Merge remote-tracking branch 'origin/master' into staging

nixos/modules/module-list.nix

@@ -328,7 +328,7 @@
   ./services/monitoring/cadvisor.nix
   ./services/monitoring/collectd.nix
   ./services/monitoring/das_watchdog.nix
-  ./services/monitoring/dd-agent.nix
+  ./services/monitoring/dd-agent/dd-agent.nix
   ./services/monitoring/grafana.nix
   ./services/monitoring/graphite.nix
   ./services/monitoring/hdaps.nix

nixos/modules/services/monitoring/dd-agent/dd-agent-defaults.nix

@@ -0,0 +1,8 @@
+# Generated using update-dd-agent-default, please re-run after updating dd-agent. DO NOT EDIT MANUALLY.
+[
+  "auto_conf"
+  "agent_metrics.yaml.default"
+  "disk.yaml.default"
+  "network.yaml.default"
+  "ntp.yaml.default"
+]

nixos/modules/services/monitoring/dd-agent/dd-agent.nix

@@ -73,9 +73,15 @@ let
   nginxConfig = pkgs.writeText "nginx.yaml" cfg.nginxConfig;
   mongoConfig = pkgs.writeText "mongo.yaml" cfg.mongoConfig;
   jmxConfig = pkgs.writeText "jmx.yaml" cfg.jmxConfig;
+  processConfig = pkgs.writeText "process.yaml" cfg.processConfig;
   
   etcfiles =
-    [ { source = ddConf;
+    let
+      defaultConfd = import ./dd-agent-defaults.nix;
+    in (map (f: { source = "${pkgs.dd-agent}/agent/conf.d-system/${f}";
+                  target = "dd-agent/conf.d/${f}";
+                }) defaultConfd) ++ [
+      { source = ddConf;
         target = "dd-agent/datadog.conf";
       }
       { source = diskConfig;
@@ -96,6 +102,10 @@ let
       { source = mongoConfig;
         target = "dd-agent/conf.d/mongo.yaml";
       }) ++
+    (optional (cfg.processConfig != null)
+      { source = processConfig;
+        target = "dd-agent/conf.d/process.yaml";
+      }) ++
     (optional (cfg.jmxConfig != null)
       { source = jmxConfig;
         target = "dd-agent/conf.d/jmx.yaml";
@@ -153,6 +163,16 @@ in {
       type = types.uniq (types.nullOr types.string);
     };
 
+    processConfig = mkOption {
+      description = ''
+        Process integration configuration
+ 
+        See http://docs.datadoghq.com/integrations/process/
+      '';
+      default = null;
+      type = types.uniq (types.nullOr types.string);
+    };
+
   };
 
   config = mkIf cfg.enable {
@@ -179,7 +199,7 @@ in {
         Restart = "always";
         RestartSec = 2;
       };
-      restartTriggers = [ pkgs.dd-agent ddConf diskConfig networkConfig postgresqlConfig nginxConfig mongoConfig jmxConfig ];
+      restartTriggers = [ pkgs.dd-agent ddConf diskConfig networkConfig postgresqlConfig nginxConfig mongoConfig jmxConfig processConfig ];
     };
 
     systemd.services.dogstatsd = {
@@ -195,7 +215,7 @@ in {
         Restart = "always";
         RestartSec = 2;
       };
-      restartTriggers = [ pkgs.dd-agent ddConf diskConfig networkConfig postgresqlConfig nginxConfig mongoConfig jmxConfig ];
+      restartTriggers = [ pkgs.dd-agent ddConf diskConfig networkConfig postgresqlConfig nginxConfig mongoConfig jmxConfig processConfig ];
     };
 
     systemd.services.dd-jmxfetch = lib.mkIf (cfg.jmxConfig != null) {

nixos/modules/services/monitoring/dd-agent/update-dd-agent-defaults

@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+dd=$(nix-build --no-out-link -A dd-agent ../../../..)
+echo '# Generated using update-dd-agent-default, please re-run after updating dd-agent. DO NOT EDIT MANUALLY.' > dd-agent-defaults.nix
+echo '[' >> dd-agent-defaults.nix
+echo '  "auto_conf"' >> dd-agent-defaults.nix
+for f in $(find $dd/agent/conf.d-system -maxdepth 1 -type f | grep -v '\.example' | sort); do
+  echo "  \"$(basename $f)\"" >> dd-agent-defaults.nix
+done
+echo ']' >> dd-agent-defaults.nix

pkgs/applications/editors/emacs-modes/elpa-generated.nix

@@ -162,10 +162,10 @@
       }) {};
     async = callPackage ({ elpaBuild, fetchurl, lib }: elpaBuild {
         pname = "async";
-        version = "1.9";
+        version = "1.9.2";
         src = fetchurl {
-          url = "https://elpa.gnu.org/packages/async-1.9.tar";
+          url = "https://elpa.gnu.org/packages/async-1.9.2.tar";
-          sha256 = "1ip5nc8xyln5szvqwp6wqva9xr84pn8ssn3nnphrszr19y4js2bm";
+          sha256 = "17fnvrj7jww29sav6a6jpizclg4w2962m6h37akpii71gf0vrffw";
         };
         packageRequires = [];
         meta = {
@@ -1404,10 +1404,10 @@
       }) {};
     org = callPackage ({ elpaBuild, fetchurl, lib }: elpaBuild {
         pname = "org";
-        version = "20170210";
+        version = "20170502";
         src = fetchurl {
-          url = "https://elpa.gnu.org/packages/org-20170210.tar";
+          url = "https://elpa.gnu.org/packages/org-20170502.tar";
-          sha256 = "15415wh3w8d4c8hd7qfrfdjnjb1zppmrkg8cdp7hw2ilyr90c0bn";
+          sha256 = "12inz804j55ycprb2m3ay54d1bhwhjssmn5nrfm7cfklyhfsy27s";
         };
         packageRequires = [];
         meta = {

pkgs/applications/networking/cluster/helm/default.nix

@@ -4,12 +4,12 @@ let
          then "linux-amd64"
          else "darwin-amd64";
   checksum = if stdenv.isLinux
-             then "fa434644d1afd92637369a033fd65b717d8dfa910127d335e8a82c8fad74cc35"
+             then "17fya0d1v2w44df5n5xb99vr8qjbnbfjvicsi9p7yz4iz2mcymd6"
-             else "64420d467e03ceb666a4f22b89e08b93c06f76f5917fe539860b04cd5e5e515f";
+             else "0299ffws37d60wim8kvdp4xrvqxa93sggrprgrsiclcp8bab0dcr";
 in
 stdenv.mkDerivation rec {
   pname = "helm";
-  version = "2.2.3";
+  version = "2.3.1";
   name = "${pname}-${version}";
 
   src = fetchurl {

pkgs/applications/science/math/R/default.nix

@@ -1,7 +1,7 @@
 { stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng
 , libtiff, ncurses, pango, pcre, perl, readline, tcl, texLive, tk, xz, zlib
 , less, texinfo, graphviz, icu, pkgconfig, bison, imake, which, jdk, openblas
-, curl, Cocoa, Foundation, cf-private, libobjc, tzdata
+, curl, Cocoa, Foundation, cf-private, libobjc, tzdata, fetchpatch
 , withRecommendedPackages ? true
 , enableStrictBarrier ? false
 }:
@@ -21,7 +21,7 @@ stdenv.mkDerivation rec {
   ] ++ stdenv.lib.optionals (!stdenv.isDarwin) [ tcl tk ]
     ++ stdenv.lib.optionals stdenv.isDarwin [ Cocoa Foundation cf-private libobjc ];
 
-  patches = [ ./no-usr-local-search-paths.patch ];
+  patches = [ ./no-usr-local-search-paths.patch ./fix-sweave-exit-code.patch ];
 
   preConfigure = ''
     configureFlagsArray=(

pkgs/applications/science/math/R/fix-sweave-exit-code.patch

@@ -0,0 +1,52 @@
+From 0ff560ba912fad126576818519035c8d3c693bed Mon Sep 17 00:00:00 2001
+From: maechler <maechler@00db46b3-68df-0310-9c12-caf00c1e9a41>
+Date: Mon, 24 Apr 2017 14:24:11 +0000
+Subject: [PATCH] R CMD Sweave status bug fix
+
+git-svn-id: https://svn.r-project.org/R/trunk@72612 00db46b3-68df-0310-9c12-caf00c1e9a41
+
+diff --git a/src/library/utils/R/Sweave.R b/src/library/utils/R/Sweave.R
+index 2beb094..8d4950b 100644
+--- a/src/library/utils/R/Sweave.R
++++ b/src/library/utils/R/Sweave.R
+@@ -1,7 +1,7 @@
+ #   File src/library/utils/R/Sweave.R
+ #  Part of the R package, https://www.R-project.org
+ #
+-#  Copyright (C) 1995-2016 The R Core Team
++#  Copyright (C) 1995-2017 The R Core Team
+ #
+ #  This program is free software; you can redistribute it and/or modify
+ #  it under the terms of the GNU General Public License as published by
+@@ -452,10 +452,10 @@ SweaveHooks <- function(options, run = FALSE, envir = .GlobalEnv)
+     }
+     do_exit <-
+ 	if(no.q)
+-	    function(status = 1L) (if(status) stop else message)(
++	    function(status = 0L) (if(status) stop else message)(
+ 		".Sweave() exit status ", status)
+ 	else
+-	    function(status = 1L) q("no", status = status, runLast = FALSE)
++	    function(status = 0L) q("no", status = status, runLast = FALSE)
+ 
+     if (!length(args)) {
+         Usage()
+@@ -577,16 +577,15 @@ SweaveHooks <- function(options, run = FALSE, envir = .GlobalEnv)
+     }
+     do_exit <-
+ 	if(no.q)
+-	    function(status = 1L) (if(status) stop else message)(
++	    function(status = 0L) (if(status) stop else message)(
+ 		".Stangle() exit status ", status)
+ 	else
+-	    function(status = 1L) q("no", status = status, runLast = FALSE)
++	    function(status = 0L) q("no", status = status, runLast = FALSE)
+ 
+     if (!length(args)) {
+         Usage()
+         do_exit(1L)
+     }
+-
+     file <- character()
+     encoding <- options <- ""
+     engine <- NULL

pkgs/applications/window-managers/stalonetray/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "stalonetray-${version}";
-  version = "0.8.1";
+  version = "0.8.3";
 
   src = fetchurl {
     url = "mirror://sourceforge/stalonetray/${name}.tar.bz2";
-    sha256 = "1wp8pnlv34w7xizj1vivnc3fkwqq4qgb9dbrsg15598iw85gi8ll";
+    sha256 = "0k7xnpdb6dvx25d67v0crlr32cdnzykdsi9j889njiididc8lm1n";
   };
 
   buildInputs = [ libX11 xproto ];
@@ -15,8 +15,10 @@ stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     description = "Stand alone tray";
-    maintainers = with maintainers; [ raskin ];
+    homepage = http://stalonetray.sourceforge.net;
+    license = licenses.gpl2;
     platforms = platforms.linux;
+    maintainers = with maintainers; [ raskin ];
   };
 
   passthru = {

pkgs/data/documentation/man-pages/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "man-pages-${version}";
-  version = "4.09";
+  version = "4.11";
 
   src = fetchurl {
     url = "mirror://kernel/linux/docs/man-pages/${name}.tar.xz";
-    sha256 = "1740gq9sq28dp5a5sjn1ya7cvrv8mbky6knb7734v8k29a7a0x55";
+    sha256 = "097m0gsbaz0gf9ir4lmph3h5jj6wmydk1rglfz82dysybx4q1pmd";
   };
 
   makeFlags = [ "MANDIR=$(out)/share/man" ];

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

@@ -684,6 +684,9 @@ self: super: {
     store = self.store_0_3_1;
   });
 
+  # It makes no sense to have intero-nix-shim in Hackage, so we publish it here only.
+  intero-nix-shim = self.callPackage ../tools/haskell/intero-nix-shim {};
+
   # The latest Hoogle needs versions not yet in LTS Haskell 7.x.
   hoogle = super.hoogle.override { haskell-src-exts = self.haskell-src-exts_1_19_1; };
 

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

@@ -37,7 +37,7 @@ core-packages:
   - ghcjs-base-0
 
 default-package-overrides:
-  # LTS Haskell 8.12
+  # LTS Haskell 8.13
   - abstract-deque ==0.3
   - abstract-par ==0.3.3
   - AC-Vector ==2.3.2
@@ -47,7 +47,7 @@ default-package-overrides:
   - acid-state ==0.14.2
   - action-permutations ==0.0.0.1
   - active ==0.2.0.12
-  - ad ==4.3.2.1
+  - ad ==4.3.3
   - adjunctions ==4.3
   - adler32 ==0.1.1.0
   - aeson ==1.0.2.1
@@ -224,7 +224,7 @@ default-package-overrides:
   - between ==0.11.0.0
   - bibtex ==0.1.0.6
   - bifunctors ==5.4.2
-  - bimap ==0.3.2
+  - bimap ==0.3.3
   - bimap-server ==0.1.0.1
   - binary-bits ==0.5
   - binary-conduit ==1.2.4.1
@@ -252,7 +252,7 @@ default-package-overrides:
   - bitcoin-script ==0.11.1
   - bitcoin-tx ==0.13.1
   - bitcoin-types ==0.9.2
-  - bits ==0.5
+  - bits ==0.5.1
   - bitx-bitcoin ==0.11.0.1
   - blake2 ==0.2.0
   - blank-canvas ==0.6
@@ -294,7 +294,7 @@ default-package-overrides:
   - byteable ==0.1.1
   - bytedump ==1.0
   - byteorder ==1.0.4
-  - bytes ==0.15.2
+  - bytes ==0.15.3
   - byteset ==0.1.1.0
   - bytestring-builder ==0.10.8.1.0
   - bytestring-conversion ==0.3.1
@@ -358,12 +358,12 @@ default-package-overrides:
   - cipher-rc4 ==0.1.4
   - circle-packing ==0.1.0.5
   - clang-pure ==0.2.0.2
-  - clash-ghc ==0.7.1
+  - clash-ghc ==0.7.2
   - clash-lib ==0.7.1
-  - clash-prelude ==0.11.1
+  - clash-prelude ==0.11.2
-  - clash-systemverilog ==0.7.1
+  - clash-systemverilog ==0.7.2
-  - clash-verilog ==0.7.1
+  - clash-verilog ==0.7.2
-  - clash-vhdl ==0.7.1
+  - clash-vhdl ==0.7.2
   - classy-prelude ==1.2.0.1
   - classy-prelude-conduit ==1.2.0
   - classy-prelude-yesod ==1.2.0
@@ -630,11 +630,11 @@ default-package-overrides:
   - esqueleto ==2.5.1
   - etc ==0.0.0.2
   - etcd ==1.0.5
-  - ether ==0.4.1.0
+  - ether ==0.4.2.0
   - euphoria ==0.8.0.0
   - event ==0.1.4
   - event-list ==0.1.1.3
-  - eventstore ==0.14.0.1
+  - eventstore ==0.14.0.2
   - exact-combinatorics ==0.2.0.8
   - exact-pi ==0.4.1.2
   - exception-mtl ==0.4.0.1
@@ -680,7 +680,7 @@ default-package-overrides:
   - filemanip ==0.3.6.3
   - fingertree ==0.1.1.0
   - fingertree-psqueue ==0.3
-  - finite-typelits ==0.1.1.0
+  - finite-typelits ==0.1.2.0
   - fixed ==0.2.1.1
   - fixed-length ==0.2
   - fixed-vector ==0.9.0.0
@@ -699,14 +699,14 @@ default-package-overrides:
   - fold-debounce-conduit ==0.1.0.5
   - foldl ==1.2.4
   - foldl-statistics ==0.1.4.2
-  - folds ==0.7.1
+  - folds ==0.7.3
   - FontyFruity ==0.5.3.2
   - force-layout ==0.4.0.6
   - foreign-store ==0.2
   - format-numbers ==0.1.0.0
   - formatting ==6.2.4
   - fortran-src ==0.1.0.4
-  - foundation ==0.0.7
+  - foundation ==0.0.8
   - Frames ==0.1.9
   - free ==4.12.4
   - free-vl ==0.1.4
@@ -725,7 +725,7 @@ default-package-overrides:
   - gd ==3000.7.3
   - Genbank ==1.0.3
   - general-games ==1.0.5
-  - generic-aeson ==0.2.0.8
+  - generic-aeson ==0.2.0.9
   - generic-deriving ==1.11.2
   - generic-random ==0.4.1.0
   - generic-xmlpickler ==0.1.0.5
@@ -733,8 +733,8 @@ default-package-overrides:
   - generics-eot ==0.2.1.1
   - generics-sop ==0.2.5.0
   - generics-sop-lens ==0.1.2.1
-  - geniplate-mirror ==0.7.4
+  - geniplate-mirror ==0.7.5
-  - getopt-generics ==0.13
+  - getopt-generics ==0.13.0.1
   - ghc-events ==0.4.4.0
   - ghc-exactprint ==0.5.3.0
   - ghc-heap-view ==0.5.9
@@ -751,18 +751,18 @@ default-package-overrides:
   - ghcjs-codemirror ==0.0.0.1
   - ghcjs-hplay ==0.3.4.2
   - ghcjs-perch ==0.3.3.2
-  - gi-atk ==2.0.11
+  - gi-atk ==2.0.12
-  - gi-cairo ==1.0.11
+  - gi-cairo ==1.0.12
-  - gi-gdk ==3.0.11
+  - gi-gdk ==3.0.12
-  - gi-gdkpixbuf ==2.0.11
+  - gi-gdkpixbuf ==2.0.12
-  - gi-gio ==2.0.11
+  - gi-gio ==2.0.12
-  - gi-glib ==2.0.11
+  - gi-glib ==2.0.12
-  - gi-gobject ==2.0.11
+  - gi-gobject ==2.0.12
-  - gi-gtk ==3.0.13
+  - gi-gtk ==3.0.14
-  - gi-javascriptcore ==3.0.11
+  - gi-javascriptcore ==3.0.12
-  - gi-pango ==1.0.12
+  - gi-pango ==1.0.13
-  - gi-soup ==2.4.11
+  - gi-soup ==2.4.12
-  - gi-webkit ==3.0.11
+  - gi-webkit ==3.0.12
   - ginger ==0.3.9.1
   - gio ==0.13.3.1
   - gipeda ==0.3.3.2
@@ -790,7 +790,7 @@ default-package-overrides:
   - gloss ==1.10.2.5
   - gloss-rendering ==1.10.3.5
   - GLURaw ==2.0.0.3
-  - GLUT ==2.7.0.11
+  - GLUT ==2.7.0.12
   - gnuplot ==0.5.4.1
   - gogol ==0.1.1
   - gogol-adexchange-buyer ==0.1.1
@@ -972,7 +972,7 @@ default-package-overrides:
   - hasql-transaction ==0.5
   - hastache ==0.6.1
   - hasty-hamiltonian ==1.3.0
-  - HaTeX ==3.17.1.0
+  - HaTeX ==3.17.2.0
   - hatex-guide ==1.3.1.6
   - haxl ==0.5.0.0
   - haxl-amazonka ==0.1.1
@@ -987,7 +987,7 @@ default-package-overrides:
   - HDBC-session ==0.1.1.0
   - hdevtools ==0.1.5.0
   - heap ==1.0.3
-  - heaps ==0.3.3
+  - heaps ==0.3.4.1
   - hebrew-time ==0.1.1
   - hedis ==0.9.8
   - here ==1.2.9
@@ -1000,6 +1000,7 @@ default-package-overrides:
   - hflags ==0.4.2
   - hformat ==0.1.0.1
   - hfsevents ==0.1.6
+  - hgal ==2.0.0.2
   - hid ==0.2.2
   - hidapi ==0.1.4
   - hidden-char ==0.1.0.0
@@ -1010,7 +1011,7 @@ default-package-overrides:
   - highlighting-kate ==0.6.4
   - hinotify ==0.3.9
   - hint ==0.6.0
-  - hip ==1.5.2.0
+  - hip ==1.5.3.0
   - histogram-fill ==0.8.5.0
   - hit ==0.6.3
   - hjpath ==3.0.1
@@ -1069,7 +1070,7 @@ default-package-overrides:
   - hslua-aeson ==0.1.0.4
   - hsndfile ==0.8.0
   - hsndfile-vector ==0.5.2
-  - HsOpenSSL ==0.11.4.7
+  - HsOpenSSL ==0.11.4.8
   - HsOpenSSL-x509-system ==0.1.0.3
   - hsp ==0.10.0
   - hspec ==2.4.3
@@ -1181,7 +1182,7 @@ default-package-overrides:
   - IntervalMap ==0.5.2.0
   - intervals ==0.7.2
   - intro ==0.1.0.10
-  - invariant ==0.4.1
+  - invariant ==0.4.2
   - invertible ==0.2.0.2
   - io-choice ==0.0.6
   - io-machine ==0.2.0.0
@@ -1235,7 +1236,7 @@ default-package-overrides:
   - kansas-comet ==0.4
   - katip ==0.3.1.4
   - katip-elasticsearch ==0.3.0.2
-  - kawhi ==0.2.2
+  - kawhi ==0.2.3
   - kdt ==0.2.4
   - keter ==1.4.3.2
   - keycode ==0.2.2
@@ -1270,8 +1271,8 @@ default-package-overrides:
   - lca ==0.3
   - leapseconds-announced ==2017
   - lens ==4.15.1
-  - lens-action ==0.2.0.2
+  - lens-action ==0.2.1
-  - lens-aeson ==1.0.0.5
+  - lens-aeson ==1.0.1
   - lens-datetime ==0.3
   - lens-family ==1.2.1
   - lens-family-core ==1.2.1
@@ -1296,7 +1297,7 @@ default-package-overrides:
   - lifted-async ==0.9.1.1
   - lifted-base ==0.2.3.10
   - line ==2.2.0
-  - linear ==1.20.5
+  - linear ==1.20.6
   - linear-accelerate ==0.2
   - linked-list-with-iterator ==0.1.1.0
   - linux-file-extents ==0.2.0.0
@@ -1325,7 +1326,7 @@ default-package-overrides:
   - lucid ==2.9.8.1
   - lucid-svg ==0.7.0.0
   - lzma-conduit ==1.1.3.1
-  - machines ==0.6.1
+  - machines ==0.6.2
   - machines-binary ==0.3.0.3
   - machines-directory ==0.2.1.0
   - machines-io ==0.2.0.13
@@ -1357,7 +1358,7 @@ default-package-overrides:
   - median-stream ==0.7.0.0
   - mega-sdist ==0.3.0.2
   - megaparsec ==5.2.0
-  - memory ==0.14.3
+  - memory ==0.14.5
   - MemoTrie ==0.6.7
   - mersenne-random ==1.0.0.1
   - mersenne-random-pure64 ==0.2.2.0
@@ -1397,7 +1398,7 @@ default-package-overrides:
   - monad-extras ==0.6.0
   - monad-http ==0.1.0.0
   - monad-journal ==0.7.2
-  - monad-logger ==0.3.22
+  - monad-logger ==0.3.23
   - monad-logger-json ==0.1.0.0
   - monad-logger-prefix ==0.1.6
   - monad-logger-syslog ==0.1.3.0
@@ -1446,7 +1447,7 @@ default-package-overrides:
   - mustache ==2.1.3
   - mutable-containers ==0.3.3
   - mwc-probability ==1.3.0
-  - mwc-random ==0.13.5.0
+  - mwc-random ==0.13.6.0
   - mwc-random-monad ==0.7.3.1
   - mysql ==0.1.4
   - mysql-haskell ==0.8.0.0
@@ -1524,7 +1525,7 @@ default-package-overrides:
   - open-browser ==0.2.1.0
   - open-witness ==0.4
   - OpenAL ==1.7.0.4
-  - OpenGL ==3.0.1.0
+  - OpenGL ==3.0.2.0
   - OpenGLRaw ==3.2.4.0
   - openpgp-asciiarmor ==0.1
   - opensource ==0.1.0.0
@@ -1560,7 +1561,7 @@ default-package-overrides:
   - parsers ==0.12.4
   - partial-handler ==1.0.2
   - partial-isomorphisms ==0.2.2
-  - patat ==0.5.0.0
+  - patat ==0.5.1.2
   - path ==0.5.13
   - path-extra ==0.0.3
   - path-io ==1.2.2
@@ -1666,8 +1667,8 @@ default-package-overrides:
   - profunctors ==5.2
   - project-template ==0.2.0
   - projectroot ==0.2.0.1
-  - prometheus-client ==0.1.0.1
+  - prometheus-client ==0.1.1
-  - prometheus-metrics-ghc ==0.1.0.1
+  - prometheus-metrics-ghc ==0.1.1
   - prompt ==0.1.1.2
   - proto-lens ==0.2.0.1
   - proto-lens-arbitrary ==0.1.0.2
@@ -1816,8 +1817,8 @@ default-package-overrides:
   - sandman ==0.2.0.1
   - say ==0.1.0.0
   - sbv ==5.14
-  - scalpel ==0.5.0
+  - scalpel ==0.5.1
-  - scalpel-core ==0.5.0
+  - scalpel-core ==0.5.1
   - scanner ==0.2
   - scientific ==0.3.4.12
   - scotty ==0.11.0
@@ -1882,7 +1883,7 @@ default-package-overrides:
   - sibe ==0.2.0.4
   - signal ==0.1.0.3
   - silently ==1.2.5
-  - simple ==0.11.1
+  - simple ==0.11.2
   - simple-download ==0.0.2
   - simple-log ==0.5.1
   - simple-reflect ==0.3.2
@@ -1943,6 +1944,8 @@ default-package-overrides:
   - stack-run-auto ==0.1.1.4
   - stack-type ==0.1.0.0
   - stackage-curator ==0.14.5
+  - stackage-query ==0.1.0
+  - stackage-types ==1.2.0
   - state-plus ==0.1.3
   - stateref ==0.3
   - statestack ==0.2.0.5
@@ -2003,7 +2006,7 @@ default-package-overrides:
   - svg-tree ==0.6.1
   - SVGFonts ==1.6.0.1
   - swagger ==0.3.0
-  - swagger2 ==2.1.3
+  - swagger2 ==2.1.4
   - syb ==0.6
   - syb-with-class ==0.6.1.7
   - symbol ==0.2.4
@@ -2053,7 +2056,7 @@ default-package-overrides:
   - tcp-streams-openssl ==0.6.0.0
   - tdigest ==0.1
   - tdigest-Chart ==0
-  - telegram-api ==0.6.1.0
+  - telegram-api ==0.6.1.1
   - template ==0.2.0.10
   - temporary ==1.2.0.4
   - temporary-rc ==1.2.0.3
@@ -2067,11 +2070,12 @@ default-package-overrides:
   - test-framework-quickcheck2 ==0.3.0.3
   - test-framework-smallcheck ==0.2
   - test-framework-th ==0.2.4
+  - test-invariant ==0.4.5.0
   - test-simple ==0.1.9
   - testing-feat ==0.4.0.3
   - texmath ==0.9.4
   - text ==1.2.2.1
-  - text-all ==0.3.0.2
+  - text-all ==0.3.1.0
   - text-binary ==0.2.1.1
   - text-conversions ==0.3.0
   - text-format ==0.3.1.1
@@ -2104,7 +2108,7 @@ default-package-overrides:
   - these ==0.7.3
   - thread-local-storage ==0.1.1
   - threads ==0.5.1.4
-  - threepenny-gui ==0.7.0.1
+  - threepenny-gui ==0.7.0.2
   - threepenny-gui-flexbox ==0.3.0.2
   - through-text ==0.1.0.0
   - thumbnail-plus ==1.0.5
@@ -2145,7 +2149,7 @@ default-package-overrides:
   - tuple ==0.3.0.2
   - tuple-th ==0.2.5
   - tuples-homogenous-h98 ==0.1.1.0
-  - turtle ==1.3.2
+  - turtle ==1.3.3
   - turtle-options ==0.1.0.4
   - twitter-feed ==0.2.0.11
   - twitter-types ==0.7.2.2
@@ -2264,7 +2268,7 @@ default-package-overrides:
   - wai-middleware-content-type ==0.5.0.1
   - wai-middleware-crowd ==0.1.4.2
   - wai-middleware-metrics ==0.2.4
-  - wai-middleware-prometheus ==0.1.0.1
+  - wai-middleware-prometheus ==0.1.1
   - wai-middleware-rollbar ==0.3.0
   - wai-middleware-static ==0.8.1
   - wai-middleware-throttle ==0.2.1.0
@@ -2299,7 +2303,7 @@ default-package-overrides:
   - websockets ==0.10.0.0
   - websockets-rpc ==0.0.2
   - websockets-snap ==0.10.2.1
-  - weigh ==0.0.3
+  - weigh ==0.0.4
   - wikicfp-scraper ==0.1.0.8
   - wild-bind ==0.1.0.3
   - wild-bind-indicator ==0.1.0.1
@@ -2330,8 +2334,8 @@ default-package-overrides:
   - writer-cps-full ==0.1.0.0
   - writer-cps-lens ==0.1.0.1
   - writer-cps-morph ==0.1.0.2
-  - writer-cps-mtl ==0.1.1.3
+  - writer-cps-mtl ==0.1.1.4
-  - writer-cps-transformers ==0.1.1.2
+  - writer-cps-transformers ==0.1.1.3
   - wuss ==1.1.4
   - X11 ==1.8
   - X11-xft ==0.3.1
@@ -2368,7 +2372,7 @@ default-package-overrides:
   - yackage ==0.8.1
   - yahoo-finance-api ==0.2.0.1
   - yaml ==0.8.22
-  - Yampa ==0.10.5
+  - Yampa ==0.10.5.1
   - YampaSynth ==0.2
   - yes-precure5-command ==5.5.3
   - yesod ==1.4.5
@@ -2412,10 +2416,10 @@ default-package-overrides:
   - zero ==0.1.4
   - zeromq4-haskell ==0.6.5
   - zip ==0.1.10
-  - zip-archive ==0.3.0.5
+  - zip-archive ==0.3.0.6
-  - zippers ==0.2.2
+  - zippers ==0.2.3
-  - ziptastic-client ==0.3.0.1
+  - ziptastic-client ==0.3.0.2
-  - ziptastic-core ==0.2.0.1
+  - ziptastic-core ==0.2.0.2
   - zlib ==0.6.1.2
   - zlib-bindings ==0.1.1.5
   - zlib-lens ==0.1.2.1
@@ -6992,8 +6996,6 @@ dont-distribute-packages:
   postgresql-simple-typed:                      [ i686-linux, x86_64-linux, x86_64-darwin ]
   postgresql-typed:                             [ i686-linux, x86_64-linux, x86_64-darwin ]
   postgresql-typed-lifted:                      [ i686-linux, x86_64-linux, x86_64-darwin ]
-  postgrest:                                    [ i686-linux, x86_64-linux, x86_64-darwin ]
-  postgrest-ws:                                 [ i686-linux, x86_64-linux, x86_64-darwin ]
   postie:                                       [ i686-linux, x86_64-linux, x86_64-darwin ]
   postmark:                                     [ i686-linux, x86_64-linux, x86_64-darwin ]
   postmark-streams:                             [ i686-linux, x86_64-linux, x86_64-darwin ]

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

@@ -63,7 +63,8 @@ assert enableSplitObjs == null;
 let
 
   inherit (stdenv.lib) optional optionals optionalString versionOlder versionAtLeast
-                       concatStringsSep enableFeature optionalAttrs toUpper;
+                       concatStringsSep enableFeature optionalAttrs toUpper
+                       filter makeLibraryPath;
 
   isGhcjs = ghc.isGhcjs or false;
   isHaLVM = ghc.isHaLVM or false;
@@ -330,6 +331,9 @@ stdenv.mkDerivation ({
         export NIX_${ghcCommandCaps}="${ghcEnv}/bin/${ghcCommand}"
         export NIX_${ghcCommandCaps}PKG="${ghcEnv}/bin/${ghcCommand}-pkg"
         export NIX_${ghcCommandCaps}_DOCDIR="${ghcEnv}/share/doc/ghc/html"
+        export LD_LIBRARY_PATH="''${LD_LIBRARY_PATH:+''${LD_LIBRARY_PATH}:}${
+          makeLibraryPath (filter (x: !isNull x) systemBuildInputs)
+        }"
         ${if isHaLVM
             then ''export NIX_${ghcCommandCaps}_LIBDIR="${ghcEnv}/lib/HaLVM-${ghc.version}"''
             else ''export NIX_${ghcCommandCaps}_LIBDIR="${ghcEnv}/lib/${ghcCommand}-${ghc.version}"''}

pkgs/development/libraries/capnproto/clang4.patch

@@ -1,22 +0,0 @@
-From 0f1fd1938b19dccdb5dbfe9cb5177c4342a2a5b5 Mon Sep 17 00:00:00 2001
-From: Eric Fiselier <eric@efcs.ca>
-Date: Thu, 29 Dec 2016 14:23:40 -0700
-Subject: [PATCH] Fix conversion build error when building with Clang 4.0
-
----
- c++/src/capnp/layout.h | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/c++/src/capnp/layout.h b/c++/src/capnp/layout.h
-index 850925a..b955f08 100644
---- a/src/capnp/layout.h
-+++ b/src/capnp/layout.h
-@@ -126,7 +126,7 @@template <> struct ElementSizeForType<Void> { static constexpr ElementSize value
- template <> struct ElementSizeForType<bool> { static constexpr ElementSize value = ElementSize::BIT; };
- 
- // Lists and blobs are pointers, not structs.
--template <typename T, bool b> struct ElementSizeForType<List<T, b>> {
-+template <typename T, Kind K> struct ElementSizeForType<List<T, K>> {
-   static constexpr ElementSize value = ElementSize::POINTER;
- };
- template <> struct ElementSizeForType<Text> {

pkgs/development/libraries/capnproto/default.nix

@@ -2,18 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "capnproto-${version}";
-  version = "0.5.3";
+  version = "0.6.0";
 
   src = fetchurl {
     url = "https://capnproto.org/capnproto-c++-${version}.tar.gz";
-    sha256 = "1yvaadhgakskqq5wpv53hd6fc3pp17mrdldw4i5cvgck4iwprcfd";
+    sha256 = "0gpp1cxsb9nfd7qkjjykzknx03y0z0n4bq5q0fmxci7w38ci22g5";
   };
 
-  patches = [
-    # Remove once they release a version above 0.5.3. See https://github.com/sandstorm-io/capnproto/issues/433
-    ./clang4.patch
-  ];
-
   meta = with stdenv.lib; {
     homepage    = "http://kentonv.github.io/capnproto";
     description = "Cap'n Proto cerealization protocol";

pkgs/development/libraries/gdal/default.nix

@@ -1,6 +1,6 @@
 { stdenv, fetchurl, composableDerivation, unzip, libjpeg, libtiff, zlib
 , postgresql, mysql, libgeotiff, pythonPackages, proj, geos, openssl
-, libpng, sqlite, libspatialite
+, libpng, sqlite, libspatialite, poppler
 , libiconv
 , netcdfSupport ? true, netcdf, hdf5 , curl
 }:
@@ -16,7 +16,8 @@ composableDerivation.composableDerivation {} (fixed: rec {
     sha256 = "0jh7filpf5dk5iz5acj7y3y49ihnzqypxckdlj0sjigbqq6hlsmf";
   };
 
-  buildInputs = [ unzip libjpeg libtiff libpng proj openssl sqlite libspatialite ]
+  buildInputs = [ unzip libjpeg libtiff libpng proj openssl sqlite
+    libspatialite poppler ]
   ++ (with pythonPackages; [ python numpy wrapPython ])
   ++ stdenv.lib.optional stdenv.isDarwin libiconv
   ++ stdenv.lib.optionals netcdfSupport [ netcdf hdf5 curl ];
@@ -30,6 +31,7 @@ composableDerivation.composableDerivation {} (fixed: rec {
     "--with-jpeg=${libjpeg.dev}"
     "--with-libtiff=${libtiff.dev}" # optional (without largetiff support)
     "--with-png=${libpng.dev}"      # optional
+    "--with-poppler=${poppler.dev}" # optional
     "--with-libz=${zlib.dev}"       # optional
     "--with-pg=${postgresql}/bin/pg_config"
     "--with-mysql=${mysql.lib.dev}/bin/mysql_config"

pkgs/development/libraries/libseccomp/default.nix

@@ -15,9 +15,8 @@ stdenv.mkDerivation rec {
     patchShebangs .
   '';
 
-  postInstall = ''
+  # Hack to ensure that patchelf --shrink-rpath get rids of a $TMPDIR reference.
-    wrapProgram $out/bin/scmp_sys_resolver --prefix LD_LIBRARY_PATH ":" $out/lib
+  preFixup = "rm -rfv src";
-  '';
 
   meta = with stdenv.lib; {
     description = "High level library for the Linux Kernel seccomp filter";
@@ -27,4 +26,3 @@ stdenv.mkDerivation rec {
     maintainers = with maintainers; [ thoughtpolice wkennington ];
   };
 }
-

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

@@ -1,21 +1,26 @@
-{ stdenv, buildPythonPackage, fetchurl, isPy3k,
+{ stdenv, buildPythonPackage, fetchurl, isPy3k, isPy33,
-  unittest2, mock, pytest, trollius, pytest-asyncio,
+  unittest2, mock, pytest, trollius, asyncio,
-  six, twisted, txaio
+  pytest-asyncio, futures,
+  six, twisted, txaio, zope_interface
 }:
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "autobahn";
-  version = "0.18.2";
+  version = "17.5.1";
 
   src = fetchurl {
     url = "mirror://pypi/a/${pname}/${name}.tar.gz";
-    sha256 = "1alp71plqnrak5nm2vn9mmkxayjb081c1kihqwf60wdpvv0w7y14";
+    sha256 = "0p2xx20g0rj6pnp4h3231mn8zk4ag8msv69f93gai2hzl5vglcia";
   };
 
-  buildInputs = [ unittest2 mock pytest trollius pytest-asyncio ];
+  # Upstream claim python2 support, but tests require pytest-asyncio which
-  propagatedBuildInputs = [ six twisted txaio ];
+  # is pythn3 only. Therefore, tests are skipped for python2.
+  doCheck = isPy3k;
+  buildInputs = stdenv.lib.optionals isPy3k [ unittest2 mock pytest pytest-asyncio ];
+  propagatedBuildInputs = [ six twisted zope_interface txaio ] ++
+    (stdenv.lib.optional isPy33 asyncio) ++
+    (stdenv.lib.optionals (!isPy3k) [ trollius futures ]);
 
-  disabled = !isPy3k;
   checkPhase = ''
     py.test $out
   '';

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

@@ -0,0 +1,30 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytest
+, jinja2
+, selenium
+}:
+
+buildPythonPackage rec {
+  pname = "branca";
+  version = "0.2.0";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "327b0bae73a519f25dc2f320d8d9f1885aad2e8e5105add1496269d5391b8ea4";
+  };
+
+  checkInputs = [ pytest selenium ];
+  propagatedBuildInputs = [ jinja2 ];
+
+  # Seems to require a browser
+  doCheck = false;
+
+  meta = {
+    description = "Generate complex HTML+JS pages with Python";
+    homepage = https://github.com/python-visualization/branca;
+    license = with lib.licenses; [ mit ];
+  };
+}

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

@@ -0,0 +1,45 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytest
+, numpy
+, nbconvert
+, pandas
+, mock
+, jinja2
+, branca
+, six
+}:
+
+buildPythonPackage rec {
+  pname = "folium";
+  version = "0.3.0";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "7729ddd6766b9c5dab17b3709e2387935fd5c655872f1cbab7b7036474415217";
+  };
+
+  postPatch = ''
+    # Causes trouble because a certain file cannot be found
+    rm tests/notebooks/test_notebooks.py
+  '';
+
+  checkInputs = [ pytest numpy nbconvert pandas mock ];
+  propagatedBuildInputs = [ jinja2 branca six ];
+
+  #
+#   doCheck = false;
+
+#   checkPhase = ''
+#     py.test -k 'not test_notebooks'
+#   '';
+
+  meta = {
+    description = "Make beautiful maps with Leaflet.js & Python";
+    homepage = https://github.com/python-visualization/folium;
+    license = with lib.licenses; [ mit ];
+    maintainers = with lib.maintainers; [ fridh ];
+  };
+}

pkgs/development/python-modules/os-testr/default.nix

@@ -0,0 +1,32 @@
+{ stdenv, buildPythonPackage, fetchurl, python,
+  pbr, Babel, testrepository, subunit, testtools,
+  coverage, oslosphinx, oslotest, testscenarios, six, ddt 
+}:
+buildPythonPackage rec {
+  name = "os-testr-${version}";
+  version = "0.8.1";
+
+  src = fetchurl {
+    url = "mirror://pypi/o/os-testr/${name}.tar.gz";
+    sha256 = "10ws7l5p25psnp6rwymwdzh4zagmmnbf56xwg06cn2292m95l4i7";
+  };
+
+  patchPhase = ''
+    sed -i 's@python@${python.interpreter}@' .testr.conf
+    sed -i 's@python@${python.interpreter}@' os_testr/tests/files/testr-conf
+  '';
+
+  checkPhase = ''
+    export PATH=$PATH:$out/bin
+    ${python.interpreter} setup.py test
+  '';
+
+  propagatedBuildInputs = [ pbr Babel testrepository subunit testtools ];
+  buildInputs = [ coverage oslosphinx oslotest testscenarios six ddt ];
+
+  meta = with stdenv.lib; {
+    description = "A testr wrapper to provide functionality for OpenStack projects";
+    homepage  = http://docs.openstack.org/developer/os-testr/;
+    license = licenses.asl20;
+  };
+}

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

@@ -0,0 +1,28 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, proj
+, python
+}:
+
+buildPythonPackage rec {
+  pname = "pyproj";
+  version = "1.9.5.1";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "53fa54c8fa8a1dfcd6af4bf09ce1aae5d4d949da63b90570ac5ec849efaf3ea8";
+  };
+
+  buildInputs = [ proj ];
+
+  # Could not get tests working
+  doCheck = false;
+
+  meta = {
+    description = "Python interface to PROJ.4 library";
+    homepage = http://github.com/jswhit/pyproj;
+    license = with lib.licenses; [ isc ];
+  };
+}

pkgs/development/python-modules/pytest-asyncio/default.nix

@@ -1,9 +1,11 @@
-{ stdenv, buildPythonPackage, fetchurl, pytest }:
+{ stdenv, buildPythonPackage, fetchurl, pytest, isPy3k }:
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "pytest-asyncio";
   version = "0.5.0";
 
+  disabled = !isPy3k;
+
   src = fetchurl {
     url = "mirror://pypi/p/${pname}/${name}.tar.gz";
     sha256 = "03sxq8fglr4lw4y6wqlbli9ypr65fxzx6hlpn5wpccx8v5472iff";

pkgs/development/python-modules/sqlalchemy-migrate/default.nix

@@ -0,0 +1,34 @@
+{ stdenv, buildPythonPackage, fetchurl, python,
+  unittest2, scripttest, pytz, pylint, tempest-lib, mock, testtools,
+  pbr, tempita, decorator, sqlalchemy, six, sqlparse 
+}:
+buildPythonPackage rec {
+  name = "sqlalchemy-migrate-${version}";
+  version = "0.11.0";
+
+  src = fetchurl {
+    url = "mirror://pypi/s/sqlalchemy-migrate/${name}.tar.gz";
+    sha256 = "0ld2bihp9kmf57ykgzrfgxs4j9kxlw79sgdj9sfn47snw3izb2p6";
+  };
+
+  buildInputs = [ unittest2 scripttest pytz pylint tempest-lib mock testtools ];
+  propagatedBuildInputs = [ pbr tempita decorator sqlalchemy six sqlparse ];
+
+  checkPhase = ''
+    export PATH=$PATH:$out/bin
+    echo sqlite:///__tmp__ > test_db.cfg
+    # depends on ibm_db_sa
+    rm migrate/tests/changeset/databases/test_ibmdb2.py
+    # wants very old testtools
+    rm migrate/tests/versioning/test_schema.py
+    # transient failures on py27
+    substituteInPlace migrate/tests/versioning/test_util.py --replace "test_load_model" "noop"
+    ${python.interpreter} setup.py test
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = http://code.google.com/p/sqlalchemy-migrate/;
+    description = "Schema migration tools for SQLAlchemy";
+    license = licenses.asl20;
+  };
+}

pkgs/development/tools/build-managers/buildbot/default.nix

@@ -13,11 +13,11 @@ let
   package = pythonPackages.buildPythonApplication (rec {
     name = "${pname}-${version}";
     pname = "buildbot";
-    version = "0.9.5";
+    version = "0.9.6";
 
     src = pythonPackages.fetchPypi {
       inherit pname version;
-      sha256 = "11r553nmh87a9pm58wycimapk2pw9hnlc7hffn97xwbqprd8qh66";
+      sha256 = "0d6ys1wjwsv4jg4bja1cqhy279hhrl1c9kwyx126srf45slcvg1w";
     };
 
     buildInputs = with pythonPackages; [
@@ -69,6 +69,12 @@ let
 
     ];
 
+    patches = [
+      # This patch disables the test that tries to reat /etc/os-release which
+      # is not accessible in sandboxed builds.
+      ./skip_test_linux_distro.patch
+    ];
+
     postPatch = ''
       substituteInPlace buildbot/scripts/logwatcher.py --replace '/usr/bin/tail' "$(type -P tail)"
 
@@ -79,6 +85,10 @@ let
       rm -fv buildbot/test/unit/test_interpolate_secrets.py
       rm -fv buildbot/test/unit/test_secret_in_file.py
       rm -fv buildbot/test/unit/test_secret_in_vault.py
+
+      # Remove this line after next update. See
+      # https://github.com/buildbot/buildbot/commit/e7fc8c8eba903c2aa6d7e6393499e5b9bffc2334
+      rm -fv buildbot/test/unit/test_mq_wamp.py
     '';
 
     passthru = { inherit withPlugins; };

pkgs/development/tools/build-managers/buildbot/skip_test_linux_distro.patch

@@ -0,0 +1,11 @@
+diff -Nur buildbot-0.9.6/buildbot/test/unit/test_buildbot_net_usage_data.py buildbot-0.9.6.patched/buildbot/test/unit/test_buildbot_net_usage_data.py
+--- buildbot-0.9.6/buildbot/test/unit/test_buildbot_net_usage_data.py	2017-04-19 16:57:02.000000000 +0200
++++ buildbot-0.9.6.patched/buildbot/test/unit/test_buildbot_net_usage_data.py	2017-05-04 12:22:54.575762551 +0200
+@@ -147,6 +147,7 @@
+         _sendBuildbotNetUsageData({'foo': 'bar'})
+ 
+     def test_linux_distro(self):
++        raise SkipTest("NixOS sandboxed builds hides /etc/os-release")
+         system = platform.system()
+         if system != "Linux":
+             raise SkipTest("test is only for linux")

pkgs/development/tools/database/sqlitebrowser/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, qt5, sqlite, cmake }:
+{ stdenv, fetchFromGitHub, qtbase, qttools, makeQtWrapper, sqlite, cmake }:
 
 stdenv.mkDerivation rec {
   version = "3.9.1";
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "1s7f2d7wx2i68x60z7wdws3il6m83k5n5w5wyjvr0mz0mih0s150";
   };
 
-  buildInputs = [ qt5.qtbase qt5.qttools sqlite cmake ];
+  buildInputs = [ qtbase qttools sqlite ];
+  nativeBuildInputs = [ makeQtWrapper cmake ];
   
   enableParallelBuilding = true;
   
@@ -19,10 +20,13 @@ stdenv.mkDerivation rec {
   
   # A regression was introduced in CMakeLists.txt on v3.9.x
   # See https://github.com/sqlitebrowser/sqlitebrowser/issues/832 and issues/755
-  patchPhase = ''
+  postPatch = ''
     substituteInPlace CMakeLists.txt --replace 'project("DB Browser for SQLite")' 'project(sqlitebrowser)'
   '';
 
+  postInstall = ''
+    wrapQtProgram $out/bin/sqlitebrowser
+  '';
 
   meta = with stdenv.lib; {
     description = "DB Browser for SQLite";

pkgs/development/tools/haskell/intero-nix-shim/default.nix

@@ -0,0 +1,21 @@
+{ mkDerivation, base, directory, filepath, optparse-applicative
+, posix-escape, split, stdenv, unix, fetchFromGitHub
+}:
+mkDerivation {
+  pname = "intero-nix-shim";
+  version = "0.1.2";
+  src = fetchFromGitHub {
+    owner = "michalrus";
+    repo = "intero-nix-shim";
+    rev = "0.1.2";
+    sha256 = "0p1h3w15bgvsbzi7f1n2dxxxz9yq7vmbxmww5igc5d3dm76skgzg";
+  };
+  isLibrary = false;
+  isExecutable = true;
+  executableHaskellDepends = [
+    base directory filepath optparse-applicative posix-escape split
+    unix
+  ];
+  homepage = "https://github.com/michalrus/intero-nix-shim";
+  license = stdenv.lib.licenses.asl20;
+}

pkgs/development/tools/misc/hydra/default.nix

@@ -104,7 +104,7 @@ in releaseTools.nixBuild rec {
 
   configureFlags = [ "--with-docbook-xsl=${docbook_xsl}/xml/xsl/docbook" ];
 
-  preHook = ''
+  shellHook = ''
     PATH=$(pwd)/src/script:$(pwd)/src/hydra-eval-jobs:$(pwd)/src/hydra-queue-runner:$(pwd)/src/hydra-evaluator:$PATH
     PERL5LIB=$(pwd)/src/lib:$PERL5LIB;
   '';

pkgs/development/tools/ocaml/camlp5/default.nix

@@ -24,6 +24,8 @@ stdenv.mkDerivation {
 
   postInstall = "cp ${metafile} $out/lib/ocaml/${ocaml.version}/site-lib/camlp5/META";
 
+  dontStrip = true;
+
   meta = with stdenv.lib; {
     description = "Preprocessor-pretty-printer for OCaml";
     longDescription = ''

pkgs/development/tools/ocaml/utop/default.nix

@@ -1,5 +1,5 @@
 { stdenv, fetchurl, bash, ocaml, findlib, ocamlbuild, camlp4, ocaml_react
-, lambdaTerm, ocaml_lwt, camomile, zed, cppo, ppx_tools
+, lambdaTerm, ocaml_lwt, camomile, zed, cppo, ppx_tools, makeWrapper
 }:
 
 stdenv.mkDerivation rec {
@@ -11,6 +11,7 @@ stdenv.mkDerivation rec {
     sha256 = "16z02vp9n97iax4fqpbi7v86r75vbabxvnd1rirh8w2miixs1g4x";
   };
 
+  nativeBuildInputs = [ makeWrapper ];
   buildInputs = [ ocaml findlib ocamlbuild cppo camlp4 ppx_tools ];
 
   propagatedBuildInputs = [ lambdaTerm ocaml_lwt ];

pkgs/os-specific/linux/kernel/linux-4.10.nix

@@ -1,12 +1,12 @@
 { stdenv, fetchurl, perl, buildLinux, ... } @ args:
 
 import ./generic.nix (args // rec {
-  version = "4.10.13";
+  version = "4.10.14";
   extraMeta.branch = "4.10";
 
   src = fetchurl {
     url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz";
-    sha256 = "1vylg3zv0n0hx9y5ngshz65hkpfm2686mvdcarhdg2mnxqd2kc6s";
+    sha256 = "1p9k7z91qxp0qqzd0qjfbasxirmhny5s3sasnlizcwsvyb4vicyk";
   };
 
   kernelPatches = args.kernelPatches;

pkgs/os-specific/linux/kernel/linux-4.4.nix

@@ -1,12 +1,12 @@
 { stdenv, fetchurl, perl, buildLinux, ... } @ args:
 
 import ./generic.nix (args // rec {
-  version = "4.4.65";
+  version = "4.4.66";
   extraMeta.branch = "4.4";
 
   src = fetchurl {
     url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz";
-    sha256 = "1vdb1804m3x991p3z0apxzsrp3ppdgngbfwj4j2ac062xgsp5x31";
+    sha256 = "10yl43sdzdy3c4vyqdzrw5vb59bbfb7z6k171a2sid9qr63hfi4s";
   };
 
   kernelPatches = args.kernelPatches;

pkgs/os-specific/linux/kernel/linux-4.9.nix

@@ -1,12 +1,12 @@
 { stdenv, fetchurl, perl, buildLinux, ... } @ args:
 
 import ./generic.nix (args // rec {
-  version = "4.9.25";
+  version = "4.9.26";
   extraMeta.branch = "4.9";
 
   src = fetchurl {
     url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz";
-    sha256 = "0drfz75k0zj2prawqmxaqgk27zk2vdj2pwip2n7hb9r1b9ly9bc2";
+    sha256 = "1lz9pj53k57y4kmns22xfx823q5gzw8w5d1sn7rdknsjjzhibinz";
   };
 
   kernelPatches = args.kernelPatches;

pkgs/servers/http/nginx/modules.nix

@@ -30,18 +30,6 @@
     inputs = [ pkgs.expat ];
   };
 
-  syslog = rec {
-    src = fetchFromGitHub {
-      owner = "yaoweibin";
-      repo = "nginx_syslog_patch";
-      rev = "3ca5ba65541637f74467038aa032e2586321d0cb";
-      sha256 = "0y8dxkx8m1jw4v5zsvw1gfah9vh3ryq0hfmrcbjzcmwp5b5lb1i8";
-    };
-    preConfigure = ''
-      patch -p1 < "${src}/syslog-1.7.0.patch"
-    '';
-  };
-
   moreheaders = {
     src = fetchFromGitHub {
       owner = "openresty";

pkgs/tools/networking/dd-agent/default.nix

@@ -64,6 +64,9 @@ in stdenv.mkDerivation rec {
     ln -s $out/agent/dogstatsd.py $out/bin/dogstatsd
     ln -s $out/agent/ddagent.py $out/bin/dd-forwarder
 
+    # Move out default conf.d so that /etc/dd-agent/conf.d is used
+    mv $out/agent/conf.d $out/agent/conf.d-system
+
     cat > $out/bin/dd-jmxfetch <<EOF
     #!/usr/bin/env bash
     exec ${python}/bin/python $out/agent/jmxfetch.py $@

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

@@ -3,6 +3,7 @@
 , autoreconfHook, autoconf-archive, bison, flex, libxml2, libxslt, docbook5, docbook5_xsl
 , storeDir ? "/nix/store"
 , stateDir ? "/nix/var"
+, confDir ? "/etc"
 }:
 
 let
@@ -43,7 +44,7 @@ let
     configureFlags =
       [ "--with-store-dir=${storeDir}"
         "--localstatedir=${stateDir}"
-        "--sysconfdir=/etc"
+        "--sysconfdir=${confDir}"
         "--disable-init-state"
         "--enable-gc"
       ]
@@ -116,9 +117,10 @@ let
     configureFlags =
       [ "--with-dbi=${perlPackages.DBI}/${perl.libPrefix}"
         "--with-dbd-sqlite=${perlPackages.DBDSQLite}/${perl.libPrefix}"
-        "--with-www-curl=${perlPackages.WWWCurl}/${perl.libPrefix}"
       ];
 
+    preConfigure = "export NIX_STATE_DIR=$TMPDIR";
+
     preBuild = "unset NIX_INDENT_MAKE";
   };
 

pkgs/top-level/all-packages.nix

@@ -5281,6 +5281,7 @@ with pkgs;
   cabal-install = haskell.lib.disableSharedExecutables haskellPackages.cabal-install;
 
   stack = haskell.lib.justStaticExecutables haskellPackages.stack;
+  hlint = haskell.lib.justStaticExecutables haskellPackages.hlint;
 
   all-cabal-hashes = callPackage ../data/misc/hackage/default.nix { };
 
@@ -6983,7 +6984,7 @@ with pkgs;
     flex = flex_2_5_35;
   };
 
-  sqlitebrowser = callPackage ../development/tools/database/sqlitebrowser { };
+  sqlitebrowser = qt5.callPackage ../development/tools/database/sqlitebrowser { };
 
   sselp = callPackage ../tools/X11/sselp{ };
 

pkgs/top-level/python-packages.nix

@@ -3264,6 +3264,8 @@ in {
     };
   };
 
+  branca = callPackage ../development/python-modules/branca { };
+
   bugwarrior = buildPythonPackage rec {
     name = "bugwarrior-${version}";
     version = "1.4.0";
@@ -11791,6 +11793,8 @@ in {
     };
   });
 
+  folium = callPackage ../development/python-modules/folium { };
+
   fontforge = pkgs.fontforge.override {
     withPython = true;
     inherit python;
@@ -16652,33 +16656,7 @@ in {
 
   };
 
-  os-testr = buildPythonPackage rec {
+  os-testr = callPackage ../development/python-modules/os-testr { };
-    name = "os-testr-${version}";
-    version = "0.4.2";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/o/os-testr/${name}.tar.gz";
-      sha256 = "0474z0mxb7y3vfk4s097wf1mzji5d135vh27cvlh9q17rq3x9r3w";
-    };
-
-    patchPhase = ''
-      sed -i 's@python@${python.interpreter}@' .testr.conf
-      sed -i 's@python@${python.interpreter}@' os_testr/tests/files/testr-conf
-    '';
-
-    checkPhase = ''
-      export PATH=$PATH:$out/bin
-      ${python.interpreter} setup.py test
-    '';
-
-    propagatedBuildInputs = with self; [ pbr Babel testrepository subunit testtools ];
-    buildInputs = with self; [ coverage oslosphinx oslotest testscenarios six ddt ];
-
-    # Requires pbr < 2
-    # Or update to latest version but that requires updating the whole of openstack / oslo
-    meta.broken = true;
-
-  };
 
   bandit = buildPythonPackage rec {
     name = "bandit-${version}";
@@ -17012,6 +16990,8 @@ in {
 
     meta = with stdenv.lib; {
       homepage = "https://launchpad.net/python-cliff";
+      # requires an update, incompatible with current dependencies (pbr)
+      broken = true;
     };
   };
 
@@ -17105,6 +17085,9 @@ in {
    meta = with stdenv.lib; {
      description = "Python bindings to the OpenStack Images API";
      homepage = "http://www.openstack.org/";
+
+     # requires an update, incompatible with current dependencies (pbr)
+     broken = true;
    };
  };
 
@@ -20236,6 +20219,8 @@ in {
 
   pyopencl = callPackage ../development/python-modules/pyopencl { };
 
+  pyproj = callPackage ../development/python-modules/pyproj { };
+
   pyrr = buildPythonPackage rec {
     name = "pyrr-${version}";
     version = "0.7.2";
@@ -24761,37 +24746,7 @@ in {
     };
   };
 
-
+  sqlalchemy_migrate = callPackage ../development/python-modules/sqlalchemy-migrate { };
-  sqlalchemy_migrate_func = sqlalchemy: buildPythonPackage rec {
-    name = "sqlalchemy-migrate-0.10.0";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/s/sqlalchemy-migrate/${name}.tar.gz";
-      sha256 = "00z0lzjs4ksr9yr31zs26csyacjvavhpz6r74xaw1r89kk75qg7q";
-    };
-
-    buildInputs = with self; [ unittest2 scripttest pytz pylint tempest-lib mock testtools ];
-    propagatedBuildInputs = with self; [ pbr tempita decorator sqlalchemy six sqlparse ];
-
-    checkPhase = ''
-      export PATH=$PATH:$out/bin
-      echo sqlite:///__tmp__ > test_db.cfg
-      # depends on ibm_db_sa
-      rm migrate/tests/changeset/databases/test_ibmdb2.py
-      # wants very old testtools
-      rm migrate/tests/versioning/test_schema.py
-      # transient failures on py27
-      substituteInPlace migrate/tests/versioning/test_util.py --replace "test_load_model" "noop"
-      ${python.interpreter} setup.py test
-    '';
-
-    meta = {
-      homepage = http://code.google.com/p/sqlalchemy-migrate/;
-      description = "Schema migration tools for SQLAlchemy";
-    };
-  };
-
-  sqlalchemy_migrate = self.sqlalchemy_migrate_func self.sqlalchemy;
 
   sqlparse = buildPythonPackage rec {
     name = "sqlparse-${version}";

pkgs/top-level/rust-packages.nix

@@ -7,9 +7,9 @@
 { runCommand, fetchFromGitHub, git }:
 
 let
-  version = "2017-04-13";
+  version = "2017-05-03";
-  rev = "5758a926a647716bd650978ad53aeb4a0c5f9b45";
+  rev = "dbc41da97da0a504d83af656b5d354ab5cf033e6";
-  sha256 = "1fnwh62k8fbflciv1qg3r9fsqn1xy72flyv15ii3mpja2vqzkdi2";
+  sha256 = "1kmy0hr155gcmilvwaj4ak5ppszrympyia7zxwhfihh00mip7xkb";
 
   src = fetchFromGitHub {
       inherit rev;