Merge staging-next into staging

maintainers/maintainer-list.nix

@@ -4260,6 +4260,12 @@
     github = "d4ilyrun";
     githubId = 34611103;
   };
+  d4rkstar = {
+    name = "Bruno Salzano";
+    email = "d4rkstar@gmail.com";
+    github = "d4rkstar";
+    githubId = 4957015;
+  };
   dadada = {
     name = "dadada";
     email = "dadada@dadada.li";
@@ -13629,6 +13635,12 @@
     githubId = 3856390;
     email = "mschwaig+nixpkgs@eml.cc";
   };
+  msciabarra = {
+    email = "msciabarra@apache.org";
+    github = "sciabarracom";
+    githubId = 30654959;
+    name = "Michele Sciabarra";
+  };
   msiedlarek = {
     email = "mikolaj@siedlarek.pl";
     github = "msiedlarek";

maintainers/scripts/pluginupdate.py

@@ -788,7 +788,10 @@ def update_plugins(editor: Editor, args):
     fetch_config = FetchConfig(args.proc, args.github_token)
     update = editor.get_update(args.input_file, args.outfile, fetch_config)
 
+    start_time = time.time()
     redirects = update()
+    duration = time.time() - start_time
+    print(f"The plugin update took {duration}s.")
     editor.rewrite_input(fetch_config, args.input_file, editor.deprecated, redirects)
 
     autocommit = not args.no_commit

nixos/doc/manual/configuration/gpu-accel.chapter.md

@@ -30,7 +30,7 @@ $ export \
 ```
 
 The second mechanism is to add the OpenCL driver package to
-[](#opt-hardware.opengl.extraPackages).
+[](#opt-hardware.graphics.extraPackages).
 This links the ICD file under `/run/opengl-driver`, where it will be visible
 to the ICD loader.
 
@@ -51,12 +51,12 @@ Platform Vendor      Advanced Micro Devices, Inc.
 Modern AMD [Graphics Core
 Next](https://en.wikipedia.org/wiki/Graphics_Core_Next) (GCN) GPUs are
 supported through the rocmPackages.clr.icd package. Adding this package to
-[](#opt-hardware.opengl.extraPackages)
+[](#opt-hardware.graphics.extraPackages)
 enables OpenCL support:
 
 ```nix
 {
-  hardware.opengl.extraPackages = [
+  hardware.graphics.extraPackages = [
     rocmPackages.clr.icd
   ];
 }
@@ -71,13 +71,13 @@ intel-compute-runtime package. The proprietary Intel OpenCL runtime, in
 the intel-ocl package, is an alternative for Gen7 GPUs.
 
 The intel-compute-runtime or intel-ocl package can be added to
-[](#opt-hardware.opengl.extraPackages)
+[](#opt-hardware.graphics.extraPackages)
 to enable OpenCL support. For example, for Gen8 and later GPUs, the following
 configuration can be used:
 
 ```nix
 {
-  hardware.opengl.extraPackages = [
+  hardware.graphics.extraPackages = [
     intel-compute-runtime
   ];
 }
@@ -90,8 +90,8 @@ compute API for GPUs. It is used directly by games or indirectly though
 compatibility layers like
 [DXVK](https://github.com/doitsujin/dxvk/wiki).
 
-By default, if [](#opt-hardware.opengl.driSupport)
+By default, if [](#opt-hardware.graphics.enable)
-is enabled, mesa is installed and provides Vulkan for supported hardware.
+is enabled, Mesa is installed and provides Vulkan for supported hardware.
 
 Similar to OpenCL, Vulkan drivers are loaded through the *Installable
 Client Driver* (ICD) mechanism. ICD files for Vulkan are JSON files that
@@ -110,7 +110,7 @@ $ export \
 ```
 
 The second mechanism is to add the Vulkan driver package to
-[](#opt-hardware.opengl.extraPackages).
+[](#opt-hardware.graphics.extraPackages).
 This links the ICD file under `/run/opengl-driver`, where it will be
 visible to the ICD loader.
 
@@ -140,18 +140,18 @@ Modern AMD [Graphics Core
 Next](https://en.wikipedia.org/wiki/Graphics_Core_Next) (GCN) GPUs are
 supported through either radv, which is part of mesa, or the amdvlk
 package. Adding the amdvlk package to
-[](#opt-hardware.opengl.extraPackages)
+[](#opt-hardware.graphics.extraPackages)
 makes amdvlk the default driver and hides radv and lavapipe from the device list.
 A specific driver can be forced as follows:
 
 ```nix
 {
-  hardware.opengl.extraPackages = [
+  hardware.graphics.extraPackages = [
     pkgs.amdvlk
   ];
 
   # To enable Vulkan support for 32-bit applications, also add:
-  hardware.opengl.extraPackages32 = [
+  hardware.graphics.extraPackages32 = [
     pkgs.driversi686Linux.amdvlk
   ];
 
@@ -171,7 +171,7 @@ graphics hardware acceleration capabilities for video processing.
 
 VA-API drivers are loaded by `libva`. The version in nixpkgs is built to search
 the opengl driver path, so drivers can be installed in
-[](#opt-hardware.opengl.extraPackages).
+[](#opt-hardware.graphics.extraPackages).
 
 VA-API can be tested using:
 
@@ -185,7 +185,7 @@ Modern Intel GPUs use the iHD driver, which can be installed with:
 
 ```nix
 {
-  hardware.opengl.extraPackages = [
+  hardware.graphics.extraPackages = [
     intel-media-driver
   ];
 }
@@ -195,7 +195,7 @@ Older Intel GPUs use the i965 driver, which can be installed with:
 
 ```nix
 {
-  hardware.opengl.extraPackages = [
+  hardware.graphics.extraPackages = [
     intel-vaapi-driver
   ];
 }

nixos/doc/manual/configuration/x-windows.chapter.md

@@ -79,7 +79,7 @@ Wine, you should also set the following:
 
 ```nix
 {
-  hardware.opengl.driSupport32Bit = true;
+  hardware.graphics.enable32Bit = true;
 }
 ```
 
@@ -183,23 +183,6 @@ If you have an older card, you may have to use one of the legacy drivers:
 You may need to reboot after enabling this driver to prevent a clash
 with other kernel modules.
 
-## Proprietary AMD drivers {#sec-x11--graphics-cards-amd}
-
-AMD provides a proprietary driver for its graphics cards that is not
-enabled by default because it's not Free Software, is often broken in
-nixpkgs and as of this writing doesn't offer more features or
-performance. If you still want to use it anyway, you need to explicitly
-set:
-
-```nix
-{
-  services.xserver.videoDrivers = [ "amdgpu-pro" ];
-}
-```
-
-You will need to reboot after enabling this driver to prevent a clash
-with other kernel modules.
-
 ## Touchpads {#sec-x11-touchpads}
 
 Support for Synaptics touchpads (found in many laptops such as the Dell

nixos/doc/manual/release-notes/rl-2405.section.md

@@ -207,6 +207,8 @@ The pre-existing [services.ankisyncd](#opt-services.ankisyncd.enable) has been m
 
 - [xdg-terminal-exec](https://github.com/Vladimir-csp/xdg-terminal-exec), the proposed Default Terminal Execution Specification.
 
+- Convenience options for `amdgpu`, open source driver for Radeon cards, is now available under `hardware.amdgpu`.
+
 - [ydotool](https://github.com/ReimuNotMoe/ydotool), a generic command-line automation tool now has a module. Available as [programs.ydotool](#opt-programs.ydotool.enable).
 
 - [your_spotify](https://github.com/Yooooomi/your_spotify), a self hosted Spotify tracking dashboard. Available as [services.your_spotify](#opt-services.your_spotify.enable)

nixos/doc/manual/release-notes/rl-2411.section.md

@@ -4,6 +4,8 @@
 
 ## Highlights {#sec-release-24.11-highlights}
 
+- Convenience options for `amdgpu`, open source driver for Radeon cards, is now available under `hardware.amdgpu`.
+
 - [AMDVLK](https://github.com/GPUOpen-Drivers/AMDVLK), AMD's open source Vulkan driver, is now available to be configured as `hardware.amdgpu.amdvlk` option.
   This also allows configuring runtime settings of AMDVLK and enabling experimental features.
 

nixos/modules/hardware/graphics.nix

@@ -0,0 +1,126 @@
+{ config, lib, pkgs, ... }:
+let
+  cfg = config.hardware.graphics;
+
+  driversEnv = pkgs.buildEnv {
+    name = "graphics-drivers";
+    paths = [ cfg.package ] ++ cfg.extraPackages;
+  };
+
+  driversEnv32 = pkgs.buildEnv {
+    name = "graphics-drivers-32bit";
+    paths = [ cfg.package32 ] ++ cfg.extraPackages32;
+  };
+in
+{
+  imports = [
+    (lib.mkRenamedOptionModule [ "services" "xserver" "vaapiDrivers" ] [ "hardware" "opengl" "extraPackages" ])
+    (lib.mkRemovedOptionModule [ "hardware" "opengl" "s3tcSupport" ] "S3TC support is now always enabled in Mesa.")
+    (lib.mkRemovedOptionModule [ "hardware" "opengl" "driSupport"] "The setting can be removed.")
+
+    (lib.mkRenamedOptionModule [ "hardware" "opengl" "enable"] [ "hardware" "graphics" "enable" ])
+    (lib.mkRenamedOptionModule [ "hardware" "opengl" "driSupport32Bit"] [ "hardware" "graphics" "enable32Bit" ])
+    (lib.mkRenamedOptionModule [ "hardware" "opengl" "package"] [ "hardware" "graphics" "package" ])
+    (lib.mkRenamedOptionModule [ "hardware" "opengl" "package32"] [ "hardware" "graphics" "package32" ])
+    (lib.mkRenamedOptionModule [ "hardware" "opengl" "extraPackages"] [ "hardware" "graphics" "extraPackages" ])
+    (lib.mkRenamedOptionModule [ "hardware" "opengl" "extraPackages32"] [ "hardware" "graphics" "extraPackages32" ])
+  ];
+
+  options.hardware.graphics = {
+    enable = lib.mkOption {
+      description = ''
+        Whether to enable hardware accelerated graphics drivers.
+
+        This is required to allow most graphical applications and
+        environments to use hardware rendering, video encode/decode
+        acceleration, etc.
+
+        This option should be enabled by default by the corresponding modules,
+        so you do not usually have to set it yourself.
+      '';
+      type = lib.types.bool;
+      default = false;
+    };
+
+    enable32Bit = lib.mkOption {
+      description = ''
+        On 64-bit systems, whether to also install 32-bit drivers for
+        32-bit applications (such as Wine).
+      '';
+      type = lib.types.bool;
+      default = false;
+    };
+
+    package = lib.mkOption {
+      description = ''
+        The package that provides the default driver set.
+      '';
+      type = lib.types.package;
+      internal = true;
+    };
+
+    package32 = lib.mkOption {
+      description = ''
+        The package that provides the 32-bit driver set. Used when {option}`enable32Bit` is enabled.
+        set.
+      '';
+      type = lib.types.package;
+      internal = true;
+    };
+
+    extraPackages = lib.mkOption {
+      description = ''
+        Additional packages to add to the default graphics driver lookup path.
+        This can be used to add OpenCL drivers, VA-API/VDPAU drivers, etc.
+
+        ::: {.note}
+        intel-media-driver supports hardware Broadwell (2014) or newer. Older hardware should use the mostly unmaintained intel-vaapi-driver driver.
+        :::
+      '';
+      type = lib.types.listOf lib.types.package;
+      default = [];
+      example = lib.literalExpression "with pkgs; [ intel-media-driver intel-ocl intel-vaapi-driver ]";
+    };
+
+    extraPackages32 = lib.mkOption {
+      description = ''
+        Additional packages to add to 32-bit graphics driver lookup path on 64-bit systems.
+        Used when {option}`enable32Bit` is set. This can be used to add OpenCL drivers, VA-API/VDPAU drivers, etc.
+
+        ::: {.note}
+        intel-media-driver supports hardware Broadwell (2014) or newer. Older hardware should use the mostly unmaintained intel-vaapi-driver driver.
+        :::
+      '';
+      type = lib.types.listOf lib.types.package;
+      default = [];
+      example = lib.literalExpression "with pkgs.pkgsi686Linux; [ intel-media-driver intel-vaapi-driver ]";
+    };
+  };
+
+  config = lib.mkIf cfg.enable {
+    assertions = [
+      {
+        assertion = cfg.enable32Bit -> pkgs.stdenv.isx86_64;
+        message = "`hardware.graphics.enable32Bit` only makes sense on a 64-bit system.";
+      }
+      {
+        assertion = cfg.enable32Bit -> (config.boot.kernelPackages.kernel.features.ia32Emulation or false);
+        message = "`hardware.graphics.enable32Bit` requires a kernel that supports 32-bit emulation";
+      }
+    ];
+
+    systemd.tmpfiles.settings.graphics-driver = {
+      "/run/opengl-driver"."L+".argument = toString driversEnv;
+      "/run/opengl-driver-32" =
+        if pkgs.stdenv.isi686 then
+          { "L+".argument = "opengl-driver"; }
+        else if cfg.enable32Bit then
+          { "L+".argument = toString driversEnv32; }
+        else
+          { "r" = {}; };
+    };
+
+    hardware.graphics.package = lib.mkDefault pkgs.mesa.drivers;
+    hardware.graphics.package32 = lib.mkDefault pkgs.pkgsi686Linux.mesa.drivers;
+  };
+}

nixos/modules/hardware/opengl.nix

@@ -1,158 +0,0 @@
-{ config, lib, pkgs, ... }:
-
-let
-
-  cfg = config.hardware.opengl;
-
-  kernelPackages = config.boot.kernelPackages;
-
-  videoDrivers = config.services.xserver.videoDrivers;
-
-  package = pkgs.buildEnv {
-    name = "opengl-drivers";
-    paths = [ cfg.package ] ++ cfg.extraPackages;
-  };
-
-  package32 = pkgs.buildEnv {
-    name = "opengl-drivers-32bit";
-    paths = [ cfg.package32 ] ++ cfg.extraPackages32;
-  };
-
-in
-
-{
-
-  imports = [
-    (lib.mkRenamedOptionModule [ "services" "xserver" "vaapiDrivers" ] [ "hardware" "opengl" "extraPackages" ])
-    (lib.mkRemovedOptionModule [ "hardware" "opengl" "s3tcSupport" ] "S3TC support is now always enabled in Mesa.")
-  ];
-
-  options = {
-
-    hardware.opengl = {
-      enable = lib.mkOption {
-        description = ''
-          Whether to enable OpenGL drivers. This is needed to enable
-          OpenGL support in X11 systems, as well as for Wayland compositors
-          like sway and Weston. It is enabled by default
-          by the corresponding modules, so you do not usually have to
-          set it yourself, only if there is no module for your wayland
-          compositor of choice. See services.xserver.enable and
-          programs.sway.enable.
-        '';
-        type = lib.types.bool;
-        default = false;
-      };
-
-      driSupport = lib.mkOption {
-        type = lib.types.bool;
-        default = true;
-        description = ''
-          Whether to enable accelerated OpenGL rendering through the
-          Direct Rendering Interface (DRI).
-        '';
-      };
-
-      driSupport32Bit = lib.mkOption {
-        type = lib.types.bool;
-        default = false;
-        description = ''
-          On 64-bit systems, whether to support Direct Rendering for
-          32-bit applications (such as Wine).  This is currently only
-          supported for the `nvidia` as well as
-          `Mesa`.
-        '';
-      };
-
-      package = lib.mkOption {
-        type = lib.types.package;
-        internal = true;
-        description = ''
-          The package that provides the OpenGL implementation.
-        '';
-      };
-
-      package32 = lib.mkOption {
-        type = lib.types.package;
-        internal = true;
-        description = ''
-          The package that provides the 32-bit OpenGL implementation on
-          64-bit systems. Used when {option}`driSupport32Bit` is
-          set.
-        '';
-      };
-
-      extraPackages = lib.mkOption {
-        type = lib.types.listOf lib.types.package;
-        default = [];
-        example = lib.literalExpression "with pkgs; [ intel-media-driver intel-ocl intel-vaapi-driver ]";
-        description = ''
-          Additional packages to add to OpenGL drivers.
-          This can be used to add OpenCL drivers, VA-API/VDPAU drivers etc.
-
-          ::: {.note}
-          intel-media-driver supports hardware Broadwell (2014) or newer. Older hardware should use the mostly unmaintained intel-vaapi-driver driver.
-          :::
-        '';
-      };
-
-      extraPackages32 =lib. mkOption {
-        type = lib.types.listOf lib.types.package;
-        default = [];
-        example = lib.literalExpression "with pkgs.pkgsi686Linux; [ intel-media-driver intel-vaapi-driver ]";
-        description = ''
-          Additional packages to add to 32-bit OpenGL drivers on 64-bit systems.
-          Used when {option}`driSupport32Bit` is set. This can be used to add OpenCL drivers, VA-API/VDPAU drivers etc.
-
-          ::: {.note}
-          intel-media-driver supports hardware Broadwell (2014) or newer. Older hardware should use the mostly unmaintained intel-vaapi-driver driver.
-          :::
-        '';
-      };
-
-      setLdLibraryPath = lib.mkOption {
-        type = lib.types.bool;
-        internal = true;
-        default = false;
-        description = ''
-          Whether the `LD_LIBRARY_PATH` environment variable
-          should be set to the locations of driver libraries. Drivers which
-          rely on overriding libraries should set this to true. Drivers which
-          support `libglvnd` and other dispatch libraries
-          instead of overriding libraries should not set this.
-        '';
-      };
-    };
-
-  };
-
-  config = lib.mkIf cfg.enable {
-    assertions = [
-      { assertion = cfg.driSupport32Bit -> pkgs.stdenv.isx86_64;
-        message = "Option driSupport32Bit only makes sense on a 64-bit system.";
-      }
-      { assertion = cfg.driSupport32Bit -> (config.boot.kernelPackages.kernel.features.ia32Emulation or false);
-        message = "Option driSupport32Bit requires a kernel that supports 32bit emulation";
-      }
-    ];
-
-    systemd.tmpfiles.settings.opengl = {
-      "/run/opengl-driver"."L+".argument = toString package;
-      "/run/opengl-driver-32" =
-        if pkgs.stdenv.isi686 then
-          { "L+".argument = "opengl-driver"; }
-        else if cfg.driSupport32Bit then
-          { "L+".argument = toString package32; }
-        else
-          { "r" = {}; };
-    };
-
-    environment.sessionVariables.LD_LIBRARY_PATH = lib.mkIf cfg.setLdLibraryPath
-      ([ "/run/opengl-driver/lib" ] ++ lib.optional cfg.driSupport32Bit "/run/opengl-driver-32/lib");
-
-    hardware.opengl.package = lib.mkDefault pkgs.mesa.drivers;
-    hardware.opengl.package32 = lib.mkDefault pkgs.pkgsi686Linux.mesa.drivers;
-
-    boot.extraModulePackages = lib.optional (lib.elem "virtualbox" videoDrivers) kernelPackages.virtualboxGuestAdditions;
-  };
-}

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

@@ -1,69 +0,0 @@
-# This module provides the proprietary AMDGPU-PRO drivers.
-
-{ config, lib, pkgs, ... }:
-
-with lib;
-
-let
-
-  drivers = config.services.xserver.videoDrivers;
-
-  enabled = elem "amdgpu-pro" drivers;
-
-  package = config.boot.kernelPackages.amdgpu-pro;
-  package32 = pkgs.pkgsi686Linux.linuxPackages.amdgpu-pro.override { kernel = null; };
-
-  opengl = config.hardware.opengl;
-
-in
-
-{
-
-  config = mkIf enabled {
-    services.xserver.drivers = singleton
-      { name = "amdgpu"; modules = [ package ]; display = true; };
-
-    hardware.opengl.package = package;
-    hardware.opengl.package32 = package32;
-    hardware.opengl.setLdLibraryPath = true;
-
-    boot.extraModulePackages = [ package.kmod ];
-
-    boot.kernelPackages = pkgs.linuxKernel.packagesFor
-      (pkgs.linuxKernel.kernels.linux_5_10.override {
-        structuredExtraConfig = {
-          DEVICE_PRIVATE = kernel.yes;
-          KALLSYMS_ALL = kernel.yes;
-        };
-      });
-
-    hardware.firmware = [ package.fw ];
-
-    systemd.tmpfiles.settings.amdgpu-pro = {
-      "/run/amdgpu"."L+".argument = "${package}/opt/amdgpu";
-      "/run/amdgpu-pro"."L+".argument = "${package}/opt/amdgpu-pro";
-    };
-
-    system.requiredKernelConfig = with config.lib.kernelConfig; [
-      (isYes "DEVICE_PRIVATE")
-      (isYes "KALLSYMS_ALL")
-    ];
-
-    boot.initrd.extraUdevRulesCommands = mkIf (!config.boot.initrd.systemd.enable) ''
-      cp -v ${package}/etc/udev/rules.d/*.rules $out/
-    '';
-    boot.initrd.services.udev.packages = [ package ];
-
-    environment.systemPackages =
-      [ package.vulkan ] ++
-      # this isn't really DRI, but we'll reuse this option for now
-      optional config.hardware.opengl.driSupport32Bit package32.vulkan;
-
-    environment.etc = {
-      "modprobe.d/blacklist-radeon.conf".source = package + "/etc/modprobe.d/blacklist-radeon.conf";
-      amd.source = package + "/etc/amd";
-    };
-
-  };
-
-}

nixos/modules/hardware/video/nvidia.nix

@@ -297,7 +297,7 @@ in
             KERNEL=="nvidia_uvm", RUN+="${pkgs.runtimeShell} -c 'mknod -m 666 /dev/nvidia-uvm c $$(grep nvidia-uvm /proc/devices | cut -d \  -f 1) 0'"
             KERNEL=="nvidia_uvm", RUN+="${pkgs.runtimeShell} -c 'mknod -m 666 /dev/nvidia-uvm-tools c $$(grep nvidia-uvm /proc/devices | cut -d \  -f 1) 1'"
           '';
-          hardware.opengl = {
+          hardware.graphics = {
             extraPackages = [ nvidia_x11.out ];
             extraPackages32 = [ nvidia_x11.lib32 ];
           };
@@ -467,7 +467,7 @@ in
             "egl/egl_external_platform.d".source = "/run/opengl-driver/share/egl/egl_external_platform.d/";
           };
 
-          hardware.opengl = {
+          hardware.graphics = {
             extraPackages = [ pkgs.nvidia-vaapi-driver ];
             extraPackages32 = [ pkgs.pkgsi686Linux.nvidia-vaapi-driver ];
           };

nixos/modules/hardware/video/virtualbox.nix

@@ -0,0 +1,7 @@
+{ lib, config, ... }:
+let
+  inherit (config.boot) kernelPackages;
+  inherit (config.services.xserver) videoDrivers;
+in {
+  boot.extraModulePackages = lib.mkIf (lib.elem "virtualbox" videoDrivers) [ kernelPackages.virtualboxGuestAdditions ];
+}

nixos/modules/module-list.nix

@@ -67,6 +67,7 @@
   ./hardware/gkraken.nix
   ./hardware/glasgow.nix
   ./hardware/gpgsmartcards.nix
+  ./hardware/graphics.nix
   ./hardware/hackrf.nix
   ./hardware/i2c.nix
   ./hardware/infiniband.nix
@@ -84,7 +85,6 @@
   ./hardware/new-lg4ff.nix
   ./hardware/nitrokey.nix
   ./hardware/onlykey/default.nix
-  ./hardware/opengl.nix
   ./hardware/openrazer.nix
   ./hardware/opentabletdriver.nix
   ./hardware/pcmcia.nix
@@ -103,7 +103,6 @@
   ./hardware/uni-sync.nix
   ./hardware/usb-modeswitch.nix
   ./hardware/usb-storage.nix
-  ./hardware/video/amdgpu-pro.nix
   ./hardware/video/bumblebee.nix
   ./hardware/video/capture/mwprocapture.nix
   ./hardware/video/displaylink.nix
@@ -111,6 +110,7 @@
   ./hardware/video/nvidia.nix
   ./hardware/video/switcheroo-control.nix
   ./hardware/video/uvcvideo/default.nix
+  ./hardware/video/virtualbox.nix
   ./hardware/video/webcam/facetimehd.nix
   ./hardware/video/webcam/ipu6.nix
   ./hardware/wooting.nix
@@ -549,6 +549,7 @@
   ./services/games/xonotic.nix
   ./services/hardware/acpid.nix
   ./services/hardware/actkbd.nix
+  ./services/hardware/amdgpu.nix
   ./services/hardware/amdvlk.nix
   ./services/hardware/argonone.nix
   ./services/hardware/asusd.nix

nixos/modules/programs/miriway.nix

@@ -65,7 +65,7 @@ in {
       };
     };
 
-    hardware.opengl.enable = lib.mkDefault true;
+    hardware.graphics.enable = lib.mkDefault true;
     fonts.enableDefaultPackages = lib.mkDefault true;
     programs.dconf.enable = lib.mkDefault true;
     programs.xwayland.enable = lib.mkDefault true;

nixos/modules/programs/steam.nix

@@ -50,7 +50,7 @@ in {
         }) // (prev.extraEnv or {});
         extraLibraries = pkgs: let
           prevLibs = if prev ? extraLibraries then prev.extraLibraries pkgs else [ ];
-          additionalLibs = with config.hardware.opengl;
+          additionalLibs = with config.hardware.graphics;
             if pkgs.stdenv.hostPlatform.is64bit
             then [ package ] ++ extraPackages
             else [ package32 ] ++ extraPackages32;
@@ -176,10 +176,9 @@ in {
   };
 
   config = lib.mkIf cfg.enable {
-    hardware.opengl = { # this fixes the "glXChooseVisual failed" bug, context: https://github.com/NixOS/nixpkgs/issues/47932
+    hardware.graphics = { # this fixes the "glXChooseVisual failed" bug, context: https://github.com/NixOS/nixpkgs/issues/47932
       enable = true;
-      driSupport = true;
+      enable32Bit = true;
-      driSupport32Bit = true;
     };
 
     security.wrappers = lib.mkIf (cfg.gamescopeSession.enable && gamescopeCfg.capSysNice) {

nixos/modules/programs/turbovnc.nix

@@ -17,7 +17,7 @@ in
           Whether to set up NixOS such that TurboVNC's built-in software OpenGL
           implementation works.
 
-          This will enable {option}`hardware.opengl.enable` so that OpenGL
+          This will enable {option}`hardware.graphics.enable` so that OpenGL
           programs can find Mesa's llvmpipe drivers.
 
           Setting this option to `false` does not mean that software
@@ -46,7 +46,7 @@ in
     # can find the llvmpipe `swrast.so` software rendering DRI lib via `libglvnd`.
     # This comment exists to explain why `hardware.` is involved,
     # even though 100% software rendering is used.
-    hardware.opengl.enable = true;
+    hardware.graphics.enable = true;
 
   };
 }

nixos/modules/programs/wayland/wayland-session.nix

@@ -11,7 +11,7 @@
     pam.services.swaylock = {};
   };
 
-  hardware.opengl.enable = lib.mkDefault true;
+  hardware.graphics.enable = lib.mkDefault true;
   fonts.enableDefaultPackages = lib.mkDefault true;
 
   programs = {

nixos/modules/services/desktop-managers/lomiri.nix

@@ -63,7 +63,7 @@ in {
     ];
 
     # Copy-pasted basic stuff
-    hardware.opengl.enable = lib.mkDefault true;
+    hardware.graphics.enable = lib.mkDefault true;
     fonts.enableDefaultPackages = lib.mkDefault true;
     programs.dconf.enable = lib.mkDefault true;
 

nixos/modules/services/display-managers/default.nix

@@ -212,9 +212,7 @@ in
       after = [ "acpid.service" "systemd-logind.service" "systemd-user-sessions.service" ];
       restartIfChanged = false;
 
-      environment = lib.optionalAttrs config.hardware.opengl.setLdLibraryPath {
+      environment = cfg.environment;
-        LD_LIBRARY_PATH = lib.makeLibraryPath [ pkgs.addOpenGLRunpath.driverLink ];
-      } // cfg.environment;
 
       preStart = cfg.preStart;
       script = lib.mkIf (config.systemd.services.display-manager.enable == true) cfg.execCmd;

nixos/modules/services/hardware/amdgpu.nix

@@ -0,0 +1,43 @@
+{ config, lib, pkgs, ... }:
+
+let
+  cfg = config.hardware.amdgpu;
+in {
+  options.hardware.amdgpu = {
+    legacySupport.enable = lib.mkEnableOption ''
+      using `amdgpu` kernel driver instead of `radeon` for Southern Islands
+      (Radeon HD 7000) series and Sea Islands (Radeon HD 8000)
+      series cards. Note: this removes support for analog video outputs,
+      which is only available in the `radeon` driver
+    '';
+    initrd.enable = lib.mkEnableOption ''
+      loading `amdgpu` kernelModule in stage 1.
+      Can fix lower resolution in boot screen during initramfs phase
+    '';
+    opencl.enable = lib.mkEnableOption ''OpenCL support using ROCM runtime library'';
+    # cfg.amdvlk option is defined in ./amdvlk.nix module
+  };
+
+  config = {
+    boot.kernelParams = lib.optionals cfg.legacySupport.enable [
+      "amdgpu.si_support=1"
+      "amdgpu.cik_support=1"
+      "radeon.si_support=0"
+      "radeon.cik_support=0"
+    ];
+
+    boot.initrd.kernelModules = lib.optionals cfg.initrd.enable [ "amdgpu" ];
+
+    hardware.opengl = lib.mkIf cfg.opencl.enable {
+      enable = lib.mkDefault true;
+      extraPackages = [
+        pkgs.rocmPackages.clr
+        pkgs.rocmPackages.clr.icd
+      ];
+    };
+  };
+
+  meta = {
+    maintainers = with lib.maintainers; [ johnrtitor ];
+  };
+}

nixos/modules/services/hardware/amdvlk.nix

@@ -31,11 +31,9 @@ in {
   };
 
   config = lib.mkIf cfg.enable {
-    hardware.opengl = {
+    hardware.graphics = {
       enable = true;
-      driSupport = true;
       extraPackages = [ cfg.package ];
-      driSupport32Bit = cfg.support32Bit.enable;
       extraPackages32 = [ cfg.support32Bit.package ];
     };
 

nixos/modules/services/misc/graphical-desktop.nix

@@ -38,7 +38,7 @@ in
 
     fonts.enableDefaultPackages = lib.mkDefault true;
 
-    hardware.opengl.enable = lib.mkDefault true;
+    hardware.graphics.enable = lib.mkDefault true;
 
     programs.gnupg.agent.pinentryPackage = lib.mkOverride 1100 pkgs.pinentry-gnome3;
 

nixos/modules/services/network-filesystems/samba.nix

@@ -201,14 +201,10 @@ in
               message   = "If samba.nsswins is enabled, then samba.enableWinbindd must also be enabled";
             }
           ];
-        # Always provide a smb.conf to shut up programs like smbclient and smbspool.
-        environment.etc."samba/smb.conf".source = mkOptionDefault (
-          if cfg.enable then configFile
-          else pkgs.writeText "smb-dummy.conf" "# Samba is disabled."
-        );
       }
 
       (mkIf cfg.enable {
+        environment.etc."samba/smb.conf".source = configFile;
 
         system.nssModules = optional cfg.nsswins samba;
         system.nssDatabases.hosts = optional cfg.nsswins "wins";

nixos/modules/services/ttys/kmscon.nix

@@ -107,7 +107,7 @@ in {
         fonts = optional (cfg.fonts != null) "font-name=${lib.concatMapStringsSep ", " (f: f.name) cfg.fonts}";
       in lib.concatStringsSep "\n" (render ++ fonts);
 
-    hardware.opengl.enable = mkIf cfg.hwRender true;
+    hardware.graphics.enable = mkIf cfg.hwRender true;
 
     fonts = mkIf (cfg.fonts != null) {
       fontconfig.enable = true;

nixos/modules/services/wayland/cage.nix

@@ -101,7 +101,7 @@ in {
       session required ${config.systemd.package}/lib/security/pam_systemd.so
     '';
 
-    hardware.opengl.enable = mkDefault true;
+    hardware.graphics.enable = mkDefault true;
 
     systemd.targets.graphical.wants = [ "cage-tty1.service" ];
 

nixos/modules/services/x11/desktop-managers/phosh.nix

@@ -216,7 +216,7 @@ in
 
     security.pam.services.phosh = {};
 
-    hardware.opengl.enable = mkDefault true;
+    hardware.graphics.enable = mkDefault true;
 
     services.gnome.core-shell.enable = true;
     services.gnome.core-os-services.enable = true;

nixos/modules/services/x11/xserver.nix

@@ -302,7 +302,7 @@ in
         default = [ "modesetting" "fbdev" ];
         example = [
           "nvidia"
-          "amdgpu-pro"
+          "amdgpu"
         ];
         # TODO(@oxij): think how to easily add the rest, like those nvidia things
         relatedPackages = concatLists
@@ -716,10 +716,7 @@ in
 
         restartIfChanged = false;
 
-        environment =
+        environment = config.services.displayManager.environment;
-          optionalAttrs config.hardware.opengl.setLdLibraryPath
-            { LD_LIBRARY_PATH = lib.makeLibraryPath [ pkgs.addOpenGLRunpath.driverLink ]; }
-          // config.services.displayManager.environment;
 
         preStart =
           ''

nixos/modules/virtualisation/docker.nix

@@ -244,8 +244,8 @@ in
       };
 
       assertions = [
-        { assertion = cfg.enableNvidia && pkgs.stdenv.isx86_64 -> config.hardware.opengl.driSupport32Bit or false;
+        { assertion = cfg.enableNvidia && pkgs.stdenv.isx86_64 -> config.hardware.graphics.enable32Bit or false;
-          message = "Option enableNvidia on x86_64 requires 32bit support libraries";
+          message = "Option enableNvidia on x86_64 requires 32-bit support libraries";
         }];
 
       virtualisation.docker.daemon.settings = {

nixos/tests/armagetronad.nix

@@ -12,7 +12,7 @@ let
     { pkgs, ... }:
 
     { imports = [ ./common/user-account.nix ./common/x11.nix ];
-      hardware.opengl.driSupport = true;
+      hardware.graphics.enable = true;
       virtualisation.memorySize = 256;
       environment = {
         systemPackages = [ pkgs.armagetronad ];

nixos/tests/cagebreak.nix

@@ -14,9 +14,7 @@ in
   };
 
   nodes.machine = { config, ... }:
-  let
+  {
-    alice = config.users.users.alice;
-  in {
     # Automatically login on tty1 as a normal user:
     imports = [ ./common/user-account.nix ];
     services.getty.autologinUser = "alice";
@@ -31,7 +29,7 @@ in
       fi
     '';
 
-    hardware.opengl.enable = true;
+    hardware.graphics.enable = true;
     programs.xwayland.enable = true;
     security.polkit.enable = true;
     environment.systemPackages = [ pkgs.cagebreak pkgs.wayland-utils ];

nixos/tests/monado.nix

@@ -5,7 +5,7 @@ import ./make-test-python.nix ({ pkgs, ... }: {
     { pkgs, ... }:
 
     {
-      hardware.opengl.enable = true;
+      hardware.graphics.enable = true;
       users.users.alice = {
         isNormalUser = true;
         uid = 1000;

nixos/tests/openarena.nix

@@ -5,7 +5,7 @@ let
     { pkgs, ... }:
 
     { imports = [ ./common/x11.nix ];
-      hardware.opengl.driSupport = true;
+      hardware.graphics.enable = true;
       environment.systemPackages = [ pkgs.openarena ];
     };
 

nixos/tests/quake3.nix

@@ -21,7 +21,7 @@ let
     { pkgs, ... }:
 
     { imports = [ ./common/x11.nix ];
-      hardware.opengl.driSupport = true;
+      hardware.graphics.enable = true;
       environment.systemPackages = [ pkgs.quake3demo ];
       nixpkgs.config.packageOverrides = overrides;
       nixpkgs.config.allowUnfreePredicate = unfreePredicate;

nixos/tests/seatd.nix

@@ -39,7 +39,7 @@ in
           dwl -s 'foot touch /tmp/foot_started'
     '';
 
-    hardware.opengl.enable = true;
+    hardware.graphics.enable = true;
     virtualisation.qemu.options = [ "-vga none -device virtio-gpu-pci" ];
     services.seatd.enable = true;
   };

nixos/tests/tinywl.nix

@@ -16,7 +16,7 @@ import ./make-test-python.nix ({ pkgs, lib, ... }:
         systemPackages = with pkgs; [ tinywl foot wayland-utils ];
       };
 
-      hardware.opengl.enable = true;
+      hardware.graphics.enable = true;
 
       # Automatically start TinyWL when logging in on tty1:
       programs.bash.loginShellInit = ''

pkgs/applications/audio/waylyrics/default.nix

@@ -9,16 +9,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "waylyrics";
-  version = "0.3.11";
+  version = "0.3.12";
 
   src = fetchFromGitHub {
     owner = "waylyrics";
     repo = "waylyrics";
     rev = "v${version}";
-    hash = "sha256-8jmB6kJUNHTT0w/1ADgjoMAP1zNpohsPl9FIGoh8UG4=";
+    hash = "sha256-FfrgeUDKiM9m0mvKlu02KEuvsq+3Gv3yPFW1DIQw05I=";
   };
 
-  cargoHash = "sha256-hH9EQAH1uSD6uRUxKv7O3ewZsijrbCSWWY7EmC0Z7tI=";
+  cargoHash = "sha256-xD46aKT18Kl+81Pfv+zleUUKhSV1Px7JFjhXw1/4cBA=";
 
   nativeBuildInputs = [ pkg-config wrapGAppsHook4 ];
   buildInputs = [ openssl dbus ];

pkgs/applications/editors/vim/plugins/generated.nix

@@ -9676,6 +9676,18 @@ final: prev:
     meta.homepage = "https://github.com/mfukar/robotframework-vim/";
   };
 
+  rocks-nvim = buildNeovimPlugin {
+    pname = "rocks.nvim";
+    version = "2024-06-19";
+    src = fetchFromGitHub {
+      owner = "nvim-neorocks";
+      repo = "rocks.nvim";
+      rev = "6737e01a76eaaae06d11b45c8b5b774fa97c283b";
+      sha256 = "0vl6rm3rv1730iw3bwzrwjsgr1hw5h4ksdgpir5spd3vqj7i97lz";
+    };
+    meta.homepage = "https://github.com/nvim-neorocks/rocks.nvim/";
+  };
+
   ron-vim = buildVimPlugin {
     pname = "ron.vim";
     version = "2022-08-19";

pkgs/applications/editors/vim/plugins/vim-plugin-names

@@ -813,6 +813,7 @@ https://github.com/vim-scripts/restore_view.vim/,HEAD,restore-view-vim
 https://github.com/gu-fan/riv.vim/,,
 https://github.com/kevinhwang91/rnvimr/,,
 https://github.com/mfukar/robotframework-vim/,,
+https://github.com/nvim-neorocks/rocks.nvim/,,
 https://github.com/ron-rs/ron.vim/,,
 https://github.com/jmederosalvarado/roslyn.nvim/,HEAD,
 https://github.com/keith/rspec.vim/,,

pkgs/applications/networking/cluster/k9s/default.nix

@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "k9s";
-  version = "0.32.4";
+  version = "0.32.5";
 
   src = fetchFromGitHub {
     owner = "derailed";
     repo = "k9s";
     rev = "v${version}";
-    hash = "sha256-0MAnN1ekzHLs25EspDN3xacmDvwXGwKO/5RsCMMwTI8=";
+    hash = "sha256-H0PimkPXs2/iirOpN82az3Bge71k1RZOhMtr0UmGOy8=";
   };
 
   ldflags = [
@@ -23,7 +23,7 @@ buildGoModule rec {
 
   proxyVendor = true;
 
-  vendorHash = "sha256-Eaz56iU862KDAlVPuMo8qPuWSFCxEFcJ3Qubl9TUiyI=";
+  vendorHash = "sha256-U/tIsYpoog3S8V2yQGGqaQ+Av7TfvCYt3zn74qWuQKs=";
 
   # TODO investigate why some config tests are failing
   doCheck = !(stdenv.isDarwin && stdenv.isAarch64);

pkgs/applications/networking/instant-messengers/deltachat-cursed/default.nix

@@ -7,7 +7,7 @@
 
 python3.pkgs.buildPythonApplication rec {
   pname = "deltachat-cursed";
-  version = "0.8.0";
+  version = "0.9.0";
 
   pyproject = true;
 
@@ -15,17 +15,17 @@ python3.pkgs.buildPythonApplication rec {
     owner = "adbenitez";
     repo = "deltachat-cursed";
     rev = "v${version}";
-    hash = "sha256-1QNhNPa6ZKn0lGQXs/cmfdSFHscwlYwFC/2DpnMoHvY=";
+    hash = "sha256-z4JKe5soR4FdIn8hugxtnxQr/9V8m8a7QRzE1liIexc=";
   };
 
-  nativeBuildInputs = with python3.pythonOnBuildForHost.pkgs; [
+  build-system = with python3.pythonOnBuildForHost.pkgs; [
     setuptools
     setuptools-scm
   ];
 
-  propagatedBuildInputs = with python3.pkgs; [
+  dependencies = with python3.pkgs; [
     appdirs
-    deltachat
+    deltachat2
     emoji
     notify-py
     setuptools # for pkg_resources

pkgs/applications/networking/instant-messengers/deltachat-desktop/default.nix

@@ -1,11 +1,12 @@
 { lib
 , buildNpmPackage
 , copyDesktopItems
-, electron_28
+, electron
 , buildGoModule
 , esbuild
 , fetchFromGitHub
 , jq
+, deltachat-rpc-server
 , libdeltachat
 , makeDesktopItem
 , makeWrapper
@@ -36,16 +37,16 @@ let
 in
 buildNpmPackage rec {
   pname = "deltachat-desktop";
-  version = "1.44.1";
+  version = "1.46.1";
 
   src = fetchFromGitHub {
     owner = "deltachat";
     repo = "deltachat-desktop";
     rev = "v${version}";
-    hash = "sha256-fL+9oPQ5dAgvQREZ7A+hKo2MnZKeVvadQDvDPsDNbnQ=";
+    hash = "sha256-90/Wmh0h75i3kvqj3Wo+A3KlKW8LLDWfPza2gDrDY6E=";
   };
 
-  npmDepsHash = "sha256-rUxJLDsAfp+brecTThYTdHIVIfVkKwZ/W5sHV0hHHIk=";
+  npmDepsHash = "sha256-UzWxMd+DYH5A8Zo1rzi8oIsoKbmzsVbGpr3uWtc02rY=";
 
   postPatch = ''
     test \
@@ -64,6 +65,7 @@ buildNpmPackage rec {
   ];
 
   buildInputs = [
+    deltachat-rpc-server
     libdeltachat
   ] ++ lib.optionals stdenv.isDarwin [
     CoreServices
@@ -77,7 +79,8 @@ buildNpmPackage rec {
   };
 
   preBuild = ''
-    rm -r node_modules/deltachat-node/node/prebuilds
+    rm node_modules/@deltachat/stdio-rpc-server-*/deltachat-rpc-server
+    ln -s ${lib.getExe deltachat-rpc-server} node_modules/@deltachat/stdio-rpc-server-linux-*
   '';
 
   npmBuildScript = "build4production";
@@ -93,6 +96,9 @@ buildNpmPackage rec {
     awk '!/^#/ && NF' build/packageignore_list \
       | xargs -I {} sh -c "rm -rf $out/lib/node_modules/deltachat-desktop/{}" || true
 
+    # required for electron to import index.js as a module
+    cp package.json $out/lib/node_modules/deltachat-desktop
+
     install -D build/icon.png \
       $out/share/icons/hicolor/scalable/apps/deltachat.png
 
@@ -103,7 +109,7 @@ buildNpmPackage rec {
         $out/lib/node_modules/deltachat-desktop/html-dist/fonts
     done
 
-    makeWrapper ${lib.getExe electron_28} $out/bin/deltachat \
+    makeWrapper ${lib.getExe electron} $out/bin/deltachat \
       --set LD_PRELOAD ${sqlcipher}/lib/libsqlcipher${stdenv.hostPlatform.extensions.sharedLibrary} \
       --add-flags $out/lib/node_modules/deltachat-desktop
 

pkgs/applications/networking/instant-messengers/signal-desktop/signal-desktop.nix

@@ -2,7 +2,7 @@
 callPackage ./generic.nix { } rec {
   pname = "signal-desktop";
   dir = "Signal";
-  version = "7.11.1";
+  version = "7.12.0";
   url = "https://updates.signal.org/desktop/apt/pool/s/signal-desktop/signal-desktop_${version}_amd64.deb";
-  hash = "sha256-ROJ2aQY0NPZD2GcjdQ1OxbeXKC+60n791Nxs93CyJ/Y=";
+  hash = "sha256-k8Dp3MiWRNpWEGqYtt5o8FtL3fJ9AkIm+hjvW8r6qG0=";
 }

pkgs/applications/science/electronics/gtkwave/default.nix

@@ -16,11 +16,11 @@
 
 stdenv.mkDerivation rec {
   pname = "gtkwave";
-  version = "3.3.119";
+  version = "3.3.120";
 
   src = fetchurl {
     url = "mirror://sourceforge/gtkwave/${pname}-gtk3-${version}.tar.gz";
-    sha256 = "sha256-6rPgnnZBEVwHhIv7MPfdDDu+K4y+RQF+leB327pqwDg=";
+    sha256 = "sha256-XalIY/suXYjMAZ4r/cZ2AiOYETiUtYXYZOEcqDQbJNg=";
   };
 
   nativeBuildInputs = [ pkg-config wrapGAppsHook3 ];

pkgs/applications/science/math/R/default.nix

@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, fetchpatch, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng
+{ lib, stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng
 , libtiff, ncurses, pango, pcre2, perl, readline, tcl, texlive, texliveSmall, tk, xz, zlib
 , less, texinfo, graphviz, icu, pkg-config, bison, imake, which, jdk, blas, lapack
 , curl, Cocoa, Foundation, libobjc, libcxx, tzdata
@@ -15,13 +15,13 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "R";
-  version = "4.3.3";
+  version = "4.4.1";
 
   src = let
     inherit (finalAttrs) pname version;
   in fetchurl {
     url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz";
-    sha256 = "sha256-gIUSMTk7hb84d+6eObKC51Dthkxexgy9aObhOfBSAzA=";
+    sha256 = "sha256-tMtnXequtymdOyZdIYzeQ/GSlRzluJt7saUUijay2U0=";
   };
 
   outputs = [ "out" "tex" ];
@@ -37,12 +37,6 @@ stdenv.mkDerivation (finalAttrs: {
 
   patches = [
     ./no-usr-local-search-paths.patch
-    (fetchpatch {
-      # https://hiddenlayer.com/research/r-bitrary-code-execution/
-      name = "CVE-2024-27322.patch";
-      url = "https://github.com/r-devel/r-svn/commit/f7c46500f455eb4edfc3656c3fa20af61b16abb7.patch";
-      hash = "sha256-CH2mMmie9E96JeGSC7UGm7/roUNhK5xv6HO53N2ixEI=";
-    })
   ];
 
   # Test of the examples for package 'tcltk' fails in Darwin sandbox. See:

pkgs/applications/science/misc/boinc/default.nix

@@ -27,14 +27,14 @@
 
 stdenv.mkDerivation rec {
   pname = "boinc";
-  version = "8.0.2";
+  version = "8.0.3";
 
   src = fetchFromGitHub {
     name = "${pname}-${version}-src";
     owner = "BOINC";
     repo = "boinc";
     rev = "client_release/${lib.versions.majorMinor version}/${version}";
-    hash = "sha256-e0zEdiN3QQHj6MNGd1pfaZf3o9rOpCTmuNSJQb3sss4=";
+    hash = "sha256-kkEEJp7NTpHwbo03BGjjJAraFQIJcoNyV+oDsCZlzPQ=";
   };
 
   nativeBuildInputs = [ libtool automake autoconf m4 pkg-config ];

pkgs/by-name/an/ananicy-cpp/match-wrappers.patch

@@ -0,0 +1,16 @@
+diff --git a/src/worker.cpp b/src/worker.cpp
+index 0cf8955..b9dc70f 100644
+--- a/src/worker.cpp
++++ b/src/worker.cpp
+@@ -29,7 +29,10 @@ void Worker::work(const std::stop_token &stop_token) {
+   while (!stop_token.stop_requested()) {
+     while ((proc = process_queue->poll(500ms)).has_value()) {
+       const auto &p = proc.value();
+-      const auto &rule = rules->get_rule(p.name);
++      auto name = p.name;
++      if (name.starts_with('.') && name.ends_with("-wrapped"))
++        name = name.substr(1, name.find_last_of('-') - 1);
++      const auto &rule = rules->get_rule(name);
+ 
+       processed_count++;
+ 

pkgs/by-name/an/ananicy-cpp/package.nix

@@ -33,6 +33,7 @@ clangStdenv.mkDerivation rec {
       url = "https://gitlab.com/ananicy-cpp/ananicy-cpp/-/commit/6ea2dccceec39b6c4913f617dad81d859aa20f24.patch";
       hash = "sha256-C+7x/VpVwewXEPwibi7GxGfjuhDkhcjTyGbZHlYL2Bs=";
     })
+    ./match-wrappers.patch
   ];
 
   strictDeps = true;
@@ -80,6 +81,7 @@ clangStdenv.mkDerivation rec {
     maintainers = with lib.maintainers; [
       artturin
       johnrtitor
+      diniamo
     ];
     mainProgram = "ananicy-cpp";
   };

pkgs/by-name/db/dbeaver-bin/package.nix

@@ -12,16 +12,7 @@
 
 stdenvNoCC.mkDerivation (finalAttrs: {
   pname = "dbeaver-bin";
-  version = "24.0.5";
+  version = "24.1.0";
-
-  nativeBuildInputs =
-    [ makeWrapper ]
-    ++ lib.optionals (!stdenvNoCC.isDarwin) [
-      gnused
-      wrapGAppsHook3
-      autoPatchelfHook
-    ]
-    ++ lib.optionals stdenvNoCC.isDarwin [ undmg ];
 
   src =
     let
@@ -34,10 +25,10 @@ stdenvNoCC.mkDerivation (finalAttrs: {
         aarch64-darwin = "macos-aarch64.dmg";
       };
       hash = selectSystem {
-        x86_64-linux = "sha256-q6VIr55hXn47kZrE2i6McEOfp2FBOvwB0CcUnRHFMZs=";
+        x86_64-linux = "sha256-cJcjUoZSpD87jy4GGIxMinZW4gxRZfcGO0GdGUGXI6g=";
-        aarch64-linux = "sha256-Xn3X1C31UALBAsZIGyMWdp0HNhJEm5N+7Go7nMs8W64=";
+        aarch64-linux = "sha256-96t/T/VzzzaSWJbPBb1CH2FXqfhiH1d0MjRoPsRMRwo=";
-        x86_64-darwin = "sha256-XOQaMNQHOC4dVJXIUn4l4Oa7Gohbq+JMDFusIy/U+tc=";
+        x86_64-darwin = "sha256-8xqSL8fTveg1Y5huBTYZLyubajt27h4XUBzyYVF394A=";
-        aarch64-darwin = "sha256-554ea5p1MR4XIHtSeByd4S/Ke4cKRZbITTNRRDoRqPI=";
+        aarch64-darwin = "sha256-r7WqJrNF1IgQHx3Na1fGk0ywsfh5t4Dl/u8hH6CPuoE=";
       };
     in
     fetchurl {
@@ -45,15 +36,25 @@ stdenvNoCC.mkDerivation (finalAttrs: {
       inherit hash;
     };
 
+  sourceRoot = lib.optional stdenvNoCC.isDarwin "dbeaver.app";
+
+  nativeBuildInputs =
+    [ makeWrapper ]
+    ++ lib.optionals (!stdenvNoCC.isDarwin) [
+      gnused
+      wrapGAppsHook3
+      autoPatchelfHook
+    ]
+    ++ lib.optionals stdenvNoCC.isDarwin [ undmg ];
+
   dontConfigure = true;
   dontBuild = true;
 
-  sourceRoot = lib.optional stdenvNoCC.isDarwin "dbeaver.app";
-
   installPhase =
     if !stdenvNoCC.isDarwin then
       ''
         runHook preInstall
+
         mkdir -p $out/opt/dbeaver $out/bin
         cp -r * $out/opt/dbeaver
         makeWrapper $out/opt/dbeaver/dbeaver $out/bin/dbeaver \

pkgs/by-name/db/dbeaver-bin/update.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/env nix-shell
-#!nix-shell -I nixpkgs=./. -i bash -p curl jq
+#!nix-shell -I nixpkgs=./. -i bash -p curl jq common-updater-scripts
 
 latestVersion=$(curl "https://api.github.com/repos/dbeaver/dbeaver/tags" | jq -r '.[0].name')
 currentVersion=$(nix-instantiate --eval -E "with import ./. {}; dbeaver-bin.version" | tr -d '"')

pkgs/by-name/de/design/package.nix

@@ -0,0 +1,58 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, wrapGAppsHook4
+, appstream-glib
+, blueprint-compiler
+, desktop-file-utils
+, meson
+, ninja
+, pkg-config
+, glib
+, gjs
+, libadwaita
+}:
+
+stdenv.mkDerivation rec {
+  pname = "design";
+  version = "46-alpha1";
+
+  src = fetchFromGitHub {
+    owner = "dubstar-04";
+    repo = "Design";
+    rev = "v${version}";
+    fetchSubmodules = true;
+    hash = "sha256-Q4R/Ztu4w8IRvq15xNXN/iP/6hIHe/W+me1jROGpYc8=";
+  };
+
+  nativeBuildInputs = [
+    appstream-glib
+    blueprint-compiler
+    desktop-file-utils
+    gjs
+    meson
+    ninja
+    pkg-config
+    wrapGAppsHook4
+  ];
+
+  buildInputs = [
+    glib
+    libadwaita
+  ];
+
+  # Use a symlink here so that the basename isn't changed by the wrapper which is used to decide the resource path.
+  postInstall = ''
+    mv $out/bin/io.github.dubstar_04.design $out/share/design/
+    ln -s $out/share/design/io.github.dubstar_04.design $out/bin
+  '';
+
+  meta = {
+    homepage = "https://github.com/dubstar-04/Design";
+    description = "2D CAD For GNOME";
+    maintainers = with lib.maintainers; [ linsui ];
+    license = lib.licenses.gpl3Plus;
+    platforms = lib.platforms.linux;
+    mainProgram = "io.github.dubstar_04.design";
+  };
+}

pkgs/by-name/go/google-chrome/package.nix

@@ -64,11 +64,11 @@ let
 
 in stdenv.mkDerivation (finalAttrs: {
   pname = "google-chrome";
-  version = "126.0.6478.61";
+  version = "126.0.6478.114";
 
   src = fetchurl {
     url = "https://dl.google.com/linux/chrome/deb/pool/main/g/google-chrome-stable/google-chrome-stable_${finalAttrs.version}-1_amd64.deb";
-    hash = "sha256-L7gBl4SMHIq0x+GZiaaK5Dxs+UJDandz0xYET7YO73o=";
+    hash = "sha256-CGqo6XnUwndOjODOxy+TCGxDXbAz4EwkZMOl7ZLFsAc=";
   };
 
   nativeBuildInputs = [ patchelf makeWrapper ];

pkgs/by-name/go/gosmee/package.nix

@@ -6,13 +6,13 @@
 
 buildGoModule rec {
   pname = "gosmee";
-  version = "0.22.0";
+  version = "0.22.1";
 
   src = fetchFromGitHub {
     owner = "chmouel";
     repo = "gosmee";
     rev = "v${version}";
-    sha256 = "sha256-PP+N8BihgSvYL7yHlBJOK4zWkuM75iaGc7Gld+c0D6Y=";
+    sha256 = "sha256-UnGzPkbw7x8l1+9xEXFiJZFzJT5yu7MCgPKkKzaFqkk=";
   };
   vendorHash = null;
 

pkgs/by-name/hy/hyprutils/package.nix

@@ -2,25 +2,34 @@
   lib,
   stdenv,
   cmake,
+  pkg-config,
+  pixman,
   fetchFromGitHub,
 }:
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "hyprutils";
-  version = "0.1.2";
+  version = "0.1.4";
 
   src = fetchFromGitHub {
     owner = "hyprwm";
     repo = "hyprutils";
-    rev = "v${finalAttrs.version}";
+    rev = "refs/tags/v${finalAttrs.version}";
-    hash = "sha256-8KvVqtApNt4FWTdn1TqVvw00rpqyG9UuUPA2ilPVD1U=";
+    hash = "sha256-CqRZne63BpYlPd/i8lXV0UInUt59oKogiwdVtBRHt60=";
   };
 
-  nativeBuildInputs = [ cmake ];
+  nativeBuildInputs = [
+    cmake
+    pkg-config
+  ];
 
-  outputs = [ "out" "dev" ];
+  buildInputs = [
+    pixman
+  ];
 
-  doCheck = false;
+  outputs = ["out" "dev"];
+
+  cmakeBuildType = "RelWithDebInfo";
 
   meta = {
     homepage = "https://github.com/hyprwm/hyprutils";

pkgs/by-name/ic/ice-bar/package.nix

@@ -0,0 +1,41 @@
+{
+  lib,
+  stdenvNoCC,
+  unzip,
+  fetchurl,
+  nix-update-script,
+}:
+
+stdenvNoCC.mkDerivation (finalAttrs: {
+  pname = "ice-bar";
+  version = "0.9.0";
+
+  src = fetchurl {
+    url = "https://github.com/jordanbaird/Ice/releases/download/${finalAttrs.version}/Ice.zip";
+    hash = "sha256-MvkJRP8Stz9VIK3vBnWezVKq2KkPfUa/NUBxJtYzHhU=";
+  };
+
+  sourceRoot = ".";
+
+  nativeBuildInputs = [ unzip ];
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p "$out/Applications"
+    cp -r *.app "$out/Applications"
+
+    runHook postInstall
+  '';
+
+  passthru.updateScript = nix-update-script { };
+
+  meta = {
+    description = "Powerful menu bar manager for macOS";
+    homepage = "https://icemenubar.app/";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ donteatoreo ];
+    platforms = lib.platforms.darwin;
+    sourceProvenance = with lib.sourceTypes; [ binaryNativeCode ];
+  };
+})

pkgs/by-name/it/itools/package.nix

@@ -0,0 +1,41 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, autoreconfHook
+, pkgs
+, pkg-config
+, perl
+, libitl
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "itools";
+  version = "1.1";
+
+  nativeBuildInputs = [ pkg-config autoreconfHook ];
+  buildInputs = [ libitl perl ];
+
+  outputs = [ "out" "man" ];
+
+  src = fetchFromGitHub {
+    owner = "arabeyes-org";
+    repo = "itools";
+    rev = finalAttrs.version;
+    hash = "sha256-DxTZaq2SlEmy9k7iAdjctpPkk+2rIaF+xEcfXj/ERWw=";
+  };
+
+  meta = {
+    description = "Islamic command-line tools for prayer times and hijri dates";
+    longDescription = ''
+      The itools package is a set of user friendly applications utilizing Arabeyes' ITL library.
+
+      The package addresses two main areas - hijri date and prayertime calculation. The package
+      is envisioned to mimick the development of the underlying ITL library and is meant to
+      always give the end-user a simple means to access its functions.
+    '';
+    homepage = "https://www.arabeyes.org/ITL";
+    license = lib.licenses.gpl2Only;
+    platforms = lib.platforms.all;
+    maintainers = with lib.maintainers; [ amyipdev ];
+  };
+})

pkgs/by-name/ja/jasp-desktop/modules.nix

@@ -33,6 +33,9 @@ let
 
     env.INCLUDE_DIR = "../inst/include/jaspColumnEncoder";
 
+    # necessary for R 4.4.0
+    hardeningDisable = [ "format" ];
+
     postPatch = ''
       mkdir -p inst/include
       cp -r --no-preserve=all ${jaspColumnEncoder-src} inst/include/jaspColumnEncoder

pkgs/by-name/ja/jasp-desktop/package.nix

@@ -66,6 +66,9 @@ stdenv.mkDerivation {
     "-DCUSTOM_R_PATH=${customREnv}"
   ];
 
+  # necessary for R 4.4.0
+  hardeningDisable = [ "format" ];
+
   nativeBuildInputs = [
     cmake
     ninja

pkgs/by-name/nu/numi/package.nix

@@ -0,0 +1,41 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  undmg,
+  nix-update-script,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "numi";
+  version = "3.32.721";
+
+  src = fetchurl {
+    url = "https://s3.numi.app/updates/${finalAttrs.version}/Numi.dmg";
+    hash = "sha256-IbX4nsrPqwOSlYdNJLeaRQwIDVJrzfMXFqRqixHd2zA=";
+  };
+
+  nativeBuildInputs = [ undmg ];
+
+  sourceRoot = ".";
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p "$out/Applications"
+    cp -R *.app "$out/Applications"
+
+    runHook postInstall
+  '';
+
+  passthru.updateScript = nix-update-script { };
+
+  meta = {
+    description = "Beautiful calculator app for macOS";
+    homepage = "https://numi.app/";
+    license = lib.licenses.unfree;
+    maintainers = with lib.maintainers; [ donteatoreo ];
+    platforms = lib.platforms.darwin;
+    sourceProvenance = with lib.sourceTypes; [ binaryNativeCode ];
+  };
+})

pkgs/by-name/nu/nuv/package.nix

@@ -0,0 +1,75 @@
+{ lib
+, stdenv
+, symlinkJoin
+, callPackage
+, fetchFromGitHub
+, fetchurl
+, buildGoModule
+, makeWrapper
+, breakpointHook
+, jq
+, curl
+, kubectl
+, eksctl
+, kind
+, k3sup
+, coreutils
+}:
+
+let
+  branch = "3.0.0";
+  version = "3.0.1-beta.2405292059";
+  pname = "nuv";
+in
+buildGoModule {
+  inherit pname version;
+
+  src = fetchFromGitHub {
+    owner = "nuvolaris";
+    repo = "nuv";
+    rev = version;
+    hash = "sha256-MdnBvlA4S2Mi/bcbE+O02x+wvlIrsK1Zc0dySz4FB/w=";
+  };
+
+  subPackages = [ "." ];
+  vendorHash = "sha256-JkQbQ2NEaumXbAfsv0fNiQf/EwMs3SDLHvu7c/bU7fU=";
+
+  nativeBuildInputs = [ makeWrapper jq curl breakpointHook ];
+
+  ldflags = [
+    "-s"
+    "-w"
+    "-X main.NuvVersion=${version}"
+    "-X main.NuvBranch=${branch}"
+  ];
+
+  # false because tests require some modifications inside nix-env
+  doCheck = false;
+
+  postInstall = let
+    nuv-bin = symlinkJoin {
+      name = "nuv-bin";
+      paths = [
+        coreutils
+        kubectl
+        eksctl
+        kind
+        k3sup
+      ];
+    };
+  in ''
+    wrapProgram $out/bin/nuv --set NUV_BIN "${nuv-bin}/bin"
+  '';
+
+  passthru.tests = {
+    simple = callPackage ./tests.nix { inherit version; };
+  };
+
+  meta = {
+    homepage = "https://nuvolaris.io/";
+    description = "A CLI tool for running tasks using the Nuvolaris serverless engine";
+    license = lib.licenses.asl20;
+    mainProgram = "nuv";
+    maintainers = with lib.maintainers; [ msciabarra d4rkstar ];
+  };
+}

pkgs/by-name/nu/nuv/tests.nix

@@ -0,0 +1,17 @@
+{ runCommand, nuv, version }:
+
+runCommand "nuv-test-run"
+{
+  nativeBuildInputs = [ nuv ];
+} ''
+  export TMP_BASE=$(mktemp -d /tmp/.nuv-XXXXX)
+  export HOME=$TMP_BASE
+  export NUV_REPO=""
+  export NUV_ROOT=$TMP_BASE/.nuv/3.0.0/olaris
+  rm -rf $TMP_BASE/.nuv && \
+    mkdir -p $TMP_BASE/.nuv/3.0.0/olaris && \
+    mkdir $TMP_BASE/.nuv/tmp
+  V=$(nuv -version 2>/dev/null)
+  diff -U3 --color=auto <(echo "$V") <(echo "${version}")
+  touch $out
+''

pkgs/by-name/ow/owncloud-client/package.nix

@@ -17,13 +17,13 @@
 
 stdenv.mkDerivation rec {
   pname = "owncloud-client";
-  version = "5.3.0";
+  version = "5.3.1";
 
   src = fetchFromGitHub {
     owner = "owncloud";
     repo = "client";
     rev = "refs/tags/v${version}";
-    hash = "sha256-2BM5XoblPwI2xr0e9VHiN4ePkyUx+NyMDY7HkWa9uZM=";
+    hash = "sha256-ot+2hxipeZ5eI6nPJ8XGE8gFMNQoblUq+koAFZpZDv4=";
   };
 
   nativeBuildInputs = [

pkgs/by-name/pi/pid1/package.nix

@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "pid1";
-  version = "0.1.2";
+  version = "0.1.3";
 
   src = fetchFromGitHub {
     owner = "fpco";
     repo = "pid1-rs";
     rev = "v${version}";
-    hash = "sha256-BljIa+4BKI7WHlOhXfN/3VKMzs5G5E4tNlQ2oPpJV2g=";
+    hash = "sha256-2dnQj3AQxedyq1YvHKt+lVXNEtuB5sMRSCqX9YeifzI=";
   };
 
-  cargoHash = "sha256-7PANlw/SKxyAqymfXIXFT/v3U0GCiGfgStguSr0lrqQ=";
+  cargoHash = "sha256-/KK9U1dgCLglgn/MJ7+sov4EEnY/nluEsz0ooMp6ggI=";
 
   meta = with lib; {
     description = "Signal handling and zombie reaping for PID1 process";

pkgs/by-name/po/powerpipe/package.nix

@@ -11,16 +11,16 @@
 
 buildGoModule rec {
   pname = "powerpipe";
-  version = "0.3.1";
+  version = "0.4.0";
 
   src = fetchFromGitHub {
     owner = "turbot";
     repo = "powerpipe";
     rev = "refs/tags/v${version}";
-    hash = "sha256-tvGCgpuWMCzBldgxf4caKiUe7EpraJJeOVBwNqU60oc=";
+    hash = "sha256-KJ024dIU0GmeHCFa/pbyFIA+LitaudHC+NBGg8yNWxM=";
   };
 
-  vendorHash = "sha256-C3memfHNSlkiwhwB5zCXCtUOII3IjFD5FHGd8uPGmpU=";
+  vendorHash = "sha256-XALFXUeWrS4nt+ONToCfYXvLWuk7ZhLWvJidnATcWtM=";
   proxyVendor = true;
 
   nativeBuildInputs = [

pkgs/by-name/sf/sfwbar/package.nix

@@ -1,28 +1,31 @@
-{ lib
+{
-, stdenv
+  lib,
-, fetchFromGitHub
+  stdenv,
-, gtk3
+  fetchFromGitHub,
-, meson
+  gtk3,
-, ninja
+  meson,
-, json_c
+  ninja,
-, pkg-config
+  json_c,
-, gtk-layer-shell
+  pkg-config,
-, libpulseaudio
+  gtk-layer-shell,
-, libmpdclient
+  libpulseaudio,
-, libxkbcommon
+  libmpdclient,
-, alsa-lib
+  libxkbcommon,
-, makeWrapper
+  alsa-lib,
-,
+  makeWrapper,
 }:
-stdenv.mkDerivation rec {
+let
+  version = "1.0_beta14";
+in
+stdenv.mkDerivation {
   pname = "sfwbar";
-  version = "1.0_beta13";
+  inherit version;
 
   src = fetchFromGitHub {
     owner = "LBCrion";
-    repo = pname;
+    repo = "sfwbar";
     rev = "v${version}";
-    hash = "sha256-7oiuTEqdXDReKdakJX6+HRaSi1XovM+MkHFkaFZtq64=";
+    hash = "sha256-4brP1SXaWq/L0D87rvlrWhLU1oFPSwNNxBSzRr4jsTM=";
   };
 
   buildInputs = [
@@ -47,12 +50,16 @@ stdenv.mkDerivation rec {
       --suffix XDG_DATA_DIRS : $out/share
   '';
 
-  meta = with lib; {
+  meta = {
     homepage = "https://github.com/LBCrion/sfwbar";
     description = "Flexible taskbar application for wayland compositors, designed with a stacking layout in mind";
+    changelog = "https://github.com/LBCrion/sfwbar/releases/tag/v${version}";
     mainProgram = "sfwbar";
-    platforms = platforms.linux;
+    platforms = lib.platforms.linux;
-    maintainers = with maintainers; [ NotAShelf ];
+    maintainers = with lib.maintainers; [
-    license = licenses.gpl3Only;
+      luftmensch-luftmensch
+      NotAShelf
+    ];
+    license = lib.licenses.gpl3Only;
   };
 }

pkgs/by-name/sp/spacedrive/package.nix

@@ -1,73 +1,136 @@
-{ lib
+{
-, pkgs
+  lib,
-, stdenv
+  stdenv,
-, fetchurl
+  fetchurl,
-, appimageTools
+  undmg,
-, undmg
+  nix-update-script,
-, nix-update-script
+  #linux required
+  autoPatchelfHook,
+  dpkg,
+  gdk-pixbuf,
+  glib,
+  gst_all_1,
+  libsoup,
+  webkitgtk_4_1,
+  xdotool,
 }:
 
 let
   pname = "spacedrive";
-  version = "0.2.14";
+  version = "0.3.1";
 
-  src = fetchurl {
+  src =
-    aarch64-darwin = {
+    fetchurl
-      url = "https://github.com/spacedriveapp/spacedrive/releases/download/${version}/Spacedrive-darwin-aarch64.dmg";
+      {
-      hash = "sha256-G0Ey7ewZeXegiqkAXFmS0MdaYllTphp7Buqs5/4/mWY=";
+        aarch64-darwin = {
-    };
+          url = "https://github.com/spacedriveapp/spacedrive/releases/download/${version}/Spacedrive-darwin-aarch64.dmg";
-    x86_64-darwin = {
+          hash = "sha256-9E7h03zJtH8b6khDcbBsB46iVWwl48s+GJuBMOmEre4=";
-      url = "https://github.com/spacedriveapp/spacedrive/releases/download/${version}/Spacedrive-darwin-x86_64.dmg";
+        };
-      hash = "sha256-ypUDb94RlGqJfkf4htWKZ0UrGZ0SyCZrrAqtMuxDzDI=";
+        x86_64-darwin = {
-    };
+          url = "https://github.com/spacedriveapp/spacedrive/releases/download/${version}/Spacedrive-darwin-x86_64.dmg";
-    x86_64-linux = {
+          hash = "sha256-h+B7tc6jXJUFNEMhG6ZNch+grtgUeAzfa37BDoZ6M8Q=";
-      url = "https://github.com/spacedriveapp/spacedrive/releases/download/${version}/Spacedrive-linux-x86_64.AppImage";
+        };
-      hash = "sha256-DFJ1/uJW0BwEtJZxGpnvGC7U8YmsJTUbcuWEOAP2Bno=";
+        x86_64-linux = {
-    };
+          url = "https://github.com/spacedriveapp/spacedrive/releases/download/${version}/Spacedrive-linux-x86_64.deb";
-  }.${stdenv.system} or (throw "${pname}-${version}: ${stdenv.system} is unsupported.");
+          hash = "sha256-E1mOODG4YzBc0TPZJmKgrt/c5hp5LwzLaYPl+J5dnkg=";
+        };
+      }
+      .${stdenv.system} or (throw "${pname}-${version}: ${stdenv.system} is unsupported.");
 
   meta = {
     description = "Open source file manager, powered by a virtual distributed filesystem";
     homepage = "https://www.spacedrive.com";
     changelog = "https://github.com/spacedriveapp/spacedrive/releases/tag/${version}";
-    platforms = [ "aarch64-darwin" "x86_64-darwin" "x86_64-linux" ];
+    platforms = [
+      "aarch64-darwin"
+      "x86_64-darwin"
+      "x86_64-linux"
+    ];
     license = lib.licenses.agpl3Plus;
     sourceProvenance = with lib.sourceTypes; [ binaryNativeCode ];
-    maintainers = with lib.maintainers; [ DataHearth heisfer mikaelfangel stepbrobd ];
+    maintainers = with lib.maintainers; [
+      DataHearth
+      heisfer
+      mikaelfangel
+      stepbrobd
+    ];
     mainProgram = "spacedrive";
   };
 
   passthru.updateScript = nix-update-script { };
 in
-if stdenv.isDarwin then stdenv.mkDerivation
+if stdenv.isDarwin then
-{
+  stdenv.mkDerivation {
-  inherit pname version src meta passthru;
+    inherit
+      pname
+      version
+      src
+      meta
+      passthru
+      ;
 
-  sourceRoot = "Spacedrive.app";
+    sourceRoot = "Spacedrive.app";
 
-  nativeBuildInputs = [ undmg ];
+    nativeBuildInputs = [ undmg ];
 
-  installPhase = ''
+    installPhase = ''
-    mkdir -p "$out/Applications/Spacedrive.app"
+      runHook preInstall
-    cp -r . "$out/Applications/Spacedrive.app"
-    mkdir -p "$out/bin"
-    ln -s "$out/Applications/Spacedrive.app/Contents/MacOS/Spacedrive" "$out/bin/spacedrive"
-  '';
-}
-else appimageTools.wrapType2 {
-  inherit pname version src meta passthru;
 
-  extraPkgs = pkgs: [ pkgs.libthai ];
+      mkdir -p "$out/Applications/Spacedrive.app"
+      cp -r . "$out/Applications/Spacedrive.app"
+      mkdir -p "$out/bin"
+      ln -s "$out/Applications/Spacedrive.app/Contents/MacOS/Spacedrive" "$out/bin/spacedrive"
 
-  extraInstallCommands =
+      runHook postInstall
-    let
-      appimageContents = appimageTools.extractType2 { inherit pname version src; };
-    in
-    ''
-      # Install .desktop files
-      install -Dm444 ${appimageContents}/com.spacedrive.desktop -t $out/share/applications
-      install -Dm444 ${appimageContents}/spacedrive.png -t $out/share/pixmaps
-      substituteInPlace $out/share/applications/com.spacedrive.desktop \
-        --replace 'Exec=usr/bin/spacedrive' 'Exec=spacedrive'
     '';
-}
+  }
+
+else
+  stdenv.mkDerivation {
+    inherit
+      pname
+      version
+      src
+      meta
+      passthru
+      ;
+
+    nativeBuildInputs = [
+      autoPatchelfHook
+      dpkg
+    ];
+
+    # Depends: libc6, libxdo3, libwebkit2gtk-4.1-0, libgtk-3-0
+    # Recommends: gstreamer1.0-plugins-ugly
+    # Suggests: gstreamer1.0-plugins-bad
+    buildInputs = [
+      xdotool
+      glib
+      libsoup
+      webkitgtk_4_1
+      gdk-pixbuf
+      gst_all_1.gst-plugins-ugly
+      gst_all_1.gst-plugins-bad
+      gst_all_1.gst-plugins-base
+      gst_all_1.gstreamer
+    ];
+
+    unpackPhase = ''
+      runHook preUnpack
+
+      dpkg-deb -x $src .
+
+      runHook postUnpack
+    '';
+
+    installPhase = ''
+      runHook preInstall
+
+      mkdir -p $out/bin
+      cp -r usr/share $out/
+      cp -r usr/lib $out/
+      cp -r usr/bin $out/
+
+      runHook postInstall
+    '';
+  }

pkgs/by-name/sy/sysmenu/001-no-runtime-config.patch

@@ -0,0 +1,13 @@
+diff --git a/src/config.hpp b/src/config.hpp
+index 6e7439b..ae01462 100644
+--- a/src/config.hpp
++++ b/src/config.hpp
+@@ -4,8 +4,6 @@
+ 	Runtime configuration can be disabled by deleting #define RUNTIME_CONFIG
+ */
+ 
+-#define RUNTIME_CONFIG
+-
+ // Current								Default
+ inline bool starthidden = false;		// false
+ inline bool searchbar = true;			// true

pkgs/by-name/sy/sysmenu/002-cflags-fix.patch

@@ -0,0 +1,13 @@
+diff --git a/Makefile b/Makefile
+index f0b6baf..71033a5 100644
+--- a/Makefile
++++ b/Makefile
+@@ -4,7 +4,7 @@ SRCS +=	$(wildcard src/*.cpp)
+ OBJS = $(SRCS:.cpp=.o)
+ DESTDIR = $(HOME)/.local
+ 
+-CXXFLAGS = -march=native -mtune=native -Os -s -Wall -flto=auto -fno-exceptions
++CXXFLAGS = -Os -s -Wall -flto=auto -fno-exceptions
+ CXXFLAGS += $(shell pkg-config --cflags $(PKGS))
+ LDFLAGS += $(shell pkg-config --libs $(PKGS)) -Wl,--gc-sections
+ 

pkgs/by-name/sy/sysmenu/package.nix

@@ -0,0 +1,56 @@
+{
+  stdenv,
+  lib,
+  fetchFromGitHub,
+  pkg-config,
+  git,
+  gtkmm4,
+  gtk4-layer-shell,
+  wrapGAppsHook4,
+  unstableGitUpdater,
+}:
+
+stdenv.mkDerivation {
+  pname = "sysmenu";
+  version = "unstable-2024-06-13";
+
+  src = fetchFromGitHub {
+    owner = "System64fumo";
+    repo = "sysmenu";
+    rev = "0b891e5d27f286b867d4a0984ee284a3456de851";
+    hash = "sha256-zI6dmS+ZqcGrG/joWouqrMNQfTRflP677kYJLJEWTBc=";
+  };
+
+  patches = [
+    ./001-no-runtime-config.patch
+    ./002-cflags-fix.patch
+  ];
+
+  nativeBuildInputs = [
+    pkg-config
+    git
+    wrapGAppsHook4
+  ];
+
+  buildInputs = [
+    gtkmm4
+    gtk4-layer-shell
+  ];
+
+  installPhase = ''
+    runHook preInstall
+    install -Dm755 sysmenu $out/bin/sysmenu
+    runHook postInstall
+  '';
+
+  passthru.updateScript = unstableGitUpdater { };
+
+  meta = {
+    description = "Simple program launcher using GTK4";
+    homepage = "https://github.com/System64fumo/sysmenu";
+    license = lib.licenses.wtfpl;
+    mainProgram = "sysmenu";
+    maintainers = with lib.maintainers; [ matteopacini ];
+    platforms = lib.platforms.linux;
+  };
+}

pkgs/by-name/wl/wl-clipboard-rs/package.nix

@@ -8,16 +8,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "wl-clipboard-rs";
-  version = "0.8.1";
+  version = "0.9.0";
 
   src = fetchFromGitHub {
     owner = "YaLTeR";
     repo = "wl-clipboard-rs";
     rev = "v${version}";
-    hash = "sha256-tNmpGBg21IuhKEzY15O2MKVpMB+eCjvRVwVUahADuJU=";
+    hash = "sha256-qwlR/PJivCgQTXe027zuQxq0iVJ3/BLg6LAD3w5tb9Y=";
   };
 
-  cargoHash = "sha256-0Ix+fF1QO1KU8FIOb8EV4iYXe4S69sZOxCdxYccL8m0=";
+  cargoHash = "sha256-C3vhZq5IHtbfg2mYYdQRqaLSA0iSER8zRaKi72FCd+E=";
 
   cargoBuildFlags = [
     "--package=wl-clipboard-rs"

pkgs/data/documentation/man-pages/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "man-pages";
-  version = "6.8";
+  version = "6.9";
 
   src = fetchurl {
     url = "mirror://kernel/linux/docs/man-pages/${pname}-${version}.tar.xz";
-    hash = "sha256-ucawpCD4ORSL4EsvwTqFaSMTco1U1HxpyKE4N5Zl0iY=";
+    hash = "sha256-0Uyv9UzGYvNLG3C89i1OJ+TC/SYGcqNbbnSvcbP3H4g=";
   };
 
   makeFlags = [

pkgs/development/libraries/libdeltachat/default.nix

@@ -31,13 +31,13 @@ let
   };
 in stdenv.mkDerivation rec {
   pname = "libdeltachat";
-  version = "1.136.3";
+  version = "1.140.2";
 
   src = fetchFromGitHub {
     owner = "deltachat";
     repo = "deltachat-core-rust";
     rev = "v${version}";
-    hash = "sha256-/ZWpPpxnOCLGswrfbEPvfUn1LpdBQeR5LecRAB0PEhI=";
+    hash = "sha256-BSbvgKiI89B+nxp5McBKTJAwgePt27C1QvSQLhTL7pQ=";
   };
 
   patches = [

pkgs/development/libraries/libdeltachat/no-static-lib.patch

@@ -1,33 +1,33 @@
 diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 44ca43e7..8b6960dd 100644
+index 5587e391..a18092f5 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -14,7 +14,6 @@ find_program(CARGO cargo)
+@@ -20,7 +20,6 @@ endif()
  
  add_custom_command(
  	OUTPUT
--	"target/release/libdeltachat.a"
+-	"${CMAKE_BINARY_DIR}/target/release/libdeltachat.a"
- 	"target/release/libdeltachat.${DYNAMIC_EXT}"
+ 	"${CMAKE_BINARY_DIR}/target/release/libdeltachat.${DYNAMIC_EXT}"
- 	"target/release/pkgconfig/deltachat.pc"
+ 	"${CMAKE_BINARY_DIR}/target/release/pkgconfig/deltachat.pc"
          COMMAND
-@@ -39,12 +38,10 @@ add_custom_target(
+@@ -35,12 +34,10 @@ add_custom_target(
  	lib_deltachat
  	ALL
  	DEPENDS
--	"target/release/libdeltachat.a"
+-	"${CMAKE_BINARY_DIR}/target/release/libdeltachat.a"
- 	"target/release/libdeltachat.${DYNAMIC_EXT}"
+ 	"${CMAKE_BINARY_DIR}/target/release/libdeltachat.${DYNAMIC_EXT}"
- 	"target/release/pkgconfig/deltachat.pc"
+ 	"${CMAKE_BINARY_DIR}/target/release/pkgconfig/deltachat.pc"
  )
  
  install(FILES "deltachat-ffi/deltachat.h" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
--install(FILES "target/release/libdeltachat.a" DESTINATION ${CMAKE_INSTALL_LIBDIR})
+-install(FILES "${CMAKE_BINARY_DIR}/target/${ARCH_DIR}/release/libdeltachat.a" DESTINATION ${CMAKE_INSTALL_LIBDIR})
- install(FILES "target/release/libdeltachat.${DYNAMIC_EXT}" DESTINATION ${CMAKE_INSTALL_LIBDIR})
+ install(FILES "${CMAKE_BINARY_DIR}/target/${ARCH_DIR}/release/libdeltachat.${DYNAMIC_EXT}" DESTINATION ${CMAKE_INSTALL_LIBDIR})
- install(FILES "target/release/pkgconfig/deltachat.pc" DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+ install(FILES "${CMAKE_BINARY_DIR}/target/${ARCH_DIR}/release/pkgconfig/deltachat.pc" DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
 diff --git a/deltachat-ffi/Cargo.toml b/deltachat-ffi/Cargo.toml
-index de0fbafe..120efec9 100644
+index d66cb00f..48347a48 100644
 --- a/deltachat-ffi/Cargo.toml
 +++ b/deltachat-ffi/Cargo.toml
-@@ -12,7 +12,7 @@ categories = ["cryptography", "std", "email"]
+@@ -11,7 +11,7 @@ categories = ["cryptography", "std", "email"]
  
  [lib]
  name = "deltachat"

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

@@ -9,7 +9,7 @@
 
 buildPythonPackage rec {
   pname = "ailment";
-  version = "9.2.106";
+  version = "9.2.107";
   pyproject = true;
 
   disabled = pythonOlder "3.11";
@@ -18,7 +18,7 @@ buildPythonPackage rec {
     owner = "angr";
     repo = "ailment";
     rev = "refs/tags/v${version}";
-    hash = "sha256-f1F1mPqrZJvXPmziyRIoPj7lIAfSWzpSpLtVs1RjzhI=";
+    hash = "sha256-yEwSHmAxbbdLVFatG4pKJokatCkO4RCZUMVAoBSOwTI=";
   };
 
   build-system = [ setuptools ];

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

@@ -36,7 +36,7 @@
 
 buildPythonPackage rec {
   pname = "angr";
-  version = "9.2.106";
+  version = "9.2.107";
   pyproject = true;
 
   disabled = pythonOlder "3.11";
@@ -45,7 +45,7 @@ buildPythonPackage rec {
     owner = "angr";
     repo = "angr";
     rev = "refs/tags/v${version}";
-    hash = "sha256-TM6Jvb260lQWDrqYASdpRqgS9PmkmPUBcncDtTwWKAU=";
+    hash = "sha256-f4RiLXEp4q3V2SiX6OSLHbAVCaZ5GLOvqm1qmBAYIZ8=";
   };
 
   pythonRelaxDeps = [ "capstone" ];

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

@@ -10,7 +10,7 @@
 
 buildPythonPackage rec {
   pname = "archinfo";
-  version = "9.2.106";
+  version = "9.2.107";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -19,7 +19,7 @@ buildPythonPackage rec {
     owner = "angr";
     repo = "archinfo";
     rev = "refs/tags/v${version}";
-    hash = "sha256-tjM0+R7m9jlhf/cXptjOoyV7o+9xU889wTwOBcFjNSQ=";
+    hash = "sha256-D29ddBceo4Bz3KUiQckdbV0e9uPXEOAAIHZrSpqw3BE=";
   };
 
   build-system = [ setuptools ];

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

@@ -10,6 +10,7 @@
   fastapi,
   fetchFromGitHub,
   grpcio,
+  httpx,
   hypothesis,
   importlib-resources,
   kubernetes,
@@ -49,7 +50,7 @@
 
 buildPythonPackage rec {
   pname = "chromadb";
-  version = "0.5.0";
+  version = "0.5.3";
   pyproject = true;
 
   disabled = pythonOlder "3.9";
@@ -58,13 +59,13 @@ buildPythonPackage rec {
     owner = "chroma-core";
     repo = "chroma";
     rev = "refs/tags/${version}";
-    hash = "sha256-gM+fexjwifF3evR8jZvMbIDz655RFKPUizrsB2q5tbw=";
+    hash = "sha256-czDL2b+Jj7mrYZCTfnaZArkOHBaWyTV0BTE2wvykHps=";
   };
 
   cargoDeps = rustPlatform.fetchCargoTarball {
     inherit src;
     name = "${pname}-${version}";
-    hash = "sha256-zyiFv/gswGupm7Y8BhviklqJzM914v0QyUsRwbGKZ48=";
+    hash = "sha256-eTVT1yowuDsajjceWojdUdX466FKneUt1i5QipBFdp4=";
   };
 
   pythonRelaxDeps = [ "orjson" ];
@@ -90,6 +91,7 @@ buildPythonPackage rec {
     chroma-hnswlib
     fastapi
     grpcio
+    httpx
     importlib-resources
     kubernetes
     mmh3
@@ -141,12 +143,13 @@ buildPythonPackage rec {
 
   disabledTestPaths = [
     # Tests require network access
-    "chromadb/test/property/test_cross_version_persist.py"
     "chromadb/test/auth/test_simple_rbac_authz.py"
+    "chromadb/test/db/test_system.py"
     "chromadb/test/ef/test_default_ef.py"
-    "chromadb/test/test_api.py"
     "chromadb/test/property/"
+    "chromadb/test/property/test_cross_version_persist.py"
     "chromadb/test/stress/"
+    "chromadb/test/test_api.py"
   ];
 
   __darwinAllowLocalNetworking = true;

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

@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "claripy";
-  version = "9.2.106";
+  version = "9.2.107";
   pyproject = true;
 
   disabled = pythonOlder "3.11";
@@ -22,7 +22,7 @@ buildPythonPackage rec {
     owner = "angr";
     repo = "claripy";
     rev = "refs/tags/v${version}";
-    hash = "sha256-y3r0/FU8GcVMv+wnccCB/SUBS+TC22S3qp4Awbhoung=";
+    hash = "sha256-89wh/SuwxOuORk3S42VA/cJh1GACFWB4ceUxp2OszQM=";
   };
 
   # z3 does not provide a dist-info, so python-runtime-deps-check will fail

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

@@ -19,14 +19,14 @@
 
 let
   # The binaries are following the argr projects release cycle
-  version = "9.2.106";
+  version = "9.2.107";
 
   # Binary files from https://github.com/angr/binaries (only used for testing and only here)
   binaries = fetchFromGitHub {
     owner = "angr";
     repo = "binaries";
     rev = "refs/tags/v${version}";
-    hash = "sha256-f8lbofU5VYWDZ4BmSRE81X/3Rk8aj9yvEn9PM0lkZoM=";
+    hash = "sha256-7b3kjPoaJ9z1wdz125XsD0hj5FXj9DmUt8Hpqd/AjKs=";
   };
 in
 buildPythonPackage rec {
@@ -40,7 +40,7 @@ buildPythonPackage rec {
     owner = "angr";
     repo = "cle";
     rev = "refs/tags/v${version}";
-    hash = "sha256-eOKAVqtGt86UJhdobKu4QYN5lC9YjZ+luZwwSm3J1xw=";
+    hash = "sha256-0dfnp0sIxO4Ln20c57Wb9B0E987v+xhrX53yriC+Qy0=";
   };
 
   build-system = [ setuptools ];

pkgs/development/python-modules/deltachat2/default.nix

@@ -0,0 +1,42 @@
+{ lib
+, fetchFromGitHub
+, buildPythonPackage
+, deltachat-rpc-server
+, libdeltachat
+, setuptools-scm
+, substituteAll
+}:
+
+buildPythonPackage rec {
+  pname = "deltachat2";
+  version = "0.6.2";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "adbenitez";
+    repo = "deltachat2";
+    rev = "refs/tags/${version}";
+    hash = "sha256-bp4bi+EeMaWP8zOaPp0eaPKn71F055QgMOOSDzIJUH4=";
+  };
+
+  patches = [
+    (substituteAll {
+      src = ./paths.patch;
+      deltachatrpcserver = lib.getExe deltachat-rpc-server;
+    })
+  ];
+
+  build-system = [
+    setuptools-scm
+  ];
+
+  pythonImportsCheck = [ "deltachat2" ];
+
+  meta = {
+    description = "Client library for Delta Chat core JSON-RPC interface";
+    homepage = "https://github.com/adbenitez/deltachat2";
+    license = lib.licenses.mpl20;
+    mainProgram = "deltachat2";
+    inherit (libdeltachat.meta) maintainers;
+  };
+}

pkgs/development/python-modules/deltachat2/paths.patch

@@ -0,0 +1,13 @@
+diff --git a/deltachat2/transport.py b/deltachat2/transport.py
+index a93dc7e..251947b 100644
+--- a/deltachat2/transport.py
++++ b/deltachat2/transport.py
+@@ -71,7 +71,7 @@ class IOTransport:
+             # `process_group` is not supported before Python 3.11.
+             kwargs = {"preexec_fn": os.setpgrp, **self._kwargs}  # noqa: PLW1509
+         self.process = subprocess.Popen(  # noqa: R1732
+-            "deltachat-rpc-server",
++            "@deltachatrpcserver@",
+             stdin=subprocess.PIPE,
+             stdout=subprocess.PIPE,
+             **kwargs,

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

@@ -26,7 +26,7 @@
 
 buildPythonPackage rec {
   pname = "jsonargparse";
-  version = "4.29.0";
+  version = "4.30.0";
   pyproject = true;
 
   disabled = pythonOlder "3.11";
@@ -35,7 +35,7 @@ buildPythonPackage rec {
     owner = "omni-us";
     repo = "jsonargparse";
     rev = "refs/tags/v${version}";
-    hash = "sha256-L+bGyn6O3lGu4FPclNFUeIzQhpznBxdkofUS5yCRM3Y=";
+    hash = "sha256-jeQOnJ8dLUbp60Nk5v4NYKVR8VYlGz08QHIfQotO2uY=";
   };
 
   build-system = [ setuptools ];

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

@@ -16,7 +16,7 @@
 
 buildPythonPackage rec {
   pname = "lacuscore";
-  version = "1.9.5";
+  version = "1.9.6";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -25,7 +25,7 @@ buildPythonPackage rec {
     owner = "ail-project";
     repo = "LacusCore";
     rev = "refs/tags/v${version}";
-    hash = "sha256-PSxNBgehKOWjf6y/RidIegE+P5rg9OzU4p8ZZrXAdq4=";
+    hash = "sha256-SCObCYcZ+aDzWOkE5tzkKMkgAP/h7HDNyHXMFmYjiHQ=";
   };
 
   pythonRelaxDeps = [

pkgs/development/python-modules/llama-index-core/default.nix

@@ -46,7 +46,7 @@ in
 
 buildPythonPackage rec {
   pname = "llama-index-core";
-  version = "0.10.45";
+  version = "0.10.46";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -55,7 +55,7 @@ buildPythonPackage rec {
     owner = "run-llama";
     repo = "llama_index";
     rev = "refs/tags/v${version}";
-    hash = "sha256-mI2Cx3ZMW8cLiA7wIo/QwxZrlBVR9W/TMAD5l0TjBQo=";
+    hash = "sha256-k9SltX3QvrCYszyJqfpzhuI0JwpzsVTMkK3pIX/wyrg=";
   };
 
   sourceRoot = "${src.name}/${pname}";

pkgs/development/python-modules/llama-index-embeddings-huggingface/default.nix

@@ -10,7 +10,7 @@
 
 buildPythonPackage rec {
   pname = "llama-index-embeddings-huggingface";
-  version = "0.2.1";
+  version = "0.2.2";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -18,7 +18,7 @@ buildPythonPackage rec {
   src = fetchPypi {
     pname = "llama_index_embeddings_huggingface";
     inherit version;
-    hash = "sha256-usaKE61RMaBV2j7xdMynDhUjBCbux9Rxs3LoHoSJ2Ig=";
+    hash = "sha256-Q7KXh0DSkpGuTHVmki0rHHVD3JeeJoeUtXjhoq37Qxk=";
   };
 
   build-system = [ poetry-core ];

pkgs/development/python-modules/llama-index-graph-stores-neo4j/default.nix

@@ -10,7 +10,7 @@
 
 buildPythonPackage rec {
   pname = "llama-index-graph-stores-neo4j";
-  version = "0.2.4";
+  version = "0.2.5";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -18,7 +18,7 @@ buildPythonPackage rec {
   src = fetchPypi {
     pname = "llama_index_graph_stores_neo4j";
     inherit version;
-    hash = "sha256-mOB08Ui6MTnCQUBlc666PRDjoSf2cjPUf1WO34VMK9s=";
+    hash = "sha256-K+k3tsELhF6TXVK/voMRYpb0vVkGQpkzYnB9syCLmoY=";
   };
 
   build-system = [ poetry-core ];

pkgs/development/python-modules/pycrdt-websocket/default.nix

@@ -19,7 +19,7 @@
 
 buildPythonPackage rec {
   pname = "pycrdt-websocket";
-  version = "0.13.4";
+  version = "0.13.5";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -28,7 +28,7 @@ buildPythonPackage rec {
     owner = "jupyter-server";
     repo = "pycrdt-websocket";
     rev = "refs/tags/v${version}";
-    hash = "sha256-nkm1ZQ6bYBRDDoREovhEthDZoHApYxzAnwVgDgpWW/s=";
+    hash = "sha256-dzlmgxrdQ97+DO/vDtoX7PIOpngEE+FGUGq1vdVmhNw=";
   };
 
   build-system = [ hatchling ];

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

@@ -12,14 +12,14 @@
 
 buildPythonPackage rec {
   pname = "pyvex";
-  version = "9.2.106";
+  version = "9.2.107";
   pyproject = true;
 
   disabled = pythonOlder "3.11";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-rFdltQQOZN8qoG5m8Uvzi+zSD2vsq2Cb9Xpt2r5t678=";
+    hash = "sha256-e8DZgHCVUcAEgo9IR7Ut/v580//oeH9l1MwGSe/RThw=";
   };
 
   build-system = [ setuptools ];
@@ -43,7 +43,7 @@ buildPythonPackage rec {
   preBuild = ''
     export CC=${stdenv.cc.targetPrefix}cc
     substituteInPlace pyvex_c/Makefile \
-      --replace 'AR=ar' 'AR=${stdenv.cc.targetPrefix}ar'
+      --replace-fail 'AR=ar' 'AR=${stdenv.cc.targetPrefix}ar'
   '';
 
   # No tests are available on PyPI, GitHub release has tests

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

@@ -19,7 +19,7 @@
 
 buildPythonPackage rec {
   pname = "rapidfuzz";
-  version = "3.9.2";
+  version = "3.9.3";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -28,7 +28,7 @@ buildPythonPackage rec {
     owner = "maxbachmann";
     repo = "RapidFuzz";
     rev = "refs/tags/v${version}";
-    hash = "sha256-mPfS/p/Gwc/aobTZMJqbUkpEq60PC7DSiAXBanlNt+8=";
+    hash = "sha256-G1WveLVoeWkaKrHRFgCt8HVBnBYNdCb7/JVCm0L4dv8=";
   };
 
   postPatch = ''

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

@@ -1,18 +1,21 @@
 {
   lib,
   buildPythonPackage,
-  fetchFromGitHub,
-  pytestCheckHook,
   pythonOlder,
-
+  fetchFromGitHub,
-  dask,
+  # build-system
-  netcdf4,
+  setuptools,
+  # dependencies
   numpy,
   packaging,
   pyproj,
   rasterio,
-  setuptools,
   xarray,
+  # tests
+  dask,
+  netcdf4,
+  pytestCheckHook,
+  stdenv,
 }:
 
 buildPythonPackage rec {
@@ -24,13 +27,13 @@ buildPythonPackage rec {
   src = fetchFromGitHub {
     owner = "corteva";
     repo = "rioxarray";
-    rev = version;
+    rev = "refs/tags/${version}";
     hash = "sha256-bumFZQktgUqo2lyoLtDXkh6Vv5oS/wobqYpvNYy7La0=";
   };
 
   build-system = [ setuptools ];
 
-  propagatedBuildInputs = [
+  dependencies = [
     numpy
     packaging
     pyproj
@@ -44,13 +47,20 @@ buildPythonPackage rec {
     pytestCheckHook
   ];
 
-  disabledTests = [ "test_clip_geojson__no_drop" ];
+  disabledTests =
+    [ "test_clip_geojson__no_drop" ]
+    ++ lib.optionals (stdenv.hostPlatform.system == "aarch64-linux") [
+      # numerical errors
+      "test_clip_geojson"
+      "test_open_rasterio_mask_chunk_clip"
+    ];
 
   pythonImportsCheck = [ "rioxarray" ];
 
   meta = {
     description = "geospatial xarray extension powered by rasterio";
     homepage = "https://corteva.github.io/rioxarray/";
+    changelog = "https://github.com/corteva/rioxarray/releases/tag/${version}";
     license = lib.licenses.asl20;
     maintainers = lib.teams.geospatial.members;
   };

pkgs/development/python-modules/rpy2/default.nix

@@ -5,6 +5,7 @@
   fetchPypi,
   isPyPy,
   R,
+  libdeflate,
   rWrapper,
   rPackages,
   pcre,
@@ -53,6 +54,7 @@ buildPythonPackage rec {
       bzip2
       zlib
       icu
+      libdeflate
     ]
     ++ (with rPackages; [
       # packages expected by the test framework
@@ -87,6 +89,13 @@ buildPythonPackage rec {
 
   doCheck = !stdenv.isDarwin;
 
+  # https://github.com/rpy2/rpy2/issues/1111
+  disabledTests = [
+    "test_parse_incomplete_error"
+    "test_parse_error"
+    "test_parse_error_when_evaluting"
+  ];
+
   nativeCheckInputs = [ pytestCheckHook ];
 
   meta = {

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

@@ -2,14 +2,19 @@
   buildPythonPackage,
   fetchFromGitLab,
   lib,
+  nix-update-script,
   pytestCheckHook,
   python-dateutil,
   pythonAtLeast,
   pythonOlder,
 }:
-buildPythonPackage rec {
+let
-  pname = "vcard";
   version = "0.15.4";
+in
+buildPythonPackage {
+  inherit version;
+
+  pname = "vcard";
   format = "setuptools";
 
   disabled = pythonOlder "3.8" || pythonAtLeast "3.12";
@@ -27,6 +32,8 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "vcard" ];
 
+  passthru.updateScript = nix-update-script { };
+
   meta = {
     homepage = "https://gitlab.com/engmark/vcard";
     description = "vCard validator, class and utility functions";

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

@@ -4,14 +4,14 @@
 # Rscript generate-r-packages.R bioc-annotation >new && mv new bioc-annotation-packages.nix
 
 { self, derive }:
-let derive2 = derive { biocVersion = "3.18"; };
+let derive2 = derive { biocVersion = "3.19"; };
 in with self; {
   AHCytoBands = derive2 { name="AHCytoBands"; version="0.99.1"; sha256="0svxxhj3mh5gqik45ikcxnlhnma8n1c0rv8pycj2034cb9ms1dbv"; depends=[]; };
-  AHEnsDbs = derive2 { name="AHEnsDbs"; version="1.1.11"; sha256="1mh8aji48a6fad6bd1333qmc3dw7b5hf4v7xw0zhmfbnld64gz0s"; depends=[AnnotationHubData ensembldb]; };
+  AHEnsDbs = derive2 { name="AHEnsDbs"; version="1.5.1"; sha256="02gvrlfld6y03gcw7931fplm220dhnhh12xljb0xm6f3inl0vwa6"; depends=[AnnotationHubData ensembldb]; };
-  AHLRBaseDbs = derive2 { name="AHLRBaseDbs"; version="1.7.0"; sha256="1nbgqv1c3nyhlniqvqdc5cf8kyys323z1ia5jw54hxwi1jdyclfg"; depends=[AnnotationHub]; };
+  AHLRBaseDbs = derive2 { name="AHLRBaseDbs"; version="1.8.0"; sha256="038i0338zyqzkvmhxcdiykb0rwa3bzi0vv18j643b1a64bsnvcxi"; depends=[AnnotationHub]; };
-  AHMeSHDbs = derive2 { name="AHMeSHDbs"; version="1.7.0"; sha256="0hxik2xzvbgv6a936mvax5kyv65drr36r9rf7rlv124jinlbxw82"; depends=[AnnotationHub]; };
+  AHMeSHDbs = derive2 { name="AHMeSHDbs"; version="1.8.0"; sha256="09acd6xipzillw9z68nqqxjxa0hbshclv504na7l2dkhpppx6934"; depends=[AnnotationHub]; };
   AHPathbankDbs = derive2 { name="AHPathbankDbs"; version="0.99.5"; sha256="10wcrglm521xcrfbzc39dkbjvg1pkz0zq70vgnh68akiwmdirp89"; depends=[AnnotationHub]; };
-  AHPubMedDbs = derive2 { name="AHPubMedDbs"; version="1.7.0"; sha256="0a14xjhh95pwnyy4c1vij6p63pmgry8fffx4zbirczzzrxsc9cvp"; depends=[AnnotationHub]; };
+  AHPubMedDbs = derive2 { name="AHPubMedDbs"; version="1.8.0"; sha256="1p9jxs8ci4yv7yi4n86gpg49jigdmw0nrfnm8ls0jxwm0371vm7l"; depends=[AnnotationHub]; };
   AHWikipathwaysDbs = derive2 { name="AHWikipathwaysDbs"; version="0.99.4"; sha256="0vz3p9sx36bwzl9rq0ffh7klbq13pv2yhgjq1cjk7ll8z226c0q4"; depends=[AnnotationHub]; };
   AlphaMissense_v2023_hg19 = derive2 { name="AlphaMissense.v2023.hg19"; version="3.18.2"; sha256="0622yzywf3655rsh1ckmfvx0crm715a227bg5zz5znz7zfnlsl8y"; depends=[AnnotationHub GenomicScores]; };
   AlphaMissense_v2023_hg38 = derive2 { name="AlphaMissense.v2023.hg38"; version="3.18.2"; sha256="080c0282hcls96pd9mjljv2y1y6sy6nhqzlqwl5a2knq1aql4mna"; depends=[AnnotationHub GenomicScores]; };
@@ -133,6 +133,7 @@ in with self; {
   ChemmineDrugs = derive2 { name="ChemmineDrugs"; version="1.0.2"; sha256="0l47ac6lkycmghra2cbcdcxcv47ari8xg6lxpzilvkf4n6ld6064"; depends=[BiocGenerics ChemmineR RSQLite]; };
   DO_db = derive2 { name="DO.db"; version="2.9"; sha256="10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"; depends=[AnnotationDbi]; };
   ENCODExplorerData = derive2 { name="ENCODExplorerData"; version="0.99.5"; sha256="00gfm5l8pxrfs4cw4jlw6n0cz5s31isg69k833n89800v26w3kvh"; depends=[data_table jsonlite RCurl]; };
+  EPICv2manifest = derive2 { name="EPICv2manifest"; version="0.99.7"; sha256="1rskd8zhdxvvf119ngsmr6bzrmabhy5zqdh1w5azcyf4c39svp6k"; depends=[AnnotationHub]; };
   EnsDb_Hsapiens_v75 = derive2 { name="EnsDb.Hsapiens.v75"; version="2.99.0"; sha256="0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"; depends=[ensembldb]; };
   EnsDb_Hsapiens_v79 = derive2 { name="EnsDb.Hsapiens.v79"; version="2.99.0"; sha256="0k94iml0417m3k086d0bzd83fndyb2kn7pimsfzcdmafgy6sxwgg"; depends=[ensembldb]; };
   EnsDb_Hsapiens_v86 = derive2 { name="EnsDb.Hsapiens.v86"; version="2.99.0"; sha256="1gp7xrzddpvmh2vrcp571wyy00skxgxfl39ksj4h0hm1qay0fb2m"; depends=[ensembldb]; };
@@ -151,9 +152,9 @@ in with self; {
   FDb_UCSC_snp137common_hg19 = derive2 { name="FDb.UCSC.snp137common.hg19"; version="1.0.0"; sha256="1q1r7rk29q0zlzxz6fvfy1kjfli6wxzvhvhhfnf3z4ksy5332q63"; depends=[AnnotationDbi GenomicFeatures]; };
   FDb_UCSC_tRNAs = derive2 { name="FDb.UCSC.tRNAs"; version="1.0.1"; sha256="1dymdalx9fzrplxyc0fd9faa4r5jimi7zyry9k65lyz1pabpkwqz"; depends=[AnnotationDbi GenomicFeatures]; };
   GGHumanMethCancerPanelv1_db = derive2 { name="GGHumanMethCancerPanelv1.db"; version="1.4.1"; sha256="0ag1pkbh4mx4aplfrrz1q4f4cl05mczq9pcsfkd1071qk51dcwvx"; depends=[AnnotationDbi AnnotationForge org_Hs_eg_db]; };
-  GO_db = derive2 { name="GO.db"; version="3.18.0"; sha256="0znqa724jvrw2xx696n48lx83kzhivfr7fc9awzgm7nigwg3907m"; depends=[AnnotationDbi]; };
+  GO_db = derive2 { name="GO.db"; version="3.19.1"; sha256="199vk4y069yik7fn25pp73nkhs1vaw9km9rcmm1cirncwm2n0vhg"; depends=[AnnotationDbi]; };
   GeneSummary = derive2 { name="GeneSummary"; version="0.99.6"; sha256="0h6afrjb00afrcw6mwslxp7cmwfzp4qfxh0aa4f41kfjd3cymmp5"; depends=[]; };
-  GenomeInfoDbData = derive2 { name="GenomeInfoDbData"; version="1.2.11"; sha256="1hkvcrp4a2g3yl1h4k5zzj5fhp3d9a1amyn19zr62q9fhj3y47ri"; depends=[]; };
+  GenomeInfoDbData = derive2 { name="GenomeInfoDbData"; version="1.2.12"; sha256="0md3jl5bz4d2wkvf4yra7rydf5dgykrijrdqwwxc7f77l30nsmgp"; depends=[]; };
   GenomicState = derive2 { name="GenomicState"; version="0.99.15"; sha256="1r7z3n6wyrd2cclj5b7sg15wpmjdh9k5b1hjlw7jjx8j384l7l1h"; depends=[AnnotationDbi AnnotationHub bumphunter derfinder GenomeInfoDb GenomicFeatures IRanges org_Hs_eg_db rtracklayer]; };
   HDO_db = derive2 { name="HDO.db"; version="0.99.1"; sha256="14ngyxailmxrbxqqi9m7mchqcvchmbg7zm34i8a927b20s6z4z61"; depends=[AnnotationDbi]; };
   HPO_db = derive2 { name="HPO.db"; version="0.99.2"; sha256="1brzrnafvyh76h8a663gk5lprhixxpi9xi65vwgxwf7jh6yw0was"; depends=[AnnotationDbi AnnotationHub BiocFileCache DBI]; };
@@ -175,9 +176,11 @@ in with self; {
   IlluminaHumanMethylationEPICanno_ilm10b3_hg19 = derive2 { name="IlluminaHumanMethylationEPICanno.ilm10b3.hg19"; version="0.6.0"; sha256="1rdkvbpbz8a8bd9ipycfmgn8a3x519abhwywka21ii9ziv3s6ah6"; depends=[minfi]; };
   IlluminaHumanMethylationEPICanno_ilm10b4_hg19 = derive2 { name="IlluminaHumanMethylationEPICanno.ilm10b4.hg19"; version="0.6.0"; sha256="0687b4k8hwfc18qgdd9ypv1skp37jd204fszba0gmrv3dc92i09c"; depends=[minfi]; };
   IlluminaHumanMethylationEPICmanifest = derive2 { name="IlluminaHumanMethylationEPICmanifest"; version="0.3.0"; sha256="0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"; depends=[minfi]; };
+  IlluminaHumanMethylationEPICv2anno_20a1_hg38 = derive2 { name="IlluminaHumanMethylationEPICv2anno.20a1.hg38"; version="1.0.0"; sha256="0vp4m3a7qal4d8qc9xaj7z3x484i33ix4c67qlbw0kskdir7rq5a"; depends=[minfi]; };
+  IlluminaHumanMethylationEPICv2manifest = derive2 { name="IlluminaHumanMethylationEPICv2manifest"; version="1.0.0"; sha256="1z4b15x8cai27cqhl2lhl02nx0lv8q5c1774vdvvdajx2hivn77l"; depends=[minfi]; };
   JASPAR2018 = derive2 { name="JASPAR2018"; version="1.1.1"; sha256="1iq5b51ryah2ccdx16yyigfa2jiapcpm94l6vgvd4v7b94jjp8l7"; depends=[]; };
   JASPAR2020 = derive2 { name="JASPAR2020"; version="0.99.10"; sha256="0nrp63z7q2ivv5h87f7inpp2qll2dfgj4227l4rbnzii38a2vfdr"; depends=[]; };
-  JASPAR2022 = derive2 { name="JASPAR2022"; version="0.99.7"; sha256="0sayaxsazcsbwdkisjfmkc01piahkqi9xks3rfj60cf56wrjlbpa"; depends=[BiocFileCache]; };
+  JASPAR2022 = derive2 { name="JASPAR2022"; version="0.99.8"; sha256="0di84aydk5brgdz1qh30fh1jizwd8w1rsz74mw4apv5s8ayryl48"; depends=[BiocFileCache]; };
   JASPAR2024 = derive2 { name="JASPAR2024"; version="0.99.6"; sha256="1l169kwymylqz67fz182fgq22nvg3cg12p2r8drgibs2d72khcpf"; depends=[BiocFileCache]; };
   JazaeriMetaData_db = derive2 { name="JazaeriMetaData.db"; version="3.2.3"; sha256="04lvcmm4ybxkfwgbiwcnpyj6kpbd0gd7jz6ijlbbvv6zdgdmvykb"; depends=[AnnotationDbi org_Hs_eg_db]; };
   LAPOINTE_db = derive2 { name="LAPOINTE.db"; version="3.2.3"; sha256="0960gy5p4ybs5zs6251cgc3nk5a9gsh1nh23gkbkr3gc8jddinfm"; depends=[AnnotationDbi org_Hs_eg_db]; };
@@ -198,7 +201,8 @@ in with self; {
   MafDb_gnomAD_r2_1_hs37d5 = derive2 { name="MafDb.gnomAD.r2.1.hs37d5"; version="3.10.0"; sha256="153dy3lx0islfdkmyik7lxp1w2yzb0bqmia673hlwi4rmvns112h"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; };
   MafDb_gnomADex_r2_1_GRCh38 = derive2 { name="MafDb.gnomADex.r2.1.GRCh38"; version="3.10.0"; sha256="1v0sdjmn9z8gqn4yj4v04zycj3ngr32r04zqmkp6y41hcgdr8lxw"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; };
   MafDb_gnomADex_r2_1_hs37d5 = derive2 { name="MafDb.gnomADex.r2.1.hs37d5"; version="3.10.0"; sha256="0y42ncmilijdxsgqsmskz7gff3il3fdf2kpflknmz1z9kybzaday"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; };
-  MafH5_gnomAD_v3_1_2_GRCh38 = derive2 { name="MafH5.gnomAD.v3.1.2.GRCh38"; version="3.15.0"; sha256="18hzw7f41ii16qpm3ch516b773900l1m1id5z6a763m01fg0mhiq"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores HDF5Array IRanges rhdf5 S4Vectors]; };
+  MafH5_gnomAD_v3_1_2_GRCh38 = derive2 { name="MafH5.gnomAD.v3.1.2.GRCh38"; version="3.15.1"; sha256="1q9hlva814sjfz8vm9bzw7xzppbcfy5qq7nnz9w742yr59cjb6mp"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores HDF5Array IRanges rhdf5 S4Vectors]; };
+  MafH5_gnomAD_v4_0_GRCh38 = derive2 { name="MafH5.gnomAD.v4.0.GRCh38"; version="3.19.0"; sha256="1hb905rvxvzh2nap52agcm488yarn2j99d23yxa133jw9d8a9zqk"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores HDF5Array IRanges rhdf5 S4Vectors]; };
   MmAgilentDesign026655_db = derive2 { name="MmAgilentDesign026655.db"; version="3.2.3"; sha256="00d0yjcb5id7zacx4bzdwy4q6f4qvnnx8ph4d4xz1fmcbspz2qiz"; depends=[AnnotationDbi org_Mm_eg_db]; };
   MoExExonProbesetLocation = derive2 { name="MoExExonProbesetLocation"; version="1.15.0"; sha256="0bvj3bji4bwwmxjz4b57n1aqypdibdmry30rfwmlxss1hav96sl7"; depends=[AnnotationDbi]; };
   Mu15v1_db = derive2 { name="Mu15v1.db"; version="3.2.3"; sha256="0qchqkbx6ybijab8qhflxj33kwksfll1d3d3917vydjac9fzw1lz"; depends=[AnnotationDbi org_Mm_eg_db]; };
@@ -206,9 +210,9 @@ in with self; {
   Mus_musculus = derive2 { name="Mus.musculus"; version="1.3.1"; sha256="143zdf83gbfqhy8jm9df7gzhw5q3a64jrjrxrzjf0zd76j8s8j6y"; depends=[AnnotationDbi GenomicFeatures GO_db org_Mm_eg_db OrganismDbi TxDb_Mmusculus_UCSC_mm10_knownGene]; };
   Norway981_db = derive2 { name="Norway981.db"; version="3.2.3"; sha256="04ngc2hilqi9m7933mnm7jcvkxlz68vqqh5b628db575vcxql9b9"; depends=[AnnotationDbi org_Hs_eg_db]; };
   OperonHumanV3_db = derive2 { name="OperonHumanV3.db"; version="3.2.3"; sha256="082gff88cwk2p50q8g9bixggacaclgqcvk6w5dc11h9fkgvd160i"; depends=[AnnotationDbi org_Hs_eg_db]; };
-  Orthology_eg_db = derive2 { name="Orthology.eg.db"; version="3.18.0"; sha256="11v6fm2403m32q9k70n5p839a4awks7avcfaa8rvrm59v0ab5czj"; depends=[AnnotationDbi]; };
+  Orthology_eg_db = derive2 { name="Orthology.eg.db"; version="3.19.1"; sha256="1zg50j46kka5y0mfgqw3vh5xibd3yk7ay051dnci6mgd7v9gns5w"; depends=[AnnotationDbi]; };
   PANTHER_db = derive2 { name="PANTHER.db"; version="1.0.12"; sha256="05ydg87cix86hp6hkkqmcniy69q5zyb3xyc3q7bykp26bvrgjvqq"; depends=[AnnotationDbi AnnotationHub BiocFileCache RSQLite]; };
-  PFAM_db = derive2 { name="PFAM.db"; version="3.18.0"; sha256="15m7qfvz53jkdmx90y7rvy62myr4y3hdy414yqi0w3ch32vy78nr"; depends=[AnnotationDbi]; };
+  PFAM_db = derive2 { name="PFAM.db"; version="3.19.1"; sha256="0jjba22p8x4cfnihsa3gah3amdr4yrqpfm0zfr990jcjkvf94wvk"; depends=[AnnotationDbi]; };
   POCRCannotation_db = derive2 { name="POCRCannotation.db"; version="3.2.3"; sha256="0ybvs4hrxpivdkhm0fxpib11vlxqqdk8prlyj78vj5qzyb3iy89d"; depends=[AnnotationDbi org_Hs_eg_db]; };
   PartheenMetaData_db = derive2 { name="PartheenMetaData.db"; version="3.2.3"; sha256="0d37c5b7s3fgkkvg7sj7gl9ksrjk5pyyv54vkys8w3qwgsm8yrdz"; depends=[AnnotationDbi org_Hs_eg_db]; };
   PolyPhen_Hsapiens_dbSNP131 = derive2 { name="PolyPhen.Hsapiens.dbSNP131"; version="1.0.2"; sha256="1kikygkli41sn3rqihz0924prmqg2264ifj29vmg1a7qccm0kf7c"; depends=[AnnotationDbi RSQLite VariantAnnotation]; };
@@ -227,7 +231,7 @@ in with self; {
   SNPlocs_Hsapiens_dbSNP150_GRCh38 = derive2 { name="SNPlocs.Hsapiens.dbSNP150.GRCh38"; version="0.99.20"; sha256="0jkwwgxxpm9ry8kizq8hs70sky41pks1ag40y5aqq91yjbpqlckj"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
   SNPlocs_Hsapiens_dbSNP155_GRCh37 = derive2 { name="SNPlocs.Hsapiens.dbSNP155.GRCh37"; version="0.99.24"; sha256="0am2r8hn5ybxlvlw7c0i91n5xii0km3iy7d9a0wc9v1ykvk6qmgz"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
   SNPlocs_Hsapiens_dbSNP155_GRCh38 = derive2 { name="SNPlocs.Hsapiens.dbSNP155.GRCh38"; version="0.99.24"; sha256="1yzywcyk1yngjys9pyykilzw0w4nfxdmwz04w3b17chsbxvckl5s"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
-  SomaScan_db = derive2 { name="SomaScan.db"; version="0.99.7"; sha256="012v0ph9mkdl13111qamzkdfpdklbq94ry6scjhbhjqm4igmz79r"; depends=[AnnotationDbi DBI org_Hs_eg_db]; };
+  SomaScan_db = derive2 { name="SomaScan.db"; version="0.99.10"; sha256="1qk4frv4hn3pfwbhqd92r8d59ksvgzs9399w4ca7knmij6zzl73p"; depends=[AnnotationDbi DBI org_Hs_eg_db]; };
   TxDb_Athaliana_BioMart_plantsmart22 = derive2 { name="TxDb.Athaliana.BioMart.plantsmart22"; version="3.0.1"; sha256="0j2zr4cddad7z1lxx9m9kfgyy7jajjnblpk9j8igd39ia3ixrpzc"; depends=[AnnotationDbi GenomicFeatures]; };
   TxDb_Athaliana_BioMart_plantsmart25 = derive2 { name="TxDb.Athaliana.BioMart.plantsmart25"; version="3.1.3"; sha256="0a6v0l6p13zmiysi3k8dxzdlxng552qqj9rnlbdavdiidla0pvm3"; depends=[AnnotationDbi GenomicFeatures]; };
   TxDb_Athaliana_BioMart_plantsmart28 = derive2 { name="TxDb.Athaliana.BioMart.plantsmart28"; version="3.2.2"; sha256="1yjyvrbx55y024lqg3b2rlf8pngqw5xi3p83j5ipan05wf0aq6ir"; depends=[AnnotationDbi GenomicFeatures]; };
@@ -253,14 +257,14 @@ in with self; {
   TxDb_Hsapiens_UCSC_hg19_knownGene = derive2 { name="TxDb.Hsapiens.UCSC.hg19.knownGene"; version="3.2.2"; sha256="1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"; depends=[AnnotationDbi GenomicFeatures]; };
   TxDb_Hsapiens_UCSC_hg19_lincRNAsTranscripts = derive2 { name="TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts"; version="3.2.2"; sha256="0bmbp7kydvviczw8axgxq2wdlwq6fdas90jk9bg56avjq5syws2g"; depends=[AnnotationDbi GenomicFeatures]; };
   TxDb_Hsapiens_UCSC_hg38_knownGene = derive2 { name="TxDb.Hsapiens.UCSC.hg38.knownGene"; version="3.18.0"; sha256="0ak6acjll2djamakpn60ks47lfs2y0r8xwhjazj6fvch34xkc2d5"; depends=[AnnotationDbi GenomicFeatures]; };
-  TxDb_Hsapiens_UCSC_hg38_refGene = derive2 { name="TxDb.Hsapiens.UCSC.hg38.refGene"; version="3.18.0"; sha256="03wfafd03gni9wpavfwjzfjhx6z8hv4f4jnh4hkjbxqld32sg1kr"; depends=[AnnotationDbi GenomicFeatures]; };
+  TxDb_Hsapiens_UCSC_hg38_refGene = derive2 { name="TxDb.Hsapiens.UCSC.hg38.refGene"; version="3.19.0"; sha256="1ylqdh23767x20npbx0527r353h4kdhc2cz6s2xdadjm3ia8zynn"; depends=[AnnotationDbi GenomicFeatures]; };
   TxDb_Mmulatta_UCSC_rheMac10_refGene = derive2 { name="TxDb.Mmulatta.UCSC.rheMac10.refGene"; version="3.14.0"; sha256="12gxs6s57l22013g40b7hb09vxhmdri73cp9rgs2icb88p7sjlib"; depends=[AnnotationDbi GenomicFeatures]; };
   TxDb_Mmulatta_UCSC_rheMac3_refGene = derive2 { name="TxDb.Mmulatta.UCSC.rheMac3.refGene"; version="3.12.0"; sha256="1a0wbh4dajpgynmw2iwbvp836nklzlk0cfhqnwmqq9l4gzzh2w07"; depends=[AnnotationDbi GenomicFeatures]; };
   TxDb_Mmulatta_UCSC_rheMac8_refGene = derive2 { name="TxDb.Mmulatta.UCSC.rheMac8.refGene"; version="3.12.0"; sha256="1k7mq3p96wfd0694zw00hs4529zvv8nnfdwlsb94bn11qjhr1zrz"; depends=[AnnotationDbi GenomicFeatures]; };
   TxDb_Mmusculus_UCSC_mm10_ensGene = derive2 { name="TxDb.Mmusculus.UCSC.mm10.ensGene"; version="3.4.0"; sha256="0saxi1fdiwd38sfvy1rynd3v44rbp158jv6sjqcivvaqnd84zg9s"; depends=[AnnotationDbi GenomicFeatures]; };
   TxDb_Mmusculus_UCSC_mm10_knownGene = derive2 { name="TxDb.Mmusculus.UCSC.mm10.knownGene"; version="3.10.0"; sha256="0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"; depends=[AnnotationDbi GenomicFeatures]; };
   TxDb_Mmusculus_UCSC_mm39_knownGene = derive2 { name="TxDb.Mmusculus.UCSC.mm39.knownGene"; version="3.18.0"; sha256="061rfyddq15sz684jchvwxww1ipi94xljcgwbz4a92k8i9cnysva"; depends=[AnnotationDbi GenomicFeatures]; };
-  TxDb_Mmusculus_UCSC_mm39_refGene = derive2 { name="TxDb.Mmusculus.UCSC.mm39.refGene"; version="3.18.0"; sha256="0f7392c9zd5489jfsdxvwwmpnzscp70ayxv78gcg50m5mkgwaydv"; depends=[AnnotationDbi GenomicFeatures]; };
+  TxDb_Mmusculus_UCSC_mm39_refGene = derive2 { name="TxDb.Mmusculus.UCSC.mm39.refGene"; version="3.19.0"; sha256="1rhfr4s0lxz86vigrbyyx27q1gbg0g512ld0rkfv2vxwdbcl9hc0"; depends=[AnnotationDbi GenomicFeatures]; };
   TxDb_Mmusculus_UCSC_mm9_knownGene = derive2 { name="TxDb.Mmusculus.UCSC.mm9.knownGene"; version="3.2.2"; sha256="16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"; depends=[AnnotationDbi GenomicFeatures]; };
   TxDb_Ptroglodytes_UCSC_panTro4_refGene = derive2 { name="TxDb.Ptroglodytes.UCSC.panTro4.refGene"; version="3.12.0"; sha256="036g5zn9rzy8qivb1snhpancsz1z60i3r7z3g91bgla4jpgwwjv6"; depends=[AnnotationDbi GenomicFeatures]; };
   TxDb_Ptroglodytes_UCSC_panTro5_refGene = derive2 { name="TxDb.Ptroglodytes.UCSC.panTro5.refGene"; version="3.12.0"; sha256="0yypv9iqn4i36hnvcr2lsfgaabl8g2pm72ya4psvia261jr2i12i"; depends=[AnnotationDbi GenomicFeatures]; };
@@ -285,15 +289,16 @@ in with self; {
   agprobe = derive2 { name="agprobe"; version="2.18.0"; sha256="1vnawamcpz16na8nmlq2czfxcr325fwdnngxl65mmnbd0f4lmy3k"; depends=[AnnotationDbi]; };
   alternativeSplicingEvents_hg19 = derive2 { name="alternativeSplicingEvents.hg19"; version="1.1.0"; sha256="0q90nw3ds66zbyn3ch19lq1qimd1hz1s3jyyd6zi3v10p5s8bm0y"; depends=[AnnotationHub]; };
   alternativeSplicingEvents_hg38 = derive2 { name="alternativeSplicingEvents.hg38"; version="1.1.0"; sha256="18qabggvs9mcg8fwd6prdca8lfxn9r9i0493l667n8jl9vy2pbfc"; depends=[AnnotationHub]; };
-  anopheles_db0 = derive2 { name="anopheles.db0"; version="3.18.0"; sha256="197p9dc3rn8vri3frmsrq9r033g2dd0dvbdabgcm8ailyphwpmqq"; depends=[AnnotationDbi]; };
+  anopheles_db0 = derive2 { name="anopheles.db0"; version="3.19.1"; sha256="190yjnl86b6vm2xmdfm43hn5xy7jsf83rwd103v537y4qhxdy0yq"; depends=[AnnotationDbi]; };
-  arabidopsis_db0 = derive2 { name="arabidopsis.db0"; version="3.18.0"; sha256="1dv2vrzq6anf422jxa9vssvwc68m1x3cp9543liq3ajprz1alh35"; depends=[AnnotationDbi]; };
+  arabidopsis_db0 = derive2 { name="arabidopsis.db0"; version="3.19.1"; sha256="1fi4akbk7yc6drkdwp0dfaxdn5axg1c5qp9b445318zszdylxbd3"; depends=[AnnotationDbi]; };
   ath1121501_db = derive2 { name="ath1121501.db"; version="3.13.0"; sha256="0v4vapbns71dpv09857lyrnliq202i8yi4ar9z81wbpbc22lhf0d"; depends=[AnnotationDbi org_At_tair_db]; };
   ath1121501cdf = derive2 { name="ath1121501cdf"; version="2.18.0"; sha256="1naq8f8dwgbmndx178nm2pw6hjx5ljx0w1wb4dfjifnl4bs5rqcc"; depends=[AnnotationDbi]; };
+  ath1121501frmavecs = derive2 { name="ath1121501frmavecs"; version="1.0.0"; sha256="0y3ka95aafiyily188536azvfqrsr2mbljhc696d2wlkjczbxq5i"; depends=[]; };
   ath1121501probe = derive2 { name="ath1121501probe"; version="2.18.0"; sha256="0a2nd8zhp3ybis780l3rrmwcxskbl3a111g8w6m8qfwsw5vnlqg1"; depends=[AnnotationDbi]; };
   barley1cdf = derive2 { name="barley1cdf"; version="2.18.0"; sha256="0rbij5cqr2sz33y5waybv85nrcgf70iwj5gk13g0xn9p1l1zxyn2"; depends=[AnnotationDbi]; };
   barley1probe = derive2 { name="barley1probe"; version="2.18.0"; sha256="1kh5r748b4vkmvlfaclmrh07ypbrzgxn90liqfz1rwkabh6rfk71"; depends=[AnnotationDbi]; };
   bovine_db = derive2 { name="bovine.db"; version="3.13.0"; sha256="06692b1n0lzhg0biixipsnwx33w9y8wkc7pc5q1lkjfzbmd2inml"; depends=[AnnotationDbi org_Bt_eg_db]; };
-  bovine_db0 = derive2 { name="bovine.db0"; version="3.18.0"; sha256="1s95x4hrv6r1mlsls2yfwbw1mn0jpqg7ancfcwc22p9pi962jjf8"; depends=[AnnotationDbi]; };
+  bovine_db0 = derive2 { name="bovine.db0"; version="3.19.1"; sha256="1qyhzbr81r302xnzg76njwj3b88rrbk02qsxsrg7728qwpwd412v"; depends=[AnnotationDbi]; };
   bovinecdf = derive2 { name="bovinecdf"; version="2.18.0"; sha256="13mf0yy0dypkm5n2ghl04xm6ayb9bn9qijqhgynksghi7s2k34mb"; depends=[AnnotationDbi]; };
   bovineprobe = derive2 { name="bovineprobe"; version="2.18.0"; sha256="0i4afa5dksnir2nfrfh2cynjm59sm6vfaqa9wyag8cxg7c2nlm1i"; depends=[AnnotationDbi]; };
   bsubtiliscdf = derive2 { name="bsubtiliscdf"; version="2.18.0"; sha256="1rihrjim37b49rhqr4nxga8sp67qri9xqlqc141mhbngh6cw3iyl"; depends=[AnnotationDbi]; };
@@ -302,7 +307,7 @@ in with self; {
   cadd_v1_6_hg19 = derive2 { name="cadd.v1.6.hg19"; version="3.18.1"; sha256="1g8pk1bmq2p6a7r1skfs54a2b8106znasympyz3dq3vahm5ia0dq"; depends=[AnnotationHub GenomicScores]; };
   cadd_v1_6_hg38 = derive2 { name="cadd.v1.6.hg38"; version="3.18.1"; sha256="0088wv3a082ircmgpx23822bvjwqd5jdvilkgvhaypksbnbdkq68"; depends=[AnnotationHub GenomicScores]; };
   canine_db = derive2 { name="canine.db"; version="3.13.0"; sha256="1x1mlh0p6r2l5kclarqwgiw9y64xc8jhp6252hhpl9bpnn638n3s"; depends=[AnnotationDbi org_Cf_eg_db]; };
-  canine_db0 = derive2 { name="canine.db0"; version="3.18.0"; sha256="1s88nj0ysvb7dwvxwkshy9w1a8qvaq3bkxki974zhhh42ssdxm2q"; depends=[AnnotationDbi]; };
+  canine_db0 = derive2 { name="canine.db0"; version="3.19.1"; sha256="0qagfxza04zncjrd97b0mrqrd5jchifv1pxbzv3npdp0801yym2f"; depends=[AnnotationDbi]; };
   canine2_db = derive2 { name="canine2.db"; version="3.13.0"; sha256="1xzz0vivdypwl6kaq2ba02jkpxw0r9r98297ilksdh8m71f244si"; depends=[AnnotationDbi org_Cf_eg_db]; };
   canine2cdf = derive2 { name="canine2cdf"; version="2.18.0"; sha256="077cmmnhjdk0vxjzm1kqf3q5kgx6chwkm59dr4s5dy019rqb6sqr"; depends=[AnnotationDbi]; };
   canine2probe = derive2 { name="canine2probe"; version="2.18.0"; sha256="1l849a1dqy4kpcsxs0lvb48ag81i0f0ys0w4757rw4kp8ry59z4b"; depends=[AnnotationDbi]; };
@@ -312,10 +317,10 @@ in with self; {
   celeganscdf = derive2 { name="celeganscdf"; version="2.18.0"; sha256="0a6w0a48azg0i21j3aqb7fnxck3ff9w3gsi89bnlfh0zx6pknx7p"; depends=[AnnotationDbi]; };
   celegansprobe = derive2 { name="celegansprobe"; version="2.18.0"; sha256="05k7si3f8pzkyb8jv0r2vkavbrqxsn4nawl92gcphfsylrwcddqb"; depends=[AnnotationDbi]; };
   chicken_db = derive2 { name="chicken.db"; version="3.13.0"; sha256="0szb7sgassw10kzm8iz8h3fdbxm6v0kz95yb3a9icj2chi5d1m2i"; depends=[AnnotationDbi org_Gg_eg_db]; };
-  chicken_db0 = derive2 { name="chicken.db0"; version="3.18.0"; sha256="1b2ypbjxmm6dg5dagc9cka9p1c9n6b9rjlw1ivcakbnpx7ipwkl2"; depends=[AnnotationDbi]; };
+  chicken_db0 = derive2 { name="chicken.db0"; version="3.19.1"; sha256="1qba9s4fmh17b3g6z6jfb2cdby0mhc80xjj0r9a2wvd8qlm5gyw1"; depends=[AnnotationDbi]; };
   chickencdf = derive2 { name="chickencdf"; version="2.18.0"; sha256="09hhim5s9xj7n2b5rhn1svf5qly2mn0rr2v2ls25hfzyrqcbxlz1"; depends=[AnnotationDbi]; };
   chickenprobe = derive2 { name="chickenprobe"; version="2.18.0"; sha256="1fdsiwfyg7fwslrr7xs3gny7sw24bzg5k1fvlyzb1477sgj0pid3"; depends=[AnnotationDbi]; };
-  chimp_db0 = derive2 { name="chimp.db0"; version="3.18.0"; sha256="1y5yi53hld1q3zi3z25zg68mb76nbh09yikn4x14q5rk2imjg9gm"; depends=[AnnotationDbi]; };
+  chimp_db0 = derive2 { name="chimp.db0"; version="3.19.1"; sha256="1vsb2235k00jxmff9i7lbc3kmiqkz5xvm21bzhryql7kgy5i64yf"; depends=[AnnotationDbi]; };
   chromhmmData = derive2 { name="chromhmmData"; version="0.99.2"; sha256="13g6x7lzmkz9qv7yr6ps8gsgilgr048lc7y0y7xsfa9ws3n08fzj"; depends=[]; };
   citruscdf = derive2 { name="citruscdf"; version="2.18.0"; sha256="1326mj1xf3k4v5iyyn46whx24qfng0x3cv6rvckdr1ycc1v887dn"; depends=[AnnotationDbi]; };
   citrusprobe = derive2 { name="citrusprobe"; version="2.18.0"; sha256="0bf1wic136cxwgs4j13wsyqasnyvr0jw1hzg6qizndmy7g8hrb87"; depends=[AnnotationDbi]; };
@@ -339,15 +344,15 @@ in with self; {
   ecoli2_db = derive2 { name="ecoli2.db"; version="3.13.0"; sha256="1i2arr26hch7lmx2bixzy4l0zaa0gynah4dfwa98cvb24ahqqj9f"; depends=[AnnotationDbi org_EcK12_eg_db]; };
   ecoli2cdf = derive2 { name="ecoli2cdf"; version="2.18.0"; sha256="1rkxrwadq9kg9685z9pg6rgc4bblkx5p3c6snsl4gv2k188dva9r"; depends=[AnnotationDbi]; };
   ecoli2probe = derive2 { name="ecoli2probe"; version="2.18.0"; sha256="11q4ka0ncjapahic49xdl9919vm9frrwlqgj101krgkg262lfm8n"; depends=[AnnotationDbi]; };
-  ecoliK12_db0 = derive2 { name="ecoliK12.db0"; version="3.18.0"; sha256="1x0jpi1j5nxvzirrjafg9w71glsshdbw98zrw1zzbp7gxrwxilpn"; depends=[AnnotationDbi]; };
+  ecoliK12_db0 = derive2 { name="ecoliK12.db0"; version="3.19.1"; sha256="0fi0cxl5hj5mx2z2r0j86qf3bfx1dz8abn86maim9b1l89whvqwd"; depends=[AnnotationDbi]; };
-  ecoliSakai_db0 = derive2 { name="ecoliSakai.db0"; version="3.18.0"; sha256="0khajmjawf0gs7bi0m4pnzl1m7p76wdybv9h3fd3p1qjv5dyifwz"; depends=[AnnotationDbi]; };
+  ecoliSakai_db0 = derive2 { name="ecoliSakai.db0"; version="3.19.1"; sha256="1kqpmmddqyfjx2y2kbp53mv1vazbjhpwl3crpx2iq0q1b2ynb63f"; depends=[AnnotationDbi]; };
   ecoliasv2cdf = derive2 { name="ecoliasv2cdf"; version="2.18.0"; sha256="16i6has9qgmzakcy24racc1h9j331wndv5c87qp5r1zrai61zyav"; depends=[AnnotationDbi]; };
   ecoliasv2probe = derive2 { name="ecoliasv2probe"; version="2.18.0"; sha256="1hfrnal170cdigc2fmnynb75jjsiq77p4x6ws9gah558hvx87nk3"; depends=[AnnotationDbi]; };
   ecolicdf = derive2 { name="ecolicdf"; version="2.18.0"; sha256="18g5prjykn356k35m131ifn128k5mhij2x26balqav0azigzjqsn"; depends=[AnnotationDbi]; };
   ecoliprobe = derive2 { name="ecoliprobe"; version="2.18.0"; sha256="17g5zxfzsak7a0w51irc0w1w2i5ngdkx9db6rhv1fyp8mfjgaphd"; depends=[AnnotationDbi]; };
   excluderanges = derive2 { name="excluderanges"; version="0.99.8"; sha256="19pdwlhqlz420yss371bsqhkx8c7wxr0sv4wsycnc0mlplwq4bsf"; depends=[GenomicRanges]; };
   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="3.18.0"; sha256="1pksr9jwdd5izf2yc7fb935pic84nvlxa458h0da9lryglc0w5rg"; depends=[AnnotationDbi]; };
+  fly_db0 = derive2 { name="fly.db0"; version="3.19.1"; sha256="0726vpqc092mq9j23ghvy5yjg3v6fm26fynlad5k4wshyfw1szxk"; depends=[AnnotationDbi]; };
   geneplast_data = derive2 { name="geneplast.data"; version="0.99.9"; sha256="1i31kx4kckfg965s9l3pilvmg847av3rpa05aql43259ccyng4hi"; depends=[ape BiocFileCache dplyr geneplast igraph purrr readr tibble tidyr treeio]; };
   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=[]; };
@@ -480,7 +485,7 @@ in with self; {
   hugene20sttranscriptcluster_db = derive2 { name="hugene20sttranscriptcluster.db"; version="8.8.0"; sha256="00fjhz7gac0rssn3kplag68vfx7gimjrm4mc7z516bs013rppgsz"; depends=[AnnotationDbi org_Hs_eg_db]; };
   hugene21stprobeset_db = derive2 { name="hugene21stprobeset.db"; version="8.8.0"; sha256="0s4zl9lv5w3fkb9axhz9siliz73brwarw8a7cam1p9b2kmdrdqs0"; depends=[AnnotationDbi org_Hs_eg_db]; };
   hugene21sttranscriptcluster_db = derive2 { name="hugene21sttranscriptcluster.db"; version="8.8.0"; sha256="1g7yfva96vhkdvcvsjwsj7sy8q6kczd5rmcwrwjc73v9qi4ywgal"; depends=[AnnotationDbi org_Hs_eg_db]; };
-  human_db0 = derive2 { name="human.db0"; version="3.18.0"; sha256="0il4v5r03976qvfd4gq8wdgrp060c1byc3v6wx6yxcxk1wvp81zf"; depends=[AnnotationDbi]; };
+  human_db0 = derive2 { name="human.db0"; version="3.19.1"; sha256="006q28yvh8l5h7pa9qdhcvjd9049bzg1v5nnvphivwn186hv47ww"; depends=[AnnotationDbi]; };
   human1mduov3bCrlmm = derive2 { name="human1mduov3bCrlmm"; version="1.0.4"; sha256="1p7qpzk6svafgdafljhh4k0z7pcs78qmwwfd80r0a1yhkssmp0v9"; depends=[]; };
   human1mv1cCrlmm = derive2 { name="human1mv1cCrlmm"; version="1.0.3"; sha256="1qlph3qrjv52ddzlj8pwa93zzh70x4mbdrdr7q9pan427lpck9gx"; depends=[]; };
   human370quadv3cCrlmm = derive2 { name="human370quadv3cCrlmm"; version="1.0.3"; sha256="1chjx9vsmqz2whslw1l7jn7nfn7zx6pcjfmqqm9mh81i74rzrdik"; depends=[]; };
@@ -518,7 +523,7 @@ in with self; {
   m20kcod_db = derive2 { name="m20kcod.db"; version="3.4.0"; sha256="1p2sm5j4b50iqzwcb984qrh74c3hf6yml7b8mvxlhhhvxz4iy1np"; depends=[AnnotationDbi org_Mm_eg_db]; };
   maizecdf = derive2 { name="maizecdf"; version="2.18.0"; sha256="0yfz5gjhsq4wz6j63s1b1hxjz03gsmrlfs2cdc8smq6azp3zdid4"; depends=[AnnotationDbi]; };
   maizeprobe = derive2 { name="maizeprobe"; version="2.18.0"; sha256="01h5dv5i0zaqlphkii9ipxy9wswv1srgprrpr5vmi01c9d98qsk0"; depends=[AnnotationDbi]; };
-  malaria_db0 = derive2 { name="malaria.db0"; version="3.18.0"; sha256="1zp2j7vbws2a56xkngfl248xskpj5r58q7sxx6xjipdjk8n13vf3"; depends=[AnnotationDbi]; };
+  malaria_db0 = derive2 { name="malaria.db0"; version="3.19.1"; sha256="0gyx0s801pzhcaa0hqbcj69hjgz63b6d764wiflpdg90c79db2is"; depends=[AnnotationDbi]; };
   medicagocdf = derive2 { name="medicagocdf"; version="2.18.0"; sha256="1clz679cc887x98c6jk93cphijkbg5r2nd9idrj5901yvh6p9n5q"; depends=[AnnotationDbi]; };
   medicagoprobe = derive2 { name="medicagoprobe"; version="2.18.0"; sha256="0w6j1pfkvb3npc8srpjifq2ywnqxhc9q090jqzmkx22x36cw9cl5"; depends=[AnnotationDbi]; };
   metaboliteIDmapping = derive2 { name="metaboliteIDmapping"; version="1.0.0"; sha256="0nflpvla3wn8i2gaja5wwjkxk0jich95f5ws3rnhh2a6rx3xi3ql"; depends=[AnnotationHub]; };
@@ -573,7 +578,7 @@ in with self; {
   mogene20sttranscriptcluster_db = derive2 { name="mogene20sttranscriptcluster.db"; version="8.8.0"; sha256="1bpzpba9aifc7w6qbrh6rnc636k6z1r9gz03sxvc3aa3977p9xag"; depends=[AnnotationDbi org_Mm_eg_db]; };
   mogene21stprobeset_db = derive2 { name="mogene21stprobeset.db"; version="8.8.0"; sha256="172bhzqqw5hz76bw8vqwx2qpw4f6rwbcm6savmkxmmhzb2nq60z5"; depends=[AnnotationDbi org_Mm_eg_db]; };
   mogene21sttranscriptcluster_db = derive2 { name="mogene21sttranscriptcluster.db"; version="8.8.0"; sha256="02g2n5nkxi9lqw9h7sbkblk99zd57lkrldqb1fmi9zww59qwagrv"; depends=[AnnotationDbi org_Mm_eg_db]; };
-  mouse_db0 = derive2 { name="mouse.db0"; version="3.18.0"; sha256="092rjbkrqbkg1997vb4zpyjldv8c541kkx7q95pdpk5qx5aapwqy"; depends=[AnnotationDbi]; };
+  mouse_db0 = derive2 { name="mouse.db0"; version="3.19.1"; sha256="00payj4mc0z5s5iv8ai8w1vg2j68xi12qbg4yxcyjc69vslcgpv0"; depends=[AnnotationDbi]; };
   mouse4302_db = derive2 { name="mouse4302.db"; version="3.13.0"; sha256="0rf22kfj6y96ap0gcwq3mnpv6fj0yax37gf51sfi0wkmp95k7rcs"; depends=[AnnotationDbi org_Mm_eg_db]; };
   mouse4302cdf = derive2 { name="mouse4302cdf"; version="2.18.0"; sha256="1mpyma4x8zfs2fmmx57xw4cfs2cf9lhw71nc3icl72d7vmwidswc"; depends=[AnnotationDbi]; };
   mouse4302frmavecs = derive2 { name="mouse4302frmavecs"; version="1.5.0"; sha256="04clwkfz1gqqwrnqbavkka3hv480w6vi6c4q947qqnhw8j5jjp7s"; depends=[]; };
@@ -611,25 +616,26 @@ in with self; {
   nugomm1a520177probe = derive2 { name="nugomm1a520177probe"; version="3.4.0"; sha256="1n70k0mhv146983myjgk1cgkr9rmmcpqdv8wpkcr320qcvgf9bn7"; depends=[AnnotationDbi]; };
   oligoData = derive2 { name="oligoData"; version="1.8.0"; sha256="1d1yfms3jv2c4s255xnh8yxwijrj35skw3nxds7l46y88lg3qn8y"; depends=[oligo]; };
   ontoProcData = derive2 { name="ontoProcData"; version="0.99.9901"; sha256="16wwh539hdm89f1vxqfgjmlbqwadnr4xqap80annsqgfn90mi8rk"; depends=[]; };
-  org_Ag_eg_db = derive2 { name="org.Ag.eg.db"; version="3.18.0"; sha256="1j9bxz8ypv323wdsp0i0jxv70s14rkq40y1b2n665237rxh0zylz"; depends=[AnnotationDbi]; };
+  org_Ag_eg_db = derive2 { name="org.Ag.eg.db"; version="3.19.1"; sha256="1j8aaraq4wrj633kwfldycsshyygx1k5bvacpha5qg6g7c00bb79"; depends=[AnnotationDbi]; };
-  org_At_tair_db = derive2 { name="org.At.tair.db"; version="3.18.0"; sha256="13lrhfyppn5f5jbnnzqwvjfrmg96a687whv2ws2a3h73i18sxfl1"; depends=[AnnotationDbi]; };
+  org_At_tair_db = derive2 { name="org.At.tair.db"; version="3.19.1"; sha256="0g4b2h08z4fy2wq9nskgp3h5vffs9zk3xx1ax1l86wl16ji2591x"; depends=[AnnotationDbi]; };
-  org_Bt_eg_db = derive2 { name="org.Bt.eg.db"; version="3.18.0"; sha256="0fgrpjfrsw837ay9cq3wd6gp6sxvwjc7r9spfs4m89vqs2xb0bfc"; depends=[AnnotationDbi]; };
+  org_Bt_eg_db = derive2 { name="org.Bt.eg.db"; version="3.19.1"; sha256="0rbbjv47fadc6jgpqrimsd91f35fw6sw8d805vf61nx5xhbl3lpc"; depends=[AnnotationDbi]; };
-  org_Ce_eg_db = derive2 { name="org.Ce.eg.db"; version="3.18.0"; sha256="1fsbrbby6ka2xdsbp8b10nid99w6lkvb7pyn8gv3dsn8p9p6mc5q"; depends=[AnnotationDbi]; };
+  org_Ce_eg_db = derive2 { name="org.Ce.eg.db"; version="3.19.1"; sha256="0vg6nw4qzj8janmkv6k2z471m3l4xnd1h232h0w5i53b20c7p6ys"; depends=[AnnotationDbi]; };
-  org_Cf_eg_db = derive2 { name="org.Cf.eg.db"; version="3.18.0"; sha256="0cfj8cg85vgdz7skpvqkbp7a371w95jywwsjvb5am2wb5hzsnwnp"; depends=[AnnotationDbi]; };
+  org_Cf_eg_db = derive2 { name="org.Cf.eg.db"; version="3.19.1"; sha256="07grx4zgba2q4xgs9x7j3ryy12xkl32mzzgfgivxq68xg7ipj2fk"; depends=[AnnotationDbi]; };
-  org_Dm_eg_db = derive2 { name="org.Dm.eg.db"; version="3.18.0"; sha256="1n0rwynw3nl4js104295kff0jk8jwymjk8imm9di6dy6b9s3qsa6"; depends=[AnnotationDbi]; };
+  org_Dm_eg_db = derive2 { name="org.Dm.eg.db"; version="3.19.1"; sha256="1sqw38z73sgq66x8qrb5xw0jxyimy7l1hs2iwm7xq9ylzrjw3yj0"; depends=[AnnotationDbi]; };
-  org_Dr_eg_db = derive2 { name="org.Dr.eg.db"; version="3.18.0"; sha256="1kk5jgbzcqhgwf5p4mpxswqhr9rkirm3fb7maflk61zcn6fs56zc"; depends=[AnnotationDbi]; };
+  org_Dr_eg_db = derive2 { name="org.Dr.eg.db"; version="3.19.1"; sha256="041hp3xhkiwh8vb4zq5kwvrsmp8paqlri6gaj1qy0a5zjlkw0fl6"; depends=[AnnotationDbi]; };
-  org_EcK12_eg_db = derive2 { name="org.EcK12.eg.db"; version="3.18.0"; sha256="12lqv06n49lwczv5l4h5h6lbfbcqyg9j4csffcdx495scmhc06mc"; depends=[AnnotationDbi]; };
+  org_EcK12_eg_db = derive2 { name="org.EcK12.eg.db"; version="3.19.1"; sha256="1af2yrbpn58z34jq39qmmwprzsffgxbrs84dsxny4rksa8k6j70s"; depends=[AnnotationDbi]; };
-  org_EcSakai_eg_db = derive2 { name="org.EcSakai.eg.db"; version="3.18.0"; sha256="03w6566b3gljs2sjz4ywjkvgr3s33n33877vvmgwapmdwvy6kfs6"; depends=[AnnotationDbi]; };
+  org_EcSakai_eg_db = derive2 { name="org.EcSakai.eg.db"; version="3.19.1"; sha256="02wbh31iqdywy0gqj43l9faijxagsa3fcgcx7y8mafwpgd7aqr7m"; depends=[AnnotationDbi]; };
-  org_Gg_eg_db = derive2 { name="org.Gg.eg.db"; version="3.18.0"; sha256="035pxjcyyhv1nd177vp3kmjjfakzdyf0xmadqqih69almkrvd9yb"; depends=[AnnotationDbi]; };
+  org_Gg_eg_db = derive2 { name="org.Gg.eg.db"; version="3.19.1"; sha256="0fnxscjps85jmd683212hsp6rs5f4bybcxj8xfqggi4l87fkzng0"; depends=[AnnotationDbi]; };
-  org_Hs_eg_db = derive2 { name="org.Hs.eg.db"; version="3.18.0"; sha256="1jn556ql6xknfd34qz4bqh6bgc9rccmz6pk41p7ivlzlslz7bp21"; depends=[AnnotationDbi]; };
+  org_Hs_eg_db = derive2 { name="org.Hs.eg.db"; version="3.19.1"; sha256="1xrbf0zmik1j70i6bg5wqvfwz4vcf3vgypan36r1lv6lspsfychr"; depends=[AnnotationDbi]; };
-  org_Mm_eg_db = derive2 { name="org.Mm.eg.db"; version="3.18.0"; sha256="0i35dfllh8wf7b61ajf33gvclzg3znyx3cgp30vs3hm8ys3nras1"; depends=[AnnotationDbi]; };
+  org_Mm_eg_db = derive2 { name="org.Mm.eg.db"; version="3.19.1"; sha256="12d8lrf6bxvqzfxzdbxqmjcywy2myhwhi99kxdwpijsczxxfikj7"; depends=[AnnotationDbi]; };
-  org_Mmu_eg_db = derive2 { name="org.Mmu.eg.db"; version="3.18.0"; sha256="1qj06dybpqv17vkmd2bk7x3f20a34p4ra054gywbp9klbgmrk60h"; depends=[AnnotationDbi]; };
+  org_Mmu_eg_db = derive2 { name="org.Mmu.eg.db"; version="3.19.1"; sha256="0fz2rrw52nsa2mnl3gmx3ap9zjj0w37zyzwnvxzhmi6wmamr1nk4"; depends=[AnnotationDbi]; };
   org_Mxanthus_db = derive2 { name="org.Mxanthus.db"; version="1.0.27"; sha256="1jqwsdjz1d8fwqhq26lavb2kq739ddlb8khsh4b096vhnwv3dxg5"; depends=[AnnotationDbi AnnotationHub BiocFileCache BiocStyle]; };
-  org_Pt_eg_db = derive2 { name="org.Pt.eg.db"; version="3.18.0"; sha256="0fv0l1fj4d5fza936gx187z3b3yd8cjs0hlb3f9vrsv1zadr3yyf"; depends=[AnnotationDbi]; };
+  org_Pf_plasmo_db = derive2 { name="org.Pf.plasmo.db"; version="3.19.1"; sha256="1klkhazb4rbmnpp3ywj266202740p1c0xsi6dlz84r2cxsrvw1kn"; depends=[AnnotationDbi]; };
-  org_Rn_eg_db = derive2 { name="org.Rn.eg.db"; version="3.18.0"; sha256="1z9wsb7f67mggcsv27zrn50j5c9a3hxc4dygaj2nbma23zxbyjc3"; depends=[AnnotationDbi]; };
+  org_Pt_eg_db = derive2 { name="org.Pt.eg.db"; version="3.19.1"; sha256="1l17ys29ms7iiyflhbk47nvy069rrjpz2f1b5cbfklpr0lzy583b"; depends=[AnnotationDbi]; };
-  org_Sc_sgd_db = derive2 { name="org.Sc.sgd.db"; version="3.18.0"; sha256="15ngfqimrjpn2fxzngj5m3pvqivbq65010qdx33xs32ax48z6p2r"; depends=[AnnotationDbi]; };
+  org_Rn_eg_db = derive2 { name="org.Rn.eg.db"; version="3.19.1"; sha256="0bq42q2j4jddzi2s4lzhmzplbhkd2drw6545ffhcpi4r7ryrzqkn"; depends=[AnnotationDbi]; };
-  org_Ss_eg_db = derive2 { name="org.Ss.eg.db"; version="3.18.0"; sha256="0jqrwh4h7shsni9zyygyggmwg89jsc90r7y0gali29yy8wa38h0q"; depends=[AnnotationDbi]; };
+  org_Sc_sgd_db = derive2 { name="org.Sc.sgd.db"; version="3.19.1"; sha256="1sbjwyf0ibivdhhxsaljgqa4lqp3hcf8gcrlcm2vd78bfm5cm7bg"; depends=[AnnotationDbi]; };
-  org_Xl_eg_db = derive2 { name="org.Xl.eg.db"; version="3.18.0"; sha256="01xr4cpjzdd1v0xw8dbmcjhmcwhi8b3vjhmgsx77c969w9sa0igr"; depends=[AnnotationDbi]; };
+  org_Ss_eg_db = derive2 { name="org.Ss.eg.db"; version="3.19.1"; sha256="0cdql2zvgsrirpby6vahkfxqwnfpbs1hmfl55j8i4n4dv184cbhf"; depends=[AnnotationDbi]; };
+  org_Xl_eg_db = derive2 { name="org.Xl.eg.db"; version="3.19.1"; sha256="0xl3xg4sa5fc7ms6c61pq633y45p2ayh8l02ws1k2yadcmykajrh"; depends=[AnnotationDbi]; };
   paeg1acdf = derive2 { name="paeg1acdf"; version="2.18.0"; sha256="127pgxxp5wp3hgmafbzdzsk4gqnllq1m1gcsfyzkvpkvmbn4aa9n"; depends=[AnnotationDbi]; };
   paeg1aprobe = derive2 { name="paeg1aprobe"; version="2.18.0"; sha256="0hbyd402wf9nzy2g93nhnf2zsi9jvhgfk0llxlyfk0kqxs0y4byy"; depends=[AnnotationDbi]; };
   pd_081229_hg18_promoter_medip_hx1 = derive2 { name="pd.081229.hg18.promoter.medip.hx1"; version="0.99.4"; sha256="1h4925dmw0vfsnhllg55gswq3sxfmx9rcjzifdvgs9y27399psrr"; depends=[Biostrings DBI IRanges oligo oligoClasses RSQLite]; };
@@ -809,7 +815,7 @@ in with self; {
   phastCons35way_UCSC_mm39 = derive2 { name="phastCons35way.UCSC.mm39"; version="3.16.0"; sha256="0lniqakqxja8inq3gn168w1xja1m2kbmww0cw971smsnddypmig7"; depends=[AnnotationHub GenomicScores]; };
   phastCons7way_UCSC_hg38 = derive2 { name="phastCons7way.UCSC.hg38"; version="3.7.1"; sha256="105isdrb3nsy30wd8yy9vrrv8b7c8izc11xqqixg6rcriacd0rl0"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; };
   phyloP35way_UCSC_mm39 = derive2 { name="phyloP35way.UCSC.mm39"; version="3.16.0"; sha256="1n0iywfs23dhc54mapirvaqcbx38zjf8lknbsz80p5lxp24n2lf9"; depends=[AnnotationHub GenomicScores]; };
-  pig_db0 = derive2 { name="pig.db0"; version="3.18.0"; sha256="05lddwcf205gid4ppq9ch5bp7cjdm36c3hfsdm2jddh4a7nky4vz"; depends=[AnnotationDbi]; };
+  pig_db0 = derive2 { name="pig.db0"; version="3.19.1"; sha256="10s39hcyia1w2wik2yxlalnli8a3bw8siqbrnmfyh0hx50plhhmv"; depends=[AnnotationDbi]; };
   plasmodiumanophelescdf = derive2 { name="plasmodiumanophelescdf"; version="2.18.0"; sha256="1vs36091djinn3g6rjhmy9xfdyi58365zbcjc9mf50adnp2i5fq9"; depends=[AnnotationDbi]; };
   plasmodiumanophelesprobe = derive2 { name="plasmodiumanophelesprobe"; version="2.18.0"; sha256="03hfq51nrpmx8ihc48jiih6bk99irrgal9x7i7mgcv8xd508gcsy"; depends=[AnnotationDbi]; };
   poplarcdf = derive2 { name="poplarcdf"; version="2.18.0"; sha256="0j28czs936j2wgwp63qbwl1mjcflcrx7ir88jzxkkw7411ch1gl1"; depends=[AnnotationDbi]; };
@@ -839,7 +845,7 @@ in with self; {
   ragene20sttranscriptcluster_db = derive2 { name="ragene20sttranscriptcluster.db"; version="8.8.0"; sha256="1bi4wy0sbhsyavxwshxvf3iqmyz26q7y2vqp1h3rjshsjdmhfd0h"; depends=[AnnotationDbi org_Rn_eg_db]; };
   ragene21stprobeset_db = derive2 { name="ragene21stprobeset.db"; version="8.8.0"; sha256="1m0hd0nlav9dhqzvs5drl8q3llx2wjxdfvb24fmjnba4h769ns7k"; depends=[AnnotationDbi org_Rn_eg_db]; };
   ragene21sttranscriptcluster_db = derive2 { name="ragene21sttranscriptcluster.db"; version="8.8.0"; sha256="14hp03pizq7kprwk26s9w6s27zzbs2kk50qhjbiwic1xbrl0dp8a"; depends=[AnnotationDbi org_Rn_eg_db]; };
-  rat_db0 = derive2 { name="rat.db0"; version="3.18.0"; sha256="1g02gq0wwb1f7hmqcpd4ad59xn295zqg1hdzixn20wgkan5yd0ac"; depends=[AnnotationDbi]; };
+  rat_db0 = derive2 { name="rat.db0"; version="3.19.1"; sha256="0vl2an3b00h94z1ba29fz83q04p4n641qs4xgp53zz3jg8lgm4si"; depends=[AnnotationDbi]; };
   rat2302_db = derive2 { name="rat2302.db"; version="3.13.0"; sha256="1k2qm1rpq3xkj52m3n629r4qcqi2azdssb2i5shj9jdaqkmr43qc"; depends=[AnnotationDbi org_Rn_eg_db]; };
   rat2302cdf = derive2 { name="rat2302cdf"; version="2.18.0"; sha256="1748rc6yypd7y8wgr1qg632pcsxx0fkxjz6b3z4fhblgdllhy9wk"; depends=[AnnotationDbi]; };
   rat2302frmavecs = derive2 { name="rat2302frmavecs"; version="0.99.11"; sha256="0qy5hf86lrkn20yg6d46kcw9fjc0qhsbzbyavaj1v2zl34xvr1ii"; depends=[affy frma]; };
@@ -847,7 +853,7 @@ in with self; {
   ratCHRLOC = derive2 { name="ratCHRLOC"; version="2.1.6"; sha256="0mgk6lwvvdwjzjh4r1q1q6nfnx4vqx9iy6gmbrb9f31jf30hqnsb"; depends=[]; };
   rattoxfxcdf = derive2 { name="rattoxfxcdf"; version="2.18.0"; sha256="0q84lfaxnnj2zbm5q8xswa1md15fjj4i0djnqr835ixzn7px4yqn"; depends=[AnnotationDbi]; };
   rattoxfxprobe = derive2 { name="rattoxfxprobe"; version="2.18.0"; sha256="1kp159553rkcn9yh6x3yph3yjz2ja21wi9j5ax03qnhwlsl1x8ik"; depends=[AnnotationDbi]; };
-  reactome_db = derive2 { name="reactome.db"; version="1.86.2"; sha256="02p8ihds0hpcfj5mib0ifql9404svlavfyj36c15jzmbci0rnc8c"; depends=[AnnotationDbi]; };
+  reactome_db = derive2 { name="reactome.db"; version="1.88.0"; sha256="1fwbf53vklhvqa6n6pijb8xqyv2pap1hskkirnm5c42wmd6g4ql7"; depends=[AnnotationDbi]; };
   rgu34a_db = derive2 { name="rgu34a.db"; version="3.13.0"; sha256="1nl28gia0zh8xkfv8llxiysxk1k1gm6cs2wvl0n1xqhnr0rhla76"; depends=[AnnotationDbi org_Rn_eg_db]; };
   rgu34acdf = derive2 { name="rgu34acdf"; version="2.18.0"; sha256="08z9f16xp1m2mwl9vlmbffxl4zyyl8cgzf6wp66rrm32lvl0nbwq"; depends=[AnnotationDbi]; };
   rgu34aprobe = derive2 { name="rgu34aprobe"; version="2.18.0"; sha256="1gjxyq9128jgv3ic386f84rajgf3wz7yi2dja80y0ff4m0a48dlh"; depends=[AnnotationDbi]; };
@@ -861,7 +867,7 @@ in with self; {
   rgug4105a_db = derive2 { name="rgug4105a.db"; version="3.2.3"; sha256="0lq8k95qm0q7j65nf16p3f09dn9zs87n3k561wxrgi2lb0pf6j40"; depends=[AnnotationDbi org_Rn_eg_db]; };
   rgug4130a_db = derive2 { name="rgug4130a.db"; version="3.2.3"; sha256="0zlcn9spw23bj3px9z1l2f5afn09zbr6rv0nbd2h6dd12wrvy1zk"; depends=[AnnotationDbi org_Rn_eg_db]; };
   rgug4131a_db = derive2 { name="rgug4131a.db"; version="3.2.3"; sha256="1r272jf9cflf1yf4bznp4d59h7bd7adh1i3rf890h5ffc0xzf5cq"; depends=[AnnotationDbi org_Rn_eg_db]; };
-  rhesus_db0 = derive2 { name="rhesus.db0"; version="3.18.0"; sha256="08l0srvyac33z7ly90pscfh46ms4yfq2pqw502px095qpk0lfvz1"; depends=[AnnotationDbi]; };
+  rhesus_db0 = derive2 { name="rhesus.db0"; version="3.19.1"; sha256="1687fgxx9rj1ghjg7vhmli360algh6piwafdsi4l347sl1yhklcd"; depends=[AnnotationDbi]; };
   rhesuscdf = derive2 { name="rhesuscdf"; version="2.18.0"; sha256="0q2alkxm80wkzaf0q80df27q30qkswybavz05x6ywsihbs9h0nb8"; depends=[AnnotationDbi]; };
   rhesusprobe = derive2 { name="rhesusprobe"; version="2.18.0"; sha256="0fd8pvwvpcmx41k80nbccjxllh39fvjf7l9dr8facisl1x7gsfil"; depends=[AnnotationDbi]; };
   ri16cod_db = derive2 { name="ri16cod.db"; version="3.4.0"; sha256="1xz533vxjdyxx1wkks0kgk6b90sxs44iqcsvyds0xcm573bx8c6q"; depends=[AnnotationDbi org_Rn_eg_db]; };
@@ -884,7 +890,7 @@ in with self; {
   sugarcanecdf = derive2 { name="sugarcanecdf"; version="2.18.0"; sha256="0wghc6wr7iwkql63m3wibjjdcdpqd53z0g5rxdh553sjb0ca2n7z"; depends=[AnnotationDbi]; };
   sugarcaneprobe = derive2 { name="sugarcaneprobe"; version="2.18.0"; sha256="17zrydd8xd7m61bp750xlpcak0m3zgl0mvknz9s7mv2a35kp02ih"; depends=[AnnotationDbi]; };
   synaptome_data = derive2 { name="synaptome.data"; version="0.99.6"; sha256="00cqgx06wysz0qyicwnxlc8hpqkj5rwqlyfzsvy7agvcjjkarwg5"; depends=[AnnotationHub]; };
-  synaptome_db = derive2 { name="synaptome.db"; version="0.99.15"; sha256="111rg62l8f0k3m0fq8g63lg15agk9bkfcx5z990157cxs0rq07h3"; depends=[AnnotationHub DBI dbplyr dplyr igraph Rdpack RSQLite synaptome_data]; };
+  synaptome_db = derive2 { name="synaptome.db"; version="0.99.16"; sha256="0sd3kwhf9gh74j6qiaf1i2qzgn69i9yyvza26aysiplirbsy1jr0"; depends=[AnnotationHub DBI dbplyr dplyr igraph Rdpack RSQLite synaptome_data]; };
   targetscan_Hs_eg_db = derive2 { name="targetscan.Hs.eg.db"; version="0.6.1"; sha256="1p14jyhn1d2m6kww9vsb96263g8crnrff7qgyiz46pp9ww8mvxf4"; depends=[AnnotationDbi]; };
   targetscan_Mm_eg_db = derive2 { name="targetscan.Mm.eg.db"; version="0.6.1"; sha256="0ad6vxpwn9x82qcrpwcy1lwg0q3ik4vabxn01k6gwmbpvydz9cf5"; depends=[AnnotationDbi]; };
   test1cdf = derive2 { name="test1cdf"; version="2.18.0"; sha256="0nmkrp4b2p09pg8ndcnfv5y7w94xah6fa5pff60dp1s2s8dcgcr4"; depends=[AnnotationDbi]; };
@@ -901,8 +907,8 @@ in with self; {
   vitisviniferaprobe = derive2 { name="vitisviniferaprobe"; version="2.18.0"; sha256="1ggz1s37dwvrkhj4vx2civyhap7bgqsshy33lk14z4fjsayfi39a"; depends=[AnnotationDbi]; };
   wheatcdf = derive2 { name="wheatcdf"; version="2.18.0"; sha256="1gmbrdilqvm54h6nkb1cm01ki8aipiywd4qj8gpwlm2hqrimr8kr"; depends=[AnnotationDbi]; };
   wheatprobe = derive2 { name="wheatprobe"; version="2.18.0"; sha256="1fifi3pvzdrg356idwz0kx7qlf5mssdxlyvwpn3cjgw0z7n7cnw8"; depends=[AnnotationDbi]; };
-  worm_db0 = derive2 { name="worm.db0"; version="3.18.0"; sha256="1kiv5a7mxak12m58c7p9m10k4ip6v63ycgj9mfawa8i70cp1dvap"; depends=[AnnotationDbi]; };
+  worm_db0 = derive2 { name="worm.db0"; version="3.19.1"; sha256="1v24lpw3kfzlzq577vqpqy5bypwfkw1khag7smpq9bgv8dmfcx8r"; depends=[AnnotationDbi]; };
-  xenopus_db0 = derive2 { name="xenopus.db0"; version="3.18.0"; sha256="1dacnx0bknhgdlaljm9r54dxxbw7vi6pgxhl2dmprkl9k02cc2q6"; depends=[AnnotationDbi]; };
+  xenopus_db0 = derive2 { name="xenopus.db0"; version="3.19.1"; sha256="1d6bhq0ppgm087zkh4nmm3qx6f2mp0lblhzvayc6fqyzrzanvjiy"; depends=[AnnotationDbi]; };
   xenopuslaeviscdf = derive2 { name="xenopuslaeviscdf"; version="2.18.0"; sha256="1bcz1hr7gxw6ac4qvw0giph6hfcf5i9b11s274ypq512qc1d32iq"; depends=[AnnotationDbi]; };
   xenopuslaevisprobe = derive2 { name="xenopuslaevisprobe"; version="2.18.0"; sha256="0prb14zn2gvgxq8w0y21x1ng51cn3bgjhkppf7zkmnq1xkzvq0pw"; depends=[AnnotationDbi]; };
   xlaevis_db = derive2 { name="xlaevis.db"; version="3.2.3"; sha256="0cdi71c8pflb8n4yfxc0wmfi51w6z0dlz7nw5hv0hkx547v79d53"; depends=[AnnotationDbi org_Xl_eg_db]; };
@@ -914,7 +920,7 @@ in with self; {
   ye6100subbcdf = derive2 { name="ye6100subbcdf"; version="2.18.0"; sha256="1169hv56981b915rlr5w5sn6ppyjd8as7f4k1hbjzadrdrl3glwp"; depends=[AnnotationDbi]; };
   ye6100subccdf = derive2 { name="ye6100subccdf"; version="2.18.0"; sha256="0mhr4zd33gfvvivc17k7fb6nvmhq6h3q0xbx2zl09zd6qk09kizm"; depends=[AnnotationDbi]; };
   ye6100subdcdf = derive2 { name="ye6100subdcdf"; version="2.18.0"; sha256="11b1fflgc34lrj4yf1p7way5n83cm9c7znsbxpzlwddwyy8qib30"; depends=[AnnotationDbi]; };
-  yeast_db0 = derive2 { name="yeast.db0"; version="3.18.0"; sha256="1lrni3i2qljkrvpm63rrwhk52m2lr4ci82lxaczbk7spk8yr7mvy"; depends=[AnnotationDbi]; };
+  yeast_db0 = derive2 { name="yeast.db0"; version="3.19.1"; sha256="00zbg60zn0yzmfdm017al4hbncrlsdfb5syj8mfxha3522q1114h"; depends=[AnnotationDbi]; };
   yeast2_db = derive2 { name="yeast2.db"; version="3.13.0"; sha256="0aqbs3p6f3sc6nyggyk7gvg191b551rwq20009fnk0li50dg1ps6"; depends=[AnnotationDbi org_Sc_sgd_db]; };
   yeast2cdf = derive2 { name="yeast2cdf"; version="2.18.0"; sha256="0c68val9x8bfnv4xx0vag9dxwsx5q8dzbj0dpha3nshh12jw48w9"; depends=[AnnotationDbi]; };
   yeast2probe = derive2 { name="yeast2probe"; version="2.18.0"; sha256="125nif693qcmxc0nnnz917f9avggcdr8g9rfvx2qdc54a2l7vdb7"; depends=[AnnotationDbi]; };
@@ -923,7 +929,7 @@ in with self; {
   ygs98frmavecs = derive2 { name="ygs98frmavecs"; version="1.3.0"; sha256="1xrm1209xnknwvad7nvg1a0mbxz15z12yd4x5bia3cq03zcmzf9m"; depends=[]; };
   ygs98probe = derive2 { name="ygs98probe"; version="2.18.0"; sha256="0awf6z4j2vb2jk9a9j2r512yd3m31660y68pasa9mp488m270a3q"; depends=[AnnotationDbi]; };
   zebrafish_db = derive2 { name="zebrafish.db"; version="3.13.0"; sha256="13a65jxr3r5qjf82h1dr0k9qq20g14canqgqdd11k9gk5h31xhc7"; depends=[AnnotationDbi org_Dr_eg_db]; };
-  zebrafish_db0 = derive2 { name="zebrafish.db0"; version="3.18.0"; sha256="0qrd1b5l936jf30dnnmmi5fighwg4zmhz62acq6qzi4r7668g6sk"; depends=[AnnotationDbi]; };
+  zebrafish_db0 = derive2 { name="zebrafish.db0"; version="3.19.1"; sha256="1bg35zyxdvdhv0a1l5v61z6g0vz2h2ikad4lyv4akrmwndcrxijy"; depends=[AnnotationDbi]; };
   zebrafishcdf = derive2 { name="zebrafishcdf"; version="2.18.0"; sha256="0sq1xqhblbilvaiabhqyl9gxdj3jg576vgq8v0cls1zvvx0isrx0"; depends=[AnnotationDbi]; };
   zebrafishprobe = derive2 { name="zebrafishprobe"; version="2.18.0"; sha256="1pb8z2rdhq11hq391xyi236scyafbp56kbhhwsnha36yygz5drw0"; depends=[AnnotationDbi]; };
   LRBase_Ath_eg_db = derive2 { name="LRBase.Ath.eg.db"; version="2.0.1"; sha256="1f9yp9rfaydzz24bhl795379clcinibi4kavxzzavrvqfvkrgw84"; depends=[LRBaseDbi RSQLite]; broken = true; };
@@ -1021,7 +1027,6 @@ in with self; {
   SNPlocs_Hsapiens_dbSNP151_GRCh38 = derive2 { name="SNPlocs.Hsapiens.dbSNP151.GRCh38"; version="0.99.21"; sha256="19j5h0dgxd2iw35p6fblj8b3z2d92zmmp60khw5zs70scd5fs9pb"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; broken = true; };
   XtraSNPlocs_Hsapiens_dbSNP141_GRCh38 = derive2 { name="XtraSNPlocs.Hsapiens.dbSNP141.GRCh38"; version="0.99.13"; sha256="1fidmrf0xr7wwd4v1y7x2wwyplplbs1z8jqpfdjpc8aclcy38m3f"; depends=[BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; broken = true; };
   greengenes13_5MgDb = derive2 { name="greengenes13.5MgDb"; version="2.0.0"; sha256="0j4pd653vlfpd9gq6gi459lra8xhyknjrzadkx9d3zjy0hcwpj7r"; depends=[]; broken = true; };
-  org_Pf_plasmo_db = derive2 { name="org.Pf.plasmo.db"; version="3.14.0"; sha256="1fs68n9xyia6v9jj8a91asmrirnh2xkqcgrjbzk7x6ss0rlwcl7w"; depends=[AnnotationDbi]; broken = true; };
   ribosomaldatabaseproject11_5MgDb = derive2 { name="ribosomaldatabaseproject11.5MgDb"; version="1.00.0"; sha256="04ppa4k8p54bmkq3jm41h0v4lb5hz95cmnakfzmqfml00ir04mxp"; depends=[]; broken = true; };
   silva128_1MgDb = derive2 { name="silva128.1MgDb"; version="1.00.0"; sha256="0pwwxxa55d3919rbczg5iskd03ignimk80m52kfi930b1kdg9qc2"; depends=[]; broken = true; };
 }

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

@@ -4,445 +4,456 @@
 # Rscript generate-r-packages.R bioc-experiment >new && mv new bioc-experiment-packages.nix
 
 { self, derive }:
-let derive2 = derive { biocVersion = "3.18"; };
+let derive2 = derive { biocVersion = "3.19"; };
 in with self; {
-  ALL = derive2 { name="ALL"; version="1.44.0"; sha256="1ny5xv338a91gc88a1y5rrd27iawrrlmxhkidvc7xdsbrwd4flkc"; depends=[Biobase]; };
+  ALL = derive2 { name="ALL"; version="1.46.0"; sha256="1yl8b8q8i19kx4viwinhyq9xn9d4axlfgjvm7cpf7pys4krhnrha"; depends=[Biobase]; };
-  ALLMLL = derive2 { name="ALLMLL"; version="1.42.0"; sha256="1sq2j4gq78d68lqlqnd6nxi66gngzqyxicsyv85xp7dhcl59fwbm"; depends=[affy]; };
+  ALLMLL = derive2 { name="ALLMLL"; version="1.44.0"; sha256="0pmdw42wrmhqm3754s3kkz7wjih63h21zlrwl1b7lkli79vbzkpd"; depends=[affy]; };
-  ARRmData = derive2 { name="ARRmData"; version="1.38.0"; sha256="0hlhc7kvw9n1bnbzingd1475qwivpx64sccnigdij8xdcm1mb4s7"; depends=[]; };
+  ARRmData = derive2 { name="ARRmData"; version="1.40.0"; sha256="02y44d0dappc3srl2d7lgipm6a62gvd8vivzaq4594dnmy8rvkw3"; depends=[]; };
-  ASICSdata = derive2 { name="ASICSdata"; version="1.22.0"; sha256="01xm27j9c37vqpqz4d9v3bsji1z6ppgf64jja5dd4rz8i3gx9f68"; depends=[]; };
+  ASICSdata = derive2 { name="ASICSdata"; version="1.24.0"; sha256="03wlk2x9bz5xjhnfgxl5zdagnwm60f23bz1qhlgqfs94zfay0jrq"; depends=[]; };
-  Affyhgu133A2Expr = derive2 { name="Affyhgu133A2Expr"; version="1.38.0"; sha256="1rvw1z3i8jz0x4ca2fy4xg2z97ffalh15prsd38sz4chj9cwybxc"; depends=[]; };
+  Affyhgu133A2Expr = derive2 { name="Affyhgu133A2Expr"; version="1.40.0"; sha256="0l55wr09j2p8dkzx8cas2whf404anf477h2bmpv267mglrs1sp32"; depends=[]; };
-  Affyhgu133Plus2Expr = derive2 { name="Affyhgu133Plus2Expr"; version="1.36.0"; sha256="10jilz65xba8a43zdvxksll9jpba9a1nj5w266d7laws056m4bh9"; depends=[]; };
+  Affyhgu133Plus2Expr = derive2 { name="Affyhgu133Plus2Expr"; version="1.38.0"; sha256="04cxyjk1dhal8iapfilzck8kxpw8jvswxxb7fhnbxqghwlhjg617"; depends=[]; };
-  Affyhgu133aExpr = derive2 { name="Affyhgu133aExpr"; version="1.40.0"; sha256="1kdp39k2s35jb3wp4qqm0lbrz94dxz1s9yygv8frfc70xv4hh7af"; depends=[]; };
+  Affyhgu133aExpr = derive2 { name="Affyhgu133aExpr"; version="1.42.0"; sha256="047yza31rrdmzjbg6chqrz61fh7j1a013fww5nj1nwp60rd6iln1"; depends=[]; };
-  AffymetrixDataTestFiles = derive2 { name="AffymetrixDataTestFiles"; version="0.40.0"; sha256="0h8i38qh3krw02v5x4rybh0pmfriy5l3ji6ahk2j0hgjfgq55z5b"; depends=[]; };
+  AffymetrixDataTestFiles = derive2 { name="AffymetrixDataTestFiles"; version="0.42.0"; sha256="1ijprvhbhq68v2g8z9yqwwqw2lz4f4a2pa7lnq2vhf54p9s96sn1"; depends=[]; };
-  Affymoe4302Expr = derive2 { name="Affymoe4302Expr"; version="1.40.0"; sha256="01zgyp6yy980iyqan7f9qiv7pqzkr4cjli9q5ncig085afp2j88r"; depends=[]; };
+  Affymoe4302Expr = derive2 { name="Affymoe4302Expr"; version="1.42.0"; sha256="11n5mx1m21j6cc4qrwzrxj3749zc42b1ivwnp47cf55h6j2c3rgm"; depends=[]; };
-  AmpAffyExample = derive2 { name="AmpAffyExample"; version="1.42.0"; sha256="028473p5k69vmm8nh0qpmq30cyjcjaccclnsc7crr6brg2xjzcb6"; depends=[affy]; };
+  AmpAffyExample = derive2 { name="AmpAffyExample"; version="1.44.0"; sha256="0j5alica5z8fzcwiva3dg1wmncwwkchb7avwvhszk7p7ym0s983q"; depends=[affy]; };
-  AneuFinderData = derive2 { name="AneuFinderData"; version="1.30.0"; sha256="03kp8qkqy2wph7lbzawgnh83qjm31ih1jp986qwphfhkfk125wg0"; depends=[]; };
+  AneuFinderData = derive2 { name="AneuFinderData"; version="1.32.0"; sha256="1qysi874hsa4a7xz0na0cxv0sx02d3b74h77s30mfww1wsg8jy69"; depends=[]; };
-  AshkenazimSonChr21 = derive2 { name="AshkenazimSonChr21"; version="1.32.0"; sha256="0yin4q6bjhbh6a6xb62ac5w0kjb23y3kslrpkf9prr1cz42kvbjx"; depends=[]; };
+  AshkenazimSonChr21 = derive2 { name="AshkenazimSonChr21"; version="1.34.0"; sha256="0bm2f7pnxibgcsi5kghjzmin01sirprym5i94qsiga7c6dknqgmn"; depends=[]; };
-  AssessORFData = derive2 { name="AssessORFData"; version="1.20.0"; sha256="0lp80w5msdisic9j827wq7gsi9v6vnrchrlcmr2h5vd26plia98x"; depends=[DECIPHER]; };
+  AssessORFData = derive2 { name="AssessORFData"; version="1.21.0"; sha256="10rbwdcjqfhq9ramrzfxd3bl2q2nqminsj3pigid6fmvyg0ykfhk"; depends=[DECIPHER]; };
-  BeadArrayUseCases = derive2 { name="BeadArrayUseCases"; version="1.40.0"; sha256="052r8snjwqzn49gjwv1fv5vhwl14vcmzwjxb4jgsbnb14wyhiliy"; depends=[beadarray GEOquery limma]; };
+  BeadArrayUseCases = derive2 { name="BeadArrayUseCases"; version="1.42.0"; sha256="1s62vqvl3zxf97syp5lymacah594m8szk23skl4bk88jkzkkx6a5"; depends=[beadarray GEOquery limma]; };
-  BeadSorted_Saliva_EPIC = derive2 { name="BeadSorted.Saliva.EPIC"; version="1.10.0"; sha256="088c6ikr7cslpx8yx89d3y00zigy6c21qa1m3dlrynghh7z8xi8w"; depends=[ExperimentHub minfi]; };
+  BeadSorted_Saliva_EPIC = derive2 { name="BeadSorted.Saliva.EPIC"; version="1.12.0"; sha256="1pjnamvgx9w3g40j82rbdysbarx11gm8k6lb3vhkgb2nxv1vij84"; depends=[ExperimentHub minfi]; };
-  BioImageDbs = derive2 { name="BioImageDbs"; version="1.10.0"; sha256="1xgm9n01if7rb6lsgj4cg5dbjl8kq6zvkj4324vrwj1c1mdaa9nv"; depends=[animation AnnotationHub EBImage einsum ExperimentHub filesstrings magick magrittr markdown rmarkdown]; };
+  BioImageDbs = derive2 { name="BioImageDbs"; version="1.12.0"; sha256="1cs6c80h34xbzpsgrpy5aj1f0nlxmy713jj1q5g156z5kiz3mzwc"; depends=[animation AnnotationHub EBImage einsum ExperimentHub filesstrings magick magrittr markdown rmarkdown]; };
-  BioPlex = derive2 { name="BioPlex"; version="1.8.0"; sha256="0wwsbv4kyi67favswb5jrcgjv6a02s8gvwc23918y0rlcmkx07m7"; depends=[BiocFileCache GenomeInfoDb GenomicRanges GEOquery graph SummarizedExperiment]; };
+  BioPlex = derive2 { name="BioPlex"; version="1.10.0"; sha256="1bkakf7yi1lhwc48pmwifk7qdnc9hzaqnlcni7sy0ypwgb1mfsh7"; depends=[BiocFileCache GenomeInfoDb GenomicRanges GEOquery graph SummarizedExperiment]; };
-  BloodCancerMultiOmics2017 = derive2 { name="BloodCancerMultiOmics2017"; version="1.22.0"; sha256="1ya62fx76ifnbdbws51nw544n12sk4a35qichfc54v0ffbz0n38c"; depends=[beeswarm Biobase DESeq2 devtools dplyr ggdendro ggplot2 glmnet gtable ipflasso RColorBrewer reshape2 scales SummarizedExperiment survival tibble]; };
+  BloodCancerMultiOmics2017 = derive2 { name="BloodCancerMultiOmics2017"; version="1.24.0"; sha256="16c6nirflpj0zf2wrj0hb5xcq2168si95np3sm76r3kvwlr48zm7"; depends=[beeswarm Biobase DESeq2 devtools dplyr ggdendro ggplot2 glmnet gtable ipflasso RColorBrewer reshape2 scales SummarizedExperiment survival tibble]; };
-  CCl4 = derive2 { name="CCl4"; version="1.40.0"; sha256="02fw0c7yy6vch31a726fpn163mi5zj13jvrpczqqshb2wz2qs58c"; depends=[Biobase limma]; };
+  CCl4 = derive2 { name="CCl4"; version="1.42.0"; sha256="0n3kx176if48gmw3qd5knlv5q7v7738c54ix8cwr2xhsqc7ah800"; depends=[Biobase limma]; };
-  CLL = derive2 { name="CLL"; version="1.42.0"; sha256="10l2a562l6hx32sxmvy8z59shq87v770rrh2fhddnj06dpx6n6cf"; depends=[affy Biobase]; };
+  CLL = derive2 { name="CLL"; version="1.44.0"; sha256="18bjaqf6cjvjfcp80b5zmb48qbywacqs6aiarsh6ksq2yj4np4zs"; depends=[affy Biobase]; };
-  CLLmethylation = derive2 { name="CLLmethylation"; version="1.22.0"; sha256="16k05g98j2zs8n827kvgishzcj0zcx12cwzvgznzjrwp56dl72xs"; depends=[ExperimentHub SummarizedExperiment]; };
+  CLLmethylation = derive2 { name="CLLmethylation"; version="1.24.0"; sha256="0pafgk4sagyrsddzg5a0nigs518ki2rikhkj02mngh9x4kipkhip"; depends=[ExperimentHub SummarizedExperiment]; };
-  COHCAPanno = derive2 { name="COHCAPanno"; version="1.38.0"; sha256="0f85l5alhzb14p30pmk11lv0wn6n4nsx8l9pc545fkwqdm5bsqh3"; depends=[]; };
+  COHCAPanno = derive2 { name="COHCAPanno"; version="1.40.0"; sha256="0gdb08vxna4rhf5lyhjr9prww58sikjiv49i4sy6hgj5a1chz288"; depends=[]; };
-  CONFESSdata = derive2 { name="CONFESSdata"; version="1.30.0"; sha256="1gjsbrrz06qsa0lwjiil0qprhiajyy7im5wh6xks0ifs8rl9f9y4"; depends=[]; };
+  CONFESSdata = derive2 { name="CONFESSdata"; version="1.32.0"; sha256="0xmbgr6iq4nzxw8gvb099c65bxsc0aqfwn55l2hyr7zskqc3apka"; depends=[]; };
-  COPDSexualDimorphism_data = derive2 { name="COPDSexualDimorphism.data"; version="1.38.0"; sha256="1mkxf577xa7k1cflrwbdngj6kfhdz2a1dg04x849zm6ahmd3x9vf"; depends=[]; };
+  COPDSexualDimorphism_data = derive2 { name="COPDSexualDimorphism.data"; version="1.40.0"; sha256="0wxhsj29yycmfgwl1sxz3yynwwwccxs1n9kcvdd6940jm4rz8nvq"; depends=[]; };
-  COSMIC_67 = derive2 { name="COSMIC.67"; version="1.38.0"; sha256="0c4nmzdhg2mam134j5p7g5h4g2f08aqj429b03cz83znqy4k25vl"; depends=[GenomicRanges SummarizedExperiment VariantAnnotation]; };
+  COSMIC_67 = derive2 { name="COSMIC.67"; version="1.40.0"; sha256="0b9w91qvxakrwwgkzfmhd7ily9yy5jmwimiykckksrhf1fr7i7zp"; depends=[GenomicRanges SummarizedExperiment VariantAnnotation]; };
-  CRCL18 = derive2 { name="CRCL18"; version="1.22.0"; sha256="1wa9988sv5maml0v0n893m5vf773z0z530dpp5cjk02cd40npcrn"; depends=[Biobase]; };
+  CRCL18 = derive2 { name="CRCL18"; version="1.24.0"; sha256="1f513yxinql9qnxmlcfarhn840bxkbwxjqs661c9zliah26hv2wp"; depends=[Biobase]; };
-  CardinalWorkflows = derive2 { name="CardinalWorkflows"; version="1.34.0"; sha256="0cyzzyki6y2a7m4w7pk7x532a0i539irmpxbba3zs05cjs3213sb"; depends=[Cardinal]; };
+  CardinalWorkflows = derive2 { name="CardinalWorkflows"; version="1.36.0"; sha256="09b0a7ss64mx0ag6rwa7nld0hfzhrr7pfy4iimd0isfz1hm55kd8"; depends=[Cardinal]; };
-  CellMapperData = derive2 { name="CellMapperData"; version="1.28.0"; sha256="12mx1m4lm51y8pazmhrd8ickvvpa2sm9cg2znhs6pzmgc5bj09dx"; depends=[CellMapper ExperimentHub]; };
+  CellMapperData = derive2 { name="CellMapperData"; version="1.30.0"; sha256="1rw0793g5bj1zwa5wi4f9d7l3y29c88c2s16ia0ph1j72zr0vyrn"; depends=[CellMapper ExperimentHub]; };
-  ChAMPdata = derive2 { name="ChAMPdata"; version="2.34.0"; sha256="175vsg2bh578fdrdchcma5q3jq7cfxa8b7g8954xv6fxrwcj0ffz"; depends=[BiocGenerics GenomicRanges]; };
+  ChAMPdata = derive2 { name="ChAMPdata"; version="2.36.0"; sha256="0x006ilgqrf15135ivxv8qrcyhssl1w6pm1gpnna96za58l2f2rr"; depends=[BiocGenerics GenomicRanges]; };
-  ChIC_data = derive2 { name="ChIC.data"; version="1.22.0"; sha256="1akqpqw9ydf23whr346psciyyp9c3r0rsas1rkdkf8g5wrcj9vhk"; depends=[caret genomeIntervals randomForest]; };
+  ChIPXpressData = derive2 { name="ChIPXpressData"; version="1.42.0"; sha256="0jfiii3akdsg4drj3x3rmjakzr85bhzdxl5w433qkrzb4dm724q0"; depends=[bigmemory]; };
-  ChIPXpressData = derive2 { name="ChIPXpressData"; version="1.40.0"; sha256="0i96lkgkzssrsa0gnc5l4f9j4x07cvq4s019v3b2fm5s288lvsnj"; depends=[bigmemory]; };
+  ChIPexoQualExample = derive2 { name="ChIPexoQualExample"; version="1.28.0"; sha256="07m4515g0gq4qv7yyx0qy0y4c2zb1dm30yhkzh43z34m6rkgsf1f"; depends=[]; };
-  ChIPexoQualExample = derive2 { name="ChIPexoQualExample"; version="1.26.0"; sha256="1v35xq0a58kf0nabv3v6aiz9cd3gvwv0asmvq27ha0w1ngwd0dzk"; depends=[]; };
+  ChimpHumanBrainData = derive2 { name="ChimpHumanBrainData"; version="1.42.0"; sha256="04cixcachip43kynlz4l6fh1y0wdzijgipvkz5rvlhqca7mpdqss"; depends=[affy hexbin limma qvalue statmod]; };
-  CluMSIDdata = derive2 { name="CluMSIDdata"; version="1.18.0"; sha256="0xahy0l8b8c7xgg6481vhliiis63brh3rszaj5d1f7sjbgzj7ahs"; depends=[]; };
+  CluMSIDdata = derive2 { name="CluMSIDdata"; version="1.20.0"; sha256="01r4cfy0ny5vh0x1ihkynyxfxgjsprhim7913vzj0d1kgdkzdr6z"; depends=[]; };
-  CoSIAdata = derive2 { name="CoSIAdata"; version="1.2.0"; sha256="07x44vn6r1d0ixfzx9h3rzzn9gjjci59c41xhqn2b3k6f5c7fa9r"; depends=[ExperimentHub]; };
+  CoSIAdata = derive2 { name="CoSIAdata"; version="1.4.0"; sha256="1mld9j54ywkgz63brf8lmfi57f1hmclyv3m9lw201wyni48nx377"; depends=[ExperimentHub]; };
-  ConnectivityMap = derive2 { name="ConnectivityMap"; version="1.38.0"; sha256="0ixvmkyps62f10c0s4z0jas2106hnvijknai6abial6i3plffnsc"; depends=[]; };
+  ConnectivityMap = derive2 { name="ConnectivityMap"; version="1.40.0"; sha256="1i7bv10kmmgb355nmp3qsm9awcba69h8chhvcmw718hg5x2axrdh"; depends=[]; };
-  CopyNeutralIMA = derive2 { name="CopyNeutralIMA"; version="1.20.0"; sha256="11l994nhi813qs1vmrqjgclw11k5hrsmcrlj5x5wqmqmnjjw1dsy"; depends=[ExperimentHub Rdpack]; };
+  CopyNeutralIMA = derive2 { name="CopyNeutralIMA"; version="1.22.0"; sha256="12pw212lrqsas08hzan6sh56iasx74adbnngvyj2dllgc30971i8"; depends=[ExperimentHub Rdpack]; };
-  CopyhelpeR = derive2 { name="CopyhelpeR"; version="1.34.0"; sha256="1zfsxi65lln93fb87l6fgp7vxldb4fvnf95h91dl424xyq6qjp1h"; depends=[]; };
+  CopyhelpeR = derive2 { name="CopyhelpeR"; version="1.36.0"; sha256="1ijlba601wknkj6ybbnarcdw1z54f76gkdgynpry1v8jpbpvcadr"; depends=[]; };
-  DAPARdata = derive2 { name="DAPARdata"; version="1.32.1"; sha256="1iwiq5z1jnsrdp3pnhxlb2rvcfg91xp7xp2k0ry7r0gr9hjnnhr7"; depends=[MSnbase]; };
+  CytoMethIC = derive2 { name="CytoMethIC"; version="1.0.0"; sha256="19ms0i2rs0b3lbg71m3k43hy0wx45yif6pv3nnchbafysnlzp04n"; depends=[BiocManager BiocParallel ExperimentHub sesame sesameData tibble]; };
-  DExMAdata = derive2 { name="DExMAdata"; version="1.10.0"; sha256="1a2hrvbkhpwmjha0iwd17xv60d1cdl7iswc942bcac80mn6sw305"; depends=[Biobase]; };
+  DAPARdata = derive2 { name="DAPARdata"; version="1.34.0"; sha256="055rlbc2sky8am6vcz09vxpj8n34y3lmajlp8n6zz086w7fgfd8d"; depends=[MSnbase]; };
-  DLBCL = derive2 { name="DLBCL"; version="1.42.2"; sha256="06x4jbyz0m9pzwxjl326rl5zahq5km5rryncbq99cz6mml2asn21"; depends=[Biobase graph]; };
+  DExMAdata = derive2 { name="DExMAdata"; version="1.12.0"; sha256="17gm48hawh42cdbqr1bbrb7nccx3lwan8nca353vyj43pjr3s46n"; depends=[Biobase]; };
-  DMRcatedata = derive2 { name="DMRcatedata"; version="2.20.3"; sha256="0fhk71j60s693vh333277ra0vgjys15h6r593v2j1y970650pq0a"; depends=[ExperimentHub GenomicFeatures Gviz IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b4_hg19 plyr readxl rtracklayer]; };
+  DLBCL = derive2 { name="DLBCL"; version="1.44.0"; sha256="0sakxhj192khn777aspzzckrjnzi89ng5wnzvzxgfdbpwh2nfl4d"; depends=[Biobase graph]; };
-  DNAZooData = derive2 { name="DNAZooData"; version="1.2.0"; sha256="0d5466b830s82laamig1rw0p0n6i4npb11iyziv1sfvs4y8pbhl8"; depends=[BiocFileCache HiCExperiment rjson S4Vectors]; };
+  DMRcatedata = derive2 { name="DMRcatedata"; version="2.22.0"; sha256="119r3c2yc5hbj5x0h7r930rwhp0k5rsnfmbmvl2rhz02wq2ychhy"; depends=[ExperimentHub GenomicFeatures Gviz IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b4_hg19 plyr readxl rtracklayer]; };
-  DeSousa2013 = derive2 { name="DeSousa2013"; version="1.38.0"; sha256="1xjygkr8rc1m9sv5bwph3wdf9hhcfdw8zji547nw0ayrg5d49689"; depends=[affy AnnotationDbi Biobase cluster ConsensusClusterPlus frma frmaTools gplots hgu133plus2_db hgu133plus2frmavecs pamr rgl ROCR siggenes survival sva]; };
+  DNAZooData = derive2 { name="DNAZooData"; version="1.4.0"; sha256="1bs2pnak2v2szp7zly8ysf8pqh7f70w70cbqqzvnxlf35npv7cxd"; depends=[BiocFileCache HiCExperiment rjson S4Vectors]; };
-  DmelSGI = derive2 { name="DmelSGI"; version="1.34.0"; sha256="1qsvw7jrn070yfrgrkw9wsdb05g8ai5hmcqmyr78qs5qny0cz919"; depends=[abind gplots igraph knitr limma rhdf5 TSP]; };
+  DeSousa2013 = derive2 { name="DeSousa2013"; version="1.40.0"; sha256="1icjl4rr8jk16hs8ri925v3gf9lasi4x39yf5a7av39byb2zwqif"; depends=[affy AnnotationDbi Biobase cluster ConsensusClusterPlus frma frmaTools gplots hgu133plus2_db hgu133plus2frmavecs pamr rgl ROCR siggenes survival sva]; };
-  DonaPLLP2013 = derive2 { name="DonaPLLP2013"; version="1.40.0"; sha256="0pxxg6rkdgafxj71mvlbm14vzv414hfh2p24rhyby7glrkzh2vq0"; depends=[EBImage]; };
+  DmelSGI = derive2 { name="DmelSGI"; version="1.36.0"; sha256="0xjj2ky0k8vazw97qsaf79c6cc3whxg0n5v6lrj6slk4hyfcmbw4"; depends=[abind gplots igraph knitr limma rhdf5 TSP]; };
-  DropletTestFiles = derive2 { name="DropletTestFiles"; version="1.12.0"; sha256="0a68xd9ks83a13s1cckmhrc50ijp7dw19yjf37v253q50xjp0z03"; depends=[AnnotationHub ExperimentHub S4Vectors]; };
+  DonaPLLP2013 = derive2 { name="DonaPLLP2013"; version="1.42.0"; sha256="0mcz0vdawz62qpdz8dmw359qim0b5wy42wp5r0h5pw05fh03b9bp"; depends=[EBImage]; };
-  DrugVsDiseasedata = derive2 { name="DrugVsDiseasedata"; version="1.38.0"; sha256="03g6syilb9v9cr2snh5w02ng6drff5i86drbmhv24yabwfgp3ndi"; depends=[]; };
+  DropletTestFiles = derive2 { name="DropletTestFiles"; version="1.14.0"; sha256="1n98mgzc6dscm6wy18mf0l5l5bvx3m35xdniarv83j8302xra9n1"; depends=[AnnotationHub ExperimentHub S4Vectors]; };
-  DuoClustering2018 = derive2 { name="DuoClustering2018"; version="1.20.0"; sha256="0248jc4frjwbv5vq0483s2flbrnd70x4bkad7aphfxvrk897sn9v"; depends=[dplyr ExperimentHub ggplot2 ggthemes magrittr mclust purrr reshape2 tidyr viridis]; };
+  DrugVsDiseasedata = derive2 { name="DrugVsDiseasedata"; version="1.40.0"; sha256="0pmydn60f80ga6la6gxn1l1baw22kqqf1v2gbcniq7qm5axj6vh2"; depends=[]; };
-  DvDdata = derive2 { name="DvDdata"; version="1.38.0"; sha256="16352h34az5sjq0bfgx9qs9njkn3nqws584cm1yydh2v60fclv63"; depends=[]; };
+  DuoClustering2018 = derive2 { name="DuoClustering2018"; version="1.22.0"; sha256="042v3dpirp68qsdbhygvx3apx94xxdmzpm0swii30kzkw1r1xfck"; depends=[dplyr ExperimentHub ggplot2 ggthemes magrittr mclust purrr reshape2 tidyr viridis]; };
-  EGSEAdata = derive2 { name="EGSEAdata"; version="1.30.0"; sha256="0m281qwvz1cdfjf605czammw107x23pjpqh1adx5rvacpzgd8gli"; depends=[]; };
+  DvDdata = derive2 { name="DvDdata"; version="1.40.0"; sha256="0l298n6fj57yz6ml5xp1gmwxkj200pwsijbxxf2k8f028m4igy0k"; depends=[]; };
-  ELMER_data = derive2 { name="ELMER.data"; version="2.26.0"; sha256="0vwzj98pds0n3wc74y84d8srb1rvvf7kn7mjy4zf4d0qrp92sa94"; depends=[GenomicRanges]; };
+  EGSEAdata = derive2 { name="EGSEAdata"; version="1.32.0"; sha256="0448hr7zz1wibi8l3plb9hsr6x0a7hz0pmqchhbzbsqwjjdrsgid"; depends=[]; };
-  EatonEtAlChIPseq = derive2 { name="EatonEtAlChIPseq"; version="0.40.0"; sha256="06mzals24cc4fl5j2w8mwa1s7q98qm80g7gnr5rz4hj66kmiak94"; depends=[GenomicRanges rtracklayer ShortRead]; };
+  ELMER_data = derive2 { name="ELMER.data"; version="2.28.0"; sha256="1ppmdqc0j3hkngg0nzx18vw8sgnfbrhxyb3l1l5mhv3gq02rslxz"; depends=[GenomicRanges]; };
-  EpiMix_data = derive2 { name="EpiMix.data"; version="1.4.0"; sha256="15qc8jjbv6b4nxszrj8lkj6cmbvvxlvknksp5pl13s3y176gm4d5"; depends=[ExperimentHub]; };
+  EatonEtAlChIPseq = derive2 { name="EatonEtAlChIPseq"; version="0.42.0"; sha256="109law5cc64xipwqyanw71h8v5nx08s1iaskh05hm1w18dsjxff1"; depends=[GenomicRanges rtracklayer ShortRead]; };
-  FANTOM3and4CAGE = derive2 { name="FANTOM3and4CAGE"; version="1.38.0"; sha256="01qz41q2cw4g7yg4nj7dlqsw6p8bh7dvm22a0vgp5dpm2pjagh15"; depends=[]; };
+  EpiMix_data = derive2 { name="EpiMix.data"; version="1.6.0"; sha256="037kp9ziawdxfxydg4jb64k6klv9j78wp45gi72prisl4hj5hlp3"; depends=[ExperimentHub]; };
-  FIs = derive2 { name="FIs"; version="1.30.0"; sha256="0pnw0p2n9r1r0a7b1g32s7s2abbvdc976igdf48agkmilkhzpbb4"; depends=[]; };
+  FANTOM3and4CAGE = derive2 { name="FANTOM3and4CAGE"; version="1.40.0"; sha256="0vmpgq694jvrcbnx2ik7cyq2axfm7xl3sibd2b9k3dpxaw62gipm"; depends=[]; };
-  FieldEffectCrc = derive2 { name="FieldEffectCrc"; version="1.12.0"; sha256="13xzypr95v5b3kynfn45b7rpg7kd0gcqmx3ap377plqs42nc7pa6"; depends=[AnnotationHub BiocStyle DESeq2 ExperimentHub RUnit SummarizedExperiment]; };
+  FIs = derive2 { name="FIs"; version="1.32.0"; sha256="0l084k6p8nsnv51fxb55lass72qhjm4ff84i4y3if5p29gzl8frz"; depends=[]; };
-  Fletcher2013a = derive2 { name="Fletcher2013a"; version="1.38.0"; sha256="04rvri7hcc5qd29c0xbkvjylh2x9flk7hf8rngd01fbhk9myxsaj"; depends=[Biobase gplots limma VennDiagram]; };
+  FieldEffectCrc = derive2 { name="FieldEffectCrc"; version="1.14.0"; sha256="0g9b5a7l802z6g2s95x4m914hwwn5qqnlxvag3qbvy3bhwx3xyi6"; depends=[AnnotationHub BiocStyle DESeq2 ExperimentHub RUnit SummarizedExperiment]; };
-  Fletcher2013b = derive2 { name="Fletcher2013b"; version="1.38.0"; sha256="1zp7wafibklwc7gr827yk1m6630c4r11nvy1i8jjhriqrjd4hnpn"; depends=[Fletcher2013a igraph RColorBrewer RedeR RTN]; };
+  Fletcher2013a = derive2 { name="Fletcher2013a"; version="1.40.0"; sha256="0l839hd76xr94qjcnscr9c40nvsx99ir6vsy1zx6dn7cha52mpar"; depends=[Biobase gplots limma VennDiagram]; };
-  FlowSorted_Blood_450k = derive2 { name="FlowSorted.Blood.450k"; version="1.40.0"; sha256="08xli4a24kkyy5q1ka0vyrpk11yfkyp0gxbs0k8khycppsq9s9sn"; depends=[minfi]; };
+  Fletcher2013b = derive2 { name="Fletcher2013b"; version="1.40.0"; sha256="0agnkc207bma3h89xxrzcywny664f42vfd63qnmyda4kvdvvk0km"; depends=[Fletcher2013a igraph RColorBrewer RedeR RTN]; };
-  FlowSorted_Blood_EPIC = derive2 { name="FlowSorted.Blood.EPIC"; version="2.6.0"; sha256="0vfx1kpy02640nkkkpksisznybv0xb6jkvvkwsybsggcr2rdkl89"; depends=[AnnotationHub ExperimentHub genefilter minfi nlme quadprog S4Vectors SummarizedExperiment]; };
+  FlowSorted_Blood_450k = derive2 { name="FlowSorted.Blood.450k"; version="1.42.0"; sha256="0lc45dg5jq0kqycpsggrhi5fa4xj1ciqrj6iw548ccjgdyy2w1xh"; depends=[minfi]; };
-  FlowSorted_CordBlood_450k = derive2 { name="FlowSorted.CordBlood.450k"; version="1.30.0"; sha256="04fx8mc21lflbxdz7fgz0jl30jk4gd09qqn5a654jlqhllnkg9rj"; depends=[minfi]; };
+  FlowSorted_Blood_EPIC = derive2 { name="FlowSorted.Blood.EPIC"; version="2.8.0"; sha256="1b0azyslk2g08i6v1vv2niw32f0zqasw85b9klw83zdy2f5dcdvh"; depends=[AnnotationHub ExperimentHub genefilter minfi nlme quadprog S4Vectors SummarizedExperiment]; };
-  FlowSorted_CordBloodCombined_450k = derive2 { name="FlowSorted.CordBloodCombined.450k"; version="1.18.0"; sha256="0gl0dwhabdik17al1f1zq2vhg3bgbirxmsa1lxfv97vq08nqfshl"; depends=[AnnotationHub ExperimentHub IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b4_hg19 minfi SummarizedExperiment]; };
+  FlowSorted_CordBlood_450k = derive2 { name="FlowSorted.CordBlood.450k"; version="1.32.0"; sha256="1bbx2s8vzkawwpywcc33xbgjbc134q6fqgnflk30sfq1pfpxcmsm"; depends=[minfi]; };
-  FlowSorted_CordBloodNorway_450k = derive2 { name="FlowSorted.CordBloodNorway.450k"; version="1.28.0"; sha256="16hrhakaxhhilfy5gb0yrwijww8ph20i3qnfkrhhz6gjqh0iyri2"; depends=[minfi]; };
+  FlowSorted_CordBloodCombined_450k = derive2 { name="FlowSorted.CordBloodCombined.450k"; version="1.20.0"; sha256="14486v4cs3j1jmifsgy3ihpm5x7i9581yz4bwsl3h2a7p86cdsbv"; depends=[AnnotationHub ExperimentHub IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b4_hg19 minfi SummarizedExperiment]; };
-  FlowSorted_DLPFC_450k = derive2 { name="FlowSorted.DLPFC.450k"; version="1.38.0"; sha256="0dj0gcz8mfd0ilihhysrbrzbkvfpwy1dx56g4dsizkg0k6aa8nha"; depends=[minfi]; };
+  FlowSorted_CordBloodNorway_450k = derive2 { name="FlowSorted.CordBloodNorway.450k"; version="1.30.0"; sha256="1r78j0786bl9420cxcmhw07bzakl71r2kar41bwkd6xwfpj2znj5"; depends=[minfi]; };
-  GIGSEAdata = derive2 { name="GIGSEAdata"; version="1.20.0"; sha256="0qisi43rbjg9y2fglkri3bb1wxn4rcylhlidw2ml4bl7d36rfxdz"; depends=[]; };
+  FlowSorted_DLPFC_450k = derive2 { name="FlowSorted.DLPFC.450k"; version="1.40.0"; sha256="0h21h2nywy9dfqw3d1xw87wah19nidl8k7d0zqpqxql6agr1p92j"; depends=[minfi]; };
-  GSBenchMark = derive2 { name="GSBenchMark"; version="1.22.0"; sha256="03ccpc69k0i0pffw0x0f49h71saz68chyppa8ncpyb5aj4lxp2gb"; depends=[]; };
+  GIGSEAdata = derive2 { name="GIGSEAdata"; version="1.22.0"; sha256="1pwi3bn7xj2m7kg02dwn17rnhirl2qf1d67p2m9194f3iwy4vrp8"; depends=[]; };
-  GSE103322 = derive2 { name="GSE103322"; version="1.8.0"; sha256="018k8vkyr0cvycvkihkajf709jsw0y9mhf8yamzc72x5mwazwhym"; depends=[Biobase GEOquery]; };
+  GSBenchMark = derive2 { name="GSBenchMark"; version="1.24.0"; sha256="1al1k9c513l3if8kag24dkrmr6m8ajck30gd8yqkcncsrrgc769j"; depends=[]; };
-  GSE13015 = derive2 { name="GSE13015"; version="1.10.0"; sha256="1jc40g1gxz7rcxcgx11blx9li3fpa605rzs9k2glaglrp373r7dk"; depends=[Biobase GEOquery preprocessCore SummarizedExperiment]; };
+  GSE103322 = derive2 { name="GSE103322"; version="1.10.0"; sha256="0iv75phj9s8yyk0h3mnv12aak26kspbqhxvc4dbjjdd4g6jawlgv"; depends=[Biobase GEOquery]; };
-  GSE159526 = derive2 { name="GSE159526"; version="1.8.0"; sha256="0z8aywaihmrzfn0pzm5z7pxkpmkrar4090wavvy4vzkqbzdicv8r"; depends=[]; };
+  GSE13015 = derive2 { name="GSE13015"; version="1.12.0"; sha256="0l1v30g1g93wk5bnhkw52pwypby6n0rxpp11aw93j733whn9j2y4"; depends=[Biobase GEOquery preprocessCore SummarizedExperiment]; };
-  GSE62944 = derive2 { name="GSE62944"; version="1.30.0"; sha256="03wy4jjg6fh1fckmy0fqs776b3mhvrksk7hgkrjg7hr7p9b9dxwp"; depends=[Biobase GEOquery]; };
+  GSE159526 = derive2 { name="GSE159526"; version="1.10.0"; sha256="1j8dy1zrw4isscspzb83n7k0x8yaf97zyyfyjh26ff7l997cqdvk"; depends=[]; };
-  GSVAdata = derive2 { name="GSVAdata"; version="1.38.0"; sha256="1a9kspbmsnsrisy5xp5r3s1l7fz34v7riyiqn22hlc87zmnj7y5q"; depends=[Biobase GSEABase hgu95a_db]; };
+  GSE62944 = derive2 { name="GSE62944"; version="1.32.0"; sha256="041sby283m8ajb96gdg3zcrs0l6760svx8wijxfabq9dygiiaqp8"; depends=[Biobase GEOquery]; };
-  GWASdata = derive2 { name="GWASdata"; version="1.40.0"; sha256="0lprcr2r0qzi7pa9pl6cp21z7vkjpn0d6ynnbbzji9ga82hd2njq"; depends=[GWASTools]; };
+  GSVAdata = derive2 { name="GSVAdata"; version="1.40.0"; sha256="0d1xgjizi58hwbralla62jch3kl4bqx0dg0lhh0h1bk9jyicyqjy"; depends=[Biobase GSEABase hgu95a_db]; };
-  GenomicDistributionsData = derive2 { name="GenomicDistributionsData"; version="1.10.0"; sha256="1c9pqmdnnpm80zzsbl3j66xdwb3kzn7jkisx31sn5jaxzc660jc4"; depends=[AnnotationFilter AnnotationHub BSgenome data_table ensembldb ExperimentHub GenomeInfoDb GenomicFeatures GenomicRanges]; };
+  GWASdata = derive2 { name="GWASdata"; version="1.42.0"; sha256="08w9qlf6vprvf383mji0hhzpn65jicqmkbljqndh7r7s4hp1z9jr"; depends=[GWASTools]; };
-  GeuvadisTranscriptExpr = derive2 { name="GeuvadisTranscriptExpr"; version="1.30.0"; sha256="12253pncfqvq7c1ajkdgfn4f861w2zk3j6p5xyra7c0d0z47a2b6"; depends=[]; };
+  GenomicDistributionsData = derive2 { name="GenomicDistributionsData"; version="1.12.0"; sha256="16cj8w6n053aciz9wclppmc22b9s4a9lh58r6wi2lhs0sp7iirzn"; depends=[AnnotationFilter AnnotationHub BSgenome data_table ensembldb ExperimentHub GenomeInfoDb GenomicFeatures GenomicRanges]; };
-  HCAData = derive2 { name="HCAData"; version="1.18.0"; sha256="1rd1qra8g7dn9pg2mhh2j40p7p6ny838n4w6mx5ryw4xky95lf41"; depends=[AnnotationHub ExperimentHub HDF5Array SingleCellExperiment]; };
+  GeuvadisTranscriptExpr = derive2 { name="GeuvadisTranscriptExpr"; version="1.32.0"; sha256="1n9yq4lqs6v9qdw9rm9hy8dww6n5axpkncms2drkjn2hv8xlqgj8"; depends=[]; };
-  HCATonsilData = derive2 { name="HCATonsilData"; version="1.0.0"; sha256="1h5hrfslhyiqc855bb23rz9hahnpcy47h2lz1k0dj8glrjldq0jp"; depends=[base64enc ExperimentHub HDF5Array htmltools rmarkdown S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
+  HCAData = derive2 { name="HCAData"; version="1.20.0"; sha256="1kdp9iwn0vy7hlxyh09vrl6cwj7ajy2zqk23w3rxa5py710prp1q"; depends=[AnnotationHub ExperimentHub HDF5Array SingleCellExperiment]; };
-  HD2013SGI = derive2 { name="HD2013SGI"; version="1.42.0"; sha256="1xxc85al19qxj17rj1k4q0xp3wgkxr007akmq3an7mqrah0y8hm8"; depends=[EBImage geneplotter gplots limma LSD RColorBrewer splots vcd]; };
+  HCATonsilData = derive2 { name="HCATonsilData"; version="1.2.0"; sha256="1wg0mvc3gwf80bgsfkvdcnnzy7qbnffbbrcy3f87jyw4a20irpp1"; depends=[base64enc ExperimentHub HDF5Array htmltools rmarkdown S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
-  HDCytoData = derive2 { name="HDCytoData"; version="1.22.1"; sha256="1048xgypsw257ihy0ysfxy5443dzhzp2rkjjvpivvrhw4dzl25ir"; depends=[ExperimentHub flowCore SummarizedExperiment]; };
+  HD2013SGI = derive2 { name="HD2013SGI"; version="1.44.0"; sha256="0r4nlbz7b70z1ii9wisk8nj218m2j5qmpfj8k2sp8k723gmsg4x0"; depends=[EBImage geneplotter gplots limma LSD RColorBrewer splots vcd]; };
-  HEEBOdata = derive2 { name="HEEBOdata"; version="1.40.0"; sha256="1xijrm32p191qydz1gkm8321b8ycb9h6y6m1qvc8shlhbbzw705h"; depends=[]; };
+  HDCytoData = derive2 { name="HDCytoData"; version="1.24.0"; sha256="0pmzgp7x1zam3b7agi8mdq14qmx8nln9lnhiglax2pvg2a5n4ii4"; depends=[ExperimentHub flowCore SummarizedExperiment]; };
-  HIVcDNAvantWout03 = derive2 { name="HIVcDNAvantWout03"; version="1.42.0"; sha256="0kyblhc6fdc5c45qyqcr2qnmp1zrwdrc0j91fml04pw5yxrf6dw0"; depends=[]; };
+  HEEBOdata = derive2 { name="HEEBOdata"; version="1.42.0"; sha256="0nkggzidbzya9g7v412iwjkm6pah5siha1jai48k3hhfa4i51jj7"; depends=[]; };
-  HMP16SData = derive2 { name="HMP16SData"; version="1.22.0"; sha256="1ns7yyw0w8rrkw87awrrzxmb44gkkb1cn6j3cbzj8fbrd9whl30d"; depends=[AnnotationHub assertthat dplyr ExperimentHub kableExtra knitr magrittr readr S4Vectors stringr SummarizedExperiment tibble]; };
+  HIVcDNAvantWout03 = derive2 { name="HIVcDNAvantWout03"; version="1.44.0"; sha256="1mrza15digswpqszff88caclfwbwxql7dx6gih4gz72cnpyx3fpj"; depends=[]; };
-  HMP2Data = derive2 { name="HMP2Data"; version="1.16.0"; sha256="1xrvslsybzy1zjvck6imrjxzd0hsiyx4ly71ndirxs7yhh13d1qk"; depends=[AnnotationHub assertthat data_table dplyr ExperimentHub kableExtra knitr magrittr MultiAssayExperiment phyloseq readr S4Vectors SummarizedExperiment]; };
+  HMP16SData = derive2 { name="HMP16SData"; version="1.24.0"; sha256="16x7mw5bdsyda1qv0v739pkr8lxq8hga84vhmaa8qnx45pwqyyh0"; depends=[AnnotationHub assertthat dplyr ExperimentHub kableExtra knitr magrittr readr S4Vectors stringr SummarizedExperiment tibble]; };
-  HSMMSingleCell = derive2 { name="HSMMSingleCell"; version="1.22.0"; sha256="1nf6jsjvy3qacwz0dl5jc9h87xhj9q73b0g49c2yrxvv1dhayq0i"; depends=[]; };
+  HMP2Data = derive2 { name="HMP2Data"; version="1.18.0"; sha256="014bf29kg9dizi3p0fdxrs42bf9a0dc2f7zd7yxzvzs3jqvniji2"; depends=[AnnotationHub assertthat data_table dplyr ExperimentHub kableExtra knitr magrittr MultiAssayExperiment phyloseq readr S4Vectors SummarizedExperiment]; };
-  HarmanData = derive2 { name="HarmanData"; version="1.30.0"; sha256="0mqv76lj2amb18k5533r6lc42g4a0jggcj7h2dh1lk1hl973asqg"; depends=[]; };
+  HSMMSingleCell = derive2 { name="HSMMSingleCell"; version="1.24.0"; sha256="18p8hk2dq26pp4fvcf1m8wsvj1mn66i8nr900knl2n9vs09j70wy"; depends=[]; };
-  HarmonizedTCGAData = derive2 { name="HarmonizedTCGAData"; version="1.24.0"; sha256="1sfb7kzmwdvv71bf56z6sd81dfrs4v53igmnxphrvjiymdjxrb3b"; depends=[ExperimentHub]; };
+  HarmanData = derive2 { name="HarmanData"; version="1.32.0"; sha256="1bf9jl9gl10gawv835hp8wxzzs1v9g3y3qzpki63j3dw5yssazh5"; depends=[]; };
-  HelloRangesData = derive2 { name="HelloRangesData"; version="1.28.0"; sha256="09jrcwrn5vjsva2fz28193llhrysswhxyq83rczi5dnimr5qqnxc"; depends=[]; };
+  HarmonizedTCGAData = derive2 { name="HarmonizedTCGAData"; version="1.26.0"; sha256="1zi0605nq51zpgap9jsbkilpxalwlpld0crvxivk6pmgrbavvlf7"; depends=[ExperimentHub]; };
-  HiBED = derive2 { name="HiBED"; version="1.0.0"; sha256="1cacjpghp5zbbcvn0fpfyhg56dx9bfa8d2qwf1dvbmwwcm85l0vw"; depends=[AnnotationHub dplyr FlowSorted_Blood_EPIC FlowSorted_DLPFC_450k minfi SummarizedExperiment tibble]; };
+  HelloRangesData = derive2 { name="HelloRangesData"; version="1.30.0"; sha256="19gk0xhvpnqqrr6pxiwyyhszi93pjjfiknfj1gvzdrj81p06qhbh"; depends=[]; };
-  HiCDataHumanIMR90 = derive2 { name="HiCDataHumanIMR90"; version="1.22.0"; sha256="1jy5hpq8vdki23yy3ivlhqj6k80z1rnby4xrk83wk0rxiz4sdxix"; depends=[]; };
+  HiBED = derive2 { name="HiBED"; version="1.2.0"; sha256="0sqxlm2nn8g7qfwhndf79dg7v57ngmznr0b297v59nhhpigs1g2q"; depends=[AnnotationHub dplyr FlowSorted_Blood_EPIC FlowSorted_DLPFC_450k minfi SummarizedExperiment tibble]; };
-  HiCDataLymphoblast = derive2 { name="HiCDataLymphoblast"; version="1.38.0"; sha256="1a6kf55sqqpqs3gk76np9payqj9i75ggn06iy46cazslnhnvmdvg"; depends=[]; };
+  HiCDataHumanIMR90 = derive2 { name="HiCDataHumanIMR90"; version="1.24.0"; sha256="1xndbds4clzpblc6gjz7lr48pkvi3j2m0a9jzavff45ds7aa6jxk"; depends=[]; };
-  HiContactsData = derive2 { name="HiContactsData"; version="1.4.0"; sha256="07i91rz7bn6g27wbjrwgck3mdmj8lrsdda6pza9k1ghh5zssrx7i"; depends=[AnnotationHub BiocFileCache ExperimentHub]; };
+  HiCDataLymphoblast = derive2 { name="HiCDataLymphoblast"; version="1.40.0"; sha256="1sb384dca5n1lanv5k4idjx1b1hmvfdv1xp14m8k00gcnacgj9v3"; depends=[]; };
-  HighlyReplicatedRNASeq = derive2 { name="HighlyReplicatedRNASeq"; version="1.14.0"; sha256="1zz6xqn9amlh7v7v8c67i4n94lxc8w46g3gqnhbrlcpi6zid36a9"; depends=[ExperimentHub S4Vectors SummarizedExperiment]; };
+  HiContactsData = derive2 { name="HiContactsData"; version="1.6.0"; sha256="0q92gvvlx4zx6sxi9sdzwjmwvdzaw6fj0nkr5d4h8j0hv7ycylmi"; depends=[AnnotationHub BiocFileCache ExperimentHub]; };
-  Hiiragi2013 = derive2 { name="Hiiragi2013"; version="1.38.0"; sha256="04ywn2nw551x082v9pxglxl83kfccsds566lwkpa87098i4wdx85"; depends=[affy Biobase boot clue cluster genefilter geneplotter gplots gtools KEGGREST lattice latticeExtra MASS mouse4302_db RColorBrewer xtable]; };
+  HighlyReplicatedRNASeq = derive2 { name="HighlyReplicatedRNASeq"; version="1.16.0"; sha256="01b09hk33p14lfrrpk0agi6prf9wbv6zs0qn07jdsm63vmawscds"; depends=[ExperimentHub S4Vectors SummarizedExperiment]; };
-  HumanAffyData = derive2 { name="HumanAffyData"; version="1.28.0"; sha256="0g24nr0jdw6509xjski83jf2r35iklmnhqikmfr90ki4rn0fqar0"; depends=[Biobase ExperimentHub]; };
+  Hiiragi2013 = derive2 { name="Hiiragi2013"; version="1.40.0"; sha256="0xn3ayh2x04cvwrr476k8vlp8lhk5lxaqg01a0ynkrrc4scf2f99"; depends=[affy Biobase boot clue cluster genefilter geneplotter gplots gtools KEGGREST lattice latticeExtra MASS mouse4302_db RColorBrewer xtable]; };
-  IHWpaper = derive2 { name="IHWpaper"; version="1.30.0"; sha256="06qbcnq2i0qjc4xqld3gd8746qpvxy4avqba82vzdk0h95kxirmj"; depends=[Biobase BiocGenerics BiocParallel cowplot DESeq2 dplyr fdrtool genefilter ggplot2 IHW qvalue Rcpp SummarizedExperiment]; };
+  HumanAffyData = derive2 { name="HumanAffyData"; version="1.30.0"; sha256="0jnikpd3djps3wp4vd3l9911jkzfm8h5pp0gv8l9bx5s2skkdrw1"; depends=[Biobase ExperimentHub]; };
-  ITALICSData = derive2 { name="ITALICSData"; version="2.40.0"; sha256="0fzx2qqykma2r2ds53wik4kb9a0wvybr63vf34s91731k21mgsqn"; depends=[]; };
+  IHWpaper = derive2 { name="IHWpaper"; version="1.32.0"; sha256="0s3x2chbr8ik3rhgzmfhaq8xlsnnkzfhjh4p327sn5aar6xhaj67"; depends=[Biobase BiocGenerics BiocParallel cowplot DESeq2 dplyr fdrtool genefilter ggplot2 IHW qvalue Rcpp SummarizedExperiment]; };
-  Illumina450ProbeVariants_db = derive2 { name="Illumina450ProbeVariants.db"; version="1.38.0"; sha256="1h0qcdmyd22x5y5iwi1w89ppb1k3nb2awwim1lcxgdinab8km52b"; depends=[]; };
+  ITALICSData = derive2 { name="ITALICSData"; version="2.42.0"; sha256="1d0awis142kgx9hi0dggl6gqg17m0awqzn8ncpqh2lwaka372dq8"; depends=[]; };
-  IlluminaDataTestFiles = derive2 { name="IlluminaDataTestFiles"; version="1.40.0"; sha256="08fb7aywjjka5lrpb46cd322sfnhcch5ilf5aq0a2sdq12m2psyi"; depends=[]; };
+  Illumina450ProbeVariants_db = derive2 { name="Illumina450ProbeVariants.db"; version="1.40.0"; sha256="1jpknhp624753rhalf81kvl02k4wj19xpncagzf85c878953vph0"; depends=[]; };
-  Iyer517 = derive2 { name="Iyer517"; version="1.44.0"; sha256="1zahcx2kjspm3bvgxklfgd34srlrxcq9xcj37qa20b08892llkk7"; depends=[Biobase]; };
+  IlluminaDataTestFiles = derive2 { name="IlluminaDataTestFiles"; version="1.42.0"; sha256="0xmyhqaa34chd2fxzbs7rk72wyx086cfhnjjh4lwjmb8acbp9xi8"; depends=[]; };
-  JASPAR2014 = derive2 { name="JASPAR2014"; version="1.38.0"; sha256="1ha5nm4v28bfxxa6jqkag7hy0b7bph15v1qs8xwd9w2wam2znazx"; depends=[Biostrings]; };
+  Iyer517 = derive2 { name="Iyer517"; version="1.46.0"; sha256="0b9j6bc0dfx5mqyd7z7bzmfp6s59cy4dqr1pxzjy05yyfznbc72p"; depends=[Biobase]; };
-  JASPAR2016 = derive2 { name="JASPAR2016"; version="1.30.0"; sha256="0dyx29f7jnyqcj85j2yrl8jcphi2kymx2y2mk7ws25xcahl5zzpy"; depends=[]; };
+  JASPAR2014 = derive2 { name="JASPAR2014"; version="1.40.0"; sha256="0m4g6vp78zsnzkfjmjfjwvd04505lz55njm7ml7dycwv6lmaxivk"; depends=[Biostrings]; };
-  KEGGandMetacoreDzPathwaysGEO = derive2 { name="KEGGandMetacoreDzPathwaysGEO"; version="1.22.0"; sha256="1rmn5zx5p4c8is5dd80nppl1r8ciyccwhiir0312bpaaplyc9qks"; depends=[Biobase BiocGenerics]; };
+  JASPAR2016 = derive2 { name="JASPAR2016"; version="1.32.0"; sha256="09q5m71drbp64n26plr0a9bz71akcs4g7pqqyjmsmjrzi40kx7hr"; depends=[]; };
-  KEGGdzPathwaysGEO = derive2 { name="KEGGdzPathwaysGEO"; version="1.40.0"; sha256="05s6cq27cdw9w9laq5hxjiynjavd873w2idpwa1k4kw0rdsni8cb"; depends=[Biobase BiocGenerics]; };
+  JohnsonKinaseData = derive2 { name="JohnsonKinaseData"; version="1.0.0"; sha256="1ry5p2zll8hazxil4sa57v50b7xr9bk4p5a509i4mvasb089al3l"; depends=[BiocParallel checkmate dplyr ExperimentHub purrr stringr tidyr]; };
-  KOdata = derive2 { name="KOdata"; version="1.28.0"; sha256="1dflsvfz7c2ahs60s4wx8mc9ar8qrz9ax8g9m67jchygcmqs4jla"; depends=[]; };
+  KEGGandMetacoreDzPathwaysGEO = derive2 { name="KEGGandMetacoreDzPathwaysGEO"; version="1.24.0"; sha256="1fqybcvwa8dls2kv8mkdydmkw0bzihr3xp3m853mffkdjjsrzkyk"; depends=[Biobase BiocGenerics]; };
-  LRcellTypeMarkers = derive2 { name="LRcellTypeMarkers"; version="1.10.0"; sha256="1wad78cpgf9pl8hl4issb0k1m0dlrk0bradkdz5b5a5pamlwh82c"; depends=[ExperimentHub]; };
+  KEGGdzPathwaysGEO = derive2 { name="KEGGdzPathwaysGEO"; version="1.42.0"; sha256="1mbvy9x8zp02337sw92hh00vvqcamldqdsdy4zp53qiskrpidkdc"; depends=[Biobase BiocGenerics]; };
-  LiebermanAidenHiC2009 = derive2 { name="LiebermanAidenHiC2009"; version="0.40.0"; sha256="06qifvjaxjz51p2vkfdzxjbj5040772y3gzc0qpzsh5fapprkxv9"; depends=[IRanges KernSmooth]; };
+  KOdata = derive2 { name="KOdata"; version="1.30.0"; sha256="1ia8fyas2yfird4a0md85s3ak96hb1pdrvay48zzsmhmpgf1yj44"; depends=[]; };
-  ListerEtAlBSseq = derive2 { name="ListerEtAlBSseq"; version="1.34.0"; sha256="15v80d554pai4584dhy3nzwva38b9r6997br7xqysj7v8x2f4392"; depends=[methylPipe]; };
+  LRcellTypeMarkers = derive2 { name="LRcellTypeMarkers"; version="1.12.0"; sha256="1cghhh1rv8w7819dzi982q862m6yj62pckx8r925j2di1him9db8"; depends=[ExperimentHub]; };
-  LungCancerACvsSCCGEO = derive2 { name="LungCancerACvsSCCGEO"; version="1.38.0"; sha256="1d0zfx6sqwanyh67996v008sjkscskm5z24n9siklc9w416nqa63"; depends=[]; };
+  LiebermanAidenHiC2009 = derive2 { name="LiebermanAidenHiC2009"; version="0.42.0"; sha256="0hx2lfpidg54r6kslz3yx6d1lv4vjdrk6s2whii0070hbr18lvjj"; depends=[IRanges KernSmooth]; };
-  LungCancerLines = derive2 { name="LungCancerLines"; version="0.40.0"; sha256="0yr7l7964nkwlz6s9hsdab2sihrngk9wqakrn4pm5h8m15f8ls46"; depends=[Rsamtools]; };
+  ListerEtAlBSseq = derive2 { name="ListerEtAlBSseq"; version="1.36.0"; sha256="0j4vvac93m8vqidwvqczggkfdk07dabycqprhsnmj8f0g8hpaq9v"; depends=[methylPipe]; };
-  M3DExampleData = derive2 { name="M3DExampleData"; version="1.28.0"; sha256="0rp1zp14wvfwy67m0ph8amm41frj76gfylacdbdjyblcpdgzzlnq"; depends=[]; };
+  LungCancerACvsSCCGEO = derive2 { name="LungCancerACvsSCCGEO"; version="1.40.0"; sha256="1h0m67ak452bbza0s3dsmh2vi9wdi1mgl4bvflhin1gxcgb6fk6p"; depends=[]; };
-  MACSdata = derive2 { name="MACSdata"; version="1.10.0"; sha256="117jy39rn972hzwcckx5wdsrsxfzhwbx4wb6air4l7xcb6qmfrj1"; depends=[]; };
+  LungCancerLines = derive2 { name="LungCancerLines"; version="0.42.0"; sha256="0gmjpagl71vddsvcx3iwql175lv0lc5m6j071wnwh10z59a9jams"; depends=[Rsamtools]; };
-  MAQCsubset = derive2 { name="MAQCsubset"; version="1.40.0"; sha256="1qqn4mf2jrdkn28n1npzag50m24j29nm0adcj276s8fgwdayv434"; depends=[affy Biobase lumi]; };
+  M3DExampleData = derive2 { name="M3DExampleData"; version="1.30.0"; sha256="0g7p7vn2im6d4gamalfm2lcssdg874fgb23wra5c34dzrzz9nr0v"; depends=[]; };
-  MAQCsubsetILM = derive2 { name="MAQCsubsetILM"; version="1.40.0"; sha256="1bb158bmy7195wnj0wap08g621xbzflvj30pv4l7mwc54lm1vqfx"; depends=[Biobase lumi]; };
+  MACSdata = derive2 { name="MACSdata"; version="1.12.0"; sha256="0wffmyshsylf118xfcdyl8bd5xy9gz726lpx3avmxz3a8x917vbr"; depends=[]; };
-  MEDIPSData = derive2 { name="MEDIPSData"; version="1.38.0"; sha256="1lrxg5vrfqxrnnpn8m3ypk3ikc6pa7pszxfi08gaa3a4c2glcc4m"; depends=[]; };
+  MAQCsubset = derive2 { name="MAQCsubset"; version="1.42.0"; sha256="0x59gbv91d90hasa2gwkv00c06zp8fj4fk18386ajfag0wpvpb2n"; depends=[affy Biobase lumi]; };
-  MEEBOdata = derive2 { name="MEEBOdata"; version="1.40.0"; sha256="0ni928njn0hm38njgbnz223pvpq1318si12z5d56h3cczi2f3a37"; depends=[]; };
+  MEDIPSData = derive2 { name="MEDIPSData"; version="1.40.0"; sha256="0x9317wgrhvqwh87d1vls5m06jyzsli2yhkc345n6iwxzz3a0brr"; depends=[]; };
-  MMAPPR2data = derive2 { name="MMAPPR2data"; version="1.16.0"; sha256="16ang08nc4jw8m4faacd0rhv47h5wlp771nd6d8bn1r6d5b9si3w"; depends=[Rsamtools]; };
+  MEEBOdata = derive2 { name="MEEBOdata"; version="1.42.0"; sha256="1cj563a0fjwdrbrwnfzk7l79mjg95hanp5rs6rvjz30b8s5gmwqm"; depends=[]; };
-  MMDiffBamSubset = derive2 { name="MMDiffBamSubset"; version="1.38.0"; sha256="1awhcc4zjmzwqc35xv1l2alybbnv1b16bbxn85xywdq0qyj8zgxp"; depends=[]; };
+  MMAPPR2data = derive2 { name="MMAPPR2data"; version="1.18.0"; sha256="0rbi0psjwk0jgjpliv0hhjvq9wmwb8w4wgqw45wqba6qfpm70wya"; depends=[Rsamtools]; };
-  MOFAdata = derive2 { name="MOFAdata"; version="1.18.0"; sha256="1pl593dlf87g88bdabqqn2a9b1vkgg4znp1l9wbyk49a35l2rqy1"; depends=[]; };
+  MMDiffBamSubset = derive2 { name="MMDiffBamSubset"; version="1.40.0"; sha256="1psm5f7wrqwqwxzkmqkaz629i1d7zn2s5zs6sgmhijqp7rzhmhc4"; depends=[]; };
-  MSMB = derive2 { name="MSMB"; version="1.20.0"; sha256="1nq9y7c3y0q1040fzsg5hiavqq4n1778cry420f03db1yg40lns0"; depends=[tibble]; };
+  MOFAdata = derive2 { name="MOFAdata"; version="1.20.0"; sha256="1sjpvs2vdmmrr5mkk734502lhs3nr3n0brscvh77y1n42abxy26x"; depends=[]; };
-  MUGAExampleData = derive2 { name="MUGAExampleData"; version="1.22.0"; sha256="1q8bqqpc14iymmmmv87yqzkpjlzq4r801hjav8kymsw66zlqi0rq"; depends=[]; };
+  MSMB = derive2 { name="MSMB"; version="1.22.0"; sha256="0kwjdgf526q63kln6j7a0v6v14x1qx5hlpannpb5grah2lyxz4rw"; depends=[tibble]; };
-  MerfishData = derive2 { name="MerfishData"; version="1.4.1"; sha256="055wmm0r8wyv8i2kil5f5lh5n2kjw36q4yrpqswf0fvdsvvrpaak"; depends=[AnnotationHub BumpyMatrix EBImage ExperimentHub S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
+  MUGAExampleData = derive2 { name="MUGAExampleData"; version="1.24.0"; sha256="0mrap1whvlzlmbrfg611cq3c9a1w2pq3wmijk842cybsx8az59xd"; depends=[]; };
-  MetaGxBreast = derive2 { name="MetaGxBreast"; version="1.22.0"; sha256="0b0s7g4ijqlsfbr8wdrs1g54hba9ry6i1af71ly0v6l7ff0j65r1"; depends=[AnnotationHub Biobase ExperimentHub impute lattice SummarizedExperiment]; };
+  MerfishData = derive2 { name="MerfishData"; version="1.6.0"; sha256="1i8war9rg7fwjdfhj5xa6sp3lmp30j0di04gckskmz6pk9pjjg4r"; depends=[AnnotationHub BumpyMatrix EBImage ExperimentHub S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
-  MetaGxOvarian = derive2 { name="MetaGxOvarian"; version="1.22.0"; sha256="0k144fi1i9c1rlsif2pfk4lyzk25lkpfp1c4yanqqzbij8z50y6k"; depends=[AnnotationHub Biobase ExperimentHub impute lattice SummarizedExperiment]; };
+  MetaGxBreast = derive2 { name="MetaGxBreast"; version="1.24.0"; sha256="05cz500r6fhlq5pfviiqj8cfv173027dqsdvhvvi57cbbx3qqn6r"; depends=[AnnotationHub Biobase ExperimentHub impute lattice SummarizedExperiment]; };
-  MetaGxPancreas = derive2 { name="MetaGxPancreas"; version="1.22.0"; sha256="0a5daghij0c6ykdh2vvd0gmrinqbvnn2hm8apga768ib04ylhb13"; depends=[AnnotationHub ExperimentHub impute S4Vectors SummarizedExperiment]; };
+  MetaGxOvarian = derive2 { name="MetaGxOvarian"; version="1.24.0"; sha256="01cnm2rf6ls1q5plgazxqkrrw3b6mcrxbq0wrmi0ra8daqh6asi7"; depends=[AnnotationHub Biobase ExperimentHub impute lattice SummarizedExperiment]; };
-  MetaScope = derive2 { name="MetaScope"; version="1.2.0"; sha256="0wpp2h3zldvcw9r8bjbbpcvkd3hgh11dp8qalcbm36kx4djc2d1a"; depends=[BiocFileCache Biostrings data_table dplyr ggplot2 magrittr Matrix MultiAssayExperiment Rbowtie2 readr rlang Rsamtools S4Vectors stringr SummarizedExperiment taxize tidyr]; };
+  MetaGxPancreas = derive2 { name="MetaGxPancreas"; version="1.24.0"; sha256="150i72jrq3qshsh0m20kxdcx7zxz1cgvlk0y2nxnacs1xbdnywxv"; depends=[AnnotationHub ExperimentHub impute S4Vectors SummarizedExperiment]; };
-  MethylAidData = derive2 { name="MethylAidData"; version="1.34.0"; sha256="0kn20wsij54c3i2w3yai97qqmnbawsz0326ai5zrlkalkra4w1r9"; depends=[MethylAid]; };
+  MetaScope = derive2 { name="MetaScope"; version="1.4.0"; sha256="1kaisvhp66g95w4dycw8jzsxh00f2c193rjcla6l5k2dn5rnsyr9"; depends=[BiocFileCache Biostrings data_table dplyr ggplot2 magrittr Matrix MultiAssayExperiment Rbowtie2 readr rlang Rsamtools S4Vectors stringr SummarizedExperiment taxize tibble tidyr]; };
-  MethylSeqData = derive2 { name="MethylSeqData"; version="1.12.0"; sha256="0bw450ada6nnz19d2b9qvx0szyldswrsmy21vsm0dw7idh4xfj6c"; depends=[ExperimentHub GenomeInfoDb GenomicRanges HDF5Array IRanges rhdf5 S4Vectors SummarizedExperiment]; };
+  MethylAidData = derive2 { name="MethylAidData"; version="1.36.0"; sha256="1f328mhf9b64scr45c9sshcgnsw9lb1g9in22xx2sak40dspjx2a"; depends=[MethylAid]; };
-  MicrobiomeBenchmarkData = derive2 { name="MicrobiomeBenchmarkData"; version="1.4.0"; sha256="1546ccbnz86scdslf17rzsvyc7h0pb4mw77b17jicfwr8h4qff25"; depends=[ape BiocFileCache S4Vectors SummarizedExperiment TreeSummarizedExperiment]; };
+  MethylSeqData = derive2 { name="MethylSeqData"; version="1.14.0"; sha256="197347pavq9hjcpwa9lq66lyjr1jb7mymd9pjz01rr9f77d7rqq5"; depends=[ExperimentHub GenomeInfoDb GenomicRanges HDF5Array IRanges rhdf5 S4Vectors SummarizedExperiment]; };
-  MouseGastrulationData = derive2 { name="MouseGastrulationData"; version="1.16.0"; sha256="0m03wrqgfhlyc0rmjjcj8b9gcc2rv644hffnff3j1bnkjg5rldi0"; depends=[BiocGenerics BumpyMatrix ExperimentHub S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
+  MicrobiomeBenchmarkData = derive2 { name="MicrobiomeBenchmarkData"; version="1.6.0"; sha256="00lr183x24yx4xd9cpxvzkcxmqp4dinfi1nz2arqqxnbfcp2s25j"; depends=[ape BiocFileCache S4Vectors SummarizedExperiment TreeSummarizedExperiment]; };
-  MouseThymusAgeing = derive2 { name="MouseThymusAgeing"; version="1.10.0"; sha256="19p7a0k565yz5201klib85z2gwqss0ywbv66sh0bvk4g5cmd9k0y"; depends=[BiocGenerics ExperimentHub S4Vectors SingleCellExperiment SummarizedExperiment]; };
+  MouseAgingData = derive2 { name="MouseAgingData"; version="1.0.0"; sha256="1867xjhwbsjlzlm8fq0j8ggbhhym427l7vcx9i9g6zwkda7p64x3"; depends=[AnnotationHub ExperimentHub SingleCellExperiment]; };
-  NCIgraphData = derive2 { name="NCIgraphData"; version="1.38.0"; sha256="1haia26flsmh553z0pn4zh4s9w3smkl5q16hmz4vpfwkgc3f9506"; depends=[]; };
+  MouseGastrulationData = derive2 { name="MouseGastrulationData"; version="1.18.0"; sha256="0adw98vym1jir1jrzaws7zrlfvls6rfl8bvkpq5sjy4crb33lxy2"; depends=[BiocGenerics BumpyMatrix ExperimentHub S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
-  NGScopyData = derive2 { name="NGScopyData"; version="1.22.0"; sha256="0858c5cqkjlk55whiravwmnia26yfkgw4656zfscpdfz2n9xm50m"; depends=[]; };
+  MouseThymusAgeing = derive2 { name="MouseThymusAgeing"; version="1.12.0"; sha256="1vkbfni6zyr9qhzxfgfj7c5y639amsgbi3chcnsch36r35bnaxp2"; depends=[BiocGenerics ExperimentHub S4Vectors SingleCellExperiment SummarizedExperiment]; };
-  NanoporeRNASeq = derive2 { name="NanoporeRNASeq"; version="1.12.0"; sha256="0jvwl6k12acinwsvs62vx7dpnhjbcvhf8sbdw13gwwknrn96hgh4"; depends=[ExperimentHub]; };
+  NCIgraphData = derive2 { name="NCIgraphData"; version="1.40.0"; sha256="0macj01775q3dzqhvsbfb2gkz0s8w49vgbfh2nhpgfykwzx5bwjm"; depends=[]; };
-  NestLink = derive2 { name="NestLink"; version="1.18.0"; sha256="1nr7ddlrbd4q963750x3cdnn7y6mf2y5q3v37ilhfplypnynlgy1"; depends=[AnnotationHub Biostrings ExperimentHub gplots protViz ShortRead]; };
+  NGScopyData = derive2 { name="NGScopyData"; version="1.24.0"; sha256="1j780dkzv08ajyz0c9dh2ygqsyycyhnzvxl1jrc3gvxdddr1syvj"; depends=[]; };
-  NetActivityData = derive2 { name="NetActivityData"; version="1.4.0"; sha256="1h3ih2y9jl5d3xk5fydgs9s9bsny3lksn67jxmrksxxrabr5zknl"; depends=[]; };
+  NanoporeRNASeq = derive2 { name="NanoporeRNASeq"; version="1.14.0"; sha256="0lpjxpw5jd4zj9pjd3xjcaxkcn135rbhz628zpl44qrdnmyjg2wk"; depends=[ExperimentHub]; };
-  Neve2006 = derive2 { name="Neve2006"; version="0.40.0"; sha256="0an77i7z2pqrgizd0z5n4iihg9zp3xbl8rgnfphsh9q3fbvwp185"; depends=[annotate Biobase hgu133a_db]; };
+  NestLink = derive2 { name="NestLink"; version="1.20.0"; sha256="1yh1nivipyrx3h0par8cf943licl1rs47jvfwz1392hi09vji15j"; depends=[AnnotationHub Biostrings ExperimentHub gplots protViz ShortRead]; };
-  NxtIRFdata = derive2 { name="NxtIRFdata"; version="1.8.0"; sha256="0gvx81w5krzdzz4v09qlscr0hklzmxq2pz4slwwy1dflq0rjswk5"; depends=[BiocFileCache ExperimentHub R_utils rtracklayer]; };
+  NetActivityData = derive2 { name="NetActivityData"; version="1.6.0"; sha256="1jcj9k5mzf30wimwwv4gix85n597bv20bjh32nrha2yqiihp9k34"; depends=[]; };
-  OMICsPCAdata = derive2 { name="OMICsPCAdata"; version="1.20.0"; sha256="1jbdyxqyjp4yn6ywk80gin29wi5szwnz661l9hb8gcfbmhv5m1sv"; depends=[MultiAssayExperiment]; };
+  Neve2006 = derive2 { name="Neve2006"; version="0.42.0"; sha256="0w3ph610lhxyg1knhsnnxpw32sw2n5p57svpbhqm3zmphx29nw3h"; depends=[annotate Biobase hgu133a_db]; };
-  ObMiTi = derive2 { name="ObMiTi"; version="1.10.0"; sha256="1sgl38mbnv99miy6n2gps9r5dzhadf1gvin95nif379kdq6xl0nz"; depends=[ExperimentHub SummarizedExperiment]; };
+  NxtIRFdata = derive2 { name="NxtIRFdata"; version="1.10.0"; sha256="0qwqpzaqp9m8202sp7pdpii90j9yh97ipk36ivh9ba3s05agwq8p"; depends=[BiocFileCache ExperimentHub R_utils rtracklayer]; };
-  OnassisJavaLibs = derive2 { name="OnassisJavaLibs"; version="1.24.0"; sha256="0ynb0n4d1ic1xhnwvqxvncr3vm5kwl3y0771rivrz6rrynfchy4c"; depends=[rJava]; };
+  OMICsPCAdata = derive2 { name="OMICsPCAdata"; version="1.22.0"; sha256="0p0pjgffxc72b3wx6wnn0d0wc27qdp5z6my1xr19604drn7sd20x"; depends=[MultiAssayExperiment]; };
-  PCHiCdata = derive2 { name="PCHiCdata"; version="1.30.0"; sha256="19xzn1agfn34y16prfcgwzbz40bw654zj28lhamiv2mvljxy60jx"; depends=[Chicago]; };
+  ObMiTi = derive2 { name="ObMiTi"; version="1.12.0"; sha256="061qyy69wlr5zhp3m499lq83dq7rwch8ll3a10vwmmwx1l40n8xa"; depends=[ExperimentHub SummarizedExperiment]; };
-  PREDAsampledata = derive2 { name="PREDAsampledata"; version="0.42.0"; sha256="1ps8m8g0s5vsxhhr80ylxcngnn7xipfc70cyxszwmhcwgy1ghwja"; depends=[affy annotate Biobase PREDA]; };
+  OnassisJavaLibs = derive2 { name="OnassisJavaLibs"; version="1.26.0"; sha256="1j2nyrkx9ish1v2yvr8wsahhclpy2mvdnrwnk19fkv8kr1hjwjws"; depends=[rJava]; };
-  PWMEnrich_Dmelanogaster_background = derive2 { name="PWMEnrich.Dmelanogaster.background"; version="4.36.0"; sha256="02aiy2qb62r8qgi5gaj2scra46qgf4wh3lzpqvsxbi7c2glnp7ig"; depends=[PWMEnrich]; };
+  PCHiCdata = derive2 { name="PCHiCdata"; version="1.32.0"; sha256="12nzy9m96jsal7sfqqdi8q7vq9rb4jc5h3hbl11aq4ik66048dyh"; depends=[Chicago]; };
-  PWMEnrich_Hsapiens_background = derive2 { name="PWMEnrich.Hsapiens.background"; version="4.36.0"; sha256="0fr775h5k98xspmjpyf363dav38j7cixnmhapfsy8ijijyl4g8jw"; depends=[PWMEnrich]; };
+  PREDAsampledata = derive2 { name="PREDAsampledata"; version="0.44.0"; sha256="0ydb4y2s8kshia7k6mr941f1fc7nsqahm1g86ig3wpcq7al33z1b"; depends=[affy annotate Biobase PREDA]; };
-  PWMEnrich_Mmusculus_background = derive2 { name="PWMEnrich.Mmusculus.background"; version="4.36.0"; sha256="1gwmilyikslgp56xrff2sqqm32lmdq589cya19cm0yi7pa17fqdw"; depends=[PWMEnrich]; };
+  PWMEnrich_Dmelanogaster_background = derive2 { name="PWMEnrich.Dmelanogaster.background"; version="4.38.0"; sha256="1wnm4jq5lzz50wzsz9v0kw104c1m67j68qlq6773ikdblsrlq23x"; depends=[PWMEnrich]; };
-  PasillaTranscriptExpr = derive2 { name="PasillaTranscriptExpr"; version="1.30.0"; sha256="17482ypqdvgc6p3fvkfdwfcpm3gn4rfd6zjsnlbqc99dpikq13sr"; depends=[]; };
+  PWMEnrich_Hsapiens_background = derive2 { name="PWMEnrich.Hsapiens.background"; version="4.38.0"; sha256="0fjzlnzv4fk9a90vnl39shx6d84bv61rc3hda6h18md5al202jyj"; depends=[PWMEnrich]; };
-  PathNetData = derive2 { name="PathNetData"; version="1.38.0"; sha256="07wq6526ihrzmyk2rql0zpkr6qkg6rdkk2f03lxkaq7fsbidb03q"; depends=[]; };
+  PWMEnrich_Mmusculus_background = derive2 { name="PWMEnrich.Mmusculus.background"; version="4.38.0"; sha256="0w815iqjfv0f0kybr84y3q4xsvxihixbiljsdz09xgafam3l80a3"; depends=[PWMEnrich]; };
-  PepsNMRData = derive2 { name="PepsNMRData"; version="1.20.0"; sha256="1xy05yd2nzrl2s0bjsr9y94rwcm68gglbijxplalyy3ppcwwm55c"; depends=[]; };
+  PasillaTranscriptExpr = derive2 { name="PasillaTranscriptExpr"; version="1.32.0"; sha256="0pwqfmcm0cw0z42571fa8w2lpy5mx516mckvk1dwys2yzdhjj24a"; depends=[]; };
-  PhyloProfileData = derive2 { name="PhyloProfileData"; version="1.16.0"; sha256="1r51zrvm8n7w66ii97wz6ncz0d7s473ppdn8b958mh15w81rk5fr"; depends=[BiocStyle Biostrings ExperimentHub]; };
+  PathNetData = derive2 { name="PathNetData"; version="1.40.0"; sha256="1pa6hrkyz1byldlch3h7brw2klxi9v2gg97j6814qiqiv84ms90y"; depends=[]; };
-  ProData = derive2 { name="ProData"; version="1.40.0"; sha256="099xf8143k2z74nb1hdlswrv1gjmg41255x0njxa4wzdwlpyp5k2"; depends=[Biobase]; };
+  PepsNMRData = derive2 { name="PepsNMRData"; version="1.22.0"; sha256="1yzdpfbfivkyvnw76c24j2rbwfkjsnh0blv2z9x8aj1s0b3m5rjy"; depends=[]; };
-  PtH2O2lipids = derive2 { name="PtH2O2lipids"; version="1.28.0"; sha256="1rx0sg5nz7i20d74y0cq6nybc1q62h0d9rpi3dk02jfngk3zzb5d"; depends=[CAMERA LOBSTAHS xcms]; };
+  PhyloProfileData = derive2 { name="PhyloProfileData"; version="1.18.0"; sha256="1bnzrqcyvhr4cnxkiwlpw5rjhrkbs6lm050yjnm79b2gd2whyk81"; depends=[BiocStyle Biostrings ExperimentHub]; };
-  QDNAseq_hg19 = derive2 { name="QDNAseq.hg19"; version="1.32.0"; sha256="01fnbbkyfpim0xh6v0bm553pmrg9n3bnwn4adds0p47lai1n7dr8"; depends=[QDNAseq]; };
+  ProData = derive2 { name="ProData"; version="1.42.0"; sha256="0ysmv66irrq7q8yzk77kkcrxdrcs1pa0z20dfhcsaqkd84yn74jz"; depends=[Biobase]; };
-  QDNAseq_mm10 = derive2 { name="QDNAseq.mm10"; version="1.32.0"; sha256="0x54ncmxqb1qci41qy7q9gskx7zp1rcpad3wvil023h81l1s5pg6"; depends=[QDNAseq]; };
+  PtH2O2lipids = derive2 { name="PtH2O2lipids"; version="1.30.0"; sha256="0garsf77h2nb1zcy3z8ypk3c95pjjnzhxvfwlznn4i1l6qi45mds"; depends=[CAMERA LOBSTAHS xcms]; };
-  QUBICdata = derive2 { name="QUBICdata"; version="1.30.0"; sha256="0apbndslrdrflmwvz456q31x3mr1p7v7kpbl0fp0hajadjb38aha"; depends=[]; };
+  QDNAseq_hg19 = derive2 { name="QDNAseq.hg19"; version="1.34.0"; sha256="054c565wqr3cadym8kmf0wm0k2n3ri6x4bla4zyhra0v8cz6axjb"; depends=[QDNAseq]; };
-  RGMQLlib = derive2 { name="RGMQLlib"; version="1.22.0"; sha256="1sys8vji70mkd100zy84ywv6ralr5k7z1044rn03wp75s1h8klwy"; depends=[]; };
+  QDNAseq_mm10 = derive2 { name="QDNAseq.mm10"; version="1.34.0"; sha256="08lj3vcnjg38fnnppa3nsg8sw6gfhklak9prpjxig9yzcg4pggwx"; depends=[QDNAseq]; };
-  RITANdata = derive2 { name="RITANdata"; version="1.26.0"; sha256="0jkcf4g2h6bpx0v8ybwnrni3qq9hajxxprfq9pszpmf4xb9cmgs2"; depends=[]; };
+  QUBICdata = derive2 { name="QUBICdata"; version="1.32.0"; sha256="0gdsyvfrwsbbm786bkkqxxsc5s3wpn7fyhf4f227gr8sg3l7fkbi"; depends=[]; };
-  RMassBankData = derive2 { name="RMassBankData"; version="1.40.0"; sha256="190q4q8201i1v3bb4snasxy2kbwvnppq9kpqmxa1hg9mlvk643fq"; depends=[]; };
+  RGMQLlib = derive2 { name="RGMQLlib"; version="1.24.0"; sha256="09149yaw2gpypp0m7cghbjqksbj0ncly8fxlv1n7l2s8kaq5jkdq"; depends=[]; };
-  RNAinteractMAPK = derive2 { name="RNAinteractMAPK"; version="1.40.0"; sha256="0s5bb73ixp2zhzj0ssq3kai6ijrpn9flg23f1n2vsi2vf66wfajj"; depends=[Biobase fields gdata genefilter lattice MASS RNAinteract sparseLDA]; };
+  RITANdata = derive2 { name="RITANdata"; version="1.28.0"; sha256="0k1rziwpb26y19j2cii9y2vffr0sdkskll41njwpkl5mla5bzylv"; depends=[]; };
-  RNAmodR_Data = derive2 { name="RNAmodR.Data"; version="1.16.0"; sha256="0p9x1j4ra11banvifh5z07i26b2s59b2knbgj44yx4qi0d3cnn81"; depends=[ExperimentHub ExperimentHubData]; };
+  RLHub = derive2 { name="RLHub"; version="1.9.0"; sha256="0hm3wplzmmzsygz8dalwf6y798p4g2bssjdsg51w17s2mgm4hl98"; depends=[AnnotationHub ExperimentHub]; };
-  RNAseqData_HNRNPC_bam_chr14 = derive2 { name="RNAseqData.HNRNPC.bam.chr14"; version="0.40.0"; sha256="1gdwsbkjnb3927ihq2gbwrksvhm61wm114bwhazypmpnnwcfv27f"; depends=[]; };
+  RMassBankData = derive2 { name="RMassBankData"; version="1.42.0"; sha256="10g42s6wq66fhvrxcwxf08073scpkinfldwwdl03r7lxy1wka426"; depends=[]; };
-  RRBSdata = derive2 { name="RRBSdata"; version="1.22.0"; sha256="1visrkyxljp3d7h7qgf72l71w91vah93qmi733s15zmsm090sf1c"; depends=[BiSeq]; };
+  RNAinteractMAPK = derive2 { name="RNAinteractMAPK"; version="1.42.0"; sha256="0vm20x1lfgl671rrwvxybcwjgk7falb3d5xi6hiq9jivvbms9120"; depends=[Biobase fields gdata genefilter lattice MASS RNAinteract sparseLDA]; };
-  RTCGA_CNV = derive2 { name="RTCGA.CNV"; version="1.30.0"; sha256="0akfifgkkhzrrw21gxm4h2liam5f7rd2ghidyr21c6660wg1444c"; depends=[RTCGA]; };
+  RNAmodR_Data = derive2 { name="RNAmodR.Data"; version="1.18.0"; sha256="0k5ykbry5si0wc6f1am3ln9pcl842hjrpmmw15j9sm565k5pmvmf"; depends=[ExperimentHub ExperimentHubData]; };
-  RTCGA_PANCAN12 = derive2 { name="RTCGA.PANCAN12"; version="1.30.0"; sha256="1iz72gbpm0msiasrc0xyiw9c3s2a59fgbz7kfrlwskspqvm9pvdl"; depends=[RTCGA]; };
+  RNAseqData_HNRNPC_bam_chr14 = derive2 { name="RNAseqData.HNRNPC.bam.chr14"; version="0.42.0"; sha256="1xc5ya20nnrhdkib7590zv5g8q6cppd6qiwglxc6fj26ncdj6s73"; depends=[]; };
-  RTCGA_RPPA = derive2 { name="RTCGA.RPPA"; version="1.30.0"; sha256="1ln4v06pf2skxaa0vcwp9m2vkczm5bc37kfczqg022n0fi7wa084"; depends=[RTCGA]; };
+  RRBSdata = derive2 { name="RRBSdata"; version="1.24.0"; sha256="1s6fjkz0dld7mlb1ylqmrw63jk3k0162rv2li6zkz66gc4aq10p0"; depends=[BiSeq]; };
-  RTCGA_clinical = derive2 { name="RTCGA.clinical"; version="20151101.32.0"; sha256="0ivfq9z66v9a867v4c6581v7pmbcwy1g6fr5bgs1fp0n7rl6b15g"; depends=[RTCGA]; };
+  RTCGA_CNV = derive2 { name="RTCGA.CNV"; version="1.32.0"; sha256="0ll5zj9d9d3ykkkq7iqq5sfvz8i4dc297nwkjpvjxrlazw28iiyl"; depends=[RTCGA]; };
-  RTCGA_mRNA = derive2 { name="RTCGA.mRNA"; version="1.30.0"; sha256="1wf5rxxxa3qgihpa9hbcabryz74k3vc1yp2mscs4w0zdym48fw78"; depends=[RTCGA]; };
+  RTCGA_PANCAN12 = derive2 { name="RTCGA.PANCAN12"; version="1.32.0"; sha256="0rmgg5j4rzqg78i43l9975vhdnh8r23lz78fkwwa94ihpqv1pbic"; depends=[RTCGA]; };
-  RTCGA_methylation = derive2 { name="RTCGA.methylation"; version="1.30.0"; sha256="1g543scp553gya9ax7c7rm93gra1mqhv93y8jj9hvv7sq5mx469j"; depends=[RTCGA]; };
+  RTCGA_RPPA = derive2 { name="RTCGA.RPPA"; version="1.32.0"; sha256="158m31hysybyh3ha5n324srrxzc76bkv9fpblida2znv9sni6c52"; depends=[RTCGA]; };
-  RTCGA_miRNASeq = derive2 { name="RTCGA.miRNASeq"; version="1.30.0"; sha256="1hvb77c44vbhyqbpqrid5vrashqng3clpqm5svr7fq6xhqaj3v34"; depends=[RTCGA]; };
+  RTCGA_clinical = derive2 { name="RTCGA.clinical"; version="20151101.34.0"; sha256="1s7fss644wkrvimqp2h3hq14gr0gjdqyj92hcrzff2qwyy5fzhky"; depends=[RTCGA]; };
-  RTCGA_mutations = derive2 { name="RTCGA.mutations"; version="20151101.32.0"; sha256="1n265xk9rr491rlcgy98nvvxmnhjf9b4x80qbc9xlb0ks3hpgx13"; depends=[RTCGA]; };
+  RTCGA_mRNA = derive2 { name="RTCGA.mRNA"; version="1.32.0"; sha256="1anwv8cg38lpwfyxicqi8kml9q9gigrc7bzmp163322lxaq79c1q"; depends=[RTCGA]; };
-  RTCGA_rnaseq = derive2 { name="RTCGA.rnaseq"; version="20151101.32.0"; sha256="1nmn9dqp6kdsz7536wln8wv1ms8nlgys7xlmc555q1irc1pz4ksc"; depends=[RTCGA]; };
+  RTCGA_methylation = derive2 { name="RTCGA.methylation"; version="1.32.0"; sha256="04q23w331vjmmmy2iy79grkgdn03iz53vw8npwx2wq1w8if8xdi4"; depends=[RTCGA]; };
-  RUVnormalizeData = derive2 { name="RUVnormalizeData"; version="1.22.0"; sha256="1sqkvkwlvwwspj6xg3xq062s2brr6yjmhw5dlccrjff0qcc9w41p"; depends=[Biobase]; };
+  RTCGA_miRNASeq = derive2 { name="RTCGA.miRNASeq"; version="1.32.0"; sha256="1bgcgsx01s7p24014rp8jiklmml822hxabrgf4xxagx4jzr91fxn"; depends=[RTCGA]; };
-  RcisTarget_hg19_motifDBs_cisbpOnly_500bp = derive2 { name="RcisTarget.hg19.motifDBs.cisbpOnly.500bp"; version="1.22.0"; sha256="0yhalgrj0p99ka7wfcnb70adjy4n7zlk9caxd5fk8hhspzkwzkfp"; depends=[data_table]; };
+  RTCGA_mutations = derive2 { name="RTCGA.mutations"; version="20151101.34.0"; sha256="19las4v4zg8wbb52wa4zmwpfpn80pyjp1kyvqkhgvpd8m3dj7951"; depends=[RTCGA]; };
-  ReactomeGSA_data = derive2 { name="ReactomeGSA.data"; version="1.16.1"; sha256="18n4shnlbgz6vv63hljzcpz1yd2y4p0gwgj6i37lvr4p7hmg7bi3"; depends=[edgeR limma ReactomeGSA Seurat]; };
+  RTCGA_rnaseq = derive2 { name="RTCGA.rnaseq"; version="20151101.34.0"; sha256="03kr2l5l5a7v98rna3a43543b7pqcwc7zhawnh92g3rdabk03w9s"; depends=[RTCGA]; };
-  RegParallel = derive2 { name="RegParallel"; version="1.20.0"; sha256="0fxvzj5vgsdq2jm467a5ddya5p6603rzhklh8hmdn9d352yzy01i"; depends=[arm data_table doParallel foreach iterators stringr survival]; };
+  RUVnormalizeData = derive2 { name="RUVnormalizeData"; version="1.24.0"; sha256="0w62ybdiq0dwd11ld48kl178qpd53xbfl51z2jwpi2pj1b86fg9l"; depends=[Biobase]; };
-  RforProteomics = derive2 { name="RforProteomics"; version="1.40.0"; sha256="11cjlhvk04r0flf0wr7n4qmlazaaw4kd5gs589h95mblsmk4andx"; depends=[BiocManager biocViews MSnbase R_utils]; };
+  RcisTarget_hg19_motifDBs_cisbpOnly_500bp = derive2 { name="RcisTarget.hg19.motifDBs.cisbpOnly.500bp"; version="1.24.0"; sha256="170wjqnrvmdjcpx0bwwky3j7cxhbqvch781dzl6il2igca9kbqhq"; depends=[data_table]; };
-  RnBeads_hg19 = derive2 { name="RnBeads.hg19"; version="1.34.0"; sha256="0mv6pqkhwiwdq72dh0m79c7inpkvz8nwy4m8b93sjy1wi76wgci6"; depends=[GenomicRanges]; };
+  ReactomeGSA_data = derive2 { name="ReactomeGSA.data"; version="1.18.0"; sha256="1410ks6s7albf6sly8ry0ln58ws9jlfn62amniqqsg46kx4xc4bh"; depends=[edgeR limma ReactomeGSA Seurat]; };
-  RnBeads_hg38 = derive2 { name="RnBeads.hg38"; version="1.34.0"; sha256="19l875n3injnn1af01jmlf62a6dgd9mn54ppcsy1x71wrcs1lk25"; depends=[GenomicRanges]; };
+  RegParallel = derive2 { name="RegParallel"; version="1.22.0"; sha256="0zaask3zpbqh6pmrx4hsi5wz7kkfhbl15xzhz10s8h9m739wm8c0"; depends=[arm data_table doParallel foreach iterators stringr survival]; };
-  RnBeads_mm10 = derive2 { name="RnBeads.mm10"; version="2.10.0"; sha256="0x1nxgdwad42k39mrfilbi1kkm9avm0cbcrhsrxs67ajng9qmci8"; depends=[GenomicRanges]; };
+  RforProteomics = derive2 { name="RforProteomics"; version="1.42.0"; sha256="0irg6wrwy82xhlkgj1vphh6ncp9s6qcpp40mxv1vq969qjjchkk9"; depends=[BiocManager biocViews MSnbase R_utils]; };
-  RnBeads_mm9 = derive2 { name="RnBeads.mm9"; version="1.34.0"; sha256="1d7lshk5a8zn4wi4f5b8q4d206i379iv6gxxsbzygrlnk74j9kzf"; depends=[GenomicRanges]; };
+  RnBeads_hg19 = derive2 { name="RnBeads.hg19"; version="1.36.0"; sha256="0yn7n3zv9i76abx9wp0vw6wa7iylbrj2ffhzbc3irc104id0i4f9"; depends=[GenomicRanges]; };
-  RnBeads_rn5 = derive2 { name="RnBeads.rn5"; version="1.34.0"; sha256="182pdfi6dvz4r5v41r62d0rsxkm5vlrl7y6pwx9nx3h1gaiybl8s"; depends=[GenomicRanges]; };
+  RnBeads_hg38 = derive2 { name="RnBeads.hg38"; version="1.36.0"; sha256="05ffx8a76z9nnl3qhfjf6vfnnc2pqkw2jy4pc0wgqc1y3w9vg60l"; depends=[GenomicRanges]; };
-  RnaSeqSampleSizeData = derive2 { name="RnaSeqSampleSizeData"; version="1.34.0"; sha256="0p2q7phn40ax94yh43xg72fmnnljfi6cfiyaad39br1hi2b6hrjf"; depends=[edgeR]; };
+  RnBeads_mm10 = derive2 { name="RnBeads.mm10"; version="2.12.0"; sha256="151ivmy35ff850f1ij403bj5g9jhw8r515jjqbvq182x1cygbdfl"; depends=[GenomicRanges]; };
-  SBGNview_data = derive2 { name="SBGNview.data"; version="1.16.0"; sha256="1nprhg7rkia9jwy8mqx7iqdh1qs81nk9al8fvv1ynq2cc9x77jfr"; depends=[bookdown knitr rmarkdown]; };
+  RnBeads_mm9 = derive2 { name="RnBeads.mm9"; version="1.36.0"; sha256="1bd5jai5jk1d3mqbx7x05ypfxma8s330na9n5bb9qzwxq7imd50b"; depends=[GenomicRanges]; };
-  SCLCBam = derive2 { name="SCLCBam"; version="1.34.0"; sha256="0jnpg8qdbd5b6809glzg68n12bavnpqaaarn2vfv5c6055qg6jgy"; depends=[]; };
+  RnBeads_rn5 = derive2 { name="RnBeads.rn5"; version="1.36.0"; sha256="098vy604ca0g408hl2g0p6kh2zzvzvbmyhbr0z081rbdpvzlnf4f"; depends=[GenomicRanges]; };
-  SFEData = derive2 { name="SFEData"; version="1.4.0"; sha256="0wkb27cs4zvvhclgk2slx8n7jx1mx3q87kn86n4rjdcx2074ndqz"; depends=[AnnotationHub BiocFileCache ExperimentHub]; };
+  RnaSeqSampleSizeData = derive2 { name="RnaSeqSampleSizeData"; version="1.36.0"; sha256="1gm55gmsxna8a53k7a7yd99nzc4mg1kw7l5lnmkipa03lafa2yff"; depends=[edgeR]; };
-  SNAData = derive2 { name="SNAData"; version="1.48.0"; sha256="0qd48ggg1wjy5h47hzl9iqzy13gsxxn4f7fq4b0ra35vhckmcvyf"; depends=[graph]; };
+  SBGNview_data = derive2 { name="SBGNview.data"; version="1.18.0"; sha256="1hycjipfz6lr1hs1r7g65l565pcx77sz8bjacg5gdcv3rs1by2ql"; depends=[bookdown knitr rmarkdown]; };
-  SNAGEEdata = derive2 { name="SNAGEEdata"; version="1.38.0"; sha256="17wbf4xsljkryzjpk57kvjbiln0ig8d717j953wy0inz7vzdkpkn"; depends=[]; };
+  SCLCBam = derive2 { name="SCLCBam"; version="1.36.0"; sha256="18im1j8j1y4hva4wg6vki59j1bifz9apijyi44wngsx68z19az35"; depends=[]; };
-  SNPhoodData = derive2 { name="SNPhoodData"; version="1.32.0"; sha256="0p8361lmlfz496ivw9qaqkg7b3hr4gb9g9r73fxp6amy2xncb00g"; depends=[]; };
+  SFEData = derive2 { name="SFEData"; version="1.6.0"; sha256="03f7f9jrdszvwqgskk12jqw8mvyrrhcjd5v1nzdiy3csg2fa7nbs"; depends=[AnnotationHub BiocFileCache ExperimentHub]; };
-  STexampleData = derive2 { name="STexampleData"; version="1.10.1"; sha256="1fr29mnczvglpkwh4vdy6klahv014ikmxwx055x4grkxvygbqm23"; depends=[ExperimentHub SpatialExperiment]; };
+  SNAData = derive2 { name="SNAData"; version="1.50.0"; sha256="1l3g5gsiv5s83b6406s23snf62zav75s28nq68s8czbm1rsv6xw5"; depends=[graph]; };
-  SVM2CRMdata = derive2 { name="SVM2CRMdata"; version="1.34.0"; sha256="1k7cjakxcqq86xvx0d0799hb94hi7w05amd9yncd0nf4dcy6zm0f"; depends=[]; };
+  SNAGEEdata = derive2 { name="SNAGEEdata"; version="1.40.0"; sha256="00m10r01sx027pnahw5ck1paplqpwsyq11dkacxq21ssvlc8kbl6"; depends=[]; };
-  SimBenchData = derive2 { name="SimBenchData"; version="1.10.0"; sha256="1g5wff2hx3sra48wcvwh3hs9lpfavq2pqflcm9wfcch9y10m8iqd"; depends=[ExperimentHub S4Vectors]; };
+  SNPhoodData = derive2 { name="SNPhoodData"; version="1.34.0"; sha256="0r036vskwlk0mp7bgcbvr7iwffcm7g7imzwh5gri05j5p0rhny72"; depends=[]; };
-  Single_mTEC_Transcriptomes = derive2 { name="Single.mTEC.Transcriptomes"; version="1.30.0"; sha256="1w3f71mfq74sjlsasi87gvqs2mhny41zm22zswz9km5msi8r2wva"; depends=[]; };
+  STexampleData = derive2 { name="STexampleData"; version="1.12.3"; sha256="1c9lbghi1ybilrc7yiff12sjyaqpr8095wdvz941lnf3cmgci79q"; depends=[ExperimentHub SingleCellExperiment SpatialExperiment]; };
-  SingleCellMultiModal = derive2 { name="SingleCellMultiModal"; version="1.14.0"; sha256="0kwff2nqv7nf7rqifyzr6klba6k1h29y4332b60k7hv3psjsm015"; depends=[AnnotationHub BiocBaseUtils BiocFileCache ExperimentHub HDF5Array Matrix MultiAssayExperiment S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
+  SVM2CRMdata = derive2 { name="SVM2CRMdata"; version="1.36.0"; sha256="18pd61cg12ghi8kjh1cjyrd248r20l39drbg9vpqmmcpai5f45wy"; depends=[]; };
-  SingleMoleculeFootprintingData = derive2 { name="SingleMoleculeFootprintingData"; version="1.10.0"; sha256="1chlik8ycsiw0kvxikiplb5xkj4afi4qniy666csyqlksaflr703"; depends=[ExperimentHub]; };
+  SimBenchData = derive2 { name="SimBenchData"; version="1.12.0"; sha256="0a3q2ajr0pzwdabx306c8bia25cbih3hfzd5jgm2cx9f5i37f11v"; depends=[ExperimentHub S4Vectors]; };
-  SomatiCAData = derive2 { name="SomatiCAData"; version="1.40.0"; sha256="0m92db12a9h7866l3vbvpqnxnvkbik8znh3l6qyl22l438wvd8b2"; depends=[]; };
+  Single_mTEC_Transcriptomes = derive2 { name="Single.mTEC.Transcriptomes"; version="1.32.0"; sha256="0h54w7lc8v5jicm6xf5i16pi8rw2fxqvssf7a0ql9qa6bv4c7sqy"; depends=[]; };
-  SomaticCancerAlterations = derive2 { name="SomaticCancerAlterations"; version="1.38.0"; sha256="140bn20n60dnsb3li0ygnymfb7wwgh523yx8pmc6zvyx6izdg618"; depends=[GenomicRanges IRanges S4Vectors]; };
+  SingleCellMultiModal = derive2 { name="SingleCellMultiModal"; version="1.16.0"; sha256="1kzfzprma01ppbpbzgfgaa3dins2915n3wqsrqapcxfks7zvaciq"; depends=[AnnotationHub BiocBaseUtils BiocFileCache ExperimentHub HDF5Array Matrix MultiAssayExperiment S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
-  SpatialDatasets = derive2 { name="SpatialDatasets"; version="1.0.0"; sha256="1szsggymx05swr4i5mgxcxk7jbz8qh6xxwpnmmzajns03gmszggy"; depends=[ExperimentHub SpatialExperiment]; };
+  SingleMoleculeFootprintingData = derive2 { name="SingleMoleculeFootprintingData"; version="1.12.0"; sha256="0xdi5rpqpj07h8j1n7wxfsmvrp6zsnc5rq1b2frdp8x3xdlf5dxn"; depends=[ExperimentHub]; };
-  SpikeIn = derive2 { name="SpikeIn"; version="1.44.0"; sha256="04saqrdzl1irdbvgr9s86sgwsvnlp5l4xbx16wj41476rbzhg2aw"; depends=[affy]; };
+  SomatiCAData = derive2 { name="SomatiCAData"; version="1.42.0"; sha256="01k9s97rd78pciv4yaij07zzrijvfidpg6hh4h67mnxc90pg3r8w"; depends=[]; };
-  SpikeInSubset = derive2 { name="SpikeInSubset"; version="1.42.0"; sha256="14w4g6n0nn1mg9wifqp2jrxb0hy2sqfcnycwhvir1znfck83fzir"; depends=[affy Biobase]; };
+  SomaticCancerAlterations = derive2 { name="SomaticCancerAlterations"; version="1.40.0"; sha256="11jvin7y5ys1lxwfjrwb4vw4gcpj09y0n6rhs87w27gcpj4dk7dm"; depends=[GenomicRanges IRanges S4Vectors]; };
-  TBX20BamSubset = derive2 { name="TBX20BamSubset"; version="1.38.0"; sha256="1f09l2ihh80cqqg6sw5ypa51c1zsspkq2g06lbfi19zgllcfh80f"; depends=[Rsamtools xtable]; };
+  SpatialDatasets = derive2 { name="SpatialDatasets"; version="1.2.0"; sha256="0qg9x657kamqqcifziagp3qrk5h2zh16jl8dprzl7nnrxhp0cra2"; depends=[ExperimentHub SpatialExperiment]; };
-  TCGAMethylation450k = derive2 { name="TCGAMethylation450k"; version="1.38.0"; sha256="0pz8xmi4zxp1qvpcwhf54sy5lhpaspdlad1dlrhxgjbfm8xl535q"; depends=[]; };
+  SpikeIn = derive2 { name="SpikeIn"; version="1.46.0"; sha256="1bnhag1cck99k6mgfnqddjxjhmpgax76p28hm686jkil416y0y47"; depends=[affy]; };
-  TCGAWorkflowData = derive2 { name="TCGAWorkflowData"; version="1.26.0"; sha256="03p3ifgr9w737v9dvx1qvj2kdyf1l9a2qnmwii0nmlak9dp1cc52"; depends=[SummarizedExperiment]; };
+  SpikeInSubset = derive2 { name="SpikeInSubset"; version="1.44.0"; sha256="118v972wwq4h2ww2nlb7mzva3d38c4hzmbq0v28500q2zc1ykv4l"; depends=[affy Biobase]; };
-  TCGAbiolinksGUI_data = derive2 { name="TCGAbiolinksGUI.data"; version="1.22.0"; sha256="04fmnqa95rb2lgflcg3d7kbz9jj990r9hlxwlhhzb79dv9wd1mfa"; depends=[]; };
+  SubcellularSpatialData = derive2 { name="SubcellularSpatialData"; version="1.0.0"; sha256="0lyg6hiv8ch7c8a7zzi02c9fmq2zqif88khhslj15gvg5dznw79v"; depends=[dplyr hexbin Matrix SpatialExperiment]; };
-  TCGAcrcmRNA = derive2 { name="TCGAcrcmRNA"; version="1.22.0"; sha256="0vwd0pi8g4pmz8g61c0mr0njha6qsm5m1z7iyf0lnwrm6y6bv6px"; depends=[Biobase]; };
+  TBX20BamSubset = derive2 { name="TBX20BamSubset"; version="1.40.0"; sha256="0hxmizdgrbv6vqlxj6hn4wiazjf3cwaaq17pagqmjlfxbqb4mlzk"; depends=[Rsamtools xtable]; };
-  TCGAcrcmiRNA = derive2 { name="TCGAcrcmiRNA"; version="1.22.0"; sha256="0qrcj2mb58dwdwfpypnwyb2f7kcjjyqnyz4v42rc43r04xy14l2m"; depends=[Biobase]; };
+  TCGAMethylation450k = derive2 { name="TCGAMethylation450k"; version="1.40.0"; sha256="1c2jgrh5fsnq4d8aw8p1147jsdz8yi60i3naxsd8kj3s9mn1vfn2"; depends=[]; };
-  TENxBUSData = derive2 { name="TENxBUSData"; version="1.16.0"; sha256="071qbq0avzbs6c64l6lrmrs1hmbrg98bnf91vpz4x7s0p5axx87n"; depends=[AnnotationHub BiocGenerics ExperimentHub]; };
+  TCGAWorkflowData = derive2 { name="TCGAWorkflowData"; version="1.28.0"; sha256="0sg9zn06rf63n9z6qggxwrh5mxjg0gq1zjj1fn141d7xdbw1j784"; depends=[SummarizedExperiment]; };
-  TENxBrainData = derive2 { name="TENxBrainData"; version="1.22.0"; sha256="1ia7a6jq7giy130avgv5brffxk5r2yql7rjppxs9nab3a6y472yy"; depends=[AnnotationHub ExperimentHub HDF5Array SingleCellExperiment]; };
+  TCGAbiolinksGUI_data = derive2 { name="TCGAbiolinksGUI.data"; version="1.24.0"; sha256="1r36f7nvvjjgkgmhha81n2iyr9k4nzy0qkkblm483rgzxav4gqa6"; depends=[]; };
-  TENxPBMCData = derive2 { name="TENxPBMCData"; version="1.20.0"; sha256="09pgf31x1zqcrnvf2fwdbx4qn7pgsaby8damxcfq5xr3iksqhdwb"; depends=[AnnotationHub ExperimentHub HDF5Array SingleCellExperiment]; };
+  TCGAcrcmRNA = derive2 { name="TCGAcrcmRNA"; version="1.24.0"; sha256="07sszvf7wd50gj5sgkj4di9a5y4yqcgi9ykssmp9n16bam1xp0a8"; depends=[Biobase]; };
-  TENxVisiumData = derive2 { name="TENxVisiumData"; version="1.10.0"; sha256="0yi7axdam9b0ps0818cgygbmjcdknn032bm2snb6xf3g4i8n45f4"; depends=[ExperimentHub SpatialExperiment]; };
+  TCGAcrcmiRNA = derive2 { name="TCGAcrcmiRNA"; version="1.24.0"; sha256="0jc6shc18kvd69v8wrgifg3cvi5idv1hlnd4x93njxbj9yyxr8xd"; depends=[Biobase]; };
-  TMExplorer = derive2 { name="TMExplorer"; version="1.12.0"; sha256="0vi99vpbfzwwqpdxgjlhcr835nnbfngwz6fag9kvd7ndicb21zy4"; depends=[BiocFileCache Matrix SingleCellExperiment]; };
+  TENxBUSData = derive2 { name="TENxBUSData"; version="1.18.0"; sha256="19a909cs0z8zy6vwlxxgk76ybj9yrhsxd2z8narf50rv96nyid0s"; depends=[AnnotationHub BiocGenerics ExperimentHub]; };
-  TabulaMurisData = derive2 { name="TabulaMurisData"; version="1.20.0"; sha256="1p0pyvgwzbnkx1687n2j7gxjzb5s49r1njklsff0di66m8nlis7k"; depends=[ExperimentHub]; };
+  TENxBrainData = derive2 { name="TENxBrainData"; version="1.24.0"; sha256="1kb5i3xrins9jd40xzyi4sj9nks83vzw1w8pk7ji6kgyjdgm1by6"; depends=[AnnotationHub ExperimentHub HDF5Array SingleCellExperiment]; };
-  TabulaMurisSenisData = derive2 { name="TabulaMurisSenisData"; version="1.8.0"; sha256="0f6gj56rgcv378ry4h1sgm3zhv083yh23qf1pj9rvabwhdfgk8p1"; depends=[AnnotationHub ExperimentHub gdata HDF5Array SingleCellExperiment SummarizedExperiment]; };
+  TENxPBMCData = derive2 { name="TENxPBMCData"; version="1.22.0"; sha256="089q81wiq7flr1a72gmj7y1ds73zzc2h96pnjm7s5sbysgy4jgx9"; depends=[AnnotationHub ExperimentHub HDF5Array SingleCellExperiment]; };
-  TargetScoreData = derive2 { name="TargetScoreData"; version="1.38.0"; sha256="19s1jxrh04gfkx7a9h59v6vl063wlf2j71bi6lxq9lm689y23z4k"; depends=[]; };
+  TENxVisiumData = derive2 { name="TENxVisiumData"; version="1.12.0"; sha256="08jcq5vq0ki4q6ndpm3799kwiy62j446v4kbfdfw7j7rwgjmhjhs"; depends=[ExperimentHub SpatialExperiment]; };
-  TargetSearchData = derive2 { name="TargetSearchData"; version="1.40.0"; sha256="12z820mwi779dlmg5hf1cq5gpvrxg9ijb38s43fbzzgagn25czff"; depends=[]; };
+  TENxXeniumData = derive2 { name="TENxXeniumData"; version="1.0.0"; sha256="1zjyry8m4f8xw6apib90rv8lyxhpdy3nqgawshhslv8w8qwk3xs9"; depends=[BumpyMatrix ExperimentHub SpatialExperiment SpatialFeatureExperiment SummarizedExperiment]; };
-  TimerQuant = derive2 { name="TimerQuant"; version="1.32.0"; sha256="18jl2x9ywfwm4ir2kwa9y4fq0lsz0295lx7f7qz08l4d1yrb1w4v"; depends=[deSolve dplyr ggplot2 gridExtra locfit shiny]; };
+  TMExplorer = derive2 { name="TMExplorer"; version="1.14.0"; sha256="0qxm46dryq7c4xrbkhgbfqxqn0p7x1nxklqhkdw8qmklszc2b870"; depends=[BiocFileCache Matrix SingleCellExperiment]; };
-  TumourMethData = derive2 { name="TumourMethData"; version="1.0.0"; sha256="100kw4552rc48sqpw9makyf9nwgrs049hkvbrd8zjmrf542cj9md"; depends=[ExperimentHub GenomicRanges HDF5Array R_utils rhdf5 SummarizedExperiment]; };
+  TabulaMurisData = derive2 { name="TabulaMurisData"; version="1.22.0"; sha256="0gnv8yfksrc59prki6w6xa5pw5nszxkx88i5av3ln21hq5idj4cm"; depends=[ExperimentHub]; };
-  VariantToolsData = derive2 { name="VariantToolsData"; version="1.26.0"; sha256="0jj8wp2mp0xgd4hixyb59bykxbbpklncjj39ra5nyw4h4ziwrbfm"; depends=[BiocGenerics GenomicRanges VariantAnnotation]; };
+  TabulaMurisSenisData = derive2 { name="TabulaMurisSenisData"; version="1.10.0"; sha256="1b1aj06qacvzpabz8r0vkqpm0pp48vx26xx84h5ihzg9232wrqmy"; depends=[AnnotationHub ExperimentHub gdata HDF5Array SingleCellExperiment SummarizedExperiment]; };
-  VectraPolarisData = derive2 { name="VectraPolarisData"; version="1.6.0"; sha256="0zr94qgyj365sy7cyzjsm9zbxyv6zbd8lwfr1nqz0p6f6hb9b8qw"; depends=[ExperimentHub SpatialExperiment]; };
+  TargetScoreData = derive2 { name="TargetScoreData"; version="1.40.0"; sha256="18y7vidhgkhpr9nlhxwhhi7z07vj6ii1vwl9c8dyyhzfc8icsmsn"; depends=[]; };
-  WES_1KG_WUGSC = derive2 { name="WES.1KG.WUGSC"; version="1.34.0"; sha256="1p8z4p1s5l4hlp78ifiy3gan1n8iljaafbqv88vxwbjh2x9gfnjl"; depends=[]; };
+  TargetSearchData = derive2 { name="TargetSearchData"; version="1.42.0"; sha256="0dzb1jazdwx37kx0xwvv9i7rfq1712bifz542x4liahvxjgz7prg"; depends=[]; };
-  WGSmapp = derive2 { name="WGSmapp"; version="1.14.0"; sha256="0yv323mkv681f20dzjh1xaz19xbn4j777xxlmq27rvmk3j1vfah9"; depends=[GenomicRanges]; };
+  TimerQuant = derive2 { name="TimerQuant"; version="1.34.0"; sha256="1gjnfmsbcj8ndj1fssclzlb5qd482c38gpi0q4x7ls98bk42r44x"; depends=[deSolve dplyr ggplot2 gridExtra locfit shiny]; };
-  WeberDivechaLCdata = derive2 { name="WeberDivechaLCdata"; version="1.4.1"; sha256="00ws47shsfnwi6c3ah56bm6dvicfhfr50jadll613fddv7cxkfsw"; depends=[ExperimentHub SingleCellExperiment SpatialExperiment]; };
+  TransOmicsData = derive2 { name="TransOmicsData"; version="1.0.1"; sha256="0sfpks0wfzlrh5qqg0id5c99l1dzj2l1nd5h3shjhp0lm4f5v8w0"; depends=[S4Vectors]; };
-  XhybCasneuf = derive2 { name="XhybCasneuf"; version="1.40.0"; sha256="1qzbsmqn9y1483108pzh8zkiw1q1xzghincrcmz8cl2a4q10hyxf"; depends=[affy ath1121501cdf RColorBrewer tinesath1cdf]; };
+  TumourMethData = derive2 { name="TumourMethData"; version="1.2.0"; sha256="1xwm2amlb1vrf3hpdw9387nglc6pbxxdxik56byr5p8856fkjdav"; depends=[ExperimentHub GenomicRanges HDF5Array R_utils rhdf5 SummarizedExperiment]; };
-  adductData = derive2 { name="adductData"; version="1.18.0"; sha256="16c79wy55p4ryglxph80dibfm1ni8c5yfk6fnmq064ihw4zwcld5"; depends=[AnnotationHub ExperimentHub]; };
+  VariantToolsData = derive2 { name="VariantToolsData"; version="1.28.0"; sha256="0k8fg4bhghva32qk4l6r4g6asdkyl2afx0frbk0f57b2hqix69fb"; depends=[BiocGenerics GenomicRanges VariantAnnotation]; };
-  affycompData = derive2 { name="affycompData"; version="1.40.0"; sha256="183wgbc4j7f9d4rwr9smndnmw1i390abak23wp6p02zk340qmvq4"; depends=[affycomp Biobase]; };
+  VectraPolarisData = derive2 { name="VectraPolarisData"; version="1.8.0"; sha256="13r0r1whcxzzhlsa3bjsq9kp3csgnynbcrxj06v5s73xf8xify00"; depends=[ExperimentHub SpatialExperiment]; };
-  affydata = derive2 { name="affydata"; version="1.50.0"; sha256="1p9gqv8xnakwhf4sani09krlrq6qs4gr8yfjmi8g3s1zq4d32h1k"; depends=[affy]; };
+  WES_1KG_WUGSC = derive2 { name="WES.1KG.WUGSC"; version="1.36.0"; sha256="1yv62ydvlsl52awzn2nsa52vaz4naf4biw57awpmz0cp4rb68kdb"; depends=[]; };
-  airway = derive2 { name="airway"; version="1.22.0"; sha256="1xs5bw6azvcdwh9325alndzrp82alxxqwpkf60zsk2q7lv43nwbr"; depends=[SummarizedExperiment]; };
+  WGSmapp = derive2 { name="WGSmapp"; version="1.16.0"; sha256="0k4zyj9dn5x710a1vv11156brz52yf9lzmlmx9axcfsch5dcvi7x"; depends=[GenomicRanges]; };
-  antiProfilesData = derive2 { name="antiProfilesData"; version="1.38.0"; sha256="0nbg37w6ij9vpj0mrbsx35naqv48kg8kkfl3x39ycbl860mrbr0b"; depends=[Biobase]; };
+  WeberDivechaLCdata = derive2 { name="WeberDivechaLCdata"; version="1.6.0"; sha256="0nkh8c329n0jh33wa0knnwi9vvk8na1d3lpm3g5lrzl8624kdllv"; depends=[ExperimentHub SingleCellExperiment SpatialExperiment]; };
-  aracne_networks = derive2 { name="aracne.networks"; version="1.28.0"; sha256="16gy79hgy07kynjf2s1lrh6a86brhz1caylginmkw547hal43nvf"; depends=[viper]; };
+  XhybCasneuf = derive2 { name="XhybCasneuf"; version="1.42.0"; sha256="0n0k6h9b9gkywy6cmlx15g09287aqzvc228j3jgjkv0ljbwsq756"; depends=[affy ath1121501cdf RColorBrewer tinesath1cdf]; };
-  bcellViper = derive2 { name="bcellViper"; version="1.38.0"; sha256="1q9ig5z03flq57nrhwnk6gdz4kamjmpwdfifwvnhac3l3f5z828h"; depends=[Biobase]; };
+  adductData = derive2 { name="adductData"; version="1.20.0"; sha256="1ydd7zxag0cmw7mj38srqs4w6lbp1ic5i8s1ay6pifv14arcncrz"; depends=[AnnotationHub ExperimentHub]; };
-  beadarrayExampleData = derive2 { name="beadarrayExampleData"; version="1.40.0"; sha256="1mb821p4hf9fmj0f7s0rxwbxv8kb5ln0x2gfnydg4jnyz7k9w5p8"; depends=[beadarray Biobase]; };
+  affycompData = derive2 { name="affycompData"; version="1.42.0"; sha256="16fri51jhp0lm3aj9hw2s6jzxjlxz2qbd36j9zcbcs7sb6jh42jy"; depends=[affycomp Biobase]; };
-  benchmarkfdrData2019 = derive2 { name="benchmarkfdrData2019"; version="1.16.0"; sha256="1p441c08bxx81z556n5wrzxkbq5g4lrwkp1wk7jh6zk6qs3jqg96"; depends=[ExperimentHub SummarizedExperiment]; };
+  affydata = derive2 { name="affydata"; version="1.52.0"; sha256="0srmrb2pf5dhjfm1l1jd06jgnah16qxillxi5zjr8vq7pgvw8x4b"; depends=[affy]; };
-  beta7 = derive2 { name="beta7"; version="1.40.0"; sha256="1q77pmvjnwyi0hm0dmi45a5fcj1phhz9r2fvz4vnmq5b632zp30v"; depends=[marray]; };
+  airway = derive2 { name="airway"; version="1.24.0"; sha256="0yj9ac58iplcakzw6yyglyiwwhiyslp2hlnszhp3258grvbfvcby"; depends=[SummarizedExperiment]; };
-  biotmleData = derive2 { name="biotmleData"; version="1.26.0"; sha256="06lnkwqzsk4v241309w174ia6x8iksh7rvk3z8l0xr6hf31sg5gw"; depends=[]; };
+  antiProfilesData = derive2 { name="antiProfilesData"; version="1.40.0"; sha256="1mlps08fra7ssbymwf260c43skp2pzw477mp090ycfaj8ncdzqqp"; depends=[Biobase]; };
-  biscuiteerData = derive2 { name="biscuiteerData"; version="1.16.0"; sha256="1wqdj1499psnf9y816k05m6h38yfsin4rwzqm1209ddxza6jbw1x"; depends=[AnnotationHub curl ExperimentHub GenomicRanges]; };
+  aracne_networks = derive2 { name="aracne.networks"; version="1.30.0"; sha256="1xfzs1n9wis3r0q4g0hg4amhx4zldbslidx1i4d90vcrgzfdh4x6"; depends=[viper]; };
-  bladderbatch = derive2 { name="bladderbatch"; version="1.40.0"; sha256="19dgvdbxsswy1fl68wwf4ifplppm1blzjw1dr06mz0yjq80a7rvl"; depends=[Biobase]; };
+  bcellViper = derive2 { name="bcellViper"; version="1.40.0"; sha256="0mx92gs9065lz0c01mzng9snalvmdb3xbsm1r3f6fnhg478da4yq"; depends=[Biobase]; };
-  blimaTestingData = derive2 { name="blimaTestingData"; version="1.22.0"; sha256="14rlw5xxgbybsrzmzncqwzkc617gfays5z8x6ifigfdlrp5h1rpl"; depends=[]; };
+  beadarrayExampleData = derive2 { name="beadarrayExampleData"; version="1.42.0"; sha256="0l5n1d7x4gc3w2kc6vq0gqxp1wdpa2sn5k75yf5fc802m11nrkd1"; depends=[beadarray Biobase]; };
-  bodymapRat = derive2 { name="bodymapRat"; version="1.18.0"; sha256="1sfq6vxkb68l0q5qbnpm3fi53k4q9a890bv2ff9c6clhc42wx3h6"; depends=[ExperimentHub SummarizedExperiment]; };
+  benchmarkfdrData2019 = derive2 { name="benchmarkfdrData2019"; version="1.18.0"; sha256="1k8gpql57jps51bh5kdn5j5mgz36a369p4sz37sbqkfrskfs8m91"; depends=[ExperimentHub SummarizedExperiment]; };
-  breakpointRdata = derive2 { name="breakpointRdata"; version="1.20.0"; sha256="13w9vp436akpnywhsr6kz763c2yakrvpyiplggfb6w50wi2xm5xj"; depends=[]; };
+  beta7 = derive2 { name="beta7"; version="1.42.0"; sha256="0c7zal2hk7knw2mcfkfh7svz3b6nz98y895mhl3ari986wqpj4nv"; depends=[marray]; };
-  breastCancerMAINZ = derive2 { name="breastCancerMAINZ"; version="1.40.0"; sha256="1nbvacb04ka0p88hailawz0i4472gaagxy0yw9qg83f9da1dzm4l"; depends=[]; };
+  biotmleData = derive2 { name="biotmleData"; version="1.28.0"; sha256="0c50778lwkapgvwn7nvhjyn7irxn85d97mfyawgfgs9kzyfxx1a3"; depends=[]; };
-  breastCancerNKI = derive2 { name="breastCancerNKI"; version="1.40.0"; sha256="0q3lvq447jw3ny2896mz009x0ijdxgy4xgk4y00sv9nsbwic1ais"; depends=[]; };
+  biscuiteerData = derive2 { name="biscuiteerData"; version="1.18.0"; sha256="1qv2ajy312diacb3mihc3q7hrrlq48k5vd9v0g6w38cqz6gnz0as"; depends=[AnnotationHub curl ExperimentHub GenomicRanges]; };
-  breastCancerTRANSBIG = derive2 { name="breastCancerTRANSBIG"; version="1.40.0"; sha256="03q9y9cbipp8a275hcw5yzwx7l5qrc6fqzdy8vy7z5ij825ygnad"; depends=[]; };
+  bladderbatch = derive2 { name="bladderbatch"; version="1.42.0"; sha256="00cgkpa6mb32q3xl5clkpdh5rkwx7c81rxmyh2qr0jpwpmd3gjwc"; depends=[Biobase]; };
-  breastCancerUNT = derive2 { name="breastCancerUNT"; version="1.40.0"; sha256="0p11hll0pjzycgqbjhcn06vcah7kfvxbzsrqvbwglajs0b5m6dra"; depends=[]; };
+  blimaTestingData = derive2 { name="blimaTestingData"; version="1.24.0"; sha256="0414hiah3yzkcdayb43vz5dafv6samaczg556wyl7ig2275k3q6h"; depends=[]; };
-  breastCancerUPP = derive2 { name="breastCancerUPP"; version="1.40.0"; sha256="0mi9dqbx7fyrxmc4l12c0x6i865f5691f94wzw88q2hwzzz80n6p"; depends=[]; };
+  bodymapRat = derive2 { name="bodymapRat"; version="1.20.0"; sha256="15kjgqq7lq94pjqg380swqrkv684kgbpkaikfxxdx4cpgx8sjzn7"; depends=[ExperimentHub SummarizedExperiment]; };
-  breastCancerVDX = derive2 { name="breastCancerVDX"; version="1.40.0"; sha256="12r8zql30ssr0cxy8v1qawwsky54321c737ny19n2yrl7sm08gf0"; depends=[]; };
+  breakpointRdata = derive2 { name="breakpointRdata"; version="1.22.0"; sha256="1hm190ji3s451x2hchmpyzx6v4n8p1n6fdqg7cbzmj19rzsb4wha"; depends=[]; };
-  brgedata = derive2 { name="brgedata"; version="1.24.0"; sha256="0nplh5km45hdb001mc86fh9yyj56mfvcr2g0zffq0nbjlpvspz0i"; depends=[Biobase SummarizedExperiment]; };
+  breastCancerMAINZ = derive2 { name="breastCancerMAINZ"; version="1.42.0"; sha256="1i2h0f38skkv1m5gas15jdjw4jl8ma4w1sv74j1x9g1zfl9xq3rg"; depends=[]; };
-  bronchialIL13 = derive2 { name="bronchialIL13"; version="1.40.0"; sha256="110791bhnpzadc2ja8i59bix42ficqxqw3il8hnqb38i7c43w0zw"; depends=[affy]; };
+  breastCancerNKI = derive2 { name="breastCancerNKI"; version="1.42.0"; sha256="0vnwyqn5wg9iqmgb6zx6rciw62n8bxkdyfxlaggl35dpwwpzdb2f"; depends=[]; };
-  bsseqData = derive2 { name="bsseqData"; version="0.40.0"; sha256="15fyv6l6bsa4fk4qxpfgxgw5aq1dd3pry84zapklijxm24g6yl6j"; depends=[bsseq]; };
+  breastCancerTRANSBIG = derive2 { name="breastCancerTRANSBIG"; version="1.42.0"; sha256="0s2h6qy19jnk5s23r0vkv6j77n5qr7ncanmkz0ybx5qyfyicz9m4"; depends=[]; };
-  cMap2data = derive2 { name="cMap2data"; version="1.38.0"; sha256="1d2yv9gq3w1b50f602ajbdqky5vwsh19qqg8a3czlphghrjrlfwd"; depends=[]; };
+  breastCancerUNT = derive2 { name="breastCancerUNT"; version="1.42.0"; sha256="0i8xw534hywfa382nyfy94g2fk0nfaid306dxrlijkfbs2b24dy9"; depends=[]; };
-  cancerdata = derive2 { name="cancerdata"; version="1.40.0"; sha256="1670df52ainxq220vzblrv2jml2bql8vid09b51dzhjhikwzxhs4"; depends=[Biobase]; };
+  breastCancerUPP = derive2 { name="breastCancerUPP"; version="1.42.0"; sha256="183dy6c3wqc2m65vihdn840wvnq64vwndwcfsvhw39znqpszhs9k"; depends=[]; };
-  ccTutorial = derive2 { name="ccTutorial"; version="1.40.0"; sha256="1rqblyk7389xqwzvib2xjyjrc8l3qd2g8z9vj96mrfyr8dpccjjs"; depends=[affy Biobase Ringo topGO]; };
+  breastCancerVDX = derive2 { name="breastCancerVDX"; version="1.42.0"; sha256="0mvm2a77mss85vi8x3i35d54z70advyshsmadhl6aysrzfiw5ifd"; depends=[]; };
-  ccdata = derive2 { name="ccdata"; version="1.28.0"; sha256="1vskwqb0n3qfgmakc8zlvfkag653gkz3l9j8lqnhxbbnnads738j"; depends=[]; };
+  brgedata = derive2 { name="brgedata"; version="1.26.0"; sha256="1h2ka8k12lx4326y50scw80n21xkf67ks7kqs2ss6sbwd536gm61"; depends=[Biobase SummarizedExperiment]; };
-  celarefData = derive2 { name="celarefData"; version="1.20.0"; sha256="11vx5hmbjsfzyxgb8qzhy3f54krcp33h8ki61irxxl06q2n59928"; depends=[]; };
+  bronchialIL13 = derive2 { name="bronchialIL13"; version="1.42.0"; sha256="0g1cfhfjycpv1jmba5jddff88m7pbz1l02kci9w73qzjcnqgpp12"; depends=[affy]; };
-  celldex = derive2 { name="celldex"; version="1.12.0"; sha256="1ckjdmiw9g1wdswijy3dvamv3kqi11j8b8p9dgr1yv5q2lfjbnwl"; depends=[AnnotationDbi AnnotationHub DelayedArray DelayedMatrixStats ExperimentHub S4Vectors SummarizedExperiment]; };
+  bsseqData = derive2 { name="bsseqData"; version="0.42.0"; sha256="06k6r288bqi9dshpdz6qlz0d3p1srz8yc1b0xrar9wy5fckdb97d"; depends=[bsseq]; };
-  cfToolsData = derive2 { name="cfToolsData"; version="1.0.0"; sha256="0icr4llq99ghyvi8nsdfnp5sydh8icr23y8ar7jg0qpwiagdl3l9"; depends=[ExperimentHub]; };
+  cMap2data = derive2 { name="cMap2data"; version="1.40.0"; sha256="1vaqqszdx3bfdqm3ckn12w9f474wnyqyi7kz0wrj1y50wnwpm38f"; depends=[]; };
-  chipenrich_data = derive2 { name="chipenrich.data"; version="2.26.0"; sha256="0hfisbzbhz501dvcwvx3cnag9643ydw6f0q122w7mrnzsag82013"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicRanges IRanges readr rtracklayer S4Vectors]; };
+  cancerdata = derive2 { name="cancerdata"; version="1.42.0"; sha256="1jgcg16v09wpga5zivx221mz2bnl37gwpjhlmq9a8h5vxlqcb9wl"; depends=[Biobase]; };
-  chipseqDBData = derive2 { name="chipseqDBData"; version="1.18.0"; sha256="114645f6db8pp263g6h2gb2cwhdgqh8risssq2vfzzdv16qqw640"; depends=[AnnotationHub ExperimentHub Rsamtools S4Vectors]; };
+  ccdata = derive2 { name="ccdata"; version="1.30.0"; sha256="0q77dk9rifwpp1c2ga1y3yxf1dwvlkmmn5sw285a1c5h6pipxsj3"; depends=[]; };
-  chromstaRData = derive2 { name="chromstaRData"; version="1.28.0"; sha256="13xrdr9xrfysh714q4p00pgvwr6ryhvd3jinfqr1gb27s7bdvsi6"; depends=[]; };
+  celarefData = derive2 { name="celarefData"; version="1.22.0"; sha256="1njq6i1803avcn2h9p3d2cnp8viwv7jak1b5kfqhcvl8jwwxlr59"; depends=[]; };
-  clustifyrdatahub = derive2 { name="clustifyrdatahub"; version="1.12.0"; sha256="004g6s917ayxiixlc8zp4h7zai9amcm6bllr9mz5j9sgm8kd8px4"; depends=[ExperimentHub]; };
+  celldex = derive2 { name="celldex"; version="1.14.0"; sha256="155hnh62ra06b52xk78f111b10gm34d1djvl5w5mabvrk4vknwj6"; depends=[alabaster_base alabaster_matrix alabaster_se AnnotationDbi AnnotationHub DBI DelayedArray DelayedMatrixStats ExperimentHub gypsum jsonlite Matrix RSQLite S4Vectors SummarizedExperiment]; };
-  cnvGSAdata = derive2 { name="cnvGSAdata"; version="1.38.0"; sha256="1aask6cx972qw62p2p16n1sk0rjmrr9hhqlaaab52rn4lfdiaba2"; depends=[cnvGSA]; };
+  cfToolsData = derive2 { name="cfToolsData"; version="1.2.0"; sha256="0hhc9fn6rm9dnzlvs3lk5v0h5m76knl5nblnda26a36wdwz547ld"; depends=[ExperimentHub]; };
-  colonCA = derive2 { name="colonCA"; version="1.44.0"; sha256="0qkjmbyh5hwfjw657qam7xpjnym4qqbv1292fbqzwdyr0019jpfn"; depends=[Biobase]; };
+  chipenrich_data = derive2 { name="chipenrich.data"; version="2.28.0"; sha256="1kpc3ljayxycadshdgyzkbagh4vd7cmyqqccy61269skpasdnwbv"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicRanges IRanges readr rtracklayer S4Vectors]; };
-  crisprScoreData = derive2 { name="crisprScoreData"; version="1.6.0"; sha256="0rrwsfp8m8z389yfr8ls6wkz7faa2iz8pnljl2776qa3zgsfmhni"; depends=[AnnotationHub ExperimentHub]; };
+  chipseqDBData = derive2 { name="chipseqDBData"; version="1.20.0"; sha256="16mfq2mdwrc40i6wyjc9g897sk2rk0way6shc0nw9d1fkf4fsf8l"; depends=[AnnotationHub ExperimentHub Rsamtools S4Vectors]; };
-  curatedAdipoArray = derive2 { name="curatedAdipoArray"; version="1.14.0"; sha256="06dcb58i86gg4ar3hyh5w8kdqd0rf1ps7l021nfwklzm622b4wzc"; depends=[]; };
+  chromstaRData = derive2 { name="chromstaRData"; version="1.30.0"; sha256="0v28zg8z5b72hci7rqbvjvcgp979zxnq6xgck4baypmkj9ac5wn3"; depends=[]; };
-  curatedAdipoChIP = derive2 { name="curatedAdipoChIP"; version="1.18.0"; sha256="16g8k2cvi890b9j30yzm7lxnxljl2k4x1yxvd8cg1ba94vzimw6k"; depends=[ExperimentHub SummarizedExperiment]; };
+  clustifyrdatahub = derive2 { name="clustifyrdatahub"; version="1.14.0"; sha256="1asssxa8kw2r5ai14kg06ajzkqfmqfvrp6ydjwgf8pkyc4m53r4p"; depends=[ExperimentHub]; };
-  curatedAdipoRNA = derive2 { name="curatedAdipoRNA"; version="1.18.0"; sha256="1dy58ppw1ck89p036y6iml9210hv7f4zvsm0wi5m13b4ij7a749p"; depends=[SummarizedExperiment]; };
+  cnvGSAdata = derive2 { name="cnvGSAdata"; version="1.40.0"; sha256="19dskn9kjk1phn2xlsx4wikwvagv48av6ar845hzwwyq7rzllyy6"; depends=[cnvGSA]; };
-  curatedBladderData = derive2 { name="curatedBladderData"; version="1.38.0"; sha256="1i9hbm8gh9f09fzyjga7rjps7hlbsivnnbpk8fgb0838msjq5bl2"; depends=[affy]; };
+  colonCA = derive2 { name="colonCA"; version="1.46.0"; sha256="17h4vcpvll01ggp280bspxsl1swiakfabs6n73874sjnik64wp2q"; depends=[Biobase]; };
-  curatedBreastData = derive2 { name="curatedBreastData"; version="2.30.0"; sha256="127kjiqb2laz77cx9lr0rs43kgwxyi52rd7ivhfpcxhivsg4hcsr"; depends=[Biobase BiocStyle ggplot2 impute XML]; };
+  crisprScoreData = derive2 { name="crisprScoreData"; version="1.8.0"; sha256="1a5ji6zbvnlbdzcqj4arpi6am7vaq31brxaxawr93knpy4lksd4f"; depends=[AnnotationHub ExperimentHub]; };
-  curatedCRCData = derive2 { name="curatedCRCData"; version="2.34.0"; sha256="1dqcdpzls41adih54wfpcb36mpysw0za14pz4wsjwisqnjwzpxvn"; depends=[BiocGenerics nlme]; };
+  curatedAdipoArray = derive2 { name="curatedAdipoArray"; version="1.16.0"; sha256="0gs68q5gfn0ba6y0p429s8v989cfnnlii9066wvqgd8ixqcig66i"; depends=[]; };
-  curatedMetagenomicData = derive2 { name="curatedMetagenomicData"; version="3.10.0"; sha256="0fgvpxc1878lm8l0bib12zzwrgsap0vw4zn77qpz1mljnz43shcb"; depends=[AnnotationHub dplyr ExperimentHub magrittr mia purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect TreeSummarizedExperiment]; };
+  curatedAdipoChIP = derive2 { name="curatedAdipoChIP"; version="1.20.0"; sha256="1yzxz6wjddf4mn6yw8zlz2yq6rhfs0639widql99hjclni1llxkc"; depends=[ExperimentHub SummarizedExperiment]; };
-  curatedOvarianData = derive2 { name="curatedOvarianData"; version="1.40.1"; sha256="18163l0g3g042m2qgz143smxia3lp8v7rddkqmkg4hzns7baxfaa"; depends=[Biobase BiocGenerics]; };
+  curatedAdipoRNA = derive2 { name="curatedAdipoRNA"; version="1.20.0"; sha256="1q22clkypj8y6am609h4748z2jc2lhhm8kdcv9s3dzx272dmm0w5"; depends=[SummarizedExperiment]; };
-  curatedTBData = derive2 { name="curatedTBData"; version="1.8.0"; sha256="116ck61pw6diili326x0x8p7f8d5w624n4w3pd212vhq8555yrqs"; depends=[AnnotationHub ExperimentHub MultiAssayExperiment rlang]; };
+  curatedBladderData = derive2 { name="curatedBladderData"; version="1.40.0"; sha256="0ma11myfh5kddksn81rspjq7l44vn0mgz2c98krpdgfv8qynf6ky"; depends=[affy]; };
-  curatedTCGAData = derive2 { name="curatedTCGAData"; version="1.24.1"; sha256="0hr66p8l54nzfsizcxxd2njy44xnia607wvfhrgv46f3f8s95z02"; depends=[AnnotationHub ExperimentHub HDF5Array MultiAssayExperiment S4Vectors SummarizedExperiment]; };
+  curatedBreastData = derive2 { name="curatedBreastData"; version="2.32.0"; sha256="0zglh1h9hw6rnpdl4v5v7cmzgcvxa0phfixfwwmi8il0rn40jd68"; depends=[Biobase BiocStyle ggplot2 impute XML]; };
-  davidTiling = derive2 { name="davidTiling"; version="1.42.0"; sha256="1xfkyncwi9zrynk6dqsmacmkxx2qvj1axda3wn55b1vbw2wimpyf"; depends=[Biobase GO_db tilingArray]; };
+  curatedCRCData = derive2 { name="curatedCRCData"; version="2.35.0"; sha256="1q6xmp32w39jsw7jrphpygyv63vd640nmpz69nlhhisbbpjd259c"; depends=[BiocGenerics nlme]; };
-  depmap = derive2 { name="depmap"; version="1.16.0"; sha256="1vb3f5ar2jlkjyhp7rv4imlylinm6fi94ki277jgdaxn12v78qxj"; depends=[AnnotationHub dplyr ExperimentHub]; };
+  curatedMetagenomicData = derive2 { name="curatedMetagenomicData"; version="3.12.0"; sha256="1hp1s5v567xidmmpn6jv7i3fid5hwg3i43y9471aabq00nsg67b1"; depends=[AnnotationHub dplyr ExperimentHub magrittr mia purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect TreeSummarizedExperiment]; };
-  derfinderData = derive2 { name="derfinderData"; version="2.20.0"; sha256="1h8rl8mnxk2lsl8xa8mihvbd77yw32fpxdbhhn4rv1v8i5j35r7l"; depends=[]; };
+  curatedOvarianData = derive2 { name="curatedOvarianData"; version="1.42.0"; sha256="0rigr8nwcr60vp164hyjw20dw54mwlfg71m4naiz6m1v47d7cg1i"; depends=[Biobase BiocGenerics]; };
-  diffloopdata = derive2 { name="diffloopdata"; version="1.30.0"; sha256="1f0gnwpjxkby7kd2bphnz4lv7gx9k297yqz0b954m7adp1sh6aqa"; depends=[]; };
+  curatedPCaData = derive2 { name="curatedPCaData"; version="1.0.0"; sha256="0wqvg0z19lxyqbbsl7fbq12jgycpqycx45vy24z4sph48kz2ag3w"; depends=[AnnotationHub ExperimentHub MultiAssayExperiment RaggedExperiment rlang S4Vectors]; };
-  diggitdata = derive2 { name="diggitdata"; version="1.34.0"; sha256="01r356zdy4pi8z90pbww8q7dfmq09zf148d5sq3w22z1ypsy6zm1"; depends=[Biobase viper]; };
+  curatedTBData = derive2 { name="curatedTBData"; version="2.0.0"; sha256="03wmr9iyhqwbpmp7azq9im5waxy4viqhx0lsmqpk2bsijmigrg0z"; depends=[AnnotationHub ExperimentHub MultiAssayExperiment rlang]; };
-  dorothea = derive2 { name="dorothea"; version="1.14.1"; sha256="0bjmnqly57y69axnz5q2rqz7j7dnz1xzbhbzcalv99kybjiyqyb5"; depends=[bcellViper decoupleR dplyr magrittr]; };
+  curatedTCGAData = derive2 { name="curatedTCGAData"; version="1.26.0"; sha256="1xdygjwqgy6kjjxzvsy25bckc0f8j5m42wrj1vrnwy5fp0q7y287"; depends=[AnnotationHub ExperimentHub HDF5Array MultiAssayExperiment S4Vectors SummarizedExperiment]; };
-  dressCheck = derive2 { name="dressCheck"; version="0.40.0"; sha256="1mb6cmyf61rb7jdwczhzcvadgqijij53w03d87xq7zqsc7jxi9z3"; depends=[Biobase]; };
+  davidTiling = derive2 { name="davidTiling"; version="1.44.0"; sha256="06r600sn2ga5jrwahxh3ysv4c713sxi0g6y6v46zpcwilkj10gp3"; depends=[Biobase GO_db tilingArray]; };
-  dyebiasexamples = derive2 { name="dyebiasexamples"; version="1.42.0"; sha256="06sp4fxsph3w84g960s65sy1vc032p2xj3sf0v94nh78f6myg0mj"; depends=[GEOquery marray]; };
+  depmap = derive2 { name="depmap"; version="1.18.0"; sha256="0imajc5kiqf45sjwxagvg5bjvmnrzrk3ls4bflwxj9rnd84v2r62"; depends=[AnnotationHub BiocFileCache curl dplyr ExperimentHub httr2 tibble]; };
-  easierData = derive2 { name="easierData"; version="1.8.0"; sha256="138x8i1zd4cvlawg9pa5ia1kmmdaxm0g9lkivzxl077s9vlpjp8d"; depends=[AnnotationHub ExperimentHub SummarizedExperiment]; };
+  derfinderData = derive2 { name="derfinderData"; version="2.22.0"; sha256="14gyw3cii7np0rw9j39hcrij9kcybbrwxwz9qa4wx98ddzfixrcn"; depends=[]; };
-  ecoliLeucine = derive2 { name="ecoliLeucine"; version="1.42.0"; sha256="02v2hv8qcwdi2z531xqvnfdymzmd5qqp868arg5r0zcrzj5kkiaw"; depends=[affy ecolicdf]; };
+  diffloopdata = derive2 { name="diffloopdata"; version="1.32.0"; sha256="0qhbdq5j900nmpfbz3bcr4jn9zd43fnr7rd94lsv69dpjmsv7ikw"; depends=[]; };
-  emtdata = derive2 { name="emtdata"; version="1.10.0"; sha256="0fjqmg9w7c1lv0b0ldr26rxsly78sw2asj3hw8h8yd623g7bkddw"; depends=[edgeR ExperimentHub SummarizedExperiment]; };
+  diggitdata = derive2 { name="diggitdata"; version="1.36.0"; sha256="0js94wbi9rfsmwj7q8mbh2fimwpiw45ahb1a1g0300zxzf9y61ax"; depends=[Biobase viper]; };
-  epimutacionsData = derive2 { name="epimutacionsData"; version="1.6.0"; sha256="1gbh1ad0kqdmyrnmvrw5lbxlafvq12gqmbw9w3bxi7q1ahclh4yh"; depends=[]; };
+  dorothea = derive2 { name="dorothea"; version="1.16.0"; sha256="08s961ra7f6q4dag39rgdrg5minvzm58g22r8xkwfiw0hfavacbg"; depends=[bcellViper decoupleR dplyr magrittr]; };
-  estrogen = derive2 { name="estrogen"; version="1.48.0"; sha256="0nbyg1pj7vqxaxgznkhz2v14cq42gg8jkn5mbkd3nrz86slzkblm"; depends=[]; };
+  dressCheck = derive2 { name="dressCheck"; version="0.42.0"; sha256="1i6lcf8lxp0v0lpkckx3yhzyzj841w3x6qj3kaxls4bfkzr3hls6"; depends=[Biobase]; };
-  etec16s = derive2 { name="etec16s"; version="1.30.0"; sha256="1amhmhl74fyfvh4w1a0r0g7ahqm5yq16i87s4mzwvc03vslps143"; depends=[Biobase metagenomeSeq]; };
+  dyebiasexamples = derive2 { name="dyebiasexamples"; version="1.44.0"; sha256="1ihkhfhgqywnp2vxrqpzvm5w3ncy6acwcns2ah1fm8xsq1bvcs5v"; depends=[GEOquery marray]; };
-  ewceData = derive2 { name="ewceData"; version="1.10.0"; sha256="1kgh5r0pplvblrrkf1qxg7c92psrwm2bjpbs30dp8mdsnjdahm9v"; depends=[ExperimentHub]; };
+  easierData = derive2 { name="easierData"; version="1.10.0"; sha256="0l6qhlaa02d2sqaa0yfxqqm1giga5jppq74sfgrih1ccqh348am7"; depends=[AnnotationHub ExperimentHub SummarizedExperiment]; };
-  faahKO = derive2 { name="faahKO"; version="1.42.0"; sha256="0m3m9382b463wbl5hrzh04lp8h052gka8b7q69s740hlb91npjx7"; depends=[xcms]; };
+  ecoliLeucine = derive2 { name="ecoliLeucine"; version="1.44.0"; sha256="09pk2ay2j5gvk60vavs03cgfhma8bvsynxabkfcvr1hkl87qfl2k"; depends=[affy ecolicdf]; };
-  fabiaData = derive2 { name="fabiaData"; version="1.40.0"; sha256="0alh11k7vj6ripj2017j6afa8wjb4xb03zfvrh10svsrr0a7qldv"; depends=[Biobase]; };
+  emtdata = derive2 { name="emtdata"; version="1.12.0"; sha256="0b3hvggndw3bzddk0vflbn0wx8fr08b6nphjhil1wqlyp3535xk4"; depends=[edgeR ExperimentHub SummarizedExperiment]; };
-  ffpeExampleData = derive2 { name="ffpeExampleData"; version="1.40.0"; sha256="16bxp2x0n77hzlf6m871wgprrhkydcbbnw88jp8nb7d0fl1vhxyr"; depends=[lumi]; };
+  epimutacionsData = derive2 { name="epimutacionsData"; version="1.8.0"; sha256="06z3lxp8lsr2nqw3yqiddy3h4y6iid3n7s1ykbaz0dpm05vdq8i2"; depends=[]; };
-  fibroEset = derive2 { name="fibroEset"; version="1.44.0"; sha256="17dzp6gjfgsnvwplk3inf7s491brf1pnn1bq1a195s8m0r5kd946"; depends=[Biobase]; };
+  estrogen = derive2 { name="estrogen"; version="1.50.0"; sha256="077mr5xz2w90iik8r6jraip377dbily14rnkpc7njicqnnq1d6m7"; depends=[]; };
-  fission = derive2 { name="fission"; version="1.22.0"; sha256="0y07zj5iw6fmr397xkxijgfy8mmv1k42mqjfpmv01kb0hzayjj8n"; depends=[SummarizedExperiment]; };
+  etec16s = derive2 { name="etec16s"; version="1.32.0"; sha256="0hlvvmgm42g0lzsb5kljdfs0fcdpwwz3b3h7x88szg7fzqlvainz"; depends=[Biobase metagenomeSeq]; };
-  flowPloidyData = derive2 { name="flowPloidyData"; version="1.28.0"; sha256="1r3w88d20jipmj7gchv0mmw9rbziq0s7vyvi5isc4lp59hc6m9h1"; depends=[]; };
+  ewceData = derive2 { name="ewceData"; version="1.12.0"; sha256="1xk4i38a1yb3zx42hfh2b427y28103h2mpjvxa03fnwkl0lcb46j"; depends=[ExperimentHub]; };
-  flowWorkspaceData = derive2 { name="flowWorkspaceData"; version="3.14.0"; sha256="0wm0s1839c14b2y05b8nini2aqp39vl7ycsp1nz1y2amxirdfpyq"; depends=[]; };
+  faahKO = derive2 { name="faahKO"; version="1.44.0"; sha256="0bd93q332m7agqgsfkgsp87wv5fx6g2qsgn2z2n0bfsn3vmjjzc4"; depends=[xcms]; };
-  fourDNData = derive2 { name="fourDNData"; version="1.2.0"; sha256="06dzm57f56y396py2mmfzls9yypkxzj032hpba8srq263zqpi9z0"; depends=[BiocFileCache GenomicRanges HiCExperiment IRanges S4Vectors]; };
+  fabiaData = derive2 { name="fabiaData"; version="1.42.0"; sha256="1wzq802q1i52jh82yh9i2kdbya7qrmcjr646dc78vr6vng2k541s"; depends=[Biobase]; };
-  frmaExampleData = derive2 { name="frmaExampleData"; version="1.38.0"; sha256="0sdh0ijkpni4xk07dyvkckr6k0dha6zbciggxaki61j99fs5nwsv"; depends=[]; };
+  ffpeExampleData = derive2 { name="ffpeExampleData"; version="1.42.0"; sha256="1dzrbqlgh114m4lvikp638bqmw0yq3rwz9bpb1cfbpqlyji97wx7"; depends=[lumi]; };
-  furrowSeg = derive2 { name="furrowSeg"; version="1.30.0"; sha256="0vvr9x50yw7h5qcgcva2505cgqk276ci7yfbzvizn3mq4n2r3n3j"; depends=[abind dplyr EBImage locfit tiff]; };
+  fibroEset = derive2 { name="fibroEset"; version="1.46.0"; sha256="09lpn8s95rbbmv0zk3mg512ddxdv7gpp16hqyh7krsrfr9r8kjxs"; depends=[Biobase]; };
-  gDNAinRNAseqData = derive2 { name="gDNAinRNAseqData"; version="1.2.0"; sha256="13v14dhwb1mkpxc5z08amqajhkncrkl38k4js48bp36s8lzb0zw8"; depends=[BiocGenerics ExperimentHub RCurl Rsamtools XML]; };
+  fission = derive2 { name="fission"; version="1.24.0"; sha256="095fd01jd105826gpv038zwj7p4iz7drbm3gy6r0w329xlv4lpp2"; depends=[SummarizedExperiment]; };
-  gDRtestData = derive2 { name="gDRtestData"; version="1.0.0"; sha256="0pwrypvc1hvrcd6dckiid5vjpwpcbw3vg61s88mms3kjs8163c0r"; depends=[checkmate]; };
+  flowPloidyData = derive2 { name="flowPloidyData"; version="1.30.0"; sha256="1qlwv4v1mgxk444scdvmdpak0rpph51mc4al1qfbavd34l4yq6zc"; depends=[]; };
-  gageData = derive2 { name="gageData"; version="2.40.0"; sha256="13g8hzkh34c0my75xnxdffa1d67xvn9hn592s25m18400lgsfif0"; depends=[]; };
+  flowWorkspaceData = derive2 { name="flowWorkspaceData"; version="3.16.0"; sha256="11p2b85h8dmajj0pakmb7i4lr2rx9ghlm8sy3pa696hpqnszimjl"; depends=[]; };
-  gaschYHS = derive2 { name="gaschYHS"; version="1.40.0"; sha256="08dgm24ycsldp6pjqhflpxqm91yqp199n2j1fg9m4wrgbyakypkm"; depends=[Biobase]; };
+  fourDNData = derive2 { name="fourDNData"; version="1.4.0"; sha256="1lixqb8n99w0qwr6hi5sql2r84dnp4zc7lqd6lhj0mgpya85b5zr"; depends=[BiocFileCache GenomicRanges HiCExperiment IRanges S4Vectors]; };
-  gcspikelite = derive2 { name="gcspikelite"; version="1.40.0"; sha256="1yfmp96k1iy6sjyafs2sflflnmnq4czkjba61vzxb4alirra9jf5"; depends=[]; };
+  frmaExampleData = derive2 { name="frmaExampleData"; version="1.40.0"; sha256="1dgirbhamg53dmfwc76s5ivclxmy7sjhjm9crzwrj1bzl6056cr3"; depends=[]; };
-  geneLenDataBase = derive2 { name="geneLenDataBase"; version="1.38.0"; sha256="0skycixz0qbm8cs10kgrkl1ab1qh0mz8641mf5194y839m81d060"; depends=[GenomicFeatures rtracklayer]; };
+  furrowSeg = derive2 { name="furrowSeg"; version="1.32.0"; sha256="125wyqi4h7kkrhbcn4gknwlw6panian2hfsapwyqfxz0mg6ssg5z"; depends=[abind dplyr EBImage locfit tiff]; };
-  genomationData = derive2 { name="genomationData"; version="1.34.0"; sha256="044q01dbcd34lxgwpg76yk0msvx7gpiibiqxp6fr9jswq6izrzq7"; depends=[]; };
+  gDNAinRNAseqData = derive2 { name="gDNAinRNAseqData"; version="1.4.0"; sha256="0wpv9p96qxnk22p7ili8ic4gr8p3wb6jfn4v9f0d4kn385vvfwyp"; depends=[BiocGenerics ExperimentHub RCurl Rsamtools XML]; };
-  golubEsets = derive2 { name="golubEsets"; version="1.44.0"; sha256="1rwhb48wz20i06whxdj1cb6qjda545w4050y87c55h3xqcair3ya"; depends=[Biobase]; };
+  gDRtestData = derive2 { name="gDRtestData"; version="1.2.0"; sha256="0kdlqbs5qj6svnhsrhnsd644kcxyd8haws5h4djm4gplyx6vwqyj"; depends=[checkmate data_table]; };
-  gpaExample = derive2 { name="gpaExample"; version="1.14.0"; sha256="0danfxw9jqlv9862pcf7sdaxnwxrpgs9gy38xpjzx3q25y4y1589"; depends=[]; };
+  gageData = derive2 { name="gageData"; version="2.42.0"; sha256="1kbs0fz1jnx3grd9mpclbahwbp3749ipwfs8ggl9299bhjrgh9i6"; depends=[]; };
-  grndata = derive2 { name="grndata"; version="1.34.0"; sha256="17g2jp99dl6kypzz4v2pf0h29vx16pwfw6apbhgggv1had9593nm"; depends=[]; };
+  gaschYHS = derive2 { name="gaschYHS"; version="1.42.0"; sha256="01r25gx65a9lcjzbjm6gckzy3hyr70cxswxkvprsbphh7pkll3np"; depends=[Biobase]; };
-  h5vcData = derive2 { name="h5vcData"; version="2.22.0"; sha256="0pflrqg6yaiw7w9b8wazf74sdgx1fqgd0iz9cdq0bx4jnra5f0gz"; depends=[]; };
+  gcspikelite = derive2 { name="gcspikelite"; version="1.42.0"; sha256="0cphbkq13jknmzs6qyv3cj1m73a1wncnj7znjnymbc0ha7rwcd5i"; depends=[]; };
-  hapmap100khind = derive2 { name="hapmap100khind"; version="1.44.0"; sha256="1qzvf4g8rd85g3qxx5gckx4w1v258h9jd9dfcxbn39ghamqhy9yb"; depends=[]; };
+  geneLenDataBase = derive2 { name="geneLenDataBase"; version="1.40.1"; sha256="0c8f0sqgrg7rc2vs9id9xzbwwv3zhy6ylqiisji20rw9ipzgv7k8"; depends=[GenomicFeatures rtracklayer txdbmaker]; };
-  hapmap100kxba = derive2 { name="hapmap100kxba"; version="1.44.0"; sha256="0743byawrk3azgrb1wdb16khd2pl887fxf4r7mf6zm08lgjyr3vv"; depends=[]; };
+  genomationData = derive2 { name="genomationData"; version="1.36.0"; sha256="16mghhik2xzin14d7mqlwfy2dah3ccnga947z9id44vyz906wws7"; depends=[]; };
-  hapmap500knsp = derive2 { name="hapmap500knsp"; version="1.44.0"; sha256="1kla7h8hv6kyc9v6ra5scg3f1dlmw160wl5c1vqq9b6irqmrah6l"; depends=[]; };
+  golubEsets = derive2 { name="golubEsets"; version="1.46.0"; sha256="1rv5y7cj4rpdg8vl0qd3071d12rvgqcffqsf1gx8kmdgz13hi4gl"; depends=[Biobase]; };
-  hapmap500ksty = derive2 { name="hapmap500ksty"; version="1.44.0"; sha256="0g13vk2gnnmpm21fngr7cfhry3sacxmbxsym5wz4sibfv3d72n7r"; depends=[]; };
+  gpaExample = derive2 { name="gpaExample"; version="1.16.0"; sha256="0q87x5k8ql01k9m503k87wn5pkrygrilqrsb0aix7xjpxa8aia1n"; depends=[]; };
-  hapmapsnp5 = derive2 { name="hapmapsnp5"; version="1.44.0"; sha256="1486k3dlnvadxl8qphzria3qrw91x8j0b3k4di8c8s0fjkrfdh33"; depends=[]; };
+  grndata = derive2 { name="grndata"; version="1.36.0"; sha256="1qkxpljvm9sipphgjygnrynbslyv5rlpvfy34q6w1rqhf6qv0n89"; depends=[]; };
-  hapmapsnp6 = derive2 { name="hapmapsnp6"; version="1.44.0"; sha256="1dx59dsm4pmca9xf5c2abk5clmczx2wh6j47xx8h064x3n5s611n"; depends=[]; };
+  h5vcData = derive2 { name="h5vcData"; version="2.24.0"; sha256="04ymiclfwwp68h8pzpxrfrb5x9njqknhyhihbcj4v51qzx0y4jid"; depends=[]; };
-  harbChIP = derive2 { name="harbChIP"; version="1.40.0"; sha256="0xb553h6ffnik8c299h5imaabb2ca0fkqk0hrbs1a1acg11xqs32"; depends=[Biobase Biostrings IRanges]; };
+  hapmap100khind = derive2 { name="hapmap100khind"; version="1.46.0"; sha256="0a8j45fxr3sm4q689v29n9gj60g21pk3ixhv7s9plig12ma7nfnz"; depends=[]; };
-  healthyControlsPresenceChecker = derive2 { name="healthyControlsPresenceChecker"; version="1.6.0"; sha256="127p0wwqf0dx9c8y3rjmsw6nl9rczr72zn8dsqf92mdj13qpxi2m"; depends=[geneExpressionFromGEO GEOquery magrittr xml2]; };
+  hapmap100kxba = derive2 { name="hapmap100kxba"; version="1.46.0"; sha256="1afvfh6mckyi575qlp579p1akya4q7h0c9zp28s7n5nyljmh572i"; depends=[]; };
-  healthyFlowData = derive2 { name="healthyFlowData"; version="1.40.0"; sha256="1w96g3m8kniz4nil682hz55pxhxgaqfgmfii990mrd0smirnckwx"; depends=[flowCore]; };
+  hapmap500knsp = derive2 { name="hapmap500knsp"; version="1.46.0"; sha256="0lbrn02lyca76xk2h2iddxpkvsj2kvz37m1dn0l5pwbz6igpllqp"; depends=[]; };
-  hgu133abarcodevecs = derive2 { name="hgu133abarcodevecs"; version="1.40.0"; sha256="1v8ssmzad3a1wwwh2rw9pkrcwjbbv9m2i5iqjsn0qmi7s9xpdn2z"; depends=[]; };
+  hapmap500ksty = derive2 { name="hapmap500ksty"; version="1.46.0"; sha256="0lnzwdcjz5f9imqprkh9qxrakg8qdh3j83bq5qaaq54mdh76kd68"; depends=[]; };
-  hgu133plus2CellScore = derive2 { name="hgu133plus2CellScore"; version="1.22.0"; sha256="08d6p5zmf674hj6qy6sz8n9fg70xr83y21d7ln22i9gzvvgbazpi"; depends=[Biobase]; };
+  hapmapsnp5 = derive2 { name="hapmapsnp5"; version="1.46.0"; sha256="03pmlz3cskxf683dpdns258gh8rv33amzpvb9mabbg0jagg2b9lw"; depends=[]; };
-  hgu133plus2barcodevecs = derive2 { name="hgu133plus2barcodevecs"; version="1.40.0"; sha256="1c3432d28n4bj363s7h493izz865i2gfrs8x2fr6n2js9p4bz8bf"; depends=[]; };
+  hapmapsnp6 = derive2 { name="hapmapsnp6"; version="1.46.0"; sha256="15npa8h6qpp1i0ir2y6knvzb5f4rn9zimyl6sw24ccqbvimjkf7f"; depends=[]; };
-  hgu2beta7 = derive2 { name="hgu2beta7"; version="1.42.0"; sha256="1xxwj4d760y6ymw2ag5xqd212yb7wns2yaxgla62v3pcalvdccfp"; depends=[]; };
+  harbChIP = derive2 { name="harbChIP"; version="1.42.0"; sha256="1pliyvn6g3gbkiinz4q24ajmq0apw035a2c9xq6b91ccm8m7ddrk"; depends=[Biobase Biostrings IRanges]; };
-  humanStemCell = derive2 { name="humanStemCell"; version="0.42.0"; sha256="0bywcagkg17gdcwbbw68fla1481llz96bhr3apbymvk8m4vbhlp0"; depends=[Biobase hgu133plus2_db]; };
+  healthyControlsPresenceChecker = derive2 { name="healthyControlsPresenceChecker"; version="1.8.0"; sha256="14gq24z99l04kcn13414zjn17184l3p5l6draxwy3820m9sijzgq"; depends=[geneExpressionFromGEO GEOquery magrittr xml2]; };
-  imcdatasets = derive2 { name="imcdatasets"; version="1.10.0"; sha256="0yvii8qxgxabf9i2z5pz37dn9s6vw3g6z2k6c5k4rjns8wmvixps"; depends=[cytomapper DelayedArray ExperimentHub HDF5Array S4Vectors SingleCellExperiment SpatialExperiment]; };
+  healthyFlowData = derive2 { name="healthyFlowData"; version="1.42.0"; sha256="01hq1nchjyzps5nvsvpgxrw1vds92fv0sggzlls21ggrjhyrx8kp"; depends=[flowCore]; };
-  kidpack = derive2 { name="kidpack"; version="1.44.0"; sha256="15c7ahrpjapqp90nanpkjb9hbcv42a84xg939fgpzkpgc7ch0m9k"; depends=[Biobase]; };
+  hgu133abarcodevecs = derive2 { name="hgu133abarcodevecs"; version="1.42.0"; sha256="1p9l32lhk5cvqfgxkk3bdz4s9dcyczh9b0a8rvb2cf6zz0i3l6fh"; depends=[]; };
-  leeBamViews = derive2 { name="leeBamViews"; version="1.38.0"; sha256="0j7q5slcb59z6vf2z123h9ld0gaazsiih7an603id1bqjprkd74b"; depends=[Biobase BSgenome GenomicAlignments GenomicRanges IRanges Rsamtools S4Vectors]; };
+  hgu133plus2CellScore = derive2 { name="hgu133plus2CellScore"; version="1.24.0"; sha256="0akf6y1pwjiffhxgd2s01kmw4aylbfbh9hv8yyfvm3r72j07lbvs"; depends=[Biobase]; };
-  leukemiasEset = derive2 { name="leukemiasEset"; version="1.38.0"; sha256="1srwn3sy929hskka9gfnqpjrh8xy0pz76ihq4amq8wbdawh1zv8b"; depends=[Biobase]; };
+  hgu133plus2barcodevecs = derive2 { name="hgu133plus2barcodevecs"; version="1.42.0"; sha256="0d6jcyb1v58f1p76mng0l327v6i1cskrgcj4p2r9z2pjbgyicgq2"; depends=[]; };
-  lumiBarnes = derive2 { name="lumiBarnes"; version="1.42.0"; sha256="1c27s7ajkmygfmd2g6dpsamwcm87xlxgr31wyn6g1rb7zw2zdpy2"; depends=[Biobase lumi]; };
+  hgu2beta7 = derive2 { name="hgu2beta7"; version="1.44.0"; sha256="0wlkv4yppzg520zbhk7v19jfxbiran9di0bm10bfb9lizdszwd75"; depends=[]; };
-  lungExpression = derive2 { name="lungExpression"; version="0.40.0"; sha256="1kzf8lsl9sh0ikn9zx5sfj5z7ld94xldhmj7awvgp0bsbqlra2qc"; depends=[Biobase]; };
+  homosapienDEE2CellScore = derive2 { name="homosapienDEE2CellScore"; version="1.0.0"; sha256="1vwasylfqv4xgmhkzykdwhlxh0kk4pl4bcndx5dpn7i386zp6chs"; depends=[BiocGenerics DESeq2 ExperimentHub getDEE2 MatrixGenerics Rtsne S4Vectors SummarizedExperiment]; };
-  lydata = derive2 { name="lydata"; version="1.28.0"; sha256="0gwaiq16q1kfx533hymqnh6zk9nimljdbidvzb23bykj99kmsiqr"; depends=[]; };
+  humanStemCell = derive2 { name="humanStemCell"; version="0.44.0"; sha256="0yr4z1j4xaxaby3ka9k6h5bshzn78ymp0ic0ycblbl6zzr0vzym2"; depends=[Biobase hgu133plus2_db]; };
-  mAPKLData = derive2 { name="mAPKLData"; version="1.34.0"; sha256="0vhysi7wyw7d3vbq4qcq3i3ic953awppg2bix40ywz1459b5p43g"; depends=[]; };
+  imcdatasets = derive2 { name="imcdatasets"; version="1.12.0"; sha256="135sffkn322g6zp6wz6ri2cg4wj9pwadmv4b6zaaxwximpx5xy04"; depends=[cytomapper DelayedArray ExperimentHub HDF5Array S4Vectors SingleCellExperiment SpatialExperiment]; };
-  mCSEAdata = derive2 { name="mCSEAdata"; version="1.22.0"; sha256="0la86384k9f0r8mgh6an023bx1sjklglgm9rwzg33hcc58lb02ki"; depends=[GenomicRanges]; };
+  kidpack = derive2 { name="kidpack"; version="1.46.0"; sha256="0802kn1n9ivjil19faphg4z4iy0y7n1hmixd9bkfv7livfl8yn0b"; depends=[Biobase]; };
-  macrophage = derive2 { name="macrophage"; version="1.18.0"; sha256="10d69v34fhxfy4nhw8h50j4q5kblm032cmjnparxm5gm7ksiqwxy"; depends=[]; };
+  leeBamViews = derive2 { name="leeBamViews"; version="1.40.0"; sha256="15prksw8pi302i8qpw3skwljyj3hfm9wld2lzpcgz7nnpzrqm8bc"; depends=[Biobase BSgenome GenomicAlignments GenomicRanges IRanges Rsamtools S4Vectors]; };
-  mammaPrintData = derive2 { name="mammaPrintData"; version="1.38.0"; sha256="0bm1lfdjhav34rqvkvygkllmwibjh0f34p58vml3ljjdhgghawrq"; depends=[]; };
+  leukemiasEset = derive2 { name="leukemiasEset"; version="1.40.0"; sha256="0r5dmd9m8fcbdns3r1vsw4xmxdbjp5gf4klsb148rpgmp5avjar4"; depends=[Biobase]; };
-  maqcExpression4plex = derive2 { name="maqcExpression4plex"; version="1.46.0"; sha256="0ihwmzndj3yxs75x3h9w03ydvy08hmi0pzy561mjsyhdrrb8i4dc"; depends=[]; };
+  lumiBarnes = derive2 { name="lumiBarnes"; version="1.44.0"; sha256="0in8rkcg1r7mjq3fzhyc8446dc09b1mm371vd6l0x541sj7x4n50"; depends=[Biobase lumi]; };
-  marinerData = derive2 { name="marinerData"; version="1.2.0"; sha256="00m1r6ijhykq96d86h17asngdm8a1ss2213nd6n6lsj4dshr74a0"; depends=[ExperimentHub]; };
+  lungExpression = derive2 { name="lungExpression"; version="0.42.0"; sha256="1r4xn6r0vwnkfbi49gjrxgdscqdpwpfwzb61mrxa9m1hgjy1dr80"; depends=[Biobase]; };
-  mcsurvdata = derive2 { name="mcsurvdata"; version="1.20.0"; sha256="06k500vivc8anxv1x639acjv55w5r6pc2ghmszkh42h1q7a27r68"; depends=[AnnotationHub Biobase ExperimentHub]; };
+  lydata = derive2 { name="lydata"; version="1.30.0"; sha256="1f13r5krfqc2f4gc03dxk8ajxlm62yxif03m0nx8lqxvijgm4abq"; depends=[]; };
-  metaMSdata = derive2 { name="metaMSdata"; version="1.38.0"; sha256="18gixjk80zzvjg39av6rhbl9zpvnx09fd6gcbnsjxag7vmk88d1d"; depends=[]; };
+  mCSEAdata = derive2 { name="mCSEAdata"; version="1.24.0"; sha256="0364bvsx286nsnyp5mh2i7i71dpdlpgn0907hnpxck1hcw19npnn"; depends=[GenomicRanges]; };
-  methylclockData = derive2 { name="methylclockData"; version="1.10.0"; sha256="0q4hiclws0fg03kwvbdwka024gghl1hbmmfficxfghslll78mc3y"; depends=[ExperimentHub ExperimentHubData]; };
+  macrophage = derive2 { name="macrophage"; version="1.20.0"; sha256="11ydl4srfxbcqnb42kwk783xd74231g6vgp1f0qs3hl8slc1hk1w"; depends=[]; };
-  miRNATarget = derive2 { name="miRNATarget"; version="1.40.0"; sha256="0qlazpmar9wi0gbh2qpkz8f44vzzg79iia1sgry42xbykx7bzx0y"; depends=[Biobase]; };
+  mammaPrintData = derive2 { name="mammaPrintData"; version="1.40.0"; sha256="1vna6vg7md9pl9hfrvbb4pi2rpnm0pm9l3ndh8ifdhqrz2vjhfpz"; depends=[]; };
-  miRcompData = derive2 { name="miRcompData"; version="1.32.0"; sha256="15w8vldxp5wp0vqfy3k7s8imjvmdaibgiw0p2li5sx2j0g6i27g6"; depends=[]; };
+  maqcExpression4plex = derive2 { name="maqcExpression4plex"; version="1.48.0"; sha256="086pkn4x1nr7qqhawhyxdcrh9pnsqdpfgy07zxyf1i2by3b7b0v9"; depends=[]; };
-  microRNAome = derive2 { name="microRNAome"; version="1.24.0"; sha256="09b0260qxdhx7sax1xmg8nz8mf0nv4yh70ibd8cyxj8fpnzifnhh"; depends=[SummarizedExperiment]; };
+  marinerData = derive2 { name="marinerData"; version="1.4.0"; sha256="1blrqzi840vcvdslyxkljbc2ihbx7yvvfxmxcs2kq8590jagl425"; depends=[ExperimentHub]; };
-  microbiomeDataSets = derive2 { name="microbiomeDataSets"; version="1.10.0"; sha256="1i118r0wfq2y57h3m1l3nzhrixmkq0dsc1dfkbfi83xl29ijhjn9"; depends=[ape BiocGenerics Biostrings ExperimentHub MultiAssayExperiment SummarizedExperiment TreeSummarizedExperiment]; };
+  mcsurvdata = derive2 { name="mcsurvdata"; version="1.22.0"; sha256="1pf4vljmfbks31rdhb1088x2lyck5bj1a5ci1z6qam8yi4kzgh1y"; depends=[AnnotationHub Biobase ExperimentHub]; };
-  minfiData = derive2 { name="minfiData"; version="0.48.0"; sha256="12lhyv3zb8vps7v61zfm8sz4r18rpgphgy7nvdpj48dj3awdnpw8"; depends=[IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest minfi]; };
+  metaMSdata = derive2 { name="metaMSdata"; version="1.40.0"; sha256="12x7p2jyzggjfb7v2ax9by5hly84jjkkm6fq3i2ycyryjl8f0p6s"; depends=[]; };
-  minfiDataEPIC = derive2 { name="minfiDataEPIC"; version="1.28.0"; sha256="1m2wl7x48rjjl3sh8r42wmw761r55821jjvbxjs7lycbmgd162ph"; depends=[IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest minfi]; };
+  methylclockData = derive2 { name="methylclockData"; version="1.12.0"; sha256="1bwrgib7k71i4i6iq4l71n0z9adq3bg9k8j10bpi79ygn9169np5"; depends=[ExperimentHub ExperimentHubData]; };
-  minionSummaryData = derive2 { name="minionSummaryData"; version="1.32.0"; sha256="1pkg77i5xi96yqn7i3xchwknh5lii35hyms8rjqqzamjr7g16ifs"; depends=[]; };
+  miRNATarget = derive2 { name="miRNATarget"; version="1.42.0"; sha256="1l8k9j7gwmg5ml68j0rj903im8q74ksanzfarwcx0hdxx4srsv2j"; depends=[Biobase]; };
-  mosaicsExample = derive2 { name="mosaicsExample"; version="1.40.0"; sha256="02x97k7s5l3ca1xws4xplmc3x14wjy0rx1kl5jmy59ncc2lwik4r"; depends=[]; };
+  miRcompData = derive2 { name="miRcompData"; version="1.34.0"; sha256="17cg4j5lgn5wf0dcrb71sqf8amkjql5zgvjr85szxlzimkjykfyd"; depends=[]; };
-  mouse4302barcodevecs = derive2 { name="mouse4302barcodevecs"; version="1.40.0"; sha256="1l2blxqsxy27lkrgd08r6a3j8va54hzhl5lx0i9bxpj1i9xiwkr6"; depends=[]; };
+  microRNAome = derive2 { name="microRNAome"; version="1.26.0"; sha256="0ry0pi7gcdwgfij7sw96pv9krqyq1lx5n81c1prhla45q26w9zpc"; depends=[SummarizedExperiment]; };
-  msPurityData = derive2 { name="msPurityData"; version="1.30.0"; sha256="1gf28bcj65vyvghdd2vqj3zsymw2y4jk8dhhkhh6ps18qh149ca0"; depends=[]; };
+  microbiomeDataSets = derive2 { name="microbiomeDataSets"; version="1.12.0"; sha256="0ng0sbdn3y2h7dyn42rq5ci12xx5y3hqb87n7xi7lc1gp1pcxcf2"; depends=[ape BiocGenerics Biostrings ExperimentHub MultiAssayExperiment SummarizedExperiment TreeSummarizedExperiment]; };
-  msd16s = derive2 { name="msd16s"; version="1.22.0"; sha256="0s7bbcxgly2xr21dkf88hpby5b4lhwy18jyji88dhqqq4jpbc8dk"; depends=[Biobase metagenomeSeq]; };
+  minfiData = derive2 { name="minfiData"; version="0.50.0"; sha256="1myxv7cqh7d1rjav9qhwqsmw3s1xh3zm34vbxwprqaqg87dg4bw0"; depends=[IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest minfi]; };
-  msdata = derive2 { name="msdata"; version="0.42.0"; sha256="1jm1zjqzkd0vy8ww0k0y1fgs6i9vkg7ir6dyga001n170g11vfzr"; depends=[]; };
+  minfiDataEPIC = derive2 { name="minfiDataEPIC"; version="1.30.0"; sha256="1sgcw9gdlgk6dyzw61c0k2q26w7vzbqzyrl5qimx466x76knz4hj"; depends=[IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest minfi]; };
-  msigdb = derive2 { name="msigdb"; version="1.10.0"; sha256="1fzgq31n059zhlkny3rfwfnriz81q9brk14r5yx2zhizlv8jcais"; depends=[AnnotationDbi AnnotationHub ExperimentHub GSEABase org_Hs_eg_db org_Mm_eg_db]; };
+  minionSummaryData = derive2 { name="minionSummaryData"; version="1.34.0"; sha256="0mmj48c1djl026g7ckn5k7shvyy7xa0fp7nsavm15a8l4blbq1ri"; depends=[]; };
-  msqc1 = derive2 { name="msqc1"; version="1.30.0"; sha256="1s6wfmrss67qz8lsiqbm3bsvw3zm9pczv0w6712dd2bd2mf2lirg"; depends=[lattice]; };
+  mosaicsExample = derive2 { name="mosaicsExample"; version="1.42.0"; sha256="0sy85jkl5z82a7y3fg8a1mfq5cpjq2c5arvwplz427rsi02ppqan"; depends=[]; };
-  mtbls2 = derive2 { name="mtbls2"; version="1.32.0"; sha256="1z4n5bykfk02b6gscwygy4r99fjk9cmiv8fzp2996q4mhzr7dh6c"; depends=[]; };
+  mouse4302barcodevecs = derive2 { name="mouse4302barcodevecs"; version="1.42.0"; sha256="1bdcfbjpz60fldj8xq3hwgvdqmv5axc8cl2l57i4xk4piggah22r"; depends=[]; };
-  muscData = derive2 { name="muscData"; version="1.16.0"; sha256="01jmd59zk4fkny984wv9iwd9bq56cq4mnqz1x9wcjkmgk5bnvwxa"; depends=[ExperimentHub SingleCellExperiment]; };
+  msPurityData = derive2 { name="msPurityData"; version="1.32.0"; sha256="0pbdx6pg3cdwx6qngn01w46bvvqv2hhyicgi39y182gbwliv0fxl"; depends=[]; };
-  mvoutData = derive2 { name="mvoutData"; version="1.38.0"; sha256="17rbb19wv8dzgkrkhgabm3fgr3l2gzvjl34ichlcfalaa17wci3w"; depends=[affy Biobase lumi]; };
+  msd16s = derive2 { name="msd16s"; version="1.24.0"; sha256="16ska3qh5bav3y891gz805pj638j4kx73izv8krpqgpycin719ar"; depends=[Biobase metagenomeSeq]; };
-  nanotubes = derive2 { name="nanotubes"; version="1.18.0"; sha256="0ah7y051mk6pl96y6h9qlxk4gg2a7al8j9ccwk0fjl7v5fa1daya"; depends=[]; };
+  msdata = derive2 { name="msdata"; version="0.44.0"; sha256="0g7mlgks3nfnfipnybs7pvsnmrvmq8888g39badca8pi73q1cm25"; depends=[]; };
-  nullrangesData = derive2 { name="nullrangesData"; version="1.8.0"; sha256="0dd9d07z2k3n34wi5mynyghc0bsmyn5fhl0510ij7zbd58i520xy"; depends=[ExperimentHub GenomicRanges InteractionSet]; };
+  msigdb = derive2 { name="msigdb"; version="1.12.0"; sha256="080wm9sjwqhaxqx1r3kly1bi1gvkssqpsadnvabx11w493356qr0"; depends=[AnnotationDbi AnnotationHub ExperimentHub GSEABase org_Hs_eg_db org_Mm_eg_db]; };
-  oct4 = derive2 { name="oct4"; version="1.18.0"; sha256="1kbv532sav3a0s1893hxjw7pf25lhff5kxnraq6h7h7vqqmim93j"; depends=[]; };
+  msqc1 = derive2 { name="msqc1"; version="1.32.0"; sha256="1wac6i792ndmv98rb3k7pz07q4l830yhkfs89ahlcalrah6m9cld"; depends=[lattice]; };
-  octad_db = derive2 { name="octad.db"; version="1.4.0"; sha256="03dih6cc71aj31l9s982qpdsyy51q83inykyz4a8pk81x3pld2n9"; depends=[ExperimentHub]; };
+  mtbls2 = derive2 { name="mtbls2"; version="1.34.0"; sha256="0bycprz32ihj7kzy5f31275sd4b855nd9vm34447x5y33wdiq9b9"; depends=[]; };
-  optimalFlowData = derive2 { name="optimalFlowData"; version="1.14.0"; sha256="0agaavlhsv1zk3xdwncn4nkz7q80bjnsg32msnnj8x79925hfgwq"; depends=[]; };
+  muleaData = derive2 { name="muleaData"; version="1.0.0"; sha256="0n5q0whp2fad980b72b9z85swkm8dc2r888javkzhb5c9sajz1w0"; depends=[]; };
-  orthosData = derive2 { name="orthosData"; version="1.0.0"; sha256="0n9vkvfxah29cjfwnxjqw0kf5kdgjvx9394kgilnbskys95fh6v3"; depends=[AnnotationHub BiocFileCache ExperimentHub HDF5Array stringr SummarizedExperiment]; };
+  multiWGCNAdata = derive2 { name="multiWGCNAdata"; version="1.2.0"; sha256="1hpm0hf8yh3308rlfcm5f9hi1mcwgcij1baikrx4nrwn7fgi30l3"; depends=[ExperimentHub]; };
-  pRolocdata = derive2 { name="pRolocdata"; version="1.40.0"; sha256="0zjys778k9xydd6r1nvklz324mq688472b8i8d1nm8ayb880bi7i"; depends=[Biobase MSnbase]; };
+  muscData = derive2 { name="muscData"; version="1.18.0"; sha256="1snpzvmxrpzspfl5gy18w2mcdpszq7wn2l3z1mbvjdp8ffh4qv00"; depends=[ExperimentHub SingleCellExperiment]; };
-  parathyroidSE = derive2 { name="parathyroidSE"; version="1.40.0"; sha256="0lv7wlbdi05a3l4pv8x4cnc6jzqk1gb82rpmj1cv0nsq7gqhqscv"; depends=[SummarizedExperiment]; };
+  mvoutData = derive2 { name="mvoutData"; version="1.40.0"; sha256="01rxr4867w2zcy4gmcg868g2xqal5vb4xw2izfmcwplxah5380wv"; depends=[affy Biobase lumi]; };
-  pasilla = derive2 { name="pasilla"; version="1.30.0"; sha256="0dga4bb7qjigy1m1yp4bs4frwynjqfy3dnnylx4maai9x2zlynd0"; depends=[DEXSeq]; };
+  nanotubes = derive2 { name="nanotubes"; version="1.20.0"; sha256="0gsgs0i3117753pxypr2q8pc3zc8bd3fkp5xj30jx142wvi4y0al"; depends=[]; };
-  pasillaBamSubset = derive2 { name="pasillaBamSubset"; version="0.40.0"; sha256="1lr7dn9s7i287k602xa1zyx5xs6wa3g58kmpamc3hcsi5nn1iv7x"; depends=[]; };
+  nullrangesData = derive2 { name="nullrangesData"; version="1.10.0"; sha256="099ynygy9ld7ckzh38rf5nglx70mjwha0jz3ngn85ncnaz64cw26"; depends=[ExperimentHub GenomicRanges InteractionSet]; };
-  pcxnData = derive2 { name="pcxnData"; version="2.24.0"; sha256="0mhqgii84ncx2na49h3qvciqz7jfbbgil12i2cb4snlmxpa66k0j"; depends=[]; };
+  oct4 = derive2 { name="oct4"; version="1.20.0"; sha256="0q6q5zg33fxq9cjnxdbc53q4wqsqcgid8ax0z2b8sbyv86knj620"; depends=[]; };
-  pd_atdschip_tiling = derive2 { name="pd.atdschip.tiling"; version="0.40.0"; sha256="03yvz9z4dmnm4cvfwkw3b7srmq7hmwk9y21lpsn5yz01wjp9wf6w"; depends=[Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; };
+  octad_db = derive2 { name="octad.db"; version="1.6.0"; sha256="1n8zwjhf7s61gaqr1zs5gvc5l3xsbzilj38lpsh8k80y175msgbx"; depends=[ExperimentHub]; };
-  pepDat = derive2 { name="pepDat"; version="1.22.0"; sha256="0ks5lxfwwgxfv0ls42fr5hj0iq2m6ylv13ybp8gq5r24p6hyigq3"; depends=[GenomicRanges]; };
+  optimalFlowData = derive2 { name="optimalFlowData"; version="1.16.0"; sha256="0b5r3hqs2pnj2s9qizrqpkkidq3r5ig75rmk1ygsppad0dl98qyh"; depends=[]; };
-  plotgardenerData = derive2 { name="plotgardenerData"; version="1.8.0"; sha256="1c8004k5kqx1lryc7x57xvlqic7km11r2b723r5ar1x5mghl9lr3"; depends=[]; };
+  orthosData = derive2 { name="orthosData"; version="1.2.0"; sha256="000jqijl7mpp0qfgg0aqx7jzn5bviybp2ndxmikyn0rmcvi9057k"; depends=[AnnotationHub BiocFileCache ExperimentHub HDF5Array stringr SummarizedExperiment]; };
-  prebsdata = derive2 { name="prebsdata"; version="1.38.0"; sha256="1jszgh5sq0fls0484zfy41cpxwfg04pky54ma2r8v0x2aksb9fnv"; depends=[]; };
+  pRolocdata = derive2 { name="pRolocdata"; version="1.42.0"; sha256="0drc8srg2frzjpq7j00pfr1371n0jiry5gz1rz2hbagcz2q51aad"; depends=[Biobase MSnbase]; };
-  preciseTADhub = derive2 { name="preciseTADhub"; version="1.10.0"; sha256="006kdb7rv63jyn4xnvrk13s5by1m85jgnfs2594h51af4sgyd2id"; depends=[ExperimentHub]; };
+  parathyroidSE = derive2 { name="parathyroidSE"; version="1.42.0"; sha256="183cyn1i0i2p8npajwmbwzr2ncrrzwgpvh8adhjxzrdqkn3qdnr5"; depends=[SummarizedExperiment]; };
-  prostateCancerCamcap = derive2 { name="prostateCancerCamcap"; version="1.30.0"; sha256="1962yhm8j1mb3yvdkvdn8i35dmwj69larlp201vwqr8a25l67isq"; depends=[Biobase]; };
+  pasilla = derive2 { name="pasilla"; version="1.32.0"; sha256="0r5i64125qq5z4c8zliazsi68035d1bsz6ingzqdh37m8prdw1cr"; depends=[DEXSeq]; };
-  prostateCancerGrasso = derive2 { name="prostateCancerGrasso"; version="1.30.0"; sha256="0mvlnfps3xa6039ysbp5hc8cy30masw9p1rhhms9f79m1xh3ldqr"; depends=[Biobase]; };
+  pasillaBamSubset = derive2 { name="pasillaBamSubset"; version="0.42.0"; sha256="0q0wawb4hj45lm9z8h0q905dvmx13x25cv64qmm1nf0342m8gccn"; depends=[]; };
-  prostateCancerStockholm = derive2 { name="prostateCancerStockholm"; version="1.30.0"; sha256="19dkx1brrwjcrjyfhajiazfpy853kmqr10npzkarnb1fw3dhn9a9"; depends=[Biobase]; };
+  pcxnData = derive2 { name="pcxnData"; version="2.25.0"; sha256="1mlqkxlkqfb8x5jp2fdx5nfrpfh8g3lghfj6sqkaf958n5yl1dg3"; depends=[]; };
-  prostateCancerTaylor = derive2 { name="prostateCancerTaylor"; version="1.30.0"; sha256="0mccc3fwrnayjlpjyncizsrnnapgb7mhywvcdwlspp2ma0xzq2kw"; depends=[Biobase]; };
+  pd_atdschip_tiling = derive2 { name="pd.atdschip.tiling"; version="0.42.0"; sha256="17sf3x7mhkjk605hmc0idx1d3pbx49hyfaxzifkc6bq1mmq5113x"; depends=[Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; };
-  prostateCancerVarambally = derive2 { name="prostateCancerVarambally"; version="1.30.0"; sha256="10irpxg5gfj10s310irjh1lacg05s6073vfqlv5jmpwgjjz8g84m"; depends=[Biobase]; };
+  pepDat = derive2 { name="pepDat"; version="1.24.0"; sha256="01svdmjhijbmjypp9hzninmagjl24zk4kjigmrjiasfski8yjln5"; depends=[GenomicRanges]; };
-  ptairData = derive2 { name="ptairData"; version="1.10.0"; sha256="11fxa0j4jl19ig21v00acbkapwi0y5d9n36q82pb8kz2krdaa9xc"; depends=[rhdf5 signal]; };
+  plotgardenerData = derive2 { name="plotgardenerData"; version="1.10.0"; sha256="14y5hh4r7j7kkbh7kl6wwh6xyva9pbqxzz4ch7dp7p0kj5kgh52s"; depends=[]; };
-  pumadata = derive2 { name="pumadata"; version="2.38.0"; sha256="0rc2qda3s3326g1ymychhxa3c1vb16vj7sllfqymridqwm907k0x"; depends=[Biobase oligo puma]; };
+  prebsdata = derive2 { name="prebsdata"; version="1.40.0"; sha256="0agdmcin4mqigrpm004wvaqd9ciy2kc7di1yiycgdnd4ccglhllk"; depends=[]; };
-  qPLEXdata = derive2 { name="qPLEXdata"; version="1.20.0"; sha256="0l6agwhqsm5z98j0hm1h7df6lrq7rgwch99a33532f5zmn6bq7xa"; depends=[dplyr knitr MSnbase qPLEXanalyzer]; };
+  preciseTADhub = derive2 { name="preciseTADhub"; version="1.12.0"; sha256="0449ppjh29rwykf5i2c8f8sfy9s87p2kxgvylfa016x3g2gbnygw"; depends=[ExperimentHub]; };
-  rRDPData = derive2 { name="rRDPData"; version="1.22.0"; sha256="18k925rd7yslvc6gl9gn9fk7672w57327rsybi5vpphvpyqsqls1"; depends=[rRDP]; };
+  prostateCancerCamcap = derive2 { name="prostateCancerCamcap"; version="1.32.0"; sha256="03pfci7cx5r2lagfzi0j8b2ry9s6c211qamfqlqrx5siw0yxllrx"; depends=[Biobase]; };
-  raerdata = derive2 { name="raerdata"; version="1.0.0"; sha256="0f8k9a714fc0wkrg2ja1193302q712aw6q4nv79qnvavqx12p0hi"; depends=[BiocGenerics ExperimentHub Rsamtools rtracklayer SingleCellExperiment]; };
+  prostateCancerGrasso = derive2 { name="prostateCancerGrasso"; version="1.32.0"; sha256="11sl00lfi85gpwh2619w3z54vb0mw05bwcgdblg1c6wnrn17qd9h"; depends=[Biobase]; };
-  rcellminerData = derive2 { name="rcellminerData"; version="2.24.0"; sha256="0fmidhiqaf2vrhz6b5qr7bhisqnr3vff1aczp02qfhj5zyrf2vp6"; depends=[Biobase]; };
+  prostateCancerStockholm = derive2 { name="prostateCancerStockholm"; version="1.32.0"; sha256="02kcm3wvz4wrdnn4cfna67gqx7p8765j4j0cl7x08j7qjlnsnq2z"; depends=[Biobase]; };
-  restfulSEData = derive2 { name="restfulSEData"; version="1.24.0"; sha256="1ydi54mbvvsn73j955qjiqgpc2qvgdxfa9gsflx5cc14c0aqyb9h"; depends=[DelayedArray ExperimentHub HDF5Array SummarizedExperiment]; };
+  prostateCancerTaylor = derive2 { name="prostateCancerTaylor"; version="1.32.0"; sha256="1ynjyrcp7d8ywzlfkv2909r1l3ihap4yiamq0jrqa27xh6lvpqfd"; depends=[Biobase]; };
-  rheumaticConditionWOLLBOLD = derive2 { name="rheumaticConditionWOLLBOLD"; version="1.40.0"; sha256="0qaxxhn31kwny0327ki5yllp4cnljdqbqmrb0arx1qggbysb31gf"; depends=[]; };
+  prostateCancerVarambally = derive2 { name="prostateCancerVarambally"; version="1.32.0"; sha256="1f0wzm4hlax0dcx3ibssiq1nmli8zhrp7b2r1znjs38v2p5skx53"; depends=[Biobase]; };
-  sampleClassifierData = derive2 { name="sampleClassifierData"; version="1.26.0"; sha256="0ir21cvcqq9xh43pidh4lrm1slzknsjm9lad3qhh7dn2x5dg8p7p"; depends=[SummarizedExperiment]; };
+  ptairData = derive2 { name="ptairData"; version="1.12.0"; sha256="1w7j8zx0x0kihsv295l389vlxii72z22gyi2mhdfviyay7g4n2gd"; depends=[rhdf5 signal]; };
-  scATAC_Explorer = derive2 { name="scATAC.Explorer"; version="1.8.0"; sha256="1qjacprh3q0g1fyq70akasfr66hxw2g8n1bwn4yhf798vly5ngf8"; depends=[BiocFileCache data_table Matrix S4Vectors SingleCellExperiment]; };
+  pumadata = derive2 { name="pumadata"; version="2.40.0"; sha256="0ryrlsfyc64kbcn6mhq5xv09n9dv58d6azhywx21kg01iayrmnvb"; depends=[Biobase oligo puma]; };
-  scMultiome = derive2 { name="scMultiome"; version="1.2.0"; sha256="0j9cwlnj0078yyzfjiwsadx34g1ddcrfm5xmzjv59dmk55iy59d7"; depends=[AnnotationHub AzureStor checkmate DelayedArray ExperimentHub GenomicRanges HDF5Array MultiAssayExperiment rhdf5 S4Vectors SingleCellExperiment SummarizedExperiment]; };
+  qPLEXdata = derive2 { name="qPLEXdata"; version="1.22.0"; sha256="1a8mzbll0s9w82y4sy153jna6677sdpp3bfzs83qaqpnjymjzfpc"; depends=[dplyr knitr MSnbase qPLEXanalyzer]; };
-  scRNAseq = derive2 { name="scRNAseq"; version="2.16.0"; sha256="0dbh3sqq7lkkdf7vls5qg7fbn6y74c7hsigb4d69pvk934ll88aw"; depends=[AnnotationDbi AnnotationHub BiocGenerics ensembldb ExperimentHub GenomicFeatures GenomicRanges S4Vectors SingleCellExperiment SummarizedExperiment]; };
+  rRDPData = derive2 { name="rRDPData"; version="1.24.0"; sha256="030hnp9sghl0f2wfg243ll6myp9gr5zzbwlfzaz8m7q8xk2if363"; depends=[rRDP]; };
-  scTHI_data = derive2 { name="scTHI.data"; version="1.14.0"; sha256="1y28wldw2xln9bp4hgymjdlgz9fjiyhb56kac6z7aiy1pifavw48"; depends=[]; };
+  raerdata = derive2 { name="raerdata"; version="1.2.0"; sha256="15j7sw3kvgqqb7m4y4kn40p8g8s1f204lfnb5zskkjfakj6c2j03"; depends=[BiocGenerics ExperimentHub Rsamtools rtracklayer SingleCellExperiment]; };
-  scanMiRData = derive2 { name="scanMiRData"; version="1.8.0"; sha256="116v4l8rqg2lsadjhhhn40fdgfar6hbx5abri5kdq7bc5fagg957"; depends=[scanMiR]; };
+  rcellminerData = derive2 { name="rcellminerData"; version="2.26.0"; sha256="1al3v586q2ak77hjbl3xlvrxqs3xid8y06lf601c5diyrd7vp7r7"; depends=[Biobase]; };
-  scpdata = derive2 { name="scpdata"; version="1.10.0"; sha256="0zwwbqss2a6vkzhz517j89gf02z4f5b9kx5wbnyi2g15ihwlvaxr"; depends=[AnnotationHub ExperimentHub QFeatures S4Vectors SingleCellExperiment]; };
+  restfulSEData = derive2 { name="restfulSEData"; version="1.26.0"; sha256="17ia2d5g0zawfpcqvpncw05qshhn09p05j2frxmz0mwjfp7mya27"; depends=[DelayedArray ExperimentHub HDF5Array SummarizedExperiment]; };
-  seq2pathway_data = derive2 { name="seq2pathway.data"; version="1.34.0"; sha256="0iaz4i5garvhai2bpwxm59h4qasbasv66a2b8mql2rqa4s6wnf0a"; depends=[]; };
+  rheumaticConditionWOLLBOLD = derive2 { name="rheumaticConditionWOLLBOLD"; version="1.42.0"; sha256="0s75faby72cv6i1y1mj5d3qfvfp6907jinnfm17zvgdvcl0xx06h"; depends=[]; };
-  seqCNA_annot = derive2 { name="seqCNA.annot"; version="1.38.0"; sha256="0kzmn5hx8ag02pz8b78cq7dbalw2w60y441cjyyvxjgycwcfvmvj"; depends=[]; };
+  sampleClassifierData = derive2 { name="sampleClassifierData"; version="1.28.0"; sha256="0bjncqk3h11gcsg8zp64f22xjsbgr20dqangg7h84d9m0rr6x0kg"; depends=[SummarizedExperiment]; };
-  seqc = derive2 { name="seqc"; version="1.36.0"; sha256="0zxmh69v45ys1hv9kkr7g6v67npcip6s11r3am502zq1dnk7khg1"; depends=[Biobase]; };
+  scATAC_Explorer = derive2 { name="scATAC.Explorer"; version="1.10.0"; sha256="0s2w9b9bb1bzqnlhlrgvp17bifhryvymzaid02ypkqaql06d6nyx"; depends=[BiocFileCache data_table Matrix S4Vectors SingleCellExperiment]; };
-  serumStimulation = derive2 { name="serumStimulation"; version="1.38.0"; sha256="0c6zg119rdmqhgrzi3s10856l9vyrqmd8c858hw20aiagvxn5nik"; depends=[]; };
+  scMultiome = derive2 { name="scMultiome"; version="1.4.0"; sha256="1fiivxs35zanssfkjv83fa898fjr93xgq5g2i9m2qkv2pxqlyan8"; depends=[AnnotationHub AzureStor checkmate DelayedArray ExperimentHub GenomicRanges HDF5Array MultiAssayExperiment rhdf5 S4Vectors SingleCellExperiment SummarizedExperiment]; };
-  sesameData = derive2 { name="sesameData"; version="1.20.0"; sha256="0a5xchdnlw9ixafk8p3ny58yqv74ba9j4z2sdyp990rbaqrx1gjw"; depends=[AnnotationHub ExperimentHub GenomeInfoDb GenomicRanges IRanges readr S4Vectors stringr]; };
+  scRNAseq = derive2 { name="scRNAseq"; version="2.18.0"; sha256="0jsq037ba4xsb3bwwf021jw2hqv30vb5nrjag97xadx75z5fzqlr"; depends=[alabaster_base alabaster_matrix alabaster_sce AnnotationDbi AnnotationHub BiocGenerics DBI DelayedArray ensembldb ExperimentHub GenomicFeatures GenomicRanges gypsum jsonlite Matrix RSQLite S4Vectors SingleCellExperiment SparseArray SummarizedExperiment]; };
-  seventyGeneData = derive2 { name="seventyGeneData"; version="1.38.2"; sha256="1zpks4fpwjb640pggwd1xldri2lf3fl8pcbvi244c6dgkf8nq93i"; depends=[]; };
+  scTHI_data = derive2 { name="scTHI.data"; version="1.16.0"; sha256="03zixwlainshb8q3jsb6w9vah790vq17p742fpa2h8f0vcamqxa4"; depends=[]; };
-  shinyMethylData = derive2 { name="shinyMethylData"; version="1.22.0"; sha256="1i6ffgi79jgpkg6nhil7v7vi23yv2j7czzibj6dxdc0kpb1n0q1h"; depends=[]; };
+  scaeData = derive2 { name="scaeData"; version="1.0.0"; sha256="0ghd2qyc9kz2d0g0whdy7cpys7j265iq9w7a02mnfwk8s0vplrk5"; depends=[ExperimentHub]; };
-  signatureSearchData = derive2 { name="signatureSearchData"; version="1.16.0"; sha256="1xn0y7mcpk4s4x9azzabxfq0hxwlx7dvpb4yjrl3x8zcyk394s3z"; depends=[affy Biobase dplyr ExperimentHub limma magrittr R_utils rhdf5]; };
+  scanMiRData = derive2 { name="scanMiRData"; version="1.10.0"; sha256="1h7bla3l5mmydwz6pgq6ja560r02i741k0259f3a5lf07y4rdab6"; depends=[scanMiR]; };
-  simpIntLists = derive2 { name="simpIntLists"; version="1.38.0"; sha256="1683dsi6bm45v5wk9fgvrmvap15w6gvwnfijg5ayj29shiaa2qif"; depends=[]; };
+  scpdata = derive2 { name="scpdata"; version="1.12.0"; sha256="1mn3a27wmdsn582v6ajavn2fxqqqlv79zyy40zfg6pnza19izpbx"; depends=[AnnotationHub ExperimentHub QFeatures S4Vectors SingleCellExperiment]; };
-  smokingMouse = derive2 { name="smokingMouse"; version="1.0.0"; sha256="0xm4a7yp6802xcmh29hwvlz39gqb5s380mzi5rck89fl6wjl4bf6"; depends=[]; };
+  seq2pathway_data = derive2 { name="seq2pathway.data"; version="1.36.0"; sha256="0i45qxvbirh4l048a2hzk9iahydsgk6az0yjlfsypa0zq6hcz3cj"; depends=[]; };
-  spatialDmelxsim = derive2 { name="spatialDmelxsim"; version="1.8.0"; sha256="110anvdbsq8mh3ibfhps9hyfhlk2np4mjs224377s1sasmpzwbbb"; depends=[ExperimentHub SummarizedExperiment]; };
+  seqc = derive2 { name="seqc"; version="1.38.0"; sha256="0g1zwzm38xqdpzfhpbwlw8zcdl8lvyd7pfncgwk7y50w1mblxqah"; depends=[Biobase]; };
-  spatialLIBD = derive2 { name="spatialLIBD"; version="1.14.1"; sha256="0zqbnj55d06xai9qlg1hcy2kczjn6zxrhqwwsi18a36511qks5qb"; depends=[AnnotationHub benchmarkme BiocFileCache BiocGenerics cowplot DT edgeR ExperimentHub fields GenomicRanges ggplot2 golem IRanges jsonlite limma magick Matrix paletteer plotly png RColorBrewer rtracklayer S4Vectors scater scuttle sessioninfo shiny shinyWidgets SingleCellExperiment SpatialExperiment statmod SummarizedExperiment tibble viridisLite]; };
+  serumStimulation = derive2 { name="serumStimulation"; version="1.40.0"; sha256="1lkwx3gc7c6scznaf1z62szi4mb944dg1jprp8zlmm51a73w9kp9"; depends=[]; };
-  spqnData = derive2 { name="spqnData"; version="1.14.0"; sha256="0kvnkz71w1c7yhl4kqdj9j51d1ix2g7q3pqr2678f31hhw7yr1ck"; depends=[SummarizedExperiment]; };
+  sesameData = derive2 { name="sesameData"; version="1.22.0"; sha256="05k67isysszzfkkbi811dkab0cmxnwz81p2ldcqz3gsq5qin3p1g"; depends=[AnnotationHub ExperimentHub GenomeInfoDb GenomicRanges IRanges readr S4Vectors stringr]; };
-  stemHypoxia = derive2 { name="stemHypoxia"; version="1.38.0"; sha256="1ak78mvgm9dv80ji44b1cb4y8bq0l4k0cpx734m8dy8mr3i8nblw"; depends=[]; };
+  seventyGeneData = derive2 { name="seventyGeneData"; version="1.40.0"; sha256="0yy9pywbr5fjkjc2gaaf8cfw5q2barw1a3yin99a7sphq062lfvj"; depends=[]; };
-  stjudem = derive2 { name="stjudem"; version="1.42.0"; sha256="0pcvvvaqalr5jklqy7vzxkp0cd9nj9dk941drgr7ndbqc2navz2c"; depends=[]; };
+  shinyMethylData = derive2 { name="shinyMethylData"; version="1.24.0"; sha256="17l63xmdi6zhaqggw45nhpiclag96xjbkngmcqhihfykkrgbb18p"; depends=[]; };
-  synapterdata = derive2 { name="synapterdata"; version="1.40.0"; sha256="1hl3r6smv25vhwxwrxw2c98db4c36392js49zj9kgf7c22qpyaqr"; depends=[synapter]; };
+  signatureSearchData = derive2 { name="signatureSearchData"; version="1.18.0"; sha256="11y1dbixj9b91whzq4lrmad5f4f6gqdv70ar4rg20ql1699dx5l5"; depends=[affy Biobase dplyr ExperimentHub limma magrittr R_utils rhdf5]; };
-  systemPipeRdata = derive2 { name="systemPipeRdata"; version="2.6.0"; sha256="004sjgvhn9hq14f4mwfakrkkm2mwr2bdcbld25b393in0k26r9hf"; depends=[BiocGenerics Biostrings jsonlite remotes]; };
+  simpIntLists = derive2 { name="simpIntLists"; version="1.40.0"; sha256="03d7whna1h2ffgci060gqfdwbjwmjg6q3yfd8l6vc25kiblc4igp"; depends=[]; };
-  tartare = derive2 { name="tartare"; version="1.16.0"; sha256="1w8z756s2c4vcxan8lid5mflyn8n718vhqn72x3mspg1pbb6k0l6"; depends=[AnnotationHub ExperimentHub]; };
+  smokingMouse = derive2 { name="smokingMouse"; version="1.2.0"; sha256="1z3kbmlqylmaingkcdm6wxlx848zipqfh6kha7f55s6aklgcv5d7"; depends=[]; };
-  timecoursedata = derive2 { name="timecoursedata"; version="1.12.0"; sha256="10i4wcdjqd2qh6rpl65xi5mj2hsam78hi3haqp4xhg0ha4f73nb3"; depends=[SummarizedExperiment]; };
+  spatialDmelxsim = derive2 { name="spatialDmelxsim"; version="1.10.0"; sha256="172hgg2wxjc32950lga8fqwygd6x07i0ilsvfp46sd7nmysy6cpn"; depends=[ExperimentHub SummarizedExperiment]; };
-  tinesath1cdf = derive2 { name="tinesath1cdf"; version="1.40.0"; sha256="12db5w6fsmpjx2xgq7f3hp5czm21jp17826mi7jdz1c0217i1h4s"; depends=[]; };
+  spatialLIBD = derive2 { name="spatialLIBD"; version="1.16.2"; sha256="0bbwh9mfz7iscv8a1jlc7g1c452hv4qr95hwv3z6h2mqf8pcr5g8"; depends=[AnnotationHub benchmarkme BiocFileCache BiocGenerics cowplot DT edgeR ExperimentHub fields GenomicRanges ggplot2 golem IRanges jsonlite limma magick Matrix MatrixGenerics paletteer plotly png RColorBrewer rlang rtracklayer S4Vectors scater scuttle sessioninfo shiny shinyWidgets SingleCellExperiment SpatialExperiment statmod SummarizedExperiment tibble viridisLite]; };
-  tinesath1probe = derive2 { name="tinesath1probe"; version="1.40.0"; sha256="1s119zkz03rq0bs3fjx85rwr7f2fxk144ykvglbzz3m6wxwi94r9"; depends=[AnnotationDbi]; };
+  spqnData = derive2 { name="spqnData"; version="1.16.0"; sha256="047dbhcfqs0zddmnfpabpjhym86m5zlxnwccidkx0b131wxb22gv"; depends=[SummarizedExperiment]; };
-  tissueTreg = derive2 { name="tissueTreg"; version="1.22.0"; sha256="17hjzwvk9pa1zhvmqrs99dnm428bm2br4xjmydp7d8j2mdsbkfs3"; depends=[]; };
+  stemHypoxia = derive2 { name="stemHypoxia"; version="1.40.0"; sha256="0i8rvz2l6hgzd4zcmfzszjck0riy2m34qf2nidrxx6bjza4iqwpy"; depends=[]; };
-  tofsimsData = derive2 { name="tofsimsData"; version="1.30.0"; sha256="18fn2krbc1mg3phx1sjpshsq9n39jlm75n9s7615h4jdcky9gzld"; depends=[]; };
+  synapterdata = derive2 { name="synapterdata"; version="1.42.0"; sha256="0p6rrnqvdifrajil2akjvrzjm1k7gyywspg5cb5p2k62lyz0f06k"; depends=[synapter]; };
-  topdownrdata = derive2 { name="topdownrdata"; version="1.24.0"; sha256="01wxdwq87yan5a71z60bzs18w1ryjvgscnrrpdksqs56009k5992"; depends=[topdownr]; };
+  systemPipeRdata = derive2 { name="systemPipeRdata"; version="2.8.0"; sha256="131p4s5cgm75f32a5dzyj059aznxjcy76h7h8dbccblqlqxgx1ix"; depends=[BiocGenerics Biostrings jsonlite remotes]; };
-  tuberculosis = derive2 { name="tuberculosis"; version="1.8.0"; sha256="15jmhn7lrdwz19hv076yf0g2wqw7c32vp4pjzj2151f4xzxrl1iz"; depends=[AnnotationHub dplyr ExperimentHub magrittr purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr]; };
+  tartare = derive2 { name="tartare"; version="1.18.0"; sha256="1wxq6sfzdah29ql9q7w3d35x7bf1bh1417ih55rg07qbs8cnxb9v"; depends=[AnnotationHub ExperimentHub]; };
-  tweeDEseqCountData = derive2 { name="tweeDEseqCountData"; version="1.40.0"; sha256="1s071578qldq564ylrkd9azn5519rdc3g1gdp9v8hj4zh8kza56v"; depends=[Biobase]; };
+  timecoursedata = derive2 { name="timecoursedata"; version="1.14.0"; sha256="0wjfc5awj4spvwwj3mp1bn3dqngjdnfz7bnlv7azqxmnd4q72ckr"; depends=[SummarizedExperiment]; };
-  tximportData = derive2 { name="tximportData"; version="1.30.0"; sha256="0ksmg3gblkqzz40pzm35y6wghjmszrimdx7bxhq5jv4piqwii0hg"; depends=[]; };
+  tinesath1cdf = derive2 { name="tinesath1cdf"; version="1.42.0"; sha256="0anb8n6kni2i56rhhd6wlvq7am6jifiqfmm6v54yh96i2m3gsbq9"; depends=[]; };
-  vulcandata = derive2 { name="vulcandata"; version="1.24.0"; sha256="18wbxwwp7bsmdbn4g6d96x45b672fyrhlh38kbcz3j5dysdg1clr"; depends=[]; };
+  tinesath1probe = derive2 { name="tinesath1probe"; version="1.42.0"; sha256="0jcjzgazj3z4ls2b0mhi15n1vh4adxv2ysm6x3r8w4a4hzm4gnmg"; depends=[AnnotationDbi]; };
-  xcoredata = derive2 { name="xcoredata"; version="1.6.0"; sha256="1chcjylfdl07q19f924hsml22lbfcjrzndp1appi3q80hzbc3pz6"; depends=[ExperimentHub]; };
+  tissueTreg = derive2 { name="tissueTreg"; version="1.24.0"; sha256="0wv7hlq4v69gwypg9lvkcxf7w191iq8j5rzh2gqvg25ajxhm0bwl"; depends=[]; };
-  yeastCC = derive2 { name="yeastCC"; version="1.42.0"; sha256="1abl3jlwznzdmfpsqy0bfvrn6xx99yc8wz70s228lalvac4lqrfn"; depends=[Biobase]; };
+  tofsimsData = derive2 { name="tofsimsData"; version="1.32.0"; sha256="02svkikiw72lpnsm3w333py7gwc52qi3qina215rp7fknrsqrw07"; depends=[]; };
-  yeastExpData = derive2 { name="yeastExpData"; version="0.48.0"; sha256="13hxrcsvxwjdr649xzl07fkl0mzx6j36hkmgmj9zj270gsvlchns"; depends=[graph]; };
+  topdownrdata = derive2 { name="topdownrdata"; version="1.26.0"; sha256="13vcis52fadfpahw31v2z3p2q47d4yp7yl719mibkwga9iyklgva"; depends=[topdownr]; };
-  yeastGSData = derive2 { name="yeastGSData"; version="0.40.0"; sha256="0i3fawlbxb6xc9wilxlc5gjr22ikp1x4rc2dich1cmpbjqd2zg1c"; depends=[]; };
+  tuberculosis = derive2 { name="tuberculosis"; version="1.10.0"; sha256="1l9gm8jlvall905053mmbn0wd053ssnsxy74gza37w669il85awn"; depends=[AnnotationHub dplyr ExperimentHub magrittr purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr]; };
-  yeastNagalakshmi = derive2 { name="yeastNagalakshmi"; version="1.38.0"; sha256="1d1y7xpggizgiv2qma31mlzri2jidir425q08fdnnm9ymcxx83z0"; depends=[]; };
+  tweeDEseqCountData = derive2 { name="tweeDEseqCountData"; version="1.42.0"; sha256="01cgv28yyqjg8f86dskafb3xy4ylcl4schcad44f9jpvc6zk48qs"; depends=[Biobase]; };
-  yeastRNASeq = derive2 { name="yeastRNASeq"; version="0.40.0"; sha256="1b7bdbyzh6lx4qp4md9b7qxd433l8wpswfq0azxjdn33yryv8spm"; depends=[]; };
+  tximportData = derive2 { name="tximportData"; version="1.32.0"; sha256="15wy0dhs9sbz27ii64b4i0zxlsm6v75m2f32gisdy9f6gnbgwkjg"; depends=[]; };
-  zebrafishRNASeq = derive2 { name="zebrafishRNASeq"; version="1.22.0"; sha256="0fhsg1j40rkzxphnq7gl98zyqijacmfrjf4ffmbvr70mxw3zysgz"; depends=[]; };
+  vulcandata = derive2 { name="vulcandata"; version="1.26.0"; sha256="13cdb630w1xy734h15dgpzzk64g1rpr5xwh9q2hvs1z3ljyws8qd"; depends=[]; };
+  xcoredata = derive2 { name="xcoredata"; version="1.8.0"; sha256="0sn3h2c0h9jpdp17jcxskcqjy31vx6wz2d5xb98ag19cfbimv3nl"; depends=[ExperimentHub]; };
+  yeastCC = derive2 { name="yeastCC"; version="1.44.0"; sha256="1y3k3dvxrv68pcsdqhyvhxvwnmhm0iv7yr3rc6b0gm8g2nv9kcqm"; depends=[Biobase]; };
+  yeastExpData = derive2 { name="yeastExpData"; version="0.50.0"; sha256="1ila3h87j9l37nvwhabrayxawx3mcklhlr3y9cqzpwkg7iayrplf"; depends=[graph]; };
+  yeastGSData = derive2 { name="yeastGSData"; version="0.42.0"; sha256="1m3hrjmibmp8zzcc6acg6m21zq83rpnclya4ivivj60nw6ardbkr"; depends=[]; };
+  yeastNagalakshmi = derive2 { name="yeastNagalakshmi"; version="1.40.0"; sha256="16n48lcyl63cmlc796xizf19rmm5qmdic0msaadz12wh743phh3a"; depends=[]; };
+  yeastRNASeq = derive2 { name="yeastRNASeq"; version="0.42.0"; sha256="1jk6451ypys3xskmlm6xpvjxxzrx1g0hnzfcsahf3gqgg63pfj7h"; depends=[]; };
+  zebrafishRNASeq = derive2 { name="zebrafishRNASeq"; version="1.24.1"; sha256="0khmilw21jnq2ivl7bh7fwz9nxlphljl5fh4w28q9gzydrv0vxci"; depends=[]; };
   ABAData = derive2 { name="ABAData"; version="1.24.0"; sha256="1wgniq7ibvjj6dx63ixr3i5yclqmg94qpifzfbzzn9yjj3wnikzr"; depends=[]; broken = true; };
-  ChimpHumanBrainData = derive2 { name="ChimpHumanBrainData"; version="1.38.0"; sha256="1hgc2a7wsbw5ivdjknv82p3pvznq29lm8g4fdxy6dyr781xghs0w"; depends=[affy hexbin limma qvalue statmod]; broken = true; };
+  ChIC_data = derive2 { name="ChIC.data"; version="1.22.0"; sha256="1akqpqw9ydf23whr346psciyyp9c3r0rsas1rkdkf8g5wrcj9vhk"; depends=[caret genomeIntervals randomForest]; broken = true; };
   DREAM4 = derive2 { name="DREAM4"; version="1.31.0"; sha256="11ypc84agvq0q0v7bk0b25cm48awxay5hhhjd95gw9s7jk196i2p"; depends=[SummarizedExperiment]; broken = true; };
   MAQCsubsetAFX = derive2 { name="MAQCsubsetAFX"; version="1.30.0"; sha256="14mwg96g7aza81vc3hpmb41scmygl8vnsi6s8p48c8v92106asmb"; depends=[affy Biobase]; broken = true; };
+  MAQCsubsetILM = derive2 { name="MAQCsubsetILM"; version="1.40.0"; sha256="1bb158bmy7195wnj0wap08g621xbzflvj30pv4l7mwc54lm1vqfx"; depends=[Biobase lumi]; broken = true; };
   MIGSAdata = derive2 { name="MIGSAdata"; version="1.24.0"; sha256="1s7fyf8n86a3znacjjs0zf22amw4rlgnvw2idld0np0yz81ggzs2"; depends=[]; broken = true; };
   MSstatsBioData = derive2 { name="MSstatsBioData"; version="1.13.0"; sha256="1jzypgfmd6d0fdj9ycp4jwihjpxyinr5kwi2x2dg2z6hvxx97gb8"; depends=[]; broken = true; };
-  RLHub = derive2 { name="RLHub"; version="1.6.0"; sha256="1lx4w9m5ddzx3v4ky7yxiq7ydd0dl7xfh9fcmf53apc6fnql13h2"; depends=[AnnotationHub ExperimentHub]; broken = true; };
   RNASeqRData = derive2 { name="RNASeqRData"; version="1.16.0"; sha256="17c5fvyqxdsg7wl0hy0i28z0kf2lmjg36lfrmsv51kzklsc6ykrp"; depends=[]; broken = true; };
   SCATEData = derive2 { name="SCATEData"; version="1.10.0"; sha256="0p0y8mkcg99dpwvp7spxx047kyr7mdflnnlfpb4i232q0yxz2z03"; depends=[ExperimentHub GenomicAlignments GenomicRanges]; broken = true; };
   alpineData = derive2 { name="alpineData"; version="1.26.0"; sha256="1337y1y8q5y8yh2r2bji8fz3nhcxbn5s6pfnnkb8kvg8r0avgmkz"; depends=[AnnotationHub ExperimentHub GenomicAlignments]; broken = true; };
   brainImageRdata = derive2 { name="brainImageRdata"; version="1.12.0"; sha256="072x7yn1ambf6hfpir6qdxl8bybv64blpbi1jdp0bvqlk66zs7zv"; depends=[ExperimentHub]; broken = true; };
+  ccTutorial = derive2 { name="ccTutorial"; version="1.40.0"; sha256="1rqblyk7389xqwzvib2xjyjrc8l3qd2g8z9vj96mrfyr8dpccjjs"; depends=[affy Biobase Ringo topGO]; broken = true; };
   gatingMLData = derive2 { name="gatingMLData"; version="2.38.0"; sha256="1dhm48nrh1y0x6p50045cn6f21bg35i0b4z7bjymn9aw0n9r5fyk"; depends=[]; broken = true; };
+  mAPKLData = derive2 { name="mAPKLData"; version="1.34.0"; sha256="0vhysi7wyw7d3vbq4qcq3i3ic953awppg2bix40ywz1459b5p43g"; depends=[]; broken = true; };
   plasFIA = derive2 { name="plasFIA"; version="1.26.0"; sha256="0vbqjbfc75pb2gk49sl6aihmvcc38ylngyr1bgdvdxr0xh11imv0"; depends=[proFIA]; broken = true; };
   ppiData = derive2 { name="ppiData"; version="0.34.0"; sha256="10xbp12wim5kj1h2vkxn9x22fd92s2038w653y81jwbh2hyidybf"; depends=[AnnotationDbi graph]; broken = true; };
   pwrEWAS_data = derive2 { name="pwrEWAS.data"; version="1.14.0"; sha256="1bldyvjsv5wwzasg9sbsivyi7m2ypc17mqjglsl22fjkykm92h4s"; depends=[ExperimentHub]; broken = true; };
+  seqCNA_annot = derive2 { name="seqCNA.annot"; version="1.38.0"; sha256="0kzmn5hx8ag02pz8b78cq7dbalw2w60y441cjyyvxjgycwcfvmvj"; depends=[]; broken = true; };
+  stjudem = derive2 { name="stjudem"; version="1.42.0"; sha256="0pcvvvaqalr5jklqy7vzxkp0cd9nj9dk941drgr7ndbqc2navz2c"; depends=[]; broken = true; };
   tcgaWGBSData_hg19 = derive2 { name="tcgaWGBSData.hg19"; version="1.12.0"; sha256="1kmh4iyh2h7vc1mlwb3sridn4nwkqdschz5md5dk53mxkn2wxcmi"; depends=[bsseq ExperimentHub knitr]; broken = true; };
 }

pkgs/development/r-modules/default.nix

@@ -310,12 +310,17 @@ let
     rmsb = [ self.rstantools ];
     gastempt = [ self.rstantools ];
     interactiveDisplay = [ self.BiocManager ];
+    disbayes = [ self.rstantools ];
+    tipsae = [ self.rstantools ];
+    TriDimRegression = [ self.rstantools ];
+    bbmix = [ self.rstantools ];
   };
 
   packagesWithNativeBuildInputs = {
     adbcpostgresql = [ pkgs.postgresql ];
     adimpro = [ pkgs.imagemagick ];
     animation = [ pkgs.which ];
+    Apollonius = with pkgs; [ pkg-config gmp.dev mpfr.dev ];
     arrow = with pkgs; [ pkg-config cmake ] ++ lib.optionals stdenv.isDarwin [ intltool ];
     audio = [ pkgs.portaudio ];
     BayesSAE = [ pkgs.gsl ];
@@ -323,6 +328,7 @@ let
     BayesXsrc = with pkgs; [ readline.dev ncurses gsl ];
     bioacoustics = [ pkgs.fftw.dev pkgs.cmake ];
     bigGP = [ pkgs.mpi ];
+    bigrquerystorage = with pkgs; [ grpc protobuf which ];
     bio3d = [ pkgs.zlib ];
     BiocCheck = [ pkgs.which ];
     Biostrings = [ pkgs.zlib ];
@@ -344,9 +350,14 @@ let
     diversitree = with pkgs; [ gsl fftw ];
     exactextractr = [ pkgs.geos ];
     EMCluster = [ pkgs.lapack ];
+    fangs = [ pkgs.cargo ];
+    fcl = [ pkgs.cargo ];
     fftw = [ pkgs.fftw.dev ];
     fftwtools = with pkgs; [ fftw.dev pkg-config ];
+    fingerPro = [ pkgs.gsl ];
     Formula = [ pkgs.gmp ];
+    frailtyMMpen = [ pkgs.gsl ];
+    gamstransfer = [ pkgs.zlib ];
     gdalraster = [ pkgs.pkg-config ];
     gdtools = with pkgs; [ cairo.dev fontconfig.lib freetype.dev ];
     GeneralizedWendland = [ pkgs.gsl ];
@@ -362,13 +373,20 @@ let
     gert = [ pkgs.libgit2 ];
     haven = with pkgs; [ zlib.dev ];
     hellorust = [ pkgs.cargo ];
+    hgwrr = [ pkgs.gsl ];
     h5vc = with pkgs; [ zlib.dev bzip2.dev xz.dev ];
     yyjsonr = with pkgs; [ zlib.dev ];
+    RNifti = with pkgs; [ zlib.dev ];
+    RNiftyReg = with pkgs; [ zlib.dev ];
     highs = [ pkgs.which pkgs.cmake ];
+    crc32c = [ pkgs.which pkgs.cmake ];
     rbedrock = [ pkgs.zlib.dev pkgs.which pkgs.cmake ];
     HiCseg = [ pkgs.gsl ];
     imager = [ pkgs.xorg.libX11.dev ];
+    imbibe = [ pkgs.zlib.dev ];
+    image_CannyEdges = with pkgs; [ fftw.dev libpng.dev ];
     iBMQ = [ pkgs.gsl ];
+    jack = [ pkgs.pkg-config ];
     JavaGD = [ pkgs.jdk ];
     jpeg = [ pkgs.libjpeg.dev ];
     jqr = [ pkgs.jq.dev ];
@@ -377,7 +395,10 @@ let
     kza = [ pkgs.fftw.dev ];
     leidenAlg = [ pkgs.gmp.dev ];
     Libra = [ pkgs.gsl ];
+    libstable4u = [ pkgs.gsl ];
+    heck = [ pkgs.cargo ];
     LOMAR = [ pkgs.gmp.dev ];
+    littler = [ pkgs.libdeflate ];
     lpsymphony = with pkgs; [ pkg-config gfortran gettext ];
     lwgeom = with pkgs; [ proj geos gdal ];
     rsbml = [ pkgs.pkg-config ];
@@ -390,6 +411,7 @@ let
     mzR = with pkgs; [ zlib netcdf ];
     nanonext = with pkgs; [ mbedtls nng ];
     ncdf4 = [ pkgs.netcdf ];
+    neojags = [ pkgs.jags ];
     nloptr = with pkgs; [ nlopt pkg-config ];
     n1qn1 = [ pkgs.gfortran ];
     odbc = [ pkgs.unixODBC ];
@@ -401,6 +423,7 @@ let
     pbdZMQ = [ pkgs.pkg-config ] ++ lib.optionals stdenv.isDarwin [ pkgs.which ];
     pcaL1 = [ pkgs.pkg-config pkgs.clp ];
     pdftools = [ pkgs.poppler.dev ];
+    PEPBVS = [ pkgs.gsl ];
     phytools = [ pkgs.which ];
     PKI = [ pkgs.openssl.dev ];
     png = [ pkgs.libpng.dev ];
@@ -425,7 +448,7 @@ let
     Rhpc = with pkgs; [ zlib bzip2.dev icu xz.dev mpi pcre.dev ];
     Rhtslib = with pkgs; [ zlib.dev automake autoconf bzip2.dev xz.dev curl.dev ];
     rjags = [ pkgs.jags ];
-    rJava = with pkgs; [ zlib bzip2.dev icu xz.dev pcre.dev jdk libzip ];
+    rJava = with pkgs; [ zlib bzip2.dev icu xz.dev pcre.dev jdk libzip libdeflate ];
     Rlibeemd = [ pkgs.gsl ];
     rmatio = [ pkgs.zlib.dev pkgs.pkg-config ];
     Rmpfr = with pkgs; [ gmp mpfr.dev ];
@@ -454,6 +477,7 @@ let
     sdcTable = with pkgs; [ gmp glpk ];
     seewave = with pkgs; [ fftw.dev libsndfile.dev ];
     seqinr = [ pkgs.zlib.dev ];
+    smcryptoR = with pkgs; [ cargo rustc which ];
     webp = [ pkgs.pkg-config ];
     seqminer = with pkgs; [ zlib.dev bzip2 ];
     sf = with pkgs; [ gdal proj geos libtiff curl ];
@@ -461,6 +485,10 @@ let
     string2path = [ pkgs.cargo ];
     terra = with pkgs; [ gdal proj geos ];
     tok = [ pkgs.cargo ];
+    rshift = [ pkgs.cargo ];
+    arcgisutils = with pkgs; [ cargo rustc ];
+    arcgisgeocode = with pkgs; [ cargo rustc ];
+    arcgisplaces = with pkgs; [ pkg-config openssl.dev cargo rustc ];
     apcf = with pkgs; [ geos ];
     SemiCompRisks = [ pkgs.gsl ];
     showtext = with pkgs; [ zlib libpng icu freetype.dev ];
@@ -497,7 +525,7 @@ let
     Rsubread = [ pkgs.zlib.dev ];
     XVector = [ pkgs.zlib.dev ];
     Rsamtools = with pkgs; [ zlib.dev curl.dev bzip2 xz ];
-    rtracklayer = [ pkgs.zlib.dev ];
+    rtracklayer = with pkgs; [ zlib.dev curl.dev ];
     affyio = [ pkgs.zlib.dev ];
     snpStats = [ pkgs.zlib.dev ];
     vcfppR = [ pkgs.curl.dev pkgs.bzip2 pkgs.zlib.dev pkgs.xz];
@@ -533,6 +561,7 @@ let
     redux = [ pkgs.pkg-config ];
     rswipl = with pkgs; [ cmake pkg-config ];
     rrd = [ pkgs.pkg-config ];
+    surveyvoi = [ pkgs.pkg-config ];
     Rbwa = [ pkgs.zlib.dev ];
     trackViewer = [ pkgs.zlib.dev ];
     themetagenomics = [ pkgs.zlib.dev ];
@@ -544,16 +573,19 @@ let
     ragg = [ pkgs.pkg-config ];
     qqconf = [ pkgs.pkg-config ];
     qspray = [ pkgs.pkg-config ];
+    ratioOfQsprays = [ pkgs.pkg-config ];
+    symbolicQspray = [ pkgs.pkg-config ];
+    sphereTessellation = [ pkgs.pkg-config ];
     vapour = [ pkgs.pkg-config ];
   };
 
   packagesWithBuildInputs = {
     # sort -t '=' -k 2
-    asciicast = with pkgs; [ xz.dev bzip2.dev zlib.dev icu.dev ];
+    asciicast = with pkgs; [ xz.dev bzip2.dev zlib.dev icu.dev libdeflate ];
     island = [ pkgs.gsl.dev ];
     svKomodo = [ pkgs.which ];
     ulid = [ pkgs.zlib.dev ];
-    unrtf = with pkgs; [ xz.dev bzip2.dev zlib.dev icu.dev ];
+    unrtf = with pkgs; [ xz.dev bzip2.dev zlib.dev icu.dev libdeflate ];
     nat = [ pkgs.which ];
     nat_templatebrains = [ pkgs.which ];
     pbdZMQ = [ pkgs.zeromq ] ++ lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ];
@@ -572,7 +604,7 @@ let
     RMark = [ pkgs.which ];
     RPushbullet = [ pkgs.which ];
     stpphawkes = [ pkgs.gsl ];
-    registr = with pkgs; [ icu.dev zlib.dev bzip2.dev xz.dev ];
+    registr = with pkgs; [ icu.dev zlib.dev bzip2.dev xz.dev libdeflate ];
     RCurl = [ pkgs.curl.dev ];
     R2SWF = [ pkgs.pkg-config ];
     rDEA = [ pkgs.glpk ];
@@ -628,6 +660,7 @@ let
     Rsymphony = with pkgs; [ symphony doxygen graphviz subversion cgl clp];
     tcltk2 = with pkgs; [ tcl tk ];
     rswipl = with pkgs; [ ncurses.dev libxcrypt zlib.dev ];
+    GrafGen = [ pkgs.zlib ];
     tikzDevice = with pkgs; [ which texliveMedium ];
     gridGraphics = [ pkgs.which ];
     adimpro = with pkgs; [ which xorg.xdpyinfo ];
@@ -670,6 +703,7 @@ let
     zlib = [ pkgs.zlib.dev ];
     divest = [ pkgs.zlib.dev ];
     hipread = [ pkgs.zlib.dev ];
+    jack = with pkgs; [ gmp.dev mpfr.dev ];
     jackalope = with pkgs; [ zlib.dev xz.dev bzip2.dev ];
     largeList = [ pkgs.zlib.dev ];
     mappoly = [ pkgs.zlib.dev ];
@@ -725,10 +759,13 @@ let
     RITCH = [ pkgs.zlib.dev ];
     RcppMeCab = [ pkgs.mecab ];
     PING = [ pkgs.gsl ];
+    PROJ = [ pkgs.proj.dev ];
     RcppAlgos = [ pkgs.gmp.dev ];
     RcppBigIntAlgos = [ pkgs.gmp.dev ];
     spaMM = [ pkgs.gsl ];
     shrinkTVP = [ pkgs.gsl ];
+    sbrl = with pkgs; [ gsl gmp.dev ];
+    surveyvoi = with pkgs; [ gmp.dev mpfr.dev ];
     unigd = with pkgs; [ cairo.dev libpng.dev ];
     HilbertVisGUI = [ pkgs.gtkmm2.dev ];
     textshaping = with pkgs; [ harfbuzz.dev freetype.dev fribidi libpng ];
@@ -739,216 +776,103 @@ let
     qqconf = [ pkgs.fftw.dev ];
     spFW = [ pkgs.fftw.dev ];
     qspray = with pkgs; [ gmp.dev mpfr.dev ];
+    ratioOfQsprays = with pkgs; [ gmp.dev mpfr.dev ];
+    symbolicQspray = with pkgs; [ gmp.dev mpfr.dev ];
+    sphereTessellation = with pkgs; [ gmp.dev mpfr.dev ];
     vapour = with pkgs; [ proj.dev gdal ];
     MedianaDesigner = [ pkgs.zlib.dev ];
     ChemmineOB = [ pkgs.eigen ];
   };
 
   packagesRequiringX = [
-    "accrual"
-    "ade4TkGUI"
-    "analogue"
     "analogueExtra"
     "AnalyzeFMRI"
     "AnnotLists"
-    "AnthropMMD"
-    "aplpack"
     "asbio"
-    "BAT"
     "BCA"
-    "betapart"
-    "BiodiversityR"
-    "bio_infer"
-    "bipartite"
     "biplotbootGUI"
-    "blender"
     "cairoDevice"
-    "canceR"
-    "CCTpack"
     "cncaGUI"
-    "cocorresp"
     "CommunityCorrelogram"
-    "confidence"
-    "constrainedKriging"
-    "ConvergenceConcepts"
-    "cpa"
-    "DALY"
     "dave"
-    "Deducer"
     "DeducerPlugInExample"
     "DeducerPlugInScaling"
     "DeducerSpatial"
     "DeducerSurvival"
     "DeducerText"
     "Demerelate"
-    "detrendeR"
+    "diveR"
     "dpa"
     "dynamicGraph"
-    "dynBiplotGUI"
     "EasyqpcR"
-    "EcoVirtual"
     "exactLoglinTest"
-    "fat2Lpoly"
-    "fbati"
-    "FD"
-    "feature"
-    "FeedbackTS"
-    "FFD"
-    "fgui"
     "fisheyeR"
     "forams"
     "forensim"
-    "FreeSortR"
-    "fscaret"
-    "gcmr"
-    "geomorph"
-    "geoR"
-    "georob"
     "GGEBiplotGUI"
-    "gnm"
-    "GrapheR"
-    "GroupSeq"
     "gsubfn"
-    "GUniFrac"
     "gWidgets2RGtk2"
     "gWidgets2tcltk"
-    "HH"
     "HiveR"
     "ic50"
     "iDynoR"
-    "in2extRemes"
     "iplots"
-    "isopam"
-    "IsotopeR"
-    "JGR"
-    "KappaGUI"
     "likeLTD"
-    "logmult"
     "loon"
     "loon_ggplot"
-    "LS2Wstat"
+    "loon_shiny"
-    "MareyMap"
+    "loon_tourr"
-    "memgene"
-    "metacom"
     "Meth27QC"
-    "migui"
-    "miniGUI"
     "mixsep"
-    "MplusAutomation"
-    "mpmcorrelogram"
-    "mritc"
-    "multgee"
     "multibiplotGUI"
     "OligoSpecificitySystem"
-    "onemap"
+    "optbdmaeAT"
-    "OpenRepGrid"
+    "optrcdmaeAT"
     "paleoMAS"
-    "pbatR"
-    "PBSadmb"
-    "PBSmodelling"
-    "PCPS"
-    "pez"
-    "phylotools"
-    "picante"
-    "plotSEMM"
-    "plsRbeta"
-    "plsRglm"
-    "PopGenReport"
-    "poppr"
-    "powerpkg"
-    "PredictABEL"
-    "prefmod"
-    "PrevMap"
-    "r4ss"
     "RandomFields"
-    "rareNMtests"
-    "rAverage"
     "rfviz"
     "RclusTool"
-    "Rcmdr"
     "RcmdrPlugin_coin"
-    "RcmdrPlugin_depthTools"
-    "RcmdrPlugin_DoE"
-    "RcmdrPlugin_EACSPIR"
-    "RcmdrPlugin_EBM"
-    "RcmdrPlugin_EcoVirtual"
-    "RcmdrPlugin_EZR"
-    "RcmdrPlugin_FactoMineR"
     "RcmdrPlugin_FuzzyClust"
-    "RcmdrPlugin_HH"
     "RcmdrPlugin_IPSUR"
-    "RcmdrPlugin_KMggplot2"
     "RcmdrPlugin_lfstat"
-    "RcmdrPlugin_MA"
-    "RcmdrPlugin_MPAStats"
-    "RcmdrPlugin_orloca"
     "RcmdrPlugin_PcaRobust"
     "RcmdrPlugin_plotByGroup"
     "RcmdrPlugin_pointG"
-    "RcmdrPlugin_ROC"
     "RcmdrPlugin_sampling"
     "RcmdrPlugin_SCDA"
     "RcmdrPlugin_SLC"
-    "RcmdrPlugin_sos"
     "RcmdrPlugin_steepness"
-    "RcmdrPlugin_survival"
-    "RcmdrPlugin_TeachingDemos"
-    "RcmdrPlugin_temis"
-    "RcmdrPlugin_UCA"
-    "recluster"
-    "relimp"
-    "RHRV"
     "rich"
-    "RNCEP"
-    "RSDA"
     "RSurvey"
     "simba"
-    "Simile"
     "SimpleTable"
     "SOLOMON"
-    "soundecology"
+    "soptdmaeA"
-    "spatsurv"
-    "sqldf"
-    "SSDforR"
-    "statcheck"
-    "StatDA"
-    "STEPCAM"
-    "stosim"
     "strvalidator"
     "stylo"
-    "svDialogstcltk"
-    "svIDE"
-    "svSocket"
-    "svWidgets"
-    "SYNCSA"
     "SyNet"
     "switchboard"
-    "tcltk2"
+    "tkImgR"
-    "TestScorer"
-    "TIMP"
-    "tkrplot"
-    "tmap"
-    "tspmeta"
     "TTAinterfaceTrendAnalysis"
     "twiddler"
     "uHMM"
-    "vcdExtra"
     "VecStatGraphs3D"
-    "vegan"
-    "vegan3d"
-    "vegclust"
-    "x12GUI"
   ];
 
   packagesRequiringHome = [
     "aroma_affymetrix"
     "aroma_cn"
     "aroma_core"
+    "avotrex"
+    "beer"
     "ceramic"
     "connections"
+    "covidmx"
     "csodata"
     "DiceView"
     "facmodTS"
+    "gasanalyzer"
     "margaret"
     "MSnID"
     "OmnipathR"
@@ -1048,6 +972,7 @@ let
     "benchmarkfdrData2019"
     "bodymapRat"
     "clustifyrdatahub"
+    "CTexploreR"
     "depmap"
     "emtdata"
     "metaboliteIDmapping"
@@ -1069,6 +994,11 @@ let
     # this is a straightforward approach. Example where patching was necessary
     # -> arrow 14.0.0.2 on CRAN; was lagging behind libarrow release:
     #   https://github.com/apache/arrow/issues/39698 )
+
+    vegan3d = old.vegan3d.overrideAttrs (attrs: {
+      RGL_USE_NULL = "true";
+    });
+
     arrow = old.arrow.overrideAttrs (attrs: {
       src = pkgs.arrow-cpp.src;
       name = "r-arrow-${pkgs.arrow-cpp.version}";
@@ -1157,10 +1087,18 @@ let
       preConfigure = "patchShebangs configure";
     });
 
+    Colossus = old.Colossus.overrideAttrs (_: {
+      postPatch = "patchShebangs configure";
+    });
+
    gmailr = old.gmailr.overrideAttrs (attrs: {
       postPatch = "patchShebangs configure";
     });
 
+    heck = old.heck.overrideAttrs (attrs: {
+      postPatch = "patchShebangs configure";
+    });
+
    surtvep = old.surtvep.overrideAttrs (attrs: {
       postPatch = "patchShebangs configure";
     });
@@ -1178,6 +1116,10 @@ let
       patchPhase = "patchShebangs configure";
     });
 
+    RcppGetconf = old.RcppGetconf.overrideAttrs (attrs: {
+      postPatch = "patchShebangs configure";
+    });
+
     SpliceWiz = old.SpliceWiz.overrideAttrs (attrs: {
       postPatch = "patchShebangs configure";
     });
@@ -1203,6 +1145,26 @@ let
       patchPhase = "patchShebangs configure";
     });
 
+    cisPath = old.cisPath.overrideAttrs (attrs: {
+      hardeningDisable = [ "format" ];
+    });
+
+    HilbertVis = old.HilbertVis.overrideAttrs (attrs: {
+      hardeningDisable = [ "format" ];
+    });
+
+    HilbertVisGUI = old.HilbertVisGUI.overrideAttrs (attrs: {
+      hardeningDisable = [ "format" ];
+    });
+
+    MANOR = old.MANOR.overrideAttrs (attrs: {
+      hardeningDisable = [ "format" ];
+    });
+
+    rGADEM = old.rGADEM.overrideAttrs (attrs: {
+      hardeningDisable = [ "format" ];
+    });
+
    rsgeo = old.rsgeo.overrideAttrs (attrs: {
       nativeBuildInputs = [ pkgs.cargo ] ++ attrs.nativeBuildInputs;
       postPatch = "patchShebangs configure";
@@ -1303,19 +1265,12 @@ let
       propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ pkgs.quarto ];
       postPatch = ''
         substituteInPlace "R/quarto.R" \
-          --replace "path_env <- Sys.getenv(\"QUARTO_PATH\", unset = NA)" "path_env <- Sys.getenv(\"QUARTO_PATH\", unset = '${lib.getBin pkgs.quarto}/bin/quarto')"
+          --replace-fail "Sys.getenv(\"QUARTO_PATH\", unset = NA_character_)" "Sys.getenv(\"QUARTO_PATH\", unset = '${lib.getBin pkgs.quarto}/bin/quarto')"
       '';
     });
 
-    # backported patch from 1.9
+    Rhisat2 = old.Rhisat2.overrideAttrs (attrs: {
-    Rhisat2= old.Rhisat2.overrideAttrs (attrs: {
+      enableParallelBuilding = false;
-      patches = [ (pkgs.fetchpatch {
-        url = "https://github.com/fmicompbio/Rhisat2/commit/a0f27b018831b39f080f99e6db8a4b876fd56fc3.patch";
-        sha256 = "sha256-FbYkP/WFmbfQmxArkHgushgVgY0XSypbK8Z5ivQK8k4=";
-      }) ];
-      env = (attrs.env or { }) // {
-        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -w";
-      };
     });
 
     s2 = old.s2.overrideAttrs (attrs: {
@@ -1335,6 +1290,14 @@ let
       ];
     });
 
+    covidsymptom = old.covidsymptom.overrideAttrs (attrs: {
+      preConfigure = "rm R/covidsymptomdata.R";
+    });
+
+    cubature = old.cubature.overrideAttrs (attrs: {
+      enableParallelBuilding = false;
+    });
+
     RVowpalWabbit = old.RVowpalWabbit.overrideAttrs (attrs: {
       configureFlags = [
         "--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.out}/lib"
@@ -1372,10 +1335,6 @@ let
       PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack";
     });
 
-    spMC = old.spMC.overrideAttrs (attrs: {
-      patches = [ ./patches/spMC.patch ];
-    });
-
     FLAMES = old.FLAMES.overrideAttrs (attrs: {
       patches = [ ./patches/FLAMES.patch ];
     });
@@ -1457,7 +1416,7 @@ let
     });
 
     rgoslin = old.rgoslin.overrideAttrs (attrs: {
-      patches = [ ./patches/rgoslin.patch ];
+      enableParallelBuilding = false;
     });
 
     rpanel = old.rpanel.overrideAttrs (attrs: {
@@ -1467,6 +1426,16 @@ let
       TCLLIBPATH = "${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}";
     });
 
+    networkscaleup = old.networkscaleup.overrideAttrs (attrs: {
+      env = (attrs.env or { }) // {
+        # needed to avoid "log limit exceeded" on Hydra
+        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-ignored-attributes";
+      };
+
+      # consumes a lot of resources in parallel
+      enableParallelBuilding = false;
+    });
+
     RPostgres = old.RPostgres.overrideAttrs (attrs: {
       preConfigure = ''
         export INCLUDE_DIR=${pkgs.postgresql}/include
@@ -1497,6 +1466,16 @@ let
         '';
     });
 
+    FlexReg = old.FlexReg.overrideAttrs (attrs: {
+      env = (attrs.env or { }) // {
+        # needed to avoid "log limit exceeded" on Hydra
+        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-ignored-attributes";
+      };
+
+      # consumes a lot of resources in parallel
+      enableParallelBuilding = false;
+    });
+
     geojsonio = old.geojsonio.overrideAttrs (attrs: {
       buildInputs = [ cacert ] ++ attrs.buildInputs;
     });
@@ -1538,6 +1517,18 @@ let
       '';
     });
 
+    nearfar = let
+      angrist = fetchurl {
+        url = "https://raw.githubusercontent.com/joerigdon/nearfar/master/angrist.csv";
+        hash = "sha256-lb+HMHnRGonc26merFGB0B7Vk1Lk+sIJlay+JtQC8m4=";
+      };
+    in old.nearfar.overrideAttrs (attrs: {
+      postPatch = ''
+        substituteInPlace "R/nearfar.R" --replace-fail \
+         'url("https://raw.githubusercontent.com/joerigdon/nearfar/master/angrist.csv")'  '"${angrist}"'
+      '';
+    });
+
     rstan = old.rstan.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
@@ -1647,6 +1638,15 @@ let
       hardeningDisable = [ "format" ];
     });
 
+    Rbwa = old.Rbwa.overrideAttrs (attrs: {
+      # Parallel build cleans up *.o before they can be packed in a library
+      postPatch = ''
+        substituteInPlace src/Makefile --replace-fail \
+          "all:\$(PROG) ../inst/bwa clean" \
+          "all:\$(PROG) ../inst/bwa" \
+      '';
+    });
+
     ROracle = old.ROracle.overrideAttrs (attrs: {
       configureFlags = [
         "--with-oci-lib=${pkgs.oracle-instantclient.lib}/lib"
@@ -1710,14 +1710,37 @@ let
       postPatch = "patchShebangs configure";
     });
 
+    SharedObject = old.SharedObject.overrideAttrs (attrs: {
+      # backport PR resolving build issues: https://github.com/Jiefei-Wang/SharedObject/pull/17
+      patches = let inherit (pkgs) fetchpatch; in [
+        (fetchpatch {
+          url = "https://github.com/Jiefei-Wang/SharedObject/pull/17/commits/50c4b2964649d7f5a14d843bd7089ab62650fcd3.patch";
+          sha256 = "sha256-zn535IeOYRvyQ2yxgoGEq2wccrl9xdu9nREmy7sV+PQ=";
+        })
+        (fetchpatch {
+          url = "https://github.com/Jiefei-Wang/SharedObject/pull/17/commits/bf096a39858e9210cbe246d4b136905d4cfbfaf4.patch";
+          sha256 = "sha256-Z+BZOkFnLgIBiVuPsAHp7bMXzADcvuHV4hILdmLvd+k=";
+        })
+      ];
+    });
+
     httr2 = old.httr2.overrideAttrs (attrs: {
       preConfigure = "patchShebangs configure";
     });
 
+    dbarts = old.dbarts.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };
+
     geomorph = old.geomorph.overrideAttrs (attrs: {
       RGL_USE_NULL = "true";
     });
 
+    gpuMagic = old.gpuMagic.overrideAttrs (_: {
+      hardeningDisable = ["format"];
+    });
+
+    Rdisop = old.Rdisop.overrideAttrs (_: {
+      hardeningDisable = ["format"];
+    });
 
     opencv = let
       opencvGtk = pkgs.opencv.override (old : { enableGtk2 = true; });
@@ -1763,6 +1786,10 @@ let
       '';
     });
 
+    oligo = old.oligo.overrideAttrs (_: {
+      hardeningDisable = ["format"];
+    });
+
     tesseract = old.tesseract.overrideAttrs (_: {
       preConfigure = ''
         substituteInPlace configure \

pkgs/development/r-modules/generate-r-packages.R

@@ -12,9 +12,9 @@ if ("release" %in% biocVersion$BiocStatus) {
   biocVersion <-  max(as.numeric(as.character(biocVersion$Bioc)))
 }
 
-mirrorUrls <- list( bioc=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/bioc/src/contrib/")
+mirrorUrls <- list( bioc=paste0("http://bioconductor.org/packages/", biocVersion, "/bioc/src/contrib/")
-                  , "bioc-annotation"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/annotation/src/contrib/")
+                  , "bioc-annotation"=paste0("http://bioconductor.org/packages/", biocVersion, "/data/annotation/src/contrib/")
-                  , "bioc-experiment"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/experiment/src/contrib/")
+                  , "bioc-experiment"=paste0("http://bioconductor.org/packages/", biocVersion, "/data/experiment/src/contrib/")
                   , cran="https://cran.r-project.org/src/contrib/"
                   )
 

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

@@ -1,12 +0,0 @@
-diff --git a/src/cppgoslin/cppgoslin/domain/StringFunctions.h b/src/cppgoslin/cppgoslin/domain/StringFunctions.h
-index 70e8544..de5c040 100644
---- a/src/cppgoslin/cppgoslin/domain/StringFunctions.h
-+++ b/src/cppgoslin/cppgoslin/domain/StringFunctions.h
-@@ -35,6 +35,7 @@ SOFTWARE.
- #include "cppgoslin/domain/Element.h"
- #include <algorithm>
- #include <cctype>
-+#include <cstdint>
- 
- 
- #define contains_val(X, Y) ((X).find(Y) != (X).end())

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

@@ -1,8 +0,0 @@
-Only in spMC_orig: spMC
-diff -ru -x '*~' spMC_orig/src/Makevars spMC/src/Makevars
---- spMC_orig/src/Makevars	2014-09-19 21:23:30.000000000 +0900
-+++ spMC/src/Makevars	2014-10-25 18:14:48.366954769 +0900
-@@ -1,2 +1,2 @@
- PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS)
--PKG_LIBS=$(SHLIB_OPENMP_CFLAGS) $(BLAS_LIBS) $(LAPACK_LIBS) $(FLIBS)
-+PKG_LIBS=$(SHLIB_OPENMP_CFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

pkgs/development/tools/language-servers/nixd/default.nix

@@ -20,13 +20,13 @@
 
 let
   common = rec {
-    version = "2.2.0";
+    version = "2.2.1";
 
     src = fetchFromGitHub {
       owner = "nix-community";
       repo = "nixd";
       rev = version;
-      hash = "sha256-/8Ty1I130vWFidedt+WEaaFHS/zMFVu9vpq4Z3EBjGw=";
+      hash = "sha256-Y5MB3BQBRkSe+10enlric1GTmJCN36clbOSos6fzoRM=";
     };
 
     nativeBuildInputs = [