Merge master into staging-next

nixos/modules/services/mail/spamassassin.nix

@@ -5,7 +5,6 @@ with lib;
 let
   cfg = config.services.spamassassin;
   spamassassin-local-cf = pkgs.writeText "local.cf" cfg.config;
-  spamassassin-init-pre = pkgs.writeText "init.pre" cfg.initPreConf;
 
   spamdEnv = pkgs.buildEnv {
     name = "spamd-env";
@@ -65,8 +64,9 @@ in
       };
 
       initPreConf = mkOption {
-        type = types.str;
+        type = with types; either str path;
         description = "The SpamAssassin init.pre config.";
+        apply = val: if builtins.isPath val then val else pkgs.writeText "init.pre" val;
         default =
         ''
           #

nixos/tests/kafka.nix

@@ -89,4 +89,5 @@ in with pkgs; {
   kafka_2_1  = makeKafkaTest "kafka_2_1"  apacheKafka_2_1;
   kafka_2_2  = makeKafkaTest "kafka_2_2"  apacheKafka_2_2;
   kafka_2_3  = makeKafkaTest "kafka_2_3"  apacheKafka_2_3;
+  kafka_2_4  = makeKafkaTest "kafka_2_4"  apacheKafka_2_4;
 }

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

@@ -175,6 +175,7 @@ in {
       ./no-buildconfig.patch
       missing-documentation-patch
     ];
+    meta.knownVulnerabilities = [ "Support ended around October 2019." ];
   };
 
   # Similarly to firefox-esr-52 above.
@@ -196,94 +197,8 @@ in {
     meta.knownVulnerabilities = [ "Support ended in August 2018." ];
   };
 
-}) // (let
+  tor-browser-7-5 = throw "firefoxPackages.tor-browser-7-5 was removed because it was out of date and inadequately maintained. Please use tor-browser-bundle-bin instead. See #77452.";
-
+  tor-browser-8-5 = throw "firefoxPackages.tor-browser-8-5 was removed because it was out of date and inadequately maintained. Please use tor-browser-bundle-bin instead. See #77452.";
-  tbcommon = args: common (args // {
+  tor-browser = throw "firefoxPackages.tor-browser was removed because it was out of date and inadequately maintained. Please use tor-browser-bundle-bin instead. See #77452.";
-    pname = "tor-browser";
-    isTorBrowserLike = true;
-
-    unpackPhase = ''
-      # fetchFromGitHub produces ro sources, root dir gets a name that
-      # is too long for shebangs. fixing
-      cp -a $src tor-browser
-      chmod -R +w tor-browser
-      cd tor-browser
-
-      # set times for xpi archives
-      find . -exec touch -d'2010-01-01 00:00' {} \;
-    '';
-
-    meta = (args.meta or {}) // {
-      description = "A web browser built from TorBrowser source tree";
-      longDescription = ''
-        This is a version of TorBrowser with bundle-related patches
-        reverted.
-
-        I.e. it's a variant of Firefox with less fingerprinting and
-        some isolation features you can't get with any extensions.
-
-        Or, alternatively, a variant of TorBrowser that works like any
-        other UNIX program and doesn't expect you to run it from a
-        bundle.
-
-        It will use your default Firefox profile if you're not careful
-        even! Be careful!
-
-        It will clash with firefox binary if you install both. But it
-        should not be a problem because you should run browsers in
-        separate users/VMs anyway.
-
-        Create new profile by starting it as
-
-        $ firefox -ProfileManager
-
-        and then configure it to use your tor instance.
-
-        Or just use `tor-browser-bundle` package that packs this
-        `tor-browser` back into a sanely-built bundle.
-      '';
-      homepage = "https://www.torproject.org/projects/torbrowser.html";
-      platforms = lib.platforms.unix;
-      license = with lib.licenses; [ mpl20 bsd3 ];
-    };
-  });
-
-in rec {
-
-  tor-browser-7-5 = (tbcommon {
-    ffversion = "52.9.0esr";
-    tbversion = "7.5.6";
-
-    # FIXME: fetchFromGitHub is not ideal, unpacked source is >900Mb
-    src = fetchFromGitHub {
-      owner = "SLNOS";
-      repo  = "tor-browser";
-      # branch "tor-browser-52.9.0esr-7.5-2-slnos"
-      rev   = "95bb92d552876a1f4260edf68fda5faa3eb36ad8";
-      sha256 = "1ykn3yg4s36g2cpzxbz7s995c33ij8kgyvghx38z4i8siaqxdddy";
-    };
-  }).override {
-    gtk3Support = false;
-  };
-
-  tor-browser-8-5 = tbcommon rec {
-    ffversion = "60.9.0esr";
-    tbversion = "8.5.6";
-
-    # FIXME: fetchFromGitHub is not ideal, unpacked source is >900Mb
-    src = fetchFromGitHub {
-      owner = "SLNOS";
-      repo  = "tor-browser";
-      # branch "tor-browser-60.9.0esr-8.5-2-slnos"
-      rev   = "0489ae3158cd8c0e16c2e78b94083d8cbf0209dc";
-      sha256 = "0y5s7d8pg8ak990dp8d801j9823igaibfhv9hsa79nib5yllifzs";
-    };
-
-    patches = [
-      missing-documentation-patch
-    ];
-  };
-
-  tor-browser = tor-browser-8-5;
 
 })

pkgs/applications/networking/browsers/mozilla-plugins/google-talk-plugin/default.nix

@@ -48,21 +48,21 @@ in
 stdenv.mkDerivation rec {
   pname = "google-talk-plugin";
 
-  # You can get the upstream version and SHA-1 hash from the following URLs:
+  # You can get the upstream version and SHA-256 hash from the following URLs:
-  # curl -s http://dl.google.com/linux/talkplugin/deb/dists/stable/main/binary-amd64/Packages | grep -E 'Version|SHA1'
+  # curl -s http://dl.google.com/linux/talkplugin/deb/dists/stable/main/binary-amd64/Packages | grep -E 'Version|SHA256'
-  # curl -s http://dl.google.com/linux/talkplugin/deb/dists/stable/main/binary-i386/Packages | grep -E 'Version|SHA1'
+  # curl -s http://dl.google.com/linux/talkplugin/deb/dists/stable/main/binary-i386/Packages | grep -E 'Version|SHA256'
   version = "5.41.3.0";
 
   src =
     if stdenv.hostPlatform.system == "x86_64-linux" then
       fetchurl {
         url = "${baseURL}/google-talkplugin_${version}-1_amd64.deb";
-        sha1 = "0bbc3d6997ba22ce712d93e5bc336c894b54fc81";
+        sha256 = "af7e23d2b6215afc547f96615b99f04e0561557cc58c0c9302364b5a3840d97d";
       }
     else if stdenv.hostPlatform.system == "i686-linux" then
       fetchurl {
         url = "${baseURL}/google-talkplugin_${version}-1_i386.deb";
-        sha1 = "6eae0544858f85c68b0cc46d7786e990bd94f139";
+        sha256 = "4c46d2b7f2018640288cd7ac49adc47e309d0beadfd979eb03030e672016b4a7";
       }
     else throw "Google Talk does not support your platform.";
 

pkgs/applications/networking/browsers/tor-browser-bundle-bin/default.nix

@@ -54,9 +54,6 @@
 
 # Extra preferences
 , extraPrefs ? ""
-
-# For meta
-, tor-browser-bundle
 }:
 
 with stdenv.lib;
@@ -93,19 +90,19 @@ let
   fteLibPath = makeLibraryPath [ stdenv.cc.cc gmp ];
 
   # Upstream source
-  version = "9.0.3";
+  version = "9.0.4";
 
   lang = "en-US";
 
   srcs = {
     x86_64-linux = fetchurl {
       url = "https://dist.torproject.org/torbrowser/${version}/tor-browser-linux64-${version}_${lang}.tar.xz";
-      sha256 = "0saipnmhjfqwrx0q8mn3zc9n0j5a754cfipdaizbcqwm9dwd70w9";
+      sha256 = "14zlf02i447hcdr4qap8af1k4aziznfp9m2ygqz05zsy8icm1j2k";
     };
 
     i686-linux = fetchurl {
       url = "https://dist.torproject.org/torbrowser/${version}/tor-browser-linux32-${version}_${lang}.tar.xz";
-      sha256 = "19r6zm81p9fv9ldsck5wilcihvb5bifmd1cms6wdkldz8crnn9l6";
+      sha256 = "1bmih91gsh698fp2mbnjcq8vmwhg822wanmn99r0xhkmgpi4zw2s";
     };
   };
 in
@@ -394,7 +391,15 @@ stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     description = "Tor Browser Bundle built by torproject.org";
-    longDescription = tor-browser-bundle.meta.longDescription;
+    longDescription = ''
+      Tor Browser Bundle is a bundle of the Tor daemon, Tor Browser (heavily patched version of
+      Firefox), several essential extensions for Tor Browser, and some tools that glue those
+      together with a convenient UI.
+
+      `tor-browser-bundle-bin` package is the official version built by torproject.org patched with
+      `patchelf` to work under nix and with bundled scripts adapted to the read-only nature of
+      the `/nix/store`.
+    '';
     homepage = "https://www.torproject.org/";
     platforms = attrNames srcs;
     maintainers = with maintainers; [ offline matejc doublec thoughtpolice joachifm hax404 cap ];

pkgs/applications/networking/browsers/tor-browser-bundle/default.nix

@@ -1,345 +0,0 @@
-{ stdenv
-, fetchgit
-, fetchurl
-, symlinkJoin
-
-, tor
-, tor-browser-unwrapped
-
-# Wrapper runtime
-, coreutils
-, hicolor-icon-theme
-, shared-mime-info
-, noto-fonts
-, noto-fonts-emoji
-
-# Audio support
-, audioSupport ? mediaSupport
-, apulse
-
-# Media support (implies audio support)
-, mediaSupport ? false
-, ffmpeg
-
-# Extensions, common
-, zip
-
-# HTTPS Everywhere
-, git
-, libxml2 # xmllint
-, python27
-, python27Packages
-, rsync
-
-# Pluggable transports
-, obfs4
-
-# Customization
-, extraPrefs ? ""
-, extraExtensions ? [ ]
-}:
-
-with stdenv.lib;
-
-let
-  tor-browser-build_src = fetchgit {
-    url = "https://git.torproject.org/builders/tor-browser-build.git";
-    rev = "refs/tags/tbb-7.5a5-build5";
-    sha256 = "0j37mqldj33fnzghxifvy6v8vdwkcz0i4z81prww64md5s8qcsa9";
-  };
-
-  firefoxExtensions = import ./extensions.nix {
-    inherit stdenv fetchurl fetchgit zip
-      git libxml2 python27 python27Packages rsync;
-  };
-
-  bundledExtensions = with firefoxExtensions; [
-    https-everywhere
-    noscript
-    torbutton
-    tor-launcher
-  ] ++ extraExtensions;
-
-  fontsEnv = symlinkJoin {
-    name = "tor-browser-fonts";
-    paths = [ noto-fonts noto-fonts-emoji ];
-  };
-
-  fontsDir = "${fontsEnv}/share/fonts";
-
-  mediaLibPath = makeLibraryPath [
-    ffmpeg
-  ];
-in
-stdenv.mkDerivation {
-  pname = "tor-browser-bundle";
-  version = tor-browser-unwrapped.version;
-
-  buildInputs = [ tor-browser-unwrapped tor ];
-
-  dontUnpack = true;
-
-  buildPhase = ":";
-
-  # The following creates a customized firefox distribution.  For
-  # simplicity, we copy the entire base firefox runtime, to work around
-  # firefox's annoying insistence on resolving the installation directory
-  # relative to the real firefox executable.  A little tacky and
-  # inefficient but it works.
-  installPhase = ''
-    TBBUILD=${tor-browser-build_src}/projects/tor-browser
-    TBDATA_PATH=TorBrowser-Data
-
-    self=$out/lib/tor-browser
-    mkdir -p $self && cd $self
-
-    TBDATA_IN_STORE=$self/$TBDATA_PATH
-
-    cp -dR ${tor-browser-unwrapped}/lib"/"*"/"* .
-    chmod -R +w .
-
-    # Prepare for autoconfig
-    cat >defaults/pref/autoconfig.js <<EOF
-    pref("general.config.filename", "mozilla.cfg");
-    pref("general.config.obscure_value", 0);
-    EOF
-
-    # Hardcoded configuration
-    cat >mozilla.cfg <<EOF
-    // First line must be a comment
-
-    // Always update via Nixpkgs
-    lockPref("app.update.auto", false);
-    lockPref("app.update.enabled", false);
-    lockPref("extensions.update.autoUpdateDefault", false);
-    lockPref("extensions.update.enabled", false);
-    lockPref("extensions.torbutton.updateNeeded", false);
-    lockPref("extensions.torbutton.versioncheck_enabled", false);
-
-    // Where to find the Nixpkgs tor executable & config
-    lockPref("extensions.torlauncher.tor_path", "${tor}/bin/tor");
-    lockPref("extensions.torlauncher.torrc-defaults_path", "$TBDATA_IN_STORE/torrc-defaults");
-
-    // Captures store paths
-    clearPref("extensions.xpiState");
-    clearPref("extensions.bootstrappedAddons");
-
-    // Insist on using IPC for communicating with Tor
-    lockPref("extensions.torlauncher.control_port_use_ipc", true);
-    lockPref("extensions.torlauncher.socks_port_use_ipc", true);
-
-    // Allow sandbox access to sound devices if using ALSA directly
-    ${if audioSupport then ''
-      pref("security.sandbox.content.write_path_whitelist", "/dev/snd/");
-    '' else ''
-      clearPref("security.sandbox.content.write_path_whitelist");
-    ''}
-
-    // User customization
-    ${extraPrefs}
-    EOF
-
-    # Preload extensions
-    find ${toString bundledExtensions} -name '*.xpi' -exec ln -s -t browser/extensions '{}' '+'
-
-    # Copy bundle data
-    bundlePlatform=linux
-    bundleData=$TBBUILD/Bundle-Data
-
-    mkdir -p $TBDATA_PATH
-    cat \
-      $bundleData/$bundlePlatform/Data/Tor/torrc-defaults \
-      >> $TBDATA_PATH/torrc-defaults
-    cat \
-      $bundleData/$bundlePlatform/Data/Browser/profile.default/preferences/extension-overrides.js \
-      $bundleData/PTConfigs/bridge_prefs.js \
-      >> defaults/pref/extension-overrides.js
-
-    # Configure geoip
-    #
-    # tor-launcher insists on resolving geoip data relative to torrc-defaults
-    # (and passes them directly on the tor command-line).
-    #
-    # Write the paths into torrc-defaults anyway, otherwise they'll be
-    # captured in the runtime torrc.
-    ln -s -t $TBDATA_PATH ${tor.geoip}/share/tor/geoip{,6}
-    cat >>$TBDATA_PATH/torrc-defaults <<EOF
-    GeoIPFile $TBDATA_IN_STORE/geoip
-    GeoIPv6File $TBDATA_IN_STORE/geoip6
-    EOF
-
-    # Configure pluggable transports
-    substituteInPlace $TBDATA_PATH/torrc-defaults \
-      --replace "./TorBrowser/Tor/PluggableTransports/obfs4proxy" \
-                "${obfs4}/bin/obfs4proxy"
-
-    # Hard-code path to TBB fonts; xref: FONTCONFIG_FILE in the wrapper below
-    sed $bundleData/$bundlePlatform/Data/fontconfig/fonts.conf \
-        -e "s,<dir>fonts</dir>,<dir>${fontsDir}</dir>," \
-        > $TBDATA_PATH/fonts.conf
-
-    # Generate a suitable wrapper
-    wrapper_PATH=${makeBinPath [ coreutils ]}
-    wrapper_XDG_DATA_DIRS=${concatMapStringsSep ":" (x: "${x}/share") [
-      hicolor-icon-theme
-      shared-mime-info
-    ]}
-
-    ${optionalString audioSupport ''
-      # apulse uses a non-standard library path ...
-      wrapper_LD_LIBRARY_PATH=${apulse}/lib/apulse''${wrapper_LD_LIBRARY_PATH:+:$wrapper_LD_LIBRARY_PATH}
-    ''}
-
-    ${optionalString mediaSupport ''
-      wrapper_LD_LIBRARY_PATH=${mediaLibPath}''${wrapper_LD_LIBRARY_PATH:+:$wrapper_LD_LIBRARY_PATH}
-    ''}
-
-    mkdir -p $out/bin
-    cat >$out/bin/tor-browser <<EOF
-    #! ${stdenv.shell} -eu
-
-    umask 077
-
-    PATH=$wrapper_PATH
-
-    readonly THE_HOME=\$HOME
-    TBB_HOME=\''${TBB_HOME:-\''${XDG_DATA_HOME:-\$HOME/.local/share}/tor-browser}
-    if [[ \''${TBB_HOME:0:1} != / ]] ; then
-      TBB_HOME=\$PWD/\$TBB_HOME
-    fi
-    readonly TBB_HOME
-
-    # Basic sanity check: never want to vomit directly onto user's homedir
-    if [[ "\$TBB_HOME" = "\$THE_HOME" ]] ; then
-      echo 'TBB_HOME=\$HOME; refusing to run' >&2
-      exit 1
-    fi
-
-    mkdir -p "\$TBB_HOME"
-
-    HOME=\$TBB_HOME
-    cd "\$HOME"
-
-    # Re-init XDG basedir envvars
-    XDG_CACHE_HOME=\$HOME/.cache
-    XDG_CONFIG_HOME=\$HOME/.config
-    XDG_DATA_HOME=\$HOME/.local/share
-
-    # Initialize empty TBB runtime state directory hierarchy.  Mirror the
-    # layout used by the official TBB, to avoid the hassle of working
-    # against the assumptions made by tor-launcher & co.
-    mkdir -p "\$HOME/TorBrowser" "\$HOME/TorBrowser/Data"
-
-    # Initialize the Tor data directory.
-    mkdir -p "\$HOME/TorBrowser/Data/Tor"
-
-    # TBB fails if ownership is too permissive
-    chmod 0700 "\$HOME/TorBrowser/Data/Tor"
-
-    # Initialize the browser profile state.  Expect TBB to generate all data.
-    mkdir -p "\$HOME/TorBrowser/Data/Browser/profile.default"
-
-    # Files that capture store paths; re-generated by firefox at startup
-    rm -rf "\$HOME/TorBrowser/Data/Browser/profile.default"/{compatibility.ini,extensions.ini,extensions.json,startupCache}
-
-    # Clear out fontconfig caches
-    rm -f "\$HOME/.cache/fontconfig/"*.cache-*
-
-    # Lift-off!
-    #
-    # TZ is set to avoid stat()ing /etc/localtime over and over ...
-    #
-    # DBUS_SESSION_BUS_ADDRESS is inherited to avoid auto-launching a new
-    # dbus instance; to prevent using the session bus, set the envvar to
-    # an empty/invalid value prior to running tor-browser.
-    #
-    # FONTCONFIG_FILE is required to make fontconfig read the TBB
-    # fonts.conf; upstream uses FONTCONFIG_PATH, but FC_DEBUG=1024
-    # indicates the system fonts.conf being used instead.
-    #
-    # HOME, TMPDIR, XDG_*_HOME are set as a form of soft confinement;
-    # ideally, tor-browser should not write to any path outside TBB_HOME
-    # and should run even under strict confinement to TBB_HOME.
-    #
-    # XDG_DATA_DIRS is set to prevent searching system directories for
-    # mime and icon data.
-    #
-    # PULSE_{SERVER,COOKIE} is necessary for audio playback w/pulseaudio
-    #
-    # APULSE_PLAYBACK_DEVICE is for audio playback w/o pulseaudio (no capture yet)
-    #
-    # TOR_* is for using an external tor instance
-    #
-    # Parameters lacking a default value below are *required* (enforced by
-    # -o nounset).
-    exec env -i \
-      LD_LIBRARY_PATH=$wrapper_LD_LIBRARY_PATH \
-      \
-      TZ=":" \
-      \
-      DISPLAY="\$DISPLAY" \
-      XAUTHORITY="\''${XAUTHORITY:-}" \
-      DBUS_SESSION_BUS_ADDRESS="\$DBUS_SESSION_BUS_ADDRESS" \
-      \
-      HOME="\$HOME" \
-      TMPDIR="\$XDG_CACHE_HOME/tmp" \
-      XDG_CONFIG_HOME="\$XDG_CONFIG_HOME" \
-      XDG_DATA_HOME="\$XDG_DATA_HOME" \
-      XDG_CACHE_HOME="\$XDG_CACHE_HOME" \
-      XDG_RUNTIME_DIR="\$HOME/run" \
-      \
-      XDG_DATA_DIRS="$wrapper_XDG_DATA_DIRS" \
-      \
-      FONTCONFIG_FILE="$TBDATA_IN_STORE/fonts.conf" \
-      \
-      APULSE_PLAYBACK_DEVICE="\''${APULSE_PLAYBACK_DEVICE:-plug:dmix}" \
-      \
-      TOR_SKIP_LAUNCH="\''${TOR_SKIP_LAUNCH:-}" \
-      TOR_CONTROL_PORT="\''${TOR_CONTROL_PORT:-}" \
-      TOR_SOCKS_PORT="\''${TOR_SOCKS_PORT:-}" \
-      \
-      $self/firefox \
-        -no-remote \
-        -profile "\$HOME/TorBrowser/Data/Browser/profile.default" \
-        "\$@"
-    EOF
-    chmod +x $out/bin/tor-browser
-
-    echo "Syntax checking wrapper ..."
-    bash -n $out/bin/tor-browser
-
-    echo "Checking wrapper ..."
-    DISPLAY="" XAUTHORITY="" DBUS_SESSION_BUS_ADDRESS="" TBB_HOME=$(mktemp -d) \
-    $out/bin/tor-browser -version >/dev/null
-  '';
-
-  passthru.execdir = "/bin";
-  meta = with stdenv.lib; {
-    description = "An unofficial version of the Tor Browser Bundle, built from source";
-    longDescription = ''
-      Tor Browser Bundle is a bundle of the Tor daemon, Tor Browser (heavily patched version of
-      Firefox), several essential extensions for Tor Browser, and some tools that glue those
-      together with a convenient UI.
-
-      `tor-browser-bundle-bin` package is the official version built by torproject.org patched with
-      `patchelf` to work under nix and with bundled scripts adapted to the read-only nature of
-      the `/nix/store`.
-
-      `tor-browser-bundle` package is the version built completely from source. It reuses the `tor`
-      package for the tor daemon, `firefoxPackages.tor-browser` package for the tor-browser, and
-      builds all the extensions from source.
-
-      Note that `tor-browser-bundle` package is not only built from source, but also bundles Tor
-      Browser differently from the official `tor-browser-bundle-bin` implementation. The official
-      Tor Browser is not a normal UNIX program and is heavily patched for its use in the Tor Browser
-      Bundle (which `tor-browser-bundle-bin` package then has to work around for the read-only
-      /nix/store). Meanwhile, `firefoxPackages.tor-browser` reverts all those patches, allowing
-      `firefoxPackages.tor-browser` to be used independently of the bundle, and then implements what
-      `tor-browser-bundle` needs for the bundling using a much simpler patch. See the
-      longDescription and expression of the `firefoxPackages.tor-browser` package for more info.
-    '';
-    inherit (tor-browser-unwrapped.meta) homepage platforms license;
-    hydraPlatforms = [ ];
-    maintainers = with maintainers; [ joachifm ];
-  };
-}

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

@@ -17,11 +17,11 @@ let
   vivaldiName = if isSnapshot then "vivaldi-snapshot" else "vivaldi";
 in stdenv.mkDerivation rec {
   pname = "vivaldi";
-  version = "2.10.1745.23-1";
+  version = "2.10.1745.26-1";
 
   src = fetchurl {
     url = "https://downloads.vivaldi.com/${branch}/vivaldi-${branch}_${version}_amd64.deb";
-    sha256 = "1dkyanasycarka6zikrk0pn6n0xin7hrnysm67rs7pam4lzpq0vh";
+    sha256 = "0zl5sqa60x9yg7acp6vxgnmfzz27v849mlpp1wgnwh019fx3wf53";
   };
 
   unpackPhase = ''

pkgs/applications/networking/mullvad-vpn/default.nix

@@ -84,7 +84,7 @@ stdenv.mkDerivation rec {
     changelog = "https://github.com/mullvad/mullvadvpn-app/blob/${version}/CHANGELOG.md";
     license = licenses.gpl3;
     platforms = [ "x86_64-linux" ];
-    maintainers = [ maintainers.xfix ];
+    maintainers = with maintainers ;[ filalex77 xfix ];
   };
 
 }

pkgs/applications/science/biology/xenomapper/default.nix

@@ -14,7 +14,7 @@ buildPythonPackage rec {
   propagatedBuildInputs = [ statistics ];
 
   meta = with lib; {
-    homepage = "http://github.com/genomematt/xenomapper";
+    homepage = "https://github.com/genomematt/xenomapper";
     description = "A utility for post processing mapped reads that have been aligned to a primary genome and a secondary genome and binning reads into species specific, multimapping in each species, unmapped and unassigned bins";
     license = licenses.gpl3;
     platforms = platforms.all;

pkgs/build-support/docker/default.nix

@@ -325,7 +325,6 @@ rec {
         | jshon -d config \
         | jshon -s "1970-01-01T00:00:01Z" -i created > generic.json
 
-
       # WARNING!
       # The following code is fiddly w.r.t. ensuring every layer is
       # created, and that no paths are missed. If you change the
@@ -625,7 +624,22 @@ rec {
           -i "$imageName" > image/repositories
 
         echo "Cooking the image..."
-        tar -C image --dereference --hard-dereference --sort=name --mtime="@$SOURCE_DATE_EPOCH" --owner=0 --group=0  --mode=a-w --xform s:'^./':: -c . | pigz -nT > $out
+        # tar exits with an exit code of 1 if files changed while it was
+        # reading them. It considers a change in the number of hard links
+        # to be a "change", which can cause this to fail if images are being
+        # built concurrently and the auto-optimise-store nix option is turned on.
+        # Since the contents of these files will not change, we can reasonably
+        # ignore this exit code.
+        set +e
+        tar -C image --dereference --hard-dereference --sort=name \
+          --mtime="@$SOURCE_DATE_EPOCH" --owner=0 --group=0  \
+          --mode=a-w --xform s:'^./':: --use-compress-program='pigz -nT' \
+          --warning=no-file-changed -cf $out .
+        RET=$?
+        if [ $RET -ne 0 ] && [ $RET -ne 1 ]; then
+          exit $RET
+        fi
+        set -e
 
         echo "Finished."
       '';

pkgs/build-support/docker/store-path-to-layer.sh

@@ -5,16 +5,43 @@ set -eu
 layerNumber=$1
 shift
 
+storePath="$1"
+shift
+
 layerPath="./layers/$layerNumber"
-echo "Creating layer #$layerNumber for $@"
+echo "Creating layer #$layerNumber for $storePath"
 
 mkdir -p "$layerPath"
-tar --no-recursion -rf "$layerPath/layer.tar" \
+
+# Make sure /nix and /nix/store appear first in the archive.
+# We create the directories here and use them because
+# when there are other things being added to the
+# nix store, tar could fail, saying,
+# "tar: /nix/store: file changed as we read it"
+mkdir -p nix/store
+tar -cf "$layerPath/layer.tar"  \
     --mtime="@$SOURCE_DATE_EPOCH" \
-    --owner=0 --group=0 /nix /nix/store
+    --owner=0 --group=0 \
-tar -rpf "$layerPath/layer.tar" --hard-dereference --sort=name \
+    --transform='s,nix,/nix,' \
+    nix
+
+# We change into the /nix/store in order to avoid a similar
+# "file changed as we read it" error as above. Namely,
+# if we use the absolute path of /nix/store/123-pkg
+# and something new is added to the nix store while tar
+# is running, it will detect a change to /nix/store and
+# fail. Instead, if we cd into the nix store and copy
+# the relative nix store path, tar will ignore changes
+# to /nix/store. In order to create the correct structure
+# in the tar file, we transform the relative nix store
+# path to the absolute store path.
+n=$(basename "$storePath")
+tar -C /nix/store -rpf "$layerPath/layer.tar" \
+    --hard-dereference --sort=name \
     --mtime="@$SOURCE_DATE_EPOCH" \
-    --owner=0 --group=0 "$@"
+    --owner=0 --group=0 \
+    --transform="s,$n,/nix/store/$n," \
+    $n
 
 # Compute a checksum of the tarball.
 tarhash=$(tarsum < $layerPath/layer.tar)

pkgs/development/compilers/go/1.12.nix

@@ -30,11 +30,11 @@ in
 
 stdenv.mkDerivation rec {
   pname = "go";
-  version = "1.12.10";
+  version = "1.12.15";
 
   src = fetchurl {
     url = "https://dl.google.com/go/go${version}.src.tar.gz";
-    sha256 = "0m1rvawvpdl7kd0asw10m50xbxlhykix6dng9p4x6ih6x3y4hvpm";
+    sha256 = "1hw4xjywcl883dnvfbb92w85sy8n231fdri4aynj8xajgr0p9fla";
   };
 
   # perl is used for testing go vet

pkgs/development/compilers/go/1.13.nix

@@ -30,11 +30,11 @@ in
 
 stdenv.mkDerivation rec {
   pname = "go";
-  version = "1.13.5";
+  version = "1.13.6";
 
   src = fetchurl {
     url = "https://dl.google.com/go/go${version}.src.tar.gz";
-    sha256 = "1zr6lravlmyld57nnymkcr092pys4pr8qy0ans1rj3dkl3i5dlr7";
+    sha256 = "03220q6n4wlpmz6zz3mw48kl3pjxia6pxdvf03wbqh6w9favxrda";
   };
 
   # perl is used for testing go vet

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

@@ -74,7 +74,7 @@ self: super: {
       name = "git-annex-${super.git-annex.version}-src";
       url = "git://git-annex.branchable.com/";
       rev = "refs/tags/" + super.git-annex.version;
-      sha256 = "1i4arhwbc05iz8hl7kk843m2f49i3ysby1kxcm9qfhpk7z9nyzj4";
+      sha256 = "0s8sv6h90l2a9xdabj0nirhpr6d2k8s5cddjdkm50x395i014w31";
     };
   }).override {
     dbus = if pkgs.stdenv.isLinux then self.dbus else null;
@@ -1261,7 +1261,7 @@ self: super: {
 
   # The LTS-14.x version of their dependencies are too old.
   cabal-plan = super.cabal-plan.overrideScope (self: super: { optparse-applicative = self.optparse-applicative_0_15_1_0; ansi-terminal = self.ansi-terminal_0_10_2; base-compat = self.base-compat_0_11_0; semialign = self.semialign_1_1; time-compat = doJailbreak super.time-compat; });
-  hoogle = super.hoogle.override { haskell-src-exts = self.haskell-src-exts_1_22_0; };
+  hoogle = super.hoogle.override { haskell-src-exts = self.haskell-src-exts_1_23_0; };
 
   # Version bounds for http-client are too strict:
   # https://github.com/bitnomial/prometheus/issues/34
@@ -1325,7 +1325,7 @@ self: super: {
   });
 
   # Needs the corresponding version of haskell-src-exts.
-  haskell-src-exts-simple = super.haskell-src-exts-simple.override { haskell-src-exts = self.haskell-src-exts_1_22_0; };
+  haskell-src-exts-simple = super.haskell-src-exts-simple.override { haskell-src-exts = self.haskell-src-exts_1_23_0; };
 
   # https://github.com/Daniel-Diaz/HaTeX/issues/144
   HaTeX = dontCheck super.HaTeX;
@@ -1365,4 +1365,8 @@ self: super: {
   ormolu = doJailbreak (super.ormolu.override {
     ghc-lib-parser = self.ghc-lib-parser_8_8_1_20191204;
   });
+
+  # krank-0.1.0 does not accept PyF-0.9.0.0.
+  krank = doJailbreak super.krank;
+
 } // import ./configuration-tensorflow.nix {inherit pkgs haskellLib;} self super

pkgs/development/haskell-modules/configuration-ghc-8.10.x.nix

@@ -16,6 +16,7 @@ self: super: {
   containers = null;
   deepseq = null;
   directory = null;
+  exceptions = null;
   filepath = null;
   ghc-boot = null;
   ghc-boot-th = null;

pkgs/development/haskell-modules/configuration-ghc-8.8.x.nix

@@ -91,7 +91,7 @@ self: super: {
   microlens-th = self.microlens-th_0_4_3_2;
   network = self.network_3_1_1_1;
   optparse-applicative = self.optparse-applicative_0_15_1_0;
-  pandoc = self.pandoc_2_9_1;
+  pandoc = self.pandoc_2_9_1_1;
   pandoc-types = self.pandoc-types_1_20;
   prettyprinter = self.prettyprinter_1_5_1;
   primitive = dontCheck super.primitive_0_7_0_0;  # evaluating the test suite gives an infinite recursion
@@ -107,7 +107,7 @@ self: super: {
   sop-core = self.sop-core_0_5_0_0;
   texmath = self.texmath_0_12;
   th-desugar = self.th-desugar_1_10;
-  tls = self.tls_1_5_2;
+  tls = self.tls_1_5_3;
   trifecta = self.trifecta_2_1;
   vty = self.vty_5_26;
   xml-conduit = overrideCabal super.xml-conduit (drv: { version = "1.9.0.0"; sha256 = "1p57v127882rxvvmwjmvnqdmk3x2wg1z4d8y03849h0xaz1vid0w"; });

pkgs/development/haskell-modules/configuration-hackage2nix.yaml

@@ -42,8 +42,32 @@ core-packages:
   # of this library are marked as "broken".
   - ghcjs-base-0
 
+# This is a list of packages with versions from the latest Stackage LTS release.
+#
+# The packages and versions in this list cause the `hackage2nix` tool to
+# generate the package at the given version.
+#
+# For instance, with a line like the following:
+#
+# - aeson ==1.4.6.0
+#
+# `hackage2nix` will generate the `aeson` package at version 1.4.6.0 in the
+# ./hackage-packages.nix file.
+#
+# Since the packages in the LTS package set are sometimes older than the latest
+# on Hackage, `hackage2nix` is smart enough to also generate the latest version
+# of a given package.
+#
+# In the above example with aeson, if there was version 1.5.0.0 of aeson
+# available on Hackage, `hackage2nix` would generate two packages, `aeson`
+# at version 1.4.6.0 and `aeson_1_5_0_0` at version 1.5.0.0.
+#
+# WARNING: This list is generated semiautomatically based on the most recent
+# LTS package set. If you want to add entries to it, you must do so before the
+# comment saying "# LTS Haskell x.y". Any changes after that commend will be
+# lost the next time `update-stackage.sh` runs.
 default-package-overrides:
-  # LTS Haskell 14.18
+  # LTS Haskell 14.20
   - abstract-deque ==0.3
   - abstract-deque-tests ==0.3
   - abstract-par ==0.3.3
@@ -73,7 +97,7 @@ default-package-overrides:
   - alarmclock ==0.7.0.2
   - alerts ==0.1.2.0
   - alex ==3.2.5
-  - alg ==0.2.13.0
+  - alg ==0.2.13.1
   - algebraic-graphs ==0.4
   - Allure ==0.9.5.0
   - almost-fix ==0.0.2
@@ -263,10 +287,9 @@ default-package-overrides:
   - bzlib-conduit ==0.3.0.2
   - c2hs ==0.28.6
   - Cabal ==2.4.1.0
-  - cabal2spec ==2.2.2.1
   - cabal-doctest ==1.0.8
   - cabal-file-th ==0.2.6
-  - cabal-rpm ==1.0.2
+  - cabal-rpm ==1.0.3
   - cache ==0.1.3.0
   - cacophony ==0.10.1
   - calendar-recycling ==0.0.0.1
@@ -283,10 +306,10 @@ default-package-overrides:
   - cassava-records ==0.1.0.4
   - cast ==0.1.0.2
   - caster ==0.0.3.0
-  - category ==0.2.4.2
+  - category ==0.2.5.0
   - cayley-client ==0.4.9
-  - cborg ==0.2.2.0
+  - cborg ==0.2.2.1
-  - cborg-json ==0.2.1.0
+  - cborg-json ==0.2.2.0
   - cereal ==0.5.8.1
   - cereal-conduit ==0.8.0
   - cereal-text ==0.1.0.2
@@ -399,7 +422,7 @@ default-package-overrides:
   - convertible ==1.1.1.0
   - cookie ==0.4.5
   - core-data ==0.2.1.4
-  - core-text ==0.2.2.4
+  - core-text ==0.2.2.6
   - countable ==1.0
   - country ==0.1.6
   - courier ==0.1.1.5
@@ -537,7 +560,7 @@ default-package-overrides:
   - direct-sqlite ==2.3.24
   - discount ==0.1.1
   - disk-free-space ==0.1.0.1
-  - distributed-closure ==0.4.1.1
+  - distributed-closure ==0.4.2.0
   - distribution-opensuse ==1.1.1
   - distributive ==0.6.1
   - dl-fedora ==0.5
@@ -562,7 +585,7 @@ default-package-overrides:
   - download ==0.3.2.7
   - drinkery ==0.4
   - dsp ==0.2.5
-  - dual ==0.1.0.2
+  - dual ==0.1.0.3
   - dual-tree ==0.2.2.1
   - dublincore-xml-conduit ==0.1.0.2
   - dunai ==0.5.1
@@ -630,7 +653,7 @@ default-package-overrides:
   - exact-pi ==0.5.0.1
   - exceptional ==0.3.0.0
   - exception-mtl ==0.4.0.1
-  - exceptions ==0.10.3
+  - exceptions ==0.10.4
   - exception-transformers ==0.4.0.8
   - executable-hash ==0.2.0.4
   - executable-path ==0.0.3.1
@@ -698,7 +721,7 @@ default-package-overrides:
   - focuslist ==0.1.0.2
   - foldable1 ==0.1.0.0
   - fold-debounce ==0.2.0.9
-  - fold-debounce-conduit ==0.2.0.3
+  - fold-debounce-conduit ==0.2.0.4
   - foldl ==1.4.5
   - folds ==0.7.5
   - follow-file ==0.0.3
@@ -804,7 +827,7 @@ default-package-overrides:
   - gitrev ==1.3.1
   - gi-vte ==2.91.25
   - gl ==0.9
-  - glabrous ==2.0.0
+  - glabrous ==2.0.1
   - glaze ==0.3.0.1
   - glazier ==1.0.0.0
   - GLFW-b ==3.2.1.1
@@ -818,7 +841,7 @@ default-package-overrides:
   - GLUT ==2.7.0.15
   - gnuplot ==0.5.6
   - google-isbn ==1.0.3
-  - google-oauth2-jwt ==0.3.1
+  - google-oauth2-jwt ==0.3.2
   - gpolyline ==0.1.0.1
   - graph-core ==0.3.0.0
   - graphite ==0.10.0.1
@@ -828,8 +851,8 @@ default-package-overrides:
   - gravatar ==0.8.0
   - graylog ==0.1.0.1
   - greskell ==0.2.3.1
-  - greskell-core ==0.1.2.7
+  - greskell-core ==0.1.3.1
-  - greskell-websocket ==0.1.1.2
+  - greskell-websocket ==0.1.2.1
   - groom ==0.1.2.1
   - groundhog ==0.10.0
   - groundhog-inspector ==0.10.0
@@ -853,7 +876,7 @@ default-package-overrides:
   - HandsomeSoup ==0.4.2
   - hapistrano ==0.3.10.0
   - happy ==1.19.12
-  - hasbolt ==0.1.4.0
+  - hasbolt ==0.1.4.1
   - hashable ==1.2.7.0
   - hashable-time ==0.2.0.2
   - hashids ==1.0.2.4
@@ -874,7 +897,7 @@ default-package-overrides:
   - haskell-src-meta ==0.8.3
   - haskey-btree ==0.3.0.1
   - haskintex ==0.8.0.0
-  - haskoin-core ==0.9.7
+  - haskoin-core ==0.9.8
   - hasql ==1.4.0.1
   - hasql-optparse-applicative ==0.3.0.5
   - hasql-pool ==0.5.1
@@ -984,7 +1007,7 @@ default-package-overrides:
   - hspec-leancheck ==0.0.3
   - hspec-megaparsec ==2.0.1
   - hspec-meta ==2.6.0
-  - hspec-need-env ==0.1.0.3
+  - hspec-need-env ==0.1.0.4
   - hspec-pg-transact ==0.1.0.2
   - hspec-smallcheck ==0.5.2
   - hspec-wai ==0.9.2
@@ -1013,7 +1036,7 @@ default-package-overrides:
   - http-conduit ==2.3.7.3
   - http-date ==0.0.8
   - http-directory ==0.1.5
-  - http-download ==0.1.0.0
+  - http-download ==0.1.0.1
   - httpd-shed ==0.4.1.1
   - http-link-header ==1.0.3.1
   - http-media ==0.8.0.0
@@ -1122,9 +1145,9 @@ default-package-overrides:
   - io-streams ==1.5.1.0
   - io-streams-haproxy ==1.0.1.0
   - ip ==1.5.1
-  - ip6addr ==1.0.0
+  - ip6addr ==1.0.1
   - iproute ==1.7.8
-  - IPv6Addr ==1.1.2
+  - IPv6Addr ==1.1.3
   - ipynb ==0.1
   - ipython-kernel ==0.10.1.0
   - irc ==0.6.1.0
@@ -1148,7 +1171,7 @@ default-package-overrides:
   - json-alt ==1.0.0
   - json-feed ==1.0.7
   - jsonpath ==0.1.0.2
-  - json-rpc ==1.0.0
+  - json-rpc ==1.0.1
   - json-rpc-client ==0.2.5.0
   - json-rpc-generic ==0.2.1.5
   - json-rpc-server ==0.2.6.0
@@ -1323,7 +1346,7 @@ default-package-overrides:
   - mime-mail-ses ==0.4.1
   - mime-types ==0.1.0.9
   - minimorph ==0.2.1.0
-  - minio-hs ==1.5.1
+  - minio-hs ==1.5.2
   - miniutter ==0.5.0.0
   - mintty ==0.1.2
   - miso ==1.2.0.0
@@ -1372,11 +1395,10 @@ default-package-overrides:
   - monoid-extras ==0.5.1
   - monoid-subclasses ==0.4.6.1
   - monoid-transformer ==0.0.4
-  - mono-traversable ==1.0.13.0
+  - mono-traversable ==1.0.15.1
   - mono-traversable-instances ==0.1.0.0
   - mono-traversable-keys ==0.1.0
   - more-containers ==0.2.2.0
-  - morpheus-graphql ==0.8.0
   - mountpoints ==1.0.2
   - mpi-hs ==0.5.3.0
   - msgpack ==1.0.1.0
@@ -1681,7 +1703,6 @@ default-package-overrides:
   - pure-zlib ==0.6.6
   - pushbullet-types ==0.4.1.0
   - pusher-http-haskell ==1.5.1.11
-  - PyF ==0.8.1.2
   - qchas ==1.1.0.1
   - qm-interpolated-string ==0.3.0.0
   - qnap-decrypt ==0.3.5
@@ -1702,7 +1723,7 @@ default-package-overrides:
   - quickcheck-text ==0.1.2.1
   - quickcheck-transformer ==0.3.1
   - quickcheck-unicode ==1.0.1.0
-  - radius ==0.6.0.3
+  - radius ==0.6.1.0
   - rainbow ==0.30.0.2
   - rainbox ==0.20.0.0
   - ramus ==0.1.2
@@ -1839,7 +1860,7 @@ default-package-overrides:
   - sdl2-image ==2.0.0
   - sdl2-mixer ==1.1.0
   - sdl2-ttf ==2.1.0
-  - secp256k1-haskell ==0.1.5
+  - secp256k1-haskell ==0.1.6
   - securemem ==0.1.10
   - selda ==0.4.0.0
   - selda-json ==0.1.1.0
@@ -1856,11 +1877,11 @@ default-package-overrides:
   - sendfile ==0.7.11.1
   - seqalign ==0.2.0.4
   - serf ==0.1.1.0
-  - serialise ==0.2.1.0
+  - serialise ==0.2.2.0
   - servant ==0.16.2
   - servant-auth ==0.3.2.0
   - servant-auth-docs ==0.2.10.0
-  - servant-auth-server ==0.4.4.0
+  - servant-auth-server ==0.4.5.0
   - servant-auth-swagger ==0.2.10.0
   - servant-auth-wordpress ==1.0.0.1
   - servant-blaze ==0.9
@@ -2030,7 +2051,7 @@ default-package-overrides:
   - stripe-wreq ==1.0.1.0
   - strive ==5.0.9
   - structs ==0.1.2
-  - structured-cli ==2.5.1.0
+  - structured-cli ==2.5.2.0
   - summoner ==1.3.0.1
   - sum-type-boilerplate ==0.1.1
   - sundown ==0.6
@@ -2139,7 +2160,7 @@ default-package-overrides:
   - thread-hierarchy ==0.3.0.1
   - thread-local-storage ==0.2
   - threads ==0.5.1.6
-  - threepenny-gui ==0.8.3.0
+  - threepenny-gui ==0.8.3.1
   - th-reify-compat ==0.0.1.5
   - th-reify-many ==0.1.9
   - throttle-io-stream ==0.2.0.1
@@ -2148,7 +2169,6 @@ default-package-overrides:
   - th-test-utils ==1.0.1
   - th-utilities ==0.2.3.1
   - thyme ==0.3.5.5
-  - tidal ==1.4.5
   - tile ==0.3.0.0
   - time-compat ==1.9.2.2
   - timeit ==2.0
@@ -2177,11 +2197,11 @@ default-package-overrides:
   - tomland ==1.1.0.1
   - tonalude ==0.1.1.0
   - tonaparser ==0.1.0.0
-  - tonatona ==0.1.0.1
+  - tonatona ==0.1.1.0
   - tonatona-logger ==0.2.0.0
   - tonatona-persistent-postgresql ==0.1.0.1
   - tonatona-persistent-sqlite ==0.1.0.1
-  - tonatona-servant ==0.1.0.2
+  - tonatona-servant ==0.1.0.3
   - torsor ==0.1
   - tostring ==0.2.1.1
   - TotalMap ==0.1.1.1
@@ -2237,7 +2257,7 @@ default-package-overrides:
   - uncertain ==0.3.1.0
   - unconstrained ==0.1.0.2
   - unicode ==0.0.1.1
-  - unicode-show ==0.1.0.3
+  - unicode-show ==0.1.0.4
   - unicode-transforms ==0.3.6
   - unification-fd ==0.10.0.1
   - union ==0.1.2
@@ -2279,7 +2299,7 @@ default-package-overrides:
   - users-test ==0.5.0.1
   - utf8-light ==0.4.2
   - utf8-string ==1.0.1.1
-  - util ==0.1.15.0
+  - util ==0.1.17.0
   - utility-ht ==0.0.14
   - uuid ==1.3.13
   - uuid-types ==1.0.3
@@ -2356,13 +2376,13 @@ default-package-overrides:
   - web-routes-hsp ==0.24.6.1
   - web-routes-wai ==0.24.3.1
   - webrtc-vad ==0.1.0.3
-  - websockets ==0.12.6.1
+  - websockets ==0.12.7.0
   - websockets-snap ==0.10.3.1
   - weigh ==0.0.16
   - wide-word ==0.1.0.9
   - wikicfp-scraper ==0.1.0.11
-  - wild-bind ==0.1.2.4
+  - wild-bind ==0.1.2.5
-  - wild-bind-x11 ==0.2.0.8
+  - wild-bind-x11 ==0.2.0.9
   - Win32 ==2.6.1.0
   - Win32-notify ==0.3.0.3
   - windns ==0.1.0.1
@@ -2444,7 +2464,7 @@ default-package-overrides:
   - yesod-gitrev ==0.2.1
   - yesod-newsfeed ==1.6.1.0
   - yesod-paginator ==1.1.0.2
-  - yesod-persistent ==1.6.0.3
+  - yesod-persistent ==1.6.0.4
   - yesod-recaptcha2 ==0.3.0
   - yesod-sitemap ==1.6.0
   - yesod-static ==1.6.0.1
@@ -2755,6 +2775,7 @@ broken-packages:
   - accelerate-arithmetic
   - accelerate-fftw
   - accelerate-fourier
+  - accelerate-kullback-liebler
   - accelerate-llvm-native
   - accelerate-random
   - accelerate-typelits
@@ -3351,6 +3372,7 @@ broken-packages:
   - boolexpr
   - boombox
   - boomslang
+  - boopadoop
   - boots-app
   - boots-cloud
   - boots-web
@@ -5318,7 +5340,6 @@ broken-packages:
   - hakyll-filestore
   - hakyll-ogmarkup
   - hakyll-R
-  - hakyll-sass
   - hakyll-series
   - hakyll-shakespeare
   - hakyll-shortcode
@@ -5652,6 +5673,7 @@ broken-packages:
   - hdr-histogram
   - HDRUtils
   - headergen
+  - heart-app
   - heartbeat-streams
   - heatitup
   - heatitup-complete
@@ -6932,6 +6954,7 @@ broken-packages:
   - llvm-base-types
   - llvm-base-util
   - llvm-data-interop
+  - llvm-extension
   - llvm-extra
   - llvm-ffi
   - llvm-general
@@ -7252,6 +7275,8 @@ broken-packages:
   - mmsyn4
   - mmsyn6ukr
   - mmsyn7h
+  - mmsyn7l
+  - mmsyn7s
   - mmsyn7ukr
   - mmtf
   - mmtl
@@ -8068,7 +8093,6 @@ broken-packages:
   - postgresql-simple-queue
   - postgresql-simple-sop
   - postgresql-simple-typed
-  - postgresql-typed
   - postgresql-typed-lifted
   - postgrest
   - postgrest-ws
@@ -8274,6 +8298,7 @@ broken-packages:
   - quicktest
   - quickwebapp
   - quipper
+  - quipper-all
   - quipper-core
   - quipper-rendering
   - quiver-binary
@@ -8417,6 +8442,7 @@ broken-packages:
   - refresht
   - refurb
   - reg-alloc
+  - reg-alloc-graph-color
   - regex-deriv
   - regex-dfa
   - regex-generator
@@ -9806,6 +9832,7 @@ broken-packages:
   - typedquery
   - typehash
   - TypeIlluminator
+  - typelevel-rewrite-rules
   - typelevel-tensor
   - TypeNat
   - typeparams
@@ -10106,7 +10133,6 @@ broken-packages:
   - WebBits
   - WebBits-Html
   - WebBits-multiplate
-  - webby
   - webcloud
   - WebCont
   - webcrank

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

@@ -695,4 +695,8 @@ self: super: builtins.intersectAttrs super {
       spagoWithoutChecks = dontCheck spagoFixHpack;
     in
     spagoWithoutChecks;
+
+  # checks SQL statements at compile time, and so requires a running PostgreSQL
+  # database to run it's test suite
+  postgresql-typed = dontCheck super.postgresql-typed;
 }

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

@@ -24,6 +24,7 @@ in
 , doCheck ? !isCross && stdenv.lib.versionOlder "7.4" ghc.version
 , doBenchmark ? false
 , doHoogle ? true
+, doHaddockQuickjump ? doHoogle && stdenv.lib.versionAtLeast ghc.version "8.6"
 , editedCabalFile ? null
 , enableLibraryProfiling ? !(ghc.isGhcjs or false)
 , enableExecutableProfiling ? false
@@ -402,6 +403,7 @@ stdenv.mkDerivation ({
     ${optionalString (doHaddock && isLibrary) ''
       ${setupCommand} haddock --html \
         ${optionalString doHoogle "--hoogle"} \
+        ${optionalString doHaddockQuickjump "--quickjump"} \
         ${optionalString (isLibrary && hyperlinkSource) "--hyperlink-source"} \
         ${stdenv.lib.concatStringsSep " " haddockFlags}
     ''}

pkgs/development/haskell-modules/with-packages-wrapper.nix

@@ -1,4 +1,4 @@
-{ lib, stdenv, ghc, llvmPackages, packages, buildEnv, makeWrapper
+{ lib, stdenv, ghc, llvmPackages, packages, symlinkJoin, makeWrapper
 , withLLVM ? false
 , postBuild ? ""
 , ghcLibdir ? null # only used by ghcjs, when resolving plugins
@@ -51,25 +51,15 @@ let
                    ++ lib.optional stdenv.targetPlatform.isDarwin llvmPackages.clang);
 in
 if paths == [] && !withLLVM then ghc else
-buildEnv {
+symlinkJoin {
   # this makes computing paths from the name attribute impossible;
   # if such a feature is needed, the real compiler name should be saved
   # as a dedicated drv attribute, like `compiler-name`
   name = ghc.name + "-with-packages";
   paths = paths ++ [ghc];
-  extraOutputsToInstall = ["doc"];
   postBuild = ''
     . ${makeWrapper}/nix-support/setup-hook
 
-    # We make changes to ghc binaries in $out/bin. buildEnv gives a
-    # symlink if only one of the paths has the subdirectory. If so,
-    # we need to remove it for our new wrappers.
-
-    if [ -L "$out/bin" ]; then
-      rm -f "$out/bin"
-      mkdir -p "$out/bin"
-    fi
-
     # wrap compiler executables with correct env variables
 
     for prg in ${ghcCommand} ${ghcCommand}i ${ghcCommand}-${ghc.version} ${ghcCommand}i-${ghc.version}; do

pkgs/development/interpreters/joker/default.nix

@@ -2,17 +2,21 @@
 
 buildGoModule rec {
   pname = "joker";
-  version = "0.12.9";
+  version = "0.14.0";
 
   src = fetchFromGitHub {
     rev = "v${version}";
     owner = "candid82";
     repo = "joker";
-    sha256 = "19n2pzs045mflyzgq3cpa4w2fbd0f77j5k6c4yc3gk0mcwgdxhs2";
+    sha256 = "1b38alajxs89a9x3f3ldk1nlynp6j90qhl1m2c6561rsm41sqfz0";
   };
 
   modSha256 = "0i16vf7n1xfz5kp9w3fvyc9y9wgz4h396glgpdaznpxjr12rb43j";
 
+  preBuild = ''
+    go generate ./...
+  '';
+
   meta = with stdenv.lib; {
     homepage = https://github.com/candid82/joker;
     description = "A small Clojure interpreter and linter written in Go";

pkgs/development/libraries/thrift/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, boost, zlib, libevent, openssl, python, cmake, pkgconfig
+{ stdenv, fetchurl, fetchpatch, boost, zlib, libevent, openssl, python, cmake, pkgconfig
 , bison, flex, twisted, static ? false }:
 
 stdenv.mkDerivation rec {
@@ -10,6 +10,15 @@ stdenv.mkDerivation rec {
     sha256 = "0yai9c3bdsrkkjshgim7zk0i7malwfprg00l9774dbrkh2w4ilvs";
   };
 
+  patches = [
+    # Fix a failing test on darwin
+    # https://issues.apache.org/jira/browse/THRIFT-4976
+    (fetchpatch {
+      url = "https://github.com/apache/thrift/commit/6701dbb8e89f6550c7843e9b75b118998df471c3.diff";
+      sha256 = "14rqma2b2zv3zxkkl5iv9kvyp3zihvad6fdc2gcdqv37nqnswx9d";
+    })
+  ];
+
   # Workaround to make the python wrapper not drop this package:
   # pythonFull.buildEnv.override { extraLibs = [ thrift ]; }
   pythonPath = [];
@@ -32,7 +41,9 @@ stdenv.mkDerivation rec {
   doCheck = !static;
   checkPhase = ''
     runHook preCheck
-    LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD/lib ctest -E PythonTestSSLSocket
+
+    ${stdenv.lib.optionalString stdenv.isDarwin "DY"}LD_LIBRARY_PATH=$PWD/lib ctest -E PythonTestSSLSocket
+
     runHook postCheck
   '';
   enableParallelChecking = false;

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

@@ -19,7 +19,7 @@ buildPythonPackage rec {
   doCheck = false;
 
   meta = {
-    homepage = http://pygments.org/;
+    homepage = https://pygments.org/;
     description = "A generic syntax highlighter";
     license = lib.licenses.bsd2;
     maintainers = with lib.maintainers; [ ];

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

@@ -6,11 +6,11 @@
 
 buildPythonPackage rec {
   pname = "catalogue";
-  version = "0.0.8";
+  version = "0.2.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c407a51c22f51b0f938104b6396c489145bae234386e68eb1d56326c3b3e128e";
+    sha256 = "0zha0gzqfkazc9da0cyjys5ghf20ihyhkgd1h5zxkxlf8zhz03s3";
   };
 
   propagatedBuildInputs = [ importlib-metadata ];

pkgs/development/python-modules/junit-xml/default.nix

@@ -0,0 +1,32 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, six
+, pytest
+, pytest-sugar
+}:
+
+buildPythonPackage rec {
+  pname = "junit-xml";
+  version = "1.8";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "08fw86azza6d3l3nx34kq69cpwmmfqpn7xrb8pdlxmhr1941qbv0";
+  };
+
+  propagatedBuildInputs = [ six ];
+
+  checkInputs = [ pytest pytest-sugar ];
+
+  checkPhase = ''
+    pytest
+  '';
+
+  meta = with lib; {
+    description = "Creates JUnit XML test result documents that can be read by tools such as Jenkins";
+    homepage = https://github.com/kyrus/python-junit-xml;
+    maintainers = with maintainers; [ multun ];
+    license = licenses.mit;
+  };
+}

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

@@ -24,7 +24,7 @@ buildPythonPackage rec {
 
   meta = with stdenv.lib; {
     description = "A pluggable command-line frontend, including commands to setup package file layouts";
-    homepage = http://pythonpaste.org/script/;
+    homepage = https://github.com/cdent/pastescript/;
     license = licenses.mit;
   };
 

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

@@ -23,7 +23,7 @@ buildPythonPackage rec {
 
   meta = with stdenv.lib; {
     description = "Parallel graph management and execution in heterogeneous computing";
-    homepage = http://www.cacr.caltech.edu/~mmckerns/pathos.htm;
+    homepage = https://github.com/uqfoundation/pathos/;
     license = licenses.bsd3;
   };
 

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

@@ -39,7 +39,7 @@ buildPythonPackage rec {
   '';
 
   meta = with stdenv.lib; {
-    homepage = http://pivy.coin3d.org/;
+    homepage = https://github.com/coin3d/pivy/;
     description = "A Python binding for Coin";
     license = licenses.bsd0;
     maintainers = with maintainers; [ gebner ];

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

@@ -15,7 +15,7 @@ buildPythonPackage rec {
   meta = with stdenv.lib; {
     description = "Utilities for filesystem exploration and automated builds";
     license = licenses.bsd3;
-    homepage = http://www.cacr.caltech.edu/~mmckerns/pox.htm;
+    homepage = https://github.com/uqfoundation/pox/;
   };
 
 }

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

@@ -26,7 +26,7 @@ buildPythonPackage rec {
   '';
 
   meta = with stdenv.lib; {
-    homepage = http://pvlib-python.readthedocs.io;
+    homepage = https://pvlib-python.readthedocs.io;
     description = "Simulate the performance of photovoltaic energy systems";
     license = licenses.bsd3;
     maintainers = with maintainers; [ jluttine ];

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

@@ -29,7 +29,7 @@ buildPythonPackage rec {
 
   meta = with stdenv.lib; {
     description = "pyenchant: Python bindings for the Enchant spellchecker";
-    homepage = https://pythonhosted.org/pyenchant/;
+    homepage = https://github.com/pyenchant/pyenchant;
     license = licenses.lgpl21;
     badPlatforms = [ "x86_64-darwin" ];
   };

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

@@ -20,7 +20,7 @@ buildPythonPackage rec {
 
   meta = {
     description = "User-space driver for modern FTDI devices";
-    homepage = "http://github.com/eblot/pyftdi";
+    homepage = "https://github.com/eblot/pyftdi";
     license = lib.licenses.lgpl2;
   };
 }

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

@@ -12,7 +12,7 @@ buildPythonPackage rec {
     doCheck = false;
 
     meta = with stdenv.lib; {
-      homepage = http://pyparsing.wikispaces.com/;
+      homepage = https://pyparsing.wikispaces.com/;
       description = "An alternative approach to creating and executing simple grammars, vs. the traditional lex/yacc approach, or the use of regular expressions";
       license = licenses.mit;
     };

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

@@ -17,7 +17,7 @@ buildPythonPackage rec {
 
   meta = with stdenv.lib; {
     description = "A package which logs to a Python logger when an exception is raised by a Pyramid application";
-    homepage = http://docs.pylonsproject.org/;
+    homepage = https://docs.pylonsproject.org/;
     license = licenses.bsd0;
     maintainers = with maintainers; [ domenkozar ];
   };

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

@@ -39,7 +39,7 @@ buildPythonPackage rec {
   '';
 
   meta = {
-    homepage = http://pysam.readthedocs.io/;
+    homepage = https://pysam.readthedocs.io/;
     description = "A python module for reading, manipulating and writing genome data sets";
     maintainers = with lib.maintainers; [ unode ];
     license = lib.licenses.mit;

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

@@ -3,12 +3,14 @@
 buildPythonPackage rec {
   pname = "python-sql";
   version = "1.0.0";
+
   src = fetchPypi {
     inherit pname version;
     sha256 = "05ni936y0ia9xmryl7mlhbj9i80nnvq1bi4zxhb96rv7yvpb3fqb";
   };
+
   meta = {
-    homepage = http://python-sql.tryton.org/;
+    homepage = https://python-sql.tryton.org/;
     description = "A library to write SQL queries in a pythonic way";
     maintainers = with lib.maintainers; [ johbo ];
     license = lib.licenses.bsd3;

pkgs/development/python-modules/pyviz-comms/default.nix

@@ -20,7 +20,7 @@ buildPythonPackage rec {
 
   meta = with lib; {
     description = "Launch jobs, organize the output, and dissect the results";
-    homepage = http://pyviz.org/;
+    homepage = https://pyviz.org/;
     license = licenses.bsd3;
     maintainers = [ maintainers.costrouc ];
   };

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

@@ -22,7 +22,7 @@ buildPythonPackage rec {
 
   meta = {
     description = "Quantities is designed to handle arithmetic and";
-    homepage = http://python-quantities.readthedocs.io/;
+    homepage = https://python-quantities.readthedocs.io/;
     license = lib.licenses.bsd2;
   };
 }

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

@@ -3,17 +3,20 @@
 buildPythonPackage rec {
   pname = "relatorio";
   version = "0.9.0";
+
   src = fetchPypi {
     inherit pname version;
     sha256 = "0q93sl7ppfvjxylgq9m5n4xdgv4af7d69yxd84zszq10vjmpsg6k";
   };
+
   propagatedBuildInputs = [
     genshi
     lxml
     python_magic
   ];
+
   meta = {
-    homepage = http://relatorio.tryton.org/;
+    homepage = https://relatorio.tryton.org/;
     description = "A templating library able to output odt and pdf files";
     maintainers = with lib.maintainers; [ johbo ];
     license = lib.licenses.gpl3;

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

@@ -12,7 +12,7 @@ buildPythonPackage rec {
 
   meta = with stdenv.lib; {
     description = "Generic test automation framework";
-    homepage = http://robotframework.org/;
+    homepage = https://robotframework.org/;
     license = licenses.asl20;
     maintainers = with maintainers; [ bjornfor ];
   };

pkgs/development/python-modules/scikit-image/default.nix

@@ -35,7 +35,7 @@ buildPythonPackage rec {
 
   meta = {
     description = "Image processing routines for SciPy";
-    homepage = http://scikit-image.org;
+    homepage = https://scikit-image.org;
     license = lib.licenses.bsd3;
   };
 }

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

@@ -34,7 +34,7 @@ buildPythonPackage rec {
 
   meta = with lib; {
     description = "Pure Python HDFS client";
-    homepage = http://github.com/spotify/snakebite;
+    homepage = https://github.com/spotify/snakebite;
     license = licenses.asl20;
     maintainers = [ maintainers.costrouc ];
   };

pkgs/development/python-modules/stups-fullstop/default.nix

@@ -0,0 +1,45 @@
+{ lib
+, fetchFromGitHub
+, buildPythonPackage
+, requests
+, stups-cli-support
+, stups-zign
+, pytest
+, pytestcov
+, isPy3k
+}:
+
+buildPythonPackage rec {
+  pname = "stups-fullstop";
+  version = "1.1.31";
+  disabled = !isPy3k;
+
+  src = fetchFromGitHub {
+    owner = "zalando-stups";
+    repo = "fullstop-cli";
+    rev = version;
+    sha256 = "1cpzz1b8g2mich7c1p74vfgw70vlxpgwi82a1ld82wv3srwqa0h3";
+  };
+
+  propagatedBuildInputs = [
+    requests
+    stups-cli-support
+    stups-zign
+  ];
+
+  preCheck = "
+    export HOME=$TEMPDIR
+  ";
+
+  checkInputs = [
+    pytest
+    pytestcov
+  ];
+
+  meta = with lib; {
+    description = "Convenience command line tool for fullstop. audit reporting.";
+    homepage = "https://github.com/zalando-stups/stups-fullstop-cli";
+    license = licenses.asl20;
+    maintainers = [ maintainers.mschuwalow ];
+  };
+}

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

@@ -28,7 +28,7 @@ buildPythonPackage rec {
 
   meta = {
     description = "A Python library for symbolic mathematics";
-    homepage    = http://www.sympy.org/;
+    homepage    = https://www.sympy.org/;
     license     = lib.licenses.bsd3;
     maintainers = with lib.maintainers; [ lovek323 timokau ];
   };

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

@@ -13,7 +13,7 @@ buildPythonPackage rec {
   };
 
   meta = with stdenv.lib; {
-    homepage = http://chrisarndt.de/projects/threadpool/;
+    homepage = https://chrisarndt.de/projects/threadpool/;
     description = "Easy to use object-oriented thread pool framework";
     license = licenses.mit;
   };

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

@@ -14,7 +14,7 @@ buildPythonPackage rec {
 
   meta = {
     description = "The official Todoist Python API library";
-    homepage = http://todoist-python.readthedocs.io/en/latest/;
+    homepage = https://todoist-python.readthedocs.io/en/latest/;
     license = stdenv.lib.licenses.mit;
     maintainers = with stdenv.lib.maintainers; [ the-kenny ];
   };

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

@@ -13,7 +13,7 @@ buildPythonPackage rec {
   };
 
   meta = with stdenv.lib; {
-    homepage = http://pylonsproject.org/;
+    homepage = https://pylonsproject.org/;
     description = "Utility library for i18n relied on by various Repoze and Pyramid packages";
     license = licenses.bsd0;
     maintainers = with maintainers; [ domenkozar ];

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

@@ -15,7 +15,7 @@ buildPythonPackage rec {
 
   meta = {
     description = "Pure python download utility";
-    homepage = http://bitbucket.org/techtonik/python-wget/;
+    homepage = https://bitbucket.org/techtonik/python-wget/;
     license = with lib.licenses; [ unlicense ];
     maintainers = with lib.maintainers; [ prusnak ];
   };

pkgs/development/python-modules/xstatic-bootstrap/default.nix

@@ -16,7 +16,7 @@ buildPythonPackage rec {
   doCheck = false;
 
   meta = with lib;{
-    homepage = http://getbootstrap.com;
+    homepage = https://getbootstrap.com;
     description = "Bootstrap packaged static files for python";
     license = licenses.mit;
     maintainers = with maintainers; [ makefu ];

pkgs/development/python-modules/xstatic-pygments/default.nix

@@ -16,7 +16,7 @@ buildPythonPackage rec {
   doCheck = false;
 
   meta = with lib;{
-    homepage = http://pygments.org;
+    homepage = https://pygments.org;
     description = "pygments packaged static files for python";
     license = licenses.mit;
     maintainers = with maintainers; [ makefu ];

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

@@ -12,6 +12,6 @@ buildPythonPackage rec {
   meta = with lib; {
     description = "Generate HTML or XML in a pythonic way. Pure python alternative to web template engines. Can fill HTML forms with default values and error messages.";
     license = [ licenses.lgpl21 ];
-    homepage = http://www.yattag.org/;
+    homepage = https://www.yattag.org/;
   };
 }

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

@@ -16,7 +16,7 @@ buildPythonPackage rec {
   propagatedBuildInputs = [ zope_schema ];
 
   meta = with stdenv.lib; {
-    homepage = http://zopefilerepresentation.readthedocs.io/;
+    homepage = https://zopefilerepresentation.readthedocs.io/;
     description = "File-system Representation Interfaces";
     license = licenses.zpl20;
     maintainers = with maintainers; [ goibhniu ];

pkgs/development/tools/misc/clojure-lsp/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "clojure-lsp";
-  version = "20200106T233511";
+  version = "20200109T185134";
 
   src = fetchurl {
     url = "https://github.com/snoe/clojure-lsp/releases/download/release-${version}/${pname}";
-    sha256 = "0z550c15sywbaxbfi1nxx19whfysq4whl4na4fjihnin8ab5sh2x";
+    sha256 = "11fzyf2qzqmxhdyssm59cqkkcjh8hw1i859abc1i2zali3fd7w68";
   };
 
   dontUnpack = true;

pkgs/development/tools/rq/default.nix

@@ -1,19 +1,17 @@
-{ stdenv, fetchFromGitHub, rustPlatform, llvmPackages, v8 }:
+{ lib, fetchFromGitHub, rustPlatform, libiconv, llvmPackages, v8 }:
 
-with rustPlatform;
+rustPlatform.buildRustPackage rec {
-
-buildRustPackage rec {
   pname = "rq";
-  version = "0.10.4";
+  version = "1.0.2";
 
   src = fetchFromGitHub {
     owner = "dflemstr";
-    repo = "rq";
+    repo = pname;
     rev = "v${version}";
-    sha256 = "066f6sdy0vrp113wlg18q9p0clyrg9iqbj17ly0yn8dxr5iar002";
+    sha256 = "0km9d751jr6c5qy4af6ks7nv3xfn13iqi03wq59a1c73rnf0zinp";
   };
 
-  cargoSha256 = "1n92d82l9wqrpsbkqiir6zsgf12xp4xb6bxq2nywg4lmwrnyapbh";
+  cargoSha256 = "0z971fpyj4v5hjp6q4yxgxv069h9idkpkcixb14gxi7kpiswprvz";
 
   buildInputs = [ llvmPackages.clang-unwrapped v8 ];
 
@@ -22,12 +20,11 @@ buildRustPackage rec {
     export V8_SOURCE="${v8}"
   '';
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "A tool for doing record analysis and transformation";
-    homepage = https://github.com/dflemstr/rq ;
+    homepage = "https://github.com/dflemstr/rq";
     license = with licenses; [ asl20 ];
-    maintainers = [ maintainers.aristid ];
+    maintainers = with maintainers; [ aristid filalex77 ];
     platforms = platforms.all;
-    broken = true;
   };
 }

pkgs/development/tools/run/default.nix

@@ -0,0 +1,22 @@
+{ stdenv, buildGoModule, fetchFromGitHub }:
+buildGoModule rec {
+  pname = "run";
+  version = "0.7.0";
+
+  src = fetchFromGitHub {
+    owner = "TekWizely";
+    repo = "run";
+    rev = "v${version}";
+    sha256 = "0365nvsqrlagrp08sifbdk3rgy7r4hmp3sx5zhizamadfcj2fsv6";
+  };
+
+  modSha256 = "0s2lw9q5jskj41jqr8bv5w45pkrp2s0yfd2hgjgsd0q4ifm07k7s";
+
+  meta = with stdenv.lib; {
+    description = "Easily manage and invoke small scripts and wrappers";
+    homepage    = https://github.com/TekWizely/run;
+    license     = licenses.mit;
+    maintainers = with maintainers; [ rawkode ];
+    platforms   = platforms.unix;
+  };
+}

pkgs/development/tools/rust/racer/default.nix

@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "racer";
-  version = "2.1.28";
+  version = "2.1.29";
 
   src = fetchFromGitHub {
     owner = "racer-rust";
     repo = "racer";
-    rev = "v${version}";
+    rev = "5db1d0cf8bd1a1030983337c2079be09a1268c8c";
-    sha256 = "1zifbcqy9hmcdbz7sl046l2631f5a3j65kyin38l7wm7vrqx9s3h";
+    sha256 = "0kxi0krpc3abanphzpmi3jhmm831bn4wjzyas469q2gvqfhm71dj";
   };
 
-  cargoSha256 = "1ys1yb939y144lhjr451cpqrayqn66r0zp71xm90fkqxsbv7wkqv";
+  cargoSha256 = "18hx0dfx6lw3azsnpqzhbjs0fpfya5y0pcyjmfywv42a8n7dr1jc";
 
   buildInputs = [ makeWrapper ]
                 ++ stdenv.lib.optional stdenv.isDarwin Security;

pkgs/development/web/nodejs/v10.nix

@@ -5,6 +5,6 @@ let
 in
   buildNodejs {
     inherit enableNpm;
-    version = "10.18.0";
+    version = "10.18.1";
-    sha256 = "1ppycqffsy7ix6whdp6id7ld1qizwvjlzxyk12kxw4wphjmn49hb";
+    sha256 = "0dgax08lkgjvafp6i0c5h8wqqs0w49j8mh8fqi6ppbrryhviibrr";
   }

pkgs/misc/vim-plugins/generated.nix

@@ -1441,6 +1441,17 @@ let
     };
   };
 
+  increment-activator = buildVimPluginFrom2Nix {
+    pname = "increment-activator";
+    version = "2019-05-09";
+    src = fetchFromGitHub {
+      owner = "nishigori";
+      repo = "increment-activator";
+      rev = "f341baf93b172aee646c90ff2ce28de0f897561b";
+      sha256 = "0hda6h3qz6ynpl996rk1rm6xnxgkaz108v28qg0w6wm7qzynbmnv";
+    };
+  };
+
   incsearch-easymotion-vim = buildVimPluginFrom2Nix {
     pname = "incsearch-easymotion-vim";
     version = "2016-01-18";
@@ -3467,6 +3478,17 @@ let
     };
   };
 
+  vim-cool = buildVimPluginFrom2Nix {
+    pname = "vim-cool";
+    version = "2018-01-11";
+    src = fetchFromGitHub {
+      owner = "romainl";
+      repo = "vim-cool";
+      rev = "06918c36b3396af0bec1e87e748a5dba55be87b9";
+      sha256 = "099sbjdk944bnivqgqgbjplczfm3k84583ryrmpqf3lgrq6pl8wr";
+    };
+  };
+
   vim-cpp-enhanced-highlight = buildVimPluginFrom2Nix {
     pname = "vim-cpp-enhanced-highlight";
     version = "2019-11-14";

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

@@ -324,6 +324,7 @@ neovim/nvim-lsp
 neutaaaaan/iosvkem
 nfnty/vim-nftables
 nicoe/deoplete-khard
+nishigori/increment-activator
 nixprime/cpsm
 NLKNguyen/papercolor-theme
 noc7c9/vim-iced-coffee-script
@@ -366,6 +367,7 @@ rhysd/vim-grammarous
 rhysd/vim-operator-surround
 Rip-Rip/clang_complete
 rodjek/vim-puppet
+romainl/vim-cool
 ron89/thesaurus_query.vim
 roxma/nvim-cm-racer
 roxma/nvim-completion-manager

pkgs/os-specific/linux/kernel/linux-libre.nix

@@ -1,7 +1,7 @@
 { stdenv, lib, fetchsvn, linux
 , scripts ? fetchsvn {
     url = "https://www.fsfla.org/svn/fsfla/software/linux-libre/releases/branches/";
-    rev = "17177";
+    rev = "17179";
     sha256 = "0hyd7wp73w4555d42xcvk4x4nxrfckbzah2ckb4d2aqzxab87789";
   }
 , ...

pkgs/servers/apache-kafka/default.nix

@@ -48,6 +48,11 @@ let
       scalaVersion = "2.12";
       sha256 = "0bldfrvd351agm237icnvn36va67crpnzmbh6dlq84ip910xsgas";
     };
+    "2.4" = {
+      kafkaVersion = "2.4.0";
+      scalaVersion = "2.12";
+      sha256 = "1vng5ipkjzqy0wijc706w2m1rjl5d0nsgbxiacci739y1jmjnn5r";
+    };
   };
 in
 

pkgs/servers/matterbridge/default.nix

@@ -1,14 +1,15 @@
-{ stdenv, buildGoPackage, fetchurl }:
+{ stdenv, buildGoModule, fetchurl }:
 
-buildGoPackage rec {
+buildGoModule rec {
   pname = "matterbridge";
-  version = "1.11.0";
+  version = "1.16.3";
 
   goPackagePath = "github.com/42wim/matterbridge";
+  modSha256 = "sha256-Q6R6AhAELirFijw5ntyjly46HCzFMpLGSJYfv864gt0=";
 
   src = fetchurl {
     url = "https://github.com/42wim/matterbridge/archive/v${version}.tar.gz";
-    sha256 = "1fjpgdaq4mfgf36gzk3hhmlbpfn44b7xll2rdpy69y460jrjfg6k";
+    sha256 = "sha256-VAbZSXilmmd2z2bK4/UZzOrjohDVcJHah9t3DE1mtOE=";
   };
 
   meta = with stdenv.lib; {

pkgs/tools/networking/shadowsocks-libev/default.nix

@@ -5,14 +5,14 @@
 
 stdenv.mkDerivation rec {
   pname = "shadowsocks-libev";
-  version = "3.3.3";
+  version = "3.3.4";
 
   # Git tag includes CMake build files which are much more convenient.
   src = fetchFromGitHub {
     owner = "shadowsocks";
     repo = pname;
     rev = "refs/tags/v${version}";
-    sha256 = "1i2431imbn4bhwmwyz63g5mh1g5ikhsiwv6mzcdc2kx34zjpibrj";
+    sha256 = "05f1vvd0r0wanbb61rf4p6y991jp7625l0i223v23r2ji43y3i5a";
     fetchSubmodules = true;
   };
 

pkgs/tools/package-management/cargo-deb/default.nix

@@ -1,21 +1,25 @@
-{ stdenv, fetchurl, fetchFromGitHub, rustPlatform, Security }:
+{ stdenv
+, lib
+, fetchFromGitHub
+, rustPlatform
+, Security }:
 
 rustPlatform.buildRustPackage rec {
   pname = "cargo-deb";
-  version = "1.23.0";
+  version = "1.23.1";
 
   src = fetchFromGitHub {
     owner = "mmstick";
-    repo = "cargo-deb";
+    repo = pname;
     rev = "v${version}";
-    sha256 = "0jjhbs48f0rprzxnfgav6mjbyvcqnr7xq1qgyjxwd61z8g3m8hx8";
+    sha256 = "0dkkbyzimnzfyrzmfn83jqg5xq53wzrknixnyh46cniqffqhd663";
   };
 
-  buildInputs = with stdenv; lib.optionals isDarwin [ Security ];
+  buildInputs = lib.optionals stdenv.isDarwin [ Security ];
 
-  cargoSha256 = "03z9hq873jfsbssnd3kr5vz9lx9mvhb1navb2glm6kkw1k2zm4d2";
+  cargoSha256 = "0j64dcczxdr9zdch4a241d5adgipzz8sgbw00min9k3p8hbljd9n";
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "Generate Debian packages from information in Cargo.toml";
     homepage = "https://github.com/mmstick/cargo-deb";
     license = licenses.mit;

pkgs/top-level/aliases.nix

@@ -532,4 +532,9 @@ mapAliases ({
 
   # added 2019-10-28
   gnatsd = nats-server;
+
+  # added 2020-01-10
+  tor-browser-bundle = throw "tor-browser-bundle was removed because it was out of date and inadequately maintained. Please use tor-browser-bundle-bin instead. See #77452.";
+  # added 2020-01-10
+  tor-browser-unwrapped = throw "tor-browser-unwrapped was removed because it was out of date and inadequately maintained. Please use tor-browser-bundle-bin instead. See #77452.";
 })

pkgs/top-level/all-packages.nix

@@ -274,6 +274,8 @@ in
 
   pet = callPackage ../development/tools/pet { };
 
+  run = callPackage ../development/tools/run { };
+
   mod = callPackage ../development/tools/mod { };
 
   broadlink-cli = callPackage ../tools/misc/broadlink-cli {};
@@ -6114,7 +6116,9 @@ in
 
   routino = callPackage ../tools/misc/routino { };
 
-  rq = callPackage ../development/tools/rq { };
+  rq = callPackage ../development/tools/rq {
+    inherit (darwin) libiconv;
+  };
 
   rsnapshot = callPackage ../tools/backup/rsnapshot { };
 
@@ -6793,11 +6797,6 @@ in
 
   tor-browser-bundle-bin = callPackage ../applications/networking/browsers/tor-browser-bundle-bin { };
 
-  tor-browser-bundle = callPackage ../applications/networking/browsers/tor-browser-bundle {
-    stdenv = stdenvNoCC;
-    tor-browser-unwrapped = firefoxPackages.tor-browser;
-  };
-
   touchegg = callPackage ../tools/inputmethods/touchegg { };
 
   torsocks = callPackage ../tools/security/tor/torsocks.nix { };
@@ -9603,7 +9602,7 @@ in
   apacheAnt_1_9 = callPackage ../development/tools/build-managers/apache-ant/1.9.nix { };
   ant = apacheAnt;
 
-  apacheKafka = apacheKafka_2_3;
+  apacheKafka = apacheKafka_2_4;
   apacheKafka_0_9 = callPackage ../servers/apache-kafka { majorVersion = "0.9"; };
   apacheKafka_0_10 = callPackage ../servers/apache-kafka { majorVersion = "0.10"; };
   apacheKafka_0_11 = callPackage ../servers/apache-kafka { majorVersion = "0.11"; };
@@ -9613,6 +9612,7 @@ in
   apacheKafka_2_1 = callPackage ../servers/apache-kafka { majorVersion = "2.1"; };
   apacheKafka_2_2 = callPackage ../servers/apache-kafka { majorVersion = "2.2"; };
   apacheKafka_2_3 = callPackage ../servers/apache-kafka { majorVersion = "2.3"; };
+  apacheKafka_2_4 = callPackage ../servers/apache-kafka { majorVersion = "2.4"; };
 
   kt = callPackage ../tools/misc/kt {};
 
@@ -19036,7 +19036,6 @@ in
   firefox-esr-52-unwrapped = firefoxPackages.firefox-esr-52;
   firefox-esr-60-unwrapped = firefoxPackages.firefox-esr-60;
   firefox-esr-68-unwrapped = firefoxPackages.firefox-esr-68;
-  tor-browser-unwrapped = firefoxPackages.tor-browser;
   icecat-unwrapped = firefoxPackages.icecat;
 
   firefox = wrapFirefox firefox-unwrapped { };

pkgs/top-level/python-packages.nix

@@ -779,6 +779,8 @@ in {
 
   jira = callPackage ../development/python-modules/jira { };
 
+  junit-xml = callPackage ../development/python-modules/junit-xml { };
+
   junitparser = callPackage ../development/python-modules/junitparser { };
 
   jwcrypto = callPackage ../development/python-modules/jwcrypto { };
@@ -1388,6 +1390,8 @@ in {
 
   stups-cli-support = callPackage ../development/python-modules/stups-cli-support { };
 
+  stups-fullstop = callPackage ../development/python-modules/stups-fullstop { };
+
   stups-tokens = callPackage ../development/python-modules/stups-tokens { };
 
   stups-zign = callPackage ../development/python-modules/stups-zign { };