Merge branch 'master.upstream' into staging.upstream

lib/attrsets.nix

@@ -221,6 +221,16 @@ rec {
   isDerivation = x: isAttrs x && x ? type && x.type == "derivation";
 
 
+  /* Convert a store path to a fake derivation. */
+  toDerivation = path:
+    let path' = builtins.storePath path; in
+    { type = "derivation";
+      name = builtins.unsafeDiscardStringContext (builtins.substring 33 (-1) (baseNameOf path'));
+      outPath = path';
+      outputs = [ "out" ];
+    };
+
+
   /* If the Boolean `cond' is true, return the attribute set `as',
      otherwise an empty attribute set. */
   optionalAttrs = cond: as: if cond then as else {};

lib/maintainers.nix

@@ -151,6 +151,7 @@
   madjar = "Georges Dubus <georges.dubus@compiletoi.net>";
   magnetophon = "Bart Brouns <bart@magnetophon.nl>";
   mahe = "Matthias Herrmann <matthias.mh.herrmann@gmail.com>";
+  makefu = "Felix Richter <makefu@syntax-fehler.de>";
   malyn = "Michael Alyn Miller <malyn@strangeGizmo.com>";
   manveru = "Michael Fellinger <m.fellinger@gmail.com>";
   marcweber = "Marc Weber <marco-oweber@gmx.de>";

lib/strings.nix

@@ -218,4 +218,9 @@ rec {
 
   # Format a number adding leading zeroes up to fixed width.
   fixedWidthNumber = width: n: fixedWidthString width "0" (toString n);
+
+
+  # Check whether a value is a store path.
+  isStorePath = x: builtins.substring 0 1 (toString x) == "/" && dirOf (builtins.toPath x) == builtins.storeDir;
+
 }

lib/types.nix

@@ -94,14 +94,16 @@ rec {
     # derivation is a reserved keyword.
     package = mkOptionType {
       name = "derivation";
-      check = isDerivation;
+      check = x: isDerivation x || isStorePath x;
-      merge = mergeOneOption;
+      merge = loc: defs:
+        let res = mergeOneOption loc defs;
+        in if isDerivation res then res else toDerivation res;
     };
 
     path = mkOptionType {
       name = "path";
       # Hacky: there is no ‘isPath’ primop.
-      check = x: builtins.unsafeDiscardStringContext (builtins.substring 0 1 (toString x)) == "/";
+      check = x: builtins.substring 0 1 (toString x) == "/";
       merge = mergeOneOption;
     };
 

nixos/doc/manual/development/option-declarations.xml

@@ -106,6 +106,15 @@ options = {
     </listitem>
   </varlistentry>
 
+  <varlistentry>
+    <term><varname>types.package</varname></term>
+    <listitem>
+      <para>A derivation (such as <literal>pkgs.hello</literal>) or a
+      store path (such as
+      <filename>/nix/store/1ifi1cfbfs5iajmvwgrbmrnrw3a147h9-hello-2.10</filename>).</para>
+    </listitem>
+  </varlistentry>
+
   <varlistentry>
     <term><varname>types.listOf</varname> <replaceable>t</replaceable></term>
     <listitem>

nixos/modules/installer/tools/auto-upgrade.nix

@@ -0,0 +1,81 @@
+{ config, lib, pkgs, ... }:
+
+with lib;
+
+let cfg = config.system.autoUpgrade; in
+
+{
+
+  options = {
+
+    system.autoUpgrade = {
+
+      enable = mkOption {
+        type = types.bool;
+        default = false;
+        description = ''
+          Whether to periodically upgrade NixOS to the latest
+          version. If enabled, a systemd timer will run
+          <literal>nixos-rebuild switch --upgrade</literal> once a
+          day.
+        '';
+      };
+
+      channel = mkOption {
+        type = types.nullOr types.str;
+        default = null;
+        example = https://nixos.org/channels/nixos-14.12-small;
+        description = ''
+          The URI of the NixOS channel to use for automatic
+          upgrades. By default, this is the channel set using
+          <command>nix-channel</command> (run <literal>nix-channel
+          --list</literal> to see the current value).
+        '';
+      };
+
+      flags = mkOption {
+        type = types.listOf types.str;
+        default = [];
+        example = [ "-I" "stuff=/home/alice/nixos-stuff" "--option" "extra-binary-caches" "http://my-cache.example.org/" ];
+        description = ''
+          Any additional flags passed to <command>nixos-rebuild</command>.
+        '';
+      };
+
+    };
+
+  };
+
+  config = {
+
+    system.autoUpgrade.flags =
+      [ "--no-build-output" ]
+      ++ (if cfg.channel == null
+          then [ "--upgrade" ]
+          else [ "-I" "nixpkgs=${cfg.channel}/nixexprs.tar.xz" ]);
+
+    systemd.services.nixos-upgrade = {
+      description = "NixOS Upgrade";
+
+      restartIfChanged = false;
+      unitConfig.X-StopOnRemoval = false;
+
+      serviceConfig.Type = "oneshot";
+
+      environment = config.nix.envVars //
+        { inherit (config.environment.sessionVariables) NIX_PATH SSL_CERT_FILE;
+          HOME = "/root";
+        };
+
+      path = [ pkgs.gnutar pkgs.xz config.nix.package ];
+
+      script = ''
+        ${config.system.build.nixos-rebuild}/bin/nixos-rebuild test ${toString cfg.flags}
+      '';
+
+      startAt = mkIf cfg.enable "04:40";
+    };
+
+  };
+
+}

nixos/modules/installer/tools/tools.nix

@@ -57,7 +57,9 @@ let
 in
 
 {
+
   config = {
+
     environment.systemPackages =
       [ nixos-build-vms
         nixos-install
@@ -70,5 +72,7 @@ in
     system.build = {
       inherit nixos-install nixos-generate-config nixos-option nixos-rebuild;
     };
+
   };
+
 }

nixos/modules/module-list.nix

@@ -41,6 +41,7 @@
   ./hardware/video/bumblebee.nix
   ./hardware/video/nvidia.nix
   ./hardware/video/ati.nix
+  ./installer/tools/auto-upgrade.nix
   ./installer/tools/nixos-checkout.nix
   ./installer/tools/tools.nix
   ./misc/assertions.nix

nixos/modules/profiles/minimal.nix

@@ -7,6 +7,8 @@ with lib;
 
 {
   environment.noXlibs = mkDefault true;
-  i18n.supportedLocales = [ config.i18n.defaultLocale ];
+
+  # This isn't perfect, but let's expect the user specifies an UTF-8 defaultLocale
+  i18n.supportedLocales = [ (config.i18n.defaultLocale + "/UTF-8") ];
   services.nixosManual.enable = mkDefault false;
 }

nixos/modules/services/networking/kippo.nix

@@ -87,7 +87,6 @@ rec {
       environment.PYTHONPATH = "${pkgs.kippo}/src/:${pkgs.pythonPackages.pycrypto}/lib/python2.7/site-packages/:${pkgs.pythonPackages.pyasn1}/lib/python2.7/site-packages/:${pkgs.pythonPackages.python}/lib/python2.7/site-packages/:${pkgs.pythonPackages.twisted}/lib/python2.7/site-packages/:.";
       preStart = ''
         if [ ! -d ${cfg.varPath}/ ] ; then
-            mkdir -p ${cfg.pidPath}
             mkdir -p ${cfg.logPath}/tty
             mkdir -p ${cfg.logPath}/dl
             mkdir -p ${cfg.varPath}/keys
@@ -97,12 +96,15 @@ rec {
             cp ${pkgs.kippo}/src/txtcmds ${cfg.varPath} -r
 
             chmod u+rw ${cfg.varPath} -R
-            chmod u+rw ${cfg.pidPath}
             chown kippo.kippo ${cfg.varPath} -R
-            chown kippo.kippo ${cfg.pidPath}
             chown kippo.kippo ${cfg.logPath} -R
             chmod u+rw ${cfg.logPath} -R
         fi
+        if [ ! -d ${cfg.pidPath}/ ] ; then
+            mkdir -p ${cfg.pidPath}
+            chmod u+rw ${cfg.pidPath}
+            chown kippo.kippo ${cfg.pidPath}
+        fi
       '';
 
       serviceConfig.ExecStart = "${pkgs.pythonPackages.twisted}/bin/twistd -y ${pkgs.kippo}/src/kippo.tac --syslog --rundir=${cfg.varPath}/ --pidfile=${cfg.pidPath}/kippo.pid --prefix=kippo -n";

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

@@ -97,7 +97,7 @@ sub parseFstab {
 sub parseUnit {
     my ($filename) = @_;
     my $info = {};
-    parseKeyValues($info, read_file($filename));
+    parseKeyValues($info, read_file($filename)) if -f $filename;
     parseKeyValues($info, read_file("${filename}.d/overrides.conf")) if -f "${filename}.d/overrides.conf";
     return $info;
 }
@@ -157,7 +157,8 @@ while (my ($unit, $state) = each %{$activePrev}) {
 
     if (-e $prevUnitFile && ($state->{state} eq "active" || $state->{state} eq "activating")) {
         if (! -e $newUnitFile || abs_path($newUnitFile) eq "/dev/null") {
-            $unitsToStop{$unit} = 1;
+            my $unitInfo = parseUnit($prevUnitFile);
+            $unitsToStop{$unit} = 1 if boolIsTrue($unitInfo->{'X-StopOnRemoval'} // "yes");
         }
 
         elsif ($unit =~ /\.target$/) {

pkgs/applications/audio/fmit/default.nix

@@ -1,32 +1,61 @@
-{ stdenv, fetchFromGitHub, alsaLib, cmake, fftw
+# FIXME: upgrading qt5Full (Qt 5.3) to qt5.{base,multimedia} (Qt 5.4) breaks
-, freeglut, libjack2, libXmu, qt4 }:
+# the default Qt audio capture source!
+{ stdenv, fetchFromGitHub, fftw, freeglut, qt5Full
+, alsaSupport ? false, alsaLib ? null
+, jackSupport ? false, libjack2 ? null }:
 
-let version = "1.0.0"; in
+assert alsaSupport -> alsaLib != null;
+assert jackSupport -> libjack2 != null;
+
+let version = "1.0.5"; in
 stdenv.mkDerivation {
   name = "fmit-${version}";
 
   src = fetchFromGitHub {
-    sha256 = "13y9csv34flz7065kg69h99hd7d9zskq12inmkf34l4qjyk7c185";
+    sha256 = "1p49ykg7mf62xrn08fqss8yr1nf53mm8w9zp2sgcy48bfsa9xbpy";
     rev = "v${version}";
     repo = "fmit";
     owner = "gillesdegottex";
   };
 
-  buildInputs = [ alsaLib fftw freeglut libjack2 libXmu qt4 ];
+  buildInputs = [ fftw freeglut qt5Full ]
-  nativeBuildInputs = [ cmake ];
+    ++ stdenv.lib.optional alsaSupport [ alsaLib ]
+    ++ stdenv.lib.optional jackSupport [ libjack2 ];
+
+  postPatch = ''
+    substituteInPlace fmit.pro --replace '$$FMITVERSIONGITPRO' '${version}'
+    substituteInPlace distrib/fmit.desktop \
+      --replace "Icon=fmit" "Icon=$out/share/pixmaps/fmit.svg"
+    substituteInPlace src/main.cpp --replace "PREFIX" "\"$out\""
+  '';
+
+  configurePhase = ''
+    qmake \
+      CONFIG+=${stdenv.lib.optionalString alsaSupport "acs_alsa"} \
+      CONFIG+=${stdenv.lib.optionalString jackSupport "acs_jack"} \
+      fmit.pro
+  '';
 
   enableParallelBuilding = true;
 
+  installPhase = ''
+    install -D fmit $out/bin/fmit
+    install -Dm644 distrib/fmit.desktop $out/share/applications/fmit.desktop
+    install -Dm644 ui/images/fmit.svg $out/share/pixmaps/fmit.svg
+    mkdir -p $out/share/fmit
+    cp -R tr $out/share/fmit
+  '';
+
   meta = with stdenv.lib; {
     inherit version;
     description = "Free Musical Instrument Tuner";
     longDescription = ''
-      FMIT is a graphical utility for tuning your musical instruments, with
+      FMIT is a graphical utility for tuning musical instruments, with error
-      error and volume history and advanced features.
+      and volume history, and advanced features.
     '';
     homepage = http://gillesdegottex.github.io/fmit/;
     license = licenses.gpl3Plus;
-    platforms = with platforms; linux;
+    platforms = platforms.linux;
     maintainers = with maintainers; [ nckx ];
   };
 }

pkgs/applications/audio/pamixer/default.nix

@@ -3,11 +3,11 @@
 stdenv.mkDerivation rec {
 
   name = "pamixer-${version}";
-  version = "1.2.1";
+  version = "1.3";
 
   src = fetchurl {
     url = "https://github.com/cdemoulins/pamixer/archive/${version}.tar.gz";
-    sha256 = "1ad6b46hh02hs1978pgihrm2bnq4z2v0imrfm3wy74xdkr6xjxy4";
+    sha256 = "091676ww4jbf4jr728gjfk7fkd5nisy70mr6f3s1p7n05hjpmfjx";
   };
 
   buildInputs = [ boost libpulseaudio ];

pkgs/applications/editors/emacs-modes/haskell/default.nix

@@ -1,19 +1,21 @@
-{ stdenv, fetchurl, emacs, texinfo }:
+{ stdenv, fetchFromGitHub, emacs, texinfo }:
 
 let
-  version = "13.10";
+  version = "13.14-130-ga03bd9b";      # git describe --tags
 in
 stdenv.mkDerivation {
   name = "haskell-mode-${version}";
 
-  src = fetchurl {
+  src = fetchFromGitHub {
-    url = "https://github.com/haskell/haskell-mode/archive/v${version}.tar.gz";
+    owner = "haskell";
-    sha256 = "0hcg7wpalcdw8j36m8vd854zrrgym074r7m903rpwfrhx9mlg02b";
+    repo = "haskell-mode";
+    rev = "v${version}";
+    sha256 = "0k4jfixzsvwpsz37f2pvbr9slz8fpcd9nwddcv2bvi4x20jp11ma";
   };
 
   buildInputs = [ emacs texinfo ];
 
-  makeFlags = "VERSION=${version} GIT_VERSION=${version}";
+  makeFlags = "VERSION=v${version} GIT_VERSION=v${version}";
 
   installPhase = ''
     mkdir -p $out/share/emacs/site-lisp
@@ -22,6 +24,11 @@ stdenv.mkDerivation {
     cp -v *.info* $out/share/info/
   '';
 
+  # The test suite must run *after* copying the generated files to $out
+  # because "make check" implies "make clean".
+  doInstallCheck = true;
+  installCheckTarget = "check";
+
   meta = {
     homepage = "http://github.com/haskell/haskell-mode";
     description = "Haskell mode for Emacs";

pkgs/applications/editors/emacs-modes/haskell/git.nix

@@ -1,39 +0,0 @@
-{ stdenv, fetchFromGitHub, emacs, texinfo }:
-
-let
-  version = "13.10-361-gfa09425";      # git describe --tags
-in
-stdenv.mkDerivation {
-  name = "haskell-mode-${version}";
-
-  src = fetchFromGitHub {
-    owner = "haskell";
-    repo = "haskell-mode";
-    rev = "v${version}";
-    sha256 = "1bq4gddzwjy2w1hbsmwxcamcy87amz7ksy1vmpwg0qij88fk4av9";
-  };
-
-  buildInputs = [ emacs texinfo ];
-
-  makeFlags = "VERSION=v${version} GIT_VERSION=v${version}";
-
-  installPhase = ''
-    mkdir -p $out/share/emacs/site-lisp
-    cp *.el *.elc *.hs $out/share/emacs/site-lisp/
-    mkdir -p $out/share/info
-    cp -v *.info* $out/share/info/
-  '';
-
-  # The test suite must run *after* copying the generated files to $out
-  # because "make check" implies "make clean".
-  doInstallCheck = true;
-  installCheckTarget = "check";
-
-  meta = {
-    homepage = "http://github.com/haskell/haskell-mode";
-    description = "Haskell mode for Emacs";
-
-    platforms = stdenv.lib.platforms.unix;
-    maintainers = [ stdenv.lib.maintainers.simons ];
-  };
-}

pkgs/applications/editors/emacs-modes/nyan-mode/default.nix

@@ -1,4 +1,4 @@
-{trivialBuild, lib, fetchFromGitHub}:
+{lib, trivialBuild, fetchFromGitHub}:
 
 trivialBuild rec {
   pname    = "nyan-mode";
@@ -23,9 +23,8 @@ trivialBuild rec {
     cp -r mus $out
   '';
 
-  meta = with lib; {
+  meta = {
     description = "An analog indicator of the position in the buffer";
-    homepage = https://github.com/TeMPOraL/nyan-mode/;
+    license = lib.licenses.gpl3Plus;
-    license = licenses.gpl3Plus;
   };
 }

pkgs/applications/editors/emacs-modes/org/default.nix

@@ -2,11 +2,11 @@
 , texLiveAggregationFun }:
 
 stdenv.mkDerivation rec {
-  name = "org-8.3";
+  name = "org-8.3.1";
 
   src = fetchurl {
     url = "http://orgmode.org/${name}.tar.gz";
-    sha256 = "0yqbl232hfppljz545jbjawwaw7qjdjsq97c0wf0cbkghgpln3wy";
+    sha256 = "0cn3k02b2dhp489rrlaz4g91h0ph99a7721gm8x7axicqhpv04rx";
   };
 
   buildInputs = [ emacs ];

pkgs/applications/gis/qgis/default.nix

@@ -1,12 +1,12 @@
 { stdenv, fetchurl, gdal, cmake, qt4, flex, bison, proj, geos, x11, sqlite, gsl,
-  pyqt4, qwt, fcgi, pythonPackages, libspatialindex, libspatialite, qscintilla, postgresql, makeWrapper }:
+  qwt, fcgi, pythonPackages, libspatialindex, libspatialite, qscintilla, postgresql, makeWrapper }:
 
 stdenv.mkDerivation rec {
   name = "qgis-2.10.1";
 
-  buildInputs = [ gdal qt4 flex bison proj geos x11 sqlite gsl pyqt4 qwt qscintilla
+  buildInputs = [ gdal qt4 flex bison proj geos x11 sqlite gsl qwt qscintilla
     fcgi libspatialindex libspatialite postgresql ] ++
-    (with pythonPackages; [ numpy psycopg2 ]);
+    (with pythonPackages; [ numpy psycopg2 ]) ++ [ pythonPackages.qscintilla ];
 
   nativeBuildInputs = [ cmake makeWrapper ];
 

pkgs/applications/graphics/openscad/default.nix

@@ -1,23 +1,22 @@
 { stdenv, fetchurl, qt4, bison, flex, eigen, boost, mesa, glew, opencsg, cgal
-, mpfr, gmp, glib, pkgconfig
+, mpfr, gmp, glib, pkgconfig, harfbuzz, qscintilla, gettext
 }:
 
 stdenv.mkDerivation rec {
-  version = "2014.03";
+  version = "2015.03-1";
   name = "openscad-${version}";
 
   src = fetchurl {
     url = "http://files.openscad.org/${name}.src.tar.gz";
-    sha256 = "1hv1lmq1ayhlvrz5sqipg650xryq25a9k22ysdw0dsrwg9ixqpw6";
+    sha256 = "61e0dd3cd107e5670d727526700104cca5ac54a1f0a84117fcc9e57bf3b6b279";
   };
 
   buildInputs = [
     qt4 bison flex eigen boost mesa glew opencsg cgal mpfr gmp glib
-    pkgconfig
+    pkgconfig harfbuzz qscintilla gettext
   ];
 
   configurePhase = ''
-    export NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE -I$(echo ${eigen}/include/eigen*) "
     qmake PREFIX="$out" VERSION=${version}
   '';
 

pkgs/applications/misc/rofi/pass.nix

@@ -2,12 +2,12 @@
 
 stdenv.mkDerivation rec {
   name = "rofi-pass-${version}";
-  version = "2015-06-08";
+  version = "1.0";
 
   src = fetchgit {
     url = "https://github.com/carnager/rofi-pass";
-    rev = "7e376b5ec64974c4e8478acf3ada8d111896f391";
+    rev = "refs/tags/${version}";
-    sha256 = "1ywsxdgy5m63a2f5vd7np2f1qffz7y95z7s1gq5d87s8xd8myadl";
+    sha256 = "16k7bj5mf5alfks8mylp549q3lmpbxjsrsgyj7gibdmhjz768jz3";
   };
 
   buildInputs = [ rofi wmctrl xprop xdotool ];

pkgs/applications/misc/rtv/default.nix

@@ -1,14 +1,14 @@
 { stdenv, fetchFromGitHub, pkgs, python, pythonPackages }:
 
 pythonPackages.buildPythonPackage rec {
-  version = "1.4";
+  version = "1.4.2";
   name = "rtv-${version}";
 
   src = fetchFromGitHub {
     owner = "michael-lazar";
     repo = "rtv";
     rev = "v${version}";
-    sha256 = "071p7idprknpra6mrdjjka8lrr80ykag62rhbsaf6zcz1d9p55cp";
+    sha256 = "103ahwaaghxpih5bkbzqyqgxqmx6kc859vjla8fy8scg21cijghh";
   };
 
   propagatedBuildInputs = with pythonPackages; [

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

@@ -41,7 +41,7 @@ let
 
   desktopItem = makeDesktopItem {
     name = "chromium";
-    exec = "chromium";
+    exec = "chromium %U";
     icon = "${chromium.browser}/share/icons/hicolor/48x48/apps/chromium.png";
     comment = "An open source web browser from Google";
     desktopName = "Chromium";

pkgs/applications/networking/browsers/chromium/source/default.nix

@@ -17,8 +17,6 @@ let
     "s,^/,,"
   ]);
 
-  pre44 = versionOlder version "44.0.0.0";
-
 in stdenv.mkDerivation {
   name = "chromium-source-${version}";
 
@@ -46,9 +44,7 @@ in stdenv.mkDerivation {
     done
   '';
 
-  patches = if pre44
+  patches = singleton ./nix_plugin_paths_44.patch;
-            then singleton ./nix_plugin_paths_42.patch
-            else singleton ./nix_plugin_paths_44.patch;
 
   patchPhase = let
     diffmod = sym: "/^${sym} /{s/^${sym} //;${transform ""};s/^/${sym} /}";

pkgs/applications/networking/browsers/chromium/source/nix_plugin_paths_42.patch

@@ -1,93 +0,0 @@
-diff --git a/chrome/common/chrome_paths.cc b/chrome/common/chrome_paths.cc
-index 8a205a6..d5c24e1 100644
---- a/chrome/common/chrome_paths.cc
-+++ b/chrome/common/chrome_paths.cc
-@@ -97,21 +97,14 @@ static base::LazyInstance<base::FilePath>
-     g_invalid_specified_user_data_dir = LAZY_INSTANCE_INITIALIZER;
- 
- // Gets the path for internal plugins.
--bool GetInternalPluginsDirectory(base::FilePath* result) {
--#if defined(OS_MACOSX) && !defined(OS_IOS)
--  // If called from Chrome, get internal plugins from a subdirectory of the
--  // framework.
--  if (base::mac::AmIBundled()) {
--    *result = chrome::GetFrameworkBundlePath();
--    DCHECK(!result->empty());
--    *result = result->Append("Internet Plug-Ins");
--    return true;
--  }
--  // In tests, just look in the module directory (below).
--#endif
--
--  // The rest of the world expects plugins in the module directory.
--  return PathService::Get(base::DIR_MODULE, result);
-+bool GetInternalPluginsDirectory(base::FilePath* result,
-+                                 const std::string& ident) {
-+  std::string full_env = std::string("NIX_CHROMIUM_PLUGIN_PATH_") + ident;
-+  const char* value = getenv(full_env.c_str());
-+  if (value == NULL)
-+      return PathService::Get(base::DIR_MODULE, result);
-+  else
-+      *result = base::FilePath(value);
- }
- 
- }  // namespace
-@@ -248,11 +241,11 @@ bool PathProvider(int key, base::FilePath* result) {
-       create_dir = true;
-       break;
-     case chrome::DIR_INTERNAL_PLUGINS:
--      if (!GetInternalPluginsDirectory(&cur))
-+      if (!GetInternalPluginsDirectory(&cur, "ALL"))
-         return false;
-       break;
-     case chrome::DIR_PEPPER_FLASH_PLUGIN:
--      if (!GetInternalPluginsDirectory(&cur))
-+      if (!GetInternalPluginsDirectory(&cur, "PEPPERFLASH"))
-         return false;
-       cur = cur.Append(kPepperFlashBaseDirectory);
-       break;
-@@ -285,7 +278,7 @@ bool PathProvider(int key, base::FilePath* result) {
-       cur = cur.Append(FILE_PATH_LITERAL("script.log"));
-       break;
-     case chrome::FILE_FLASH_PLUGIN:
--      if (!GetInternalPluginsDirectory(&cur))
-+      if (!GetInternalPluginsDirectory(&cur, "FILEFLASH"))
-         return false;
-       cur = cur.Append(kInternalFlashPluginFileName);
-       break;
-@@ -295,7 +288,7 @@ bool PathProvider(int key, base::FilePath* result) {
-       cur = cur.Append(chrome::kPepperFlashPluginFilename);
-       break;
-     case chrome::FILE_EFFECTS_PLUGIN:
--      if (!GetInternalPluginsDirectory(&cur))
-+      if (!GetInternalPluginsDirectory(&cur, "FILE_EFFECTS"))
-         return false;
-       cur = cur.Append(kEffectsPluginFileName);
-       break;
-@@ -308,7 +301,7 @@ bool PathProvider(int key, base::FilePath* result) {
-     // We currently need a path here to look up whether the plugin is disabled
-     // and what its permissions are.
-     case chrome::FILE_NACL_PLUGIN:
--      if (!GetInternalPluginsDirectory(&cur))
-+      if (!GetInternalPluginsDirectory(&cur, "NACL"))
-         return false;
-       cur = cur.Append(kInternalNaClPluginFileName);
-       break;
-@@ -343,7 +336,7 @@ bool PathProvider(int key, base::FilePath* result) {
-         cur = cur.DirName();
-       }
- #else
--      if (!GetInternalPluginsDirectory(&cur))
-+      if (!GetInternalPluginsDirectory(&cur, "PNACL"))
-         return false;
- #endif
-       cur = cur.Append(FILE_PATH_LITERAL("pnacl"));
-@@ -372,7 +365,7 @@ bool PathProvider(int key, base::FilePath* result) {
-     // In the component case, this is the source adapter. Otherwise, it is the
-     // actual Pepper module that gets loaded.
-     case chrome::FILE_WIDEVINE_CDM_ADAPTER:
--      if (!GetInternalPluginsDirectory(&cur))
-+      if (!GetInternalPluginsDirectory(&cur, "WIDEVINE"))
-         return false;
-       cur = cur.AppendASCII(kWidevineCdmAdapterFileName);
-       break;

pkgs/applications/networking/browsers/chromium/source/sources.nix

@@ -13,9 +13,9 @@
     sha256bin64 = "14l8lka8jci1d90vbz5kpl20mk98n1ak4mw667dkz89cch5gal4s";
   };
   stable = {
-    version = "44.0.2403.125";
+    version = "44.0.2403.130";
-    sha256 = "0li483phq72xlg0bpsgfk1rlxrmldk4g45ijx1xmnfs42g38wmkq";
+    sha256 = "055lccfiqdqwcjnx9l9xgzcilm2m341rg66nfnnadqa490prnxrp";
-    sha256bin32 = "0h5a2wm13bvrq013skp3lq40bzx9519mb9kh8x3n4800lnanbjcb";
+    sha256bin32 = "0yzjhqyw2aaiwfv395c75avizcg28f3bn9zkqk2p3ifcv231w15v";
-    sha256bin64 = "1p9gfqpgyihvby4pb3fdn4ibg84fh4gksy18cvyi9zq7cibww2ff";
+    sha256bin64 = "1dzwlrdvnqyz6rpcl3pavpvqsx6la1d04cvgca3iaanq5xcana8b";
   };
 }

pkgs/applications/networking/browsers/chromium/update.sh

@@ -11,22 +11,6 @@ source "$(nix-build --no-out-link "$base_path/update.nix" -A updateHelpers)";
 
 ver_sha_table=""; # list of version:sha256
 
-sha_lookup()
-{
-    version="$1";
-
-    for ver_sha in $ver_sha_table;
-    do
-        if [ "x${ver_sha%:*}" = "x$version" ];
-        then
-            echo "${ver_sha##*:}";
-            return 0;
-        fi;
-    done;
-
-    return 1;
-}
-
 sha_insert()
 {
     version="$1";
@@ -72,22 +56,15 @@ get_channel_exprs()
         channel="${chline%%,*}";
         version="${chline##*,}";
 
-        echo -n "Checking if sha256 of version $version is cached..." >&2;
+        sha256="$(get_sha256 "$channel" "$version")";
-        if sha256="$(sha_lookup "$version")";
+        if [ $? -ne 0 ];
         then
-            echo " yes: $sha256" >&2;
+            echo "Whoops, failed to fetch $version, trying previous" \
-        else
+                 "versions:" >&2;
-            echo " no." >&2;
-            sha256="$(get_sha256 "$channel" "$version")";
-            if [ $? -ne 0 ];
-            then
-                echo "Whoops, failed to fetch $version, trying previous" \
-                     "versions:" >&2;
 
-                sha_ver="$(get_prev_sha256 "$channel" "$version")";
+            sha_ver="$(get_prev_sha256 "$channel" "$version")";
-                sha256="${sha_ver%:*}";
+            sha256="${sha_ver%:*}";
-                version="${sha_ver#*:}";
+            version="${sha_ver#*:}";
-            fi;
         fi;
 
         sha_insert "$version" "$sha256";

pkgs/applications/networking/browsers/firefox-bin/sources.nix

@@ -4,185 +4,185 @@
 # ruby generate_source.rb > source.nix
 
 {
-  version = "39.0";
+  version = "39.0.3";
   sources = [
-    { locale = "ach"; arch = "linux-i686"; sha1 = "802ac533ba95ecfb4780f84d52698a2cc2d7ac82"; }
+    { locale = "ach"; arch = "linux-i686"; sha1 = "4b732557876ff3e4d02ad480b7c73bd7abd6782d"; }
-    { locale = "ach"; arch = "linux-x86_64"; sha1 = "3c000ef496165cb4e0e104d72a381040a3bc6787"; }
+    { locale = "ach"; arch = "linux-x86_64"; sha1 = "0a63b048b33638ade924bcf7ae435423c9da906c"; }
-    { locale = "af"; arch = "linux-i686"; sha1 = "6fa249f63fe690f3459f4b0112f4945a502a79eb"; }
+    { locale = "af"; arch = "linux-i686"; sha1 = "87349773cdb5e07aaa1387e75e08d03786df700d"; }
-    { locale = "af"; arch = "linux-x86_64"; sha1 = "f22b92d0fb0ed21f0e6a3a47c5f2fe873b3bfb56"; }
+    { locale = "af"; arch = "linux-x86_64"; sha1 = "137d3558eb674036d43e5764ca691a66f9a07782"; }
-    { locale = "an"; arch = "linux-i686"; sha1 = "650c772ef89bc5ef6efe5129ddf8feaf993c8f1d"; }
+    { locale = "an"; arch = "linux-i686"; sha1 = "db99f86de92b0d1782611926b3053b25ad302e8b"; }
-    { locale = "an"; arch = "linux-x86_64"; sha1 = "e722d65e3b9b706e6b9214ae79543130ad6dba95"; }
+    { locale = "an"; arch = "linux-x86_64"; sha1 = "d000f9e8a983be0fa7d05176fb6cc0954bb06ad7"; }
-    { locale = "ar"; arch = "linux-i686"; sha1 = "8ff6fbc92e5b9cedfa17eda240fc89f14eb68f73"; }
+    { locale = "ar"; arch = "linux-i686"; sha1 = "b794a584da47ee9197666ab6976863f23ff1972c"; }
-    { locale = "ar"; arch = "linux-x86_64"; sha1 = "a1e94f56148a554e522cd317d0f2384073020278"; }
+    { locale = "ar"; arch = "linux-x86_64"; sha1 = "0319aec1942cd8311b236aef5772850897b36f64"; }
-    { locale = "as"; arch = "linux-i686"; sha1 = "c6815876c23117a462d79eb5da291610c1d96feb"; }
+    { locale = "as"; arch = "linux-i686"; sha1 = "83b83af48caf75bcdc39efb9c8a09333d6ae97b7"; }
-    { locale = "as"; arch = "linux-x86_64"; sha1 = "629997b112da84852a01606f7fa4f15448c0ebb3"; }
+    { locale = "as"; arch = "linux-x86_64"; sha1 = "827463330470ab2abd4a71a92e15fea451957fb5"; }
-    { locale = "ast"; arch = "linux-i686"; sha1 = "acda6aefe872e4982d0e8f3ac337d4243bb5e00f"; }
+    { locale = "ast"; arch = "linux-i686"; sha1 = "9f994c9374c53afa094271907fc6aecbf5a93eb4"; }
-    { locale = "ast"; arch = "linux-x86_64"; sha1 = "181d998305bb75ea5e99bb1b4b5059b54a724ab9"; }
+    { locale = "ast"; arch = "linux-x86_64"; sha1 = "611835134f1008fcff72f3ab264ce9448a6a0948"; }
-    { locale = "az"; arch = "linux-i686"; sha1 = "230ebfaf61efac65c9daae983ec2fd854a9c1dac"; }
+    { locale = "az"; arch = "linux-i686"; sha1 = "67339f5005bf8c805b6c8ed24fbed597865f5dd0"; }
-    { locale = "az"; arch = "linux-x86_64"; sha1 = "a8ddb38542bce008924e4b593691ae84a839e564"; }
+    { locale = "az"; arch = "linux-x86_64"; sha1 = "ecdd763f7d40bcb1ff6004fd0a3f511f5cbb9d9b"; }
-    { locale = "be"; arch = "linux-i686"; sha1 = "47a242cd2c91cd7435c8c959d5eaa8595710f6aa"; }
+    { locale = "be"; arch = "linux-i686"; sha1 = "d6a7d84744c0ac6e4cb7f0a1f0025bbee053cdc2"; }
-    { locale = "be"; arch = "linux-x86_64"; sha1 = "db62ad921f9df2683522db1968db9b79edfbadf2"; }
+    { locale = "be"; arch = "linux-x86_64"; sha1 = "051646e7d213099433bc198c74f85d99aeb6e846"; }
-    { locale = "bg"; arch = "linux-i686"; sha1 = "c2fddb3667c5bb50fee3011cfb782b2dff7f4063"; }
+    { locale = "bg"; arch = "linux-i686"; sha1 = "28e48822cc2977037db1493ddc06ef106a11e8bf"; }
-    { locale = "bg"; arch = "linux-x86_64"; sha1 = "1b891a9df513e9f099f68fe2f0429b00bd12505b"; }
+    { locale = "bg"; arch = "linux-x86_64"; sha1 = "7b59deab0fd2b35d2ec087947f5c5a85bd70cf4a"; }
-    { locale = "bn-BD"; arch = "linux-i686"; sha1 = "0ad965be5c9ce5468e65667dcb0390a9afabd7b0"; }
+    { locale = "bn-BD"; arch = "linux-i686"; sha1 = "4c5bff7f6b3f664138a881479701cfea81ff60b8"; }
-    { locale = "bn-BD"; arch = "linux-x86_64"; sha1 = "301b659d5689de81ca60f7092176efaf48a50a18"; }
+    { locale = "bn-BD"; arch = "linux-x86_64"; sha1 = "3a659a5335d4b215ac2a0452264a61c702420c60"; }
-    { locale = "bn-IN"; arch = "linux-i686"; sha1 = "df99d9e80ebda8c146724f893ae2de77cf2518ab"; }
+    { locale = "bn-IN"; arch = "linux-i686"; sha1 = "a641b87769d90db720fc5294ab06f6dae2a597d3"; }
-    { locale = "bn-IN"; arch = "linux-x86_64"; sha1 = "4b4cc8e588a518af8a922d32163249af115fac42"; }
+    { locale = "bn-IN"; arch = "linux-x86_64"; sha1 = "1c1e47f4012c765ce96e4d2581e47f9b61344370"; }
-    { locale = "br"; arch = "linux-i686"; sha1 = "39976bf6a0c7bdfc1832a6f2c48e92324f4a6727"; }
+    { locale = "br"; arch = "linux-i686"; sha1 = "0491cf87e0815079eba8f57ae8c6f392d2e5251f"; }
-    { locale = "br"; arch = "linux-x86_64"; sha1 = "ea66a36ea70486f39c7cf7abbf637d37c04d32ef"; }
+    { locale = "br"; arch = "linux-x86_64"; sha1 = "abe34c6d4998ac2f4e2d1f2d4655f8ace9f0a857"; }
-    { locale = "bs"; arch = "linux-i686"; sha1 = "71eeeccd5bf5757d6ec4f9e1442c4fcfbf312d79"; }
+    { locale = "bs"; arch = "linux-i686"; sha1 = "40f2eb7fd72f4a05ee47cb136c73e75f139e9ed1"; }
-    { locale = "bs"; arch = "linux-x86_64"; sha1 = "10911d28d56d4083aea7eb2174d0d7dd78772215"; }
+    { locale = "bs"; arch = "linux-x86_64"; sha1 = "3a737c33921af68621d906702fb1298f5bf161f9"; }
-    { locale = "ca"; arch = "linux-i686"; sha1 = "434532ff2cca7a0401a7aed8753d1c5578e98c1a"; }
+    { locale = "ca"; arch = "linux-i686"; sha1 = "46cf625eea24a819d93741f2d11bc315a21361cc"; }
-    { locale = "ca"; arch = "linux-x86_64"; sha1 = "2a6aaed334856d06ce8c426282f3345d9bcaa435"; }
+    { locale = "ca"; arch = "linux-x86_64"; sha1 = "be84a0a6e32fbbb977b654f195064add8881a853"; }
-    { locale = "cs"; arch = "linux-i686"; sha1 = "e2445b13ab680f5dfd5d67e4e796170fbd6bd120"; }
+    { locale = "cs"; arch = "linux-i686"; sha1 = "ce507b8801646f3156bb38776c17dd7955ba9678"; }
-    { locale = "cs"; arch = "linux-x86_64"; sha1 = "ef1df48bd465a3b05d1046bf4627c1ae4f60ee06"; }
+    { locale = "cs"; arch = "linux-x86_64"; sha1 = "5b1599282512c66a8619202b494042dbe959adc0"; }
-    { locale = "cy"; arch = "linux-i686"; sha1 = "f95974e478e2d0fec7400424a33202e1e2b1e5b9"; }
+    { locale = "cy"; arch = "linux-i686"; sha1 = "9eb6a71214122e02e7e94b526b4ff1e0bad71680"; }
-    { locale = "cy"; arch = "linux-x86_64"; sha1 = "c521abab2bffe24863c087f02d57ffafae47def7"; }
+    { locale = "cy"; arch = "linux-x86_64"; sha1 = "4f21da86ab876bf916157fe7e1fd84502e8fb923"; }
-    { locale = "da"; arch = "linux-i686"; sha1 = "f11b050caae304029ccf23ce2906fe18115adbc8"; }
+    { locale = "da"; arch = "linux-i686"; sha1 = "d175b55ebf05905531f28a74f9a075c4dd4467d1"; }
-    { locale = "da"; arch = "linux-x86_64"; sha1 = "800e0f3b649c9a03d4e9cd2a4ccd8f14bbb5ed95"; }
+    { locale = "da"; arch = "linux-x86_64"; sha1 = "62039edbacf4d5ed9b32f5ef2d993c0b6fc7a0cc"; }
-    { locale = "de"; arch = "linux-i686"; sha1 = "b9502be9396e00b69946f0094c5939a8a57da64b"; }
+    { locale = "de"; arch = "linux-i686"; sha1 = "933cc29a7902f4de25fc593ffbaf6e62ccceb2fc"; }
-    { locale = "de"; arch = "linux-x86_64"; sha1 = "84fab2779bc055821afdb5d7ff45e3ffe95e2858"; }
+    { locale = "de"; arch = "linux-x86_64"; sha1 = "eb69a42286f7d4a7106ddd24ec0c1f1356101956"; }
-    { locale = "dsb"; arch = "linux-i686"; sha1 = "5eee946bc2182990b310ed57fbf527e82f93bc8b"; }
+    { locale = "dsb"; arch = "linux-i686"; sha1 = "6683f985caece486b068a3ddd85e732903b1f738"; }
-    { locale = "dsb"; arch = "linux-x86_64"; sha1 = "8b3219b071e836ecc4966e153ec0adb4e691de89"; }
+    { locale = "dsb"; arch = "linux-x86_64"; sha1 = "fd92cd5ab674762fce35fddc54b7dcdfa4829dcf"; }
-    { locale = "el"; arch = "linux-i686"; sha1 = "9759c69061d6419edb949c55f7e797302b477c78"; }
+    { locale = "el"; arch = "linux-i686"; sha1 = "91416a56f0221772a0f9691ad418602327d193e2"; }
-    { locale = "el"; arch = "linux-x86_64"; sha1 = "db5025d393a763c7cd4ed447d61b640ee77e7e79"; }
+    { locale = "el"; arch = "linux-x86_64"; sha1 = "ce89cdb9c8c88d7c4dcd089eef006b98171f5d04"; }
-    { locale = "en-GB"; arch = "linux-i686"; sha1 = "4fdc423d6d15bd6a14030a526ad7017fd5bdf937"; }
+    { locale = "en-GB"; arch = "linux-i686"; sha1 = "8322cad2eacba0c064eb9ef2f5cd1d426411c648"; }
-    { locale = "en-GB"; arch = "linux-x86_64"; sha1 = "0d8637f1ca6acfe494f963c936d8510c6c11f8bf"; }
+    { locale = "en-GB"; arch = "linux-x86_64"; sha1 = "c4102cc705610d7ad5b0cc530c600b2170f55419"; }
-    { locale = "en-US"; arch = "linux-i686"; sha1 = "e05722e42ea1d844d8fe40672026cacb19575ccf"; }
+    { locale = "en-US"; arch = "linux-i686"; sha1 = "571067007e0dff64095b8eeb760aec7f78f367fd"; }
-    { locale = "en-US"; arch = "linux-x86_64"; sha1 = "8143b339d0ceedaf797b49ca4b54bcc0c91925e3"; }
+    { locale = "en-US"; arch = "linux-x86_64"; sha1 = "64a0422e42cf1d19e558377d5ecee6536917b414"; }
-    { locale = "en-ZA"; arch = "linux-i686"; sha1 = "fac507eebec642fd50f248ac184dbde4538ad0bb"; }
+    { locale = "en-ZA"; arch = "linux-i686"; sha1 = "9f5611cd3043b1c267724b198ab04c16078b7818"; }
-    { locale = "en-ZA"; arch = "linux-x86_64"; sha1 = "2670a80c7ca5d5390df9fcee907afbe7a01f9f37"; }
+    { locale = "en-ZA"; arch = "linux-x86_64"; sha1 = "3a22150e16a12d8fba9d21cef0c8e7ac434edf35"; }
-    { locale = "eo"; arch = "linux-i686"; sha1 = "a134117ddd446b63f325a38f818a80921adb5b2f"; }
+    { locale = "eo"; arch = "linux-i686"; sha1 = "6502874b051c281e565cd0e0953698b88b69e5f5"; }
-    { locale = "eo"; arch = "linux-x86_64"; sha1 = "5b073a912221e8e734ba17ecfe735d820f5febf3"; }
+    { locale = "eo"; arch = "linux-x86_64"; sha1 = "3bdbcf6d324c43fbf7f3c71243df10a760f7fec2"; }
-    { locale = "es-AR"; arch = "linux-i686"; sha1 = "0e518d9fe0644a6ada9463ae14fa67c2c49bfd5f"; }
+    { locale = "es-AR"; arch = "linux-i686"; sha1 = "83edce65b276d9989e66d11bfd4e9c1c87955364"; }
-    { locale = "es-AR"; arch = "linux-x86_64"; sha1 = "fa33935aa4abb696ea9a399cff0c1dc29beffab0"; }
+    { locale = "es-AR"; arch = "linux-x86_64"; sha1 = "6281d1d560fb7dd1a8bc1af0be046491a4ee4382"; }
-    { locale = "es-CL"; arch = "linux-i686"; sha1 = "3c7df32ed5d2570e62e35dcb9f9d91588d7584d2"; }
+    { locale = "es-CL"; arch = "linux-i686"; sha1 = "d394d731f7cde2b17bafd9d9d4cb6819fdbcbfd5"; }
-    { locale = "es-CL"; arch = "linux-x86_64"; sha1 = "ced3821f7e334b2f0d5b5115cc04cbaf5bcdbe15"; }
+    { locale = "es-CL"; arch = "linux-x86_64"; sha1 = "b969107e5e840e1701672b3d5ba81ae3e53889be"; }
-    { locale = "es-ES"; arch = "linux-i686"; sha1 = "6af75a3e116162591dd6a15c8903ee5182afe03b"; }
+    { locale = "es-ES"; arch = "linux-i686"; sha1 = "a9c801142df7a932b2eba4d8f540b2579d0fabeb"; }
-    { locale = "es-ES"; arch = "linux-x86_64"; sha1 = "fa1ddbc5a3d9bd7c9cc424fe6c5e94c87d51eab2"; }
+    { locale = "es-ES"; arch = "linux-x86_64"; sha1 = "96cb7bb0bd079d683304168b2b14255a1217fa92"; }
-    { locale = "es-MX"; arch = "linux-i686"; sha1 = "8110bdf4c8657e88f71b8a6bec1ca92f2eac0538"; }
+    { locale = "es-MX"; arch = "linux-i686"; sha1 = "c233e4da88f3fcc5eb5f2c45766c9197b5910dfc"; }
-    { locale = "es-MX"; arch = "linux-x86_64"; sha1 = "30df4777fde7eba8724fab002cb7387203eeb82e"; }
+    { locale = "es-MX"; arch = "linux-x86_64"; sha1 = "e04973316a340325888f0f2e06590773f81a7cf0"; }
-    { locale = "et"; arch = "linux-i686"; sha1 = "2f16472e5cd030a14e3cfa761a32c0ef5ffd395e"; }
+    { locale = "et"; arch = "linux-i686"; sha1 = "22c59e40b39aefe356e8b5305ce720d4a2cdd0b7"; }
-    { locale = "et"; arch = "linux-x86_64"; sha1 = "19a96b008a49e7a223ea2463edab7cda504e2ba5"; }
+    { locale = "et"; arch = "linux-x86_64"; sha1 = "74256cbb8a76d835887727aa01f6e6a22936a43e"; }
-    { locale = "eu"; arch = "linux-i686"; sha1 = "786db5ad8d92324d3086f7b2b8da71767829a8f2"; }
+    { locale = "eu"; arch = "linux-i686"; sha1 = "fa14a31fe15106f224df47a62c3e5ec16da1cb95"; }
-    { locale = "eu"; arch = "linux-x86_64"; sha1 = "31273f797cb90615032611d2d86cac8cf6d28994"; }
+    { locale = "eu"; arch = "linux-x86_64"; sha1 = "c8b6216d448f6f192e584ceb81fb22e5ac79a280"; }
-    { locale = "fa"; arch = "linux-i686"; sha1 = "e2980430f1cd25edb401862b83fb49f2d730ff5e"; }
+    { locale = "fa"; arch = "linux-i686"; sha1 = "a1c67f4bec3f46de3cf6297e8a711d55f8189e3b"; }
-    { locale = "fa"; arch = "linux-x86_64"; sha1 = "dae850824c3eaaa31fec4aad19e38e2073d96f10"; }
+    { locale = "fa"; arch = "linux-x86_64"; sha1 = "70d3b99652e8c690bbd05af7af9c65eeb780d455"; }
-    { locale = "ff"; arch = "linux-i686"; sha1 = "f865672eaa7815f3bb527baf3946c62c01c76dbb"; }
+    { locale = "ff"; arch = "linux-i686"; sha1 = "1f42b51648eb296dfc339982c331e7d63bfbbd96"; }
-    { locale = "ff"; arch = "linux-x86_64"; sha1 = "aa207b51d24ca275b0cbd5ba4cd93ce16a6bd28a"; }
+    { locale = "ff"; arch = "linux-x86_64"; sha1 = "bd176a2bda1246e15dbbfb1b068f6b196a0ce266"; }
-    { locale = "fi"; arch = "linux-i686"; sha1 = "30ef856ecdadeba171977859324f010d441a51e9"; }
+    { locale = "fi"; arch = "linux-i686"; sha1 = "2cd7757360efeca608b8a9b4b56c04f9aca89a79"; }
-    { locale = "fi"; arch = "linux-x86_64"; sha1 = "3ebbabc2346eeac01aaf88e91fd1fd55538c0770"; }
+    { locale = "fi"; arch = "linux-x86_64"; sha1 = "dc130d8ab31c739e4406f8cc72dc32d3795db208"; }
-    { locale = "fr"; arch = "linux-i686"; sha1 = "4dd376ccc6811d46be052fcf1aab82e50a3e0999"; }
+    { locale = "fr"; arch = "linux-i686"; sha1 = "6dccfb2944006379271c308fa31d8f6a4bd6bb3d"; }
-    { locale = "fr"; arch = "linux-x86_64"; sha1 = "f6409e276b400ecaa689d92fe5387662d1b5f2ab"; }
+    { locale = "fr"; arch = "linux-x86_64"; sha1 = "aca6deabd521e29611fccbdeca3bf036a2239c1d"; }
-    { locale = "fy-NL"; arch = "linux-i686"; sha1 = "751cd1092a58a8b6cde5d9e80790715d249ac11b"; }
+    { locale = "fy-NL"; arch = "linux-i686"; sha1 = "4ffb659a341308a097ad26f1873ae243e581bba9"; }
-    { locale = "fy-NL"; arch = "linux-x86_64"; sha1 = "3cc75c55220f81b0291c16d2f237cb6a2d2609f0"; }
+    { locale = "fy-NL"; arch = "linux-x86_64"; sha1 = "340caff2afeb8f9f01c84f780b6aef079ab257e6"; }
-    { locale = "ga-IE"; arch = "linux-i686"; sha1 = "2bfa436c566a4e2f0fe7847feccf3c157e026d4b"; }
+    { locale = "ga-IE"; arch = "linux-i686"; sha1 = "7adb1a44e0367b570437fdeae9f04c6f94f6702f"; }
-    { locale = "ga-IE"; arch = "linux-x86_64"; sha1 = "0b2ce0b246e107d99b13e497c64ad169e85eec51"; }
+    { locale = "ga-IE"; arch = "linux-x86_64"; sha1 = "d427e6ca8287d97b27949ccb412207ef48d0cebe"; }
-    { locale = "gd"; arch = "linux-i686"; sha1 = "3afc8ad8747bfcbc5a7e6f2e6de37cbefb3967e7"; }
+    { locale = "gd"; arch = "linux-i686"; sha1 = "2741c8bdcfad1edc36968bfac70c71b1a2837df4"; }
-    { locale = "gd"; arch = "linux-x86_64"; sha1 = "5bec8bcc0a67f304485b1efa7be5d952ce7985ce"; }
+    { locale = "gd"; arch = "linux-x86_64"; sha1 = "430817ee768fd76dd29e76ae00488d6397f7b6f1"; }
-    { locale = "gl"; arch = "linux-i686"; sha1 = "8fa3dfdc0d2da19f6c98dc76363c9e0d9d10f978"; }
+    { locale = "gl"; arch = "linux-i686"; sha1 = "725c194c1e08293b44cbeb2a6791f4340a773b81"; }
-    { locale = "gl"; arch = "linux-x86_64"; sha1 = "4345cf5673267fb41c2c38f5fb92a3b0a9208cf0"; }
+    { locale = "gl"; arch = "linux-x86_64"; sha1 = "611e5f92796707379a9fd60ade840896eac4eabd"; }
-    { locale = "gu-IN"; arch = "linux-i686"; sha1 = "e57883626a22d3935716417194e78a689c5535c2"; }
+    { locale = "gu-IN"; arch = "linux-i686"; sha1 = "720ee20fa7a74dc321ab7fa8a95732ff2e9e5250"; }
-    { locale = "gu-IN"; arch = "linux-x86_64"; sha1 = "be6095129ee3f3fc80f6705594a53c6ced996cb2"; }
+    { locale = "gu-IN"; arch = "linux-x86_64"; sha1 = "778496274c362d9d854b1cc6ac9b1806ce8e708c"; }
-    { locale = "he"; arch = "linux-i686"; sha1 = "7ca70c0648b2f3928c1dc33288b48f488cf1d19b"; }
+    { locale = "he"; arch = "linux-i686"; sha1 = "f31729cecde50073e49d1387356c13060cf50c61"; }
-    { locale = "he"; arch = "linux-x86_64"; sha1 = "f2eb7c6c33e8b4bc9a03bee587de4fe5b442ac95"; }
+    { locale = "he"; arch = "linux-x86_64"; sha1 = "72e9c8c602c403d16e4d60fbeb1bf5a415aabf25"; }
-    { locale = "hi-IN"; arch = "linux-i686"; sha1 = "32b242a2c6865fdad63ba4de701c566ffb33ef99"; }
+    { locale = "hi-IN"; arch = "linux-i686"; sha1 = "f2498d503005d0a1d7432bbc5a981be350421cfa"; }
-    { locale = "hi-IN"; arch = "linux-x86_64"; sha1 = "f83ceece81a71e6fb1494863b2970b2dc384d4c4"; }
+    { locale = "hi-IN"; arch = "linux-x86_64"; sha1 = "b003f7d484ec995fe4f10808d1141e20c6ed9bfc"; }
-    { locale = "hr"; arch = "linux-i686"; sha1 = "77f9c855e5f728dcd3b4ff27ed656aa67217dd35"; }
+    { locale = "hr"; arch = "linux-i686"; sha1 = "de191039fb5acb5ca9ab556ef4ef6b6211b5b697"; }
-    { locale = "hr"; arch = "linux-x86_64"; sha1 = "f48bcf72d740f4a34bb7f888d977d4d39c141567"; }
+    { locale = "hr"; arch = "linux-x86_64"; sha1 = "d5cd94ddd0b301dc0edf2f64bafa678864aa4595"; }
-    { locale = "hsb"; arch = "linux-i686"; sha1 = "2db09bd59f3761bfdba8bad565e27e1b42a93727"; }
+    { locale = "hsb"; arch = "linux-i686"; sha1 = "cf66178d0a18fcabcde897d4ba869da8d82fe999"; }
-    { locale = "hsb"; arch = "linux-x86_64"; sha1 = "99e0f119e5e79df5b20f686dd065fee5bda4511f"; }
+    { locale = "hsb"; arch = "linux-x86_64"; sha1 = "b83bbf3fb4d3aabdc961b9ef669dd2aa9f05ee52"; }
-    { locale = "hu"; arch = "linux-i686"; sha1 = "0d601a679675c517a535bf706e7cbad9882a5d7c"; }
+    { locale = "hu"; arch = "linux-i686"; sha1 = "0550d016ad044fdac193beee822171a0d891a34d"; }
-    { locale = "hu"; arch = "linux-x86_64"; sha1 = "dbd3d180342d0946ab857bdd8d6bc30373e991b5"; }
+    { locale = "hu"; arch = "linux-x86_64"; sha1 = "4f5916dac9d8efb333e2ad21370bd8a3d961b68f"; }
-    { locale = "hy-AM"; arch = "linux-i686"; sha1 = "5f3e01cf375af38bee7014ff21fe75daf4e27071"; }
+    { locale = "hy-AM"; arch = "linux-i686"; sha1 = "b72515f5e194a4c543c8a6487c858abe07e24db0"; }
-    { locale = "hy-AM"; arch = "linux-x86_64"; sha1 = "a78fbb1cc4e6d10056cc7a3ccecf4750979c5953"; }
+    { locale = "hy-AM"; arch = "linux-x86_64"; sha1 = "aef7fdc2f59edbde165c4e98de10f7e20e203f9d"; }
-    { locale = "id"; arch = "linux-i686"; sha1 = "7efc031614247ddb93a27531d3fa1d19ce21d516"; }
+    { locale = "id"; arch = "linux-i686"; sha1 = "1db4444dbc9479cad1122925a9af73e358e09cbf"; }
-    { locale = "id"; arch = "linux-x86_64"; sha1 = "e409bb73aad373791d83569dfb4a475bc617eac8"; }
+    { locale = "id"; arch = "linux-x86_64"; sha1 = "a826b23b1783fff4d51451284301610cd26b578f"; }
-    { locale = "is"; arch = "linux-i686"; sha1 = "0e5c4e9173379457b6c8edd1812121fce84cda07"; }
+    { locale = "is"; arch = "linux-i686"; sha1 = "2943bbe86e052280d610cbf3adceb89e949615b3"; }
-    { locale = "is"; arch = "linux-x86_64"; sha1 = "dc6cbffde61b6188080e458b4a31b634f4c0434c"; }
+    { locale = "is"; arch = "linux-x86_64"; sha1 = "c1b0bb2f22c11974e5e3a2d9b221601da07a858d"; }
-    { locale = "it"; arch = "linux-i686"; sha1 = "d75318f8421f634eeacf15aaa91a28261324044c"; }
+    { locale = "it"; arch = "linux-i686"; sha1 = "2e3568872301c3897e83ee5692638a76fbef15fc"; }
-    { locale = "it"; arch = "linux-x86_64"; sha1 = "b024d0e3498c3dd32757997a273d9f1051ccd47f"; }
+    { locale = "it"; arch = "linux-x86_64"; sha1 = "5af762e2487171f6b41a6c1654b672c86e6964f8"; }
-    { locale = "ja"; arch = "linux-i686"; sha1 = "f74c1c567582a207efb501892845d1c28d7b8751"; }
+    { locale = "ja"; arch = "linux-i686"; sha1 = "40c042713ee07d4d375327515c7425d6733b926f"; }
-    { locale = "ja"; arch = "linux-x86_64"; sha1 = "cb4151c0c1c6efa4c8ec5e4656de60b1abd65bac"; }
+    { locale = "ja"; arch = "linux-x86_64"; sha1 = "0dd2808378e870f553e02066f5ee78b11543e420"; }
-    { locale = "kk"; arch = "linux-i686"; sha1 = "1e9d43eedb0bab9f428a80ee3c2721a944961562"; }
+    { locale = "kk"; arch = "linux-i686"; sha1 = "294eb8f7345f6baffc183605988bd1a57bbdd880"; }
-    { locale = "kk"; arch = "linux-x86_64"; sha1 = "18a55f6ea18663922052411ebaed18c16c9f3050"; }
+    { locale = "kk"; arch = "linux-x86_64"; sha1 = "fbd9524ac8c1286e4c4bcf77efa8c9bf86d03948"; }
-    { locale = "km"; arch = "linux-i686"; sha1 = "f4f6af5a09072e004e7c8db7a10edc9ab8d474c3"; }
+    { locale = "km"; arch = "linux-i686"; sha1 = "09b63d181398b1ff6a83849aa209952c0c5ce9b0"; }
-    { locale = "km"; arch = "linux-x86_64"; sha1 = "43694f66fea7caf9b2f4d976564c00a99f7092e7"; }
+    { locale = "km"; arch = "linux-x86_64"; sha1 = "d7478ba2f1b59ef83b1447789034bbdca78fab77"; }
-    { locale = "kn"; arch = "linux-i686"; sha1 = "3a94f8a0cadc729e97bb6a7b273b02d79c9012dd"; }
+    { locale = "kn"; arch = "linux-i686"; sha1 = "72e1e6e225790e4438da20cd2f69dce6e455fe53"; }
-    { locale = "kn"; arch = "linux-x86_64"; sha1 = "ec51644f69354aebac67f36e387d1a5b45d0dfa8"; }
+    { locale = "kn"; arch = "linux-x86_64"; sha1 = "3ef27144bb335d7a3f168bbadc0592a5fd554d78"; }
-    { locale = "ko"; arch = "linux-i686"; sha1 = "599de739c08799b8e4082190a53de3ae0dfc6617"; }
+    { locale = "ko"; arch = "linux-i686"; sha1 = "5ef7f628aeb20d20ffa01316c234afafc2a6e2c7"; }
-    { locale = "ko"; arch = "linux-x86_64"; sha1 = "338825804362d34911beaad146ca6d104bc69788"; }
+    { locale = "ko"; arch = "linux-x86_64"; sha1 = "cbf6a8d123e98ef1b99221083c743e962ccec58c"; }
-    { locale = "lij"; arch = "linux-i686"; sha1 = "f2a6112a81043cc9608594cd56680a2e075dfd36"; }
+    { locale = "lij"; arch = "linux-i686"; sha1 = "46f34520fc023f9d20781c9d5f13c683bc7f86bd"; }
-    { locale = "lij"; arch = "linux-x86_64"; sha1 = "8650de76d89abdcba3d0e4bba8c2b90533e54ce6"; }
+    { locale = "lij"; arch = "linux-x86_64"; sha1 = "c07c7ca26034e53d29e868315201605b95d83e65"; }
-    { locale = "lt"; arch = "linux-i686"; sha1 = "0ea6e49b51dfd12150334b6023e26419716cdb65"; }
+    { locale = "lt"; arch = "linux-i686"; sha1 = "8ab47bda33eeec6d135049f775f06478480394b2"; }
-    { locale = "lt"; arch = "linux-x86_64"; sha1 = "a16c9e916462e3780159677528ffa35b9569a80b"; }
+    { locale = "lt"; arch = "linux-x86_64"; sha1 = "82b0c898ebf2e3714763640f2cabd00dd14c9078"; }
-    { locale = "lv"; arch = "linux-i686"; sha1 = "0255634959aa739ae6807a1c249e4c78f51f8316"; }
+    { locale = "lv"; arch = "linux-i686"; sha1 = "1dba01bbf772b38c67b90d5e68f7e1a5c20f0b02"; }
-    { locale = "lv"; arch = "linux-x86_64"; sha1 = "ada8dc2d3ea22c2afffac88b581dfc72a27f2f89"; }
+    { locale = "lv"; arch = "linux-x86_64"; sha1 = "ade71dce8572628f99bf59132e8c0efd01a77016"; }
-    { locale = "mai"; arch = "linux-i686"; sha1 = "fa932b9e6d9798753e7b89b91a5db6565fe2b695"; }
+    { locale = "mai"; arch = "linux-i686"; sha1 = "486411e211d5505ca696a936db64682e04d43392"; }
-    { locale = "mai"; arch = "linux-x86_64"; sha1 = "8a9252658d549d2cbc764197265275461db605b6"; }
+    { locale = "mai"; arch = "linux-x86_64"; sha1 = "0239e14c627499220518d1f9a3f643315c1846c6"; }
-    { locale = "mk"; arch = "linux-i686"; sha1 = "641c882870dfa7fb23bed9c07def585477ff459d"; }
+    { locale = "mk"; arch = "linux-i686"; sha1 = "d7f314a0caec40e367faa29e071a81da2e50d802"; }
-    { locale = "mk"; arch = "linux-x86_64"; sha1 = "4b68d11f2a613bc8350d37dae899c2c65afe5dc9"; }
+    { locale = "mk"; arch = "linux-x86_64"; sha1 = "4ad6c120360f90dea82282a6891419f17d0b5068"; }
-    { locale = "ml"; arch = "linux-i686"; sha1 = "f636e9b8d5e268f7c124ef3f35f6933de83fed62"; }
+    { locale = "ml"; arch = "linux-i686"; sha1 = "14a6534cba54ff08695b4322f6566a375f9cb713"; }
-    { locale = "ml"; arch = "linux-x86_64"; sha1 = "ed98b20d8eb88a73b119c3a1435904f69529eabd"; }
+    { locale = "ml"; arch = "linux-x86_64"; sha1 = "badad6dfe2d794d508c4f8b061ef2a91209a8c32"; }
-    { locale = "mr"; arch = "linux-i686"; sha1 = "d5ef4d4dbf4d0b63f526d102e95f28078096032a"; }
+    { locale = "mr"; arch = "linux-i686"; sha1 = "1602ac0a3ac5c8c49a370a64d450aa06b490c8b5"; }
-    { locale = "mr"; arch = "linux-x86_64"; sha1 = "8e92bf456593359afb256c387578042c6085916f"; }
+    { locale = "mr"; arch = "linux-x86_64"; sha1 = "a8108ecee8557be024c35818a99c30dfd811da83"; }
-    { locale = "ms"; arch = "linux-i686"; sha1 = "d94320d0c8aee23b6d3c603664caab45180b6069"; }
+    { locale = "ms"; arch = "linux-i686"; sha1 = "02952ca95545f83231b36e9c05adc51ab955f9e5"; }
-    { locale = "ms"; arch = "linux-x86_64"; sha1 = "b9fdc0248d9656b3555c475643c7e07ca3c6b222"; }
+    { locale = "ms"; arch = "linux-x86_64"; sha1 = "164c31da7ad4272500b8906ee5d29c69ac285618"; }
-    { locale = "nb-NO"; arch = "linux-i686"; sha1 = "d49719c255a43151ed5e94d7024c39914ea27ec7"; }
+    { locale = "nb-NO"; arch = "linux-i686"; sha1 = "c09a24b8f00409c7c93686586b091bfc33f22e52"; }
-    { locale = "nb-NO"; arch = "linux-x86_64"; sha1 = "f2b1f00254ef350f817b5c1958384a9f5144f83e"; }
+    { locale = "nb-NO"; arch = "linux-x86_64"; sha1 = "9124e6b86f947dd4a7d2d7c9b8860dd28647d2f4"; }
-    { locale = "nl"; arch = "linux-i686"; sha1 = "cc54828041f57f623de691a49e4bb055bd059c54"; }
+    { locale = "nl"; arch = "linux-i686"; sha1 = "fb2dbbda6817d8fbcf9870a3233396051ce7c67f"; }
-    { locale = "nl"; arch = "linux-x86_64"; sha1 = "5728a30bf53644a3b13bc00f5652e067cbe9100b"; }
+    { locale = "nl"; arch = "linux-x86_64"; sha1 = "bbf1e039a02556df8c68d6d49aa30f821bfdfae9"; }
-    { locale = "nn-NO"; arch = "linux-i686"; sha1 = "0f69ddbd963a19d104ee96589c405c55aa7140b2"; }
+    { locale = "nn-NO"; arch = "linux-i686"; sha1 = "9ff1ae86d0989f81ae3324e9ccbda2d2069281be"; }
-    { locale = "nn-NO"; arch = "linux-x86_64"; sha1 = "26af2b8cf928fedb5442c5257289f5e38c4f8432"; }
+    { locale = "nn-NO"; arch = "linux-x86_64"; sha1 = "2be8ac327c7aa90abb38ee6ccfb0181194d5592e"; }
-    { locale = "or"; arch = "linux-i686"; sha1 = "2da0842ebe8ae5a8e80061d0fc159a5d408c4464"; }
+    { locale = "or"; arch = "linux-i686"; sha1 = "a6ff7bf9c96b1baa2d22e897d1083c9907300de5"; }
-    { locale = "or"; arch = "linux-x86_64"; sha1 = "b7cc446178a493589d8654236f6e9113aee48455"; }
+    { locale = "or"; arch = "linux-x86_64"; sha1 = "4ab6eff3bf8c99f3404a313f54ea3e0d48842d9f"; }
-    { locale = "pa-IN"; arch = "linux-i686"; sha1 = "dd81dc403366a7fd0d395338878b8b8fcb858365"; }
+    { locale = "pa-IN"; arch = "linux-i686"; sha1 = "7ed256e6b3a5aec16eb0c5d3cab8c4cd5bf07999"; }
-    { locale = "pa-IN"; arch = "linux-x86_64"; sha1 = "2ca8cc4c491f0ded4cef8e3826a3c1419a580051"; }
+    { locale = "pa-IN"; arch = "linux-x86_64"; sha1 = "da6511f215e206df0fe450225f2b2e4d8d541838"; }
-    { locale = "pl"; arch = "linux-i686"; sha1 = "468d45392126ac7852012ed43d76d83e238dc2ac"; }
+    { locale = "pl"; arch = "linux-i686"; sha1 = "d3df1cc8647d6dc8576fcfd0c6a1e28a28c0ce8a"; }
-    { locale = "pl"; arch = "linux-x86_64"; sha1 = "ed20af16563516671f32bb588728e90f29955964"; }
+    { locale = "pl"; arch = "linux-x86_64"; sha1 = "af999c2bcb0d865d38e336eaad5d6766fed291cc"; }
-    { locale = "pt-BR"; arch = "linux-i686"; sha1 = "b197bca20e972ce2f8851dc128fb212a7d293454"; }
+    { locale = "pt-BR"; arch = "linux-i686"; sha1 = "7369a73558f6df1218dac14c3259e08cfa80ac52"; }
-    { locale = "pt-BR"; arch = "linux-x86_64"; sha1 = "2cd05329c3612330fdc1354fe651cc13ab8d9a5f"; }
+    { locale = "pt-BR"; arch = "linux-x86_64"; sha1 = "bd21ac0aca091de913201d2df5f914b9eeb83c8d"; }
-    { locale = "pt-PT"; arch = "linux-i686"; sha1 = "1087ba6ba17aa102888e929ccf7acc6b2476e447"; }
+    { locale = "pt-PT"; arch = "linux-i686"; sha1 = "8b9a5cf1259a824edb54d4db9aa7db3637ab041a"; }
-    { locale = "pt-PT"; arch = "linux-x86_64"; sha1 = "aa1907c10e980a8466c1604519ffa08aaabb2d7c"; }
+    { locale = "pt-PT"; arch = "linux-x86_64"; sha1 = "f8004907aac63d8e9e4196424aa94db4fa1ff8c0"; }
-    { locale = "rm"; arch = "linux-i686"; sha1 = "fdb717a0f40b94a53077ff036a55c0f93b61a2cc"; }
+    { locale = "rm"; arch = "linux-i686"; sha1 = "3403690013738c55f87c56d52ed8f9923a496b42"; }
-    { locale = "rm"; arch = "linux-x86_64"; sha1 = "af10206080a7ad21e5fda9cdf66a734ee33b07ac"; }
+    { locale = "rm"; arch = "linux-x86_64"; sha1 = "3b00a49b87fa900ecea9fdedce1b49d2560a81dd"; }
-    { locale = "ro"; arch = "linux-i686"; sha1 = "f08c67c6ea2a63c216f944453b4ce8b36f4ed840"; }
+    { locale = "ro"; arch = "linux-i686"; sha1 = "6e5f1e0460792c080aa9ac82d3be69c047862203"; }
-    { locale = "ro"; arch = "linux-x86_64"; sha1 = "07efb37804ffab35f117eb32f9f645b554ac1dd8"; }
+    { locale = "ro"; arch = "linux-x86_64"; sha1 = "2f09d74e5e39f9016ab5594f95f61b369cd6467c"; }
-    { locale = "ru"; arch = "linux-i686"; sha1 = "874f588d7ac5554ae4e8e134bfc272897f839f97"; }
+    { locale = "ru"; arch = "linux-i686"; sha1 = "df7b6c0806b27ade147dc6d42d181d599cc2c28b"; }
-    { locale = "ru"; arch = "linux-x86_64"; sha1 = "af64b6eb8d33d6bd78ce86e4785be50babe5c919"; }
+    { locale = "ru"; arch = "linux-x86_64"; sha1 = "1dedbe2a377cee5b32ca4aa0ec54eb24261238b0"; }
-    { locale = "si"; arch = "linux-i686"; sha1 = "672523b996c7021e06b4a713f7ac1239a3b1800f"; }
+    { locale = "si"; arch = "linux-i686"; sha1 = "0309c2c97affcfa4c0d155eec2f9f4f586c940eb"; }
-    { locale = "si"; arch = "linux-x86_64"; sha1 = "2e594b56230c079a9f1735e9bab9dc4a9d9e31ab"; }
+    { locale = "si"; arch = "linux-x86_64"; sha1 = "890a17e8f1d771e12d3e9c03ee0c8069654dae66"; }
-    { locale = "sk"; arch = "linux-i686"; sha1 = "6edffa576d9829673c65400d4570b34dc787faad"; }
+    { locale = "sk"; arch = "linux-i686"; sha1 = "73fbaabb4644ae3726681bd6c49f6efa25a74a1a"; }
-    { locale = "sk"; arch = "linux-x86_64"; sha1 = "7b506fedbf3a25cd1ed54b05c9b5cb7b8c237ad8"; }
+    { locale = "sk"; arch = "linux-x86_64"; sha1 = "573ba7d8526147e47f49fedb5f8c2e3bf0aaee82"; }
-    { locale = "sl"; arch = "linux-i686"; sha1 = "e8d1fea389b7cb75b7ccbf22ad5b8691e9bf1b6a"; }
+    { locale = "sl"; arch = "linux-i686"; sha1 = "abacb4f8ad9ed7eb42d5bbf3ebdce4136557bff5"; }
-    { locale = "sl"; arch = "linux-x86_64"; sha1 = "20163798733ee36ffa510987b18d1eb67b82aca1"; }
+    { locale = "sl"; arch = "linux-x86_64"; sha1 = "cd1dc2a385e1911b5eaf69bc0cab13f257d8f68d"; }
-    { locale = "son"; arch = "linux-i686"; sha1 = "9076d0e9de6adb7fbd26dbd3cd89dd5728939aab"; }
+    { locale = "son"; arch = "linux-i686"; sha1 = "5c1aff5bbf858e1e7f6fa2c2d996a396b8710124"; }
-    { locale = "son"; arch = "linux-x86_64"; sha1 = "352aeb9f5ccb1e3bb87c8e47f93e96a049991412"; }
+    { locale = "son"; arch = "linux-x86_64"; sha1 = "a6d7e023615936b0d61e956a4dadb6431febaa0c"; }
-    { locale = "sq"; arch = "linux-i686"; sha1 = "838c4c525a9f93117704851ad81b2c199a9c28fc"; }
+    { locale = "sq"; arch = "linux-i686"; sha1 = "19a7147c4a7de505ef0106b121640f5f651d6dbd"; }
-    { locale = "sq"; arch = "linux-x86_64"; sha1 = "0139a064056da0ed1730fd768da1322a9661bca9"; }
+    { locale = "sq"; arch = "linux-x86_64"; sha1 = "f1120ddacc1d5a124512c405855a4014fc910034"; }
-    { locale = "sr"; arch = "linux-i686"; sha1 = "7d74018cd9948ee31e05b30ff1fb45a84d417494"; }
+    { locale = "sr"; arch = "linux-i686"; sha1 = "d21616842495521d3b71877ff2b694e019a4c2c2"; }
-    { locale = "sr"; arch = "linux-x86_64"; sha1 = "85c43e2359f444faf111efd83fb0dc3e1b0edb48"; }
+    { locale = "sr"; arch = "linux-x86_64"; sha1 = "43b9236a33a803fc0b0dd41cef93a5bf9fd91472"; }
-    { locale = "sv-SE"; arch = "linux-i686"; sha1 = "bc95ee926f82aba58691d923eb4cb963aa4cb64a"; }
+    { locale = "sv-SE"; arch = "linux-i686"; sha1 = "17e06ab17369c234bef72b1a284bef39d5810671"; }
-    { locale = "sv-SE"; arch = "linux-x86_64"; sha1 = "7c8946d6180e2c48a80958b6a790bf6c9231591e"; }
+    { locale = "sv-SE"; arch = "linux-x86_64"; sha1 = "8f8e2cb6acd475d7d75116c6494ab237b9531364"; }
-    { locale = "ta"; arch = "linux-i686"; sha1 = "dfaad8f934869d714c94a95a775bcdcd67fda3c4"; }
+    { locale = "ta"; arch = "linux-i686"; sha1 = "77fb9f32965af6a70275fbca308caf5bf88c3c8e"; }
-    { locale = "ta"; arch = "linux-x86_64"; sha1 = "5523c6df4e2b03ae71c865aabe6bb0dd0446fc87"; }
+    { locale = "ta"; arch = "linux-x86_64"; sha1 = "4a65de127708cbee44cc7238d14b9c0942d2673b"; }
-    { locale = "te"; arch = "linux-i686"; sha1 = "7a61ca88c832af3d15f197ba01d66c6fc43465d3"; }
+    { locale = "te"; arch = "linux-i686"; sha1 = "37a556dafc73e5de983cb62fdd545d01f32f698d"; }
-    { locale = "te"; arch = "linux-x86_64"; sha1 = "696823890791a05c6cf0230d1063a30012873090"; }
+    { locale = "te"; arch = "linux-x86_64"; sha1 = "2f4549d5ef998449b553a5d6f62d01d0313c6c95"; }
-    { locale = "th"; arch = "linux-i686"; sha1 = "4a3b932813ad0ab07f467a598e9e85b847bbe142"; }
+    { locale = "th"; arch = "linux-i686"; sha1 = "f6a10236fe0fcc9d11c3c5aee3bd84365bb06013"; }
-    { locale = "th"; arch = "linux-x86_64"; sha1 = "f847f3f0fb07f97053066f4b4314d93e9614e6cf"; }
+    { locale = "th"; arch = "linux-x86_64"; sha1 = "c2694589cc28b938fd7a079378e5fa99cdd7c98b"; }
-    { locale = "tr"; arch = "linux-i686"; sha1 = "59eee567e30cf6321c234c60002b416faec07aa4"; }
+    { locale = "tr"; arch = "linux-i686"; sha1 = "e7888b70a1a90613fd7d38a5a7735857385ae683"; }
-    { locale = "tr"; arch = "linux-x86_64"; sha1 = "b64dfdbdc75f87003f00883173084646a2617a29"; }
+    { locale = "tr"; arch = "linux-x86_64"; sha1 = "6ebef5649484bfda154c44232a9e3aae239c0990"; }
-    { locale = "uk"; arch = "linux-i686"; sha1 = "44e6b53ede97835847ed84defe4235cad513c653"; }
+    { locale = "uk"; arch = "linux-i686"; sha1 = "fe5ffb931bd7e5bb403f6aef6b879c2c9446721e"; }
-    { locale = "uk"; arch = "linux-x86_64"; sha1 = "bb6f84f58a19c6287bbc84e0e7101fcd48bd720a"; }
+    { locale = "uk"; arch = "linux-x86_64"; sha1 = "4b53989b554929b085b120788e1e30d5232dedb4"; }
-    { locale = "uz"; arch = "linux-i686"; sha1 = "1aec3ba9efd52a1f386e0bb075745a7c01c443a2"; }
+    { locale = "uz"; arch = "linux-i686"; sha1 = "bed269a3a7e3fc82d2fb1931632be9b04fe6b6da"; }
-    { locale = "uz"; arch = "linux-x86_64"; sha1 = "2ce2caccb638c0467ba1382a15146ef1cc33fa72"; }
+    { locale = "uz"; arch = "linux-x86_64"; sha1 = "786d51639cd7e952f4c73e9d91b50f6da0ba9242"; }
-    { locale = "vi"; arch = "linux-i686"; sha1 = "d8b339892c152254c89ec1d42ff9b7f128455aab"; }
+    { locale = "vi"; arch = "linux-i686"; sha1 = "db04c29c9038c856c67e99c77c0628c377bcd8f7"; }
-    { locale = "vi"; arch = "linux-x86_64"; sha1 = "e4503686f2a997e1c793ef8e3c80bccd3dc0e2f0"; }
+    { locale = "vi"; arch = "linux-x86_64"; sha1 = "d9525ad0b0069ae05cad173ab567198b67fc13dc"; }
-    { locale = "xh"; arch = "linux-i686"; sha1 = "d130fae691b91a1f1f7d15ca84f643ccf299b0e3"; }
+    { locale = "xh"; arch = "linux-i686"; sha1 = "2a8bbe15f2b2b242e9787704e542a6c0a9ed93bc"; }
-    { locale = "xh"; arch = "linux-x86_64"; sha1 = "18b5d09571f4db7b18dbbdb3f3c29c80480a16aa"; }
+    { locale = "xh"; arch = "linux-x86_64"; sha1 = "532e224a166addee7b6068bbcee7e6c0b1c3f6df"; }
-    { locale = "zh-CN"; arch = "linux-i686"; sha1 = "303816f99659e2bbb8ecc4f9b1c83932a0c9205d"; }
+    { locale = "zh-CN"; arch = "linux-i686"; sha1 = "514bc01fe7055a050898a01f0c1ed4773fb33b7e"; }
-    { locale = "zh-CN"; arch = "linux-x86_64"; sha1 = "238b50b8bb745f2d80099354592c9b710c55f1d8"; }
+    { locale = "zh-CN"; arch = "linux-x86_64"; sha1 = "0d5154d3d5062c7e1ff33112ad0a1399ba548b29"; }
-    { locale = "zh-TW"; arch = "linux-i686"; sha1 = "9159a6fea44a97a33390c527abf7730cdbbc9216"; }
+    { locale = "zh-TW"; arch = "linux-i686"; sha1 = "291ee73bc5540f8089f6b7bbdf8160c931cc4dd7"; }
-    { locale = "zh-TW"; arch = "linux-x86_64"; sha1 = "74e3c2292aed9c2a7de24d6f3693ac1d0ba4c41f"; }
+    { locale = "zh-TW"; arch = "linux-x86_64"; sha1 = "16df041eeaf6a3885d52569db1781635e519fd3f"; }
   ];
 }

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

@@ -3,7 +3,7 @@
 , freetype, fontconfig, file, alsaLib, nspr, nss, libnotify
 , yasm, mesa, sqlite, unzip, makeWrapper, pysqlite
 , hunspell, libevent, libstartup_notification, libvpx
-, cairo, gstreamer, gst_plugins_base, icu
+, cairo, gst_all_1, icu, libpng, jemalloc
 , enableGTK3 ? false
 , debugBuild ? false
 , # If you want the resulting program to call itself "Firefox" instead
@@ -16,14 +16,14 @@
 
 assert stdenv.cc ? libc && stdenv.cc.libc != null;
 
-let version = "39.0"; in
+let version = "39.0.3"; in
 
 stdenv.mkDerivation rec {
   name = "firefox-${version}";
 
   src = fetchurl {
     url = "http://ftp.mozilla.org/pub/mozilla.org/firefox/releases/${version}/source/firefox-${version}.source.tar.bz2";
-    sha1 = "32785daee7ddb9da8d7509ef095258fc58fe838e";
+    sha1 = "e024e528317d6c531fb36a26d2ce3317d3510b42";
   };
 
   buildInputs =
@@ -34,7 +34,8 @@ stdenv.mkDerivation rec {
       xlibs.libXScrnSaver xlibs.scrnsaverproto pysqlite
       xlibs.libXext xlibs.xextproto sqlite unzip makeWrapper
       hunspell libevent libstartup_notification libvpx cairo
-      gstreamer gst_plugins_base icu
+      gst_all_1.gstreamer gst_all_1.gst-plugins-base icu libpng
+      jemalloc
     ]
     ++ lib.optional enableGTK3 gtk3;
 
@@ -48,26 +49,27 @@ stdenv.mkDerivation rec {
       "--with-system-nss"
       "--with-system-libevent"
       "--with-system-libvpx"
-      # "--with-system-png" # needs APNG support
+      "--with-system-png" # needs APNG support
-      # "--with-system-icu" # causes ‘ar: invalid option -- 'L'’ in Firefox 28.0
+      "--with-system-icu"
       "--enable-system-ffi"
       "--enable-system-hunspell"
       "--enable-system-pixman"
       "--enable-system-sqlite"
       "--enable-system-cairo"
-      "--enable-gstreamer"
+      "--enable-gstreamer=1.0"
       "--enable-startup-notification"
-      # "--enable-content-sandbox"            # available since 26.0, but not much info available
+      "--enable-content-sandbox"            # available since 26.0, but not much info available
-      # "--enable-content-sandbox-reporter"   # keeping disabled for now
+      "--disable-content-sandbox-reporter"  # keeping disabled for now
       "--disable-crashreporter"
       "--disable-tests"
       "--disable-necko-wifi" # maybe we want to enable this at some point
       "--disable-installer"
       "--disable-updater"
       "--disable-pulseaudio"
+      "--enable-jemalloc"
     ]
     ++ lib.optional enableGTK3 "--enable-default-toolkit=cairo-gtk3"
-    ++ (if debugBuild then [ "--enable-debug" "--enable-profiling"]
+    ++ (if debugBuild then [ "--enable-debug" "--enable-profiling" ]
                       else [ "--disable-debug" "--enable-release"
                              "--enable-optimize${lib.optionalString (stdenv.system == "i686-linux") "=-O1"}"
                              "--enable-strip" ])

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

@@ -19,6 +19,11 @@ in stdenv.mkDerivation rec {
     sha256 = "1v5xpn4wal4vcrvcklchx9slkpa8xlwqkdbnxzy9zkzpq5g3arxr";
   };
 
+  patches = [
+    # https://reviews.apache.org/r/36610/
+    ./rb36610.patch
+  ];
+
   buildInputs = [
     makeWrapper autoconf automake114x libtool curl sasl jdk maven
     python wrapPython boto distutils-cfg setuptools leveldb

pkgs/applications/networking/cluster/mesos/rb36610.patch

@@ -0,0 +1,11 @@
+diff --git a/src/linux/fs.cpp b/src/linux/fs.cpp
+index ea0891e320154b85a21ed2d138c192821efae9cd..7b24c377c9a28cad91738305c273fb53a4dc7365 100644
+--- a/src/linux/fs.cpp
++++ b/src/linux/fs.cpp
+@@ -19,6 +19,7 @@
+ #include <errno.h>
+ #include <stdio.h>
+ #include <string.h>
++#include <syscall.h>
+
+ #include <linux/limits.h>

pkgs/applications/networking/dropbox/default.nix

@@ -19,11 +19,11 @@
 
 let
   # NOTE: When updating, please also update in current stable, as older versions stop working
-  version = "3.6.9";
+  version = "3.8.5";
   sha256 =
     {
-      "x86_64-linux" = "1i260mi40siwcx9b2sj4zwszxmj1l88mpmyqncsfa72k02jz22j3";
+      "x86_64-linux" = "1r0wz2fsx2piasl04qsgwbl88bi0ajr0dm2swbslxwkf789vk18y";
-      "i686-linux" = "0qqc8qbfaighbhjq9y22ka6n6apl8b6cr80a9rkpk2qsk99k8h1z";
+      "i686-linux" = "1dvfgp9dg3frhwmchwa6fyws4im9vgicchfsv0zzflvc7rm9fcig";
     }."${stdenv.system}" or (throw "system ${stdenv.system} not supported");
 
   arch =

pkgs/applications/networking/mailreaders/notmuch/default.nix

@@ -28,6 +28,7 @@ stdenv.mkDerivation rec {
 
     for src in \
       crypto.c \
+      notmuch-config.c \
       emacs/notmuch-crypto.el
     do
       substituteInPlace "$src" \

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

@@ -0,0 +1,36 @@
+{ pkgs, lib, mercurial, pyPackages ? pkgs.python27Packages }:
+
+pkgs.buildPythonPackage rec {
+    name = "tortoisehg-${version}";
+    version = "3.4.2";
+    namePrefix = "";
+
+    src = pkgs.fetchurl {
+      url = "https://bitbucket.org/tortoisehg/targz/downloads/${name}.tar.gz";
+      sha256 = "18a587c8fybfjxbcj8i2smypxy7vfzmmrzibs74n3zy6dlb949nj";
+    };
+
+    pythonPath = [ pkgs.pyqt4 mercurial ]
+       ++ (with pyPackages; [qscintilla iniparse]);
+
+    propagatedBuildInputs = with pyPackages; [ qscintilla iniparse ];
+    
+    doCheck = false;
+
+    postUnpack = ''
+     substituteInPlace $sourceRoot/setup.py \
+       --replace "/usr/share/" "$out/share/"
+    '';
+
+    postInstall = ''
+     ln -s $out/bin/thg $out/bin/tortoisehg     #convenient alias
+    '';
+
+    meta = {
+      description = "Qt based graphical tool for working with Mercurial";
+      homepage = http://tortoisehg.bitbucket.org/;
+      license = lib.licenses.gpl2;
+      platforms = lib.platforms.linux;
+      maintainers = [ "abcz2.uprola@gmail.com" ];
+    };
+}

pkgs/applications/video/kodi/default.nix

@@ -15,6 +15,7 @@
 , lzo, libcdio, libmodplug, libass, libbluray
 , sqlite, mysql, nasm, gnutls, libva, wayland
 , curl, bzip2, zip, unzip, glxinfo, xdpyinfo
+, libcec, libcec_platform
 , dbus_libs ? null, dbusSupport ? true
 , udev, udevSupport ? true
 , libusb ? null, usbSupport ? false
@@ -24,7 +25,6 @@
 , rtmpdump ? null, rtmpSupport ? true
 , libvdpau ? null, vdpauSupport ? true
 , libpulseaudio ? null, pulseSupport ? true
-, libcec ? null, cecSupport ? true
 }:
 
 assert dbusSupport  -> dbus_libs != null;
@@ -33,7 +33,6 @@ assert usbSupport   -> libusb != null && ! udevSupport; # libusb won't be used i
 assert sambaSupport -> samba != null;
 assert vdpauSupport -> libvdpau != null;
 assert pulseSupport -> libpulseaudio != null;
-assert cecSupport   -> libcec != null;
 assert rtmpSupport  -> rtmpdump != null;
 
 let
@@ -69,6 +68,7 @@ in stdenv.mkDerivation rec {
       lzo libcdio libmodplug libass libbluray
       sqlite mysql.lib nasm avahi libdvdcss lame
       curl bzip2 zip unzip glxinfo xdpyinfo
+      libcec libcec_platform
     ]
     ++ lib.optional dbusSupport dbus_libs
     ++ lib.optional udevSupport udev
@@ -76,7 +76,6 @@ in stdenv.mkDerivation rec {
     ++ lib.optional sambaSupport samba
     ++ lib.optional vdpauSupport libvdpau
     ++ lib.optional pulseSupport libpulseaudio
-    ++ lib.optional cecSupport libcec
     ++ lib.optional rtmpSupport rtmpdump;
 
     dontUseCmakeConfigure = true;
@@ -93,9 +92,7 @@ in stdenv.mkDerivation rec {
       ./bootstrap
     '';
 
-    configureFlags = [
+    configureFlags = [ ]
-      "--enable-external-libraries"
-    ]
     ++ lib.optional (!sambaSupport) "--disable-samba"
     ++ lib.optional vdpauSupport "--enable-vdpau"
     ++ lib.optional pulseSupport "--enable-pulse"
@@ -112,6 +109,7 @@ in stdenv.mkDerivation rec {
           --prefix LD_LIBRARY_PATH ":" "${libmad}/lib" \
           --prefix LD_LIBRARY_PATH ":" "${libvdpau}/lib" \
           --prefix LD_LIBRARY_PATH ":" "${libcec}/lib" \
+          --prefix LD_LIBRARY_PATH ":" "${libcec_platform}/lib" \
           --prefix LD_LIBRARY_PATH ":" "${rtmpdump}/lib"
       done
     '';

pkgs/build-support/emacs/generic.nix

@@ -16,10 +16,14 @@ with lib;
 }@args:
 
 let
+
   defaultMeta = {
     broken = false;
     platforms = emacs.meta.platforms;
+  } // optionalAttrs ((args.src.meta.homepage or "") != "") {
+    homepage = args.src.meta.homepage;
   };
+
 in
 
 stdenv.mkDerivation ({

pkgs/build-support/emacs/melpa.nix

@@ -31,7 +31,7 @@ let
   targets = concatStringsSep " " (if files == null then fileSpecs else files);
 
   defaultMeta = {
-    homepage = "http://melpa.org/#/${pname}";
+    homepage = args.src.meta.homepage or "http://melpa.org/#/${pname}";
   };
 
 in

pkgs/data/misc/geolite-legacy/default.nix

@@ -37,7 +37,7 @@ stdenv.mkDerivation {
     description = "GeoLite Legacy IP geolocation databases";
     homepage = https://geolite.maxmind.com/download/geoip;
     license = licenses.cc-by-sa-30;
-    platforms = with platforms; linux;
+    platforms = platforms.all;
     maintainers = with maintainers; [ nckx ];
   };
 

pkgs/desktops/e19/econnman.nix

@@ -8,9 +8,9 @@ stdenv.mkDerivation rec {
   };
 
   buildInputs = [ makeWrapper pkgconfig e19.efl python27 dbus ];
-  propagatedBuildInputs = [ python27Packages.pythonefl_1_14 python27Packages.dbus e19.elementary ];
+  propagatedBuildInputs = [ python27Packages.pythonefl_1_15 python27Packages.dbus e19.elementary ];
   postInstall = ''
-    wrapProgram $out/bin/econnman-bin --prefix PYTHONPATH : ${python27Packages.dbus}/lib/python2.7/site-packages:${python27Packages.pythonefl_1_14}/lib/python2.7/site-packages
+    wrapProgram $out/bin/econnman-bin --prefix PYTHONPATH : ${python27Packages.dbus}/lib/python2.7/site-packages:${python27Packages.pythonefl_1_15}/lib/python2.7/site-packages
   '';
 
   meta = {

pkgs/desktops/e19/efl.nix

@@ -3,10 +3,10 @@
 
 stdenv.mkDerivation rec {
   name = "efl-${version}";
-  version = "1.14.1";
+  version = "1.15.0";
   src = fetchurl {
     url = "http://download.enlightenment.org/rel/libs/efl/${name}.tar.gz";
-    sha256 = "16rj4qnpw1ya0bsp9a69w6zjmmhzni7vnc0z4wg819jg5k2njzjf";
+    sha256 = "1x5n2afy5z1akam5y187ajk52mq2k9lwmz7nlrxp92rvx1jf6li5";
   };
 
   buildInputs = [ pkgconfig openssl zlib freetype fontconfig fribidi SDL2 SDL mesa

pkgs/desktops/e19/elementary.nix

@@ -1,12 +1,12 @@
-{ stdenv, fetchurl, pkgconfig, e19, libcap, automake114x, autoconf, libdrm, gdbm }:
+{ stdenv, fetchurl, pkgconfig, e19, libcap, automake, autoconf, libdrm, gdbm }:
 stdenv.mkDerivation rec {
   name = "elementary-${version}";
-  version = "1.14.1";
+  version = "1.15.0";
   src = fetchurl {
     url = "http://download.enlightenment.org/rel/libs/elementary/${name}.tar.gz";
-    sha256 = "100bfzw6q57dnzcqg4zm0rqpvkk7zykfklnn6kcymv80j43xg0p1";
+    sha256 = "085s2xw3dhv8xiy7ikaaim5gil423g08wclhk0psi76g0vavgd32";
   };
-  buildInputs = [ pkgconfig e19.efl libdrm gdbm automake114x autoconf ] ++ stdenv.lib.optionals stdenv.isLinux [ libcap ];
+  buildInputs = [ pkgconfig e19.efl libdrm gdbm automake autoconf ] ++ stdenv.lib.optionals stdenv.isLinux [ libcap ];
   NIX_CFLAGS_COMPILE = [ "-I${libdrm}/include/libdrm" ];
   patches = [ ./elementary.patch ];
   enableParallelBuilding = true;

pkgs/desktops/e19/emotion.nix

@@ -1,10 +1,10 @@
 { stdenv, fetchurl, pkgconfig, e19, vlc }:
 stdenv.mkDerivation rec {
   name = "emotion_generic_players-${version}";
-  version = "1.14.0";
+  version = "1.15.0";
   src = fetchurl {
     url = "http://download.enlightenment.org/rel/libs/emotion_generic_players/${name}.tar.gz";
-    sha256 = "1n1a5n2wi68n8gjw4yk6cyf11djpqpac0025vysn5w6dqgccfic3";
+    sha256 = "08yl473aiklj0yfxbn88000hmnhl7dbhqixsn22ias8a90rxdfhh";
   };
   buildInputs = [ pkgconfig e19.efl vlc ];
   NIX_CFLAGS_COMPILE = [ "-I${e19.efl}/include/eo-1" ];

pkgs/desktops/e19/enlightenment.nix

@@ -3,10 +3,10 @@
 
 stdenv.mkDerivation rec {
   name = "enlightenment-${version}";
-  version = "0.19.5";
+  version = "0.19.8";
   src = fetchurl {
     url = "http://download.enlightenment.org/rel/apps/enlightenment/${name}.tar.xz";
-    sha256 = "0j66x7x76fbgqfw6fi77v8qy50slw3jnsq3vvs82rrfvniabm8wc";
+    sha256 = "1y83jnq01k9i328adgjgpfwgpvvd2a1ixpm029pjcar8p1mvgadi";
   };
   buildInputs = [ pkgconfig e19.efl e19.elementary xlibs.libXdmcp xlibs.libxcb
     xlibs.xcbutilkeysyms xlibs.libXrandr libffi pam alsaLib luajit bzip2

pkgs/desktops/e19/evas.nix

@@ -1,10 +1,10 @@
 { stdenv, fetchurl, pkgconfig, e19, zlib, libspectre, gstreamer, gst_plugins_base, gst_ffmpeg, gst_plugins_good, poppler, librsvg, libraw }:
 stdenv.mkDerivation rec {
   name = "evas_generic_loaders-${version}";
-  version = "1.14.0";
+  version = "1.15.0";
   src = fetchurl {
     url = "http://download.enlightenment.org/rel/libs/evas_generic_loaders/${name}.tar.gz";
-    sha256 = "04m8vsrigbsg9hm94lxac56frdxil1bib0bjmspa6xsfgi12afwl";
+    sha256 = "1k9bmswrgfara4a7znqcv3qbhq3zjbm0ks1zdb0jk5mfl6djr8na";
   };
   buildInputs = [ pkgconfig e19.efl zlib libspectre gstreamer gst_plugins_base gst_ffmpeg gst_plugins_good poppler librsvg libraw ];
   meta = {

pkgs/desktops/gnome-3/3.16/apps/cheese/default.nix

@@ -1,6 +1,6 @@
 { stdenv, intltool, fetchurl, wrapGAppsHook, gnome-video-effects, libcanberra_gtk3
 , pkgconfig, gtk3, glib, clutter_gtk, clutter-gst_2, udev, gst_all_1, itstool
-, adwaita-icon-theme, librsvg, gdk_pixbuf, gnome3, gnome_desktop, libxml2, libtool }:
+, adwaita-icon-theme, librsvg, gdk_pixbuf, gnome3, gnome_desktop, libxml2 }:
 
 stdenv.mkDerivation rec {
   name = "cheese-${gnome3.version}.1";
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
                   gdk_pixbuf adwaita-icon-theme librsvg udev gst_all_1.gstreamer libxml2
                   gst_all_1.gst-plugins-base gst_all_1.gst-plugins-good gnome_desktop
                   gst_all_1.gst-plugins-bad clutter_gtk clutter-gst_2
-                  libtool libcanberra_gtk3 ];
+                  libcanberra_gtk3 ];
 
   enableParallelBuilding = true;
 

pkgs/desktops/gnome-3/3.16/core/yelp/default.nix

@@ -3,11 +3,11 @@
 , bash, makeWrapper, itstool, libxml2, libxslt, icu }:
 
 stdenv.mkDerivation rec {
-  name = "yelp-${gnome3.version}.0";
+  name = "yelp-${gnome3.version}.1";
 
   src = fetchurl {
     url = "mirror://gnome/sources/yelp/${gnome3.version}/${name}.tar.xz";
-    sha256 = "0az2f1g8gz341i93zxnm6sabrqx416a348ylwfr8vzlg592am2r3";
+    sha256 = "1jk7aad1srykhgc3x0hd3q3dnlshmy1ak00alwjzaasxvy6hp0b0";
   };
 
   propagatedUserEnvPkgs = [ gnome3.gnome_themes_standard ];

pkgs/desktops/gnome-3/3.16/misc/gnome-tweak-tool/default.nix

@@ -4,11 +4,11 @@
 , gnome3, librsvg, gdk_pixbuf, file, libnotify }:
 
 stdenv.mkDerivation rec {
-  name = "gnome-tweak-tool-${gnome3.version}.0";
+  name = "gnome-tweak-tool-${gnome3.version}.2";
 
   src = fetchurl {
     url = "mirror://gnome/sources/gnome-tweak-tool/${gnome3.version}/${name}.tar.xz";
-    sha256 = "0pc62qwxgjrgxdhn3qqdzxpx0prrn6c948hqj66w2dy8r0yrdiqw";
+    sha256 = "0r5x67aj79dsw2xl98q4harxv3hjs52g0m6pw43vx29lbir07r5i";
   };
 
   doCheck = true;

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

@@ -14,6 +14,9 @@ self: super: {
   # Link statically to avoid runtime dependency on GHC.
   jailbreak-cabal = disableSharedExecutables super.jailbreak-cabal;
 
+  # Apply NixOS-specific patches.
+  ghc-paths = appendPatch super.ghc-paths ./patches/ghc-paths-nix.patch;
+
   # Break infinite recursions.
   Dust-crypto = dontCheck super.Dust-crypto;
   hasql-postgres = dontCheck super.hasql-postgres;
@@ -250,24 +253,24 @@ self: super: {
   # https://github.com/tibbe/ekg/commit/95018646f48f60d9ccf6209cc86747e0f132e737, not yet in hackage
   ekg = doJailbreak super.ekg;
 
-  # https://github.com/diagrams/diagrams-rasterific/commit/2758e5760c64f8ca2528628bd11de502f354ab15, not yet in hackage
-  diagrams-rasterific = doJailbreak super.diagrams-rasterific;
-
   # https://github.com/NixOS/cabal2nix/issues/136
   glib = addBuildDepends super.glib [pkgs.pkgconfig pkgs.glib];
   gtk3 = super.gtk3.override { inherit (pkgs) gtk3; };
   gtk = addBuildDepends super.gtk [pkgs.pkgconfig pkgs.gtk];
   gtksourceview3 = super.gtksourceview3.override { inherit (pkgs.gnome3) gtksourceview; };
 
+  # webkit does not recognize its system library build input any more.
+  webkit = markBroken super.webkit; # http://hydra.cryp.to/build/1041942/nixlog/1/raw
+  ghcjs-dom-hello = dontDistribute super.ghcjs-dom-hello;       # depends on broken webkit
+  ghcjs-dom = dontDistribute super.ghcjs-dom;                   # depends on broken webkit
+  jsaddle-hello = dontDistribute super.jsaddle-hello;           # depends on broken webkit
+  reflex-dom = dontDistribute super.reflex-dom;                 # depends on broken webkit
+
   # Need WebkitGTK, not just webkit.
-  webkit = super.webkit.override { webkit = pkgs.webkitgtk24x; };
   webkitgtk3 = super.webkitgtk3.override { webkit = pkgs.webkitgtk24x; };
   webkitgtk3-javascriptcore = super.webkitgtk3-javascriptcore.override { webkit = pkgs.webkitgtk24x; };
   websnap = super.websnap.override { webkit = pkgs.webkitgtk24x; };
 
-  # https://github.com/jgm/zip-archive/issues/21
-  zip-archive = addBuildTool super.zip-archive pkgs.zip;
-
   # https://github.com/mvoidex/hsdev/issues/11
   hsdev = dontHaddock super.hsdev;
 
@@ -300,6 +303,7 @@ self: super: {
   dbmigrations = dontCheck super.dbmigrations;
   euler = dontCheck super.euler;                        # https://github.com/decomputed/euler/issues/1
   filestore = dontCheck super.filestore;
+  getopt-generics = dontCheck super.getopt-generics;
   graceful = dontCheck super.graceful;
   hakyll = dontCheck super.hakyll;
   Hclip = dontCheck super.Hclip;
@@ -331,6 +335,7 @@ self: super: {
   hasql = dontCheck super.hasql;                        # http://hydra.cryp.to/build/502489/nixlog/4/raw
   hjsonschema = overrideCabal super.hjsonschema (drv: { testTarget = "local"; });
   holy-project = dontCheck super.holy-project;          # http://hydra.cryp.to/build/502002/nixlog/1/raw
+  hoogle = overrideCabal super.hoogle (drv: { testTarget = "--test-option=--no-net"; });
   http-client = dontCheck super.http-client;            # http://hydra.cryp.to/build/501430/nixlog/1/raw
   http-conduit = dontCheck super.http-conduit;          # http://hydra.cryp.to/build/501966/nixlog/1/raw
   js-jquery = dontCheck super.js-jquery;
@@ -526,6 +531,7 @@ self: super: {
   stable-tree = dontDistribute super.stable-tree;
   synthesizer-llvm = dontDistribute super.synthesizer-llvm;
   optimal-blocks = dontDistribute super.optimal-blocks;
+  hs-blake2 = dontDistribute super.hs-blake2;
 
   # https://ghc.haskell.org/trac/ghc/ticket/9625
   vty = dontCheck super.vty;
@@ -561,7 +567,7 @@ self: super: {
   duplo = dontCheck super.duplo;
 
   # Nix-specific workaround
-  xmonad = appendPatch super.xmonad ./xmonad-nix.patch;
+  xmonad = appendPatch super.xmonad ./patches/xmonad-nix.patch;
 
   # https://github.com/evanrinehart/mikmod/issues/1
   mikmod = addExtraLibrary super.mikmod pkgs.libmikmod;
@@ -582,31 +588,6 @@ self: super: {
   # no haddock since this is an umbrella package.
   cloud-haskell = dontHaddock super.cloud-haskell;
 
-  # Disable tests which couldn't be built.
-  distributed-process-async = dontCheck super.distributed-process-async;
-
-  # Disable tests which couldn't be built.
-  distributed-process-client-server = dontCheck super.distributed-process-client-server;
-
-  # Disable tests which couldn't be built.
-  distributed-process-extras = dontCheck super.distributed-process-extras;
-
-  # Make distributed-process-platform compile until next version
-  distributed-process-platform = overrideCabal super.distributed-process-platform (drv: {
-    patchPhase = "mv Setup.hs Setup.lhs";
-    doCheck = false;
-    doHaddock = false;
-  });
-
-  # Disable tests due to a failure (Sequential Shutdown Ordering test.)
-  distributed-process-supervisor = dontCheck super.distributed-process-supervisor;
-
-  # Disable network test and errorneous haddock.
-  distributed-process-tests = overrideCabal super.distributed-process-tests (drv: {
-    doCheck = false;
-    doHaddock = false;
-  });
-
   # This packages compiles 4+ hours on a fast machine. That's just unreasonable.
   CHXHtml = dontDistribute super.CHXHtml;
 
@@ -616,9 +597,6 @@ self: super: {
   # https://github.com/NixOS/nixpkgs/issues/6350
   paypal-adaptive-hoops = overrideCabal super.paypal-adaptive-hoops (drv: { testTarget = "local"; });
 
-  # https://github.com/seanparsons/wiring/issues/1
-  wiring = markBrokenVersion super.wiring;
-
   # https://github.com/jwiegley/simple-conduit/issues/2
   simple-conduit = markBroken super.simple-conduit;
 
@@ -631,12 +609,8 @@ self: super: {
   # https://github.com/vincenthz/hs-asn1/issues/12
   asn1-encoding = dontCheck super.asn1-encoding;
 
-  # wxc needs help deciding which version of GTK to use.
+  # wxc supports wxGTX >= 2.9, but our current default version points to 2.8.
-  wxc = overrideCabal (super.wxc.override { wxGTK = pkgs.wxGTK29; }) (drv: {
+  wxc = super.wxc.override { wxGTK = pkgs.wxGTK29; };
-    patches = [ ./wxc-no-ldconfig.patch ];
-    doHaddock = false;
-    postInstall = "cp -v dist/build/libwxc.so.${drv.version} $out/lib/libwxc.so";
-  });
   wxcore = super.wxcore.override { wxGTK = pkgs.wxGTK29; };
 
   # Depends on QuickCheck 1.x.
@@ -783,7 +757,7 @@ self: super: {
   leksah = dontCheck super.leksah;
 
   # Patch to consider NIX_GHC just like xmonad does
-  dyre = appendPatch super.dyre ./dyre-nix.patch;
+  dyre = appendPatch super.dyre ./patches/dyre-nix.patch;
 
   # Test suite won't compile against tasty-hunit 0.9.x.
   zlib = dontCheck super.zlib;
@@ -903,4 +877,49 @@ self: super: {
   # https://github.com/hspec/mockery/issues/6
   mockery = overrideCabal super.mockery (drv: { preCheck = "export TRAVIS=true"; });
 
+  # https://github.com/diagrams/diagrams-lib/issues/258
+  # https://github.com/diagrams/diagrams-lib/issues/259
+  diagrams-lib = markBroken super.diagrams-lib;
+  diagrams-cairo = dontDistribute super.diagrams-cairo;
+  diagrams-gtk = dontDistribute super.diagrams-gtk;
+  diagrams-html5 = dontDistribute super.diagrams-html5;
+  diagrams-pandoc = dontDistribute super.diagrams-pandoc;
+  diagrams-postscript = dontDistribute super.diagrams-postscript;
+  diagrams-rasterific = dontDistribute super.diagrams-rasterific;
+  diagrams-rubiks-cube = dontDistribute super.diagrams-rubiks-cube;
+  diagrams-svg = dontDistribute super.diagrams-svg;
+  halma = dontDistribute super.halma;
+  midi-music-box = dontDistribute super.midi-music-box;
+  potrace-diagrams = dontDistribute super.potrace-diagrams;
+  SVGFonts = dontDistribute super.SVGFonts;
+  yesod-media-simple = dontDistribute super.yesod-media-simple;
+
+  # https://github.com/alphaHeavy/lzma-conduit/issues/5
+  lzma-conduit = dontCheck super.lzma-conduit;
+
+  # https://github.com/kazu-yamamoto/logger/issues/42
+  logger = dontCheck super.logger;
+
+  # https://github.com/edwinb/EpiVM/issues/13
+  # https://github.com/edwinb/EpiVM/issues/14
+  epic = addExtraLibraries (addBuildTool super.epic self.happy) [pkgs.boehmgc pkgs.gmp];
+
+  # Upstream has no issue tracker.
+  dpkg = markBroken super.dpkg;
+
+  # https://github.com/ekmett/wl-pprint-terminfo/issues/7
+  wl-pprint-terminfo = addExtraLibrary super.wl-pprint-terminfo pkgs.ncurses;
+
+  # https://github.com/bos/pcap/issues/5
+  pcap = addExtraLibrary super.pcap pkgs.libpcap;
+
+  # https://github.com/bscarlet/llvm-general/issues/143
+  llvm-general-pure = dontCheck super.llvm-general-pure;
+
+  # https://github.com/skogsbaer/hscurses/issues/24
+  hscurses = markBroken super.hscurses;
+
+  # https://github.com/qnikst/imagemagick/issues/34
+  imagemagick = dontCheck super.imagemagick;
+
 }

pkgs/development/haskell-modules/configuration-ghc-7.10.x.nix

@@ -47,13 +47,14 @@ self: super: {
   idris =
     let idris' = overrideCabal super.idris (drv: {
       # "idris" binary cannot find Idris library otherwise while building.
-      # After installing it's completely fine though.
+      # After installing it's completely fine though. Seems like Nix-specific
-      # Seems like Nix-specific issue so not reported.
+      # issue so not reported.
-      preBuild = ''
+      preBuild = "export LD_LIBRARY_PATH=$PWD/dist/build:$LD_LIBRARY_PATH";
-        export LD_LIBRARY_PATH=$PWD/dist/build:$LD_LIBRARY_PATH
+      # https://github.com/idris-lang/Idris-dev/issues/2499
-      '';
+      librarySystemDepends = (drv.librarySystemDepends or []) ++ [pkgs.gmp];
     });
     in idris'.overrideScope (self: super: {
+      # https://github.com/idris-lang/Idris-dev/issues/2500
       zlib = self.zlib_0_5_4_2;
     });
 
@@ -205,7 +206,7 @@ self: super: {
   tasty-rerun = dontHaddock (appendConfigureFlag super.tasty-rerun "--ghc-option=-XFlexibleContexts");
 
   # http://hub.darcs.net/ivanm/graphviz/issue/5
-  graphviz = dontCheck (dontJailbreak (appendPatch super.graphviz ./graphviz-fix-ghc710.patch));
+  graphviz = dontCheck (dontJailbreak (appendPatch super.graphviz ./patches/graphviz-fix-ghc710.patch));
 
   # Broken with GHC 7.10.x.
   aeson_0_7_0_6 = markBroken super.aeson_0_7_0_6;
@@ -219,6 +220,9 @@ self: super: {
   seqid-streams_0_1_0 = markBroken super.seqid-streams_0_1_0;
   vector_0_10_9_3 = markBroken super.vector_0_10_9_3;
 
+  # http://hub.darcs.net/shelarcy/regex-tdfa-text/issue/1 -- upstream seems to be asleep
+  regex-tdfa-text = appendPatch super.regex-tdfa-text ./patches/regex-tdfa-text.patch;
+
   # https://github.com/HugoDaniel/RFC3339/issues/14
   timerep = dontCheck super.timerep;
 
@@ -264,4 +268,7 @@ self: super: {
   # GHC 7.10.1 is affected by https://github.com/srijs/hwsl2/issues/1.
   hwsl2 = dontCheck super.hwsl2;
 
+  # https://github.com/haskell/haddock/issues/427
+  haddock = dontCheck super.haddock;
+
 }

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

@@ -7,7 +7,7 @@ self: super: {
   # LLVM is not supported on this GHC; use the latest one.
   inherit (pkgs) llvmPackages;
 
-  inherit (pkgs.haskell-ng.packages.ghc7101) jailbreak-cabal alex happy;
+  inherit (pkgs.haskell.packages.ghc7102) jailbreak-cabal alex happy;
 
   # Many packages fail with:
   #   haddock: internal error: expectJust getPackageDetails
@@ -87,7 +87,7 @@ self: super: {
   });
 
   ghc-paths = overrideCabal super.ghc-paths (drv: {
-    patches = [ ./ghc-paths-nix-ghcjs.patch ];
+    patches = [ ./patches/ghc-paths-nix-ghcjs.patch ];
   });
 
   reflex-dom = overrideCabal super.reflex-dom (drv: {

pkgs/development/haskell-modules/default.nix

@@ -3,8 +3,6 @@
 , overrides ? (self: super: {})
 }:
 
-with ./lib.nix;
-
 let
 
   fix = f: let x = f x // { __unfix__ = f; }; in x;

pkgs/development/haskell-modules/edit-distance-fix-boundaries.patch

@@ -1,30 +0,0 @@
-diff -ru3 edit-distance-0.2.1.2-old/edit-distance.cabal edit-distance-0.2.1.2/edit-distance.cabal
---- edit-distance-0.2.1.2-old/edit-distance.cabal	2015-04-17 22:46:50.964116064 +0300
-+++ edit-distance-0.2.1.2/edit-distance.cabal	2015-04-17 22:41:31.216027373 +0300
-@@ -36,7 +36,7 @@
-                                 Text.EditDistance.ArrayUtilities
-         
-         if flag(splitBase)
--                Build-Depends:  base >= 3 && < 4.8, array >= 0.1, random >= 1.0, containers >= 0.1.0.1
-+                Build-Depends:  base >= 3 && < 5, array >= 0.1, random >= 1.0, containers >= 0.1.0.1
-         else
-                 Build-Depends:  base < 3
-         
-@@ -54,7 +54,7 @@
-         else            
-                 Build-Depends:          test-framework >= 0.1.1, QuickCheck >= 1.1 && < 2.0, test-framework-quickcheck
-                 if flag(splitBase)
--                        Build-Depends:  base >= 3 && < 4.8, array >= 0.1, random >= 1.0
-+                        Build-Depends:  base >= 3 && < 5, array >= 0.1, random >= 1.0
-                 else
-                         Build-Depends:  base < 3
- 
-@@ -65,7 +65,7 @@
-                 Buildable:      False
-         else
-                 if flag(splitBase)
--                        Build-Depends:  base >= 3 && < 4.8, array >= 0.1, random >= 1.0, time >= 1.0, process >= 1.0,
-+                        Build-Depends:  base >= 3 && < 5, array >= 0.1, random >= 1.0, time >= 1.0, process >= 1.0,
-                                         deepseq >= 1.2, unix >= 2.3, criterion >= 0.6
-                 else
-                         Build-Depends:  base < 3,

pkgs/development/haskell-modules/generic-builder.nix

@@ -113,7 +113,7 @@ let
   otherBuildInputs = extraLibraries ++ librarySystemDepends ++ executableSystemDepends ++
                      buildTools ++ libraryToolDepends ++ executableToolDepends ++
                      optionals (allPkgconfigDepends != []) ([pkgconfig] ++ allPkgconfigDepends) ++
-                     optionals doCheck (testDepends ++ testHaskellDepends ++ testSystemDepends);
+                     optionals doCheck (testDepends ++ testHaskellDepends ++ testSystemDepends ++ testToolDepends);
   allBuildInputs = propagatedBuildInputs ++ otherBuildInputs;
 
   haskellBuildInputs = stdenv.lib.filter isHaskellPkg allBuildInputs;

pkgs/development/haskell-modules/haskell-src-meta-ghc710.patch

@@ -1,55 +0,0 @@
-From 24e6f45408083745080ff2f3710f58209041113c Mon Sep 17 00:00:00 2001
-From: Luite Stegeman <stegeman@gmail.com>
-Date: Sun, 28 Dec 2014 21:33:22 +0100
-Subject: [PATCH] updates for GHC 7.10 and Template Haskell 2.10
-
----
- haskell-src-meta.cabal                        | 4 ++--
- src/Language/Haskell/Meta/Syntax/Translate.hs | 6 ++++++
- src/Language/Haskell/Meta/Utils.hs            | 5 ++++-
- 3 files changed, 12 insertions(+), 3 deletions(-)
-
-diff --git a/src/Language/Haskell/Meta/Syntax/Translate.hs b/src/Language/Haskell/Meta/Syntax/Translate.hs
-index 189d32e..36a08f1 100644
---- a/src/Language/Haskell/Meta/Syntax/Translate.hs
-+++ b/src/Language/Haskell/Meta/Syntax/Translate.hs
-@@ -384,9 +384,15 @@ a .->. b = AppT (AppT ArrowT a) b
- toCxt :: Hs.Context -> Cxt
- toCxt = fmap toPred
-  where
-+#if MIN_VERSION_template_haskell(2,10,0)
-+  toPred (Hs.ClassA n ts) = foldl' AppT (ConT (toName n)) (fmap toType ts)
-+  toPred (Hs.InfixA t1 n t2) = foldl' AppT (ConT (toName n)) (fmap toType [t1,t2])
-+  toPred (Hs.EqualP t1 t2) = foldl' AppT EqualityT (fmap toType [t1,t2])
-+#else
-   toPred (Hs.ClassA n ts) = ClassP (toName n) (fmap toType ts)
-   toPred (Hs.InfixA t1 n t2) = ClassP (toName n) (fmap toType [t1, t2])
-   toPred (Hs.EqualP t1 t2) = EqualP (toType t1) (toType t2)
-+#endif
-   toPred a@Hs.IParam{} = noTH "toCxt" a
- 
- foldAppT :: Type -> [Type] -> Type
-diff --git a/src/Language/Haskell/Meta/Utils.hs b/src/Language/Haskell/Meta/Utils.hs
-index 36f7e96..d194f3e 100644
---- a/src/Language/Haskell/Meta/Utils.hs
-+++ b/src/Language/Haskell/Meta/Utils.hs
-@@ -166,6 +166,9 @@ renameT env new (ForallT ns cxt t) =
-     unVarT (VarT n) = PlainTV n
-     renamePreds = renameThings renamePred
- 
-+#if MIN_VERSION_template_haskell(2,10,0)
-+    renamePred = renameT
-+#else
-     renamePred env new (ClassP n ts) = let
-         (ts', env', new') = renameTs env new [] ts
-       in (ClassP (normaliseName n) ts', env', new')
-@@ -174,7 +177,7 @@ renameT env new (ForallT ns cxt t) =
-         (t1', env1, new1) = renameT env new t1
-         (t2', env2, new2) = renameT env1 new1 t2
-       in (EqualP t1' t2', env2, new2)
--
-+#endif
- 
- -- | Remove qualification, etc.
- normaliseName :: Name -> Name
-

pkgs/development/haskell-modules/lib.nix

@@ -31,6 +31,9 @@ rec {
   addBuildDepend = drv: x: addBuildDepends drv [x];
   addBuildDepends = drv: xs: overrideCabal drv (drv: { buildDepends = (drv.buildDepends or []) ++ xs; });
 
+  addPkgconfigDepend = drv: x: addPkgconfigDepends drv [x];
+  addPkgconfigDepends = drv: xs: overrideCabal drv (drv: { buildDepends = (drv.pkgconfigDepends or []) ++ xs; });
+
   enableCabalFlag = drv: x: appendConfigureFlag (removeConfigureFlag drv "-f-${x}") "-f${x}";
   disableCabalFlag = drv: x: appendConfigureFlag (removeConfigureFlag drv "-f${x}") "-f-${x}";
 

pkgs/development/haskell-modules/patches/regex-tdfa-text.patch

@@ -0,0 +1,21 @@
+--- regex-tdfa-text-1.0.0.2/Text/Regex/TDFA/Text/Lazy.orig.hs	2015-08-05 20:30:01.228983428 +0100
++++ regex-tdfa-text-1.0.0.2/Text/Regex/TDFA/Text/Lazy.hs	2015-08-05 20:39:25.682563005 +0100
+@@ -26,7 +26,7 @@
+ import Data.Array.IArray((!),elems,amap)
+ import qualified Data.Text.Lazy as L(Text,empty,take,drop,uncons,unpack)
+
+-import Text.Regex.Base(MatchArray,RegexContext(..),Extract(..),RegexMaker(..),RegexLike(..))
++import Text.Regex.Base(MatchText,MatchArray,RegexContext(..),Extract(..),RegexMaker(..),RegexLike(..))
+ import Text.Regex.Base.Impl(polymatch,polymatchM)
+ import Text.Regex.TDFA.ReadRegex(parseRegex)
+ import Text.Regex.TDFA.String() -- piggyback on RegexMaker for String
+@@ -74,7 +74,8 @@
+                ,after (o+l) source))
+          (matchOnce regex source)
+   matchAllText regex source =
+-    let go i _ _ | i `seq` False = undefined
++    let go :: Int -> L.Text -> [MatchArray] -> [MatchText L.Text]
++        go i _ _ | i `seq` False = undefined
+         go _i _t [] = []
+         go i t (x:xs) =
+           let (off0,len0) = x!0

pkgs/development/haskell-modules/wxc-no-ldconfig.patch

@@ -1,10 +0,0 @@
-Only in wxc-0.91.0.0: dist
-diff -ubr wxc-0.91.0.0-orig/Setup.hs wxc-0.91.0.0/Setup.hs
---- wxc-0.91.0.0-orig/Setup.hs	2014-10-31 13:30:15.514809137 +0100
-+++ wxc-0.91.0.0/Setup.hs	2014-10-31 13:33:53.606372005 +0100
-@@ -507,5 +507,3 @@
-         inst_lib_dir = libdir $ absoluteInstallDirs pkg_descr local_bld_info NoCopyDest
- 
-     installOrdinaryFile (verbosity flags) (bld_dir </> lib_name) (inst_lib_dir </> lib_name)
--    ldconfig inst_lib_dir
--

pkgs/development/interpreters/picoc/default.nix

@@ -39,7 +39,9 @@ stdenv.mkDerivation {
 
   enableParallelBuilding = true;
 
-  doCheck = true;
+  # Tests are currently broken on i686 see
+  # http://hydra.nixos.org/build/24003763/nixlog/1
+  doCheck = if stdenv.isi686 then false else true;
   checkTarget = "test";
 
   installPhase = ''

pkgs/development/libraries/gsl/default.nix

@@ -11,10 +11,9 @@ stdenv.mkDerivation rec {
   patches = [
     # ToDo: there might be more impurities than FMA support check
     ./disable-fma.patch # http://lists.gnu.org/archive/html/bug-gsl/2011-11/msg00019.html
-
     (fetchpatch {
       name = "bug-39055.patch";
-      url = "http://git.savannah.gnu.org/cgit/gsl.git/patch/?id=9cc12d0377";
+      url = "http://git.savannah.gnu.org/cgit/gsl.git/patch/?id=9cc12d";
       sha256 = "1bmrmihi28cly9g9pq54kkix2jy59y7cd7h5fw4v1c7h5rc2qvs8";
     })
   ];

pkgs/development/libraries/libcanberra/default.nix

@@ -16,6 +16,12 @@ stdenv.mkDerivation rec {
 
   configureFlags = "--disable-oss";
 
+  postInstall = ''
+    for f in $out/lib/*.la; do
+      sed 's|-lltdl|-L${libtool}/lib -lltdl|' -i $f
+    done
+  '';
+
   passthru = {
     gtkModule = "/lib/gtk-2.0/";
   };

pkgs/development/libraries/libcec/default.nix

@@ -1,16 +1,18 @@
-{ stdenv, fetchurl, autoreconfHook, pkgconfig, udev }:
+{ stdenv, fetchurl, cmake, pkgconfig, udev, libcec_platform }:
 
-let version = "2.2.0"; in
+let version = "3.0.1"; in
 
 stdenv.mkDerivation {
   name = "libcec-${version}";
 
   src = fetchurl {
-    url = "https://github.com/Pulse-Eight/libcec/archive/libcec-${version}-repack.tar.gz";
+    url = "https://github.com/Pulse-Eight/libcec/archive/libcec-${version}.tar.gz";
-    sha256 = "1kdfak8y96v14d5vp2apkjjs0fvvim9phc0nkhlq5pjlagk8v32x";
+    sha256 = "0gi5gq8pz6vfdx80pimx23d5g243zzgmc7s8wpb686csjk470dky";
   };
 
-  buildInputs = [ autoreconfHook pkgconfig udev ];
+  buildInputs = [ cmake pkgconfig udev libcec_platform ];
+
+  cmakeFlags = [ "-DBUILD_SHARED_LIBS=1" ];
 
   # Fix dlopen path
   patchPhase = ''

pkgs/development/libraries/libcec/platform.nix

@@ -0,0 +1,23 @@
+{ stdenv, fetchurl, cmake }:
+
+let version = "1.0.10"; in
+
+stdenv.mkDerivation {
+  name = "libcec-${version}";
+
+  src = fetchurl {
+    url = "https://github.com/Pulse-Eight/platform/archive/${version}.tar.gz";
+    sha256 = "1kdmi9b62nky4jrb5519ddnw5n7s7m6qyj7rzhg399f0n6f278vb";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  meta = with stdenv.lib; {
+    description = "Platform library for libcec and Kodi addons";
+    homepage = "https://github.com/Pulse-Eight/platform";
+    repositories.git = "https://github.com/Pulse-Eight/libcec.git";
+    license = stdenv.lib.licenses.gpl2Plus;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.titanous ];
+  };
+}

pkgs/development/libraries/libpng/12.nix

@@ -3,11 +3,11 @@
 assert !(stdenv ? cross) -> zlib != null;
 
 stdenv.mkDerivation rec {
-  name = "libpng-1.2.52";
+  name = "libpng-1.2.53";
 
   src = fetchurl {
     url = "mirror://sourceforge/libpng/${name}.tar.xz";
-    sha256 = "1h0fa67x4bh7gcdh7qx87m4xpkdfqa7ihd4h678dcyh52jzhzyyl";
+    sha256 = "02jwfqk1ahqfvbs9gdyb5v0123by9ws6m7jnfvainig7i7v4jpml";
   };
 
   propagatedBuildInputs = [ zlib ];

pkgs/development/libraries/libpng/default.nix

@@ -1,13 +1,13 @@
-{ stdenv, fetchurl, zlib, apngSupport ? false }:
+{ stdenv, fetchurl, zlib, apngSupport ? true }:
 
 assert zlib != null;
 
 let
-  version = "1.6.16";
+  version = "1.6.18";
-  sha256 = "0q5ygy15jkpqbj5701ywrjzqp4nl5yz3r4g58h2p0kiycggm9xs2";
+  sha256 = "0qq96rf31483kxz32h6l6921hy6p2v2pfqfvc74km229g4xw241f";
   patch_src = fetchurl {
     url = "mirror://sourceforge/libpng-apng/libpng-${version}-apng.patch.gz";
-    sha256 = "1sf27a5gvwvcm4wsf2pyq87d3g4l2fym8cirq9sli54bi753ikbh";
+    sha256 = "0g2ljh2vhclas1hacys1c4gk6l6hyy6sngb2yvdsnjz50nyq16kv";
   };
   whenPatched = stdenv.lib.optionalString apngSupport;
 

pkgs/development/libraries/libpsl/default.nix

@@ -1,16 +1,48 @@
-{ stdenv, fetchFromGitHub, autoreconfHook, icu, libxslt, pkgconfig }:
+{ stdenv, fetchurl, fetchFromGitHub, autoreconfHook, docbook_xsl, gtk_doc
+, icu, libxslt, pkgconfig }:
 
-let version = "0.7.1"; in
+let
-stdenv.mkDerivation rec {
+
+  version = "${libVersion}-list-${listVersion}";
+
+  listVersion = "2015-08-03";
+  listArchive = let
+    rev = "447962d71bf512fe41e828afc7fa66a1701c7c3c";
+  in fetchurl {
+    sha256 = "0gp0cb6p8yvyy5kvgdwg45ian9rb07bb0a9ibdj58g21l54mx3r2";
+    url = "https://codeload.github.com/publicsuffix/list/tar.gz/${rev}";
+  };
+
+  libVersion = "0.8.0";
+
+in stdenv.mkDerivation {
   name = "libpsl-${version}";
 
   src = fetchFromGitHub {
-    sha256 = "0hbsidbmwgpg0h48wh2pzsq59j8az7naz3s5q3yqn99yyjji2vgw";
+    sha256 = "0mjnj36igk6w3c0d4k2fqqg1kl6bpnxfrcgcgz1zdw33gfa5gdi7";
-    rev = name;
+    rev = "libpsl-${libVersion}";
     repo = "libpsl";
     owner = "rockdaboot";
   };
 
+  buildInputs = [ icu libxslt ];
+  nativeBuildInputs = [ autoreconfHook docbook_xsl gtk_doc pkgconfig ];
+
+  preAutoreconf = ''
+    mkdir m4
+    gtkdocize
+  '';
+
+  preConfigure = ''
+    # The libpsl check phase requires the list's test scripts (tests/) as well
+    tar --directory=list --strip-components=1 -xf "${listArchive}"
+  '';
+  configureFlags = "--disable-static --enable-gtk-doc --enable-man";
+
+  enableParallelBuilding = true;
+
+  doCheck = true;
+
   meta = with stdenv.lib; {
     inherit version;
     description = "C library for the Publix Suffix List";
@@ -26,13 +58,4 @@ stdenv.mkDerivation rec {
     platforms = with platforms; linux ++ darwin;
     maintainers = with maintainers; [ nckx ];
   };
-
-  buildInputs = [ icu libxslt ];
-  nativeBuildInputs = [ autoreconfHook pkgconfig ];
-
-  configureFlags = "--disable-static --enable-man";
-
-  enableParallelBuilding = true;
-
-  doCheck = true;
 }

pkgs/development/libraries/libtap/default.nix

@@ -0,0 +1,28 @@
+{ stdenv, fetchurl, pkgconfig, cmake, perl }:
+
+with stdenv.lib;
+stdenv.mkDerivation rec{
+
+  name = "libtap-${version}";
+  version = "1.12.0";
+
+  src = fetchurl {
+    url = "http://web-cpan.shlomifish.org/downloads/${name}.tar.bz2";
+    sha256 = "1ms1770cx8c6q3lhn1chkzy12vzmjgvlms7cqhd2d3260j2wwv5s";
+  };
+
+  buildInputs = [ pkgconfig ];
+  propagatedBuildInputs = [ cmake perl ];
+
+  meta = {
+    description = "A library to implement a test protocol";
+    longDescription = ''
+      libtap is a library to implement the Test Anything Protocol for
+      C originally created by Nik Clayton. This is a maintenance
+      branch by Shlomi Fish.
+    '';
+    homepage = "http://www.shlomifish.org/open-source/projects/libtap/";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.AndersonTorres ];
+  };
+}

pkgs/development/libraries/qscintilla/default.nix

@@ -23,8 +23,6 @@ stdenv.mkDerivation rec {
     qmake qscintilla.pro
   '';
 
-  # TODO PyQt Support.
-
   meta = {
     description = "A Qt port of the Scintilla text editing library";
     longDescription = ''

pkgs/development/pure-modules/octave/default.nix

@@ -21,5 +21,8 @@ stdenv.mkDerivation rec {
     license = stdenv.lib.licenses.gpl3Plus;
     platforms = stdenv.lib.platforms.linux;
     maintainers = with stdenv.lib.maintainers; [ asppsa ];
+
+    # See https://bitbucket.org/purelang/pure-lang/issues/38
+    broken = true;
   };
 }

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

@@ -21,12 +21,12 @@ AffyExpress = derive { name="AffyExpress"; version="1.35.0"; sha256="1ysn3c8mpnq
 AffyRNADegradation = derive { name="AffyRNADegradation"; version="1.15.0"; sha256="0x7mwlzvcxplvijprch0anwbfmj1qkrxqd9rc6f4p0zf88z2csal"; depends=[affy]; };
 AffyTiling = derive { name="AffyTiling"; version="1.27.0"; sha256="1jqil9hd10cwsqdlxjd7c8s0p9fvrfcqxiw8rfrq117c8dlgl7w6"; depends=[affxparser affy preprocessCore]; };
 AgiMicroRna = derive { name="AgiMicroRna"; version="2.19.0"; sha256="1m1fi6pdqwnfn21a4i7psxdg12bn6bhvcsi43bhwlzxzkrz00257"; depends=[affy affycoretools Biobase limma preprocessCore]; };
-AllelicImbalance = derive { name="AllelicImbalance"; version="1.7.17"; sha256="0fgqsdlnch5rh04pnzjypgba2n67j3m2aab2yddl0kf0wsmb8zwg"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges Gviz IRanges lattice Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; };
+AllelicImbalance = derive { name="AllelicImbalance"; version="1.7.19"; sha256="09kjl7rka00vqysg13naqqcks5mjygg45yb6z6k1qmbc7xd19ggl"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges Gviz IRanges lattice Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; };
-AnalysisPageServer = derive { name="AnalysisPageServer"; version="1.1.2"; sha256="057xik4hxaqz1f9m8clq504xa4km2byag546iw20v6i0qa9s1dwi"; depends=[Biobase graph log4r rjson]; };
+AnalysisPageServer = derive { name="AnalysisPageServer"; version="1.1.3"; sha256="1k07v1flb7zvni6gmmpjrwl5hrs7adfhcjcg58vqj0b3nbij7aa0"; depends=[Biobase graph log4r rjson]; };
 AnnotationDbi = derive { name="AnnotationDbi"; version="1.31.17"; sha256="04xkhqnr9hmgxihfhn35a6s68s8x5layl7mf5whwhwxmlcd76lx4"; depends=[Biobase BiocGenerics DBI IRanges RSQLite S4Vectors]; };
-AnnotationForge = derive { name="AnnotationForge"; version="1.11.7"; sha256="00agvwzmnvs8vx2y62x5qd9y09045j74kk9kp69v8m1iqpigs1v0"; depends=[AnnotationDbi Biobase BiocGenerics DBI RSQLite S4Vectors]; };
+AnnotationForge = derive { name="AnnotationForge"; version="1.11.15"; sha256="02z3kxqcn87ykdsxfzs9j0qzpjkb2k79sz89lxrggk24jxk0rr35"; depends=[AnnotationDbi Biobase BiocGenerics DBI RSQLite S4Vectors]; };
 AnnotationFuncs = derive { name="AnnotationFuncs"; version="1.19.0"; sha256="1qjvkbqpyhwibdqv1c4n2z5wjnzx0h3kdas3fs33jhb597bxhl1y"; depends=[AnnotationDbi]; };
-AnnotationHub = derive { name="AnnotationHub"; version="2.1.28"; sha256="055biw0izf0la405igpp22azgharwhr6xfks32lr4dgbh8n70qjd"; depends=[AnnotationDbi BiocGenerics BiocInstaller httr interactiveDisplayBase RSQLite S4Vectors]; };
+AnnotationHub = derive { name="AnnotationHub"; version="2.1.32"; sha256="1a8hxbj97fhg64zxfhwk107ih8y4zgq48yx6xgpzm2pdsx5x9ndx"; depends=[AnnotationDbi BiocGenerics BiocInstaller httr interactiveDisplayBase RSQLite S4Vectors]; };
 ArrayExpress = derive { name="ArrayExpress"; version="1.29.1"; sha256="0gyckxsmmh81ykf7mj952h2a4z58xrf9lbnmv884hz7zj317lf83"; depends=[affy Biobase limma XML]; };
 ArrayExpressHTS = derive { name="ArrayExpressHTS"; version="1.19.0"; sha256="0qyd9jhkvw4lxqjvix28yzdx08hi7vf77ynlqxcl2q1lb3gmbxar"; depends=[Biobase BiocGenerics biomaRt Biostrings bitops DESeq edgeR GenomicRanges Hmisc IRanges R2HTML RColorBrewer rJava Rsamtools sampling sendmailR ShortRead snow svMisc XML]; };
 ArrayTV = derive { name="ArrayTV"; version="1.7.0"; sha256="11dlq4lmzw0x8z2qrxff6xlcilp95nd71jpdvg3i5yni3ws6z5m1"; depends=[DNAcopy foreach oligoClasses]; };
@@ -41,14 +41,14 @@ BEclear = derive { name="BEclear"; version="1.1.0"; sha256="1icaxkxwr2rkii4fffln
 BGmix = derive { name="BGmix"; version="1.29.0"; sha256="0s2s6ylbw2wvdkn28842ghsflhcmcn156zw3fxmbdnz7xs29qs1f"; depends=[KernSmooth]; };
 BHC = derive { name="BHC"; version="1.21.0"; sha256="0f8qqid4qxw52zjvvm024wcmn0afr7avkr4hr2jfyvs0ga49khx8"; depends=[]; };
 BRAIN = derive { name="BRAIN"; version="1.15.0"; sha256="09yd3xf3h85wdf56p38mnspyqbswl2v8zb81yg0a008p0l5ax8xr"; depends=[Biostrings lattice PolynomF]; };
-BSgenome = derive { name="BSgenome"; version="1.37.3"; sha256="1a0qk3lh2qhynsink8ysc16d4pmam2midakh26adn1hqrf6n22gb"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools rtracklayer S4Vectors XVector]; };
+BSgenome = derive { name="BSgenome"; version="1.37.4"; sha256="09vwkl517nnq9krxwyaf70xaqnk3r3ddxdd834pwrhyij7r49sqr"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools rtracklayer S4Vectors XVector]; };
 BUS = derive { name="BUS"; version="1.25.0"; sha256="1n3s0pw4ijgh927mahwqybks8i6ysybp7xn4a86nrbpr2kqhznrd"; depends=[infotheo minet]; };
 BaseSpaceR = derive { name="BaseSpaceR"; version="1.13.2"; sha256="17g87vfx6yy4cdqxchl9ig6s2vhnpfbarssw80ha6kbqw81jh55h"; depends=[RCurl RJSONIO]; };
 Basic4Cseq = derive { name="Basic4Cseq"; version="1.5.1"; sha256="0a4b11rv5ilv84qqpvf320c3knaajg4hlby5km0zzms3vbisr4hi"; depends=[Biostrings caTools GenomicAlignments GenomicRanges RCircos]; };
 BayesPeak = derive { name="BayesPeak"; version="1.21.0"; sha256="0mz00mk6gmc5g79iifn5hzfwf7s568n6s6wy46vrnnnnr3sk9w49"; depends=[IRanges]; };
 BeadDataPackR = derive { name="BeadDataPackR"; version="1.21.1"; sha256="16dh7byvigd6161qznd1k9cz9hp0r50nbrd8nqlsh28zr60pvrj3"; depends=[]; };
 BiGGR = derive { name="BiGGR"; version="1.5.0"; sha256="1q9m870pyhxd1627n94c259094k8jyrg22ni26qpnxkapj18lr0b"; depends=[hyperdraw hypergraph LIM rsbml stringr]; };
-BiRewire = derive { name="BiRewire"; version="2.1.2"; sha256="08innw83yr3imrgklva9djjx3a5sd7mqfnb70ggi6hia729kar01"; depends=[igraph slam]; };
+BiRewire = derive { name="BiRewire"; version="2.3.6"; sha256="1i2fn3lfc93gxy3llc6wwviq7pn3d3na556i2fl538ia66asm2ax"; depends=[igraph slam tsne]; };
 BiSeq = derive { name="BiSeq"; version="1.9.2"; sha256="1z401p2y9sa2cs1zwnkvf3968nyv5c7wcbxvldjyl5dg04qw88wn"; depends=[betareg Biobase BiocGenerics Formula GenomeInfoDb GenomicRanges globaltest IRanges lokern rtracklayer S4Vectors SummarizedExperiment]; };
 BicARE = derive { name="BicARE"; version="1.27.0"; sha256="19hslc78nijcs6gyxzzcd8856wa1gf5dsrvm4x6r9lprfrk7d7fb"; depends=[Biobase GSEABase multtest]; };
 BioMVCClass = derive { name="BioMVCClass"; version="1.37.0"; sha256="1k4ba98cjaqhy33vsmflnwasi0vxr30dvj6861pz625m87fyp2g6"; depends=[Biobase graph MVCClass Rgraphviz]; };
@@ -57,10 +57,10 @@ BioSeqClass = derive { name="BioSeqClass"; version="1.27.0"; sha256="1pv7zibcrgb
 Biobase = derive { name="Biobase"; version="2.29.1"; sha256="12cckssh7x4dd8vaapp5nfc5bfcqls8k3rblcfi17z5cpi0jply6"; depends=[BiocGenerics]; };
 BiocCaseStudies = derive { name="BiocCaseStudies"; version="1.31.0"; sha256="05nj9i9y8clf406bjcflj8lsrp9x9iw6my1bdqnxg3nv2krp37xn"; depends=[Biobase]; };
 BiocCheck = derive { name="BiocCheck"; version="1.5.6"; sha256="0gpmrqvj31n73bqljf23wbsw3hp44hl3z1jhc2q86s3mw6hlcfip"; depends=[BiocInstaller biocViews codetools devtools graph httr knitr optparse]; };
-BiocGenerics = derive { name="BiocGenerics"; version="0.15.3"; sha256="1wk7mr3jmjr2ljqqlmnpvb3x2cflkkhsyjl2cd4ns0gld4rmmm8x"; depends=[]; };
+BiocGenerics = derive { name="BiocGenerics"; version="0.15.5"; sha256="0l8gqzqqnxx99ziamclsf4krmlyrq6fjzifh19xg7wqiyp59h41x"; depends=[]; };
-BiocInstaller = derive { name="BiocInstaller"; version="1.19.8"; sha256="1jmzvs3sv324n9j6j8mrjpc648650k0sv23xni09x55zq41nm672"; depends=[]; };
+BiocInstaller = derive { name="BiocInstaller"; version="1.19.9"; sha256="14z4wgvry2mbbv847mlns6ff0irwfpyk1yfcxbr27wmlisk14wxz"; depends=[]; };
-BiocParallel = derive { name="BiocParallel"; version="1.3.31"; sha256="0s47gbrj8cs8wpsac14nj2blqwwr2fkg8fsr61fz5v0j21wrk3kd"; depends=[futile_logger snow]; };
+BiocParallel = derive { name="BiocParallel"; version="1.3.47"; sha256="0y3nv2ff8r2mijhljrgkky6b1vyb22iywbq38rv1ac6kbbpf680p"; depends=[futile_logger snow]; };
-BiocStyle = derive { name="BiocStyle"; version="1.7.4"; sha256="0wlydy1a3pspnyjg5vl0657z620n5vlhx99hxisskbrsr026mhmg"; depends=[]; };
+BiocStyle = derive { name="BiocStyle"; version="1.7.6"; sha256="1bdsz8s74wfgbq6afihi40ra1kljf8w8vxrgna34aks49908rxnd"; depends=[]; };
 Biostrings = derive { name="Biostrings"; version="2.37.2"; sha256="0j6701qgrnphsy9p34sf3s6d91j1zbd824zwv9rsfdmdffbkqq3b"; depends=[BiocGenerics IRanges S4Vectors XVector zlibbioc]; };
 BitSeq = derive { name="BitSeq"; version="1.13.0"; sha256="1d397bcdyi3d35l1q1661spm3xhr7hqlsrjr5a2ybsjs3wqkf4fj"; depends=[IRanges Rsamtools S4Vectors zlibbioc]; };
 BrainStars = derive { name="BrainStars"; version="1.13.0"; sha256="07wygi0fw0ilg404gx1ifswr61w6qlg8j0vkmnsr0migm70rgzzg"; depends=[Biobase RCurl RJSONIO]; };
@@ -73,7 +73,7 @@ BufferedMatrixMethods = derive { name="BufferedMatrixMethods"; version="1.33.0";
 CAFE = derive { name="CAFE"; version="1.5.0"; sha256="1kzy0g0kwvzvlls316cpvwrvnv5m9vklzjjsiiykvfq1wd21s96f"; depends=[affy annotate Biobase biovizBase GenomicRanges ggbio ggplot2 gridExtra IRanges]; };
 CAGEr = derive { name="CAGEr"; version="1.11.0"; sha256="1rz1r55aji1av70c661d7czwipxah9507h5i9hcngy84ic1m72f1"; depends=[beanplot BSgenome data_table GenomicRanges IRanges Rsamtools rtracklayer som VGAM]; };
 CALIB = derive { name="CALIB"; version="1.35.0"; sha256="08fgzq80ws4i6i1ppbqxdq3ba9qfdv4h0dyi08f9k91kfh1y31x4"; depends=[limma]; };
-CAMERA = derive { name="CAMERA"; version="1.25.0"; sha256="1nl5va3f436vwpcirhcpcph13s2vbh8965v8iizi29vk83gbyfza"; depends=[Biobase graph Hmisc igraph RBGL xcms]; };
+CAMERA = derive { name="CAMERA"; version="1.25.1"; sha256="0g8w5g6kr1s039cyvxk3pkw1mbskrij2vlc657bbxvs6pb3h2mrm"; depends=[Biobase graph Hmisc igraph RBGL xcms]; };
 CAnD = derive { name="CAnD"; version="1.1.1"; sha256="1zyp4z86fda83wdhjfdh1ck9ynvdvrrxcvdlgld7h4x295r35r3s"; depends=[ggplot2 reshape]; };
 CFAssay = derive { name="CFAssay"; version="1.3.0"; sha256="04zgyvm0rrs780z1vn4zzrh3w01lnhaywyn5ar6dvxcyxnr2y3qs"; depends=[]; };
 CGEN = derive { name="CGEN"; version="3.3.0"; sha256="03sdyw6z5xw9ndwkwdli7bz6v0ki8w2slx30v5lgm31lqgl4lpf6"; depends=[mvtnorm survival]; };
@@ -97,7 +97,7 @@ COHCAP = derive { name="COHCAP"; version="1.7.0"; sha256="0clr1jh4jnq54phsnl90zf
 COMPASS = derive { name="COMPASS"; version="1.7.2"; sha256="0c83fsrmi7d2888pa3lnln42mlbnjgvpxw337vdh3dar1185a5b0"; depends=[abind clue data_table knitr plyr RColorBrewer Rcpp scales]; };
 CORREP = derive { name="CORREP"; version="1.35.0"; sha256="0hlij2ch8r3lv130hvyshb82lfqz2c7kr56bka1ghmg6jp0xf1n6"; depends=[e1071]; };
 COSNet = derive { name="COSNet"; version="1.3.3"; sha256="0l9sn0cki0mxacxv0bwp3cczcl8rscx8g3lnr0r448f13j8198f4"; depends=[]; };
-CRISPRseek = derive { name="CRISPRseek"; version="1.9.2"; sha256="1h004gznxrm2k3l4xdr6iyn97rkkh8n85phskiink815ysm2l9z4"; depends=[BiocGenerics Biostrings BSgenome seqinr]; };
+CRISPRseek = derive { name="CRISPRseek"; version="1.9.7"; sha256="164f12s8arg1460fcsaa9l3igav4vjn4niwwpxaj19i4iar1f3pw"; depends=[BiocGenerics Biostrings BSgenome seqinr]; };
 CRImage = derive { name="CRImage"; version="1.17.0"; sha256="1sab95gngwi7c333n9hnbd9fdvdy9i69pjpx5ic5799s7qr03llw"; depends=[aCGH DNAcopy e1071 EBImage foreach MASS sgeostat]; };
 CSAR = derive { name="CSAR"; version="1.21.0"; sha256="1wn7zxmy5ssj2jkk2624j42yv67wdcigp5ksb6fc2kzpgnvqmxl1"; depends=[GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
 CSSP = derive { name="CSSP"; version="1.7.0"; sha256="1ydxj358sfaygzjvh0b042p7gymjyl7nr5cnxrh8c7x2mv2hdh4d"; depends=[]; };
@@ -111,7 +111,7 @@ ChAMP = derive { name="ChAMP"; version="1.7.0"; sha256="0ll50qyq9k8x4bv30dap6g6l
 ChIPQC = derive { name="ChIPQC"; version="1.5.2"; sha256="0g630lpzwfbg5hgicg0s906a3a6gidswmidszx0hmn3479fah74m"; depends=[Biobase BiocGenerics BiocParallel chipseq DiffBind GenomicAlignments GenomicRanges ggplot2 gtools IRanges Nozzle_R1 reshape2 Rsamtools S4Vectors]; };
 ChIPXpress = derive { name="ChIPXpress"; version="1.11.0"; sha256="11aifr69ss1hakrhba985bwz6k1sqkpzvv7gnzn8cgqnzxyr2i6b"; depends=[affy biganalytics bigmemory Biobase frma GEOquery]; };
 ChIPpeakAnno = derive { name="ChIPpeakAnno"; version="3.3.2"; sha256="0ww3ddnvdc561lhz27h8n3ywi1xpx1cbsqk2i8m5rkpykkkkr2dh"; depends=[AnnotationDbi BiocGenerics BiocInstaller biomaRt Biostrings BSgenome GenomicFeatures GenomicRanges graph IRanges limma multtest RBGL VennDiagram]; };
-ChIPseeker = derive { name="ChIPseeker"; version="1.5.6"; sha256="0ppv51hd44h15mkw15samdq1awsh1kdfy5p87pj60nmvbl0qj39h"; depends=[AnnotationDbi BiocGenerics boot dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gtools IRanges magrittr plotrix plyr RColorBrewer rtracklayer S4Vectors]; };
+ChIPseeker = derive { name="ChIPseeker"; version="1.5.8"; sha256="14prgyzrhh5r6mmrf88my8a0r3n6m45rx2ik0ajlz76avjpzdawr"; depends=[AnnotationDbi BiocGenerics boot dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gridBase gtools IRanges magrittr plotrix plyr RColorBrewer rtracklayer S4Vectors UpSetR]; };
 ChIPseqR = derive { name="ChIPseqR"; version="1.23.2"; sha256="1k1vbck7kjyzzgm0hg8hxpq6zfg71rca76q3998fcnnlzsmgvcf4"; depends=[BiocGenerics Biostrings fBasics GenomicRanges HilbertVis IRanges S4Vectors ShortRead timsac]; };
 ChIPsim = derive { name="ChIPsim"; version="1.23.1"; sha256="13kniwvwa49n1kc9114ljn1fmzaiyb2nh33if596llql60p7nd23"; depends=[Biostrings IRanges ShortRead XVector]; };
 ChemmineOB = derive { name="ChemmineOB"; version="1.7.1"; sha256="04agfsdzccsvvvis6vy1gg83gfs4nrph950v6bbzgk15ki32rsjz"; depends=[BH BiocGenerics Rcpp zlibbioc]; };
@@ -124,13 +124,13 @@ CoCiteStats = derive { name="CoCiteStats"; version="1.41.0"; sha256="0shp06qy8cv
 CoGAPS = derive { name="CoGAPS"; version="2.3.2"; sha256="0jh5ij66x3isz67mj0jwypyshplk1l1p47n2hvwgq87xmjzv6c8p"; depends=[BH gplots RColorBrewer Rcpp]; };
 CoRegNet = derive { name="CoRegNet"; version="1.5.0"; sha256="14yq1f005fcfmfp88h2fy05gdgbskjws11qbdh0ndx3sf93nzxm2"; depends=[arules igraph shiny]; };
 CompGO = derive { name="CompGO"; version="1.5.0"; sha256="128ib7w0jxba0p32s796i864b73zjfxac56znd0v4wv4vxv3jiv6"; depends=[GenomicFeatures ggplot2 pathview pcaMethods RDAVIDWebService reshape2 Rgraphviz rtracklayer]; };
-ComplexHeatmap = derive { name="ComplexHeatmap"; version="1.2.2"; sha256="0v1mj0n5gjdarwdrl9ir9gms0f3v0gplx4n34zvyszxivh4ph4jj"; depends=[circlize colorspace dendextend GetoptLong RColorBrewer]; };
+ComplexHeatmap = derive { name="ComplexHeatmap"; version="1.2.6"; sha256="0n0bn69ms6ny42i0rvajhvrwivxd21spgk9s9xzqbln7758fvnw2"; depends=[circlize colorspace dendextend GetoptLong RColorBrewer]; };
 ConsensusClusterPlus = derive { name="ConsensusClusterPlus"; version="1.23.0"; sha256="13iikfh234d2z4k487lb3shmnrfijygrf6gz3x481gba2psnbjyw"; depends=[Biobase cluster]; };
 CopyNumber450k = derive { name="CopyNumber450k"; version="1.5.0"; sha256="0mjhmh4shgckv43zvg4yqr17jfi9p9xnc40fwy9fw9c4vjcfsvsj"; depends=[Biobase BiocGenerics DNAcopy minfi preprocessCore]; };
-CopywriteR = derive { name="CopywriteR"; version="2.1.2"; sha256="0lja77qdfbsl9cc1nv4jbrjwiq8bb93ja6na8hqksrrm9g1qs4q4"; depends=[BiocParallel chipseq data_table DNAcopy futile_logger GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges matrixStats Rsamtools S4Vectors]; };
+CopywriteR = derive { name="CopywriteR"; version="2.1.3"; sha256="0qhl3lbdf9fsm6hx45sk2nihikbzh08lbnwaz1as3wf5cx7zm08c"; depends=[BiocParallel chipseq data_table DNAcopy futile_logger GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges matrixStats Rsamtools S4Vectors]; };
 CorMut = derive { name="CorMut"; version="1.11.0"; sha256="0s92bh3610frxbm0gqvlznay70dy7x61hvc0qgh6xmcyz0llx27g"; depends=[igraph seqinr]; };
 Cormotif = derive { name="Cormotif"; version="1.15.0"; sha256="1v36ylwkxr6yqasckmmj2dkr7s72f39srhwvm93rs1rl7kw4dc4p"; depends=[affy limma]; };
-CoverageView = derive { name="CoverageView"; version="1.5.1"; sha256="0qi8r6vw5c6kmlw12j81jmgn555wd51w80m80gm5n7hqnggpwkh4"; depends=[BiocGenerics GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors]; };
+CoverageView = derive { name="CoverageView"; version="1.5.2"; sha256="1bxx35h9d7gwm5m16i4hkf54zghij95jfxxc46x83glccsirah2f"; depends=[BiocGenerics GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors]; };
 DART = derive { name="DART"; version="1.17.1"; sha256="1z7lf4d9yjcyikq9j3348z5sxjqaly46c0ls7f9cl8nnqdpw7w42"; depends=[igraph]; };
 DASiR = derive { name="DASiR"; version="1.9.0"; sha256="0b3b7kmhsd6bb1s57c89h495j1ax6779wfca112fq6ba3z4dih3n"; depends=[Biostrings GenomicRanges IRanges XML]; };
 DAVIDQuery = derive { name="DAVIDQuery"; version="1.29.0"; sha256="0gvm6qjx8y61nbnbz66md74pfc4awj4900pjr8q1m5sip5yzbxj2"; depends=[RCurl]; };
@@ -138,20 +138,21 @@ DBChIP = derive { name="DBChIP"; version="1.13.0"; sha256="0gk9kgmyp9540sq5gpbn7
 DECIPHER = derive { name="DECIPHER"; version="1.15.0"; sha256="1kbdsqvkznzsk4ljy91r5ipndwxb8hhkm46qqkakgr24mia3yvl1"; depends=[Biostrings DBI IRanges RSQLite S4Vectors XVector]; };
 DEDS = derive { name="DEDS"; version="1.43.0"; sha256="1z049ppkrbyp0xjpiygz5i6rbxbv3vvnvspwz2vv77495v7ykj6z"; depends=[]; };
 DEGraph = derive { name="DEGraph"; version="1.21.0"; sha256="17f04qngcx8y4glr5wiryi8fifbla8fxh8nb6wagnrai5x6vhzis"; depends=[graph KEGGgraph lattice mvtnorm NCIgraph R_methodsS3 R_utils RBGL Rgraphviz rrcov]; };
-DEGreport = derive { name="DEGreport"; version="1.4.0"; sha256="06l803iy18kkv05b4h46vmzws20c0735m6csfkn2vp3bik8xh4lp"; depends=[coda edgeR ggplot2 Nozzle_R1 plyr quantreg]; };
+DEGreport = derive { name="DEGreport"; version="1.5.0"; sha256="14mrfnmkik74yf5vml03x96brq7qlja2hpvndbffxr5a8ddb7117"; depends=[coda edgeR ggplot2 Nozzle_R1 plyr quantreg]; };
 DEGseq = derive { name="DEGseq"; version="1.23.0"; sha256="0993f140wwv9z9l53f9g74x7l28bflxq7wdcbilfz7ijhh7isr7p"; depends=[qvalue samr]; };
 DESeq = derive { name="DESeq"; version="1.21.0"; sha256="13f6phdf9g325dlpn38l7zrq3mzldhldil134acxi9p3l50bx23y"; depends=[Biobase BiocGenerics genefilter geneplotter lattice locfit MASS RColorBrewer]; };
-DESeq2 = derive { name="DESeq2"; version="1.9.21"; sha256="0ywhakri35cz37zlwv760zgmk1z9ldivl0i24mawavccc0hcvrhk"; depends=[Biobase BiocGenerics BiocParallel genefilter geneplotter GenomicRanges ggplot2 Hmisc IRanges locfit Rcpp RcppArmadillo S4Vectors SummarizedExperiment]; };
+DESeq2 = derive { name="DESeq2"; version="1.9.26"; sha256="0b7w0csg7q5nqbrmc83rviiwhahq88zlqmxwlkz5g01w9zzkgc80"; depends=[Biobase BiocGenerics BiocParallel genefilter geneplotter GenomicRanges ggplot2 Hmisc IRanges locfit Rcpp RcppArmadillo S4Vectors SummarizedExperiment]; };
-DEXSeq = derive { name="DEXSeq"; version="1.15.9"; sha256="0ml4ibzhw38w0mfp0vdbbkisz40rw65yyd71q3ppj7jg4r4ch39a"; depends=[Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools statmod stringr]; };
+DEXSeq = derive { name="DEXSeq"; version="1.15.10"; sha256="1sddciia2zxn5jxpzyrg3mxcrl28kcvxfbc6nk5dwrnqd9mj53jj"; depends=[Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools statmod stringr]; };
 DFP = derive { name="DFP"; version="1.27.0"; sha256="0xcipbhfzvrpbm6dh2y3lbvfbwpn4wly32sssfm702zik5wm9dy1"; depends=[Biobase]; };
 DMRcaller = derive { name="DMRcaller"; version="1.1.1"; sha256="1g7q7cwivvb0m2y4fixvbxp51zfag1jv66bdlai3gawr94pcx56y"; depends=[GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; };
-DMRcate = derive { name="DMRcate"; version="1.5.0"; sha256="12q6if9lljia37zwhcc9fpcp9vhkp1qhzchpypwwyn2j4344bmp3"; depends=[limma minfi]; };
+DMRcate = derive { name="DMRcate"; version="1.5.61"; sha256="0ss8zk2b1y83q49pv9fdm2rqw5hlnd189knfg1y8y0psfjhc9knp"; depends=[limma minfi]; };
 DMRforPairs = derive { name="DMRforPairs"; version="1.5.0"; sha256="0d14qgx07xq7wa687a2znpfw0zcg8ccvxjawkjdbi6ayjwpb6zd7"; depends=[GenomicRanges Gviz R2HTML]; };
 DNAcopy = derive { name="DNAcopy"; version="1.43.0"; sha256="1v1i4bfkblimdmazv29csqr46jaiv8lncihgywvq5wfn8ccr7xl9"; depends=[]; };
 DOQTL = derive { name="DOQTL"; version="1.3.0"; sha256="0g3nyamqdhjg8105kcq6nsgjgqzcxkp04194j82v1xb31baj53bg"; depends=[annotate annotationTools Biobase BiocGenerics biomaRt corpcor GenomicRanges hwriter IRanges mclust QTLRel Rsamtools RUnit S4Vectors XML]; };
-DOSE = derive { name="DOSE"; version="2.7.9"; sha256="0l0rkd7siz251pxgmfv4ijq1l68w3lkjlc83zmhf4ddjf3db07ig"; depends=[AnnotationDbi ggplot2 GOSemSim igraph plyr qvalue reshape2 scales]; };
+DOSE = derive { name="DOSE"; version="2.7.10"; sha256="093gyplk5ylwndynlcvm8s44ra8b6i6xrkqswc7zprndkawc4bgp"; depends=[AnnotationDbi ggplot2 GOSemSim igraph plyr qvalue reshape2 scales]; };
-DSS = derive { name="DSS"; version="2.7.2"; sha256="01czzgkx6rqpps93vfn8dg2n2hm2nkd887mc955z67845jkrgi2j"; depends=[Biobase bsseq]; };
+DSS = derive { name="DSS"; version="2.8.1"; sha256="0nhrq05b5rsfdcxc96pdsppnfwz106k7xdxccgr0xjypbhm01hsk"; depends=[Biobase bsseq]; };
 DTA = derive { name="DTA"; version="2.15.0"; sha256="0amibwj5mnm2plkf3ys8sgy4lpwr60fnvika0psdrahgb4blmkzp"; depends=[LSD scatterplot3d]; };
+DeMAND = derive { name="DeMAND"; version="0.99.9"; sha256="013zwa4flbsf9rwlnbzhg1sgfqwvrr01v9bhgpk73kx312zg30sg"; depends=[KernSmooth]; };
 DeconRNASeq = derive { name="DeconRNASeq"; version="1.11.0"; sha256="0665chwpbs2pw753nb2x65cs9r9ghb5123bsrzrv6pz2p3ni8yz7"; depends=[ggplot2 limSolve pcaMethods]; };
 DiffBind = derive { name="DiffBind"; version="1.15.3"; sha256="1akx65vi8razwpfxnvilh4x1vb8qbsfr2q8lygsb3imfrrb83q44"; depends=[amap edgeR GenomicAlignments GenomicRanges gplots IRanges lattice limma locfit RColorBrewer Rsamtools SummarizedExperiment systemPipeR zlibbioc]; };
 DirichletMultinomial = derive { name="DirichletMultinomial"; version="1.11.2"; sha256="01wmvs7alq7gy1nmb5gdbglfs51qdhwysbmmjvh7yyhb8dqbvrj4"; depends=[IRanges S4Vectors]; };
@@ -159,8 +160,8 @@ DriverNet = derive { name="DriverNet"; version="1.9.0"; sha256="0visiafw9m7i0yy7
 DrugVsDisease = derive { name="DrugVsDisease"; version="2.9.0"; sha256="1wmw1r0x7kkmp47743aq0pp71wamnf5gsk6bhz6rdvswzb12iyqk"; depends=[affy annotate ArrayExpress BiocGenerics biomaRt GEOquery limma qvalue RUnit xtable]; };
 DupChecker = derive { name="DupChecker"; version="1.7.0"; sha256="02wwwnx3w8rxiassd62xr295paw8py9pqsk1396qb5k773l6bfxv"; depends=[R_utils RCurl]; };
 DynDoc = derive { name="DynDoc"; version="1.47.0"; sha256="0gpmhqav4dx8p86pkh18fpmlki60zqaz00m2zhziiawigbrz41ph"; depends=[]; };
-EBImage = derive { name="EBImage"; version="4.11.5"; sha256="15npg7r76avlxq036yis85b91bgl10y4wjjcdnrcn39dbvb50zav"; depends=[abind BiocGenerics fftwtools jpeg locfit png tiff]; };
+EBImage = derive { name="EBImage"; version="4.11.7"; sha256="1zddydckv3zy8wf0wh34g5yg8s1p255h66ym6lnw3l5id7v32wz8"; depends=[abind BiocGenerics fftwtools jpeg locfit png tiff]; };
-EBSeq = derive { name="EBSeq"; version="1.9.2"; sha256="0n3y9ikamcfm786fvqp5b2b4g2fx8hvnicsx1sh4rvrpyab9f5jm"; depends=[blockmodeling gplots]; };
+EBSeq = derive { name="EBSeq"; version="1.9.4"; sha256="01pzjhqx61005jbw3l3m24h10225fkml9889aqvxdxzv5n4rvc03"; depends=[blockmodeling gplots testthat]; };
 EBSeqHMM = derive { name="EBSeqHMM"; version="1.3.1"; sha256="0lyf363f1wfgacrj5cyq8n3f3ssl5q400mn2q94cpai6k0qmvgs1"; depends=[EBSeq]; };
 EBarrays = derive { name="EBarrays"; version="2.33.0"; sha256="1zvfqf49chiks5vmj5ki89pvy14bm1cman47n3ybba1gg8z8mw94"; depends=[Biobase cluster lattice]; };
 EBcoexpress = derive { name="EBcoexpress"; version="1.13.0"; sha256="0fl0a7xasqcwvjlgf3h51akyhwpras2865m2idz1nmacm42q1w79"; depends=[EBarrays mclust minqa]; };
@@ -168,12 +169,12 @@ EDASeq = derive { name="EDASeq"; version="2.3.2"; sha256="0l1mmpy71pqqmqnx4xxn1v
 EDDA = derive { name="EDDA"; version="1.7.0"; sha256="0dyyhnc9v232njqnrcaq78g2m1qws30qcf6bsswq2di235ymk2g0"; depends=[baySeq DESeq edgeR Rcpp ROCR snow]; };
 ELBOW = derive { name="ELBOW"; version="1.5.0"; sha256="0lnc5hw2x4p9yd561w9dwplf7q2slcaghxsh5796bmyxjxhxanpy"; depends=[]; };
 ELMER = derive { name="ELMER"; version="1.00.0"; sha256="1kb7rixq02cc0cwm52acji69p89jq07zsagg7a8qva6gshs94k86"; depends=[GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra IRanges minfi reshape S4Vectors]; };
-EMDomics = derive { name="EMDomics"; version="1.1.0"; sha256="1i2dy2vqig0lkd13xy4yfwq58zyjiqavpmcvg6pvkh2l48ap1jds"; depends=[BiocParallel emdist ggplot2 matrixStats]; };
+EMDomics = derive { name="EMDomics"; version="1.1.2"; sha256="14gh59gq0wjhkmrclpmlixn3mbabwwq01bwq6hilf9s2s0i8qkpv"; depends=[BiocParallel CDFt emdist ggplot2 matrixStats preprocessCore]; };
 ENCODExplorer = derive { name="ENCODExplorer"; version="1.1.3"; sha256="054cm1ldas26gv4xn16w3i25kykwnikj4s83g7sxxdij93m5rmlb"; depends=[jsonlite RSQLite]; };
 ENVISIONQuery = derive { name="ENVISIONQuery"; version="1.17.0"; sha256="1dnlw62hwysij63yc856c2sncgfwdq0rpmcds6i6wigdcfd21w8q"; depends=[rJava XML]; };
-ENmix = derive { name="ENmix"; version="1.1.6"; sha256="069dniqyg0pljbwnl24bv5kfdh5v2j9vbvyxc127ag1isggh9m7b"; depends=[Biobase doParallel foreach geneplotter impute MASS minfi preprocessCore sva wateRmelon]; };
+ENmix = derive { name="ENmix"; version="1.1.7"; sha256="0p5ywjnm0xknr6k7bnkhcn69870f5wwlq70yfqiah7syqmyim67d"; depends=[Biobase doParallel foreach geneplotter impute MASS minfi preprocessCore sva wateRmelon]; };
 EasyqpcR = derive { name="EasyqpcR"; version="1.11.1"; sha256="0s2jyg6b14wbyl0c1n89c7bi7p88g7s1rz8d830p9hh2x75ly6zj"; depends=[gWidgetsRGtk2 matrixStats plotrix plyr]; };
-EnrichmentBrowser = derive { name="EnrichmentBrowser"; version="1.3.0"; sha256="1a6w3drh5x20wvxpx1cb5q2h9k6jh65v9hh81924lcp4baplpx31"; depends=[Biobase graph KEGGgraph KEGGREST limma MASS mixtools neaGUI qvalue RColorBrewer Rgraphviz safe SPIA stringr]; };
+EnrichmentBrowser = derive { name="EnrichmentBrowser"; version="1.99.6"; sha256="17xchpf0ddxihz6p0lm0nhhyrbaahcar1phl842b30ccv877ibrs"; depends=[AnnotationDbi Biobase biocGraph biomaRt ComplexHeatmap DESeq2 EDASeq edgeR geneplotter graph GSEABase hwriter KEGGgraph KEGGREST limma MASS mixtools neaGUI npGSEA PathNet pathview ReportingTools Rgraphviz S4Vectors safe SPIA stringr SummarizedExperiment topGO]; };
 ExiMiR = derive { name="ExiMiR"; version="2.11.0"; sha256="1gmfrn3jq4pz5wmijywhxr0kx79534fhrfnqyhjmqq3s9sjn2cbh"; depends=[affy affyio Biobase limma preprocessCore]; };
 ExpressionView = derive { name="ExpressionView"; version="1.21.0"; sha256="026w9f119j26c1078nwg4rhfc54wlb3i56iy8bi0cjpvbm4p698f"; depends=[AnnotationDbi bitops caTools eisa isa2]; };
 FEM = derive { name="FEM"; version="2.3.0"; sha256="112mmah33ar36cpqjwanrfyhdwjfympnvmxwirxbbnk0nfp9cvpr"; depends=[AnnotationDbi corrplot igraph impute limma marray Matrix]; };
@@ -182,12 +183,12 @@ FISHalyseR = derive { name="FISHalyseR"; version="1.3.0"; sha256="0xnmww7ldyxghq
 FRGEpistasis = derive { name="FRGEpistasis"; version="1.5.0"; sha256="1vvcphgirvghzjvic5yq6nl229ryc0y4kp5qd25kgspbcgblg01q"; depends=[fda MASS]; };
 FlowRepositoryR = derive { name="FlowRepositoryR"; version="1.1.1"; sha256="1xxljbdbvxg1dbm82r86frw2bskmfrl6rv98xz0z4jfc0w4ag3pd"; depends=[RCurl XML]; };
 FlowSOM = derive { name="FlowSOM"; version="1.1.0"; sha256="0k5pw46dbhm6nssr5szj251v3479xgky2iipihrdvp5lr5lhxilq"; depends=[BiocGenerics ConsensusClusterPlus flowCore igraph tsne]; };
-FourCSeq = derive { name="FourCSeq"; version="1.3.4"; sha256="1csxfr23b3g1k54h4ksnhg7c7d6aw28v32lrrqyq7x7xls9cx2lg"; depends=[Biobase Biostrings DESeq2 fda GenomicAlignments GenomicRanges ggbio ggplot2 gtools LSD Matrix reshape2 Rsamtools rtracklayer SummarizedExperiment]; };
+FourCSeq = derive { name="FourCSeq"; version="1.3.5"; sha256="1mjvgi1cbfi5brl7l0v8026hjjksh81kpslm6w6i6b1llcn1sf65"; depends=[Biobase Biostrings DESeq2 fda GenomicAlignments GenomicRanges ggbio ggplot2 gtools LSD Matrix reshape2 Rsamtools rtracklayer SummarizedExperiment]; };
 FunciSNP = derive { name="FunciSNP"; version="1.11.0"; sha256="19kl14yzqr59ngrd5ygr858zbvx23rihlr4vw5bfdy9cgwlvlzab"; depends=[AnnotationDbi ChIPpeakAnno GenomicRanges ggplot2 IRanges plyr reshape Rsamtools rtracklayer scales snpStats VariantAnnotation]; };
 GENE_E = derive { name="GENE.E"; version="1.9.0"; sha256="10c9mw9f619z2ai43qvagj7p1lsqpv90z8vzsyyxym614lvlqfzm"; depends=[RCurl rhdf5]; };
 GENESIS = derive { name="GENESIS"; version="1.1.0"; sha256="01d3yc5rc4y22znr7zf980m458qvnmjxpml353k7bkwyz6xyn0fj"; depends=[GWASTools]; };
 GEOmetadb = derive { name="GEOmetadb"; version="1.29.0"; sha256="1s9x3dbh61xisk5hwzqv3991savygdcwv5cww447w4bfgwffzplg"; depends=[GEOquery RSQLite]; };
-GEOquery = derive { name="GEOquery"; version="2.35.4"; sha256="1ny592c1s36a1hkgaqqyss65c190bw5612l23qc9y9qhf4sarq38"; depends=[Biobase RCurl XML]; };
+GEOquery = derive { name="GEOquery"; version="2.35.5"; sha256="0c1jyvl5sm0yjlk4ji8qjwxm4rqakmjz04aq6m8biyf04cdd2crk"; depends=[Biobase RCurl XML]; };
 GEOsubmission = derive { name="GEOsubmission"; version="1.21.0"; sha256="1rr8k4myw7jibibclphj63hp4byk3v0cg37vnyc5b0iacdp8s9gn"; depends=[affy Biobase]; };
 GEWIST = derive { name="GEWIST"; version="1.13.0"; sha256="1mlzyjggv0rh9xk9pifshhdri3vapvzk2h47g75wx57yfapamcwn"; depends=[car]; };
 GGBase = derive { name="GGBase"; version="3.31.2"; sha256="0xbkj7dr7xaq3pj4jph5ii78c4ax5b0p6jqmvkv2hr3j70qk3mh2"; depends=[AnnotationDbi Biobase BiocGenerics digest genefilter GenomicRanges IRanges limma Matrix S4Vectors snpStats SummarizedExperiment]; };
@@ -201,14 +202,14 @@ GOexpress = derive { name="GOexpress"; version="1.3.2"; sha256="151hqhyjaq3ggigi
 GOstats = derive { name="GOstats"; version="2.35.1"; sha256="1almz6gc2xm3njz8pjvynpnniz7xdd8z5293cfvx91v11lz70v7f"; depends=[annotate AnnotationDbi AnnotationForge Biobase Category graph RBGL]; };
 GOsummaries = derive { name="GOsummaries"; version="2.3.0"; sha256="09c4grz9ljwrz37yv9k6gna9zxk708vxfz2190xz7za0mrql1k3k"; depends=[ggplot2 gProfileR gtable limma plyr Rcpp reshape2]; };
 GRENITS = derive { name="GRENITS"; version="1.21.0"; sha256="1lm0074dw0248vyj9wl99if489dx38ia8wscx61842jyi4qz7r2q"; depends=[ggplot2 Rcpp RcppArmadillo reshape2]; };
-GSAR = derive { name="GSAR"; version="1.3.2"; sha256="0fqv6lwi94ibwjjv6g0qmc8plc0ghszvjpd73m88080jiaw44yfl"; depends=[igraph]; };
+GSAR = derive { name="GSAR"; version="1.3.4"; sha256="1hgakyl4ply01m77ffy2vjflwzn5iqnfbsp4a4smi762innm5f3z"; depends=[igraph]; };
 GSCA = derive { name="GSCA"; version="1.7.0"; sha256="1hv9r59fx1hbjnga26shb8crxji1bzmzjmwfbk1wrlm8dsikjnyg"; depends=[ggplot2 gplots RColorBrewer reshape2 rhdf5 shiny sp]; };
 GSEABase = derive { name="GSEABase"; version="1.31.3"; sha256="1jq3s3pha624gns7d7yf8qqgzq0fm3qgjrkwdkxgbpc7b09baiz0"; depends=[annotate AnnotationDbi Biobase BiocGenerics graph XML]; };
 GSEAlm = derive { name="GSEAlm"; version="1.29.0"; sha256="13ixp6vq9g9ag5rndc40gw64vny70zcj6lll7r7vz06p5i9b6kyk"; depends=[Biobase]; };
 GSRI = derive { name="GSRI"; version="2.17.0"; sha256="158dipqi9mh79d42pv5qsa1gwxz660kl474rdnkd59rnxh7ziyf3"; depends=[Biobase fdrtool genefilter GSEABase les]; };
 GSReg = derive { name="GSReg"; version="1.3.0"; sha256="07s60j68i1r64y8x8r1r9s6w020n41137cf2aj9hrsw6gn4ajh15"; depends=[]; };
 GSVA = derive { name="GSVA"; version="1.17.0"; sha256="0rk1srk95qia5ap69c2lysgv7r8qh50f50v9b569d2v2vjb0hpq5"; depends=[Biobase BiocGenerics GSEABase]; };
-GWASTools = derive { name="GWASTools"; version="1.15.12"; sha256="04k5grfbrcpwnxxpirzb7x9488q8sq19lg00yn4mhpr7y1znrmpc"; depends=[Biobase DBI DNAcopy gdsfmt GWASExactHW lmtest logistf ncdf quantsmooth RSQLite sandwich survival]; };
+GWASTools = derive { name="GWASTools"; version="1.15.14"; sha256="1ir5czbs3z9myq8659xc15i61bk0yifwcdycbgzmfd9frf9mw8ji"; depends=[Biobase DBI DNAcopy gdsfmt GWASExactHW lmtest logistf ncdf quantsmooth RSQLite sandwich survival]; };
 GeneAnswers = derive { name="GeneAnswers"; version="2.11.1"; sha256="15rf8syxhj3332d7f4jkvyby05r3iia7p1ryz1zv629waz6mr4nh"; depends=[annotate Biobase downloader Heatplus igraph MASS RBGL RColorBrewer RCurl RSQLite XML]; };
 GeneExpressionSignature = derive { name="GeneExpressionSignature"; version="1.15.0"; sha256="0wni584412af8a2wzk5r8nf63grw86d6fk74cmwksirw2734mmqs"; depends=[Biobase PGSEA]; };
 GeneGA = derive { name="GeneGA"; version="1.19.0"; sha256="0irfr4q55rda8acchgcqsksh6ija87fryj822nb3d4zklv9raqfv"; depends=[hash seqinr]; };
@@ -222,23 +223,23 @@ GeneticsDesign = derive { name="GeneticsDesign"; version="1.37.0"; sha256="08awf
 GeneticsPed = derive { name="GeneticsPed"; version="1.31.0"; sha256="17fs4gvirji3qp9ik480jpz6qrbq209sjhn57ipkaafvx7rw5j4i"; depends=[gdata genetics MASS]; };
 GenoView = derive { name="GenoView"; version="1.3.0"; sha256="09k9xjmx3qmsfr3a4vrfgs73r0xsymf5m4gl0zjjk4cnfk7bs41v"; depends=[biovizBase GenomicRanges ggbio ggplot2 gridExtra]; };
 GenomeGraphs = derive { name="GenomeGraphs"; version="1.29.0"; sha256="0kl2gapg7hnl4zfsamb3vwmj7z0vag7vd8viwh0pwqj0pd45dswa"; depends=[biomaRt]; };
-GenomeInfoDb = derive { name="GenomeInfoDb"; version="1.5.8"; sha256="0kdz1mkn3ljwxcz6v0np7gbb7b7sqxfj80sxrah3bnck2bzg1yra"; depends=[BiocGenerics IRanges S4Vectors]; };
+GenomeInfoDb = derive { name="GenomeInfoDb"; version="1.5.9"; sha256="1mnskpj4qb6fyg7a6qkzs6cmxzn0bjff0zzgnp17bm94vx0334zh"; depends=[BiocGenerics IRanges S4Vectors]; };
-GenomicAlignments = derive { name="GenomicAlignments"; version="1.5.11"; sha256="1w4wmxcyj0ja9nkn35n5qhhax0b7sh4pjxk2hib71323y80mxlld"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; };
+GenomicAlignments = derive { name="GenomicAlignments"; version="1.5.12"; sha256="0p1vnkh5h8w69is254zkzpj5y2a9c2yc2s7lvqhkf861x6fgkz1l"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; };
-GenomicFeatures = derive { name="GenomicFeatures"; version="1.21.13"; sha256="1swk94rqpvfysr3x1r61ypq9vlw1ryc0iw0x6dazfjjchaln0h07"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors]; };
+GenomicFeatures = derive { name="GenomicFeatures"; version="1.21.14"; sha256="0lnkidki4pl40878nd6bzswkdxgkz75nn052693glcvzw3qm6wg5"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors]; };
 GenomicFiles = derive { name="GenomicFiles"; version="1.5.4"; sha256="13lglgxkqsxgi453dk56ry7amnv6lyddy74fnhhsqinj5ip9k3vw"; depends=[BiocGenerics BiocParallel GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; };
-GenomicInteractions = derive { name="GenomicInteractions"; version="1.3.4"; sha256="1dh9l0abwfc9dkznvpnzsxlggifvh8zfcmb22mc36lnkq42r033d"; depends=[BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra igraph IRanges plotrix Rsamtools rtracklayer S4Vectors stringr]; };
+GenomicInteractions = derive { name="GenomicInteractions"; version="1.3.6"; sha256="0003hd22c3nfdb5h84pvd754gcpj3b6flzg8nhf7d0s99nzddr6a"; depends=[BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph IRanges Rsamtools rtracklayer S4Vectors stringr]; };
-GenomicRanges = derive { name="GenomicRanges"; version="1.21.16"; sha256="11s14ikk2pj3hycanyjv6s1pild3987gfvf4vnzm6a6ilmqsyqzy"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; };
+GenomicRanges = derive { name="GenomicRanges"; version="1.21.17"; sha256="1hp2knf1qnph62480hzmn68lxp193x4zv3b0yx2a7khj4sgy7566"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; };
 GenomicTuples = derive { name="GenomicTuples"; version="1.3.1"; sha256="0i91qs1c84lyh0irhgnbnnvag0j3f48gfxxndk5x0yjf9kpa0hca"; depends=[Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; };
 Genominator = derive { name="Genominator"; version="1.23.0"; sha256="03pacbd3d5q7ykrflg258zcf8yfzm8kc976aw3d38q7agkia69h2"; depends=[BiocGenerics DBI GenomeGraphs IRanges RSQLite]; };
 GlobalAncova = derive { name="GlobalAncova"; version="3.37.0"; sha256="1j35r39plsxlkla2bv7wvg0if5gs2mfy71g6zb65g6ml5cqws45r"; depends=[annotate AnnotationDbi corpcor globaltest]; };
-GoogleGenomics = derive { name="GoogleGenomics"; version="1.1.1"; sha256="06mcg36x41k9s9ick6y3vrg5r4fnkz5qb77a7dh7kk2skinvzips"; depends=[Biostrings GenomeInfoDb GenomicAlignments GenomicRanges httr IRanges rjson Rsamtools S4Vectors VariantAnnotation]; };
+GoogleGenomics = derive { name="GoogleGenomics"; version="1.1.3"; sha256="1y5jkxhrfi5gkckfmilqsshv5l5ql25iwpmqbr5slch1h4myskbl"; depends=[Biostrings GenomeInfoDb GenomicAlignments GenomicRanges httr IRanges rjson Rsamtools S4Vectors VariantAnnotation]; };
 GraphAT = derive { name="GraphAT"; version="1.41.0"; sha256="1mjd54zy4l7ivy347zn5rv6gn65sjhxn2cxm417fm83hm542327l"; depends=[graph MCMCpack]; };
 GraphAlignment = derive { name="GraphAlignment"; version="1.33.0"; sha256="14zxbw8cj12wr6c2a0a6mfskr9sqf6cdfyz0ccbzy91d1lnrxzdf"; depends=[]; };
 GraphPAC = derive { name="GraphPAC"; version="1.11.0"; sha256="1p0rkc1qz0yf0lxyjfvrpd7nqky855kmhb1pdwxg3ckifnypw5mc"; depends=[igraph iPAC RMallow TSP]; };
 GreyListChIP = derive { name="GreyListChIP"; version="1.1.1"; sha256="0kbl9m37aiyv6yrqg4z352k7dpdpxm7yywymjfa9gdd0rv1cy401"; depends=[BSgenome GenomeInfoDb GenomicAlignments GenomicRanges MASS Rsamtools rtracklayer]; };
 Gviz = derive { name="Gviz"; version="1.13.3"; sha256="0qbad4r0k7j1z4gg785iv57azp9ljlxv5jngnk9kfif05rd3k7v3"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; };
 HCsnip = derive { name="HCsnip"; version="1.9.0"; sha256="14f881v776xn8lw4lvjc26s72laxs9zph902875f76ykbzygayd9"; depends=[Biobase clusterRepro coin fpc impute randomForestSRC sigaR sm survival]; };
-HDTD = derive { name="HDTD"; version="1.3.2"; sha256="19kzd1sjl0riwisdbrsy9j2pd39lpxwmizrnnj65hrfv6dwaqsgq"; depends=[]; };
+HDTD = derive { name="HDTD"; version="1.3.3"; sha256="0b9z2bkfislxn9w5bjcd5jcpby2yq5bhn6zxvylngjwqz98v30hl"; depends=[]; };
 HELP = derive { name="HELP"; version="1.27.0"; sha256="1n2fj316ha2l941biyr9d56pry6n39drwa820rgyrwd116rzx79d"; depends=[Biobase]; };
 HEM = derive { name="HEM"; version="1.41.0"; sha256="0qi6q305p0vdhyah3860dpd3z0lyyn6wn5x0m3mj3p739pk288ik"; depends=[Biobase]; };
 HIBAG = derive { name="HIBAG"; version="1.5.0"; sha256="0rrpz4brij408szfmzv7gpk0hrhikjyx061gkamb02ry1my722j1"; depends=[]; };
@@ -250,22 +251,23 @@ HTqPCR = derive { name="HTqPCR"; version="1.23.0"; sha256="0zp7jbnh5zbrqaq84q114
 Harshlight = derive { name="Harshlight"; version="1.41.0"; sha256="12wpfg785dfn5gwp014dfzk9x8zqvr9qrrs0pq32by576knida5z"; depends=[affy altcdfenvs Biobase]; };
 Heatplus = derive { name="Heatplus"; version="2.15.1"; sha256="1jcrajxvll0hhrsq8qvvyc1sj1nd3dm06n8q25qi9nacnfi865y7"; depends=[]; };
 HiTC = derive { name="HiTC"; version="1.13.2"; sha256="1bkd680n81cd7sdji6gjjljxhlbsrdgn5hwpmi37i83hnryfgf5x"; depends=[Biostrings GenomeInfoDb GenomicRanges IRanges Matrix RColorBrewer rtracklayer]; };
+HilbertCurve = derive { name="HilbertCurve"; version="0.99.1"; sha256="0nws4y2nc726z6igj3fdkrpv9l4i694g17nz3z1r006ss78gzzf2"; depends=[GenomicRanges HilbertVis IRanges png]; };
 HilbertVis = derive { name="HilbertVis"; version="1.27.0"; sha256="1qcyzn86v0xhb9zc1vcia1n53i33sgncbb7lpink5llmjpalacq6"; depends=[lattice]; };
 HilbertVisGUI = derive { name="HilbertVisGUI"; version="1.27.0"; sha256="03jxn398xv97mmvbpl0qymmydhm4i4c36qnw4s22ch7wy3h9x6h8"; depends=[HilbertVis]; };
 HybridMTest = derive { name="HybridMTest"; version="1.13.0"; sha256="0r4j8yllxzwn5r2rvpkqx6w23836lmly8wlshib6p917ky0djw4s"; depends=[Biobase fdrtool MASS survival]; };
 IMPCdata = derive { name="IMPCdata"; version="1.3.0"; sha256="003qvf47bcfcwxkw7zpzdvpnw7xhd2y12n9by2b1ns5i5jka754b"; depends=[rjson]; };
 INPower = derive { name="INPower"; version="1.5.0"; sha256="0msz24bixp7b5a83n40675xq8fglrhbg8972a93x2k8jgb5gdh38"; depends=[mvtnorm]; };
 INSPEcT = derive { name="INSPEcT"; version="0.99.8"; sha256="0pzh0xkh4py6rwnjqz4wqfnk2h08dp5q9gc4cgxls6gl3574i9ny"; depends=[Biobase BiocParallel deSolve GenomicFeatures GenomicRanges IRanges preprocessCore pROC rootSolve]; };
-IONiseR = derive { name="IONiseR"; version="0.99.6"; sha256="1fzp7ncznqw7pmb4sh1qphrk0ham1158q71kiylggbm88wlisky3"; depends=[BiocGenerics Biostrings data_table dplyr ggplot2 magrittr rhdf5 ShortRead tidyr XVector]; };
+IONiseR = derive { name="IONiseR"; version="0.99.7"; sha256="0b4lxdhajd4mhdnfa8c3zm8n5s398arrxjig2bv6il933lhxi6ps"; depends=[BiocGenerics Biostrings data_table dplyr ggplot2 magrittr rhdf5 ShortRead tidyr XVector]; };
 IPPD = derive { name="IPPD"; version="1.17.0"; sha256="0afhz5ishr1my9gnksa4dl92lfnb2fnvdpsh3n7kj4j2s8xx0crc"; depends=[bitops digest MASS Matrix XML]; };
-IRanges = derive { name="IRanges"; version="2.3.14"; sha256="0pg6zbdhhpk7h64nma9zrdjxvfk2nwad9b9x8y1qnkki8917a1xd"; depends=[BiocGenerics S4Vectors]; };
+IRanges = derive { name="IRanges"; version="2.3.17"; sha256="1fjz4whvw68xw6w0anzcrympk6xfsa7rgx0mxbzlwkpj96j2805k"; depends=[BiocGenerics S4Vectors]; };
 ITALICS = derive { name="ITALICS"; version="2.29.0"; sha256="16l0wq7bxi3nz8f5hggnzddhg07vrcca480ygvmi03cxajxbjr9h"; depends=[affxparser DBI GLAD oligo oligoClasses]; };
 IVAS = derive { name="IVAS"; version="1.1.0"; sha256="15jnmi40bsnyf5yw86gvqppv0g8250lsi74gsjzhm7gijhlxfnrm"; depends=[AnnotationDbi BiocGenerics doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges lme4 Matrix S4Vectors]; };
 Icens = derive { name="Icens"; version="1.41.0"; sha256="1vi2hnzs8z5prggswa6wzr2y53jczkgg09f4vw0pjzkzi7p8bphy"; depends=[survival]; };
 IdMappingAnalysis = derive { name="IdMappingAnalysis"; version="1.13.0"; sha256="1kwalcvb7cxkg89kz5hpk0cvsfzxz5g2cbiflrs2dyaxx96pm5gm"; depends=[Biobase boot mclust R_oo rChoiceDialogs RColorBrewer]; };
 IdMappingRetrieval = derive { name="IdMappingRetrieval"; version="1.17.0"; sha256="0fclrkv53q9aq3xw95k25rw52sjzy40r37kajnrk0kc41cyzf2vv"; depends=[AffyCompatible biomaRt DAVIDQuery ENVISIONQuery R_methodsS3 R_oo rChoiceDialogs RCurl XML]; };
 IdeoViz = derive { name="IdeoViz"; version="1.3.0"; sha256="1ynqg2a0jq23mlqzgf7k05jc2nkby8hkbc6h0p76ms33fwqj2qxz"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges RColorBrewer rtracklayer]; };
-InPAS = derive { name="InPAS"; version="1.1.3"; sha256="1fyhrf1n7hb34l742d3jrjyyznhjvf6z8bdmjawsqr10dvk1j2mv"; depends=[AnnotationDbi BiocParallel BSgenome cleanUpdTSeq GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges limma S4Vectors seqinr]; };
+InPAS = derive { name="InPAS"; version="1.1.5"; sha256="1s9jx90r7g9v9ipnnld2kdrbhyjl0vdwbgism6ab2hbpdxc33w7k"; depends=[AnnotationDbi Biobase BiocParallel BSgenome cleanUpdTSeq depmixS4 GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges limma preprocessCore S4Vectors seqinr]; };
 IsoGeneGUI = derive { name="IsoGeneGUI"; version="2.5.0"; sha256="05k6qdnsr2aywdmhdlimx5axrk07mf14rvia10afhf56380sdf3s"; depends=[Biobase ff geneplotter goric Iso IsoGene jpeg multtest ORCME ORIClust orQA RColorBrewer Rcpp relimp tkrplot xlsx]; };
 KCsmart = derive { name="KCsmart"; version="2.27.0"; sha256="1igsmg1l39yladz4dlc9j01nxkwfaciy575d7k6764jhrs6pv39m"; depends=[BiocGenerics KernSmooth multtest siggenes]; };
 KEGGREST = derive { name="KEGGREST"; version="1.9.0"; sha256="0ms60slsf7lpw0yidpy47hyxi7cm9r0gyb0q6ajxv52vn9diz29v"; depends=[Biostrings httr png]; };
@@ -277,6 +279,7 @@ LMGene = derive { name="LMGene"; version="2.25.0"; sha256="17djx1fkjxpmmp56vphcb
 LPE = derive { name="LPE"; version="1.43.0"; sha256="13z3h3mabbwhb5p40a7hil0aq10mya1zqgb8qj2qwnc50sbmgjx2"; depends=[]; };
 LPEadj = derive { name="LPEadj"; version="1.29.0"; sha256="1734ihzvid5bz2wyh7yskk7agd82xmw7dibzb7aivhcfyxs8g8p4"; depends=[LPE]; };
 LVSmiRNA = derive { name="LVSmiRNA"; version="1.19.0"; sha256="1z74y8zbg5amsmslb309gi630v8qa1qqgj37214bv5g9ab8xajmj"; depends=[affy Biobase BiocGenerics limma MASS quantreg SparseM vsn zlibbioc]; };
+LedPred = derive { name="LedPred"; version="1.0.0"; sha256="1wglgnl5y61g4jcqfgnf3gqvmfpdvcb6h43n44cv46icybdk0bzs"; depends=[akima e1071 GenomicRanges irr jsonlite plot3D plyr RCurl ROCR testthat]; };
 LiquidAssociation = derive { name="LiquidAssociation"; version="1.23.0"; sha256="178gx8n0ga1ppjk368xacidms1rc2kn301fmdc8rwbcknwvxrwck"; depends=[Biobase geepack]; };
 LowMACA = derive { name="LowMACA"; version="1.1.0"; sha256="0i0pka0jf1yq7vjw1kb9sd2p21gpy4pw855ap815k02i0n7jyny4"; depends=[Biostrings cgdsr data_table motifStack RColorBrewer reshape2 stringr]; };
 M3D = derive { name="M3D"; version="1.3.5"; sha256="1pjfl0kdhzw9l59qzgxjkf60w0rjdswm8wc12cyk39190hnalh49"; depends=[BiSeq GenomicRanges IRanges]; };
@@ -291,7 +294,7 @@ MEDME = derive { name="MEDME"; version="1.29.0"; sha256="1fpi4ri134ii28nfiq2p875
 MEIGOR = derive { name="MEIGOR"; version="1.3.0"; sha256="1kif7m78w0w0qv4fqfby3rknqk56zk83dds3cm4pgv2cii61i9jy"; depends=[CNORode deSolve Rsolnp snowfall]; };
 MGFM = derive { name="MGFM"; version="1.3.0"; sha256="1h2bi2cchfxl0z31pgj6q6pb1jnmqvjy7jv2khp80h7sdr65356i"; depends=[annotate AnnotationDbi]; };
 MIMOSA = derive { name="MIMOSA"; version="1.7.1"; sha256="1gzm90ii18vvpfd2nnl34mcvbvi49ck4hd7c5yziac8m3gx2f9f2"; depends=[Biobase coda data_table Formula ggplot2 Kmisc MASS MCMCpack modeest plyr pracma Rcpp RcppArmadillo reshape scales testthat]; };
-MLInterfaces = derive { name="MLInterfaces"; version="1.49.3"; sha256="1c7l9xwyx72hmv4rs24xm4bzj3lzaaj0ax71yw1p008rkgj8ifxz"; depends=[annotate Biobase BiocGenerics cluster fpc gdata genefilter ggvis htmltools MASS pls rda rpart sfsmisc shiny]; };
+MLInterfaces = derive { name="MLInterfaces"; version="1.49.8"; sha256="0asl6mibg1r2i9kmgax2qmsnj80spkn4n2pg237wxs9pm70qgpnv"; depends=[annotate Biobase BiocGenerics cluster fpc gbm gdata genefilter ggvis hwriter MASS pls RColorBrewer rda rgl rpart sfsmisc shiny]; };
 MLP = derive { name="MLP"; version="1.17.0"; sha256="1wb6bzxn1paba2fxh62ldsfr4kr0nq2sy21v0pp0qwhfxndyzpdn"; depends=[affy AnnotationDbi gdata gmodels gplots gtools plotrix]; };
 MLSeq = derive { name="MLSeq"; version="1.7.0"; sha256="0vc5rz4l574hmzwn3q7c4giib0lzs720j0j3alvarb3lmfzx9mhq"; depends=[Biobase caret DESeq2 edgeR limma randomForest]; };
 MMDiff = derive { name="MMDiff"; version="1.9.0"; sha256="0xvnv024cv540m0jv9lrb4s5rvc0mq4gwp6wvdgpnsnqnwi9j556"; depends=[Biobase DiffBind GenomicRanges GMD IRanges Rsamtools]; };
@@ -299,7 +302,7 @@ MPFE = derive { name="MPFE"; version="1.5.0"; sha256="123a6qg761j46bs1ckd6yyr2ig
 MSGFgui = derive { name="MSGFgui"; version="1.3.0"; sha256="0r7izs3wpd7l9agrm3mrr3kmm00s9fzljsjxhk4pzxkjg1ran4hp"; depends=[MSGFplus mzID mzR shiny shinyFiles xlsx]; };
 MSGFplus = derive { name="MSGFplus"; version="1.3.0"; sha256="0q75mygrd56kr9hrrxlmckkgvhcrgvpgvbjdxjmz6jaqp5wfbkf5"; depends=[mzID]; };
 MSnID = derive { name="MSnID"; version="1.3.1"; sha256="0a0r2ikyb0spm110xzn3zzhl8g6xsvmh781d65f10l1iqnd2cqza"; depends=[Biobase data_table doParallel foreach iterators MSnbase mzID ProtGenerics R_cache Rcpp reshape2]; };
-MSnbase = derive { name="MSnbase"; version="1.17.11"; sha256="1yrzmanv87rpahpqg40vqx23baahq41w3j7zag8chygr2xhxkjxy"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant mzID mzR pcaMethods plyr preprocessCore ProtGenerics Rcpp reshape2 S4Vectors vsn]; };
+MSnbase = derive { name="MSnbase"; version="1.17.13"; sha256="0ijh800jbdjw4nlcx69f3dp9q5zhghvfprgpjvx407a32i47dz3k"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant mzID mzR pcaMethods plyr preprocessCore ProtGenerics Rcpp reshape2 S4Vectors vsn]; };
 MSstats = derive { name="MSstats"; version="2.7.0"; sha256="0zhv2c769biv6avb4csi7alabk76bfn0ykzwp0lc6ymzggbj9pil"; depends=[ggplot2 gplots limma lme4 marray MSnbase preprocessCore Rcpp reshape]; };
 MVCClass = derive { name="MVCClass"; version="1.43.0"; sha256="1mbhfkvdkxw9xd76dd2pxk947w9wahwdsk9x1wcryrmwcdvaqqcz"; depends=[]; };
 MantelCorr = derive { name="MantelCorr"; version="1.39.0"; sha256="0l255m63q9idv56svs5m5bc4izwqnm3jy2z3kka7sw4xcx13l39g"; depends=[]; };
@@ -332,25 +335,27 @@ NCIgraph = derive { name="NCIgraph"; version="1.17.0"; sha256="103p0i4y9frkvdpzh
 NGScopy = derive { name="NGScopy"; version="1.3.0"; sha256="09b323rx0v5dnck2dgq9rzzjk7dbpry74q6c4dkgvjvxkf7khh8m"; depends=[changepoint rbamtools Xmisc]; };
 NOISeq = derive { name="NOISeq"; version="2.11.1"; sha256="13q3v2jphridbjk1059c475xgw9ywkdyqf0b6pbl3pk9l3ag9dr9"; depends=[Biobase Matrix]; };
 NTW = derive { name="NTW"; version="1.19.0"; sha256="027rdvy8xpsa70g6x33v4fmzk8gyvd8p3lgf65ac36wcy120gyhl"; depends=[mvtnorm]; };
-NanoStringQCPro = derive { name="NanoStringQCPro"; version="1.1.1"; sha256="0mmbbxhxd7nh7mqzckw0as68ac0nv005liif0laadbz49y6p4rwm"; depends=[AnnotationDbi Biobase knitr NMF png RColorBrewer]; };
+NanoStringQCPro = derive { name="NanoStringQCPro"; version="1.1.2"; sha256="1xk7rzaschgb39982jkb25xaz1l547dl020nl4wn0fdmy8kalp86"; depends=[AnnotationDbi Biobase knitr NMF png RColorBrewer]; };
 NarrowPeaks = derive { name="NarrowPeaks"; version="1.13.2"; sha256="0cryjprj8y1fgn5xxzsyyv4zdzv5qy8405qkj47kvjbrk0kbr97s"; depends=[BiocGenerics CSAR fda GenomeInfoDb GenomicRanges ICSNP IRanges S4Vectors]; };
 NetPathMiner = derive { name="NetPathMiner"; version="1.5.2"; sha256="0k3vq5l95hapw8hbc00m4pchxwzylp97y20w21g0g1yaf1cf9br0"; depends=[igraph]; };
 NetSAM = derive { name="NetSAM"; version="1.9.0"; sha256="1bdch37kk1clb8cyffrlcr6d5qykk5a5ql3dfi94bw1l0w6v4fjq"; depends=[graph igraph seriation]; };
 NormqPCR = derive { name="NormqPCR"; version="1.15.0"; sha256="0nfjnx5id04nbkda9v66418yzpp88mq2ijsfn8jyg0sfika405nl"; depends=[Biobase qpcR RColorBrewer ReadqPCR]; };
 NuPoP = derive { name="NuPoP"; version="1.19.0"; sha256="1dpqmhbwr1l95vgjxlw3xayjxksa909xj05jbf4x3gafnlkkdvbk"; depends=[]; };
 OCplus = derive { name="OCplus"; version="1.43.0"; sha256="1x7yqb6hkbglvr0kkq5s7caxambdvzc0f38gahq68wfsfwln7b49"; depends=[akima multtest]; };
+OGSA = derive { name="OGSA"; version="0.99.7"; sha256="03iqpsp1864605yjc7ji064dkiia8y7m66jyi1mskha7hk5mqk5x"; depends=[Biobase gplots limma]; };
 OLIN = derive { name="OLIN"; version="1.47.0"; sha256="19wjz96104rn88pdflixb790qhj24ff4s3hc09ldcii1pfzm0sdw"; depends=[limma locfit marray]; };
 OLINgui = derive { name="OLINgui"; version="1.43.0"; sha256="0714bzbsmd7bsdm5zk05g83yy48z3rlazpv17xbn38ljpykawzjb"; depends=[marray OLIN tkWidgets widgetTools]; };
 OSAT = derive { name="OSAT"; version="1.17.0"; sha256="1ky9xb5ls3xnzinsrxrgggb4r0fmm1q33vxb3ajav7nygyxijq0d"; depends=[]; };
 OTUbase = derive { name="OTUbase"; version="1.19.0"; sha256="0xmp446v57z875lmjkg47f9hx961af9nda658v8qlbjxf1wjw9zb"; depends=[Biobase Biostrings IRanges S4Vectors ShortRead vegan]; };
 OmicCircos = derive { name="OmicCircos"; version="1.7.0"; sha256="1xil5043hgpypaww1a1wvcxw9im9jmzgdp83p3z71giqiq36dvh4"; depends=[GenomicRanges]; };
-OmicsMarkeR = derive { name="OmicsMarkeR"; version="1.1.0"; sha256="1fw6zfp5jrkvxjb6j48q3n1fqkm1qmmjjvmr70v93hi5jg0an8gy"; depends=[assertive caret caTools data_table DiscriMiner e1071 foreach gbm glmnet pamr permute plyr randomForest]; };
+OmicsMarkeR = derive { name="OmicsMarkeR"; version="1.1.2"; sha256="09mdsvcp7n5qh845lpa1zsjk7jmbi0ni0601jlr1jija0hmkv1zx"; depends=[assertive assertive_base caret caTools data_table DiscriMiner e1071 foreach gbm glmnet pamr permute plyr randomForest]; };
 OncoSimulR = derive { name="OncoSimulR"; version="1.99.5"; sha256="0pjn2kirf1b72fvqxjawxcbrsn42brhz09kjnywm611kap329dq2"; depends=[data_table graph gtools igraph Rcpp Rgraphviz]; };
 OperaMate = derive { name="OperaMate"; version="0.99.6"; sha256="0xh57d82rmfcs1a6gj0qcjf585drhzns5k69bwxb7x1xw63wp4kp"; depends=[ggplot2 MASS pheatmap RDAVIDWebService]; };
 OrderedList = derive { name="OrderedList"; version="1.41.0"; sha256="1cw8y5f5h15z0qwg8n4dq7g3ixx2wa332rdsb4w2qqmcqlz79bfp"; depends=[Biobase twilight]; };
 OrganismDbi = derive { name="OrganismDbi"; version="1.11.42"; sha256="0y0v5ngall7iyvx2bqhfkxdnw9alkyab5f6qgpq8dpvr6pvyamyl"; depends=[AnnotationDbi Biobase BiocGenerics BiocInstaller GenomicFeatures GenomicRanges graph IRanges RBGL RSQLite S4Vectors]; };
+Oscope = derive { name="Oscope"; version="0.99.1"; sha256="0kv586yv17cf61jnvglsr08175dq0qz5zif8xflnliac9whj7yvf"; depends=[BiocParallel cluster EBSeq testthat]; };
 OutlierD = derive { name="OutlierD"; version="1.33.0"; sha256="0bljxmrnlqcngzzv6yxjsim7gd4icyi384vimn5gs869mq9gyrj3"; depends=[Biobase quantreg]; };
-PAA = derive { name="PAA"; version="1.3.2"; sha256="1p9900wiy5mmcmwb4l5n8kvsjs3ay6k0k551mpjbwijhk2si7wja"; depends=[e1071 limma MASS mRMRe randomForest Rcpp ROCR sva]; };
+PAA = derive { name="PAA"; version="1.3.3"; sha256="1v5gw9f2glzsz05kqyvvhwzfdfj4ypwbfgy5q16lr1y64slabzq2"; depends=[e1071 limma MASS mRMRe randomForest Rcpp ROCR sva]; };
 PADOG = derive { name="PADOG"; version="1.11.0"; sha256="0x84k32fmd1zrwjc4f71mq4jslh9bxr4gjbl48k1f5kl5j6hlxj3"; depends=[AnnotationDbi Biobase doRNG foreach GSA limma nlme]; };
 PANR = derive { name="PANR"; version="1.15.0"; sha256="0nc2a10z7i16dz41yhz3zw9h51myxzxbxd1vpc2d8gczks07n6ch"; depends=[igraph MASS pvclust RedeR]; };
 PAPi = derive { name="PAPi"; version="1.9.0"; sha256="1553fxm3ma3p5j10acyk5m2wx4dafp346x0pyxj9aah856h4zkw5"; depends=[KEGGREST svDialogs]; };
@@ -378,7 +383,7 @@ ProCoNA = derive { name="ProCoNA"; version="1.7.0"; sha256="1x2wmlhlizd09v4d7q98
 ProtGenerics = derive { name="ProtGenerics"; version="1.1.0"; sha256="1l77j3zl78v86jbxpwnyc0a5q66yds79nirlcvan789hxbggr0i4"; depends=[BiocGenerics]; };
 Pviz = derive { name="Pviz"; version="1.3.0"; sha256="0pvmpxw4dpxxs9lrn9nn44rn36r3l09rwlkh5ph054h56nm80xs1"; depends=[Biostrings biovizBase data_table GenomicRanges Gviz IRanges]; };
 QDNAseq = derive { name="QDNAseq"; version="1.5.1"; sha256="1gykm8r410s9aw75km0f8wnhd0p8gqirszp70g5x97n83r4k6rnq"; depends=[Biobase CGHbase CGHcall DNAcopy matrixStats R_utils Rsamtools]; };
-QUALIFIER = derive { name="QUALIFIER"; version="1.13.0"; sha256="0vk3xx0dmxadxk1wmcnf9cxv7rr4z8624npkmdbqlzb6mxix7p6d"; depends=[Biobase data_table flowCore flowViz flowWorkspace hwriter lattice latticeExtra MASS ncdfFlow reshape XML]; };
+QUALIFIER = derive { name="QUALIFIER"; version="1.13.1"; sha256="0b25cgjafs3k2kwbmbla713gxy9xbjclsx6k4pxydz5flz8w8grg"; depends=[Biobase data_table flowCore flowViz flowWorkspace hwriter lattice latticeExtra MASS ncdfFlow reshape XML]; };
 QuartPAC = derive { name="QuartPAC"; version="1.1.0"; sha256="0w92hggwihp2nia9dzg8yjbfsyrcgwq4kpxh96jb8kkmq6kl2l8p"; depends=[data_table GraphPAC iPAC SpacePAC]; };
 QuasR = derive { name="QuasR"; version="1.9.9"; sha256="13md1pq0bg9xdlhvwsys3f7ibqll80viica03h2l4cnhgw26zj52"; depends=[Biobase BiocGenerics BiocInstaller BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rbowtie Rsamtools rtracklayer S4Vectors ShortRead zlibbioc]; };
 R3CPET = derive { name="R3CPET"; version="1.1.0"; sha256="0vwyrqsihnabzqh5r329v3f5zcg2ik51aakvscpp482z0dm2naqh"; depends=[clues clValid data_table DAVIDQuery GenomicRanges ggbio ggplot2 Hmisc igraph IRanges pheatmap Rcpp reshape2 S4Vectors]; };
@@ -386,8 +391,8 @@ R453Plus1Toolbox = derive { name="R453Plus1Toolbox"; version="1.19.1"; sha256="0
 RBGL = derive { name="RBGL"; version="1.45.1"; sha256="0y90pvl3i8pyzxwssciygcd1c1lb8a0rqhpiqgif56075amm71rl"; depends=[graph]; };
 RBM = derive { name="RBM"; version="1.1.0"; sha256="03q7prkrj8y3k8jrnnbjrkmlyv72cxfa8l042df4wajhcbpa4g4l"; depends=[limma marray]; };
 RBioinf = derive { name="RBioinf"; version="1.29.0"; sha256="1cyd18lz3h9b20g6s9azzv9rv9bachh3qsczz84y8lj4kay3qssx"; depends=[graph]; };
-RCASPAR = derive { name="RCASPAR"; version="1.15.1"; sha256="125vrkz5gicizf0acpv0f0ijiky5my7rpfyim25vihcsz5fkb0w1"; depends=[]; };
+RCASPAR = derive { name="RCASPAR"; version="1.15.2"; sha256="151mil4v8iz5lrn7827imvvnjh171qdgjg927fic3fwyfx0kkyqs"; depends=[]; };
-RCyjs = derive { name="RCyjs"; version="1.1.12"; sha256="1gv31yj0ms7llsg2rca96rh77h1qw3hkjbiskzc3zmpycx5m9m8b"; depends=[BiocGenerics BrowserViz graph httpuv igraph jsonlite Rcpp]; };
+RCyjs = derive { name="RCyjs"; version="1.1.18"; sha256="0d6zh2ryy9583i2cxahi4gl5ldp1r0yyyz8mjzklp47rkm2cxmkx"; depends=[BiocGenerics BrowserViz graph httpuv igraph jsonlite Rcpp]; };
 RCytoscape = derive { name="RCytoscape"; version="1.19.0"; sha256="0yfmlksi7sz0p9nbgjz2cpqwbwyzzxij3zaqmkp3wqfdk89mxgi7"; depends=[BiocGenerics graph]; };
 RDAVIDWebService = derive { name="RDAVIDWebService"; version="1.7.0"; sha256="07hnj7flfacg9j8c6155nw23zjxcb1v4wj4rkfi8xz5clp80v6xh"; depends=[Category ggplot2 GOstats graph RBGL rJava]; };
 RDRToolbox = derive { name="RDRToolbox"; version="1.19.0"; sha256="186cj6xri4prv7y9jvspyql8mkqy3aqs2kd6m5fliqicqbfia2z8"; depends=[MASS rgl]; };
@@ -399,8 +404,8 @@ RLMM = derive { name="RLMM"; version="1.31.0"; sha256="01plzmxz5dzvvxzx4wxsqhhyp
 RMassBank = derive { name="RMassBank"; version="1.11.0"; sha256="1df5kfm4gb5kz1z5sq38wddi4njq3y8nzy7fr2dxk1z2j4b1977z"; depends=[mzR rcdk Rcpp RCurl rjson XML yaml]; };
 RNASeqPower = derive { name="RNASeqPower"; version="1.9.0"; sha256="0nn5wq81cm81wjwc43ky597fyq1l4ya36k64bp6k80ri94qx2vzg"; depends=[]; };
 RNAinteract = derive { name="RNAinteract"; version="1.17.0"; sha256="03rz6xyy9f48ns0r9xcxrghikxlna8cx62rwswq2i1xkh7c5lfiy"; depends=[abind Biobase cellHTS2 geneplotter gplots hwriter ICS ICSNP lattice latticeExtra limma locfit RColorBrewer splots]; };
-RNAither = derive { name="RNAither"; version="2.17.0"; sha256="028qf3sj2cms9h6wh4bynxaky8mvlr0axci8yw9bjp4bdlrjland"; depends=[biomaRt car geneplotter limma prada RankProd splots topGO]; };
+RNAither = derive { name="RNAither"; version="2.17.2"; sha256="01h9l5inafhzpych76rpkrml442ld6jaxrd31ambspn9hsv8js6z"; depends=[biomaRt car geneplotter limma prada RankProd splots topGO]; };
-RNAprobR = derive { name="RNAprobR"; version="1.1.1"; sha256="1n0ra0jb6y01nbdx9qbmkh5w4zy381nzkwcawvdg2bfzva1734mp"; depends=[BiocGenerics Biostrings GenomicFeatures GenomicRanges plyr Rsamtools rtracklayer]; };
+RNAprobR = derive { name="RNAprobR"; version="1.1.2"; sha256="0cjxf53q9g5g2092grbwp2z9q0sgw4bj5fism0a34w5r1varr9nb"; depends=[BiocGenerics Biostrings GenomicFeatures GenomicRanges plyr Rsamtools rtracklayer]; };
 ROC = derive { name="ROC"; version="1.45.0"; sha256="1vcv5q7ylr2b1fb4vmrc8j4j7s3v5szzpkwblnfkcp2y8d03i9a1"; depends=[]; };
 ROntoTools = derive { name="ROntoTools"; version="1.9.0"; sha256="07l9j4d26hn8d5ma3z19ipy4rrw29k66zb2ib8n3ba24pjm0h8w3"; depends=[boot graph KEGGgraph KEGGREST Rgraphviz]; };
 RPA = derive { name="RPA"; version="1.25.0"; sha256="1bzjb0064xdn5zk9y9dpxjdw79i8kkfb29f13balx78nq5xznxh4"; depends=[affy]; };
@@ -416,7 +421,7 @@ RUVnormalize = derive { name="RUVnormalize"; version="1.3.0"; sha256="1fqk68rpzn
 RWebServices = derive { name="RWebServices"; version="1.33.1"; sha256="1bxp4zj7r1lrxb7r7l32h6b8hdxb1ryf7dxxj0qhwimh7pmxln31"; depends=[RCurl SJava TypeInfo]; };
 RamiGO = derive { name="RamiGO"; version="1.15.0"; sha256="1q9f2ii5b1xway407gzfpzz6vm6an8p13vmgkw7vb9rldxn85hab"; depends=[graph gsubfn igraph png RCurl RCytoscape]; };
 RankProd = derive { name="RankProd"; version="2.41.0"; sha256="05r8mrgnpfkd7yhcch7nrn9jbapfhvi67h0z9a9nlxlp44mz0qq7"; depends=[]; };
-RareVariantVis = derive { name="RareVariantVis"; version="1.0.0"; sha256="09hww69169c225dmi3rmjhv5j2bxq1c773s1q7048rysgv0har5y"; depends=[BiocGenerics GenomeInfoDb GenomicRanges googleVis IRanges S4Vectors SummarizedExperiment VariantAnnotation]; };
+RareVariantVis = derive { name="RareVariantVis"; version="1.0.3"; sha256="1wc2rb80xvwbnsc93fl04cf6y74qpwhhi4172whxb6affq2682cq"; depends=[BiocGenerics GenomeInfoDb GenomicRanges googleVis IRanges S4Vectors VariantAnnotation]; };
 Rariant = derive { name="Rariant"; version="1.5.0"; sha256="1xwy2xrdk1m1mscnql8cp3az1jx639a9w4mb8bz7jf62z4z4npsi"; depends=[dplyr exomeCopy GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges reshape2 Rsamtools S4Vectors shiny SomaticSignatures VariantAnnotation VGAM]; };
 RbcBook1 = derive { name="RbcBook1"; version="1.37.0"; sha256="03q82zjd725w585rgdn9mbx7ddsv1kdxylsndh26csz573j2myhh"; depends=[Biobase graph rpart]; };
 Rbowtie = derive { name="Rbowtie"; version="1.9.0"; sha256="02wc0pzw9vm1mc7y84ic79jjdi1mh77v8h4gk2pl117pdkgg7nl7"; depends=[]; };
@@ -436,27 +441,27 @@ ReportingTools = derive { name="ReportingTools"; version="2.9.1"; sha256="05p005
 Rgraphviz = derive { name="Rgraphviz"; version="2.13.0"; sha256="08apr3v2h5jwah96c2596ggz7xaz41k5zywcqsjm6g8xhd3hs522"; depends=[graph]; };
 Rhtslib = derive { name="Rhtslib"; version="1.1.8"; sha256="1n6mimlkyaxcfwfr4hclmch3h14qaffakkd899p9fwlf1d60j9xw"; depends=[zlibbioc]; };
 Ringo = derive { name="Ringo"; version="1.33.0"; sha256="12qh3aayy317pzb137ds9vqrrwn93c4l4fdcl6yyp8p4fqpki03j"; depends=[Biobase BiocGenerics genefilter lattice limma Matrix RColorBrewer vsn]; };
-Risa = derive { name="Risa"; version="1.11.0"; sha256="1rgyh3yv4ii0xw6ycm0g9b0y6c9nqdq4k8lidmifk0gx835lw7vf"; depends=[affy Biobase biocViews Rcpp xcms]; };
+Risa = derive { name="Risa"; version="1.11.1"; sha256="1bx7n7fjsaig5zq6xgwva2fvy0dlg9f1niwl9m6bi1h04spybp2c"; depends=[affy Biobase biocViews Rcpp xcms]; };
 Rmagpie = derive { name="Rmagpie"; version="1.25.0"; sha256="13mb9aaqmwx1ad4mk0fhxqfql8pjpyaiibip7jawiyji7ghp9iw7"; depends=[Biobase e1071 kernlab pamr]; };
 RmiR = derive { name="RmiR"; version="1.25.0"; sha256="1xc19w8la239ia793qpnpx2h0aavwhidrjf4i87jry2j29npjfzz"; depends=[DBI RSVGTipsDevice]; };
-RnBeads = derive { name="RnBeads"; version="1.1.3"; sha256="1yd5gmi2vvkqrv384ndsn7qgp8rzjj6d0i4zsgr33avxnah757m2"; depends=[BiocGenerics cluster ff fields GenomicRanges ggplot2 gplots gridExtra illuminaio IRanges limma MASS matrixStats methylumi plyr RColorBrewer]; };
+RnBeads = derive { name="RnBeads"; version="1.1.4"; sha256="1v4cgfrarybansrxk2r77g79xkwhkh28qaffk93mfwf163rq3391"; depends=[BiocGenerics cluster ff fields GenomicRanges ggplot2 gplots gridExtra illuminaio IRanges limma MASS matrixStats methylumi plyr RColorBrewer]; };
 RnaSeqSampleSize = derive { name="RnaSeqSampleSize"; version="1.1.0"; sha256="0q2w1yd5p9k3pls6ki8yci3r2v4rxi3iy4zk5mafmr7ip0q1rwpp"; depends=[biomaRt edgeR heatmap3 KEGGREST matlab Rcpp]; };
 Rnits = derive { name="Rnits"; version="1.3.0"; sha256="0hxll8hlv5nc6vijznhzmvbjh1hxmfy9shm2g8al291yi0gfdmk3"; depends=[affy Biobase boot ggplot2 impute limma qvalue reshape2]; };
 Roleswitch = derive { name="Roleswitch"; version="1.7.0"; sha256="01b21yyg0d2v10abcbw08zhswh9nb7wj7s3x5kcaaas7671f06ha"; depends=[Biobase biomaRt Biostrings DBI microRNA plotrix pracma reshape]; };
 Rolexa = derive { name="Rolexa"; version="1.25.0"; sha256="1qrf7byimw9s5jp15zmwqk95x34r3yx2npr46gwf1zih06n7kc05"; depends=[Biostrings IRanges mclust ShortRead]; };
 RpsiXML = derive { name="RpsiXML"; version="2.11.0"; sha256="0rvma7vynfh5sjhqnbpagilq54dh0wrvvb3jzykwmrak0dbyk7zh"; depends=[annotate AnnotationDbi Biobase graph hypergraph RBGL XML]; };
 Rqc = derive { name="Rqc"; version="1.3.1"; sha256="02kc0ki021m4hxhzlmxfrb9p7p2ibdqan5hr9h67vd2dcnp9yaij"; depends=[BiocGenerics BiocParallel BiocStyle Biostrings ggplot2 IRanges knitr markdown plyr reshape2 S4Vectors ShortRead]; };
-Rsamtools = derive { name="Rsamtools"; version="1.21.13"; sha256="0fv0a5f1jb8mj3b2qn6bf9vzzpvn8fgrlhxz492rd3ndvvgnabxc"; depends=[BiocGenerics BiocParallel Biostrings bitops GenomeInfoDb GenomicRanges IRanges S4Vectors XVector zlibbioc]; };
+Rsamtools = derive { name="Rsamtools"; version="1.21.14"; sha256="1s2xwz0njbml9x0yw08kk8ykbr5zgzfy5glhzkdhcdfdz7m19ma9"; depends=[BiocGenerics BiocParallel Biostrings bitops GenomeInfoDb GenomicRanges IRanges S4Vectors XVector zlibbioc]; };
-Rsubread = derive { name="Rsubread"; version="1.19.2"; sha256="1xcj13mzw7a8q93kimr61kcl2xvr0mdzvrrqi4j3psbcyf5zn86k"; depends=[]; };
+Rsubread = derive { name="Rsubread"; version="1.19.3"; sha256="1qb43g5868m3590p1kzb1g5dcl1dkpggk8qq2lnmbw5v761ryamp"; depends=[]; };
 Rtreemix = derive { name="Rtreemix"; version="1.31.0"; sha256="1z08y8qhc3sv4pwvji4pks46hxpcpwb9yx8y0927bc96a8mqgax4"; depends=[Biobase graph Hmisc]; };
-S4Vectors = derive { name="S4Vectors"; version="0.7.10"; sha256="15hyi728raya0x0fl0pp58kk6w4chvx7xv2f7kmp1432pkgvif9p"; depends=[BiocGenerics]; };
+S4Vectors = derive { name="S4Vectors"; version="0.7.12"; sha256="1ym0kph98ab7rdm8b2h3g8zhx92dax7c2nbdmkrahfnldiq60sgn"; depends=[BiocGenerics]; };
 SAGx = derive { name="SAGx"; version="1.43.0"; sha256="111pgl7rzmscgadkbivwa736gpyw1z7zkcj648zq3jhqix569dvd"; depends=[Biobase multtest]; };
-SANTA = derive { name="SANTA"; version="2.5.2"; sha256="0y49ly3ll8qhbnd5yv5nfzc0bq2xcp2nwdg26338qmif4xklzs43"; depends=[igraph Matrix snow]; };
+SANTA = derive { name="SANTA"; version="2.6.0"; sha256="0zx9azk7j82bzq424rf42nsaw05qyfgzdsy38h6r352mfbmip2dl"; depends=[igraph Matrix snow]; };
 SBMLR = derive { name="SBMLR"; version="1.65.0"; sha256="1nmw5c32ka6l12cid54mc4diahjhmyg6fngsd646v70rbzgffn7q"; depends=[deSolve XML]; };
 SCAN_UPC = derive { name="SCAN.UPC"; version="2.11.0"; sha256="1gwjd78qfaqv6xh4ys6rr29b82wc8qxk7ysfjcl06j6n0qk1v4s6"; depends=[affy affyio Biobase Biostrings foreach GEOquery IRanges MASS oligo sva]; };
 SELEX = derive { name="SELEX"; version="1.1.0"; sha256="13v2aqphpblwslbnm9yk9lfg31vrc3lz9ds4m8j7584iszmlgnar"; depends=[Biostrings rJava]; };
 SEPA = derive { name="SEPA"; version="0.99.0"; sha256="1mc44amd39x1dvl0kamhbsn2cplg7h5j5v5y2lv1gminfl4xs0sw"; depends=[ggplot2 reshape2 segmented shiny topGO]; };
-SGSeq = derive { name="SGSeq"; version="1.3.12"; sha256="19i39vv0ds79hgjjkp37j49apr1jr5n93zc2dmn1llglyp9qqwyl"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges igraph IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; };
+SGSeq = derive { name="SGSeq"; version="1.3.14"; sha256="0m4dsjyww001bqm3ra01jajl0ys9kx605kjb3fjl4dk6adfkn8h8"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges igraph IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; };
 SIM = derive { name="SIM"; version="1.39.0"; sha256="1r08h5hkciycv4lh998vm742flim07plysgjvrq9dp4c5q4qrzr5"; depends=[globaltest quantreg quantsmooth]; };
 SIMAT = derive { name="SIMAT"; version="1.1.5"; sha256="074r9fyrgkay1xr0i3ps1sn7n24y26w595nssy7bryrvhhd8izbr"; depends=[ggplot2 mzR Rcpp reshape2]; };
 SJava = derive { name="SJava"; version="0.95.1"; sha256="1cl0qybi71srf1ggawxdy128kz8crn8if4yi8c2m6w9ppah9m763"; depends=[]; };
@@ -464,12 +469,12 @@ SLGI = derive { name="SLGI"; version="1.29.0"; sha256="0jhi3nmgnqf8qix90kpz8gqib
 SLqPCR = derive { name="SLqPCR"; version="1.35.0"; sha256="1p35xgwf3i8ksznz1gi3bddj0816hdljamcb7smdrq0md5fqmpzb"; depends=[]; };
 SMAP = derive { name="SMAP"; version="1.33.0"; sha256="0znl289fclws2vnqgpjnrl8b0s5q4cna3ps3il5783vr64ir88cg"; depends=[]; };
 SNAGEE = derive { name="SNAGEE"; version="1.9.0"; sha256="0sn5b8ah9idbz63y1rjx8brz3h58zvh2sk59l4i48nvrm38g169r"; depends=[]; };
-SNPRelate = derive { name="SNPRelate"; version="1.3.5"; sha256="0xr839g6a2m5p7fd2dzaz0c263b2cfdpakq5ydk0k1c3xppzly9y"; depends=[gdsfmt]; };
+SNPRelate = derive { name="SNPRelate"; version="1.3.8"; sha256="0rmqx5s4748jpcbqjjpkm4snkvbs8c0xpdm5qfg18cgkx3jbpxpr"; depends=[gdsfmt]; };
 SNPchip = derive { name="SNPchip"; version="2.15.2"; sha256="1px5ifdsly1z8iwd22vj2xb4pk5jhsa3h2z31scw37b0v4daks50"; depends=[Biobase foreach GenomeInfoDb GenomicRanges IRanges lattice oligoClasses SummarizedExperiment]; };
 SPEM = derive { name="SPEM"; version="1.9.0"; sha256="09klaxlz1ff77jhjsr95g3s4b5m285zf3fl9w4mv5pc8r1viqplf"; depends=[Biobase Rsolnp]; };
 SPIA = derive { name="SPIA"; version="2.21.0"; sha256="0v8m9wfl2kqzzl3k0v7lr7g33ymdnmqi9r2fqyb42mggpq5pwxlm"; depends=[KEGGgraph]; };
 SQUADD = derive { name="SQUADD"; version="1.19.0"; sha256="0xss3vhn6471z44gd44i8j5bni8471nb1sq3cx99f2gyk817nxp8"; depends=[RColorBrewer]; };
-SRAdb = derive { name="SRAdb"; version="1.23.0"; sha256="042y06ds1jdj26jzi51wxb6mlmlr751jyf7ggjaq7zrz267dmj76"; depends=[GEOquery graph RCurl RSQLite]; };
+SRAdb = derive { name="SRAdb"; version="1.25.0"; sha256="1gkg3qyk98zc8gjlmgg34xgjmh92iy2bl9larhdv5inqv2jn3yj3"; depends=[GEOquery graph RCurl RSQLite]; };
 SSPA = derive { name="SSPA"; version="2.9.0"; sha256="1kkvj3s2l6zzvv6pybx38qrnm3i5dxckx2fpc4snlx7km2w175xz"; depends=[lattice limma qvalue]; };
 STAN = derive { name="STAN"; version="1.3.0"; sha256="02qg79aa0j2ns1xswdirgbpwb0dlghd0lbdxgnpmy225wgb7nak6"; depends=[Rsolnp]; };
 STATegRa = derive { name="STATegRa"; version="1.3.1"; sha256="0kfwi5qimg4myx5x0gjwrkhz8cxh2hz1mvxla8yn8v8fkb3ryshj"; depends=[affy Biobase calibrate edgeR foreach ggplot2 gplots gridExtra limma MASS]; };
@@ -478,7 +483,7 @@ SVM2CRM = derive { name="SVM2CRM"; version="1.1.0"; sha256="0k3mg9b8i406ssvkzacz
 SamSPECTRAL = derive { name="SamSPECTRAL"; version="1.23.4"; sha256="0fqnqffw6q5sja3jkw6ddrachs075s5s7rnpg9fli9lgax5r4rbp"; depends=[]; };
 ScISI = derive { name="ScISI"; version="1.41.0"; sha256="05snqj8qphcmnkrmv42p6zs92dmi09sd06abn5ll5234my5d0vvn"; depends=[annotate AnnotationDbi apComplex RpsiXML]; };
 SemDist = derive { name="SemDist"; version="1.3.0"; sha256="0dvnp3d2s7bc4jv2vm8jikyac2cd23hx7r480g2lkcaic99wbl0s"; depends=[annotate AnnotationDbi]; };
-SeqArray = derive { name="SeqArray"; version="1.9.7"; sha256="0gpn5dispfd8scqhgxw8pfgrwkz479ly5q8431mifmbkq8zh34pd"; depends=[Biostrings gdsfmt GenomicRanges IRanges S4Vectors VariantAnnotation]; };
+SeqArray = derive { name="SeqArray"; version="1.9.10"; sha256="0r4308fich1wwdrqfw6d6c88cq8xsyg2p8wvfnhn1ah4lng9s6z3"; depends=[Biostrings gdsfmt GenomicRanges IRanges S4Vectors VariantAnnotation]; };
 SeqGSEA = derive { name="SeqGSEA"; version="1.9.0"; sha256="0znabm84qgzf9m4dk64jppn3s5vzz1sjvrdlr7s6jls8jwi8kqqi"; depends=[Biobase biomaRt DESeq doParallel]; };
 SeqVarTools = derive { name="SeqVarTools"; version="1.7.1"; sha256="04xfph2iphpmlqws5xmibq1jdkclbal2nrf18w7sblqcv67cff7x"; depends=[gdsfmt GenomicRanges GWASExactHW IRanges S4Vectors SeqArray VariantAnnotation]; };
 ShortRead = derive { name="ShortRead"; version="1.27.5"; sha256="0r9gmbg9fd3n6v8c0l1mjkk9x1v6qrisamm5a1nasqbg3wmhmz5k"; depends=[Biobase BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges hwriter IRanges lattice latticeExtra Rsamtools S4Vectors XVector zlibbioc]; };
@@ -486,7 +491,7 @@ SigCheck = derive { name="SigCheck"; version="2.1.0"; sha256="012n75gmsifvymbk20
 SigFuge = derive { name="SigFuge"; version="1.7.0"; sha256="1b966n3rl4xs3q1vjgkxxfravqr02rdgwyzvr469y757qdqi1day"; depends=[GenomicRanges ggplot2 matlab reshape sigclust]; };
 SimBindProfiles = derive { name="SimBindProfiles"; version="1.7.0"; sha256="04m7h5zil05sg9yfgjjzm1p65302fp50vxf8y1jafp1nwqialxwh"; depends=[Biobase limma mclust Ringo]; };
 SomatiCA = derive { name="SomatiCA"; version="1.13.0"; sha256="06b3mz199qm2ynal8iq4kp8rv40wbc5zipzwm22nccf97krxl9a4"; depends=[DNAcopy doParallel foreach GenomicRanges IRanges lars rebmix sn]; };
-SomaticSignatures = derive { name="SomaticSignatures"; version="2.5.4"; sha256="1kr4z1b9b5a8gb1m9vfk9bxhinh5ccba2mrwnq3cqhb7c3slbjs3"; depends=[Biobase Biostrings GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges NMF pcaMethods proxy reshape2 S4Vectors VariantAnnotation]; };
+SomaticSignatures = derive { name="SomaticSignatures"; version="2.5.6"; sha256="17w3dszcaxpkyk9chb7bfdii9zr1hppqhgsarzls4s4p4472f7d1"; depends=[Biobase Biostrings GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges NMF pcaMethods proxy reshape2 S4Vectors VariantAnnotation]; };
 SpacePAC = derive { name="SpacePAC"; version="1.7.0"; sha256="1ay5hlbm2x9g5mjrq5qksgrrr84vwfk49g9qb2sc9wyc46n5af6k"; depends=[iPAC]; };
 SpeCond = derive { name="SpeCond"; version="1.23.0"; sha256="0nbbqazxql9mc5idvrcycrm9fkrnm2vi9zrad3awhc378ippdk8k"; depends=[Biobase fields hwriter mclust RColorBrewer]; };
 SplicingGraphs = derive { name="SplicingGraphs"; version="1.9.1"; sha256="1s3kvaxrrvfndp4imavj0r9zw0rg37cn9xwxhi5zpfd7a784z1xk"; depends=[BiocGenerics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph igraph IRanges Rgraphviz Rsamtools S4Vectors]; };
@@ -495,17 +500,18 @@ Streamer = derive { name="Streamer"; version="1.15.2"; sha256="0mah1sq797ihy82mv
 SummarizedExperiment = derive { name="SummarizedExperiment"; version="0.3.2"; sha256="0k7dmly8g1qhpqx4qv376ixkwvx073ydc5xqi29s81mwp5fq08zi"; depends=[Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
 Sushi = derive { name="Sushi"; version="1.6.1"; sha256="0g1fk0xrn584l49r73crj0bc5z2y6rdzyf54d221r7k119njp3dw"; depends=[biomaRt zoo]; };
 SwimR = derive { name="SwimR"; version="1.7.0"; sha256="07kh24m9d1q3swj3srjybj6lq68s89750fbvlg449px4aq23yrq0"; depends=[gplots heatmap_plus R2HTML signal]; };
-TCC = derive { name="TCC"; version="1.9.0"; sha256="1bihqfvrq3sjs38m2a60swxqcxmgabb1lmsnfrb669imiqc7ramj"; depends=[baySeq DESeq DESeq2 edgeR ROC samr]; };
+TCC = derive { name="TCC"; version="1.9.2"; sha256="1srlaiavii6sr0d3fiqngp1rchdfxgnmsf7h29szyy34aajqygbw"; depends=[baySeq DESeq DESeq2 edgeR ROC samr]; };
 TDARACNE = derive { name="TDARACNE"; version="1.19.0"; sha256="0nwg355n0qs781801pmmwfwp66sa2ci7g6gfdh4669067j4qbqhb"; depends=[Biobase GenKern Rgraphviz]; };
 TEQC = derive { name="TEQC"; version="3.9.0"; sha256="0dkmh901jkf529jcshvr79jmkvw0824r4dxgp6l6vgv9j5c6nf25"; depends=[Biobase BiocGenerics hwriter IRanges Rsamtools]; };
 TFBSTools = derive { name="TFBSTools"; version="1.7.0"; sha256="1c38n6xlm4cfrhh9qih0d8xh3d7r7w797fjcbmhsr2zhd7qssrqb"; depends=[BiocParallel Biostrings BSgenome caTools CNEr DirichletMultinomial GenomicRanges gtools IRanges RSQLite rtracklayer S4Vectors seqLogo TFMPvalue XVector]; };
 TIN = derive { name="TIN"; version="1.1.0"; sha256="0npf3gwh2izvsa5j0zjy1gkm69nrxhcjlm2ha621fc1gz7lx1i2y"; depends=[aroma_affymetrix data_table impute squash stringr WGCNA]; };
-TPP = derive { name="TPP"; version="1.1.0"; sha256="06xm73jx4f2pldi7yifvx7zh62zmigidnfd7klpp0jpfxx3xjw61"; depends=[Biobase doParallel foreach ggplot2 gridExtra nls2 openxlsx plyr reshape2 VennDiagram VGAM]; };
+TPP = derive { name="TPP"; version="1.1.3"; sha256="152dpyn6ldw4b3ys0b1ylriq0l1hr9l0qjgfh19bvs2gflhbzyah"; depends=[Biobase doParallel foreach ggplot2 gridExtra nls2 openxlsx plyr reshape2 VennDiagram VGAM]; };
 TRONCO = derive { name="TRONCO"; version="1.1.0"; sha256="18zmn1cxysar3a19n9i47r2gda5r5jvz0bk209wh6kqlhs001q9v"; depends=[graph lattice Rgraphviz]; };
 TSCAN = derive { name="TSCAN"; version="1.5.0"; sha256="1hkmfn9svbgpvxpszfdxjc23qq8x60prsbrgv7z5n3na4sl7y5z5"; depends=[combinat fastICA ggplot2 gplots igraph mclust mgcv plyr shiny]; };
 TSSi = derive { name="TSSi"; version="1.15.0"; sha256="0475zw1s34ayiz0v9i770rmha4rx9i3zzkjvyskgvsdpgsq9wl4j"; depends=[Biobase BiocGenerics Hmisc IRanges minqa plyr S4Vectors]; };
 TargetScore = derive { name="TargetScore"; version="1.7.0"; sha256="0lkkxzi3fi0dxika09fkbakq54c2sjw4g4y9bafcy3f225fac8x8"; depends=[Matrix pracma]; };
 TargetSearch = derive { name="TargetSearch"; version="1.25.0"; sha256="071p06gb1rn6sdhdpi7g05rflp6jgs0cdff13gj8hr5jykyw5ix7"; depends=[mzR]; };
+TimerQuant = derive { name="TimerQuant"; version="0.99.3"; sha256="03qa5k4xc8pv677azdc0ar66p23jdyqyblckdnrqlwnscln0y77g"; depends=[deSolve dplyr ggplot2 gridExtra locfit shiny]; };
 TitanCNA = derive { name="TitanCNA"; version="1.7.1"; sha256="0a64bqgyn18qdvgzmc6kqr6c16jlqyz0vah0fm2qwdjz3zmjd081"; depends=[foreach GenomeInfoDb IRanges Rsamtools]; };
 ToPASeq = derive { name="ToPASeq"; version="1.3.0"; sha256="1m6mh30fpf9mmgg2wsv08qvizw0cpa6dz5abspgbw3q0vaskm2db"; depends=[Biobase clipper DESeq DESeq2 edgeR fields GenomicRanges graph graphite gRbase KEGGgraph limma locfit qpgraph R_utils RBGL Rcpp Rgraphviz TeachingDemos]; };
 TransView = derive { name="TransView"; version="1.13.0"; sha256="14fanxl8lqam3492c5sbvhsjwbayrx7dcp5wpsbqrcvbssmfa3cx"; depends=[GenomicRanges gplots IRanges Rsamtools zlibbioc]; };
@@ -514,12 +520,12 @@ TypeInfo = derive { name="TypeInfo"; version="1.35.0"; sha256="0rxwfaqg8sg70hiq8
 UNDO = derive { name="UNDO"; version="1.11.0"; sha256="173cdpp0gipwplxdf7ynxqnv8fqfkbyx7xmr5cx396zi8gpq3am4"; depends=[Biobase BiocGenerics boot MASS nnls]; };
 UniProt_ws = derive { name="UniProt.ws"; version="2.9.2"; sha256="0pby1c7y8fxkpdd2knbv8gbxs78ry1dz8q9zqw6bakp831v5kbgw"; depends=[AnnotationDbi BiocGenerics RCurl RSQLite]; };
 VanillaICE = derive { name="VanillaICE"; version="1.31.3"; sha256="0niimjngjx8wq2fylzjdijb2za4w4ia53aqkdnjwjfl78rg2hwch"; depends=[Biobase BiocGenerics crlmm data_table foreach GenomeInfoDb GenomicRanges IRanges lattice matrixStats oligoClasses S4Vectors SummarizedExperiment]; };
-VariantAnnotation = derive { name="VariantAnnotation"; version="1.15.19"; sha256="1hqpjwrnyl5hp8vwl68v2cnf868vjf7k0vckjczdcc66wp3g9r70"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; };
+VariantAnnotation = derive { name="VariantAnnotation"; version="1.15.21"; sha256="0b5i9q2xnclkrziri6575irmm5y3r2g9x45dr5qnq91g9rxi4m7v"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; };
-VariantFiltering = derive { name="VariantFiltering"; version="1.5.15"; sha256="1dawzsv358h3p5x7kcml17snpbypgwjl5b0aam2wrsb7qp80sqh7"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges graph Gviz IRanges RBGL Rsamtools RSQLite S4Vectors shiny VariantAnnotation XVector]; };
+VariantFiltering = derive { name="VariantFiltering"; version="1.5.16"; sha256="1fvzhxvirzxcrqw3bm86f5id29s993gpmbwjar5maj86881l1c2f"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges graph Gviz IRanges RBGL Rsamtools RSQLite S4Vectors shiny VariantAnnotation XVector]; };
 VariantTools = derive { name="VariantTools"; version="1.11.0"; sha256="1yyx9l6q3v4igm2ppnrsj9c7p4p0zpkqwjyf9d7b7rqvrk9yjyrv"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicFeatures GenomicRanges gmapR IRanges Matrix Rsamtools rtracklayer S4Vectors VariantAnnotation]; };
 Vega = derive { name="Vega"; version="1.17.0"; sha256="1c39112czlw9hgh9gmkwxhhz9kwki48k8lsfmy3hkzxqpxx61h01"; depends=[]; };
 VegaMC = derive { name="VegaMC"; version="3.7.0"; sha256="046wly5sn4vwk3h4bcick8q5dpjrfjq393rqjl8y4v24iqynlyqd"; depends=[Biobase biomaRt genoset]; };
-XBSeq = derive { name="XBSeq"; version="0.99.6"; sha256="1j8hwy2wi4vmc1nnc5xij578w445vqj0v6ngz06rlbdi5kb9k7ls"; depends=[Biobase BiocGenerics DESeq2 ggplot2 locfit matrixStats pracma]; };
+XBSeq = derive { name="XBSeq"; version="0.99.7"; sha256="01vi1p5h1lin0d62mm92y745crv21qqf24kwaj0nlhny93aq45gp"; depends=[Biobase BiocGenerics Delaporte DESeq2 dplyr ggplot2 locfit magrittr matrixStats pracma]; };
 XDE = derive { name="XDE"; version="2.15.0"; sha256="17i8zxb6q4wpsa8lymcnilmr39ip1a54h6rqyl3m7qa8xwb0gv50"; depends=[Biobase BiocGenerics genefilter gtools MergeMaid mvtnorm]; };
 XVector = derive { name="XVector"; version="0.9.1"; sha256="0l5l45i7sx1j51s3wkab207qwbk77i8iazd26isf0yp3rsb84a4c"; depends=[BiocGenerics IRanges S4Vectors]; };
 a4 = derive { name="a4"; version="1.17.0"; sha256="0pn0gm4xkngz72i92h58d0xbpcx04938x4vm0mqsilrjapchripj"; depends=[a4Base a4Classif a4Core a4Preproc a4Reporting]; };
@@ -531,7 +537,7 @@ a4Reporting = derive { name="a4Reporting"; version="1.17.0"; sha256="1fpdkw048gv
 aCGH = derive { name="aCGH"; version="1.47.0"; sha256="095arlryay4gdr6kva7vf9lcby60pyx5bs4vcx586zgwskzpb2ln"; depends=[Biobase cluster multtest survival]; };
 acde = derive { name="acde"; version="0.99.5"; sha256="1bbsfr7a2sivb6dpn06hwj0i95wdlfxzba4a36pakx7nzn6nv76p"; depends=[boot]; };
 adSplit = derive { name="adSplit"; version="1.39.0"; sha256="1jprbqwhksyp9jf05r5dbfzgn30xm16shqsf8yi9b3nr7z2swvwm"; depends=[AnnotationDbi Biobase cluster multtest]; };
-affxparser = derive { name="affxparser"; version="1.41.5"; sha256="0naiv8z07zr1xjnmimx17awnsb9dryiz4w9jx17whrjwdpddx1p5"; depends=[]; };
+affxparser = derive { name="affxparser"; version="1.41.6"; sha256="1d1jnsx3dq52yfcchnagidlsw73dk7j5pagqfzba6pa6vv8l3sl0"; depends=[]; };
 affy = derive { name="affy"; version="1.47.1"; sha256="1c9ggyqhj65mj0nq9xsqfmzp4a5705qj67swjpk5bmqajxr390a3"; depends=[affyio Biobase BiocGenerics BiocInstaller preprocessCore zlibbioc]; };
 affyContam = derive { name="affyContam"; version="1.27.0"; sha256="1hd9kchhdjcnkxlf6kcc59jb5a9v67671shvzprraa1lg4800j5x"; depends=[affy Biobase]; };
 affyILM = derive { name="affyILM"; version="1.21.0"; sha256="1gvagg83p4vxp6q72s7camcg5lhxdfy7rmm3a2p2n29267xvcz5x"; depends=[affxparser affy Biobase gcrma]; };
@@ -540,8 +546,8 @@ affyPara = derive { name="affyPara"; version="1.29.0"; sha256="06382vyfjrng72hhm
 affyQCReport = derive { name="affyQCReport"; version="1.47.0"; sha256="09f3pbacsrjs5bv1bv3dz7jmd849rnix6pqlkszr507s6by5i47y"; depends=[affy affyPLM Biobase genefilter lattice RColorBrewer simpleaffy xtable]; };
 affycomp = derive { name="affycomp"; version="1.45.0"; sha256="0wwgijr7h2hbv2l0w5p509f70yy873w8kahs7nnhrgl4kzbjiymc"; depends=[Biobase]; };
 affycoretools = derive { name="affycoretools"; version="1.41.9"; sha256="16zdm1idmssg9jp86kkfc2h2dhjz2rl6qnrbybfbkiiklj2gagq7"; depends=[affy AnnotationDbi Biobase gcrma ggplot2 GOstats gplots hwriter lattice limma oligoClasses ReportingTools xtable]; };
-affyio = derive { name="affyio"; version="1.37.0"; sha256="0p6wgrl8xag85y5vadfxdvvr430d7sa4wh2fw3ijyi3hr83sdr4z"; depends=[zlibbioc]; };
+affyio = derive { name="affyio"; version="1.39.0"; sha256="07m032wbfgi06yl79waskb2h1r4qi65pzr1j2ry60cr9jv50sizc"; depends=[zlibbioc]; };
-affylmGUI = derive { name="affylmGUI"; version="1.43.0"; sha256="04np48b2v04w77vhpacdx8790i8jb58rw7da76qvahiqja857vlq"; depends=[affy affyio affyPLM AnnotationDbi BiocInstaller gcrma limma R2HTML tkrplot xtable]; };
+affylmGUI = derive { name="affylmGUI"; version="1.43.2"; sha256="1mkg2addri3x8vchgcdy4wih1pzagbp0i54w3nh9kf64r89m35br"; depends=[affy affyio affyPLM AnnotationDbi BiocInstaller gcrma limma R2HTML tkrplot xtable]; };
 affypdnn = derive { name="affypdnn"; version="1.43.0"; sha256="01myf9dxzgc2jgdswphinz7ap7bdaqnw0gcfk32sxbykr4g4zyiy"; depends=[affy]; };
 agilp = derive { name="agilp"; version="3.1.0"; sha256="13jnq7v0qfyllbldx2abnia0rg40yxxgkq4i1whsy5qnk1fp0n77"; depends=[]; };
 alsace = derive { name="alsace"; version="1.5.0"; sha256="17ah7dl02w6qysfbs92h4c3wxfb6f1m6vz6yl07s0zd86k12g4nm"; depends=[ALS ptw]; };
@@ -549,7 +555,7 @@ altcdfenvs = derive { name="altcdfenvs"; version="2.31.0"; sha256="05gr6j1w1y289
 ampliQueso = derive { name="ampliQueso"; version="1.7.0"; sha256="1bk0svxg7n6b610d5czkk1mgkrgdsjlghbj38g4hxxw3vciaxhkk"; depends=[DESeq doParallel edgeR foreach genefilter ggplot2 gplots knitr rgl rnaSeqMap samr statmod VariantAnnotation xtable]; };
 annaffy = derive { name="annaffy"; version="1.41.1"; sha256="1rqp0lrhahkimnhifpipf2vw0lhprdx9slz3s4bwylvn0k5balcm"; depends=[AnnotationDbi Biobase]; };
 annmap = derive { name="annmap"; version="1.11.0"; sha256="0s0ifbwra3zczw9h0nqcs88rb3h74ry1gap1bvqvcxqirdwq9nw4"; depends=[Biobase BiocGenerics DBI digest genefilter GenomicRanges IRanges lattice RMySQL Rsamtools]; };
-annotate = derive { name="annotate"; version="1.47.0"; sha256="06nrzkl9g26rrnqvakwkn2yinvgka02a5iivhi9kgjk4g5plcmkw"; depends=[AnnotationDbi Biobase BiocGenerics DBI XML xtable]; };
+annotate = derive { name="annotate"; version="1.47.4"; sha256="01imryfc18jg8hmxk82arkpvdxfh448fhiv5z0xmkbx03hrrin7b"; depends=[AnnotationDbi Biobase BiocGenerics DBI XML xtable]; };
 annotationTools = derive { name="annotationTools"; version="1.43.0"; sha256="1dqs8f4p1ks03q0lfwm3hs116ahks39hk17knkqs492zcqr83qay"; depends=[Biobase]; };
 anota = derive { name="anota"; version="1.17.0"; sha256="0grdmpdg03wqjs6rk558nvl8vvdi6my0jv06f3h364pk44hrijdn"; depends=[multtest qvalue]; };
 antiProfiles = derive { name="antiProfiles"; version="1.9.1"; sha256="07gzl7wsvv3x7in7n1fwq4cm8bqhlrxwq6ra1k2556z9z8ad7y33"; depends=[locfit matrixStats]; };
@@ -567,7 +573,7 @@ beadarraySNP = derive { name="beadarraySNP"; version="1.35.0"; sha256="0g6ba4iyn
 betr = derive { name="betr"; version="1.25.0"; sha256="0jd7r069jlfp5fj51xw8k6jpxq5kb364xi9331l06hwijp3msrk6"; depends=[Biobase limma mvtnorm]; };
 bgafun = derive { name="bgafun"; version="1.31.0"; sha256="18wk42h1i06j3swlsac9vnkc7riimk7qap59lygji1p3zvy1nkpx"; depends=[ade4 made4 seqinr]; };
 bgx = derive { name="bgx"; version="1.35.0"; sha256="1cawfanrxq82b24ny050hv4p607k2zhfxllgl8j1j9qm9n4yk4yk"; depends=[affy Biobase gcrma]; };
-bigmemoryExtras = derive { name="bigmemoryExtras"; version="1.13.2"; sha256="0qmrpm4bir0si5xd5v8ih6wnwfprwp4q9hcxbylf1721v9m9wpwv"; depends=[bigmemory Biobase]; };
+bigmemoryExtras = derive { name="bigmemoryExtras"; version="1.13.3"; sha256="0jniyz1b11yk00azqxswfdipri84a28ni30kxpazb57d5m6s53h2"; depends=[bigmemory Biobase]; };
 bioDist = derive { name="bioDist"; version="1.41.0"; sha256="14a18ky9x36fa8yx3kry23c0vfazxy0lg0j2zkdnr1irngc9wnw5"; depends=[Biobase KernSmooth]; };
 bioassayR = derive { name="bioassayR"; version="1.7.7"; sha256="1pflygamq0l0pdps4ay3rl4f8c1njrb55lnl0p2z7mgpj6dbgvf8"; depends=[BiocGenerics DBI Matrix rjson RSQLite XML]; };
 biocGraph = derive { name="biocGraph"; version="1.31.0"; sha256="069n4867pkygrsgfjp6arnnmcvlij03r1a2kbs9jgnpx4knck09i"; depends=[BiocGenerics geneplotter graph Rgraphviz]; };
@@ -577,13 +583,13 @@ biomvRCNS = derive { name="biomvRCNS"; version="1.9.1"; sha256="0ni7ncip0vx1ipyr
 biosvd = derive { name="biosvd"; version="2.5.0"; sha256="0xnc3vpbj5p14w2fwql8vpz9lyvivq3kjmwsr62abn418ampa941"; depends=[Biobase BiocGenerics NMF]; };
 biovizBase = derive { name="biovizBase"; version="1.17.1"; sha256="0fffqm8z7x849rd0k7vhpbzwyrx5s0w75iz78627rglczjff6ddp"; depends=[AnnotationDbi BiocGenerics Biostrings dichromat GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges Hmisc IRanges RColorBrewer Rsamtools S4Vectors scales SummarizedExperiment VariantAnnotation]; };
 birta = derive { name="birta"; version="1.13.0"; sha256="01lrwg4naks85gcrlg3sk3pr328j40b1ji4m4bn3s74rqn6sb52h"; depends=[Biobase limma MASS]; };
-birte = derive { name="birte"; version="1.3.0"; sha256="0azkl9x2hk826sdpw96ls868jf83yf1v79inyjg7xsilal2slqgf"; depends=[Biobase limma MASS nem Rcpp RcppArmadillo ridge]; };
+birte = derive { name="birte"; version="1.4.0"; sha256="0fyz2chcgcp98lk6zj21lsixmkr06hd80dbg2j25a4rx2pv6qn5s"; depends=[Biobase limma MASS nem Rcpp RcppArmadillo ridge]; };
 blima = derive { name="blima"; version="1.3.0"; sha256="1i7njg1lw76717irmfbpy9pmv8hy7nzyini2wm6625cafizp5xq8"; depends=[beadarray Biobase BiocGenerics]; };
 bridge = derive { name="bridge"; version="1.33.0"; sha256="06iz67amv80az14s8yim25jfsgbxhxbfifbqazsc78ip9gd7lfyv"; depends=[rama]; };
-bsseq = derive { name="bsseq"; version="1.5.4"; sha256="1hr9h4h099506id4xvh6xm9x40dv5hsiyz8rzj4dxxkq7095h9d1"; depends=[Biobase BiocGenerics data_table GenomeInfoDb GenomicRanges gtools IRanges locfit matrixStats S4Vectors scales SummarizedExperiment]; };
+bsseq = derive { name="bsseq"; version="1.5.5"; sha256="1yhrysqrbv38p7k7g8sywp6ly6prll1kgjpkk7ff9gklpgmdygkq"; depends=[Biobase BiocGenerics data_table GenomeInfoDb GenomicRanges gtools IRanges locfit matrixStats R_utils S4Vectors scales SummarizedExperiment]; };
 bumphunter = derive { name="bumphunter"; version="1.9.1"; sha256="0phq9dhrj8fa253a64vwfp75j85vp9142g5gmfy1g1n861xy8r26"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; };
 caOmicsV = derive { name="caOmicsV"; version="0.99.2"; sha256="0y96f64m0liv53vbby866v1ga5nml1506pp6ff4ax7dbg0niiwwn"; depends=[bc3net igraph]; };
-canceR = derive { name="canceR"; version="1.1.2"; sha256="07wikalgmf3vw2dzmri1ia80hfman53mynsk40y549qn8hjija1k"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase GSEAlm phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; };
+canceR = derive { name="canceR"; version="1.1.3"; sha256="1cagv58133w80acjzlyvx2752ap4dhkpvsfr34306gwbvs4gin3j"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase GSEAlm phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; };
 cancerclass = derive { name="cancerclass"; version="1.13.0"; sha256="066v9dz49ap0db31jrdlx2zbv8l3bwd75sf9gqa1dw3g8m9zq7hg"; depends=[binom Biobase]; };
 casper = derive { name="casper"; version="2.3.1"; sha256="12nz9ypg685c1bly3fp9x76cilh6imlw4hqdmd7sbp2d0z89dcgf"; depends=[Biobase BiocGenerics EBarrays gaga GenomeInfoDb GenomicFeatures GenomicRanges gtools IRanges limma mgcv Rsamtools rtracklayer S4Vectors sqldf survival VGAM]; };
 categoryCompare = derive { name="categoryCompare"; version="1.13.0"; sha256="08r5payxn40xdpaph6zind8miqlqdhnmka9jcijj396rbbhvb480"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category colorspace GOstats graph GSEABase hwriter RCytoscape]; };
@@ -603,21 +609,21 @@ cisPath = derive { name="cisPath"; version="1.9.0"; sha256="1jdq159ixiixh9ppfc5g
 cleanUpdTSeq = derive { name="cleanUpdTSeq"; version="1.7.1"; sha256="0inszzss1fqyhw18lx40iycvpzkm18djxmad1li8bd22hss759c2"; depends=[BiocGenerics BSgenome e1071 GenomicRanges seqinr]; };
 cleaver = derive { name="cleaver"; version="1.7.0"; sha256="14vbdagy61imql6z2qazzlqzp0r9ridydn7phvajc84lnwbf8xa3"; depends=[Biostrings IRanges]; };
 clippda = derive { name="clippda"; version="1.19.0"; sha256="1gd5b2n2qa9bv1n93vcdz8lg8kmn1lv923i3gzq8pcy7fbz7m5cs"; depends=[Biobase lattice limma rgl scatterplot3d statmod]; };
-clipper = derive { name="clipper"; version="1.9.0"; sha256="0py5hdbf8wypw5r9r2d7b3239b83lyrybcvksrmiklv7snw9c2qx"; depends=[Biobase corpcor graph gRbase igraph KEGGgraph Matrix qpgraph RBGL Rcpp]; };
+clipper = derive { name="clipper"; version="1.9.1"; sha256="1z0wjkzx9v0wlsx2wdjxch7j6m3hlkmg5zy8fddgbv3fdc750ppm"; depends=[Biobase corpcor graph gRbase igraph KEGGgraph Matrix qpgraph RBGL Rcpp]; };
 clonotypeR = derive { name="clonotypeR"; version="1.7.0"; sha256="1pwwjgln7r7035fdqqfb69fgql91cxfablbwid2m5xkdrwzpb57s"; depends=[]; };
 clst = derive { name="clst"; version="1.17.1"; sha256="08gqxcjchzywvc67nfjmr2i1xxm71i1j00qxdq3zs6p9y4n65qa0"; depends=[lattice ROC]; };
 clstutils = derive { name="clstutils"; version="1.17.1"; sha256="04gwj8mlbqd5l2nas146vk0vzad0z1y4225g935h9baspcmdh3f8"; depends=[ape clst lattice rjson RSQLite]; };
 clusterProfiler = derive { name="clusterProfiler"; version="2.3.6"; sha256="1hfknmad6wix5ciwcfjn80s0y78966gfkifhxa6wxpkddmdhklqw"; depends=[AnnotationDbi DOSE ggplot2 GOSemSim KEGGREST magrittr plyr qvalue topGO]; };
 clusterStab = derive { name="clusterStab"; version="1.41.0"; sha256="0sgj2k70fc3r3s19vxcx95z8s3a42yshl78swxp0qp55kidbhvdp"; depends=[Biobase]; };
 cn_farms = derive { name="cn.farms"; version="1.17.0"; sha256="09xasmanimx3mzis786iwy2nvxqa5rzvrvrz1hpsiyh5y77yrbnb"; depends=[affxparser Biobase DBI DNAcopy ff lattice oligo oligoClasses preprocessCore snow]; };
-cn_mops = derive { name="cn.mops"; version="1.15.1"; sha256="03gr4i1vpyg6h3yyqrdjq1z1dzq9jzdazcrv9045v652qf4jbshr"; depends=[Biobase BiocGenerics GenomicRanges IRanges Rsamtools]; };
+cn_mops = derive { name="cn.mops"; version="1.15.3"; sha256="0swin9qyzi2fcc0frq0xnzmj789vbjj0mi2wnmmy131blp7iy6x9"; depends=[Biobase BiocGenerics GenomicRanges IRanges Rsamtools]; };
 cnvGSA = derive { name="cnvGSA"; version="1.13.0"; sha256="1sswh1xwimki8ys08l2h95ajpnm5gr0bscvwilhjw4g2a0y7nibr"; depends=[brglm doParallel foreach GenomicRanges splitstackshape]; };
 coGPS = derive { name="coGPS"; version="1.13.0"; sha256="160cf9ijn5crvhwbqldix1n36jrmn51085sr4whgm765si57wwb4"; depends=[]; };
 coMET = derive { name="coMET"; version="1.1.0"; sha256="01baf156p0ldqhczrin2lsf4jir7158b0db5732jddnl5ayghsi3"; depends=[biomaRt colortools GenomicRanges ggbio ggplot2 gridExtra Gviz hash IRanges psych rtracklayer S4Vectors trackViewer]; };
 coRNAi = derive { name="coRNAi"; version="1.19.0"; sha256="1vidwyq8rnkbi0pfbh3mk8m3qj8acwqn7q6jm35gahy4y3p0nq7x"; depends=[cellHTS2 gplots lattice limma locfit MASS]; };
 cobindR = derive { name="cobindR"; version="1.7.1"; sha256="0mya51pynfdxfap3paylinqg10fpir7flsz1bng0sk34y15jnxbz"; depends=[BiocGenerics biomaRt Biostrings BSgenome gmp gplots IRanges mclust rtfbs seqinr yaml]; };
-codelink = derive { name="codelink"; version="1.37.4"; sha256="0rn2cbjgb7f9yypdrvk5ahgpghd3pn45pb183rs9fdywivys9a0v"; depends=[annotate Biobase BiocGenerics limma]; };
+codelink = derive { name="codelink"; version="1.37.5"; sha256="1nh7cfhamy5l8qsxixwl4bg8k524hlr4l8v5mqf4qis9f3zp3l3x"; depends=[annotate Biobase BiocGenerics limma]; };
-cogena = derive { name="cogena"; version="1.1.3"; sha256="074knrfvnhf4fp98dypwzjsp9z15lj7xlgm1wfmnijcwrwf5566p"; depends=[amap Biobase biwt class cluster corrplot devtools doParallel dplyr fastcluster foreach ggplot2 gplots igraph kohonen mclust reshape2 STRINGdb]; };
+cogena = derive { name="cogena"; version="1.1.6"; sha256="0sf0513qhqpb8mm2ydchdnv20dj9s510nv4rcs5b89vnwm62j0i0"; depends=[amap Biobase biwt class cluster corrplot devtools doParallel dplyr fastcluster foreach ggplot2 gplots igraph jsonlite kohonen mclust reshape2 STRINGdb]; };
 compEpiTools = derive { name="compEpiTools"; version="1.3.4"; sha256="0y12sn2dh0x2y7nghkh6dm98b4ilg41694shw3m0fcgaz22c30kp"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges gplots IRanges methylPipe Rsamtools S4Vectors topGO XVector]; };
 compcodeR = derive { name="compcodeR"; version="1.5.3"; sha256="0208sxff40mjizr47zf6yf87irnnjm0gizdk9h5frbizdxl2i9nn"; depends=[caTools edgeR gdata ggplot2 gplots gtools KernSmooth knitr lattice limma markdown MASS modeest ROCR sm stringr vioplot]; };
 conumee = derive { name="conumee"; version="1.1.0"; sha256="1sxl5m7yfqbzg76n06y1jcv0v75y7wf3ad66zw8v004nz84diaix"; depends=[DNAcopy GenomeInfoDb GenomicRanges IRanges minfi rtracklayer]; };
@@ -628,7 +634,7 @@ cosmiq = derive { name="cosmiq"; version="1.3.0"; sha256="1868sxwlmaqas3w3nrw4bv
 cpvSNP = derive { name="cpvSNP"; version="1.1.0"; sha256="066y409zfz0bway990ygck5lf0vzl6whh212v4rpis1l9bzfv434"; depends=[BiocParallel corpcor GenomicFeatures ggplot2 GSEABase plyr]; };
 cqn = derive { name="cqn"; version="1.15.1"; sha256="1g1ip7lxs82qq0qbhnx90hxmjiypc76p1sgx7yvj5nmp6wp1m5xy"; depends=[mclust nor1mix preprocessCore quantreg]; };
 crlmm = derive { name="crlmm"; version="1.27.0"; sha256="16i3ijqhwp6c2dshk8r7idrjwga3sm1qcafqz9gl4q6b04s5jvym"; depends=[affyio Biobase BiocGenerics ellipse ff foreach illuminaio lattice matrixStats mvtnorm oligoClasses preprocessCore RcppEigen SNPchip VGAM]; };
-csaw = derive { name="csaw"; version="1.3.9"; sha256="10ad0nflzy5ygq7rcn5swpdhxd4rr4y65759pvhji17scsinhswp"; depends=[AnnotationDbi edgeR GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges limma Rsamtools S4Vectors SummarizedExperiment]; };
+csaw = derive { name="csaw"; version="1.3.10"; sha256="01vap3h0j9pklmdh5i90p6j9mppvyld000cbhhyj7rmx7z8bsswy"; depends=[AnnotationDbi edgeR GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges limma Rsamtools S4Vectors SummarizedExperiment]; };
 ctc = derive { name="ctc"; version="1.43.0"; sha256="139rxdvyvv3wvlc5q3581y5hkjkd5smxvb606mlxjb8lww4qmcj8"; depends=[amap]; };
 cummeRbund = derive { name="cummeRbund"; version="2.11.1"; sha256="0nd1a9wi2qvvdhfvkb18ql82bfzhz6fivc7wdfv90mibrd7ypb2a"; depends=[Biobase BiocGenerics fastcluster ggplot2 Gviz plyr reshape2 RSQLite rtracklayer]; };
 customProDB = derive { name="customProDB"; version="1.9.4"; sha256="0ws620i6s9p477zfns0m6qpzzhrsivjziv2gv3gmy19dhfh0ln08"; depends=[AnnotationDbi biomaRt Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges plyr RCurl Rsamtools RSQLite rtracklayer stringr VariantAnnotation]; };
@@ -643,32 +649,33 @@ deltaGseg = derive { name="deltaGseg"; version="1.9.0"; sha256="0y8fw4gxmhsr5xrb
 derfinder = derive { name="derfinder"; version="1.3.3"; sha256="11npavkr27f3c48bp40vgn9klgmpqs2w17gl96qn5g1y2gyvrhk5"; depends=[AnnotationDbi BiocParallel bumphunter derfinderHelper GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges Hmisc IRanges qvalue Rsamtools rtracklayer S4Vectors]; };
 derfinderHelper = derive { name="derfinderHelper"; version="1.3.1"; sha256="03kijh42x1v4ix4gxs1729rifwckaz9npcrd9b3j6xsizx97b4cr"; depends=[IRanges Matrix S4Vectors]; };
 derfinderPlot = derive { name="derfinderPlot"; version="1.3.4"; sha256="1f7x609sknmbn8gsxq75073vfr0qd0k9j7gfi0fxvgnm5f4lkizx"; depends=[derfinder GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 IRanges limma plyr RColorBrewer reshape2 scales]; };
+destiny = derive { name="destiny"; version="0.99.14"; sha256="1k44mwmvrh3fyjdslk8vh2kw075nijzsviy7i0glsbj9q1lhfnzk"; depends=[Biobase BiocGenerics FNN igraph Matrix proxy Rcpp RcppEigen scatterplot3d VIM]; };
 dexus = derive { name="dexus"; version="1.9.0"; sha256="1xnjs6gmzkdj1snwakq73bz8ypnxzzxh8ki9wv0ljfbfwv1j7z53"; depends=[BiocGenerics]; };
 diffGeneAnalysis = derive { name="diffGeneAnalysis"; version="1.51.0"; sha256="1k5as63cd87nnigc0yzaxvhskpnbr7l1ym2bqc57zsm3bwh8xxwb"; depends=[minpack_lm]; };
-diffHic = derive { name="diffHic"; version="1.1.9"; sha256="0azagkb87v2lxmb5bvjqc9bz8pqnn1a9j3p5r4v8izpqwq23hf75"; depends=[BiocGenerics Biostrings BSgenome csaw edgeR GenomeInfoDb GenomicRanges IRanges limma locfit rhdf5 Rsamtools S4Vectors]; };
+diffHic = derive { name="diffHic"; version="1.1.12"; sha256="1ywa1c9g4v19w3xmgxvk202h2dd9ax3h99d4rff9xjp2ywkxy2qz"; depends=[BiocGenerics Biostrings BSgenome csaw edgeR GenomeInfoDb GenomicRanges IRanges limma locfit rhdf5 Rsamtools S4Vectors]; };
 diggit = derive { name="diggit"; version="1.1.1"; sha256="0c3zy1d9bzb6asa4clgq738h7dj6md55gclwa244qyx857b58rqv"; depends=[Biobase ks viper]; };
 dks = derive { name="dks"; version="1.15.0"; sha256="1d66jfca6q8ni5vz5zh7fmxwh3y0yvl2p7gal7w55py6wvyssnl3"; depends=[cubature]; };
 domainsignatures = derive { name="domainsignatures"; version="1.29.0"; sha256="1wkypbm5ldwx8y2n16fajf450pwv6zipjdk0176a5rqihaflz80l"; depends=[AnnotationDbi biomaRt prada]; };
 dualKS = derive { name="dualKS"; version="1.29.0"; sha256="1a2wb137x98nmdm8dvnl4msl89mlyvm8f1kqzr6jhdj4wjv2hrg1"; depends=[affy Biobase]; };
 dyebias = derive { name="dyebias"; version="1.27.0"; sha256="095qcnri2g19m363ipdi31xgn20b51mbfv5mgkk21m6fww1npc92"; depends=[Biobase marray]; };
-easyRNASeq = derive { name="easyRNASeq"; version="2.5.5"; sha256="0g2n3ayl06bn8khf5pail119i1611nq71vvqfkdh0v30nj9rsbw2"; depends=[Biobase BiocGenerics BiocParallel biomaRt Biostrings DESeq edgeR GenomeInfoDb genomeIntervals GenomicAlignments GenomicRanges IRanges locfit LSD Rsamtools S4Vectors ShortRead SummarizedExperiment]; };
+easyRNASeq = derive { name="easyRNASeq"; version="2.5.6"; sha256="0b93i80fjvljjm4il1ad9g3apznj23hcyhpq3z10zsw81clfya1j"; depends=[Biobase BiocGenerics BiocParallel biomaRt Biostrings DESeq edgeR GenomeInfoDb genomeIntervals GenomicAlignments GenomicRanges IRanges locfit LSD Rsamtools S4Vectors ShortRead SummarizedExperiment]; };
 ecolitk = derive { name="ecolitk"; version="1.41.0"; sha256="0jga35q98bidqjlqynq0cack4gwsm3hw34vgns67v37krjs4hn9f"; depends=[Biobase]; };
 edge = derive { name="edge"; version="2.1.0"; sha256="1xxz8qyagrfr92ldaxlgb8dfpm6nx3lyk6fa4dl0m8yvlr6lw2fa"; depends=[Biobase MASS qvalue snm sva]; };
 edgeR = derive { name="edgeR"; version="3.11.2"; sha256="0df181xjga322phjinlffl0j2mg61pq4p8h3sxx3xz100c6xrahr"; depends=[limma]; };
 eiR = derive { name="eiR"; version="1.9.1"; sha256="01wkz9lc6gi1a98q02c6zyzfsnkk52px60xg3lawp2419dvj2ww3"; depends=[BH BiocGenerics ChemmineR DBI digest RCurl RUnit snow snowfall]; };
 eisa = derive { name="eisa"; version="1.21.0"; sha256="03366q5qj4wdfm4d9lwysmgz3bgwc53zynw2cmsj7w3yg6dj63km"; depends=[AnnotationDbi Biobase BiocGenerics Category DBI genefilter isa2]; };
 ensemblVEP = derive { name="ensemblVEP"; version="1.9.2"; sha256="10xjxafm97jnk7dfi0j1ahyd6hp45r5rpfr206fbiipcq3ha2p9h"; depends=[BiocGenerics Biostrings GenomicRanges VariantAnnotation]; };
-ensembldb = derive { name="ensembldb"; version="1.1.5"; sha256="1q32pcg07lgzzavcgx5843ljchklgbscw0qgifrs6d1hidbldjvq"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics DBI GenomeInfoDb GenomicFeatures GenomicRanges Rsamtools RSQLite rtracklayer S4Vectors]; };
+ensembldb = derive { name="ensembldb"; version="1.1.6"; sha256="1kr0yfdfhmd8g5pqazpbmaqcjw6ydv5whxf4c29d77x83alfncyh"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics DBI GenomeInfoDb GenomicFeatures GenomicRanges Rsamtools RSQLite rtracklayer S4Vectors]; };
 epigenomix = derive { name="epigenomix"; version="1.9.2"; sha256="0l7pa2nyllf7imapbxqavyg3h0ba3wc1bhrhz7a7bc8rr8qyq0w1"; depends=[beadarray Biobase BiocGenerics GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; };
 epivizr = derive { name="epivizr"; version="1.7.8"; sha256="01z80dbahjbf60d71hiqai5h5i546hvl2j737b4xjca9017g2wsg"; depends=[Biobase GenomeInfoDb GenomicFeatures GenomicRanges httpuv mime OrganismDbi R6 rjson rtracklayer S4Vectors SummarizedExperiment]; };
-erccdashboard = derive { name="erccdashboard"; version="1.3.1"; sha256="10ya8gzd9z3b7kwm9yf7v1cbxpqi1r7ghxwy1sg6b646gf3g580v"; depends=[edgeR ggplot2 gplots gridExtra gtools limma locfit MASS plyr QuasiSeq qvalue reshape2 ROCR scales stringr]; };
+erccdashboard = derive { name="erccdashboard"; version="1.3.2"; sha256="0vsjk6ba739c2hvx87gz0n3sn2cwfm1nhwk2jcb8ynv7gxww3p4l"; depends=[edgeR ggplot2 gplots gridExtra gtools limma locfit MASS plyr QuasiSeq qvalue reshape2 ROCR scales stringr]; };
 erma = derive { name="erma"; version="0.1.2"; sha256="046m88bjfkv8xkmz8il6l0zbp0wcr7n6wvsv2lavcyl09qnjghs0"; depends=[BiocGenerics GenomicFiles GenomicRanges ggplot2 rtracklayer S4Vectors]; };
 exomeCopy = derive { name="exomeCopy"; version="1.15.0"; sha256="1047k3whc8pjcrvb10dmykbc3c7ah4fgzsiqxw7asp4ksiqpj5ii"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; };
 exomePeak = derive { name="exomePeak"; version="1.9.1"; sha256="1lvzr8zsa61vj5qhd4yh9n8vmfw759b8gbpp6q9yxz1py1ky16y6"; depends=[GenomicAlignments GenomicFeatures Rsamtools rtracklayer]; };
 explorase = derive { name="explorase"; version="1.33.0"; sha256="0405q21ivvchmb37jksv46kwxgbmyiavznizn39asv6wrsvw62az"; depends=[limma rggobi RGtk2]; };
 fCI = derive { name="fCI"; version="0.99.10"; sha256="1gknc8pqznxkgdgc403s59xl6x9s8cdb5iql0q88kk8jcqc2fgyl"; depends=[FNN gtools psych rgl VennDiagram zoo]; };
 fabia = derive { name="fabia"; version="2.15.0"; sha256="1631f6q30cxzaw7vqjacr44hwzrjbvk0sw3v41zagpbqbbr11swx"; depends=[Biobase]; };
-facopy = derive { name="facopy"; version="1.3.0"; sha256="0nm7jds5c4p471qyzv61byl61frwnf71kkvcdrc876168bd6s9y3"; depends=[annotate cgdsr coin data_table DOSE FactoMineR ggplot2 GOstats graphite gridExtra igraph IRanges MASS nnet reshape2 Rgraphviz scales]; };
+facopy = derive { name="facopy"; version="1.3.1"; sha256="091pgih7daxhz1lhynq98d5yfxv851dv64vl18dafsg3bp4k5ig5"; depends=[annotate cgdsr coin data_table DOSE FactoMineR ggplot2 GOstats graphite gridExtra igraph IRanges MASS nnet reshape2 Rgraphviz scales]; };
 factDesign = derive { name="factDesign"; version="1.45.0"; sha256="08d7ma718s8rdbmk00jdbwn9d1g431iaff7hc4ra421drl95yql1"; depends=[Biobase]; };
 farms = derive { name="farms"; version="1.21.0"; sha256="1c0k2ffjqfrhkw0d7h6a6sffh50qvbc7jqd3glgrvbwjnmsys34v"; depends=[affy Biobase MASS]; };
 fastLiquidAssociation = derive { name="fastLiquidAssociation"; version="1.5.0"; sha256="0477z4inv374bv5qs6wr5lcndk0d4if4hf1qbwlvv070sh5001gi"; depends=[Hmisc LiquidAssociation WGCNA]; };
@@ -683,7 +690,7 @@ flowCHIC = derive { name="flowCHIC"; version="1.3.0"; sha256="1g6kkmcja3am6dawdk
 flowCL = derive { name="flowCL"; version="1.7.0"; sha256="0n7gsvsfvfcn1ysc2kzv564hnn963rg6zwzx70vzp8lzvg55z8db"; depends=[Rgraphviz SPARQL]; };
 flowClean = derive { name="flowClean"; version="1.5.0"; sha256="1ggzsm1zrvg7x0x9jvjiqm5172cm6lvkmzkk5v38pjvhplqgx4hi"; depends=[bit changepoint flowCore sfsmisc]; };
 flowClust = derive { name="flowClust"; version="3.7.01"; sha256="06y8sg5mdjzn3d18m5b3753q2g4s4yxm1v8vb6pkdszq88255w6k"; depends=[Biobase BiocGenerics clue corpcor ellipse flowCore flowViz graph MCMCpack mnormt RBGL]; };
-flowCore = derive { name="flowCore"; version="1.35.5"; sha256="1w9x5ynbfglj620i4ffg3p18q16ig553rfd52j7r0adlx8w1hm9d"; depends=[BH Biobase BiocGenerics corpcor graph Rcpp rrcov]; };
+flowCore = derive { name="flowCore"; version="1.35.7"; sha256="1j7819bwyrphwwh6hkcjyc7f7yy5bv2sy1qfc66519wswjr90qzn"; depends=[BH Biobase BiocGenerics corpcor graph Rcpp rrcov]; };
 flowCyBar = derive { name="flowCyBar"; version="1.5.0"; sha256="160vyp9pglsrv23m0118506bikwzi2mm9b1qgsrxjnzls2lqvjfa"; depends=[gplots vegan]; };
 flowDensity = derive { name="flowDensity"; version="1.3.0"; sha256="1z8s1d4qwavi5z8zmvac9yqyd19sma18z1jl129w6sl5964spi86"; depends=[car flowCore GEOmap gplots RFOC]; };
 flowFP = derive { name="flowFP"; version="1.27.0"; sha256="15n57slfn0z4vzqhk38mfqzb22r6krafqyp11hv1xsllp8my2a5g"; depends=[Biobase BiocGenerics flowCore flowViz]; };
@@ -702,41 +709,42 @@ flowType = derive { name="flowType"; version="2.7.0"; sha256="0zrwf7h62jd5xgs0kq
 flowUtils = derive { name="flowUtils"; version="1.33.0"; sha256="0r7l8fbi3p1y7ql60czlqhxx4l0fzxv50phwkr5w85jxxldk2pjm"; depends=[Biobase corpcor flowCore flowViz graph RUnit XML]; };
 flowVS = derive { name="flowVS"; version="1.1.0"; sha256="0g1zmcr1wd3xccx2z1akwk177innzrngmxc5r4hjanl37l0skrpq"; depends=[flowCore flowStats flowViz]; };
 flowViz = derive { name="flowViz"; version="1.33.2"; sha256="11qbpf0yw1gjzgw3pb7mnqfvwd60nms4cwrwag8h36a5whfd158c"; depends=[Biobase flowCore hexbin IDPmisc KernSmooth lattice latticeExtra MASS RColorBrewer]; };
-flowWorkspace = derive { name="flowWorkspace"; version="3.15.12"; sha256="1fw5xg93x92acg2vimp6ks9sxqkqc4vbkghvj4shagnck2zjs0dw"; depends=[BH Biobase BiocGenerics data_table dplyr flowCore flowViz graph gridExtra lattice latticeExtra ncdfFlow plyr RBGL RColorBrewer Rcpp Rgraphviz stringr XML]; };
+flowWorkspace = derive { name="flowWorkspace"; version="3.15.15"; sha256="1chjfhij0d4li1q2nz5yqwgmmd4vlf5rcg81z1zfs2kc3c19is18"; depends=[BH Biobase BiocGenerics data_table dplyr flowCore flowViz graph gridExtra lattice latticeExtra ncdfFlow RBGL RColorBrewer Rcpp Rgraphviz stringr XML]; };
-flowcatchR = derive { name="flowcatchR"; version="1.3.0"; sha256="0zgbnfh3sq6s8y81al379lrif67w5xffc6n3fd5y8bp2wmdqmx8b"; depends=[abind BiocParallel colorRamps EBImage rgl]; };
+flowcatchR = derive { name="flowcatchR"; version="1.3.2"; sha256="1l1m709jfx6k13d9ayv9v355lhws6xnmz2bsklrzrkls25pfm04v"; depends=[abind BiocParallel colorRamps EBImage rgl]; };
 fmcsR = derive { name="fmcsR"; version="1.11.4"; sha256="1ah1gyrhcyv4kqxi4n8yj14mgjh6v9l820k5hzb7fwbw74kh2pa5"; depends=[BiocGenerics ChemmineR RUnit]; };
 focalCall = derive { name="focalCall"; version="1.3.0"; sha256="1g3vk72xnzy2vsjjq7dnmmxiy29qg2bqij1iim9psb2zd6w387r5"; depends=[CGHcall]; };
 frma = derive { name="frma"; version="1.21.0"; sha256="0glsdwzlfba9j850s393jm6ada4j04nz4lilym81qvs9y9jccscp"; depends=[affy Biobase BiocGenerics DBI MASS oligo oligoClasses preprocessCore]; };
-frmaTools = derive { name="frmaTools"; version="1.21.0"; sha256="1k5ghz0ddcypisw2l64cg3r9lhvvmdiv1gpbb9b56rw0sk27w0cr"; depends=[affy Biobase DBI preprocessCore]; };
+frmaTools = derive { name="frmaTools"; version="1.21.1"; sha256="13x1k763gdkh9mab1nvsa45z7b0v2q4ilvhv47fvwagi5r11jf5w"; depends=[affy Biobase DBI preprocessCore]; };
 gCMAP = derive { name="gCMAP"; version="1.13.0"; sha256="06qb51rxxjqanh92g0cj6kwnrcbgkc2f0slav2bxkh2rkrjpyvcn"; depends=[annotate AnnotationDbi Biobase Category DESeq genefilter GSEABase GSEAlm limma Matrix]; };
 gCMAPWeb = derive { name="gCMAPWeb"; version="1.9.0"; sha256="0xn1iyvrw3idhwszvipf3y69i1w1azr5hhgklg57v9wibnq02q9g"; depends=[annotate AnnotationDbi Biobase BiocGenerics brew gCMAP GSEABase hwriter Rook yaml]; };
 gQTLBase = derive { name="gQTLBase"; version="1.1.1"; sha256="033lfnn0zkkkzay25fkj7wizyd63jxr2nkgga22iwm8ffjgpyac0"; depends=[BatchJobs BBmisc BiocGenerics doParallel ff ffbase foreach GenomicRanges S4Vectors]; };
-gQTLstats = derive { name="gQTLstats"; version="1.1.0"; sha256="1hc2lwvq5bzxjl7xap8ykr7ja9jxpp6ydalc582v2jz6r8yp0wx8"; depends=[AnnotationDbi BatchJobs Biobase BiocGenerics doParallel dplyr foreach gam GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gQTLBase IRanges limma reshape2 S4Vectors snpStats VariantAnnotation]; };
+gQTLstats = derive { name="gQTLstats"; version="1.1.1"; sha256="0sav44fxh5m9402gip2qaql4rm81ymw7339732nw2lrjk2vm7l7l"; depends=[AnnotationDbi BatchJobs Biobase BiocGenerics doParallel dplyr foreach gam GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gQTLBase IRanges limma reshape2 S4Vectors snpStats SummarizedExperiment VariantAnnotation]; };
 gaga = derive { name="gaga"; version="2.15.1"; sha256="17ccfnvrqq6p9dynlacxw4797n1h9773ilmsh53mzs52w1k2cybm"; depends=[Biobase coda EBarrays mgcv]; };
 gage = derive { name="gage"; version="2.19.0"; sha256="1g8i3w715s10azw7xyzq6gjmz5ilxll4qcf367jn6dwz8xnf15dr"; depends=[AnnotationDbi graph KEGGREST]; };
 gaggle = derive { name="gaggle"; version="1.37.0"; sha256="1429xffj08m3dgfp6z34ngwzaq0wyjm3wv3cwfxzl5pzzy200k41"; depends=[graph rJava RUnit]; };
 gaia = derive { name="gaia"; version="2.13.0"; sha256="10vpz16plzi651aj1f5h3iwz6nzrrdnl9sgx3sgv5wmks2haqij4"; depends=[]; };
 gaucho = derive { name="gaucho"; version="1.5.0"; sha256="0kl8fw1n6dkqmrjp0xri3w2fhx25llrjag7j50m2xh371zfw9chc"; depends=[GA graph heatmap_plus png Rgraphviz]; };
 gcrma = derive { name="gcrma"; version="2.41.0"; sha256="03ncgd26hmj4l0mnnif1cf5qg99ir66d0mafx7wamrr930m17v8x"; depends=[affy affyio Biobase BiocInstaller Biostrings XVector]; };
-gdsfmt = derive { name="gdsfmt"; version="1.5.6"; sha256="0xncblhsfzwzxmki0mir6khpjb4d5sjc452br8jq0hp9khl9j937"; depends=[]; };
+gdsfmt = derive { name="gdsfmt"; version="1.5.9"; sha256="1j849lizdsyqqp8wyssk00jc0l3mqk0ya0p8ca005i11vz8rivv3"; depends=[]; };
-geNetClassifier = derive { name="geNetClassifier"; version="1.9.2"; sha256="04k1j2hqbs75k250i8b17bb8b84mij0hyb3yk1jl1368mpn5vmhc"; depends=[Biobase e1071 EBarrays minet]; };
+geNetClassifier = derive { name="geNetClassifier"; version="1.9.3"; sha256="1vcbh910g6hsgqian6kf4vd62bf16m3bbycg7rn69rd5nhyn9b8x"; depends=[Biobase e1071 EBarrays minet]; };
 geecc = derive { name="geecc"; version="1.3.0"; sha256="0s955yg31papyny42nnqq711hawk5nn3dqgsf24ldz93vjiif9dr"; depends=[gplots hypergea MASS]; };
 genArise = derive { name="genArise"; version="1.45.0"; sha256="07xyy6wa22sa0ziqvy1dvpmpq11j56aw70kvj834da003yvabmg1"; depends=[locfit tkrplot xtable]; };
 geneRecommender = derive { name="geneRecommender"; version="1.41.0"; sha256="0c06xg7jbcn4lnrkwgwwdjq383a7d34svf9cdqlaz5fc662nl5v0"; depends=[Biobase]; };
 geneRxCluster = derive { name="geneRxCluster"; version="1.5.0"; sha256="1m5jxv0qhm68iv6rwy91nkx2mz9b7zh9mdz98gva8mb6gm88iiig"; depends=[GenomicRanges IRanges]; };
 genefilter = derive { name="genefilter"; version="1.51.0"; sha256="0zrav2zw7v67i564v20y02cn2ycyk9ms8cnj2b2l7ajd1lq5cp9s"; depends=[annotate AnnotationDbi Biobase survival]; };
-genefu = derive { name="genefu"; version="1.19.0"; sha256="05rzq0dy4v7z57zqdg9v2csj3ncv2n76igbz2a9nvjpmqrgfcqlc"; depends=[amap biomaRt mclust survcomp]; };
+genefu = derive { name="genefu"; version="2.0.0"; sha256="0vrp2di9pz4xdy2shkl7ccc4ri19q2mv75xl9fkzkan4gnamlkbj"; depends=[amap biomaRt mclust survcomp]; };
 geneplotter = derive { name="geneplotter"; version="1.47.0"; sha256="03vl60rhhfh8imp0ihx83gq9r64gdnh2gjdm7pzi4yc03afqgaw8"; depends=[annotate AnnotationDbi Biobase BiocGenerics lattice RColorBrewer]; };
 genoCN = derive { name="genoCN"; version="1.21.0"; sha256="10q16kch3gn6phx1zk3aii87f4liy5l6mp0kvjf29x6aam11l7c7"; depends=[]; };
-genomation = derive { name="genomation"; version="1.1.5"; sha256="0x4pgs7g46giv6z92hqa0fgq3fbw5p2jm5h8qzbwsvir3y7fnf79"; depends=[GenomicAlignments GenomicRanges ggplot2 gridBase impute IRanges plyr readr reshape2 Rsamtools rtracklayer]; };
+genomation = derive { name="genomation"; version="1.1.10"; sha256="1cxhap9h1g8a5q0jc7xpg00vcp9jrwqmn1v0vlh5ck54vnp672ks"; depends=[data_table GenomicAlignments GenomicRanges ggplot2 gridBase impute IRanges matrixStats plotrix plyr readr reshape2 Rsamtools rtracklayer]; };
-genomeIntervals = derive { name="genomeIntervals"; version="1.25.2"; sha256="145xg7pjihfg6qmjfmswf33hkxsnq8ml02x6s6y90giyxlmjqisk"; depends=[BiocGenerics GenomeInfoDb GenomicRanges intervals IRanges S4Vectors]; };
+genomeIntervals = derive { name="genomeIntervals"; version="1.25.3"; sha256="14ql99gny196nl8ss3pb9m0277nczx6qj9sj2vhwfrr9q9c3ja9a"; depends=[BiocGenerics GenomeInfoDb GenomicRanges intervals IRanges S4Vectors]; };
 genomes = derive { name="genomes"; version="2.15.0"; sha256="1a172fz97b6xg4w91dcjbdr9kx0grzf71qn2j7zlyz52dcqppybb"; depends=[Biostrings GenomicRanges IRanges RCurl XML]; };
-genoset = derive { name="genoset"; version="1.23.2"; sha256="0j23ym7v47fv2f2j25hfc4xh1113614ixdd1accx9gindbqf72cl"; depends=[Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
+genoset = derive { name="genoset"; version="1.23.5"; sha256="1vs1yffrjmqz70qc9rbzrabv7271jrqyscb43g3dw5q1mjwifjvn"; depends=[Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
-gespeR = derive { name="gespeR"; version="1.1.0"; sha256="0hp2pw4z5kgj4av339v7r43is082c47ms422pwwa5f2pljijz2z6"; depends=[Biobase biomaRt cellHTS2 doParallel foreach ggplot2 glmnet Matrix reshape2]; };
+genotypeeval = derive { name="genotypeeval"; version="0.99.3"; sha256="1a0dxfdlcdxmsih8imhvd4mk40lzg9p8sryccqmycw360nwbxh1h"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges ggplot2 IRanges rtracklayer VariantAnnotation]; };
-ggbio = derive { name="ggbio"; version="1.17.1"; sha256="1pc98v500l476sa1krxrj24lfsnbs13ws9hdix3vxfkbklvqjww7"; depends=[Biobase BiocGenerics Biostrings biovizBase BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra gtable Hmisc IRanges OrganismDbi reshape2 Rsamtools rtracklayer S4Vectors scales SummarizedExperiment VariantAnnotation]; };
+gespeR = derive { name="gespeR"; version="1.1.2"; sha256="1mfsy2jca89qh22l95y8cd6bjgdss0p1zhprh87jq973w2saj1kf"; depends=[Biobase biomaRt cellHTS2 doParallel dplyr foreach ggplot2 glmnet Matrix reshape2]; };
-ggtree = derive { name="ggtree"; version="1.1.8"; sha256="1y9h93wn0zmmaz4hdn2xgz226y8pak0lnix5wvv1xax7myzhkbyl"; depends=[ape Biostrings colorspace EBImage ggplot2 gridExtra jsonlite magrittr reshape2]; };
+ggbio = derive { name="ggbio"; version="1.17.2"; sha256="09ffhppri2ibprpwps0zxsrpvbrymsnycriy4709x2ldp1ifjn9l"; depends=[Biobase BiocGenerics Biostrings biovizBase BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra gtable Hmisc IRanges OrganismDbi reshape2 Rsamtools rtracklayer S4Vectors scales SummarizedExperiment VariantAnnotation]; };
+ggtree = derive { name="ggtree"; version="1.1.13"; sha256="1vbv7qawd3zrppxlgy2gjf31q1v74ww8r2cn4w3q5dlv883pxcvm"; depends=[ape Biostrings colorspace EBImage ggplot2 gridExtra jsonlite magrittr reshape2]; };
 girafe = derive { name="girafe"; version="1.21.0"; sha256="11j9aiy6s5cdhwc9591vv344qnwlgn4hvwlp2rx47gccrnxxaqxi"; depends=[Biobase BiocGenerics Biostrings genomeIntervals intervals IRanges Rsamtools S4Vectors ShortRead]; };
-globaltest = derive { name="globaltest"; version="5.23.0"; sha256="1cwgqq5i3v6pp5kp4qi0jxqfh09zgaj719mk4kci3wxb18dc6ql7"; depends=[annotate AnnotationDbi Biobase multtest survival]; };
+globaltest = derive { name="globaltest"; version="5.23.1"; sha256="1zcyiixjia9lznaaksfb6mnwpsa4nsqzv92l86kgrvq9a5655pzd"; depends=[annotate AnnotationDbi Biobase survival]; };
 gmapR = derive { name="gmapR"; version="1.11.0"; sha256="0vn5iz44gcp4k0y5y4pjw6m60w75k82kv25hmnjshh8cpcwqkxkp"; depends=[Biobase BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors VariantAnnotation]; };
 goProfiles = derive { name="goProfiles"; version="1.31.0"; sha256="0nnc5idd3p969nhcsw2bjv7ws1qlb30sywhvpy8kcvk64wzz4jgw"; depends=[AnnotationDbi Biobase]; };
 goTools = derive { name="goTools"; version="1.43.0"; sha256="104xj0q1151ch0b4sswnky6shscx6fps25ycmig1s1ingd8dqnby"; depends=[AnnotationDbi]; };
@@ -745,7 +753,7 @@ gpls = derive { name="gpls"; version="1.41.0"; sha256="050db8ag8wpngfkw686r9vjvd
 gprege = derive { name="gprege"; version="1.13.0"; sha256="0z27521mjn5ipjq8wi3fbh2qw4k1q694l8268f8lypr9f357i1q4"; depends=[gptk]; };
 graph = derive { name="graph"; version="1.47.2"; sha256="0db15kd5qf993qdbr7dl2wbw6bgyg3kiqvd1iziqdq6d2vvbpzbj"; depends=[BiocGenerics]; };
 graphite = derive { name="graphite"; version="1.15.1"; sha256="1q3ybshd9yxivs1b5vj659c45qa8bf7r1dy3idg8g7glh9f2bgnl"; depends=[AnnotationDbi BiocGenerics graph]; };
-groHMM = derive { name="groHMM"; version="1.3.0"; sha256="0kx574xs0k51wwkvm6rbrrgr76ziwkkyqhiy076yzfsfkm3d1jvf"; depends=[GenomicAlignments GenomicRanges IRanges MASS rtracklayer S4Vectors]; };
+groHMM = derive { name="groHMM"; version="1.3.1"; sha256="1bwa2dc2hmp34grl1ki8wzqn5v12afrmcw0igdiv4j8sfgybw3w7"; depends=[GenomicAlignments GenomicRanges IRanges MASS rtracklayer S4Vectors]; };
 gtrellis = derive { name="gtrellis"; version="1.1.1"; sha256="17jflcq97a3a7k735klj6pphn6ixyshggwi0n7b45jgkqi9j5s08"; depends=[circlize GetoptLong]; };
 gwascat = derive { name="gwascat"; version="2.1.4"; sha256="13hvh6rvlh13n9dxx9g1q68qz4mxsvv4sh0kc1931b3vz2mfs0m0"; depends=[AnnotationHub BiocGenerics Biostrings GenomeInfoDb GenomicRanges gQTLstats Gviz IRanges Rsamtools rtracklayer S4Vectors snpStats VariantAnnotation]; };
 h5vc = derive { name="h5vc"; version="2.3.0"; sha256="1cl00k13x03sm60gfkxmaf6ba9kw4186cnik08zn446fipxqypla"; depends=[abind BatchJobs BiocParallel Biostrings GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges reshape rhdf5 Rsamtools S4Vectors]; };
@@ -775,10 +783,10 @@ inSilicoDb = derive { name="inSilicoDb"; version="2.5.0"; sha256="1w5irx042z8if0
 inSilicoMerging = derive { name="inSilicoMerging"; version="1.13.0"; sha256="0zaqwachxn3anbjyn0akv0n2djg08475cdxz7c44ja635r1f6y1j"; depends=[Biobase]; };
 intansv = derive { name="intansv"; version="1.9.0"; sha256="0vb5hls1yyw0x0ff2xcjmxplg0gar9g9xvs1bqw96bf9akcr12r9"; depends=[BiocGenerics GenomicRanges ggbio IRanges plyr]; };
 interactiveDisplay = derive { name="interactiveDisplay"; version="1.7.2"; sha256="1ql4qr5m1xsn3z57p2ndfc4b0zmxgjj0d3gb937ikfljm43jkwyk"; depends=[AnnotationDbi BiocGenerics Category ggplot2 gridSVG interactiveDisplayBase plyr RColorBrewer reshape2 shiny XML]; };
-interactiveDisplayBase = derive { name="interactiveDisplayBase"; version="1.7.0"; sha256="0032ljfx6pj0c11imfhxsxvrcn3gwyb6j29xl8xv48x8z44r0vas"; depends=[BiocGenerics shiny]; };
+interactiveDisplayBase = derive { name="interactiveDisplayBase"; version="1.7.1"; sha256="00b32z45xh0n1hrj166ax71p2aka3df9b2440wq0zribb9jf1s02"; depends=[BiocGenerics shiny]; };
 inveRsion = derive { name="inveRsion"; version="1.17.0"; sha256="1km1h75dh5q505x1ddlhvyqxy4c10wvlviiz2l8sv3g3m9mbd26h"; depends=[haplo_stats]; };
 iontree = derive { name="iontree"; version="1.15.0"; sha256="0frq4f357n5w08nwz3m7s0hv858kgcnlvxb4907yrg1b11zpfvmm"; depends=[rJava RSQLite XML]; };
-isobar = derive { name="isobar"; version="1.15.0"; sha256="0zkj2i1hhs9nwflnwidzpnqcs08vbv3vqwz244shs9i7h0c5fd16"; depends=[Biobase distr plyr]; };
+isobar = derive { name="isobar"; version="1.15.1"; sha256="1i4zlfxbx94yb70bvd3wzlald2fi9ix4bhdlyim490rcdhb0lhyr"; depends=[Biobase distr plyr]; };
 iterativeBMA = derive { name="iterativeBMA"; version="1.27.0"; sha256="18g04l2bksjc2563kd2fmjygpci6pdw9lxv4ax0kpbfvc7zwbz17"; depends=[Biobase BMA leaps]; };
 iterativeBMAsurv = derive { name="iterativeBMAsurv"; version="1.27.0"; sha256="1l36lmxlwq16kzh8i8nbi8bbrgqc7im1b5pcc170q89x6rfgvyf7"; depends=[BMA leaps survival]; };
 jmosaics = derive { name="jmosaics"; version="1.9.0"; sha256="00c84fh5798yyzmsy985b79fcf2yz8y8am13dj7xgnzxl5nj32v1"; depends=[mosaics]; };
@@ -787,15 +795,15 @@ kebabs = derive { name="kebabs"; version="1.3.3"; sha256="10pnr5fd2ni4w69qp30q81
 keggorthology = derive { name="keggorthology"; version="2.21.0"; sha256="1d3dz61llgmdnyqxqwv03pacfs97lzynzpjpmn7grf7bbpybjk2q"; depends=[AnnotationDbi DBI graph]; };
 lapmix = derive { name="lapmix"; version="1.35.0"; sha256="1sps41l210h782bry6n8h55ghnlqn7s5dx0bx2805y5izz01linm"; depends=[Biobase]; };
 les = derive { name="les"; version="1.19.0"; sha256="1b3zcvflwyybrh9pf33a0fn5qz6918sszjf0n666iqd3hh7zph8z"; depends=[boot fdrtool gplots RColorBrewer]; };
-limma = derive { name="limma"; version="3.25.12"; sha256="1gl13qnbj4w2bzdxf1ml603r1ccyq0wv1ynlrgb8j9sa7z228ri9"; depends=[]; };
+limma = derive { name="limma"; version="3.25.14"; sha256="136pvfqqf9jwdir543wblrv6z4fpha5x2dbwldj980yhj4aqz76d"; depends=[]; };
-limmaGUI = derive { name="limmaGUI"; version="1.45.0"; sha256="05pqzb5nq3paddq2zw80gvdaf8rvynga8zs24rwzjpz3ylakqngr"; depends=[AnnotationDbi BiocInstaller gcrma limma R2HTML tkrplot xtable]; };
+limmaGUI = derive { name="limmaGUI"; version="1.45.2"; sha256="1s1dn14d5yhmfqj4r3kaxavpxaxsjw2492fpijgq0v8dnwqhz190"; depends=[AnnotationDbi BiocInstaller gcrma limma R2HTML tkrplot xtable]; };
 lmdme = derive { name="lmdme"; version="1.11.0"; sha256="0j41rfvbhz31vniax7njnslxd94lws4jjfv3hc2s1ihxnj41dcma"; depends=[limma pls]; };
 logicFS = derive { name="logicFS"; version="1.39.0"; sha256="1sz4bxsg76437j42i6cpbqvj5a35q7dwhya4yh1gmknqjrrcrv56"; depends=[LogicReg mcbiopi]; };
 logitT = derive { name="logitT"; version="1.27.0"; sha256="13gglwkvwrc5xr44ynz10qzyksry0wamk9mjlsfb18c2ncbnyypq"; depends=[affy]; };
 lol = derive { name="lol"; version="1.17.1"; sha256="0adj2bg8akb3z0w3wqj6bdlypf9c587k5c2npx0l21hgy4qv7p8k"; depends=[Matrix penalized]; };
 lpNet = derive { name="lpNet"; version="2.1.2"; sha256="0qy2ardh00gf3xkhqphvmdsnsxa4pjrdpcxpjs53nw68bcsbgy9g"; depends=[lpSolve nem]; };
 lumi = derive { name="lumi"; version="2.21.2"; sha256="0nfkzf11lnpvyqng8ns6nf23qkap04fir8cbqngnzm6yddfk33dq"; depends=[affy annotate AnnotationDbi Biobase DBI GenomicFeatures GenomicRanges KernSmooth lattice MASS methylumi mgcv nleqslv preprocessCore RSQLite]; };
-mAPKL = derive { name="mAPKL"; version="1.1.0"; sha256="1knjvwd0z4i70py0dqcngz56j78ylhcxsw8dyxj80ns5jzsdppbx"; depends=[AnnotationDbi apcluster Biobase clusterSim e1071 igraph limma multtest parmigene]; };
+mAPKL = derive { name="mAPKL"; version="1.1.1"; sha256="1wya7fhr6xbjdc61q0hk7k2y3iivashdksqj6b8459c9cr1mn5sl"; depends=[AnnotationDbi apcluster Biobase clusterSim e1071 igraph limma multtest parmigene]; };
 mBPCR = derive { name="mBPCR"; version="1.23.0"; sha256="0c0idj213l8gwxkh9sb03dr4jhlbwvkpghldccbjrqnk4jqs4zpp"; depends=[Biobase oligoClasses SNPchip]; };
 mQTL_NMR = derive { name="mQTL.NMR"; version="1.3.0"; sha256="05q3p6pxi5x89z3zyrvdv5p2lzwr3as3zwcg8k0zm70liyczqcbx"; depends=[GenABEL MASS outliers qtl]; };
 maCorrPlot = derive { name="maCorrPlot"; version="1.39.0"; sha256="14p6cliik2ar0x8q4x66p43lsdbz11sqa7szafqvk7aw3pbszgh4"; depends=[lattice]; };
@@ -823,27 +831,28 @@ metabomxtr = derive { name="metabomxtr"; version="1.3.2"; sha256="0wbpb79k9026ql
 metagene = derive { name="metagene"; version="2.1.0"; sha256="0fk7cgf96g1ax009g6f45jppb0w80akv5n3iwaaryy5b9pvsfk21"; depends=[BiocParallel biomaRt GenomicAlignments GenomicRanges ggplot2 gplots muStat R6 Rsamtools rtracklayer]; };
 metagenomeSeq = derive { name="metagenomeSeq"; version="1.11.10"; sha256="0b9vylijb6gzri61qn8wkj9si1zrgznzqhxzib1aw9y71v8y8k05"; depends=[Biobase foreach glmnet gplots limma Matrix matrixStats RColorBrewer]; };
 metahdep = derive { name="metahdep"; version="1.27.0"; sha256="0kjd27brcvhfqbqk9r3fclbzf2np2zj88gi522y1c6vh3pc6fd22"; depends=[]; };
-metaseqR = derive { name="metaseqR"; version="1.9.0"; sha256="0p8bpnjm73jkng2xrypnz14rmrw1pppkrx1r88vnx33hzpkx83zx"; depends=[baySeq biomaRt brew corrplot DESeq EDASeq edgeR gplots limma log4r NBPSeq NOISeq qvalue rjson vsn]; };
+metaseqR = derive { name="metaseqR"; version="1.9.1"; sha256="1qaa28wnvafi7239lla8xfi8kxxwvi6ar684fg8f5a98s8vjk8i2"; depends=[baySeq biomaRt brew corrplot DESeq EDASeq edgeR gplots limma log4r NBPSeq NOISeq qvalue rjson vsn]; };
 methVisual = derive { name="methVisual"; version="1.21.0"; sha256="18kin1ibcc4ilfh59qgb0zilhvhvs0a1gmbg0lbvj2r0kbsk1ryy"; depends=[Biostrings ca gridBase gsubfn IRanges plotrix sqldf]; };
 methyAnalysis = derive { name="methyAnalysis"; version="1.11.0"; sha256="0ka0svxvb76j0xkdx4pbwf2cyplihh45mb953csrapyh5r6hxwkn"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt genefilter GenomeInfoDb GenomicFeatures GenomicRanges genoset Gviz IRanges lumi methylumi rtracklayer S4Vectors VariantAnnotation]; };
 methylMnM = derive { name="methylMnM"; version="1.7.0"; sha256="08y13kkmafn2h55wwkgs1mpskb4i2wpxzzgjdr9gb3ns06qc9799"; depends=[edgeR statmod]; };
 methylPipe = derive { name="methylPipe"; version="1.3.4"; sha256="17y9xsvl6wgm7kn8g35h3zh7bcqhy7qp2lia6dzx609i04a9br9f"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicRanges gplots Gviz IRanges marray Rsamtools S4Vectors SummarizedExperiment]; };
 methylumi = derive { name="methylumi"; version="2.15.2"; sha256="174hikk5flwylifv7n8n67aps4np06klw240bdzfr347r8yrvikp"; depends=[annotate AnnotationDbi Biobase BiocGenerics genefilter GenomeInfoDb GenomicRanges ggplot2 illuminaio IRanges lattice matrixStats minfi reshape2 S4Vectors scales SummarizedExperiment]; };
 mgsa = derive { name="mgsa"; version="1.17.0"; sha256="1nic4bgk3g3j2l6vr3i3msmid2bz0n7bq8f8zq26n45sr37wb4wq"; depends=[gplots]; };
+miRLAB = derive { name="miRLAB"; version="0.99.2"; sha256="0q255w5myzv9hg27xz4k3ykxf6arpr3nf28ykf23szcw8p01dc80"; depends=[energy entropy glmnet gplots Hmisc httr impute limma pcalg RCurl Roleswitch stringr]; };
 miRNApath = derive { name="miRNApath"; version="1.29.0"; sha256="07r37gzn0y5cp4awj2i638i2cn019rnp7b4hnaqi3gc71sdzb25c"; depends=[]; };
 miRNAtap = derive { name="miRNAtap"; version="1.3.0"; sha256="0hmnhbbai04wp8hxrpgq04czfx2c49aihq7iiz86x9hzlj6xhgn6"; depends=[AnnotationDbi DBI plyr RSQLite sqldf stringr]; };
 microRNA = derive { name="microRNA"; version="1.27.0"; sha256="1akq1yxc03v7jmpypmr8a9lx5h2nfdjp1y0433lyffbd49wia2gm"; depends=[Biostrings]; };
 minet = derive { name="minet"; version="3.27.0"; sha256="1wnn3nlpa0ymk465ax2s65i3w9xplhwssvng9qs7p3v2z72p9nqp"; depends=[infotheo]; };
-minfi = derive { name="minfi"; version="1.15.9"; sha256="1q21b57iw8lbzbjq96qmlmccijz0apr9clasrz4nbmbgyn97gba2"; depends=[beanplot Biobase BiocGenerics Biostrings bumphunter genefilter GenomeInfoDb GenomicRanges GEOquery illuminaio IRanges lattice limma MASS matrixStats mclust mixOmics nlme nor1mix preprocessCore quadprog RColorBrewer reshape S4Vectors siggenes SummarizedExperiment]; };
+minfi = derive { name="minfi"; version="1.15.11"; sha256="14j5vw6vmfz2h85n4dmsnx7138mxwzfl961p8y5wh1brz4vr31iy"; depends=[beanplot Biobase BiocGenerics Biostrings bumphunter genefilter GenomeInfoDb GenomicRanges GEOquery illuminaio IRanges lattice limma MASS matrixStats mclust mixOmics nlme nor1mix preprocessCore quadprog RColorBrewer reshape S4Vectors siggenes SummarizedExperiment]; };
 mirIntegrator = derive { name="mirIntegrator"; version="0.99.5"; sha256="0r8l1lgf9rdxnr0dvc8r05ahjf3q0r4syy9mzx4p3f04s0c78q3h"; depends=[AnnotationDbi ggplot2 graph Rgraphviz ROntoTools]; };
 missMethyl = derive { name="missMethyl"; version="1.3.2"; sha256="05xk70z813jgwz9darqwh0f9ybycq9krig486b3751dd0xnjgmcq"; depends=[limma methylumi minfi ruv statmod stringr]; };
 mitoODE = derive { name="mitoODE"; version="1.7.0"; sha256="182ifqh1g1yz8rbsxdqgk4hzlz3dwy0d03iklbg39cxy6qhgxqg4"; depends=[KernSmooth MASS minpack_lm]; };
 mmnet = derive { name="mmnet"; version="1.7.0"; sha256="0za8a3j2fzyi15hd7l3ccw5qy3lyl7vihbcbixaw2kb81hmpphsa"; depends=[Biobase biom flexmix ggplot2 igraph KEGGREST Matrix plyr RCurl reshape2 RJSONIO stringr XML]; };
-mogsa = derive { name="mogsa"; version="1.1.3"; sha256="0rzqlm0c4skjgic334nfd2s7p0xk86mv1zbwjk036nwf5lnmdd0i"; depends=[Biobase BiocGenerics cluster corpcor genefilter gplots graphite GSEABase svd]; };
+mogsa = derive { name="mogsa"; version="1.1.5"; sha256="1xn2rrp9s3d84i7ln37iblnxadl1dsi7qd98k5xz71kq0v1ljpy4"; depends=[Biobase BiocGenerics cluster corpcor genefilter gplots graphite GSEABase svd]; };
 monocle = derive { name="monocle"; version="1.3.0"; sha256="1ir0f80nsrvpl4i441irprd4pk1f53dxf1jnvnjg5zrkj7dz3wrw"; depends=[Biobase BiocGenerics cluster combinat fastICA ggplot2 igraph irlba limma matrixStats plyr reshape2 VGAM]; };
 mosaics = derive { name="mosaics"; version="2.3.0"; sha256="1jv5sv6xyh5i5m7kypgwc5g3sfsf0n5n683gijxcvrrwpvvfpnqy"; depends=[IRanges lattice MASS Rcpp]; };
 motifRG = derive { name="motifRG"; version="1.13.0"; sha256="01k47padfs393pprjyz9pp9z6vjqlxi6x10y51mhg0anqfb1sar2"; depends=[Biostrings BSgenome IRanges seqLogo XVector]; };
-motifStack = derive { name="motifStack"; version="1.13.3"; sha256="08ddwy3yyydxaxs6qfh99va3v7xx57kq1pizqknxaar0p79x278w"; depends=[ade4 Biostrings grImport MotIV scales XML]; };
+motifStack = derive { name="motifStack"; version="1.13.6"; sha256="0yp3k22i35hdmx5b5a9dk9mkdvglry6s8ck57gsl039ypf58kpja"; depends=[ade4 Biostrings grImport MotIV scales XML]; };
 msa = derive { name="msa"; version="1.1.1"; sha256="0nqgx1zb3n8kk2l3dgilsamwzadnddif39q5br7qs9xl38hag4nr"; depends=[BiocGenerics Biostrings IRanges Rcpp S4Vectors]; };
 msmsEDA = derive { name="msmsEDA"; version="1.7.0"; sha256="1hywj0vvrqq1zg62gr1rk4sblm201hgwz5kd78819apw5jf50fwd"; depends=[gplots MASS MSnbase RColorBrewer]; };
 msmsTests = derive { name="msmsTests"; version="1.7.0"; sha256="1qvi91shpy02irppq6g6lq43sp3rk2j7n1nfnm2p9767rdhbj13b"; depends=[edgeR msmsEDA MSnbase qvalue]; };
@@ -852,14 +861,14 @@ multiscan = derive { name="multiscan"; version="1.29.0"; sha256="0rp1nc8vjr8b0v9
 multtest = derive { name="multtest"; version="2.25.2"; sha256="1gby3am0rp62lsijhbr8yx8y457yhrv2ghdb41kl53r59mw8ba4z"; depends=[Biobase BiocGenerics MASS survival]; };
 muscle = derive { name="muscle"; version="3.11.0"; sha256="1s3apdcd0qj08bswn7smj7b93yv9qar7wrzyfkp5z3m16jgz979x"; depends=[Biostrings]; };
 mvGST = derive { name="mvGST"; version="1.3.0"; sha256="1chskyx9hgymxg57p6y98rw743lapssx18axvl0r9f2zsmmfz9bn"; depends=[annotate AnnotationDbi GOstats gProfileR graph Rgraphviz stringr topGO]; };
-mygene = derive { name="mygene"; version="1.5.1"; sha256="0f1ck375fqbz3ydjjg9qd9av8jbpc840nv3j83qic8g3r2pck8ij"; depends=[GenomicFeatures Hmisc httr jsonlite S4Vectors sqldf]; };
+mygene = derive { name="mygene"; version="1.5.2"; sha256="0x40bnll85v94dnfpqrs8d9kx0zmdjbvgnqhcin1k9bshxqkypd9"; depends=[GenomicFeatures Hmisc httr jsonlite plyr S4Vectors sqldf]; };
 mzID = derive { name="mzID"; version="1.7.1"; sha256="1pp0zfffz91g16y1kr81mbham64g00mm3q539ykj5az34g5q1fcm"; depends=[doParallel foreach iterators plyr ProtGenerics XML]; };
-mzR = derive { name="mzR"; version="2.3.1"; sha256="19piyqgdxpi777nd4860d6mp0g4zzcf3wf7q7ilm99jqav9lfrn8"; depends=[Biobase BiocGenerics ProtGenerics Rcpp zlibbioc]; };
+mzR = derive { name="mzR"; version="2.3.2"; sha256="0hl3g2fn90lpka5r96cfzcw3msw8wnvq6d52p5axhb1214v5zpr6"; depends=[Biobase BiocGenerics ProtGenerics Rcpp zlibbioc]; };
-ncdfFlow = derive { name="ncdfFlow"; version="2.15.2"; sha256="0s65c26r6q8di73iwpkrx4g3d9dy6v18vna7yy7di5vsgy0phr9l"; depends=[BH Biobase flowCore flowViz Rcpp RcppArmadillo zlibbioc]; };
+ncdfFlow = derive { name="ncdfFlow"; version="2.15.3"; sha256="0xhqis5pj5m4ib4xpkgg1afxzjc1827jw5k569aijr11qmi6jjxw"; depends=[BH Biobase flowCore flowViz Rcpp RcppArmadillo zlibbioc]; };
 neaGUI = derive { name="neaGUI"; version="1.7.0"; sha256="198b0vrr5qp66z4sccwy6rh8sjxpw3qjkdryygg1baxq91ra76p1"; depends=[hwriter]; };
 nem = derive { name="nem"; version="2.43.0"; sha256="1d357gh8binh0fwg1z0mzjzq3nyhazg9dnnf7aqk6gjfgsjda9i8"; depends=[boot e1071 graph limma plotrix RBGL RColorBrewer Rgraphviz statmod]; };
 netbenchmark = derive { name="netbenchmark"; version="1.1.6"; sha256="07q5a9kxq5r0ch32q68vxb4gxl6r5zhw6d06b8c89h42cby2qdfp"; depends=[c3net GeneNet minet PCIT pracma randomForest Rcpp]; };
-netbiov = derive { name="netbiov"; version="1.3.0"; sha256="0d6xc74ivzvi0n9ndfgc0m9y79mwdbs344lxv9nps4igd7aaxh34"; depends=[igraph]; };
+netbiov = derive { name="netbiov"; version="1.3.1"; sha256="1v1iddwgz7nn0flgald0nrg96wm8pvdlwjnh8bql8y5x5sm58lmv"; depends=[igraph]; };
 nethet = derive { name="nethet"; version="1.1.0"; sha256="1xklqhwfmv1sk5h3x2g1jjbl5higrzhfj0mvap15vr2agax5hbg5"; depends=[CompQuadForm GeneNet ggm ggplot2 glasso glmnet GSA huge ICSNP limma mclust multtest mvtnorm network parcor]; };
 netresponse = derive { name="netresponse"; version="1.19.0"; sha256="0blgcfbhwns4khnsd3m2yafmihr63kh3zsf7imphim0cdrx67xks"; depends=[dmt ggplot2 graph igraph mclust minet plyr qvalue RColorBrewer reshape Rgraphviz]; };
 networkBMA = derive { name="networkBMA"; version="1.11.0"; sha256="09wf696s8n30nnadfds58flv8sv2gamgnw6pzz80isfc3178h1n6"; depends=[BMA Rcpp RcppArmadillo RcppEigen]; };
@@ -874,12 +883,12 @@ oligoClasses = derive { name="oligoClasses"; version="1.31.1"; sha256="0likyfm4x
 omicade4 = derive { name="omicade4"; version="1.9.3"; sha256="00dr419qd563d75srypc02j6m5v281995mrh0r6fylz5bmi9bbks"; depends=[ade4 made4]; };
 oneChannelGUI = derive { name="oneChannelGUI"; version="1.35.0"; sha256="1diclgl4zkzzyz705cyqx983bw4zqw03rx7fn9515w0ifl0bk1r4"; depends=[affylmGUI Biobase Biostrings chimera IRanges Rsamtools siggenes tkrplot tkWidgets]; };
 ontoCAT = derive { name="ontoCAT"; version="1.21.0"; sha256="10d0a0fxg2h9gf6d1jbilxxg8irbqb1k526689qkdn2zh0qjvv04"; depends=[rJava]; };
-openCyto = derive { name="openCyto"; version="1.7.2"; sha256="1x92yam7zdmsf6x0xqydwz70qmh3gzzi64mbiwrihr8abcjmhjhd"; depends=[Biobase clue data_table flowClust flowCore flowStats flowViz flowWorkspace graph gtools ks lattice MASS ncdfFlow plyr R_utils RBGL RColorBrewer Rcpp rrcov]; };
+openCyto = derive { name="openCyto"; version="1.7.4"; sha256="1q07s7rv19yahlpjpvsrhbvld6n2bf7jv7lfrgs6syfl3fwrs008"; depends=[Biobase clue data_table flowClust flowCore flowStats flowViz flowWorkspace graph gtools ks lattice MASS ncdfFlow plyr R_utils RBGL RColorBrewer Rcpp rrcov]; };
-oposSOM = derive { name="oposSOM"; version="1.5.2"; sha256="0zvclv05sfgk0mq169igaqhqmx2hqj3iwrxrjgryy276xjywhxcr"; depends=[ape Biobase biomaRt fastICA fdrtool igraph KernSmooth pixmap scatterplot3d som]; };
+oposSOM = derive { name="oposSOM"; version="1.5.4"; sha256="0f06wmy1n9gl41x4x7q1fcfxaw6y6qkrmb4ypg9j6v7xjhjpfj03"; depends=[ape Biobase biomaRt fastICA fdrtool igraph KernSmooth pixmap scatterplot3d som]; };
-pRoloc = derive { name="pRoloc"; version="1.9.3"; sha256="09pi362w1vfcx6fsr6bbsjqq9wq93dzhw0myavxsj11g3pnqh66n"; depends=[Biobase BiocGenerics BiocParallel biomaRt caret class e1071 FNN ggplot2 gtools kernlab knitr lattice MASS mclust MLInterfaces MSnbase mvtnorm nnet plyr proxy randomForest RColorBrewer Rcpp RcppArmadillo sampling scales]; };
+pRoloc = derive { name="pRoloc"; version="1.9.6"; sha256="01gk4xnij5l4sk0c4km94i5b26vjfm8qhh3irb7xwfijank7mxd9"; depends=[Biobase BiocGenerics BiocParallel biomaRt caret class e1071 FNN ggplot2 gtools kernlab knitr lattice MASS mclust MLInterfaces MSnbase mvtnorm nnet plyr proxy randomForest RColorBrewer Rcpp RcppArmadillo sampling scales]; };
-pRolocGUI = derive { name="pRolocGUI"; version="1.3.0"; sha256="1k7r8fhj4fqizk1w76mfcdd9sj3y7vxiq3kzfrkbk674gl1jsgmq"; depends=[MSnbase pRoloc shiny]; };
+pRolocGUI = derive { name="pRolocGUI"; version="1.3.2"; sha256="08q1cavlxryx9isn2wsw8r0bv795hgzkyfx95ycxxdwh6vdvnnyl"; depends=[DT MSnbase pRoloc scales shiny]; };
 paircompviz = derive { name="paircompviz"; version="1.7.0"; sha256="0sf80ji20q6kaqw2747an9b51xxwhl55yj5y7q6j68gif1ndkzl4"; depends=[Rgraphviz]; };
-pandaR = derive { name="pandaR"; version="1.1.0"; sha256="03aa0s1mifq5hyg4xshbjqz9javphgb11135zvfg8cqdq34dzg4m"; depends=[]; };
+pandaR = derive { name="pandaR"; version="1.1.1"; sha256="0rp8qk5cn5zj0nypkhmxjpja6lkjxd3hw2dkl4gaisayhiqlfk3g"; depends=[igraph matrixStats]; };
 panp = derive { name="panp"; version="1.39.0"; sha256="163yii12bhw0skzhwrjbavpsgsl2aygj8x9cilzj9pqsqakvinna"; depends=[affy Biobase]; };
 parglms = derive { name="parglms"; version="1.1.0"; sha256="1msk5ygl030rczm10rp9xnb461cbzcs7qqk6jqk8xhv5dycnwnbd"; depends=[BatchJobs BiocGenerics BiocParallel]; };
 parody = derive { name="parody"; version="1.27.0"; sha256="06lrzix8ydc41siy21fqkf3z6krj07p5v38pzan8jzzhqpwlq4iz"; depends=[]; };
@@ -890,7 +899,7 @@ paxtoolsr = derive { name="paxtoolsr"; version="1.3.1"; sha256="0pv4zcl12yxidiy3
 pcaGoPromoter = derive { name="pcaGoPromoter"; version="1.13.1"; sha256="0a1yfi16sadp5fj112mlq9har0yggp8amn8v4v18jzfrb8aiacsj"; depends=[AnnotationDbi Biostrings ellipse]; };
 pcaMethods = derive { name="pcaMethods"; version="1.59.0"; sha256="12b8qdd38xgpzisz0lm9xkwq22z5ciq7b8i11z3na1wynvim3nll"; depends=[Biobase BiocGenerics MASS Rcpp]; };
 pcot2 = derive { name="pcot2"; version="1.37.0"; sha256="023ly5jgq8zc7k73mfqvra13mask54l7f62dznjh1dcjpv6xgw4p"; depends=[amap Biobase]; };
-pdInfoBuilder = derive { name="pdInfoBuilder"; version="1.33.1"; sha256="1vyw3ggh247km4qag1gy3wz9v338na4hlxmqz57mv51gp7fw6v1l"; depends=[affxparser Biobase BiocGenerics Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; };
+pdInfoBuilder = derive { name="pdInfoBuilder"; version="1.33.2"; sha256="026l6klpf93h42xgrbjyl022l0d0722gp7cqqgq4j8nb0wydg8l2"; depends=[affxparser Biobase BiocGenerics Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; };
 pdmclass = derive { name="pdmclass"; version="1.41.0"; sha256="0361s7d6n9wn65pxks3alr8ycqjcgv9dvvb2n9xqiqawyki1nvpm"; depends=[Biobase mda]; };
 pepStat = derive { name="pepStat"; version="1.3.0"; sha256="003gqcs5m5b8mil9r1ydadhcc086nqmdk6i1xz4kkdpkcyxbyz7p"; depends=[Biobase data_table fields GenomicRanges ggplot2 IRanges limma plyr]; };
 pepXMLTab = derive { name="pepXMLTab"; version="1.3.0"; sha256="0rbcj59vsbq8zqxq4h1v077jgpz7l607zalc4lhw9yn8l5lij4j8"; depends=[XML]; };
@@ -934,8 +943,9 @@ qusage = derive { name="qusage"; version="1.9.0"; sha256="1dg8qchhqfvak5cqjs9v30
 qvalue = derive { name="qvalue"; version="2.1.0"; sha256="0qgsqjb90qnf5a77n3zf5dcb5agdbj4hlk3swh1hrjg9iqcs76g0"; depends=[ggplot2 reshape2]; };
 r3Cseq = derive { name="r3Cseq"; version="1.15.0"; sha256="0pi5aq3dbivk23x6axwbqa4danbsvn623icw6xvlh3i71v8m5rkw"; depends=[Biostrings data_table GenomeInfoDb GenomicRanges IRanges qvalue RColorBrewer Rsamtools rtracklayer sqldf VGAM]; };
 rBiopaxParser = derive { name="rBiopaxParser"; version="2.7.0"; sha256="1ni8kaivdxqxv8fj2qf5vnwzmmamfd073l1p4072pnfxpn7rn0p4"; depends=[data_table XML]; };
+rCGH = derive { name="rCGH"; version="0.99.7"; sha256="1bn8rwln7zh686hz87zz3ymv5lylk64xfmwjj357q7kx5r75n2hz"; depends=[aCGH affy AnnotationDbi BiocGenerics DNAcopy GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 lattice limma mclust plyr RUnit shiny]; };
 rGADEM = derive { name="rGADEM"; version="2.17.0"; sha256="1xwypnpf7sdaqszfmallgg2314g866xbi9q342yhds2fkiw9sp65"; depends=[Biostrings BSgenome IRanges seqLogo]; };
-rGREAT = derive { name="rGREAT"; version="1.1.0"; sha256="1rd4cjwh4rrqgfg15k32br0iv15j99797z7lx7789wc1zxkpzvg3"; depends=[GenomicRanges GetoptLong IRanges RCurl rjson]; };
+rGREAT = derive { name="rGREAT"; version="1.1.2"; sha256="0wwwpbxp8263jgkja6szcwqvijig8cfxdb66hvjqq69h9lqg9bkx"; depends=[GenomicRanges GetoptLong IRanges RCurl rjson]; };
 rHVDM = derive { name="rHVDM"; version="1.35.0"; sha256="0y2vm6xsdsz174xrs22p54z5f5rxqcx937yf02ilv0bnfa0r06hj"; depends=[affy Biobase minpack_lm R2HTML]; };
 rMAT = derive { name="rMAT"; version="3.19.0"; sha256="0nhmf1hbiqwzb9035405f8asnhh2ywj4bm9wdlgbafyhiw6qik98"; depends=[affxparser Biobase BiocGenerics IRanges]; };
 rRDP = derive { name="rRDP"; version="1.3.0"; sha256="0q373nfs4ynjnmq9rp0c0ficnnylwb2gf1j0bzlnxcd2cwz215zv"; depends=[Biostrings]; };
@@ -943,7 +953,7 @@ rSFFreader = derive { name="rSFFreader"; version="0.17.1"; sha256="105qlrjq4777k
 rTANDEM = derive { name="rTANDEM"; version="1.9.0"; sha256="08r73kv83w8rfglbqf2zvczj4yix7sfhvrz93wk22nry04jfgccr"; depends=[data_table Rcpp XML]; };
 rTRM = derive { name="rTRM"; version="1.7.1"; sha256="06p38i0hif1kjsy4xa88jhfl5giprq8gfa15zh1yv1qdqhaf1v1m"; depends=[AnnotationDbi DBI igraph RSQLite]; };
 rTRMui = derive { name="rTRMui"; version="1.7.0"; sha256="132cm40hxhb4apdidifbw90jyxhlz0dqxgqsr6awv8q6dy9jpfw4"; depends=[MotifDb rTRM shiny]; };
-rain = derive { name="rain"; version="1.3.0"; sha256="0ak8wbhsglnylzy1jzh9hb2yxqjzmspvj98x10vf3qmgbqc30i4y"; depends=[gmp multtest]; };
+rain = derive { name="rain"; version="1.3.1"; sha256="0hzfrab9b67wk9kkkx7bn1w2imhlq4j8mi3fch3ij42081g8plww"; depends=[gmp multtest]; };
 rama = derive { name="rama"; version="1.43.0"; sha256="1siqzb0b9j51b06aijz85xn6c9v4dqvcw7scmrlfpf18dihqaig1"; depends=[]; };
 randPack = derive { name="randPack"; version="1.15.0"; sha256="0m9729h3fia15rcgxznz4hmlz7abz8xkbn1ffc3l8qhqks5j50f7"; depends=[Biobase]; };
 rbsurv = derive { name="rbsurv"; version="2.27.0"; sha256="1v97vrralg445zn8s3km7vmhlxhkv8bdwcj90fyvd6kfk7gm4xc7"; depends=[Biobase survival]; };
@@ -953,16 +963,17 @@ regionReport = derive { name="regionReport"; version="1.3.8"; sha256="0gpifx0x2k
 regioneR = derive { name="regioneR"; version="1.1.1"; sha256="1wylrkqiv5lc9rw3mc1by88ckx437jwhlgyg5kasvpry003rm72c"; depends=[BSgenome GenomicRanges memoise rtracklayer]; };
 rfPred = derive { name="rfPred"; version="1.7.0"; sha256="0k1z7bqdjmm668kipz8c74kd9k1vw2pcjbirxdi88clrclz3i47y"; depends=[data_table GenomicRanges IRanges Rsamtools]; };
 rgsepd = derive { name="rgsepd"; version="1.1.0"; sha256="1rvzlzh43j3sj2vrhmg13hl4wq3bg9hml3xq2dpx28lapynywm41"; depends=[AnnotationDbi biomaRt DESeq2 GenomicRanges goseq gplots hash]; };
-rhdf5 = derive { name="rhdf5"; version="2.13.4"; sha256="0vby0cpsc22jrq37p3sxj6f3q0l238d28lx0p558mh8nks9fkai1"; depends=[zlibbioc]; };
+rhdf5 = derive { name="rhdf5"; version="2.13.5"; sha256="1k2hjzzj2irs7jap7g4ys0gd3iymnnbbyvyv986y9pq68p4f1nr0"; depends=[zlibbioc]; };
 riboSeqR = derive { name="riboSeqR"; version="1.3.0"; sha256="0jlh5q1hkxkfvy496hlbwfkl17k36n304yiyz9f0azq5kv7jz1y2"; depends=[abind GenomicRanges]; };
 rnaSeqMap = derive { name="rnaSeqMap"; version="2.27.0"; sha256="1638vikgizcgg4bpfm61ak98smwy74dk5hyx73qjbisd49zvy5nk"; depends=[Biobase DBI DESeq edgeR GenomicAlignments GenomicRanges IRanges Rsamtools]; };
-rnaseqcomp = derive { name="rnaseqcomp"; version="0.99.3"; sha256="0gyz91ayyr1834hr6jg1bnjiiiw4k75j3kn5pfmw9q8v9vg2fcsj"; depends=[RColorBrewer]; };
+rnaseqcomp = derive { name="rnaseqcomp"; version="0.99.4"; sha256="0m3xz7fnry89i7b4f51x90mwiqlv2z4d3p2r41mdm4xvwmqj4ghf"; depends=[RColorBrewer]; };
 roar = derive { name="roar"; version="1.5.2"; sha256="0g0ylr49dvnbyb1kwj20hrh3y3x49n4rbdvg7mpdg1byrygcli3c"; depends=[GenomicAlignments GenomicRanges rtracklayer S4Vectors SummarizedExperiment]; };
 rols = derive { name="rols"; version="1.11.6"; sha256="0wgzvwfq677dkqzzcq071xbh6v47vkcrzw66ch1vg348pcj58z0f"; depends=[Biobase XML]; };
+ropls = derive { name="ropls"; version="1.1.2"; sha256="06z0ay0rdaawyvpy7dbdpxkwa8311rlb9plk4v52v830zibamhvs"; depends=[]; };
 rpx = derive { name="rpx"; version="1.5.1"; sha256="048qldpx4zsp55jkr8g8vljiyidm9kzv4p1vwh1983y38qbz882v"; depends=[RCurl XML]; };
 rqubic = derive { name="rqubic"; version="1.15.0"; sha256="19n613m7x48wkrfrhnd0ab9018m5dd7rf08qjbgphakwycssfgcw"; depends=[biclust Biobase BiocGenerics]; };
 rsbml = derive { name="rsbml"; version="2.27.0"; sha256="10qmv5gpgqffnr5wqh7zik0l2d1cg0c0m3xak4r4bqmsd1y4dw01"; depends=[BiocGenerics graph]; };
-rtracklayer = derive { name="rtracklayer"; version="1.29.12"; sha256="0gz3284d5cy3n0hr5w7x86lraryfi2jdg1yzj2jg6cq0hgga40c1"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl Rsamtools S4Vectors XML XVector zlibbioc]; };
+rtracklayer = derive { name="rtracklayer"; version="1.29.13"; sha256="04f7fxl5k7yl4jr4la57k1z613m39zvrmrf8n5pmdy0j25lxk2z6"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl Rsamtools S4Vectors XML XVector zlibbioc]; };
 sRAP = derive { name="sRAP"; version="1.9.0"; sha256="0rvnq41gns4ccr6gnfw0xbbi2c2wjl14qh0yr7wj7s4yrxzqr866"; depends=[gplots pls qvalue ROCR WriteXLS]; };
 sSeq = derive { name="sSeq"; version="1.7.0"; sha256="0wcw77cz47wklwsrwwimwryqmyc0lrd9mk2aawk0vx1zkqci1yca"; depends=[caTools RColorBrewer]; };
 safe = derive { name="safe"; version="3.9.0"; sha256="0x1gdzpgrm4m2m64h6y5rayp64j6ckxlr081d3w46zvfb935294a"; depends=[AnnotationDbi Biobase SparseM]; };
@@ -970,7 +981,7 @@ sagenhaft = derive { name="sagenhaft"; version="1.39.1"; sha256="15aimbx6wn4il0j
 sangerseqR = derive { name="sangerseqR"; version="1.5.0"; sha256="0wiqaqzn6n63k1389nqj35k5wn93bq7c99gayblwjrhks0y9fll0"; depends=[Biostrings shiny]; };
 sapFinder = derive { name="sapFinder"; version="1.7.0"; sha256="1xg3scw5ijm1z2l4ha4ik52s97vr10plr9ifs9rdk2l6vh8na6kh"; depends=[pheatmap Rcpp rTANDEM]; };
 saps = derive { name="saps"; version="2.1.0"; sha256="0r6525n8ksxaa5dcvs9419bca1v369251psvwphfsdnfa4xg2n14"; depends=[piano reshape2 survcomp survival]; };
-savR = derive { name="savR"; version="1.7.4"; sha256="1v0rzrh27yl0fx5gcwb04yq2vln3ngisg59614qmmdppc36qf5k6"; depends=[ggplot2 gridExtra reshape2 scales XML]; };
+savR = derive { name="savR"; version="1.7.5"; sha256="0pdkf8rkqd3fl1p8h1adfixmi0fgj1hwfbn2qn5y326w6aq6cqrs"; depends=[ggplot2 gridExtra reshape2 scales XML]; };
 scsR = derive { name="scsR"; version="1.5.0"; sha256="1n9clp1ldspxbrv4chihv1xhw2fmys13p884cmn037xhwv5b7j3r"; depends=[BiocGenerics Biostrings ggplot2 hash IRanges plyr RColorBrewer sqldf STRINGdb]; };
 segmentSeq = derive { name="segmentSeq"; version="2.3.1"; sha256="005b9a7rhhhcpkac8xyvl9lbzgwjbfpqr49wyn0i9j99v9zw1lfv"; depends=[baySeq GenomicRanges IRanges S4Vectors ShortRead]; };
 seq2pathway = derive { name="seq2pathway"; version="1.1.2"; sha256="1ghanxmfs99h8w2fxn6im3ml7brhhx131k7djbvsm695lvxgqm7a"; depends=[biomaRt GenomicRanges GSA nnet WGCNA]; };
@@ -997,7 +1008,7 @@ snm = derive { name="snm"; version="1.17.0"; sha256="0ckn29nymlml8ldxqq5la1h3bwm
 snpStats = derive { name="snpStats"; version="1.19.1"; sha256="1i4v737mrjjp8b24mihiv53ifgjcs7gaf9c4h2ling6gpasf39z8"; depends=[BiocGenerics Matrix survival zlibbioc]; };
 soGGi = derive { name="soGGi"; version="1.1.2"; sha256="0vqsdlnbdimz1y2q37ycddc3ifykbr9d0hsg47kqh5wjzgsrl4h7"; depends=[BiocGenerics BiocParallel Biostrings chipseq GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges preprocessCore reshape2 Rsamtools rtracklayer S4Vectors SummarizedExperiment]; };
 spade = derive { name="spade"; version="1.17.0"; sha256="02ba8ybgcldjmfsxywb0q7drm5nyhg6i72brvbrcgsq2ni0b7cpf"; depends=[Biobase flowCore igraph Rclusterpp]; };
-specL = derive { name="specL"; version="1.3.3"; sha256="17067na171pn55w7znyhrn9bcibjpk7spvdw5l6gzrr5slh49qg8"; depends=[DBI protViz Rcpp RSQLite seqinr]; };
+specL = derive { name="specL"; version="1.3.5"; sha256="0afaxclb4h797hm6rdybvp5dp85r1hmwgykj0q5h9ialqbjkmsv7"; depends=[DBI protViz Rcpp RSQLite seqinr]; };
 spikeLI = derive { name="spikeLI"; version="2.29.0"; sha256="1f7in8zcbdz9i1cqdhvdcjl6g71vhz9hgd8whc0x9nf12qa87l7p"; depends=[]; };
 spkTools = derive { name="spkTools"; version="1.25.0"; sha256="1a260c41jxg0yi2li1159pdp8dqbrxgvda88047k5pjrpzwg0738"; depends=[Biobase gtools RColorBrewer]; };
 spliceR = derive { name="spliceR"; version="1.11.0"; sha256="0zfvbnlslpav4kz385sa5h1v73wrzirahxc6fx752zvn4kqbxdkj"; depends=[cummeRbund GenomicRanges IRanges plyr RColorBrewer rtracklayer VennDiagram]; };
@@ -1011,12 +1022,12 @@ ssviz = derive { name="ssviz"; version="1.3.0"; sha256="1sl181mq7qsibn6f51mp8srl
 staRank = derive { name="staRank"; version="1.11.0"; sha256="0hi3nzm0bdqrgjqjfvgz0qwymdrsd2c4csndw85hw9dj5ml1czqd"; depends=[cellHTS2]; };
 stepNorm = derive { name="stepNorm"; version="1.41.0"; sha256="05g9qgxwfahyfq97pz3xmg49y7ml93w8n5hs5fv6f60l1nz59va1"; depends=[marray MASS]; };
 stepwiseCM = derive { name="stepwiseCM"; version="1.15.0"; sha256="0r0ca29xpzki7lpr91rf99a1dvc5lmyls2v22pd1nxq4fb3g265l"; depends=[Biobase e1071 glmpath MAclinical pamr penalized randomForest snowfall tspair]; };
-supraHex = derive { name="supraHex"; version="1.7.1"; sha256="02jv0mb17d79031b6a8sam0710a0njm2akkcj4bji40bx0bkqsna"; depends=[ape hexbin MASS]; };
+supraHex = derive { name="supraHex"; version="1.7.2"; sha256="1ivi3lcck3ygxbask4v3kf8fkjni5ac9qz2pv55lnarws3s0xns7"; depends=[ape hexbin MASS]; };
-survcomp = derive { name="survcomp"; version="1.19.0"; sha256="1czy90l49f0c31kh9p461wkdxb1iih64pvpbz31wv0mhyi2633i5"; depends=[bootstrap ipred KernSmooth prodlim rmeta SuppDists survival survivalROC]; };
+survcomp = derive { name="survcomp"; version="1.19.1"; sha256="0nl3i8pbjyvpbn7d9fck5l1z3ayav2s2d943h6jvqdzc24qhb21w"; depends=[bootstrap ipred KernSmooth prodlim rmeta SuppDists survival survivalROC]; };
 sva = derive { name="sva"; version="3.15.0"; sha256="0bskn3famgz24kjaz4lrrm94vw07g5d2103h9gh5qzhajdsc2d03"; depends=[genefilter mgcv]; };
 switchBox = derive { name="switchBox"; version="1.3.0"; sha256="0bnb1wqxl3rv8w5rm0jw3x22yy8q27j11hpqnd792fvsz8ssr5h1"; depends=[]; };
 synapter = derive { name="synapter"; version="1.11.0"; sha256="05gv788mx1bzizr07cg5cw98i4xm3qdh8hpys4xvr06as7q65h2g"; depends=[Biobase BiocParallel Biostrings cleaver hwriter knitr lattice MSnbase multtest qvalue RColorBrewer]; };
-systemPipeR = derive { name="systemPipeR"; version="1.3.11"; sha256="1ssxavb1dwfma6dvd6jp4vnh4xz1nns0d14ccrrslssnch8knn3g"; depends=[annotate BatchJobs BiocGenerics Biostrings DESeq2 edgeR GenomicRanges ggplot2 GOstats limma pheatmap rjson Rsamtools ShortRead SummarizedExperiment VariantAnnotation]; };
+systemPipeR = derive { name="systemPipeR"; version="1.3.20"; sha256="164xjy8vsjr1ri196xhklisiqjj3frcm3nbpvixc6kd4zjgn0r0q"; depends=[annotate BatchJobs BiocGenerics Biostrings DESeq2 edgeR GenomicRanges ggplot2 GOstats limma pheatmap rjson Rsamtools ShortRead SummarizedExperiment VariantAnnotation]; };
 tRanslatome = derive { name="tRanslatome"; version="1.7.0"; sha256="1pcr1ghwkmkpsbkqh85yninvgb2za2vdsnax5bjkdj60wfj0d5bc"; depends=[anota Biobase DESeq edgeR GOSemSim gplots Heatplus limma plotrix RankProd samr sigPathway topGO]; };
 ternarynet = derive { name="ternarynet"; version="1.13.0"; sha256="13pnzzlfzgkvqn323xhjvbaqzrk2fjq440ff9hjf09a53g14q7li"; depends=[igraph]; };
 tigre = derive { name="tigre"; version="1.23.0"; sha256="177phidn72rcghb4mqfcr2wbfx5pz2vdw6jh7ahnki7s5q6fkldl"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI gplots RSQLite]; };
@@ -1026,6 +1037,7 @@ tkWidgets = derive { name="tkWidgets"; version="1.47.0"; sha256="08vhxl7bdhnx0vk
 topGO = derive { name="topGO"; version="2.21.0"; sha256="0hhglb4zqbjwqywn37h3klz7qgkypl2zmv1afibxjn70xc6wxq46"; depends=[AnnotationDbi Biobase BiocGenerics graph lattice SparseM]; };
 trackViewer = derive { name="trackViewer"; version="1.5.2"; sha256="0kr6mkim32khr5zqm7wzrv03g9fvn4imxr0b7h8jl7sl896hv5ks"; depends=[GenomicAlignments GenomicFeatures GenomicRanges Gviz gWidgetstcltk pbapply Rsamtools rtracklayer scales]; };
 tracktables = derive { name="tracktables"; version="1.3.0"; sha256="125z9b0rjvrrbg91bdzqrf3rrw0aajivpyxd1m9k1gcs6jmsaaj3"; depends=[GenomicRanges IRanges RColorBrewer Rsamtools stringr tractor_base XML XVector]; };
+traseR = derive { name="traseR"; version="0.99.7"; sha256="0rj4jcjgpkqyhclbpmz2ha0afj5jzr9qcc7kl1cw6dbf1syxcj8p"; depends=[GenomicRanges IRanges]; };
 triform = derive { name="triform"; version="1.11.3"; sha256="0j8arzd9zbd37kzz1ndr6ljzz21h7bi33p0iqzy83l5ifidd4kaj"; depends=[BiocGenerics IRanges yaml]; };
 trigger = derive { name="trigger"; version="1.15.0"; sha256="1gsvp2rvry8pg9wfl9rggjfjxd0dcq3lrfkygfsl4jqcwnankpvc"; depends=[corpcor qtl qvalue sva]; };
 trio = derive { name="trio"; version="3.7.1"; sha256="1g3q1pvqq2kp1vck9c7sj000inw5b7q0wvd14yr8096mm6ax8zka"; depends=[]; };
@@ -1034,8 +1046,9 @@ tspair = derive { name="tspair"; version="1.27.0"; sha256="0kx2iw2g0nji25qds5z6q
 tweeDEseq = derive { name="tweeDEseq"; version="1.15.0"; sha256="17mmkz0qpww2qwzk1vd5945wqpr59v091rlvn1s2013h248173vm"; depends=[cqn edgeR limma MASS]; };
 twilight = derive { name="twilight"; version="1.45.0"; sha256="0dzgapk34jzxhdadraq072fcj6rwqhkx2795rbn0dkk4vazqz4sn"; depends=[Biobase]; };
 unifiedWMWqPCR = derive { name="unifiedWMWqPCR"; version="1.5.0"; sha256="055yvgwqjh91cf8d2hsacnbzq2z9c911cy3qd206azqlr6qyjiip"; depends=[BiocGenerics HTqPCR]; };
+variancePartition = derive { name="variancePartition"; version="0.99.4"; sha256="1xy99saci2cihx95dy7yn92b09fan317iiacnyabsrd6z8l7ypp4"; depends=[Biobase dendextend doParallel foreach ggplot2 iterators limma lme4 reshape]; };
 vbmp = derive { name="vbmp"; version="1.37.0"; sha256="1i4akvqrwj1r0ahi4vjxl7q780sa5bryj3rd2c5wg0ifd5l95h6s"; depends=[]; };
-viper = derive { name="viper"; version="1.5.1"; sha256="0494601adg93i5gwam73x4x3m7vfg25xly6v2gj4aclaq9v6fpyf"; depends=[Biobase e1071 KernSmooth mixtools]; };
+viper = derive { name="viper"; version="1.5.2"; sha256="0zcb03c469nz5ka85m54n8if1188hprh4qgdwap5zc7xgyc0lhya"; depends=[Biobase e1071 KernSmooth mixtools]; };
 vsn = derive { name="vsn"; version="3.37.3"; sha256="09mzv7l5j20sx14m63q9ycpacrh2zayywiyckglfgndpc8v9wp08"; depends=[affy Biobase ggplot2 hexbin lattice limma]; };
 vtpnet = derive { name="vtpnet"; version="0.9.0"; sha256="0gbs4pdwy88pjwsn3r2yspnfscz127awhlwym6g1lk8sxkb4mjxc"; depends=[doParallel foreach GenomicRanges graph gwascat]; };
 wateRmelon = derive { name="wateRmelon"; version="1.9.0"; sha256="1lgadzv28j5qqqqsrjzakxmyj1q9j0hps3waa2nn9r7dq4cvallh"; depends=[limma lumi matrixStats methylumi ROC]; };

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

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, jdk, zip, zlib, protobuf, pkgconfig, libarchive, unzip, makeWrapper }:
+{ stdenv, fetchFromGitHub, jdk, zip, zlib, protobuf2_5, pkgconfig, libarchive, unzip, which, makeWrapper }:
 
 stdenv.mkDerivation rec {
   name = "bazel-20150326.981b7bc1";
@@ -10,19 +10,20 @@ stdenv.mkDerivation rec {
     sha256 = "0i9gxgqhfmix7hmkb15s7h9f8ssln08pixqm26pd1d20g0kfyxj7";
   };
 
-  buildInputs = [ pkgconfig protobuf zlib zip jdk libarchive unzip makeWrapper ];
+  buildInputs = [ pkgconfig protobuf2_5 zlib zip jdk libarchive unzip which makeWrapper ];
 
   installPhase = ''
     PROTOC=protoc bash compile.sh
     mkdir -p $out/bin $out/share
     cp -R output $out/share/bazel
     ln -s $out/share/bazel/bazel $out/bin/bazel
-    wrapProgram $out/bin/bazel --set JAVA_HOME "${jdk}"
+    wrapProgram $out/bin/bazel --set JAVA_HOME "${jdk.home}"
   '';
 
   meta = {
     homepage = http://github.com/google/bazel/;
     description = "Build tool that builds code quickly and reliably";
     license = stdenv.lib.licenses.asl20;
+    maintainers = [ stdenv.lib.maintainers.philandstuff ];
   };
 }

pkgs/development/tools/haskell/cabal2nix/default.nix

@@ -1,35 +1,41 @@
-{ mkDerivation, fetchgit, aeson, base, bytestring, Cabal, containers
+{ mkDerivation, fetchgit, aeson, ansi-wl-pprint, base, bytestring, Cabal
-, deepseq, deepseq-generics, directory, doctest, filepath, gitMinimal
+, containers, deepseq, deepseq-generics, directory, doctest, filepath
-, hackage-db, hspec, lens, monad-par, monad-par-extras, mtl, pretty
+, hackage-db, hspec, lens, monad-par, monad-par-extras, mtl
-, process, QuickCheck, regex-posix, SHA, split, stdenv, transformers
+, optparse-applicative, pretty, process, QuickCheck, regex-posix, SHA, split
-, utf8-string, cartel, nix-prefetch-scripts, optparse-applicative
+, stdenv, transformers, utf8-string, makeWrapper, gitMinimal, cartel
-, makeWrapper
+, nix-prefetch-scripts
 }:
 
 mkDerivation rec {
   pname = "cabal2nix";
-  version = "20150531";
+  version = "20150807";
   src = fetchgit {
     url = "http://github.com/NixOS/cabal2nix.git";
-    rev = "513a5fce6cfabe0b062424f6deb191a12f7e2187";
+    rev = "796dabfc3fb0a98174b680c5d722954096465103";
-    sha256 = "1rsnzgfzw6zrjwwr3a4qbhw4l07pqi9ddm2p9l3sw3agzwmc7z49";
+    sha256 = "1blyjq80w9534ap4cg0m6awks0zj2135kxld1i9d2z88x1ijzx9v";
     deepClone = true;
   };
+  isLibrary = true;
   isExecutable = true;
-  enableSharedLibraries = false;
+  libraryHaskellDepends = [
-  enableSharedExecutables = false;
+    aeson ansi-wl-pprint base bytestring Cabal containers
-  buildDepends = [
+    deepseq-generics directory filepath hackage-db lens monad-par
-    aeson base bytestring Cabal containers deepseq-generics directory
+    monad-par-extras mtl optparse-applicative pretty process
-    filepath hackage-db lens monad-par monad-par-extras mtl pretty
+    regex-posix SHA split transformers utf8-string
-    process regex-posix SHA split transformers utf8-string cartel
-    optparse-applicative
   ];
-  testDepends = [
+  executableHaskellDepends = [
-    aeson base bytestring Cabal containers deepseq deepseq-generics
+    aeson ansi-wl-pprint base bytestring Cabal containers
-    directory doctest filepath hackage-db hspec lens monad-par
+    deepseq-generics directory filepath hackage-db lens monad-par
-    monad-par-extras mtl pretty process QuickCheck regex-posix SHA
+    monad-par-extras mtl optparse-applicative pretty process
-    split transformers utf8-string
+    regex-posix SHA split transformers utf8-string
   ];
+  testHaskellDepends = [
+    aeson ansi-wl-pprint base bytestring Cabal containers deepseq
+    deepseq-generics directory doctest filepath hackage-db hspec lens
+    monad-par monad-par-extras mtl optparse-applicative pretty process
+    QuickCheck regex-posix SHA split transformers utf8-string
+  ];
+  buildDepends = [ cartel ];
   buildTools = [ gitMinimal makeWrapper ];
   preConfigure = ''
     git reset --hard # Re-create the index that fetchgit destroyed in the name of predictable hashes.

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

@@ -23,7 +23,7 @@ stdenv.mkDerivation {
   passthru = {
     # A derivation that provides gcc and g++ commands, but that
     # will end up calling ccache for the given cacheDir
-    links = extraConfig : (runCommand "ccache-links" { passthru.gcc = gcc; }
+    links = extraConfig : (runCommand "ccache-links" { passthru.gcc = gcc; passthru.isGNU = true; }
       ''
         mkdir -p $out/bin
         if [ -x "${gcc.cc}/bin/gcc" ]; then

pkgs/development/tools/ocaml/camlp4/default.nix

@@ -1,15 +1,17 @@
-{stdenv, fetchurl, which, ocaml}:
+{stdenv, fetchzip, which, ocaml}:
 let
   ocaml_version = (stdenv.lib.getVersion ocaml);
+  version = "4.02+6";
+
 in
 
 assert stdenv.lib.versionAtLeast ocaml_version "4.02";
 
 stdenv.mkDerivation {
-  name = "camlp4-4.02.0+1";
+  name = "camlp4-${version}";
-  src = fetchurl {
+  src = fetchzip {
-    url = https://github.com/ocaml/camlp4/archive/4.02.0+1.tar.gz;
+    url = "https://github.com/ocaml/camlp4/archive/${version}.tar.gz";
-    sha256 = "0055f4jiz82rgn581xhq3mr4qgq2qgdxqppmp8i2x1xnsim4h9pn";
+    sha256 = "06yl4q0qazl7g25b0axd1gdkfd4qpqzs1gr5fkvmkrcbz113h1hj";
   };
 
   buildInputs = [ which ocaml ];
@@ -27,10 +29,6 @@ stdenv.mkDerivation {
   postConfigure = ''
     substituteInPlace camlp4/META.in \
     --replace +camlp4 $out/lib/ocaml/${ocaml_version}/site-lib/camlp4
-    substituteInPlace camlp4/config/Camlp4_config.ml \
-    --replace \
-      "Filename.concat ocaml_standard_library" \
-      "Filename.concat \"$out/lib/ocaml/${ocaml_version}/site-lib\""
   '';
 
 

pkgs/development/tools/ocaml/utop/default.nix

@@ -1,22 +1,24 @@
 {stdenv, fetchurl, ocaml, findlib, lambdaTerm, ocaml_lwt, makeWrapper,
- ocaml_react, camomile, zed
+ ocaml_react, camomile, zed, cppo, camlp4
 }:
 
 stdenv.mkDerivation rec {
-  version = "1.15";
+  version = "1.17";
   name = "utop-${version}";
 
   src = fetchurl {
-    url = https://github.com/diml/utop/archive/1.15.tar.gz;
+    url = "https://github.com/diml/utop/archive/${version}.tar.gz";
-    sha256 = "106v0x6sa2x10zgmjf73mpzws7xiqanxswivd00iqnpc0bcpkmrr";
+    sha256 = "0l9lz2nypl2ls3kqzmp738m02yvscabhsfpj70ckp0p98pimnnfd";
   };
 
-  buildInputs = [ ocaml findlib makeWrapper];
+  buildInputs = [ ocaml findlib makeWrapper cppo camlp4 ];
 
   propagatedBuildInputs = [ lambdaTerm ocaml_lwt ];
 
   createFindlibDestdir = true;
 
+  configureFlags = "--enable-camlp4";
+
   buildPhase = ''
     make
     make doc

pkgs/games/freecell-solver/default.nix

@@ -0,0 +1,30 @@
+{ stdenv, fetchurl, pkgconfig, cmake, perl, gmp, libtap, perlPackages }:
+
+with stdenv.lib;
+stdenv.mkDerivation rec{
+
+  name = "freecell-solver-${version}";
+  version = "3.26.0";
+
+  src = fetchurl {
+    url = "http://fc-solve.shlomifish.org/downloads/fc-solve/${name}.tar.bz2";
+    sha256 = "0pm6xk4fmwgzva70qxb0pqymdfvpasnvqiwwmm8hpx7g37y11wqk";
+  };
+
+  buildInputs = [ pkgconfig cmake perl gmp libtap
+    perlPackages.TemplateToolkit perlPackages.StringShellQuote
+    perlPackages.GamesSolitaireVerify ];
+
+  meta = {
+    description = "A FreeCell automatic solver";
+    longDescription = ''
+      FreeCell Solver is a program that automatically solves layouts
+      of Freecell and similar variants of Card Solitaire such as Eight
+      Off, Forecell, and Seahaven Towers, as well as Simple Simon
+      boards.
+    '';
+    homepage = http://fc-solve.shlomifish.org/;
+    license = licenses.mit;
+    maintainers = [ maintainers.AndersonTorres ];
+  };
+}

pkgs/misc/emulators/wine/builder-wow.sh

@@ -1,5 +1,7 @@
 #!/bin/sh
 
+## build described at http://wiki.winehq.org/Wine64
+
 source $stdenv/setup
 
 unpackPhase

pkgs/misc/emulators/wine/versions.nix

@@ -1,7 +1,7 @@
 {
   unstable = {
-    wineVersion = "1.7.47";
+    wineVersion = "1.7.48";
-    wineSha256  = "0bmvgcag0kv0671dj6fbfdz86ij91rb2kp2dssqw83a0xidgfx5s";
+    wineSha256  = "13kcjirif57p8mg4yhzxf0hjpghlwc18iskz66dx94i0dvjmrxg3";
     geckoVersion = "2.36";
     geckoSha256 = "12hjks32yz9jq4w3xhk3y1dy2g3iakqxd7aldrdj51cqiz75g95g";
     gecko64Version = "2.36";
@@ -18,13 +18,10 @@
     gecko64Sha256 = "0grc86dkq90i59zw43hakh62ra1ajnk11m64667xjrlzi7f0ndxw";
     monoVersion = "4.5.6";
     monoSha256 = "09dwfccvfdp3walxzp6qvnyxdj2bbyw9wlh6cxw2sx43gxriys5c";
-    ## TESTME wine stable should work with most recent mono
-    #monoVersion = "0.0.8";
-    #monoSha256 = "00jl24qp7vh3hlqv7wsw1s529lr5p0ybif6s73jy85chqaxj7z1x";
   };
   staging = {
-    version = "1.7.47";
+    version = "1.7.48";
-    sha256 = "0m47v4jbc70b7qxj0lqnc7an1xlcb81b6k7dwzjyk3pv3ixp2snp";
+    sha256 = "06p1h92vaqlzk09aj4na6z7k3a81y9nw19rfg9q2szpcqjdd437w";
   };
   winetricks = {
     version = "20150706";

pkgs/misc/vim-plugins/default.nix

@@ -85,6 +85,17 @@ rec {
   yankring            = YankRing;
 
 
+  CheckAttach = buildVimPluginFrom2Nix { # created by nix#NixDerivation
+    name = "CheckAttach-2015-06-22";
+    src = fetchgit {
+      url = "git://github.com/chrisbra/CheckAttach";
+      rev = "a1d86be7e69b25b41ce1a7fe2d2844330f783b68";
+      sha256 = "b8921c826f5a122e9b128301c620b8b3d3fd88a15a2b0634fdea01062fba2c1f";
+    };
+    dependencies = [];
+
+  };
+
   CSApprox = buildVimPluginFrom2Nix { # created by nix#NixDerivation
     name = "CSApprox-2013-07-26";
     src = fetchgit {
@@ -1351,6 +1362,17 @@ rec {
 
   };
 
+  vimwiki = buildVimPluginFrom2Nix { # created by nix#NixDerivation
+    name = "vimwiki-2014-02-21";
+    src = fetchgit {
+      url = "git://github.com/vimwiki/vimwiki";
+      rev = "2c03d82a0e4662adf1e347487d73a9bf4bf6fdac";
+      sha256 = "8f94fe1204ae3770b114370382f9c616f971eb9b940d8d08ca96ac83405a0cdf";
+    };
+    dependencies = [];
+
+  };
+
   vundle = buildVimPluginFrom2Nix { # created by nix#NixDerivation
     name = "vundle-2015-03-21";
     src = fetchgit {

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

@@ -1,3 +1,4 @@
+"CheckAttach"
 "CSApprox"
 "Gist"
 "Gundo"
@@ -100,4 +101,5 @@
 "vim-signature"
 "vim-snippets"
 "vim2hs"
+"vimwiki"
 "vundle"

pkgs/os-specific/linux/kernel/common-config.nix

@@ -141,6 +141,8 @@ with stdenv.lib;
   # Video configuration.
   # Enable KMS for devices whose X.org driver supports it.
   DRM_I915_KMS y
+  # Allow specifying custom EDID on the kernel command line
+  DRM_LOAD_EDID_FIRMWARE y
   ${optionalString (versionOlder version "3.9") ''
     DRM_RADEON_KMS? y
   ''}

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

@@ -1,12 +1,12 @@
 { stdenv, fetchFromGitHub, pkgconfig, gettext, ncurses, libdrm, libpciaccess }:
 
-let version = "2015-06-24"; in
+let version = "2015-08-06"; in
 stdenv.mkDerivation {
   name = "radeontop-${version}";
 
   src = fetchFromGitHub {
-    sha256 = "06cn7lixxx94c1fki0plg9f4rdy459mgi9yl80m0k1a20jqykz2a";
+    sha256 = "01s0j28lk66wb46qymkk1nyk91iv22y3m56z4lqd16yaxmhl0v2f";
-    rev = "976cae0be0ffb9142d5e63e435960c6b2bb0eb34";
+    rev = "93c8ff2f07da8d4c204ee4872aed7eec834ff57d";
     repo = "radeontop";
     owner = "clbr";
   };

pkgs/servers/nosql/rethinkdb/default.nix

@@ -11,21 +11,12 @@ stdenv.mkDerivation rec {
     sha256 = "19qhia4lfa8a0rzp2v6lnlxp2lf4z4vqhgfxnicfdnx07q4r847i";
   };
 
-  postPatch = ''
-    # Remove the dependence on bundled libraries
-    sed -i '/must_fetch_list/ s/ v8//' configure
-
-    # Don't use the default command line args
-    rm configure.default
-  '';
-
   preConfigure = ''
     export ALLOW_WARNINGS=1
     patchShebangs .
   '';
 
   configureFlags = [
-    "--dynamic=all"
     "--with-jemalloc"
     "--lib-path=${jemalloc}/lib"
   ];

pkgs/servers/pulseaudio/default.nix

@@ -1,5 +1,5 @@
 { lib, stdenv, fetchurl, pkgconfig, intltool, autoreconfHook
-, json_c, libsndfile
+, json_c, libsndfile, libtool
 , xlibs, libcap, alsaLib, glib
 , avahi, libjack2, libasyncns, lirc, dbus
 , sbc, bluez5, udev, openssl, fftwFloat
@@ -109,6 +109,7 @@ stdenv.mkDerivation rec {
 
   postInstall = lib.optionalString libOnly ''
     rm -rf $out/{bin,share,etc,lib/{pulse-*,systemd}}
+    sed 's|-lltdl|-L${libtool}/lib -lltdl|' -i $out/lib/libpulsecore-6.0.la
   '';
 
   meta = {

pkgs/servers/serfdom/default.nix

@@ -3,7 +3,7 @@
 with goPackages;
 
 buildGoPackage rec {
-  version = "0.6.3";
+  version = "0.6.4";
   name = "serfdom-${version}";
   goPackagePath = "github.com/hashicorp/serf";
 
@@ -11,10 +11,10 @@ buildGoPackage rec {
     owner = "hashicorp";
     repo = "serf";
     rev = "v${version}";
-    sha256 = "0ck77ji28bvm4ahzxyyi4sm17c3fxc16k0k5mihl1nlkgdd73m8y";
+    sha256 = "1fhz8wrvsmgaky22n255w9hkyfph2n45c47ivdyzrrxisg5j2438";
   };
 
-  buildInputs = [ cli mapstructure memberlist logutils go-syslog mdns columnize circbuf ];
+  buildInputs = [ cli mapstructure memberlist_v2 logutils go-syslog mdns columnize circbuf ugorji.go ];
 
   dontInstallSrc = true;
 

pkgs/tools/X11/ckbcomp/default.nix

@@ -2,12 +2,12 @@
 
 stdenv.mkDerivation rec {
   name = "ckbcomp-${version}";
-  version = "1.129";
+  version = "1.131";
 
   src = fetchgit {
     url = "git://anonscm.debian.org/d-i/console-setup.git";
     rev = "refs/tags/${version}";
-    sha256 = "1shbqnjhdmy7qwz2kwfhrdxbjw1vv98rpz1x7wlgqxr812aqcfdd";
+    sha256 = "0xmdnzhm1wsdpjb0wsi24xzk1xpv5h2bxgwm9f4awb7aj7wv59ma";
   };
 
   buildInputs = [ perl ];

pkgs/tools/backup/obnam/default.nix

@@ -2,13 +2,13 @@
 
 pythonPackages.buildPythonPackage rec {
   name = "obnam-${version}";
-  version = "1.12";
+  version = "1.13";
 
   namePrefix = "";
 
   src = fetchurl rec {
     url = "http://code.liw.fi/debian/pool/main/o/obnam/obnam_${version}.orig.tar.xz";
-    sha256 = "09b9j2mygv1dsrq424j535c92wvlbzpwgzcgg7x922dxrnsdsxpr";
+    sha256 = "13a9icgp7kvxaw700sdhxll0in00ghk0aacg26s4kxmxc85w92i4";
   };
 
   buildInputs = [ pythonPackages.sphinx attr ];

pkgs/tools/filesystems/ceph/0.94-pre.nix

@@ -4,9 +4,9 @@ callPackage ./generic.nix (args // rec {
   version = "0.94.3";
 
   src = fetchgit {
-    url = "https://github.com/ceph/ceph.git";
+    url = "https://github.com/wkennington/ceph.git";
-    rev = "c19b0fc1aa2834ae3027b07a02aebe9639fc2ca7";
+    rev = "6218aa41e04533f0d6e62b5c7be591c2e99716ec";
-    sha256 = "1h1y5jh2bszia622rmwdblb3cpkpd0mijahkaiasr30jwpkmzh0i";
+    sha256 = "0cyl5i1q6lap5a6vk8fjxfpikhxzwm9zkybg37nibahi2bwjr7rr";
   };
 
   patches = [ ./fix-pgrefdebugging.patch ];

pkgs/tools/filesystems/ceph/generic.nix

@@ -164,50 +164,55 @@ stdenv.mkDerivation {
   '';
 
   configureFlags = [
-    (mkOther                               "exec_prefix"        "\${out}")
+    (mkOther                               "exec_prefix"         "\${out}")
-    (mkOther                               "sysconfdir"         "/etc")
+    (mkOther                               "sysconfdir"          "/etc")
-    (mkOther                               "localstatedir"      "/var")
+    (mkOther                               "localstatedir"       "/var")
-    (mkOther                               "libdir"             "\${lib}/lib")
+    (mkOther                               "libdir"              "\${lib}/lib")
-    (mkOther                               "includedir"         "\${lib}/include")
+    (mkOther                               "includedir"          "\${lib}/include")
-    (mkWith   true                         "rbd"                 null)
+    (mkWith   true                         "rbd"                  null)
-    (mkWith   true                         "cephfs"              null)
+    (mkWith   true                         "cephfs"               null)
-    (mkWith   hasRadosgw                   "radosgw"             null)
+    (mkWith   hasRadosgw                   "radosgw"              null)
-    (mkWith   true                         "radosstriper"        null)
+    (mkWith   true                         "radosstriper"         null)
-    (mkWith   hasServer                    "mon"                 null)
+    (mkWith   hasServer                    "mon"                  null)
-    (mkWith   hasServer                    "osd"                 null)
+    (mkWith   hasServer                    "osd"                  null)
-    (mkWith   hasServer                    "mds"                 null)
+    (mkWith   hasServer                    "mds"                  null)
-    (mkEnable true                         "client"              null)
+    (mkEnable true                         "client"               null)
-    (mkEnable hasServer                    "server"              null)
+    (mkEnable hasServer                    "server"               null)
-    (mkWith   (cryptoStr == "cryptopp")    "cryptopp"            null)
+    (mkWith   (cryptoStr == "cryptopp")    "cryptopp"             null)
-    (mkWith   (cryptoStr == "nss")         "nss"                 null)
+    (mkWith   (cryptoStr == "nss")         "nss"                  null)
-    (mkEnable false                        "root-make-check"     null)
+    (mkEnable false                        "root-make-check"      null)
-    (mkWith   false                        "profiler"            null)
+    (mkWith   false                        "profiler"             null)
-    (mkWith   false                        "debug"               null)
+    (mkWith   false                        "debug"                null)
-    (mkEnable false                        "coverage"            null)
+    (mkEnable false                        "coverage"             null)
-    (mkWith   (optFuse != null)            "fuse"                null)
+    (mkWith   (optFuse != null)            "fuse"                 null)
-    (mkWith   (malloc == optJemalloc)      "jemalloc"            null)
+    (mkWith   (malloc == optJemalloc)      "jemalloc"             null)
-    (mkWith   (malloc == optGperftools)    "tcmalloc"            null)
+    (mkWith   (malloc == optGperftools)    "tcmalloc"             null)
-    (mkEnable false                        "pgrefdebugging"      null)
+    (mkEnable false                        "pgrefdebugging"       null)
-    (mkEnable false                        "cephfs-java"         null)
+    (mkEnable false                        "cephfs-java"          null)
-    (mkEnable hasXio                       "xio"                 null)
+    (mkEnable hasXio                       "xio"                  null)
-    (mkWith   (optLibatomic_ops != null)   "libatomic-ops"       null)
+    (mkWith   (optLibatomic_ops != null)   "libatomic-ops"        null)
-    (mkWith   true                         "ocf"                 null)
+    (mkWith   true                         "ocf"                  null)
-    (mkWith   hasKinetic                   "kinetic"             null)
+    (mkWith   hasKinetic                   "kinetic"              null)
-    (mkWith   hasRocksdb                   "librocksdb"          null)
+    (mkWith   hasRocksdb                   "librocksdb"           null)
-    (mkWith   false                        "librocksdb-static"   null)
+    (mkWith   false                        "librocksdb-static"    null)
   ] ++ optional stdenv.isLinux [
-    (mkWith   (optLibaio != null)          "libaio"              null)
+    (mkWith   (optLibaio != null)          "libaio"               null)
-    (mkWith   (optLibxfs != null)          "libxfs"              null)
+    (mkWith   (optLibxfs != null)          "libxfs"               null)
-    (mkWith   (optZfs != null)             "libzfs"              null)
+    (mkWith   (optZfs != null)             "libzfs"               null)
+  ] ++ optional (versionAtLeast version "0.94.3") [
+    (mkWith   false                        "tcmalloc-minimal"     null)
   ] ++ optional (versionAtLeast version "9.0.1") [
-    (mkWith   false                        "tcmalloc-minimal"    null)
+    (mkWith   false                        "valgrind"             null)
-    (mkWith   false                        "valgrind"            null)
   ] ++ optional (versionAtLeast version "9.0.2") [
-    (mkWith   true                         "man-pages"           null)
+    (mkWith   true                         "man-pages"            null)
-    (mkWith   true                         "systemd-libexec-dir" "\${TMPDIR}")
+    (mkWith   true                         "systemd-libexec-dir"  "\${out}/libexec")
   ] ++ optional (versionOlder version "10.0.0") [
-    (mkWith   (optLibs3 != null)           "system-libs3"        null)
+    (mkWith   (optLibs3 != null)           "system-libs3"         null)
-    (mkWith   true                         "rest-bench"          null)
+    (mkWith   true                         "rest-bench"           null)
+  ] ++ optional (versionAtLeast version "10.0.0") [
+    (mkWith   true                         "rgw-user"             "rgw")
+    (mkWith   true                         "rgw-group"            "rgw")
+    (mkWith   true                         "systemd-unit-dir"     "\${out}/etc/systemd/system")
   ];
 
   preBuild = optionalString (versionAtLeast version "9.0.0") ''

pkgs/tools/filesystems/ceph/git.nix

@@ -1,12 +1,12 @@
 { callPackage, fetchgit, ... } @ args:
 
 callPackage ./generic.nix (args // rec {
-  version = "2015-07-31";
+  version = "2015-08-05";
 
   src = fetchgit {
-    url = "git://github.com/ceph/ceph.git";
+    url = "git://github.com/wkennington/ceph.git";
-    rev = "ef86e29259d0e863e62115926bf67287dc9a7e41";
+    rev = "043a780feb973b7ad571bb696437476da3260133";
-    sha256 = "14h387ngx3fmdm0b0sgl0l743j3d22gnp3lv68ah59yc4crfgdcx";
+    sha256 = "02kk24wm6mxsclklsz5zzpj3wm6f341blj2anx3v5x20cixzdnhp";
   };
 
   patches = [ ./fix-pythonpath.patch ];

pkgs/tools/filesystems/hubicfuse/default.nix

@@ -0,0 +1,25 @@
+{ stdenv, fetchurl, pkgconfig, curl, openssl, fuse, libxml2, json_c, file }:
+
+stdenv.mkDerivation rec {
+  name = "hubicfuse-${version}";
+  version = "2.1.0";
+
+  src = fetchurl {
+    url = https://github.com/TurboGit/hubicfuse/archive/v2.1.0.tar.gz;
+    sha256 = "1mnijcwac6k3f6xknvdrsbmkkizpwbayqkb5l6jic15ymxv1fs7d";
+  };
+
+  buildInputs = [ pkgconfig curl openssl fuse libxml2 json_c file ];
+  postInstall = ''
+    install hubic_token $out/bin
+    mkdir -p $out/sbin
+    ln -sf $out/bin/hubicfuse $out/sbin/mount.hubicfuse
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/TurboGit/hubicfuse;
+    description = "FUSE-based filesystem to access hubic cloud storage";
+    platforms = platforms.linux;
+    license = licenses.mit;
+  };
+}

pkgs/tools/misc/debbindiff/default.nix

@@ -1,46 +0,0 @@
-{ stdenv, fetchgit, pythonPackages, docutils
-, acl, binutils, bzip2, cdrkit, cpio, diffutils, e2fsprogs, file, gettext
-, gnupg, gzip, pdftk, poppler_utils, rpm, squashfsTools, unzip, vim, xz
-}:
-
-pythonPackages.buildPythonPackage rec {
-  name = "debbindiff-${version}";
-  version = "26";
-
-  namePrefix = "";
-
-  src = fetchgit {
-    url = "git://anonscm.debian.org/reproducible/debbindiff.git";
-    rev = "refs/tags/${version}";
-    sha256 = "18637gc7c92mwcpx3dvh6xild0sb9bwsgfcrjplmh7s8frvlvkv6";
-  };
-
-  postPatch = ''
-    # Different pkg name in debian
-    sed -i setup.py -e "s@'magic'@'Magic-file-extensions'@"
-
-    # Upstream doesn't provide a PKG-INFO file
-    sed -i setup.py -e "/'rpm',/d"
-  '';
-
-  # Still missing these tools: ghc javap showttf sng
-  propagatedBuildInputs = (with pythonPackages; [ debian magic ]) ++
-    [ acl binutils bzip2 cdrkit cpio diffutils e2fsprogs file gettext gnupg
-      gzip pdftk poppler_utils rpm squashfsTools unzip vim xz ];
-
-  doCheck = false; # Calls 'mknod' in squashfs tests, which needs root
-
-  postInstall = ''
-    mv $out/bin/debbindiff.py $out/bin/debbindiff
-    mkdir -p $out/share/man/man1
-    ${docutils}/bin/rst2man.py debian/debbindiff.1.rst $out/share/man/man1/debbindiff.1
-  '';
-
-  meta = with stdenv.lib; {
-    description = "Highlight differences between two builds of Debian packages, and even other kind of files";
-    homepage = https://wiki.debian.org/ReproducibleBuilds;
-    license = licenses.gpl3Plus;
-    maintainers = [ maintainers.dezgeg ];
-    platforms = platforms.linux;
-  };
-}

pkgs/tools/misc/diffoscope/default.nix

@@ -0,0 +1,56 @@
+{ stdenv, fetchgit, pythonPackages, docutils
+, acl, binutils, bzip2, cdrkit, cpio, diffutils, e2fsprogs, file, gettext
+, gnupg, gzip, pdftk, poppler_utils, rpm, sqlite, squashfsTools, unzip, vim, xz
+}:
+
+pythonPackages.buildPythonPackage rec {
+  name = "diffoscope-${version}";
+  version = "29";
+
+  namePrefix = "";
+
+  src = fetchgit {
+    url = "git://anonscm.debian.org/reproducible/diffoscope.git";
+    rev = "refs/tags/${version}";
+    sha256 = "0q7hx2wm9gvzl1f7iilr9pjwpv8i2anscqan7cgk80v90s2pakrf";
+  };
+
+  postPatch = ''
+    # Different pkg name in debian
+    sed -i setup.py -e "s@'magic'@'Magic-file-extensions'@"
+
+    # Upstream doesn't provide a PKG-INFO file
+    sed -i setup.py -e "/'rpm',/d"
+  '';
+
+  # Still missing these tools: ghc javap showttf sng
+  propagatedBuildInputs = (with pythonPackages; [ debian libarchive-c magic ssdeep ]) ++
+    [ acl binutils bzip2 cdrkit cpio diffutils e2fsprogs file gettext gnupg
+      gzip pdftk poppler_utils rpm sqlite squashfsTools unzip vim xz ];
+
+  doCheck = false; # Calls 'mknod' in squashfs tests, which needs root
+
+  postInstall = ''
+    mv $out/bin/diffoscope.py $out/bin/diffoscope
+    mkdir -p $out/share/man/man1
+    ${docutils}/bin/rst2man.py debian/diffoscope.1.rst $out/share/man/man1/diffoscope.1
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Perform in-depth comparison of files, archives, and directories";
+    longDescription = ''
+      diffoscope will try to get to the bottom of what makes files or directories
+      different. It will recursively unpack archives of many kinds and transform
+      various binary formats into more human readable form to compare them. It can
+      compare two tarballs, ISO images, or PDF just as easily. The differences can
+      be shown in a text or HTML report.
+
+      diffoscope is developed as part of the "reproducible builds" Debian
+      project and was formerly known as "debbindiff".
+    '';
+    homepage = https://wiki.debian.org/ReproducibleBuilds;
+    license = licenses.gpl3Plus;
+    maintainers = [ maintainers.dezgeg ];
+    platforms = platforms.linux;
+  };
+}

pkgs/tools/misc/vdirsyncer/default.nix

@@ -1,13 +1,13 @@
 { stdenv, fetchurl, pythonPackages }:
 
 pythonPackages.buildPythonPackage rec {
-  version = "0.5.2";
+  version = "0.6.0";
   name = "vdirsyncer-${version}";
   namePrefix = "";
 
   src = fetchurl {
-    url = "https://github.com/untitaker/vdirsyncer/archive/${version}.tar.gz";
+    url = "https://pypi.python.org/packages/source/v/vdirsyncer/${name}.tar.gz";
-    sha256 = "02k6ijj0z0r08l50ignm2ngd4ax84l0r1wshh1is0wcfr70d94h9";
+    sha256 = "1mb0pws5vsgnmyp5dp5m5jvgl6jcvdamxjz7wmgvxkw6n1vrcahd";
   };
 
   propagatedBuildInputs = with pythonPackages; [