NixOS · Nov 3, 2019 · Nov 7, 2019 · Nov 7, 2019 · Nov 15, 2019 · Nov 15, 2019
diff --git a/nixos/modules/services/networking/bitcoind.nix b/nixos/modules/services/networking/bitcoind.nix
@@ -177,9 +177,6 @@ in {
         NoNewPrivileges = "true";
         PrivateDevices = "true";
         MemoryDenyWriteExecute = "true";
-
-        # Permission for preStart
-        PermissionsStartOnly = "true";
       };
     };
     users.users.${cfg.user} = {

diff --git a/nixos/modules/services/web-servers/nginx/location-options.nix b/nixos/modules/services/web-servers/nginx/location-options.nix
@@ -1,4 +1,4 @@
-# This file defines the options that can be used both for the Apache
+# This file defines the options that can be used both for the Nginx
 # main server configuration, and for the virtual hosts.  (The latter
 # has additional options that affect the web server as a whole, like
 # the user/group to run under.)
@@ -92,4 +92,3 @@ with lib;
     };
   };
 }
-
diff --git a/nixos/modules/services/web-servers/nginx/vhost-options.nix b/nixos/modules/services/web-servers/nginx/vhost-options.nix
@@ -1,4 +1,4 @@
-# This file defines the options that can be used both for the Apache
+# This file defines the options that can be used both for the Nginx
 # main server configuration, and for the virtual hosts.  (The latter
 # has additional options that affect the web server as a whole, like
 # the user/group to run under.)

diff --git a/pkgs/applications/audio/vcv-rack/default.nix b/pkgs/applications/audio/vcv-rack/default.nix
@@ -3,17 +3,10 @@
 , libzip, rtaudio, rtmidi, speex, libsamplerate }:
 
 let
-  glfw-git = glfw.overrideAttrs (oldAttrs: rec {
-    name = "glfw-git-${version}";
-    version = "2019-06-30";
-    src = fetchFromGitHub {
-      owner = "glfw";
-      repo = "glfw";
-      rev = "d25248343e248337284dfbe5ecd1eddbd37ae66d";
-      sha256 = "0gbz353bfmqbpm0af2nqf5draz3k4f3lqwiqj68s8nwn7878aqm3";
-    };
-    buildInputs = oldAttrs.buildInputs ++ [ libXext libXi ];
-  });
+  # The package repo vendors some of the package dependencies as submodules.
+  # Others are downloaded with `make deps`. Due to previous issues with the
+  # `glfw` submodule (see above) and because we can not access the network when
+  # building in a sandbox, we fetch the dependency source manually.
   pfft-source = fetchFromBitbucket {
     owner = "jpommier";
     repo = "pffft";
@@ -47,24 +40,22 @@ let
 in
 with stdenv.lib; stdenv.mkDerivation rec {
   pname = "VCV-Rack";
-  version = "1.1.5";
+  version = "1.1.6";
 
   src = fetchFromGitHub {
     owner = "VCVRack";
     repo = "Rack";
     rev = "v${version}";
-    sha256 = "1g3mkghgiycbxyvzjhanc1b10jynkfkw03bpnha06qgd6gd9wv7k";
+    sha256 = "0ji64prr74qzxf5bx1sw022kbslx9nzll16lmk5in78hbl137b3i";
   };
 
   patches = [
     ./rack-minimize-vendoring.patch
-    # We patch out a call to a custom function, that is not needed on Linux.
-    # This avoids needing a patched version of glfw. The version we previously used disappeared
-    # on GitHub. See https://github.com/NixOS/nixpkgs/issues/71189
-    ./remove-custom-glfw-function.patch
   ];
 
   prePatch = ''
+    # As we can't use `make dep` to set up the dependencies (as explained
+    # above), we do it here manually
     mkdir -p dep/include
 
     cp -r ${pfft-source} dep/jpommier-pffft-source
@@ -86,7 +77,7 @@ with stdenv.lib; stdenv.mkDerivation rec {
   enableParallelBuilding = true;
 
   nativeBuildInputs = [ makeWrapper pkgconfig ];
-  buildInputs = [ glfw-git alsaLib curl glew gtk2-x11 jansson libjack2 libzip rtaudio rtmidi speex libsamplerate ];
+  buildInputs = [ alsaLib curl glew glfw gtk2-x11 jansson libjack2 libsamplerate libzip rtaudio rtmidi speex ];
 
   buildFlags = "Rack";
 

diff --git a/pkgs/applications/audio/vcv-rack/remove-custom-glfw-function.patch b/pkgs/applications/audio/vcv-rack/remove-custom-glfw-function.patch
diff --git a/pkgs/applications/misc/gpscorrelate/default.nix b/pkgs/applications/misc/gpscorrelate/default.nix
@@ -3,17 +3,15 @@
 
 stdenv.mkDerivation rec {
   pname = "gpscorrelate";
-  version = "unstable-2019-09-03";
+  version = "2.0";
 
   src = fetchFromGitHub {
     owner = "dfandrich";
     repo = pname;
-    rev = "e1dd44a34f67b1ab7201440e60a840258ee448d2";
-    sha256 = "0gjwwdqh9dprzylmmnk3gm41khka9arkij3i9amd8y7d49pm9rlv";
+    rev = version;
+    sha256 = "1wkpb0nqnm0ik46hp2sibf96h2gxi6n951zm8c72scgmh4ciq4fl";
   };
 
-  patches = [ ./fix-localedir.diff ];
-
   nativeBuildInputs = [
     desktop-file-utils
     docbook_xml_dtd_42
@@ -30,7 +28,6 @@ stdenv.mkDerivation rec {
 
   makeFlags = [
     "prefix=${placeholder "out"}"
-    "GTK=3"
     "CC=cc"
     "CXX=c++"
     "CFLAGS=-DENABLE_NLS"
@@ -60,7 +57,7 @@ stdenv.mkDerivation rec {
     '';
 
     license = licenses.gpl2Plus;
-    homepage = "https://github.com/dfandrich/gpscorrelate";
+    homepage = "https://dfandrich.github.io/gpscorrelate/";
     platforms = platforms.linux;
     maintainers = with maintainers; [ sikmir ];
   };

diff --git a/pkgs/applications/misc/gpscorrelate/fix-localedir.diff b/pkgs/applications/misc/gpscorrelate/fix-localedir.diff
diff --git a/pkgs/applications/networking/instant-messengers/signal-cli/default.nix b/pkgs/applications/networking/instant-messengers/signal-cli/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, lib, fetchurl, makeWrapper, jre_headless }:
+{ stdenv, lib, fetchurl, makeWrapper, jre_headless, libmatthew_java, dbus, dbus_java }:
 
 stdenv.mkDerivation rec {
   pname = "signal-cli";
@@ -10,16 +10,24 @@ stdenv.mkDerivation rec {
     sha256 = "1gvdifscyxmxn2dwlkqi684ahy5kbcj84mqda0m8l4aa8iaq1d59";
   };
 
-  buildInputs = [ makeWrapper ];
+  buildInputs = lib.optional stdenv.isLinux [ libmatthew_java dbus dbus_java ];
+  nativeBuildInputs = [ makeWrapper ];
 
   installPhase = ''
     mkdir -p $out/bin
     cp -r lib $out/lib
     cp bin/signal-cli $out/bin/signal-cli
+  '' + (if stdenv.isLinux then ''
+    makeWrapper ${jre_headless}/bin/java $out/bin/signal-cli \
+      --set JAVA_HOME "${jre_headless}" \
+      --add-flags "-classpath '$out/lib/*:${libmatthew_java}/lib/jni'" \
+      --add-flags "-Djava.library.path=${libmatthew_java}/lib/jni:${dbus_java}/share/java/dbus:$out/lib" \
+      --add-flags "org.asamk.signal.Main"
+  '' else ''
     wrapProgram $out/bin/signal-cli \
       --prefix PATH : ${lib.makeBinPath [ jre_headless ]} \
       --set JAVA_HOME ${jre_headless}
-  '';
+  '');
 
   # Execution in the macOS (10.13) sandbox fails with
   # dyld: Library not loaded: /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa
@@ -29,6 +37,7 @@ stdenv.mkDerivation rec {
   #         /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa: file system sandbox blocked stat()
   # /nix/store/in41dz8byyyz4c0w132l7mqi43liv4yr-stdenv-darwin/setup: line 1310:  2231 Abort trap: 6           signal-cli --version
   doInstallCheck = stdenv.isLinux;
+
   installCheckPhase = ''
     export PATH=$PATH:$out/bin
     # --help returns non-0 exit code even when working
@@ -39,7 +48,7 @@ stdenv.mkDerivation rec {
     homepage = https://github.com/AsamK/signal-cli;
     description = "Command-line and dbus interface for communicating with the Signal messaging service";
     license = licenses.gpl3;
-    maintainers = with maintainers; [ ivan ];
+    maintainers = with maintainers; [ ivan erictapen ];
     platforms = platforms.all;
   };
 }
diff --git a/pkgs/desktops/gnome-3/extensions/system-monitor/default.nix b/pkgs/desktops/gnome-3/extensions/system-monitor/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, substituteAll, fetchFromGitHub, glib, glib-networking, libgtop, gnome3 }:
+{ stdenv, substituteAll, fetchFromGitHub, glib, glib-networking, libgtop }:
 
 stdenv.mkDerivation rec {
   pname = "gnome-shell-system-monitor";
@@ -41,6 +41,5 @@ stdenv.mkDerivation rec {
     license = licenses.gpl3Plus;
     maintainers = with maintainers; [ aneeshusa tiramiseb ];
     homepage = https://github.com/paradoxxxzero/gnome-shell-system-monitor-applet;
-    broken = versionAtLeast gnome3.gnome-shell.version "3.32";
   };
 }
diff --git a/pkgs/development/haskell-modules/configuration-ghc-8.8.x.nix b/pkgs/development/haskell-modules/configuration-ghc-8.8.x.nix
@@ -102,11 +102,6 @@ self: super: {
   vault = dontHaddock super.vault;
   monad-par = dontCheck super.monad-par;   # test suite does not compile in monad-par-0.3.4.8
 
-  # TODO dont fetch patch if https://github.com/simonmar/alex/issues/140 is resolved
-  alex = appendPatch super.alex (pkgs.fetchpatch {
-    url = "https://github.com/simonmar/alex/commit/deaae6eddef5186bfd0e42e2c3ced39e26afa4d6.patch";
-    sha256 = "1v40gmnw4lqyk271wngdwz8whpfdhmza58srbkka8icwwwrck3l5";
-  });
   # https://github.com/snapframework/snap-core/issues/288
   snap-core = overrideCabal super.snap-core (drv: { prePatch = "substituteInPlace src/Snap/Internal/Core.hs --replace 'fail   = Fail.fail' ''"; });
   # needs a release

diff --git a/pkgs/development/interpreters/elixir/1.9.nix b/pkgs/development/interpreters/elixir/1.9.nix
@@ -1,7 +1,9 @@
 { mkDerivation }:
 
+# How to obtain `sha256`:
+# nix-prefetch-url --unpack https://github.com/elixir-lang/elixir/archive/v${version}.tar.gz
 mkDerivation {
-  version = "1.9.2";
-  sha256 = "19yn6nx6r627f5zbyc7ckgr96d6b45sgwx95n2gp2imqwqvpj8wc";
+  version = "1.9.4";
+  sha256 = "1l4318g35y4h0vi2w07ayc3jizw1xc3s7hdb47w6j3iw33y06g6b";
   minimumOTPVersion = "20";
 }
diff --git a/pkgs/development/interpreters/erlang/R22.nix b/pkgs/development/interpreters/erlang/R22.nix
@@ -1,8 +1,10 @@
 { mkDerivation }:
 
+# How to obtain `sha256`:
+# nix-prefetch-url --unpack https://github.com/erlang/otp/archive/OTP-${version}.tar.gz
 mkDerivation {
-  version = "22.0.4";
-  sha256 = "1aqkhd6nwdn4xp5yz02zbymd4x8ij8fjw9ji8kh860n1a513k9ai";
+  version = "22.1.7";
+  sha256 = "18aqy2s8nqd82v4lzzxknrwjva8mv1y2hvai9cakz5nkyd3vwq62";
 
   prePatch = ''
     substituteInPlace make/configure.in --replace '`sw_vers -productVersion`' "''${MACOSX_DEPLOYMENT_TARGET:-10.12}"

diff --git a/pkgs/development/libraries/ffmpeg/2.8.nix b/pkgs/development/libraries/ffmpeg/2.8.nix
@@ -1,7 +1,7 @@
 { callPackage, ... } @ args:
 
-callPackage ./generic.nix (args // rec {
+callPackage ./generic.nix (rec {
   version = "${branch}.14";
   branch = "2.8";
   sha256 = "1g6x3lyjl1zlfksizj1ys61kj97yg0xf4dlr6sr5acpbja3a26yn";
-})
+} // args)
diff --git a/pkgs/development/libraries/ffmpeg/3.4.nix b/pkgs/development/libraries/ffmpeg/3.4.nix
@@ -4,9 +4,9 @@
 , ...
 }@args:
 
-callPackage ./generic.nix (args // rec {
+callPackage ./generic.nix (rec {
   version = branch;
   branch = "3.4.6";
   sha256 = "1s20wzgxxrm56gckyb8cf1lh36hdnkdxvmmnnvdxvia4zb3grf1b";
   darwinFrameworks = [ Cocoa CoreMedia ];
-})
+} // args)
diff --git a/pkgs/development/libraries/ffmpeg/4.nix b/pkgs/development/libraries/ffmpeg/4.nix
@@ -4,9 +4,9 @@
 , ...
 }@args:
 
-callPackage ./generic.nix (args // rec {
+callPackage ./generic.nix (rec {
   version = "4.2.1";
   branch = "4.2";
   sha256 = "090naa6rj46pzkgh03bf51hbqdz356qqckr2pw6pykc6ysiryak8";
   darwinFrameworks = [ Cocoa CoreMedia VideoToolbox ];
-})
+} // args)
diff --git a/pkgs/development/libraries/science/biology/elastix/default.nix b/pkgs/development/libraries/science/biology/elastix/default.nix
@@ -1,15 +1,15 @@
-{ stdenv, fetchurl, cmake, itk, python }:
+{ stdenv, fetchFromGitHub, cmake, itk, python }:
 
 stdenv.mkDerivation rec {
   pname    = "elastix";
-  pversion = "4.9.0";
-  name  = "${pname}-${pversion}";
+  version = "5.0.0";
 
-  src = fetchurl {
-    url    = "https://github.com/SuperElastix/${pname}/archive/${pversion}.tar.gz";
-    sha256 = "02pbln36nq98xxfyqwlxg7b6gmigdq4fgfqr9mym1qn58aj04shg";
+  src = fetchFromGitHub {
+    owner  = "SuperElastix";
+    repo   = pname;
+    rev    = version;
+    sha256 = "1zrl7rz4lwsx88b2shnl985f3a97lmp4ksbd437h9y0hfjq8l0lj";
   };
-
   nativeBuildInputs = [ cmake python ];
   buildInputs = [ itk ];
 
@@ -19,6 +19,5 @@ stdenv.mkDerivation rec {
     maintainers = with maintainers; [ bcdarwin ];
     platforms = platforms.linux;
     license = licenses.asl20;
-    broken = true;
   };
 }
diff --git a/pkgs/development/python-modules/cliff/default.nix b/pkgs/development/python-modules/cliff/default.nix
@@ -9,6 +9,10 @@
 , pyyaml
 , unicodecsv
 , cmd2
+, pytest
+, mock
+, testtools
+, fixtures
 }:
 
 buildPythonPackage rec {
@@ -31,10 +35,17 @@ buildPythonPackage rec {
     unicodecsv
   ];
 
-  # test dependencies are complex
-  # and would require about 20 packages
-  # to be added
-  doCheck = false;
+  # remove version constraints
+  postPatch = ''
+    sed -i '/cmd2/c\cmd2' requirements.txt
+  '';
+
+  checkInputs = [ fixtures mock pytest testtools ];
+  # add some tests
+  checkPhase = ''
+    pytest cliff/tests/test_{utils,app,command,help,lister}.py \
+      -k 'not interactive_mode'
+  '';
 
   meta = with lib; {
     description = "Command Line Interface Formulation Framework";

diff --git a/pkgs/development/python-modules/wrf-python/default.nix b/pkgs/development/python-modules/wrf-python/default.nix
@@ -1,19 +1,20 @@
-{lib, fetchFromGitHub, pythonOlder, buildPythonPackage, gfortran, mock, xarray, wrapt, numpy, netcdf4}:
+{lib, fetchFromGitHub, pythonOlder, buildPythonPackage, gfortran, mock, xarray, wrapt, numpy, netcdf4, setuptools}:
 
 buildPythonPackage rec {
   pname = "wrf-python";
-  version = "1.3.1.1";
+  version = "1.3.2";
 
   src = fetchFromGitHub {
     owner = "NCAR";
     repo = "wrf-python";
     rev = version;
-    sha256 = "12mm7x1r5md6x28vmwyh6k655pgsv6knj8ycmjbxxk8bk7qsj74h";
+    sha256 = "1rklkki54z5392cpwwy78bnmsy2ghc187l3j7nv0rzn6jk5bvyi7";
   };
 
   propagatedBuildInputs = [
     wrapt
     numpy
+    setuptools
     xarray
   ];
 
@@ -39,4 +40,4 @@ buildPythonPackage rec {
     license = lib.licenses.asl20;
     maintainers = with lib.maintainers; [ mhaselsteiner ];
 	};
-}
+}