Merge older staging

Enough rebuilds have finished on Hydra now.

nixos/modules/module-list.nix

@@ -283,6 +283,7 @@
   ./services/misc/etcd.nix
   ./services/misc/felix.nix
   ./services/misc/folding-at-home.nix
+  ./services/misc/fstrim.nix
   ./services/misc/gammu-smsd.nix
   ./services/misc/geoip-updater.nix
   #./services/misc/gitit.nix

nixos/modules/services/misc/fstrim.nix

@@ -0,0 +1,45 @@
+{ config, lib, pkgs, ... }:
+
+with lib;
+
+let
+
+  cfg = config.services.fstrim;
+
+in {
+
+  options = {
+
+    services.fstrim = {
+      enable = mkEnableOption "periodic SSD TRIM of mounted partitions in background";
+
+      interval = mkOption {
+        type = types.string;
+        default = "weekly";
+        description = ''
+          How often we run fstrim. For most desktop and server systems
+          a sufficient trimming frequency is once a week.
+
+          The format is described in
+          <citerefentry><refentrytitle>systemd.time</refentrytitle>
+          <manvolnum>7</manvolnum></citerefentry>.
+        '';
+      };
+    };
+
+  };
+
+  config = mkIf cfg.enable {
+
+    systemd.packages = [ pkgs.utillinux ];
+
+    systemd.timers.fstrim = {
+      timerConfig = {
+        OnCalendar = cfg.interval;
+      };
+      wantedBy = [ "timers.target" ];
+    };
+
+  };
+
+}

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

@@ -1,5 +1,6 @@
 { stdenv, fetch, cmake, libxml2, libedit, llvm, version, release_version, clang-tools-extra_src, python
 , fixDarwinDylibNames
+, enableManpages ? true
 }:
 
 let
@@ -15,25 +16,28 @@ let
       mv clang-tools-extra-* $sourceRoot/tools/extra
     '';
 
-    nativeBuildInputs = [ cmake python python.pkgs.sphinx ];
+    nativeBuildInputs = [ cmake python ]
+      ++ stdenv.lib.optional enableManpages python.pkgs.sphinx;
+
     buildInputs = [ libedit libxml2 llvm ]
       ++ stdenv.lib.optional stdenv.isDarwin fixDarwinDylibNames;
 
     cmakeFlags = [
       "-DCMAKE_CXX_FLAGS=-std=c++11"
+    ] ++ stdenv.lib.optionals enableManpages [
       "-DCLANG_INCLUDE_DOCS=ON"
       "-DLLVM_ENABLE_SPHINX=ON"
       "-DSPHINX_OUTPUT_MAN=ON"
       "-DSPHINX_OUTPUT_HTML=OFF"
       "-DSPHINX_WARNINGS_AS_ERRORS=OFF"
-    ] ++
+    ]
     # Maybe with compiler-rt this won't be needed?
-    (stdenv.lib.optional stdenv.isLinux "-DGCC_INSTALL_PREFIX=${gcc}") ++
-    (stdenv.lib.optional (stdenv.cc.libc != null) "-DC_INCLUDE_DIRS=${stdenv.cc.libc}/include");
+    ++ stdenv.lib.optional stdenv.isLinux "-DGCC_INSTALL_PREFIX=${gcc}"
+    ++ stdenv.lib.optional (stdenv.cc.libc != null) "-DC_INCLUDE_DIRS=${stdenv.cc.libc}/include";
 
     patches = [ ./purity.patch ];
 
-    postBuild = ''
+    postBuild = stdenv.lib.optionalString enableManpages ''
       cmake --build . --target docs-clang-man
     '';
 
@@ -45,7 +49,8 @@ let
       sed -i '1s,^,find_package(Sphinx REQUIRED)\n,' docs/CMakeLists.txt
     '';
 
-    outputs = [ "out" "man" "python" ];
+    outputs = [ "out" "python" ]
+      ++ stdenv.lib.optional enableManpages "man";
 
     # Clang expects to find LLVMgold in its own prefix
     # Clang expects to find sanitizer libraries in its own prefix
@@ -62,7 +67,8 @@ let
       mv $out/share/clang/*.py $python/share/clang
 
       rm $out/bin/c-index-test
-
+    ''
+    + stdenv.lib.optionalString enableManpages ''
       # Manually install clang manpage
       cp docs/man/*.1 $out/share/man/man1/
 

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

@@ -16,6 +16,7 @@
 , compiler-rt_src
 , libcxxabi
 , debugVersion ? false
+, enableManpages ? true
 , enableSharedLibraries ? true
 , darwin
 }:
@@ -38,9 +39,13 @@ in stdenv.mkDerivation rec {
     mv compiler-rt-* $sourceRoot/projects/compiler-rt
   '';
 
-  outputs = [ "out" "man" ] ++ stdenv.lib.optional enableSharedLibraries "lib";
+  outputs = [ "out" ]
+    ++ stdenv.lib.optional enableSharedLibraries "lib"
+    ++ stdenv.lib.optional enableManpages "man";
+
+  nativeBuildInputs = [ perl groff cmake python ]
+    ++ stdenv.lib.optional enableManpages python.pkgs.sphinx;
 
-  nativeBuildInputs = [ perl groff cmake python python.pkgs.sphinx ];
   buildInputs = [ libxml2 libffi ]
     ++ stdenv.lib.optionals stdenv.isDarwin [ libcxxabi ];
 
@@ -81,16 +86,19 @@ in stdenv.mkDerivation rec {
     "-DLLVM_ENABLE_FFI=ON"
     "-DLLVM_ENABLE_RTTI=ON"
     "-DCOMPILER_RT_INCLUDE_TESTS=OFF" # FIXME: requires clang source code
+  ]
+  ++ stdenv.lib.optional enableSharedLibraries
+    "-DLLVM_LINK_LLVM_DYLIB=ON"
+  ++ stdenv.lib.optionals enableManpages [
     "-DLLVM_BUILD_DOCS=ON"
     "-DLLVM_ENABLE_SPHINX=ON"
     "-DSPHINX_OUTPUT_MAN=ON"
     "-DSPHINX_OUTPUT_HTML=OFF"
     "-DSPHINX_WARNINGS_AS_ERRORS=OFF"
-  ] ++ stdenv.lib.optional enableSharedLibraries [
-    "-DLLVM_LINK_LLVM_DYLIB=ON"
-  ] ++ stdenv.lib.optional (!isDarwin)
+  ]
+  ++ stdenv.lib.optional (!isDarwin)
     "-DLLVM_BINUTILS_INCDIR=${binutils.dev}/include"
-    ++ stdenv.lib.optionals (isDarwin) [
+  ++ stdenv.lib.optionals (isDarwin) [
     "-DLLVM_ENABLE_LIBCXX=ON"
     "-DCAN_TARGET_i386=false"
   ];
@@ -109,10 +117,10 @@ in stdenv.mkDerivation rec {
     export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD/lib
   '';
 
-  postInstall = ''
+  postInstall = stdenv.lib.optionalString enableManpages ''
     moveToOutput "share/man" "$man"
   ''
-  + stdenv.lib.optionalString (enableSharedLibraries) ''
+  + stdenv.lib.optionalString enableSharedLibraries ''
     moveToOutput "lib/libLLVM-*" "$lib"
     moveToOutput "lib/libLLVM.${shlib}" "$lib"
     substituteInPlace "$out/lib/cmake/llvm/LLVMExports-release.cmake" \

pkgs/development/libraries/gnutls/3.5.nix

@@ -1,11 +1,11 @@
 { callPackage, fetchurl, libunistring, ... } @ args:
 
 callPackage ./generic.nix (args // rec {
-  version = "3.5.12";
+  version = "3.5.13";
 
   src = fetchurl {
     url = "ftp://ftp.gnutls.org/gcrypt/gnutls/v3.5/gnutls-${version}.tar.xz";
-    sha256 = "1jspvrmydqgz30c1ji94b55gr2dynz7p96p4y8fkhad0xajkkjv3";
+    sha256 = "15ihq6p0hnnhs8cnjrkj40dmlcaa1jjg8xg0g2ydbnlqs454ixbr";
   };
 
   # Skip two tests introduced in 3.5.11.  Probable reasons of failure:

pkgs/development/libraries/icu/default.nix

@@ -33,18 +33,9 @@ stdenv.mkDerivation ({
     echo Source root reset to ''${sourceRoot}
   '';
 
-  # This pre/postPatch shenanigans is to handle that the patches expect
-  # to be outside of `source`.
-  prePatch = ''
-    pushd ..
-  '';
-  postPatch = ''
-    popd
-    patch -p4 < ${keywordFix}
-  '';
+  patchFlags = "-p4";
 
-  patches = [
-  ];
+  patches = [ keywordFix ];
 
   preConfigure = ''
     sed -i -e "s|/bin/sh|${stdenv.shell}|" configure

pkgs/development/libraries/libgcrypt/default.nix

@@ -4,11 +4,11 @@ assert enableCapabilities -> stdenv.isLinux;
 
 stdenv.mkDerivation rec {
   name = "libgcrypt-${version}";
-  version = "1.7.6";
+  version = "1.7.7";
 
   src = fetchurl {
     url = "mirror://gnupg/libgcrypt/${name}.tar.bz2";
-    sha256 = "1g05prhgqw4ryd0w433q8nhds0h93kf47hfjagi2r7dghkpaysk2";
+    sha256 = "16ndaj93asw122mwjz172x2ilpm03w1yp5mqcrp3xslk0yx5xf5r";
   };
 
   outputs = [ "out" "dev" "info" ];

pkgs/development/libraries/libtiff/default.nix

@@ -1,21 +1,20 @@
 { stdenv, fetchurl, fetchpatch, pkgconfig, zlib, libjpeg, xz }:
 
 let
-  version = "4.0.7";
+  version = "4.0.8";
 in
 stdenv.mkDerivation rec {
   name = "libtiff-${version}";
 
   src = fetchurl {
     url = "http://download.osgeo.org/libtiff/tiff-${version}.tar.gz";
-    sha256 = "06ghqhr4db1ssq0acyyz49gr8k41gzw6pqb6mbn5r7jqp77s4hwz";
+    sha256 = "0419mh6kkhz5fkyl77gv0in8x4d2jpdpfs147y8mj86rrjlabmsr";
   };
 
   prePatch =let
-      # https://lwn.net/Vulnerabilities/711777/ and more patched in *-6 -> *-7
       debian = fetchurl {
-        url = http://http.debian.net/debian/pool/main/t/tiff/tiff_4.0.7-6.debian.tar.xz;
-        sha256 = "9c9048c28205bdbeb5ba36c7a194d0cd604bd137c70961607bfc8a079be5fa31";
+        url = http://http.debian.net/debian/pool/main/t/tiff/tiff_4.0.8-2.debian.tar.xz;
+        sha256 = "1ssjh6vn9rvl2jwm34i3p89g8lj0c7fj3cziva9rj4vasfps58ng";
       };
     in ''
       tar xf '${debian}'

pkgs/development/libraries/openssl/default.nix

@@ -109,8 +109,8 @@ let
 in {
 
   openssl_1_0_2 = common {
-    version = "1.0.2k";
-    sha256 = "1h6qi35w6hv6rd73p4cdgdzg732pdrfgpp37cgwz1v9a3z37ffbb";
+    version = "1.0.2l";
+    sha256 = "037kvpisc6qh5dkppcwbm5bg2q800xh2hma3vghz8xcycmdij1yf";
   };
 
   openssl_1_1_0 = common {

pkgs/development/python-modules/bootstrapped-pip/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, python, fetchPypi, makeWrapper, unzip }:
+{ stdenv, python, fetchPypi, fetchurl, makeWrapper, unzip }:
 
 let
   wheel_source = fetchPypi {
@@ -13,6 +13,15 @@ let
     format = "wheel";
     sha256 = "f2900e560efc479938a219433c48f15a4ff4ecfe575a65de385eeb44f2425587";
   };
+
+  # TODO: Shouldn't be necessary anymore for pip > 9.0.1!
+  # https://github.com/NixOS/nixpkgs/issues/26392
+  # https://github.com/pypa/setuptools/issues/885
+  pkg_resources = fetchurl {
+    url = https://raw.githubusercontent.com/pypa/setuptools/v36.0.1/pkg_resources/__init__.py;
+    sha256 = "1wdnq3mammk75mifkdmmjx7yhnpydvnvi804na8ym4mj934l2jkv";
+  };
+
 in stdenv.mkDerivation rec {
   pname = "pip";
   version = "9.0.1";
@@ -29,6 +38,8 @@ in stdenv.mkDerivation rec {
     unzip -d $out/${python.sitePackages} $src
     unzip -d $out/${python.sitePackages} ${setuptools_source}
     unzip -d $out/${python.sitePackages} ${wheel_source}
+    # TODO: Shouldn't be necessary anymore for pip > 9.0.1!
+    cp ${pkg_resources} $out/${python.sitePackages}/pip/_vendor/pkg_resources/__init__.py
   '';
 
   patchPhase = ''

pkgs/development/tools/build-managers/cmake/default.nix

@@ -3,7 +3,7 @@
 # darwin attributes
 , ps
 , isBootstrap ? false
-, useSharedLibraries ? !stdenv.isCygwin
+, useSharedLibraries ? (!isBootstrap && !stdenv.isCygwin)
 , useNcurses ? false, ncurses
 , useQt4 ? false, qt4
 }:

pkgs/os-specific/linux/nfs-utils/default.nix

@@ -39,6 +39,9 @@ in stdenv.mkDerivation rec {
       sed -i "s,^PATH=.*,PATH=$out/bin:${statdPath}," utils/statd/start-statd
 
       configureFlags="--with-start-statd=$out/bin/start-statd $configureFlags"
+
+      substituteInPlace utils/mount/Makefile.in \
+        --replace "chmod 4511" "chmod 0511"
     '';
 
   makeFlags = [

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

@@ -41,6 +41,11 @@ stdenv.mkDerivation rec {
       })
     ];
 
+  # The nix daemon often forbids even creating set[ug]id files.
+  postPatch =
+    ''sed 's/^\(s[ug]idperms\) = [0-9]755/\1 = 0755/' -i src/Makefile.am
+    '';
+
   outputs = [ "out" "su" "man" ];
 
   enableParallelBuilding = true;

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

@@ -29,31 +29,30 @@ stdenv.mkDerivation rec {
     preConfigure = "export scanf_cv_type_modifier=ms";
   };
 
+  preConfigure = lib.optionalString (systemd != null) ''
+    configureFlags+=" --with-systemd --with-systemdsystemunitdir=$bin/lib/systemd/system/"
+  '';
+
   # !!! It would be better to obtain the path to the mount helpers
   # (/sbin/mount.*) through an environment variable, but that's
   # somewhat risky because we have to consider that mount can setuid
   # root...
-  configureFlags = ''
-    --enable-write
-    --enable-last
-    --enable-mesg
-    --disable-use-tty-group
-    --enable-fs-paths-default=/run/wrappers/bin:/var/run/current-system/sw/bin:/sbin
-    ${if ncurses == null then "--without-ncurses" else ""}
-    ${if systemd == null then "" else ''
-      --with-systemd
-      --with-systemdsystemunitdir=$out/lib/systemd/system/
-    ''}
-  '';
+  configureFlags = [
+    "--enable-write"
+    "--enable-last"
+    "--enable-mesg"
+    "--disable-use-tty-group"
+    "--enable-fs-paths-default=/run/wrappers/bin:/var/run/current-system/sw/bin:/sbin"
+    "--disable-makeinstall-setuid" "--disable-makeinstall-chown"
+  ]
+    ++ lib.optional (ncurses == null) "--without-ncurses";
 
   makeFlags = "usrbin_execdir=$(bin)/bin usrsbin_execdir=$(bin)/sbin";
 
   nativeBuildInputs = [ pkgconfig ];
   buildInputs =
     [ zlib pam ]
-    ++ lib.optional (ncurses != null) ncurses
-    ++ lib.optional (systemd != null) systemd
-    ++ lib.optional (perl != null) perl;
+    ++ lib.filter (p: p != null) [ ncurses systemd perl ];
 
   postInstall = ''
     rm "$bin/bin/su" # su should be supplied by the su package (shadow)

pkgs/stdenv/darwin/default.nix

@@ -233,11 +233,11 @@ in rec {
       libcxxabi libcxx ncurses libffi zlib gmp pcre gnugrep
       coreutils findutils diffutils patchutils;
 
-    llvmPackages = let llvmOverride = llvmPackages.llvm.override { inherit libcxxabi; };
-    in super.llvmPackages // {
-      llvm = llvmOverride;
-      clang-unwrapped = llvmPackages.clang-unwrapped.override { llvm = llvmOverride; };
-    };
+    llvmPackages = let llvmOverride = llvmPackages.llvm.override { enableManpages = false; inherit libcxxabi; }; in
+      super.llvmPackages // {
+        llvm = llvmOverride;
+        clang-unwrapped = llvmPackages.clang-unwrapped.override { enableManpages = false; llvm = llvmOverride; };
+      };
 
     darwin = super.darwin // {
       inherit (darwin) dyld Libsystem libiconv locale;
@@ -313,7 +313,7 @@ in rec {
       xz.out xz.bin libcxx libcxxabi gmp.out gnumake findutils bzip2.out
       bzip2.bin llvmPackages.llvm llvmPackages.llvm.lib zlib.out zlib.dev libffi.out coreutils ed diffutils gnutar
       gzip ncurses.out ncurses.dev ncurses.man gnused bash gawk
-      gnugrep llvmPackages.clang-unwrapped llvmPackages.clang-unwrapped.man patch pcre.out binutils-raw.out
+      gnugrep llvmPackages.clang-unwrapped patch pcre.out binutils-raw.out
       binutils-raw.dev binutils gettext
     ]) ++ (with pkgs.darwin; [
       dyld Libsystem CF cctools ICU libiconv locale

pkgs/tools/networking/openssh/default.nix

@@ -49,6 +49,13 @@ stdenv.mkDerivation rec {
     ]
     ++ optional withGssapiPatches gssapiSrc;
 
+  postPatch =
+    # On Hydra this makes installation fail (sometimes?),
+    # and nix store doesn't allow such fancy permission bits anyway.
+    ''
+      substituteInPlace Makefile.in --replace '$(INSTALL) -m 4711' '$(INSTALL) -m 0711'
+    '';
+
   buildInputs = [ zlib openssl libedit pkgconfig pam ]
     ++ optional withKerberos kerberos
     ++ optional hpnSupport autoreconfHook;

pkgs/tools/system/vboot_reference/default.nix

@@ -12,11 +12,10 @@ stdenv.mkDerivation rec {
     sha256 = "14d3a93ha5k4al4ib43nyn1ppx7kgb12xw6mkflhx8nxmx8827nc";
   };
 
-  buildInputs = [ pkgconfig openssl stdenv.cc.libc.static ] ++
-                (if libuuid == null
-                 then []
-                 else [ (stdenv.lib.overrideDerivation libuuid
-                          (args: { configureFlags = args.configureFlags + " --enable-static"; })) ]);
+  buildInputs = [ pkgconfig openssl stdenv.cc.libc.static ]
+    ++ stdenv.lib.optional (libuuid != null)
+         (libuuid.overrideAttrs (attrs:
+           { configureFlags = attrs.configureFlags ++ [ "--enable-static" ]; }));
 
   arch = if stdenv.system == "x86_64-linux" then "x86_64"
     else if stdenv.system == "i686-linux" then "x86"

pkgs/top-level/all-packages.nix

@@ -5649,7 +5649,7 @@ with pkgs;
   llvmPackages_4 = callPackage ../development/compilers/llvm/4 ({
     inherit (stdenvAdapters) overrideCC;
   } // stdenv.lib.optionalAttrs stdenv.isDarwin {
-    cmake = cmake.override { isBootstrap = true; useSharedLibraries = false; };
+    cmake = cmake.override { isBootstrap = true; };
     libxml2 = libxml2.override { pythonSupport = false; };
     python2 = callPackage ../development/interpreters/python/cpython/2.7/boot.nix { inherit (darwin) CF configd; };
   });

pkgs/top-level/python-packages.nix

@@ -12468,11 +12468,11 @@ in {
   };
 
   ipaddress = if (pythonAtLeast "3.3") then null else buildPythonPackage rec {
-    name = "ipaddress-1.0.16";
+    name = "ipaddress-1.0.18";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/i/ipaddress/${name}.tar.gz";
-      sha256 = "1c3imabdrw8nfksgjjflzg7h4ynjckqacb188rf541m74arq4cas";
+      sha256 = "1q8klj9d84cmxgz66073x1j35cplr3r77vx1znhxiwl5w74391ax";
     };
 
     checkPhase = ''