Merge branch 'staging-next' into staging

9 files changed, 233 insertions, 44 deletions

diff --git a/pkgs/development/compilers/intel-graphics-compiler/default.nix b/pkgs/development/compilers/intel-graphics-compiler/default.nix
index 183e1f2a085..a365761b014 100644
--- a/pkgs/development/compilers/intel-graphics-compiler/default.nix
+++ b/pkgs/development/compilers/intel-graphics-compiler/default.nix
@@ -24,13 +24,13 @@ in
 
 stdenv.mkDerivation rec {
   pname = "intel-graphics-compiler";
-  version = "1.0.2714.1";
+  version = "1.0.2878";
 
   src = fetchFromGitHub {
     owner = "intel";
     repo = "intel-graphics-compiler";
     rev = "igc-${version}";
-    sha256 = "0ys03sv08fg8q06lb6k5088xirnwms4nzazxp3kbdjm973n7imxc";
+    sha256 = "0rgij1013fy2x2szfchy3z6390mjfqw3nz4zprcb5v2v6mpvcj4l";
   };
 
   nativeBuildInputs = [ clang cmake bison flex llvm python ];
diff --git a/pkgs/development/interpreters/jimtcl/default.nix b/pkgs/development/interpreters/jimtcl/default.nix
index 91b4c0b9a9e..09d7fa622fc 100644
--- a/pkgs/development/interpreters/jimtcl/default.nix
+++ b/pkgs/development/interpreters/jimtcl/default.nix
@@ -5,35 +5,53 @@ let
 
 in stdenv.mkDerivation rec {
   pname = "jimtcl";
-  version = "0.78";
+  version = "0.79";
 
   src = fetchFromGitHub {
     owner = "msteveb";
     repo = "jimtcl";
     rev = version;
-    sha256 = "1nrjxjfh69i35ig8sxdlal4ydd3cl0x68c05s6svnf1y2i1bl23j";
+    sha256 = "1k88hz0v3bi19xdvlp0i9nsx38imzwpjh632w7326zwbv2wldf0h";
   };
 
-  buildInputs = [
-    sqlite readline asciidoc SDL SDL_gfx
+  nativeBuildInputs = [
+    asciidoc
   ];
 
-  NIX_CFLAGS_COMPILE = makeSDLFlags [ SDL SDL_gfx ];
+  buildInputs = [
+    sqlite readline SDL SDL_gfx
+  ];
 
   configureFlags = [
+    "--shared"
     "--with-ext=oo"
     "--with-ext=tree"
     "--with-ext=binary"
     "--with-ext=sqlite3"
     "--with-ext=readline"
     "--with-ext=sdl"
+    "--with-ext=json"
     "--enable-utf8"
     "--ipv6"
   ];
 
+  NIX_CFLAGS_COMPILE = makeSDLFlags [ SDL SDL_gfx ];
+
+  enableParallelBuilding = true;
+
+  doCheck = true;
+  preCheck = ''
+    # test exec2-3.2 fails depending on platform or sandboxing (?)
+    rm tests/exec2.test
+  '';
+
+  postInstall = ''
+    ln -sr $out/lib/libjim.so.${version} $out/lib/libjim.so
+  '';
+
   meta = {
     description = "An open source small-footprint implementation of the Tcl programming language";
-    homepage = http://jim.tcl.tk/;
+    homepage = "http://jim.tcl.tk/";
     license = stdenv.lib.licenses.bsd2;
     platforms = stdenv.lib.platforms.all;
     maintainers = with stdenv.lib.maintainers; [ dbohdan vrthra ];
diff --git a/pkgs/development/libraries/at-spi2-core/default.nix b/pkgs/development/libraries/at-spi2-core/default.nix
index bda809b1a5a..84a8a6b9026 100644
--- a/pkgs/development/libraries/at-spi2-core/default.nix
+++ b/pkgs/development/libraries/at-spi2-core/default.nix
@@ -10,6 +10,7 @@
 
 , dbus
 , glib
+, dconf
 , libX11
 , libXtst # at-spi2-core can be build without X support, but due it is a client-side library, GUI-less usage is a very rare case
 , libXi
@@ -48,7 +49,7 @@ stdenv.mkDerivation rec {
   postFixup = ''
     # Cannot use wrapGAppsHook'due to a dependency cycle
     wrapProgram $out/libexec/at-spi-bus-launcher \
-      --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib gnome3.dconf}/lib/gio/modules" \
+      --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib dconf}/lib/gio/modules" \
       --prefix XDG_DATA_DIRS : ${gsettings-desktop-schemas}/share/gsettings-schemas/${gsettings-desktop-schemas.name}
   '';
 
diff --git a/pkgs/development/libraries/dconf/default.nix b/pkgs/development/libraries/dconf/default.nix
new file mode 100644
index 00000000000..7ce498da9f3
--- /dev/null
+++ b/pkgs/development/libraries/dconf/default.nix
@@ -0,0 +1,50 @@
+{ stdenv, fetchurl, meson, ninja, python3, vala, libxslt, pkgconfig, glib, bash-completion, dbus, gnome3
+, libxml2, gtk-doc, docbook_xsl, docbook_xml_dtd_42, fetchpatch }:
+
+let
+  pname = "dconf";
+in
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  version = "0.34.0";
+
+  src = fetchurl {
+    url = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${name}.tar.xz";
+    sha256 = "0lnsl85cp2vpzgp8pkf6l6yd2i3lp02jdvga1icfa78j2smr8fll";
+  };
+
+  patches = [
+  ];
+
+  postPatch = ''
+    chmod +x meson_post_install.py tests/test-dconf.py
+    patchShebangs meson_post_install.py
+    patchShebangs tests/test-dconf.py
+  '';
+
+  outputs = [ "out" "lib" "dev" "devdoc" ];
+
+  nativeBuildInputs = [ meson ninja vala pkgconfig python3 libxslt libxml2 gtk-doc docbook_xsl docbook_xml_dtd_42 ];
+  buildInputs = [ glib bash-completion dbus ];
+
+  mesonFlags = [
+    "--sysconfdir=/etc"
+    "-Dgtk_doc=true"
+  ];
+
+  doCheck = !stdenv.isAarch32 && !stdenv.isAarch64 && !stdenv.isDarwin;
+
+  passthru = {
+    updateScript = gnome3.updateScript {
+      packageName = pname;
+      attrPath = "gnome3.${pname}";
+    };
+  };
+
+  meta = with stdenv.lib; {
+    homepage = https://wiki.gnome.org/Projects/dconf;
+    license = licenses.lgpl21Plus;
+    platforms = platforms.linux ++ platforms.darwin;
+    maintainers = gnome3.maintainers;
+  };
+}
diff --git a/pkgs/development/libraries/flatpak/default.nix b/pkgs/development/libraries/flatpak/default.nix
index c0cbb763d36..945f1d4931f 100644
--- a/pkgs/development/libraries/flatpak/default.nix
+++ b/pkgs/development/libraries/flatpak/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchurl, autoreconfHook, docbook_xml_dtd_412, docbook_xml_dtd_42, docbook_xml_dtd_43, docbook_xsl, which, libxml2
 , gobject-introspection, gtk-doc, intltool, libxslt, pkgconfig, xmlto, appstream-glib, substituteAll, glibcLocales, yacc, xdg-dbus-proxy, p11-kit
 , bubblewrap, bzip2, dbus, glib, gpgme, json-glib, libarchive, libcap, libseccomp, coreutils, gettext, hicolor-icon-theme, fuse, nixosTests
-, libsoup, lzma, ostree, polkit, python3, systemd, xorg, valgrind, glib-networking, wrapGAppsHook, gnome3, gsettings-desktop-schemas, librsvg }:
+, libsoup, lzma, ostree, polkit, python3, systemd, xorg, valgrind, glib-networking, wrapGAppsHook, dconf, gsettings-desktop-schemas, librsvg }:
 
 stdenv.mkDerivation rec {
   pname = "flatpak";
@@ -42,7 +42,7 @@ stdenv.mkDerivation rec {
   ];
 
   buildInputs = [
-    bubblewrap bzip2 dbus gnome3.dconf glib gpgme json-glib libarchive libcap libseccomp
+    bubblewrap bzip2 dbus dconf glib gpgme json-glib libarchive libcap libseccomp
     libsoup lzma ostree polkit python3 systemd xorg.libXau fuse
     gsettings-desktop-schemas glib-networking
     librsvg # for flatpak-validate-icon
diff --git a/pkgs/development/python-modules/rpy2/2.nix b/pkgs/development/python-modules/rpy2/2.nix
new file mode 100644
index 00000000000..aef184d4afc
--- /dev/null
+++ b/pkgs/development/python-modules/rpy2/2.nix
@@ -0,0 +1,108 @@
+{ lib
+, python
+, buildPythonPackage
+, fetchPypi
+, isPyPy
+, isPy27
+, readline
+, R
+, rWrapper
+, rPackages
+, pcre
+, lzma
+, bzip2
+, zlib
+, icu
+, singledispatch
+, six
+, jinja2
+, pytz
+, numpy
+, pytest
+, mock
+, extraRPackages ? []
+}:
+
+buildPythonPackage rec {
+    version = "2.8.6"; # python2 support dropped in 2.9.x
+    pname = "rpy2";
+    disabled = isPyPy;
+    src = fetchPypi {
+      inherit version pname;
+      sha256 = "162zki5c1apgv6qbafi7n66y4hgpgp43xag7q75qb6kv99ri6k80";
+    };
+    buildInputs = [
+      readline
+      R
+      pcre
+      lzma
+      bzip2
+      zlib
+      icu
+    ] ++ (with rPackages; [
+      # packages expected by the test framework
+      ggplot2
+      dplyr
+      RSQLite
+      broom
+      DBI
+      dbplyr
+      hexbin
+      lme4
+      tidyr
+
+      # is in upstream's `requires` although it shouldn't be -- this is easier than patching it away
+      pytest
+    ]) ++ extraRPackages ++ rWrapper.recommendedPackages;
+
+    nativeBuildInputs = [
+      R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)
+    ];
+
+    patches = [
+      # R_LIBS_SITE is used by the nix r package to point to the installed R libraries.
+      # This patch sets R_LIBS_SITE when rpy2 is imported.
+      ./r-libs-site.patch
+    ];
+    postPatch = ''
+      substituteInPlace ${ if isPy27 then "rpy/rinterface/__init__.py" else "rpy2/rinterface_lib/embedded.py" } --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
+    '';
+
+    doPatchelf = false; # fails because of "missing filename"
+    patchelfPhase = "";
+
+    propagatedBuildInputs = [
+      singledispatch
+      six
+      jinja2
+      pytz
+      numpy
+    ];
+
+    checkInputs = [
+      pytest
+      mock
+    ];
+    # One remaining test failure caused by different unicode encoding.
+    # https://bitbucket.org/rpy2/rpy2/issues/488
+    doCheck = false;
+    checkPhase = ''
+      ${python.interpreter} -m 'rpy2'
+    '';
+
+    # For some reason libreadline.so is not found. Curiously `ldd _rinterface.so | grep readline` shows two readline entries:
+    # libreadline.so.6 => not found
+    # libreadline.so.6 => /nix/store/z2zhmrg6jcrn5iq2779mav0nnq4vm2q6-readline-6.3p08/lib/libreadline.so.6 (0x00007f333ac43000)
+    # There must be a better way to fix this, but I don't know it.
+    postFixup = ''
+      patchelf --add-needed ${readline}/lib/libreadline.so "$out/${python.sitePackages}/rpy2/rinterface/"_rinterface*.so
+    '';
+
+    meta = {
+      homepage = http://rpy.sourceforge.net/rpy2;
+      description = "Python interface to R";
+      license = lib.licenses.gpl2Plus;
+      platforms = lib.platforms.unix;
+      maintainers = with lib.maintainers; [ joelmo ];
+    };
+  }
diff --git a/pkgs/development/python-modules/rpy2/default.nix b/pkgs/development/python-modules/rpy2/default.nix
index 1b4ab4d40db..bc4bc0bcb5b 100644
--- a/pkgs/development/python-modules/rpy2/default.nix
+++ b/pkgs/development/python-modules/rpy2/default.nix
@@ -3,8 +3,6 @@
 , buildPythonPackage
 , fetchPypi
 , isPyPy
-, isPy27
-, readline
 , R
 , rWrapper
 , rPackages
@@ -13,38 +11,38 @@
 , bzip2
 , zlib
 , icu
-, singledispatch
-, six
+, ipython
 , jinja2
 , pytz
+, pandas
 , numpy
+, cffi
+, tzlocal
+, simplegeneric
 , pytest
-, mock
 , extraRPackages ? []
 }:
 
 buildPythonPackage rec {
-    version = if isPy27 then
-      "2.8.6" # python2 support dropped in 2.9.x
-    else
-      "2.9.5";
+    version = "3.2.2";
     pname = "rpy2";
+
     disabled = isPyPy;
     src = fetchPypi {
       inherit version pname;
-      sha256 = if isPy27 then
-        "162zki5c1apgv6qbafi7n66y4hgpgp43xag7q75qb6kv99ri6k80" # 2.8.x
-      else
-        "1nrj8pgyxrwrfdrxzb4j3z1adjwjx1mr8d1n5cmrz4nhlzy8w7xr"; # 2.9.x
+      sha256 = "0b3jpn9x7m2pccriyzgfsdb68qp6nq4ffhvjy1q2ar8wdxvmf5xp";
     };
+
     buildInputs = [
-      readline
       R
       pcre
       lzma
       bzip2
       zlib
       icu
+
+      # is in the upstream `requires` although it shouldn't be -- this is easier than patching it away
+      pytest
     ] ++ (with rPackages; [
       # packages expected by the test framework
       ggplot2
@@ -58,6 +56,10 @@ buildPythonPackage rec {
       tidyr
     ]) ++ extraRPackages ++ rWrapper.recommendedPackages;
 
+    checkPhase = ''
+      pytest
+    '';
+
     nativeBuildInputs = [
       R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)
     ];
@@ -65,38 +67,26 @@ buildPythonPackage rec {
     patches = [
       # R_LIBS_SITE is used by the nix r package to point to the installed R libraries.
       # This patch sets R_LIBS_SITE when rpy2 is imported.
-      ./r-libs-site.patch
+      ./rpy2-3.x-r-libs-site.patch
     ];
     postPatch = ''
-      substituteInPlace rpy/rinterface/__init__.py --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
+      substituteInPlace 'rpy2/rinterface_lib/embedded.py' --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
     '';
 
     propagatedBuildInputs = [
-      singledispatch
-      six
+      ipython
       jinja2
       pytz
+      pandas
       numpy
+      cffi
+      tzlocal
+      simplegeneric
     ];
 
     checkInputs = [
       pytest
-      mock
     ];
-    # One remaining test failure caused by different unicode encoding.
-    # https://bitbucket.org/rpy2/rpy2/issues/488
-    doCheck = false;
-    checkPhase = ''
-      ${python.interpreter} -m 'rpy2.tests'
-    '';
-
-    # For some reason libreadline.so is not found. Curiously `ldd _rinterface.so | grep readline` shows two readline entries:
-    # libreadline.so.6 => not found
-    # libreadline.so.6 => /nix/store/z2zhmrg6jcrn5iq2779mav0nnq4vm2q6-readline-6.3p08/lib/libreadline.so.6 (0x00007f333ac43000)
-    # There must be a better way to fix this, but I don't know it.
-    postFixup = ''
-      patchelf --add-needed ${readline}/lib/libreadline.so "$out/${python.sitePackages}/rpy2/rinterface/"_rinterface*.so
-    '';
 
     meta = {
       homepage = http://rpy.sourceforge.net/rpy2;
diff --git a/pkgs/development/python-modules/rpy2/rpy2-3.x-r-libs-site.patch b/pkgs/development/python-modules/rpy2/rpy2-3.x-r-libs-site.patch
new file mode 100644
index 00000000000..177e4f9a83d
--- /dev/null
+++ b/pkgs/development/python-modules/rpy2/rpy2-3.x-r-libs-site.patch
@@ -0,0 +1,21 @@
+diff --git a/rpy2/rinterface_lib/embedded.py b/rpy2/rinterface_lib/embedded.py
+index cc32b6d..3969ad0 100644
+--- a/rpy2/rinterface_lib/embedded.py
++++ b/rpy2/rinterface_lib/embedded.py
+@@ -113,6 +113,16 @@ def _initr(interactive: bool = True,
+         if isinitialized():
+             return None
+         os.environ['R_HOME'] = openrlib.R_HOME
++
++        # path to libraries
++        existing = os.environ.get('R_LIBS_SITE')
++        if existing is not None:
++            prefix = existing + ':'
++        else:
++            prefix = ''
++        additional = '@NIX_R_LIBS_SITE@'
++        os.environ['R_LIBS_SITE'] = prefix + additional
++
+         options_c = [ffi.new('char[]', o.encode('ASCII')) for o in _options]
+         n_options = len(options_c)
+         n_options_c = ffi.cast('int', n_options)
diff --git a/pkgs/development/tools/analysis/rr/default.nix b/pkgs/development/tools/analysis/rr/default.nix
index 844fd38d9be..a8d95eb05de 100644
--- a/pkgs/development/tools/analysis/rr/default.nix
+++ b/pkgs/development/tools/analysis/rr/default.nix
@@ -25,6 +25,7 @@ stdenv.mkDerivation rec {
   buildInputs = [
     cmake libpfm zlib python2Packages.python python2Packages.pexpect which procps gdb capnproto
   ];
+  propagatedBuildInputs = [ gdb ]; # needs GDB to replay programs at runtime
   cmakeFlags = [
     "-DCMAKE_C_FLAGS_RELEASE:STRING="
     "-DCMAKE_CXX_FLAGS_RELEASE:STRING="