Merge master into staging-next

32 files changed, 274 insertions, 186 deletions

diff --git a/pkgs/development/compilers/binaryen/default.nix b/pkgs/development/compilers/binaryen/default.nix
index 7c3203fe62e..8ebed6f4b5b 100644
--- a/pkgs/development/compilers/binaryen/default.nix
+++ b/pkgs/development/compilers/binaryen/default.nix
@@ -1,11 +1,11 @@
 { stdenv, cmake, python, fetchFromGitHub, emscriptenRev ? null }:
 
 let
-  defaultVersion = "83";
+  defaultVersion = "84";
 
   # Map from git revs to SHA256 hashes
   sha256s = {
-    "version_83" = "0vggd9n6anfxsdk4kiyylysi4cfm2rp39f66sq9zkg0h7vw5x5sm";
+    "version_84" = "189zqc5gp8fm7clsgby9h2s758ijil7ma4liwbf81wnwkb4kqxc0";
     "1.38.28" = "172s7y5f38736ic8ri3mnbdqcrkadd40a26cxcfwbscc53phl11v";
   };
 in
diff --git a/pkgs/development/compilers/llvm/7/llvm.nix b/pkgs/development/compilers/llvm/7/llvm.nix
index c288fd3e2a5..d3d9a4c506d 100644
--- a/pkgs/development/compilers/llvm/7/llvm.nix
+++ b/pkgs/development/compilers/llvm/7/llvm.nix
@@ -84,6 +84,14 @@ in stdenv.mkDerivation (rec {
     substituteInPlace unittests/Support/CMakeLists.txt \
       --replace "add_subdirectory(DynamicLibrary)" ""
     rm unittests/Support/DynamicLibrary/DynamicLibraryTest.cpp
+  '' + optionalString stdenv.hostPlatform.isAarch32 ''
+    # skip failing X86 test cases on armv7l
+    rm test/DebugInfo/X86/debug_addr.ll
+    rm test/tools/llvm-dwarfdump/X86/debug_addr.s
+    rm test/tools/llvm-dwarfdump/X86/debug_addr_address_size_mismatch.s
+    rm test/tools/llvm-dwarfdump/X86/debug_addr_dwarf4.s
+    rm test/tools/llvm-dwarfdump/X86/debug_addr_unsupported_version.s
+    rm test/tools/llvm-dwarfdump/X86/debug_addr_version_mismatch.s
   '' + ''
     patchShebangs test/BugPoint/compile-custom.ll.py
   '';
diff --git a/pkgs/development/compilers/orc/default.nix b/pkgs/development/compilers/orc/default.nix
index 83869e1b621..4540a301610 100644
--- a/pkgs/development/compilers/orc/default.nix
+++ b/pkgs/development/compilers/orc/default.nix
@@ -15,8 +15,9 @@ stdenv.mkDerivation rec {
     sed "/^toolsdir=/ctoolsdir=$dev/bin" -i "$dev"/lib/pkgconfig/orc*.pc
   '';
 
-  # https://bugzilla.gnome.org/show_bug.cgi?id=728129#c15
-  doCheck = stdenv.hostPlatform.system != "i686-linux"; # not sure about cross-compiling
+  # i686   https://gitlab.freedesktop.org/gstreamer/orc/issues/18
+  # armv7l https://gitlab.freedesktop.org/gstreamer/orc/issues/9
+  doCheck = (!stdenv.hostPlatform.isi686 && !stdenv.hostPlatform.isAarch32);
 
   meta = with stdenv.lib; {
     description = "The Oil Runtime Compiler";
diff --git a/pkgs/development/haskell-modules/configuration-common.nix b/pkgs/development/haskell-modules/configuration-common.nix
index 26e0f56d506..4028859e338 100644
--- a/pkgs/development/haskell-modules/configuration-common.nix
+++ b/pkgs/development/haskell-modules/configuration-common.nix
@@ -1181,7 +1181,6 @@ self: super: {
   # Jailbreak tasty < 1.2: https://github.com/phadej/tdigest/issues/30
   tdigest = doJailbreak super.tdigest; # until tdigest > 0.2.1
   these = doJailbreak super.these; # until these >= 0.7.6
-  insert-ordered-containers = appendPatch super.insert-ordered-containers ./patches/insert-ordered-containers-fix-test.patch;
 
   uri-bytestring = appendPatch super.uri-bytestring (pkgs.fetchpatch {
     url = "https://github.com/Soostone/uri-bytestring/commit/e5c5602a97160a6a6304a24947e33e47c9155460.patch";
diff --git a/pkgs/development/haskell-modules/patches/insert-ordered-containers-fix-test.patch b/pkgs/development/haskell-modules/patches/insert-ordered-containers-fix-test.patch
deleted file mode 100644
index 1e9ac5aa66a..00000000000
--- a/pkgs/development/haskell-modules/patches/insert-ordered-containers-fix-test.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-diff --git a/insert-ordered-containers.cabal b/insert-ordered-containers.cabal
-index 0e8923a..bfbbec4 100644
---- a/insert-ordered-containers.cabal
-+++ b/insert-ordered-containers.cabal
-@@ -21,8 +21,8 @@ tested-with:
-   GHC==7.10.3,
-   GHC==8.0.1,
-   GHC==8.2.2,
--  GHC==8.4.3,
--  GHC==8.6.1
-+  GHC==8.4.4,
-+  GHC==8.6.3
- 
- extra-source-files:
-     CHANGELOG.md
-@@ -70,7 +70,7 @@ test-suite ins-ord-containers-tests
-     , unordered-containers
-     , base
-     , insert-ordered-containers
--    , tasty             >= 0.10.1.2 && <1.2
-+    , tasty             >= 0.10.1.2 && <1.3
-     , tasty-quickcheck  >= 0.8.3.2  && <0.11
-     , QuickCheck        >=2.7.6     && <2.13
-   default-language: Haskell2010
-
diff --git a/pkgs/development/interpreters/erlang/R21.nix b/pkgs/development/interpreters/erlang/R21.nix
index 8c4e1561ec0..60eb6c8a6a5 100644
--- a/pkgs/development/interpreters/erlang/R21.nix
+++ b/pkgs/development/interpreters/erlang/R21.nix
@@ -1,8 +1,8 @@
 { mkDerivation }:
 
 mkDerivation rec {
-  version = "21.3.7.1";
-  sha256 = "03vbp22vwra3zz76q3sjv23lmic60gi96a7dncry8whbfp4i4j8a";
+  version = "21.3.8.3";
+  sha256 = "1szybirrcpqsl2nmlmpbkxjqnm6i7l7bma87m5cpwi0kpvlxwmcw";
 
   prePatch = ''
     substituteInPlace configure.in --replace '`sw_vers -productVersion`' '10.10'
diff --git a/pkgs/development/libraries/beignet/clang_llvm.patch b/pkgs/development/libraries/beignet/clang_llvm.patch
index 88876f157cd..bcdad510e10 100644
--- a/pkgs/development/libraries/beignet/clang_llvm.patch
+++ b/pkgs/development/libraries/beignet/clang_llvm.patch
@@ -47,16 +47,3 @@ index a148321..96cafb8 100644
    set(CLANG_LIBRARIES ${CLANG_LIBRARIES} ${CLANG_LIB})
  	unset(CLANG_LIB CACHE)
  endmacro()
-diff --git a/./CMakeLists.txt b/../Beignet-1.1.2-Source_new/CMakeLists.txt
-index 88985d7..01bca9e 100644
---- a/./CMakeLists.txt
-+++ b/../Beignet-1.1.2-Source_new/CMakeLists.txt
-@@ -205,7 +205,7 @@ IF(OCLIcd_FOUND)
-     "intel-beignet.icd.in"
-     "${ICD_FILE_NAME}"
-   )
--  install (FILES ${CMAKE_CURRENT_BINARY_DIR}/${ICD_FILE_NAME} DESTINATION /etc/OpenCL/vendors)
-+  install (FILES ${CMAKE_CURRENT_BINARY_DIR}/${ICD_FILE_NAME} DESTINATION ${CMAKE_INSTALL_PREFIX}/etc/OpenCL/vendors)
- ELSE(OCLIcd_FOUND)
-   MESSAGE(STATUS "Looking for OCL ICD header file - not found")
- ENDIF(OCLIcd_FOUND)
diff --git a/pkgs/development/libraries/beignet/default.nix b/pkgs/development/libraries/beignet/default.nix
index ba6fc7cb541..05ff5593205 100644
--- a/pkgs/development/libraries/beignet/default.nix
+++ b/pkgs/development/libraries/beignet/default.nix
@@ -1,5 +1,5 @@
 { stdenv
-, fetchurl
+, fetchFromGitHub
 , cmake
 , pkgconfig
 , clang-unwrapped
@@ -19,11 +19,13 @@
 
 stdenv.mkDerivation rec {
   name = "beignet-${version}";
-  version = "1.3.2";
+  version = "unstable-2018.08.20";
 
-  src = fetchurl {
-    url = "https://01.org/sites/default/files/${name}-source.tar.gz"; 
-    sha256 = "0hqb04jhjjslnmi3fnpzphanz84zywwkyw2sjr1k5qlx2jxfsmf5";
+  src = fetchFromGitHub {
+    owner  = "intel";
+    repo   = "beignet";
+    rev    = "fc5f430cb7b7a8f694d86acbb038bd5b38ec389c";
+    sha256 = "1z64v69w7f52jrskh1jfyh1x46mzfhjrqxj9hhgzh3xxv9yla32h";
   };
 
   patches = [ ./clang_llvm.patch ];
@@ -31,6 +33,7 @@ stdenv.mkDerivation rec {
   enableParallelBuilding = true;
 
   postPatch = ''
+    substituteInPlace CMakeLists.txt --replace /etc/OpenCL/vendors "\''${CMAKE_INSTALL_PREFIX}/etc/OpenCL/vendors"
     patchShebangs src/git_sha1.sh
   '';
 
@@ -101,8 +104,8 @@ stdenv.mkDerivation rec {
     homepage = https://cgit.freedesktop.org/beignet/;
     description = "OpenCL Library for Intel Ivy Bridge and newer GPUs";
     longDescription = ''
-      The package provides an open source implementation of the OpenCL specification for Intel GPUs. 
-      It supports the Intel OpenCL runtime library and compiler. 
+      The package provides an open source implementation of the OpenCL specification for Intel GPUs.
+      It supports the Intel OpenCL runtime library and compiler.
     '';
     license = licenses.lgpl21Plus;
     maintainers = with maintainers; [ artuuge zimbatm ];
diff --git a/pkgs/development/libraries/faad2/default.nix b/pkgs/development/libraries/faad2/default.nix
index 50323846e98..e7e4835d2ed 100644
--- a/pkgs/development/libraries/faad2/default.nix
+++ b/pkgs/development/libraries/faad2/default.nix
@@ -12,6 +12,30 @@ stdenv.mkDerivation rec {
     sha256 = "1db37ydb6mxhshbayvirm5vz6j361bjim4nkpwjyhmy4ddfinmhl";
   };
 
+  patches = let
+    fp = { ver ? "2.8.8-3", pname, name ? (pname + ".patch"), sha256 }: fetchurl {
+      url = "https://salsa.debian.org/multimedia-team/faad2/raw/debian/${ver}"
+          + "/debian/patches/${pname}.patch?inline=false";
+      inherit name sha256;
+    };
+  in [
+    (fp {
+      # critical bug addressed in vlc 3.0.7 (but we use system-provided faad)
+      pname = "0004-Fix-a-couple-buffer-overflows";
+      sha256 = "1mwycdfagz6wpda9j3cp7lf93crgacpa8rwr58p3x0i5cirnnmwq";
+    })
+    (fp {
+      name = "CVE-2018-20362.patch";
+      pname = "0009-syntax.c-check-for-syntax-element-inconsistencies";
+      sha256 = "1z849l5qyvhyn5pvm6r07fa50nrn8nsqnrka2nnzgkhxlhvzpa81";
+    })
+    (fp {
+      name = "CVE-2018-20194.patch";
+      pname = "0010-sbr_hfadj-sanitize-frequency-band-borders";
+      sha256 = "1b1kbz4mv0zhpq8h3djnvqafh1gn12nikk9v3jrxyryywacirah4";
+    })
+  ];
+
   configureFlags = []
     ++ optional drmSupport "--with-drm";
 
diff --git a/pkgs/development/libraries/hwloc/default.nix b/pkgs/development/libraries/hwloc/default.nix
index 81e30d675d2..5866d6b8fed 100644
--- a/pkgs/development/libraries/hwloc/default.nix
+++ b/pkgs/development/libraries/hwloc/default.nix
@@ -7,7 +7,7 @@ assert x11Support -> libX11 != null && cairo != null;
 with stdenv.lib;
 
 let
-  version = "2.0.3";
+  version = "2.0.4";
   versmm = versions.major version + "." + versions.minor version;
   name = "hwloc-${version}";
 
@@ -16,7 +16,7 @@ in stdenv.mkDerivation {
 
   src = fetchurl {
     url = "http://www.open-mpi.org/software/hwloc/v${versmm}/downloads/${name}.tar.bz2";
-    sha256 = "09f7ajak8wv5issr0hw72vs3jkldc7crcc7z5fd34sspkvrsm4z3";
+    sha256 = "1aa7s208gdijk19vvzzahyl8pglk1va3yd6kdbpfa5pz5ms0ag35";
   };
 
   configureFlags = [
diff --git a/pkgs/development/libraries/liburcu/default.nix b/pkgs/development/libraries/liburcu/default.nix
index 0cc18d82720..0cc1b0d08f9 100644
--- a/pkgs/development/libraries/liburcu/default.nix
+++ b/pkgs/development/libraries/liburcu/default.nix
@@ -1,12 +1,12 @@
 { stdenv, fetchurl, perl }:
 
 stdenv.mkDerivation rec {
-  version = "0.10.2";
+  version = "0.11.0";
   name = "liburcu-${version}";
 
   src = fetchurl {
     url = "https://lttng.org/files/urcu/userspace-rcu-${version}.tar.bz2";
-    sha256 = "1k31faqz9plx5dwxq8g1fnczxda1is4s1x4ph0gjrq3gmy6qixmk";
+    sha256 = "1rxk5vbkbmqlsnjnvkjz0pkx2076mqnq6jzblpmz8rk29x66kx8s";
   };
 
   checkInputs = [ perl ];
diff --git a/pkgs/development/libraries/mpich/default.nix b/pkgs/development/libraries/mpich/default.nix
index ffe6b5edf96..1c6b8df1511 100644
--- a/pkgs/development/libraries/mpich/default.nix
+++ b/pkgs/development/libraries/mpich/default.nix
@@ -4,11 +4,11 @@
 
 stdenv.mkDerivation  rec {
   name = "mpich-${version}";
-  version = "3.3";
+  version = "3.3.1";
 
   src = fetchurl {
     url = "https://www.mpich.org/static/downloads/${version}/mpich-${version}.tar.gz";
-    sha256 = "02zs118q9n4xz9qnfc24i2r84vnzgnwnyyqanfv03lf3wqpy17ij";
+    sha256 = "1raism1r4jsx4cybc9ddyr1xkccbxm0l8j3ryrw8kslfkkr1wmgy";
   };
 
   configureFlags = [
diff --git a/pkgs/development/libraries/nss/default.nix b/pkgs/development/libraries/nss/default.nix
index 87bc1a16f23..f3fc4caf315 100644
--- a/pkgs/development/libraries/nss/default.nix
+++ b/pkgs/development/libraries/nss/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, nspr, perl, zlib, sqlite, fixDarwinDylibNames }:
+{ stdenv, fetchurl, nspr, perl, zlib, sqlite, fixDarwinDylibNames, buildPackages }:
 
 let
   nssPEM = fetchurl {
@@ -17,7 +17,11 @@ in stdenv.mkDerivation rec {
     sha256 = "1zvabgxlyvz3fnv4w89y4a5qkscjmm88naf929dgvvgfnrchwqm5";
   };
 
-  buildInputs = [ perl zlib sqlite ]
+  depsBuildBuild = [ buildPackages.stdenv.cc ];
+
+  nativeBuildInputs = [ perl ];
+
+  buildInputs = [ zlib sqlite ]
     ++ stdenv.lib.optional stdenv.isDarwin fixDarwinDylibNames;
 
   propagatedBuildInputs = [ nspr ];
@@ -43,7 +47,9 @@ in stdenv.mkDerivation rec {
 
   preConfigure = "cd nss";
 
-  makeFlags = [
+  makeFlags = let
+    cpu = stdenv.hostPlatform.parsed.cpu.name;
+  in [
     "NSPR_INCLUDE_DIR=${nspr.dev}/include"
     "NSPR_LIB_DIR=${nspr.out}/lib"
     "NSDISTMODE=copy"
@@ -52,6 +58,12 @@ in stdenv.mkDerivation rec {
     "NSS_ENABLE_ECC=1"
     "USE_SYSTEM_ZLIB=1"
     "NSS_USE_SYSTEM_SQLITE=1"
+    "NATIVE_CC=${buildPackages.stdenv.cc}/bin/cc"
+  ] ++ stdenv.lib.optional (stdenv.hostPlatform != stdenv.buildPlatform) [
+    "OS_TEST=${cpu}"
+    "CPU_ARCH=${cpu}"
+    "CROSS_COMPILE=1"
+    "NSS_DISABLE_GTESTS=1" # don't want to build tests when cross-compiling
   ] ++ stdenv.lib.optional stdenv.is64bit "USE_64=1"
     ++ stdenv.lib.optional stdenv.isDarwin "CCC=clang++";
 
@@ -95,7 +107,10 @@ in stdenv.mkDerivation rec {
     chmod 0755 $out/bin/nss-config
   '';
 
-  postFixup = ''
+  postFixup = let
+    isCross = stdenv.hostPlatform != stdenv.buildPlatform;
+    nss = if isCross then buildPackages.nss.tools else "$out";
+  in ''
     for libname in freebl3 nssdbm3 softokn3
     do '' +
     (if stdenv.isDarwin
@@ -106,7 +121,7 @@ in stdenv.mkDerivation rec {
        libfile="$out/lib/lib$libname.so"
        LD_LIBRARY_PATH=$out/lib:${nspr.out}/lib \
      '') + ''
-        $out/bin/shlibsign -v -i "$libfile"
+        ${nss}/bin/shlibsign -v -i "$libfile"
     done
 
     moveToOutput bin "$tools"
diff --git a/pkgs/development/libraries/physics/rivet/default.nix b/pkgs/development/libraries/physics/rivet/default.nix
index 54bf1cc442b..40ccd8cfd20 100644
--- a/pkgs/development/libraries/physics/rivet/default.nix
+++ b/pkgs/development/libraries/physics/rivet/default.nix
@@ -17,12 +17,16 @@ stdenv.mkDerivation rec {
     scheme-basic
     collection-pstricks
     collection-fontsrecommended
+    l3kernel
+    l3packages
     mathastext
     pgf
     relsize
     sfmath
+    siunitx
     xcolor
     xkeyval
+    xstring
     ;};
   buildInputs = [ hepmc imagemagick python2 latex makeWrapper ];
   propagatedBuildInputs = [ fastjet ghostscript gsl yoda ];
diff --git a/pkgs/development/python-modules/acme-tiny/default.nix b/pkgs/development/python-modules/acme-tiny/default.nix
index 759ed2086fc..e212e83c270 100644
--- a/pkgs/development/python-modules/acme-tiny/default.nix
+++ b/pkgs/development/python-modules/acme-tiny/default.nix
@@ -1,34 +1,26 @@
-{ stdenv, buildPythonPackage, fetchFromGitHub
-, python, openssl }:
+{ stdenv, buildPythonPackage, fetchPypi, setuptools_scm, fusepy, fuse
+, openssl }:
 
 buildPythonPackage rec {
   pname = "acme-tiny";
-  version = "2016-03-26";
+  version = "4.0.4";
 
-  src = fetchFromGitHub {
-    sha256 = "0ngmr3kxcvlqa9mrv3gx0rg4r67xvdjplqfminxliri3ipak853g";
-    rev = "7a5a2558c8d6e5ab2a59b9fec9633d9e63127971";
-    repo = "acme-tiny";
-    owner = "diafygi";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0vqlmvk34jgvgx3qdsh50q7m4aiy02786jyjjcq45dcws7a4f9f1";
   };
 
-  # source doesn't have any python "packaging" as such
-  configurePhase = " ";
-  buildPhase = " ";
-  # the tests are... complex
-  doCheck = false;
-
   patchPhase = ''
-    substituteInPlace acme_tiny.py --replace "openssl" "${openssl.bin}/bin/openssl"
+    substituteInPlace acme_tiny.py --replace '"openssl"' '"${openssl.bin}/bin/openssl"'
+    substituteInPlace tests/monkey.py --replace '"openssl"' '"${openssl.bin}/bin/openssl"'
+    substituteInPlace tests/test_module.py --replace '"openssl"' '"${openssl.bin}/bin/openssl"'
+    substituteInPlace tests/monkey.py --replace /etc/ssl/openssl.cnf ${openssl.out}/etc/ssl/openssl.cnf
   '';
 
-  installPhase = ''
-    mkdir -p $out/${python.sitePackages}/
-    cp acme_tiny.py $out/${python.sitePackages}/
-    mkdir -p $out/bin
-    ln -s $out/${python.sitePackages}/acme_tiny.py $out/bin/acme_tiny
-    chmod +x $out/bin/acme_tiny
-  '';
+  buildInputs = [ setuptools_scm ];
+  checkInputs = [ fusepy fuse ];
+
+  doCheck = false; # seems to hang, not sure
 
   meta = with stdenv.lib; {
     description = "A tiny script to issue and renew TLS certs from Let's Encrypt";
diff --git a/pkgs/development/python-modules/cmd2/old.nix b/pkgs/development/python-modules/cmd2/old.nix
deleted file mode 100644
index 8f75170c58c..00000000000
--- a/pkgs/development/python-modules/cmd2/old.nix
+++ /dev/null
@@ -1,50 +0,0 @@
-{ stdenv, buildPythonPackage, pythonOlder
-, pyperclip, six, pyparsing, vim
-, contextlib2 ? null, subprocess32 ? null
-, pytest, mock, which, fetchFromGitHub, glibcLocales
-, runtimeShell
-}:
-buildPythonPackage rec {
-  pname = "cmd2";
-  version = "0.8.0";
-
-  src = fetchFromGitHub {
-    owner = "python-cmd2";
-    repo = "cmd2";
-    rev = version;
-    sha256 = "0nw2b7n7zg51bc3glxw0l9fn91mwjnjshklhmxhyvjbsg7khf64z";
-  };
-
-  LC_ALL="en_US.UTF-8";
-
-  postPatch = stdenv.lib.optional stdenv.isDarwin ''
-    # Fake the impure dependencies pbpaste and pbcopy
-    mkdir bin
-    echo '#${runtimeShell}' > bin/pbpaste
-    echo '#${runtimeShell}' > bin/pbcopy
-    chmod +x bin/{pbcopy,pbpaste}
-    export PATH=$(realpath bin):$PATH
-  '';
-
-  checkInputs= [ pytest mock which vim glibcLocales ];
-  checkPhase = ''
-    # test_path_completion_user_expansion might be fixed in the next release
-    py.test -k 'not test_path_completion_user_expansion'
-  '';
-  doCheck = !stdenv.isDarwin;
-
-  propagatedBuildInputs = [
-    pyperclip
-    six
-    pyparsing
-  ]
-  ++ stdenv.lib.optional (pythonOlder "3.5") contextlib2
-  ++ stdenv.lib.optional (pythonOlder "3.0") subprocess32
-  ;
-
-  meta = with stdenv.lib; {
-    description = "Enhancements for standard library's cmd module";
-    homepage = https://github.com/python-cmd2/cmd2;
-    maintainers = with maintainers; [ teto ];
-  };
-}
diff --git a/pkgs/development/python-modules/cx_oracle/default.nix b/pkgs/development/python-modules/cx_oracle/default.nix
index ca28f231831..5708bf12d6b 100644
--- a/pkgs/development/python-modules/cx_oracle/default.nix
+++ b/pkgs/development/python-modules/cx_oracle/default.nix
@@ -22,7 +22,7 @@ buildPythonPackage rec {
   meta = with stdenv.lib; {
     description = "Python interface to Oracle";
     homepage = "https://oracle.github.io/python-cx_Oracle";
-    license = licenses.bsdOriginal;
+    license = licenses.bsd3;
     maintainers = with maintainers; [ y0no ];
   };
 }
diff --git a/pkgs/development/python-modules/http-ece/default.nix b/pkgs/development/python-modules/http-ece/default.nix
new file mode 100644
index 00000000000..1f50608d3d1
--- /dev/null
+++ b/pkgs/development/python-modules/http-ece/default.nix
@@ -0,0 +1,24 @@
+{ lib, fetchPypi, buildPythonPackage
+, coverage, flake8, mock, nose
+, cryptography }:
+
+buildPythonPackage rec {
+  pname = "http_ece";
+  version = "1.1.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1y5ln09ji4dwpzhxr77cggk02kghq7lql60a6969a5n2lwpvqblk";
+  };
+
+  propagatedBuildInputs = [ cryptography ];
+
+  checkInputs = [ coverage flake8 mock nose ];
+
+  meta = with lib; {
+    description = "Encipher HTTP Messages";
+    homepage = https://github.com/martinthomson/encrypted-content-encoding;
+    license = licenses.mit;
+    maintainers = with maintainers; [ peterhoeg ];
+  };
+}
diff --git a/pkgs/development/python-modules/nltk/default.nix b/pkgs/development/python-modules/nltk/default.nix
index 9ae4f00b495..2c6858915ce 100644
--- a/pkgs/development/python-modules/nltk/default.nix
+++ b/pkgs/development/python-modules/nltk/default.nix
@@ -1,26 +1,17 @@
 { fetchPypi, buildPythonPackage, lib, six, singledispatch, isPy3k, fetchpatch }:
 
 buildPythonPackage rec {
-  version = "3.4";
+  version = "3.4.3";
   pname = "nltk";
 
   src = fetchPypi {
     inherit pname version;
     extension = "zip";
-    sha256 = "286f6797204ffdb52525a1d21ec0a221ec68b8e3fa4f2d25f412ac8e63c70e8d";
+    sha256 = "1cjkv4jmmlr0w4qi399ncgb6lp41mb9i352934288wh9xad15mqj";
   };
 
   propagatedBuildInputs = [ six ] ++ lib.optional (!isPy3k) singledispatch;
 
-  # TODO: remove patch during update to new version
-  patches = [
-    (fetchpatch {
-      url = https://github.com/nltk/nltk/commit/3966111cbf2f35fb86082b2f12acd90d75e9b8bb.patch;
-      includes = [ "setup.py" ];
-      sha256 = "1sxafnvf6nzv6d996xc1rys06x62s36swgpfqhsyh6l1lj7y38jw";
-    })
-  ];
-
   # Tests require some data, the downloading of which is impure. It would
   # probably make sense to make the data another derivation, but then feeding
   # that into the tests (given that we need nltk itself to download the data,
diff --git a/pkgs/development/python-modules/py-vapid/default.nix b/pkgs/development/python-modules/py-vapid/default.nix
new file mode 100644
index 00000000000..d5af1c1c33d
--- /dev/null
+++ b/pkgs/development/python-modules/py-vapid/default.nix
@@ -0,0 +1,24 @@
+{ lib, buildPythonPackage, fetchPypi
+, flake8, mock, nose, pytest
+, cryptography
+}:
+
+buildPythonPackage rec {
+  pname = "py-vapid";
+  version = "1.5.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1b3g4ljkpi6ka5n63bl5y47r3qhxjmr6qfamqwxnmna2567b5las";
+  };
+
+  propagatedBuildInputs = [ cryptography ];
+
+  checkInputs = [ flake8 mock nose pytest ];
+
+  meta = with lib; {
+    description = "VAPID is a voluntary standard for WebPush subscription providers";
+    homepage = https://github.com/mozilla-services/vapid;
+    license = licenses.mpl20;
+  };
+}
diff --git a/pkgs/development/python-modules/pywebpush/default.nix b/pkgs/development/python-modules/pywebpush/default.nix
new file mode 100644
index 00000000000..c9077c7a17c
--- /dev/null
+++ b/pkgs/development/python-modules/pywebpush/default.nix
@@ -0,0 +1,28 @@
+{ lib, fetchPypi, buildPythonPackage
+, coverage, flake8, mock, nose
+, http-ece, py-vapid, requests }:
+
+buildPythonPackage rec {
+  pname = "pywebpush";
+  version = "1.9.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "03qkijz56fx7p8405sknw2wji4pfj5knajk2lmj9y58mjxydbpp3";
+  };
+
+  propagatedBuildInputs = [
+    http-ece py-vapid requests
+  ];
+
+  checkInputs = [
+    coverage flake8 mock nose
+  ];
+
+  meta = with lib; {
+    description = "Webpush Data encryption library for Python";
+    homepage = https://github.com/web-push-libs/pywebpush;
+    license = licenses.mpl20;
+    maintainers = with maintainers; [ peterhoeg ];
+  };
+}
diff --git a/pkgs/development/python-modules/wsproto/default.nix b/pkgs/development/python-modules/wsproto/default.nix
index ca9872bfbf0..36aaf0ec8ce 100644
--- a/pkgs/development/python-modules/wsproto/default.nix
+++ b/pkgs/development/python-modules/wsproto/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "wsproto";
-  version = "0.14.0";
+  version = "0.14.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1p24dmym6pfsqsyxps6m2cxfl36cmkri0kdy5y5q7s300j3xmhsm";
+    sha256 = "051s127qb5dladxa14n9nqajwq7xki1dz1was5r5v9df5a0jq8pd";
   };
 
   propagatedBuildInputs = [ h11 enum34 ];
diff --git a/pkgs/development/tools/analysis/flow/default.nix b/pkgs/development/tools/analysis/flow/default.nix
index dfe1a6a10c7..ac9680c404c 100644
--- a/pkgs/development/tools/analysis/flow/default.nix
+++ b/pkgs/development/tools/analysis/flow/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "flow";
-  version = "0.100.0";
+  version = "0.101.0";
 
   src = fetchFromGitHub {
     owner  = "facebook";
     repo   = "flow";
     rev    = "refs/tags/v${version}";
-    sha256 = "10i2r0w979lhqgkq25s1a7j5vxlnjmr2w7nknhc1cvfp3z17k9ay";
+    sha256 = "09m9arpb26fqwc16f2zgjgkrlmjg0gj55zd9rfv2s8x1l0lrx5z6";
   };
 
   installPhase = ''
diff --git a/pkgs/development/tools/build-managers/bear/ignore_wrapper.patch b/pkgs/development/tools/build-managers/bear/ignore_wrapper.patch
index f70e3811f65..8effc723bba 100644
--- a/pkgs/development/tools/build-managers/bear/ignore_wrapper.patch
+++ b/pkgs/development/tools/build-managers/bear/ignore_wrapper.patch
@@ -1,6 +1,6 @@
---- Bear-2.3.11-src/bear/main.py.in	1970-01-01 01:00:01.000000000 +0100
-+++ Bear-2.3.11-src-patch/bear/main.py.in	1970-01-01 01:00:01.000000000 +0100
-@@ -49,6 +49,7 @@
+--- a/bear/main.py.in
++++ b/bear/main.py.in
+@@ -49,6 +49,7 @@ import tempfile
  import shutil
  import contextlib
  import logging
@@ -8,16 +8,20 @@
  
  # Map of ignored compiler option for the creation of a compilation database.
  # This map is used in _split_command method, which classifies the parameters
-@@ -540,7 +541,11 @@
-                 any(pattern.match(cmd) for pattern in COMPILER_PATTERNS_CXX)
+@@ -569,7 +570,15 @@ class Compilation:
+                 (compiler, language, rest of the command) otherwise """
  
          if command:  # not empty list will allow to index '0' and '1:'
 -            executable = os.path.basename(command[0])  # type: str
-+            absolute_executable = os.path.realpath(find_executable(command[0]))
-+            if 'wrapper' in absolute_executable:
-+                return None
-+
-+            executable = os.path.basename(absolute_executable) # type: str
++            executable_file = find_executable(command[0])
++            if executable_file:
++                absolute_executable = os.path.realpath(executable_file)
++                # Ignore Nix wrappers.
++                if 'wrapper' in absolute_executable:
++                    return None
++                executable = os.path.basename(absolute_executable)
++            else:
++                executable = os.path.basename(command[0])
              parameters = command[1:]  # type: List[str]
              # 'wrapper' 'parameters' and
              # 'wrapper' 'compiler' 'parameters' are valid.
\ No newline at end of file
diff --git a/pkgs/development/tools/build-managers/rebar3/default.nix b/pkgs/development/tools/build-managers/rebar3/default.nix
index 60b6fd1953e..341585744a6 100644
--- a/pkgs/development/tools/build-managers/rebar3/default.nix
+++ b/pkgs/development/tools/build-managers/rebar3/default.nix
@@ -3,7 +3,7 @@
   tree, hexRegistrySnapshot }:
 
 let
-  version = "3.10.0";
+  version = "3.11.1";
 
   bootstrapper = ./rebar3-nix-bootstrap;
 
@@ -74,10 +74,10 @@ stdenv.mkDerivation rec {
   inherit version erlang;
 
   src = fetchFromGitHub {
-    owner = "rebar";
+    owner = "erlang";
     repo = pname;
     rev = version;
-    sha256 = "1p34kfkrdmsixg95ad76rifjwfh484vp688lxsjaxg0kf2xjr2d2";
+    sha256 = "124l1alf7wx4hqjpf63l0nx70q68lilmgh582c1d413fz5ip0byd";
   };
 
   inherit bootstrapper;
diff --git a/pkgs/development/tools/continuous-integration/gitlab-runner/default.nix b/pkgs/development/tools/continuous-integration/gitlab-runner/default.nix
index 42e8f26970f..07be22ae43f 100644
--- a/pkgs/development/tools/continuous-integration/gitlab-runner/default.nix
+++ b/pkgs/development/tools/continuous-integration/gitlab-runner/default.nix
@@ -1,16 +1,16 @@
 { lib, buildGoPackage, fetchFromGitLab, fetchurl }:
 
 let
-  version = "11.11.0";
+  version = "11.11.2";
   # Gitlab runner embeds some docker images these are prebuilt for arm and x86_64
   docker_x86_64 = fetchurl {
     url = "https://gitlab-runner-downloads.s3.amazonaws.com/v${version}/helper-images/prebuilt-x86_64.tar.xz";
-    sha256 = "0h35y3ifqqsirkbgg75jj30n1ggyyncbwjnnxwdhc3r9hbbc545y";
+    sha256 = "0q5i9517jsz3mw7hglbnjih7q114350dfd9nyzv7xfk56kc0172w";
   };
 
   docker_arm = fetchurl {
     url = "https://gitlab-runner-downloads.s3.amazonaws.com/v${version}/helper-images/prebuilt-arm.tar.xz";
-    sha256 = "1lphzy5xxyc4qgmnf7rrplida2zdn2mfl9p9fr3gyjs7gbcr92d7";
+    sha256 = "0q7g0ggaxg6akda06an867vbdqjrfcxf4c81b1cxfhbk7whxgxhv";
   };
 in
 buildGoPackage rec {
@@ -29,7 +29,7 @@ buildGoPackage rec {
     owner = "gitlab-org";
     repo = "gitlab-runner";
     rev = "v${version}";
-    sha256 = "0i45p4z8f7ggdh7624473d8qhz7d75hlhz98p3z69dggx38vv49y";
+    sha256 = "0bnn89z7p2mrjjlq7i9yfr6ra903vr278qhhy2i126w56dlac6vf";
   };
 
   patches = [ ./fix-shell-path.patch ];
diff --git a/pkgs/development/tools/libsigrok/default.nix b/pkgs/development/tools/libsigrok/default.nix
index 93c8c6a6c71..a80b638625e 100644
--- a/pkgs/development/tools/libsigrok/default.nix
+++ b/pkgs/development/tools/libsigrok/default.nix
@@ -1,20 +1,20 @@
 { stdenv, fetchurl, pkgconfig, libzip, glib, libusb1, libftdi1, check
 , libserialport, librevisa, doxygen, glibmm, python
-, version ? "0.5.0", sha256 ? "197kr5ip98lxn7rv10zs35d1w0j7265s0xvckx0mq2l8kdvqd32c"
+, version ? "0.5.1", sha256 ? "171b553dir5gn6w4f7n37waqk62nq2kf1jykx4ifjacdz5xdw3z4"
 }:
 
 stdenv.mkDerivation rec {
   inherit version;
-  name = "libsigrok-${version}";
+  pname = "libsigrok";
 
   src = fetchurl {
-    url = "https://sigrok.org/download/source/libsigrok/${name}.tar.gz";
+    url = "https://sigrok.org/download/source/${pname}/${pname}-${version}.tar.gz";
     inherit sha256;
   };
 
   firmware = fetchurl {
-    url = "https://sigrok.org/download/binary/sigrok-firmware-fx2lafw/sigrok-firmware-fx2lafw-bin-0.1.3.tar.gz";
-    sha256 = "1qr02ny97navqxr56xq1a227yzf6h09m8jlvc9bnjl0bsk6887bl";
+    url = "https://sigrok.org/download/binary/sigrok-firmware-fx2lafw/sigrok-firmware-fx2lafw-bin-0.1.6.tar.gz";
+    sha256 = "14sd8xqph4kb109g073daiavpadb20fcz7ch1ipn0waz7nlly4sw";
   };
 
   nativeBuildInputs = [ pkgconfig ];
diff --git a/pkgs/development/tools/misc/libwhich/default.nix b/pkgs/development/tools/misc/libwhich/default.nix
index 58aca8a8b5a..c751c275558 100644
--- a/pkgs/development/tools/misc/libwhich/default.nix
+++ b/pkgs/development/tools/misc/libwhich/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "libwhich";
-  version = "2019-03-20";
+  version = "1.1.0";
 
   src = fetchFromGitHub {
     owner = "vtjnash";
     repo = pname;
-    rev = "b348872107c77cba50b60475aa8ce2ddba86aac0";
-    sha256 = "0fd8hsdc9b9v83j89mxvisgrz77q9rlxnbzd6j63wq66h95r02r9";
+    rev = "v${version}";
+    sha256 = "0s0pqai61jszmi495k621rdlf288ij67adkz72hwqqarqp54idhb";
   };
 
   installPhase = ''
diff --git a/pkgs/development/tools/qtcreator/0001-Fix-clang-libcpp-regexp.patch b/pkgs/development/tools/qtcreator/0001-Fix-clang-libcpp-regexp.patch
new file mode 100644
index 00000000000..8744b753a6e
--- /dev/null
+++ b/pkgs/development/tools/qtcreator/0001-Fix-clang-libcpp-regexp.patch
@@ -0,0 +1,15 @@
+diff --git a/src/plugins/cpptools/headerpathfilter.cpp b/src/plugins/cpptools/headerpathfilter.cpp
+index b514c46..5f96358 100644
+--- a/src/plugins/cpptools/headerpathfilter.cpp
++++ b/src/plugins/cpptools/headerpathfilter.cpp
+@@ -92,8 +92,8 @@ HeaderPaths::iterator resourceIterator(HeaderPaths &headerPaths, bool isMacOs)
+ {
+     // include/c++, include/g++, libc++\include and libc++abi\include
+     static const QString cppIncludes = R"((.*\/include\/.*(g\+\+|c\+\+).*))"
+-                                       R"(|(.*libc\+\+\/include))"
+-                                       R"(|(.*libc\+\+abi\/include))";
++                                       R"(|(.*libc\+\+.*\/include))"
++                                       R"(|(.*libc\+\+abi.*\/include))";
+     static const QRegularExpression includeRegExp("\\A(" + cppIncludes + ")\\z");
+ 
+     // The same as includeRegExp but also matches /usr/local/include
diff --git a/pkgs/development/tools/qtcreator/default.nix b/pkgs/development/tools/qtcreator/default.nix
index 3c892592d88..03b758cbdc6 100644
--- a/pkgs/development/tools/qtcreator/default.nix
+++ b/pkgs/development/tools/qtcreator/default.nix
@@ -1,5 +1,5 @@
-{ stdenv, fetchurl, makeWrapper
-, qtbase, qtquickcontrols, qtscript, qtdeclarative, qmake
+{ stdenv, fetchurl, fetchgit, fetchpatch, makeWrapper
+, qtbase, qtquickcontrols, qtscript, qtdeclarative, qmake, llvmPackages_8
 , withDocumentation ? false
 }:
 
@@ -8,6 +8,17 @@ with stdenv.lib;
 let
   baseVersion = "4.9";
   revision = "1";
+
+  # Fetch clang from qt vendor, this contains submodules like this:
+  # clang<-clang-tools-extra<-clazy. 
+  clang_qt_vendor = llvmPackages_8.clang-unwrapped.overrideAttrs (oldAttrs: rec {
+    src = fetchgit {
+      url = "https://code.qt.io/clang/clang.git";
+      rev = "c12b012bb7465299490cf93c2ae90499a5c417d5";
+      sha256 = "0mgmnazgr19hnd03xcrv7d932j6dpz88nhhx008b0lv4bah9mqm0";
+    };
+    unpackPhase = "";
+  });
 in
 
 stdenv.mkDerivation rec {
@@ -19,10 +30,29 @@ stdenv.mkDerivation rec {
     sha256 = "10ddp1365rf0z4bs7yzc9hajisp3j6mzjshyd0vpi4ki126j5f3r";
   };
 
-  buildInputs = [ qtbase qtscript qtquickcontrols qtdeclarative ];
+  buildInputs = [ qtbase qtscript qtquickcontrols qtdeclarative llvmPackages_8.libclang clang_qt_vendor llvmPackages_8.llvm ];
 
   nativeBuildInputs = [ qmake makeWrapper ];
 
+  # 0001-Fix-clang-libcpp-regexp.patch is for fixing regexp that is used to 
+  # find clang libc++ library include paths. By default it's not covering paths
+  # like libc++-version, which is default name for libc++ folder in nixos.
+  patches = [ ./0001-Fix-clang-libcpp-regexp.patch 
+
+    # Fix clazy plugin name. This plugin was renamed with clang8 
+    # release, and patch didn't make it into 4.9.1 release. Should be removed 
+    # on qtcreator update, if this problem is fixed.
+    (fetchpatch {
+      url = "https://code.qt.io/cgit/qt-creator/qt-creator.git/patch/src/plugins/clangcodemodel/clangeditordocumentprocessor.cpp?id=53c407bc0c87e0b65b537bf26836ddd8e00ead82";
+      sha256 = "1lanp7jg0x8jffajb852q8p4r34facg41l410xsz6s1k91jskbi9";
+    })
+
+    (fetchpatch {
+      url = "https://code.qt.io/cgit/qt-creator/qt-creator.git/patch/src/plugins/clangtools/clangtidyclazyrunner.cpp?id=53c407bc0c87e0b65b537bf26836ddd8e00ead82";
+      sha256 = "1rl0rc2l297lpfhhawvkkmj77zb081hhp0bbi7nnykf3q9ch0clh";
+    })
+  ]; 
+
   doCheck = true;
 
   enableParallelBuilding = true;
@@ -34,6 +64,20 @@ stdenv.mkDerivation rec {
   preConfigure = ''
     substituteInPlace src/plugins/plugins.pro \
       --replace '$$[QT_INSTALL_QML]/QtQuick/Controls' '${qtquickcontrols}/${qtbase.qtQmlPrefix}/QtQuick/Controls'
+
+    # Fix paths for llvm/clang includes directories.
+    substituteInPlace src/shared/clang/clang_defines.pri \
+      --replace '$$clean_path($${LLVM_LIBDIR}/clang/$${LLVM_VERSION}/include)' '${clang_qt_vendor}/lib/clang/8.0.0/include' \
+      --replace '$$clean_path($${LLVM_BINDIR})' '${clang_qt_vendor}/bin'
+
+    # Fix include path to find clang and clang-c include directories.  
+    substituteInPlace src/plugins/clangtools/clangtools.pro \
+      --replace 'INCLUDEPATH += $$LLVM_INCLUDEPATH' 'INCLUDEPATH += $$LLVM_INCLUDEPATH ${clang_qt_vendor}'
+
+    # Fix paths to libclang library.
+    substituteInPlace src/shared/clang/clang_installation.pri \
+      --replace 'LIBCLANG_LIBS = -L$${LLVM_LIBDIR}' 'LIBCLANG_LIBS = -L${llvmPackages_8.libclang}/lib' \
+      --replace 'LIBCLANG_LIBS += $${CLANG_LIB}' 'LIBCLANG_LIBS += -lclang'
   '';
 
   preBuild = optional withDocumentation ''
diff --git a/pkgs/development/tools/rust/cargo-make/default.nix b/pkgs/development/tools/rust/cargo-make/default.nix
index ab625d7ea35..da42e819ced 100644
--- a/pkgs/development/tools/rust/cargo-make/default.nix
+++ b/pkgs/development/tools/rust/cargo-make/default.nix
@@ -2,7 +2,7 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "cargo-make";
-  version = "0.19.4";
+  version = "0.19.5";
 
   src =
     let
@@ -10,11 +10,11 @@ rustPlatform.buildRustPackage rec {
         owner = "sagiegurari";
         repo = pname;
         rev = version;
-        sha256 = "019dn401p4bds144fbvqxbnn8vswcj0lxr8cvgpxb2y22640z60l";
+        sha256 = "0xjyzsi3n3lb5g4gl6v0s4p87nazkqgjf244m792iji9i568ynjb";
       };
       cargo-lock = fetchurl {
-        url = "https://gist.githubusercontent.com/xrelkd/e4c9c7738b21f284d97cb7b1d181317d/raw/c5b9fde279a9f6d55d97e0ba4e0b4cd62e0ab2bf/cargo-make-Cargo.lock";
-        sha256 = "1d5md3m8hxwf3pwvx059fsk1b3vvqm17pxbbyiisn9v4psrsmld5";
+        url = "https://gist.githubusercontent.com/xrelkd/e4c9c7738b21f284d97cb7b1d181317d/raw/285cf8f9b0ab33db0d656fdc8e759feed55c0167/cargo-make-Cargo.lock";
+        sha256 = "0l2i2hq43k482m2w6hpapaq53r8bjljfcszp6csljj4fvxcl62yj";
       };
     in
     runCommand "cargo-make-src" {} ''
@@ -25,7 +25,7 @@ rustPlatform.buildRustPackage rec {
 
   buildInputs = stdenv.lib.optionals stdenv.isDarwin [ Security ];
 
-  cargoSha256 = "0wf60ck0w3m9fa19dz99q84kw05sxlj2pp6bd8r1db3cfy8f8h8j";
+  cargoSha256 = "1rmdmvr5wc2m0yv3dy07cv9y1xrwlfri3hk97zjwv5f73wgncspy";
 
   # Some tests fail because they need network access.
   # However, Travis ensures a proper build.
diff --git a/pkgs/development/web/grails/default.nix b/pkgs/development/web/grails/default.nix
index b4d78ef0850..018c7f96969 100644
--- a/pkgs/development/web/grails/default.nix
+++ b/pkgs/development/web/grails/default.nix
@@ -11,11 +11,11 @@ let
 in
 stdenv.mkDerivation rec {
   name = "grails-${version}";
-  version = "3.3.9";
+  version = "3.3.10";
 
   src = fetchurl {
     url = "https://github.com/grails/grails-core/releases/download/v${version}/grails-${version}.zip";
-    sha256 = "0xnwi9m9l8rz4wdwjp2i3yfzsq1szz37z886nc6lbfxd5mj19hnn";
+    sha256 = "1lykawfi47c2k6lq4vrnghlz8gcnmqsslxsnaq4d2n78g0y3yyr2";
   };
 
   buildInputs = [ unzip ];