Merge staging-next-21.11 into staging-21.11

github-actions[bot] · web-flow · commit ee8ff1d82826 · 2021-12-15T00:10:31.000Z
diff --git a/nixos/doc/manual/from_md/release-notes/rl-2111.section.xml b/nixos/doc/manual/from_md/release-notes/rl-2111.section.xml
@@ -2040,6 +2040,17 @@ Superuser created successfully.
           hydrus manual</link>.
         </para>
       </listitem>
+      <listitem>
+        <para>
+          <literal>pkgs.emacsPackages.orgPackages</literal> is removed
+          because org elpa is deprecated. The packages in the top level
+          of <literal>pkgs.emacsPackages</literal>, such as org and
+          org-contrib, refer to the ones in
+          <literal>pkgs.emacsPackages.elpaPackages</literal> and
+          <literal>pkgs.emacsPackages.nongnuPackages</literal> where the
+          new versions will release.
+        </para>
+      </listitem>
     </itemizedlist>
   </section>
 </section>
diff --git a/nixos/doc/manual/release-notes/rl-2111.section.md b/nixos/doc/manual/release-notes/rl-2111.section.md
@@ -551,3 +551,5 @@ In addition to numerous new and upgraded packages, this release has the followin
 - RetroArch has been upgraded from version `1.8.5` to `1.9.13.2`. Since the previous release was quite old, if you're having issues after the upgrade, please delete your `$XDG_CONFIG_HOME/retroarch/retroarch.cfg` file.
 
 - hydrus has been upgraded from version `438` to `463`. Since upgrading between releases this old is advised against, be sure to have a backup of your data before upgrading. For details, see [the hydrus manual](https://hydrusnetwork.github.io/hydrus/help/getting_started_installing.html#big_updates).
+
+- `pkgs.emacsPackages.orgPackages` is removed because org elpa is deprecated. The packages in the top level of `pkgs.emacsPackages`, such as org and org-contrib, refer to the ones in `pkgs.emacsPackages.elpaPackages` and `pkgs.emacsPackages.nongnuPackages` where the new versions will release.
diff --git a/pkgs/applications/editors/emacs/27.nix b/pkgs/applications/editors/emacs/27.nix
@@ -2,7 +2,6 @@ import ./generic.nix (rec {
   version = "27.2";
   sha256 = "sha256-tKfMTnjmPzeGJOCRkhW5EK9bsqCvyBn60pgnLp9Awbk=";
   patches = fetchpatch: [
-    ./tramp-detect-wrapped-gvfsd.patch
     (fetchpatch {
       name = "fix-aarch64-darwin-triplet.patch";
       url = "https://git.savannah.gnu.org/cgit/emacs.git/patch/?id=a88f63500e475f842e5fbdd9abba4ce122cdb082";
diff --git a/pkgs/applications/editors/emacs/elisp-packages/org-packages.nix b/pkgs/applications/editors/emacs/elisp-packages/org-packages.nix
diff --git a/pkgs/applications/editors/emacs/elisp-packages/update-from-overlay b/pkgs/applications/editors/emacs/elisp-packages/update-from-overlay
@@ -11,10 +11,6 @@ curl -s -O https://raw.githubusercontent.com/nix-community/emacs-overlay/master/
 nix-instantiate ../../../../../ -A emacs.pkgs.elpaPackages --show-trace
 git diff --exit-code elpa-generated.nix > /dev/null || git commit -m "emacs.pkgs.elpa-packages: $(date --iso)" -- elpa-generated.nix
 
-curl -s -O https://raw.githubusercontent.com/nix-community/emacs-overlay/master/repos/org/org-generated.nix
-nix-instantiate ../../../../../ -A emacs.pkgs.orgPackages --show-trace
-git diff --exit-code org-generated.nix > /dev/null || git commit -m "emacs.pkgs.org-packages: $(date --iso)" -- org-generated.nix
-
 curl -s -O https://raw.githubusercontent.com/nix-community/emacs-overlay/master/repos/melpa/recipes-archive-melpa.json
 nix-instantiate --show-trace ../../../../../ -A emacs.pkgs.melpaStablePackages
 nix-instantiate --show-trace ../../../../../ -A emacs.pkgs.melpaPackages
diff --git a/pkgs/applications/editors/emacs/elisp-packages/update-org b/pkgs/applications/editors/emacs/elisp-packages/update-org
diff --git a/pkgs/applications/editors/emacs/generic.nix b/pkgs/applications/editors/emacs/generic.nix
@@ -64,6 +64,16 @@ let emacs = stdenv.mkDerivation (lib.optionalAttrs nativeComp {
       rm -fr .git
     '')
 
+    # Add the name of the wrapped gvfsd
+    # This used to be carried as a patch but it often got out of sync with upstream
+    # and was hard to maintain for emacs-overlay.
+    (lib.concatStrings (map (fn: ''
+      sed -i 's#(${fn} "gvfs-fuse-daemon")#(${fn} "gvfs-fuse-daemon") (${fn} ".gvfsd-fuse-wrapped")#' lisp/net/tramp-gvfs.el
+    '') [
+      "tramp-compat-process-running-p"
+      "tramp-process-running-p"
+    ]))
+
     # Reduce closure size by cleaning the environment of the emacs dumper
     ''
       substituteInPlace src/Makefile.in \
diff --git a/pkgs/applications/editors/emacs/tramp-detect-wrapped-gvfsd-26.patch b/pkgs/applications/editors/emacs/tramp-detect-wrapped-gvfsd-26.patch
diff --git a/pkgs/applications/editors/emacs/tramp-detect-wrapped-gvfsd.patch b/pkgs/applications/editors/emacs/tramp-detect-wrapped-gvfsd.patch
diff --git a/pkgs/applications/misc/calibre/default.nix b/pkgs/applications/misc/calibre/default.nix
@@ -42,6 +42,13 @@ mkDerivation rec {
       url = "https://raw.githubusercontent.com/debian-calibre/calibre/debian/${version}%2Bdfsg-1/debian/patches/0001-only-plugin-update.patch";
       sha256 = "sha256-dLzO1TWP7Q4nw2a3oN7qlhGCmcA0NKJrZidUnD6hUMA=";
     })
+
+    # fix for CVE-2021-44686
+    (fetchpatch {
+      name = "0002-CVE-2021-44686.patch";
+      url = "https://github.com/kovidgoyal/calibre/commit/235b7e38c197ba4a3c17531e516610af8795e348.patch";
+      sha256 = "07ncv6r2v05m8rnv4syjfalkpksqpjag6icf1z57nv7k9dkkfmfw";
+    })
   ]
   ++ lib.optional (!unrarSupport) ./dont_build_unrar_plugin.patch;
 
diff --git a/pkgs/applications/misc/latte-dock/default.nix b/pkgs/applications/misc/latte-dock/default.nix
@@ -3,11 +3,11 @@
 
 mkDerivation rec {
   pname = "latte-dock";
-  version = "0.10.0";
+  version = "0.10.4";
 
   src = fetchurl {
     url = "https://download.kde.org/stable/${pname}/${pname}-${version}.tar.xz";
-    sha256 = "04kq86qmrjbzidrkknj000pv1b5z0r7nfidhy2zv67ks8fdi4zln";
+    sha256 = "XRop+MNcbeCcbnL2LM1i67QvMudW3CjWYEPLkT/qbGM=";
     name = "${pname}-${version}.tar.xz";
   };
 
diff --git a/pkgs/applications/networking/browsers/chromium/upstream-info.json b/pkgs/applications/networking/browsers/chromium/upstream-info.json
@@ -1,8 +1,8 @@
 {
   "stable": {
-    "version": "96.0.4664.93",
-    "sha256": "14rlm91pzpdll6x2r1sxdswiv19h1ykxcq0csi9k9g0a9s71yyvw",
-    "sha256bin64": "15233njj6ln7q3c112ssfh9s4m3shhp920zw8648z9dr7k8512qb",
+    "version": "96.0.4664.110",
+    "sha256": "1s3ilq0ik36qgqp7l88gfd1yx97zscn8yr2kprsrjfp9q8lrva9n",
+    "sha256bin64": "17cyj1jx47fz6y26f196xhlngrw5gnjgcvapvgkgswlwd7y67jcb",
     "deps": {
       "gn": {
         "version": "2021-09-24",
diff --git a/pkgs/applications/virtualization/runc/default.nix b/pkgs/applications/virtualization/runc/default.nix
@@ -16,13 +16,13 @@
 
 buildGoModule rec {
   pname = "runc";
-  version = "1.0.2";
+  version = "1.0.3";
 
   src = fetchFromGitHub {
     owner = "opencontainers";
     repo = "runc";
     rev = "v${version}";
-    sha256 = "sha256-l+Uq7aiXFrI+qbKSOZpYFIXz0VJBBR7ZZxlAJeGb7K4=";
+    sha256 = "sha256-Tl/JKbIpao+FCjngPzaVkxse50zo3XQ9Mg/AdkblMcI=";
   };
 
   vendorSha256 = null;
diff --git a/pkgs/development/python-modules/mahotas/default.nix b/pkgs/development/python-modules/mahotas/default.nix
@@ -1,4 +1,15 @@
-{ buildPythonPackage, fetchFromGitHub, pillow, scipy, numpy, pytestCheckHook, imread, freeimage, lib, stdenv }:
+{ buildPythonPackage
+, fetchFromGitHub
+, fetchpatch
+, pillow
+, scipy
+, numpy
+, pytestCheckHook
+, imread
+, freeimage
+, lib
+, stdenv
+}:
 
 buildPythonPackage rec {
   pname = "mahotas";
@@ -11,11 +22,22 @@ buildPythonPackage rec {
     sha256 = "029gvy1fb855pvxvy8zwj44k4s7qpqi0161bg5wldfiprrysn1kw";
   };
 
+  patches = [
+    (fetchpatch {
+      name = "fix-freeimage-tests.patch";
+      url = "https://github.com/luispedro/mahotas/commit/08cc4aa0cbd5dbd4c37580d52b822810c03b2c69.patch";
+      sha256 = "0389sz7fyl8h42phw8sn4pxl4wc3brcrj9d05yga21gzil9bfi23";
+      excludes = [ "ChangeLog" ];
+    })
+  ];
+
   propagatedBuildInputs = [ numpy imread pillow scipy freeimage ];
   checkInputs = [ pytestCheckHook ];
 
   postPatch = ''
-    substituteInPlace mahotas/io/freeimage.py --replace "/opt/local/lib" "${freeimage}/lib"
+    substituteInPlace mahotas/io/freeimage.py \
+      --replace "ctypes.util.find_library('freeimage')" 'True' \
+      --replace 'ctypes.CDLL(libname)' 'np.ctypeslib.load_library("libfreeimage", "${freeimage}/lib")'
   '';
 
   # tests must be run in the build directory
@@ -29,6 +51,12 @@ buildPythonPackage rec {
     "test_ellipse_axes"
     "test_normalize"
     "test_haralick3d"
+    "test_uint16"
+  ];
+
+  pythonImportsCheck = [
+    "mahotas"
+    "mahotas.freeimage"
   ];
 
   disabled = stdenv.isi686; # Failing tests
diff --git a/pkgs/servers/keycloak/default.nix b/pkgs/servers/keycloak/default.nix
@@ -18,11 +18,11 @@ let
 in
 stdenv.mkDerivation rec {
   pname   = "keycloak";
-  version = "15.0.2";
+  version = "15.1.0";
 
   src = fetchzip {
     url    = "https://github.com/keycloak/keycloak/releases/download/${version}/keycloak-${version}.zip";
-    sha256 = "sha256-GlnSsvAYBjRTtabMVrpWUH0EWEdLIe6ud+HIXJqTsqY=";
+    sha256 = "0s8nvp1ca30569k1a7glbn2zvvchz35s2r8d08fbs5zjngnz3276";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/pkgs/servers/nosql/apache-jena/binary.nix b/pkgs/servers/nosql/apache-jena/binary.nix
@@ -3,10 +3,10 @@ let
   s = # Generated upstream information
   rec {
     baseName="apache-jena";
-    version = "4.2.0";
+    version = "4.3.1";
     name="${baseName}-${version}";
-    url="http://archive.apache.org/dist/jena/binaries/apache-jena-${version}.tar.gz";
-    sha256 = "1yiqlsp1g2fladal8mj164b9s0qsl5csllg54p7x7w63wf7gixnq";
+    url="https://dlcdn.apache.org/jena/binaries/apache-jena-${version}.tar.gz";
+    sha256 = "02asp88smayn68hc019fwp0si9mc79vxn8py7qhx3qzwjk6j9p71";
   };
   buildInputs = [
     makeWrapper
diff --git a/pkgs/servers/nosql/apache-jena/fuseki-binary.nix b/pkgs/servers/nosql/apache-jena/fuseki-binary.nix
@@ -3,10 +3,10 @@ let
   s = # Generated upstream information
   rec {
     baseName="apache-jena-fuseki";
-    version = "4.2.0";
+    version = "4.3.1";
     name="${baseName}-${version}";
-    url="http://archive.apache.org/dist/jena/binaries/apache-jena-fuseki-${version}.tar.gz";
-    sha256 = "1x3va4yqmxh55lhr6ms85ks9v0lqkl3y41h0bpjdycp8j96lsy3h";
+    url="https://dlcdn.apache.org/jena/binaries/apache-jena-fuseki-${version}.tar.gz";
+    sha256 = "1r0vfa7d55lzw22yfx46mxxmz8x8pkr666vggqw2m1rzzj52z9nx";
   };
   buildInputs = [
     makeWrapper
diff --git a/pkgs/tools/networking/gping/default.nix b/pkgs/tools/networking/gping/default.nix
@@ -2,6 +2,7 @@
 , stdenv
 , rustPlatform
 , fetchFromGitHub
+, fetchpatch
 , libiconv
 }:
 
@@ -18,6 +19,13 @@ rustPlatform.buildRustPackage rec {
 
   cargoSha256 = "sha256-xEASs6r5zxYJXS+at6aX5n0whGp5qwuNwq6Jh0GM+/4=";
 
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/orf/gping/commit/b843beb9617e4b7b98d4f6d3942067cad59c9d60.patch";
+      sha256 = "sha256-9DIeeweCuGqymvUj4EBct82XVevkFSbHWaV76ExjGbs=";
+    })
+  ];
+
   buildInputs = lib.optional stdenv.isDarwin libiconv;
 
   meta = with lib; {
diff --git a/pkgs/top-level/emacs-packages.nix b/pkgs/top-level/emacs-packages.nix
@@ -45,10 +45,6 @@ let
     inherit lib pkgs;
   };
 
-  mkOrgPackages = { lib }: import ../applications/editors/emacs/elisp-packages/org-packages.nix {
-    inherit lib;
-  };
-
   mkManualPackages = { pkgs, lib }: import ../applications/editors/emacs/elisp-packages/manual-packages.nix {
     inherit lib pkgs;
   };
@@ -66,14 +62,12 @@ in makeScope pkgs'.newScope (self: makeOverridable ({
   , nongnuPackages ? mkNongnuPackages { inherit pkgs lib; } self
   , melpaStablePackages ? melpaGeneric { inherit pkgs lib; } "stable" self
   , melpaPackages ? melpaGeneric { inherit pkgs lib; } "unstable" self
-  , orgPackages ? mkOrgPackages { inherit lib; } self
   , manualPackages ? mkManualPackages { inherit pkgs lib; } self
 }: ({}
   // elpaPackages // { inherit elpaPackages; }
   // nongnuPackages // { inherit nongnuPackages; }
   // melpaStablePackages // { inherit melpaStablePackages; }
   // melpaPackages // { inherit melpaPackages; }
-  // orgPackages // { inherit orgPackages; }
   // manualPackages // { inherit manualPackages; }
   // {
 
