Merge older staging (finished on Hydra)

https://hydra.nixos.org/eval/1427837?filter=&compare=1427817
Fixes #34087.

pkgs/applications/version-management/git-and-tools/git/default.nix

@@ -13,7 +13,7 @@
 }:
 
 let
-  version = "2.15.1";
+  version = "2.16.0";
   svn = subversionClient.override { perlBindings = true; };
 in
 
@@ -22,7 +22,7 @@ stdenv.mkDerivation {
 
   src = fetchurl {
     url = "https://www.kernel.org/pub/software/scm/git/git-${version}.tar.xz";
-    sha256 = "0p04linqdywdf7m1hqa904fzqvgzplsxlzdqrn96j1j5gpyr174r";
+    sha256 = "1y1hdr8ydff5q7y762cwfdgaxam4mxvir6nrw3g51mmkcr77c40d";
   };
 
   hardeningDisable = [ "format" ];

pkgs/applications/version-management/git-and-tools/git/git-send-email-honor-PATH.patch

@@ -1,47 +1,28 @@
-From 9a4396ddaedaf59ebee16d69900884e990b79cdd Mon Sep 17 00:00:00 2001
-From: Florian Klink <flokli@flokli.de>
-Date: Fri, 17 Nov 2017 13:21:37 +0100
-Subject: [PATCH] git-send-email: honor $PATH
-
-This will search $PATH for a sendmail binary, instead of the (previously
-fixed) list of paths.
-
-Signed-off-by: Florian Klink <flokli@flokli.de>
----
- Documentation/git-send-email.txt | 5 ++---
- git-send-email.perl              | 3 ++-
- 2 files changed, 4 insertions(+), 4 deletions(-)
-
 diff --git a/Documentation/git-send-email.txt b/Documentation/git-send-email.txt
-index bac9014ac..b9b1f2c41 100644
+index 8060ea35c..c81067a19 100644
 --- a/Documentation/git-send-email.txt
 +++ b/Documentation/git-send-email.txt
-@@ -203,9 +203,8 @@ a password is obtained using 'git-credential'.
+@@ -203,8 +203,7 @@ a password is obtained using 'git-credential'.
  	specify a full pathname of a sendmail-like program instead;
  	the program must support the `-i` option.  Default value can
  	be specified by the `sendemail.smtpServer` configuration
--	option; the built-in default is `/usr/sbin/sendmail` or
+-	option; the built-in default is to search for `sendmail` in
--	`/usr/lib/sendmail` if such program is available, or
+-	`/usr/sbin`, `/usr/lib` and $PATH if such program is
--	`localhost` otherwise.
++        option; the built-in default is to search in $PATH if such program is
-+	option; the built-in default is to search in $PATH if such program is
+ 	available, falling back to `localhost` otherwise.
-+	available, or `localhost` otherwise.
+
- 
  --smtp-server-port=<port>::
- 	Specifies a port different from the default port (SMTP
 diff --git a/git-send-email.perl b/git-send-email.perl
-index 2208dcc21..8e357aeab 100755
+index edcc6d346..8e357aeab 100755
 --- a/git-send-email.perl
 +++ b/git-send-email.perl
-@@ -885,7 +885,8 @@ if (defined $initial_reply_to) {
+@@ -885,8 +885,7 @@ if (defined $initial_reply_to) {
  }
- 
+
  if (!defined $smtp_server) {
--	foreach (qw( /usr/sbin/sendmail /usr/lib/sendmail )) {
+-	my @sendmail_paths = qw( /usr/sbin/sendmail /usr/lib/sendmail );
+-	push @sendmail_paths, map {"$_/sendmail"} split /:/, $ENV{PATH};
 +	my @sendmail_paths = map {"$_/sendmail"} split /:/, $ENV{PATH};
-+	foreach (@sendmail_paths) {
+ 	foreach (@sendmail_paths) {
  		if (-x $_) {
  			$smtp_server = $_;
- 			last;
--- 
-2.15.0
-

pkgs/applications/version-management/git-and-tools/git/ssh-path.patch

@@ -1,21 +1,21 @@
 diff --git a/connect.c b/connect.c
-index fd7ffe1..20cd992 100644
+index c3a014c5b..fbca3262b 100644
 --- a/connect.c
 +++ b/connect.c
-@@ -768,7 +768,7 @@
+@@ -1010,7 +1010,7 @@ static void fill_ssh_args(struct child_process *conn, const char *ssh_host,
+
+ 		ssh = getenv("GIT_SSH");
+ 		if (!ssh)
+-			ssh = "ssh";
++			ssh = "@ssh@";
+ 		variant = determine_ssh_variant(ssh, 0);
+ 	}
 
- 				ssh = getenv("GIT_SSH");
- 				if (!ssh)
--					ssh = "ssh";
-+					ssh = "@ssh@";
-				else
-					handle_ssh_variant(ssh, 0,
-								&port_option,
 diff --git a/git-gui/lib/remote_add.tcl b/git-gui/lib/remote_add.tcl
-index 50029d0..17b9594 100644
+index 480a6b30d..781720424 100644
 --- a/git-gui/lib/remote_add.tcl
 +++ b/git-gui/lib/remote_add.tcl
-@@ -139,7 +139,7 @@
+@@ -139,7 +139,7 @@ method _add {} {
  		# Parse the location
  		if { [regexp {(?:git\+)?ssh://([^/]+)(/.+)} $location xx host path]
  		     || [regexp {([^:][^:]+):(.+)} $location xx host path]} {

pkgs/development/compilers/llvm/3.8/clang/default.nix

@@ -40,6 +40,8 @@ let
 
       # Move libclang to 'lib' output
       moveToOutput "lib/libclang.*" "$lib"
+      substituteInPlace $out/share/clang/cmake/ClangTargets-release.cmake \
+          --replace "\''${_IMPORT_PREFIX}/lib/libclang." "$lib/lib/libclang."
 
       mkdir -p $python/bin $python/share/clang/
       mv $out/bin/{git-clang-format,scan-view} $python/bin

pkgs/development/compilers/llvm/3.9/clang/default.nix

@@ -42,6 +42,8 @@ let
 
       # Move libclang to 'lib' output
       moveToOutput "lib/libclang.*" "$lib"
+      substituteInPlace $out/lib/cmake/clang/ClangTargets-release.cmake \
+          --replace "\''${_IMPORT_PREFIX}/lib/libclang." "$lib/lib/libclang."
 
       mkdir -p $python/bin $python/share/clang/
       mv $out/bin/{git-clang-format,scan-view} $python/bin

pkgs/development/compilers/llvm/4/clang/default.nix

@@ -59,6 +59,8 @@ let
 
       # Move libclang to 'lib' output
       moveToOutput "lib/libclang.*" "$lib"
+      substituteInPlace $out/lib/cmake/clang/ClangTargets-release.cmake \
+          --replace "\''${_IMPORT_PREFIX}/lib/libclang." "$lib/lib/libclang."
 
       mkdir -p $python/bin $python/share/clang/
       mv $out/bin/{git-clang-format,scan-view} $python/bin

pkgs/development/compilers/llvm/5/clang/default.nix

@@ -60,6 +60,8 @@ let
 
       # Move libclang to 'lib' output
       moveToOutput "lib/libclang.*" "$lib"
+      substituteInPlace $out/lib/cmake/clang/ClangTargets-release.cmake \
+          --replace "\''${_IMPORT_PREFIX}/lib/libclang." "$lib/lib/libclang."
 
       mkdir -p $python/bin $python/share/clang/
       mv $out/bin/{git-clang-format,scan-view} $python/bin

pkgs/development/interpreters/guile/default.nix

@@ -10,11 +10,11 @@
 
 (rec {
   name = "guile-${version}";
-  version = "2.2.0";
+  version = "2.2.3";
 
   src = fetchurl {
     url = "mirror://gnu/guile/${name}.tar.xz";
-    sha256 = "05dmvhd1y135x7w5qfw4my42cfp6l8bbhjfxvchcc1cbdvzri0f1";
+    sha256 = "11j01agvnci2cx32wwpqs9078856yxmvs15gcsz7ganpkj2ahlw3";
   };
 
   outputs = [ "out" "dev" "info" ];

pkgs/development/libraries/libnftnl/default.nix

@@ -1,11 +1,12 @@
 { stdenv, fetchurl, pkgconfig, libmnl }:
 
 stdenv.mkDerivation rec {
-  name = "libnftnl-1.0.8";
+  version = "1.0.9";
+  name = "libnftnl-${version}";
 
   src = fetchurl {
-    url = "http://netfilter.org/projects/libnftnl/files/${name}.tar.bz2";
+    url = "https://netfilter.org/projects/libnftnl/files/${name}.tar.bz2";
-    sha256 = "0f10cfiyl4c0f8k3brxfrw28x7a6qvrakaslg4jgqncwxycxggg6";
+    sha256 = "0d9nkdbdck8sg6msysqyv3m9kjr9sjif5amf26dfa0g3mqjdihgy";
   };
 
   nativeBuildInputs = [ pkgconfig ];

pkgs/os-specific/linux/apparmor/default.nix

@@ -2,14 +2,15 @@
 , pkgconfig, which
 , flex, bison
 , linuxHeaders ? stdenv.cc.libc.linuxHeaders
-, pythonPackages
+, python
+, gawk
 , perl
 , swig
+, ncurses
 , pam
 }:
 
 let
-
   apparmor-series = "2.12";
   apparmor-patchver = "0";
   apparmor-version = apparmor-series + "." + apparmor-patchver;
@@ -46,12 +47,13 @@ let
       flex
       pkgconfig
       swig
+      ncurses
       which
     ];
 
     buildInputs = [
       perl
-      pythonPackages.python
+      python
     ];
 
     # required to build apparmor-parser
@@ -61,7 +63,6 @@ let
       substituteInPlace ./libraries/libapparmor/src/Makefile.am --replace "/usr/include/netinet/in.h" "${stdenv.cc.libc.dev}/include/netinet/in.h"
       substituteInPlace ./libraries/libapparmor/src/Makefile.in --replace "/usr/include/netinet/in.h" "${stdenv.cc.libc.dev}/include/netinet/in.h"
     '';
-
     postPatch = "cd ./libraries/libapparmor";
     configureFlags = "--with-python --with-perl";
 
@@ -83,7 +84,7 @@ let
 
     buildInputs = [
       perl
-      pythonPackages.python
+      python
       libapparmor
       libapparmor.python
     ];
@@ -95,7 +96,7 @@ let
 
     postInstall = ''
       for prog in aa-audit aa-autodep aa-cleanprof aa-complain aa-disable aa-enforce aa-genprof aa-logprof aa-mergeprof aa-status aa-unconfined ; do
-        wrapProgram $out/bin/$prog --prefix PYTHONPATH : "$out/lib/${pythonPackages.python.libPrefix}/site-packages:$PYTHONPATH"
+        wrapProgram $out/bin/$prog --prefix PYTHONPATH : "$out/lib/${python.libPrefix}/site-packages:$PYTHONPATH"
       done
 
       for prog in aa-notify ; do
@@ -106,6 +107,29 @@ let
     meta = apparmor-meta "user-land utilities";
   };
 
+  apparmor-bin-utils = stdenv.mkDerivation {
+    name = "apparmor-bin-utils-${apparmor-version}";
+    src = apparmor-sources;
+
+    nativeBuildInputs = [
+      pkgconfig
+      libapparmor
+      gawk
+      which
+    ];
+
+    buildInputs = [
+      libapparmor
+    ];
+
+    prePatch = prePatchCommon;
+    postPatch = "cd ./binutils";
+    makeFlags = ''LANGS= USE_SYSTEM=1'';
+    installFlags = ''DESTDIR=$(out) BINDIR=$(out)/bin'';
+
+    meta = apparmor-meta "binary user-land utilities";
+  };
+
   apparmor-parser = stdenv.mkDerivation {
     name = "apparmor-parser-${apparmor-version}";
     src = apparmor-sources;
@@ -172,6 +196,12 @@ let
 in
 
 {
-  inherit libapparmor apparmor-utils apparmor-parser apparmor-pam
+  inherit
-  apparmor-profiles apparmor-kernel-patches;
+    libapparmor
+    apparmor-utils
+    apparmor-bin-utils
+    apparmor-parser
+    apparmor-pam
+    apparmor-profiles
+    apparmor-kernel-patches;
 }

pkgs/os-specific/linux/audit/default.nix

@@ -6,11 +6,11 @@
 assert enablePython -> python != null;
 
 stdenv.mkDerivation rec {
-  name = "audit-2.8.1";
+  name = "audit-2.8.2";
 
   src = fetchurl {
     url = "http://people.redhat.com/sgrubb/audit/${name}.tar.gz";
-    sha256 = "0v1vng43fjsh158zb5k5d81ngn4p4jmj1247m27pk0bfzy9dxv0v";
+    sha256 = "1fmw8whraz1q3y3z5mgdpgsa3wz6r3zq0kgsgbc9xvmgfwmrpdb7";
   };
 
   outputs = [ "bin" "dev" "out" "man" ];

pkgs/os-specific/linux/kmod/default.nix

@@ -6,11 +6,11 @@ let
 
 in stdenv.mkDerivation rec {
   name = "kmod-${version}";
-  version = "24";
+  version = "25";
 
   src = fetchurl {
     url = "mirror://kernel/linux/utils/kernel/kmod/${name}.tar.xz";
-    sha256 = "15xkkkzvca9flvkm48gkh8y8f13vlm3sl7nz9ydc7b3jy4fqs2v1";
+    sha256 = "1kgixs4m3jvwk7fb3d18n6j77qhgi9qfv4csj35rs5ancr4ycrbi";
   };
 
   nativeBuildInputs = [ autoreconfHook pkgconfig libxslt ];

pkgs/os-specific/linux/util-linux/default.nix

@@ -5,14 +5,14 @@ let
   version = lib.concatStringsSep "." ([ majorVersion ]
     ++ lib.optional (patchVersion != "") patchVersion);
   majorVersion = "2.31";
-  patchVersion = "";
+  patchVersion = "1";
 
 in stdenv.mkDerivation rec {
   name = "util-linux-${version}";
 
   src = fetchurl {
     url = "mirror://kernel/linux/utils/util-linux/v${majorVersion}/${name}.tar.xz";
-    sha256 = "12nw108xjhm63sh2n5a0qs33vpvbvb6rln96l9j50p7wykf7rgpr";
+    sha256 = "04fzrnrr3pvqskvjn9f81y0knh0jvvqx4lmbz5pd4lfdm5pv2l8s";
   };
 
   patches = [

pkgs/top-level/all-packages.nix

@@ -12511,8 +12511,9 @@ with pkgs;
 
   microcodeIntel = callPackage ../os-specific/linux/microcode/intel.nix { };
 
-  inherit (callPackages ../os-specific/linux/apparmor { pythonPackages = python27Packages; swig = swig2; })
+  inherit (callPackages ../os-specific/linux/apparmor { python = python3; })
-    libapparmor apparmor-pam apparmor-parser apparmor-profiles apparmor-utils;
+    libapparmor apparmor-utils apparmor-bin-utils apparmor-parser apparmor-pam
+    apparmor-profiles apparmor-kernel-patches;
 
   atop = callPackage ../os-specific/linux/atop { };