Merge branch 'master' into security-updates

Makefile.am

@@ -56,6 +56,7 @@ MODULES =					\
   guix/graph.scm				\
   guix/cve.scm					\
   guix/build-system.scm				\
+  guix/build-system/ant.scm			\
   guix/build-system/cmake.scm			\
   guix/build-system/emacs.scm			\
   guix/build-system/glib-or-gtk.scm		\
@@ -75,6 +76,7 @@ MODULES =					\
   guix/cvs-download.scm				\
   guix/svn-download.scm				\
   guix/ui.scm					\
+  guix/build/ant-build-system.scm		\
   guix/build/download.scm			\
   guix/build/cmake-build-system.scm		\
   guix/build/emacs-build-system.scm		\
@@ -171,8 +173,10 @@ dist_noinst_DATA = guix/tests.scm
 
 # Linux-Libre configurations.
 KCONFIGS =					\
-  gnu/packages/linux-libre-i686.conf		\
+  gnu/packages/linux-libre-4.5-i686.conf	\
-  gnu/packages/linux-libre-x86_64.conf		\
+  gnu/packages/linux-libre-4.5-x86_64.conf	\
+  gnu/packages/linux-libre-4.4-i686.conf	\
+  gnu/packages/linux-libre-4.4-x86_64.conf	\
   gnu/packages/linux-libre-4.1-i686.conf	\
   gnu/packages/linux-libre-4.1-x86_64.conf
 

doc/guix.texi

@@ -16,8 +16,9 @@ Copyright @copyright{} 2013 Nikita Karetnikov@*
 Copyright @copyright{} 2015, 2016 Mathieu Lirzin@*
 Copyright @copyright{} 2014 Pierre-Antoine Rault@*
 Copyright @copyright{} 2015 Taylan Ulrich Bayırlı/Kammer@*
-Copyright @copyright{} 2015, 2016 Leo Famulari
+Copyright @copyright{} 2015, 2016 Leo Famulari@*
-Copyright @copyright{} 2016 Ben Woodcroft
+Copyright @copyright{} 2016 Ben Woodcroft@*
+Copyright @copyright{} 2016 Chris Marusich
 
 Permission is granted to copy, distribute and/or modify this document
 under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -154,6 +155,12 @@ Utilities
 * Invoking guix challenge::     Challenging substitute servers.
 * Invoking guix container::     Process isolation.
 
+Invoking @command{guix build}
+
+* Common Build Options::        Build options for most commands.
+* Package Transformation Options::    Creating variants of packages.
+* Additional Build Options::    Options specific to 'guix build'.
+
 GNU Distribution
 
 * System Installation::         Installing the whole operating system.
@@ -165,6 +172,15 @@ GNU Distribution
 * Bootstrapping::               GNU/Linux built from scratch.
 * Porting::                     Targeting another platform or kernel.
 
+System Installation
+
+* Limitations::                 What you can expect.
+* Hardware Considerations::     Supported hardware.
+* USB Stick Installation::      Preparing the installation medium.
+* Preparing for Installation::  Networking, partitioning, etc.
+* Proceeding with the Installation::  The real thing.
+* Building the Installation Image::  How this comes to be.
+
 System Configuration
 
 * Using the Configuration System::  Customizing your GNU system.
@@ -2720,6 +2736,27 @@ of @var{gnu-build-system}, and differ mainly in the set of inputs
 implicitly added to the build process, and in the list of phases
 executed.  Some of these build systems are listed below.
 
+@defvr {Scheme Variable} ant-build-system
+This variable is exported by @code{(guix build-system ant)}.  It
+implements the build procedure for Java packages that can be built with
+@url{http://ant.apache.org/, Ant build tool}.
+
+It adds both @code{ant} and the @dfn{Java Development Kit} (JDK) as
+provided by the @code{icedtea} package to the set of inputs.  Different
+packages can be specified with the @code{#:ant} and @code{#:jdk}
+parameters, respectively.
+
+When the original package does not provide a suitable Ant build file,
+the parameter @code{#:jar-name} can be used to generate a minimal Ant
+build file @file{build.xml} with tasks to build the specified jar
+archive.
+
+The parameter @code{#:build-target} can be used to specify the Ant task
+that should be run during the @code{build} phase.  By default the
+``jar'' task will be run.
+
+@end defvr
+
 @defvr {Scheme Variable} cmake-build-system
 This variable is exported by @code{(guix build-system cmake)}.  It
 implements the build procedure for packages using the
@@ -5636,11 +5673,12 @@ link that follows: @pxref{Help,,, info, Info: An Introduction}.  Hit
 @end ifinfo
 
 @menu
-* Limitations::                         What you can expect.
+* Limitations::                 What you can expect.
-* USB Stick Installation::              Preparing the installation medium.
+* Hardware Considerations::     Supported hardware.
-* Preparing for Installation::          Networking, partitioning, etc.
+* USB Stick Installation::      Preparing the installation medium.
-* Proceeding with the Installation::    The real thing.
+* Preparing for Installation::  Networking, partitioning, etc.
-* Building the Installation Image::     How this comes to be.
+* Proceeding with the Installation::  The real thing.
+* Building the Installation Image::  How this comes to be.
 @end menu
 
 @node Limitations
@@ -5686,6 +5724,40 @@ You have been warned!  But more than a disclaimer, this is an invitation
 to report issues (and success stories!), and to join us in improving it.
 @xref{Contributing}, for more info.
 
+
+@node Hardware Considerations
+@subsection Hardware Considerations
+
+@cindex hardware support on GuixSD
+GNU@tie{}GuixSD focuses on respecting the user's computing freedom.  It
+builds around the kernel Linux-libre, which means that only hardware for
+which free software drivers and firmware exists is supported.  Nowadays,
+a wide range of off-the-shelf hardware is supported on
+GNU/Linux-libre---from keyboards to graphics cards to scanners and
+Ethernet controllers.  Unfortunately, there are still areas where
+hardware vendors deny users control over their own computing, and such
+hardware is not supported on GuixSD.
+
+@cindex WiFi, hardware support
+One of the main areas where free drivers or firmware is lacking is WiFi
+devices.  WiFi devices known to work include those using Atheros chips
+(AR9271 and AR7010), which corresponds to the @code{ath9k} Linux-libre
+driver, and for which free firmware exists and is available
+out-of-the-box on GuixSD, as part of @var{%base-firmware}
+(@pxref{operating-system Reference, @code{firmware}}).
+
+@cindex RYF, Respects Your Freedom
+The @uref{https://www.fsf.org/, Free Software Foundation} runs
+@uref{https://www.fsf.org/ryf, @dfn{Respect Your Freedom}} (RYF), a
+certification program for hardware products that respect your freedom
+and your privacy and ensure that you have control over your device.  We
+encourage you to check the list of RYF-certified hardware.
+
+Another useful resource is the @uref{https://www.h-node.org/, H-Node}
+web site.  It contains a catalog of hardware devices with information
+about their support in GNU/Linux.
+
+
 @node USB Stick Installation
 @subsection USB Stick Installation
 
@@ -5967,8 +6039,8 @@ system} command, specifically:
 guix system disk-image --image-size=850MiB gnu/system/install.scm
 @end example
 
-@xref{Invoking guix system} and
+Have a look at @file{gnu/system/install.scm} in the source tree,
-@file{gnu/system/install.scm} in the source tree for more information
+and see also @ref{Invoking guix system} for more information
 about the installation image.
 
 @node System Configuration
@@ -6087,28 +6159,42 @@ generated as needed (@pxref{Defining Services}).
 @cindex customization, of services
 @findex modify-services
 Occasionally, instead of using the base services as is, you will want to
-customize them.  For instance, to change the configuration of
+customize them.  To do this, use @code{modify-services} (@pxref{Service
-@code{guix-daemon} and Mingetty (the console log-in), you may write the
+Reference, @code{modify-services}}) to modify the list.
-following instead of @var{%base-services}:
+
+For example, suppose you want to modify @code{guix-daemon} and Mingetty
+(the console log-in) in the @var{%base-services} list (@pxref{Base
+Services, @code{%base-services}}).  To do that, you can write the
+following in your operating system declaration:
 
 @lisp
-(modify-services %base-services
+(define %my-services
-  (guix-service-type config =>
+  ;; My very own list of services.
-                     (guix-configuration
+  (modify-services %base-services
-                      (inherit config)
+    (guix-service-type config =>
-                      (use-substitutes? #f)
+                       (guix-configuration
-                      (extra-options '("--gc-keep-outputs"))))
+                        (inherit config)
-  (mingetty-service-type config =>
+                        (use-substitutes? #f)
-                         (mingetty-configuration
+                        (extra-options '("--gc-keep-derivations"))))
-                          (inherit config)
+    (mingetty-service-type config =>
-                          (motd (plain-file "motd" "Hi there!")))))
+                           (mingetty-configuration
+                            (inherit config)
+                            (motd (plain-file "motd" "Howdy!"))))))
+
+(operating-system
+  ;; @dots{}
+  (services %my-services))
 @end lisp
 
-@noindent
+This changes the configuration---i.e., the service parameters---of the
-The effect here is to change the options passed to @command{guix-daemon}
+@code{guix-service-type} instance, and that of all the
-when it is started, as well as the ``message of the day'' that appears
+@code{mingetty-service-type} instances in the @var{%base-services} list.
-when logging in at the console.  @xref{Service Reference,
+Observe how this is accomplished: first, we arrange for the original
-@code{modify-services}}, for more on that.
+configuration to be bound to the identifier @code{config} in the
+@var{body}, and then we write the @var{body} so that it evaluates to the
+desired configuration.  In particular, notice how we use @code{inherit}
+to create a new configuration which has the same values as the old
+configuration, but with a few modifications.
 
 The configuration for a typical ``desktop'' usage, with the X11 display
 server, a desktop environment, network management, power management, and
@@ -6214,7 +6300,8 @@ the Linux kernel.  @xref{Initial RAM Disk}.
 List of firmware packages loadable by the operating system kernel.
 
 The default includes firmware needed for Atheros-based WiFi devices
-(Linux-libre module @code{ath9k}.)
+(Linux-libre module @code{ath9k}).  @xref{Hardware Considerations}, for
+more info on supported hardware.
 
 @item @code{host-name}
 The host name.
@@ -9963,11 +10050,12 @@ Here is an example of how a service is created and manipulated:
 
 The @code{modify-services} form provides a handy way to change the
 parameters of some of the services of a list such as
-@var{%base-services} (@pxref{Base Services, @code{%base-services}}).  Of
+@var{%base-services} (@pxref{Base Services, @code{%base-services}}).  It
-course, you could always use standard list combinators such as
+evalutes to a list of services.  Of course, you could always use
-@code{map} and @code{fold} to do that (@pxref{SRFI-1, List Library,,
+standard list combinators such as @code{map} and @code{fold} to do that
-guile, GNU Guile Reference Manual}); @code{modify-services} simply
+(@pxref{SRFI-1, List Library,, guile, GNU Guile Reference Manual});
-provides a more concise form for this common pattern.
+@code{modify-services} simply provides a more concise form for this
+common pattern.
 
 @deffn {Scheme Syntax} modify-services @var{services} @
   (@var{type} @var{variable} => @var{body}) @dots{}
@@ -9979,16 +10067,21 @@ clauses.  Each clause has the form:
 (@var{type} @var{variable} => @var{body})
 @end example
 
-where @var{type} is a service type, such as @var{guix-service-type}, and
+where @var{type} is a service type---e.g.,
-@var{variable} is an identifier that is bound within @var{body} to the
+@code{guix-service-type}---and @var{variable} is an identifier that is
-value of the service of that @var{type}.  @xref{Using the Configuration
+bound within the @var{body} to the service parameters---e.g., a
-System}, for an example.
+@code{guix-configuration} instance---of the original service of that
+@var{type}.
 
-This is a shorthand for:
+The @var{body} should evaluate to the new service parameters, which will
+be used to configure the new service.  This new service will replace the
+original in the resulting list.  Because a service's service parameters
+are created using @code{define-record-type*}, you can write a succint
+@var{body} that evaluates to the new service parameters by using the
+@code{inherit} feature that @code{define-record-type*} provides.
+
+@xref{Using the Configuration System} for example usage.
 
-@example
-(map (lambda (service) @dots{}) @var{services})
-@end example
 @end deffn
 
 Next comes the programming interface for service types.  This is

gnu-system.am

@@ -484,7 +484,6 @@ dist_patch_DATA =						\
   gnu/packages/patches/geoclue-config.patch			\
   gnu/packages/patches/ghostscript-CVE-2015-3228.patch		\
   gnu/packages/patches/ghostscript-runpath.patch		\
-  gnu/packages/patches/gitolite-openssh-6.8-compat.patch	\
   gnu/packages/patches/glib-networking-ssl-cert-file.patch	\
   gnu/packages/patches/glib-tests-desktop.patch			\
   gnu/packages/patches/glib-tests-homedir.patch			\

gnu/build/install.scm

@@ -159,7 +159,7 @@ (define (reset-timestamps directory)
                 ;; read-only store.
                 (unless (eq? (stat:type s) 'symlink)
                   (utime file 0 0 0 0))))
-            (find-files directory "")))
+            (find-files directory #:directories? #t)))
 
 (define* (register-closure store closure
                            #:key (deduplicate? #t))

gnu/packages/aspell.scm

@@ -139,3 +139,11 @@ (define-public aspell-dict-it
                      #:sha256
                      (base32
                       "1gdf7bc1a0kmxsmphdqq8pl01h667mjsj6hihy6kqy14k5qdq69v")))
+
+(define-public aspell-dict-nl
+  (aspell-dictionary "nl" "Dutch"
+                     #:version "0.50-2"
+                     #:prefix "aspell-"
+                     #:sha256
+                     (base32
+                      "0ffb87yjsh211hllpc4b9khqqrblial4pzi1h9r3v465z1yhn3j4")))

gnu/packages/audio.scm

@@ -2073,3 +2073,38 @@ (define-public shntool
     (home-page "http://etree.org/shnutils/shntool/")
     ;; 'install-sh' bears the x11 license
     (license (list license:gpl2+ license:x11))))
+
+(define-public dcadec
+  (package
+    (name "dcadec")
+    (version "0.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/foo86/dcadec/archive/v"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0i0dpypgqkhhi4v1fmsp2way6w9kbcix3c7q79pmg39yvrzj17gd"))))
+    (build-system gnu-build-system)
+    (arguments
+     ;; Test files are missing: https://github.com/foo86/dcadec/issues/53
+     '(#:tests? #f
+       #:make-flags
+       (list "CC=gcc"
+             ;; Build shared library.
+             "CONFIG_SHARED=1"
+             (string-append "PREFIX=" (assoc-ref %outputs "out"))
+             ;; Set proper runpath.
+             (string-append "LDFLAGS=-Wl,-rpath="
+                            (assoc-ref %outputs "out")
+                            "/lib"))
+       #:phases
+       (modify-phases %standard-phases
+         ;; No configure script, just a hand-written Makefile.
+         (delete 'configure))))
+    (synopsis "DTS Coherent Acoustics decoder")
+    (description "Dcadec is a DTS Coherent Acoustics surround sound decoder
+with support for HD extensions.")
+    (home-page "https://github.com/foo86/dcadec")
+    (license license:lgpl2.1+)))

gnu/packages/bioinformatics.scm

@@ -26,6 +26,7 @@ (define-module (gnu packages bioinformatics)
   #:use-module (guix utils)
   #:use-module (guix download)
   #:use-module (guix git-download)
+  #:use-module (guix build-system ant)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system perl)
@@ -2002,24 +2003,17 @@ (define-public htsjdk
               (snippet '(substitute* "build.xml"
                           (("failifexecutionfails=\"true\"")
                            "failifexecutionfails=\"false\"")))))
-    (build-system gnu-build-system)
+    (build-system ant-build-system)
     (arguments
-     `(#:modules ((srfi srfi-1)
+     `(#:tests? #f ; test require Internet access
-                  (guix build gnu-build-system)
+       #:make-flags
-                  (guix build utils))
+       (list (string-append "-Ddist=" (assoc-ref %outputs "out")
-       #:phases (alist-replace
+                            "/share/java/htsjdk/"))
-                 'build
+       #:build-target "all"
-                 (lambda _
+       #:phases
-                   (setenv "JAVA_HOME" (assoc-ref %build-inputs "jdk"))
+       (modify-phases %standard-phases
-                   (zero? (system* "ant" "all"
+         ;; The build phase also installs the jars
-                                   (string-append "-Ddist="
+         (delete 'install))))
-                                                  (assoc-ref %outputs "out")
-                                                  "/share/java/htsjdk/"))))
-                 (fold alist-delete %standard-phases
-                       '(configure install check)))))
-    (native-inputs
-     `(("ant" ,ant)
-       ("jdk" ,icedtea "jdk")))
     (home-page "http://samtools.github.io/htsjdk/")
     (synopsis "Java API for high-throughput sequencing data (HTS) formats")
     (description
@@ -2556,6 +2550,44 @@ (define-public pbtranscript-tofu
 generated using the PacBio Iso-Seq protocol.")
       (license license:bsd-3))))
 
+(define-public pyicoteo
+  (package
+    (name "pyicoteo")
+    (version "2.0.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
+                           "pyicoteo/get/v" version ".tar.bz2"))
+       (file-name (string-append name "-" version ".tar.bz2"))
+       (sha256
+        (base32
+         "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2 ; does not work with Python 3
+       #:tests? #f))      ; there are no tests
+    (inputs
+     `(("python2-matplotlib" ,python2-matplotlib)))
+    (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo")
+    (synopsis "Analyze high-throughput genetic sequencing data")
+    (description
+     "Pyicoteo is a suite of tools for the analysis of high-throughput genetic
+sequencing data.  It works with genomic coordinates.  There are currently six
+different command-line tools:
+
+@enumerate
+@item pyicoregion: for generating exploratory regions automatically;
+@item pyicoenrich: for differential enrichment between two conditions;
+@item pyicoclip: for calling CLIP-Seq peaks without a control;
+@item pyicos: for genomic coordinates manipulation;
+@item pyicoller: for peak calling on punctuated ChIP-Seq;
+@item pyicount: to count how many reads from N experiment files overlap in a
+  region file;
+@item pyicotrocol: to combine operations from pyicoteo.
+@end enumerate\n")
+    (license license:gpl3+)))
+
 (define-public prodigal
   (package
     (name "prodigal")

gnu/packages/cdrom.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2013, 2014 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
-;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -44,14 +44,14 @@ (define-module (gnu packages cdrom)
 (define-public libcddb
   (package
     (name "libcddb")
-    (version "1.3.0")
+    (version "1.3.2")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/libcddb/libcddb-"
                                  version ".tar.bz2"))
              (sha256
               (base32
-               "1y8bfy12dwm41m1jahayn3v47dm34fmz7m9cjxyh7xcw6fp3lzaf"))))
+               "0fr21a7vprdyy1bq6s99m0x420c9jm5fipsd63pqv8qyfkhhxkim"))))
     (build-system gnu-build-system)
     (arguments '(#:tests? #f))      ; tests rely on access to external servers
     (home-page "http://libcddb.sourceforge.net/")
@@ -189,14 +189,14 @@ (define-public cdparanoia
 (define-public dvdisaster
   (package
     (name "dvdisaster")
-    (version "0.72.6")
+    (version "0.79.5")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://dvdisaster.net/downloads/dvdisaster-"
                                  version ".tar.bz2"))
              (sha256
               (base32
-               "0sqrprc5rh3shnfli25m2wy0i5f83db54iv04s5s7bxf77m7sy79"))))
+               "0f8gjnia2fxcbmhl8b3qkr5b7idl8m855dw7xw2fnmbqwvcm6k4w"))))
     (build-system gnu-build-system)
     (inputs
      `(("gtk+" ,gtk+-2)))
@@ -208,14 +208,7 @@ (define-public dvdisaster
      `(;; Parallel builds appear to be unsafe, see
        ;; <http://hydra.gnu.org/build/49331/nixlog/1/raw>.
        #:parallel-build? #f
-       #:tests? #f ; no check target
+       #:tests? #f)) ; no check target
-       #:phases
-         (alist-cons-before
-          'patch-source-shebangs 'sanitise
-          (lambda _
-            ;; delete dangling symlink
-            (delete-file ".#GNUmakefile"))
-          %standard-phases)))
     (home-page "http://dvdisaster.net/en/index.html")
     (synopsis "Error correcting codes for optical media images")
     (description "Optical media (CD,DVD,BD) keep their data only for a
@@ -240,9 +233,8 @@ (define-public libcue
     (version "1.4.0")
     (source (origin
              (method url-fetch)
-             (uri (string-append "https://github.com/lipnitsk/libcue/releases"
+             (uri (string-append "https://github.com/lipnitsk/libcue/archive/v"
-                                 "/download/v" version
+                                 version ".tar.bz2"))
-                                 "/libcue-" version ".tar.bz2"))
              (sha256
               (base32
                "17kjd7rjz1bvfn44n3n2bjb7a1ywd0yc0g4sqp5ihf9b5bn7cwlb"))))
@@ -287,15 +279,15 @@ (define-public cd-discid
 (define-public abcde
   (package
     (name "abcde")
-    (version "2.7")
+    (version "2.7.1")
-    (home-page "http://abcde.einval.com/")
+    (home-page "https://abcde.einval.com/")
     (source (origin
               (method url-fetch)
               (uri (string-append home-page "/download/abcde-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0ikpffzvacadh6vj9qlary8126j1zrd2knp9gvivmp7y1656jj01"))
+                "0l7j0nk8p30s97285i418rv9ym9bgns7bn6l8gldw3mjhnby609l"))
               (modules '((guix build utils)))
               (snippet
                '(substitute* "Makefile"
@@ -305,37 +297,36 @@ (define-public abcde
                    (string-append "etcdir = $(prefix)/etc\n"))))))
     (build-system gnu-build-system)
     (arguments
-     '(#:phases (alist-replace
+     '(#:phases
-                 'configure
+       (modify-phases %standard-phases
-                 (lambda* (#:key outputs inputs #:allow-other-keys)
+         (replace 'configure
-                   (substitute* "Makefile"
+           (lambda* (#:key outputs inputs #:allow-other-keys)
-                     (("^prefix = .*$")
+             (substitute* "Makefile"
-                      (string-append "prefix = "
+               (("^prefix = .*$")
-                                     (assoc-ref outputs "out")
+                (string-append "prefix = "
-                                     "\n"))))
+                               (assoc-ref outputs "out")
-                 (alist-cons-after
+                               "\n")))))
-                  'install 'wrap
+         (add-after 'install 'wrap
-                  (lambda* (#:key inputs outputs #:allow-other-keys)
+           (lambda* (#:key inputs outputs #:allow-other-keys)
-                    (let ((wget   (assoc-ref inputs "wget"))
+             (let ((wget   (assoc-ref inputs "wget"))
-                          (vorbis (assoc-ref inputs "vorbis-tools"))
+                   (vorbis (assoc-ref inputs "vorbis-tools"))
-                          (parano (assoc-ref inputs "cdparanoia"))
+                   (parano (assoc-ref inputs "cdparanoia"))
-                          (which  (assoc-ref inputs "which"))
+                   (which  (assoc-ref inputs "which"))
-                          (discid (assoc-ref inputs "cd-discid"))
+                   (discid (assoc-ref inputs "cd-discid"))
-                          (out    (assoc-ref outputs "out")))
+                   (out    (assoc-ref outputs "out")))
-                      (define (wrap file)
+               (define (wrap file)
-                        (wrap-program file
+                 (wrap-program file
-                                      `("PATH" ":" prefix
+                               `("PATH" ":" prefix
-                                        (,(string-append out "/bin:"
+                                 (,(string-append out "/bin:"
-                                                         wget "/bin:"
+                                                  wget "/bin:"
-                                                         which "/bin:"
+                                                  which "/bin:"
-                                                         vorbis "/bin:"
+                                                  vorbis "/bin:"
-                                                         discid "/bin:"
+                                                  discid "/bin:"
-                                                         parano "/bin")))))
+                                                  parano "/bin")))))
 
-                      (for-each wrap
+               (for-each wrap
-                                (find-files (string-append out "/bin")
+                         (find-files (string-append out "/bin")
-                                            ".*"))))
+                                     ".*"))))))
-                  %standard-phases))
        #:tests? #f))
 
     (inputs `(("wget" ,wget)

gnu/packages/dav.scm

@@ -52,21 +52,16 @@ (define-public radicale
 (define-public vdirsyncer
   (package
     (name "vdirsyncer")
-    (version "0.9.0")
+    (version "0.9.2")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "vdirsyncer" version))
              (sha256
               (base32
-               "0s9awjr9v60rr80xcpwmdhkf4v1yqnydahjmxwvxmh64565is465"))))
+               "1g1107cz4sk41d2z6k6pn9n2fzd26m72j8aj33zn483vfvmyrc4q"))))
     (build-system python-build-system)
     (arguments
       `(#:phases (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             (setenv "DAV_SERVER" "radicale")
-             (setenv "REMOTESTORAGE_SERVER" "skip")
-             (zero? (system* "py.test"))))
          ;; vdirsyncer requires itself to be installed in order to build
          ;; the manpage.
          (add-after 'install 'manpage
@@ -80,17 +75,24 @@ (define-public vdirsyncer
                "docs/_build/man/vdirsyncer.1"
                (string-append
                  (assoc-ref outputs "out")
-                 "/share/man/man1")))))))
+                 "/share/man/man1"))))
+         ;; vdirsyncer requires itself to be installed in order to run the test
+         ;; suite.
+         (delete 'check)
+         (add-after 'install 'check-later
+           (lambda _
+             (setenv "DETERMINISTIC_TESTS" "true")
+             (setenv "DAV_SERVER" "radicale")
+             (setenv "REMOTESTORAGE_SERVER" "skip")
+             (zero? (system* "make" "test")))))))
     (native-inputs
-     `(("python-oauthlib" ,python-oauthlib)
+     `(("python-setuptools-scm" ,python-setuptools-scm)
-       ("python-setuptools-scm" ,python-setuptools-scm)
        ("python-sphinx" ,python-sphinx)
        ;; Required for testing
        ("python-hypothesis" ,python-hypothesis)
        ("python-pytest" ,python-pytest)
        ("python-pytest-localserver" ,python-pytest-localserver)
        ("python-pytest-subtesthack" ,python-pytest-subtesthack)
-       ("python-pytest-xprocess" ,python-pytest-xprocess)
        ("python-wsgi-intercept" ,python-wsgi-intercept)
        ("radicale" ,radicale)))
     (propagated-inputs
@@ -98,7 +100,7 @@ (define-public vdirsyncer
        ("python-click" ,python-click)
        ("python-click-log" ,python-click-log)
        ("python-click-threading" ,python-click-threading)
-       ("python-lxml" ,python-lxml) ; which one?
+       ("python-lxml" ,python-lxml)
        ("python-requests-toolbelt" ,python-requests-toolbelt)))
     (synopsis "Synchronize calendars and contacts")
     (description "Vdirsyncer synchronizes your calendars and addressbooks

gnu/packages/emacs.scm

@@ -308,7 +308,7 @@ (define-public paredit
 (define-public git-modes
   (package
     (name "git-modes")
-    (version "1.2.0")
+    (version "1.2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -317,7 +317,7 @@ (define-public git-modes
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "09dv7ikbj2bi4y3lmvjfzqpdmx2f9bd4w7jkp10bkap62d05iqhk"))))
+                "088wyddh8y0yw77i0hx449n9zg4wzyc90h63wlmxba1ijg4dzm0p"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((guix build gnu-build-system)

gnu/packages/enlightenment.scm

@@ -273,7 +273,7 @@ (define-public rage
 (define-public enlightenment
   (package
     (name "enlightenment")
-    (version "0.20.5")
+    (version "0.20.6")
     (source (origin
               (method url-fetch)
               (uri
@@ -281,7 +281,7 @@ (define-public enlightenment
                               name "/" name "-" version ".tar.xz"))
               (sha256
                (base32
-                 "1l02m2d7d5r0vnfgn44glhvqhc8ygbjxjkf6cdd2vxpxsa29ax12"))))
+                 "11ahll68nlci214ka05whp5l32hy9lznmcdfqx3hxsmq2p7bl7zj"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--enable-mount-eeze")))

gnu/packages/fonts.scm

@@ -7,6 +7,7 @@
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Nils Gillmann <niasterisk@grrlz.net>
+;;; Copyright © 2016 Jookia <166291@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -67,14 +68,15 @@ (define-public font-inconsolata
 (define-public font-ubuntu
   (package
     (name "font-ubuntu")
-    (version "0.80")
+    (version "0.83")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://font.ubuntu.com/download/ubuntu-font-family-"
+              (uri (string-append
-                                  version ".zip"))
+                    "http://font.ubuntu.com/download/ubuntu-font-family-"
+                    version ".zip"))
               (sha256
                (base32
-                "0k4f548riq23gmw4zhn30qqkcpaj4g2ab5rbc3lflfxwkc4p0w8h"))))
+                "0hjvq2x758dx0sfwqhzflns0ns035qm7h6ygskbx1svzg517sva5"))))
     (build-system trivial-build-system)
     (arguments
      `(#:modules ((guix build utils))
@@ -628,3 +630,113 @@ (define-public font-gnu-unifont
 utilities to ease adding new glyphs to the font.")
     (home-page "http://unifoundry.com/unifont.html")
     (license license:gpl2+)))
+
+(define-public font-google-noto
+  (package
+    (name "font-google-noto")
+    (version "20150929")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://noto-website-2.storage.googleapis.com/"
+                                  "pkgs/Noto-hinted.zip"))
+              (sha256
+               (base32
+                "13jhpqzhsqhyby8n0ksqg155a3jyaif3nzj9anzbq8s2gn1xjyd9"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder (begin
+                   (use-modules (guix build utils)
+                                (srfi srfi-26))
+
+                   (let ((PATH     (string-append (assoc-ref %build-inputs
+                                                             "unzip")
+                                                  "/bin"))
+                         (font-dir (string-append %output
+                                                  "/share/fonts/truetype")))
+                     (setenv "PATH" PATH)
+                     (system* "unzip" (assoc-ref %build-inputs "source"))
+
+                     (mkdir-p font-dir)
+                     (for-each (lambda (ttf)
+                                 (copy-file ttf
+                                            (string-append font-dir "/" ttf)))
+                               (find-files "." "\\.ttf$"))
+                     (for-each (lambda (otf)
+                                 (copy-file otf
+                                            (string-append font-dir "/" otf)))
+                               (find-files "." "\\.otf$"))))))
+    (native-inputs `(("unzip" ,unzip)))
+    (home-page "https://www.google.com/get/noto/")
+    (synopsis "Fonts aimed to cover all languages")
+    (description "Googe Noto Fonts is a family of fonts aimed to support all
+languages with a consistent look and aesthetic.  It's goal is to have no Unicode
+symbols unable to be displayed properly.")
+    (license license:silofl1.1)))
+
+(define-public font-un
+  (package
+    (name "font-un")
+    (version "1.0.2-080608")
+    ;; The upstream server at kldp.net is serving us broken MIME.
+    ;; See <http://bugs.gnu.org/22908>.
+    (source (origin
+              (method url-fetch)
+              (uri (list
+                    (string-append
+                     "http://krosos.sdf.org/static/unix/"
+                     "un-fonts-core-" version ".tar.gz")
+                    ;; XXX: The upstream server at kldp.net
+                    (string-append
+                     "https://kldp.net/projects/unfonts/download/4695?filename="
+                     "un-fonts-core-" version ".tar.gz")))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "13liaz2pmww3aqabm55la5npd08m1skh334ky7qfidxaz5s742iv"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+
+         (let ((tar      (string-append (assoc-ref %build-inputs "tar")
+                                        "/bin/tar"))
+               (PATH     (string-append (assoc-ref %build-inputs "gzip")
+                                        "/bin"))
+               (font-dir (string-append %output "/share/fonts/truetype"))
+               (doc-dir  (string-append %output "/share/doc/" ,name)))
+           (setenv "PATH" PATH)
+           (system* tar "xvf" (assoc-ref %build-inputs "source"))
+           (mkdir-p font-dir)
+           (mkdir-p doc-dir)
+           (chdir (string-append "un-fonts"))
+           (for-each (lambda (ttf)
+                       (copy-file ttf
+                                  (string-append font-dir "/"
+                                                 (basename ttf))))
+                     (find-files "." "\\.ttf$"))
+           (for-each (lambda (doc)
+                       (copy-file doc
+                                  (string-append doc-dir "/"
+                                                 (basename doc))))
+                     '("COPYING" "README"))))))
+    (native-inputs
+     `(("tar" ,tar)
+       ("gzip" ,gzip)))
+    (home-page "https://kldp.net/projects/unfonts/")
+    (synopsis "Collection of Korean fonts")
+    (description
+     "Un-fonts is a family of mainly Korean fonts.
+It contains the following fonts and styles:
+
+@enumerate
+@item UnBatang, UnBatangBold: serif;
+@item UnDotum, UnDotumBold: sans-serif;
+@item UnGraphic, UnGraphicBold: sans-serif style;
+@item UnDinaru, UnDinaruBold, UnDinaruLight;
+@item UnPilgi, UnPilgiBold: script;
+@item UnGungseo: cursive, brush-stroke.
+@end enumerate\n")
+    (license license:gpl2+)))

gnu/packages/fontutils.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -305,7 +306,7 @@ (define-public libspiro
 (define-public libuninameslist
   (package
     (name "libuninameslist")
-    (version "0.4.20140731")
+    (version "0.5.20150701")
     (source
      (origin
        (method url-fetch)
@@ -314,7 +315,7 @@ (define-public libuninameslist
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "016zxffpc8iwpxxmnjkdirn6dsbcvdb2wjdrp123sf79f4nsynyj"))))
+         "1j6147l100rppw7axlrkdx0p35fax6bz2zh1xgpg7a3b4pmqaj3v"))))
     (build-system gnu-build-system)
     (native-inputs `(("autoconf" ,autoconf)
                      ("automake" ,automake)

gnu/packages/freedesktop.scm

@@ -451,7 +451,7 @@ (define-public libmbim
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "http://www.freedesktop.org/software/" name "/"
+                    "https://www.freedesktop.org/software/" name "/"
                     name "-" version ".tar.xz"))
               (sha256
                (base32

gnu/packages/games.scm

@@ -1185,7 +1185,7 @@ (define-public raincat
 (define-public manaplus
   (package
     (name "manaplus")
-    (version "1.6.1.16")
+    (version "1.6.3.12")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1193,7 +1193,7 @@ (define-public manaplus
                     version "/manaplus-" version ".tar.xz"))
               (sha256
                (base32
-                "1vrsjvdbdzbnqmr8sp110b2d93kp5yfnifsn6zjm60kdvvbphdir"))))
+                "02bnd4nk1qzrfqckqkwb6sbjzsmacv968ih74cdgcykslpsr684d"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags

gnu/packages/java.scm

@@ -139,9 +139,8 @@ (define-public ant
     (version "1.9.6")
     (source (origin
               (method url-fetch)
-              (uri (string-append
+              (uri (string-append "mirror://apache/ant/source/apache-ant-"
-                    "https://www.apache.org/dist/ant/source/apache-ant-"
+                                  version "-src.tar.gz"))
-                    version "-src.tar.gz"))
               (sha256
                (base32
                 "1396wflczyxjxl603dhxjvd559f289lha9y2f04f71c7hapjl3am"))))

gnu/packages/jrnl.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Eric Bavier <address@hidden>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,7 +28,7 @@ (define-module (gnu packages jrnl)
 (define-public jrnl
   (package
     (name "jrnl")
-    (version "1.8.4")
+    (version "1.9.7")
     (source
      (origin
       (method url-fetch)
@@ -36,11 +37,10 @@ (define-public jrnl
       (file-name (string-append name "-" version ".tar.gz"))
       (sha256
        (base32
-        "019ky09sj5i7frmca0imv4jm46mn3f4lzah2wmiwxh22cisj7ksn"))))
+        "0mfq7hhw5np2dj9jlxpyyk2cg9i0xgz2brb894d928hczszy97bq"))))
     (build-system python-build-system)
     (native-inputs
-     `(("python-setuptools" ,python-setuptools)
+     `(("behave" ,behave)))
-       ("behave" ,behave)))
     (inputs
      `(("python" ,python)
        ("python-keyring" ,python-keyring)

gnu/packages/kodi.scm

@@ -21,6 +21,7 @@ (define-module (gnu packages kodi)
   #:use-module (guix utils)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages audio)
@@ -68,18 +69,67 @@ (define-module (gnu packages kodi)
   #:use-module (gnu packages yasm)
   #:use-module (gnu packages zip))
 
+(define-public crossguid
+  (let ((commit "8f399e8bd4252be9952f3dfa8199924cc8487ca4"))
+    (package
+      (name "crossguid")
+      (version (string-append "0.0-1." (string-take commit 7)))
+      ;; There's no official release.  Just a Git repository.
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/graeme-hill/crossguid.git")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1i29y207qqddvaxbn39pk2fbh3gx8zvdprfp35wasj9rw2wjk3s9"))))
+      (build-system gnu-build-system)
+      (arguments
+       '(#:phases
+         (modify-phases %standard-phases
+           (delete 'configure) ; no configure script
+           ;; There's no build system here, so we have to do it ourselves.
+           (replace 'build
+             (lambda _
+               (and (zero? (system* "g++" "-c" "guid.cpp" "-o" "guid.o"
+                                    "-std=c++11" "-DGUID_LIBUUID"))
+                    (zero? (system* "ar" "rvs" "libcrossguid.a" "guid.o")))))
+           (replace 'check
+             (lambda _
+               (and (zero? (system* "g++" "-c" "test.cpp" "-o" "test.o"
+                                    "-std=c++11"))
+                    (zero? (system* "g++" "-c" "testmain.cpp" "-o" "testmain.o"
+                                    "-std=c++11"))
+                    (zero? (system* "g++" "test.o" "guid.o" "testmain.o"
+                                    "-o" "test" "-luuid"))
+                    (zero? (system* (string-append (getcwd) "/test"))))))
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((out (assoc-ref outputs "out")))
+                 (install-file "guid.h" (string-append out "/include"))
+                 (install-file "libcrossguid.a"
+                               (string-append out "/lib"))
+                 #t))))))
+      (inputs
+       `(("util-linux" ,util-linux)))
+      (synopsis "Lightweight universal identifier library")
+      (description "CrossGuid is a minimal @acronym{GUID}/@acronym{UUID}
+generator library for C++.")
+      (home-page "https://github.com/graeme-hill/crossguid")
+      (license license:expat))))
+
 (define-public kodi
   (package
     (name "kodi")
-    (version "15.2")
+    (version "16.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://mirrors.kodi.tv/releases/source/"
-                                  version "-Isengard.tar.gz"))
+                                  version "-Jarvis.tar.gz"))
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "043i0f1crx9glwxil4xm45z5kxpkrx316gi4ir4d3rbd5safp2nx"))
+                "0iirspvv7czf785l2lqf232dvdaj87srbn9ni97ngvnd6w9yl884"))
               (snippet
                ;; Delete bundled ffmpeg.
                ;; TODO: Delete every other bundled library.
@@ -161,7 +211,9 @@ (define (run-make makefile)
        ("bluez" ,bluez)
        ("boost" ,boost)
        ("bzip2" ,bzip2)
+       ("crossguid" ,crossguid)
        ("curl" ,curl)
+       ("dcadec" ,dcadec)
        ("dbus" ,dbus)
        ("enca" ,enca)
        ("eudev" ,eudev)
@@ -213,6 +265,7 @@ (define (run-make makefile)
        ("taglib" ,taglib)
        ("tinyxml" ,tinyxml)
        ("unzip" ,unzip)
+       ("util-linux" ,util-linux)
        ("zip" ,zip)
        ("zlib" ,zlib)))
     (synopsis "Media center for home theater computers")

gnu/packages/linux.scm

@@ -220,7 +220,7 @@ (define* (kernel-config system #:key variant)
     (search-path %load-path file)))
 
 (define-public linux-libre
-  (let* ((version "4.4.5")
+  (let* ((version "4.5")
          (build-phase
           '(lambda* (#:key system inputs #:allow-other-keys #:rest args)
              ;; Apply the neat patch.
@@ -294,7 +294,7 @@ (define-public linux-libre
              (uri (linux-libre-urls version))
              (sha256
               (base32
-               "19yyw6yssyxr9k5y3whgz2p731mb1pnq3xajpv8g01m13cxs32dd"))))
+               "0km863vwy557flpygkr869yshpjs1v11ni78p8k9p9nm31ai6yn3"))))
     (build-system gnu-build-system)
     (supported-systems '("x86_64-linux" "i686-linux"))
     (native-inputs `(("perl" ,perl)
@@ -303,8 +303,10 @@ (define-public linux-libre
                      ("module-init-tools" ,module-init-tools)
                      ("patch/freedo+gnu" ,%boot-logo-patch)
 
-                     ,@(let ((conf (kernel-config (or (%current-target-system)
+                     ,@(let ((conf (kernel-config
-                                                      (%current-system)))))
+                                    (or (%current-target-system)
+                                        (%current-system))
+                                    #:variant (version-major+minor version))))
                          (if conf
                              `(("kconfig" ,conf))
                              '()))))
@@ -326,6 +328,23 @@ (define-public linux-libre
     (license license:gpl2)
     (home-page "http://www.gnu.org/software/linux-libre/"))))
 
+(define-public linux-libre-4.4
+  (package
+    (inherit linux-libre)
+    (version "4.4.5")
+    (source (origin
+              (method url-fetch)
+              (uri (linux-libre-urls version))
+              (sha256
+               (base32
+                "19yyw6yssyxr9k5y3whgz2p731mb1pnq3xajpv8g01m13cxs32dd"))))
+    (native-inputs
+     (let ((conf (kernel-config (or (%current-target-system)
+                                    (%current-system))
+                                #:variant "4.4")))
+       `(,@(alist-delete "kconfig" (package-native-inputs linux-libre))
+         ("kconfig" ,conf))))))
+
 (define-public linux-libre-4.1
   (package
     (inherit linux-libre)

gnu/packages/mail.scm

@@ -71,8 +71,8 @@ (define-module (gnu packages mail)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
   #:use-module ((guix licenses)
-                #:select (gpl2 gpl2+ gpl3+ lgpl2.1 lgpl2.1+ lgpl3+ non-copyleft
+                #:select (gpl2 gpl2+ gpl3 gpl3+ lgpl2.1 lgpl2.1+ lgpl3+
-                          (expat . license:expat)))
+                           non-copyleft (expat . license:expat)))
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
@@ -1150,5 +1150,46 @@ (define-public procmail
                       ;; nonfree Artistic License 1.0
                       ;; as alternative to the GPL2+.
                       ;; This option is not listed here.
-;;; mail.scm ends here
 
+(define-public khard
+  (package
+    (name "khard")
+    (version "0.8.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri name version))
+              (sha256
+               (base32
+                "098gs94qmnspdfn6ar8lycx7dbsz9bcff90aps0cmn47mw7llch0"))))
+    (build-system python-build-system)
+    (arguments
+      `(#:python ,python-2 ; only python-2 is supported.
+        #:phases
+        (modify-phases %standard-phases
+          (add-before 'build 'disable-egg-compression
+            ;; Do not compress the egg.
+            (lambda _
+              (let ((port (open-file "setup.cfg" "a")))
+                (display "\n[easy_install]\nzip_ok = 0\n"
+                         port)
+                (close-port port)
+                #t)))
+          (add-after 'install 'install-doc
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let* ((out (assoc-ref outputs "out"))
+                     (doc (string-append out "/share/doc/khard")))
+                (copy-recursively "misc/khard" doc)))))))
+    (native-inputs
+     `(("python2-setuptools" ,python2-setuptools)))
+    (propagated-inputs
+     `(("python2-vobject" ,python2-vobject)
+       ("python2-pyyaml" ,python2-pyyaml)
+       ("python2-atomicwrites" ,python2-atomicwrites)
+       ("python2-configobj" ,python2-configobj)))
+    (synopsis "Console address book using CardDAV")
+    (description "Khard is an address book for the console.  It creates, reads,
+modifies and removes CardDAV address book entries at your local machine.  For
+synchronizing with a remote address book, @command{vdirsyncer} is recommended.
+Khard can also be used from within the email client @command{mutt}.")
+    (home-page "https://github.com/scheibler/khard")
+    (license gpl3+)))

gnu/packages/maths.scm

@@ -177,7 +177,7 @@ (define-public gsl
 (define-public glpk
   (package
     (name "glpk")
-    (version "4.58")
+    (version "4.59")
     (source
      (origin
       (method url-fetch)
@@ -185,7 +185,7 @@ (define-public glpk
                           version ".tar.gz"))
       (sha256
        (base32
-        "1jmrya04hgwnrxrqqs40i6m9cqka3q601cx3nh9ijyvlg90zlq24"))))
+        "1bpbp5z0378kaj5bqmc5m2j5h9c7553p0s2j6a28badqghpbx673"))))
     (build-system gnu-build-system)
     (inputs
      `(("gmp" ,gmp)))

gnu/packages/music.scm

@@ -817,7 +817,7 @@ (define-public pd
 (define-public frescobaldi
   (package
     (name "frescobaldi")
-    (version "2.18.1")
+    (version "2.18.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -825,7 +825,7 @@ (define-public frescobaldi
                     version "/frescobaldi-" version ".tar.gz"))
               (sha256
                (base32
-                "1hflc6gck6dn17czc2ldai5j0ynfg3df8lqcggdry06qxsdbnns7"))))
+                "1yns7nq2a2hz5rv4xjp21bgcdi1xj6fq48lqjrld7ypqqi5nfjp5"))))
     (build-system python-build-system)
     (inputs
      `(("lilypond" ,lilypond)

gnu/packages/patches/gitolite-openssh-6.8-compat.patch

@@ -1,25 +0,0 @@
-From ed807a40c6683960e357bc995b3acf721ec088b4 Mon Sep 17 00:00:00 2001
-From: Sitaram Chamarty <sitaram@atc.tcs.com>
-Date: Thu, 19 Mar 2015 05:17:59 +0530
-Subject: [PATCH] openssh 6.8 compat
-
----
- src/triggers/post-compile/ssh-authkeys | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/triggers/post-compile/ssh-authkeys b/src/triggers/post-compile/ssh-authkeys
-index 84dda73..d5f5d8b 100755
---- a/src/triggers/post-compile/ssh-authkeys
-+++ b/src/triggers/post-compile/ssh-authkeys
-@@ -115,7 +115,7 @@ sub fp_file {
-     my $f  = shift;
-     my $fp = `ssh-keygen -l -f '$f'`;
-     chomp($fp);
--    _die "fingerprinting failed for '$f'" unless $fp =~ /([0-9a-f][0-9a-f](:[0-9a-f][0-9a-f])+)/;
-+    _die "fingerprinting failed for '$f'" unless $fp =~ /([0-9a-f][0-9a-f](:[0-9a-f][0-9a-f])+)/ or $fp =~ m(SHA256:([A-ZA-z0-9+/]+));
-     $fp = $1;
-     return $fp;
- }
---
-2.2.1
-

gnu/packages/python.scm

@@ -1133,10 +1133,10 @@ (define-public python2-simplejson
   (package-with-python2 python-simplejson))
 
 
-(define-public python2-pyicu
+(define-public python-pyicu
   (package
-    (name "python2-pyicu")
+    (name "python-pyicu")
-    (version "1.8")
+    (version "1.9.2")
     (source
      (origin
       (method url-fetch)
@@ -1144,19 +1144,22 @@ (define-public python2-pyicu
                           version ".tar.gz"))
       (sha256
        (base32
-        "1y361x82lnh9k9srmdx3q92z5iag112z7r5fxm0n1sfwb349yjdw"))))
+        "1diba0g8md614fvm9yf50paiwdkhj6rd7xwf1rg9mc0pxc0hhn4v"))))
     (build-system python-build-system)
     (inputs
      `(("icu4c" ,icu4c)))
-    (arguments
-     `(#:python ,python-2 ; Python 3 works also, but needs special care for
-                          ; linking with libpython3.3m
-       #:tests? #f)) ; no check target
     (home-page "http://pyicu.osafoundation.org/")
     (synopsis "Python extension wrapping the ICU C++ API")
     (description
      "PyICU is a python extension wrapping the ICU C++ API.")
-    (license x11)))
+    (license x11)
+    (properties `((python2-variant . ,(delay python2-pyicu))))))
+
+(define-public python2-pyicu
+  (package
+    (inherit (package-with-python2
+              (strip-python2-variant python-pyicu)))
+    (native-inputs `(("python2-setuptools" ,python2-setuptools)))))
 
 (define-public python2-dogtail
   ;; Python 2 only, as it leads to "TabError: inconsistent use of tabs and
@@ -6756,7 +6759,14 @@ (define-public python-atomicwrites
     (description "Library for atomic file writes using platform dependent tools
 for atomic filesystem operations.")
     (home-page "https://github.com/untitaker/python-atomicwrites")
-    (license license:expat)))
+    (license license:expat)
+    (properties `((python2-variant . ,(delay python2-atomicwrites))))))
+
+(define-public python2-atomicwrites
+  (package (inherit (package-with-python2
+                     (strip-python2-variant python-atomicwrites)))
+    (native-inputs
+     `(("python2-setuptools" ,python2-setuptools)))))
 
 (define-public python-requests-toolbelt
   (package
@@ -7457,13 +7467,13 @@ (define-public awscli
 (define-public python-hypothesis
   (package
     (name "python-hypothesis")
-    (version "3.0.4")
+    (version "3.1.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "hypothesis" version))
               (sha256
                (base32
-                "0bh6pqyc56cqlbpg0ffzjs6466blyylix4nsw11qrqwf01cg9gdq"))))
+                "0qyqq9akm4vshhn8cngjc1qykcvsn7cz6dlm6njfsgpbraqrmbbw"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-flake8" ,python-flake8)
@@ -8193,3 +8203,33 @@ (define-public python2-psycopg2
     (inherit (package-with-python2
               (strip-python2-variant python-psycopg2)))
     (native-inputs `(("python2-setuptools" ,python2-setuptools)))))
+
+(define-public python-vobject
+  (package
+    (name "python-vobject")
+    (version "0.9.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "vobject" version))
+              (sha256
+               (base32
+                "1cwzjnrdr9yg2x21wbf3kf59ibnchvj33mygd69yzi178a9gs9gz"))))
+    (build-system python-build-system)
+    (inputs
+     `(("python-dateutil-2" ,python-dateutil-2)
+       ("python-pyicu" ,python-pyicu)))
+    (synopsis "Parse and generate vCard and vCalendar files")
+    (description "Vobject is intended to be a full featured Python package for
+parsing and generating vCard and vCalendar files.  Currently, iCalendar files
+are supported and well tested. vCard 3.0 files are supported, and all data
+should be imported, but only a few components are understood in a sophisticated
+way.")
+    (home-page "http://eventable.github.io/vobject/")
+    (license asl2.0)
+    (properties `((python2-variant . ,(delay python2-vobject))))))
+
+(define-public python2-vobject
+  (package
+    (inherit (package-with-python2
+              (strip-python2-variant python-vobject)))
+    (native-inputs `(("python2-setuptools" ,python2-setuptools)))))

gnu/packages/version-control.scm

@@ -324,7 +324,7 @@ (define-public git-manpages
 (define-public libgit2
   (package
     (name "libgit2")
-    (version "0.23.4")
+    (version "0.24.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/libgit2/libgit2/"
@@ -332,7 +332,7 @@ (define-public libgit2
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0aa0i5bvmzrrirqk5w13pm0qmblkk57x24w0hxz4vg0x73by5xf7"))))
+                "1c5jx0pcpz83x7s36jimfz5bj0vy7vwpchq9p4sgdqxy8gwr6rhw"))))
     (build-system cmake-build-system)
     (arguments
      `(#:phases
@@ -351,7 +351,7 @@ (define-public libgit2
     (inputs
      `(("libssh2" ,libssh2)
        ("libcurl" ,curl)
-       ("python" ,python)
+       ("python" ,python-wrapper)
        ("openssl" ,openssl)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -367,14 +367,14 @@ (define-public libgit2
 (define-public shflags
   (package
     (name "shflags")
-    (version "1.0.3")
+    (version "1.2.0")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://shflags.googlecode.com/files/"
+              (uri (string-append "https://github.com/kward/shflags/archive/v"
-                                  "shflags-" version ".tgz"))
+                                  version ".tar.gz"))
               (sha256
                (base32
-                "08laxhf1hifh3w4j0hri5ppcklaqz0mnkmbaz8j0wxih29vi8slm"))))
+                "0zxw12haylaq60a335xlqcs4afw2zrgwqymmpw0m21r51w6irdmr"))))
     (build-system trivial-build-system)
     (native-inputs `(("tar" ,tar)
                      ("gzip" ,gzip)))
@@ -396,7 +396,7 @@ (define-public shflags
                        (copy-file "src/shflags"
                                   (string-append srcdir "/shflags"))
                        #t)))))
-    (home-page "https://code.google.com/p/shflags/")
+    (home-page "https://github.com/kward/shflags")
     (synopsis "Command-line flags library for shell scripts")
     (description
      "Shell Flags (shFlags) is a library written to greatly simplify the
@@ -489,19 +489,16 @@ (define-public git-test-sequence
 (define-public gitolite
   (package
     (name "gitolite")
-    (version "3.6.2")
+    (version "3.6.5")
     (source (origin
               (method url-fetch)
               (uri (string-append
                     "https://github.com/sitaramc/gitolite/archive/v"
                     version ".tar.gz"))
               (file-name (string-append name "-" version ".tar.gz"))
-              ;; Commit ed807a4 upstream
-              (patches
-               (list (search-patch "gitolite-openssh-6.8-compat.patch")))
               (sha256
                (base32
-                "1gsgzi9ayb4rablki3mqr11b0h8db4xg43df660marfpacmkfb01"))))
+                "0xpqg04gyr4dhdhxx5lbk61lwwd5ml32530bigg2qy663icngwqm"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f ; no tests

gnu/packages/xfce.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2014, 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2016 Florian Paul Schmidt <mista.tapas@gmx.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -704,6 +705,7 @@ (define-public xfce
        ("tumlber"              ,tumbler)
        ("xfce4-appfinder"      ,xfce4-appfinder)
        ("xfce4-panel"          ,xfce4-panel)
+       ("xfce4-power-manager"  ,xfce4-power-manager)
        ("xfce4-session"        ,xfce4-session)
        ("xfce4-settings"       ,xfce4-settings)
        ("xfce4-terminal"       ,xfce4-terminal)
@@ -721,3 +723,37 @@ (define-public xfce
      "Xfce is a lightweight desktop environment.  It aims to be fast and low on
 system resources, while still being visually appealing and user friendly.")
     (license gpl2+)))
+
+(define-public xfce4-power-manager
+  (package
+    (name "xfce4-power-manager")
+    (version "1.4.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://archive.xfce.org/xfce/4.12"
+                                  "/src/" name "-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "04909sfc2nrj2wg9cw6y9y2r9yrp3l3vc201sy1gaiap67fi33h1"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:configure-flags '("--enable-gtk3")))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("intltool" ,intltool)))
+    (inputs
+     `(("lbxrandr" ,libxrandr)
+       ("upower" ,upower)
+       ("libnotify" ,libnotify)
+       ("libxfce4ui" ,libxfce4ui)))
+    (home-page "http://www.xfce.org/")
+    (synopsis "Xfce Power Manager")
+    (description
+     "This is a power manager for the Xfce desktop.  It manages the power
+sources on the computer and the devices that can be controlled to reduce their
+power consumption (such as LCD brightness level, monitor sleep, CPU frequency
+scaling, etc).  In addition, xfce4-power-manager provides a set of
+freedesktop-compliant DBus interfaces to inform other applications about current
+power level so that they can adjust their power consumption, and it provides the
+inhibit interface which allows applications to prevent automatic sleep.")
+    (license gpl2+)))

gnu/services.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016 Chris Marusich <cmmarusich@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -153,8 +154,8 @@ (define-syntax %modify-service
 
 (define-syntax modify-services
   (syntax-rules ()
-    "Modify the services listed in SERVICES according to CLAUSES.  Each clause
+    "Modify the services listed in SERVICES according to CLAUSES and return
-must have the form:
+the resulting list of services.  Each clause must have the form:
 
   (TYPE VARIABLE => BODY)
 

guix/build-system/ant.scm

@@ -0,0 +1,149 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
+;;;
+;;; 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 (guix build-system ant)
+  #:use-module (guix store)
+  #:use-module (guix utils)
+  #:use-module (guix packages)
+  #:use-module (guix derivations)
+  #:use-module (guix search-paths)
+  #:use-module (guix build-system)
+  #:use-module (guix build-system gnu)
+  #:use-module (ice-9 match)
+  #:use-module (srfi srfi-26)
+  #:export (%ant-build-system-modules
+            ant-build
+            ant-build-system))
+
+;; Commentary:
+;;
+;; Standard build procedure for Java packages using Ant.
+;;
+;; Code:
+
+(define %ant-build-system-modules
+  ;; Build-side modules imported by default.
+  `((guix build ant-build-system)
+    (guix build syscalls)
+    ,@%gnu-build-system-modules))
+
+(define (default-jdk)
+  "Return the default JDK package."
+  ;; Lazily resolve the binding to avoid a circular dependency.
+  (let ((jdk-mod (resolve-interface '(gnu packages java))))
+    (module-ref jdk-mod 'icedtea)))
+
+(define (default-ant)
+  "Return the default Ant package."
+  ;; Lazily resolve the binding to avoid a circular dependency.
+  (let ((jdk-mod (resolve-interface '(gnu packages java))))
+    (module-ref jdk-mod 'ant)))
+
+(define* (lower name
+                #:key source inputs native-inputs outputs system target
+                (jdk (default-jdk))
+                (ant (default-ant))
+                #:allow-other-keys
+                #:rest arguments)
+  "Return a bag for NAME."
+  (define private-keywords
+    '(#:source #:target #:jdk #:ant #:inputs #:native-inputs))
+
+  (and (not target)                               ;XXX: no cross-compilation
+       (bag
+         (name name)
+         (system system)
+         (host-inputs `(,@(if source
+                              `(("source" ,source))
+                              '())
+                        ,@inputs
+
+                        ;; Keep the standard inputs of 'gnu-build-system'.
+                        ,@(standard-packages)))
+         (build-inputs `(("jdk" ,jdk "jdk")
+                         ("ant" ,ant)
+                         ,@native-inputs))
+         (outputs outputs)
+         (build ant-build)
+         (arguments (strip-keyword-arguments private-keywords arguments)))))
+
+(define* (ant-build store name inputs
+                    #:key
+                    (tests? #t)
+                    (test-target "tests")
+                    (configure-flags ''())
+                    (make-flags ''())
+                    (build-target "jar")
+                    (jar-name #f)
+                    (phases '(@ (guix build ant-build-system)
+                                %standard-phases))
+                    (outputs '("out"))
+                    (search-paths '())
+                    (system (%current-system))
+                    (guile #f)p
+                    (imported-modules %ant-build-system-modules)
+                    (modules '((guix build ant-build-system)
+                               (guix build utils))))
+  "Build SOURCE with INPUTS."
+  (define builder
+    `(begin
+       (use-modules ,@modules)
+       (ant-build #:name ,name
+                  #:source ,(match (assoc-ref inputs "source")
+                              (((? derivation? source))
+                               (derivation->output-path source))
+                              ((source)
+                               source)
+                              (source
+                               source))
+                  #:make-flags ,make-flags
+                  #:configure-flags ,configure-flags
+                  #:system ,system
+                  #:tests? ,tests?
+                  #:test-target ,test-target
+                  #:build-target ,build-target
+                  #:jar-name ,jar-name
+                  #:phases ,phases
+                  #:outputs %outputs
+                  #:search-paths ',(map search-path-specification->sexp
+                                        search-paths)
+                  #:inputs %build-inputs)))
+
+  (define guile-for-build
+    (match guile
+      ((? package?)
+       (package-derivation store guile system #:graft? #f))
+      (#f                               ; the default
+       (let* ((distro (resolve-interface '(gnu packages commencement)))
+              (guile  (module-ref distro 'guile-final)))
+         (package-derivation store guile system #:graft? #f)))))
+
+  (build-expression->derivation store name builder
+                                #:inputs inputs
+                                #:system system
+                                #:modules imported-modules
+                                #:outputs outputs
+                                #:guile-for-build guile-for-build))
+
+(define ant-build-system
+  (build-system
+    (name 'ant)
+    (description "The standard Ant build system")
+    (lower lower)))
+
+;;; ant.scm ends here

guix/build/ant-build-system.scm

@@ -0,0 +1,160 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
+;;;
+;;; 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 (guix build ant-build-system)
+  #:use-module ((guix build gnu-build-system) #:prefix gnu:)
+  #:use-module (guix build syscalls)
+  #:use-module (guix build utils)
+  #:use-module (sxml simple)
+  #:use-module (ice-9 match)
+  #:use-module (ice-9 ftw)
+  #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-26)
+  #:export (%standard-phases
+            ant-build))
+
+;; Commentary:
+;;
+;; Builder-side code of the standard build procedure for Java packages using
+;; Ant.
+;;
+;; Code:
+
+(define (default-build.xml jar-name prefix)
+  "Create a simple build.xml with standard targets for Ant."
+  (call-with-output-file "build.xml"
+    (lambda (port)
+      (sxml->xml
+       `(project (@ (basedir "."))
+                 (property (@ (name "classes.dir")
+                              (value "${basedir}/build/classes")))
+                 (property (@ (name "jar.dir")
+                              (value "${basedir}/build/jar")))
+                 (property (@ (name "dist.dir")
+                              (value ,prefix)))
+
+                 ;; respect the CLASSPATH environment variable
+                 (property (@ (name "build.sysclasspath")
+                              (value "first")))
+                 (property (@ (environment "env")))
+                 (path (@ (id "classpath"))
+                       (pathelement (@ (location "${env.CLASSPATH}"))))
+
+                 (target (@ (name "compile"))
+                         (mkdir (@ (dir "${classes.dir}")))
+                         (javac (@ (includeantruntime "false")
+                                   (srcdir "src")
+                                   (destdir "${classes.dir}")
+                                   (classpath (@ (refid "classpath"))))))
+
+                 (target (@ (name "jar")
+                            (depends "compile"))
+                         (mkdir (@ (dir "${jar.dir}")))
+                         ;; We cannot use the simpler "jar" task here, because
+                         ;; there is no way to disable generation of a
+                         ;; manifest.  We do not include a generated manifest
+                         ;; to ensure determinism, because we cannot easily
+                         ;; reset the ctime/mtime before creating the archive.
+                         (exec (@ (executable "jar"))
+                               (arg (@ (line ,(string-append "-Mcf ${jar.dir}/" jar-name
+                                                             " -C ${classes.dir} ."))))))
+
+                 (target (@ (name "install"))
+                         (copy (@ (todir "${dist.dir}"))
+                               (fileset (@ (dir "${jar.dir}"))
+                                        (include (@ (name "**/*.jar")))))))
+       port)))
+  (utime "build.xml" 0 0)
+  #t)
+
+(define (generate-classpath inputs)
+  "Return a colon-separated string of full paths to jar files found among the
+INPUTS."
+  (string-join
+   (apply append (map (match-lambda
+                        ((_ . dir)
+                         (find-files dir "\\.*jar$")))
+                      inputs)) ":"))
+
+(define* (configure #:key inputs outputs (jar-name #f)
+                    #:allow-other-keys)
+  (when jar-name
+    (default-build.xml jar-name
+                       (string-append (assoc-ref outputs "out")
+                                      "/share/java")))
+  (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
+  (setenv "CLASSPATH" (generate-classpath inputs)))
+
+(define* (build #:key (make-flags '()) (build-target "jar")
+                #:allow-other-keys)
+  (zero? (apply system* `("ant" ,build-target ,@make-flags))))
+
+(define* (strip-jar-timestamps #:key outputs
+                 #:allow-other-keys)
+  "Unpack all jar archives, reset the timestamp of all contained files, and
+repack them.  This is necessary to ensure that archives are reproducible."
+  (define (repack-archive jar)
+    (format #t "repacking ~a\n" jar)
+    (let ((dir (mkdtemp! "jar-contents.XXXXXX")))
+      (and (with-directory-excursion dir
+             (zero? (system* "jar" "xf" jar)))
+           ;; The manifest file contains timestamps
+           (for-each delete-file (find-files dir "MANIFEST.MF"))
+           (delete-file jar)
+           ;; XXX: copied from (gnu build install)
+           (for-each (lambda (file)
+                       (let ((s (lstat file)))
+                         (unless (eq? (stat:type s) 'symlink)
+                           (utime file 0 0 0 0))))
+                     (find-files dir #:directories? #t))
+           (unless (zero? (system* "jar" "-Mcf" jar "-C" dir "."))
+             (error "'jar' failed"))
+           (utime jar 0 0)
+           #t)))
+
+  (every (match-lambda
+           ((output . directory)
+            (every repack-archive (find-files directory "\\.jar$"))))
+         outputs))
+
+(define* (check #:key target (make-flags '()) (tests? (not target))
+                (test-target "check")
+                #:allow-other-keys)
+  (if tests?
+      (zero? (apply system* `("ant" ,test-target ,@make-flags)))
+      (begin
+        (format #t "test suite not run~%")
+        #t)))
+
+(define* (install #:key (make-flags '()) #:allow-other-keys)
+  (zero? (apply system* `("ant" "install" ,@make-flags))))
+
+(define %standard-phases
+  (modify-phases gnu:%standard-phases
+    (replace 'configure configure)
+    (replace 'build build)
+    (replace 'check check)
+    (replace 'install install)
+    (add-after 'install 'strip-jar-timestamps strip-jar-timestamps)))
+
+(define* (ant-build #:key inputs (phases %standard-phases)
+                    #:allow-other-keys #:rest args)
+  "Build the given Java package, applying all of PHASES in order."
+  (apply gnu:gnu-build #:inputs inputs #:phases phases args))
+
+;;; ant-build-system.scm ends here

guix/grafts.scm

@@ -189,6 +189,12 @@ (define (references* items)
     (guard (c ((nix-protocol-error? c)
                ;; As a last resort, build DRV and query the references of the
                ;; build result.
+
+               ;; Warm up the narinfo cache, otherwise each derivation build
+               ;; will result in one HTTP request to get one narinfo, which is
+               ;; much less efficient than fetching them all upfront.
+               (substitution-oracle store (list drv))
+
                (and (build-derivations store (list drv))
                     (map (cut references store <>) items))))
       (references/substitutes store items)))

guix/http-client.scm

@@ -222,11 +222,14 @@ (define (read-header-line port)
 (module-define! (resolve-module '(web client))
                 'shutdown (const #f))
 
-(define* (http-fetch uri #:key port (text? #f) (buffered? #t))
+(define* (http-fetch uri #:key port (text? #f) (buffered? #t)
+                     keep-alive?)
   "Return an input port containing the data at URI, and the expected number of
 bytes available or #f.  If TEXT? is true, the data at URI is considered to be
 textual.  Follow any HTTP redirection.  When BUFFERED? is #f, return an
-unbuffered port, suitable for use in `filtered-port'.
+unbuffered port, suitable for use in `filtered-port'.  When KEEP-ALIVE? is
+true, send a 'Connection: keep-alive' HTTP header, in which case PORT may be
+reused for future HTTP requests.
 
 Raise an '&http-get-error' condition if downloading fails."
   (let loop ((uri (if (string? uri)
@@ -246,8 +249,10 @@ (define* (http-fetch uri #:key port (text? #f) (buffered? #t))
                      ;; Try hard to use the API du jour to get an input port.
                      (if (guile-version>? "2.0.7")
                          (http-get uri #:streaming? #t #:port port
+                                   #:keep-alive? #t
                                    #:headers auth-header) ; 2.0.9+
                          (http-get* uri #:decode-body? text?        ; 2.0.7
+                                    #:keep-alive? #t
                                     #:port port #:headers auth-header)))
                     ((code)
                      (response-code resp)))

guix/scripts/size.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2015, 2016 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -22,6 +22,7 @@ (define-module (guix scripts size)
   #:use-module (guix store)
   #:use-module (guix monads)
   #:use-module (guix utils)
+  #:use-module (guix grafts)
   #:use-module (guix packages)
   #:use-module (guix derivations)
   #:use-module (gnu packages)
@@ -274,19 +275,23 @@ (define (guix-size . args)
          (leave (_ "missing store item argument\n")))
         ((file)
          (leave-on-EPIPE
-          (with-store store
+          ;; Turn off grafts because (1) hydra.gnu.org does not serve grafted
-            (set-build-options store
+          ;; packages, and (2) they do not make any difference on the
-                               #:use-substitutes? #t
+          ;; resulting size.
-                               #:substitute-urls urls)
+          (parameterize ((%graft? #f))
+            (with-store store
+              (set-build-options store
+                                 #:use-substitutes? #t
+                                 #:substitute-urls urls)
 
-            (run-with-store store
+              (run-with-store store
-              (mlet* %store-monad ((item    (ensure-store-item file))
+                (mlet* %store-monad ((item    (ensure-store-item file))
-                                   (profile (store-profile item)))
+                                     (profile (store-profile item)))
-                (if map-file
+                  (if map-file
-                    (begin
+                      (begin
-                      (profile->page-map profile map-file)
+                        (profile->page-map profile map-file)
-                      (return #t))
+                        (return #t))
-                    (display-profile* profile)))
+                      (display-profile* profile)))
-              #:system system))))
+                #:system system)))))
         ((files ...)
          (leave (_ "too many arguments\n")))))))

guix/scripts/substitute.scm

@@ -164,10 +164,9 @@ (define-syntax-rule (with-timeout duration handler body ...)
         (sigaction SIGALRM SIG_DFL)
         (apply values result)))))
 
-(define* (fetch uri #:key (buffered? #t) (timeout? #t) (quiet-404? #f))
+(define* (fetch uri #:key (buffered? #t) (timeout? #t))
   "Return a binary input port to URI and the number of bytes it's expected to
-provide.  If QUIET-404? is true, HTTP 404 error conditions are passed through
+provide."
-to the caller without emitting an error message."
   (case (uri-scheme uri)
     ((file)
      (let ((port (open-file (uri-path uri)
@@ -175,12 +174,10 @@ (define* (fetch uri #:key (buffered? #t) (timeout? #t) (quiet-404? #f))
        (values port (stat:size (stat port)))))
     ((http https)
      (guard (c ((http-get-error? c)
-                (let ((code (http-get-error-code c)))
+                (leave (_ "download from '~a' failed: ~a, ~s~%")
-                  (if (and (= code 404) quiet-404?)
+                       (uri->string (http-get-error-uri c))
-                      (raise c)
+                       (http-get-error-code c)
-                      (leave (_ "download from '~a' failed: ~a, ~s~%")
+                       (http-get-error-reason c))))
-                             (uri->string (http-get-error-uri c))
-                             code (http-get-error-reason c))))))
        ;; Test this with:
        ;;   sudo tc qdisc add dev eth0 root netem delay 1500ms
        ;; and then cancel with:
@@ -219,19 +216,46 @@ (define-record-type <cache-info>
   (wants-mass-query? cache-info-wants-mass-query?))
 
 (define (download-cache-info url)
-  "Download the information for the cache at URL.  Return a <cache-info>
+  "Download the information for the cache at URL.  On success, return a
-object on success, or #f on failure."
+<cache-info> object and a port on which to send further HTTP requests.  On
-  (define (download url)
+failure, return #f and #f."
-    ;; Download the `nix-cache-info' from URL, and return its contents as an
+  (define uri
-    ;; list of key/value pairs.
+    (string->uri (string-append url "/nix-cache-info")))
-    (and=> (false-if-exception (fetch (string->uri url)))
-           fields->alist))
 
-  (and=> (download (string-append url "/nix-cache-info"))
+  (define (read-cache-info port)
-         (lambda (properties)
+    (alist->record (fields->alist port)
-           (alist->record properties
+                   (cut %make-cache-info url <...>)
-                          (cut %make-cache-info url <...>)
+                   '("StoreDir" "WantMassQuery")))
-                          '("StoreDir" "WantMassQuery")))))
+
+  (catch #t
+    (lambda ()
+      (case (uri-scheme uri)
+        ((file)
+         (values (call-with-input-file (uri-path uri)
+                   read-cache-info)
+                 #f))
+        ((http https)
+         (let ((port (open-connection-for-uri uri
+                                              #:timeout %fetch-timeout)))
+           (guard (c ((http-get-error? c)
+                      (warning (_ "while fetching '~a': ~a (~s)~%")
+                               (uri->string (http-get-error-uri c))
+                               (http-get-error-code c)
+                               (http-get-error-reason c))
+                      (close-port port)
+                      (warning (_ "ignoring substitute server at '~s'~%") url)
+                      (values #f #f)))
+             (values (read-cache-info (http-fetch uri
+                                                  #:port port
+                                                  #:keep-alive? #t))
+                     port))))))
+    (lambda (key . args)
+      (case key
+        ((getaddrinfo-error system-error)
+         ;; Silently ignore the error: probably due to lack of network access.
+         (values #f #f))
+        (else
+         (apply throw key args))))))
 
 
 (define-record-type <narinfo>
@@ -480,16 +504,19 @@ (define (narinfo-request cache-url path)
                             ".narinfo")))
     (build-request (string->uri url) #:method 'GET)))
 
-(define (http-multiple-get base-uri proc seed requests)
+(define* (http-multiple-get base-uri proc seed requests
+                            #:key port)
   "Send all of REQUESTS to the server at BASE-URI.  Call PROC for each
 response, passing it the request object, the response, a port from which to
 read the response body, and the previous result, starting with SEED, à la
-'fold'.  Return the final result."
+'fold'.  Return the final result.  When PORT is specified, use it as the
-  (let connect ((requests requests)
+initial connection on which HTTP requests are sent."
+  (let connect ((port     port)
+                (requests requests)
                 (result   seed))
     ;; (format (current-error-port) "connecting (~a requests left)..."
     ;;         (length requests))
-    (let ((p (open-connection-for-uri base-uri)))
+    (let ((p (or port (open-connection-for-uri base-uri))))
       ;; For HTTPS, P is not a file port and does not support 'setvbuf'.
       (when (file-port? p)
         (setvbuf p _IOFBF (expt 2 16)))
@@ -523,7 +550,7 @@ (define (http-multiple-get base-uri proc seed requests)
              (match (assq 'connection (response-headers resp))
                (('connection 'close)
                 (close-port p)
-                (connect tail result))            ;try again
+                (connect #f tail result))         ;try again
                (_
                 (loop tail result))))))))))       ;keep going
 
@@ -582,14 +609,17 @@ (define (handle-narinfo-response request response port result)
              (read-to-eof port))
          result))))
 
-  (define (do-fetch uri)
+  (define (do-fetch uri port)
     (case (and=> uri uri-scheme)
       ((http https)
        (let ((requests (map (cut narinfo-request url <>) paths)))
          (update-progress!)
          (let ((result (http-multiple-get uri
                                           handle-narinfo-response '()
-                                          requests)))
+                                          requests
+                                          #:port port)))
+           (unless (port-closed? port)
+             (close-port port))
            (newline (current-error-port))
            result)))
       ((file #f)
@@ -602,17 +632,17 @@ (define (do-fetch uri)
        (leave (_ "~s: unsupported server URI scheme~%")
               (if uri (uri-scheme uri) url)))))
 
-  (define cache-info
+  (let-values (((cache-info port)
-    (download-cache-info url))
+                (download-cache-info url)))
-
+    (and cache-info
-  (and cache-info
+         (if (string=? (cache-info-store-directory cache-info)
-       (if (string=? (cache-info-store-directory cache-info)
+                       (%store-prefix))
-                     (%store-prefix))
+             (do-fetch (string->uri url) port)    ;reuse PORT
-           (do-fetch (string->uri url))
+             (begin
-           (begin
+               (warning (_ "'~a' uses different store '~a'; ignoring it~%")
-             (warning (_ "'~a' uses different store '~a'; ignoring it~%")
+                        url (cache-info-store-directory cache-info))
-                      url (cache-info-store-directory cache-info))
+               (close-port port)
-             #f))))
+               #f)))))
 
 (define (lookup-narinfos cache paths)
   "Return the narinfos for PATHS, invoking the server at CACHE when no

guix/store.scm

@@ -726,14 +726,23 @@ (define references
              "Return the list of references of PATH."
              store-path-list))
 
+(define %reference-cache
+  ;; Brute-force cache mapping store items to their list of references.
+  ;; Caching matters because when building a profile in the presence of
+  ;; grafts, we keep calling 'graft-derivation', which in turn calls
+  ;; 'references/substitutes' many times with the same arguments.  Ideally we
+  ;; would use a cache associated with the daemon connection instead (XXX).
+  (make-hash-table 100))
+
 (define (references/substitutes store items)
   "Return the list of list of references of ITEMS; the result has the same
 length as ITEMS.  Query substitute information for any item missing from the
 store at once.  Raise a '&nix-protocol-error' exception if reference
 information for one of ITEMS is missing."
   (let* ((local-refs (map (lambda (item)
-                            (guard (c ((nix-protocol-error? c) #f))
+                            (or (hash-ref %reference-cache item)
-                              (references store item)))
+                                (guard (c ((nix-protocol-error? c) #f))
+                                  (references store item))))
                           items))
          (missing    (fold-right (lambda (item local-ref result)
                                    (if local-ref
@@ -757,7 +766,10 @@ (define (references/substitutes store items)
                (result      '()))
       (match items
         (()
-         (reverse result))
+         (let ((result (reverse result)))
+           (for-each (cut hash-set! %reference-cache <> <>)
+                     items result)
+           result))
         ((item items ...)
          (match local-refs
            ((#f tail ...)