From 9a68fb6c3002f3e440bb01d8c25c660800101c1b Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 7 Jun 2017 18:18:39 -0400
Subject: gnu: Rename 's' to 's-shell'.

* gnu/packages/shells.scm (s): Rename to ...
(s-shell): ... this.
[name]: Change to "s-shell".
---
 gnu/packages/shells.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm
index 5e04e86539..41d1758250 100644
--- a/gnu/packages/shells.scm
+++ b/gnu/packages/shells.scm
@@ -503,11 +503,11 @@ (define-public linenoise
 @end enumerate\n")
     (license bsd-2)))
 
-(define-public s
+(define-public s-shell
   (let ((commit "6604341edb3a775ff94415762af3ee9bd86bfb3c")
         (revision "1"))
     (package
-      (name "s")
+      (name "s-shell")
       (version (string-append "0.0.0-" revision "." (string-take commit 7)))
       (source
        (origin
-- 
cgit v1.2.3


From 517c66c03d16604e0f59db313368a676b761f79b Mon Sep 17 00:00:00 2001
From: Clément Lassieur <clement@lassieur.org>
Date: Wed, 7 Jun 2017 23:42:30 +0200
Subject: gnu: livemedia-utils: Change source URL to one that is archived.

* gnu/packages/video.scm (livemedia-utils)[source]: Change it.
---
 gnu/packages/video.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 4b3d83df28..1053f76bb7 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -2176,7 +2176,7 @@ (define-public livemedia-utils
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "http://www.live555.com/liveMedia/public/live."
+                    "https://download.videolan.org/contrib/live555/live."
                     version ".tar.gz"))
               (sha256
                (base32
-- 
cgit v1.2.3


From 1577a65809f8ef1883d18cf81095f632b65c042a Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 7 Jun 2017 19:13:59 -0400
Subject: gnu: guile-2.2: Increase max-silent-time to 6 hours.

* gnu/packages/guile.scm (guile-2.2)[properties]: Increase max-silent-time
to 6 hours.
---
 gnu/packages/guile.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 5b85a61c12..b9cd664604 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -240,7 +240,8 @@ (define-public guile-2.2
               (snippet '(for-each delete-file
                                   (find-files "prebuilt" "\\.go$")))))
     (properties '((timeout . 72000)               ;20 hours
-                  (max-silent-time . 10800)))     ;3 hours (needed on ARM)
+                  (max-silent-time . 21600)))     ;6 hours (needed on ARM
+                                                  ;  when heavily loaded)
     (native-search-paths
      (list (search-path-specification
             (variable "GUILE_LOAD_PATH")
-- 
cgit v1.2.3


From f69ff11af7a06b285c4d370f5c68788c3f4503d0 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 8 Jun 2017 09:38:41 +1000
Subject: gnu: diamond: Update to 0.9.6.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.6.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a5c28afc6e..bf4dd87eb3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2093,7 +2093,7 @@ (define-public deeptools
 (define-public diamond
   (package
     (name "diamond")
-    (version "0.9.3")
+    (version "0.9.6")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2102,7 +2102,7 @@ (define-public diamond
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1fs5ilvda50vfdg9wll35w8hcpq3jlkp8q2kim4llkwljkj8bls3"))))
+                "1y8a10b695pvgn7kk2s87jdwbdf7iszpnr6139pw8ina1ajs4w8y"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; no "check" target
-- 
cgit v1.2.3


From 4391a0295e090e7440685ff886f0c99c753c40a3 Mon Sep 17 00:00:00 2001
From: Clément Lassieur <clement@lassieur.org>
Date: Thu, 8 Jun 2017 11:23:27 +0200
Subject: gnu: the-silver-searcher: Update to 2.0.0.

* gnu/packages/code.scm (the-silver-searcher): Update to 2.0.0.
---
 gnu/packages/code.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm
index 1576c23b35..6f25b7cd82 100644
--- a/gnu/packages/code.scm
+++ b/gnu/packages/code.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -191,7 +192,7 @@ (define ref
 (define-public the-silver-searcher
   (package
     (name "the-silver-searcher")
-    (version "1.0.2")
+    (version "2.0.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -199,7 +200,7 @@ (define-public the-silver-searcher
                     version ".tar.gz"))
               (sha256
                (base32
-                "0v54himv65w294l0k4lhdyc6kvpgijn8b9g5356479fzy7hphjkg"))))
+                "04wm3r5p2mgv8mdkvysak0d5199h5y0yzl032624brfxpzmqfcq0"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From dfe93c9ac0578b624f952d0bf98142f8f1c20775 Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Thu, 8 Jun 2017 10:33:36 +0200
Subject: gnu: Add nftables.

* gnu/packages/linux.scm (nftables): New variable

Signed-off-by: Kei Kebreau <kei@openmailbox.org>
---
 gnu/packages/linux.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 217647e071..14e921ecd3 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -72,6 +72,7 @@ (define-module (gnu packages linux)
   #:use-module (gnu packages libusb)
   #:use-module (gnu packages man)
   #:use-module (gnu packages maths)
+  #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages networking)
   #:use-module (gnu packages ninja)
@@ -3854,6 +3855,36 @@ (define-public libnftnl
 used by nftables.")
     (license license:gpl2+)))
 
+(define-public nftables
+  (package
+    (name "nftables")
+    (version "0.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://www.nftables.org/projects/nftables"
+                           "/files/nftables-" version ".tar.bz2"))
+       (sha256
+        (base32
+         "0hzdqigdx4i6jbpxbdyq4zy4p4waqn8l6vvz7685ikh1v0wr4qzy"))))
+    (build-system gnu-build-system)
+    (inputs `(("bison", bison)
+              ("flex", flex)
+              ("gmp", gmp)
+              ("libmnl", libmnl)
+              ("libnftnl", libnftnl)
+              ("readline", readline)))
+    (native-inputs `(("pkg-config", pkg-config)))
+    (home-page "http://www.nftables.org")
+    (synopsis "Userspace utility for Linux packet filtering")
+    (description "nftables is the project that aims to replace the existing
+{ip,ip6,arp,eb}tables framework.  Basically, this project provides a new packet
+filtering framework, a new userspace utility and also a compatibility layer for
+{ip,ip6}tables.  nftables is built upon the building blocks of the Netfilter
+infrastructure such as the existing hooks, the connection tracking system, the
+userspace queueing component and the logging subsystem.")
+    (license license:gpl2)))
+
 (define-public proot
   (package
     (name "proot")
-- 
cgit v1.2.3


From 45f523d9f018c262900e94b0f70f17b05118941c Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Sun, 4 Jun 2017 20:57:03 -0700
Subject: gnu: emacs: Fix ert-runner by adding 'reporters' subdirectory.

Previous this change, ert-runner would fail with error:
"Invalid reporter: dot".

* gnu/packages/emacs.scm (ert-runner)[include]: Add regexp to match elisp
files under the 'reporters' subdirectory.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
---
 gnu/packages/emacs.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 987aaf4226..a4cb4a0b3a 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -4814,7 +4814,8 @@ (define-public ert-runner
                           ;; determined by emacs' standard initialization
                           ;; procedure
                           (list ""))))
-                 #t))))))
+                 #t))))
+         #:include (cons* "^reporters/.*\\.el$" %default-include)))
       (home-page "https://github.com/rejeep/ert-runner.el")
       (synopsis "Opinionated Ert testing workflow")
       (description "@code{ert-runner} is a tool for Emacs projects tested
-- 
cgit v1.2.3


From 758798a9cb9af09e146506d08a4fe7bfdd3d38ba Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Thu, 8 Jun 2017 18:00:01 +0200
Subject: gnu: geoclue: Create typelib files.

* gnu/packages/gnome.scm (geoclue)[native-inputs]: Add GOBJECT-INTROSPECTION.
---
 gnu/packages/gnome.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 84ae1cf2f1..4069abab82 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -2634,6 +2634,7 @@ (define-public geoclue
                          (("/bin/true") (which "true"))))))))
     (native-inputs
      `(("pkg-config" ,pkg-config)
+       ("gobject-introspection" ,gobject-introspection)
        ("intltool" ,intltool)))
     (inputs
      `(("avahi" ,avahi)
-- 
cgit v1.2.3


From 30e760f0cf6d7c1beae275853b86046ab3b9d7eb Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Thu, 8 Jun 2017 18:04:20 +0200
Subject: gnu: gnome-shell: Fix startup failure.

Fixes <https://bugs.gnu.org/27264>.

* gnu/packages/gnome.scm (gnome-shell)[inputs]: Add LIBRSVG and GEOCLUE.
---
 gnu/packages/gnome.scm | 4 ++++
 1 file changed, 4 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 4069abab82..9ea3bb07a5 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -5111,6 +5111,10 @@ (define-public gnome-shell
        ("startup-notification" ,startup-notification)
        ("telepathy-logger" ,telepathy-logger)
        ("upower" ,upower)
+       ;; XXX: These requirements were added in 3.24, but no mention in NEWS.
+       ;; Missing propagation? See also: <https://bugs.gnu.org/27264>
+       ("librsvg" ,librsvg)
+       ("geoclue" ,geoclue)
        ;; XXX: required by libgjs.la.
        ("readline" ,readline)))
     (synopsis "Desktop shell for GNOME")
-- 
cgit v1.2.3


From e7aab7736214d021d43bef598064f9daa95adc19 Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Mon, 15 May 2017 17:27:55 +0200
Subject: gnu: kguiaddons: Add more optional inputs.

* gnu/packages/kde-frameworks.scm (kguiaddons)
  [native-inputs]: Add pkg-config. [inputs]:Add qtx11extras.
---
 gnu/packages/kde-frameworks.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 07943e1e5e..d44692ac6d 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -641,9 +641,11 @@ (define-public kguiaddons
     (build-system cmake-build-system)
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)
+       ("pkg-config" ,pkg-config)
        ("xorg-server" ,xorg-server)))
     (inputs
-     `(("qtbase" ,qtbase)))
+     `(("qtbase" ,qtbase)
+       ("qtx11extras" ,qtx11extras)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-- 
cgit v1.2.3


From 986447c8a61a3746173c960aa9c064843123b77b Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Mon, 15 May 2017 18:12:20 +0200
Subject: gnu: kguiaddons: Remove unused native input.

The xorg server is not required since change
1de5b667f896aa2c612416bffac5f77cae94c5f4.

* gnu/packages/kde-frameworks.scm (kguiaddons)[native-inputs]: Remove
  xorg-server.
---
 gnu/packages/kde-frameworks.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index d44692ac6d..f7f5598fe8 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -641,8 +641,7 @@ (define-public kguiaddons
     (build-system cmake-build-system)
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)
-       ("pkg-config" ,pkg-config)
-       ("xorg-server" ,xorg-server)))
+       ("pkg-config" ,pkg-config)))
     (inputs
      `(("qtbase" ,qtbase)
        ("qtx11extras" ,qtx11extras)))
-- 
cgit v1.2.3


From 0cd3e818e7bfdfc8812e00b209e75a4298514b07 Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Mon, 15 May 2017 17:31:36 +0200
Subject: gnu: kitemmodels: Add more optional inputs.

* gnu/packages/kde-frameworks.scm (kitemmodels)[inputs]: Add qtdeclarative.
---
 gnu/packages/kde-frameworks.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index f7f5598fe8..1547c0154c 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -747,7 +747,8 @@ (define-public kitemmodels
      `(("extra-cmake-modules" ,extra-cmake-modules)
        ("xorg-server" ,xorg-server)))
     (inputs
-     `(("qtbase" ,qtbase)))
+     `(("qtbase" ,qtbase)
+       ("qtdeclarative" ,qtdeclarative)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-- 
cgit v1.2.3


From 72b073ca9e6a3a9702d4f206602fa105e9af48ab Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Mon, 15 May 2017 18:14:17 +0200
Subject: gnu: kcompletion: Remove unused native input.

The xorg server is not required since change
548f99b3e0d3647f29ddc3c3864ca36b655f14ec.

* gnu/packages/kde-frameworks.scm (kcompletion)[native-inputs]: Remove
  xorg-server.
---
 gnu/packages/kde-frameworks.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 1547c0154c..0354e1d7fd 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -1303,8 +1303,7 @@ (define-public kcompletion
     (build-system cmake-build-system)
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)
-       ("qttools" ,qttools)
-       ("xorg-server" ,xorg-server)))
+       ("qttools" ,qttools)))
     (inputs
      `(("kconfig" ,kconfig)
        ("kwidgetsaddons" ,kwidgetsaddons)
-- 
cgit v1.2.3


From 03ac48248b104becf026418ef0cef9fedfff9bbb Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Mon, 15 May 2017 22:25:28 +0200
Subject: gnu: kde frameworks: Avoid requiring xorg-server for tests.

Some packages started a x.org server for testing, which can be
avoided by setting QT_QPA_PLATFORM=offscreen.

* gnu/packages/kde-frameworks.scm (kitemmodels)
  [native-inputs]: Remove xorg-server.
  [arguments]<#phases> 'start-xorg-server' replace by 'check-setup'.
  (kplotting, kcrash, kimageformats): Likewise.
  (kitemviews)[native-inputs]: Remove xorg-server.
  [arguments]<#phases> 'start-xorg-server': Remove phase; 'check-setup':
  set QT_QPA_PLATFORM=offscreen.
---
 gnu/packages/kde-frameworks.scm | 64 +++++++++++++++--------------------------
 1 file changed, 23 insertions(+), 41 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 0354e1d7fd..5fe457fb3b 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -744,20 +744,17 @@ (define-public kitemmodels
                 "1liq1ppa7xb1dcncv25c2a0xy3l9bvb2a56cff90c0b0vwr239q5"))))
     (build-system cmake-build-system)
     (native-inputs
-     `(("extra-cmake-modules" ,extra-cmake-modules)
-       ("xorg-server" ,xorg-server)))
+     `(("extra-cmake-modules" ,extra-cmake-modules)))
     (inputs
      `(("qtbase" ,qtbase)
        ("qtdeclarative" ,qtdeclarative)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'check 'start-xorg-server
-           (lambda* (#:key inputs #:allow-other-keys)
-             ;; The test suite requires a running X server.
-             (system (string-append (assoc-ref inputs "xorg-server")
-                                    "/bin/Xvfb :1 &"))
-             (setenv "DISPLAY" ":1")
+         (add-before 'check 'check-setup
+           (lambda _
+             ;; make Qt render "offscreen", required for tests
+             (setenv "QT_QPA_PLATFORM" "offscreen")
              #t)))))
     (home-page "https://community.kde.org/Frameworks")
     (synopsis "Set of item models extending the Qt model-view framework")
@@ -807,8 +804,7 @@ (define-public kitemviews
     (build-system cmake-build-system)
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)
-       ("qttools" ,qttools)
-       ("xorg-server" ,xorg-server)))
+       ("qttools" ,qttools)))
     (inputs
      `(("qtbase" ,qtbase)))
     (arguments
@@ -817,13 +813,8 @@ (define-public kitemviews
          (add-before 'check 'check-setup
            (lambda _
              (setenv "DBUS_FATAL_WARNINGS" "0")
-             #t))
-         (add-before 'check 'start-xorg-server
-           (lambda* (#:key inputs #:allow-other-keys)
-             ;; The test suite requires a running X server.
-             (system (string-append (assoc-ref inputs "xorg-server")
-                                    "/bin/Xvfb :1 &"))
-             (setenv "DISPLAY" ":1")
+             ;; make Qt render "offscreen", required for tests
+             (setenv "QT_QPA_PLATFORM" "offscreen")
              #t)))))
     (home-page "https://community.kde.org/Frameworks")
     (synopsis "Set of item views extending the Qt model-view framework")
@@ -847,19 +838,16 @@ (define-public kplotting
                 "1ffy9b08128ym024wlfgnzk52vpy0mbaa91dhndpr40qcz0i67sh"))))
     (build-system cmake-build-system)
     (native-inputs
-     `(("extra-cmake-modules" ,extra-cmake-modules)
-       ("xorg-server" ,xorg-server)))
+     `(("extra-cmake-modules" ,extra-cmake-modules)))
     (inputs
      `(("qtbase" ,qtbase)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'check 'start-xorg-server
-           (lambda* (#:key inputs #:allow-other-keys)
-             ;; The test suite requires a running X server.
-             (system (string-append (assoc-ref inputs "xorg-server")
-                                    "/bin/Xvfb :1 &"))
-             (setenv "DISPLAY" ":1")
+         (add-before 'check 'check-setup
+           (lambda _ ; kplotting
+             ;; make Qt render "offscreen", required for tests
+             (setenv "QT_QPA_PLATFORM" "offscreen")
              #t)))))
     (home-page "https://community.kde.org/Frameworks")
     (synopsis "Data plotting library")
@@ -1338,8 +1326,7 @@ (define-public kcrash
                 "1cshay7dhbqgh62nq85vd9sm20gq9s9f70mdnzjjh1q7cajybkp3"))))
     (build-system cmake-build-system)
     (native-inputs
-     `(("extra-cmake-modules" ,extra-cmake-modules)
-       ("xorg-server" ,xorg-server)))
+     `(("extra-cmake-modules" ,extra-cmake-modules)))
     (inputs
      `(("kcoreaddons" ,kcoreaddons)
        ("kwindowsystem" ,kwindowsystem)
@@ -1348,12 +1335,10 @@ (define-public kcrash
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'check 'start-xorg-server
-           (lambda* (#:key inputs #:allow-other-keys)
-             ;; The test suite requires a running X server.
-             (system "Xvfb :1 &")
-             (sleep 2)              ;XXX: give the server enough time to start
-             (setenv "DISPLAY" ":1")
+         (add-before 'check 'check-setup
+           (lambda _
+             ;; make Qt render "offscreen", required for tests
+             (setenv "QT_QPA_PLATFORM" "offscreen")
              #t)))))
     (home-page "https://community.kde.org/Frameworks")
     (synopsis "Graceful handling of application crashes")
@@ -1476,19 +1461,16 @@ (define-public kimageformats
                 "0q9ng4clqk2dqw43nk1pmq1d61rahc3qr4dmg4y3kjvz3ahnnijw"))))
     (build-system cmake-build-system)
     (native-inputs
-     `(("extra-cmake-modules" ,extra-cmake-modules)
-       ("xorg-server" ,xorg-server)))
+     `(("extra-cmake-modules" ,extra-cmake-modules)))
     (inputs
      `(("qtbase" ,qtbase)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'check 'start-xorg-server
-           (lambda* (#:key inputs #:allow-other-keys)
-             ;; The test suite requires a running X server.
-             (system (string-append (assoc-ref inputs "xorg-server")
-                                    "/bin/Xvfb :1 &"))
-             (setenv "DISPLAY" ":1")
+         (add-before 'check 'check-setup
+           (lambda _
+             ;; make Qt render "offscreen", required for tests
+             (setenv "QT_QPA_PLATFORM" "offscreen")
              #t)))))
     (home-page "https://community.kde.org/Frameworks")
     (synopsis "Plugins to allow QImage to support extra file formats")
-- 
cgit v1.2.3


From 92605669e117cd3f00c5b895bc2833a3d105b4f3 Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Mon, 29 May 2017 12:23:14 +0200
Subject: gnu: kimageformats: Add more optional and recommended inputs.

* gnu/packages/kde-frameworks.scm (kimageformats)
  [native-inputs]: Add pkg-config.
  [inputs]: Add karchive, openexr.
  [arguments]<#:configure-flags>: Set include-flags.
---
 gnu/packages/kde-frameworks.scm | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 5fe457fb3b..8aa4419c27 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -43,6 +43,7 @@ (define-module (gnu packages kde-frameworks)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
+  #:use-module (gnu packages graphics)
   #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages image)
   #:use-module (gnu packages linux)
@@ -1461,9 +1462,12 @@ (define-public kimageformats
                 "0q9ng4clqk2dqw43nk1pmq1d61rahc3qr4dmg4y3kjvz3ahnnijw"))))
     (build-system cmake-build-system)
     (native-inputs
-     `(("extra-cmake-modules" ,extra-cmake-modules)))
+     `(("extra-cmake-modules" ,extra-cmake-modules)
+       ("pkg-config" ,pkg-config)))
     (inputs
-     `(("qtbase" ,qtbase)))
+     `(("karchive" ,karchive) ; for Krita and OpenRaster images
+       ("openexr" ,openexr) ; for OpenEXR high dynamic-range images
+       ("qtbase" ,qtbase)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -1471,7 +1475,14 @@ (define-public kimageformats
            (lambda _
              ;; make Qt render "offscreen", required for tests
              (setenv "QT_QPA_PLATFORM" "offscreen")
-             #t)))))
+             #t)))
+       ;; FIXME: The header files of ilmbase (propagated by openexr) are not
+       ;; found when included by the header files of openexr, and an explicit
+       ;; flag needs to be set.
+       #:configure-flags
+       (list (string-append "-DCMAKE_CXX_FLAGS=-I"
+                            (assoc-ref %build-inputs "ilmbase")
+                            "/include/OpenEXR"))))
     (home-page "https://community.kde.org/Frameworks")
     (synopsis "Plugins to allow QImage to support extra file formats")
     (description "This framework provides additional image format plugins for
-- 
cgit v1.2.3


From 786cb78386f2819375d0b9f6612b4d0c06e0d9e9 Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Sat, 3 Jun 2017 11:20:07 +0200
Subject: gnu: kio: Add more optional and recommended inputs.

* gnu/packages/kde-frameworks.scm (kio)[inputs]: Add mit-krb5, qtscript.
---
 gnu/packages/kde-frameworks.scm | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 8aa4419c27..601c61ee3d 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -46,6 +46,7 @@ (define-module (gnu packages kde-frameworks)
   #:use-module (gnu packages graphics)
   #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages kerberos)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages mp3)
   #:use-module (gnu packages pdf)
@@ -2304,6 +2305,7 @@ (define-public kio
        ("extra-cmake-modules" ,extra-cmake-modules)))
     (inputs
      `(("acl" ,acl)
+       ("krb5" ,mit-krb5)
        ("karchive" ,karchive)
        ("kauth" ,kauth)
        ("kcodecs" ,kcodecs)
@@ -2320,6 +2322,7 @@ (define-public kio
        ("libxml2" ,libxml2)
        ("libxslt" ,libxslt)
        ("qtbase" ,qtbase)
+       ("qtscript" ,qtscript)
        ("qtx11extras" ,qtx11extras)
        ("sonnet" ,sonnet)))
     (arguments
-- 
cgit v1.2.3


From 7cf6793b4e63a74fed35fd143b92fa7be92cb05d Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Sat, 3 Jun 2017 11:38:58 +0200
Subject: gnu: kinit: Add more optional inputs.

* gnu/packages/kde-frameworks.scm (kinit)
  [native-inputs]: Add pkg-config.
  [inputs]: Add kdoctools, libcap.
---
 gnu/packages/kde-frameworks.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 601c61ee3d..e4a2e99379 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -2247,7 +2247,8 @@ (define-public kinit
                 "08429kjihpaip73wszr3rsii8sdlwgm3kxx7g0hpjhkj9d2jq3m1"))))
     (build-system cmake-build-system)
     (native-inputs
-     `(("extra-cmake-modules" ,extra-cmake-modules)))
+     `(("extra-cmake-modules" ,extra-cmake-modules)
+       ("pkg-config" ,pkg-config)))
     (inputs
      `(("kauth" ,kauth)
        ("kbookmarks" ,kbookmarks)
@@ -2257,6 +2258,7 @@ (define-public kinit
        ("kconfigwidgets" ,kconfigwidgets)
        ("kcoreaddons" ,kcoreaddons)
        ("kcrash" ,kcrash)
+       ("kdoctools" ,kdoctools)
        ("kio" ,kio)
        ("kitemviews" ,kitemviews)
        ("ki18n" ,ki18n)
@@ -2265,6 +2267,7 @@ (define-public kinit
        ("kwidgetsaddons" ,kwidgetsaddons)
        ("kwindowsystem" ,kwindowsystem)
        ("kxmlgui" ,kxmlgui)
+       ("libcap" ,libcap) ; to install start_kdeinit with CAP_SYS_RESOURCE
        ("qtbase" ,qtbase)
        ("solid" ,solid)))
     (home-page "https://community.kde.org/Frameworks")
-- 
cgit v1.2.3


From 37aa54b7221bb1709889d6ba21107b8eb80d6b97 Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Sun, 4 Jun 2017 17:55:33 +0200
Subject: gnu: ktexteditor: Add more optional inputs.

* gnu/packages/kde-frameworks.scm (ktexteditor)[native-inputs]: Add
  pkg-config.
---
 gnu/packages/kde-frameworks.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index e4a2e99379..995d45276e 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -2664,7 +2664,8 @@ (define-public ktexteditor
     (propagated-inputs
      `(("kparts" ,kparts)))
     (native-inputs
-     `(("extra-cmake-modules" ,extra-cmake-modules)))
+     `(("extra-cmake-modules" ,extra-cmake-modules)
+       ("pkg-config" ,pkg-config)))
     (inputs
      `(("karchive" ,karchive)
        ("kauth" ,kauth)
-- 
cgit v1.2.3


From faec8b8f0728f63b01f5616c2a927612aff83d90 Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Sat, 3 Jun 2017 11:42:46 +0200
Subject: gnu: plasma-framework: Add more optional inputs.

* gnu/packages/kde-frameworks.scm (plasma-frameworks)[native-inputs]: Add
  pkg-config. [inputs]: Add kwayland.
---
 gnu/packages/kde-frameworks.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 995d45276e..0e7bcb9210 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -2916,7 +2916,8 @@ (define-public plasma-framework
      `(("kpackage" ,kpackage)
        ("kservice" ,kservice)))
     (native-inputs
-     `(("extra-cmake-modules" ,extra-cmake-modules)))
+     `(("extra-cmake-modules" ,extra-cmake-modules)
+       ("pkg-config" ,pkg-config)))
     (inputs
      `(("kactivities" ,kactivities)
        ("karchive" ,karchive)
@@ -2938,6 +2939,7 @@ (define-public plasma-framework
        ("ki18n" ,ki18n)
        ("kjobwidgets" ,kjobwidgets)
        ("knotificantions" ,knotifications)
+       ("kwayland" ,kwayland)
        ("kwidgetsaddons" ,kwidgetsaddons)
        ("kwindowsystem" ,kwindowsystem)
        ("kxmlgui" ,kxmlgui)
-- 
cgit v1.2.3


From 73a3598df8dc86ed72d0779c8db0932fa69952c7 Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Sun, 4 Jun 2017 18:14:44 +0200
Subject: gnu: kpackage: Add more optional inputs.

* gnu/packages/kde-frameworks.scm (kpackage)[inputs]: Add kdoctools.
---
 gnu/packages/kde-frameworks.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 0e7bcb9210..1aa438b77d 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -1583,6 +1583,7 @@ (define-public kpackage
      `(("karchive" ,karchive)
        ("kconfig" ,kconfig)
        ("kcoreaddons" ,kcoreaddons)
+       ("kdoctools" ,kdoctools)
        ("ki18n" ,ki18n)
        ("qtbase" ,qtbase)))
     (arguments
-- 
cgit v1.2.3


From ab313cd0ba59098e7b88627a223204bacd3a7eb9 Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Sun, 4 Jun 2017 18:43:09 +0200
Subject: gnu: sonnet: Add optional input (spell-checker).

* gnu/packages/kde-frameworks.scm (sonnet)[inputs]: Add hunspell; add
  todo comment for other language's spell-checker.
---
 gnu/packages/kde-frameworks.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 1aa438b77d..c5b14eae7f 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -47,6 +47,7 @@ (define-module (gnu packages kde-frameworks)
   #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages image)
   #:use-module (gnu packages kerberos)
+  #:use-module (gnu packages libreoffice)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages mp3)
   #:use-module (gnu packages pdf)
@@ -1192,7 +1193,9 @@ (define-public sonnet
      `(("extra-cmake-modules" ,extra-cmake-modules)
        ("qttools" ,qttools)))
     (inputs
-     `(("qtbase" ,qtbase)))
+     `(("hunspell" ,hunspell)
+       ;; TODO: hspell (for Hebrew), Voikko (for Finish)
+       ("qtbase" ,qtbase)))
     (home-page "https://community.kde.org/Frameworks")
     (synopsis "Multi-language spell checker")
     (description "Sonnet is a plugin-based spell checking library for Qt-based
-- 
cgit v1.2.3


From 73577a66f171be57b7d54a53b0d2f655916a06df Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Sun, 4 Jun 2017 20:30:43 +0200
Subject: gnu: gpgmepp: Superseded by gpgme.

The C++-bindings are part of gpgme since version 1.7.

* gnu/packages/kde-frameworks.scm (gpgmepp)[properties]: New field.
---
 gnu/packages/kde-frameworks.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index c5b14eae7f..4090f88554 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -205,7 +205,8 @@ (define-public gpgmepp
     (home-page "https://community.kde.org/Frameworks")
     (synopsis "C++ bindings/wrapper for gpgme")
     (description "C++ bindings/wrapper for gpgme.")
-    (license license:lgpl2.1+)))
+    (license license:lgpl2.1+)
+    (properties `((superseded . ,gpgme)))))
 
 (define-public kpmcore
   (package
-- 
cgit v1.2.3


From 51361afd78f84ef26bf5f0408cd2c9418b2af700 Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Sun, 4 Jun 2017 20:29:08 +0200
Subject: gnu: kwallet: Use gpgme instead of gpgmepp.

The C++-bindings are part of gpgme since version 1.7.

* gnu/packages/kde-frameworks.scm(kwallet)[inputs]: Replace gpgmepp by
  gpgme.
---
 gnu/packages/kde-frameworks.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 4090f88554..60b2ca012a 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -2784,7 +2784,7 @@ (define-public kwallet
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)))
     (inputs
-     `(("gpgmepp" ,gpgmepp)
+     `(("gpgme" ,gpgme) ;; TODO: Add gpgme Qt-bindings
        ("kauth" ,kauth)
        ("kcodecs" ,kcodecs)
        ("kconfig" ,kconfig)
-- 
cgit v1.2.3


From 9ebffc504d8f27a10d2bf66ddd74ca138a6d448f Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Mon, 5 Jun 2017 13:17:58 +0200
Subject: gnu: kiconthemes: Re-enable tests.

* gnu/packages/kde-frameworks.scm (kiconthemes)[arguments]: Test-suite
  is now passing; reenable it.
---
 gnu/packages/kde-frameworks.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 60b2ca012a..8f5f480058 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -2219,8 +2219,7 @@ (define-public kiconthemes
        ("qtbase" ,qtbase)
        ("qtsvg" ,qtsvg)))
     (arguments
-     `(#:tests? #f ; FIXME: Test failure
-       #:phases
+     `(#:phases
        (modify-phases %standard-phases
          (add-before 'check 'check-setup
            (lambda* (#:key inputs #:allow-other-keys)
-- 
cgit v1.2.3


From 3406d0b3a97b93f43c1cd3c20293ec6f6d125b53 Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Sun, 4 Jun 2017 21:10:51 +0200
Subject: gnu: kwidgetsaddons: Re-enable tests.

* gnu/packages/kde-frameworks.scm (kwidgetsaddons)[arguments]: Test-suite
   is now passing; reenable it.
---
 gnu/packages/kde-frameworks.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 8f5f480058..e9c8b887bc 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -970,8 +970,7 @@ (define-public kwidgetsaddons
     (inputs
      `(("qtbase" ,qtbase)))
     (arguments
-     `(#:tests? #f ; FIXME: Regression after update to qt 5.7
-       #:phases
+     `(#:phases
        (modify-phases %standard-phases
          (add-before 'check 'check-setup
            (lambda _
-- 
cgit v1.2.3


From ed4a3ec68c24693fcefe8ca7c1f55d62cc5bf482 Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Mon, 5 Jun 2017 00:42:08 +0200
Subject: gnu: kwindowsystem: Fix some test-cases (test-suite still disabled).
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Make five tests pass, three are still failing – thus the test-suite is still
disabled. This commit's aim is to retain the progress.

* gnu/packages/kde-frameworks.scm (kwindowsystem)[native-inputs]: Add dbus.
  [arguments]<#:test?>: Change comment. <#:phases>: Replace phase `check` by
  new one befind 'install'.
---
 gnu/packages/kde-frameworks.scm | 27 ++++++++++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index e9c8b887bc..18e445e215 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -1013,6 +1013,7 @@ (define-public kwindowsystem
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)
        ("pkg-config" ,pkg-config)
+       ("dbus" ,dbus) ; for the tests
        ("qttools" ,qttools)
        ("xorg-server" ,xorg-server))) ; for the tests
     (inputs
@@ -1021,7 +1022,31 @@ (define-public kwindowsystem
        ("qtx11extras" ,qtx11extras)
        ("xcb-utils-keysyms" ,xcb-util-keysyms)))
     (arguments
-     `(#:tests? #f)) ; FIXME: 8/10 tests fail.
+     `(#:tests? #f ; FIXME: 3/12 tests fail.
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             ;; TODO: Simplify and use "common" phases when test-suite passes
+             (if tests?
+                 (begin
+                   (let ((out (assoc-ref outputs "out")))
+                     (setenv "QT_PLUGIN_PATH"
+                             (string-append out "/lib/plugins:"
+                                            (getenv "QT_PLUGIN_PATH"))))
+                   ;; The test suite requires a running X server, setting
+                   ;; QT_QPA_PLATFORM=offscreen does not suffice and even make
+                   ;; some tests fail.
+                   (system (string-append (assoc-ref inputs "xorg-server")
+                                          "/bin/Xvfb :1 -screen 0 640x480x24 &"))
+                   (setenv "DISPLAY" ":1")
+                   (setenv "CTEST_OUTPUT_ON_FAILURE" "1")
+                   (setenv "DBUS_FATAL_WARNINGS" "0")
+                   (zero? (system* "dbus-launch" "ctest" ".")))
+                 (begin
+                   (format #t "test suite not run~%")
+                   #t)))))))
     (home-page "https://community.kde.org/Frameworks")
     (synopsis "KDE access to the windowing system")
     (description "KWindowSystem provides information about and allows
-- 
cgit v1.2.3


From 1e0ae3b352d4521aa2a88158ab49277cea7cd0bd Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Sun, 4 Jun 2017 17:55:56 +0200
Subject: gnu: kde.scm, kde-frameworks.scm: Add and update comments.

* gnu/packages/kde-frameworks.scm
  (kpackage,plasma-framework)[arguments]: Update comment (number of failed
  tests).
  (kdeclarative)[arguments]<#:phases>: Update comment.
  (bluez-qt,knotifications,kpty,ktexteditor,ktextwidgets,solid)[inputs]: Add a
  todo comment.
  (kguiaddons): Add a todo comment.
  (phonon)[native-inputs]: Add a todo comment.
* gnu/packages/kde-frameworks.scm (kauth)[arguments]<#:phases>: Add a todo
  comment.
---
 gnu/packages/kde-frameworks.scm | 23 +++++++++++++++++++----
 gnu/packages/kde.scm            |  2 ++
 2 files changed, 21 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 18e445e215..8fe71d5b5d 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -123,6 +123,8 @@ (define-public phonon
                 "177647r2jqfm32hqcz2nqfqv6v48hn5ab2vc31svba2wz23fkgk7"))))
     (build-system cmake-build-system)
     (native-inputs
+     ;; TODO: Add qttools to build the Qt Designer plugin.
+     ;; TODO: Think about adding pulseaudio. Is it required for sound?
      `(("extra-cmake-modules" ,extra-cmake-modules)))
     (inputs
      `(("qtbase" ,qtbase)))
@@ -296,6 +298,7 @@ (define-public bluez-qt
      `(("dbus" ,dbus)
        ("extra-cmake-modules" ,extra-cmake-modules)))
     (inputs
+     ;; TODO: qtdeclarative (yields one failing test)
      `(("qtbase" ,qtbase)))
     (arguments
      `(#:configure-flags
@@ -643,6 +646,10 @@ (define-public kguiaddons
                (base32
                 "1nmlwvy2jdmh0m6bmahvk68vl2rs9s28c10dkncpi6gvhsdkigqx"))))
     (build-system cmake-build-system)
+    ;; TODO: Build packages for the Python bindings.  Ideally this will be
+    ;; done for all versions of python guix supports.  Requires python,
+    ;; python-sip, clang-python, libclang.  Requires python-2 in all cases for
+    ;; clang-python.
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)
        ("pkg-config" ,pkg-config)))
@@ -1193,6 +1200,7 @@ (define-public solid
     (inputs
      `(("qtbase" ,qtbase)
        ("udev" ,eudev)))
+    ;; TODO: Add runtime-only dependency MediaPlayerInfo
     (home-page "https://community.kde.org/Frameworks")
     (synopsis "Desktop hardware abstraction")
     (description "Solid is a device integration framework.  It provides a way of
@@ -1573,6 +1581,9 @@ (define-public knotifications
        ("kwindowsystem" ,kwindowsystem)
        ("phonon" ,phonon)
        ("qtbase" ,qtbase)
+       ;; TODO: qtspeech (new in Qt 5.9)
+       ;; TODO: Think about adding dbusmenu-qt5 from
+       ;; https://launchpad.net/libdbusmenu-qt
        ("qtx11extras" ,qtx11extras)))
     (arguments
      `(#:phases
@@ -1615,7 +1626,7 @@ (define-public kpackage
        ("ki18n" ,ki18n)
        ("qtbase" ,qtbase)))
     (arguments
-     `(#:tests? #f ; FIXME: 1/4 tests fail.
+     `(#:tests? #f ; FIXME: 3/9 tests fail.
        #:phases
        (modify-phases %standard-phases
          (add-before 'check 'check-setup
@@ -1648,6 +1659,7 @@ (define-public kpty
     (inputs
      `(("kcoreaddons" ,kcoreaddons)
        ("ki18n" ,ki18n)
+       ;; TODO: utempter, for managing UTMP entries
        ("qtbase" ,qtbase)))
     (arguments
      `(#:tests? #f ; FIXME: 1/1 tests fail.
@@ -2013,7 +2025,8 @@ (define-public kdeclarative
        (modify-phases %standard-phases
          (add-before 'check 'start-xorg-server
            (lambda* (#:key inputs #:allow-other-keys)
-             ;; The test suite requires a running X server.
+             ;; The test suite requires a running X server, setting
+             ;; QT_QPA_PLATFORM=offscreen does not suffice.
              (system (string-append (assoc-ref inputs "xorg-server")
                                     "/bin/Xvfb :1 -screen 0 640x480x24 &"))
              (setenv "DISPLAY" ":1")
@@ -2695,7 +2708,8 @@ (define-public ktexteditor
      `(("extra-cmake-modules" ,extra-cmake-modules)
        ("pkg-config" ,pkg-config)))
     (inputs
-     `(("karchive" ,karchive)
+     `(;; TODO: editor-config
+       ("karchive" ,karchive)
        ("kauth" ,kauth)
        ("kbookmarks" ,kbookmarks)
        ("kcodecs" ,kcodecs)
@@ -2774,6 +2788,7 @@ (define-public ktextwidgets
        ("kservice" ,kservice)
        ("kwidgetsaddons" ,kwidgetsaddons)
        ("kwindowsystem" ,kwindowsystem)
+       ;; TODO: qtspeech (new in Qt 5.9)
        ("qtbase" ,qtbase)))
     (arguments
      `(#:phases
@@ -2978,7 +2993,7 @@ (define-public plasma-framework
        ("qtx11extras" ,qtx11extras)
        ("solid" ,solid)))
     (arguments
-     `(#:tests? #f ; FIXME: 13/14 tests fail.
+     `(#:tests? #f ; FIXME: 9/15 tests fail.
        #:phases
        (modify-phases %standard-phases
          (add-before 'check 'check-setup
diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm
index b481bb98db..a5ad8da062 100644
--- a/gnu/packages/kde.scm
+++ b/gnu/packages/kde.scm
@@ -293,6 +293,8 @@ (define-public libksysguard
        (modify-phases %standard-phases
          (add-before 'configure 'patch-cmakelists
            (lambda _
+             ;; TODO: Verify: This should no longer be necessary, since
+             ;; KF5AuthConfig.cmake.in contains this already.
              (substitute* "processcore/CMakeLists.txt"
                (("KAUTH_HELPER_INSTALL_DIR") "KDE_INSTALL_LIBEXECDIR"))))
          (replace 'check
-- 
cgit v1.2.3


From 6175937011bc7891006468ea700f90d3335e6886 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Thu, 8 Jun 2017 15:25:30 -0400
Subject: gnu: certbot, python-acme: Update to 0.15.0.

* gnu/packages/tls.scm (certbot, python-acme, python2-acme): Update to 0.15.0.
(python-acme, python2-acme)[arguments]: Remove 'patch-dependency' phase.
This issue was fixed upstream:
https://github.com/certbot/certbot/commit/d0e471dc8093bd0d08c5a739e5cf9677240d9c0e
---
 gnu/packages/tls.scm | 14 +++-----------
 1 file changed, 3 insertions(+), 11 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index 7f62b37690..cdb4becb07 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -484,25 +484,17 @@ (define-public python-acme
   (package
     (name "python-acme")
     ;; Remember to update the hash of certbot when updating python-acme.
-    (version "0.14.2")
+    (version "0.15.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "acme" version))
       (sha256
        (base32
-        "1kbgpjabbly7r757vyr1050ixnm9hyvrbf9n6aq49cgmb147ysqn"))))
+        "11zwgj663vr575pbqw74ia10wxaw16i8rnkcivsrbsx148rxdbcz"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'patch-dependency
-           ;; This module is part of the Python standard library, so we don't
-           ;; need to use an external package.
-           ;; https://github.com/certbot/certbot/pull/2249
-           (lambda _
-             (substitute* "setup.py"
-               (("'argparse',") ""))
-             #t))
          (add-after 'build 'build-documentation
            (lambda _
              (zero? (system* "make" "-C" "docs" "man" "info"))))
@@ -549,7 +541,7 @@ (define-public certbot
               (uri (pypi-uri name version))
               (sha256
                (base32
-                "1b39hybswzm8mkarg1mwpx47wffqg57jcgi52mz5iz60rxym9j2v"))))
+                "1srvmjxz75dbafx7xfg1w3n9h3srr9p2ljnfsih9dwwd5cxh9i5q"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2
-- 
cgit v1.2.3


From 28c98738009e522c48fc484033a0009ab7cea99d Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kei@openmailbox.org>
Date: Thu, 8 Jun 2017 15:58:45 -0400
Subject: gnu: minetest: Update to 0.4.16.

* gnu/packages/games.scm (minetest-data, minetest): Update to 0.4.16.
---
 gnu/packages/games.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 9153a2b5cf..d63c6d0ddf 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -959,7 +959,7 @@ (define-public mars
 (define minetest-data
   (package
     (name "minetest-data")
-    (version "0.4.15")
+    (version "0.4.16")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -968,7 +968,7 @@ (define minetest-data
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "12kxklcd1b5n0f369zf3xxhvkrizxj4d9xv0dh8crfqiymaym0zm"))))
+                "0nibpm600rbv9dg1zgcsl5grlbqx0b5l6cg1lp6sqkwvjialb4ga"))))
     (build-system trivial-build-system)
     (native-inputs
      `(("source" ,source)
@@ -1000,7 +1000,7 @@ (define minetest-data
 (define-public minetest
   (package
     (name "minetest")
-    (version "0.4.15")
+    (version "0.4.16")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1009,7 +1009,7 @@ (define-public minetest
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1ag3jcj7kpq3ph12zirk1c0mj9i0g50wmw932f8gi11liq8yd12n"))))
+                "0mbnf1ma4gsw9ah68ply04059xkfx5psdxwalxp78sgmx4ypkwqf"))))
     (build-system cmake-build-system)
     (arguments
      '(#:configure-flags
-- 
cgit v1.2.3


From 525da27c25bf16dfcb08472dec546e3ed4cebc65 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Thu, 8 Jun 2017 19:11:52 +0200
Subject: gnu: php: Update to 7.1.6.

* gnu/packages/php.scm (php): Update to 7.1.6.
---
 gnu/packages/php.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm
index 1b55cd4eb9..b6f64bc0ef 100644
--- a/gnu/packages/php.scm
+++ b/gnu/packages/php.scm
@@ -53,7 +53,7 @@ (define-module (gnu packages php)
 (define-public php
   (package
     (name "php")
-    (version "7.1.5")
+    (version "7.1.6")
     (home-page "https://secure.php.net/")
     (source (origin
               (method url-fetch)
@@ -61,7 +61,7 @@ (define-public php
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1b7njiqgy66ga5c8wsm78mqqjr7lj3hlpwbbvksi2mn4jv1s6jfi"))
+                "0nr49gqhk4pv8kcdc60cl1mgwlinawpraq9ba15whzmb472lsn01"))
               (modules '((guix build utils)))
               (snippet
                '(with-directory-excursion "ext"
-- 
cgit v1.2.3


From ea4678a427b5c95f13a25faf4dca792f0bb9bbd8 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Thu, 8 Jun 2017 23:33:31 +0200
Subject: gnu: gnuastro: Update to 0.3.

* gnu/packages/astronomy.scm (gnuastro): Update to 0.3.
Adjust as suggested by 'guix lint'.
---
 gnu/packages/astronomy.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 6984f10742..2aa65d5880 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -93,7 +93,7 @@ (define-public wcslib
 (define-public gnuastro
   (package
     (name "gnuastro")
-    (version "0.2")
+    (version "0.3")
     (source
      (origin
        (method url-fetch)
@@ -101,7 +101,7 @@ (define-public gnuastro
                            version ".tar.gz"))
        (sha256
         (base32
-         "0099g7zqg1gr9y94ybhyjgx9pkn9zv4rj1xb00fkybfw8w6ij9iv"))))
+         "109xjwbs36gbkx5sd5yzf6ailfcldc5d28vl1n19z0ylfzww4nwa"))))
     (inputs
      `(("cfitsio" ,cfitsio)
        ("gsl" ,gsl)
@@ -109,7 +109,7 @@ (define-public gnuastro
        ("wcslib" ,wcslib)))
     (build-system gnu-build-system)
     (home-page "https://www.gnu.org/software/gnuastro/")
-    (synopsis "Astronomical data manipulation programs")
+    (synopsis "Astronomy utilities")
     (description "The GNU Astronomy Utilities (Gnuastro) is a suite of
 programs for the manipulation and analysis of astronomical data.")
     (license license:gpl3+)))
-- 
cgit v1.2.3


From dfcd02c0f69a36bf91bfd1dfc9f8144fa6888df5 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Thu, 8 Jun 2017 23:54:56 +0200
Subject: gnu: artanis: Update to 0.2.1.

* gnu/packages/guile.scm (artanis): Update to 0.2.1.
[inputs]: Switch to GUILE-2.2.
[arguments]: Adjust #:make-flags for Guile 2.2.  Take .go files from
lib/guile/2.2.  Add 'wrap-art' phase.
* gnu/packages/patches/artanis-fix-Makefile.in.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                       |  1 -
 gnu/packages/guile.scm                             | 29 +++++----
 gnu/packages/patches/artanis-fix-Makefile.in.patch | 70 ----------------------
 3 files changed, 19 insertions(+), 81 deletions(-)
 delete mode 100644 gnu/packages/patches/artanis-fix-Makefile.in.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index ab3fbb2d39..01bcff584a 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -504,7 +504,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/agg-am_c_prototype.patch			\
   %D%/packages/patches/antiword-CVE-2014-8123.patch			\
   %D%/packages/patches/apr-skip-getservbyname-test.patch	\
-  %D%/packages/patches/artanis-fix-Makefile.in.patch		\
   %D%/packages/patches/aspell-default-dict-dir.patch		\
   %D%/packages/patches/ath9k-htc-firmware-binutils.patch	\
   %D%/packages/patches/ath9k-htc-firmware-gcc.patch		\
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index b9cd664604..b57f4c3b6c 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -387,18 +387,17 @@ (define-public guildhall
 (define-public artanis
   (package
     (name "artanis")
-    (version "0.1.2")
+    (version "0.2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "ftp://alpha.gnu.org/gnu/artanis/artanis-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "19m3ak12cqk8js9d2mdg11kh4fjsq8frfpd10qw75h0zpr5cywpp"))
-              (patches (search-patches "artanis-fix-Makefile.in.patch"))))
+                "041ajcg2pz918kd9iqcj4inpzddc3impvz3r2nhlpbv8zrz011hn"))))
     (build-system gnu-build-system)
     ;; TODO: Add guile-dbi and guile-dbd optional dependencies.
-    (inputs `(("guile" ,guile-2.0)))
+    (inputs `(("guile" ,guile-2.2)))
     (native-inputs `(("bash"       ,bash)         ;for the `source' builtin
                      ("pkgconfig"  ,pkg-config)
                      ("util-linux" ,util-linux))) ;for the `script' command
@@ -406,15 +405,15 @@ (define-public artanis
      '(#:make-flags
        ;; TODO: The documentation must be built with the `docs' target.
        (let* ((out (assoc-ref %outputs "out"))
-              (dir (string-append out "/share/guile/site/2.0")))
+              (scm (string-append out "/share/guile/site/2.2"))
+              (go  (string-append out "/lib/guile/2.2/site-ccache")))
          ;; Don't use (%site-dir) for site paths.
-         (list (string-append "MOD_PATH=" dir)
-               (string-append "MOD_COMPILED_PATH=" dir)))
+         (list (string-append "MOD_PATH=" scm)
+               (string-append "MOD_COMPILED_PATH=" go)))
        #:test-target "test"
        #:phases
        (modify-phases %standard-phases
-         (add-before
-          'install 'substitute-root-dir
+         (add-before 'install 'substitute-root-dir
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out  (assoc-ref outputs "out")))
               (substitute* "Makefile"   ;ignore the execution of bash.bashrc
@@ -422,7 +421,17 @@ (define-public artanis
               (substitute* "Makefile"   ;set the root of config files to OUT
                 ((" /etc") (string-append " " out "/etc")))
               (mkdir-p (string-append out "/bin")) ;for the `art' executable
-              #t))))))
+              #t)))
+         (add-after 'install 'wrap-art
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (scm (string-append out "/share/guile/site/2.2"))
+                    (go  (string-append out "/lib/guile/2.2/site-ccache")))
+               (wrap-program (string-append bin "/art")
+                 `("GUILE_LOAD_PATH" ":" prefix (,scm))
+                 `("GUILE_LOAD_COMPILED_PATH" ":" prefix (,go)))
+               #t))))))
     (synopsis "Web application framework written in Guile")
     (description "GNU Artanis is a web application framework written in Guile
 Scheme.  A web application framework (WAF) is a software framework that is
diff --git a/gnu/packages/patches/artanis-fix-Makefile.in.patch b/gnu/packages/patches/artanis-fix-Makefile.in.patch
deleted file mode 100644
index 7e4800d364..0000000000
--- a/gnu/packages/patches/artanis-fix-Makefile.in.patch
+++ /dev/null
@@ -1,70 +0,0 @@
-Applies until an Artanis release comes with the following patches
-applied:
-* <https://savannah.gnu.org/patch/?func=detailitem&item_id=9130>
-* <https://savannah.gnu.org/patch/?func=detailitem&item_id=9131>
-diff -ru artanis-0.1.2/Makefile.in artanis-0.1.2.1/Makefile.in
---- artanis-0.1.2/Makefile.in	2016-02-10 12:35:18.800490571 -0200
-+++ artanis-0.1.2.1/Makefile.in	2016-10-15 19:44:35.140907367 -0300
-@@ -19,9 +19,18 @@
- MOD_OBJ := $(OBJ)/artanis
- BIN := bin
- TEMP_LIB_PATH := $(OBJ)
--MOD_PATH := $(shell guile -c "(display (%site-dir))")
- MOD_COMPILED_PATH := $(shell guile -c "(display (%site-ccache-dir))")
-+
-+ifdef DESTDIR
-+INFO_DIR := $(DESTDIR)/share/info/
-+MOD_PATH := $(DESTDIR)/$(shell guile -c "(display (%site-dir))")
- MOD_TARGET_PATH := $(DESTDIR)/$(MOD_COMPILED_PATH)
-+else
-+INFO_DIR := $(PREFIX)/share/info/
-+MOD_PATH := $(shell guile -c "(display (%site-dir))")
-+MOD_TARGET_PATH := $(MOD_COMPILED_PATH)
-+endif
-+
- GUILE_CFLAGS := -Wunsupported-warning -Wunbound-variable -Warity-mismatch -Wduplicate-case-datum -Wbad-case-datum -Wformat
- GUILEC := GUILE_LOAD_COMPILED_PATH=$(TEMP_LIB_PATH) guild compile $(GUILE_CFLAGS)
- ARTANIS_ETC := $(SRC)/etc/artanis
-@@ -36,7 +45,6 @@
- GENDOCS :=$(BUILD_AUX)/gendocs.sh
- CHK_TEXINFO := $(BUILD_AUX)/check_texinfo.scm
- CP := cp -frd -P
--INFO_DIR := $(PREFIX)/share/info/
- TARBALL_NAME := artanis-$(VERSION)
- TMP_DIR := $(shell mktemp -d)
- ANN_GEN := $(BUILD_AUX)/announce-gen
-@@ -124,18 +132,29 @@
- 	-rm -f config.{h,log}
- 
- install: $(ALL_TARGETS)
--	mkdir -p $(DESTDIR)/$(MOD_PATH)
--	$(CP) $(MOD) $(DESTDIR)/$(MOD_PATH)/
-+	mkdir -p $(MOD_PATH)
-+	$(CP) $(MOD) $(MOD_PATH)/
- 	mkdir -p $(MOD_TARGET_PATH)/
- 	$(CP) $(MOD_OBJ) $(MOD_TARGET_PATH)/
-+
-+ifdef DESTDIR
- 	$(CP) $(ARTANIS_ETC) $(DESTDIR)/etc/
- 	$(CP) $(ARTANIS_PAGES) $(DESTDIR)/etc/artanis/
--	mkdir -p $(DESTDIR)/$(PREFIX)/bin/
--	$(CP) $(BIN)/art $(DESTDIR)/$(PREFIX)/bin/
-+	mkdir -p $(DESTDIR)/bin/
-+	$(CP) $(BIN)/art $(DESTDIR)/bin/
- 	mkdir -p $(DESTDIR)/etc/bash_completion.d/
- 	$(CP) $(CMDCOMP) $(DESTDIR)/etc/bash_completion.d/
-+else
-+	$(CP) $(ARTANIS_ETC) $(PREFIX)/etc/
-+	$(CP) $(ARTANIS_PAGES) $(PREFIX)/etc/artanis/
-+	mkdir -p $(PREFIX)/bin/
-+	$(CP) $(BIN)/art $(PREFIX)/bin/
-+	mkdir -p $(PREFIX)/etc/bash_completion.d/
-+	$(CP) $(CMDCOMP) $(PREFIX)/etc/bash_completion.d/
-+endif
-+
- 	if [ -e /etc/bash.bashrc ]; then source /etc/bash.bashrc; fi
--	if [ -e artanis.info ]; then mkdir -p $(DESTDIR)/$(INFO_DIR); $(CP) artanis.info $(DESTDIR)/$(INFO_DIR)/; fi
-+	if [ -e artanis.info ]; then mkdir -p $(INFO_DIR); $(CP) artanis.info $(INFO_DIR)/; fi
- 
- distclean: distclean-mk clean clean-config clean-tarball
- 	-rm -f $(BIN)/art
-- 
cgit v1.2.3


From 099c9fdae623e06e4fded8b0d4e55d9d5b56715b Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Thu, 8 Jun 2017 18:50:52 +0200
Subject: gnu: raptor2: Fix heap overflow bug.

* gnu/packages/patches/raptor2-heap-overflow.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/rdf.scm (raptor2): Use it.
---
 gnu/local.mk                                     |  1 +
 gnu/packages/patches/raptor2-heap-overflow.patch | 51 ++++++++++++++++++++++++
 gnu/packages/rdf.scm                             |  2 +
 3 files changed, 54 insertions(+)
 create mode 100644 gnu/packages/patches/raptor2-heap-overflow.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 01bcff584a..93a58440e2 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -966,6 +966,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/qtscript-disable-tests.patch		\
   %D%/packages/patches/quickswitch-fix-dmenu-check.patch	\
   %D%/packages/patches/rapicorn-isnan.patch			\
+  %D%/packages/patches/raptor2-heap-overflow.patch		\
   %D%/packages/patches/ratpoison-shell.patch			\
   %D%/packages/patches/rcs-5.9.4-noreturn.patch			\
   %D%/packages/patches/readline-link-ncurses.patch		\
diff --git a/gnu/packages/patches/raptor2-heap-overflow.patch b/gnu/packages/patches/raptor2-heap-overflow.patch
new file mode 100644
index 0000000000..ce2a4516f8
--- /dev/null
+++ b/gnu/packages/patches/raptor2-heap-overflow.patch
@@ -0,0 +1,51 @@
+This patch addresses two heap overflow bugs in raptor2:
+
+http://seclists.org/oss-sec/2017/q2/424
+
+Patch copied from libreoffice:
+
+https://github.com/LibreOffice/core/blob/master/external/redland/raptor/0001-Calcualte-max-nspace-declarations-correctly-for-XML-.patch.1
+
+From 590681e546cd9aa18d57dc2ea1858cb734a3863f Mon Sep 17 00:00:00 2001
+From: Dave Beckett <dave@dajobe.org>
+Date: Sun, 16 Apr 2017 23:15:12 +0100
+Subject: [PATCH] Calcualte max nspace declarations correctly for XML writer
+
+(raptor_xml_writer_start_element_common): Calculate max including for
+each attribute a potential name and value.
+
+Fixes Issues #0000617 http://bugs.librdf.org/mantis/view.php?id=617
+and #0000618 http://bugs.librdf.org/mantis/view.php?id=618
+---
+ src/raptor_xml_writer.c | 7 ++++---
+ 1 file changed, 4 insertions(+), 3 deletions(-)
+
+diff --git a/src/raptor_xml_writer.c b/src/raptor_xml_writer.c
+index 693b946..0d3a36a 100644
+--- a/src/raptor_xml_writer.c
++++ b/src/raptor_xml_writer.c
+@@ -181,9 +181,10 @@ raptor_xml_writer_start_element_common(raptor_xml_writer* xml_writer,
+   size_t nspace_declarations_count = 0;  
+   unsigned int i;
+ 
+-  /* max is 1 per element and 1 for each attribute + size of declared */
+   if(nstack) {
+-    int nspace_max_count = element->attribute_count+1;
++    int nspace_max_count = element->attribute_count * 2; /* attr and value */
++    if(element->name->nspace)
++      nspace_max_count++;
+     if(element->declared_nspaces)
+       nspace_max_count += raptor_sequence_size(element->declared_nspaces);
+     if(element->xml_language)
+@@ -237,7 +238,7 @@ raptor_xml_writer_start_element_common(raptor_xml_writer* xml_writer,
+         }
+       }
+ 
+-      /* Add the attribute + value */
++      /* Add the attribute's value */
+       nspace_declarations[nspace_declarations_count].declaration=
+         raptor_qname_format_as_xml(element->attributes[i],
+                                    &nspace_declarations[nspace_declarations_count].length);
+-- 
+2.9.3
+
diff --git a/gnu/packages/rdf.scm b/gnu/packages/rdf.scm
index 7b7fe60855..6b5cfb013c 100644
--- a/gnu/packages/rdf.scm
+++ b/gnu/packages/rdf.scm
@@ -53,6 +53,8 @@ (define-public raptor2
              (method url-fetch)
              (uri (string-append "http://download.librdf.org/source/" name
                                  "-" version ".tar.gz"))
+             (patches
+              (search-patches "raptor2-heap-overflow.patch"))
              (sha256
               (base32
                "1vc02im4mpc28zxzgli68k6j0dakh0k3s389bm436yvqajxg19xd"))))
-- 
cgit v1.2.3


From 0377d5006efe29e249316352b3abaf64eac1c63d Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kei@openmailbox.org>
Date: Thu, 8 Jun 2017 19:56:28 -0400
Subject: gnu: crawl: Update to 0.20.0.

* gnu/packages/games.scm (crawl, crawl-tiles): Update to 0.20.0.
---
 gnu/packages/games.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index d63c6d0ddf..a76ab1ddc2 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -4035,7 +4035,7 @@ (define-public fillets-ng
 (define-public crawl
   (package
     (name "crawl")
-    (version "0.19.5")
+    (version "0.20.0")
     (source
      (origin
        (method url-fetch)
@@ -4049,7 +4049,7 @@ (define-public crawl
                             version "-nodeps.tar.xz")))
        (sha256
         (base32
-         "00yl2lb2shglxlxzpyk99zvglfx4amjybqwnzdcasvbiggb4cj18"))))
+         "0127dgldij2h4m7cf32yy9ndv4vcz03g4km71lmxrsi5mw7ljgpd"))))
     (build-system gnu-build-system)
     (inputs
      `(("lua51" ,lua-5.1)
-- 
cgit v1.2.3


From db0bb6f0afad658eddfa350a8ba8c05e151f6a28 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 31 May 2017 17:12:07 +0200
Subject: gnu: Add r-lubridate.

* gnu/packages/statistics.scm (r-lubridate): New variable.
---
 gnu/packages/statistics.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index b81bb42073..625f9f4884 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -5231,3 +5231,29 @@ (define-public r-cairo
 anti-aliasing.  Backends are modular such that any subset of backends
 is supported.")
     (license license:gpl2)))
+
+(define-public r-lubridate
+  (package
+    (name "r-lubridate")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "lubridate" version))
+       (sha256
+        (base32
+         "0ci6rwij9i1inn840m0mlh1nqgh6vm2lada9kdnjpcjp5kyfv1qs"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-stringr" ,r-stringr)))
+    (home-page
+     "http://cran.r-project.org/web/packages/lubridate")
+    (synopsis "Make dealing with dates a little easier")
+    (description
+     "This package provides functions to work with date-times and time-spans:
+fast and user friendly parsing of date-time data, extraction and updating of
+components of a date-time (years, months, days, hours, minutes, and seconds),
+algebraic manipulation on date-time and time-span objects.  The 'lubridate'
+package has a consistent and memorable syntax that makes working with dates
+easy and fun.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 1dacc269567683cedc439545a8077e523a1ed94e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 31 May 2017 17:12:08 +0200
Subject: gnu: Add r-fdrtool.

* gnu/packages/statistics.scm (r-fdrtool): New variable.
---
 gnu/packages/statistics.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 625f9f4884..ae44bfb01f 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -5257,3 +5257,31 @@ (define-public r-lubridate
 package has a consistent and memorable syntax that makes working with dates
 easy and fun.")
     (license license:gpl2)))
+
+(define-public r-fdrtool
+  (package
+    (name "r-fdrtool")
+    (version "1.2.15")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fdrtool" version))
+       (sha256
+        (base32
+         "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
+    (build-system r-build-system)
+    (home-page "http://strimmerlab.org/software/fdrtool/")
+    (synopsis "Estimation of false discovery rates and higher criticism")
+    (description
+     "This package provides tools to estimate both tail area-based false
+discovery rates (Fdr) as well as local false discovery rates (fdr) for a
+variety of null models (p-values, z-scores, correlation coefficients,
+t-scores).  The proportion of null values and the parameters of the null
+distribution are adaptively estimated from the data.  In addition, the package
+contains functions for non-parametric density estimation (Grenander
+estimator), for monotone regression (isotonic regression and antitonic
+regression with weights), for computing the greatest convex minorant (GCM) and
+the least concave majorant (LCM), for the half-normal and correlation
+distributions, and for computing empirical higher criticism (HC) scores and
+the corresponding decision threshold.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From b8fffd3a53a6b588e3613272802db580994b9cb0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 13 Apr 2017 14:16:12 +0200
Subject: gnu: Add ritornello.

* gnu/packages/bioinformatics.scm (ritornello): New variable.
---
 gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bf4dd87eb3..d61f91fcad 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9223,3 +9223,48 @@ (define-public sambamba
 an important subset of samtools functionality, including view, index,
 sort, markdup, and depth.")
     (license license:gpl2+)))
+
+(define-public ritornello
+  (package
+    (name "ritornello")
+    (version "1.0.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/KlugerLab/"
+                                  "Ritornello/archive/v"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ; there are no tests
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-samtools-references
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* '("src/SamStream.h"
+                            "src/BufferedGenomeReader.h")
+               (("<sam.h>") "<samtools/sam.h>"))
+             #t))
+         (delete 'configure)
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out    (assoc-ref outputs "out"))
+                    (bin    (string-append out "/bin/")))
+               (mkdir-p bin)
+               (install-file "bin/Ritornello" bin)
+               #t))))))
+    (inputs
+     `(("samtools" ,samtools-0.1)
+       ("fftw" ,fftw)
+       ("boost" ,boost)
+       ("zlib" ,zlib)))
+    (home-page "https://github.com/KlugerLab/Ritornello")
+    (synopsis "Control-free peak caller for ChIP-seq data")
+    (description "Ritornello is a ChIP-seq peak calling algorithm based on
+signal processing that can accurately call binding events without the need to
+do a pair total DNA input or IgG control sample.  It has been tested for use
+with narrow binding events such as transcription factor ChIP-seq.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From 44f6c88909061bb37facc180f3af948a55eb3caa Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 13 Apr 2017 14:16:32 +0200
Subject: gnu: Add trim-galore.

* gnu/packages/bioinformatics.scm (trim-galore): New variable.
---
 gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d61f91fcad..fbff587302 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9268,3 +9268,63 @@ (define-public ritornello
 do a pair total DNA input or IgG control sample.  It has been tested for use
 with narrow binding events such as transcription factor ChIP-seq.")
     (license license:gpl3+)))
+
+(define-public trim-galore
+  (package
+    (name "trim-galore")
+    (version "0.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://www.bioinformatics.babraham.ac.uk/"
+                           "projects/trim_galore/trim_galore_v"
+                           version ".zip"))
+       (sha256
+        (base32
+         "0b9qdxi4521gsrjvbhgky8g7kry9b5nx3byzaxkgxz7p4k8bn1mn"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ; no tests
+       #:phases
+       (modify-phases %standard-phases
+         ;; The archive contains plain files.
+         (replace 'unpack
+           (lambda* (#:key source #:allow-other-keys)
+             (zero? (system* "unzip" source))))
+         (delete 'configure)
+         (delete 'build)
+         (add-after 'unpack 'hardcode-tool-references
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "trim_galore"
+               (("\\$path_to_cutadapt = 'cutadapt'")
+                (string-append "$path_to_cutadapt = '"
+                               (assoc-ref inputs "cutadapt")
+                               "/bin/cutadapt'"))
+               (("\\| gzip")
+                (string-append "| "
+                               (assoc-ref inputs "gzip")
+                               "/bin/gzip"))
+               (("\"gunzip")
+                (string-append "\""
+                               (assoc-ref inputs "gzip")
+                               "/bin/gunzip")))
+             #t))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out")
+                                       "/bin")))
+               (mkdir-p bin)
+               (install-file "trim_galore" bin)
+               #t))))))
+    (inputs
+     `(("gzip" ,gzip)
+       ("perl" ,perl)
+       ("cutadapt" ,cutadapt)))
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/")
+    (synopsis "Wrapper around Cutadapt and FastQC")
+    (description "Trim Galore! is a wrapper script to automate quality and
+adapter trimming as well as quality control, with some added functionality to
+remove biased methylation positions for RRBS sequence files.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From 3420c905cdc37027bd630e9c5f3ac0e6fc066405 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 13 Apr 2017 14:18:10 +0200
Subject: gnu: Add gess.

* gnu/packages/bioinformatics.scm (gess): New variable.
---
 gnu/packages/bioinformatics.scm | 61 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fbff587302..2844c46075 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9328,3 +9328,64 @@ (define-public trim-galore
 adapter trimming as well as quality control, with some added functionality to
 remove biased methylation positions for RRBS sequence files.")
     (license license:gpl3+)))
+
+(define-public gess
+  (package
+    (name "gess")
+    (version "1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://compbio.uthscsa.edu/"
+                                  "GESS_Web/files/"
+                                  "gess-" version ".src.tar.gz"))
+              (sha256
+               (base32
+                "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ; no tests
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'build)
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((python (assoc-ref inputs "python"))
+                    (out    (assoc-ref outputs "out"))
+                    (bin    (string-append out "/bin/"))
+                    (target (string-append
+                             out "/lib/python2.7/site-packages/gess/")))
+               (mkdir-p target)
+               (copy-recursively "." target)
+               ;; Make GESS.py executable
+               (chmod (string-append target "GESS.py") #o555)
+               ;; Add Python shebang to the top and make Matplotlib
+               ;; usable.
+               (substitute* (string-append target "GESS.py")
+                 (("\"\"\"Description:" line)
+                  (string-append "#!" (which "python") "
+import matplotlib
+matplotlib.use('Agg')
+" line)))
+               ;; Make sure GESS has all modules in its path
+               (wrap-program (string-append target "GESS.py")
+                 `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH"))))
+               (mkdir-p bin)
+               (symlink (string-append target "GESS.py")
+                        (string-append bin "GESS.py"))
+               #t))))))
+    (inputs
+     `(("python" ,python-2)
+       ("python2-pysam" ,python2-pysam)
+       ("python2-scipy" ,python2-scipy)
+       ("python2-numpy" ,python2-numpy)
+       ("python2-networkx" ,python2-networkx)
+       ("python2-biopython" ,python2-biopython)))
+    (home-page "http://compbio.uthscsa.edu/GESS_Web/")
+    (synopsis "Detect exon-skipping events from raw RNA-seq data")
+    (description
+     "GESS is an implementation of a novel computational method to detect de
+novo exon-skipping events directly from raw RNA-seq data without the prior
+knowledge of gene annotation information.  GESS stands for the graph-based
+exon-skipping scanner detection scheme.")
+    (license license:bsd-3)))
-- 
cgit v1.2.3


From 282b01515ba48f17638631c40cfc17e99d4a6cce Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 13 Apr 2017 14:21:27 +0200
Subject: gnu: Add phylip.

* gnu/packages/bioinformatics.scm (phylip): New variable.
---
 gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2844c46075..b7d39ea359 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9389,3 +9389,40 @@ (define-public gess
 knowledge of gene annotation information.  GESS stands for the graph-based
 exon-skipping scanner detection scheme.")
     (license license:bsd-3)))
+
+(define-public phylip
+  (package
+    (name "phylip")
+    (version "3.696")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://evolution.gs.washington.edu/phylip/"
+                           "download/phylip-" version ".tar.gz"))
+       (sha256
+        (base32
+         "01jar1rayhr2gba2pgbw49m56rc5z4p5wn3ds0m188hrlln4a2nd"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ; no check target
+       #:make-flags (list "-f" "Makefile.unx" "install")
+       #:parallel-build? #f             ; not supported
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'enter-dir
+           (lambda _ (chdir "src") #t))
+         (delete 'configure)
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((target (string-append (assoc-ref outputs "out")
+                                          "/bin")))
+               (mkdir-p target)
+               (for-each (lambda (file)
+                           (install-file file target))
+                         (find-files "../exe" ".*")))
+             #t)))))
+    (home-page "http://evolution.genetics.washington.edu/phylip/")
+    (synopsis "Tools for inferring phylogenies")
+    (description "PHYLIP (the PHYLogeny Inference Package) is a package of
+programs for inferring phylogenies (evolutionary trees).")
+    (license license:bsd-2)))
-- 
cgit v1.2.3


From aa163424b249bb11525fccc0a87cf60aa687ac60 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 13 Apr 2017 22:56:54 +0200
Subject: gnu: Add imp.

* gnu/packages/bioinformatics.scm (imp): New variable.
---
 gnu/packages/bioinformatics.scm | 48 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b7d39ea359..7b36d6bbdc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -85,6 +85,7 @@ (define-module (gnu packages bioinformatics)
   #:use-module (gnu packages ruby)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages statistics)
+  #:use-module (gnu packages swig)
   #:use-module (gnu packages tbb)
   #:use-module (gnu packages tex)
   #:use-module (gnu packages texinfo)
@@ -9426,3 +9427,50 @@ (define-public phylip
     (description "PHYLIP (the PHYLogeny Inference Package) is a package of
 programs for inferring phylogenies (evolutionary trees).")
     (license license:bsd-2)))
+
+(define-public imp
+  (package
+    (name "imp")
+    (version "2.6.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://integrativemodeling.org/"
+                           version "/download/imp-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(;; FIXME: Some tests fail because they produce warnings, others fail
+       ;; because the PYTHONPATH does not include the modeller's directory.
+       #:tests? #f
+       ;; Do not place libraries in an architecture-specific directory.
+       #:configure-flags
+       (list "-DCMAKE_INSTALL_LIBDIR=lib")))
+    (inputs
+     `(("boost" ,boost)
+       ("gsl" ,gsl)
+       ("swig" ,swig)
+       ("hdf5" ,hdf5)
+       ("fftw" ,fftw)
+       ("python" ,python-2)))
+    (propagated-inputs
+     `(("python2-numpy" ,python2-numpy)
+       ("python2-scipy" ,python2-scipy)
+       ("python2-pandas" ,python2-pandas)
+       ("python2-scikit-learn" ,python2-scikit-learn)
+       ("python2-networkx" ,python2-networkx)))
+    (home-page "https://integrativemodeling.org")
+    (synopsis "Integrative modeling platform")
+    (description "IMP's broad goal is to contribute to a comprehensive
+structural characterization of biomolecules ranging in size and complexity
+from small peptides to large macromolecular assemblies, by integrating data
+from diverse biochemical and biophysical experiments.  IMP provides a C++ and
+Python toolbox for solving complex modeling problems, and a number of
+applications for tackling some common problems in a user-friendly way.")
+    ;; IMP is largely available under the GNU Lesser GPL; see the file
+    ;; COPYING.LGPL for the full text of this license. Some IMP modules are
+    ;; available under the GNU GPL (see the file COPYING.GPL).
+    (license (list license:lgpl2.1+
+                   license:gpl3+))))
-- 
cgit v1.2.3


From 8befd0940b4d443d5c2f1e91f9fe1b375f30fe1f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 13 Apr 2017 23:15:06 +0200
Subject: gnu: Add tadbit.

* gnu/packages/bioinformatics.scm (tadbit): New variable.
---
 gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7b36d6bbdc..b47f136935 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9474,3 +9474,61 @@ (define-public imp
     ;; available under the GNU GPL (see the file COPYING.GPL).
     (license (list license:lgpl2.1+
                    license:gpl3+))))
+
+(define-public tadbit
+  (package
+    (name "tadbit")
+    (version "0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/3DGenomes/TADbit/"
+                                  "archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f"))))
+    (build-system python-build-system)
+    (arguments
+     `(;; Tests are included and must be run after installation, but
+       ;; they are incomplete and thus cannot be run.
+       #:tests? #f
+       #:python ,python-2
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-problems-with-setup.py
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; setup.py opens these files for writing
+             (chmod "_pytadbit/_version.py" #o664)
+             (chmod "README.rst" #o664)
+
+             ;; Don't attempt to install the bash completions to
+             ;; the home directory.
+             (rename-file "extras/.bash_completion"
+                          "extras/tadbit")
+             (substitute* "setup.py"
+               (("\\(path.expanduser\\('~'\\)")
+                (string-append "(\""
+                               (assoc-ref outputs "out")
+                               "/etc/bash_completion.d\""))
+               (("extras/\\.bash_completion")
+                "extras/tadbit"))
+             #t)))))
+    (inputs
+     ;; TODO: add Chimera for visualization
+     `(("imp" ,imp)
+       ("mcl" ,mcl)
+       ("python2-scipy" ,python2-scipy)
+       ("python2-numpy" ,python2-numpy)
+       ("python2-matplotlib" ,python2-matplotlib)
+       ("python2-pysam" ,python2-pysam)))
+    (home-page "http://3dgenomes.github.io/TADbit/")
+    (synopsis "Analyze, model, and explore 3C-based data")
+    (description
+     "TADbit is a complete Python library to deal with all steps to analyze,
+model, and explore 3C-based data.  With TADbit the user can map FASTQ files to
+obtain raw interaction binned matrices (Hi-C like matrices), normalize and
+correct interaction matrices, identify adn compare the so-called
+@dfn{Topologically Associating Domains} (TADs), build 3D models from the
+interaction matrices, and finally, extract structural properties from the
+models.  TADbit is complemented by TADkit for visualizing 3D models.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From f1a710c3210795c8c501a06799a1ac55b06bc83b Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Fri, 9 Jun 2017 01:29:47 -0400
Subject: gnu: linux-libre@4.4: Update to 4.4.71.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.71.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 14e921ecd3..ea2de00214 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -374,8 +374,8 @@ (define-public linux-libre-4.9
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.70"
-                    "1dvcj3mk42m91y1x41yh52frjdcwip1wj57qwlkmrpg02icr0b3s"
+  (make-linux-libre "4.4.71"
+                    "0nrd165crx9m9s1px98if6q5dcdqwmas9kh8i4rw51gz2xinh0gx"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
-- 
cgit v1.2.3


From e2d57d12ce5dc63c8c96c77a3dc5a269b3cc5f49 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Fri, 9 Jun 2017 01:30:29 -0400
Subject: gnu: linux-libre@4.9: Update to 4.9.31.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.31.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index ea2de00214..51dd781777 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -368,8 +368,8 @@ (define-public linux-libre
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.30"
-                    "1m1ii9n65lwkbwx0ifj13vgdfr0mnx8n7sfvhf5mn4r8krhxi77a"
+  (make-linux-libre "4.9.31"
+                    "0amc35c9f2rym6grb277yscnx8ybn8d4fbc2a59sgkg1lsdv7n4q"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
-- 
cgit v1.2.3


From 6fe5c49ab487154074eaab2ef80e9a2f8163320c Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Fri, 9 Jun 2017 01:31:08 -0400
Subject: gnu: linux-libre: Update to 4.11.4.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.11.4.
(%linux-libre-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 51dd781777..2bbc3b6ef6 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -358,8 +358,8 @@ (define* (make-linux-libre version hash supported-systems
 
 (define %intel-compatible-systems '("x86_64-linux" "i686-linux"))
 
-(define %linux-libre-version "4.11.3")
-(define %linux-libre-hash "14fbn9s7n86p5yivr4vmh4axdavny6xw1qk63cfwlcma7426wmva")
+(define %linux-libre-version "4.11.4")
+(define %linux-libre-hash "11nd9pv18vz3g82ja71dkz9mbs0ffb8yamsd44d381szmmm2kpj8")
 
 (define-public linux-libre
   (make-linux-libre %linux-libre-version
-- 
cgit v1.2.3


From b22cdf0c4240016ca321639682bc58b0384ea36b Mon Sep 17 00:00:00 2001
From: 宋文武 <iyzsong@member.fsf.org>
Date: Fri, 9 Jun 2017 20:50:11 +0800
Subject: gnu: python-paramiko: Update to 2.1.2.

* gnu/packages.scm (python-paramiko, python2-paramiko):
Update to 2.1.2.  Enable tests.
---
 gnu/packages/python.scm | 20 +++++++++-----------
 1 file changed, 9 insertions(+), 11 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 19ffe729bf..44adcba01e 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -533,26 +533,24 @@ (define-public python2-py-bcrypt
 (define-public python-paramiko
   (package
     (name "python-paramiko")
-    (version "1.17.4")
+    (version "2.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "paramiko" version))
        (sha256
         (base32
-         "1rs2qcmskcmq66q6g5al08wa41l9am0fad5r719m8wf91msyylqw"))))
+         "04734n0wy3hxk6rij4fr29in5jmr70nxpc7pqi2ksbjysfz4kbjz"))))
     (build-system python-build-system)
     (arguments
-     '(;; FIXME: One test fails with "EOFError not raised by connect".
-       #:tests? #f))
-       ;; #:phases
-       ;; (modify-phases %standard-phases
-       ;;   (replace 'check
-       ;;     (lambda _
-       ;;       (zero? (system* "python" "test.py")))))))
+     '(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (zero? (system* "python" "test.py")))))))
     (propagated-inputs
-     `(("python-pycrypto" ,python-pycrypto)
-       ("python-ecdsa" ,python-ecdsa)))
+     `(("python-pyasn1" ,python-pyasn1)
+       ("python-cryptography" ,python-cryptography)))
     (home-page "http://www.paramiko.org/")
     (synopsis "SSHv2 protocol library")
     (description "Paramiko is a python implementation of the SSHv2 protocol,
-- 
cgit v1.2.3


From e6ad9bda4992a8170c40b5775cce991b9c48d128 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Fri, 9 Jun 2017 23:26:14 +0200
Subject: gnu: p11-kit: Update to 0.23.7.

Newer releases are only available on GitHub. See release announcements:
https://lists.freedesktop.org/archives/p11-glue/2017-June/000661.html

* gnu/packages/tls.scm (p11-kit): Update to 0.23.7.
[source]: Remove obsolete substitution.
---
 gnu/packages/tls.scm | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index cdb4becb07..8964abb2f2 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -112,23 +112,15 @@ (define-public asn1c
 (define-public p11-kit
   (package
     (name "p11-kit")
-    (version "0.23.2")
+    (version "0.23.7")
     (source
      (origin
       (method url-fetch)
-      (uri (string-append "https://p11-glue.freedesktop.org/releases/p11-kit-"
-                          version ".tar.gz"))
+      (uri (string-append "https://github.com/p11-glue/p11-kit/releases/"
+                          "download/" version "/p11-kit-" version ".tar.gz"))
       (sha256
        (base32
-        "1w7szm190phlkg7qx05ychlj2dbvkgkhx9gw6dx4d5rw62l6wwms"))
-      (modules '((guix build utils))) ; for substitute*
-      (snippet
-        '(begin
-           ;; Drop one test that fails, also when trying to compile manually.
-           ;; Reported upstream at
-           ;; https://bugs.freedesktop.org/show_bug.cgi?id=89027
-           (substitute* "Makefile.in"
-             (("test-module\\$\\(EXEEXT\\) ") ""))))))
+        "0hdy4h8byvcvd4av504xqfqyd1h6xy914j034mq3c6v4ya37r3lq"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From ad27449ef10e469d9e937700ee3a0f3015cf0945 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Fri, 9 Jun 2017 23:28:55 +0200
Subject: gnu: ffmpeg: Update to 3.3.2.

* gnu/packages/video.scm (ffmpeg): Update to 3.3.2.
---
 gnu/packages/video.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 1053f76bb7..8a91a97017 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -461,14 +461,14 @@ (define-public libva
 (define-public ffmpeg
   (package
     (name "ffmpeg")
-    (version "3.3.1")
+    (version "3.3.2")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "0bwgm6z6k3khb91qh9xv15inykkfchpkm0lcdckkxhkacpyaf0mp"))))
+               "11974vcfsy8w0i6f4lfwqmg80xkfybqw7vw6zzrcn5i6ncddx60r"))))
     (build-system gnu-build-system)
     (inputs
      `(("fontconfig" ,fontconfig)
-- 
cgit v1.2.3


From 0866dd46a97082a963acc631ecae02820c718079 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Fri, 9 Jun 2017 23:33:36 +0200
Subject: gnu: capnproto: Update to 0.6.1.

* gnu/packages/serialization.scm (capnproto): Update to 0.6.1.
---
 gnu/packages/serialization.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index a6b5270199..6a3d8f900d 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -282,7 +282,7 @@ (define-public jsoncpp
 (define-public capnproto
   (package
     (name "capnproto")
-    (version "0.6.0")
+    (version "0.6.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -290,7 +290,7 @@ (define-public capnproto
                     version ".tar.gz"))
               (sha256
                (base32
-                "0gpp1cxsb9nfd7qkjjykzknx03y0z0n4bq5q0fmxci7w38ci22g5"))))
+                "010s9yhq4531wvdfrdf2477zswhck6cjfby79w73rff3v06090l0"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From e5eede3fb37e5f50542f138f86ee752696442580 Mon Sep 17 00:00:00 2001
From: ng0 <ng0@no-reply.pragmatique.xyz>
Date: Thu, 8 Jun 2017 17:14:06 +0000
Subject: gnu: Rename (gnu packages markdown) to (gnu packages markup).

* gnu/packages/markdown.scm: Rename this ...
* gnu/packages/markup.scm: ... to this.
* gnu-system.am (GNU_SYSTEM_MODULES): Change markdown.scm to markup.scm.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/local.mk              |   2 +-
 gnu/packages/markdown.scm | 132 ----------------------------------------------
 gnu/packages/markup.scm   | 132 ++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 133 insertions(+), 133 deletions(-)
 delete mode 100644 gnu/packages/markdown.scm
 create mode 100644 gnu/packages/markup.scm

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 93a58440e2..686c3c6396 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -256,7 +256,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/man.scm				\
   %D%/packages/mail.scm				\
   %D%/packages/make-bootstrap.scm		\
-  %D%/packages/markdown.scm			\
+  %D%/packages/markup.scm			\
   %D%/packages/marst.scm			\
   %D%/packages/mate.scm             \
   %D%/packages/maths.scm			\
diff --git a/gnu/packages/markdown.scm b/gnu/packages/markdown.scm
deleted file mode 100644
index 4a020198e4..0000000000
--- a/gnu/packages/markdown.scm
+++ /dev/null
@@ -1,132 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
-;;; Copyright © 2015 David Thompson <davet@gnu.org>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
-;;;
-;;; This file is part of GNU Guix.
-;;;
-;;; GNU Guix is free software; you can redistribute it and/or modify it
-;;; under the terms of the GNU General Public License as published by
-;;; the Free Software Foundation; either version 3 of the License, or (at
-;;; your option) any later version.
-;;;
-;;; GNU Guix is distributed in the hope that it will be useful, but
-;;; WITHOUT ANY WARRANTY; without even the implied warranty of
-;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;;; GNU General Public License for more details.
-;;;
-;;; You should have received a copy of the GNU General Public License
-;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
-
-(define-module (gnu packages markdown)
-  #:use-module (guix licenses)
-  #:use-module (guix download)
-  #:use-module (guix packages)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix build-system trivial)
-  #:use-module (guix build-system cmake)
-  #:use-module (gnu packages perl)
-  #:use-module (gnu packages python)
-  #:use-module (gnu packages web)
-  #:use-module (gnu packages zip))
-
-(define-public hoedown
-  (package
-    (name "hoedown")
-    (version "3.0.7")
-    (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/hoedown/hoedown/archive/"
-                                 version ".tar.gz"))
-             (file-name (string-append name "-" version ".tar.gz"))
-             (sha256
-              (base32
-               "0859dc2xjasd6kgkshi8mb20kbyw5sql1ln0hw3bfaf33qdh5dh1"))))
-    (build-system gnu-build-system)
-    (arguments
-     '(#:make-flags (list "CC=gcc" (string-append "PREFIX=" %output))
-       #:phases (modify-phases %standard-phases
-                  (delete 'configure)) ; no configure script
-       #:test-target "test"))
-    (native-inputs
-     `(("python" ,python-2)
-       ("tidy" ,tidy)))
-    (synopsis "Markdown processing library")
-    (description "Hoedown is a standards compliant, fast, secure markdown
-processing library written in C.")
-    (home-page "https://github.com/hoedown/hoedown")
-    (license expat)))
-
-(define-public markdown
-  (package
-    (name "markdown")
-    (version "1.0.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "http://daringfireball.net/projects/downloads/"
-             (string-capitalize name) "_" version ".zip"))
-       (sha256
-        (base32 "0dq1pj91pvlwkv0jwcgdfpv6gvnxzrk3s8mnh7imamcclnvfj835"))))
-    (build-system trivial-build-system)
-    (arguments
-     '(#:modules ((guix build utils))
-       #:builder
-       (begin
-         (use-modules (guix build utils))
-         (let ((source (assoc-ref %build-inputs "source"))
-               (out    (assoc-ref %outputs "out"))
-               (perlbd (string-append (assoc-ref %build-inputs "perl") "/bin"))
-               (unzip  (string-append (assoc-ref %build-inputs "unzip")
-                                      "/bin/unzip")))
-           (mkdir-p out)
-           (with-directory-excursion out
-             (system* unzip source)
-             (mkdir "bin")
-             (mkdir-p "share/doc")
-             (rename-file "Markdown_1.0.1/Markdown.pl" "bin/markdown")
-             (rename-file "Markdown_1.0.1/Markdown Readme.text"
-                          "share/doc/README")
-             (patch-shebang "bin/markdown" (list perlbd))
-             (delete-file-recursively "Markdown_1.0.1"))))))
-    (native-inputs `(("unzip" ,unzip)))
-    (inputs `(("perl" ,perl)))
-    (home-page "http://daringfireball.net/projects/markdown")
-    (synopsis "Text-to-HTML conversion tool")
-    (description
-     "Markdown is a text-to-HTML conversion tool for web writers.  It allows
-you to write using an easy-to-read, easy-to-write plain text format, then
-convert it to structurally valid XHTML (or HTML).")
-    (license (non-copyleft "file://License.text"
-                           "See License.text in the distribution."))))
-
-(define-public cmark
-  (package
-    (name "cmark")
-    (version "0.27.1")
-    (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/jgm/cmark/archive/"
-                                 version ".tar.gz"))
-             (file-name (string-append name "-" version ".tar.gz"))
-             (sha256
-              (base32
-               "1da62ispca9aal2a36gaj87175rv5013pl7x740vk32y6lclr6v6"))))
-    (build-system cmake-build-system)
-    (arguments
-     '(#:test-target "test"))
-    (native-inputs `(("python" ,python)))
-    (synopsis "CommonMark Markdown reference implementation")
-    (description "CommonMark is a strongly defined, highly compatible
-specification of Markdown.  cmark is the C reference implementation of
-CommonMark.  It provides @code{libcmark} shared library for parsing
-CommonMark to an abstract syntax tree (AST) and rendering the document
-as HTML, groff man, LaTeX, CommonMark, or an XML representation of the
-AST.  The package also provides the command-line program @command{cmark}
-for parsing and rendering CommonMark.")
-    (home-page "http://commonmark.org")
-    ;; cmark is distributed with a BSD-2 license, but some components are Expat
-    ;; licensed. The CommonMark specification is Creative Commons CC-BY-SA 4.0
-    ;; licensed. See 'COPYING' in the source distribution for more information.
-    (license (list bsd-2 expat cc-by-sa4.0))))
diff --git a/gnu/packages/markup.scm b/gnu/packages/markup.scm
new file mode 100644
index 0000000000..de40de670d
--- /dev/null
+++ b/gnu/packages/markup.scm
@@ -0,0 +1,132 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
+;;; Copyright © 2015 David Thompson <davet@gnu.org>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages markup)
+  #:use-module (guix licenses)
+  #:use-module (guix download)
+  #:use-module (guix packages)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system trivial)
+  #:use-module (guix build-system cmake)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages web)
+  #:use-module (gnu packages zip))
+
+(define-public hoedown
+  (package
+    (name "hoedown")
+    (version "3.0.7")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append "https://github.com/hoedown/hoedown/archive/"
+                                 version ".tar.gz"))
+             (file-name (string-append name "-" version ".tar.gz"))
+             (sha256
+              (base32
+               "0859dc2xjasd6kgkshi8mb20kbyw5sql1ln0hw3bfaf33qdh5dh1"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:make-flags (list "CC=gcc" (string-append "PREFIX=" %output))
+       #:phases (modify-phases %standard-phases
+                  (delete 'configure)) ; no configure script
+       #:test-target "test"))
+    (native-inputs
+     `(("python" ,python-2)
+       ("tidy" ,tidy)))
+    (synopsis "Markdown processing library")
+    (description "Hoedown is a standards compliant, fast, secure markdown
+processing library written in C.")
+    (home-page "https://github.com/hoedown/hoedown")
+    (license expat)))
+
+(define-public markdown
+  (package
+    (name "markdown")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://daringfireball.net/projects/downloads/"
+             (string-capitalize name) "_" version ".zip"))
+       (sha256
+        (base32 "0dq1pj91pvlwkv0jwcgdfpv6gvnxzrk3s8mnh7imamcclnvfj835"))))
+    (build-system trivial-build-system)
+    (arguments
+     '(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let ((source (assoc-ref %build-inputs "source"))
+               (out    (assoc-ref %outputs "out"))
+               (perlbd (string-append (assoc-ref %build-inputs "perl") "/bin"))
+               (unzip  (string-append (assoc-ref %build-inputs "unzip")
+                                      "/bin/unzip")))
+           (mkdir-p out)
+           (with-directory-excursion out
+             (system* unzip source)
+             (mkdir "bin")
+             (mkdir-p "share/doc")
+             (rename-file "Markdown_1.0.1/Markdown.pl" "bin/markdown")
+             (rename-file "Markdown_1.0.1/Markdown Readme.text"
+                          "share/doc/README")
+             (patch-shebang "bin/markdown" (list perlbd))
+             (delete-file-recursively "Markdown_1.0.1"))))))
+    (native-inputs `(("unzip" ,unzip)))
+    (inputs `(("perl" ,perl)))
+    (home-page "http://daringfireball.net/projects/markdown")
+    (synopsis "Text-to-HTML conversion tool")
+    (description
+     "Markdown is a text-to-HTML conversion tool for web writers.  It allows
+you to write using an easy-to-read, easy-to-write plain text format, then
+convert it to structurally valid XHTML (or HTML).")
+    (license (non-copyleft "file://License.text"
+                           "See License.text in the distribution."))))
+
+(define-public cmark
+  (package
+    (name "cmark")
+    (version "0.27.1")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append "https://github.com/jgm/cmark/archive/"
+                                 version ".tar.gz"))
+             (file-name (string-append name "-" version ".tar.gz"))
+             (sha256
+              (base32
+               "1da62ispca9aal2a36gaj87175rv5013pl7x740vk32y6lclr6v6"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:test-target "test"))
+    (native-inputs `(("python" ,python)))
+    (synopsis "CommonMark Markdown reference implementation")
+    (description "CommonMark is a strongly defined, highly compatible
+specification of Markdown.  cmark is the C reference implementation of
+CommonMark.  It provides @code{libcmark} shared library for parsing
+CommonMark to an abstract syntax tree (AST) and rendering the document
+as HTML, groff man, LaTeX, CommonMark, or an XML representation of the
+AST.  The package also provides the command-line program @command{cmark}
+for parsing and rendering CommonMark.")
+    (home-page "http://commonmark.org")
+    ;; cmark is distributed with a BSD-2 license, but some components are Expat
+    ;; licensed. The CommonMark specification is Creative Commons CC-BY-SA 4.0
+    ;; licensed. See 'COPYING' in the source distribution for more information.
+    (license (list bsd-2 expat cc-by-sa4.0))))
-- 
cgit v1.2.3


From 83f0d3a5c8a1f551d7a92283d445fb605f9fb069 Mon Sep 17 00:00:00 2001
From: ng0 <ng0@no-reply.pragmatique.xyz>
Date: Tue, 30 May 2017 13:56:26 +0000
Subject: gnu: Add smu.

* gnu/packages/markup.scm (smu): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/markup.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/markup.scm b/gnu/packages/markup.scm
index de40de670d..cd883b23ec 100644
--- a/gnu/packages/markup.scm
+++ b/gnu/packages/markup.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
 ;;; Copyright © 2015 David Thompson <davet@gnu.org>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017 ng0 <ng0@no-reply.pragmatique.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -130,3 +131,39 @@ (define-public cmark
     ;; licensed. The CommonMark specification is Creative Commons CC-BY-SA 4.0
     ;; licensed. See 'COPYING' in the source distribution for more information.
     (license (list bsd-2 expat cc-by-sa4.0))))
+
+(define-public smu
+  (package
+    (name "smu")
+    (version "1.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/Gottox/smu/archive/v"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0iazl45rkz8ngsb5hpykl76w0ngvdvqqhym1qz5wykgmrzk293rp"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:make-flags (list "CC=gcc"
+                          (string-append "PREFIX="
+                                         (assoc-ref %outputs "out")))
+       #:tests? #f ;No tests included
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure))))
+    (home-page "https://github.com/Gottox/smu")
+    (synopsis "Simple markup")
+    (description
+     "Smu is a very simple and minimal markup language.  It is
+designed for using in wiki-like environments.  Smu makes it very
+easy to write your documents on the fly and convert them into HTML.
+Smu is capable to parse very large documents.  As long as you avoid an huge
+amount of indents it scales just great.
+
+Smu was started as a rewrite of Markdown but became something more
+lightweight and consistent.  The biggest difference between Markdown
+and smu is that smu doesn't support reference style links.")
+    (license x11)))
-- 
cgit v1.2.3


From b2193c359a3a6c6bc6db68b22b3dc29b8421dc1a Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Jun 2017 01:06:40 +0200
Subject: gnu: xclip: Update to 0.13.

Yet another GitHub casualty. See: https://sourceforge.net/projects/xclip/

* gnu/packages/xdisorg.scm (xclip): Update to 0.13.
[source, home-page]: Change to new home.
[native-inputs]: Add AUTOCONF and AUTOMAKE.
[arguments]: Add "bootstrap" phase.
---
 gnu/packages/xdisorg.scm | 24 ++++++++++++++++--------
 1 file changed, 16 insertions(+), 8 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index 91abf66945..97f68e872a 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -14,7 +14,7 @@
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Alex Kost <alezost@gmail.com>
-;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2016 Petter <petter@mykolab.ch>
 ;;; Copyright © 2017 Mekeor Melire <mekeor.melire@gmail.com>
 ;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net>
@@ -47,6 +47,7 @@ (define-module (gnu packages xdisorg)
   #:use-module (gnu packages)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages algebra)
+  #:use-module (gnu packages autotools)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages image)
   #:use-module (gnu packages pkg-config)
@@ -117,22 +118,29 @@ (define-public arandr
 (define-public xclip
   (package
     (name "xclip")
-    (version "0.12")
+    (version "0.13")
     (source
       (origin
         (method url-fetch)
-        (uri (string-append
-              "mirror://sourceforge/" name "/" name "/" version "/"
-              name "-" version ".tar.gz"))
+        (uri (string-append "https://github.com/astrand/xclip"
+                            "/archive/" version ".tar.gz"))
         (sha256
           (base32
-           "0ibcf46rldnv0r424qcnai1fa5iq3lm5q5rdd7snsi5sb78gmixp"))))
+           "0n7pczk9vv30zf8qfln8ba3hnif9yfdxg0m84djac469wc28hnya"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:tests? #f))   ; There is no test suite
+     '(#:tests? #f     ; There is no test suite
+       #:phases
+       (modify-phases %standard-phases
+         ;; Since version 0.13, bootstrapped releases are no longer available.
+         (add-after 'unpack 'bootstrap
+           (lambda _ (zero? (system* "autoreconf" "-v")))))))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)))
     (inputs `(("libxmu" ,libxmu)
               ("libxt" ,libxt)))
-    (home-page "http://xclip.sourceforge.net/")
+    (home-page "https://github.com/astrand/xclip")
     (synopsis "Command line interface to X11 clipboard")
     (description "Xclip is a command line interface to the X11 clipboard.  It
 can also be used for copying files, as an alternative to sftp/scp, thus
-- 
cgit v1.2.3


From b634408158346ab6e28fd5b9b3fdf60f11f53ccb Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Jun 2017 01:32:24 +0200
Subject: gnu: slop: Update to 6.3.43.

* gnu/packages/xdisorg.scm (slop): Update to 6.3.43.
---
 gnu/packages/xdisorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index 97f68e872a..aaa961bb2b 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -449,7 +449,7 @@ (define-public scrot
 (define-public slop
   (package
     (name "slop")
-    (version "6.3.41")
+    (version "6.3.43")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -458,7 +458,7 @@ (define-public slop
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1yiv0ak1z7zbmcdw0dwx2gpblrh7l7s3l7y7sgpx071dy8s4rqpb"))))
+                "0kazcnnarc61d3rjysaym9vadf31wisfd3sn076rsjnsldm4y66h"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f)) ; no "check" target
-- 
cgit v1.2.3


From bddcaf76259eabf87f4c2b591d0b8cf8d1eab9d8 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Jun 2017 01:47:40 +0200
Subject: gnu: xf86-video-ati: Update to 7.9.0.

* gnu/packages/xorg.scm (xf86-video-ati): Update to 7.9.0.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index f243222fb3..1b126d85d5 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -2621,7 +2621,7 @@ (define-public xf86-video-ark
 (define-public xf86-video-ati
   (package
     (name "xf86-video-ati")
-    (version "7.8.0")
+    (version "7.9.0")
     (source
       (origin
         (method url-fetch)
@@ -2631,7 +2631,7 @@ (define-public xf86-video-ati
                ".tar.bz2"))
         (sha256
           (base32
-            "1ynnm4v4261xmg94b7jam9hjyym4n2nqba23rv23v3wjfbkms7s0"))))
+            "0xcq0lncb5p4sas5866qpkjyp1v8ksalw7m1gmqb3brhccp8gb9w"))))
     (build-system gnu-build-system)
     (inputs `(("mesa" ,mesa)
               ("xxf86driproto" ,xf86driproto)
-- 
cgit v1.2.3


From 8caf5bac4c89512793276054770386c343c73e7b Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Jun 2017 01:49:16 +0200
Subject: gnu: xf86-video-openchrome: Update to 0.6.0.

* gnu/packages/xorg.scm (xf86-video-openchrome): Update to 0.6.0.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 1b126d85d5..cc785a998b 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -3019,7 +3019,7 @@ (define-public xf86-video-nouveau
 (define-public xf86-video-openchrome
   (package
     (name "xf86-video-openchrome")
-    (version "0.5.0")
+    (version "0.6.0")
     (source
       (origin
         (method url-fetch)
@@ -3029,7 +3029,7 @@ (define-public xf86-video-openchrome
                ".tar.bz2"))
         (sha256
          (base32
-          "1fsmr455lk89zl795d6b5ypyqjim40j3h2vjch52lcssjw9xdza9"))))
+          "0x9gq3hw6k661k82ikd1y2kkk4dmgv310xr5q59dwn4k6z37aafs"))))
     (build-system gnu-build-system)
     (inputs `(("libx11" ,libx11)
               ("libxext" ,libxext)
-- 
cgit v1.2.3