From 581176c00b424ea6ddbeec38ba5dfaea43b53bcc Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 25 Oct 2015 19:07:29 +0200
Subject: gnu: youtube-dl: Upgrade to 2015.10.24.

* gnu/packages/video.scm (youtube-dl): Upgrade to 2015.10.24.
---
 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 e3e67becf5..d22975afd9 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -797,7 +797,7 @@ (define-public libvpx
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2015.10.16")
+    (version "2015.10.24")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://youtube-dl.org/downloads/"
@@ -805,7 +805,7 @@ (define-public youtube-dl
                                   version ".tar.gz"))
               (sha256
                (base32
-                "001a4md0yl3zx129mksmwc85grss67r3c9rynvranf9vlpv202vn"))))
+                "1q9srq08vb2yzl81hmjrgqwajckq52fhh9ag2ppbbxjibf91w5gs"))))
     (build-system python-build-system)
     (inputs `(("setuptools" ,python-setuptools)))
     (home-page "http://youtube-dl.org")
-- 
cgit v1.2.3


From 554093b7e139ca2224b754fdeb8a3c6f2d53bde5 Mon Sep 17 00:00:00 2001
From: Paul van der Walt <paul@denknerd.org>
Date: Fri, 23 Oct 2015 19:55:34 +0200
Subject: gnu: ghc-async: Fix description formatting.

* gnu/packages/haskell.scm (ghc-async): Formatting.
---
 gnu/packages/haskell.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 83ec3f9ca3..4303093d99 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3645,7 +3645,7 @@ (define-public ghc-async
     (home-page "https://github.com/simonmar/async")
     (synopsis "Library to run IO operations asynchronously")
     (description "Async provides a library to run IO operations
-asynchronously, and wait for their results. It is a higher-level interface
+asynchronously, and wait for their results.  It is a higher-level interface
 over threads in Haskell, in which @code{Async a} is a concurrent thread that
 will eventually deliver a value of type @code{a}.")
     (license bsd-3)))
-- 
cgit v1.2.3


From fd59d2ee65d6c86b115a19394d31c270cc8d95e2 Mon Sep 17 00:00:00 2001
From: Paul van der Walt <paul@denknerd.org>
Date: Fri, 23 Oct 2015 19:57:15 +0200
Subject: gnu: haskell: Remove CONFIG_SHELL patches.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

A previous commit to the haskell-build-system made sure that if
necessary, the CONFIG_SHELL environment variable is set.  That obviates
the individual patches applied to some packages.  Remove them.

* gnu/packages/haskell.scm (ghc-network, ghc-old-time, ghc-sdl-image,
  ghc-sdl-mixer, ghc-sdl, ghc-unix-time, ghc-x11)[arguments]: Remove
  ‘fix-/bin/sh’ phase.
---
 gnu/packages/haskell.scm | 53 +++++-------------------------------------------
 1 file changed, 5 insertions(+), 48 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 4303093d99..652efc3fbd 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -865,14 +865,6 @@ (define-public ghc-sdl
         (base32
          "1sa3zx3vrs1gbinxx33zwq0x2bsf3i964bff7419p7vzidn36k46"))))
     (build-system haskell-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after
-          'unpack 'fix-/bin/sh
-          (lambda _
-            ;; Use `sh', not `/bin/sh'.
-            (setenv "CONFIG_SHELL" "sh"))))))
     (inputs
      `(("sdl" ,sdl)))
     (home-page "https://hackage.haskell.org/package/SDL")
@@ -903,14 +895,7 @@ (define-public ghc-sdl-mixer
      `(#:configure-flags
        (let* ((sdl-mixer (assoc-ref %build-inputs "sdl-mixer"))
               (sdl-mixer-include (string-append sdl-mixer "/include/SDL")))
-         (list (string-append "--extra-include-dirs=" sdl-mixer-include)))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after
-          'unpack 'fix-/bin/sh
-          (lambda _
-            ;; Use `sh', not `/bin/sh'.
-            (setenv "CONFIG_SHELL" "sh"))))))
+         (list (string-append "--extra-include-dirs=" sdl-mixer-include)))))
     (propagated-inputs
      `(("ghc-sdl" ,ghc-sdl)))
     (inputs
@@ -942,14 +927,7 @@ (define-public ghc-sdl-image
      `(#:configure-flags
        (let* ((sdl-image (assoc-ref %build-inputs "sdl-image"))
               (sdl-image-include (string-append sdl-image "/include/SDL")))
-         (list (string-append "--extra-include-dirs=" sdl-image-include)))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after
-          'unpack 'fix-/bin/sh
-          (lambda _
-            ;; Use `sh', not `/bin/sh'.
-            (setenv "CONFIG_SHELL" "sh"))))))
+         (list (string-append "--extra-include-dirs=" sdl-image-include)))))
     (propagated-inputs
      `(("ghc-sdl" ,ghc-sdl)))
     (inputs
@@ -1216,12 +1194,6 @@ (define-public ghc-old-time
         (base32
          "1h9b26s3kfh2k0ih4383w90ibji6n0iwamxp6rfp2lbq1y5ibjqw"))))
     (build-system haskell-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-/bin/sh
-                    (lambda _
-                      (setenv "CONFIG_SHELL" "sh"))))))
     (propagated-inputs
      `(("ghc-old-locale" ,ghc-old-locale)))
     (home-page "http://hackage.haskell.org/package/old-time")
@@ -1433,12 +1405,6 @@ (define-public ghc-x11
                            "X11-" version ".tar.gz"))
        (sha256
         (base32 "1kzjcynm3rr83ihqx2y2d852jc49da4p18gv6jzm7g87z22x85jj"))))
-    (arguments
-     `(#:phases (modify-phases %standard-phases
-                  (add-before 'configure 'set-sh
-                              (lambda _
-                                (setenv "CONFIG_SHELL" "sh")
-                                #t)))))
     (build-system haskell-build-system)
     (inputs
      `(("libx11" ,libx11)
@@ -1801,13 +1767,8 @@ (define-public ghc-unix-time
          "0dyvyxwaffb94bgri1wc4b9wqaasy32pyjn0lww3dqblxv8fn5ax"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:tests? #f ; FIXME: Test fails with "System.Time not found".  This is
-                   ; weird, that should be provided by GHC 7.10.2.
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-/bin/sh
-                    (lambda _
-                      (setenv "CONFIG_SHELL" "sh"))))))
+     `(#:tests? #f)) ; FIXME: Test fails with "System.Time not found".  This
+                     ; is weird, that should be provided by GHC 7.10.2.
     (propagated-inputs
      `(("ghc-old-time" ,ghc-old-time)
        ("ghc-old-locale" ,ghc-old-locale)))
@@ -3162,11 +3123,7 @@ (define-public ghc-network
     (inputs
      `(("ghc-hunit" ,ghc-hunit)))
     (arguments
-     `(#:tests? #f  ; FIXME: currently missing libraries used for tests.
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'configure 'set-sh
-                     (lambda _ (setenv "CONFIG_SHELL" "sh"))))))
+     `(#:tests? #f))      ; FIXME: currently missing libraries used for tests.
     (home-page "https://github.com/haskell/network")
     (synopsis "Low-level networking interface")
     (description
-- 
cgit v1.2.3


From 64a719203fc5bbb6ace1e18727de6c216ad484fc Mon Sep 17 00:00:00 2001
From: Paul van der Walt <paul@denknerd.org>
Date: Mon, 26 Oct 2015 13:28:20 +0100
Subject: gnu: racket: Update to 6.2.1.

* gnu/packages/scheme.scm (racket): Update to 6.2.1.
---
 gnu/packages/scheme.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm
index 7465b1b58c..aea8b54433 100644
--- a/gnu/packages/scheme.scm
+++ b/gnu/packages/scheme.scm
@@ -334,7 +334,7 @@ (define-public scheme48
 (define-public racket
   (package
     (name "racket")
-    (version "6.1.1")
+    (version "6.2.1")
     (source (origin
              (method url-fetch)
              (uri (list (string-append "http://mirror.racket-lang.org/installers/"
@@ -344,7 +344,7 @@ (define-public racket
                          version "/racket/racket-" version "-src-unix.tgz")))
              (sha256
               (base32
-               "0xfsfdqkngz0xw2lqmc7bsznwx25cw91l9fjhp7abrr05m96j0h9"))))
+               "0555j63k7fs10iv0icmivlxpzgp6s7gwcbfddmbwxlf2rk80qhq0"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
-- 
cgit v1.2.3


From e3e1ecf67c03836295b513d10403194a513afa2d Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Mon, 26 Oct 2015 00:13:03 +0100
Subject: gnu: Add RPM.

* gnu/packages/package-management.scm (rpm): New variable.
* gnu/packages/backup.scm (libarchive): Add comment.
---
 gnu/packages/backup.scm             |  1 +
 gnu/packages/package-management.scm | 83 ++++++++++++++++++++++++++++++++++++-
 2 files changed, 83 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 84d27c08a6..99a10e1c7f 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -147,6 +147,7 @@ (define-public libarchive
               (search-patch "libarchive-fix-lzo-test-case.patch")
               (search-patch "libarchive-CVE-2013-0211.patch")))))
     (build-system gnu-build-system)
+    ;; TODO: Add -L/path/to/nettle in libarchive.pc.
     (inputs
      `(("zlib" ,zlib)
        ("nettle" ,nettle)
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 8fbe5b3064..4e69d6de59 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -23,9 +23,12 @@ (define-module (gnu packages package-management)
   #:use-module (guix git-download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
-  #:use-module ((guix licenses) #:select (gpl2+ gpl3+ lgpl2.1+))
+  #:use-module (guix build-system python)
+  #:use-module ((guix licenses) #:select (gpl2+ gpl3+ lgpl2.1+ asl2.0))
   #:use-module (gnu packages)
   #:use-module (gnu packages guile)
+  #:use-module (gnu packages file)
+  #:use-module (gnu packages backup)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages databases)
@@ -34,12 +37,17 @@ (define-module (gnu packages package-management)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages texinfo)
+  #:use-module (gnu packages nettle)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages web)
   #:use-module (gnu packages man)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages bdw-gc)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages popt)
+  #:use-module (gnu packages gnuzilla)
+  #:use-module (gnu packages cpio)
   #:use-module (gnu packages tls))
 
 (define (boot-guile-uri arch)
@@ -275,3 +283,76 @@ (define-public stow
 letting you install them apart in distinct directories and then create
 symlinks to the files in a common directory such as /usr/local.")
     (license gpl2+)))
+
+(define-public rpm
+  (package
+    (name "rpm")
+    (version "4.12.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://rpm.org/releases/rpm-4.12.x/rpm-"
+                                  version ".tar.bz2"))
+              (sha256
+               (base32
+                "18hk47hc755nslvb7xkq4jb095z7va0nlcyxdpxayc4lmb8mq3bp"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:configure-flags '("--with-external-db"   ;use the system's bdb
+                           "--enable-python"
+                           "--without-lua")
+       #:phases (modify-phases %standard-phases
+                  (add-before 'configure 'set-nspr-search-path
+                    (lambda* (#:key inputs #:allow-other-keys)
+                      ;; nspr.pc contains the right -I flag pointing to
+                      ;; 'include/nspr', but unfortunately 'configure' doesn't
+                      ;; use 'pkg-config'.  Thus, augment CPATH.
+                      ;; Likewise for NSS.
+                      (let ((nspr (assoc-ref inputs "nspr"))
+                            (nss  (assoc-ref inputs "nss")))
+                        (setenv "CPATH"
+                                (string-append (getenv "CPATH") ":"
+                                               nspr "/include/nspr:"
+                                               nss "/include/nss"))
+                        (setenv "LIBRARY_PATH"
+                                (string-append (getenv "LIBRARY_PATH") ":"
+                                               nss "/lib/nss"))
+                        #t)))
+                  (add-after 'install 'fix-rpm-symlinks
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      ;; 'make install' gets these symlinks wrong.  Fix them.
+                      (let* ((out (assoc-ref outputs "out"))
+                             (bin (string-append out "/bin")))
+                        (with-directory-excursion bin
+                          (for-each (lambda (file)
+                                      (delete-file file)
+                                      (symlink "rpm" file))
+                                    '("rpmquery" "rpmverify"))
+                          #t)))))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("python" ,python-2)
+       ("xz" ,xz)
+       ("bdb" ,bdb)
+       ("popt" ,popt)
+       ("nss" ,nss)
+       ("nspr" ,nspr)
+       ("libarchive" ,libarchive)
+       ("nettle" ,nettle)            ;XXX: actually a dependency of libarchive
+       ("file" ,file)
+       ("bzip2" ,bzip2)
+       ("zlib" ,zlib)
+       ("cpio" ,cpio)))
+    (home-page "http://www.rpm.org/")
+    (synopsis "The RPM Package Manager")
+    (description
+     "The RPM Package Manager (RPM) is a command-line driven package
+management system capable of installing, uninstalling, verifying, querying,
+and updating computer software packages.  Each software package consists of an
+archive of files along with information about the package like its version, a
+description.  There is also a library permitting developers to manage such
+transactions from C or Python.")
+
+    ;; The whole is GPLv2+; librpm itself is dual-licensed LGPLv2+ | GPLv2+.
+    (license gpl2+)))
+
-- 
cgit v1.2.3


From 5e1c936712d824e7ccbb3cbb8ac7ffa375237469 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Mon, 26 Oct 2015 09:58:55 +0100
Subject: gnu: Add python-file.

* gnu/packages/python.scm (python-file, python2-file): New variables.
---
 gnu/packages/python.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 9721343235..23150a3dfe 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -39,6 +39,7 @@ (define-module (gnu packages python)
   #:use-module (gnu packages backup)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages databases)
+  #:use-module (gnu packages file)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gdbm)
   #:use-module (gnu packages gcc)
@@ -5750,3 +5751,29 @@ (define-public python-libarchive-c
 
 (define-public python2-libarchive-c
   (package-with-python2 python-libarchive-c))
+
+(define-public python-file
+  (package
+    (inherit file)
+    (name "python-file")
+    (build-system python-build-system)
+    (arguments
+     '(#:tests? #f                                ;no tests
+       #:phases (modify-phases %standard-phases
+                  (add-before 'build 'change-directory
+                    (lambda _
+                      (chdir "python")
+                      #t))
+                  (add-before 'build 'set-library-file-name
+                    (lambda* (#:key inputs #:allow-other-keys)
+                      (let ((file (assoc-ref inputs "file")))
+                        (substitute* "magic.py"
+                          (("find_library\\('magic'\\)")
+                           (string-append "'" file "/lib/libmagic.so'")))
+                        #t))))))
+    (inputs `(("file" ,file)))
+    (self-native-input? #f)
+    (synopsis "Python bindings to the libmagic file type guesser")))
+
+(define-public python2-file
+  (package-with-python2 python-file))
-- 
cgit v1.2.3


From 7dae1f4301323e5789b93e04786977c87aa8c8da Mon Sep 17 00:00:00 2001
From: Cyrill Schenkel <cyrill.schenkel@gmail.com>
Date: Fri, 23 Oct 2015 16:38:16 +0200
Subject: gnu: Add xcompmgr.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/xorg.scm (xcompmgr): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/xorg.scm | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index b39bbd436f..a891fcc06b 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
+;;; Copyright © 2015 Cyrill Schenkel <cyrill.schenkel@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -5439,3 +5440,44 @@ (define-public perl-x11-protocol
     ;; of the extension modules in the directory Protocol/Ext: see those files
     ;; for details)."
     (license (package-license perl))))
+
+(define-public xcompmgr
+  (package
+    (name "xcompmgr")
+    (version "1.1.7")
+    (source
+     (origin
+       ;; there's no current tarball
+       (method git-fetch)
+       (uri (git-reference
+             (url "http://anongit.freedesktop.org/git/xorg/app/xcompmgr.git")
+             (commit (string-append name "-" version))))
+       (sha256
+        (base32
+         "04swkrm3gk689wrjc418bd3n25w8r20kg1xfbn5j8d7mx1r5gf16"))
+       (file-name (string-append name "-" version))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'autogen
+                              (lambda _
+                                (setenv "NOCONFIGURE" "t")
+                                (zero? (system* "sh" "autogen.sh")))))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("autoconf" ,autoconf)
+       ("automake" ,automake)))
+    (inputs
+     `(("libX11" ,libx11)
+       ("libXext" ,libxext)
+       ("libXcomposite" ,libxcomposite)
+       ("libXfixes" ,libxfixes)
+       ("libXdamage" ,libxdamage)
+       ("libXrender" ,libxrender)))
+    (synopsis "X Compositing manager using RENDER")
+    (description "xcompmgr is a sample compositing manager for X servers
+supporting the XFIXES, DAMAGE, RENDER, and COMPOSITE extensions.  It enables
+basic eye-candy effects.")
+    (home-page "http://cgit.freedesktop.org/xorg/app/xcompmgr/")
+    (license (license:x11-style
+              "http://cgit.freedesktop.org/xorg/app/xcompmgr/tree/COPYING"))))
-- 
cgit v1.2.3


From 7e9b07bdcbe6b5339fdc70d880089282ebc82578 Mon Sep 17 00:00:00 2001
From: Aljosha Papsch <misc@rpapsch.de>
Date: Mon, 26 Oct 2015 22:27:05 +0100
Subject: gnu: Add yapet.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/password-utils.scm (yapet): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/password-utils.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm
index 921ade1030..3cb319aeda 100644
--- a/gnu/packages/password-utils.scm
+++ b/gnu/packages/password-utils.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Steve Sprang <scs@stevesprang.com>
 ;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015 Aljosha Papsch <misc@rpapsch.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -26,6 +27,9 @@ (define-module (gnu packages password-utils)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages guile)
+  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages tls)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages xorg))
@@ -104,3 +108,31 @@ (define-public shroud
 applications, there is xclip integration." )
     (home-page "http://dthompson.us/pages/software/shroud.html")
     (license license:gpl3+)))
+
+(define-public yapet
+  (package
+    (name "yapet")
+    (version "1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://www.guengel.ch/myapps/yapet/downloads/yapet-"
+                                  version
+                                  ".tar.bz2"))
+              (sha256
+               (base32
+                "0ydbnqw6icdh07pnv2w6dhvq501bdfvrklv4xmyr8znca9d753if"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("ncurses" ,ncurses)
+       ("openssl" ,openssl)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (synopsis "Yet Another Password Encryption Tool")
+    (description "YAPET is a text based password manager using the Blowfish
+encryption algorithm.  Because of its small footprint and very few library
+dependencies, it is suited for installing on desktop and server systems alike.
+The text based user interface allows you to run YAPET easily in a Secure Shell
+session.  Two companion utilities enable users to convert CSV files to YAPET
+and vice versa.")
+    (home-page "http://www.guengel.ch/myapps/yapet/")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From 61d5fd03bf2840849b82c7d9ed5eebc313e043b9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 27 Oct 2015 11:12:32 +0100
Subject: gnu: crossmap: Update to 0.2.1.

* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.1.
---
 gnu/packages/bioinformatics.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 48edd56854..4b7e70f072 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -805,15 +805,16 @@ (define-public clustal-omega
 (define-public crossmap
   (package
     (name "crossmap")
-    (version "0.1.6")
+    (version "0.2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "163hi5gjgij6cndxlvbkp5jjwr0k4wbm9im6d2210278q7k9kpnp"))
-              ;; patch has been sent upstream already
+                "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f"))
+              ;; This patch has been sent upstream already and is available
+              ;; for download from Sourceforge, but it has not been merged.
               (patches (list
                         (search-patch "crossmap-allow-system-pysam.patch")))
               (modules '((guix build utils)))
-- 
cgit v1.2.3


From 104c1986ac0c786440ece5d3fe88e9d501ba65e3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 23 Oct 2015 14:16:27 +0200
Subject: gnu: subread: Use SSE optimizations on x86_64 only.

* gnu/packages/bioinformatics.scm (subread)[arguments]: Override CC and
  CCFLAGS conditionally dependent on target system.
---
 gnu/packages/bioinformatics.scm | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4b7e70f072..9765f1a178 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2704,7 +2704,24 @@ (define-public subread
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ;no "check" target
-       #:make-flags '("-f" "Makefile.Linux")
+      ;; The CC and CCFLAGS variables are set to contain a lot of x86_64
+      ;; optimizations by default, so we override these flags such that x86_64
+      ;; flags are only added when the build target is an x86_64 system.
+       #:make-flags
+       (list (let ((system ,(or (%current-target-system)
+                                (%current-system)))
+                   (flags '("-ggdb" "-fomit-frame-pointer"
+                            "-ffast-math" "-funroll-loops"
+                            "-fmessage-length=0"
+                            "-O9" "-Wall" "-DMAKE_FOR_EXON"
+                            "-DMAKE_STANDALONE"
+                            "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\""))
+                   (flags64 '("-mmmx" "-msse" "-msse2" "-msse3")))
+               (if (string-prefix? "x86_64" system)
+                   (string-append "CCFLAGS=" (string-join (append flags flags64)))
+                   (string-append "CCFLAGS=" (string-join flags))))
+             "-f" "Makefile.Linux"
+             "CC=gcc ${CCFLAGS}")
        #:phases
        (alist-cons-after
         'unpack 'enter-dir
-- 
cgit v1.2.3


From 9a9e143b7501eef808159d74932f30948820dfba Mon Sep 17 00:00:00 2001
From: Christopher Allan Webber <cwebber@dustycloud.org>
Date: Mon, 26 Oct 2015 14:04:56 -0500
Subject: gnu: guile-next: Update to 20151025.e5bccb6

* gnu/packages/guile.scm (guile-next): Update to 20151025.e5bccb6.
---
 gnu/packages/guile.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index e778bf0f6e..da75addc94 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -189,15 +189,15 @@ (define-public guile-2.0/fixed
 (define-public guile-next
   (package (inherit guile-2.0)
     (name "guile-next")
-    (version "20150815.00884bb")
+    (version "20151025.e5bccb6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "git://git.sv.gnu.org/guile.git")
-                    (commit "00884bb79fff41fdf5f22f24a74e366a94a14c9b")))
+                    (commit "e5bccb6e5df3485152bc6501e1f36275e09c6352")))
               (sha256
                (base32
-                "0qk8m9aq3i7pzw6npim58xmsvjqfz5kl1pkyb6b43awn2vydydi5"))))
+                "0z7ywryfcargrpz8hdrz6sfs06c2h2y9baqin3mbjvvg96a5bx47"))))
 
     (arguments
      (substitute-keyword-arguments `(;; Tests aren't passing for now.
-- 
cgit v1.2.3


From c364a287ad6ed581af4de457e7d968d815578f39 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 22 Oct 2015 13:02:37 +0200
Subject: gnu: gcj: Run libjava tests.

* gnu/packages/gcc.scm (gcj)[native-inputs]: Add dejagnu.
  [arguments]: Enable tests and set test target to
  "check-target-libjava".
---
 gnu/packages/gcc.scm | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm
index 7e4f18b887..419e2c9cbf 100644
--- a/gnu/packages/gcc.scm
+++ b/gnu/packages/gcc.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2014 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -27,6 +27,7 @@ (define-module (gnu packages gcc)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages texinfo)
+  #:use-module (gnu packages dejagnu)
   #:use-module (gnu packages doxygen)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages docbook)
@@ -460,6 +461,9 @@ (define-public gcj
        ("javac.in" ,javac.in)
        ("ecj-bootstrap" ,ecj-bootstrap)
        ,@(package-inputs gcc)))
+    (native-inputs
+     `(("dejagnu" ,dejagnu)
+       ,@(package-native-inputs gcc)))
     ;; Suppress the separate "lib" output, because otherwise the
     ;; "lib" and "out" outputs would refer to each other, creating
     ;; a cyclic dependency.  <http://debbugs.gnu.org/18101>
@@ -471,7 +475,9 @@ (define-public gcj
                                                 (ice-9 regex)
                                                 (srfi srfi-1)
                                                 (srfi srfi-26))
-                                               ,@(package-arguments gcc))
+                                     #:test-target "check-target-libjava"
+                                     ,@(package-arguments gcc))
+       ((#:tests? _) #t)
        ((#:configure-flags flags)
         `(let ((ecj (assoc-ref %build-inputs "ecj-bootstrap")))
            `("--enable-java-home"
-- 
cgit v1.2.3


From 85d4aeacc49f2793b7d67914fd4086e2d7b2e6f8 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Tue, 27 Oct 2015 20:43:11 +0100
Subject: gnu: Add python-debian.

* gnu/packages/python.scm (python-debian, python2-debian): New
  variables.
---
 gnu/packages/python.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 23150a3dfe..8fc87599fd 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5777,3 +5777,43 @@ (define-public python-file
 
 (define-public python2-file
   (package-with-python2 python-file))
+
+(define-public python-debian
+  (package
+    (name "python-debian")
+    (version "0.1.23")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/source/p/python-debian/python-debian-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "193faznwnjc3n5991wyzim6h9gyq1zxifmfrnpm3avgkh7ahyynh"))))
+    (build-system python-build-system)
+    (inputs
+     `(("python-six" ,python-six)))
+    (native-inputs
+     `(("python-setuptools" ,python-setuptools)))
+    (home-page "http://packages.debian.org/sid/python-debian")
+    (synopsis "Debian package related modules")
+    (description
+     "This package provides Python modules that abstract many formats of
+Debian-related files, such as:
+
+@itemize
+@item Debtags information;
+@item @file{debian/changelog} files;
+@item packages files, pdiffs;
+@item control files of single or multiple RFC822-style paragraphs---e.g.
+   @file{debian/control}, @file{.changes}, @file{.dsc};
+@item Raw @file{.deb} and @file{.ar} files, with (read-only) access to
+   contained files and meta-information.
+@end itemize\n")
+
+    ;; Modules are either GPLv2+ or GPLv3+.
+    (license gpl3+)))
+
+(define-public python2-debian
+  (package-with-python2 python-debian))
-- 
cgit v1.2.3


From 816a653884558feab29ccf470c972262708309f9 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Tue, 27 Oct 2015 20:53:48 +0100
Subject: gnu: Add python-chardet.

* gnu/packages/python.scm (python-chardet, python2-chardet): New
  variables.
---
 gnu/packages/python.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 8fc87599fd..45fd417e86 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5817,3 +5817,30 @@ (define-public python-debian
 
 (define-public python2-debian
   (package-with-python2 python-debian))
+
+(define-public python-chardet
+  (package
+    (name "python-chardet")
+    (version "2.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/source/c/chardet/chardet-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "1ak87ikcw34fivcgiz2xvi938dmclh078az65l9x3rmgljrkhgp5"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-setuptools" ,python-setuptools)))
+    (home-page "https://github.com/chardet/chardet")
+    (synopsis "Universal encoding detector for Python 2 and 3")
+    (description
+     "This package provides @code{chardet}, a Python module that can
+automatically detect a wide range of file encodings.")
+    (license lgpl2.1+)))
+
+(define-public python2-chardet
+  (package-with-python2 python-chardet))
-- 
cgit v1.2.3


From 08dcff47445b4029f7f4b4a42750b29a2a184131 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Tue, 27 Oct 2015 21:01:55 +0100
Subject: gnu: Add Diffoscope.

* gnu/packages/package-management.scm (diffoscope): New variable.
---
 gnu/packages/package-management.scm | 54 +++++++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 4e69d6de59..65464f7691 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -356,3 +356,57 @@ (define-public rpm
     ;; The whole is GPLv2+; librpm itself is dual-licensed LGPLv2+ | GPLv2+.
     (license gpl2+)))
 
+(define-public diffoscope
+  (package
+    (name "diffoscope")
+    (version "34")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url
+                     "https://anonscm.debian.org/cgit/reproducible/diffoscope.git")
+                    (commit version)))
+              (sha256
+               (base32
+                "1g8b7bpkmns0355gkr3a244affwx4xzqwahwsl6ivw4z0qv7dih8"))
+              (file-name (string-append name "-" version "-checkout"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:phases (modify-phases %standard-phases
+                  (add-before 'build 'disable-egg-zipping
+                    (lambda _
+                      ;; Leave the .egg file uncompressed.
+                      (let ((port (open-file "setup.cfg" "a")))
+                        (display "\n[easy_install]\nzip_ok = 0\n"
+                                 port)
+                        (close-port port)
+                        #t)))
+                  (add-before 'build 'dependency-on-rpm
+                    (lambda _
+                      (substitute* "setup.py"
+                        ;; Somehow this requirement is reported as not met,
+                        ;; even though rpm.py is in the search path.  So
+                        ;; delete it.
+                        (("'rpm-python',") ""))
+                      #t)))
+       ;; FIXME: Some obscure test failures.
+       #:tests? #f))
+    (inputs `(("rpm" ,rpm)                        ;for rpm-python
+              ("python-file" ,python2-file)
+              ("python-debian" ,python2-debian)
+              ("python-libarchive-c" ,python2-libarchive-c)
+              ("python-tlsh" ,python2-tlsh)
+
+              ;; Below are modules used for tests.
+              ("python-pytest" ,python2-pytest)
+              ("python-chardet" ,python2-chardet)))
+    (native-inputs `(("python-setuptools" ,python2-setuptools)))
+    (home-page "http://diffoscope.org/")
+    (synopsis "Compare files, archives, and directories in depth")
+    (description
+     "Diffoscope tries to get to the bottom of what makes files or directories
+different.  It recursively unpacks archives of many kinds and transforms
+various binary formats into more human readable forms to compare them.  It can
+compare two tarballs, ISO images, or PDFs just as easily.")
+    (license gpl3+)))
-- 
cgit v1.2.3


From b1b9e5c8d243d37efc07568a9b96e061cf24c264 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Tue, 27 Oct 2015 20:19:01 -0400
Subject: gnu: linux-libre: Update to 4.2.5.

* gnu/packages/linux.scm (linux-libre): Update to 4.2.5.
---
 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 f6f2555b1c..790a500ba8 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -210,7 +210,7 @@ (define (lookup file)
      #f)))
 
 (define-public linux-libre
-  (let* ((version "4.2.4")
+  (let* ((version "4.2.5")
          (build-phase
           '(lambda* (#:key system inputs #:allow-other-keys #:rest args)
              ;; Apply the neat patch.
@@ -283,7 +283,7 @@ (define-public linux-libre
              (uri (linux-libre-urls version))
              (sha256
               (base32
-               "11r9yhi4c2zwfb8i21zk014gcm1kvnabq410wjy6g6a015d5v37w"))))
+               "13ar9sghm2g5w2km9x2d07q3lh81rz286d6slklv56qanm24chzx"))))
     (build-system gnu-build-system)
     (native-inputs `(("perl" ,perl)
                      ("bc" ,bc)
-- 
cgit v1.2.3


From 6c8d70b0b69bb842b7b5ddd8e6f354962b0a3b29 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sun, 23 Aug 2015 13:47:13 -0400
Subject: gnu: linux-libre: Add 'supported-systems' field: Intel only for now.

* gnu/packages/linux.scm (linux-libre)[supported-systems]: New field.
---
 gnu/packages/linux.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 790a500ba8..8b7fe35309 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -285,6 +285,7 @@ (define-public linux-libre
               (base32
                "13ar9sghm2g5w2km9x2d07q3lh81rz286d6slklv56qanm24chzx"))))
     (build-system gnu-build-system)
+    (supported-systems '("x86_64-linux" "i686-linux"))
     (native-inputs `(("perl" ,perl)
                      ("bc" ,bc)
                      ("module-init-tools" ,module-init-tools)
-- 
cgit v1.2.3


From 726029b2bac3584d7d13e577d7321ed84c80aebd Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 6 Aug 2015 18:15:51 -0400
Subject: gnu: linux-libre: Add case for ARCH=mips.

* gnu/packages/linux.scm (linux-libre)[build-phase]: When setting ARCH, add a
  case for MIPS.
---
 gnu/packages/linux.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 8b7fe35309..d66fac5ceb 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -220,6 +220,7 @@ (define-public linux-libre
              (let ((arch (car (string-split system #\-))))
                (setenv "ARCH"
                        (cond ((string=? arch "i686") "i386")
+                             ((string=? arch "mips64el") "mips")
                              (else arch)))
                (format #t "`ARCH' set to `~a'~%" (getenv "ARCH")))
 
-- 
cgit v1.2.3


From 44a88ce49e6a6a4595a9ea6e02ea59be89614eae Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sun, 23 Aug 2015 22:54:59 -0400
Subject: gnu: linux-libre: On MIPS, the linux image name is vmlinuz, not
 bzImage.

* gnu/packages/linux.scm (linux-libre)[install-phase]: Add vmlinuz to the list
  of file names to be copied.
---
 gnu/packages/linux.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index d66fac5ceb..24fed02dca 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -267,7 +267,7 @@ (define-public linux-libre
                (for-each (lambda (file)
                            (copy-file file
                                       (string-append out "/" (basename file))))
-                         (find-files "." "^(bzImage|System\\.map)$"))
+                         (find-files "." "^(bzImage|vmlinuz|System\\.map)$"))
                (copy-file ".config" (string-append out "/config"))
                (zero? (system* "make"
                                (string-append "DEPMOD=" mit "/sbin/depmod")
-- 
cgit v1.2.3


From 04e0eac1ed80c0ecba5a21658e951959b5e3a059 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 15 Aug 2015 01:22:06 -0400
Subject: gnu: grub: Use modify-phases and other minor cleanups.

* gnu/packages/grub.scm (grub)[arguments]: Use modify-phases.  Return #t from
  'patch-stuff' phase.  Add 'patch-stuff' phase after 'unpack' instead of
  before 'patch-source-shebangs'.
  [inputs]: Add comment noting that 'fuse' would be a desirable input.
---
 gnu/packages/grub.scm | 28 ++++++++++++++++------------
 1 file changed, 16 insertions(+), 12 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/grub.scm b/gnu/packages/grub.scm
index b1da394835..4a7dca8945 100644
--- a/gnu/packages/grub.scm
+++ b/gnu/packages/grub.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -84,25 +85,28 @@ (define-public grub
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--disable-werror")
-       #:phases (alist-cons-before
-                 'patch-source-shebangs 'patch-stuff
-                 (lambda* (#:key inputs #:allow-other-keys)
-                   (substitute* "grub-core/Makefile.in"
-                     (("/bin/sh") (which "sh")))
+       #:phases (modify-phases %standard-phases
+                  (add-after
+                   'unpack 'patch-stuff
+                   (lambda* (#:key inputs #:allow-other-keys)
+                     (substitute* "grub-core/Makefile.in"
+                       (("/bin/sh") (which "sh")))
 
-                   ;; Make the font visible.
-                   (copy-file (assoc-ref inputs "unifont") "unifont.bdf.gz")
-                   (system* "gunzip" "unifont.bdf.gz")
+                     ;; Make the font visible.
+                     (copy-file (assoc-ref inputs "unifont") "unifont.bdf.gz")
+                     (system* "gunzip" "unifont.bdf.gz")
 
-                   ;; TODO: Re-enable this test when we have Parted.
-                   (substitute* "tests/partmap_test.in"
-                     (("set -e") "exit 77")))
-                 %standard-phases)))
+                     ;; TODO: Re-enable this test when we have Parted.
+                     (substitute* "tests/partmap_test.in"
+                       (("set -e") "exit 77"))
+
+                     #t)))))
     (inputs
      `(;; ("lvm2" ,lvm2)
        ("gettext" ,gnu-gettext)
        ("freetype" ,freetype)
        ;; ("libusb" ,libusb)
+       ;; ("fuse" ,fuse)
        ("ncurses" ,ncurses)))
     (native-inputs
      `(("unifont" ,unifont)
-- 
cgit v1.2.3


From 58301666dd3e372ee05aa23e4043781c8d24be97 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 19 Aug 2015 13:57:30 -0400
Subject: gnu: grub: Install documentation.

* gnu/packages/grub.scm (grub)[native-inputs]: Add help2man and texinfo.
---
 gnu/packages/grub.scm | 4 ++++
 1 file changed, 4 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/grub.scm b/gnu/packages/grub.scm
index 4a7dca8945..7875a64186 100644
--- a/gnu/packages/grub.scm
+++ b/gnu/packages/grub.scm
@@ -29,6 +29,8 @@ (define-module (gnu packages grub)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages qemu)
+  #:use-module (gnu packages man)
+  #:use-module (gnu packages texinfo)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages cdrom)
   #:use-module (srfi srfi-1))
@@ -112,6 +114,8 @@ (define-public grub
      `(("unifont" ,unifont)
        ("bison" ,bison)
        ("flex" ,flex)
+       ("texinfo" ,texinfo)
+       ("help2man" ,help2man)
 
        ;; Dependencies for the test suite.  The "real" QEMU is needed here,
        ;; because several targets are used.
-- 
cgit v1.2.3


From 5c7bdc9a7fb2ed4f963dbacc7c1bee8cc9223303 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Wed, 28 Oct 2015 11:59:42 +0100
Subject: gnu: python-debian: Avoid @itemize in description.

* gnu/packages/python.scm (python-debian): Use @enumerate instead of
  @itemize.
---
 gnu/packages/python.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 45fd417e86..08f0146641 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5799,10 +5799,12 @@ (define-public python-debian
     (home-page "http://packages.debian.org/sid/python-debian")
     (synopsis "Debian package related modules")
     (description
+     ;; XXX: Use @enumerate instead of @itemize to work around
+     ;; <http://bugs.gnu.org/21772>.
      "This package provides Python modules that abstract many formats of
 Debian-related files, such as:
 
-@itemize
+@enumerate
 @item Debtags information;
 @item @file{debian/changelog} files;
 @item packages files, pdiffs;
@@ -5810,7 +5812,7 @@ (define-public python-debian
    @file{debian/control}, @file{.changes}, @file{.dsc};
 @item Raw @file{.deb} and @file{.ar} files, with (read-only) access to
    contained files and meta-information.
-@end itemize\n")
+@end enumerate\n")
 
     ;; Modules are either GPLv2+ or GPLv3+.
     (license gpl3+)))
-- 
cgit v1.2.3


From fb8d1be8e125722226fe3d2ae7dedb6ba7015290 Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Wed, 28 Oct 2015 15:56:22 +0100
Subject: gnu: pari-gp: Add X11 input.

* gnu/packages/algebra.scm (pari-gp)[inputs]: Add libx11, which enables
  plotting functions.
---
 gnu/packages/algebra.scm | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 2f52f5545c..daa5ddd072 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -26,6 +26,7 @@ (define-module (gnu packages algebra)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages flex)
+  #:use-module (gnu packages xorg)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
@@ -125,6 +126,7 @@ (define-public pari-gp
                 "0k1qqagfl6zn7gvwmsqffj6g9yrzqvszwh2mblhmxpjlw1pigfh8"))))
    (build-system gnu-build-system)
    (inputs `(("gmp" ,gmp)
+             ("libx11" ,libx11)
              ("perl" ,perl)
              ("readline" ,readline)))
    (arguments
-- 
cgit v1.2.3


From 9a067efdb2076293e505c29a51a9819ff025b056 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 28 Oct 2015 14:39:13 +0100
Subject: gnu: pbtranscript-tofu: Update to 2.2.3.

* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Update to 2.2.3.
  [source]: Remove bundled Cython sources in a snippet.  Replace
  ".tar.gz" extension in file-name field with "-checkout".
  [arguments]: Replace "enter-directory-and-clean-up" phase with
  "enter-directory" phase, and add "patch-setuppy" phase.
  [inputs]: Add python2-h5py.  Move python2-cython ...
  [native-inputs]: ... to this field.
---
 gnu/packages/bioinformatics.scm | 55 +++++++++++++++++++++--------------------
 1 file changed, 28 insertions(+), 27 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9765f1a178..fdb42562e8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1839,19 +1839,25 @@ (define-public python2-warpedlmm
     (license license:asl2.0)))
 
 (define-public pbtranscript-tofu
-  (let ((commit "c7bbd5472"))
+  (let ((commit "8f5467fe6"))
     (package
       (name "pbtranscript-tofu")
-      (version (string-append "0.4.1." commit))
+      (version (string-append "2.2.3." commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
                       (url "https://github.com/PacificBiosciences/cDNA_primer.git")
                       (commit commit)))
-                (file-name (string-append name "-" version ".tar.gz"))
+                (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "148xkzi689c49g6fdhckp6mnmj2qhjdf1j4wifm6ja7ij95d7fxx"))))
+                  "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f"))
+                (modules '((guix build utils)))
+                (snippet
+                 '(begin
+                    ;; remove bundled Cython sources
+                    (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz")
+                    #t))))
       (build-system python-build-system)
       (arguments
        `(#:python ,python-2
@@ -1861,34 +1867,29 @@ (define-public pbtranscript-tofu
          #:configure-flags '("--single-version-externally-managed"
                              "--record=pbtranscript-tofu.txt")
          #:phases
-         (alist-cons-after
-          'unpack 'enter-directory-and-clean-up
-          (lambda _
-            (chdir "pbtranscript-tofu/pbtranscript/")
-            ;; Delete clutter
-            (delete-file-recursively "dist/")
-            (delete-file-recursively "build/")
-            (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/")
-            (delete-file-recursively "pbtools.pbtranscript.egg-info")
-            (delete-file "Cython-0.20.1.tar.gz")
-            (delete-file "setuptools_cython-0.2.1-py2.7.egg")
-            (delete-file "setuptools_cython-0.2.1.tar.gz")
-            (delete-file "setup.cfg")
-            (for-each delete-file
-                      (find-files "." "\\.so$"))
-            ;; files should be writable for install phase
-            (for-each (lambda (f) (chmod f #o755))
-                      (find-files "." "\\.py$")))
-          %standard-phases)))
+         (modify-phases %standard-phases
+           (add-after 'unpack 'enter-directory
+            (lambda _
+              (chdir "pbtranscript-tofu/pbtranscript/")
+              #t))
+           ;; With setuptools version 18.0 and later this setup.py hack causes
+           ;; a build error, so we disable it.
+           (add-after 'enter-directory 'patch-setuppy
+            (lambda _
+              (substitute* "setup.py"
+                (("if 'setuptools.extension' in sys.modules:")
+                 "if False:"))
+              #t)))))
       (inputs
-       `(("python-cython" ,python2-cython)
-         ("python-numpy" ,python2-numpy)
+       `(("python-numpy" ,python2-numpy)
          ("python-bx-python" ,python2-bx-python)
          ("python-networkx" ,python2-networkx)
          ("python-scipy" ,python2-scipy)
-         ("python-pbcore" ,python2-pbcore)))
+         ("python-pbcore" ,python2-pbcore)
+         ("python-h5py" ,python2-h5py)))
       (native-inputs
-       `(("python-nose" ,python2-nose)
+       `(("python-cython" ,python2-cython)
+         ("python-nose" ,python2-nose)
          ("python-setuptools" ,python2-setuptools)))
       (home-page "https://github.com/PacificBiosciences/cDNA_primer")
       (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
-- 
cgit v1.2.3


From 1fda9b1f46fb5fabbc08153b2fdf19c31f873e6c Mon Sep 17 00:00:00 2001
From: Alex Kost <alezost@gmail.com>
Date: Thu, 29 Oct 2015 00:07:20 +0300
Subject: gnu: magit: Update to 2.3.0.

* gnu/packages/emacs.scm (magit): Update to 2.3.0.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 6416b00ee0..ae6d0db612 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -316,7 +316,7 @@ (define-public git-modes
 (define-public magit
   (package
     (name "magit")
-    (version "2.2.2")
+    (version "2.3.0")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -324,7 +324,7 @@ (define-public magit
                    version "/" name "-" version ".tar.gz"))
              (sha256
               (base32
-               "1imkj4prprnivhbpdn1mdpiryxkckzy5hbnqaahv7gixwac1irh8"))))
+               "0bi0vqp9802f00vnii3x80iqycji20bw4pjysy6al0d86mkggjx5"))))
     (build-system gnu-build-system)
     (native-inputs `(("texinfo" ,texinfo)
                      ("emacs" ,emacs-no-x)))
-- 
cgit v1.2.3


From b7f16845c837e8f640b20df6c9cdeb11690df2f8 Mon Sep 17 00:00:00 2001
From: Alex Kost <alezost@gmail.com>
Date: Thu, 29 Oct 2015 00:08:03 +0300
Subject: gnu: magit-svn: Update to 2.1.1.

* gnu/packages/emacs.scm (magit-svn): Update to 2.1.1.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index ae6d0db612..f8be743ce5 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -372,7 +372,7 @@ (define-public magit
 (define-public magit-svn
   (package
     (name "magit-svn")
-    (version "2.1.0")
+    (version "2.1.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -381,7 +381,7 @@ (define-public magit-svn
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "09sz93g7x7g9q75jsw8bdh7yr4jr1igfb4fpg5i302a7l2ahxfr8"))))
+                "04y88j7q9h8xjbx5dbick6n5nr1522sn9i1znp0qwk3vjb4b5mzz"))))
     (build-system trivial-build-system)
     (native-inputs `(("emacs" ,emacs-no-x)
                      ("tar" ,tar)
-- 
cgit v1.2.3


From a0d3eff99c956847e092450a7e6b874313c69c82 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 28 Oct 2015 23:55:27 +0200
Subject: gnu: bluez: Update to 5.35.

* gnu/packages/linux.scm (bluez): Update to 5.35.
---
 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 24fed02dca..9b0af0d507 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -2357,7 +2357,7 @@ (define-public libaio
 (define-public bluez
   (package
     (name "bluez")
-    (version "5.30")
+    (version "5.35")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2365,7 +2365,7 @@ (define-public bluez
                     version ".tar.xz"))
               (sha256
                (base32
-                "0b1qbnq1xzcdw5rajg9yyg31bf21jnff0n6gnf1snz89bbdllfhy"))))
+                "1qphz25hganfnd5ipfscbj7s70anv5favmwqmi9ig2saciaf1zhs"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags
-- 
cgit v1.2.3


From dd169b73e0104738e2be5fee4ded6143beeca044 Mon Sep 17 00:00:00 2001
From: Paul van der Walt <paul@denknerd.org>
Date: Thu, 29 Oct 2015 11:08:05 +0100
Subject: gnu: ghc-glut: Propagate freeglut input.

* gnu/packages/haskell.scm (ghc-glut): Move freeglut to
  propagated-inputs.
---
 gnu/packages/haskell.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 652efc3fbd..b9387f8d43 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1009,10 +1009,10 @@ (define-public ghc-glut
     (build-system haskell-build-system)
     (propagated-inputs
      `(("ghc-statevar" ,ghc-statevar)
-       ("ghc-openglraw" ,ghc-openglraw)))
-    (inputs
-     `(("ghc-opengl" ,ghc-opengl)
+       ("ghc-openglraw" ,ghc-openglraw)
        ("freeglut" ,freeglut)))
+    (inputs
+     `(("ghc-opengl" ,ghc-opengl)))
     (home-page "http://www.haskell.org/haskellwiki/Opengl")
     (synopsis "Haskell bindings for the OpenGL Utility Toolkit")
     (description "This library provides Haskell bindings for the OpenGL
-- 
cgit v1.2.3


From 8a3a9e84cbe0b46b6ae933136210115206ab6846 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 29 Oct 2015 14:51:23 +0100
Subject: gnu: icedtea7: Update to 2.6.2.

* gnu/packages/java.scm (icedtea7): Update to 2.6.2.
---
 gnu/packages/java.scm | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 5fa546a98c..6d3446055a 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -576,7 +576,7 @@ (define-public icedtea6
     (license license:gpl2+)))
 
 (define-public icedtea7
-  (let* ((version "2.6.1")
+  (let* ((version "2.6.2")
          (drop (lambda (name hash)
                  (origin
                    (method url-fetch)
@@ -594,7 +594,7 @@ (define-public icedtea7
                       version ".tar.xz"))
                 (sha256
                  (base32
-                  "0s107vi1530a5dyxacysc4m64zshgg2d3xpndsc0ws99wz0zmr6c"))
+                  "0xi0w8gpxx3r68hyi7fb991hxb3rqfp7895nfsl4wj3sa1f5ds5y"))
                 (modules '((guix build utils)))
                 (snippet
                  '(substitute* "Makefile.in"
@@ -728,24 +728,24 @@ (define-public icedtea7
       (native-inputs
        `(("openjdk-drop"
           ,(drop "openjdk"
-                 "0gs6vbj5c09516r460r68i7vm652sb25h973kq9hfx749qbs0s01"))
+                 "0jabxc8iw7ciz6f2qshcpla66qniy686vnxnfx3h2yw7syvas4a9"))
          ("corba-drop"
           ,(drop "corba"
-                 "1y7nf6hqry1az28i3b6ln5cs82cww1jj4r61jk54ab8s2xydj0yd"))
+                 "1bw22djg8mfqqn8kp8mpbj9vi4pl8dk67qwwrny67d0fvirixylj"))
          ("jaxp-drop"
           ,(drop "jaxp"
-                 "1szs2w0p496k1qi3yl1fymj0g10lgq31am35zlalcz7pi4l4q360"))
+                 "1h3g2dwbj8ihicl73qbr4cvvc3i5bs5ckrpja1nx6g5b56xa7kcl"))
          ("jaxws-drop"
           ,(drop "jaxws"
-                 "17xfy9q2zdpap7m2prbf937x55jm3pwrqpp1fdlridraqrfzjprd"))
+                 "1m1h7455qn4pdhb5yamdl9965iz9260lzwl3njcs35vi14v7fihl"))
          ("jdk-drop"
           ,(drop "jdk"
-                 "0qskhwr4nml49zhbppnq8ldj0x001bl37mrcpxslbnsdw5skw258"))
+                 "1wcaxf2chnlpk34q04c23im6z32dy8fr6f9giz3ih65nyvah3n3s"))
          ("langtools-drop"
           ,(drop "langtools"
-                 "0hyxrrb0zrx1pq1s90bmim94hwfligr0ajzs1874da4gclbbvfbd"))
+                 "0da3cmm8nwz7dk2sqnywvidaa0kjnyzzi33p2lkdi4415f8yhgx5"))
          ("hotspot-drop"
           ,(drop "hotspot"
-                 "1cv8df2s89mnjzg4rja4i89d4fr8n0c3v5y2cqbww1ma1463n100"))
+                 "0fn3cjhqsgbkfzychkvvw6whxil2n9dr6q0196ywxzkinny1hjcq"))
          ,@(fold alist-delete (package-native-inputs icedtea6)
                  '("openjdk6-src")))))))
-- 
cgit v1.2.3


From 69851c59c7445229f798e5ea0ca918989e6772d7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 29 Oct 2015 15:41:31 +0100
Subject: gnu: openblas: Update to 0.2.15.

* gnu/packages/maths.scm (openblas): Update to 0.2.15.
---
 gnu/packages/maths.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 5fa37d1535..4935f8019f 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1461,7 +1461,7 @@ (define-public muparser
 (define-public openblas
   (package
     (name "openblas")
-    (version "0.2.14")
+    (version "0.2.15")
     (source
      (origin
        (method url-fetch)
@@ -1470,7 +1470,7 @@ (define-public openblas
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0av3pd96j8rx5i65f652xv9wqfkaqn0w4ma1gvbyz73i6j2hi9db"))))
+         "1k5f6vjlk54qlplk5m7xkbaw6g2y7dl50lwwdv6xsbcsgsbxfcpy"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f  ;no "check" target
-- 
cgit v1.2.3


From b416aadf7455470b702a557f4f475b04198ce698 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Thu, 29 Oct 2015 16:48:32 +0100
Subject: gnu: Move gdbm to (gnu packages databases).

* gnu/packages/gdbm.scm: Remove.
* gnu/packages/databases.scm (gdbm): New variable, from gdbm.scm.
* gnu/packages/avahi.scm, gnu/packages/cyrus-sasl.scm,
  gnu/packages/guile.scm, gnu/packages/mail.scm,
  gnu/packages/man.scm, gnu/packages/pulseaudio.scm,
  gnu/packages/python.scm, gnu/packages/ruby.scm,
  gnu/packages/sawfish.scm: Adjust accordingly.
* gnu-system.am (GNU_SYSTEM_MODULES): Remove gdbm.scm.
---
 gnu-system.am               |  1 -
 gnu/packages/avahi.scm      |  2 +-
 gnu/packages/cyrus-sasl.scm |  4 ++--
 gnu/packages/databases.scm  | 22 ++++++++++++++++++++++
 gnu/packages/gdbm.scm       | 46 ---------------------------------------------
 gnu/packages/guile.scm      |  2 +-
 gnu/packages/mail.scm       |  2 --
 gnu/packages/man.scm        |  2 +-
 gnu/packages/pulseaudio.scm |  2 +-
 gnu/packages/python.scm     |  1 -
 gnu/packages/ruby.scm       |  3 +--
 gnu/packages/sawfish.scm    |  2 +-
 12 files changed, 30 insertions(+), 59 deletions(-)
 delete mode 100644 gnu/packages/gdbm.scm

(limited to 'gnu/packages')

diff --git a/gnu-system.am b/gnu-system.am
index 3e976e9fb7..d8430b4732 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -121,7 +121,6 @@ GNU_SYSTEM_MODULES =				\
   gnu/packages/gcc.scm				\
   gnu/packages/gd.scm				\
   gnu/packages/gdb.scm				\
-  gnu/packages/gdbm.scm				\
   gnu/packages/geeqie.scm			\
   gnu/packages/gettext.scm			\
   gnu/packages/ghostscript.scm			\
diff --git a/gnu/packages/avahi.scm b/gnu/packages/avahi.scm
index b6eef1a6ad..2d480192af 100644
--- a/gnu/packages/avahi.scm
+++ b/gnu/packages/avahi.scm
@@ -23,7 +23,7 @@ (define-module (gnu packages avahi)
   #:use-module (guix download)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages)
-  #:use-module (gnu packages gdbm)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages libdaemon)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages glib)
diff --git a/gnu/packages/cyrus-sasl.scm b/gnu/packages/cyrus-sasl.scm
index cd0f1bb401..8f3e1a1b70 100644
--- a/gnu/packages/cyrus-sasl.scm
+++ b/gnu/packages/cyrus-sasl.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -19,7 +19,7 @@
 
 (define-module (gnu packages cyrus-sasl)
   #:use-module (gnu packages)
-  #:use-module (gnu packages gdbm)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages mit-krb5)
   #:use-module (gnu packages tls)
   #:use-module ((guix licenses) #:prefix license:)
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index a17424196a..51e2a3e058 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -53,6 +53,28 @@ (define-module (gnu packages databases)
   #:use-module (srfi srfi-26)
   #:use-module (ice-9 match))
 
+(define-public gdbm
+  (package
+    (name "gdbm")
+    (version "1.11")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://gnu/gdbm/gdbm-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1hz3jgh3pd4qzp6jy0l8pd8x01g9abw7csnrlnj1a2sxy122z4cd"))))
+    (arguments `(#:configure-flags '("--enable-libgdbm-compat")))
+    (build-system gnu-build-system)
+    (home-page "http://www.gnu.org/software/gdbm/")
+    (synopsis
+     "Hash library of database functions compatible with traditional dbm")
+    (description
+     "GDBM is a library for manipulating hashed databases.  It is used to
+store key/value pairs in a file in a manner similar to the Unix dbm library
+and provides interfaces to the traditional file format.")
+    (license gpl3+)))
+
 (define-public bdb
   (package
     (name "bdb")
diff --git a/gnu/packages/gdbm.scm b/gnu/packages/gdbm.scm
deleted file mode 100644
index 62d02001c8..0000000000
--- a/gnu/packages/gdbm.scm
+++ /dev/null
@@ -1,46 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012 Ludovic Courtès <ludo@gnu.org>
-;;;
-;;; 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 gdbm)
-  #:use-module (guix licenses)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module (guix build-system gnu))
-
-(define-public gdbm
-  (package
-    (name "gdbm")
-    (version "1.11")
-    (source
-     (origin
-      (method url-fetch)
-      (uri (string-append "mirror://gnu/gdbm/gdbm-"
-                          version ".tar.gz"))
-      (sha256
-       (base32
-        "1hz3jgh3pd4qzp6jy0l8pd8x01g9abw7csnrlnj1a2sxy122z4cd"))))
-    (arguments `(#:configure-flags '("--enable-libgdbm-compat")))
-    (build-system gnu-build-system)
-    (home-page "http://www.gnu.org/software/gdbm/")
-    (synopsis
-     "Hash library of database functions compatible with traditional dbm")
-    (description
-     "GDBM is a library for manipulating hashed databases.  It is used to
-store key/value pairs in a file in a manner similar to the Unix dbm library
-and provides interfaces to the traditional file format.")
-    (license gpl3+)))
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index da75addc94..ac9e9c7b42 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -38,7 +38,7 @@ (define-module (gnu packages guile)
   #:use-module (gnu packages base)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages gettext)
-  #:use-module (gnu packages gdbm)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages python)
   #:use-module (guix packages)
   #:use-module (guix download)
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 25407b835a..699b8802b7 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -36,7 +36,6 @@ (define-module (gnu packages mail)
   #:use-module (gnu packages dejagnu)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages enchant)
-  #:use-module (gnu packages gdbm)
   #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
@@ -48,7 +47,6 @@ (define-module (gnu packages mail)
   #:use-module (gnu packages libidn)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages m4)
-  #:use-module (gnu packages databases)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages perl)
diff --git a/gnu/packages/man.scm b/gnu/packages/man.scm
index 46b7d8b9b0..3298268d28 100644
--- a/gnu/packages/man.scm
+++ b/gnu/packages/man.scm
@@ -24,9 +24,9 @@ (define-module (gnu packages man)
   #:use-module (guix download)
   #:use-module (guix packages)
   #:use-module (guix build-system gnu)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages gawk)
-  #:use-module (gnu packages gdbm)
   #:use-module (gnu packages groff)
   #:use-module (gnu packages less)
   #:use-module (gnu packages lynx)
diff --git a/gnu/packages/pulseaudio.scm b/gnu/packages/pulseaudio.scm
index d832228278..27b269afc2 100644
--- a/gnu/packages/pulseaudio.scm
+++ b/gnu/packages/pulseaudio.scm
@@ -27,7 +27,7 @@ (define-module (gnu packages pulseaudio)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages avahi)
   #:use-module (gnu packages check)
-  #:use-module (gnu packages gdbm)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages libcanberra)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 08f0146641..24a342b8d5 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -41,7 +41,6 @@ (define-module (gnu packages python)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages file)
   #:use-module (gnu packages fontutils)
-  #:use-module (gnu packages gdbm)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages glib)
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 701b7ee6ef..8bf85233ea 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015 Pjotr Prins <pjotr.guix@thebird.nl>
-;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014, 2015 David Thompson <davet@gnu.org>
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
@@ -30,7 +30,6 @@ (define-module (gnu packages ruby)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages java)
   #:use-module (gnu packages libffi)
-  #:use-module (gnu packages gdbm)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages version-control)
   #:use-module (guix packages)
diff --git a/gnu/packages/sawfish.scm b/gnu/packages/sawfish.scm
index e2cb62c62c..9b09b6171e 100644
--- a/gnu/packages/sawfish.scm
+++ b/gnu/packages/sawfish.scm
@@ -22,7 +22,7 @@ (define-module (gnu packages sawfish)
   #:use-module (guix download)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages)
-  #:use-module (gnu packages gdbm)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages libffi)
-- 
cgit v1.2.3


From 362f496da9fc929d9548b8a56990779718b13c95 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Thu, 29 Oct 2015 17:07:08 +0100
Subject: gnu: Add libchop.

* gnu/packages/backup.scm (libchop): New variable.
---
 gnu/packages/backup.scm | 44 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 99a10e1c7f..40cfc4ee14 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -30,9 +30,12 @@ (define-module (gnu packages backup)
   #:use-module (gnu packages acl)
   #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages dejagnu)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnupg)
+  #:use-module (gnu packages gperf)
+  #:use-module (gnu packages guile)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages mcrypt)
   #:use-module (gnu packages nettle)
@@ -353,3 +356,44 @@ (define-public attic
 changes are stored.")
     (home-page "https://attic-backup.org/")
     (license license:bsd-3)))
+
+(define-public libchop
+  (package
+    (name "libchop")
+    (version "0.5.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://savannah/libchop/libchop-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "0fpdyxww41ba52d98blvnf543xvirq1v9xz1i3x1gm9lzlzpmc2g"))
+              (patches
+               (list (search-patch "diffutils-gets-undeclared.patch")))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("guile" ,guile-2.0)
+       ("gperf" ,gperf)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("guile" ,guile-2.0)
+       ("util-linux" ,util-linux)
+       ("gnutls" ,gnutls)
+       ("tdb" ,tdb)
+       ("bdb" ,bdb)
+       ("gdbm" ,gdbm)
+       ("libgcrypt" ,libgcrypt)
+       ("lzo" ,lzo)
+       ("bzip2" ,bzip2)
+       ("zlib" ,zlib)))
+    (home-page "http://nongnu.org/libchop/")
+    (synopsis "Tools & library for data backup and distributed storage")
+    (description
+     "Libchop is a set of utilities and library for data backup and
+distributed storage.  Its main application is @command{chop-backup}, an
+encrypted backup program that supports data integrity checks, versioning,
+distribution among several sites, selective sharing of stored data, adaptive
+compression, and more.  The library itself implements storage techniques such
+as content-addressable storage, content hash keys, Merkle trees, similarity
+detection, and lossless compression.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From 12f92e38d7b7add735b0cfe9a09a27c99d6f9977 Mon Sep 17 00:00:00 2001
From: Andy Patterson <ajpatter@uwaterloo.ca>
Date: Wed, 28 Oct 2015 22:42:42 -0400
Subject: gnu: ffmpeg: Move flags into their own argument.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/video.scm (ffmpeg)[arguments]: Move the configurable
  configure flag literals into the configure-flags argument. Call
  configure with these flags from the configure phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/video.scm | 168 ++++++++++++++++++++++++++-----------------------
 1 file changed, 91 insertions(+), 77 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index d22975afd9..554a2eaab2 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015 Andy Patterson <ajpatter@uwaterloo.ca>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -412,6 +413,89 @@ (define-public ffmpeg
        ("yasm" ,yasm)))
     (arguments
      `(#:test-target "fate"
+       #:configure-flags
+       ;; possible additional inputs:
+       ;;   --enable-avisynth        enable reading of AviSynth script
+       ;;                            files [no]
+       ;;   --enable-frei0r          enable frei0r video filtering
+       ;;   --enable-libaacplus      enable AAC+ encoding via libaacplus [no]
+       ;;   --enable-libcelt         enable CELT decoding via libcelt [no]
+       ;;   --enable-libdc1394       enable IIDC-1394 grabbing using libdc1394
+       ;;                            and libraw1394 [no]
+       ;;   --enable-libfaac         enable AAC encoding via libfaac [no]
+       ;;   --enable-libfdk-aac      enable AAC de/encoding via libfdk-aac [no]
+       ;;   --enable-libflite        enable flite (voice synthesis) support via
+       ;;                            libflite [no]
+       ;;   --enable-libgme          enable Game Music Emu via libgme [no]
+       ;;   --enable-libgsm          enable GSM de/encoding via libgsm [no]
+       ;;   --enable-libiec61883     enable iec61883 via libiec61883 [no]
+       ;;   --enable-libilbc         enable iLBC de/encoding via libilbc [no]
+       ;;   --enable-libmodplug      enable ModPlug via libmodplug [no]
+       ;;   --enable-libnut          enable NUT (de)muxing via libnut,
+       ;;                            native (de)muxer exists [no]
+       ;;   --enable-libopencore-amrnb    enable AMR-NB de/encoding via
+       ;;                                 libopencore-amrnb [no]
+       ;;   --enable-libopencore-amrwb    enable AMR-WB decoding via
+       ;;                                 libopencore-amrwb [no]
+       ;;   --enable-libopencv       enable video filtering via libopencv [no]
+       ;;   --enable-libopenjpeg     enable JPEG 2000 de/encoding via
+       ;;                            OpenJPEG [no]
+       ;;   --enable-librtmp         enable RTMP[E] support via librtmp [no]
+       ;;   --enable-libschroedinger enable Dirac de/encoding via
+       ;;                            libschroedinger [no]
+       ;;   --enable-libshine        enable fixed-point MP3 encoding via
+       ;;                            libshine [no]
+       ;;   --enable-libssh          enable SFTP protocol via libssh [no]
+       ;;                            (libssh2 does not work)
+       ;;   --enable-libstagefright-h264  enable H.264 decoding via
+       ;;                                 libstagefright [no]
+       ;;   --enable-libutvideo      enable Ut Video encoding and decoding via
+       ;;                            libutvideo [no]
+       ;;   --enable-libv4l2         enable libv4l2/v4l-utils [no]
+       ;;   --enable-libvidstab      enable video stabilization using
+       ;;                            vid.stab [no]
+       ;;   --enable-libvo-aacenc    enable AAC encoding via libvo-aacenc [no]
+       ;;   --enable-libvo-amrwbenc  enable AMR-WB encoding via
+       ;;                            libvo-amrwbenc [no]
+       ;;   --enable-libwavpack      enable wavpack encoding via libwavpack [no]
+       ;;   --enable-libxavs         enable AVS encoding via xavs [no]
+       ;;   --enable-libzmq          enable message passing via libzmq [no]
+       ;;   --enable-libzvbi         enable teletext support via libzvbi [no]
+       ;;   --enable-opencl          enable OpenCL code
+       ;;   --enable-x11grab         enable X11 grabbing [no]
+       '("--enable-avresample"
+         "--enable-gpl" ; enable optional gpl licensed parts
+         "--enable-shared"
+         "--enable-fontconfig"
+         ;; "--enable-gnutls" ; causes test failures
+         "--enable-ladspa"
+         "--enable-libass"
+         "--enable-libbluray"
+         "--enable-libcaca"
+         "--enable-libcdio"
+         "--enable-libfreetype"
+         "--enable-libmp3lame"
+         "--enable-libopus"
+         "--enable-libpulse"
+         "--enable-libquvi"
+         "--enable-libsoxr"
+         "--enable-libspeex"
+         "--enable-libtheora"
+         "--enable-libtwolame"
+         "--enable-libvorbis"
+         "--enable-libvpx"
+         "--enable-libxvid"
+         "--enable-libx264"
+         "--enable-openal"
+
+         "--enable-runtime-cpudetect"
+
+         ;; Runtime cpu detection is not implemented on
+         ;; MIPS, so we disable some features.
+         "--disable-mips32r2"
+         "--disable-mipsdspr1"
+         "--disable-mipsdspr2"
+         "--disable-mipsfpu")
        #:phases
        (modify-phases %standard-phases
          (replace
@@ -424,83 +508,13 @@ (define-public ffmpeg
                 (("#! /bin/sh") (string-append "#!" (which "bash"))))
               (setenv "SHELL" (which "bash"))
               (setenv "CONFIG_SHELL" (which "bash"))
-              ;; possible additional inputs:
-              ;;   --enable-avisynth        enable reading of AviSynth script files [no]
-              ;;   --enable-frei0r          enable frei0r video filtering
-              ;;   --enable-libaacplus      enable AAC+ encoding via libaacplus [no]
-              ;;   --enable-libcelt         enable CELT decoding via libcelt [no]
-              ;;   --enable-libdc1394       enable IIDC-1394 grabbing using libdc1394
-              ;;                            and libraw1394 [no]
-              ;;   --enable-libfaac         enable AAC encoding via libfaac [no]
-              ;;   --enable-libfdk-aac      enable AAC de/encoding via libfdk-aac [no]
-              ;;   --enable-libflite        enable flite (voice synthesis) support via libflite [no]
-              ;;   --enable-libgme          enable Game Music Emu via libgme [no]
-              ;;   --enable-libgsm          enable GSM de/encoding via libgsm [no]
-              ;;   --enable-libiec61883     enable iec61883 via libiec61883 [no]
-              ;;   --enable-libilbc         enable iLBC de/encoding via libilbc [no]
-              ;;   --enable-libmodplug      enable ModPlug via libmodplug [no]
-              ;;   --enable-libnut          enable NUT (de)muxing via libnut,
-              ;;                            native (de)muxer exists [no]
-              ;;   --enable-libopencore-amrnb enable AMR-NB de/encoding via libopencore-amrnb [no]
-              ;;   --enable-libopencore-amrwb enable AMR-WB decoding via libopencore-amrwb [no]
-              ;;   --enable-libopencv       enable video filtering via libopencv [no]
-              ;;   --enable-libopenjpeg     enable JPEG 2000 de/encoding via OpenJPEG [no]
-              ;;   --enable-librtmp         enable RTMP[E] support via librtmp [no]
-              ;;   --enable-libschroedinger enable Dirac de/encoding via libschroedinger [no]
-              ;;   --enable-libshine        enable fixed-point MP3 encoding via libshine [no]
-              ;;   --enable-libssh          enable SFTP protocol via libssh [no]
-              ;;                            (libssh2 does not work)
-              ;;   --enable-libstagefright-h264  enable H.264 decoding via libstagefright [no]
-              ;;   --enable-libutvideo      enable Ut Video encoding and decoding via libutvideo [no]
-              ;;   --enable-libv4l2         enable libv4l2/v4l-utils [no]
-              ;;   --enable-libvidstab      enable video stabilization using vid.stab [no]
-              ;;   --enable-libvo-aacenc    enable AAC encoding via libvo-aacenc [no]
-              ;;   --enable-libvo-amrwbenc  enable AMR-WB encoding via libvo-amrwbenc [no]
-              ;;   --enable-libwavpack      enable wavpack encoding via libwavpack [no]
-              ;;   --enable-libxavs         enable AVS encoding via xavs [no]
-              ;;   --enable-libzmq          enable message passing via libzmq [no]
-              ;;   --enable-libzvbi         enable teletext support via libzvbi [no]
-              ;;   --enable-opencl          enable OpenCL code
-              ;;   --enable-x11grab         enable X11 grabbing [no]
-              (zero? (system*
-                      "./configure"
-                      (string-append "--prefix=" out)
-                      ;; Add $libdir to the RUNPATH of all the binaries.
-                      (string-append "--extra-ldflags=-Wl,-rpath="
-                                     %output "/lib")
-                      "--enable-avresample"
-                      "--enable-gpl" ; enable optional gpl licensed parts
-                      "--enable-shared"
-                      "--enable-fontconfig"
-                      ;; "--enable-gnutls" ; causes test failures
-                      "--enable-ladspa"
-                      "--enable-libass"
-                      "--enable-libbluray"
-                      "--enable-libcaca"
-                      "--enable-libcdio"
-                      "--enable-libfreetype"
-                      "--enable-libmp3lame"
-                      "--enable-libopus"
-                      "--enable-libpulse"
-                      "--enable-libquvi"
-                      "--enable-libsoxr"
-                      "--enable-libspeex"
-                      "--enable-libtheora"
-                      "--enable-libtwolame"
-                      "--enable-libvorbis"
-                      "--enable-libvpx"
-                      "--enable-libxvid"
-                      "--enable-libx264"
-                      "--enable-openal"
-
-                      "--enable-runtime-cpudetect"
-
-                      ;; Runtime cpu detection is not implemented on
-                      ;; MIPS, so we disable some features.
-                      "--disable-mips32r2"
-                      "--disable-mipsdspr1"
-                      "--disable-mipsdspr2"
-                      "--disable-mipsfpu")))))
+              (zero? (apply system*
+                            "./configure"
+                            (string-append "--prefix=" out)
+                            ;; Add $libdir to the RUNPATH of all the binaries.
+                            (string-append "--extra-ldflags=-Wl,-rpath="
+                                           out "/lib")
+                            configure-flags)))))
          (add-before
           'check 'set-ld-library-path
           (lambda _
-- 
cgit v1.2.3


From 0bdab089622deed12383d4067ca241d639d40d7d Mon Sep 17 00:00:00 2001
From: Eric Bavier <bavier@member.fsf.org>
Date: Thu, 29 Oct 2015 17:26:30 -0500
Subject: gnu: fish: Add python input.

* gnu/packages/fish.scm (inputs): Add python.
---
 gnu/packages/fish.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/fish.scm b/gnu/packages/fish.scm
index 94e418a8b1..6392efe308 100644
--- a/gnu/packages/fish.scm
+++ b/gnu/packages/fish.scm
@@ -20,6 +20,7 @@ (define-module (gnu packages fish)
   #:use-module (guix licenses)
   #:use-module (gnu packages doxygen)
   #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages python)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix utils)
@@ -45,7 +46,8 @@ (define-public fish
     (native-inputs
      `(("doxygen" ,doxygen)))
     (inputs
-     `(("ncurses" ,ncurses)))
+     `(("ncurses" ,ncurses)
+       ("python" ,python-wrapper)))   ;for fish_config and manpage completions
     (arguments
      '(#:tests? #f ; no check target
        #:configure-flags '("--sysconfdir=/etc")))
-- 
cgit v1.2.3


From cd4cb1b597f3d42ade7e71dac718a41070ce6acc Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Fri, 30 Oct 2015 13:12:44 +0200
Subject: gnu: freeipmi: Update to 1.4.11.

* gnu/packages/freeipmi.scm (freeipmi): Update to 1.4.11.
---
 gnu/packages/freeipmi.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/freeipmi.scm b/gnu/packages/freeipmi.scm
index badecc60ba..6e2610409d 100644
--- a/gnu/packages/freeipmi.scm
+++ b/gnu/packages/freeipmi.scm
@@ -27,14 +27,14 @@ (define-module (gnu packages freeipmi)
 (define-public freeipmi
   (package
     (name "freeipmi")
-    (version "1.4.10")
+    (version "1.4.11")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/freeipmi/freeipmi-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "1l98l8g8lha85q1d288wr7dyx00x36smh9g5wza15n4wm35c9wqs"))))
+               "0bkghpbj1zkxcgmx2crg0mf97y6dhnxdqvdk5mkw1pyqdxncwq3l"))))
     (build-system gnu-build-system)
     (inputs
      `(("readline" ,readline) ("libgcrypt" ,libgcrypt)))
-- 
cgit v1.2.3


From 7ea3099b0516f98cad378a347659b9011a01a1d3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 29 Oct 2015 17:12:17 +0100
Subject: gnu: Add pcre2.

* gnu/packages/pcre.scm (pcre2): New variable.
---
 gnu/packages/pcre.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/pcre.scm b/gnu/packages/pcre.scm
index d07e434190..d7d974fc5c 100644
--- a/gnu/packages/pcre.scm
+++ b/gnu/packages/pcre.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -57,3 +58,37 @@ (define-public pcre
 POSIX regular expression API.")
    (license license:bsd-3)
    (home-page "http://www.pcre.org/")))
+
+(define-public pcre2
+  (package
+    (name "pcre2")
+    (version "10.20")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/pcre/pcre2/"
+                                  version "/pcre2-" version ".tar.bz2"))
+
+              (sha256
+               (base32
+                "0yj8mm9ll9zj3v47rvmmqmr1ybxk72rr2lym3rymdsf905qjhbik"))))
+   (build-system gnu-build-system)
+   (inputs `(("bzip2" ,bzip2)
+             ("readline" ,readline)
+             ("zlib" ,zlib)))
+   (arguments
+    `(#:configure-flags '("--enable-unicode"
+                          "--enable-pcregrep-libz"
+                          "--enable-pcregrep-libbz2"
+                          "--enable-pcretest-libreadline"
+                          "--enable-unicode-properties"
+                          "--enable-pcre2-16"
+                          "--enable-pcre2-32"
+                          "--enable-jit")))
+   (synopsis "Perl Compatible Regular Expressions")
+   (description
+    "The PCRE library is a set of functions that implement regular expression
+pattern matching using the same syntax and semantics as Perl 5.  PCRE has its
+own native API, as well as a set of wrapper functions that correspond to the
+POSIX regular expression API.")
+   (license license:bsd-3)
+   (home-page "http://www.pcre.org/")))
-- 
cgit v1.2.3


From b90e7e5d49e951a24f58d3cd29d37127982ef240 Mon Sep 17 00:00:00 2001
From: David Thompson <dthompson2@worcester.edu>
Date: Fri, 30 Oct 2015 08:40:58 -0400
Subject: gnu: xfce4-session: Fix xflock4.

* gnu/packages/patches/xfce4-session-fix-xflock4.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/xfce.scm (xfce4-session)[source]: Add patch.
---
 gnu-system.am                                      |  1 +
 .../patches/xfce4-session-fix-xflock4.patch        | 31 ++++++++++++++++++++++
 gnu/packages/xfce.scm                              |  5 +++-
 3 files changed, 36 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/xfce4-session-fix-xflock4.patch

(limited to 'gnu/packages')

diff --git a/gnu-system.am b/gnu-system.am
index d8430b4732..575c6f53f6 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -687,6 +687,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/xf86-video-trident-remove-mibstore.patch	\
   gnu/packages/patches/xf86-video-vmware-glibc-2.20.patch	\
   gnu/packages/patches/xfce4-panel-plugins.patch		\
+  gnu/packages/patches/xfce4-session-fix-xflock4.patch		\
   gnu/packages/patches/xfce4-settings-defaults.patch		\
   gnu/packages/patches/xmodmap-asprintf.patch 			\
   gnu/packages/patches/zathura-plugindir-environment-variable.patch
diff --git a/gnu/packages/patches/xfce4-session-fix-xflock4.patch b/gnu/packages/patches/xfce4-session-fix-xflock4.patch
new file mode 100644
index 0000000000..74769e4257
--- /dev/null
+++ b/gnu/packages/patches/xfce4-session-fix-xflock4.patch
@@ -0,0 +1,31 @@
+From cbb9c769316b4d32956a2c78aa01a38b473f0cfc Mon Sep 17 00:00:00 2001
+From: David Thompson <dthompson2@worcester.edu>
+Date: Fri, 30 Oct 2015 08:30:43 -0400
+Subject: [PATCH] xflock4: Do not override PATH with hardcoded value.
+
+The PATH "/bin:/usr/bin" may not be a valid search path on the user's
+machine.  The screen locking program may be in /usr/local/bin or
+elsewhere.  Distros that do not conform to the FHS, such as GuixSD and
+NixOS, will not have their executables in either location.  Thus, we
+simply leave PATH alone.
+---
+ scripts/xflock4 | 3 ---
+ 1 file changed, 3 deletions(-)
+
+diff --git a/scripts/xflock4 b/scripts/xflock4
+index ec4d05d..e7981ac 100644
+--- a/scripts/xflock4
++++ b/scripts/xflock4
+@@ -21,9 +21,6 @@
+ #  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ #
+ 
+-PATH=/bin:/usr/bin
+-export PATH
+-
+ # Lock by xscreensaver or gnome-screensaver, if a respective daemon is running
+ for lock_cmd in \
+     "xscreensaver-command -lock" \
+-- 
+2.5.0
+
diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm
index e42c58050d..914012625f 100644
--- a/gnu/packages/xfce.scm
+++ b/gnu/packages/xfce.scm
@@ -421,7 +421,10 @@ (define-public xfce4-session
                                   "/src/" name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "01kvbd09c06j20n155hracsgrq06rlmfgdywffjsvlwpn19m9j38"))))
+                "01kvbd09c06j20n155hracsgrq06rlmfgdywffjsvlwpn19m9j38"))
+              (patches
+               ;; See: https://bugzilla.xfce.org/show_bug.cgi?id=12282
+               (list (search-patch "xfce4-session-fix-xflock4.patch")))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags
-- 
cgit v1.2.3