Merge remote-tracking branch 'upstream/master' into staging

2018-03-17 09:58:02 +02:00 · 2018-03-17 09:58:02 +02:00 · 07e2f29772
commit 07e2f29772
parent 017d678a00 548607d830
69 changed files with 3234 additions and 2303 deletions
--- a/nixos/doc/manual/release-notes/rl-1809.xml
+++ b/nixos/doc/manual/release-notes/rl-1809.xml
@ -4,7 +4,7 @@
         version="5.0"
         xml:id="sec-release-18.09">

-<title>Release 18.09 (“Jackrabbit”, 2018/09/??)</title>
+<title>Release 18.09 (“Jellyfish”, 2018/09/??)</title>

 <section xmlns="http://docbook.org/ns/docbook"
         xmlns:xlink="http://www.w3.org/1999/xlink"
--- a/nixos/modules/misc/version.nix
+++ b/nixos/modules/misc/version.nix
@ -85,8 +85,8 @@ in
      revision      = mkIf (pathIsDirectory gitRepo) (mkDefault            gitCommitId);
      versionSuffix = mkIf (pathIsDirectory gitRepo) (mkDefault (".git." + gitCommitId));

-      # Note: code names must only increase in alphabetical order.
-      codeName = "Jackrabbit";
+      # Note: the first letter is bumped on every release.  It's an animal.
+      codeName = "Jellyfish";
    };

    # Generate /etc/os-release.  See
--- a/pkgs/applications/audio/drumkv1/default.nix
+++ b/pkgs/applications/audio/drumkv1/default.nix
@ -2,11 +2,11 @@

 stdenv.mkDerivation rec {
  name = "drumkv1-${version}";
-  version = "0.8.6";
+  version = "0.9.0";

  src = fetchurl {
    url = "mirror://sourceforge/drumkv1/${name}.tar.gz";
-    sha256 = "0fwxrfyp15a4m77mzz4mwj36mhdrj646whlrkvcys33p2w75f8cq";
+    sha256 = "1vm8lrk3lykdic6fyfpl12jx1xg6rcaid242s8sij30p1ix4zdab";
  };

  buildInputs = [ libjack2 alsaLib libsndfile liblo lv2 qt5.qtbase qt5.qttools ];
--- a/pkgs/applications/audio/synthv1/default.nix
+++ b/pkgs/applications/audio/synthv1/default.nix
@ -2,11 +2,11 @@

 stdenv.mkDerivation rec {
  name = "synthv1-${version}";
-  version = "0.8.6";
+  version = "0.9.0";

  src = fetchurl {
    url = "mirror://sourceforge/synthv1/${name}.tar.gz";
-    sha256 = "141ah1gnv5r2k846v5ay15q9q90h01p74240a56vlxqh20z43g92";
+    sha256 = "1skynjg6ip0qfbqqkybfjh6xcwxagq89ghl08f7sp7j0sz5qdcwp";
  };

  buildInputs = [ qt5.qtbase qt5.qttools libjack2 alsaLib liblo lv2 ];
--- a/pkgs/applications/editors/eclipse/plugins.nix
+++ b/pkgs/applications/editors/eclipse/plugins.nix
@ -160,6 +160,29 @@ rec {
    };
  };

+  antlr-runtime_4_7 = buildEclipsePluginBase rec {
+    name = "antlr-runtime-4.7.1";
+
+    src = fetchurl {
+      url = "http://www.antlr.org/download/${name}.jar";
+      sha256 = "07f91mjclacrvkl8a307w2abq5wcqp0gcsnh0jg90ddfpqcnsla3";
+    };
+
+    buildCommand = ''
+      dropinDir="$out/eclipse/dropins/"
+      mkdir -p $dropinDir
+      cp -v $src $dropinDir/${name}.jar
+    '';
+
+    meta = with stdenv.lib; {
+      description = "A powerful parser generator for processing structured text or binary files";
+      homepage = http://www.antlr.org/;
+      license = licenses.bsd3;
+      platforms = platforms.all;
+      maintainers = [ maintainers.rycee ];
+    };
+  };
+
  anyedittools = buildEclipsePlugin rec {
    name = "anyedit-${version}";
    version = "2.7.1.201709201439";
@ -409,11 +432,11 @@ rec {

  jsonedit = buildEclipsePlugin rec {
    name = "jsonedit-${version}";
-    version = "1.0.2";
+    version = "1.1.0";

    srcFeature = fetchurl {
      url = "https://boothen.github.io/Json-Eclipse-Plugin/features/jsonedit-feature_${version}.jar";
-      sha256 = "0zh9ihvaji2v4d4980va8p1c38x5dn2mcw74qmqkwxlz4nglpsr0";
+      sha256 = "1qqbzh9sv0s9p0irim7kimvzdkw0hg6yv090bz5ifpzqdxc4v9r5";
    };

    srcPlugins =
@ -425,16 +448,16 @@ rec {
          };
      in
        map fetch [
-          { n = "core"; h = "0zc1jpda6sviazsgvvig8zk2zmz0ac1mch5qs8lbcbdmrpq732ni"; }
-          { n = "editor"; h = "06k2mx7ka0bn0i8dfbv89jna9kmy8wnlwkg9yp1n1pgqmr01944s"; }
-          { n = "folding"; h = "1525blyhrl495vz5r98dyfws6kcgnhmyf9qgm5vkplhb27474yca"; }
-          { n = "model"; h = "0rnnkdl3hrp0sxchfzfad97ya5swsw56wfb5zvjwffbby4vln8fd"; }
-          { n = "outline"; h = "06bday90a7sdpv4idp69m2831z3r99q248n2avw2npc3gzkfy3kl"; }
-          { n = "preferences"; h = "1d9pcnq6j5p2smkfldb9dw8gdw5nqlmpcy9kh5n34jcyzf37cdac"; }
-          { n = "text"; h = "0r3g2qhnhl6misi0rrmw152gw0nb7zlcjy7019qvprn9mhwn1n84"; }
+          { n = "core"; h = "1fl4api6j0wp4vfbyabxqsrjvvpclp8p3b4xnxxpn4v8g12q526m"; }
+          { n = "editor"; h = "1kn15qampdlpxblj2bv94b3bb15qfwng27lk0n578585yqmb3p66"; }
+          { n = "folding"; h = "1qnzdx4xx9ma3p6lg1ab8xf3nik1yrww33nksi0j3vnvh8i9ihdm"; }
+          { n = "model"; h = "0n8855ma1h2as0skrrp2qy3sdkmnhl5vlqxcjv8xlc3faa72174a"; }
+          { n = "outline"; h = "07i2spmzghs49pkxl8z9c29n6l38x26v20prkh4a7i1rf9whg1q8"; }
+          { n = "preferences"; h = "0d1m8pb903wpc4vvhsp0gx0h65r432ax898wif3a23c5wxj4nh9i"; }
+          { n = "text"; h = "0z80d9qgpbx88jrq8b4r478lrcrf52gxqkl94l13wrk7rszjpldh"; }
        ];

-    propagatedBuildInputs = [ antlr-runtime_4_5 ];
+    propagatedBuildInputs = [ antlr-runtime_4_7 ];

    meta = with stdenv.lib; {
      description = "Adds support for JSON files to Eclipse";
--- a/pkgs/applications/graphics/feh/default.nix
+++ b/pkgs/applications/graphics/feh/default.nix
@ -6,11 +6,11 @@ with stdenv.lib;

 stdenv.mkDerivation rec {
  name = "feh-${version}";
-  version = "2.25";
+  version = "2.25.1";

  src = fetchurl {
    url = "https://feh.finalrewind.org/${name}.tar.bz2";
-    sha256 = "102rwi30n09l8rih6kv6bb7lhv3djklgzill4p2zag0h700yqfq6";
+    sha256 = "197sm78bm33dvahr5nxqkbmpmdn4b13ahc9mrgn1l7n104bg4phc";
  };

  outputs = [ "out" "man" "doc" ];
--- a/pkgs/applications/graphics/inkscape/default.nix
+++ b/pkgs/applications/graphics/inkscape/default.nix
@ -10,11 +10,11 @@ let
 in

 stdenv.mkDerivation rec {
-  name = "inkscape-0.92.2";
+  name = "inkscape-0.92.3";

  src = fetchurl {
    url = "https://media.inkscape.org/dl/resources/file/${name}.tar.bz2";
-    sha256 = "1lyghk6yarcv9nwkh6k366p6hb7rfilqcvbyji09hki59khd0a56";
+    sha256 = "1chng2yw8dsjxc9gf92aqv7plj11cav8ax321wmakmv5bb09cch6";
  };

  unpackPhase = ''
--- a/pkgs/applications/misc/xca/default.nix
+++ b/pkgs/applications/misc/xca/default.nix
@ -3,11 +3,11 @@

 mkDerivation rec {
  name = "xca-${version}";
-  version = "1.4.0";
+  version = "1.4.1";

  src = fetchurl {
    url = "mirror://sourceforge/xca/${name}.tar.gz";
-    sha256 = "1gygj6kljj3r1y0pg67mks36vfcz4vizjsqnqdvrk6zlgqjbzm7z";
+    sha256 = "11niik2m4yswkp71hrdh54z5kgkvdg8y0b6wdqbrn6vy1n8gz63q";
  };

  enableParallelBuilding = true;
--- a/pkgs/applications/misc/xfontsel/default.nix
+++ b/pkgs/applications/misc/xfontsel/default.nix
@ -4,11 +4,11 @@

 {stdenv, fetchurl, makeWrapper, libX11, pkgconfig, libXaw}:
 stdenv.mkDerivation rec {
-  name = "xfontsel-1.0.5";
+  name = "xfontsel-1.0.6";

  src = fetchurl {
    url = "mirror://xorg/individual/app/${name}.tar.bz2";
-    sha256 = "1grir464hy52a71r3mpm9mzvkf7nwr3vk0b1vc27pd3gp588a38p";
+    sha256 = "0700lf6hx7dg88wq1yll7zjvf9gbwh06xff20yffkxb289y0pai5";
  };

  nativeBuildInputs = [ pkgconfig ];
--- a/pkgs/applications/networking/browsers/firefox-bin/release_sources.nix
+++ b/pkgs/applications/networking/browsers/firefox-bin/release_sources.nix
--- a/pkgs/applications/networking/browsers/firefox/common.nix
+++ b/pkgs/applications/networking/browsers/firefox/common.nix
@ -221,7 +221,7 @@ stdenv.mkDerivation (rec {

  postInstall = ''
    # For grsecurity kernels
-    paxmark m $out/lib/firefox-[0-9]*/{firefox,firefox-bin,plugin-container}
+    paxmark m $out/lib/firefox*/{firefox,firefox-bin,plugin-container}

    # Remove SDK cruft. FIXME: move to a separate output?
    rm -rf $out/share/idl $out/include $out/lib/firefox-devel-*
@ -233,8 +233,8 @@ stdenv.mkDerivation (rec {
  postFixup = ''
    # Fix notifications. LibXUL uses dlopen for this, unfortunately; see #18712.
    patchelf --set-rpath "${lib.getLib libnotify
-      }/lib:$(patchelf --print-rpath "$out"/lib/firefox-*/libxul.so)" \
-        "$out"/lib/firefox-*/libxul.so
+      }/lib:$(patchelf --print-rpath "$out"/lib/firefox*/libxul.so)" \
+        "$out"/lib/firefox*/libxul.so
  '';

  doInstallCheck = true;
--- a/pkgs/applications/networking/browsers/firefox/packages.nix
+++ b/pkgs/applications/networking/browsers/firefox/packages.nix
@ -18,28 +18,15 @@ rec {

  firefox = common rec {
    pname = "firefox";
-    version = "58.0.2";
+    version = "59.0";
    src = fetchurl {
-      url = "mirror://mozilla/firefox/releases/${version}/source/firefox-${version}.source.tar.xz";
-      sha512 = "ff748780492fc66b3e44c7e7641f16206e4c09514224c62d37efac2c59877bdf428a3670bfb50407166d7b505d4e2ea020626fd776b87f6abb6bc5d2e54c773f";
+      url = "https://hg.mozilla.org/releases/mozilla-release/archive/c61f5f5ead48c78a80c80db5c489bdc7cfaf8175.tar.bz2";
+      sha512 = "03yybi1yp9g29jzdfgrq32r7a0gl2jz64w6ai8219cvhx8y95ahxfznj3vm29frrp6c18dk2nlpv2s89iczwm00lnn42r7dn6s6ppl9";
    };

    patches = nixpkgsPatches ++ [
      ./no-buildconfig.patch
-
-      # https://bugzilla.mozilla.org/show_bug.cgi?id=1430274
-      # Scheduled for firefox 59
-      (fetchpatch {
-        url = "https://bug1430274.bmoattachments.org/attachment.cgi?id=8943426";
-        sha256 = "12yfss3k61yilrb337dh2rffy5hh83d2f16gqrf5i56r9c33f7hf";
-      })
-
-      # https://bugzilla.mozilla.org/show_bug.cgi?id=1388981
-      # Should have been fixed in firefox 57
-    ] ++ lib.optional stdenv.isi686 (fetchpatch {
-      url = "https://hg.mozilla.org/mozilla-central/raw-rev/15517c5a5d37";
-      sha256 = "1ba487p3hk4w2w7qqfxgv1y57vp86b8g3xhav2j20qd3j3phbbn7";
-    });
+    ];

    meta = {
      description = "A web browser built from Firefox source tree";
@ -54,10 +41,10 @@ rec {

  firefox-esr = common rec {
    pname = "firefox-esr";
-    version = "52.6.0esr";
+    version = "52.7.1esr";
    src = fetchurl {
      url = "mirror://mozilla/firefox/releases/${version}/source/firefox-${version}.source.tar.xz";
-      sha512 = "cf583df34272b7ff8841c3b093ca0819118f9c36d23c6f9b3135db298e84ca022934bcd189add6473922b199b47330c0ecf14c303ab4177c03dbf26e64476fa4";
+      sha512 = "0275ca9c093fd0dcf09cfd31a4bca8c6ddb87aa74ace6b273a62f61079eeed11c2c0330c52c5f76aa73ed97e9cd18aa63cee69387e1fe346a30e4f9affc91ba7";
    };

    patches = nixpkgsPatches;
@ -149,9 +136,26 @@ in rec {
    src = fetchFromGitHub {
      owner = "SLNOS";
      repo  = "tor-browser";
-      # branch "tor-browser-52.6.2esr-7.5-2-slnos";
-      rev   = "cf1a504aaa26af962ae909a3811c0038db2d2eec";
-      sha256 = "0llbk7skh1n7yj137gv7rnxfasxsnvfjp4ss7h1fbdnw19yba115";
+      # branch "tor-browser-52.7.0esr-7.5-1-slnos";
+      rev   = "211b2be3fea45a450915b0addcd7783aa939e24a";
+      sha256 = "18gv4r8cjf89mamjh93a856a5yfp7dm3jrk8g05w89vxb3lrl74v";
+    };
+
+    patches = nixpkgsPatches;
+  } // commonAttrs) {};
+
+  tor-browser-8-0 = common (rec {
+    pname = "tor-browser";
+    version = "8.0.1";
+    isTorBrowserLike = true;
+
+    # FIXME: fetchFromGitHub is not ideal, unpacked source is >900Mb
+    src = fetchFromGitHub {
+      owner = "SLNOS";
+      repo  = "tor-browser";
+      # branch "tor-browser-52.7.0esr-8.0-1-slnos";
+      rev   = "58314ccb043882e830ee9a21c37a92d6e0d34e94";
+      sha256 = "09gb7chw2kly53b599xwpi75azj00957rnxly9fqv8zi3n5k2pdb";
    };

    patches = nixpkgsPatches;
--- a/pkgs/applications/networking/browsers/firefox/update.nix
+++ b/pkgs/applications/networking/browsers/firefox/update.nix
@ -22,13 +22,15 @@ writeScript "update-${attrPath}" ''
  #  - removes trailing slash
  #  - sorts everything with semver in mind
  #  - picks up latest release
-  version=`xidel -q $url --extract "//a" | \
+  version=`xidel -s $url --extract "//a" | \
           grep "^[0-9.]*${versionSuffix}/$" | \
           sed s/[/]$// | \
           sort --version-sort | \
           tail -n 1`

+  source_url=`curl --silent $url$version/SOURCE | grep -o 'https://.*\.tar\.bz2'`
+
  shasum=`curl --silent $url$version/SHA512SUMS | grep 'source\.tar\.xz' | cut -d ' ' -f 1`

-  update-source-version ${attrPath} "$version" "$shasum"
+  update-source-version ${attrPath} "$version" "$shasum" "$source_url"
 ''
--- a/pkgs/applications/networking/cluster/kubernetes/default.nix
+++ b/pkgs/applications/networking/cluster/kubernetes/default.nix
@ -1,4 +1,4 @@
-{ stdenv, lib, fetchFromGitHub, fetchpatch, removeReferencesTo, which, go, go-bindata, makeWrapper, rsync
+{ stdenv, lib, fetchFromGitHub, fetchpatch, removeReferencesTo, which, go_1_9, go-bindata, makeWrapper, rsync
 , iptables, coreutils
 , components ? [
    "cmd/kubeadm"
@ -25,7 +25,8 @@ stdenv.mkDerivation rec {
    sha256 = "1dmq2g138h7fsswmq4l47b44gsl9anmm3ywqyi7y48f1rkvc11mk";
  };

-  buildInputs = [ removeReferencesTo makeWrapper which go rsync go-bindata ];
+  # go > 1.10 should be fixed by https://github.com/kubernetes/kubernetes/pull/60373
+  buildInputs = [ removeReferencesTo makeWrapper which go_1_9 rsync go-bindata ];

  outputs = ["out" "man" "pause"];

@ -35,6 +36,13 @@ stdenv.mkDerivation rec {
      url = "https://github.com/kubernetes/kubernetes/commit/a990b04dc8a7d8408a71eee40db93621cf2b6d1b.patch";
      sha256 = "0piqilc5c9frikl74hamkffawwg1mvdwfxqvjnmk6wdma43dbb7w";
    })
+    (fetchpatch {
+      # https://github.com/kubernetes/kubernetes/pull/60978
+      # Fixes critical kube-proxy failure on iptables-restore >= 1.6.2 and
+      # non-critical failures on prior versions.
+      url = "https://github.com/kubernetes/kubernetes/commit/34ce573e9992ecdbc06dff1b4e3d0e9baa8353dd.patch";
+      sha256 = "1sd9qgc28zr6fkk0441f89bw8kq2kadys0qs7bgivy9cmcpw5x5p";
+    })
  ];

  postPatch = ''
@ -69,7 +77,7 @@ stdenv.mkDerivation rec {
  '';

  preFixup = ''
-    find $out/bin $pause/bin -type f -exec remove-references-to -t ${go} '{}' +
+    find $out/bin $pause/bin -type f -exec remove-references-to -t ${go_1_9} '{}' +
  '';

  meta = {
--- a/pkgs/applications/networking/instant-messengers/dino/default.nix
+++ b/pkgs/applications/networking/instant-messengers/dino/default.nix
@ -13,13 +13,13 @@
 }:

 stdenv.mkDerivation rec {
-  name = "dino-unstable-2018-02-11";
+  name = "dino-unstable-2018-03-10";

  src = fetchFromGitHub {
    owner = "dino";
    repo = "dino";
-    rev = "5436d716c0f508eb8ab70f322da862f996ce421e";
-    sha256 = "0yxkhl9xm5f0j2i9vxgyabpa5fwja0329fmg0878mqsm89nzz3am";
+    rev = "4ccdc1d0920a93b313d81b4014b6f45efb49b1fe";
+    sha256 = "0d9698zi09s107zva6cgip7xxmdby0zfmqvka4n0khxrsnii5awq";
    fetchSubmodules = true;
  };

--- a/pkgs/applications/science/logic/ltl2ba/default.nix
+++ b/pkgs/applications/science/logic/ltl2ba/default.nix
@ -2,11 +2,11 @@

 stdenv.mkDerivation rec {
  name = "ltl2ba-${version}";
-  version = "1.1";
+  version = "1.2b1";

  src = fetchurl {
    url    = "http://www.lsv.ens-cachan.fr/~gastin/ltl2ba/${name}.tar.gz";
-    sha256 = "16z0gc7a9dkarwn0l6rvg5jdhw1q4qyn4501zlchy0zxqddz0sx6";
+    sha256 = "1f4jnkfkyj8lcc5qfqbiypfc11rhhpqqi6xs9xx5dysg6r6303wm";
  };

  hardeningDisable = [ "format" ];
--- a/pkgs/applications/science/math/R/default.nix
+++ b/pkgs/applications/science/math/R/default.nix
@ -7,11 +7,11 @@
 }:

 stdenv.mkDerivation rec {
-  name = "R-3.4.3";
+  name = "R-3.4.4";

  src = fetchurl {
    url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz";
-    sha256 = "09pl0w01fr09bsrwd7nz2r5psysj0z93w4chz3hm2havvqqvhg3s";
+    sha256 = "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk";
  };

  buildInputs = [
--- a/pkgs/common-updater/scripts/update-source-version
+++ b/pkgs/common-updater/scripts/update-source-version
@ -6,10 +6,11 @@ die() {
    exit 1
 }

-# Usage: update-source-hash <attr> <version> [<new-source-hash>]
+# Usage: update-source-hash <attr> <version> [<new-source-hash>] [<new-source-url>]
 attr=$1
 newVersion=$2
 newHash=$3
+newUrl=$4

 nixFile=$(nix-instantiate --eval --strict -A "$attr.meta.position" | sed -re 's/^"(.*):[0-9]+"$/\1/')
 if [ ! -f "$nixFile" ]; then
@ -27,6 +28,12 @@ if [ $(grep -c "$oldHash" "$nixFile") != 1 ]; then
    die "Couldn't locate old source hash '$oldHash' (or it appeared more than once) in '$nixFile'!"
 fi

+oldUrl=$(nix-instantiate --eval -E "with import ./. {}; builtins.elemAt $attr.src.drvAttrs.urls 0" | tr -d '"')
+
+if [ -z "$oldUrl" ]; then
+    die "Couldn't evaluate source url from '$attr.name'!"
+fi
+
 drvName=$(nix-instantiate --eval -E "with import ./. {}; (builtins.parseDrvName $attr.name).name" | tr -d '"')
 oldVersion=$(nix-instantiate --eval -E "with import ./. {}; $attr.version or (builtins.parseDrvName $attr.name).version" | tr -d '"')

@ -41,6 +48,7 @@ fi

 # Escape regex metacharacter that are allowed in store path names
 oldVersion=$(echo "$oldVersion" | sed -re 's|[.+]|\\&|g')
+oldUrl=$(echo "$oldUrl" | sed -re 's|[${}.+]|\\&|g')

 if [ $(grep -c -E "^\s*(let\b)?\s*version\s*=\s*\"$oldVersion\"" "$nixFile") = 1 ]; then
    pattern="/\bversion\b\s*=/ s|\"$oldVersion\"|\"$newVersion\"|"
@ -56,6 +64,15 @@ if cmp -s "$nixFile" "$nixFile.bak"; then
    die "Failed to replace version '$oldVersion' to '$newVersion' in '$attr'!"
 fi

+# Replace new URL
+if [ -n "$newUrl" ]; then
+    sed -i "$nixFile" -re "s|\"$oldUrl\"|\"$newUrl\"|"
+
+    if cmp -s "$nixFile" "$nixFile.bak"; then
+        die "Failed to replace source URL '$oldUrl' to '$newUrl' in '$attr'!"
+    fi
+fi
+
 case "$oldHashAlgo" in
    sha256) hashLength=64 ;;
    sha512) hashLength=128 ;;
@ -74,7 +91,7 @@ fi
 if [ -z "$newHash" ]; then
    nix-build --no-out-link -A "$attr.src" 2>"$attr.fetchlog" >/dev/null || true
    # FIXME: use nix-build --hash here once https://github.com/NixOS/nix/issues/1172 is fixed
-    newHash=$(egrep -v "killing process|dependencies couldn't be built" "$attr.fetchlog" | tail -n2 | sed "s~output path .* has .* hash \(.*\) when .* was expected\|fixed-output derivation produced path '.*' with .* hash '\(.*\)' instead of the expected hash '.*'~\1\2~" | head -n1)
+    newHash=$(egrep -v "killing process|dependencies couldn't be built" "$attr.fetchlog" | tail -n2 | sed "s~output path .* has .* hash ‘\(.*\)’ when .* was expected\|fixed-output derivation produced path '.*' with .* hash '\(.*\)' instead of the expected hash '.*'~\1\2~" | head -n1)
 fi

 if [ -z "$newHash" ]; then
--- a/pkgs/data/misc/cacert/default.nix
+++ b/pkgs/data/misc/cacert/default.nix
@ -9,8 +9,8 @@ let

  certdata2pem = fetchurl {
    name = "certdata2pem.py";
-    url = "https://anonscm.debian.org/cgit/collab-maint/ca-certificates.git/plain/mozilla/certdata2pem.py?h=debian/20160104";
-    sha256 = "0bw11mgfrf19qziyvdnq22kirp0nn54lfsanrg5h6djs6ig1c2im";
+    url = "https://anonscm.debian.org/cgit/collab-maint/ca-certificates.git/plain/mozilla/certdata2pem.py?h=debian/20170717";
+    sha256 = "1d4q27j1gss0186a5m8bs5dk786w07ccyq0qi6xmd2zr1a8q16wy";
  };

 in
--- a/pkgs/development/compilers/ats2/default.nix
+++ b/pkgs/development/compilers/ats2/default.nix
@ -3,11 +3,11 @@
 , withContrib ? true }:

 let
-  versionPkg = "0.3.7" ;
+  versionPkg = "0.3.9" ;

  contrib = fetchurl {
    url = "mirror://sourceforge/ats2-lang/ATS2-Postiats-contrib-${versionPkg}.tgz" ;
-    sha256 = "1w59ir9ij5bvvnxj6fb1rvzycfqa57i31wmpwawxbsb10bqwzyr6";
+    sha256 = "627bb99ecf2e3d5976f95f2faa13c7c330726601e8bb05a2113c9b69c98749b5";
  };

  postInstallContrib = stdenv.lib.optionalString withContrib
@ -31,7 +31,7 @@ stdenv.mkDerivation rec {

  src = fetchurl {
    url = "mirror://sourceforge/ats2-lang/ATS2-Postiats-${version}.tgz";
-    sha256 = "19nxyi39fn42sp38kl14a6pvbxq9wr8y405wx0zz7mqb77r0m0h5";
+    sha256 = "c69a7c58964df26227e77656659129ca4c05205d2ebcacc7084edba818fb6e81";
  };

  buildInputs = [ gmp ];
--- a/pkgs/development/compilers/ghc/7.0.4-binary.nix
+++ b/pkgs/development/compilers/ghc/7.0.4-binary.nix
@ -1,146 +0,0 @@
-{ stdenv
-, fetchurl, perl
-, ncurses5, gmp, libiconv
-}:
-
-# Prebuilt only does native
-assert stdenv.targetPlatform == stdenv.hostPlatform;
-
-let
-  libPath = stdenv.lib.makeLibraryPath ([
-    ncurses5 gmp
-  ] ++ stdenv.lib.optional (stdenv.hostPlatform.isDarwin) libiconv);
-
-  libEnvVar = stdenv.lib.optionalString stdenv.hostPlatform.isDarwin "DY"
-    + "LD_LIBRARY_PATH";
-
-in
-
-stdenv.mkDerivation rec {
-  version = "7.0.4";
-
-  name = "ghc-${version}-binary";
-
-  src = fetchurl ({
-    "i686-linux" = {
-      url = "http://haskell.org/ghc/dist/${version}/ghc-${version}-i386-unknown-linux.tar.bz2";
-      sha256 = "0mfnihiyjl06f5w1yrjp36sw9g67g2ymg5sdl0g23h1pab99jx63";
-    };
-    "x86_64-linux" = {
-      url = "http://haskell.org/ghc/dist/${version}/ghc-${version}-x86_64-unknown-linux.tar.bz2";
-      sha256 = "0mc4rhqcxz427wq4zgffmnn0d2yjqvy6af4x9mha283p1gdj5q99";
-    };
-    "i686-darwin" = {
-      url = "http://haskell.org/ghc/dist/${version}/ghc-${version}-i386-apple-darwin.tar.bz2";
-      sha256 = "0qj45hslrrr8zfks8m1jcb3awwx9rh35ndnpfmb0gwb6j7azq5n3";
-    };
-    "x86_64-darwin" = {
-      url = "http://haskell.org/ghc/dist/${version}/ghc-${version}-x86_64-apple-darwin.tar.bz2";
-      sha256 = "1m2ml88p1swf4dnv2vq8hz4drcp46n3ahpfi05wh01ajkf8hnn3l";
-    };
-  }.${stdenv.hostPlatform.system}
-    or (throw "cannot bootstrap GHC on this platform"));
-
-  nativeBuildInputs = [ perl ];
-
-  # Cannot patchelf beforehand due to relative RPATHs that anticipate
-  # the final install location/
-  ${libEnvVar} = libPath;
-
-  postUnpack =
-    # GHC has dtrace probes, which causes ld to try to open /usr/lib/libdtrace.dylib
-    # during linking
-    stdenv.lib.optionalString stdenv.isDarwin ''
-      export NIX_LDFLAGS+=" -no_dtrace_dof"
-    '' +
-
-    # Strip is harmful, see also below. It's important that this happens
-    # first. The GHC Cabal build system makes use of strip by default and
-    # has hardcoded paths to /usr/bin/strip in many places. We replace
-    # those below, making them point to our dummy script.
-    ''
-      mkdir "$TMP/bin"
-      for i in strip; do
-        echo '#! ${stdenv.shell}' > "$TMP/bin/$i"
-        chmod +x "$TMP/bin/$i"
-      done
-      PATH="$TMP/bin:$PATH"
-    '' +
-    # We have to patch the GMP paths for the integer-gmp package.
-    ''
-      find . -name integer-gmp.buildinfo \
-          -exec sed -i "s@extra-lib-dirs: @extra-lib-dirs: ${gmp.out}/lib@" {} \;
-    '' + stdenv.lib.optionalString stdenv.isDarwin ''
-      find . -name base.buildinfo \
-          -exec sed -i "s@extra-lib-dirs: @extra-lib-dirs: ${libiconv}/lib@" {} \;
-    '' +
-    # Rename needed libraries and binaries, fix interpreter
-    stdenv.lib.optionalString stdenv.isLinux ''
-      find . -type f -perm -0100 -exec patchelf \
-          --interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" {} \;
-
-      paxmark m ./ghc-${version}/ghc/stage2/build/tmp/ghc-stage2
-
-      sed -i "s|/usr/bin/perl|perl\x00        |" ghc-${version}/ghc/stage2/build/tmp/ghc-stage2
-      sed -i "s|/usr/bin/gcc|gcc\x00        |" ghc-${version}/ghc/stage2/build/tmp/ghc-stage2
-      for prog in ld ar gcc strip ranlib; do
-        find . -name "setup-config" -exec sed -i "s@/usr/bin/$prog@$(type -p $prog)@g" {} \;
-      done
-    '';
-
-  configurePlatforms = [ ];
-  configureFlags = [
-    "--with-gmp-libraries=${stdenv.lib.getLib gmp}/lib"
-    "--with-gmp-includes=${stdenv.lib.getDev gmp}/include"
-  ] ++ stdenv.lib.optional stdenv.isDarwin "--with-gcc=${./gcc-clang-wrapper.sh}";
-
-  # Stripping combined with patchelf breaks the executables (they die
-  # with a segfault or the kernel even refuses the execve). (NIXPKGS-85)
-  dontStrip = true;
-
-  # No building is necessary, but calling make without flags ironically
-  # calls install-strip ...
-  dontBuild = true;
-
-  # On Linux, use patchelf to modify the executables so that they can
-  # find editline/gmp.
-  preFixup = stdenv.lib.optionalString stdenv.isLinux ''
-    find "$out" -type f -executable \
-        -exec patchelf --set-rpath "${libPath}" {} \;
-  '' + stdenv.lib.optionalString stdenv.isDarwin ''
-    # not enough room in the object files for the full path to libiconv :(
-    for exe in $(find "$out" -type f -executable); do
-      isScript $exe && continue
-      ln -fs ${libiconv}/lib/libiconv.dylib $(dirname $exe)/libiconv.dylib
-      install_name_tool -change /usr/lib/libiconv.2.dylib @executable_path/libiconv.dylib $exe
-    done
-
-    for file in $(find "$out" -name setup-config); do
-      substituteInPlace $file --replace /usr/bin/ranlib "$(type -P ranlib)"
-    done
-  '';
-
-  doInstallCheck = true;
-  installCheckPhase = ''
-    # Sanity check, can ghc create executables?
-    cd $TMP
-    mkdir test-ghc; cd test-ghc
-    cat > main.hs << EOF
-      module Main where
-      main = putStrLn "yes"
-    EOF
-    $out/bin/ghc --make main.hs
-    echo compilation ok
-    [ $(./main) == "yes" ]
-  '';
-
-  passthru = {
-    targetPrefix = "";
-
-    # Our Cabal compiler name
-    haskellCompilerName = "ghc-7.0.4";
-  };
-
-  meta.license = stdenv.lib.licenses.bsd3;
-  meta.platforms = ["x86_64-linux" "i686-linux" "x86_64-darwin"];
-}
--- a/pkgs/development/compilers/ghc/7.0.4.nix
+++ b/pkgs/development/compilers/ghc/7.0.4.nix
@ -1,67 +0,0 @@
-{ stdenv, fetchurl, ghc, perl, gmp, ncurses, libiconv }:
-
-# TODO(@Ericson2314): Cross compilation support
-assert stdenv.targetPlatform == stdenv.hostPlatform;
-
-stdenv.mkDerivation rec {
-  version = "7.0.4";
-  name = "ghc-${version}";
-
-  src = fetchurl {
-    url = "https://downloads.haskell.org/~ghc/${version}/ghc-${version}-src.tar.bz2";
-    sha256 = "1a9b78d9d66c9c21de6c0932e36bb87406a4856f1611bf83bd44539bdc6ed0ed";
-  };
-
-  patches = [ ./fix-7.0.4-clang.patch ./relocation.patch ];
-
-  buildInputs = [ ghc perl gmp ncurses ];
-
-  buildMK = ''
-    libraries/integer-gmp_CONFIGURE_OPTS += --configure-option=--with-gmp-libraries="${gmp.out}/lib"
-    libraries/integer-gmp_CONFIGURE_OPTS += --configure-option=--with-gmp-includes="${gmp.dev}/include"
-    libraries/terminfo_CONFIGURE_OPTS += --configure-option=--with-curses-includes="${ncurses.dev}/include"
-    libraries/terminfo_CONFIGURE_OPTS += --configure-option=--with-curses-libraries="${ncurses.out}/lib"
-    ${stdenv.lib.optionalString stdenv.isDarwin ''
-      libraries/base_CONFIGURE_OPTS += --configure-option=--with-iconv-includes="${libiconv}/include"
-      libraries/base_CONFIGURE_OPTS += --configure-option=--with-iconv-libraries="${libiconv}/lib"
-    ''}
-  '';
-
-  preConfigure = ''
-    echo -n "${buildMK}" > mk/build.mk
-    sed -i -e 's|-isysroot /Developer/SDKs/MacOSX10.5.sdk||' configure
-  '' + stdenv.lib.optionalString stdenv.isDarwin ''
-    find . -name '*.hs'  | xargs sed -i -e 's|ASSERT (|ASSERT(|' -e 's|ASSERT2 (|ASSERT2(|' -e 's|WARN (|WARN(|'
-    find . -name '*.lhs' | xargs sed -i -e 's|ASSERT (|ASSERT(|' -e 's|ASSERT2 (|ASSERT2(|' -e 's|WARN (|WARN(|'
-    export NIX_LDFLAGS+=" -no_dtrace_dof"
-  '';
-
-  configureFlags = if stdenv.isDarwin then "--with-gcc=${./gcc-clang-wrapper.sh}"
-                                      else "--with-gcc=${stdenv.cc}/bin/gcc";
-
-  NIX_CFLAGS_COMPILE = "-fomit-frame-pointer";
-
-  # required, because otherwise all symbols from HSffi.o are stripped, and
-  # that in turn causes GHCi to abort
-  stripDebugFlags=["-S" "--keep-file-symbols"];
-
-  passthru = {
-    targetPrefix = "";
-
-    # Our Cabal compiler name
-    haskellCompilerName = "ghc-7.0.4";
-  };
-
-  meta = {
-    homepage = http://haskell.org/ghc;
-    description = "The Glasgow Haskell Compiler";
-    maintainers = [
-      stdenv.lib.maintainers.marcweber
-      stdenv.lib.maintainers.andres
-      stdenv.lib.maintainers.peti
-    ];
-    platforms = ["x86_64-linux" "i686-linux"];  # Darwin is not supported.
-    inherit (ghc.meta) license;
-  };
-
-}
--- a/pkgs/development/compilers/ghc/7.4.2-binary.nix
+++ b/pkgs/development/compilers/ghc/7.4.2-binary.nix
@ -1,148 +0,0 @@
-{ stdenv
-, fetchurl, perl
-, ncurses5, gmp, libiconv
-}:
-
-# Prebuilt only does native
-assert stdenv.targetPlatform == stdenv.hostPlatform;
-
-let
-  libPath = stdenv.lib.makeLibraryPath ([
-    ncurses5 gmp
-  ] ++ stdenv.lib.optional (stdenv.hostPlatform.isDarwin) libiconv);
-
-  libEnvVar = stdenv.lib.optionalString stdenv.hostPlatform.isDarwin "DY"
-    + "LD_LIBRARY_PATH";
-
-in
-
-stdenv.mkDerivation rec {
-  version = "7.4.2";
-
-  name = "ghc-${version}-binary";
-
-  src = fetchurl ({
-    "i686-linux" = {
-      url = "http://haskell.org/ghc/dist/${version}/ghc-${version}-i386-unknown-linux.tar.bz2";
-      sha256 = "0gny7knhss0w0d9r6jm1gghrcb8kqjvj94bb7hxf9syrk4fxlcxi";
-    };
-    "x86_64-linux" = {
-      url = "http://haskell.org/ghc/dist/${version}/ghc-${version}-x86_64-unknown-linux.tar.bz2";
-      sha256 = "043jabd0lh6n1zlqhysngbpvlsdznsa2mmsj08jyqgahw9sjb5ns";
-    };
-    "i686-darwin" = {
-      url = "http://haskell.org/ghc/dist/${version}/ghc-${version}-i386-apple-darwin.tar.bz2";
-      sha256 = "1vrbs3pzki37hzym1f1nh07lrqh066z3ypvm81fwlikfsvk4djc0";
-    };
-    "x86_64-darwin" = {
-      url = "http://haskell.org/ghc/dist/${version}/ghc-${version}-x86_64-apple-darwin.tar.bz2";
-      sha256 = "1imzqc0slpg0r6p40n5a9m18cbcm0m86z8dgyhfxcckksw54mzwf";
-    };
-  }.${stdenv.hostPlatform.system}
-    or (throw "cannot bootstrap GHC on this platform"));
-
-  nativeBuildInputs = [ perl ];
-
-  # Cannot patchelf beforehand due to relative RPATHs that anticipate
-  # the final install location/
-  ${libEnvVar} = libPath;
-
-  postUnpack =
-    # GHC has dtrace probes, which causes ld to try to open /usr/lib/libdtrace.dylib
-    # during linking
-    stdenv.lib.optionalString stdenv.isDarwin ''
-      export NIX_LDFLAGS+=" -no_dtrace_dof"
-    '' +
-
-    # Strip is harmful, see also below. It's important that this happens
-    # first. The GHC Cabal build system makes use of strip by default and
-    # has hardcoded paths to /usr/bin/strip in many places. We replace
-    # those below, making them point to our dummy script.
-    ''
-      mkdir "$TMP/bin"
-      for i in strip; do
-        echo '#! ${stdenv.shell}' > "$TMP/bin/$i"
-        chmod +x "$TMP/bin/$i"
-      done
-      PATH="$TMP/bin:$PATH"
-    '' +
-    # We have to patch the GMP paths for the integer-gmp package.
-    ''
-      find . -name integer-gmp.buildinfo \
-          -exec sed -i "s@extra-lib-dirs: @extra-lib-dirs: ${gmp.out}/lib@" {} \;
-    '' + stdenv.lib.optionalString stdenv.isDarwin ''
-      find . -name base.buildinfo \
-          -exec sed -i "s@extra-lib-dirs: @extra-lib-dirs: ${libiconv}/lib@" {} \;
-    '' +
-    # Rename needed libraries and binaries, fix interpreter
-    stdenv.lib.optionalString stdenv.isLinux ''
-      find . -type f -perm -0100 -exec patchelf \
-          --replace-needed libncurses${stdenv.lib.optionalString stdenv.is64bit "w"}.so.5 libncurses.so \
-          --interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" {} \;
-
-      paxmark m ./ghc-${version}/ghc/stage2/build/tmp/ghc-stage2
-
-      sed -i "s|/usr/bin/perl|perl\x00        |" ghc-${version}/ghc/stage2/build/tmp/ghc-stage2
-      sed -i "s|/usr/bin/gcc|gcc\x00        |" ghc-${version}/ghc/stage2/build/tmp/ghc-stage2
-      for prog in ld ar gcc strip ranlib; do
-        find . -name "setup-config" -exec sed -i "s@/usr/bin/$prog@$(type -p $prog)@g" {} \;
-      done
-    '';
-
-  configurePlatforms = [ ];
-  configureFlags = [
-    "--with-gmp-libraries=${stdenv.lib.getLib gmp}/lib"
-    "--with-gmp-includes=${stdenv.lib.getDev gmp}/include"
-  ] ++ stdenv.lib.optional stdenv.isDarwin "--with-gcc=${./gcc-clang-wrapper.sh}";
-
-  # Stripping combined with patchelf breaks the executables (they die
-  # with a segfault or the kernel even refuses the execve). (NIXPKGS-85)
-  dontStrip = true;
-
-  # No building is necessary, but calling make without flags ironically
-  # calls install-strip ...
-  dontBuild = true;
-
-  # On Linux, use patchelf to modify the executables so that they can
-  # find editline/gmp.
-  preFixup = stdenv.lib.optionalString stdenv.isLinux ''
-    find "$out" -type f -executable \
-        -exec patchelf --set-rpath "${libPath}" {} \;
-  '' + stdenv.lib.optionalString stdenv.isDarwin ''
-    # not enough room in the object files for the full path to libiconv :(
-    for exe in $(find "$out" -type f -executable); do
-      isScript $exe && continue
-      ln -fs ${libiconv}/lib/libiconv.dylib $(dirname $exe)/libiconv.dylib
-      install_name_tool -change /usr/lib/libiconv.2.dylib @executable_path/libiconv.dylib $exe
-    done
-
-    for file in $(find "$out" -name setup-config); do
-      substituteInPlace $file --replace /usr/bin/ranlib "$(type -P ranlib)"
-    done
-  '';
-
-  doInstallCheck = true;
-  installCheckPhase = ''
-    # Sanity check, can ghc create executables?
-    cd $TMP
-    mkdir test-ghc; cd test-ghc
-    cat > main.hs << EOF
-      {-# LANGUAGE TemplateHaskell #-}
-      module Main where
-      main = putStrLn \$([|"yes"|])
-    EOF
-    $out/bin/ghc --make main.hs || exit 1
-    echo compilation ok
-    [ $(./main) == "yes" ]
-  '';
-
-  passthru = {
-    targetPrefix = "";
-
-    # Our Cabal compiler name
-    haskellCompilerName = "ghc-7.4.2";
-  };
-
-  meta.license = stdenv.lib.licenses.bsd3;
-  meta.platforms = ["x86_64-linux" "i686-linux" "x86_64-darwin"];
-}
--- a/pkgs/development/compilers/ghc/7.4.2.nix
+++ b/pkgs/development/compilers/ghc/7.4.2.nix
@ -1,77 +0,0 @@
-{ stdenv, fetchurl, ghc, perl, ncurses, libiconv
-
-, # If enabled, GHC will be built with the GPL-free but slower integer-simple
-  # library instead of the faster but GPLed integer-gmp library.
-  enableIntegerSimple ? false, gmp ? null
-}:
-
-# TODO(@Ericson2314): Cross compilation support
-assert stdenv.targetPlatform == stdenv.hostPlatform;
-assert !enableIntegerSimple -> gmp != null;
-
-stdenv.mkDerivation rec {
-  version = "7.4.2";
-
-  name = "ghc-${version}";
-
-  src = fetchurl {
-    url = "https://downloads.haskell.org/~ghc/${version}/ghc-${version}-src.tar.bz2";
-    sha256 = "0vc3zmxqi4gflssmj35n5c8idbvyrhd88abi50whbirwlf4i5vpj";
-  };
-
-  patches = [ ./fix-7.4.2-clang.patch ./relocation.patch ];
-
-  buildInputs = [ ghc perl ncurses ]
-                ++ stdenv.lib.optional (!enableIntegerSimple) gmp;
-
-  buildMK = ''
-    libraries/terminfo_CONFIGURE_OPTS += --configure-option=--with-curses-includes="${ncurses.dev}/include"
-    libraries/terminfo_CONFIGURE_OPTS += --configure-option=--with-curses-libraries="${ncurses.out}/lib"
-    ${stdenv.lib.optionalString stdenv.isDarwin ''
-      libraries/base_CONFIGURE_OPTS += --configure-option=--with-iconv-includes="${libiconv}/include"
-      libraries/base_CONFIGURE_OPTS += --configure-option=--with-iconv-libraries="${libiconv}/lib"
-    ''}
-  '' + (if enableIntegerSimple then ''
-    INTEGER_LIBRARY = integer-simple
-  '' else ''
-    libraries/integer-gmp_CONFIGURE_OPTS += --configure-option=--with-gmp-libraries="${gmp.out}/lib"
-    libraries/integer-gmp_CONFIGURE_OPTS += --configure-option=--with-gmp-includes="${gmp.dev}/include"
-  '');
-
-  preConfigure = ''
-    echo -n "${buildMK}" > mk/build.mk
-    sed -i -e 's|-isysroot /Developer/SDKs/MacOSX10.5.sdk||' configure
-  '' + stdenv.lib.optionalString (!stdenv.isDarwin) ''
-    export NIX_LDFLAGS+=" -rpath $out/lib/ghc-${version}"
-  '' + stdenv.lib.optionalString stdenv.isDarwin ''
-    find . -name '*.hs'  | xargs sed -i -e 's|ASSERT (|ASSERT(|' -e 's|ASSERT2 (|ASSERT2(|' -e 's|WARN (|WARN(|'
-    find . -name '*.lhs' | xargs sed -i -e 's|ASSERT (|ASSERT(|' -e 's|ASSERT2 (|ASSERT2(|' -e 's|WARN (|WARN(|'
-    export NIX_LDFLAGS+=" -no_dtrace_dof"
-  '';
-
-  configureFlags = if stdenv.isDarwin then "--with-gcc=${./gcc-clang-wrapper.sh}"
-                                      else "--with-gcc=${stdenv.cc}/bin/gcc";
-
-  # required, because otherwise all symbols from HSffi.o are stripped, and
-  # that in turn causes GHCi to abort
-  stripDebugFlags = [ "-S" ] ++ stdenv.lib.optional (!stdenv.isDarwin) "--keep-file-symbols";
-
-  passthru = {
-    targetPrefix = "";
-
-    # Our Cabal compiler name
-    haskellCompilerName = "ghc-7.4.2";
-  };
-
-  meta = {
-    homepage = http://haskell.org/ghc;
-    description = "The Glasgow Haskell Compiler";
-    maintainers = [
-      stdenv.lib.maintainers.marcweber
-      stdenv.lib.maintainers.andres
-      stdenv.lib.maintainers.peti
-    ];
-    inherit (ghc.meta) license platforms;
-  };
-
-}
--- a/pkgs/development/compilers/ghc/7.6.3.nix
+++ b/pkgs/development/compilers/ghc/7.6.3.nix
@ -1,103 +0,0 @@
-{ stdenv, fetchurl, ghc, perl, ncurses, libiconv
-
-, # If enabled, GHC will be built with the GPL-free but slower integer-simple
-  # library instead of the faster but GPLed integer-gmp library.
-  enableIntegerSimple ? false, gmp ? null
-}:
-
-# TODO(@Ericson2314): Cross compilation support
-assert stdenv.targetPlatform == stdenv.hostPlatform;
-assert !enableIntegerSimple -> gmp != null;
-
-let
-  # The "-Wa,--noexecstack" options might be needed only with GNU ld (as opposed
-  # to the gold linker). It prevents binaries' stacks from being marked as
-  # executable, which fails to run on a grsecurity/PaX kernel.
-  ghcFlags = "-optc-Wa,--noexecstack -opta-Wa,--noexecstack";
-  cFlags = "-Wa,--noexecstack";
-
-in stdenv.mkDerivation rec {
-  version = "7.6.3";
-
-  name = "ghc-${version}";
-
-  src = fetchurl {
-    url = "https://downloads.haskell.org/~ghc/${version}/ghc-${version}-src.tar.bz2";
-    sha256 = "1669m8k9q72rpd2mzs0bh2q6lcwqiwd1ax3vrard1dgn64yq4hxx";
-  };
-
-  patches = [ ./fix-7.6.3-clang.patch ./relocation.patch ];
-
-  buildInputs = [ ghc perl ncurses ]
-                ++ stdenv.lib.optional (!enableIntegerSimple) gmp;
-
-  buildMK = ''
-    libraries/terminfo_CONFIGURE_OPTS += --configure-option=--with-curses-includes="${ncurses.dev}/include"
-    libraries/terminfo_CONFIGURE_OPTS += --configure-option=--with-curses-libraries="${ncurses.out}/lib"
-    ${stdenv.lib.optionalString stdenv.isDarwin ''
-      libraries/base_CONFIGURE_OPTS += --configure-option=--with-iconv-includes="${libiconv}/include"
-      libraries/base_CONFIGURE_OPTS += --configure-option=--with-iconv-libraries="${libiconv}/lib"
-    ''}
-  '' + stdenv.lib.optionalString stdenv.isLinux ''
-    # Set ghcFlags for building ghc itself
-    SRC_HC_OPTS += ${ghcFlags}
-    SRC_CC_OPTS += ${cFlags}
-  '' + (if enableIntegerSimple then ''
-    INTEGER_LIBRARY = integer-simple
-  '' else ''
-    libraries/integer-gmp_CONFIGURE_OPTS += --configure-option=--with-gmp-libraries="${gmp.out}/lib"
-    libraries/integer-gmp_CONFIGURE_OPTS += --configure-option=--with-gmp-includes="${gmp.dev}/include"
-  '');
-
-  preConfigure = ''
-    echo -n "${buildMK}" > mk/build.mk
-    sed -i -e 's|-isysroot /Developer/SDKs/MacOSX10.5.sdk||' configure
-
-  '' + stdenv.lib.optionalString stdenv.isLinux ''
-    # Set ghcFlags for binaries that ghc builds
-    sed -i -e 's|"\$topdir"|"\$topdir" ${ghcFlags}|' ghc/ghc.wrapper
-
-  '' + stdenv.lib.optionalString (!stdenv.isDarwin) ''
-    export NIX_LDFLAGS+=" -rpath $out/lib/ghc-${version}"
-  '' + stdenv.lib.optionalString stdenv.isDarwin ''
-    find . -name '*.hs'  | xargs sed -i -e 's|ASSERT (|ASSERT(|' -e 's|ASSERT2 (|ASSERT2(|' -e 's|WARN (|WARN(|'
-    find . -name '*.lhs' | xargs sed -i -e 's|ASSERT (|ASSERT(|' -e 's|ASSERT2 (|ASSERT2(|' -e 's|WARN (|WARN(|'
-    export NIX_LDFLAGS+=" -no_dtrace_dof"
-  '';
-
-  configureFlags = if stdenv.isDarwin then "--with-gcc=${./gcc-clang-wrapper.sh}"
-                                      else "--with-gcc=${stdenv.cc}/bin/gcc";
-
-  postInstall = ''
-    # ghci uses mmap with rwx protection at it implements dynamic
-    # linking on its own. See:
-    # - https://bugs.gentoo.org/show_bug.cgi?id=299709
-    # - https://ghc.haskell.org/trac/ghc/ticket/4244
-    # Therefore, we have to pax-mark the resulting binary.
-    # Haddock also seems to run with ghci, so mark it as well.
-    paxmark m $out/lib/${name}/{ghc,haddock}
-  '';
-
-  # required, because otherwise all symbols from HSffi.o are stripped, and
-  # that in turn causes GHCi to abort
-  stripDebugFlags = [ "-S" ] ++ stdenv.lib.optional (!stdenv.isDarwin) "--keep-file-symbols";
-
-  passthru = {
-    targetPrefix = "";
-
-    # Our Cabal compiler name
-    haskellCompilerName = "ghc-7.6.3";
-  };
-
-  meta = {
-    homepage = http://haskell.org/ghc;
-    description = "The Glasgow Haskell Compiler";
-    maintainers = [
-      stdenv.lib.maintainers.marcweber
-      stdenv.lib.maintainers.andres
-      stdenv.lib.maintainers.peti
-    ];
-    inherit (ghc.meta) license platforms;
-  };
-
-}
--- a/pkgs/development/compilers/ghc/7.8.4-binary.nix
+++ b/pkgs/development/compilers/ghc/7.8.4-binary.nix
@ -1,156 +0,0 @@
-{ stdenv
-, fetchurl, perl
-, ncurses5, gmp, libiconv
-}:
-
-# Prebuilt only does native
-assert stdenv.targetPlatform == stdenv.hostPlatform;
-
-let
-  libPath = stdenv.lib.makeLibraryPath ([
-    ncurses5 gmp
-  ] ++ stdenv.lib.optional (stdenv.hostPlatform.isDarwin) libiconv);
-
-  libEnvVar = stdenv.lib.optionalString stdenv.hostPlatform.isDarwin "DY"
-    + "LD_LIBRARY_PATH";
-
-in
-
-stdenv.mkDerivation rec {
-  version = "7.8.4";
-
-  name = "ghc-${version}-binary";
-
-  src = fetchurl ({
-    "i686-linux" = {
-      url = "http://haskell.org/ghc/dist/${version}/ghc-${version}-i386-unknown-linux-deb7.tar.bz2";
-      sha256 = "5da2cf45986f33319a92a666f1f0149915334a7b64b41892ab94f4557242b406";
-    };
-    "x86_64-linux" = {
-      url = "http://haskell.org/ghc/dist/${version}/ghc-${version}-x86_64-unknown-linux-deb7.tar.bz2";
-      sha256 = "20b5731d268613bbf6e977dbb192a3a3b7b78d954c35edbfca4fb36b652e24f7";
-    };
-    "x86_64-darwin" = {
-      url = "http://haskell.org/ghc/dist/${version}/ghc-${version}-x86_64-apple-darwin.tar.bz2";
-      sha256 = "dfa161c2a136ee16214a49d5902e2377407c8292dbbdbb14fa0fa6b17220cae6";
-    };
-  }.${stdenv.hostPlatform.system}
-    or (throw "cannot bootstrap GHC on this platform"));
-
-  nativeBuildInputs = [ perl ];
-
-  # Cannot patchelf beforehand due to relative RPATHs that anticipate
-  # the final install location/
-  ${libEnvVar} = libPath;
-
-  postUnpack =
-    # GHC has dtrace probes, which causes ld to try to open /usr/lib/libdtrace.dylib
-    # during linking
-    stdenv.lib.optionalString stdenv.isDarwin ''
-      export NIX_LDFLAGS+=" -no_dtrace_dof"
-      # not enough room in the object files for the full path to libiconv :(
-      for exe in $(find . -type f -executable); do
-        isScript $exe && continue
-        ln -fs ${libiconv}/lib/libiconv.dylib $(dirname $exe)/libiconv.dylib
-        install_name_tool -change /usr/lib/libiconv.2.dylib @executable_path/libiconv.dylib $exe
-        for file in $(find . -name setup-config); do
-          substituteInPlace $file --replace /usr/bin/ranlib "$(type -P ranlib)"
-        done
-      done
-    '' +
-
-    # Some scripts used during the build need to have their shebangs patched
-    ''
-      patchShebangs ghc-${version}/utils/
-    '' +
-
-    # Strip is harmful, see also below. It's important that this happens
-    # first. The GHC Cabal build system makes use of strip by default and
-    # has hardcoded paths to /usr/bin/strip in many places. We replace
-    # those below, making them point to our dummy script.
-    ''
-      mkdir "$TMP/bin"
-      for i in strip; do
-        echo '#! ${stdenv.shell}' > "$TMP/bin/$i"
-        chmod +x "$TMP/bin/$i"
-      done
-      PATH="$TMP/bin:$PATH"
-    '' +
-    # We have to patch the GMP paths for the integer-gmp package.
-    ''
-      find . -name integer-gmp.buildinfo \
-          -exec sed -i "s@extra-lib-dirs: @extra-lib-dirs: ${gmp.out}/lib@" {} \;
-    '' + stdenv.lib.optionalString stdenv.isDarwin ''
-      find . -name base.buildinfo \
-          -exec sed -i "s@extra-lib-dirs: @extra-lib-dirs: ${libiconv}/lib@" {} \;
-    '' +
-    # Rename needed libraries and binaries, fix interpreter
-    stdenv.lib.optionalString stdenv.isLinux ''
-      find . -type f -perm -0100 -exec patchelf \
-          --replace-needed libncurses${stdenv.lib.optionalString stdenv.is64bit "w"}.so.5 libncurses.so \
-          --replace-needed libtinfo.so libtinfo.so.5 \
-          --interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" {} \;
-
-      paxmark m ./ghc-${version}/ghc/stage2/build/tmp/ghc-stage2
-
-      sed -i "s|/usr/bin/perl|perl\x00        |" ghc-${version}/ghc/stage2/build/tmp/ghc-stage2
-      sed -i "s|/usr/bin/gcc|gcc\x00        |" ghc-${version}/ghc/stage2/build/tmp/ghc-stage2
-    '';
-
-  configurePlatforms = [ ];
-  configureFlags = [
-    "--with-gmp-libraries=${stdenv.lib.getLib gmp}/lib"
-    "--with-gmp-includes=${stdenv.lib.getDev gmp}/include"
-  ] ++ stdenv.lib.optional stdenv.isDarwin "--with-gcc=${./gcc-clang-wrapper.sh}";
-
-  # Stripping combined with patchelf breaks the executables (they die
-  # with a segfault or the kernel even refuses the execve). (NIXPKGS-85)
-  dontStrip = true;
-
-  # No building is necessary, but calling make without flags ironically
-  # calls install-strip ...
-  dontBuild = true;
-
-  # On Linux, use patchelf to modify the executables so that they can
-  # find editline/gmp.
-  preFixup = stdenv.lib.optionalString stdenv.isLinux ''
-    for p in $(find "$out" -type f -executable); do
-      if isELF "$p"; then
-        echo "Patchelfing $p"
-        patchelf --set-rpath "${libPath}:$(patchelf --print-rpath $p)" $p
-      fi
-    done
-  '' + stdenv.lib.optionalString stdenv.isDarwin ''
-    # not enough room in the object files for the full path to libiconv :(
-    for exe in $(find "$out" -type f -executable); do
-      isScript $exe && continue
-      ln -fs ${libiconv}/lib/libiconv.dylib $(dirname $exe)/libiconv.dylib
-      install_name_tool -change /usr/lib/libiconv.2.dylib @executable_path/libiconv.dylib $exe
-    done
-
-    for file in $(find "$out" -name setup-config); do
-      substituteInPlace $file --replace /usr/bin/ranlib "$(type -P ranlib)"
-    done
-  '';
-
-  doInstallCheck = true;
-  installCheckPhase = ''
-    unset ${libEnvVar}
-    # Sanity check, can ghc create executables?
-    cd $TMP
-    mkdir test-ghc; cd test-ghc
-    cat > main.hs << EOF
-      {-# LANGUAGE TemplateHaskell #-}
-      module Main where
-      main = putStrLn \$([|"yes"|])
-    EOF
-    $out/bin/ghc --make main.hs || exit 1
-    echo compilation ok
-    [ $(./main) == "yes" ]
-  '';
-
-  passthru = { targetPrefix = ""; };
-
-  meta.license = stdenv.lib.licenses.bsd3;
-  meta.platforms = ["x86_64-linux" "i686-linux" "x86_64-darwin"];
-}
--- a/pkgs/development/compilers/ghc/7.8.4.nix
+++ b/pkgs/development/compilers/ghc/7.8.4.nix
@ -1,91 +0,0 @@
-{ stdenv, targetPackages
-
-, fetchurl, ghc, perl
-, libffi, libiconv ? null, ncurses
-
-, # If enabled, GHC will be built with the GPL-free but slower integer-simple
-  # library instead of the faster but GPLed integer-gmp library.
-  enableIntegerSimple ? false, gmp ? null
-}:
-
-# TODO(@Ericson2314): Cross compilation support
-assert stdenv.targetPlatform == stdenv.hostPlatform;
-assert !enableIntegerSimple -> gmp != null;
-
-let
-  buildMK = ''
-    libraries/terminfo_CONFIGURE_OPTS += --configure-option=--with-curses-includes="${ncurses.dev}/include"
-    libraries/terminfo_CONFIGURE_OPTS += --configure-option=--with-curses-libraries="${ncurses.out}/lib"
-    DYNAMIC_BY_DEFAULT = NO
-    ${stdenv.lib.optionalString (stdenv.hostPlatform.libc != "glibc") ''
-      libraries/base_CONFIGURE_OPTS += --configure-option=--with-iconv-includes="${libiconv}/include"
-      libraries/base_CONFIGURE_OPTS += --configure-option=--with-iconv-libraries="${libiconv}/lib"
-    ''}
-  '' + (if enableIntegerSimple then ''
-    INTEGER_LIBRARY = integer-simple
-  '' else ''
-    libraries/integer-gmp_CONFIGURE_OPTS += --configure-option=--with-gmp-libraries="${gmp.out}/lib"
-    libraries/integer-gmp_CONFIGURE_OPTS += --configure-option=--with-gmp-includes="${gmp.dev}/include"
-  '');
-
-  # Splicer will pull out correct variations
-  libDeps = [ ncurses ]
-    ++ stdenv.lib.optional (!enableIntegerSimple) gmp
-    ++ stdenv.lib.optional (stdenv.hostPlatform.libc != "glibc") libiconv;
-
-in
-
-stdenv.mkDerivation rec {
-  version = "7.8.4";
-  name = "ghc-${version}";
-
-  src = fetchurl {
-    url = "http://www.haskell.org/ghc/dist/${version}/${name}-src.tar.xz";
-    sha256 = "1i4254akbb4ym437rf469gc0m40bxm31blp6s1z1g15jmnacs6f3";
-  };
-
-  enableParallelBuilding = true;
-
-  patches = [ ./relocation.patch ]
-    ++ stdenv.lib.optional stdenv.isDarwin ./hpc-7.8.4.patch;
-
-  preConfigure = ''
-    echo -n "${buildMK}" > mk/build.mk
-    sed -i -e 's|-isysroot /Developer/SDKs/MacOSX10.5.sdk||' configure
-  '' + stdenv.lib.optionalString (!stdenv.isDarwin) ''
-    export NIX_LDFLAGS+=" -rpath $out/lib/ghc-${version}"
-  '' + stdenv.lib.optionalString stdenv.isDarwin ''
-    export NIX_LDFLAGS+=" -no_dtrace_dof"
-  '';
-
-  # TODO(@Ericson2314): Always pass "--target" and always prefix.
-  configurePlatforms = [ "build" "host" ];
-
-  nativeBuildInputs = [ ghc perl ];
-  depsBuildTarget = [ targetPackages.stdenv.cc ];
-
-  buildInputs = libDeps;
-  propagatedBuildInputs = [ targetPackages.stdenv.cc ];
-
-  depsTargetTarget = map stdenv.lib.getDev libDeps;
-  depsTargetTargetPropagated = map (stdenv.lib.getOutput "out") libDeps;
-
-  # required, because otherwise all symbols from HSffi.o are stripped, and
-  # that in turn causes GHCi to abort
-  stripDebugFlags = [ "-S" ] ++ stdenv.lib.optional (!stdenv.isDarwin) "--keep-file-symbols";
-
-  passthru = {
-    targetPrefix = "";
-
-    # Our Cabal compiler name
-    haskellCompilerName = "ghc-7.8.4";
-  };
-
-  meta = {
-    homepage = http://haskell.org/ghc;
-    description = "The Glasgow Haskell Compiler";
-    maintainers = with stdenv.lib.maintainers; [ marcweber andres peti ];
-    inherit (ghc.meta) license platforms;
-  };
-
-}
--- a/pkgs/development/compilers/ghc/fix-7.0.4-clang.patch
+++ b/pkgs/development/compilers/ghc/fix-7.0.4-clang.patch
@ -1,74 +0,0 @@
-diff --git a/compiler/codeGen/CgInfoTbls.hs b/compiler/codeGen/CgInfoTbls.hs
-index f704a69..37753fd 100644
--- a/compiler/codeGen/CgInfoTbls.hs
-+++ b/compiler/codeGen/CgInfoTbls.hs
-@@ -211,9 +211,7 @@ mkStackLayout = do
-                     [(offset - frame_sp - retAddrSizeW, b)
-                     | (offset, b) <- binds]
- 
-  WARN( not (all (\bind -> fst bind >= 0) rel_binds),
-	ppr binds $$ ppr rel_binds $$
-        ppr frame_size $$ ppr real_sp $$ ppr frame_sp )
-+  WARN( not (all (\bind -> fst bind >= 0) rel_binds), ppr binds $$ ppr rel_binds $$ ppr frame_size $$ ppr real_sp $$ ppr frame_sp )
-     return $ stack_layout rel_binds frame_size
- 
- stack_layout :: [(VirtualSpOffset, CgIdInfo)]
-diff --git a/compiler/main/GHC.hs b/compiler/main/GHC.hs
-index 638e1db..0aee4b7 100644
--- a/compiler/main/GHC.hs
-+++ b/compiler/main/GHC.hs
-@@ -788,8 +788,7 @@ load2 how_much mod_graph = do
- 	    -- is stable).
- 	    partial_mg
- 		| LoadDependenciesOf _mod <- how_much
-		= ASSERT( case last partial_mg0 of 
-			    AcyclicSCC ms -> ms_mod_name ms == _mod; _ -> False )
-+		= ASSERT( case last partial_mg0 of AcyclicSCC ms -> ms_mod_name ms == _mod; _ -> False )
- 		  List.init partial_mg0
- 		| otherwise
- 		= partial_mg0
-@@ -879,8 +878,7 @@ load2 how_much mod_graph = do
- 	      liftIO $ cleanTempFilesExcept dflags (ppFilesFromSummaries mods_to_keep)
- 
- 	      -- there should be no Nothings where linkables should be, now
-	      ASSERT(all (isJust.hm_linkable) 
-			(eltsUFM (hsc_HPT hsc_env))) do
-+	      ASSERT(all (isJust.hm_linkable) (eltsUFM (hsc_HPT hsc_env))) do
- 	
- 	      -- Link everything together
-               linkresult <- liftIO $ link (ghcLink dflags) dflags False hpt4
-diff --git a/compiler/simplCore/SimplUtils.lhs b/compiler/simplCore/SimplUtils.lhs
-index 99a63e4..3268726 100644
--- a/compiler/simplCore/SimplUtils.lhs
-+++ b/compiler/simplCore/SimplUtils.lhs
-@@ -388,8 +388,7 @@ mkArgInfo fun rules n_val_args call_cont
- 		   else
- 			map isStrictDmd demands ++ vanilla_stricts
- 	       | otherwise
-	       -> WARN( True, text "More demands than arity" <+> ppr fun <+> ppr (idArity fun) 
-				<+> ppr n_val_args <+> ppr demands ) 
-+	       -> WARN( True, text "More demands than arity" <+> ppr fun <+> ppr (idArity fun) <+> ppr n_val_args <+> ppr demands ) 
- 		   vanilla_stricts	-- Not enough args, or no strictness
- 
-     add_type_str :: Type -> [Bool] -> [Bool]
-@@ -1812,4 +1811,4 @@ without getting changed to c1=I# c2.
- I don't think this is worth fixing, even if I knew how. It'll
- all come out in the next pass anyway.
- 
-  
-\ No newline at end of file
-+  
-diff --git a/compiler/simplCore/Simplify.lhs b/compiler/simplCore/Simplify.lhs
-index d0fbd8d..ef87996 100644
--- a/compiler/simplCore/Simplify.lhs
-+++ b/compiler/simplCore/Simplify.lhs
-@@ -2071,8 +2071,7 @@ mkDupableAlt env case_bndr (con, bndrs', rhs')
- 		      	     rhs = mkConApp dc (map Type (tyConAppArgs scrut_ty)
- 			     	   	        ++ varsToCoreExprs bndrs')
- 
-		      LitAlt {} -> WARN( True, ptext (sLit "mkDupableAlt")
-		      	     	   	        <+> ppr case_bndr <+> ppr con )
-+		      LitAlt {} -> WARN( True, ptext (sLit "mkDupableAlt") <+> ppr case_bndr <+> ppr con )
- 			           case_bndr
- 		      	   -- The case binder is alive but trivial, so why has 
- 		      	   -- it not been substituted away?
--- a/pkgs/development/compilers/ghc/fix-7.2.2-clang.patch
+++ b/pkgs/development/compilers/ghc/fix-7.2.2-clang.patch
@ -1,74 +0,0 @@
-diff --git a/compiler/codeGen/CgInfoTbls.hs b/compiler/codeGen/CgInfoTbls.hs
-index dbd22f3..42208f9 100644
--- a/compiler/codeGen/CgInfoTbls.hs
-+++ b/compiler/codeGen/CgInfoTbls.hs
-@@ -210,9 +210,7 @@ mkStackLayout = do
-                     [(offset - frame_sp - retAddrSizeW, b)
-                     | (offset, b) <- binds]
- 
-  WARN( not (all (\bind -> fst bind >= 0) rel_binds),
-	ppr binds $$ ppr rel_binds $$
-        ppr frame_size $$ ppr real_sp $$ ppr frame_sp )
-+  WARN( not (all (\bind -> fst bind >= 0) rel_binds), ppr binds $$ ppr rel_binds $$ ppr frame_size $$ ppr real_sp $$ ppr frame_sp )
-     return $ stack_layout rel_binds frame_size
- 
- stack_layout :: [(VirtualSpOffset, CgIdInfo)]
-diff --git a/compiler/main/GhcMake.hs b/compiler/main/GhcMake.hs
-index dece548..9643f30 100644
--- a/compiler/main/GhcMake.hs
-+++ b/compiler/main/GhcMake.hs
-@@ -236,8 +236,7 @@ load2 how_much mod_graph = do
- 	    -- is stable).
- 	    partial_mg
- 		| LoadDependenciesOf _mod <- how_much
-		= ASSERT( case last partial_mg0 of 
-			    AcyclicSCC ms -> ms_mod_name ms == _mod; _ -> False )
-+		= ASSERT( case last partial_mg0 of AcyclicSCC ms -> ms_mod_name ms == _mod; _ -> False )
- 		  List.init partial_mg0
- 		| otherwise
- 		= partial_mg0
-@@ -331,8 +330,7 @@ load2 how_much mod_graph = do
-               liftIO $ intermediateCleanTempFiles dflags mods_to_keep hsc_env1
- 
- 	      -- there should be no Nothings where linkables should be, now
-	      ASSERT(all (isJust.hm_linkable) 
-			(eltsUFM (hsc_HPT hsc_env))) do
-+	      ASSERT(all (isJust.hm_linkable) (eltsUFM (hsc_HPT hsc_env))) do
- 	
- 	      -- Link everything together
-               linkresult <- liftIO $ link (ghcLink dflags) dflags False hpt4
-diff --git a/compiler/simplCore/SimplUtils.lhs b/compiler/simplCore/SimplUtils.lhs
-index dd0ce4b..9501e73 100644
--- a/compiler/simplCore/SimplUtils.lhs
-+++ b/compiler/simplCore/SimplUtils.lhs
-@@ -393,8 +393,7 @@ mkArgInfo fun rules n_val_args call_cont
- 		   else
- 			map isStrictDmd demands ++ vanilla_stricts
- 	       | otherwise
-	       -> WARN( True, text "More demands than arity" <+> ppr fun <+> ppr (idArity fun) 
-				<+> ppr n_val_args <+> ppr demands ) 
-+	       -> WARN( True, text "More demands than arity" <+> ppr fun <+> ppr (idArity fun) <+> ppr n_val_args <+> ppr demands ) 
- 		   vanilla_stricts	-- Not enough args, or no strictness
- 
-     add_type_str :: Type -> [Bool] -> [Bool]
-@@ -1845,4 +1844,4 @@ without getting changed to c1=I# c2.
- I don't think this is worth fixing, even if I knew how. It'll
- all come out in the next pass anyway.
- 
-  
-\ No newline at end of file
-+  
-diff --git a/compiler/simplCore/Simplify.lhs b/compiler/simplCore/Simplify.lhs
-index adcaf13..06d939d 100644
--- a/compiler/simplCore/Simplify.lhs
-+++ b/compiler/simplCore/Simplify.lhs
-@@ -2185,8 +2185,7 @@ mkDupableAlt env case_bndr (con, bndrs', rhs')
- 		      	     rhs = mkConApp dc (map Type (tyConAppArgs scrut_ty)
- 			     	   	        ++ varsToCoreExprs bndrs')
- 
-		      LitAlt {} -> WARN( True, ptext (sLit "mkDupableAlt")
-		      	     	   	        <+> ppr case_bndr <+> ppr con )
-+		      LitAlt {} -> WARN( True, ptext (sLit "mkDupableAlt") <+> ppr case_bndr <+> ppr con )
- 			           case_bndr
- 		      	   -- The case binder is alive but trivial, so why has 
- 		      	   -- it not been substituted away?
--- a/pkgs/development/compilers/ghc/fix-7.4.2-clang.patch
+++ b/pkgs/development/compilers/ghc/fix-7.4.2-clang.patch
@ -1,57 +0,0 @@
-diff --git a/compiler/codeGen/CgInfoTbls.hs b/compiler/codeGen/CgInfoTbls.hs
-index 25ba154..fbb7874 100644
--- a/compiler/codeGen/CgInfoTbls.hs
-+++ b/compiler/codeGen/CgInfoTbls.hs
-@@ -178,9 +178,7 @@ mkStackLayout = do
-                     [(offset - frame_sp - retAddrSizeW, b)
-                     | (offset, b) <- binds]
- 
-  WARN( not (all (\bind -> fst bind >= 0) rel_binds),
-        pprPlatform platform binds $$ pprPlatform platform rel_binds $$
-        ppr frame_size $$ ppr real_sp $$ ppr frame_sp )
-+  WARN( not (all (\bind -> fst bind >= 0) rel_binds), pprPlatform platform binds $$ pprPlatform platform rel_binds $$ ppr frame_size $$ ppr real_sp $$ ppr frame_sp )
-     return $ stack_layout rel_binds frame_size
- 
- stack_layout :: [(VirtualSpOffset, CgIdInfo)]
-diff --git a/compiler/main/GhcMake.hs b/compiler/main/GhcMake.hs
-index 091e1be..23447e4 100644
--- a/compiler/main/GhcMake.hs
-+++ b/compiler/main/GhcMake.hs
-@@ -338,8 +338,7 @@ load2 how_much mod_graph = do
-               liftIO $ intermediateCleanTempFiles dflags mods_to_keep hsc_env1
- 
-               -- there should be no Nothings where linkables should be, now
-              ASSERT(all (isJust.hm_linkable) 
-                        (eltsUFM (hsc_HPT hsc_env))) do
-+              ASSERT(all (isJust.hm_linkable) (eltsUFM (hsc_HPT hsc_env))) do
-         
-               -- Link everything together
-               linkresult <- liftIO $ link (ghcLink dflags) dflags False hpt4
-diff --git a/compiler/simplCore/SimplUtils.lhs b/compiler/simplCore/SimplUtils.lhs
-index 86dc88d..ecde4fd 100644
--- a/compiler/simplCore/SimplUtils.lhs
-+++ b/compiler/simplCore/SimplUtils.lhs
-@@ -407,8 +407,7 @@ mkArgInfo fun rules n_val_args call_cont
- 		   else
- 			map isStrictDmd demands ++ vanilla_stricts
- 	       | otherwise
-	       -> WARN( True, text "More demands than arity" <+> ppr fun <+> ppr (idArity fun) 
-				<+> ppr n_val_args <+> ppr demands ) 
-+	       -> WARN( True, text "More demands than arity" <+> ppr fun <+> ppr (idArity fun) <+> ppr n_val_args <+> ppr demands ) 
- 		   vanilla_stricts	-- Not enough args, or no strictness
- 
-     add_type_str :: Type -> [Bool] -> [Bool]
-diff --git a/compiler/simplCore/Simplify.lhs b/compiler/simplCore/Simplify.lhs
-index 3bd95a7..4c9ee7c 100644
--- a/compiler/simplCore/Simplify.lhs
-+++ b/compiler/simplCore/Simplify.lhs
-@@ -2336,8 +2336,7 @@ mkDupableAlt env case_bndr (con, bndrs', rhs')
- 		      	     rhs = mkConApp dc (map Type (tyConAppArgs scrut_ty)
- 			     	   	        ++ varsToCoreExprs bndrs')
- 
-		      LitAlt {} -> WARN( True, ptext (sLit "mkDupableAlt")
-		      	     	   	        <+> ppr case_bndr <+> ppr con )
-+		      LitAlt {} -> WARN( True, ptext (sLit "mkDupableAlt") <+> ppr case_bndr <+> ppr con )
- 			           case_bndr
- 		      	   -- The case binder is alive but trivial, so why has 
- 		      	   -- it not been substituted away?
--- a/pkgs/development/compilers/ghc/fix-7.6.3-clang.patch
+++ b/pkgs/development/compilers/ghc/fix-7.6.3-clang.patch
@ -1,71 +0,0 @@
-diff --git a/compiler/codeGen/CgInfoTbls.hs b/compiler/codeGen/CgInfoTbls.hs
-index 7cdb1b6..e953507 100644
--- a/compiler/codeGen/CgInfoTbls.hs
-+++ b/compiler/codeGen/CgInfoTbls.hs
-@@ -157,9 +157,7 @@ mkStackLayout = do
-                     [(offset - frame_sp - retAddrSizeW, b)
-                     | (offset, b) <- binds]
- 
-  WARN( not (all (\bind -> fst bind >= 0) rel_binds),
-        ppr binds $$ ppr rel_binds $$
-        ppr frame_size $$ ppr real_sp $$ ppr frame_sp )
-+  WARN( not (all (\bind -> fst bind >= 0) rel_binds), ppr binds $$ ppr rel_binds $$ ppr frame_size $$ ppr real_sp $$ ppr frame_sp )
-     return $ stack_layout rel_binds frame_size
- 
- stack_layout :: [(VirtualSpOffset, CgIdInfo)]
-diff --git a/compiler/main/GhcMake.hs b/compiler/main/GhcMake.hs
-index f563cd9..4ac7812 100644
--- a/compiler/main/GhcMake.hs
-+++ b/compiler/main/GhcMake.hs
-@@ -331,8 +331,7 @@ load how_much = do
-           liftIO $ intermediateCleanTempFiles dflags mods_to_keep hsc_env1
- 
-           -- there should be no Nothings where linkables should be, now
-          ASSERT(all (isJust.hm_linkable) 
-                    (eltsUFM (hsc_HPT hsc_env))) do
-+          ASSERT(all (isJust.hm_linkable) (eltsUFM (hsc_HPT hsc_env))) do
-     
-           -- Link everything together
-           linkresult <- liftIO $ link (ghcLink dflags) dflags False hpt4
-diff --git a/compiler/simplCore/SimplUtils.lhs b/compiler/simplCore/SimplUtils.lhs
-index 87aefba..479d2ef 100644
--- a/compiler/simplCore/SimplUtils.lhs
-+++ b/compiler/simplCore/SimplUtils.lhs
-@@ -415,8 +415,7 @@ mkArgInfo fun rules n_val_args call_cont
- 		   else
- 			map isStrictDmd demands ++ vanilla_stricts
- 	       | otherwise
-	       -> WARN( True, text "More demands than arity" <+> ppr fun <+> ppr (idArity fun) 
-				<+> ppr n_val_args <+> ppr demands ) 
-+	       -> WARN( True, text "More demands than arity" <+> ppr fun <+> ppr (idArity fun) <+> ppr n_val_args <+> ppr demands ) 
- 		   vanilla_stricts	-- Not enough args, or no strictness
- 
-     add_type_str :: Type -> [Bool] -> [Bool]
-diff --git a/compiler/simplCore/Simplify.lhs b/compiler/simplCore/Simplify.lhs
-index f2ed224..464fad6 100644
--- a/compiler/simplCore/Simplify.lhs
-+++ b/compiler/simplCore/Simplify.lhs
-@@ -2359,8 +2359,7 @@ mkDupableAlt env case_bndr (con, bndrs', rhs')
- 		      	     rhs = mkConApp dc (map Type (tyConAppArgs scrut_ty)
- 			     	   	        ++ varsToCoreExprs bndrs')
- 
-		      LitAlt {} -> WARN( True, ptext (sLit "mkDupableAlt")
-		      	     	   	        <+> ppr case_bndr <+> ppr con )
-+		      LitAlt {} -> WARN( True, ptext (sLit "mkDupableAlt") <+> ppr case_bndr <+> ppr con )
- 			           case_bndr
- 		      	   -- The case binder is alive but trivial, so why has 
- 		      	   -- it not been substituted away?
-diff --git a/compiler/types/Coercion.lhs b/compiler/types/Coercion.lhs
-index 42e54ba..9b420ae 100644
--- a/compiler/types/Coercion.lhs
-+++ b/compiler/types/Coercion.lhs
-@@ -498,8 +498,7 @@ splitForAllCo_maybe _                = Nothing
- coVarKind :: CoVar -> (Type,Type) 
- coVarKind cv
-  | Just (tc, [_kind,ty1,ty2]) <- splitTyConApp_maybe (varType cv)
- = ASSERT (tc `hasKey` eqPrimTyConKey)
-   (ty1,ty2)
-+ = ASSERT (tc `hasKey` eqPrimTyConKey) (ty1,ty2)
-  | otherwise = panic "coVarKind, non coercion variable"
- 
- -- | Makes a coercion type from two types: the types whose equality 
--- a/pkgs/development/compilers/ghc/hpc-7.8.4.patch
+++ b/pkgs/development/compilers/ghc/hpc-7.8.4.patch
@ -1,13 +0,0 @@
-diff --git a/compiler/cmm/CLabel.hs b/compiler/cmm/CLabel.hs
-index 991fc57..0aad221 100644
--- a/compiler/cmm/CLabel.hs
-+++ b/compiler/cmm/CLabel.hs
-@@ -877,7 +877,7 @@ labelDynamic dflags this_pkg this_mod lbl =
- 
-    PlainModuleInitLabel m -> not (gopt Opt_Static dflags) && this_pkg /= (modulePackageId m)
- 
-   HpcTicksLabel m        -> not (gopt Opt_Static dflags) && this_pkg /= (modulePackageId m)
-+   HpcTicksLabel m        -> not (gopt Opt_Static dflags) && this_mod /= m
- 
-    -- Note that DynamicLinkerLabels do NOT require dynamic linking themselves.
-    _                 -> False
--- a/pkgs/development/compilers/teyjus/default.nix
+++ b/pkgs/development/compilers/teyjus/default.nix
@ -1,11 +1,15 @@
 { stdenv, fetchurl, omake, ocaml, flex, bison }:

+let
+  version = "2.1";
+in
+
 stdenv.mkDerivation {
-  name = "teyjus-2.1";
+  name = "teyjus-${version}";

  src = fetchurl {
-    url = "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/teyjus/teyjus-source-2.0-b2.tar.gz";
-    sha256 = "0llhm5nrfyj7ihz2qq1q9ijrh6y4f8vl39mpfkkad5bh1m3gp2gm";
+    url = "https://github.com/teyjus/teyjus/archive/v${version}.tar.gz";
+    sha256 = "0393wpg8v1vvarqy2xh4fdmrwlrl6jaj960kql7cq79mb9p3m269";
  };

  patches = [ ./fix-lex-to-flex.patch ];
--- a/pkgs/development/compilers/teyjus/fix-lex-to-flex.patch
+++ b/pkgs/development/compilers/teyjus/fix-lex-to-flex.patch
@ -1,9 +1,9 @@
 diff --git a/source/OMakefile b/source/OMakefile
-index 6b19d84..095b8b6 100644
+index e6bd37e..1bbc0a8 100644
 --- a/source/OMakefile
 +++ b/source/OMakefile
-@@ -164,12 +164,17 @@ LNK_MAIN = $(FNT)/linkerfront
- DEP_MAIN = $(FNT)/dependfront
+@@ -184,6 +184,12 @@ DEP_MAIN = $(FNT)/dependfront
+ PAR_MAIN = $(FNT)/parsefront
 
 ############################################################
 +# Nixpkgs specific changes
@ -15,9 +15,11 @@ index 6b19d84..095b8b6 100644
 # Platform specific changes
 #
 
+@@ -194,7 +200,6 @@ if $(mem $(SYSNAME), Linux)
+ 
 if $(mem $(OSTYPE), Cygwin Win32)
     YACC = bison -by
 -    LEX = flex
-     CFLAGS += -mno-cygwin
+     CC = i686-pc-mingw32-gcc
     INC_C[] += $(INC)/byteswap $(INC)/search
     export
--- a/pkgs/development/haskell-modules/configuration-common.nix
+++ b/pkgs/development/haskell-modules/configuration-common.nix
@ -80,7 +80,7 @@ self: super: {
      name = "git-annex-${drv.version}-src";
      url = "git://git-annex.branchable.com/";
      rev = "refs/tags/" + drv.version;
-      sha256 = "0fdcv9nig896ckl9x51ximxsvja1ii8qysf6c9ickvc0511hvr9w";
+      sha256 = "0qi5wpsvw6g8xrri1pr0401370acs5sg75myr0h5mjad6pvqc667";
    };
  })).overrideScope (self: super: {
    aws = dontCheck (self.aws_0_18);
@ -618,7 +618,7 @@ self: super: {
  }));

  # Need newer versions of their dependencies than the ones we have in LTS-11.x.
-  cabal2nix = super.cabal2nix.overrideScope (self: super: { hpack = self.hpack_0_28_1; hackage-db = self.hackage-db_2_0_1; });
+  cabal2nix = super.cabal2nix.overrideScope (self: super: { hpack = self.hpack_0_28_2; hackage-db = self.hackage-db_2_0_1; });

  # https://github.com/bos/configurator/issues/22
  configurator = dontCheck super.configurator;
@ -827,9 +827,6 @@ self: super: {
  fluid-idl-http-client = markBroken super.fluid-idl-http-client;
  fluid-idl-scotty = markBroken super.fluid-idl-scotty;

-  # Build with gi overloading feature disabled.
-  ltk = super.ltk.overrideScope (self: super: { haskell-gi-overloading = self.haskell-gi-overloading_0_0; });
-
  # missing dependencies: Glob >=0.7.14 && <0.8, data-fix ==0.0.4
  stack2nix = doJailbreak super.stack2nix;

@ -928,7 +925,7 @@ self: super: {
  haddock-api = super.haddock-api.override { haddock-library = self.haddock-library_1_4_4; };

  # Jailbreak "unix-compat >=0.1.2 && <0.5".
-  darcs = overrideCabal super.darcs (drv: { preConfigure = "sed -i -e 's/unix-compat .*,/unix-compat,/' darcs.cabal"; });
+  darcs = overrideCabal super.darcs (drv: { preConfigure = "sed -i -e 's/unix-compat .*,/unix-compat,/' -e 's/fgl .*,/fgl,/' darcs.cabal"; });

  # https://github.com/Twinside/Juicy.Pixels/issues/149
  JuicyPixels = dontHaddock super.JuicyPixels;
--- a/pkgs/development/haskell-modules/configuration-ghc-8.4.x.nix
+++ b/pkgs/development/haskell-modules/configuration-ghc-8.4.x.nix
@ -42,9 +42,6 @@ self: super: {
  unix = null;
  xhtml = null;

-  # https://github.com/bitemyapp/esqueleto/issues/77
-  esqueleto = markBrokenVersion "2.5.3" super.esqueleto;
-
  # Need newer version.
  haskell-src = super.haskell-src_1_0_3_0;

@ -733,6 +730,6 @@ self: super: {
    });

  # https://github.com/jgm/pandoc-types/issues/37
-  pandoc-types = self.pandoc-types_1_17_4;
+  pandoc-types = self.pandoc-types_1_17_4_1;

 }
--- a/pkgs/development/haskell-modules/configuration-hackage2nix.yaml
+++ b/pkgs/development/haskell-modules/configuration-hackage2nix.yaml
--- a/pkgs/development/haskell-modules/generic-builder.nix
+++ b/pkgs/development/haskell-modules/generic-builder.nix
@ -24,13 +24,13 @@ in
 , doBenchmark ? false
 , doHoogle ? true
 , editedCabalFile ? null
-, enableLibraryProfiling ? false
+, enableLibraryProfiling ? true
 , enableExecutableProfiling ? false
+, profilingDetail ? "all-functions"
 # TODO enable shared libs for cross-compiling
-, enableSharedExecutables ? ((ghc.isGhcjs or false) || stdenv.lib.versionOlder "7.7" ghc.version)
+, enableSharedExecutables ? false
 , enableSharedLibraries ? ((ghc.isGhcjs or false) || stdenv.lib.versionOlder "7.7" ghc.version)
-, enableSplitObjs ? null # OBSOLETE, use enableDeadCodeElimination
-, enableDeadCodeElimination ? (!stdenv.isDarwin)  # TODO: use -dead_strip  for darwin
+, enableDeadCodeElimination ? (!stdenv.isDarwin)  # TODO: use -dead_strip for darwin
 , enableStaticLibraries ? true
 , extraLibraries ? [], librarySystemDepends ? [], executableSystemDepends ? []
 , homepage ? "http://hackage.haskell.org/package/${pname}"
@ -66,8 +66,6 @@ in
 } @ args:

 assert editedCabalFile != null -> revision != null;
-# OBSOLETE, use enableDeadCodeElimination
-assert enableSplitObjs == null;

 let

@ -135,12 +133,15 @@ let
    (optionalString useCpphs "--with-cpphs=${cpphs}/bin/cpphs --ghc-options=-cpp --ghc-options=-pgmP${cpphs}/bin/cpphs --ghc-options=-optP--cpp")
    (enableFeature (enableDeadCodeElimination && !hostPlatform.isArm && !hostPlatform.isAarch64 && (versionAtLeast "8.0.1" ghc.version)) "split-objs")
    (enableFeature enableLibraryProfiling "library-profiling")
+    (optionalString (enableExecutableProfiling || enableLibraryProfiling) "--profiling-detail=${profilingDetail}")
    (enableFeature enableExecutableProfiling (if versionOlder ghc.version "8" then "executable-profiling" else "profiling"))
    (enableFeature enableSharedLibraries "shared")
    (optionalString (versionAtLeast ghc.version "7.10") (enableFeature doCoverage "coverage"))
-    (optionalString (isGhcjs || versionOlder "7" ghc.version) (enableFeature enableStaticLibraries "library-vanilla"))
+    (optionalString (versionOlder "8.4" ghc.version) (enableFeature enableStaticLibraries "static"))
    (optionalString (isGhcjs || versionOlder "7.4" ghc.version) (enableFeature enableSharedExecutables "executable-dynamic"))
    (optionalString (isGhcjs || versionOlder "7" ghc.version) (enableFeature doCheck "tests"))
+    "--enable-library-vanilla"  # TODO: Should this be configurable?
+    "--enable-library-for-ghci" # TODO: Should this be configurable?
  ] ++ optionals (enableDeadCodeElimination && (stdenv.lib.versionOlder "8.0.1" ghc.version)) [
     "--ghc-option=-split-sections"
  ] ++ optionals isGhcjs [
--- a/pkgs/development/haskell-modules/hackage-packages.nix
+++ b/pkgs/development/haskell-modules/hackage-packages.nix
--- a/pkgs/development/interpreters/elixir/1.6.nix
+++ b/pkgs/development/interpreters/elixir/1.6.nix
@ -1,7 +1,7 @@
 { mkDerivation }:

 mkDerivation rec {
-  version = "1.6.2";
-  sha256 = "18f5afmvra78y0x73bfnwbddlyqfndyaj1h8n1ybj32w4nvy96y7";
+  version = "1.6.4";
+  sha256 = "0li2zb5ha7fdkjnzjbj3dxb9xls8xn6xr23fqwl7gp2697vcw3ws";
  minimumOTPVersion = "18";
 }
--- a/pkgs/development/libraries/CGAL/default.nix
+++ b/pkgs/development/libraries/CGAL/default.nix
@ -1,14 +1,14 @@
 { stdenv, fetchFromGitHub, cmake, boost, gmp, mpfr }:

 stdenv.mkDerivation rec {
-  version = "4.11";
+  version = "4.11.1";
  name = "cgal-" + version;

  src = fetchFromGitHub {
    owner = "CGAL";
    repo = "releases";
    rev = "CGAL-${version}";
-    sha256 = "126r06aba5h8l73xmm5mwmxkir7sy122jn2j18cd4gz3z9p23npr";
+    sha256 = "04nn1lzsjdglzjygc72cq09xrvpqwwnbf6l0xz8bfwfp4x9g10jf";
  };

  # note: optional component libCGAL_ImageIO would need zlib and opengl;
--- a/pkgs/development/libraries/aws-sdk-cpp/default.nix
+++ b/pkgs/development/libraries/aws-sdk-cpp/default.nix
@ -15,13 +15,13 @@ let
        else throw "Unsupported system!";
 in stdenv.mkDerivation rec {
  name = "aws-sdk-cpp-${version}";
-  version = "1.3.22";
+  version = "1.4.10";

  src = fetchFromGitHub {
    owner = "awslabs";
    repo = "aws-sdk-cpp";
    rev = version;
-    sha256 = "0sdgy8kqhxnw7n0sw4m3p3ay7yic3rhad5ab8m5lbx61ad9bq3c2";
+    sha256 = "0gw0ph6v2w4zqmixqfw5ab08c0r3d7iy2z1hll5pydlp5vwfmn7g";
  };

  # FIXME: might be nice to put different APIs in different outputs
--- a/pkgs/development/libraries/nss/85_security_load.patch
+++ b/pkgs/development/libraries/nss/85_security_load.patch
@ -13,10 +13,10 @@ diff -ru -x '*~' -x '*.orig' -x '*.rej' nss/cmd/shlibsign/shlibsign.c nss/cmd/sh
 diff -ru -x '*~' -x '*.orig' -x '*.rej' nss/coreconf/config.mk nss/coreconf/config.mk
 --- nss/coreconf/config.mk	2017-01-04 15:24:24.000000000 +0100
 +++ nss/coreconf/config.mk	2017-01-24 14:43:47.989432372 +0100
-@@ -208,3 +208,6 @@
- # exported symbols, which causes problem when NSS is built as part of Mozilla.
- # So we add a NSS_SSL_ENABLE_ZLIB variable to allow Mozilla to turn this off.
- NSS_SSL_ENABLE_ZLIB = 1
+@@ -202,3 +202,6 @@
+ 
+ # Hide old, deprecated, TLS cipher suite names when building NSS
+ DEFINES += -DSSL_DISABLE_DEPRECATED_CIPHER_SUITE_NAMES
 +
 +# Nix specific stuff.
 +DEFINES += -DNIX_NSS_LIBDIR=\"$(out)/lib/\"
--- a/pkgs/development/libraries/nss/default.nix
+++ b/pkgs/development/libraries/nss/default.nix
@ -9,11 +9,11 @@ let

 in stdenv.mkDerivation rec {
  name = "nss-${version}";
-  version = "3.34.1";
+  version = "3.35";

  src = fetchurl {
-    url = "mirror://mozilla/security/nss/releases/NSS_3_34_1_RTM/src/${name}.tar.gz";
-    sha256 = "186x33wsk4mzjz7dzbn8p0py9a0nzkgzpfkdv4rlyy5gghv5vhd3";
+    url = "mirror://mozilla/security/nss/releases/NSS_3_35_RTM/src/${name}.tar.gz";
+    sha256 = "1ypn68z9ncbbshi3184ywrhx5i846lyd72gps1grzqzdkgh7s4pl";
  };

  buildInputs = [ perl zlib sqlite ]
--- a/pkgs/development/r-modules/bioc-annotation-packages.nix
+++ b/pkgs/development/r-modules/bioc-annotation-packages.nix
@ -131,6 +131,7 @@ in with self; {
  IlluminaHumanMethylationEPICanno_ilm10b3_hg19 = derive2 { name="IlluminaHumanMethylationEPICanno.ilm10b3.hg19"; version="0.6.0"; sha256="1rdkvbpbz8a8bd9ipycfmgn8a3x519abhwywka21ii9ziv3s6ah6"; depends=[minfi]; };
  IlluminaHumanMethylationEPICanno_ilm10b4_hg19 = derive2 { name="IlluminaHumanMethylationEPICanno.ilm10b4.hg19"; version="0.6.0"; sha256="0687b4k8hwfc18qgdd9ypv1skp37jd204fszba0gmrv3dc92i09c"; depends=[minfi]; };
  IlluminaHumanMethylationEPICmanifest = derive2 { name="IlluminaHumanMethylationEPICmanifest"; version="0.3.0"; sha256="0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"; depends=[minfi]; };
+  JASPAR2018 = derive2 { name="JASPAR2018"; version="1.0.0"; sha256="1j82wsayzn6zn7irihpc8jivvwfsdrckik0ypajsv3pgrb5b3naa"; depends=[]; };
  JazaeriMetaData_db = derive2 { name="JazaeriMetaData.db"; version="3.2.3"; sha256="04lvcmm4ybxkfwgbiwcnpyj6kpbd0gd7jz6ijlbbvv6zdgdmvykb"; depends=[AnnotationDbi org_Hs_eg_db]; };
  KEGG_db = derive2 { name="KEGG.db"; version="3.2.3"; sha256="0qv9in1nmnqcbjxh0y45x33xyw9zdp4jf5hmlvcsh1pclcq4dsh2"; depends=[AnnotationDbi]; };
  LAPOINTE_db = derive2 { name="LAPOINTE.db"; version="3.2.3"; sha256="0960gy5p4ybs5zs6251cgc3nk5a9gsh1nh23gkbkr3gc8jddinfm"; depends=[AnnotationDbi org_Hs_eg_db]; };
--- a/pkgs/development/r-modules/bioc-packages.nix
+++ b/pkgs/development/r-modules/bioc-packages.nix
@ -23,7 +23,7 @@ in with self; {
  ASSET = derive2 { name="ASSET"; version="1.16.0"; sha256="12863h5f7ib3p26ghim2h0l7zn51y3624rihsybj5lpycnxkam9q"; depends=[MASS msm mvtnorm rmeta tmvnsim]; };
  ASSIGN = derive2 { name="ASSIGN"; version="1.14.0"; sha256="12g1dh35azv1z5bc7n7gyr0vnyyi2r2jrvi6x0gyikbdszxwfysx"; depends=[ggplot2 gplots msm Rlab sva]; };
  ASpli = derive2 { name="ASpli"; version="1.4.0"; sha256="19v9p4brgrzijin759n1q8zjrlksrzhmczi1nwhsjgbg47f35vs7"; depends=[AnnotationDbi BiocGenerics BiocStyle edgeR GenomicAlignments GenomicFeatures GenomicRanges Gviz IRanges Rsamtools S4Vectors]; };
-  ATACseqQC = derive2 { name="ATACseqQC"; version="1.2.8"; sha256="11l1cpfcadhdrcy5qdmq9gd18if8rs5xw4b5m0ky8gxgxmfpd2wq"; depends=[BiocGenerics Biostrings BSgenome ChIPpeakAnno GenomeInfoDb GenomicAlignments GenomicRanges GenomicScores IRanges limma motifStack randomForest Rsamtools rtracklayer S4Vectors]; };
+  ATACseqQC = derive2 { name="ATACseqQC"; version="1.2.10"; sha256="0f1j89an2rckjrmvvmy6crmrgz2jxgmmajhx333crl8jjqi1aqm8"; depends=[BiocGenerics Biostrings BSgenome ChIPpeakAnno GenomeInfoDb GenomicAlignments GenomicRanges GenomicScores IRanges limma motifStack randomForest Rsamtools rtracklayer S4Vectors]; };
  AUCell = derive2 { name="AUCell"; version="1.0.0"; sha256="0b6az665vpdkp82xcr4xgric3nw9204g47rj4316s30l5w5l1j2v"; depends=[data_table GSEABase mixtools R_utils SummarizedExperiment]; };
  AffyCompatible = derive2 { name="AffyCompatible"; version="1.38.0"; sha256="1lxxpldgrsl0nf63cfhbqpraylfb3118y4j8q4xknr7x8pj95gns"; depends=[Biostrings RCurl XML]; };
  AffyExpress = derive2 { name="AffyExpress"; version="1.44.0"; sha256="0nwvgkh9nc9gag9dh85g3x4d5125p00c9jc55knpr11jraj2xifw"; depends=[affy limma]; };
@ -54,7 +54,7 @@ in with self; {
  BEclear = derive2 { name="BEclear"; version="1.10.0"; sha256="1skkqzph89lx9cwlgyd2xmn1808sn5byfa8mqdq6w60j6vwplpzn"; depends=[Matrix snowfall]; };
  BGmix = derive2 { name="BGmix"; version="1.38.0"; sha256="1778bm1hx8bw00n0l3d5jvfldc7hqmpg2w1nbsc3c017rd1l2ryk"; depends=[KernSmooth]; };
  BHC = derive2 { name="BHC"; version="1.30.0"; sha256="0j8sb6ifq2nxvlarm1zqa89yzfs3si4w43ily9nnbmlnhngr6d0m"; depends=[]; };
-  BLMA = derive2 { name="BLMA"; version="1.3.2"; sha256="1dwhhqsvah7ds7v2jd2khkabcg7222g2bfi0q5dd1xqkd15mq0j3"; depends=[Biobase graph GSA limma PADOG ROntoTools]; };
+  BLMA = derive2 { name="BLMA"; version="1.3.3"; sha256="1qxj3izpv4pphq515kqq5qcsg1p847knpm961pcipmikbzxrvfqw"; depends=[Biobase graph GSA limma PADOG ROntoTools]; };
  BPRMeth = derive2 { name="BPRMeth"; version="1.4.0"; sha256="0b7p2z69zjxrza2qfgpg6dfk96r9gfjm3v4qzafjy0hrbcfi2d74"; depends=[assertthat data_table doParallel e1071 earth foreach GenomicRanges IRanges MASS randomForest S4Vectors]; };
  BRAIN = derive2 { name="BRAIN"; version="1.24.0"; sha256="0cxci3clyz98r8vx6cq49ypc3s3bkhx8rx0h60r54va6gbp1j2lm"; depends=[Biostrings lattice PolynomF]; };
  BSgenome = derive2 { name="BSgenome"; version="1.46.0"; sha256="1jbzq7lm2iajajn2bifxnkss0k9fdvgqr30mral17cbhp5f6w4lq"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools rtracklayer S4Vectors XVector]; };
@ -69,7 +69,7 @@ in with self; {
  BayesKnockdown = derive2 { name="BayesKnockdown"; version="1.4.0"; sha256="1dkch2md8fi23i3pg90rzxy185v6953jhz4l2icgglxhp15ydmfp"; depends=[Biobase]; };
  BayesPeak = derive2 { name="BayesPeak"; version="1.30.0"; sha256="1f8r1z7mmh40nrfqj1b3drjli6zb6hm645a9xi39claid2kvfh9z"; depends=[IRanges]; };
  BeadDataPackR = derive2 { name="BeadDataPackR"; version="1.30.0"; sha256="153ks6bbhqzdkl88wvszjg5f67hr0gnf1mnhn6crq7i3pjy1jw0m"; depends=[]; };
-  BgeeDB = derive2 { name="BgeeDB"; version="2.4.0"; sha256="1jha16jqbj5jzanky16ihn0sqvx0k50hh1p5xw1m4ssi86dnx42x"; depends=[Biobase data_table digest dplyr graph RCurl tidyr topGO]; };
+  BgeeDB = derive2 { name="BgeeDB"; version="2.5.0"; sha256="08q93yk0hb4sbavk7i1z2qdklhl87f70ywr7xnq26r5frxcpcxm6"; depends=[Biobase data_table digest dplyr graph RCurl tidyr topGO]; };
  BiGGR = derive2 { name="BiGGR"; version="1.14.0"; sha256="1frxzj99qh94ll1xsvvnmgnfai7wfzchsqdrk2s0cp7z40yng13b"; depends=[hyperdraw hypergraph LIM limSolve rsbml stringr]; };
  BiRewire = derive2 { name="BiRewire"; version="3.10.0"; sha256="08z2h5fq1nm192s2vwzv1q6sp82axkk81p05bib71wl5vg0j5fpk"; depends=[igraph Matrix slam tsne]; };
  BiSeq = derive2 { name="BiSeq"; version="1.18.0"; sha256="0277lknj60gniwx4vr3ffd46gldzgjr7lbw8xy5xzdd0wa45wanz"; depends=[betareg Biobase BiocGenerics Formula GenomeInfoDb GenomicRanges globaltest IRanges lokern rtracklayer S4Vectors SummarizedExperiment]; };
@ -106,7 +106,7 @@ in with self; {
  CATALYST = derive2 { name="CATALYST"; version="1.2.0"; sha256="1q31zzi15q2z46wsk3p4fvq8imxjkyywi849h5jyrvnxhca28mbz"; depends=[drc flowCore ggplot2 gridExtra matrixStats plotly RColorBrewer reshape2]; };
  CAnD = derive2 { name="CAnD"; version="1.10.0"; sha256="17nzlplz9d8dhzm546bznwmz20p7lxnsvq35qd09a3rdcf1abz77"; depends=[ggplot2 reshape]; };
  CCPROMISE = derive2 { name="CCPROMISE"; version="1.4.0"; sha256="0r0aardhmz76zd5lj1qzwyva8la0jv9wczfmak3r0pp2axaw13yr"; depends=[Biobase CCP GSEABase PROMISE]; };
-  CEMiTool = derive2 { name="CEMiTool"; version="1.0.1"; sha256="1pqdnyxmpcp5gjf2w00cf1msbc96d8q9vdqbafg4x2fv83m9ivbq"; depends=[clusterProfiler data_table DT fgsea ggdendro ggplot2 ggpmisc ggrepel ggthemes gRbase gridExtra gtable htmltools igraph intergraph knitr matrixStats network pracma rmarkdown scales sna stringr WGCNA]; };
+  CEMiTool = derive2 { name="CEMiTool"; version="1.0.3"; sha256="07ighg7y1rpx00xylg1yhd03fvs2yi215rfyii8ckzwf8l9829l4"; depends=[clusterProfiler data_table DT fgsea ggdendro ggplot2 ggpmisc ggrepel ggthemes gRbase gridExtra gtable htmltools igraph intergraph knitr matrixStats network pracma rmarkdown scales sna stringr WGCNA]; };
  CFAssay = derive2 { name="CFAssay"; version="1.12.0"; sha256="01yakrkpbs43013936rh8qd4giiz7y7cp9jrdx9i4p6h5h8jzj28"; depends=[]; };
  CGEN = derive2 { name="CGEN"; version="3.14.0"; sha256="14s1j2h5cb2gfgn73yvb933ng63cr9i8lx8hisd0g8lcfi2b5rxw"; depends=[mvtnorm survival]; };
  CGHbase = derive2 { name="CGHbase"; version="1.38.0"; sha256="0fynvcsjdbgp69i0nxrc8ni58rhb1kx9k5r3nb91n9i8s43gjqlm"; depends=[Biobase marray]; };
@ -152,9 +152,9 @@ in with self; {
  ChIPQC = derive2 { name="ChIPQC"; version="1.14.0"; sha256="1nnmgzad7kzydrmz374f9xvf8s13q6vhanz93v6d9jqh6jnd5di0"; depends=[Biobase BiocGenerics BiocParallel chipseq DiffBind GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gtools IRanges Nozzle_R1 reshape2 Rsamtools S4Vectors TxDb_Celegans_UCSC_ce6_ensGene TxDb_Dmelanogaster_UCSC_dm3_ensGene TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Mmusculus_UCSC_mm10_knownGene TxDb_Mmusculus_UCSC_mm9_knownGene TxDb_Rnorvegicus_UCSC_rn4_ensGene]; };
  ChIPXpress = derive2 { name="ChIPXpress"; version="1.22.0"; sha256="0wcs7gw0kgvbk1f4i8j9cr8kwv1lj45zv9q069cify78rdb106rb"; depends=[affy biganalytics bigmemory Biobase ChIPXpressData frma GEOquery]; };
  ChIPanalyser = derive2 { name="ChIPanalyser"; version="1.0.0"; sha256="02w4k41wx9cqfk0zjzcv8vdfgwv9rswijmdrsbmcpbrmbwn2jlxi"; depends=[Biostrings BSgenome GenomicRanges IRanges RcppRoll S4Vectors]; };
-  ChIPexoQual = derive2 { name="ChIPexoQual"; version="1.2.0"; sha256="0n0bpwiff3lbirvmzbamjvxa2957wsl0kixfh1hnsr0hqgs3swqf"; depends=[BiocParallel biovizBase broom data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 hexbin IRanges RColorBrewer rmarkdown Rsamtools S4Vectors scales viridis]; };
+  ChIPexoQual = derive2 { name="ChIPexoQual"; version="1.3.2"; sha256="0hh7ppc4fsil7vczng897dkzz2a1x0s2j2qvw1v2g8hm82mv070k"; depends=[BiocParallel biovizBase broom data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 hexbin IRanges RColorBrewer rmarkdown Rsamtools S4Vectors scales viridis]; };
  ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.12.7"; sha256="1zab489d7a6bh6ylc68x6yn47gdkmr7p3677grx9l2qafrryjr04"; depends=[AnnotationDbi Biobase BiocGenerics BiocInstaller biomaRt Biostrings BSgenome DBI DelayedArray ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GO_db graph idr IRanges limma matrixStats multtest RBGL regioneR Rsamtools S4Vectors seqinr SummarizedExperiment VennDiagram]; };
-  ChIPseeker = derive2 { name="ChIPseeker"; version="1.14.1"; sha256="1819hny2azpj3wpp09yyqllx668p98ja3ds5a65c0hxy8vbmjxpz"; depends=[AnnotationDbi BiocGenerics boot DOSE dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gridBase gtools IRanges magrittr plotrix RColorBrewer rtracklayer S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene UpSetR]; };
+  ChIPseeker = derive2 { name="ChIPseeker"; version="1.14.2"; sha256="1db2k7j0rr9q8jlfxlji62zyhzfh7yhsacyg1dj5sgwbhhn0xliy"; depends=[AnnotationDbi BiocGenerics boot DOSE dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gridBase gtools IRanges magrittr plotrix RColorBrewer rtracklayer S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene UpSetR]; };
  ChIPseqR = derive2 { name="ChIPseqR"; version="1.32.0"; sha256="0igqlfr5grhkr7dsdyg3c31d3r1wpn413vxmzlckiimfwdi35rqv"; depends=[BiocGenerics Biostrings fBasics GenomicRanges HilbertVis IRanges S4Vectors ShortRead timsac]; };
  ChIPsim = derive2 { name="ChIPsim"; version="1.32.0"; sha256="01kmhzyvnp03v9xydm9xrrkdmlf5dpsnzzcf13i9r03x3m44r4ga"; depends=[Biostrings IRanges ShortRead XVector]; };
  ChemmineOB = derive2 { name="ChemmineOB"; version="1.16.2"; sha256="0zrg6f5cg54f1bpwjhx2h97w267jr2gyncgfyjs7njkjwwrl9ads"; depends=[BH BiocGenerics Rcpp zlibbioc]; };
@ -179,7 +179,7 @@ in with self; {
  CoverageView = derive2 { name="CoverageView"; version="1.16.0"; sha256="1091mxiclb3zhr48bdj7z8gi3v69l4w25cfpfbxhhp70rffn9xfr"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors]; };
  CrispRVariants = derive2 { name="CrispRVariants"; version="1.6.0"; sha256="15za6ysnnjfwmiq2dhbpr3kww6c2jvc2y1mf8rfpqx56bd1dh3cb"; depends=[AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges reshape2 Rsamtools S4Vectors]; };
  CytoML = derive2 { name="CytoML"; version="1.4.1"; sha256="1jj79adwrzwx012xvw3czv0m94jc3j2ibpijdfbz8fpjhynrzwqb"; depends=[base64enc Biobase data_table flowCore flowUtils flowWorkspace ggcyto graph jsonlite ncdfFlow openCyto plyr RBGL Rgraphviz XML]; };
-  DAPAR = derive2 { name="DAPAR"; version="1.10.3"; sha256="1xkfw2zjy8wj8x5mddyzw1632zhb2dvdnqp5ikmf1n1bi1mq0ya4"; depends=[AnnotationDbi Cairo clusterProfiler cp4p DAPARdata doParallel dplyr foreach ggplot2 gplots graph highcharter imp4p impute imputeLCMD knitr lattice limma lme4 Matrix MSnbase norm openxlsx pcaMethods png preprocessCore RColorBrewer readxl reshape2 scales siggenes tidyr tmvtnorm vioplot]; };
+  DAPAR = derive2 { name="DAPAR"; version="1.10.4"; sha256="15ghdx2yccsk98bmynljiwdfkjjfqafq62wc87zsgydql59c10kh"; depends=[AnnotationDbi Cairo clusterProfiler cp4p DAPARdata doParallel dplyr foreach ggplot2 gplots graph highcharter imp4p impute imputeLCMD knitr lattice limma lme4 Matrix MSnbase norm openxlsx pcaMethods png preprocessCore RColorBrewer readxl reshape2 scales siggenes tidyr tmvtnorm vioplot]; };
  DART = derive2 { name="DART"; version="1.26.0"; sha256="15hqsdi7pa1qn5c5af2izhf609c7lmb0zsv2qwyc9xbf7dn42qmf"; depends=[igraph]; };
  DASC = derive2 { name="DASC"; version="0.99.11"; sha256="1wm43kgvq3wkwp8hmz70m9c7yxxjsanpqxvcm6x63bna02ysb90y"; depends=[Biobase cvxclustr NMF]; };
  DBChIP = derive2 { name="DBChIP"; version="1.22.0"; sha256="07psmmvcdl4r5m71kccd9rd3vk521ilhwmcll37pfrmb16s1856x"; depends=[DESeq edgeR]; };
@ -193,7 +193,7 @@ in with self; {
  DEP = derive2 { name="DEP"; version="1.0.1"; sha256="0glkq6xlhcsr364zl4nkc7g3gnscv0yb3kcyvhzgm3bbfvd9q7ac"; depends=[assertthat Biobase broom circlize ComplexHeatmap dplyr DT fdrtool ggplot2 ggrepel gridExtra imputeLCMD limma MSnbase purrr RColorBrewer readr rmarkdown shiny shinydashboard SummarizedExperiment tibble tidyr vsn]; };
  DESeq = derive2 { name="DESeq"; version="1.30.0"; sha256="0mn5w3cy16iwwk8zxs7za6aa6cnrca75z0g45zd5zh1py5d7nfv9"; depends=[Biobase BiocGenerics genefilter geneplotter lattice locfit MASS RColorBrewer]; };
  DESeq2 = derive2 { name="DESeq2"; version="1.18.1"; sha256="1iyimg1s0x5pdmvl8x08s8h0v019y0nhjzs50chagbpk2x91fsmv"; depends=[Biobase BiocGenerics BiocParallel genefilter geneplotter GenomicRanges ggplot2 Hmisc IRanges locfit Rcpp RcppArmadillo S4Vectors SummarizedExperiment]; };
-  DEXSeq = derive2 { name="DEXSeq"; version="1.24.2"; sha256="18nh8ynxirfwkmc4sawdxgl7w1sl9ny5zpv8zbhv9vi5vgb8pxmj"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; };
+  DEXSeq = derive2 { name="DEXSeq"; version="1.24.3"; sha256="0xip73hlbr3zry9d7ly9vvvsbb3xjcmfa09lr9fdy528dwjrf084"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; };
  DEsubs = derive2 { name="DEsubs"; version="1.4.0"; sha256="1i9blymzj18r9646vac9grrjxw6xar8m6chn1dgdila17jag1wlp"; depends=[circlize DESeq DESeq2 EBSeq edgeR ggplot2 graph igraph jsonlite limma locfit Matrix NBPSeq pheatmap RBGL samr]; };
  DFP = derive2 { name="DFP"; version="1.36.0"; sha256="117gmzcgr9wr9wb7g0rm7wlrakd76ys1frhmhx1k6ps97ibxlz1k"; depends=[Biobase]; };
  DMCHMM = derive2 { name="DMCHMM"; version="1.0.0"; sha256="1y0wmxks51h0d21v8g4mryq7kzq49khhpa88fbhza9xp2bmwk358"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; };
@ -255,7 +255,7 @@ in with self; {
  FGNet = derive2 { name="FGNet"; version="3.12.0"; sha256="1f33k7dx7f97kzjpq1jvs614vjsyg3yd03s2y7xxwhydmx02n7vs"; depends=[hwriter igraph plotrix png R_utils RColorBrewer reshape2 XML]; };
  FISHalyseR = derive2 { name="FISHalyseR"; version="1.12.0"; sha256="07q5paypybw8qq17wyl7qqlrdy5kfg2k24rj2ic4gjgb6qiic38b"; depends=[abind EBImage]; };
  FRGEpistasis = derive2 { name="FRGEpistasis"; version="1.14.0"; sha256="1nyw8h4kjddn75878adhlilwjnm4wlyhksyp2ygx6cm35fbqa2v3"; depends=[fda MASS]; };
-  FamAgg = derive2 { name="FamAgg"; version="1.6.0"; sha256="0p87aidqbzdwhihsnaammv1i5yb0rvhs0xrjlmq64z6q9ffj7k32"; depends=[BiocGenerics gap igraph kinship2 Matrix survey]; };
+  FamAgg = derive2 { name="FamAgg"; version="1.6.1"; sha256="02fy27g8vi9byhnfav0121291jbwiypnj1r9i56hbgwwzplqbr5z"; depends=[BiocGenerics gap igraph kinship2 Matrix survey]; };
  FindMyFriends = derive2 { name="FindMyFriends"; version="1.8.0"; sha256="13f6hdjn4l5xfrdskq2abpzczxcm8sy71fqpfj6hsxzj06fz9a36"; depends=[Biobase BiocGenerics BiocParallel Biostrings digest dplyr filehash ggdendro ggplot2 gtable igraph IRanges kebabs Matrix Rcpp reshape2 S4Vectors]; };
  FitHiC = derive2 { name="FitHiC"; version="1.4.0"; sha256="12ylhrppi051m7nqsgq95kzd9g9wmp34i0zzfi55cjqawlpx7c6n"; depends=[data_table fdrtool Rcpp]; };
  FlowRepositoryR = derive2 { name="FlowRepositoryR"; version="1.10.0"; sha256="0mgqnmznqpy8ikzg1829bjgxnznm43wkgirhpgfskdxfzr4zqs3a"; depends=[jsonlite RCurl XML]; };
@ -270,7 +270,7 @@ in with self; {
  GENESIS = derive2 { name="GENESIS"; version="2.8.1"; sha256="0w3xrw6a1fkcp49nyarkp4yykjk79gqq7rzwixdk4363d5pnm7gp"; depends=[Biobase BiocGenerics gdsfmt GenomicRanges graph GWASTools IRanges S4Vectors SeqArray SeqVarTools]; };
  GENIE3 = derive2 { name="GENIE3"; version="1.0.0"; sha256="1lxbkhlvb082nrmlq2b57chi0vpyaqwj56ngbzli8qdmp1gz4qd3"; depends=[reshape2]; };
  GEOmetadb = derive2 { name="GEOmetadb"; version="1.40.0"; sha256="003inwm8qkjdaihlx4009nwj3rgjn3xdk0m8k696qhniq99gcd0a"; depends=[GEOquery RSQLite]; };
-  GEOquery = derive2 { name="GEOquery"; version="2.46.14"; sha256="12m6l95qjip33rw97qymc2i0wpmdmsvswlcp93b3gssxslpzkqzi"; depends=[Biobase dplyr httr limma magrittr readr tidyr xml2]; };
+  GEOquery = derive2 { name="GEOquery"; version="2.46.15"; sha256="1l5vcksida44zkrqvrp9krqd4yhn6xh24y9jfvkyjvhq4x8fl18z"; depends=[Biobase dplyr httr limma magrittr readr tidyr xml2]; };
  GEOsearch = derive2 { name="GEOsearch"; version="1.1.4"; sha256="0k0vn99rz2821gswb834nn9ib099a152y2828ka7qvhag4shzdy9"; depends=[org_Hs_eg_db org_Mm_eg_db RCurl]; };
  GEOsubmission = derive2 { name="GEOsubmission"; version="1.30.0"; sha256="0sl9m7lk7jczpcfhn50yn322v1s65d9swjidcnzk3ydv47z419p8"; depends=[affy Biobase]; };
  GEWIST = derive2 { name="GEWIST"; version="1.22.0"; sha256="0lfm19s4z5j7zhpzhfa7rqdz09ip05cf2zbnsqv9widdmkcw2wnk"; depends=[car]; };
@ -323,7 +323,7 @@ in with self; {
  GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.30.3"; sha256="010vn8hlwbnw12pd1d8pv6m12yp3xwx557gba5rbjq9p4qypnn3z"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RMySQL RSQLite rtracklayer S4Vectors XVector]; };
  GenomicFiles = derive2 { name="GenomicFiles"; version="1.14.0"; sha256="0r0wmrs5jycf1kckhnc2sgjmp336srlcjdkpbb1ymm7kazdd0s9n"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; };
  GenomicInteractions = derive2 { name="GenomicInteractions"; version="1.12.0"; sha256="0f0ki2zsaxg6f4qr47xgyhxm6jvms0s1zab7f0vcnw8jd7vhmnzn"; depends=[Biobase BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph InteractionSet IRanges Rsamtools rtracklayer S4Vectors stringr]; };
-  GenomicRanges = derive2 { name="GenomicRanges"; version="1.30.2"; sha256="0c3r155603vb4zjs3adqa72770bh8karc11y8gl62l1m24jrkbnj"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; };
+  GenomicRanges = derive2 { name="GenomicRanges"; version="1.30.3"; sha256="07cszc9ri94nzk4dffwnsj247ih6pchnrzrvnb0q4dkk33gwy8n1"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; };
  GenomicScores = derive2 { name="GenomicScores"; version="1.2.2"; sha256="0g6i90vn29pasiqbq0088bgdisr356539z94scv7cila968inh7n"; depends=[AnnotationHub Biobase BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors XML]; };
  GenomicTuples = derive2 { name="GenomicTuples"; version="1.12.0"; sha256="0962l9204vm5x7vcqzlvlgblhdczwp4zbq4i262gqh79lnx4yq1y"; depends=[BiocGenerics data_table GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; };
  Genominator = derive2 { name="Genominator"; version="1.32.0"; sha256="1gh56xyfgx5f8rb0wbpvkg8h2q1ci2qf3ngkg3sficn65pbj9iha"; depends=[BiocGenerics DBI GenomeGraphs IRanges RSQLite]; };
@ -517,7 +517,7 @@ in with self; {
  PCAN = derive2 { name="PCAN"; version="1.6.0"; sha256="0inm1kfi9xvd3jhqivxh4vzc6vsijh1z7fwzsqb35rlbi2cl7snd"; depends=[BiocParallel]; };
  PCpheno = derive2 { name="PCpheno"; version="1.40.0"; sha256="1sgw116qif7w52va7qg8n51a40nvmhybvgr5nxlvgvrwylkhqfai"; depends=[annotate AnnotationDbi Biobase Category GO_db graph GSEABase KEGG_db ppiData ppiStats ScISI SLGI]; };
  PECA = derive2 { name="PECA"; version="1.14.0"; sha256="1c3nbsvng951fsg9vk3yki215f3abgsxqhd025gyvs120nw4c9kv"; depends=[affy aroma_affymetrix aroma_core genefilter limma preprocessCore ROTS]; };
-  PGA = derive2 { name="PGA"; version="1.8.0"; sha256="0x410vnwgdzdkx2i9pqj22mv8jzflswl35a6xkhkr0in47hgz806"; depends=[AnnotationDbi biomaRt Biostrings customProDB data_table GenomicFeatures GenomicRanges ggplot2 IRanges Nozzle_R1 pheatmap RCurl Rsamtools RSQLite rTANDEM rtracklayer S4Vectors stringr VariantAnnotation]; };
+  PGA = derive2 { name="PGA"; version="1.8.1"; sha256="14lm4ab7lib80wmkim4j72n4msmbx7nhlbv349cxrpc9k0dxmycm"; depends=[AnnotationDbi biomaRt Biostrings customProDB data_table GenomicFeatures GenomicRanges ggplot2 IRanges Nozzle_R1 pheatmap RCurl Rsamtools RSQLite rTANDEM rtracklayer S4Vectors stringr VariantAnnotation]; };
  PGSEA = derive2 { name="PGSEA"; version="1.52.0"; sha256="1g0kfhrvq8hv4lpwq3p3p6fkm2bmfjmkfw9312jrwnbjj0hfwd34"; depends=[annaffy AnnotationDbi Biobase GO_db KEGG_db]; };
  PICS = derive2 { name="PICS"; version="2.22.0"; sha256="0jb4hzswiyrqpnazfpd6wd11gdlmv18za7fyr4slxv0rc9rkf8qm"; depends=[BiocGenerics GenomicAlignments GenomicRanges IRanges Rsamtools S4Vectors]; };
  PING = derive2 { name="PING"; version="2.22.0"; sha256="1lvbl3g2m643nypc0nfmhjpfv4zl7qk457kg9i7y7l1lzqwqsk0s"; depends=[BiocGenerics BSgenome chipseq fda GenomicRanges Gviz IRanges PICS S4Vectors]; };
@ -545,7 +545,7 @@ in with self; {
  Polyfit = derive2 { name="Polyfit"; version="1.12.0"; sha256="1gkn6g5hwa8ss156armxam9ky5fd7dj0k3gh1b0gy5plpzzyzv1h"; depends=[DESeq]; };
  Prize = derive2 { name="Prize"; version="1.8.0"; sha256="1vaf4n69pb2sa6fd79988picz08d3c46cjmxfr5qf7hxay9lbwc6"; depends=[diagram ggplot2 gplots matrixcalc reshape2 stringr]; };
  ProCoNA = derive2 { name="ProCoNA"; version="1.16.0"; sha256="06jlzcr9b6nfrlgb1wqxp7r2z8042ygjx4d2z7jzg07hqn3gymjz"; depends=[BiocGenerics flashClust GOstats MSnbase WGCNA]; };
-  Prostar = derive2 { name="Prostar"; version="1.10.4"; sha256="12kdq40qnd7a1x0qcwfjiim03sh5hi9pix61mwdmmq0zc7pg54s3"; depends=[DAPAR DAPARdata data_table DT highcharter htmlwidgets rhandsontable shiny shinyAce shinyjs webshot]; };
+  Prostar = derive2 { name="Prostar"; version="1.10.5"; sha256="1z9qli85if894j6s4a21yq6990hamz3ql1399m2wjjzka3w8kd29"; depends=[DAPAR DAPARdata data_table DT highcharter htmlwidgets rhandsontable shiny shinyAce shinyjs webshot]; };
  ProtGenerics = derive2 { name="ProtGenerics"; version="1.10.0"; sha256="16ijp50448wnabp43klx943rhdvh7x45hvy7cnpq1s4dckxhhyni"; depends=[]; };
  ProteomicsAnnotationHubData = derive2 { name="ProteomicsAnnotationHubData"; version="1.8.0"; sha256="1myd5gqr3nmbp6f1n7ilp6qjcfgm401frm4ldvxbjyppxh6m1wh5"; depends=[AnnotationHub AnnotationHubData Biobase BiocInstaller Biostrings GenomeInfoDb MSnbase mzR RCurl]; };
  PureCN = derive2 { name="PureCN"; version="1.8.1"; sha256="12wpqwz771vzz5yad67d9j1jhgi5ccxngyqcjcddqwsiws65prwc"; depends=[BiocGenerics Biostrings data_table DNAcopy edgeR futile_logger GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges limma RColorBrewer Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation VGAM]; };
@ -562,7 +562,7 @@ in with self; {
  RBGL = derive2 { name="RBGL"; version="1.54.0"; sha256="18jad23i3899ypv4bg3l47cvvs3qnj1pqis2p9x0135yv5y6wnv7"; depends=[graph]; };
  RBM = derive2 { name="RBM"; version="1.10.0"; sha256="1nqmf9yiaam767f2wkwggnw6v0rymszx7chnkis0xbdsllzqb0j4"; depends=[limma marray]; };
  RBioinf = derive2 { name="RBioinf"; version="1.38.0"; sha256="01qk9ddk8bm9sl70rlwgmrkz2y7dnqzrhi13hhh0ii62s0z0gdwh"; depends=[graph]; };
-  RCAS = derive2 { name="RCAS"; version="1.4.2"; sha256="0d8mm3f0lxdvngldlazql2vcfv3w7172ari0g2lp3cj101d7pyd3"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot data_table DBI DT genomation GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo knitr motifRG org_Hs_eg_db pbapply pheatmap plotly plotrix proxy rmarkdown RSQLite rtracklayer S4Vectors topGO]; };
+  RCAS = derive2 { name="RCAS"; version="1.4.3"; sha256="0ajnhi8i9p755lr0l2j5j52d5j6rsilrjhm3zrjr1zsgwqm2an6z"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot data_table DBI DT genomation GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo knitr motifRG org_Hs_eg_db pbapply pheatmap plotly plotrix proxy rmarkdown RSQLite rtracklayer S4Vectors topGO]; };
  RCASPAR = derive2 { name="RCASPAR"; version="1.24.0"; sha256="1v19pv81q0g965mks88ablznzhcdk3kfd7j2dgxx4r12bl1afawg"; depends=[]; };
  RCy3 = derive2 { name="RCy3"; version="1.8.0"; sha256="09p66zxh82j5pcjz1zn3cg43rpsp0gnkwja836m6g1i450zrialv"; depends=[graph httr RCurl RJSONIO]; };
  RCyjs = derive2 { name="RCyjs"; version="1.10.0"; sha256="0vlyh32byw49j3vfw0avknixflpjs5h599xxlbf2zc6irvncg1wg"; depends=[base64enc BiocGenerics BrowserViz graph httpuv igraph jsonlite Rcpp]; };
@ -610,7 +610,7 @@ in with self; {
  Rariant = derive2 { name="Rariant"; version="1.14.0"; sha256="1kfw2gfvdgzi5ldarmmwnksgg256vfaripcridlsb2pgwzay52k4"; depends=[dplyr exomeCopy GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges reshape2 Rsamtools S4Vectors shiny SomaticSignatures VariantAnnotation VGAM]; };
  RbcBook1 = derive2 { name="RbcBook1"; version="1.46.0"; sha256="0qj8zvhq9cq3akdl6zpspvvz9jlvc0lxrn4ap7qd984406jihyg4"; depends=[Biobase graph rpart]; };
  Rbowtie = derive2 { name="Rbowtie"; version="1.18.0"; sha256="0v3x9i6wmps7x0zpvgimzfwarg4246nbk4cpa1kim46r5jkl5m4v"; depends=[]; };
-  Rbowtie2 = derive2 { name="Rbowtie2"; version="1.0.1"; sha256="1xplrih6sijbwj24k4lb0cml5pmyszmw5jzkaii5m3vign6m7wmh"; depends=[]; };
+  Rbowtie2 = derive2 { name="Rbowtie2"; version="1.0.2"; sha256="1cc2z55qzp3psnhii0d71dmb71d0s3wzl8dsyxyxcr95clp4irsi"; depends=[]; };
  Rcade = derive2 { name="Rcade"; version="1.20.0"; sha256="0awsdg6wfm6hykj96s8cgz2mhn2i4jl1yabg7xfj0nmd776gv5fa"; depends=[baySeq GenomeInfoDb GenomicAlignments GenomicRanges IRanges plotrix rgl Rsamtools S4Vectors]; };
  Rchemcpp = derive2 { name="Rchemcpp"; version="2.16.0"; sha256="1k5rgk944x0xy0y7l4fba1gfbiq6vnpbgmwwm520vv061v9g72nz"; depends=[ChemmineR Rcpp]; };
  RchyOptimyx = derive2 { name="RchyOptimyx"; version="2.18.0"; sha256="0lghahggrh3142rn9f2rnh517740d62bh7rc97zd2sjk3rfdb761"; depends=[flowType graph Rgraphviz sfsmisc]; };
@ -632,7 +632,7 @@ in with self; {
  Risa = derive2 { name="Risa"; version="1.20.0"; sha256="10ypbd9qwh1rk27fwm8naf3gl05w9zlw79qyr55pk5m6x5lnn9cb"; depends=[affy Biobase biocViews Rcpp xcms]; };
  Rmagpie = derive2 { name="Rmagpie"; version="1.34.0"; sha256="1hvv8pps0q7xnsl33rammqvyj191j5gs78r2333jgscxnw4byqb7"; depends=[Biobase e1071 kernlab pamr]; };
  RmiR = derive2 { name="RmiR"; version="1.34.0"; sha256="10n8i7qirbd8xrb73ccxyj7c6bi1szx263nwjh8w2j9x4dgzx22x"; depends=[DBI RmiR_Hs_miRNA RSVGTipsDevice]; };
-  RnBeads = derive2 { name="RnBeads"; version="1.10.7"; sha256="1rlxa161sgbz7p59svihk2ym70d1c5yi02rcajgp0fraf8ln8xhc"; depends=[BiocGenerics cluster ff fields GenomicRanges ggplot2 gplots gridExtra illuminaio IRanges limma MASS matrixStats methylumi plyr S4Vectors]; };
+  RnBeads = derive2 { name="RnBeads"; version="1.10.8"; sha256="1kawb781y7pscbmll69pzk4gnb0xz3s8llj3icy3c8y0arkg98xz"; depends=[BiocGenerics cluster ff fields GenomicRanges ggplot2 gplots gridExtra illuminaio IRanges limma MASS matrixStats methylumi plyr S4Vectors]; };
  RnaSeqGeneEdgeRQL = derive2 { name="RnaSeqGeneEdgeRQL"; version="1.1.0"; sha256="06i2fy89wck0jhpc174d81ka7jim8gjamjk0ym1j0fh3ldiw9yvm"; depends=[edgeR GO_db gplots org_Mm_eg_db]; };
  RnaSeqSampleSize = derive2 { name="RnaSeqSampleSize"; version="1.10.0"; sha256="1r0bn121bf5fcp4im4hm2c6rccgf7fb1vvxj2iri8ippc2k60d2c"; depends=[biomaRt edgeR heatmap3 KEGGREST matlab Rcpp RnaSeqSampleSizeData]; };
  Rnits = derive2 { name="Rnits"; version="1.12.0"; sha256="00ddzbjms9wpiinc021s4b50wbzdafnml96ngsmi7rd8ipr3k3vp"; depends=[affy Biobase boot ggplot2 impute limma qvalue reshape2]; };
@ -689,7 +689,7 @@ in with self; {
  SeqGSEA = derive2 { name="SeqGSEA"; version="1.18.0"; sha256="1vaqa6jkvwxpbqnz9wz3i6p26mky6d7d704cjv5as67j04v99b2a"; depends=[Biobase biomaRt DESeq doParallel]; };
  SeqSQC = derive2 { name="SeqSQC"; version="1.0.0"; sha256="0qj1y9zsjxkh08jkw80hl62072viincq1pvcz9r3i0m28nhk7pg5"; depends=[e1071 ExperimentHub gdsfmt GenomicRanges GGally ggplot2 IRanges rbokeh RColorBrewer reshape2 rmarkdown S4Vectors SNPRelate]; };
  SeqVarTools = derive2 { name="SeqVarTools"; version="1.16.0"; sha256="14n70xzj91f4rshl0kx549rqzy9rrv5mv0b0xvj891i8anxahb2n"; depends=[Biobase dplyr gdsfmt GenomicRanges GWASExactHW IRanges logistf S4Vectors SeqArray tidyr]; };
-  ShortRead = derive2 { name="ShortRead"; version="1.36.0"; sha256="06mknlsmd4hnaxzdjapgvp2kgdnf9w103y500dsac5jgsz4vwzcz"; depends=[Biobase BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges hwriter IRanges lattice latticeExtra Rsamtools S4Vectors XVector zlibbioc]; };
+  ShortRead = derive2 { name="ShortRead"; version="1.36.1"; sha256="1cyv47632m9ljkxfsvnvmd19sb607ys5kz8fwh6v39dnw16g0a6m"; depends=[Biobase BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges hwriter IRanges lattice latticeExtra Rsamtools S4Vectors XVector zlibbioc]; };
  SigCheck = derive2 { name="SigCheck"; version="2.10.0"; sha256="1k2xmb7jcjbdxafr8fspf9pbc0jwcll914lqc42gvhhjq6rnf8q4"; depends=[Biobase BiocParallel e1071 MLInterfaces survival]; };
  SigFuge = derive2 { name="SigFuge"; version="1.16.0"; sha256="0ddy6bayb05gsgh06p5awhjwyx57z0l8fb5x6p0dci2fgzy6gr4f"; depends=[GenomicRanges ggplot2 matlab reshape sigclust]; };
  SimBindProfiles = derive2 { name="SimBindProfiles"; version="1.16.0"; sha256="0jkd78wl5ksm05qjmsx7s8aznh3kfpi34yvxaxv763pqjqzkxa82"; depends=[Biobase limma mclust Ringo]; };
@ -840,7 +840,7 @@ in with self; {
  cghMCR = derive2 { name="cghMCR"; version="1.36.0"; sha256="10c6cnm2qbg0gb3klfv1xlwhbzj9x6aimxg7jnz29fgnn3xnd8cs"; depends=[BiocGenerics CNTools DNAcopy limma]; };
  charm = derive2 { name="charm"; version="2.24.0"; sha256="0zr96pwq7zd45lffl67fxvzrxhmjk8pmh8rfawhc7mmazds2ip9a"; depends=[Biobase Biostrings BSgenome ff fields genefilter gtools IRanges limma nor1mix oligo oligoClasses preprocessCore RColorBrewer siggenes SQN sva]; };
  chimera = derive2 { name="chimera"; version="1.20.0"; sha256="0z50pwynvyx2gc619b7w6chwdb7pxs2gf1ywh9vp7vzghkdv0wx4"; depends=[AnnotationDbi Biobase BSgenome_Hsapiens_UCSC_hg19 GenomicAlignments GenomicRanges Homo_sapiens Rsamtools TxDb_Hsapiens_UCSC_hg19_knownGene]; };
-  chimeraviz = derive2 { name="chimeraviz"; version="1.4.2"; sha256="1qqv2wzagq5kf4xijrvcm17bb1qgjjp2kx4fm2a8ky1rcwf50251"; depends=[AnnotationDbi AnnotationFilter ArgumentCheck BiocStyle Biostrings dplyr DT ensembldb GenomeInfoDb GenomicAlignments GenomicRanges graph Gviz IRanges org_Hs_eg_db plyr RCircos RColorBrewer readr Rgraphviz rmarkdown Rsamtools S4Vectors]; };
+  chimeraviz = derive2 { name="chimeraviz"; version="1.4.3"; sha256="1jwgra30lqi4zyyda2xcy7zkgnbidlxqfhh48bq8scfym0b34kjf"; depends=[AnnotationDbi AnnotationFilter ArgumentCheck BiocStyle Biostrings dplyr DT ensembldb GenomeInfoDb GenomicAlignments GenomicRanges graph Gviz IRanges org_Hs_eg_db plyr RCircos RColorBrewer readr Rgraphviz rmarkdown Rsamtools S4Vectors]; };
  chipenrich = derive2 { name="chipenrich"; version="2.2.0"; sha256="0q24il68grjqdxpy7qjk6lw6l5zlmw6yybrbrbb8l42gljyi6s74"; depends=[AnnotationDbi BiocGenerics chipenrich_data GenomeInfoDb GenomicRanges IRanges lattice latticeExtra mgcv org_Dm_eg_db org_Dr_eg_db org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db plyr rms rtracklayer S4Vectors stringr]; };
  chipseq = derive2 { name="chipseq"; version="1.28.0"; sha256="1ymcq77krwjzrkzzcw7i9909cmkqa7c0675z9wzvrrk81hgdssfq"; depends=[BiocGenerics GenomicRanges IRanges lattice S4Vectors ShortRead]; };
  chopsticks = derive2 { name="chopsticks"; version="1.42.0"; sha256="0awwk8k7vnsc0c1ic17m2mhmpin0s0ijd2gn7my9yysqzld9sncd"; depends=[survival]; };
@ -913,7 +913,7 @@ in with self; {
  derfinder = derive2 { name="derfinder"; version="1.12.6"; sha256="1bp8qw3m5crncwz586b4f4w1x0kcm6r39md3w8il2d9xlvjvmml0"; depends=[AnnotationDbi BiocParallel bumphunter derfinderHelper GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges Hmisc IRanges qvalue Rsamtools rtracklayer S4Vectors]; };
  derfinderHelper = derive2 { name="derfinderHelper"; version="1.12.0"; sha256="06aj2h98vm27pc1laxi7pjxhwxm756scl2r9d8f1x1gsg2aa0k1b"; depends=[IRanges Matrix S4Vectors]; };
  derfinderPlot = derive2 { name="derfinderPlot"; version="1.12.3"; sha256="1p0pqy2rdd4lmz91gyxwcm1gpnyb89qzy9j9fsm1jy84iaanan40"; depends=[derfinder GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 IRanges limma plyr RColorBrewer reshape2 S4Vectors scales]; };
-  destiny = derive2 { name="destiny"; version="2.6.1"; sha256="1gyjh9lgqql67zsm4zz4lg77kdw5wbgkl9mraaww1aich167aqfl"; depends=[Biobase BiocGenerics ggplot2 Hmisc igraph Matrix proxy Rcpp RcppEigen scales scatterplot3d smoother VIM]; };
+  destiny = derive2 { name="destiny"; version="2.6.2"; sha256="18id35mjlwnavqi04lzr47vj6y3j8y8g1rxb6hdc6dklajnvyyln"; depends=[Biobase BiocGenerics ggplot2 Hmisc igraph Matrix proxy Rcpp RcppEigen scales scatterplot3d smoother VIM]; };
  dexus = derive2 { name="dexus"; version="1.18.0"; sha256="1l9x51w1q58zvh53slcmw8rbb2v1sii380acap1frp4idi56wmig"; depends=[BiocGenerics]; };
  diffGeneAnalysis = derive2 { name="diffGeneAnalysis"; version="1.60.0"; sha256="0bfs3n9crca46q0cgkpknl4xf5vc4dr5anly9kn77prb1zp9b0p3"; depends=[minpack_lm]; };
  diffHic = derive2 { name="diffHic"; version="1.10.0"; sha256="0j7vmgpxakzk3gazdy06xhpcqnb19pib0jxfz67nc7fgkyrmhzqi"; depends=[BiocGenerics Biostrings BSgenome csaw edgeR GenomeInfoDb GenomicRanges InteractionSet IRanges limma locfit Rcpp rhdf5 Rhtslib Rsamtools S4Vectors SummarizedExperiment zlibbioc]; };
@ -930,7 +930,7 @@ in with self; {
  easyRNASeq = derive2 { name="easyRNASeq"; version="2.14.0"; sha256="11l0bj9wcp5k0a5nq0adn4w891cllfdn7qrqg76k7klx5h0p37bx"; depends=[Biobase BiocGenerics BiocParallel biomaRt Biostrings DESeq edgeR GenomeInfoDb genomeIntervals GenomicAlignments GenomicRanges IRanges locfit LSD Rsamtools S4Vectors ShortRead SummarizedExperiment]; };
  ecolitk = derive2 { name="ecolitk"; version="1.50.0"; sha256="0xagah7nrj6dghl2ib75l8wlwj7kzdssnlbpjdwhm67nsys3hvx4"; depends=[Biobase]; };
  edge = derive2 { name="edge"; version="2.10.0"; sha256="1knr03yiw0cq0kj9hklmkaap4qiphm2ph51bjn1m5cn7nyckramz"; depends=[Biobase jackstraw MASS qvalue snm sva]; };
-  edgeR = derive2 { name="edgeR"; version="3.20.8"; sha256="0g7bj6w61blw3m22hw9rc01n554k9qkjizh7njr3j4shmhads58d"; depends=[limma locfit Rcpp]; };
+  edgeR = derive2 { name="edgeR"; version="3.20.9"; sha256="0y52snwbz37xzdd7gihdkqczbndlfzmmypv6hri3ymjyfmlx6qaw"; depends=[limma locfit Rcpp]; };
  eegc = derive2 { name="eegc"; version="1.4.0"; sha256="1v3586qddx1l74ha083x36m3lqdblrhmwd63k22jzfpkh30adz09"; depends=[AnnotationDbi clusterProfiler DESeq2 DOSE edgeR ggplot2 gplots igraph limma org_Hs_eg_db org_Mm_eg_db pheatmap R_utils S4Vectors sna wordcloud]; };
  eiR = derive2 { name="eiR"; version="1.18.0"; sha256="1ypd7yq9c6mqp7nm984dm60qzvwy4qb81zrp2mvp7g87c5vdj2a3"; depends=[BiocGenerics ChemmineR DBI digest gespeR RcppAnnoy RCurl RUnit snow snowfall]; };
  eisa = derive2 { name="eisa"; version="1.30.0"; sha256="11ydmv5kddq75sknbax1aiyxq60rx146qa7pd3m09axjzvk83mq5"; depends=[AnnotationDbi Biobase BiocGenerics Category DBI genefilter isa2]; };
@ -945,7 +945,7 @@ in with self; {
  epivizrStandalone = derive2 { name="epivizrStandalone"; version="1.6.0"; sha256="0rbd2kmdi0y97mx72gkg93s97slfig1k1bgcv5maknsqqqcwzz8j"; depends=[BiocGenerics epivizr epivizrServer GenomeInfoDb GenomicFeatures git2r S4Vectors]; };
  erccdashboard = derive2 { name="erccdashboard"; version="1.12.0"; sha256="07dc80l8618rlv3sywr0gp9i49kq66i9glx3md2r0k5c4l67mw37"; depends=[edgeR ggplot2 gplots gridExtra gtools limma locfit MASS plyr qvalue reshape2 ROCR scales stringr]; };
  erma = derive2 { name="erma"; version="0.10.0"; sha256="0gcfs9g8vvdv5vmq9b21kd8sq5mizjj49nfzd4in9zvp4b9v7x1g"; depends=[AnnotationDbi Biobase BiocGenerics foreach GenomicFiles GenomicRanges ggplot2 Homo_sapiens rtracklayer S4Vectors shiny SummarizedExperiment]; };
-  esATAC = derive2 { name="esATAC"; version="1.0.19"; sha256="1ikihh939c8iqm9w582s0kjmnh7yqgnj3dq8y8vfvpbill4f2zyd"; depends=[AnnotationDbi BiocGenerics BiocInstaller Biostrings BSgenome ChIPseeker clusterProfiler corrplot DiagrammeR digest GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 igraph IRanges JASPAR2016 knitr magrittr R_utils Rbowtie2 Rcpp rJava rmarkdown Rsamtools rtracklayer S4Vectors ShortRead TFBSTools VennDiagram]; };
+  esATAC = derive2 { name="esATAC"; version="1.0.23"; sha256="1g2pai0b98dfnng4h7w2xs73qp2dqacmx8x3ackqi6a515x0cyaf"; depends=[AnnotationDbi BiocGenerics BiocInstaller Biostrings BSgenome ChIPseeker clusterProfiler corrplot DiagrammeR digest GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 igraph IRanges JASPAR2016 knitr magrittr R_utils Rbowtie2 Rcpp rJava rmarkdown Rsamtools rtracklayer S4Vectors ShortRead TFBSTools VennDiagram]; };
  esetVis = derive2 { name="esetVis"; version="1.4.0"; sha256="1yb238lxy8sqmxim3zd25rp642cpz8p25vdffjlija2wivq8phn1"; depends=[Biobase hexbin MASS MLP mpm Rtsne]; };
  eudysbiome = derive2 { name="eudysbiome"; version="1.8.0"; sha256="13ayrigzy55h6an3am9f77r6mzcvyfcpxpby71xilhaf6mjhyj39"; depends=[Biostrings plyr R_utils Rsamtools]; };
  exomeCopy = derive2 { name="exomeCopy"; version="1.24.0"; sha256="17rpa7mck2rrivrv5vqk4abb094v79v8dbzh6n5dj4hnw53b9wif"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; };
@ -971,7 +971,7 @@ in with self; {
  flowCL = derive2 { name="flowCL"; version="1.16.2"; sha256="1zaic9cf7xw4qmdcrhi9a9zcxvxlnn9iii0a6lnwwkpsspgn1bnj"; depends=[graph Rgraphviz SPARQL]; };
  flowClean = derive2 { name="flowClean"; version="1.16.0"; sha256="1crpgaw1bilvgcyr93c2qx6jbx18ca52dzr6r8cqznlfxdnz48jj"; depends=[bit changepoint flowCore sfsmisc]; };
  flowClust = derive2 { name="flowClust"; version="3.16.0"; sha256="1c8ppgy4i42l250m71ri3gbw8mw1yw2saplx9wrhnykvwxnsx210"; depends=[Biobase BiocGenerics clue ellipse flowCore flowViz graph MCMCpack mnormt RBGL]; };
-  flowCore = derive2 { name="flowCore"; version="1.44.1"; sha256="1ain06wjny8f5khpf6cmz683rzq1jfidk4p3mz1v5ybw54dxvl7z"; depends=[BH Biobase BiocGenerics corpcor graph matrixStats Rcpp rrcov]; };
+  flowCore = derive2 { name="flowCore"; version="1.44.2"; sha256="09vp822nrhyfxibwh22g2rdl4yv6n4w1rm7hy9hkz8rsbpbdbwv4"; depends=[BH Biobase BiocGenerics corpcor graph matrixStats Rcpp rrcov]; };
  flowCyBar = derive2 { name="flowCyBar"; version="1.14.0"; sha256="06wzxlw02x5nzn5qc91yjawrmimsns2kmw4rm3rgbh10d4qh8r09"; depends=[gplots vegan]; };
  flowDensity = derive2 { name="flowDensity"; version="1.12.0"; sha256="1df181ilq7mnwlfvyjjvgd262f2sq09c5wg5fpf531m5jiaj6qpk"; depends=[car flowCore flowWorkspace GEOmap gplots RFOC rgeos sp]; };
  flowFP = derive2 { name="flowFP"; version="1.36.0"; sha256="0kpw90pxappz3mbidfqjv8l6cpc4qg2hgi1wqh4rzx8b2bdl5a8f"; depends=[Biobase BiocGenerics flowCore flowViz]; };
@ -981,7 +981,7 @@ in with self; {
  flowMeans = derive2 { name="flowMeans"; version="1.38.0"; sha256="0mqgblmfili3nxnfz5h0hrhdl6wz4ylnslyx17kw7pyd0wskd26v"; depends=[Biobase feature flowCore rrcov]; };
  flowMerge = derive2 { name="flowMerge"; version="2.26.0"; sha256="0lpgipgrirhc5i5qzby1krg7vbd4jg566y3i5k18lxsccws12zx6"; depends=[feature flowClust flowCore foreach graph Rgraphviz rrcov snow]; };
  flowPeaks = derive2 { name="flowPeaks"; version="1.22.0"; sha256="0cs0sbs9cx3syjv3dhl9b56s8ccpb00cwz9z18j31yaijl1h13vi"; depends=[]; };
-  flowPloidy = derive2 { name="flowPloidy"; version="1.4.1"; sha256="1iqyc6b8lp22lr4xik4ibixc4x6grxvmg18bp2dflp6xkyy7vrq5"; depends=[car caTools flowCore knitr minpack_lm rmarkdown shiny]; };
+  flowPloidy = derive2 { name="flowPloidy"; version="1.4.2"; sha256="15z3laz0g3agv9dhga29myhmri5w6ivj10rivq4r0kv7lql1wzlx"; depends=[car caTools flowCore knitr minpack_lm rmarkdown shiny]; };
  flowPlots = derive2 { name="flowPlots"; version="1.26.0"; sha256="0bg523vxnk3kjwwplqykamdfqmyr7b0laxkml06rfr0rbj5lcdc5"; depends=[]; };
  flowQ = derive2 { name="flowQ"; version="1.38.0"; sha256="1vxc7fn747x7i2v0nv821nx9z1d5d4dyd6fa0vbmn7smjkbdxbzd"; depends=[BiocGenerics bioDist flowCore flowViz geneplotter IRanges lattice latticeExtra mvoutlier outliers parody RColorBrewer]; };
  flowQB = derive2 { name="flowQB"; version="2.6.0"; sha256="04hjsswngbxi40rxcb13hzvzm8y7yzpr6qzwhnishp0a5614rzka"; depends=[extremevalues flowCore]; };
@ -992,7 +992,7 @@ in with self; {
  flowUtils = derive2 { name="flowUtils"; version="1.42.0"; sha256="0d4ab30xp722h9avi785wj8z1qz7dy65z5faqf3jc6j6v40bzikq"; depends=[Biobase corpcor flowCore graph RUnit XML]; };
  flowVS = derive2 { name="flowVS"; version="1.10.0"; sha256="07vcqcxzd9cw4hvc1yld2v05zcxqs5p9spka2l80pmsjr0aij043"; depends=[flowCore flowStats flowViz]; };
  flowViz = derive2 { name="flowViz"; version="1.42.0"; sha256="1fbr0snid9vgb133sb5dwkk469n465p8r490r67vsmm8wqsf6iyl"; depends=[Biobase flowCore hexbin IDPmisc KernSmooth lattice latticeExtra MASS RColorBrewer]; };
-  flowWorkspace = derive2 { name="flowWorkspace"; version="3.26.5"; sha256="1j1gq3izyngjbspy6c8l8wjdhv3jm21i6aqv8sz262z2g9krqdyf"; depends=[BH Biobase BiocGenerics cytolib data_table dplyr flowCore flowViz graph gridExtra lattice latticeExtra ncdfFlow RBGL RColorBrewer Rcpp Rgraphviz RProtoBufLib scales stringr XML]; };
+  flowWorkspace = derive2 { name="flowWorkspace"; version="3.26.6"; sha256="11r9c9h1ffp3i1p7gw0f93l5g30waawl7f2vbyh06p5mcr732dmp"; depends=[BH Biobase BiocGenerics cytolib data_table dplyr flowCore flowViz graph gridExtra lattice latticeExtra ncdfFlow RBGL RColorBrewer Rcpp Rgraphviz RProtoBufLib scales stringr XML]; };
  flowcatchR = derive2 { name="flowcatchR"; version="1.12.0"; sha256="0i6r86b1g98kaw8nhbnjjrw8gw6vvhfpr5r7dn4whl4hwlizc5qx"; depends=[abind BiocParallel colorRamps EBImage rgl]; };
  fmcsR = derive2 { name="fmcsR"; version="1.20.0"; sha256="0cbbil337zbb968zibkysrmpc8bwlpn7rl908zyvzvj8v11lxzcc"; depends=[BiocGenerics ChemmineR RUnit]; };
  focalCall = derive2 { name="focalCall"; version="1.12.0"; sha256="07lb0ijdsryd31dxp5fgp393p9f21b7in3rnf9j43qn8wmz48hnl"; depends=[CGHcall]; };
@ -1017,7 +1017,7 @@ in with self; {
  geNetClassifier = derive2 { name="geNetClassifier"; version="1.18.0"; sha256="14qvrjbcvkqp2azfqi33y7pwg4wlf1vabddbirinw73za5b4jf48"; depends=[Biobase e1071 EBarrays minet]; };
  geecc = derive2 { name="geecc"; version="1.12.0"; sha256="1njvcwfdbpvmvvx8lcfw0baigjldr0v0rkqbk2rhb0h6wsiljfm2"; depends=[gplots hypergea MASS Rcpp]; };
  genArise = derive2 { name="genArise"; version="1.54.0"; sha256="101dammhv29w78cm2xylln4s7rzcy6sqw44navzs260xccdipxab"; depends=[locfit tkrplot xtable]; };
-  genbankr = derive2 { name="genbankr"; version="1.6.0"; sha256="0yy9mjcd354g7gw73rx00q079xjaaka20imn3afmxv80gprhss5f"; depends=[Biobase BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges rtracklayer S4Vectors VariantAnnotation]; };
+  genbankr = derive2 { name="genbankr"; version="1.6.1"; sha256="1f88ix4c4pfy5hhc2wlj2zrdz1jjfzzkrj4swk34ril24gf6av2z"; depends=[Biobase BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges rtracklayer S4Vectors VariantAnnotation]; };
  geneAttribution = derive2 { name="geneAttribution"; version="1.4.0"; sha256="11p8zqmmcfccl0fnyjm5kv8rbasamj6mra3bvk5jxsi4cqmbx9wx"; depends=[BiocGenerics GenomeInfoDb GenomicFeatures GenomicRanges IRanges org_Hs_eg_db rtracklayer]; };
  geneClassifiers = derive2 { name="geneClassifiers"; version="1.2.0"; sha256="1canrqw0g6v32vy2p2xd4pz6kw5k2zyzgff5ii0p86w519dzg16v"; depends=[Biobase BiocGenerics]; };
  geneRecommender = derive2 { name="geneRecommender"; version="1.50.0"; sha256="16cf2zkjffmdr2lhm7b4ckcw6p0kx40whw36m6y9510i8pmzy3y9"; depends=[Biobase]; };
@ -1035,9 +1035,9 @@ in with self; {
  genotypeeval = derive2 { name="genotypeeval"; version="1.10.0"; sha256="1pff2n1s350j6i7klsnwqlizkdvvfpyqqrvc7kq5gj7yh508dxy9"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges ggplot2 IRanges rtracklayer Rtsne VariantAnnotation]; };
  genphen = derive2 { name="genphen"; version="1.6.0"; sha256="0m1g1hfhhbq3xjdr2fjf3wbng6d953kci965h298c168dv3864k6"; depends=[Biostrings e1071 effsize ggplot2 randomForest rjags]; };
  gespeR = derive2 { name="gespeR"; version="1.10.0"; sha256="09xd080b08bfpqqbha4rxn4vmglv7c5asd4gibfjgjkasd78g40m"; depends=[Biobase biomaRt cellHTS2 doParallel dplyr foreach ggplot2 glmnet Matrix reshape2]; };
-  ggbio = derive2 { name="ggbio"; version="1.26.0"; sha256="1bqxfqy0hff87ax92z4lfbjz01ndrz7x8pzm6dlkdmi52p30krm9"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings biovizBase BSgenome ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra gtable Hmisc IRanges OrganismDbi reshape2 Rsamtools rtracklayer S4Vectors scales SummarizedExperiment VariantAnnotation]; };
+  ggbio = derive2 { name="ggbio"; version="1.26.1"; sha256="1xlmlngn27iwnr21s9di4059kav1a7c1sajx08wja8yn8f7j06hp"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings biovizBase BSgenome ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra gtable Hmisc IRanges OrganismDbi reshape2 Rsamtools rtracklayer S4Vectors scales SummarizedExperiment VariantAnnotation]; };
  ggcyto = derive2 { name="ggcyto"; version="1.6.1"; sha256="07rsg673hnrn1kf82nb59sxa925hjlb3qnjwlxvzlr2lzs958rcd"; depends=[data_table flowCore flowWorkspace ggplot2 gridExtra ncdfFlow plyr RColorBrewer scales]; };
-  ggtree = derive2 { name="ggtree"; version="1.10.4"; sha256="1ja6ynzhqyrf4gl0haf18h36zwrc0cj9969an94c23h4ksppw0m1"; depends=[ape ggplot2 magrittr rvcheck scales tidyr treeio]; };
+  ggtree = derive2 { name="ggtree"; version="1.10.5"; sha256="1gkfjgihykkvqrhvzhr5brwzsgva0mxvfpa664k08jan9brjg22f"; depends=[ape ggplot2 magrittr rvcheck scales tidyr treeio]; };
  girafe = derive2 { name="girafe"; version="1.30.0"; sha256="0k8fjn7d1hxwin0vywly7vc570048i7nckhyw9j4cind6fi6f75v"; depends=[Biobase BiocGenerics Biostrings genomeIntervals intervals IRanges Rsamtools S4Vectors ShortRead]; };
  globalSeq = derive2 { name="globalSeq"; version="1.6.0"; sha256="19aws180r5gwxrz6xmfgic0mp8piki2qmzrxyy1f75866blk3r4f"; depends=[]; };
  globaltest = derive2 { name="globaltest"; version="5.32.0"; sha256="1fk9yk6n3aqigcly5zsb0jnb6jmdbn3jgbp1wyv6sby124sr4hmr"; depends=[annotate AnnotationDbi Biobase survival]; };
@ -1095,7 +1095,7 @@ in with self; {
  iterativeBMAsurv = derive2 { name="iterativeBMAsurv"; version="1.36.0"; sha256="096qnp9wisc4hnpgy37a4h1xb1f01kqc9rhrhfkp25wkf1yxgwmi"; depends=[BMA leaps survival]; };
  ivygapSE = derive2 { name="ivygapSE"; version="1.0.0"; sha256="1y82cm0xmddhfz12iqqwpq9ifaml3r0yxs4c3cvp6k2c0wlhl173"; depends=[ggplot2 hwriter plotly S4Vectors shiny SummarizedExperiment survival survminer UpSetR]; };
  joda = derive2 { name="joda"; version="1.26.0"; sha256="0qwfkq40zl16lngrmhw8lxx1qn5lh076nl6bydrzksvh1bjs78b6"; depends=[bgmm RBGL]; };
-  karyoploteR = derive2 { name="karyoploteR"; version="1.4.1"; sha256="0sq6iinign7ndw2wg1gfz7chbalyqycb8j0cai6zakaxjxav2dsc"; depends=[bezier biovizBase digest GenomeInfoDb GenomicRanges IRanges memoise regioneR Rsamtools rtracklayer S4Vectors]; };
+  karyoploteR = derive2 { name="karyoploteR"; version="1.4.2"; sha256="18g6dm6bl5qyr50gydlvq948cmvg21iyb6l33cyh7p4haajf7xaa"; depends=[bezier biovizBase digest GenomeInfoDb GenomicRanges IRanges memoise regioneR Rsamtools rtracklayer S4Vectors]; };
  kebabs = derive2 { name="kebabs"; version="1.12.0"; sha256="1mbymzrbwzzfd5ygf8fk89igv7x0damgskri39fj913aqifgkf42"; depends=[apcluster Biostrings e1071 IRanges kernlab LiblineaR Matrix Rcpp S4Vectors XVector]; };
  keggorthology = derive2 { name="keggorthology"; version="2.30.0"; sha256="117s7b32nkv95adh2j91b87r90svhfb91ag28brsq3r333m2q8cn"; depends=[AnnotationDbi DBI graph hgu95av2_db]; };
  kimod = derive2 { name="kimod"; version="1.6.0"; sha256="0mb9bv6bz7k27vs8rl26kh2zm8mvpkgzqhgc471lp4qz8f4fsbxc"; depends=[Biobase cluster]; };
@ -1103,7 +1103,7 @@ in with self; {
  ldblock = derive2 { name="ldblock"; version="1.8.0"; sha256="18nfsixh6d2wfrb9laqsgly5w1frzihhak683k0p8fdf51h4aqba"; depends=[erma GenomeInfoDb GenomicFiles GO_db Homo_sapiens Matrix Rsamtools snpStats VariantAnnotation]; };
  les = derive2 { name="les"; version="1.28.0"; sha256="0xy7ggc2b20i1c78mww84xvc0jhbinxn00nbfvnbw997vjqr7r79"; depends=[boot fdrtool gplots RColorBrewer]; };
  lfa = derive2 { name="lfa"; version="1.8.0"; sha256="06w0032wwqm2cxid7brb6iq6bkhqc5x3a08wwyjbib6lnj5n7rvh"; depends=[corpcor]; };
-  limma = derive2 { name="limma"; version="3.34.8"; sha256="0bmxsgz2yll83sd3wbxsrsfd35468igb0d8lldym0d0lqfz906bw"; depends=[]; };
+  limma = derive2 { name="limma"; version="3.34.9"; sha256="1y2fm61g5i0fn0j3l31xvwh9zww9bpkc4nwzb1d0yv1cag20jkdc"; depends=[]; };
  limmaGUI = derive2 { name="limmaGUI"; version="1.54.0"; sha256="1mhqxy4bfb38lp57wrm6jm57xbwhqz6z78cxjdjr8r9inysddjlp"; depends=[AnnotationDbi BiocInstaller gcrma limma R2HTML tkrplot xtable]; };
  lmdme = derive2 { name="lmdme"; version="1.20.0"; sha256="1742ffw592cpp0bxd38g4k51h28iaax995lzmgxb3di6kj6h8an3"; depends=[limma pls stemHypoxia]; };
  logicFS = derive2 { name="logicFS"; version="1.48.0"; sha256="1qkbc6xgmppicg30613ak0dy8fn1irq6n8kf2qvwd95y210zlcfv"; depends=[LogicReg mcbiopi]; };
@ -1121,7 +1121,7 @@ in with self; {
  maanova = derive2 { name="maanova"; version="1.48.0"; sha256="1vvjk6y8mp5h7l8yk4f1y48jx5k9fl9s12x2mgsbap306paw860q"; depends=[Biobase]; };
  macat = derive2 { name="macat"; version="1.52.0"; sha256="168jw5bi1nbj2dfhipnvja7w0avmiw6vrvdany73d41fvigmagj5"; depends=[annotate Biobase]; };
  made4 = derive2 { name="made4"; version="1.52.0"; sha256="1ns7f47l7ig2fm95l67ppym5gbkbr8lp18vx51pqwjg8r5rvj9sc"; depends=[ade4 gplots RColorBrewer scatterplot3d]; };
-  maftools = derive2 { name="maftools"; version="1.4.21"; sha256="0xcqfnp7qx9gr5nr8bd00cqa7b1d32nb14cj0ymhazsyd2ja9wv5"; depends=[Biostrings changepoint cometExactTest ComplexHeatmap cowplot data_table ggplot2 ggrepel gridExtra mclust NMF RColorBrewer rjson Rsamtools survival VariantAnnotation wordcloud]; };
+  maftools = derive2 { name="maftools"; version="1.4.25"; sha256="0k4ry5pnh3lxyzkab094wpjiaqjrymq9hbgpz8xv9g67fhg2g8ah"; depends=[Biostrings changepoint cometExactTest ComplexHeatmap cowplot data_table ggplot2 ggrepel gridExtra mclust NMF RColorBrewer rjson Rsamtools survival VariantAnnotation wordcloud]; };
  maigesPack = derive2 { name="maigesPack"; version="1.42.0"; sha256="1c92kkr2rmfydckmbvri8g0lzz1v3hx93zpmb1pwrnlfpm01j95j"; depends=[convert graph limma marray]; };
  makecdfenv = derive2 { name="makecdfenv"; version="1.54.0"; sha256="17fmzd12acdpq3vfnqrafmmg5jcmdgkf83mrqjpw92zah2w8490a"; depends=[affy affyio Biobase zlibbioc]; };
  manta = derive2 { name="manta"; version="1.24.0"; sha256="060x5rdzkx882pa8x9w7j3sgj0clar6w35yblbcggq579r9jpx06"; depends=[caroline edgeR Hmisc]; };
@ -1160,7 +1160,7 @@ in with self; {
  methyvim = derive2 { name="methyvim"; version="1.0.0"; sha256="1hz6c4bdgslxrbkr0q9fx6ffrrilxcanm8f5alady5qndm4vmiw1"; depends=[BiocGenerics BiocParallel bumphunter cluster doFuture dplyr future GenomeInfoDb ggplot2 gridExtra gtools IRanges limma magrittr minfi SummarizedExperiment superheat tmle wesanderson]; };
  mfa = derive2 { name="mfa"; version="1.0.0"; sha256="17mwf4p4cr4xz1g32p4j0jaxvzfvjzilyrl9nv686nr7cplgkbgp"; depends=[Biobase coda dplyr ggmcmc ggplot2 magrittr MCMCglmm MCMCpack Rcpp tibble]; };
  mgsa = derive2 { name="mgsa"; version="1.26.0"; sha256="087hmvrrd5x1s6198g9q8nwrpd36zywg39dl4l6x8qkr7zgjzakb"; depends=[gplots]; };
-  miRBaseConverter = derive2 { name="miRBaseConverter"; version="1.0.0"; sha256="0nx31s6lq6270qj0lx0f8f14959vwhfcyzs1n9h3rs0jwagr41kx"; depends=[]; };
+  miRBaseConverter = derive2 { name="miRBaseConverter"; version="1.0.4"; sha256="1cjjikbw6anb1cgwl4718lv1k5acc2fhl6c0gmszdl16x8z2yyz1"; depends=[]; };
  miRLAB = derive2 { name="miRLAB"; version="1.8.0"; sha256="0fj96h1xan56sc71ycc4c5b2q7chncsknmdlj318lz95mydbiwdv"; depends=[energy entropy glmnet gplots Hmisc httr impute limma pcalg RCurl Roleswitch stringr]; };
  miRNAmeConverter = derive2 { name="miRNAmeConverter"; version="1.6.0"; sha256="1chsigqmfxajd8gll2rq7ccbrsgp9k0cddn4ds4zkiiz6a79iiww"; depends=[AnnotationDbi DBI miRBaseVersions_db]; };
  miRNApath = derive2 { name="miRNApath"; version="1.38.0"; sha256="11137kg0a1l8z2aiz6qisg1gq21rpgzhwr4z8dg0bkh9137jwnx8"; depends=[]; };
@ -1169,7 +1169,7 @@ in with self; {
  miRmine = derive2 { name="miRmine"; version="1.0.0"; sha256="09sxjj2pj4s03dqqphywyhvmk3q2gvdn2nph5nplqwny6q9m2i1v"; depends=[SummarizedExperiment]; };
  miRsponge = derive2 { name="miRsponge"; version="1.2.0"; sha256="0c3213hpf78ynqlaj12p0j9172gvlrhrx4rn4kmr6g1ja9xk80k7"; depends=[clusterProfiler corpcor DOSE igraph ProNet ReactomePA survival varhandle]; };
  microRNA = derive2 { name="microRNA"; version="1.36.0"; sha256="0mc81fy9y3jgc3ll074ksmw72d8yp29pyaankn3na24r96lfcxnj"; depends=[Biostrings]; };
-  microbiome = derive2 { name="microbiome"; version="1.0.0"; sha256="13hfia6y1bnzx68gkbb9jhpg9m4mbjn6js69zmhg68c3s7l7s1lk"; depends=[dplyr ggplot2 phyloseq reshape2 tidyr vegan]; };
+  microbiome = derive2 { name="microbiome"; version="1.0.2"; sha256="185igm8dr5irc4bhgjflkxax0gk4lgm3zznqazv378j435194xgh"; depends=[dplyr ggplot2 phyloseq reshape2 tidyr vegan]; };
  mimager = derive2 { name="mimager"; version="1.2.0"; sha256="14r0h676nhsbg175hj7jmkp1ny5wfhykmy2jm2s9qgdsfrgacgv2"; depends=[affy affyPLM Biobase BiocGenerics DBI gtable oligo oligoClasses preprocessCore S4Vectors scales]; };
  minet = derive2 { name="minet"; version="3.36.0"; sha256="1ig9kwh7fvhpglxkda9l5nkaz3rmhl6bc006h6mrz9hl130vmnn8"; depends=[infotheo]; };
  minfi = derive2 { name="minfi"; version="1.24.0"; sha256="1pk5savz9ziarx2iajqnck4vjmh3bnrmzy5m06vx3vmcww46ddi7"; depends=[beanplot Biobase BiocGenerics Biostrings bumphunter data_table genefilter GenomeInfoDb GenomicRanges GEOquery illuminaio IRanges lattice limma MASS matrixStats mclust nlme nor1mix preprocessCore quadprog RColorBrewer reshape S4Vectors siggenes SummarizedExperiment]; };
@ -1177,10 +1177,10 @@ in with self; {
  missMethyl = derive2 { name="missMethyl"; version="1.12.0"; sha256="1fvpny7x56l55zhgabm6al2i2n0hix7fp7d01bzirsn7chxpwny3"; depends=[AnnotationDbi BiasedUrn GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest limma methylumi minfi org_Hs_eg_db ruv statmod stringr]; };
  mitoODE = derive2 { name="mitoODE"; version="1.16.0"; sha256="11kyihynbl3kcrngv8dhiqn3ghpkvv0xi35pf8np2p41zdhbrpyv"; depends=[KernSmooth MASS minpack_lm mitoODEdata]; };
  mogsa = derive2 { name="mogsa"; version="1.12.2"; sha256="0a29q9jak4vr05ngh2pcsfifa9i6p086acjk2qrzwnc3lcfm00bm"; depends=[Biobase BiocGenerics cluster corpcor genefilter gplots graphite GSEABase svd]; };
-  monocle = derive2 { name="monocle"; version="2.6.1"; sha256="1s3g488jyb0lbdsx4jkpzfl47kpcrnmn2n3bi85if1jmgvlxahvv"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree densityClust dplyr fastICA ggplot2 HSMMSingleCell igraph irlba limma MASS Matrix matrixStats pheatmap plyr proxy qlcMatrix RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; };
+  monocle = derive2 { name="monocle"; version="2.6.3"; sha256="1qag8q6wy1wf1zx16h2lwki6rn4nxkjff7yhpn8m30hp3v01fvhn"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree densityClust dplyr fastICA ggplot2 HSMMSingleCell igraph irlba limma MASS Matrix matrixStats pheatmap plyr proxy qlcMatrix RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; };
  mosaics = derive2 { name="mosaics"; version="2.16.0"; sha256="08q48zakyfydrj8vix3a5w0j4ix5h1hpqccv0jxgj55gpdc062kj"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges lattice MASS Rcpp Rsamtools S4Vectors]; };
  motifRG = derive2 { name="motifRG"; version="1.22.0"; sha256="193zl2rlzwxv9p9q5i7rilj3w05ndqfyp9bdpvagp5s5cin4hf44"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 IRanges seqLogo XVector]; };
-  motifStack = derive2 { name="motifStack"; version="1.22.2"; sha256="05kbp0j0hqpx22fn47r4fcws3hgv5j0496n5srwz1qdlm10igs23"; depends=[ade4 Biostrings grImport htmlwidgets MotIV scales XML]; };
+  motifStack = derive2 { name="motifStack"; version="1.22.4"; sha256="13wrpdgyhzrqdp7k0d7iym2pjjla46rh3i1qwm34j22n7j0pxs8x"; depends=[ade4 Biostrings grImport htmlwidgets MotIV scales XML]; };
  motifbreakR = derive2 { name="motifbreakR"; version="1.8.0"; sha256="1jfff6jgvrylhnpyc5zq1fah33xq8vf7hypv22vg7js6m8bmcx5j"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges grImport Gviz IRanges matrixStats MotifDb motifStack rtracklayer S4Vectors stringr TFMPvalue VariantAnnotation]; };
  motifcounter = derive2 { name="motifcounter"; version="1.2.1"; sha256="1k47yca1w59w0k7w4cxahhq4r2jyb8vflpzmrl7wnypb4lf9mbc0"; depends=[Biostrings]; };
  motifmatchr = derive2 { name="motifmatchr"; version="1.0.1"; sha256="0a7hg307f274n8vxknl0381xpvgphsim07pk7dnh0af3a63lh2ji"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment TFBSTools]; };
@ -1196,7 +1196,7 @@ in with self; {
  multiscan = derive2 { name="multiscan"; version="1.38.0"; sha256="07fb0a7kn8bjvq9cx4dvdjrf92830vwpz5n31mgk58aw3vg3mz66"; depends=[Biobase]; };
  multtest = derive2 { name="multtest"; version="2.34.0"; sha256="0n11rd49xl2vn3ldmfips7d3yb70l8npjcqsxyswr9ypjhgzkv9j"; depends=[Biobase BiocGenerics MASS survival]; };
  muscle = derive2 { name="muscle"; version="3.20.0"; sha256="16kawdvm08hag2kghdn438z0ysby67p989v3xlcf9r8f62isw6b7"; depends=[Biostrings]; };
-  mvGST = derive2 { name="mvGST"; version="1.12.0"; sha256="12fm1xgini0l5x2xbp9qkxigdvii7yjdwww420bn7ymz4z97865c"; depends=[annotate AnnotationDbi GO_db GOstats gProfileR graph Rgraphviz stringr topGO]; };
+  mvGST = derive2 { name="mvGST"; version="1.12.2"; sha256="132s30c116gmbimzf1jw70p0pz4fv6lbfqb90sxnzbqvb8alvs0h"; depends=[annotate AnnotationDbi GO_db GOstats gProfileR graph Rgraphviz stringr topGO]; };
  mygene = derive2 { name="mygene"; version="1.14.0"; sha256="0qqkpsqk99575rc49kj7s5yl22jb96gmk47i5lm700qi4v9fyim4"; depends=[GenomicFeatures Hmisc httr jsonlite plyr S4Vectors sqldf]; };
  myvariant = derive2 { name="myvariant"; version="1.8.0"; sha256="1r4hqy5jz4xqswj3pfzxmncjapjmcksbx428f7lfncj844198g1q"; depends=[GenomeInfoDb Hmisc httr jsonlite magrittr plyr S4Vectors VariantAnnotation]; };
  mzID = derive2 { name="mzID"; version="1.16.0"; sha256="0yk70dka56zd8w62f03ggx3mandj91gfa767h9ajj0sd3mjmfqb9"; depends=[doParallel foreach iterators plyr ProtGenerics XML]; };
@ -1278,7 +1278,7 @@ in with self; {
  plw = derive2 { name="plw"; version="1.38.0"; sha256="1mys9rslhc3rb23wbvlnxwl4dcca2m395bxfg7i4217hvzai7b25"; depends=[affy MASS]; };
  pmm = derive2 { name="pmm"; version="1.10.0"; sha256="1bzmh0p0c649sqp1lhz8zdqh4k7b3n78akgn2wlhawjbx3lb5f6i"; depends=[lme4]; };
  podkat = derive2 { name="podkat"; version="1.10.0"; sha256="0c93gnrcw8rwq9r4f7kkpsdjflarwixjpadaa05w98vqa9x5ycc4"; depends=[Biobase BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp Rsamtools]; };
-  polyester = derive2 { name="polyester"; version="1.14.0"; sha256="1pxlkncfnrd15l1n4j5mj04in9pr6fxmxcwlrsqrqn58x4hk4kxs"; depends=[Biostrings IRanges limma logspline S4Vectors zlibbioc]; };
+  polyester = derive2 { name="polyester"; version="1.14.1"; sha256="10dj2qy5b94qd0j0rm7a6j50zqaxdjjwy583cgci158cf8s8y915"; depends=[Biostrings IRanges limma logspline S4Vectors zlibbioc]; };
  ppiStats = derive2 { name="ppiStats"; version="1.44.0"; sha256="14xrvcfbp177mpdlzi2kxmv0v9j93i4r1xsw06fr3gw9a7l6zg3r"; depends=[Biobase Category graph lattice ppiData RColorBrewer ScISI]; };
  pqsfinder = derive2 { name="pqsfinder"; version="1.6.3"; sha256="0rf0sjd1gsdvn1qilckp5y9vb7j3wgs9h12gcxcjfrcaax8b3h6h"; depends=[BH Biostrings GenomicRanges IRanges Rcpp S4Vectors]; };
  prada = derive2 { name="prada"; version="1.54.0"; sha256="19f8h411mzbrim1wvncr7wa3ah0qc1vy9kzcbx64pcif2xfb5qin"; depends=[Biobase BiocGenerics MASS RColorBrewer rrcov]; };
@ -1329,7 +1329,7 @@ in with self; {
  rcellminer = derive2 { name="rcellminer"; version="2.0.0"; sha256="1y5rzv9ggfxgyy4z5hm7awd8zb8n57qr2954p2j4ikhj62b6h6z2"; depends=[Biobase fingerprint ggplot2 gplots rcdk rcellminerData shiny stringr]; };
  readat = derive2 { name="readat"; version="1.4.0"; sha256="10pib536kmkpi3ij8cccxyap7zw0q1jfd1bcv4c38vn04jm3smaa"; depends=[assertive_base assertive_files assertive_numbers assertive_properties assertive_sets assertive_types Biobase data_table dplyr magrittr openxlsx pathological reshape2 stringi SummarizedExperiment testthat tidyr]; };
  reb = derive2 { name="reb"; version="1.56.0"; sha256="0sh9r77r2s3fmkbkwrazl705dqwr2wh0mx34pxhjfvfic0jc1r5x"; depends=[Biobase idiogram]; };
-  recount = derive2 { name="recount"; version="1.4.4"; sha256="1pm7p4qfnqajmm8ym5bq71hi8bjrm6xjax838x79b67d825nhsw9"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; };
+  recount = derive2 { name="recount"; version="1.4.6"; sha256="0gqv59rm9k5kcfiq99vxz9g86p2vy7znq5cd84bc7hg6qkva1ah0"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; };
  recoup = derive2 { name="recoup"; version="1.6.0"; sha256="09i0c2wv9c6hqc4mq6kklp0maqskpfxj871j44256dxlfh81xm3b"; depends=[BiocGenerics biomaRt circlize ComplexHeatmap GenomicAlignments GenomicRanges ggplot2 plyr rtracklayer]; };
  regionReport = derive2 { name="regionReport"; version="1.12.2"; sha256="1fvkmd2yfkvkj44ldywr1z0l1cn7c64nq3920fhlarqygv92d7xx"; depends=[BiocStyle DEFormats derfinder DESeq2 GenomeInfoDb GenomicRanges knitcitations knitr knitrBootstrap RefManageR rmarkdown S4Vectors SummarizedExperiment]; };
  regioneR = derive2 { name="regioneR"; version="1.10.0"; sha256="1vprp3l929hwzmvgskbhawfgnrymwc9n2rxd16rgagnv1dxnjxfp"; depends=[BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; };
@ -1339,7 +1339,7 @@ in with self; {
  rfPred = derive2 { name="rfPred"; version="1.16.0"; sha256="1m79rykh534iss41nw62j0dyx6v0vqk543m7dlgl7zm2kpyzdpc3"; depends=[data_table GenomicRanges IRanges Rsamtools]; };
  rgsepd = derive2 { name="rgsepd"; version="1.10.0"; sha256="0r1adlc7dxwnm8h6nh4w05z3bffvr10cch7i68a7dli968yza2vj"; depends=[AnnotationDbi biomaRt DESeq2 GO_db goseq gplots hash org_Hs_eg_db SummarizedExperiment]; };
  rhdf5 = derive2 { name="rhdf5"; version="2.22.0"; sha256="145858qg1xan6imxcbprzq3yn3mdf532aahdr6cibvdjg47hs4c1"; depends=[zlibbioc]; };
-  rhdf5client = derive2 { name="rhdf5client"; version="1.0.6"; sha256="1h2dvz4rx11gsxj2fy61jwbkxgdx1jq0xahxyq7mclkbc4p8v4xy"; depends=[httr rjson S4Vectors]; };
+  rhdf5client = derive2 { name="rhdf5client"; version="1.0.7"; sha256="0hq812larfzim4cpq26mx6ckcrpz6p1m55xl2z9dk7zwqapnd2ri"; depends=[httr rjson S4Vectors]; };
  riboSeqR = derive2 { name="riboSeqR"; version="1.12.0"; sha256="0fg2zn5az1djdjnsrli26rl53ljrrjzmspx02dmgwf1a7nm7qmfz"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools seqLogo]; };
  rnaSeqMap = derive2 { name="rnaSeqMap"; version="2.36.0"; sha256="0y0mxzs24jz9nxcvjxymj0zxjfn1rlx3d8dzvdmfn98lbgyzm4dv"; depends=[Biobase DBI DESeq edgeR GenomicAlignments GenomicRanges IRanges Rsamtools]; };
  rnaseqcomp = derive2 { name="rnaseqcomp"; version="1.8.0"; sha256="050dc6asknh8snk6xkvpp5ivyikalslsawadh11lnw5wb4fixmhm"; depends=[RColorBrewer]; };
@ -1369,7 +1369,7 @@ in with self; {
  scmap = derive2 { name="scmap"; version="1.1.5"; sha256="0jqgk9sjb5bp5gbzq14vsif5gd5ry4213glvnpmhgqm23hmwbfhi"; depends=[Biobase BiocGenerics dplyr e1071 ggplot2 googleVis matrixStats proxy randomForest Rcpp RcppArmadillo reshape2 S4Vectors SingleCellExperiment SummarizedExperiment]; };
  scone = derive2 { name="scone"; version="1.2.0"; sha256="1xq48d3z78p54iclb1ii074i7f88qfzh5djfiyrwf3k6gsapadfi"; depends=[aroma_light BiocParallel boot class cluster compositions diptest edgeR fpc gplots hexbin limma matrixStats mixtools rARPACK RColorBrewer rhdf5 RUVSeq SummarizedExperiment]; };
  scoreInvHap = derive2 { name="scoreInvHap"; version="1.0.0"; sha256="04q2rs1gw7v97lwcialyswqzl0kd5c5298v60cm6wha25i6lwgbs"; depends=[BiocParallel Biostrings GenomicRanges snpStats SummarizedExperiment VariantAnnotation]; };
-  scran = derive2 { name="scran"; version="1.6.7"; sha256="0zfm5i8xrnzb3894xygqd6zkbwaa2x3z74wbxw39fcjhyhxv2hmb"; depends=[beachmat BiocGenerics BiocParallel DT dynamicTreeCut edgeR FNN ggplot2 igraph limma Matrix Rcpp Rhdf5lib S4Vectors scater shiny SingleCellExperiment statmod SummarizedExperiment viridis zoo]; };
+  scran = derive2 { name="scran"; version="1.6.9"; sha256="0cs64cnf0xjcgmawr210y99j3gxs6aqgh8081n9827kkqnx2y5dm"; depends=[beachmat BiocGenerics BiocParallel DT dynamicTreeCut edgeR FNN ggplot2 igraph limma Matrix Rcpp Rhdf5lib S4Vectors scater shiny SingleCellExperiment statmod SummarizedExperiment viridis zoo]; };
  scsR = derive2 { name="scsR"; version="1.14.0"; sha256="05xqrv1babqvlvr4m5k0r7yy4fbr0y46f3i4v4zcjilda1qf54pb"; depends=[BiocGenerics Biostrings ggplot2 hash IRanges plyr RColorBrewer sqldf STRINGdb]; };
  segmentSeq = derive2 { name="segmentSeq"; version="2.12.0"; sha256="0jqdddzrxahf6i7cmaay5v9ig9969avhv8ddh72v6ndfphlkfb64"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors ShortRead]; };
  semisup = derive2 { name="semisup"; version="1.2.0"; sha256="14q2p38a8r4ry8swwi88k96rchmcnplknq1a62lvm98k09k1887r"; depends=[SummarizedExperiment VGAM]; };
@ -1441,15 +1441,15 @@ in with self; {
  timescape = derive2 { name="timescape"; version="1.2.0"; sha256="0v3a7gn2d852h8m0053a57w153z4nlmp5mb5g96kjw06vvwr71jd"; depends=[dplyr gtools htmlwidgets jsonlite stringr]; };
  tkWidgets = derive2 { name="tkWidgets"; version="1.56.0"; sha256="0z1vd0nymyvvrn5jc97q33y9xl6w8pd4wzb6yyfjg8jy85kswfgf"; depends=[DynDoc widgetTools]; };
  tofsims = derive2 { name="tofsims"; version="1.6.0"; sha256="1zpq0c01fqm3yl2mkvx1yl2ajj2a933wa6h7hinrh3mdyix8pzrn"; depends=[ALS ChemometricsWithR KernSmooth ProtGenerics Rcpp RcppArmadillo signal]; };
-  topGO = derive2 { name="topGO"; version="2.30.0"; sha256="1hqffz5qp7glxdvjp37005g8qk5nam3f9wpf6d1wjnzpar04f3dz"; depends=[AnnotationDbi Biobase BiocGenerics DBI GO_db graph lattice matrixStats SparseM]; };
+  topGO = derive2 { name="topGO"; version="2.30.1"; sha256="1cgz4knxr328xfqlhl6ypxl6x86rfrlqz748kn94ainxjzz55i6x"; depends=[AnnotationDbi Biobase BiocGenerics DBI GO_db graph lattice matrixStats SparseM]; };
  topdownr = derive2 { name="topdownr"; version="1.0.0"; sha256="1yshm8a6dirnmda5ydx1ksndbbcrqlp25lrj1rqxnaclqb9xn0g2"; depends=[Biobase BiocGenerics Biostrings ggplot2 Matrix MSnbase mzR S4Vectors]; };
  trackViewer = derive2 { name="trackViewer"; version="1.14.1"; sha256="029yff299x23imqyk62cmxcsvdx34a6b4l9zp4p46iq3jb841h66"; depends=[AnnotationDbi GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges grImport Gviz htmlwidgets IRanges pbapply Rsamtools rtracklayer S4Vectors scales]; };
  tracktables = derive2 { name="tracktables"; version="1.12.0"; sha256="02l5n4sbwzig5kdnjyhhqpiwskaf8f4pqkra3m511vrqfpmd39f3"; depends=[GenomicRanges IRanges RColorBrewer Rsamtools stringr tractor_base XML XVector]; };
  transcriptR = derive2 { name="transcriptR"; version="1.6.0"; sha256="0malha3w4vm21bmqdvn8y9q37m0ilghbyzmwgayvx9lvy3mfnk2s"; depends=[BiocGenerics caret chipseq e1071 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges pROC reshape2 Rsamtools rtracklayer S4Vectors]; };
  transcriptogramer = derive2 { name="transcriptogramer"; version="1.0.0"; sha256="08yab83dkwjwbbgf05k05c32yn74ls8xy7lm3yr39sb3nfqmra9n"; depends=[biomaRt data_table doSNOW foreach igraph limma progress RedeR snow topGO]; };
  traseR = derive2 { name="traseR"; version="1.8.0"; sha256="1zqcz7w8pwc2vzjr137iv1bpfddh17kvmqaz7hgs9z1962704l0y"; depends=[BSgenome_Hsapiens_UCSC_hg19 GenomicRanges IRanges]; };
-  treeio = derive2 { name="treeio"; version="1.2.1"; sha256="1m36jqdn9png95zy0n19x4p6ggc8f9sz9708l1kf8as8bhan9rlx"; depends=[ape ggplot2 jsonlite magrittr rvcheck]; };
-  trena = derive2 { name="trena"; version="1.0.0"; sha256="0b7bwm5xfav3m0gnz4mnc6959ha0larqpzlny3r8kxj4gx6cql4j"; depends=[AnnotationDbi BiocParallel biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI flare GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RMySQL RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 stringr vbsr]; };
+  treeio = derive2 { name="treeio"; version="1.2.2"; sha256="1m92hrfgy3lca7x674qp41j2x4gpanfvvc7gsmxw3d1q7fwqlvwl"; depends=[ape ggplot2 jsonlite magrittr rvcheck]; };
+  trena = derive2 { name="trena"; version="1.0.3"; sha256="1yk88mc3lcgm75wzqgl6xz4f1vk1i5q9qybr5m7s71m4dvwszgpb"; depends=[AnnotationDbi BiocParallel biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI flare GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RMySQL RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 stringr vbsr]; };
  triform = derive2 { name="triform"; version="1.20.0"; sha256="09hlnkrbzgk0vn1jcbja2i0hv54pfr2nzf33ik0rabrvv75zhb46"; depends=[BiocGenerics IRanges yaml]; };
  trigger = derive2 { name="trigger"; version="1.24.0"; sha256="16r7b0wy37pbylz9ch6516nygpxrb31qm42i8amh04jy60zw64rw"; depends=[corpcor qtl qvalue sva]; };
  trio = derive2 { name="trio"; version="3.16.0"; sha256="1bw0cy95qrzmg6qiy9j8n4ydi734z3q78l1pnaxagdk1ji5ab577"; depends=[]; };
@ -1467,14 +1467,14 @@ in with self; {
  vsn = derive2 { name="vsn"; version="3.46.0"; sha256="18y62phzirj75gg6v5l41jwybmk23ia6w7qhch0kxc4bl2rysw6j"; depends=[affy Biobase ggplot2 lattice limma]; };
  vtpnet = derive2 { name="vtpnet"; version="0.18.0"; sha256="02nws97nmlrpzwb5jqm3fmg38mp1qdf41hzwmmprhfhsymnmc4ch"; depends=[doParallel foreach GenomicRanges graph gwascat]; };
  vulcan = derive2 { name="vulcan"; version="1.0.0"; sha256="1yxm6yg7d65wh9rl6k5b6831y4hr5l9nnmfi0azxz1h4x1ghqbdj"; depends=[Biobase caTools ChIPpeakAnno csaw DESeq DiffBind GenomicRanges gplots locfit S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene viper wordcloud zoo]; };
-  wateRmelon = derive2 { name="wateRmelon"; version="1.22.0"; sha256="1043wwkavdkdwlps5hcqn6hi2jk8w1m1lfb8fp6i4yp82r82zn5h"; depends=[Biobase IlluminaHumanMethylation450kanno_ilmn12_hg19 illuminaio limma lumi matrixStats methylumi ROC]; };
+  wateRmelon = derive2 { name="wateRmelon"; version="1.22.1"; sha256="08imbxhs4ikm6panz3y64b24d2ghy1s2ksgd8siff53hg2v59rqr"; depends=[Biobase IlluminaHumanMethylation450kanno_ilmn12_hg19 illuminaio limma lumi matrixStats methylumi ROC]; };
  wavClusteR = derive2 { name="wavClusteR"; version="2.11.0"; sha256="0f1lk45a9yqr0ysjq8kjpqys8qln2b8ix03nywcqnkl1lk2b5ymi"; depends=[BiocGenerics Biostrings foreach GenomicFeatures GenomicRanges ggplot2 Hmisc IRanges mclust Rsamtools rtracklayer S4Vectors seqinr stringr wmtsa]; };
  waveTiling = derive2 { name="waveTiling"; version="1.20.0"; sha256="1dlz548vjnarz15mscmj56jp2hn810w0dy7xprxx22n51h7kb7jg"; depends=[affy Biobase Biostrings GenomeGraphs GenomicRanges IRanges oligo oligoClasses preprocessCore waveslim]; };
  weaver = derive2 { name="weaver"; version="1.44.0"; sha256="06fg8z4gp2mabiy9jrfwkrrz1r4qzzgjk3lxj6d53ii2xhq95vy6"; depends=[codetools digest]; };
  webbioc = derive2 { name="webbioc"; version="1.50.0"; sha256="1kg6apnhq97ypmpx6qm2f7wip81f910mjlg9kmd9zzmhnkrhqamd"; depends=[affy annaffy Biobase BiocInstaller gcrma multtest qvalue vsn]; };
  widgetTools = derive2 { name="widgetTools"; version="1.56.0"; sha256="0xkasd8z4sy9dsb2r7k3x2vhbqh9md39bz3qqwjsz8hgl6f0ggsr"; depends=[]; };
  wiggleplotr = derive2 { name="wiggleplotr"; version="1.2.0"; sha256="1scqvmh16y6c81qlvfa8y9z47p8wl4lccq0sm5wy4jay6zch8mn2"; depends=[assertthat cowplot dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges purrr rtracklayer S4Vectors]; };
-  xcms = derive2 { name="xcms"; version="3.0.0"; sha256="0yy45y7shh70ql8wrpr8bjqsx7i30hjqdgvwaxv4kypf4pxy7rx0"; depends=[Biobase BiocGenerics BiocParallel lattice MassSpecWavelet MSnbase multtest mzR plyr ProtGenerics RANN RColorBrewer S4Vectors]; };
+  xcms = derive2 { name="xcms"; version="3.0.2"; sha256="0qk9mjg4qdv88vmcsdalf59za46ifikxp7snwf5a6n3jaykzx4xl"; depends=[Biobase BiocGenerics BiocParallel lattice MassSpecWavelet MSnbase multtest mzR plyr ProtGenerics RANN RColorBrewer S4Vectors]; };
  xmapbridge = derive2 { name="xmapbridge"; version="1.36.0"; sha256="0jv07kgjh3jkk61bw92kr3s10sai427f93r5j5hjzjhn6wzpahqy"; depends=[]; };
  xps = derive2 { name="xps"; version="1.38.0"; sha256="1xmsbjkcy04nz1npbr2bia1p4x4q6b55mmk0vqkphjl6x93dw6c8"; depends=[]; };
  yamss = derive2 { name="yamss"; version="1.4.0"; sha256="08mq0f27if86wacck1317fhm6gchxqzbj2vj9sxasr865jdzr1r9"; depends=[BiocGenerics data_table EBImage IRanges limma Matrix mzR S4Vectors SummarizedExperiment]; };
--- a/pkgs/development/r-modules/cran-packages.nix
+++ b/pkgs/development/r-modules/cran-packages.nix
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@ -366,7 +366,6 @@ let
    udunits2 = [ pkgs.udunits pkgs.expat ];
    V8 = [ pkgs.v8_3_14 ];
    VBLPCM = [ pkgs.gsl_1 ];
-    VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ];
    WhopGenome = [ pkgs.zlib.dev ];
    XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
    xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ];
@ -404,7 +403,6 @@ let
    RGtk2 = [ pkgs.pkgconfig ];
    RProtoBuf = [ pkgs.pkgconfig ];
    Rpoppler = [ pkgs.pkgconfig ];
-    VBmix = [ pkgs.pkgconfig ];
    XML = [ pkgs.pkgconfig ];
    cairoDevice = [ pkgs.pkgconfig ];
    chebpol = [ pkgs.pkgconfig ];
@ -493,7 +491,6 @@ let
    "EasyqpcR"
    "EcoVirtual"
    "ENiRG"
-    "EnQuireR"
    "eVenn"
    "exactLoglinTest"
    "fat2Lpoly"
--- a/pkgs/development/tools/haskell/multi-ghc-travis/default.nix
+++ b/pkgs/development/tools/haskell/multi-ghc-travis/default.nix
@ -8,9 +8,10 @@ mkDerivation {
  src = fetchFromGitHub {
    owner = "haskell-CI";
    repo = "haskell-ci";
-    rev = "a4962f1478089654d138da7a3807dfcf2cef4284";
-    sha256 = "1qwknajabxcfz5w5g0yn30r8p0180wxp7pncr6nwfhszlhay0vb7";
+    rev = "7ca5d751c35c6dc43392397b4641c4611ed55121";
+    sha256 = "04f9jcxqv1mn0rw31x23ns6xdhgqjv55blsksadwr25qn2521zxb";
  };
+  jailbreak = true;
  isLibrary = true;
  isExecutable = true;
  libraryHaskellDepends = [
--- a/pkgs/development/tools/misc/fsatrace/default.nix
+++ b/pkgs/development/tools/misc/fsatrace/default.nix
@ -0,0 +1,31 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  name = "fsatrace-${version}";
+  version = "0.0.1-160";
+
+  src = fetchFromGitHub {
+    owner = "jacereda";
+    repo = "fsatrace";
+    rev = "2bf89d836e0156e68f121b0ffeedade7c9381f77";
+    sha256 = "0bndfmm0y738azwzf6m6xg6gjnrwcqlfjsampk67vga40yylwkbw";
+  };
+
+  preConfigure = ''
+    mkdir -p $out/libexec/${name}
+    export makeFlags=INSTALLDIR=$out/libexec/${name}
+  '';
+
+  postInstall = ''
+    mkdir -p $out/bin
+    ln -s $out/libexec/${name}/fsatrace $out/bin/
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/jacereda/fsatrace;
+    description = "filesystem access tracer";
+    license = licenses.isc;
+    maintainers = [ maintainers.peti ];
+    platforms = platforms.linux;
+  };
+}
--- a/pkgs/development/web/nodejs/v6.nix
+++ b/pkgs/development/web/nodejs/v6.nix
@ -5,7 +5,7 @@ let
 in
  buildNodejs {
    inherit enableNpm;
-    version = "6.13.0";
-    sha256 = "012dpfqxsrmd3xc4dmq0mik1kab4czf56s8wm2jvm7xjqvi6y5mp";
+    version = "6.13.1";
+    sha256 = "0ikasm20wq56gvn3j28hxjwbvqqzqj5w0p2sc3ss00v58w5kady4";
    patches = lib.optionals stdenv.isDarwin [ ./no-xcode.patch ./no-xcodebuild.patch ];
  }
--- a/pkgs/development/web/nodejs/v8.nix
+++ b/pkgs/development/web/nodejs/v8.nix
@ -5,7 +5,7 @@ let
 in
  buildNodejs {
    inherit enableNpm;
-    version = "8.9.4";
-    sha256 = "0vy8rlg58kg75j4sw3xadmbrwxfa56iaykmjl18g9a8wkjfdxp3c";
+    version = "8.10.0";
+    sha256 = "06lhnasmbpwvyv5dfc9kmjj32djllwgvb1xl778cnswdc5qlwbdp";
    patches = lib.optionals stdenv.isDarwin [ ./no-xcode-v7.patch ./no-xcodebuild.patch ];
  }
--- a/pkgs/development/web/nodejs/v9.nix
+++ b/pkgs/development/web/nodejs/v9.nix
@ -5,7 +5,7 @@ let
 in
  buildNodejs {
    inherit enableNpm;
-    version = "9.7.1";
-    sha256 = "0hlhj817s5bji2qdghxkwxjj40kwkyzgax4zyv32r5pbl6af3yh6";
+    version = "9.8.0";
+    sha256 = "1b0ynhvnq25w29rmshim0dn4m1dknkn1p52idi6acpzswi4vn1h7";
    patches = lib.optionals stdenv.isDarwin [ ./no-xcode-v7.patch ];
  }
--- a/pkgs/misc/cups/filters.nix
+++ b/pkgs/misc/cups/filters.nix
@ -9,11 +9,11 @@ let

 in stdenv.mkDerivation rec {
  name = "cups-filters-${version}";
-  version = "1.20.0";
+  version = "1.20.1";

  src = fetchurl {
    url = "http://openprinting.org/download/cups-filters/${name}.tar.xz";
-    sha256 = "0g6npicm1cwmxqi6ymfvf9wkplp4z2rzvjjl9v4yfvqdjq85gxnp";
+    sha256 = "0qix1whz5n4ijnl6d44f1v8nzkpv99wqjyrby8vx6xnpskw5hsxk";
  };

  nativeBuildInputs = [ pkgconfig makeWrapper ];
--- a/pkgs/os-specific/linux/nvidiabl/default.nix
+++ b/pkgs/os-specific/linux/nvidiabl/default.nix
@ -2,18 +2,19 @@

 stdenv.mkDerivation rec {
  name = "nvidiabl-${version}-${kernel.version}";
-  version = "0.87";
+  version = "2017-09-26";

+  # We use a fork which adds support for newer kernels -- upstream has been abandoned.
  src = fetchFromGitHub {
-    owner = "guillaumezin";
+    owner = "yorickvP";
    repo = "nvidiabl";
-    rev = "v${version}";
-    sha256 = "1hs61dxn84vsyvrd2s899dhgg342mhfkbdn1nkhcvly45hdp2nca";
+    rev = "2d909f4dfceb24ce98479fd571411c6ec3b71bea";
+    sha256 = "0dsar8fsaxwywjh6rbrxkhdp142vqjnsyxfz6bgpbqml6slpiqs1";
  };

  hardeningDisable = [ "pic" ];

-  patches = [ ./linux4compat.patch ];
+  nativeBuildInputs = kernel.moduleBuildDependencies;

  preConfigure = ''
    sed -i 's|/sbin/depmod|#/sbin/depmod|' Makefile
@ -25,11 +26,11 @@ stdenv.mkDerivation rec {
    "KVER=${kernel.modDirVersion}"
  ];

-  meta = {
+  meta = with stdenv.lib; {
    description = "Linux driver for setting the backlight brightness on laptops using NVIDIA GPU";
    homepage = https://github.com/guillaumezin/nvidiabl;
-    license = stdenv.lib.licenses.gpl2;
-    platforms = stdenv.lib.platforms.linux;
-    broken = !stdenv.lib.versionOlder kernel.version "4.9";
+    license = licenses.gpl2;
+    platforms = [ "x86_64-linux" "i686-linux" ];
+    maintainers = with maintainers; [ yorickvp ];
  };
 }
--- a/pkgs/os-specific/linux/nvidiabl/linux4compat.patch
+++ b/pkgs/os-specific/linux/nvidiabl/linux4compat.patch
@ -1,22 +0,0 @@
-From 2bf6f08b2492cc04a2c39fdcb22a2d0c18963d1c Mon Sep 17 00:00:00 2001
-From: sonic414 <sonic414@gmail.com>
-Date: Tue, 28 Apr 2015 19:30:15 +0530
-Subject: [PATCH] strnicmp to strncasecmp in Linux 4.0.0
-
---
- nvidiabl-module.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/nvidiabl-module.c b/nvidiabl-module.c
-index b789ea4..b306579 100644
--- a/nvidiabl-module.c
-+++ b/nvidiabl-module.c
-@@ -214,7 +214,7 @@ static int __init nvidiabl_init(void)
- #if LINUX_VERSION_CODE >= KERNEL_VERSION(2,6,39)
- 	
- 	for (iii = 0 ; iii < sizeof(backlight_type_ids) ; iii++) {
-		if (strnicmp(bl_type, backlight_type_ids[iii].id, sizeof(bl_type)) == 0) {
-+		if (strncasecmp(bl_type, backlight_type_ids[iii].id, sizeof(bl_type)) == 0) {
- 			props.type = backlight_type_ids[iii].type;
- 			printk(KERN_INFO "nvidiabl: backlight type is %s\n", backlight_type_ids[iii].id);
- 		}
--- a/pkgs/servers/memcached/default.nix
+++ b/pkgs/servers/memcached/default.nix
@ -1,12 +1,12 @@
 {stdenv, fetchurl, cyrus_sasl, libevent}:

 stdenv.mkDerivation rec {
-  version = "1.5.5";
+  version = "1.5.6";
  name = "memcached-${version}";

  src = fetchurl {
    url = "http://memcached.org/files/${name}.tar.gz";
-    sha256 = "1v87gvhxih5jav20cp9zdddna31s968xdm2iskc9mqzb5li6di72";
+    sha256 = "00szy9d4szaixi260dcd4846zci04y0sd47ia2lzg0bxkn2ywxcn";
  };

  buildInputs = [cyrus_sasl libevent];
--- a/pkgs/tools/graphics/vips/default.nix
+++ b/pkgs/tools/graphics/vips/default.nix
@ -5,11 +5,11 @@

 stdenv.mkDerivation rec {
  name = "vips-${version}";
-  version = "8.6.2";
+  version = "8.6.3";

  src = fetchurl {
    url = "https://github.com/jcupitt/libvips/releases/download/v${version}/${name}.tar.gz";
-    sha256 = "18hjwk000w49yjjb41qrk4s39mr1xccisrvwy2x063vyjbdbr1ll";
+    sha256 = "14h9w61gaimldmqaym0zhf9fkxjj1pkd5lhglhs6pxphynwxnnpq";
  };

  buildInputs =
--- a/pkgs/tools/misc/profile-cleaner/default.nix
+++ b/pkgs/tools/misc/profile-cleaner/default.nix
@ -1,14 +1,14 @@
 { stdenv, fetchFromGitHub, makeWrapper, parallel, sqlite, bc, file }:

 stdenv.mkDerivation rec {
-  version = "2.36";
+  version = "2.37";
  name = "profile-cleaner-${version}";

  src = fetchFromGitHub {
    owner = "graysky2";
    repo = "profile-cleaner";
    rev = "v${version}";
-    sha256 = "0vm4ca99dyr6i0sfjsr0w06i0rbmqf40kp37h04bk4c8yassq1zq";
+    sha256 = "1fbsn2xvcjkqhhkhidn04iwc0zha68cpkyc9vs5yly38qr1q238a";
  };

  buildInputs = [ makeWrapper ];
--- a/pkgs/tools/misc/qt5ct/default.nix
+++ b/pkgs/tools/misc/qt5ct/default.nix
@ -4,11 +4,11 @@ let inherit (stdenv.lib) getDev; in

 stdenv.mkDerivation rec {
  name = "qt5ct-${version}";
-  version = "0.34";
+  version = "0.35";

  src = fetchurl {
    url = "mirror://sourceforge/qt5ct/${name}.tar.bz2";
-    sha256 = "0aqbilz7acx077zg5rwf2909xabw16047yjdn9nx2gmhp31y00pl";
+    sha256 = "0xzgd12cvm4vyzl8qax6izdmaf46bf18h055z6k178s8pybm1sqw";
  };

  nativeBuildInputs = [ qmake qttools ];
--- a/pkgs/tools/misc/xvfb-run/default.nix
+++ b/pkgs/tools/misc/xvfb-run/default.nix
@ -14,6 +14,7 @@ stdenv.mkDerivation {
    cp ${xvfb_run} $out/bin/xvfb-run

    chmod a+x $out/bin/xvfb-run
+    patchShebangs $out/bin/xvfb-run
    wrapProgram $out/bin/xvfb-run \
      --set FONTCONFIG_FILE "${fontsConf}" \
      --prefix PATH : ${stdenv.lib.makeBinPath [ getopt xorgserver xauth which utillinux gawk coreutils ]}
--- a/pkgs/tools/networking/network-manager/default.nix
+++ b/pkgs/tools/networking/network-manager/default.nix
@ -7,13 +7,13 @@

 let
  pname   = "NetworkManager";
-  version = "1.10.4";
+  version = "1.10.2";
 in stdenv.mkDerivation rec {
  name    = "network-manager-${version}";

  src = fetchurl {
    url    = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
-    sha256 = "1zimmpmpd84dscdky7zad5zr1gk1bnsk0insjm0s9415gjvsgq3x";
+    sha256 = "0nv2jm2lsidlrzn4dkbc5rpj8ma4cpzjqz8z8dmwkqvh0zsk970n";
  };

  outputs = [ "out" "dev" ];
--- a/pkgs/tools/networking/network-manager/fortisslvpn.nix
+++ b/pkgs/tools/networking/network-manager/fortisslvpn.nix
@ -3,13 +3,13 @@ networkmanager, ppp, lib, libsecret, withGnome ? true, gnome3, procps, kmod }:

 let
  pname   = "NetworkManager-fortisslvpn";
-  version = "1.2.8";
+  version = "1.2.4";
 in stdenv.mkDerivation rec {
  name    = "${pname}${if withGnome then "-gnome" else ""}-${version}";

  src = fetchurl {
    url    = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
-    sha256 = "01gvdv9dknvzx05plq863jh1xz1v8vgj5w7v9fmw5v601ggybf4w";
+    sha256 = "0wsbj5lvf9l1w8k5nmaqnzmldilh482bn4z4k8a3wnm62xfxgscr";
  };

  buildInputs = [ openfortivpn networkmanager ppp libtool libsecret ]
--- a/pkgs/tools/networking/whois/default.nix
+++ b/pkgs/tools/networking/whois/default.nix
@ -18,8 +18,8 @@ stdenv.mkDerivation rec {
    for i in Makefile po/Makefile; do
      substituteInPlace $i --replace "prefix = /usr" "prefix = $out"
    done
-
-    substituteInPlace Makefile --replace "DEFS += HAVE_ICONV" "DEFS += HAVE_ICONV\nwhois_LDADD += -liconv"
+  '' + stdenv.lib.optionalString (stdenv.isDarwin || stdenv.hostPlatform.isMusl) ''
+    echo "whois_LDADD += -liconv" >> Makefile
  '';

  makeFlags = [ "HAVE_ICONV=1" ];
@ -39,6 +39,6 @@ stdenv.mkDerivation rec {
    homepage = https://packages.qa.debian.org/w/whois.html;
    license = licenses.gpl2;
    maintainers = with maintainers; [ fpletz ];
-    platforms = platforms.linux;
+    platforms = platforms.unix;
  };
 }
--- a/pkgs/tools/package-management/rpm/default.nix
+++ b/pkgs/tools/package-management/rpm/default.nix
@ -5,11 +5,11 @@

 stdenv.mkDerivation rec {
  name = "rpm-${version}";
-  version = "4.14.0";
+  version = "4.14.1";

  src = fetchurl {
    url = "http://ftp.rpm.org/releases/rpm-4.14.x/rpm-${version}.tar.bz2";
-    sha256 = "053396glswgszzg6wizn76vc8zc5m2bicw025vj44g0dc1aav806";
+    sha256 = "0fvrjq6jsvbllb5q6blchzh7p5flk61rz34g4g9mp9iwrhn0xx23";
  };

  outputs = [ "out" "dev" "man" ];
--- a/pkgs/tools/security/sshuttle/default.nix
+++ b/pkgs/tools/security/sshuttle/default.nix
@ -16,6 +16,11 @@ python3Packages.buildPythonApplication rec {
      url = "https://github.com/sshuttle/sshuttle/commit/91aa6ff625f7c89a19e6f8702425cfead44a146f.patch";
      sha256 = "0sqcc6kj53wlas2d3klbyilhns6vakzwbbp8y7j9wlmbnc530pks";
    })
+    # fix macos patch
+    (fetchpatch {
+      url = "https://github.com/sshuttle/sshuttle/commit/884bd6deb0b699a5648bb1c7bdfbc7be8ea0e7df.patch";
+      sha256 = "1nn0wx0rckxl9yzw9dxjji44zw4xqz7ws4qwjdvfn48w1f786lmz";
+    })
  ];

  nativeBuildInputs = [ makeWrapper python3Packages.setuptools_scm ] ++ stdenv.lib.optional (stdenv.system != "i686-linux") pandoc;
@ -25,14 +30,6 @@ python3Packages.buildPythonApplication rec {

  checkInputs = with python3Packages; [ mock pytest pytestrunner ];

-  # Tests only run with Python 3. Server-side Python 2 still works if client
-  # uses Python 3, so it should be fine.
-  doCheck = true;
-
-  checkPhase = ''
-    py.test -k "${stdenv.lib.optionalString stdenv.isDarwin "not test_parse_subnetport_ip6"}"
-  '';
-
  postInstall = let
    mapPath = f: x: stdenv.lib.concatStringsSep ":" (map f x);
  in ''
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@ -7722,6 +7722,8 @@ with pkgs;

  frame = callPackage ../development/libraries/frame { };

+  fsatrace = callPackage ../development/tools/misc/fsatrace { };
+
  fswatch = callPackage ../development/tools/misc/fswatch { };

  funnelweb = callPackage ../development/tools/literate-programming/funnelweb { };
--- a/pkgs/top-level/haskell-packages.nix
+++ b/pkgs/top-level/haskell-packages.nix
@ -6,16 +6,11 @@
 let
  # These are attributes in compiler and packages that don't support integer-simple.
  integerSimpleExcludes = [
-    "ghc704Binary"
-    "ghc742Binary"
-    "ghc784Binary"
    "ghc7103Binary"
    "ghc821Binary"
-    "ghc704"
-    "ghc763"
+    "ghcCross"
    "ghcjs"
    "ghcjsHEAD"
-    "ghcCross"
    "integer-simple"
  ];

@ -26,29 +21,25 @@ let

  callPackage = newScope { inherit haskellLib; };

+  bootstrapPackageSet = self: super: {
+    mkDerivation = drv: super.mkDerivation (drv // {
+      doCheck = false;
+      doHaddock = false;
+      enableExecutableProfiling = false;
+      enableLibraryProfiling = false;
+      enableSharedExecutables = false;
+      enableSharedLibraries = false;
+    });
+  };
+
 in rec {
  lib = haskellLib;

  compiler = {

-    ghc704Binary = callPackage ../development/compilers/ghc/7.0.4-binary.nix { gmp = pkgs.gmp4; };
-    ghc742Binary = callPackage ../development/compilers/ghc/7.4.2-binary.nix { gmp = pkgs.gmp4; };
-    ghc784Binary = callPackage ../development/compilers/ghc/7.8.4-binary.nix { };
    ghc7103Binary = callPackage ../development/compilers/ghc/7.10.3-binary.nix { };
    ghc821Binary = callPackage ../development/compilers/ghc/8.2.1-binary.nix { };

-    ghc704 = callPackage ../development/compilers/ghc/7.0.4.nix {
-      ghc = compiler.ghc704Binary;
-    };
-    ghc742 = callPackage ../development/compilers/ghc/7.4.2.nix {
-      ghc = compiler.ghc704Binary;
-    };
-    ghc763 = callPackage ../development/compilers/ghc/7.6.3.nix {
-      ghc = compiler.ghc704Binary;
-    };
-    ghc784 = callPackage ../development/compilers/ghc/7.8.4.nix {
-      ghc = compiler.ghc742Binary;
-    };
    ghc7103 = callPackage ../development/compilers/ghc/7.10.3.nix rec {
      bootPkgs = packages.ghc7103Binary;
      inherit (bootPkgs) hscolour;
@ -114,6 +105,7 @@ in rec {
      buildHaskellPackages = bh.packages.ghc7103Binary;
      ghc = bh.compiler.ghc7103Binary;
      compilerConfig = callPackage ../development/haskell-modules/configuration-ghc-7.10.x.nix { };
+      packageSetConfig = bootstrapPackageSet;
    };
    ghc802 = callPackage ../development/haskell-modules {
      buildHaskellPackages = bh.packages.ghc802;
@ -124,6 +116,7 @@ in rec {
      buildHaskellPackages = bh.packages.ghc821Binary;
      ghc = bh.compiler.ghc821Binary;
      compilerConfig = callPackage ../development/haskell-modules/configuration-ghc-8.2.x.nix { };
+      packageSetConfig = bootstrapPackageSet;
    };
    ghc822 = callPackage ../development/haskell-modules {
      buildHaskellPackages = bh.packages.ghc822;
--- a/pkgs/top-level/perl-packages.nix
+++ b/pkgs/top-level/perl-packages.nix
@ -7654,7 +7654,7 @@ let self = _self // overrides; _self = with self; {
      echo "1;" > lib/JSON/backportPP.pm
    '';
    postConfigure = ''
-      cp lib/JSON/backportPP.pm{,orig}
+      cp lib/JSON/backportPP.pm{orig,}
    '';
    buildInputs = [ TestPod ];
    meta = {