From 64fa24b516f6fa53a850ca86eab8c359745e4812 Mon Sep 17 00:00:00 2001
From: Ioannis Koutras <ioannis.koutras@gmail.com>
Date: Sun, 26 Nov 2017 01:57:54 +0200
Subject: [PATCH 01/12] xmonad-log: init at 0.1.0

---
 pkgs/tools/misc/xmonad-log/default.nix | 25 +++++++++++++++++++++++++
 pkgs/tools/misc/xmonad-log/deps.nix    | 12 ++++++++++++
 pkgs/top-level/all-packages.nix        |  2 ++
 3 files changed, 39 insertions(+)
 create mode 100644 pkgs/tools/misc/xmonad-log/default.nix
 create mode 100644 pkgs/tools/misc/xmonad-log/deps.nix

diff --git a/pkgs/tools/misc/xmonad-log/default.nix b/pkgs/tools/misc/xmonad-log/default.nix
new file mode 100644
index 00000000000..c39da71e179
--- /dev/null
+++ b/pkgs/tools/misc/xmonad-log/default.nix
@@ -0,0 +1,25 @@
+{ stdenv, buildGoPackage, fetchFromGitHub }:
+
+buildGoPackage rec {
+  name = "xmonad-log-${version}";
+  version = "0.1.0";
+
+  goPackagePath = "github.com/xintron/xmonad-log";
+
+  src = fetchFromGitHub {
+    owner = "xintron";
+    repo = "xmonad-log";
+    rev = version;
+    sha256 = "1il6v0zcjw0pfb1hjj198y94jmlcx255h422ph0f1zr7afqkzmaw";
+  };
+
+  goDeps = ./deps.nix;
+
+  meta = with stdenv.lib; {
+    description = "xmonad DBus monitoring solution";
+    homepage = https://github.com/xintron/xmonad-log;
+    license = licenses.mit;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ joko ];
+  };
+}
diff --git a/pkgs/tools/misc/xmonad-log/deps.nix b/pkgs/tools/misc/xmonad-log/deps.nix
new file mode 100644
index 00000000000..f5a7c7e5dd1
--- /dev/null
+++ b/pkgs/tools/misc/xmonad-log/deps.nix
@@ -0,0 +1,12 @@
+# This file was generated by https://github.com/kamilchm/go2nix v1.2.1
+[
+  {
+    goPackagePath = "github.com/godbus/dbus";
+    fetch = {
+      type = "git";
+      url = "https://github.com/godbus/dbus";
+      rev = "a389bdde4dd695d414e47b755e95e72b7826432c";
+      sha256 = "1ckvg15zdsgmbn4mi36cazkb407ixc9mmyf7vwj8b8wi3d00rgn9";
+    };
+  }
+]
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 25fb245eb9e..bdde51d2271 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -17921,6 +17921,8 @@ with pkgs;
 
   xkblayout-state = callPackage ../applications/misc/xkblayout-state { };
 
+  xmonad-log = callPackage ../tools/misc/xmonad-log { };
+
   xmonad-with-packages = callPackage ../applications/window-managers/xmonad/wrapper.nix {
     inherit (haskellPackages) ghcWithPackages;
     packages = self: [];

From 12c5dc343fdbbbd5f012d8ff6ed784424950ab86 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Arcadio=20Rubio=20Garc=C3=ADa?= <arc@well.ox.ac.uk>
Date: Mon, 22 Jan 2018 12:16:26 +0000
Subject: [PATCH 02/12] picard-tools: 2.7.1 -> 2.17.4

---
 pkgs/applications/science/biology/picard-tools/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix
index 3f17825202e..5578a41f444 100644
--- a/pkgs/applications/science/biology/picard-tools/default.nix
+++ b/pkgs/applications/science/biology/picard-tools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "picard-tools-${version}";
-  version = "2.7.1";
+  version = "2.17.4";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "0rcfcvy9zacqmh7nyqlm93hzsx6gfygmcf8d2p02h5l69gvygnb9";
+    sha256 = "00ffi8kkrlh72vjjkjpgi8zys3r9hkdk4xi82kcahch8pix4qzf2";
   };
 
   buildInputs = [ jre makeWrapper ];

From 612953567d823b5f8a8dc6602bcbd3028dec4563 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Arcadio=20Rubio=20Garc=C3=ADa?= <arc@well.ox.ac.uk>
Date: Mon, 22 Jan 2018 12:28:06 +0000
Subject: [PATCH 03/12] bowtie2: 2.3.3.1 -> 2.3.4

---
 pkgs/applications/science/biology/bowtie2/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/science/biology/bowtie2/default.nix b/pkgs/applications/science/biology/bowtie2/default.nix
index 05a85cafedf..f04b81ea979 100644
--- a/pkgs/applications/science/biology/bowtie2/default.nix
+++ b/pkgs/applications/science/biology/bowtie2/default.nix
@@ -2,14 +2,14 @@
 
 stdenv.mkDerivation rec {
   pname = "bowtie2";
-  version = "2.3.3.1";
+  version = "2.3.4";
   name = "${pname}-${version}";
 
   src = fetchFromGitHub {
     owner = "BenLangmead";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1pcyks76bnnkq6h0gqjw4fkdddjjnw7k5ibim7ajkbvfw58a99y0";
+    sha256 = "15k86ln1xgqkyk8ms09cgdhagz49jpvr6ij6mha1f9ga5fxnnp1m";
   };
 
   buildInputs = [ zlib tbb ];

From 960d7d66d5ccdccf1b9ee40e7536ba424500d923 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Arcadio=20Rubio=20Garc=C3=ADa?= <arc@well.ox.ac.uk>
Date: Mon, 22 Jan 2018 14:50:51 +0000
Subject: [PATCH 04/12] libreoffice: Add Spanish (es) language support and sort
 langs list

---
 pkgs/applications/office/libreoffice/default.nix | 2 +-
 pkgs/applications/office/libreoffice/still.nix   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/office/libreoffice/default.nix b/pkgs/applications/office/libreoffice/default.nix
index cd59f78b6c6..c8948d13cf7 100644
--- a/pkgs/applications/office/libreoffice/default.nix
+++ b/pkgs/applications/office/libreoffice/default.nix
@@ -13,7 +13,7 @@
 , librevenge, libe-book, libmwaw, glm, glew, gst_all_1
 , gdb, commonsLogging, librdf_rasqal, wrapGAppsHook
 , defaultIconTheme, glib, ncurses, xmlsec, epoxy, gpgme
-, langs ? [ "en-US" "en-GB" "ca" "ru" "eo" "fr" "nl" "de" "sl" "pl" "hu" "it" ]
+, langs ? [ "ca" "de" "en-GB" "en-US" "eo" "es" "fr" "hu" "it" "nl" "pl" "ru" "sl" ]
 , withHelp ? true
 , kdeIntegration ? false
 }:
diff --git a/pkgs/applications/office/libreoffice/still.nix b/pkgs/applications/office/libreoffice/still.nix
index 679afaa2dce..5070de5262e 100644
--- a/pkgs/applications/office/libreoffice/still.nix
+++ b/pkgs/applications/office/libreoffice/still.nix
@@ -13,7 +13,7 @@
 , librevenge, libe-book, libmwaw, glm, glew, gst_all_1
 , gdb, commonsLogging, librdf_rasqal, wrapGAppsHook
 , defaultIconTheme, glib, ncurses
-, langs ? [ "en-US" "en-GB" "ca" "ru" "eo" "fr" "nl" "de" "sl" "pl" "hu" "it" ]
+, langs ? [ "ca" "de" "en-GB" "en-US" "eo" "es" "fr" "hu" "it" "nl" "pl" "ru" "sl" ]
 , withHelp ? true
 }:
 

From 360b86e51562d25d6d674ac80b8e4c9b9ae0088d Mon Sep 17 00:00:00 2001
From: Will Dietz <w@wdtz.org>
Date: Mon, 22 Jan 2018 11:12:43 -0600
Subject: [PATCH 05/12] vim: 8.0.1257 -> 8.0.1428

---
 pkgs/applications/editors/vim/common.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/editors/vim/common.nix b/pkgs/applications/editors/vim/common.nix
index 417f2d80516..21b0f7a85d2 100644
--- a/pkgs/applications/editors/vim/common.nix
+++ b/pkgs/applications/editors/vim/common.nix
@@ -1,12 +1,12 @@
 { lib, fetchFromGitHub }:
 rec {
-  version = "8.0.1257";
+  version = "8.0.1428";
 
   src = fetchFromGitHub {
     owner = "vim";
     repo = "vim";
     rev = "v${version}";
-    sha256 = "1y4c7wn5gr7n4c2ni36kadr26aldydxlf06yj7nsmw22ywwg78ig";
+    sha256 = "0pqqh7g96w8jfc5kvv2il6fcbhccwhk4k5skk52g1c1ixsblwz3y";
   };
 
   enableParallelBuilding = true;

From c8d5121c1d184cf48b63a03ab2aa575d5189e9ee Mon Sep 17 00:00:00 2001
From: WilliButz <wbutz@cyberfnord.de>
Date: Sat, 20 Jan 2018 16:50:32 +0100
Subject: [PATCH 06/12] deis: 1.13.3 -> 1.13.4

---
 pkgs/development/tools/deis/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/tools/deis/default.nix b/pkgs/development/tools/deis/default.nix
index fe4ec06322f..91037e6dfaa 100644
--- a/pkgs/development/tools/deis/default.nix
+++ b/pkgs/development/tools/deis/default.nix
@@ -2,7 +2,7 @@
 
 buildGoPackage rec {
   name = "deis-${version}";
-  version = "1.13.3";
+  version = "1.13.4";
   rev = "v${version}";
 
   goPackagePath = "github.com/deis/deis";
@@ -18,7 +18,7 @@ buildGoPackage rec {
     inherit rev;
     owner = "deis";
     repo = "deis";
-    sha256 = "15q44jyjms8fdmly0z4sn4ymf1dx6cmdavgixjixdj2wbjw0yi2p";
+    sha256 = "0hndzvlgpfm83c4i1c88byv8j9clagswa79nny8wrw33dx90dym1";
   };
 
   preBuild = ''

From 3e173f39be8946dcf6841a3652a3199f06f9ba8f Mon Sep 17 00:00:00 2001
From: WilliButz <wbutz@cyberfnord.de>
Date: Sat, 20 Jan 2018 16:55:07 +0100
Subject: [PATCH 07/12] irqbalance: 1.2.0 -> 1.3.0

---
 pkgs/os-specific/linux/irqbalance/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/os-specific/linux/irqbalance/default.nix b/pkgs/os-specific/linux/irqbalance/default.nix
index 26cedf41a5a..76c10f0a06e 100644
--- a/pkgs/os-specific/linux/irqbalance/default.nix
+++ b/pkgs/os-specific/linux/irqbalance/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "irqbalance-${version}";
-  version = "1.2.0";
+  version = "1.3.0";
 
   src = fetchFromGitHub {
     owner = "irqbalance";
     repo = "irqbalance";
     rev = "v${version}";
-    sha256 = "1xznxjbjzg6sds3fymdq9rk3g4cgq7xj7rz3dwbqqjqvd3k2nxw6";
+    sha256 = "009777p5v72x4r58skqgaf03qv3app9b8lkxkpxq0226l0x3j4qh";
   };
 
   nativeBuildInputs = [ autoreconfHook pkgconfig ];

From 4361cc5ffa17d6b525b426aef49ed43632cfa891 Mon Sep 17 00:00:00 2001
From: WilliButz <wbutz@cyberfnord.de>
Date: Sat, 20 Jan 2018 17:06:23 +0100
Subject: [PATCH 08/12] scanmem: 0.16 -> 0.17

---
 pkgs/tools/misc/scanmem/default.nix | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/pkgs/tools/misc/scanmem/default.nix b/pkgs/tools/misc/scanmem/default.nix
index 132012de123..bd760adecf7 100644
--- a/pkgs/tools/misc/scanmem/default.nix
+++ b/pkgs/tools/misc/scanmem/default.nix
@@ -1,26 +1,26 @@
 { stdenv, autoconf, automake, intltool, libtool, fetchFromGitHub, readline }:
 
 stdenv.mkDerivation rec {
-  version = "0.16";
+  version = "0.17";
   name = "scanmem-${version}";
- 
+
   src = fetchFromGitHub {
     owner  = "scanmem";
     repo   = "scanmem";
     rev    = "v${version}";
-    sha256 = "131rx6cpnlz2x36r0ry80gqapmxpz2qc3h0040xhvp7ydmd4fyjd";
+    sha256 = "17p8sh0rj8yqz36ria5bp48c8523zzw3y9g8sbm2jwq7sc27i7s9";
   };
 
   nativeBuildInputs = [ autoconf automake intltool libtool ];
   buildInputs = [ readline ];
-  
+
   preConfigure = ''
     ./autogen.sh
   '';
   meta = with stdenv.lib; {
     homepage = https://github.com/scanmem/scanmem;
     description = "Memory scanner for finding and poking addresses in executing processes";
-    maintainers = [ maintainers.chattered  ];
+    maintainers = [ maintainers.chattered ];
     platforms = platforms.linux;
     license = licenses.gpl3;
   };

From 0c27903ac04557f2a3de5b385f0fb28321079131 Mon Sep 17 00:00:00 2001
From: Daiderd Jordan <daiderd@gmail.com>
Date: Mon, 22 Jan 2018 19:45:40 +0100
Subject: [PATCH 09/12] python-cffi: remove patch for clang

Builds fine without it now.
---
 pkgs/development/python-modules/cffi/clang.patch | 13 -------------
 pkgs/development/python-modules/cffi/default.nix |  2 --
 2 files changed, 15 deletions(-)
 delete mode 100644 pkgs/development/python-modules/cffi/clang.patch

diff --git a/pkgs/development/python-modules/cffi/clang.patch b/pkgs/development/python-modules/cffi/clang.patch
deleted file mode 100644
index 27674edb58b..00000000000
--- a/pkgs/development/python-modules/cffi/clang.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/testing/cffi1/test_recompiler.py b/testing/cffi1/test_recompiler.py
-index a3277b0..0d6e2c3 100644
---- a/testing/cffi1/test_recompiler.py
-+++ b/testing/cffi1/test_recompiler.py
-@@ -2270,7 +2270,7 @@ def test_char16_char32_type(no_cpp=False):
-         char32_t foo_4bytes(char32_t);
-     """)
-     lib = verify(ffi, "test_char16_char32_type" + no_cpp * "_nocpp", """
--    #if !defined(__cplusplus) || __cplusplus < 201103L
-+    #if !defined(__cplusplus)
-     typedef uint_least16_t char16_t;
-     typedef uint_least32_t char32_t;
-     #endif
diff --git a/pkgs/development/python-modules/cffi/default.nix b/pkgs/development/python-modules/cffi/default.nix
index cc6ad6a32a7..6658b76c31e 100644
--- a/pkgs/development/python-modules/cffi/default.nix
+++ b/pkgs/development/python-modules/cffi/default.nix
@@ -10,8 +10,6 @@ if isPyPy then null else buildPythonPackage rec {
     sha256 = "df9083a992b17a28cd4251a3f5c879e0198bb26c9e808c4647e0a18739f1d11d";
   };
 
-  patches = stdenv.lib.optional (isPy27 && stdenv.cc.isClang) ./clang.patch;
-
   outputs = [ "out" "dev" ];
 
   propagatedBuildInputs = [ libffi pycparser ];

From f8514573682173267572aea06a019949a0ad8308 Mon Sep 17 00:00:00 2001
From: Will Dietz <w@wdtz.org>
Date: Mon, 22 Jan 2018 12:45:48 -0600
Subject: [PATCH 10/12] vim: fix for cross, add missing configure test override

This is one of the variables mentioned to set
when cross-compiling:

https://github.com/vim/vim/blob/master/src/INSTALLx.txt
---
 pkgs/applications/editors/vim/default.nix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pkgs/applications/editors/vim/default.nix b/pkgs/applications/editors/vim/default.nix
index 2f110749277..067179974b1 100644
--- a/pkgs/applications/editors/vim/default.nix
+++ b/pkgs/applications/editors/vim/default.nix
@@ -29,6 +29,7 @@ stdenv.mkDerivation rec {
     "vim_cv_toupper_broken=no"
     "--with-tlib=ncurses"
     "vim_cv_terminfo=yes"
+    "vim_cv_tgetent=zero" # it does on native anyway
     "vim_cv_tty_group=tty"
     "vim_cv_tty_mode=0660"
     "vim_cv_getcwd_broken=no"

From 505c82efe44b2366360c22f73cce8cd72bd8ac8c Mon Sep 17 00:00:00 2001
From: Daiderd Jordan <daiderd@gmail.com>
Date: Mon, 22 Jan 2018 19:55:47 +0100
Subject: [PATCH 11/12] python-cffi: add lnl7 to maintainers

---
 pkgs/development/python-modules/cffi/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/python-modules/cffi/default.nix b/pkgs/development/python-modules/cffi/default.nix
index 6658b76c31e..28d4a36aca7 100644
--- a/pkgs/development/python-modules/cffi/default.nix
+++ b/pkgs/development/python-modules/cffi/default.nix
@@ -37,7 +37,7 @@ if isPyPy then null else buildPythonPackage rec {
   '';
 
   meta = with stdenv.lib; {
-    maintainers = with maintainers; [ domenkozar ];
+    maintainers = with maintainers; [ domenkozar lnl7 ];
     homepage = https://cffi.readthedocs.org/;
     license = with licenses; [ mit ];
     description = "Foreign Function Interface for Python calling C code";

From bd67bf5ca00e8895e2e9156a014a2871fe911f53 Mon Sep 17 00:00:00 2001
From: Will Dietz <github@wdtz.org>
Date: Mon, 22 Jan 2018 13:07:03 -0600
Subject: [PATCH 12/12] julia-git: mark broken, hasn't built since 2017-04-08.
 (#34150)

* julia-git: mark broken, hasn't built since 2017-04-08.

First broken: https://hydra.nixos.org/build/51447624
Last successful: https://hydra.nixos.org/build/51385779

cc #34135
---
 pkgs/development/compilers/julia/git.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/compilers/julia/git.nix b/pkgs/development/compilers/julia/git.nix
index cfddb862f59..19519823f37 100644
--- a/pkgs/development/compilers/julia/git.nix
+++ b/pkgs/development/compilers/julia/git.nix
@@ -175,6 +175,6 @@ stdenv.mkDerivation rec {
     license = stdenv.lib.licenses.mit;
     maintainers = with stdenv.lib.maintainers; [ raskin ];
     platforms = [ "i686-linux" "x86_64-linux" "x86_64-darwin" ];
-    broken = stdenv.isi686;
+    broken = true; # since 2017-04-08.
   };
 }