Merge branch 'master' into staging

Makefile.am

@@ -4,6 +4,7 @@
 # Copyright © 2015, 2017 Alex Kost <alezost@gmail.com>
 # Copyright © 2016 Mathieu Lirzin <mthl@gnu.org>
 # Copyright © 2016, 2017 Mark H Weaver <mhw@netris.org>
+# Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 #
 # This file is part of GNU Guix.
 #
@@ -394,11 +395,11 @@ EXTRA_DIST =						\
   TODO							\
   CODE-OF-CONDUCT					\
   .dir-locals.el					\
+  gnu/build/svg.scm					\
   build-aux/build-self.scm				\
   build-aux/compile-all.scm				\
   build-aux/hydra/evaluate.scm				\
   build-aux/hydra/gnu-system.scm			\
-  build-aux/hydra/demo-os.scm				\
   build-aux/hydra/guix.scm				\
   build-aux/check-available-binaries.scm		\
   build-aux/check-final-inputs-self-contained.scm	\
@@ -489,11 +490,13 @@ AM_DISTCHECK_CONFIGURE_FLAGS =			\
   --with-nix-prefix="$(NIX_PREFIX)"		\
   --enable-daemon
 
-# The self-contained tarball.
+# The self-contained tarball.  Add 'glibc-utf8-locales' along with glibc just
+# so 'etc/profile' defines 'GUIX_LOCPATH' pointing to a valid set of locales.
 guix-binary.%.tar.xz:
 	$(AM_V_GEN)GUIX_PACKAGE_PATH=				\
 	tarball=`$(top_builddir)/pre-inst-env guix pack -C xz	\
-	  -s "$*" --localstatedir guix` ;			\
+	  -s "$*" --localstatedir guix glibc-utf8-locales	\
+	  -e  '(@@ (gnu packages commencement) glibc-final)'` ;	\
 	cp "$$tarball" "$@.tmp" ; mv "$@.tmp" "$@"
 
 

build-aux/download.scm

@@ -42,17 +42,15 @@
   (match (string-tokenize file (char-set-complement (char-set #\/)))
     ((_ ... system basename)
      (string->uri
-       (match system
+      (string-append %url-base "/" system
-        ("aarch64-linux"
+                     (match system
-         (string-append "http://flashner.co.il/guix/bootstrap/aarch64-linux"
+                       ("aarch64-linux"
-                        "/20170217/" basename))
+                        "/20170217/")
-        (_ (string-append %url-base "/" system
+                       ("armhf-linux"
-                          (match system
+                        "/20150101/")
-                                 ("armhf-linux"
+                       (_
-                                  "/20150101/")
+                        "/20131110/"))
-                                 (_
+                     basename)))))
-                                  "/20131110/"))
-                          basename)))))))
 
 (match (command-line)
   ((_ file expected-hash)

doc/guix.texi

@@ -165,6 +165,7 @@ GNU Distribution
 
 * System Installation::         Installing the whole operating system.
 * System Configuration::        Configuring the operating system.
+* Documentation::                Browsing software user manuals.
 * Installing Debugging Files::  Feeding the debugger.
 * Security Updates::            Deploying security fixes quickly.
 * Package Modules::             Packages from the programmer's viewpoint.
@@ -233,7 +234,7 @@ Packaging Guidelines
 * Package Naming::              What's in a name?
 * Version Numbers::             When the name is not enough.
 * Synopses and Descriptions::   Helping users find the right package.
-* Python Modules::              Taming the snake.
+* Python Modules::              A touch of British comedy.
 * Perl Modules::                Little pearls.
 * Java Packages::               Coffee break.
 * Fonts::                       Fond of fonts.
@@ -438,6 +439,14 @@ Make @code{root}'s profile available under @file{~/.guix-profile}:
          ~root/.guix-profile
 @end example
 
+Source @file{etc/profile} to augment @code{PATH} and other relevant
+environment variables:
+
+@example
+# GUIX_PROFILE=$HOME/.guix-profile \
+  source $GUIX_PROFILE/etc/profile
+@end example
+
 @item
 Create the group and user accounts for build users as explained below
 (@pxref{Build Environment Setup}).
@@ -2475,6 +2484,14 @@ This produces a tarball that follows the
 Docker Image Specification}.
 @end table
 
+@item --expression=@var{expr}
+@itemx -e @var{expr}
+Consider the package @var{expr} evaluates to.
+
+This has the same purpose as the same-named option in @command{guix
+build} (@pxref{Additional Build Options, @code{--expression} in
+@command{guix build}}).
+
 @item --system=@var{system}
 @itemx -s @var{system}
 Attempt to build for @var{system}---e.g., @code{i686-linux}---instead of
@@ -2946,6 +2963,16 @@ with @var{libressl}.  Then we use it to define a @dfn{variant} of the
 This is exactly what the @option{--with-input} command-line option does
 (@pxref{Package Transformation Options, @option{--with-input}}).
 
+A more generic procedure to rewrite a package dependency graph is
+@code{package-mapping}: it supports arbitrary changes to nodes in the
+graph.
+
+@deffn {Scheme Procedure} package-mapping @var{proc} [@var{cut?}]
+Return a procedure that, given a package, applies @var{proc} to all the packages
+depended on and returns the resulting package.  The procedure stops recursion
+when @var{cut?} returns true for a given package.
+@end deffn
+
 @menu
 * package Reference ::          The package data type.
 * origin Reference::            The origin data type.
@@ -4011,8 +4038,15 @@ in this example:
 @deffnx {Scheme Syntax} mlet* @var{monad} ((@var{var} @var{mval}) ...) @
        @var{body} ...
 Bind the variables @var{var} to the monadic values @var{mval} in
-@var{body}.  The form (@var{var} -> @var{val}) binds @var{var} to the
+@var{body}, which is a sequence of expressions.  As with the bind
-``normal'' value @var{val}, as per @code{let}.
+operator, this can be thought of as ``unpacking'' the raw, non-monadic
+value ``contained'' in @var{mval} and making @var{var} refer to that
+raw, non-monadic value within the scope of the @var{body}.  The form
+(@var{var} -> @var{val}) binds @var{var} to the ``normal'' value
+@var{val}, as per @code{let}.  The binding operations occur in sequence
+from left to right.  The last expression of @var{body} must be a monadic
+expression, and its result will become the result of the @code{mlet} or
+@code{mlet*} when run in the @var{monad}.
 
 @code{mlet*} is to @code{mlet} what @code{let*} is to @code{let}
 (@pxref{Local Bindings,,, guile, GNU Guile Reference Manual}).
@@ -4020,13 +4054,28 @@ Bind the variables @var{var} to the monadic values @var{mval} in
 
 @deffn {Scheme System} mbegin @var{monad} @var{mexp} ...
 Bind @var{mexp} and the following monadic expressions in sequence,
-returning the result of the last expression.
+returning the result of the last expression.  Every expression in the
+sequence must be a monadic expression.
 
 This is akin to @code{mlet}, except that the return values of the
 monadic expressions are ignored.  In that sense, it is analogous to
 @code{begin}, but applied to monadic expressions.
 @end deffn
 
+@deffn {Scheme System} mwhen @var{condition} @var{mexp0} @var{mexp*} ...
+When @var{condition} is true, evaluate the sequence of monadic
+expressions @var{mexp0}..@var{mexp*} as in an @code{mbegin}.  When
+@var{condition} is false, return @code{*unspecified*} in the current
+monad.  Every expression in the sequence must be a monadic expression.
+@end deffn
+
+@deffn {Scheme System} munless @var{condition} @var{mexp0} @var{mexp*} ...
+When @var{condition} is false, evaluate the sequence of monadic
+expressions @var{mexp0}..@var{mexp*} as in an @code{mbegin}.  When
+@var{condition} is true, return @code{*unspecified*} in the current
+monad.  Every expression in the sequence must be a monadic expression.
+@end deffn
+
 @cindex state monad
 The @code{(guix monads)} module provides the @dfn{state monad}, which
 allows an additional value---the state---to be @emph{threaded} through
@@ -6897,6 +6946,7 @@ For information on porting to other architectures or kernels,
 @menu
 * System Installation::         Installing the whole operating system.
 * System Configuration::        Configuring the operating system.
+* Documentation::                Browsing software user manuals.
 * Installing Debugging Files::  Feeding the debugger.
 * Security Updates::            Deploying security fixes quickly.
 * Package Modules::             Packages from the programmer's viewpoint.
@@ -15226,6 +15276,11 @@ of the given @var{size}.  @var{size} may be a number of bytes, or it may
 include a unit as a suffix (@pxref{Block size, size specifications,,
 coreutils, GNU Coreutils}).
 
+@item --root=@var{file}
+@itemx -r @var{file}
+Make @var{file} a symlink to the result, and register it as a garbage
+collector root.
+
 @item --on-error=@var{strategy}
 Apply @var{strategy} when an error occurs when reading @var{file}.
 @var{strategy} may be one of the following:
@@ -15895,6 +15950,70 @@ This service represents PID@tie{}1.
 @end defvr
 
 
+@node Documentation
+@section Documentation
+
+@cindex documentation, searching for
+@cindex searching for documentation
+@cindex Info, documentation format
+@cindex man pages
+@cindex manual pages
+In most cases packages installed with Guix come with documentation.
+There are two main documentation formats: ``Info'', a browseable
+hypertext format used for GNU software, and ``manual pages'' (or ``man
+pages''), the linear documentation format traditionally found on Unix.
+Info manuals are accessed with the @command{info} command or with Emacs,
+and man pages are accessed using @command{man}.
+
+You can look for documentation of software installed on your system by
+keyword.  For example, the following command searches for information
+about ``TLS'' in Info manuals:
+
+@example
+$ info -k TLS
+"(emacs)Network Security" -- STARTTLS
+"(emacs)Network Security" -- TLS
+"(gnutls)Core TLS API" -- gnutls_certificate_set_verify_flags
+"(gnutls)Core TLS API" -- gnutls_certificate_set_verify_function
+@dots{}
+@end example
+
+@noindent
+The command below searches for the same keyword in man pages:
+
+@example
+$ man -k TLS
+SSL (7)              - OpenSSL SSL/TLS library
+certtool (1)         - GnuTLS certificate tool
+@dots {}
+@end example
+
+These searches are purely local to your computer so you have the
+guarantee that documentation you find corresponds to what you have
+actually installed, you can access it off-line, and your privacy is
+respected.
+
+Once you have these results, you can view the relevant documentation by
+running, say:
+
+@example
+$ info "(gnutls)Core TLS API"
+@end example
+
+@noindent
+or:
+
+@example
+$ man certtool
+@end example
+
+Info manuals contain sections and indices as well as hyperlinks like
+those found in Web pages.  The @command{info} reader (@pxref{Top, Info
+reader,, info-stnd, Stand-alone GNU Info}) and its Emacs counterpart
+(@pxref{Misc Help,,, emacs, The GNU Emacs Manual}) provide intuitive key
+bindings to navigate manuals.  @xref{Getting Started,,, info, Info: An
+Introduction}, for an introduction to Info navigation.
+
 @node Installing Debugging Files
 @section Installing Debugging Files
 
@@ -16206,7 +16325,7 @@ needed is to review and apply the patch.
 * Package Naming::              What's in a name?
 * Version Numbers::             When the name is not enough.
 * Synopses and Descriptions::   Helping users find the right package.
-* Python Modules::              Taming the snake.
+* Python Modules::              A touch of British comedy.
 * Perl Modules::                Little pearls.
 * Java Packages::               Coffee break.
 * Fonts::                       Fond of fonts.

gnu/build/file-systems.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2017 David Craven <david@craven.ch>
+;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -47,12 +48,7 @@
 
             mount-flags->bit-mask
             check-file-system
-            mount-file-system)
+            mount-file-system))
-  #:re-export (mount
-               umount
-               MS_BIND
-               MS_MOVE
-               MS_RDONLY))
 
 ;;; Commentary:
 ;;;
@@ -61,13 +57,6 @@
 ;;;
 ;;; Code:
 
-;; 'mount' is already defined in the statically linked Guile used for initial
-;; RAM disks, in which case the bindings in (guix build syscalls) do not work
-;; (the FFI bindings do not work there).  Override them in that case.
-(when (module-defined? the-scm-module 'mount)
-  (set! mount (@ (guile) mount))
-  (set! umount (@ (guile) umount)))
-
 (define (bind-mount source target)
   "Bind-mount SOURCE at TARGET."
   (mount source target "" MS_BIND))
@@ -576,10 +565,6 @@ corresponds to the symbols listed in FLAGS."
       (()
        0))))
 
-(define (regular-file? file-name)
-  "Return #t if FILE-NAME is a regular file."
-  (eq? (stat:type (stat file-name)) 'regular))
-
 (define* (mount-file-system spec #:key (root "/root"))
   "Mount the file system described by SPEC under ROOT.  SPEC must have the
 form:
@@ -619,9 +604,9 @@ run a file system check."
          (check-file-system source type))
 
        ;; Create the mount point.  Most of the time this is a directory, but
-       ;; in the case of a bind mount, a regular file may be needed.
+       ;; in the case of a bind mount, a regular file or socket may be needed.
        (if (and (= MS_BIND (logand flags MS_BIND))
-                (regular-file? source))
+                (not (file-is-directory? source)))
            (unless (file-exists? mount-point)
              (mkdir-p (dirname mount-point))
              (call-with-output-file mount-point (const #t)))

gnu/build/linux-boot.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -26,6 +27,7 @@
   #:use-module (ice-9 match)
   #:use-module (ice-9 ftw)
   #:use-module (guix build utils)
+  #:use-module (guix build syscalls)
   #:use-module (gnu build linux-modules)
   #:use-module (gnu build file-systems)
   #:export (mount-essential-file-systems

gnu/build/linux-modules.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -18,6 +19,7 @@
 
 (define-module (gnu build linux-modules)
   #:use-module (guix elf)
+  #:use-module (guix build syscalls)
   #:use-module (rnrs io ports)
   #:use-module (rnrs bytevectors)
   #:use-module (srfi srfi-1)

gnu/build/vm.scm

@@ -21,6 +21,7 @@
 (define-module (gnu build vm)
   #:use-module (guix build utils)
   #:use-module (guix build store-copy)
+  #:use-module (guix build syscalls)
   #:use-module (gnu build linux-boot)
   #:use-module (gnu build install)
   #:use-module (guix records)

gnu/local.mk

@@ -53,7 +53,6 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/assembly.scm			\
   %D%/packages/astronomy.scm			\
   %D%/packages/attr.scm				\
-  %D%/packages/audacity.scm			\
   %D%/packages/audio.scm			\
   %D%/packages/augeas.scm			\
   %D%/packages/autogen.scm			\
@@ -71,6 +70,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/boost.scm			\
   %D%/packages/bootloaders.scm			\
   %D%/packages/bootstrap.scm			\
+  %D%/packages/build-tools.scm			\
   %D%/packages/busybox.scm			\
   %D%/packages/c.scm				\
   %D%/packages/calcurse.scm			\
@@ -106,7 +106,6 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/dejagnu.scm			\
   %D%/packages/dico.scm				\
   %D%/packages/dictionaries.scm			\
-  %D%/packages/dillo.scm			\
   %D%/packages/disk.scm				\
   %D%/packages/display-managers.scm		\
   %D%/packages/django.scm			\
@@ -390,6 +389,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/w3m.scm				\
   %D%/packages/wdiff.scm			\
   %D%/packages/web.scm				\
+  %D%/packages/web-browsers.scm			\
   %D%/packages/webkit.scm			\
   %D%/packages/wget.scm				\
   %D%/packages/wicd.scm				\
@@ -460,7 +460,6 @@ GNU_SYSTEM_MODULES =				\
   %D%/build/linux-modules.scm			\
   %D%/build/marionette.scm			\
   %D%/build/shepherd.scm			\
-  %D%/build/svg.scm				\
   %D%/build/vm.scm				\
 						\
   %D%/tests.scm					\
@@ -495,7 +494,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/ath9k-htc-firmware-binutils.patch	\
   %D%/packages/patches/ath9k-htc-firmware-gcc.patch		\
   %D%/packages/patches/ath9k-htc-firmware-objcopy.patch		\
-  %D%/packages/patches/audacity-fix-ffmpeg-binding.patch	\
   %D%/packages/patches/automake-skip-amhello-tests.patch	\
   %D%/packages/patches/automake-regexp-syntax.patch		\
   %D%/packages/patches/automake-test-gzip-warning.patch		\
@@ -609,11 +607,11 @@ dist_patch_DATA =						\
   %D%/packages/patches/glibc-locales.patch			\
   %D%/packages/patches/glibc-o-largefile.patch			\
   %D%/packages/patches/glibc-versioned-locpath.patch		\
+  %D%/packages/patches/glog-gcc-5-demangling.patch		\
   %D%/packages/patches/gmp-arm-asm-nothumb.patch		\
   %D%/packages/patches/gmp-faulty-test.patch			\
   %D%/packages/patches/gnome-tweak-tool-search-paths.patch	\
   %D%/packages/patches/gnucash-price-quotes-perl.patch		\
-  %D%/packages/patches/gnupg-2.1-fix-Y2038-test-failure.patch	\
   %D%/packages/patches/gobject-introspection-absolute-shlib-path.patch \
   %D%/packages/patches/gobject-introspection-cc.patch		\
   %D%/packages/patches/gobject-introspection-girepository.patch	\
@@ -662,12 +660,16 @@ dist_patch_DATA =						\
   %D%/packages/patches/id3lib-CVE-2007-4460.patch			\
   %D%/packages/patches/ilmbase-fix-tests.patch			\
   %D%/packages/patches/isl-0.11.1-aarch64-support.patch	\
+  %D%/packages/patches/jasper-CVE-2017-6850.patch		\
   %D%/packages/patches/jbig2dec-ignore-testtest.patch		\
   %D%/packages/patches/jbig2dec-CVE-2016-9601.patch		\
   %D%/packages/patches/jq-CVE-2015-8863.patch			\
   %D%/packages/patches/kdbusaddons-kinit-file-name.patch	\
   %D%/packages/patches/khmer-use-libraries.patch                \
-  %D%/packages/patches/kio-CVE-2017-6410.patch			\
+  %D%/packages/patches/kiki-level-selection-crash.patch		\
+  %D%/packages/patches/kiki-makefile.patch			\
+  %D%/packages/patches/kiki-missing-includes.patch		\
+  %D%/packages/patches/kiki-portability-64bit.patch		\
   %D%/packages/patches/kmod-module-directory.patch		\
   %D%/packages/patches/kobodeluxe-paths.patch			\
   %D%/packages/patches/kobodeluxe-enemies-pipe-decl.patch	\
@@ -759,8 +761,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/luajit-no_ldconfig.patch			\
   %D%/packages/patches/luajit-symlinks.patch			\
   %D%/packages/patches/luit-posix.patch				\
+  %D%/packages/patches/luminance-hdr-qt-printer.patch		\
   %D%/packages/patches/lvm2-static-link.patch			\
   %D%/packages/patches/lxsession-use-gapplication.patch         \
+  %D%/packages/patches/lz4-fix-test-failures.patch		\
   %D%/packages/patches/make-impure-dirs.patch			\
   %D%/packages/patches/mars-install.patch			\
   %D%/packages/patches/mars-sfml-2.3.patch			\
@@ -794,6 +798,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/netsurf-system-utf8proc.patch		\
   %D%/packages/patches/netsurf-y2038-tests.patch		\
   %D%/packages/patches/netsurf-longer-test-timeout.patch	\
+  %D%/packages/patches/networkmanager-qt-activeconnection-test-1.patch \
+  %D%/packages/patches/networkmanager-qt-activeconnection-test-2.patch \
   %D%/packages/patches/ngircd-handle-zombies.patch		\
   %D%/packages/patches/ninja-zero-mtime.patch			\
   %D%/packages/patches/node-9077.patch				\
@@ -821,11 +827,12 @@ dist_patch_DATA =						\
   %D%/packages/patches/ots-no-include-missing-file.patch	\
   %D%/packages/patches/p7zip-CVE-2016-9296.patch			\
   %D%/packages/patches/p7zip-remove-unused-code.patch		\
-  %D%/packages/patches/password-store-gnupg-compat.patch	\
   %D%/packages/patches/patchelf-page-size.patch			\
   %D%/packages/patches/patchelf-rework-for-arm.patch		\
   %D%/packages/patches/patchutils-xfail-gendiff-tests.patch	\
   %D%/packages/patches/patch-hurd-path-max.patch		\
+  %D%/packages/patches/pcre-CVE-2017-7186.patch			\
+  %D%/packages/patches/pcre2-CVE-2017-7186.patch		\
   %D%/packages/patches/perl-autosplit-default-time.patch	\
   %D%/packages/patches/perl-deterministic-ordering.patch	\
   %D%/packages/patches/perl-finance-quote-unuse-mozilla-ca.patch \
@@ -878,6 +885,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch	\
   %D%/packages/patches/python-statsmodels-fix-tests.patch	\
   %D%/packages/patches/python-configobj-setuptools.patch	\
+  %D%/packages/patches/python-cython-fix-tests-32bit.patch	\
   %D%/packages/patches/python-fake-factory-fix-build-32bit.patch	\
   %D%/packages/patches/python-faker-fix-build-32bit.patch	\
   %D%/packages/patches/python-pandas-skip-failing-tests.patch	\
@@ -891,18 +899,13 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-pygpgme-fix-pinentry-tests.patch	\
   %D%/packages/patches/python2-subprocess32-disable-input-test.patch	\
   %D%/packages/patches/qemu-CVE-2016-10155.patch			\
-  %D%/packages/patches/qemu-CVE-2017-2615.patch			\
-  %D%/packages/patches/qemu-CVE-2017-2620.patch			\
-  %D%/packages/patches/qemu-CVE-2017-2630.patch			\
   %D%/packages/patches/qemu-CVE-2017-5525.patch			\
   %D%/packages/patches/qemu-CVE-2017-5526.patch			\
   %D%/packages/patches/qemu-CVE-2017-5552.patch			\
   %D%/packages/patches/qemu-CVE-2017-5578.patch			\
   %D%/packages/patches/qemu-CVE-2017-5579.patch			\
-  %D%/packages/patches/qemu-CVE-2017-5667.patch			\
   %D%/packages/patches/qemu-CVE-2017-5856.patch			\
   %D%/packages/patches/qemu-CVE-2017-5898.patch			\
-  %D%/packages/patches/qemu-CVE-2017-5931.patch			\
   %D%/packages/patches/qt4-ldflags.patch			\
   %D%/packages/patches/quickswitch-fix-dmenu-check.patch	\
   %D%/packages/patches/rapicorn-isnan.patch			\
@@ -921,6 +924,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/ruby-tzinfo-data-ignore-broken-test.patch\
   %D%/packages/patches/scheme48-tests.patch			\
   %D%/packages/patches/scotch-test-threading.patch		\
+  %D%/packages/patches/screen-fix-info-syntax-error.patch	\
   %D%/packages/patches/sdl-libx11-1.6.patch			\
   %D%/packages/patches/seq24-rename-mutex.patch			\
   %D%/packages/patches/serf-comment-style-fix.patch		\
@@ -952,6 +956,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/tcsh-fix-autotest.patch			\
   %D%/packages/patches/tcsh-fix-out-of-bounds-read.patch	\
   %D%/packages/patches/teensy-loader-cli-help.patch		\
+  %D%/packages/patches/teeworlds-use-latest-wavpack.patch	\
   %D%/packages/patches/texlive-texmf-CVE-2016-10243.patch	\
   %D%/packages/patches/texi2html-document-encoding.patch	\
   %D%/packages/patches/texi2html-i18n.patch			\

gnu/packages/admin.scm

@@ -8,13 +8,14 @@
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
-;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Peter Feigl <peter.feigl@nexoid.at>
 ;;; Copyright © 2016 John J. Foerch <jjfoerch@earthlink.net>
 ;;; Coypright © 2016, 2017 ng0 <contact.ng0@cryptolab.net>
 ;;; Coypright © 2016 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Coypright © 2016 John Darrington <jmd@gnu.org>
+;;; Coypright © 2017 Ben Sturmfels <ben@sturm.com.au>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -67,10 +68,12 @@
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages groff)
   #:use-module (gnu packages pciutils)
+  #:use-module (gnu packages libunwind)
   #:use-module (gnu packages libusb)
   #:use-module (gnu packages libftdi)
   #:use-module (gnu packages image)
   #:use-module (gnu packages xorg)
+  #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages python)
   #:use-module (gnu packages man)
   #:use-module (gnu packages autotools)
@@ -477,7 +480,7 @@ connection alive.")
          (bind-minor-version "9")
          (bind-patch-version "9")
          (bind-release-type "-P")         ; for patch release, use "-P"
-         (bind-release-version "6")      ; for patch release, e.g. "6"
+         (bind-release-version "8")      ; for patch release, e.g. "6"
          (bind-version (string-append bind-major-version
                                       "."
                                       bind-minor-version
@@ -593,7 +596,7 @@ connection alive.")
                                         "/bind-" bind-version ".tar.gz"))
                     (sha256
                      (base32
-                      "1qf9j0nyqx0qy871mj22xh4dg0n1pqlv94lpiijb8vr7n7m3svhr"))))
+                      "1f5i64f6y4rmy61y63r5if1lifw8dw8r8dh6ns3x4002hanzrpgz"))))
 
                 ;; When cross-compiling, we need the cross Coreutils and sed.
                 ;; Otherwise just use those from %FINAL-INPUTS.
@@ -1997,3 +2000,86 @@ with all the commands and parameters identified for your viewing pleasure.
 With sedsed you can master any sed script.  No more secrets, no more hidden
 buffers.")
     (license license:expat)))
+
+(define-public intel-gpu-tools
+  (package
+    (name "intel-gpu-tools")
+    (version "1.18")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://cgit.freedesktop.org/xorg/app/"
+                                  "intel-gpu-tools/snapshot/"
+                                  "intel-gpu-tools-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0w7djk0y5w76hzn1b3cm39zd5c6w9za1wfn80wd857h0v313rzq3"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; many of the tests try to load kernel modules
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'autogen
+           (lambda _
+             ;; Don't run configure in this phase
+             (setenv "NOCONFIGURE" "1")
+             (zero? (system* "sh" "autogen.sh")))))))
+    (inputs
+     `(("util-macros" ,util-macros)
+       ("libdrm" ,libdrm)
+       ("libpciaccess" ,libpciaccess)
+       ("kmod" ,kmod)
+       ("procps" ,procps)
+       ("cairo" ,cairo)
+       ("libunwind" ,libunwind)
+       ("libxrandr" ,libxrandr)
+       ("glib" ,glib)))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
+    (home-page "https://cgit.freedesktop.org/xorg/app/intel-gpu-tools/")
+    (synopsis "Tools for development and testing of the Intel DRM driver")
+    (description "Intel GPU Tools is a collection of tools for development and
+testing of the Intel DRM driver.  There are many macro-level test suites that
+get used against the driver, including xtest, rendercheck, piglit, and
+oglconform, but failures from those can be difficult to track down to kernel
+changes, and many require complicated build procedures or specific testing
+environments to get useful results.  Therefore, Intel GPU Tools includes
+low-level tools and tests specifically for development and testing of the
+Intel DRM Driver.")
+    (license license:expat)))
+
+(define-public fabric
+  (package
+    (name "fabric")
+    (version "1.13.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "Fabric" version))
+       (sha256
+        (base32
+         "1z17hw0yiqp1blq217zxkg2jzkv8qd79saqhscgsw14mwlcqpwd0"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f     ;XXX: Tests attempt to download Python "fudge" package.
+       #:python ,python-2))                       ;Python 2 only
+    (propagated-inputs
+     ;; Required upgrading python-paramiko 1.17.4 to fix an incompatibility
+     ;; between python-paramiko and newer python-pycrypto. Without this, the
+     ;; `fab` command fails with "ValueError: CTR mode needs counter
+     ;; parameter, not IV". See:
+     ;; https://github.com/paramiko/paramiko/pull/714#issuecomment-281191548.
+     `(("python2-paramiko" ,python2-paramiko)))
+    (home-page "http://fabfile.org")
+    (synopsis "Simple Pythonic remote execution and deployment tool")
+    (description
+     "Fabric is designed to upload files and run shell commands on a number of
+servers in parallel or serially.  These commands are grouped in tasks (which
+are regular Python functions) and specified in a @dfn{fabfile}.
+
+It is similar to Capistrano, except it's implemented in Python and doesn't
+expect you to be deploying Rails applications.  Fabric is a simple, Pythonic
+tool for remote execution and deployment.")
+    (license license:bsd-2)))

gnu/packages/algebra.scm

@@ -4,6 +4,7 @@
 ;;; Copyright © 2016 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,26 +26,26 @@
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages documentation)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fltk)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages image)
-  #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
+  #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages perl)
-  #:use-module (gnu packages readline)
-  #:use-module (gnu packages flex)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages readline)
   #:use-module (gnu packages shells)
   #:use-module (gnu packages tex)
   #:use-module (gnu packages xiph)
   #:use-module (gnu packages xorg)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages)
-  #:use-module (guix download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
+  #:use-module (guix download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
   #:use-module (guix utils))
 
 
@@ -494,7 +495,9 @@ binary.")
                             ;; PREFIX/share/{man,info}.
                             (string-append "--mandir=" out "/share/man")
                             (string-append "--infodir=" out "/share/info")))))
-                      %standard-phases)))
+                      %standard-phases)
+       #:configure-flags
+       (list "--with-readline")))
     (home-page "https://www.gnu.org/software/bc/")
     (synopsis "Arbitrary precision numeric processing language")
     (description

gnu/packages/audacity.scm

@@ -1,103 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
-;;;
-;;; 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 audacity)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix build-system gnu)
-  #:use-module (gnu packages)
-  #:use-module (gnu packages audio)
-  #:use-module (gnu packages base)
-  #:use-module (gnu packages gettext)
-  #:use-module (gnu packages gtk)
-  #:use-module (gnu packages linux)
-  #:use-module (gnu packages mp3)
-  #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages pulseaudio)
-  #:use-module (gnu packages python)
-  #:use-module (gnu packages xiph)
-  #:use-module (gnu packages xml)
-  #:use-module (gnu packages video)
-  #:use-module (gnu packages wxwidgets))
-
-(define-public audacity
-  (package
-    (name "audacity")
-    (version "2.1.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/audacity/audacity/archive"
-                           "/Audacity-" version ".zip"))
-       (sha256
-        (base32 "1642i9d5cdmqzj6r0qdl2ldnqsvpb08znnczncysi72x6zpvb5qq"))
-       (patches (search-patches "audacity-fix-ffmpeg-binding.patch"))))
-    (build-system gnu-build-system)
-    (inputs
-     ;; TODO: Add portSMF and libwidgetextra once they're packaged.  In-tree
-     ;; versions shipping with Audacity are used for now.
-     `(("wxwidgets" ,wxwidgets-gtk2)
-       ("gtk" ,gtk+-2)
-       ("alsa-lib" ,alsa-lib)
-       ("jack" ,jack-1)
-       ("expat" ,expat)
-       ("ffmpeg" ,ffmpeg)
-       ("lame" ,lame)
-       ("flac" ,flac)
-       ("libid3tag" ,libid3tag)
-       ("libmad" ,libmad)
-       ("libsbsms" ,libsbsms)
-       ("libsndfile" ,libsndfile)
-       ("soundtouch" ,soundtouch)
-       ("soxr" ,soxr)                   ;replaces libsamplerate
-       ("twolame" ,twolame)
-       ("vamp" ,vamp)
-       ("libvorbis" ,libvorbis)
-       ("lv2" ,lv2)
-       ("lilv" ,lilv)
-       ("portaudio" ,portaudio)))
-    (native-inputs
-     `(("gettext" ,gettext-minimal)     ;for msgfmt
-       ("pkg-config" ,pkg-config)
-       ("python" ,python-2)
-       ("which" ,which)))
-    (arguments
-     '(#:configure-flags
-       (let ((libid3tag (assoc-ref %build-inputs "libid3tag"))
-             (libmad (assoc-ref %build-inputs "libmad")))
-         (list
-          ;; Loading FFmpeg dynamically is problematic.
-          "--disable-dynamic-loading"
-          ;; libid3tag and libmad provide no .pc files, so pkg-config fails to
-          ;; find them.  Force their inclusion.
-          (string-append "ID3TAG_CFLAGS=-I" libid3tag "/include")
-          (string-append "ID3TAG_LIBS=-L" libid3tag "/lib -lid3tag -lz")
-          (string-append "LIBMAD_CFLAGS=-I" libmad "/include")
-          (string-append "LIBMAD_LIBS=-L" libmad "/lib -lmad")))
-       ;; The test suite is not "well exercised" according to the developers,
-       ;; and fails with various errors.  See
-       ;; <http://sourceforge.net/p/audacity/mailman/message/33524292/>.
-       #:tests? #f))
-    (home-page "http://audacity.sourceforge.net/")
-    (synopsis "Software for recording and editing sounds")
-    (description
-     "Audacity is a multi-track audio editor designed for recording, playing
-and editing digital audio.  It features digital effects and spectrum analysis
-tools.")
-    (license license:gpl2+)))

gnu/packages/audio.scm

@@ -4,7 +4,7 @@
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2015, 2016 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2016 ng0 <ng0@we.make.ritual.n0.is>
 ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org>
@@ -75,6 +75,7 @@
   #:use-module (gnu packages video)
   #:use-module (gnu packages vim) ;xxd
   #:use-module (gnu packages webkit)
+  #:use-module (gnu packages wxwidgets)
   #:use-module (gnu packages xiph)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
@@ -269,6 +270,80 @@ record, edit, mix and master audio and MIDI projects.  It is targeted at audio
 engineers, musicians, soundtrack editors and composers.")
     (license license:gpl2+)))
 
+(define-public audacity
+  (package
+    (name "audacity")
+    (version "2.1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/audacity/audacity/archive"
+                           "/Audacity-" version ".tar.gz"))
+       (sha256
+        (base32 "11mx7gb4dbqrgfp7hm0154x3m76ddnmhf2675q5zkxn7jc5qfc6b"))))
+    (build-system gnu-build-system)
+    (inputs
+     ;; TODO: Add portSMF and libwidgetextra once they're packaged.  In-tree
+     ;; versions shipping with Audacity are used for now.
+     `(("wxwidgets" ,wxwidgets-gtk2)
+       ("gtk" ,gtk+-2)
+       ("alsa-lib" ,alsa-lib)
+       ("jack" ,jack-1)
+       ("expat" ,expat)
+       ("ffmpeg" ,ffmpeg)
+       ("lame" ,lame)
+       ("flac" ,flac)
+       ("libid3tag" ,libid3tag)
+       ("libmad" ,libmad)
+       ("libsbsms" ,libsbsms)
+       ("libsndfile" ,libsndfile)
+       ("soundtouch" ,soundtouch)
+       ("soxr" ,soxr)                   ;replaces libsamplerate
+       ("twolame" ,twolame)
+       ("vamp" ,vamp)
+       ("libvorbis" ,libvorbis)
+       ("lv2" ,lv2)
+       ("lilv" ,lilv)
+       ("portaudio" ,portaudio)))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("gettext" ,gettext-minimal)     ;for msgfmt
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)
+       ("python" ,python-2)
+       ("which" ,which)))
+    (arguments
+     '(#:configure-flags
+       (let ((libid3tag (assoc-ref %build-inputs "libid3tag"))
+             (libmad (assoc-ref %build-inputs "libmad")))
+         (list
+          ;; Loading FFmpeg dynamically is problematic.
+          "--disable-dynamic-loading"
+          ;; libid3tag and libmad provide no .pc files, so pkg-config fails to
+          ;; find them.  Force their inclusion.
+          (string-append "ID3TAG_CFLAGS=-I" libid3tag "/include")
+          (string-append "ID3TAG_LIBS=-L" libid3tag "/lib -lid3tag -lz")
+          (string-append "LIBMAD_CFLAGS=-I" libmad "/include")
+          (string-append "LIBMAD_LIBS=-L" libmad "/lib -lmad")))
+       #:phases
+       (modify-phases %standard-phases
+         ;; FFmpeg is only detected if autoreconf runs.
+         (add-before 'configure 'autoreconf
+           (lambda _
+             (zero? (system* "autoreconf" "-vfi")))))
+       ;; The test suite is not "well exercised" according to the developers,
+       ;; and fails with various errors.  See
+       ;; <http://sourceforge.net/p/audacity/mailman/message/33524292/>.
+       #:tests? #f))
+    (home-page "http://audacity.sourceforge.net/")
+    (synopsis "Software for recording and editing sounds")
+    (description
+     "Audacity is a multi-track audio editor designed for recording, playing
+and editing digital audio.  It features digital effects and spectrum analysis
+tools.")
+    (license license:gpl2+)))
+
 (define-public azr3
   (package
     (name "azr3")
@@ -1091,7 +1166,6 @@ patches that can be used with softsynths such as Timidity and WildMidi.")
        ("jack" ,jack-1)
        ("gtkmm" ,gtkmm-2)
        ("gtk+" ,gtk+-2)
-       ("webkitgtk/gtk+-2" ,webkitgtk/gtk+-2)
        ("fftwf" ,fftwf)
        ("lrdf" ,lrdf)
        ("zita-resampler" ,zita-resampler)
@@ -1227,7 +1301,7 @@ especially for creating reverb effects.  It supports impulse responses with 1,
 (define-public jack-1
   (package
     (name "jack")
-    (version "0.124.1")
+    (version "0.125.0")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -1236,7 +1310,7 @@ especially for creating reverb effects.  It supports impulse responses with 1,
                    ".tar.gz"))
              (sha256
               (base32
-               "1mk1wnx33anp6haxfjjkfhwbaknfblsvj35nxvz0hvspcmhdyhpb"))))
+               "0i6l25dmfk2ji2lrakqq9icnwjxklgcjzzk65dmsff91z2zva5rm"))))
     (build-system gnu-build-system)
     (inputs
      `(("alsa-lib" ,alsa-lib)
@@ -1328,14 +1402,14 @@ synchronous execution of all clients, and low latency operation.")
 (define-public jalv
   (package
     (name "jalv")
-    (version "1.4.6")
+    (version "1.6.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://download.drobilla.net/jalv-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "1f1hcq74n3ziw8bk97mn5a1vgw028dxikv3fchaxd430pbbhqgl9"))))
+                "1x2wpzzx2cgvz3dgdcgsj8dr0w3zsasy62mvl199bsdj5fbjaili"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f ; no check target
@@ -1351,8 +1425,8 @@ synchronous execution of all clients, and low latency operation.")
      `(("lv2" ,lv2)
        ("lilv" ,lilv)
        ("suil" ,suil)
-       ("gtk" ,gtk+-2)
+       ("gtk" ,gtk+)
-       ("gtkmm" ,gtkmm-2)
+       ("gtkmm" ,gtkmm)
        ("jack" ,jack-1)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -1526,15 +1600,14 @@ included are the command line utilities @code{send_osc} and @code{dump_osc}.")
 (define-public lilv
   (package
     (name "lilv")
-    (version "0.22.0")
+    (version "0.24.2")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://download.drobilla.net/lilv-"
-                                 version
+                                 version ".tar.bz2"))
-                                 ".tar.bz2"))
              (sha256
               (base32
-               "1d3ss7vv8drf1c5340lyd0gv736n2qy7sxji2nh1rw9y48hr69yd"))))
+               "08m5a372pr1l7aii9s3pic5nm68gynx1n1bc7bnlswziq6qnbv7p"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f ; no check target
@@ -1792,6 +1865,36 @@ buffers, and audio capture.")
 and ALSA.")
     (license license:gpl3+)))
 
+(define-public qjackctl
+  (package
+    (name "qjackctl")
+    (version "0.4.4")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append
+                "mirror://sourceforge/qjackctl/qjackctl/"
+                version "/qjackctl-" version ".tar.gz"))
+              (sha256
+               (base32
+                "19bbljb3iz5ss4s5fmra1dxabg2fnp61sa51d63zsm56xkvv47ak"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f)) ; no check target
+    (inputs
+     `(("jack-2" ,jack-2)
+       ("qtbase" ,qtbase)
+       ("qtx11extras" ,qtx11extras)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("qttools" ,qttools)))
+    (home-page "https://qjackctl.sourceforge.io/")
+    (synopsis "Jack server control application")
+    (description "Control a Jack server.  Allows you to plug various sources
+into various outputs and to start, stop and configure jackd")
+    (license license:gpl2+)))
+
+
 (define-public raul
   (package
     (name "raul")
@@ -1918,15 +2021,14 @@ input/output.")
 (define-public sratom
   (package
     (name "sratom")
-    (version "0.4.6")
+    (version "0.6.0")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://download.drobilla.net/sratom-"
-                                 version
+                                 version ".tar.bz2"))
-                                 ".tar.bz2"))
              (sha256
               (base32
-               "080jjiyxjnj7hf25844hd9rb01grvzz1rk8mxcdnakywmspbxfd4"))))
+               "0hrxd9i66s06bpn6i3s9ka95134g3sm8yscmif7qgdzhyjqw42j4"))))
     (build-system waf-build-system)
     (arguments `(#:tests? #f)) ; no check target
     (inputs
@@ -1945,15 +2047,14 @@ the Turtle syntax.")
 (define-public suil
   (package
     (name "suil")
-    (version "0.8.2")
+    (version "0.8.4")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://download.drobilla.net/suil-"
-                                 version
+                                 version ".tar.bz2"))
-                                 ".tar.bz2"))
              (sha256
               (base32
-               "1s3adyiw7sa5gfvm5wasa61qa23629kprxyv6w8hbxdiwp0hhxkq"))))
+               "1kji3lhha26qr6xm9j8ic5c40zbrrb5qnwm2qxzmsfxgmrz29wkf"))))
     (build-system waf-build-system)
     (arguments `(#:tests? #f)) ; no check target
     (inputs

gnu/packages/bioinformatics.scm

@@ -2084,7 +2084,7 @@ identify enrichments with functional annotations of the genome.")
 (define-public diamond
   (package
     (name "diamond")
-    (version "0.8.36")
+    (version "0.8.37")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2093,7 +2093,7 @@ identify enrichments with functional annotations of the genome.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "092smzzjcg51n3x4h84k52ijpz9m40ri838j9k2i463ribc3c8rh"))))
+                "1zn7q8m41ayfnjvf9snrsnq00mm68alf9rhdadx5q1sk23lyvp2l"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; no "check" target
@@ -3196,7 +3196,7 @@ sequencing tag position and orientation.")
 (define-public mafft
   (package
     (name "mafft")
-    (version "7.305")
+    (version "7.310")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3205,7 +3205,7 @@ sequencing tag position and orientation.")
               (file-name (string-append name "-" version ".tgz"))
               (sha256
                (base32
-                "0ziim7g58n3z8gppsa713f5fxprl60ldj3xck186z0n9dpp06i8r"))))
+                "0gbsaz6z2qa307kd7wfb06c3y4ikmv1hsdvlns11f6zq4w1z9pwc"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no automated tests, though there are tests in the read me
@@ -4041,7 +4041,7 @@ extremely diverse sets of genomes.")
 (define-public raxml
   (package
     (name "raxml")
-    (version "8.2.9")
+    (version "8.2.10")
     (source
      (origin
        (method url-fetch)
@@ -4052,7 +4052,7 @@ extremely diverse sets of genomes.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1pv8p2fy67y21a9y4cm7xpvxqjwz2v4201flfjshdq1p8j52rqf7"))))
+         "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; There are no tests.
@@ -4790,50 +4790,61 @@ sequence itself can be retrieved from these databases.")
                                  "/lib64"
                                  "/lib32")))
        #:phases
-       (alist-replace
+       (modify-phases %standard-phases
-        'configure
+         (replace 'configure
-        (lambda* (#:key inputs outputs #:allow-other-keys)
+           (lambda* (#:key inputs outputs #:allow-other-keys)
-          ;; The build system expects a directory containing the sources and
+             ;; The build system expects a directory containing the sources and
-          ;; raw build output of ncbi-vdb, including files that are not
+             ;; raw build output of ncbi-vdb, including files that are not
-          ;; installed.  Since we are building against an installed version of
+             ;; installed.  Since we are building against an installed version of
-          ;; ncbi-vdb, the following modifications are needed.
+             ;; ncbi-vdb, the following modifications are needed.
-          (substitute* "setup/konfigure.perl"
+             (substitute* "setup/konfigure.perl"
-            ;; Make the configure script look for the "ilib" directory of
+               ;; Make the configure script look for the "ilib" directory of
-            ;; "ncbi-vdb" without first checking for the existence of a
+               ;; "ncbi-vdb" without first checking for the existence of a
-            ;; matching library in its "lib" directory.
+               ;; matching library in its "lib" directory.
-            (("^            my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
+               (("^            my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
-             "my $f = File::Spec->catdir($ilibdir, $ilib);")
+                "my $f = File::Spec->catdir($ilibdir, $ilib);")
-            ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
+               ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
-            (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
+               (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
-             "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
+                "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
 
-          ;; Dynamic linking
+             ;; Dynamic linking
-          (substitute* "tools/copycat/Makefile"
+             (substitute* "tools/copycat/Makefile"
-            (("smagic-static") "lmagic"))
+               (("smagic-static") "lmagic"))
 
-          ;; The 'configure' script doesn't recognize things like
+             ;; The 'configure' script doesn't recognize things like
-          ;; '--enable-fast-install'.
+             ;; '--enable-fast-install'.
-          (zero? (system*
+             (zero? (system*
-                  "./configure"
+                     "./configure"
-                  (string-append "--build-prefix=" (getcwd) "/build")
+                     (string-append "--build-prefix=" (getcwd) "/build")
-                  (string-append "--prefix=" (assoc-ref outputs "out"))
+                     (string-append "--prefix=" (assoc-ref outputs "out"))
-                  (string-append "--debug")
+                     (string-append "--debug")
-                  (string-append "--with-fuse-prefix="
+                     (string-append "--with-fuse-prefix="
-                                 (assoc-ref inputs "fuse"))
+                                    (assoc-ref inputs "fuse"))
-                  (string-append "--with-magic-prefix="
+                     (string-append "--with-magic-prefix="
-                                 (assoc-ref inputs "libmagic"))
+                                    (assoc-ref inputs "libmagic"))
-                  ;; TODO: building with libxml2 fails with linker errors
+                     ;; TODO: building with libxml2 fails with linker errors
-                  ;; (string-append "--with-xml2-prefix="
+                     ;; (string-append "--with-xml2-prefix="
-                  ;;                (assoc-ref inputs "libxml2"))
+                     ;;                (assoc-ref inputs "libxml2"))
-                  (string-append "--with-ncbi-vdb-sources="
+                     (string-append "--with-ncbi-vdb-sources="
-                                 (assoc-ref inputs "ncbi-vdb"))
+                                    (assoc-ref inputs "ncbi-vdb"))
-                  (string-append "--with-ncbi-vdb-build="
+                     (string-append "--with-ncbi-vdb-build="
-                                 (assoc-ref inputs "ncbi-vdb"))
+                                    (assoc-ref inputs "ncbi-vdb"))
-                  (string-append "--with-ngs-sdk-prefix="
+                     (string-append "--with-ngs-sdk-prefix="
-                                 (assoc-ref inputs "ngs-sdk"))
+                                    (assoc-ref inputs "ngs-sdk"))
-                  (string-append "--with-hdf5-prefix="
+                     (string-append "--with-hdf5-prefix="
-                                 (assoc-ref inputs "hdf5")))))
+                                    (assoc-ref inputs "hdf5"))))))
-        %standard-phases)))
+         ;; This version of sra-tools fails to build with glibc because of a
+         ;; naming conflict.  glibc-2.25/include/bits/mathcalls.h already
+         ;; contains a definition of "canonicalize", so we rename it.
+         ;;
+         ;; See upstream bug report:
+         ;; https://github.com/ncbi/sra-tools/issues/67
+         (add-after 'unpack 'patch-away-glibc-conflict
+           (lambda _
+             (substitute* "tools/bam-loader/bam.c"
+               (("canonicalize\\(" line)
+                (string-append "sra_tools_" line)))
+             #t)))))
     (native-inputs `(("perl" ,perl)))
     (inputs
      `(("ngs-sdk" ,ngs-sdk)
@@ -5345,40 +5356,18 @@ information as possible.")
 (define-public r-vegan
   (package
     (name "r-vegan")
-    (version "2.4-2")
+    (version "2.4-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vegan" version))
        (sha256
         (base32
-         "12wf64izrpq9z3ix7mgm5421mq0xsm8dw5qblvcrz452nfhjf5w9"))))
+         "15zcxfix2d854897k1lr0sfmj2n00339nlsppcr3zrb238lb2mi5"))))
     (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'revert-test-deletion
-           ;; The distributed sources do not include tests with the CRAN
-           ;; package.  Here we revert the commit
-           ;; `591d0e8ba1deaaf82445474ec6619c0b43db4e63' which deletes these
-           ;; tests.  There are plans to not delete tests in future as
-           ;; documented at https://github.com/vegandevs/vegan/issues/181.
-           (lambda* (#:key inputs #:allow-other-keys)
-             (zero?
-              (system* "patch" "-R" "-p1" "-i"
-                       (assoc-ref inputs "r-vegan-delete-tests-patch"))))))))
     (native-inputs
      `(("gfortran" ,gfortran)
-       ("r-knitr" ,r-knitr)
+       ("r-knitr" ,r-knitr)))
-       ("r-vegan-delete-tests-patch"
-        ,(origin
-           (method url-fetch)
-           (uri (string-append
-                 "https://github.com/vegandevs/vegan/commit/"
-                 "591d0e8ba1deaaf82445474ec6619c0b43db4e63.patch"))
-           (sha256
-            (base32
-             "0b1bi7y4jjdl3ph721vm9apm51dr2z9piwvhy4355sf2b4kyyj5a"))))))
     (propagated-inputs
      `(("r-cluster" ,r-cluster)
        ("r-lattice" ,r-lattice)
@@ -5486,14 +5475,6 @@ high-throughput sequencing experiments.")
          "1walwkqryn1gnwz7zryr5764a0p6ia7ag4w6w9n8fskg8dkg0fqs"))))
     (properties `((upstream-name . "DESeq2")))
     (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'link-against-armadillo
-           (lambda _
-             (substitute* "src/Makevars"
-               (("PKG_LIBS =" prefix)
-                (string-append prefix "-larmadillo"))))))))
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
@@ -5521,14 +5502,14 @@ distribution.")
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.16.0")
+    (version "1.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "02msyb9p3hywrryx00zpjkjl126mrv827i1ah1092s0cplm6xxvf"))))
+         "0l1g9hy88sh5g567svyfd8pnjvkyklkn6a3gjn8zalvh62qqjjq1"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
@@ -5660,14 +5641,14 @@ testing and other simple calculations.")
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.32.0")
+    (version "1.32.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "0mjdlg92x5qw4x2djc4dv5lxwl7ai6ix56nnf86zr07jk8vc7yls"))))
+         "1m7lbfxs7xwcy9xs76zy5rky2mb96anvh457xfw60lh3kygwfpxc"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs
@@ -5807,7 +5788,7 @@ track.  The database is exposed as a @code{TxDb} object.")
 (define-public vsearch
   (package
     (name "vsearch")
-    (version "2.4.2")
+    (version "2.4.3")
     (source
      (origin
        (method url-fetch)
@@ -5817,7 +5798,7 @@ track.  The database is exposed as a @code{TxDb} object.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "15zy2d9xvgbgdjlxvrhj8s5ga42p13k7a3xv015ingn0bi1p3n6w"))
+         "0hc110ycqpa54nr6x173qg7190hk08qp7yz7zzqxlsypqnpc5zzp"))
        (patches (search-patches "vsearch-unbundle-cityhash.patch"))
        (snippet
         '(begin
@@ -6131,13 +6112,13 @@ functionality.")
 (define-public r-bioccheck
   (package
     (name "r-bioccheck")
-    (version "1.10.0")
+    (version "1.10.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocCheck" version))
               (sha256
                (base32
-                "1rfy37xg1nc2cmgbclvzsi7sgmdcdjiahsx9crgx3yaw7kxgiack"))))
+                "197kpiycyl3qawm6801fxyxj81d2g57a00qxaqprapsf1d140l52"))))
     (properties
      `((upstream-name . "BiocCheck")))
     (build-system r-build-system)
@@ -6165,10 +6146,8 @@ functionality.")
     (propagated-inputs
      `(("r-codetools" ,r-codetools)
        ("r-graph" ,r-graph)
-       ("r-knitr" ,r-knitr)
        ("r-httr" ,r-httr)
        ("r-optparse" ,r-optparse)
-       ("r-devtools" ,r-devtools)
        ("r-biocinstaller" ,r-biocinstaller)
        ("r-biocviews" ,r-biocviews)))
     (home-page "http://bioconductor.org/packages/BiocCheck")
@@ -6247,13 +6226,13 @@ abnormal copy number.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.12.1")
+    (version "0.12.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "0i36y3w36h3d8rmazxcrip4gvn54rd9av1wz4lygsprrjmylfhcc"))))
+                "0syx0qgipx97zsp3b8afhzamsr30835a2a99yb9wnq7b50g3v3p1"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -6274,14 +6253,14 @@ S4Vectors package itself.")
 (define-public r-seqinr
   (package
     (name "r-seqinr")
-    (version "3.3-3")
+    (version "3.3-6")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "seqinr" version))
         (sha256
           (base32
-            "0rk4yba8km26c0rh1f4h474zsb5n6kjmqsi55bnzr6p8pymp18hj"))))
+            "13d0qxm2244wgdl2dy2s8vnrnf5fx4n47if9gkb49dqx6c0sx8s2"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ade4" ,r-ade4)
@@ -6299,13 +6278,13 @@ utilities for sequence data management under the ACNUC system.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.8.1")
+    (version "2.8.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "0cryqnpqb3p6l9jjw27hyqd550sxlljls3ka7b9rb38hkji7b5hw"))))
+                "0x8h74ik3xwdnwrkn89hq5ll0qa1lp9jgzlbmpa02dpws7snfwyr"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
@@ -6328,19 +6307,20 @@ possible.")
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.10.2")
+    (version "1.10.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "0zh894qd1sgpjbn0wfvq6hs2dzn7y1pyicvzk2aa48y3zbidanv7"))))
+                "18g24cf6b3vi13w85ki2mam6i2gl4yxr1zchyga34xc3dkdngzrw"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-iranges" ,r-iranges)
+       ("r-rcurl" ,r-rcurl)
        ("r-s4vectors" ,r-s4vectors)))
     (home-page "http://bioconductor.org/packages/GenomeInfoDb")
     (synopsis "Utilities for manipulating chromosome identifiers")
@@ -6381,13 +6361,13 @@ CAGE.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.20.2")
+    (version "1.20.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "165wda1d2jagd907pnra4m3sla66icyqxvd60xpv09jl5agd5mn9"))))
+                "10v8apgfw57nd4dxmdxdrijxpw135jpp2p8wrk3wjpb3hhfjp1qj"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (inputs
@@ -6419,13 +6399,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.30.7")
+    (version "3.30.13")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1xg9w4lmn9n4hwyflxiwi6g969lcy569cg4z1x47crwwg7z7qdka"))))
+                "1ji8kb19anwq2505zii2kzqlrnk75mk1mpz8vy4s1mckzs1cz4m0"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -6438,13 +6418,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-xvector
   (package
     (name "r-xvector")
-    (version "0.14.0")
+    (version "0.14.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "XVector" version))
               (sha256
                (base32
-                "09lbqxpqr80g0kw77mpz0p1a8cq706j33kz8194wp71il67cdzi7"))))
+                "1j14ip4c260kdp3zcmgfa2v8ky88csa0gfdg6a1xsb64s03hdbm6"))))
     (properties
      `((upstream-name . "XVector")))
     (build-system r-build-system)
@@ -6474,13 +6454,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.26.2")
+    (version "1.26.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "0if5dswkp77lyqppd0z2iyvnwag9h1gsr03707s8npcx13mzpsia"))))
+                "1789ycqzv20d8p1axkxrhsz9v0ww6w1dk2mfvm85p8j53zd1f67c"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -6525,13 +6505,13 @@ on Bioconductor or which replace R functions.")
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.36.0")
+    (version "1.36.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "0ydrqw1k1j5p6w76bwc753cx545c055x88q87wzya93858synj6r"))))
+                "0574lmyisn3nv9aicz9x3iivx990da4q2j4i0f1jz0mpj9v3vc2w"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)
@@ -6582,13 +6562,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.8.1")
+    (version "1.8.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "123i928rwi4h4sy4fpysv6pinw5nns0sm3myxi2ghqhm34ws8gyl"))))
+                "18zpa0vl375n9pvxsgbid1k96m17nqqgv1g1sfnlmm7kj34jxg6v"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -6632,13 +6612,13 @@ biological sequences or sets of sequences.")
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "1.26.1")
+    (version "1.26.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "0pf4f6brf4bl5zgjrah0f38qslazrs49ayqgyh0xfqgrh63yx4ck"))))
+                "118nsajgghi4cy3h0wi7777kc70a5j1fdyxv5n1dy01glix2z4qk"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
@@ -6706,13 +6686,13 @@ samples.")
 (define-public r-genomicalignments
   (package
     (name "r-genomicalignments")
-    (version "1.10.0")
+    (version "1.10.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicAlignments" version))
               (sha256
                (base32
-                "11vb0a0zd36i4yhg4mfijv787v0nihn6pkjj6q7rfy19gwy61xlc"))))
+                "1dilghbsyf64iz5c0kib2c7if72x7almd5w3ali09a2b2ff2mcjk"))))
     (properties
      `((upstream-name . "GenomicAlignments")))
     (build-system r-build-system)
@@ -6739,13 +6719,13 @@ alignments.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.34.1")
+    (version "1.34.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "0x59k2fd0iaqi93gy6bm58p2j2z90z1b7a6w5b4c098y98n096rc"))))
+                "1j3cyvg1wg1d9l0lkcjk3jn7pb96zi17nd1qsa5lglsimja19mpl"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -6784,13 +6764,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.26.2")
+    (version "1.26.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "1ybi6r3bax07wlv2qcd34y5qjdvcqcfayfvlrjc39ifrkk65wv4f"))))
+                "1y16lqach0v3ym5zhdhj4r2imfi0kpa0djlb51hj85yf7xkzwdlb"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -8295,14 +8275,14 @@ unmodeled, or latent sources of noise.")
 (define-public r-seqminer
   (package
     (name "r-seqminer")
-    (version "5.3")
+    (version "5.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "seqminer" version))
        (sha256
         (base32
-         "0y0gc5lws3hdxasjb84m532ics6imb7qg9sl1zy62h503jh4j9gw"))))
+         "0p75wyl70cvp36mwg5y74nv573j1gdqi15ac2a7xf61jmsq7ycpy"))))
     (build-system r-build-system)
     (inputs
      `(("zlib" ,zlib)))
@@ -8349,14 +8329,14 @@ trait.")
 (define-public r-maldiquant
   (package
     (name "r-maldiquant")
-    (version "1.16")
+    (version "1.16.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MALDIquant" version))
        (sha256
         (base32
-         "067xbmy10mpsvmv77g62chd7wwhdhcfn5hmp5fisbnz2h5rq0q60"))))
+         "0z5srzsfgsgi4bssr4chls4ry6d18y2g9143znqmraylppwrrqzr"))))
     (properties `((upstream-name . "MALDIquant")))
     (build-system r-build-system)
     (home-page "http://cran.r-project.org/web/packages/MALDIquant")

gnu/packages/build-tools.scm

@@ -0,0 +1,64 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2017 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 (gnu packages build-tools)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix utils)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages python)
+  #:use-module (guix build-system gnu))
+
+(define-public bam
+  (package
+    (name "bam")
+    (version "0.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://github.com/downloads/matricks/"
+                                  "bam/bam-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "0z90wvyd4nfl7mybdrv9dsd4caaikc6fxw801b72gqi1m9q0c0sn"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'build
+           (lambda _
+             (zero? (system* "bash" "make_unix.sh"))))
+         (replace 'check
+           (lambda _
+             (zero? (system* "python" "scripts/test.py"))))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+               (mkdir-p bin)
+               (install-file "bam" bin)
+               #t))))))
+    (native-inputs
+     `(("python" ,python-2)))
+    (home-page "https://matricks.github.io/bam/")
+    (synopsis "Fast and flexible build system")
+    (description "Bam is a fast and flexible build system.  Bam uses Lua to
+describe the build process.  It takes its inspiration for the script files
+from scons.  While scons focuses on being 100% correct when building, bam
+makes a few sacrifices to acquire fast full and incremental build times.")
+    (license license:bsd-3)))

gnu/packages/calendar.scm

@@ -85,13 +85,13 @@ data units.")
 (define-public khal
   (package
     (name "khal")
-    (version "0.9.3")
+    (version "0.9.5")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "khal" version))
              (sha256
               (base32
-               "1iva6cw2x3p2jzjj6bsyx7lc7yxin4fsd37j9c96j07x16p4imyl"))))
+               "0fvv0kjym9q8v20zbpr5m8ig65b8hva4p0c935qsdvgdni68jidr"))))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases

gnu/packages/certs.scm

@@ -74,7 +74,7 @@
 (define-public nss-certs
   (package
     (name "nss-certs")
-    (version "3.29.3")
+    (version "3.30.1")
     (source (origin
               (method url-fetch)
               (uri (let ((version-with-underscores
@@ -85,7 +85,7 @@
                       "nss-" version ".tar.gz")))
               (sha256
                (base32
-                "1sz1r2iml9bhd4iqiqz75gii855a25895vpy9scjky0y4lqwrp9m"))))
+                "1djypq081m22iw0wg0q7gnpndam5f8qjhqfd5v9by4c6l6lp78hz"))))
     (build-system gnu-build-system)
     (outputs '("out"))
     (native-inputs

gnu/packages/compression.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015, 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2015 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2015, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
 ;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
@@ -673,14 +673,16 @@ writing of compressed data created with the zlib and bzip2 libraries.")
 (define-public lz4
   (package
     (name "lz4")
-    (version "1.7.4.2")
+    (version "1.7.5")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://github.com/Cyan4973/lz4/archive/"
+       (uri (string-append "https://github.com/lz4/lz4/archive/"
                            "v" version ".tar.gz"))
+       (patches (search-patches "lz4-fix-test-failures.patch"))
        (sha256
-        (base32 "0l39bymif15rmmfz7h6wvrr853rix4wj8wbqq8z8fm49xa7gx9fb"))
+        (base32
+         "0zkykqqjfa1q3ji0qmb1ml3l9063qqfh99agyj3cnb02cg6wm401"))
        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system gnu-build-system)
     (native-inputs `(("valgrind" ,valgrind)))   ; for tests
@@ -691,7 +693,7 @@ writing of compressed data created with the zlib and bzip2 libraries.")
                           (string-append "PREFIX=" (assoc-ref %outputs "out")))
        #:phases (modify-phases %standard-phases
                   (delete 'configure))))        ; no configure script
-    (home-page "https://github.com/Cyan4973/lz4")
+    (home-page "https://github.com/lz4/lz4")
     (synopsis "Compression algorithm focused on speed")
     (description "LZ4 is a lossless compression algorithm, providing
 compression speed at 400 MB/s per core (0.16 Bytes/cycle).  It also features an

gnu/packages/databases.scm

@@ -290,7 +290,7 @@ mapping from string keys to string values.")
 (define-public mysql
   (package
     (name "mysql")
-    (version "5.7.17")
+    (version "5.7.18")
     (source (origin
              (method url-fetch)
              (uri (list (string-append
@@ -302,7 +302,7 @@ mapping from string keys to string values.")
                           name "-" version ".tar.gz")))
              (sha256
               (base32
-               "0lcn9cm36n14g22bcppq5vf4nxbrl3khvlsp9hsixqdfb3l27gyf"))))
+               "18m1mr55k9zmvnyqs0wr50csqsz3scs09fykh60wsml6c3np2p8b"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
@@ -438,14 +438,14 @@ as a drop-in replacement of MySQL.")
 (define-public postgresql
   (package
     (name "postgresql")
-    (version "9.5.6")
+    (version "9.6.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "0bz1b9r249ffjfvldaiah2g78ccwq30ddh8hdvlq61z26inmz7mv"))))
+                "1jahzqqw5inyvmacic2ihhj5f8z50lapci2fwws91h719ccbb1q1"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -960,7 +960,7 @@ columns, primary keys, unique constraints and relationships.")
 (define-public perl-dbd-pg
   (package
     (name "perl-dbd-pg")
-    (version "3.5.1")
+    (version "3.5.3")
     (source
      (origin
        (method url-fetch)
@@ -968,7 +968,7 @@ columns, primary keys, unique constraints and relationships.")
                            "DBD-Pg-" version ".tar.gz"))
        (sha256
         (base32
-         "0z0kf1kjgbi5f6nr63i2fnrx7629d9lvxg1q8sficwb3zdf1ggzx"))))
+         "03m9w1cd0yyrbqwkwcl92j1cpmasmm69f3hwvcrlfsi5fnwsk63y"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-dbi" ,perl-dbi)))
@@ -1008,7 +1008,7 @@ columns, primary keys, unique constraints and relationships.")
 (define-public perl-dbd-sqlite
   (package
     (name "perl-dbd-sqlite")
-    (version "1.52")
+    (version "1.54")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1016,7 +1016,7 @@ columns, primary keys, unique constraints and relationships.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "0kimb2qr1rh07yylbbfybwcizpmy61ck667amypn4clmkfg0knm6"))))
+                "0sbj9lx9syzpknvjv8cz9jndg32qz775vy2prgq305npv3dsca9r"))))
     (build-system perl-build-system)
     (inputs `(("sqlite" ,sqlite)))
     (propagated-inputs `(("perl-dbi" ,perl-dbi)))
@@ -1280,7 +1280,7 @@ trees (LSM), for sustained throughput under random insert workloads.")
 (define-public perl-db-file
  (package
   (name "perl-db-file")
-  (version "1.838")
+  (version "1.840")
   (source
     (origin
       (method url-fetch)
@@ -1290,7 +1290,7 @@ trees (LSM), for sustained throughput under random insert workloads.")
              ".tar.gz"))
       (sha256
         (base32
-          "0yp5d5zr8dk9g6xdh7ygi5bq63q7nxvhd58dk2i3ki4nb7yv2yh9"))))
+          "1i5jz85z4hpx15lw6ix27pyvrf0ziyh4z33lii4d3wnhz83lg1mp"))))
   (build-system perl-build-system)
   (inputs `(("bdb" ,bdb)))
   (native-inputs `(("perl-test-pod" ,perl-test-pod)))

gnu/packages/django.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,13 +30,13 @@
 (define-public python-django
   (package
     (name "python-django")
-    (version "1.10.5")
+    (version "1.10.7")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "Django" version))
               (sha256
                (base32
-                "12szjsmnfhh2yr54sfynyjr8vl0q9gb6qak3ayqcifcinrs97f0d"))))
+                "1f5hnn2dzfr5szk4yc47bs4kk2nmrayjcvgpqi2s4l13pjfpfgar"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
@@ -80,7 +81,8 @@ development and clean, pragmatic design.  It provides many tools for building
 any Web site.  Django focuses on automating as much as possible and adhering
 to the @dfn{don't repeat yourself} (DRY) principle.")
     (license license:bsd-3)
-    (properties `((python2-variant . ,(delay python2-django))))))
+    (properties `((python2-variant . ,(delay python2-django))
+                  (cpe-name . "django")))))
 
 (define-public python2-django
   (let ((base (package-with-python2 (strip-python2-variant python-django))))
@@ -188,3 +190,58 @@ them do this.")
 
 (define-public python2-django-filter
   (package-with-python2 python-django-filter))
+
+(define-public python-django-allauth
+  (package
+    (name "python-django-allauth")
+    (version "0.30.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "django-allauth" version))
+       (sha256
+        (base32
+         "1fslqc5qqb0b66yscvkyjwfv8cnbfx5nlkpnwimyb3pf1nc1w7r3"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-openid" ,python-openid)
+       ("python-requests" ,python-requests)
+       ("python-requests-oauthlib" ,python-requests-oauthlib)))
+    (native-inputs
+     `(("python-mock" ,python-mock)))
+    (inputs
+     `(("python-django" ,python-django)))
+    (home-page "https://github.com/pennersr/django-allauth")
+    (synopsis "Set of Django applications addressing authentication")
+    (description
+     "Integrated set of Django applications addressing authentication,
+registration, account management as well as 3rd party (social)
+account authentication.")
+    (license license:expat)))
+
+(define-public python2-django-allauth
+  (package-with-python2 python-django-allauth))
+
+(define-public python-django-gravatar2
+  (package
+    (name "python-django-gravatar2")
+    (version "1.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "django-gravatar2" version))
+       (sha256
+        (base32
+         "1v4qyj6kms321yw0z2g1kch6b2dskmv6fjd6sfxzwr4xshq9mccl"))))
+    (build-system python-build-system)
+    (inputs
+     `(("python-django" ,python-django)))
+    (home-page "https://github.com/twaddington/django-gravatar")
+    (synopsis "Gravatar support for Django, improved version")
+    (description
+     "Essential Gravatar support for Django.  Features helper methods,
+templatetags and a full test suite.")
+    (license license:expat)))
+
+(define-public python2-django-gravatar2
+  (package-with-python2 python-django-gravatar2))

gnu/packages/dns.scm

@@ -90,7 +90,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
 (define-public bind
   (package
     (name "bind")
-    (version "9.10.4-P6")
+    (version "9.10.4-P8")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -98,7 +98,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "0rgffdm0h6dks0np4h9q4kd8nyb3azrdxw2skqnjzd8ws78vzpx1"))))
+                "1sv6fp5gznjj1kmx9q8wr2c6js10wqckgy25sqj83bbf8smmdlvx"))))
     (build-system gnu-build-system)
     (outputs `("out" "utils"))
     (inputs
@@ -318,14 +318,14 @@ Extensions} (DNSSEC).")
 (define-public knot
   (package
     (name "knot")
-    (version "2.4.2")
+    (version "2.4.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://secure.nic.cz/files/knot-dns/"
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0licfnjl0mq9lzdn6frzdasrj65253xc9n33dhvxcjqr3z7pznip"))
+                "0kvhibnnk77nqi9gdw2zbnp0dydfcy6zy96qv0f3a7wwnay5h0pr"))
               (modules '((guix build utils)))
               (snippet
                '(begin

gnu/packages/emacs.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2014, 2015, 2016, 2017 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016 Chris Marusich <cmmarusich@gmail.com>
+;;; Copyright © 2016, 2017 Chris Marusich <cmmarusich@gmail.com>
 ;;; Copyright © 2015, 2016 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2016 humanitiesNerd <catonano@gmail.com>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
@@ -22,6 +22,8 @@
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 Vasile Dumitrascu <va511e@yahoo.com>
 ;;; Copyright © 2017 Kyle Meyer <kyle@kyleam.com>
+;;; Copyright © 2017 Kei Kebreau <kei@openmailbox.org>
+;;; Copyright © 2017 George Clemmer <myglc2@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -51,13 +53,16 @@
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
+  #:use-module (gnu packages audio)
   #:use-module (gnu packages code)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages python)
   #:use-module (gnu packages tex)
   #:use-module (gnu packages texinfo)
+  #:use-module (gnu packages tcl)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages xorg)
@@ -725,7 +730,7 @@ the body are let-bound and this search is done at compile time.")
 (define-public flycheck
   (package
     (name "emacs-flycheck")
-    (version "28")
+    (version "30")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -733,7 +738,7 @@ the body are let-bound and this search is done at compile time.")
                     version "/flycheck-" version ".tar"))
               (sha256
                (base32
-                "1yjxivk11d7w39zfhj2xr4h6xhwx1aj6yhyzd63rjrad7xpjfl86"))))
+                "1rxzkaqsj48z3nska5wsgwafvwkam014dzqd32baycmxjl0jxvy7"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-dash" ,emacs-dash)
@@ -1125,9 +1130,22 @@ than @code{electric-indent-mode}.")
                ("ag-executable"
                 (string-append (assoc-ref inputs "the-silver-searcher")
                                "/bin/ag")))
-             #t)))))
+             #t))
+         (add-before 'install 'make-info
+           (lambda _
+             (with-directory-excursion "docs"
+               (zero? (system* "make" "info")))))
+         (add-after 'install 'install-info
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out  (assoc-ref outputs "out"))
+                    (info (string-append out "/share/info")))
+               (install-file "docs/_build/texinfo/agel.info" info)
+               #t))))))
     (inputs
      `(("the-silver-searcher" ,the-silver-searcher)))
+    (native-inputs
+     `(("python-sphinx" ,python-sphinx)
+       ("texinfo" ,texinfo)))
     (propagated-inputs
      `(("dash" ,emacs-dash)
        ("s" ,emacs-s)))
@@ -1487,17 +1505,18 @@ strings.")
 (define-public emacs-symon
   (package
     (name "emacs-symon")
-    (version "20170224.33")
+    (version "20160630")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "http://melpa.org/packages/symon-"
+       (uri (string-append "https://github.com/zk-phi/symon/archive/"
-                           version ".el"))
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "109jd7yjhdrrf5jqpqyv543nb28g7065z58bji9pvxanzi4zl2iz"))))
+         "0h4jcgdnq98wc9rj72nwyazq8498yg55jfljiij5qwbn1xf1g5zz"))))
     (build-system emacs-build-system)
-    (home-page "http://hins11.yu-yake.com/")
+    (home-page "https://github.com/zk-phi/symon")
     (synopsis "Tiny graphical system monitor")
     (description
      "Tiny graphical system monitor for the Emacs minibuffer when idle.")
@@ -1979,14 +1998,14 @@ source code using IPython.")
 (define-public emacs-debbugs
   (package
     (name "emacs-debbugs")
-    (version "0.12")
+    (version "0.14")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://elpa.gnu.org/packages/debbugs-"
                                   version ".tar"))
               (sha256
                (base32
-                "1swi4d7fhahimid9j12cypmkz7dlqgffrnhfxy5ra44y3j2b35ph"))))
+                "07wgcvg038l88gxvjr0gjpjhyk743w22x1rqghz3gkmif0g70say"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-async" ,emacs-async)))
@@ -2058,7 +2077,7 @@ build jobs.")
 (define-public emacs-company
   (package
     (name "emacs-company")
-    (version "0.8.12")
+    (version "0.9.3")
     (source
      (origin
        (method url-fetch)
@@ -2067,8 +2086,20 @@ build jobs.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1vwmbqm7h4lrszv2qxy6fqzznm9raigi84cadx982c9m7shp0zzz"))))
+         "1fyrpchpdmvszssy1qmsw41aqpv6q5rybvs1bw00nv9xdhiaq4vh"))))
     (build-system emacs-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'install 'check
+           (lambda _
+             ;; The company-files-candidates-normal-root test looks
+             ;; for the /bin directory, but the build environment has
+             ;; no /bin directory. Modify the test to look for the
+             ;; /tmp directory.
+             (substitute* "test/files-tests.el"
+               (("/bin/") "/tmp/"))
+             (zero? (system* "make" "test-batch")))))))
     (home-page "http://company-mode.github.io/")
     (synopsis "Modular text completion framework")
     (description
@@ -2442,7 +2473,7 @@ organizer.")
 (define-public emacs-zenburn-theme
   (package
     (name "emacs-zenburn-theme")
-    (version "2.4")
+    (version "2.5")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2451,7 +2482,7 @@ organizer.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0lyi84bm8sa7vj40n6zg6rlbsmi53mi1y9xn6gkjj29s5zbcnlg7"))))
+                "03kfhzgbbbl8ivpzzky6qxw4j9mmp452m1sk7wikxmcalfnix0gn"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/bbatsov/zenburn-emacs")
     (synopsis "Low contrast color theme for Emacs")
@@ -2655,7 +2686,7 @@ automatically.")
 (define-public emacs-ivy
   (package
     (name "emacs-ivy")
-    (version "0.8.0")
+    (version "0.9.1")
     (source
      (origin
        (method url-fetch)
@@ -2664,7 +2695,7 @@ automatically.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "18nqwl05is71dzswnvpfhlg7b0v3apvbsfxrwab9c0apwavi892q"))))
+         "1abi1rvjarwfxxylpx8qlhck0kbavnj0nmlaaizk9q5zr02xfx1j"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-hydra" ,emacs-hydra)))
@@ -2792,7 +2823,7 @@ S-expression.")
 (define-public emacs-clojure-mode
   (package
     (name "emacs-clojure-mode")
-    (version "5.3.0")
+    (version "5.4.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2801,7 +2832,7 @@ S-expression.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0gi8ra3ap5m3mz4qh1yxp2cldn7z9xcxvypznr6rrlc6a9l8s5a6"))))
+                "117mvjqh4nm8mvmwmmvy4qmkdg23ldlzk08y91g8b8ac8kxwqg81"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/clojure-emacs/clojure-mode")
     (synopsis "Major mode for Clojure code")
@@ -3064,7 +3095,7 @@ in Emacs.")
 (define-public emacs-projectile
   (package
     (name "emacs-projectile")
-    (version "0.13.0")
+    (version "0.14.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://raw.githubusercontent.com/bbatsov"
@@ -3072,7 +3103,7 @@ in Emacs.")
               (file-name (string-append "projectile-" version ".el"))
               (sha256
                (base32
-                "1pc6xb61hzxzc5hkqkli1ab0s7wz0rfgx4kcn9y30ksvhw18smbz"))))
+                "1ql1wnzhblbwnv66hf2y0wq45g71hh6s9inc090lmhm1vgylbd1f"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-dash" ,emacs-dash)
@@ -3100,6 +3131,12 @@ If you want to mark a folder manually as a project just create an empty
                (base32
                 "145glas04zd0s2rmnif46vhyijs4z03v871gfp1dcrwxvvvns8ap"))))
     (build-system emacs-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'install 'check
+           (lambda _
+             (zero? (system* "make" "test")))))))
     (home-page "https://github.com/skeeto/elfeed")
     (synopsis "Atom/RSS feed reader for Emacs")
     (description
@@ -4051,3 +4088,275 @@ jQuery and Bootstrap resources included via osscdn.")
     (description
      "This Emacs package highlights the s-exp at the current position.")
     (license license:gpl3+)))
+
+(define-public emacspeak
+  (package
+    (name "emacspeak")
+    (version "45.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/tvraman/emacspeak/releases/download/"
+             version "/emacspeak-" version ".tar.bz2"))
+       (sha256
+        (base32
+         "0npcr867xbbhwa0i7v26hnk4z2d51522jwcfwc594j74kbv3g6ka"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:make-flags (list (string-append "prefix="
+                                         (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "Makefile"
+               (("\\$\\(INSTALL\\) -d \\$\\(libdir\\)/servers/linux-outloud")
+                "")
+               (("\\$\\(INSTALL\\)  -m 755 \\$\\{OUTLOUD\\}.*$") "")
+               (("\\*info\\*") "*"))
+             (substitute* "etc/emacspeak.sh.def"
+               (("<emacspeak-dir>")
+                (string-append (assoc-ref outputs "out")
+                               "/share/emacs/site-lisp/emacspeak/lisp")))
+             (zero? (system* "make" "config"))))
+         (add-after 'install 'install-espeak-server
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (with-directory-excursion "servers/linux-espeak"
+                 (and (zero? (system* "make"))
+                      (zero? (system* "make" "install"
+                                      (string-append "PREFIX=" out))))))))
+         (add-after 'install-espeak-server 'wrap-program
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (emacspeak (string-append out "/bin/emacspeak"))
+                    (espeak (string-append (assoc-ref inputs "espeak")
+                                           "/bin/espeak")))
+               ;; The environment variable DTK_PROGRAM tells emacspeak what
+               ;; program to use for speech.
+               (wrap-program emacspeak
+                 `("DTK_PROGRAM" ":" prefix (,espeak)))
+               #t))))
+       #:tests? #f)) ; no check target
+    (inputs
+     `(("espeak" ,espeak)
+       ("tcl" ,tcl)
+       ("tclx" ,tclx)))
+    (native-inputs `(("emacs" ,emacs-minimal)))
+    (home-page "http://emacspeak.sourceforge.net")
+    (synopsis "Audio desktop interface for Emacs")
+    (description
+     "Emacspeak is a speech interface that allows visually impaired users to
+interact independently and efficiently with the computer.  Audio formatting
+--a technique pioneered by AsTeR-- and full support for W3C's Aural CSS (ACSS)
+allows Emacspeak to produce rich aural presentations of electronic information.
+By seamlessly blending all aspects of the Internet such as Web-surfing and
+messaging, Emacspeak speech-enables local and remote information via a
+consistent and well-integrated user interface.")
+    (license license:gpl2+)))
+
+(define-public emacs-adaptive-wrap
+  (package
+    (name "emacs-adaptive-wrap")
+    (version "0.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://elpa.gnu.org/packages/adaptive-wrap-"
+                    version ".el"))
+              (sha256
+               (base32
+                "0frgmp8vrrml4iykm60j4d6cl9rbcivy9yh24q6kd10bcyx59ypy"))))
+    (build-system emacs-build-system)
+    (home-page "http://elpa.gnu.org/packages/adaptive-wrap.html")
+    (synopsis "Smart line-wrapping with wrap-prefix")
+    (description
+     "This Emacs package provides the @code{adaptive-wrap-prefix-mode}
+minor mode which sets the wrap-prefix property on the fly so that
+single-long-line paragraphs get word-wrapped in a way similar to what
+you'd get with @kbd{M-q} using @code{adaptive-fill-mode}, but without
+actually changing the buffer's text.")
+    (license license:gpl3+)))
+
+(define-public emacs-diminish
+  (package
+    (name "emacs-diminish")
+    (version "0.45")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/myrjola/diminish.el/archive/v"
+             version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0i3629sv5cfrrb00hcnmaqzgs8mk36yasc1ax3ry1ga09nr6rkj9"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/myrjola/diminish.el")
+    (synopsis "Diminish minor modes with no modeline display")
+    (description "@code{emacs-diminish} implements hiding or
+abbreviation of the mode line displays (lighters) of minor modes.")
+    (license license:gpl2+)))
+
+(define-public emacs-use-package
+  (package
+    (name "emacs-use-package")
+    (version "2.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/jwiegley/use-package/archive/"
+             version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0x4h136jb3imyli6zsh7dyzjrra6pv0v6b0yk94jdng3rdfcmsf5"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-diminish" ,emacs-diminish)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'install 'check
+           (lambda _
+             (zero? (system* "emacs" "--batch" "-L" "."
+                             "-l" "use-package-tests.el"
+                             "-f" "ert-run-tests-batch-and-exit"))
+             ;; Tests fail in this release, but have been fixed in
+             ;; upstream commit 7956d40eed57d6c06bef36ebc174cf57d934e30d
+             #t)))))
+    (home-page "https://github.com/jwiegley/use-package")
+    (synopsis "Declaration for simplifying your .emacs")
+    (description "The use-package macro allows you to isolate package
+configuration in your @file{.emacs} file in a way that is both
+performance-oriented and tidy.")
+    (license license:gpl2+)))
+
+(define-public emacs-strace-mode
+  (let* ((commit "6a69b4b06db6797af56f33eda5cb28af94e59f11")
+         (revision "1"))
+    (package
+      (name "emacs-strace-mode")
+      (version (string-append "0.0.2-" revision "." (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/pkmoore/strace-mode")
+                      (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
+                (sha256
+                 (base32
+                  "1lbk2kzdznf2bkfazizfbimaxxzfzv00lrz1ran9dc2zqbc0bj9f"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/pkmoore/strace-mode")
+      (synopsis "Emacs major mode to highlight strace outputs")
+      (description "@code{emacs-strace-mode} provides an Emacs major mode
+ highlighting strace outputs.")
+      (license license:gpl3+))))
+
+(define-public emacs-default-encrypt
+  (package
+    (name "emacs-default-encrypt")
+    (version "4.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://www.informationelle-selbstbestimmung-im-internet.de"
+             "/emacs/jl-encrypt" version "/jl-encrypt.el"))
+       (file-name (string-append "jl-encrypt-" version ".el"))
+       (sha256
+        (base32
+         "16i3rlfp3jxlqvndn8idylhmczync3gwmy8a019v29vyr48rnnr0"))))
+    (build-system emacs-build-system)
+    (home-page "https://www.informationelle-selbstbestimmung-im-internet.de/Emacs.html")
+    (synopsis "Automatically encrypt or sign Gnus messages in Emacs")
+    (description
+     "DefaultEncrypt is designed to be used with Gnus in Emacs.  It
+automatically encrypts messages that you send (e.g., email) when public keys
+for all recipients are available, and it protects you from accidentally
+sending un-encrypted messages.  It can also be configured to automatically
+sign messages that you send.  For details and instructions on how to use
+DefaultEncrypt, please refer to the home page or read the comments in the
+source file, @file{jl-encrypt.el}.")
+    (license license:gpl3+)))
+
+(define-public emacs-htmlize
+  (package
+    (name "emacs-htmlize")
+    (version "1.51")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/hniksic/emacs-htmlize/archive/release/"
+             version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1fy1lybzrxl8a8r88f6p19nz8ygmvcxhxbnymkxh7jqaz25viwld"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/hniksic/emacs-htmlize")
+    (synopsis "Convert buffer text and decorations to HTML")
+    (description "@code{emacs-htmlize} converts the buffer text and
+the associated decorations to HTML.  Output to CSS, inline CSS and
+fonts is supported.")
+    (license license:gpl2+)))
+
+(define-public emacs-xmlgen
+  (package
+    (name "emacs-xmlgen")
+    (version "0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/philjackson/xmlgen/archive/"
+             version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0zay490vjby3f7455r0vydmjg7q1gwc78hilpfb0rg4gwz224z8r"))))
+    (build-system emacs-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'install 'check
+           (lambda _
+             (zero? (system* "emacs" "--batch" "-L" "."
+                             "-l" "xmlgen-test.el"
+                             "-f" "ert-run-tests-batch-and-exit")))))))
+    (home-page "https://github.com/philjackson/xmlgen")
+    (synopsis "S-expression to XML domain specific language (DSL) in
+Emacs Lisp")
+    (description "@code{emacs-xmlgen} provides S-expression to XML
+conversion for Emacs Lisp.")
+    (license license:gpl2+)))
+
+(define-public emacs-cdlatex
+  (package
+    (name "emacs-cdlatex")
+    (version "4.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/cdominik/cdlatex/archive/"
+             version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0pivapphmykc6vhvpx7hdyl55ls37vc4jcrxpvs4yk7jzcmwa9xp"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/cdominik/cdlatex")
+    (synopsis "Fast Emacs input methods for LaTeX environments and
+math")
+    (description "CDLaTeX is an Emacs minor mode supporting fast
+insertion of environment templates and math in LaTeX.  Similar
+commands are also offered as part of the AUCTeX package, but it is not
+the same - CDLaTeX focuses on speediness for inserting LaTeX
+constructs.")
+    (license license:gpl3+)))

gnu/packages/games.scm

@@ -21,7 +21,7 @@
 ;;; Copyright © 2016 Albin Söderqvist <albin@fripost.org>
 ;;; Copyright © 2016, 2017 Kei Kebreau <kei@openmailbox.org>
 ;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2016 Steve Webber <webber.sl@gmail.com>
 ;;; Copyright © 2017 Adonay "adfeno" Felipe Nogueira <https://libreplanet.org/wiki/User:Adfeno> <adfeno@openmailbox.org>
@@ -56,6 +56,7 @@
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages backup)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages build-tools)
   #:use-module (gnu packages admin)
   #:use-module (gnu packages audio)
   #:use-module (gnu packages avahi)
@@ -89,6 +90,7 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages sdl)
+  #:use-module (gnu packages swig)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages check)
   #:use-module (gnu packages fonts)
@@ -225,7 +227,7 @@ representation of the playing board.")
 (define-public gnubik
   (package
     (name "gnubik")
-    (version "2.4.2")
+    (version "2.4.3")
     (source
      (origin
       (method url-fetch)
@@ -233,7 +235,7 @@ representation of the playing board.")
                           version ".tar.gz"))
       (sha256
        (base32
-        "0mhpfnxzbns0wfrsjv5vafqr34770rbvkmdzxk0x0aq67hb3zyl5"))))
+        "1vlf924mq8hg93bsjj0rzvs0crc6psmlxyc6zn0fr7msnmpx6gib"))))
     (build-system gnu-build-system)
     (inputs `(("gtk+" ,gtk+-2)
               ("mesa" ,mesa)
@@ -3458,3 +3460,350 @@ starting a decryption sequence to reveal the original plaintext characters.")
 game, where you control the armies of one of seven different factions: Tech,
 Magic, Egypt, Indians, Norsemen, Persian or Romans.")
     (license license:gpl2+)))
+
+(define-public freegish
+  (let ((commit "8795cd7adc95957883f2d3465eb9036a774667a7")
+        (revision "1"))
+    (package
+      (name "freegish")
+      (version (string-append "0-" revision "." (string-take commit 9)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/freegish/freegish.git")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1p1zf5qqagmcpi1db2bs02cnalpy3qiymp6yzan7k1bhmv859gsx"))
+                (modules '((guix build utils)))
+                ;; The audio files in the "music" directory are licensed under
+                ;; CC-BY-NC, so we delete them.
+                (snippet
+                 '(begin
+                    (delete-file-recursively "music")
+                    #t))))
+      (build-system cmake-build-system)
+      (arguments
+       `(#:tests? #f ; no tests included
+         #:configure-flags
+         (list "-DCMAKE_INSTALL_FHS=ON")
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'set-DATAPATH
+             (lambda* (#:key outputs #:allow-other-keys)
+               (substitute* "CMakeLists.txt"
+                 (("^option\\(INSTALL_FHS" line)
+                  (string-append "add_definitions(-DDATAPATH=\""
+                                 (assoc-ref outputs "out") "/share/freegish\")\n"
+                                 line)))
+               #t)))))
+      (inputs
+       `(("sdl-union" ,(sdl-union (list sdl sdl-mixer)))
+         ("openal" ,openal)
+         ("libvorbis" ,libvorbis)
+         ("libogg" ,libogg)
+         ("mesa" ,mesa)
+         ("libpng" ,libpng)
+         ("zlib" ,zlib)))
+      (home-page "https://github.com/freegish/freegish")
+      (synopsis "Side-scrolling physics platformer with a ball of tar")
+      (description "In FreeGish you control Gish, a ball of tar who lives
+happily with his girlfriend Brea, until one day a mysterious dark creature
+emerges from a sewer hole and pulls her below ground.")
+      ;; The textures are available under the Expat license.  All other assets
+      ;; (including levels) are covered under CC-BY-SA or public domain.  The
+      ;; source code is under GPLv2+.
+      (license (list license:gpl2+
+                     license:expat
+                     license:public-domain
+                     license:cc-by-sa3.0)))))
+
+(define-public cdogs-sdl
+  (package
+    (name "cdogs-sdl")
+    (version "0.6.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/cxong/cdogs-sdl/"
+                                  "archive/" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "08c3y8ijimx6mp0gm90abz4lsnbflqka519q2v0id0096vsc2pxn"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "-DCDOGS_DATA_DIR="
+                            (assoc-ref %outputs "out")
+                            "/share/cdogs-sdl/"))))
+    (inputs
+     `(("sdl2" ,sdl2)
+       ("sdl2-image" ,sdl2-image)
+       ("sdl2-mixer" ,sdl2-mixer)))
+    (home-page "http://cxong.github.io/cdogs-sdl/")
+    (synopsis "Classic overhead run-and-gun game")
+    (description "C-Dogs SDL is a classic overhead run-and-gun game,
+supporting up to 4 players in co-op and deathmatch modes.  Customize your
+player, choose from many weapons, and blast, slide and slash your way through
+over 100 user-created campaigns.")
+    ;; GPLv2+ for code (includes files under BSD-2 and BSD-3),
+    ;; CC0/CC-BY/CC-BY-SA for assets.
+    (license (list license:gpl2+
+                   license:bsd-2
+                   license:bsd-3
+                   license:cc0
+                   license:cc-by3.0
+                   license:cc-by-sa3.0))))
+
+(define-public kiki
+  (package
+    (name "kiki")
+    (version "1.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/kiki/kiki-src/"
+                                  version "/kiki-" version "-src.tgz"))
+              (sha256
+               (base32
+                "0ihjdsxbn8z3cz0gpcprafiipcqaiskgdnh1rhmw4qff8dszalbn"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (for-each delete-file (find-files "." "\\.dll$"))
+                  #t))
+              (patches
+               (search-patches "kiki-level-selection-crash.patch"
+                               "kiki-makefile.patch"
+                               "kiki-missing-includes.patch"
+                               "kiki-portability-64bit.patch"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; there are no tests
+       #:make-flags '("CXX=g++")
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (setenv "CPLUS_INCLUDE_PATH"
+                     (string-append (assoc-ref inputs "sdl-union")
+                                    "/include/SDL:"
+                                    (assoc-ref inputs "python")
+                                    "/include/python2.7:"
+                                    (getenv "CPLUS_INCLUDE_PATH")))
+             (substitute* "src/main/main.cpp"
+               (("#include <SDL.h>" line)
+                (string-append line "
+#define K_INCLUDE_GLUT
+#include \"KIncludeTools.h\""))
+               (("// initialize SDL" line)
+                (string-append "glutInit(&argc,argv);\n" line)))
+             (substitute* "src/main/KikiController.cpp"
+               (("getenv\\(\"KIKI_HOME\"\\)")
+                (string-append "\"" (assoc-ref outputs "out") "/share/kiki/\"")))
+             (substitute* "linux/Makefile"
+               (("CXXOPTS =" line)
+                (string-append line " -fpermissive"))
+               (("PYTHON_VERSION=.*") "PYTHON_VERSION=2.7")
+               (("PYTHONHOME =.*")
+                (string-append "PYTHONHOME = "
+                               (assoc-ref inputs "python")
+                               "/lib/python2.7/"))
+               (("\\$\\(GLLIBS\\)" line)
+                (string-append line " -lm -lpython2.7")))
+             (substitute* "src/main/KikiPythonWidget.h"
+               (("#define __KikiPythonWidget" line)
+                (string-append line "\n#include \"KikiPython.h\"")))
+             #t))
+         (add-before 'build 'build-kodilib
+           (lambda* (#:key make-flags #:allow-other-keys)
+             (with-directory-excursion "kodilib/linux"
+               (zero? (apply system* "make" make-flags)))))
+         (add-after 'build-kodilib 'chdir
+           (lambda _ (chdir "linux") #t))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out   (assoc-ref outputs "out"))
+                    (bin   (string-append out "/bin"))
+                    (share (string-append out "/share/kiki")))
+               (mkdir-p bin)
+               (mkdir-p share)
+               (install-file "kiki" bin)
+               (copy-recursively "../py" (string-append share "/py"))
+               (copy-recursively "../sound" (string-append share "/sound"))
+               #t))))))
+    (inputs
+     `(("glu" ,glu)
+       ;; Kiki builds fine with freeglut 3.0.0 but segfaults on start.
+       ("freeglut" ,freeglut-2.8)
+       ("sdl-union" ,(sdl-union (list sdl
+                                      sdl-mixer
+                                      sdl-image)))
+       ("python" ,python-2)))
+    (native-inputs
+     `(("swig" ,swig)))
+    (home-page "http://kiki.sourceforge.net/")
+    (synopsis "3D puzzle game")
+    (description "Kiki the nano bot is a 3D puzzle game.  It is basically a
+mixture of the games Sokoban and Kula-World.  Your task is to help Kiki, a
+small robot living in the nano world, repair its maker.")
+    ;; See <http://metadata.ftp-master.debian.org/changelogs/main/k/
+    ;; kiki-the-nano-bot/kiki-the-nano-bot_1.0.2+dfsg1-4_copyright>
+    ;; for a statement from the author.
+    (license license:public-domain)))
+
+(define-public teeworlds
+  (package
+    (name "teeworlds")
+    (version "0.6.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/teeworlds/teeworlds/"
+                                  "archive/" version "-release.tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1mqhp6xjl75l49050cid36wxyjn1qr0vjx1c709dfg1lkvmgs6l3"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (for-each delete-file-recursively
+                            '("src/engine/external/wavpack/"
+                              "src/engine/external/zlib/"))
+                  #t))
+              (patches
+               (search-patches "teeworlds-use-latest-wavpack.patch"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; no tests included
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Embed path to assets.
+             (substitute* "src/engine/shared/storage.cpp"
+               (("#define DATA_DIR.*")
+                (string-append "#define DATA_DIR \""
+                               (assoc-ref outputs "out")
+                               "/share/teeworlds/data"
+                               "\"")))
+
+             ;; Bam expects all files to have a recent time stamp.
+             (for-each (lambda (file)
+                         (utime file 1 1))
+                       (find-files "."))
+
+             ;; Do not use bundled libraries.
+             (substitute* "bam.lua"
+               (("if config.zlib.value == 1 then")
+                "if true then")
+               (("wavpack = .*")
+                "wavpack = {}
+settings.link.libs:Add(\"wavpack\")\n"))
+             (substitute* "src/engine/client/sound.cpp"
+               (("#include <engine/external/wavpack/wavpack.h>")
+                "#include <wavpack/wavpack.h>"))
+             #t))
+         (replace 'build
+           (lambda _
+             (zero? (system* "bam" "-a" "-v" "release"))))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out  (assoc-ref outputs "out"))
+                    (bin  (string-append out "/bin"))
+                    (data (string-append out "/share/teeworlds/data")))
+               (mkdir-p bin)
+               (mkdir-p data)
+               (for-each (lambda (file)
+                           (install-file file bin))
+                         '("teeworlds" "teeworlds_srv"))
+               (copy-recursively "data" data)
+               #t))))))
+    ;; FIXME: teeworlds bundles the sources of "pnglite", a two-file PNG
+    ;; library without a build system.
+    (inputs
+     `(("freetype" ,freetype)
+       ("glu" ,glu)
+       ("mesa" ,mesa)
+       ("sdl-union" ,(sdl-union (list sdl
+                                      sdl-mixer
+                                      sdl-image)))
+       ("wavpack" ,wavpack)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("bam" ,bam)
+       ("python" ,python-2)))
+    (home-page "https://www.teeworlds.com")
+    (synopsis "2D retro multiplayer shooter game")
+    (description "Teeworlds is an online multiplayer game.  Battle with up to
+16 players in a variety of game modes, including Team Deathmatch and Capture
+The Flag.  You can even design your own maps!")
+    (license license:bsd-3)))
+
+(define-public fillets-ng
+  (package
+    (name "fillets-ng")
+    (version "1.0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/fillets/"
+                                  "Fish%20Fillets%20-%20Next%20Generation/"
+                                  version "/fillets-ng-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1nljp75aqqb35qq3x7abhs2kp69vjcj0h1vxcpdyn2yn2nalv6ij"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "--with-lua="
+                            (assoc-ref %build-inputs "lua")))
+       #:make-flags
+       (list (string-append "CFLAGS=-I"
+                            (assoc-ref %build-inputs "sdl-union")
+                            "/include/SDL")
+             (string-append "CXXFLAGS=-I"
+                            (assoc-ref %build-inputs "sdl-union")
+                            "/include/SDL"))
+       #:phases
+       (modify-phases %standard-phases
+         ;; Lua 5.1 does not provide it.
+         (add-after 'unpack 'do-not-link-with-lualib
+           (lambda _
+             (substitute* "configure"
+               (("-llualib") ""))
+             #t))
+         (add-after 'install 'install-data
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((data (string-append (assoc-ref outputs "out")
+                                        "/share/games/fillets-ng")))
+               (mkdir-p data)
+               (zero? (system* "tar" "-xvf"
+                               (assoc-ref inputs "fillets-ng-data")
+                               "--strip-components=1"
+                               "-C" data))))))))
+    (inputs
+     `(("sdl-union" ,(sdl-union (list sdl
+                                      sdl-mixer
+                                      sdl-image
+                                      sdl-ttf)))
+       ("fribidi" ,fribidi)
+       ("libx11" ,libx11)
+       ("lua" ,lua-5.1)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("fillets-ng-data"
+        ,(origin
+           (method url-fetch)
+           (uri (string-append "mirror://sourceforge/fillets/"
+                               "Fish%20Fillets%20-%20Next%20Generation/"
+                               version "/fillets-ng-data-" version ".tar.gz"))
+           (sha256
+            (base32
+             "169p0yqh2gxvhdilvjc2ld8aap7lv2nhkhkg4i1hlmgc6pxpkjgh"))))))
+    (home-page "http://fillets.sourceforge.net/")
+    (synopsis "Puzzle game")
+    (description "Fish Fillets NG is strictly a puzzle game.  The goal in
+every of the seventy levels is always the same: find a safe way out.  The fish
+utter witty remarks about their surroundings, the various inhabitants of their
+underwater realm quarrel among themselves or comment on the efforts of your
+fish.  The whole game is accompanied by quiet, comforting music.")
+    (license license:gpl2+)))

gnu/packages/gl.scm

@@ -7,6 +7,7 @@
 ;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 David Thompson <davet@gnu.org>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,12 +28,14 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages bison)
+  #:use-module (gnu packages compression)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages guile)
+  #:use-module (gnu packages image)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages llvm)
   #:use-module (gnu packages pkg-config)
@@ -121,6 +124,21 @@ the mouse, keyboard and joystick functions.  Freeglut is released under
 the X-Consortium license.")
     (license license:x11)))
 
+;; Needed for "kiki".
+(define-public freeglut-2.8
+  (package (inherit freeglut)
+    (name "freeglut")
+    (version "2.8.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://sourceforge/freeglut/freeglut/"
+                    version "/freeglut-" version ".tar.gz"))
+              (sha256
+               (base32
+                "16lrxxxd9ps9l69y3zsw6iy0drwjsp6m26d1937xj71alqk6dr6x"))))
+    (build-system gnu-build-system)))
+
 (define-public ftgl
   (package
     (name "ftgl")
@@ -612,3 +630,35 @@ library for OpenGL.  It has lean API modeled after HTML5 canvas API.  It is
 aimed to be a practical and fun toolset for building scalable user interfaces
 and visualizations.")
     (license license:zlib)))
+
+(define-public gl2ps
+  (package
+    (name "gl2ps")
+    (version "1.3.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://geuz.org/gl2ps/src/gl2ps-"
+             version ".tgz"))
+       (sha256
+        (base32
+         "0h1nrhmkc4qjw2ninwpj2zbgwhc0qg6pdhpsibbvry0d2bzhns4a"))))
+    (build-system cmake-build-system)
+    (inputs
+     `(("libpng" ,libpng)
+       ("mesa" ,mesa)
+       ("zlib" ,zlib)))
+    (arguments
+     `(#:tests? #f))  ;; no tests
+    (home-page "http://www.geuz.org/gl2ps/")
+    (synopsis "OpenGL to PostScript printing library")
+    (description "GL2PS is a C library providing high quality vector
+output for any OpenGL application.  GL2PS uses sorting algorithms
+capable of handling intersecting and stretched polygons, as well as
+non-manifold objects.  GL2PS provides many features including advanced
+smooth shading and text rendering, culling of invisible primitives and
+mixed vector/bitmap output.")
+    (license (list license:lgpl2.0+
+                   (license:fsf-free "http://www.geuz.org/gl2ps/COPYING.GL2PS"
+                                     "GPL-incompatible copyleft license")))))

gnu/packages/gnome.scm

@@ -23,6 +23,7 @@
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2016 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
+;;; Copyright © 2017 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -89,6 +90,7 @@
   #:use-module (gnu packages lirc)
   #:use-module (gnu packages lua)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages networking)
   #:use-module (gnu packages password-utils)
   #:use-module (gnu packages pcre)
@@ -723,6 +725,29 @@ update-desktop-database: updates the database containing a cache of MIME types
     (native-inputs
      `(("gtk-encode-symbolic-svg" ,gtk+ "bin")))))
 
+(define-public tango-icon-theme
+  (package
+    (name "tango-icon-theme")
+    (version "0.8.90")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://tango.freedesktop.org/releases/"
+                                  "tango-icon-theme-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "034r9s944b4yikyfgn602yv7s54wdzlq0qfvqh52b9x6kbx08h79"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("icon-naming-utils" ,icon-naming-utils)
+       ("intltool" ,intltool)
+       ("imagemagick" ,imagemagick)
+       ("pkg-config" ,pkg-config)))
+    (home-page "http://tango-project.org/")
+    (synopsis "Tango icon theme")
+    (description "This is an icon theme that follows the Tango visual
+guidelines.")
+    (license license:public-domain)))
+
 (define-public shared-mime-info
   (package
     (name "shared-mime-info")
@@ -4549,7 +4574,7 @@ users.")
 (define-public network-manager
   (package
     (name "network-manager")
-    (version "1.4.4")
+    (version "1.6.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/NetworkManager/"
@@ -4557,7 +4582,7 @@ users.")
                                   "NetworkManager-" version ".tar.xz"))
               (sha256
                (base32
-                "029k2f1arx1m5hppmr778i9yg34jj68nmji3i89qs06c33rpi4w2"))
+                "1y96k82rav8if334jl500zc024d210c4pgprh94yqyz3rmanyaxj"))
               (snippet
               '(begin
                  (use-modules (guix build utils))
@@ -4601,12 +4626,14 @@ users.")
              ;; cope with being already in the Guix build jail as that jail
              ;; lacks some features that they would like to proxy over (like
              ;; a /sys mount).
-             (substitute* '("src/platform/Makefile.in"
+             (substitute* '("Makefile.in")
-                            "src/devices/Makefile.in")
+               (("src/platform/tests/test-address-linux") " ")
-               (("SUBDIRS = tests") ""))
+               (("src/platform/tests/test-cleanup-linux") " ")
-             (substitute* '("src/tests/Makefile.in")
+               (("src/platform/tests/test-link-linux") " ")
-               (("\ttest-route-manager-linux") "\t")
+               (("src/platform/tests/test-route-linux") " ")
-               (("\ttest-route-manager-fake") "\t"))
+               (("src/devices/tests/test-arping") " ")
+               (("src/devices/tests/test-lldp") " ")
+               (("src/tests/test-route-manager-linux") " "))
              #t))
          (add-before 'check 'pre-check
            (lambda _
@@ -4619,13 +4646,17 @@ users.")
                              "sysconfdir=/tmp"
                              "rundir=/tmp"
                              "statedir=/tmp"
+                             "nmstatedir=/tmp/nm"
                              "install")))))))
     (propagated-inputs
      `(("glib" ,glib)))
     (native-inputs
      `(("glib:bin" ,glib "bin") ; for gdbus-codegen
        ("gobject-introspection" ,gobject-introspection)
+       ("docbook-xsl" ,docbook-xsl)
        ("intltool" ,intltool)
+       ("libxslt" ,libxslt)
+       ("libxml2" ,libxml2)
        ("pkg-config" ,pkg-config)
        ;; For testing.
        ("python" ,python-wrapper)
@@ -4637,6 +4668,7 @@ users.")
        ("gnutls" ,gnutls)
        ("iptables" ,iptables)
        ("isc-dhcp" ,isc-dhcp)
+       ("jansson" ,jansson)
        ("libgcrypt" ,libgcrypt)
        ("libgudev" ,libgudev)
        ("libndp" ,libndp)

gnu/packages/gnucash.scm

@@ -42,7 +42,7 @@
 (define-public gnucash
   (package
     (name "gnucash")
-    (version "2.6.15")
+    (version "2.6.16")
     (source
      (origin
       (method url-fetch)
@@ -50,7 +50,7 @@
                           version "/gnucash-" version ".tar.bz2"))
       (sha256
        (base32
-        "1bnvnv1sxv85bgpfklykbhymjl4sbfqc1z9as5ym97s3cf1fn68n"))
+        "1088rssg9xgwi3wdfrhdcga46gby6lrd9a1fvn9zq456lscn4m9c"))
       (patches (search-patches "gnucash-price-quotes-perl.patch"))))
     (build-system gnu-build-system)
     (inputs

gnu/packages/gnupg.scm

@@ -217,15 +217,14 @@ compatible to GNU Pth.")
 (define-public gnupg
   (package
     (name "gnupg")
-    (version "2.1.19")
+    (version "2.1.20")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnupg/gnupg/gnupg-" version
                                   ".tar.bz2"))
-              (patches (search-patches "gnupg-2.1-fix-Y2038-test-failure.patch"))
               (sha256
                (base32
-                "1w4vccmb5l50lm4yrz9vkdj7whbfvzx543r55362kkj1aqgyvk26"))))
+                "03cnd6gz8f4lf69inskssw57idrswcdimhccdyglmrlv6rlrmkr4"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -371,7 +370,7 @@ libskba (working with X.509 certificates and CMS data).")
 (define-public gpgme
   (package
     (name "gpgme")
-    (version "1.8.0")
+    (version "1.9.0")
     (source
      (origin
       (method url-fetch)
@@ -379,7 +378,7 @@ libskba (working with X.509 certificates and CMS data).")
                           ".tar.bz2"))
       (sha256
        (base32
-        "0csx3qnycwm0n90ql6gs65if5xi4gqyzzy21fxs2xqicghjrfq2r"))))
+        "1ssc0gs02r4fasabk7c6v6r865k2j02mpb5g1vkpbmzsigdzwa8v"))))
     (build-system gnu-build-system)
     (propagated-inputs
      ;; Needs to be propagated because gpgme.h includes gpg-error.h.

gnu/packages/gnuzilla.scm

@@ -5,6 +5,7 @@
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
+;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -193,7 +194,7 @@ in the Mozilla clients.")
 (define-public nss
   (package
     (name "nss")
-    (version "3.29.3")
+    (version "3.30.1")
     (source (origin
               (method url-fetch)
               (uri (let ((version-with-underscores
@@ -204,7 +205,7 @@ in the Mozilla clients.")
                       "nss-" version ".tar.gz")))
               (sha256
                (base32
-                "1sz1r2iml9bhd4iqiqz75gii855a25895vpy9scjky0y4lqwrp9m"))
+                "1djypq081m22iw0wg0q7gnpndam5f8qjhqfd5v9by4c6l6lp78hz"))
               ;; Create nss.pc and nss-config.
               (patches (search-patches "nss-pkgconfig.patch"
                                        "nss-increase-test-timeout.patch"))))
@@ -375,7 +376,22 @@ standards.")
         (mozilla-patch "icecat-bug-1292534.patch"        "c709d4b36145" "18cdck3fr4a1ygszb6qk07g6fi3kv6i697pjfcipvqrk358qb0hq")
         (mozilla-patch "icecat-bug-1336830.patch"        "18e355831dd5" "042487xhq9zkky3pxiqy1rpy69z0j20w0jnl7kwg2j1bzfbnniip")
         (mozilla-patch "icecat-bug-1336832.patch"        "ebeb0b45a84b" "17ch2aqsrnkiwbnkf6x7a1cpi8jgfjhwr6wp0bsa89s8v1dax6w4")
-        (mozilla-patch "icecat-bug-1349946.patch"        "ccbecbe17a45" "19vwmhvqarpzai8mcq6i7szkrp1h9m8v5lyimkmmdlmagrivjw7f")))
+        (mozilla-patch "icecat-bug-1349946.patch"        "ccbecbe17a45" "19vwmhvqarpzai8mcq6i7szkrp1h9m8v5lyimkmmdlmagrivjw7f")
+        (mozilla-patch "icecat-bug-1350683.patch"        "00ed655efad1" "0nfk9345lshim8xl29qka5man73jgxcppv3pzfrgjhk97z7h6ifq")
+        (mozilla-patch "icecat-bug-1342823.patch"        "609145968cfe" "1y5kw8khzxnx5cbrv4zmdd1nzha85r3cmxn3inami9fx8vikxjq8")
+        (mozilla-patch "icecat-bug-1336828.patch"        "982cfe33c513" "0amj3qx5399mrdcqakvfn5pabp562i1s87a8zd65jyqs4mwgcjap")
+        (mozilla-patch "icecat-bug-1348894.patch"        "eed8086d0af7" "18p567nhj7nvh740fhh3l0mqx0b7370b45005j43ll08rf2nhygl")
+        (mozilla-patch "icecat-bug-1344467.patch"        "38664f88d8f5" "0zdkmiqjr6h1bfs4qw74p5bnw74kcx9fxr4mcnshpavv2gvc6dn4")
+        (mozilla-patch "icecat-bug-1350844.patch"        "c071fab59d05" "16hf5c4appca8vwxl5yvl5ig5bw8cb8hl8apvknsn5rdsjwjlrpr")
+        (mozilla-patch "icecat-bug-1352926.patch"        "8fade3eebca2" "165v18545g4br1j6nbbhq2h9098iqvqpbd54zmgwwk9c973qhp3c")
+        (mozilla-patch "icecat-bug-1343642.patch"        "6172686bf59c" "0iwihvx11am28cbmgg68llf3mr4ghrclimr51vms1nq9ji767wdb")
+        (mozilla-patch "icecat-bug-1349340.patch"        "260b50fb6d39" "0lq08bkj1ihhwmf0yhxcnvngzym222q3n66ql9fbda4n7prlfhzl")
+        (mozilla-patch "icecat-bug-1353088.patch"        "44a90ca714b9" "1rb27bnrm9a5nnwrsxx7z36yhhz8x6lv0df98jv1128zvd373blp")
+        (mozilla-patch "icecat-bug-1347617.patch"        "e40b00161221" "0nm6jqbkb6rdahzd39gnhmy1gwawa5jbd7i80c7g1igj3x8ab50y")
+        (mozilla-patch "icecat-bug-1278157.patch"        "a7803c36d797" "10l8jbqlmfkvi4jj0vhkl0a9vdsh3niy5rjr26br3633nyyr4747")
+        (mozilla-patch "icecat-bug-1348941.patch"        "4fe9b979b84d" "069rzn60vn90gcck2wakr6m83q0cy32x5r54ccia9nc26a01p6p5")
+        (mozilla-patch "icecat-bug-1347075.patch"        "a017569d3535" "1j7q02q2ybpfx9cr6dn9x27jva1d6dzs4pdxx2a1xmk5va03lrmq")
+        (mozilla-patch "icecat-bug-1333858.patch"        "413dc18f25c8" "0g1q1y22m5gds8p07nq5c8f84jc152x4sac40b17gawj1005n5v9")))
       (modules '((guix build utils)))
       (snippet
        '(begin
@@ -472,7 +488,6 @@ standards.")
     (arguments
      `(#:tests? #f          ; no check target
        #:out-of-source? #t  ; must be built outside of the source directory
-       #:parallel-build? #f
 
        ;; XXX: There are RUNPATH issues such as
        ;; $prefix/lib/icecat-31.6.0/plugin-container NEEDing libmozalloc.so,
@@ -509,7 +524,11 @@ standards.")
                            "--with-system-jpeg"        ; must be libjpeg-turbo
                            "--with-system-libevent"
                            "--with-system-libvpx"
-                           "--with-system-icu"
+
+                           ;; FIXME: It is preferable to build with system
+                           ;; libraries, but this fixes crashes.
+                           ;; "--with-system-icu"
+
                            "--with-system-nspr"
                            "--with-system-nss"
                            "--enable-system-pixman"

gnu/packages/guile.scm

@@ -11,6 +11,7 @@
 ;;; Copyright © 2016 Amirouche <amirouche@hypermove.net>
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2017 Andy Wingo <wingo@igalia.com>
+;;; Copyright © 2017 David Thompson <davet@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -470,17 +471,17 @@ many readers as needed).")
 (define-public guile-ncurses
   (package
     (name "guile-ncurses")
-    (version "2.1")
+    (version "2.2")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/guile-ncurses/guile-ncurses-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "1h7rnq4g7xlxxybcb3vjq6nscm9zhlmfaxb7258c8ax7him4azg6"))))
+               "1wvggbr4xv8idh1hzd8caj4xfp4pln78a7w1wqzd4zgzwmnzxr2f"))))
     (build-system gnu-build-system)
     (inputs `(("ncurses" ,ncurses)
-              ("guile" ,guile-2.0)))
+              ("guile" ,guile-2.2)))
     (native-inputs `(("pkg-config" ,pkg-config)))
     (arguments
      '(#:configure-flags (list "--with-ncursesw"  ; Unicode support
@@ -498,7 +499,7 @@ many readers as needed).")
                          (files (find-files dir ".scm")))
                     (substitute* files
                       (("\"libguile-ncurses\"")
-                       (format #f "\"~a/lib/guile/2.0/libguile-ncurses\""
+                       (format #f "\"~a/lib/guile/2.2/libguile-ncurses\""
                                out)))
                     #t)))))))
     (home-page "https://www.gnu.org/software/guile-ncurses/")
@@ -1520,7 +1521,7 @@ type system, elevating types to first-class status.")
 (define-public guile-aspell
   (package
     (name "guile-aspell")
-    (version "0.3")
+    (version "0.4")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1528,23 +1529,27 @@ type system, elevating types to first-class status.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "1wknn57x2qcsbn7zw6sbn1ma6fjsg8cvpnf78ak47s8jw6k6j75n"))))
+                "0vpk5xj9m9qc702z3khmkwhgpb949qbsyz8kw2qycda6qnxk0077"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:configure-flags (list (string-append "--with-guilesitedir="
+     '(#:phases (modify-phases %standard-phases
-                                              (assoc-ref %outputs "out")
+                  (add-before 'configure 'set-guilesitedir
-                                              "/share/guile/site/2.0"))
+                    (lambda _
-       #:phases (modify-phases %standard-phases
+                      (substitute* "Makefile.in"
+                        (("^guilesitedir =.*$")
+                         "guilesitedir = \
+$(datadir)/guile/site/$(GUILE_EFFECTIVE_VERSION)\n"))
+                      #t))
                   (add-before 'build 'set-libaspell-file-name
                     (lambda* (#:key inputs #:allow-other-keys)
                       (let ((aspell (assoc-ref inputs "aspell")))
-                        (substitute* "aspell/aspell.scm"
+                        (substitute* "aspell.scm"
                           (("\"libaspell\\.so\"")
                            (string-append "\"" aspell
                                           "/lib/libaspell\"")))
                         #t))))))
     (native-inputs `(("pkg-config" ,pkg-config)))
-    (inputs `(("guile" ,guile-2.0)
+    (inputs `(("guile" ,guile-2.2)
               ("aspell" ,aspell)))
     (home-page "https://github.com/spk121/guile-aspell")
     (synopsis "Spell-checking from Guile")
@@ -1728,4 +1733,39 @@ is not available for Guile 2.0.")
 manipulate repositories of the Git version control system.")
       (license license:gpl3+))))
 
+(define-public guile-syntax-highlight
+  (let ((commit "a047675e66861b647426372aa2ba7820f749616d")
+        (revision "0"))
+    (package
+      (name "guile-syntax-highlight")
+      (version (string-append "0.0." revision "."
+                              (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "git://dthompson.us/guile-syntax-highlight.git")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1zjr6sg3n7xbdsliy45i39dqanxvcms58ayx36wxrz72zpq58vq3"))))
+      (build-system gnu-build-system)
+      (arguments
+       '(#:phases (modify-phases %standard-phases
+                    (add-after 'unpack 'bootstrap
+                      (lambda _
+                        (zero? (system* "sh" "bootstrap")))))))
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("pkg-config" ,pkg-config)))
+      (inputs
+       `(("guile" ,guile-2.2)))
+      (synopsis "General-purpose syntax highlighter for GNU Guile")
+      (description "Guile-syntax-highlight is a general-purpose syntax
+highlighting library for GNU Guile.  It can parse code written in various
+programming languages into a simple s-expression that can be converted to
+HTML (via SXML) or any other format for rendering.")
+      (home-page "http://dthompson.us/software/guile-syntax-highlight")
+      (license license:lgpl3+))))
+
 ;;; guile.scm ends here

gnu/packages/image-viewers.scm

@@ -1,10 +1,11 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net>
 ;;; Copyright © 2015, 2016 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net>
+;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,22 +29,29 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
   #:use-module (gnu packages autotools)
+  #:use-module (gnu packages algebra)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages boost)
+  #:use-module (gnu packages compression)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gtk)
+  #:use-module (gnu packages graphics)
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
+  #:use-module (gnu packages maths)
   #:use-module (gnu packages photo)
   #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages xorg))
+  #:use-module (gnu packages qt)
+  #:use-module (gnu packages xorg)
+  #:use-module (gnu packages))
 
 (define-public feh
   (package
     (name "feh")
-    (version "2.18.2")
+    (version "2.18.3")
     (home-page "https://feh.finalrewind.org/")
     (source (origin
               (method url-fetch)
@@ -51,7 +59,7 @@
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "09f5rfzls4h5jcrp7ylwbiljp5qzc2nbw9p2csv0pnlaixj69gil"))))
+                "0qq567d0g181k6llr6p759lnni39va5xakjqngd6063fm73nhbyq"))))
     (build-system gnu-build-system)
     (arguments
       '(#:phases (alist-delete 'configure %standard-phases)
@@ -122,6 +130,29 @@ image formats; tools for image comparison, sorting and managing photo
 collection.  Geeqie was initially based on GQview.")
     (license license:gpl2+)))
 
+(define-public gpicview
+  (package
+    (name "gpicview")
+    (version "0.2.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/lxde/"
+                                  "GPicView%20%28image%20Viewer%29/0.2.x/"
+                                  name "-" version ".tar.xz"))
+              (sha256
+               (base32
+                "0hi9v0rdx47nys0wvm9xasdrafa34r5kq6crb074a0ipwmc60iiq"))))
+    (build-system gnu-build-system)
+    (inputs `(("gtk+" ,gtk+-2)
+              ("libjpeg" ,libjpeg)))
+    (native-inputs `(("intltool"   ,intltool)
+                     ("pkg-config" ,pkg-config)))
+    (synopsis "Simple and fast image viewer for X")
+    (description "gpicview is a lightweight GTK+ 2.x based image viewer.
+It is the default image viewer on LXDE desktop environment.")
+    (home-page "http://lxde.sourceforge.net/gpicview/")
+    (license license:gpl2+)))
+
 (define-public sxiv
   (package
     (name "sxiv")
@@ -266,3 +297,66 @@ your images.  Among its features are:
      "Catimg is a little program that prints images in the terminal.
 It supports JPEG, PNG and GIF formats.")
     (license license:expat)))
+
+(define-public luminance-hdr
+  (package
+    (name "luminance-hdr")
+    (version "2.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://sourceforge/qtpfsgui/luminance/"
+                    version "/luminance-hdr-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "00fldbcizrx8jcnjgq74n3zmbm27dxzl96fxa7q49689mfnlw08l"))
+              (patches (search-patches "luminance-hdr-qt-printer.patch"))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("qttools" ,qttools)))
+    (inputs
+     `(("qtbase" ,qtbase)
+       ("qtdeclarative" ,qtdeclarative)
+       ("qtwebkit" ,qtwebkit)
+       ("boost" ,boost)
+       ;; ("gtest" ,gtest)
+       ("libraw" ,libraw)
+       ("zlib" ,zlib)
+       ("exiv2" ,exiv2)
+       ("libpng" ,libpng)
+       ("libjpeg" ,libjpeg)
+       ("lcms" ,lcms)
+       ("openexr" ,openexr)
+       ("fftw" ,fftwf)
+       ("gsl" ,gsl)
+       ("libtiff" ,libtiff)))
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'set-paths 'add-ilmbase-include-path
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; 'OpenEXR.pc' has a -I for IlmBase but 'FindOpenEXR.cmake' does
+             ;; not use 'OpenEXR.pc'.  Thus, we need to add
+             ;; "$ilmbase/include/OpenEXR/" to the CPATH.
+             (setenv "CPATH"
+                     (string-append (assoc-ref inputs "ilmbase")
+                                    "/include/OpenEXR"
+                                    ":" (or (getenv "CPATH") "")))
+             #t)))))
+    (home-page "http://qtpfsgui.sourceforge.net")
+    (synopsis "High dynamic range (HDR) imaging application")
+    (description
+     "Luminance HDR (formerly QtPFSGui) is a graphical user interface
+application that aims to provide a workflow for high dynamic range (HDR)
+imaging.  It supports several HDR and LDR image formats, and it can:
+
+@itemize
+@item Create an HDR file from a set of images (formats: JPEG, TIFF 8bit and
+16bit, RAW) of the same scene taken at different exposure setting;
+@item Save load HDR images;
+@item Rotate, resize and crop HDR images;
+@item Tone-map HDR images;
+@item Copy EXIF data between sets of images.
+@end itemize\n")
+    (license license:gpl2+)))

gnu/packages/image.scm

@@ -905,7 +905,8 @@ convert, manipulate, filter and display a wide variety of image formats.")
                                   "/software/jasper-" version ".tar.gz"))
               (sha256
                (base32
-                "1njdbxv7d4anzrd476wjww2qsi96dd8vfnp4hri0srrqxpszl92v"))))
+                "1njdbxv7d4anzrd476wjww2qsi96dd8vfnp4hri0srrqxpszl92v"))
+              (patches (search-patches "jasper-CVE-2017-6850.patch"))))
     (build-system cmake-build-system)
     (inputs `(("libjpeg" ,libjpeg)))
     (synopsis "JPEG-2000 library")

gnu/packages/julia.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -83,7 +83,7 @@
 (define-public julia
   (package
     (name "julia")
-    (version "0.5.0")
+    (version "0.5.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -91,7 +91,7 @@
                     version "/julia-" version ".tar.gz"))
               (sha256
                (base32
-                "0bhickil88lalp9jdj1kmf4is70zinhx8ha9rng0g3z50r4a2qmv"))))
+                "1a9m7hzzrwk71gvwwrd1p45s64yid61i41n95gm5pzbry6p9fpl0"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"

gnu/packages/kde.scm

@@ -39,7 +39,7 @@
 (define-public kdevelop
   (package
     (name "kdevelop")
-    (version "5.0.4")
+    (version "5.1.0")
     (source
       (origin
         (method url-fetch)
@@ -48,7 +48,7 @@
                             version ".tar.xz"))
         (sha256
          (base32
-          "0max4g1i8xf5g7a8zm60qkr2j8w5bsqzxz914z43fj5ipnr4448r"))))
+          "1s4cbkx2a0p73b52yxmf5dhv08xk9pxgrkjsnbzy76ssfr545g60"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)
@@ -148,7 +148,7 @@ for some KDevelop language plugins (Ruby, PHP, CSS...).")
 (define-public kdevplatform
   (package
     (name "kdevplatform")
-    (version "5.0.4")
+    (version "5.1.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://kde/stable/kdevelop"
@@ -156,7 +156,7 @@ for some KDevelop language plugins (Ruby, PHP, CSS...).")
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0wfl5azblnpmc7hydfvm7450343m1v7cr2g9gw0qs1432gbzraq1"))))
+                "1nxf66vk6p7lmckdsha9fpq3zchwbg79qhy49f4hndlxgj03p7zh"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)

gnu/packages/language.scm

@@ -28,7 +28,7 @@
 (define-public perl-lingua-en-findnumber
   (package
     (name "perl-lingua-en-findnumber")
-    (version "1.30")
+    (version "1.32")
     (source
      (origin
        (method url-fetch)
@@ -36,7 +36,7 @@
                            "Lingua-EN-FindNumber-" version ".tar.gz"))
        (sha256
         (base32
-         "0g5h6bwwggizwh3dd3xyx92537s4qy8nspshp1lrm9qlxh3prc28"))))
+         "015ximzdp42v824llwlg2pd77vd0d172lb4xs55q9f9zhqf6s5qx"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-lingua-en-words2nums" ,perl-lingua-en-words2nums)))
@@ -50,7 +50,7 @@ manipulating such numbers.")
 (define-public perl-lingua-en-inflect
   (package
     (name "perl-lingua-en-inflect")
-    (version "1.895")
+    (version "1.901")
     (source
      (origin
        (method url-fetch)
@@ -58,7 +58,7 @@ manipulating such numbers.")
                            "Lingua-EN-Inflect-" version ".tar.gz"))
        (sha256
         (base32
-         "0drzg9a2dkjxgf00n6jg0jzhd8972bh3j4wdnmdxpqi3zmfqhwcy"))))
+         "0mcwlgf6hkh4zm3s1x899f25xj4hyzrc2vssiwfxysqja36yf5ys"))))
     (build-system perl-build-system)
     (native-inputs `(("perl-module-build" ,perl-module-build)))
     (home-page "http://search.cpan.org/dist/Lingua-EN-Inflect")
@@ -73,7 +73,7 @@ provided.  Where appropriate, \"classical\" variants (for example: \"brother\"
 (define-public perl-lingua-en-inflect-number
   (package
     (name "perl-lingua-en-inflect-number")
-    (version "1.11")
+    (version "1.12")
     (source
      (origin
        (method url-fetch)
@@ -81,7 +81,7 @@ provided.  Where appropriate, \"classical\" variants (for example: \"brother\"
                            "Lingua-EN-Inflect-Number-" version ".tar.gz"))
        (sha256
         (base32
-         "0rvgrff96ja7fqr79dszmiyv2wz4izw82znah0mx9szkir657gfz"))))
+         "1gxccynkaqav43ww43jp4rzkyr36x97jd03yb5f6yx0jhn1k7yv6"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-lingua-en-inflect" ,perl-lingua-en-inflect)))
@@ -122,7 +122,7 @@ English phrases.")
 (define-public perl-lingua-en-number-isordinal
   (package
     (name "perl-lingua-en-number-isordinal")
-    (version "0.04")
+    (version "0.05")
     (source
      (origin
        (method url-fetch)
@@ -130,7 +130,7 @@ English phrases.")
                            "Lingua-EN-Number-IsOrdinal-" version ".tar.gz"))
        (sha256
         (base32
-         "1321fm4pyqcamffd0qsjm1gb07ijqndlb29qkcqf22kaibngfm4i"))))
+         "1mhqjvh2ad30gjab5b3a6mbr4aysyrscp4wp42yy5x6001a6km98"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-try-tiny" ,perl-try-tiny)
@@ -146,7 +146,7 @@ digits, is a cardinal or ordinal number.")
 (define-public perl-lingua-en-tagger
   (package
     (name "perl-lingua-en-tagger")
-    (version "0.24")
+    (version "0.28")
     (source
      (origin
        (method url-fetch)
@@ -154,7 +154,7 @@ digits, is a cardinal or ordinal number.")
                            "Lingua-EN-Tagger-" version ".tar.gz"))
        (sha256
         (base32
-         "0qksqh1zi8fz76a29s2ll4g6yr8y6agmzgq7ngccvgj3gza5q241"))))
+         "1rm223d871s150dgnhbar71w56bim950cp45f0904w6px5fifcqa"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-memoize-expirelru" ,perl-memoize-expirelru)

gnu/packages/ldc.scm

@@ -2,6 +2,8 @@
 ;;; Copyright © 2015, 2016 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2015 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2017 Frederick Muriithi <fredmanglis@gmail.com>
+;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -120,6 +122,8 @@ and freshness without requiring additional information from the user.")
                 (string-append (assoc-ref inputs "tzdata") "/share/zoneinfo")))
              (substitute* "tests/d2/dmd-testsuite/Makefile"
                (("/bin/bash") (which "bash")))
+             ;; FIXME: this test cannot be linked.
+             (delete-file "tests/d2/dmd-testsuite/runnable/cppa.d")
              #t)))))
     (inputs
      `(("libconfig" ,libconfig)
@@ -276,7 +280,7 @@ latest DMD frontend and uses LLVM as backend.")
 (define-public dub
   (package
     (name "dub")
-    (version "1.2.2")
+    (version "1.3.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/dlang/dub/archive/"
@@ -284,28 +288,33 @@ latest DMD frontend and uses LLVM as backend.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "02k11x34nck0lbv13ww103niiswnwnslbnswj3b5faszzadbi1v4"))))
+                "056mvf01z51qc3i1qnx7yaqr728q8pss8zabiv5zpfx2ynfsw3k7"))))
    (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; it would have tested itself by installing some packages (vibe etc)
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure)
+         (delete 'configure)            ; no configure script
          (replace 'build
            (lambda _
              (zero? (system* "./build.sh"))))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
-                    (outbin (string-append out "/bin")))
+                    (bin (string-append out "/bin")))
-               (mkdir-p outbin)
+               (install-file "bin/dub" bin)
-               (install-file "bin/dub" outbin)
                #t))))))
     (inputs
      `(("curl" ,curl)))
     (native-inputs
      `(("ldc" ,ldc)))
     (home-page "https://code.dlang.org/getting_started")
-    (synopsis "DUB package manager")
+    (synopsis "Package and build manager for D projects")
-    (description "This package provides the D package manager.")
+    (description
+     "DUB is a package and build manager for applications and libraries written
+in the D programming language.  It can automatically retrieve a project's
+dependencies and integrate them in the build process.
+
+The design emphasis is on maximum simplicity for simple projects, while
+providing the opportunity to customize things when needed. ")
     (license license:expat)))

gnu/packages/libusb.scm

@@ -42,7 +42,7 @@
 (define-public libusb
   (package
     (name "libusb")
-    (version "1.0.19")
+    (version "1.0.21")
     (source
      (origin
       (method url-fetch)
@@ -50,7 +50,7 @@
                           "libusb-" version "/libusb-" version ".tar.bz2"))
       (sha256
        (base32
-        "0h38p9rxfpg9vkrbyb120i1diq57qcln82h5fr7hvy82c20jql3c"))))
+        "0jw2n5kdnrqvp7zh792fd6mypzzfap6jp4gfcmq4n6c1kb79rkkx"))))
     (build-system gnu-build-system)
 
     ;; XXX: Enabling udev is now recommended, but eudev indirectly depends on
@@ -58,7 +58,7 @@
     (arguments `(#:configure-flags '("--disable-udev")))
     ;; (inputs `(("eudev" ,eudev)))
 
-    (home-page "http://www.libusb.org")
+    (home-page "http://libusb.info")
     (synopsis "User-space USB library")
     (description
      "Libusb is a library that gives applications easy access to USB
@@ -136,14 +136,14 @@ version of libusb to run with newer libusb.")
 (define-public libmtp
   (package
     (name "libmtp")
-    (version "1.1.11")
+    (version "1.1.13")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/libmtp/libmtp/" version
                                  "/libmtp-" version ".tar.gz"))
              (sha256
               (base32
-               "1sc768q2cixwanlwrz95mp389iaadl4s95486caavxx4g7znvn8m"))))
+               "0h3dv9py5mmvxhfxmkr8ky4s80hgq3d66cmrfnnnlcdwpwpy0kj9"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))

gnu/packages/linux.scm

@@ -352,8 +352,8 @@ It has been modified to remove all non-free binary blobs.")
 
 (define %intel-compatible-systems '("x86_64-linux" "i686-linux"))
 
-(define %linux-libre-version "4.10.8")
+(define %linux-libre-version "4.10.10")
-(define %linux-libre-hash "0936i2h9l4gn67gby9kx70w6zqv1nbzbgwssry6k11wrjwa2p8n4")
+(define %linux-libre-hash "1py6hzv39hbyafkvz69pmcidwxbd7psp9jzmnm4dg4jj7j92m6b7")
 
 (define-public linux-libre
   (make-linux-libre %linux-libre-version
@@ -362,14 +362,14 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.20"
+  (make-linux-libre "4.9.22"
-                    "0hnxylfnyz3xf7k3qcq2wri2wpbi2islngxjmqp445v1pzr4k9xp"
+                    "1dvsbqkw7wvg40nmzdyiyvb0i54j5w6d9dvsvv7z87d2id56lqm0"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.59"
+  (make-linux-libre "4.4.61"
-                    "1nrg7mg6cn0xzsdklg24aj5fqx05hab11j9nq4b8dabjf4crlkx5"
+                    "12555h3yxymxgfgq3g33sy78g7rj6l8dpqr29z98kr9ybs93q7vj"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
@@ -2224,6 +2224,7 @@ in a digital read-out.")
        ;; ("newt" ,newt)
        ("python" ,python-2)                    ;'perf' links against libpython
        ("elfutils" ,elfutils)
+       ("libiberty" ,libiberty)      ;used alongside BDF for symbol demangling
 
        ;; Documentation.
        ("libxml2" ,libxml2)                       ;for $XML_CATALOG_FILES

gnu/packages/lisp.scm

@@ -6,6 +6,7 @@
 ;;; Copyright © 2016, 2017 ng0 <contact.ng0@cryptolab.net>
 ;;; Copyright © 2016 Andy Patterson <ajpatter@uwaterloo.ca>
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -87,34 +88,32 @@
      `(#:parallel-build? #f  ; The build system seems not to be thread safe.
        #:tests? #f  ; There does not seem to be make check or anything similar.
        #:configure-flags '("--enable-ansi") ; required for use by the maxima package
-       #:phases (alist-cons-before
+       #:phases (modify-phases %standard-phases
-                'configure 'pre-conf
+                  (add-before 'configure 'pre-conf
-                (lambda _
+                    (lambda _
-                  ;; Patch bug when building readline support.  This bug was
+                      (substitute*
-                  ;; also observed by Debian
+                        (append
-                  ;; https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=741819
+                         '("pcl/impl/kcl/makefile.akcl"
-                  (substitute* "o/gcl_readline.d"
+                           "add-defs"
-                    (("rl_attempted_completion_function = \
+                           "unixport/makefile.dos"
-\\(CPPFunction \\*\\)rl_completion;")
+                           "add-defs.bat"
-                      "rl_attempted_completion_function = rl_completion;"))
+                           "gcl-tk/makefile.prev"
-                  (substitute*
+                           "add-defs1")
-                      (append
+                         (find-files "h" "\\.defs"))
-                       '("pcl/impl/kcl/makefile.akcl"
+                        (("SHELL=/bin/bash")
-                         "add-defs"
+                         (string-append "SHELL=" (which "bash")))
-                         "unixport/makefile.dos"
+                        (("SHELL=/bin/sh")
-                         "add-defs.bat"
+                         (string-append "SHELL=" (which "sh"))))
-                         "gcl-tk/makefile.prev"
+                      #t))
-                         "add-defs1")
+                  ;; drop strip phase to make maxima build, see
-                       (find-files "h" "\\.defs"))
+                  ;; https://www.ma.utexas.edu/pipermail/maxima/2008/009769.html
-                    (("SHELL=/bin/(ba)?sh")
+                  (delete 'strip))))
-                     (string-append "SHELL=" (which "bash")))))
+    (inputs
-                ;; drop strip phase to make maxima build, see
+     `(("gmp" ,gmp)
-                ;; https://www.ma.utexas.edu/pipermail/maxima/2008/009769.html
+       ("readline" ,readline)))
-                (alist-delete 'strip
-                 %standard-phases))))
     (native-inputs
-     `(("m4" ,m4)
+     `(("gcc" ,gcc-4.9)
-       ("readline" ,readline)
+       ("m4" ,m4)
        ("texinfo" ,texinfo)
        ("texlive" ,texlive)))
     (home-page "https://www.gnu.org/software/gcl/")

gnu/packages/logging.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -24,6 +24,7 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
+  #:use-module (gnu packages)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages autotools))
 
@@ -62,7 +63,8 @@ staying as close to their API as is reasonable.")
               (sha256
                (base32
                 "0ym5g15m7c8kjfr2c3zq6bz08ghin2d1r1nb6v2vnkfh1vn945x1"))
-              (file-name (string-append name "-" version "-checkout"))))
+              (file-name (string-append name "-" version "-checkout"))
+              (patches (search-patches "glog-gcc-5-demangling.patch"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("perl" ,perl)                             ;for tests

gnu/packages/lxde.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net>
+;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -26,10 +27,12 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gtk)
+  #:use-module (gnu packages image-viewers)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages openbox)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages polkit)
+  #:use-module (gnu packages text-editors)
   #:use-module (gnu packages wm)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
@@ -433,9 +436,11 @@ in LXDE.")
     (arguments '(#:builder (mkdir %output)))
     (propagated-inputs
      ;; TODO:
-     ;; lxshortcut, lxsession-edit, gpicview, leafpad,
+     ;; lxshortcut, lxsession-edit
      ;; lxappearance-obconf
      `(("menu-cache" ,menu-cache)
+       ("gpicview" ,gpicview)
+       ("leafpad" ,leafpad)
        ("lxappearance" ,lxappearance)
        ("lxde-icon-theme" ,lxde-icon-theme)
        ("lxde-common" ,lxde-common)

gnu/packages/mail.scm

@@ -15,7 +15,7 @@
 ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org>
 ;;; Copyright © 2016 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2016 Troy Sankey <sankeytms@gmail.com>
-;;; Copyright © 2016, 2017 <contact.ng0@cryptolab.net>
+;;; Copyright © 2016, 2017 ng0 <contact.ng0@cryptolab.net>
 ;;; Copyright © 2016 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2016, 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2016 John Darrington <jmd@gnu.org>
@@ -40,6 +40,7 @@
 
 (define-module (gnu packages mail)
   #:use-module (gnu packages)
+  #:use-module (gnu packages aspell)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages backup)
@@ -50,6 +51,7 @@
   #:use-module (gnu packages cyrus-sasl)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages dejagnu)
+  #:use-module (gnu packages django)
   #:use-module (gnu packages dns)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages emacs)
@@ -63,6 +65,7 @@
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages flex)
+  #:use-module (gnu packages kerberos)
   #:use-module (gnu packages libcanberra)
   #:use-module (gnu packages libevent)
   #:use-module (gnu packages libidn)
@@ -70,6 +73,7 @@
   #:use-module (gnu packages lua)
   #:use-module (gnu packages m4)
   #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages openldap)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
@@ -85,6 +89,7 @@
   #:use-module (gnu packages ruby)
   #:use-module (gnu packages samba)
   #:use-module (gnu packages screen)
+  #:use-module (gnu packages tcl)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages networking)
   #:use-module (gnu packages web)
@@ -95,7 +100,7 @@
                 #:select (gpl2 gpl2+ gpl3 gpl3+ lgpl2.1 lgpl2.1+ lgpl3+
                            non-copyleft (expat . license:expat) bsd-3
                            public-domain bsd-4 isc (openssl . license:openssl)
-                           bsd-2 x11-style agpl3))
+                           bsd-2 x11-style agpl3 asl2.0))
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
@@ -1081,7 +1086,7 @@ facilities for checking incoming mail.")
 (define-public dovecot
   (package
     (name "dovecot")
-    (version "2.2.28")
+    (version "2.2.29.1")
     (source
      (origin
        (method url-fetch)
@@ -1089,7 +1094,7 @@ facilities for checking incoming mail.")
                            (version-major+minor version) "/"
                            name "-" version ".tar.gz"))
        (sha256 (base32
-                "098zpkmkk93372qnv6drgbfg8hp5mynspzc1735qgar6wdcqya70"))))
+                "127kn3fgmahw9fvgz2w3zaghq98ip4j8640wqa3rw7mrgvxrzync"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -1132,44 +1137,41 @@ It supports mbox/Maildir and its own dbox/mdbox formats.")
     (license (list lgpl2.1 license:expat (non-copyleft "file://COPYING")))))
 
 (define-public dovecot-trees
-  (let ((commit "006059c8a47d68f14f73c09743e45b9a73014dbf")
+  (package
-        (revision "1"))
+    (name "dovecot-trees")
-    (package
+    (version "2.1.0")
-      (name "dovecot-trees")
+    (source
-      (version (string-append "2.0.0-" revision "." (string-take commit 7)))
+     (origin
-      (source
+       (method url-fetch)
-       (origin
+       (uri (string-append "https://0xacab.org/riseuplabs/trees/repository/"
-         (method git-fetch)
+                           "archive.tar.gz?ref=v" version))
-         (uri (git-reference
+       (file-name (string-append name "-" version ".tar.gz"))
-               (url "https://0xacab.org/riseuplabs/trees.git")
+       (sha256
-               (commit commit)))
+        (base32
-         (file-name (string-append name "-" version "-checkout"))
+         "0rkk10b1bsjz979sc864vpgcdchy7yxwmyv4ik50lar1h6awdnrf"))))
-         (sha256
+    (build-system gnu-build-system)
-          (base32
+    (native-inputs
-           "0ax90bzc66x179wi1m7ywqwa8nssyhjngs7ij109hqqxg5ymfp73"))))
+     `(("automake" ,automake)
-      (build-system gnu-build-system)
+       ("autoconf" ,autoconf)
-      (native-inputs
+       ("libtool" ,libtool)
-       `(("automake" ,automake)
+       ("dovecot" ,dovecot)
-         ("autoconf" ,autoconf)
+       ("pkg-config" ,pkg-config)))
-         ("libtool" ,libtool)
+    (inputs
-         ("dovecot" ,dovecot)
+     `(("libsodium" ,libsodium)))
-         ("pkg-config" ,pkg-config)))
+    (arguments
-      (inputs
+     `(#:tests? #f ;No tests exist.
-       `(("libsodium" ,libsodium)))
+       #:configure-flags (list (string-append "--with-dovecot="
-      (arguments
+                                              (assoc-ref %build-inputs "dovecot")
-       `(#:tests? #f ;No tests exist.
+                                              "/lib/dovecot"))
-         #:configure-flags (list (string-append "--with-dovecot="
+       #:phases
-                                                (assoc-ref %build-inputs "dovecot")
+       (modify-phases %standard-phases
-                                                "/lib/dovecot"))
+         (add-before 'configure 'autogen
-         #:phases
+           (lambda _
-         (modify-phases %standard-phases
+             (zero? (system* "./autogen.sh")))))))
-           (add-before 'configure 'autogen
+    (home-page "https://0xacab.org/riseuplabs/trees")
-             (lambda _
+    (synopsis "NaCL-based Dovecot email storage encryption plugin")
-               (zero? (system* "./autogen.sh")))))))
+    (description
-      (home-page "https://0xacab.org/riseuplabs/trees")
+     "Technology for Resting Email Encrypted Storage (TREES) is a NaCL-based
-      (synopsis "NaCL-based Dovecot email storage encryption plugin")
-      (description
-       "Technology for Resting Email Encrypted Storage (TREES) is a NaCL-based
 Dovecot encryption plugin.  This plugin adds individually encrypted mail
 storage to the Dovecot IMAP server.  It is inspired by Posteo's scrambler
 which uses OpenSSL and RSA keypairs.  TREES works in a similar way, but uses
@@ -1185,7 +1187,7 @@ How it works:
 using lidsodium sealed boxes.
 @item New mail is encrypted as it arrives using the Curve25519 public key.
 @end enumerate\n")
-      (license agpl3))))
+    (license agpl3)))
 
 (define-public dovecot-libsodium-plugin
   (let ((commit "044de73c01c35385df0105f6b387bec5d5317ce7")
@@ -1335,7 +1337,7 @@ identify a message uniquely.")
 (define-public perl-email-mime
   (package
     (name "perl-email-mime")
-    (version "1.937")
+    (version "1.940")
     (source
      (origin
        (method url-fetch)
@@ -1343,7 +1345,7 @@ identify a message uniquely.")
                            "Email-MIME-" version ".tar.gz"))
        (sha256
         (base32
-         "0s50i3nxi9dr81p4rn017nrarc40yrwz0qcw34q8k3pvdf46fr9n"))))
+         "0pnxbr16cn5qy96xqhp9zmd94ashc9ivqh10qbgbc3f637a0mfir"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-email-address" ,perl-email-address)
@@ -1436,7 +1438,7 @@ Email::Send library.")
 (define-public perl-email-simple
   (package
     (name "perl-email-simple")
-    (version "2.211")
+    (version "2.213")
     (source
      (origin
        (method url-fetch)
@@ -1444,7 +1446,7 @@ Email::Send library.")
                            "Email-Simple-" version ".tar.gz"))
        (sha256
         (base32
-         "1if4a2wh4iwlcycqrd2fhkx04ngmd75q444gh43w0r9p15ym5f8w"))))
+         "1ibwsng63gvqqc6r2135mjwfdzazxkb1x8q7f87wqcbjcjfpmffd"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-email-date-format" ,perl-email-date-format)))
@@ -2065,6 +2067,74 @@ installation on systems where resources are limited.  Its features include:
 @end enumerate\n")
     (license license:expat)))
 
+(define-public python-django-mailman3
+  (package
+    (name "python-django-mailman3")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "django-mailman3" version))
+       (sha256
+        (base32
+         "1adxyh8knw9knjlh73xq0jpn5adml0ck4alsv0swakm95wfyx46z"))))
+    (build-system python-build-system)
+    (inputs
+     `(("python-django" ,python-django)))
+    (propagated-inputs
+     `(("python-requests" ,python-requests)
+       ("python-requests-oauthlib" ,python-requests-oauthlib)
+       ("python-openid" ,python-openid)
+       ("python-mailmanclient" ,python-mailmanclient)
+       ("python-django-allauth" ,python-django-allauth)
+       ("python-django-gravatar2" ,python-django-gravatar2)
+       ("python-pytz" ,python-pytz)))
+    (home-page "https://gitlab.com/mailman/django-mailman3")
+    (synopsis "Django library for Mailman UIs")
+    (description
+     "Libraries and templates for Django-based interfaces
+interacting with Mailman.")
+    (license gpl3+)))
+
+(define-public python2-django-mailman3
+  (let ((base (package-with-python2
+               python-django-mailman3)))
+    (package
+      (inherit base)
+      (propagated-inputs
+       `(("python2-openid" ,python2-openid)
+         ,@(package-propagated-inputs base))))))
+
+(define-public postorius
+  (package
+    (name "postorius")
+    (version "1.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "postorius" version "+post2.tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1wymcpv2icjjy8h1ni52p6dr7wwxf71ivqgbqhzx4i82yqphcaq5"))))
+    (build-system python-build-system)
+    (arguments
+     `(; One test dependency relies on Persona, which was shut down in
+       ;; November 2016.
+       #:tests? #f
+       ;; The part of the frontend of Mailman is still python 2.7.
+       #:python ,python-2))
+    (inputs
+     `(("python2-django" ,python2-django)
+       ("python2-django-mailman3" ,python2-django-mailman3)
+       ("python2-mailmanclient" ,python2-mailmanclient)))
+    (home-page "https://gitlab.com/mailman/postorius")
+    (synopsis "Web user interface for GNU Mailman")
+    (description
+     "Postorius is a Django app which provides a web user interface
+to access GNU Mailman.")
+    (license (list gpl3+ lgpl3+))))
+
 (define-public blists
   (package
     (name "blists")
@@ -2148,3 +2218,68 @@ Options can be specified in environment variables, configuration files, and
 the command line allowing maximum configurability and ease of use for
 operators and scripters.")
     (license gpl2+)))
+
+(define-public alpine
+  (package
+    (name "alpine")
+    (version "2.21")
+    (source
+     (origin
+       (method url-fetch)
+       ;; There are two versions: the plain continuation of Alpine without extra
+       ;; patches and the version which adds extra fixes. Every distro uses
+       ;; the patched version, and so do we to not break expectations.
+       ;; http://patches.freeiz.com/alpine/readme/README.patches
+       (uri (string-append "http://patches.freeiz.com/alpine/patches/alpine-"
+                           version "/alpine-" version ".tar.xz"))
+       (sha256
+        (base32
+         "1k9hcfjywfk3mpsl71hjza3nk6icgf1b6xxzgx10kdzg5yci5x5m"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:make-flags (list "CC=gcc")
+       #:configure-flags (list (string-append "--with-ssl-include-dir="
+                                              (assoc-ref %build-inputs "openssl")
+                                              "/include/openssl")
+                               (string-append "--with-ssl-dir="
+                                              (assoc-ref %build-inputs "openssl"))
+                               (string-append "--with-ssl-certs-dir="
+                                              "/etc/ssl/certs/")
+                               (string-append "--with-ssl-lib-dir="
+                                              (assoc-ref %build-inputs "openssl")
+                                              "/lib")
+                               (string-append "--with-interactive-spellcheck="
+                                              (assoc-ref %build-inputs "aspell")
+                                              "/bin/aspell"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'make-reproducible
+           (lambda _
+             ;; This removes time-dependent code to make alpine reproducible.
+             (substitute* "pico/blddate.c"
+               (("%02d-%s-%d") "1970-01-01"))
+             (substitute* (list "alpine/Makefile.in"
+                                "web/src/alpined.d/Makefile.in")
+               (("`date`") "1970-01-01"))
+             #t)))))
+    (inputs
+     `(("ncurses" ,ncurses)
+       ("openssl" ,openssl)
+       ("gnutls" ,gnutls)
+       ("openldap" ,openldap)
+       ("cyrus-sasl" ,cyrus-sasl)
+       ("mit-krb5" ,mit-krb5)
+       ("aspell" ,aspell)
+       ("tcl" ,tcl)
+       ("linux-pam" ,linux-pam)))
+    (home-page "http://patches.freeiz.com/alpine/")
+    (synopsis "Alternatively Licensed Program for Internet News and Email")
+    (description
+     "Alpine is a text-based mail and news client.  Alpine includes several
+tools and applications:
+@enumerate
+@item alpine, the Alpine mailer
+@item pico, the standalone text editor, GNU nano's predecessor
+@item pilot, the standalone file system navigator
+@end enumerate\n")
+    (license asl2.0)))

gnu/packages/maths.scm

@@ -1001,6 +1001,7 @@ can solve two kinds of problems:
     (inputs
      `(("lapack" ,lapack)
        ("readline" ,readline)
+       ("gl2ps" ,gl2ps)
        ("glpk" ,glpk)
        ("fftw" ,fftw)
        ("fftwf" ,fftwf)
@@ -1583,12 +1584,12 @@ programming problems.")
 (define-public r-pracma
   (package
     (name "r-pracma")
-    (version "1.9.5")
+    (version "2.0.4")
     (source (origin
       (method url-fetch)
       (uri (cran-uri "pracma" version))
       (sha256
-        (base32 "19nr2jlkbcdgvw3gx5hry12av565lmvqd5q4h7zlch3q13avwwl2"))))
+        (base32 "1z3i90mkzwvp9di17caf4934z2xlb2imm3hwxllcrbwvmnmhrwyc"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-quadprog" ,r-quadprog)))
@@ -2159,14 +2160,14 @@ full text searching.")
 (define-public armadillo
   (package
     (name "armadillo")
-    (version "7.600.2")
+    (version "7.800.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/arma/armadillo-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0bac9y46m61zxinj51l82w06v01ra9vw7a9j6rrwdjhznkkdb437"))))
+                "1qqzy7dp891j9v7062mv1599hdwr97vqzrd3j2fl8c3gmc00dmzg"))))
     (build-system cmake-build-system)
     (arguments `(#:tests? #f)) ;no test target
     (inputs
@@ -2183,18 +2184,7 @@ environments.  It can be used for machine learning, pattern recognition,
 signal processing, bioinformatics, statistics, econometrics, etc.  The library
 provides efficient classes for vectors, matrices and cubes, as well as 150+
 associated functions (eg. contiguous and non-contiguous submatrix views).")
-    (license license:mpl2.0)))
+    (license license:asl2.0)))
-
-(define-public armadillo-for-rcpparmadillo
-  (package (inherit armadillo)
-    (version "7.600.1")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://sourceforge/arma/armadillo-"
-                                  version ".tar.xz"))
-              (sha256
-               (base32
-                "1dxgfd2r9lbh24nszvqm2lag439s0srxaf1l86f6ww6waqm5r8zk"))))))
 
 (define-public muparser
   ;; When switching download sites, muparser re-issued a 2.2.5 release with a
@@ -2730,6 +2720,8 @@ in finite element programs.")
           (base32
             "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))))
     (build-system cmake-build-system)
+    (outputs '("out"
+               "octave"))                  ;46 MiB .mex file that pulls Octave
     (native-inputs
      `(("unzip" ,unzip)))
     (inputs
@@ -2747,6 +2739,14 @@ in finite element programs.")
        ;; Save 12 MiB by not installing .a files.  Passing
        ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
        #:phases (modify-phases %standard-phases
+                  (add-before 'configure 'set-octave-directory
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      ;; Install the .mex file in the "octave" output.
+                      (let ((out (assoc-ref outputs "octave")))
+                        (substitute* "src/matlab/CMakeLists.txt"
+                          (("share/flann/octave")
+                           (string-append out "/share/flann/octave")))
+                        #t)))
                   (add-after 'install 'remove-static-libraries
                     (lambda* (#:key outputs #:allow-other-keys)
                       (let* ((out (assoc-ref outputs "out"))

gnu/packages/mpd.scm

@@ -54,7 +54,7 @@
 (define-public libmpdclient
   (package
     (name "libmpdclient")
-    (version "2.10")
+    (version "2.11")
     (source (origin
               (method url-fetch)
               (uri
@@ -63,7 +63,7 @@
                               "/libmpdclient-" version ".tar.xz"))
               (sha256
                (base32
-                "10pzs9z815a8hgbbbiliapyiw82bnplsccj5irgqjw5f5plcs22g"))))
+                "1xms8q44g6zc7sc212qpcihq6ch3pmph3i1m9hzymmy0jcw6kzhm"))))
     (build-system gnu-build-system)
     (native-inputs `(("doxygen" ,doxygen)))
     (synopsis "Music Player Daemon client library")
@@ -172,7 +172,7 @@ player daemon.")
 (define-public ncmpc
   (package
     (name "ncmpc")
-    (version "0.25")
+    (version "0.27")
     (source (origin
               (method url-fetch)
               (uri
@@ -181,7 +181,7 @@ player daemon.")
                               "/ncmpc-" version ".tar.xz"))
               (sha256
                (base32
-                "196f9s0qmc4srr10n4vk3amvqy5f52y9kvgwqpkfjsnhf75qlckf"))))
+                "1n8m7syhpgx24hfipixv66h2izn229jkxsmh2q5dzkv9r0znm8pr"))))
     (build-system gnu-build-system)
     (inputs `(("glib" ,glib)
               ("libmpdclient" ,libmpdclient)

gnu/packages/music.scm

@@ -1513,7 +1513,7 @@ using a system-independent interface.")
 (define-public frescobaldi
   (package
     (name "frescobaldi")
-    (version "2.19.0")
+    (version "3.0.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1521,17 +1521,17 @@ using a system-independent interface.")
                     version "/frescobaldi-" version ".tar.gz"))
               (sha256
                (base32
-                "1rnk8i8dlshzx16n2qxcsqcs7kywgyazzyzw2vy4vp2gsm9vs9ml"))))
+                "15cqhbjbjikr7ljgiq56bz2gxrr38j8p0f78p2vhyzydaviy9a2z"))))
     (build-system python-build-system)
     (arguments `(#:tests? #f)) ; no tests included
     (inputs
      `(("lilypond" ,lilypond)
        ("portmidi" ,portmidi)
-       ("python-pyqt-4" ,python-pyqt-4)
+       ("python-pyqt" ,python-pyqt)
        ("python-ly" ,python-ly)
        ("python-pyportmidi" ,python-pyportmidi)
        ("poppler" ,poppler)
-       ("python-poppler-qt4" ,python-poppler-qt4)
+       ("python-poppler-qt5" ,python-poppler-qt5)
        ("python-sip" ,python-sip)))
     (home-page "http://www.frescobaldi.org/")
     (synopsis "LilyPond sheet music text editor")
@@ -1639,7 +1639,7 @@ capabilities, custom envelopes, effects, etc.")
 (define-public yoshimi
   (package
     (name "yoshimi")
-    (version "1.5.1")
+    (version "1.5.1.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/yoshimi/"
@@ -1647,7 +1647,7 @@ capabilities, custom envelopes, effects, etc.")
                                   "/yoshimi-" version ".tar.bz2"))
               (sha256
                (base32
-                "09kmq5bwgwwpa5z2mm1pxhnqcryd0cm5ixlafb3g6d3aspja2mkn"))))
+                "1gjanmbn08x11iz4bjlkx3m66x0yk401ddkz8fqkj7y3p5ih1kna"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ; there are no tests
@@ -1824,7 +1824,7 @@ follows a traditional multi-track tape recorder control paradigm.")
 (define-public ams-lv2
   (package
     (name "ams-lv2")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
@@ -1833,7 +1833,7 @@ follows a traditional multi-track tape recorder control paradigm.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1392spswkhfd38fggf584wb3m8aqpg7csfrs9zxnzyvhgmp0fgqk"))))
+         "1xacxyzqcj83g9c1gwfn36gg1c6yi15v7km4vidfidrjzb4x27fq"))))
     (build-system waf-build-system)
     (arguments
      `(#:phases
@@ -1902,8 +1902,8 @@ analogue-like user interface.")
 (define-public mod-host
   ;; The last release was in 2014 but since then more than 140 commits have
   ;; been made.
-  (let ((commit "72aca771e3a4e3889641b9bab84985586c9bb926")
+  (let ((commit "299a3977476e8eb0285837fbd7522cec506a11de")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "mod-host")
       (version (string-append "0.10.6-" revision "." (string-take commit 9)))
@@ -1914,7 +1914,7 @@ analogue-like user interface.")
                       (commit commit)))
                 (sha256
                  (base32
-                  "19szi8cy65jlchbrmbjbma03g6gxj9zyyp4dgw1k06r0cxbx82gq"))
+                  "128q7p5mph086v954rqnafalfbkyvhgwclaq6ks6swrhj45wnag6"))
                 (file-name (string-append name "-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments
@@ -1951,7 +1951,7 @@ socket or command line.")
 (define-public pianobar
   (package
     (name "pianobar")
-    (version "2015.11.22")
+    (version "2016.06.02")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/PromyLOPh/"
@@ -1959,7 +1959,7 @@ socket or command line.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "022df19bhxqvkhy0qy21xahba5s1fm17b13y0p9p9dnf2yl44wfv"))))
+                "1hi5rr6jcr0kwf4xfz007ndwkjkp287lhwlsgfz6iryqa5n6jzcp"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no tests
@@ -2261,6 +2261,8 @@ with a number of bugfixes and changes to improve IT playback.")
        ("libmodplug" ,libmodplug)
        ("libmpcdec" ,libmpcdec)
        ("libmad" ,libmad)
+       ("libogg" ,libogg)
+       ("libvorbis" ,libvorbis)
        ("ncurses" ,ncurses)
        ("openssl" ,openssl)
        ("sasl" ,cyrus-sasl)
@@ -2305,44 +2307,39 @@ standard MIDI file with the csvmidi program.")
     (license license:public-domain)))
 
 (define-public gx-guvnor-lv2
-  (let ((commit "9f528a7623a201383e119bb6a2df32b18396a9d5")
+  (package
-        (revision "1"))
+    (name "gx-guvnor-lv2")
-    (package
+    (version "0.1")
-      (name "gx-guvnor-lv2")
+    (source (origin
-      (version (string-append "0-" revision "." (string-take commit 9)))
+              (method url-fetch)
-      (source (origin
+              (uri (string-append "https://github.com/brummer10/GxGuvnor.lv2/"
-                (method git-fetch)
+                                  "archive/v" version ".tar.gz"))
-                (uri (git-reference
+              (file-name (string-append name "-" version ".tar.gz"))
-                      (url "https://github.com/brummer10/GxGuvnor.lv2")
+              (sha256
-                      (commit commit)))
+               (base32
-                (sha256
+                "0rnfvrvs8qmmldyfmx4llyly33zp68448gx40ywdwj42x0mam92p"))))
-                 (base32
+    (build-system gnu-build-system)
-                  "10zx84p2vd7i1yqc5ma9p17927265j4g0zfwv9rxladw0nm8y45k"))
+    (arguments
-                (file-name (string-append name "-" version "-checkout"))))
+     `(;; The check target is used only to output a warning.
-      (build-system gnu-build-system)
+       #:tests? #f
-      (arguments
+       #:make-flags
-       `(;; The check target is used only to output a warning.
+       (list (string-append "DESTDIR=" (assoc-ref %outputs "out")))
-         #:tests? #f
+       #:phases
-         #:make-flags
+       (modify-phases %standard-phases
-         (list (string-append "DESTDIR=" (assoc-ref %outputs "out")))
+         (replace 'configure
-         #:phases
+           (lambda _
-         (modify-phases %standard-phases
+             (substitute* "Makefile"
-           (replace 'configure
+               (("INSTALL_DIR = .*") "INSTALL_DIR=/lib/lv2\n"))
-             (lambda _
+             #t)))))
-               (substitute* "Makefile"
+    (inputs
-                 (("INSTALL_DIR = .*") "INSTALL_DIR=/lib/lv2\n")
+     `(("lv2" ,lv2)))
-                 ;; Avoid rebuilding everything
+    (home-page "https://github.com/brummer10/GxGuvnor.lv2")
-                 (("install : all") "install:"))
+    (synopsis "Overdrive/distortion pedal simulation")
-               #t)))))
+    (description "This package provides the LV2 plugin \"GxGuvnor\", a
-      (inputs
-       `(("lv2" ,lv2)))
-      (home-page "https://github.com/brummer10/GxGuvnor.lv2")
-      (synopsis "Overdrive/distortion pedal simulation")
-      (description "This package provides the LV2 plugin \"GxGuvnor\", a
 simulation of an overdrive or distortion pedal for guitars.")
-      ;; The LICENSE file says GPLv3 but the license headers in the files say
+    ;; The LICENSE file says GPLv3 but the license headers in the files say
-      ;; GPLv2 or later.
+    ;; GPLv2 or later.
-      (license license:gpl2+))))
+    (license license:gpl2+)))
 
 (define-public gx-vbass-preamp-lv2
   (let ((commit "0e599abab10c7669dd444e5d06f671c2fc1b9c6c")
@@ -2359,6 +2356,16 @@ simulation of an overdrive or distortion pedal for guitars.")
                  (base32
                   "1dzksdfrva666gpi62fd2ni9rhf18sl917f1894qr0b17pbdh9k1"))
                 (file-name (string-append name "-" version "-checkout"))))
+      (arguments
+       (substitute-keyword-arguments (package-arguments gx-guvnor-lv2)
+         ((#:phases phases)
+          `(modify-phases ,phases
+             (replace 'configure
+               (lambda _
+                 (substitute* "Makefile"
+                   (("INSTALL_DIR = .*") "INSTALL_DIR=/lib/lv2\n")
+                   (("install : all") "install :"))
+                 #t))))))
       (home-page "https://github.com/brummer10/GxVBassPreAmp.lv2")
       (synopsis "Simulation of the Vox Venue Bass 100 Pre Amp Section")
       (description "This package provides the LV2 plugin \"GxVBassPreAmp\", a
@@ -2368,7 +2375,7 @@ Section."))))
 (define-public gx-overdriver-lv2
   (let ((commit "ed71801987449414bf3adaa0dbfac68e8775f1ce")
         (revision "1"))
-    (package (inherit gx-guvnor-lv2)
+    (package (inherit gx-vbass-preamp-lv2)
       (name "gx-overdriver-lv2")
       (version (string-append "0-" revision "." (string-take commit 9)))
       (source (origin
@@ -2388,7 +2395,7 @@ overdrive effect."))))
 (define-public gx-tone-mender-lv2
   (let ((commit "b6780b4a3e4782b3ed0e5882d6788f178aed138f")
         (revision "1"))
-    (package (inherit gx-guvnor-lv2)
+    (package (inherit gx-vbass-preamp-lv2)
       (name "gx-tone-mender-lv2")
       (version (string-append "0-" revision "." (string-take commit 9)))
       (source (origin
@@ -2408,7 +2415,7 @@ clean boost effect with a 3-knob tonestack."))))
 (define-public gx-push-pull-lv2
   (let ((commit "7f76ae2068498643ac8671ee0930b13ee3fd8eb5")
         (revision "1"))
-    (package (inherit gx-guvnor-lv2)
+    (package (inherit gx-vbass-preamp-lv2)
       (name "gx-push-pull-lv2")
       (version (string-append "0-" revision "." (string-take commit 9)))
       (source (origin
@@ -2426,30 +2433,28 @@ clean boost effect with a 3-knob tonestack."))))
 simulation of a push pull transistor fuzz effect with added high octave."))))
 
 (define-public gx-suppa-tone-bender-lv2
-  (let ((commit "4e6dc713ec24e7fcf5ea23b7e685af627c01b9c9")
+  (package (inherit gx-guvnor-lv2)
-        (revision "1"))
+    (name "gx-suppa-tone-bender-lv2")
-    (package (inherit gx-guvnor-lv2)
+    (version "0.1")
-      (name "gx-suppa-tone-bender-lv2")
+    (source (origin
-      (version (string-append "0-" revision "." (string-take commit 9)))
+              (method url-fetch)
-      (source (origin
+              (uri (string-append "https://github.com/brummer10/"
-                (method git-fetch)
+                                  "GxSuppaToneBender.lv2/archive/v"
-                (uri (git-reference
+                                  version ".tar.gz"))
-                      (url "https://github.com/brummer10/GxSuppaToneBender.lv2")
+              (sha256
-                      (commit commit)))
+               (base32
-                (sha256
+                "1j90fns87035sfr6bxs4cvqxbyy3pqjhihx1nis8xajn202nl1hx"))
-                 (base32
+              (file-name (string-append name "-" version ".tar.gz"))))
-                  "1i22xr252nkbazkwidll2zb3i96610gx65qn5djdkijlz7j77138"))
+    (home-page "https://github.com/brummer10/GxSuppaToneBender.lv2")
-                (file-name (string-append name "-" version "-checkout"))))
+    (synopsis "Simulation of the Vox Suppa Tone Bender pedal")
-      (home-page "https://github.com/brummer10/GxSuppaToneBender.lv2")
+    (description "This package provides the LV2 plugin
-      (synopsis "Simulation of the Vox Suppa Tone Bender pedal")
-      (description "This package provides the LV2 plugin
 \"GxSuppaToneBender\", a simulation modelled after the Vox Suppa Tone Bender
-pedal."))))
+pedal.")))
 
 (define-public gx-saturator-lv2
   (let ((commit "0b581ac85c515325b9f16e51937cae6e1bf81a0a")
         (revision "2"))
-    (package (inherit gx-guvnor-lv2)
+    (package (inherit gx-vbass-preamp-lv2)
       (name "gx-saturator-lv2")
       (version (string-append "0-" revision "." (string-take commit 9)))
       (source (origin
@@ -2467,93 +2472,85 @@ pedal."))))
 saturation effect."))))
 
 (define-public gx-hyperion-lv2
-  (let ((commit "6a096a664e553e551e179e85cf390bd1683410fb")
+  (package (inherit gx-guvnor-lv2)
-        (revision "2"))
+    (name "gx-hyperion-lv2")
-    (package (inherit gx-guvnor-lv2)
+    (version "0.1")
-      (name "gx-hyperion-lv2")
+    (source (origin
-      (version (string-append "0-" revision "." (string-take commit 9)))
+              (method url-fetch)
-      (source (origin
+              (uri (string-append "https://github.com/brummer10/"
-                (method git-fetch)
+                                  "GxHyperion.lv2/archive/v"
-                (uri (git-reference
+                                  version ".tar.gz"))
-                      (url "https://github.com/brummer10/GxHyperion.lv2")
+              (sha256
-                      (commit commit)))
+               (base32
-                (sha256
+                "1pd7l33a14kq73wavgqq7csw4n3mwjz9d5rxaj0jgsyxd3llp3wh"))
-                 (base32
+              (file-name (string-append name "-" version ".tar.gz"))))
-                  "1ksv3wmylhwbf6kjl2lnhr14h9rfl291cfm21471gnb1r68yqfxh"))
+    (home-page "https://github.com/brummer10/GxHyperion.lv2")
-                (file-name (string-append name "-" version "-checkout"))))
+    (synopsis "Simulation of the Hyperion Fuzz pedal")
-      (home-page "https://github.com/brummer10/GxHyperion.lv2")
+    (description "This package provides the LV2 plugin \"GxHyperion\", a
-      (synopsis "Simulation of the Hyperion Fuzz pedal")
+simulation of the Hyperion Fuzz pedal.")))
-      (description "This package provides the LV2 plugin \"GxHyperion\", a
-simulation of the Hyperion Fuzz pedal."))))
 
 (define-public gx-voodoo-fuzz-lv2
-  (let ((commit "aec7889b489385e8add06126e7a36ae2e26254b1")
+  (package (inherit gx-guvnor-lv2)
-        (revision "2"))
+    (name "gx-voodoo-fuzz-lv2")
-    (package (inherit gx-guvnor-lv2)
+    (version "0.1")
-      (name "gx-voodoo-fuzz-lv2")
+    (source (origin
-      (version (string-append "0-" revision "." (string-take commit 9)))
+              (method url-fetch)
-      (source (origin
+              (uri (string-append "https://github.com/brummer10/"
-                (method git-fetch)
+                                  "GxVoodoFuzz.lv2/archive/v"
-                (uri (git-reference
+                                  version ".tar.gz"))
-                      (url "https://github.com/brummer10/GxVoodoFuzz.lv2")
+              (sha256
-                      (commit commit)))
+               (base32
-                (sha256
+                "0cc8sg7q493bs6pcq4ipqp6czpxv04nh9yvn8kq2x65ni2208n2f"))
-                 (base32
+              (file-name (string-append name "-" version ".tar.gz"))))
-                  "0mc41ldlv89069iaysnfiqxy5h5sr8mdi5cxm3ij5q5v4jv3viwx"))
+    (home-page "https://github.com/brummer10/GxVoodoFuzz.lv2")
-                (file-name (string-append name "-" version "-checkout"))))
+    (synopsis "Fuzz effect modelled after the Voodoo Lab SuperFuzz")
-      (home-page "https://github.com/brummer10/GxVoodoFuzz.lv2")
+    (description "This package provides the LV2 plugin \"GxVoodooFuzz\", a
-      (synopsis "Fuzz effect modelled after the Voodoo Lab SuperFuzz")
-      (description "This package provides the LV2 plugin \"GxVoodooFuzz\", a
 simulation modelled after the Voodoo Lab SuperFuzz pedal.  It's basically a
 Bosstone circuit, followed by the tone control of the FoxToneMachine in
-parallel with a DarkBooster, followed by a volume control."))))
+parallel with a DarkBooster, followed by a volume control.")))
 
 (define-public gx-super-fuzz-lv2
-  (let ((commit "f40389575812c909007d140d327ce579930b71f7")
+  (package (inherit gx-guvnor-lv2)
-        (revision "2"))
+    (name "gx-super-fuzz-lv2")
-    (package (inherit gx-guvnor-lv2)
+    (version "0.1")
-      (name "gx-super-fuzz-lv2")
+    (source (origin
-      (version (string-append "0-" revision "." (string-take commit 9)))
+              (method url-fetch)
-      (source (origin
+              (uri (string-append "https://github.com/brummer10/"
-                (method git-fetch)
+                                  "GxSuperFuzz.lv2/archive/v"
-                (uri (git-reference
+                                  version ".tar.gz"))
-                      (url "https://github.com/brummer10/GxSuperFuzz.lv2")
+              (sha256
-                      (commit commit)))
+               (base32
-                (sha256
+                "0pnivq05f1kji8c5jxsqdzhdfk3xn422v2d1x20x3jfsxnaf115x"))
-                 (base32
+              (file-name (string-append name "-" version ".tar.gz"))))
-                  "174bibj8qzm8zr6f5h8bcj94iry17zravk8flpdy84n6yg7cixji"))
+    (home-page "https://github.com/brummer10/GxSuperFuzz.lv2")
-                (file-name (string-append name "-" version "-checkout"))))
+    (synopsis "Fuzz effect modelled after the UniVox SuperFuzz")
-      (home-page "https://github.com/brummer10/GxSuperFuzz.lv2")
+    (description "This package provides the LV2 plugin \"GxSuperFuzz\", an
-      (synopsis "Fuzz effect modelled after the UniVox SuperFuzz")
-      (description "This package provides the LV2 plugin \"GxVoodooFuzz\", an
 analog simulation of the UniVox SuperFuzz pedal.  In this simulation the trim
 pot, which is usualy in the housing, is exposed as a control parameter.  It
-adjusts the amount of harmonics."))))
+adjusts the amount of harmonics.")))
 
 (define-public gx-vintage-fuzz-master-lv2
-  (let ((commit "0fec0bc1e8a8ba909a68e916e036138a3425d7db")
+  (package (inherit gx-guvnor-lv2)
-        (revision "2"))
+    (name "gx-vintage-fuzz-master-lv2")
-    (package (inherit gx-guvnor-lv2)
+    (version "0.1")
-      (name "gx-vintage-fuzz-master-lv2")
+    (source (origin
-      (version (string-append "0-" revision "." (string-take commit 9)))
+              (method url-fetch)
-      (source (origin
+              (uri (string-append "https://github.com/brummer10/"
-                (method git-fetch)
+                                  "GxVintageFuzzMaster.lv2/archive/v"
-                (uri (git-reference
+                                  version ".tar.gz"))
-                      (url "https://github.com/brummer10/GxVintageFuzzMaster.lv2")
+              (sha256
-                      (commit commit)))
+               (base32
-                (sha256
+                "0bdkfj6xi2g4izfw3pmr4i0nqzg8jnkdwc23x9ifxwc6p1kbayzk"))
-                 (base32
+              (file-name (string-append name "-" version ".tar.gz"))))
-                  "06szi6d2iwkygbw5azhwzhcl2as4lmk2gs9hanngsf46a1zbdcp7"))
+    (home-page "https://github.com/brummer10/GxVintageFuzzMaster.lv2")
-                (file-name (string-append name "-" version "-checkout"))))
+    (synopsis "Fuzz effect simulation of the vintage Fuzz Master")
-      (home-page "https://github.com/brummer10/GxVintageFuzzMaster.lv2")
+    (description "This package provides the LV2 plugin
-      (synopsis "Fuzz effect simulation of the vintage Fuzz Master")
+\"GxVintageFuzzMaster\", a simulation of the vintage Fuzz Master pedal.")))
-      (description "This package provides the LV2 plugin
-\"GxVintageFuzzMaster\", a simulation of the vintage Fuzz Master pedal."))))
 
 (define-public gx-slow-gear-lv2
   (let ((commit "cb852e0426f4e6fe077e7f1ede73a4da335cfc5e")
         (revision "2"))
-    (package (inherit gx-guvnor-lv2)
+    (package (inherit gx-vbass-preamp-lv2)
       (name "gx-slow-gear-lv2")
       (version (string-append "0-" revision "." (string-take commit 9)))
       (source (origin
@@ -2573,7 +2570,7 @@ slow gear audio effect to produce volume swells."))))
 (define-public gx-switchless-wah-lv2
   (let ((commit "7b08691203314612999f0ce2328cdc1161cd6665")
         (revision "2"))
-    (package (inherit gx-guvnor-lv2)
+    (package (inherit gx-vbass-preamp-lv2)
       (name "gx-switchless-wah-lv2")
       (version (string-append "0-" revision "." (string-take commit 9)))
       (source (origin

gnu/packages/nano.scm

@@ -29,7 +29,7 @@
 (define-public nano
   (package
     (name "nano")
-    (version "2.8.0")
+    (version "2.8.1")
     (source
      (origin
       (method url-fetch)
@@ -37,7 +37,7 @@
                           version ".tar.gz"))
       (sha256
        (base32
-        "0dlid11c8jkv0b9n73lc3mj274y5c7y08n7pzv947qz50m446yqb"))))
+        "042rbhhkiw6nvwklm8zmmdlhjr8gdhdp486hafwrn1pwnpd511m4"))))
     (build-system gnu-build-system)
     (inputs
      `(("gettext" ,gettext-minimal)

gnu/packages/package-management.scm

@@ -61,9 +61,8 @@
                         arch "-linux"
                         "/20150101/guile-2.0.11.tar.xz"))
         ((string=? "aarch64" arch)
-         (let ((suffix "/bootstrap/aarch64-linux/20170217/guile-2.0.14.tar.xz"))
+         (string-append "http://alpha.gnu.org/gnu/guix/bootstrap/"
-           (list (string-append "http://alpha.gnu.org/gnu/guix" suffix)
+                        arch "-linux/20170217/guile-2.0.14.tar.xz"))
-                 (string-append "http://flashner.co.il/guix" suffix))))
         (else
          (string-append "http://alpha.gnu.org/gnu/guix/bootstrap/"
                         arch "-linux"

gnu/packages/password-utils.scm

@@ -284,7 +284,7 @@ any X11 window.")
 (define-public password-store
   (package
     (name "password-store")
-    (version "1.7")
+    (version "1.7.1")
     (source (origin
               (method url-fetch)
               (uri
@@ -292,8 +292,7 @@ any X11 window.")
                               name "-" version ".tar.xz"))
               (sha256
                (base32
-                "002mw7j0m33bw483rllzhcf41wp3ixka8yma6kqrfaj57jyw66hn"))
+                "0scqkpll2q8jhzcgcsh9kqz0gwdpvynivqjmmbzax2irjfaiklpn"))))
-              (patches (search-patches "password-store-gnupg-compat.patch"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases

gnu/packages/patches/audacity-fix-ffmpeg-binding.patch

@@ -1,32 +0,0 @@
-This resolves some "declaration of C function conflicts with previous
-declaration" errors during compilation.
-
---- a/src/FFmpeg.h	2015-02-21 00:33:33.853857529 +0100
-+++ b/src/FFmpeg.h	2015-02-21 00:35:09.626497205 +0100
-@@ -688,7 +688,7 @@
-    FFMPEG_FUNCTION_WITH_RETURN(
-       AVOutputFormat*,
-       av_oformat_next,
--      (AVOutputFormat *f),
-+      (const AVOutputFormat *f),
-       (f)
-    );
-    FFMPEG_FUNCTION_WITH_RETURN(
-@@ -755,7 +755,7 @@
-    FFMPEG_FUNCTION_WITH_RETURN(
-       int,
-       av_fifo_size,
--      (AVFifoBuffer *f),
-+      (const AVFifoBuffer *f),
-       (f)
-    );
-    FFMPEG_FUNCTION_WITH_RETURN(
-@@ -801,7 +801,7 @@
-    FFMPEG_FUNCTION_WITH_RETURN(
-       AVDictionaryEntry *,
-       av_dict_get,
--      (AVDictionary *m, const char *key, const AVDictionaryEntry *prev, int flags),
-+      (const AVDictionary *m, const char *key, const AVDictionaryEntry *prev, int flags),
-       (m, key, prev, flags)
-    );
-    FFMPEG_FUNCTION_WITH_RETURN(

gnu/packages/patches/glog-gcc-5-demangling.patch

@@ -0,0 +1,64 @@
+Fix symbol demangling for GCC 5, as reported at:
+
+  https://github.com/google/glog/issues/14
+
+Patch from:
+
+  https://github.com/google/glog/pull/50
+
+From b1639e3014996fbc7635870e013559c54e7e3b2f Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?David=20Mart=C3=ADnez=20Moreno?= <ender@debian.org>
+Date: Thu, 13 Aug 2015 09:31:26 -0700
+Subject: [PATCH] Fix ABI demangling for the GCC 5.x case.
+
+When glog is compiled with gcc-5.2 in cxx11 ABI mode, it barfs about unmangled symbols.  This patches it getting inspiration from binutils and demangle.cc itself, although it may be totally wrong or maybe have to use ParseAbiTag in more places.  I haven't read the spec for the symbols, though.
+
+This patch makes the demangle unit test pass correctly.
+---
+ src/demangle.cc | 19 +++++++++++++++++++
+ 1 file changed, 19 insertions(+)
+
+diff --git a/src/demangle.cc b/src/demangle.cc
+index e858181..0f0c831 100644
+--- a/src/demangle.cc
++++ b/src/demangle.cc
+@@ -439,6 +439,7 @@ static bool ParseExprPrimary(State *state);
+ static bool ParseLocalName(State *state);
+ static bool ParseDiscriminator(State *state);
+ static bool ParseSubstitution(State *state);
++static bool ParseAbiTag(State *state);
+ 
+ // Implementation note: the following code is a straightforward
+ // translation of the Itanium C++ ABI defined in BNF with a couple of
+@@ -567,6 +568,8 @@ static bool ParseNestedName(State *state) {
+ static bool ParsePrefix(State *state) {
+   bool has_something = false;
+   while (true) {
++    if (ParseAbiTag(state))
++      continue;
+     MaybeAppendSeparator(state);
+     if (ParseTemplateParam(state) ||
+         ParseSubstitution(state) ||
+@@ -585,6 +588,22 @@ static bool ParsePrefix(State *state) {
+   return true;
+ }
+ 
++// <abi-tag>          ::= B <source-name>
++static bool ParseAbiTag(State *state) {
++  State copy = *state;
++
++  Append(state, "[", 1);
++  if (ParseOneCharToken(state, 'B') &&
++      ParseSourceName(state))
++  {
++    Append(state, "]", 1);
++    return true;
++  }
++
++  *state = copy;
++  return false;
++}
++
+ // <unqualified-name> ::= <operator-name>
+ //                    ::= <ctor-dtor-name>
+ //                    ::= <source-name>

gnu/packages/patches/gnupg-2.1-fix-Y2038-test-failure.patch

@@ -1,67 +0,0 @@
-Fix a Y2038 test failure on systems where time_t is a signed 32-bit value:
-
-https://bugs.gnupg.org/gnupg/issue2988
-
-Patch copied from upstream source repository:
-
-https://git.gnupg.org/cgi-bin/gitweb.cgi?p=gnupg.git;a=commit;h=de3838372ae3cdecbd83eea2c53c8e2656d93052
-
-From de3838372ae3cdecbd83eea2c53c8e2656d93052 Mon Sep 17 00:00:00 2001
-From: Justus Winter <justus@g10code.com>
-Date: Tue, 7 Mar 2017 12:18:59 +0100
-Subject: [PATCH] tests: Avoid overflowing signed 32 bit time_t.
-
-* tests/openpgp/quick-key-manipulation.scm: Use expiration times in
-the year 2038 instead of 2105 to avoid overflowing 32 bit time_t.
-time_t is used internally to parse the expiraton time from the iso
-timestamp.
-
-GnuPG-bug-id: 2988
-Signed-off-by: Justus Winter <justus@g10code.com>
----
- tests/openpgp/quick-key-manipulation.scm | 15 +++++++++++----
- 1 file changed, 11 insertions(+), 4 deletions(-)
-
-diff --git a/tests/openpgp/quick-key-manipulation.scm b/tests/openpgp/quick-key-manipulation.scm
-index 10f0bfe21..08ef62613 100755
---- a/tests/openpgp/quick-key-manipulation.scm
-+++ b/tests/openpgp/quick-key-manipulation.scm
-@@ -125,8 +125,13 @@
-    (default default never)
-    (rsa "sign auth encr" "seconds=600") ;; GPGME uses this
-    (rsa "auth,encr" "2") ;; "without a letter, days is assumed"
--   (rsa "sign" "2105-01-01") ;; "last year GnuPG can represent is 2105"
--   (rsa "sign" "21050101T115500") ;; "last year GnuPG can represent is 2105"
-+   ;; Sadly, the timestamp is truncated by the use of time_t on
-+   ;; systems where time_t is a signed 32 bit value.
-+   (rsa "sign" "2038-01-01")      ;; unix millennium
-+   (rsa "sign" "20380101T115500") ;; unix millennium
-+   ;; Once fixed, we can use later timestamps:
-+   ;; (rsa "sign" "2105-01-01")      ;; "last year GnuPG can represent is 2105"
-+   ;; (rsa "sign" "21050101T115500") ;; "last year GnuPG can represent is 2105"
-    (rsa sign "2d")
-    (rsa1024 sign "2w")
-    (rsa2048 encr "2m")
-@@ -157,7 +162,8 @@
-   (lambda (subkey)
-     (assert (= 1 (:alg subkey)))
-     (assert (string-contains? (:cap subkey) "s"))
--    (assert (time-matches? 4260207600 ;; 2105-01-01
-+    (assert (time-matches? 2145916800    ;; 2038-01-01
-+			   ;; 4260207600 ;; 2105-01-01
- 			   (string->number (:expire subkey))
- 			   ;; This is off by 12h, but I guess it just
- 			   ;; choses the middle of the day.
-@@ -165,7 +171,8 @@
-   (lambda (subkey)
-     (assert (= 1 (:alg subkey)))
-     (assert (string-contains? (:cap subkey) "s"))
--    (assert (time-matches? 4260254100 ;; UTC 2105-01-01 11:55:00
-+    (assert (time-matches? 2145959700    ;; UTC 2038-01-01 11:55:00
-+			   ;; 4260254100 ;; UTC 2105-01-01 11:55:00
- 			   (string->number (:expire subkey))
- 			   (minutes->seconds 5))))
-   (lambda (subkey)
--- 
-2.12.0
-

gnu/packages/patches/jasper-CVE-2017-6850.patch

@@ -0,0 +1,284 @@
+This patch is from upstream and should be fixed included in the next release
+
+From e96fc4fdd525fa0ede28074a7e2b1caf94b58b0d Mon Sep 17 00:00:00 2001
+From: Michael Adams <mdadams@ece.uvic.ca>
+Date: Sat, 4 Mar 2017 14:43:24 -0800
+Subject: [PATCH] Fixed bugs due to uninitialized data in the JP2 decoder.
+ Also, added some comments marking I/O stream interfaces that probably need to
+ be changed (in the long term) to fix integer overflow problems.
+
+---
+ src/libjasper/base/jas_stream.c | 18 +++++++++++++++++
+ src/libjasper/jp2/jp2_cod.c     | 44 ++++++++++++++++++++++++++++-------------
+ 2 files changed, 48 insertions(+), 14 deletions(-)
+
+diff --git a/src/libjasper/base/jas_stream.c b/src/libjasper/base/jas_stream.c
+index 327ee57..d70408f 100644
+--- a/src/libjasper/base/jas_stream.c
++++ b/src/libjasper/base/jas_stream.c
+@@ -664,6 +664,7 @@ int jas_stream_ungetc(jas_stream_t *stream, int c)
+ 	return 0;
+ }
+ 
++/* FIXME integral type */
+ int jas_stream_read(jas_stream_t *stream, void *buf, int cnt)
+ {
+ 	int n;
+@@ -690,6 +691,7 @@ int jas_stream_read(jas_stream_t *stream, void *buf, int cnt)
+ 	return n;
+ }
+ 
++/* FIXME integral type */
+ int jas_stream_write(jas_stream_t *stream, const void *buf, int cnt)
+ {
+ 	int n;
+@@ -742,6 +744,7 @@ int jas_stream_puts(jas_stream_t *stream, const char *s)
+ 	return 0;
+ }
+ 
++/* FIXME integral type */
+ char *jas_stream_gets(jas_stream_t *stream, char *buf, int bufsize)
+ {
+ 	int c;
+@@ -765,6 +768,7 @@ char *jas_stream_gets(jas_stream_t *stream, char *buf, int bufsize)
+ 	return buf;
+ }
+ 
++/* FIXME integral type */
+ int jas_stream_gobble(jas_stream_t *stream, int n)
+ {
+ 	int m;
+@@ -783,6 +787,7 @@ int jas_stream_gobble(jas_stream_t *stream, int n)
+ 	return n;
+ }
+ 
++/* FIXME integral type */
+ int jas_stream_pad(jas_stream_t *stream, int n, int c)
+ {
+ 	int m;
+@@ -885,6 +890,7 @@ long jas_stream_tell(jas_stream_t *stream)
+ * Buffer initialization code.
+ \******************************************************************************/
+ 
++/* FIXME integral type */
+ static void jas_stream_initbuf(jas_stream_t *stream, int bufmode, char *buf,
+   int bufsize)
+ {
+@@ -1060,6 +1066,7 @@ static int jas_strtoopenmode(const char *s)
+ 	return openmode;
+ }
+ 
++/* FIXME integral type */
+ int jas_stream_copy(jas_stream_t *out, jas_stream_t *in, int n)
+ {
+ 	int all;
+@@ -1085,6 +1092,7 @@ int jas_stream_copy(jas_stream_t *out, jas_stream_t *in, int n)
+ 	return 0;
+ }
+ 
++/* FIXME integral type */
+ long jas_stream_setrwcount(jas_stream_t *stream, long rwcnt)
+ {
+ 	int old;
+@@ -1094,6 +1102,7 @@ long jas_stream_setrwcount(jas_stream_t *stream, long rwcnt)
+ 	return old;
+ }
+ 
++/* FIXME integral type */
+ int jas_stream_display(jas_stream_t *stream, FILE *fp, int n)
+ {
+ 	unsigned char buf[16];
+@@ -1168,6 +1177,7 @@ long jas_stream_length(jas_stream_t *stream)
+ * Memory stream object.
+ \******************************************************************************/
+ 
++/* FIXME integral type */
+ static int mem_read(jas_stream_obj_t *obj, char *buf, int cnt)
+ {
+ 	ssize_t n;
+@@ -1209,6 +1219,7 @@ static int mem_resize(jas_stream_memobj_t *m, size_t bufsize)
+ 	return 0;
+ }
+ 
++/* FIXME integral type */
+ static int mem_write(jas_stream_obj_t *obj, char *buf, int cnt)
+ {
+ 	size_t n;
+@@ -1264,6 +1275,7 @@ static int mem_write(jas_stream_obj_t *obj, char *buf, int cnt)
+ 	return ret;
+ }
+ 
++/* FIXME integral type */
+ static long mem_seek(jas_stream_obj_t *obj, long offset, int origin)
+ {
+ 	jas_stream_memobj_t *m = (jas_stream_memobj_t *)obj;
+@@ -1310,6 +1322,7 @@ static int mem_close(jas_stream_obj_t *obj)
+ * File stream object.
+ \******************************************************************************/
+ 
++/* FIXME integral type */
+ static int file_read(jas_stream_obj_t *obj, char *buf, int cnt)
+ {
+ 	jas_stream_fileobj_t *fileobj;
+@@ -1318,6 +1331,7 @@ static int file_read(jas_stream_obj_t *obj, char *buf, int cnt)
+ 	return read(fileobj->fd, buf, cnt);
+ }
+ 
++/* FIXME integral type */
+ static int file_write(jas_stream_obj_t *obj, char *buf, int cnt)
+ {
+ 	jas_stream_fileobj_t *fileobj;
+@@ -1326,6 +1340,7 @@ static int file_write(jas_stream_obj_t *obj, char *buf, int cnt)
+ 	return write(fileobj->fd, buf, cnt);
+ }
+ 
++/* FIXME integral type */
+ static long file_seek(jas_stream_obj_t *obj, long offset, int origin)
+ {
+ 	jas_stream_fileobj_t *fileobj;
+@@ -1352,6 +1367,7 @@ static int file_close(jas_stream_obj_t *obj)
+ * Stdio file stream object.
+ \******************************************************************************/
+ 
++/* FIXME integral type */
+ static int sfile_read(jas_stream_obj_t *obj, char *buf, int cnt)
+ {
+ 	FILE *fp;
+@@ -1367,6 +1383,7 @@ static int sfile_read(jas_stream_obj_t *obj, char *buf, int cnt)
+ 	return result;
+ }
+ 
++/* FIXME integral type */
+ static int sfile_write(jas_stream_obj_t *obj, char *buf, int cnt)
+ {
+ 	FILE *fp;
+@@ -1377,6 +1394,7 @@ static int sfile_write(jas_stream_obj_t *obj, char *buf, int cnt)
+ 	return (n != JAS_CAST(size_t, cnt)) ? (-1) : cnt;
+ }
+ 
++/* FIXME integral type */
+ static long sfile_seek(jas_stream_obj_t *obj, long offset, int origin)
+ {
+ 	FILE *fp;
+diff --git a/src/libjasper/jp2/jp2_cod.c b/src/libjasper/jp2/jp2_cod.c
+index 7f3608a..8d98a2c 100644
+--- a/src/libjasper/jp2/jp2_cod.c
++++ b/src/libjasper/jp2/jp2_cod.c
+@@ -183,15 +183,28 @@ jp2_boxinfo_t jp2_boxinfo_unk = {
+ * Box constructor.
+ \******************************************************************************/
+ 
+-jp2_box_t *jp2_box_create(int type)
++jp2_box_t *jp2_box_create0()
+ {
+ 	jp2_box_t *box;
+-	jp2_boxinfo_t *boxinfo;
+-
+ 	if (!(box = jas_malloc(sizeof(jp2_box_t)))) {
+ 		return 0;
+ 	}
+ 	memset(box, 0, sizeof(jp2_box_t));
++	box->type = 0;
++	box->len = 0;
++	// Mark the box data as never having been constructed
++	// so that we will not errantly attempt to destroy it later.
++	box->ops = &jp2_boxinfo_unk.ops;
++	return box;
++}
++
++jp2_box_t *jp2_box_create(int type)
++{
++	jp2_box_t *box;
++	jp2_boxinfo_t *boxinfo;
++	if (!(box = jp2_box_create0())) {
++		return 0;
++	}
+ 	box->type = type;
+ 	box->len = 0;
+ 	if (!(boxinfo = jp2_boxinfolookup(type))) {
+@@ -248,14 +261,9 @@ jp2_box_t *jp2_box_get(jas_stream_t *in)
+ 	box = 0;
+ 	tmpstream = 0;
+ 
+-	if (!(box = jas_malloc(sizeof(jp2_box_t)))) {
++	if (!(box = jp2_box_create0())) {
+ 		goto error;
+ 	}
+-
+-	// Mark the box data as never having been constructed
+-	// so that we will not errantly attempt to destroy it later.
+-	box->ops = &jp2_boxinfo_unk.ops;
+-
+ 	if (jp2_getuint32(in, &len) || jp2_getuint32(in, &box->type)) {
+ 		goto error;
+ 	}
+@@ -263,10 +271,12 @@ jp2_box_t *jp2_box_get(jas_stream_t *in)
+ 	box->info = boxinfo;
+ 	box->len = len;
+ 	JAS_DBGLOG(10, (
+-	  "preliminary processing of JP2 box: type=%c%s%c (0x%08x); length=%d\n",
++	  "preliminary processing of JP2 box: "
++	  "type=%c%s%c (0x%08x); length=%"PRIuFAST32"\n",
+ 	  '"', boxinfo->name, '"', box->type, box->len
+ 	  ));
+ 	if (box->len == 1) {
++		JAS_DBGLOG(10, ("big length\n"));
+ 		if (jp2_getuint64(in, &extlen)) {
+ 			goto error;
+ 		}
+@@ -382,6 +392,7 @@ static int jp2_bpcc_getdata(jp2_box_t *box, jas_stream_t *in)
+ {
+ 	jp2_bpcc_t *bpcc = &box->data.bpcc;
+ 	unsigned int i;
++	bpcc->bpcs = 0;
+ 	bpcc->numcmpts = box->datalen;
+ 	if (!(bpcc->bpcs = jas_alloc2(bpcc->numcmpts, sizeof(uint_fast8_t)))) {
+ 		return -1;
+@@ -462,6 +473,7 @@ static int jp2_cdef_getdata(jp2_box_t *box, jas_stream_t *in)
+ 	jp2_cdef_t *cdef = &box->data.cdef;
+ 	jp2_cdefchan_t *chan;
+ 	unsigned int channo;
++	cdef->ents = 0;
+ 	if (jp2_getuint16(in, &cdef->numchans)) {
+ 		return -1;
+ 	}
+@@ -518,7 +530,9 @@ int jp2_box_put(jp2_box_t *box, jas_stream_t *out)
+ 	}
+ 
+ 	if (dataflag) {
+-		if (jas_stream_copy(out, tmpstream, box->len - JP2_BOX_HDRLEN(false))) {
++		if (jas_stream_copy(out, tmpstream, box->len -
++		  JP2_BOX_HDRLEN(false))) {
++			jas_eprintf("cannot copy box data\n");
+ 			goto error;
+ 		}
+ 		jas_stream_close(tmpstream);
+@@ -777,6 +791,7 @@ static int jp2_cmap_getdata(jp2_box_t *box, jas_stream_t *in)
+ 	jp2_cmap_t *cmap = &box->data.cmap;
+ 	jp2_cmapent_t *ent;
+ 	unsigned int i;
++	cmap->ents = 0;
+ 
+ 	cmap->numchans = (box->datalen) / 4;
+ 	if (!(cmap->ents = jas_alloc2(cmap->numchans, sizeof(jp2_cmapent_t)))) {
+@@ -835,6 +850,7 @@ static int jp2_pclr_getdata(jp2_box_t *box, jas_stream_t *in)
+ 	int_fast32_t x;
+ 
+ 	pclr->lutdata = 0;
++	pclr->bpc = 0;
+ 
+ 	if (jp2_getuint16(in, &pclr->numlutents) ||
+ 	  jp2_getuint8(in, &pclr->numchans)) {
+@@ -869,9 +885,9 @@ static int jp2_pclr_putdata(jp2_box_t *box, jas_stream_t *out)
+ #if 0
+ 	jp2_pclr_t *pclr = &box->data.pclr;
+ #endif
+-/* Eliminate warning about unused variable. */
+-box = 0;
+-out = 0;
++	/* Eliminate warning about unused variable. */
++	box = 0;
++	out = 0;
+ 	return -1;
+ }
+ 

gnu/packages/patches/kiki-level-selection-crash.patch

@@ -0,0 +1,19 @@
+Downloaded from https://anonscm.debian.org/viewvc/pkg-games/packages/trunk/kiki-the-nano-bot/debian/patches/level-selection-with-no-levels-solved.patch?revision=8291&view=co
+
+Kiki crashes if the user tries to use the level selection menu before
+finishing any level.
+
+Peter De Wachter (pdewacht@gmail.com)
+placed in the public domain
+
+--- a/py/levelselection.py
++++ b/py/levelselection.py
+@@ -25,6 +25,8 @@
+     # ............................................................................................................    
+     
+     last_level = highscore.getLastAvailableLevel()
++    if last_level < 0:
++        last_level = 0
+     current_level = (level_index >= 0) and level_index or last_level 
+         
+     world.max_level_index = last_level

gnu/packages/patches/kiki-makefile.patch

@@ -0,0 +1,57 @@
+Downloaded from https://anonscm.debian.org/viewvc/pkg-games/packages/trunk/kiki-the-nano-bot/debian/patches/Makefile.patch?revision=15681&view=co
+
+Makefile fixes:
+ - Make CXXFLAGS, CPPFLAGS, LDFLAGS available for user-specified flags.
+ - run SWIG before compiling
+
+Peter De Wachter (pdewacht@gmail.com)
+placed in the public domain
+
+--- a/kodilib/linux/Makefile
++++ b/kodilib/linux/Makefile
+@@ -21,7 +21,7 @@
+ 
+ INCLUDES = $(KODI_INCLUDES) $(X11_INCLUDES) $(SDL_INCLUDES)
+ 
+-CXXFLAGS = $(INCLUDES) $(SDL_CFLAGS)
++CXXOPTS = -Wall $(INCLUDES) $(SDL_CFLAGS) $(CPPFLAGS) $(CXXFLAGS)
+ 
+ src =  \
+ 	$(KODISRCDIR)/handler/KEventHandler.cpp \
+@@ -95,4 +95,4 @@
+ 	$(RM) -f $(obj) libkodi.a
+ 
+ %.o:    %.cpp
+-	$(CXX) -c $(CXXFLAGS) -o $@ $<
++	$(CXX) -c $(CXXOPTS) -o $@ $<
+--- a/linux/Makefile
++++ b/linux/Makefile
+@@ -46,7 +46,7 @@
+ 
+ INCLUDES = $(KIKI_INCLUDES) $(X11_INCLUDES) $(PYTHON_INCLUDES)
+ 
+-CXXFLAGS = $(INCLUDES) $(SDLCFLAGS)
++CXXOPTS = -Wall $(INCLUDES) $(SDLCFLAGS) $(CPPFLAGS) $(CXXFLAGS)
+ 
+ src =  \
+ 	$(KIKISRC)/base/KikiAction.cpp \
+@@ -105,8 +105,10 @@
+ obj = $(src:.cpp=.o)
+ 
+ kiki: $(KIKISRC)/../SWIG/KikiPy_wrap.cpp $(obj)
+-	-(cd ../SWIG; swig -c++ -python -globals kiki -o KikiPy_wrap.cpp KikiPy.i; cp kiki.py ../py)
+-	$(CXX) $(obj) $(KODILIB) -o kiki $(GLLIBS) $(SDLLIBS) $(PYTHONLIBS)
++	$(CXX) $(LDFLAGS) $(obj) $(KODILIB) -o kiki $(GLLIBS) $(SDLLIBS) $(PYTHONLIBS)
++
++$(KIKISRC)/../SWIG/KikiPy_wrap.cpp: $(wildcard ../SWIG/*.i)
++	(cd ../SWIG && swig -c++ -python -globals kiki -DSWIG_PYTHON_LEGACY_BOOL -o KikiPy_wrap.cpp KikiPy.i && cp kiki.py ../py)
+ 
+ obj-clean:
+ 	$(RM) -f $(obj)
+@@ -115,5 +117,5 @@
+ 	$(RM) -f $(obj) kiki
+ 
+ %.o:    %.cpp
+-	$(CXX) -c $(CXXFLAGS) -o $@ $<
++	$(CXX) -c $(CXXOPTS) -o $@ $<
+ 

gnu/packages/patches/kiki-missing-includes.patch

@@ -0,0 +1,55 @@
+Downloaded from https://anonscm.debian.org/viewvc/pkg-games/packages/trunk/kiki-the-nano-bot/debian/patches/missing-includes.patch?revision=7984&view=co
+
+Status: in upstream CVS
+
+--- a/kodilib/src/handler/KPickable.h
++++ b/kodilib/src/handler/KPickable.h
+@@ -8,6 +8,7 @@
+ 
+ #include "KIntrospection.h"
+ #include <vector>
++#include <limits.h>
+ 
+ #define DEBUG_PICKING		false
+ 
+--- a/kodilib/src/tools/KIntrospection.h
++++ b/kodilib/src/tools/KIntrospection.h
+@@ -11,6 +11,7 @@
+ #endif
+ 
+ #include <string>
++#include <string.h>
+ 
+ // --------------------------------------------------------------------------------------------------------
+ class KClassInfo
+--- a/kodilib/src/tools/KStringTools.cpp
++++ b/kodilib/src/tools/KStringTools.cpp
+@@ -6,7 +6,7 @@
+ #include "KStringTools.h"
+ #include "KVector.h"
+ 
+-#include <sys/types.h> 	// INT_MAX
++#include <limits.h> // INT_MAX
+ #include <stdio.h>
+ 
+ // --------------------------------------------------------------------------------------------------------
+--- a/kodilib/src/tools/KStringTools.h
++++ b/kodilib/src/tools/KStringTools.h
+@@ -9,6 +9,7 @@
+ #include <string>
+ #include <vector>
+ #include <stdarg.h>
++#include <string.h>
+ 
+ // --------------------------------------------------------------------------------------------------------
+ 
+--- a/kodilib/src/tools/KXMLTools.cpp
++++ b/kodilib/src/tools/KXMLTools.cpp
+@@ -7,6 +7,7 @@
+ #include "KConsole.h"
+ #include "KSeparatedMatrix.h"
+ #include <stdio.h>
++#include <stdlib.h>
+ 
+ // --------------------------------------------------------------------------------------------------------
+ std::string kXMLTag ( const std::string & name, const std::string & attributes, int depth )

gnu/packages/patches/kiki-portability-64bit.patch

@@ -0,0 +1,328 @@
+This patch was downloaded from Debian:
+https://anonscm.debian.org/viewvc/pkg-games/packages/trunk/kiki-the-nano-bot/debian/patches/portability-64bit.patch?revision=7984&view=co
+
+Make 64-bit clean (string positions don't fit in an int on 64-bit machines)
+
+Peter De Wachter (pdewacht@gmail.com)
+placed in the public domain
+
+Status: in upstream CVS
+
+--- a/kodilib/src/tools/KFileTools.cpp
++++ b/kodilib/src/tools/KFileTools.cpp
+@@ -214,8 +214,8 @@
+ // --------------------------------------------------------------------------------------------------------
+ string kFileSuffix ( const string & path )
+ {
+-    unsigned int lastDotPos = path.rfind(".");
+-    unsigned int lastSlashPos = path.rfind(kPathSep);
++    std::string::size_type lastDotPos = path.rfind(".");
++    std::string::size_type lastSlashPos = path.rfind(kPathSep);
+ 
+     if (lastDotPos < path.size() - 1 && (lastDotPos > lastSlashPos || lastSlashPos == string::npos))
+     {
+@@ -228,7 +228,7 @@
+ string kFileDirName ( const string & path )
+ {
+ 	string native = kFileNativePath(path);
+-    unsigned int lastSlashPos = native.rfind(kPathSep);
++    std::string::size_type lastSlashPos = native.rfind(kPathSep);
+     if (lastSlashPos < native.size())
+     {
+         return native.substr(0, lastSlashPos+1);
+@@ -241,7 +241,7 @@
+ {
+ 	string native = kFileNativePath(path);
+     string baseName = native;
+-    unsigned int lastSlashPos = native.rfind(kPathSep);
++    std::string::size_type lastSlashPos = native.rfind(kPathSep);
+     if (lastSlashPos < native.size() - 1) 
+     {
+         baseName = native.substr(lastSlashPos+1);
+--- a/kodilib/src/tools/KKeyTools.cpp
++++ b/kodilib/src/tools/KKeyTools.cpp
+@@ -170,7 +170,7 @@
+ // --------------------------------------------------------------------------------------------------------
+ int kKeyGetDisplayWidthForKey ( const std::string & keyName )
+ {
+-    unsigned int keyPos = keyName.find('_', 0);
++    std::string::size_type keyPos = keyName.find('_', 0);
+     if (keyPos == std::string::npos) 
+     {
+         return kKeyGetDisplayWidthForPureKey(keyName) + KDL_MOD_KEY_SPACING;
+@@ -313,7 +313,7 @@
+ int kKeyDisplayKey ( const std::string & keyName, const KPosition & pos )
+ {
+     KPosition start = pos;
+-    unsigned int keyPos = keyName.find('_', 0);
++    std::string::size_type keyPos = keyName.find('_', 0);
+     if (keyPos == std::string::npos) 
+     {
+         return start.x + kKeyDisplayPureKey(keyName, start) + KDL_MOD_KEY_SPACING;
+@@ -380,7 +380,7 @@
+ // --------------------------------------------------------------------------------------------------------
+ SDL_keysym kKeyGetKeysymForKeyName ( const std::string & keyName )
+ {
+-    unsigned int pos = keyName.find('_');
++    std::string::size_type pos = keyName.find('_');
+     
+     std::string modString;
+     std::string symString = keyName;
+--- a/kodilib/src/tools/KStringTools.cpp
++++ b/kodilib/src/tools/KStringTools.cpp
+@@ -13,7 +13,7 @@
+ void kStringInsertStringBehindTags ( std::string & str, const std::string & insertString, 
+                                      const std::string & tag )
+ {
+-    unsigned int oldPos = 0;
++    std::string::size_type oldPos = 0;
+     while ((oldPos = str.find(tag, oldPos)) != std::string::npos)
+     {
+         oldPos += tag.size();
+@@ -34,8 +34,8 @@
+ {
+     std::vector<std::string> components;
+     
+-    unsigned int dividerLength = divider.size();
+-    unsigned int oldpos = 0, pos;
++    std::string::size_type dividerLength = divider.size();
++    std::string::size_type oldpos = 0, pos;
+     
+     while ((pos = str.find(divider, oldpos)) != std::string::npos)
+     {
+@@ -50,7 +50,7 @@
+ // --------------------------------------------------------------------------------------------------------
+ void kStringReplace ( std::string & str, const std::string & toReplace, const std::string & replacement )
+ {
+-    unsigned int pos = 0, chars = toReplace.size();
++    std::string::size_type pos = 0, chars = toReplace.size();
+     while ((pos = str.find(toReplace, pos)) != std::string::npos)
+     {
+         str.replace(pos, chars, replacement);
+@@ -60,11 +60,11 @@
+ // --------------------------------------------------------------------------------------------------------
+ void kStringReplaceTabs ( std::string & str, unsigned int tabWidth )
+ {
+-    unsigned int tabPos;
++    std::string::size_type tabPos;
+     while ((tabPos = str.find('\t')) != std::string::npos)
+     {
+-        unsigned int lastNewlinePos = str.rfind('\n', tabPos-1);
+-        unsigned int relPos = (lastNewlinePos == std::string::npos) ? tabPos : tabPos - lastNewlinePos; 
++        std::string::size_type lastNewlinePos = str.rfind('\n', tabPos-1);
++        std::string::size_type relPos = (lastNewlinePos == std::string::npos) ? tabPos : tabPos - lastNewlinePos; 
+         str.replace(tabPos, 1, std::string(tabWidth-(relPos % tabWidth), ' '));
+     }
+ }
+@@ -114,7 +114,7 @@
+ // --------------------------------------------------------------------------------------------------------
+ unsigned int kStringNthCharPos ( const std::string & str, unsigned int n, char c )
+ {
+-    unsigned int loc = n, oloc = 0;
++    std::string::size_type loc = n, oloc = 0;
+     while (n > 0 && (loc = str.find(c, oloc)) != std::string::npos)
+     { 
+         n--; 
+@@ -138,7 +138,7 @@
+ // --------------------------------------------------------------------------------------------------------
+ void kStringCropCols ( std::string & str, unsigned int columns )
+ {        
+-    unsigned int oloc = 0, nloc = 0;
++    std::string::size_type oloc = 0, nloc = 0;
+     while ((nloc = str.find('\n', oloc)) != std::string::npos)
+     {
+         if ((nloc - oloc) > columns)
+@@ -160,10 +160,10 @@
+ unsigned int kStringCols ( const std::string & str )
+ {
+     if (str.size() == 0) return 0;
+-    int oloc = 0, nloc;
++    long oloc = 0, nloc;
+     std::string substring;
+     int maxlength = 0, length;
+-    while ((nloc = str.find('\n', oloc)) != (int)std::string::npos) 
++    while ((nloc = str.find('\n', oloc)) != (long)std::string::npos) 
+     {
+         substring = str.substr(oloc, nloc - oloc);
+         length = substring.size();
+@@ -181,7 +181,7 @@
+ unsigned int kStringRows ( const std::string & str )
+ {
+     if (str.size() == 0) return 1;
+-    unsigned int loc = 0, lines = 0;
++    std::string::size_type loc = 0, lines = 0;
+     while ((loc = str.find('\n', loc)) != std::string::npos) { lines++; loc++; }
+     if (str[str.size()-1] == '\n') return lines;
+     return lines+1;
+@@ -204,8 +204,8 @@
+ {
+     static char str[256];
+     std::string format(fmt), subformat, text;
+-    unsigned int oloc = 0;
+-    unsigned int nloc = 0;
++    std::string::size_type oloc = 0;
++    std::string::size_type nloc = 0;
+     
+     kStringReplaceTabs(format);
+     
+@@ -260,7 +260,7 @@
+ // --------------------------------------------------------------------------------------------------------
+ bool kStringHasSuffix ( const std::string & str, const std::string & suffix )
+ {
+-    unsigned int result = str.rfind(suffix);
++    std::string::size_type result = str.rfind(suffix);
+     if (result == std::string::npos) return false;
+     return (result == str.size()-suffix.size());
+ }
+--- a/kodilib/src/tools/KXMLTools.cpp
++++ b/kodilib/src/tools/KXMLTools.cpp
+@@ -58,11 +58,11 @@
+ std::string kXMLParseToTagsInVector ( std::string & xml, const std::vector<std::string> & tags )
+ {
+     std::string open("<");
+-    unsigned int minLoc = std::string::npos; 
++    std::string::size_type minLoc = std::string::npos; 
+     std::vector<std::string>::const_iterator iter = tags.begin();
+     while (iter != tags.end())
+     {
+-        unsigned int loc = xml.find(open+(*iter));
++        std::string::size_type loc = xml.find(open+(*iter));
+         if (loc < minLoc) minLoc = loc;
+         iter++;
+     }
+@@ -77,7 +77,7 @@
+     std::string value;
+     std::string nameStr(name);
+     nameStr += "='";
+-    unsigned int loc = xml.find(nameStr);
++    std::string::size_type loc = xml.find(nameStr);
+     if (loc != std::string::npos)
+     {	
+         loc += nameStr.size();
+@@ -90,7 +90,7 @@
+ // --------------------------------------------------------------------------------------------------------
+ bool kXMLParseNamedCloseTag ( std::string & xml, const std::string & name, bool printError )
+ {
+-    unsigned int loc = xml.find('<');
++    std::string::size_type loc = xml.find('<');
+     if (loc == std::string::npos) 
+     {
+         if (printError) KConsole::printError(kStringPrintf("invalid XML:\nmissing close tag '%s'", 
+@@ -117,7 +117,7 @@
+ // --------------------------------------------------------------------------------------------------------
+ bool kXMLReadNamedOpenTag ( const std::string & xml, const std::string & name, std::string * attributes )
+ {
+-    unsigned int loc = xml.find('<'), endloc;
++    std::string::size_type loc = xml.find('<'), endloc;
+     
+     if (loc == std::string::npos || xml[loc+1] == '/') return false;
+     
+@@ -140,7 +140,7 @@
+ // --------------------------------------------------------------------------------------------------------
+ std::string kXMLParseNamedOpenTag ( std::string & xml, const std::string & name, std::string * attributes, bool printError )
+ {
+-    unsigned int loc = xml.find('<');
++    std::string::size_type loc = xml.find('<');
+     if (loc == std::string::npos || xml[loc+1] == '/') 
+     {
+         if (printError) KConsole::printError(kStringPrintf("invalid XML:\nmissing tag '%s'", name.c_str()));
+@@ -191,7 +191,7 @@
+ // --------------------------------------------------------------------------------------------------------
+ bool kXMLParseOpenTag ( std::string & xml, std::string & name, std::string * attributes, bool printError )
+ {
+-    unsigned int loc = xml.find('<');
++    std::string::size_type loc = xml.find('<');
+     if (loc == std::string::npos || xml[loc+1] == '/') 
+     {
+         if (printError) KConsole::printError("invalid XML:\nmissing open tag");
+@@ -295,7 +295,7 @@
+ // --------------------------------------------------------------------------------------------------------
+ bool kXMLParseValue( std::string & xml, const std::string & name, int type, void * value, bool printError )
+ {
+-    unsigned int loc = xml.find('<');
++    std::string::size_type loc = xml.find('<');
+     if (loc == std::string::npos || xml[loc+1] == '/')     
+     {
+         if (printError) KConsole::printError(kStringPrintf("invalid XML:\nmissing value '%s'", name.c_str()));
+@@ -379,8 +379,8 @@
+         }
+         else if (typeString == "string")
+         {
+-            unsigned int first = substring.find("\"")+1;
+-            unsigned int last  = substring.rfind("\"", std::string::npos);
++            std::string::size_type first = substring.find("\"")+1;
++            std::string::size_type last  = substring.rfind("\"", std::string::npos);
+             *((std::string*)value) = substring.substr(first, last-first);
+         }
+         
+--- a/kodilib/src/types/KKey.cpp
++++ b/kodilib/src/types/KKey.cpp
+@@ -31,7 +31,7 @@
+ // --------------------------------------------------------------------------------------------------------
+ std::string KKey::getUnmodifiedName () const
+ {
+-    unsigned int keyPos = name.find('_', 0);
++    std::string::size_type keyPos = name.find('_', 0);
+     if (keyPos == std::string::npos) 
+     {
+         return name;
+@@ -42,7 +42,7 @@
+ // --------------------------------------------------------------------------------------------------------
+ std::string KKey::getModifierName () const
+ {
+-    unsigned int keyPos = name.find('_', 0);
++    std::string::size_type keyPos = name.find('_', 0);
+     if (keyPos == std::string::npos) 
+     {
+         return "";
+--- a/kodilib/src/widgets/KFileNameField.cpp
++++ b/kodilib/src/widgets/KFileNameField.cpp
+@@ -41,7 +41,7 @@
+         std::string restPath; 				 // path behind cursor
+         
+         // map cropped path to current directory and rest path to file prefix
+-        unsigned int lastSlashPos = croppedPath.rfind("/");
++        std::string::size_type lastSlashPos = croppedPath.rfind("/");
+         if (lastSlashPos < croppedPath.size()-1)
+         {
+             restPath = croppedPath.substr(lastSlashPos+1);
+@@ -88,7 +88,7 @@
+         }
+ 
+         // ............................collect list of entries in searchDir that match prefix restPath
+-        unsigned int restLength = restPath.size();
++        std::string::size_type restLength = restPath.size();
+         std::vector<std::string> matchingEntries;
+         std::vector<std::string>::iterator iter = dir_entries.begin();
+         while (iter != dir_entries.end())
+@@ -223,7 +223,7 @@
+ // --------------------------------------------------------------------------------------------------------
+ void KFileNameField::selectLastPathComponent ()
+ {
+-    unsigned int lastSlashPos = text.rfind("/");
++    std::string::size_type lastSlashPos = text.rfind("/");
+     if (lastSlashPos == text.size()-1) lastSlashPos = text.rfind("/", lastSlashPos-1);
+     if (lastSlashPos < text.size()) cursor_pos = lastSlashPos+1;
+     else cursor_pos = 0;
+--- a/src/gui/KikiMenu.cpp
++++ b/src/gui/KikiMenu.cpp
+@@ -54,7 +54,7 @@
+ {
+     std::string item_text (itemText);
+     std::string event_name (itemText);
+-    unsigned int pos;
++    std::string::size_type pos;
+     float scale_factor = 1.0;
+ 
+     KikiMenuItem * menu_item = new KikiMenuItem ();
+--- a/src/gui/KikiTextLine.cpp
++++ b/src/gui/KikiTextLine.cpp
+@@ -46,7 +46,7 @@
+ void KikiTextLine::setText ( const std::string & str )
+ {
+     text = str;
+-    unsigned int pos;
++    std::string::size_type pos;
+  
+     if ((pos = text.find ("$scale(")) != std::string::npos)
+     {

gnu/packages/patches/kio-CVE-2017-6410.patch

@@ -1,53 +0,0 @@
-Fix CVE-2017-6410, "Information Leak when accessing https when using a
-malicious PAC file":
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-6410
-https://www.kde.org/info/security/advisory-20170228-1.txt
-
-Patch copied from upstream source repository:
-
-https://cgit.kde.org/kio.git/commit/?id=f9d0cb47cf94e209f6171ac0e8d774e68156a6e4
-
-From f9d0cb47cf94e209f6171ac0e8d774e68156a6e4 Mon Sep 17 00:00:00 2001
-From: Albert Astals Cid <aacid@kde.org>
-Date: Tue, 28 Feb 2017 19:00:48 +0100
-Subject: Sanitize URLs before passing them to FindProxyForURL
-
-Remove user/password information
-For https: remove path and query
-
-Thanks to safebreach.com for reporting the problem
-
-CCMAIL: yoni.fridburg@safebreach.com
-CCMAIL: amit.klein@safebreach.com
-CCMAIL: itzik.kotler@safebreach.com
----
- src/kpac/script.cpp | 11 +++++++++--
- 1 file changed, 9 insertions(+), 2 deletions(-)
-
-diff --git a/src/kpac/script.cpp b/src/kpac/script.cpp
-index a0235f7..2485c54 100644
---- a/src/kpac/script.cpp
-+++ b/src/kpac/script.cpp
-@@ -754,9 +754,16 @@ QString Script::evaluate(const QUrl &url)
-         }
-     }
- 
-+    QUrl cleanUrl = url;
-+    cleanUrl.setUserInfo(QString());
-+    if (cleanUrl.scheme() == QLatin1String("https")) {
-+        cleanUrl.setPath(QString());
-+        cleanUrl.setQuery(QString());
-+    }
-+
-     QScriptValueList args;
--    args << url.url();
--    args << url.host();
-+    args << cleanUrl.url();
-+    args << cleanUrl.host();
- 
-     QScriptValue result = func.call(QScriptValue(), args);
-     if (result.isError()) {
--- 
-cgit v0.11.2
-

gnu/packages/patches/luminance-hdr-qt-printer.patch

@@ -0,0 +1,28 @@
+Allow the 'QtPrinter' header to be found, as described
+at <https://github.com/LuminanceHDR/LuminanceHDR/issues/11>.
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index fbad8a2..8379c8a 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -29,6 +29,7 @@ find_package(Qt5Xml)
+ find_package(Qt5Sql)
+ find_package(Qt5Network)
+ find_package(Qt5LinguistTools)
++find_package(Qt5PrintSupport REQUIRED)
+ IF(WIN32)
+ 	find_package(Qt5WinExtras)
+ ENDIF()
+diff --git a/src/HelpBrowser/CMakeLists.txt b/src/HelpBrowser/CMakeLists.txt
+index 04319a8..5537dae 100644
+--- a/src/HelpBrowser/CMakeLists.txt
++++ b/src/HelpBrowser/CMakeLists.txt
+@@ -29,7 +29,7 @@ QT5_WRAP_UI(FILES_UI_H ${FILES_UI})
+ 
+ 
+ ADD_LIBRARY(helpbrowser ${FILES_H} ${FILES_CPP} ${FILES_MOC} ${FILES_UI_H} ${FILES_HXX})
+-qt5_use_modules(helpbrowser Core Concurrent Gui Widgets Xml WebKit WebKitWidgets)
++qt5_use_modules(helpbrowser Core Concurrent Gui Widgets Xml WebKit WebKitWidgets PrintSupport)
+ 
+ SET(FILES_TO_TRANSLATE ${FILES_TO_TRANSLATE} ${FILES_CPP} ${FILES_H} ${FILES_UI} ${FILES_HXX} PARENT_SCOPE)
+ SET(LUMINANCE_MODULES_GUI ${LUMINANCE_MODULES_GUI} helpbrowser PARENT_SCOPE)

gnu/packages/patches/lz4-fix-test-failures.patch

@@ -0,0 +1,136 @@
+These two patches fix some bugs in lz4's test suite:
+
+https://github.com/lz4/lz4/issues/308
+
+Patches copied from upstream source repository:
+
+https://github.com/lz4/lz4/commit/b89cac7b2e92b792af98bb0a12e4d14684d07629
+https://github.com/lz4/lz4/commit/0dfb0b9dad2a8cb7cc347d2139bf9b84de7e1481
+
+From b89cac7b2e92b792af98bb0a12e4d14684d07629 Mon Sep 17 00:00:00 2001
+From: Eric Siegerman <pub08-git@davor.org>
+Date: Tue, 14 Feb 2017 14:17:06 -0500
+Subject: [PATCH] Don't use "foo && false || true"
+
+Replace it with either:
+    test ! -f $FILE_THAT_SHOULD_NOT_EXIST
+or:
+    ! $COMMAND_THAT_SHOULD_FAIL
+
+as appropriate.
+---
+ tests/Makefile | 38 +++++++++++++++++++-------------------
+ 1 file changed, 19 insertions(+), 19 deletions(-)
+
+diff --git a/tests/Makefile b/tests/Makefile
+index 77e6ae7..ebab278 100644
+--- a/tests/Makefile
++++ b/tests/Makefile
+@@ -236,17 +236,17 @@ test-lz4-basic: lz4 datagen unlz4 lz4cat
+ 	./datagen -g256MB | $(LZ4) -vqB4D | $(LZ4) -t
+ 	@echo "hello world" > tmp
+ 	$(LZ4) --rm -f tmp
+-	ls -ls tmp         && false || true   # must fail (--rm)
+-	ls -ls tmp.lz4
+-	$(PRGDIR)/lz4cat tmp.lz4              # must display hello world
+-	ls -ls tmp.lz4
++	test ! -f tmp                      # must fail (--rm)
++	test   -f tmp.lz4
++	$(PRGDIR)/lz4cat tmp.lz4           # must display hello world
++	test   -f tmp.lz4
+ 	$(PRGDIR)/unlz4 --rm tmp.lz4
+-	ls -ls tmp
+-	ls -ls tmp.lz4     && false || true   # must fail (--rm)
+-	ls -ls tmp.lz4.lz4 && false || true   # must fail (unlz4)
+-	$(PRGDIR)/lz4cat tmp                  # pass-through mode
+-	ls -ls tmp
+-	ls -ls tmp.lz4     && false || true   # must fail (lz4cat)
++	test   -f tmp
++	test ! -f tmp.lz4                  # must fail (--rm)
++	test ! -f tmp.lz4.lz4              # must fail (unlz4)
++	$(PRGDIR)/lz4cat tmp               # pass-through mode
++	test   -f tmp
++	test ! -f tmp.lz4                  # must fail (lz4cat)
+ 	$(LZ4) tmp                         # creates tmp.lz4
+ 	$(PRGDIR)/lz4cat < tmp.lz4 > tmp3  # checks lz4cat works with stdin (#285)
+ 	$(DIFF) -q tmp tmp3
+@@ -262,22 +262,22 @@ test-lz4-hugefile: lz4 datagen
+ 
+ test-lz4-testmode: lz4 datagen
+ 	@echo "\n ---- bench mode ----"
+-	$(LZ4) -bi1
++	  $(LZ4) -bi1
+ 	@echo "\n ---- test mode ----"
+-	./datagen | $(LZ4) -t             && false || true
+-	./datagen | $(LZ4) -tf            && false || true
++	! ./datagen | $(LZ4) -t
++	! ./datagen | $(LZ4) -tf
+ 	@echo "\n ---- pass-through mode ----"
+-	./datagen | $(LZ4) -d  > $(VOID)  && false || true
+-	./datagen | $(LZ4) -df > $(VOID)
++	! ./datagen | $(LZ4) -d  > $(VOID)
++	  ./datagen | $(LZ4) -df > $(VOID)
+ 	@echo "Hello World !" > tmp1
+ 	$(LZ4) -dcf tmp1
+ 	@echo "from underground..." > tmp2
+ 	$(LZ4) -dcfm tmp1 tmp2
+ 	@echo "\n ---- test cli ----"
+-	$(LZ4)     file-does-not-exist    && false || true
+-	$(LZ4) -f  file-does-not-exist    && false || true
+-	$(LZ4) -fm file1-dne file2-dne    && false || true
+-	$(LZ4) -fm file1-dne file2-dne    && false || true
++	! $(LZ4)     file-does-not-exist
++	! $(LZ4) -f  file-does-not-exist
++	! $(LZ4) -fm file1-dne file2-dne
++	! $(LZ4) -fm file1-dne file2-dne
+ 
+ test-lz4-opt-parser: lz4 datagen
+ 	@echo "\n ---- test opt-parser ----"
+-- 
+2.12.2
+
+From 0dfb0b9dad2a8cb7cc347d2139bf9b84de7e1481 Mon Sep 17 00:00:00 2001
+From: "Dmitry V. Levin" <ldv@altlinux.org>
+Date: Sun, 5 Mar 2017 23:20:10 +0000
+Subject: [PATCH] Fix test-lz4-basic
+
+When no output filename is specified and stdout is not a terminal,
+lz4 doesn't attempt to guess an output filename and uses stdout for
+output.
+
+This change fixes test-lz4-basic when run without a terminal
+by specifying output filenames.
+---
+ tests/Makefile | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/tests/Makefile b/tests/Makefile
+index ebab278..d68c700 100644
+--- a/tests/Makefile
++++ b/tests/Makefile
+@@ -235,19 +235,19 @@ test-lz4-basic: lz4 datagen unlz4 lz4cat
+ 	./datagen -g33M   | $(LZ4) --no-frame-crc | $(LZ4) -t
+ 	./datagen -g256MB | $(LZ4) -vqB4D | $(LZ4) -t
+ 	@echo "hello world" > tmp
+-	$(LZ4) --rm -f tmp
++	$(LZ4) --rm -f tmp tmp.lz4
+ 	test ! -f tmp                      # must fail (--rm)
+ 	test   -f tmp.lz4
+ 	$(PRGDIR)/lz4cat tmp.lz4           # must display hello world
+ 	test   -f tmp.lz4
+-	$(PRGDIR)/unlz4 --rm tmp.lz4
++	$(PRGDIR)/unlz4 --rm tmp.lz4 tmp
+ 	test   -f tmp
+ 	test ! -f tmp.lz4                  # must fail (--rm)
+ 	test ! -f tmp.lz4.lz4              # must fail (unlz4)
+ 	$(PRGDIR)/lz4cat tmp               # pass-through mode
+ 	test   -f tmp
+ 	test ! -f tmp.lz4                  # must fail (lz4cat)
+-	$(LZ4) tmp                         # creates tmp.lz4
++	$(LZ4) tmp tmp.lz4                 # creates tmp.lz4
+ 	$(PRGDIR)/lz4cat < tmp.lz4 > tmp3  # checks lz4cat works with stdin (#285)
+ 	$(DIFF) -q tmp tmp3
+ 	$(PRGDIR)/lz4cat < tmp > tmp2      # checks lz4cat works with stdin (#285)
+-- 
+2.12.2
+

gnu/packages/patches/networkmanager-qt-activeconnection-test-1.patch

@@ -0,0 +1,60 @@
+From 61337983ba74361938b7d5323de5d2819a235fdc Mon Sep 17 00:00:00 2001
+From: Jan Grulich <jgrulich@redhat.com>
+Date: Mon, 3 Apr 2017 12:53:12 +0200
+Subject: Fix unit test for active connections
+
+Instead of sending PropertiesChanged signal for an active connection we
+added recently we should set all properties initially and just advertise
+that we have a new active connection once everything is set
+---
+ src/fakenetwork/fakenetwork.cpp | 26 +++++++-------------------
+ 1 file changed, 7 insertions(+), 19 deletions(-)
+
+diff --git a/src/fakenetwork/fakenetwork.cpp b/src/fakenetwork/fakenetwork.cpp
+index bc1144e..261fe8e 100644
+--- a/src/fakenetwork/fakenetwork.cpp
++++ b/src/fakenetwork/fakenetwork.cpp
+@@ -215,8 +215,14 @@ void FakeNetwork::unregisterService()
+ 
+ QDBusObjectPath FakeNetwork::ActivateConnection(const QDBusObjectPath &connection, const QDBusObjectPath &device, const QDBusObjectPath &specific_object)
+ {
+-    ActiveConnection *newActiveConnection = new ActiveConnection(this);
+     QString newActiveConnectionPath = QString("/org/kde/fakenetwork/ActiveConnection/") + QString::number(m_activeConnectionsCounter++);
++    ActiveConnection *newActiveConnection = new ActiveConnection(this);
++    newActiveConnection->addDevice(device);
++    newActiveConnection->setActiveConnectionPath(newActiveConnectionPath);
++    newActiveConnection->setConnection(connection);
++    newActiveConnection->setSpecificObject(specific_object);
++    newActiveConnection->setState(NetworkManager::ActiveConnection::Activating);
++
+     m_activeConnections.insert(QDBusObjectPath(newActiveConnectionPath), newActiveConnection);
+     QDBusConnection::sessionBus().registerObject(newActiveConnectionPath, newActiveConnection, QDBusConnection::ExportScriptableContents);
+ 
+@@ -227,24 +233,6 @@ QDBusObjectPath FakeNetwork::ActivateConnection(const QDBusObjectPath &connectio
+     map.insert(QLatin1Literal("ActivatingConnection"), QVariant::fromValue(QDBusObjectPath(newActiveConnectionPath)));
+     Q_EMIT PropertiesChanged(map);
+ 
+-    newActiveConnection->addDevice(device);
+-    newActiveConnection->setActiveConnectionPath(newActiveConnectionPath);
+-    newActiveConnection->setConnection(connection);
+-    newActiveConnection->setSpecificObject(specific_object);
+-    newActiveConnection->setState(NetworkManager::ActiveConnection::Activating);
+-
+-    map.clear();
+-    const QList<QDBusObjectPath> deviceList { device };
+-    map.insert(QLatin1Literal("Devices"), QVariant::fromValue<QList<QDBusObjectPath> >(deviceList));
+-    map.insert(QLatin1Literal("Connection"), QVariant::fromValue<QDBusObjectPath>(connection));
+-    if (!specific_object.path().isEmpty()) {
+-        map.insert(QLatin1Literal("SpecificObject"), QVariant::fromValue<QDBusObjectPath>(connection));
+-    }
+-    map.insert(QLatin1Literal("State"), NetworkManager::ActiveConnection::Activating);
+-    QDBusMessage message = QDBusMessage::createSignal(newActiveConnectionPath, QLatin1Literal("org.kde.fakenetwork.Connection.Active"), QLatin1Literal("PropertiesChanged"));
+-    message << map;
+-    QDBusConnection::sessionBus().send(message);
+-
+     Device *usedDevice = static_cast<Device *>(QDBusConnection::sessionBus().objectRegisteredAt(device.path()));
+     if (usedDevice) {
+         m_activatedDevice = usedDevice->devicePath();
+-- 
+cgit v0.11.2
+

gnu/packages/patches/networkmanager-qt-activeconnection-test-2.patch

@@ -0,0 +1,57 @@
+From 3f6155389abc8e2b3dafc5eefa1ce0c929b007fa Mon Sep 17 00:00:00 2001
+From: Jan Grulich <jgrulich@redhat.com>
+Date: Mon, 3 Apr 2017 14:13:54 +0200
+Subject: One more attempt to fix unit test for active connections
+
+---
+ src/activeconnection.cpp | 10 ++++++++++
+ 1 file changed, 10 insertions(+)
+
+diff --git a/src/activeconnection.cpp b/src/activeconnection.cpp
+index 05582fa..3a8e6b2 100644
+--- a/src/activeconnection.cpp
++++ b/src/activeconnection.cpp
+@@ -79,11 +79,13 @@ NetworkManager::ActiveConnection::ActiveConnection(const QString &path, QObject
+     connect(&d->iface, &OrgFreedesktopNetworkManagerConnectionActiveInterface::PropertiesChanged, d, &ActiveConnectionPrivate::propertiesChanged);
+ #endif
+ 
++#ifndef NMQT_STATIC
+     /*
+      * Workaround: Re-check connection state before we watch changes in case it gets changed too quickly
+      * BUG:352326
+      */
+     d->recheckProperties();
++#endif
+ }
+ 
+ NetworkManager::ActiveConnection::ActiveConnection(ActiveConnectionPrivate &dd, QObject *parent)
+@@ -91,18 +93,26 @@ NetworkManager::ActiveConnection::ActiveConnection(ActiveConnectionPrivate &dd,
+ {
+     Q_D(ActiveConnection);
+ 
++#ifndef NMQT_STATIC
+ #if NM_CHECK_VERSION(1, 4, 0)
+     QDBusConnection::systemBus().connect(NetworkManagerPrivate::DBUS_SERVICE, d->path, NetworkManagerPrivate::FDO_DBUS_PROPERTIES,
+                                          QLatin1String("PropertiesChanged"), d, SLOT(dbusPropertiesChanged(QString,QVariantMap,QStringList)));
+ #else
+     connect(&d->iface, &OrgFreedesktopNetworkManagerConnectionActiveInterface::PropertiesChanged, d, &ActiveConnectionPrivate::propertiesChanged);
+ #endif
++#endif
++
++#ifdef NMQT_STATIC
++    connect(&d->iface, &OrgFreedesktopNetworkManagerConnectionActiveInterface::PropertiesChanged, d, &ActiveConnectionPrivate::propertiesChanged);
++#endif
+ 
++#ifndef NMQT_STATIC
+     /*
+      * Workaround: Re-check connection state before we watch changes in case it gets changed too quickly
+      * BUG:352326
+      */
+     d->recheckProperties();
++#endif
+ }
+ 
+ NetworkManager::ActiveConnection::~ActiveConnection()
+-- 
+cgit v0.11.2
+

gnu/packages/patches/nss-increase-test-timeout.patch

@@ -14,12 +14,12 @@ Increase timeouts to increase chances of a successful build.
  }
  
  void TlsConnectTestBase::EnableExtendedMasterSecret() {
-@@ -387,7 +387,7 @@
+@@ -385,7 +385,7 @@
-   } else {
+   if (failing_side == TlsAgent::CLIENT) {
-     fail_agent = server_;
+     failing_agent = client_;
    }
--  ASSERT_TRUE_WAIT(fail_agent->state() == TlsAgent::STATE_ERROR, 5000);
+-  ASSERT_TRUE_WAIT(failing_agent->state() == TlsAgent::STATE_ERROR, 5000);
-+  ASSERT_TRUE_WAIT(fail_agent->state() == TlsAgent::STATE_ERROR, 25000);
++  ASSERT_TRUE_WAIT(failing_agent->state() == TlsAgent::STATE_ERROR, 25000);
  }
  
  void TlsConnectTestBase::ConfigureVersion(uint16_t version) {

gnu/packages/patches/password-store-gnupg-compat.patch

@@ -1,53 +0,0 @@
-Copied from upstream mailing list:
-https://lists.zx2c4.com/pipermail/password-store/2017-March/002844.html.
-
-The patch actually restores compatibility with GnuPG 2.1.19, the '2.2.19' in
-the commit message is a typo.
-
-From 8723d8e8192683891904aff321446b0fac37d1ad Mon Sep 17 00:00:00 2001
-From: Andreas Stieger <astieger@suse.com>
-Date: Fri, 10 Mar 2017 15:43:26 +0100
-Subject: [PATCH] Fix compatibility with GnuPG 2.2.19
-
-GnuPG 2.2.19 added a warning when no command was given.
-
-* src/password-store.sh (reencrypt_path): Add --decrypt to --list-only
-* tests/t0300-reencryption.sh (gpg_keys_from_encrypted_file): same
-
-https://bugs.gnupg.org/gnupg/msg9873
-http://git.gnupg.org/cgi-bin/gitweb.cgi?p=gnupg.git;a=commit;h=810adfd47801fc01e45fb71af9f05c91f7890cdb
-https://bugzilla.suse.com/show_bug.cgi?id=1028867
----
- src/password-store.sh       | 2 +-
- tests/t0300-reencryption.sh | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/src/password-store.sh b/src/password-store.sh
-index 1ab6fb5..bad8d4f 100755
---- a/src/password-store.sh
-+++ b/src/password-store.sh
-@@ -125,7 +125,7 @@ reencrypt_path() {
- 			done
- 			gpg_keys="$($GPG $PASSWORD_STORE_GPG_OPTS --list-keys --with-colons "${GPG_RECIPIENTS[@]}" | sed -n 's/sub:[^:]*:[^:]*:[^:]*:\([^:]*\):[^:]*:[^:]*:[^:]*:[^:]*:[^:]*:[^:]*:[a-zA-Z]*e[a-zA-Z]*:.*/\1/p' | LC_ALL=C sort -u)"
- 		fi
--		current_keys="$($GPG $PASSWORD_STORE_GPG_OPTS -v --no-secmem-warning --no-permission-warning --list-only --keyid-format long "$passfile" 2>&1 | cut -d ' ' -f 5 | LC_ALL=C sort -u)"
-+		current_keys="$($GPG $PASSWORD_STORE_GPG_OPTS -v --no-secmem-warning --no-permission-warning --decrypt --list-only --keyid-format long "$passfile" 2>&1 | cut -d ' ' -f 5 | LC_ALL=C sort -u)"
- 
- 		if [[ $gpg_keys != "$current_keys" ]]; then
- 			echo "$passfile_display: reencrypting to ${gpg_keys//$'\n'/ }"
-diff --git a/tests/t0300-reencryption.sh b/tests/t0300-reencryption.sh
-index 9d46580..6d5811d 100755
---- a/tests/t0300-reencryption.sh
-+++ b/tests/t0300-reencryption.sh
-@@ -10,7 +10,7 @@ canonicalize_gpg_keys() {
- 	$GPG --list-keys --with-colons "$@" | sed -n 's/sub:[^:]*:[^:]*:[^:]*:\([^:]*\):[^:]*:[^:]*:[^:]*:[^:]*:[^:]*:[^:]*:[a-zA-Z]*e[a-zA-Z]*:.*/\1/p' | LC_ALL=C sort -u
- }
- gpg_keys_from_encrypted_file() {
--	$GPG -v --no-secmem-warning --no-permission-warning --list-only --keyid-format long "$1" 2>&1 | cut -d ' ' -f 5 | LC_ALL=C sort -u
-+	$GPG -v --no-secmem-warning --no-permission-warning --decrypt --list-only --keyid-format long "$1" 2>&1 | cut -d ' ' -f 5 | LC_ALL=C sort -u
- }
- gpg_keys_from_group() {
- 	local output="$($GPG --list-config --with-colons | sed -n "s/^cfg:group:$1:\\(.*\\)/\\1/p" | head -n 1)"
--- 
-2.12.0
-

gnu/packages/patches/pcre-CVE-2017-7186.patch

@@ -0,0 +1,56 @@
+Patch for <https://nvd.nist.gov/vuln/detail?vulnId=CVE-2017-7186>
+from <https://vcs.pcre.org/pcre?view=revision&revision=1688>.
+
+--- trunk/pcre_internal.h	2016/05/21 13:34:44	1649
++++ trunk/pcre_internal.h	2017/02/24 17:30:30	1688
+@@ -2772,6 +2772,9 @@
+ extern const pcre_uint16 PRIV(ucd_stage2)[];
+ extern const pcre_uint32 PRIV(ucp_gentype)[];
+ extern const pcre_uint32 PRIV(ucp_gbtable)[];
++#ifdef COMPILE_PCRE32
++extern const ucd_record  PRIV(dummy_ucd_record)[];
++#endif
+ #ifdef SUPPORT_JIT
+ extern const int         PRIV(ucp_typerange)[];
+ #endif
+@@ -2780,9 +2783,15 @@
+ /* UCD access macros */
+ 
+ #define UCD_BLOCK_SIZE 128
+-#define GET_UCD(ch) (PRIV(ucd_records) + \
++#define REAL_GET_UCD(ch) (PRIV(ucd_records) + \
+         PRIV(ucd_stage2)[PRIV(ucd_stage1)[(int)(ch) / UCD_BLOCK_SIZE] * \
+         UCD_BLOCK_SIZE + (int)(ch) % UCD_BLOCK_SIZE])
++        
++#ifdef COMPILE_PCRE32
++#define GET_UCD(ch) ((ch > 0x10ffff)? PRIV(dummy_ucd_record) : REAL_GET_UCD(ch))
++#else
++#define GET_UCD(ch) REAL_GET_UCD(ch)
++#endif 
+ 
+ #define UCD_CHARTYPE(ch)    GET_UCD(ch)->chartype
+ #define UCD_SCRIPT(ch)      GET_UCD(ch)->script
+
+--- trunk/pcre_ucd.c	2014/06/19 07:51:39	1490
++++ trunk/pcre_ucd.c	2017/02/24 17:30:30	1688
+@@ -38,6 +38,20 @@
+ const pcre_uint32 PRIV(ucd_caseless_sets)[] = {0};
+ #else
+ 
++/* If the 32-bit library is run in non-32-bit mode, character values
++greater than 0x10ffff may be encountered. For these we set up a
++special record. */
++
++#ifdef COMPILE_PCRE32
++const ucd_record PRIV(dummy_ucd_record)[] = {{
++  ucp_Common,    /* script */
++  ucp_Cn,        /* type unassigned */
++  ucp_gbOther,   /* grapheme break property */
++  0,             /* case set */
++  0,             /* other case */
++  }};
++#endif
++
+ /* When recompiling tables with a new Unicode version, please check the
+ types in this structure definition from pcre_internal.h (the actual
+ field names will be different):

gnu/packages/patches/pcre2-CVE-2017-7186.patch

@@ -0,0 +1,68 @@
+Patch for <https://nvd.nist.gov/vuln/detail?vulnId=CVE-2017-7186>
+taken from <https://vcs.pcre.org/pcre2?view=revision&revision=670>.
+
+--- trunk/src/pcre2_internal.h	2016/11/19 12:46:24	600
++++ trunk/src/pcre2_internal.h	2017/02/24 18:25:32	670
+@@ -1774,10 +1774,17 @@
+ /* UCD access macros */
+ 
+ #define UCD_BLOCK_SIZE 128
+-#define GET_UCD(ch) (PRIV(ucd_records) + \
++#define REAL_GET_UCD(ch) (PRIV(ucd_records) + \
+         PRIV(ucd_stage2)[PRIV(ucd_stage1)[(int)(ch) / UCD_BLOCK_SIZE] * \
+         UCD_BLOCK_SIZE + (int)(ch) % UCD_BLOCK_SIZE])
+ 
++#if PCRE2_CODE_UNIT_WIDTH == 32
++#define GET_UCD(ch) ((ch > MAX_UTF_CODE_POINT)? \
++  PRIV(dummy_ucd_record) : REAL_GET_UCD(ch))
++#else
++#define GET_UCD(ch) REAL_GET_UCD(ch)
++#endif
++
+ #define UCD_CHARTYPE(ch)    GET_UCD(ch)->chartype
+ #define UCD_SCRIPT(ch)      GET_UCD(ch)->script
+ #define UCD_CATEGORY(ch)    PRIV(ucp_gentype)[UCD_CHARTYPE(ch)]
+@@ -1834,6 +1841,9 @@
+ #define _pcre2_default_compile_context PCRE2_SUFFIX(_pcre2_default_compile_context_)
+ #define _pcre2_default_match_context   PCRE2_SUFFIX(_pcre2_default_match_context_)
+ #define _pcre2_default_tables          PCRE2_SUFFIX(_pcre2_default_tables_)
++#if PCRE2_CODE_UNIT_WIDTH == 32
++#define _pcre2_dummy_ucd_record        PCRE2_SUFFIX(_pcre2_dummy_ucd_record_)
++#endif
+ #define _pcre2_hspace_list             PCRE2_SUFFIX(_pcre2_hspace_list_)
+ #define _pcre2_vspace_list             PCRE2_SUFFIX(_pcre2_vspace_list_)
+ #define _pcre2_ucd_caseless_sets       PCRE2_SUFFIX(_pcre2_ucd_caseless_sets_)
+@@ -1858,6 +1868,9 @@
+ extern const uint32_t                  PRIV(vspace_list)[];
+ extern const uint32_t                  PRIV(ucd_caseless_sets)[];
+ extern const ucd_record                PRIV(ucd_records)[];
++#if PCRE2_CODE_UNIT_WIDTH == 32
++extern const ucd_record                PRIV(dummy_ucd_record)[];
++#endif
+ extern const uint8_t                   PRIV(ucd_stage1)[];
+ extern const uint16_t                  PRIV(ucd_stage2)[];
+ extern const uint32_t                  PRIV(ucp_gbtable)[];
+
+--- trunk/src/pcre2_ucd.c	2015/07/17 15:44:51	316
++++ trunk/src/pcre2_ucd.c	2017/02/24 18:25:32	670
+@@ -41,6 +41,20 @@
+ 
+ const char *PRIV(unicode_version) = "8.0.0";
+ 
++/* If the 32-bit library is run in non-32-bit mode, character values
++greater than 0x10ffff may be encountered. For these we set up a
++special record. */
++
++#if PCRE2_CODE_UNIT_WIDTH == 32
++const ucd_record PRIV(dummy_ucd_record)[] = {{
++  ucp_Common,    /* script */
++  ucp_Cn,        /* type unassigned */
++  ucp_gbOther,   /* grapheme break property */
++  0,             /* case set */
++  0,             /* other case */
++  }};
++#endif
++
+ /* When recompiling tables with a new Unicode version, please check the
+ types in this structure definition from pcre2_internal.h (the actual
+ field names will be different):

gnu/packages/patches/python-cython-fix-tests-32bit.patch

@@ -0,0 +1,27 @@
+This fixes a test failure on 32-bit platforms.
+
+Upstream bug URL: https://github.com/cython/cython/issues/1548
+
+Patch copied from upstream source repository:
+
+https://github.com/cython/cython/commit/d92a718a26c9354fbf35f31a17de5c069865a447
+
+From d92a718a26c9354fbf35f31a17de5c069865a447 Mon Sep 17 00:00:00 2001
+From: Robert Bradshaw <robertwb@gmail.com>
+Date: Tue, 24 Jan 2017 16:57:00 -0800
+Subject: [PATCH] Normalize possible L suffix.
+
+---
+ tests/run/cpdef_enums.pyx | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/tests/run/cpdef_enums.pyx b/tests/run/cpdef_enums.pyx
+index 167c762..c264ec5 100644
+--- a/tests/run/cpdef_enums.pyx
++++ b/tests/run/cpdef_enums.pyx
+@@ -93,4 +93,4 @@ def verify_resolution_GH1533():
+     3
+     """
+     THREE = 100
+-    return PyxEnum.THREE
++    return int(PyxEnum.THREE)

gnu/packages/patches/qemu-CVE-2017-2615.patch

@@ -1,52 +0,0 @@
-http://git.qemu.org/?p=qemu.git;a=patch;h=62d4c6bd5263bb8413a06c80144fc678df6dfb64
-this patch is from qemu-git.
-
-
-From 62d4c6bd5263bb8413a06c80144fc678df6dfb64 Mon Sep 17 00:00:00 2001
-From: Li Qiang <liqiang6-s@360.cn>
-Date: Wed, 1 Feb 2017 09:35:01 +0100
-Subject: [PATCH] cirrus: fix oob access issue (CVE-2017-2615)
-
-When doing bitblt copy in backward mode, we should minus the
-blt width first just like the adding in the forward mode. This
-can avoid the oob access of the front of vga's vram.
-
-Signed-off-by: Li Qiang <liqiang6-s@360.cn>
-
-{ kraxel: with backward blits (negative pitch) addr is the topmost
-          address, so check it as-is against vram size ]
-
-Cc: qemu-stable@nongnu.org
-Cc: P J P <ppandit@redhat.com>
-Cc: Laszlo Ersek <lersek@redhat.com>
-Cc: Paolo Bonzini <pbonzini@redhat.com>
-Cc: Wolfgang Bumiller <w.bumiller@proxmox.com>
-Fixes: d3532a0db02296e687711b8cdc7791924efccea0 (CVE-2014-8106)
-Signed-off-by: Gerd Hoffmann <kraxel@redhat.com>
-Message-id: 1485938101-26602-1-git-send-email-kraxel@redhat.com
-Reviewed-by: Laszlo Ersek <lersek@redhat.com>
----
- hw/display/cirrus_vga.c | 7 +++----
- 1 file changed, 3 insertions(+), 4 deletions(-)
-
-diff --git a/hw/display/cirrus_vga.c b/hw/display/cirrus_vga.c
-index 7db6409dc5..16f27e8ac5 100644
---- a/hw/display/cirrus_vga.c
-+++ b/hw/display/cirrus_vga.c
-@@ -274,10 +274,9 @@ static bool blit_region_is_unsafe(struct CirrusVGAState *s,
- {
-     if (pitch < 0) {
-         int64_t min = addr
--            + ((int64_t)s->cirrus_blt_height-1) * pitch;
--        int32_t max = addr
--            + s->cirrus_blt_width;
--        if (min < 0 || max > s->vga.vram_size) {
-+            + ((int64_t)s->cirrus_blt_height - 1) * pitch
-+            - s->cirrus_blt_width;
-+        if (min < -1 || addr >= s->vga.vram_size) {
-             return true;
-         }
-     } else {
--- 
-2.11.0
-

gnu/packages/patches/qemu-CVE-2017-2620.patch

@@ -1,134 +0,0 @@
-Fix CVE-2017-2620:
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-2620
-https://lists.gnu.org/archive/html/qemu-devel/2017-02/msg04700.html
-
-Both patches copied from upstream source repository:
-
-Fixes CVE-2017-2620:
-http://git.qemu-project.org/?p=qemu.git;a=commit;h=92f2b88cea48c6aeba8de568a45f2ed958f3c298
-
-The CVE-2017-2620 bug-fix depends on this earlier patch:
-http://git.qemu-project.org/?p=qemu.git;a=commit;h=913a87885f589d263e682c2eb6637c6e14538061
-
-From 92f2b88cea48c6aeba8de568a45f2ed958f3c298 Mon Sep 17 00:00:00 2001
-From: Gerd Hoffmann <kraxel@redhat.com>
-Date: Wed, 8 Feb 2017 11:18:36 +0100
-Subject: [PATCH] cirrus: add blit_is_unsafe call to cirrus_bitblt_cputovideo
- (CVE-2017-2620)
-
-CIRRUS_BLTMODE_MEMSYSSRC blits do NOT check blit destination
-and blit width, at all.  Oops.  Fix it.
-
-Security impact: high.
-
-The missing blit destination check allows to write to host memory.
-Basically same as CVE-2014-8106 for the other blit variants.
-
-Cc: qemu-stable@nongnu.org
-Signed-off-by: Gerd Hoffmann <kraxel@redhat.com>
----
- hw/display/cirrus_vga.c | 8 ++++++++
- 1 file changed, 8 insertions(+)
-
-diff --git a/hw/display/cirrus_vga.c b/hw/display/cirrus_vga.c
-index 1deb52070a..b9e7cb1df1 100644
---- a/hw/display/cirrus_vga.c
-+++ b/hw/display/cirrus_vga.c
-@@ -900,6 +900,10 @@ static int cirrus_bitblt_cputovideo(CirrusVGAState * s)
- {
-     int w;
- 
-+    if (blit_is_unsafe(s, true)) {
-+        return 0;
-+    }
-+
-     s->cirrus_blt_mode &= ~CIRRUS_BLTMODE_MEMSYSSRC;
-     s->cirrus_srcptr = &s->cirrus_bltbuf[0];
-     s->cirrus_srcptr_end = &s->cirrus_bltbuf[0];
-@@ -925,6 +929,10 @@ static int cirrus_bitblt_cputovideo(CirrusVGAState * s)
- 	}
-         s->cirrus_srccounter = s->cirrus_blt_srcpitch * s->cirrus_blt_height;
-     }
-+
-+    /* the blit_is_unsafe call above should catch this */
-+    assert(s->cirrus_blt_srcpitch <= CIRRUS_BLTBUFSIZE);
-+
-     s->cirrus_srcptr = s->cirrus_bltbuf;
-     s->cirrus_srcptr_end = s->cirrus_bltbuf + s->cirrus_blt_srcpitch;
-     cirrus_update_memory_access(s);
--- 
-2.12.0
-
-From 913a87885f589d263e682c2eb6637c6e14538061 Mon Sep 17 00:00:00 2001
-From: Bruce Rogers <brogers@suse.com>
-Date: Mon, 9 Jan 2017 13:35:20 -0700
-Subject: [PATCH] display: cirrus: ignore source pitch value as needed in
- blit_is_unsafe
-
-Commit 4299b90 added a check which is too broad, given that the source
-pitch value is not required to be initialized for solid fill operations.
-This patch refines the blit_is_unsafe() check to ignore source pitch in
-that case. After applying the above commit as a security patch, we
-noticed the SLES 11 SP4 guest gui failed to initialize properly.
-
-Signed-off-by: Bruce Rogers <brogers@suse.com>
-Message-id: 20170109203520.5619-1-brogers@suse.com
-Signed-off-by: Gerd Hoffmann <kraxel@redhat.com>
----
- hw/display/cirrus_vga.c | 11 +++++++----
- 1 file changed, 7 insertions(+), 4 deletions(-)
-
-diff --git a/hw/display/cirrus_vga.c b/hw/display/cirrus_vga.c
-index bdb092ee9d..379910db2d 100644
---- a/hw/display/cirrus_vga.c
-+++ b/hw/display/cirrus_vga.c
-@@ -294,7 +294,7 @@ static bool blit_region_is_unsafe(struct CirrusVGAState *s,
-     return false;
- }
- 
--static bool blit_is_unsafe(struct CirrusVGAState *s)
-+static bool blit_is_unsafe(struct CirrusVGAState *s, bool dst_only)
- {
-     /* should be the case, see cirrus_bitblt_start */
-     assert(s->cirrus_blt_width > 0);
-@@ -308,6 +308,9 @@ static bool blit_is_unsafe(struct CirrusVGAState *s)
-                               s->cirrus_blt_dstaddr & s->cirrus_addr_mask)) {
-         return true;
-     }
-+    if (dst_only) {
-+        return false;
-+    }
-     if (blit_region_is_unsafe(s, s->cirrus_blt_srcpitch,
-                               s->cirrus_blt_srcaddr & s->cirrus_addr_mask)) {
-         return true;
-@@ -673,7 +676,7 @@ static int cirrus_bitblt_common_patterncopy(CirrusVGAState * s,
- 
-     dst = s->vga.vram_ptr + (s->cirrus_blt_dstaddr & s->cirrus_addr_mask);
- 
--    if (blit_is_unsafe(s))
-+    if (blit_is_unsafe(s, false))
-         return 0;
- 
-     (*s->cirrus_rop) (s, dst, src,
-@@ -691,7 +694,7 @@ static int cirrus_bitblt_solidfill(CirrusVGAState *s, int blt_rop)
- {
-     cirrus_fill_t rop_func;
- 
--    if (blit_is_unsafe(s)) {
-+    if (blit_is_unsafe(s, true)) {
-         return 0;
-     }
-     rop_func = cirrus_fill[rop_to_index[blt_rop]][s->cirrus_blt_pixelwidth - 1];
-@@ -795,7 +798,7 @@ static int cirrus_do_copy(CirrusVGAState *s, int dst, int src, int w, int h)
- 
- static int cirrus_bitblt_videotovideo_copy(CirrusVGAState * s)
- {
--    if (blit_is_unsafe(s))
-+    if (blit_is_unsafe(s, false))
-         return 0;
- 
-     return cirrus_do_copy(s, s->cirrus_blt_dstaddr - s->vga.start_addr,
--- 
-2.12.0
-

gnu/packages/patches/qemu-CVE-2017-2630.patch

@@ -1,47 +0,0 @@
-Fix CVE-2017-2630:
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-2630
-https://lists.gnu.org/archive/html/qemu-devel/2017-02/msg01246.html
-
-Patch copied from upstream source repository:
-
-http://git.qemu-project.org/?p=qemu.git;a=commit;h=2563c9c6b8670400c48e562034b321a7cf3d9a85
-
-From 2563c9c6b8670400c48e562034b321a7cf3d9a85 Mon Sep 17 00:00:00 2001
-From: Vladimir Sementsov-Ogievskiy <vsementsov@virtuozzo.com>
-Date: Tue, 7 Mar 2017 09:16:27 -0600
-Subject: [PATCH] nbd/client: fix drop_sync [CVE-2017-2630]
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-Comparison symbol is misused. It may lead to memory corruption.
-Introduced in commit 7d3123e.
-
-Signed-off-by: Vladimir Sementsov-Ogievskiy <vsementsov@virtuozzo.com>
-Message-Id: <20170203154757.36140-6-vsementsov@virtuozzo.com>
-[eblake: add CVE details, update conditional]
-Signed-off-by: Eric Blake <eblake@redhat.com>
-Reviewed-by: Marc-André Lureau <marcandre.lureau@redhat.com>
-Message-Id: <20170307151627.27212-1-eblake@redhat.com>
-Signed-off-by: Paolo Bonzini <pbonzini@redhat.com>
----
- nbd/client.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/nbd/client.c b/nbd/client.c
-index 5c9dee37fa..3dc2564cd0 100644
---- a/nbd/client.c
-+++ b/nbd/client.c
-@@ -94,7 +94,7 @@ static ssize_t drop_sync(QIOChannel *ioc, size_t size)
-     char small[1024];
-     char *buffer;
- 
--    buffer = sizeof(small) < size ? small : g_malloc(MIN(65536, size));
-+    buffer = sizeof(small) >= size ? small : g_malloc(MIN(65536, size));
-     while (size > 0) {
-         ssize_t count = read_sync(ioc, buffer, MIN(65536, size));
- 
--- 
-2.12.0
-

gnu/packages/patches/qemu-CVE-2017-5667.patch

@@ -1,46 +0,0 @@
-Fix CVE-2017-5667 (sdhci OOB access during multi block SDMA transfer):
-
-http://seclists.org/oss-sec/2017/q1/243
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-5667
-
-Patch copied from upstream source repository:
-
-http://git.qemu-project.org/?p=qemu.git;a=commitdiff;h=42922105beb14c2fc58185ea022b9f72fb5465e9
-
-From 42922105beb14c2fc58185ea022b9f72fb5465e9 Mon Sep 17 00:00:00 2001
-From: Prasad J Pandit <pjp@fedoraproject.org>
-Date: Tue, 7 Feb 2017 18:29:59 +0000
-Subject: [PATCH] sd: sdhci: check data length during dma_memory_read
-
-While doing multi block SDMA transfer in routine
-'sdhci_sdma_transfer_multi_blocks', the 's->fifo_buffer' starting
-index 'begin' and data length 's->data_count' could end up to be same.
-This could lead to an OOB access issue. Correct transfer data length
-to avoid it.
-
-Cc: qemu-stable@nongnu.org
-Reported-by: Jiang Xin <jiangxin1@huawei.com>
-Signed-off-by: Prasad J Pandit <pjp@fedoraproject.org>
-Reviewed-by: Peter Maydell <peter.maydell@linaro.org>
-Message-id: 20170130064736.9236-1-ppandit@redhat.com
-Signed-off-by: Peter Maydell <peter.maydell@linaro.org>
----
- hw/sd/sdhci.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/hw/sd/sdhci.c b/hw/sd/sdhci.c
-index 01fbf228be..5bd5ab6319 100644
---- a/hw/sd/sdhci.c
-+++ b/hw/sd/sdhci.c
-@@ -536,7 +536,7 @@ static void sdhci_sdma_transfer_multi_blocks(SDHCIState *s)
-                 boundary_count -= block_size - begin;
-             }
-             dma_memory_read(&address_space_memory, s->sdmasysad,
--                            &s->fifo_buffer[begin], s->data_count);
-+                            &s->fifo_buffer[begin], s->data_count - begin);
-             s->sdmasysad += s->data_count - begin;
-             if (s->data_count == block_size) {
-                 for (n = 0; n < block_size; n++) {
--- 
-2.11.1
-

gnu/packages/patches/qemu-CVE-2017-5931.patch

@@ -1,55 +0,0 @@
-Fix CVE-2017-5931 (integer overflow in handling virtio-crypto requests):
-
-http://seclists.org/oss-sec/2017/q1/337
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-5931
-
-Patch copied from upstream source repository:
-
-http://git.qemu-project.org/?p=qemu.git;a=commit;h=a08aaff811fb194950f79711d2afe5a892ae03a4
-
-From a08aaff811fb194950f79711d2afe5a892ae03a4 Mon Sep 17 00:00:00 2001
-From: Gonglei <arei.gonglei@huawei.com>
-Date: Tue, 3 Jan 2017 14:50:03 +0800
-Subject: [PATCH] virtio-crypto: fix possible integer and heap overflow
-
-Because the 'size_t' type is 4 bytes in 32-bit platform, which
-is the same with 'int'. It's easy to make 'max_len' to zero when
-integer overflow and then cause heap overflow if 'max_len' is zero.
-
-Using uint_64 instead of size_t to avoid the integer overflow.
-
-Cc: qemu-stable@nongnu.org
-Reported-by: Li Qiang <liqiang6-s@360.cn>
-Signed-off-by: Gonglei <arei.gonglei@huawei.com>
-Tested-by: Li Qiang <liqiang6-s@360.cn>
-Reviewed-by: Michael S. Tsirkin <mst@redhat.com>
-Signed-off-by: Michael S. Tsirkin <mst@redhat.com>
----
- hw/virtio/virtio-crypto.c | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/hw/virtio/virtio-crypto.c b/hw/virtio/virtio-crypto.c
-index 2f2467e859..c23e1ad458 100644
---- a/hw/virtio/virtio-crypto.c
-+++ b/hw/virtio/virtio-crypto.c
-@@ -416,7 +416,7 @@ virtio_crypto_sym_op_helper(VirtIODevice *vdev,
-     uint32_t hash_start_src_offset = 0, len_to_hash = 0;
-     uint32_t cipher_start_src_offset = 0, len_to_cipher = 0;
- 
--    size_t max_len, curr_size = 0;
-+    uint64_t max_len, curr_size = 0;
-     size_t s;
- 
-     /* Plain cipher */
-@@ -441,7 +441,7 @@ virtio_crypto_sym_op_helper(VirtIODevice *vdev,
-         return NULL;
-     }
- 
--    max_len = iv_len + aad_len + src_len + dst_len + hash_result_len;
-+    max_len = (uint64_t)iv_len + aad_len + src_len + dst_len + hash_result_len;
-     if (unlikely(max_len > vcrypto->conf.max_size)) {
-         virtio_error(vdev, "virtio-crypto too big length");
-         return NULL;
--- 
-2.11.1
-

gnu/packages/patches/screen-fix-info-syntax-error.patch

@@ -0,0 +1,47 @@
+Fix errors when building the info manual:
+
+[...]
+./screen.texinfo:5799: unknown command `suse'
+./screen.texinfo:5800: unknown command `deuxchevaux'
+make[2]: *** [Makefile:31: screen.info] Error 1
+[...]
+
+Patch copied from upstream source repository:
+
+http://git.savannah.gnu.org/cgit/screen.git/commit/?id=a7d2f9e6ecfa794dd0bd3dbeaf6780c88a6f3152
+
+From a7d2f9e6ecfa794dd0bd3dbeaf6780c88a6f3152 Mon Sep 17 00:00:00 2001
+From: Andreas Stieger <astieger@suse.com>
+Date: Tue, 28 Feb 2017 19:23:01 +0100
+Subject: [PATCH] fix texinfo syntax errors
+
+thanks to Andreas Stieger <astieger@suse.com>
+---
+ src/doc/screen.texinfo | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/src/doc/screen.texinfo b/src/doc/screen.texinfo
+index bc4cbae..aadad33 100644
+--- a/doc/screen.texinfo
++++ b/doc/screen.texinfo
+@@ -5795,7 +5795,7 @@ and Alexander Naumov <alexander_naumov@@opensuse.org>.
+ Contributors @*
+ ============
+ 
+-@example
++@verbatim
+      Thomas Renninger <treen@suse.com>,
+      Axel Beckert <abe@deuxchevaux.org>,
+      Ken Beal <kbeal@@amber.ssd.csd.harris.com>,
+@@ -5826,7 +5826,7 @@ Contributors @*
+      Jason Merrill <jason@@jarthur.Claremont.EDU>,
+      Johannes Zellner <johannes@@zellner.org>,
+      Pablo Averbuj <pablo@@averbuj.com>.
+-@end example
++@end verbatim
+ 
+ @noindent
+ Version @*
+-- 
+cgit v1.0-41-gc330
+

gnu/packages/patches/teeworlds-use-latest-wavpack.patch

@@ -0,0 +1,84 @@
+Downloaded from https://anonscm.debian.org/cgit/pkg-games/teeworlds.git/plain/debian/patches/new-wavpack.patch.
+
+This patch lets us build teeworlds with wavpack 5.1.0.
+
+--- a/src/engine/client/sound.cpp
++++ b/src/engine/client/sound.cpp
+@@ -328,17 +328,14 @@ void CSound::RateConvert(int SampleID)
+ 	pSample->m_NumFrames = NumFrames;
+ }
+ 
+-int CSound::ReadData(void *pBuffer, int Size)
+-{
+-	return io_read(ms_File, pBuffer, Size);
+-}
+-
+ int CSound::LoadWV(const char *pFilename)
+ {
+ 	CSample *pSample;
+ 	int SampleID = -1;
+ 	char aError[100];
+ 	WavpackContext *pContext;
++	char aWholePath[1024];
++	IOHANDLE File;
+ 
+ 	// don't waste memory on sound when we are stress testing
+ 	if(g_Config.m_DbgStress)
+@@ -351,19 +348,23 @@ int CSound::LoadWV(const char *pFilename
+ 	if(!m_pStorage)
+ 		return -1;
+ 
+-	ms_File = m_pStorage->OpenFile(pFilename, IOFLAG_READ, IStorage::TYPE_ALL);
+-	if(!ms_File)
++	File = m_pStorage->OpenFile(pFilename, IOFLAG_READ, IStorage::TYPE_ALL, aWholePath, sizeof(aWholePath));
++	if(!File)
+ 	{
+ 		dbg_msg("sound/wv", "failed to open file. filename='%s'", pFilename);
+ 		return -1;
+ 	}
++	else
++	{
++		io_close(File);
++	}
+ 
+ 	SampleID = AllocID();
+ 	if(SampleID < 0)
+ 		return -1;
+ 	pSample = &m_aSamples[SampleID];
+ 
+-	pContext = WavpackOpenFileInput(ReadData, aError);
++	pContext = WavpackOpenFileInput(aWholePath, aError, OPEN_2CH_MAX, 0);
+ 	if (pContext)
+ 	{
+ 		int m_aSamples = WavpackGetNumSamples(pContext);
+@@ -419,9 +420,6 @@ int CSound::LoadWV(const char *pFilename
+ 		dbg_msg("sound/wv", "failed to open %s: %s", pFilename, aError);
+ 	}
+ 
+-	io_close(ms_File);
+-	ms_File = NULL;
+-
+ 	if(g_Config.m_Debug)
+ 		dbg_msg("sound/wv", "loaded %s", pFilename);
+ 
+@@ -527,7 +525,5 @@ void CSound::StopAll()
+ 	lock_unlock(m_SoundLock);
+ }
+ 
+-IOHANDLE CSound::ms_File = 0;
+-
+ IEngineSound *CreateEngineSound() { return new CSound; }
+ 
+--- a/src/engine/client/sound.h
++++ b/src/engine/client/sound.h
+@@ -21,10 +21,6 @@ public:
+ 
+ 	static void RateConvert(int SampleID);
+ 
+-	// TODO: Refactor: clean this mess up
+-	static IOHANDLE ms_File;
+-	static int ReadData(void *pBuffer, int Size);
+-
+ 	virtual bool IsSoundEnabled() { return m_SoundEnabled != 0; }
+ 
+ 	virtual int LoadWV(const char *pFilename);

gnu/packages/pcre.scm

@@ -4,6 +4,7 @@
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2017 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -33,6 +34,7 @@
   (package
    (name "pcre")
    (version "8.40")
+   (replacement pcre/fixed)
    (source (origin
             (method url-fetch)
             (uri (list
@@ -70,6 +72,14 @@ POSIX regular expression API.")
    (license license:bsd-3)
    (home-page "http://www.pcre.org/")))
 
+(define pcre/fixed
+  (package
+    (inherit pcre)
+    (replacement #f)
+    (source (origin
+              (inherit (package-source pcre))
+              (patches (search-patches "pcre-CVE-2017-7186.patch"))))))
+
 (define-public pcre2
   (package
     (name "pcre2")
@@ -81,7 +91,8 @@ POSIX regular expression API.")
 
               (sha256
                (base32
-                "0vn5g0mkkp99mmzpissa06hpyj6pk9s4mlwbjqrjvw3ihy8rpiyz"))))
+                "0vn5g0mkkp99mmzpissa06hpyj6pk9s4mlwbjqrjvw3ihy8rpiyz"))
+              (patches (search-patches "pcre2-CVE-2017-7186.patch"))))
    (build-system gnu-build-system)
    (inputs `(("bzip2" ,bzip2)
              ("readline" ,readline)

gnu/packages/pdf.scm

@@ -184,6 +184,53 @@
 Poppler PDF rendering library.")
     (license license:lgpl2.1+)))
 
+(define-public python-poppler-qt5
+  (package
+    (name "python-poppler-qt5")
+    (version "0.24.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "python-poppler-qt5" version))
+        (sha256
+         (base32
+          "0l69llw1fzwz8y90q0qp9q5pifbrqjjbwii7di54dwghw5fc6w1r"))))
+    (build-system python-build-system)
+    (arguments
+     `(;; There are no tests.  The check phase just causes a rebuild.
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'build
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "setup.py"
+               ;; This check always fails, so disable it.
+               (("if not check_qtxml\\(\\)")
+                "if True")
+               ;; Enable C++11, which is needed because of Qt5.
+               (("\\*\\*ext_args" line)
+                (string-append "extra_compile_args=['-std=gnu++11'], " line)))
+             ;; We need to pass an extra flag here.  This cannot be in
+             ;; configure-flags because it should not be passed for the
+             ;; installation phase.
+             ((@@ (guix build python-build-system) call-setuppy)
+              "build_ext" (list (string-append "--pyqt-sip-dir="
+                                               (assoc-ref inputs "python-pyqt")
+                                               "/share/sip")) #t))))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("python-sip" ,python-sip)
+       ("python-pyqt" ,python-pyqt)
+       ("poppler-qt5" ,poppler-qt5)
+       ("qtbase" ,qtbase)))
+    (home-page "https://pypi.python.org/pypi/python-poppler-qt5")
+    (synopsis "Python bindings for Poppler-Qt5")
+    (description
+     "This package provides Python bindings for the Qt5 interface of the
+Poppler PDF rendering library.")
+    (license license:lgpl2.1+)))
+
 (define-public libharu
   (package
    (name "libharu")

gnu/packages/php.scm

@@ -53,7 +53,7 @@
 (define-public php
   (package
     (name "php")
-    (version "7.1.3")
+    (version "7.1.4")
     (home-page "https://secure.php.net/")
     (source (origin
               (method url-fetch)
@@ -61,7 +61,7 @@
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1c0brdq5aqh4i127pq1g904dfb6klz2gbg9gjvykg3kp6hk7r274"))
+                "02rh1lcfj2hakyls73gwn6w00yblnfh4883w13gn7sgkmn346lbi"))
               (modules '((guix build utils)))
               (snippet
                '(with-directory-excursion "ext"

gnu/packages/pulseaudio.scm

@@ -4,6 +4,7 @@
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
+;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;

gnu/packages/python.scm

@@ -529,14 +529,14 @@ John the Ripper).")
 (define-public python-paramiko
   (package
     (name "python-paramiko")
-    (version "1.16.0")
+    (version "1.17.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "paramiko" version))
        (sha256
         (base32
-         "14k8z7ndc3zk5xivnm4d8lncchx475ll5izpf8vmfbq7rp9yp5rj"))))
+         "1rs2qcmskcmq66q6g5al08wa41l9am0fad5r719m8wf91msyylqw"))))
     (build-system python-build-system)
     (arguments
      '(;; FIXME: One test fails with "EOFError not raised by connect".
@@ -3401,14 +3401,15 @@ is designed to have a low barrier to entry.")
 (define-public python-cython
   (package
     (name "python-cython")
-    (version "0.24.1")
+    (version "0.25.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Cython" version))
+       (patches (search-patches "python-cython-fix-tests-32bit.patch"))
        (sha256
         (base32
-         "1fg7fmpvfcq9md4ncyqnnylyjy4z3ksdrshzis95g1sh03d8z044"))))
+         "01h3lrf6d98j07iakifi81qjszh6faa37ibx7ylva1vsqbwx2hgi"))))
     (build-system python-build-system)
     ;; we need the full python package and not just the python-wrapper
     ;; because we need libpython3.3m.so
@@ -4905,7 +4906,7 @@ cluster without needing to write any wrapper code yourself.")
          (replace 'check (lambda _ (zero? (system* "nosetests" "-v")))))))
     (native-inputs
      `(("python-nose" ,python-nose)
-       ("python-pytest" ,python-pytest)
+       ("python-pytest" ,python-pytest-3.0)
        ("man-db" ,man-db)
        ("which" ,which)))
     (propagated-inputs
@@ -13947,3 +13948,20 @@ recognize TestCases.")
 
 (define-public python2-mando
   (package-with-python2 python-mando))
+
+(define-public python-mando-0.3.1
+  ;; python-radon (version 1.5.0) has a requirement
+  ;; for mando<0.4,>=0.3
+  (package
+    (inherit python-mando)
+    (name "python-mando")
+    (version "0.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/rubik/mando/archive/v"
+                           version
+                           ".tar.gz"))
+       (sha256
+        (base32
+         "17jlkdpqw22z1nyml5ybslilqkzmnk0dxxjml8bfghav1l5hbwd2"))))))

gnu/packages/qemu.scm

@@ -69,27 +69,23 @@
 (define-public qemu
   (package
     (name "qemu")
-    (version "2.8.0")
+    (version "2.8.1")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://wiki.qemu-project.org/download/qemu-"
-                                 version ".tar.bz2"))
+                                 version ".tar.xz"))
              (sha256
               (base32
-               "0qjy3rcrn89n42y5iz60kgr0rrl29hpnj8mq2yvbc1wrcizmvzfs"))
+               "0h342v4n44kh89yyfas4iazvhhsy5m5qk94vsjqpz5zpq1i2ykad"))
              (patches (search-patches "qemu-CVE-2016-10155.patch"
-                                      "qemu-CVE-2017-2615.patch"
-                                      "qemu-CVE-2017-2620.patch"
-                                      "qemu-CVE-2017-2630.patch"
                                       "qemu-CVE-2017-5525.patch"
                                       "qemu-CVE-2017-5526.patch"
                                       "qemu-CVE-2017-5552.patch"
                                       "qemu-CVE-2017-5578.patch"
                                       "qemu-CVE-2017-5579.patch"
-                                      "qemu-CVE-2017-5667.patch"
                                       "qemu-CVE-2017-5856.patch"
                                       "qemu-CVE-2017-5898.patch"
-                                      "qemu-CVE-2017-5931.patch"))))
+                                      ))))
     (build-system gnu-build-system)
     (arguments
      '(;; Running tests in parallel can occasionally lead to failures, like:

gnu/packages/ratpoison.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
+;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -43,14 +44,14 @@
 (define-public ratpoison
   (package
     (name "ratpoison")
-    (version "1.4.8")
+    (version "1.4.9")
     (source
      (origin (method url-fetch)
              (uri (string-append "mirror://savannah/ratpoison/ratpoison-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "1w502z55vv7zs45l80nsllqh9fvfwjfdfi11xy1qikhzdmirains"))
+               "1wfir1gvh5h7izgvx2kd1pr2k7wlncd33zq7qi9s9k2y0aza93yr"))
              (patches (search-patches "ratpoison-shell.patch"))))
     (build-system gnu-build-system)
     (arguments
@@ -70,7 +71,7 @@
        ("freetype" ,freetype)
        ("libXft" ,libxft)
        ("libXi" ,libxi)
-       ("libxinerama" ,libxinerama)
+       ("libxrandr" ,libxrandr)
        ("libXpm" ,libxpm)
        ("libXt" ,libxt)
        ("libXtst" ,libxtst)

gnu/packages/rdf.scm

@@ -233,15 +233,14 @@ and triple stores.")
 (define-public serd
   (package
     (name "serd")
-    (version "0.22.0")
+    (version "0.26.0")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://download.drobilla.net/serd-"
-                                 version
+                                 version ".tar.bz2"))
-                                 ".tar.bz2"))
              (sha256
               (base32
-               "1lmgca2s6r7ysakcld2lrj06bgn0pr45c51b47k3apxpnj3h40vv"))))
+               "164j43am4hka2vbzw4n52zy7rafgp6kmkgbcbvap368az644mr73"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f ; no check target
@@ -267,15 +266,14 @@ ideal (e.g. in LV2 implementations or embedded applications).")
 (define-public sord
   (package
     (name "sord")
-    (version "0.14.0")
+    (version "0.16.0")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://download.drobilla.net/sord-"
-                                 version
+                                 version ".tar.bz2"))
-                                 ".tar.bz2"))
              (sha256
               (base32
-               "16piw1s3l95cf9x3rdcplp9l52k2lxq8drwg2q50ygm4avndhmkn"))))
+               "0nh3i867g9z4kdlnk82cg2kcw8r02qgifxvkycvzb4vfjv4v4g4x"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f ; no check target

gnu/packages/regex.scm

@@ -28,7 +28,7 @@
 (define-public re2
    (package
      (name "re2")
-     (version "2017-03-01")
+     (version "2017-04-01")
      (source (origin
                (method url-fetch)
                (uri
@@ -38,7 +38,7 @@
                (file-name (string-append name "-" version ".tar.gz"))
                (sha256
                 (base32
-                 "1s3kdcrz2mwi30k6pz9jkv5vk8b704bz65xgcr67wbn2pn3hpnqr"))))
+                 "14i9pf9ap8h48j1584ifsq7c7a884cr1s4r7zvpcb9x1xr9232wh"))))
      (build-system gnu-build-system)
      (arguments
       `(#:test-target "test"

gnu/packages/rust.scm

@@ -44,7 +44,7 @@
   #:use-module (srfi srfi-26))
 
 ;; Should be one less than the current released version.
-(define %rust-bootstrap-binaries-version "1.14.0")
+(define %rust-bootstrap-binaries-version "1.15.0")
 
 (define %rust-bootstrap-binaries
   (origin
@@ -55,7 +55,7 @@
           "-i686-unknown-linux-gnu.tar.gz"))
     (sha256
      (base32
-      "0h384prpabcl08mxs1bilyb0dbk0knpdylcnz4b84ij4idr7ap4d"))))
+      "0wmkfx8pxmkkw021mrq9s3xhra8f0daqdl6j56pxyn4w39i0rzrw"))))
 
 (define (increment-rust-version rust-version major patch)
   (match (string-split rust-version #\.)
@@ -205,7 +205,7 @@ rustc-bootstrap and cargo-bootstrap packages.")
                     "rustc-" version "-src.tar.gz"))
               (sha256
                (base32
-                "0wvn8m1nfg664b95qrdpfh72q1a6ir09rqkrnlzbkay2r7xf8mgn"))))
+                "1d78jq7mc34n265by68amr9r4nzbiqrilfbwh7gx56ydn4gb6rpr"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("cmake" ,cmake)
@@ -226,7 +226,22 @@ rustc-bootstrap and cargo-bootstrap packages.")
            (lambda _
              (substitute* "configure"
                (("/usr/bin/env") (which "env")) ; Detect target CPU correctly.
-               (("probe_need CFG_CURL curl") "")) ; Avoid curl as a build dependency.
+               (("probe_need CFG_CURL curl") "") ; Avoid curl build dependency.
+               ;; Newer LLVM has a NVPTX (NVIDIA) backend which the Rust
+               ;; Makefiles don't know about, causing a linker failure
+               ;; if we don't intervene.
+               ;; Therefore, we add NVPTX here.
+               ;; See <https://github.com/rust-lang/rust/issues/40698>.
+               ;; For the next release, we will have to use rustbuild.
+               ;; Right now, rustbuild doesn't work yet.
+               (("-DLLVM_TARGETS_TO_BUILD='")
+                "-DLLVM_TARGETS_TO_BUILD='NVPTX;")) ; Make LLVM >= 3.8.1 work.
+             (substitute* "src/tools/compiletest/src/util.rs"
+               (("(\"amd64\", \"x86_64\"),") "(\"amd64\", \"x86_64\"),
+(\"nvptx\", \"nvptx\"),")) ; Make LLVM >= 3.8.1 work.
+             (substitute* "mk/main.mk"
+               (("LLVM_OPTIONAL_COMPONENTS=")
+                "LLVM_OPTIONAL_COMPONENTS=nvptx ")) ; Make LLVM >= 3.8.1 work.
              #t))
          (add-after 'unpack 'set-env
            (lambda _
@@ -263,7 +278,7 @@ rustc-bootstrap and cargo-bootstrap packages.")
                             "--release-channel=stable"
                             "--enable-rpath"
                             "--enable-local-rust"
-                            "--disable-rustbuild" ; use Makefiles
+                            "--disable-rustbuild" ; rustbuild doesn't work yet.
                             "--disable-manage-submodules")))
                ;; Rust uses a custom configure script (no autoconf).
                (zero? (apply system* "./configure" flags)))))
@@ -297,7 +312,7 @@ safety and thread safety guarantees.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "194i06y9nql0p93gahh0vm4qwv6c1kpd9rprpf22w5gav9lpcyjz"))))
+                "1y0zy8gk1ly0wh57y78fisk7cdd92qk0x7z664f6l7lzl2krqs7w"))))
     (build-system cargo-build-system)
     (propagated-inputs
      `(("cmake" ,cmake)
@@ -313,10 +328,10 @@ safety and thread safety guarantees.")
      `(("rust-openssl"
         ,(origin
            (method url-fetch)
-           (uri (crate-uri "openssl" "0.9.1"))
+           (uri (crate-uri "openssl" "0.9.6"))
            (sha256
             (base32
-             "1m2mhiar87qnw4gxci286q9g85ljafbc41salbj2hmcgh8aagchy"))))
+             "0g28g692gby6izp9qmnwnyxyhf9b0870yhd500p18j9l69lxl00c"))))
        ("rust-strsim"
         ,(origin
            (method url-fetch)
@@ -411,17 +426,17 @@ safety and thread safety guarantees.")
        ("rust-libssh2-sys"
         ,(origin
            (method url-fetch)
-           (uri (crate-uri "libssh2-sys" "0.2.4"))
+           (uri (crate-uri "libssh2-sys" "0.2.5"))
            (sha256
             (base32
-             "1pmmh0hcx14856wg9bp740yf618qfl2765vhf67sfs5lmf39227d"))))
+             "0d2r36hrh9vc1821r0v4kywv30svpf37d31calwql69fbij3bqci"))))
        ("rust-libz-sys"
         ,(origin
            (method url-fetch)
-           (uri (crate-uri "libz-sys" "1.0.10"))
+           (uri (crate-uri "libz-sys" "1.0.13"))
            (sha256
             (base32
-             "1rl85x045sk5d345hgcahx99plpbdg2a3bx5vjfxig30qah74p4h"))))
+             "034pgvxzgsv37iafgs0lmvd1ifm0bg0zm1xcsn9x71nn8lm93vp5"))))
        ("rust-curl-sys"
         ,(origin
            (method url-fetch)
@@ -429,13 +444,27 @@ safety and thread safety guarantees.")
            (sha256
             (base32
              "0fi8kjz3f8m8vfazycs3ddm0h6j3x78hw78gwbvybx71129192i1"))))
+       ("rust-error-chain"
+        ,(origin
+           (method url-fetch)
+           (uri (crate-uri "error-chain" "0.7.2"))
+           (sha256
+            (base32
+             "03qjh6l2a9fkiyg0428p7q3dcpi47cbmrqf9zmlymkg43v3v731i"))))
+       ("rust-metadeps"
+        ,(origin
+           (method url-fetch)
+           (uri (crate-uri "metadeps" "1.1.1"))
+           (sha256
+            (base32
+             "0l818461bslb7nrs7r1amkqv45n53fcp5sabyqipwx0xxbkzz7w2"))))
        ("rust-openssl-sys"
         ,(origin
            (method url-fetch)
-           (uri (crate-uri "openssl-sys" "0.9.1"))
+           (uri (crate-uri "openssl-sys" "0.9.6"))
            (sha256
             (base32
-             "1sdhgalfm2zdqf144xhdnxdha7ifjgsfbmlrqbx0j9f3mh4gpscm"))))
+             "1hzpyf9z8xg1yn5r9g17bl5j20nifd6s2zp10xh90v7m0sd2yj5i"))))
        ("rust-fs2"
         ,(origin
            (method url-fetch)
@@ -635,10 +664,10 @@ safety and thread safety guarantees.")
        ("rust-libgit2-sys"
         ,(origin
            (method url-fetch)
-           (uri (crate-uri "libgit2-sys" "0.6.5"))
+           (uri (crate-uri "libgit2-sys" "0.6.6"))
            (sha256
             (base32
-             "0yl80n12ih4jh1halpbj3zqlqvw5zxdr6m6xdcvdz67svjy50bjh"))))
+             "074h9q4p60xh6canb0sj4vrc801wqv6p53l9lp0q724bkwzf7967"))))
        ("rust-env_logger"
         ,(origin
            (method url-fetch)
@@ -785,7 +814,14 @@ safety and thread safety guarantees.")
            (uri (crate-uri "num-complex" "0.1.35"))
            (sha256
             (base32
-             "0bzrjfppnnzf9vmkpklhp2dw9sb1lqzydb8r6k83z76i9l2qxizh"))))))
+             "0bzrjfppnnzf9vmkpklhp2dw9sb1lqzydb8r6k83z76i9l2qxizh"))))
+       ("rust-shell-escape"
+        ,(origin
+           (method url-fetch)
+           (uri (crate-uri "shell-escape" "0.1.3"))
+           (sha256
+            (base32
+             "1y2fp2brv639icv4a0fdqs1zhlrxq8qbz27ygfa86ifmh5jcjp6x"))))))
     (arguments
      `(#:cargo ,cargo-bootstrap
        #:tests? #f ; FIXME

gnu/packages/samba.scm

@@ -3,6 +3,7 @@
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Adonay "adfeno" Felipe Nogueira <https://libreplanet.org/wiki/User:Adfeno> <adfeno@openmailbox.org>
+;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -26,6 +27,8 @@
   #:use-module (guix licenses)
   #:use-module (gnu packages acl)
   #:use-module (gnu packages admin)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages crypto)
   #:use-module (gnu packages cups)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages tls)
@@ -33,10 +36,54 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages openldap)
   #:use-module (gnu packages readline)
+  #:use-module (gnu packages kerberos)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python))
 
+(define-public cifs-utils
+  (package
+    (name "cifs-utils")
+    (version "6.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://download.samba.org/pub/linux-cifs/"
+                           name "/" name "-" version ".tar.bz2"))
+       (sha256 (base32
+                "1ayghnkryy1n1zm5dyvyyr7n3807nsm6glfcbbki5c2a8w91dwmj"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("keytuils" ,keyutils)
+       ("linux-pam" ,linux-pam)
+       ("libcap-ng" ,libcap-ng)
+       ("mit-krb5" ,mit-krb5)
+       ("samba" ,samba)
+       ("talloc" ,talloc)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; The 6.7 tarball is missing ‘install.sh’. Create it.
+         (add-before 'configure 'autoreconf
+           (lambda _
+             (zero? (system* "autoreconf" "-i"))))
+         (add-before 'configure 'set-root-sbin
+           (lambda _ ; Don't try to install in "/sbin".
+             (setenv "ROOTSBINDIR"
+                     (string-append (assoc-ref %outputs "out") "/sbin"))
+             #t)))))
+    (synopsis "User-space utilities for Linux CIFS (Samba) mounts")
+    (description "@code{cifs-utils} is a set of user-space utilities for
+mounting and managing @dfn{Common Internet File System} (CIFS) shares using
+the Linux kernel CIFS client.")
+    (home-page "https://wiki.samba.org/index.php/LinuxCIFS_utils")
+    ;; cifs-utils is licensed as GPL3 or later, but 3 files contain LGPL code.
+    (license gpl3+)))
+
 (define-public iniparser
   (package
     (name "iniparser")

gnu/packages/screen.scm

@@ -40,6 +40,7 @@
              (method url-fetch)
              (uri (string-append "mirror://gnu/screen/screen-"
                                  version ".tar.gz"))
+             (patches (search-patches "screen-fix-info-syntax-error.patch"))
              (sha256
               (base32 "0bbv16gpxrh64sn4bvjy3qjy7jsxjlqlilyysin02fwnvla23nwp"))))
     (build-system gnu-build-system)

gnu/packages/statistics.scm

@@ -406,13 +406,13 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
 (define-public r-lattice
   (package
     (name "r-lattice")
-    (version "0.20-34")
+    (version "0.20-35")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "lattice" version))
               (sha256
                (base32
-                "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja"))))
+                "0pcnmaz3lr62ly0dcy5hnnqxshc4yqd43hrvlz3almgc9l7sna88"))))
     (build-system r-build-system)
     (home-page "http://lattice.r-forge.r-project.org/")
     (synopsis "High-level data visualization system")
@@ -426,14 +426,14 @@ also flexible enough to handle most nonstandard requirements.")
 (define-public r-matrix
   (package
     (name "r-matrix")
-    (version "1.2-7.1")
+    (version "1.2-8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Matrix" version))
        (sha256
         (base32
-         "09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa"))))
+         "1dyv42d7ranb85y8hvi57hbg5xnvhdzqn56wcq3qmhazqj3s3liw"))))
     (properties `((upstream-name . "Matrix")))
     (build-system r-build-system)
     (propagated-inputs
@@ -471,14 +471,14 @@ nonlinear mixed-effects models.")
 (define-public r-mgcv
   (package
    (name "r-mgcv")
-   (version "1.8-16")
+   (version "1.8-17")
    (source
     (origin
      (method url-fetch)
      (uri (cran-uri "mgcv" version))
      (sha256
       (base32
-       "0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj"))))
+       "1zj223l4a3j15d3c01wv7dkzn9w6084gxrq5600ck9rvr0lfpwwg"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-matrix" ,r-matrix)
@@ -553,14 +553,14 @@ analysis.")
 (define-public r-survival
   (package
     (name "r-survival")
-    (version "2.40-1")
+    (version "2.41-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "survival" version))
        (sha256
         (base32
-         "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci"))))
+         "07cnr0hnki6ybbjll54l4s5lllhk19vni5f8m0mvsfp99ls7qygk"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)))
@@ -684,13 +684,13 @@ effects of different types of color-blindness.")
 (define-public r-digest
   (package
     (name "r-digest")
-    (version "0.6.10")
+    (version "0.6.12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "digest" version))
        (sha256
-        (base32 "07825781nl85gx3pqskc04ywgs0f874qj9z2nyrwz7h0aqks0l8c"))))
+        (base32 "1awy9phxdvqnadby7rvwy2hkbrj210bqf4xvi27asdq028zlcyd4"))))
     (build-system r-build-system)
     ;; Vignettes require r-knitr, which requires r-digest, so we have to
     ;; disable them and the tests.
@@ -814,13 +814,13 @@ Munsell colour system.")
 (define-public r-rcpp
   (package
     (name "r-rcpp")
-    (version "0.12.8")
+    (version "0.12.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rcpp" version))
        (sha256
-        (base32 "0is1vql1q82g7yakad4skx707ip0fx3rgdwv9a8mi8259gly2qji"))))
+        (base32 "108p485agxwgmnl9p54vsyy94w96lcimlk08v71ddm77gfl13y2f"))))
     (build-system r-build-system)
     (home-page "http://www.rcpp.org")
     (synopsis "Seamless R and C++ Integration")
@@ -943,14 +943,14 @@ solution for sending email, including attachments, from within R.")
 (define-public r-stringi
   (package
     (name "r-stringi")
-    (version "1.1.2")
+    (version "1.1.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stringi" version))
        (sha256
         (base32
-         "13i1p6j8mx31hsw2s4c2phm2llrrdakzixkm6i0axsxprri722z5"))))
+         "1wh20is24lmzhcd9487ckv7r19009fyz4is3ianp3ky69vy8a7k5"))))
     (build-system r-build-system)
     (inputs `(("icu4c" ,icu4c)))
     (native-inputs `(("pkg-config" ,pkg-config)))
@@ -969,13 +969,13 @@ transliteration, concatenation, date-time formatting and parsing, etc.")
 (define-public r-stringr
   (package
     (name "r-stringr")
-    (version "1.1.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stringr" version))
        (sha256
-        (base32 "0css5j4psl80br75chg6s1s3ipzf89f71bnbys34flp9yghg1cfc"))))
+        (base32 "16hj2rmv8x03lp6cp2jk0k2plibvbggf444kp05przdvd03v7l31"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-magrittr" ,r-magrittr)
@@ -1073,14 +1073,14 @@ aesthetic attributes.")
 (define-public r-gdtools
   (package
     (name "r-gdtools")
-    (version "0.1.3")
+    (version "0.1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gdtools" version))
        (sha256
         (base32
-         "1prh814lw3qkgnf0760cvpic1k68jhlkpcxlksv8chjkvsrnnf09"))))
+         "0l8c4bh6765x9s6rw3mfm1bgicdzdngir1kxh9pxx4sidrdndcip"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-rcpp" ,r-rcpp)
@@ -1162,13 +1162,13 @@ evaluation (NSE) in R.")
 (define-public r-dbi
   (package
     (name "r-dbi")
-    (version "0.5-1")
+    (version "0.6-1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "DBI" version))
               (sha256
                (base32
-                "1idwm9lkmz6ns6h0vvgml18mg0k7vjqiv9p5svrdcmx7r1rirpdi"))))
+                "1fg158k4n6l3rzx9nrwhp4nwkwpbmv1q7z2xz5rw138zws68fkgr"))))
     (build-system r-build-system)
     (home-page "https://github.com/rstats-db/DBI")
     (synopsis "R database interface")
@@ -1525,18 +1525,17 @@ defined in different packages.")
 (define-public r-tibble
   (package
     (name "r-tibble")
-    (version "1.2")
+    (version "1.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tibble" version))
        (sha256
         (base32
-         "011i352ylq9b4xfcj7h10h7qsqd9qkc1rzc0pr1gf8qjb788p2pd"))))
+         "1q25i1cv3qms6d3lw7jd3z142w188znkcbyam460gn9si8l8g2bk"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-assertthat" ,r-assertthat)
+     `(("r-lazyeval" ,r-lazyeval)
-       ("r-lazyeval" ,r-lazyeval)
        ("r-rcpp" ,r-rcpp)))
     (home-page "https://github.com/hadley/tibble")
     (synopsis "Simple data frames")
@@ -1602,14 +1601,14 @@ transformations.")
 (define-public r-cluster
   (package
     (name "r-cluster")
-    (version "2.0.5")
+    (version "2.0.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cluster" version))
        (sha256
         (base32
-         "1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b"))))
+         "1z4gbz7chxxi4ly6c0yjlikwgf8aa8dlg05cn5cd6pjr21zvh97l"))))
     (build-system r-build-system)
     (inputs
      `(("gfortran" ,gfortran)))
@@ -1687,13 +1686,13 @@ and density estimation.")
 (define-public r-chron
   (package
     (name "r-chron")
-    (version "2.3-48")
+    (version "2.3-50")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "chron" version))
               (sha256
                (base32
-                "1q1d0p2wq19w3mpfqnrg8nmspxqmhv4ap52r393s6y3abl36ccac"))))
+                "1w3sl60gsirniqslb3pa75caiqbzbvc44phpd4czvwkb62xx1vx9"))))
     (build-system r-build-system)
     (home-page "http://cran.r-project.org/web/packages/chron")
     (synopsis "Chronological R objects which can handle dates and times")
@@ -1705,13 +1704,13 @@ times.")
 (define-public r-data-table
   (package
     (name "r-data-table")
-    (version "1.10.0")
+    (version "1.10.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "data.table" version))
               (sha256
                (base32
-                "1168arn4wjd1jj7kgr4sb8xd52hr8p8iqp85g5jwp3mkz4p76qfg"))))
+                "0ykbjr1x50ajxbri385vi3mnxj7zg1dcgh9y0snp341qmmmdypw6"))))
     (build-system r-build-system)
     (home-page "https://github.com/Rdatatable/data.table/wiki")
     (synopsis "Enhanced version of data.frame R object")
@@ -1867,14 +1866,14 @@ chain.")
 (define-public r-ade4
   (package
     (name "r-ade4")
-    (version "1.7-5")
+    (version "1.7-6")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "ade4" version))
         (sha256
           (base32
-            "0aaqbnydm5fb37nrvqj4bx6hxax7255j426cwh2lh88nyvznbq37"))))
+            "0lnc37d6waajmagy8qvw206pyc4vgrpzl3hk3j9frh6wa0b8x140"))))
     (build-system r-build-system)
     (home-page "http://pbil.univ-lyon1.fr/ADE-4")
     (synopsis "Multivariate data analysis and graphical display")
@@ -1886,14 +1885,14 @@ and environmental data in the framework of Euclidean exploratory methods.")
 (define-public r-xml2
   (package
     (name "r-xml2")
-    (version "1.0.0")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xml2" version))
        (sha256
         (base32
-         "0f2alsrk3yykznbhnz4pcsg9mb72cv607vbapqx5kqfv39772kgr"))))
+         "05iifrcgzx53w5ciw8bbm4vdwc3giv4xsvazv8chqxkndfvf7wq0"))))
     (build-system r-build-system)
     (inputs
      `(("libxml2" ,libxml2)))
@@ -1910,14 +1909,14 @@ files in R.  It is built on top of the libxml2 C library.")
 (define-public r-multitaper
   (package
     (name "r-multitaper")
-    (version "1.0-12")
+    (version "1.0-13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "multitaper" version))
        (sha256
         (base32
-         "011qpkwpjclfc24y2qqigmdnikqwdnanflfhihigh5b5k7qwgm5j"))))
+         "1ckf9bhvd5k7ypaw2viqh3cyj9jij0ygcp4q9pxwqs508s6yx3a5"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -1976,14 +1975,14 @@ limited to R.")
 (define-public r-backports
   (package
     (name "r-backports")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "backports" version))
        (sha256
         (base32
-         "0fssh5rnnvpp8wm0ml9gk765idwrgj07xyxpkhpidl9zwydxzif2"))))
+         "1pn1ii8vbkgxcqvx52kzsbwf9gkn9fp33388087zky2hmdzdirn0"))))
     (build-system r-build-system)
     (home-page "http://cran.r-project.org/web/packages/backports")
     (synopsis "Reimplementations of functions introduced since R 3.0.0")
@@ -2021,14 +2020,14 @@ worries about execution time overhead.")
 (define-public r-bbmisc
   (package
     (name "r-bbmisc")
-    (version "1.10")
+    (version "1.11")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "BBmisc" version))
        (sha256
         (base32
-         "0cw2mhw7qhdrx91zzd5iwyh7ch9fy4wxga8j63731q6sxr1airjl"))))
+         "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
     (properties `((upstream-name . "BBmisc")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2112,23 +2111,76 @@ code for report generation.  The template syntax is similar to PHP, Ruby's erb
 module, Java Server Pages, and Python's psp module.")
     (license license:gpl2+)))
 
+(define-public r-desc
+  (package
+    (name "r-desc")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "desc" version))
+       (sha256
+        (base32
+         "0mc1jmiwqyj7s6gzxz6fyamzjpmdn3rpfpllby2fq11ml30c6jpr"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-assertthat" ,r-assertthat)
+       ("r-crayon" ,r-crayon)
+       ("r-r6" ,r-r6)
+       ("r-rprojroot" ,r-rprojroot)))
+    (home-page "https://github.com/r-pkgs/desc")
+    (synopsis "Manipulate DESCRIPTION Files")
+    (description
+     "This package provides tools to read, write, create, and manipulate
+DESCRIPTION files.  It is intended for packages that create or manipulate
+other packages.")
+    (license license:expat)))
+
+(define-public r-commonmark
+  (package
+    (name "r-commonmark")
+    (version "1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "commonmark" version))
+       (sha256
+        (base32
+         "12q5mncxvkwdxc35is6y5idx8a1h99hyz5x6ri0arni6k25krchk"))))
+    (build-system r-build-system)
+    ;;(inputs `(("zlib" ,zlib)))
+    (home-page "http://cran.r-project.org/web/packages/commonmark")
+    (synopsis "CommonMark and Github Markdown Rendering in R")
+    (description
+     "The CommonMark specification defines a rationalized version of markdown
+syntax.  This package uses the 'cmark' reference implementation for converting
+markdown text into various formats including HTML, LaTeX and groff man.  In
+addition, it exposes the markdown parse tree in XML format.  The latest
+version of this package also adds support for Github extensions including
+tables, autolinks and strikethrough text.")
+    (license license:bsd-2)))
+
 (define-public r-roxygen2
   (package
     (name "r-roxygen2")
-    (version "5.0.1")
+    (version "6.0.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "roxygen2" version))
               (sha256
                (base32
-                "19gblyrrn29msbpawcb1hn5m1rshiqwxy0lby0vf92rm13fmsxcz"))))
+                "0xpzziminf225kjwhyl51kgkzhplyzhk5farhf5s822krl2xqbfj"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-brew" ,r-brew)
+       ("r-commonmark" ,r-commonmark)
+       ("r-desc" ,r-desc)
        ("r-digest" ,r-digest)
+       ("r-r6" ,r-r6)
        ("r-rcpp" ,r-rcpp)
        ("r-stringi" ,r-stringi)
-       ("r-stringr" ,r-stringr)))
+       ("r-stringr" ,r-stringr)
+       ("r-xml2" ,r-xml2)))
     (home-page "https://github.com/klutometis/roxygen")
     (synopsis "In-source documentation system for R")
     (description
@@ -2308,17 +2360,16 @@ time-of-day values, based on the @code{difftime} class.")
 (define-public r-readr
   (package
     (name "r-readr")
-    (version "1.0.0")
+    (version "1.1.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "readr" version))
               (sha256
                (base32
-                "0xji0dbal6xcxnsmjj678fw29n7wrj45wrd5ng99yhqqijcm9f6g"))))
+                "1g7g3gdmvq7nj8asw6fi13k38c420sy9696nqgkrhlvv5h13yqs7"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-curl" ,r-curl)
+     `(("r-rcpp" ,r-rcpp)
-       ("r-rcpp" ,r-rcpp)
        ("r-hms" ,r-hms)
        ("r-tibble" ,r-tibble)
        ("r-r6" ,r-r6)
@@ -2392,32 +2443,17 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.7.600.1.0")
+    (version "0.7.700.0.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "0k1wniip184j0ckcg9kcjy2q4mcfj5jpd1nkk4l0ab75ad8znywv"))
+                "03cvl2xgmvh4sylw7ff7s020y7k2wzyj34l0zngm09qs44pa9q0m"))))
-              (modules '((guix build utils)))
-              ;; Remove bundled armadillo sources
-              (snippet
-               '(begin
-                  (delete-file-recursively "inst/include/armadillo_bits")
-                  (delete-file "inst/include/armadillo")))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'link-against-armadillo
-           (lambda _
-             (substitute* "src/Makevars"
-               (("PKG_LIBS=" prefix)
-                (string-append prefix "-larmadillo"))))))))
     (propagated-inputs
-     `(("r-rcpp" ,r-rcpp)
+     `(("r-rcpp" ,r-rcpp)))
-       ("armadillo" ,armadillo-for-rcpparmadillo)))
     (home-page "https://github.com/RcppCore/RcppArmadillo")
     (synopsis "Rcpp integration for the Armadillo linear algebra library")
     (description
@@ -2476,14 +2512,14 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.")
 (define-public r-rprojroot
   (package
     (name "r-rprojroot")
-    (version "1.1")
+    (version "1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rprojroot" version))
        (sha256
         (base32
-         "04ywfpar4d2hyi4rh4fbixrbzd665gpa2jhx67g8857cr70pp0nh"))))
+         "1fgyxv1zv04sllcclzz089xl6hpdzac7xk61l0l4acb7rqsx5d18"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-backports" ,r-backports)))
@@ -2499,14 +2535,14 @@ certain criterion, e.g., it contains a certain regular file.")
 (define-public r-rmarkdown
   (package
     (name "r-rmarkdown")
-    (version "1.3")
+    (version "1.4")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "rmarkdown" version))
         (sha256
           (base32
-            "1vvxyf3zhyxx6k697lia299456hryp8nh3zr0fc27f3107a8mcjf"))))
+            "1dvs9cq88g61wfimifagq6y98yxavxzjan39jvpdsg98mafckq9g"))))
     (properties `((upstream-name . "rmarkdown")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2592,13 +2628,13 @@ error stream.")
 (define-public r-rsqlite
   (package
     (name "r-rsqlite")
-    (version "1.1-1")
+    (version "1.1-2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RSQLite" version))
               (sha256
                (base32
-                "11vnzds5gidgakdmsbdn0bvnsz064ym1savwb7l6gc1bjn7xa2k4"))))
+                "0mg9yhdvny3vjn72agai5ghqxd3vk8cd4x1lsc0gzc2b2dm2w0p4"))))
     (properties `((upstream-name . "RSQLite")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2649,13 +2685,13 @@ ldap, and also supports cookies, redirects, authentication, etc.")
 (define-public r-xml
   (package
     (name "r-xml")
-    (version "3.98-1.5")
+    (version "3.98-1.6")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "XML" version))
               (sha256
                (base32
-                "0dcdj7ryn8lm7wmv4hqhh9jxa5k97l6ad8xyvb932yfkwj1g1byy"))))
+                "1amxx7fpik162nimrr7m5lvv6rhx9cwdyg44fxp1i5wm3y4skwnz"))))
     (properties
      `((upstream-name . "XML")))
     (build-system r-build-system)
@@ -2808,13 +2844,13 @@ worker processes and collect and return the results on the master.")
 (define-public r-sparsem
   (package
     (name "r-sparsem")
-    (version "1.74")
+    (version "1.76")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "SparseM" version))
               (sha256
                (base32
-                "1fpfhld887y5lyb8jydprmv5krqm1fk6n53z942b4g4z1v4g04j7"))))
+                "16xnl9cacim35aawq6bmd2y6rrhnh1kg6dwsy3k5yslkfr1y9j62"))))
     (properties
      `((upstream-name . "SparseM")))
     (inputs
@@ -3139,14 +3175,14 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
 (define-public r-e1071
   (package
     (name "r-e1071")
-    (version "1.6-7")
+    (version "1.6-8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "e1071" version))
        (sha256
         (base32
-         "1069qwj9gsjq6par2cgfah8nn5x2w38830761x1f7mqpmk0gnj3h"))))
+         "08n6i26nfckjpxjkzi8phhanc3ahsrirkv5rz38y2jcv7ds031pn"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-class" ,r-class)))
@@ -3426,13 +3462,13 @@ vignettes.")
 (define-public r-mvtnorm
   (package
     (name "r-mvtnorm")
-    (version "1.0-5")
+    (version "1.0-6")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mvtnorm" version))
               (sha256
                (base32
-                "1pc1mi2h063gh4a40009xk5j6pf5bm4274i5kycln38dixsry3yh"))))
+                "0i74s9dl4jf1gln6agra8h38qn9ifd5v0gi13caj1da5nrbmn0aa"))))
     (build-system r-build-system)
     (inputs
      `(("gfortran" ,gfortran)))
@@ -3445,13 +3481,13 @@ t-probabilities, quantiles, random deviates and densities.")
 (define-public r-matrixstats
   (package
     (name "r-matrixstats")
-    (version "0.51.0")
+    (version "0.52.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "matrixStats" version))
               (sha256
                (base32
-                "0bsalx605kgb9nl7mfnq1qinkyd9s97p8plymsyfja1gmcnjrcpj"))))
+                "0ihxnbbc1czfbccm8mrh7hjwdik3y90964xhbjday6fci0xjcsi5"))))
     (properties `((upstream-name . "matrixStats")))
     (build-system r-build-system)
     (native-inputs
@@ -3469,17 +3505,18 @@ memory usage.")
 (define-public r-viridis
   (package
     (name "r-viridis")
-    (version "0.3.4")
+    (version "0.4.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "viridis" version))
               (sha256
                (base32
-                "1a9hqn2pccpc51vh8ghw698ni6xzdnp8v0n8kgjh51nlz5hhc87j"))))
+                "03mha2935k1mw7mjjkq7mrx185hl0m3vq3967iiwbknpivbdxllk"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)))
+       ("r-gridextra" ,r-gridextra)
+       ("r-viridislite" ,r-viridislite)))
     (home-page "https://github.com/sjmgarnier/viridis")
     (synopsis "Matplotlib default color map")
     (description
@@ -3495,14 +3532,14 @@ most common form of color blindness.")
 (define-public r-viridislite
   (package
     (name "r-viridislite")
-    (version "0.1.3")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "viridisLite" version))
        (sha256
         (base32
-         "1b0fhj8i1m9jsz91gzag60k7vy7kk5xkdg31rc3h3spq96l66psp"))))
+         "1546h44ng4dxs130jkh6lkh990hmp90m1w45sq5p47n546gr0k9d"))))
     (properties `((upstream-name . "viridisLite")))
     (build-system r-build-system)
     (home-page "https://github.com/sjmgarnier/viridisLite")
@@ -3520,21 +3557,22 @@ the 'lite' version of the more complete @code{viridis} package.")
 (define-public r-tidyr
   (package
     (name "r-tidyr")
-    (version "0.6.0")
+    (version "0.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidyr" version))
        (sha256
         (base32
-         "1bpwbphgl43ym433b0nrshwhr7pprmj1wkpkamdzix1zvf9dcbc2"))))
+         "11hs3gqpbaw3w281as4m7j9n594ix5axfpwbyjsd0l62pwnzj217"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
        ("r-lazyeval" ,r-lazyeval)
        ("r-magrittr" ,r-magrittr)
        ("r-rcpp" ,r-rcpp)
-       ("r-stringi" ,r-stringi)))
+       ("r-stringi" ,r-stringi)
+       ("r-tibble" ,r-tibble)))
     (home-page "https://github.com/hadley/tidyr")
     (synopsis "Tidy data with `spread()` and `gather()` functions")
     (description
@@ -4153,13 +4191,13 @@ with alternating row colors) in LaTeX and HTML formats easily from
 (define-public r-vipor
   (package
     (name "r-vipor")
-    (version "0.4.4")
+    (version "0.4.5")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "vipor" version))
               (sha256
                (base32
-                "0p1z9a3fazl78pj8a1i2n62v8hrs8cinq82j9wpawhmfkn3dggss"))))
+                "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
     (build-system r-build-system)
     (home-page "http://cran.r-project.org/web/packages/vipor")
     (synopsis "Plot categorical data using noise and density estimates")
@@ -4191,14 +4229,14 @@ closely-packed, non-overlapping points.")
 (define-public r-sourcetools
   (package
     (name "r-sourcetools")
-    (version "0.1.5")
+    (version "0.1.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sourcetools" version))
        (sha256
         (base32
-         "0jx6kslygfqaic3cmjwag3dy98q1a2dw20cz7z8agsknmmbk6dy2"))))
+         "0l8c6fql82cb246qh7hfgxb4s35qn0qfgy6dzvkx0zkz1cpqvx69"))))
     (build-system r-build-system)
     (home-page "http://cran.r-project.org/web/packages/sourcetools")
     (synopsis "Tools for reading, tokenizing and parsing R code")
@@ -4234,13 +4272,13 @@ data at that region, and avoids over-plotting.")
 (define-public r-ggthemes
   (package
     (name "r-ggthemes")
-    (version "3.3.0")
+    (version "3.4.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "ggthemes" version))
               (sha256
                (base32
-                "1qdxg2siwsiq32fmgcxn4vihgxad9v8q0aqigl7a94c26bwxs7y2"))))
+                "1jj8lp7jbk3489kpgbw4b5phpn01gkfmksc21c6sn3x6wmzyn6hs"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -4259,13 +4297,13 @@ Wall Street Journal, among others.  This package also provides
 (define-public r-statmod
   (package
     (name "r-statmod")
-    (version "1.4.27")
+    (version "1.4.29")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "statmod" version))
               (sha256
                (base32
-                "14yilq9d3z20hig4rs8bjqyydw3dfx90mhmzvw9w8p16h0s595sn"))))
+                "1fgzkwriba39d7946lq892f0si2fjdy37pvxki6ix8xyj8qgnci4"))))
     (build-system r-build-system)
     (home-page "http://cran.r-project.org/web/packages/statmod")
     (native-inputs
@@ -4378,19 +4416,19 @@ letters, as is often required for scientific publications.")
 (define-public r-mixtools
   (package
     (name "r-mixtools")
-    (version "1.0.4")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mixtools" version))
        (sha256
         (base32
-         "133rr17ywmlhsc6457hs8qxi8ng443ql9ashxpwc8875gjhv1x32"))))
+         "13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-boot" ,r-boot)
+     `(("r-mass" ,r-mass)
-       ("r-mass" ,r-mass)
+       ("r-segmented" ,r-segmented)
-       ("r-segmented" ,r-segmented)))
+       ("r-survival" ,r-survival)))
     (home-page "http://cran.r-project.org/web/packages/mixtools")
     (synopsis "Tools for analyzing finite mixture models")
     (description
@@ -4536,14 +4574,14 @@ models, generalized linear models and model-based clustering.")
 (define-public r-mclust
   (package
     (name "r-mclust")
-    (version "5.2.2")
+    (version "5.2.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mclust" version))
        (sha256
         (base32
-         "19cbg7p5h2b6h9mvcx9rjppyd3awma18ymaljakbnclpvhwbqpwd"))))
+         "0045msdw1xndfmlylbnm1ss716iiqzqwj454a97gmcq5kph86qzz"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -4772,14 +4810,14 @@ based on an interface to Fortran implementations by M. J. D. Powell.")
 (define-public r-rcppeigen
   (package
     (name "r-rcppeigen")
-    (version "0.3.2.9.0")
+    (version "0.3.2.9.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RcppEigen" version))
        (sha256
         (base32
-         "0fy9kr03160f1ywzff3p380s8a59jz7d2d0rggb14g2y0slzpbr5"))))
+         "1ih940yjbc530cmpl6kx1jic7pz2ps1w5vrvy32qizh6m5s3lk7x"))))
     (properties `((upstream-name . "RcppEigen")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4923,14 +4961,14 @@ C++ library for numerical linear algebra and RcppEigen glue.")
 (define-public r-pbkrtest
   (package
     (name "r-pbkrtest")
-    (version "0.4-6")
+    (version "0.4-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pbkrtest" version))
        (sha256
         (base32
-         "00cw18q7wvddzjrbxz917wkix6r7672vi2wmsp4gwgzady8vha4x"))))
+         "1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lme4" ,r-lme4)
@@ -5114,14 +5152,14 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
 (define-public r-ranger
   (package
     (name "r-ranger")
-    (version "0.6.0")
+    (version "0.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ranger" version))
        (sha256
         (base32
-         "1fwqwbi0dnla16x6zj14rf95qr5gmilfmlrwnv7s960h4yiw4n97"))))
+         "0g1rnpk4c06lmy0r5n0j7i2xna190kqalmxp42d9gnk3drnb1x43"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)))

gnu/packages/suckless.scm

@@ -266,7 +266,7 @@ drawing.")
 (define-public surf
   (package
     (name "surf")
-    (version "0.7")
+    (version "2.0")
     (source
      (origin
        (method url-fetch)
@@ -274,7 +274,7 @@ drawing.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "0jj93izd8fizxfa6ln9w1h9bwki81sz5dhskh5x1rl34zd38aq4m"))))
+         "07cmajyafljigy10d21kkyvv5jf3hxkx06pz3rwwk3y3c9x4rvps"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      '(#:tests? #f ; no tests
@@ -294,7 +294,7 @@ drawing.")
      `(("dmenu" ,dmenu)
        ("glib-networking" ,glib-networking)
        ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
-       ("webkitgtk" ,webkitgtk/gtk+-2)
+       ("webkitgtk" ,webkitgtk)
        ("xprop" ,xprop)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))

gnu/packages/tcl.scm

@@ -4,6 +4,7 @@
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2017 Kei Kebreau <kei@openmailbox.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -290,3 +291,35 @@ callback is evaluated.")
     (license (non-copyleft
               "file://LICENCE"
               "See LICENCE in the distribution."))))
+
+(define-public tclx
+  (package
+    (name "tclx")
+    (version "8.4.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/tclx/TclX/"
+                                  version "/tclx" version ".tar.bz2"))
+              (sha256
+               (base32
+                "1v2qwzzidz0is58fd1p7wfdbscxm3ip2wlbqkj5jdhf6drh1zd59"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f ; a test named profile.test segfaults
+       #:configure-flags (list (string-append "--with-tcl="
+                                              (assoc-ref %build-inputs "tcl")
+                                              "/lib")
+                               (string-append "--libdir="
+                                              (assoc-ref %outputs "out")
+                                              "/lib"))))
+    (inputs
+     `(("tcl" ,tcl)
+       ("tk" ,tk)))
+    (home-page "http://tclx.sourceforge.net/")
+    (synopsis "System programming extensions for Tcl")
+    (description
+     "Extended Tcl is oriented towards system programming tasks and large
+application development.  TclX provides additional interfaces to the operating
+system, and adds many new programming constructs, text manipulation tools, and
+debugging tools.")
+    (license tcl/tk)))

gnu/packages/text-editors.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2016 José Miguel Sánchez García <jmi2k@openmailbox.org>
 ;;; Copyright © 2016 Carlo Zancanaro <carlo@zancanaro.id.au>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2017 Feng Shu <tumashu@163.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,8 +30,11 @@
   #:use-module (gnu packages boost)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages glib)
+  #:use-module (gnu packages gtk)
   #:use-module (gnu packages lua)
   #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages ruby)
   #:use-module (gnu packages terminals)
   #:use-module (gnu packages xml))
@@ -161,3 +165,28 @@ competitive (as in keystroke count) with Vim.")
 interface similar to many user-friendly editors.  JOE has some of the key
 bindings and many of the powerful features of GNU Emacs.")
     (license license:gpl3+)))
+
+(define-public leafpad
+  (package
+    (name "leafpad")
+    (version "0.8.18.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://download.savannah.gnu.org/releases/"
+                                  "leafpad/leafpad-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0b0az2wvqgvam7w0ns1j8xp2llslm1rx6h7zcsy06a7j0yp257cm"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("intltool" ,intltool)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("gtk+" ,gtk+-2)))
+    (home-page "http://tarot.freeshell.org/leafpad/")
+    (synopsis "GTK+ based text editor")
+    (description "Leafpad is a GTK+ text editor that emphasizes simplicity.  As
+development focuses on keeping weight down to a minimum, only the most essential
+features are implemented in the editor.  Leafpad is simple to use, is easily
+compiled, requires few libraries, and starts up quickly. ")
+    (license license:gpl2+)))

gnu/packages/tls.scm

@@ -431,7 +431,7 @@ required structures.")
 (define-public libressl
   (package
     (name "libressl")
-    (version "2.5.2")
+    (version "2.5.3")
     (source
      (origin
       (method url-fetch)
@@ -440,7 +440,7 @@ required structures.")
              version ".tar.gz"))
       (sha256
        (base32
-        "10hw434azw0gvfkmfm46r85r7my1c6592rg9jsna914jh1q7vyhg"))))
+        "0c4awq45cl757fv7f7f75i5i0ibc6v7ns13n7xvfak7chv2lrqql"))))
     (build-system gnu-build-system)
     (native-search-paths
       ;; FIXME: These two variables must designate a single file or directory
@@ -469,26 +469,37 @@ security, and applying best practice development processes.")
   (package
     (name "python-acme")
     ;; Remember to update the hash of certbot when updating python-acme.
-    (version "0.12.0")
+    (version "0.13.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "acme" version))
       (sha256
        (base32
-        "1pzv8fcfwdqzvvpyhgjz412is0b98yj9495k8sidzzqgbdmvlp50"))))
+        "05cqadwzgfcianw3v0qxwja65dxnzw429f7dk8w0mnh21pib72bl"))))
     (build-system python-build-system)
+
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-after 'install 'docs
+         (add-after 'unpack 'patch-dependency
+           ;; This module is part of the Python standard library, so we don't
+           ;; need to use an external package.
+           ;; https://github.com/certbot/certbot/pull/2249
+           (lambda _
+             (substitute* "setup.py"
+               (("'argparse',") ""))
+             #t))
+         (add-after 'build 'build-documentation
+           (lambda _
+             (zero? (system* "make" "-C" "docs" "man" "info"))))
+         (add-after 'install 'install-documentation
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (man (string-append out "/share/man/man1"))
                     (info (string-append out "/info")))
-               (and (zero? (system* "make" "-C" "docs" "man" "info"))
+               (install-file "docs/_build/texinfo/acme-python.info" info)
-                    (install-file "docs/_build/texinfo/acme-python.info" info)
+               (install-file "docs/_build/man/acme-python.1" man)
-                    (install-file "docs/_build/man/acme-python.1" man)
+               #t))))))
-                    #t)))))))
     ;; TODO: Add optional inputs for testing.
     (native-inputs
      `(("python-mock" ,python-mock)
@@ -498,9 +509,7 @@ security, and applying best practice development processes.")
        ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme)
        ("texinfo" ,texinfo)))
     (propagated-inputs
-     `(("python-ndg-httpsclient" ,python-ndg-httpsclient)
+     `(("python-six" ,python-six)
-       ("python-werkzeug" ,python-werkzeug)
-       ("python-six" ,python-six)
        ("python-requests" ,python-requests)
        ("python-pytz" ,python-pytz)
        ("python-pyrfc3339" ,python-pyrfc3339)
@@ -526,24 +535,23 @@ security, and applying best practice development processes.")
               (uri (pypi-uri name version))
               (sha256
                (base32
-                "1dw86gb8lyap5ckjawmli1hxgbchw2g62g1lqfvxyqjv0df94waa"))))
+                "1wq0khcf4ixda71cgfd9rkqqzx6j8hp8ha0cssvjzjnsgrsdffpn"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2
-       #:phases
+       ,@(substitute-keyword-arguments (package-arguments python-acme)
-       (modify-phases %standard-phases
+           ((#:phases phases)
-         (add-after 'build 'docs
+            `(modify-phases ,phases
-           (lambda* (#:key outputs #:allow-other-keys)
+              (replace 'install-documentation
-             (let* ((out (assoc-ref outputs "out"))
+                (lambda* (#:key outputs #:allow-other-keys)
-                    (man1 (string-append out "/share/man/man1"))
+                  (let* ((out (assoc-ref outputs "out"))
-                    (man7 (string-append out "/share/man/man7"))
+                         (man1 (string-append out "/share/man/man1"))
-                    (info (string-append out "/info")))
+                         (man7 (string-append out "/share/man/man7"))
-               (and
+                         (info (string-append out "/info")))
-                 (zero? (system* "make" "-C" "docs" "man" "info"))
+                    (install-file "docs/_build/texinfo/Certbot.info" info)
-                 (install-file "docs/_build/texinfo/Certbot.info" info)
+                    (install-file "docs/_build/man/certbot.1" man1)
-                 (install-file "docs/_build/man/certbot.1" man1)
+                    (install-file "docs/_build/man/certbot.7" man7)
-                 (install-file "docs/_build/man/certbot.7" man7)
+                    #t))))))))
-                 #t)))))))
     ;; TODO: Add optional inputs for testing.
     (native-inputs
      `(("python2-nose" ,python2-nose)
@@ -557,7 +565,6 @@ security, and applying best practice development processes.")
     (propagated-inputs
      `(("python2-acme" ,python2-acme)
        ("python2-zope-interface" ,python2-zope-interface)
-       ("python2-pythondialog" ,python2-pythondialog)
        ("python2-pyrfc3339" ,python2-pyrfc3339)
        ("python2-pyopenssl" ,python2-pyopenssl)
        ("python2-configobj" ,python2-configobj)

gnu/packages/tor.scm

@@ -4,6 +4,7 @@
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017 ng0 <contact.ng0@cryptolab.net>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,7 +29,9 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages libevent)
+  #:use-module (gnu packages linux)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages python)
@@ -88,6 +91,19 @@ the application layer) you need to install @code{torsocks}.")
                (base32
                 "0byr9ga9w79qz4vp0m11sbmspad7fsal9wm67r4znzb7zb7cis19"))))
     (build-system gnu-build-system)
+    (inputs
+     `(("which" ,which)
+       ("libcap" ,libcap)))
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (add-after 'build 'absolutize
+                    (lambda* (#:key inputs #:allow-other-keys)
+                      (substitute* "src/bin/torsocks"
+                        (("getcap=`.*`")
+                         (string-append "getcap=" (which "getcap")))
+                        (("`which")
+                         (string-append "`" (which "which"))))
+                      #t)))))
     (home-page "https://www.torproject.org/")
     (synopsis "Use socks-friendly applications with Tor")
     (description

gnu/packages/version-control.scm

@@ -35,6 +35,7 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system haskell)
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages apr)
@@ -50,6 +51,7 @@
   #:use-module (gnu packages flex)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages groff)
+  #:use-module (gnu packages haskell)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages nano)
   #:use-module (gnu packages ncurses)
@@ -1171,24 +1173,24 @@ modification time.")
 (define-public myrepos
   (package
     (name "myrepos")
-    (version "1.20160123")
+    (version "1.20170129")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append
+       (uri (git-reference
-             "https://github.com/joeyh/myrepos/archive/"
+             (url "git://myrepos.branchable.com/myrepos")
-             version ".tar.gz"))
+             (commit version)))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (file-name (string-append name "-" version "-checkout"))
        (sha256
-        (base32 "1723cg5haplz2w9dwdzp6ds1ip33cx3awmj4wnb0h4yq171v5lqk"))))
+        (base32 "15i9bs2i25l7ibv530ghy8280kklcgm5kr6j86s7iwcqqckd0czp"))))
     (build-system gnu-build-system)
     (inputs
      `(("perl" ,perl)))
     (arguments
-     `(#:test-target "test"
+     '(#:test-target "test"
-       #:phases (alist-delete 'configure %standard-phases)
+       #:phases (modify-phases %standard-phases (delete 'configure))
        #:make-flags (list (string-append "PREFIX=" %output))))
-    (home-page "http://myrepos.branchable.com/")
+    (home-page "https://myrepos.branchable.com/")
     (synopsis "Multiple repository management tool")
     (description
      "Myrepos provides the @code{mr} command, which maps an operation (e.g.,
@@ -1307,3 +1309,104 @@ a built-in wiki, built-in file browsing, built-in tickets system, etc.")
     (description "Stagit creates static pages for git repositories, the results can
 be served with a HTTP file server of your choice.")
     (license license:expat)))
+
+;; Darcs has no https support: http://irclog.perlgeek.de/darcs/2016-09-17
+;; http://darcs.net/manual/Configuring_darcs.html#SECTION00440070000000000000
+;; and results of search engines will show that if the protocol is http, https
+;; is never mentioned.
+(define-public darcs
+  (package
+    (name "darcs")
+    (version "2.12.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/darcs/"
+                           "darcs-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0jfwiwl5k8wspciq1kpmvh5yap4japrf97s9pvhcybxxhaj3ds28"))
+       (modules '((guix build utils)))
+       ;; Remove time-dependent code for reproducibility.
+       (snippet
+        '(begin
+           (substitute* "darcs/darcs.hs"
+             (("__DATE__") "\"1970-01-01\"")
+             (("__TIME__") "\"00:00:00\""))
+           (substitute* "src/impossible.h"
+             (("__DATE__") "\"\"")
+             (("__TIME__") "\"\""))))))
+    (build-system haskell-build-system)
+    (arguments
+     `(#:configure-flags '("-fpkgconfig" "-fcurl" "-flibiconv" "-fthreaded"
+                           "-fnetwork-uri" "-fhttp" "--flag=executable"
+                           "--flag=library")
+       #:tests? #f)) ; 20 failing shell tests out of over 400
+    (inputs
+     `(("ghc-cmdargs" ,ghc-cmdargs)
+       ("ghc-split" ,ghc-split)
+       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-findbin" ,ghc-findbin)
+       ("ghc-hunit" ,ghc-hunit)
+       ("ghc-array" ,ghc-array)
+       ("ghc-async" ,ghc-async)
+       ("ghc-attoparsec" ,ghc-attoparsec)
+       ("ghc-base16-bytestring" ,ghc-base16-bytestring)
+       ("ghc-binary" ,ghc-binary)
+       ("ghc-bytestring-builder" ,ghc-bytestring-builder)
+       ("ghc-cryptohash" ,ghc-cryptohash)
+       ("ghc-data-ordlist" ,ghc-data-ordlist)
+       ("ghc-directory" ,ghc-directory)
+       ("ghc-fgl" ,ghc-fgl)
+       ("ghc-system-filepath" ,ghc-system-filepath)
+       ("ghc-graphviz" ,ghc-graphviz)
+       ("ghc-hashable" ,ghc-hashable)
+       ("ghc-haskeline" ,ghc-haskeline)
+       ("ghc-html" ,ghc-html)
+       ("ghc-mmap" ,ghc-mmap)
+       ("ghc-mtl" ,ghc-mtl)
+       ("ghc-old-time" ,ghc-old-time)
+       ("ghc-parsec" ,ghc-parsec)
+       ("ghc-process" ,ghc-process)
+       ("ghc-random" ,ghc-random)
+       ("ghc-regex-applicative" ,ghc-regex-applicative)
+       ("ghc-regex-compat-tdfa" ,ghc-regex-compat-tdfa)
+       ("ghc-sandi" ,ghc-sandi)
+       ("ghc-shelly" ,ghc-shelly)
+       ("ghc-tar" ,ghc-tar)
+       ("ghc-transformers-compat" ,ghc-transformers-compat)
+       ("ghc-unix-compat" ,ghc-unix-compat)
+       ("ghc-utf8-string" ,ghc-utf8-string)
+       ("ghc-vector" ,ghc-vector)
+       ("ghc-zip-archive" ,ghc-zip-archive)
+       ("ghc-zlib" ,ghc-zlib)
+       ("ghc-http" ,ghc-http)
+       ("curl" ,curl)
+       ("ghc" ,ghc)
+       ("ncurses" ,ncurses)
+       ("perl" ,perl)
+       ("libiconv" ,libiconv)
+       ("ghc-network" ,ghc-network)
+       ("ghc-network-uri" ,ghc-network-uri)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://darcs.net")
+    (synopsis "Distributed Revision Control System")
+    (description
+     "Darcs is a revision control system.  It is:
+
+@enumerate
+@item Distributed: Every user has access to the full command set, removing boundaries
+between server and client or committer and non-committers.
+@item Interactive: Darcs is easy to learn and efficient to use because it asks you
+questions in response to simple commands, giving you choices in your work flow.
+You can choose to record one change in a file, while ignoring another.  As you update
+from upstream, you can review each patch name, even the full diff for interesting
+patches.
+@item Smart: Originally developed by physicist David Roundy, darcs is based on a
+unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}.
+@end enumerate")
+    (license license:gpl2)))

gnu/packages/video.scm

@@ -14,6 +14,7 @@
 ;;; Copyright © 2016, 2017 ng0 <contact.ng0@cryptolab.net>
 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2017 Feng Shu <tumashu@163.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -984,7 +985,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2017.03.26")
+    (version "2017.04.14")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://yt-dl.org/downloads/"
@@ -992,7 +993,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "00ysv18p4rqg7sswbpjpmmvaih6nm135bpllqdlj4ns8kjqmh59j"))))
+                "1rjc4ilafzrig02znrlxwjyzk5rpcc3li55n8rw2c4dmjmvjppkh"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion
@@ -1023,6 +1024,31 @@ YouTube.com and a few more sites.")
     (home-page "https://yt-dl.org")
     (license license:public-domain)))
 
+(define-public you-get
+  (package
+    (name "you-get")
+    (version "0.4.652")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/soimort/you-get/releases/download/v"
+                    version "/you-get-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0brkz98lycx8mmxjwmn7jlhqfdbvl0hy070n7skwr1k75kh99q30"))))
+    (build-system python-build-system)
+    (arguments
+     ;; no tests
+     '(#:tests? #f))
+    (inputs
+     `(("ffmpeg" ,ffmpeg)))
+    (synopsis "Download videos, audios, or images from Web sites")
+    (description
+     "You-Get is a command-line utility to download media contents (videos,
+audio, images) from the Web.  It can use either mpv or vlc for playback.")
+    (home-page "https://you-get.org/")
+    (license license:expat)))
+
 (define-public libbluray
   (package
     (name "libbluray")

gnu/packages/web-browsers.scm

@@ -16,7 +16,7 @@
 ;;; 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 dillo)
+(define-module (gnu packages web-browsers)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (gnu packages)

gnu/packages/web.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2013 Aljosha Papsch <misc@rpapsch.de>
 ;;; Copyright © 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015, 2016, 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
@@ -14,7 +14,7 @@
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2016 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2016, 2017 ng0 <contact.ng0@cryptolab.net>
-;;; Copyright © 2016 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2016, 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2016 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016 Bake Timmons <b3timmons@speedymail.org>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
@@ -130,14 +130,14 @@ and its related documentation.")
 (define-public nginx
   (package
     (name "nginx")
-    (version "1.11.11")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://nginx.org/download/nginx-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0qkj4xqv2f986dwqwlkidmr6jpxhv3ds67pxd1pd4a4f4j0c8yjs"))))
+                "0c2vg6530qplwk8rhldww5r3cwcbw1avka53qg9sh85nzlk2w8ml"))))
     (build-system gnu-build-system)
     (inputs `(("pcre" ,pcre)
               ("openssl" ,openssl)
@@ -3316,13 +3316,13 @@ particularly easy to create complete web applications using httpuv alone.")
 (define-public r-jsonlite
   (package
     (name "r-jsonlite")
-    (version "1.2")
+    (version "1.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "jsonlite" version))
               (sha256
                (base32
-                "0k966hzp3qnwck7fgd76w49zrz39s7pqyywws17bhbcd8rh4csyb"))))
+                "11rgkjp5qir79niad0aizjxvjzyvkl6l9nsrv3ikv446vllmrasn"))))
     (build-system r-build-system)
     (home-page "http://arxiv.org/abs/1403.2805")
     (synopsis "Robust, high performance JSON parser and generator for R")
@@ -3422,18 +3422,20 @@ applications.")
 (define-public r-htmltable
   (package
     (name "r-htmltable")
-    (version "1.7")
+    (version "1.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "htmlTable" version))
        (sha256
         (base32
-         "0x2f2hrbhvm53zqwn0ny9wxbk34nwf6zww8cx4bjy5ax15asdllm"))))
+         "0ciic1f4iczq14j81fg7kxibn65sy8z1zxkvk1yxnxxg6dzplj2v"))))
     (properties `((upstream-name . "htmlTable")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-knitr" ,r-knitr)
+     `(("r-checkmate" ,r-checkmate)
+       ("r-htmlwidgets" ,r-htmlwidgets)
+       ("r-knitr" ,r-knitr)
        ("r-magrittr" ,r-magrittr)
        ("r-stringr" ,r-stringr)))
     (home-page "http://gforge.se/packages/")
@@ -3451,13 +3453,13 @@ LaTeX.")
 (define-public r-curl
   (package
     (name "r-curl")
-    (version "2.3")
+    (version "2.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "curl" version))
               (sha256
                (base32
-                "0gbw5l0wnsw26fbr08gj9vgxrzxg8axvqxfshmd8g9khpgbdl0gr"))))
+                "0j1i24irpn4hvpcs61rzq0n19rmgmn29v48qc36csjk3r661l4pm"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -4218,17 +4220,12 @@ and similar services.")
     (version "1.12")
     (source
      (origin
-       ;; The darkhttpd release tarball URL fails to download with a
+       (method url-fetch)
-       ;; 'TLS warning alert'. Download from the darkhttpd git repo
+       (uri (string-append "https://unix4lyfe.org/darkhttpd/darkhttpd-"
-       ;; until the problem has been fixed upstream.
+                           version ".tar.bz2"))
-       (method git-fetch)
-       (uri (git-reference
-             (url (string-append "https://unix4lyfe.org/git/darkhttpd"))
-             (commit "41b68476c35270f47dcd2ddebe27cbcd87e43d41")))
        (sha256
         (base32
-         "0wi8dfgj4ic0fsy4dszl69xgxdxlwxz4c30vsw2i2dpnczgjm04k"))
+         "0185wlyx4iqiwfigp1zvql14zw7gxfacncii3d15yaxk4av1f155"))))
-       (file-name (string-append name "-" version "-checkout"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags '("CC=gcc")

gnu/packages/webkit.scm

@@ -53,14 +53,14 @@
 (define-public webkitgtk
   (package
     (name "webkitgtk")
-    (version "2.16.0")
+    (version "2.16.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.webkitgtk.org/releases/"
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1p3w23n5bq30xg4qg0i9lmrk13vgck2l4wh8gmzwxwqfj7c738sy"))))
+                "0i99kmv4dvb9m2sd36kig4j6d59pxmq47ih3nxayd31j68r3i4pb"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; no tests

gnu/packages/xml.scm

@@ -11,7 +11,7 @@
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
-;;; Copyright © 2016 ng0 <ng0@we.make.ritual.n0.is>
+;;; Copyright © 2016, 2017 ng0 <contact.ng0@cryptolab.net>
 ;;; Copyright © 2016 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
 ;;;
@@ -39,6 +39,7 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web)
+  #:use-module (gnu packages zip)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
@@ -1068,3 +1069,56 @@ XSLT and EXSLT.")
 XLSM) format spreadsheets into plaintext @dfn{comma separated values} (CSV)
 files.  It is designed to be fast and to handle large input files.")
     (license license:gpl2+)))
+
+(define-public python-defusedxml
+  (package
+    (name "python-defusedxml")
+    (version "0.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "defusedxml" version))
+       (sha256
+        (base32
+         "0y147zy3jqmk6ly7fbhqmzn1hf41xcb53f2vcc3m8x4ba5d1smfd"))))
+    (build-system python-build-system)
+    (home-page "https://bitbucket.org/tiran/defusedxml")
+    (synopsis "XML bomb protection for Python stdlib modules")
+    (description
+     "Defusedxml provides XML bomb protection for Python stdlib modules.")
+    (license license:psfl)))
+
+(define-public python2-defusedxml
+  (package-with-python2 python-defusedxml))
+
+(define-public libxls
+  (package
+    (name "libxls")
+    (version "1.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://sourceforge.net/projects/"
+                                  name "/files/" name "-"
+                                  version ".zip"))
+              (sha256
+               (base32
+                "1g8ds7wbhsa4hdcn77xc2c0l3vvz5bx2hx9ng9c9n7aii92ymfnk"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; Bootstrapping is required in order to fix the test driver script.
+         (add-after 'unpack 'bootstrap
+           (lambda _
+             (zero? (system* "bash" "bootstrap")))))))
+    (native-inputs
+     `(("unzip" ,unzip)
+       ("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (home-page "http://libxls.sourceforge.net/")
+    (synopsis "Read Excel files")
+    (description
+     "libxls is a C library which can read Excel (xls) files since Excel 97 (the BIFF8 format).
+libxls cannot write Excel files.")
+    (license license:bsd-2)))

gnu/services.scm

@@ -403,16 +403,13 @@ ACTIVATION-SCRIPT-TYPE."
       ;; Let users debug their own processes!
       (activate-ptrace-attach)))
 
-(define linux-bare-metal-service-type
-  (service-type (name 'linux-bare-metal)
-                (extensions
-                 (list (service-extension activation-service-type
-                                          (const %linux-kernel-activation))))))
-
 (define %linux-bare-metal-service
   ;; The service that does things that are needed on the "bare metal", but not
   ;; necessary or impossible in a container.
-  (service linux-bare-metal-service-type #f))
+  (simple-service 'linux-bare-metal
+                  activation-service-type
+                  %linux-kernel-activation))
+
 
 (define special-files-service-type
   ;; Service to install "special files" such as /bin/sh and /usr/bin/env.

gnu/services/cuirass.scm

@@ -87,7 +87,7 @@
      (list (shepherd-service
             (documentation "Run Cuirass.")
             (provision '(cuirass))
-            (requirement '(guix-daemon))
+            (requirement '(guix-daemon networking))
             (start #~(make-forkexec-constructor
                       (list (string-append #$cuirass "/bin/cuirass")
                             "--cache-directory" #$cache-directory

gnu/services/networking.scm

@@ -595,17 +595,31 @@ HiddenServicePort ~a ~a~%"
   (match config
     (($ <tor-configuration> tor)
      (let ((torrc (tor-configuration->torrc config)))
-       (list (shepherd-service
+       (with-imported-modules (source-module-closure
-              (provision '(tor))
+                               '((gnu build shepherd)
+                                 (gnu system file-systems)))
+         (list (shepherd-service
+                (provision '(tor))
 
-              ;; Tor needs at least one network interface to be up, hence the
+                ;; Tor needs at least one network interface to be up, hence the
-              ;; dependency on 'loopback'.
+                ;; dependency on 'loopback'.
-              (requirement '(user-processes loopback syslogd))
+                (requirement '(user-processes loopback syslogd))
 
-              (start #~(make-forkexec-constructor
+                (modules '((gnu build shepherd)
-                        (list (string-append #$tor "/bin/tor") "-f" #$torrc)))
+                           (gnu system file-systems)))
-              (stop #~(make-kill-destructor))
+
-              (documentation "Run the Tor anonymous network overlay.")))))))
+                (start #~(make-forkexec-constructor/container
+                          (list #$(file-append tor "/bin/tor") "-f" #$torrc)
+
+                          #:mappings (list (file-system-mapping
+                                            (source "/var/lib/tor")
+                                            (target source)
+                                            (writable? #t))
+                                           (file-system-mapping
+                                            (source "/dev/log") ;for syslog
+                                            (target source)))))
+                (stop #~(make-kill-destructor))
+                (documentation "Run the Tor anonymous network overlay."))))))))
 
 (define (tor-hidden-service-activation config)
   "Return the activation gexp for SERVICES, a list of hidden services."

gnu/system/examples/bare-bones.tmpl

@@ -43,5 +43,7 @@
   ;; Add services to the baseline: a DHCP client and
   ;; an SSH server.
   (services (cons* (dhcp-client-service)
-                   (lsh-service #:port-number 2222)
+                   (service openssh-service-type
+                            (openssh-configuration
+                              (port-number 2222)))
                    %base-services)))