Merge branch 'master' into staging

.gitignore

@@ -69,7 +69,6 @@
 /etc/guix-publish.conf
 /etc/guix-publish.service
 /guix-daemon
-/guix-register
 /guix/config.scm
 /libformat.a
 /libstore.a
@@ -147,3 +146,4 @@ tmp
 /nix/scripts/download
 /etc/indent-code.el
 /.version
+/doc/stamp-[0-9]

Makefile.am

@@ -11,6 +11,7 @@
 # Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
 # Copyright © 2018 Nils Gillmann <ng0@n0.is>
 # Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
+# Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
 #
 # This file is part of GNU Guix.
 #
@@ -262,11 +263,7 @@ STORE_MODULES =					\
   guix/store/database.scm			\
   guix/store/deduplication.scm
 
-if HAVE_GUILE_SQLITE3
 MODULES += $(STORE_MODULES)
-else
-MODULES_NOT_COMPILED += $(STORE_MODULES)
-endif !HAVE_GUILE_SQLITE3
 
 # Internal modules with test suite support.
 dist_noinst_DATA = guix/tests.scm guix/tests/http.scm
@@ -300,6 +297,7 @@ EXAMPLES =					\
 GOBJECTS = $(MODULES:%.scm=%.go) guix/config.go $(dist_noinst_DATA:%.scm=%.go)
 
 nobase_dist_guilemodule_DATA =					\
+  guix/store/schema.sql						\
   $(MODULES) $(MODULES_NOT_COMPILED) $(AUX_FILES) $(EXAMPLES)	\
   $(MISC_DISTRO_FILES)
 nobase_nodist_guilemodule_DATA = guix/config.scm
@@ -378,7 +376,9 @@ SCM_TESTS =					\
   tests/scripts-build.scm			\
   tests/containers.scm				\
   tests/pack.scm				\
-  tests/import-utils.scm
+  tests/import-utils.scm			\
+  tests/store-database.scm			\
+  tests/store-deduplication.scm
 
 if HAVE_GUILE_JSON
 
@@ -390,14 +390,6 @@ SCM_TESTS += 					\
 
 endif
 
-if HAVE_GUILE_SQLITE3
-
-SCM_TESTS +=					\
-  tests/store-database.scm			\
-  tests/store-deduplication.scm
-
-endif
-
 SH_TESTS =					\
   tests/guix-build.sh				\
   tests/guix-download.sh			\
@@ -414,13 +406,6 @@ SH_TESTS =					\
   tests/guix-graph.sh				\
   tests/guix-lint.sh
 
-if BUILD_DAEMON
-
-SH_TESTS += tests/guix-register.sh
-
-endif BUILD_DAEMON
-
-
 TESTS = $(SCM_TESTS) $(SH_TESTS)
 
 AM_TESTS_ENVIRONMENT = abs_top_srcdir="$(abs_top_srcdir)" GUILE_AUTO_COMPILE=0
@@ -470,7 +455,8 @@ dist_pkgdata_DATA =				\
   berlin.guixsd.org.pub
 
 # Bash completion file.
-dist_bashcompletion_DATA = etc/completion/bash/guix
+dist_bashcompletion_DATA = etc/completion/bash/guix	\
+  etc/completion/bash/guix-daemon
 
 # Zsh completion file.
 dist_zshcompletion_DATA = etc/completion/zsh/_guix

README

@@ -23,7 +23,8 @@ GNU Guix currently depends on the following packages:
   - [[https://gnu.org/software/guile/][GNU Guile 2.2.x or 2.0.x]], version 2.0.13 or later
   - [[https://gnupg.org/][GNU libgcrypt]]
   - [[https://www.gnu.org/software/make/][GNU Make]]
-  - [[https://www.gnutls.org][GnuTLS]] compiled with guile support enabled.
+  - [[https://www.gnutls.org][GnuTLS]] compiled with guile support enabled
+  - [[https://notabug.org/civodul/guile-sqlite3][Guile-SQLite3]]
   - [[https://gitlab.com/guile-git/guile-git][Guile-Git]]
   - [[http://www.zlib.net/][zlib]]
   - optionally [[https://savannah.nongnu.org/projects/guile-json/][Guile-JSON]], for the 'guix import pypi' command

build-aux/hydra/gnu-system.scm

@@ -43,7 +43,8 @@
 
   (and=> (assoc-ref (current-source-location) 'filename)
          (lambda (file)
-           (let ((dir (string-append (dirname file) "/../..")))
+           (let ((dir (canonicalize-path
+                       (string-append (dirname file) "/../.."))))
              (format (current-error-port) "prepending ~s to the load path~%"
                      dir)
              (set! %load-path (cons dir %load-path))))))

build-aux/pre-inst-env.in

@@ -1,7 +1,7 @@
 #!/bin/sh
 
 # GNU Guix --- Functional package management for GNU
-# Copyright © 2012, 2013, 2014, 2015, 2017 Ludovic Courtès <ludo@gnu.org>
+# Copyright © 2012, 2013, 2014, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 # Copyright © 2017 Eric Bavier <bavier@cray.com>
 #
 # This file is part of GNU Guix.
@@ -55,10 +55,6 @@ NIX_BUILD_HOOK="$abs_top_builddir/nix/scripts/offload"
 @BUILD_DAEMON_OFFLOAD_FALSE@# No offloading support.
 @BUILD_DAEMON_OFFLOAD_FALSE@unset NIX_BUILD_HOOK
 
-# The 'guix-register' program.
-GUIX_REGISTER="$abs_top_builddir/guix-register"
-export GUIX_REGISTER
-
 # The following variables need only be defined when compiling Guix
 # modules, but we define them to be on the safe side in case of
 # auto-compilation.

configure.ac

@@ -126,8 +126,9 @@ AM_CONDITIONAL([HAVE_GUILE_JSON], [test "x$have_guile_json" = "xyes"])
 
 dnl Guile-Sqlite3 is used by the (guix store ...) modules.
 GUIX_CHECK_GUILE_SQLITE3
-AM_CONDITIONAL([HAVE_GUILE_SQLITE3],
+if test "x$guix_cv_have_recent_guile_sqlite3" != "xyes"; then
-  [test "x$guix_cv_have_recent_guile_sqlite3" = "xyes"])
+  AC_MSG_ERROR([A recent Guile-SQLite3 could not be found; please install it.])
+fi
 
 dnl Make sure we have a full-fledged Guile.
 GUIX_ASSERT_GUILE_FEATURES([regex posix socket net-db threads])

doc/contributing.texi

@@ -407,12 +407,19 @@ changes).  This branch is intended to be merged in @code{master} every
 2.5 months or so.
 @end table
 
-All these branches are tracked by our build farm
+All these branches are @uref{https://hydra.gnu.org/project/gnu,
-and merged into @code{master} once
+tracked by our build farm} and merged into @code{master} once
 everything has been successfully built.  This allows us to fix issues
 before they hit users, and to reduce the window during which pre-built
 binaries are not available.
 
+Generally, branches other than @code{master} are considered
+@emph{frozen} if there has been a recent evaluation, or there is a
+corresponding @code{-next} branch.  Please ask on the mailing list or
+IRC if unsure where to place a patch.
+@c TODO: It would be good with badges on the website that tracks these
+@c branches.  Or maybe even a status page.
+
 @item
 @cindex determinism, of build processes
 @cindex reproducible builds, checking

doc/guix.texi

@@ -37,7 +37,7 @@ Copyright @copyright{} 2017 Carlo Zancanaro@*
 Copyright @copyright{} 2017 Thomas Danckaert@*
 Copyright @copyright{} 2017 humanitiesNerd@*
 Copyright @copyright{} 2017 Christopher Allan Webber@*
-Copyright @copyright{} 2017 Marius Bakke@*
+Copyright @copyright{} 2017, 2018 Marius Bakke@*
 Copyright @copyright{} 2017 Hartmut Goebel@*
 Copyright @copyright{} 2017 Maxim Cournoyer@*
 Copyright @copyright{} 2017, 2018 Tobias Geerinckx-Rice@*
@@ -615,6 +615,9 @@ later, including 2.2.x;
 Guile,, gnutls-guile, GnuTLS-Guile});
 @item
 @c FIXME: Specify a version number once a release has been made.
+@uref{https://notabug.org/civodul/guile-sqlite3, Guile-SQLite3};
+@item
+@c FIXME: Specify a version number once a release has been made.
 @uref{https://gitlab.com/guile-git/guile-git, Guile-Git}, from August
 2017 or later;
 @item @url{http://zlib.net, zlib};
@@ -2756,25 +2759,40 @@ export PATH="$HOME/.config/guix/current/bin:$PATH"
 export INFOPATH="$HOME/.config/guix/current/share/info:$INFOPATH"
 @end example
 
+The @code{--list-generations} or @code{-l} option lists past generations
+produced by @command{guix pull}, along with details about their provenance:
+
+@example
+$ guix pull -l
+Generation 1	Jun 10 2018 00:18:18
+  guix 65956ad
+    repository URL: https://git.savannah.gnu.org/git/guix.git
+    branch: origin/master
+    commit: 65956ad3526ba09e1f7a40722c96c6ef7c0936fe
+
+Generation 2	Jun 11 2018 11:02:49
+  guix e0cc7f6
+    repository URL: https://git.savannah.gnu.org/git/guix.git
+    branch: origin/master
+    commit: e0cc7f669bec22c37481dd03a7941c7d11a64f1d
+
+Generation 3	Jun 13 2018 23:31:07	(current)
+  guix 844cc1c
+    repository URL: https://git.savannah.gnu.org/git/guix.git
+    branch: origin/master
+    commit: 844cc1c8f394f03b404c5bb3aee086922373490c
+@end example
+
 This @code{~/.config/guix/current} profile works like any other profile
 created by @command{guix package} (@pxref{Invoking guix package}).  That
 is, you can list generations, roll back to the previous
 generation---i.e., the previous Guix---and so on:
 
 @example
-$ guix package -p ~/.config/guix/current -l
-Generation 1	May 25 2018 10:06:41
-  guix	221951a	out	/gnu/store/i4dfk7vw5k112s49jrhl6hwsfnh6wr7l-guix-221951af4
-
-Generation 2	May 27 2018 19:07:47
- + guix	2fbae00	out	/gnu/store/44cv9hyvxg34xf5kblf5dz57hc52y4bm-guix-2fbae006f
- - guix	221951a	out	/gnu/store/i4dfk7vw5k112s49jrhl6hwsfnh6wr7l-guix-221951af4
-
-Generation 3	May 30 2018 16:11:39	(current)
- + guix	a076f19	out	/gnu/store/332czkicwwg6lc3x4aqbw5q2mq12s7fj-guix-a076f1990
- - guix	2fbae00	out	/gnu/store/44cv9hyvxg34xf5kblf5dz57hc52y4bm-guix-2fbae006f
 $ guix package -p ~/.config/guix/current --roll-back
 switched from generation 3 to 2
+$ guix package -p ~/.config/guix/current --delete-generations=1
+deleting /home/charlie/.config/guix/current-1-link
 @end example
 
 The @command{guix pull} command is usually invoked with no arguments,
@@ -2800,6 +2818,13 @@ string.
 Deploy the tip of @var{branch}, the name of a Git branch available on
 the repository at @var{url}.
 
+@item --list-generations[=@var{pattern}]
+@itemx -l [@var{pattern}]
+List all the generations of @file{~/.config/guix/current} or, if @var{pattern}
+is provided, the subset of generations that match @var{pattern}.
+The syntax of @var{pattern} is the same as with @code{guix package
+--list-generations} (@pxref{Invoking guix package}).
+
 @item --bootstrap
 Use the bootstrap Guile to build the latest Guix.  This option is only
 useful to Guix developers.
@@ -8856,6 +8881,22 @@ Have a look at @file{gnu/system/install.scm} in the source tree,
 and see also @ref{Invoking guix system} for more information
 about the installation image.
 
+@subsection Building the Installation Image for ARM Boards
+
+Many ARM boards require a specific variant of the
+@uref{http://www.denx.de/wiki/U-Boot/, U-Boot} bootloader.
+
+If you build a disk image and the bootloader is not available otherwise
+(on another boot drive etc), it's advisable to build an image that
+includes the bootloader, specifically:
+
+@example
+guix system disk-image --system=armhf-linux -e '((@@ (gnu system install) os-with-u-boot) (@@ (gnu system install) installation-os) "A20-OLinuXino-Lime2")'
+@end example
+
+@code{A20-OLinuXino-Lime2} is the name of the board.  If you specify an invalid
+board, a list of possible boards will be printed.
+
 @node System Configuration
 @section System Configuration
 
@@ -15938,6 +15979,10 @@ use the size of the processors cache line.
 @item @code{server-names-hash-bucket-max-size} (default: @code{#f})
 Maximum bucket size for the server names hash tables.
 
+@item @code{extra-content} (default: @code{""})
+Extra content for the @code{http} block.  Should be string or a string
+valued G-expression.
+
 @end table
 @end deffn
 

etc/completion/bash/guix-daemon

@@ -0,0 +1,30 @@
+# GNU Guix --- Functional package management for GNU
+# Copyright © 2018 Oleg Pykhalov <go.wigust@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/>.
+
+# Bash completion for guix-daemon command.
+
+_guix_daemon_complete ()
+{
+    local options="$(${COMP_WORDS[0]} --help 2> /dev/null \
+                            | grep '^  \+-' \
+                            | sed -e's/^.*--\([a-zA-Z0-9_-]\+\)\(=\?\).*/--\1\2/g')"
+    compopt -o nospace
+    COMPREPLY=($(compgen -W "$options" -- "${COMP_WORDS[${#COMP_WORDS[*]} - 1]}"))
+}
+
+complete -F _guix_daemon_complete guix-daemon

gnu/build/install.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Chris Marusich <cmmarusich@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -18,6 +18,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu build install)
+  #:use-module (guix store database)
   #:use-module (guix build utils)
   #:use-module (guix build store-copy)
   #:use-module (srfi srfi-26)
@@ -25,7 +26,6 @@
   #:export (install-boot-config
             evaluate-populate-directive
             populate-root-file-system
-            reset-timestamps
             register-closure
             populate-single-profile-directory))
 
@@ -110,9 +110,6 @@ STORE."
 
     ("/var/guix/gcroots/booted-system" -> "/run/booted-system")
     ("/var/guix/gcroots/current-system" -> "/run/current-system")
-
-    ;; XXX: 'guix-register' creates this symlink with a wrong target, so
-    ;; create it upfront to be sure.
     ("/var/guix/gcroots/profiles" -> "/var/guix/profiles")
 
     (directory "/bin")
@@ -144,37 +141,27 @@ includes /etc, /var, /run, /bin/sh, etc., and all the symlinks to SYSTEM."
                 (try))
               (apply throw args)))))))
 
-(define (reset-timestamps directory)
+(define* (register-closure prefix closure
-  "Reset the timestamps of all the files under DIRECTORY, so that they appear
+                           #:key
-as created and modified at the Epoch."
+                           (deduplicate? #t) (reset-timestamps? #t)
-  (display "clearing file timestamps...\n")
+                           (schema (sql-schema)))
-  (for-each (lambda (file)
+  "Register CLOSURE in PREFIX, where PREFIX is the directory name of the
-              (let ((s (lstat file)))
+target store and CLOSURE is the name of a file containing a reference graph as
-                ;; XXX: Guile uses libc's 'utime' function (not 'futime'), so
+produced by #:references-graphs..  As a side effect, if RESET-TIMESTAMPS? is
-                ;; the timestamp of symlinks cannot be changed, and there are
+true, reset timestamps on store files and, if DEDUPLICATE? is true,
-                ;; symlinks here pointing to /gnu/store, which is the host,
+deduplicates files common to CLOSURE and the rest of PREFIX."
-                ;; read-only store.
+  (let ((items (call-with-input-file closure read-reference-graph)))
-                (unless (eq? (stat:type s) 'symlink)
+    (register-items items
-                  (utime file 0 0 0 0))))
+                    #:prefix prefix
-            (find-files directory #:directories? #t)))
+                    #:deduplicate? deduplicate?
-
+                    #:reset-timestamps? reset-timestamps?
-(define* (register-closure store closure
+                    #:registration-time %epoch
-                           #:key (deduplicate? #t))
+                    #:schema schema)))
-  "Register CLOSURE in STORE, where STORE is the directory name of the target
-store and CLOSURE is the name of a file containing a reference graph as used
-by 'guix-register'.  As a side effect, this resets timestamps on store files
-and, if DEDUPLICATE? is true, deduplicates files common to CLOSURE and the
-rest of STORE."
-  (let ((status (apply system* "guix-register" "--prefix" store
-                       (append (if deduplicate? '() '("--no-deduplication"))
-                               (list closure)))))
-    (unless (zero? status)
-      (error "failed to register store items" closure))))
 
 (define* (populate-single-profile-directory directory
                                             #:key profile closure
                                             deduplicate?
-                                            register?)
+                                            register? schema)
   "Populate DIRECTORY with a store containing PROFILE, whose closure is given
 in the file called CLOSURE (as generated by #:references-graphs.)  DIRECTORY
 is initialized to contain a single profile under /root pointing to PROFILE.
@@ -200,11 +187,11 @@ This is used to create the self-contained tarballs with 'guix pack'."
 
   (when register?
     (register-closure (canonicalize-path directory) closure
-                      #:deduplicate? deduplicate?)
+                      #:deduplicate? deduplicate?
+                      #:schema schema)
 
-    ;; XXX: 'guix-register' registers profiles as GC roots but the symlink
+    (mkdir-p* "/var/guix/profiles")
-    ;; target uses $TMPDIR.  Fix that.
+    (mkdir-p* "/var/guix/gcroots")
-    (delete-file (scope "/var/guix/gcroots/profiles"))
     (symlink* "/var/guix/profiles"
               "/var/guix/gcroots/profiles"))
 

gnu/build/linux-modules.scm

@@ -32,6 +32,7 @@
             ensure-dot-ko
             module-aliases
             module-dependencies
+            normalize-module-name
             recursive-module-dependencies
             modules-loaded
             module-loaded?

gnu/build/vm.scm

@@ -25,6 +25,7 @@
   #:use-module (guix build utils)
   #:use-module (guix build store-copy)
   #:use-module (guix build syscalls)
+  #:use-module ((guix store database) #:select (reset-timestamps))
   #:use-module (gnu build linux-boot)
   #:use-module (gnu build install)
   #:use-module (gnu system uuid)
@@ -345,7 +346,7 @@ SYSTEM-DIRECTORY is the name of the directory of the 'system' derivation."
     ;; Optionally, register the inputs in the image's store.
     (when register-closures?
       (unless copy-closures?
-        ;; XXX: 'guix-register' wants to palpate the things it registers, so
+        ;; XXX: 'register-closure' wants to palpate the things it registers, so
         ;; bind-mount the store on the target.
         (mkdir-p target-store)
         (mount (%store-directory) target-store "" MS_BIND))
@@ -354,6 +355,7 @@ SYSTEM-DIRECTORY is the name of the directory of the 'system' derivation."
       (for-each (lambda (closure)
                   (register-closure target
                                     (string-append "/xchg/" closure)
+                                    #:reset-timestamps? copy-closures?
                                     #:deduplicate? deduplicate?))
                 closures)
       (unless copy-closures?
@@ -363,7 +365,7 @@ SYSTEM-DIRECTORY is the name of the directory of the 'system' derivation."
     (display "populating...\n")
     (populate-root-file-system system-directory target)
 
-    ;; 'guix-register' resets timestamps and everything, so no need to do it
+    ;; 'register-closure' resets timestamps and everything, so no need to do it
     ;; once more in that case.
     (unless register-closures?
       (reset-timestamps target))))

gnu/local.mk

@@ -581,6 +581,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/azr3.patch				\
   %D%/packages/patches/bash-completion-directories.patch	\
   %D%/packages/patches/bazaar-CVE-2017-14176.patch		\
+  %D%/packages/patches/bind-CVE-2018-5738.patch			\
+  %D%/packages/patches/binutils-aarch64-symbol-relocation.patch	\
   %D%/packages/patches/binutils-loongson-workaround.patch	\
   %D%/packages/patches/blast+-fix-makefile.patch		\
   %D%/packages/patches/boost-fix-icu-build.patch		\
@@ -641,7 +643,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/e2fsprogs-glibc-2.27.patch		\
   %D%/packages/patches/eigen-arm-neon-fixes.patch		\
   %D%/packages/patches/elfutils-tests-ptrace.patch		\
-  %D%/packages/patches/elixir-disable-failing-tests.patch	\
   %D%/packages/patches/elogind-glibc-2.27.patch			\
   %D%/packages/patches/einstein-build.patch			\
   %D%/packages/patches/emacs-browse-at-remote-cgit-gnu.patch	\
@@ -671,6 +672,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/file-CVE-2017-1000249.patch		\
   %D%/packages/patches/findutils-localstatedir.patch		\
   %D%/packages/patches/findutils-test-xargs.patch		\
+  %D%/packages/patches/flann-cmake-3.11.patch			\
   %D%/packages/patches/flint-ldconfig.patch			\
   %D%/packages/patches/fltk-shared-lib-defines.patch		\
   %D%/packages/patches/fltk-xfont-on-demand.patch		\
@@ -744,7 +746,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/gnome-todo-libical-compat.patch		\
   %D%/packages/patches/gnome-tweak-tool-search-paths.patch	\
   %D%/packages/patches/gnucash-price-quotes-perl.patch		\
-  %D%/packages/patches/gnupg-1.4-CVE-2018-12020.patch		\
   %D%/packages/patches/gnutls-skip-trust-store-test.patch	\
   %D%/packages/patches/gnutls-skip-pkgconfig-test.patch		\
   %D%/packages/patches/gobject-introspection-absolute-shlib-path.patch \
@@ -982,12 +983,12 @@ dist_patch_DATA =						\
   %D%/packages/patches/p7zip-CVE-2016-9296.patch		\
   %D%/packages/patches/p7zip-CVE-2017-17969.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/perf-gcc-ice.patch			\
+  %D%/packages/patches/perl-archive-tar-CVE-2018-12015.patch	\
   %D%/packages/patches/perl-file-path-CVE-2017-6512.patch	\
   %D%/packages/patches/perl-autosplit-default-time.patch	\
   %D%/packages/patches/perl-dbd-mysql-CVE-2017-10788.patch	\
@@ -1050,7 +1051,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-genshi-stripping-of-unsafe-script-tags.patch	\
   %D%/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch \
   %D%/packages/patches/python-networkx2-reproducible-build.patch	\
-  %D%/packages/patches/python-nose-timer-drop-ordereddict.patch \
   %D%/packages/patches/python-pillow-fix-failing-tests.patch	\
   %D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch	\
   %D%/packages/patches/python-scikit-learn-fix-test-non-determinism.patch	\
@@ -1111,7 +1111,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/slim-login.patch				\
   %D%/packages/patches/sooperlooper-build-with-wx-30.patch 	\
   %D%/packages/patches/steghide-fixes.patch			\
-  %D%/packages/patches/strace-kernel-4.16.patch			\
   %D%/packages/patches/superlu-dist-scotchmetis.patch		\
   %D%/packages/patches/swish-e-search.patch			\
   %D%/packages/patches/swish-e-format-security.patch		\
@@ -1157,6 +1156,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/ustr-fix-build-with-gcc-5.patch		\
   %D%/packages/patches/util-linux-tests.patch			\
   %D%/packages/patches/upower-builddir.patch			\
+  %D%/packages/patches/upx-fix-CVE-2017-15056.patch		\
   %D%/packages/patches/valgrind-enable-arm.patch		\
   %D%/packages/patches/valgrind-glibc-compat.patch		\
   %D%/packages/patches/vinagre-revert-1.patch                   \

gnu/packages/admin.scm

@@ -21,6 +21,7 @@
 ;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
+;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -822,41 +823,36 @@ by bandwidth they use.")
 (define-public clusterssh
   (package
     (name "clusterssh")
-    (version "3.28")
+    (version "4.13.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/clusterssh/"
-                                  "1.%20ClusterSSH%20Series%203/" version
+                                  "2.%20ClusterSSH%20Series%204/"
-                                  "/clusterssh-" version ".tar.gz"))
+                                  "App-ClusterSSH-v" version ".tar.gz"))
               (sha256
                (base32
-                "1bwggpvaj2al5blg1ynapviv2kpydffpzq2zkhi81najnvzc1rr7"))))
+                "0rmk2p3f2wz1h092anidjclh212rv3gxyk0c641qk3frlrjnw6mp"))))
-    (build-system gnu-build-system)
+    (build-system perl-build-system)
-    (inputs `(("perl" ,perl)))
+    (native-inputs
-    (propagated-inputs `(("xterm" ,xterm)
+     `(("perl-cpan-changes" ,perl-cpan-changes)
+       ("perl-file-slurp" ,perl-file-slurp)
+       ("perl-file-which" ,perl-file-which)
+       ("perl-module-build" ,perl-module-build)
+       ("perl-readonly" ,perl-readonly)
+       ("perl-test-differences" ,perl-test-differences)
+       ("perl-test-distmanifest" ,perl-test-distmanifest)
+       ("perl-test-perltidy" ,perl-test-perltidy)
+       ("perl-test-pod" ,perl-test-pod)
+       ("perl-test-pod-coverage" ,perl-test-pod-coverage)
+       ("perl-test-trap" ,perl-test-trap)
+       ("perltidy" ,perltidy)))
+    (propagated-inputs
+     `(("xterm" ,xterm)
+       ("perl-exception-class" ,perl-exception-class)
        ("perl-tk" ,perl-tk)
-                         ("perl-x11-protocol" ,perl-x11-protocol)))
+       ("perl-try-tiny" ,perl-try-tiny)
-    (arguments
+       ("perl-x11-protocol" ,perl-x11-protocol)
-     `(#:phases
+       ("perl-x11-protocol-other" ,perl-x11-protocol-other)))
-       (modify-phases %standard-phases
-         (add-after 'install 'set-load-paths
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             ;; Put the perl-tk and perl-x11-protocol modules in the perl inc
-             ;; path for PROG
-             (let* ((out  (assoc-ref outputs "out"))
-                    (prog (string-append out "/bin/cssh"))
-                    (perl-ver ,(package-version perl))
-                    (x11-inc (string-append
-                              (assoc-ref inputs "perl-x11-protocol")
-                              "/lib/perl5/site_perl/" perl-ver))
-                    (tk-inc (string-append
-                             (assoc-ref inputs "perl-tk")
-                             "/lib/perl5/site_perl/" perl-ver
-                             "/x86_64-linux")))
-               (wrap-program
-                   prog
-                 `("PERL5LIB" ":" prefix (,x11-inc ,tk-inc))))
-             #t)))))
     ;; The clusterssh.sourceforge.net address requires login to view
     (home-page "https://sourceforge.net/projects/clusterssh/")
     (synopsis "Secure concurrent multi-server terminal control")
@@ -2359,11 +2355,23 @@ Intel DRM Driver.")
          "13r0b0hllgf8j9rh6x1knmbgvingbdmx046aazv6vck2ll120mw1"))))
     (build-system python-build-system)
     (arguments
-     `(#:python ,python-2))             ; Python 2 only
+     `(#:python ,python-2               ; Python 2 only
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (invoke
+              "nosetests" "-v" "tests/"
+              ;; This test hangs indefinitely when run on a single core VM
+              ;; (see GNU bug #26647 and Debian bug #850230).
+              "--exclude=test_nested_execution_with_explicit_ports"
+              ;; This test randomly fails in certain environments causing too
+              ;; much noise to be useful (see Debian bug #854686).
+              "--exclude=test_should_use_sentinel_for_tasks_that_errored"))))))
     (native-inputs
-     `(("python2-fudge" ,python2-fudge)
+     `(("python2-fudge" ,python2-fudge) ; Requires < 1.0
-       ("python2-jinja2" ,python2-jinja2)
+       ("python2-jinja2" ,python2-jinja2) ; Requires < 3.0
-       ("python2-nose" ,python2-nose)
+       ("python2-nose" ,python2-nose) ; Requires < 2.0
        ("python2-pynacl" ,python2-pynacl)
        ("python2-bcrypt" ,python2-bcrypt)))
     (propagated-inputs
@@ -2383,7 +2391,7 @@ tool for remote execution and deployment.")
 (define-public neofetch
   (package
     (name "neofetch")
-    (version "3.4.0")
+    (version "4.0.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/dylanaraps/neofetch/"
@@ -2391,7 +2399,7 @@ tool for remote execution and deployment.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "18rhamy910ig03rr55y9x5i6pf78yj9xc6jpm6nfh3gqja7340rb"))))
+                "014hlbzs6j4b669b64hnq8vc5knwiv9ncw9m9d193p9jsybxpm1w"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; there are no tests

gnu/packages/aidc.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2014 John Darringon <jmd@gnu.org>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Hartmut Goebel <h.goebel@crazy-compilers.com>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -51,7 +52,7 @@ formats.")
 (define-public qrencode
   (package
     (name "qrencode")
-    (version "4.0.0")
+    (version "4.0.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -59,7 +60,7 @@ formats.")
                     ".tar.bz2"))
               (sha256
                (base32
-                "02vx69fl52jbcrmnydsaxcmy6nxqm9jyxzd7hr07s491d7hka069"))))
+                "1d2q5d3v8g3hsi3h5jq4n177bjhf3kawms09immw7p187f6jgjy9"))))
     (build-system gnu-build-system)
     (inputs `(("libpng" ,libpng)))
     (native-inputs `(("pkg-config" ,pkg-config)))

gnu/packages/audio.scm

@@ -1890,7 +1890,7 @@ lv2-c++-tools.")
 (define-public openal
   (package
     (name "openal")
-    (version "1.17.2")
+    (version "1.18.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1898,7 +1898,7 @@ lv2-c++-tools.")
                     version ".tar.bz2"))
               (sha256
                (base32
-                "051k5fy8pk4fd9ha3qaqcv08xwbks09xl5qs4ijqq2qz5xaghhd3"))))
+                "10kydm8701a2kppiss9sdidn1820cmzhqgx1b2bsa5dsgzic32lz"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f  ; no check target

gnu/packages/backup.scm

@@ -10,6 +10,7 @@
 ;;; Copyright © 2017 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -32,6 +33,7 @@
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system go)
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages acl)
@@ -45,6 +47,7 @@
   #:use-module (gnu packages ftp)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnupg)
+  #:use-module (gnu packages golang)
   #:use-module (gnu packages gperf)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages linux)
@@ -472,13 +475,13 @@ detection, and lossless compression.")
 (define-public borg
   (package
     (name "borg")
-    (version "1.1.5")
+    (version "1.1.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "borgbackup" version))
        (sha256
-        (base32 "0gbdnq7ks46diz6y2pf6wpwkb9hy6hp3immi7jg3h7w72b3ycmj3"))
+        (base32 "0c09j46fi8i7klas0bh82a4whlwnajshk0izkgax6fjxr1sf9lm1"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -511,17 +514,6 @@ detection, and lossless compression.")
                ;; HOME=/homeless-shelter.
                (setenv "HOME" "/tmp")
                #t)))
-         ;; Later versions of msgpack were disallowed to some warnings and lack
-         ;; of support for Python versions that we don't support anyways. So,
-         ;; it's okay to to keep using more recents versions of msgpack for
-         ;; Borg. Also see the note about msgpack in the list of inputs.
-         ;; https://github.com/borgbackup/borg/issues/3517#issuecomment-357221978
-         (add-before 'build 'adjust-msgpack-dependency
-           (lambda _
-             (substitute* "setup.py"
-               (("msgpack-python>=0.4.6,<0.5.0")
-                 "msgpack-python>=0.4.6"))
-             #t))
          ;; The tests need to be run after Borg is installed.
          (delete 'check)
          (add-after 'install 'check
@@ -833,3 +825,112 @@ file systems with unattended creation and expiration.  A dirvish backup vault
 is like a time machine for your data. ")
     (license (license:fsf-free "file://COPYING"
                                "Open Software License 2.0"))))
+
+(define-public restic ; bundled / vendored dependencies
+  (package
+    (name "restic")
+    (version "0.9.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/restic/restic/releases/download/"
+                    "v" version "/restic-" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "15f0rsm2lxk4lmn4773q28g49p68pqyyx0ccp7r556asan73p79m"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "github.com/restic/restic"
+       #:unpack-path "github.com/restic"
+      ;; We don't need to install the source code for end-user applications.
+       #:install-source? #f
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'build
+           (lambda* (#:key inputs #:allow-other-keys)
+             (with-directory-excursion (string-append
+                                        "src/github.com/restic/restic-"
+                                        ,version)
+               (invoke "go" "run" "build.go"))))
+
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (src (string-append "src/github.com/restic/restic-"
+                                       ,version)))
+               (install-file (string-append src "/restic")
+                             (string-append out "/bin"))
+               #t)))
+
+         (add-after 'install 'install-docs
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (man "/share/man")
+                    (man-section (string-append man "/man"))
+                    (src (string-append "src/github.com/restic/restic-"
+                                        ,version "/doc/man/")))
+               ;; Install all the man pages to "out".
+               (for-each
+                 (lambda (file)
+                   (install-file file
+                                 (string-append out man-section
+                                                (string-take-right file 1))))
+                 (find-files src "\\.[1-9]"))
+               #t)))
+
+         (add-after 'install-docs 'install-shell-completion
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (etc (string-append out "/etc"))
+                    (share (string-append out "/share")))
+               (for-each
+                (lambda (shell)
+                  (let* ((shell-name (symbol->string shell))
+                         (dir (string-append "etc/completion/" shell-name)))
+                    (mkdir-p dir)
+                    (invoke (string-append bin "/restic") "generate"
+                            (string-append "--" shell-name "-completion")
+                            (string-append dir "/"
+                                           (case shell
+                                             ((bash) "restic")
+                                             ((zsh) "_restic"))))))
+                '(bash zsh))
+               (with-directory-excursion "etc/completion"
+                 (install-file "bash/restic"
+                               (string-append etc "/bash_completion.d"))
+                 (install-file "zsh/_restic"
+                               (string-append share "/zsh/site-functions")))
+               #t))))))
+    (home-page "https://restic.net/")
+    (synopsis "Backup program with multiple revisions, encryption and more")
+    (description "Restic is a program that does backups right and was designed
+with the following principles in mind:
+
+@itemize
+@item Easy: Doing backups should be a frictionless process, otherwise you
+might be tempted to skip it.  Restic should be easy to configure and use, so
+that, in the event of a data loss, you can just restore it.  Likewise,
+restoring data should not be complicated.
+
+@item Fast: Backing up your data with restic should only be limited by your
+network or hard disk bandwidth so that you can backup your files every day.
+Nobody does backups if it takes too much time.  Restoring backups should only
+transfer data that is needed for the files that are to be restored, so that
+this process is also fast.
+
+@item Verifiable: Much more important than backup is restore, so restic
+enables you to easily verify that all data can be restored.  @item Secure:
+Restic uses cryptography to guarantee confidentiality and integrity of your
+data.  The location the backup data is stored is assumed not to be a trusted
+environment (e.g.  a shared space where others like system administrators are
+able to access your backups).  Restic is built to secure your data against
+such attackers.
+
+@item Efficient: With the growth of data, additional snapshots should only
+take the storage of the actual increment.  Even more, duplicate data should be
+de-duplicated before it is actually written to the storage back end to save
+precious backup space.
+@end itemize")
+    (license license:bsd-2)))

gnu/packages/base.scm

@@ -480,6 +480,17 @@ included.")
    (license gpl3+)
    (home-page "https://www.gnu.org/software/binutils/")))
 
+(define-public binutils/fixed
+  ;; TODO: Incorporate this in binutils during the next rebuild cycle.
+  (hidden-package
+   (package
+     (inherit binutils)
+     (source (origin
+               (inherit (package-source binutils))
+               (patches (append (origin-patches (package-source binutils))
+                                (search-patches
+                                 "binutils-aarch64-symbol-relocation.patch"))))))))
+
 (define* (make-ld-wrapper name #:key
                           (target (const #f))
                           binutils

gnu/packages/benchmark.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Dave Love <fx@gnu.org>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -34,15 +35,14 @@
 (define-public fio
   (package
     (name "fio")
-    (version "3.6")
+    (version "3.7")
     (source (origin
               (method url-fetch)
-              (uri (string-append
+              (uri (string-append "http://brick.kernel.dk/snaps/"
-                       "http://brick.kernel.dk/snaps/"
+                                  "fio-" version ".tar.gz"))
-                       "fio-" version ".tar.bz2"))
               (sha256
                (base32
-                "1d2jibp1b2dq97f22wj6pcjl7gbd2kmhfggj2c7q3j8v9axjqsh2"))))
+                "0rw9jf2ikm19lq4jizavdvvp3vfvlm3annq7jsxl2y5nf1pi2qr7"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"

gnu/packages/bioconductor.scm

@@ -24,10 +24,11 @@
   #:use-module (guix download)
   #:use-module (guix build-system r)
   #:use-module (gnu packages)
+  #:use-module (gnu packages bioinformatics)
   #:use-module (gnu packages cran)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages statistics)
+  #:use-module (gnu packages graph)
-  #:use-module (gnu packages bioinformatics))
+  #:use-module (gnu packages statistics))
 
 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
   (package
@@ -61,6 +62,111 @@ melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
 objects.")
     (license license:artistic2.0)))
 
+(define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
+  (package
+    (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
+    (version "1.3.99")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/annotation/" instead of "bioc/".
+              (uri (string-append "http://www.bioconductor.org/packages/"
+                                  "release/data/annotation/src/contrib/"
+                                  "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
+    (properties
+     `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bsgenome" ,r-bsgenome)
+       ("r-bsgenome-dmelanogaster-ucsc-dm3"
+        ,r-bsgenome-dmelanogaster-ucsc-dm3)))
+    (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
+    (synopsis "Full masked genome sequences for Fly")
+    (description
+     "This package provides full masked genome sequences for Drosophila
+melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
+Biostrings objects.  The sequences are the same as in
+BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
+masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
+intra-contig ambiguities (AMB mask), (3) the mask of repeats from
+RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
+Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by default.")
+    (license license:artistic2.0)))
+
+(define-public r-bsgenome-hsapiens-ucsc-hg19-masked
+  (package
+    (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
+    (version "1.3.99")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/annotation/" instead of "bioc/".
+              (uri (string-append "http://www.bioconductor.org/packages/"
+                                  "release/data/annotation/src/contrib/"
+                                  "BSgenome.Hsapiens.UCSC.hg19.masked_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
+    (properties
+     `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bsgenome" ,r-bsgenome)
+       ("r-bsgenome-hsapiens-ucsc-hg19"
+        ,r-bsgenome-hsapiens-ucsc-hg19)))
+    (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
+    (synopsis "Full masked genome sequences for Homo sapiens")
+    (description
+     "This package provides full genome sequences for Homo sapiens (Human) as
+provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects.  The
+sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
+them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
+mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
+repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
+Repeats Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by
+default.")
+    (license license:artistic2.0)))
+
+(define-public r-bsgenome-mmusculus-ucsc-mm9-masked
+  (package
+    (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
+    (version "1.3.99")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/annotation/" instead of "bioc/".
+              (uri (string-append "http://www.bioconductor.org/packages/"
+                                  "release/data/annotation/src/contrib/"
+                                  "BSgenome.Mmusculus.UCSC.mm9.masked_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
+    (properties
+     `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bsgenome" ,r-bsgenome)
+       ("r-bsgenome-mmusculus-ucsc-mm9"
+        ,r-bsgenome-mmusculus-ucsc-mm9)))
+    (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
+    (synopsis "Full masked genome sequences for Mouse")
+    (description
+     "This package provides full genome sequences for Mus musculus (Mouse) as
+provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects.  The
+sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
+them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
+mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
+repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
+Repeats Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by
+default."  )
+    (license license:artistic2.0)))
+
 (define-public r-hpar
   (package
     (name "r-hpar")
@@ -371,3 +477,201 @@ filtered to remove spurious regions in the genome.  Downstream steps of
 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
 respectively.")
     (license license:gpl2+)))
+
+(define-public r-bayseq
+  (package
+    (name "r-bayseq")
+    (version "2.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "baySeq" version))
+       (sha256
+        (base32
+         "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg"))))
+    (properties `((upstream-name . "baySeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-abind" ,r-abind)
+       ("r-edger" ,r-edger)
+       ("r-genomicranges" ,r-genomicranges)))
+    (home-page "https://bioconductor.org/packages/baySeq/")
+    (synopsis "Bayesian analysis of differential expression patterns in count data")
+    (description
+     "This package identifies differential expression in high-throughput count
+data, such as that derived from next-generation sequencing machines,
+calculating estimated posterior likelihoods of differential expression (or
+more complex hypotheses) via empirical Bayesian methods.")
+    (license license:gpl3)))
+
+(define-public r-chipcomp
+  (package
+    (name "r-chipcomp")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ChIPComp" version))
+       (sha256
+        (base32
+         "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs"))))
+    (properties `((upstream-name . "ChIPComp")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+       ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-limma" ,r-limma)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/ChIPComp")
+    (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
+    (description
+     "ChIPComp implements a statistical method for quantitative comparison of
+multiple ChIP-seq datasets.  It detects differentially bound sharp binding
+sites across multiple conditions considering matching control in ChIP-seq
+datasets.")
+    ;; Any version of the GPL.
+    (license license:gpl3+)))
+
+(define-public r-riboprofiling
+  (package
+    (name "r-riboprofiling")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "RiboProfiling" version))
+       (sha256
+        (base32
+         "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0"))))
+    (properties `((upstream-name . "RiboProfiling")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-data-table" ,r-data-table)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggbio" ,r-ggbio)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-iranges" ,r-iranges)
+       ("r-plyr" ,r-plyr)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-sqldf" ,r-sqldf)))
+    (home-page "https://bioconductor.org/packages/RiboProfiling/")
+    (synopsis "Ribosome profiling data analysis")
+    (description "Starting with a BAM file, this package provides the
+necessary functions for quality assessment, read start position recalibration,
+the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
+of count data: pairs, log fold-change, codon frequency and coverage
+assessment, principal component analysis on codon coverage.")
+    (license license:gpl3)))
+
+(define-public r-riboseqr
+  (package
+    (name "r-riboseqr")
+    (version "1.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "riboSeqR" version))
+       (sha256
+        (base32
+         "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn"))))
+    (properties `((upstream-name . "riboSeqR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-abind" ,r-abind)
+       ("r-bayseq" ,r-bayseq)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-seqlogo" ,r-seqlogo)))
+    (home-page "https://bioconductor.org/packages/riboSeqR/")
+    (synopsis "Analysis of sequencing data from ribosome profiling experiments")
+    (description
+     "This package provides plotting functions, frameshift detection and
+parsing of genetic sequencing data from ribosome profiling experiments.")
+    (license license:gpl3)))
+
+(define-public r-interactionset
+  (package
+    (name "r-interactionset")
+    (version "1.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "InteractionSet" version))
+       (sha256
+        (base32
+         "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n"))))
+    (properties
+     `((upstream-name . "InteractionSet")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://bioconductor.org/packages/InteractionSet")
+    (synopsis "Base classes for storing genomic interaction data")
+    (description
+     "This packages provides the @code{GInteractions},
+@code{InteractionSet} and @code{ContactMatrix} objects and associated methods
+for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
+experiments.")
+    (license license:gpl3)))
+
+(define-public r-genomicinteractions
+  (package
+    (name "r-genomicinteractions")
+    (version "1.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "GenomicInteractions" version))
+       (sha256
+        (base32
+         "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q"))))
+    (properties
+     `((upstream-name . "GenomicInteractions")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-data-table" ,r-data-table)
+       ("r-dplyr" ,r-dplyr)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-gviz" ,r-gviz)
+       ("r-igraph" ,r-igraph)
+       ("r-interactionset" ,r-interactionset)
+       ("r-iranges" ,r-iranges)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-stringr" ,r-stringr)))
+    (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
+    (synopsis "R package for handling genomic interaction data")
+    (description
+     "This R package provides tools for handling genomic interaction data,
+such as ChIA-PET/Hi-C, annotating genomic features with interaction
+information and producing various plots and statistics.")
+    (license license:gpl3)))

gnu/packages/bioinformatics.scm

@@ -6939,13 +6939,13 @@ Bioconductor, CRAN, and Github.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.48.0")
+    (version "1.48.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "1yx2lir67ny0j150wyfqca0wsxp84byri8nscbs9qlndkh2jppq9"))))
+                "1q5z6xxhjyibr165di7iyachw4gd4bdrxkd8rjkcklnngsrx1azm"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -7128,13 +7128,13 @@ abnormal copy number.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.18.2")
+    (version "0.18.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "0qvj2j0zl4djjl7vrwc6xak6h8dxr53iwypfbcvfb3sh7jwhdiz5"))))
+                "02bps2rpjqx2npwxq3x62ncwi9ggr165cwi56h6hld28bw2gddy8"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -9705,13 +9705,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "2.3.1")
+    (version "2.3.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "0hi59rgdrr2iqfvx5bq7yq02hbjxkjl1fzidqj14z0ypq0nzbjys"))
+                "1sjpy5rrpvlpm6hs7qy7qpglgbp7zrgfybcsalpmjb51rhxhgcg1"))
               ;; Delete pre-built jar.
               (snippet
                '(begin (delete-file "inst/java/ModularityOptimizer.jar")
@@ -9755,6 +9755,7 @@ Main-Class: ModularityOptimizer\n")))
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggridges" ,r-ggridges)
        ("r-gplots" ,r-gplots)
+       ("r-hdf5r" ,r-hdf5r)
        ("r-hmisc" ,r-hmisc)
        ("r-ica" ,r-ica)
        ("r-igraph" ,r-igraph)
@@ -12905,7 +12906,7 @@ expression report comparing samples in an easily configurable manner.")
 (define-public pigx-chipseq
   (package
     (name "pigx-chipseq")
-    (version "0.0.15")
+    (version "0.0.16")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
@@ -12913,7 +12914,7 @@ expression report comparing samples in an easily configurable manner.")
                                   "/pigx_chipseq-" version ".tar.gz"))
               (sha256
                (base32
-                "11v9v3vyda0sv4cl45nki7mm4v4bjfcdq7a70kcvi9h465nq66wg"))))
+                "0s53840z53pih0jkllmcfb2la7c36zxmf229fshhyq8n6a2hgr8f"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; parts of the tests rely on access to the network
@@ -12985,7 +12986,7 @@ in an easily configurable manner.")
 (define-public pigx-bsseq
   (package
     (name "pigx-bsseq")
-    (version "0.0.8")
+    (version "0.0.9")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
@@ -12993,7 +12994,7 @@ in an easily configurable manner.")
                                   "/pigx_bsseq-" version ".tar.gz"))
               (sha256
                (base32
-                "0irlnlhhw9fd4ha7hksrxn3y7j76mz5qq1wjswbs9p364laqg69y"))))
+                "0j1dfjk8m1p1h6d5yw63scjlbx56z8gixmbw626w1vcyblg0frmz"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -13052,7 +13053,7 @@ methylation and segmentation.")
 (define-public pigx-scrnaseq
   (package
     (name "pigx-scrnaseq")
-    (version "0.0.4")
+    (version "0.0.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
@@ -13060,7 +13061,7 @@ methylation and segmentation.")
                                   "/pigx_scrnaseq-" version ".tar.gz"))
               (sha256
                (base32
-                "1pvjm6f3mascprs65vflggwwg5v925knvgal7k7a6nnlmw5qndrf"))))
+                "0a73rilv0vnw42d5rsdq205h4f0x8j3jqv998janh4s324c6w2kj"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -13088,6 +13089,7 @@ methylation and segmentation.")
        ("python-wrapper" ,python-wrapper)
        ("python-pyyaml" ,python-pyyaml)
        ("python-pandas" ,python-pandas)
+       ("python-magic" ,python-magic)
        ("python-numpy" ,python-numpy)
        ("python-loompy" ,python-loompy)
        ("ghc-pandoc" ,ghc-pandoc-1)
@@ -13245,3 +13247,62 @@ rate speciation and extinction.")
 junctions in RNA-seq data.  It is annotation-agnostic and offset-aware.  This
 version does count multisplits.")
       (license license:gpl3+))))
+
+(define-public minimap2
+  (package
+    (name "minimap2")
+    (version "2.10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/lh3/minimap2/"
+                           "releases/download/v" version "/"
+                           "minimap2-" version ".tar.bz2"))
+       (sha256
+        (base32
+         "080w9066irkbhbyr4nmf19pzkdd2s4v31hpzlajgq2y0drr6zcsj"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ; there are none
+       #:make-flags
+       (list "CC=gcc"
+             (let ((system ,(or (%current-target-system)
+                                (%current-system))))
+               (cond
+                ((string-prefix? "x86_64" system)
+                 "all")
+                ((or (string-prefix? "armhf" system)
+                     (string-prefix? "aarch64" system))
+                 "arm_neon=1")
+                (_ "sse2only=1"))))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (man (string-append out "/share/man/man1")))
+               (install-file "minimap2" bin)
+               (mkdir-p man)
+               (install-file "minimap2.1" man))
+             #t)))))
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://lh3.github.io/minimap2/")
+    (synopsis "Pairwise aligner for genomic and spliced nucleotide sequences")
+    (description "Minimap2 is a versatile sequence alignment program that
+aligns DNA or mRNA sequences against a large reference database.  Typical use
+cases include:
+
+@enumerate
+@item mapping PacBio or Oxford Nanopore genomic reads to the human genome;
+@item finding overlaps between long reads with error rate up to ~15%;
+@item splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA
+  reads against a reference genome;
+@item aligning Illumina single- or paired-end reads;
+@item assembly-to-assembly alignment;
+@item full-genome alignment between two closely related species with
+  divergence below ~15%.
+@end enumerate\n")
+    (license license:expat)))

gnu/packages/bootloaders.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
@@ -61,7 +61,8 @@
   #:use-module (guix packages)
   #:use-module (guix utils)
   #:use-module (srfi srfi-1)
-  #:use-module (srfi srfi-26))
+  #:use-module (srfi srfi-26)
+  #:use-module (ice-9 regex))
 
 (define unifont
   ;; GNU Unifont, <http://gnu.org/s/unifont>.
@@ -144,6 +145,22 @@
        ("texinfo" ,texinfo)
        ("help2man" ,help2man)
 
+       ;; XXX: When building GRUB 2.02 on 32-bit x86, we need a binutils
+       ;; capable of assembling 64-bit instructions.  However, our default
+       ;; binutils on 32-bit x86 is not 64-bit capable.
+       ,@(if (string-match "^i[3456]86-" (%current-system))
+             (let ((binutils (package/inherit
+                              binutils
+                              (name "binutils-i386")
+                              (arguments
+                               (substitute-keyword-arguments (package-arguments binutils)
+                                 ((#:configure-flags flags ''())
+                                  `(cons "--enable-64-bit-bfd" ,flags)))))))
+               `(("ld-wrapper" ,(make-ld-wrapper "ld-wrapper-i386"
+                                                 #:binutils binutils))
+                 ("binutils" ,binutils)))
+             '())
+
        ;; Dependencies for the test suite.  The "real" QEMU is needed here,
        ;; because several targets are used.
        ("parted" ,parted)
@@ -439,7 +456,7 @@ def test_ctrl_c"))
 also initializes the boards (RAM etc).  This package provides its
 board-independent tools.")))
 
-(define (make-u-boot-package board triplet)
+(define-public (make-u-boot-package board triplet)
   "Returns a u-boot package for BOARD cross-compiled for TRIPLET."
   (let ((same-arch? (if (string-prefix? (%current-system)
                                         (gnu-triplet->nix-system triplet))

gnu/packages/check.scm

@@ -293,13 +293,13 @@ format.")
 (define-public cppcheck
   (package
     (name "cppcheck")
-    (version "1.83")
+    (version "1.84")
     (source (origin
       (method url-fetch)
       (uri (string-append "https://github.com/danmar/cppcheck/archive/"
                           version ".tar.gz"))
       (sha256
-       (base32 "15ghxwmyy09cd9mi008k4jn09c441j86qyaa4dz0is7f5dv5cdkx"))
+       (base32 "1ibz07dgs1dpfb8bmjh3qsma37wl5p6s6b4qlv5ccpshj4yjk9ma"))
       (file-name (string-append name "-" version ".tar.gz"))))
     (build-system cmake-build-system)
     (home-page "http://cppcheck.sourceforge.net")
@@ -1902,19 +1902,14 @@ create data based on random numbers and yet remain repeatable.")
 (define-public python-nose-timer
   (package
     (name "python-nose-timer")
-    (version "0.7.0")
+    (version "0.7.2")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "nose-timer" version))
-        (patches
-         (search-patches
-          ;; This patch will not be needed in the next version.
-          ;; It is taken from the master branch.
-          "python-nose-timer-drop-ordereddict.patch"))
         (sha256
           (base32
-            "1s32ymsnby8lz2qk55ifj9zi50dqcg6swnj5cz2rmwxg2jsslsxp"))))
+            "0ywg223p528014z5s0vzck74r4xyw3kvcp2casfnc85dkvir1zj7"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-nose" ,python-nose)
@@ -1930,14 +1925,14 @@ create data based on random numbers and yet remain repeatable.")
 (define-public python-freezegun
   (package
     (name "python-freezegun")
-    (version "0.3.9")
+    (version "0.3.10")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "freezegun" version))
        (sha256
         (base32
-         "1vhf3kgdy7gpy70n3bxa3y1n6aza316137md97z8p5k0gz6wqg3q"))))
+         "08m6b42yxb9hk5lv747v9n2qsxyadmkb0k6yg0gxdanwap0slg3h"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-mock" ,python-mock)
@@ -1953,7 +1948,7 @@ create data based on random numbers and yet remain repeatable.")
          ;; package does not include the Makefile.
          (replace 'check
            (lambda _
-             (zero? (system* "nosetests" "./tests/")))))))
+             (invoke "nosetests" "./tests/"))))))
     (home-page "https://github.com/spulec/freezegun")
     (synopsis "Test utility for mocking the datetime module")
     (description

gnu/packages/compression.scm

@@ -2111,7 +2111,7 @@ single-member files which can't be decompressed in parallel.")
 (define-public innoextract
   (package
    (name "innoextract")
-   (version "1.6")
+   (version "1.7")
    (source
     (origin
      (method url-fetch)
@@ -2119,7 +2119,7 @@ single-member files which can't be decompressed in parallel.")
                          version ".tar.gz"))
      (sha256
       (base32
-       "08sp5vbfjvq1irhhraqkn5m2x1z209r4axhx7laf1adcw30ccapi"))
+       "0khwi9f0q0h6xfbixrrc1rfpgj0b7ajwilq7yhmxnn5lpc807f6x"))
      (file-name (string-append name "-" version ".tar.gz"))))
    (build-system cmake-build-system)
    (arguments
@@ -2209,7 +2209,8 @@ decompression is a little bit slower.")
                                  version "/" name "-" version "-src.tar.xz"))
              (sha256
               (base32
-               "08anybdliqsbsl6x835iwzljahnm9i7v26icdjkcv33xmk6p5vw1"))))
+               "08anybdliqsbsl6x835iwzljahnm9i7v26icdjkcv33xmk6p5vw1"))
+             (patches (search-patches "upx-fix-CVE-2017-15056.patch"))))
     (build-system gnu-build-system)
     (native-inputs `(("perl" ,perl)
                      ("ucl" ,ucl)))
@@ -2241,6 +2242,11 @@ decompression is a little bit slower.")
              #t))
          )))
     (home-page "https://upx.github.io/")
+    ;; CVE-2017-16869 is about Mach-O files which is not of a big concern for Guix.
+    ;; See https://github.com/upx/upx/issues/146 and
+    ;; https://nvd.nist.gov/vuln/detail?vulnId=CVE-2017-16869.
+    ;; The issue will be fixed after version 3.94.
+    (properties `((lint-hidden-cve . ("CVE-2017-16869"))))
     (synopsis "Compression tool for executables")
     (description
      "The Ultimate Packer for eXecutables (UPX) is an executable file

gnu/packages/cran.scm

@@ -30,6 +30,7 @@
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix build-system r)
+  #:use-module (gnu packages compression)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
@@ -556,14 +557,14 @@ ellipses, circles, cylinders, arrows, ...")
 (define-public r-globaloptions
   (package
     (name "r-globaloptions")
-    (version "0.0.13")
+    (version "0.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "GlobalOptions" version))
        (sha256
         (base32
-         "04jvha0mafslqz5nr99xjylg9n2x31gj9v4mgyg7qcmfwpqyw3ch"))))
+         "1wlyqz1yhmhjwslrd7q69jbd9vsbjkjfc01g60kl3cdpyr8hlyjn"))))
     (properties `((upstream-name . "GlobalOptions")))
     (build-system r-build-system)
     (home-page "https://github.com/jokergoo/GlobalOptions")
@@ -576,14 +577,14 @@ validation and filtering on the values, making options invisible or private.")
 (define-public r-circlize
   (package
     (name "r-circlize")
-    (version "0.4.3")
+    (version "0.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "circlize" version))
        (sha256
         (base32
-         "0pg947gkryygikfbv6admx8gsg02b6g219j6a1sdnqij2908yxna"))))
+         "1l28maiqi549z191srncxgabx5fnvf0lld7smzwfd3vr5cx8nqww"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-colorspace" ,r-colorspace)
@@ -681,14 +682,14 @@ compare different dendrograms to one another.")
 (define-public r-getoptlong
   (package
     (name "r-getoptlong")
-    (version "0.1.6")
+    (version "0.1.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "GetoptLong" version))
        (sha256
         (base32
-         "1d98gcvlvp9nz5lbnzr0kkpc2hbkx74hlhrnybqhg1gdwc3g09pm"))))
+         "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr"))))
     (properties `((upstream-name . "GetoptLong")))
     (build-system r-build-system)
     (inputs
@@ -896,14 +897,14 @@ most popular ones.")
 (define-public r-sp
   (package
     (name "r-sp")
-    (version "1.2-7")
+    (version "1.3-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sp" version))
        (sha256
         (base32
-         "0q04yfgyjannsrzl0ppwcv0simrxrrbx2iz5mzaafc5x38zf0q3d"))))
+         "17xm1ig80p9wc860hm3bgishz6lj9fxgwqidj7rkbk4ap99qp62p"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -1009,14 +1010,14 @@ SpatialVx.")
 (define-public r-extremes
   (package
     (name "r-extremes")
-    (version "2.0-8")
+    (version "2.0-9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "extRemes" version))
        (sha256
         (base32
-         "0pnpib3g2r9x8hfqhvq23j8m3jh62lp28ipnqir5yadnzv850gfm"))))
+         "0cpvcajk9xyy7662nqkyx333vrxpwsc5nmv0bfnhsbgijz5y0hvm"))))
     (properties `((upstream-name . "extRemes")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1595,14 +1596,14 @@ Core algorithms are executed in parallel on systems supporting OpenMP.")
 (define-public r-rcpproll
   (package
     (name "r-rcpproll")
-    (version "0.2.2")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RcppRoll" version))
        (sha256
         (base32
-         "19xzvxym8zbighndygkq4imfwc0abh4hqyq3qrr8aakyd096iisi"))))
+         "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
     (properties `((upstream-name . "RcppRoll")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1822,14 +1823,14 @@ color labels, layout, etc.")
 (define-public r-stringdist
   (package
     (name "r-stringdist")
-    (version "0.9.4.7")
+    (version "0.9.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stringdist" version))
        (sha256
         (base32
-         "1qg80wmcrpkba9njvgjdg15bgw7ddks40kkfh5x61as9lhchy4i4"))))
+         "0gap1g9xwhp0zxqsznkc2carpvi80z03prr4q8m528684lznx2xa"))))
     (build-system r-build-system)
     (home-page "https://github.com/markvanderloo/stringdist")
     (synopsis "Approximate string matching and string distance functions")
@@ -2718,17 +2719,19 @@ supports arbitrary vertex/edge/graph attributes.")
 (define-public r-statnet-common
   (package
     (name "r-statnet-common")
-    (version "4.0.0")
+    (version "4.1.2")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "statnet.common" version))
         (sha256
           (base32
-            "0yw6l5b4qv0jqlg4zyczas7m12a5pyqghs6ydxy2f6v6vxkijvi0"))))
+            "0h3g687214rlycca0fjrpy1lqbqsrginxqhmhl2mb2jinqqxcfgd"))))
     (properties
       `((upstream-name . "statnet.common")))
     (build-system r-build-system)
+    (propagated-inputs
+     `(("r-coda" ,r-coda)))
     (home-page "https://statnet.org")
     (synopsis "R scripts and utilities used by the Statnet software")
     (description "This package provides non-statistical utilities used by the
@@ -2971,14 +2974,14 @@ Cryer and Kung-Sik Chan.")
 (define-public r-extradistr
   (package
     (name "r-extradistr")
-    (version "1.8.8")
+    (version "1.8.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "extraDistr" version))
        (sha256
         (base32
-         "0ywn4qwnamv36l1hw27l9y5kh3v6ha5781wsv2bz6szqjgg7kdb3"))))
+         "1fg8vjpal33y51iqzglk1yvy46d7js0l0wfbdy698lq8a06hq19p"))))
     (properties `((upstream-name . "extraDistr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3041,14 +3044,14 @@ applied econometric analysis.")
 (define-public r-cubature
   (package
     (name "r-cubature")
-    (version "1.3-11")
+    (version "1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cubature" version))
        (sha256
         (base32
-         "06f6gsvbb732p80r6hxvzh4ik546icxfvx21dyh65ypmw3kgm64k"))))
+         "1hd23b8v2kpqp5gr0va8p2q7j8w9rik6ks7zrr4b8mb2mwrakk74"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)))
@@ -3324,14 +3327,14 @@ environment within Shiny.")
 (define-public r-radiant-data
   (package
     (name "r-radiant-data")
-    (version "0.8.1")
+    (version "0.9.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "radiant.data" version))
        (sha256
         (base32
-         "1ylina1jlrmvjkj8pwg0ip5jv1038vnzyckmf542xl7g11x8rvw1"))
+         "0mbxfqn79nphii4hb6kxl2wc0w0ra16y378rp2yw9a9926zdb7mb"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -3347,6 +3350,7 @@ environment within Shiny.")
        ("r-curl" ,r-curl)
        ("r-dplyr" ,r-dplyr)
        ("r-dt" ,r-dt)
+       ("r-glue" ,r-glue)
        ("r-ggplot2" ,r-ggplot2)
        ("r-gridextra" ,r-gridextra)
        ("r-import" ,r-import)
@@ -3355,16 +3359,19 @@ environment within Shiny.")
        ("r-lubridate" ,r-lubridate)
        ("r-magrittr" ,r-magrittr)
        ("r-markdown" ,r-markdown)
-       ("r-pryr" ,r-pryr)
+       ("r-plotly" ,r-plotly)
        ("r-psych" ,r-psych)
        ("r-readr" ,r-readr)
+       ("r-readxl" ,r-readxl)
+       ("r-rlang" ,r-rlang)
        ("r-rmarkdown" ,r-rmarkdown)
        ("r-rstudioapi" ,r-rstudioapi)
        ("r-scales" ,r-scales)
        ("r-shiny" ,r-shiny)
        ("r-shinyace" ,r-shinyace)
        ("r-tibble" ,r-tibble)
-       ("r-tidyr" ,r-tidyr)))
+       ("r-tidyr" ,r-tidyr)
+       ("r-writexl" ,r-writexl)))
     (home-page "https://github.com/radiant-rstats/radiant.data")
     (synopsis "Data menu for Radiant: business analytics using R and Shiny")
     (description
@@ -3915,14 +3922,14 @@ exchanging spatial objects with other R packages.")
 (define-public r-later
   (package
     (name "r-later")
-    (version "0.7.2")
+    (version "0.7.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "later" version))
        (sha256
         (base32
-         "0l5ln7sjyi2rj7bx8iamxykqlfarv05zb9882ikizppb1cr1hgyw"))))
+         "04j2phymxgkk4hv9pfa5w3s98w5d7fvm11blrdhxmray4n618msw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bh" ,r-bh)
@@ -4125,14 +4132,14 @@ obtain a better initial configuration in non-metric MDS.")
 (define-public r-reticulate
   (package
     (name "r-reticulate")
-    (version "1.7")
+    (version "1.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "reticulate" version))
        (sha256
         (base32
-         "1ghhc4hbmwpp79ilbdbshynhs61i8sv8z6p1al04jy7ij0lcglxy"))))
+         "0zwb4ikf021nw7axdn7qlr6bq4xkph3anfy314idkspy1iil4nmr"))))
     (build-system r-build-system)
     (inputs `(("python" ,python)))
     (propagated-inputs
@@ -4190,3 +4197,267 @@ generating multiple logo plots, and aiding the visualisation with annotations.
 Sequence logos can easily be combined with other ggplot2 plots.")
     ;; Unspecified version of the LGPL.
     (license license:lgpl3+)))
+
+(define-public r-ggsci
+  (package
+    (name "r-ggsci")
+    (version "2.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggsci" version))
+       (sha256
+        (base32
+         "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-scales" ,r-scales)))
+    (home-page "https://nanx.me/ggsci/")
+    (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
+    (description
+     "This package provides a collection of ggplot2 color palettes inspired by
+plots in scientific journals, data visualization libraries, science fiction
+movies, and TV shows.")
+    (license license:gpl3)))
+
+(define-public r-ggsignif
+  (package
+    (name "r-ggsignif")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggsignif" version))
+       (sha256
+        (base32
+         "1rn58d7pb3axk6chiihryykrzw76adaa2yiafq4d0j6qbhax78f7"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)))
+    (home-page "https://github.com/const-ae/ggsignif")
+    (synopsis "Significance brackets for ggplot2")
+    (description
+     "Enrich your ggplots with group-wise comparisons.  This package provides
+an easy way to indicate if two groups are significantly different.  Commonly
+this is shown by a bracket on top connecting the groups of interest which
+itself is annotated with the level of significance.  The package provides a
+single layer that takes the groups for comparison and the test as arguments
+and adds the annotation to the plot.")
+    (license license:gpl3)))
+
+(define-public r-ggpubr
+  (package
+    (name "r-ggpubr")
+    (version "0.1.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggpubr" version))
+       (sha256
+        (base32
+         "0mvw215bj887958p34f0dzlrb8mgyfcz9b5zvsschvbhamqinqna"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cowplot" ,r-cowplot)
+       ("r-dplyr" ,r-dplyr)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggrepel" ,r-ggrepel)
+       ("r-ggsci" ,r-ggsci)
+       ("r-ggsignif" ,r-ggsignif)
+       ("r-gridextra" ,r-gridextra)
+       ("r-magrittr" ,r-magrittr)
+       ("r-purrr" ,r-purrr)
+       ("r-scales" ,r-scales)
+       ("r-tidyr" ,r-tidyr)))
+    (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
+    (synopsis "ggplot2-based publication-ready plots")
+    (description
+     "The ggplot2 package is an excellent and flexible package for elegant
+data visualization in R.  However the default generated plots require some
+formatting before we can send them for publication.  The ggpubr package
+provides some easy-to-use functions for creating and customizing ggplot2-based
+publication-ready plots.")
+    (license license:gpl2)))
+
+(define-public r-ellipse
+  (package
+    (name "r-ellipse")
+    (version "0.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ellipse" version))
+       (sha256
+        (base32
+         "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/ellipse/")
+    (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
+    (description
+     "This package contains various routines for drawing ellipses and
+ellipse-like confidence regions, implementing the plots described in Murdoch
+and Chow (1996), A graphical display of large correlation matrices, The
+American Statistician 50, 178-180.  There are also routines implementing the
+profile plots described in Bates and Watts (1988), Nonlinear Regression
+Analysis and its Applications.")
+    (license license:gpl2+)))
+
+(define-public r-flashclust
+  (package
+    (name "r-flashclust")
+    (version "1.01-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "flashClust" version))
+       (sha256
+        (base32
+         "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
+    (properties `((upstream-name . "flashClust")))
+    (build-system r-build-system)
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/flashClust/")
+    (synopsis "Implementation of optimal hierarchical clustering")
+    (description
+     "This package provides a fast implementation of hierarchical
+clustering.")
+    (license license:gpl2+)))
+
+(define-public r-factominer
+  (package
+    (name "r-factominer")
+    (version "1.41")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "FactoMineR" version))
+       (sha256
+        (base32
+         "1h20hydav6l2b7bngqw1av4l5rrh0wk58nhailga1f4qw9lrv259"))))
+    (properties `((upstream-name . "FactoMineR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-car" ,r-car)
+       ("r-cluster" ,r-cluster)
+       ("r-ellipse" ,r-ellipse)
+       ("r-flashclust" ,r-flashclust)
+       ("r-lattice" ,r-lattice)
+       ("r-leaps" ,r-leaps)
+       ("r-mass" ,r-mass)
+       ("r-scatterplot3d" ,r-scatterplot3d)))
+    (home-page "http://factominer.free.fr")
+    (synopsis "Multivariate exploratory data analysis and data mining")
+    (description
+     "This package provides exploratory data analysis methods to summarize,
+visualize and describe datasets.  The main principal component methods are
+available, those with the largest potential in terms of applications:
+principal component analysis (PCA) when variables are quantitative,
+correspondence analysis (CA) and multiple correspondence analysis (MCA) when
+variables are categorical, Multiple Factor Analysis when variables are
+structured in groups, etc. and hierarchical cluster analysis.")
+    (license license:gpl2+)))
+
+(define-public r-factoextra
+  (package
+    (name "r-factoextra")
+    (version "1.0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "factoextra" version))
+       (sha256
+        (base32
+         "1l6m8k7qhdw8ndar8nhmym0lfyd1i2iszl1cicjax0vq23ss6xw1"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-abind" ,r-abind)
+       ("r-cluster" ,r-cluster)
+       ("r-dendextend" ,r-dendextend)
+       ("r-factominer" ,r-factominer)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggpubr" ,r-ggpubr)
+       ("r-ggrepel" ,r-ggrepel)
+       ("r-reshape2" ,r-reshape2)
+       ("r-tidyr" ,r-tidyr)))
+    (home-page "http://www.sthda.com/english/rpkgs/factoextra")
+    (synopsis "Extract and visualize the results of multivariate data analyses")
+    (description
+     "This package provides some easy-to-use functions to extract and
+visualize the output of multivariate data analyses, including
+@code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
+Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
+Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
+@code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
+packages.  It contains also functions for simplifying some clustering analysis
+steps and provides ggplot2-based elegant data visualization.")
+    (license license:gpl2)))
+
+(define-public r-nbclust
+  (package
+    (name "r-nbclust")
+    (version "3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "NbClust" version))
+       (sha256
+        (base32
+         "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
+    (properties `((upstream-name . "NbClust")))
+    (build-system r-build-system)
+    (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
+    (synopsis "Determine the best number of clusters in a data set")
+    (description
+     "NbClust provides 30 indexes for determining the optimal number of
+clusters in a data set and offers the best clustering scheme from different
+results to the user.")
+    (license license:gpl2)))
+
+(define-public r-hdf5r
+  (package
+    (name "r-hdf5r")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "hdf5r" version))
+       (sha256
+        (base32
+         "1s6p4cj909kc635fh5xpl87bqlcdj3dn3r1wk5g40abimk2b0pva"))))
+    (build-system r-build-system)
+    (inputs
+     `(("hdf5" ,hdf5)
+       ("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-bit64" ,r-bit64)
+       ("r-r6" ,r-r6)))
+    (home-page "https://hhoeflin.github.io/hdf5r")
+    (synopsis "Interface to the HDF5 binary data format")
+    (description
+     "HDF5 is a data model, library and file format for storing and managing
+large amounts of data.  This package provides a nearly feature complete,
+object oriented wrapper for the HDF5 API using R6 classes.  Additionally,
+functionality is added so that HDF5 objects behave very similar to their
+corresponding R counterparts.")
+    (license license:asl2.0)))
+
+(define-public r-writexl
+  (package
+    (name "r-writexl")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "writexl" version))
+       (sha256
+        (base32
+         "0r2v12dc4zqmr1agp6vbw0fc48i278018684x84psjjqfmnv14cf"))))
+    (build-system r-build-system)
+    (inputs `(("zlib" ,zlib)))
+    (home-page "https://github.com/ropensci/writexl")
+    (synopsis "Export data frames to xlsx format")
+    (description
+     "This package provides a data frame to xlsx exporter based on
+libxlsxwriter.")
+    (license license:bsd-2)))

gnu/packages/crypto.scm

@@ -32,6 +32,7 @@
   #:use-module (gnu packages attr)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages boost)
+  #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cryptsetup)
   #:use-module (gnu packages databases)
@@ -217,7 +218,7 @@ communication.")
 (define-public encfs
   (package
     (name "encfs")
-    (version "1.9.1")
+    (version "1.9.5")
     (source
      (origin
        (method url-fetch)
@@ -226,13 +227,13 @@ communication.")
                        version "/encfs-" version ".tar.gz"))
        (sha256
         (base32
-         "1906254dg5hwljh0h4gyrw09ms3b57dlhjfzhfzffv50yzpkl837"))
+         "0qzxavvv20577bxvly8s7d3y7bqasqclc2mllp0ddfncjm9z02a7"))
        (modules '((guix build utils)))
        ;; Remove bundled dependencies in favour of proper inputs.
        (snippet '(begin
                    (for-each delete-file-recursively
-                             (find-files "internal" "^tinyxml2-[0-9]"
+                             '("vendor/github.com/leethomason/tinyxml2"
-                                         #:directories? #t))
+                               "vendor/github.com/google/googletest"))
                    #t))))
     (build-system cmake-build-system)
     (native-inputs
@@ -240,6 +241,7 @@ communication.")
 
        ;; Test dependencies.
        ("expect" ,expect)
+       ("googletest-source" ,(package-source googletest))
        ("perl" ,perl)))
     (inputs
      `(("attr" ,attr)
@@ -247,7 +249,18 @@ communication.")
        ("openssl" ,openssl)
        ("tinyxml2" ,tinyxml2)))
     (arguments
-     `(#:configure-flags (list "-DUSE_INTERNAL_TINYXML=OFF")))
+     `(#:configure-flags (list "-DUSE_INTERNAL_TINYXML=OFF")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'unpack-googletest
+           (lambda* (#:key inputs #:allow-other-keys)
+             (mkdir-p "vendor/github.com/google/googletest")
+             (invoke "tar" "xvf" (assoc-ref inputs "googletest-source")
+                     "-C" "vendor/github.com/google/googletest"
+                     "--strip-components=1")))
+         (add-before 'check 'make-unittests
+           (lambda _
+             (invoke "make" "unittests"))))))
     (home-page "https://vgough.github.io/encfs")
     (synopsis "Encrypted virtual file system")
     (description
@@ -713,14 +726,14 @@ SHA256, SHA512, SHA3, AICH, ED2K, Tiger, DC++ TTH, BitTorrent BTIH, GOST R
 (define-public botan
   (package
     (name "botan")
-    (version "2.5.0")
+    (version "2.6.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://botan.randombit.net/releases/"
                                   "Botan-" version ".tgz"))
               (sha256
                (base32
-                "06zvwknhwfrkdvq2sybqbqhnd2d4nq2cszlnsddql13z7vh1z8xq"))))
+                "1iawmymmnp5j2mcjj70slivn6bgg8gbpppldc1rjqw5sbdan3wn1"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases

gnu/packages/databases.scm

@@ -1107,7 +1107,7 @@ extremely small.")
 (define-public perl-dbi
   (package
     (name "perl-dbi")
-    (version "1.637")
+    (version "1.641")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1115,7 +1115,7 @@ extremely small.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "1ikbsb6sb0bd2m1dqknl4vx7ikmnd41y0xq8np1l40g8jcjp2mr5"))))
+                "1hf2x29bnqf2x1v4bdhji802z7n2mbg7h1amv8gdkqyhrlrfa2am"))))
     (build-system perl-build-system)
     (synopsis "Database independent interface for Perl")
     (description "This package provides an database interface for Perl.")

gnu/packages/dav.scm

@@ -57,13 +57,13 @@ clients.")
 (define-public vdirsyncer
   (package
     (name "vdirsyncer")
-    (version "0.16.4")
+    (version "0.16.6")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri name version))
              (sha256
               (base32
-               "03wva48bgv1ad3df6plc9b8xxh6k8bcaxrhlzwh81c9mzn5bspzv"))))
+               "07iqq5c53cfrb5xnmam1rsl683hc3rykmdak896n2gm81r361c66"))))
     (build-system python-build-system)
     (arguments
       `(#:phases (modify-phases %standard-phases
@@ -76,7 +76,6 @@ clients.")
              (zero? (system* "make" "test"))))
          (add-after 'install 'manpage
            (lambda* (#:key inputs outputs #:allow-other-keys)
-             (add-installed-pythonpath inputs outputs)
              (zero? (system* "make" "--directory=docs/" "man"))
              (install-file
                "docs/_build/man/vdirsyncer.1"

gnu/packages/dns.scm

@@ -50,6 +50,7 @@
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
+  #:use-module (gnu packages)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
@@ -104,6 +105,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
               (uri (string-append
                     "ftp://ftp.isc.org/isc/bind9/" version "/" name "-"
                     version ".tar.gz"))
+              (patches (search-patches "bind-CVE-2018-5738.patch"))
               (sha256
                (base32
                 "0a9dvyg1dk7vpqn9gz7p5jas3bz7z22bjd66b98g1qk16i2w7rqd"))))

gnu/packages/elixir.scm

@@ -40,15 +40,7 @@
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0acnxfwvkx1m1d0h5z051mz95n35zm468hcvc3wpmn17c15h5ihg"))
+                "0acnxfwvkx1m1d0h5z051mz95n35zm468hcvc3wpmn17c15h5ihg"))))
-              ;; FIXME: 27 tests (out of 4K) had to be disabled as
-              ;; they fail in the build environment.  Common failures
-              ;; are:
-              ;; - Mix.Shell.cmd() fails with error 130
-              ;; - The git_repo fixture cannot be found
-              ;; - Communication with spawned processes fails with EPIPE
-              ;; - Failure to copy files
-              (patches (search-patches "elixir-disable-failing-tests.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
@@ -70,27 +62,6 @@
                  (("#!/usr/bin/env elixir")
                   (string-append "#!" out "/bin/elixir"))))
              #t))
-         (add-after 'unpack 'fix-or-disable-tests
-           (lambda* (#:key inputs #:allow-other-keys)
-             ;; Some tests require access to a home directory.
-             (setenv "HOME" "/tmp")
-
-             ;; FIXME: These tests fail because the "git_repo" fixture does
-             ;; not exist or cannot be found.
-             (delete-file "lib/mix/test/mix/tasks/deps.git_test.exs")
-
-             ;; FIXME: Mix.Shell.cmd() always fails with error code 130.
-             (delete-file "lib/mix/test/mix/shell_test.exs")
-
-             ;; FIXME:
-             ;; disabled failing impure tests to make it build again.
-             ;; related discussion: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=28034#14
-             (delete-file "lib/elixir/test/elixir/kernel/cli_test.exs")
-             (delete-file "lib/elixir/test/elixir/kernel/dialyzer_test.exs")
-             (delete-file "lib/iex/test/iex/helpers_test.exs")
-             (delete-file "lib/ex_unit/test/ex_unit/capture_io_test.exs")
-
-             #t))
          (add-before 'build 'make-current
            ;; The Elixir compiler checks whether or not to compile files by
            ;; inspecting their timestamps.  When the timestamp is equal to the
@@ -102,6 +73,11 @@
                            (utime file recent recent 0 0)))
                        (find-files "." ".*"))
              #t))
+         (add-before 'check 'set-home
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; Some tests require access to a home directory.
+             (setenv "HOME" "/tmp")
+             #t))
          (delete 'configure))))
     (inputs
      `(("erlang" ,erlang)

gnu/packages/emacs.scm

@@ -436,7 +436,7 @@ on stdout instead of using a socket as the Emacsclient does.")
 (define-public magit
   (package
     (name "magit")
-    (version "2.12.1")
+    (version "2.13.0")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -444,7 +444,7 @@ on stdout instead of using a socket as the Emacsclient does.")
                    version "/" name "-" version ".tar.gz"))
              (sha256
               (base32
-               "1czzknmhzbggcv3bxl5amvfpp0zrkdwl1x05qarsq6qakvc85xy3"))))
+               "1ygaah3dd3nxpyd17297xgvdcgr7pgzzwlmpnmchki0kiwgg3sbc"))))
     (build-system gnu-build-system)
     (native-inputs `(("texinfo" ,texinfo)
                      ("emacs" ,emacs-minimal)))
@@ -3014,6 +3014,33 @@ This provides a basic API and common UI widgets such as popup tooltips
 and popup menus.")
     (license license:gpl3+)))
 
+(define-public emacs-puppet-mode
+  (let ((commit "b3ed5057166a4f49dfa9be638523a348b55a2fd2")
+        (revision "1"))
+    (package
+      (name "emacs-puppet-mode")
+      ;; The last release, 0.3 was several years ago, and there have been many
+      ;; commits since
+      (version (git-version "0.3" revision commit))
+      (source
+       (origin
+         (method url-fetch)
+         (uri (string-append
+               "https://raw.githubusercontent.com/voxpupuli/puppet-mode/"
+               commit "/puppet-mode.el"))
+         (sha256
+          (base32
+           "1indycxawsl0p2aqqg754f6735q3cmah9vd886rpn0ncc3ipi1xm"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/voxpupuli/puppet-mode")
+      (synopsis "Emacs major mode for the Puppet configuration language")
+      (description
+       "This package provides support for the Puppet configuration language,
+including syntax highlighting, indentation of expressions and statements,
+linting of manifests and integration with Puppet Debugger.")
+      ;; Also incorporates work covered by the Apache License, Version 2.0
+      (license license:gpl3+))))
+
 (define-public emacs-god-mode
   (let ((commit "6cf0807b6555eb6fcf8387a4e3b667071ef38964")
         (revision "1"))
@@ -4797,7 +4824,7 @@ distribution, primarily targeting Clojure users")
 (define-public emacs-orgalist
   (package
     (name "emacs-orgalist")
-    (version "1.7")
+    (version "1.8")
     (source
      (origin
        (method url-fetch)
@@ -4805,7 +4832,7 @@ distribution, primarily targeting Clojure users")
                            "orgalist-" version ".el"))
        (sha256
         (base32
-         "13dl0l727vlny3y88gqpngcy90ly5r719s1pbmkva5gmcryb68xr"))))
+         "1wqwnmn08i0qkxm8b2iclvf6cydcn68h1p3h7r1kig2bdn5b8948"))))
     (build-system emacs-build-system)
     (home-page "http://elpa.gnu.org/packages/orgalist.html")
     (synopsis "Manage Org-like lists in non-Org buffers")
@@ -5609,7 +5636,7 @@ highlights quasi-quoted expressions.")
 (define-public emacspeak
   (package
     (name "emacspeak")
-    (version "47.0")
+    (version "48.0")
     (source
      (origin
        (method url-fetch)
@@ -5618,7 +5645,7 @@ highlights quasi-quoted expressions.")
              version "/emacspeak-" version ".tar.bz2"))
        (sha256
         (base32
-         "0xbcc266x752y68s3g096m161irzvsqym3axzqn8rb276a8x55n7"))))
+         "07imi3hji06b3r7v7v59978q76s8a7ynmxwfc9j03pgnv965lpjy"))))
     (build-system gnu-build-system)
     (arguments
      '(#:make-flags (list (string-append "prefix="
@@ -5626,30 +5653,35 @@ highlights quasi-quoted expressions.")
        #:phases
        (modify-phases %standard-phases
          (replace 'configure
-           (lambda _
+           (lambda* (#:key outputs #:allow-other-keys)
-             ;; Configure Emacspeak according to etc/install.org.
+             (let* ((out (assoc-ref outputs "out"))
+                    (lisp (string-append out
+                                         "/share/emacs/site-lisp/emacspeak")))
                (setenv "SHELL" (which "sh"))
-             (zero? (system* "make" "config"))))
+               ;; Configure Emacspeak according to etc/install.org.
+               (invoke "make" "config"))))
          (add-after 'build 'build-espeak
            (lambda _
-             (zero? (system* "make" "espeak"))))
+             (invoke "make" "espeak")))
          (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
+           (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (bin (string-append out "/bin"))
                     (lisp (string-append out "/share/emacs/site-lisp/emacspeak"))
-                    (info (string-append out "/share/info")))
+                    (info (string-append out "/share/info"))
+                    (emacs (string-append (assoc-ref inputs "emacs")
+                                          "/bin/emacs")))
                ;; According to etc/install.org, the Emacspeak directory should
                ;; be copied to its installation destination.
                (for-each
                 (lambda (file)
                   (copy-recursively file (string-append lisp "/" file)))
-                '("etc" "info" "lisp" "media" "servers" "sounds" "stumpwm"
+                '("etc" "info" "js" "lisp" "media" "scapes" "servers" "sounds"
-                  "xsl"))
+                  "stumpwm" "xsl"))
                ;; Make sure emacspeak is loaded from the correct directory.
                (substitute* "etc/emacspeak.sh"
-                 (("exec emacs.*$")
+                 (("exec FLAVOR.*")
-                  (string-append "exec emacs -l " lisp
+                  (string-append "exec " emacs " -l " lisp
                                  "/lisp/emacspeak-setup.el $CL_ALL")))
                ;; Install the convenient startup script.
                (mkdir-p bin)
@@ -5668,10 +5700,11 @@ highlights quasi-quoted expressions.")
                #t))))
        #:tests? #f)) ; no check target
     (inputs
-     `(("espeak" ,espeak)
+     `(("emacs" ,emacs)
+       ("espeak" ,espeak)
+       ("perl" ,perl)
        ("tcl" ,tcl)
        ("tclx" ,tclx)))
-    (native-inputs `(("emacs" ,emacs-minimal)))
     (home-page "http://emacspeak.sourceforge.net")
     (synopsis "Audio desktop interface for Emacs")
     (description
@@ -7917,7 +7950,7 @@ close, copy, cut, paste, undo, redo.")
 (define-public emacs-password-store
   (package
     (name "emacs-password-store")
-    (version "1.7.1")
+    (version "1.7.2")
     (source (origin
               (method url-fetch)
               (uri
@@ -7925,7 +7958,7 @@ close, copy, cut, paste, undo, redo.")
                               "password-store-" version ".tar.xz"))
               (sha256
                (base32
-                "0scqkpll2q8jhzcgcsh9kqz0gwdpvynivqjmmbzax2irjfaiklpn"))))
+                "1sl0d7nc85c6c2bmmmyb8rpmn47vhkj831l153mjlkawjvhwas27"))))
     (build-system emacs-build-system)
     (arguments
      `(#:phases
@@ -7940,6 +7973,7 @@ close, copy, cut, paste, undo, redo.")
     (propagated-inputs
      `(("emacs-f" ,emacs-f)
        ("emacs-s" ,emacs-s)
+       ("emacs-with-editor" ,emacs-with-editor)
        ("password-store" ,password-store)))
     (home-page "https://git.zx2c4.com/password-store/tree/contrib/emacs")
     (synopsis "Password store (pass) support for Emacs")
@@ -9934,11 +9968,11 @@ perform regression test for packages that provide font-lock rules.")
       (license license:gpl3+))))
 
 (define-public emacs-racket-mode
-  (let ((commit "33877b1bb24faea68842e0396bd5718b84e47451")
+  (let ((commit "48f0cb99d3b2ca6066249546d2063d85437251c1")
         (revision "1"))
     (package
       (name "emacs-racket-mode")
-      (version (string-append "0.0.1" "-" revision "."
+      (version (string-append "0.0.2" "-" revision "."
                               (string-take commit 7)))
       (source
        (origin
@@ -9949,8 +9983,10 @@ perform regression test for packages that provide font-lock rules.")
          (file-name (string-append name "-" version "-checkout"))
          (sha256
           (base32
-           "0681mzwx08zwbh8qg3s26jw1jn4fw2ljp1akxqkhy08sxhafqvb1"))))
+           "0fxky8xj639bjhiab9way9daqda22301b7w85vm4b4ydgjgnc59x"))))
       (build-system emacs-build-system)
+      (arguments
+       `(#:include '("\\.el$" "\\.rkt$")))
       (propagated-inputs
        `(("emacs-faceup" ,emacs-faceup)
          ("emacs-s" ,emacs-s)))
@@ -10807,23 +10843,36 @@ Org-mode.  It features:
       (license license:gpl3+))))
 
 (define-public emacs-fish-completion
+  (let ((commit "bac15fda1392a891070574dfe5d2d50b10831e8b"))
     (package
       (name "emacs-fish-completion")
-    (version "20180329")
+      (version (git-version "20180616" "1" commit))
       (source
        (origin
          (method url-fetch)
          (uri (string-append
-             "https://github.com/Ambrevar/emacs-fish-completion/archive/"
+               "https://gitlab.com/Ambrevar/emacs-fish-completion/repository/"
-             "3e3ed1f19fa778b7c35ad88e033dce5a6b1fc153"
+               "archive.tar.gz?ref="
-             ".tar.gz"))
+               commit))
          (sha256
           (base32
-         "16329py7fvid0bap1qhqxhdc68m9qqy1p8gc2bhng81zhm5a5zsm"))))
+           "093qzdrbkl7dhjk16zq8i13kh1phyigkblcfrbgbrxjqd2ndrfdi"))))
       (build-system emacs-build-system)
-    (propagated-inputs `(("fish" ,fish)))
+      (inputs `(("fish" ,fish)))
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'configure
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let ((fish (assoc-ref inputs "fish")))
+                 ;; Specify the absolute file names of the various
+                 ;; programs so that everything works out-of-the-box.
+                 (emacs-substitute-variables
+                     "fish-completion.el"
+                   ("fish-completion-command"
+                    (string-append fish "/bin/fish")))))))))
       (home-page
-     "https://github.com/Ambrevar/emacs-fish-completion")
+       "https://gitlab.com/Ambrevar/emacs-fish-completion")
       (synopsis "Fish completion for Emacs pcomplete")
       (description
        "This package provides completion for the Fish shell to pcomplete (used
@@ -10841,7 +10890,7 @@ shell/Eshell mode hook.
 The package @code{emacs-bash-completion} is an optional dependency: if available,
 @code{fish-completion-complete} can be configured to fall back on bash to further
 try completing.  See @code{fish-completion-fallback-on-bash-p}.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-gif-screencast
   (let ((commit "825e606950ec842304bf75cf85baef707b853b03"))

gnu/packages/emulators.scm

@@ -1235,7 +1235,8 @@ play them on systems for which they were never designed!")
                            (find-files "keymaps" ".*LINUX\\.map")))
                (let ((fonts (string-append share "/fonts")))
                  (install-file "uismall.bdf" fonts))
-               (rename-file "mame64" "mame")
+               (when (file-exists? "mame64")
+                 (rename-file "mame64" "mame"))
                (install-file "mame" (string-append out "/bin")))
              #t))
          (add-after 'install 'install-documentation

gnu/packages/erlang.scm

@@ -89,6 +89,7 @@
                   (guix build gnu-build-system))
        #:phases
        (modify-phases %standard-phases
+         (delete 'bootstrap)
          ;; The are several code fragments that embed timestamps into the
          ;; output. Here, we alter those fragments to use the value of
          ;; SOURCE_DATE_EPOCH instead.
@@ -127,6 +128,29 @@
                   (date->string source-date-epoch
                                 "{H,Mi,S} = {~H,~M,~S},")))
                #t)))
+         (add-after 'unpack 'patch-/bin/sh
+           (lambda _
+             (substitute* "erts/etc/unix/run_erl.c"
+               (("sh = \"/bin/sh\";")
+                (string-append "sh = \""
+                               (which "sh")
+                               "\";")))
+
+             (substitute* "erts/emulator/sys/unix/sys_drivers.c"
+               (("SHELL \"/bin/sh\"")
+                (string-append "SHELL \""
+                               (which "sh")
+                               "\"")))
+             (substitute* "erts/emulator/sys/unix/erl_child_setup.c"
+               (("SHELL \"/bin/sh\"")
+                (string-append "SHELL \""
+                               (which "sh")
+                               "\"")))
+
+             (substitute* "lib/kernel/src/os.erl"
+               (("/bin/sh") (which "sh")))
+
+             #t))
          (add-after 'patch-source-shebangs 'patch-source-env
            (lambda _
              (let ((escripts

gnu/packages/fcitx.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -35,14 +36,14 @@
 (define-public fcitx
   (package
     (name "fcitx")
-    (version "4.2.8.6")
+    (version "4.2.9.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://download.fcitx-im.org/fcitx/"
                                   name "-" version "_dict.tar.xz"))
               (sha256
                (base32
-                "15ymd42kg920ri0f8fymq3i68g8k1kgpmdlnk9jf5fvnz6g4w0wi"))))
+                "0hyrh3v82a32ylnlvzrp6cmq56x4p1a42q5xc6njmmj2msxm34x5"))))
     (build-system cmake-build-system)
     (outputs '("out" "gtk2" "gtk3"))
     (arguments
@@ -65,6 +66,11 @@
              "-DENABLE_QT_IM_MODULE=OFF")))
     (native-inputs
      `(("doxygen"    ,doxygen)
+       ("extra-cmake-modules"
+        ;; XXX: We can't simply #:use-module due to a cycle somewhere.
+        ,(module-ref
+          (resolve-interface '(gnu packages kde-frameworks))
+          'extra-cmake-modules))
        ("glib:bin"   ,glib "bin")       ; for glib-genmarshal
        ("pkg-config" ,pkg-config)))
     (inputs
@@ -78,7 +84,7 @@
        ("libxkbfile"       ,libxkbfile)
        ("libxml2"          ,libxml2)
        ("xkeyboard-config" ,xkeyboard-config)))
-    (home-page "http://fcitx-im.org")
+    (home-page "https://fcitx-im.org")
     (synopsis "Input method framework")
     (description
      "Fcitx is an input method framework with extension support.  It has
@@ -89,14 +95,14 @@ built-in.")
 (define-public fcitx-configtool
   (package
    (name "fcitx-configtool")
-   (version "0.4.8")
+   (version "0.4.10")
    (source (origin
             (method url-fetch)
             (uri (string-append "https://download.fcitx-im.org/fcitx-configtool/"
                   name "-" version ".tar.xz"))
             (sha256
              (base32
-              "1vaim0namw58bfafbvws1vgd4010p19zwqfbx6bd1zi5sgchdg0f"))))
+              "1yyi9jhkwn49lx9a47k1zbvwgazv4y4z72gnqgzdpgdzfrlrgi5w"))))
    (build-system cmake-build-system)
    (arguments
     `(#:configure-flags

gnu/packages/fonts.scm

@@ -617,7 +617,7 @@ languages, plus Greek and Cyrillic.")
 (define-public font-gnu-unifont
   (package
     (name "font-gnu-unifont")
-    (version "10.0.07")
+    (version "11.0.01")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -625,7 +625,7 @@ languages, plus Greek and Cyrillic.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "1js8dn4v4pv8jqprsxa1fv4fs3hqhm9x4dj19fg9qgc8fx7k0v0k"))))
+                "1nkapra0ic4fp3lmnvfc6jly62yskhcdkwrnq29hvh3xs51ncc52"))))
     (build-system gnu-build-system)
     (outputs '("out" ; TrueType version
                "pcf" ; PCF (bitmap) version
@@ -650,7 +650,7 @@ languages, plus Greek and Cyrillic.")
                    (psf (string-append (assoc-ref outputs "psf")
                                        "/share/consolefonts"))
                    (bin (assoc-ref outputs "bin")))
-              (system* "make"
+              (invoke "make"
                       (string-append "PREFIX=" bin)
                       (string-append "TTFDEST=" ttf)
                       (string-append "PCFDEST=" pcf)

gnu/packages/games.scm

@@ -1822,7 +1822,7 @@ falling, themeable graphics and sounds, and replays.")
 (define-public wesnoth
   (package
     (name "wesnoth")
-    (version "1.14.1")
+    (version "1.14.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/wesnoth/wesnoth-"
@@ -1831,7 +1831,7 @@ falling, themeable graphics and sounds, and replays.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "1mzrnbv71b4s41c5x8clhb53l8lidiwzny1hl828228pvys5bxkb"))))
+                "06648041nr77sgzr7jpmcn37cma3hp41qynp50xzddx28l17zwg9"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f)) ; no check target
@@ -2229,6 +2229,88 @@ Transport Tycoon Deluxe.")
        ("opensfx" ,openttd-opensfx)
        ,@(package-native-inputs openttd-engine)))))
 
+(define openrct2-title-sequences
+  (package
+   (name "openrct2-title-sequences")
+   (version "0.1.2")
+   (source
+    (origin
+     (method url-fetch)
+     (uri (string-append "https://github.com/OpenRCT2/title-sequences/releases/download/v"
+                         version "/title-sequence-v" version ".zip"))
+     (file-name (string-append name "-" version ".zip"))
+     (sha256
+      (base32
+       "0qbyxrsw8hlgaq0r5d7lx7an3idy4qbfv7yiw9byhldk763n9cfw"))))
+   (build-system trivial-build-system)
+   (native-inputs
+    `(("bash" ,bash)
+      ("coreutils" ,coreutils)
+      ("unzip" ,unzip)))
+   (arguments
+    `(#:modules ((guix build utils))
+      #:builder
+      (begin
+        (use-modules (guix build utils))
+        (let* ((out (assoc-ref %outputs "out"))
+               (openrct2-title-sequences (string-append out
+                                         "/share/openrct2/title-sequences"))
+               (source (assoc-ref %build-inputs "source"))
+               (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip")))
+          (copy-file source (string-append ,name "-" ,version ".zip"))
+          (invoke unzip (string-append ,name "-" ,version ".zip"))
+          (delete-file (string-append ,name "-" ,version ".zip"))
+          (mkdir-p openrct2-title-sequences)
+          (copy-recursively "."
+                            openrct2-title-sequences)
+          #t))))
+   (home-page "https://github.com/OpenRCT2/OpenRCT2")
+   (synopsis "Title sequences for OpenRCT2")
+   (description
+    "openrct2-title-sequences is a set of title sequences for OpenRCT2.")
+   (license license:gpl3+)))
+
+(define openrct2-objects
+  (package
+   (name "openrct2-objects")
+   (version "1.0.2")
+   (source
+    (origin
+     (method url-fetch)
+     (uri (string-append "https://github.com/OpenRCT2/objects/releases/download/v"
+                         version "/objects.zip"))
+     (file-name (string-append name "-" version ".zip"))
+     (sha256
+      (base32
+       "1z92afhbv13j1ig6fz0x8w9vdmfchssv16vwwhb0vj40pn1g1rwy"))))
+   (build-system trivial-build-system)
+   (native-inputs
+    `(("bash" ,bash)
+      ("coreutils" ,coreutils)
+      ("unzip" ,unzip)))
+   (arguments
+    `(#:modules ((guix build utils))
+      #:builder
+      (begin
+        (use-modules (guix build utils))
+        (let* ((out (assoc-ref %outputs "out"))
+               (openrct2-objects (string-append out
+                                         "/share/openrct2/objects"))
+               (source (assoc-ref %build-inputs "source"))
+               (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip")))
+          (copy-file source (string-append ,name "-" ,version ".zip"))
+          (invoke unzip (string-append ,name "-" ,version ".zip"))
+          (delete-file (string-append ,name "-" ,version ".zip"))
+          (mkdir-p openrct2-objects)
+          (copy-recursively "."
+                            openrct2-objects)
+          #t))))
+   (home-page "https://github.com/OpenRCT2/OpenRCT2")
+   (synopsis "Objects for OpenRCT2")
+   (description
+    "openrct2-objects is a set of objects for OpenRCT2.")
+   (license license:gpl3+)))
+
 (define-public openrct2
   (package
     (name "openrct2")
@@ -2244,29 +2326,33 @@ Transport Tycoon Deluxe.")
        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:tests? #f ;; no tests available
+     `(#:configure-flags '("-DDOWNLOAD_TITLE_SEQUENCES=OFF")
+       #:tests? #f ; Tests require network.
        #:phases
         (modify-phases %standard-phases
-          (add-after 'unpack 'fix-usr-share-paths
+          (add-after 'unpack 'fix-usr-share-paths&add-data
-            (lambda* (#:key make-flags outputs #:allow-other-keys)
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (let ((titles (assoc-ref inputs "openrct2-title-sequences"))
+                    (objects (assoc-ref inputs "openrct2-objects")))
               ;; Fix some references to /usr/share.
+              ;; Change to Platform.Linux.cpp on 0.1.2+
               (substitute* "src/openrct2/platform/linux.c"
                 (("/usr/share")
-                (string-append (assoc-ref %outputs "out") "/share")))))
+                 (string-append (assoc-ref %outputs "out") "/share")))
-          (add-after 'build 'fix-cmake-install-file
+              (copy-recursively (string-append titles
-            (lambda _
+                                "/share/openrct2/title-sequences") "data/title")
-              ;; The build system tries to download a file and compare hashes.
+              (copy-recursively (string-append objects
-              ;; Since we have no network, remove this so the install doesn't fail.
+                                "/share/openrct2/objects") "data/object")))))))
-              (substitute* "cmake_install.cmake"
-                (("EXPECTED_HASH SHA1=b587d83de508d0b104d14c599b76f8565900fce0")
-                "")))))))
     (inputs `(("curl" ,curl)
               ("fontconfig" ,fontconfig)
               ("freetype" ,freetype)
+              ("icu4c" ,icu4c)
               ("jansson" ,jansson)
               ("libpng" ,libpng)
               ("libzip" ,libzip)
               ("mesa" ,mesa)
+              ("openrct2-objects" ,openrct2-objects)
+              ("openrct2-title-sequences" ,openrct2-title-sequences)
               ("openssl" ,openssl)
               ("sdl2" ,sdl2)
               ("speexdsp" ,speexdsp)
@@ -3166,53 +3252,6 @@ application that locks the keyboard and mouse and instead displays bright
 colors, pictures, and sounds.")
     (license license:gpl3+)))
 
-(define-public mrrescue
-  (package
-    (name "mrrescue")
-    (version "1.02e")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/SimonLarsen/mrrescue/releases/"
-                    "download/" version "/" name version ".love"))
-              (file-name (string-append name "-" version ".love"))
-              (sha256
-               (base32
-                "0jwzbwkgp1l5ia6c7s760gmdirbsncp6nfqp7vqdqsfb63la9gl2"))))
-    (build-system trivial-build-system)
-    (arguments
-     '(#:modules ((guix build utils))
-       #:builder
-       (begin
-         (use-modules (guix build utils))
-         (let* ((out     (assoc-ref %outputs "out"))
-                (bindir  (string-append out "/bin"))
-                (prog    (string-append bindir "/mrrescue"))
-                (source  (assoc-ref %build-inputs "source"))
-                (bash    (string-append (assoc-ref %build-inputs "bash")
-                                        "/bin/bash"))
-                (love    (string-append (assoc-ref %build-inputs "love")
-                                        "/bin/love")))
-           (mkdir-p bindir)
-           (with-output-to-file prog
-             (lambda ()
-               (format #t "#!~a~%" bash)
-               (format #t "exec -a mrrescue \"~a\" \"~a\"~%" love source)))
-           (chmod prog #o755)
-           #t))))
-    (inputs
-     `(("bash" ,bash)
-       ("love" ,love)))
-    (home-page "http://tangramgames.dk/games/mrrescue")
-    (synopsis "Arcade-style fire fighting game")
-    (description
-     "Mr. Rescue is an arcade styled 2d action game centered around evacuating
-civilians from burning buildings.  The game features fast paced fire
-extinguishing action, intense boss battles, a catchy soundtrack and lots of
-throwing people around in pseudo-randomly generated buildings.")
-    (license (list license:zlib             ; for source code
-                   license:cc-by-sa3.0))))  ; for graphics and music assets
-
 (define-public hyperrogue
   (package
     (name "hyperrogue")
@@ -4481,7 +4520,7 @@ some graphical niceities, and numerous bug-fixes and other improvements.")
   (package
     (inherit quakespasm)
     (name "vkquake")
-    (version "0.97.3")
+    (version "1.00.0")
     (source
      (origin
        (method url-fetch)
@@ -4490,7 +4529,7 @@ some graphical niceities, and numerous bug-fixes and other improvements.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1p0nh2v2ilylw62fxc5qpfcmyhs0s64w8sgh036nc6kn21kbjc0d"))))
+         "0bviv18jvp41jvrabgl7l5kq4n1p6p3rywij481yswawdw6l5idh"))))
     (arguments
      `(#:make-flags
        (let ((vulkanlib (string-append (assoc-ref %build-inputs

gnu/packages/geo.scm

@@ -544,14 +544,14 @@ coordinates.")
 (define-public r-rgooglemaps
   (package
    (name "r-rgooglemaps")
-   (version "1.4.1")
+   (version "1.4.2")
    (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RgoogleMaps" version))
        (sha256
         (base32
-         "0fsmlnhl4kw2j4972kfanzw9njhnzk695gsyw8g6yppsmz2clcaq"))))
+         "112mdm53qx92n2m4ms02sbppckp44l1z19vy99j6gw3jrdprjydl"))))
    (properties `((upstream-name . "RgoogleMaps")))
    (build-system r-build-system)
    (propagated-inputs `(("r-png" ,r-png)))

gnu/packages/gnome.scm

@@ -7140,7 +7140,7 @@ photo-booth-like software, such as Cheese.")
 (define-public cheese
   (package
     (name "cheese")
-    (version "3.26.0")
+    (version "3.28.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -7148,7 +7148,7 @@ photo-booth-like software, such as Cheese.")
                                   version ".tar.xz"))
               (sha256
                (base32
-                "01f6lsp9jkhq5v2zxlghw15bca4xqavkxqkl8977r0g13p22zxcf"))))
+                "06da5qc5hdvwwd5vkbgbx8pjx1l3mvr07yrnnv3v1hfc3wp7l7jw"))))
     (arguments
      ;; Tests require GDK.
      `(#:tests? #f

gnu/packages/gnupg.scm

@@ -108,6 +108,7 @@ Daemon and possibly more in the future.")
 
 (define-public libgcrypt
   (package
+    (replacement libgcrypt/fixed)
     (name "libgcrypt")
     (version "1.8.2")
     (source (origin
@@ -142,6 +143,19 @@ generation.")
     (properties '((ftp-server . "ftp.gnupg.org")
                   (ftp-directory . "/gcrypt/libgcrypt")))))
 
+(define libgcrypt/fixed
+  (package
+    (inherit libgcrypt)
+    (name "libgcrypt")
+    (version "1.8.3")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append "mirror://gnupg/libgcrypt/libgcrypt-"
+                                 version ".tar.bz2"))
+             (sha256
+              (base32
+               "0z5gs1khzyknyfjr19k8gk4q148s6q987ya85cpn0iv70fz91v36"))))))
+
 (define-public libassuan
   (package
     (name "libassuan")
@@ -349,15 +363,14 @@ libskba (working with X.509 certificates and CMS data).")
 
 (define-public gnupg-1
   (package (inherit gnupg)
-    (version "1.4.22")
+    (version "1.4.23")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnupg/gnupg/gnupg-" version
                                   ".tar.bz2"))
-              (patches (search-patches "gnupg-1.4-CVE-2018-12020.patch"))
               (sha256
                (base32
-                "1d1hz4szh1kvwhsw7w2zxa6q5ndrk3qy6hj289l1b8k3xi5s554m"))))
+                "1fkq4sqldvf6a25mm2qz95swv1qjg464736091w51djiwqbjyin9"))))
     (native-inputs '())
     (inputs
      `(("zlib" ,zlib)
@@ -508,14 +521,14 @@ decrypt messages using the OpenPGP format by making use of GPGME.")
 (define-public python-gnupg
   (package
     (name "python-gnupg")
-    (version "0.3.8")
+    (version "0.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "python-gnupg" version))
        (sha256
         (base32
-         "0nkbs9c8f30lra7ca39kg91x8cyxn0jb61vih4qky839gpbwwwiq"))))
+         "03dc8whhvk7ccspbk8vzfhkxli8cd9zfbss5p597g4jldgy8s59d"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -523,16 +536,14 @@ decrypt messages using the OpenPGP format by making use of GPGME.")
          (replace 'check
            (lambda _
              (substitute* "test_gnupg.py"
-               ;; Exported keys don't have a version line!
-               (("del k1\\[1\\]") "#")
                ;; Unsure why this test fails.
                (("'test_search_keys'") "True")
                (("def test_search_keys") "def disabled__search_keys"))
              (setenv "USERNAME" "guixbuilder")
              ;; The doctests are extremely slow and sometimes time out,
              ;; so we disable them.
-             (zero? (system* "python"
+             (invoke "python"
-                             "test_gnupg.py" "--no-doctests")))))))
+                     "test_gnupg.py" "--no-doctests"))))))
     (native-inputs
      `(("gnupg" ,gnupg-1)))
     (home-page "https://packages.python.org/python-gnupg/index.html")

gnu/packages/golang.scm

@@ -215,7 +215,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
   (package
     (inherit go-1.4)
     (name "go")
-    (version "1.9.6")
+    (version "1.9.7")
     (source
      (origin
        (method url-fetch)
@@ -223,7 +223,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
                            name version ".src.tar.gz"))
        (sha256
         (base32
-         "0a2qkvzr0g5cbd66wi7b6r40qyp9p55y0zz2j5qg1xsqwsdhbx1n"))))
+         "08kpy874x0rx43zpyv5kwd8xj2ma91xm33i0ka2v1v788px18a2q"))))
     (arguments
      (substitute-keyword-arguments (package-arguments go-1.4)
        ((#:phases phases)
@@ -384,7 +384,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
   (package
     (inherit go-1.9)
     (name "go")
-    (version "1.10.2")
+    (version "1.10.3")
     (source
      (origin
        (method url-fetch)
@@ -392,7 +392,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
                            name version ".src.tar.gz"))
        (sha256
         (base32
-         "1gcqbac3wbhbcr0ri9zgfj6qkqbwf9fn116a0a7fvn4wdff60r32"))))
+         "1wjmw65nfkkzz084695gdgn13sbjcaafy2y5370d214pdk31qysn"))))
     (arguments
      (substitute-keyword-arguments (package-arguments go-1.9)
        ((#:phases phases)

gnu/packages/graphics.scm

@@ -373,7 +373,7 @@ storage of the \"EXR\" file format for storing 16-bit floating-point images.")
 (define-public openimageio
   (package
     (name "openimageio")
-    (version "1.6.15")
+    (version "1.7.19")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/OpenImageIO/oiio/"
@@ -381,7 +381,7 @@ storage of the \"EXR\" file format for storing 16-bit floating-point images.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "144crq0205d0w5aq4iglh2rhzf54a8rv3pksy6d533b75w5d7rq7"))))
+                "1qlmfhvl2wva4aifyiq7c4sdy61ddl7wykwvlpfys9p701xghvj7"))))
     (build-system cmake-build-system)
     ;; FIXME: To run all tests successfully, test image sets from multiple
     ;; third party sources have to be present.  For details see

gnu/packages/groovy.scm

@@ -1107,7 +1107,7 @@ and modify groovy's @dfn{Abstract Syntax Tree} (AST).")))
                      "groovy-jmx" "groovy-json" "groovy-jsr223"
                      "groovy-nio" "groovy-servlet" "groovy-sql"
                      "groovy-swing" "groovy-templates" "groovy-testng"
-                     "java-commons-cli" "java-asm"
+                     "groovy-xml" "java-commons-cli" "java-asm"
                      "java-classpathx-servletapi" "java-xstream"
                      "java-jansi" "java-jline-2"))
                  ;; antlr.jar is present twice in antlr2.  Symlink doesn't like
@@ -1140,6 +1140,7 @@ and modify groovy's @dfn{Abstract Syntax Tree} (AST).")))
        ("groovy-swing" ,groovy-swing)
        ("groovy-templates" ,groovy-templates)
        ("groovy-testng" ,groovy-testng)
+       ("groovy-xml" ,groovy-xml)
        ("java-commons-cli" ,java-commons-cli)
        ("java-asm" ,java-asm)
        ("java-classpathx-servletapi" ,java-classpathx-servletapi)

gnu/packages/gtk.scm

@@ -8,7 +8,7 @@
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2015 Andy Wingo <wingo@igalia.com>
 ;;; Copyright © 2015 David Hashe <david.hashe@dhashe.com>
-;;; Coypright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Fabian Harfert <fhmgufs@web.de>
 ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>

gnu/packages/guile.scm

@@ -1786,7 +1786,7 @@ is no support for parsing block and inline level HTML.")
 (define-public guile-bytestructures
   (package
     (name "guile-bytestructures")
-    (version "1.0.1")
+    (version "1.0.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/TaylanUB/scheme-bytestructures"
@@ -1794,7 +1794,7 @@ is no support for parsing block and inline level HTML.")
                                   "/bytestructures-" version ".tar.gz"))
               (sha256
                (base32
-                "1lnfcy65mqj823lamy2n2vaghdz0g7mj011bgnhmd6hwpnaidnh2"))))
+                "0xf6s8gd3656j8k2ar6y7i62r68azawyzxhsagsk8nvldnrs1r18"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -2002,20 +2002,6 @@ is not available for Guile 2.0.")
                   "0z1dvn0scx59pbgjkpacam7p5n7630z4qm8fazim7ixq9xv3s8wx"))
                 (file-name (git-file-name name version))))
       (build-system gnu-build-system)
-      (arguments
-       `(#:phases (modify-phases %standard-phases
-                    ;; FIXME: On i686, bytestructures miscalculates the offset
-                    ;; of the 'old-file' and 'new-file' fields within the
-                    ;; '%diff-delta' structure.  See
-                    ;; <https://github.com/TaylanUB/scheme-bytestructures/issues/30>.
-                    ,@(if (string=? (%current-system) "x86_64-linux")
-                          '()
-                          '((add-before 'check 'skip-tests
-                              (lambda _
-                                (substitute* "Makefile"
-                                  (("tests/status\\.scm")
-                                   ""))
-                                #t)))))))
       (native-inputs
        `(("autoconf" ,autoconf)
          ("automake" ,automake)

gnu/packages/java.scm

@@ -3304,6 +3304,39 @@ Compiler component.")))
 This component decrypts a string passed to it.")
     (license license:asl2.0)))
 
+(define-public java-plexus-cli
+  (package
+    (name "java-plexus-cli")
+    (version "1.7")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/sonatype/plexus-cli")
+                     (commit "a776afa6bca84e5107bedb69440329cdb24ed645")))
+              (file-name (string-append name "-" version))
+              (sha256
+               (base32
+                "0xjrlay605rypv3zd7y24vlwf0039bil3n2cqw54r1ddpysq46vx"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "plexus-cli.jar"
+       #:source-dir "src/main/java"
+       #:jdk ,icedtea-8
+       #:test-dir "src/test"))
+    (inputs
+     `(("java-commons-cli" ,java-commons-cli)
+       ("java-plexus-container-default" ,java-plexus-container-default)
+       ("java-plexus-classworlds" ,java-plexus-classworlds)))
+    (native-inputs
+     `(("java-plexus-utils" ,java-plexus-utils)
+       ("java-junit" ,java-junit)
+       ("java-guava" ,java-guava)))
+    (home-page "https://codehaus-plexus.github.io/plexus-cli")
+    (synopsis "CLI building library for plexus")
+    (description "This package is a library to help creating CLI around
+Plexus components.")
+    (license license:asl2.0)))
+
 (define-public java-sisu-build-api
   (package
     (name "java-sisu-build-api")
@@ -10195,3 +10228,32 @@ This module can be assimilated to a significantly improved version of log4j.
 Moreover, @code{logback-classic} natively implements the slf4j API so that you
 can readily switch back and forth between logback and other logging frameworks
 such as log4j or @code{java.util.logging} (JUL).")))
+
+(define-public java-qdox
+  (package
+    (name "java-qdox")
+    ; Newer version exists, but this version is required by java-plexus-component-metadata
+    (version "2.0-M2")
+    (source (origin
+              (method url-fetch)
+              ;; 2.0-M4, -M5 at https://github.com/paul-hammant/qdox
+              ;; Older releases at https://github.com/codehaus/qdox/
+              ;; Note: The release at maven is pre-generated. The release at
+              ;; github requires jflex.
+              (uri (string-append "http://central.maven.org/maven2/"
+                                  "com/thoughtworks/qdox/qdox/" version
+                                  "/qdox-" version "-sources.jar"))
+              (sha256
+               (base32
+                "10xxrcaicq6axszcr2jpygisa4ch4sinyx5q7kqqxv4lknrmxp5x"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "qdox.jar"
+       #:tests? #f)); no tests
+    (home-page "http://qdox.codehaus.org/")
+    (synopsis "Parse definitions from Java source files")
+    (description "QDox is a high speed, small footprint parser for extracting
+class/interface/method definitions from source files complete with JavaDoc
+@code{@@tags}.  It is designed to be used by active code generators or
+documentation tools.")
+    (license license:asl2.0)))

gnu/packages/libedit.scm

@@ -28,7 +28,7 @@
 (define-public libedit
   (package
     (name "libedit")
-    (version "20170329-3.1")
+    (version "20180525-3.1")
     (source
      (origin
       (method url-fetch)
@@ -36,7 +36,7 @@
                           "/" name "-" version ".tar.gz"))
       (sha256
        (base32
-        "1gnlgl0x8g9ky59s70nriy5gv47676d1s4ypvbv8y11apl7xkwli"))))
+        "05iicng4kag5hxdc7adbyj1gm3qbmvcc33m9cyx5gys0s67yl6y4"))))
     (build-system gnu-build-system)
     (inputs
      `(("ncurses" ,ncurses)))

gnu/packages/linux.scm

@@ -295,6 +295,12 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration."
                  (or (%current-target-system) (%current-system)))
            ((or "x86_64" "i386")
             `(("gcc" ,gcc-7)))
+           ("arm64"
+            ;; Work around a binutils 2.30 bug where some kernel symbols would
+            ;; be incorrectly marked as relocatable:
+            ;; <https://sourceware.org/bugzilla/show_bug.cgi?id=22764>.
+            `(("ld-wrapper" ,(make-ld-wrapper "ld-wrapper"
+                                              #:binutils binutils/fixed))))
            (_
             '()))
        ,@(match (and configuration-file
@@ -395,8 +401,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.17")
+(define %linux-libre-version "4.17.2")
-(define %linux-libre-hash "0abbqrq96kn97jr02mf4ahqg7hl9vhq95c1l2z0s7jqrmhv1n8pb")
+(define %linux-libre-hash "0xkswi9vhbzi466pqvyli7glkvdyxhphn8yjg69kpw37rpw8ix5l")
 
 (define-public linux-libre
   (make-linux-libre %linux-libre-version
@@ -404,8 +410,8 @@ It has been modified to remove all non-free binary blobs.")
                     %linux-compatible-systems
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.48")
+(define %linux-libre-4.14-version "4.14.50")
-(define %linux-libre-4.14-hash "011lkq30gpvbgvg2p1nw2kqkig9a3qridy678rkx3fpah0ya4rhd")
+(define %linux-libre-4.14-hash "19k7s33dyykm2vh1zpxxh3qrbjcx2p2md2r8s8z5mbv8yaldgvmj")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
@@ -414,14 +420,14 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.107"
+  (make-linux-libre "4.9.109"
-                    "0560sy53l42wi1jidwdbhjaa9p6kf46snk2hfcjk9f0ciiiiz5gi"
+                    "1i27fmlr0b05n4qri2vxdbg0qddwk1clyaramwbl3w0w10k63qkc"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.136"
+  (make-linux-libre "4.4.138"
-                    "0bc278l9arl8bb2gvcg02x57h66b4r8iaan3r4kzqbmkfspkl2gi"
+                    "1030ra5gn24qmx8lsnhr6kfnfm60avzs23r81dl7mvzr5dci8vsl"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
@@ -914,16 +920,15 @@ Zerofree requires the file system to be unmounted or mounted read-only.")
 (define-public strace
   (package
     (name "strace")
-    (version "4.22")
+    (version "4.23")
     (home-page "https://strace.io")
     (source (origin
              (method url-fetch)
              (uri (string-append home-page "/files/" version
                                  "/strace-" version ".tar.xz"))
-             (patches (search-patches "strace-kernel-4.16.patch"))
              (sha256
               (base32
-               "17dkpnsjxmys1ydidm9wcvc3wscsz44fmlxw3dclspn9cj9d1306"))))
+               "1bcsq2gbpcb81ayryvn56a6kjx42fc21la6qgds35n0xbybacq3q"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -2995,7 +3000,10 @@ arrays when needed.")
              (let ((lvm2 (assoc-ref inputs "lvm2"))
                    (udev (assoc-ref inputs "udev")))
                (substitute* "Makefile.inc"
-                 (("\\$\\(prefix\\)/usr") "$(prefix)"))
+                 (("\\$\\(prefix\\)/usr") "$(prefix)")
+                 ;; Do not save timestamp to avoid gzip "timestamp
+                 ;; out-of-range" warnings.
+                 (("gzip -9") "gzip -9n"))
                (substitute* '("kpartx/Makefile" "libmultipath/Makefile")
                  (("/usr/include/libdevmapper.h")
                   (string-append lvm2 "/include/libdevmapper.h"))
@@ -3364,7 +3372,7 @@ disks and SD cards.  This package provides the userland utilities.")
   (package
     (inherit f2fs-tools-1.7)
     (name "f2fs-tools")
-    (version "1.8.0")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3372,7 +3380,7 @@ disks and SD cards.  This package provides the userland utilities.")
                     "/f2fs-tools.git/snapshot/" name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1bir9ladb58ijlcvrjrq1fb1xv5ys50zdjaq0yzliib0apsyrnyl"))))
+                "05ikaim0qq3dx9x3sp43ralwz43r3b0viv62n99kabp0vf3b0hg8"))))
     (inputs
      `(("libuuid" ,util-linux)))))
 
@@ -4033,15 +4041,15 @@ monitoring tools for Linux.  These include @code{mpstat}, @code{iostat},
 (define-public light
   (package
     (name "light")
-    (version "1.0")
+    (version "1.1")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/haikarainen/" name
+              (uri (git-reference
-                                  "/archive/v" version ".tar.gz"))
+                    (url "https://github.com/haikarainen/light")
+                    (commit version)))
               (sha256
                (base32
-                "0r5gn6c0jcxknzybl6059dplxv46dpahchqq4gymrs7z8bp0hilp"))
+                "1qra8yzsga29bxlvq63v1db071a1xdji7i60p4kzrciidm1206js"))))
-              (file-name (string-append name "-" version ".tar.gz"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f                      ; no tests
@@ -4049,10 +4057,11 @@ monitoring tools for Linux.  These include @code{mpstat}, @code{iostat},
                           (string-append "PREFIX=" %output))
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure)
+         (delete 'configure)            ; no configure script
          (add-after 'unpack 'patch-makefile
            (lambda _
-             (substitute* "Makefile" (("chown") "#")))))))
+             (substitute* "Makefile" (("chown") "#"))
+             #t)))))
     (native-inputs
      `(("help2man" ,help2man)))
     (home-page "https://haikarainen.github.io/light")
@@ -4405,14 +4414,14 @@ available in the kernel Linux.")
 (define-public cpuid
   (package
     (name "cpuid")
-    (version "20180419")
+    (version "20180519")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://www.etallen.com/cpuid/cpuid-"
                                   version ".src.tar.gz"))
               (sha256
                (base32
-                "0cnxj72pjalsszhn862r6shw64zbrkw0k3mm36fn93bivswjnj12"))))
+                "16pzwyifc9glpk1hm6bqb5d1a7cw0qnqiamh5sbvqg7j6sz26y4n"))))
     (build-system gnu-build-system)
     (arguments
      '(#:make-flags '("CC=gcc")

gnu/packages/machine-learning.scm

@@ -47,6 +47,7 @@
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages image)
   #:use-module (gnu packages maths)
+  #:use-module (gnu packages mpi)
   #:use-module (gnu packages ocaml)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
@@ -786,3 +787,78 @@ main intended application of Autograd is gradient-based optimization.")
 
 (define-public python2-autograd
   (package-with-python2 python-autograd))
+
+(define-public lightgbm
+  (package
+    (name "lightgbm")
+    (version "2.0.12")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/Microsoft/LightGBM/archive/v"
+                    version ".tar.gz"))
+              (sha256
+               (base32
+                "132zf0yk0545mg72hyzxm102g3hpb6ixx9hnf8zd2k55gas6cjj1"))
+              (file-name (string-append name "-" version ".tar.gz"))))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-nose" ,python-nose)))
+    (inputs
+     `(("openmpi" ,openmpi)))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-scipy" ,python-scipy)))
+    (arguments
+     `(#:configure-flags
+       '("-DUSE_MPI=ON")
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key outputs #:allow-other-keys)
+             (with-directory-excursion ,(string-append "../LightGBM-" version)
+               (invoke "pytest" "tests/c_api_test/test_.py")))))))
+    (build-system cmake-build-system)
+    (home-page "https://github.com/Microsoft/LightGBM")
+    (synopsis "Gradient boosting framework based on decision tree algorithms")
+    (description "LightGBM is a gradient boosting framework that uses tree
+based learning algorithms.  It is designed to be distributed and efficient with
+the following advantages:
+
+@itemize
+@item Faster training speed and higher efficiency
+@item Lower memory usage
+@item Better accuracy
+@item Parallel and GPU learning supported (not enabled in this package)
+@item Capable of handling large-scale data
+@end itemize\n")
+    (license license:expat)))
+
+(define-public vowpal-wabbit
+  ;; Language bindings not included.
+  (package
+    (name "vowpal-wabbit")
+    (version "8.5.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/JohnLangford/vowpal_wabbit/archive/"
+                    version ".tar.gz"))
+              (sha256
+               (base32
+                "0clp2kb7rk5sckhllxjr5a651awf4s8dgzg4659yh4hf5cqnf0gr"))
+              (file-name (string-append name "-" version ".tar.gz"))))
+    (inputs
+     `(("boost" ,boost)
+       ("zlib" ,zlib)))
+    (arguments
+     `(#:configure-flags
+       (list (string-append "--with-boost="
+                            (assoc-ref %build-inputs "boost")))))
+    (build-system gnu-build-system)
+    (home-page "https://github.com/JohnLangford/vowpal_wabbit")
+    (synopsis "Fast machine learning library for online learning")
+    (description "Vowpal Wabbit is a machine learning system with techniques
+such as online, hashing, allreduce, reductions, learning2search, active, and
+interactive learning.")
+    (license license:bsd-3)))

gnu/packages/mail.scm

@@ -491,7 +491,7 @@ and corrections.  It is based on a Bayesian filter.")
 (define-public offlineimap
   (package
     (name "offlineimap")
-    (version "7.2.0")
+    (version "7.2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/OfflineIMAP/offlineimap/"
@@ -499,7 +499,7 @@ and corrections.  It is based on a Bayesian filter.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1i7pzm1vrj98jcyn1ygsg1yp0gqlsssnc25451icvivysvdwdj5n"))))
+                "1022xf2w1xax4vx4kzhlfbhaf0b72wkpvrcscvs4q8qk2ja68h8x"))))
     (build-system python-build-system)
     (native-inputs
      `(("asciidoc" ,asciidoc)))

gnu/packages/maths.scm

@@ -294,14 +294,14 @@ semiconductors.")
 (define-public gsl
   (package
     (name "gsl")
-    (version "2.4")
+    (version "2.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/gsl/gsl-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "16yfs5n444s03np1naj6yp1fsysd42kdscxzkg0k2yvfjixx0ijd"))
+                "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
               (patches (search-patches "gsl-test-i686.patch"))))
     (build-system gnu-build-system)
     (arguments
@@ -3372,7 +3372,8 @@ in finite element programs.")
             version "-src.zip"))
         (sha256
           (base32
-            "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))))
+            "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
+        (patches (search-patches "flann-cmake-3.11.patch"))))
     (build-system cmake-build-system)
     (outputs '("out"
                "octave"))                  ;46 MiB .mex file that pulls Octave

gnu/packages/maven.scm

@@ -24,7 +24,54 @@
   #:use-module (guix build-system ant)
   #:use-module (gnu packages)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages java))
+  #:use-module (gnu packages java)
+  #:use-module (gnu packages web)
+  #:use-module (gnu packages xml))
+
+(define-public java-plexus-component-metadata
+  (package
+    (inherit java-plexus-container-default)
+    (name "java-plexus-component-metadata")
+    (arguments
+     `(#:jar-name "plexus-component-metadata.jar"
+       #:source-dir "src/main/java"
+       #:test-dir "src/test"
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'chdir
+           (lambda _
+             (chdir "plexus-component-metadata")
+             #t))
+         (add-before 'build 'copy-resources
+           (lambda _
+             (copy-recursively "src/main/resources"
+                               "build/classes/")
+             #t)))))
+    (inputs
+     `(("java-plexus-container-default" ,java-plexus-container-default)
+       ("java-plexu-component-annotations" ,java-plexus-component-annotations)
+       ("java-plexus-utils" ,java-plexus-utils)
+       ("java-plexus-cli" ,java-plexus-cli)
+       ("java-plexus-classworlds" ,java-plexus-classworlds)
+       ("maven-plugin-api" ,maven-plugin-api)
+       ("maven-plugin-annotations" ,maven-plugin-annotations)
+       ("maven-core-bootstrap" ,maven-core-bootstrap)
+       ("maven-model" ,maven-model)
+       ("java-commons-cli" ,java-commons-cli)
+       ("java-qdox" ,java-qdox)
+       ("java-jdom2" ,java-jdom2)
+       ("java-asm" ,java-asm)))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-guava" ,java-guava)
+       ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect)))
+    (synopsis "Inversion-of-control container for Maven")
+    (description "The Plexus project provides a full software stack for creating
+and executing software projects.  Based on the Plexus container, the
+applications can utilise component-oriented programming to build modular,
+reusable components that can easily be assembled and reused.  This package
+provides the Maven plugin generating the component metadata.")))
 
 (define-public maven-resolver-api
   (package
@@ -190,6 +237,89 @@ for repositories using URI-based layouts.")))
        ("java-hamcrest-core" ,java-hamcrest-core)
        ("maven-resolver-test-util" ,maven-resolver-test-util)))))
 
+(define-public maven-resolver-transport-wagon
+  (package
+    (inherit maven-resolver-api)
+    (name "maven-resolver-transport-wagon")
+    (arguments
+     `(#:jar-name "maven-resolver-transport-wagon.jar"
+       #:source-dir "maven-resolver-transport-wagon/src/main/java"
+       #:test-dir "maven-resolver-transport-wagon/src/test"
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'generate-sisu
+           (lambda _
+             (mkdir-p "build/classes/META-INF/sisu")
+             (with-output-to-file "build/classes/META-INF/sisu/javax.inject.Named"
+               (lambda _
+                 (display "org.eclipse.aether.transport.wagon.WagonTransporterFactory\n")))
+             #t))
+         (add-before 'build 'generate-components.xml
+           (lambda _
+             (mkdir-p "build/classes/META-INF/plexus")
+             (with-output-to-file "build/classes/META-INF/plexus/components.xml"
+               (lambda _
+                 (display
+                   (string-append
+                     "<?xml version=\"1.0\" encoding=\"UTF-8\"?>
+<component-set>
+  <components>
+    <component>
+      <role>org.eclipse.aether.transport.wagon.WagonConfigurator</role>
+      <role-hint>plexus</role-hint>
+      <implementation>org.eclipse.aether.internal.transport.wagon.PlexusWagonConfigurator</implementation>
+      <description />
+      <isolated-realm>false</isolated-realm>
+      <requirements>
+        <requirement>
+          <role>org.codehaus.plexus.PlexusContainer</role>
+          <role-hint />
+          <field-name>container</field-name>
+        </requirement>
+      </requirements>
+    </component>
+    <component>
+      <role>org.eclipse.aether.transport.wagon.WagonProvider</role>
+      <role-hint>plexus</role-hint>
+      <implementation>org.eclipse.aether.internal.transport.wagon.PlexusWagonProvider</implementation>
+      <description />
+      <isolated-realm>false</isolated-realm>
+      <requirements>
+        <requirement>
+          <role>org.codehaus.plexus.PlexusContainer</role>
+          <role-hint />
+          <field-name>container</field-name>
+        </requirement>
+      </requirements>
+    </component>
+  </components>
+</component-set>\n"))))
+             #t)))))
+    (inputs
+     `(("maven-resolver-api" ,maven-resolver-api)
+       ("maven-resolver-spi" ,maven-resolver-spi)
+       ("maven-resolver-util" ,maven-resolver-util)
+       ("java-javax-inject" ,java-javax-inject)
+       ("mavne-wagon-provider-api" ,maven-wagon-provider-api)
+       ("java-plexus-component-annotation" ,java-plexus-component-annotations)
+       ("java-plexus-classworld" ,java-plexus-classworlds)
+       ("java-plexus-plexus-util" ,java-plexus-utils)
+       ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject)
+       ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus)))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-hamcrest-core" ,java-hamcrest-core)
+       ("maven-resolver-test-util" ,maven-resolver-test-util)
+       ("java-guava" ,java-guava)
+       ("java-cglib" ,java-cglib)
+       ("java-asm" ,java-asm)
+       ("java-aopalliance" ,java-aopalliance)
+       ("java-guice" ,java-guice)))
+    (synopsis "Transport implementation for Maven")
+    (description "This package contains a transport implementation based on
+Maven Wagon, for use in Maven.")))
+
 (define-public maven-shared-utils
   (package
     (name "maven-shared-utils")
@@ -230,6 +360,317 @@ plexus-utils in Maven.  It is not a 100% API compatible replacement but a
 replacement with improvements.")
     (license license:asl2.0)))
 
+(define-public maven-plugin-annotations
+  (package
+    (name "maven-plugin-annotations")
+    (version "3.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://archive.apache.org/dist/maven/"
+                                  "plugin-tools/maven-plugin-tools-" version
+                                  "-source-release.zip"))
+              (sha256 (base32 "1ryqhs62j5pas93brhf5dsnvp99hxbvssf681yj5rk3r9h24hqm2"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "maven-plugin-annotations.jar"
+       #:source-dir "maven-plugin-annotations/src/main/java"
+       #:tests? #f))
+    (inputs
+     `(("maven-artifact" ,maven-artifact)))
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (home-page "https://maven.apache.org/plugin-tools/maven-plugin-annotations/")
+    (synopsis "Java 5 annotations to use in Mojos")
+    (description "This package contains Java 5 annotations for use in Mojos.")
+    (license license:asl2.0)))
+
+(define-public maven-wagon-provider-api
+  (package
+    (name "maven-wagon-provider-api")
+    (version "3.0.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://archive.apache.org/dist/maven/wagon/"
+                                  "wagon-" version "-source-release.zip"))
+              (sha256 (base32 "1qb0q4m7vmf290xp3fnfdi3pwl3hkskia5g3z2v82q1ch3y2knqv"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "maven-wagon-provider-api.jar"
+       #:source-dir "wagon-provider-api/src/main/java"
+       #:test-dir "wagon-provider-api/src/test"))
+    (inputs
+     `(("java-plexus-utils" ,java-plexus-utils)))
+    (native-inputs
+     `(("unzip" ,unzip)
+       ("java-junit" ,java-junit)
+       ("java-easymock" ,java-easymock)))
+    (home-page "https://maven.apache.org/wagon")
+    (synopsis "Transport abstraction for Maven")
+    (description "Maven Wagon is a transport abstraction that is used in Maven's
+artifact and repository handling code.")
+    (license license:asl2.0)))
+
+(define-public maven-wagon-provider-test
+  (package
+    (inherit maven-wagon-provider-api)
+    (name "maven-wagon-provider-test")
+    (arguments
+     `(#:jar-name "maven-wagon-provider-test.jar"
+       #:source-dir "wagon-provider-test/src/main/java"
+       #:tests? #f; no tests
+       #:jdk ,icedtea-8))
+    (inputs
+     `(("java-plexus-utils" ,java-plexus-utils)
+       ("java-plexus-container-default" ,java-plexus-container-default)
+       ("java-eclipse-jetty-util-9.2" ,java-eclipse-jetty-util-9.2)
+       ("java-eclipse-jetty-security-9.2" ,java-eclipse-jetty-security-9.2)
+       ("java-eclipse-jetty-server-9.2" ,java-eclipse-jetty-server-9.2)
+       ("java-eclipse-jetty-servlet-9.2" ,java-eclipse-jetty-servlet-9.2)
+       ("java-slf4j-api" ,java-slf4j-api)
+       ("java-tomcat" ,java-tomcat)
+       ("maven-wagon-provider-api" ,maven-wagon-provider-api)))
+    (synopsis "Test classes from maven-wagon")
+    (description "Maven Wagon is a transport abstraction that is used in Maven's
+artifact and repository handling code.  This package contains common test
+classes used in multiple maven-wagon components.")))
+
+(define-public maven-wagon-file
+  (package
+    (inherit maven-wagon-provider-api)
+    (name "maven-wagon-file")
+    (arguments
+     `(#:jar-name "maven-wagon-file.jar"
+       #:source-dir "wagon-providers/wagon-file/src/main/java"
+       #:test-dir "wagon-providers/wagon-file/src/test"
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'fix-paths
+           (lambda _
+             ;; Tests assume they are run by maven, which copies test resources
+             ;; to target.  Our ant-build-system does the same, but with the
+             ;; build directory.
+             (substitute* "wagon-providers/wagon-file/src/test/java/org/apache/maven/wagon/providers/file/FileWagonTest.java"
+               (("target") "build"))
+             #t))
+         (add-after 'build 'generate-metadata
+           (lambda _
+             (invoke "java" "-cp" (string-append (getenv "CLASSPATH") ":build/classes")
+                     "org.codehaus.plexus.metadata.PlexusMetadataGeneratorCli"
+                     "--source" "wagon-providers/wagon-file/src/main/java"
+                     "--output" "build/classes/META-INF/plexus/components.xml"
+                     "--classes" "build/classes"
+                     "--descriptors" "build/classes/META-INF")
+             #t))
+         (add-after 'generate-metadata 'rebuild
+           (lambda _
+             (invoke "ant" "jar")
+             #t)))))
+    (inputs
+     `(("java-plexus-utils" ,java-plexus-utils)
+       ("maven-wagon-provider-api" ,maven-wagon-provider-api)))
+    (native-inputs
+     `(("maven-wagon-provider-test" ,maven-wagon-provider-test)
+       ("java-plexus-component-metadata" ,java-plexus-component-metadata)
+       ("java-plexus-component-annotations" ,java-plexus-component-annotations)
+       ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus)
+       ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject)
+       ("java-plexus-classworlds" ,java-plexus-classworlds)
+       ("java-guava" ,java-guava)
+       ("java-guice" ,java-guice)
+       ("java-javax-inject" ,java-javax-inject)
+       ("java-cglib" ,java-cglib)
+       ("java-slf4j-api" ,java-slf4j-api)
+       ("java-plexus-utils" ,java-plexus-utils)
+       ("java-plexus-cli" ,java-plexus-cli)
+       ("maven-plugin-api" ,maven-plugin-api)
+       ("maven-plugin-annotations" ,maven-plugin-annotations)
+       ("maven-core" ,maven-core)
+       ("maven-model" ,maven-model)
+       ("java-commons-cli" ,java-commons-cli)
+       ("java-qdox" ,java-qdox)
+       ("java-jdom2" ,java-jdom2)
+       ("java-asm" ,java-asm)
+       ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect)
+       ,@(package-native-inputs maven-wagon-provider-api)))
+    (synopsis "Wagon provider that gets and puts artifacts using the file system")
+    (description "Maven Wagon is a transport abstraction that is used in Maven's
+artifact and repository handling code.  It uses providers, that are tools to
+manage artifacts and deployment.  This package contains the file provider which
+gets and puts artifacts using the file system.")))
+
+(define-public maven-wagon-tck-http
+  (package
+    (inherit maven-wagon-provider-api)
+    (name "maven-wagon-tck-http")
+    (arguments
+     `(#:jar-name "maven-wagon-tck-http.jar"
+       #:source-dir "wagon-tcks/wagon-tck-http/src/main/java"
+       #:tests? #f; no tests
+       #:jdk ,icedtea-8))
+    (inputs
+     `(("java-plexus-util" ,java-plexus-utils)
+       ("maven-wagon-provider-api" ,maven-wagon-provider-api)
+       ("java-tomcat" ,java-tomcat)
+       ("java-slf4j-api" ,java-slf4j-api)
+       ("java-commons-codec" ,java-commons-codec)
+       ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus)
+       ("java-plexus-classworlds" ,java-plexus-classworlds)
+       ("java-eclipse-jetty-util-9.2" ,java-eclipse-jetty-util-9.2)
+       ("java-eclipse-jetty-webapp-9.2" ,java-eclipse-jetty-webapp-9.2)
+       ("java-eclipse-jetty-security-9.2" ,java-eclipse-jetty-security-9.2)
+       ("java-eclipse-jetty-server-9.2" ,java-eclipse-jetty-server-9.2)
+       ("java-eclipse-jetty-servlet-9.2" ,java-eclipse-jetty-servlet-9.2)))
+    (synopsis "Wagon HTTP Test Compatibility Kit")
+    (description "Maven Wagon is a transport abstraction that is used in Maven's
+artifact and repository handling code.  This package contains the HTTP
+Test Compatibility Kit.")))
+
+(define-public maven-wagon-http-shared
+  (package
+    (inherit maven-wagon-provider-api)
+    (name "maven-wagon-http-shared")
+    (arguments
+     `(#:jar-name "maven-wagon-http-shared.jar"
+       #:source-dir "wagon-providers/wagon-http-shared/src/main/java"
+       #:test-dir "wagon-providers/wagon-http-shared/src/test"
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'build 'generate-metadata
+           (lambda _
+             (invoke "java" "-cp" (string-append (getenv "CLASSPATH") ":build/classes")
+                     "org.codehaus.plexus.metadata.PlexusMetadataGeneratorCli"
+                     "--source" "wagon-providers/wagon-http-shared/src/main/java"
+                     "--output" "build/classes/META-INF/plexus/components.xml"
+                     "--classes" "build/classes"
+                     "--descriptors" "build/classes/META-INF")
+             #t))
+         (add-after 'generate-metadata 'rebuild
+           (lambda _
+             (invoke "ant" "jar")
+             #t)))))
+    (inputs
+     `(("java-plexus-utils" ,java-plexus-utils)
+       ("java-httpcomponents-httpclient" ,java-httpcomponents-httpclient)
+       ("java-httpcomponents-httpcore" ,java-httpcomponents-httpcore)
+       ("java-commons-io" ,java-commons-io)
+       ("java-jsoup" ,java-jsoup)
+       ("maven-wagon-provider-api" ,maven-wagon-provider-api)))
+    (native-inputs
+     `(("maven-wagon-provider-test" ,maven-wagon-provider-test)
+       ("java-plexus-component-metadata" ,java-plexus-component-metadata)
+       ("java-plexus-component-annotations" ,java-plexus-component-annotations)
+       ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus)
+       ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject)
+       ("java-plexus-classworlds" ,java-plexus-classworlds)
+       ("java-guava" ,java-guava)
+       ("java-guice" ,java-guice)
+       ("java-javax-inject" ,java-javax-inject)
+       ("java-cglib" ,java-cglib)
+       ("java-slf4j-api" ,java-slf4j-api)
+       ("java-plexus-utils" ,java-plexus-utils)
+       ("java-plexus-cli" ,java-plexus-cli)
+       ("maven-plugin-api" ,maven-plugin-api)
+       ("maven-plugin-annotations" ,maven-plugin-annotations)
+       ("maven-core" ,maven-core)
+       ("maven-model" ,maven-model)
+       ("java-commons-cli" ,java-commons-cli)
+       ("java-qdox" ,java-qdox)
+       ("java-jdom2" ,java-jdom2)
+       ("java-asm" ,java-asm)
+       ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect)
+       ,@(package-native-inputs maven-wagon-provider-api)))
+    (synopsis "Shared Library for wagon providers supporting HTTP.")
+    (description "Maven Wagon is a transport abstraction that is used in Maven's
+artifact and repository handling code.  It uses providers, that are tools to
+manage artifacts and deployment.  This package contains a shared library for
+wagon providers supporting HTTP.")))
+
+(define-public maven-wagon-http
+  (package
+    (inherit maven-wagon-provider-api)
+    (name "maven-wagon-http")
+    (arguments
+     `(#:jar-name "maven-wagon-http.jar"
+       #:source-dir "wagon-providers/wagon-http/src/main/java"
+       #:test-dir "wagon-providers/wagon-http/src/test"
+       #:test-exclude (list
+                        "**/Abstract*.java"
+                        ;; FIXME: javax.net.ssl.SSLHandshakeException:
+                        ;; sun.security.validator.ValidatorException:
+                        ;; PKIX path building failed:
+                        ;; sun.security.provider.certpath.SunCertPathBuilderException:
+                        ;; unable to find valid certification path to requested target
+                        "**/HttpsWagonPreemptiveTest.java"
+                        "**/HttpsWagonTest.java"
+                        ;; Injection errors
+                        "**/TckTest.java")
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (install-file "wagon-providers/wagon-http/src/main/resources/META-INF/plexus/components.xml"
+                           "build/classes/META-INF/plexus")
+             #t))
+         (add-before 'check 'fix-resource-path
+           (lambda _
+             (substitute* '("wagon-providers/wagon-http/src/test/java/org/apache/maven/wagon/providers/http/HttpsWagonPreemptiveTest.java"
+                            "wagon-providers/wagon-http/src/test/java/org/apache/maven/wagon/providers/http/HttpsWagonTest.java")
+               (("src/test") "wagon-providers/wagon-http/src/test"))
+             #t)))))
+    (inputs
+     `(("java-plexus-utils" ,java-plexus-utils)
+       ("java-httpcomponents-httpclient" ,java-httpcomponents-httpclient)
+       ("java-httpcomponents-httpcore" ,java-httpcomponents-httpcore)
+       ("maven-wagon-http-shared" ,maven-wagon-http-shared)
+       ("maven-wagon-tck-http" ,maven-wagon-tck-http)
+       ("maven-wagon-provider-api" ,maven-wagon-provider-api)))
+    (native-inputs
+     `(("maven-wagon-provider-test" ,maven-wagon-provider-test)
+       ("java-plexus-component-metadata" ,java-plexus-component-metadata)
+       ("java-plexus-component-annotations" ,java-plexus-component-annotations)
+       ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus)
+       ("java-plexus-container-default" ,java-plexus-container-default)
+       ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject)
+       ("java-plexus-classworlds" ,java-plexus-classworlds)
+       ("java-guava" ,java-guava)
+       ("java-guice" ,java-guice)
+       ("java-inject" ,java-javax-inject)
+       ("java-cglib" ,java-cglib)
+       ("java-slf4j-api" ,java-slf4j-api)
+       ("java-plexus-utils" ,java-plexus-utils)
+       ("java-plexus-cli" ,java-plexus-cli)
+       ("maven-plugin-api" ,maven-plugin-api)
+       ("maven-plugin-annotations" ,maven-plugin-annotations)
+       ("maven-core" ,maven-core)
+       ("maven-model" ,maven-model)
+       ("java-commons-cli" ,java-commons-cli)
+       ("java-qdox" ,java-qdox)
+       ("java-jdom2" ,java-jdom2)
+       ("java-asm" ,java-asm)
+       ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect)
+       ("java-tomcat" ,java-tomcat)
+       ("java-eclipse-jetty-util-9.2" ,java-eclipse-jetty-util-9.2)
+       ("java-eclipse-jetty-io-9.2" ,java-eclipse-jetty-io-9.2)
+       ("java-eclipse-jetty-http-9.2" ,java-eclipse-jetty-http-9.2)
+       ("java-eclipse-jetty-server-9.2" ,java-eclipse-jetty-server-9.2)
+       ("java-eclipse-jetty-servlet-9.2" ,java-eclipse-jetty-servlet-9.2)
+       ("java-eclipse-jetty-security-9.2" ,java-eclipse-jetty-security-9.2)
+       ("java-hamcrest-core" ,java-hamcrest-core)
+       ("java-commons-logging-minimal" ,java-commons-logging-minimal)
+       ("java-commons-codec" ,java-commons-codec)
+       ("java-commons-io" ,java-commons-io)
+       ("java-jsoup" ,java-jsoup)
+       ("java-slf4j-simple" ,java-slf4j-simple)
+       ,@(package-native-inputs maven-wagon-provider-api)))
+    (synopsis "Wagon provider that gets and puts artifacts through HTTP(S)")
+    (description "Maven Wagon is a transport abstraction that is used in Maven's
+artifact and repository handling code.  It uses providers, that are tools to
+manage artifacts and deployment.  This package contains a Wagon provider that
+gets and puts artifacts through HTTP(S) using Apache HttpClient-4.x.")))
+
 (define-public maven-artifact
   (package
     (name "maven-artifact")
@@ -562,3 +1003,508 @@ so really just plain objects.")))
        ("java-guava" ,java-guava)
        ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject)
        ("java-javax-inject" ,java-javax-inject)))))
+
+(define-public maven-plugin-api
+  (package
+    (inherit maven-artifact)
+    (name "maven-plugin-api")
+    (arguments
+     `(#:jar-name "maven-plugin-api.jar"
+       #:source-dir "maven-plugin-api/src/main/java"
+       #:jdk ,icedtea-8
+       #:test-dir "maven-plugin-api/src/test"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'generate-models
+           (lambda* (#:key inputs #:allow-other-keys)
+             (define (modello-single-mode file version mode)
+               (invoke "java" "org.codehaus.modello.ModelloCli"
+                       file mode "maven-plugin-api/src/main/java" version
+                       "false" "true"))
+             (let ((file "maven-plugin-api/src/main/mdo/lifecycle.mdo"))
+               (modello-single-mode file "1.0.0" "java")
+               (modello-single-mode file "1.0.0" "xpp3-reader")
+               (modello-single-mode file "1.0.0" "xpp3-writer"))
+             #t)))))
+    (inputs
+     `(("maven-artifact" ,maven-artifact)
+       ("maven-model" ,maven-model)
+       ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus)
+       ("java-plexus-component-annotations" ,java-plexus-component-annotations)
+       ("guice" ,java-guice)
+       ("java-cglib" ,java-cglib)
+       ("java-asm" ,java-asm)
+       ("sisu-inject" ,java-eclipse-sisu-inject)
+       ("javax-inject" ,java-javax-inject)
+       ("utils" ,java-plexus-utils)))
+    (native-inputs
+     `(("modello" ,java-modello-core)
+       ;; for modello:
+       ("classworlds" ,java-plexus-classworlds)
+       ("guava" ,java-guava)
+       ("xbean" ,java-geronimo-xbean-reflect)
+       ("build-api" ,java-sisu-build-api)
+       ;; modello plugins:
+       ("java" ,java-modello-plugins-java)
+       ("xml" ,java-modello-plugins-xml)
+       ("xpp3" ,java-modello-plugins-xpp3)
+       ;; for tests
+       ("java-junit" ,java-junit)))
+    (description "Apache Maven is a software project management and comprehension
+tool.  This package contains strictly the API for plugins -- composed of goals
+implemented by Mojos -- development.
+
+A plugin is described in a @file{META-INF/maven/plugin.xml} plugin descriptor,
+generally generated from plugin sources using maven-plugin-plugin.")))
+
+(define maven-core-bootstrap
+  (package
+    (inherit maven-artifact)
+    (name "maven-core")
+    (arguments
+     `(#:jar-name "maven-core.jar"
+       #:source-dir "src/main/java"
+       #:jdk ,icedtea-8
+       ;; Tests need maven-compat, which requires maven-core
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'chdir
+           (lambda _
+             ;; Required for generating components.xml in maven-core
+             (chdir "maven-core")
+             #t))
+         (add-before 'build 'copy-resources
+           (lambda _
+             (mkdir-p "build/classes/")
+             (copy-recursively "src/main/resources" "build/classes")
+             #t))
+         (add-before 'build 'generate-sisu-named
+           (lambda _
+             (mkdir-p "build/classes/META-INF/sisu")
+             (chmod "../sisu.sh" #o755)
+             (invoke "../sisu.sh" "src/main/java"
+                     "build/classes/META-INF/sisu/javax.inject.Named")
+             #t))
+         (add-before 'build 'generate-models
+           (lambda* (#:key inputs #:allow-other-keys)
+             (define (modello-single-mode file version mode)
+               (invoke "java" "org.codehaus.modello.ModelloCli"
+                       file mode "src/main/java" version
+                       "false" "true"))
+             (let ((file "src/main/mdo/toolchains.mdo"))
+               (modello-single-mode file "1.1.0" "java")
+               (modello-single-mode file "1.1.0" "xpp3-reader")
+               (modello-single-mode file "1.1.0" "xpp3-writer"))
+             #t)))))
+    (inputs
+     `(("maven-artifact" ,maven-artifact)
+       ("maven-resolver-provider" ,maven-resolver-provider)
+       ("maven-builder-support" ,maven-builder-support)
+       ("maven-model" ,maven-model)
+       ("maven-model-builder" ,maven-model-builder)
+       ("maven-settings" ,maven-settings)
+       ("maven-settings-builder" ,maven-settings-builder)
+       ("maven-plugin-api" ,maven-plugin-api)
+       ("maven-repository-metadata" ,maven-repository-metadata)
+       ("maven-shared-utils" ,maven-shared-utils)
+       ("java-plexus-component-annotations" ,java-plexus-component-annotations)
+       ("java-plexus-utils" ,java-plexus-utils)
+       ("java-commons-lang3" ,java-commons-lang3)
+       ("java-guava" ,java-guava)
+       ("java-guice" ,java-guice)
+       ("maven-resolver-api" ,maven-resolver-api)
+       ("maven-resolver-spi" ,maven-resolver-spi)
+       ("maven-resolver-util" ,maven-resolver-util)
+       ("maven-resolver-impl" ,maven-resolver-impl)
+       ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject)
+       ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus)
+       ("java-javax-inject" ,java-javax-inject)
+       ("java-plexus-classworld" ,java-plexus-classworlds)))
+    (native-inputs
+     `(("java-modello-core" ,java-modello-core)
+       ("java-cglib" ,java-cglib)
+       ("java-asm" ,java-asm)
+       ("java-plexus-classworlds" ,java-plexus-classworlds)
+       ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect)
+       ("java-sisu-build-api" ,java-sisu-build-api)
+       ("java-modello-plugins-java" ,java-modello-plugins-java)
+       ("java-modello-plugins-xml" ,java-modello-plugins-xml)
+       ("java-modello-plugins-xpp3" ,java-modello-plugins-xpp3)
+       ;; tests
+       ("java-junit" ,java-junit)
+       ("java-mockito-1" ,java-mockito-1)
+       ("java-commons-jxpath" ,java-commons-jxpath)))
+    (description "Apache Maven is a software project management and comprehension
+tool.  This package contains the maven core classes managing the whole build
+process.")))
+
+(define-public maven-core
+  (package
+    (inherit maven-core-bootstrap)
+    (arguments
+      (substitute-keyword-arguments (package-arguments maven-core-bootstrap)
+        ((#:phases phases)
+         `(modify-phases ,phases
+            (add-before 'build 'modify-metainf
+              (lambda _
+                (substitute* "build.xml"
+                  (("message=\"\"") "message=\"Implementation-Version: 3.5.3\n\""))
+                #t))
+            (add-before 'build 'add-maven-files
+              (lambda _
+                (mkdir-p "build/classes/META-INF/maven/org.apache.maven/maven-core")
+                (copy-file "pom.xml"
+                           "build/classes/META-INF/maven/org.apache.maven/maven-core/pom.xml")
+                (with-output-to-file "build/classes/META-INF/maven/org.apache.maven/maven-core/pom.properties"
+                  (lambda _
+                    (format #t "version=~a~%
+groupId=org.apache.maven~%
+artifactId=maven-core" ,(package-version maven-core-bootstrap))))
+                #t))
+            (add-after 'build 'generate-metadata
+              (lambda _
+                (define (components file)
+                  (let ((sxml (with-input-from-file file
+                                (lambda _ (xml->sxml (current-input-port)
+                                                     #:trim-whitespace? #t)))))
+                    ;; Select the list of <component>s inside the <component-set>
+                    ;; and <components>.
+                    ((@ (ice-9 match) match) sxml
+                     (('*TOP*
+                       ('*PI* foo ...)
+                       ('component-set
+                        ('components x ...))) x))))
+                (use-modules (sxml simple))
+                (delete-file "build/classes/META-INF/plexus/components.xml")
+                (invoke "java" "-cp" (string-append (getenv "CLASSPATH") ":build/classes")
+                        "org.codehaus.plexus.metadata.PlexusMetadataGeneratorCli"
+                        "--source" "build/classes/META-INF/plexus"
+                        "--output" "build/classes/META-INF/plexus/components.t.xml"
+                        "--classes" "build/classes"
+                        "--descriptors" "build/classes")
+                ;; Now we merge all other components from hand-written xml
+                (let ((generated-xml (components "build/classes/META-INF/plexus/components.t.xml"))
+                      (components-xml (components "src/main/resources/META-INF/plexus/components.xml"))
+                      (default-bindings-xml (components "src/main/resources/META-INF/plexus/default-bindings.xml"))
+                      (artifact-handlers-xml (components "src/main/resources/META-INF/plexus/artifact-handlers.xml")))
+                  (with-output-to-file "build/classes/META-INF/plexus/components.xml"
+                    (lambda _
+                      (display "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
+                      (sxml->xml
+                        `(component-set
+                           (components
+                             ,@(append generated-xml components-xml
+                                       default-bindings-xml
+                                       artifact-handlers-xml)))))))
+                #t))
+            (add-after 'generate-metadata 'rebuild
+              (lambda _
+                (invoke "ant" "jar")
+                #t))))))
+    (native-inputs
+     `(("java-plexus-component-metadata" ,java-plexus-component-metadata)
+       ("java-commons-cli" ,java-commons-cli)
+       ("java-plexus-cli" ,java-plexus-cli)
+       ("java-jdom2" ,java-jdom2)
+       ("java-qdox" ,java-qdox)
+       ("maven-core-boot" ,maven-core-bootstrap)
+       ,@(package-native-inputs maven-core-bootstrap)))))
+
+(define-public maven-embedder
+  (package
+    (inherit maven-artifact)
+    (name "maven-embedder")
+    (arguments
+     `(#:jar-name "maven-embedder.jar"
+       #:source-dir "maven-embedder/src/main/java"
+       #:test-dir "maven-embedder/src/test"
+       #:test-exclude (list "**/MavenCliTest.java")
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'generate-sisu-named
+           (lambda _
+             (mkdir-p "build/classes/META-INF/sisu")
+             (chmod "sisu.sh" #o755)
+             (invoke "./sisu.sh" "maven-embedder/src/main/java"
+                     "build/classes/META-INF/sisu/javax.inject.Named")
+             #t))
+         (add-before 'build 'generate-models
+           (lambda* (#:key inputs #:allow-other-keys)
+             (define (modello-single-mode file version mode)
+               (invoke "java" "org.codehaus.modello.ModelloCli"
+                       file mode "maven-embedder/src/main/java" version
+                       "false" "true"))
+             (let ((file "maven-embedder/src/main/mdo/core-extensions.mdo"))
+               (modello-single-mode file "1.0.0" "java")
+               (modello-single-mode file "1.0.0" "xpp3-reader")
+               (modello-single-mode file "1.0.0" "xpp3-writer"))
+             #t))
+         (add-before 'check 'fix-test-paths
+           (lambda _
+             (substitute* "maven-embedder/src/test/java/org/apache/maven/cli/CLIManagerDocumentationTest.java"
+               (("target/test-classes") "build/test-classes"))
+             #t))
+         (add-before 'check 'fix-test-compilation
+           (lambda _
+             ;; Tests are in the java/ subdir. Other subdirectories contain
+             ;; additional test plugins, with duplicate classes, so we can't
+             ;; compile them. Also, they are meant to be built with maven, to
+             ;; test its build process.
+             (substitute* "build.xml"
+               (("srcdir=\"maven-embedder/src/test\"")
+                "srcdir=\"maven-embedder/src/test/java\""))
+             #t)))))
+    (inputs
+     `(("maven-core" ,maven-core)
+       ("maven-artifact" ,maven-artifact)
+       ("maven-plugin-api" ,maven-plugin-api)
+       ("maven-builder-support" ,maven-builder-support)
+       ("maven-model" ,maven-model)
+       ("maven-model-builder" ,maven-model-builder)
+       ("maven-settings" ,maven-settings)
+       ("maven-settings-builder" ,maven-settings-builder)
+       ("maven-shared-utils" ,maven-shared-utils)
+       ("java-plexus-classworlds" ,java-plexus-classworlds)
+       ("java-plexus-util" ,java-plexus-utils)
+       ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus)
+       ("java-plexus-cipher" ,java-plexus-cipher)
+       ("java-plexus-component-annotations" ,java-plexus-component-annotations)
+       ("java-plexus-sec-dispatcher" ,java-plexus-sec-dispatcher)
+       ("maven-resolevr-util" ,maven-resolver-util)
+       ("maven-resolevr-api" ,maven-resolver-api)
+       ("java-logback-core" ,java-logback-core)
+       ("java-logback-classic" ,java-logback-classic)
+       ("java-commons-cli" ,java-commons-cli)
+       ("java-commons-io" ,java-commons-io)
+       ("java-commons-lang3" ,java-commons-lang3)
+       ("java-guava" ,java-guava)
+       ("java-guice" ,java-guice)
+       ("java-javax-inject" ,java-javax-inject)
+       ("java-slf4j-api" ,java-slf4j-api)
+       ("java-slf4j-simple" ,java-slf4j-simple)))
+    (native-inputs
+     `(("java-modello-core" ,java-modello-core)
+       ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect)
+       ("java-sisu-build-api" ,java-sisu-build-api)
+       ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus)
+       ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject)
+       ("java-cglib" ,java-cglib)
+       ("java-asm" ,java-asm)
+       ("java-modello-plugins-java" ,java-modello-plugins-java)
+       ("java-modello-plugins-xml" ,java-modello-plugins-xml)
+       ("java-modello-plugins-xpp3" ,java-modello-plugins-xpp3)
+       ;; tests
+       ("java-junit" ,java-junit)
+       ("java-objenesis" ,java-objenesis)
+       ("java-mockito-1" ,java-mockito-1)
+       ("java-hamcrest-core" ,java-hamcrest-core)))
+    (description "Apache Maven is a software project management and comprehension
+tool.  This package contains a Maven embeddable component, with CLI and
+logging support.")))
+
+(define-public maven-compat
+  (package
+    (inherit maven-artifact)
+    (name "maven-compat")
+    (arguments
+     `(#:jar-name "maven-compat.jar"
+       #:source-dir "src/main/java"
+       #:jdk ,icedtea-8
+       #:test-dir "src/test"
+       #:phases
+       (modify-phases %standard-phases
+         ;; Tests assume we're in this directory
+         (add-before 'configure 'chdir
+           (lambda _
+             (chdir "maven-compat")
+             #t))
+         (add-before 'build 'generate-models
+           (lambda* (#:key inputs #:allow-other-keys)
+             (define (modello-single-mode file version mode)
+               (invoke "java" "org.codehaus.modello.ModelloCli"
+                       file mode "src/main/java" version
+                       "false" "true"))
+             (let ((file "src/main/mdo/profiles.mdo"))
+               (modello-single-mode file "1.0.0" "java")
+               (modello-single-mode file "1.0.0" "xpp3-reader")
+               (modello-single-mode file "1.0.0" "xpp3-writer"))
+             (let ((file "src/main/mdo/paramdoc.mdo"))
+               (modello-single-mode file "1.0.0" "java")
+               (modello-single-mode file "1.0.0" "xpp3-reader")
+               (modello-single-mode file "1.0.0" "xpp3-writer"))
+             #t))
+         (add-after 'build 'generate-metadata
+           (lambda _
+             (invoke "java" "-cp" (string-append (getenv "CLASSPATH") ":build/classes")
+                     "org.codehaus.plexus.metadata.PlexusMetadataGeneratorCli"
+                     "--source" "src/main/java"
+                     "--output" "build/classes/META-INF/plexus/components.xml"
+                     "--classes" "build/classes"
+                     "--descriptors" "build/classes/META-INF")
+             #t))
+         (add-before 'check 'build-tests
+          (lambda _
+            (invoke "ant" "compile-tests")
+            #t))
+         (add-after 'build-tests 'generate-test-metadata
+           (lambda _
+             (invoke "java" "-cp" (string-append (getenv "CLASSPATH")
+                                                 ":build/classes"
+                                                 ":build/test-classes")
+                     "org.codehaus.plexus.metadata.PlexusMetadataGeneratorCli"
+                     "--source" "src/test/java"
+                     "--output" "build/test-classes/META-INF/plexus/components.xml"
+                     "--classes" "build/test-classes"
+                     "--descriptors" "build/test-classes/META-INF")
+             #t))
+         (add-after 'generate-metadata 'rebuild
+           (lambda _
+             (invoke "ant" "jar")
+             #t)))))
+    (inputs
+     `(("maven-artifact" ,maven-artifact)
+       ("maven-repository-metadata" ,maven-repository-metadata)
+       ("maven-builder-support" ,maven-builder-support)
+       ("maven-model" ,maven-model)
+       ("maven-model-builder" ,maven-model-builder)
+       ("maven-settings" ,maven-settings)
+       ("maven-settings-builder" ,maven-settings-builder)
+       ("maven-core" ,maven-core)
+       ("maven-wagon-provider-api" ,maven-wagon-provider-api)
+       ("maven-wagon-file" ,maven-wagon-file)
+       ("maven-resolver-api" ,maven-resolver-api)
+       ("maven-resolver-util" ,maven-resolver-util)
+       ("maven-resolver-spi" ,maven-resolver-spi)
+       ("java-plexus-interpolation" ,java-plexus-interpolation)))
+    (native-inputs
+     `(("java-modello-core" ,java-modello-core)
+       ("java-plexus-utils" ,java-plexus-utils)
+       ("java-plexus-component-annotations" ,java-plexus-component-annotations)
+       ("java-plexus-classworlds" ,java-plexus-classworlds)
+       ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect)
+       ("java-sisu-build-api" ,java-sisu-build-api)
+       ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus)
+       ("java-exclispe-sisu-inject" ,java-eclipse-sisu-inject)
+       ("java-javax-inject" ,java-javax-inject)
+       ("java-guice" ,java-guice)
+       ("java-guava" ,java-guava)
+       ("java-cglib" ,java-cglib)
+       ("java-asm" ,java-asm)
+       ("java-modello-plugins-java" ,java-modello-plugins-java)
+       ("java-modello-plugins-xml" ,java-modello-plugins-xml)
+       ("java-modello-plugins-xpp3" ,java-modello-plugins-xpp3)
+       ;; metadata
+       ("java-plexus-component-metadata" ,java-plexus-component-metadata)
+       ("java-commons-cli" ,java-commons-cli)
+       ("java-plexus-cli" ,java-plexus-cli)
+       ("java-jdom2" ,java-jdom2)
+       ("maven-plugin-api" ,maven-plugin-api)
+       ("java-qdox" ,java-qdox)
+       ;; tests
+       ("java-plexus-cipher" ,java-plexus-cipher)
+       ("java-plexus-sec-dispatcher" ,java-plexus-sec-dispatcher)
+       ("java-jsr250", java-jsr250)
+       ("java-cdi-api" ,java-cdi-api)
+       ("java-junit" ,java-junit)
+       ("maven-resolver-impl" ,maven-resolver-impl)
+       ("maven-resolver-connector-basic" ,maven-resolver-connector-basic)
+       ("maven-resolver-transport-wagon" ,maven-resolver-transport-wagon)
+       ("java-commons-lang3" ,java-commons-lang3)
+       ("java-aop" ,java-aopalliance)
+       ("maven-resolver-provider" ,maven-resolver-provider)
+       ("java-slf4j-api" ,java-slf4j-api)
+       ("java-slf4j-simple" ,java-slf4j-simple)
+       ,@(package-inputs java-slf4j-api)))
+    (description "Apache Maven is a software project management and comprehension
+tool.  This package contains Maven2 classes maintained as compatibility
+layer for plugins that need to keep Maven2 compatibility.")))
+
+(define-public maven
+  (package
+    (inherit maven-artifact)
+    (name "maven")
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'build
+           (lambda _
+             (substitute* "apache-maven/src/bin/mvn"
+               (("cygwin=false;")
+                (string-append
+                  "CLASSPATH=" (getenv "CLASSPATH") "\n"
+                  "cygwin=false;"))
+               (("-classpath.*") "-classpath ${CLASSPATH} \\\n"))
+             #t))
+         (delete 'check)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))
+                   (conf (string-append (assoc-ref outputs "out") "/conf/")))
+               (mkdir-p (string-append (assoc-ref outputs "out") "/lib"))
+               (for-each (lambda (file)
+                           (install-file (string-append "apache-maven/src/bin/" file)
+                                         bin)
+                           (chmod (string-append bin file) #o755))
+                '("mvn" "mvnDebug" "mvnyjp"))
+               (install-file "apache-maven/src/bin/m2.conf" bin)
+               (copy-recursively "apache-maven/src/conf" conf))
+             #t)))))
+    (inputs
+     `(("java-plexus-classworlds" ,java-plexus-classworlds)
+       ("maven-artifact" ,maven-artifact)
+       ("maven-embedder" ,maven-embedder)
+       ("maven-core" ,maven-core)
+       ("maven-compat" ,maven-compat)
+       ("maven-builder-support" ,maven-builder-support)
+       ("maven-model" ,maven-model)
+       ("maven-model-builder" ,maven-model-builder)
+       ("maven-settings" ,maven-settings)
+       ("maven-settings-builder" ,maven-settings-builder)
+       ("maven-plugin-api" ,maven-plugin-api)
+       ("maven-repository-metadata", maven-repository-metadata)
+       ("maven-shared-utils" ,maven-shared-utils)
+       ("maven-resolver-api" ,maven-resolver-api)
+       ("maven-resolver-spi" ,maven-resolver-spi)
+       ("maven-resolver-util" ,maven-resolver-util)
+       ("maven-resolver-impl" ,maven-resolver-impl)
+       ("maven-resolver-connector-basic" ,maven-resolver-connector-basic)
+       ("maven-resolver-provider" ,maven-resolver-provider)
+       ("maven-resolver-transport-wagon" ,maven-resolver-transport-wagon)
+       ("maven-wagon-provider-api" ,maven-wagon-provider-api)
+       ("maven-wagon-file" ,maven-wagon-file)
+       ("maven-wagon-http" ,maven-wagon-http)
+       ("java-commons-logging-minimal" ,java-commons-logging-minimal)
+       ("java-httpcomponents-httpclient" ,java-httpcomponents-httpclient)
+       ("java-httpcomponents-httpcore" ,java-httpcomponents-httpcore)
+       ("maven-wagon-http-shared" ,maven-wagon-http-shared)
+       ("maven-wagon-tck-http" ,maven-wagon-tck-http)
+       ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus)
+       ("java-guice" ,java-guice)
+       ("java-aopalliance" ,java-aopalliance)
+       ("java-cglib" ,java-cglib)
+       ("java-asm" ,java-asm)
+       ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject)
+       ("java-javax-inject" ,java-javax-inject)
+       ("java-plexus-component-annotations" ,java-plexus-component-annotations)
+       ("java-plexus-utils" ,java-plexus-utils)
+       ("java-plexus-interpolation" ,java-plexus-interpolation)
+       ("java-plexus-sec-dispatcher" ,java-plexus-sec-dispatcher)
+       ("java-plexus-cipher" ,java-plexus-cipher)
+       ("java-guava" ,java-guava)
+       ("java-jansi" ,java-jansi)
+       ("java-jsr250" ,java-jsr250)
+       ("java-cdi-api" ,java-cdi-api)
+       ("java-commons-cli" ,java-commons-cli)
+       ("java-commons-io" ,java-commons-io)
+       ("java-commons-lang3" ,java-commons-lang3)
+       ("java-slf4j-api" ,java-slf4j-api)
+       ;; TODO: replace with maven-slf4j-provider
+       ("java-slf4j-simple" ,java-slf4j-simple)))
+    (description "Apache Maven is a software project management and comprehension
+tool.  Based on the concept of a project object model: builds, dependency
+management, documentation creation, site publication, and distribution
+publication are all controlled from the @file{pom.xml} declarative file.  Maven
+can be extended by plugins to utilise a number of other development tools for
+reporting or the build process.")))

gnu/packages/mes.scm

@@ -73,7 +73,7 @@ extensive examples, including parsers for the Javascript and C99 languages.")
   (let ((triplet "i686-unknown-linux-gnu"))
     (package
       (name "mes")
-      (version "0.14")
+      (version "0.15")
       (source (origin
                 (method url-fetch)
                 (uri (string-append "https://gitlab.com/janneke/mes"
@@ -81,7 +81,7 @@ extensive examples, including parsers for the Javascript and C99 languages.")
                                     "/mes-" version ".tar.gz"))
                 (sha256
                  (base32
-                  "1i23jk61iibjza2s3lka56ry4ma424g2fyk8pjd5bd1dyjd0yrzf"))))
+                  "0kj2ywgii1795gxj6k29zxa0848h2j0ihbwlgn55wdalswl165dq"))))
       (build-system gnu-build-system)
       (supported-systems '("i686-linux" "x86_64-linux"))
       (propagated-inputs
@@ -98,9 +98,7 @@ extensive examples, including parsers for the Javascript and C99 languages.")
                '())
          ("perl" ,perl)))               ;build-aux/gitlog-to-changelog
       (arguments
-       `(#:make-flags (list
+       `(#:phases
-                       (string-append "PREFIX=" (assoc-ref %outputs "out")))
-         #:phases
          (modify-phases %standard-phases
            (add-before 'install 'generate-changelog
              (lambda _

gnu/packages/networking.scm

@@ -1350,16 +1350,17 @@ networks.")
 (define-public speedtest-cli
   (package
     (name "speedtest-cli")
-    (version "2.0.0")
+    (version "2.0.2")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append
+       (uri (git-reference
-             "https://github.com/sivel/speedtest-cli/archive/v" version ".tar.gz"))
+             (url "https://github.com/sivel/speedtest-cli")
-       (file-name (string-append name "-" version ".tar.gz"))
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "16kcpba7nmszz2h0fq7qvv6src20syck2wlknaacg69kk88aybbk"))))
+         "0vv2z37g2kgm2dzkfa4bhri92hs0d1acxi8z66gznsl5148q7sdi"))))
     (build-system python-build-system)
     (home-page "https://github.com/sivel/speedtest-cli")
     (synopsis "Internet bandwidth tester")
@@ -1901,3 +1902,36 @@ eight bytes) tools
 low-level I/O programming that provides developers with a consistent
 asynchronous model using a modern C++ approach.")
     (license license:boost1.0)))
+
+(define-public shadowsocks
+  ;; There are some security fixes after the last release.
+  (let* ((commit "e332ec93e9c90f1cbee676b022bf2c5d5b7b1239")
+         (revision "0")
+         (version (git-version "2.8.2" revision commit)))
+    (package
+      (name "shadowsocks")
+      (version version)
+      (home-page "https://github.com/shadowsocks/shadowsocks")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url home-page)
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1idd9b4f2pnhcpk1bh030hqg5zq25gkwxd53xi3c0cj242w7sp2j"))
+                (file-name (git-file-name name version))))
+      (build-system python-build-system)
+      (synopsis "Fast tunnel proxy that helps you bypass firewalls")
+      (description
+       "This package is a fast tunnel proxy that helps you bypass firewalls.
+
+Features:
+@itemize
+@item TCP & UDP support
+@item User management API
+@item TCP Fast Open
+@item Workers and graceful restart
+@item Destination IP blacklist
+@end itemize")
+      (license license:asl2.0))))

gnu/packages/nickle.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Nils Gillmann <ng0@n0.is>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,14 +28,14 @@
 (define-public nickle
   (package
     (name "nickle")
-    (version "2.77")
+    (version "2.81")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://nickle.org/release/nickle-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0rhij7cn1zkn8wzxyjkamz9fs262zyg80p6v6i864hdalg4plpm3"))))
+                "1daqsflnqqgfkq6w6dknbm42avz70f5qxn7qidvgp472i4a37acr"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("readline" ,readline)))

gnu/packages/package-management.scm

@@ -7,6 +7,7 @@
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
+;;; Copyright © 2018 Sou Bunnbu <iyzsong@member.fsf.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -26,9 +27,12 @@
 (define-module (gnu packages package-management)
   #:use-module (gnu packages)
   #:use-module (gnu packages acl)
+  #:use-module (gnu packages attr)
+  #:use-module (gnu packages avahi)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages backup)
   #:use-module (gnu packages bdw-gc)
+  #:use-module (gnu packages bison)
   #:use-module (gnu packages bootstrap)          ;for 'bootstrap-guile-origin'
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
@@ -36,6 +40,7 @@
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages databases)
+  #:use-module (gnu packages docbook)
   #:use-module (gnu packages file)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages glib)
@@ -208,12 +213,13 @@
                         (let* ((out    (assoc-ref outputs "out"))
                                (guile  (assoc-ref inputs "guile"))
                                (json   (assoc-ref inputs "guile-json"))
+                               (sqlite (assoc-ref inputs "guile-sqlite3"))
                                (git    (assoc-ref inputs "guile-git"))
                                (bs     (assoc-ref inputs
                                                   "guile-bytestructures"))
                                (ssh    (assoc-ref inputs "guile-ssh"))
                                (gnutls (assoc-ref inputs "gnutls"))
-                               (deps   (list json gnutls git bs ssh))
+                               (deps   (list json sqlite gnutls git bs ssh))
                                (effective
                                 (read-line
                                  (open-pipe* OPEN_READ
@@ -270,6 +276,7 @@
       (propagated-inputs
        `(("gnutls" ,gnutls)
          ("guile-json" ,guile-json)
+         ("guile-sqlite3" ,guile-sqlite3)
          ("guile-ssh" ,guile-ssh)
          ("guile-git" ,guile-git)))
 
@@ -287,23 +294,24 @@ the Nix package manager.")
 ;; Alias for backward compatibility.
 (define-public guix-devel guix)
 
-(define-public guix-register
+(define-public guix-daemon
   ;; This package is for internal consumption: it allows us to quickly build
-  ;; the 'guix-register' program, which is referred to by (guix config).
+  ;; the 'guix-daemon' program and use that in (guix self), used by 'guix
-  ;; TODO: Remove this hack when 'guix-register' has been superseded by Scheme
+  ;; pull'.
-  ;; code.
   (package
     (inherit guix)
     (properties `((hidden? . #t)))
-    (name "guix-register")
+    (name "guix-daemon")
 
     ;; Use a minimum set of dependencies.
     (native-inputs
      (fold alist-delete (package-native-inputs guix)
            '("po4a" "graphviz" "help2man")))
-    (propagated-inputs
+    (inputs
      `(("gnutls" ,gnutls)
-       ("guile-git" ,guile-git)))
+       ("guile-git" ,guile-git)
+       ,@(package-inputs guix)))
+    (propagated-inputs '())
 
     (arguments
      (substitute-keyword-arguments (package-arguments guix)
@@ -316,11 +324,21 @@ the Nix package manager.")
                (invoke "make" "nix/libstore/schema.sql.hh")
                (invoke "make" "-j" (number->string
                                     (parallel-job-count))
-                       "guix-register")))
+                       "guix-daemon")))
            (delete 'copy-bootstrap-guile)
            (replace 'install
-             (lambda _
+             (lambda* (#:key outputs #:allow-other-keys)
-               (invoke "make" "install-sbinPROGRAMS")))
+               (invoke "make" "install-binPROGRAMS"
+                       "install-nodist_pkglibexecSCRIPTS")
+
+               ;; We need to tell 'guix-daemon' which 'guix' command to use.
+               ;; Here we use a questionable hack where we hard-code
+               ;; "~root/.config", which could be wrong (XXX).
+               (let ((out (assoc-ref outputs "out")))
+                 (substitute* (find-files (string-append out "/libexec"))
+                   (("exec \".*/bin/guix\"")
+                    "exec ~root/.config/current/bin/guix"))
+                 #t)))
            (delete 'wrap-program)))))))
 
 (define-public guile2.0-guix
@@ -528,13 +546,13 @@ transactions from C or Python.")
 (define-public diffoscope
   (package
     (name "diffoscope")
-    (version "95")
+    (version "96")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri name version))
               (sha256
                (base32
-                "0aksxxivxli6l3fylxgl771hw0h7l8x35l76cmj0d12zgx54w0a1"))))
+                "1x66f2x8miy3giff14higpcs70c0zb5d3gj6yn8ac6p183sngl72"))))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
@@ -883,3 +901,57 @@ Microsoft cabinet (.@dfn{CAB}) files.")
 and sign Windows@tie{}Installer (.@dfn{MSI}) files.  It aims to be a solution
 for packaging and deployment of cross-compiled Windows applications.")
     (license license:lgpl2.1+)))
+
+(define-public libostree
+  (package
+    (name "libostree")
+    (version "2018.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/ostreedev/ostree/releases/download/v"
+                    version "/libostree-" version ".tar.xz"))
+              (sha256
+               (base32
+                "0q82d6rvp119nx7ck7j63a591kz8vg7v465kf9ygh8kzg875l3xd"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'pre-check
+           (lambda _
+             ;; Don't try to use the non-existing '/var/tmp' as test
+             ;; directory.
+             (setenv "TEST_TMPDIR" (getenv "TMPDIR"))
+             #t)))
+       ;; XXX: fails with:
+       ;;     tap-driver.sh: internal error getting exit status
+       ;;     tap-driver.sh: fatal: I/O or internal error
+       #:tests? #f))
+    (native-inputs
+     `(("attr" ,attr)                   ; for tests
+       ("bison" ,bison)
+       ("glib:bin" ,glib "bin")          ; for 'glib-mkenums'
+       ("gobject-introspection" ,gobject-introspection)
+       ("pkg-config" ,pkg-config)
+       ("xsltproc" ,libxslt)))
+    (inputs
+     `(("avahi" ,avahi)
+       ("docbook-xml" ,docbook-xml-4.2)
+       ("docbook-xsl" ,docbook-xsl)
+       ("e2fsprogs" ,e2fsprogs)
+       ("fuse" ,fuse)
+       ("glib" ,glib)
+       ("gpgme" ,gpgme)
+       ("libarchive" ,libarchive)
+       ("libsoup" ,libsoup)
+       ("nettle" ,nettle)               ; required by 'libarchive.la'
+       ("util-linux" ,util-linux)))
+    (home-page "https://ostree.readthedocs.io/en/latest/")
+    (synopsis "Operating system and container binary deployment and upgrades")
+    (description
+     "@code{libostree} is both a shared library and suite of command line
+tools that combines a \"git-like\" model for committing and downloading
+bootable filesystem trees, along with a layer for deploying them and managing
+the bootloader configuration.")
+    (license license:lgpl2.0+)))

gnu/packages/password-utils.scm

@@ -358,7 +358,7 @@ any X11 window.")
 (define-public password-store
   (package
     (name "password-store")
-    (version "1.7.1")
+    (version "1.7.2")
     (source (origin
               (method url-fetch)
               (uri
@@ -366,8 +366,7 @@ any X11 window.")
                               name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0scqkpll2q8jhzcgcsh9kqz0gwdpvynivqjmmbzax2irjfaiklpn"))
+                "1sl0d7nc85c6c2bmmmyb8rpmn47vhkj831l153mjlkawjvhwas27"))))
-              (patches (search-patches "password-store-gnupg-compat.patch"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases

gnu/packages/patches/bind-CVE-2018-5738.patch

@@ -0,0 +1,100 @@
+Fix CVE-2018-5738:
+
+https://kb.isc.org/article/AA-01616/0/CVE-2018-5738
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-5738
+
+diff --git a/bin/named/server.c b/bin/named/server.c
+index f63554e..847c4ff 100644
+--- a/bin/named/server.c
++++ b/bin/named/server.c
+@@ -3725,10 +3725,6 @@ configure_view(dns_view_t *view, dns_viewlist_t *viewlist,
+ 	CHECKM(named_config_getport(config, &port), "port");
+ 	dns_view_setdstport(view, port);
+ 
+-	CHECK(configure_view_acl(vconfig, config, named_g_config,
+-				 "allow-query", NULL, actx,
+-				 named_g_mctx, &view->queryacl));
+-
+ 	/*
+ 	 * Make the list of response policy zone names for a view that
+ 	 * is used for real lookups and so cares about hints.
+@@ -4692,21 +4688,35 @@ configure_view(dns_view_t *view, dns_viewlist_t *viewlist,
+ 				 "allow-query-cache-on", NULL, actx,
+ 				 named_g_mctx, &view->cacheonacl));
+ 	/*
+-	 * Set "allow-query-cache", "allow-recursion", and
+-	 * "allow-recursion-on" acls if configured in named.conf.
+-	 * (Ignore the global defaults for now, because these ACLs
+-	 * can inherit from each other when only some of them set at
+-	 * the options/view level.)
++	 * Set the "allow-query", "allow-query-cache", "allow-recursion",
++	 * and "allow-recursion-on" ACLs if configured in named.conf, but
++	 * NOT from the global defaults. This is done by leaving the third
++	 * argument to configure_view_acl() NULL.
++	 *
++	 * We ignore the global defaults here because these ACLs
++	 * can inherit from each other.  If any are still unset after
++	 * applying the inheritance rules, we'll look up the defaults at
++	 * that time.
+ 	 */
+-	CHECK(configure_view_acl(vconfig, config, NULL, "allow-query-cache",
+-				 NULL, actx, named_g_mctx, &view->cacheacl));
++
++	/* named.conf only */
++	CHECK(configure_view_acl(vconfig, config, NULL,
++				 "allow-query", NULL, actx,
++				 named_g_mctx, &view->queryacl));
++
++	/* named.conf only */
++	CHECK(configure_view_acl(vconfig, config, NULL,
++				 "allow-query-cache", NULL, actx,
++				 named_g_mctx, &view->cacheacl));
+ 
+ 	if (strcmp(view->name, "_bind") != 0 &&
+ 	    view->rdclass != dns_rdataclass_chaos)
+ 	{
++		/* named.conf only */
+ 		CHECK(configure_view_acl(vconfig, config, NULL,
+ 					 "allow-recursion", NULL, actx,
+ 					 named_g_mctx, &view->recursionacl));
++		/* named.conf only */
+ 		CHECK(configure_view_acl(vconfig, config, NULL,
+ 					 "allow-recursion-on", NULL, actx,
+ 					 named_g_mctx, &view->recursiononacl));
+@@ -4744,18 +4754,21 @@ configure_view(dns_view_t *view, dns_viewlist_t *viewlist,
+ 		 * the global config.
+ 		 */
+ 		if (view->recursionacl == NULL) {
++			/* global default only */
+ 			CHECK(configure_view_acl(NULL, NULL, named_g_config,
+ 						 "allow-recursion", NULL,
+ 						 actx, named_g_mctx,
+ 						 &view->recursionacl));
+ 		}
+ 		if (view->recursiononacl == NULL) {
++			/* global default only */
+ 			CHECK(configure_view_acl(NULL, NULL, named_g_config,
+ 						 "allow-recursion-on", NULL,
+ 						 actx, named_g_mctx,
+ 						 &view->recursiononacl));
+ 		}
+ 		if (view->cacheacl == NULL) {
++			/* global default only */
+ 			CHECK(configure_view_acl(NULL, NULL, named_g_config,
+ 						 "allow-query-cache", NULL,
+ 						 actx, named_g_mctx,
+@@ -4769,6 +4782,14 @@ configure_view(dns_view_t *view, dns_viewlist_t *viewlist,
+ 		CHECK(dns_acl_none(mctx, &view->cacheacl));
+ 	}
+ 
++	if (view->queryacl == NULL) {
++		/* global default only */
++		CHECK(configure_view_acl(NULL, NULL, named_g_config,
++					 "allow-query", NULL,
++					 actx, named_g_mctx,
++					 &view->queryacl));
++	}
++
+ 	/*
+ 	 * Ignore case when compressing responses to the specified
+ 	 * clients. This causes case not always to be preserved,

gnu/packages/patches/binutils-aarch64-symbol-relocation.patch

@@ -0,0 +1,36 @@
+Fix a regression in Binutils 2.30 where some symbols are incorrectly assumed
+to be addresses:
+
+https://sourceware.org/bugzilla/show_bug.cgi?id=22764
+
+Patch taken from upstream (with ChangeLog entries and tests omitted):
+
+https://sourceware.org/git/gitweb.cgi?p=binutils-gdb.git;a=commitdiff;h=279b2f94168ee91e02ccd070d27c983fc001fe12
+
+diff --git a/bfd/elfnn-aarch64.c b/bfd/elfnn-aarch64.c
+index af448f9..2737773 100644
+--- a/bfd/elfnn-aarch64.c
++++ b/bfd/elfnn-aarch64.c
+@@ -7189,10 +7189,19 @@ elfNN_aarch64_check_relocs (bfd *abfd, struct bfd_link_info *info,
+ #if ARCH_SIZE == 64
+ 	case BFD_RELOC_AARCH64_32:
+ #endif
+-	  if (bfd_link_pic (info)
+-	      && (sec->flags & SEC_ALLOC) != 0
+-	      && (sec->flags & SEC_READONLY) != 0)
++	  if (bfd_link_pic (info) && (sec->flags & SEC_ALLOC) != 0)
+ 	    {
++	      if (h != NULL
++		  /* This is an absolute symbol.  It represents a value instead
++		     of an address.  */
++		  && ((h->root.type == bfd_link_hash_defined
++		       && bfd_is_abs_section (h->root.u.def.section))
++		      /* This is an undefined symbol.  */
++		      || h->root.type == bfd_link_hash_undefined))
++		break;
++
++	      /* For local symbols, defined global symbols in a non-ABS section,
++		 it is assumed that the value is an address.  */
+ 	      int howto_index = bfd_r_type - BFD_RELOC_AARCH64_RELOC_START;
+ 	      _bfd_error_handler
+ 		/* xgettext:c-format */

gnu/packages/patches/elixir-disable-failing-tests.patch

@@ -1,284 +0,0 @@
-Most of these tests fail for unknown reasons when run in the chroot
-environment of a Guix build process.
-
-Common failures are:
-
- * Mix.Shell.cmd() fails with error 130
- * The git_repo fixture cannot be found
- * Communication with spawned processes fails with EPIPE
- * Failure to copy files
-
-
-diff --git a/lib/elixir/test/elixir/kernel/cli_test.exs b/lib/elixir/test/elixir/kernel/cli_test.exs
-index 3ffd56c..1232d19 100644
---- a/lib/elixir/test/elixir/kernel/cli_test.exs
-+++ b/lib/elixir/test/elixir/kernel/cli_test.exs
-@@ -39,6 +39,7 @@ end
- defmodule Kernel.CLI.OptionParsingTest do
-   use ExUnit.Case, async: true
-
-+  @tag :skip
-   test "properly parses paths" do
-     root = fixture_path("../../..") |> to_charlist
-     list = elixir('-pa "#{root}/*" -pz "#{root}/lib/*" -e "IO.inspect(:code.get_path, limit: :infinity)"')
-@@ -57,6 +58,7 @@ end
- defmodule Kernel.CLI.AtExitTest do
-   use ExUnit.Case, async: true
-
-+  @tag :skip
-   test "invokes at_exit callbacks" do
-     assert elixir(fixture_path("at_exit.exs") |> to_charlist) ==
-            'goodbye cruel world with status 1\n'
-@@ -66,6 +68,7 @@ end
- defmodule Kernel.CLI.ErrorTest do
-   use ExUnit.Case, async: true
-
-+  @tag :skip
-   test "properly format errors" do
-     assert :string.str('** (throw) 1', elixir('-e "throw 1"')) == 0
-     assert :string.str('** (ErlangError) erlang error: 1', elixir('-e "error 1"')) == 0
-@@ -86,6 +89,7 @@ defmodule Kernel.CLI.CompileTest do
-     {:ok, [tmp_dir_path: tmp_dir_path, beam_file_path: beam_file_path, fixture: fixture]}
-   end
-
-+  @tag :skip
-   test "compiles code", context do
-     assert elixirc('#{context[:fixture]} -o #{context[:tmp_dir_path]}') == ''
-     assert File.regular?(context[:beam_file_path])
-@@ -96,6 +100,7 @@ defmodule Kernel.CLI.CompileTest do
-     Code.delete_path context[:tmp_dir_path]
-   end
-
-+  @tag :skip
-   test "fails on missing patterns", context do
-     output = elixirc('#{context[:fixture]} non_existing.ex -o #{context[:tmp_dir_path]}')
-     assert :string.str(output, 'non_existing.ex') > 0, "expected non_existing.ex to be mentioned"
-@@ -103,6 +108,7 @@ defmodule Kernel.CLI.CompileTest do
-     refute File.exists?(context[:beam_file_path]), "expected the sample to not be compiled"
-   end
-
-+  @tag :skip
-   test "fails on missing write access to .beam file", context do
-     compilation_args = '#{context[:fixture]} -o #{context[:tmp_dir_path]}'
-
-diff --git a/lib/elixir/test/elixir/kernel/dialyzer_test.exs b/lib/elixir/test/elixir/kernel/dialyzer_test.exs
-index 801d852..40fc5bc 100644
---- a/lib/elixir/test/elixir/kernel/dialyzer_test.exs
-+++ b/lib/elixir/test/elixir/kernel/dialyzer_test.exs
-@@ -60,16 +60,19 @@ defmodule Kernel.DialyzerTest do
-     assert_dialyze_no_warnings! context
-   end
-
-+  @tag :skip
-   test "no warnings on rewrites", context do
-     copy_beam! context, Dialyzer.Rewrite
-     assert_dialyze_no_warnings! context
-   end
-
-+  @tag :skip
-   test "no warnings on raise", context do
-     copy_beam! context, Dialyzer.Raise
-     assert_dialyze_no_warnings! context
-   end
-
-+  @tag :skip
-   test "no warnings on macrocallback", context do
-     copy_beam! context, Dialyzer.Macrocallback
-     copy_beam! context, Dialyzer.Macrocallback.Impl
-diff --git a/lib/elixir/test/elixir/system_test.exs b/lib/elixir/test/elixir/system_test.exs
-index aafa559..0f9c178 100644
---- a/lib/elixir/test/elixir/system_test.exs
-+++ b/lib/elixir/test/elixir/system_test.exs
-@@ -53,7 +53,8 @@ defmodule SystemTest do
-     assert System.endianness in [:little, :big]
-     assert System.endianness == System.compiled_endianness
-   end
--
-+
-+  @tag :skip
-   test "argv/0" do
-     list = elixir('-e "IO.inspect System.argv" -- -o opt arg1 arg2 --long-opt 10')
-     {args, _} = Code.eval_string list, []
-diff --git a/lib/mix/test/mix/dep_test.exs b/lib/mix/test/mix/dep_test.exs
-index fff3351..d6ed1b3 100644
---- a/lib/mix/test/mix/dep_test.exs
-+++ b/lib/mix/test/mix/dep_test.exs
-@@ -244,6 +244,7 @@ defmodule Mix.DepTest do
-     end
-   end
-
-+  @tag :skip
-   test "remote converger" do
-     deps = [{:deps_repo, "0.1.0", path: "custom/deps_repo"},
-             {:git_repo, "0.2.0", git: MixTest.Case.fixture_path("git_repo")}]
-@@ -301,6 +302,7 @@ defmodule Mix.DepTest do
-     end
-   end
-
-+  @tag :skip
-   test "remote converger is not invoked if deps diverge" do
-     deps = [{:deps_repo, "0.1.0", path: "custom/deps_repo"},
-             {:git_repo, "0.2.0", git: MixTest.Case.fixture_path("git_repo"), only: :test}]
-
-diff --git a/lib/mix/test/mix/shell/io_test.exs b/lib/mix/test/mix/shell/io_test.exs
-index 9bfb6b4..d982ef3 100644
---- a/lib/mix/test/mix/shell/io_test.exs
-+++ b/lib/mix/test/mix/shell/io_test.exs
-@@ -29,6 +29,7 @@ defmodule Mix.Shell.IOTest do
-     assert capture_io("", fn -> refute yes?("Ok?") end)
-   end
-
-+  @tag :skip
-   test "runs a given command" do
-     assert capture_io("", fn -> assert cmd("echo hello") == 0 end) == "hello\n"
-
-diff --git a/lib/mix/test/mix/shell/quiet_test.exs b/lib/mix/test/mix/shell/quiet_test.exs
-index 626429b..99fab35 100644
---- a/lib/mix/test/mix/shell/quiet_test.exs
-+++ b/lib/mix/test/mix/shell/quiet_test.exs
-@@ -29,6 +29,7 @@ defmodule Mix.Shell.QuietTest do
-     assert capture_io("", fn -> refute yes?("Ok?") end)
-   end
-
-+  @tag :skip
-   test "runs a given command" do
-     assert capture_io("", fn -> assert cmd("echo hello") == 0 end) == ""
-
-diff --git a/lib/mix/test/mix/tasks/cmd_test.exs b/lib/mix/test/mix/tasks/cmd_test.exs
-index db4bf06..4d441f7 100644
---- a/lib/mix/test/mix/tasks/cmd_test.exs
-+++ b/lib/mix/test/mix/tasks/cmd_test.exs
-@@ -3,6 +3,7 @@ Code.require_file "../../test_helper.exs", __DIR__
- defmodule Mix.Tasks.CmdTest do
-   use MixTest.Case
-
-+  @tag :skip
-   test "runs the command for each app" do
-     in_fixture "umbrella_dep/deps/umbrella", fn ->
-       Mix.Project.in_project(:umbrella, ".", fn _ ->
-diff --git a/lib/mix/test/mix/tasks/deps.tree_test.exs b/lib/mix/test/mix/tasks/deps.tree_test.exs
-index 4f09ff3..c371997 100644
---- a/lib/mix/test/mix/tasks/deps.tree_test.exs
-+++ b/lib/mix/test/mix/tasks/deps.tree_test.exs
-@@ -29,6 +29,7 @@ defmodule Mix.Tasks.Deps.TreeTest do
-     end
-   end
-
-+  @tag :skip
-   test "shows the dependency tree", context do
-     Mix.Project.push ConvergedDepsApp
-
-@@ -109,6 +110,7 @@ defmodule Mix.Tasks.Deps.TreeTest do
-     end
-   end
-
-+  @tag :skip
-   test "shows the dependency tree in DOT graph format", context do
-     Mix.Project.push ConvergedDepsApp
-
-diff --git a/lib/mix/test/mix/tasks/deps_test.exs b/lib/mix/test/mix/tasks/deps_test.exs
-index b061777..cc45cf8 100644
---- a/lib/mix/test/mix/tasks/deps_test.exs
-+++ b/lib/mix/test/mix/tasks/deps_test.exs
-@@ -96,6 +96,7 @@
-     end
-   end
-
-+  @tag :skip
-   test "prints list of dependencies and their lock status" do
-     Mix.Project.push DepsApp
-
-@@ -409,6 +409,7 @@ defmodule Mix.Tasks.DepsTest do
-     end
-   end
-
-+  @tag :skip
-   test "fails on diverged dependencies by requirement" do
-     Mix.Project.push ConvergedDepsApp
-
-@@ -440,6 +441,7 @@ defmodule Mix.Tasks.DepsTest do
-     end
-   end
-
-+  @tag :skip
-   test "fails on diverged dependencies even when optional" do
-     Mix.Project.push ConvergedDepsApp
-
-@@ -469,6 +471,7 @@ defmodule Mix.Tasks.DepsTest do
-     end
-   end
-
-+  @tag :skip
-   test "works with converged dependencies" do
-     Mix.Project.push ConvergedDepsApp
-
-@@ -491,6 +494,7 @@ defmodule Mix.Tasks.DepsTest do
-     purge [GitRepo, GitRepo.Mixfile]
-   end
-
-+  @tag :skip
-   test "works with overridden dependencies" do
-     Mix.Project.push OverriddenDepsApp
-
-diff --git a/lib/mix/test/mix/umbrella_test.exs b/lib/mix/test/mix/umbrella_test.exs
-index 69f9428..406668a 100644
---- a/lib/mix/test/mix/umbrella_test.exs
-+++ b/lib/mix/test/mix/umbrella_test.exs
-@@ -98,6 +98,7 @@ defmodule Mix.UmbrellaTest do
-     end
-   end
-
-+  @tag :skip
-   test "loads umbrella child dependencies in all environments" do
-     in_fixture "umbrella_dep/deps/umbrella", fn ->
-       Mix.Project.in_project :umbrella, ".", fn _ ->
-
-diff --git a/lib/elixir/test/elixir/kernel/dialyzer_test.exs b/lib/elixir/test/elixir/kernel/dialyzer_test.exs
-index 792222c..e90beb9 100644
---- a/lib/elixir/test/elixir/kernel/dialyzer_test.exs
-+++ b/lib/elixir/test/elixir/kernel/dialyzer_test.exs
-@@ -54,6 +54,7 @@ defmodule Kernel.DialyzerTest do
-     {:ok, [outdir: dir, dialyzer: dialyzer]}
-   end
-
-+  @tag :skip
-   test "no warnings on valid remote calls", context do
-     copy_beam! context, Dialyzer.RemoteCall
-     assert_dialyze_no_warnings! context
-@@ -78,11 +79,13 @@ defmodule Kernel.DialyzerTest do
-     assert_dialyze_no_warnings! context
-   end
-
-+  @tag :skip
-   test "no warnings on struct update", context do
-     copy_beam! context, Dialyzer.StructUpdate
-     assert_dialyze_no_warnings! context
-   end
-
-+  @tag :skip
-   test "no warnings on protocol calls with opaque types", context do
-     copy_beam! context, Dialyzer.ProtocolOpaque
-     copy_beam! context, Dialyzer.ProtocolOpaque.Entity
-@@ -90,6 +93,7 @@ defmodule Kernel.DialyzerTest do
-     assert_dialyze_no_warnings! context
-   end
-
-+  @tag :skip
-   test "no warnings on and/2 and or/2", context do
-     copy_beam! context, Dialyzer.BooleanCheck
-     assert_dialyze_no_warnings! context
-
-diff --git a/Makefile b/Makefile
-index 2fc4f9a..aef8366 100644
---- a/Makefile
-+++ b/Makefile
-@@ -201,7 +201,7 @@ $(TEST_EBIN)/%.beam: $(TEST_ERL)/%.erl
-        $(Q) mkdir -p $(TEST_EBIN)
-        $(Q) $(ERLC) -o $(TEST_EBIN) $<
-
--test_elixir: test_stdlib test_ex_unit test_logger test_mix test_eex test_iex
-+test_elixir: test_stdlib test_ex_unit test_logger test_eex test_iex
-
- test_stdlib: compile
-        @ echo "==> elixir (exunit)"
-

gnu/packages/patches/flann-cmake-3.11.patch

@@ -0,0 +1,84 @@
+Fixes this issue:
+ <https://github.com/mariusmuja/flann/issues/369>.
+Patch from Buildroot:
+ <https://github.com/buildroot/buildroot/commit/45a39b3e2ba42b72d19bfcef30db1b8da9ead51a>.
+
+From fa5ec96a94646492a3f908e12905b3e48a8e800b Mon Sep 17 00:00:00 2001
+From: Romain Naour <romain.naour@gmail.com>
+Date: Wed, 18 Apr 2018 20:24:13 +0200
+Subject: [PATCH] src/cpp: fix cmake >= 3.11 build
+
+CMake < 3.11 doesn't support add_library() without any source file
+(i.e add_library(foo SHARED)). But flann CMake use a trick that use
+an empty string "" as source list (i.e add_library(foo SHARED "")).
+This look like a bug in CMake < 3.11.
+
+With CMake >= 3.11, the new behaviour of add_library() break the
+existing flann CMake code.
+
+From CMake Changelog [1]:
+"add_library() and add_executable() commands can now be called without
+ any sources and will not complain as long as sources are added later
+ via the target_sources() command."
+
+Note: flann CMake code doesn't use target_sources() since no source file
+are provided intentionally since the flann shared library is created by
+linking with the flann_cpp_s static library with this line:
+
+target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive)
+
+If you try to use "add_library(flann_cpp SHARED ${CPP_SOURCES})" (as it should
+be normally done), the link fail due to already defined symbol.
+
+They are building the shared version using the static library "to speedup the
+build time" [3]
+
+This issue is already reported upstream [2] with a proposed solution.
+
+Upstream status: Pending
+
+Fixes:
+http://autobuild.buildroot.net/results/b2f/b2febfaf8c44ce477b3e4a5b9b976fd25e8d7454
+
+[1] https://cmake.org/cmake/help/v3.11/release/3.11.html
+[2] https://github.com/mariusmuja/flann/issues/369
+[3] https://github.com/mariusmuja/flann/commit/0fd62b43be2fbb0b8d791ee36290791224dc030c
+
+Signed-off-by: Romain Naour <romain.naour@gmail.com>
+---
+ src/cpp/CMakeLists.txt | 4 ++--
+ src/cpp/empty.cpp      | 1 +
+ 2 files changed, 3 insertions(+), 2 deletions(-)
+ create mode 100644 src/cpp/empty.cpp
+
+diff --git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt
+index b44a735..a816863 100644
+--- a/src/cpp/CMakeLists.txt
++++ b/src/cpp/CMakeLists.txt
+@@ -29,7 +29,7 @@ if (BUILD_CUDA_LIB)
+ endif()
+ 
+ if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC)
+-    add_library(flann_cpp SHARED "")
++    add_library(flann_cpp SHARED "empty.cpp")
+     set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX)
+     target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive)
+ 
+@@ -85,7 +85,7 @@ if (BUILD_C_BINDINGS)
+     set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC)
+ 
+     if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC)
+-        add_library(flann SHARED "")
++        add_library(flann SHARED "empty.cpp")
+         set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX)
+         target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive)
+     else()
+diff --git a/src/cpp/empty.cpp b/src/cpp/empty.cpp
+new file mode 100644
+index 0000000..40a8c17
+--- /dev/null
++++ b/src/cpp/empty.cpp
+@@ -0,0 +1 @@
++/* empty */
+-- 
+2.14.3

gnu/packages/patches/gnupg-1.4-CVE-2018-12020.patch

@@ -1,50 +0,0 @@
-Fix CVE-2018-12020:
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-12020
-https://lists.gnupg.org/pipermail/gnupg-announce/2018q2/000425.html
-
-Patch copied from upstream source repository:
-
-https://git.gnupg.org/cgi-bin/gitweb.cgi?p=gnupg.git;a=commit;h=2326851c60793653069494379b16d84e4c10a0ac
-
-From 2326851c60793653069494379b16d84e4c10a0ac Mon Sep 17 00:00:00 2001
-From: Werner Koch <wk@gnupg.org>
-Date: Fri, 8 Jun 2018 10:45:21 +0200
-Subject: [PATCH] gpg: Sanitize diagnostic with the original file name.
-
-* g10/mainproc.c (proc_plaintext): Sanitize verbose output.
---
-
-This fixes a forgotten sanitation of user supplied data in a verbose
-mode diagnostic.  The mention CVE is about using this to inject
-status-fd lines into the stderr output.  Other harm good as well be
-done.  Note that GPGME based applications are not affected because
-GPGME does not fold status output into stderr.
-
-CVE-id: CVE-2018-12020
-GnuPG-bug-id: 4012
-(cherry picked from commit 13f135c7a252cc46cff96e75968d92b6dc8dce1b)
----
- g10/mainproc.c | 6 +++++-
- 1 file changed, 5 insertions(+), 1 deletion(-)
-
-diff --git a/g10/mainproc.c b/g10/mainproc.c
-index 33a654b34..ffa7ef6d8 100644
---- a/g10/mainproc.c
-+++ b/g10/mainproc.c
-@@ -638,7 +638,11 @@ proc_plaintext( CTX c, PACKET *pkt )
-     if( pt->namelen == 8 && !memcmp( pt->name, "_CONSOLE", 8 ) )
- 	log_info(_("NOTE: sender requested \"for-your-eyes-only\"\n"));
-     else if( opt.verbose )
--	log_info(_("original file name='%.*s'\n"), pt->namelen, pt->name);
-+      {
-+        char *tmp = make_printable_string (pt->name, pt->namelen, 0);
-+        log_info (_("original file name='%.*s'\n"), (int)strlen (tmp), tmp);
-+        xfree (tmp);
-+      }
-     free_md_filter_context( &c->mfx );
-     c->mfx.md = md_open( 0, 0);
-     /* fixme: we may need to push the textfilter if we have sigclass 1
--- 
-2.17.1
-

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

@@ -1,28 +0,0 @@
-Copied from upstream mailing list:
-https://lists.zx2c4.com/pipermail/password-store/2018-February/003216.html.
-
-From 9b0c86159d754cc88dd3642564eed527153dfb7f Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= <clement@lassieur.org>
-Date: Sat, 24 Feb 2018 12:05:46 +0100
-Subject: [PATCH] tests: fix compatibility with GnuPG 2.2.5
-
----
- tests/t0300-reencryption.sh | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tests/t0300-reencryption.sh b/tests/t0300-reencryption.sh
-index 6d5811d..6d15364 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 --decrypt --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 "$1" 2>&1 | grep "public key is" | cut -d ' ' -f 5 | LC_ALL=C sort -u
- }
- gpg_keys_from_group() {
- 	local output="$($GPG --list-config --with-colons | sed -n "s/^cfg:group:$1:\\(.*\\)/\\1/p" | head -n 1)"
--- 
-2.16.2
-

gnu/packages/patches/perl-archive-tar-CVE-2018-12015.patch

@@ -0,0 +1,36 @@
+Fix CVE-2018-12015:
+
+https://security-tracker.debian.org/tracker/CVE-2018-12015
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-12015
+https://rt.cpan.org/Ticket/Display.html?id=125523
+
+Patch taken from this upstream commit and adapted to apply to
+the bundled copy in the Perl distribution:
+
+https://github.com/jib/archive-tar-new/commit/ae65651eab053fc6dc4590dbb863a268215c1fc5
+
+diff --git a/cpan/Archive-Tar/lib/Archive/Tar.pm b/cpan/Archive-Tar/lib/Archive/Tar.pm
+index 6244369..a83975f 100644
+--- a/cpan/Archive-Tar/lib/Archive/Tar.pm
++++ b/cpan/Archive-Tar/lib/Archive/Tar.pm
+@@ -845,6 +845,20 @@ sub _extract_file {
+         return;
+     }
+ 
++    ### If a file system already contains a block device with the same name as
++    ### the being extracted regular file, we would write the file's content
++    ### to the block device. So remove the existing file (block device) now.
++    ### If an archive contains multiple same-named entries, the last one
++    ### should replace the previous ones. So remove the old file now.
++    ### If the old entry is a symlink to a file outside of the CWD, the new
++    ### entry would create a file there. This is CVE-2018-12015
++    ### <https://rt.cpan.org/Ticket/Display.html?id=125523>.
++    if (-l $full || -e _) {
++	if (!unlink $full) {
++	    $self->_error( qq[Could not remove old file '$full': $!] );
++	    return;
++	}
++    }
+     if( length $entry->type && $entry->is_file ) {
+         my $fh = IO::File->new;
+         $fh->open( $full, '>' ) or (

gnu/packages/patches/python-nose-timer-drop-ordereddict.patch

@@ -1,44 +0,0 @@
-From 700076019b5aff72aac7651cc830aaef21ee9a47 Mon Sep 17 00:00:00 2001
-From: jakirkham <jakirkham@gmail.com>
-Date: Fri, 7 Jul 2017 05:57:56 -0400
-Subject: [PATCH] Drop ordereddict requirement (#84)
-
-* Drop ordereddict requirement
-
-As Python 2.7 is the minimum Python supported, every version of Python
-should have `ordereddict` preincluded in the standard library one way or
-another. So we can drop this dependency and just handle the differences
-between Python 2 and Python 3.
----
- nosetimer/plugin.py | 5 +----
- setup.py            | 1 -
- 2 files changed, 1 insertion(+), 5 deletions(-)
-
-diff --git a/nosetimer/plugin.py b/nosetimer/plugin.py
-index ef28e11..d093a51 100644
---- a/nosetimer/plugin.py
-+++ b/nosetimer/plugin.py
-@@ -12,10 +12,7 @@
- except ImportError:
-     import queue as Queue
- 
--try:
--    from collections import OrderedDict
--except ImportError:
--    from ordereddict import OrderedDict
-+from collections import OrderedDict
- 
- 
- # define constants
-diff --git a/setup.py b/setup.py
-index 6a55b82..d249325 100755
---- a/setup.py
-+++ b/setup.py
-@@ -27,7 +27,6 @@
-     install_requires=[
-         'nose',
-         'termcolor',
--        'ordereddict',
-     ],
-     license='MIT',
-     entry_points={

gnu/packages/patches/strace-kernel-4.16.patch

@@ -1,92 +0,0 @@
-Fix test failure when using Linux-Libre >= 4.16.
-
-Taken from upstream:
-https://github.com/strace/strace/commit/bcff87c31c0f27c678a43d6b7f67dab363a974fa
-
-From bcff87c31c0f27c678a43d6b7f67dab363a974fa Mon Sep 17 00:00:00 2001
-From: Masatake YAMATO <yamato@redhat.com>
-Date: Wed, 2 May 2018 17:11:07 +0900
-Subject: [PATCH] tests/ioctl_kvm_run.c: handle cpuid at the end of vcpu dentry
-
-Since Linux 4.16, kernel appends the cpuid as suffix to the entry
-for a kvm vcpu in /proc/$pid/fd like:
-
-    anon_inode:kvm-vcpu:0
-
-That was
-
-    anon_inode:kvm-vcpu
-
-This kernel change causes the test case failure on newer kernels.
-Update the test to deal with the new name as well as the old one.
-
-* tests/ioctl_kvm_run.c: Include unistd.h for using readlink(2).
-(vcpu_dev_should_have_cpuid): New function for detecting whether
-a proc entry for given fd has the cpuid suffix or not.
-(main): Trim vcpu_dev to remove the cpuid suffix if needed.
-(vcpu_dev): Remove const modifier.
----
- tests/ioctl_kvm_run.c | 29 ++++++++++++++++++++++++++++-
- 1 file changed, 28 insertions(+), 1 deletion(-)
-
-diff --git a/tests/ioctl_kvm_run.c b/tests/ioctl_kvm_run.c
-index 179461430..e1bef5796 100644
---- a/tests/ioctl_kvm_run.c
-+++ b/tests/ioctl_kvm_run.c
-@@ -40,6 +40,7 @@
- # include <string.h>
- # include <sys/ioctl.h>
- # include <sys/mman.h>
-+# include <unistd.h>
- # include <linux/kvm.h>
- 
- static int
-@@ -56,7 +57,7 @@ kvm_ioctl(int fd, unsigned long cmd, const char *cmd_str, void *arg)
- 
- static const char dev[] = "/dev/kvm";
- static const char vm_dev[] = "anon_inode:kvm-vm";
--static const char vcpu_dev[] = "anon_inode:kvm-vcpu";
-+static char vcpu_dev[] = "anon_inode:kvm-vcpu:0";
- static size_t page_size;
- 
- extern const char code[];
-@@ -165,6 +166,23 @@ run_kvm(const int vcpu_fd, struct kvm_run *const run, const size_t mmap_size,
- 	}
- }
- 
-+static int
-+vcpu_dev_should_have_cpuid(int fd)
-+{
-+	int r = 0;
-+	char *filename = NULL;
-+	char buf[sizeof(vcpu_dev)];
-+
-+	if (asprintf(&filename, "/proc/%d/fd/%d", getpid(), fd) < 0)
-+		error_msg_and_fail("asprintf");
-+
-+	if (readlink(filename, buf, sizeof(buf)) == sizeof(buf) - 1
-+	    && (memcmp(buf, vcpu_dev, sizeof(buf) - 1) == 0))
-+		r = 1;
-+	free(filename);
-+	return r;
-+}
-+
- int
- main(void)
- {
-@@ -208,6 +226,15 @@ main(void)
- 	       (unsigned long) page_size, (unsigned long) page_size, mem);
- 
- 	int vcpu_fd = KVM_IOCTL(vm_fd, KVM_CREATE_VCPU, NULL);
-+	if (!vcpu_dev_should_have_cpuid(vcpu_fd))
-+		/*
-+		 * This is an older kernel that doesn't place a cpuid
-+		 * at the end of the dentry associated with vcpu_fd.
-+		 * Trim the cpuid part of vcpu_dev like:
-+		 * "anon_inode:kvm-vcpu:0" -> "anon_inode:kvm-vcpu"
-+		 */
-+		vcpu_dev[strlen (vcpu_dev) - 2] = '\0';
-+
- 	printf("ioctl(%d<%s>, KVM_CREATE_VCPU, 0) = %d<%s>\n",
- 	       vm_fd, vm_dev, vcpu_fd, vcpu_dev);
- 

gnu/packages/patches/upx-fix-CVE-2017-15056.patch

@@ -0,0 +1,96 @@
+From 3e0c2966dffb5dadb512a476ef4be3d0cc51c2be Mon Sep 17 00:00:00 2001
+From: Pierre Neidhardt <ambrevar@gmail.com>
+Date: Sat, 16 Jun 2018 16:35:00 +0200
+Subject: [PATCH] Protect against bad crafted input
+
+Also check for wrap-around when checking oversize involving e_shoff and e_shnum.
+
+raised by https://github.com/upx/upx/pull/190
+	modified:   p_lx_elf.cpp
+---
+ src/p_lx_elf.cpp | 30 ++++++++++++++++++++++++++++++
+ 1 file changed, 30 insertions(+)
+
+diff --git a/src/p_lx_elf.cpp b/src/p_lx_elf.cpp
+index 822a7652..41e805ee 100644
+--- a/src/p_lx_elf.cpp
++++ b/src/p_lx_elf.cpp
+@@ -235,8 +235,17 @@ PackLinuxElf32::PackLinuxElf32help1(InputFile *f)
+         sz_phdrs = 0;
+         return;
+     }
++    if (0==e_phnum) throwCantUnpack("0==e_phnum");
+     e_phoff = get_te32(&ehdri.e_phoff);
++    unsigned const last_Phdr = e_phoff + e_phnum * sizeof(Elf32_Phdr);
++    if (last_Phdr < e_phoff || (unsigned long)file_size < last_Phdr) {
++        throwCantUnpack("bad e_phoff");
++    }
+     e_shoff = get_te32(&ehdri.e_shoff);
++    unsigned const last_Shdr = e_shoff + e_shnum * sizeof(Elf32_Shdr);
++    if (last_Shdr < e_shoff || (unsigned long)file_size < last_Shdr) {
++        throwCantUnpack("bad e_shoff");
++    }
+     sz_phdrs = e_phnum * e_phentsize;
+ 
+     if (f && Elf32_Ehdr::ET_DYN!=e_type) {
+@@ -599,8 +608,17 @@ PackLinuxElf64::PackLinuxElf64help1(InputFile *f)
+         sz_phdrs = 0;
+         return;
+     }
++    if (0==e_phnum) throwCantUnpack("0==e_phnum");
+     e_phoff = get_te64(&ehdri.e_phoff);
++    upx_uint64_t const last_Phdr = e_phoff + e_phnum * sizeof(Elf64_Phdr);
++    if (last_Phdr < e_phoff || (unsigned long)file_size < last_Phdr) {
++        throwCantUnpack("bad e_phoff");
++    }
+     e_shoff = get_te64(&ehdri.e_shoff);
++    upx_uint64_t const last_Shdr = e_shoff + e_shnum * sizeof(Elf64_Shdr);
++    if (last_Shdr < e_shoff || (unsigned long)file_size < last_Shdr) {
++        throwCantUnpack("bad e_shoff");
++    }
+     sz_phdrs = e_phnum * e_phentsize;
+ 
+     if (f && Elf64_Ehdr::ET_DYN!=e_type) {
+@@ -3763,6 +3781,9 @@ void PackLinuxElf64::pack4(OutputFile *fo, Filter &ft)
+ 
+ void PackLinuxElf64::unpack(OutputFile *fo)
+ {
++    if (e_phoff != sizeof(Elf64_Ehdr)) {// Phdrs not contiguous with Ehdr
++        throwCantUnpack("bad e_phoff");
++    }
+     unsigned const c_phnum = get_te16(&ehdri.e_phnum);
+     upx_uint64_t old_data_off = 0;
+     upx_uint64_t old_data_len = 0;
+@@ -3828,6 +3849,9 @@ void PackLinuxElf64::unpack(OutputFile *fo)
+     unsigned total_out = 0;
+     unsigned c_adler = upx_adler32(NULL, 0);
+     unsigned u_adler = upx_adler32(NULL, 0);
++    if ((MAX_ELF_HDR - sizeof(Elf64_Ehdr))/sizeof(Elf64_Phdr) < u_phnum) {
++        throwCantUnpack("bad compressed e_phnum");
++    }
+ 
+     // Packed ET_EXE has no PT_DYNAMIC.
+     // Packed ET_DYN has original PT_DYNAMIC for info needed by rtld.
+@@ -4383,6 +4407,9 @@ Elf64_Sym const *PackLinuxElf64::elf_lookup(char const *name) const
+ 
+ void PackLinuxElf32::unpack(OutputFile *fo)
+ {
++    if (e_phoff != sizeof(Elf32_Ehdr)) {// Phdrs not contiguous with Ehdr
++        throwCantUnpack("bad e_phoff");
++    }
+     unsigned const c_phnum = get_te16(&ehdri.e_phnum);
+     unsigned old_data_off = 0;
+     unsigned old_data_len = 0;
+@@ -4449,6 +4476,9 @@ void PackLinuxElf32::unpack(OutputFile *fo)
+     unsigned total_out = 0;
+     unsigned c_adler = upx_adler32(NULL, 0);
+     unsigned u_adler = upx_adler32(NULL, 0);
++    if ((MAX_ELF_HDR - sizeof(Elf32_Ehdr))/sizeof(Elf32_Phdr) < u_phnum) {
++        throwCantUnpack("bad compressed e_phnum");
++    }
+ 
+     // Packed ET_EXE has no PT_DYNAMIC.
+     // Packed ET_DYN has original PT_DYNAMIC for info needed by rtld.
+-- 
+2.17.0
+

gnu/packages/perl-check.scm

@@ -13,6 +13,7 @@
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -364,6 +365,30 @@ modified or tested with this API, making it simple to test both individual
 files, as well as to verify that there are no missing or unknown files.")
     (license perl-license)))
 
+(define-public perl-test-distmanifest
+  (package
+    (name "perl-test-distmanifest")
+    (version "1.014")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/E/ET/ETHER/Test-DistManifest-"
+             version ".tar.gz"))
+       (sha256
+        (base32 "1ifpff5simjslabwy7ac6kdylv4c0b5b39fgpwf9ha16yh6w49ix"))))
+    (build-system perl-build-system)
+    (native-inputs
+     `(("perl-module-build" ,perl-module-build)))
+    (propagated-inputs
+     `(("perl-module-manifest" ,perl-module-manifest)))
+    (home-page "https://github.com/jawnsy/Test-DistManifest")
+    (synopsis "Author test that validates a package @file{MANIFEST}")
+    (description
+     "@code{Test::DistManifest} provides a simple method of testing that a
+@file{MANIFEST} file matches its distribution.")
+    (license perl-license)))
+
 (define-public perl-test-eol
   (package
     (name "perl-test-eol")
@@ -1140,6 +1165,32 @@ a minimum of effort.")
     ;; "Under the same license as Perl itself"
     (license perl-license)))
 
+(define-public perl-test-perltidy
+  (package
+    (name "perl-test-perltidy")
+    (version "20130104")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/L/LA/LARRYL/Test-PerlTidy-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "1j5rsb4km9rzcbd1ljavj8vm42bmilji40v2jj2k87l1ykrxj59z"))))
+    (build-system perl-build-system)
+    (propagated-inputs
+     `(("perl-file-finder" ,perl-file-finder)
+       ("perl-file-slurp" ,perl-file-slurp)
+       ("perltidy" ,perltidy)
+       ("perl-text-diff" ,perl-text-diff)))
+    (home-page "http://search.cpan.org/dist/Test-PerlTidy/")
+    (synopsis "Check that all your Perl files are tidy")
+    (description
+     "Using @code{Test::PerlTidy}, any file ending in .pl, .pm, .t or .PL will
+cause a test fail unless it is exactly as @code{perltidy} would like it to be.")
+    (license perl-license)))
+
 (define-public perl-test-trap
   (package
     (name "perl-test-trap")

gnu/packages/perl.scm

@@ -20,6 +20,7 @@
 ;;; Copyright © 2017 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -170,6 +171,8 @@
               (inherit (package-source perl))
               (uri (string-append "mirror://cpan/src/5.0/perl-"
                                   version ".tar.gz"))
+              (patches (append (origin-patches (package-source perl))
+                               (search-patches "perl-archive-tar-CVE-2018-12015.patch")))
               (sha256
                (base32
                 "03gpnxx1g6hvlh0v4aqx00580h787sfywp1vlvw64q2xcbm9qbsp"))))))
@@ -1522,6 +1525,27 @@ provides a means of converting those data streams back into into binary
 data.")
     (license perl-license)))
 
+(define-public perl-cpan-changes
+  (package
+    (name "perl-cpan-changes")
+    (version "0.400002")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/H/HA/HAARG/CPAN-Changes-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "13dy78amkhwg278sv5im0ylyskhxpfivyl2aissqqih71nlxxvh1"))))
+    (build-system perl-build-system)
+    (home-page "http://search.cpan.org/dist/CPAN-Changes/")
+    (synopsis "Read and write @file{Changes} files")
+    (description
+     "@code{CPAN::Changes} helps users programmatically read and write
+@file{Changes} files that conform to a common specification.")
+    (license perl-license)))
+
 (define-public perl-cpan-meta-check
   (package
     (name "perl-cpan-meta-check")
@@ -5213,6 +5237,36 @@ strictly correct manner with ExtUtils::MakeMaker, and will run on any Perl
 installation version 5.005 or newer.")
     (license (package-license perl))))
 
+(define-public perl-module-manifest
+  (package
+    (name "perl-module-manifest")
+    (version "1.09")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/E/ET/ETHER/Module-Manifest-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "16skpm804a19gsgxzn1wba3lmvc7cx5q8ly4srpyd82yy47zi5d3"))))
+    (build-system perl-build-system)
+    (native-inputs
+     `(("perl-test-exception" ,perl-test-exception)
+       ("perl-test-warn" ,perl-test-warn)))
+    (propagated-inputs
+     `(("perl-params-util" ,perl-params-util)))
+    (home-page "http://search.cpan.org/dist/Module-Manifest/")
+    (synopsis "Parse and examine a Perl distribution @file{MANIFEST} file")
+    (description
+     "@code{Module::Manifest} is a simple utility module created originally for
+use in @code{Module::Inspector}.
+
+It can load a @file{MANIFEST} file that comes in a Perl distribution tarball,
+examine the contents, and perform some simple tasks.  It can also load the
+@file{MANIFEST.SKIP} file and check that.")
+    (license perl-license)))
+
 (define-public perl-module-pluggable
   (package
     (name "perl-module-pluggable")
@@ -8461,14 +8515,14 @@ as exceptions to standard program flow.")
 (define-public perltidy
   (package
     (name "perltidy")
-    (version "20160302")
+    (version "20180220")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/perltidy/" version
                                   "/Perl-Tidy-" version ".tar.gz"))
               (sha256
                (base32
-                "19yw63yh5s3pq7k3nkw6nsamg5b8vvwyhgbizslgxg0mqgc4xl3d"))))
+                "0w1k5ffcrpx0fm9jgprrwy0290k6cmy7dyk83s61063migi3r5z9"))))
     (build-system perl-build-system)
     (home-page "http://perltidy.sourceforge.net/")
     (synopsis "Perl script tidier")
@@ -9476,6 +9530,38 @@ File::Find replacement in Perl.")
 interface to File::Find::Object.")
   (license (package-license perl))))
 
+(define-public perl-file-finder
+  (package
+    (name "perl-file-finder")
+    (version "0.53")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/M/ME/MERLYN/File-Finder-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "0x3a2xgzrka73lcmmwalq2mmpzxa7s6pm01ahxf677ksqsdc3jrf"))))
+    (build-system perl-build-system)
+    (propagated-inputs
+     `(("perl-text-glob" ,perl-text-glob)))
+    (home-page "http://search.cpan.org/dist/File-Finder/")
+    (synopsis "Wrapper for @code{File::Find} ala @code{find(1)}")
+    (description
+     "@code{File::Find} is great, but constructing the wanted routine can
+sometimes be a pain.  @code{File::Finder} provides a wanted-writer, using
+syntax that is directly mappable to the @code{find(1)} command's syntax.
+
+A @code{File::Finder} object contains a hash of @code{File::Find} options, and
+a series of steps that mimic find's predicates.  Initially, a
+@code{File::Finder} object has no steps.  Each step method clones the previous
+object's options and steps, and then adds the new step, returning the new
+object.  In this manner, an object can be grown, step by step, by chaining
+method calls.  Furthermore, a partial sequence can be created and held, and
+used as the head of many different sequences.")
+    (license perl-license)))
+
 (define-public perl-font-ttf
   (package
     (name "perl-font-ttf")

gnu/packages/python.scm

@@ -53,6 +53,7 @@
 ;;; Copyright © 2016, 2018 Tomáš Čech <sleep_walker@gnu.org>
 ;;; Copyright © 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
+;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -4871,26 +4872,15 @@ computing.")
 (define-public python-urwid
   (package
     (name "python-urwid")
-    (version "1.3.1")
+    (version "2.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "urwid" version))
        (sha256
         (base32
-         "18cnd1wdjcas08x5qwa5ayw6jsfcn33w4d9f7q3s29fy6qzc1kng"))))
+         "1g6cpicybvbananpjikmjk8npmjk4xvak1wjzji62wc600wkwkb4"))))
     (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; Disable failing test. Bug filed upstream:
-         ;; https://github.com/wardi/urwid/issues/164
-         ;; TODO: check again for python-urwid > 1.3.1 or python > 3.4.3.
-         (add-after 'unpack 'disable-failing-test
-          (lambda _
-            (substitute* "urwid/tests/test_event_loops.py"
-              (("test_remove_watch_file")
-                "disable_remove_watch_file")))))))
     (home-page "http://urwid.org")
     (synopsis "Console user interface library for Python")
     (description
@@ -4899,22 +4889,7 @@ features useful for text console applications.")
     (license license:lgpl2.1+)))
 
 (define-public python2-urwid
-  (let ((python2-urwid (package-with-python2 python-urwid)))
+  (package-with-python2 python-urwid))
-    (package
-      (inherit python2-urwid)
-      (arguments
-       (append
-        `(;; Explicitly using Python 2 is necessary due the argument list being
-          ;; built from only the 'delete-test_vterm.py' phase and python-urwid's
-          ;; package arguments, which by default assumes the use of Python 3.
-          #:python ,python-2
-          #:phases
-          (modify-phases %standard-phases
-            ;; Disable the vterm tests because of non-deterministic failures
-            ;; with Python 2. See https://github.com/urwid/urwid/issues/230.
-            (add-after 'unpack 'delete-test_vterm.py
-              (delete-file "urwid/tests/test_vterm.py"))))
-        (package-arguments python-urwid))))))
 
 (define-public python-urwidtrees
   (package
@@ -6033,13 +6008,13 @@ should be stored on various operating systems.")
 (define-public python-llfuse
   (package
     (name "python-llfuse")
-    (version "1.3.2")
+    (version "1.3.3")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "llfuse" version ".tar.bz2"))
               (sha256
                (base32
-                "0qxvnbz41bpvpc1vbi8qkhmpr9gj1qrrp5jdj085iqibd8l2l9cn"))))
+                "1rqww632y2zz71xmr6ch7yq80kvza9mhqr2z773k0d8l1lwzl575"))))
     (build-system python-build-system)
     (inputs
      `(("fuse" ,fuse)
@@ -7285,13 +7260,13 @@ applications.")
 (define-public python-click-log
   (package
     (name "python-click-log")
-    (version "0.2.1")
+    (version "0.3.2")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "click-log" version))
              (sha256
               (base32
-               "1r1x85023cslb2pwldd089jjk573mk3w78cnashs77wrx7yz8fj9"))))
+               "091i03bhxyzsdbc6kilxhivfda2f8ymz3b33xa6cj5kbzjiirz8n"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-click" ,python-click)))
@@ -13657,3 +13632,120 @@ introspection.")
 
 (define-public python2-fasteners
   (package-with-python2 python-fasteners))
+
+(define-public python-requests-file
+  (package
+    (name "python-requests-file")
+    (version "1.4.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "requests-file" version))
+       (sha256
+        (base32
+         "1yp2jaxg3v86pia0q512dg3hz6s9y5vzdivsgrba1kds05ial14g"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-requests" ,python-requests)
+       ("python-six" ,python-six)))
+    (home-page
+     "https://github.com/dashea/requests-file")
+    (synopsis "File transport adapter for Requests")
+    (description
+     "Requests-File is a transport adapter for use with the Requests Python
+library to allow local filesystem access via file:// URLs.")
+    (license license:asl2.0)))
+
+(define-public python2-requests-file
+  (package-with-python2 python-requests-file))
+
+(define-public python-tldextract
+  (package
+    (name "python-tldextract")
+    (version "2.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "tldextract" version))
+       (sha256
+        (base32
+         "1d5s8v6kpsgazyahflhji1cfdcf89rv7l7z55v774bhzvcjp2y99"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-responses" ,python-responses)))
+    (propagated-inputs
+     `(("python-idna" ,python-idna)
+       ("python-requests" ,python-requests)
+       ("python-requests-file" ,python-requests-file)))
+    (home-page
+     "https://github.com/john-kurkowski/tldextract")
+    (synopsis
+     "Separate the TLD from the registered domain and subdomains of a URL")
+    (description
+     "TLDExtract accurately separates the TLD from the registered domain and
+subdomains of a URL, using the Public Suffix List.  By default, this includes
+the public ICANN TLDs and their exceptions.  It can optionally support the
+Public Suffix List's private domains as well.")
+    (license license:bsd-3)))
+
+(define-public python2-tldextract
+  (package-with-python2 python-tldextract))
+
+(define-public python-pynamecheap
+  (package
+    (name "python-pynamecheap")
+    (version "0.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "PyNamecheap" version))
+       (sha256
+        (base32
+         "0wkbwz208j8nfrsmzmclvxg22ymknn0mlz76wbdza9k2bx2zja6l"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-requests" ,python-requests)))
+    (home-page
+     "https://github.com/Bemmu/PyNamecheap")
+    (synopsis
+     "Namecheap API client in Python")
+    (description
+     "PyNamecheap is a Namecheap API client in Python.")
+    (license license:expat)))
+
+(define-public python2-pynamecheap
+  (package-with-python2 python-pynamecheap))
+
+(define-public python-dns-lexicon
+  (package
+    (name "python-dns-lexicon")
+    (version "2.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "dns-lexicon" version))
+       (sha256
+        (base32
+         "0jdn3ns71bsybr7njgsqr9xlxsqh7zh6phn4ld0liazqdn2l5f6m"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f))                    ;requires internet access
+    (propagated-inputs
+     `(("python-future" ,python-future)
+       ("python-pynamecheap" ,python-pynamecheap)
+       ("python-requests" ,python-requests)
+       ("python-tldextract" ,python-tldextract)
+       ("python-urllib3" ,python-urllib3)))
+    (home-page "https://github.com/AnalogJ/lexicon")
+    (synopsis
+     "Manipulate DNS records on various DNS providers")
+    (description
+     "Lexicon provides a way to manipulate DNS records on multiple DNS
+providers in a standardized way.  It has a CLI but it can also be used as a
+Python library.  It was designed to be used in automation, specifically with
+Let's Encrypt.")
+    (license license:expat)))
+
+(define-public python2-dns-lexicon
+  (package-with-python2 python-dns-lexicon))

gnu/packages/qt.scm

@@ -9,6 +9,7 @@
 ;;; Copyright © 2017 Quiliro <quiliro@fsfla.org>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2018 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1069,6 +1070,55 @@ between the host (QML/C++ application) and the client (HTML/JavaScript
 application).  The transport mechanism is supported out of the box by the two
 popular web engines, Qt WebKit 2 and Qt WebEngine.")))
 
+(define-public qtwebglplugin
+  (package (inherit qtsvg)
+    (name "qtwebglplugin")
+    (version "5.11.0")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append "https://download.qt.io/official_releases/qt/"
+                                 (version-major+minor version) "/" version
+                                 "/submodules/" name "-everywhere-src-"
+                                 version ".tar.xz"))
+             (sha256
+              (base32
+               "1al7dv7i9rg4z4p8vnipbjbbgc6113lbfjggxxap3sn6hqs986fm"))))
+    (native-inputs '())
+    (inputs
+     `(("mesa" ,mesa)
+       ("qtbase" ,qtbase)
+       ("qtwebsockets" ,qtwebsockets)))
+    (synopsis "QPA plugin for running an application via a browser using
+streamed WebGL commands")
+    (description "Qt back end that uses WebGL for rendering. It allows Qt
+applications (with some limitations) to run in a web browser that supports
+WebGL.  WebGL is a JavaScript API for rendering 2D and 3D graphics within any
+compatible web browser without the use of plug-ins.  The API is similar to
+OpenGL ES 2.0 and can be used in HTML5 canvas elements")))
+
+(define-public qtwebview
+  (package (inherit qtsvg)
+    (name "qtwebview")
+    (version "5.11.0")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append "https://download.qt.io/official_releases/qt/"
+                                 (version-major+minor version) "/" version
+                                 "/submodules/" name "-everywhere-src-"
+                                 version ".tar.xz"))
+             (sha256
+              (base32
+               "0a89v8mj5pb7a7whyhasf4ms0n34ghfmv2qp0pyxnq56f2bsjbl4"))))
+    (native-inputs
+     `(("perl" ,perl)))
+    (inputs
+     `(("qtbase" ,qtbase)
+       ("qtdeclarative" ,qtdeclarative)))
+    (synopsis "Display web content in a QML application")
+    (description "Qt WebView provides a way to display web content in a QML
+application without necessarily including a full web browser stack by using
+native APIs where it makes sense.")))
+
 (define-public qtlocation
   (package (inherit qtsvg)
     (name "qtlocation")

gnu/packages/samba.scm

@@ -362,7 +362,10 @@ many event types, including timers, signals, and the classic file descriptor eve
                   #t))))
     (build-system gnu-build-system)
     (arguments
-     '(#:phases
+     '(;; LMDB is only supported on 64-bit systems, yet the test suite
+       ;; requires it.
+       #:tests? (assoc-ref %build-inputs "lmdb")
+       #:phases
        (modify-phases %standard-phases
          (replace 'configure
            ;; ldb use a custom configuration script that runs waf.
@@ -382,7 +385,9 @@ many event types, including timers, signals, and the classic file descriptor eve
      `(("talloc" ,talloc)
        ("tdb" ,tdb)))
     (inputs
-     `(("lmdb" ,lmdb)
+     `(,@(if (target-64bit?)
+             `(("lmdb" ,lmdb))
+             '())
        ("popt" ,popt)
        ("tevent" ,tevent)))
     (synopsis "LDAP-like embedded database")

gnu/packages/spice.scm

@@ -128,7 +128,7 @@ system to use the host GPU to accelerate 3D rendering.")
 (define-public spice-protocol
   (package
     (name "spice-protocol")
-    (version "0.12.13")
+    (version "0.12.14")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -136,7 +136,7 @@ system to use the host GPU to accelerate 3D rendering.")
                 "spice-protocol-" version ".tar.bz2"))
               (sha256
                (base32
-                "0cwrgkp558mblcf4vrhacb3iizz12khsrrl82w38w9nj0ar13vl9"))))
+                "170ckpgazvqv7hxy209myg67pqnd6c0gvr4ysbqgsfch6320nd90"))))
     (build-system gnu-build-system)
     (synopsis "Protocol headers for the SPICE protocol")
     (description "SPICE (the Simple Protocol for Independent Computing

gnu/packages/sssd.scm

@@ -81,14 +81,14 @@ fundamental object types for C.")
 (define-public sssd
   (package
     (name "sssd")
-    (version "1.16.1")
+    (version "1.16.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://releases.pagure.org/SSSD/sssd/"
                                   "sssd-" version ".tar.gz"))
               (sha256
                (base32
-                "0vjh1c5960wh86zjsamdjhljls7bb5fz5jpcazgzrpmga5w6ggrd"))))
+                "032ppk57qs1lnvz7pb7lw9ldwm9i1yagh9fzgqgn6na3bg61ynzy"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
@@ -165,6 +165,7 @@ fundamental object types for C.")
      `(("check" ,check)
        ("docbook-xsl" ,docbook-xsl)
        ("docbook-xml" ,docbook-xml)
+       ("libxml2" ,libxml2)             ; for xmllint
        ("libxslt" ,libxslt)
        ("pkg-config" ,pkg-config)
        ("util-linux" ,util-linux)))     ; for uuid.h, reqired for KCM

gnu/packages/statistics.scm

@@ -835,13 +835,13 @@ see package vignette.  To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
 (define-public r-munsell
   (package
     (name "r-munsell")
-    (version "0.4.3")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "munsell" version))
        (sha256
-        (base32 "0jdxlbjslkzaqgp058da1cgm85qvqi09wpcgpvp4hvwnmy83qz1r"))))
+        (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-colorspace" ,r-colorspace)))
@@ -960,14 +960,14 @@ solution for sending email, including attachments, from within R.")
 (define-public r-stringi
   (package
     (name "r-stringi")
-    (version "1.2.2")
+    (version "1.2.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stringi" version))
        (sha256
         (base32
-         "1z8yqnh3alq0xriz77vifgl27msf3av6maz07fld78m90ajb6y8r"))))
+         "1sgg4krw03qkz1n4dwiya0djggk7giwd0w21qlp0pfjqi0rxq6qx"))))
     (build-system r-build-system)
     (inputs `(("icu4c" ,icu4c)))
     (native-inputs `(("pkg-config" ,pkg-config)))
@@ -1289,13 +1289,13 @@ There is also a Shiny app as a user interface in this package.")
 (define-public r-highr
   (package
     (name "r-highr")
-    (version "0.6")
+    (version "0.7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "highr" version))
               (sha256
                (base32
-                "0n9v44dxdy5fhkdmpbpa2p78whyd9z3rhhy42ipdz5m5vsr55qa3"))))
+                "1dzknqk4x7iiiq1jkh9bqm5qcvs7mbqxbkn5955050payavabfya"))))
     (build-system r-build-system)
     (home-page "https://github.com/yihui/highr")
     (synopsis "Syntax highlighting for R source code")
@@ -2603,14 +2603,14 @@ certain criterion, e.g., it contains a certain regular file.")
 (define-public r-rmarkdown
   (package
     (name "r-rmarkdown")
-    (version "1.9")
+    (version "1.10")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "rmarkdown" version))
         (sha256
           (base32
-            "0wq6kbhrkv3fhcy4hg5yyv9gdvf8gr4nsjwdifs4ih8lnn0dmdyb"))))
+            "0mh2f3k98w7pgz0ri34149s4kx5y0kfm27nwq64k0qwxd16hwd9r"))))
     (properties `((upstream-name . "rmarkdown")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2622,6 +2622,7 @@ certain criterion, e.g., it contains a certain regular file.")
        ("r-mime" ,r-mime)
        ("r-rprojroot" ,r-rprojroot)
        ("r-stringr" ,r-stringr)
+       ("r-tinytex" ,r-tinytex)
        ("r-yaml" ,r-yaml)
        ;; rmarkdown works with the 2.x release of Pandoc, but with degraded
        ;; functionality.  For example, tabbed plots do not currently work with
@@ -4222,13 +4223,13 @@ mechanism.")
 (define-public r-zoo
   (package
     (name "r-zoo")
-    (version "1.8-1")
+    (version "1.8-2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "zoo" version))
               (sha256
                (base32
-                "16nc5jnpkf5j9vgq3pzssv7knj30mi055wj7q3sygz3l0d88hgfr"))))
+                "1lpwigxmi5sc23xrha4gcsccsm4yfsg0sa97y6vac3pg1lliblvx"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))

gnu/packages/terminals.scm

@@ -10,6 +10,7 @@
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Petter <petter@mykolab.ch>
 ;;; Copyright © 2018 Hartmut Goebel <h.goebel@crazy-compilers.com>
+;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -47,6 +48,7 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gtk)
+  #:use-module (gnu packages libevent)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
@@ -55,6 +57,8 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages qt)
+  #:use-module (gnu packages serialization)
+  #:use-module (gnu packages ssh)
   #:use-module (gnu packages textutils)
   #:use-module (gnu packages wm)
   #:use-module (gnu packages xdisorg)
@@ -845,3 +849,33 @@ per-line fullscreen terminal rendering, and keyboard input event reporting.")
 
 (define-public python2-curtsies
   (package-with-python2 python-curtsies))
+
+(define-public tmate
+  (package
+    (name "tmate")
+    (version "2.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/tmate-io/tmate/archive/"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "01f3hhm3x0sd6apyb1ajkjfdfvq5m2759w00yp2slr9fyicsrhnr"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("libevent" ,libevent)
+       ("libssh" ,libssh)
+       ("msgpack" ,msgpack)
+       ("ncurses" ,ncurses)))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("pkg-config" ,pkg-config)))
+    (home-page "https://tmate.io/")
+    (synopsis "Terminal sharing application")
+    (description "tmate is a terminal sharing application that allows you to
+share your terminal with other users over the Internet.  tmate is a fork of
+tmux.")
+    (license license:isc)))

gnu/packages/tex.scm

@@ -176,14 +176,17 @@
                            (string-prefix? "mips64" s))))
       #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'fix-unix-detection
+         (add-after 'unpack 'configure-ghostscript-executable
            ;; ps2eps.pl uses the "gswin32c" ghostscript executable on Windows,
            ;; and the "gs" ghostscript executable on Unix. It detects Unix by
            ;; checking for the existence of the /usr/bin directory. Since
            ;; GuixSD does not have /usr/bin, it is also detected as Windows.
-           (lambda _
+           (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "utils/ps2eps/ps2eps-src/bin/ps2eps.pl"
                (("gswin32c") "gs"))
+             (substitute* "texk/texlive/linked_scripts/epstopdf/epstopdf.pl"
+               (("\"gs\"")
+                (string-append "\"" (assoc-ref inputs "ghostscript") "/bin/gs\"")))
              #t))
          (add-after 'install 'postint
            (lambda* (#:key inputs outputs #:allow-other-keys #:rest args)

gnu/packages/time.scm

@@ -287,14 +287,14 @@ value (in fractional seconds) of a clock which never goes backwards.")
 (define-public python-pyrfc3339
   (package
     (name "python-pyrfc3339")
-    (version "1.0")
+    (version "1.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyRFC3339" version))
        (sha256
         (base32
-         "0dgm4l9y8jiax5cp6yxjd2i27cq8h33sh81n1wfbmnmqb32cdywd"))))
+         "06jv7ar7lpvvk0dixzwdr3wgm0g1lipxs429s2z7knwwa7hwpf41"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-pytz" ,python-pytz)))

gnu/packages/tls.scm

@@ -12,6 +12,7 @@
 ;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
+;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -38,10 +39,14 @@
   #:use-module (guix build-system python)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system haskell)
+  #:use-module (guix build-system trivial)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages)
+  #:use-module (gnu packages bash)
   #:use-module (gnu packages check)
+  #:use-module (gnu packages curl)
   #:use-module (gnu packages dns)
+  #:use-module (gnu packages gawk)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages haskell)
   #:use-module (gnu packages haskell-check)
@@ -459,14 +464,14 @@ required structures.")
 (define-public libressl
   (package
     (name "libressl")
-    (version "2.7.3")
+    (version "2.7.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://openbsd/LibreSSL/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1597kj9jy3jyw52ys19sd4blg2gkam5q0rqdxbnrnvnyw67hviqn"))))
+                "19kxa5i97q7p6rrps9qm0nd8zqhdjvzx02j72400c73cl2nryfhy"))))
     (build-system gnu-build-system)
     (arguments
      ;; Do as if 'getentropy' was missing since older Linux kernels lack it
@@ -503,13 +508,13 @@ netcat implementation that supports TLS.")
   (package
     (name "python-acme")
     ;; Remember to update the hash of certbot when updating python-acme.
-    (version "0.24.0")
+    (version "0.25.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "acme" version))
               (sha256
                (base32
-                "1jq1nlly5146k08dw31fc1pw78plya5jswznnd512c08giif0mfn"))))
+                "0d177dhy8a7472pz9v4blrlk02d8fp6s52li7z8v3dv97pvz7da7"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -528,6 +533,7 @@ netcat implementation that supports TLS.")
     ;; TODO: Add optional inputs for testing.
     (native-inputs
      `(("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)
        ;; For documentation
        ("python-sphinx" ,python-sphinx)
        ("python-sphinxcontrib-programoutput" ,python-sphinxcontrib-programoutput)
@@ -537,6 +543,7 @@ netcat implementation that supports TLS.")
      `(("python-josepy" ,python-josepy)
        ("python-six" ,python-six)
        ("python-requests" ,python-requests)
+       ("python-requests-toolbelt" ,python-requests-toolbelt)
        ("python-pytz" ,python-pytz)
        ("python-pyrfc3339" ,python-pyrfc3339)
        ("python-pyasn1" ,python-pyasn1)
@@ -558,7 +565,7 @@ netcat implementation that supports TLS.")
               (uri (pypi-uri name version))
               (sha256
                (base32
-                "0w3dbz74rpabjnc3l3ybnzjdypbr65lsjqf9yn243b5kid9d8wm0"))))
+                "0kp56gwn1bnlrag9qidhm1i5ifdp5z6y1ravh3yimfrkc4cfa8sw"))))
     (build-system python-build-system)
     (arguments
      `(,@(substitute-keyword-arguments (package-arguments python-acme)
@@ -873,3 +880,69 @@ implement the SSL3.0, TLS1.0, TLS1.1 and TLS1.2 protocol, and support RSA and
 Ephemeral (Elliptic curve and regular) Diffie Hellman key exchanges, and many
 extensions.")
     (license license:bsd-3)))
+
+(define-public dehydrated
+  (package
+    (name "dehydrated")
+    (version "0.6.2")
+    (source (origin
+              (method url-fetch/tarbomb)
+              (uri (string-append
+                    "https://github.com/lukas2511/dehydrated/archive/v"
+                    version ".tar.gz"))
+              (sha256
+               (base32
+                "03p80yj6bnzjc6dkp5hb9wpplmlrla8n5src71cnzw4rj53q8cqn"))
+              (file-name (string-append name "-" version ".tar.gz"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let* ((source (assoc-ref %build-inputs "source"))
+                (out (assoc-ref %outputs "out"))
+                (bin (string-append out "/bin"))
+                (bash (in-vicinity (assoc-ref %build-inputs "bash") "bin")))
+           (mkdir-p bin)
+           (with-directory-excursion bin
+             (copy-file
+              (in-vicinity source (string-append "/dehydrated-" ,version
+                                                 "/dehydrated"))
+              (in-vicinity bin "dehydrated"))
+             (patch-shebang "dehydrated" (list bash))
+
+             ;; Do not try to write in the store.
+             (substitute* "dehydrated"
+               (("SCRIPTDIR=\"\\$.*\"") "SCRIPTDIR=~/.dehydrated"))
+
+             (setenv "PATH" bash)
+             (wrap-program "dehydrated"
+               `("PATH" ":" prefix
+                 ,(map (lambda (dir)
+                         (string-append dir "/bin"))
+                       (map (lambda (input)
+                              (assoc-ref %build-inputs input))
+                            '("coreutils"
+                              "curl"
+                              "diffutils"
+                              "gawk"
+                              "grep"
+                              "openssl"
+                              "sed"))))))
+           #t))))
+    (inputs
+     `(("bash" ,bash)
+       ("coreutils" ,coreutils)
+       ("curl" ,curl)
+       ("diffutils" ,diffutils)
+       ("gawk" ,gawk)
+       ("grep" ,grep)
+       ("openssl" ,openssl)
+       ("sed" ,sed)))
+    (home-page "https://dehydrated.io/")
+    (synopsis "Let's Encrypt/ACME client implemented as a shell script")
+    (description "Dehydrated is a client for signing certificates with an
+ACME-server (currently only provided by Let's Encrypt) implemented as a
+relatively simple Bash script.")
+    (license license:expat)))

gnu/packages/tor.scm

@@ -47,14 +47,14 @@
 (define-public tor
   (package
     (name "tor")
-    (version "0.3.3.6")
+    (version "0.3.3.7")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://dist.torproject.org/tor-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "1drk2h8zd05xrfpx7xn77pcxz0hs4nrq6figw56qk5gkvgv5kg4r"))))
+               "036ybfvldj7yfci9ipjki8smpzyxdg8c5r12bghc9yxdqh9basza"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags (list "--enable-gcc-hardening"

gnu/packages/version-control.scm

@@ -1911,7 +1911,7 @@ network protocols, and core version control algorithms.")
 (define-public gource
   (package
     (name "gource")
-    (version "0.48")
+    (version "0.49")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1919,7 +1919,7 @@ network protocols, and core version control algorithms.")
                     "/gource-" version "/gource-" version ".tar.gz"))
               (sha256
                (base32
-                "04qxcm05qiyr9rg2kv6abfy7kkzqr8ziw4iyp1d14lniv93m61dp"))))
+                "12hf5ipcsp9dxsqn84n4kr63xaiskrnf5a084wr29qk171lj7pd9"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags

gnu/packages/video.scm

@@ -606,14 +606,14 @@ standards (MPEG-2, MPEG-4 ASP/H.263, MPEG-4 AVC/H.264, and VC-1/VMW3).")
 (define-public ffmpeg
   (package
     (name "ffmpeg")
-    (version "4.0")
+    (version "4.0.1")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "0gx4ngnhi5glmxh38603qy5n6vq8bl1cr4sqd1xff95i82pmv57d"))))
+               "1vn04n0n46zdxq14cma3w8ml2ckh5jxwlybsc4xmvcqdqq0mqpv0"))))
     (build-system gnu-build-system)
     (inputs
      `(("fontconfig" ,fontconfig)

gnu/packages/vim.scm

@@ -450,23 +450,20 @@ trouble using them, because you do not have to remember each snippet name.")
       (home-page "https://github.com/Shougo/context_filetype.vim")
       (license license:expat)))) ; ??? check again
 
-;; The 2.2 release was in 2015, no new releases planned.
 (define-public vim-fugitive
-  (let ((commit "de6c05720cdf74c0218218d7207f700232a5b6dc")
-        (revision "1"))
   (package
     (name "vim-fugitive")
-      (version (string-append "2.2-" revision "." (string-take commit 7)))
+    (version "2.3")
     (source
       (origin
         (method git-fetch)
         (uri (git-reference
                (url "https://github.com/tpope/vim-fugitive.git")
-                 (commit commit)))
+               (commit (string-append "v" version))))
-          (file-name (string-append name "-" version "-checkout"))
+        (file-name (git-file-name name version))
         (sha256
          (base32
-           "0zg9vv7hirnx45vc2mwgg0xijmwwz55bssyd6cpdz71wbhrcpxxb"))))
+          "17s94a8g5z0lrs7yy4nyqyvp9ykys5ws2ar3m3c0bjsn0iazd7m3"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f
@@ -488,21 +485,22 @@ trouble using them, because you do not have to remember each snippet name.")
     (description "Vim-fugitive is a wrapper for Vim that complements the
 command window, where you can stage and review your changes before the next
 commit or run any Git arbitrary command.")
-      (license license:vim)))) ; distributed under the same license as vim
+    (license license:vim))) ; distributed under the same license as vim
 
 (define-public vim-airline
   (package
     (name "vim-airline")
-    (version "0.8")
+    (version "0.9")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/vim-airline/vim-airline/"
+       (uri (git-reference
-                           "archive/v" version ".tar.gz"))
+              (url "https://github.com/vim-airline/vim-airline")
-       (file-name (string-append name "-" version ".tar.gz"))
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "053sfq3jmgdc5y7zbg6jrk7r2hp0raj3y3mxa2h1c1bnkb6wvcaz"))))
+         "0hq3304rhakx7x1v7wll7gxinmfz6561bq97qpj8jrk19rhcab75"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f
@@ -575,16 +573,17 @@ and powerline symbols, etc.")
 (define-public vim-syntastic
   (package
     (name "vim-syntastic")
-    (version "3.8.0")
+    (version "3.9.0")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/vim-syntastic/syntastic/archive/"
+       (uri (git-reference
-                           version ".tar.gz"))
+             (url "https://github.com/vim-syntastic/syntastic")
-       (file-name (string-append name "-" version ".tar.gz"))
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0wsnd9bsp5x6yiw96h1bnd1vyxdkh130hb82kyyxydgsplx92ima"))))
+         "121a1mxgfng2y5zmivyyk02mca8pyw72crivf4f1q9nhn0barf57"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f

gnu/packages/virtualization.scm

@@ -45,6 +45,7 @@
   #:use-module (gnu packages gl)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
+  #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages image)
@@ -52,6 +53,7 @@
   #:use-module (gnu packages linux)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages networking)
+  #:use-module (gnu packages package-management)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages polkit)
@@ -71,6 +73,7 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system python)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module ((guix licenses) #:select (gpl2 gpl2+ gpl3+ lgpl2.1 lgpl2.1+
                                                asl2.0))
   #:use-module (guix packages)
@@ -864,3 +867,110 @@ packaged according to the
 Container Initiative (OCI) format} and is a compliant implementation of the
 Open Container Initiative specification.")
     (license asl2.0)))
+
+(define-public umoci
+  (package
+    (name "umoci")
+    (version "0.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/openSUSE/umoci/releases/download/v"
+                    version "/umoci.tar.xz"))
+              (file-name (string-append "umoci-" version ".tar.xz"))
+              (sha256
+               (base32
+                "0hg7hs4dagj2fgymm4b4s68k1v2k2093s3jg0d94j0ixhfmyg9nd"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/openSUSE/umoci"
+       #:install-source? #f
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'unpack
+           (lambda* (#:key source import-path #:allow-other-keys)
+             ;; Unpack the tarball into 'umoci' instead of "runc-${version}".
+             (let ((dest (string-append "src/" import-path)))
+               (mkdir-p dest)
+               (invoke "tar" "-C" (string-append "src/" import-path)
+                       "--strip-components=1"
+                       "-xvf" source))))
+         (replace 'build
+           (lambda* (#:key import-path #:allow-other-keys)
+             (chdir (string-append "src/" import-path))
+             ;; TODO: build manpages with 'go-md2man'.
+             (invoke "make" "SHELL=bash")))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bindir (string-append out "/bin")))
+               (install-file "umoci" bindir)
+               #t))))))
+    (home-page "https://umo.ci/")
+    (synopsis "Tool for modifying Open Container images")
+    (description
+     "@command{umoci} is a tool that allows for high-level modification of an
+Open Container Initiative (OCI) image layout and its tagged images.")
+    (license asl2.0)))
+
+(define-public skopeo
+  (package
+    (name "skopeo")
+    (version "0.1.28")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/projectatomic/skopeo")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "068nwrr3nr27alravcq1sxyhdd5jjr24213vdgn1dqva3885gbi0"))))
+    (build-system go-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("btrfs-progs" ,btrfs-progs)
+       ("eudev" ,eudev)
+       ("libassuan" ,libassuan)
+       ("libselinux" ,libselinux)
+       ("libostree" ,libostree)
+       ("lvm2" ,lvm2)
+       ("glib" ,glib)
+       ("gpgme" ,gpgme)))
+    (arguments
+     '(#:import-path "github.com/projectatomic/skopeo"
+       #:install-source? #f
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'build
+           (lambda* (#:key import-path #:allow-other-keys)
+             (chdir (string-append "src/" import-path))
+             ;; TODO: build manpages with 'go-md2man'.
+             (invoke "make" "binary-local")))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (invoke "make" "install-binary" "install-completions"
+                       (string-append "PREFIX=" out))))))))
+    (home-page "https://github.com/projectatomic/skopeo")
+    (synopsis "Interact with container images and container image registries")
+    (description
+     "@command{skopeo} is a command line utility providing various operations
+with container images and container image registries.  It can:
+@enumerate
+
+@item Copy container images between various containers image stores,
+converting them as necessary.
+
+@item Convert a Docker schema 2 or schema 1 container image to an OCI image.
+
+@item Inspect a repository on a container registry without needlessly pulling
+the image.
+
+@item Sign and verify container images.
+
+@item Delete container images from a remote container registry.
+
+@end enumerate")
+    (license asl2.0)))

gnu/packages/web.scm

@@ -4024,14 +4024,14 @@ objects in HTML format.")
 (define-public r-rjson
   (package
     (name "r-rjson")
-    (version "0.2.19")
+    (version "0.2.20")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rjson" version))
        (sha256
         (base32
-         "1g29vp3gfbh73a5br68jydsrigia4vnr5avc84avgwl6353749jw"))))
+         "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/rjson")
     (synopsis "JSON library for R")
@@ -6117,6 +6117,11 @@ infrastructure")))
     (inherit java-eclipse-jetty-security)
     (version (package-version java-eclipse-jetty-util-9.2))
     (source (package-source java-eclipse-jetty-util-9.2))
+    (arguments
+     `(#:test-exclude
+       ;; This test fails.
+       (list "**/ConstraintTest.*")
+       ,@(package-arguments java-eclipse-jetty-security)))
     (inputs
      `(("util" ,java-eclipse-jetty-util-9.2)
        ("http" ,java-eclipse-jetty-http-9.2)
@@ -6182,6 +6187,107 @@ container.")))
        ("server" ,java-eclipse-jetty-server-9.2)
        ,@(package-inputs java-eclipse-jetty-util-9.2)))))
 
+(define-public java-eclipse-jetty-xml
+  (package
+    (inherit java-eclipse-jetty-util)
+    (name "java-eclipse-jetty-xml")
+    (arguments
+     `(#:jar-name "eclipse-jetty-xml.jar"
+       #:source-dir "src/main/java"
+       #:jdk ,icedtea-8
+       #:tests? #f; most tests require network
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'chdir
+           (lambda _
+             (chdir "jetty-xml")
+             #t)))))
+    (inputs
+     `(("java-eclipse-jetty-util" ,java-eclipse-jetty-util)))
+    (native-inputs
+     `(("java-eclipse-jetty-io" ,java-eclipse-jetty-io)
+       ,@(package-native-inputs java-eclipse-jetty-util)))))
+
+(define-public java-eclipse-jetty-xml-9.2
+  (package
+    (inherit java-eclipse-jetty-xml)
+    (version (package-version java-eclipse-jetty-util-9.2))
+    (source (package-source java-eclipse-jetty-util-9.2))
+    (arguments
+     `(#:jar-name "eclipse-jetty-xml.jar"
+       #:source-dir "src/main/java"
+       #:jdk ,icedtea-8
+       #:tests? #f; most tests require network
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'chdir
+           (lambda _
+             (chdir "jetty-xml")
+             #t)))))
+    (inputs
+     `(("java-eclipse-jetty-util-9.2" ,java-eclipse-jetty-util-9.2)
+       ,@(package-inputs java-eclipse-jetty-util-9.2)))
+    (native-inputs
+     `(("java-eclipse-jetty-io-9.2" ,java-eclipse-jetty-io-9.2)
+       ,@(package-native-inputs java-eclipse-jetty-util-9.2)))))
+
+(define-public java-eclipse-jetty-webapp
+  (package
+    (inherit java-eclipse-jetty-util)
+    (name "java-eclipse-jetty-webapp")
+    (arguments
+     `(#:jar-name "eclipse-jetty-webapp.jar"
+       #:source-dir "src/main/java"
+       #:jdk ,icedtea-8
+       ;; One test fails
+       #:test-exclude (list "**/WebAppContextTest.java")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'chdir
+           (lambda _
+             (chdir "jetty-webapp")
+             #t)))))
+    (inputs
+     `(("java-eclipse-jetty-util" ,java-eclipse-jetty-util)
+       ("java-eclipse-jetty-http" ,java-eclipse-jetty-http)
+       ("java-eclipse-jetty-server" ,java-eclipse-jetty-server)
+       ("java-eclipse-jetty-servlet" ,java-eclipse-jetty-servlet)
+       ("java-eclipse-jetty-security" ,java-eclipse-jetty-security)
+       ("java-eclipse-jetty-xml" ,java-eclipse-jetty-xml)
+       ("java-tomcat" ,java-tomcat)))
+    (native-inputs
+     `(("java-eclipse-jetty-io" ,java-eclipse-jetty-io)
+       ,@(package-native-inputs java-eclipse-jetty-util)))))
+
+(define-public java-eclipse-jetty-webapp-9.2
+  (package
+    (inherit java-eclipse-jetty-webapp)
+    (version (package-version java-eclipse-jetty-util-9.2))
+    (source (package-source java-eclipse-jetty-util-9.2))
+    (arguments
+     `(#:jar-name "eclipse-jetty-webapp.jar"
+       #:source-dir "src/main/java"
+       #:jdk ,icedtea-8
+       #:test-exclude (list "**/WebAppContextTest.java")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'chdir
+           (lambda _
+             (chdir "jetty-webapp")
+             #t)))))
+    (inputs
+     `(("java-eclipse-jetty-util-9.2" ,java-eclipse-jetty-util-9.2)
+       ("java-eclipse-jetty-http-9.2" ,java-eclipse-jetty-http-9.2)
+       ("java-eclipse-jetty-server-9.2" ,java-eclipse-jetty-server-9.2)
+       ("java-eclipse-jetty-servlet-9.2" ,java-eclipse-jetty-servlet-9.2)
+       ("java-eclipse-jetty-security-9.2" ,java-eclipse-jetty-security-9.2)
+       ("java-eclipse-jetty-xml-9.2" ,java-eclipse-jetty-xml-9.2)
+       ("java-tomcat" ,java-tomcat)
+       ,@(package-inputs java-eclipse-jetty-util-9.2)))
+    (native-inputs
+     `(("java-eclipse-jetty-io-9.2" ,java-eclipse-jetty-io-9.2)
+       ,@(package-native-inputs java-eclipse-jetty-util-9.2)))))
+
 (define-public java-jsoup
   (package
     (name "java-jsoup")

gnu/packages/wine.scm

@@ -223,7 +223,7 @@ integrate Windows applications into your desktop.")
 (define-public wine-staging-patchset-data
   (package
    (name "wine-staging-patchset-data")
-   (version "3.9")
+   (version "3.10")
    (source
     (origin
      (method url-fetch)
@@ -232,7 +232,7 @@ integrate Windows applications into your desktop.")
      (file-name (string-append name "-" version ".zip"))
      (sha256
       (base32
-       "0akccqrp1ymjrra2c99f6hxlaa77jyihfs3q8x93vkgb9c0lq5xx"))))
+       "14rf3g9szxygbd6ypg6zbqw1h84rn8gqgrzwi607xwgh8wm59sli"))))
    (build-system trivial-build-system)
    (native-inputs
     `(("bash" ,bash)
@@ -279,7 +279,7 @@ integrate Windows applications into your desktop.")
               (file-name (string-append name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0ddphvlp9lsjyqc6zckinc36bggpkg925v0x2vqr8nkdjs0w5bfc"))))
+                "1df6g8g5nfb4ca218m78giqp3k1fmv0grv26387rbn3wkk3mql6p"))))
     (inputs `(("autoconf" ,autoconf) ; for autoreconf
               ("gtk+" ,gtk+)
               ("libva" ,libva)

gnu/packages/xdisorg.scm

@@ -531,7 +531,7 @@ selection's dimensions to stdout.")
 (define-public maim
   (package
     (name "maim")
-    (version "5.5.1")
+    (version "5.5.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -540,7 +540,7 @@ selection's dimensions to stdout.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1dvw0axnr9hhjg6zdcq9lwvaq0x7vrzlz00p8n3hj25qzsi4z5as"))))
+                "14zdhsx1cndg5m8wbv1rqmza7wgknwfj5h0knzxg3p2jkjw66i95"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f))            ; no "check" target

gnu/packages/xml.scm

@@ -263,13 +263,11 @@ the @code{Graph} class and write it out in a specific file format.")
                                     (getenv "PERL5LIB")))
              #t)))))
     (native-inputs
-     `(("perl-datetime" ,perl-datetime)
      ;; TODO package: perl-datetime-format-atom
-       ("perl-html-tagset" ,perl-html-tagset)
+     `(("perl-html-tagset" ,perl-html-tagset)
        ("perl-module-build-tiny" ,perl-module-build-tiny)
-       ("perl-module-install" ,perl-module-install)
+       ("perl-module-install" ,perl-module-install)))
-       ("perl-xml-xpath" ,perl-xml-xpath)))
+    (propagated-inputs
-    (inputs
      `(("perl-class-data-inheritable" ,perl-class-data-inheritable)
        ("perl-datetime" ,perl-datetime)
        ("perl-datetime-timezone" ,perl-datetime-timezone)
@@ -418,14 +416,14 @@ XML parser and the high performance DOM implementation.")
 (define-public perl-xml-libxml-simple
   (package
     (name "perl-xml-libxml-simple")
-    (version "0.97")
+    (version "0.99")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cpan/authors/id/M/MA/MARKOV/"
                                   "XML-LibXML-Simple-" version ".tar.gz"))
               (sha256
                (base32
-                "1g8nlk3zdz2cclxf7azvsb3jfxmvy6ml8wmj774k4qjqcsqmzk0w"))))
+                "0i4ybiqdnvnbfxqslw2y392kvy7i752dl8n99bqiqv5kzk4lbzhl"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-file-slurp-tiny" ,perl-file-slurp-tiny)
@@ -815,18 +813,18 @@ RSS 0.91, RSS 1.0, RSS 2.0, Atom")
 (define-public perl-xml-xpath
   (package
     (name "perl-xml-xpath")
-    (version "1.40")
+    (version "1.42")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cpan/authors/id/M/MA/MANWAR/"
                                   "XML-XPath-" version ".tar.gz"))
               (sha256
                (base32
-                "07pa0bl42jka8mj7jshjynx8vpfh8b4cdyiv4zlkqvkqz98nzxib"))))
+                "04mm91kxav598ax7nlg81dhnvanwvg6bkf30l0cgkmga5iyccsly"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-path-tiny" ,perl-path-tiny)))
-    (inputs
+    (propagated-inputs
      `(("perl-xml-parser" ,perl-xml-parser)))
     (home-page "http://search.cpan.org/dist/XML-XPath")
     (synopsis "Parse and evaluate XPath statements")

gnu/packages/xorg.scm

@@ -15,6 +15,7 @@
 ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -5855,6 +5856,34 @@ perl programs to display windows and graphics on X11 servers.")
     ;; for details)."
     (license license:perl-license)))
 
+(define-public perl-x11-protocol-other
+  (package
+    (name "perl-x11-protocol-other")
+    (version "30")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/K/KR/KRYDE/X11-Protocol-Other-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "1mambi57cdkj82wiw1l8y2f70a60qsamdas0165hlj10drryfgrj"))))
+    (build-system perl-build-system)
+    (native-inputs
+     `(("perl-encode-hanextra" ,perl-encode-hanextra)
+       ("perl-module-util" ,perl-module-util)))
+    (propagated-inputs
+     `(("perl-x11-protocol" ,perl-x11-protocol)))
+    (home-page "http://search.cpan.org/dist/X11-Protocol-Other/")
+    (synopsis "Miscellaneous helpers for @code{X11::Protocol} connections")
+    (description
+     "@code{X11::Protocol::Other} contains window manager related functions for
+use by client programs, as per the @dfn{ICCCM} (Inter-Client Communication
+Conventions Manual) and some of the @dfn{EWMH}
+(Extended Window Manager Hints).")
+    (license license:gpl3+)))
+
 (define-public xcompmgr
   (package
     (name "xcompmgr")

gnu/services/base.scm

@@ -1592,8 +1592,9 @@ failed to register hydra.gnu.org public key: ~a~%" status))))))))
 
                            (call-with-output-file #$output
                              (lambda (port)
-                               (write (call-with-input-file "graph"
+                               (write (map store-info-item
-                                        read-reference-graph)
+                                           (call-with-input-file "graph"
+                                             read-reference-graph))
                                       port)))))
                      #:options `(#:local-build? #f
                                  #:references-graphs (("graph" ,item))))

gnu/services/networking.scm

@@ -6,6 +6,7 @@
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -608,7 +609,7 @@ demand.")))
             (call-with-output-file #$output
               (lambda (port)
                 (display "\
-# The beginning was automatically added.
+### These lines were generated from your system configuration:
 User tor
 DataDirectory /var/lib/tor
 Log notice syslog\n" port)
@@ -628,6 +629,9 @@ HiddenServicePort ~a ~a~%"
                                      (cons name mapping)))
                                   services))
 
+                (display "\
+### End of automatically generated lines.\n\n" port)
+
                 ;; Append the user's config file.
                 (call-with-input-file #$config-file
                   (lambda (input)

gnu/services/web.scm

@@ -77,6 +77,7 @@
             nginx-configuration-upstream-blocks
             nginx-configuration-server-names-hash-bucket-size
             nginx-configuration-server-names-hash-bucket-max-size
+            nginx-configuration-extra-content
             nginx-configuration-file
 
             <nginx-server-configuration>
@@ -431,6 +432,8 @@
                                  (default #f))
   (server-names-hash-bucket-max-size nginx-configuration-server-names-hash-bucket-max-size
                                      (default #f))
+  (extra-content nginx-configuration-extra-content
+                 (default ""))
   (file          nginx-configuration-file         ;#f | string | file-like
                  (default #f)))
 
@@ -521,7 +524,8 @@ of index files."
                 (nginx log-directory run-directory
                  server-blocks upstream-blocks
                  server-names-hash-bucket-size
-                 server-names-hash-bucket-max-size)
+                 server-names-hash-bucket-max-size
+                 extra-content)
    (apply mixed-text-file "nginx.conf"
           (flatten
            "user nginx nginx;\n"
@@ -550,7 +554,8 @@ of index files."
            "\n"
            (map emit-nginx-upstream-config upstream-blocks)
            (map emit-nginx-server-config server-blocks)
-           "}\n"
+           extra-content
+           "\n}\n"
            "events {}\n"))))
 
 (define %nginx-accounts

gnu/system.scm

@@ -602,7 +602,7 @@ directory."
 # because they would require combining both profiles.
 # FIXME: See <http://bugs.gnu.org/20255>.
 export MANPATH=$HOME/.guix-profile/share/man:/run/current-system/profile/share/man
-export INFOPATH=$HOME/.config/guix/current/share/info:$HOME/.guix-profile/share/info:/run/current-system/profile/share/info
+export INFOPATH=$HOME/.guix-profile/share/info:/run/current-system/profile/share/info
 export XDG_DATA_DIRS=$HOME/.guix-profile/share:/run/current-system/profile/share
 export XDG_CONFIG_DIRS=$HOME/.guix-profile/etc/xdg:/run/current-system/profile/etc/xdg
 
@@ -630,7 +630,8 @@ then
   export `cat /etc/environment | cut -d= -f1`
 fi
 
-for profile in \"$HOME/.config/guix/current\" \"$HOME/.guix-profile\"
+# Arrange so that ~/.config/guix/current comes first.
+for profile in \"$HOME/.guix-profile\" \"$HOME/.config/guix/current\"
 do
   if [ -f \"$profile/etc/profile\" ]
   then
@@ -644,6 +645,9 @@ do
   fi
 done
 
+# Arrange so that ~/.config/guix/current/share/info comes first.
+export INFOPATH=\"$HOME/.config/guix/current/share/info:$INFOPATH\"
+
 # Set the umask, notably for users logging in via 'lsh'.
 # See <http://bugs.gnu.org/22650>.
 umask 022

gnu/system/file-systems.scm

@@ -194,10 +194,15 @@
 ;; differs from user to user.
 (define (%store-prefix)
   "Return the store prefix."
-  (cond ((resolve-module '(guix store) #:ensure #f)
+  ;; Note: If we have (guix store database) in the search path and we do *not*
-         =>
+  ;; have (guix store) proper, 'resolve-module' returns an empty (guix store)
+  ;; with one sub-module.
+  (cond ((and=> (resolve-module '(guix store) #:ensure #f)
                 (lambda (store)
-           ((module-ref store '%store-prefix))))
+                  (module-variable store '%store-prefix)))
+         =>
+         (lambda (variable)
+           ((variable-ref variable))))
         ((getenv "NIX_STORE")
          => identity)
         (else

gnu/system/install.scm

@@ -54,7 +54,8 @@
             novena-installation-os
             pine64-plus-installation-os
             rk3399-puma-installation-os
-            wandboard-installation-os))
+            wandboard-installation-os
+            os-with-u-boot))
 
 ;;; Commentary:
 ;;;
@@ -386,6 +387,19 @@ You have been warned.  Thanks for being so brave.\x1b[0m
                      nvi                          ;:wq!
                      %base-packages))))
 
+(define* (os-with-u-boot os board #:key (bootloader-target "/dev/mmcblk0")
+                         (triplet "arm-linux-gnueabihf"))
+  "Given OS, amend it with the u-boot bootloader for BOARD,
+installed to BOOTLOADER-TARGET (a drive), compiled for TRIPLET.
+
+If you want a serial console, make sure to specify one in your
+operating-system's kernel-arguments (\"console=ttyS0\" or similar)."
+  (operating-system (inherit os)
+    (bootloader (bootloader-configuration
+                 (bootloader (bootloader (inherit u-boot-bootloader)
+                              (package (make-u-boot-package board triplet))))
+                 (target bootloader-target)))))
+
 (define* (embedded-installation-os bootloader bootloader-target tty
                                    #:key (extra-modules '()))
   "Return an installation os for embedded systems.

gnu/system/mapped-devices.scm

@@ -32,7 +32,8 @@
   #:use-module (gnu system uuid)
   #:autoload   (gnu build file-systems) (find-partition-by-luks-uuid)
   #:autoload   (gnu build linux-modules)
-                 (device-module-aliases matching-modules known-module-aliases)
+                 (device-module-aliases matching-modules known-module-aliases
+                  normalize-module-name)
   #:autoload   (gnu packages cryptsetup) (cryptsetup-static)
   #:autoload   (gnu packages linux) (mdadm-static)
   #:use-module (srfi srfi-1)
@@ -129,8 +130,13 @@ DEVICE must be a \"/dev\" file name."
   (when aliases
     (let ((modules  (delete-duplicates
                      (append-map (cut matching-modules <> aliases)
-                                (device-module-aliases device)))))
+                                 (device-module-aliases device))))
-      (unless (every (cute member <> linux-modules) modules)
+
+          ;; Module names (not file names) are supposed to use underscores
+          ;; instead of hyphens.  MODULES is a list of module names, whereas
+          ;; LINUX-MODULES is file names without '.ko', so normalize them.
+          (provided (map normalize-module-name linux-modules)))
+      (unless (every (cut member <> provided) modules)
         (raise (condition
                 (&message
                  (message (format #f (G_ "you may need these modules \

gnu/system/vm.scm

@@ -34,6 +34,7 @@
   #:use-module (guix utils)
   #:use-module (guix hash)
   #:use-module (guix base32)
+  #:use-module ((guix self) #:select (make-config.scm))
 
   #:use-module ((gnu build vm)
                 #:select (qemu-command))
@@ -50,7 +51,6 @@
   #:use-module (gnu packages disk)
   #:use-module (gnu packages zile)
   #:use-module (gnu packages linux)
-  #:use-module (gnu packages package-management)
   #:use-module ((gnu packages make-bootstrap)
                 #:select (%guile-static-stripped))
   #:use-module (gnu packages admin)
@@ -116,6 +116,19 @@
           (options "trans=virtio")
           (check? #f))))
 
+(define not-config?
+  ;; Select (guix …) and (gnu …) modules, except (guix config).
+  (match-lambda
+    (('guix 'config) #f)
+    (('guix rest ...) #t)
+    (('gnu rest ...) #t)
+    (rest #f)))
+
+(define guile-sqlite3&co
+  ;; Guile-SQLite3 and its propagated inputs.
+  (cons guile-sqlite3
+        (package-transitive-propagated-inputs guile-sqlite3)))
+
 (define* (expression->derivation-in-linux-vm name exp
                                              #:key
                                              (system (%current-system))
@@ -151,12 +164,28 @@ based on the size of the closure of REFERENCES-GRAPHS.
 When REFERENCES-GRAPHS is true, it must be a list of file name/store path
 pairs, as for `derivation'.  The files containing the reference graphs are
 made available under the /xchg CIFS share."
+  (define config
+    ;; (guix config) module for consumption by (guix gcrypt).
+    (make-config.scm #:libgcrypt libgcrypt))
+
+  (define user-builder
+    (program-file "builder-in-linux-vm" exp))
+
+  (define loader
+    ;; Invoke USER-BUILDER instead using 'primitive-load'.  The reason for
+    ;; this is to allow USER-BUILDER to dlopen stuff by using a full-featured
+    ;; Guile, which it couldn't do using the statically-linked guile used in
+    ;; the initrd.  See example at
+    ;; <https://lists.gnu.org/archive/html/guix-devel/2017-10/msg00233.html>.
+    (program-file "linux-vm-loader"
+                  ;; When USER-BUILDER succeeds, reboot (indicating a
+                  ;; success), otherwise die, which causes a kernel panic
+                  ;; ("Attempted to kill init!").
+                  #~(when (zero? (system* #$user-builder))
+                      (reboot))))
+
   (mlet* %store-monad
-      ((user-builder (gexp->file "builder-in-linux-vm" exp))
+      ((initrd       (if initrd                   ; use the default initrd?
-       (loader       (gexp->file "linux-vm-loader"
-                                 #~(primitive-load #$user-builder)))
-       (coreutils -> (canonical-package coreutils))
-       (initrd       (if initrd                   ; use the default initrd?
                          (return initrd)
                          (base-initrd file-systems
                                       #:on-error 'backtrace
@@ -166,13 +195,17 @@ made available under the /xchg CIFS share."
 
     (define builder
       ;; Code that launches the VM that evaluates EXP.
-      (with-imported-modules (source-module-closure '((guix build utils)
+      (with-extensions guile-sqlite3&co
-                                                      (gnu build vm)))
+        (with-imported-modules `(,@(source-module-closure
+                                    '((guix build utils)
+                                      (gnu build vm))
+                                    #:select? not-config?)
+                                 ((guix config) => ,config))
           #~(begin
               (use-modules (guix build utils)
                            (gnu build vm))
 
-            (let* ((inputs  '#$(list qemu coreutils))
+              (let* ((inputs  '#$(list qemu (canonical-package coreutils)))
                      (linux   (string-append #$linux "/"
                                              #$(system-linux-image-file-name)))
                      (initrd  (string-append #$initrd "/initrd"))
@@ -199,7 +232,7 @@ made available under the /xchg CIFS share."
                                   #:target-arm32? #$(target-arm32?)
                                   #:disk-image-format #$disk-image-format
                                   #:disk-image-size size
-                                #:references-graphs graphs)))))
+                                  #:references-graphs graphs))))))
 
     (gexp->derivation name builder
                       ;; TODO: Require the "kvm" feature.
@@ -222,19 +255,33 @@ made available under the /xchg CIFS share."
   "Return a bootable, stand-alone iso9660 image.
 
 INPUTS is a list of inputs (as for packages)."
+  (define config
+    (make-config.scm #:libgcrypt libgcrypt))
+
+  (define schema
+    (and register-closures?
+         (local-file (search-path %load-path
+                                  "guix/store/schema.sql"))))
+
   (expression->derivation-in-linux-vm
    name
-   (with-imported-modules (source-module-closure '((gnu build vm)
+   (with-extensions guile-sqlite3&co
-                                                   (guix build utils)))
+     (with-imported-modules `(,@(source-module-closure '((gnu build vm)
+                                                         (guix store database)
+                                                         (guix build utils))
+                                                       #:select? not-config?)
+                              ((guix config) => ,config))
        #~(begin
            (use-modules (gnu build vm)
+                        (guix store database)
                         (guix build utils))
 
+           (sql-schema #$schema)
+
            (let ((inputs
                   '#$(append (list qemu parted e2fsprogs dosfstools xorriso)
                              (map canonical-package
-                                (list sed grep coreutils findutils gawk))
+                                  (list sed grep coreutils findutils gawk))))
-                           (if register-closures? (list guix) '())))
 
 
                  (graphs     '#$(match inputs
@@ -257,8 +304,7 @@ INPUTS is a list of inputs (as for packages)."
                                  #:closures graphs
                                  #:volume-id #$file-system-label
                                  #:volume-uuid #$(and=> file-system-uuid
-                                                      uuid-bytevector))
+                                                        uuid-bytevector))))))
-           (reboot))))
    #:system system
 
    ;; Keep a local file system for /tmp so that we can populate it directly as
@@ -301,23 +347,37 @@ INPUTS is a list of inputs (as for packages).  When COPY-INPUTS? is true, copy
 all of INPUTS into the image being built.  When REGISTER-CLOSURES? is true,
 register INPUTS in the store database of the image so that Guix can be used in
 the image."
+  (define config
+    (make-config.scm #:libgcrypt libgcrypt))
+
+  (define schema
+    (and register-closures?
+         (local-file (search-path %load-path
+                                  "guix/store/schema.sql"))))
+
   (expression->derivation-in-linux-vm
    name
-   (with-imported-modules (source-module-closure '((gnu build bootloader)
+   (with-extensions guile-sqlite3&co
-                                                   (gnu build vm)
+     (with-imported-modules `(,@(source-module-closure '((gnu build vm)
-                                                   (guix build utils)))
+                                                         (gnu build bootloader)
+                                                         (guix store database)
+                                                         (guix build utils))
+                                                       #:select? not-config?)
+                              ((guix config) => ,config))
        #~(begin
            (use-modules (gnu build bootloader)
                         (gnu build vm)
+                        (guix store database)
                         (guix build utils)
                         (srfi srfi-26)
                         (ice-9 binary-ports))
 
+           (sql-schema #$schema)
+
            (let ((inputs
                   '#$(append (list qemu parted e2fsprogs dosfstools)
                              (map canonical-package
-                                (list sed grep coreutils findutils gawk))
+                                  (list sed grep coreutils findutils gawk))))
-                           (if register-closures? (list guix) '())))
 
                  ;; This variable is unused but allows us to add INPUTS-TO-COPY
                  ;; as inputs.
@@ -384,8 +444,7 @@ the image."
                                      #:bootcfg-location
                                      #$(bootloader-configuration-file bootloader)
                                      #:bootloader-installer
-                                   #$(bootloader-installer bootloader))
+                                     #$(bootloader-installer bootloader)))))))
-             (reboot)))))
    #:system system
    #:make-disk-image? #t
    #:disk-image-size disk-image-size
@@ -403,49 +462,41 @@ makes sense when you want to build a GuixSD Docker image that has Guix
 installed inside of it.  If you don't need Guix (e.g., your GuixSD Docker
 image just contains a web server that is started by the Shepherd), then you
 should set REGISTER-CLOSURES? to #f."
-  (define not-config?
-    (match-lambda
-      (('guix 'config) #f)
-      (('guix rest ...) #t)
-      (('gnu rest ...) #t)
-      (rest #f)))
-
   (define config
     ;; (guix config) module for consumption by (guix gcrypt).
-    (scheme-file "gcrypt-config.scm"
+    (make-config.scm #:libgcrypt libgcrypt))
-                 #~(begin
-                     (define-module (guix config)
-                       #:export (%libgcrypt))
 
-                     ;; XXX: Work around <http://bugs.gnu.org/15602>.
+  (define schema
-                     (eval-when (expand load eval)
+    (and register-closures?
-                       (define %libgcrypt
+         (local-file (search-path %load-path
-                         #+(file-append libgcrypt "/lib/libgcrypt"))))))
+                                  "guix/store/schema.sql"))))
 
   (mlet %store-monad ((os-drv (operating-system-derivation os #:container? #t))
                       (name -> (string-append name ".tar.gz"))
                       (graph -> "system-graph"))
     (define build
-      (with-extensions (list guile-json)          ;for (guix docker)
+      (with-extensions (cons guile-json          ;for (guix docker)
+                             guile-sqlite3&co)   ;for (guix store database)
         (with-imported-modules `(,@(source-module-closure
                                     '((guix docker)
+                                      (guix store database)
                                       (guix build utils)
+                                      (guix build store-copy)
                                       (gnu build vm))
                                     #:select? not-config?)
-                                 (guix build store-copy)
                                  ((guix config) => ,config))
           #~(begin
               (use-modules (guix docker)
                            (guix build utils)
                            (gnu build vm)
                            (srfi srfi-19)
-                           (guix build store-copy))
+                           (guix build store-copy)
+                           (guix store database))
 
-              (let* ((inputs '#$(append (list tar)
+              ;; Set the SQL schema location.
-                                        (if register-closures?
+              (sql-schema #$schema)
-                                            (list guix)
+
-                                            '())))
+              (let* (;; This initializer requires elevated privileges that are
-                     ;; This initializer requires elevated privileges that are
                      ;; not normally available in the build environment (e.g.,
                      ;; it needs to create device nodes).  In order to obtain
                      ;; such privileges, we run it as root in a VM.
@@ -460,33 +511,22 @@ should set REGISTER-CLOSURES? to #f."
                      ;; lack of privileges if we use a root-directory that is on
                      ;; a file system that is shared with the host (e.g., /tmp).
                      (root-directory "/guixsd-system-root"))
-                (set-path-environment-variable "PATH" '("bin" "sbin") inputs)
+                (set-path-environment-variable "PATH" '("bin" "sbin") '(#+tar))
                 (mkdir root-directory)
                 (initialize root-directory)
                 (build-docker-image
                  (string-append "/xchg/" #$name) ;; The output file.
                  (cons* root-directory
-                        (call-with-input-file (string-append "/xchg/" #$graph)
+                        (map store-info-item
-                          read-reference-graph))
+                             (call-with-input-file
+                                 (string-append "/xchg/" #$graph)
+                               read-reference-graph)))
                  #$os-drv
                  #:compressor '(#+(file-append gzip "/bin/gzip") "-9n")
                  #:creation-time (make-time time-utc 0 1)
                  #:transformations `((,root-directory -> ""))))))))
     (expression->derivation-in-linux-vm
-     name
+     name build
-     ;; The VM's initrd Guile doesn't support dlopen, but our "build" gexp
-     ;; needs to be run by a Guile that can dlopen libgcrypt.  The following
-     ;; hack works around that problem by putting the "build" gexp into an
-     ;; executable script (created by program-file) which, when executed, will
-     ;; run using a Guile that supports dlopen.  That way, the VM's initrd
-     ;; Guile can just execute it via invoke, without using dlopen.  See:
-     ;; https://lists.gnu.org/archive/html/guix-devel/2017-10/msg00233.html
-     (with-imported-modules `((guix build utils))
-       #~(begin
-           (use-modules (guix build utils))
-           ;; If we use execl instead of invoke here, the VM will crash with a
-           ;; kernel panic.
-           (invoke #$(program-file "build-docker-image" build))))
      #:make-disk-image? #f
      #:single-file-output? #t
      #:references-graphs `((,graph ,os-drv)))))

gnu/tests/admin.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017 Christopher Baines <mail@cbaines.net>
+;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -74,13 +75,11 @@ HTTP-PORT."
 
           (test-begin "tailon")
 
-          (test-eq "service running"
+          (test-assert "service running"
-            'running!
             (marionette-eval
              '(begin
                 (use-modules (gnu services herd))
-                (start-service 'tailon)
+                (start-service 'tailon))
-                'running!)
              marionette))
 
           (define* (retry-on-error f #:key times delay)

gnu/tests/base.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -517,13 +518,11 @@ in a loop.  See <http://bugs.gnu.org/26931>.")
 
           (test-begin "mcron")
 
-          (test-eq "service running"
+          (test-assert "service running"
-            'running!
             (marionette-eval
              '(begin
                 (use-modules (gnu services herd))
-                (start-service 'mcron)
+                (start-service 'mcron))
-                'running!)
              marionette))
 
           ;; Make sure root's mcron job runs, has its cwd set to "/root", and
@@ -619,32 +618,43 @@ in a loop.  See <http://bugs.gnu.org/26931>.")
 
           (test-begin "avahi")
 
-          (test-assert "wait for services"
+          (test-assert "nscd PID file is created"
             (marionette-eval
              '(begin
                 (use-modules (gnu services herd))
+                (start-service 'nscd))
+             marionette))
 
-                (start-service 'nscd)
+          (test-assert "nscd is listening on its socket"
-
+            (marionette-eval
              ;; XXX: Work around a race condition in nscd: nscd creates its
              ;; PID file before it is listening on its socket.
-                (let ((sock (socket PF_UNIX SOCK_STREAM 0)))
+             '(let ((sock (socket PF_UNIX SOCK_STREAM 0)))
                 (let try ()
                   (catch 'system-error
                     (lambda ()
                       (connect sock AF_UNIX "/var/run/nscd/socket")
                       (close-port sock)
-                        (format #t "nscd is ready~%"))
+                      (format #t "nscd is ready~%")
+                      #t)
                     (lambda args
                       (format #t "waiting for nscd...~%")
                       (usleep 500000)
                       (try)))))
+             marionette))
 
-                ;; Wait for the other useful things.
+          (test-assert "avahi is running"
-                (start-service 'avahi-daemon)
+            (marionette-eval
-                (start-service 'networking)
+             '(begin
+                (use-modules (gnu services herd))
+                (start-service 'avahi-daemon))
+             marionette))
 
-                #t)
+          (test-assert "network is up"
+            (marionette-eval
+             '(begin
+                (use-modules (gnu services herd))
+                (start-service 'networking))
              marionette))
 
           (test-equal "avahi-resolve-host-name"

gnu/tests/dict.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -84,13 +85,11 @@
           (test-begin "dicod")
 
           ;; Wait for the service to be started.
-          (test-eq "service is running"
+          (test-assert "service is running"
-            'running!
             (marionette-eval
              '(begin
                 (use-modules (gnu services herd))
-                (start-service 'dicod)
+                (start-service 'dicod))
-                'running!)
              marionette))
 
           ;; Wait until dicod is actually listening.

gnu/tests/mail.scm

@@ -3,6 +3,7 @@
 ;;; Copyright © 2017 Carlo Zancanaro <carlo@zancanaro.id.au>
 ;;; Copyright © 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
+;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -84,8 +85,7 @@ accept from any for local deliver to mbox
             (marionette-eval
              '(begin
                 (use-modules (gnu services herd))
-                (start-service 'smtpd)
+                (start-service 'smtpd))
-                #t)
              marionette))
 
           (test-assert "mbox is empty"
@@ -224,8 +224,7 @@ acl_check_data:
             (marionette-eval
              '(begin
                 (use-modules (gnu services herd))
-                (start-service 'exim)
+                (start-service 'exim))
-                #t)
              marionette))
 
           (sleep 1) ;; give the service time to start talking
@@ -330,13 +329,11 @@ Subject: Hello Nice to meet you!")
           (test-begin "dovecot")
 
           ;; Wait for dovecot to be up and running.
-          (test-eq "dovecot running"
+          (test-assert "dovecot running"
-            'running!
             (marionette-eval
              '(begin
                 (use-modules (gnu services herd))
-                (start-service 'dovecot)
+                (start-service 'dovecot))
-                'running!)
              marionette))
 
           ;; Check Dovecot service's PID.