@@ -160,5 +160,5 @@ stdenvNoCC.mkDerivation {
   '';
 
   inherit meta;
-  inherit passthru;
+  passthru = { inherit url; } // passthru;
 }

pkgs/build-support/setup-hooks/desktop-to-darwin-bundle.sh

@@ -163,7 +163,7 @@ convertIconTheme() {
     }
 
     iconsdir=$(getIcons "$sharePath" "apps/${iconName}" "$theme")
-    if [[ -n "$(ls -1 "$iconsdir/"*)" ]]; then
+    if [[ -n "$(ls -A1 "$iconsdir")" ]]; then
         icnsutil compose --toc "$out/${iconName}.icns" "$iconsdir/"*
     else
         echo "Warning: no icons were found. Creating an empty icon for ${iconName}.icns."
@@ -171,12 +171,32 @@ convertIconTheme() {
     fi
 }
 
+processExecFieldCodes() {
+  local -r file=$1
+  local -r execRaw=$(getDesktopParam "${file}" "Exec")
+  local -r execNoK="${execRaw/\%k/${file}}"
+  local -r execNoKC="${execNoK/\%c/$(getDesktopParam "${file}" "Name")}"
+  local -r icon=$(getDesktopParam "${file}" "Icon")
+  local -r execNoKCI="${execNoKC/\%i/${icon:+--icon }${icon}}"
+  local -r execNoKCIfu="${execNoKCI/\%[fu]/\$1}"
+  local -r exec="${execNoKCIfu/\%[FU]/\$@}"
+  if [[ "$exec" != "$execRaw" ]]; then
+    echo 1>&2 "desktopToDarwinBundle: Application bundles do not understand desktop entry field codes. Changed '$execRaw' to '$exec'."
+  fi
+  echo "$exec"
+}
+
 # For a given .desktop file, generate a darwin '.app' bundle for it.
 convertDesktopFile() {
     local -r file=$1
     local -r sharePath=$(dirname "$(dirname "$file")")
     local -r name=$(getDesktopParam "${file}" "^Name")
-    local -r exec=$(getDesktopParam "${file}" "Exec")
+    local -r macOSExec=$(getDesktopParam "${file}" "X-macOS-Exec")
+    if [[ "$macOSExec" ]]; then
+      local -r exec="$macOSExec"
+    else
+      local -r exec=$(processExecFieldCodes "${file}")
+    fi
     local -r iconName=$(getDesktopParam "${file}" "^Icon")
     local -r squircle=$(getDesktopParam "${file}" "X-macOS-SquircleIcon")
 

pkgs/build-support/testers/default.nix

@@ -0,0 +1,4 @@
+{ pkgs, lib, callPackage }:
+{
+  testEqualDerivation = callPackage ./test-equal-derivation.nix { };
+}

pkgs/data/fonts/unifont/default.nix

@@ -4,18 +4,16 @@
 
 stdenv.mkDerivation rec {
   pname = "unifont";
-  version = "14.0.02";
+  version = "14.0.03";
 
   ttf = fetchurl {
-    # Unfortunately the 14.0.02 TTF file is not available on the GNU mirror.
-    # Restore this for next version: "mirror://gnu/unifont/${pname}-${version}/${pname}-${version}.ttf";
-    url = "https://unifoundry.com/pub/unifont/${pname}-${version}/font-builds/${pname}-${version}.ttf";
-    sha256 = "1c8rdk3xg6j8lrzxddd73jppfgpk253jdkch63rr7n2d7ljp9gc3";
+    url = "mirror://gnu/unifont/${pname}-${version}/${pname}-${version}.ttf";
+    sha256 = "1qyc7nqyhjnarwgpkah52qv7hr0yfzak7084ilrj7z0nii4f5y57";
   };
 
   pcf = fetchurl {
     url = "mirror://gnu/unifont/${pname}-${version}/${pname}-${version}.pcf.gz";
-    sha256 = "0hcl1zihm91xwvh5ds01sybgs0j8zsrrhn4wlz5j6ji99rh797jr";
+    sha256 = "1sgvxpr4ydjnbk70j0lpgxz5x851lmrmxjb5x8lsz0i2hm32jdbc";
   };
 
   nativeBuildInputs = [ libfaketime fonttosfnt mkfontscale ];

pkgs/data/fonts/unifont_upper/default.nix

@@ -1,7 +1,7 @@
 { lib, fetchzip }:
 
 let
-  version = "14.0.02";
+  version = "14.0.03";
 in fetchzip rec {
   name = "unifont_upper-${version}";
 
@@ -9,7 +9,7 @@ in fetchzip rec {
 
   postFetch = "install -Dm644 $downloadedFile $out/share/fonts/truetype/unifont_upper.ttf";
 
-  sha256 = "0p1c2kkg20jqddy828yj6sxfwgv8k5gxwmg0cybalrjb0s09kcs8";
+  sha256 = "1lwx7syb9ij4dlqiiybp6xgvar2sszxphvaqh64vivzj9gp0g0ai";
 
   meta = with lib; {
     description = "Unicode font for glyphs above the Unicode Basic Multilingual Plane";

pkgs/data/misc/wireless-regdb/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "wireless-regdb";
-  version = "2021.08.28";
+  version = "2022.02.18";
 
   src = fetchurl {
     url = "https://www.kernel.org/pub/software/network/${pname}/${pname}-${version}.tar.xz";
-    sha256 = "sha256-z/NwxBDR5tMWrgp/qKxieP3x78pdPWZKynz9Kq+lREY=";
+    sha256 = "sha256-iCjCWk7iUCAEQAT1c3S7nerIUoCfrXD409AXcL+ayX8=";
   };
 
   dontBuild = true;

pkgs/development/beam-modules/erlang-ls/default.nix

@@ -1,7 +1,7 @@
 { fetchFromGitHub, fetchgit, fetchHex, rebar3Relx, buildRebar3, rebar3-proper
 , stdenv, writeScript, lib }:
 let
-  version = "0.23.1";
+  version = "0.24.0";
   owner = "erlang-ls";
   repo = "erlang_ls";
   deps = import ./rebar-deps.nix {
@@ -19,7 +19,7 @@ rebar3Relx {
   inherit version;
   src = fetchFromGitHub {
     inherit owner repo;
-    sha256 = "sha256-N0jkdzwNi9dx0dmN4qL+mb8S60OII4C/MnR/y8G3GUY=";
+    sha256 = "sha256-fKe6vsY40lexnkUP4PEsc53WFaUAw5LGLEC/zJauogg=";
     rev = version;
   };
   releaseType = "escript";

pkgs/development/compilers/cudatoolkit/versions.toml

@@ -44,16 +44,16 @@ gcc = "gcc9"
 version = "11.4.2"
 url = "https://developer.download.nvidia.com/compute/cuda/11.4.2/local_installers/cuda_11.4.2_470.57.02_linux.run"
 sha256 = "sha256-u9h8oOkT+DdFSnljZ0c1E83e9VUILk2G7Zo4ZZzIHwo="
-gcc = "gcc10" # can bump to 11 along with stdenv.cc
+gcc = "gcc11"
 
 ["11.5"]
 version = "11.5.0"
 url = "https://developer.download.nvidia.com/compute/cuda/11.5.0/local_installers/cuda_11.5.0_495.29.05_linux.run"
 sha256 = "sha256-rgoWk9lJfPPYHmlIlD43lGNpANtxyY1Y7v2sr38aHkw="
-gcc = "gcc10" # can bump to 11 along with stdenv.cc
+gcc = "gcc11"
 
 ["11.6"]
 version = "11.6.1"
 url = "https://developer.download.nvidia.com/compute/cuda/11.6.1/local_installers/cuda_11.6.1_510.47.03_linux.run"
 sha256 = "sha256-qyGa/OALdCABEyaYZvv/derQN7z8I1UagzjCaEyYTX4="
-gcc = "gcc10" # can bump to 11 along with stdenv.cc
+gcc = "gcc11"

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

@@ -6,10 +6,13 @@ with lib; mkCoqDerivation {
   owner = "uwplse";
   inherit version;
   defaultVersion = with versions; switch coq.coq-version [
+    { case = range "8.7" "8.15"; out = "20211026"; }
     { case = range "8.7" "8.14"; out = "20210524"; }
     { case = range "8.7" "8.13"; out = "20200131"; }
     { case = "8.6"; out = "20181102"; }
   ] null;
+  release."20211026".rev    = "064cc4fb2347453bf695776ed820ffb5fbc1d804";
+  release."20211026".sha256 = "sha256:13xrcyzay5sjszf5lg4s44wl9nrcz22n6gi4h95pkpj0ni5clinx";
   release."20210524".rev    = "54597d8ac7ab7dd4dae683f651237644bf77701e";
   release."20210524".sha256 = "sha256:05wb0km2jkhvi8807glxk9fi1kll4lwisiyzkxhqvymz4x6v8xqv";
   release."20200131".rev    = "fdb4ede19d2150c254f0ebcfbed4fb9547a734b0";

pkgs/development/interpreters/dart/default.nix

@@ -13,6 +13,10 @@
     version = "2.15.1";
   in
   {
+    "${version}-aarch64-darwin" = fetchurl {
+      url = "${base}/stable/release/${version}/sdk/dartsdk-macos-${aarch64}-release.zip";
+      sha256 = "sha256-DDE4DpA2m8wKkUZuQDn4NpXVvtaJ6sIHeKNjk3RbpYE=";
+    };
     "${version}-x86_64-darwin" = fetchurl {
       url = "${base}/stable/release/${version}/sdk/dartsdk-macos-${x86_64}-release.zip";
       sha256 = "sha256-s6bkwh2m5KdRr/WxWXwItO9YaDpp/HI3xjnS2UHmN+I=";
@@ -47,6 +51,7 @@ stdenv.mkDerivation {
     mkdir -p $out
     cp -R * $out/
     echo $libPath
+  '' + lib.optionalString(stdenv.isLinux) ''
     find $out/bin -executable -type f -exec patchelf --set-interpreter $(cat $NIX_CC/nix-support/dynamic-linker) {} \;
   '';
 
@@ -63,7 +68,7 @@ stdenv.mkDerivation {
       with C-style syntax. It offers compilation to JavaScript, interfaces,
       mixins, abstract classes, reified generics, and optional typing.
     '';
-    platforms = [ "x86_64-linux" "i686-linux" "aarch64-linux" "x86_64-darwin" ];
+    platforms = [ "x86_64-linux" "i686-linux" "aarch64-linux" "x86_64-darwin" "aarch64-darwin" ];
     license = licenses.bsd3;
   };
 }

pkgs/development/interpreters/luajit/2.0.nix

@@ -1,10 +1,10 @@
 { self, callPackage, lib }:
 callPackage ./default.nix {
   inherit self;
-  version = "2.0.5-2021-10-02";
-  rev = "d3294fa63b344173db68dd612c6d3801631e28d4";
+  version = "2.0.5-2022-03-13";
+  rev = "93a65d3cc263aef2d2feb3d7ff2206aca3bee17e";
   isStable = true;
-  sha256 = "0ja6x7bv3iqnf6m8xk6qp1dgan2b7mys0ff86dw671fqqrfw28fn";
+  hash = "sha256-Gp7OdfxBGkW59zxWUml2ugPABLUv2SezMiDblA/FZ7g=";
   extraMeta = { # this isn't precise but it at least stops the useless Hydra build
     platforms = with lib; filter (p: !hasPrefix "aarch64-" p)
       (platforms.linux ++ platforms.darwin);

pkgs/development/interpreters/luajit/2.1.nix

@@ -1,8 +1,8 @@
 { self, callPackage }:
 callPackage ./default.nix {
   inherit self;
-  version = "2.1.0-2021-10-27";
-  rev = "b4b2dce9fc3ffaaaede39b36d06415311e2aa516";
+  version = "2.1.0-2022-04-05";
+  rev = "5e3c45c43bb0e0f1f2917d432e9d2dba12c42a6e";
   isStable = false;
-  sha256 = "185s071aa0yffz8npgdxj7l98cs987vddb2l5pzfcdqfj41gn55q";
+  hash = "sha256-Q+34hJDgyCqmtThHbxR16Nn7zhq4Ql142No2rO57HL0=";
 }

pkgs/development/interpreters/luajit/default.nix

@@ -4,7 +4,7 @@
 , buildPackages
 , name ? "luajit-${version}"
 , isStable
-, sha256
+, hash
 , rev
 , version
 , extraMeta ? { }
@@ -46,7 +46,7 @@ stdenv.mkDerivation rec {
   src = fetchFromGitHub {
     owner = "LuaJIT";
     repo = "LuaJIT";
-    inherit sha256 rev;
+    inherit hash rev;
   };
 
   luaversion = "5.1";

pkgs/development/libraries/SDL_audiolib/default.nix

@@ -0,0 +1,53 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, cmake
+, SDL2
+, pkg-config
+}:
+
+stdenv.mkDerivation rec {
+  pname = "SDL_audiolib";
+  version = "unstable-2022-04-17";
+
+  src = fetchFromGitHub {
+    owner = "realnc";
+    repo = "SDL_audiolib";
+    rev = "908214606387ef8e49aeacf89ce848fb36f694fc";
+    sha256 = "sha256-11KkwIhG1rX7yDFSj92NJRO9L2e7XZGq2gOJ54+sN/A=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    pkg-config
+  ];
+
+  buildInputs = [
+    SDL2
+  ];
+
+  cmakeFlags = [
+    "-DUSE_RESAMP_SRC=OFF"
+    "-DUSE_RESAMP_SOXR=OFF"
+    "-DUSE_DEC_DRFLAC=OFF"
+    "-DUSE_DEC_OPENMPT=OFF"
+    "-DUSE_DEC_XMP=OFF"
+    "-DUSE_DEC_MODPLUG=OFF"
+    "-DUSE_DEC_MPG123=OFF"
+    "-DUSE_DEC_SNDFILE=OFF"
+    "-DUSE_DEC_LIBVORBIS=OFF"
+    "-DUSE_DEC_LIBOPUSFILE=OFF"
+    "-DUSE_DEC_MUSEPACK=OFF"
+    "-DUSE_DEC_FLUIDSYNTH=OFF"
+    "-DUSE_DEC_BASSMIDI=OFF"
+    "-DUSE_DEC_WILDMIDI=OFF"
+    "-DUSE_DEC_ADLMIDI=OFF"
+  ];
+
+  meta = with lib; {
+    description = "Audio decoding, resampling and mixing library for SDL";
+    homepage = "https://github.com/realnc/SDL_audiolib";
+    license = licenses.lgpl3Plus;
+    maintainers = with maintainers; [ SuperSandro2000 ];
+  };
+}

pkgs/development/libraries/aws-sdk-cpp/default.nix

@@ -1,7 +1,19 @@
-{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, curl, openssl, s2n-tls, zlib
+{ lib
+, stdenv
+, fetchFromGitHub
+, cmake
+, curl
+, openssl
+, s2n-tls
+, zlib
 , aws-crt-cpp
-, aws-c-cal, aws-c-common, aws-c-event-stream, aws-c-io, aws-checksums
-, CoreAudio, AudioToolbox
+, aws-c-cal
+, aws-c-common
+, aws-c-event-stream
+, aws-c-io
+, aws-checksums
+, CoreAudio
+, AudioToolbox
 , # Allow building a limited set of APIs, e.g. ["s3" "ec2"].
   apis ? ["*"]
 , # Whether to enable AWS' custom memory management.
@@ -18,16 +30,31 @@ in
 
 stdenv.mkDerivation rec {
   pname = "aws-sdk-cpp";
-  version = "1.9.150";
+  version = "1.9.238";
 
   src = fetchFromGitHub {
     owner = "aws";
     repo = "aws-sdk-cpp";
     rev = version;
-    sha256 = "sha256-fgLdXWQKHaCwulrw9KV3vpQ71DjnQAL4heIRW7Rk7UY=";
+    sha256 = "sha256-pEmsTfZXsvJMV79dGkjDNbUVajwyoYgzE5DCsC53pGY=";
   };
 
   postPatch = ''
+    # Missing includes for GCC11
+    sed '5i#include <thread>' -i \
+      aws-cpp-sdk-cloudfront-integration-tests/CloudfrontOperationTest.cpp \
+      aws-cpp-sdk-cognitoidentity-integration-tests/IdentityPoolOperationTest.cpp \
+      aws-cpp-sdk-dynamodb-integration-tests/TableOperationTest.cpp \
+      aws-cpp-sdk-elasticfilesystem-integration-tests/ElasticFileSystemTest.cpp \
+      aws-cpp-sdk-lambda-integration-tests/FunctionTest.cpp \
+      aws-cpp-sdk-mediastore-data-integration-tests/MediaStoreDataTest.cpp \
+      aws-cpp-sdk-queues/source/sqs/SQSQueue.cpp \
+      aws-cpp-sdk-redshift-integration-tests/RedshiftClientTest.cpp \
+      aws-cpp-sdk-s3-crt-integration-tests/BucketAndObjectOperationTest.cpp \
+      aws-cpp-sdk-s3-integration-tests/BucketAndObjectOperationTest.cpp \
+      aws-cpp-sdk-s3control-integration-tests/S3ControlTest.cpp \
+      aws-cpp-sdk-sqs-integration-tests/QueueOperationTest.cpp \
+      aws-cpp-sdk-transfer-tests/TransferTests.cpp
     # Flaky on Hydra
     rm aws-cpp-sdk-core-tests/aws/auth/AWSCredentialsProviderTest.cpp
     # Includes aws-c-auth private headers, so only works with submodule build
@@ -82,12 +109,6 @@ stdenv.mkDerivation rec {
 
   patches = [
     ./cmake-dirs.patch
-
-    # fix cmake config
-    (fetchpatch {
-      url = "https://github.com/aws/aws-sdk-cpp/commit/b102aaf5693c4165c84b616ab9ffb9edfb705239.diff";
-      sha256 = "sha256-38QBo3MEFpyHPb8jZEURRPkoeu4DqWhVeErJayiHKF0=";
-    })
   ];
 
   # Builds in 2+h with 2 cores, and ~10m with a big-parallel builder.

pkgs/development/libraries/faudio/default.nix

@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   pname = "faudio";
-  version = "21.10";
+  version = "22.02";
 
   src = fetchFromGitHub {
     owner = "FNA-XNA";
     repo = "FAudio";
     rev = version;
-    sha256 = "sha256-gh/QYH25j9A+XalW6ajRjs+yOYEfkZmw11CHjR6LK1E=";
+    sha256 = "sha256-qjXFpxoFF70aOaEq9/JfI2DtFxxHjyK2OnDaXMiqQMM=";
   };
 
   nativeBuildInputs = [cmake];

pkgs/development/libraries/gspell/default.nix

@@ -16,14 +16,14 @@
 
 stdenv.mkDerivation rec {
   pname = "gspell";
-  version = "1.9.1";
+  version = "1.10.0";
 
   outputs = [ "out" "dev" ];
   outputBin = "dev";
 
   src = fetchurl {
     url = "mirror://gnome/sources/${pname}/${lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
-    sha256 = "1pdb4gbjrs8mk6r0ipw5vxyvzav1wvkjq46kiq53r3nyznfpdfyw";
+    sha256 = "gDu4hMAhXT/SKoXX8wQjr/iNl5LwWlGZ2KSJov+q4do=";
   };
 
   patches = [

pkgs/development/libraries/qt-5/modules/qtmultimedia.nix

@@ -15,8 +15,9 @@ qtModule {
   pname = "qtmultimedia";
   qtInputs = [ qtbase qtdeclarative ];
   nativeBuildInputs = [ pkg-config ];
-  buildInputs = [ gstreamer gst-plugins-base libpulseaudio ]
-    ++ lib.optional (stdenv.isLinux) alsa-lib
+  buildInputs = [ gstreamer gst-plugins-base ]
+    # https://github.com/NixOS/nixpkgs/pull/169336 regarding libpulseaudio
+    ++ lib.optionals stdenv.isLinux [ libpulseaudio alsa-lib ]
     ++ lib.optional (lib.versionAtLeast qtbase.version "5.14.0" && stdenv.isLinux) wayland;
   outputs = [ "bin" "dev" "out" ];
   qmakeFlags = [ "GST_VERSION=1.0" ];

pkgs/development/libraries/sundials/default.nix

@@ -59,6 +59,19 @@ stdenv.mkDerivation rec {
   )]
   ;
 
+  # disable stackprotector on aarch64-darwin for now
+  # https://github.com/NixOS/nixpkgs/issues/127608
+  #
+  # build error:
+  #
+  # /private/tmp/nix-build-sundials-5.7.0.drv-0/ccD2dUtR.s:21:15: error: index must be an integer in range [-256, 255].
+  #         ldr     x0, [x0, ___stack_chk_guard];momd
+  #                          ^
+  # /private/tmp/nix-build-sundials-5.7.0.drv-0/ccD2dUtR.s:46:15: error: index must be an integer in range [-256, 255].
+  #         ldr     x0, [x0, ___stack_chk_guard];momd
+
+  hardeningDisable = lib.optionals (stdenv.isAarch64 && stdenv.isDarwin) [ "stackprotector" ];
+
   doCheck = true;
   checkTarget = "test";
 

pkgs/development/ocaml-modules/brisk-reconciler/default.nix

@@ -0,0 +1,33 @@
+{ buildDunePackage, fetchFromGitHub, lib, reason, ppxlib }:
+
+buildDunePackage rec {
+  pname = "brisk-reconciler";
+  version = "unstable-2020-12-02";
+
+  src = fetchFromGitHub {
+    owner = "briskml";
+    repo = "brisk-reconciler";
+    rev = "c9d5c4cf5dd17ff2da994de2c3b0f34c72778f70";
+    sha256 = "sha256-AAB4ZzBnwfwFXOAqX/sIT6imOl70F0YNMt96SWOOE9w=";
+  };
+
+  nativeBuildInputs = [ reason ];
+
+  buildInputs = [
+    ppxlib
+  ];
+
+  meta = with lib; {
+    description = "React.js-like reconciler implemented in OCaml/Reason";
+    longDescription = ''
+      Easily model any `tree-shaped state` with simple `stateful functions`.
+
+      Definitions:
+      * tree-shaped state: Any tree shaped-state like the DOM tree, app navigation state, or even rich text document!
+      * stateful functions: Functions that maintain state over time. Imagine that you can take any variable in your function and manage its value over the function's invocation. Now, imagine that any function invocation really creates its own "instance" of the function which will track this state separately from other invocations of this function.
+    '';
+    homepage = "https://github.com/briskml/brisk-reconciler";
+    maintainers = with maintainers; [ superherointj ];
+    license = licenses.mit;
+  };
+}

pkgs/development/ocaml-modules/ctypes/default.nix

@@ -6,13 +6,13 @@ else
 
 stdenv.mkDerivation rec {
   pname = "ocaml${ocaml.version}-ctypes";
-  version = "0.18.0";
+  version = "0.20.0";
 
   src = fetchFromGitHub {
     owner = "ocamllabs";
     repo = "ocaml-ctypes";
     rev = version;
-    sha256 = "sha256-eu5RAuPYC97IM4XUsUw3HQ1BJlEHQ+eBpsdUE6hd+Q8=";
+    sha256 = "sha256-fr60H/hiSVjEg11qM8LF1Y5CotS3FEyFdCcIh0A0uI4=";
   };
 
   nativeBuildInputs = [ pkg-config ocaml findlib ];

pkgs/development/ocaml-modules/flex/default.nix

@@ -0,0 +1,22 @@
+{ buildDunePackage, fetchFromGitHub, lib, reason }:
+
+buildDunePackage rec {
+  pname = "flex";
+  version = "unstable-2020-09-12";
+
+  src = fetchFromGitHub {
+    owner = "jordwalke";
+    repo = "flex";
+    rev = "6ff12fe4f96749ffd3c0ea3d9962742767937b4a";
+    sha256 = "sha256-GomTOdlU5ZwElKK8CM4DEMr51YDIrFKmTxUCGMLL3c4=";
+  };
+
+  nativeBuildInputs = [ reason ];
+
+  meta = with lib; {
+    description = "Native Reason implementation of CSS Flexbox layout. An Yoga project port";
+    homepage = "https://github.com/jordwalke/flex";
+    maintainers = with maintainers; [ superherointj ];
+    license = licenses.mit;
+  };
+}

pkgs/development/ocaml-modules/hacl-star/raw.nix

@@ -14,6 +14,9 @@ stdenv.mkDerivation rec {
 
   minimalOCamlVersion = "4.08";
 
+  # strictoverflow is disabled because it breaks aarch64-darwin
+  hardeningDisable = [ "strictoverflow" ];
+
   postPatch = ''
     patchShebangs ./
   '';

pkgs/development/ocaml-modules/pure-splitmix/default.nix

@@ -0,0 +1,22 @@
+{ lib, fetchFromGitHub, buildDunePackage }:
+
+buildDunePackage rec {
+  pname = "pure-splitmix";
+  version = "0.3";
+
+  src = fetchFromGitHub {
+    owner = "Lysxia";
+    repo = pname;
+    rev = version;
+    sha256 = "RUnsAB4hMV87ItCyGhc47bHGY1iOwVv9kco2HxnzqbU=";
+  };
+
+  doCheck = true;
+
+  meta = with lib; {
+    homepage = "https://github.com/Lysxia/pure-splitmix";
+    description = "Purely functional splittable PRNG";
+    license = licenses.mit;
+    maintainers = [ maintainers.ulrikstrid ];
+  };
+}

pkgs/development/ocaml-modules/toml/default.nix

@@ -4,15 +4,13 @@
 
 buildDunePackage rec {
   pname = "toml";
-  version = "6.0.0";
-
-  useDune2 = true;
+  version = "7.0.0";
 
   src = fetchFromGitHub {
     owner = "ocaml-toml";
     repo = "to.ml";
     rev = version;
-    sha256 = "08ywzqckllvwawl1wpgg7qzvx6jhq7d6vysa0d5hj7qdwq213ggm";
+    sha256 = "sha256-VEZQTFPwAGShCBGbKUiNOIY1zA/JdTpXU0ZIGNWopnQ=";
   };
 
   nativeBuildInputs = [ menhir ];

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

@@ -12,7 +12,7 @@
 
 buildPythonPackage rec {
   pname = "aiohomekit";
-  version = "0.7.16";
+  version = "0.7.17";
   format = "pyproject";
 
   disabled = pythonOlder "3.7";
@@ -20,8 +20,8 @@ buildPythonPackage rec {
   src = fetchFromGitHub {
     owner = "Jc2k";
     repo = pname;
-    rev = version;
-    sha256 = "sha256-dakxPhnI1m6KiOj6oQkfQ0UVA7NEBTHFGYnF6L6c8Ck=";
+    rev = "refs/tags/${version}";
+    sha256 = "sha256-vgRiqA3xNvuw3nIzl45RXdmcbDW6OTxvReSH5SVcNEs=";
   };
 
   nativeBuildInputs = [

pkgs/development/python-modules/cyclonedx-python-lib/default.nix

@@ -18,7 +18,7 @@
 
 buildPythonPackage rec {
   pname = "cyclonedx-python-lib";
-  version = "2.2.0";
+  version = "2.3.0";
   format = "pyproject";
 
   disabled = pythonOlder "3.9";
@@ -26,8 +26,8 @@ buildPythonPackage rec {
   src = fetchFromGitHub {
     owner = "CycloneDX";
     repo = pname;
-    rev = "v${version}";
-    hash = "sha256-QylA3bf0P65prR74H5+Sm51xWjjhOYpe4jHX7m/f6mI=";
+    rev = "refs/tags/v${version}";
+    hash = "sha256-eZy+m6AkSlZM/i64FyFL+ZgeW86MOSM6sDYPT4ckaHE=";
   };
 
   nativeBuildInputs = [

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

@@ -24,13 +24,13 @@
 
 buildPythonPackage rec {
   pname = "dragonfly";
-  version = "0.32.0";
+  version = "0.35.0";
 
   src = fetchFromGitHub {
     owner = "dictation-toolbox";
     repo = pname;
     rev = version;
-    sha256 = "BUbIhc8as/DVx8/4VeQS9emOLGcWFujNCxesSEEBqKQ=";
+    sha256 = "sha256-sqEEEr5/KG3cn4rmOGJt9zMNAjeLO6h3NJgg0EyewrM=";
   };
 
   postPatch = ''

pkgs/development/python-modules/faraday-plugins/default.nix

@@ -16,14 +16,14 @@
 
 buildPythonPackage rec {
   pname = "faraday-plugins";
-  version = "1.6.2";
+  version = "1.6.3";
   format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "infobyte";
     repo = "faraday_plugins";
-    rev = "v${version}";
-    sha256 = "sha256-1YROdQvwfV5Wp7vsNYCy2X6yR6mplunchD0U4xGUNBc=";
+    rev = "refs/tags/v${version}";
+    sha256 = "sha256-oynDX1miBvBmiN22ILQH1Q2y+PmWOfBunjZmVSnlvKk=";
   };
 
   propagatedBuildInputs = [

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

@@ -62,6 +62,11 @@ buildPythonPackage rec {
     wtf-peewee
   ];
 
+  disabledTests = [
+    # Incompatible with werkzeug 2.1
+    "test_mockview"
+  ];
+
   disabledTestPaths = [
     # Tests have additional requirements
     "flask_admin/tests/geoa/test_basic.py"

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

@@ -8,13 +8,13 @@
 
 buildPythonPackage rec {
   pname = "flask-bcrypt";
-  version = "0.7.1";
+  version = "1.0.1";
 
   src = fetchFromGitHub {
     owner = "maxcountryman";
     repo = pname;
     rev = version;
-    sha256 = "0036gag3nj7fzib23lbbpwhlrn1s0kkrfwk5pd90y4cjcfqh8z9x";
+    sha256 = "sha256-WlIholi/nzq6Ikc0LS6FhG0Q5Kz0kvvAlA2YJ7EksZ4=";
   };
 
   propagatedBuildInputs = [
@@ -23,9 +23,15 @@ buildPythonPackage rec {
   ];
 
   checkPhase = ''
-    ${python.interpreter} test_bcrypt.py
+    runHook preCheck
+    ${python.interpreter} -m unittest discover
+    runHook postCheck
   '';
 
+  pythonImportsCheck = [
+    "flask_bcrypt"
+  ];
+
   meta = with lib; {
     description = "Brcrypt hashing for Flask";
     homepage = "https://github.com/maxcountryman/flask-bcrypt";

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

@@ -1,19 +1,29 @@
-{ lib, fetchFromGitHub, buildPythonPackage, isPy3k, flask }:
+{ lib, fetchFromGitHub, buildPythonPackage, isPy3k, flask, mock, python }:
 
 buildPythonPackage rec {
   pname = "Flask-SeaSurf";
-  version = "0.3.0";
+  version = "1.1.1";
   disabled = !isPy3k;
 
   src = fetchFromGitHub {
     owner = "maxcountryman";
     repo = "flask-seasurf";
     rev = version;
-    sha256 = "02hsvppsz1d93v641f14fdnd22gbc12ilc9k9kn7wl119n5s3pd8";
+    sha256 = "sha256-L/ZUEqqHmsyXG5eShcITII36ttwQlZN5GBngo+GcCdw=";
   };
 
   propagatedBuildInputs = [ flask ];
 
+  checkInputs = [
+    mock
+  ];
+
+  checkPhase = ''
+    runHook preCheck
+    ${python.interpreter} -m unittest discover
+    runHook postCheck
+  '';
+
   pythonImportsCheck = [ "flask_seasurf" ];
 
   meta = with lib; {

pkgs/development/python-modules/flask-security-too/default.nix

@@ -43,12 +43,12 @@
 
 buildPythonPackage rec {
   pname = "flask-security-too";
-  version = "4.1.3";
+  version = "4.1.4";
 
   src = fetchPypi {
     pname = "Flask-Security-Too";
     inherit version;
-    sha256 = "sha256-mW2NKGeJpyR4Ri7m+KE3ElSg3E+P7qbzNTTCo3cskc8=";
+    sha256 = "sha256-j6My1CD+GY2InHlN0IXPcNqfq+ytdoDD3y+5s2o3WRI=";
   };
 
   propagatedBuildInputs = [
@@ -98,28 +98,6 @@ buildPythonPackage rec {
   ++ passthru.extras-require.fsqla
   ++ passthru.extras-require.mfa;
 
-  disabledTests = [
-    # flask 2.1.0 incompatibilities https://github.com/Flask-Middleware/flask-security/issues/594
-    "test_admin_setup_reset"
-    "test_authn_freshness"
-    "test_authn_freshness_nc"
-    "test_bad_sender"
-    "test_change_invalidates_auth_token"
-    "test_change_invalidates_session"
-    "test_default_authn_bp"
-    "test_default_unauthn"
-    "test_default_unauthn_bp"
-    "test_email_not_identity"
-    "test_next"
-    "test_post_security_with_application_root"
-    "test_post_security_with_application_root_and_views"
-    "test_recover_invalidates_session"
-    "test_two_factor_flag"
-    "test_unauthorized_access_with_referrer"
-    "test_verify"
-    "test_verify_link"
-    "test_view_configuration"
-  ];
 
   pythonImportsCheck = [ "flask_security" ];
 

pkgs/development/python-modules/geoalchemy2/default.nix

@@ -34,6 +34,12 @@ buildPythonPackage rec {
     pytestCheckHook
   ];
 
+  pytestFlagsArray = [
+    # tests require live postgis database
+    "--deselect=tests/test_pickle.py::TestPickle::test_pickle_unpickle"
+    "--deselect=tests/gallery/test_specific_compilation.py::test_specific_compilation"
+  ];
+
   disabledTestPaths = [
     # tests require live postgis database
     "tests/gallery/test_decipher_raster.py"
@@ -41,6 +47,11 @@ buildPythonPackage rec {
     "tests/gallery/test_summarystatsagg.py"
     "tests/gallery/test_type_decorator.py"
     "tests/test_functional.py"
+    "tests/test_functional_postgresql.py"
+  ];
+
+  pythonImportsCheck = [
+    "geoalchemy2"
   ];
 
   meta = with lib; {

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

@@ -7,13 +7,13 @@
 
 buildPythonPackage rec {
   pname = "gym";
-  version = "0.22.0";
+  version = "0.21.0";
 
   src = fetchFromGitHub {
     owner = "openai";
     repo = pname;
-    rev = version;
-    sha256 = "sha256-JbPWLuQGo+fErUlCKKpMwWdu0KvXBDuH2MeAHdJCTgM=";
+    rev = "v${version}";
+    sha256 = "12b545xz0r2g4z5r7f8amxl7nm0lqymkzwcwhg1bni9h0sxwpv6c";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/httpx-ntlm/default.nix

@@ -17,7 +17,7 @@ buildPythonPackage rec {
   src = fetchPypi {
     pname = "httpx_ntlm";
     inherit version;
-    sha256 = "sha256-pv/OxgcO0JWk2nCZp+bKlOdX7NqV6V5xZRDy5dd13qQ=";
+    hash = "sha256-pv/OxgcO0JWk2nCZp+bKlOdX7NqV6V5xZRDy5dd13qQ=";
   };
 
   propagatedBuildInputs = [
@@ -26,6 +26,12 @@ buildPythonPackage rec {
     pyspnego
   ];
 
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "pyspnego==0.3.*" "pyspnego>=0.3.*" \
+      --replace "cryptography==36.0.*" "cryptography>=36.0.*"
+  '';
+
   # https://github.com/ulodciv/httpx-ntlm/issues/5
   doCheck = false;
 

pkgs/development/python-modules/kaldi-active-grammar/default.nix

@@ -5,6 +5,7 @@
 , cmake
 , ush
 , requests
+, six
 , numpy
 , cffi
 , openfst
@@ -12,6 +13,11 @@
 , callPackage
 }:
 
+#
+# Maintainer note: only in-tree dependant is `dragonfly`, try to
+# update the two alongside eachother.
+#
+
 let
   kaldi = callPackage ./fork.nix { };
 in
@@ -48,7 +54,7 @@ buildPythonPackage rec {
 
   buildInputs = [ openfst kaldi ];
   nativeBuildInputs = [ scikit-build cmake ];
-  propagatedBuildInputs = [ ush requests numpy cffi ];
+  propagatedBuildInputs = [ ush requests numpy cffi six ];
 
   doCheck = false;  # no tests exist
 

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

@@ -0,0 +1,69 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+
+# build
+, setuptools-scm
+
+# propagates
+, azure-storage-blob
+, boto3
+, requests
+
+# tests
+, responses
+, python
+}:
+
+buildPythonPackage rec {
+    pname = "sapi-python-client";
+    version = "0.4.1";
+    format = "setuptools";
+
+    src = fetchFromGitHub {
+      owner = "keboola";
+      repo = pname;
+      rev  = version;
+      sha256 = "189dzj06vzp7366h2qsfvbjmw9qgl7jbp8syhynn9yvrjqp4k8h3";
+    };
+
+    SETUPTOOLS_SCM_PRETEND_VERSION = version;
+
+    nativeBuildInputs = [
+      setuptools-scm
+    ];
+
+    propagatedBuildInputs = [
+      azure-storage-blob
+      boto3
+      requests
+    ];
+
+    # requires API token and an active keboola bucket
+    # ValueError: Root URL is required.
+    doCheck = false;
+
+    checkInputs = [
+      responses
+    ];
+
+    checkPhase = ''
+      runHook preCheck
+      ${python.interpreter} -m unittest discover
+      runHook postCheck
+    '';
+
+    pythonImportsCheck = [
+      "kbcstorage"
+      "kbcstorage.buckets"
+      "kbcstorage.client"
+      "kbcstorage.tables"
+    ];
+
+    meta = with lib; {
+      description = "Keboola Connection Storage API client";
+      homepage = "https://github.com/keboola/sapi-python-client";
+      maintainers = with maintainers; [ mrmebelman ];
+      license = licenses.mit;
+    };
+}

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

@@ -7,14 +7,14 @@
 
 buildPythonPackage rec {
   pname = "pex";
-  version = "2.1.80";
+  version = "2.1.81";
   format = "flit";
 
   disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-m9HMvLoFpg5aUoNknLdF7X++XEk9j70+qaid627uYvs=";
+    hash = "sha256-EW7kOUTzLjmBVKcdRrcdx+AAMSp1hw2LJ/mHMuKViLE=";
   };
 
   nativeBuildInputs = [

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

@@ -0,0 +1,38 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, blessed
+, docopt
+, pillow
+, requests
+, dataclasses
+, pythonOlder
+}:
+
+buildPythonPackage rec {
+  pname = "pixcat";
+  version = "0.1.4";
+
+  disabled = pythonOlder "3.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "657c8fe04513caecccd6086b347aa4b85db6b4c0f761b162cb9cd789abe7abb6";
+  };
+
+  propagatedBuildInputs = [
+    blessed
+    docopt
+    pillow
+    requests
+  ];
+
+  pythonImportsCheck = [ "pixcat" ];
+
+  meta = with lib; {
+    description = "Display images on a kitty terminal with optional resizing";
+    homepage = "https://github.com/mirukan/pixcat";
+    license = licenses.lgpl3;
+    maintainers = [ maintainers.tilcreator ];
+  };
+}

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

@@ -9,7 +9,7 @@
 
 buildPythonPackage rec {
   pname = "pycfmodel";
-  version = "0.19.0";
+  version = "0.19.1";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -18,7 +18,7 @@ buildPythonPackage rec {
     owner = "Skyscanner";
     repo = pname;
     rev = "refs/tags/${version}";
-    hash = "sha256-u1XuUW5OFl5NDP11nd6HK17NBXjqvzLFp2jUmecWP8E=";
+    hash = "sha256-k059AfI3dTPMLAOColmTG4kz0z2bLO1oi8Bg0QeLork=";
   };
 
   propagatedBuildInputs = [

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

@@ -5,6 +5,7 @@
 , numpy
 , setuptools-scm
 , six
+, glibcLocales
 , pytestCheckHook
 }:
 
@@ -27,16 +28,15 @@ buildPythonPackage rec {
   ];
 
   checkInputs = [
+    glibcLocales
     nose
     numpy
     pytestCheckHook
   ];
 
-  disabledTests = [
-    # PyPI releases don't ship all the needed files for the tests
-    "test_index_zero_length"
-    "test_fetch_zero_length"
-    "test_read_back_index"
+  disabledTestPaths = [
+    # FileNotFoundError: [Errno 2] No such file or directory: 'data/genes.fasta.gz'
+    "tests/test_Fasta_bgzip.py"
   ];
 
   pythonImportsCheck = [

pkgs/development/python-modules/pytest-testmon/default.nix

@@ -16,16 +16,11 @@ buildPythonPackage rec {
     sha256 = "sha256-6gWWCtm/GHknhjLyRdVf42koeaSKzk5/V0173DELmj0=";
   };
 
-  propagatedBuildInputs = [ coverage ];
+  propagatedBuildInputs = [ pytest coverage ];
 
-  checkInputs = [ pytest ];
-
-  # avoid tests which try to import unittest_mixins
-  # unittest_mixins doesn't seem to be very active
-  checkPhase = ''
-    cd test
-    pytest test_{core,process_code,pytest_assumptions}.py
-  '';
+  # The project does not include tests since version 1.3.0
+  doCheck = false;
+  pythonImportsCheck = [ "testmon" ];
 
   meta = with lib; {
     homepage = "https://github.com/tarpas/pytest-testmon/";

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

@@ -1,24 +1,24 @@
 { lib
-, buildPythonPackage
-, pythonOlder
-, fetchPypi
-, poetry-core
-, click
-, cryptography
-, construct
-, zeroconf
-, attrs
-, pytz
-, appdirs
-, tqdm
-, netifaces
 , android-backup
-, importlib-metadata
+, appdirs
+, attrs
+, buildPythonPackage
+, click
+, construct
 , croniter
+, cryptography
 , defusedxml
-, pytestCheckHook
+, fetchPypi
+, importlib-metadata
+, netifaces
+, poetry-core
 , pytest-mock
+, pytestCheckHook
+, pythonOlder
+, pytz
 , pyyaml
+, tqdm
+, zeroconf
 }:
 
 
@@ -57,13 +57,16 @@ buildPythonPackage rec {
   ];
 
   checkInputs = [
-    pytestCheckHook
     pytest-mock
+    pytestCheckHook
   ];
 
   postPatch = ''
     substituteInPlace pyproject.toml \
-      --replace 'defusedxml = "^0"' 'defusedxml = "*"' \
+      --replace 'defusedxml = "^0"' 'defusedxml = "*"'
+    # Will be fixed with the next release, https://github.com/rytilahti/python-miio/pull/1378
+    substituteInPlace miio/integrations/vacuum/roborock/vacuum_cli.py \
+      --replace "resultcallback" "result_callback"
   '';
 
   pythonImportsCheck = [

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

@@ -3,6 +3,7 @@
 buildPythonPackage rec {
   version = "1.0.0";
   pname = "python-vagrant";
+  format = "pyproject";
 
   src = fetchPypi {
     inherit pname version;
@@ -12,6 +13,10 @@ buildPythonPackage rec {
   # The tests try to connect to qemu
   doCheck = false;
 
+  pythonImportsCheck = [
+    "vagrant"
+  ];
+
   meta = {
     description = "Python module that provides a thin wrapper around the vagrant command line executable";
     homepage = "https://github.com/todddeluca/python-vagrant";

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

@@ -7,14 +7,14 @@
 
 buildPythonPackage rec {
   pname = "pyvesync";
-  version = "2.0.1";
+  version = "2.0.2";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-7eGsRy8S6IZQ+UVNN8SoS7tBIYLlujSFr2qFldaxtJE=";
+    sha256 = "sha256-SsSzwuJvDbQ1AzF+q5bjOnFaR6M2UFixtlmk6sgjKOg=";
   };
 
   propagatedBuildInputs = [

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

@@ -3,14 +3,17 @@
 , buildPythonPackage
 , setuptools-scm
 , astropy
+, numpy
+, scipy
+, six
 , pytestCheckHook
 , pytest-doctestplus
-, scipy
 }:
 
 buildPythonPackage rec {
   pname = "radio_beam";
   version = "0.3.3";
+  format = "pyproject";
 
   src = fetchPypi {
     inherit version;
@@ -22,9 +25,17 @@ buildPythonPackage rec {
     setuptools-scm
   ];
 
-  propagatedBuildInputs = [ astropy ];
+  propagatedBuildInputs = [
+    astropy
+    numpy
+    scipy
+    six
+  ];
 
-  checkInputs = [ pytestCheckHook pytest-doctestplus scipy ];
+  checkInputs = [
+    pytestCheckHook
+    pytest-doctestplus
+  ];
 
   # Tests must be run in the build directory
   preCheck = ''

pkgs/development/python-modules/sapi-python-client/default.nix

@@ -1,30 +0,0 @@
-{ lib, git, setuptools, setuptools-scm, fetchFromGitHub, requests, boto3, buildPythonPackage, responses }:
-
-buildPythonPackage rec {
-    pname = "sapi-python-client";
-    version = "0.4.1";
-
-    src = fetchFromGitHub {
-        owner = "keboola";
-        repo = pname;
-        rev  = version;
-        sha256 = "189dzj06vzp7366h2qsfvbjmw9qgl7jbp8syhynn9yvrjqp4k8h3";
-    };
-
-    postPatch = ''
-        sed -i 's|use_scm_version=True|version="${version}"|' setup.py
-    '';
-
-    doCheck = false; # requires API token and an active keboola bucket
-
-    nativeBuildInputs = [ git setuptools-scm ];
-
-    propagatedBuildInputs = [ setuptools requests boto3 responses ];
-
-    meta = with lib; {
-        description = "Keboola Connection Storage API client";
-        homepage = "https://github.com/keboola/sapi-python-client";
-        maintainers = with maintainers; [ mrmebelman ];
-        license = licenses.mit;
-    };
-}

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

@@ -7,6 +7,7 @@
 , pythonOlder
 , pyyaml
 , starkbank-ecdsa
+, six
 , werkzeug
 }:
 
@@ -27,6 +28,7 @@ buildPythonPackage rec {
   propagatedBuildInputs = [
     python-http-client
     starkbank-ecdsa
+    six
   ];
 
   checkInputs = [

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

@@ -7,6 +7,7 @@
 , pytestCheckHook
 , pythonOlder
 , setuptools-scm
+, six
 }:
 
 buildPythonPackage rec {
@@ -36,6 +37,7 @@ buildPythonPackage rec {
     mock
     pep440
     pytestCheckHook
+    six
   ];
 
   preCheck = ''
@@ -45,6 +47,7 @@ buildPythonPackage rec {
   disabledTests = [
     # Tests want to scan site-packages
     "test_check_dependencies"
+    "test_clean"
     "test_scenario"
     "test_git_versioning"
   ];

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

@@ -10,7 +10,7 @@
 
 buildPythonPackage rec {
   pname = "shtab";
-  version = "1.5.3";
+  version = "1.5.4";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -19,7 +19,7 @@ buildPythonPackage rec {
     owner = "iterative";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-Wuc4m3VdOGEcevYXUpbL4gTvyW9t13pj57zPYdqx0UY=";
+    hash = "sha256-MYLAQSz55913fOhRnH+Y9xugOdfO43gkavitazIgeqg=";
   };
 
   SETUPTOOLS_SCM_PRETEND_VERSION = version;

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

@@ -29,6 +29,7 @@ in with self; {
   BSgenome_Btaurus_UCSC_bosTau6_masked = derive2 { name="BSgenome.Btaurus.UCSC.bosTau6.masked"; version="1.3.99"; sha256="07isv0lcvlsl0aha1p474l0pps0j7bsh455m33vfxwahivqsfy27"; depends=[BSgenome BSgenome_Btaurus_UCSC_bosTau6]; };
   BSgenome_Btaurus_UCSC_bosTau8 = derive2 { name="BSgenome.Btaurus.UCSC.bosTau8"; version="1.4.2"; sha256="16wjy1aw9nvx03r7w8yh5w7sw3pn8i9nczd0n0728l6nnyqxlsz6"; depends=[BSgenome]; };
   BSgenome_Btaurus_UCSC_bosTau9 = derive2 { name="BSgenome.Btaurus.UCSC.bosTau9"; version="1.4.2"; sha256="0vx9z101faybqqdqfk306m7m3j490svmx7bn7knh5if66g0mzi7g"; depends=[BSgenome]; };
+  BSgenome_Btaurus_UCSC_bosTau9_masked = derive2 { name="BSgenome.Btaurus.UCSC.bosTau9.masked"; version="1.4.4"; sha256="04wzhrp0kb8mv7dg732daqr58djs5dwjm54hgmzbaafv1715i74k"; depends=[BSgenome BSgenome_Btaurus_UCSC_bosTau9]; };
   BSgenome_Carietinum_NCBI_v1 = derive2 { name="BSgenome.Carietinum.NCBI.v1"; version="1.0.0"; sha256="1asyyb1p1bzc7dv9s2igjxrf9f144vvz2xbv9qxg15w9qzzx7r33"; depends=[BSgenome]; };
   BSgenome_Celegans_UCSC_ce10 = derive2 { name="BSgenome.Celegans.UCSC.ce10"; version="1.4.0"; sha256="1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"; depends=[BSgenome]; };
   BSgenome_Celegans_UCSC_ce11 = derive2 { name="BSgenome.Celegans.UCSC.ce11"; version="1.4.2"; sha256="0d4bxfglpqiv1f0n6imdgz101g9383hfj3ra91268wryzlm0yk5w"; depends=[BSgenome]; };
@@ -330,7 +331,7 @@ in with self; {
   excluderanges = derive2 { name="excluderanges"; version="0.99.6"; sha256="1ryp2ghbx1b1268fpgza5rn6brhalff9hsr6fxpr5x5mc35hkd68"; depends=[]; };
   fitCons_UCSC_hg19 = derive2 { name="fitCons.UCSC.hg19"; version="3.7.1"; sha256="19isa4x8js0pdb4k8a11bw3bzmzv6jc4jphzrvav7piqkvrgykzx"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; };
   fly_db0 = derive2 { name="fly.db0"; version="3.14.0"; sha256="0jk5k5zpr4r9yn2l7vpb01xdmhi0pm3jg333jr7rv0c6fzjq5279"; depends=[AnnotationDbi]; };
-  geneplast_data = derive2 { name="geneplast.data"; version="0.99.5"; sha256="0bwhc20jkjs3n1n4xv7xmkgjzf6ghssvbsmx3dm347smk54wgjsw"; depends=[]; };
+  geneplast_data = derive2 { name="geneplast.data"; version="0.99.6"; sha256="1vq2l828d25lsmmac6079vip8bbvqhiyr1x58s467cwcl1mgayrk"; depends=[]; };
   geneplast_data_string_v91 = derive2 { name="geneplast.data.string.v91"; version="0.99.6"; sha256="0mc26d0sgmpmfmqsqinqv5k6vhg0hlc8hsjkcnvf369yav224nq1"; depends=[]; };
   genomewidesnp5Crlmm = derive2 { name="genomewidesnp5Crlmm"; version="1.0.6"; sha256="06dmwnjy3gb53y6nr02dmp22qzfl5d63wppazrabcqbzwimhnvp8"; depends=[]; };
   genomewidesnp6Crlmm = derive2 { name="genomewidesnp6Crlmm"; version="1.0.7"; sha256="16qcxa32fmbdcv5dck0grsnqyfcqql7wpxa1l6andv9hrvabv2jx"; depends=[]; };

pkgs/development/r-modules/bioc-experiment-packages.nix

@@ -153,7 +153,7 @@ in with self; {
   QDNAseq_mm10 = derive2 { name="QDNAseq.mm10"; version="1.24.0"; sha256="1iamvkpj5gij2x7j3fixgn3djgly684wrvr888w9cfir6wf5pk94"; depends=[QDNAseq]; };
   QUBICdata = derive2 { name="QUBICdata"; version="1.22.0"; sha256="15saydq9vv1lvqgvv5d51km52aqzwjx7q7ijpka6why442lrys9r"; depends=[]; };
   RGMQLlib = derive2 { name="RGMQLlib"; version="1.14.0"; sha256="0l317dma9cnwhr24k65lhs26n1511chiq8fp0xx4bnxzvw3q7g5b"; depends=[]; };
-  RITANdata = derive2 { name="RITANdata"; version="1.18.0"; sha256="0jpw3lsm7npwn44j7ydi2630qmkjymm1hm2hv73gfk464zr40xf4"; depends=[]; };
+  RITANdata = derive2 { name="RITANdata"; version="1.18.1"; sha256="1dx743cjhi9713sa0ndvk5w8m8p0zxbp9xdw1ssincgqyv1n02qb"; depends=[]; };
   RLHub = derive2 { name="RLHub"; version="1.0.0"; sha256="1i3i1dp5b04xmkgz6lf3fdk0bag23as4f42pcqncalxavgf3c3vm"; depends=[AnnotationHub ExperimentHub]; };
   RMassBankData = derive2 { name="RMassBankData"; version="1.32.0"; sha256="1m268dd3wl92l3vihqijcxy1iif7qw3i3vlqhjq18qmc11i55qp2"; depends=[]; };
   RNASeqRData = derive2 { name="RNASeqRData"; version="1.12.0"; sha256="0546d7p29vra6n54ffnjxz0ajb9ih90m01xx3b9p56v2s4x0wia4"; depends=[]; };
@@ -200,7 +200,7 @@ in with self; {
   TBX20BamSubset = derive2 { name="TBX20BamSubset"; version="1.30.0"; sha256="1y1dgnqa3f80x8j8pw02dd4zb40q86v1qp7102lkhnppvb3b3f2j"; depends=[Rsamtools xtable]; };
   TCGAMethylation450k = derive2 { name="TCGAMethylation450k"; version="1.30.0"; sha256="1qymmnvpic4nz93079r5kxb9yi7y6qcjq39rz5mmcp15q73lpfqk"; depends=[]; };
   TCGAWorkflowData = derive2 { name="TCGAWorkflowData"; version="1.18.0"; sha256="17iq6g93bxzzgsv255ab68crcr5haim57fxx6shjy8ww2ab6522k"; depends=[SummarizedExperiment]; };
-  TCGAbiolinksGUI_data = derive2 { name="TCGAbiolinksGUI.data"; version="1.14.0"; sha256="08zmlvycq3jz1zy0715x9f21nf3465c51k7w2jq12sfbap36pmjm"; depends=[]; };
+  TCGAbiolinksGUI_data = derive2 { name="TCGAbiolinksGUI.data"; version="1.14.1"; sha256="0h8k8bq64c9l70li2jzjmwillxsdmp06f3kikzxhys0xhdkcaanm"; depends=[]; };
   TCGAcrcmRNA = derive2 { name="TCGAcrcmRNA"; version="1.14.0"; sha256="09ccilwf4kvwgaglk5ar5b6c7pyh3b21r0vg6ibb57ilbv85srqd"; depends=[Biobase]; };
   TCGAcrcmiRNA = derive2 { name="TCGAcrcmiRNA"; version="1.14.0"; sha256="0njs301kfbchhcy4i8ldlpv7z9lsj4hm1ivb4w2r75qkaalmgi7s"; depends=[Biobase]; };
   TENxBUSData = derive2 { name="TENxBUSData"; version="1.8.0"; sha256="1smvgqym0jd5m3as8pjyl9dhnfbh02sdh2sxb2hr89133fh6mx6a"; depends=[AnnotationHub BiocGenerics ExperimentHub]; };
@@ -394,7 +394,7 @@ in with self; {
   stemHypoxia = derive2 { name="stemHypoxia"; version="1.30.0"; sha256="05jly60gg5xr9511jlymzbpjysapfz2qq81rxhdz7cjbjkkgvykr"; depends=[]; };
   stjudem = derive2 { name="stjudem"; version="1.34.0"; sha256="005wy7b8naaph9krsdw234sk8fprccclnj7y4rfrs2f3lbrw4b2g"; depends=[]; };
   synapterdata = derive2 { name="synapterdata"; version="1.31.0"; sha256="03bdx8a1hrnlbcfq92d2yrjydw978pifbgr257r55p15khkigl86"; depends=[]; };
-  systemPipeRdata = derive2 { name="systemPipeRdata"; version="1.22.0"; sha256="09p653i4drnfjvx3kd20f4jg7lw1254f44qknl3ghiqppa6rz9g9"; depends=[BiocGenerics GenomicFeatures GenomicRanges IRanges jsonlite remotes Rsamtools rtracklayer ShortRead]; };
+  systemPipeRdata = derive2 { name="systemPipeRdata"; version="1.22.2"; sha256="1hkmgj6dzrn2wnpasl418hxzv9ym0007swg9ayjjy6i4w0q1mvs3"; depends=[BiocGenerics GenomicFeatures GenomicRanges IRanges jsonlite remotes Rsamtools rtracklayer ShortRead]; };
   tartare = derive2 { name="tartare"; version="1.8.0"; sha256="0zaiy4wkikrcx2lc8mcsikpfp8yz3l17bd1z1l0g9r41ixysq105"; depends=[AnnotationHub ExperimentHub]; };
   tcgaWGBSData_hg19 = derive2 { name="tcgaWGBSData.hg19"; version="1.12.0"; sha256="1kmh4iyh2h7vc1mlwb3sridn4nwkqdschz5md5dk53mxkn2wxcmi"; depends=[bsseq ExperimentHub knitr]; };
   timecoursedata = derive2 { name="timecoursedata"; version="1.4.0"; sha256="007dh5wmjd6s7jr0p8af6irm25my20j1ifxhm6rxscgijskqb410"; depends=[SummarizedExperiment]; };

pkgs/development/r-modules/bioc-packages.nix

@@ -14,7 +14,7 @@ in with self; {
   ADAM = derive2 { name="ADAM"; version="1.10.0"; sha256="18zwci0ab54q7rdwj0n63w0i14lfrb4cccp09bcrq10gl1ki07f5"; depends=[dplyr DT GO_db KEGGREST knitr pbapply Rcpp stringr SummarizedExperiment]; };
   ADAMgui = derive2 { name="ADAMgui"; version="1.10.0"; sha256="0n06bb9djigha0249lxx84pn9q0xiryxbv25qsc3p2h46iaxi3wq"; depends=[ADAM colorRamps data_table dplyr DT ggplot2 ggpubr ggrepel ggsignif GO_db gridExtra knitr RColorBrewer reshape2 shiny shinyjs stringi stringr testthat varhandle]; };
   ADImpute = derive2 { name="ADImpute"; version="1.4.0"; sha256="1bkq1hd8sqg9r28r70a9vd3gb2nsmg6dybf002d621p88cdfjib2"; depends=[BiocParallel checkmate data_table DrImpute kernlab MASS Matrix rsvd S4Vectors SAVER SingleCellExperiment SummarizedExperiment]; };
-  ADaCGH2 = derive2 { name="ADaCGH2"; version="2.34.0"; sha256="0a01wds33i2h2whigznbrxq38irlxm20qpwix33x6vlxbjgrckal"; depends=[aCGH bit cluster DNAcopy ff ffbase GLAD snapCGH tilingArray waveslim]; };
+  ADaCGH2 = derive2 { name="ADaCGH2"; version="2.34.0"; sha256="0a01wds33i2h2whigznbrxq38irlxm20qpwix33x6vlxbjgrckal"; depends=[aCGH bit cluster DNAcopy ff GLAD snapCGH tilingArray waveslim]; };
   AGDEX = derive2 { name="AGDEX"; version="1.42.0"; sha256="0y0q4zdybr5hlsi7qy2hf6c2sqr2z2211wz36dz70jkqyr0ggw64"; depends=[Biobase GSEABase]; };
   AIMS = derive2 { name="AIMS"; version="1.26.0"; sha256="1jsvyddv4cy3a53agprqkpfv1a7p384d462675k73dh8paid90nq"; depends=[Biobase e1071]; };
   ALDEx2 = derive2 { name="ALDEx2"; version="1.26.0"; sha256="1k57ifczqj47r8v2m08kmqr4vsrc5vsh7zs18vspvd6xd0qd03xf"; depends=[BiocParallel GenomicRanges IRanges multtest Rfast S4Vectors SummarizedExperiment zCompositions]; };
@@ -32,7 +32,7 @@ in with self; {
   ASSIGN = derive2 { name="ASSIGN"; version="1.30.0"; sha256="0j8kvn5pq29wqjdcsq6smawdvxb7ccam3m5z223mkwww24m92qyw"; depends=[ggplot2 gplots msm Rlab sva yaml]; };
   ASpediaFI = derive2 { name="ASpediaFI"; version="1.8.0"; sha256="0q33ir3chlix9qvw9drjrwzckk5s1vkj7gfdsffrslxsyl0nizx7"; depends=[BiocParallel biomaRt dplyr DRaWR e1071 fgsea GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 Gviz igraph IRanges IVAS limma Matrix mGSZ reshape2 ROCR Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; };
   ASpli = derive2 { name="ASpli"; version="2.4.0"; sha256="0548p8k3a379qqw7d80rbc7hm1g9bx4vmadxm0gmjph9akx56f3h"; depends=[AnnotationDbi BiocGenerics BiocStyle data_table DT edgeR GenomicAlignments GenomicFeatures GenomicRanges Gviz htmltools igraph IRanges limma MASS pbmcapply Rsamtools S4Vectors tidyr UpSetR]; };
-  ATACseqQC = derive2 { name="ATACseqQC"; version="1.18.0"; sha256="0i1i3bfkp1xsjdl1nd56mlh66qz3aasd1hp09d4i31njz2f9znwn"; depends=[BiocGenerics Biostrings BSgenome ChIPpeakAnno edgeR GenomeInfoDb GenomicAlignments GenomicRanges GenomicScores IRanges KernSmooth limma motifStack preseqR randomForest Rsamtools rtracklayer S4Vectors]; };
+  ATACseqQC = derive2 { name="ATACseqQC"; version="1.18.1"; sha256="1jmlialnhs9df1hv6l4qk2c4qjyjbz9mdj8vr52ms8vlxlxplz6c"; depends=[BiocGenerics Biostrings BSgenome ChIPpeakAnno edgeR GenomeInfoDb GenomicAlignments GenomicRanges GenomicScores IRanges KernSmooth limma motifStack preseqR randomForest Rsamtools rtracklayer S4Vectors]; };
   AUCell = derive2 { name="AUCell"; version="1.16.0"; sha256="1lclf8hkhrm6g5fp8yhvjxnwgf8p0j9ffxsmcybz4rjvmwkiz5dp"; depends=[BiocGenerics data_table GSEABase mixtools R_utils S4Vectors shiny SummarizedExperiment]; };
   AWFisher = derive2 { name="AWFisher"; version="1.8.0"; sha256="1i9niknq2bnhwjdvl4f5hmdhg0p5vn9p6b6bb8fanfsijq0cn37p"; depends=[edgeR limma]; };
   AffiXcan = derive2 { name="AffiXcan"; version="1.12.0"; sha256="06yn87briv2141jqad934gg5rcd90w5nghrgmbhqnmwafn72gj9d"; depends=[BiocParallel crayon MultiAssayExperiment SummarizedExperiment]; };
@@ -42,7 +42,7 @@ in with self; {
   AllelicImbalance = derive2 { name="AllelicImbalance"; version="1.32.0"; sha256="1s6arjd0nxgxyqy7vhqcb78k0ss7vwrhv41pm346hs1nyr5dkzaq"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridExtra Gviz IRanges lattice latticeExtra nlme Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; };
   AlphaBeta = derive2 { name="AlphaBeta"; version="1.8.0"; sha256="0ya3dqvdf8iyd5bscc9lc476vkc7kamiqgjvxhxl4ay5j4vn02nr"; depends=[BiocParallel data_table dplyr expm ggplot2 gtools igraph optimx plotly stringr]; };
   AlpsNMR = derive2 { name="AlpsNMR"; version="3.4.0"; sha256="0h8y9hi97zbv3qzjskxh81qjarmwx2w790kpspljgxa214f58fzv"; depends=[assertthat baseline BiocParallel dplyr fs furrr future GGally ggplot2 ggrepel glue htmltools magrittr matrixStats mixOmics pcaPP plyr purrr readxl reshape2 rlang rmarkdown S4Vectors signal speaq stringr SummarizedExperiment tibble tidyr tidyselect vctrs writexl zip]; };
-  AnVIL = derive2 { name="AnVIL"; version="1.6.5"; sha256="0ipf3916xwmg22kmc0qk7x8sw3bb6579cffmdwsizr1mw84cdjwd"; depends=[BiocManager dplyr futile_logger httr jsonlite rapiclient rlang tibble tidyr tidyselect]; };
+  AnVIL = derive2 { name="AnVIL"; version="1.6.7"; sha256="0sy3338vg6g9rsc8ixh1l51xkjcyzxk2mcdw7xxxi6bpcg3zhqv9"; depends=[BiocManager dplyr futile_logger httr jsonlite rapiclient rlang tibble tidyr tidyselect]; };
   AnVILBilling = derive2 { name="AnVILBilling"; version="1.4.0"; sha256="0pg5r6qn18i91z2ixapdkranaacv9z8ljmdb33vdn2dqwv2w85b1"; depends=[bigrquery DBI dplyr DT ggplot2 lubridate magrittr plotly shiny shinytoastr]; };
   AnVILPublish = derive2 { name="AnVILPublish"; version="1.4.1"; sha256="0jvh22kz9mg4r49mbzvbvzbn58lzj5mvk7qb4pizn4sd8xsbvmyq"; depends=[AnVIL httr jsonlite readr rmarkdown whisker yaml]; };
   Anaquin = derive2 { name="Anaquin"; version="2.18.0"; sha256="0b9clpqy2jfhign30nab1369xswrkmqm6dx14mf6wjrvcl9xpm2s"; depends=[DESeq2 ggplot2 knitr locfit plyr qvalue ROCR]; };
@@ -88,10 +88,10 @@ in with self; {
   BayesSpace = derive2 { name="BayesSpace"; version="1.4.1"; sha256="1nif6d4hb9zpfx9lczs6j6xniiv0spq6s39jvrs1qazdyysmf4qy"; depends=[assertthat BiocFileCache BiocSingular coda DirichletReg ggplot2 Matrix mclust purrr Rcpp RcppArmadillo RcppDist RcppProgress RCurl rhdf5 S4Vectors scales scater scran SingleCellExperiment SummarizedExperiment xgboost]; };
   BeadDataPackR = derive2 { name="BeadDataPackR"; version="1.46.0"; sha256="004cppgdy79fqw2szkgkxir0rxvn91bmfrq4g20sdr7cvh8kpfyi"; depends=[]; };
   BgeeCall = derive2 { name="BgeeCall"; version="1.10.0"; sha256="0rbbl8m48qcvl26lnf27jq108p7pi84m9ac3qcpjc0ax5wywbv16"; depends=[biomaRt Biostrings data_table dplyr GenomicFeatures jsonlite rhdf5 rslurm rtracklayer sjmisc tximport]; };
-  BgeeDB = derive2 { name="BgeeDB"; version="2.20.0"; sha256="0pjymal01sjl5dc37g66wykgxnksarlbvwnbvhg7w0i7y92zavqk"; depends=[Biobase curl data_table digest dplyr graph R_utils RCurl RSQLite tidyr topGO]; };
+  BgeeDB = derive2 { name="BgeeDB"; version="2.20.1"; sha256="0mrw7fwjx8k0a5c3iw2j94h1yn5pkvqil7fbzih9xiafnpbn374m"; depends=[Biobase curl data_table digest dplyr graph R_utils RCurl RSQLite tidyr topGO]; };
   BiFET = derive2 { name="BiFET"; version="1.14.0"; sha256="0vidypvphnj76g4ra5ijrgqx2dnzw0fmvdvz35gsqswrr3k20jkk"; depends=[GenomicRanges poibin]; };
   BiGGR = derive2 { name="BiGGR"; version="1.30.0"; sha256="1g01666wwznk148776s4vr1hfi3dfl448dhgk4d1qy2wv6sxh9kr"; depends=[hyperdraw hypergraph LIM limSolve rsbml stringr]; };
-  BiRewire = derive2 { name="BiRewire"; version="3.26.2"; sha256="114qljg6yqx55yi0w5nmhdz9260dzkj73bjgqh8w9kpfvcb0439l"; depends=[igraph Matrix slam tsne]; };
+  BiRewire = derive2 { name="BiRewire"; version="3.26.5"; sha256="041i5d08bsc5jqx3309fixjacizs4yi992cwazxghm8mrk3kicbr"; depends=[igraph Matrix Rtsne slam]; };
   BiSeq = derive2 { name="BiSeq"; version="1.34.0"; sha256="05namdzj196rzjg3wqvamj3xpn039dbfhfpmc6p8ifxn9c9dnd3c"; depends=[betareg Biobase BiocGenerics Formula GenomeInfoDb GenomicRanges globaltest IRanges lokern rtracklayer S4Vectors SummarizedExperiment]; };
   BicARE = derive2 { name="BicARE"; version="1.52.0"; sha256="1g8vrsc05cysb36gsw8sfmr6dgbh4aji37vcq9qwkmkv3jgvnlf6"; depends=[Biobase GSEABase multtest]; };
   BindingSiteFinder = derive2 { name="BindingSiteFinder"; version="1.0.0"; sha256="0mvl2mh2px315ilfmf9ax5qjz3282l56qm1a0v142bb7cxld13v7"; depends=[GenomicRanges ggforce ggplot2 matrixStats rtracklayer S4Vectors tidyr]; };
@@ -147,7 +147,7 @@ in with self; {
   CGHnormaliter = derive2 { name="CGHnormaliter"; version="1.48.0"; sha256="1zz4iaxyf5b03xalq58idnkrwcpsvh8zlz6hlxz487caw7c8xx6p"; depends=[Biobase CGHbase CGHcall]; };
   CGHregions = derive2 { name="CGHregions"; version="1.52.0"; sha256="1g337b6fjmbbkpn9pw20z6bvacrlfh582n6lss3qw0s6x6w5cygs"; depends=[Biobase CGHbase]; };
   CHRONOS = derive2 { name="CHRONOS"; version="1.22.0"; sha256="18fdvbdbl0rms1fs27yi6lvf3xnn3pjfm1qngaaz4c06v207mg9w"; depends=[biomaRt circlize doParallel foreach graph igraph openxlsx RBGL RCurl rJava XML]; };
-  CIMICE = derive2 { name="CIMICE"; version="1.2.0"; sha256="0d2sglrp8ansh8nibbqyg3pvhaaw33q5mzci382pwky05mpy9sjk"; depends=[assertthat dplyr ggcorrplot ggplot2 ggraph glue igraph maftools Matrix networkD3 purrr relations tidyr visNetwork]; };
+  CIMICE = derive2 { name="CIMICE"; version="1.2.1"; sha256="1np9wp7phlhvhk58v853iz55i5jhkc75kw5xnyz8zjc30gb5nz9k"; depends=[assertthat dplyr expm ggcorrplot ggplot2 ggraph glue igraph maftools Matrix networkD3 purrr tidygraph tidyr visNetwork]; };
   CINdex = derive2 { name="CINdex"; version="1.22.0"; sha256="0a73rdhmsprbbq69yvnnhgp86wic255yxrj82k1i1k62f3bsi74c"; depends=[bitops dplyr GenomeInfoDb GenomicRanges gplots gridExtra IRanges png S4Vectors som stringr]; };
   CMA = derive2 { name="CMA"; version="1.52.0"; sha256="09w0wj2mars83rfws8k6fpfgkbyp7fw97zfcf6d8lbsza639f3cm"; depends=[Biobase]; };
   CNAnorm = derive2 { name="CNAnorm"; version="1.40.0"; sha256="0nrkqycsssrrsf8h2w2wgi4lfyjlqakjx1iacb754pp2jfsr2nl2"; depends=[DNAcopy]; };
@@ -242,7 +242,7 @@ in with self; {
   DEComplexDisease = derive2 { name="DEComplexDisease"; version="1.14.0"; sha256="0qbmw70rqmfixrbnb2jzvvqi54j2rl6gy1bspb143gsadh8z2s9i"; depends=[BiocParallel ComplexHeatmap DESeq2 edgeR Rcpp SummarizedExperiment]; };
   DEFormats = derive2 { name="DEFormats"; version="1.22.0"; sha256="0c9ajkrjzw3rdnfnjj7xn9pdsykdzn230mi01138srrkvcpra856"; depends=[checkmate data_table DESeq2 edgeR GenomicRanges S4Vectors SummarizedExperiment]; };
   DEGraph = derive2 { name="DEGraph"; version="1.46.0"; sha256="1p8zzx8vbzhxnpvd7cbr4g1r87lys41cx4n60rkx53c0pqlnabsn"; depends=[graph KEGGgraph lattice mvtnorm NCIgraph R_methodsS3 R_utils RBGL Rgraphviz rrcov]; };
-  DEGreport = derive2 { name="DEGreport"; version="1.30.0"; sha256="0zmqz8gvpbka5cnwxx7w00xjaxlhmrni1lvacnippy63lpl2w4sz"; depends=[Biobase BiocGenerics broom circlize cluster ComplexHeatmap ConsensusClusterPlus cowplot DESeq2 dplyr edgeR ggdendro ggplot2 ggrepel knitr lasso2 logging magrittr Nozzle_R1 psych RColorBrewer reshape rlang S4Vectors scales stringr SummarizedExperiment tibble tidyr]; };
+  DEGreport = derive2 { name="DEGreport"; version="1.30.3"; sha256="08g0ldj4867jsw2h1368pcirvcbdz5w9pbz3pgyxjg9mdbnllaka"; depends=[Biobase BiocGenerics broom circlize cluster ComplexHeatmap ConsensusClusterPlus cowplot DESeq2 dplyr edgeR ggdendro ggplot2 ggrepel knitr lasso2 logging magrittr Nozzle_R1 psych RColorBrewer reshape rlang S4Vectors scales stringr SummarizedExperiment tibble tidyr]; };
   DEGseq = derive2 { name="DEGseq"; version="1.48.0"; sha256="1bx6xj71k7126ckpr1b7dh1ndmb9yvp9wrrr8lyfcq5birgpf22n"; depends=[qvalue]; };
   DEP = derive2 { name="DEP"; version="1.16.0"; sha256="122gxaslxl3q66ncqndkmnjf6kx2gkj880cf2khwivh58sg6y410"; depends=[assertthat circlize cluster ComplexHeatmap dplyr DT fdrtool ggplot2 ggrepel gridExtra imputeLCMD limma MSnbase purrr RColorBrewer readr rmarkdown shiny shinydashboard SummarizedExperiment tibble tidyr vsn]; };
   DEScan2 = derive2 { name="DEScan2"; version="1.14.1"; sha256="017pxb1z1vflxcqbhc1vrdxw146rb50zgxzalpmh0njzc333v3j1"; depends=[BiocGenerics BiocParallel ChIPpeakAnno data_table DelayedArray GenomeInfoDb GenomicAlignments GenomicRanges glue IRanges plyr Rcpp RcppArmadillo rtracklayer S4Vectors SummarizedExperiment]; };
@@ -274,7 +274,7 @@ in with self; {
   DeMixT = derive2 { name="DeMixT"; version="1.10.0"; sha256="0x3kjcn0878w36rqd808ca1iicv4dki1f8066s3ry7806dhcxiln"; depends=[base64enc ggplot2 KernSmooth knitr matrixcalc matrixStats Rcpp rmarkdown SummarizedExperiment truncdist]; };
   DeconRNASeq = derive2 { name="DeconRNASeq"; version="1.36.0"; sha256="1ax9lx5qg4k5c1mv35bhpfh9q8dbfbv4rf4y1vy994qxmnq4rwsv"; depends=[ggplot2 limSolve pcaMethods]; };
   DeepBlueR = derive2 { name="DeepBlueR"; version="1.20.0"; sha256="16sdsvmp54k6zj1xcxmq0pdpm91q9ff11p3c83ii30brshj69bhi"; depends=[data_table diffr dplyr filehash foreach GenomeInfoDb GenomicRanges R_utils RCurl rjson rtracklayer settings stringr withr XML]; };
-  DeepPINCS = derive2 { name="DeepPINCS"; version="1.2.1"; sha256="0ic9v6ikpb4r51j39f54z3va5ybcpd7i11xigwgb85wp3ri3nkvw"; depends=[CatEncoders keras matlab PRROC purrr rcdk reticulate stringdist tensorflow tokenizers ttgsea webchem]; };
+  DeepPINCS = derive2 { name="DeepPINCS"; version="1.2.2"; sha256="1daxagyhcf6ma4r504ypr4gpfjzrbmp1x57r0siccrpgqc1ds817"; depends=[CatEncoders keras matlab PRROC purrr rcdk reticulate stringdist tensorflow tokenizers ttgsea webchem]; };
   DegNorm = derive2 { name="DegNorm"; version="1.4.0"; sha256="0f3vpynm5g83lpja5xg9nvpssyj6lh5cw9syg242j3mlrjim9bif"; depends=[data_table doParallel foreach GenomicAlignments GenomicFeatures GenomicRanges ggplot2 heatmaply IRanges plotly plyr Rcpp RcppArmadillo Rsamtools S4Vectors viridis]; };
   DelayedArray = derive2 { name="DelayedArray"; version="0.20.0"; sha256="1cm6zh01mvhiq7zrik7q3dmgxinyjz1nyg6rfj93kpkvcb5d4wpj"; depends=[BiocGenerics IRanges Matrix MatrixGenerics S4Vectors]; };
   DelayedDataFrame = derive2 { name="DelayedDataFrame"; version="1.10.0"; sha256="1vifbqka5k1rmimqcpl6218ragr9dq9rzxizx9nff5ilsva21f9b"; depends=[BiocGenerics DelayedArray S4Vectors]; };
@@ -306,7 +306,7 @@ in with self; {
   EGSEA = derive2 { name="EGSEA"; version="1.22.0"; sha256="17q0cjvkrqhmzcgvip4mkdz02aa9rm3svfv2s689fhz2kmwljca8"; depends=[AnnotationDbi Biobase DT edgeR EGSEAdata gage ggplot2 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="2.18.0"; sha256="0kn5yr9yf49kcipjn4z7bcpzj74kcfkhb8q9cfnx659xnksfb27d"; 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="2.24.0"; sha256="0rf83brhzdqsnwg3vlby0a4kf8khv2g7rmxkk31r44apkyspzapl"; depends=[BiocParallel CDFt emdist ggplot2 matrixStats preprocessCore]; };
-  ENmix = derive2 { name="ENmix"; version="1.30.01"; sha256="14p1imjqylqwfap662w94mss0f8gl4z2laz8mhhxz5gk1xym5i9n"; depends=[AnnotationHub Biobase doParallel dynamicTreeCut ExperimentHub foreach genefilter geneplotter gplots gtools illuminaio impute IRanges matrixStats minfi preprocessCore quadprog RPMM S4Vectors SummarizedExperiment]; };
+  ENmix = derive2 { name="ENmix"; version="1.30.03"; sha256="1mqfvvdrmwc4qcrb6826sq9yr244p3x6vrcw523ybcs0qvzw25yg"; depends=[AnnotationHub Biobase doParallel dynamicTreeCut ExperimentHub foreach genefilter geneplotter gplots gtools illuminaio impute IRanges matrixStats minfi preprocessCore quadprog RPMM S4Vectors SummarizedExperiment]; };
   ERSSA = derive2 { name="ERSSA"; version="1.12.0"; sha256="11lak418vmswi9mz4h97pxb68m7ihqbg6z93bvnakka65w997ki8"; depends=[BiocParallel DESeq2 edgeR ggplot2 plyr RColorBrewer]; };
   EWCE = derive2 { name="EWCE"; version="1.2.0"; sha256="02kfcj2wldqfrkrlwss5k5vb5mgi37jrp2c3kx556k25xkzh19vq"; depends=[AnnotationHub biomaRt cowplot ewceData ExperimentHub future ggdendro ggplot2 gridExtra HGNChelper limma Matrix reshape2 RNOmni scales stringr SummarizedExperiment]; };
   EmpiricalBrownsMethod = derive2 { name="EmpiricalBrownsMethod"; version="1.22.0"; sha256="0yra1mp1iz4rh6dvlxv0i0f1ibqgl9giz3r4csg5l0wxz60fbxzm"; depends=[]; };
@@ -352,7 +352,7 @@ in with self; {
   GDCRNATools = derive2 { name="GDCRNATools"; version="1.14.0"; sha256="1h0gfi6mhr5kzwhqxkzgxz12abkn7svnbbzga70pp7az8m8vxmnn"; depends=[BiocParallel biomaRt clusterProfiler DESeq2 DOSE DT edgeR GenomicDataCommons ggplot2 gplots jsonlite limma org_Hs_eg_db pathview rjson shiny survival survminer XML]; };
   GDSArray = derive2 { name="GDSArray"; version="1.14.1"; sha256="0v8kxy7xfhgghz4qg2djc4nxh2w3bk48b0cx1jx7lc45hm2qsdfx"; depends=[BiocGenerics DelayedArray gdsfmt S4Vectors SeqArray SNPRelate]; };
   GEM = derive2 { name="GEM"; version="1.20.0"; sha256="19jars2vajfgy2v9xrgp45gc2yn2hq31d9ikdpnkd9gvpqm99nkv"; depends=[ggplot2]; };
-  GENESIS = derive2 { name="GENESIS"; version="2.24.1"; sha256="10b72yy6bx9alw8zr9rz22wgkqm1m6b2lr1flrf80mvxjihfy7as"; depends=[Biobase BiocGenerics BiocParallel data_table gdsfmt GenomicRanges GWASTools igraph IRanges Matrix reshape2 S4Vectors SeqArray SeqVarTools SNPRelate]; };
+  GENESIS = derive2 { name="GENESIS"; version="2.24.2"; sha256="13xjn9a0njpm6w0i2ikkjsp77ykdaigf5x5d39g6qqdj2rc2pz7w"; depends=[Biobase BiocGenerics BiocParallel data_table gdsfmt GenomicRanges GWASTools igraph IRanges Matrix reshape2 S4Vectors SeqArray SeqVarTools SNPRelate]; };
   GENIE3 = derive2 { name="GENIE3"; version="1.16.0"; sha256="0ms769267pimrx3xwwkgjy03qilkxxs7xwhzfca01f65i4n3l6fw"; depends=[dplyr reshape2]; };
   GEOexplorer = derive2 { name="GEOexplorer"; version="1.0.0"; sha256="01hgjdp14b9r2044h0sd136f0px983n0il08wiii41vq1jgisvhb"; depends=[Biobase DT factoextra GEOquery ggplot2 heatmaply htmltools impute limma maptools pheatmap plotly scales shiny shinyBS shinybusy shinyHeatmaply stringr umap]; };
   GEOfastq = derive2 { name="GEOfastq"; version="1.2.0"; sha256="03ya7x7dph6g97aa3gf3d7dinjcy8qipd0dyxqpdhdm1w1gx83by"; depends=[doParallel foreach plyr RCurl rvest stringr xml2]; };
@@ -407,7 +407,7 @@ in with self; {
   GeneRegionScan = derive2 { name="GeneRegionScan"; version="1.50.0"; sha256="0bkhadr61i9jsfwp3i3clz4b0yjdav8rnnrmfplh86sq700y58v5"; depends=[affxparser Biobase Biostrings RColorBrewer S4Vectors]; };
   GeneSelectMMD = derive2 { name="GeneSelectMMD"; version="2.38.0"; sha256="1nq6n4bp3ydgpjbsgg3222dd345l5z5yp4mvs4haps6wlc6bin4i"; depends=[Biobase limma MASS]; };
   GeneStructureTools = derive2 { name="GeneStructureTools"; version="1.14.0"; sha256="1w7nckmjc4zg5a20f4hjqjavmkdwngkjp70akrf3bh1qmbvpdr2a"; depends=[Biostrings BSgenome_Mmusculus_UCSC_mm10 data_table GenomicRanges Gviz IRanges plyr rtracklayer S4Vectors stringdist stringr]; };
-  GeneTonic = derive2 { name="GeneTonic"; version="1.6.1"; sha256="1kcl87bjjy933z8xkqc3nx5yy6b89f62iaf7p6hc69z4vw5xrydf"; depends=[AnnotationDbi backbone bs4Dash circlize colorspace colourpicker ComplexHeatmap dendextend DESeq2 dplyr DT dynamicTreeCut expm ggforce ggplot2 ggrepel GO_db igraph matrixStats plotly RColorBrewer rintrojs rlang rmarkdown S4Vectors scales shiny shinyAce shinycssloaders shinyWidgets SummarizedExperiment tidyr tippy viridis visNetwork]; };
+  GeneTonic = derive2 { name="GeneTonic"; version="1.6.4"; sha256="1qj12jpd5q95lf0fwq26ykpnw6kjp54pdnbh0ipgn37fl9v5vbcx"; depends=[AnnotationDbi backbone bs4Dash circlize colorspace colourpicker ComplexHeatmap dendextend DESeq2 dplyr DT dynamicTreeCut expm ggforce ggplot2 ggrepel GO_db igraph matrixStats plotly RColorBrewer rintrojs rlang rmarkdown S4Vectors scales shiny shinyAce shinycssloaders shinyWidgets SummarizedExperiment tidyr tippy viridis visNetwork]; };
   GeneticsPed = derive2 { name="GeneticsPed"; version="1.56.0"; sha256="1gvk3wg5mqyc8j95l4djfc55ymv4i08az67znnly3r8376m07mqw"; depends=[gdata genetics MASS]; };
   GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.30.1"; sha256="1ly851w6xy144qvmpdv7p64yc45bqxmvny2rzgz691h3qbin3x55"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; };
   GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.30.0"; sha256="1jwksis94mk8bmdggk0w3kvxqwp4di6x78xgsjk6ij54710adyq9"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; };
@@ -418,12 +418,12 @@ in with self; {
   GenomicInteractions = derive2 { name="GenomicInteractions"; version="1.28.0"; sha256="090kxq5jn1jfr9fgbkvbjr5g4bcxzgsaal3gc9yx1n7pgmhccfmb"; depends=[Biobase BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph InteractionSet IRanges Rsamtools rtracklayer S4Vectors stringr]; };
   GenomicOZone = derive2 { name="GenomicOZone"; version="1.8.0"; sha256="1dx72y7kmj7ng3r6qn9bzlmgq9pf7g738myhgrnmk4ivjl6f615w"; depends=[biomaRt Ckmeans_1d_dp GenomeInfoDb GenomicRanges ggbio ggplot2 gridExtra IRanges lsr plyr Rdpack S4Vectors]; };
   GenomicRanges = derive2 { name="GenomicRanges"; version="1.46.1"; sha256="133r27wsdyppjv9kq0d2xamx007lkf416nnlaygs4hs3a76p9xwx"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; };
-  GenomicScores = derive2 { name="GenomicScores"; version="2.6.0"; sha256="18fzi2qi95851ci7qrzwpb7v6fhwp6xi1d1vk11xbygpbvql5mls"; depends=[AnnotationHub Biobase BiocFileCache BiocGenerics BiocManager Biostrings DelayedArray GenomeInfoDb GenomicRanges HDF5Array IRanges rhdf5 S4Vectors XML]; };
+  GenomicScores = derive2 { name="GenomicScores"; version="2.6.1"; sha256="17v2v7aklljy17nivwmani2jxkbffqs2yr38hlspjlvgpidpf9ln"; depends=[AnnotationHub Biobase BiocFileCache BiocGenerics BiocManager Biostrings DelayedArray GenomeInfoDb GenomicRanges HDF5Array IRanges rhdf5 S4Vectors XML]; };
   GenomicSuperSignature = derive2 { name="GenomicSuperSignature"; version="1.2.1"; sha256="08z1h70j82s405q0hqahb4n580ibqaqml7skq0p4w8rgchrvbs7q"; depends=[Biobase BiocFileCache ComplexHeatmap dplyr flextable ggplot2 ggpubr plotly S4Vectors SummarizedExperiment]; };
   GenomicTuples = derive2 { name="GenomicTuples"; version="1.28.0"; sha256="15rv41z4mxj8nn1mkvs73warygd1cmwi9m7lshgld1wf6zk43ypl"; depends=[BiocGenerics data_table GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; };
   GeoDiff = derive2 { name="GeoDiff"; version="1.0.0"; sha256="0ci1x5q8k6rjarciasg72j0ngrv79ya2j8plhgjck41v8g10mbi0"; depends=[Biobase GeomxTools lme4 Matrix NanoStringNCTools plyr Rcpp RcppArmadillo robust roptim testthat withr]; };
   GeomxTools = derive2 { name="GeomxTools"; version="2.0.0"; sha256="0pzad7m77aib9pa0p37sa2wcmlcydy5nvz4xiax11szjc0y4ay7f"; depends=[Biobase BiocGenerics data_table dplyr EnvStats lmerTest NanoStringNCTools outliers readxl reshape2 rjson S4Vectors]; };
-  GladiaTOX = derive2 { name="GladiaTOX"; version="1.10.0"; sha256="0cybhqzw403vm0w6wimdjb8k0fvfgig53g83k5v9m3i3wp8vk0pz"; depends=[brew data_table DBI ggplot2 ggrepel numDeriv RColorBrewer RCurl RJSONIO RMySQL RSQLite stringr tidyr XML xtable]; };
+  GladiaTOX = derive2 { name="GladiaTOX"; version="1.10.2"; sha256="0hdbfsjn3xfmaprhq3vz78hwshp1dgvvmbrs8n76dnsvh8bxwsgx"; depends=[brew data_table DBI ggplot2 ggrepel numDeriv RColorBrewer RCurl RJSONIO RMySQL RSQLite stringr tidyr XML xtable]; };
   Glimma = derive2 { name="Glimma"; version="2.4.0"; sha256="0qkbx9n2vb7kvb5f00csnbffy5bm7hhbdvkx2isgzi0wv0y59kx9"; depends=[DESeq2 edgeR htmlwidgets jsonlite limma S4Vectors SummarizedExperiment]; };
   GlobalAncova = derive2 { name="GlobalAncova"; version="4.12.0"; sha256="12r62a67k3p85lcs8mffai3bzrxq52vm3blgvia3by16nids42d0"; depends=[annotate AnnotationDbi Biobase corpcor dendextend globaltest GSEABase VGAM]; };
   GmicR = derive2 { name="GmicR"; version="1.8.0"; sha256="18rfbdljfc6hl4p9c66j36j0yg19fp8nhv4gny6f8qa9x3n172sd"; depends=[AnnotationDbi ape bnlearn Category data_table doParallel DT foreach GOstats gRain gRbase GSEABase org_Hs_eg_db org_Mm_eg_db reshape2 shiny WGCNA]; };
@@ -494,7 +494,7 @@ in with self; {
   IntramiRExploreR = derive2 { name="IntramiRExploreR"; version="1.16.0"; sha256="18x08rfxvqf1g7haidbzmlg5zd22w8140rhba5jzxpcyx8mcz6h7"; depends=[FGNet igraph knitr]; };
   IsoCorrectoR = derive2 { name="IsoCorrectoR"; version="1.12.0"; sha256="0z2aw2ldar3qq7ddza0k87gksix1j829j76arqyg4w2w0yp9r2q6"; depends=[dplyr magrittr pracma quadprog readr readxl stringr tibble WriteXLS]; };
   IsoCorrectoRGUI = derive2 { name="IsoCorrectoRGUI"; version="1.10.0"; sha256="0mbfm2v8hhmff3yix9znvb6fbjwlgf76bgjyzx000dvpnp7pjrz7"; depends=[IsoCorrectoR readxl tcltk2]; };
-  IsoGeneGUI = derive2 { name="IsoGeneGUI"; version="2.30.0"; sha256="0970w1g6na4iwqcyml2b9amx816n05n78ara1qrxvdx6swxw3r8s"; depends=[Biobase ff geneplotter goric Iso IsoGene jpeg multtest ORCME ORIClust orQA RColorBrewer Rcpp relimp tkrplot xlsx]; };
+  IsoGeneGUI = derive2 { name="IsoGeneGUI"; version="2.30.0"; sha256="0970w1g6na4iwqcyml2b9amx816n05n78ara1qrxvdx6swxw3r8s"; depends=[Biobase ff geneplotter goric Iso IsoGene jpeg multtest ORCME ORIClust RColorBrewer Rcpp relimp tkrplot xlsx]; };
   IsoformSwitchAnalyzeR = derive2 { name="IsoformSwitchAnalyzeR"; version="1.16.0"; sha256="14bqf39gw5ab5r9sr3afkig1jbzdvds1bmcvc6bpb45kschx7fwf"; 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="1.2.0"; sha256="1c4l5lwiarm6l6nbqcw85sf16am3x06a1wfsfcm91pchkdl1jx08"; depends=[]; };
   KCsmart = derive2 { name="KCsmart"; version="2.52.0"; sha256="17glg0m4c5k5ridr3k25r4wpwsp1bsl51lgi270sl590rbj2634n"; depends=[BiocGenerics KernSmooth multtest siggenes]; };
@@ -535,6 +535,7 @@ in with self; {
   MBASED = derive2 { name="MBASED"; version="1.28.0"; sha256="11rbsaki3nbzil2p8fv7b7biykb60398ayq8sc8drqpiam15myy7"; depends=[BiocGenerics BiocParallel GenomicRanges RUnit SummarizedExperiment]; };
   MBAmethyl = derive2 { name="MBAmethyl"; version="1.28.0"; sha256="1jkvx523spv55qrikg26xc2r9qb72y7kfa161ha6jjm8l57rb6bv"; depends=[]; };
   MBCB = derive2 { name="MBCB"; version="1.48.0"; sha256="06idlf8s0a59q45rckflxi5m3i7rgn8lphzyw2fgajvv4df5j7q3"; depends=[preprocessCore tcltk2]; };
+  MBQN = derive2 { name="MBQN"; version="2.6.2"; sha256="1wzpa45nxn8z96q6f08h8h5c77nfbwapxb494nrk1gdpszcqsq7l"; depends=[BiocFileCache ggplot2 limma PairedData preprocessCore rappdirs RCurl rmarkdown SummarizedExperiment xml2]; };
   MBttest = derive2 { name="MBttest"; version="1.22.0"; sha256="115bkavx4pqy7sh70m5jmghk784f4cqm6z91z5s44m8c00a58vnp"; depends=[gplots gtools]; };
   MCbiclust = derive2 { name="MCbiclust"; version="1.18.0"; sha256="1sswmmdkxw41pzqzqxs8rq581jx1wprcmafagnn4n39h2mw00wwy"; depends=[AnnotationDbi BiocParallel cluster GGally ggplot2 GO_db org_Hs_eg_db scales WGCNA]; };
   MDTS = derive2 { name="MDTS"; version="1.14.0"; sha256="124ixdshragwgnr4rz5qii2j0j74ybm5h8y3k2h1kba56632ff1s"; depends=[Biostrings DNAcopy GenomicAlignments GenomicRanges IRanges Rsamtools stringr]; };
@@ -554,7 +555,7 @@ in with self; {
   MLSeq = derive2 { name="MLSeq"; version="2.12.0"; sha256="0z722cbbvkkfpzli47n9dhyj3n02gibffy1l06imwvzxcvahcfyj"; depends=[Biobase caret DESeq2 edgeR foreach ggplot2 limma pamr plyr sSeq SummarizedExperiment testthat VennDiagram xtable]; };
   MMAPPR2 = derive2 { name="MMAPPR2"; version="1.8.0"; sha256="1fl8dmbxr407f0vzv4q3jpaia28igzqxjb6azbck7zgn64wh5i3c"; depends=[Biobase BiocGenerics BiocParallel data_table dplyr ensemblVEP GenomeInfoDb GenomicRanges gmapR IRanges magrittr Rsamtools S4Vectors stringr tidyr VariantAnnotation VariantTools]; };
   MMDiff2 = derive2 { name="MMDiff2"; version="1.22.0"; sha256="1a74q87mlf1pvgy47gyncllsdz460iyk1nrh4m75jywhbxjf36z0"; depends=[Biobase Biostrings BSgenome GenomicRanges ggplot2 locfit RColorBrewer Rsamtools S4Vectors shiny]; };
-  MMUPHin = derive2 { name="MMUPHin"; version="1.8.1"; sha256="161s7505hyacn9632yaq8a0arqac1g11vbz4awjrhqjlma12c9m1"; depends=[cowplot dplyr fpc ggplot2 igraph Maaslin2 metafor tidyr]; };
+  MMUPHin = derive2 { name="MMUPHin"; version="1.8.2"; sha256="1bdcg7mcnpj5n26klc6s2gvind5wdh8ic96glpq6cjgcayaqbd9a"; depends=[cowplot dplyr fpc ggplot2 igraph Maaslin2 metafor tidyr]; };
   MODA = derive2 { name="MODA"; version="1.20.0"; sha256="00v40gsp1x5gbjg4ilnsjq1j512lwl3sbhqmavyxs20i8c8xjcqf"; depends=[AMOUNTAIN cluster dynamicTreeCut igraph RColorBrewer WGCNA]; };
   MOFA2 = derive2 { name="MOFA2"; version="1.4.0"; sha256="0vl2ffvh9nsdgw94yavkdkkhihpcb8fdbn3f19aygmwbfg78j3w9"; 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="1.4.0"; sha256="0jq863ql6ydykrbriw5h6ibinchkhsgxq8908gyg5f5jl2sgc8pc"; depends=[BiocParallel igraph RCy3 RUnit stringr]; };
@@ -582,7 +583,7 @@ in with self; {
   Maaslin2 = derive2 { name="Maaslin2"; version="1.8.0"; sha256="08zncj3ywc5pcywi3zgqvvlmqgp9j165b3vrkipvwv15b647jqvp"; depends=[biglm car chemometrics cplm data_table dplyr edgeR ggplot2 glmmTMB hash lme4 lmerTest logging lpsymphony MASS metagenomeSeq optparse pbapply pcaPP pheatmap pscl robustbase vegan]; };
   MantelCorr = derive2 { name="MantelCorr"; version="1.64.0"; sha256="10n1f04088wzki7mw27zwlahv6mmkwjjljkj0g65az5arki02rbl"; depends=[]; };
   MassArray = derive2 { name="MassArray"; version="1.46.0"; sha256="1m3a0h5jmjifm16z9l37rij00jka0k22qryq0lmhvfmidzvn7pbf"; depends=[]; };
-  MassSpecWavelet = derive2 { name="MassSpecWavelet"; version="1.60.0"; sha256="1icqyxkx5a9y3wahkxpxngw85c7l4hih1ym9nwwn9qy93pnw1zi4"; depends=[waveslim]; };
+  MassSpecWavelet = derive2 { name="MassSpecWavelet"; version="1.60.1"; sha256="00irq3i5kfck7rnm8ll7rqhqfpp3bisv2h8is50a7wbd7480z7ij"; depends=[waveslim]; };
   MatrixGenerics = derive2 { name="MatrixGenerics"; version="1.6.0"; sha256="1s75p8rrmj24r0vcbaiyw8xg8y84j388mv6iawai7pypfcl8s1z3"; depends=[matrixStats]; };
   MatrixQCvis = derive2 { name="MatrixQCvis"; version="1.2.2"; sha256="1czw4v7dyggk6dkhvqsx01wd5rp9rds3h4g9dbycgb9gz5qmza0h"; depends=[ComplexHeatmap dplyr ggplot2 Hmisc htmlwidgets impute imputeLCMD limma openxlsx pcaMethods plotly proDA rlang rmarkdown Rtsne S4Vectors shiny shinydashboard shinyhelper shinyjs SummarizedExperiment tibble tidyr umap UpSetR vegan vsn]; };
   MatrixRider = derive2 { name="MatrixRider"; version="1.26.0"; sha256="0mv0w3m7waqfm8gy39hmdn00p6cq0a0ndr01scfg1js29jm6sgc2"; depends=[Biostrings IRanges S4Vectors TFBSTools XVector]; };
@@ -629,7 +630,7 @@ in with self; {
   MultiBaC = derive2 { name="MultiBaC"; version="1.4.0"; sha256="0pwg6zmrfqrzra1r6ai68ya5fjf6dy2sl035xnxl617iii96jada"; depends=[ggplot2 Matrix MultiAssayExperiment plotrix ropls]; };
   MultiDataSet = derive2 { name="MultiDataSet"; version="1.22.0"; sha256="17asldnxqvp3sijx7nbi2lbbgnq4iq8z72qlg9080sm5lga1yy1s"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggrepel IRanges limma qqman S4Vectors SummarizedExperiment]; };
   MultiMed = derive2 { name="MultiMed"; version="2.16.0"; sha256="1dkvvrvjfc04ad48zywbrmbvm1lcnni6rvvl9gdax11y9lz19341"; depends=[]; };
-  MungeSumstats = derive2 { name="MungeSumstats"; version="1.2.3"; sha256="04lv8yqpjwa6p9n6jpd9mpnnn0r1yv8b6rig6w1zgmhi31cigz7j"; depends=[Biostrings BSgenome data_table dplyr GenomeInfoDb GenomicRanges googleAuthR httr jsonlite magrittr R_utils RCurl rtracklayer stringr VariantAnnotation]; };
+  MungeSumstats = derive2 { name="MungeSumstats"; version="1.2.4"; sha256="00skqhqkh6fbxifqf8dkc79vyizha4cqpwzyb3h6w7v3yzs6bd7x"; depends=[Biostrings BSgenome data_table dplyr GenomeInfoDb GenomicRanges googleAuthR httr jsonlite magrittr R_utils RCurl rtracklayer stringr VariantAnnotation]; };
   MutationalPatterns = derive2 { name="MutationalPatterns"; version="3.4.1"; sha256="0i6fq6736gvrqn45r7nrhl0ns45qwj1bl4yc6qlalw2g46mjxf6k"; depends=[BiocGenerics Biostrings BSgenome cowplot dplyr GenomeInfoDb GenomicRanges ggalluvial ggdendro ggplot2 IRanges magrittr NMF pracma purrr RColorBrewer S4Vectors stringr tibble tidyr VariantAnnotation]; };
   NADfinder = derive2 { name="NADfinder"; version="1.18.0"; sha256="0glcjxgydj2k7h4963fl465y398xqvq4g393ainvwcgz77kx4sk0"; depends=[ATACseqQC baseline BiocGenerics corrplot csaw EmpiricalBrownsMethod GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma metap Rsamtools rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; };
   NBAMSeq = derive2 { name="NBAMSeq"; version="1.10.0"; sha256="1him4qg3xmgisl3jsws690ciknvj2876xn8n9gxc8l08cihfminf"; depends=[BiocParallel DESeq2 genefilter mgcv S4Vectors SummarizedExperiment]; };
@@ -748,7 +749,7 @@ in with self; {
   RCASPAR = derive2 { name="RCASPAR"; version="1.40.0"; sha256="0iw17mh880x1pjqs5ffjlc8xicy8qrks8yigb1aiyn4xd00ihf1s"; depends=[]; };
   RCM = derive2 { name="RCM"; version="1.10.0"; sha256="082qnzy5q3k5g2qazralj4jwhrdxm1y9xc8dxry5d4l6l6vf77wp"; depends=[alabama edgeR ggplot2 MASS nleqslv phyloseq RColorBrewer reshape2 tensor tseries VGAM]; };
   RCSL = derive2 { name="RCSL"; version="1.2.0"; sha256="01v45b42g0gvhz6h0p1j4865l2cm185ai40bf1fcvjd8747850h4"; depends=[ggplot2 igraph NbClust pracma RcppAnnoy Rtsne umap]; };
-  RCy3 = derive2 { name="RCy3"; version="2.14.1"; sha256="1avfplsg0pl6naxbwvwl3r29idq57r6vpiqnhbzfvj28hra4gdqi"; depends=[base64enc base64url BiocGenerics fs glue graph httr IRdisplay IRkernel RColorBrewer RCurl RJSONIO uchardet uuid XML]; };
+  RCy3 = derive2 { name="RCy3"; version="2.14.2"; sha256="13yjr01svgz36g5irr8jg1c3zpwwb9q424qj75k8nrf2zrz72l7w"; depends=[base64enc base64url BiocGenerics fs glue graph httr IRdisplay IRkernel RColorBrewer RCurl RJSONIO uchardet uuid XML]; };
   RCyjs = derive2 { name="RCyjs"; version="2.16.0"; sha256="1xb98gyf847sy5ijv2ka1vsvz64n6fi356qmcgm4k1qhz1jizm6z"; depends=[base64enc BiocGenerics BrowserViz graph httpuv]; };
   RDRToolbox = derive2 { name="RDRToolbox"; version="1.44.0"; sha256="1mlfzvn6imnkj2mrma6nr5cm0qdxjca7vy6hlaidicvwn3jz4129"; depends=[MASS rgl]; };
   REBET = derive2 { name="REBET"; version="1.12.0"; sha256="19hsykk770jyrvd5lbaybggs4j1f1rnrbcq2mb0cz8w288lh4i5p"; depends=[ASSET]; };
@@ -845,11 +846,11 @@ in with self; {
   RpsiXML = derive2 { name="RpsiXML"; version="2.36.0"; sha256="19jc5dhwyy2z1cwbvgvw54v7kkbgh7g0wzy4frxv91zdgaj7wmhy"; depends=[annotate AnnotationDbi Biobase graph hypergraph RBGL XML]; };
   Rqc = derive2 { name="Rqc"; version="1.28.0"; sha256="0hcxkrfja0gmd8r2llijdvaw2xiiplk037305inimz0qna6w2071"; depends=[BiocGenerics BiocParallel BiocStyle Biostrings biovizBase GenomicAlignments GenomicFiles ggplot2 IRanges knitr markdown plyr Rcpp reshape2 Rsamtools S4Vectors shiny ShortRead]; };
   Rsamtools = derive2 { name="Rsamtools"; version="2.10.0"; sha256="0v6b3j45ivd9f04fpfs1vjwby5pi30mf5683bjxim01vi2krj9yh"; depends=[BiocGenerics BiocParallel Biostrings bitops GenomeInfoDb GenomicRanges IRanges Rhtslib S4Vectors XVector zlibbioc]; };
-  Rsubread = derive2 { name="Rsubread"; version="2.8.1"; sha256="0lpx0dp5570kbrq7v0g573axkhi00qrf38si59vmvnqxhmkvsixn"; depends=[Matrix]; };
+  Rsubread = derive2 { name="Rsubread"; version="2.8.2"; sha256="078zcchw9xl6vs2wihzzji349vq0m1a039m86jdlvb7nc3i1imfk"; depends=[Matrix]; };
   Rtpca = derive2 { name="Rtpca"; version="1.4.0"; sha256="05i25sfgdqsnw9ky0p25aix8qrzkirmcl5vvpqrv8bwvs335glm4"; depends=[Biobase dplyr fdrtool ggplot2 pROC tibble tidyr]; };
   Rtreemix = derive2 { name="Rtreemix"; version="1.56.0"; sha256="15kr8y8w059bxhl9x7j7qg01b55jsxfmfzgdyxk6l40i3l4i0wh1"; depends=[Biobase graph Hmisc]; };
-  S4Vectors = derive2 { name="S4Vectors"; version="0.32.3"; sha256="0wp29v41f9cf6khq2ww0f63nsq6219l1ycajzdqp3a2xda734ncw"; depends=[BiocGenerics]; };
-  SAIGEgds = derive2 { name="SAIGEgds"; version="1.8.0"; sha256="08jhqpi13kg69nfl425m6rvgyvzfspfylgnzkk1v6v0kaz5876f2"; depends=[gdsfmt Rcpp RcppArmadillo RcppParallel SeqArray SPAtest]; };
+  S4Vectors = derive2 { name="S4Vectors"; version="0.32.4"; sha256="17dvypxcwp8c7ih23hi2366110by6zq1mjgxkmlbiklzachg9780"; depends=[BiocGenerics]; };
+  SAIGEgds = derive2 { name="SAIGEgds"; version="1.8.1"; sha256="1fyhscqvhmpwd7zykj7mglk6liq6nccmic741mds5hqlx8zxhy7d"; depends=[gdsfmt Rcpp RcppArmadillo RcppParallel SeqArray SPAtest]; };
   SANTA = derive2 { name="SANTA"; version="2.30.0"; sha256="0w0rd0vmjvz98ijk53ikpin7x5acl0yfkb2v7y77ma6lizy70rgl"; depends=[igraph Matrix]; };
   SBGNview = derive2 { name="SBGNview"; version="1.8.0"; sha256="17jh1ad1a951r89xd9127c1wv5s4rzd03qq8rh5zjn2zxzpwswr4"; depends=[AnnotationDbi bookdown httr igraph KEGGREST knitr pathview Rdpack rmarkdown rsvg SBGNview_data SummarizedExperiment xml2]; };
   SBMLR = derive2 { name="SBMLR"; version="1.90.0"; sha256="08cvhlrh13v571jc0fgfiwzc041nq2ndxpy5nsxmgpbsw5ryfgff"; depends=[deSolve XML]; };
@@ -894,7 +895,7 @@ in with self; {
   SRAdb = derive2 { name="SRAdb"; version="1.56.0"; sha256="18z62c2w6spsmnyqcmc57w41vli5vrcrl3hpy1al1n1yy9fgil0y"; depends=[GEOquery graph RCurl RSQLite]; };
   STAN = derive2 { name="STAN"; version="2.22.0"; sha256="1inqjw11a791c6svw0y4p3m8rd09fjcna3j4p5950f975aph1q4g"; depends=[BiocGenerics GenomeInfoDb GenomicRanges Gviz IRanges poilog Rsolnp S4Vectors]; };
   STATegRa = derive2 { name="STATegRa"; version="1.30.0"; sha256="10a230bvfjvjwsjkh0v3fjbrjkwcvsdch8bfv1s6h4yav1m4wca7"; depends=[affy Biobase calibrate edgeR foreach ggplot2 gplots gridExtra limma MASS]; };
-  STRINGdb = derive2 { name="STRINGdb"; version="2.6.1"; sha256="14yn0fi6ghlv41z5vk4wvrx51hlpx7z9k5fk5jyb50l2g8wwzjhi"; depends=[gplots hash igraph plotrix plyr png RColorBrewer RCurl sqldf]; };
+  STRINGdb = derive2 { name="STRINGdb"; version="2.6.5"; sha256="0n2r2zc2sx1a2a8wqqxz6z7i4ynaj18iwbwgif7469n13agji5mv"; depends=[gplots hash igraph plotrix plyr png RColorBrewer RCurl sqldf]; };
   STROMA4 = derive2 { name="STROMA4"; version="1.18.0"; sha256="10v8kgmx79zd2vgzwij3il80l724sdl0k4a3rm73kd4jw2wvhkrh"; depends=[Biobase BiocParallel cluster matrixStats]; };
   SWATH2stats = derive2 { name="SWATH2stats"; version="1.24.0"; sha256="0ifl1y3rs0r2zqkpcpiibyv12mjqz6wxs296f691k1qfz9qvx8kg"; depends=[biomaRt data_table ggplot2 reshape2]; };
   SamSPECTRAL = derive2 { name="SamSPECTRAL"; version="1.48.0"; sha256="1xxz5ggxj10psrz5rm0xjr8mxwc3cfyl9chsa9w2wxrrixypdnah"; depends=[]; };
@@ -949,7 +950,7 @@ in with self; {
   TCC = derive2 { name="TCC"; version="1.34.0"; sha256="0298zfvrs7x6050s3222fg5yp60siz85pfh6541wmah7j0wzpgsd"; depends=[baySeq DESeq2 edgeR ROC]; };
   TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.22.4"; sha256="071wz6dm6dypbfzvxd6j67l1iawlb6d5sfzq871zh06fzaxjm332"; 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="1.20.0"; sha256="0941xcd42kz72vlhlm93681dwgi4afli5j8cfs331fpddpv7l4af"; 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="1.14.0"; sha256="0gjmgz20hmy8c7igy5xvwql37k0v7662qkxwsc2vi01x6y781bcj"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; };
+  TCGAutils = derive2 { name="TCGAutils"; version="1.14.1"; sha256="1i8cl01l9qnpvbirxka5raaa8xp88wwn6914cqsq3qz44ji4gi79"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; };
   TCseq = derive2 { name="TCseq"; version="1.18.0"; sha256="1kzz3fl19d1ivb6l55xadwg202vq4wza3r7wgf6fx196s20vnvng"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; };
   TDARACNE = derive2 { name="TDARACNE"; version="1.44.0"; sha256="0rjlwj05fw0y4q02lhvdg0blpqrgxjq5kdq0hff94qjwp7fgn5gn"; depends=[Biobase GenKern Rgraphviz]; };
   TEQC = derive2 { name="TEQC"; version="4.16.0"; sha256="08jllnzsfz0zkn2m8n5c6cppjbh5cm8kpgwq652bgw5jmkkpg3f2"; depends=[Biobase BiocGenerics hwriter IRanges Rsamtools]; };
@@ -961,7 +962,7 @@ in with self; {
   TIN = derive2 { name="TIN"; version="1.26.0"; sha256="07m8q3lgcflmrchpw88y4w62iwq5cxd0sw1lbassvgych7dnq3ks"; depends=[aroma_affymetrix data_table impute squash stringr WGCNA]; };
   TMixClust = derive2 { name="TMixClust"; version="1.16.0"; sha256="1i69q92ss9q2vv6hyxvq8wv55w1937rmda43a8qfblzy0jr5avww"; depends=[Biobase BiocParallel cluster flexclust gss mvtnorm SPEM zoo]; };
   TNBC_CMS = derive2 { name="TNBC.CMS"; version="1.10.0"; sha256="1iz2jb895hsliavk9g93mvvccla461cmifmsam3qdscj09gfl17x"; depends=[e1071 forestplot GGally ggplot2 ggpubr GSVA pheatmap pracma quadprog R_utils RColorBrewer SummarizedExperiment survival]; };
-  TOAST = derive2 { name="TOAST"; version="1.8.2"; sha256="1j0a3ll0mkp0jgw8hfl8xs5yj4baqjxfvg09zb8sh82jim1my77z"; depends=[corpcor doParallel EpiDISH GGally ggplot2 limma nnls quadprog SummarizedExperiment tidyr]; };
+  TOAST = derive2 { name="TOAST"; version="1.8.3"; sha256="13vdkygyz0qiwyniz4ahydpfkj6k1ap91hsnkzr6ym765cpdan01"; depends=[corpcor doParallel EpiDISH GGally ggplot2 limma nnls quadprog SummarizedExperiment tidyr]; };
   TPP = derive2 { name="TPP"; version="3.22.1"; sha256="0vr8sv22rhhrv63arz33vbkp5i3cwd03bz54qwx3zbdcf5l3snhy"; depends=[Biobase biobroom broom data_table doParallel dplyr foreach futile_logger ggplot2 gridExtra knitr limma magrittr MASS mefa nls2 openxlsx plyr purrr RColorBrewer RCurl reshape2 rmarkdown stringr tibble tidyr VennDiagram VGAM]; };
   TPP2D = derive2 { name="TPP2D"; version="1.10.0"; sha256="183gf3v1nj0nqll817whxdif0kiwscil88ig0vjj1hn3936q59v6"; depends=[BiocParallel doParallel dplyr foreach ggplot2 limma MASS openxlsx RCurl stringr tidyr]; };
   TRESS = derive2 { name="TRESS"; version="1.0.0"; sha256="0zmzbpzhcsykbpifs5m8md2lhami0ya7y9sf2rdmadgbx17gvzj7"; depends=[AnnotationDbi GenomicFeatures GenomicRanges IRanges Matrix matrixStats Rsamtools rtracklayer S4Vectors]; };
@@ -1105,7 +1106,7 @@ in with self; {
   biomformat = derive2 { name="biomformat"; version="1.22.0"; sha256="0xf99j4lhf8kh9h1317hrbzxdv6rljs1fn68r8s40x6y4db3l817"; depends=[jsonlite Matrix plyr rhdf5]; };
   biomvRCNS = derive2 { name="biomvRCNS"; version="1.34.0"; sha256="01nhjhfyzs67p97bk9bjqdxk239ckl8sgfj55azk1zmw92aw2hfy"; depends=[GenomicRanges Gviz IRanges mvtnorm]; };
   biosigner = derive2 { name="biosigner"; version="1.22.0"; sha256="189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z"; depends=[Biobase e1071 MultiDataSet randomForest ropls]; };
-  biotmle = derive2 { name="biotmle"; version="1.18.0"; sha256="0p3iavf9059qa8qvfvqzskfc5gki3z0ivkkqdwg5anvf0wv2k47g"; depends=[assertthat BiocGenerics BiocParallel dplyr drtmle ggplot2 ggsci limma S4Vectors SummarizedExperiment superheat tibble]; };
+  biotmle = derive2 { name="biotmle"; version="1.18.0"; sha256="0p3iavf9059qa8qvfvqzskfc5gki3z0ivkkqdwg5anvf0wv2k47g"; depends=[assertthat BiocGenerics BiocParallel dplyr ggplot2 ggsci limma S4Vectors SummarizedExperiment superheat tibble]; };
   biovizBase = derive2 { name="biovizBase"; version="1.42.0"; sha256="0kg71p7sqfvxal0c19zrws1ffaqgyi8p605l3z6mkq5ldi26pajz"; depends=[AnnotationDbi AnnotationFilter BiocGenerics Biostrings dichromat ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges Hmisc IRanges RColorBrewer rlang Rsamtools S4Vectors scales SummarizedExperiment VariantAnnotation]; };
   biscuiteer = derive2 { name="biscuiteer"; version="1.8.0"; sha256="16ds322b21g8ys5c3lkrvi70i82f9rxvnknbiqx4sp6f2l01j5yj"; depends=[Biobase BiocGenerics BiocParallel biscuiteerData bsseq data_table DelayedMatrixStats dmrseq GenomeInfoDb GenomicRanges gtools HDF5Array Homo_sapiens impute Matrix matrixStats Mus_musculus QDNAseq qualV R_utils readr Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; };
   blacksheepr = derive2 { name="blacksheepr"; version="1.8.0"; sha256="0j623s9vjxknqx3p3d2nbwiqqjp1326bbyvqjm75n1iyj33z1844"; depends=[circlize ComplexHeatmap pasilla RColorBrewer SummarizedExperiment viridis]; };
@@ -1126,7 +1127,7 @@ in with self; {
   caOmicsV = derive2 { name="caOmicsV"; version="1.24.0"; sha256="0snr67g9bqwyvrr1gxmgdjhrybgcpl38dwik583752sgdyf84c6p"; depends=[bc3net igraph]; };
   cageminer = derive2 { name="cageminer"; version="1.0.0"; sha256="140w8ccm5j5kl3gyn6437a2zqlzf5277k3g3c9i22n1jkdp947yn"; depends=[BioNERO GenomeInfoDb GenomicRanges ggbio ggplot2 ggtext IRanges reshape2]; };
   calm = derive2 { name="calm"; version="1.8.0"; sha256="1sq78fv4s6ja9yw84k20zl10pbkk8g2kf38p6nbxkhi4rvz8b5r2"; depends=[mgcv]; };
-  canceR = derive2 { name="canceR"; version="1.28.02"; sha256="00h8jklisp1vapqz8z4l4qk2273p2n33f0sfrgc6gpraiypvqr10"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; };
+  canceR = derive2 { name="canceR"; version="1.28.04"; sha256="0si885h0nkfzvy3snhsp7638fdzc66l90hswd0va42d3ahq8hr8v"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase phenoTest plyr rpart RUnit survival tkrplot]; };
   cancerclass = derive2 { name="cancerclass"; version="1.38.0"; sha256="1kp764g9jms7r95wh58c4d1yli7xfvhfvi50x2s8rzi4bhi3zik6"; depends=[binom Biobase]; };
   casper = derive2 { name="casper"; version="2.28.0"; sha256="0z85zq5crf3806c16hv0gpv072k2bf7hdyhq958y33282wybr4zd"; depends=[Biobase BiocGenerics coda EBarrays gaga GenomeInfoDb GenomicFeatures GenomicRanges gtools IRanges limma mgcv Rsamtools rtracklayer S4Vectors sqldf survival VGAM]; };
   categoryCompare = derive2 { name="categoryCompare"; version="1.38.0"; sha256="1175is4gr6nr393lk5ha2c3rqsdzsl1mfnhkajcym8n0927rx8n8"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category colorspace GOstats graph GSEABase hwriter RCy3]; };
@@ -1144,7 +1145,7 @@ in with self; {
   cellity = derive2 { name="cellity"; version="1.22.0"; sha256="18nivw8c2iv6ibp6hj2m0f04qb28dcq3ya1imfwsvanm9qb2z8zr"; depends=[AnnotationDbi e1071 ggplot2 mvoutlier org_Hs_eg_db org_Mm_eg_db robustbase topGO]; };
   cellmigRation = derive2 { name="cellmigRation"; version="1.2.0"; sha256="0wwfp4jffdxjhzpjpa9136i7ji7bkgbmkdrc4k058kwncv65iajp"; depends=[doParallel FactoMineR FME foreach Hmisc matrixStats reshape2 sp SpatialTools tiff vioplot]; };
   cellscape = derive2 { name="cellscape"; version="1.18.0"; sha256="1p8ib244yxfzl5xswl1ifhj7grc8435npw82kmj5vqg8mqbkhgh7"; depends=[dplyr gtools htmlwidgets jsonlite plyr reshape2 stringr]; };
-  censcyt = derive2 { name="censcyt"; version="1.2.0"; sha256="0yrkv3122iniqgfsp8hhglndpklhlvr2d1f661ghn73dhwbabmww"; depends=[BiocParallel broom_mixed diffcyt dirmult dplyr edgeR fitdistrplus lme4 magrittr MASS mice multcomp purrr rlang S4Vectors stringr SummarizedExperiment survival tibble tidyr]; };
+  censcyt = derive2 { name="censcyt"; version="1.2.1"; sha256="0sd412jhhgax0szslks8bmg81yrqs3hj54ahdgsnbqf846kccrzw"; depends=[BiocParallel broom_mixed diffcyt dirmult dplyr edgeR fitdistrplus lme4 magrittr MASS mice multcomp purrr rlang S4Vectors stringr SummarizedExperiment survival tibble tidyr]; };
   cfDNAPro = derive2 { name="cfDNAPro"; version="1.0.0"; sha256="0klzwax2wblcq8j51ig7qkxml7yb3qc2p66g2ds8sfai0y3hslf9"; depends=[dplyr ggplot2 magrittr quantmod rlang Rsamtools stringr]; };
   cghMCR = derive2 { name="cghMCR"; version="1.52.0"; sha256="1j3pdj1c5wpl0mmirbssysval6fh2vyfb4d6w6jkqikchbcal8pk"; depends=[BiocGenerics CNTools DNAcopy limma]; };
   chimeraviz = derive2 { name="chimeraviz"; version="1.20.0"; sha256="0gsd2bwjzh6f8gqclnhm8gq2q3c1ddp4qqflmbgfk16jja8516va"; depends=[AnnotationDbi AnnotationFilter BiocStyle Biostrings checkmate data_table dplyr DT ensembldb GenomeInfoDb GenomicAlignments GenomicRanges graph gtools Gviz IRanges magick org_Hs_eg_db org_Mm_eg_db plyr RCircos RColorBrewer Rgraphviz rmarkdown Rsamtools S4Vectors]; };
@@ -1228,7 +1229,7 @@ in with self; {
   daMA = derive2 { name="daMA"; version="1.66.0"; sha256="0m7192md5956mbklw0j7z0b82inr6h0p2c9vvjsmd5ivlbz1zdri"; depends=[MASS]; };
   dada2 = derive2 { name="dada2"; version="1.22.0"; sha256="1mj2fiqanr8lp1883bali00la38d9g1krqz9v7f396s1f5x8yll6"; depends=[BiocGenerics Biostrings ggplot2 IRanges Rcpp RcppParallel reshape2 ShortRead XVector]; };
   dagLogo = derive2 { name="dagLogo"; version="1.32.0"; sha256="1gqb56zg11cl7ldww15zmn09f1f5i60mshwrv7gsb3yc79zs48s1"; depends=[BiocGenerics biomaRt Biostrings motifStack pheatmap UniProt_ws]; };
-  dasper = derive2 { name="dasper"; version="1.4.2"; sha256="1c0kz52wwz7b8fxgzj7drs8mqr5r2cl25n58rralqb7mgn926v62"; depends=[basilisk BiocFileCache BiocParallel data_table dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggpubr ggrepel IRanges magrittr megadepth plyranges readr reticulate rtracklayer S4Vectors stringr SummarizedExperiment tidyr]; };
+  dasper = derive2 { name="dasper"; version="1.4.3"; sha256="0rry987mmwrrg15wm5vwmwds2dk6vqpvayvkhzgw2zm5gabis27n"; depends=[basilisk BiocFileCache BiocParallel data_table dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggpubr ggrepel IRanges magrittr megadepth plyranges readr reticulate rtracklayer S4Vectors stringr SummarizedExperiment tidyr]; };
   dcGSA = derive2 { name="dcGSA"; version="1.22.0"; sha256="0j697q02zys9brmc7xn1yh7lir7k1m7hlr752ykydqx9qzzw0m77"; depends=[BiocParallel Matrix]; };
   dcanr = derive2 { name="dcanr"; version="1.10.0"; sha256="0xrfdwcs4qxgasm318nd2cdqmr9ksaxig1frs8h6a7lg8wvh5f2x"; depends=[circlize doRNG foreach igraph Matrix plyr RColorBrewer reshape2 stringr]; };
   dce = derive2 { name="dce"; version="1.2.0"; sha256="0wzi9hv975ib7nvd6qqnlhzfzgx9wydxxs1pkklzzgwlwm4gr971"; depends=[assertthat CombinePValue dplyr edgeR epiNEM expm ggplot2 ggraph glm2 glue graph graphite harmonicmeanp igraph logger MASS Matrix metap mnem naturalsort org_Hs_eg_db pcalg ppcor purrr reshape2 Rgraphviz rlang tidygraph tidyverse]; };
@@ -1236,12 +1237,12 @@ in with self; {
   ddPCRclust = derive2 { name="ddPCRclust"; version="1.14.0"; sha256="13s2h8bfd6i6shbm9iwlz99nvyif6c934ccgkdihgbxfq2zacmdj"; depends=[clue flowCore flowDensity flowPeaks ggplot2 openxlsx plotrix R_utils SamSPECTRAL]; };
   dearseq = derive2 { name="dearseq"; version="1.6.0"; sha256="07vr27rv3z86ajd62c0ilvfgz9z35qsiwwi5pv4sygbhnnjwh3rc"; depends=[ggplot2 KernSmooth matrixStats patchwork pbapply statmod survey viridisLite]; };
   debCAM = derive2 { name="debCAM"; version="1.12.0"; sha256="1nqc2r9wr4q71zsya0ylwkxc91sqa4zkal26wiv5h10bk5nxig5r"; depends=[apcluster Biobase BiocParallel corpcor DMwR2 geometry NMF nnls pcaPP rJava SummarizedExperiment]; };
-  debrowser = derive2 { name="debrowser"; version="1.22.4"; sha256="0wrwyq7kz8qqhgg2pjif8hz53ci33r6fgzwpsdxywds1arv54yb2"; depends=[annotate AnnotationDbi apeglm ashr clusterProfiler colourpicker DESeq2 DOSE DT edgeR enrichplot GenomicRanges ggplot2 gplots Harman heatmaply igraph IRanges jsonlite limma org_Hs_eg_db org_Mm_eg_db pathview plotly RColorBrewer RCurl reshape2 S4Vectors shiny shinyBS shinydashboard shinyjs stringi SummarizedExperiment sva]; };
+  debrowser = derive2 { name="debrowser"; version="1.22.5"; sha256="1aqjnq13yvgw0rjq90l7kgf8c56fhjxhv7r3g1xa5pbdqzfdbv99"; depends=[annotate AnnotationDbi apeglm ashr clusterProfiler colourpicker DESeq2 DOSE DT edgeR enrichplot GenomicRanges ggplot2 gplots Harman heatmaply igraph IRanges jsonlite limma org_Hs_eg_db org_Mm_eg_db pathview plotly RColorBrewer RCurl reshape2 S4Vectors shiny shinyBS shinydashboard shinyjs stringi SummarizedExperiment sva]; };
   deco = derive2 { name="deco"; version="1.10.0"; sha256="1bvn5wipvyxy5h74wl1433pv5lzdp82m8yxwr3b8cljnlqcqh9da"; depends=[ade4 AnnotationDbi Biobase BiocParallel BiocStyle cluster foreign gdata ggplot2 gplots gridExtra limma locfit made4 RColorBrewer reshape2 scatterplot3d sfsmisc SummarizedExperiment]; };
   decompTumor2Sig = derive2 { name="decompTumor2Sig"; version="2.10.0"; sha256="125913q735vazmlnvg8vdca8j88y0mx24zdlqzsgzw9ylkwbq86p"; depends=[BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg19 data_table GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo gridExtra Matrix plyr quadprog readxl S4Vectors SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; };
   decontam = derive2 { name="decontam"; version="1.14.0"; sha256="0k8rp91ap3dwzhhhg3s7ikbphxvgha7m118ayrghshp8929g3cdm"; depends=[ggplot2 reshape2]; };
   deconvR = derive2 { name="deconvR"; version="1.0.1"; sha256="1ibp59d0q8bax7rphg140jb5ylkhmaa4lmc0khqffq440j9fnrr5"; depends=[assertthat BiocGenerics data_table dplyr e1071 foreach GenomicRanges IRanges magrittr MASS matrixStats methylKit nnls quadprog rsq S4Vectors tidyr]; };
-  decoupleR = derive2 { name="decoupleR"; version="2.0.0"; sha256="0a9jxhfa2qfafvc35vqky8dfqhpl5vw6zmm1q5gq26bc58pswqar"; depends=[AUCell broom dplyr fgsea GSVA magrittr Matrix purrr ranger rlang RobustRankAggreg rpart speedglm stringr SummarizedExperiment tibble tidyr tidyselect viper withr]; };
+  decoupleR = derive2 { name="decoupleR"; version="2.0.1"; sha256="0d4jl94598rxzw4y0qs2g4c67dhlsnlzj01qqcmi156am3a13pkr"; depends=[broom dplyr magrittr Matrix purrr rlang stringr tibble tidyr tidyselect withr]; };
   deepSNV = derive2 { name="deepSNV"; version="1.40.0"; sha256="1wi6j6yb6i9fs9yszfywqz3w50mhl85dkfmr4w3phwvkf0xkn81w"; depends=[Biostrings GenomicRanges IRanges Rhtslib SummarizedExperiment VariantAnnotation VGAM]; };
   deltaCaptureC = derive2 { name="deltaCaptureC"; version="1.8.0"; sha256="1gfh788xxamsf919bznwl1n5ycd81bcxw4mxcsib46fqmzxgh7vh"; depends=[DESeq2 GenomicRanges ggplot2 IRanges SummarizedExperiment tictoc]; };
   deltaGseg = derive2 { name="deltaGseg"; version="1.34.0"; sha256="090bkkd0sxkjxnparn7jyi59rk18vd3nid2sw66malvc4zx0b22y"; depends=[changepoint fBasics ggplot2 pvclust reshape scales tseries wavethresh]; };
@@ -1281,11 +1282,11 @@ in with self; {
   eegc = derive2 { name="eegc"; version="1.20.0"; sha256="0x35z9nwylb3jq56w31z9zb2q6b52fqk0sb70l3axqamb8yym0lc"; depends=[AnnotationDbi clusterProfiler DESeq2 DOSE edgeR ggplot2 gplots igraph limma org_Hs_eg_db org_Mm_eg_db pheatmap R_utils S4Vectors sna wordcloud]; };
   eiR = derive2 { name="eiR"; version="1.34.0"; sha256="1dppl1x5s0apz7djdi3qzdv8i0q7iqh6q9dcxx1g0hfn2v945jfn"; depends=[BiocGenerics ChemmineR DBI digest RcppAnnoy RCurl RUnit snow snowfall]; };
   eisaR = derive2 { name="eisaR"; version="1.6.0"; sha256="1gfcmxdbzpb8rfdk7c1y7jhqanipa6jyxy2cg6f9jsp9x73fs61w"; depends=[BiocGenerics edgeR GenomicRanges IRanges limma S4Vectors SummarizedExperiment]; };
-  enhancerHomologSearch = derive2 { name="enhancerHomologSearch"; version="1.0.0"; sha256="1v8zgp33kabf5qjf7aklb1lbzsvlh1jv30g0f79djf2i9khcxlkm"; depends=[BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges httr IRanges jsonlite Matrix motifmatchr Rcpp rtracklayer S4Vectors]; };
+  enhancerHomologSearch = derive2 { name="enhancerHomologSearch"; version="1.0.1"; sha256="080cfazmj13mcymfrcajfmwrj6jq0nkhf4qqv12nb3vchd8dbvjk"; depends=[BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges httr IRanges jsonlite Matrix motifmatchr Rcpp rtracklayer S4Vectors]; };
   enrichTF = derive2 { name="enrichTF"; version="1.10.0"; sha256="0ssjsl5vh0wdq0584yl6c61d8bp5n3qvkgfrqdlpjfwb7b7gh4xv"; 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="1.14.2"; sha256="1rjiqmc32c9gxckgrgbypxpp0m8y0kahvhzvjzymda25xp8zqjs2"; depends=[aplot DOSE ggplot2 ggraph ggtree GOSemSim igraph magrittr plyr purrr RColorBrewer reshape2 scatterpie shadowtext yulab_utils]; };
-  ensemblVEP = derive2 { name="ensemblVEP"; version="1.36.0"; sha256="1b9i8qv16mrr31qpvvcimcd80nkykky8dygi90jinkzgvkzdxi64"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; };
-  ensembldb = derive2 { name="ensembldb"; version="2.18.3"; sha256="0rbd8ycvl1aydbd8xcbkhgqxqkrflymgah3wm6nx76csapbzh4q9"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; };
+  ensemblVEP = derive2 { name="ensemblVEP"; version="1.36.1"; sha256="1g38psw45g4yvwilj47ka8xbbmjmna2rdabjfjjal47x9p0yf01a"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; };
+  ensembldb = derive2 { name="ensembldb"; version="2.18.4"; sha256="1nsdcsghhh3ikv0hbn1aazdam7a6pqf1p6rz68ll2h6965kl4qzp"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; };
   epiNEM = derive2 { name="epiNEM"; version="1.18.0"; sha256="0xs9jzy0d9iv45d5ina7ki79wix96318yp17mxhp1l4vdkpm3fk7"; depends=[BoolNet e1071 graph gtools igraph latex2exp lattice latticeExtra minet mnem pcalg RColorBrewer]; };
   epialleleR = derive2 { name="epialleleR"; version="1.2.0"; sha256="1zgwwzrg9ngsfq186qsmvgwxcz0b9avr8wk1yadjlrjc9avgh2d3"; depends=[BH BiocGenerics data_table GenomeInfoDb GenomicRanges Rcpp Rhtslib stringi SummarizedExperiment VariantAnnotation zlibbioc]; };
   epidecodeR = derive2 { name="epidecodeR"; version="1.2.0"; sha256="1fy3i7djpj2inlcpa2h4n5hzp0q6a555sc5axg1jwxiala9l8siv"; depends=[dplyr EnvStats GenomicRanges ggplot2 ggpubr IRanges rstatix rtracklayer]; };
@@ -1381,7 +1382,7 @@ in with self; {
   geneXtendeR = derive2 { name="geneXtendeR"; version="1.20.0"; sha256="03vfb2si6wwn2ilqpiwacmbd3fj2lgzx71jf19sk7ypmnwld3zgc"; depends=[AnnotationDbi BiocStyle data_table dplyr GO_db networkD3 org_Rn_eg_db RColorBrewer rtracklayer SnowballC tm wordcloud]; };
   genefilter = derive2 { name="genefilter"; version="1.76.0"; sha256="05ba33m99dg414lasn36mjmkd9lvrxgpamy1qj2zvi31i9vkq6y2"; depends=[annotate AnnotationDbi Biobase BiocGenerics survival]; };
   genefu = derive2 { name="genefu"; version="2.26.0"; sha256="0l9a20fncrifrmfawsx3azaxvs2v2i41xifgk6zi6dfyj1k4h3sk"; depends=[AIMS amap biomaRt iC10 impute limma mclust survcomp]; };
-  geneplast = derive2 { name="geneplast"; version="1.20.0"; sha256="13gfxsc3i2c25h51sx46lsaivy78vy8mbj9frh5kqc2i6lwrcmpi"; depends=[ape data_table igraph snow]; };
+  geneplast = derive2 { name="geneplast"; version="1.20.1"; sha256="00ajcyxwqpkl40bq42493r7mrcvmq3nx7a1kg080vkjyskqf40m0"; depends=[ape data_table igraph snow]; };
   geneplotter = derive2 { name="geneplotter"; version="1.72.0"; sha256="1b7ngp9l00vrymx3d3nsda546s7p4ifr90idn3x2v4ilf38rfhp8"; depends=[annotate AnnotationDbi Biobase BiocGenerics lattice RColorBrewer]; };
   genoCN = derive2 { name="genoCN"; version="1.46.0"; sha256="159hrdlyc6gh5j3qmrq2s1xpbyd29ahlggr7ccr0wlcl1m9zjfgm"; depends=[]; };
   genomation = derive2 { name="genomation"; version="1.26.0"; sha256="0ynwsrlnp98iyz4bl2s7plin0k9iy9zix4jy4v38lcqg6n4iz00j"; depends=[Biostrings BSgenome data_table GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridBase impute IRanges matrixStats plotrix plyr Rcpp readr reshape2 Rsamtools rtracklayer S4Vectors seqPattern]; };
@@ -1402,7 +1403,7 @@ in with self; {
   ggtreeExtra = derive2 { name="ggtreeExtra"; version="1.4.2"; sha256="0c7kf0a5hr63y9w6f09z8dfd3apbhx6i6cd31fvl1wiy977pn2ly"; depends=[ggnewscale ggplot2 ggtree rlang]; };
   girafe = derive2 { name="girafe"; version="1.46.0"; sha256="1al296zsp454lap05mh58y5lmrd0bfc4vmwaq5icnna56i4bi9m9"; depends=[Biobase BiocGenerics Biostrings genomeIntervals intervals IRanges Rsamtools S4Vectors ShortRead]; };
   glmGamPoi = derive2 { name="glmGamPoi"; version="1.6.0"; sha256="1yffzcy910cawz2lzjqg8h1hrjvrkhz3pdif5q352kpzjklr5qjm"; depends=[beachmat BiocGenerics DelayedArray DelayedMatrixStats HDF5Array matrixStats Rcpp RcppArmadillo SummarizedExperiment]; };
-  glmSparseNet = derive2 { name="glmSparseNet"; version="1.12.0"; sha256="14qyj2jgjapjjznjzhslhcfbyxm9z0p28z8qrjqkxcb5z2hw9arq"; depends=[biomaRt dplyr forcats futile_logger ggplot2 glmnet glue httr loose_rock Matrix MultiAssayExperiment readr reshape2 sparsebn sparsebnUtils stringr SummarizedExperiment survminer]; };
+  glmSparseNet = derive2 { name="glmSparseNet"; version="1.12.0"; sha256="14qyj2jgjapjjznjzhslhcfbyxm9z0p28z8qrjqkxcb5z2hw9arq"; depends=[biomaRt dplyr forcats futile_logger ggplot2 glmnet glue httr Matrix MultiAssayExperiment readr reshape2 sparsebnUtils stringr SummarizedExperiment survminer]; };
   globalSeq = derive2 { name="globalSeq"; version="1.22.0"; sha256="16l9pa6siahmfl8k6m0s2cch5jfqz4pcx4xzqi8gsqn9szy6f6jq"; depends=[]; };
   globaltest = derive2 { name="globaltest"; version="5.48.0"; sha256="0wpd1b0wcwkhixd6qkaw0j3y94d5b4aabgz2gq0r72k84jbaxb9f"; depends=[annotate AnnotationDbi Biobase survival]; };
   gmapR = derive2 { name="gmapR"; version="1.36.0"; sha256="0vyw54ijfydb9mvp0znvk850na1iw51higjm3wx69l8jny9l8w60"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors VariantAnnotation]; };
@@ -1427,7 +1428,7 @@ in with self; {
   gwasurvivr = derive2 { name="gwasurvivr"; version="1.12.0"; sha256="1q31ydns5i8jk4p4731i57f80iwx6qm0r9fka4xd4wdxzk5kps8z"; depends=[GWASTools matrixStats SNPRelate SummarizedExperiment survival VariantAnnotation]; };
   h5vc = derive2 { name="h5vc"; version="2.28.0"; sha256="0i4p122cavihc29javrgg5ywqn1fkg73hp46hfj3v2qmwakihk4w"; depends=[abind BatchJobs BiocParallel Biostrings GenomeInfoDb GenomicRanges ggplot2 gridExtra h5vcData IRanges reshape rhdf5 Rhtslib Rsamtools S4Vectors]; };
   hapFabia = derive2 { name="hapFabia"; version="1.36.0"; sha256="0niwlfy2ljsx1ivdxrpm0f8w75bs03xb2l43dkcm5gclwac2ys1v"; depends=[Biobase fabia]; };
-  hca = derive2 { name="hca"; version="1.2.2"; sha256="0jdn93r48id24n8ha2yn2d256mz446j6hfvn0dz0y1kniff154cc"; depends=[BiocFileCache digest dplyr httr jsonlite readr tibble tidyr]; };
+  hca = derive2 { name="hca"; version="1.2.3"; sha256="1raj7z4n1hrfvb18ml3ywnxzidc4ay9ixb74gh0d8m8ps662r701"; depends=[BiocFileCache digest dplyr httr jsonlite readr tibble tidyr]; };
   heatmaps = derive2 { name="heatmaps"; version="1.18.0"; sha256="11fi0kzqx6ihvvwc852xhj34xv4aik0zyv47ad4zbhvb1mvxqv8a"; depends=[BiocGenerics Biostrings EBImage GenomeInfoDb GenomicRanges IRanges KernSmooth Matrix plotrix RColorBrewer]; };
   hiAnnotator = derive2 { name="hiAnnotator"; version="1.28.0"; sha256="1hjgn9gszr38q9syjl9qqw3lml5falp08asn01mq4h1m53akwxxv"; depends=[BSgenome dplyr foreach GenomicRanges ggplot2 iterators rtracklayer scales]; };
   hiReadsProcessor = derive2 { name="hiReadsProcessor"; version="1.30.0"; sha256="02y6gy9h841aag0v88j1g0hw0ckd4zd3agjgvzi9mcmb76zhxz8k"; depends=[BiocGenerics BiocParallel Biostrings dplyr GenomicAlignments GenomicRanges hiAnnotator readxl sonicLength]; };
@@ -1563,7 +1564,7 @@ in with self; {
   methylclock = derive2 { name="methylclock"; version="1.0.1"; sha256="00j1crflmpk02xxs0gfidrd04s8gaw3l1hiqs7qj522j13ks1q45"; depends=[Biobase devtools dplyr dynamicTreeCut ExperimentHub ggplot2 ggpmisc ggpubr impute methylclockData minfi PerformanceAnalytics preprocessCore quadprog Rcpp RPMM tibble tidyr tidyverse]; };
   methylscaper = derive2 { name="methylscaper"; version="1.2.0"; sha256="0ygkx6fs8rjbqp4ry3am7vd3jsqx3nac1z1hdiib2pvgr7b6h1r7"; depends=[BiocParallel Biostrings data_table Rfast seqinr seriation shiny shinyFiles shinyjs SummarizedExperiment]; };
   methylumi = derive2 { name="methylumi"; version="2.40.1"; sha256="1lfcsv8k9c4ndfwlbdk3vd7fq58100bfijyxklna41zf8m8kkkka"; depends=[annotate AnnotationDbi Biobase BiocGenerics FDb_InfiniumMethylation_hg19 genefilter GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 illuminaio IRanges lattice matrixStats minfi reshape2 S4Vectors scales SummarizedExperiment]; };
-  mfa = derive2 { name="mfa"; version="1.16.0"; sha256="1a672zd33bdg0pa490pxrr0jp8vnmnkngb3x12jsqqq56p4dzpjb"; depends=[Biobase coda dplyr ggmcmc ggplot2 magrittr MCMCglmm MCMCpack Rcpp tibble]; };
+  mfa = derive2 { name="mfa"; version="1.16.3"; sha256="0jpnwxzm6iyqcbi6lf89w7xi4gmgi0fhb7rln6g0s81jarqxggib"; depends=[Biobase coda dplyr ggmcmc ggplot2 magrittr MCMCglmm MCMCpack Rcpp tibble]; };
   mgsa = derive2 { name="mgsa"; version="1.42.0"; sha256="02yc49w9yccvhq6iwf09kfb7hkq35aswxymcrkf4j54q7mqhiflc"; depends=[gplots]; };
   miQC = derive2 { name="miQC"; version="1.2.0"; sha256="1a9f6w3j3w2wwqgl2hnl2jrrzycnzwhjv2cds2xk6lakz6x7h9hd"; depends=[flexmix ggplot2 SingleCellExperiment]; };
   miRBaseConverter = derive2 { name="miRBaseConverter"; version="1.18.0"; sha256="07snnvgnmxj0w0f9400vcqgchbfvhmqlh3wrk4wqacqc0ldcxb7a"; depends=[]; };
@@ -1626,7 +1627,7 @@ in with self; {
   multiscan = derive2 { name="multiscan"; version="1.54.0"; sha256="0qjh302hpld7zdrfqkbx8a5hrp3bwfn539pv36mwizjigjznnsi9"; depends=[Biobase]; };
   multtest = derive2 { name="multtest"; version="2.50.0"; sha256="03z71r7g318nwwgiz0k8qwbhghw1hhdhh1an4qnb0nc62c5x9kns"; depends=[Biobase BiocGenerics MASS survival]; };
   mumosa = derive2 { name="mumosa"; version="1.2.0"; sha256="093mzbkx7sf5gg5qcvyzgkfzzdpjm8pd6hb7dwavcjxf90y14l1h"; depends=[batchelor beachmat BiocGenerics BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats igraph IRanges Matrix metapod S4Vectors ScaledMatrix scran scuttle SingleCellExperiment SummarizedExperiment uwot]; };
-  muscat = derive2 { name="muscat"; version="1.8.1"; sha256="0dpzid0zxcyb395yaz4gbgqlv7ngfxw1i5rfybp6cf37cfrk4m70"; depends=[BiocParallel blme ComplexHeatmap data_table DESeq2 dplyr edgeR ggplot2 glmmTMB limma lme4 lmerTest Matrix matrixStats progress purrr S4Vectors scales scater sctransform scuttle SingleCellExperiment SummarizedExperiment variancePartition viridis]; };
+  muscat = derive2 { name="muscat"; version="1.8.2"; sha256="1dlzr1swv0mfaj1kj5m0plvmh72djfwqkl1517r0kf74xj6hab7k"; depends=[BiocParallel blme ComplexHeatmap data_table DESeq2 dplyr edgeR ggplot2 glmmTMB limma lme4 lmerTest Matrix matrixStats progress purrr S4Vectors scales scater sctransform scuttle SingleCellExperiment SummarizedExperiment variancePartition viridis]; };
   muscle = derive2 { name="muscle"; version="3.36.0"; sha256="0a081ay0360h0r9731d145prdg15d1g96s7zzcn411qa8fwg7rv0"; depends=[Biostrings]; };
   musicatk = derive2 { name="musicatk"; version="1.4.0"; sha256="168578fg6gmg48gwd6944ln30g75nyq16yzyjw175yanj09g9qfs"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 BSgenome_Mmusculus_UCSC_mm9 cluster ComplexHeatmap cowplot data_table decompTumor2Sig deconstructSigs dplyr factoextra GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel gridExtra gtools IRanges maftools magrittr MASS matrixTests MCMCprecision NMF philentropy plotly rlang S4Vectors shiny shinyalert shinyBS shinybusy shinydashboard shinyjqui shinyjs sortable stringi stringr SummarizedExperiment TCGAbiolinks tibble tidyr topicmodels TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene uwot VariantAnnotation withr]; };
   mygene = derive2 { name="mygene"; version="1.30.0"; sha256="1s9hlcj9g2a3q2aa3ahjk3j2ksk4v9mpax1cxm739gywaf4sbknp"; depends=[GenomicFeatures Hmisc httr jsonlite plyr S4Vectors sqldf]; };
@@ -1698,7 +1699,7 @@ in with self; {
   pathview = derive2 { name="pathview"; version="1.34.0"; sha256="1jdl81lvrsz03b1nws90nssf2clipipzaqvwm1pq57mvshnlnkjr"; depends=[AnnotationDbi graph KEGGgraph KEGGREST org_Hs_eg_db png Rgraphviz XML]; };
   pathwayPCA = derive2 { name="pathwayPCA"; version="1.10.0"; sha256="01m2g8icx7gq4fpxxxm356wr8wc5dmq3lnvr1s5dj1qqm4hk70xr"; depends=[lars survival]; };
   paxtoolsr = derive2 { name="paxtoolsr"; version="1.28.0"; sha256="0c72fp6nisv6j0rkzw4yip3f94wq990nkmaw3h7lv5r5gpj9b69x"; depends=[httr igraph jsonlite plyr R_utils rappdirs readr rJava rjson XML]; };
-  pcaExplorer = derive2 { name="pcaExplorer"; version="2.20.1"; sha256="1ada0prp16yq21cvrgy19i570y6lsn2ph1s79vmmbw4q4i6xgcwx"; depends=[AnnotationDbi base64enc biomaRt DESeq2 DT genefilter GenomicRanges ggplot2 ggrepel GO_db GOstats heatmaply IRanges knitr limma NMF pheatmap plotly plyr rmarkdown S4Vectors scales shiny shinyAce shinyBS shinydashboard SummarizedExperiment threejs tidyr topGO]; };
+  pcaExplorer = derive2 { name="pcaExplorer"; version="2.20.2"; sha256="1ayixqyds0ma3ph66i3456jfl5bf528vkwi3ja792av5qsn701jx"; depends=[AnnotationDbi base64enc biomaRt DESeq2 DT genefilter GenomicRanges ggplot2 ggrepel GO_db GOstats heatmaply IRanges knitr limma NMF pheatmap plotly plyr rmarkdown S4Vectors scales shiny shinyAce shinyBS shinydashboard SummarizedExperiment threejs tidyr topGO]; };
   pcaMethods = derive2 { name="pcaMethods"; version="1.86.0"; sha256="1fj2v6sna4lbw7ar9h93y2g4pzylqqp7760ih425gcai7s19xdrg"; depends=[Biobase BiocGenerics MASS Rcpp]; };
   pcxn = derive2 { name="pcxn"; version="2.16.0"; sha256="1n61gn1k74k61rrfp340kjchafrfmfidslkqxdr0ijbacbp017qw"; depends=[pcxnData pheatmap]; };
   pdInfoBuilder = derive2 { name="pdInfoBuilder"; version="1.58.0"; sha256="1vk0kppsg9vynwzflkv3frv16hsl43lpk9awr6x22a1frmpndj10"; depends=[affxparser Biobase BiocGenerics Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; };
@@ -1710,12 +1711,13 @@ in with self; {
   periodicDNA = derive2 { name="periodicDNA"; version="1.4.0"; sha256="1v6rl234qs0la2r7qwiahslw7yr8mppcdcpand2lk8w862k67nda"; depends=[BiocParallel Biostrings BSgenome cowplot GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr rtracklayer S4Vectors zoo]; };
   pgca = derive2 { name="pgca"; version="1.18.0"; sha256="1wrp4k0b1sj75yhw799aqcb6dmimza6gvcxkn5ayfn6x3hfifwwl"; depends=[]; };
   phantasus = derive2 { name="phantasus"; version="1.14.0"; sha256="0p8xa0jqasgn61qzzva7wrjk8d2xcsn9kd20c4dbc61sg3cxrcir"; depends=[AnnotationDbi assertthat Biobase ccaPP curl DESeq2 fgsea GEOquery ggplot2 gtable htmltools httpuv httr jsonlite limma Matrix opencpu pheatmap protolite rhdf5 Rook scales stringr svglite]; };
+  phemd = derive2 { name="phemd"; version="1.10.0"; sha256="1n3xvw9x3600pwv2wk7mbgal0lr6zpkwziy0whlkdkxzbgy9xzaw"; depends=[Biobase BiocGenerics cluster cowplot destiny ggplot2 igraph maptree monocle phateR pheatmap pracma RANN RColorBrewer reticulate Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; };
   phenoTest = derive2 { name="phenoTest"; version="1.42.0"; sha256="0ci44hwicvz32sgv6mywawyygd1wzz2bayx6rshwvpmz1mixncq6"; depends=[annotate AnnotationDbi Biobase biomaRt BMA Category ellipse genefilter ggplot2 gplots GSEABase Heatplus hgu133a_db Hmisc hopach limma mgcv survival xtable]; };
   phenopath = derive2 { name="phenopath"; version="1.18.0"; sha256="1c0cxm3cwxprjkkwimzgjz0h67dykx2jy7jin13h7vzpwwvphh2p"; depends=[dplyr ggplot2 Rcpp SummarizedExperiment tibble tidyr]; };
   philr = derive2 { name="philr"; version="1.20.1"; sha256="1ra7wnnn0blxvxvsa570cf6jiqd9fh0ki90j2vbckrzh33z6plyv"; depends=[ape ggplot2 ggtree phangorn tidyr]; };
   phosphonormalizer = derive2 { name="phosphonormalizer"; version="1.18.0"; sha256="0qbls06h7fkqsg8yhnc8dmbqhkgxxxa29j3h7cwxdq4nvg66frjl"; depends=[matrixStats plyr]; };
   phyloseq = derive2 { name="phyloseq"; version="1.38.0"; sha256="0k0aj8f7g1vr7l0qcc507b3w67zc1k9x7sdblm7mjb20zqr3916s"; depends=[ade4 ape Biobase BiocGenerics biomformat Biostrings cluster data_table foreach ggplot2 igraph multtest plyr reshape2 scales vegan]; };
-  piano = derive2 { name="piano"; version="2.10.0"; sha256="13nnysbr2ljh0r303aja797bjxppksc6ac0qms8qy8nkn155gcw3"; depends=[Biobase BiocGenerics DT fgsea gplots htmlwidgets igraph marray relations scales shiny shinydashboard shinyjs visNetwork]; };
+  piano = derive2 { name="piano"; version="2.10.1"; sha256="0x4d7p273mh6pw2gi5rlv493j9kzpzbzkzgwl82snsqab4ljdg2r"; depends=[Biobase BiocGenerics DT fgsea gplots htmlwidgets igraph marray relations scales shiny shinydashboard shinyjs visNetwork]; };
   pickgene = derive2 { name="pickgene"; version="1.66.0"; sha256="0l5gk659gxh7i0sq3j1dg1v69p108ig84d735dv3x8mf9bq1mfhk"; depends=[MASS]; };
   pipeComp = derive2 { name="pipeComp"; version="1.4.0"; sha256="1r61m3468b4v3vw60yywgxs4r4w1lr55wgwndll6wfh62pzgvrf2"; depends=[aricode BiocParallel circlize clue cluster ComplexHeatmap cowplot dplyr ggplot2 intrinsicDimension knitr Matrix matrixStats randomcoloR RColorBrewer reshape2 Rtsne S4Vectors scales scater scran Seurat SingleCellExperiment SummarizedExperiment uwot viridisLite]; };
   pipeFrame = derive2 { name="pipeFrame"; version="1.10.0"; sha256="0463z7kyaar474yfa05j754df49yasl3qmsfxz0qb3y1d7p37grr"; depends=[Biostrings BSgenome digest GenomeInfoDb magrittr rmarkdown visNetwork]; };
@@ -1725,12 +1727,12 @@ in with self; {
   plgem = derive2 { name="plgem"; version="1.66.0"; sha256="06w8xlw4j1fc9ipdgw55dvhp07f04icmhr20lqzwwhqd5pskrra3"; depends=[Biobase MASS]; };
   plier = derive2 { name="plier"; version="1.64.0"; sha256="1sw89kici1h2xfg7zvrfdm7b7iw5n3mzwhyz82676w2vk0lgkpn4"; depends=[affy Biobase]; };
   plotGrouper = derive2 { name="plotGrouper"; version="1.12.0"; sha256="191grbs8sy8jfxz9a6vsp9qf3zaqppp23fcl5qdrmfzims9krhlw"; depends=[colourpicker dplyr egg ggplot2 ggpubr gridExtra gtable Hmisc magrittr readr readxl rlang scales shiny shinythemes stringr tibble tidyr]; };
-  plotgardener = derive2 { name="plotgardener"; version="1.0.15"; sha256="0gwvxvfcvcank7dny901kr74a3n52l16bf9lmas660ydhfn7g4x0"; depends=[curl data_table dplyr ggplotify IRanges plyranges purrr RColorBrewer Rcpp rlang strawr]; };
+  plotgardener = derive2 { name="plotgardener"; version="1.0.17"; sha256="0jlmakxvwsm1gyhkyncdiipljidf0ymab2illj0gpiwaij9fhd67"; depends=[curl data_table dplyr ggplotify IRanges plyranges purrr RColorBrewer Rcpp rlang strawr]; };
   plyranges = derive2 { name="plyranges"; version="1.14.0"; sha256="1s4zyr57x71v9ywdz6s27z158nhazwhmhkx3944l8zsqd5ciwnnc"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges IRanges magrittr rlang Rsamtools rtracklayer S4Vectors tidyselect]; };
   pmm = derive2 { name="pmm"; version="1.26.0"; sha256="0vmkpqxf0lfgkbmyvham128201d33dv3wf9g31nrlwnxd0jcxszn"; depends=[lme4]; };
   pmp = derive2 { name="pmp"; version="1.6.0"; sha256="15yggymqh329f2ibhmg9wmh76hbyn0gpz9k1cxzkvh787lss1w72"; depends=[ggplot2 impute matrixStats missForest pcaMethods reshape2 S4Vectors SummarizedExperiment]; };
   podkat = derive2 { name="podkat"; version="1.26.0"; sha256="0xj0cvw5wj29qfdjs25gawxm2fpbd1dypga54j0fi7nzp94y8ydr"; depends=[Biobase BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp Rhtslib Rsamtools]; };
-  pogos = derive2 { name="pogos"; version="1.14.0"; sha256="0chvlasp42j63hjv7s9swas9m91wkl264wng2r7461pa5kq9x2pp"; depends=[ggplot2 httr ontoProc rjson S4Vectors shiny]; };
+  pogos = derive2 { name="pogos"; version="1.14.1"; sha256="0h4h5j7mv50zg0sm2hzcpwpdj6738crr1szjj13zkh828p7khd55"; depends=[ggplot2 httr ontoProc rjson S4Vectors shiny]; };
   polyester = derive2 { name="polyester"; version="1.30.0"; sha256="0399jal3f2f4bxfxclx54rxxs8azvm63whjiqwrnkq0s3n7wd08y"; depends=[Biostrings IRanges limma logspline S4Vectors zlibbioc]; };
   powerTCR = derive2 { name="powerTCR"; version="1.14.0"; sha256="0c7crgiwpizynl1bd4i5si96kw7cffnnhsbz4w44a3wd1d6ibk4g"; depends=[cubature doParallel evmix foreach magrittr purrr truncdist vegan VGAM]; };
   ppcseq = derive2 { name="ppcseq"; version="1.2.0"; sha256="1rjqyq31lm54apznp3ymk8mm3vcyq4yxz026awy3dh4s53nzsv0a"; depends=[benchmarkme BH dplyr edgeR foreach furrr future ggplot2 lifecycle magrittr purrr Rcpp RcppEigen rlang rstan rstantools StanHeaders tibble tidybayes tidyr]; };
@@ -1753,16 +1755,16 @@ in with self; {
   progeny = derive2 { name="progeny"; version="1.16.0"; sha256="0zhr5i5v87akzqjb6wid67nhg2icrw6w0awdy87x848c6c1i6j9y"; depends=[Biobase dplyr ggplot2 ggrepel gridExtra tidyr]; };
   projectR = derive2 { name="projectR"; version="1.10.0"; sha256="1ny6fdjqc4smd2b7s5zknm0m8mi1wrapcbzlj4n8d1mhd1xxms0d"; depends=[cluster CoGAPS dplyr ggalluvial ggplot2 limma NMF RColorBrewer reshape2 ROCR scales viridis]; };
   proteinProfiles = derive2 { name="proteinProfiles"; version="1.34.0"; sha256="049q579x3m1sw0l5n22ldsrdkmcx61j8jlabq8kydwdhr6d9mbli"; depends=[]; };
-  psichomics = derive2 { name="psichomics"; version="1.20.1"; sha256="1ycsazxm3ghjwawsxjyk5jm1m7nrk03y77x1lfzyqy87s1vzfy9i"; 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]; };
+  psichomics = derive2 { name="psichomics"; version="1.20.2"; sha256="1dlxgrlqrkippiw577r94phlh6i029kpgd9sps2qi3d0n4hmlfx9"; 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="1.26.0"; sha256="1fs2ljshqfyq4hnlm882fc0vd7x4sif5k3qlliqbxai6k5sdh3li"; depends=[BgeeDB Biobase biomaRt ggplot2 GO_db igraph labeling RCurl reshape2 stringr topGO]; };
   ptairMS = derive2 { name="ptairMS"; version="1.2.0"; sha256="1y6wpg85058migpgyankns5v84jv4fk8n7raxxfryn85bqsn0ida"; 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="1.8.0"; sha256="0k2rq76bxg9cq6vjvwwx51hph6s0z1xmka62x6hv19qwakc64qnn"; depends=[cowplot ggplot2 ggridges MuMIn R_utils robustbase S4Vectors SummarizedExperiment taRifx UpSetR]; };
+  pulsedSilac = derive2 { name="pulsedSilac"; version="1.8.0"; sha256="0k2rq76bxg9cq6vjvwwx51hph6s0z1xmka62x6hv19qwakc64qnn"; depends=[cowplot ggplot2 ggridges MuMIn R_utils robustbase S4Vectors SummarizedExperiment UpSetR]; };
   puma = derive2 { name="puma"; version="3.36.0"; sha256="0li5xxvvf1346ilc6ksg0w9ri2r2w9l7cm0d7i3s2y3bai7g36ka"; depends=[affy affyio Biobase mclust oligo oligoClasses]; };
   pvac = derive2 { name="pvac"; version="1.42.0"; sha256="0zic1p12nn6yb5spkz01wr6c15cq7ilhhb2xxkxj0fsw1qalfgnb"; depends=[affy Biobase]; };
   pvca = derive2 { name="pvca"; version="1.34.0"; sha256="12d4rc29qj8sf3y3j3gfnihs7gy7gq3hnlb1ivzsqqw8rwk53cyg"; depends=[Biobase lme4 Matrix vsn]; };
   pwOmics = derive2 { name="pwOmics"; version="1.26.0"; sha256="1r38hbkyai2cf9izljp8sr2mx9ql6bznnfm9gra6kmnhlz0lrw1c"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics biomaRt data_table GenomicRanges gplots graph igraph rBiopaxParser STRINGdb]; };
   pwrEWAS = derive2 { name="pwrEWAS"; version="1.8.0"; sha256="08z5phrwvpc3xaw7vzq4jam2aaba8i6vb46zm420fby7lxrc2bbx"; depends=[abind BiocManager CpGassoc doParallel doSNOW foreach genefilter ggplot2 limma pwrEWAS_data shiny shinyBS shinyWidgets truncnorm]; };
-  qPLEXanalyzer = derive2 { name="qPLEXanalyzer"; version="1.12.0"; sha256="03v1q13xxnbi3r43b4y5psfmcpavnvx2ccr8r0gd6hfhx4wg98a2"; depends=[assertthat Biobase BiocGenerics Biostrings dplyr ggdendro ggplot2 IRanges limma magrittr MSnbase preprocessCore purrr RColorBrewer readr rlang scales stringr tibble tidyr tidyselect]; };
+  qPLEXanalyzer = derive2 { name="qPLEXanalyzer"; version="1.12.1"; sha256="0r1pvvlvccbsc1srim98ahsd7wg9sinnkh8mwbkkm53442r3p7fm"; depends=[assertthat Biobase BiocGenerics Biostrings dplyr ggdendro ggplot2 IRanges limma magrittr MSnbase preprocessCore purrr RColorBrewer readr rlang scales stringr tibble tidyr tidyselect]; };
   qckitfastq = derive2 { name="qckitfastq"; version="1.10.0"; sha256="177agr9q2rjdk67kc2nv6idnqqk2aq595yc83r8pq6h2wp2ynmn0"; depends=[data_table dplyr ggplot2 magrittr Rcpp reshape2 rlang RSeqAn seqTools zlibbioc]; };
   qcmetrics = derive2 { name="qcmetrics"; version="1.32.0"; sha256="1wfc8v1z77wpqfslls8vkw9vi51ylnr8ssr6lm8xz1jd9zijf9ny"; depends=[Biobase knitr pander S4Vectors xtable]; };
   qpcrNorm = derive2 { name="qpcrNorm"; version="1.52.0"; sha256="0zbp5kd6lm1qg9xzg9mibcqm7r3ap9gz7fhaf07ls5q1zk63cdj9"; depends=[affy Biobase limma]; };
@@ -1802,7 +1804,7 @@ in with self; {
   reconsi = derive2 { name="reconsi"; version="1.6.0"; sha256="0djiq9l70wvicbqia14n1bbd9c7ykvsyrp0r2arw2b2pqh8281fh"; depends=[ggplot2 KernSmooth matrixStats phyloseq reshape2]; };
   recount = derive2 { name="recount"; version="1.20.0"; sha256="1maa0fi6dqkcsjlbm52gl0r37qcv951xrc6m4rc6fvp6cb83x68p"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; };
   recount3 = derive2 { name="recount3"; version="1.4.0"; sha256="0ciaab6q0pix7zhz7948b8w3qki8dfy9lpa0wffhqjr7fvfh2km2"; depends=[BiocFileCache data_table GenomicRanges Matrix R_utils RCurl rtracklayer S4Vectors sessioninfo SummarizedExperiment]; };
-  recountmethylation = derive2 { name="recountmethylation"; version="1.4.2"; sha256="11z8ssn7s5mgb92jcr6jcw2rxja8kdddv7bwrqhgns2qkgj52n6w"; depends=[BiocFileCache HDF5Array IlluminaHumanMethylation450kmanifest minfi R_utils RCurl rhdf5 S4Vectors]; };
+  recountmethylation = derive2 { name="recountmethylation"; version="1.4.5"; sha256="1pmrdjiz57ig4rgbn0kkkpls26pfjc4hmx6cpczywqipdyrv6aha"; depends=[BiocFileCache HDF5Array IlluminaHumanMethylation450kmanifest minfi R_utils RCurl rhdf5 S4Vectors]; };
   recoup = derive2 { name="recoup"; version="1.22.0"; sha256="00qxkjjb4bx6vak50jjpl2l9y7myri9x7m17h01j2v2cncg48s55"; depends=[BiocGenerics biomaRt Biostrings circlize ComplexHeatmap GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 httr IRanges Rsamtools RSQLite rtracklayer S4Vectors stringr]; };
   regionReport = derive2 { name="regionReport"; version="1.28.1"; sha256="03d7nbfsk55mrlhzzr81mx3ndswkfj7fajyh1yz4jakjdclvzlxm"; depends=[BiocStyle DEFormats derfinder DESeq2 GenomeInfoDb GenomicRanges knitr knitrBootstrap RefManageR rmarkdown S4Vectors SummarizedExperiment]; };
   regioneR = derive2 { name="regioneR"; version="1.26.1"; sha256="0k500fdmv5l0v7b9pj73bjk3h9k261mfqi6vl52khlw0fafn9b6p"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; };
@@ -1813,7 +1815,7 @@ in with self; {
   rfPred = derive2 { name="rfPred"; version="1.32.0"; sha256="12ppidpn8piw1w450nm35qxzfgyki4ihvp7cri8qk9gipvd3kq9z"; depends=[data_table GenomicRanges IRanges Rsamtools]; };
   rfaRm = derive2 { name="rfaRm"; version="1.6.0"; sha256="095p3nsax57m74j4dj7klpwkl8w2326c9yhc8s0c236kwyszz9rv"; depends=[Biostrings data_table httr IRanges magick rsvg rvest S4Vectors stringi xml2]; };
   rgsepd = derive2 { name="rgsepd"; version="1.26.0"; sha256="149065kmlzdzb9bjwm7x5y3l5j1y7qxzh8xz5liicz5rc4s7pb4i"; depends=[AnnotationDbi biomaRt DESeq2 GO_db goseq gplots hash org_Hs_eg_db SummarizedExperiment]; };
-  rhdf5 = derive2 { name="rhdf5"; version="2.38.0"; sha256="13zm993l3i9f98gqdpxgsrzf9fgqppx2ajvrl0i3f7cvpifcgxqg"; depends=[rhdf5filters Rhdf5lib]; };
+  rhdf5 = derive2 { name="rhdf5"; version="2.38.1"; sha256="1mlwp7bblhbpmd90sxj02zpq1q3fyg8v7ankyjb1y284xaymp02y"; depends=[rhdf5filters Rhdf5lib]; };
   rhdf5client = derive2 { name="rhdf5client"; version="1.16.0"; sha256="1pbgjhcqilr1kzx3a5m4113p6alcr30z1mdd33qqllcarnc0pf4n"; depends=[DelayedArray httr R6 rjson S4Vectors]; };
   rhdf5filters = derive2 { name="rhdf5filters"; version="1.6.0"; sha256="05b015pyp3g1crmm2d3ldsa7r5w0khmf87qbl4fv16r6pdggha78"; depends=[Rhdf5lib]; };
   riboSeqR = derive2 { name="riboSeqR"; version="1.28.0"; sha256="0nnhjvjl4c9yyfzjf8kcj4yky5cdimicp7lz008sczy19jq4vjhd"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools seqLogo]; };
@@ -1824,7 +1826,7 @@ in with self; {
   rnaEditr = derive2 { name="rnaEditr"; version="1.4.0"; sha256="0hs3g7cr6c8gcvg1svv88r4h68364gfnqsmdjc6llwg2l1j36a8w"; depends=[BiocGenerics bumphunter corrplot GenomeInfoDb GenomicRanges IRanges logistf plyr S4Vectors survival]; };
   rnaseqcomp = derive2 { name="rnaseqcomp"; version="1.24.0"; sha256="0asx51fxg9hc0brbqlxl0jyfyidh4fbwyclrvczzzqasf277f23w"; depends=[RColorBrewer]; };
   roar = derive2 { name="roar"; version="1.30.0"; sha256="0hqh4vsnxl2sn1bf6s6wxl2nskb40rhvrysdvb6dr60zkih3g347"; depends=[BiocGenerics GenomeInfoDb GenomicAlignments GenomicRanges IRanges rtracklayer S4Vectors SummarizedExperiment]; };
-  rols = derive2 { name="rols"; version="2.22.0"; sha256="08asfjl6smdg05m41m0bdc2awiqbhyb016z9f77adx3vc73mh613"; depends=[Biobase BiocGenerics httr jsonlite progress]; };
+  rols = derive2 { name="rols"; version="2.22.1"; sha256="1qam4aajg2sp8xii3rkarq5qjxdncy4mp6n5pinmm1iwynlsv217"; depends=[Biobase BiocGenerics httr jsonlite progress]; };
   ropls = derive2 { name="ropls"; version="1.26.4"; sha256="19f3wd55860x959h5n7mrivyjdas5b3jmx74lf24xnx23g26f8rn"; depends=[Biobase MultiDataSet]; };
   rpx = derive2 { name="rpx"; version="2.2.2"; sha256="05qgfchg4pyff0xqrnycxzpan0w5ry1f9w30irhpjiglp7ggf882"; depends=[BiocFileCache curl jsonlite RCurl xml2]; };
   rqt = derive2 { name="rqt"; version="1.20.0"; sha256="0v2bm774y2ikwppp0w0ydqzak96ax7ga1d303vgll13xan50d391"; depends=[car CompQuadForm glmnet Matrix metap pls ropls RUnit SummarizedExperiment]; };
@@ -1840,7 +1842,7 @@ in with self; {
   sagenhaft = derive2 { name="sagenhaft"; version="1.64.0"; sha256="110xg6kagap9795saxmh1dl77r4c2gzmk49rvqjlwqvbifnn4mvw"; depends=[SparseM]; };
   sampleClassifier = derive2 { name="sampleClassifier"; version="1.18.0"; sha256="1plsyjjbjrjq1mydv19lsv0alq98vr2132c3m9j0w4akvs7zcv6q"; depends=[annotate e1071 ggplot2 MGFM MGFR]; };
   sangeranalyseR = derive2 { name="sangeranalyseR"; version="1.4.0"; sha256="14bmz98rhpnkdqxkq67qvzkyld1a56h3y8kvjnhz5hzw8q1aihyd"; depends=[ape BiocStyle Biostrings data_table DECIPHER DT excelR ggdendro gridExtra knitr logger openxlsx phangorn plotly reshape2 rmarkdown sangerseqR seqinr shiny shinycssloaders shinydashboard shinyjs shinyWidgets stringr zeallot]; };
-  sangerseqR = derive2 { name="sangerseqR"; version="1.30.0"; sha256="0j0hzpcsz9z04yf6jp26xscp62slgx4i4i33f6s1ajbgx00sq70n"; depends=[Biostrings shiny]; };
+  sangerseqR = derive2 { name="sangerseqR"; version="1.30.1"; sha256="0anrwj63s0rd9dz6iiq6mvzp1jv5zqadjwrhc1cypvz57zf8ja02"; depends=[Biostrings shiny]; };
   sarks = derive2 { name="sarks"; version="1.6.0"; sha256="026px0b7cbfvf7zqcm2p1y00hna1wgpyfr4bkirwrbmskb7f32lp"; depends=[binom Biostrings cluster IRanges rJava]; };
   satuRn = derive2 { name="satuRn"; version="1.2.0"; sha256="1i2prsjxf6h0ynkcx4g1sj0mpb3v9rm6hwb9ppha2p86ffqxvrjn"; depends=[BiocParallel boot ggplot2 limma locfdr Matrix pbapply SummarizedExperiment]; };
   savR = derive2 { name="savR"; version="1.32.0"; sha256="0dwl94j5dm5ngn8lyyc4bd9ihd1nqincvq26najjn6lw0x55ciky"; depends=[ggplot2 gridExtra reshape2 scales XML]; };
@@ -1859,7 +1861,7 @@ in with self; {
   scMAGeCK = derive2 { name="scMAGeCK"; version="1.6.0"; sha256="1vx90l5d010dp6snasvaymlh16w5law19shdz0fhg3ngkc1v9jg0"; depends=[ggplot2 Seurat]; };
   scMerge = derive2 { name="scMerge"; version="1.10.0"; sha256="031wlfilcagl3mq14yqybz2z7r0l420p5v8f128f841lmhqclg55"; depends=[BiocParallel BiocSingular cluster DelayedArray DelayedMatrixStats distr igraph M3Drop pdist proxy ruv S4Vectors SingleCellExperiment SummarizedExperiment]; };
   scPCA = derive2 { name="scPCA"; version="1.8.0"; sha256="1qgb03c446yv1zkzgiin05vlj7njlz3krvwj183s9y43d95mfny1"; depends=[assertthat BiocParallel cluster coop DelayedArray dplyr elasticnet kernlab Matrix MatrixGenerics matrixStats origami purrr Rdpack RSpectra ScaledMatrix sparsepca stringr tibble]; };
-  scPipe = derive2 { name="scPipe"; version="1.16.0"; sha256="0ckl6crm5rx53dlbbx0b4bfkllr5krai2bnxq5r5yqffv9p7n6mi"; depends=[AnnotationDbi BiocGenerics biomaRt dplyr GenomicRanges GGally ggplot2 glue hash magrittr MASS mclust org_Hs_eg_db org_Mm_eg_db Rcpp reshape Rhtslib rlang robustbase rtracklayer S4Vectors scales scater SingleCellExperiment stringr SummarizedExperiment testthat zlibbioc]; };
+  scPipe = derive2 { name="scPipe"; version="1.16.1"; sha256="0anw36azfp4adsxdl3c58jmgvmvjv0vrcgp2bq90wnxky9xipmna"; depends=[AnnotationDbi BiocGenerics biomaRt dplyr GenomicRanges GGally ggplot2 glue hash magrittr MASS mclust org_Hs_eg_db org_Mm_eg_db Rcpp reshape Rhtslib rlang robustbase rtracklayer S4Vectors scales scater SingleCellExperiment stringr SummarizedExperiment testthat zlibbioc]; };
   scReClassify = derive2 { name="scReClassify"; version="1.0.0"; sha256="0v2cz8h18p3q6a437db1z1ca85j7yrpz9sg7418q2hdv74wd645c"; depends=[e1071 randomForest SingleCellExperiment SummarizedExperiment]; };
   scRecover = derive2 { name="scRecover"; version="1.10.0"; sha256="0x8hlbjhf9jfin075sikc7gpl9qbpppcvhy3rd4cgy1nzq6dqwq1"; depends=[bbmle BiocParallel doParallel foreach gamlss kernlab MASS Matrix penalized preseqR pscl Rmagic rsvd SAVER]; };
   scRepertoire = derive2 { name="scRepertoire"; version="1.4.0"; sha256="17il73lv0pxbqaza21i0fg5zh2v3jf7n30nwngi1jqics4l5ahsl"; depends=[doParallel dplyr ggalluvial ggplot2 igraph plyr powerTCR reshape2 rlang SeuratObject stringdist stringr SummarizedExperiment vegan]; };
@@ -1896,8 +1898,8 @@ in with self; {
   seqPattern = derive2 { name="seqPattern"; version="1.26.0"; sha256="1mik575qaxw9h9qyjn971207pfgbc8p1mx60jrb20jbrrihgg2na"; depends=[Biostrings GenomicRanges IRanges KernSmooth plotrix]; };
   seqTools = derive2 { name="seqTools"; version="1.28.0"; sha256="1m8pxyq11bq4wz3w4n4ls5wf9ws2b7pazazv1d6icrrr9z3278ma"; depends=[zlibbioc]; };
   seqbias = derive2 { name="seqbias"; version="1.42.0"; sha256="1q608c1madij8l52ljl3w52vi3cssr6ikny84yj6n8s7yvpx5jpr"; depends=[Biostrings GenomicRanges Rhtslib]; };
-  seqcombo = derive2 { name="seqcombo"; version="1.16.0"; sha256="0xyrjbvgrld5sy6g6sp79f43j93jnyccwg21il65fqrzb7z4d7xk"; depends=[Biostrings cowplot dplyr ggplot2 igraph magrittr yulab_utils]; };
-  seqsetvis = derive2 { name="seqsetvis"; version="1.14.1"; sha256="1ja286qz7m15k97ms7rm81l0picsjjpm7fmsdpbklc66y3syl089"; depends=[data_table eulerr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 ggplotify IRanges limma pbapply pbmcapply png RColorBrewer Rsamtools rtracklayer S4Vectors UpSetR]; };
+  seqcombo = derive2 { name="seqcombo"; version="1.16.1"; sha256="18iixqj84b4ldg8q0dj8fivxrgqzba6qnj9zin9dhsyfqg5wz6z0"; depends=[Biostrings cowplot dplyr ggplot2 igraph magrittr yulab_utils]; };
+  seqsetvis = derive2 { name="seqsetvis"; version="1.14.2"; sha256="1l3fxskqwh5am1zxyz3l95whlw8wdylagx9n7fvlrfs4lfqbzphr"; depends=[data_table eulerr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 ggplotify IRanges limma pbapply pbmcapply png RColorBrewer Rsamtools rtracklayer S4Vectors UpSetR]; };
   sesame = derive2 { name="sesame"; version="1.12.9"; sha256="0sqmykp5nc87ixhf330bhz0vh28si3c6kfvr8rrfhhf3jvy34a2k"; depends=[BiocParallel DNAcopy e1071 fgsea GenomicRanges ggplot2 ggrepel illuminaio IRanges KernSmooth MASS matrixStats preprocessCore randomForest reshape2 S4Vectors sesameData stringr SummarizedExperiment tibble wheatmap]; };
   sevenC = derive2 { name="sevenC"; version="1.14.0"; sha256="06m6479ps7896zaks8jnnak8l7c6abbsdx56k3l5ir78681g4bq1"; depends=[BiocGenerics boot data_table GenomeInfoDb GenomicRanges InteractionSet IRanges purrr readr rtracklayer S4Vectors]; };
   sevenbridges = derive2 { name="sevenbridges"; version="1.24.0"; sha256="03p7p1mwa3m8zvyz5761xmqhch6cfgy42cv0swwgj0n9jr83sc23"; depends=[curl data_table docopt httr jsonlite objectProperties S4Vectors stringr uuid yaml]; };
@@ -1929,7 +1931,7 @@ in with self; {
   snpStats = derive2 { name="snpStats"; version="1.44.0"; sha256="0ha34b5cg26940xihgky45adns1nflrgq2qjq77w4bncxpaacsqq"; depends=[BiocGenerics Matrix survival zlibbioc]; };
   soGGi = derive2 { name="soGGi"; version="1.26.0"; sha256="1g2lsi8nqpi2vm284jv1ab3i9k03kwqsy9zf51vfnpqq31lrdlki"; depends=[BiocGenerics BiocParallel Biostrings chipseq GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges preprocessCore reshape2 Rsamtools rtracklayer S4Vectors SummarizedExperiment]; };
   sojourner = derive2 { name="sojourner"; version="1.8.0"; sha256="0ld1gh6vznmvd09xrza5xs93n3g0vf8zqymn58b23rilsrvm2cbc"; depends=[dplyr EBImage fitdistrplus ggplot2 gridExtra lattice MASS mclust minpack_lm mixtools mltools nls2 pixmap plyr R_matlab Rcpp reshape2 rlang sampSurf scales shiny shinyjs sp truncnorm]; };
-  sparrow = derive2 { name="sparrow"; version="1.0.1"; sha256="1i0dzj5wnphfhxdl6gmwf3qy8x9v5vb7c35mkq5xml6miwl3x5ha"; depends=[babelgene BiocGenerics BiocParallel BiocSet checkmate circlize ComplexHeatmap data_table DelayedMatrixStats edgeR ggplot2 GSEABase irlba limma Matrix plotly viridis]; };
+  sparrow = derive2 { name="sparrow"; version="1.0.3"; sha256="0mlsbicas04l3c1bhvnqnprjnlqzd6h61k7n3j51bkahrds33nbf"; depends=[babelgene BiocGenerics BiocParallel BiocSet checkmate circlize ComplexHeatmap data_table DelayedMatrixStats edgeR ggplot2 GSEABase irlba limma Matrix plotly viridis]; };
   sparseDOSSA = derive2 { name="sparseDOSSA"; version="1.18.0"; sha256="1rn8jv2b3fmyibgc6h91mhnl9nzqkds02pvj6vbq12pfvhhb021i"; depends=[MASS MCMCpack optparse tmvtnorm]; };
   sparseMatrixStats = derive2 { name="sparseMatrixStats"; version="1.6.0"; sha256="0ifqj4a6mn4749sr62gq3dwd6mmbbzdx5mh5b5663vcgl1kw96x1"; depends=[Matrix MatrixGenerics matrixStats Rcpp]; };
   sparsenetgls = derive2 { name="sparsenetgls"; version="1.12.0"; sha256="0g8vbzhzyccyi77x49c8idhwy357a2azywvllinjapgwiy88s02a"; depends=[glmnet huge MASS Matrix]; };
@@ -1972,9 +1974,9 @@ in with self; {
   switchBox = derive2 { name="switchBox"; version="1.30.0"; sha256="09z9wi8yzjq49rjmn707a1kvf7c203lbxcnc7znwhy7lv51svj67"; depends=[gplots pROC]; };
   switchde = derive2 { name="switchde"; version="1.20.0"; sha256="1n815zwj5znddgc3pz87089q8bvb14n2g61zfang8d8pna4zbf7v"; depends=[dplyr ggplot2 SingleCellExperiment SummarizedExperiment]; };
   synapsis = derive2 { name="synapsis"; version="1.0.0"; sha256="1kqapzcd2zvmyaqshcrfxkkaf6k7kwaqnd6g4dhnjcf2wqnf6fs5"; depends=[EBImage]; };
-  synergyfinder = derive2 { name="synergyfinder"; version="3.2.8"; sha256="07fjam0c6j5ga75601vsbp4x1x8h31gxwxanwjxmixnv7md0pdms"; 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="3.2.10"; sha256="0nc2c8y3msffl8ghp60wmvwnjahxg9w5xfmrpx36r7z81ggdqs9d"; 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="1.24.0"; sha256="1xidxlkppap0x8h9iiyl78lcx50ckpg46n8pl49vz4435vd6grp2"; depends=[doBy dplyr ggplot2 magrittr RankProd RColorBrewer reshape2]; };
-  systemPipeR = derive2 { name="systemPipeR"; version="2.0.5"; sha256="1j91pyfjsqngxxlxjqc477pznlfax4vayrks2q12rxw76ija80hf"; depends=[BiocGenerics Biostrings crayon GenomicRanges ggplot2 htmlwidgets magrittr Rsamtools S4Vectors ShortRead stringr SummarizedExperiment yaml]; };
+  systemPipeR = derive2 { name="systemPipeR"; version="2.0.6"; sha256="0l9m74cz5qf1hcr6f2jng7kd9vc3ppkpjgxh7gla8x0y329q0znz"; depends=[BiocGenerics Biostrings crayon GenomicRanges ggplot2 htmlwidgets magrittr Rsamtools S4Vectors ShortRead stringr SummarizedExperiment yaml]; };
   systemPipeShiny = derive2 { name="systemPipeShiny"; version="1.4.0"; sha256="0h803ijajf32igfknkaivlzrc323apzligq1j8ghpf02q7f5q830"; 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]; };
   systemPipeTools = derive2 { name="systemPipeTools"; version="1.2.0"; sha256="1n53nwb00zmrhb8h1fq4lqzdd87f74c4l1z24sid4xrjssylrnwr"; depends=[ape DESeq2 dplyr DT GGally ggplot2 ggrepel ggtree glmpca magrittr pheatmap plotly Rtsne SummarizedExperiment tibble]; };
   tLOH = derive2 { name="tLOH"; version="1.2.0"; sha256="0k3lqlivxbv4gaipiskhpl34rjrmrn1x4243awxnvbhhvaqq5r50"; depends=[data_table dplyr GenomicRanges ggplot2 MatrixGenerics purrr scales VariantAnnotation]; };
@@ -2070,7 +2072,6 @@ in with self; {
   GenoGAM = derive2 { name="GenoGAM"; version="2.11.0"; sha256="058qix2h0zm2k9csmbdhci2wqih3lyggjj591cqn0ls2nv7bnyvj"; depends=[BiocParallel Biostrings data_table DelayedArray DESeq2 futile_logger GenomeInfoDb GenomicAlignments GenomicRanges HDF5Array IRanges Matrix Rcpp RcppArmadillo rhdf5 Rsamtools S4Vectors sparseinv SummarizedExperiment]; broken = true; };
   Herper = derive2 { name="Herper"; version="1.3.0"; sha256="038cavnbz7gvmv9mpnf88n8dzrg7yl306y68zsq5hpkrj6qax9vr"; depends=[reticulate rjson withr]; broken = true; };
   HiCBricks = derive2 { name="HiCBricks"; version="1.11.0"; sha256="12s01r9z569pp6amlvcs7fqmwivw9jb2ahnnyq6nzflsyn5277kl"; depends=[BiocParallel curl data_table digest GenomeInfoDb GenomicRanges ggplot2 IRanges jsonlite R_utils R6 RColorBrewer readr reshape2 rhdf5 S4Vectors scales stringr tibble viridis]; broken = true; };
-  MBQN = derive2 { name="MBQN"; version="2.5.0"; sha256="01pf9wkk3dsxgx1y8mxfxn9m2j2hqipc5kajm7w8g60bj9flg09j"; depends=[BiocFileCache ggplot2 limma PairedData preprocessCore rappdirs RCurl rpx SummarizedExperiment xml2]; broken = true; };
   MSEADbi = derive2 { name="MSEADbi"; version="1.2.0"; sha256="1g1kg3nh7iwg5nrpmig6srw6as4yfwmbqn965pffrk0zp19llsbf"; depends=[AnnotationDbi Biobase DBI RSQLite]; broken = true; };
   MSstatsTMTPTM = derive2 { name="MSstatsTMTPTM"; version="1.1.2"; sha256="16qnddwhwhjjfr5akdrmp93gkxq2r41s82hb1blbz47lwbj5kaj5"; depends=[dplyr ggplot2 gridExtra MSstatsTMT Rcpp reshape2 stringr]; broken = true; };
   MethCP = derive2 { name="MethCP"; version="1.7.0"; sha256="1smhwmrgckgivf6xfk54sz197cw1mar95chzkrfpf4wxw3jzbbkn"; depends=[BiocParallel bsseq DNAcopy DSS GenomeInfoDb GenomicRanges IRanges methylKit S4Vectors]; broken = true; };
@@ -2085,5 +2086,4 @@ in with self; {
   methyAnalysis = derive2 { name="methyAnalysis"; version="1.34.0"; sha256="05k3n7iy5ijidbnblbqqas8dsj8drwzbhyrbs8wl1ypkg51havi0"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt genefilter GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges lumi methylumi org_Hs_eg_db rtracklayer SummarizedExperiment VariantAnnotation]; broken = true; };
   methylPipe = derive2 { name="methylPipe"; version="1.27.0"; sha256="0z2md9n1flzfsgsbzwffn4q6yfcjyj03bg1vi4phcknigbhg1viy"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicRanges gplots Gviz IRanges marray Rsamtools S4Vectors SummarizedExperiment]; broken = true; };
   perturbatr = derive2 { name="perturbatr"; version="1.13.0"; sha256="0ssk8cr42hibn917s2z2nzcdan54c7xiydypbi8f3g4w68q4ly31"; depends=[assertthat diffusr doParallel dplyr foreach formula_tools ggplot2 igraph lazyeval lme4 magrittr rlang scales tibble tidyr]; broken = true; };
-  phemd = derive2 { name="phemd"; version="1.9.0"; sha256="0hqivlc9hzcfcprng1499nas84fwvgisg8976vsjciyn903355jr"; depends=[Biobase BiocGenerics cluster cowplot destiny ggplot2 igraph maptree monocle phateR pheatmap pracma RANN RColorBrewer reticulate Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; broken = true; };
 }

pkgs/development/tools/continuous-integration/github-runner/default.nix

@@ -13,13 +13,16 @@
 , linkFarmFromDrvs
 , lttng-ust
 , makeWrapper
-, nodejs-12_x
 , nodejs-16_x
 , openssl
 , stdenv
 , zlib
 , writeShellApplication
 , nuget-to-nix
+# Keeping this option until upstream removes support for EoL Node.js 12 entirely
+# Also refer to: https://github.com/actions/runner/pull/1716
+, withNode12 ? false
+, nodejs-12_x
 }:
 let
   nugetSource = linkFarmFromDrvs "nuget-packages" (
@@ -187,15 +190,17 @@ stdenv.mkDerivation rec {
     ++ lib.optionals (stdenv.hostPlatform.system == "aarch64-linux") [
       # "JavaScript Actions in Alpine containers are only supported on x64 Linux runners. Detected Linux Arm64"
       "GitHub.Runner.Common.Tests.Worker.StepHostL0.DetermineNodeRuntimeVersionInAlpineContainerAsync"
+    ]
+    ++ lib.optionals (!withNode12) [
+      "GitHub.Runner.Common.Tests.ProcessExtensionL0.SuccessReadProcessEnv"
     ];
-
   checkInputs = [ git ];
 
   checkPhase = ''
     runHook preCheck
 
     mkdir -p _layout/externals
-    ln -s ${nodejs-12_x} _layout/externals/node12
+    ${lib.optionalString withNode12 "ln -s ${nodejs-12_x} _layout/externals/node12"}
     ln -s ${nodejs-16_x} _layout/externals/node16
 
     printf 'Disabled tests:\n%s\n' '${lib.concatMapStringsSep "\n" (x: " - ${x}") disabledTests}'
@@ -244,7 +249,7 @@ stdenv.mkDerivation rec {
     # externals/node{12,16}. As opposed to the official releases, we don't
     # link the Alpine Node flavors.
     mkdir -p $out/externals
-    ln -s ${nodejs-12_x} $out/externals/node12
+    ${lib.optionalString withNode12 "ln -s ${nodejs-12_x} $out/externals/node12"}
     ln -s ${nodejs-16_x} $out/externals/node16
 
     # Install Nodejs scripts called from workflows

pkgs/development/tools/metal-cli/default.nix

@@ -2,23 +2,29 @@
 
 buildGoModule rec {
   pname = "metal-cli";
-  version = "0.7.3";
+  version = "0.7.4";
 
   src = fetchFromGitHub {
     owner = "equinix";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-PsTQuEbo1ReWwZV4D14mEGsU99j49kleiL/6Xyk+g9s=";
+    sha256 = "sha256-muhHBUb5Ttj4n6fJzIJMqics5rKupeSBZAd4JxZUe64=";
   };
 
-  ldflags = [
-    "-X github.com/equinix/metal-cli/cmd.Version=${version}"
-  ];
-
   vendorSha256 = "sha256-F8d5i9jvjY11Pv6w0ZXI3jr0Wix++B/w9oRTuJGpQfE=";
 
+  ldflags = [
+    "-s" "-w"
+    "-X github.com/equinix/metal-cli/cmd.Version=${version}"
+  ];
+
   doCheck = false;
 
+  doInstallCheck = true;
+  installCheckPhase = ''
+      $out/bin/metal --version | grep ${version}
+  '';
+
   meta = with lib; {
     description = "Official Equinix Metal CLI";
     homepage = "https://github.com/equinix/metal-cli/";

pkgs/development/tools/misc/sccache/default.nix

@@ -16,7 +16,8 @@ rustPlatform.buildRustPackage rec {
   nativeBuildInputs = [ pkg-config ];
   buildInputs = [ openssl ] ++ lib.optional stdenv.isDarwin Security;
 
-  buildFeatures = lib.optionals (!stdenv.isDarwin) [ "dist-client" "dist-server" ];
+  # sccache-dist is only supported on x86_64 Linux machines.
+  buildFeatures = lib.optionals (stdenv.system == "x86_64-linux") [ "dist-client" "dist-server" ];
 
   # Tests fail because of client server setup which is not possible inside the pure environment,
   # see https://github.com/mozilla/sccache/issues/460

pkgs/development/tools/richgo/default.nix

@@ -13,10 +13,6 @@ buildGoModule rec {
 
   vendorSha256 = "sha256-O63QEo0/+m9cYktMg4+RloLuUfAlCG0eGkxpHPFg/Cw=";
 
-  doCheck = false;
-
-  subPackages = [ "." ];
-
   meta = with lib; {
     description = "Enrich `go test` outputs with text decorations";
     homepage = "https://github.com/kyoh86/richgo";