Merge staging-next into staging

maintainers/maintainer-list.nix

@@ -4022,6 +4022,12 @@
     github = "fitzgibbon";
     githubId = 617048;
   };
+  fkautz = {
+    name = "Frederick F. Kautz IV";
+    email = "fkautz@alumni.cmu.edu";
+    github = "fkautz";
+    githubId = 135706;
+  };
   Flakebi = {
     email = "flakebi@t-online.de";
     github = "Flakebi";

nixos/doc/manual/development/activation-script.section.md

@@ -0,0 +1,72 @@
+# Activation script {#sec-activation-script}
+
+The activation script is a bash script called to activate the new
+configuration which resides in a NixOS system in `$out/activate`. Since its
+contents depend on your system configuration, the contents may differ.
+This chapter explains how the script works in general and some common NixOS
+snippets. Please be aware that the script is executed on every boot and system
+switch, so tasks that can be performed in other places should be performed
+there (for example letting a directory of a service be created by systemd using
+mechanisms like `StateDirectory`, `CacheDirectory`, ... or if that's not
+possible using `preStart` of the service).
+
+Activation scripts are defined as snippets using
+[](#opt-system.activationScripts). They can either be a simple multiline string
+or an attribute set that can depend on other snippets. The builder for the
+activation script will take these dependencies into account and order the
+snippets accordingly. As a simple example:
+
+```nix
+system.activationScripts.my-activation-script = {
+  deps = [ "etc" ];
+  # supportsDryActivation = true;
+  text = ''
+    echo "Hallo i bims"
+  '';
+};
+```
+
+This example creates an activation script snippet that is run after the `etc`
+snippet. The special variable `supportsDryActivation` can be set so the snippet
+is also run when `nixos-rebuild dry-activate` is run. To differentiate between
+real and dry activation, the `$NIXOS_ACTION` environment variable can be
+read which is set to `dry-activate` when a dry activation is done.
+
+An activation script can write to special files instructing
+`switch-to-configuration` to restart/reload units. The script will take these
+requests into account and will incorperate the unit configuration as described
+above. This means that the activation script will "fake" a modified unit file
+and `switch-to-configuration` will act accordingly. By doing so, configuration
+like [systemd.services.\<name\>.restartIfChanged](#opt-systemd.services) is
+respected. Since the activation script is run **after** services are already
+stopped, [systemd.services.\<name\>.stopIfChanged](#opt-systemd.services)
+cannot be taken into account anymore and the unit is always restarted instead
+of being stopped and started afterwards.
+
+The files that can be written to are `/run/nixos/activation-restart-list` and
+`/run/nixos/activation-reload-list` with their respective counterparts for
+dry activation being `/run/nixos/dry-activation-restart-list` and
+`/run/nixos/dry-activation-reload-list`. Those files can contain
+newline-separated lists of unit names where duplicates are being ignored. These
+files are not create automatically and activation scripts must take the
+possiblility into account that they have to create them first.
+
+## NixOS snippets {#sec-activation-script-nixos-snippets}
+
+There are some snippets NixOS enables by default because disabling them would
+most likely break you system. This section lists a few of them and what they
+do:
+
+- `binsh` creates `/bin/sh` which points to the runtime shell
+- `etc` sets up the contents of `/etc`, this includes systemd units and
+  excludes `/etc/passwd`, `/etc/group`, and `/etc/shadow` (which are managed by
+  the `users` snippet)
+- `hostname` sets the system's hostname in the kernel (not in `/etc`)
+- `modprobe` sets the path to the `modprobe` binary for module auto-loading
+- `nix` prepares the nix store and adds a default initial channel
+- `specialfs` is responsible for mounting filesystems like `/proc` and `sys`
+- `users` creates and removes users and groups by managing `/etc/passwd`,
+  `/etc/group` and `/etc/shadow`. This also creates home directories
+- `usrbinenv` creates `/usr/bin/env`
+- `var` creates some directories in `/var` that are not service-specific
+- `wrappers` creates setuid wrappers like `ping` and `sudo`

nixos/doc/manual/development/development.xml

@@ -12,6 +12,7 @@
  <xi:include href="../from_md/development/sources.chapter.xml" />
  <xi:include href="../from_md/development/writing-modules.chapter.xml" />
  <xi:include href="../from_md/development/building-parts.chapter.xml" />
+ <xi:include href="../from_md/development/what-happens-during-a-system-switch.chapter.xml" />
  <xi:include href="../from_md/development/writing-documentation.chapter.xml" />
  <xi:include href="../from_md/development/building-nixos.chapter.xml" />
  <xi:include href="../from_md/development/nixos-tests.chapter.xml" />

nixos/doc/manual/development/unit-handling.section.md

@@ -0,0 +1,57 @@
+# Unit handling {#sec-unit-handling}
+
+To figure out what units need to be started/stopped/restarted/reloaded, the
+script first checks the current state of the system, similar to what `systemctl
+list-units` shows. For each of the units, the script goes through the following
+checks:
+
+- Is the unit file still in the new system? If not, **stop** the service unless
+  it sets `X-StopOnRemoval` in the `[Unit]` section to `false`.
+
+- Is it a `.target` unit? If so, **start** it unless it sets
+  `RefuseManualStart` in the `[Unit]` section to `true` or `X-OnlyManualStart`
+  in the `[Unit]` section to `true`. Also **stop** the unit again unless it
+  sets `X-StopOnReconfiguration` to `false`.
+
+- Are the contents of the unit files different? They are compared by parsing
+  them and comparing their contents. If they are different but only
+  `X-Reload-Triggers` in the `[Unit]` section is changed, **reload** the unit.
+  The NixOS module system allows setting these triggers with the option
+  [systemd.services.\<name\>.reloadTriggers](#opt-systemd.services). If the
+  unit files differ in any way, the following actions are performed:
+
+  - `.path` and `.slice` units are ignored. There is no need to restart them
+    since changes in their values are applied by systemd when systemd is
+    reloaded.
+
+  - `.mount` units are **reload**ed. These mostly come from the `/etc/fstab`
+    parser.
+
+  - `.socket` units are currently ignored. This is to be fixed at a later
+    point.
+
+  - The rest of the units (mostly `.service` units) are then **reload**ed if
+    `X-ReloadIfChanged` in the `[Service]` section is set to `true` (exposed
+    via [systemd.services.\<name\>.reloadIfChanged](#opt-systemd.services)).
+
+  - If the reload flag is not set, some more flags decide if the unit is
+    skipped. These flags are `X-RestartIfChanged` in the `[Service]` section
+    (exposed via
+    [systemd.services.\<name\>.restartIfChanged](#opt-systemd.services)),
+    `RefuseManualStop` in the `[Unit]` section, and `X-OnlyManualStart` in the
+    `[Unit]` section.
+
+  - The rest of the behavior is decided whether the unit has `X-StopIfChanged`
+    in the `[Service]` section set (exposed via
+    [systemd.services.\<name\>.stopIfChanged](#opt-systemd.services)). This is
+    set to `true` by default and must be explicitly turned off if not wanted.
+    If the flag is enabled, the unit is **stop**ped and then **start**ed. If
+    not, the unit is **restart**ed. The goal of the flag is to make sure that
+    the new unit never runs in the old environment which is still in place
+    before the activation script is run.
+
+  - The last thing that is taken into account is whether the unit is a service
+    and socket-activated. Due to a bug, this is currently only done when
+    `X-StopIfChanged` is set. If the unit is socket-activated, the socket is
+    stopped and started, and the service is stopped and to be started by socket
+    activation.

nixos/doc/manual/development/what-happens-during-a-system-switch.chapter.md

@@ -0,0 +1,53 @@
+# What happens during a system switch? {#sec-switching-systems}
+
+Running `nixos-rebuild switch` is one of the more common tasks under NixOS.
+This chapter explains some of the internals of this command to make it simpler
+for new module developers to configure their units correctly and to make it
+easier to understand what is happening and why for curious administrators.
+
+`nixos-rebuild`, like many deployment solutions, calls `switch-to-configuration`
+which resides in a NixOS system at `$out/bin/switch-to-configuration`. The
+script is called with the action that is to be performed like `switch`, `test`,
+`boot`. There is also the `dry-activate` action which does not really perform
+the actions but rather prints what it would do if you called it with `test`.
+This feature can be used to check what service states would be changed if the
+configuration was switched to.
+
+If the action is `switch` or `boot`, the bootloader is updated first so the
+configuration will be the next one to boot. Unless `NIXOS_NO_SYNC` is set to
+`1`, `/nix/store` is synced to disk.
+
+If the action is `switch` or `test`, the currently running system is inspected
+and the actions to switch to the new system are calculated. This process takes
+two data sources into account: `/etc/fstab` and the current systemd status.
+Mounts and swaps are read from `/etc/fstab` and the corresponding actions are
+generated. If a new mount is added, for example, the proper `.mount` unit is
+marked to be started. The current systemd state is inspected, the difference
+between the current system and the desired configuration is calculated and
+actions are generated to get to this state. There are a lot of nuances that can
+be controlled by the units which are explained here.
+
+After calculating what should be done, the actions are carried out. The order
+of actions is always the same:
+- Stop units (`systemctl stop`)
+- Run activation script (`$out/activate`)
+- See if the activation script requested more units to restart
+- Restart systemd if needed (`systemd daemon-reexec`)
+- Forget about the failed state of units (`systemctl reset-failed`)
+- Reload systemd (`systemctl daemon-reload`)
+- Reload systemd user instances (`systemctl --user daemon-reload`)
+- Set up tmpfiles (`systemd-tmpfiles --create`)
+- Reload units (`systemctl reload`)
+- Restart units (`systemctl restart`)
+- Start units (`systemctl start`)
+- Inspect what changed during these actions and print units that failed and
+  that were newly started
+
+Most of these actions are either self-explaining but some of them have to do
+with our units or the activation script. For this reason, these topics are
+explained in the next sections.
+
+```{=docbook}
+<xi:include href="unit-handling.section.xml" />
+<xi:include href="activation-script.section.xml" />
+```

nixos/doc/manual/from_md/development/activation-script.section.xml

@@ -0,0 +1,150 @@
+<section xmlns="http://docbook.org/ns/docbook" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="sec-activation-script">
+  <title>Activation script</title>
+  <para>
+    The activation script is a bash script called to activate the new
+    configuration which resides in a NixOS system in
+    <literal>$out/activate</literal>. Since its contents depend on your
+    system configuration, the contents may differ. This chapter explains
+    how the script works in general and some common NixOS snippets.
+    Please be aware that the script is executed on every boot and system
+    switch, so tasks that can be performed in other places should be
+    performed there (for example letting a directory of a service be
+    created by systemd using mechanisms like
+    <literal>StateDirectory</literal>,
+    <literal>CacheDirectory</literal>, … or if that’s not possible using
+    <literal>preStart</literal> of the service).
+  </para>
+  <para>
+    Activation scripts are defined as snippets using
+    <xref linkend="opt-system.activationScripts" />. They can either be
+    a simple multiline string or an attribute set that can depend on
+    other snippets. The builder for the activation script will take
+    these dependencies into account and order the snippets accordingly.
+    As a simple example:
+  </para>
+  <programlisting language="bash">
+system.activationScripts.my-activation-script = {
+  deps = [ &quot;etc&quot; ];
+  # supportsDryActivation = true;
+  text = ''
+    echo &quot;Hallo i bims&quot;
+  '';
+};
+</programlisting>
+  <para>
+    This example creates an activation script snippet that is run after
+    the <literal>etc</literal> snippet. The special variable
+    <literal>supportsDryActivation</literal> can be set so the snippet
+    is also run when <literal>nixos-rebuild dry-activate</literal> is
+    run. To differentiate between real and dry activation, the
+    <literal>$NIXOS_ACTION</literal> environment variable can be read
+    which is set to <literal>dry-activate</literal> when a dry
+    activation is done.
+  </para>
+  <para>
+    An activation script can write to special files instructing
+    <literal>switch-to-configuration</literal> to restart/reload units.
+    The script will take these requests into account and will
+    incorperate the unit configuration as described above. This means
+    that the activation script will <quote>fake</quote> a modified unit
+    file and <literal>switch-to-configuration</literal> will act
+    accordingly. By doing so, configuration like
+    <link linkend="opt-systemd.services">systemd.services.&lt;name&gt;.restartIfChanged</link>
+    is respected. Since the activation script is run
+    <emphasis role="strong">after</emphasis> services are already
+    stopped,
+    <link linkend="opt-systemd.services">systemd.services.&lt;name&gt;.stopIfChanged</link>
+    cannot be taken into account anymore and the unit is always
+    restarted instead of being stopped and started afterwards.
+  </para>
+  <para>
+    The files that can be written to are
+    <literal>/run/nixos/activation-restart-list</literal> and
+    <literal>/run/nixos/activation-reload-list</literal> with their
+    respective counterparts for dry activation being
+    <literal>/run/nixos/dry-activation-restart-list</literal> and
+    <literal>/run/nixos/dry-activation-reload-list</literal>. Those
+    files can contain newline-separated lists of unit names where
+    duplicates are being ignored. These files are not create
+    automatically and activation scripts must take the possiblility into
+    account that they have to create them first.
+  </para>
+  <section xml:id="sec-activation-script-nixos-snippets">
+    <title>NixOS snippets</title>
+    <para>
+      There are some snippets NixOS enables by default because disabling
+      them would most likely break you system. This section lists a few
+      of them and what they do:
+    </para>
+    <itemizedlist spacing="compact">
+      <listitem>
+        <para>
+          <literal>binsh</literal> creates <literal>/bin/sh</literal>
+          which points to the runtime shell
+        </para>
+      </listitem>
+      <listitem>
+        <para>
+          <literal>etc</literal> sets up the contents of
+          <literal>/etc</literal>, this includes systemd units and
+          excludes <literal>/etc/passwd</literal>,
+          <literal>/etc/group</literal>, and
+          <literal>/etc/shadow</literal> (which are managed by the
+          <literal>users</literal> snippet)
+        </para>
+      </listitem>
+      <listitem>
+        <para>
+          <literal>hostname</literal> sets the system’s hostname in the
+          kernel (not in <literal>/etc</literal>)
+        </para>
+      </listitem>
+      <listitem>
+        <para>
+          <literal>modprobe</literal> sets the path to the
+          <literal>modprobe</literal> binary for module auto-loading
+        </para>
+      </listitem>
+      <listitem>
+        <para>
+          <literal>nix</literal> prepares the nix store and adds a
+          default initial channel
+        </para>
+      </listitem>
+      <listitem>
+        <para>
+          <literal>specialfs</literal> is responsible for mounting
+          filesystems like <literal>/proc</literal> and
+          <literal>sys</literal>
+        </para>
+      </listitem>
+      <listitem>
+        <para>
+          <literal>users</literal> creates and removes users and groups
+          by managing <literal>/etc/passwd</literal>,
+          <literal>/etc/group</literal> and
+          <literal>/etc/shadow</literal>. This also creates home
+          directories
+        </para>
+      </listitem>
+      <listitem>
+        <para>
+          <literal>usrbinenv</literal> creates
+          <literal>/usr/bin/env</literal>
+        </para>
+      </listitem>
+      <listitem>
+        <para>
+          <literal>var</literal> creates some directories in
+          <literal>/var</literal> that are not service-specific
+        </para>
+      </listitem>
+      <listitem>
+        <para>
+          <literal>wrappers</literal> creates setuid wrappers like
+          <literal>ping</literal> and <literal>sudo</literal>
+        </para>
+      </listitem>
+    </itemizedlist>
+  </section>
+</section>

nixos/doc/manual/from_md/development/unit-handling.section.xml

@@ -0,0 +1,119 @@
+<section xmlns="http://docbook.org/ns/docbook" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="sec-unit-handling">
+  <title>Unit handling</title>
+  <para>
+    To figure out what units need to be
+    started/stopped/restarted/reloaded, the script first checks the
+    current state of the system, similar to what
+    <literal>systemctl list-units</literal> shows. For each of the
+    units, the script goes through the following checks:
+  </para>
+  <itemizedlist>
+    <listitem>
+      <para>
+        Is the unit file still in the new system? If not,
+        <emphasis role="strong">stop</emphasis> the service unless it
+        sets <literal>X-StopOnRemoval</literal> in the
+        <literal>[Unit]</literal> section to <literal>false</literal>.
+      </para>
+    </listitem>
+    <listitem>
+      <para>
+        Is it a <literal>.target</literal> unit? If so,
+        <emphasis role="strong">start</emphasis> it unless it sets
+        <literal>RefuseManualStart</literal> in the
+        <literal>[Unit]</literal> section to <literal>true</literal> or
+        <literal>X-OnlyManualStart</literal> in the
+        <literal>[Unit]</literal> section to <literal>true</literal>.
+        Also <emphasis role="strong">stop</emphasis> the unit again
+        unless it sets <literal>X-StopOnReconfiguration</literal> to
+        <literal>false</literal>.
+      </para>
+    </listitem>
+    <listitem>
+      <para>
+        Are the contents of the unit files different? They are compared
+        by parsing them and comparing their contents. If they are
+        different but only <literal>X-Reload-Triggers</literal> in the
+        <literal>[Unit]</literal> section is changed,
+        <emphasis role="strong">reload</emphasis> the unit. The NixOS
+        module system allows setting these triggers with the option
+        <link linkend="opt-systemd.services">systemd.services.&lt;name&gt;.reloadTriggers</link>.
+        If the unit files differ in any way, the following actions are
+        performed:
+      </para>
+      <itemizedlist>
+        <listitem>
+          <para>
+            <literal>.path</literal> and <literal>.slice</literal> units
+            are ignored. There is no need to restart them since changes
+            in their values are applied by systemd when systemd is
+            reloaded.
+          </para>
+        </listitem>
+        <listitem>
+          <para>
+            <literal>.mount</literal> units are
+            <emphasis role="strong">reload</emphasis>ed. These mostly
+            come from the <literal>/etc/fstab</literal> parser.
+          </para>
+        </listitem>
+        <listitem>
+          <para>
+            <literal>.socket</literal> units are currently ignored. This
+            is to be fixed at a later point.
+          </para>
+        </listitem>
+        <listitem>
+          <para>
+            The rest of the units (mostly <literal>.service</literal>
+            units) are then <emphasis role="strong">reload</emphasis>ed
+            if <literal>X-ReloadIfChanged</literal> in the
+            <literal>[Service]</literal> section is set to
+            <literal>true</literal> (exposed via
+            <link linkend="opt-systemd.services">systemd.services.&lt;name&gt;.reloadIfChanged</link>).
+          </para>
+        </listitem>
+        <listitem>
+          <para>
+            If the reload flag is not set, some more flags decide if the
+            unit is skipped. These flags are
+            <literal>X-RestartIfChanged</literal> in the
+            <literal>[Service]</literal> section (exposed via
+            <link linkend="opt-systemd.services">systemd.services.&lt;name&gt;.restartIfChanged</link>),
+            <literal>RefuseManualStop</literal> in the
+            <literal>[Unit]</literal> section, and
+            <literal>X-OnlyManualStart</literal> in the
+            <literal>[Unit]</literal> section.
+          </para>
+        </listitem>
+        <listitem>
+          <para>
+            The rest of the behavior is decided whether the unit has
+            <literal>X-StopIfChanged</literal> in the
+            <literal>[Service]</literal> section set (exposed via
+            <link linkend="opt-systemd.services">systemd.services.&lt;name&gt;.stopIfChanged</link>).
+            This is set to <literal>true</literal> by default and must
+            be explicitly turned off if not wanted. If the flag is
+            enabled, the unit is
+            <emphasis role="strong">stop</emphasis>ped and then
+            <emphasis role="strong">start</emphasis>ed. If not, the unit
+            is <emphasis role="strong">restart</emphasis>ed. The goal of
+            the flag is to make sure that the new unit never runs in the
+            old environment which is still in place before the
+            activation script is run.
+          </para>
+        </listitem>
+        <listitem>
+          <para>
+            The last thing that is taken into account is whether the
+            unit is a service and socket-activated. Due to a bug, this
+            is currently only done when
+            <literal>X-StopIfChanged</literal> is set. If the unit is
+            socket-activated, the socket is stopped and started, and the
+            service is stopped and to be started by socket activation.
+          </para>
+        </listitem>
+      </itemizedlist>
+    </listitem>
+  </itemizedlist>
+</section>

nixos/doc/manual/from_md/development/what-happens-during-a-system-switch.chapter.xml

@@ -0,0 +1,122 @@
+<chapter xmlns="http://docbook.org/ns/docbook"  xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xi="http://www.w3.org/2001/XInclude" xml:id="sec-switching-systems">
+  <title>What happens during a system switch?</title>
+  <para>
+    Running <literal>nixos-rebuild switch</literal> is one of the more
+    common tasks under NixOS. This chapter explains some of the
+    internals of this command to make it simpler for new module
+    developers to configure their units correctly and to make it easier
+    to understand what is happening and why for curious administrators.
+  </para>
+  <para>
+    <literal>nixos-rebuild</literal>, like many deployment solutions,
+    calls <literal>switch-to-configuration</literal> which resides in a
+    NixOS system at <literal>$out/bin/switch-to-configuration</literal>.
+    The script is called with the action that is to be performed like
+    <literal>switch</literal>, <literal>test</literal>,
+    <literal>boot</literal>. There is also the
+    <literal>dry-activate</literal> action which does not really perform
+    the actions but rather prints what it would do if you called it with
+    <literal>test</literal>. This feature can be used to check what
+    service states would be changed if the configuration was switched
+    to.
+  </para>
+  <para>
+    If the action is <literal>switch</literal> or
+    <literal>boot</literal>, the bootloader is updated first so the
+    configuration will be the next one to boot. Unless
+    <literal>NIXOS_NO_SYNC</literal> is set to <literal>1</literal>,
+    <literal>/nix/store</literal> is synced to disk.
+  </para>
+  <para>
+    If the action is <literal>switch</literal> or
+    <literal>test</literal>, the currently running system is inspected
+    and the actions to switch to the new system are calculated. This
+    process takes two data sources into account:
+    <literal>/etc/fstab</literal> and the current systemd status. Mounts
+    and swaps are read from <literal>/etc/fstab</literal> and the
+    corresponding actions are generated. If a new mount is added, for
+    example, the proper <literal>.mount</literal> unit is marked to be
+    started. The current systemd state is inspected, the difference
+    between the current system and the desired configuration is
+    calculated and actions are generated to get to this state. There are
+    a lot of nuances that can be controlled by the units which are
+    explained here.
+  </para>
+  <para>
+    After calculating what should be done, the actions are carried out.
+    The order of actions is always the same:
+  </para>
+  <itemizedlist spacing="compact">
+    <listitem>
+      <para>
+        Stop units (<literal>systemctl stop</literal>)
+      </para>
+    </listitem>
+    <listitem>
+      <para>
+        Run activation script (<literal>$out/activate</literal>)
+      </para>
+    </listitem>
+    <listitem>
+      <para>
+        See if the activation script requested more units to restart
+      </para>
+    </listitem>
+    <listitem>
+      <para>
+        Restart systemd if needed
+        (<literal>systemd daemon-reexec</literal>)
+      </para>
+    </listitem>
+    <listitem>
+      <para>
+        Forget about the failed state of units
+        (<literal>systemctl reset-failed</literal>)
+      </para>
+    </listitem>
+    <listitem>
+      <para>
+        Reload systemd (<literal>systemctl daemon-reload</literal>)
+      </para>
+    </listitem>
+    <listitem>
+      <para>
+        Reload systemd user instances
+        (<literal>systemctl --user daemon-reload</literal>)
+      </para>
+    </listitem>
+    <listitem>
+      <para>
+        Set up tmpfiles (<literal>systemd-tmpfiles --create</literal>)
+      </para>
+    </listitem>
+    <listitem>
+      <para>
+        Reload units (<literal>systemctl reload</literal>)
+      </para>
+    </listitem>
+    <listitem>
+      <para>
+        Restart units (<literal>systemctl restart</literal>)
+      </para>
+    </listitem>
+    <listitem>
+      <para>
+        Start units (<literal>systemctl start</literal>)
+      </para>
+    </listitem>
+    <listitem>
+      <para>
+        Inspect what changed during these actions and print units that
+        failed and that were newly started
+      </para>
+    </listitem>
+  </itemizedlist>
+  <para>
+    Most of these actions are either self-explaining but some of them
+    have to do with our units or the activation script. For this reason,
+    these topics are explained in the next sections.
+  </para>
+  <xi:include href="unit-handling.section.xml" />
+  <xi:include href="activation-script.section.xml" />
+</chapter>

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

@@ -42,6 +42,14 @@
           upgrade notes</link>.
         </para>
       </listitem>
+      <listitem>
+        <para>
+          systemd services can now set
+          <link linkend="opt-systemd.services">systemd.services.&lt;name&gt;.reloadTriggers</link>
+          instead of <literal>reloadIfChanged</literal> for a more
+          granular distinction between reloads and restarts.
+        </para>
+      </listitem>
     </itemizedlist>
   </section>
   <section xml:id="sec-release-22.05-new-services">
@@ -550,6 +558,15 @@
               honors <literal>restartIfChanged</literal> and
               <literal>reloadIfChanged</literal> of the units.
             </para>
+            <itemizedlist spacing="compact">
+              <listitem>
+                <para>
+                  Preferring to reload instead of restarting can still
+                  be achieved using
+                  <literal>/run/nixos/activation-reload-list</literal>.
+                </para>
+              </listitem>
+            </itemizedlist>
           </listitem>
           <listitem>
             <para>

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

@@ -17,6 +17,8 @@ In addition to numerous new and upgraded packages, this release has the followin
   Migrations may take a while, see the [changelog](https://docs.mattermost.com/install/self-managed-changelog.html#release-v6-3-extended-support-release)
   and [important upgrade notes](https://docs.mattermost.com/upgrade/important-upgrade-notes.html).
 
+- systemd services can now set [systemd.services.\<name\>.reloadTriggers](#opt-systemd.services) instead of `reloadIfChanged` for a more granular distinction between reloads and restarts.
+
 ## New Services {#sec-release-22.05-new-services}
 
 - [aesmd](https://github.com/intel/linux-sgx#install-the-intelr-sgx-psw), the Intel SGX Architectural Enclave Service Manager. Available as [services.aesmd](#opt-services.aesmd.enable).
@@ -179,6 +181,7 @@ In addition to numerous new and upgraded packages, this release has the followin
 
 - `switch-to-configuration` (the script that is run when running `nixos-rebuild switch` for example) has been reworked
     * The interface that allows activation scripts to restart units has been streamlined. Restarting and reloading is now done by a single file `/run/nixos/activation-restart-list` that honors `restartIfChanged` and `reloadIfChanged` of the units.
+        * Preferring to reload instead of restarting can still be achieved using `/run/nixos/activation-reload-list`.
     * The script now uses a proper ini-file parser to parse systemd units. Some values are now only searched in one section instead of in the entire unit. This is only relevant for units that don't use the NixOS systemd moule.
         * `RefuseManualStop`, `X-OnlyManualStart`, `X-StopOnRemoval`, `X-StopOnReconfiguration` are only searched in the `[Unit]` section
         * `X-ReloadIfChanged`, `X-RestartIfChanged`, `X-StopIfChanged` are only searched in the `[Service]` section

nixos/lib/systemd-unit-options.nix

@@ -201,6 +201,17 @@ in rec {
       '';
     };
 
+    reloadTriggers = mkOption {
+      default = [];
+      type = types.listOf unitOption;
+      description = ''
+        An arbitrary list of items such as derivations.  If any item
+        in the list changes between reconfigurations, the service will
+        be reloaded.  If anything but a reload trigger changes in the
+        unit file, the unit will be restarted instead.
+      '';
+    };
+
     onFailure = mkOption {
       default = [];
       type = types.listOf unitNameType;
@@ -338,6 +349,11 @@ in rec {
         configuration switch if its definition has changed.  If
         enabled, the value of <option>restartIfChanged</option> is
         ignored.
+
+        This option should not be used anymore in favor of
+        <option>reloadTriggers</option> which allows more granular
+        control of when a service is reloaded and when a service
+        is restarted.
       '';
     };
 

nixos/modules/system/activation/switch-to-configuration.pl

@@ -2,10 +2,11 @@
 
 use strict;
 use warnings;
+use Array::Compare;
 use Config::IniFiles;
 use File::Path qw(make_path);
 use File::Basename;
-use File::Slurp;
+use File::Slurp qw(read_file write_file edit_file);
 use Net::DBus;
 use Sys::Syslog qw(:standard :macros);
 use Cwd 'abs_path';
@@ -20,12 +21,19 @@ my $restartListFile = "/run/nixos/restart-list";
 my $reloadListFile = "/run/nixos/reload-list";
 
 # Parse restart/reload requests by the activation script.
-# Activation scripts may write newline-separated units to this
+# Activation scripts may write newline-separated units to the restart
 # file and switch-to-configuration will handle them. While
 # `stopIfChanged = true` is ignored, switch-to-configuration will
 # handle `restartIfChanged = false` and `reloadIfChanged = true`.
+# This is the same as specifying a restart trigger in the NixOS module.
+#
+# The reload file asks the script to reload a unit. This is the same as
+# specifying a reload trigger in the NixOS module and can be ignored if
+# the unit is restarted in this activation.
 my $restartByActivationFile = "/run/nixos/activation-restart-list";
+my $reloadByActivationFile = "/run/nixos/activation-reload-list";
 my $dryRestartByActivationFile = "/run/nixos/dry-activation-restart-list";
+my $dryReloadByActivationFile = "/run/nixos/dry-activation-reload-list";
 
 make_path("/run/nixos", { mode => oct(755) });
 
@@ -131,6 +139,10 @@ sub parseSystemdIni {
 
     # Copy over all sections
     foreach my $sectionName (keys %fileContents) {
+        if ($sectionName eq "Install") {
+            # Skip the [Install] section because it has no relevant keys for us
+            next;
+        }
         # Copy over all keys
         foreach my $iniKey (keys %{$fileContents{$sectionName}}) {
             # Ensure the value is an array so it's easier to work with
@@ -192,16 +204,92 @@ sub recordUnit {
     write_file($fn, { append => 1 }, "$unit\n") if $action ne "dry-activate";
 }
 
-# As a fingerprint for determining whether a unit has changed, we use
-# its absolute path. If it has an override file, we append *its*
-# absolute path as well.
-sub fingerprintUnit {
-    my ($s) = @_;
-    return abs_path($s) . (-f "${s}.d/overrides.conf" ? " " . abs_path "${s}.d/overrides.conf" : "");
+# The opposite of recordUnit, removes a unit name from a file
+sub unrecord_unit {
+    my ($fn, $unit) = @_;
+    edit_file { s/^$unit\n//msx } $fn if $action ne "dry-activate";
+}
+
+# Compare the contents of two unit files and return whether the unit
+# needs to be restarted or reloaded. If the units differ, the service
+# is restarted unless the only difference is `X-Reload-Triggers` in the
+# `Unit` section. If this is the only modification, the unit is reloaded
+# instead of restarted.
+# Returns:
+# - 0 if the units are equal
+# - 1 if the units are different and a restart action is required
+# - 2 if the units are different and a reload action is required
+sub compare_units {
+    my ($old_unit, $new_unit) = @_;
+    my $comp = Array::Compare->new;
+    my $ret = 0;
+
+    # Comparison hash for the sections
+    my %section_cmp = map { $_ => 1 } keys %{$new_unit};
+    # Iterate over the sections
+    foreach my $section_name (keys %{$old_unit}) {
+        # Missing section in the new unit?
+        if (not exists $section_cmp{$section_name}) {
+            if ($section_name eq 'Unit' and %{$old_unit->{'Unit'}} == 1 and defined(%{$old_unit->{'Unit'}}{'X-Reload-Triggers'})) {
+                # If a new [Unit] section was removed that only contained X-Reload-Triggers,
+                # do nothing.
+                next;
+            } else {
+                return 1;
+            }
+        }
+        delete $section_cmp{$section_name};
+        # Comparison hash for the section contents
+        my %ini_cmp = map { $_ => 1 } keys %{$new_unit->{$section_name}};
+        # Iterate over the keys of the section
+        foreach my $ini_key (keys %{$old_unit->{$section_name}}) {
+            delete $ini_cmp{$ini_key};
+            my @old_value = @{$old_unit->{$section_name}{$ini_key}};
+            # If the key is missing in the new unit, they are different...
+            if (not $new_unit->{$section_name}{$ini_key}) {
+                # ... unless the key that is now missing was the reload trigger
+                if ($section_name eq 'Unit' and $ini_key eq 'X-Reload-Triggers') {
+                    next;
+                }
+                return 1;
+            }
+            my @new_value = @{$new_unit->{$section_name}{$ini_key}};
+            # If the contents are different, the units are different
+            if (not $comp->compare(\@old_value, \@new_value)) {
+                # Check if only the reload triggers changed
+                if ($section_name eq 'Unit' and $ini_key eq 'X-Reload-Triggers') {
+                    $ret = 2;
+                } else {
+                    return 1;
+                }
+            }
+        }
+        # A key was introduced that was missing in the old unit
+        if (%ini_cmp) {
+            if ($section_name eq 'Unit' and %ini_cmp == 1 and defined($ini_cmp{'X-Reload-Triggers'})) {
+                # If the newly introduced key was the reload triggers, reload the unit
+                $ret = 2;
+            } else {
+                return 1;
+            }
+        };
+    }
+    # A section was introduced that was missing in the old unit
+    if (%section_cmp) {
+        if (%section_cmp == 1 and defined($section_cmp{'Unit'}) and %{$new_unit->{'Unit'}} == 1 and defined(%{$new_unit->{'Unit'}}{'X-Reload-Triggers'})) {
+            # If a new [Unit] section was introduced that only contains X-Reload-Triggers,
+            # reload instead of restarting
+            $ret = 2;
+        } else {
+            return 1;
+        }
+    }
+
+    return $ret;
 }
 
 sub handleModifiedUnit {
-    my ($unit, $baseName, $newUnitFile, $activePrev, $unitsToStop, $unitsToStart, $unitsToReload, $unitsToRestart, $unitsToSkip) = @_;
+    my ($unit, $baseName, $newUnitFile, $newUnitInfo, $activePrev, $unitsToStop, $unitsToStart, $unitsToReload, $unitsToRestart, $unitsToSkip) = @_;
 
     if ($unit eq "sysinit.target" || $unit eq "basic.target" || $unit eq "multi-user.target" || $unit eq "graphical.target" || $unit =~ /\.path$/ || $unit =~ /\.slice$/) {
         # Do nothing.  These cannot be restarted directly.
@@ -219,8 +307,8 @@ sub handleModifiedUnit {
         # Revert of the attempt: https://github.com/NixOS/nixpkgs/pull/147609
         # More details: https://github.com/NixOS/nixpkgs/issues/74899#issuecomment-981142430
     } else {
-        my %unitInfo = parseUnit($newUnitFile);
-        if (parseSystemdBool(\%unitInfo, "Service", "X-ReloadIfChanged", 0)) {
+        my %unitInfo = $newUnitInfo ? %{$newUnitInfo} : parseUnit($newUnitFile);
+        if (parseSystemdBool(\%unitInfo, "Service", "X-ReloadIfChanged", 0) and not $unitsToRestart->{$unit} and not $unitsToStop->{$unit}) {
             $unitsToReload->{$unit} = 1;
             recordUnit($reloadListFile, $unit);
         }
@@ -234,6 +322,11 @@ sub handleModifiedUnit {
                 # stopped and started.
                 $unitsToRestart->{$unit} = 1;
                 recordUnit($restartListFile, $unit);
+                # Remove from units to reload so we don't restart and reload
+                if ($unitsToReload->{$unit}) {
+                    delete $unitsToReload->{$unit};
+                    unrecord_unit($reloadListFile, $unit);
+                }
             } else {
                 # If this unit is socket-activated, then stop the
                 # socket unit(s) as well, and restart the
@@ -254,6 +347,11 @@ sub handleModifiedUnit {
                                 recordUnit($startListFile, $socket);
                                 $socketActivated = 1;
                             }
+                            # Remove from units to reload so we don't restart and reload
+                            if ($unitsToReload->{$unit}) {
+                                delete $unitsToReload->{$unit};
+                                unrecord_unit($reloadListFile, $unit);
+                            }
                         }
                     }
                 }
@@ -268,6 +366,11 @@ sub handleModifiedUnit {
                 }
 
                 $unitsToStop->{$unit} = 1;
+                # Remove from units to reload so we don't restart and reload
+                if ($unitsToReload->{$unit}) {
+                    delete $unitsToReload->{$unit};
+                    unrecord_unit($reloadListFile, $unit);
+                }
             }
         }
     }
@@ -344,8 +447,16 @@ while (my ($unit, $state) = each %{$activePrev}) {
             }
         }
 
-        elsif (fingerprintUnit($prevUnitFile) ne fingerprintUnit($newUnitFile)) {
-            handleModifiedUnit($unit, $baseName, $newUnitFile, $activePrev, \%unitsToStop, \%unitsToStart, \%unitsToReload, \%unitsToRestart, \%unitsToSkip);
+        else {
+            my %old_unit_info = parseUnit($prevUnitFile);
+            my %new_unit_info = parseUnit($newUnitFile);
+            my $diff = compare_units(\%old_unit_info, \%new_unit_info);
+            if ($diff eq 1) {
+                handleModifiedUnit($unit, $baseName, $newUnitFile, \%new_unit_info, $activePrev, \%unitsToStop, \%unitsToStart, \%unitsToReload, \%unitsToRestart, \%unitsToSkip);
+            } elsif ($diff eq 2 and not $unitsToRestart{$unit}) {
+                $unitsToReload{$unit} = 1;
+                recordUnit($reloadListFile, $unit);
+            }
         }
     }
 }
@@ -361,17 +472,6 @@ sub pathToUnitName {
     return $escaped;
 }
 
-sub unique {
-    my %seen;
-    my @res;
-    foreach my $name (@_) {
-        next if $seen{$name};
-        $seen{$name} = 1;
-        push @res, $name;
-    }
-    return @res;
-}
-
 # Compare the previous and new fstab to figure out which filesystems
 # need a remount or need to be unmounted.  New filesystems are mounted
 # automatically by starting local-fs.target.  FIXME: might be nicer if
@@ -407,8 +507,12 @@ foreach my $device (keys %$prevSwaps) {
         # "systemctl stop" here because systemd has lots of alias
         # units that prevent a stop from actually calling
         # "swapoff".
-        print STDERR "stopping swap device: $device\n";
-        system("@utillinux@/sbin/swapoff", $device);
+        if ($action ne "dry-activate") {
+            print STDERR "would stop swap device: $device\n";
+        } else {
+            print STDERR "stopping swap device: $device\n";
+            system("@utillinux@/sbin/swapoff", $device);
+        }
     }
     # FIXME: update swap options (i.e. its priority).
 }
@@ -469,10 +573,20 @@ if ($action eq "dry-activate") {
             next;
         }
 
-        handleModifiedUnit($unit, $baseName, $newUnitFile, $activePrev, \%unitsToRestart, \%unitsToRestart, \%unitsToReload, \%unitsToRestart, \%unitsToSkip);
+        handleModifiedUnit($unit, $baseName, $newUnitFile, undef, $activePrev, \%unitsToRestart, \%unitsToRestart, \%unitsToReload, \%unitsToRestart, \%unitsToSkip);
     }
     unlink($dryRestartByActivationFile);
 
+    foreach (split('\n', read_file($dryReloadByActivationFile, err_mode => 'quiet') // "")) {
+        my $unit = $_;
+
+        if (defined($activePrev->{$unit}) and not $unitsToRestart{$unit} and not $unitsToStop{$unit}) {
+            $unitsToReload{$unit} = 1;
+            recordUnit($reloadListFile, $unit);
+        }
+    }
+    unlink($dryReloadByActivationFile);
+
     print STDERR "would restart systemd\n" if $restartSystemd;
     print STDERR "would reload the following units: ", join(", ", sort(keys %unitsToReload)), "\n"
         if scalar(keys %unitsToReload) > 0;
@@ -525,11 +639,22 @@ foreach (split('\n', read_file($restartByActivationFile, err_mode => 'quiet') //
         next;
     }
 
-    handleModifiedUnit($unit, $baseName, $newUnitFile, $activePrev, \%unitsToRestart, \%unitsToRestart, \%unitsToReload, \%unitsToRestart, \%unitsToSkip);
+    handleModifiedUnit($unit, $baseName, $newUnitFile, undef, $activePrev, \%unitsToRestart, \%unitsToRestart, \%unitsToReload, \%unitsToRestart, \%unitsToSkip);
 }
 # We can remove the file now because it has been propagated to the other restart/reload files
 unlink($restartByActivationFile);
 
+foreach (split('\n', read_file($reloadByActivationFile, err_mode => 'quiet') // "")) {
+    my $unit = $_;
+
+    if (defined($activePrev->{$unit}) and not $unitsToRestart{$unit} and not $unitsToStop{$unit}) {
+        $unitsToReload{$unit} = 1;
+        recordUnit($reloadListFile, $unit);
+    }
+}
+# We can remove the file now because it has been propagated to the other reload file
+unlink($reloadByActivationFile);
+
 # Restart systemd if necessary. Note that this is done using the
 # current version of systemd, just in case the new one has trouble
 # communicating with the running pid 1.

nixos/modules/system/activation/top-level.nix

@@ -117,7 +117,7 @@ let
     configurationName = config.boot.loader.grub.configurationName;
 
     # Needed by switch-to-configuration.
-    perl = pkgs.perl.withPackages (p: with p; [ FileSlurp NetDBus XMLParser XMLTwig ConfigIniFiles ]);
+    perl = pkgs.perl.withPackages (p: with p; [ ArrayCompare ConfigIniFiles FileSlurp NetDBus ]);
   };
 
   # Handle assertions and warnings

nixos/modules/system/boot/systemd.nix

@@ -243,6 +243,8 @@ let
           { Requisite = toString config.requisite; }
         // optionalAttrs (config.restartTriggers != [])
           { X-Restart-Triggers = toString config.restartTriggers; }
+        // optionalAttrs (config.reloadTriggers != [])
+          { X-Reload-Triggers = toString config.reloadTriggers; }
         // optionalAttrs (config.description != "") {
           Description = config.description; }
         // optionalAttrs (config.documentation != []) {
@@ -917,6 +919,9 @@ in
               (optional hasDeprecated
                 "Service '${name}.service' uses the attribute 'StartLimitInterval' in the Service section, which is deprecated. See https://github.com/NixOS/nixpkgs/issues/45786."
               )
+              (optional (service.reloadIfChanged && service.reloadTriggers != [])
+                "Service '${name}.service' has both 'reloadIfChanged' and 'reloadTriggers' set. This is probably not what you want, because 'reloadTriggers' behave the same whay as 'restartTriggers' if 'reloadIfChanged' is set."
+              )
             ]
         )
         cfg.services

nixos/tests/switch-test.nix

@@ -18,6 +18,7 @@ import ./make-test-python.nix ({ pkgs, ...} : {
               Type = "oneshot";
               RemainAfterExit = true;
               ExecStart = "${pkgs.coreutils}/bin/true";
+              ExecReload = "${pkgs.coreutils}/bin/true";
             };
           };
         };
@@ -70,6 +71,80 @@ import ./make-test-python.nix ({ pkgs, ...} : {
           };
         };
 
+        simpleServiceWithExtraSection.configuration = {
+          imports = [ simpleServiceNostop.configuration ];
+          systemd.packages = [ (pkgs.writeTextFile {
+            name = "systemd-extra-section";
+            destination = "/etc/systemd/system/test.service";
+            text = ''
+              [X-Test]
+              X-Test-Value=a
+            '';
+          }) ];
+        };
+
+        simpleServiceWithExtraSectionOtherName.configuration = {
+          imports = [ simpleServiceNostop.configuration ];
+          systemd.packages = [ (pkgs.writeTextFile {
+            name = "systemd-extra-section";
+            destination = "/etc/systemd/system/test.service";
+            text = ''
+              [X-Test2]
+              X-Test-Value=a
+            '';
+          }) ];
+        };
+
+        simpleServiceWithInstallSection.configuration = {
+          imports = [ simpleServiceNostop.configuration ];
+          systemd.packages = [ (pkgs.writeTextFile {
+            name = "systemd-extra-section";
+            destination = "/etc/systemd/system/test.service";
+            text = ''
+              [Install]
+              WantedBy=multi-user.target
+            '';
+          }) ];
+        };
+
+        simpleServiceWithExtraKey.configuration = {
+          imports = [ simpleServiceNostop.configuration ];
+          systemd.services.test.serviceConfig."X-Test" = "test";
+        };
+
+        simpleServiceWithExtraKeyOtherValue.configuration = {
+          imports = [ simpleServiceNostop.configuration ];
+          systemd.services.test.serviceConfig."X-Test" = "test2";
+        };
+
+        simpleServiceWithExtraKeyOtherName.configuration = {
+          imports = [ simpleServiceNostop.configuration ];
+          systemd.services.test.serviceConfig."X-Test2" = "test";
+        };
+
+        simpleServiceReloadTrigger.configuration = {
+          imports = [ simpleServiceNostop.configuration ];
+          systemd.services.test.reloadTriggers = [ "/dev/null" ];
+        };
+
+        simpleServiceReloadTriggerModified.configuration = {
+          imports = [ simpleServiceNostop.configuration ];
+          systemd.services.test.reloadTriggers = [ "/dev/zero" ];
+        };
+
+        simpleServiceReloadTriggerModifiedAndSomethingElse.configuration = {
+          imports = [ simpleServiceNostop.configuration ];
+          systemd.services.test = {
+            reloadTriggers = [ "/dev/zero" ];
+            serviceConfig."X-Test" = "test";
+          };
+        };
+
+        simpleServiceReloadTriggerModifiedSomethingElse.configuration = {
+          imports = [ simpleServiceNostop.configuration ];
+          systemd.services.test.serviceConfig."X-Test" = "test";
+        };
+
         restart-and-reload-by-activation-script.configuration = {
           systemd.services = rec {
             simple-service = {
@@ -93,6 +168,17 @@ import ./make-test-python.nix ({ pkgs, ...} : {
             no-restart-service = simple-service // {
               restartIfChanged = false;
             };
+
+            reload-triggers = simple-service // {
+              wantedBy = [ "multi-user.target" ];
+            };
+
+            reload-triggers-and-restart-by-as = simple-service;
+
+            reload-triggers-and-restart = simple-service // {
+              stopIfChanged = false; # easier to check for this
+              wantedBy = [ "multi-user.target" ];
+            };
           };
 
           system.activationScripts.restart-and-reload-test = {
@@ -101,19 +187,33 @@ import ./make-test-python.nix ({ pkgs, ...} : {
             text = ''
               if [ "$NIXOS_ACTION" = dry-activate ]; then
                 f=/run/nixos/dry-activation-restart-list
+                g=/run/nixos/dry-activation-reload-list
               else
                 f=/run/nixos/activation-restart-list
+                g=/run/nixos/activation-reload-list
               fi
               cat <<EOF >> "$f"
               simple-service.service
               simple-restart-service.service
               simple-reload-service.service
               no-restart-service.service
+              reload-triggers-and-restart-by-as.service
+              EOF
+
+              cat <<EOF >> "$g"
+              reload-triggers.service
+              reload-triggers-and-restart-by-as.service
+              reload-triggers-and-restart.service
               EOF
             '';
           };
         };
 
+        restart-and-reload-by-activation-script-modified.configuration = {
+          imports = [ restart-and-reload-by-activation-script.configuration ];
+          systemd.services.reload-triggers-and-restart.serviceConfig.X-Modified = "test";
+        };
+
         mount.configuration = {
           systemd.mounts = [
             {
@@ -241,6 +341,8 @@ import ./make-test-python.nix ({ pkgs, ...} : {
             raise Exception(f"Unexpected string '{needle}' was found")
 
 
+    machine.wait_for_unit("multi-user.target")
+
     machine.succeed(
         "${stderrRunner} ${originalSystem}/bin/switch-to-configuration test"
     )
@@ -379,6 +481,130 @@ import ./make-test-python.nix ({ pkgs, ...} : {
         assert_contains(out, "Main PID:")  # output of systemctl
         assert_lacks(out, "as well:")
 
+    with subtest("unit file parser"):
+        # Switch to a well-known state
+        switch_to_specialisation("${machine}", "simpleServiceNostop")
+
+        # Add a section
+        out = switch_to_specialisation("${machine}", "simpleServiceWithExtraSection")
+        assert_lacks(out, "stopping the following units:")
+        assert_lacks(out, "NOT restarting the following changed units:")
+        assert_lacks(out, "reloading the following units:")
+        assert_contains(out, "\nrestarting the following units: test.service\n")
+        assert_lacks(out, "\nstarting the following units:")
+        assert_lacks(out, "the following new units were started:")
+        assert_lacks(out, "as well:")
+
+        # Rename it
+        out = switch_to_specialisation("${machine}", "simpleServiceWithExtraSectionOtherName")
+        assert_lacks(out, "stopping the following units:")
+        assert_lacks(out, "NOT restarting the following changed units:")
+        assert_lacks(out, "reloading the following units:")
+        assert_contains(out, "\nrestarting the following units: test.service\n")
+        assert_lacks(out, "\nstarting the following units:")
+        assert_lacks(out, "the following new units were started:")
+        assert_lacks(out, "as well:")
+
+        # Remove it
+        out = switch_to_specialisation("${machine}", "simpleServiceNostop")
+        assert_lacks(out, "stopping the following units:")
+        assert_lacks(out, "NOT restarting the following changed units:")
+        assert_lacks(out, "reloading the following units:")
+        assert_contains(out, "\nrestarting the following units: test.service\n")
+        assert_lacks(out, "\nstarting the following units:")
+        assert_lacks(out, "the following new units were started:")
+        assert_lacks(out, "as well:")
+
+        # [Install] section is ignored
+        out = switch_to_specialisation("${machine}", "simpleServiceWithInstallSection")
+        assert_lacks(out, "stopping the following units:")
+        assert_lacks(out, "NOT restarting the following changed units:")
+        assert_lacks(out, "reloading the following units:")
+        assert_lacks(out, "\nrestarting the following units:")
+        assert_lacks(out, "\nstarting the following units:")
+        assert_lacks(out, "the following new units were started:")
+        assert_lacks(out, "as well:")
+
+        # Add a key
+        out = switch_to_specialisation("${machine}", "simpleServiceWithExtraKey")
+        assert_lacks(out, "stopping the following units:")
+        assert_lacks(out, "NOT restarting the following changed units:")
+        assert_lacks(out, "reloading the following units:")
+        assert_contains(out, "\nrestarting the following units: test.service\n")
+        assert_lacks(out, "\nstarting the following units:")
+        assert_lacks(out, "the following new units were started:")
+        assert_lacks(out, "as well:")
+
+        # Change its value
+        out = switch_to_specialisation("${machine}", "simpleServiceWithExtraKeyOtherValue")
+        assert_lacks(out, "stopping the following units:")
+        assert_lacks(out, "NOT restarting the following changed units:")
+        assert_lacks(out, "reloading the following units:")
+        assert_contains(out, "\nrestarting the following units: test.service\n")
+        assert_lacks(out, "\nstarting the following units:")
+        assert_lacks(out, "the following new units were started:")
+        assert_lacks(out, "as well:")
+
+        # Rename it
+        out = switch_to_specialisation("${machine}", "simpleServiceWithExtraKeyOtherName")
+        assert_lacks(out, "stopping the following units:")
+        assert_lacks(out, "NOT restarting the following changed units:")
+        assert_lacks(out, "reloading the following units:")
+        assert_contains(out, "\nrestarting the following units: test.service\n")
+        assert_lacks(out, "\nstarting the following units:")
+        assert_lacks(out, "the following new units were started:")
+        assert_lacks(out, "as well:")
+
+        # Remove it
+        out = switch_to_specialisation("${machine}", "simpleServiceNostop")
+        assert_lacks(out, "stopping the following units:")
+        assert_lacks(out, "NOT restarting the following changed units:")
+        assert_lacks(out, "reloading the following units:")
+        assert_contains(out, "\nrestarting the following units: test.service\n")
+        assert_lacks(out, "\nstarting the following units:")
+        assert_lacks(out, "the following new units were started:")
+        assert_lacks(out, "as well:")
+
+        # Add a reload trigger
+        out = switch_to_specialisation("${machine}", "simpleServiceReloadTrigger")
+        assert_lacks(out, "stopping the following units:")
+        assert_lacks(out, "NOT restarting the following changed units:")
+        assert_contains(out, "reloading the following units: test.service\n")
+        assert_lacks(out, "\nrestarting the following units:")
+        assert_lacks(out, "\nstarting the following units:")
+        assert_lacks(out, "the following new units were started:")
+        assert_lacks(out, "as well:")
+
+        # Modify the reload trigger
+        out = switch_to_specialisation("${machine}", "simpleServiceReloadTriggerModified")
+        assert_lacks(out, "stopping the following units:")
+        assert_lacks(out, "NOT restarting the following changed units:")
+        assert_contains(out, "reloading the following units: test.service\n")
+        assert_lacks(out, "\nrestarting the following units:")
+        assert_lacks(out, "\nstarting the following units:")
+        assert_lacks(out, "the following new units were started:")
+        assert_lacks(out, "as well:")
+
+        # Modify the reload trigger and something else
+        out = switch_to_specialisation("${machine}", "simpleServiceReloadTriggerModifiedAndSomethingElse")
+        assert_lacks(out, "stopping the following units:")
+        assert_lacks(out, "NOT restarting the following changed units:")
+        assert_lacks(out, "reloading the following units:")
+        assert_contains(out, "\nrestarting the following units: test.service\n")
+        assert_lacks(out, "\nstarting the following units:")
+        assert_lacks(out, "the following new units were started:")
+        assert_lacks(out, "as well:")
+
+        # Remove the reload trigger
+        out = switch_to_specialisation("${machine}", "simpleServiceReloadTriggerModifiedSomethingElse")
+        assert_lacks(out, "stopping the following units:")
+        assert_lacks(out, "NOT restarting the following changed units:")
+        assert_lacks(out, "reloading the following units:")
+        assert_lacks(out, "\nrestarting the following units:")
+        assert_lacks(out, "\nstarting the following units:")
+        assert_lacks(out, "the following new units were started:")
+        assert_lacks(out, "as well:")
+
     with subtest("restart and reload by activation script"):
         switch_to_specialisation("${machine}", "simpleServiceNorestart")
         out = switch_to_specialisation("${machine}", "restart-and-reload-by-activation-script")
@@ -386,23 +612,32 @@ import ./make-test-python.nix ({ pkgs, ...} : {
         assert_lacks(out, "NOT restarting the following changed units:")
         assert_lacks(out, "reloading the following units:")
         assert_lacks(out, "restarting the following units:")
-        assert_contains(out, "\nstarting the following units: no-restart-service.service, simple-reload-service.service, simple-restart-service.service, simple-service.service\n")
+        assert_contains(out, "\nstarting the following units: no-restart-service.service, reload-triggers-and-restart-by-as.service, simple-reload-service.service, simple-restart-service.service, simple-service.service\n")
         assert_lacks(out, "as well:")
         # Switch to the same system where the example services get restarted
-        # by the activation script
+        # and reloaded by the activation script
         out = switch_to_specialisation("${machine}", "restart-and-reload-by-activation-script")
         assert_lacks(out, "stopping the following units:")
         assert_lacks(out, "NOT restarting the following changed units:")
-        assert_contains(out, "reloading the following units: simple-reload-service.service\n")
-        assert_contains(out, "restarting the following units: simple-restart-service.service, simple-service.service\n")
+        assert_contains(out, "reloading the following units: reload-triggers-and-restart.service, reload-triggers.service, simple-reload-service.service\n")
+        assert_contains(out, "restarting the following units: reload-triggers-and-restart-by-as.service, simple-restart-service.service, simple-service.service\n")
+        assert_lacks(out, "\nstarting the following units:")
+        assert_lacks(out, "as well:")
+        # Switch to the same system and see if the service gets restarted when it's modified
+        # while the fact that it's supposed to be reloaded by the activation script is ignored.
+        out = switch_to_specialisation("${machine}", "restart-and-reload-by-activation-script-modified")
+        assert_lacks(out, "stopping the following units:")
+        assert_lacks(out, "NOT restarting the following changed units:")
+        assert_contains(out, "reloading the following units: reload-triggers.service, simple-reload-service.service\n")
+        assert_contains(out, "restarting the following units: reload-triggers-and-restart-by-as.service, reload-triggers-and-restart.service, simple-restart-service.service, simple-service.service\n")
         assert_lacks(out, "\nstarting the following units:")
         assert_lacks(out, "as well:")
         # The same, but in dry mode
         out = switch_to_specialisation("${machine}", "restart-and-reload-by-activation-script", action="dry-activate")
         assert_lacks(out, "would stop the following units:")
         assert_lacks(out, "would NOT stop the following changed units:")
-        assert_contains(out, "would reload the following units: simple-reload-service.service\n")
-        assert_contains(out, "would restart the following units: simple-restart-service.service, simple-service.service\n")
+        assert_contains(out, "would reload the following units: reload-triggers.service, simple-reload-service.service\n")
+        assert_contains(out, "would restart the following units: reload-triggers-and-restart-by-as.service, reload-triggers-and-restart.service, simple-restart-service.service, simple-service.service\n")
         assert_lacks(out, "\nwould start the following units:")
         assert_lacks(out, "as well:")
 

pkgs/applications/misc/eureka-editor/default.nix

@@ -1,25 +1,21 @@
-{ lib, stdenv, fetchzip, fltk, zlib, xdg-utils, xorg, libjpeg, libGL }:
+{ lib, stdenv, fetchzip, fltk, zlib, xdg-utils, xorg, libjpeg, libGLU }:
 
 stdenv.mkDerivation rec {
   pname = "eureka-editor";
-  version = "1.21";
-  shortver = "121";
+  version = "1.27b";
 
   src = fetchzip {
-    url = "mirror://sourceforge/eureka-editor/Eureka/${version}/eureka-${shortver}-source.tar.gz";
-    sha256 = "0fpj13aq4wh3f7473cdc5jkf1c71jiiqmjc0ihqa0nm3hic1d4yv";
+    url = "mirror://sourceforge/eureka-editor/Eureka/${lib.versions.majorMinor version}/eureka-${version}-source.tar.gz";
+    sha256 = "075w7xxsgbgh6dhndc1pfxb2h1s5fhsw28yl1c025gmx9bb4v3bf";
   };
 
-  buildInputs = [ fltk zlib xdg-utils libjpeg xorg.libXinerama libGL ];
+  buildInputs = [ fltk zlib xdg-utils libjpeg xorg.libXinerama libGLU ];
 
   enableParallelBuilding = true;
 
-  preBuild = ''
-    substituteInPlace src/main.cc \
-      --replace /usr/local $out
-    substituteInPlace Makefile \
-      --replace /usr/local $out \
-      --replace "-o root " ""
+  postPatch = ''
+    substituteInPlace src/main.cc --replace /usr/local $out
+    substituteInPlace Makefile    --replace /usr/local $out
   '';
 
   preInstall = ''
@@ -32,9 +28,9 @@ stdenv.mkDerivation rec {
   meta = with lib; {
     homepage = "http://eureka-editor.sourceforge.net";
     description = "A map editor for the classic DOOM games, and a few related games such as Heretic and Hexen";
-    license = licenses.gpl2;
+    license = licenses.gpl2Plus;
     platforms = platforms.all;
-    broken = stdenv.isDarwin;
+    badPlatforms = platforms.darwin;
     maintainers = with maintainers; [ neonfuz ];
   };
 }

pkgs/applications/networking/browsers/chromium/upstream-info.json

@@ -19,9 +19,9 @@
     }
   },
   "beta": {
-    "version": "99.0.4844.17",
-    "sha256": "18bhfy64rz4bilbzml33856azwzq4bhiisc2jlbncdnmk3x6n71s",
-    "sha256bin64": "1vaxcfgiww4skanny5ks431jyrnf0rgx7g850m29v8v49c3qflm8",
+    "version": "99.0.4844.27",
+    "sha256": "07srkycb92sajbxcjbwgjcj0xgb17k9i4b7cg50dvz3pwdvm7y8y",
+    "sha256bin64": "1a3a66kmcim3f8wvi19330m2iixxngsfiwv44g8zz51qk4rg4wx3",
     "deps": {
       "gn": {
         "version": "2022-01-10",

pkgs/data/themes/zuki/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "zuki-themes";
-  version = "3.38-1";
+  version = "4.0";
 
   src = fetchFromGitHub {
     owner = "lassekongo83";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0890i8kavgnrhm8ic4zpl16wc4ngpnf1zi8js9gvki2cl7dlj1xm";
+    sha256 = "1q026wa8xgyb6f5k7pqpm5zav30dbnm3b8w59as3sh8rhfgpbf80";
   };
 
   nativeBuildInputs = [ meson ninja sassc ];

pkgs/development/interpreters/elixir/1.13.nix

@@ -3,7 +3,7 @@
 # How to obtain `sha256`:
 # nix-prefetch-url --unpack https://github.com/elixir-lang/elixir/archive/v${version}.tar.gz
 mkDerivation {
-  version = "1.13.2";
-  sha256 = "sha256-qv85aDP3RPCa1YBo45ykWRRZNanL6brNKDMPu9SZdbQ=";
+  version = "1.13.3";
+  sha256 = "sha256-xOIGMpjemPi1xLiYmFpQR4FD6PzeFBxSJP4QpNnEUSE=";
   minimumOTPVersion = "22";
 }

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

@@ -49,6 +49,7 @@ stdenv.mkDerivation rec {
                             piqi-ocaml uuidm frontc yojson ];
 
   installPhase = ''
+    runHook preInstall
     export OCAMLPATH=$OCAMLPATH:$OCAMLFIND_DESTDIR;
     export PATH=$PATH:$out/bin
     export CAML_LD_LIBRARY_PATH=''${CAML_LD_LIBRARY_PATH-}''${CAML_LD_LIBRARY_PATH:+:}$OCAMLFIND_DESTDIR/bap-plugin-llvm/:$OCAMLFIND_DESTDIR/bap/
@@ -58,6 +59,7 @@ stdenv.mkDerivation rec {
     makeWrapper ${utop}/bin/utop $out/bin/baptop --prefix OCAMLPATH : $OCAMLPATH --prefix PATH : $PATH --add-flags "-ppx ppx-bap -short-paths -require \"bap.top\""
     wrapProgram $out/bin/bapbuild --prefix OCAMLPATH : $OCAMLPATH --prefix PATH : $PATH
     ln -s $sigs $out/share/bap/sigs.zip
+    runHook postInstall
   '';
 
   disableIda = "--disable-ida";

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

@@ -16,7 +16,11 @@ stdenv.mkDerivation rec {
 
   createFindlibDestdir = true;
 
-  installPhase = "DESTDIR=$out make install";
+  installPhase = ''
+    runHook preInstall
+    DESTDIR=$out make install
+    runHook postInstall
+  '';
 
   meta = with lib; {
     homepage = "https://piqi.org";

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

@@ -19,15 +19,9 @@ stdenv.mkDerivation rec {
 
   createFindlibDestdir = true;
 
-  buildPhase = ''
-    make
-    make -C piqilib piqilib.cma
-  '';
+  postBuild = "make -C piqilib piqilib.cma";
 
-  installPhase = ''
-    make install;
-    make ocaml-install;
-  '';
+  installTargets = [ "install" "ocaml-install" ];
 
   meta = with lib; {
     homepage = "https://piqi.org";

pkgs/development/ocaml-modules/xml-light/default.nix

@@ -1,10 +1,8 @@
 { stdenv, lib, fetchFromGitHub, ocaml, findlib }:
-let
-  pname = "xml-light";
+
+stdenv.mkDerivation rec {
+  pname = "ocaml${ocaml.version}-xml-light";
   version = "2.4";
-in
-stdenv.mkDerivation {
-  name = "ocaml-${pname}-${version}";
 
   src = fetchFromGitHub {
     owner = "ncannasse";
@@ -17,15 +15,12 @@ stdenv.mkDerivation {
 
   createFindlibDestdir = true;
 
-  buildPhase = ''
-    make all
-    make opt
-  '';
-
   installPhase = ''
+    runHook preInstall
     make install_ocamlfind
     mkdir -p $out/share
     cp -vai doc $out/share/
+    runHook postInstall
   '';
 
   meta = {
@@ -40,6 +35,6 @@ stdenv.mkDerivation {
     homepage = "http://tech.motion-twin.com/xmllight.html";
     license = lib.licenses.lgpl21;
     maintainers = [ lib.maintainers.romildo ];
-    platforms = ocaml.meta.platforms or [ ];
+    inherit (ocaml.meta) platforms;
   };
 }

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

@@ -9,14 +9,14 @@
 
 buildPythonPackage rec {
   pname = "flexmock";
-  version = "0.11.2";
+  version = "0.11.3";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-RPcCwNCt3nCFtMev6a2rULAbckrO635Jsp9WMuYyXOg=";
+    hash = "sha256-sf419qXzJUe1zTGhXAYNmrhj3Aiv8BjNc9x40bZR7dQ=";
   };
 
   checkInputs = [

pkgs/development/python-modules/google-nest-sdm/default.nix

@@ -16,7 +16,7 @@
 
 buildPythonPackage rec {
   pname = "google-nest-sdm";
-  version = "1.7.0";
+  version = "1.7.1";
   format = "setuptools";
 
   disabled = pythonOlder "3.8";
@@ -25,7 +25,7 @@ buildPythonPackage rec {
     owner = "allenporter";
     repo = "python-google-nest-sdm";
     rev = version;
-    sha256 = "sha256-SDxYPncC/VVTbI4Ka/mgcVfU1KUNRXVvQl78LCoD/RQ=";
+    sha256 = "sha256-c/Btc2CiYGb9ZGzNYDd1xJoGID6amTyv/Emdh1M6e/U=";
   };
 
   propagatedBuildInputs = [

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

@@ -2,12 +2,13 @@
 , buildPythonPackage
 , fetchFromGitHub
 , pythonOlder
+, strenum
 , token-bucket
 }:
 
 buildPythonPackage rec {
   pname = "limiter";
-  version = "0.2.0";
+  version = "0.3.0";
   format = "setuptools";
 
   disabled = pythonOlder "3.10";
@@ -16,19 +17,15 @@ buildPythonPackage rec {
     owner = "alexdelorenzo";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-h3XiCR/8rcCBwdhO6ExrrUE9piba5mssad3+t41scSk=";
+    hash = "sha256-9EkA7S549JLi6MxAXBC+2euPDrcJjW8IsQzMtij8+hA=";
   };
 
   propagatedBuildInputs = [
+    strenum
     token-bucket
   ];
 
-  postPatch = ''
-    substituteInPlace requirements.txt \
-      --replace "token-bucket==0.2.0" "token-bucket>=0.2.0"
-  '';
-
-  # Project has no tests
+  # Module has no tests
   doCheck = false;
 
   pythonImportsCheck = [

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

@@ -46,6 +46,7 @@ buildPythonPackage rec {
   postPatch = ''
     substituteInPlace pyproject.toml \
       --replace 'asyncio-dgram = "1.2.0"' 'asyncio-dgram = ">=1.2.0"' \
+      --replace 'dnspython = "2.1.0"' 'dnspython = "^2.1.0"' \
       --replace 'six = "1.14.0"' 'six = ">=1.14.0"' \
       --replace 'click = "7.1.2"' 'click = ">=7.1.2"'
   '';

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

@@ -7,7 +7,7 @@
 
 buildPythonPackage rec {
   pname = "motionblinds";
-  version = "0.5.11";
+  version = "0.5.12";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -16,7 +16,7 @@ buildPythonPackage rec {
     owner = "starkillerOG";
     repo = "motion-blinds";
     rev = version;
-    sha256 = "sha256-XvxEYOIYjr1NcviyQ6N8xHPCnUO+IgMKFsiRa5YnLDM=";
+    sha256 = "sha256-MnW5Un5iLapfvU2TTP6NekCFPUIunfRNp7+L4LUA0bc=";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/mypy-protobuf/default.nix

@@ -2,14 +2,14 @@
 
 buildPythonApplication rec {
   pname = "mypy-protobuf";
-  version = "3.1.0";
+  version = "3.2.0";
   format = "pyproject";
 
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "558dcc390290e43c7def0d4238cc41a79abde06ff509b3014c3dff0553c7b0c1";
+    sha256 = "sha256-cwqhUzfDjwRG++CPbGwjcO4B05USU2nUtw4IseLuMO4=";
   };
 
   propagatedBuildInputs = [ protobuf types-protobuf grpcio-tools ];

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

@@ -12,14 +12,14 @@
 
 buildPythonPackage rec {
   pname = "natsort";
-  version = "8.0.2";
+  version = "8.1.0";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-/rh+DOHcH48/IeGKhSFseQ50bXal/2iJVjOUYF9QSis=";
+    hash = "sha256-x8Hz8nw3Vxmk38qzU5Cf458mwgMqBiqMgMyETqrKBEU=";
   };
 
   propagatedBuildInputs = [

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

@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "oci";
-  version = "2.54.0";
+  version = "2.56.0";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
@@ -22,7 +22,7 @@ buildPythonPackage rec {
     owner = "oracle";
     repo = "oci-python-sdk";
     rev = "v${version}";
-    hash = "sha256-LTfJSlVT4I00ftshU0mbtxzy92G8lOmQiKMTMC+ZFHk=";
+    hash = "sha256-olrWv4c2DoZ7ddm58Wpb5jZntw8WEKJ6IzAND11tdjk=";
   };
 
   propagatedBuildInputs = [

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

@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "pvo";
-  version = "0.2.1";
+  version = "0.2.2";
   format = "pyproject";
 
   disabled = pythonOlder "3.8";
@@ -22,7 +22,7 @@ buildPythonPackage rec {
     owner = "frenck";
     repo = "python-pvoutput";
     rev = "v${version}";
-    sha256 = "sha256-IXK4DvmwSLdxyW4418pe1/UOeQELUBSnTO+P6TzPnKw=";
+    sha256 = "sha256-2/O81MnFYbdOrzLiTSoX7IW+3ZGyyE/tIqgKr/sEaHI=";
   };
 
   nativeBuildInputs = [

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

@@ -10,7 +10,7 @@
 
 buildPythonPackage rec {
   pname = "pyskyqremote";
-  version = "0.3.0";
+  version = "0.3.1";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -19,7 +19,7 @@ buildPythonPackage rec {
     owner = "RogerSelwyn";
     repo = "skyq_remote";
     rev = version;
-    sha256 = "sha256-rTNEqLN7FgCJkW2nMNNO7U5q8Fp/EqZEfiPVZqW5BtM=";
+    sha256 = "sha256-yPdyO78QdaLPBJQSeUP48uDr0Zhrj9nPxWbhKAMw0ww=";
   };
 
   propagatedBuildInputs = [

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

@@ -12,14 +12,14 @@
 
 buildPythonPackage rec {
   pname = "pyvera";
-  version = "0.3.14";
+  version = "0.3.15";
   format = "pyproject";
 
   src = fetchFromGitHub {
     owner = "pavoni";
     repo = pname;
     rev = version;
-    sha256 = "sha256-CuXsyHlRw5zqDrQfMT4BzHsmox8MLRKxFKwR5M0XoEM=";
+    sha256 = "sha256-1+xIqOogRUt+blX7AZSKIiU8lpR4AzKIIW/smCSft94=";
   };
 
   nativeBuildInputs = [ poetry-core ];

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

@@ -7,14 +7,14 @@
 
 buildPythonPackage rec {
   pname = "pyvesync";
-  version = "1.4.2";
+  version = "1.4.3";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-O5zt1FiCQAlCaGaiEyrannqZjm4oGq36d4Fa77ys+HE=";
+    sha256 = "sha256-DEDgZXMQrINYImXaWmv/7W7q8RvqK8oMG/B2XsDdZDM=";
   };
 
   propagatedBuildInputs = [

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

@@ -10,7 +10,7 @@
 
 buildPythonPackage rec {
   pname = "pywizlight";
-  version = "0.5.5";
+  version = "0.5.6";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -19,7 +19,7 @@ buildPythonPackage rec {
     owner = "sbidy";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-1iu+Ztwwm97fyBWyYkFiATxjJYVLiW1y0QmSO2LzjMo=";
+    sha256 = "sha256-yXEtBztfXlpM5DHSy8z+iuWsQxoAQKa9v/8lYod/gvQ=";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/qiskit-aer/default.nix

@@ -88,9 +88,11 @@ buildPythonPackage rec {
   ];
   # Slow tests
   disabledTests = [
-    "test_clifford" # fails on cvxpy >= 1.1.15. https://github.com/Qiskit/qiskit-aer/pull/1318. Remove in future.
     "test_snapshot" # TODO: these ~30 tests fail on setup due to pytest fixture issues?
     "test_initialize_2" # TODO: simulations appear incorrect, off by >10%.
+    # These tests fail on cvxpy >= 1.1.15
+    "test_clifford"
+    "test_approx_random"
 
     # these fail for some builds. Haven't been able to reproduce error locally.
     "test_kraus_gate_noise"

pkgs/development/python-modules/qiskit-aqua/default.nix

@@ -1,185 +0,0 @@
-{ lib
-, pythonOlder
-, buildPythonPackage
-, fetchFromGitHub
-, cvxpy
-, dlx
-, docplex
-, fastdtw
-, h5py
-, networkx
-, numpy
-, psutil
-, qiskit-ignis
-, qiskit-terra
-, quandl
-, scikit-learn
-, yfinance
-  # Optional inputs
-, withTorch ? false
-, pytorch
-, withPyscf ? false
-, pyscf
-, withScikitQuant ? false
-, scikit-quant ? null
-, withCplex ? false
-, cplex ? null
-  # Check Inputs
-, ddt
-, pytestCheckHook
-, pytest-timeout
-, qiskit-aer
-}:
-
-buildPythonPackage rec {
-  pname = "qiskit-aqua";
-  version = "0.9.5";
-
-  disabled = pythonOlder "3.6";
-
-  # Pypi's tarball doesn't contain tests
-  src = fetchFromGitHub {
-    owner = "Qiskit";
-    repo = "qiskit-aqua";
-    rev = version;
-    sha256 = "sha256-7QmRwlbAVAR5KfM7tuObkb6+UgiuIm82iGWBuqfve08=";
-  };
-
-  # Optional packages: pyscf (see below NOTE) & pytorch. Can install via pip/nix if needed.
-  propagatedBuildInputs = [
-    cvxpy
-    docplex
-    dlx # Python Dancing Links package
-    fastdtw
-    h5py
-    networkx
-    numpy
-    psutil
-    qiskit-terra
-    qiskit-ignis
-    quandl
-    scikit-learn
-    yfinance
-  ] ++ lib.optionals (withTorch) [ pytorch ]
-  ++ lib.optionals (withPyscf) [ pyscf ]
-  ++ lib.optionals (withScikitQuant) [ scikit-quant ]
-  ++ lib.optionals (withCplex) [ cplex ];
-
-  # *** NOTE ***
-  # We make pyscf optional in this package, due to difficulties packaging it in Nix (test failures, complicated flags, etc).
-  # See nixpkgs#78772, nixpkgs#83447. You are welcome to try to package it yourself,
-  # or use the Nix User Repository version (https://github.com/drewrisinger/nur-packages).
-  # It can also be installed at runtime from the pip wheel.
-  # We disable appropriate tests below to allow building without pyscf installed
-
-  postPatch = ''
-    # Because this is a legacy/final release, the maintainers restricted the maximum
-    # versions of all dependencies to the latest current version. That will not
-    # work with nixpkgs' rolling release/update system.
-    # Unlock all versions for compatibility
-    substituteInPlace setup.py --replace "<=" ">="
-    sed -i 's/\(\w\+-*\w*\).*/\1/' requirements.txt
-    substituteInPlace requirements.txt --replace "dataclasses" ""
-
-    # Add ImportWarning when running qiskit.chemistry (pyscf is a chemistry package) that pyscf is not included
-    echo -e "\nimport warnings\ntry: import pyscf;\nexcept ImportError:\n    " \
-      "warnings.warn('pyscf is not supported on Nixpkgs so some qiskit features will fail." \
-        "You must install it yourself via pip or add it to your environment from the Nix User Repository." \
-        "See https://github.com/NixOS/nixpkgs/pull/83447 for details', ImportWarning)\n" \
-      >> qiskit/chemistry/__init__.py
-
-    # Add ImportWarning when running qiskit.optimization that cplex (optimization package) is not included
-    echo -e "\nimport warnings\ntry: import cplex;\nexcept ImportError:\n    " \
-      "warnings.warn('cplex is not supported on Nixpkgs so some qiskit features will fail." \
-        "You must install it yourself via pip or add it to your environment from the Nix User Repository." \
-        "', ImportWarning)\n" \
-      >> qiskit/optimization/__init__.py
-  '';
-
-  checkInputs = [
-    pytestCheckHook
-    ddt
-    pytest-timeout
-    qiskit-aer
-  ];
-  pythonImportsCheck = [
-    "qiskit.aqua"
-    "qiskit.aqua.algorithms"
-    "qiskit.chemistry"
-    "qiskit.finance"
-    "qiskit.ml"
-    "qiskit.optimization"
-  ];
-  pytestFlagsArray = [
-    "--timeout=30"  # limit test duration to 30 seconds. Some tests previously would run indefinitely
-    "--durations=10"
-  ];
-  disabledTestPaths = lib.optionals (!withPyscf) [
-    "test/chemistry/test_qeom_ee.py"
-    "test/chemistry/test_qeom_vqe.py"
-    "test/chemistry/test_vqe_uccsd_adapt.py"
-    "test/chemistry/test_bopes_sampler.py"
-  ];
-  disabledTests = [
-    # TODO: figure out why failing, only fail with upgrade to qiskit-terra > 0.16.1 & qiskit-aer > 0.7.2
-    # In test.aqua.test_amplitude_estimation.TestSineIntegral
-    "test_confidence_intervals_1"
-    "test_statevector_1"
-
-    # fails due to approximation error with latest qiskit-aer?
-    "test_application"
-
-    # Fail on CI for some reason, not locally
-    "test_binary"
-
-    # Online tests
-    "test_exchangedata"
-    "test_yahoo"
-
-    # Disabling slow tests > 10 seconds
-    "TestVQE"
-    "TestOOVQE"
-    "TestVQC"
-    "TestQSVM"
-    "TestOptimizerAQGD"
-    "test_graph_partition_vqe"
-    "TestLookupRotation"
-    "_vqe"
-    "TestHHL"
-    "TestQGAN"
-    "test_evaluate_qasm_mode"
-    "test_measurement_error_mitigation_auto_refresh"
-    "test_wikipedia"
-    "test_shor_factoring_1__15___qasm_simulator____3__5__"
-    "test_readme_sample"
-    "test_ecev"
-    "test_expected_value"
-    "test_qubo_gas_int_paper_example"
-    "test_shor_no_factors_1_5"
-    "test_shor_no_factors_2_7"
-    "test_evolve_2___suzuki___1__3_"
-    "test_delta"
-    "test_swaprz"
-    "test_deprecated_algo_result"
-    "test_unsorted_grouping"
-    "test_ad_hoc_data"
-    "test_nft"
-    "test_oh"
-    "test_confidence_intervals_00001"
-    "test_eoh"
-    "test_qasm_5"
-    "test_uccsd_hf"
-    "test_lih"
-    "test_lih_freeze_core"
-  ] ++ lib.optionals (!withPyscf) [
-    "test_validate" # test/chemistry/test_inputparser.py
-  ];
-
-  meta = with lib; {
-    description = "An extensible library of quantum computing algorithms";
-    homepage = "https://github.com/QISKit/qiskit-aqua";
-    changelog = "https://qiskit.org/documentation/release_notes.html";
-    license = licenses.asl20;
-    maintainers = with maintainers; [ drewrisinger ];
-  };
-}

pkgs/development/python-modules/qiskit-nature/default.nix

@@ -16,6 +16,7 @@
 , pytestCheckHook
 , ddt
 , pylatexenc
+, qiskit-aer
 }:
 
 buildPythonPackage rec {
@@ -31,10 +32,6 @@ buildPythonPackage rec {
     sha256 = "1lr198l2z9j1hw389vv6mgz6djkq4bw91r0hif58jpg8w6kmzsx9";
   };
 
-  postPatch = ''
-    substituteInPlace requirements.txt --replace "h5py<3.3" "h5py"
-  '';
-
   propagatedBuildInputs = [
     h5py
     numpy
@@ -49,30 +46,23 @@ buildPythonPackage rec {
     pytestCheckHook
     ddt
     pylatexenc
+    qiskit-aer
   ];
 
   pythonImportsCheck = [ "qiskit_nature" ];
 
   pytestFlagsArray = [
     "--durations=10"
-  ] ++ lib.optionals (!withPyscf) [
-    "--ignore=test/algorithms/excited_state_solvers/test_excited_states_eigensolver.py"
   ];
 
   disabledTests = [
-    # small math error < 0.05 (< 9e-6 %)
-    "test_vqe_uvccsd_factory"
-    # unsure of failure reason. Might be related to recent cvxpy update?
-    "test_two_qubit_reduction"
-  ] ++ lib.optionals (!withPyscf) [
-    "test_h2_bopes_sampler"
-    "test_potential_interface"
+    "test_two_qubit_reduction"  # unsure of failure reason. Might be related to recent cvxpy update?
   ];
 
   meta = with lib; {
     description = "Software for developing quantum computing programs";
     homepage = "https://qiskit.org";
-    downloadPage = "https://github.com/QISKit/qiskit-optimization/releases";
+    downloadPage = "https://github.com/QISKit/qiskit-nature/releases";
     changelog = "https://qiskit.org/documentation/release_notes.html";
     license = licenses.asl20;
     maintainers = with maintainers; [ drewrisinger ];

pkgs/development/python-modules/qiskit-terra/default.nix

@@ -1,13 +1,10 @@
 { lib
-, stdenv
 , pythonOlder
 , buildPythonPackage
 , fetchFromGitHub
   # Python requirements
 , cython
 , dill
-, fastjsonschema
-, jsonschema
 , numpy
 , networkx
 , ply
@@ -17,6 +14,7 @@
 , retworkx
 , scipy
 , scikit-quant ? null
+, stevedore
 , symengine
 , sympy
 , tweedledum
@@ -61,7 +59,7 @@ buildPythonPackage rec {
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
-    owner = "Qiskit";
+    owner = "qiskit";
     repo = pname;
     rev = version;
     sha256 = "16d8dghjn81v6hxfg4bpj3cl2csy2rkc279qvijnwp2i9x4y8iyq";
@@ -71,8 +69,6 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [
     dill
-    fastjsonschema
-    jsonschema
     numpy
     networkx
     ply
@@ -82,6 +78,7 @@ buildPythonPackage rec {
     retworkx
     scipy
     scikit-quant
+    stevedore
     symengine
     sympy
     tweedledum
@@ -112,6 +109,9 @@ buildPythonPackage rec {
   ];
   pytestFlagsArray = [ "--durations=10" ];
   disabledTests = [
+    "TestUnitarySynthesisPlugin" # uses unittest mocks for transpiler.run(), seems incompatible somehow w/ pytest infrastructure
+    "test_copy" # assertNotIn doesn't seem to work as expected w/ pytest vs unittest
+
     # Flaky tests
     "test_pulse_limits" # Fails on GitHub Actions, probably due to minor floating point arithmetic error.
     "test_cx_equivalence"  # Fails due to flaky test
@@ -154,6 +154,17 @@ buildPythonPackage rec {
     "test_sample_counts_memory_superposition"
     "test_piecewise_polynomial_function"
     "test_vqe_qasm"
+    "test_piecewise_chebyshev_mutability"
+    "test_bit_conditional_no_cregbundle"
+    "test_gradient_wrapper2"
+    "test_two_qubit_weyl_decomposition_abmb"
+    "test_two_qubit_weyl_decomposition_abb"
+    "test_two_qubit_weyl_decomposition_aac"
+    "test_aqc"
+    "test_gradient"
+    "test_piecewise_polynomial_rotations_mutability"
+    "test_confidence_intervals_1"
+    "test_trotter_from_bound"
   ];
 
   # Moves tests to $PACKAGEDIR/test. They can't be run from /build because of finding
@@ -163,7 +174,6 @@ buildPythonPackage rec {
     echo "Moving Qiskit test files to package directory"
     cp -r $TMP/$sourceRoot/test $PACKAGEDIR
     cp -r $TMP/$sourceRoot/examples $PACKAGEDIR
-    cp -r $TMP/$sourceRoot/qiskit/schemas/examples $PACKAGEDIR/qiskit/schemas/
 
     # run pytest from Nix's $out path
     pushd $PACKAGEDIR

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

@@ -4,7 +4,6 @@
 , fetchFromGitHub
   # Python Inputs
 , qiskit-aer
-, qiskit-aqua
 , qiskit-ibmq-provider
 , qiskit-ignis
 , qiskit-terra
@@ -42,7 +41,6 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [
     qiskit-aer
-    qiskit-aqua
     qiskit-ibmq-provider
     qiskit-ignis
     qiskit-terra
@@ -52,7 +50,6 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [
     "qiskit"
-    "qiskit.aqua"
     "qiskit.circuit"
     "qiskit.ignis"
     "qiskit.providers.aer"

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

@@ -11,15 +11,16 @@
 
 buildPythonPackage rec {
   pname = "roonapi";
-  version = "0.0.39";
+  version = "0.1.1";
   format = "pyproject";
+
   disabled = pythonOlder "3.7";
 
   src = fetchFromGitHub {
     owner = "pavoni";
     repo = "pyroon";
     rev = version;
-    sha256 = "03m00qbdkm0vdflc48ds186kh9qjxqr6z602yn3l6fzj5f93zgh5";
+    sha256 = "sha256-GEgm250uALTXIEMBWmluqGw/dw2TfGmUIcItfzonGkU=";
   };
 
   nativeBuildInputs = [
@@ -36,7 +37,9 @@ buildPythonPackage rec {
   # Tests require access to the Roon API
   doCheck = false;
 
-  pythonImportsCheck = [ "roonapi" ];
+  pythonImportsCheck = [
+    "roonapi"
+  ];
 
   meta = with lib; {
     description = "Python library to interface with the Roon API";

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

@@ -12,7 +12,7 @@
 
 buildPythonPackage rec {
   pname = "skodaconnect";
-  version = "1.1.18";
+  version = "1.1.19";
   format = "setuptools";
 
   disabled = pythonOlder "3.8";
@@ -21,7 +21,7 @@ buildPythonPackage rec {
     owner = "lendy007";
     repo = pname;
     rev = version;
-    hash = "sha256-etcNdiuCgOe08HkOL+kXACoBAouDGUBqpaKUercud84=";
+    hash = "sha256-IbCGveRcn6Kn0kGw+/kWTBTqCdWqsPTv6aPq71vc1mw=";
   };
 
   SETUPTOOLS_SCM_PRETEND_VERSION = version;

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

@@ -2,6 +2,7 @@
 , buildPythonPackage
 , dataclasses-json
 , fetchFromGitHub
+, fetchpatch
 , limiter
 , pythonOlder
 , requests
@@ -32,11 +33,21 @@ buildPythonPackage rec {
   # Tests requires an API token
   doCheck = false;
 
+  patches = [
+    # Update limiter import and rate limit, https://github.com/spyse-com/spyse-python/pull/11
+    (fetchpatch {
+      name = "support-later-limiter.patch";
+      url = "https://github.com/spyse-com/spyse-python/commit/ff68164c514dfb28ab77d8690b3a5153962dbe8c.patch";
+      sha256 = "sha256-PoWPJCK/Scsh4P7lr97u4JpVHXNlY0C9rJgY4TDYmv0=";
+    })
+  ];
+
   postPatch = ''
     substituteInPlace setup.py \
       --replace "'dataclasses~=0.6'," "" \
       --replace "responses~=0.13.3" "responses>=0.13.3" \
-      --replace "limiter~=0.1.2" "limiter>=0.1.2"
+      --replace "limiter~=0.1.2" "limiter>=0.1.2" \
+      --replace "requests~=2.26.0" "requests>=2.26.0"
   '';
 
   pythonImportsCheck = [

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

@@ -0,0 +1,43 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytestCheckHook
+, pythonOlder
+}:
+
+buildPythonPackage rec {
+  pname = "strenum";
+  version = "0.4.7";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
+
+  src = fetchFromGitHub {
+    owner = "irgeek";
+    repo = "StrEnum";
+    rev = "v${version}";
+    hash = "sha256-ktsPROIv/BbPinZfrBknI4c/WwRYGhWgmw209Hfg8EQ=";
+  };
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace '"pytest-runner"' ""
+    substituteInPlace pytest.ini \
+      --replace " --cov=strenum --cov-report term-missing --black --pylint" ""
+  '';
+
+  checkInputs = [
+    pytestCheckHook
+  ];
+
+  pythonImportsCheck = [
+    "strenum"
+  ];
+
+  meta = with lib; {
+    description = "MOdule for enum that inherits from str";
+    homepage = "https://github.com/irgeek/StrEnum";
+    license = with licenses; [ mit ];
+    maintainers = with maintainers; [ fab ];
+  };
+}

pkgs/development/python-modules/swagger-spec-validator/default.nix

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "swagger-spec-validator";
-  version = "2.5.0";
+  version = "2.7.4";
 
   src = fetchFromGitHub {
     owner = "Yelp";
     repo = "swagger_spec_validator";
     rev = "v" + version;
-    sha256 = "0qlkiyncdh7cdyjvnwjpv9i7y75ghwnpyqkkpfaa8hg698na13pw";
+    sha256 = "sha256-7+kFmtzeze0QlGf6z/M4J4F7z771a5NWewB1S3+bxn4=";
   };
 
   checkInputs = [

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

@@ -8,7 +8,7 @@
 
 buildPythonPackage rec {
   pname = "twitterapi";
-  version = "2.7.11";
+  version = "2.7.12";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -17,7 +17,7 @@ buildPythonPackage rec {
     owner = "geduldig";
     repo = "TwitterAPI";
     rev = "v${version}";
-    sha256 = "sha256-Rxc0ld0U8fhE3yJV+rgGsOfOdN6xGk0NQuHscpvergs=";
+    sha256 = "sha256-WqeoIZt2OGDXKPAbjm3cHI1kgiCEJC6+ROXXx4TR4b4=";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/velbus-aio/default.nix

@@ -10,7 +10,7 @@
 
 buildPythonPackage rec {
   pname = "velbus-aio";
-  version = "2022.2.3";
+  version = "2022.2.4";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -19,7 +19,7 @@ buildPythonPackage rec {
     owner = "Cereal2nd";
     repo = pname;
     rev = version;
-    sha256 = "sha256-EgykuIz/IGFy4GTZZYpY3D5QvsCmY4H9d9Wxbof3DyQ=";
+    sha256 = "sha256-oWHyEw1DjMynLPAARcVaqsFccpnTk1/7gpq+8TU95d0=";
     fetchSubmodules = true;
   };
 

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

@@ -7,6 +7,7 @@
 , buildPythonPackage
 , fetchFromGitHub
 , pubnub
+, pyjwt
 , pytestCheckHook
 , python-dateutil
 , pythonOlder
@@ -16,7 +17,7 @@
 
 buildPythonPackage rec {
   pname = "yalexs";
-  version = "1.1.20";
+  version = "1.1.22";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
@@ -25,13 +26,14 @@ buildPythonPackage rec {
     owner = "bdraco";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-0wcvlgKlWhj9jZ53c+uEk9F28+m7BwsmlwTRlBMPoho=";
+    sha256 = "sha256-qtJSGvvYcdGYUUHnRnKe+z+twFqLGAn1Zl47F4CGnvc=";
   };
 
   propagatedBuildInputs = [
     aiofiles
     aiohttp
     pubnub
+    pyjwt
     python-dateutil
     requests
   ];

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

@@ -330,7 +330,7 @@ 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="0.99.4"; sha256="070g5a1xh1m3yar6dk3p1m86hpw8ll4xjir2n6sh2rfjw5kijmld"; depends=[]; };
+  geneplast_data = derive2 { name="geneplast.data"; version="0.99.5"; sha256="0bwhc20jkjs3n1n4xv7xmkgjzf6ghssvbsmx3dm347smk54wgjsw"; 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

@@ -314,7 +314,7 @@ in with self; {
   humanStemCell = derive2 { name="humanStemCell"; version="0.34.0"; sha256="0lvy1n389wsc85yi7kmwq2qda0nl3hpl5bqak01fr3d6040v7g27"; depends=[Biobase hgu133plus2_db]; };
   imcdatasets = derive2 { name="imcdatasets"; version="1.2.0"; sha256="1qgg2cnalx9kiv73g0n9axc6y5b25kwxbmn7cg9syvlrfn0iynlz"; depends=[cytomapper DelayedArray ExperimentHub HDF5Array S4Vectors SingleCellExperiment]; };
   kidpack = derive2 { name="kidpack"; version="1.36.0"; sha256="094b1jhyal4h3k4ilmayz77mbjqkmn7b5bsw799jmsqyg93f4r7g"; depends=[Biobase]; };
-  leeBamViews = derive2 { name="leeBamViews"; version="1.30.0"; sha256="1f0lc8k14canmp124qqys6pwp9v88z7cwr7kgxi5mrzk92r2jiz6"; depends=[Biobase BSgenome GenomicAlignments GenomicRanges IRanges Rsamtools S4Vectors]; };
+  leeBamViews = derive2 { name="leeBamViews"; version="1.30.1"; sha256="1pa1i7mb7ixs7zrj9h93s4kgbc1dq3nx40knsm5i7a43jxsl6ggw"; depends=[Biobase BSgenome GenomicAlignments GenomicRanges IRanges Rsamtools S4Vectors]; };
   leukemiasEset = derive2 { name="leukemiasEset"; version="1.30.0"; sha256="0hnqi0qm7caipjkp3asabby5jrjl57vvshnwiwqnjsf87xx19cjx"; depends=[Biobase]; };
   lumiBarnes = derive2 { name="lumiBarnes"; version="1.34.0"; sha256="103iz7vjhh1w8zyb4n3kf1w9qfa7li9p2jql48cjsadvil4bfl09"; depends=[Biobase lumi]; };
   lungExpression = derive2 { name="lungExpression"; version="0.32.1"; sha256="00dm271n1lnj5myscmkm9g4a361lfsfg8cl7ii5z8br9v4wyw2y8"; depends=[Biobase]; };
@@ -374,7 +374,7 @@ in with self; {
   restfulSEData = derive2 { name="restfulSEData"; version="1.16.0"; sha256="1bx41xwxnvx6712wsy5qljji2w3wiybvddkxic8xc9l2hrcmfhrz"; depends=[ExperimentHub SummarizedExperiment]; };
   rheumaticConditionWOLLBOLD = derive2 { name="rheumaticConditionWOLLBOLD"; version="1.32.0"; sha256="0k2klx4rpyzcq346c3ak2lf6w47zkhnhiqn4rs70xnxnsbjn2ca5"; depends=[]; };
   sampleClassifierData = derive2 { name="sampleClassifierData"; version="1.18.0"; sha256="12k7xhd2axmcpmv970xbhx5r9b0jdmkxxqm01a0v2jfx3imzz9jb"; depends=[SummarizedExperiment]; };
-  scATAC_Explorer = derive2 { name="scATAC.Explorer"; version="1.0.0"; sha256="16qscpjbbphrd1qfp85r9bw8v98866kzsf20fk270m2aq378y4i8"; depends=[BiocFileCache data_table Matrix S4Vectors SingleCellExperiment]; };
+  scATAC_Explorer = derive2 { name="scATAC.Explorer"; version="1.0.1"; sha256="0iz0i58afr58y4mc6iyajzdblpd1s2mng693nhb49rka4bf1fx0j"; depends=[BiocFileCache data_table Matrix S4Vectors SingleCellExperiment]; };
   scRNAseq = derive2 { name="scRNAseq"; version="2.8.0"; sha256="19caas79yarf3vww60bnn92v9ns82pawqbbw78kmy0x94hvsfdbk"; depends=[AnnotationDbi AnnotationHub BiocGenerics ensembldb ExperimentHub GenomicFeatures GenomicRanges S4Vectors SingleCellExperiment SummarizedExperiment]; };
   scTHI_data = derive2 { name="scTHI.data"; version="1.6.0"; sha256="0n794kicpylibqgi4z9mwdgmk5ni3yhqzaqcdr2mij844s079fx4"; depends=[]; };
   scanMiRData = derive2 { name="scanMiRData"; version="1.0.0"; sha256="0z6nl4w4r8m1mara0zyzlg7xx6y9fa8psvln0695wvpxzmps4y9h"; depends=[scanMiR]; };
@@ -389,7 +389,7 @@ in with self; {
   signatureSearchData = derive2 { name="signatureSearchData"; version="1.8.4"; sha256="0k5j35jsdfk3qza3kzp2ih9irz4d4xbwr64wd4ibmzydkjrjdrcz"; depends=[affy Biobase dplyr ExperimentHub limma magrittr R_utils rhdf5]; };
   simpIntLists = derive2 { name="simpIntLists"; version="1.30.0"; sha256="0q2lqfhsjncdj42hblrh389j2m47x26nn58s31s1448pddhrp7z1"; depends=[]; };
   spatialDmelxsim = derive2 { name="spatialDmelxsim"; version="1.0.0"; sha256="1h5crcjrzapj5j31285ana48g3b2iscxwlzxxdx9i03jsl39dlp8"; depends=[ExperimentHub SummarizedExperiment]; };
-  spatialLIBD = derive2 { name="spatialLIBD"; version="1.6.4"; sha256="0lpp5w04szgqs0nvlhc6a7hsybsvpy9vdx4dqs9ncrb4qg6fxchp"; depends=[AnnotationHub benchmarkme BiocFileCache BiocGenerics cowplot DT ExperimentHub fields GenomicRanges ggplot2 golem IRanges jsonlite magick Matrix plotly png Polychrome RColorBrewer rtracklayer S4Vectors scater sessioninfo shiny shinyWidgets SingleCellExperiment SpatialExperiment SummarizedExperiment tibble viridisLite]; };
+  spatialLIBD = derive2 { name="spatialLIBD"; version="1.6.5"; sha256="1m25wk2np5yj0wygw3gg3kq8ykzx14jqj73aqs0yhsr04pp7qm8x"; depends=[AnnotationHub benchmarkme BiocFileCache BiocGenerics cowplot DT ExperimentHub fields GenomicRanges ggplot2 golem IRanges jsonlite magick Matrix plotly png Polychrome RColorBrewer rtracklayer S4Vectors scater sessioninfo shiny shinyWidgets SingleCellExperiment SpatialExperiment SummarizedExperiment tibble viridisLite]; };
   spqnData = derive2 { name="spqnData"; version="1.6.0"; sha256="0dwmgwz88g8fzpa2nl2zs4y32wrlf4ca142d8siak14wl089nm4y"; depends=[SummarizedExperiment]; };
   stemHypoxia = derive2 { name="stemHypoxia"; version="1.30.0"; sha256="05jly60gg5xr9511jlymzbpjysapfz2qq81rxhdz7cjbjkkgvykr"; depends=[]; };
   stjudem = derive2 { name="stjudem"; version="1.34.0"; sha256="005wy7b8naaph9krsdw234sk8fprccclnj7y4rfrs2f3lbrw4b2g"; depends=[]; };

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

@@ -50,8 +50,8 @@ in with self; {
   AnnotationDbi = derive2 { name="AnnotationDbi"; version="1.56.2"; sha256="01zwq14msbbwzxv8rgpmyr74ymvhq0vnmxkxxwd886iac5vjlgi8"; depends=[Biobase BiocGenerics DBI IRanges KEGGREST RSQLite S4Vectors]; };
   AnnotationFilter = derive2 { name="AnnotationFilter"; version="1.18.0"; sha256="15fp1228yb06jm5cblvhw3qv9mlpbjfggaz2nvi3p46mby1vs64w"; depends=[GenomicRanges lazyeval]; };
   AnnotationForge = derive2 { name="AnnotationForge"; version="1.36.0"; sha256="02wvni5q560idi6677g5f4md73z4qzjl5yycxv5dbvgbl2picisz"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; };
-  AnnotationHub = derive2 { name="AnnotationHub"; version="3.2.0"; sha256="0ks8yzvvs2r66pb9687mkskf0n3wgvp7h92k83b0a1q32sca5wng"; depends=[AnnotationDbi BiocFileCache BiocGenerics BiocManager BiocVersion curl dplyr httr interactiveDisplayBase rappdirs RSQLite S4Vectors yaml]; };
-  AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.24.1"; sha256="008jkpqzk1dxrkmbpzyjnqyrdw7rb4ci88fmnn27arx6psbl096g"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocCheck BiocGenerics BiocManager biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges jsonlite OrganismDbi RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; };
+  AnnotationHub = derive2 { name="AnnotationHub"; version="3.2.1"; sha256="08d9hfjj79c1rrmq3gf132zfx0gld5q0jwmqgghfvmn8zrppz8sf"; depends=[AnnotationDbi BiocFileCache BiocGenerics BiocManager BiocVersion curl dplyr httr interactiveDisplayBase rappdirs RSQLite S4Vectors yaml]; };
+  AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.24.2"; sha256="00n195xbja01r64mjsjvk3xpwx9mwj5x8n4l810jspf4cdjv5cbl"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocCheck BiocGenerics BiocManager biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges jsonlite OrganismDbi RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; };
   ArrayExpress = derive2 { name="ArrayExpress"; version="1.54.0"; sha256="1rfvycrjlw0x1sqjrmiyf8i7yjiwjqf8x83i7pfg78yg9k5sh9vi"; depends=[Biobase limma oligo XML]; };
   ArrayExpressHTS = derive2 { name="ArrayExpressHTS"; version="1.44.0"; sha256="1mjnddy05y06bn25xcjdx8kz538z3k4gvyqrb1lg4z8593xaw40i"; depends=[Biobase BiocGenerics biomaRt Biostrings bitops edgeR GenomicRanges Hmisc IRanges R2HTML RColorBrewer Rhtslib rJava Rsamtools sampling sendmailR ShortRead snow svMisc XML]; };
   AssessORF = derive2 { name="AssessORF"; version="1.12.0"; sha256="0rn2ijnpa8a6w2zv3cvm1s5bhcvzmb4xk18d96wjc60gxk51i5wy"; depends=[Biostrings DECIPHER GenomicRanges IRanges]; };
@@ -108,7 +108,7 @@ in with self; {
   Biobase = derive2 { name="Biobase"; version="2.54.0"; sha256="0kar2kgaayp5l7xv9zcxj61l01m8jlwnppql6qf01wsz36dacgww"; depends=[BiocGenerics]; };
   BiocCheck = derive2 { name="BiocCheck"; version="1.30.0"; sha256="0w9ddicyp9i8rxf92n9pghd9s6bb8jdjikaylrmkydhb7jbhan0y"; depends=[BiocManager biocViews codetools graph httr knitr optparse stringdist]; };
   BiocDockerManager = derive2 { name="BiocDockerManager"; version="1.6.0"; sha256="1kpdmpcngnl667bfffp9bkf8c31ipmhsncq0h9bf3a4k8b83pi0w"; depends=[dplyr httr memoise readr whisker]; };
-  BiocFileCache = derive2 { name="BiocFileCache"; version="2.2.0"; sha256="11qayqmgv274hc4h1v222sma07wkxjm8002fl6w3yvi225zq1qc1"; depends=[curl DBI dbplyr dplyr filelock httr rappdirs RSQLite]; };
+  BiocFileCache = derive2 { name="BiocFileCache"; version="2.2.1"; sha256="0gaj0z6dk2p2vhvqz685xwd5q2mkvpimh2493p3w04s2rlsvi3jb"; depends=[curl DBI dbplyr dplyr filelock httr rappdirs RSQLite]; };
   BiocGenerics = derive2 { name="BiocGenerics"; version="0.40.0"; sha256="0nr5x4r8f2krnfrxm7wrzgzr7nbljypi985cbwx5hxhn95zmfifh"; depends=[]; };
   BiocIO = derive2 { name="BiocIO"; version="1.4.0"; sha256="1qg6v961sbj7qwyjx4z720f6h0kq693p7gc8q99my7gqkbbcxrfr"; depends=[BiocGenerics S4Vectors]; };
   BiocNeighbors = derive2 { name="BiocNeighbors"; version="1.12.0"; sha256="04in8l6j7frgm0a5dzphazfhn9cm8w775z5yir712jxa37mh1agr"; depends=[BiocParallel Matrix Rcpp RcppHNSW S4Vectors]; };
@@ -137,7 +137,7 @@ in with self; {
   CAGEr = derive2 { name="CAGEr"; version="2.0.2"; sha256="0s959bqgmafc2hwh42fwildq8h8wxvdiciimgpr71ka2p1vg9sk7"; depends=[BiocGenerics BiocParallel BSgenome data_table DelayedArray DelayedMatrixStats formula_tools GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges KernSmooth memoise MultiAssayExperiment plyr reshape2 Rsamtools rtracklayer S4Vectors som stringdist stringi SummarizedExperiment vegan VGAM]; };
   CAMERA = derive2 { name="CAMERA"; version="1.50.0"; sha256="1mgdmzlbj8yhk6jmnqaw4xmss77v7csdajd240kiswvm1f317z3h"; depends=[Biobase graph Hmisc igraph RBGL xcms]; };
   CARNIVAL = derive2 { name="CARNIVAL"; version="2.4.0"; sha256="10wbdjripgndfaqx2aysmqhc9v8i94db8bf0bb89csmvmnia68c6"; depends=[dplyr igraph lpSolve readr rjson rmarkdown stringr]; };
-  CATALYST = derive2 { name="CATALYST"; version="1.18.0"; sha256="15lah45lf16zh1ankbpjvz8zp38lldvq074nmvb99rhhqys2gbgi"; depends=[circlize ComplexHeatmap ConsensusClusterPlus cowplot data_table dplyr drc flowCore FlowSOM ggplot2 ggrepel ggridges gridExtra magrittr Matrix matrixStats nnls purrr RColorBrewer reshape2 Rtsne S4Vectors scales scater SingleCellExperiment SummarizedExperiment]; };
+  CATALYST = derive2 { name="CATALYST"; version="1.18.1"; sha256="0dvcs7nz1yawcrsf9lqiwdcrvjmbs8ajrmvj0ji4qq2a86n3dkg0"; depends=[circlize ComplexHeatmap ConsensusClusterPlus cowplot data_table dplyr drc flowCore FlowSOM ggplot2 ggrepel ggridges gridExtra magrittr Matrix matrixStats nnls purrr RColorBrewer reshape2 Rtsne S4Vectors scales scater SingleCellExperiment SummarizedExperiment]; };
   CAnD = derive2 { name="CAnD"; version="1.26.0"; sha256="19c47m0i8sfp2frw6mnzr1bz3n196kgd53bisil6nix1pqsgjqba"; depends=[ggplot2 reshape]; };
   CCPROMISE = derive2 { name="CCPROMISE"; version="1.20.0"; sha256="0wkwgm85kkf7p3vwjvsaq6p7cb2qfzjfqcaba2wgkh8lzjjrglw9"; depends=[Biobase CCP GSEABase PROMISE]; };
   CEMiTool = derive2 { name="CEMiTool"; version="1.18.1"; sha256="0w2y7wkz9r75jblh5mvx096lxlsbx8hn0jp85sfqhnq6ngvil99a"; depends=[clusterProfiler data_table dplyr DT fastcluster fgsea ggdendro ggplot2 ggpmisc ggrepel ggthemes gridExtra gtable htmltools igraph intergraph knitr matrixStats network pracma rmarkdown scales sna stringr WGCNA]; };
@@ -193,7 +193,7 @@ in with self; {
   CellScore = derive2 { name="CellScore"; version="1.14.0"; sha256="17zs6y08z1l4s51ishb5cp2k70yc1cinh211r76mrdlpdp9rxx5c"; depends=[Biobase gplots lsa RColorBrewer squash]; };
   CellTrails = derive2 { name="CellTrails"; version="1.12.0"; sha256="0rwirbvrfn03xrc0jjiw24dg9c49wznckhjm9kibd10n135x6l4g"; depends=[Biobase BiocGenerics cba dendextend dtw EnvStats ggplot2 ggrepel igraph maptree mgcv reshape2 Rtsne SingleCellExperiment SummarizedExperiment]; };
   CellaRepertorium = derive2 { name="CellaRepertorium"; version="1.4.0"; sha256="1gqr12dbm1g2gz4ixx3r8f9as7m5nd0vcj0k3hsk9njs938lfzk4"; depends=[BiocGenerics Biostrings dplyr forcats Matrix progress purrr Rcpp reshape2 rlang S4Vectors stringr tibble tidyr]; };
-  CelliD = derive2 { name="CelliD"; version="1.2.0"; sha256="06jdqxa38pjvx0z1yqmhghn6x3dkq0zinc84kvxs9ls81hi6h20l"; depends=[BiocParallel data_table fastmatch fgsea ggplot2 glue irlba Matrix matrixStats pbapply Rcpp RcppArmadillo reticulate Rtsne scater Seurat SingleCellExperiment stringr SummarizedExperiment tictoc umap]; };
+  CelliD = derive2 { name="CelliD"; version="1.2.1"; sha256="1q03kv0m8v7w2ycgln86xshr0c7v14hiw56szxljgby9p3bxz85g"; depends=[BiocParallel data_table fastmatch fgsea ggplot2 glue irlba Matrix matrixStats pbapply Rcpp RcppArmadillo reticulate Rtsne scater Seurat SingleCellExperiment stringr SummarizedExperiment tictoc umap]; };
   Cepo = derive2 { name="Cepo"; version="1.0.0"; sha256="091hbppf6jmsw7bh3m1xasf9vwh4xf6m6sgqrqi8hvvp37vb7k67"; depends=[BiocParallel DelayedArray DelayedMatrixStats ggplot2 GSEABase HDF5Array patchwork reshape2 rlang S4Vectors SingleCellExperiment SummarizedExperiment]; };
   CexoR = derive2 { name="CexoR"; version="1.32.0"; sha256="18x5qj2z4nxbgj0i7si0rk57hlqwxmmz97dvsfvbkw1akcw8psb9"; depends=[genomation GenomeInfoDb GenomicRanges idr IRanges RColorBrewer Rsamtools rtracklayer S4Vectors]; };
   ChAMP = derive2 { name="ChAMP"; version="2.24.0"; sha256="10wyfcc36qfcwpzgsj2vnmjy694igk81zd35aij51fs4s1mhmf2k"; depends=[bumphunter ChAMPdata combinat dendextend DMRcate DNAcopy doParallel DT GenomicRanges ggplot2 globaltest goseq Hmisc Illumina450ProbeVariants_db IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b4_hg19 IlluminaHumanMethylationEPICmanifest illuminaio impute isva kpmt limma marray matrixStats minfi missMethyl plotly plyr preprocessCore prettydoc quadprog qvalue RColorBrewer rmarkdown RPMM shiny shinythemes sva wateRmelon]; };
@@ -203,7 +203,7 @@ in with self; {
   ChIPXpress = derive2 { name="ChIPXpress"; version="1.38.0"; sha256="1wypkh9pq3v9lwmhwdrnf6a2jm2i2nc7kv9nppcyknf9qhpkn97z"; depends=[affy biganalytics bigmemory Biobase ChIPXpressData frma GEOquery]; };
   ChIPanalyser = derive2 { name="ChIPanalyser"; version="1.16.0"; sha256="1ibbfsl2gz5634rljy4bin9h9g5bxzig3z65bvayp4ldmfiz91dm"; depends=[BiocManager Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges RcppRoll ROCR rtracklayer S4Vectors]; };
   ChIPexoQual = derive2 { name="ChIPexoQual"; version="1.18.0"; sha256="1hh3mhfcngyx7cpzns8mjqviy8vfzrvxpv6nyizflpfmsr39mxfk"; depends=[BiocParallel biovizBase broom data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 hexbin IRanges RColorBrewer rmarkdown Rsamtools S4Vectors scales viridis]; };
-  ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.28.0"; sha256="05fbq8zvww1nlyykrri0hf4248i1i7w5cr453giagmjq7lgg4v3b"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings DBI dplyr ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 graph InteractionSet IRanges KEGGREST matrixStats multtest RBGL regioneR Rsamtools rtracklayer S4Vectors SummarizedExperiment VennDiagram]; };
+  ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.28.1"; sha256="0v2qz3rp5lmj3s1ziahjqym6cjlh4wdvf050k1x6dx8404jhi8kw"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings DBI dplyr ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 graph InteractionSet IRanges KEGGREST matrixStats multtest RBGL regioneR Rsamtools rtracklayer S4Vectors SummarizedExperiment VennDiagram]; };
   ChIPseeker = derive2 { name="ChIPseeker"; version="1.30.3"; sha256="1f9m1p1viiigkmv15r2mknjrfw047jw1fylpqz5ipigc3jrphj1g"; depends=[AnnotationDbi BiocGenerics boot dplyr enrichplot GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gtools IRanges magrittr plotrix RColorBrewer rtracklayer S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene]; };
   ChIPseqR = derive2 { name="ChIPseqR"; version="1.48.0"; sha256="05hxxqmjxpry0j80kyz2400azni0dc64ps7cxfi11h243japhbsf"; depends=[BiocGenerics Biostrings fBasics GenomicRanges HilbertVis IRanges S4Vectors ShortRead timsac]; };
   ChIPsim = derive2 { name="ChIPsim"; version="1.48.0"; sha256="1pdsfsk8c92pz22qz2x5rsmk7j9v3dw9c1p96il533ycjafq1xqd"; depends=[Biostrings IRanges ShortRead XVector]; };
@@ -252,7 +252,7 @@ in with self; {
   DESeq2 = derive2 { name="DESeq2"; version="1.34.0"; sha256="0whk29zrmv9mrlc4w5ghy0fd29v8hfr8jccwgrn59mf3mkmfb2b9"; depends=[Biobase BiocGenerics BiocParallel genefilter geneplotter GenomicRanges ggplot2 IRanges locfit Rcpp RcppArmadillo S4Vectors SummarizedExperiment]; };
   DEWSeq = derive2 { name="DEWSeq"; version="1.8.0"; sha256="1ggj4in0sj9wb367s19v56f0jnfdcsylndjwpp4j02kwmc2wfl0j"; depends=[BiocGenerics BiocParallel data_table DESeq2 GenomeInfoDb GenomicRanges R_utils S4Vectors SummarizedExperiment]; };
   DEXSeq = derive2 { name="DEXSeq"; version="1.40.0"; sha256="1wd4bjd0a53s689yvb2lxzdiy0synh6ncfcly3cfw37kpdj8lds1"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; };
-  DEqMS = derive2 { name="DEqMS"; version="1.11.1"; sha256="0nm49sxxi0j4czly8rjyxp41wlcihbn802qmljs8x6y6wvp3464l"; depends=[ggplot2 limma matrixStats]; };
+  DEqMS = derive2 { name="DEqMS"; version="1.12.1"; sha256="07klzl8qb121c3jk7g16fx4g5a89m8iv8mjhqcc7f4501bpbkyb2"; depends=[ggplot2 limma matrixStats]; };
   DEsingle = derive2 { name="DEsingle"; version="1.14.0"; sha256="0x0xnylf036k320r59pqa273i59jcwxiwsw4fyfqqrliyw7fxa4c"; depends=[bbmle BiocParallel gamlss MASS Matrix maxLik pscl VGAM]; };
   DEsubs = derive2 { name="DEsubs"; version="1.20.0"; sha256="1b11hhs7r1r24z7w9mimj1bpj7y5j7i9vq9sw6ll2dlghyazc7di"; depends=[circlize DESeq2 EBSeq edgeR ggplot2 graph igraph jsonlite limma locfit Matrix NBPSeq pheatmap RBGL]; };
   DExMA = derive2 { name="DExMA"; version="1.2.1"; sha256="1afxv356bkswnbyh3mkf98xqq1arcgak980hkryn4i69531kkc0w"; depends=[Biobase bnstruct DExMAdata GEOquery impute limma pheatmap plyr scales snpStats sva swamp]; };
@@ -262,7 +262,7 @@ in with self; {
   DMCHMM = derive2 { name="DMCHMM"; version="1.16.0"; sha256="0r12m3ldbi1h0fdg4hgxfq1f0lrz49a08i7kr6imdspzm8hl2j65"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; };
   DMRScan = derive2 { name="DMRScan"; version="1.16.0"; sha256="0iza3yyjmggkxgn24raiwzppf4lvdj1lgq34lpk08mf6p5v0v601"; depends=[GenomeInfoDb GenomicRanges IRanges MASS Matrix mvtnorm RcppRoll]; };
   DMRcaller = derive2 { name="DMRcaller"; version="1.26.0"; sha256="0qn3y2nj0pyy9kqpbv8nwsiypwl6kixxs2yj3bvhkhb5dgqj6p6w"; depends=[betareg GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; };
-  DMRcate = derive2 { name="DMRcate"; version="2.8.1"; sha256="12i5h9m4xgxlxs3n48rbqlk622qi8jx7vfnn6qhib0f3m73rws1i"; depends=[bsseq DSS edgeR ExperimentHub GenomeInfoDb GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors SummarizedExperiment]; };
+  DMRcate = derive2 { name="DMRcate"; version="2.8.4"; sha256="03nh7q8mlpc2ffs5gh3aqvks2wd20zyq9vqhkhxq69xxi53wrbm3"; depends=[bsseq DMRcatedata DSS edgeR ExperimentHub GenomeInfoDb GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors SummarizedExperiment]; };
   DMRforPairs = derive2 { name="DMRforPairs"; version="1.30.0"; sha256="1f8b63chg3jrqbf669l2nk3a8wy5rya545zbypgzr2r51s284k7b"; depends=[GenomicRanges Gviz R2HTML]; };
   DNABarcodeCompatibility = derive2 { name="DNABarcodeCompatibility"; version="1.10.0"; sha256="1dj4c8h648ckzrz0k6qrzvfgqz00wj0pdahhp35nlrldcavp90p6"; depends=[DNABarcodes dplyr numbers purrr stringr tidyr]; };
   DNABarcodes = derive2 { name="DNABarcodes"; version="1.24.0"; sha256="07yaz98r18mjny1ilmfnjxcra7xpklnd183pw0kasvsri01ccwxg"; depends=[BH Matrix Rcpp]; };
@@ -285,7 +285,7 @@ in with self; {
   DelayedRandomArray = derive2 { name="DelayedRandomArray"; version="1.2.0"; sha256="1hi9pvxny8nm4akhshicksd04p7vflqa3m38k6kcs50slhgdp5ys"; depends=[BH DelayedArray dqrng Rcpp]; };
   DelayedTensor = derive2 { name="DelayedTensor"; version="1.0.0"; sha256="0yg7r6j7r1sikc4wi6khh3dsbflzpj51sdh41q337lkmlxagwpbb"; depends=[BiocSingular DelayedArray DelayedRandomArray einsum HDF5Array irlba Matrix rTensor]; };
   DepecheR = derive2 { name="DepecheR"; version="1.10.0"; sha256="1500jivij7zdycdd0i0b7mgp44w4z0hqnpzqbq8nhvzzdigic8x9"; depends=[beanplot doSNOW dplyr FNN foreach ggplot2 gmodels gplots MASS matrixStats mixOmics moments Rcpp RcppEigen reshape2 robustbase viridis]; };
-  DiffBind = derive2 { name="DiffBind"; version="3.4.3"; sha256="1bz03ls7pkb09p6nkz7gfnhjlh06mgbp3j98ppnzibiar3cjrnfj"; depends=[amap apeglm ashr BiocParallel DESeq2 dplyr GenomicAlignments GenomicRanges ggplot2 ggrepel gplots GreyListChIP IRanges lattice limma locfit RColorBrewer Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment systemPipeR]; };
+  DiffBind = derive2 { name="DiffBind"; version="3.4.9"; sha256="1fpr96hfi7hy3pzf4rgnmrz2fk3qajwgsy32yqr839vjfsvw532z"; depends=[amap apeglm ashr BiocParallel DESeq2 dplyr GenomicAlignments GenomicRanges ggplot2 ggrepel gplots GreyListChIP IRanges lattice limma locfit RColorBrewer Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment systemPipeR]; };
   DiffLogo = derive2 { name="DiffLogo"; version="2.18.0"; sha256="1axpyjr86a176rgv9wnrk04dv9llgkw9vr7h00scr6jw77wqya4n"; depends=[cba]; };
   Dino = derive2 { name="Dino"; version="1.0.0"; sha256="1k83rhva7bxk1w6qvvdhx0r95p9nbzfdm3m7g6wpyq3qp0ifx5xp"; depends=[BiocParallel BiocSingular Matrix matrixStats S4Vectors scran Seurat SingleCellExperiment SummarizedExperiment]; };
   Director = derive2 { name="Director"; version="1.20.0"; sha256="1f0a8rkpz698c5a41j7ii7ahxxaqn92rhx8sh3q66gpv0br8h44g"; depends=[htmltools]; };
@@ -294,7 +294,7 @@ in with self; {
   DominoEffect = derive2 { name="DominoEffect"; version="1.14.0"; sha256="13lksli177d11rw5692bc5qmp0x5bfkasriccaa28hklnqmbyjsc"; depends=[AnnotationDbi biomaRt Biostrings data_table GenomeInfoDb GenomicRanges IRanges SummarizedExperiment VariantAnnotation]; };
   Doscheda = derive2 { name="Doscheda"; version="1.16.0"; sha256="0lpmxnid43fvi41mc5r89mvvxn19baja8f4zr38j3dkb126dr476"; depends=[affy calibrate corrgram drc DT ggplot2 gridExtra httr jsonlite limma matrixStats prodlim readxl reshape2 shiny shinydashboard stringr vsn]; };
   DriverNet = derive2 { name="DriverNet"; version="1.34.0"; sha256="1qfjg5x3m2z5yjm0lgnw7rqhclic2fgzcdnq0nnwlqyp4i5na10q"; depends=[]; };
-  DropletUtils = derive2 { name="DropletUtils"; version="1.14.1"; sha256="1nfv5d04jzbd5nv1fazj5qchv59s4cds698r44zfw36z6v83w2d6"; depends=[beachmat BH BiocGenerics BiocParallel DelayedArray DelayedMatrixStats dqrng edgeR GenomicRanges HDF5Array IRanges Matrix R_utils Rcpp rhdf5 Rhdf5lib S4Vectors scuttle SingleCellExperiment SummarizedExperiment]; };
+  DropletUtils = derive2 { name="DropletUtils"; version="1.14.2"; sha256="0vljd0zlafqr0g5d14jf8qwahjc56i7i1xan00ql351y8hmi4qmi"; depends=[beachmat BH BiocGenerics BiocParallel DelayedArray DelayedMatrixStats dqrng edgeR GenomicRanges HDF5Array IRanges Matrix R_utils Rcpp rhdf5 Rhdf5lib S4Vectors scuttle SingleCellExperiment SummarizedExperiment]; };
   DrugVsDisease = derive2 { name="DrugVsDisease"; version="2.36.0"; sha256="19plcigawh4c4z1dxn1c0kxbdnrsz2fgfyvmcnj0025xscdk4zay"; depends=[affy annotate ArrayExpress BiocGenerics biomaRt cMap2data DrugVsDiseasedata GEOquery hgu133a_db hgu133a2_db hgu133plus2_db limma qvalue RUnit xtable]; };
   Dune = derive2 { name="Dune"; version="1.6.0"; sha256="0n267fw1yna1fpg5gcilmf0ijavy2c1ry0wcccp2cdzhs77cx7fi"; depends=[aricode BiocParallel dplyr gganimate ggplot2 magrittr purrr RColorBrewer SummarizedExperiment tidyr]; };
   DynDoc = derive2 { name="DynDoc"; version="1.72.0"; sha256="1ix1kcjrmbv7hqsmihgazh7igrh13bxhgw36ibihh07sflrgf1hm"; depends=[]; };
@@ -322,7 +322,7 @@ in with self; {
   EventPointer = derive2 { name="EventPointer"; version="3.2.0"; sha256="0kg5psygc410gx6prb8as00csh6v3s1psbcn2ym4i4k5wnyzmbn3"; depends=[abind affxparser Biostrings BSgenome cobs doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges glmnet graph igraph IRanges iterators limma lpSolve MASS Matrix matrixStats nnls poibin prodlim qvalue RBGL rhdf5 S4Vectors SGSeq speedglm stringr SummarizedExperiment tximport]; };
   ExCluster = derive2 { name="ExCluster"; version="1.12.0"; sha256="1fmijpvkn2qjwl8cqzwclybnfqyrdckxwfc6f1zird770bqyagjv"; depends=[GenomicRanges IRanges matrixStats Rsubread rtracklayer]; };
   ExiMiR = derive2 { name="ExiMiR"; version="2.36.0"; sha256="1vf1241n6f0w7p8m8vwb30dlhybw5ddhp2bgwmn7ml6rfbkidmnk"; depends=[affy affyio Biobase limma preprocessCore]; };
-  ExperimentHub = derive2 { name="ExperimentHub"; version="2.2.0"; sha256="15las4qmqvrn81hczxa3ylikqh54kp1lg9r8rcyfvrx5l0kgwlfq"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocManager curl rappdirs S4Vectors]; };
+  ExperimentHub = derive2 { name="ExperimentHub"; version="2.2.1"; sha256="0lvd6hyqdfsn5ji714v46qdrb8vr1y38lv0pgw8priab0hpqrbm5"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocManager curl rappdirs S4Vectors]; };
   ExperimentHubData = derive2 { name="ExperimentHubData"; version="1.20.1"; sha256="12gnp7zh0ligpmgnd59gp6c3cdq9sz0nzzpskjkdf7kzn08mk41m"; depends=[AnnotationHubData BiocGenerics BiocManager curl DBI ExperimentHub httr S4Vectors]; };
   ExperimentSubset = derive2 { name="ExperimentSubset"; version="1.4.0"; sha256="1ccz555f5mfvii99w66f076cb22f0ksjxmq9f6bsfxjzsbc7ssnh"; depends=[Matrix S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment TreeSummarizedExperiment]; };
   ExploreModelMatrix = derive2 { name="ExploreModelMatrix"; version="1.6.0"; sha256="162g6zfdhr6gibyqkfwk4y2fd4wmbzwx1frf8rkw6m7ny3mc7s3g"; depends=[cowplot dplyr DT ggplot2 limma magrittr MASS rintrojs S4Vectors scales shiny shinydashboard shinyjs tibble tidyr]; };
@@ -354,14 +354,14 @@ in with self; {
   GCSFilesystem = derive2 { name="GCSFilesystem"; version="1.4.0"; sha256="0k2dmiyxfpdr1jzrkkkpj0rqd1s13rwmqfrbc5xkanc5z6wqd8hc"; depends=[]; };
   GCSscore = derive2 { name="GCSscore"; version="1.8.0"; sha256="0zb2fcwqbxl59bvhj73yrb9sq2zld451abb1nmxj92yipbmwjgn6"; depends=[affxparser Biobase BiocManager data_table devtools dplR RSQLite stringr]; };
   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="1.14.0"; sha256="07b3025fcjrq1kvpb7g6kxqwmk6pwibnv8krmn11ddgl2606k8c3"; depends=[BiocGenerics DelayedArray gdsfmt S4Vectors SeqArray SNPRelate]; };
+  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="2.24.0"; sha256="1n1h9aiyn8f8cznm8dkvndm3708nls2xr4v21sspz4vj8ahwvgaz"; 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]; };
   GEOmetadb = derive2 { name="GEOmetadb"; version="1.56.0"; sha256="18v3h7518cc4fzdi7ivng81316012mry4ihyrldm85zgm4c5dign"; depends=[GEOquery RSQLite]; };
-  GEOquery = derive2 { name="GEOquery"; version="2.62.1"; sha256="0plmh4x37r848g6ilvl1x8cim90rp85gikfc5m8lgi2i4xkq7hbq"; depends=[Biobase data_table dplyr httr limma magrittr R_utils readr tidyr xml2]; };
+  GEOquery = derive2 { name="GEOquery"; version="2.62.2"; sha256="1hncr0p54qdg82a771yjjm4w1k2myrc26jzvci3g37mq7bgv3mxw"; depends=[Biobase data_table dplyr httr limma magrittr R_utils readr tidyr xml2]; };
   GEOsubmission = derive2 { name="GEOsubmission"; version="1.46.0"; sha256="0p0w55j7ij1242sa76bhgqwnj5zi0bh7s7qa14iga4ldigpxr63b"; depends=[affy Biobase]; };
   GEWIST = derive2 { name="GEWIST"; version="1.38.0"; sha256="0xcywidrs6jvps93iv3qvr9ai1bdzn95icvswy8ganx09v5hfpy9"; depends=[car]; };
   GGPA = derive2 { name="GGPA"; version="1.6.0"; sha256="0spiix8vlncrc2h1chmkfz8k79lpvq3qya33yyg7avf8dqdqaw31"; depends=[GGally matrixStats network Rcpp RcppArmadillo scales sna]; };
@@ -414,11 +414,11 @@ in with self; {
   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]; };
   GeneticsPed = derive2 { name="GeneticsPed"; version="1.56.0"; sha256="1gvk3wg5mqyc8j95l4djfc55ymv4i08az67znnly3r8376m07mqw"; depends=[gdata genetics MASS]; };
   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]; };
-  GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.30.0"; sha256="1r0wblz9w4hqxm15wdssz0invx7hxhg3bnblkia6w3aazh30s6ns"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; };
+  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]; };
   GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.18.0"; sha256="1nr504dchiifbagrjq0cck5rzd23dcfnvx6bsw9wikw5mg4gib9l"; depends=[dplyr GenomicRanges httr IRanges jsonlite magrittr rappdirs readr rlang S4Vectors SummarizedExperiment tibble xml2]; };
   GenomicDistributions = derive2 { name="GenomicDistributions"; version="1.2.0"; sha256="07c3rxvgm2abs01kzczbpy7kmn3yzcdf5z35dlk1bc2ry3s5dsd1"; depends=[Biostrings data_table dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges plyr reshape2]; };
-  GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.46.3"; sha256="0a3shdzc1r0f12q9w679hgj8ywrwbg36z7k0yp47dgfjl14lachk"; depends=[AnnotationDbi Biobase BiocGenerics BiocIO biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; };
+  GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.46.4"; sha256="0r0vi6hkp5yhgdw1df2y8ivz7fbcbxs9zqpavlkyklpfbrs32yay"; depends=[AnnotationDbi Biobase BiocGenerics BiocIO biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; };
   GenomicFiles = derive2 { name="GenomicFiles"; version="1.30.0"; sha256="0i5y6dk6z18yqj5k4zy756c6l57z9jq2w5a5dksh2di4qgdgjx3x"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges MatrixGenerics Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; };
   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]; };
@@ -437,13 +437,13 @@ in with self; {
   GraphPAC = derive2 { name="GraphPAC"; version="1.36.0"; sha256="19925ha3mr7j399nlwb2vjvsrf7s4xjbq8b6z1k304kxk7d13yp5"; depends=[igraph iPAC RMallow TSP]; };
   GreyListChIP = derive2 { name="GreyListChIP"; version="1.26.0"; sha256="1h7h27q6l9d8j0shklyrh135zrwx56v4zzmm21cj1b7dvmwvpbcv"; depends=[BSgenome GenomeInfoDb GenomicAlignments GenomicRanges MASS Rsamtools rtracklayer SummarizedExperiment]; };
   Guitar = derive2 { name="Guitar"; version="2.10.0"; sha256="082yja4mmsq77sllv3c88agxjbb6jxwil2krb8fkfsijvyyx11c9"; depends=[AnnotationDbi dplyr GenomicFeatures GenomicRanges ggplot2 knitr magrittr rtracklayer]; };
-  Gviz = derive2 { name="Gviz"; version="1.38.0"; sha256="0nqa7m300d7gpsayb6c6rv64d3y8c390wvwgz7v29zs9c025s9a8"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; };
+  Gviz = derive2 { name="Gviz"; version="1.38.3"; sha256="0fmykq3b697n6lf33n5ldv2zxp7ccihpad1n95dqmrgfq4919kis"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; };
   HDF5Array = derive2 { name="HDF5Array"; version="1.22.1"; sha256="1al4a88pgdl7hfhphsnwl1gg1c1kmw37wcdr4v4pfsw5l8ff7nx4"; depends=[BiocGenerics DelayedArray IRanges Matrix rhdf5 rhdf5filters Rhdf5lib S4Vectors]; };
   HDTD = derive2 { name="HDTD"; version="1.28.0"; sha256="1pd0bbni121b5yq3j3sn8n67xgjfm4zygcpx7zgddcnq250544vl"; depends=[Rcpp RcppArmadillo]; };
   HELP = derive2 { name="HELP"; version="1.52.0"; sha256="17bhh9phny0cw3n61582wywl395ls0ak68y8fqv1ibbqiip193ag"; depends=[Biobase]; };
   HEM = derive2 { name="HEM"; version="1.66.0"; sha256="1jv8fwqsk05g7l7bbl7z928m83gk0gw70pix0dp901j9hm1xqjpb"; depends=[Biobase]; };
   HGC = derive2 { name="HGC"; version="1.2.0"; sha256="0skvfx81xvfi8bwlskq1ylr6c5sblh3qzidbz1nb2xa2m4pck2q0"; depends=[ape dendextend dplyr ggplot2 Matrix mclust patchwork RANN Rcpp RcppEigen]; };
-  HIBAG = derive2 { name="HIBAG"; version="1.30.1"; sha256="1ca0gin0hd2vh2pvx4xrca6iqr2nncfzsk5s7az8v2mwm9q6i09s"; depends=[RcppParallel]; };
+  HIBAG = derive2 { name="HIBAG"; version="1.30.2"; sha256="0wg0p650dlnky62rbhfs1gg4hmq93dkmmxswkhdqkkbdqi62d107"; depends=[RcppParallel]; };
   HIPPO = derive2 { name="HIPPO"; version="1.6.0"; sha256="0fr1zhavdzf7rmf0diy4r9qphfcphzbcqcs4370fyd4vyz5bid6l"; depends=[dplyr ggplot2 ggrepel gridExtra irlba magrittr Matrix reshape2 rlang Rtsne SingleCellExperiment umap]; };
   HIREewas = derive2 { name="HIREewas"; version="1.12.0"; sha256="0bjj5h9vc1fhzcn31hvkpcmnx6gzmz3fhczgy21q0ngp26ny10yd"; depends=[gplots quadprog]; };
   HMMcopy = derive2 { name="HMMcopy"; version="1.36.0"; sha256="0kbvdsvvrrzy05a5qiybc9chjfiidcz5mk09nj9s2x6vsj2whwxi"; depends=[data_table]; };
@@ -459,7 +459,7 @@ in with self; {
   HelloRanges = derive2 { name="HelloRanges"; version="1.20.0"; sha256="1f9fyafp3spxb76xl8ncww0dzfi4dbzh9ijqzs89dc7m10saq89p"; depends=[BiocGenerics Biostrings BSgenome docopt GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; };
   Herper = derive2 { name="Herper"; version="1.3.0"; sha256="038cavnbz7gvmv9mpnf88n8dzrg7yl306y68zsq5hpkrj6qax9vr"; depends=[reticulate rjson withr]; };
   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]; };
-  HiCDCPlus = derive2 { name="HiCDCPlus"; version="1.2.0"; sha256="0csm0ffbn3ya8fb936dy9g5sbvszsn274wszm871n248s9vqn8k7"; depends=[bbmle Biostrings BSgenome data_table dplyr GenomeInfoDb GenomicInteractions GenomicRanges InteractionSet IRanges MASS pscl R_utils Rcpp rlang rtracklayer S4Vectors tibble tidyr]; };
+  HiCDCPlus = derive2 { name="HiCDCPlus"; version="1.2.1"; sha256="0ywy0xwymrd9pknnz654vz31463js3rl3f1avmzjzd4krkf2vdgh"; depends=[bbmle Biostrings BSgenome data_table dplyr GenomeInfoDb GenomicInteractions GenomicRanges InteractionSet IRanges MASS pscl R_utils Rcpp rlang rtracklayer S4Vectors tibble tidyr]; };
   HiCcompare = derive2 { name="HiCcompare"; version="1.16.0"; sha256="0g2gsy27prk8b4anywim0qskishc52zh0p3854v04l6jax26675r"; depends=[BiocParallel data_table dplyr GenomicRanges ggplot2 gridExtra gtools InteractionSet IRanges KernSmooth mgcv pheatmap QDNAseq rhdf5 S4Vectors]; };
   HiLDA = derive2 { name="HiLDA"; version="1.8.0"; sha256="02yss2nr6f9zb6kd11id4p3zcgdvr66zlf4s404nh1aag221bc7h"; depends=[abind BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot forcats GenomicFeatures GenomicRanges ggplot2 R2jags Rcpp S4Vectors stringr tidyr TxDb_Hsapiens_UCSC_hg19_knownGene XVector]; };
   HiTC = derive2 { name="HiTC"; version="1.38.0"; sha256="1ckiwqfq86k8p3y36iwr7k3y6g4z80n8hb047c0i2491lrn23rhx"; depends=[Biostrings GenomeInfoDb GenomicRanges IRanges Matrix RColorBrewer rtracklayer]; };
@@ -481,7 +481,7 @@ in with self; {
   IPO = derive2 { name="IPO"; version="1.20.0"; sha256="0cmdz3d5ayjgk4dwdscczxz1zcrfcsq2ajj5rzwhz9jxh8j272c9"; depends=[BiocParallel CAMERA rsm xcms]; };
   IRISFGM = derive2 { name="IRISFGM"; version="1.2.0"; sha256="1yqn4yy7bi6xkywr8pr742a87vxfynwxk67ddld7642dz0mfcb85"; depends=[AdaptGauss AnnotationDbi anocva clusterProfiler colorspace DEsingle DrImpute ggplot2 ggpubr ggraph igraph knitr Matrix MCL mixtools org_Hs_eg_db org_Mm_eg_db pheatmap Polychrome RColorBrewer Rcpp scater scran Seurat SingleCellExperiment]; };
   IRanges = derive2 { name="IRanges"; version="2.28.0"; sha256="07zs231wbfwwc1c1165rhp711fbss40p9l8kyjjv9flzpr3hr1pg"; depends=[BiocGenerics S4Vectors]; };
-  ISAnalytics = derive2 { name="ISAnalytics"; version="1.4.2"; sha256="0czvf3r4aj6xdfny28irkf8k0jrkjvmdxzrcdfqnm0mh7vmqbgaq"; depends=[BiocParallel data_table dplyr fs ggplot2 ggrepel lifecycle lubridate magrittr psych purrr Rcapture readr readxl rlang stringr tibble tidyr zip]; };
+  ISAnalytics = derive2 { name="ISAnalytics"; version="1.4.3"; sha256="1ki8b92qd361pmb9azy2kd4nsxjr9rz3cvxg5ih92k0ps4yhadak"; depends=[BiocParallel data_table dplyr fs ggplot2 ggrepel lifecycle lubridate magrittr psych purrr Rcapture readr readxl rlang stringr tibble tidyr zip]; };
   ISoLDE = derive2 { name="ISoLDE"; version="1.22.0"; sha256="16qfv44341n1l69zh86k445kspaygy0y4by7jms8fhnyiw7pd261"; depends=[]; };
   ITALICS = derive2 { name="ITALICS"; version="2.54.0"; sha256="17d12vcbwmvqfg5bfp5854g2n3c6mg30gdm5cm07k29h1y6q25h7"; depends=[affxparser DBI GLAD ITALICSData oligo oligoClasses pd_mapping50k_xba240]; };
   IVAS = derive2 { name="IVAS"; version="2.14.0"; sha256="02cwi01iamig91hwjsx481l61cxxzrhazxfnw2p1q18ydkc9w6fv"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges ggfortify ggplot2 IRanges lme4 Matrix S4Vectors]; };
@@ -575,7 +575,7 @@ in with self; {
   MSGFplus = derive2 { name="MSGFplus"; version="1.28.0"; sha256="1k0qm049gk4gjhd88zhxxrpc944r7ndq8dys08ai2kbaqignvb7y"; depends=[mzID ProtGenerics]; };
   MSPrep = derive2 { name="MSPrep"; version="1.4.0"; sha256="0nkmmjzkdxizk2yv1ahgsp8zsr4jjazpzqqwcsx86dhrgf5jk5cz"; depends=[crmn ddpcr dplyr magrittr missForest pcaMethods preprocessCore rlang S4Vectors stringr SummarizedExperiment sva tibble tidyr VIM]; };
   MSnID = derive2 { name="MSnID"; version="1.28.0"; sha256="0dks5h3vp9ly8x24px2rl5blqicxybpxjnxvg2p1bwq8zvjkm38p"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics BiocStyle Biostrings data_table doParallel dplyr foreach ggplot2 iterators msmsTests MSnbase mzID mzR ProtGenerics purrr R_cache Rcpp reshape2 rlang RUnit stringr tibble xtable]; };
-  MSnbase = derive2 { name="MSnbase"; version="2.20.1"; sha256="0ip614mdwisz2hlmyfgngysq1s3hajb88cgdmygfc8i6kyxjkjzl"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS MsCoreUtils mzID mzR pcaMethods plyr ProtGenerics Rcpp S4Vectors scales vsn XML]; };
+  MSnbase = derive2 { name="MSnbase"; version="2.20.4"; sha256="0d3b0i154dyz1wvy2jwf5831bzbmalw7rzvxj8rd7658zjhghgzc"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS MsCoreUtils mzID mzR pcaMethods plyr ProtGenerics Rcpp S4Vectors scales vsn XML]; };
   MSstats = derive2 { name="MSstats"; version="4.2.0"; sha256="1i36a0vhqb2sjllyh6ascfm5fbzf8awazbk1vjq5n8mh2cq72ri9"; depends=[checkmate data_table ggplot2 ggrepel gplots limma lme4 marray MASS MSstatsConvert preprocessCore Rcpp RcppArmadillo survival]; };
   MSstatsConvert = derive2 { name="MSstatsConvert"; version="1.4.0"; sha256="0p44g7kv2zyknmiki94w0v4zq1qpa2ly17hbfqkfy9c1xql7b38g"; depends=[checkmate data_table log4r stringi]; };
   MSstatsLOBD = derive2 { name="MSstatsLOBD"; version="1.2.0"; sha256="0d78hd9ip2amkj5pjmwy376qhzfd46wqmzl38rbm52d946c69sb8"; depends=[ggplot2 minpack_lm Rcpp]; };
@@ -621,7 +621,7 @@ in with self; {
   MiPP = derive2 { name="MiPP"; version="1.66.0"; sha256="1m42rv20f9cwnr97ckx4lm193zf0kjr2v33fisymyaq5rrl7ppfn"; depends=[Biobase e1071 MASS]; };
   MiRaGE = derive2 { name="MiRaGE"; version="1.36.0"; sha256="10laq0b1acsirykb5cjxlpj91lqvmhsd3ammk331njaaczh4mjrx"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager S4Vectors]; };
   MicrobiomeProfiler = derive2 { name="MicrobiomeProfiler"; version="1.0.0"; sha256="13awswgm1n30fy73xxlph5aay8a4nkb1gjjzhqy9w7djpm99nw8g"; depends=[clusterProfiler config DT enrichplot ggplot2 golem htmltools magrittr shiny shinycustomloader shinyWidgets]; };
-  MicrobiotaProcess = derive2 { name="MicrobiotaProcess"; version="1.6.3"; sha256="0k67ajgz87lanfkg38zhihnfvq31n7x4093a42bh0dx69m92rcbh"; depends=[ape Biostrings coin dplyr dtplyr foreach ggplot2 ggrepel ggsignif ggstar ggtree ggtreeExtra magrittr MASS patchwork pillar rlang SummarizedExperiment tibble tidyr tidyselect tidytree treeio vegan zoo]; };
+  MicrobiotaProcess = derive2 { name="MicrobiotaProcess"; version="1.6.4"; sha256="0vfmsdbn5czz90kg6mzgrfgrv1y5l9vxplj1j17k0s19z525w1kj"; depends=[ape Biostrings coin dplyr dtplyr foreach ggplot2 ggrepel ggsignif ggstar ggtree ggtreeExtra magrittr MASS patchwork pillar rlang SummarizedExperiment tibble tidyr tidyselect tidytree treeio vegan zoo]; };
   MineICA = derive2 { name="MineICA"; version="1.34.0"; sha256="00pbhbz44dx5gfzzf1drwny4a779zxk4hjavb1fkpg15cm7c152x"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt cluster colorspace fastICA foreach fpc ggplot2 GOstats graph gtools Hmisc igraph JADE lumi lumiHumanAll_db marray mclust plyr RColorBrewer Rgraphviz scales xtable]; };
   MinimumDistance = derive2 { name="MinimumDistance"; version="1.38.0"; sha256="077prww1k374czkd8dlpy081ki101vpl2gpi4dmjbzzq5q45ld7f"; depends=[Biobase BiocGenerics data_table DNAcopy ff foreach GenomeInfoDb GenomicRanges IRanges lattice MatrixGenerics matrixStats oligoClasses S4Vectors SummarizedExperiment VanillaICE]; };
   ModCon = derive2 { name="ModCon"; version="1.2.0"; sha256="1pgvkscvsacm7ag6yyqlpxs6c5vyb3hlmk6gzkiarsc1b29iqhm4"; depends=[data_table]; };
@@ -671,7 +671,7 @@ in with self; {
   OMICsPCA = derive2 { name="OMICsPCA"; version="1.12.0"; sha256="0d5hplm94k7hz6lap31jsb5pdh8lb7xl9i0swznm5vzrxrjdifyd"; depends=[cluster clValid corrplot cowplot data_table factoextra FactoMineR fpc GenomeInfoDb ggplot2 HelloRanges IRanges kableExtra magick MASS MultiAssayExperiment NbClust OMICsPCAdata pdftools PerformanceAnalytics reshape2 rgl rmarkdown rtracklayer tidyr]; };
   OPWeight = derive2 { name="OPWeight"; version="1.16.0"; sha256="1zkbhb70aam3g1arfb8bc8z4c4bd1qyr1zidz6srx1n25pkhp4ii"; depends=[MASS qvalue tibble]; };
   ORFhunteR = derive2 { name="ORFhunteR"; version="1.2.0"; sha256="0jkpq3hiv6n5c4hy3khs59020p98ig91w78ab37jam3sibykr0c6"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg38 data_table Peptides randomForest Rcpp rtracklayer stringr xfun]; };
-  ORFik = derive2 { name="ORFik"; version="1.14.6"; sha256="11f0p5m0r0qhf86n56s6pwiswn3sp1x8pz4gksa5yvhqrkbq6q8q"; depends=[AnnotationDbi BiocGenerics BiocParallel biomartr Biostrings BSgenome cowplot data_table DESeq2 fst GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra httr IRanges jsonlite R_utils Rcpp Rsamtools rtracklayer S4Vectors SummarizedExperiment xml2]; };
+  ORFik = derive2 { name="ORFik"; version="1.14.7"; sha256="0n04h94jdq99rggq4bydric0f957kd34yzfqpgafn7hy15p23a7z"; depends=[AnnotationDbi BiocGenerics BiocParallel biomartr Biostrings BSgenome cowplot data_table DESeq2 fst GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra httr IRanges jsonlite R_utils Rcpp Rsamtools rtracklayer S4Vectors SummarizedExperiment xml2]; };
   OSAT = derive2 { name="OSAT"; version="1.42.0"; sha256="1ibhrrlfjjils0w6n586s5ws0ybv7ija2p2f0jq3m3m9l324iyx9"; depends=[]; };
   OTUbase = derive2 { name="OTUbase"; version="1.44.0"; sha256="18wmllkc3h8x9ihrg0lzk4jvxjwrccl1jr37inkdmzv4aq5b7ygs"; depends=[Biobase Biostrings IRanges S4Vectors ShortRead vegan]; };
   OUTRIDER = derive2 { name="OUTRIDER"; version="1.12.0"; sha256="0ygsk0q1n8h02y4x3ccajkyyryn8gq0dz397l3jryb248g564a4h"; depends=[BBmisc BiocGenerics BiocParallel data_table DESeq2 generics GenomicFeatures GenomicRanges ggplot2 heatmaply IRanges matrixStats pcaMethods pheatmap plotly plyr PRROC RColorBrewer Rcpp RcppArmadillo reshape2 S4Vectors scales SummarizedExperiment]; };
@@ -680,7 +680,7 @@ in with self; {
   OmicCircos = derive2 { name="OmicCircos"; version="1.32.0"; sha256="1lkncbdq93azp1gv0z4bwdi6l1gpywm096hhn45q7w6f0dy5ydqs"; depends=[GenomicRanges]; };
   OmicsLonDA = derive2 { name="OmicsLonDA"; version="1.10.0"; sha256="1vdnpsbpm4zyc17nah5qnlw66bihc7svqvbwgbxmyfp84c2vbxjy"; depends=[BiocGenerics BiocParallel ggplot2 gss plyr pracma SummarizedExperiment zoo]; };
   Omixer = derive2 { name="Omixer"; version="1.4.0"; sha256="1pdsxcih642csqga7wy93bbhib2v08pywa8aw67zy7p62hvrxwim"; depends=[dplyr forcats ggplot2 gridExtra magrittr readr stringr tibble tidyselect]; };
-  OmnipathR = derive2 { name="OmnipathR"; version="3.2.0"; sha256="1q89mxnp8cig9r1499g7fb9p9x9ryz1dmc3w6ps5ww9n6rl8jqk8"; depends=[checkmate crayon curl digest dplyr httr igraph jsonlite later logger magrittr progress purrr rappdirs readr readxl rlang stringr tibble tidyr tidyselect xml2 yaml]; };
+  OmnipathR = derive2 { name="OmnipathR"; version="3.2.5"; sha256="0kmkbgkn6dw4jc0kd8p6pb2qvwyz1is24qld22h018v4rry3xa9s"; depends=[checkmate crayon curl digest dplyr httr igraph jsonlite later logger magrittr progress purrr rappdirs readr readxl rlang stringr tibble tidyr tidyselect xml2 yaml]; };
   OncoScore = derive2 { name="OncoScore"; version="1.22.0"; sha256="0pva48qjbxibgk2wxpaxr4xfq9i8dxbml418wx2nrjj20dn2dhcv"; depends=[biomaRt]; };
   OncoSimulR = derive2 { name="OncoSimulR"; version="3.2.0"; sha256="0dcx1qg42pxlcdpl07f53zkk32qpa8hd7fzdz5acvq3zm8yjmhlk"; depends=[car data_table dplyr ggplot2 ggrepel graph gtools igraph RColorBrewer Rcpp Rgraphviz smatr stringr]; };
   OpenStats = derive2 { name="OpenStats"; version="1.6.0"; sha256="17gvfvii7z8w9l6w5p0i05374d6sw704w627fnasbrcmkfqnvwka"; depends=[AICcmodavg car Hmisc jsonlite knitr MASS nlme rlist summarytools]; };
@@ -724,7 +724,7 @@ in with self; {
   PhenStat = derive2 { name="PhenStat"; version="2.30.0"; sha256="0b423kkbyyjk4ns4pdwh1lag2k0v7wn17h4l4aca3zkjrsf5522n"; depends=[car corrplot ggplot2 graph knitr lme4 logistf MASS msgps nlme nortest pingr reshape SmoothWin]; };
   PhenoGeneRanker = derive2 { name="PhenoGeneRanker"; version="1.2.0"; sha256="1x5fbipgsiz2ipg9yh2r8wr8w1s6q01vq4149gjjxgx779xz250n"; depends=[doParallel dplyr foreach igraph Matrix]; };
   PhosR = derive2 { name="PhosR"; version="1.4.0"; sha256="0ssfvc9qqj25j48srjjissq034f7giddx45w236yssaynw3ykslr"; depends=[BiocGenerics circlize dendextend dplyr e1071 GGally ggdendro ggplot2 ggpubr ggtext igraph limma network pcaMethods pheatmap preprocessCore RColorBrewer reshape2 rlang ruv S4Vectors SummarizedExperiment tidyr]; };
-  PhyloProfile = derive2 { name="PhyloProfile"; version="1.8.3"; sha256="0mnfqbyarknjh6zxq399msl2kbqa1rnw7gqw6k3z2slal2x53ris"; depends=[ape BiocStyle bioDist Biostrings colourpicker data_table DT energy ExperimentHub ggplot2 gridExtra OmaDB pbapply plyr RColorBrewer RCurl shiny shinyBS shinyjs xml2 yaml zoo]; };
+  PhyloProfile = derive2 { name="PhyloProfile"; version="1.8.5"; sha256="06ky4bhhmk251j1rfa0l9vsy9zvc99l6b280l7p8zfhj2kbpr6h1"; depends=[ape BiocStyle bioDist Biostrings colourpicker data_table DT energy ExperimentHub ggplot2 gridExtra OmaDB pbapply plyr RColorBrewer RCurl shiny shinyBS shinyFiles shinyjs xml2 yaml zoo]; };
   Pi = derive2 { name="Pi"; version="2.6.0"; sha256="14bpqzwx59shx5467nj0g6wj58qh9zqhy1i9l1n1gk7wd52ig5ql"; depends=[BiocGenerics caret dnet dplyr GenomeInfoDb GenomicRanges ggnetwork ggplot2 ggrepel glmnet igraph IRanges lattice MASS Matrix osfr plot3D purrr randomForest RCircos readr ROCR scales supraHex tibble tidyr]; };
   Pigengene = derive2 { name="Pigengene"; version="1.20.0"; sha256="1rdz2d5fy6gpdvzv5vfgxngwkag062i6bvvjqkyflabn0yijjpmi"; depends=[BiocStyle bnlearn C50 clusterProfiler DBI dplyr gdata ggplot2 GO_db graph impute MASS matrixStats openxlsx partykit pheatmap preprocessCore ReactomePA Rgraphviz WGCNA]; };
   PloGO2 = derive2 { name="PloGO2"; version="1.6.0"; sha256="0i5b7nfifjx1ywvdq4mhvy3wzdg8cqdcc7sw1awsz9xfnrjnhcdp"; depends=[GO_db GOstats httr lattice openxlsx xtable]; };
@@ -732,7 +732,7 @@ in with self; {
   PoTRA = derive2 { name="PoTRA"; version="1.10.0"; sha256="0qqr9mjqhfk76pnpzd0hzxw180swqr9b1dhakj65lha5mha4vgid"; depends=[BiocGenerics graph graphite igraph org_Hs_eg_db]; };
   PrInCE = derive2 { name="PrInCE"; version="1.10.0"; sha256="09fvk96zxj0bglbs8kgnbg3xxri2pial14g4kcsynaac0m2lmdyk"; depends=[Biobase dplyr forecast Hmisc LiblineaR magrittr MSnbase naivebayes progress purrr ranger Rdpack robustbase speedglm tester tidyr]; };
   PrecisionTrialDrawer = derive2 { name="PrecisionTrialDrawer"; version="1.10.0"; sha256="1zr1jpbnjjrgrbm99n8182akp7xg75bf54gy0wc66r7dxj4vivfl"; depends=[BiocParallel biomaRt brglm cgdsr data_table DT GenomicRanges ggplot2 ggrepel googleVis httr IRanges jsonlite LowMACAAnnotation magrittr matrixStats RColorBrewer reshape2 S4Vectors shiny shinyBS stringr XML]; };
-  Prostar = derive2 { name="Prostar"; version="1.26.2"; sha256="0wm9kmd3f4zwwn80b13n0am9vl2786pm9gl620qdc7s2pva9y1vc"; depends=[BiocManager colourpicker DAPAR DAPARdata data_table DT future highcharter htmlwidgets later promises R_utils rclipboard rhandsontable sass shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes shinyTree shinyWidgets tibble webshot XML]; };
+  Prostar = derive2 { name="Prostar"; version="1.26.4"; sha256="0488x3dsbfydymc7bvh70v77rc3gfqkc56ykvfalrzl85r9zmlk0"; depends=[BiocManager colourpicker DAPAR DAPARdata data_table DT future highcharter htmlwidgets later promises R_utils rclipboard rhandsontable sass shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes shinyTree shinyWidgets tibble webshot XML]; };
   ProtGenerics = derive2 { name="ProtGenerics"; version="1.26.0"; sha256="0x53pk7h47gjza1q5pz7jb1qqhwa9z2rr5fr61qc92zl3mqk57m0"; depends=[]; };
   ProteoDisco = derive2 { name="ProteoDisco"; version="1.0.0"; sha256="14rizjlwf87qhi929b4vafjzvx7p112bsq0zb2wppxh3m7izs4zp"; depends=[BiocGenerics BiocParallel Biostrings checkmate cleaver dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges ParallelLogger plyr rlang S4Vectors tibble tidyr VariantAnnotation XVector]; };
   ProteoMM = derive2 { name="ProteoMM"; version="1.12.0"; sha256="1y7w6rs11kclh5nipnrh02ny12bgf2rkb2dghqcybl80s6r8m6bm"; depends=[biomaRt gdata ggplot2 ggrepel gtools matrixStats]; };
@@ -803,7 +803,7 @@ in with self; {
   RTN = derive2 { name="RTN"; version="2.18.0"; sha256="0yjbvcaci77xbxkl35i03vdmd2ascaphv2lpagcib4wlj2qsg57y"; depends=[car data_table igraph IRanges limma minet mixtools pheatmap pwr RedeR S4Vectors snow SummarizedExperiment viper]; };
   RTNduals = derive2 { name="RTNduals"; version="1.18.0"; sha256="1h646yysi879v1w60sc1f6wckyz788cq2psyihnp873k001yzgv9"; depends=[RTN]; };
   RTNsurvival = derive2 { name="RTNsurvival"; version="1.18.0"; sha256="158ffqrysprfx5g5m9mc645bjcpdjr3cksl521jc4ak401va7l7l"; depends=[data_table dunn_test egg ggplot2 pheatmap RColorBrewer RTN RTNduals scales survival]; };
-  RTopper = derive2 { name="RTopper"; version="1.40.0"; sha256="18x3qmqxh6y64bmp2a8d7f794inglx7mvaiva5rs04y26qlwww9s"; depends=[Biobase limma multtest]; };
+  RTopper = derive2 { name="RTopper"; version="1.40.1"; sha256="1mdp498x90rvlq8v1mfs067r4vprliiqf30f3smqh1b2bljcfpcc"; depends=[Biobase limma multtest]; };
   RUVSeq = derive2 { name="RUVSeq"; version="1.28.0"; sha256="1a19klscykdgsd7izcxyr45ml7g0gpdj65gvbaw124mal2p4zi9q"; depends=[Biobase EDASeq edgeR MASS]; };
   RUVcorr = derive2 { name="RUVcorr"; version="1.26.0"; sha256="0va76nl1j4f5cs1d7cxz2gx7v80r42ia178c9nb2fb91lmahalsn"; depends=[BiocParallel bladderbatch corrplot gridExtra lattice MASS psych reshape2 snowfall]; };
   RUVnormalize = derive2 { name="RUVnormalize"; version="1.28.0"; sha256="1yqnp1fpln7g4h20fikr9hh7x80s93pdip9g612m0djp5p2xlvlx"; depends=[Biobase RUVnormalizeData]; };
@@ -868,7 +868,7 @@ in with self; {
   SCAN_UPC = derive2 { name="SCAN.UPC"; version="2.36.0"; sha256="16d161x1npa4lh6ckp0p9ykdrj3x36gsylmq1kjm2vw8g4zknszv"; depends=[affy affyio Biobase Biostrings foreach GEOquery IRanges MASS oligo sva]; };
   SCANVIS = derive2 { name="SCANVIS"; version="1.8.0"; sha256="08cpq7cklv1z108cy0d6abv8xq8ins4ihdwzr04fr8bg2ikbi21z"; depends=[IRanges plotrix RCurl rtracklayer]; };
   SCATE = derive2 { name="SCATE"; version="1.4.0"; sha256="1b04bggi0rw9jmgak5j2ca6msqdrq1qdphg3g9w77a1rqyxza86s"; depends=[GenomicAlignments GenomicRanges mclust preprocessCore Rtsne SCATEData splines2 xgboost]; };
-  SCArray = derive2 { name="SCArray"; version="1.2.0"; sha256="1jji2cikxkc40zaqwcknrpz5a6nyrqhbirx5ivsdnwslm8l79xmk"; depends=[BiocGenerics DelayedArray DelayedMatrixStats gdsfmt IRanges S4Vectors SingleCellExperiment SummarizedExperiment]; };
+  SCArray = derive2 { name="SCArray"; version="1.2.1"; sha256="1p69m8jp3fz71a726h2r8zjgxj01bbsnnjz9714siz6awswm816l"; depends=[BiocGenerics DelayedArray DelayedMatrixStats gdsfmt IRanges S4Vectors SingleCellExperiment SummarizedExperiment]; };
   SCBN = derive2 { name="SCBN"; version="1.12.0"; sha256="19jpbr5nr59dc9khbbx60gzbsg8llfd1zqwb9v88nr43v059k13f"; depends=[]; };
   SCFA = derive2 { name="SCFA"; version="1.4.0"; sha256="1850c78niv5hp3c6axi5nmv4qawqca1ip3xppp2nar8f9xiqjd6l"; depends=[BiocParallel cluster clusterCrit glmnet igraph keras Matrix matrixStats psych RhpcBLASctl survival tensorflow]; };
   SCOPE = derive2 { name="SCOPE"; version="1.6.0"; sha256="01sj416q0qzpji7k34xz37l4955fa3l2imms96k8zz1gs2a1xm3j"; depends=[BiocGenerics Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 DescTools DNAcopy doParallel foreach GenomeInfoDb GenomicRanges gplots IRanges RColorBrewer Rsamtools S4Vectors]; };
@@ -905,7 +905,7 @@ 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="2.6.0"; sha256="1hvb73anhbf1g82nn5m11s783z6ihvlavf7p30w29qggxggnl6lm"; depends=[gplots hash igraph plotrix plyr png RColorBrewer RCurl sqldf]; };
+  STRINGdb = derive2 { name="STRINGdb"; version="2.6.1"; sha256="14yn0fi6ghlv41z5vk4wvrx51hlpx7z9k5fk5jyb50l2g8wwzjhi"; 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=[]; };
@@ -929,7 +929,7 @@ in with self; {
   SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.16.0"; sha256="01075vbs8hy399pxalav9rbkz4djvl84ip559jkz51fypd0m4i39"; depends=[BiocGenerics DelayedArray GenomicRanges S4Vectors SummarizedExperiment]; };
   SingleCellSignalR = derive2 { name="SingleCellSignalR"; version="1.6.0"; sha256="1iw9yis5d6m2bzqkyncz5cy49rncnjrbzwah4c3il8aq5a21hrfh"; depends=[BiocManager circlize data_table edgeR foreach gplots igraph limma multtest pheatmap Rtsne scran SIMLR stringr]; };
   SingleMoleculeFootprinting = derive2 { name="SingleMoleculeFootprinting"; version="1.2.0"; sha256="0abaxk5ck81libsfhy1w9jx1jjf7cix7znl2gydh2fd5qaafzfd3"; depends=[BiocGenerics Biostrings BSgenome data_table GenomeInfoDb GenomicRanges IRanges plyr QuasR RColorBrewer]; };
-  SingleR = derive2 { name="SingleR"; version="1.8.0"; sha256="19lsn3cpghkhfbx4jqgbwwrnacrl7vj3r91ymd1gk02c9pn5dmci"; depends=[beachmat BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats Matrix Rcpp S4Vectors SummarizedExperiment]; };
+  SingleR = derive2 { name="SingleR"; version="1.8.1"; sha256="0j0h6ipm65wv38qx40z16h01mfirpshfn4lhlwlg2nri4vmihlpi"; depends=[beachmat BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats Matrix Rcpp S4Vectors SummarizedExperiment]; };
   SomaticSignatures = derive2 { name="SomaticSignatures"; version="2.30.0"; sha256="1dxzfkvljnydv7kfybfa52dwcbkkci2r8gjspjf90k2bxf10phql"; depends=[Biobase Biostrings GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges NMF pcaMethods proxy reshape2 S4Vectors VariantAnnotation]; };
   SpacePAC = derive2 { name="SpacePAC"; version="1.32.0"; sha256="1pgpfxyw621f7ljwy4y6q9fdlk263b4rwz9vg1f2h61nz097nk2l"; depends=[iPAC]; };
   Spaniel = derive2 { name="Spaniel"; version="1.8.0"; sha256="0js302hgxn0q9xy7s6pdxidvhfcvm711bci6cw3a3bwhq2kacvnc"; depends=[dplyr DropletUtils ggplot2 igraph jpeg jsonlite magrittr png S4Vectors scater scran Seurat shiny SingleCellExperiment SummarizedExperiment]; };
@@ -959,7 +959,7 @@ in with self; {
   TAPseq = derive2 { name="TAPseq"; version="1.6.0"; sha256="0y40z1xpqif09yins9jf4k0h7wljdf3qwgzykxcq5lfgns66cx91"; depends=[BiocGenerics BiocParallel Biostrings BSgenome dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges S4Vectors tidyr]; };
   TBSignatureProfiler = derive2 { name="TBSignatureProfiler"; version="1.6.0"; sha256="0sdgbkg0mv742y9b7frp4i2zrknfw87ghz6wvw4w0y0gjrbasj9r"; depends=[ASSIGN BiocGenerics BiocParallel ComplexHeatmap DESeq2 DT edgeR gdata ggplot2 GSVA magrittr RColorBrewer reshape2 rlang ROCit S4Vectors singscore SummarizedExperiment]; };
   TCC = derive2 { name="TCC"; version="1.34.0"; sha256="0298zfvrs7x6050s3222fg5yp60siz85pfh6541wmah7j0wzpgsd"; depends=[baySeq DESeq2 edgeR ROC]; };
-  TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.22.2"; sha256="0l7hfwgd8aiqv2k98jchkr3sdp9hwdg7pzm3bnvr6k7p93ifr6wc"; depends=[biomaRt data_table downloader dplyr GenomicRanges ggplot2 httr IRanges jsonlite knitr plyr purrr R_utils readr rvest S4Vectors stringr SummarizedExperiment TCGAbiolinksGUI_data tibble tidyr XML xml2]; };
+  TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.22.4"; 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]; };
   TCseq = derive2 { name="TCseq"; version="1.18.0"; sha256="1kzz3fl19d1ivb6l55xadwg202vq4wza3r7wgf6fx196s20vnvng"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; };
@@ -985,7 +985,7 @@ in with self; {
   TarSeqQC = derive2 { name="TarSeqQC"; version="1.24.0"; sha256="0303kqwgs442vf0j0rpw15qjk6snvayd9rrjbll8gjnv34xzmw7d"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; };
   TargetDecoy = derive2 { name="TargetDecoy"; version="1.0.0"; sha256="0bvby24gqwkxmcq0d9c5ix5kx1svc59vcil5xv0fmsdzp9bgv4c4"; depends=[ggplot2 ggpubr mzID mzR]; };
   TargetScore = derive2 { name="TargetScore"; version="1.32.0"; sha256="15yh0ms1i38541kf7lxjk3xs9gpm4ixaykq6mhn572slkxdx737y"; depends=[Matrix pracma]; };
-  TargetSearch = derive2 { name="TargetSearch"; version="1.50.0"; sha256="0ikwbgrjp8i5g27acs4qzr8v7gzky209w3zdb6877y9hpvl5kvyv"; depends=[assertthat ncdf4]; };
+  TargetSearch = derive2 { name="TargetSearch"; version="1.50.1"; sha256="1l84lajyrx9x6b3spbjc3zf83bmy4s5qv1a3hz8i56pc9wmqpfyz"; depends=[assertthat ncdf4]; };
   TileDBArray = derive2 { name="TileDBArray"; version="1.4.0"; sha256="007qdq6w0i9b2mbcdbdjm62nzwy15scsxml6fqr0fwgzjfzvzb0z"; depends=[DelayedArray Rcpp S4Vectors tiledb]; };
   TimeSeriesExperiment = derive2 { name="TimeSeriesExperiment"; version="1.12.0"; sha256="0fphnkkd3i7zf33a9lhw95n80vzv1z7fmn7mhrfb949yz4jdvk7d"; depends=[DESeq2 dplyr dynamicTreeCut edgeR ggplot2 Hmisc limma magrittr proxy S4Vectors SummarizedExperiment tibble tidyr vegan viridis]; };
   TimiRGeN = derive2 { name="TimiRGeN"; version="1.4.0"; sha256="1lpvw24gnm1rdl4p2vxh07z82x7wcwcpmak7rjh3yq409lwi72i0"; depends=[biomaRt clusterProfiler dplyr FreqProf ggdendro gghighlight ggplot2 gplots gtools igraph Mfuzz MultiAssayExperiment RCy3 readxl reshape2 rWikiPathways scales stringr tidyr]; };
@@ -1060,7 +1060,7 @@ in with self; {
   amplican = derive2 { name="amplican"; version="1.16.0"; sha256="1p4n0bm4hsw20iyxghnc7k06q2w3hs044zsyl5ysd9xxiggi628l"; depends=[BiocGenerics BiocParallel Biostrings clusterCrit data_table dplyr GenomeInfoDb GenomicRanges ggplot2 ggthemes gridExtra gtable IRanges knitr Matrix matrixStats Rcpp rmarkdown S4Vectors ShortRead stringr waffle]; };
   animalcules = derive2 { name="animalcules"; version="1.10.0"; sha256="0l7lyw1a51piq20lh49ss4c2i75lrs1xq532jgf65n8vkm8asc88"; depends=[ape assertthat biomformat caret covr DESeq2 dplyr DT forcats ggplot2 glmnet GUniFrac lattice limma magrittr Matrix MultiAssayExperiment plotly plotROC rentrez reshape2 S4Vectors scales shiny shinyjs SummarizedExperiment tibble tsne umap vegan XML]; };
   annaffy = derive2 { name="annaffy"; version="1.66.0"; sha256="0crj37v571005brdd0ypfx2a7d1f829xxj2hahp2gy8aj9xm4s8l"; depends=[AnnotationDbi Biobase BiocManager DBI GO_db]; };
-  annmap = derive2 { name="annmap"; version="1.36.0"; sha256="0j8zvg3670dg0smyrdwsc42h64n4c6rm855zawlwgchx3vdgb8gn"; depends=[Biobase BiocGenerics DBI digest genefilter GenomicRanges IRanges lattice RMySQL Rsamtools]; };
+  annmap = derive2 { name="annmap"; version="1.36.99"; sha256="1q129ah96d1vz5d73a5xngz0fzh2zvq793xxha80r3lx2bgld7an"; depends=[Biobase BiocGenerics DBI digest genefilter GenomicRanges IRanges lattice RMySQL Rsamtools]; };
   annotate = derive2 { name="annotate"; version="1.72.0"; sha256="0p7q5hdk7003q72vg4hrgdzn463spybxhrkvcq3a6l6jkgy9sf84"; depends=[AnnotationDbi Biobase BiocGenerics DBI httr XML xtable]; };
   annotationTools = derive2 { name="annotationTools"; version="1.68.0"; sha256="0grdswbf8nj0qwl0n5pqsir9242dry85j6m688j81gwwjgmzidvh"; depends=[Biobase]; };
   annotatr = derive2 { name="annotatr"; version="1.20.0"; sha256="1ha2wn56cdab4p3wdwv4xlqjsgl7sd8phbx71qbclrbdwpq2mi7i"; depends=[AnnotationDbi AnnotationHub dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges readr regioneR reshape2 rtracklayer S4Vectors]; };
@@ -1082,7 +1082,7 @@ in with self; {
   awst = derive2 { name="awst"; version="1.2.0"; sha256="0qxi4f7ngfsx17q9szhl95bhihcfx36bw4n175zyfdnac6cb9kap"; depends=[SummarizedExperiment]; };
   bacon = derive2 { name="bacon"; version="1.22.0"; sha256="13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc"; depends=[BiocParallel ellipse ggplot2]; };
   ballgown = derive2 { name="ballgown"; version="2.26.0"; sha256="0fiky82arvgzgxrm4bqn74m5kngqpdaqf6ks4cr89nlnhfq0v6rf"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges limma RColorBrewer rtracklayer S4Vectors sva]; };
-  bambu = derive2 { name="bambu"; version="2.0.1"; sha256="0bzbaw57syaw2c8d4484dl229brw2d33105ak6krjpl9kd6av9y9"; depends=[BiocGenerics BiocParallel data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment tidyr xgboost]; };
+  bambu = derive2 { name="bambu"; version="2.0.3"; sha256="0yfkmihy8gn55hps2cmldhq26f8lp2ad4iyp601rrmim6s7axwsc"; depends=[BiocGenerics BiocParallel data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment tidyr xgboost]; };
   bamsignals = derive2 { name="bamsignals"; version="1.26.0"; sha256="03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv"; depends=[BiocGenerics GenomicRanges IRanges Rcpp Rhtslib zlibbioc]; };
   banocc = derive2 { name="banocc"; version="1.18.0"; sha256="0p5v601j1lkgh9prlvalp3xpqw87xq7ql0bak212443n15pfj3a4"; depends=[coda mvtnorm rstan stringr]; };
   barcodetrackR = derive2 { name="barcodetrackR"; version="1.2.0"; sha256="1z7sj2ykp34g9bf0x0s3qavrprbiaksgk5r4hsakb24jjbi65jnh"; depends=[circlize cowplot dplyr ggdendro ggplot2 ggridges magrittr plyr proxy RColorBrewer rlang S4Vectors scales shiny SummarizedExperiment tibble tidyr vegan viridis]; };
@@ -1114,7 +1114,7 @@ in with self; {
   biodbKegg = derive2 { name="biodbKegg"; version="1.0.0"; sha256="16xmm3ymzd4jf55plahbxi844hpv0hpqq6v2ygcjf6wrs0yy2mhd"; depends=[biodb chk lifecycle R6]; };
   biodbLipidmaps = derive2 { name="biodbLipidmaps"; version="1.0.1"; sha256="14086f88r7mavpzp823mhpi4b9zq8q2kqxlwnmp02i03jj8mjnr8"; depends=[biodb lifecycle R6]; };
   biodbUniprot = derive2 { name="biodbUniprot"; version="1.0.0"; sha256="1aydkqqb8vs5b844ff1j09a7g8rmf7qr6rg2aw8nqshihq510v4d"; depends=[biodb R6]; };
-  biomaRt = derive2 { name="biomaRt"; version="2.50.1"; sha256="1lm8axjmi2k1d2x0gdlvs0fzsd68xvxx7sn1wn6v4wr0pv85qhkz"; depends=[AnnotationDbi BiocFileCache digest httr progress rappdirs stringr XML xml2]; };
+  biomaRt = derive2 { name="biomaRt"; version="2.50.3"; sha256="01mv05fj5iqvjb5xz9k92kx1a9d95mprb6isy57n0x20vd3cxdx1"; depends=[AnnotationDbi BiocFileCache digest httr progress rappdirs stringr XML xml2]; };
   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]; };
@@ -1134,7 +1134,7 @@ in with self; {
   bsseq = derive2 { name="bsseq"; version="1.30.0"; sha256="1i30zf6457a0qd64s89x9l544y1h0hj9rfgf1m8l4krd487a9b9d"; depends=[beachmat Biobase BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats GenomeInfoDb GenomicRanges gtools HDF5Array IRanges limma locfit permute R_utils Rcpp rhdf5 S4Vectors scales SummarizedExperiment]; };
   bugsigdbr = derive2 { name="bugsigdbr"; version="1.0.1"; sha256="1wrk9m4ja129d4al3w286hzg2gjcnq5riaa99q35psqcwm1bp94f"; depends=[BiocFileCache vroom]; };
   bumphunter = derive2 { name="bumphunter"; version="1.36.0"; sha256="0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; };
-  cBioPortalData = derive2 { name="cBioPortalData"; version="2.6.0"; sha256="0bapc4c9x328l0wrnm6zzq1byf1l33rza8xmadrfqfiq6j56qakq"; depends=[AnVIL BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges MultiAssayExperiment RaggedExperiment readr RTCGAToolbox S4Vectors SummarizedExperiment TCGAutils tibble tidyr]; };
+  cBioPortalData = derive2 { name="cBioPortalData"; version="2.6.1"; sha256="1sscczza5a2drm5h8h628nc8ajxx20gr48j2srli8a7c47lzyv6f"; depends=[AnVIL BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges MultiAssayExperiment RaggedExperiment readr RTCGAToolbox S4Vectors SummarizedExperiment TCGAutils tibble tidyr]; };
   cTRAP = derive2 { name="cTRAP"; version="1.12.0"; sha256="13q0pyc6vvxl41hg8cz4rdqrq0vppnna5fw2cin58dm2mayhd6p9"; depends=[AnnotationDbi AnnotationHub binr cowplot data_table dplyr DT fastmatch fgsea ggplot2 ggrepel highcharter htmltools httr limma pbapply purrr qs R_utils readxl reshape2 rhdf5 rlang scales shiny shinycssloaders tibble]; };
   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]; };
@@ -1183,7 +1183,7 @@ in with self; {
   clstutils = derive2 { name="clstutils"; version="1.42.0"; sha256="0zbyppajhkzims3cb631ylfl132a07b1w91kp3ba6hg4f7zxw06q"; depends=[ape clst lattice rjson RSQLite]; };
   clustComp = derive2 { name="clustComp"; version="1.22.0"; sha256="0n1qpjxffx8jm8m3gw891irpzagpi91r46xa6iznsskh8nhmh44y"; depends=[sm]; };
   clusterExperiment = derive2 { name="clusterExperiment"; version="2.14.0"; sha256="0riray1f841d5fx6mbcki5xmqz21kg5q5l0qz4pkgg9c1d9f7mbc"; depends=[ape BiocGenerics BiocSingular cluster DelayedArray edgeR HDF5Array howmany kernlab limma locfdr Matrix matrixStats mbkmeans NMF phylobase pracma RColorBrewer Rcpp S4Vectors scales SingleCellExperiment stringr SummarizedExperiment zinbwave]; };
-  clusterProfiler = derive2 { name="clusterProfiler"; version="4.2.1"; sha256="08jhcbanz24x7zdkxznxz787g0nk3jfzd7zsap13sra7qnwaswq4"; depends=[AnnotationDbi DOSE downloader dplyr enrichplot GO_db GOSemSim magrittr plyr qvalue rlang tidyr yulab_utils]; };
+  clusterProfiler = derive2 { name="clusterProfiler"; version="4.2.2"; sha256="1y8ay3fxvcc7a7yqvfc95jfn800ikvs56j17byyp6v08w2j00y76"; depends=[AnnotationDbi DOSE downloader dplyr enrichplot GO_db GOSemSim magrittr plyr qvalue rlang tidyr yulab_utils]; };
   clusterSeq = derive2 { name="clusterSeq"; version="1.18.0"; sha256="1qyycc8wrik54bc2rvzisv6p05jnh1kf68jafqgw9lqpp5gk40bl"; depends=[baySeq BiocGenerics BiocParallel]; };
   clusterStab = derive2 { name="clusterStab"; version="1.66.0"; sha256="1863jpdwx27snpil38waj3zr0w2m0q7xj8g1zm8c5cbx9as1cwkd"; depends=[Biobase]; };
   clustifyr = derive2 { name="clustifyr"; version="1.6.0"; sha256="1jz6wfv1b585yf6m9f265ig29p5qxilri40lnpry6h0am2s72xr3"; depends=[cowplot dplyr entropy fgsea ggplot2 httr Matrix matrixStats proxy readr rlang S4Vectors scales SingleCellExperiment stringr SummarizedExperiment tibble tidyr]; };
@@ -1217,7 +1217,7 @@ in with self; {
   coseq = derive2 { name="coseq"; version="1.18.0"; sha256="0g3bningjbnjys7ksdxx68lnp7qfg2fwpp2m82s61rpyb06j5v4r"; depends=[BiocParallel capushe compositions corrplot DESeq2 e1071 edgeR ggplot2 HTSCluster HTSFilter mvtnorm Rmixmod S4Vectors scales SummarizedExperiment]; };
   cosmiq = derive2 { name="cosmiq"; version="1.28.0"; sha256="0b0d7d7fdf0rgkrpp92n6k1vkxswm63p1qmqb3b2c0nwpj68ybph"; depends=[faahKO MassSpecWavelet pracma Rcpp xcms]; };
   cosmosR = derive2 { name="cosmosR"; version="1.2.0"; sha256="0y1a3yr23zbyg0b7yl7rbbfn930g72fpw8dz6vcfz73yjj6psxv1"; depends=[AnnotationDbi biomaRt CARNIVAL dorothea dplyr ggplot2 GSEABase igraph magrittr org_Hs_eg_db plyr purrr readr rlang scales stringr tibble visNetwork]; };
-  countsimQC = derive2 { name="countsimQC"; version="1.12.0"; sha256="0ldjav5wsj1shjiyxi0mh3yxhmpwgwfvp9ijml6jii60hnbkrqck"; depends=[caTools DESeq2 dplyr DT edgeR genefilter GenomeInfoDbData ggplot2 randtests rmarkdown SummarizedExperiment tidyr]; };
+  countsimQC = derive2 { name="countsimQC"; version="1.12.1"; sha256="1ayjhbh6dc8grnizgc77460qn24ll3brybp8p7j2wmpc97dhs6kr"; depends=[caTools DESeq2 dplyr DT edgeR genefilter GenomeInfoDbData ggplot2 randtests rmarkdown SummarizedExperiment tidyr]; };
   covEB = derive2 { name="covEB"; version="1.20.0"; sha256="0r0b1hih0wijcpn2xxjq56z185a5ij3l49g6wxbp5kcd7w5apmhp"; depends=[Biobase gsl igraph LaplacesDemon Matrix mvtnorm]; };
   covRNA = derive2 { name="covRNA"; version="1.20.0"; sha256="16d5pdq2zhymxpv1xx66bb8kn037559mbp3lrcmhddy46xb519cv"; depends=[ade4 Biobase genefilter]; };
   cpvSNP = derive2 { name="cpvSNP"; version="1.26.0"; sha256="1z3lzj2izqmy1m8y73za4pfk158rfxbs8janvq776aqzcaa5pf0k"; depends=[BiocParallel corpcor GenomicFeatures ggplot2 GSEABase plyr]; };
@@ -1243,7 +1243,7 @@ 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="1.4.0"; sha256="02gfagylbmpylq0cszppyxindiw3swm5n36cnfc9w08jfyisz571"; 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="1.4.1"; sha256="03k6gw6csllqysx6mcn8h5a2wq01r3pmk6b0jvqr4iwppn8jspry"; 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]; };
@@ -1264,7 +1264,7 @@ in with self; {
   derfinder = derive2 { name="derfinder"; version="1.28.0"; sha256="1hxf40ijrlmyrv3rprv5wx3am2vraplbsfg77kk9qd3gjq6q3ylp"; depends=[AnnotationDbi BiocGenerics BiocParallel bumphunter derfinderHelper GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges Hmisc IRanges qvalue Rsamtools rtracklayer S4Vectors]; };
   derfinderHelper = derive2 { name="derfinderHelper"; version="1.28.0"; sha256="06x0wy2wzpngak1pnrj2p0xzlx1nbcz0hs3p9q5ic6ib2rgwrh35"; depends=[IRanges Matrix S4Vectors]; };
   derfinderPlot = derive2 { name="derfinderPlot"; version="1.28.1"; sha256="021w4vb8al3gc6rsc6qgywd5wxmysf2jif7cazxl4xhh37g1anni"; depends=[derfinder GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 IRanges limma plyr RColorBrewer reshape2 S4Vectors scales]; };
-  destiny = derive2 { name="destiny"; version="3.8.0"; sha256="01662p5j9l12ylf5a5djg4cjppd2n3chrygzw8nnrcf1806xn58y"; depends=[Biobase BiocGenerics ggplot_multistats ggplot2 ggthemes irlba knn_covertree Matrix pcaMethods proxy Rcpp RcppEigen RcppHNSW RSpectra scales scatterplot3d SingleCellExperiment smoother SummarizedExperiment tidyr tidyselect VIM]; };
+  destiny = derive2 { name="destiny"; version="3.8.1"; sha256="1f2mp2sxbf1zi61npj5rl5pl7z30rkj5953521iiv0w99mdfwhsc"; depends=[Biobase BiocGenerics ggplot_multistats ggplot2 ggthemes irlba knn_covertree Matrix pcaMethods proxy Rcpp RcppEigen RcppHNSW RSpectra scales scatterplot3d SingleCellExperiment smoother SummarizedExperiment tidyr tidyselect VIM]; };
   diffGeneAnalysis = derive2 { name="diffGeneAnalysis"; version="1.76.0"; sha256="1aprngqc2aqdw91q9c57y15xpkm4da4czf8ki55vnyngb9nlpabp"; depends=[minpack_lm]; };
   diffHic = derive2 { name="diffHic"; version="1.26.0"; sha256="0xhm6jgalgb2v8k99k1z99rwhcaqjhhklm5ih8b6ayfmgmf6x7ih"; depends=[BiocGenerics Biostrings BSgenome csaw edgeR GenomeInfoDb GenomicRanges InteractionSet IRanges limma locfit Rcpp rhdf5 Rhtslib Rsamtools rtracklayer S4Vectors SummarizedExperiment zlibbioc]; };
   diffUTR = derive2 { name="diffUTR"; version="1.2.0"; sha256="0lmsbaaqzzvk25bxjb8ngvx0l5aqsmk7nng5kv4nghm7y7ipp1gf"; depends=[ComplexHeatmap DEXSeq dplyr edgeR ensembldb GenomeInfoDb GenomicRanges ggplot2 ggrepel IRanges limma matrixStats Rsubread rtracklayer S4Vectors stringi SummarizedExperiment viridisLite]; };
@@ -1301,12 +1301,12 @@ in with self; {
   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="1.14.1"; sha256="0nsx96mkcg0hhg3x8jndzq3xvq9bq7m4yf1b3ry73b17ladx81ch"; 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="2.18.2"; sha256="0q56gv0isa9ayw505py7i7x65pvcshmd2j1mna1wpbk66wqj4qzx"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; };
+  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]; };
   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]; };
   epigenomix = derive2 { name="epigenomix"; version="1.34.0"; sha256="0yyxm97cqyy9r6bxsw40dl8nh2f1lxw41w3i3av8lixp72wxy3ml"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; };
-  epigraHMM = derive2 { name="epigraHMM"; version="1.2.1"; sha256="1cxj50wfvgcajxgnhk3gpdhql6z6jbmdaarw09ls0wvnga9sn24p"; depends=[bamsignals csaw data_table GenomeInfoDb GenomicRanges ggplot2 ggpubr GreyListChIP IRanges limma magrittr MASS Matrix pheatmap Rcpp RcppArmadillo rhdf5 Rhdf5lib Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; };
+  epigraHMM = derive2 { name="epigraHMM"; version="1.2.2"; sha256="0cymyvhcv9msrkbh0sp3wr02924arrls3id9563givkrzl48gab3"; depends=[bamsignals csaw data_table GenomeInfoDb GenomicRanges ggplot2 ggpubr GreyListChIP IRanges limma magrittr MASS Matrix pheatmap Rcpp RcppArmadillo rhdf5 Rhdf5lib Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; };
   epihet = derive2 { name="epihet"; version="1.10.0"; sha256="086x87yzjmg0l95kd0mdxysqgdj7bmc4mr95h6mkyv70nsdfyfs4"; depends=[data_table doParallel EntropyExplorer foreach GenomicRanges ggplot2 igraph IRanges pheatmap qvalue ReactomePA Rtsne S4Vectors WGCNA]; };
   epistack = derive2 { name="epistack"; version="1.0.0"; sha256="0g5v30v7afx5wppg1fxpqba0inn6k25ljy7x3fim6vcwdhdnl95n"; depends=[BiocGenerics GenomicRanges IRanges plotrix S4Vectors viridisLite]; };
   epivizr = derive2 { name="epivizr"; version="2.24.0"; sha256="1xxs34580gm2l222qf9m63id8282n2vg41s8ng6mrrd239pxpv2f"; depends=[bumphunter epivizrData epivizrServer GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
@@ -1450,7 +1450,7 @@ in with self; {
   hierGWAS = derive2 { name="hierGWAS"; version="1.24.0"; sha256="1mxlk73p4vhnhs5yv5fbxdz3i8d425535r0zwinpi1jhshimr1mw"; depends=[fastcluster fmsb glmnet]; };
   hierinf = derive2 { name="hierinf"; version="1.12.0"; sha256="1qmpxajvclk3m7yl6h5hp4yixgf1v5whiaqh8k7z8g9kz148hi45"; depends=[fmsb glmnet]; };
   hipathia = derive2 { name="hipathia"; version="2.10.0"; sha256="1w14rgl96xssijjgzqdjjs15p33nrqg2wnvv70z5k2i7xzrjwfff"; depends=[AnnotationHub coin DelayedArray igraph limma matrixStats MultiAssayExperiment preprocessCore S4Vectors servr SummarizedExperiment]; };
-  hmdbQuery = derive2 { name="hmdbQuery"; version="1.14.0"; sha256="07xvfxpajwchi570739a2ax25bam852q1ifa8w5a02zb32rfbb6l"; depends=[S4Vectors XML]; };
+  hmdbQuery = derive2 { name="hmdbQuery"; version="1.14.2"; sha256="0q741bwana06i4l07h1ckkfkhmhxqshkq94brd1ym6kvayaqrxb5"; depends=[S4Vectors XML]; };
   hopach = derive2 { name="hopach"; version="2.54.0"; sha256="1mj8glhsxkhfbj8mlghplz1dghdr7041r48njzzprx06x94aandi"; depends=[Biobase BiocGenerics cluster]; };
   hpar = derive2 { name="hpar"; version="1.36.0"; sha256="1inajapdhjxg0vwhsdnhfq22h3fv7ad7m1lv58y5v41p59av1w76"; depends=[]; };
   hummingbird = derive2 { name="hummingbird"; version="1.4.0"; sha256="1cp3agr0nzsqgs4s253vwdbzw5fkjdkas03svy8iwlzncgd000j5"; depends=[GenomicRanges IRanges Rcpp SummarizedExperiment]; };
@@ -1481,7 +1481,7 @@ in with self; {
   idr2d = derive2 { name="idr2d"; version="1.8.1"; sha256="1cbzyf9nwqgqvz03526v3hxgkrrpfs4m8ajw186cxa4h6kdm232x"; depends=[dplyr futile_logger GenomeInfoDb GenomicRanges ggplot2 idr IRanges magrittr reticulate scales stringr]; };
   igvR = derive2 { name="igvR"; version="1.14.0"; sha256="0i55zx2y92cl22d4x4h4gjdaknyxidsxqz22fpgyfd5abryx5ni3"; depends=[BiocGenerics BrowserViz GenomicAlignments GenomicRanges httpuv MotifDb RColorBrewer rtracklayer seqLogo VariantAnnotation]; };
   illuminaio = derive2 { name="illuminaio"; version="0.36.0"; sha256="0icsp610am5vrd8x2h9c450phn4vl9c5wnzqmkix5hkqzrykk34m"; depends=[base64]; };
-  imageHTS = derive2 { name="imageHTS"; version="1.44.0"; sha256="1dg4p6qdhyhqdnpf3gaa1nlnw7d01yxhbhsbaiqnw9q9aprgi8hk"; depends=[Biobase cellHTS2 e1071 EBImage hwriter vsn]; };
+  imageHTS = derive2 { name="imageHTS"; version="1.44.1"; sha256="0m64d9csya84s2vsbmkflys03a27z8r9pa6mdd28aqaqwv0ww9dr"; depends=[Biobase cellHTS2 e1071 EBImage hwriter vsn]; };
   imcRtools = derive2 { name="imcRtools"; version="1.0.2"; sha256="05xw15d0sbjnrb8ffnajzz4wd1fygn3092za9y9sz3pcmkzbmhkf"; depends=[abind BiocNeighbors BiocParallel concaveman cytomapper data_table dplyr DT EBImage ggplot2 ggraph igraph magrittr pheatmap readr RTriangle S4Vectors scuttle sf SingleCellExperiment SpatialExperiment stringr SummarizedExperiment tidygraph viridis vroom]; };
   immunoClust = derive2 { name="immunoClust"; version="1.26.0"; sha256="0vqn8455spray252b6kg771mwz4b6f51d4k7srg2i3rn7kyp7r38"; depends=[flowCore lattice]; };
   immunotation = derive2 { name="immunotation"; version="1.2.0"; sha256="1rdmy46grqjf8ydgq0pgaja3jv4jna0yffw7fmiirfh96m2qvb00"; depends=[curl ggplot2 maps ontologyIndex readr rlang rvest stringr tidyr xml2]; };
@@ -1501,8 +1501,8 @@ in with self; {
   iterativeBMAsurv = derive2 { name="iterativeBMAsurv"; version="1.52.0"; sha256="0jrjyrg2kfmgiybwdglrbfvfziy8i6jnkzb2ddr8z0670bmv8wxw"; depends=[BMA leaps survival]; };
   iteremoval = derive2 { name="iteremoval"; version="1.14.0"; sha256="15ls501y27lc9iyvz9fmk8w09512bg7cxl763amck1f6r3qnm8hl"; depends=[GenomicRanges ggplot2 magrittr SummarizedExperiment]; };
   ivygapSE = derive2 { name="ivygapSE"; version="1.16.0"; sha256="1a35z2ndvdqj84g5327cpz3s6aqn953ycwgglcqxpaabf2jh18sq"; depends=[ggplot2 hwriter plotly S4Vectors shiny SummarizedExperiment survival survminer UpSetR]; };
-  karyoploteR = derive2 { name="karyoploteR"; version="1.20.0"; sha256="0x3mld9q55r2fy452wxq5sjzmms10zmpkzs71c3w1fdli5hwszdq"; depends=[AnnotationDbi bamsignals bezier biovizBase digest GenomeInfoDb GenomicFeatures GenomicRanges IRanges memoise regioneR Rsamtools rtracklayer S4Vectors VariantAnnotation]; };
-  kebabs = derive2 { name="kebabs"; version="1.28.0"; sha256="0454drbsl9fz0s7k00qd56wj0lwvwmyzn4nlsww7nfgszw95ac4q"; depends=[apcluster Biostrings e1071 IRanges kernlab LiblineaR Matrix Rcpp S4Vectors XVector]; };
+  karyoploteR = derive2 { name="karyoploteR"; version="1.20.3"; sha256="0bcc1ln7602lrbm9wckgyfd9slsqiljjmymj28rfpax1n8rbq44m"; depends=[AnnotationDbi bamsignals bezier biovizBase digest GenomeInfoDb GenomicFeatures GenomicRanges IRanges memoise regioneR Rsamtools rtracklayer S4Vectors VariantAnnotation]; };
+  kebabs = derive2 { name="kebabs"; version="1.28.1"; sha256="19i62ga793vza60bzq0hpr5y85vrrcsmjckyyasjzfipn3nwf98f"; depends=[apcluster Biostrings e1071 IRanges kernlab LiblineaR Matrix Rcpp S4Vectors XVector]; };
   keggorthology = derive2 { name="keggorthology"; version="2.46.0"; sha256="1rckw5yg9swf86cmh4nmrzb37w8m023c7q0pis1nqbcx9lgdgiw5"; depends=[AnnotationDbi DBI graph hgu95av2_db]; };
   kissDE = derive2 { name="kissDE"; version="1.14.0"; sha256="1k6aljlhj3k06a95imnna1jmx1xwvnbc72sbp2jqn2hc69pkyi2j"; depends=[aod Biobase DESeq2 doParallel DSS foreach ggplot2 gplots matrixStats]; };
   lapmix = derive2 { name="lapmix"; version="1.60.0"; sha256="17niykbr8c388qbvjix2hc3zmpa5335bhmwsvnna4qa9v9fi9ln2"; depends=[Biobase]; };
@@ -1549,7 +1549,7 @@ in with self; {
   mdp = derive2 { name="mdp"; version="1.14.0"; sha256="0q721w901pxyjygz63d7a39h762ngqk8dqhn0grad82n90bywx0m"; depends=[ggplot2 gridExtra]; };
   mdqc = derive2 { name="mdqc"; version="1.56.0"; sha256="06yvmgn8qhh1lmm338sdp50jfw7v148sn2mwmcps3l56vh4bci74"; depends=[cluster MASS]; };
   megadepth = derive2 { name="megadepth"; version="1.4.0"; sha256="0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r"; depends=[cmdfun dplyr fs GenomicRanges magrittr readr xfun]; };
-  memes = derive2 { name="memes"; version="1.2.4"; sha256="1bdgxhy2w5yg3j41zrc7mcrgi5plc9dxg7w40skh8kdpa5s3dvmz"; depends=[Biostrings cmdfun dplyr GenomicRanges ggplot2 ggseqlogo magrittr matrixStats patchwork processx purrr readr rlang tibble tidyr universalmotif usethis xml2]; };
+  memes = derive2 { name="memes"; version="1.2.5"; sha256="1524h2qq8ymy1vdqpja1yjn0wj07aawfiwjgc4lmclpjbkn57yhg"; depends=[Biostrings cmdfun dplyr GenomicRanges ggplot2 ggseqlogo magrittr matrixStats patchwork processx purrr readr rlang tibble tidyr universalmotif usethis xml2]; };
   meshes = derive2 { name="meshes"; version="1.20.0"; sha256="1mwdrpqj7vphb30ii958hglzr0h4z7nv99v5sqvgjql76m8z0hcg"; depends=[AnnotationDbi AnnotationHub DOSE enrichplot GOSemSim MeSHDbi yulab_utils]; };
   meshr = derive2 { name="meshr"; version="2.0.2"; sha256="030wxk7aj6d5wkfmzdji4dharmwhh9hx6rgy0igjb4lp4ih6wram"; depends=[BiocGenerics BiocStyle Category fdrtool knitr markdown MeSHDbi rmarkdown RSQLite S4Vectors]; };
   messina = derive2 { name="messina"; version="1.30.0"; sha256="1k00l4qq5jn6lkna7ch9dyycrgfs446hajwki836hm1bvdfsz2q9"; depends=[foreach ggplot2 plyr Rcpp survival]; };
@@ -1620,7 +1620,7 @@ in with self; {
   monaLisa = derive2 { name="monaLisa"; version="1.0.0"; sha256="0idfq3l3sxx2gxcksvvk6ayyv2zb9hb5bls6dkincv7mraa20max"; depends=[BiocGenerics BiocParallel Biostrings BSgenome circlize ComplexHeatmap GenomeInfoDb GenomicRanges glmnet IRanges S4Vectors stabs SummarizedExperiment TFBSTools vioplot XVector]; };
   monocle = derive2 { name="monocle"; version="2.22.0"; sha256="0wb2c1jf502lrfx3d0amb09fvhalrwxvpsp99jsab162v4hddg85"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree densityClust dplyr fastICA ggplot2 HSMMSingleCell igraph irlba limma MASS Matrix matrixStats pheatmap plyr proxy qlcMatrix RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; };
   mosaics = derive2 { name="mosaics"; version="2.32.0"; sha256="09qz4xl9xhzidw0w41bp0adkbhnasa309yn8rdi9nsfpswhaiysb"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges lattice MASS Rcpp Rsamtools S4Vectors]; };
-  mosbi = derive2 { name="mosbi"; version="1.0.1"; sha256="1sazkkwm95j6yrnmin22dh0ir08d6l3i85imqzlvyf1qigqgyk2d"; depends=[akmbiclust BH biclust fabia igraph isa2 QUBIC RColorBrewer Rcpp RcppParallel xml2]; };
+  mosbi = derive2 { name="mosbi"; version="1.0.3"; sha256="1l3zvc2pwd0z37v28fabrxnzfq53fmg58p3jhwb6mzi8rdmq6vak"; depends=[akmbiclust BH biclust fabia igraph isa2 QUBIC RColorBrewer Rcpp RcppParallel xml2]; };
   motifStack = derive2 { name="motifStack"; version="1.38.0"; sha256="1ck6bbnrab8mbf70alfdsrcv6lq0fkvcy3klhcwyxxir7r9sgbaz"; depends=[ade4 Biostrings ggplot2 htmlwidgets XML]; };
   motifbreakR = derive2 { name="motifbreakR"; version="2.8.0"; sha256="0lrgy64sv2ma6kylp4lsbwkg6ci1kn6qkk0cvzw3m4k3bgia1npj"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges grImport Gviz IRanges matrixStats MotifDb motifStack rtracklayer S4Vectors stringr SummarizedExperiment TFMPvalue VariantAnnotation]; };
   motifcounter = derive2 { name="motifcounter"; version="1.18.0"; sha256="17yhhg423yjhaix9x2w2484l22vj6ra086ymzdfhygnjz5vanpmd"; depends=[Biostrings]; };
@@ -1643,7 +1643,7 @@ 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="1.8.0"; sha256="0m5i1sqi3nzxlja9nvz9msmic9mf8y9s6f60c9b2mgbfp2kyf55w"; 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="1.8.1"; 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]; };
   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]; };
@@ -1731,7 +1731,7 @@ in with self; {
   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]; };
   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="1.20.0"; sha256="0dndab3wsj9mvgjpkmazd55w72cjh5xwjqs0xzjbfmkx7786rk09"; depends=[ape ggplot2 ggtree phangorn 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]; };
@@ -1744,7 +1744,7 @@ 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="1.0.9"; sha256="0xv1ygbk0hv57jqfjbya85wjilyang8hbfh3fv1zpy143khmy8di"; depends=[curl data_table dplyr ggplotify plyranges purrr RColorBrewer Rcpp rlang strawr]; };
+  plotgardener = derive2 { name="plotgardener"; version="1.0.12"; sha256="0rayzw2bkkkv3rvgsdv8zmm3j9vflasf8wdrf4yz5hacshr3ng7i"; 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]; };
@@ -1772,7 +1772,7 @@ 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="1.20.0"; sha256="158a9v201z1ad3fm572nz57l8czs8d5nhk9ig162cl1mpfhfrh35"; 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="1.20.1"; 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]; };
   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]; };
@@ -1824,7 +1824,7 @@ in with self; {
   recountmethylation = derive2 { name="recountmethylation"; version="1.4.0"; sha256="14b06842a97q9cggz6l7kfrlal1kaiq49j2f8sql4b2p6qdh4dpn"; depends=[BiocFileCache HDF5Array 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="1.26.0"; sha256="0y1mawzfvxrympc47q3isk96sl9d1bc8kdsxpm8rnhqg5bmgwya6"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; };
+  regioneR = derive2 { name="regioneR"; version="1.26.1"; sha256="0k500fdmv5l0v7b9pj73bjk3h9k261mfqi6vl52khlw0fafn9b6p"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; };
   regsplice = derive2 { name="regsplice"; version="1.20.0"; sha256="1vm1vvi5gfw5ssyi0qng3jmanvyl2mx08w9bi5990pj0j6ycc70y"; depends=[edgeR glmnet limma pbapply S4Vectors SummarizedExperiment]; };
   regutools = derive2 { name="regutools"; version="1.6.0"; sha256="03gjlpn1pk2xkcbg4i1az505nq2gi6ajplq3asbg1fl9p2dbw8kh"; depends=[AnnotationDbi AnnotationHub BiocFileCache Biostrings DBI GenomicRanges Gviz IRanges RCy3 RSQLite S4Vectors]; };
   restfulSE = derive2 { name="restfulSE"; version="1.16.0"; sha256="118zmj9jhgblkgi1arwndrigc1gl37q6gydhw3xfdiml4lp2zags"; depends=[AnnotationDbi AnnotationHub bigrquery Biobase DBI DelayedArray dplyr ExperimentHub GO_db magrittr reshape2 rhdf5client rlang S4Vectors SummarizedExperiment]; };
@@ -1844,8 +1844,8 @@ in with self; {
   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]; };
-  ropls = derive2 { name="ropls"; version="1.26.0"; sha256="0mz5lrdsihx66sgx9klnvpxvw1mjjcbijcsdbgxwaimzl9k1kr05"; depends=[Biobase MultiDataSet]; };
-  rpx = derive2 { name="rpx"; version="2.1.12"; sha256="0ykafx304g8gdry2r1l91zbnr6zv7jkknjyv5p0dkf0wvpqy82iy"; depends=[BiocFileCache curl jsonlite RCurl xml2]; };
+  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]; };
   rqubic = derive2 { name="rqubic"; version="1.40.0"; sha256="0drzggalrvijqvq2x38r2l07rr2248rrw8lvhnfkszabb5qg4a71"; depends=[biclust Biobase BiocGenerics]; };
   rrvgo = derive2 { name="rrvgo"; version="1.6.0"; sha256="0sxybvvbgrxpddfr80cla6pmf8q3kiqrd9r9ca0hq8m4av9nv9cc"; depends=[AnnotationDbi ggplot2 ggrepel GO_db GOSemSim pheatmap shiny tm treemap wordcloud]; };
@@ -1917,7 +1917,7 @@ in with self; {
   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]; };
-  sesame = derive2 { name="sesame"; version="1.12.7"; sha256="1gcf761alh6b86ncg8nknfshqg34102zgwcy3xjapjn37ncl7qan"; depends=[BiocParallel DNAcopy e1071 fgsea GenomicRanges ggplot2 ggrepel illuminaio IRanges KernSmooth MASS matrixStats preprocessCore randomForest reshape2 S4Vectors sesameData stringr SummarizedExperiment tibble wheatmap]; };
+  sesame = derive2 { name="sesame"; version="1.12.8"; sha256="047wpk7lvl5fik7iy0bf8jhqf3yp86gka0pkr0y9xl0a17gd5imz"; 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]; };
   shinyMethyl = derive2 { name="shinyMethyl"; version="1.30.0"; sha256="0ihs4l4r46qyv7j8a2g590x86y0dwki2gzllwq2a31il34jrbgq5"; depends=[BiocGenerics IlluminaHumanMethylation450kmanifest matrixStats minfi RColorBrewer shiny]; };
@@ -1935,7 +1935,7 @@ in with self; {
   singleCellTK = derive2 { name="singleCellTK"; version="2.4.0"; sha256="1a3j012jgysfbrknv1pp1az0zsk48yj1sjcjjchakl6lm7anzvhz"; depends=[AnnotationDbi ape batchelor Biobase BiocParallel celda celldex circlize cluster colorspace colourpicker ComplexHeatmap cowplot data_table DelayedArray DelayedMatrixStats DESeq2 dplyr DropletUtils DT enrichR ExperimentHub fields fishpond ggplot2 ggplotify ggrepel ggtree gridExtra GSEABase GSVA GSVAdata igraph KernSmooth limma magrittr MAST Matrix matrixStats metap msigdbr multtest plotly R_utils RColorBrewer reshape2 reticulate rlang rmarkdown ROCR Rtsne S4Vectors scater scDblFinder scds scMerge scran scRNAseq Seurat shiny shinyalert shinycssloaders shinyjs SingleCellExperiment SingleR SummarizedExperiment sva TENxPBMCData tibble tximport VAM withr yaml zinbwave]; };
   singscore = derive2 { name="singscore"; version="1.14.0"; sha256="1mmp0sgx684d1yxpminllzb6pnl66jlrqhxifvv7g5iivqqsrm2p"; depends=[Biobase BiocParallel edgeR ggplot2 ggrepel GSEABase magrittr matrixStats plotly plyr RColorBrewer reshape reshape2 S4Vectors SummarizedExperiment tidyr]; };
   sitadela = derive2 { name="sitadela"; version="1.2.0"; sha256="14r07kxj0fy1i2zmm1v8i7cwx5ff14xlmg5cdrjyzi6zws09vdp8"; depends=[Biobase BiocGenerics biomaRt Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rsamtools RSQLite rtracklayer S4Vectors]; };
-  sitePath = derive2 { name="sitePath"; version="1.10.0"; sha256="063nry7xxnic984qm29axki5rrp2dmp7kgdcjkvh8bi6y41a58sj"; depends=[ape aplot ggplot2 ggrepel ggtree gridExtra RColorBrewer Rcpp seqinr tidytree]; };
+  sitePath = derive2 { name="sitePath"; version="1.10.2"; sha256="0xwv469sb0zyhzn62ps4hfbsh2vivghlflhm16l9fkaix1mgmd4j"; depends=[ape aplot ggplot2 ggrepel ggtree gridExtra RColorBrewer Rcpp seqinr tidytree]; };
   sizepower = derive2 { name="sizepower"; version="1.64.0"; sha256="1jcv4hy4gq5javqvdla122d36m3gfpwwa5qv5d21fh2s90ycm3rm"; depends=[]; };
   skewr = derive2 { name="skewr"; version="1.26.0"; sha256="10mfb1yklns9zhy3p9gxxdk3gihlszynilb8b20gb7522yrd124x"; depends=[IlluminaHumanMethylation450kmanifest methylumi minfi mixsmsn RColorBrewer S4Vectors wateRmelon]; };
   slalom = derive2 { name="slalom"; version="1.16.0"; sha256="130qqbm63iwymwk0lwlp8sns62853l1fabij7iy30ax8hgi681kc"; depends=[BH ggplot2 GSEABase Rcpp RcppArmadillo rsvd SingleCellExperiment SummarizedExperiment]; };
@@ -1954,13 +1954,13 @@ in with self; {
   sparsenetgls = derive2 { name="sparsenetgls"; version="1.12.0"; sha256="0g8vbzhzyccyi77x49c8idhwy357a2azywvllinjapgwiy88s02a"; depends=[glmnet huge MASS Matrix]; };
   spatialDE = derive2 { name="spatialDE"; version="1.0.0"; sha256="01dqrs8a23b0j5a0zk31g1ld5783dd6fsjiaj1vgc767mjwh0vsx"; depends=[basilisk checkmate ggplot2 ggrepel gridExtra Matrix reticulate S4Vectors scales SpatialExperiment SummarizedExperiment]; };
   spatialHeatmap = derive2 { name="spatialHeatmap"; version="2.0.0"; sha256="0a67dk5jvww8lrjqq8yxbqnm2lasjhypi1k16qa7gwd2x84phghf"; depends=[av BiocFileCache data_table DESeq2 distinct dynamicTreeCut edgeR flashClust genefilter ggdendro ggplot2 ggplotify gplots gridExtra grImport HDF5Array htmlwidgets igraph limma magick plotly rappdirs reshape2 rols rsvg S4Vectors shiny shinydashboard SummarizedExperiment UpSetR visNetwork WGCNA xml2 yaml]; };
-  spatzie = derive2 { name="spatzie"; version="1.0.0"; sha256="1k88ibhm8k19i1jb1xsp6xqva8gdmgcp6gqmza7snh2hk5a4r9ll"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicFeatures GenomicInteractions GenomicRanges ggplot2 IRanges matrixStats motifmatchr S4Vectors SummarizedExperiment TFBSTools]; };
+  spatzie = derive2 { name="spatzie"; version="1.0.1"; sha256="08fk50y10pkpwq5cvlafs24kvzha9p6nk982vhjl0dbhlysa86vc"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicFeatures GenomicInteractions GenomicRanges ggplot2 IRanges matrixStats motifmatchr S4Vectors SummarizedExperiment TFBSTools]; };
   specL = derive2 { name="specL"; version="1.28.0"; sha256="1fsv1vi7wghrn6xgkdfsr5c53jv1kfpxygzpvnc8pa37l6jfzdfg"; depends=[DBI protViz RSQLite seqinr]; };
   spicyR = derive2 { name="spicyR"; version="1.6.0"; sha256="1a7nidfa0vq7qbs5j1yl429q1adic8p3pagrvw3362b59j36ryxx"; depends=[BiocGenerics BiocParallel concaveman data_table dplyr ggplot2 IRanges lme4 lmerTest mgcv pheatmap rlang S4Vectors scam spatstat_core spatstat_geom tidyr]; };
   spikeLI = derive2 { name="spikeLI"; version="2.54.0"; sha256="1ndxvamn2q6ad86dfql1qa7c87xfg8q3zk6f33ip458ikmx16h3f"; depends=[]; };
   spiky = derive2 { name="spiky"; version="1.0.0"; sha256="0r8n6icjkhwaq395ikcw64wgks89s84a97xc8lwgrb4lkmnlkgyj"; depends=[bamlss Biostrings BlandAltmanLeh BSgenome GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges Rsamtools S4Vectors scales]; };
   spkTools = derive2 { name="spkTools"; version="1.50.0"; sha256="1fbh8lfhl3j7dgx7my3ajjfvzfl0x5rm3m0hszm9dk7zvn6zl67x"; depends=[Biobase gtools RColorBrewer]; };
-  splatter = derive2 { name="splatter"; version="1.18.1"; sha256="1cbq3yfgpv54xkgax1m4c4vh29afdfffs7f8xi7fp7acvp365azx"; depends=[BiocGenerics BiocParallel checkmate crayon edgeR fitdistrplus ggplot2 locfit matrixStats S4Vectors scales scater SingleCellExperiment SummarizedExperiment]; };
+  splatter = derive2 { name="splatter"; version="1.18.2"; sha256="1azcn3fckqaz8kyqzlmb25fbncyyk9ai7d9gj9bq9xnqhjr5ni1a"; depends=[BiocGenerics BiocParallel checkmate crayon edgeR fitdistrplus ggplot2 locfit matrixStats S4Vectors scales scater SingleCellExperiment SummarizedExperiment]; };
   splineTimeR = derive2 { name="splineTimeR"; version="1.22.0"; sha256="0pbfflicb2zpiddslivyh9i2vly6h8jfbmpm38ljijzshmsvra6v"; depends=[Biobase FIs GeneNet GSEABase gtools igraph limma longitudinal]; };
   splots = derive2 { name="splots"; version="1.60.0"; sha256="0ng1shqpjmgbfs4hlcfncq4ipl59a9xwv42h7zcc45hzm7013fq9"; depends=[RColorBrewer]; };
   spqn = derive2 { name="spqn"; version="1.6.0"; sha256="081b87w4gsrqp9ny9gqc85g4nm17kxrs2bagxgja280hf7ry2f08"; depends=[BiocGenerics ggplot2 ggridges matrixStats SummarizedExperiment]; };
@@ -1977,7 +1977,7 @@ in with self; {
   stepNorm = derive2 { name="stepNorm"; version="1.66.0"; sha256="1v5a5zcczd65kzmpkjhr793z74f1758mbql0izwavc609ai5a241"; depends=[marray MASS]; };
   strandCheckR = derive2 { name="strandCheckR"; version="1.12.0"; sha256="1j7h8psn90zdz78j2115gwpdikkvpcfbv8izpwazawgl59byb4w8"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges magrittr reshape2 rmarkdown Rsamtools S4Vectors stringr TxDb_Hsapiens_UCSC_hg38_knownGene]; };
   struct = derive2 { name="struct"; version="1.6.0"; sha256="1vnszdh24f8hh2kcpxr9whbpbws3qnm0zldjg5pdvkfvnsq6fa00"; depends=[knitr ontologyIndex rols S4Vectors SummarizedExperiment]; };
-  structToolbox = derive2 { name="structToolbox"; version="1.6.0"; sha256="06b29kxi0gsai959vpqaknpccb20r7ij1dhj73nwcy9a0lc92n0z"; depends=[ggplot2 ggthemes gridExtra scales sp struct]; };
+  structToolbox = derive2 { name="structToolbox"; version="1.6.1"; sha256="1p39d2w0q1hi7jm6chm29pf68wp241hzr0p65hjfqdcq4bq39jkp"; depends=[ggplot2 ggthemes gridExtra scales sp struct]; };
   subSeq = derive2 { name="subSeq"; version="1.24.0"; sha256="1yyj74cff2zjl7i5ms44805jb65f1xbd0f9yh084n4f3qn0vp7jh"; depends=[Biobase data_table digest dplyr ggplot2 magrittr qvalue tidyr]; };
   supersigs = derive2 { name="supersigs"; version="1.2.0"; sha256="0g622ci7761nk8baxi3w4m9qfalv2l97irkrpjsglmqf3rnc1h47"; depends=[assertthat Biostrings caret dplyr rlang rsample SummarizedExperiment tidyr]; };
   supraHex = derive2 { name="supraHex"; version="1.32.0"; sha256="00z4dir261xr5v2ajs8vifhyy35agcqjph9jlwg8q9f3s2n89c6x"; depends=[ape dplyr hexbin igraph magrittr MASS purrr readr stringr tibble tidyr]; };
@@ -1991,7 +1991,7 @@ 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="3.2.2"; sha256="0kpvp0lamchbgs4p34pbq14y3zrmgk0pgil0qhsrm3kv1pizk1w8"; 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="3.2.6"; sha256="05jzj18lc0dznq32g5jp14dpqx816yqln8kfk7mayqx7rfwh52lf"; 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]; };
   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]; };
@@ -2037,7 +2037,7 @@ in with self; {
   trio = derive2 { name="trio"; version="3.32.0"; sha256="16bnh1q53b2pkw4v7why5b1srl39zw6iza34yxynv34b8529sl46"; depends=[LogicReg siggenes survival]; };
   triplex = derive2 { name="triplex"; version="1.34.0"; sha256="0niyiafps242y9gnrc85ncb28c1q9ny1b20la53397h5w46sqq6i"; depends=[Biostrings GenomicRanges IRanges S4Vectors XVector]; };
   tripr = derive2 { name="tripr"; version="1.0.0"; sha256="0lcyjqn2my782hq8bmab08hpp0sgaz3c6wbcywn3pidcc0zqr56p"; depends=[config data_table dplyr DT golem gridExtra plot3D plotly plyr pryr RColorBrewer shiny shinyBS shinyFiles shinyjs stringdist stringr]; };
-  tscR = derive2 { name="tscR"; version="1.6.0"; sha256="0mbyl00mylw0cvlbh93vxbc86y7fgn6n0zw7k0ix9cx7dx7kjwfm"; depends=[class cluster dplyr dtw GenomicRanges ggplot2 gridExtra IRanges kmlShape knitr latex2exp prettydoc RColorBrewer rmarkdown S4Vectors SummarizedExperiment]; };
+  tscR = derive2 { name="tscR"; version="1.6.1"; sha256="1k9f79gy0ickf8mizkmxzazkrbpl0rssdjafpcvx37a1ykgn9qax"; depends=[class cluster dplyr dtw GenomicRanges ggplot2 gridExtra IRanges kmlShape knitr latex2exp prettydoc RColorBrewer rmarkdown S4Vectors SummarizedExperiment]; };
   tspair = derive2 { name="tspair"; version="1.52.0"; sha256="0pm1rdiiza2737nar790zi2b37n25gpdxbg8ljg3a84mlji5jsws"; depends=[Biobase]; };
   ttgsea = derive2 { name="ttgsea"; version="1.2.1"; sha256="0b6c55vzay7jaacff3nrd0ks6l4qsmhjja38rs2qlabzqhyrfzi4"; depends=[data_table DiagrammeR keras purrr stopwords text2vec textstem tm tokenizers]; };
   tweeDEseq = derive2 { name="tweeDEseq"; version="1.40.0"; sha256="0xqd0i5d5q5fm58gxpxac24zpqpyj5dgab0kziwyn8pfyp1w5s4h"; depends=[cqn edgeR limma MASS]; };
@@ -2049,7 +2049,7 @@ in with self; {
   uSORT = derive2 { name="uSORT"; version="1.20.0"; sha256="0y6a6ksvbrxyqri0mc01nbls107sacs66zmbjs4qxq52rmy5xvcd"; depends=[Biobase BiocGenerics cluster fpc gplots igraph Matrix monocle plyr RANN RSpectra VGAM]; };
   uncoverappLib = derive2 { name="uncoverappLib"; version="1.4.0"; sha256="0nh5z1iirqdiv5q66k1r8byv9dasnzyinl0plan68gxvia770cnb"; depends=[BiocFileCache BSgenome_Hsapiens_UCSC_hg19 condformat DT EnsDb_Hsapiens_v75 EnsDb_Hsapiens_v86 GenomicRanges Gviz Homo_sapiens markdown openxlsx org_Hs_eg_db OrganismDbi processx rappdirs rlist Rsamtools shiny shinyBS shinycssloaders shinyjs shinyWidgets stringr TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; };
   unifiedWMWqPCR = derive2 { name="unifiedWMWqPCR"; version="1.30.0"; sha256="0kw26bm2yyna38q5r4zb2alpa3j4gx7v970419mnjlif4g0hmggk"; depends=[BiocGenerics HTqPCR]; };
-  universalmotif = derive2 { name="universalmotif"; version="1.12.2"; sha256="1p9zdrsxqn4ayvbj05xgpzpbzkzrh7k0d62x10069687vfl6dlxg"; depends=[BiocGenerics Biostrings ggplot2 IRanges MASS Rcpp RcppThread rlang S4Vectors yaml]; };
+  universalmotif = derive2 { name="universalmotif"; version="1.12.3"; sha256="00kdhjyjgxjiab4n9lxagc1bb629xnwc68cqy2gc0wnxx1j3v262"; depends=[BiocGenerics Biostrings ggplot2 IRanges MASS Rcpp RcppThread rlang S4Vectors yaml]; };
   variancePartition = derive2 { name="variancePartition"; version="1.24.0"; sha256="0f5y61dpzwmr8v7npim18zvxa8n49rbzclb9j72haba0px6ibhvw"; depends=[Biobase BiocParallel doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS Matrix pbkrtest progress reshape2 rlang scales]; };
   vbmp = derive2 { name="vbmp"; version="1.62.0"; sha256="0yavhi3n9nlgq2s0xvglsnfi9yxdl0di8vs30h9p6a0hh3d1c8ql"; depends=[]; };
   velociraptor = derive2 { name="velociraptor"; version="1.4.0"; sha256="16v1qxl8z5pr3ygvby5n2klw0wm468fbsch1b9a67il8bjxslg0j"; depends=[basilisk BiocGenerics BiocParallel BiocSingular DelayedArray Matrix reticulate S4Vectors scuttle SingleCellExperiment SummarizedExperiment zellkonverter]; };

pkgs/development/r-modules/default.nix

@@ -1096,12 +1096,6 @@ let
       ];
     });
 
-    nloptr = old.nloptr.overrideDerivation (attrs: {
-      # Drop bundled nlopt source code. Probably unnecessary, but I want to be
-      # sure we're using the system library, not this one.
-      preConfigure = "rm -r src/nlopt_src";
-    });
-
     V8 = old.V8.overrideDerivation (attrs: {
       postPatch = ''
         substituteInPlace configure \

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

@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "bazel-buildtools";
-  version = "4.2.5";
+  version = "5.0.0";
 
   src = fetchFromGitHub {
     owner = "bazelbuild";
     repo = "buildtools";
     rev = version;
-    sha256 = "sha256-KY2Sldg3ChKR+rPalCkIVaLuR37s67FjB9aA20ZWD8Y=";
+    sha256 = "sha256-3f4EIk/0IlgGnGNIT8ag0ya2Xgac033Tb7LluxXarIw=";
   };
 
   vendorSha256 = "sha256-buMkRxVLlS2LBJGaGWeR41BsmE/0vgDS8s1VcRYN0fA=";

pkgs/development/tools/clj-kondo/default.nix

@@ -2,11 +2,11 @@
 
 buildGraalvmNativeImage rec {
   pname = "clj-kondo";
-  version = "2022.01.15";
+  version = "2022.02.09";
 
   src = fetchurl {
     url = "https://github.com/clj-kondo/${pname}/releases/download/v${version}/${pname}-${version}-standalone.jar";
-    sha256 = "sha256-s1SdCy4GaxFL9M3Fp/WGu1C6qY2Kst5PXFShrGCizUE=";
+    sha256 = "sha256-WfPjn0S7Jd6zFcfaudcSsx9d5luyZuaeB8lFaOLg21w=";
   };
 
   extraNativeImageBuildArgs = [

pkgs/misc/vim-plugins/generated.nix

@@ -3645,6 +3645,18 @@ final: prev:
     meta.homepage = "https://github.com/shaunsingh/moonlight.nvim/";
   };
 
+  mru = buildVimPluginFrom2Nix {
+    pname = "mru";
+    version = "2022-01-22";
+    src = fetchFromGitHub {
+      owner = "yegappan";
+      repo = "mru";
+      rev = "30315ad4c07f0045c203a443291ad0c8d2fe7279";
+      sha256 = "1k3x8v9c9c3mn2nakcsr5f9wqckxlx3b86smml4d985q90372fqn";
+    };
+    meta.homepage = "https://github.com/yegappan/mru/";
+  };
+
   Navigator-nvim = buildVimPluginFrom2Nix {
     pname = "Navigator.nvim";
     version = "2021-11-18";

pkgs/misc/vim-plugins/vim-plugin-names

@@ -974,6 +974,7 @@ Xuyuanp/scrollbar.nvim
 yamatsum/nvim-cursorline
 yamatsum/nvim-nonicons
 ycm-core/YouCompleteMe
+yegappan/mru
 Yggdroot/hiPairs
 Yggdroot/indentLine
 Yggdroot/LeaderF

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

@@ -2,16 +2,16 @@
 
 stdenv.mkDerivation rec {
   pname = "extrace";
-  version = "0.8";
+  version = "0.9";
 
   src = fetchFromGitHub {
     owner = "leahneukirchen";
     repo = "extrace";
     rev = "v${version}";
-    sha256 = "sha256-Kg5yzVg9sqlOCzAq/HeFUPZ89Enfkt/r7EunCfOqdA0=";
+    hash = "sha256-Jy/Ac3NcqBkW0kHyypMAVUGAQ41qWM96BbLAym06ogM=";
   };
 
-  makeFlags = [ "PREFIX=$(out)" ];
+  makeFlags = [ "PREFIX=${placeholder "out"}" ];
 
   postInstall = ''
     install -dm755 "$out/share/licenses/extrace/"
@@ -21,7 +21,7 @@ stdenv.mkDerivation rec {
   meta = with lib; {
     homepage = "https://github.com/leahneukirchen/extrace";
     description = "Trace exec() calls system-wide";
-    license = with licenses; [ gpl2 bsd2 ];
+    license = with licenses; [ gpl2Plus bsd2 ];
     platforms = platforms.linux;
     maintainers = [ maintainers.leahneukirchen ];
   };

pkgs/servers/home-assistant/component-packages.nix

@@ -2,7 +2,7 @@
 # Do not edit!
 
 {
-  version = "2022.2.5";
+  version = "2022.2.6";
   components = {
     "abode" = ps: with ps; [ abodepy ];
     "accuweather" = ps: with ps; [ accuweather ];

pkgs/servers/home-assistant/default.nix

@@ -57,8 +57,18 @@ let
     # Pinned due to API changes in 0.1.0
     (mkOverride "poolsense" "0.0.8" "09y4fq0gdvgkfsykpxnvmfv92dpbknnq5v82spz43ak6hjnhgcyp")
 
-    # Requirements for recorder not found: ['sqlalchemy==1.4.27'].
-    #(mkOverride "sqlalchemy" "1.4.27" "031jbd0svrvwr3n52iibp9mkwsj9wicnck45yd26da5kmsfkas6p")
+    # Pinned due to API changes >0.3.5.3
+    (self: super: {
+      pyatag = super.pyatag.overridePythonAttrs (oldAttrs: rec {
+        version = "0.3.5.3";
+        src = fetchFromGitHub {
+          owner = "MatsNl";
+          repo = "pyatag";
+          rev = version;
+          sha256 = "00ly4injmgrj34p0lyx7cz2crgnfcijmzc0540gf7hpwha0marf6";
+        };
+      });
+    })
 
     # Pinned due to API changes in 0.4.0
     (self: super: {
@@ -92,9 +102,9 @@ let
     })
   ];
 
-  mkOverride = attrname: version: sha256:
+  mkOverride = attrName: version: sha256:
     self: super: {
-      ${attrname} = super.${attrname}.overridePythonAttrs (oldAttrs: {
+      ${attrName} = super.${attrName}.overridePythonAttrs (oldAttrs: {
         inherit version;
         src = oldAttrs.src.override {
           inherit version sha256;
@@ -121,7 +131,7 @@ let
   extraBuildInputs = extraPackages python.pkgs;
 
   # Don't forget to run parse-requirements.py after updating
-  hassVersion = "2022.2.5";
+  hassVersion = "2022.2.6";
 
 in python.pkgs.buildPythonApplication rec {
   pname = "homeassistant";
@@ -139,7 +149,7 @@ in python.pkgs.buildPythonApplication rec {
     owner = "home-assistant";
     repo = "core";
     rev = version;
-    hash = "sha256-BQrhZCmPbhu7fB5/tqr6LxpzOKPq9fPDXBrQPOv0yA4=";
+    hash = "sha256-UUiYp1YP+ak/2MncnGB0kE9+l2zQAyGjfD5srb5ArSI=";
   };
 
   # leave this in, so users don't have to constantly update their downstream patch handling

pkgs/servers/jackett/default.nix

@@ -9,13 +9,13 @@
 
 buildDotnetModule rec {
   pname = "jackett";
-  version = "0.20.539";
+  version = "0.20.546";
 
   src = fetchFromGitHub {
     owner = pname;
     repo = pname;
     rev = "v${version}";
-    sha256 = "TTaPXPEnxKYQFtYD+7AkTydtQbQgdrkaoZL6p3EFkYc=";
+    sha256 = "fNA7e+SO0eZtI5AmaA3BOtS4D9ri4Ri8PxCN7xcuH6E=";
   };
 
   projectFile = "src/Jackett.Server/Jackett.Server.csproj";

pkgs/tools/admin/oci-cli/default.nix

@@ -23,14 +23,14 @@ with py.pkgs;
 
 buildPythonApplication rec {
   pname = "oci-cli";
-  version = "3.4.1";
+  version = "3.5.0";
   format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "oracle";
     repo = "oci-cli";
     rev = "v${version}";
-    hash = "sha256-ibk5WfNPa02D7UcP+4xg8Pi9P45yUPEm56l76IwNuRE=";
+    hash = "sha256-udvYfYFUulGfnc1gzjG3UxOc68JuecpPJ1/s57qvX0k=";
   };
 
   propagatedBuildInputs = [

pkgs/tools/security/exploitdb/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "exploitdb";
-  version = "2022-02-09";
+  version = "2022-02-11";
 
   src = fetchFromGitHub {
     owner = "offensive-security";
     repo = pname;
     rev = version;
-    sha256 = "sha256-+E8MmkXnynCudGfKnCa6usmyPVM+y6kRB8eAm4F9glY=";
+    sha256 = "sha256-pSvjTL/vS3E9jYGxae9RUw+DD9u49PoF7oNM/UZOzDg=";
   };
 
   nativeBuildInputs = [ makeWrapper ];

pkgs/tools/security/kubescape/default.nix

@@ -6,20 +6,20 @@
 
 buildGoModule rec {
   pname = "kubescape";
-  version = "2.0.146";
+  version = "2.0.147";
 
   src = fetchFromGitHub {
     owner = "armosec";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-OSpT6S0jCw/svWl4q9CyZUwUB/cFAyiyWt+oXKVPSJ0=";
+    hash = "sha256-5ESAvLCAQ6ttpuc3YGkUwUvvhHZj+QYXyx30fhVSP1Y=";
   };
 
   nativeBuildInputs = [
     installShellFiles
   ];
 
-  vendorSha256 = "sha256-p2bLZfwsSevaiAqciCfEvpdOx3WlVdWBHVXtLBMjLGA=";
+  vendorSha256 = "sha256-xbOUggbu/4bNT07bD3TU/7CIDvgi6OtZLQzSqQykwRY=";
 
   ldflags = [
     "-s"

pkgs/tools/security/scilla/default.nix

@@ -5,16 +5,16 @@
 
 buildGoModule rec {
   pname = "scilla";
-  version = "1.1.1";
+  version = "1.2.1";
 
   src = fetchFromGitHub {
     owner = "edoardottt";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-xg8qnpYRdSGaFkjmQLbjMFIU419ASEHtFA8h8ads/50=";
+    sha256 = "sha256-1gSuKxNpls7B+pSGnGj3k/E93lnj2FPNtAAciPPNAeM=";
   };
 
-  vendorSha256 = "sha256-PFfzlqBuasTNeCNnu5GiGyQzBQkbe83q1EqCsWTor18=";
+  vendorSha256 = "sha256-gHZj8zpc7yFthCCBM8WGw4WwoW46bdQWe4yWjOkkQE8=";
 
   meta = with lib; {
     description = "Information gathering tool for DNS, ports and more";

pkgs/tools/security/witness/default.nix

@@ -0,0 +1,25 @@
+{ lib, buildGoModule, fetchFromGitHub }:
+
+buildGoModule rec {
+  pname = "witness";
+  version = "0.1.1";
+
+  src = fetchFromGitHub {
+    owner = "testifysec";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "sha256-NnDsiDUTCdjsHVA/mHnB8WRnvwFTzETkWUOd7IgMIWE=";
+  };
+
+  vendorSha256 = "sha256-zkLparWJsuqrhOQxxV37dBqt6fwpSinTO+paJkbl+sM=";
+
+  # We only want the witness binary, not the helper utilities for generating docs.
+  subPackages = [ "cmd/witness" ];
+
+  meta = with lib; {
+    description = "A pluggable framework for software supply chain security. Witness prevents tampering of build materials and verifies the integrity of the build process from source to target";
+    homepage = "https://github.com/testifysec/witness";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ fkautz ];
+  };
+}

pkgs/top-level/all-packages.nix

@@ -10755,6 +10755,8 @@ with pkgs;
     SDL = SDL_sixel;
   };
 
+  witness = callPackage ../tools/security/witness { };
+
   openconnect = openconnect_gnutls;
 
   openconnect_openssl = callPackage ../tools/networking/openconnect {

pkgs/top-level/python-aliases.nix

@@ -97,6 +97,7 @@ mapAliases ({
   pytest_xdist = pytest-xdist; # added 2021-01-04
   python_simple_hipchat = python-simple-hipchat; # added 2021-07-21
   qasm2image = throw "qasm2image is no longer maintained (since November 2018), and is not compatible with the latest pythonPackages.qiskit versions."; # added 2020-12-09
+  qiskit-aqua = throw "qiskit-aqua has been removed due to deprecation, with its functionality moved to different qiskit packages";
   rdflib-jsonld = throw "rdflib-jsonld is not compatible with rdflib 6"; # added 2021-11-05
   repeated_test = throw "repeated_test is no longer maintained"; # added 2022-01-11
   requests_toolbelt = requests-toolbelt; # added 2017-09-26

pkgs/top-level/python-packages.nix

@@ -8376,8 +8376,6 @@ in {
 
   qiskit-aer = callPackage ../development/python-modules/qiskit-aer { };
 
-  qiskit-aqua = callPackage ../development/python-modules/qiskit-aqua { };
-
   qiskit-finance = callPackage ../development/python-modules/qiskit-finance { };
 
   qiskit-ibmq-provider = callPackage ../development/python-modules/qiskit-ibmq-provider { };
@@ -9476,6 +9474,8 @@ in {
 
   streamz = callPackage ../development/python-modules/streamz { };
 
+  strenum =  callPackage ../development/python-modules/strenum { };
+
   strict-rfc3339 = callPackage ../development/python-modules/strict-rfc3339 { };
 
   strictyaml = callPackage ../development/python-modules/strictyaml { };