Merge staging-next into staging

pkgs/applications/networking/mailreaders/notmuch/default.nix

···
 with lib;
 
 stdenv.mkDerivation rec {
-  version = "0.32.1";
+  version = "0.32.2";
   pname = "notmuch";
 
   passthru = {
···
     inherit version;
   };
 
-  src = fetchgit {
-    url = "https://git.notmuchmail.org/git/notmuch";
-    sha256 = "sha256:06r0hdz8mxnzag74md62a9m6c2zm0fxn45n4n1c26j5cmrys7j16";
-    rev = version;
+  src = fetchurl {
+    url = "https://notmuchmail.org/releases/notmuch-${version}.tar.xz";
+    sha256 = "1myylb19hj5nb1vriqng252vfjwwkgbi3gxj93pi2q1fzyw7w2lf";
   };
 
   nativeBuildInputs = [
···
     doxygen                   # (optional) api docs
     pythonPackages.sphinx     # (optional) documentation -> doc/INSTALL
     texinfo                   # (optional) documentation -> doc/INSTALL
-  ] ++ optional withEmacs [ emacs ];
+  ] ++ optional withEmacs emacs;
 
   buildInputs = [
     gnupg                     # undefined dependencies
···
     gdb man emacs
   ];
 
-  # Expects there to always be a thread with ID
-  # thread:0000000000000009, but notmuch new is non-deterministic so
-  # this isn't always the case.  Upstream bug report:
-  # https://nmbug.notmuchmail.org/nmweb/show/871reno6g7.fsf%40alyssa.is
-  NOTMUCH_SKIP_TESTS = "lib-thread";
-
   installTargets = [ "install" "install-man" "install-info" ];
 
   postInstall = lib.optionalString withEmacs ''
···
   meta = {
     description = "Mail indexer";
     homepage    = "https://notmuchmail.org/";
-    license     = licenses.gpl3;
+    license     = licenses.gpl3Plus;
     maintainers = with maintainers; [ flokli puckipedia ];
     platforms   = platforms.unix;
   };

pkgs/development/beam-modules/erlang-ls/default.nix

···
-{ fetchFromGitHub, fetchHex, rebar3Relx, buildRebar3, rebar3-proper, lib }:
+{ fetchFromGitHub, fetchHex, rebar3Relx, buildRebar3, rebar3-proper, stdenv, lib }:
 let
   version = "0.17.0";
   owner = "erlang-ls";
···
     HOME=. rebar3 ct
     HOME=. rebar3 proper --constraint_tries 100
   '';
-  doCheck = true;
+  # tests seem to be a bit flaky on darwin, skip them for now
+  doCheck = !stdenv.isDarwin;
   installPhase = ''
     mkdir -p $out/bin
     cp _build/default/bin/erlang_ls $out/bin/

pkgs/development/tools/gotestsum/default.nix

···
 
 buildGoModule rec {
   pname = "gotestsum";
-  version = "1.6.4";
+  version = "1.7.0";
 
   src = fetchFromGitHub {
     owner = "gotestyourself";
     repo = "gotestsum";
     rev = "v${version}";
-    sha256 = "sha256-5iSUk/J73enbc/N3bn7M4oj2A0yoF1jTWpnXD380hFI=";
+    sha256 = "sha256-nZaVi39dOytJTM69xpl+d9XoUt+yHdndPgY2ggfNeMQ=";
   };
 
-  vendorSha256 = "sha256-sHi8iW+ZV/coeAwDUYnSH039UNtUO9HK0Bhz9Gmtv8k=";
+  vendorSha256 = "sha256-wP5y8Ec6eSe+rdMEQQdX0fFTQ0HWuiyBRHxGlraZd+o=";
 
   doCheck = false;
 

pkgs/tools/misc/findutils/default.nix

···
     substituteInPlace xargs/xargs.c --replace 'char default_cmd[] = "echo";' 'char default_cmd[] = "${coreutils}/bin/echo";'
   '';
 
-  patches = [ ./no-install-statedir.patch ]
-    # fix gnulib tests on 32-bit ARM. Included on findutils master.
-    # https://lists.gnu.org/r/bug-gnulib/2020-08/msg00225.html
-    ++ lib.optional stdenv.hostPlatform.isAarch32 ./fix-gnulib-tests-arm.patch;
+  patches = [ ./no-install-statedir.patch ];
 
   buildInputs = [ coreutils ]; # bin/updatedb script needs to call sort
 

pkgs/tools/misc/findutils/fix-gnulib-tests-arm.patch

···
->From 175e0bc72808d564074c4adcc72aeadb74adfcc6 Mon Sep 17 00:00:00 2001
-From: Paul Eggert <[e-mail]>
-Date: Thu, 27 Aug 2020 17:52:58 -0700
-Subject: [PATCH] perror, strerror_r: remove unportable tests
-
-Problem reported by Florian Weimer in:
-https://lists.gnu.org/r/bug-gnulib/2020-08/msg00220.html
-* tests/test-perror2.c (main):
-* tests/test-strerror_r.c (main): Omit unportable tests.
----
- tests/test-perror2.c    | 3 ---
- tests/test-strerror_r.c | 3 ---
- 2 files changed, 6 deletions(-)
-
-diff --git a/gnulib-tests/test-perror2.c b/gnulib-tests/test-perror2.c
-index 1d14eda7b..c6214dd25 100644
---- a/gnulib-tests/test-perror2.c
-+++ b/gnulib-tests/test-perror2.c
-@@ -79,9 +79,6 @@ main (void)
-     errno = -5;
-     perror ("");
-     ASSERT (!ferror (stderr));
--    ASSERT (msg1 == msg2 || msg1 == msg4 || STREQ (msg1, str1));
--    ASSERT (msg2 == msg4 || STREQ (msg2, str2));
--    ASSERT (msg3 == msg4 || STREQ (msg3, str3));
-     ASSERT (STREQ (msg4, str4));
- 
-     free (str1);
-diff --git a/gnulib-tests/test-strerror_r.c b/gnulib-tests/test-strerror_r.c
-index b11d6fd9f..c1dbcf837 100644
---- a/gnulib-tests/test-strerror_r.c
-+++ b/gnulib-tests/test-strerror_r.c
-@@ -165,9 +165,6 @@ main (void)
- 
-     strerror_r (EACCES, buf, sizeof buf);
-     strerror_r (-5, buf, sizeof buf);
--    ASSERT (msg1 == msg2 || msg1 == msg4 || STREQ (msg1, str1));
--    ASSERT (msg2 == msg4 || STREQ (msg2, str2));
--    ASSERT (msg3 == msg4 || STREQ (msg3, str3));
-     ASSERT (STREQ (msg4, str4));
- 
-     free (str1);
--- 
-2.17.1
-

pkgs/tools/networking/dnsproxy/default.nix

···
 
 buildGoModule rec {
   pname = "dnsproxy";
-  version = "0.38.3";
+  version = "0.39.0";
 
   src = fetchFromGitHub {
     owner = "AdguardTeam";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-VfEfxcewKo8D8kNsMuCvrLOZNl632ZIFyD+RG8qzjQ4=";
+    sha256 = "sha256-rHU07rh8wZPaaxZmXVBu4tpt02Jq7Yu//dwWeVDUpw4=";
   };
 
   vendorSha256 = null;

pkgs/tools/package-management/nix/default.nix

···
         [ "out" "dev" ]
         ++ lib.optionals enableDocumentation [ "man" "doc" ];
 
+      hardeningEnable = [ "pie" ];
+
       nativeBuildInputs =
         [ pkg-config ]
         ++ lib.optionals stdenv.isLinux [ util-linuxMinimal ]

pkgs/tools/virtualization/udocker/default.nix

···
-{ lib, fetchFromGitHub, proot, patchelf, fakechroot, runc, simplejson, pycurl, coreutils, nose, mock, buildPythonApplication }:
-
-buildPythonApplication rec {
+{ lib
+, fetchFromGitHub
+, singularity
+, python3Packages
+}:
 
-  version = "1.1.3";
+python3Packages.buildPythonApplication rec {
   pname = "udocker";
+  version = "1.3.1";
 
   src = fetchFromGitHub {
     owner = "indigo-dc";
-    repo = "udocker" ;
+    repo = "udocker";
     rev = "v${version}";
-    sha256 = "1c8y1p3brj987drikwrby8m1hdr40ja4anx0p4xsij3ll2h62w6z";
+    sha256 = "0dfsjgidsnah8nrclrq10yz3ja859123z81kq4zdifbrhnrn5a2x";
   };
 
-  buildInputs = [ proot patchelf fakechroot runc simplejson pycurl coreutils ];
+  # crun patchelf proot runc fakechroot
+  # are download statistically linked during runtime
+  buildInputs = [
+    singularity
+  ] ++ (with python3Packages; [
+    pytest-runner
+    pycurl
+  ]);
 
-  postPatch = ''
-      substituteInPlace udocker.py --replace /usr/sbin:/sbin:/usr/bin:/bin $PATH
-      substituteInPlace udocker.py --replace /bin/chmod ${coreutils}/bin/chmod
-      substituteInPlace udocker.py --replace /bin/rm ${coreutils}/bin/rm
-      substituteInPlace tests/unit_tests.py --replace /bin/rm ${coreutils}/bin/rm
-      substituteInPlace udocker.py --replace "autoinstall = True" "autoinstall = False"
-  '';
+  checkInputs = with python3Packages; [
+    pytestCheckHook
+  ];
 
-  checkInputs = [
-    nose
-    mock
+  disabledTests = [
+    "test_05__get_volume_bindings"
   ];
 
-  checkPhase = ''
-    NOSE_EXCLUDE=test_03_create_repo,test_04_is_repo,test_02__get_group_from_host nosetests -v tests/unit_tests.py
-  '';
+  disabledTestPaths = [
+    # Network
+    "tests/unit/test_curl.py"
+    "tests/unit/test_dockerioapi.py"
+  ];
 
   meta = with lib; {
     description = "basic user tool to execute simple docker containers in user space without root privileges";

pkgs/top-level/all-packages.nix

···
 
   umurmur = callPackage ../applications/networking/umurmur { };
 
-  udocker = pythonPackages.callPackage ../tools/virtualization/udocker { };
+  udocker = callPackage ../tools/virtualization/udocker { };
 
   uefitoolPackages = recurseIntoAttrs (callPackage ../tools/system/uefitool/variants.nix {});
   uefitool = uefitoolPackages.new-engine;