NixOS
diff --git a/nixos/doc/manual/release-notes/rl-1903.xml b/nixos/doc/manual/release-notes/rl-1903.xml
@@ -343,6 +343,13 @@
      <literal><![CDATA[security.pam.services.<name?>.text]]></literal>.
    </para>
   </listitem>
+   <listitem>
+    <para>
+     <literal>fish</literal> has been upgraded to 3.0.
+     It comes with a number of improvements and backwards incompatible changes.
+     See the <literal>fish</literal> <link xlink:href="https://github.com/fish-shell/fish-shell/releases/tag/3.0.0">release notes</link> for more information.
+    </para>
+   </listitem>
   </itemizedlist>
  </section>
 

diff --git a/nixos/modules/services/networking/ddclient.nix b/nixos/modules/services/networking/ddclient.nix
@@ -182,10 +182,9 @@ with lib;
       serviceConfig = rec {
         DynamicUser = true;
         RuntimeDirectory = StateDirectory;
-        RuntimeDirectoryMode = "0750";
         StateDirectory = builtins.baseNameOf dataDir;
         Type = "oneshot";
-        ExecStartPre = "!${lib.getBin pkgs.coreutils}/bin/install -m660 ${cfg.configFile} /run/${RuntimeDirectory}/ddclient.conf";
+        ExecStartPre = "!${lib.getBin pkgs.coreutils}/bin/install -m666 ${cfg.configFile} /run/${RuntimeDirectory}/ddclient.conf";
         ExecStart = "${lib.getBin pkgs.ddclient}/bin/ddclient -file /run/${RuntimeDirectory}/ddclient.conf";
       };
     };

diff --git a/pkgs/applications/networking/p2p/synapse-bt/default.nix b/pkgs/applications/networking/p2p/synapse-bt/default.nix
@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   name = "synapse-bt-unstable-${version}";
-  version = "2018-06-04";
+  version = "2018-10-17";
 
   src = fetchFromGitHub {
     owner = "Luminarys";
     repo = "synapse";
-    rev = "ec8f23a14af21426ab0c4f8953dd954f747850ab";
-    sha256 = "0d1rrwnk333zz9g8s40i75xgdkpz6a1j01ajsh32yvzvbi045zkw";
+    rev = "76d5e9a23ad00c25cfd0469b1adb479b9ded113a";
+    sha256 = "1lsfvcsmbsg51v8c2hkpwkx0zg25sdjc3q7x72b5bwwnw9l0iglz";
   };
 
-  cargoSha256 = "1psrmgf6ddzqwx7gf301rx84asfnvxpsvkx2fan453v65819k960";
+  cargoSha256 = "1sc8c0w2dbvcdv16idw02y35x0jx5ff6ddzij09pmqjx55zgsjf7";
 
   buildInputs = [ pkgconfig openssl ] ++ stdenv.lib.optional stdenv.isDarwin Security;
 

diff --git a/pkgs/applications/science/math/gap/default.nix b/pkgs/applications/science/math/gap/default.nix
@@ -1,6 +1,8 @@
 { stdenv
+, lib
 , fetchurl
 , fetchpatch
+, makeWrapper
 , m4
 , gmp
 # don't remove any packages -- results in a ~1.3G size increase
@@ -11,24 +13,17 @@
 stdenv.mkDerivation rec {
   pname = "gap";
   # https://www.gap-system.org/Releases/
-  # newer versions (4.9.0) are available, but still considered beta (https://github.com/gap-system/gap/wiki/GAP-4.9-release-notes)
-  version = "4r8p10";
-  pkgVer = "2018_01_15-13_02";
-  name = "${pname}-${version}";
-
-  src = let
-    # 4r8p10 -> 48
-    majorminor = stdenv.lib.replaceStrings ["r"] [""] (
-      builtins.head (stdenv.lib.splitString "p" version) # 4r8p10 -> 4r8
-    );
-  in
-    fetchurl {
-    url = "https://www.gap-system.org/pub/gap/gap${majorminor}/tar.bz2/gap${version}_${pkgVer}.tar.bz2";
-    sha256 = "0wzfdjnn6sfiaizbk5c7x44rhbfayis4lf57qbqqg84c7dqlwr6f";
+  version = "4.10.0";
+
+  src = fetchurl {
+    url = "https://www.gap-system.org/pub/gap/gap-${lib.versions.major version}.${lib.versions.minor version}/tar.bz2/gap-${version}.tar.bz2";
+    sha256 = "1dmb8v4p7j1nnf7sx8sg54b49yln36bi9acwp7w1d3a1nxj17ird";
   };
 
   # remove all non-essential packages (which take up a lot of space)
-  preConfigure = stdenv.lib.optionalString (!keepAllPackages) ''
+  preConfigure = ''
+    patchShebangs .
+  '' + lib.optionalString (!keepAllPackages) ''
     find pkg -type d -maxdepth 1 -mindepth 1 \
        -not -name 'GAPDoc-*' \
        -not -name 'autpgrp*' \
@@ -37,26 +32,63 @@ stdenv.mkDerivation rec {
   '';
 
   configureFlags = [ "--with-gmp=system" ];
-  buildInputs = [ m4 gmp ];
+
+  buildInputs = [
+    m4
+    gmp
+  ];
+
+  nativeBuildInputs = [
+    makeWrapper
+  ];
 
   patches = [
-    #  fix infinite loop in writeandcheck() when writing an error message fails.
+    # bugfix: https://github.com/gap-system/gap/pull/3102
+    (fetchpatch {
+      name = "fix-infinite-loop-in-writeandcheck.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/gap/patches/0001-a-version-of-the-writeandcheck.patch-from-Sage-that-.patch?id=5e61d7b6a0da3aa53d8176fa1fb9353cc559b098";
+      sha256 = "1zkv8bbiw3jdn54sqqvfkdkfsd7jxzq0bazwsa14g4sh2265d28j";
+    })
+
+    # needed for libgap (sage): https://github.com/gap-system/gap/pull/3043
     (fetchpatch {
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/gap/patches/writeandcheck.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
-      sha256 = "1r1511x4kc2i2mbdq1b61rb6p3misvkf1v5qy3z6fmn6vqwziaz1";
+      name = "add-error-messages-helper.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/gap/patches/0002-kernel-add-helper-function-for-writing-error-message.patch?id=5e61d7b6a0da3aa53d8176fa1fb9353cc559b098";
+      sha256 = "0c4ry5znb6hwwp8ld6k62yw8w6cqldflw3x49bbzizbmipfpidh5";
+    })
+
+    # needed for libgap (sage): https://github.com/gap-system/gap/pull/3096
+    (fetchpatch {
+      name = "gap-enter.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/gap/patches/0003-Prototype-for-GAP_Enter-Leave-macros-to-bracket-use-.patch?id=5e61d7b6a0da3aa53d8176fa1fb9353cc559b098";
+      sha256 = "12fg8mb8rm6khsz1r4k3k26jrkx4q1rv13hcrfnlhn0m7iikvc3q";
     })
   ];
 
-  doCheck = true;
-  checkTarget = "testinstall";
   # "teststandard" is a superset of testinstall. It takes ~1h instead of ~1min.
   # tests are run twice, once with all packages loaded and once without
   # checkTarget = "teststandard";
 
-  preCheck = ''
+  doInstallCheck = true;
+  installCheckTarget = "testinstall";
+
+  preInstallCheck = ''
     # gap tests check that the home directory exists
     export HOME="$TMP/gap-home"
     mkdir -p "$HOME"
+
+    # make sure gap is in PATH
+    export PATH="$out/bin:$PATH"
+
+    # make sure we don't accidentally use the wrong gap binary
+    rm -r bin
+
+    # like the defaults the Makefile, but use gap from PATH instead of the
+    # one from builddir
+    installCheckFlagsArray+=(
+      "TESTGAP=gap --quitonbreak -b -m 100m -o 1g -q -x 80 -r -A"
+      "TESTGAPauto=gap --quitonbreak -b -m 100m -o 1g -q -x 80 -r"
+    )
   '';
 
   postCheck = ''
@@ -78,14 +110,20 @@ stdenv.mkDerivation rec {
   installPhase = ''
     mkdir -p "$out/bin" "$out/share/gap/"
 
-    cp -r . "$out/share/gap/build-dir"
+    mkdir -p "$out/share/gap"
+    echo "Copying files to target directory"
+    cp -ar . "$out/share/gap/build-dir"
 
-    sed -e "/GAP_DIR=/aGAP_DIR='$out/share/gap/build-dir/'" -i "$out/share/gap/build-dir/bin/gap.sh"
+    makeWrapper "$out/share/gap/build-dir/bin/gap.sh" "$out/bin/gap" \
+      --set GAP_DIR $out/share/gap/build-dir
+  '';
 
-    ln -s "$out/share/gap/build-dir/bin/gap.sh" "$out/bin/gap"
+  preFixup = ''
+    # patchelf won't strip references to the build dir if it still exists
+    rm -rf pkg
   '';
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "Computational discrete algebra system";
     maintainers = with maintainers;
     [
@@ -96,7 +134,7 @@ stdenv.mkDerivation rec {
     # keeping all packages increases the package size considerably, wchich
     # is why a local build is preferable in that situation. The timeframe
     # is reasonable and that way the binary cache doesn't get overloaded.
-    hydraPlatforms = stdenv.lib.optionals (!keepAllPackages) meta.platforms;
+    hydraPlatforms = lib.optionals (!keepAllPackages) meta.platforms;
     license = licenses.gpl2;
     homepage = http://gap-system.org/;
   };

diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix
@@ -70,7 +70,7 @@ let
   sage-env = callPackage ./sage-env.nix {
     sagelib = python.pkgs.sagelib;
     inherit env-locations;
-    inherit python rWrapper ecl singular palp flint pynac pythonEnv;
+    inherit python ecl singular palp flint pynac pythonEnv;
     pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
   };
 
@@ -124,19 +124,6 @@ let
     ignoreCollisions = true;
   } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
 
-  # needs to be rWrapper, standard "R" doesn't include default packages
-  rWrapper = pkgs.rWrapper.override {
-    # https://trac.sagemath.org/ticket/25674
-    R = pkgs.R.overrideAttrs (attrs: rec {
-      name = "R-3.4.4";
-      doCheck = false;
-      src = fetchurl {
-        url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz";
-        sha256 = "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk";
-      };
-    });
-  };
-
   arb = pkgs.arb.override { inherit flint; };
 
   singular = pkgs.singular.override { inherit flint; };

diff --git a/pkgs/applications/science/math/sage/patches/dont-test-guess-gaproot.patch b/pkgs/applications/science/math/sage/patches/dont-test-guess-gaproot.patch
@@ -0,0 +1,13 @@
+diff --git a/src/sage/libs/gap/util.pyx b/src/sage/libs/gap/util.pyx
+index 5ff67107c1..1318df86fd 100644
+--- a/src/sage/libs/gap/util.pyx
++++ b/src/sage/libs/gap/util.pyx
+@@ -165,7 +165,7 @@ def _guess_gap_root():
+     EXAMPLES::
+
+         sage: from sage.libs.gap.util import _guess_gap_root
+-        sage: _guess_gap_root()
++        sage: _guess_gap_root() # not tested (not necessary on nixos)
+         The gap-4.5.5.spkg (or later) seems to be not installed!
+         ...
+     """