Merge commit '00e27c78d3d2de6964096ceee8d70e5b487365e3'

Conflicts:
	nixpkgs/nixos/modules/system/boot/systemd.nix
	nixpkgs/pkgs/applications/networking/browsers/firefox/common.nix
	nixpkgs/pkgs/applications/version-management/git-and-tools/cgit/common.nix
	nixpkgs/pkgs/applications/version-management/git-and-tools/cgit/default.nix
	nixpkgs/pkgs/applications/version-management/git-and-tools/cgit/pink.nix
	nixpkgs/pkgs/top-level/all-packages.nix

8 files changed, 34 insertions, 40 deletions

diff --git a/nixpkgs/pkgs/applications/science/math/R/default.nix b/nixpkgs/pkgs/applications/science/math/R/default.nix
index 4bd237f87834..f91d72ff3f63 100644
--- a/nixpkgs/pkgs/applications/science/math/R/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/R/default.nix
@@ -14,11 +14,11 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "R";
-  version = "4.1.2";
+  version = "4.1.3";
 
   src = fetchurl {
     url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz";
-    sha256 = "sha256-IDYiXp9yB9TOCX5Ulyrs2qi0DX2ZEc0mSR+sWg+rOK8=";
+    sha256 = "sha256-Ff9bMzxhCUBgsqUunB2OxVzELdAp45yiKr2qkJUm/tY=";
   };
 
   dontUseImakeConfigure = true;
diff --git a/nixpkgs/pkgs/applications/science/math/cemu/default.nix b/nixpkgs/pkgs/applications/science/math/cemu/default.nix
index 35b9200a4774..374b245e2499 100644
--- a/nixpkgs/pkgs/applications/science/math/cemu/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/cemu/default.nix
@@ -7,7 +7,7 @@
 , qtbase
 , qmake
 , git
-, libpng_apng
+, libpng
 , pkg-config
 , wrapQtAppsHook
 , stdenv
@@ -37,7 +37,7 @@ stdenv.mkDerivation rec {
     libarchive
     libusb-compat-0_1
     qtbase
-    libpng_apng
+    libpng
   ];
 
   qmakeFlags = [
diff --git a/nixpkgs/pkgs/applications/science/math/cntk/default.nix b/nixpkgs/pkgs/applications/science/math/cntk/default.nix
index ba2225b903fa..eb14982575a2 100644
--- a/nixpkgs/pkgs/applications/science/math/cntk/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/cntk/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchgit, fetchFromGitHub, cmake
+{ lib, stdenv, fetchFromGitHub, cmake
 , fetchpatch
 , openblas, blas, lapack, opencv3, libzip, boost, protobuf, mpi
 , onebitSGDSupport ? false
@@ -22,11 +22,12 @@ in stdenv.mkDerivation rec {
   pname = "CNTK";
   version = "2.7";
 
-  # Submodules
-  src = fetchgit {
-    url = "https://github.com/Microsoft/CNTK";
+  src = fetchFromGitHub {
+    owner = "Microsoft";
+    repo = "CNTK";
     rev = "v${version}";
-    sha256 = "18l9k7s966a26ywcf7flqyhm61788pcb9fj3wk61jrmgkhy2pcns";
+    sha256 = "sha256-2rIrPJyvZhnM5EO6tNhF6ARTocfUHce4N0IZk/SZiaI=";
+    fetchSubmodules = true;
   };
 
   patches = [
diff --git a/nixpkgs/pkgs/applications/science/math/fricas/default.nix b/nixpkgs/pkgs/applications/science/math/fricas/default.nix
index 79d5664426be..8c2541fe4129 100644
--- a/nixpkgs/pkgs/applications/science/math/fricas/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/fricas/default.nix
@@ -1,14 +1,11 @@
 { lib, stdenv, fetchurl, sbcl, libX11, libXpm, libICE, libSM, libXt, libXau, libXdmcp }:
 
-let
+stdenv.mkDerivation rec {
+  pname = "fricas";
   version = "1.3.7";
-  name = "fricas-" + version;
-in
-stdenv.mkDerivation {
-  inherit name;
 
   src = fetchurl {
-    url = "mirror://sourceforge/fricas/fricas/${version}/${name}-full.tar.bz2";
+    url = "mirror://sourceforge/fricas/fricas/${version}/fricas-${version}-full.tar.bz2";
     sha256 = "sha256-cOqMvSe3ef/ZeVy5cj/VU/aTRtxgfxZfRbE4lWE5TU4=";
   };
 
diff --git a/nixpkgs/pkgs/applications/science/math/nasc/default.nix b/nixpkgs/pkgs/applications/science/math/nasc/default.nix
index 2fe027365cdc..3e7a8b56af1c 100644
--- a/nixpkgs/pkgs/applications/science/math/nasc/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/nasc/default.nix
@@ -48,7 +48,6 @@ stdenv.mkDerivation rec {
     gtk3
     gtksourceview
     libgee
-    pantheon.elementary-icon-theme
     pantheon.granite
     webkitgtk
     # We add libqalculate's runtime dependencies because nasc has it as a modified subproject.
diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
index 7ba5838faba1..4f68eb6ae78d 100644
--- a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "qalculate-gtk";
-  version = "4.0.0";
+  version = "4.1.0";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "qalculate-gtk";
     rev = "v${version}";
-    sha256 = "sha256-l9lR5MVHWiRz5RG/I/nXRY4GQSSaXXP7PlRNoAu9+yo=";
+    sha256 = "sha256-EOiExp8JBc3SybSiBVbuRxBqTujzLjysWM0v94goups=";
   };
 
   hardeningDisable = [ "format" ];
diff --git a/nixpkgs/pkgs/applications/science/math/sage/README.md b/nixpkgs/pkgs/applications/science/math/sage/README.md
index 26e91fc63133..c3a81c2109ee 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/README.md
+++ b/nixpkgs/pkgs/applications/science/math/sage/README.md
@@ -17,7 +17,7 @@ If the build broke as a result of a package update, try those solutions in order
 - fix the problem yourself. First clone the sagemath source and then check out the sage version you want to patch:
 
 ```
-[user@localhost ~]$ git clone git://github.com/sagemath/sage.git
+[user@localhost ~]$ git clone https://github.com/sagemath/sage.git
 [user@localhost ~]$ cd sage
 [user@localhost sage]$ git checkout 8.2 # substitute the relevant version here
 ```
@@ -41,7 +41,7 @@ You can [login the sage trac using GitHub](https://trac.sagemath.org/login). You
 Here's the gist, assuming you want to use ssh key authentication. First, [add your public ssh key](https://trac.sagemath.org/prefs/sshkeys). Then:
 
 ```
-[user@localhost ~]$ git clone git://github.com/sagemath/sage.git
+[user@localhost ~]$ git clone https://github.com/sagemath/sage.git
 [user@localhost ~]$ cd sage
 [user@localhost sage]$ git remote add trac git@trac.sagemath.org:sage.git -t master
 [user@localhost sage]$ git checkout -b u/gh-<your-github-username>/<your-branch-name> develop
diff --git a/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix b/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix
index 18dba2952cad..65d8c145bef6 100644
--- a/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix
@@ -1,11 +1,7 @@
 { stdenv, fetchurl, lib, xorg }:
 
 let
-  name = "scilab-bin-${ver}";
-
-  ver = "6.1.1";
-
-  badArch = throw "${name} requires i686-linux or x86_64-linux";
+  badArch = throw "scilab-bin requires i686-linux or x86_64-linux";
 
   architecture =
     if stdenv.hostPlatform.system == "i686-linux" then
@@ -15,11 +11,12 @@ let
     else
       badArch;
 in
-stdenv.mkDerivation {
-  inherit name;
+stdenv.mkDerivation rec {
+  pname = "scilab-bin";
+  version = "6.1.1";
 
   src = fetchurl {
-    url = "https://www.scilab.org/download/${ver}/scilab-${ver}.bin.linux-${architecture}.tar.gz";
+    url = "https://www.scilab.org/download/${version}/scilab-${version}.bin.linux-${architecture}.tar.gz";
     sha256 =
       if stdenv.hostPlatform.system == "i686-linux" then
         "0fgjc2ak3b2qi6yin3fy50qwk2bcj0zbz1h4lyyic9n1n1qcliib"
@@ -43,7 +40,7 @@ stdenv.mkDerivation {
     sed -i 's|\$(/bin/|$(|g' bin/scilab
     sed -i 's|/usr/bin/||g' bin/scilab
 
-    sci="$out/opt/scilab-${ver}"
+    sci="$out/opt/scilab-${version}"
     fullLibPath="$sci/lib/scilab:$sci/lib/thirdparty:$libPath"
     fullLibPath="$fullLibPath:$sci/lib/thirdparty/redist"
 
@@ -55,31 +52,31 @@ stdenv.mkDerivation {
   '';
 
   installPhase = ''
-    mkdir -p "$out/opt/scilab-${ver}"
-    cp -r . "$out/opt/scilab-${ver}/"
+    mkdir -p "$out/opt/scilab-${version}"
+    cp -r . "$out/opt/scilab-${version}/"
 
     # Create bin/ dir
     mkdir "$out/bin"
 
     # Creating executable symlinks
-    ln -s "$out/opt/scilab-${ver}/bin/scilab" "$out/bin/scilab"
-    ln -s "$out/opt/scilab-${ver}/bin/scilab-cli" "$out/bin/scilab-cli"
-    ln -s "$out/opt/scilab-${ver}/bin/scilab-adv-cli" "$out/bin/scilab-adv-cli"
+    ln -s "$out/opt/scilab-${version}/bin/scilab" "$out/bin/scilab"
+    ln -s "$out/opt/scilab-${version}/bin/scilab-cli" "$out/bin/scilab-cli"
+    ln -s "$out/opt/scilab-${version}/bin/scilab-adv-cli" "$out/bin/scilab-adv-cli"
 
     # Creating desktop config dir
     mkdir -p "$out/share/applications"
 
     # Moving desktop config files
-    mv $out/opt/scilab-${ver}/share/applications/*.desktop $out/share/applications
+    mv $out/opt/scilab-${version}/share/applications/*.desktop $out/share/applications
 
     # Fixing Exec paths and launching each app with a terminal
-    sed -i -e "s|Exec=|Exec=$out/opt/scilab-${ver}/bin/|g" \
+    sed -i -e "s|Exec=|Exec=$out/opt/scilab-${version}/bin/|g" \
            -e "s|Terminal=.*$|Terminal=true|g" $out/share/applications/*.desktop
 
     # Moving icons to the appropriate locations
-    for path in $out/opt/scilab-${ver}/share/icons/hicolor/*/*/*
+    for path in $out/opt/scilab-${version}/share/icons/hicolor/*/*/*
     do
-      newpath=$(echo $path | sed 's|/opt/scilab-${ver}||g')
+      newpath=$(echo $path | sed 's|/opt/scilab-${version}||g')
       filename=$(echo $path | sed 's|.*/||g')
       dir=$(echo $newpath | sed "s|$filename||g")
       mkdir -p $dir
@@ -87,10 +84,10 @@ stdenv.mkDerivation {
     done
 
     # Removing emptied folders
-    rm -rf $out/opt/scilab-${ver}/share/{applications,icons}
+    rm -rf $out/opt/scilab-${version}/share/{applications,icons}
 
     # Moving other share/ folders
-    mv $out/opt/scilab-${ver}/share/{appdata,locale,mime} $out/share
+    mv $out/opt/scilab-${version}/share/{appdata,locale,mime} $out/share
   '';
 
   meta = {