NixOS · Jan 2, 2019 · Mar 20, 2019 · Mar 21, 2019 · Mar 21, 2019 · Mar 21, 2019
diff --git a/doc/multiple-output.xml b/doc/multiple-output.xml
@@ -101,6 +101,13 @@
    contain <varname>$outputBin</varname> and <varname>$outputLib</varname> are
    also added. (See <xref linkend="multiple-output-file-type-groups" />.)
   </para>
+
+  <para>
+   In some cases it may be desirable to combine different outputs under a
+   single store path. A function <literal>symlinkJoin</literal> can be used to
+   do this. (Note that it may negate some closure size benefits of using a
+   multiple-output package.)
+  </para>
  </section>
  <section xml:id="sec-multiple-outputs-">
   <title>Writing a split derivation</title>

diff --git a/nixos/modules/rename.nix b/nixos/modules/rename.nix
@@ -4,11 +4,6 @@ with lib;
 
 {
   imports = [
-    # !!! These were renamed the other way, but got reverted later.
-    # !!! Drop these before 18.09 is released.
-    (mkRenamedOptionModule [ "system" "nixos" "stateVersion" ] [ "system" "stateVersion" ])
-    (mkRenamedOptionModule [ "system" "nixos" "defaultChannel" ] [ "system" "defaultChannel" ])
-
     (mkRenamedOptionModule [ "networking" "enableRT73Firmware" ] [ "hardware" "enableRedistributableFirmware" ])
     (mkRenamedOptionModule [ "networking" "enableIntel3945ABGFirmware" ] [ "hardware" "enableRedistributableFirmware" ])
     (mkRenamedOptionModule [ "networking" "enableIntel2100BGFirmware" ] [ "hardware" "enableRedistributableFirmware" ])

diff --git a/pkgs/applications/audio/lollypop/default.nix b/pkgs/applications/audio/lollypop/default.nix
@@ -5,7 +5,7 @@
 
 python3.pkgs.buildPythonApplication rec  {
   pname = "lollypop";
-  version = "1.0";
+  version = "1.0.3";
 
   format = "other";
   doCheck = false;
@@ -14,7 +14,7 @@ python3.pkgs.buildPythonApplication rec  {
     url = "https://gitlab.gnome.org/World/lollypop";
     rev = "refs/tags/${version}";
     fetchSubmodules = true;
-    sha256 = "00hjxpgmhzhyjjdpm92cbbxwnc17xdhhk8svk5ih3n18yk5655fs";
+    sha256 = "1gjxcwl467h7011j9v4zy1j0fjlz480ibvk4akr6xwjg894jykbx";
   };
 
   nativeBuildInputs = [

diff --git a/pkgs/applications/editors/typora/default.nix b/pkgs/applications/editors/typora/default.nix
@@ -1,32 +1,44 @@
-{ stdenv, fetchurl, makeWrapper, electron_3, dpkg, gtk3, glib, gnome3, wrapGAppsHook }:
+{ stdenv, fetchurl, makeWrapper, electron_3, dpkg, gtk3, glib, gsettings-desktop-schemas, wrapGAppsHook }:
 
 stdenv.mkDerivation rec {
   pname = "typora";
-  version = "0.9.64";
+  version = "0.9.68";
 
   src = fetchurl {
     url = "https://www.typora.io/linux/typora_${version}_amd64.deb";
-    sha256 = "0dffydc11ys2i38gdy8080ph1xlbbzhcdcc06hyfv0dr0nf58a09";
+    sha256 = "09hkmnh9avzb7nc8i67vhbv6nc1v90kk88aq01mpmyibpdqp03zp";
   };
 
-  nativeBuildInputs = [ dpkg makeWrapper wrapGAppsHook ];
+  nativeBuildInputs = [
+    dpkg
+    makeWrapper
+    wrapGAppsHook
+  ];
 
-  buildInputs = [ gtk3 glib gnome3.gsettings-desktop-schemas ];
+  buildInputs = [
+    glib
+    gsettings-desktop-schemas
+    gtk3
+  ];
 
   unpackPhase = "dpkg-deb -x $src .";
 
   dontWrapGApps = true;
 
   installPhase = ''
-    mkdir -p $out/bin $out/share/typora
+    runHook preInstall
+
+    mkdir -p $out/bin $out/share
     {
       cd usr
-      mv share/typora/resources/app/* $out/share/typora
-      mv share/applications $out/share
-      mv share/icons $out/share
-      mv share/doc $out/share
+      mv share/typora/resources/app $out/share/typora
+      mv share/{applications,icons,doc} $out/share/
     }
 
+    runHook postInstall
+  '';
+
+  postFixup = ''
     makeWrapper ${electron_3}/bin/electron $out/bin/typora \
       --add-flags $out/share/typora \
       "''${gappsWrapperArgs[@]}" \
@@ -37,7 +49,7 @@ stdenv.mkDerivation rec {
     description = "A minimal Markdown reading & writing app";
     homepage = https://typora.io;
     license = licenses.unfree;
-    maintainers = with maintainers; [ jensbin ];
+    maintainers = with maintainers; [ jensbin worldofpeace ];
     inherit (electron_3.meta) platforms;
   };
 }
diff --git a/pkgs/applications/misc/iterm2/default.nix b/pkgs/applications/misc/iterm2/default.nix
@@ -15,6 +15,7 @@ stdenv.mkDerivation rec {
   postPatch = ''
     sed -i -e 's/CODE_SIGN_IDENTITY = "Developer ID Application"/CODE_SIGN_IDENTITY = ""/g' ./iTerm2.xcodeproj/project.pbxproj
   '';
+  preConfigure = "LD=$CC";
   makeFlagsArray = ["Deployment"];
   installPhase = ''
     mkdir -p "$out/Applications"

diff --git a/pkgs/applications/networking/browsers/chromium/common.nix b/pkgs/applications/networking/browsers/chromium/common.nix
@@ -25,7 +25,7 @@
 # package customization
 , enableNaCl ? false
 , enableWideVine ? false
-, useVaapi ? true
+, useVaapi ? false
 , gnomeSupport ? false, gnome ? null
 , gnomeKeyringSupport ? false, libgnome-keyring3 ? null
 , proprietaryCodecs ? true

diff --git a/pkgs/applications/networking/browsers/chromium/default.nix b/pkgs/applications/networking/browsers/chromium/default.nix
@@ -11,7 +11,7 @@
 , proprietaryCodecs ? true
 , enablePepperFlash ? false
 , enableWideVine ? false
-, useVaapi ? true
+, useVaapi ? false # test video on radeon, before enabling this
 , cupsSupport ? true
 , pulseSupport ? config.pulseaudio or stdenv.isLinux
 , commandLineArgs ? ""

diff --git a/pkgs/applications/networking/browsers/eolie/default.nix b/pkgs/applications/networking/browsers/eolie/default.nix
@@ -5,7 +5,7 @@
 
 python3.pkgs.buildPythonApplication rec {
   pname = "eolie";
-  version = "0.9.45";
+  version = "0.9.60";
 
   format = "other";
   doCheck = false;
@@ -14,7 +14,7 @@ python3.pkgs.buildPythonApplication rec {
     url = "https://gitlab.gnome.org/World/eolie";
     rev = "refs/tags/${version}";
     fetchSubmodules = true;
-    sha256 = "0x6f2qqqxpjf28mqxs4jlrz2z8wa9nvb9h24nf8qwmzavjjbraqg";
+    sha256 = "1mhl7p8pwp8lqx5z15r0lx1y4mb2c1gjwy3w6041cyc4hyb91693";
   };
 
   nativeBuildInputs = [

diff --git a/pkgs/applications/networking/cluster/minikube/default.nix b/pkgs/applications/networking/cluster/minikube/default.nix
@@ -14,17 +14,17 @@ let
 in buildGoPackage rec {
   pname   = "minikube";
   name    = "${pname}-${version}";
-  version = "0.35.0";
+  version = "1.0.0";
 
-  kubernetesVersion = "1.13.4";
+  kubernetesVersion = "1.14.0";
 
   goPackagePath = "k8s.io/minikube";
 
   src = fetchFromGitHub {
     owner  = "kubernetes";
     repo   = "minikube";
     rev    = "v${version}";
-    sha256 = "1qb342zs50sdfvfb8vbn7vrx11qqjy1hw518c053s7p34ljb24qd";
+    sha256 = "170iy0h27gkz2hg485rnawdw069gxwgkwsjmfj5yag2kkgl7gxa3";
   };
 
   buildInputs = [ go-bindata makeWrapper gpgme ] ++ stdenv.lib.optional stdenv.hostPlatform.isDarwin vmnet;

diff --git a/pkgs/applications/networking/p2p/gnunet/default.nix b/pkgs/applications/networking/p2p/gnunet/default.nix
@@ -4,11 +4,11 @@
 , libpulseaudio, libopus, libogg }:
 
 stdenv.mkDerivation rec {
-  name = "gnunet-0.10.1";
+  name = "gnunet-0.11.0";
 
   src = fetchurl {
     url = "mirror://gnu/gnunet/${name}.tar.gz";
-    sha256 = "04wxzm3wkgqbn42b8ksr4cx6m5cckyig5cls1adh0nwdczwvnp7n";
+    sha256 = "16kydkrjlf2vxflgls46bwaf9kjczf621p456q0qlphd7cy7lixp";
   };
 
   buildInputs = [

diff --git a/pkgs/applications/networking/spideroak/default.nix b/pkgs/applications/networking/spideroak/default.nix
@@ -4,31 +4,21 @@
 }:
 
 let
-  arch = if stdenv.hostPlatform.system == "x86_64-linux" then "x64"
-    else if stdenv.hostPlatform.system == "i686-linux" then "x86"
-    else throw "Spideroak client for: ${stdenv.hostPlatform.system} not supported!";
-
-  interpreter = if stdenv.hostPlatform.system == "x86_64-linux" then "ld-linux-x86-64.so.2"
-    else if stdenv.hostPlatform.system == "i686-linux" then "ld-linux.so.2"
-    else throw "Spideroak client for: ${stdenv.hostPlatform.system} not supported!";
-
-  sha256 = if stdenv.hostPlatform.system == "x86_64-linux" then "a88e5a8fe4a565ac500668bd53cf5784752d7c9253304ddce39ee7b01d078533"
-    else if stdenv.hostPlatform.system == "i686-linux" then "668f3b83a974a3877d16c8743c233a427ea0a44ab84b7f9aec19a2995db66c16"
-    else throw "Spideroak client for: ${stdenv.hostPlatform.system} not supported!";
+  sha256 = "6d6ca2b383bcc81af1217c696eb77864a2b6db7428f4b5bde5b5913ce705eec5";
 
   ldpath = stdenv.lib.makeLibraryPath [
     fontconfig freetype glib libICE libSM
     libX11 libXext libXrender zlib
   ];
 
-  version = "7.1.0";
+  version = "7.5.0";
 
 in stdenv.mkDerivation {
   name = "spideroak-${version}";
 
   src = fetchurl {
-    name = "SpiderOakONE-${version}-slack_tar_${arch}.tgz";
-    url = "https://spideroak.com/release/spideroak/slack_tar_${arch}";
+    name = "SpiderOakONE-${version}-slack_tar_x64.tgz";
+    url = "https://spideroak.com/release/spideroak/slack_tar_x64";
     inherit sha256;
   };
 
@@ -46,7 +36,7 @@ in stdenv.mkDerivation {
 
     rm -f $out/opt/SpiderOakONE/lib/libz*
 
-    patchelf --set-interpreter ${stdenv.glibc.out}/lib/${interpreter} \
+    patchelf --set-interpreter ${stdenv.glibc.out}/lib/ld-linux-x86-64.so.2 \
       "$out/opt/SpiderOakONE/lib/SpiderOakONE"
 
     RPATH=$out/opt/SpiderOakONE/lib:${ldpath}

diff --git a/pkgs/applications/office/notes-up/default.nix b/pkgs/applications/office/notes-up/default.nix
@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation rec {
   pname = "notes-up";
-  version = "1.6.3";
+  version = "2.0.0";
 
   src = fetchFromGitHub {
     owner = "Philip-Scott";
     repo = "Notes-up";
     rev = version;
-    sha256 = "06fzdb823kkami0jch9ccblsvw3x7zd1d4xz8fv3giscl3f36x4q";
+    sha256 = "16bb9ffsg2csps1cb636rff5vc6f1yyhg65g3y5b4wf2hlbmzgql";
   };
 
   nativeBuildInputs = [

diff --git a/pkgs/applications/science/biology/bowtie2/default.nix b/pkgs/applications/science/biology/bowtie2/default.nix
@@ -2,14 +2,14 @@
 
 stdenv.mkDerivation rec {
   pname = "bowtie2";
-  version = "2.3.4.3";
+  version = "2.3.5";
   name = "${pname}-${version}";
 
   src = fetchFromGitHub {
     owner = "BenLangmead";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1zl3cf327y2p7p03cavymbh7b00djc7lncfaqih33n96iy9q8ibp";
+    sha256 = "12v240wnbc541hl4z2fiymxd3bd6czazs13fjkygldflg48w45m0";
   };
 
   buildInputs = [ zlib tbb python perl ];

diff --git a/pkgs/applications/science/misc/root/5.nix b/pkgs/applications/science/misc/root/5.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, cmake, pcre, pkgconfig, python2
+{ stdenv, fetchurl, fetchpatch, cmake, pcre, pkgconfig, python2
 , libX11, libXpm, libXft, libXext, libGLU_combined, zlib, libxml2, lzma, gsl_1
 , Cocoa, OpenGL, cf-private, noSplash ? false }:
 
@@ -19,11 +19,30 @@ stdenv.mkDerivation rec {
 
   patches = [
     ./sw_vers_root5.patch
+
+    (fetchpatch {
+      name = "enable_new_gcc.patch";
+      url = "https://aur.archlinux.org/cgit/aur.git/plain/enable_new_gcc.patch?h=root5&id=91c50876081a0af36f84ec4f0f9dba869107fa4f";
+      sha256 = "1rnp0xlw0yqi7mjs4w145njd79i8kkir1qik7zwicdik9axf8ygm";
+    })
+
+    # prevents rootcint from looking in /usr/includes and such
+    ./purify_include_paths_root5.patch
+
+    # disable dictionary generation for stuff that includes libc headers
+    # our glibc requires a modern compiler
+    ./disable_libc_dicts_root5.patch
   ];
 
   preConfigure = ''
     patchShebangs build/unix/
     ln -s ${stdenv.lib.getDev stdenv.cc.libc}/include/AvailabilityMacros.h cint/cint/include/
+  ''
+  # Fix CINTSYSDIR for "build" version of rootcint
+  # This is probably a bug that breaks out-of-source builds
+  + ''
+    substituteInPlace cint/cint/src/loadfile.cxx\
+      --replace 'env = "cint";' 'env = "'`pwd`'/cint";'
   '' + stdenv.lib.optionalString noSplash ''
     substituteInPlace rootx/src/rootx.cxx --replace "gNoLogo = false" "gNoLogo = true"
   '';
@@ -73,8 +92,5 @@ stdenv.mkDerivation rec {
     description = "A data analysis framework";
     platforms = platforms.unix;
     maintainers = with maintainers; [ veprbl ];
-    # needs to be adapted to work with modern glibc
-    # it works on darwin by impurely picking up system's libc headers
-    broken = stdenv.isLinux;
   };
 }
diff --git a/pkgs/applications/science/misc/root/disable_libc_dicts_root5.patch b/pkgs/applications/science/misc/root/disable_libc_dicts_root5.patch
@@ -0,0 +1,27 @@
+diff --git a/cint/ROOT/CMakeLists.txt b/cint/ROOT/CMakeLists.txt
+--- a/cint/ROOT/CMakeLists.txt
++++ b/cint/ROOT/CMakeLists.txt
+@@ -47,21 +47,13 @@ set(CINTSTLDLLHEADERS
+     ${CMAKE_SOURCE_DIR}/cint/cint/lib/stdstrct/stdcxxfunc.h
+   )
+ set(CINTINCDLLNAMES 
+-    stdfunc 
++#    stdfunc 
+ #    stdcxxfunc
+    )
+ set(CINTINCDLLHEADERS
+-    ${CMAKE_SOURCE_DIR}/cint/cint/lib/stdstrct/stdfunc.h 
++#    ${CMAKE_SOURCE_DIR}/cint/cint/lib/stdstrct/stdfunc.h 
+ #    ${CMAKE_SOURCE_DIR}/cint/cint/lib/stdstrct/stdcxxfunc.h
+    )
+-if(NOT WIN32)
+-  set(CINTSTLDLLNAMES ${CINTSTLDLLNAMES}  valarray)
+-  set(CINTSTLDLLHEADERS ${CINTSTLDLLHEADERS} ${CINTDLLDIR}/vary.h)
+-  set(CINTINCDLLNAMES ${CINTINCDLLNAMES} posix ipc)
+-  set(CINTINCDLLHEADERS ${CINTINCDLLHEADERS} 
+-    ${CMAKE_SOURCE_DIR}/cint/cint/lib/posix/exten.h 
+-    ${CMAKE_SOURCE_DIR}/cint/cint/lib/ipc/ipcif.h)
+-endif()
+
+ set(CINTBUILDLOADER
+     vector