Merge staging-next into master (#44009)

* substitute(): --subst-var was silently coercing to "" if the variable does not exist.

* libffi: simplify using `checkInputs`

* pythonPackges.hypothesis, pythonPackages.pytest: simpify dependency cycle fix

* utillinux: 2.32 -> 2.32.1

https://lkml.org/lkml/2018/7/16/532

* busybox: 1.29.0 -> 1.29.1

* bind: 9.12.1-P2 -> 9.12.2

https://ftp.isc.org/isc/bind9/9.12.2/RELEASE-NOTES-bind-9.12.2.html

* curl: 7.60.0 -> 7.61.0

* gvfs: make tests run, but disable

* ilmbase: disable tests on i686. Spooky!

* mdds: fix tests

* git: disable checks as tests are run in installcheck

* ruby: disable tests

* libcommuni: disable checks as tests are run in installcheck

* librdf: make tests run, but disable

* neon, neon_0_29: make tests run, but disable

* pciutils: 3.6.0 -> 3.6.1

Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/pciutils/versions.

* mesa: more include fixes

mostly from void-linux (thanks!)

* npth: 1.5 -> 1.6

minor bump

* boost167: Add lockfree next_prior patch

* stdenv: cleanup darwin bootstrapping

Also gets rid of the full python and some of it's dependencies in the
stdenv build closure.

* Revert "pciutils: use standardized equivalent for canonicalize_file_name"

This reverts commit f8db20fb3ae382eba1ba2b160fe24739f43c0bd7.
Patching should no longer be needed with 3.6.1.

* binutils-wrapper: Try to avoid adding unnecessary -L flags

(cherry picked from commit f3758258b8895508475caf83e92bfb236a27ceb9)
Signed-off-by: Domen Kožar <domen@dev.si>

* libffi: don't check on darwin

libffi usages in stdenv broken darwin. We need to disable doCheck for that case.

* "rm $out/share/icons/hicolor/icon-theme.cache" -> hicolor-icon-theme setup-hook

* python.pkgs.pytest: setupHook to prevent creation of .pytest-cache folder, fixes #40273

When `py.test` was run with a folder as argument, it would not only
search for tests in that folder, but also create a .pytest-cache folder.
Not only is this state we don't want, but it was also causing
collisions.

* parity-ui: fix after merge

* python.pkgs.pytest-flake8: disable test, fix build

* Revert "meson: 0.46.1 -> 0.47.0"

With meson 0.47.0 (or 0.47.1, or git)
things are very wrong re:rpath handling
resulting in at best missing libs but
even corrupt binaries :(.

When we run patchelf it masks the problem
by removing obviously busted paths.
Which is probably why this wasn't noticed immediately.

Unfortunately the binary already
has a long series of paths scribbled
in a space intended for a much smaller string;
in my testing it was something like
lengths were 67 with 300+ written to it.

I think we've reported the relevant issues upstream,
but unfortunately it appears our patches
are what introduces the overwrite/corruption
(by no longer being correct in what they assume)

This doesn't look so bad to fix but it's
not something I can spend more time on
at the moment.

--

Interestingly the overwritten string data
(because it is scribbled past the bounds)
remains in the binary and is why we're suddenly
seeing unexpected references in various builds
-- notably this is is the reason we're
seeing the "extra-utils" breakage
that entirely crippled NixOS on master
(and probably on staging before?).

Fixes #43650.

This reverts commit 305ac4dade5758c58e8ab1666ad0197fd305828d.

(cherry picked from commit 273d68eff8f7b6cd4ebed3718e5078a0f43cb55d)
Signed-off-by: Domen Kožar <domen@dev.si>

19 files changed, 119 insertions, 29 deletions

diff --git a/pkgs/development/interpreters/python/cpython/2.7/boot.nix b/pkgs/development/interpreters/python/cpython/2.7/boot.nix
index 79aa85def3c1..66f358e4b95b 100644
--- a/pkgs/development/interpreters/python/cpython/2.7/boot.nix
+++ b/pkgs/development/interpreters/python/cpython/2.7/boot.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, CF, configd, coreutils }:
+{ stdenv, fetchurl, configd, CF, coreutils }:
 
 with stdenv.lib;
 
diff --git a/pkgs/development/interpreters/ruby/default.nix b/pkgs/development/interpreters/ruby/default.nix
index bb6f2758f4cf..9e6d35b818f4 100644
--- a/pkgs/development/interpreters/ruby/default.nix
+++ b/pkgs/development/interpreters/ruby/default.nix
@@ -133,6 +133,11 @@ let
           ++ op (stdenv.hostPlatform != stdenv.buildPlatform)
              "--with-baseruby=${buildRuby}";
 
+        # fails with "16993 tests, 2229489 assertions, 105 failures, 14 errors, 89 skips"
+        # mostly TZ- and patch-related tests
+        # TZ- failures are caused by nix sandboxing, I didn't investigate others
+        doCheck = false;
+
         preInstall = ''
           # Ruby installs gems here itself now.
           mkdir -pv "$out/${passthru.gemPath}"
diff --git a/pkgs/development/libraries/boost/1.67.nix b/pkgs/development/libraries/boost/1.67.nix
index 8b9e7ccca7f1..150272df6ca3 100644
--- a/pkgs/development/libraries/boost/1.67.nix
+++ b/pkgs/development/libraries/boost/1.67.nix
@@ -1,8 +1,14 @@
-{ stdenv, callPackage, fetchurl, hostPlatform, buildPlatform, ... } @ args:
+{ stdenv, callPackage, fetchurl, fetchpatch, hostPlatform, buildPlatform, ... } @ args:
 
 callPackage ./generic.nix (args // rec {
   version = "1.67_0";
 
+  patches = [ (fetchpatch {
+    url = "https://github.com/boostorg/lockfree/commit/12726cda009a855073b9bedbdce57b6ce7763da2.patch";
+    sha256 = "0x65nkwzv8fdacj8sw5njl3v63jj19dirrpklbwy6qpsncw7fc7h";
+    stripLen = 1;
+  })];
+
   src = fetchurl {
     url = "mirror://sourceforge/boost/boost_1_67_0.tar.bz2";
     # SHA256 from http://www.boost.org/users/history/version_1_66_0.html
diff --git a/pkgs/development/libraries/gvfs/default.nix b/pkgs/development/libraries/gvfs/default.nix
index 4c858242bb54..86cbd01a6026 100644
--- a/pkgs/development/libraries/gvfs/default.nix
+++ b/pkgs/development/libraries/gvfs/default.nix
@@ -4,7 +4,7 @@
 , libxml2, libxslt, docbook_xsl, docbook_xml_dtd_42, samba, libmtp
 , gnomeSupport ? false, gnome, makeWrapper
 , libimobiledevice, libbluray, libcdio-paranoia, libnfs, openssh
-, libsecret, libgdata
+, libsecret, libgdata, python3
 # Remove when switching back to meson
 , autoreconfHook, lzma, bzip2
 }:
@@ -28,6 +28,10 @@ stdenv.mkDerivation rec {
     sha256 = "1xq105596sk9yram5a143b369wpaiiwc9gz86n0j1kfr7nipkqn4";
   };
 
+  postPatch = ''
+    patchShebangs test test-driver
+  '';
+
   # Uncomment when switching back to meson
   # postPatch = ''
   #   chmod +x meson_post_install.py # patchShebangs requires executable file
@@ -73,6 +77,10 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
+  checkInputs = [ python3 ];
+  doCheck = false; # fails with "ModuleNotFoundError: No module named 'gi'"
+  doInstallCheck = doCheck;
+
   preFixup = ''
     for f in $out/libexec/*; do
       wrapProgram $f \
diff --git a/pkgs/development/libraries/ilmbase/default.nix b/pkgs/development/libraries/ilmbase/default.nix
index 956a8667be5f..156b4f72749a 100644
--- a/pkgs/development/libraries/ilmbase/default.nix
+++ b/pkgs/development/libraries/ilmbase/default.nix
@@ -20,6 +20,11 @@ stdenv.mkDerivation rec {
 
   patches = [ ./bootstrap.patch ];
 
+  # fails 1 out of 1 tests with
+  # "lt-ImathTest: testBoxAlgo.cpp:892: void {anonymous}::boxMatrixTransform(): Assertion `b21 == b2' failed"
+  # at least on i686. spooky!
+  doCheck = stdenv.isx86_64;
+
   meta = with stdenv.lib; {
     homepage = http://www.openexr.com/;
     license = licenses.bsd3;
diff --git a/pkgs/development/libraries/libcommuni/default.nix b/pkgs/development/libraries/libcommuni/default.nix
index 0788236b6017..f247c48821f7 100644
--- a/pkgs/development/libraries/libcommuni/default.nix
+++ b/pkgs/development/libraries/libcommuni/default.nix
@@ -27,6 +27,7 @@ stdenv.mkDerivation rec {
 
   # The tests fail on darwin because of install_name if they run
   # before the frameworks are installed.
+  doCheck = false;
   doInstallCheck = true;
   installCheckTarget = "check";
 
diff --git a/pkgs/development/libraries/libffi/default.nix b/pkgs/development/libraries/libffi/default.nix
index 1c7c0715e75b..6f1aeefa6758 100644
--- a/pkgs/development/libraries/libffi/default.nix
+++ b/pkgs/development/libraries/libffi/default.nix
@@ -1,5 +1,9 @@
-{ stdenv, fetchurl, fetchpatch,  dejagnu, doCheck ? false
+{ stdenv, fetchurl, fetchpatch
 , buildPlatform, hostPlatform, autoreconfHook
+
+# libffi is used in darwin stdenv
+# we cannot run checks within it
+, doCheck ? !stdenv.isDarwin, dejagnu
 }:
 
 stdenv.mkDerivation rec {
@@ -40,8 +44,6 @@ stdenv.mkDerivation rec {
 
   outputs = [ "out" "dev" "man" "info" ];
 
-  buildInputs = stdenv.lib.optional doCheck dejagnu;
-
   nativeBuildInputs = stdenv.lib.optional hostPlatform.isRiscV autoreconfHook;
 
   configureFlags = [
@@ -54,6 +56,8 @@ stdenv.mkDerivation rec {
     NIX_HARDENING_ENABLE=''${NIX_HARDENING_ENABLE/fortify/}
   '';
 
+  checkInputs = [ dejagnu ];
+
   inherit doCheck;
 
   dontStrip = hostPlatform != buildPlatform; # Don't run the native `strip' when cross-compiling.
diff --git a/pkgs/development/libraries/librdf/rasqal.nix b/pkgs/development/libraries/librdf/rasqal.nix
index 07f560fe2724..124fd0178182 100644
--- a/pkgs/development/libraries/librdf/rasqal.nix
+++ b/pkgs/development/libraries/librdf/rasqal.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, librdf_raptor2, gmp, pkgconfig, pcre, libxml2 }:
+{ stdenv, fetchurl, librdf_raptor2, gmp, pkgconfig, pcre, libxml2, perl }:
 
 stdenv.mkDerivation rec {
   name = "rasqal-0.9.33";
@@ -16,6 +16,10 @@ stdenv.mkDerivation rec {
 
   postInstall = "rm -rvf $out/share/gtk-doc";
 
+  checkInputs = [ perl ];
+  doCheck = false; # fails with "No testsuite plan file sparql-query-plan.ttl could be created in build/..."
+  doInstallCheck = false; # fails with "rasqal-config does not support (--help|--version)"
+
   meta = {
     description = "Library that handles Resource Description Framework (RDF)";
     homepage = http://librdf.org/rasqal;
diff --git a/pkgs/development/libraries/mdds/default.nix b/pkgs/development/libraries/mdds/default.nix
index 90d86ea9165c..43fee9ccead8 100644
--- a/pkgs/development/libraries/mdds/default.nix
+++ b/pkgs/development/libraries/mdds/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl }:
+{ stdenv, fetchurl, boost }:
 
 stdenv.mkDerivation rec {
   version = "1.3.1";
@@ -14,6 +14,8 @@ stdenv.mkDerivation rec {
    cp "$out/share/pkgconfig/"* "$out/lib/pkgconfig"
   '';
 
+  checkInputs = [ boost ];
+
   meta = {
     inherit version;
     homepage = https://gitlab.com/mdds/mdds;
diff --git a/pkgs/development/libraries/mesa/default.nix b/pkgs/development/libraries/mesa/default.nix
index 028930ba066d..480afcf607a6 100644
--- a/pkgs/development/libraries/mesa/default.nix
+++ b/pkgs/development/libraries/mesa/default.nix
@@ -92,7 +92,7 @@ let self = stdenv.mkDerivation {
   patches = [
     ./glx_ro_text_segm.patch # fix for grsecurity/PaX
     ./symlink-drivers.patch
-    ./missing-include.patch # dev_t needs sys/stat.h, fixes build w/musl
+    ./missing-includes.patch # dev_t needs sys/stat.h, time_t needs time.h, etc.-- fixes build w/musl
   ];
 
   outputs = [ "out" "dev" "drivers" "osmesa" ];
diff --git a/pkgs/development/libraries/mesa/missing-include.patch b/pkgs/development/libraries/mesa/missing-include.patch
deleted file mode 100644
index dd3e6bb64af8..000000000000
--- a/pkgs/development/libraries/mesa/missing-include.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ./src/gallium/winsys/svga/drm/vmw_screen.h.orig
-+++ ./src/gallium/winsys/svga/drm/vmw_screen.h
-@@ -34,7 +34,7 @@
- #ifndef VMW_SCREEN_H_
- #define VMW_SCREEN_H_
- 
--
-+#include <sys/stat.h>
- #include "pipe/p_compiler.h"
- #include "pipe/p_state.h"
- 
diff --git a/pkgs/development/libraries/mesa/missing-includes.patch b/pkgs/development/libraries/mesa/missing-includes.patch
new file mode 100644
index 000000000000..feb6ffe428c0
--- /dev/null
+++ b/pkgs/development/libraries/mesa/missing-includes.patch
@@ -0,0 +1,55 @@
+--- ./src/gallium/winsys/svga/drm/vmw_screen.h.orig
++++ ./src/gallium/winsys/svga/drm/vmw_screen.h
+@@ -34,7 +34,7 @@
+ #ifndef VMW_SCREEN_H_
+ #define VMW_SCREEN_H_
+ 
+-
++#include <sys/stat.h>
+ #include "pipe/p_compiler.h"
+ #include "pipe/p_state.h"
+ 
+--- ./src/gallium/state_trackers/nine/threadpool.h.orig	2015-05-07 14:10:53.443337212 +0200
++++ ./src/gallium/state_trackers/nine/threadpool.h	2015-05-07 14:11:04.210307653 +0200
+@@ -24,6 +24,8 @@
+ #ifndef _THREADPOOL_H_
+ #define _THREADPOOL_H_
+ 
++#include <pthread.h>
++
+ #define MAXTHREADS 1
+ 
+ struct threadpool {
+--- ./src/util/rand_xor.c.orig	2017-06-20 00:38:57.199474067 +0200
++++ ./src/util/rand_xor.c	2017-06-20 00:40:31.351279557 +0200
+@@ -23,7 +23,9 @@
+  */
+ 
+ #if defined(__linux__)
++#include <sys/types.h>
+ #include <sys/file.h>
++#include <sys/stat.h>
+ #include <unistd.h>
+ #include <fcntl.h>
+ #else
+--- ./src/mesa/drivers/dri/i965/brw_bufmgr.h
++++ ./src/mesa/drivers/dri/i965/brw_bufmgr.h
+@@ -37,6 +37,7 @@
+ #include <stdbool.h>
+ #include <stdint.h>
+ #include <stdio.h>
++#include <time.h>
+ #include "util/u_atomic.h"
+ #include "util/list.h"
+
+--- ./src/amd/vulkan/winsys/amdgpu/radv_amdgpu_winsys.h
++++ ./src/amd/vulkan/winsys/amdgpu/radv_amdgpu_winsys.h
+@@ -28,6 +28,8 @@
+ #ifndef RADV_AMDGPU_WINSYS_H
+ #define RADV_AMDGPU_WINSYS_H
+ 
++#include <sys/types.h>
++
+ #include "radv_radeon_winsys.h"
+ #include "ac_gpu_info.h"
+ #include "addrlib/addrinterface.h"<Paste>
diff --git a/pkgs/development/libraries/neon/0.29.nix b/pkgs/development/libraries/neon/0.29.nix
index e393d50bf9d2..dbde83c2d94b 100644
--- a/pkgs/development/libraries/neon/0.29.nix
+++ b/pkgs/development/libraries/neon/0.29.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, libxml2, pkgconfig
+{ stdenv, fetchurl, libxml2, pkgconfig, perl
 , compressionSupport ? true, zlib ? null
 , sslSupport ? true, openssl ? null
 , static ? false
@@ -38,6 +38,9 @@ stdenv.mkDerivation rec {
 
   passthru = {inherit compressionSupport sslSupport;};
 
+  checkInputs = [ perl ];
+  doCheck = false; # fails, needs the net
+
   meta = {
     description = "An HTTP and WebDAV client library";
     homepage = http://www.webdav.org/neon/;
diff --git a/pkgs/development/libraries/neon/default.nix b/pkgs/development/libraries/neon/default.nix
index 2351e3b0800b..9c2a3265491a 100644
--- a/pkgs/development/libraries/neon/default.nix
+++ b/pkgs/development/libraries/neon/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, libxml2, pkgconfig
+{ stdenv, fetchurl, libxml2, pkgconfig, perl
 , compressionSupport ? true, zlib ? null
 , sslSupport ? true, openssl ? null
 , static ? false
@@ -38,6 +38,9 @@ stdenv.mkDerivation rec {
 
   passthru = {inherit compressionSupport sslSupport;};
 
+  checkInputs = [ perl ];
+  doCheck = false; # fails, needs the net
+
   meta = {
     description = "An HTTP and WebDAV client library";
     homepage = http://www.webdav.org/neon/;
diff --git a/pkgs/development/libraries/npth/default.nix b/pkgs/development/libraries/npth/default.nix
index 203be8b6907b..c02998184fc5 100644
--- a/pkgs/development/libraries/npth/default.nix
+++ b/pkgs/development/libraries/npth/default.nix
@@ -1,11 +1,11 @@
 { stdenv, fetchurl }:
 
 stdenv.mkDerivation rec {
-  name = "npth-1.5";
+  name = "npth-1.6";
 
   src = fetchurl {
     url = "mirror://gnupg/npth/${name}.tar.bz2";
-    sha256 = "1hmkkp6vzyrh8v01c2ynzf9vwikyagp7p1lxhbnr4ysk3w66jji9";
+    sha256 = "1lg2lkdd3z1s3rpyf88786l243adrzyk9p4q8z9n41ygmpcsp4qk";
   };
 
   doCheck = true;
diff --git a/pkgs/development/python-modules/hypothesis/default.nix b/pkgs/development/python-modules/hypothesis/default.nix
index 88705962627f..6701c5a5b7e9 100644
--- a/pkgs/development/python-modules/hypothesis/default.nix
+++ b/pkgs/development/python-modules/hypothesis/default.nix
@@ -20,9 +20,9 @@ buildPythonPackage rec {
     sha256 = "063sn5m1966gvm3wrlxczdq4vw0r94h3nd9xpr94qxahpg2r4bpb";
   };
 
-  checkInputs = [ pytest pytest_xdist flaky mock ];
   propagatedBuildInputs = [ attrs coverage ] ++ lib.optional (!isPy3k) [ enum34 ];
 
+  checkInputs = [ pytest pytest_xdist flaky mock ];
   inherit doCheck;
 
   # https://github.com/DRMacIver/hypothesis/issues/300
diff --git a/pkgs/development/python-modules/pytest-flake8/default.nix b/pkgs/development/python-modules/pytest-flake8/default.nix
index 101594750fd5..1d7447293dfa 100644
--- a/pkgs/development/python-modules/pytest-flake8/default.nix
+++ b/pkgs/development/python-modules/pytest-flake8/default.nix
@@ -16,7 +16,7 @@ buildPythonPackage rec {
   };
 
   checkPhase = ''
-    pytest .
+    pytest . -k "not test_mtime_caching"
   '';
 
   meta = {
diff --git a/pkgs/development/python-modules/pytest/default.nix b/pkgs/development/python-modules/pytest/default.nix
index b5a8cc252b97..1c0ceef83657 100644
--- a/pkgs/development/python-modules/pytest/default.nix
+++ b/pkgs/development/python-modules/pytest/default.nix
@@ -1,6 +1,6 @@
 { stdenv, buildPythonPackage, fetchPypi, attrs, hypothesis, py
 , setuptools_scm, setuptools, six, pluggy, funcsigs, isPy3k, more-itertools
-, atomicwrites, mock
+, atomicwrites, mock, writeText
 }:
 buildPythonPackage rec {
   version = "3.6.2";
@@ -27,6 +27,11 @@ buildPythonPackage rec {
     runHook postCheck
   '';
 
+  # Don't create .pytest-cache when using py.test in a Nix build
+  setupHook = writeText "pytest-hook" ''
+    export PYTEST_ADDOPTS="-p no:cacheprovider"
+  '';
+
   meta = with stdenv.lib; {
     maintainers = with maintainers; [ domenkozar lovek323 madjar lsix ];
     platforms = platforms.unix;
diff --git a/pkgs/development/tools/build-managers/meson/default.nix b/pkgs/development/tools/build-managers/meson/default.nix
index 2ccd6637d088..3cb906d50edf 100644
--- a/pkgs/development/tools/build-managers/meson/default.nix
+++ b/pkgs/development/tools/build-managers/meson/default.nix
@@ -2,12 +2,12 @@
   targetPrefix = lib.optionalString stdenv.isCross
                    (targetPlatform.config + "-");
 in python3Packages.buildPythonApplication rec {
-  version = "0.47.0";
+  version = "0.46.1";
   pname = "meson";
 
   src = python3Packages.fetchPypi {
     inherit pname version;
-    sha256 = "1mxsvsw7mg3q4yj8qrkrwv79qwws14qnbihryn2i7504b3r204h6";
+    sha256 = "1jdxs2mkniy1hpdjc4b4jb95axsjp6j5fzphmm6d4gqmqyykjvqc";
   };
 
   postFixup = ''