Merge remote-tracking branch 'upstream/master' into HEAD

42 files changed, 311 insertions, 195 deletions

diff --git a/pkgs/applications/editors/neovim/default.nix b/pkgs/applications/editors/neovim/default.nix
index 3f2058af1336..ca915b3e6d1b 100644
--- a/pkgs/applications/editors/neovim/default.nix
+++ b/pkgs/applications/editors/neovim/default.nix
@@ -24,8 +24,8 @@ let
     src = fetchFromGitHub {
       owner = "neovim";
       repo = "libvterm";
-      rev = "11682793d84668057c5aedc3d7f8071bb54eaf2c";
-      sha256 = "0pd90yx6xsagrqjipi26sxri1l4wdnx23ziad1zbxnqx9njxa7g3";
+      rev = "5a748f97fbf27003e141002b58933a99f3addf8d";
+      sha256 = "1fnd57f5n9h7z50a4vj7g96k6ndsdknjqsibgnxi9ndhyz244qbx";
     };
 
     buildInputs = [ perl ];
@@ -81,13 +81,13 @@ let
 
   neovim = stdenv.mkDerivation rec {
     name = "neovim-${version}";
-    version = "0.1.7";
+    version = "0.2.0";
 
     src = fetchFromGitHub {
       owner = "neovim";
       repo = "neovim";
       rev = "v${version}";
-      sha256 = "0bk0raxlb1xsqyw9pmqmxvcq5szqhimidrasnvzrci84gld8cwz4";
+      sha256 = "0fhjkgjwqqmzbfn9wk10l2vq9v74zkriz5j12b1rx0gdwzlfybn8";
     };
 
     enableParallelBuilding = true;
diff --git a/pkgs/applications/editors/neovim/neovim-remote.nix b/pkgs/applications/editors/neovim/neovim-remote.nix
index 487d9c842b8c..cf4ea9df544e 100644
--- a/pkgs/applications/editors/neovim/neovim-remote.nix
+++ b/pkgs/applications/editors/neovim/neovim-remote.nix
@@ -4,17 +4,17 @@ with stdenv.lib;
 
 pythonPackages.buildPythonPackage rec {
   name = "neovim-remote-${version}";
-  version = "v1.4.0";
+  version = "v1.6.0";
   disabled = !pythonPackages.isPy3k;
 
   src = fetchFromGitHub {
     owner = "mhinz";
     repo = "neovim-remote";
     rev = version;
-    sha256 = "0msvfh27f56xj5ki59ikzavxz863nal5scm57n43618m49qzg8iz";
+    sha256 = "0x01zpmxi37jr7j2az2bd8902h7zhkpg6kpvc8xmll9f7703zz2l";
   };
 
-  propagatedBuildInputs = [ pythonPackages.neovim ];
+  propagatedBuildInputs = with pythonPackages; [ neovim psutil ];
 
   meta = {
     description = "A tool that helps controlling nvim processes from a terminal";
diff --git a/pkgs/applications/editors/neovim/qt.nix b/pkgs/applications/editors/neovim/qt.nix
index 26f2a3b69411..57f52f0e5fcf 100644
--- a/pkgs/applications/editors/neovim/qt.nix
+++ b/pkgs/applications/editors/neovim/qt.nix
@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation rec {
   name = "neovim-qt-${version}";
-  version = "0.2.6";
+  version = "0.2.7";
 
   src = fetchFromGitHub {
     owner  = "equalsraf";
     repo   = "neovim-qt";
     rev    = "v${version}";
-    sha256 = "1wsxhy8fdayy4dsr2dxgh5k4jysybjlyzj134vk325v6cqz9bsgm";
+    sha256 = "1bfni38l7cs0wbd9c6hgz2jfc8h3ixmg94izdvydm8j7amdz0cb6";
   };
 
   cmakeFlags = [
@@ -17,7 +17,13 @@ stdenv.mkDerivation rec {
     "-DMSGPACK_LIBRARIES=${libmsgpack}/lib/libmsgpackc.so"
   ];
 
-  doCheck = true;
+  # The following tests FAILED:
+  #       2 - tst_neovimconnector (Failed)
+  #       3 - tst_callallmethods (Failed)
+  #       4 - tst_encoding (Failed)
+  #
+  # Tests failed when upgraded to neovim 0.2.0
+  doCheck = false;
 
   buildInputs = with pythonPackages; [
     neovim qtbase libmsgpack
diff --git a/pkgs/applications/editors/rstudio/default.nix b/pkgs/applications/editors/rstudio/default.nix
index f7ede1a8ea56..eab1228da1ac 100644
--- a/pkgs/applications/editors/rstudio/default.nix
+++ b/pkgs/applications/editors/rstudio/default.nix
@@ -1,13 +1,5 @@
 { stdenv, fetchurl, makeDesktopItem, cmake, boost163, zlib, openssl,
-R, qt5, libuuid, hunspellDicts, unzip, ant, jdk, gnumake, makeWrapper, pandoc,
-# If you have set up an R wrapper with other packages by following
-# something like https://nixos.org/nixpkgs/manual/#r-packages, RStudio
-# by default not be able to access any of those R packages. In order
-# to do this, override the argument "R" here with your respective R
-# wrapper, and set "useRPackages" to true.  This will add the
-# environment variable R_PROFILE_USER to the RStudio wrapper, pointing
-# to an R script which will allow R to use these packages.
-useRPackages ? false
+R, qt5, libuuid, hunspellDicts, unzip, ant, jdk, gnumake, makeWrapper, pandoc
 }:
 
 let
@@ -111,14 +103,8 @@ stdenv.mkDerivation rec {
     mimeType = "text/x-r-source;text/x-r;text/x-R;text/x-r-doc;text/x-r-sweave;text/x-r-markdown;text/x-r-html;text/x-r-presentation;application/x-r-data;application/x-r-project;text/x-r-history;text/x-r-profile;text/x-tex;text/x-markdown;text/html;text/css;text/javascript;text/x-chdr;text/x-csrc;text/x-c++hdr;text/x-c++src;";
   };
 
-  postInstall = let rProfile =
-    # RStudio seems to bypass the environment variables that the R
-    # wrapper already applies, and so this sets R_PROFILE_USER to
-    # again make those R packages accessible:
-    if useRPackages
-    then "--set R_PROFILE_USER ${R}/${R.passthru.fixLibsR}" else "";
-    in ''
-      wrapProgram $out/bin/rstudio --suffix PATH : ${gnumake}/bin ${rProfile}
+  postInstall = ''
+      wrapProgram $out/bin/rstudio --suffix PATH : ${gnumake}/bin
       mkdir $out/share
       cp -r ${desktopItem}/share/applications $out/share
       mkdir $out/share/icons
diff --git a/pkgs/applications/kde/kgpg.nix b/pkgs/applications/kde/kgpg.nix
index c44285982293..58e9cb0d1e9b 100644
--- a/pkgs/applications/kde/kgpg.nix
+++ b/pkgs/applications/kde/kgpg.nix
@@ -1,7 +1,7 @@
 {
-  kdeApp, lib,
+  kdeApp, lib, makeQtWrapper,
   extra-cmake-modules, kdoctools, ki18n,
-  akonadi-contacts, gpgme, karchive, kcodecs, kcontacts, kcoreaddons, kcrash,
+  akonadi-contacts, gnupg1, gpgme, karchive, kcodecs, kcontacts, kcoreaddons, kcrash,
   kdbusaddons, kiconthemes, kjobwidgets, kio, knotifications, kservice,
   ktextwidgets, kxmlgui, kwidgetsaddons, kwindowsystem
 }:
@@ -10,10 +10,13 @@ kdeApp {
   name = "kgpg";
   nativeBuildInputs = [ extra-cmake-modules kdoctools ki18n ];
   buildInputs = [
-    akonadi-contacts gpgme karchive kcodecs kcontacts kcoreaddons kcrash kdbusaddons
+    akonadi-contacts gnupg1 gpgme karchive kcodecs kcontacts kcoreaddons kcrash kdbusaddons
     kiconthemes kjobwidgets kio knotifications kservice ktextwidgets kxmlgui
-    kwidgetsaddons kwindowsystem
+    kwidgetsaddons kwindowsystem makeQtWrapper
   ];
+  postInstall = ''
+    wrapQtProgram $out/bin/kgpg --suffix PATH : ${lib.makeBinPath [ gnupg1 ]}
+  '';
   meta = {
     license = [ lib.licenses.gpl2 ];
     maintainers = [ lib.maintainers.ttuegel ];
diff --git a/pkgs/applications/misc/urh/default.nix b/pkgs/applications/misc/urh/default.nix
index e12b95754edf..9015bb9956b3 100644
--- a/pkgs/applications/misc/urh/default.nix
+++ b/pkgs/applications/misc/urh/default.nix
@@ -22,7 +22,7 @@ python3Packages.buildPythonApplication rec {
     inherit (src.meta) homepage;
     description = "Universal Radio Hacker: investigate wireless protocols like a boss";
     license = licenses.asl20;
-    platform = platforms.all;
+    platforms = platforms.all;
     maintainers = with maintainers; [ fpletz ];
   };
 }
diff --git a/pkgs/applications/networking/browsers/google-chrome/default.nix b/pkgs/applications/networking/browsers/google-chrome/default.nix
index 32d3a8e1540f..e7b74562bd5b 100644
--- a/pkgs/applications/networking/browsers/google-chrome/default.nix
+++ b/pkgs/applications/networking/browsers/google-chrome/default.nix
@@ -4,7 +4,7 @@
 , glib, fontconfig, freetype, pango, cairo, libX11, libXi, atk, gconf, nss, nspr
 , libXcursor, libXext, libXfixes, libXrender, libXScrnSaver, libXcomposite, libxcb
 , alsaLib, libXdamage, libXtst, libXrandr, expat, cups
-, dbus_libs, gtk2, gtk3, gdk_pixbuf, gcc
+, dbus_libs, gtk2, gtk3, gdk_pixbuf, gcc-unwrapped
 
 # command line arguments which are always set e.g "--disable-gpu"
 , commandLineArgs ? ""
@@ -43,11 +43,10 @@ let
   };
 
   deps = [
-    stdenv.cc.cc
     glib fontconfig freetype pango cairo libX11 libXi atk gconf nss nspr
     libXcursor libXext libXfixes libXrender libXScrnSaver libXcomposite libxcb
     alsaLib libXdamage libXtst libXrandr expat cups
-    dbus_libs gdk_pixbuf gcc
+    dbus_libs gdk_pixbuf gcc-unwrapped.lib
     systemd
     libexif
     liberation_ttf curl utillinux xdg_utils wget
diff --git a/pkgs/applications/networking/dropbox/default.nix b/pkgs/applications/networking/dropbox/default.nix
index a4bbe15544a3..a97b29e3d3a2 100644
--- a/pkgs/applications/networking/dropbox/default.nix
+++ b/pkgs/applications/networking/dropbox/default.nix
@@ -23,11 +23,11 @@
 let
   # NOTE: When updating, please also update in current stable,
   # as older versions stop working
-  version = "24.4.17";
+  version = "25.4.28";
   sha256 =
     {
-      "x86_64-linux" = "1wjr92vrbxyjbwyqf134h8fp1zi4d5wyyirii545wqadbgg9grh9";
-      "i686-linux"   = "1qsdidpy251irzkv0hx0ch0xnrwq6wq6b22g0n8b9d0a7xi08k7h";
+      "x86_64-linux" = "0r0bdl37rkar3nijxslp493mic5qd20l125p1kghqbradvh57rl3";
+      "i686-linux"   = "1difq6ky1klvminbzjivvq6ap3l296gij0ghgyy1n4lca3jqq648";
     }."${stdenv.system}" or (throw "system ${stdenv.system} not supported");
 
   arch =
diff --git a/pkgs/applications/networking/feedreaders/rawdog/default.nix b/pkgs/applications/networking/feedreaders/rawdog/default.nix
index 39543f256fa2..4e22a95d4d86 100644
--- a/pkgs/applications/networking/feedreaders/rawdog/default.nix
+++ b/pkgs/applications/networking/feedreaders/rawdog/default.nix
@@ -12,12 +12,12 @@ python2Packages.buildPythonApplication rec {
   propagatedBuildInputs = with python2Packages; [ feedparser ];
 
   namePrefix = "";
-  
+
   meta = with stdenv.lib; {
     homepage = "http://offog.org/code/rawdog/";
     description = "RSS Aggregator Without Delusions Of Grandeur";
     license = licenses.gpl2;
-    platform = platforms.unix;
+    platforms = platforms.unix;
     maintainers = with maintainers; [ nckx ];
   };
 }
diff --git a/pkgs/applications/networking/irc/qweechat/default.nix b/pkgs/applications/networking/irc/qweechat/default.nix
index 83d459a97fe3..acf030222a1b 100644
--- a/pkgs/applications/networking/irc/qweechat/default.nix
+++ b/pkgs/applications/networking/irc/qweechat/default.nix
@@ -26,6 +26,6 @@ python27Packages.buildPythonApplication rec {
     description = "Qt remote GUI for WeeChat";
     license = licenses.gpl3;
     maintainers = with maintainers; [ ramkromberg ];
-    platform = with platforms; linux;
+    platforms = with platforms; linux;
   };
 }
diff --git a/pkgs/build-support/emacs/wrapper.nix b/pkgs/build-support/emacs/wrapper.nix
index b13def07bb88..4fb77ccfe214 100644
--- a/pkgs/build-support/emacs/wrapper.nix
+++ b/pkgs/build-support/emacs/wrapper.nix
@@ -21,7 +21,7 @@ set which contains `emacsWithPackages`. For example, to override
 `emacsPackagesNg.emacsWithPackages`,
 ```
 let customEmacsPackages =
-      emacsPackagesNg.override (super: self: {
+      emacsPackagesNg.overrideScope (super: self: {
         # use a custom version of emacs
         emacs = ...;
         # use the unstable MELPA version of magit
diff --git a/pkgs/development/libraries/gdal/default.nix b/pkgs/development/libraries/gdal/default.nix
index e39d39ab81b5..599a2c70f139 100644
--- a/pkgs/development/libraries/gdal/default.nix
+++ b/pkgs/development/libraries/gdal/default.nix
@@ -1,12 +1,12 @@
 { stdenv, fetchurl, composableDerivation, unzip, libjpeg, libtiff, zlib
 , postgresql, mysql, libgeotiff, pythonPackages, proj, geos, openssl
 , libpng, sqlite, libspatialite
-, netcdf, hdf5 , curl
-, netcdfSupport ? true
- }:
+, libiconv
+, netcdfSupport ? true, netcdf, hdf5 , curl
+}:
 
 with stdenv.lib;
- 
+
 composableDerivation.composableDerivation {} (fixed: rec {
   version = "2.1.3";
   name = "gdal-${version}";
@@ -18,7 +18,8 @@ composableDerivation.composableDerivation {} (fixed: rec {
 
   buildInputs = [ unzip libjpeg libtiff libpng proj openssl sqlite libspatialite ]
   ++ (with pythonPackages; [ python numpy wrapPython ])
-  ++ (stdenv.lib.optionals netcdfSupport [ netcdf hdf5 curl ]);
+  ++ stdenv.lib.optional stdenv.isDarwin libiconv
+  ++ stdenv.lib.optionals netcdfSupport [ netcdf hdf5 curl ];
 
   hardeningDisable = [ "format" ];
 
diff --git a/pkgs/development/libraries/libidn2/fix-error-darwin.patch b/pkgs/development/libraries/libidn2/fix-error-darwin.patch
index db3edd6e4a08..e2202abd947c 100644
--- a/pkgs/development/libraries/libidn2/fix-error-darwin.patch
+++ b/pkgs/development/libraries/libidn2/fix-error-darwin.patch
@@ -10,17 +10,6 @@ index 6abbc72..804f0f2 100644
  #include "gettext.h"
  #define _(String) dgettext (PACKAGE, String)
  #include "progname.h"
-@@ -161,9 +160,7 @@ process_input (char *readbuf, int flags)
-       free (output);
-     }
-   else
--    error (EXIT_FAILURE, 0, "%s: %s",
--	   args_info.register_given ? "register" : "lookup",
--	   idn2_strerror (rc));
-+    perror (idn2_strerror (rc));
- }
- 
- int
 @@ -222,7 +219,7 @@ main (int argc, char *argv[])
      }
  
diff --git a/pkgs/development/libraries/qtinstaller/default.nix b/pkgs/development/libraries/qtinstaller/default.nix
index 29db95e6919c..3379cbc9acfe 100644
--- a/pkgs/development/libraries/qtinstaller/default.nix
+++ b/pkgs/development/libraries/qtinstaller/default.nix
@@ -2,7 +2,10 @@
 
 stdenv.mkDerivation rec {
   name = "qtinstaller";
-  buildInputs = [ qtdeclarative qttools qtbase qmakeHook ];
+
+  propagatedBuildInputs = [qtdeclarative qttools];
+  nativeBuildInputs = [ qmakeHook ];
+
   version = "2.0.3";
   src = fetchurl {
     url = "http://download.qt.io/official_releases/qt-installer-framework/${version}/qt-installer-framework-opensource-${version}-src.tar.gz";
@@ -12,6 +15,10 @@ stdenv.mkDerivation rec {
 
   outputs = [ "out" "dev" "doc" ];
 
+  setOutputFlags = false;
+  enableParallelBuilding = true;
+  NIX_QT_SUBMODULE = true;
+
   installPhase = ''
     mkdir -p $out/{bin,lib,share/qt-installer-framework}
     cp -a bin/{archivegen,binarycreator,devtool,installerbase,repogen} $out/bin
diff --git a/pkgs/development/python-modules/certifi/default.nix b/pkgs/development/python-modules/certifi/default.nix
new file mode 100644
index 000000000000..8658c76df798
--- /dev/null
+++ b/pkgs/development/python-modules/certifi/default.nix
@@ -0,0 +1,22 @@
+{ lib
+, fetchPypi
+, buildPythonPackage
+}:
+
+buildPythonPackage rec {
+  pname = "certifi";
+  version = "2017.1.23";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1klrzl3hgvcf2mjk00g0k3kk1p2z27vzwnxivwar4vhjmjvpz1w1";
+  };
+
+  meta = {
+    homepage = http://certifi.io/;
+    description = "Python package for providing Mozilla's CA Bundle";
+    license = lib.licenses.isc;
+    maintainers = with lib.maintainers; [ koral ];
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/line_profiler/default.nix b/pkgs/development/python-modules/line_profiler/default.nix
index e6d6f1e1d7e6..570bba2a8c42 100644
--- a/pkgs/development/python-modules/line_profiler/default.nix
+++ b/pkgs/development/python-modules/line_profiler/default.nix
@@ -3,6 +3,8 @@
 , fetchPypi
 , cython
 , isPyPy
+, ipython
+, python
 }:
 
 buildPythonPackage rec {
@@ -17,8 +19,14 @@ buildPythonPackage rec {
 
   buildInputs = [ cython ];
 
+  propagatedBuildInputs = [ ipython ];
+
   disabled = isPyPy;
 
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover -s tests
+  '';
+
   meta = {
     description = "Line-by-line profiler";
     homepage = https://github.com/rkern/line_profiler;
diff --git a/pkgs/development/python-modules/magic-wormhole/default.nix b/pkgs/development/python-modules/magic-wormhole/default.nix
index 483e9aa3a3b9..99da5e83a875 100644
--- a/pkgs/development/python-modules/magic-wormhole/default.nix
+++ b/pkgs/development/python-modules/magic-wormhole/default.nix
@@ -1,18 +1,34 @@
-{ stdenv, fetchurl, nettools, glibcLocales, pythonPackages }:
+{ lib
+, buildPythonPackage
+, fetchPypi
+, nettools
+, glibcLocales
+, autobahn
+, cffi
+, click
+, hkdf
+, pynacl
+, spake2
+, tqdm
+, python
+, mock
+}:
 
-pythonPackages.buildPythonApplication rec {
-  name = "magic-wormhole-${version}";
+buildPythonPackage rec {
+  pname = "magic-wormhole";
   version = "0.8.1";
+  name = "${pname}-${version}";
 
-  src = fetchurl {
-    url = "mirror://pypi/m/magic-wormhole/${name}.tar.gz";
+  src = fetchPypi {
+    inherit pname version;
     sha256 = "1yh5nbhh9z1am2pqnb5qqyq1zjl1m7z6jnkmvry2q14qwspw9had";
   };
 
+  checkInputs = [ mock ];
   buildInputs = [ nettools glibcLocales ];
-  propagatedBuildInputs = with pythonPackages; [ autobahn cffi click hkdf pynacl spake2 tqdm ];
+  propagatedBuildInputs = [ autobahn cffi click hkdf pynacl spake2 tqdm ];
 
-  patchPhase = ''
+  postPatch = ''
     sed -i -e "s|'ifconfig'|'${nettools}/bin/ifconfig'|" src/wormhole/ipaddrs.py
     sed -i -e "s|if (os.path.dirname(os.path.abspath(wormhole))|if not os.path.abspath(wormhole).startswith('/nix/store') and (os.path.dirname(os.path.abspath(wormhole))|" src/wormhole/test/test_scripts.py
     # XXX: disable one test due to warning:
@@ -24,10 +40,10 @@ pythonPackages.buildPythonApplication rec {
     export PATH="$PATH:$out/bin"
     export LANG="en_US.UTF-8"
     export LC_ALL="en_US.UTF-8"
-    ${pythonPackages.python.interpreter} -m wormhole.test.run_trial wormhole
+    ${python.interpreter} -m wormhole.test.run_trial wormhole
   '';
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "Securely transfer data between computers";
     homepage = "https://github.com/warner/magic-wormhole";
     license = licenses.mit;
diff --git a/pkgs/development/python-modules/pydot/default.nix b/pkgs/development/python-modules/pydot/default.nix
new file mode 100644
index 000000000000..38123acd32ec
--- /dev/null
+++ b/pkgs/development/python-modules/pydot/default.nix
@@ -0,0 +1,27 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, chardet
+, pyparsing
+, graphviz
+}:
+
+buildPythonPackage rec {
+  pname = "pydot";
+  version = "1.2.3";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "edb5d3f249f97fbd9c4bb16959e61bc32ecf40eee1a9f6d27abe8d01c0a73502";
+  };
+  checkInputs = [ chardet ];
+  # No tests in archive
+  doCheck = false;
+  propagatedBuildInputs = [pyparsing graphviz];
+  meta = {
+    homepage = https://github.com/erocarrera/pydot;
+    description = "Allows to easily create both directed and non directed graphs from Python";
+    licenses = with lib.licenses; [ mit ];
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/pyroute2/default.nix b/pkgs/development/python-modules/pyroute2/default.nix
index 91bfa97cb970..1b47b7f3f7df 100644
--- a/pkgs/development/python-modules/pyroute2/default.nix
+++ b/pkgs/development/python-modules/pyroute2/default.nix
@@ -16,6 +16,6 @@ buildPythonPackage rec {
     homepage = https://github.com/svinota/pyroute2;
     license = licenses.asl20;
     maintainers = [maintainers.mic92];
-    platform = platforms.linux;
+    platforms = platforms.linux;
   };
 }
diff --git a/pkgs/development/python-modules/stevedore/default.nix b/pkgs/development/python-modules/stevedore/default.nix
new file mode 100644
index 000000000000..c6ce6c0d922e
--- /dev/null
+++ b/pkgs/development/python-modules/stevedore/default.nix
@@ -0,0 +1,23 @@
+{ stdenv, buildPythonPackage, fetchPypi, oslosphinx, pbr, six, argparse }:
+
+buildPythonPackage rec {
+  pname = "stevedore";
+  version = "1.21.0";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "12sg88ax0lv2sxr685rqdaxm9gryjrpj4fvax459zvwy1r4n83ma";
+  };
+
+  doCheck = false;
+
+  buildInputs = [ oslosphinx ];
+  propagatedBuildInputs = [ pbr six argparse ];
+
+  meta = with stdenv.lib; {
+    description = "Manage dynamic plugins for Python applications";
+    homepage = "https://pypi.python.org/pypi/stevedore";
+    license = licenses.asl20;
+  };
+}
diff --git a/pkgs/development/r-modules/README.md b/pkgs/development/r-modules/README.md
index fc046ed0627e..477059cbb2c8 100644
--- a/pkgs/development/r-modules/README.md
+++ b/pkgs/development/r-modules/README.md
@@ -55,28 +55,23 @@ available.
 
 ## RStudio
 
-RStudio by default will not use the libraries installed like above.
-You must override its R version with your custom R environment, and
-set `useRPackages` to `true`, like below:
+RStudio uses a standard set of packages and ignores any custom R
+environments or installed packages you may have.  To create a custom
+environment, see `rstudioWrapper`, which functions similarly to
+`rWrapper`:
 
 ```nix
 {
     packageOverrides = super: let self = super.pkgs; in
     {
 
-        rEnv = super.rWrapper.override {
+        rstudioEnv = super.rstudioWrapper.override {
             packages = with self.rPackages; [
-                devtools
+                dplyr
                 ggplot2
                 reshape2
-                yaml
-                optparse
                 ];
         };
-        rstudioEnv = super.rstudio.override {
-            R = rEnv;
-            useRPackages = true;
-        };
     };
 }
 ```
diff --git a/pkgs/development/r-modules/wrapper-rstudio.nix b/pkgs/development/r-modules/wrapper-rstudio.nix
new file mode 100644
index 000000000000..dd9b0e9c5381
--- /dev/null
+++ b/pkgs/development/r-modules/wrapper-rstudio.nix
@@ -0,0 +1,33 @@
+{ stdenv, R, rstudio, makeWrapper, recommendedPackages, packages }:
+
+stdenv.mkDerivation rec {
+
+  name = rstudio.name + "-wrapper";
+
+  buildInputs = [makeWrapper R rstudio] ++ recommendedPackages ++ packages;
+
+  unpackPhase = ":";
+
+  # rWrapper points R to a specific set of packages by using a wrapper
+  # (as in https://nixos.org/nixpkgs/manual/#r-packages) which sets
+  # R_LIBS_SITE.  Ordinarily, it would be possible to make RStudio use
+  # this same set of packages by simply overriding its version of R
+  # with the wrapped one, however, RStudio internally overrides
+  # R_LIBS_SITE.  The below works around this by turning R_LIBS_SITE
+  # into an R file (fixLibsR) which achieves the same effect, then
+  # uses R_PROFILE_USER to load this code at startup in RStudio.
+  fixLibsR = "fix_libs.R";
+  installPhase = ''
+    mkdir $out
+    echo "# Autogenerated by wrapper-rstudio.nix from R_LIBS_SITE" > $out/${fixLibsR}
+    echo -n ".libPaths(c(.libPaths(), \"" >> $out/${fixLibsR}
+    echo -n $R_LIBS_SITE | sed -e 's/:/", "/g' >> $out/${fixLibsR}
+    echo -n "\"))" >> $out/${fixLibsR}
+    echo >> $out/${fixLibsR}
+    makeWrapper ${rstudio}/bin/rstudio $out/bin/rstudio --set R_PROFILE_USER $out/${fixLibsR}
+  '';
+  
+  meta = {
+    platforms = stdenv.lib.platforms.unix;
+  };
+}
diff --git a/pkgs/development/r-modules/wrapper.nix b/pkgs/development/r-modules/wrapper.nix
index 25c765060279..3b9a9b184506 100644
--- a/pkgs/development/r-modules/wrapper.nix
+++ b/pkgs/development/r-modules/wrapper.nix
@@ -1,19 +1,12 @@
 { stdenv, R, makeWrapper, recommendedPackages, packages }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   name = R.name + "-wrapper";
 
   buildInputs = [makeWrapper R] ++ recommendedPackages ++ packages;
 
   unpackPhase = ":";
 
-  # This filename is used in 'installPhase', but needs to be
-  # referenced elsewhere.  This will be relative to this package's
-  # path.
-  passthru = {
-    fixLibsR = "fix_libs.R";
-  };
-  
   installPhase = ''
     mkdir -p $out/bin
     cd ${R}/bin
@@ -21,17 +14,6 @@ stdenv.mkDerivation rec {
       makeWrapper ${R}/bin/$exe $out/bin/$exe \
         --prefix "R_LIBS_SITE" ":" "$R_LIBS_SITE"
     done
-    # RStudio (and perhaps other packages) overrides the R_LIBS_SITE
-    # which the wrapper above applies, and as a result packages
-    # installed in the wrapper (as in the method described in
-    # https://nixos.org/nixpkgs/manual/#r-packages) aren't visible.
-    # The below turns R_LIBS_SITE into some R startup code which can
-    # correct this.
-    echo "# Autogenerated by wrapper.nix from R_LIBS_SITE" > $out/${passthru.fixLibsR}
-    echo -n ".libPaths(c(.libPaths(), \"" >> $out/${passthru.fixLibsR}
-    echo -n $R_LIBS_SITE | sed -e 's/:/", "/g' >> $out/${passthru.fixLibsR}
-    echo -n "\"))" >> $out/${passthru.fixLibsR}
-    echo >> $out/${passthru.fixLibsR}
   '';
 
   meta = {
diff --git a/pkgs/development/tools/ammonite/default.nix b/pkgs/development/tools/ammonite/default.nix
index 4c64141fd4d2..04916b1ef75f 100644
--- a/pkgs/development/tools/ammonite/default.nix
+++ b/pkgs/development/tools/ammonite/default.nix
@@ -1,12 +1,13 @@
 { stdenv, lib, fetchurl, makeWrapper, jre }:
 
 stdenv.mkDerivation rec {
-  name = "ammonite-repl-${version}";
-  version = "0.8.3";
+  name = "ammonite-${version}";
+  version = "0.8.4";
+  scalaVersion = "2.12";
 
   src = fetchurl {
-    url = "https://github.com/lihaoyi/Ammonite/releases/download/${version}/2.12-${version}";
-    sha256 = "0y4524y2w7aq300djcazb7ckkr3gqpim2grcgb237mxq3fdvb0r8";
+    url = "https://github.com/lihaoyi/Ammonite/releases/download/${version}/${scalaVersion}-${version}";
+    sha256 = "04kni08yd53w8dhkkgbydzkka4cnp31l2d8g23iinkn10ckmz5jm";
   };
 
   propagatedBuildInputs = [ jre ] ;
diff --git a/pkgs/development/tools/build-managers/buildbot/default.nix b/pkgs/development/tools/build-managers/buildbot/default.nix
index ed24e917a1cb..8c8caf063035 100644
--- a/pkgs/development/tools/build-managers/buildbot/default.nix
+++ b/pkgs/development/tools/build-managers/buildbot/default.nix
@@ -5,17 +5,19 @@ let
     buildInputs = [ makeWrapper ] ++ plugins;
     passthru.withPlugins = moarPlugins: withPlugins (moarPlugins ++ plugins);
   } ''
-    makeWrapper ${package}/bin/buildbot $out/bin/buildbot --prefix PYTHONPATH : $PYTHONPATH
+    makeWrapper ${package}/bin/buildbot $out/bin/buildbot \
+      --prefix PYTHONPATH : "${package}/lib/python2.7/site-packages:$PYTHONPATH"
+    ln -sfv ${package}/lib $out/lib
   '';
 
   package = pythonPackages.buildPythonApplication (rec {
     name = "${pname}-${version}";
     pname = "buildbot";
-    version = "0.9.4";
+    version = "0.9.5";
 
     src = pythonPackages.fetchPypi {
       inherit pname version;
-      sha256 = "0wklrn4fszac9wi8zw3vbsznwyff6y57cz0i81zvh46skb6n3086";
+      sha256 = "11r553nmh87a9pm58wycimapk2pw9hnlc7hffn97xwbqprd8qh66";
     };
 
     buildInputs = with pythonPackages; [
@@ -49,6 +51,7 @@ let
       txaio
       autobahn
       pyjwt
+      distro
 
       # tls
       pyopenssl
@@ -68,6 +71,14 @@ let
 
     postPatch = ''
       substituteInPlace buildbot/scripts/logwatcher.py --replace '/usr/bin/tail' "$(type -P tail)"
+
+      # NOTE: secrets management tests currently broken
+      rm -fv buildbot/test/integration/test_integration_secrets.py
+      rm -fv buildbot/test/integration/test_integration_secrets_with_vault.py
+      rm -fv buildbot/test/unit/test_fake_secrets_manager.py
+      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
     '';
 
     passthru = { inherit withPlugins; };
diff --git a/pkgs/development/tools/build-managers/buildbot/plugins.nix b/pkgs/development/tools/build-managers/buildbot/plugins.nix
index b22759af8fec..77e97ed7ac3c 100644
--- a/pkgs/development/tools/build-managers/buildbot/plugins.nix
+++ b/pkgs/development/tools/build-managers/buildbot/plugins.nix
@@ -1,14 +1,14 @@
-{ stdenv, fetchurl, pythonPackages }:
+{ stdenv, pythonPackages }:
 
 let
   buildbot-pkg = pythonPackages.buildPythonPackage rec {
     name = "${pname}-${version}";
     pname = "buildbot-pkg";
-    version = "0.9.4";
+    version = "0.9.5";
 
-    src = fetchurl {
-      url = "mirror://pypi/b/${pname}/${name}.tar.gz";
-      sha256 = "09a3yvs5hhf8syrkyydznmymgg86dpvgrwy9rb3bryq00wpjb3wn";
+    src = pythonPackages.fetchPypi {
+      inherit pname version;
+      sha256 = "1xpi4w0lc6z97pmmms85dvdspacbzlvs8zi3kv1r4rypk3znwmi1";
     };
 
     propagatedBuildInputs = with pythonPackages; [ setuptools ];
@@ -25,15 +25,14 @@ in {
   www = pythonPackages.buildPythonPackage rec {
     name = "${pname}-${version}";
     pname = "buildbot_www";
-    version = "0.9.4";
+    version = "0.9.5";
 
     # NOTE: wheel is used due to buildbot circular dependency
     format = "wheel";
 
     src = pythonPackages.fetchPypi {
       inherit pname version format;
-      python = "py2";
-      sha256 = "08m4h2pf6hgi8igh2j0qzfq49izc2z0qqj6ddxk0di5l306jx4im";
+      sha256 = "1d7yjxka6slflm3wbdpq4sr1kagmgbqdv2zgx9bq77jvjh7ga0py";
     };
 
     meta = with stdenv.lib; {
@@ -47,11 +46,11 @@ in {
   console-view = pythonPackages.buildPythonPackage rec {
     name = "${pname}-${version}";
     pname = "buildbot-console-view";
-    version = "0.9.4";
+    version = "0.9.5";
 
-    src = fetchurl {
-      url = "mirror://pypi/b/${pname}/${name}.tar.gz";
-      sha256 = "1w2vv8iyzl7ak4161avp9n6mhh08adav2fl82bbm17a3064apl8n";
+    src = pythonPackages.fetchPypi {
+      inherit pname version;
+      sha256 = "1s6mvw955dsgk7hvb1xa32bbd7w2yma62py5s0vmi5shv8nwq3hb";
     };
 
     propagatedBuildInputs = with pythonPackages; [ buildbot-pkg ];
@@ -67,11 +66,11 @@ in {
   waterfall-view = pythonPackages.buildPythonPackage rec {
     name = "${pname}-${version}";
     pname = "buildbot-waterfall-view";
-    version = "0.9.4";
+    version = "0.9.5";
 
-    src = fetchurl {
-      url = "mirror://pypi/b/${pname}/${name}.tar.gz";
-      sha256 = "17xn6vrr0k2xabw6hr9sdyy0ry3llyjfmc79qrpgp5bsly2qv3jf";
+    src = pythonPackages.fetchPypi {
+      inherit pname version;
+      sha256 = "116846d987wp1bz78f0h4lypqcns5073vzhb4vsqbf08sppgr67k";
     };
 
     propagatedBuildInputs = with pythonPackages; [ buildbot-pkg ];
diff --git a/pkgs/development/tools/build-managers/buildbot/worker.nix b/pkgs/development/tools/build-managers/buildbot/worker.nix
index b9b4b86aa442..145221c63537 100644
--- a/pkgs/development/tools/build-managers/buildbot/worker.nix
+++ b/pkgs/development/tools/build-managers/buildbot/worker.nix
@@ -3,11 +3,11 @@
 pythonPackages.buildPythonApplication (rec {
   name = "${pname}-${version}";
   pname = "buildbot-worker";
-  version = "0.9.4";
+  version = "0.9.5";
 
   src = pythonPackages.fetchPypi {
     inherit pname version;
-    sha256 = "0rdrr8x7sn2nxl51p6h9ad42s3c28lb6sys84zrg0d7fm4zhv7hj";
+    sha256 = "1al7jam351sf781axj4kfhj70cc0g21zv81ynk410kdccjyxp2dy";
   };
 
   buildInputs = with pythonPackages; [ setuptoolsTrial mock ];
diff --git a/pkgs/os-specific/linux/mwprocapture/default.nix b/pkgs/os-specific/linux/mwprocapture/default.nix
index f09e9543c48d..bed40fd02e4d 100644
--- a/pkgs/os-specific/linux/mwprocapture/default.nix
+++ b/pkgs/os-specific/linux/mwprocapture/default.nix
@@ -23,6 +23,8 @@ stdenv.mkDerivation rec {
     sha256 = "0i1y50mf559flhxgaxy2gdpa7dvpp12ix9xfzgxa61rc135x0im4";
   };
 
+  patches = [ ./linux_4_11_include_fix.patch ];
+
   preConfigure =
   ''
     cd ./src
diff --git a/pkgs/os-specific/linux/mwprocapture/linux_4_11_include_fix.patch b/pkgs/os-specific/linux/mwprocapture/linux_4_11_include_fix.patch
new file mode 100644
index 000000000000..726efd9f537c
--- /dev/null
+++ b/pkgs/os-specific/linux/mwprocapture/linux_4_11_include_fix.patch
@@ -0,0 +1,30 @@
+diff -Naur ProCaptureForLinux_3269/src/sources/avstream/capture.c ProCaptureForLinux_3269_new/src/sources/avstream/capture.c
+--- ProCaptureForLinux_3269/src/sources/avstream/capture.c	2016-12-12 17:17:18.000000000 -0800
++++ ProCaptureForLinux_3269_new/src/sources/avstream/capture.c	2017-05-02 23:58:28.270827491 -0700
+@@ -154,7 +154,9 @@
+     if (IS_ERR_OR_NULL(fp))
+         return IS_ERR(fp) ? PTR_ERR(fp) : -1;
+
+-#if LINUX_VERSION_CODE >= KERNEL_VERSION(3,9,0)
++#if LINUX_VERSION_CODE >= KERNEL_VERSION(4,11,0)
++    ret = vfs_getattr(&fp->f_path, &stat, STATX_BASIC_STATS, AT_STATX_SYNC_AS_STAT);
++#elif LINUX_VERSION_CODE >= KERNEL_VERSION(3,9,0)
+     ret = vfs_getattr(&fp->f_path, &stat);
+ #else
+     ret = vfs_getattr(fp->f_path.mnt, fp->f_path.dentry, &stat);
+diff -Naur ProCaptureForLinux_3269/src/sources/ospi/ospi-linux.c ProCaptureForLinux_3269_new/src/sources/ospi/ospi-linux.c
+--- ProCaptureForLinux_3269/src/sources/ospi/ospi-linux.c	2016-12-12 17:17:18.000000000 -0800
++++ ProCaptureForLinux_3269_new/src/sources/ospi/ospi-linux.c	2017-05-02 23:51:02.197633628 -0700
+@@ -21,6 +21,12 @@
+ #include <linux/freezer.h>
+ #include <linux/pci.h>
+
++// some functions were moved from linux/sched.h out to their own headers in 4.11.x
++#if LINUX_VERSION_CODE >= KERNEL_VERSION(4,11,0)
++#include <linux/sched/signal.h>
++#include <linux/sched/debug.h>
++#endif
++
+ unsigned int debug_level = 0;
+
+ struct kmem_cache *g_spin_cache = NULL;
diff --git a/pkgs/os-specific/linux/tomb/default.nix b/pkgs/os-specific/linux/tomb/default.nix
index 5ed7ad5b959c..141af86a337b 100644
--- a/pkgs/os-specific/linux/tomb/default.nix
+++ b/pkgs/os-specific/linux/tomb/default.nix
@@ -1,15 +1,15 @@
 { stdenv, fetchurl, zsh, pinentry, cryptsetup, gnupg1orig, makeWrapper }:
 
 let
-    version = "2.2";
+    version = "2.4";
 in
 
 stdenv.mkDerivation rec {
   name = "tomb-${version}";
 
   src = fetchurl {
-    url = "https://files.dyne.org/tomb/tomb-${version}.tar.gz";
-    sha256 = "11msj38fdmymiqcmwq1883kjqi5zr01ybdjj58rfjjrw4zw2w5y0";
+    url = "https://files.dyne.org/tomb/Tomb-${version}.tar.gz";
+    sha256 = "1hv1w79as7swqj0n137vz8n8mwvcgwlvd91sdyssz41jarg7f1vr";
   };
 
   buildInputs = [ makeWrapper ];
diff --git a/pkgs/os-specific/linux/zfs/default.nix b/pkgs/os-specific/linux/zfs/default.nix
index 5c178f47b506..c70e96aa9fd9 100644
--- a/pkgs/os-specific/linux/zfs/default.nix
+++ b/pkgs/os-specific/linux/zfs/default.nix
@@ -139,7 +139,7 @@ in
     };
     zfsUnstable = common {
       # comment/uncomment if breaking kernel versions are known
-      incompatibleKernelVersion = null;
+      incompatibleKernelVersion = "4.11";
 
       version = "0.7.0-rc3";
 
diff --git a/pkgs/servers/radicale/default.nix b/pkgs/servers/radicale/default.nix
index a701ad5d833a..e49e399194de 100644
--- a/pkgs/servers/radicale/default.nix
+++ b/pkgs/servers/radicale/default.nix
@@ -28,7 +28,7 @@ pythonPackages.buildPythonApplication rec {
       on mobile phones or computers.
     '';
     license = licenses.gpl3Plus;
-    platform = platforms.all;
+    platforms = platforms.all;
     maintainers = with maintainers; [ edwtjo pSub aneeshusa ];
   };
 }
diff --git a/pkgs/tools/networking/fakeroute/default.nix b/pkgs/tools/networking/fakeroute/default.nix
index 1cb614e88c03..9737108e6acf 100644
--- a/pkgs/tools/networking/fakeroute/default.nix
+++ b/pkgs/tools/networking/fakeroute/default.nix
@@ -16,6 +16,6 @@ stdenv.mkDerivation rec {
     '';
     homepage = https://moxie.org/software/fakeroute/;
     license = licenses.bsd3;
-    platform = platforms.linux;
+    platforms = platforms.linux;
   };
 }
diff --git a/pkgs/tools/networking/mosh/default.nix b/pkgs/tools/networking/mosh/default.nix
index 7ef001971180..5f3975a1df86 100644
--- a/pkgs/tools/networking/mosh/default.nix
+++ b/pkgs/tools/networking/mosh/default.nix
@@ -2,11 +2,11 @@
 , makeWrapper, perl, openssl, autoreconfHook, openssh }:
 
 stdenv.mkDerivation rec {
-  name = "mosh-1.2.6";
+  name = "mosh-1.3.0";
 
   src = fetchurl {
     url = "https://mosh.org/${name}.tar.gz";
-    sha256 = "118fhpm754wpklf1blnlq5xbvrxqml6rdfs3b07wg666zkxvg0ky";
+    sha256 = "0xikz40q873g9ihvz3x6bwkcb9hb8kcnp5wpcmb72pg5c7s143ij";
   };
 
   buildInputs = [ autoreconfHook protobuf ncurses zlib pkgconfig IOTty makeWrapper perl openssl ];
diff --git a/pkgs/tools/security/encryptr/default.nix b/pkgs/tools/security/encryptr/default.nix
index 95d0299e8733..2cf07c63a84a 100644
--- a/pkgs/tools/security/encryptr/default.nix
+++ b/pkgs/tools/security/encryptr/default.nix
@@ -52,6 +52,6 @@ in stdenv.mkDerivation rec {
     description = "Free, private and secure password management tool and e-wallet";
     license = licenses.unfree;
     maintainers = with maintainers; [ guillaumekoenig ];
-    platform = platforms.linux;
+    platforms = platforms.linux;
   };
 }
diff --git a/pkgs/tools/system/efivar/default.nix b/pkgs/tools/system/efivar/default.nix
index 744e34a9c60a..6b062513483d 100644
--- a/pkgs/tools/system/efivar/default.nix
+++ b/pkgs/tools/system/efivar/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "efivar-${version}";
-  version = "31";
+  version = "30";
 
   src = fetchFromGitHub {
     owner = "rhinstaller";
     repo = "efivar";
     rev = version;
-    sha256 = "0dhycikylm87jmds4ii5ygwq59g4sa5sv9mzryjzgqlgppw5arli";
+    sha256 = "1pghj019qr7qpqd9rxfhsr1hm3s0w1hd5cdndpl07vhys8hy4a8a";
   };
 
   nativeBuildInputs = [ pkgconfig ];
diff --git a/pkgs/tools/text/grin/default.nix b/pkgs/tools/text/grin/default.nix
index 7c1df7f8819c..56ea13de40e5 100644
--- a/pkgs/tools/text/grin/default.nix
+++ b/pkgs/tools/text/grin/default.nix
@@ -15,7 +15,7 @@ python2Packages.buildPythonApplication rec {
   meta = {
     homepage = https://pypi.python.org/pypi/grin;
     description = "A grep program configured the way I like it";
-    platform = stdenv.lib.platforms.all;
+    platforms = stdenv.lib.platforms.all;
     maintainers = [ stdenv.lib.maintainers.sjagoe ];
   };
 }
diff --git a/pkgs/tools/text/xml/jing-trang/default.nix b/pkgs/tools/text/xml/jing-trang/default.nix
index 36ff976a6c16..4c4f6ed7e19c 100644
--- a/pkgs/tools/text/xml/jing-trang/default.nix
+++ b/pkgs/tools/text/xml/jing-trang/default.nix
@@ -35,7 +35,7 @@ stdenv.mkDerivation rec {
     # The homepage is www.thaiopensource.com, but it links to googlecode.com
     # for downloads and call it the "project site".
     homepage = http://www.thaiopensource.com/relaxng/jing.html;
-    platforms = platforms.linux;
+    platforms = platforms.unix;
     maintainers = [ maintainers.bjornfor ];
   };
 }
diff --git a/pkgs/tools/text/xsv/default.nix b/pkgs/tools/text/xsv/default.nix
index 388917e68050..9e15649133f6 100644
--- a/pkgs/tools/text/xsv/default.nix
+++ b/pkgs/tools/text/xsv/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, rustPlatform, makeWrapper }:
+{ stdenv, fetchFromGitHub, rustPlatform }:
 
 with rustPlatform;
 
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index 94fedabd562d..7fb271682d0f 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -20,6 +20,7 @@ doNotDisplayTwice rec {
   accounts-qt = libsForQt5.accounts-qt;  # added 2015-12-19
   adobeReader = adobe-reader;
   aircrackng = aircrack-ng; # added 2016-01-14
+  ammonite-repl = ammonite; # added 2017-05-02
   arduino_core = arduino-core;  # added 2015-02-04
   asciidocFull = asciidoc-full;  # added 2014-06-22
   bar = lemonbar;  # added 2015-01-16
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 82c75fecfec2..4b1b331a227b 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -402,7 +402,7 @@ with pkgs;
 
   amazon-glacier-cmd-interface = callPackage ../tools/backup/amazon-glacier-cmd-interface { };
 
-  ammonite-repl = callPackage ../development/tools/ammonite {};
+  ammonite = callPackage ../development/tools/ammonite {};
 
   amtterm = callPackage ../tools/system/amtterm {};
 
@@ -1117,6 +1117,8 @@ with pkgs;
     pythonPackages = python2Packages;
   };
 
+  bfg-repo-cleaner = gitAndTools.bfg-repo-cleaner;
+
   bgs = callPackage ../tools/X11/bgs { };
 
   biber = callPackage ../tools/typesetting/biber {
@@ -4736,7 +4738,7 @@ with pkgs;
 
   xsel = callPackage ../tools/misc/xsel { };
 
-  xsv = callPackages ../tools/text/xsv { };
+  xsv = callPackage ../tools/text/xsv { };
 
   xtreemfs = callPackage ../tools/filesystems/xtreemfs {};
 
@@ -10610,6 +10612,15 @@ with pkgs;
     packages = [];
   };
 
+  rstudioWrapper = callPackage ../development/r-modules/wrapper-rstudio.nix {
+    recommendedPackages = with rPackages; [
+      boot class cluster codetools foreign KernSmooth lattice MASS
+      Matrix mgcv nlme nnet rpart spatial survival
+    ];
+    # Override this attribute to register additional libraries.
+    packages = [];
+  };
+
   rPackages = callPackage ../development/r-modules {
     overrides = (config.rPackageOverrides or (p: {})) pkgs;
   };
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 18d8fa92c203..c1b4def764ce 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -3695,22 +3695,7 @@ in {
     };
   };
 
-  certifi = buildPythonPackage rec {
-    name = "certifi-${version}";
-    version = "2017.1.23";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/c/certifi/${name}.tar.gz";
-      sha256 = "1klrzl3hgvcf2mjk00g0k3kk1p2z27vzwnxivwar4vhjmjvpz1w1";
-    };
-
-    meta = {
-      homepage = http://certifi.io/;
-      description = "Python package for providing Mozilla's CA Bundle";
-      license = licenses.isc;
-      maintainers = with maintainers; [ koral ];
-    };
-  };
+  certifi = callPackage ../development/python-modules/certifi { };
 
   characteristic = buildPythonPackage rec {
     name = "characteristic-14.1.0";
@@ -5439,8 +5424,8 @@ in {
       sha256 = "03c2qc42r4bczyw93gd7n0qi1h1jfhw7fnbhi33c3vp1hs81gm2k";
     };
 
-   buildInputs = with self; [ pytest_xdist virtualenv process-tests ];
-   propagatedBuildInputs = with self; [ pytest coverage ];
+   propagatedBuildInputs = with self; [ coverage ];
+   buildInputs = with self; [ pytest covCore virtualenv process-tests helper ];
 
    # xdist related tests fail with the following error
    # OSError: [Errno 13] Permission denied: 'py/_code'
@@ -16688,6 +16673,11 @@ in {
 
     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 {
@@ -19858,20 +19848,7 @@ in {
     };
    });
 
-  pydot = buildPythonPackage rec {
-    name = "pydot-1.2.3";
-    disabled = isPy3k;
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/p/pydot/${name}.tar.gz";
-      sha256 = "edb5d3f249f97fbd9c4bb16959e61bc32ecf40eee1a9f6d27abe8d01c0a73502";
-    };
-    propagatedBuildInputs = with self; [pyparsing pkgs.graphviz];
-    meta = {
-      homepage = https://github.com/erocarrera/pydot;
-      description = "Allows to easily create both directed and non directed graphs from Python";
-    };
-  };
+  pydot = callPackage ../development/python-modules/pydot { };
 
   pydot_ng = buildPythonPackage rec {
     name = "pydot_ng-1.0.0";
@@ -21741,6 +21718,8 @@ in {
       homepage = "http://github.com/diyan/pywinrm/";
       description = "Python library for Windows Remote Management";
       license = licenses.mit;
+      # error: libgssapi_krb5.so: cannot open shared object file: No such file or directory
+      broken = true; #
     };
   };
 
@@ -23319,11 +23298,15 @@ in {
       url = "mirror://pypi/s/${pname}/${name}.tar.gz";
       sha256 = "14220f8f761c48ba1e2526f087195077cf54fad7098b382ce220422f0ff59b12";
     };
-    buildInputs = with self; [ pytest_29 virtualenv pytestrunner pytest-virtualenv ];
+    buildInputs = with self; [ pytest virtualenv pytestrunner pytest-virtualenv ];
     propagatedBuildInputs = with self; [ twisted pathlib2 ];
     postPatch = ''
       sed -i '12,$d' tests/test_main.py
     '';
+
+    # Couldn't get tests working
+    doCheck = false;
+
     meta = {
       description = "Setuptools plugin that makes unit tests execute with trial instead of pyunit.";
       homepage = "https://github.com/rutsky/setuptools-trial";
@@ -23768,25 +23751,7 @@ in {
     };
   };
 
-  stevedore = buildPythonPackage rec {
-    name = "stevedore-1.7.0";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/s/stevedore/${name}.tar.gz";
-      sha256 = "149pjc0c3z6khjisn4yil3f94qjnzwafz093wc8rrzbw828qdkv8";
-    };
-
-    doCheck = false;
-
-    buildInputs = with self; [ oslosphinx ];
-    propagatedBuildInputs = with self; [ pbr six argparse ];
-
-    meta = {
-      description = "Manage dynamic plugins for Python applications";
-      homepage = "https://pypi.python.org/pypi/stevedore";
-      license = licenses.asl20;
-    };
-  };
+  stevedore = callPackage ../development/python-modules/stevedore {};
 
   Theano = self.TheanoWithoutCuda;
 
@@ -26845,9 +26810,7 @@ EOF
     };
   });
 
-  magic-wormhole = callPackage ../development/python-modules/magic-wormhole {
-    pythonPackages = self;
-  };
+  magic-wormhole = callPackage ../development/python-modules/magic-wormhole { };
 
   wsgiproxy2 = buildPythonPackage rec {
     name = "WSGIProxy2-0.4.2";
@@ -31348,6 +31311,7 @@ EOF
       rev = "8eab90908f2a3adcc414347566f4434636202344";
       sha256 = "18n14ha2d3j3ghg2f2aqnf2mks94nn7ma9ii7vkiwcay93zm82cf";
     };
+    disabled = isPy3k; # Judging from SyntaxError
     buildInputs = with self; [ pkgs.swig1 pkgs.coin3d pkgs.soqt pkgs.mesa pkgs.xorg.libXi ];
   };