Merge staging-next into staging

46 files changed, 354 insertions, 328 deletions

diff --git a/pkgs/applications/audio/gnome-podcasts/default.nix b/pkgs/applications/audio/gnome-podcasts/default.nix
index eeafdc80344..7a44ebe6769 100644
--- a/pkgs/applications/audio/gnome-podcasts/default.nix
+++ b/pkgs/applications/audio/gnome-podcasts/default.nix
@@ -1,45 +1,74 @@
-{ stdenv, fetchurl, fetchpatch, meson, ninja, gettext, cargo, rustc, python3, pkgconfig, gnome3
-, glib, libhandy, gtk3, dbus, openssl, sqlite, gst_all_1, wrapGAppsHook }:
+{ stdenv
+, rustPlatform
+, fetchFromGitLab
+, fetchpatch
+, meson
+, ninja
+, gettext
+, cargo
+, rustc
+, python3
+, pkgconfig
+, gnome3
+, glib
+, libhandy
+, gtk3
+, dbus
+, openssl
+, sqlite
+, gst_all_1
+, wrapGAppsHook
+}:
 
-# TODO: build from git for easier updates
-# rustPlatform.buildRustPackage rec {
-stdenv.mkDerivation {
-  version = "0.4.6";
+rustPlatform.buildRustPackage rec {
+  version = "0.4.7";
   pname = "gnome-podcasts";
 
-  src = fetchurl {
-    url = https://gitlab.gnome.org/World/podcasts/uploads/e59ac5d618d7daf4c7f33ba72957c466/gnome-podcasts-0.4.6.tar.xz;
-    sha256 = "0g2rk3w251fp5jwbxs5ya1adv8nsgdqjy1vmfg8qqab6qyndhbrc";
+  src = fetchFromGitLab {
+    domain = "gitlab.gnome.org";
+    owner = "World";
+    repo = "podcasts";
+    rev = version;
+    sha256 = "0vy5i77bv8c22ldhrnr4z6kx22zqnb1lg3s7y8673bqjgd7dppi0";
   };
 
-  patches = [
-    # podcasts-data would fail to build because it errors on warnings
-    (fetchpatch {
-      url = "https://gitlab.gnome.org/World/podcasts/commit/7dc1b25ee7fc59a188312d31b1fa00c3110ae63e.patch";
-      sha256 = "03ibbh1snk1391vnni529agqs14lzg5g0axjgpf3gn8dwwh1yvd5";
-    })
-  ];
-
-  # src = fetchFromGitLab {
-  #   domain = "gitlab.gnome.org";
-  #   owner = "World";
-  #   repo = "podcasts";
-  #   rev = version;
-  #   sha256 = "15xj98dhxvys0cnya9488qsfsm0ys1wy69wkc39z8j6hwdm7byq2";
-  # };
+  cargoSha256 = "1h0n8zclb8a1b1ri83viiwwzlj3anm38m4cp38aqyf6q40qga35q";
 
   nativeBuildInputs = [
-    meson ninja pkgconfig gettext cargo rustc python3 wrapGAppsHook
+    meson
+    ninja
+    pkgconfig
+    gettext
+    cargo
+    rustc
+    python3
+    wrapGAppsHook
   ];
+
   buildInputs = [
-    glib gtk3 libhandy dbus openssl sqlite gst_all_1.gstreamer gst_all_1.gst-plugins-base gst_all_1.gst-plugins-bad
+    glib
+    gtk3
+    libhandy
+    dbus
+    openssl
+    sqlite
+    gst_all_1.gstreamer
+    gst_all_1.gst-plugins-base
+    gst_all_1.gst-plugins-bad
   ];
 
-  # cargoSha256 = "0721b5f700vvvzvmdl8nfjaa6j412q1fjssgrjv8n6rmn9z13d2v";
+  # use Meson/Ninja phases
+  configurePhase = null;
+  buildPhase = null;
+  checkPhase = null;
+  installPhase = null;
+
+  # tests require network
+  doCheck = false;
 
   postPatch = ''
     chmod +x scripts/compile-gschema.py # patchShebangs requires executable file
-    patchShebangs scripts/compile-gschema.py
+    patchShebangs scripts/compile-gschema.py scripts/cargo.sh scripts/test.sh
   '';
 
   meta = with stdenv.lib; {
diff --git a/pkgs/applications/audio/strawberry/default.nix b/pkgs/applications/audio/strawberry/default.nix
index c62eba99845..315bb624e51 100644
--- a/pkgs/applications/audio/strawberry/default.nix
+++ b/pkgs/applications/audio/strawberry/default.nix
@@ -22,7 +22,7 @@
 , libpulseaudio ? null
 , libselinux ? null
 , libsepol ? null
-, p11_kit ? null
+, p11-kit ? null
 , utillinux ? null
 , qtbase
 , qtx11extras
@@ -66,7 +66,7 @@ mkDerivation rec {
     libpulseaudio
     libselinux
     libsepol
-    p11_kit
+    p11-kit
     utillinux
   ]
   ++ lib.optionals withGstreamer (with gst_all_1; [
diff --git a/pkgs/applications/backup/deja-dup/default.nix b/pkgs/applications/backup/deja-dup/default.nix
index 7120a1934f6..d19314ce9ce 100644
--- a/pkgs/applications/backup/deja-dup/default.nix
+++ b/pkgs/applications/backup/deja-dup/default.nix
@@ -1,20 +1,46 @@
-{ stdenv, fetchFromGitLab, substituteAll, meson, ninja, pkgconfig, vala_0_40, gettext
-, gnome3, libnotify, itstool, glib, gtk3, libxml2, gnome-online-accounts
-, coreutils, libpeas, libsecret, pcre, libxkbcommon, wrapGAppsHook
-, libpthreadstubs, libXdmcp, epoxy, at-spi2-core, dbus, libgpgerror
-, appstream-glib, desktop-file-utils, duplicity
+{ stdenv
+, fetchFromGitLab
+, substituteAll
+, meson
+, ninja
+, pkgconfig
+, vala
+, gettext
+, gnome3
+, libnotify
+, itstool
+, glib
+, gtk3
+, libxml2
+, gnome-online-accounts
+, coreutils
+, libsoup
+, libsecret
+, pcre
+, libxkbcommon
+, wrapGAppsHook
+, libpthreadstubs
+, libXdmcp
+, epoxy
+, at-spi2-core
+, dbus
+, libgpgerror
+, json-glib
+, appstream-glib
+, desktop-file-utils
+, duplicity
 }:
 
 stdenv.mkDerivation rec {
   pname = "deja-dup";
-  version = "38.3";
+  version = "40.4";
 
   src = fetchFromGitLab {
     domain = "gitlab.gnome.org";
     owner = "World";
     repo = pname;
     rev = version;
-    sha256 = "1bnvmdlm67k1b6115x75j3nl92x5yl4psq5pna2w6cg9npxdd3fa";
+    sha256 = "0x9z8z1mh1sxi28ilml3pvbc0g6ghcbyiy002rziwwlarxnbwkky";
   };
 
   patches = [
@@ -22,37 +48,55 @@ stdenv.mkDerivation rec {
       src = ./fix-paths.patch;
       inherit coreutils;
     })
+
+    # Hardcode GSettings path for Nautilus extension to avoid crashes from missing schemas
     ./hardcode-gsettings.patch
   ];
 
   postPatch = ''
-    substituteInPlace deja-dup/nautilus/NautilusExtension.c --subst-var-by DEJA_DUP_GSETTINGS_PATH ${glib.makeSchemaPath "$out" "${pname}-${version}"}
+    # substitute variable from hardcode-gsettings.patch
+    substituteInPlace deja-dup/nautilus/NautilusExtension.c --subst-var-by DEJA_DUP_GSETTINGS_PATH "${glib.makeSchemaPath (placeholder "out") "${pname}-${version}"}"
   '';
 
   nativeBuildInputs = [
-    meson ninja pkgconfig vala_0_40 gettext itstool
-    appstream-glib desktop-file-utils libxml2 wrapGAppsHook
+    meson
+    ninja
+    pkgconfig
+    vala
+    gettext
+    itstool
+    appstream-glib
+    desktop-file-utils
+    libxml2
+    wrapGAppsHook
   ];
 
   buildInputs = [
-   libnotify libpeas glib gtk3 libsecret
-   pcre libxkbcommon libpthreadstubs libXdmcp epoxy gnome3.nautilus
-   at-spi2-core dbus gnome-online-accounts libgpgerror
+    libnotify
+    libsoup
+    glib
+    gtk3
+    libsecret
+    pcre
+    libxkbcommon
+    libpthreadstubs
+    libXdmcp
+    epoxy
+    gnome3.nautilus
+    at-spi2-core
+    dbus
+    gnome-online-accounts # GOA not used any more, only for transferring legacy keys
+    libgpgerror
+    json-glib
   ];
 
+  # TODO: hard code the path
+  # https://gitlab.gnome.org/World/deja-dup/merge_requests/32
   propagatedUserEnvPkgs = [ duplicity ];
 
+  # install nautilus plug-in to correct path
   PKG_CONFIG_LIBNAUTILUS_EXTENSION_EXTENSIONDIR = "${placeholder "out"}/lib/nautilus/extensions-3.0";
 
-  postInstall = ''
-    glib-compile-schemas $out/share/glib-2.0/schemas
-  '';
-
-  postFixup = ''
-    # Unwrap accidentally wrapped library
-    mv $out/libexec/deja-dup/tools/.libduplicity.so-wrapped $out/libexec/deja-dup/tools/libduplicity.so
-  '';
-
   meta = with stdenv.lib; {
     description = "A simple backup tool";
     longDescription = ''
@@ -60,7 +104,7 @@ stdenv.mkDerivation rec {
       of backing up the Right Way (encrypted, off-site, and regular) \
       and uses duplicity as the backend.
     '';
-    homepage = https://wiki.gnome.org/Apps/DejaDup;
+    homepage = "https://wiki.gnome.org/Apps/DejaDup";
     license = licenses.gpl3Plus;
     maintainers = with maintainers; [ jtojnar joncojonathan ];
     platforms = platforms.linux;
diff --git a/pkgs/applications/backup/deja-dup/hardcode-gsettings.patch b/pkgs/applications/backup/deja-dup/hardcode-gsettings.patch
index 50bf2ba4fbd..f74dbf73543 100644
--- a/pkgs/applications/backup/deja-dup/hardcode-gsettings.patch
+++ b/pkgs/applications/backup/deja-dup/hardcode-gsettings.patch
@@ -1,38 +1,16 @@
 --- a/deja-dup/nautilus/NautilusExtension.c
 +++ b/deja-dup/nautilus/NautilusExtension.c
-@@ -24,6 +24,8 @@
- #include <glib/gi18n-lib.h>
- 
- GList *dirs = NULL;
-+GSettingsSchemaSource *schema_source = NULL;
-+GSettingsSchema *schema = NULL;
- GSettings *settings = NULL;
- 
- // This will treat a < b iff a is 'lower' in the file tree than b
-@@ -313,7 +315,13 @@
+@@ -313,7 +313,12 @@
    bindtextdomain(GETTEXT_PACKAGE, LOCALE_DIR);
    bind_textdomain_codeset(GETTEXT_PACKAGE, "UTF-8");
  
--  settings = g_settings_new("org.gnome.DejaDup");
-+  schema_source = g_settings_schema_source_new_from_directory ("@DEJA_DUP_GSETTINGS_PATH@",
+-  settings = g_settings_new(APPLICATION_ID);
++  g_autoptr (GSettingsSchemaSource) schema_source = g_settings_schema_source_new_from_directory ("@DEJA_DUP_GSETTINGS_PATH@",
 +    g_settings_schema_source_get_default (), TRUE, NULL);
 +
-+  schema = g_settings_schema_source_lookup (schema_source,
-+                                            "org.gnome.DejaDup", FALSE);
++  g_autoptr (GSettingsSchema) schema = g_settings_schema_source_lookup (schema_source, APPLICATION_ID, FALSE);
 +
 +  settings = g_settings_new_full (schema, NULL, NULL);
    g_signal_connect(settings, "changed::include-list",
                     update_include_excludes, NULL);
    g_signal_connect(settings, "changed::exclude-list",
-@@ -329,7 +337,11 @@
- 
- void nautilus_module_shutdown(void)
- {
-+  g_settings_schema_source_unref(schema_source);
-+  g_settings_schema_unref(schema);
-   g_object_unref(settings);
-+  schema_source = NULL;
-+  schema = NULL;
-   settings = NULL;
- 
-   update_include_excludes(); /* will clear it now that settings is NULL */
diff --git a/pkgs/applications/blockchains/parity/beta.nix b/pkgs/applications/blockchains/parity/beta.nix
index a26a1b7cc77..c9da6f0e7a8 100644
--- a/pkgs/applications/blockchains/parity/beta.nix
+++ b/pkgs/applications/blockchains/parity/beta.nix
@@ -1,6 +1,6 @@
 let
-  version     = "2.6.4";
-  sha256      = "11l93w97961zig4gqf345j9l20g0mjp7fayl1mdwdp14hhd5zk5g";
-  cargoSha256 = "1q6cbms7j1h726bvq38npxkjkmz14b5ir9c4z7pb0jcy7gkplyxx";
+  version     = "2.6.5";
+  sha256      = "1ykrsphqil68051wwp9b0259gsmfrj9xmx0pfhh2yvmmjzv7k4fv";
+  cargoSha256 = "1xqmnirx2r91q5gy1skxl0f79xvaqzimq3l0cj4xvfms7mpdfbg1";
 in
   import ./parity.nix { inherit version sha256 cargoSha256; }
diff --git a/pkgs/applications/blockchains/parity/default.nix b/pkgs/applications/blockchains/parity/default.nix
index 299bb0639b6..ba3491e084d 100644
--- a/pkgs/applications/blockchains/parity/default.nix
+++ b/pkgs/applications/blockchains/parity/default.nix
@@ -1,6 +1,6 @@
 let
-  version     = "2.5.9";
-  sha256      = "06gmfw5l8n5i35dimsmj6dn0fxhbp53zjrdvbkff63r5kfqnwnx2";
-  cargoSha256 = "1kdy0bnmyqx4rhpq0a8gliy6mws68n035kfkxrfa6cxr2cn53dyb";
+  version     = "2.5.10";
+  sha256      = "0s8llcb1xdzs2zb6rnbsa9hck7dj4m8mamzkkvr0xjmgvigskf64";
+  cargoSha256 = "16nf6y0hyffwdhxn1w4ms4zycs5lkzir8sj6c2lgsabig057hb6z";
 in
   import ./parity.nix { inherit version sha256 cargoSha256; }
diff --git a/pkgs/applications/display-managers/lightdm/default.nix b/pkgs/applications/display-managers/lightdm/default.nix
index 4d221e97099..952aa285637 100644
--- a/pkgs/applications/display-managers/lightdm/default.nix
+++ b/pkgs/applications/display-managers/lightdm/default.nix
@@ -27,6 +27,7 @@
 , qt4
 , withQt5 ? false
 , qtbase
+, yelp-tools
 }:
 
 with stdenv.lib;
@@ -47,7 +48,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [
     autoconf
     automake
-    gnome3.yelp-tools
+    yelp-tools
     gnome3.yelp-xsl
     gobject-introspection
     gtk-doc
diff --git a/pkgs/applications/editors/gobby/default.nix b/pkgs/applications/editors/gobby/default.nix
index 3abe2834db4..f194227932d 100644
--- a/pkgs/applications/editors/gobby/default.nix
+++ b/pkgs/applications/editors/gobby/default.nix
@@ -1,5 +1,5 @@
 { avahiSupport ? false # build support for Avahi in libinfinity
-, stdenv, fetchFromGitHub, autoconf, automake, pkgconfig, wrapGAppsHook
+, stdenv, fetchFromGitHub, autoconf, automake, pkgconfig, wrapGAppsHook, yelp-tools
 , gtkmm3, gsasl, gtksourceview3, libxmlxx, libinfinity, intltool, itstool, gnome3 }:
 
 let
@@ -13,7 +13,7 @@ in stdenv.mkDerivation {
     sha256 = "0q7lq64yn16lxvj4jphs8y9194h0xppj8k7y9x8b276krraak2az";
   };
 
-  nativeBuildInputs = [ autoconf automake pkgconfig intltool itstool gnome3.yelp-tools wrapGAppsHook ];
+  nativeBuildInputs = [ autoconf automake pkgconfig intltool itstool yelp-tools wrapGAppsHook ];
   buildInputs = [ gtkmm3 gsasl gtksourceview3 libxmlxx libinf ];
 
   preConfigure = "./autogen.sh";
diff --git a/pkgs/applications/editors/neovim/default.nix b/pkgs/applications/editors/neovim/default.nix
index 99b04059730..b3e2ed51015 100644
--- a/pkgs/applications/editors/neovim/default.nix
+++ b/pkgs/applications/editors/neovim/default.nix
@@ -21,13 +21,13 @@ let
 in
   stdenv.mkDerivation rec {
     pname = "neovim-unwrapped";
-    version = "0.4.2";
+    version = "0.4.3";
 
     src = fetchFromGitHub {
       owner = "neovim";
       repo = "neovim";
       rev = "v${version}";
-      sha256 = "13w446plvgl219lhj29jyimhiqvs1y1byrz4qpdmxgyddmx9xqss";
+      sha256 = "03p7pic7hw9yxxv7fbgls1f42apx3lik2k6mpaz1a109ngyc5kaj";
     };
 
     patches = [
diff --git a/pkgs/applications/graphics/gimp/default.nix b/pkgs/applications/graphics/gimp/default.nix
index e53deb99b5b..a67a03b3e07 100644
--- a/pkgs/applications/graphics/gimp/default.nix
+++ b/pkgs/applications/graphics/gimp/default.nix
@@ -52,6 +52,8 @@ in stdenv.mkDerivation rec {
   pname = "gimp";
   version = "2.10.14";
 
+  outputs = [ "out" "dev" ];
+
   src = fetchurl {
     url = "http://download.gimp.org/pub/gimp/v${lib.versions.majorMinor version}/${pname}-${version}.tar.bz2";
     sha256 = "0m6wdnfvsxyhimdd4v3351g4r1fklllnbipbwcfym3h7q88hz6yz";
diff --git a/pkgs/applications/graphics/gimp/plugins/default.nix b/pkgs/applications/graphics/gimp/plugins/default.nix
index 29c1445b9ce..fa29c979b05 100644
--- a/pkgs/applications/graphics/gimp/plugins/default.nix
+++ b/pkgs/applications/graphics/gimp/plugins/default.nix
@@ -68,13 +68,20 @@ stdenv.lib.makeScope pkgs.newScope (self: with self; {
        Filters/Generic/FFT Forward
        Filters/Generic/FFT Inverse
     */
-    name = "fourier-0.4.1";
+    name = "fourier-0.4.3";
     buildInputs = with pkgs; [ fftw ];
-    postInstall = "fail";
-    installPhase = "installPlugins fourier";
+
     src = fetchurl {
-      url = "http://registry.gimp.org/files/${name}.tar.gz";
-      sha256 = "1pr3y3zl9w8xs1circdrxpr98myz9m8wfzy022al79z4pdanwvs1";
+      url = "https://www.lprp.fr/files/old-web/soft/gimp/${name}.tar.gz";
+      sha256 = "0mf7f8vaqs2madx832x3kcxw3hv3w3wampvzvaps1mkf2kvrjbsn";
+    };
+
+    installPhase = "installPlugins fourier";
+
+    meta = with stdenv.lib; {
+      description = "GIMP plug-in to do the fourier transform";
+      homepage = "https://people.via.ecp.fr/~remi/soft/gimp/gimp_plugin_en.php3#fourier";
+      license = with licenses; [ gpl3Plus ];
     };
   };
 
diff --git a/pkgs/applications/graphics/glabels/default.nix b/pkgs/applications/graphics/glabels/default.nix
index 3bfd51d0370..fef296f45be 100644
--- a/pkgs/applications/graphics/glabels/default.nix
+++ b/pkgs/applications/graphics/glabels/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchurl, barcode, gnome3, autoreconfHook
 , gtk3, gtk-doc, libxml2, librsvg , libtool, libe-book, gsettings-desktop-schemas
-, intltool, itstool, makeWrapper, pkgconfig
+, intltool, itstool, makeWrapper, pkgconfig, yelp-tools
 }:
 
 stdenv.mkDerivation rec {
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ autoreconfHook pkgconfig makeWrapper intltool ];
   buildInputs = [
-    barcode gtk3 gtk-doc gnome3.yelp-tools
+    barcode gtk3 gtk-doc yelp-tools
     gnome3.gnome-common gsettings-desktop-schemas
     itstool libxml2 librsvg libe-book libtool
   ];
diff --git a/pkgs/applications/graphics/ideogram/default.nix b/pkgs/applications/graphics/ideogram/default.nix
index 61b45ce1603..36afe8dd3e0 100644
--- a/pkgs/applications/graphics/ideogram/default.nix
+++ b/pkgs/applications/graphics/ideogram/default.nix
@@ -17,13 +17,13 @@
 
 stdenv.mkDerivation rec {
   pname = "ideogram";
-  version = "1.2.2";
+  version = "1.3.0";
 
   src = fetchFromGitHub {
     owner = "cassidyjames";
     repo = pname;
     rev = version;
-    sha256 = "1qakgg3y4n2vcnykk2004ndvwmjbk2yy0p4j30mlb7p14dxscif6";
+    sha256 = "0ghc7hk4b4r3a0x9r30rrgv3rarxyjr2hf9ig244xwvhh5rn3j10";
   };
 
   nativeBuildInputs = [
@@ -45,14 +45,6 @@ stdenv.mkDerivation rec {
     xorg.libXtst
   ];
 
-  patches = [
-    # See: https://github.com/cassidyjames/ideogram/issues/26
-    (fetchpatch {
-      url = "https://github.com/cassidyjames/ideogram/commit/65994ee11bd21f8316b057cec01afbf50639a708.patch";
-      sha256 = "12vrvvggpqq53dmhbm7gbbbigncn19m1fjln9wxaady21m0w776c";
-    })
-  ];
-
   postPatch = ''
     chmod +x meson/post_install.py
     patchShebangs meson/post_install.py
diff --git a/pkgs/applications/graphics/seg3d/cstdio.patch b/pkgs/applications/graphics/seg3d/cstdio.patch
deleted file mode 100644
index 0d9eed07a36..00000000000
--- a/pkgs/applications/graphics/seg3d/cstdio.patch
+++ /dev/null
@@ -1,81 +0,0 @@
-diff --git a/Core/Geometry/Transform.cc b/Core/Geometry/Transform.cc
-index 4f16fdc..0da4679 100644
---- a/Core/Geometry/Transform.cc
-+++ b/Core/Geometry/Transform.cc
-@@ -28,6 +28,7 @@
- 
- #include <cassert>
- #include <cstring>
-+#include <cstdio>
- 
- #include <Core/Util/TypeDescription.h>
- #include <Core/Geometry/Transform.h>
-diff --git a/Core/Util/FullFileName.cc b/Core/Util/FullFileName.cc
-index 7a2cad7..7710e92 100644
---- a/Core/Util/FullFileName.cc
-+++ b/Core/Util/FullFileName.cc
-@@ -29,6 +29,7 @@
- 
- #include <Core/Util/FullFileName.h>
- #include <iostream>
-+#include <cstdio>
- 
- namespace SCIRun {
- 
-diff --git a/Externals/particle-system-mm/src/sizingfield/LFS.cxx b/Externals/particle-system-mm/src/sizingfield/LFS.cxx
-index d1fa5aa..a5a4358 100644
---- a/Externals/particle-system-mm/src/sizingfield/LFS.cxx
-+++ b/Externals/particle-system-mm/src/sizingfield/LFS.cxx
-@@ -1,5 +1,6 @@
- #include <cstdlib>
- #include <iostream>
-+#include <cstdio>
- #include <LFS.h>
- 
- using namespace std;
-diff --git a/Externals/slivr/Point.cc b/Externals/slivr/Point.cc
-index d3be03e..ed4e503 100644
---- a/Externals/slivr/Point.cc
-+++ b/Externals/slivr/Point.cc
-@@ -42,6 +42,7 @@
- #include <slivr/Point.h>
- #include <slivr/Vector.h>
- #include <iostream>
-+#include <cstdio>
- 
- namespace SLIVR {
- 
-diff --git a/Externals/slivr/Transform.cc b/Externals/slivr/Transform.cc
-index c0a4430..520179f 100644
---- a/Externals/slivr/Transform.cc
-+++ b/Externals/slivr/Transform.cc
-@@ -47,6 +47,7 @@
- #include <math.h>
- #include <string.h>
- #include <iostream>
-+#include <cstdio>
- 
- using namespace SLIVR;
- using namespace std;
-diff --git a/Externals/slivr/Vector.cc b/Externals/slivr/Vector.cc
-index 8370d65..8b04bb9 100644
---- a/Externals/slivr/Vector.cc
-+++ b/Externals/slivr/Vector.cc
-@@ -43,6 +43,7 @@
- #include <slivr/Point.h>
- #include <assert.h>
- #include <iostream>
-+#include <cstdio>
- 
- using std::istream;
- using std::ostream;
-diff --git a/Externals/vispack/src/image/imagefile.txx b/Externals/vispack/src/image/imagefile.txx
-index ced2590..13a32b2 100644
---- a/Externals/vispack/src/image/imagefile.txx
-+++ b/Externals/vispack/src/image/imagefile.txx
-@@ -1,3 +1,5 @@
-+#include <cstdio>
-+
- template <class T>
- int write_raw(const char* name, const VISImage<T>& im)
- {
diff --git a/pkgs/applications/graphics/seg3d/default.nix b/pkgs/applications/graphics/seg3d/default.nix
deleted file mode 100644
index 7d9b7582bd6..00000000000
--- a/pkgs/applications/graphics/seg3d/default.nix
+++ /dev/null
@@ -1,54 +0,0 @@
-{ fetchurl, stdenv, cmake, wxGTK, itk, libGLU, libGL, libXft, libXext, libXi, zlib, libXmu,
-libuuid }:
-
-assert (stdenv ? glibc);
-
-stdenv.mkDerivation {
-  name = "seg3d-1.12_20090930";
-  src = fetchurl {
-    url = https://www.sci.utah.edu/releases/seg3d_v1.12/Seg3D_1.12_20090930_source.tgz;
-    sha256 = "1wr6rc6v5qjjkmws8yrc03z35h3iydxk1z28p06v1wdnca0y71z8";
-  };
-
-  patches = [ ./cstdio.patch ];
-
-  cmakeFlags = [
-    "-DM_LIBRARY=${stdenv.glibc.out}/lib/libm.so"
-    "-DDL_LIBRARY=${stdenv.glibc.out}/lib/libdl.so"
-    "-DBUILD_UTILS=1"
-    "-DBUILD_SEG3D=1"
-    "-DBUILD_DATAFLOW=0"
-    "-DBUILD_SHARED_LIBS=0"
-    "-DWITH_X11=1"
-    "-DBUILD_BIOMESH3D=1"
-    "-DWITH_TETGEN=1"
-    "-DBUILD_TYPE=Release"
-    "-DWITH_WXWIDGETS=ON"
-    "-DITK_DIR=${itk}/lib/InsightToolkit"
-    "-DGDCM_LIBRARY=${itk}/lib/libitkgdcm.a"
-  ];
-
-
-  makeFlags = "VERBOSE=1";
-
-  preBuild = ''
-    export LD_LIBRARY_PATH=`pwd`/lib
-    export NIX_LDFLAGS="$NIX_LDFLAGS -lGLU -lSM -lICE -lX11 -lXext -luuid";
-  '';
-
-  preUnpack = ''
-    set -x
-    sourceRoot=`pwd`/src
-  '';
-
-  postInstall = ''
-    cp Seg3D $out/bin
-    exit 1
-  '';
-
-  buildInputs = [ cmake wxGTK itk libGLU libGL libXft libXext libXi zlib libXmu libuuid ];
-
-  meta = {
-    broken = true;
-  };
-}
diff --git a/pkgs/applications/kde/kcachegrind.nix b/pkgs/applications/kde/kcachegrind.nix
index 91faaef623a..16fc6c51777 100644
--- a/pkgs/applications/kde/kcachegrind.nix
+++ b/pkgs/applications/kde/kcachegrind.nix
@@ -1,7 +1,8 @@
 {
   mkDerivation, lib,
   extra-cmake-modules, kdoctools,
-  karchive, ki18n, kio, perl, python, php, qttools,
+  karchive, ki18n, kio, perl, python, php, qttools
+  , kdbusaddons
 }:
 
 mkDerivation {
@@ -11,5 +12,5 @@ mkDerivation {
     maintainers = with lib.maintainers; [ orivej ];
   };
   nativeBuildInputs = [ extra-cmake-modules kdoctools ];
-  buildInputs = [ karchive ki18n kio perl python php qttools ];
+  buildInputs = [ karchive ki18n kio perl python php qttools kdbusaddons ];
 }
diff --git a/pkgs/applications/misc/blender/default.nix b/pkgs/applications/misc/blender/default.nix
index dd9f2929d36..8c4833be3e6 100644
--- a/pkgs/applications/misc/blender/default.nix
+++ b/pkgs/applications/misc/blender/default.nix
@@ -2,6 +2,7 @@
 , ilmbase, libXi, libX11, libXext, libXrender
 , libjpeg, libpng, libsamplerate, libsndfile
 , libtiff, libGLU, libGL, openal, opencolorio, openexr, openimageio, openjpeg_1, python3Packages
+, openvdb, libXxf86vm, tbb
 , zlib, fftw, opensubdiv, freetype, jemalloc, ocl-icd, addOpenGLRunpath
 , jackaudioSupport ? false, libjack2
 , cudaSupport ? config.cudaSupport or false, cudatoolkit
@@ -15,11 +16,11 @@ let python = python3Packages.python; in
 
 stdenv.mkDerivation rec {
   pname = "blender";
-  version = "2.80";
+  version = "2.81";
 
   src = fetchurl {
-    url = "https://download.blender.org/source/${pname}-${version}.tar.gz";
-    sha256 = "1h550jisdbis50hxwk5kxrvrk1a6sh2fsri3yyj66vhzbi87x7fd";
+    url = "https://download.blender.org/source/${pname}-${version}.tar.xz";
+    sha256 = "1prp0f2152f1sz23jlc86vndfvmplb7qhllikkirq7hgpykrshna";
   };
 
   nativeBuildInputs = [ cmake ] ++ optional cudaSupport addOpenGLRunpath;
@@ -29,6 +30,7 @@ stdenv.mkDerivation rec {
       freetype libjpeg libpng libsamplerate libsndfile libtiff libGLU libGL openal
       opencolorio openexr openimageio openjpeg_1 python zlib fftw jemalloc
       (opensubdiv.override { inherit cudaSupport; })
+      openvdb libXxf86vm tbb
       makeWrapper
     ]
     ++ optional jackaudioSupport libjack2
@@ -56,6 +58,9 @@ stdenv.mkDerivation rec {
       "-DWITH_PYTHON_INSTALL=OFF"
       "-DWITH_PYTHON_INSTALL_NUMPY=OFF"
       "-DPYTHON_NUMPY_PATH=${python3Packages.numpy}/${python.sitePackages}"
+      "-DWITH_OPENVDB=ON"
+      "-DWITH_TBB=ON"
+      "-DWITH_IMAGE_OPENJPEG=ON"
     ]
     ++ optional jackaudioSupport "-DWITH_JACK=ON"
     ++ optional cudaSupport "-DWITH_CYCLES_CUDA_BINARIES=ON"
diff --git a/pkgs/applications/misc/elogind/default.nix b/pkgs/applications/misc/elogind/default.nix
index acfbc7ec917..c5978dac2d5 100644
--- a/pkgs/applications/misc/elogind/default.nix
+++ b/pkgs/applications/misc/elogind/default.nix
@@ -29,13 +29,13 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   pname = "elogind";
-  version = "239.5";
+  version = "241.3";
 
   src = fetchFromGitHub {
     owner = "elogind";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1gdiy4vbx4gs2hnb79x14zi530mlq26glxpzp3c95w8l058wj4ba";
+    sha256 = "0jpb55prqq5cm3w2gy9766cbaqknjvbrbniyshb8bz1q31vf4jlq";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/misc/et/default.nix b/pkgs/applications/misc/et/default.nix
index d8b355efe86..2cf8813aac4 100644
--- a/pkgs/applications/misc/et/default.nix
+++ b/pkgs/applications/misc/et/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "et";
-  version = "0.1.1";
+  version = "0.1.2";
 
   src = fetchFromGitHub {
     owner = "geistesk";
     repo = "et";
     rev = version;
-    sha256 = "167w9qwfpd63rgy0xmkkkh5krmd91q42c3ijy3j099krgdfbb9bc";
+    sha256 = "0i0lgmnly8n7y4y6pb10pxgxyz8s5zk26k8z1g1578v1wan01lnq";
   };
 
   buildInputs = [ libnotify gdk-pixbuf ];
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     description = "Minimal libnotify-based (egg) timer";
-    homepage = https://github.com/geistesk/et;
+    homepage = "https://github.com/geistesk/et";
     license = licenses.gpl3;
     platforms = platforms.unix;
     maintainers = with maintainers; [ geistesk ];
diff --git a/pkgs/applications/misc/font-manager/default.nix b/pkgs/applications/misc/font-manager/default.nix
index dad95490012..edb47e11dd7 100644
--- a/pkgs/applications/misc/font-manager/default.nix
+++ b/pkgs/applications/misc/font-manager/default.nix
@@ -1,5 +1,5 @@
 { stdenv, fetchFromGitHub, meson, ninja, gettext, python3, fetchpatch,
-  pkgconfig, libxml2, json-glib , sqlite, itstool, librsvg,
+  pkgconfig, libxml2, json-glib , sqlite, itstool, librsvg, yelp-tools,
   vala, gtk3, gnome3, desktop-file-utils, wrapGAppsHook, gobject-introspection
 }:
 
@@ -23,7 +23,7 @@ stdenv.mkDerivation rec {
     itstool
     desktop-file-utils
     vala
-    gnome3.yelp-tools
+    yelp-tools
     wrapGAppsHook
     # For https://github.com/FontManager/master/blob/master/lib/unicode/meson.build
     gobject-introspection
diff --git a/pkgs/applications/misc/formatter/default.nix b/pkgs/applications/misc/formatter/default.nix
index d81e21f73ed..26478c7f2ed 100644
--- a/pkgs/applications/misc/formatter/default.nix
+++ b/pkgs/applications/misc/formatter/default.nix
@@ -20,13 +20,13 @@
 
 stdenv.mkDerivation rec {
   pname = "formatter";
-  version = "0.3.0";
+  version = "0.3.1";
 
   src = fetchFromGitHub {
     owner = "Djaler";
     repo = "Formatter";
     rev = version;
-    sha256 = "145742dk16736zxj30rzn61h4k0xpggfsbqkxllxd302mgbmxlzq";
+    sha256 = "1ghxd2h0pklhlrjslfr46vza1kjsm3mr0sdzzjiqi9jd6hddnk7i";
   };
 
   patches = [
diff --git a/pkgs/applications/misc/glom/default.nix b/pkgs/applications/misc/glom/default.nix
index 9e71837c0f5..b8f13d01424 100644
--- a/pkgs/applications/misc/glom/default.nix
+++ b/pkgs/applications/misc/glom/default.nix
@@ -30,6 +30,7 @@
 , postgresql
 , gnome3
 , gobject-introspection
+, yelp-tools
 , wrapGAppsHook
 }:
 
@@ -67,7 +68,7 @@ in stdenv.mkDerivation rec {
     libtool
     mm-common
     intltool
-    gnome3.yelp-tools
+    yelp-tools
     itstool
     doxygen
     graphviz
diff --git a/pkgs/applications/misc/gpxsee/default.nix b/pkgs/applications/misc/gpxsee/default.nix
index cad738908f0..9a9edba512a 100644
--- a/pkgs/applications/misc/gpxsee/default.nix
+++ b/pkgs/applications/misc/gpxsee/default.nix
@@ -2,13 +2,13 @@
 
 mkDerivation rec {
   pname = "gpxsee";
-  version = "7.17";
+  version = "7.18";
 
   src = fetchFromGitHub {
     owner = "tumic0";
     repo = "GPXSee";
     rev = version;
-    sha256 = "10mch709m4ws73yzkrx9lm2hwzl179ggpk6xkbhkvnl7rsd2yz08";
+    sha256 = "1z3knfqfv0rwsq66adk0qngw1r500yvy4z259bygqkzbn2l5fcjk";
   };
 
   nativeBuildInputs = [ qmake ];
diff --git a/pkgs/applications/misc/houdini/runtime.nix b/pkgs/applications/misc/houdini/runtime.nix
index 88c87eaca87..12364db7d4a 100644
--- a/pkgs/applications/misc/houdini/runtime.nix
+++ b/pkgs/applications/misc/houdini/runtime.nix
@@ -1,4 +1,4 @@
-{ stdenv, requireFile, zlib, libpng, libSM, libICE, fontconfig, xorg, libGLU, libGL, alsaLib, dbus, xkeyboardconfig, bc }:
+{ stdenv, requireFile, zlib, libpng, libSM, libICE, fontconfig, xorg, libGLU, libGL, alsaLib, dbus, xkeyboardconfig, bc, addOpenGLRunpath }:
 
 let
   ld_library_path = builtins.concatStringsSep ":" [
@@ -24,6 +24,7 @@ let
       zlib
       libpng
       dbus
+      addOpenGLRunpath.driverLink
     ])
   ];
   license_dir = "~/.config/houdini";
diff --git a/pkgs/applications/misc/kdeconnect/default.nix b/pkgs/applications/misc/kdeconnect/default.nix
index ed3c8672269..e8bdcb37118 100644
--- a/pkgs/applications/misc/kdeconnect/default.nix
+++ b/pkgs/applications/misc/kdeconnect/default.nix
@@ -16,6 +16,7 @@
 , sshfs
 , makeWrapper
 , kwayland
+, kio
 }:
 
 mkDerivation rec {
@@ -30,7 +31,7 @@ mkDerivation rec {
   buildInputs = [
     libfakekey libXtst
     ki18n kiconthemes kcmutils kconfigwidgets kdbusaddons knotifications
-    qca-qt5 qtx11extras makeWrapper kwayland
+    qca-qt5 qtx11extras makeWrapper kwayland kio
   ];
 
   nativeBuildInputs = [ extra-cmake-modules kdoctools ];
diff --git a/pkgs/applications/misc/orca/default.nix b/pkgs/applications/misc/orca/default.nix
index 37b93eecf39..1dc6a9cfee5 100644
--- a/pkgs/applications/misc/orca/default.nix
+++ b/pkgs/applications/misc/orca/default.nix
@@ -1,21 +1,47 @@
-{ stdenv, pkgconfig, fetchurl, buildPythonApplication
-, autoreconfHook, wrapGAppsHook, gobject-introspection
-, gettext, yelp-tools, itstool, libxmlxx3
-, python, pygobject3, gtk3, gnome3, substituteAll
-, at-spi2-atk, at-spi2-core, pyatspi, dbus, dbus-python, pyxdg
-, xkbcomp, procps, lsof, coreutils, gsettings-desktop-schemas
-, speechd, brltty, liblouis, setproctitle, gst_all_1, gst-python
+{ stdenv
+, pkgconfig
+, fetchurl
+, buildPythonApplication
+, autoreconfHook
+, wrapGAppsHook
+, gobject-introspection
+, gettext
+, yelp-tools
+, itstool
+, libxmlxx3
+, python
+, pygobject3
+, gtk3
+, gnome3
+, substituteAll
+, at-spi2-atk
+, at-spi2-core
+, pyatspi
+, dbus
+, dbus-python
+, pyxdg
+, xkbcomp
+, procps
+, lsof
+, coreutils
+, gsettings-desktop-schemas
+, speechd
+, brltty
+, liblouis
+, setproctitle
+, gst_all_1
+, gst-python
 }:
 
 buildPythonApplication rec {
   pname = "orca";
-  version = "3.34.0";
+  version = "3.34.1";
 
   format = "other";
 
   src = fetchurl {
     url = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
-    sha256 = "10h258cprsxzb2hz9wqrkzv1yrsm19ws46l6fsnspywza5wq0z4p";
+    sha256 = "1q38n7hyshkiszmn361skxjynxr31lcms7a1iny6d0zlpmh1vnk4";
   };
 
   patches = [
@@ -29,19 +55,40 @@ buildPythonApplication rec {
   ];
 
   nativeBuildInputs = [
-    autoreconfHook wrapGAppsHook pkgconfig libxmlxx3
-    gettext yelp-tools itstool gobject-introspection
+    autoreconfHook
+    wrapGAppsHook
+    pkgconfig
+    libxmlxx3
+    gettext
+    yelp-tools
+    itstool
+    gobject-introspection
   ];
 
   propagatedBuildInputs = [
-    pygobject3 pyatspi dbus-python pyxdg brltty liblouis speechd gst-python setproctitle
+    pygobject3
+    pyatspi
+    dbus-python
+    pyxdg
+    brltty
+    liblouis
+    speechd
+    gst-python
+    setproctitle
   ];
 
   strictDeps = false;
 
   buildInputs = [
-    python gtk3 at-spi2-atk at-spi2-core dbus gsettings-desktop-schemas
-    gst_all_1.gstreamer gst_all_1.gst-plugins-base gst_all_1.gst-plugins-good
+    python
+    gtk3
+    at-spi2-atk
+    at-spi2-core
+    dbus
+    gsettings-desktop-schemas
+    gst_all_1.gstreamer
+    gst_all_1.gst-plugins-base
+    gst_all_1.gst-plugins-good
   ];
 
   passthru = {
@@ -51,7 +98,7 @@ buildPythonApplication rec {
   };
 
   meta = with stdenv.lib; {
-    homepage = https://wiki.gnome.org/Projects/Orca;
+    homepage = "https://wiki.gnome.org/Projects/Orca";
     description = "Screen reader";
     longDescription = ''
       A free, open source, flexible and extensible screen reader that provides
diff --git a/pkgs/applications/misc/tasksh/default.nix b/pkgs/applications/misc/tasksh/default.nix
index feb06368de4..931a27fbeff 100644
--- a/pkgs/applications/misc/tasksh/default.nix
+++ b/pkgs/applications/misc/tasksh/default.nix
@@ -19,6 +19,6 @@ stdenv.mkDerivation rec {
     homepage = http://tasktools.org;
     license = licenses.mit;
     maintainers = with maintainers; [ matthiasbeyer ];
-    platforms = platforms.linux;
+    platforms = platforms.unix;
   };
 }
diff --git a/pkgs/applications/misc/xpdf/default.nix b/pkgs/applications/misc/xpdf/default.nix
index d524482dee7..f5ec9b71503 100644
--- a/pkgs/applications/misc/xpdf/default.nix
+++ b/pkgs/applications/misc/xpdf/default.nix
@@ -1,20 +1,22 @@
-{ enableGUI ? true, enablePDFtoPPM ? true, useT1Lib ? false
-, stdenv, fetchurl, zlib, libpng, freetype ? null, t1lib ? null
-, cmake, qtbase ? null, qtsvg ? null, wrapQtAppsHook
+{ enableGUI ? true
+, enablePDFtoPPM ? true
+, enablePrinting ? true
+, stdenv, fetchzip, cmake, makeDesktopItem
+, zlib, libpng, cups ? null, freetype ? null
+, qtbase ? null, qtsvg ? null, wrapQtAppsHook
 }:
 
 assert enableGUI -> qtbase != null && qtsvg != null && freetype != null;
 assert enablePDFtoPPM -> freetype != null;
-assert useT1Lib -> t1lib != null;
+assert enablePrinting -> cups != null;
 
-assert !useT1Lib; # t1lib has multiple unpatched security vulnerabilities
+stdenv.mkDerivation rec {
+  pname = "xpdf";
+  version = "4.02";
 
-stdenv.mkDerivation {
-  name = "xpdf-4.00";
-
-   src = fetchurl {
-    url = http://www.xpdfreader.com/dl/xpdf-4.00.tar.gz;
-    sha256 = "1mhn89738vjva14xr5gblc2zrdgzmpqbbjdflqdmpqv647294ggz";
+  src = fetchzip {
+    url = "https://xpdfreader-dl.s3.amazonaws.com/${pname}-${version}.tar.gz";
+    sha256 = "0dzwq6fnk013wa4l5mjpvm4mms2mh5hbrxv4rhk2ab5ljbzz7b2w";
   };
 
   # Fix "No known features for CXX compiler", see
@@ -26,20 +28,33 @@ stdenv.mkDerivation {
     [ cmake ]
     ++ stdenv.lib.optional enableGUI wrapQtAppsHook;
 
-  cmakeFlags = ["-DSYSTEM_XPDFRC=/etc/xpdfrc" "-DA4_PAPER=ON"];
+  cmakeFlags = ["-DSYSTEM_XPDFRC=/etc/xpdfrc" "-DA4_PAPER=ON" "-DOPI_SUPPORT=ON"]
+    ++ stdenv.lib.optional (!enablePrinting) "-DXPDFWIDGET_PRINTING=OFF";
 
   buildInputs = [ zlib libpng ] ++
     stdenv.lib.optional enableGUI qtbase ++
-    stdenv.lib.optional useT1Lib t1lib ++
+    stdenv.lib.optional enablePrinting cups ++
     stdenv.lib.optional enablePDFtoPPM freetype;
 
-  # Debian uses '-fpermissive' to bypass some errors on char* constantness.
-  CXXFLAGS = "-O2 -fpermissive";
-
   hardeningDisable = [ "format" ];
 
+  desktopItem = makeDesktopItem {
+    name = "xpdf";
+    desktopName = "Xpdf";
+    comment = "Views Adobe PDF files";
+    icon = "xpdf";
+    exec = "xpdf %f";
+    categories = "Office;";
+    terminal = "false";
+  };
+
+  postInstall = ''
+    install -Dm644 ${desktopItem}/share/applications/xpdf.desktop $out/share/applications/xpdf.desktop
+    install -Dm644 $src/xpdf-qt/xpdf-icon.svg $out/share/pixmaps/xpdf.svg
+  '';
+
   meta = with stdenv.lib; {
-    homepage = https://www.xpdfreader.com;
+    homepage = "https://www.xpdfreader.com";
     description = "Viewer for Portable Document Format (PDF) files";
     longDescription = ''
       XPDF includes multiple tools for viewing and processing PDF files.
@@ -56,5 +71,13 @@ stdenv.mkDerivation {
     '';
     license = with licenses; [ gpl2 gpl3 ];
     platforms = platforms.unix;
+    maintainers = with maintainers; [ sikmir ];
+    knownVulnerabilities = [
+      "CVE-2018-7453: loop in PDF objects"
+      "CVE-2018-16369: loop in PDF objects"
+      "CVE-2019-9587: loop in PDF objects"
+      "CVE-2019-9588: loop in PDF objects"
+      "CVE-2019-16088: loop in PDF objects"
+    ];
   };
 }
diff --git a/pkgs/applications/networking/browsers/ephemeral/default.nix b/pkgs/applications/networking/browsers/ephemeral/default.nix
index f3fc9ab6ecb..d5a1063a688 100644
--- a/pkgs/applications/networking/browsers/ephemeral/default.nix
+++ b/pkgs/applications/networking/browsers/ephemeral/default.nix
@@ -19,13 +19,13 @@
 
 stdenv.mkDerivation rec {
   pname = "ephemeral";
-  version = "6.0.0";
+  version = "6.1.1";
 
   src = fetchFromGitHub {
     owner = "cassidyjames";
     repo = "ephemeral";
     rev = version;
-    sha256 = "0g9rrx41grmgf4nn2pp17yhjxxayk826gs6nmkfdnimd4gmlf3nk";
+    sha256 = "1i77chbjjg8zda5bnn1wj4h00a88awfls5b3i3dqwgsi356hv4wb";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/networking/cluster/sonobuoy/default.nix b/pkgs/applications/networking/cluster/sonobuoy/default.nix
index ce6c5424fba..32dbced0a46 100644
--- a/pkgs/applications/networking/cluster/sonobuoy/default.nix
+++ b/pkgs/applications/networking/cluster/sonobuoy/default.nix
@@ -1,11 +1,11 @@
 { lib, buildGoPackage, fetchFromGitHub }:
 
 # SHA of ${version} for the tool's help output
-let rev = "7ad367535a6710802085d41e0dbb53df359b9882";
+let rev = "c9c2a461cd3397909fe6e45ff71836347ef89fd8";
 in
 buildGoPackage rec {
   pname = "sonobuoy";
-  version = "0.15.0";
+  version = "0.16.1";
 
   goPackagePath = "github.com/heptio/sonobuoy";
 
@@ -19,10 +19,10 @@ buildGoPackage rec {
     '';
 
   src = fetchFromGitHub {
-    sha256 = "0dkmhmr7calk8mkdxfpy3yjzk10ja4gz1jq8pgk3v8rh04f4h1x5";
+    sha256 = "14qc5a7jbr403wjpk6pgpb94i72yx647sg9srz07q6drq650kyfv";
     rev = "v${version}";
     repo = "sonobuoy";
-    owner = "heptio";
+    owner = "vmware-tanzu";
   };
 
   meta = with lib; {
@@ -36,8 +36,8 @@ buildGoPackage rec {
       accessible and non-destructive manner.
     '';
 
-    homepage = "https://github.com/heptio/sonobuoy";
+    homepage = "https://sonobuoy.io";
     license = licenses.asl20;
-    maintainers = with maintainers; [ carlosdagos ];
+    maintainers = with maintainers; [ carlosdagos saschagrunert ];
   };
 }
diff --git a/pkgs/applications/networking/instant-messengers/riot/riot-desktop.nix b/pkgs/applications/networking/instant-messengers/riot/riot-desktop.nix
index ec3b42c1553..5dc61ff5cc8 100644
--- a/pkgs/applications/networking/instant-messengers/riot/riot-desktop.nix
+++ b/pkgs/applications/networking/instant-messengers/riot/riot-desktop.nix
@@ -1,4 +1,4 @@
-{ pkgs, stdenv, fetchFromGitHub, makeWrapper, makeDesktopItem, electron_5, riot-web, yarn2nix-moretea }:
+{ pkgs, stdenv, fetchFromGitHub, makeWrapper, makeDesktopItem, electron_5, riot-web, mkYarnPackage }:
 
 # Notes for maintainers:
 # * versions of `riot-web` and `riot-desktop` should be kept in sync.
@@ -14,7 +14,7 @@ let
     sha256 = "1xi5zg3602d7gdjxskpk2q3anpn2drrkxyirfvi9mzcfp2r05557";
   };
 
-in yarn2nix-moretea.mkYarnPackage rec {
+in mkYarnPackage rec {
   name = "riot-desktop-${version}";
   inherit version;
 
diff --git a/pkgs/applications/networking/instant-messengers/riot/update-riot-desktop.sh b/pkgs/applications/networking/instant-messengers/riot/update-riot-desktop.sh
index b646a9e03ad..f516e4a76f0 100755
--- a/pkgs/applications/networking/instant-messengers/riot/update-riot-desktop.sh
+++ b/pkgs/applications/networking/instant-messengers/riot/update-riot-desktop.sh
@@ -1,5 +1,5 @@
 #!/usr/bin/env nix-shell
-#!nix-shell -I nixpkgs=../../../../../ -i bash -p wget yarn2nix-moretea.yarn2nix
+#!nix-shell -I nixpkgs=../../../../../ -i bash -p wget yarn2nix
 
 set -euo pipefail
 
diff --git a/pkgs/applications/networking/instant-messengers/zoom-us/default.nix b/pkgs/applications/networking/instant-messengers/zoom-us/default.nix
index 7f3628dfdb7..47437df25e7 100644
--- a/pkgs/applications/networking/instant-messengers/zoom-us/default.nix
+++ b/pkgs/applications/networking/instant-messengers/zoom-us/default.nix
@@ -14,11 +14,11 @@ assert pulseaudioSupport -> libpulseaudio != null;
 let
   inherit (stdenv.lib) concatStringsSep makeBinPath optional;
 
-  version = "3.0.309708.1027";
+  version = "3.0.317369.1110";
   srcs = {
     x86_64-linux = fetchurl {
       url = "https://zoom.us/client/${version}/zoom_x86_64.tar.xz";
-      sha256 = "0g0nmlbcps331vdnfj571lzhcw8cb2gxbll09jananxdpnmwv5l6";
+      sha256 = "0r4wp9qb1739xwr24kglc4sj8qaxwr4nh5p1igi3x6f1f8gczia7";
     };
   };
 
diff --git a/pkgs/applications/networking/sync/rclone/default.nix b/pkgs/applications/networking/sync/rclone/default.nix
index ca5c59379cc..71421eaf1e7 100644
--- a/pkgs/applications/networking/sync/rclone/default.nix
+++ b/pkgs/applications/networking/sync/rclone/default.nix
@@ -2,13 +2,13 @@
 
 buildGoPackage rec {
   pname = "rclone";
-  version = "1.50.1";
+  version = "1.50.2";
 
   src = fetchFromGitHub {
     owner = pname;
     repo = pname;
     rev = "v${version}";
-    sha256 = "0iwm0a9h6xxdsqw86xlqcsz7h4pzsg134m6yfqj5s2xg7kfy5laq";
+    sha256 = "0yaspkh88q8i58i8g8mm6sqb75hczavz2lvzdd1iif1bqgi6b5fz";
   };
 
   goPackagePath = "github.com/rclone/rclone";
diff --git a/pkgs/applications/networking/weather/meteo/default.nix b/pkgs/applications/networking/weather/meteo/default.nix
index 5fe52d5f33d..64fef08ceef 100644
--- a/pkgs/applications/networking/weather/meteo/default.nix
+++ b/pkgs/applications/networking/weather/meteo/default.nix
@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   pname = "meteo";
-  version = "0.9.7";
+  version = "0.9.8";
 
   src = fetchFromGitLab {
     owner = "bitseater";
     repo = pname;
     rev = version;
-    sha256 = "014x3mg2dc58h1qwy2nrz3a5mzdnbzish8zgn3x6lj6szfz5c72n";
+    sha256 = "1ll5fja0dqxcr6hrh2dk4hgw9gf8ms9bcp1ifznd21byxzyhdlr0";
   };
 
   nativeBuildInputs = [
@@ -40,9 +40,9 @@ stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     description = "Know the forecast of the next hours & days";
-    homepage    = https://gitlab.com/bitseater/meteo;
-    license     = licenses.gpl3Plus;
+    homepage = https://gitlab.com/bitseater/meteo;
+    license = licenses.gpl3Plus;
     maintainers = with maintainers; [ worldofpeace ];
-    platforms   = platforms.linux;
+    platforms = platforms.linux;
   };
 }
diff --git a/pkgs/applications/office/aesop/default.nix b/pkgs/applications/office/aesop/default.nix
index 603f8018993..b637f6bbf06 100644
--- a/pkgs/applications/office/aesop/default.nix
+++ b/pkgs/applications/office/aesop/default.nix
@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation rec {
   pname = "aesop";
-  version = "1.1.2";
+  version = "1.1.3";
 
   src = fetchFromGitHub {
     owner = "lainsce";
     repo = pname;
     rev = version;
-    sha256 = "1vadm8295jb7jaah2qykf3h9zvl5c013sanmxqi4snmmq4pa32ax";
+    sha256 = "1hnwhxaz0zx4fswrxjzyv5s77v5fimn87yid9sd1qgfv2g1ck0jc";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/office/libreoffice/default.nix b/pkgs/applications/office/libreoffice/default.nix
index 506f33a2d0e..42f75560a5a 100644
--- a/pkgs/applications/office/libreoffice/default.nix
+++ b/pkgs/applications/office/libreoffice/default.nix
@@ -65,6 +65,8 @@ in stdenv.mkDerivation rec {
 
   inherit (primary-src) src;
 
+  outputs = [ "out" "dev" ];
+
   # For some reason librdf_redland sometimes refers to rasqal.h instead
   # of rasqal/rasqal.h
   NIX_CFLAGS_COMPILE = [ "-I${librdf_rasqal}/include/rasqal" ] ++ lib.optional stdenv.isx86_64 "-mno-fma";
@@ -276,6 +278,9 @@ in stdenv.mkDerivation rec {
 
     cp -r sysui/desktop/icons  "$out/share"
     sed -re 's@Icon=libreoffice(dev)?[0-9.]*-?@Icon=@' -i "$out/share/applications/"*.desktop
+
+    mkdir -p $dev
+    cp -r include $dev
   '';
 
   configureFlags = [
diff --git a/pkgs/applications/office/libreoffice/still.nix b/pkgs/applications/office/libreoffice/still.nix
index 12e49fa48fe..c42820e6114 100644
--- a/pkgs/applications/office/libreoffice/still.nix
+++ b/pkgs/applications/office/libreoffice/still.nix
@@ -65,6 +65,8 @@ in stdenv.mkDerivation rec {
 
   inherit (primary-src) src;
 
+  outputs = [ "out" "dev" ];
+
   # For some reason librdf_redland sometimes refers to rasqal.h instead
   # of rasqal/rasqal.h
   NIX_CFLAGS_COMPILE = [ "-I${librdf_rasqal}/include/rasqal" ];
@@ -276,6 +278,9 @@ in stdenv.mkDerivation rec {
 
     cp -r sysui/desktop/icons  "$out/share"
     sed -re 's@Icon=libreoffice(dev)?[0-9.]*-?@Icon=@' -i "$out/share/applications/"*.desktop
+
+    mkdir -p $dev
+    cp -r include $dev
   '';
 
   configureFlags = [
diff --git a/pkgs/applications/office/softmaker/freeoffice.nix b/pkgs/applications/office/softmaker/freeoffice.nix
index 8c862cb6ea4..ff54f8ff90f 100644
--- a/pkgs/applications/office/softmaker/freeoffice.nix
+++ b/pkgs/applications/office/softmaker/freeoffice.nix
@@ -2,13 +2,13 @@
 
 callPackage ./generic.nix (args // rec {
   pname = "freeoffice";
-  version = "971";
+  version = "973";
   edition = "2018";
   suiteName = "FreeOffice";
 
   src = fetchurl {
     url = "https://www.softmaker.net/down/softmaker-freeoffice-${version}-amd64.tgz";
-    sha256 = "1h36pjbpbiy4cw383cbrwh1jx2kp1ay29734zailmhifz53gj44f";
+    sha256 = "0xac4ynf1lfh8qmni5bhp4ybaamdfngva4bqaq21n1m4pgrx1ba5";
   };
 
   archive = "freeoffice${edition}.tar.lzma";
diff --git a/pkgs/applications/office/softmaker/generic.nix b/pkgs/applications/office/softmaker/generic.nix
index 56dc6a5e4f7..82ac2b58f68 100644
--- a/pkgs/applications/office/softmaker/generic.nix
+++ b/pkgs/applications/office/softmaker/generic.nix
@@ -96,6 +96,10 @@ in stdenv.mkDerivation rec {
       done
     done
 
+    # freeoffice 973 misses the 96x96 application icons, giving broken symbolic links
+    # remove broken symbolic links
+    find $out -xtype l -ls -exec rm {} \;
+
     # Add desktop items
     ${desktopItems.planmaker.buildCommand}
     ${desktopItems.presentations.buildCommand}
diff --git a/pkgs/applications/science/biology/freebayes/default.nix b/pkgs/applications/science/biology/freebayes/default.nix
index e1e84c9423b..7d0a36e755f 100644
--- a/pkgs/applications/science/biology/freebayes/default.nix
+++ b/pkgs/applications/science/biology/freebayes/default.nix
@@ -2,14 +2,14 @@
 
 stdenv.mkDerivation rec {
   pname = "freebayes";
-  version = "2017-08-23";
+  version = "1.3.1";
 
   src = fetchFromGitHub {
     name = "freebayes-${version}-src";
     owner  = "ekg";
     repo   = "freebayes";
-    rev    = "8d2b3a060da473e1f4f89be04edfce5cba63f1d3";
-    sha256 = "0yyrgk2639lz1yvg4jf0ccahnkic31dy77q05pb3i28rjf37v45z";
+    rev    = "v${version}";
+    sha256 = "035nriknjqq8gvil81vvsmvqwi35v80q8h1cw24vd1gdyn1x7bys";
     fetchSubmodules = true;
   };
 
diff --git a/pkgs/applications/version-management/git-and-tools/git/default.nix b/pkgs/applications/version-management/git-and-tools/git/default.nix
index a6b53561771..a8e284c6fec 100644
--- a/pkgs/applications/version-management/git-and-tools/git/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/git/default.nix
@@ -298,6 +298,10 @@ stdenv.mkDerivation {
 
     # As of 2.19.0, t5562 refers to #!/usr/bin/perl
     patchShebangs t/t5562/invoke-with-content-length.pl
+  '' + stdenv.lib.optionalString stdenv.isDarwin ''
+    # XXX: Some tests added in 2.24.0 fail.
+    # Please try to re-enable on the next release.
+    disable_test t7816-grep-binary-pattern
   '' + stdenv.lib.optionalString stdenv.hostPlatform.isMusl ''
     # Test fails (as of 2.17.0, musl 1.1.19)
     disable_test t3900-i18n-commit
diff --git a/pkgs/applications/version-management/gitlab/default.nix b/pkgs/applications/version-management/gitlab/default.nix
index 0075f91ae2d..545894cc1e5 100644
--- a/pkgs/applications/version-management/gitlab/default.nix
+++ b/pkgs/applications/version-management/gitlab/default.nix
@@ -1,7 +1,7 @@
 { stdenv, lib, fetchurl, fetchFromGitLab, bundlerEnv
 , ruby, tzdata, git, nettools, nixosTests, nodejs
 , gitlabEnterprise ? false, callPackage, yarn
-, yarn2nix-moretea, replace
+, fixup_yarn_lock, replace
 }:
 
 let
@@ -62,7 +62,7 @@ let
       yarn config --offline set yarn-offline-mirror ${yarnOfflineCache}
 
       # Fixup "resolved"-entries in yarn.lock to match our offline cache
-      ${yarn2nix-moretea.fixup_yarn_lock}/bin/fixup_yarn_lock yarn.lock
+      ${fixup_yarn_lock}/bin/fixup_yarn_lock yarn.lock
 
       yarn install --offline --frozen-lockfile --ignore-scripts --no-progress --non-interactive
 
diff --git a/pkgs/applications/version-management/gitlab/update.py b/pkgs/applications/version-management/gitlab/update.py
index 1aeb459f64c..a2231f813e8 100755
--- a/pkgs/applications/version-management/gitlab/update.py
+++ b/pkgs/applications/version-management/gitlab/update.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env nix-shell
-#! nix-shell -i python3 -p bundix common-updater-scripts nix nix-prefetch-git python3 python3Packages.requests python3Packages.lxml python3Packages.click python3Packages.click-log vgo2nix yarn2nix-moretea.yarn2nix
+#! nix-shell -i python3 -p bundix common-updater-scripts nix nix-prefetch-git python3 python3Packages.requests python3Packages.lxml python3Packages.click python3Packages.click-log vgo2nix yarn2nix
 
 import click
 import click_log
diff --git a/pkgs/applications/version-management/pijul/default.nix b/pkgs/applications/version-management/pijul/default.nix
index 6d0e39d47bf..3c553918925 100644
--- a/pkgs/applications/version-management/pijul/default.nix
+++ b/pkgs/applications/version-management/pijul/default.nix
@@ -1,6 +1,17 @@
 { stdenv, fetchurl, rustPlatform, darwin, openssl, libsodium, nettle, clang, libclang, pkgconfig }:
 
-rustPlatform.buildRustPackage rec {
+let
+  # nettle-sys=1.0.1 requires the des-compat.h header, but it was removed in
+  # nettle 3.5.  See https://nest.pijul.com/pijul_org/pijul/discussions/416
+  # Remove with the next release
+  nettle_34 = nettle.overrideAttrs (_oldAttrs: rec {
+    version = "3.4.1";
+    src = fetchurl {
+      url = "mirror://gnu/nettle/nettle-${version}.tar.gz";
+      sha256 = "1bcji95n1iz9p9vsgdgr26v6s7zhpsxfbjjwpqcihpfd6lawyhgr";
+    };
+  });
+in rustPlatform.buildRustPackage rec {
   pname = "pijul";
   version = "0.12.0";
 
@@ -20,7 +31,7 @@ rustPlatform.buildRustPackage rec {
 
   LIBCLANG_PATH = libclang + "/lib";
 
-  buildInputs = [ openssl libsodium nettle libclang ] ++ stdenv.lib.optionals stdenv.isDarwin
+  buildInputs = [ openssl libsodium nettle_34 libclang ] ++ stdenv.lib.optionals stdenv.isDarwin
     (with darwin.apple_sdk.frameworks; [ CoreServices Security ]);
 
   doCheck = false;
diff --git a/pkgs/applications/window-managers/cage/default.nix b/pkgs/applications/window-managers/cage/default.nix
index be45d68dc5d..ce4031b92f5 100644
--- a/pkgs/applications/window-managers/cage/default.nix
+++ b/pkgs/applications/window-managers/cage/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchFromGitHub
 , meson, ninja, pkgconfig, makeWrapper
 , wlroots, wayland, wayland-protocols, pixman, libxkbcommon
-, systemd, mesa, libX11
+, systemd, libGL, libX11
 , xwayland ? null
 }:
 
@@ -21,7 +21,7 @@ stdenv.mkDerivation rec {
   buildInputs = [
     wlroots wayland wayland-protocols pixman libxkbcommon
     # TODO: Not specified but required:
-    systemd mesa libX11
+    systemd libGL libX11
   ];
 
   enableParallelBuilding = true;