Merge branch 'master' into staging

.dir-locals.el

@@ -37,7 +37,7 @@
    (eval . (put 'with-file-lock 'scheme-indent-function 1))
    (eval . (put 'with-file-lock/no-wait 'scheme-indent-function 1))
    (eval . (put 'with-profile-lock 'scheme-indent-function 1))
-   (eval . (put 'with-writable-file 'scheme-indent-function 1))
+   (eval . (put 'with-writable-file 'scheme-indent-function 2))
 
    (eval . (put 'package 'scheme-indent-function 0))
    (eval . (put 'package/inherit 'scheme-indent-function 1))
@@ -90,9 +90,9 @@
    (eval . (put 'let-system 'scheme-indent-function 1))
 
    (eval . (put 'with-database 'scheme-indent-function 2))
-   (eval . (put 'call-with-transaction 'scheme-indent-function 2))
+   (eval . (put 'call-with-transaction 'scheme-indent-function 1))
    (eval . (put 'with-statement 'scheme-indent-function 3))
-   (eval . (put 'call-with-retrying-transaction 'scheme-indent-function 2))
+   (eval . (put 'call-with-retrying-transaction 'scheme-indent-function 1))
    (eval . (put 'call-with-savepoint 'scheme-indent-function 1))
    (eval . (put 'call-with-retrying-savepoint 'scheme-indent-function 1))
 

.gitignore

@@ -74,6 +74,7 @@
 /etc/guix-publish.conf
 /etc/guix-publish.service
 /etc/init.d/guix-daemon
+/etc/openrc/guix-daemon
 /guix-daemon
 /guix/config.scm
 /libformat.a

Makefile.am

@@ -571,6 +571,7 @@ EXTRA_DIST +=						\
   build-aux/hydra/guix-modular.scm			\
   build-aux/cuirass/gnu-system.scm			\
   build-aux/cuirass/guix-modular.scm			\
+  build-aux/cuirass/hurd-manifest.scm			\
   build-aux/cuirass/hydra-to-cuirass.scm		\
   build-aux/check-final-inputs-self-contained.scm	\
   build-aux/check-channel-news.scm			\
@@ -833,8 +834,7 @@ release: dist-with-updated-version
 	      -v1 --no-grafts --fallback
 	for system in $(GUIX_SYSTEM_SUPPORTED_SYSTEMS) ; do				\
 	  image=`$(top_builddir)/pre-inst-env						\
-	    guix system disk-image							\
+	    guix system disk-image -t iso9660                                           \
-	    --file-system-type=iso9660							\
 	    --label="GUIX_$${system}_$(VERSION)"					\
             --system=$$system --fallback						\
 	    gnu/system/install.scm` ;							\

build-aux/cuirass/hurd-manifest.scm

@@ -0,0 +1,74 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+;;; Commentary:
+;;;
+;;; This file defines a manifest with a selection of packages for Cuirass to
+;;; build for GNU/Hurd.
+;;;
+;;; Code:
+
+(use-modules (gnu)
+             (gnu system hurd)
+             (guix packages)
+             (guix utils)
+             (ice-9 match)
+             (srfi srfi-1))
+
+(use-package-modules
+ base commencement compression file gawk gdb gettext guile
+ hurd less m4 package-management python ssh version-control)
+
+(define (input->package input)
+  "Return the INPUT as package, or #f."
+  (match input
+    ((label (and (? package?) package))
+     package)
+    ((label (and (? package?) package . output))
+     (cons package output))
+    (_ #f)))
+
+(define guix-dependencies
+  (filter-map input->package
+              (fold alist-delete (package-direct-inputs guix)
+                    '("glibc-utf8-locales" "graphviz" "po4a"))))
+
+(define (package-without-tests p)
+  (package/inherit p
+    (arguments
+     (substitute-keyword-arguments (package-arguments p)
+       ((#:tests? _ #f) #f)))))
+
+(packages->manifest
+ (cons*
+  ;; where it all starts
+  hello
+
+  ;; development utililities
+  diffutils file findutils gawk grep gzip less m4 openssh-sans-x tar xz
+
+  ;; development packages
+  gcc-toolchain gdb-minimal git-minimal gnu-make
+
+  ;; guix environment guix --without-tests=python-minimal --without-tests=gettext-minimal
+  (package-without-tests gettext-minimal)
+  (package-without-tests python-minimal)
+
+  (append
+   guix-dependencies
+   (delete guile-3.0 %base-packages/hurd))))

build-aux/hydra/guix-modular.scm

@@ -43,17 +43,25 @@ for SYSTEM.  Use VERSION as the version identifier."
     (define build
       (primitive-load (string-append source "/build-aux/build-self.scm")))
 
-    `((derivation . ,(derivation-file-name
+    (let ((drv (run-with-store store
-                      (run-with-store store
                  (build source #:version version #:system system
                         #:pull-version 1
-                               #:guile-version "2.2")))) ;the latest 2.2.x
+                        #:guile-version "2.2"))))
+      `((derivation . ,(derivation-file-name drv)) ;the latest 2.2.x
+        (log . ,(log-file store (derivation-file-name drv)))
+        (outputs . ,(filter-map (lambda (res)
+                                  (match res
+                                    ((name . path)
+                                     `(,name . ,path))))
+                                (derivation->output-paths drv)))
+        (nix-name . ,(derivation-name drv))
+        (system . ,(derivation-system drv))
         (description . "Modular Guix")
         (long-description
          . "This is the modular Guix package as produced by 'guix pull'.")
         (license . ,license:gpl3+)
         (home-page . ,%guix-home-page-url)
-      (maintainers . (,%guix-bug-report-address)))))
+        (maintainers . (,%guix-bug-report-address))))))
 
 (define (hydra-jobs store arguments)
   "Return Hydra jobs."

doc/contributing.texi

@@ -353,7 +353,7 @@ Once your package builds correctly, please send us a patch
 (@pxref{Submitting Patches}).  Well, if you need help, we will be happy to
 help you too.  Once the patch is committed in the Guix repository, the
 new package automatically gets built on the supported platforms by
-@url{@value{SUBSTITUTE-SERVER}, our continuous integration system}.
+@url{@value{SUBSTITUTE-URL}, our continuous integration system}.
 
 @cindex substituter
 Users can obtain the new package definition simply by running
@@ -1016,7 +1016,7 @@ changes).  This branch is intended to be merged in @code{master} every
 6 months or so.
 @end table
 
-All these branches are @uref{@value{SUBSTITUTE-SERVER},
+All these branches are @uref{@value{SUBSTITUTE-URL},
 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

etc/completion/bash/guix

@@ -28,7 +28,8 @@ _guix_complete_command ()
     then
 	# Cache the list of commands to speed things up.
 	_guix_commands="$(guix --help 2> /dev/null  \
-                                     | grep '^  ' | cut -c 2-)"
+                                     | grep '^    ' \
+				     | sed '-es/^ *\([a-z-]\+\).*$/\1/g')"
     fi
     COMPREPLY=($(compgen -W "$_guix_commands" -- "$word_at_point"))
 }
@@ -181,7 +182,7 @@ _guix_complete ()
 	*)
 	    if _guix_is_command "package"
 	    then
-		if _guix_is_dash_L || _guix_is_dash_m
+		if _guix_is_dash_L || _guix_is_dash_m || _guix_is_dash_p
 		then
 		    _guix_complete_file
 		elif _guix_is_removing

etc/guix-install.sh

@@ -4,6 +4,7 @@
 # Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 # Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 # Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
+# Copyright © 2020 Morgan Smith <Morgan.J.Smith@outlook.com>
 #
 # This file is part of GNU Guix.
 #
@@ -150,6 +151,10 @@ chk_init_sys()
         _msg "${INF}init system is: sysv-init"
         INIT_SYS="sysv-init"
         return 0
+    elif [[ $(openrc --version 2>/dev/null) =~ \(OpenRC\) ]]; then
+        _msg "${INF}init system is: OpenRC"
+        INIT_SYS="openrc"
+        return 0
     else
         INIT_SYS="NA"
         _err "${ERR}Init system could not be detected."
@@ -212,7 +217,7 @@ guix_get_bin_list()
         | sort -Vu)")
 
     latest_ver="$(echo "$bin_ver_ls" \
-                       | grep -oP "([0-9]{1,2}\.){2}[0-9]{1,2}" \
+                       | grep -oE "([0-9]{1,2}\.){2}[0-9]{1,2}" \
                        | tail -n1)"
 
     default_ver="guix-binary-${latest_ver}.${ARCH_OS}"
@@ -268,8 +273,7 @@ sys_create_store()
     _debug "--- [ $FUNCNAME ] ---"
 
     cd "$tmp_path"
-    tar --warning=no-timestamp \
+    tar --extract \
-        --extract \
         --file "$pkg" &&
     _msg "${PAS}unpacked archive"
 
@@ -384,6 +388,16 @@ sys_enable_guix_daemon()
                   service guix-daemon start; } &&
                 _msg "${PAS}enabled Guix daemon via sysv"
             ;;
+        openrc)
+            { mkdir -p /etc/init.d;
+              cp "${ROOT_HOME}/.config/guix/current/etc/openrc/guix-daemon" \
+                 /etc/init.d/guix-daemon;
+              chmod 775 /etc/init.d/guix-daemon;
+
+              rc-update add guix-daemon default &&
+                  rc-service guix-daemon start; } &&
+                _msg "${PAS}enabled Guix daemon via OpenRC"
+            ;;
         NA|*)
             _msg "${ERR}unsupported init system; run the daemon manually:"
             echo "  ${ROOT_HOME}/.config/guix/current/bin/guix-daemon --build-users-group=guixbuild"

etc/news.scm

@@ -13,6 +13,180 @@
 (channel-news
  (version 0)
 
+ (entry (commit "8e1907a72430aa989125b053573ef0897c480697")
+        (title (en "Package transformation options now recorded in profiles")
+               (de "Paketumwandlungsoptionen werden nun in Profilen gesichert")
+               (fr "Options de transformation sauvegardées dans les profils"))
+        (body
+         (en "When installing packages in a profile, package transformation
+options such as @option{--with-input} are now recorded in the profile.  When
+you eventually run @command{guix upgrade}, those transformations will be
+automatically applied to the upgraded packages.
+
+Run @command{info \"(guix) Package Transformation Options\"} for more info.")
+         (de "Wenn Sie ein Paket in ein Profil installieren, werden nun
+Paketumwandlungsoptionen wie @option{--with-input} im Profil gespeichert.
+Sobald Sie später @command{guix upgrade} ausführen, werden dieselben
+Umwandlungen automatisch auf die aktualisierten Pakete angewandt.
+
+Führen Sie für mehr Informationen @command{info \"(guix.de)
+Paketumwandlungsoptionen\"} aus.")
+         (fr "Lorsqu'on installe des paquets dans un profil, les options de
+transformation telles que @option{--with-input} sont désormais enregistrées
+dans le profil.  Quand on le met plus tard à jour avec @command{guix upgrade},
+ces transformations sont automatiquement appliquées aux nouveaux paquets.
+
+Voir @command{info \"(guix.fr) Options de transformation de paquets\"} pour
+plus de détails.")))
+
+ (entry (commit "313f492657f1d0863c641fa5ee7f5b7028e27c94")
+        (title (en "New @option{--image-type} option for @command{guix system disk-image}.")
+               (de "Neue Option @option{--image-type} für @command{guix system disk-image}.")
+               (fr "Nouvelle option @option{--image-type} pour @command{guix system disk-image}."))
+        (body
+         (en "The @option{--file-system-type} option for @command{guix system
+disk-image} command has been replaced by the new @option{--image-type} option.
+By default, @code{raw} disk images are produced, but @code{hurd-qcow2},
+@code{hurd-raw}, @code{uncompressed-iso9660} and @code{iso9660} image types
+are also available.
+
+The @option{--list-image-types} option lists all the available image types.")
+         (de "Anstelle der Befehlszeilenoption @option{--file-system-type} für
+@command{guix system disk-image} gibt es nun die neue Option
+@option{--image-type}.  In der Vorgabeeinstellung @code{raw} werden rohe
+Disk-Images erzeugt, aber es können auch die Abbildtypen @code{hurd-qcow2},
+@code{hurd-raw}, @code{uncompressed-iso9660} und @code{iso9660} ausgewählt
+werden.
+
+Mit der Option @option{--list-image-types} werden alle verfügbaren Abbildtypen
+aufgelistet.")
+         (fr "L'option @option{--file-system-type} pour la commande
+@command{guix system disk-image} a été remplacée par la nouvelle option
+@option{--image-type}. Par défaut, l'option @code{raw}, produisant des images
+disque brutes est sélectionnée. Les options @code{hurd-qcow2},
+@code{hurd-raw}, @code{uncompressed-iso9660} et @code{iso9660} sont également
+disponibles.
+
+La nouvelle option @option{--list-image-types} énumère les types d'image
+disponibles.")))
+
+ (entry (commit "8819551c8d2a12cd4e84e09b51e434d05a012c9d")
+        (title (en "Package transformations now apply to implicit inputs")
+               (de "Paketumwandlungen betreffen jetzt auch implizite Eingaben")
+               (fr "Les transformations de paquets s'appliquent aux
+dépendances implicites"))
+        (body
+         (en "Package transformation options such as @option{--with-branch},
+@option{--with-input}, and so on now apply to implicit inputs---previously
+only a package's explicit inputs would be affected.  This allows for things
+such as replacing the Python dependency of a package that uses
+@code{python-build-system}:
+
+@example
+guix install --with-input=python=python2 python-itsdangerous
+@end example
+
+Another example is grafting a different version of the GNU C
+Library (@code{glibc} is an implicit input of almost all the packages and is
+``deep down'' in the dependency graph):
+
+@example
+guix build --with-graft=glibc=glibc@@2.31 hello
+@end example
+
+Run @command{info \"(guix) Package Transformation Options\"} for more
+info.")
+         (de "Paketumwandlungsoptionen wie @option{--with-branch},
+@option{--with-input} und so weiter betreffen nun auch implizite Eingaben —
+zuvor haben sie sich nur auf die expliziten Eingaben eines Pakets
+ausgewirkt. Dadurch kann jetzt zum Beispiel die Python-Abhängigkeit eines
+Pakets, welches @code{python-build-system} benutzt, ersetzt werden:
+
+@example
+guix install --with-input=python=python2 python-itsdangerous
+@end example
+
+Ein weiteres Beispiel ist, mit einer anderen Version der GNU-C-Bibliothek zu
+veredeln (@code{glibc} ist eine implizite Eingabe fast aller Pakete und steckt
+„ganz tief“ im Abhängigkeitsgraphen):
+
+@example
+guix build --with-graft=glibc=glibc@@2.31 hello
+@end example
+
+Führen Sie für mehr Informationen @command{info \"(guix.de)
+Paketumwandlungsoptionen\"} aus.")
+         (fr "Les options de transformation de paquets telles que
+@option{--with-branch} et @option{--with-input} s'appliquent désormais aux
+dépendances implicites — jusque là seules les dépendances explicites des
+paquets étaient prises en compte.  Cela permet certaines choses telles que
+remplacer la dépendance sur Python d'un paquet utilisant
+@code{python-build-system} :
+
+@example
+guix install --with-input=python=python2 python-itsdangerous
+@end example
+
+Un autre exemple est la possibilité de greffer une version différente de la
+bibliothèque C GNU (la @code{glibc} est une dépendance implicite de tous les
+paquets et se trouve « tout en bas » du graphe de dépendance) :
+
+@example
+guix build --with-graft=glibc=glibc@@2.31 hello
+@end example
+
+Voir @command{info \"(guix.fr) Options de transformation de paquets\"} pour
+plus de détails.")))
+
+ (entry (commit "f458cfbcc54ed87b1a87dd9e150ea276f17eab74")
+        (title (en "New @option{--without-tests} transformation option")
+               (de "Neue Paketumwandlungsoption @option{--without-tests}")
+               (fr "Nouvelle option de transformation @option{--without-tests}"))
+        (body
+         (en "The new @option{--without-tests} package transformation option
+instructs Guix to skip the test suite of a given package.  In the example
+below, @code{guile-gcrypt} is built using a variant of @code{automake} itself
+built without running its (lengthy) test suite:
+
+@example
+guix build guile-gcrypt --without-tests=automake
+@end example
+
+This is primarily useful as a way to speed up development cycles, or to work
+around flaky test suites---skipping tests can hide real issues, so use with
+care.  Run @command{info \"(guix) Package Transformation Options\"} for more
+info.")
+         (de "Mit der neuen Paketumwandlungsoption @option{--without-tests}
+wird Guix angewiesen, den Testkatalog des angegebenen Pakets zu
+überspringen. Im folgenden Beispiel wird @code{guile-gcrypt} mit einer
+Variante von @code{automake} erstellt, die wiederum ohne Durchlauf ihres (viel
+Zeit in Anspruch nehmenden) Testkatalogs erstellt wird:
+
+@example
+guix build guile-gcrypt --without-tests=automake
+@end example
+
+Der hauptsächliche Nutzen liegt in der Beschleunigung von Entwicklungszyklen
+oder im Umgehen unzuverlässiger Testkataloge. Allerdings kann das Überspringen
+dazu führen, dass echte Probleme verborgen bleiben. Setzen Sie es mit Bedacht
+ein. Führen Sie @command{info \"(guix.de) Paketumwandlungsoptionen\"} aus, um
+mehr Informationen zu erhalten.")
+         (fr "La nouvelle option de transformation de paquets
+@option{--without-tests} demande à Guix de sauter la suite de tests d'un
+paquet.  Dans l'exemple ci-dessous, @code{guile-gcrypt} est construit en
+utilisant une variante de @code{automake} construite sans lancer sa suite de
+tests :
+
+@example
+guix build guile-gcrypt --without-tests=automake
+@end example
+
+Cette option est surtout intéressante pour raccourcir le cycle de
+développement ou pour contourner une suite de tests qui n'est pas
+fiable — sauter les tests peut cacher des vrais problèmes, à utiliser avec
+précaution donc.  Voir @command{info \"(guix.fr) Options de transformation de
+paquets\"} pour plus de détails.")))
+
  (entry (commit "a98712785e0b042a290420fd74e5a4a5da4fc68f")
         (title (en "New @command{guix git authenticate} command")
                (de "Neuer Befehl @command{guix git authenticate}")

etc/openrc/guix-daemon.in

@@ -0,0 +1,28 @@
+#!/sbin/openrc-run
+# GNU Guix --- Functional package management for GNU
+# Copyright © 2020 Morgan Smith <Morgan.J.Smith@outlook.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/>.
+
+export GUIX_LOCPATH=@localstatedir@/guix/profiles/per-user/root/guix-profile/lib/locale
+export LC_ALL=en_US.utf8
+command="@localstatedir@/guix/profiles/per-user/root/current-guix/bin/guix-daemon"
+command_args="--build-users-group=guixbuild"
+command_background="yes"
+pidfile="/var/run/guix-daemon.pid"
+
+output_log="/var/log/guix-daemon-stdout.log"
+error_log="/var/log/guix-daemon-stderr.log"

gnu/bootloader/grub.scm

@@ -23,8 +23,10 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu bootloader grub)
+  #:use-module (guix build union)
   #:use-module (guix records)
-  #:use-module ((guix utils) #:select (%current-system))
+  #:use-module (guix store)
+  #:use-module (guix utils)
   #:use-module (guix gexp)
   #:use-module (gnu artwork)
   #:use-module (gnu bootloader)
@@ -46,8 +48,11 @@
             grub-theme-color-highlight
             grub-theme-gfxmode
 
+            install-grub-efi-netboot
+
             grub-bootloader
             grub-efi-bootloader
+            grub-efi-netboot-bootloader
             grub-mkrescue-bootloader
             grub-minimal-bootloader
 
@@ -295,6 +300,35 @@ code."
         ((? file-system-label? label)
          (format #f "search --label --set ~a"
                  (file-system-label->string label)))
+        ((? (lambda (device)
+              (and (string? device) (string-contains device ":/"))) nfs-uri)
+         ;; If the device is an NFS share, then we assume that the expected
+         ;; file on that device (e.g. the GRUB background image or the kernel)
+         ;; has to be loaded over the network.  Otherwise we would need an
+         ;; additional device information for some local disk to look for that
+         ;; file, which we do not have.
+         ;;
+         ;; We explicitly set "root=(tftp)" here even though if grub.cfg
+         ;; had been loaded via TFTP, Grub would have set "root=(tftp)"
+         ;; automatically anyway.  The reason is if you have a system that
+         ;; used to be on NFS but now is local, root would be set to local
+         ;; disk.  If you then selected an older system generation that is
+         ;; supposed to boot from network in the Grub boot menu, Grub still
+         ;; wouldn't load those files from network otherwise.
+         ;;
+         ;; TFTP is preferred to HTTP because it is used more widely and
+         ;; specified in standards more widely--especially BOOTP/DHCPv4
+         ;; defines a TFTP server for DHCP option 66, but not HTTP.
+         ;;
+         ;; Note: DHCPv6 specifies option 59 to contain a boot-file-url,
+         ;; which can contain a HTTP or TFTP URL.
+         ;;
+         ;; Note: It is assumed that the file paths are of a similar
+         ;; setup on both the TFTP server and the NFS server (it is
+         ;; not possible to search for files on TFTP).
+         ;;
+         ;; TODO: Allow HTTP.
+         "set root=(tftp)")
         ((or #f (? string?))
          #~(format #f "search --file --set ~a" #$file)))))
 
@@ -501,6 +535,99 @@ fi~%"))))
                       "--bootloader-id=Guix"
                       "--efi-directory" target-esp))))
 
+(define (install-grub-efi-netboot subdir)
+  "Define a grub-efi-netboot bootloader installer for installation in SUBDIR,
+which is usually efi/Guix or efi/boot."
+  (let* ((system (string-split (nix-system->gnu-triplet
+                                (or (%current-target-system)
+                                    (%current-system)))
+                               #\-))
+         (arch (first system))
+         (boot-efi-link (match system
+                          ;; These are the supportend systems and the names
+                          ;; defined by the UEFI standard for removable media.
+                          (("i686" _ ...)        "/bootia32.efi")
+                          (("x86_64" _ ...)      "/bootx64.efi")
+                          (("arm" _ ...)         "/bootarm.efi")
+                          (("aarch64" _ ...)     "/bootaa64.efi")
+                          (("riscv" _ ...)       "/bootriscv32.efi")
+                          (("riscv64" _ ...)     "/bootriscv64.efi")
+                          ;; Other systems are not supported, although defined.
+                          ;; (("riscv128" _ ...) "/bootriscv128.efi")
+                          ;; (("ia64" _ ...)     "/bootia64.efi")
+                          ((_ ...)               #f)))
+         (core-efi (string-append
+                    ;; This is the arch dependent file name of GRUB, e.g.
+                    ;; i368-efi/core.efi or arm64-efi/core.efi.
+                    (match arch
+                      ("i686"    "i386")
+                      ("aarch64" "arm64")
+                      ("riscv"   "riscv32")
+                      (_         arch))
+                    "-efi/core.efi")))
+    (with-imported-modules
+     '((guix build union))
+     #~(lambda (bootloader target mount-point)
+         "Install the BOOTLOADER, which must be the package grub, as e.g.
+bootx64.efi or bootaa64.efi into SUBDIR, which is usually efi/Guix or efi/boot,
+below the directory TARGET for the system whose root is mounted at MOUNT-POINT.
+
+MOUNT-POINT is the last argument in 'guix system init /etc/config.scm mnt/point'
+or '/' for other 'guix system' commands.
+
+TARGET is the target argument given to the bootloader-configuration in
+
+(operating-system
+ (bootloader (bootloader-configuration
+              (target \"/boot\")
+              …))
+ …)
+
+TARGET is required to be an absolute directory name, usually mounted via NFS,
+and finally needs to be provided by a TFTP server as the TFTP root directory.
+
+GRUB will load tftp://server/SUBDIR/grub.cfg and this file will instruct it to
+load more files from the store like tftp://server/gnu/store/…-linux…/Image.
+
+To make this possible two symlinks will be created. The first symlink points
+relatively form MOUNT-POINT/TARGET/SUBDIR/grub.cfg to
+MOUNT-POINT/boot/grub/grub.cfg, and the second symlink points relatively from
+MOUNT-POINT/TARGET/%store-prefix to MOUNT-POINT/%store-prefix.
+
+It is important to note that these symlinks need to be relativ, as the absolute
+paths on the TFTP server side are unknown.
+
+It is also important to note that both symlinks will point outside the TFTP root
+directory and that the TARGET/%store-prefix symlink makes the whole store
+accessible via TFTP. Possibly the TFTP server must be configured
+to allow accesses outside its TFTP root directory. This may need to be
+considered for security aspects."
+         (use-modules ((guix build union) #:select (symlink-relative)))
+         (let* ((net-dir (string-append mount-point target "/"))
+                (sub-dir (string-append net-dir #$subdir "/"))
+                (store (string-append mount-point (%store-prefix)))
+                (store-link (string-append net-dir (%store-prefix)))
+                (grub-cfg (string-append mount-point "/boot/grub/grub.cfg"))
+                (grub-cfg-link (string-append sub-dir (basename grub-cfg)))
+                (boot-efi-link (string-append sub-dir #$boot-efi-link)))
+           ;; Prepare the symlink to the store.
+           (mkdir-p (dirname store-link))
+           (false-if-exception (delete-file store-link))
+           (symlink-relative store store-link)
+           ;; Prepare the symlink to the grub.cfg, which points into the store.
+           (mkdir-p (dirname grub-cfg-link))
+           (false-if-exception (delete-file grub-cfg-link))
+           (symlink-relative grub-cfg grub-cfg-link)
+           ;; Install GRUB, which refers to the grub.cfg, with support for
+           ;; encrypted partitions,
+           (setenv "GRUB_ENABLE_CRYPTODISK" "y")
+           (invoke/quiet (string-append bootloader "/bin/grub-mknetdir")
+                         (string-append "--net-directory=" net-dir)
+                         (string-append "--subdir=" #$subdir))
+           ;; Prepare the bootloader symlink, which points to core.efi of GRUB.
+           (false-if-exception (delete-file boot-efi-link))
+           (symlink #$core-efi boot-efi-link))))))
+
 
 
 ;;;
@@ -533,6 +660,12 @@ fi~%"))))
    (name 'grub-efi)
    (package grub-efi)))
 
+(define grub-efi-netboot-bootloader
+  (bootloader
+   (inherit grub-efi-bootloader)
+   (name 'grub-efi-netboot-bootloader)
+   (installer (install-grub-efi-netboot "efi/Guix"))))
+
 (define grub-mkrescue-bootloader
   (bootloader
    (inherit grub-efi-bootloader)

gnu/bootloader/u-boot.scm

@@ -45,7 +45,7 @@
             u-boot-wandboard-bootloader))
 
 (define install-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (if bootloader
         (error "Failed to install U-Boot"))))
 
@@ -56,74 +56,74 @@
   ;; the MLO and is expected at 0x60000.  Write both first stage ("MLO") and
   ;; second stage ("u-boot.img") images, read in BOOTLOADER directory, to the
   ;; specified DEVICE.
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((mlo (string-append bootloader "/libexec/MLO"))
             (u-boot (string-append bootloader "/libexec/u-boot.img")))
         (write-file-on-device mlo (* 256 512)
-                              device (* 256 512))
+                              image (* 256 512))
         (write-file-on-device u-boot (* 1024 512)
-                              device (* 768 512)))))
+                              image (* 768 512)))))
 
 (define install-allwinner-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((u-boot (string-append bootloader
                                    "/libexec/u-boot-sunxi-with-spl.bin")))
         (write-file-on-device u-boot (stat:size (stat u-boot))
-                              device (* 8 1024)))))
+                              image (* 8 1024)))))
 
 (define install-allwinner64-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((spl (string-append bootloader "/libexec/spl/sunxi-spl.bin"))
             (u-boot (string-append bootloader "/libexec/u-boot.itb")))
         (write-file-on-device spl (stat:size (stat spl))
-                              device (* 8 1024))
+                              image (* 8 1024))
         (write-file-on-device u-boot (stat:size (stat u-boot))
-                              device (* 40 1024)))))
+                              image (* 40 1024)))))
 
 (define install-imx-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((spl (string-append bootloader "/libexec/SPL"))
             (u-boot (string-append bootloader "/libexec/u-boot.img")))
         (write-file-on-device spl (stat:size (stat spl))
-                              device (* 1 1024))
+                              image (* 1 1024))
         (write-file-on-device u-boot (stat:size (stat u-boot))
-                              device (* 69 1024)))))
+                              image (* 69 1024)))))
 
 (define install-puma-rk3399-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((spl (string-append bootloader "/libexec/u-boot-spl.rksd"))
             (u-boot (string-append bootloader "/libexec/u-boot.itb")))
         (write-file-on-device spl (stat:size (stat spl))
-                              device (* 64 512))
+                              image (* 64 512))
         (write-file-on-device u-boot (stat:size (stat u-boot))
-                              device (* 512 512)))))
+                              image (* 512 512)))))
 
 (define install-firefly-rk3399-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((idb (string-append bootloader "/libexec/idbloader.img"))
             (u-boot (string-append bootloader "/libexec/u-boot.itb")))
         (write-file-on-device idb (stat:size (stat idb))
-                              device (* 64 512))
+                              image (* 64 512))
         (write-file-on-device u-boot (stat:size (stat u-boot))
-                              device (* 16384 512)))))
+                              image (* 16384 512)))))
 
 (define install-rock64-rk3328-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((idb (string-append bootloader "/libexec/idbloader.img"))
             (u-boot (string-append bootloader "/libexec/u-boot.itb")))
         (write-file-on-device idb (stat:size (stat idb))
-                              device (* 64 512))
+                              image (* 64 512))
         (write-file-on-device u-boot (stat:size (stat u-boot))
-                              device (* 16384 512)))))
+                              image (* 16384 512)))))
 
 (define install-rockpro64-rk3399-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((idb (string-append bootloader "/libexec/idbloader.img"))
             (u-boot (string-append bootloader "/libexec/u-boot.itb")))
         (write-file-on-device idb (stat:size (stat idb))
-                              device (* 64 512))
+                              image (* 64 512))
         (write-file-on-device u-boot (stat:size (stat u-boot))
-                              device (* 16384 512)))))
+                              image (* 16384 512)))))
 
 (define install-pinebook-pro-rk3399-u-boot install-rockpro64-rk3399-u-boot)
 
@@ -138,28 +138,29 @@
    (inherit extlinux-bootloader)
    (name 'u-boot)
    (package #f)
-   (installer install-u-boot)))
+   (installer #f)
+   (disk-image-installer install-u-boot)))
 
 (define u-boot-beaglebone-black-bootloader
   (bootloader
    (inherit u-boot-bootloader)
    (package u-boot-am335x-boneblack)
-   (installer install-beaglebone-black-u-boot)))
+   (disk-image-installer install-beaglebone-black-u-boot)))
 
 (define u-boot-allwinner-bootloader
   (bootloader
    (inherit u-boot-bootloader)
-   (installer install-allwinner-u-boot)))
+   (disk-image-installer install-allwinner-u-boot)))
 
 (define u-boot-allwinner64-bootloader
   (bootloader
    (inherit u-boot-bootloader)
-   (installer install-allwinner64-u-boot)))
+   (disk-image-installer install-allwinner64-u-boot)))
 
 (define u-boot-imx-bootloader
   (bootloader
    (inherit u-boot-bootloader)
-   (installer install-imx-u-boot)))
+   (disk-image-installer install-imx-u-boot)))
 
 (define u-boot-nintendo-nes-classic-edition-bootloader
   (bootloader
@@ -196,7 +197,7 @@
   (bootloader
    (inherit u-boot-bootloader)
    (package u-boot-firefly-rk3399)
-   (installer install-firefly-rk3399-u-boot)))
+   (disk-image-installer install-firefly-rk3399-u-boot)))
 
 (define u-boot-mx6cuboxi-bootloader
   (bootloader
@@ -232,25 +233,25 @@
   (bootloader
    (inherit u-boot-bootloader)
    (package u-boot-puma-rk3399)
-   (installer install-puma-rk3399-u-boot)))
+   (disk-image-installer install-puma-rk3399-u-boot)))
 
 (define u-boot-rock64-rk3328-bootloader
   ;; SD and eMMC use the same format
   (bootloader
    (inherit u-boot-bootloader)
    (package u-boot-rock64-rk3328)
-   (installer install-rock64-rk3328-u-boot)))
+   (disk-image-installer install-rock64-rk3328-u-boot)))
 
 (define u-boot-rockpro64-rk3399-bootloader
   ;; SD and eMMC use the same format
   (bootloader
    (inherit u-boot-bootloader)
    (package u-boot-rockpro64-rk3399)
-   (installer install-rockpro64-rk3399-u-boot)))
+   (disk-image-installer install-rockpro64-rk3399-u-boot)))
 
 (define u-boot-pinebook-pro-rk3399-bootloader
   ;; SD and eMMC use the same format
   (bootloader
    (inherit u-boot-bootloader)
    (package u-boot-pinebook-pro-rk3399)
-   (installer install-pinebook-pro-rk3399-u-boot)))
+   (disk-image-installer install-pinebook-pro-rk3399-u-boot)))

gnu/build/bootloader.scm

@@ -22,6 +22,8 @@
   #:use-module (guix utils)
   #:use-module (ice-9 binary-ports)
   #:use-module (ice-9 format)
+  #:use-module (rnrs io ports)
+  #:use-module (rnrs io simple)
   #:export (write-file-on-device
             install-efi-loader))
 
@@ -35,11 +37,14 @@
   (call-with-input-file file
     (lambda (input)
       (let ((bv (get-bytevector-n input size)))
-        (call-with-output-file device
+        (call-with-port
+         (open-file-output-port device
+                                (file-options no-truncate no-create)
+                                (buffer-mode block)
+                                (native-transcoder))
          (lambda (output)
            (seek output offset SEEK_SET)
-            (put-bytevector output bv))
+           (put-bytevector output bv)))))))
-          #:binary #t)))))
 
 
 ;;;

gnu/build/image.scm

@@ -37,6 +37,7 @@
   #:use-module (srfi srfi-34)
   #:use-module (srfi srfi-35)
   #:export (make-partition-image
+            convert-disk-image
             genimage
             initialize-efi-partition
             initialize-root-partition
@@ -120,13 +121,22 @@ ROOT directory to populate the image."
       (format (current-error-port)
               "Unsupported partition type~%.")))))
 
-(define* (genimage config target)
+(define (convert-disk-image image format output)
+  "Convert IMAGE to OUTPUT according to the given FORMAT."
+  (case format
+    ((compressed-qcow2)
+     (begin
+       (invoke "qemu-img" "convert" "-c" "-f" "raw"
+               "-O" "qcow2" image output)))
+    (else
+     (copy-file image output))))
+
+(define* (genimage config)
   "Use genimage to generate in TARGET directory, the image described in the
 given CONFIG file."
   ;; genimage needs a 'root' directory.
   (mkdir "root")
-  (invoke "genimage" "--config" config
+  (invoke "genimage" "--config" config))
-          "--outputpath" target))
 
 (define* (register-closure prefix closure
                            #:key

gnu/build/linux-container.scm

@@ -170,7 +170,8 @@ for the process."
     (pivot-root root put-old)
     (chdir "/")
     (umount "real-root" MNT_DETACH)
-    (rmdir "real-root")))
+    (rmdir "real-root")
+    (chmod "/" #o755)))
 
 (define* (initialize-user-namespace pid host-uids
                                     #:key (guest-uid 0) (guest-gid 0))

gnu/build/secret-service.scm

@@ -35,44 +35,86 @@
 ;;;
 ;;; Code:
 
-(define* (secret-service-send-secrets port secret-root #:key (retry 60))
+(define-syntax log
-  "Copy all files under SECRET-ROOT using TCP to secret-service listening at
+  (lambda (s)
-local PORT.  If connect fails, sleep 1s and retry RETRY times."
+    "Log the given message."
+    (syntax-case s ()
+      ((_ fmt args ...)
+       (with-syntax ((fmt (string-append "secret service: "
+                                         (syntax->datum #'fmt))))
+         ;; Log to the current output port.  That way, when
+         ;; 'secret-service-send-secrets' is called from shepherd, output goes
+         ;; to syslog.
+         #'(format (current-output-port) fmt args ...))))))
 
+(define* (secret-service-send-secrets port secret-root
+                                      #:key (retry 60)
+                                      (handshake-timeout 120))
+  "Copy all files under SECRET-ROOT using TCP to secret-service listening at
+local PORT.  If connect fails, sleep 1s and retry RETRY times; once connected,
+wait for at most HANDSHAKE-TIMEOUT seconds for handshake to complete.  Return
+#f on failure."
   (define (file->file+size+mode file-name)
     (let ((stat (stat file-name))
           (target (substring file-name (string-length secret-root))))
       (list target (stat:size stat) (stat:mode stat))))
 
-  (format (current-error-port) "sending secrets to ~a~%" port)
+  (define (send-files sock)
-  (let ((sock (socket AF_INET SOCK_STREAM 0))
-        (addr (make-socket-address AF_INET INADDR_LOOPBACK port)))
-    ;; connect to wait for port
-    (let loop ((retry retry))
-      (catch 'system-error
-        (cute connect sock addr)
-        (lambda (key . args)
-          (when (zero? retry)
-            (apply throw key args))
-          (format (current-error-port) "retrying connection~%")
-          (sleep 1)
-          (loop (1- retry)))))
-
-    (format (current-error-port) "connected!  sending files in ~s %~"
-            secret-root)
     (let* ((files (if secret-root (find-files secret-root) '()))
            (files-sizes-modes (map file->file+size+mode files))
            (secrets `(secrets
                       (version 0)
                       (files ,files-sizes-modes))))
       (write secrets sock)
-      (for-each (compose (cute dump-port <> sock)
+      (for-each (lambda (file)
-                         (cute open-input-file <>))
+                  (call-with-input-file file
-                files))))
+                    (lambda (input)
+                      (dump-port input sock))))
+                files)))
+
+  (log "sending secrets to ~a~%" port)
+  (let ((sock (socket AF_INET SOCK_STREAM 0))
+        (addr (make-socket-address AF_INET INADDR_LOOPBACK port)))
+    ;; Connect to QEMU on the forwarded port.  The 'connect' call succeeds as
+    ;; soon as QEMU is ready, even if there's no server listening on the
+    ;; forward port inside the guest.
+    (let loop ((retry retry))
+      (catch 'system-error
+        (cute connect sock addr)
+        (lambda (key . args)
+          (when (zero? retry)
+            (apply throw key args))
+          (log "retrying connection [~a attempts left]~%"
+               (- retry 1))
+          (sleep 1)
+          (loop (1- retry)))))
+
+    (log "connected; waiting for handshake...~%")
+
+    ;; Wait for "hello" message from the server.  This is the only way to know
+    ;; that we're really connected to the server inside the guest.
+    (match (select (list sock) '() '() handshake-timeout)
+      (((_) () ())
+       (match (read sock)
+         (('secret-service-server ('version version ...))
+          (log "sending files from ~s...~%" secret-root)
+          (send-files sock)
+          (log "done sending files to port ~a~%" port)
+          (close-port sock)
+          secret-root)
+         (x
+          (log "invalid handshake ~s~%" x)
+          (close-port sock)
+          #f)))
+      ((() () ())                                 ;timeout
+       (log "timeout while sending files to ~a~%" port)
+       (close-port sock)
+       #f))))
 
 (define (secret-service-receive-secrets port)
   "Listen to local PORT and wait for a secret service client to send secrets.
-Write them to the file system."
+Write them to the file system.  Return the list of files installed on success,
+and #f otherwise."
 
   (define (wait-for-client port)
     ;; Wait for a TCP connection on PORT.  Note: We cannot use the
@@ -81,16 +123,26 @@ Write them to the file system."
     (let ((sock (socket AF_INET SOCK_STREAM 0)))
       (bind sock AF_INET INADDR_ANY port)
       (listen sock 1)
-      (format (current-error-port)
+      (log "waiting for secrets on port ~a...~%" port)
-              "waiting for secrets on port ~a...~%"
+      (match (select (list sock) '() '() 60)
-              port)
+        (((_) () ())
          (match (accept sock)
            ((client . address)
-         (format (current-error-port) "client connection from ~a~%"
+            (log "client connection from ~a~%"
                  (inet-ntop (sockaddr:fam address)
                             (sockaddr:addr address)))
+
+            ;; Send a "hello" message.  This allows the client running on the
+            ;; host to know that it's now actually connected to server running
+            ;; in the guest.
+            (write '(secret-service-server (version 0)) client)
+            (force-output client)
             (close-port sock)
-         client))))
+            client)))
+        ((() () ())
+         (log "did not receive any secrets; time out~%")
+         (close-port sock)
+         #f))))
 
   ;; TODO: Remove when (@ (guix build utils) dump-port) has a 'size'
   ;; parameter.
@@ -115,23 +167,24 @@ Write them to the file system."
       (('secrets ('version 0)
                  ('files ((files sizes modes) ...)))
        (for-each (lambda (file size mode)
-                   (format (current-error-port)
+                   (log "installing file '~a' (~a bytes)...~%"
-                           "installing file '~a' (~a bytes)...~%"
                         file size)
                    (mkdir-p (dirname file))
                    (call-with-output-file file
                      (lambda (output)
                        (dump port output size)
                        (chmod file mode))))
-                 files sizes modes))
+                 files sizes modes)
+       (log "received ~a secret files~%" (length files))
+       files)
       (_
-       (format (current-error-port)
+       (log "invalid secrets received~%")
-               "invalid secrets received~%")
        #f)))
 
   (let* ((port   (wait-for-client port))
-         (result (read-secrets port)))
+         (result (and=> port read-secrets)))
-    (close-port port)
+    (when port
+      (close-port port))
     result))
 
 ;;; secret-service.scm ends here

gnu/build/shepherd.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2020 Mathieu Othacehe <othacehe@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -196,11 +197,16 @@ namespace, in addition to essential bind-mounts such /proc."
                                       #:allow-other-keys
                                       #:rest args)
   "This is a variant of 'fork+exec-command' procedure, that joins the
-namespaces of process PID beforehand."
+namespaces of process PID beforehand.  If there is no support for containers,
-  (container-excursion* pid
+on Hurd systems for instance, fallback to direct forking."
-    (lambda ()
+  (let ((container-support?
+         (file-exists? "/proc/self/ns"))
+        (fork-proc (lambda ()
                      (apply fork+exec-command command
                             (strip-keyword-arguments '(#:pid) args)))))
+    (if container-support?
+        (container-excursion* pid fork-proc)
+        (fork-proc))))
 
 ;; Local Variables:
 ;; eval: (put 'container-excursion* 'scheme-indent-function 1)

gnu/ci.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2017 Jan Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2017, 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2018, 2019 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2020 Julien Lepiller <julien@lepiller.eu>
 ;;;
@@ -75,9 +75,17 @@
                          #:optional (package-derivation package-derivation))
   "Convert PACKAGE to an alist suitable for Hydra."
   (parameterize ((%graft? #f))
-    `((derivation . ,(derivation-file-name
+    (let ((drv (package-derivation store package system
-                      (package-derivation store package system
                                    #:graft? #f)))
+      `((derivation . ,(derivation-file-name drv))
+        (log . ,(log-file store (derivation-file-name drv)))
+        (outputs . ,(filter-map (lambda (res)
+                                  (match res
+                                    ((name . path)
+                                     `(,name . ,path))))
+                                (derivation->output-paths drv)))
+        (nix-name . ,(derivation-name drv))
+        (system . ,(derivation-system drv))
         (description . ,(package-synopsis package))
         (long-description . ,(package-description package))
 
@@ -96,7 +104,7 @@
                                            'max-silent-time)
                                 3600))              ;1 hour by default
         (timeout . ,(or (assoc-ref (package-properties package) 'timeout)
-                      72000)))))                  ;20 hours by default
+                        72000))))))                  ;20 hours by default
 
 (define (package-job store job-name package system)
   "Return a job called JOB-NAME that builds PACKAGE on SYSTEM."
@@ -195,12 +203,20 @@ SYSTEM."
   '("x86_64-linux" "i686-linux"))
 
 (define %guix-system-images
-  (list hurd-barebones-disk-image))
+  (list hurd-barebones-qcow2-image))
 
 (define (image-jobs store system)
   "Return a list of jobs that build images for SYSTEM."
   (define (->alist drv)
     `((derivation . ,(derivation-file-name drv))
+      (log . ,(log-file store (derivation-file-name drv)))
+      (outputs . ,(filter-map (lambda (res)
+                                (match res
+                                  ((name . path)
+                                   `(,name . ,path))))
+                              (derivation->output-paths drv)))
+      (nix-name . ,(derivation-name drv))
+      (system . ,(derivation-system drv))
       (description . "Stand-alone image of the GNU system")
       (long-description . "This is a demo stand-alone image of the GNU
 system.")
@@ -304,6 +320,14 @@ system.")
             (system-test-value test))))
 
       `((derivation . ,(derivation-file-name drv))
+        (log . ,(log-file store (derivation-file-name drv)))
+        (outputs . ,(filter-map (lambda (res)
+                                  (match res
+                                    ((name . path)
+                                     `(,name . ,path))))
+                                (derivation->output-paths drv)))
+        (nix-name . ,(derivation-name drv))
+        (system . ,(derivation-system drv))
         (description . ,(format #f "Guix '~a' system test"
                                 (system-test-name test)))
         (long-description . ,(system-test-description test))
@@ -333,6 +357,14 @@ system.")
   "Return Hydra jobs to build the self-contained Guix binary tarball."
   (define (->alist drv)
     `((derivation . ,(derivation-file-name drv))
+      (log . ,(log-file store (derivation-file-name drv)))
+      (outputs . ,(filter-map (lambda (res)
+                                (match res
+                                  ((name . path)
+                                   `(,name . ,path))))
+                              (derivation->output-paths drv)))
+      (nix-name . ,(derivation-name drv))
+      (system . ,(derivation-system drv))
       (description . "Stand-alone binary Guix tarball")
       (long-description . "This is a tarball containing binaries of Guix and
 all its dependencies, and ready to be installed on \"foreign\" distributions.")
@@ -511,20 +543,16 @@ Return #f if no such checkout is found."
                              (cross-jobs store system)))
                     ((hello)
                      ;; Build hello package only.
-                     (if (string=? system (%current-system))
                      (let ((hello (specification->package "hello")))
-                           (list (package-job store (job-name hello) hello system)))
+                       (list (package-job store (job-name hello) hello system))))
-                         '()))
                     ((list)
                      ;; Build selected list of packages only.
-                     (if (string=? system (%current-system))
                      (let* ((names (assoc-ref arguments 'subset))
                             (packages (map specification->package names)))
                        (map (lambda (package)
                               (package-job store (job-name package)
                                            package system))
-                                  packages))
+                            packages)))
-                         '()))
                     ((manifests)
                      ;; Build packages in the list of manifests.
                      (let* ((manifests (arguments->manifests arguments))

gnu/image.scm

@@ -39,7 +39,14 @@
             image-partitions
             image-compression?
             image-volatile-root?
-            image-substitutable?))
+            image-substitutable?
+
+            image-type
+            image-type?
+            image-type-name
+            image-type-constructor
+
+            os->image))
 
 
 ;;;
@@ -84,3 +91,23 @@
                       (default #t))
   (substitutable?     image-substitutable? ;boolean
                       (default #t)))
+
+
+;;;
+;;; Image type.
+;;;
+
+(define-record-type* <image-type>
+  image-type make-image-type
+  image-type?
+  (name           image-type-name) ;symbol
+  (constructor    image-type-constructor)) ;<operating-system> -> <image>
+
+
+;;;
+;;; Image creation.
+;;;
+
+(define* (os->image os #:key type)
+  (let ((constructor (image-type-constructor type)))
+    (constructor os)))

gnu/installer.scm

@@ -71,7 +71,7 @@
     (_ #f)))
 
 (define* (build-compiled-file name locale-builder)
-  "Return a file-like object that evalutes the gexp LOCALE-BUILDER and store
+  "Return a file-like object that evaluates the gexp LOCALE-BUILDER and store
 its result in the scheme file NAME. The derivation will also build a compiled
 version of this file."
   (define set-utf8-locale

gnu/installer/connman.scm

@@ -180,7 +180,7 @@ Return the corresponding association list of '((KEY . VALUE) (KEY2 . VALUE2)
 (define (connman-state)
   "Return the state of connman. The nominal states are 'offline, 'idle,
 'ready, 'oneline.  If an unexpected state is read, 'unknown is
-returned. Finally, an error is raised if the comman output could not be
+returned. Finally, an error is raised if the connman output could not be
 parsed, usually because the connman daemon is not responding."
   (let* ((output (connman "state"))
          (state-keys (parse-keys output)))

gnu/installer/newt.scm

@@ -107,7 +107,7 @@ problem. The backtrace is displayed below. Please report it by email to \
   (run-user-page))
 
 (define (partition-page)
-  (run-partioning-page))
+  (run-partitioning-page))
 
 (define (services-page)
   (run-services-page))

gnu/installer/newt/locale.scm

@@ -106,7 +106,7 @@ symbol.")
 territory, codeset and modifier. Use SUPPORTED-LOCALES as the list of glibc
 available locales. ISO639-LANGUAGES is an association list associating a
 locale code to a locale name. ISO3166-TERRITORIES is an association list
-associating a territory code with a territory name. The formated locale, under
+associating a territory code with a territory name. The formatted locale, under
 glibc format is returned."
 
   (define (break-on-locale-found locales)

gnu/installer/newt/partition.scm

@@ -32,7 +32,7 @@
   #:use-module (srfi srfi-35)
   #:use-module (newt)
   #:use-module (parted)
-  #:export (run-partioning-page))
+  #:export (run-partitioning-page))
 
 (define (button-exit-action)
   "Raise the &installer-step-abort condition."
@@ -725,7 +725,7 @@ by pressing the Exit button.~%~%")))
           (run-disk-page result-disks new-user-partitions
                          #:guided? guided?)))))
 
-(define (run-partioning-page)
+(define (run-partitioning-page)
   "Run a page asking the user for a partitioning method."
   (define (run-page devices)
     (let* ((items

gnu/installer/parted.scm

@@ -1201,13 +1201,13 @@ the FS-TYPE field set to 'swap, return the empty list if none found."
           user-partitions))
 
 (define (start-swapping user-partitions)
-  "Start swaping on <user-partition> records with FS-TYPE equal to 'swap."
+  "Start swapping on <user-partition> records with FS-TYPE equal to 'swap."
   (let* ((swap-user-partitions (find-swap-user-partitions user-partitions))
          (swap-devices (map user-partition-file-name swap-user-partitions)))
     (for-each swapon swap-devices)))
 
 (define (stop-swapping user-partitions)
-  "Stop swaping on <user-partition> records with FS-TYPE equal to 'swap."
+  "Stop swapping on <user-partition> records with FS-TYPE equal to 'swap."
   (let* ((swap-user-partitions (find-swap-user-partitions user-partitions))
          (swap-devices (map user-partition-file-name swap-user-partitions)))
     (for-each swapoff swap-devices)))

gnu/installer/steps.scm

@@ -88,7 +88,7 @@
                               (rewind-strategy 'previous)
                               (menu-proc (const #f)))
   "Run the COMPUTE procedure of all <installer-step> records in STEPS
-sequencially. If the &installer-step-abort condition is raised, fallback to a
+sequentially.  If the &installer-step-abort condition is raised, fallback to a
 previous install-step, accordingly to the specified REWIND-STRATEGY.
 
 REWIND-STRATEGY possible values are 'previous, 'menu and 'start.  If 'previous

gnu/local.mk

@@ -144,6 +144,8 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/cppi.scm				\
   %D%/packages/cran.scm				\
   %D%/packages/crates-io.scm			\
+  %D%/packages/crates-graphics.scm		\
+  %D%/packages/crates-gtk.scm			\
   %D%/packages/cross-base.scm			\
   %D%/packages/crypto.scm			\
   %D%/packages/cryptsetup.scm			\
@@ -646,6 +648,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/system/vm.scm				\
 						\
   %D%/system/images/hurd.scm			\
+  %D%/system/images/pine64.scm			\
 						\
   %D%/machine.scm				\
 						\
@@ -967,6 +970,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/foomatic-filters-CVE-2015-8560.patch	\
   %D%/packages/patches/fontconfig-hurd-path-max.patch		\
   %D%/packages/patches/fpc-reproducibility.patch		\
+  %D%/packages/patches/fplll-std-fenv.patch     		\
   %D%/packages/patches/freedink-engine-fix-sdl-hints.patch	\
   %D%/packages/patches/freeimage-unbundle.patch		\
   %D%/packages/patches/fuse-overlapping-headers.patch				\
@@ -1067,6 +1071,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gmp-faulty-test.patch			\
   %D%/packages/patches/gnome-shell-theme.patch			\
   %D%/packages/patches/gnome-shell-disable-test.patch		\
+  %D%/packages/patches/gnome-settings-daemon-gc.patch		\
   %D%/packages/patches/gnome-todo-delete-esource-duplicate.patch \
   %D%/packages/patches/gnome-tweaks-search-paths.patch		\
   %D%/packages/patches/gnupg-default-pinentry.patch		\
@@ -1082,6 +1087,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gpsbabel-qstring.patch     		\
   %D%/packages/patches/grantlee-merge-theme-dirs.patch		\
   %D%/packages/patches/grep-timing-sensitive-test.patch		\
+  %D%/packages/patches/grim-revert-output-rotation.patch	\
   %D%/packages/patches/grocsvs-dont-use-admiral.patch		\
   %D%/packages/patches/gromacs-tinyxml2.patch			\
   %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch	\
@@ -1130,6 +1136,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/hubbub-sort-entities.patch		\
   %D%/packages/patches/hurd-cross.patch				\
   %D%/packages/patches/hurd-xattr.patch				\
+  %D%/packages/patches/hplip-fix-bug-1898438.patch		\
   %D%/packages/patches/hplip-remove-imageprocessor.patch	\
   %D%/packages/patches/hydra-disable-darcs-test.patch		\
   %D%/packages/patches/icecat-makeicecat.patch			\
@@ -1159,6 +1166,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/jamvm-2.0.0-aarch64-support.patch	\
   %D%/packages/patches/jamvm-2.0.0-disable-branch-patching.patch	\
   %D%/packages/patches/jamvm-2.0.0-opcode-guard.patch		\
+  %D%/packages/patches/java-antlr4-Add-standalone-generator.patch	\
+  %D%/packages/patches/java-antlr4-fix-code-too-large.java	\
   %D%/packages/patches/java-apache-ivy-port-to-latest-bouncycastle.patch	\
   %D%/packages/patches/java-commons-collections-fix-java8.patch \
   %D%/packages/patches/java-jeromq-fix-tests.patch		\
@@ -1200,7 +1209,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/kodi-increase-test-timeout.patch		\
   %D%/packages/patches/kodi-set-libcurl-ssl-parameters.patch		\
   %D%/packages/patches/kodi-skip-test-449.patch		\
-  %D%/packages/patches/konversation-Fix-build-with-Qt-5.11.patch	\
   %D%/packages/patches/laby-make-install.patch			\
   %D%/packages/patches/lcalc-default-parameters-1.patch		\
   %D%/packages/patches/lcalc-default-parameters-2.patch		\
@@ -1227,7 +1235,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/libgnomeui-utf8.patch			\
   %D%/packages/patches/libjxr-fix-function-signature.patch	\
   %D%/packages/patches/libjxr-fix-typos.patch			\
-  %D%/packages/patches/liblouisutdml-fix-tests.patch		\
   %D%/packages/patches/libofa-ftbfs-1.diff		\
   %D%/packages/patches/libofa-curl.diff		\
   %D%/packages/patches/libofa-ftbfs-2.diff		\
@@ -1292,6 +1299,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/luajit-no_ldconfig.patch			\
   %D%/packages/patches/luit-posix.patch				\
   %D%/packages/patches/lvm2-static-link.patch			\
+  %D%/packages/patches/mailutils-fix-uninitialized-variable.patch	\
   %D%/packages/patches/make-impure-dirs.patch			\
   %D%/packages/patches/mariadb-client-test-32bit.patch		\
   %D%/packages/patches/mars-install.patch			\
@@ -1356,6 +1364,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/nsis-env-passthru.patch			\
   %D%/packages/patches/nss-increase-test-timeout.patch		\
   %D%/packages/patches/nss-pkgconfig.patch			\
+  %D%/packages/patches/nss-3.56-pkgconfig.patch			\
   %D%/packages/patches/ntfs-3g-CVE-2019-9755.patch		\
   %D%/packages/patches/nvi-assume-preserve-path.patch		\
   %D%/packages/patches/nvi-dbpagesize-binpower.patch		\
@@ -1402,6 +1411,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/pango-skip-libthai-test.patch		\
   %D%/packages/patches/pciutils-hurd-configure.patch		\
   %D%/packages/patches/ppsspp-disable-upgrade-and-gold.patch		\
+  %D%/packages/patches/samba-fix-fcntl-hint-detection.patch		\
   %D%/packages/patches/sdl-pango-api_additions.patch		\
   %D%/packages/patches/sdl-pango-blit_overflow.patch		\
   %D%/packages/patches/sdl-pango-fillrect_crash.patch		\
@@ -1423,6 +1433,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/perl-module-pluggable-search.patch	\
   %D%/packages/patches/perl-reproducible-build-date.patch	\
   %D%/packages/patches/perl-www-curl-remove-symbol.patch	\
+  %D%/packages/patches/picard-fix-id3-rename-test.patch		\
   %D%/packages/patches/picprog-non-intel-support.patch		\
   %D%/packages/patches/pidgin-add-search-path.patch		\
   %D%/packages/patches/pidgin-libnm.patch			\
@@ -1507,6 +1518,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-unittest2-remove-argparse.patch	\
   %D%/packages/patches/python-waitress-fix-tests.patch		\
   %D%/packages/patches/pypy3-7.3.1-fix-tests.patch		\
+  %D%/packages/patches/qemu-build-info-manual.patch		\
   %D%/packages/patches/qemu-glibc-2.27.patch 			\
   %D%/packages/patches/qrcodegen-cpp-make-install.patch		\
   %D%/packages/patches/qt4-ldflags.patch			\

gnu/packages/abduco.scm

@@ -19,6 +19,7 @@
 
 (define-module (gnu packages abduco)
   #:use-module (guix build-system gnu)
+  #:use-module (guix utils)
   #:use-module (guix download)
   #:use-module (guix licenses)
   #:use-module (guix packages))
@@ -37,7 +38,7 @@
               "1x1m58ckwsprljgmdy93mvgjyg9x3cqrzdf3mysp0mx97zhhj2f9"))))
    (build-system gnu-build-system)
    (arguments
-    `(#:make-flags (list "CC=gcc"
+    `(#:make-flags (list (string-append "CC=" ,(cc-for-target))
                          (string-append "PREFIX=" (assoc-ref %outputs "out")))
       #:phases (modify-phases %standard-phases
                  (delete 'configure)

gnu/packages/accessibility.scm

@@ -3,6 +3,7 @@
 ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Andrew Miloradovsky <andrew@interpretmath.pw>
+;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -272,7 +273,7 @@ available to help to click.")
        `(("hidapi" ,hidapi)))
       (arguments
        `(#:tests? #f ; no tests
-         #:make-flags (list "CC=gcc")
+         #:make-flags (list (string-append "CC=" ,(cc-for-target)))
          #:phases (modify-phases %standard-phases
                     (delete 'configure)
                     ;; Install target in the Makefile does not work for Guix
@@ -308,7 +309,7 @@ devices have vendorId:productId = 0c45:7403 or 0c45:7404.")
     (arguments
      `(#:tests? #f ; none included
        #:make-flags
-       (list "CC=gcc"
+       (list (string-append "CC=" ,(cc-for-target))
              (string-append "prefix=" (assoc-ref %outputs "out")))
        #:phases
        (modify-phases %standard-phases

gnu/packages/admin.scm

@@ -9,7 +9,7 @@
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Peter Feigl <peter.feigl@nexoid.at>
 ;;; Copyright © 2016 John J. Foerch <jjfoerch@earthlink.net>
 ;;; Copyright © 2016, 2017 Nikita <nikita@n0.is>
@@ -443,7 +443,7 @@ graphs and can export its output to different formats.")
 (define-public facter
   (package
     (name "facter")
-    (version "4.0.35")
+    (version "4.0.41")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -452,7 +452,7 @@ graphs and can export its output to different formats.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1f203g2hp96cp8w4x1myhqdj5j09z9s23kylwkrxr69fjhn0vhnb"))))
+                "09i3kv91g2y5hgl75ccd59gjjvkkri4cj80m7smlx6p14hmbgdif"))))
     (build-system ruby-build-system)
     (arguments
      `(#:phases
@@ -514,7 +514,7 @@ or via the @code{facter} Ruby library.")
 (define-public htop
   (package
     (name "htop")
-    (version "3.0.1")
+    (version "3.0.2")
     (source
      (origin
        (method git-fetch)
@@ -522,15 +522,14 @@ or via the @code{facter} Ruby library.")
              (url "https://github.com/htop-dev/htop")
              (commit version)))
        (sha256
-        (base32 "0kjlphdvwwbj91kk91s4ksc954d3c2bznddzx2223jmb1bn9rcsa"))
+        (base32 "1qmqhbnc5yw4brd24yrp85k09770c1c00nl03mkv5pdz2bvqivk7"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (inputs
      `(("ncurses" ,ncurses)))
     (native-inputs
      `(("autoconf" ,autoconf)
-       ("automake" ,automake)
+       ("automake" ,automake)))
-       ("python" ,python-wrapper)))     ; for scripts/MakeHeader.py
     (home-page "https://htop.dev")
     (synopsis "Interactive process viewer")
     (description
@@ -828,7 +827,7 @@ would need and has several interesting built-in capabilities.")
 (define-public netcat-openbsd
   (package
     (name "netcat-openbsd")
-    (version "1.217-1")
+    (version "1.217-2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -837,12 +836,12 @@ would need and has several interesting built-in capabilities.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0kcvi3pav2fdx5c22psjv5dggk4cmrqiaq2cklhqngsk4a7vrjan"))))
+                "19sr52ix14w344pv13ppb0c1wyg5dxhic1fw2q0s3qfmx57b9hhp"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no test suite
        #:make-flags
-       (list "CC=gcc")
+       (list (string-append "CC=" ,(cc-for-target)))
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
@@ -1398,7 +1397,7 @@ system administrator.")
 (define-public sudo
   (package
     (name "sudo")
-    (version "1.9.2")
+    (version "1.9.3p1")
     (source (origin
               (method url-fetch)
               (uri
@@ -1408,7 +1407,7 @@ system administrator.")
                                     version ".tar.gz")))
               (sha256
                (base32
-                "05432672iilb7s52j9l9xzrlambb1wg3k7qvf5973i41y40x563w"))
+                "17mldsg5d08s23cskmjxfa81ibnqw3slgf3l4023j72ywi9xxffw"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -2607,14 +2606,14 @@ done with the @code{auditctl} utility.")
 (define-public nmap
   (package
     (name "nmap")
-    (version "7.80")
+    (version "7.90")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://nmap.org/dist/nmap-" version
                                   ".tar.bz2"))
               (sha256
                (base32
-                "1aizfys6l9f9grm82bk878w56mg0zpkfns3spzj157h98875mypw"))
+                "1s20i84m9bci70lrl0p2j7h3kpbi9snmvyhc3lzc9s3mh92w6msm"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -3589,7 +3588,7 @@ Python loading in HPC environments.")
   (let ((real-name "inxi"))
     (package
       (name "inxi-minimal")
-      (version "3.1.06-1")
+      (version "3.1.07-1")
       (source
        (origin
          (method git-fetch)
@@ -3598,7 +3597,7 @@ Python loading in HPC environments.")
                (commit version)))
          (file-name (git-file-name real-name version))
          (sha256
-          (base32 "0h65n03q9kdsv0i1q5f88i11iv79ca7fqq97rdkzkmiqb4whhnm2"))))
+          (base32 "0hs4m2vmfc6srscaz72r6zpkn6n7msgzlps376ks38gj1l103xfn"))))
       (build-system trivial-build-system)
       (inputs
        `(("bash" ,bash-minimal)

gnu/packages/algebra.scm

@@ -123,15 +123,15 @@ greatest common divisor operations.")
 (define-public cm
   (package
    (name "cm")
-   (version "0.3")
+   (version "0.3.1")
    (source (origin
             (method url-fetch)
             (uri (string-append
-                  "http://www.multiprecision.org/cm/download/cm-"
+                  "http://www.multiprecision.org/downloads/cm-"
                   version ".tar.gz"))
             (sha256
              (base32
-              "1nf5kr0nqmhbzrsrinky18z0ighjpsmb5cr8zyg8jf04bfbyrfmc"))))
+              "0qq6b1kwb1byj8ws33ya5awq0ilkpm32037pi1l4cf2737fg9m42"))))
    (build-system gnu-build-system)
    (propagated-inputs
      `(("mpfrcx" ,mpfrcx)
@@ -151,12 +151,7 @@ line applications.")
 (define-public fplll
   (package
     (name "fplll")
-    ;; The most recent version 5.3.3 fails in the configure phase:
+    (version "5.3.3")
-    ;; ./configure: line 12956: syntax error near unexpected token `LIBQD,'
-    ;; ./configure: line 12956: `  PKG_CHECK_MODULES(LIBQD, qd, have_libqd="yes",'
-    ;; The error disappears when adding qd as an input; but this is
-    ;; supposed to be an optional input.
-    (version "5.3.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -165,13 +160,15 @@ line applications.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "00iyz218ywspizjiimrjdcqvdqmrsb2367zyy3vkmypnf9i9l680"))))
+                "06nyfidagp8pc2kfcw88ldgb2b1xm0a8z31n0sln7j72ihlmd8zj"))
+              (patches (search-patches "fplll-std-fenv.patch"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
-       ("libtool" ,libtool)))
+       ("libtool" ,libtool)
-    (inputs
+       ("pkg-config" ,pkg-config)))
+    (propagated-inputs ; header files pulled in by fplll/defs.h
      `(("gmp" ,gmp)
        ("mpfr" ,mpfr)))
     (home-page "https://github.com/fplll/fplll")
@@ -357,7 +354,7 @@ precision.")
 (define-public giac
   (package
     (name "giac")
-    (version "1.6.0-7")
+    (version "1.6.0-23")
     (source
      (origin
        (method url-fetch)
@@ -369,7 +366,7 @@ precision.")
                            "~parisse/debian/dists/stable/main/source/"
                            "giac_" version ".tar.gz"))
        (sha256
-        (base32 "1pvgp137zcl0rbhdn1j41xxfml7fp771a7x4ph8qrhhlx0hxzn3p"))))
+        (base32 "0bgc3jw9r0f2bkqv0m4hla7r7mxi3fzscnkjfc5cvffp3nk2gwvf"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)
@@ -380,7 +377,8 @@ precision.")
          (add-after 'unpack 'patch-bin-cp
            ;; Some Makefiles contain hard-coded "/bin/cp".
            (lambda _
-             (substitute* (find-files "doc" "^Makefile")
+             (substitute* (cons "micropython-1.12/xcas/Makefile"
+                                (find-files "doc" "^Makefile"))
                (("/bin/cp") (which "cp")))
              #t))
          (add-after 'unpack 'disable-failing-test
@@ -409,7 +407,7 @@ precision.")
                (delete-file (string-append out "/bin/xcasnew"))
                #t))))))
     (inputs
-;;; TODO: Add libnauty.
+     ;; TODO: Add libnauty, unbundle "libmicropython.a".
      `(("fltk" ,fltk)
        ("glpk" ,glpk)
        ("gmp" ,gmp)
@@ -433,6 +431,7 @@ precision.")
     (native-inputs
      `(("bison" ,bison)
        ("flex" ,flex)
+       ("python" ,python-wrapper)
        ("readline" ,readline)
        ("texlive" ,texlive-tiny)))
     (home-page "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html")

gnu/packages/antivirus.scm

@@ -44,14 +44,14 @@
 (define-public clamav
   (package
     (name "clamav")
-    (version "0.102.4")
+    (version "0.103.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.clamav.net/downloads/production/"
                                   "clamav-" version ".tar.gz"))
               (sha256
                (base32
-                "06rrzyrhnr0rswryijpbbzywr6387rv8qjq8sb8cl3h2d1m45ggf"))
+                "0ih5x1rscg2m64y0z20njj7435q8k7ss575cfw7aipdzfx979a9j"))
               (modules '((guix build utils)))
               (snippet
                '(begin

gnu/packages/astronomy.scm

@@ -159,7 +159,7 @@ programs for the manipulation and analysis of astronomical data.")
 (define-public stellarium
   (package
     (name "stellarium")
-    (version "0.20.2")
+    (version "0.20.3")
     (source
      (origin
        (method url-fetch)
@@ -167,7 +167,7 @@ programs for the manipulation and analysis of astronomical data.")
                            "/releases/download/v" version
                            "/stellarium-" version ".tar.gz"))
        (sha256
-        (base32 "16symz212vjvhfabh39a68qf7d0rm574c6djlibj2qd1q9jgj3j0"))))
+        (base32 "0z5r7b1ac43l330xphxnw54xg7jm87ajix8yl4hkq82cs5ja7097"))))
     (build-system cmake-build-system)
     (inputs
      `(("qtbase" ,qtbase)

gnu/packages/audio.scm

@@ -33,6 +33,7 @@
 ;;; Copyright © 2020 Jonathan Frederickson <jonathan@terracrypt.net>
 ;;; Copyright © 2020 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1046,7 +1047,7 @@ tools (analyzer, mono/stereo tools, crossovers).")
      `(("lv2" ,lv2)))
     ;; home-page of the original LADSPA version: http://quitte.de/dsp/caps.html
     (home-page "https://github.com/moddevices/caps-lv2")
-    (synopsis "LV2 port of the CAPS audio plugin colection")
+    (synopsis "LV2 port of the CAPS audio plugin collection")
     (description
      "LV2 port of CAPS, a collection of audio plugins comprising basic virtual
 guitar amplification and a small range of classic effects, signal processors and
@@ -1631,7 +1632,7 @@ follower.")
 (define-public fluidsynth
   (package
     (name "fluidsynth")
-    (version "2.1.4")
+    (version "2.1.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1640,7 +1641,7 @@ follower.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1r3khwyw57ybg5m4x0rvdzq7hgw2484sd52k6bm19akbw8yicfna"))))
+                "0ccpq4p1h1g53ng3961g3lh590qnwvpzwdzpl6ai4j6iazq0bh73"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f                      ; no check target
@@ -2030,7 +2031,7 @@ synchronous execution of all clients, and low latency operation.")
 (define-public jack-2
   (package (inherit jack-1)
     (name "jack2")
-    (version "1.9.13")
+    (version "1.9.14")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/jackaudio/jack2/releases/"
@@ -2039,7 +2040,7 @@ synchronous execution of all clients, and low latency operation.")
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
-               "1d1d403jn4366mqig6g8ghr8057b3rn7gs26b5p3rkal34j20qw2"))))
+               "0z11hf55a6mi8h50hfz5wry9pshlwl4mzfwgslghdh40cwv342m2"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f  ; no check target
@@ -2049,6 +2050,10 @@ synchronous execution of all clients, and low latency operation.")
        (modify-phases %standard-phases
          (add-before 'configure 'set-linkflags
            (lambda _
+             ;; Ensure -lstdc++ is the tail of LDFLAGS or the simdtests.cpp
+             ;; will not link with undefined reference to symbol
+             ;; '__gxx_personality_v0@@CXXABI_1.3'
+             (setenv "LDFLAGS" "-lstdc++")
              ;; Add $libdir to the RUNPATH of all the binaries.
              (substitute* "wscript"
                ((".*CFLAGS.*-Wall.*" m)
@@ -2676,20 +2681,21 @@ different audio devices such as ALSA or PulseAudio.")
 (define-public qjackctl
   (package
     (name "qjackctl")
-    (version "0.5.9")
+    (version "0.6.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/qjackctl/qjackctl/"
                                   version "/qjackctl-" version ".tar.gz"))
               (sha256
                (base32
-                "1saywsda9m124rmjp7i3n0llryaliabjxhqhvqr6dm983qy7pypk"))))
+                "0zbb4jlx56qvcqyhx34mbagkqf3wbxgj84hk0ppf5cmcrxv67d4x"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f))                    ; no check target
     (inputs
      `(("jack" ,jack-1)
        ("alsa-lib" ,alsa-lib)
+       ("portaudio" ,portaudio)
        ("qtbase" ,qtbase)
        ("qtx11extras" ,qtx11extras)))
     (native-inputs
@@ -4464,6 +4470,36 @@ supports both of ID3v1/v2 and APEv2 tags.")
     (home-page "http://tausoft.org/")
     (license license:gpl2+)))
 
+(define-public libsoundio
+  (package
+    (name "libsoundio")
+    (version "2.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/andrewrk/libsoundio")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "12l4rvaypv87vigdrmjz48d4d6sq4gfxf5asvnc4adyabxb73i4x"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f)) ;no tests included
+    (inputs
+     `(("alsa-lib" ,alsa-lib)
+       ("jack" ,jack-1)
+       ("pulseaudio" ,pulseaudio)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://libsound.io")
+    (synopsis "C library for real-time audio input and output")
+    (description "@code{libsoundio} is a C library providing audio input and
+output.  The API is suitable for real-time software such as digital audio
+workstations as well as consumer software such as music players.")
+    (license license:expat)))
+
 (define-public redkite
   (package
     (name "redkite")
@@ -4610,7 +4646,7 @@ in the package.")
 (define-public libaudec
   (package
     (name "libaudec")
-    (version "0.2.2")
+    (version "0.2.3")
     (source
       (origin
         (method git-fetch)
@@ -4620,14 +4656,14 @@ in the package.")
         (file-name (git-file-name name version))
         (sha256
           (base32
-            "04mpmfmqc43asw0m3zxhb6jj4qms7x4jw7mx4xb1d3lh16xllniz"))))
+            "04hw61db8wscj28qjyiaiafx8xl87njgmvqszxyhs4gmg8xgjip7"))))
    (build-system meson-build-system)
    (arguments
-    `(#:configure-flags `("-Denable_tests=true -Denable_ffmpeg=true")))
+     ;; Compile tests.
+    `(#:configure-flags `("-Dtests=true")))
    (inputs
     `(("libsamplerate" ,libsamplerate)
-      ("libsndfile" ,libsndfile)
+      ("libsndfile" ,libsndfile)))
-      ("ffmpeg" ,ffmpeg)))
    (native-inputs
      `(("pkg-config" ,pkg-config)))
    (synopsis "Library for reading and resampling audio files")
@@ -4778,6 +4814,37 @@ edited, converted, compressed and saved.")
        ,@(package-inputs ztoolkit)))
     (synopsis "ZToolkit with SVG support")))
 
+(define-public lsp-dsp-lib
+  (package
+    (name "lsp-dsp-lib")
+    (version "0.5.8")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://github.com/sadko4u/lsp-dsp-lib/"
+                            "releases/download/lsp-dsp-lib-" version
+                            "/lsp-dsp-lib-" version "-src.tar.gz"))
+        (sha256
+         (base32
+          "07w3d2i0z0xmvi1ngcgs7lc5a0da8jvf7rv4dnjk01md43b7fkh1"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; no tests
+       #:make-flags
+       (list (string-append "CC=" ,(cc-for-target)))
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             (invoke "make" "config"
+                     (string-append "PREFIX=" (assoc-ref outputs "out"))))))))
+    (home-page "https://github.com/sadko4u/lsp-dsp-lib")
+    (synopsis "Digital signal processing library")
+    (description "The LSP DSP library provides a set of functions that perform
+SIMD-optimized computing on several hardware architectures.  All functions
+currently operate on IEEE-754 single-precision floating-point numbers.")
+    (license license:lgpl3+)))
+
 (define-public codec2
   (package
     (name "codec2")

gnu/packages/axoloti.scm

@@ -527,7 +527,7 @@ patcher application.")))
                (install-file "dist/Axoloti.jar" share)
 
                ;; Install old firmware
-               (let ((target (string-append share "/old_firmware/"))
+               (let ((target (string-append share "/old_firmware/firmware-1.0.12"))
                      (old-firmware
                       (string-append (assoc-ref inputs "axoloti-runtime")
                                      "/share/axoloti/firmware/")))
@@ -557,7 +557,7 @@ patcher application.")))
                                         toolchain
                                         "/arm-none-eabi/include:"
                                         toolchain
-                                        "/arm-none-eabi/include/arm-none-eabi/armv7e-m")))
+                                        "/arm-none-eabi/include/arm-none-eabi/thumb/v7e-m")))
                        (display
                         (string-append "#!" (which "sh") "\n"
                                        "export CROSS_CPATH=" includes "\n"

gnu/packages/backup.scm

@@ -1066,7 +1066,7 @@ other storage medium.  Subsequent incremental backups can then be layered on
 top of the full backup.  The restore command performs the inverse function of
 dump; it can restore a full backup of a file system.  Single files and
 directory subtrees may also be restored from full or partial backups in
-interractive mode.")
+interactive mode.")
     (license license:bsd-3)))
 
 (define-public burp

gnu/packages/benchmark.scm

@@ -46,14 +46,14 @@
 (define-public fio
   (package
     (name "fio")
-    (version "3.22")
+    (version "3.23")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://brick.kernel.dk/snaps/"
                                   "fio-" version ".tar.bz2"))
               (sha256
                (base32
-                "0f2x917600y6k0xs34ixgfjm4v1ylbh8svpkqi07xy3474g5s2rv"))))
+                "0cy32431hv0i84yrryna5byj4r610n6i1rm8nfflnrznbf051axs"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"

gnu/packages/bioconductor.scm

@@ -4,6 +4,8 @@
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
+;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1795,14 +1797,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.22.3")
+    (version "3.22.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "0q3f55hh0a2hl96272js6gagmgps9cxs8s13pf6fii64rzaz5m7y"))))
+         "0wxgjdikinkqj7jvs2725ak0291q6zhikyf1c93w8cngwvd9i1gq"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2734,7 +2736,7 @@ gene and isoform level using RNA-seq data")
     (home-page "https://bioconductor.org/packages/karyoploteR/")
     (synopsis "Plot customizable linear genomes displaying arbitrary data")
     (description "This package creates karyotype plots of arbitrary genomes and
-offers a complete set of functions to plot arbitrary data on them.  It mimicks
+offers a complete set of functions to plot arbitrary data on them.  It mimics
 many R base graphics functions coupling them with a coordinate change function
 automatically mapping the chromosome and data coordinates into the plot
 coordinates.")
@@ -3672,7 +3674,7 @@ sets of GO terms, gene products and gene clusters.")
     (description
      "Genome wide studies of translational control is emerging as a tool to
 study various biological conditions.  The output from such analysis is both
-the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
+the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
 involved in translation (the actively translating mRNA level) for each mRNA.
 The standard analysis of such data strives towards identifying differential
 translational between two or more sample classes - i.e.  differences in
@@ -4841,7 +4843,7 @@ a more complex way than the simple GC content.  Instead, the base types (A, T,
 G or C) at each position along the probe determine the affinity of each probe.
 The parameters of the position-specific base contributions to the probe
 affinity is estimated in an NSB experiment in which only NSB but no
-gene-specific bidning is expected.")
+gene-specific binding is expected.")
     ;; Any version of the LGPL
     (license license:lgpl2.1+)))
 
@@ -7159,14 +7161,14 @@ data.")
 (define-public r-activedriverwgs
   (package
     (name "r-activedriverwgs")
-    (version "1.0.1")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ActiveDriverWGS" version))
        (sha256
         (base32
-         "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1"))))
+         "0l6h0f54zjvcx19ngq3kp01dypsjqf28vssjm8yzccmpyacfypag"))))
     (properties
      `((upstream-name . "ActiveDriverWGS")))
     (build-system r-build-system)
@@ -7177,8 +7179,9 @@ data.")
        ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicranges" ,r-genomicranges)
        ("r-iranges" ,r-iranges)
-       ("r-plyr" ,r-plyr)
        ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
     (synopsis "Driver discovery tool for cancer whole genomes")
     (description
@@ -7475,7 +7478,7 @@ networks and estimated fluxes can be visualized with hypergraphs.")
 safety and convenience features to the @code{filebacked.big.matrix} class from
 the @code{bigmemory} package.  @code{BigMatrix} protects against segfaults by
 monitoring and gracefully restoring the connection to on-disk data and it also
-protects against accidental data modification with a filesystem-based
+protects against accidental data modification with a file-system-based
 permissions system.  Utilities are provided for using @code{BigMatrix}-derived
 classes as @code{assayData} matrices within the @code{Biobase} package's
 @code{eSet} family of classes.  @code{BigMatrix} provides some optimizations
@@ -8241,3 +8244,483 @@ with:
 @end itemize
 ")
     (license license:gpl2+)))
+
+(define-public r-fourcseq
+  (package
+    (name "r-fourcseq")
+    (version "1.22.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "FourCSeq" version))
+       (sha256
+        (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
+    (properties `((upstream-name . "FourCSeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biostrings" ,r-biostrings)
+       ("r-deseq2" ,r-deseq2)
+       ("r-fda" ,r-fda)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggbio" ,r-ggbio)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gtools" ,r-gtools)
+       ("r-lsd" ,r-lsd)
+       ("r-matrix" ,r-matrix)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page
+     "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
+    (synopsis "Analysis of multiplexed 4C sequencing data")
+    (description
+     "This package is an R package dedicated to the analysis of (multiplexed)
+4C sequencing data.  @code{r-fourcseq} provides a pipeline to detect specific
+interactions between DNA elements and identify differential interactions
+between conditions.  The statistical analysis in R starts with individual bam
+files for each sample as inputs.  To obtain these files, the package contains
+a Python script to demultiplex libraries and trim off primer sequences.  With
+a standard alignment software the required bam files can be then be
+generated.")
+    (license license:gpl3+)))
+
+(define-public r-preprocesscore
+  (package
+    (name "r-preprocesscore")
+    (version "1.50.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "preprocessCore" version))
+       (sha256
+        (base32
+         "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl"))))
+    (properties
+     `((upstream-name . "preprocessCore")))
+    (build-system r-build-system)
+    (home-page "https://github.com/bmbolstad/preprocessCore")
+    (synopsis "Collection of pre-processing functions")
+    (description
+     "This package provides a library of core pre-processing and normalization
+routines.")
+    (license license:lgpl2.0+)))
+
+;; This is a CRAN package, but it depends on preprocessorcore, which is a
+;; Bioconductor package.
+(define-public r-wgcna
+  (package
+    (name "r-wgcna")
+    (version "1.69")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "WGCNA" version))
+       (sha256
+        (base32
+         "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
+    (properties `((upstream-name . "WGCNA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-doparallel" ,r-doparallel)
+       ("r-dynamictreecut" ,r-dynamictreecut)
+       ("r-fastcluster" ,r-fastcluster)
+       ("r-foreach" ,r-foreach)
+       ("r-go-db" ,r-go-db)
+       ("r-hmisc" ,r-hmisc)
+       ("r-impute" ,r-impute)
+       ("r-rcpp" ,r-rcpp)
+       ("r-survival" ,r-survival)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-preprocesscore" ,r-preprocesscore)))
+    (home-page
+     "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
+    (synopsis "Weighted correlation network analysis")
+    (description
+     "This package provides functions necessary to perform Weighted
+Correlation Network Analysis on high-dimensional data.  It includes functions
+for rudimentary data cleaning, construction and summarization of correlation
+networks, module identification and functions for relating both variables and
+modules to sample traits.  It also includes a number of utility functions for
+data manipulation and visualization.")
+    (license license:gpl2+)))
+
+(define-public r-rgraphviz
+  (package
+    (name "r-rgraphviz")
+    (version "2.32.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Rgraphviz" version))
+       (sha256
+        (base32
+         "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
+    (properties `((upstream-name . "Rgraphviz")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'make-reproducible
+           (lambda _
+             ;; The replacement value is taken from src/graphviz/builddate.h
+             (substitute* "src/graphviz/configure"
+               (("VERSION_DATE=.*")
+                "VERSION_DATE=20200427.2341\n"))
+             #t)))))
+    ;; FIXME: Rgraphviz bundles the sources of an older variant of
+    ;; graphviz.  It does not build with the latest version of graphviz, so
+    ;; we do not add graphviz to the inputs.
+    (inputs `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-graph" ,r-graph)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "https://bioconductor.org/packages/Rgraphviz")
+    (synopsis "Plotting capabilities for R graph objects")
+    (description
+     "This package interfaces R with the graphviz library for plotting R graph
+objects from the @code{graph} package.")
+    (license license:epl1.0)))
+
+(define-public r-fithic
+  (package
+    (name "r-fithic")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "FitHiC" version))
+              (sha256
+               (base32
+                "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp"))))
+    (properties `((upstream-name . "FitHiC")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-data-table" ,r-data-table)
+       ("r-fdrtool" ,r-fdrtool)
+       ("r-rcpp" ,r-rcpp)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/FitHiC")
+    (synopsis "Confidence estimation for intra-chromosomal contact maps")
+    (description
+     "Fit-Hi-C is a tool for assigning statistical confidence estimates to
+intra-chromosomal contact maps produced by genome-wide genome architecture
+assays such as Hi-C.")
+    (license license:gpl2+)))
+
+(define-public r-hitc
+  (package
+    (name "r-hitc")
+    (version "1.32.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "HiTC" version))
+              (sha256
+               (base32
+                "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy"))))
+    (properties `((upstream-name . "HiTC")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-matrix" ,r-matrix)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rtracklayer" ,r-rtracklayer)))
+    (home-page "https://bioconductor.org/packages/HiTC")
+    (synopsis "High throughput chromosome conformation capture analysis")
+    (description
+     "The HiTC package was developed to explore high-throughput \"C\" data
+such as 5C or Hi-C.  Dedicated R classes as well as standard methods for
+quality controls, normalization, visualization, and further analysis are also
+provided.")
+    (license license:artistic2.0)))
+
+(define-public r-hdf5array
+  (package
+    (name "r-hdf5array")
+    (version "1.16.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "HDF5Array" version))
+       (sha256
+        (base32
+         "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn"))))
+    (properties `((upstream-name . "HDF5Array")))
+    (build-system r-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-iranges" ,r-iranges)
+       ("r-matrix" ,r-matrix)
+       ("r-rhdf5" ,r-rhdf5)
+       ("r-rhdf5lib" ,r-rhdf5lib)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/HDF5Array")
+    (synopsis "HDF5 back end for DelayedArray objects")
+    (description "This package provides an array-like container for convenient
+access and manipulation of HDF5 datasets.  It supports delayed operations and
+block processing.")
+    (license license:artistic2.0)))
+
+(define-public r-rhdf5lib
+  (package
+    (name "r-rhdf5lib")
+    (version "1.10.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Rhdf5lib" version))
+       (sha256
+        (base32
+         "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; Delete bundled binaries
+           (delete-file-recursively "src/wininclude/")
+           (delete-file-recursively "src/winlib-4.9.3/")
+           (delete-file-recursively "src/winlib-8.3.0/")
+           (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
+           #t))))
+    (properties `((upstream-name . "Rhdf5lib")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'do-not-use-bundled-hdf5
+           (lambda* (#:key inputs #:allow-other-keys)
+             (for-each delete-file '("configure" "configure.ac"))
+             ;; Do not make other packages link with the proprietary libsz.
+             (substitute* "R/zzz.R"
+               ((" \"%s/libsz.a\"") ""))
+             (with-directory-excursion "src"
+               (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
+               (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
+                            "hdf5")
+               ;; Remove timestamp and host system information to make
+               ;; the build reproducible.
+               (substitute* "hdf5/src/libhdf5.settings.in"
+                 (("Configured on: @CONFIG_DATE@")
+                  "Configured on: Guix")
+                 (("Uname information:.*")
+                  "Uname information: Linux\n")
+                 ;; Remove unnecessary store reference.
+                 (("C Compiler:.*")
+                  "C Compiler: GCC\n"))
+               (rename-file "Makevars.in" "Makevars")
+               (substitute* "Makevars"
+                 (("@ZLIB_LIB@") "-lz")
+                 (("@ZLIB_INCLUDE@") "")
+                 (("HDF5_CXX_LIB=.*")
+                  (string-append "HDF5_CXX_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
+                 (("HDF5_LIB=.*")
+                  (string-append "HDF5_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
+                 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
+                 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
+                 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
+                 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
+                 (("HDF5_HL_LIB=.*")
+                  (string-append "HDF5_HL_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
+                 (("HDF5_HL_CXX_LIB=.*")
+                  (string-append "HDF5_HL_CXX_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
+                 ;; szip is non-free software
+                 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
+                 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
+             #t)))))
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("hdf5" ,hdf5-1.10)))
+    (native-inputs
+     `(("hdf5-source" ,(package-source hdf5-1.10))
+       ("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/Rhdf5lib")
+    (synopsis "HDF5 library as an R package")
+    (description "This package provides C and C++ HDF5 libraries for use in R
+packages.")
+    (license license:artistic2.0)))
+
+(define-public r-beachmat
+  (package
+    (name "r-beachmat")
+    (version "2.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "beachmat" version))
+       (sha256
+        (base32
+         "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-matrix" ,r-matrix)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/beachmat")
+    (synopsis "Compiling Bioconductor to handle each matrix type")
+    (description "This package provides a consistent C++ class interface for a
+variety of commonly used matrix types, including sparse and HDF5-backed
+matrices.")
+    (license license:gpl3)))
+
+(define-public r-singlecellexperiment
+  (package
+    (name "r-singlecellexperiment")
+    (version "1.10.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "SingleCellExperiment" version))
+       (sha256
+        (base32
+         "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp"))))
+    (properties
+     `((upstream-name . "SingleCellExperiment")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/SingleCellExperiment")
+    (synopsis "S4 classes for single cell data")
+    (description "This package defines an S4 class for storing data from
+single-cell experiments.  This includes specialized methods to store and
+retrieve spike-in information, dimensionality reduction coordinates and size
+factors for each cell, along with the usual metadata for genes and
+libraries.")
+    (license license:gpl3)))
+
+(define-public r-scater
+  (package
+    (name "r-scater")
+    (version "1.16.2")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "scater" version))
+              (sha256
+               (base32
+                "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-beachmat" ,r-beachmat)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocneighbors" ,r-biocneighbors)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biocsingular" ,r-biocsingular)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+       ("r-ggbeeswarm" ,r-ggbeeswarm)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rlang" ,r-rlang)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-viridis" ,r-viridis)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/davismcc/scater")
+    (synopsis "Single-cell analysis toolkit for gene expression data in R")
+    (description "This package provides a collection of tools for doing
+various analyses of single-cell RNA-seq gene expression data, with a focus on
+quality control.")
+    (license license:gpl2+)))
+
+(define-public r-scran
+  (package
+    (name "r-scran")
+    (version "1.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "scran" version))
+       (sha256
+        (base32
+         "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-beachmat" ,r-beachmat)
+       ("r-bh" ,r-bh)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocneighbors" ,r-biocneighbors)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biocsingular" ,r-biocsingular)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+       ("r-dqrng" ,r-dqrng)
+       ("r-edger" ,r-edger)
+       ("r-igraph" ,r-igraph)
+       ("r-iranges" ,r-iranges)
+       ("r-limma" ,r-limma)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scater" ,r-scater)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-statmod" ,r-statmod)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/scran")
+    (synopsis "Methods for single-cell RNA-Seq data analysis")
+    (description "This package implements a variety of low-level analyses of
+single-cell RNA-seq data.  Methods are provided for normalization of
+cell-specific biases, assignment of cell cycle phase, and detection of highly
+variable and significantly correlated genes.")
+    (license license:gpl3)))
+
+(define-public r-delayedmatrixstats
+  (package
+    (name "r-delayedmatrixstats")
+    (version "1.10.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DelayedMatrixStats" version))
+       (sha256
+        (base32
+         "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx"))))
+    (properties
+     `((upstream-name . "DelayedMatrixStats")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocparallel" ,r-biocparallel)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-hdf5array" ,r-hdf5array)
+       ("r-iranges" ,r-iranges)
+       ("r-matrix" ,r-matrix)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
+    (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
+    (description
+     "This package provides a port of the @code{matrixStats} API for use with
+@code{DelayedMatrix} objects from the @code{DelayedArray} package.  It
+contains high-performing functions operating on rows and columns of
+@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
+@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}.  Functions
+are optimized per data type and for subsetted calculations such that both
+memory usage and processing time is minimized.")
+    (license license:expat)))

gnu/packages/bioinformatics.scm

@@ -11,7 +11,7 @@
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
-;;; Copyright © 2018, 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
 ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
@@ -4496,7 +4496,7 @@ sequencing tag position and orientation.")
 (define-public mafft
   (package
     (name "mafft")
-    (version "7.394")
+    (version "7.471")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -4505,7 +4505,7 @@ sequencing tag position and orientation.")
               (file-name (string-append name "-" version ".tgz"))
               (sha256
                (base32
-                "0bacjkxfg944p5khhyh5rd4y7wkjc9qk4v2jjj442sqlq0f8ar7b"))))
+                "0r1973fx2scq4712zdqfy67wkzqj0c0bhrdy4jxhvq40mdxyry30"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no automated tests, though there are tests in the read me
@@ -4568,7 +4568,7 @@ sequencing tag position and orientation.")
        ("gawk" ,gawk)
        ("grep" ,grep)
        ("coreutils" ,coreutils)))
-    (home-page "http://mafft.cbrc.jp/alignment/software/")
+    (home-page "https://mafft.cbrc.jp/alignment/software/")
     (synopsis "Multiple sequence alignment program")
     (description
      "MAFFT offers a range of multiple alignment methods for nucleotide and
@@ -4576,7 +4576,7 @@ protein sequences.  For instance, it offers L-INS-i (accurate; for alignment
 of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000
 sequences).")
     (license (license:non-copyleft
-              "http://mafft.cbrc.jp/alignment/software/license.txt"
+              "https://mafft.cbrc.jp/alignment/software/license.txt"
               "BSD-3 with different formatting"))))
 
 (define-public mash
@@ -10599,343 +10599,6 @@ EMBL-EBI GWAS catalog.")
 visualizations for publication-quality multi-panel figures.")
     (license license:gpl2+)))
 
-(define-public r-fithic
-  (package
-    (name "r-fithic")
-    (version "1.14.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "FitHiC" version))
-              (sha256
-               (base32
-                "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp"))))
-    (properties `((upstream-name . "FitHiC")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-data-table" ,r-data-table)
-       ("r-fdrtool" ,r-fdrtool)
-       ("r-rcpp" ,r-rcpp)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/FitHiC")
-    (synopsis "Confidence estimation for intra-chromosomal contact maps")
-    (description
-     "Fit-Hi-C is a tool for assigning statistical confidence estimates to
-intra-chromosomal contact maps produced by genome-wide genome architecture
-assays such as Hi-C.")
-    (license license:gpl2+)))
-
-(define-public r-hitc
-  (package
-    (name "r-hitc")
-    (version "1.32.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "HiTC" version))
-              (sha256
-               (base32
-                "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy"))))
-    (properties `((upstream-name . "HiTC")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rtracklayer" ,r-rtracklayer)))
-    (home-page "https://bioconductor.org/packages/HiTC")
-    (synopsis "High throughput chromosome conformation capture analysis")
-    (description
-     "The HiTC package was developed to explore high-throughput \"C\" data
-such as 5C or Hi-C.  Dedicated R classes as well as standard methods for
-quality controls, normalization, visualization, and further analysis are also
-provided.")
-    (license license:artistic2.0)))
-
-(define-public r-hdf5array
-  (package
-    (name "r-hdf5array")
-    (version "1.16.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "HDF5Array" version))
-       (sha256
-        (base32
-         "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn"))))
-    (properties `((upstream-name . "HDF5Array")))
-    (build-system r-build-system)
-    (inputs
-     `(("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-rhdf5" ,r-rhdf5)
-       ("r-rhdf5lib" ,r-rhdf5lib)
-       ("r-s4vectors" ,r-s4vectors)))
-    (home-page "https://bioconductor.org/packages/HDF5Array")
-    (synopsis "HDF5 back end for DelayedArray objects")
-    (description "This package provides an array-like container for convenient
-access and manipulation of HDF5 datasets.  It supports delayed operations and
-block processing.")
-    (license license:artistic2.0)))
-
-(define-public r-rhdf5lib
-  (package
-    (name "r-rhdf5lib")
-    (version "1.10.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "Rhdf5lib" version))
-       (sha256
-        (base32
-         "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           ;; Delete bundled binaries
-           (delete-file-recursively "src/wininclude/")
-           (delete-file-recursively "src/winlib-4.9.3/")
-           (delete-file-recursively "src/winlib-8.3.0/")
-           (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
-           #t))))
-    (properties `((upstream-name . "Rhdf5lib")))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'do-not-use-bundled-hdf5
-           (lambda* (#:key inputs #:allow-other-keys)
-             (for-each delete-file '("configure" "configure.ac"))
-             ;; Do not make other packages link with the proprietary libsz.
-             (substitute* "R/zzz.R"
-               ((" \"%s/libsz.a\"") ""))
-             (with-directory-excursion "src"
-               (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
-               (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
-                            "hdf5")
-               ;; Remove timestamp and host system information to make
-               ;; the build reproducible.
-               (substitute* "hdf5/src/libhdf5.settings.in"
-                 (("Configured on: @CONFIG_DATE@")
-                  "Configured on: Guix")
-                 (("Uname information:.*")
-                  "Uname information: Linux\n")
-                 ;; Remove unnecessary store reference.
-                 (("C Compiler:.*")
-                  "C Compiler: GCC\n"))
-               (rename-file "Makevars.in" "Makevars")
-               (substitute* "Makevars"
-                 (("@ZLIB_LIB@") "-lz")
-                 (("@ZLIB_INCLUDE@") "")
-                 (("HDF5_CXX_LIB=.*")
-                  (string-append "HDF5_CXX_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
-                 (("HDF5_LIB=.*")
-                  (string-append "HDF5_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
-                 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
-                 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
-                 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
-                 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
-                 (("HDF5_HL_LIB=.*")
-                  (string-append "HDF5_HL_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
-                 (("HDF5_HL_CXX_LIB=.*")
-                  (string-append "HDF5_HL_CXX_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
-                 ;; szip is non-free software
-                 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
-                 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
-             #t)))))
-    (inputs
-     `(("zlib" ,zlib)))
-    (propagated-inputs
-     `(("hdf5" ,hdf5-1.10)))
-    (native-inputs
-     `(("hdf5-source" ,(package-source hdf5-1.10))
-       ("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/Rhdf5lib")
-    (synopsis "HDF5 library as an R package")
-    (description "This package provides C and C++ HDF5 libraries for use in R
-packages.")
-    (license license:artistic2.0)))
-
-(define-public r-beachmat
-  (package
-    (name "r-beachmat")
-    (version "2.4.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "beachmat" version))
-       (sha256
-        (base32
-         "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-matrix" ,r-matrix)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/beachmat")
-    (synopsis "Compiling Bioconductor to handle each matrix type")
-    (description "This package provides a consistent C++ class interface for a
-variety of commonly used matrix types, including sparse and HDF5-backed
-matrices.")
-    (license license:gpl3)))
-
-(define-public r-singlecellexperiment
-  (package
-    (name "r-singlecellexperiment")
-    (version "1.10.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "SingleCellExperiment" version))
-       (sha256
-        (base32
-         "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp"))))
-    (properties
-     `((upstream-name . "SingleCellExperiment")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/SingleCellExperiment")
-    (synopsis "S4 classes for single cell data")
-    (description "This package defines an S4 class for storing data from
-single-cell experiments.  This includes specialized methods to store and
-retrieve spike-in information, dimensionality reduction coordinates and size
-factors for each cell, along with the usual metadata for genes and
-libraries.")
-    (license license:gpl3)))
-
-(define-public r-scater
-  (package
-    (name "r-scater")
-    (version "1.16.2")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "scater" version))
-              (sha256
-               (base32
-                "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-beachmat" ,r-beachmat)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocneighbors" ,r-biocneighbors)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biocsingular" ,r-biocsingular)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
-       ("r-ggbeeswarm" ,r-ggbeeswarm)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rlang" ,r-rlang)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-viridis" ,r-viridis)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/davismcc/scater")
-    (synopsis "Single-cell analysis toolkit for gene expression data in R")
-    (description "This package provides a collection of tools for doing
-various analyses of single-cell RNA-seq gene expression data, with a focus on
-quality control.")
-    (license license:gpl2+)))
-
-(define-public r-scran
-  (package
-    (name "r-scran")
-    (version "1.16.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "scran" version))
-       (sha256
-        (base32
-         "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-beachmat" ,r-beachmat)
-       ("r-bh" ,r-bh)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocneighbors" ,r-biocneighbors)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biocsingular" ,r-biocsingular)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
-       ("r-dqrng" ,r-dqrng)
-       ("r-edger" ,r-edger)
-       ("r-igraph" ,r-igraph)
-       ("r-iranges" ,r-iranges)
-       ("r-limma" ,r-limma)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scater" ,r-scater)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-statmod" ,r-statmod)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/scran")
-    (synopsis "Methods for single-cell RNA-Seq data analysis")
-    (description "This package implements a variety of low-level analyses of
-single-cell RNA-seq data.  Methods are provided for normalization of
-cell-specific biases, assignment of cell cycle phase, and detection of highly
-variable and significantly correlated genes.")
-    (license license:gpl3)))
-
-(define-public r-delayedmatrixstats
-  (package
-    (name "r-delayedmatrixstats")
-    (version "1.10.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "DelayedMatrixStats" version))
-       (sha256
-        (base32
-         "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx"))))
-    (properties
-     `((upstream-name . "DelayedMatrixStats")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-hdf5array" ,r-hdf5array)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-s4vectors" ,r-s4vectors)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
-    (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
-    (description
-     "This package provides a port of the @code{matrixStats} API for use with
-@code{DelayedMatrix} objects from the @code{DelayedArray} package.  It
-contains high-performing functions operating on rows and columns of
-@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
-@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}.  Functions
-are optimized per data type and for subsetted calculations such that both
-memory usage and processing time is minimized.")
-    (license license:expat)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))

gnu/packages/bootloaders.scm

@@ -465,7 +465,6 @@ tree binary files.  These are board description files used by Linux and BSD.")
        ("python" ,python)
        ("python-coverage" ,python-coverage)
        ("python-pytest" ,python-pytest)
-       ("sdl2" ,sdl2)
        ("swig" ,swig)))
     (build-system  gnu-build-system)
     (home-page "https://www.denx.de/wiki/U-Boot/")
@@ -478,6 +477,9 @@ also initializes the boards (RAM etc).")
   (package
     (inherit u-boot)
     (name "u-boot-tools")
+    (native-inputs
+     `(("sdl2" ,sdl2)
+       ,@(package-native-inputs u-boot)))
     (arguments
      `(#:make-flags '("HOSTCC=gcc")
        #:test-target "tests"

gnu/packages/build-tools.scm

@@ -89,7 +89,7 @@ makes a few sacrifices to acquire fast full and incremental build times.")
 (define-public bear
   (package
     (name "bear")
-    (version "2.4.3")
+    (version "2.4.4")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -98,7 +98,7 @@ makes a few sacrifices to acquire fast full and incremental build times.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "19fk4flfykbzhb89ppmzqf0zlrkbjm6ajl9fsayndj9km5ys0041"))))
+                "184dqjcpxiwcfziyi67zzran2c4fal1r3j8nhjdjadcmfxf4389d"))))
     (build-system cmake-build-system)
     (inputs
      `(("python" ,python-wrapper)))
@@ -211,6 +211,21 @@ files}, are written in a custom domain-specific language (@dfn{DSL}) that
 resembles Python.")
     (license license:asl2.0)))
 
+;; Added temporarily for packages that need it.
+;; TODO: Remove when core-updates is merged.
+(define-public meson-0.55
+  (package
+    (inherit meson)
+    (version "0.55.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/mesonbuild/meson/"
+                                  "releases/download/" version  "/meson-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1070kjiirxxdfppmrhi3wsc6rykay1zlciqrzayjhjg0hkw42mrv"))))))
+
 (define-public meson-for-build
   (package
     (inherit meson)

gnu/packages/ccache.scm

@@ -30,14 +30,14 @@
 (define-public ccache
   (package
     (name "ccache")
-    (version "3.7.11")
+    (version "3.7.12")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/ccache/ccache/releases/download/v"
                            version "/ccache-" version ".tar.xz"))
        (sha256
-        (base32 "0s1g0ylrayzax68xlqnxx46f5bhvr2pcm1yzswmj0kcs14404icd"))))
+        (base32 "005liq8csgxdn7m9hj2ah07hishww855p8sc96y1hrnwc21lwbx0"))))
     (build-system gnu-build-system)
     (native-inputs `(("perl" ,perl)     ; for test/run
                      ("which" ,(@ (gnu packages base) which))))

gnu/packages/check.scm

@@ -349,7 +349,7 @@ a multi-paradigm automated test framework for C++ and Objective-C.")
 (define-public catch-framework2
   (package
     (name "catch2")
-    (version "2.13.0")
+    (version "2.13.1")
     (home-page "https://github.com/catchorg/Catch2")
     (source (origin
               (method git-fetch)
@@ -359,7 +359,7 @@ a multi-paradigm automated test framework for C++ and Objective-C.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0i4w0c9280a5fyi00mvvf13wlnfzyifr487n1iyr30zvvj5s5f1h"))))
+                "1fbzdqzvad3nxsxlwd5ws7csj6rbyyrza0ckq6km2cf5bhhxagrs"))))
     (build-system cmake-build-system)
     (inputs
      `(("python" ,python-wrapper)))
@@ -2693,7 +2693,7 @@ provides a simple way to achieve this.")
 (define-public umockdev
   (package
     (name "umockdev")
-    (version "0.14.2")
+    (version "0.14.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/martinpitt/umockdev/"
@@ -2701,7 +2701,7 @@ provides a simple way to achieve this.")
                                   "umockdev-" version ".tar.xz"))
               (sha256
                (base32
-                "1nh6xsssmssmk0lxp9c9dmq3wzlpbpkg77nmmd09csbpybibgxfp"))))
+                "15smnxwplk48nas2c8ji6a5fqcsh770f1yl5nc2j5iprjspbm4mg"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/ci.scm

@@ -39,6 +39,7 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages perl-compression)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages sqlite)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages version-control)
@@ -46,9 +47,29 @@
   #:use-module (gnu packages xml)
   #:use-module (guix build-system gnu))
 
+;; Guile-Sqlite3 package adding SQL query logging support.
+;; Remove it when next Guile-Sqlite3 release is out.
+(define-public guile-sqlite3-dev
+  (let ((commit "22ef45d268de7707cbbb943c404f9b0c1668e2e1")
+        (revision "1"))
+    (package
+      (inherit guile-sqlite3)
+      (name "guile-sqlite3")
+      (version (git-version "0.1.2" revision commit))
+      (home-page "https://notabug.org/mothacehe/guile-sqlite3.git")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url home-page)
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1q90f8zhw9n1c39szd2ba7aj5fi92m09pnlv0z7jbhnnjam5jwcd"))
+                (file-name (string-append name "-" version "-checkout")))))))
+
 (define-public cuirass
-  (let ((commit "00c7b4bb4432ff3f5ba28dca3625479e1fa129d8")
+  (let ((commit "71aac24f3fe8cb396c9d232453d8721519cae914")
-        (revision "44"))
+        (revision "50"))
     (package
       (name "cuirass")
       (version (git-version "0.0.1" revision commit))
@@ -60,7 +81,7 @@
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0xjl2in9hg24liahrhfr637ddwib3904ax9rpggyphamnvcxygzr"))))
+                  "0d9s39zi44fvck3dqd58j35wdiwa1s4f86lms3gagvkzbc0mwdia"))))
       (build-system gnu-build-system)
       (arguments
        '(#:modules ((guix build utils)
@@ -122,11 +143,11 @@
                    `("GUILE_LOAD_COMPILED_PATH" ":" prefix (,objs)))
                  #t))))))
       (inputs
-       `(("guile" ,@(assoc-ref (package-native-inputs guix) "guile"))
+       `(("guile" ,guile-3.0/libgc-7)
          ("guile-fibers" ,guile-fibers)
          ("guile-gcrypt" ,guile-gcrypt)
          ("guile-json" ,guile-json-4)
-         ("guile-sqlite3" ,guile-sqlite3)
+         ("guile-sqlite3" ,guile-sqlite3-dev)
          ("guile-git" ,guile-git)
          ("guile-zlib" ,guile-zlib)
          ;; FIXME: this is propagated by "guile-git", but it needs to be among

gnu/packages/code.scm

@@ -233,7 +233,7 @@ COCOMO model or user-provided parameters.")
 (define-public cloc
   (package
     (name "cloc")
-    (version "1.86")
+    (version "1.88")
     (source
      (origin
        (method git-fetch)
@@ -242,7 +242,7 @@ COCOMO model or user-provided parameters.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "082gj2b3x11bilz8c572dd60vn6n0fhld5zhi7wk7g1wy9wlgm9w"))))
+        (base32 "1ixgswzbzv63bl50gb2kgaqr0jcicjz6w610hi9fal1i7744zraw"))))
     (build-system gnu-build-system)
     (inputs
      `(("coreutils" ,coreutils)
@@ -470,24 +470,17 @@ stack traces.")
     (license license:gpl3+)))
 
 (define-public lcov
-  ;; Use a recent commit from upstream since the latest official release
-  ;; (1.14) doesn't support GCC 9 (see:
-  ;; https://github.com/linux-test-project/lcov/issues/58).
-  (let* ((commit "40580cd65909bc8324ae09b36bca2e178652ff3f")
-         (revision "0")
-         (version (git-version "1.14" revision commit)))
   (package
     (name "lcov")
-      (version "1.14")
+    (version "1.15")
-      (source (origin
+    (source
-                (method git-fetch)
+     (origin
-                (uri (git-reference
+       (method url-fetch)
-                      (url "https://github.com/linux-test-project/lcov")
+       (uri (string-append "https://github.com/linux-test-project/lcov"
-                      (commit commit)))
+                           "/releases/download/v" version
-                (file-name (git-file-name name version))
+                           "/lcov-" version ".tar.gz"))
        (sha256
-                 (base32
+        (base32 "0fh5z0q5wg2jxr2nn5w7321y0zg9rwk75j3k5hnamjdy6gxa5kf1"))))
-                  "0shgmh6fzhnj1qfdl90jgjmlbb1ih1qh879dca8hc58yggy3hqgb"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"
@@ -513,8 +506,8 @@ stack traces.")
                  `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))))
              #t)))))
     (inputs `(("perl" ,perl)
-                ("perl-json" ,perl-json)
+              ("perl-io-compress" ,perl-io-compress)
-                ("perl-perlio-gzip" ,perl-perlio-gzip)))
+              ("perl-json" ,perl-json)))
     (home-page "http://ltp.sourceforge.net/coverage/lcov.php")
     (synopsis "Code coverage tool that enhances GNU gcov")
     (description "LCOV is an extension of @command{gcov}, a tool part of the
@@ -523,7 +516,7 @@ are actually executed (i.e., \"covered\") while running a particular test
 case.  The extension consists of a set of Perl scripts which build on the
 textual @command{gcov} output to implement the following enhanced
 functionality such as HTML output.")
-      (license license:gpl2+))))
+    (license license:gpl2+)))
 
 (define-public kcov
   (package

gnu/packages/commencement.scm

@@ -381,7 +381,7 @@ $MES -e '(mescc)' module/mescc.scm -- \"$@\"
     (inputs '())
     (propagated-inputs '())
     (native-inputs
-     `(("nyacc-source" ,(origin (inherit (package-source nyacc))
+     `(("nyacc-source" ,(origin (inherit (package-source nyacc-0.99))
                                 (snippet #f)))
        ("mes" ,%bootstrap-mes-rewired)
        ("mescc-tools" ,%bootstrap-mescc-tools)
@@ -477,7 +477,7 @@ $MES -e '(mescc)' module/mescc.scm -- \"$@\"
     (propagated-inputs '())
     (native-inputs
      `(("mes" ,mes-boot)
-       ("nyacc-source" ,(origin (inherit (package-source nyacc))
+       ("nyacc-source" ,(origin (inherit (package-source nyacc-0.99))
                                 (snippet #f)))
        ("mescc-tools" ,%bootstrap-mescc-tools)
        ,@(%boot-gash-inputs)))
@@ -788,14 +788,17 @@ $MES -e '(mescc)' module/mescc.scm -- \"$@\"
              (substitute* "config.h"
                (("#define GETCWD_BROKEN 1") "#undef GETCWD_BROKEN"))
              (let ((config.h (open-file "config.h" "a")))
-               (display (string-append "
+               (display (string-append
+                         ;; XXX TODO: remove nested ,(string-append ...) and
+                         ;; store file name on next rebuild cycle
+                         ,(string-append "
 // tcc: error: undefined symbol 'enable_hostname_completion'
 #define enable_hostname_completion(on_or_off) 0
 
-// /gnu/store/cq0cmv35s9dhilx14zaghlc08gpc0hwr-tcc-boot0-0.9.26-6.c004e9a/lib/libc.a: error: 'sigprocmask' defined twice
+// /gnu/store/" "cq0cmv35s9dhilx14zaghlc08gpc0hwr-tcc-boot0-0.9.26-6.c004e9a/lib/libc.a: error: 'sigprocmask' defined twice
 #define HAVE_POSIX_SIGNALS 1
 #define endpwent(x) 0
-")
+"))
                         config.h)
                (close config.h))
              #t))
@@ -3861,7 +3864,8 @@ COREUTILS-FINAL vs. COREUTILS, etc."
       (description
        "This package provides a complete GCC tool chain for C/C++ development to
 be installed in user profiles.  This includes GCC, as well as libc (headers and
-binaries, plus debugging symbols in the @code{debug} output), and Binutils.")
+binaries, plus debugging symbols in the @code{debug} output), and Binutils.  GCC
+is the GNU Compiler Collection.")
       (home-page "https://gcc.gnu.org/")
       (outputs '("out" "debug" "static"))
 

gnu/packages/compression.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2017, 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2017, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
@@ -28,6 +28,7 @@
 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2020 Lars-Dominik Braun <lars@6xq.net>
+;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1762,7 +1763,8 @@ Clzip is intended to be fully compatible with the regular lzip package.")
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
-       (list "CC=gcc"
+       (list (string-append "CC=" ,(cc-for-target))
+             "--disable-static"
              "--enable-shared")))       ; only static (.a) is built by default
     (home-page "https://www.nongnu.org/lzip/lzlib.html")
     (synopsis "Lzip data compression C library")
@@ -2249,3 +2251,31 @@ computations.")
 with their error correction data losslessly rearranged for better compression,
 to their original, binary CD format.")
     (license license:gpl3+)))
+
+(define-public tarlz
+  (package
+    (name "tarlz")
+    (version "0.17")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://savannah/lzip/tarlz/"
+                           "tarlz-" version ".tar.lz"))
+       (sha256
+        (base32 "0gpdm6z9pdr5bn31kxg73wm686hhpb5pdf5782pbl5a4xqqhqj90"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("lzip" ,lzip)))
+    (inputs
+     `(("lzlib" ,lzlib)))
+    (home-page "https://www.nongnu.org/lzip/tarlz.html")
+    (synopsis "Combination of the tar archiver and the lzip compressor")
+    (description
+     "Tarlz is a massively parallel (multi-threaded) combined implementation of
+the tar archiver and the lzip compressor.  Tarlz creates, lists, and extracts
+archives in a simplified and safer variant of the POSIX pax format compressed
+with lzip, keeping the alignment between tar members and lzip members.  The
+resulting multimember tar.lz archive is fully backward compatible with standard
+tar tools like GNU tar, which treat it like any other tar.lz archive.  Tarlz
+can append files to the end of such compressed archives.")
+    (license license:gpl2+)))

gnu/packages/coq.scm

@@ -5,6 +5,7 @@
 ;;; Copyright © 2020 Brett Gilio <brettg@gnu.org>
 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2020 raingloom <raingloom@riseup.net>
+;;; Copyright © 2020 Robin Green <greenrd@greenrd.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -34,6 +35,7 @@
   #:use-module (gnu packages ocaml)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages rsync)
   #:use-module (gnu packages texinfo)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system ocaml)
@@ -47,7 +49,7 @@
 (define-public coq
   (package
     (name "coq")
-    (version "8.10.2")
+    (version "8.11.2")
     (source
      (origin
        (method git-fetch)
@@ -57,7 +59,7 @@
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0ji2rzd70b3hcwfw97qk7rv3m2977ylqnq82l1555dp3njr8nm3q"))))
+         "1gia82dkmzqspw2w3s4gjyh39ghbmw4i41i4hyzc91g7mza17nbz"))))
     (native-search-paths
      (list (search-path-specification
             (variable "COQPATH")
@@ -70,7 +72,9 @@
        ("camlp5" ,camlp5)
        ("ocaml-num" ,ocaml-num)))
     (native-inputs
-     `(("ocaml-ounit" ,ocaml-ounit)))
+     `(("ocaml-ounit" ,ocaml-ounit)
+       ("rsync" ,rsync)
+       ("which" ,which)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -125,7 +129,7 @@
                ;; Fails because the output is not formatted as expected.
                (delete-file-recursively "coq-makefile/timing")
                ;; Fails because we didn't build coqtop.byte.
-               (delete-file-recursively "coq-makefile/findlib-package")
+               (delete-file "misc/printers.sh")
                (invoke "make")))))))
     (home-page "https://coq.inria.fr")
     (synopsis "Proof assistant for higher-order logic")
@@ -215,7 +219,7 @@ provers.")
 (define-public coq-flocq
   (package
     (name "coq-flocq")
-    (version "3.2.0")
+    (version "3.3.1")
     (source
      (origin
        (method git-fetch)
@@ -225,7 +229,7 @@ provers.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "15bi36x7zj0glsb3s2gwqd4wswhfzh36rbp7imbyff53a7nna95l"))))
+         "01gdykva0lcw6y3dm8j0djxayb87szfg9vn0mxd6z3pks644misl"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -272,7 +276,7 @@ inside Coq.")
 (define-public coq-gappa
   (package
     (name "coq-gappa")
-    (version "1.4.2")
+    (version "1.4.4")
     (source
      (origin
        (method git-fetch)
@@ -282,7 +286,7 @@ inside Coq.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0r7jwp5xssdfzivs2flp7mzrscqhgl63mryhhf1cvndpgzqwfk2f"))))
+         "0f3g3wjkvfkm961l4jpckhsqd43jnvm7f5qqk78qc32zh1fg339n"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -332,7 +336,7 @@ assistant.")
 (define-public coq-mathcomp
   (package
     (name "coq-mathcomp")
-    (version "1.10.0")
+    (version "1.11.0")
     (source
      (origin
        (method git-fetch)
@@ -341,7 +345,7 @@ assistant.")
              (commit (string-append "mathcomp-" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1h5h1c2025r1ms5qryvwy6pikxmpmmjav6yl127xpzmqdi6w732d"))))
+        (base32 "1axywpa1jcpnidd86irpd1gdbbg2sfbwc652675xisq5wnmfmf6f"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("ocaml" ,ocaml)
@@ -374,7 +378,7 @@ part of the distribution.")
 (define-public coq-coquelicot
   (package
     (name "coq-coquelicot")
-    (version "3.0.3")
+    (version "3.1.0")
     (source
      (origin
        (method git-fetch)
@@ -384,7 +388,7 @@ part of the distribution.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0m5wbr2s8lnf8b7cfwv15hyzsmbcaz6hgdn7aazcrkxnwr87vgkp"))))
+         "0mz3pxan1237fr5fi79c66y7b9z7bmi0sc45kwrmkczsjm5462jm"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -427,7 +431,7 @@ theorems between the two libraries.")
 (define-public coq-bignums
   (package
     (name "coq-bignums")
-    (version "8.10.0")
+    (version "8.11.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -436,7 +440,7 @@ theorems between the two libraries.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0bpb4flckn4nqxbs3wjiznyx1k7r8k93qdigp3qwmikp2lxvcbw5"))))
+                "1xcd7c7qlvs0narfba6px34zq0mz8rffnhxw0kzhhg6i4iw115dp"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("ocaml" ,ocaml)
@@ -460,7 +464,7 @@ provides BigN, BigZ, BigQ that used to be part of Coq standard library.")
 (define-public coq-interval
   (package
     (name "coq-interval")
-    (version "3.4.1")
+    (version "4.0.0")
     (source
      (origin
        (method git-fetch)
@@ -470,7 +474,7 @@ provides BigN, BigZ, BigQ that used to be part of Coq standard library.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "03q3dfqi3r3f7aji5s06ig4aav9ajcwswwdzi5lrgr69z0m487k4"))))
+         "01iz6qmnsm6b9s1vmdjs79vjx9xgwzn5rwyjp6bvs8hg3zlmhpip"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -556,16 +560,16 @@ uses Ltac to synthesize the substitution operation.")
 (define-public coq-equations
   (package
     (name "coq-equations")
-    (version "1.2.1")
+    (version "1.2.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/mattam82/Coq-Equations")
-                    (commit (string-append "v" version "-8.10-2"))))
+                    (commit (string-append "v" version "-8.11"))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0j3z4l5nrbyi9zbbyqkc6kassjanwld2188mwmrbqspaypm2ys68"))))
+                "1srxz1rws8jsh7402g2x2vcqgjbbsr64dxxj5d2zs48pmhb20csf"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("ocaml"  ,ocaml)

gnu/packages/cpp.scm

@@ -14,6 +14,7 @@
 ;;; Copyright © 2020 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
 ;;; Copyright © 2020 Alexandros Theodotou <alex@zrythm.org>
+;;; Copyright © 2020 Greg Hogan <code@greghogan.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -361,7 +362,7 @@ intuitive syntax and trivial integration.")
 (define-public xtl
   (package
     (name "xtl")
-    (version "0.6.18")
+    (version "0.6.19")
     (source (origin
               (method git-fetch)
               (uri
@@ -370,7 +371,7 @@ intuitive syntax and trivial integration.")
                 (commit version)))
               (sha256
                (base32
-                "0s9gnv1wq0cmpw878dmx0lnci86895hhdrwyc9x8lfbc1hr7ypnh"))
+                "1g98lfrp13fqfqrirg0rw90m7bajmjmy12yhrlj5jzwcby4dfs81"))
               (file-name (git-file-name name version))))
     (native-inputs
      `(("googletest" ,googletest)
@@ -647,3 +648,24 @@ Google's C++ code base.")
 a zero-dependency C++ header-only parser combinator library for creating
 parsers according to a Parsing Expression Grammar (PEG).")
     (license license:expat)))
+
+(define-public cxxopts
+  (package
+    (name "cxxopts")
+    (version "2.2.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/jarro2783/cxxopts")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0d3y747lsh1wkalc39nxd088rbypxigm991lk3j91zpn56whrpha"))))
+    (build-system cmake-build-system)
+    (synopsis "Lightweight C++ command line option parser")
+    (description
+     "A lightweight header-only C++ option parser library, supporting the
+standard GNU style syntax for options.")
+    (home-page "https://github.com/jarro2783/cxxopts/wiki")
+    (license license:expat)))

gnu/packages/cran.scm

@@ -253,17 +253,18 @@ series of numeric vectors/matrices and factors.")
 (define-public r-ggpmisc
   (package
     (name "r-ggpmisc")
-    (version "0.3.5")
+    (version "0.3.6")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "ggpmisc" version))
               (sha256
                (base32
-                "0ma2d3a3v8n85sghxr9anl6vgbs8gi82i1dllw99n81gsm59wgin"))))
+                "05i81q9rg8zf35vgcxhn3yhkc9dlvcpwpxncq1q3zs0rxhfkf208"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-broom" ,r-broom)
        ("r-dplyr" ,r-dplyr)
+       ("r-glue" ,r-glue)
        ("r-ggplot2" ,r-ggplot2)
        ("r-gridextra" ,r-gridextra)
        ("r-lubridate" ,r-lubridate)
@@ -783,14 +784,14 @@ same time tries to group instances from the same class together.")
 (define-public r-callr
   (package
     (name "r-callr")
-    (version "3.4.3")
+    (version "3.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "callr" version))
        (sha256
         (base32
-         "1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1"))))
+         "1hgc4mfwv83104fh93v8g2srpwzjayq7krgzi9r0apq784r61642"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-r6" ,r-r6)
@@ -917,13 +918,13 @@ particularly easy to create complete web applications using httpuv alone.")
 (define-public r-jsonlite
   (package
     (name "r-jsonlite")
-    (version "1.7.0")
+    (version "1.7.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "jsonlite" version))
               (sha256
                (base32
-                "1izfrk5yahsz6s69wanfspn72qdffjglbr5305akj72ig9fnladq"))))
+                "1wygpnycmyf339x92hwapqk7nc1gs9cadx890b809a9spjhah41a"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -2260,14 +2261,14 @@ on (non-orthogonal) variable vectors in scatterplots and biplots.")
 (define-public r-shape
   (package
     (name "r-shape")
-    (version "1.4.4")
+    (version "1.4.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shape" version))
        (sha256
         (base32
-         "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
+         "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/shape")
     (synopsis "Functions for plotting graphical shapes")
@@ -2788,14 +2789,14 @@ or excesses over a high threshold.")
 (define-public r-lmtest
   (package
     (name "r-lmtest")
-    (version "0.9-37")
+    (version "0.9-38")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lmtest" version))
        (sha256
         (base32
-         "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
+         "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-zoo" ,r-zoo)))
@@ -2833,13 +2834,13 @@ by Li, Brown, Huang, and Bickel")
 (define-public r-inline
   (package
     (name "r-inline")
-    (version "0.3.15")
+    (version "0.3.16")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "inline" version))
               (sha256
                (base32
-                "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
+                "0x9m2hwin6anfhkf61cnsbqn4qp1pr2gy1pbwbdgbdz2cmns85nj"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/inline")
     (synopsis "Functions to inline C, C++, Fortran function calls from R")
@@ -3400,7 +3401,7 @@ Optimization problems by using the simplex algorithm.")
        ("r-rcpp" ,r-rcpp)
        ("r-rcppprogress" ,r-rcppprogress)))
     (home-page "http://geometry.r-forge.r-project.org/")
-    (synopsis "Mesh generation and surface tesselation")
+    (synopsis "Mesh generator and surface tessellator")
     (description
      "This package makes the qhull library available in R, in a similar manner
 as in Octave.  Qhull computes convex hulls, Delaunay triangulations, halfspace
@@ -3524,14 +3525,14 @@ problems as well as resampling based estimators of prediction error.")
 (define-public r-psych
   (package
     (name "r-psych")
-    (version "2.0.7")
+    (version "2.0.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "psych" version))
        (sha256
         (base32
-         "13z26yk9nrgviyakkij3jc7mja8wy7al9ripab07mvy21kli79bc"))))
+         "0ymds7ql2dv994m73h68dnhbsws8bl09p2rqvl6xsq6c6xr0yryg"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)
@@ -3742,7 +3743,7 @@ color labels, layout, etc.")
     (description
      "This package implements an approximate string matching version of R's
 native @code{match} function.  It can calculate various string distances based
-on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
+on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
 Jaro-Winkler).  An implementation of soundex is provided as well.  Distances
 can be computed between character vectors while taking proper care of encoding
@@ -4111,14 +4112,14 @@ training models for classification or ranking.")
 (define-public r-xts
   (package
     (name "r-xts")
-    (version "0.12-0")
+    (version "0.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xts" version))
        (sha256
         (base32
-         "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
+         "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-zoo" ,r-zoo)))
     (home-page "https://github.com/joshuaulrich/xts")
@@ -4408,13 +4409,13 @@ constants, and control debugging of packages via environment variables.")
 (define-public r-processx
   (package
     (name "r-processx")
-    (version "3.4.3")
+    (version "3.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "processx" version))
        (sha256
-        (base32 "07dhzijqnj2zkm3qrk4ppsv8wscn8ysdsjbidlg9zrbj1wcg4izj"))))
+        (base32 "0as8lzfpbz5rcpcpczvrrgd67whngkmw12q33r2yn3k7lq80z95a"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ps" ,r-ps)
@@ -4555,13 +4556,13 @@ iVAT).")
 (define-public r-xfun
   (package
     (name "r-xfun")
-    (version "0.16")
+    (version "0.17")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xfun" version))
        (sha256
-        (base32 "1x7b71xhbl44fyccz69l24nbgyxawm2km90s4h1l3zr5z2vly0sg"))))
+        (base32 "1zd5qi1rrz3b1lpisapa2yscanz39ghaamf28g7aq3z9ai2a2ymj"))))
     (build-system r-build-system)
     ;; knitr itself depends on xfun
     #;
@@ -5077,20 +5078,21 @@ University Press, 2000.")
 (define-public r-tsa
   (package
     (name "r-tsa")
-    (version "1.2")
+    (version "1.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TSA" version))
        (sha256
         (base32
-         "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
+         "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
     (properties `((upstream-name . "TSA")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-leaps" ,r-leaps)
        ("r-locfit" ,r-locfit)
-       ("r-mgcv" ,r-mgcv)))
+       ("r-mgcv" ,r-mgcv)
+       ("r-tseries" ,r-tseries)))
     (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
     (synopsis "Time series analysis")
     (description
@@ -5102,14 +5104,14 @@ Cryer and Kung-Sik Chan.")
 (define-public r-extradistr
   (package
     (name "r-extradistr")
-    (version "1.8.11")
+    (version "1.9.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "extraDistr" version))
        (sha256
         (base32
-         "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
+         "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
     (properties `((upstream-name . "extraDistr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6857,14 +6859,14 @@ references and Rd files.")
 (define-public r-officer
   (package
     (name "r-officer")
-    (version "0.3.13")
+    (version "0.3.14")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "officer" version))
        (sha256
         (base32
-         "15v5dishdsrw95nj6f7x23llzla3sgbvw35ibdk8ld3miwzxb2kr"))))
+         "1nyv4710bcd2afh1l1qiy5zrspjcdvc7mrzz5189dwy9xvgxi31h"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-magrittr" ,r-magrittr)
@@ -7124,14 +7126,14 @@ other add-on packages.")
 (define-public r-insight
   (package
     (name "r-insight")
-    (version "0.9.1")
+    (version "0.9.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "insight" version))
        (sha256
         (base32
-         "0d6yzg5s0mz07bzxwfc77rpv4l20jpzrnhviqgkp02qw6a4nrwa6"))))
+         "0853kq4j8kic8z2gh5mxfqkwxjs4bdphlajzyvxka7af4r04bfmi"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -7258,14 +7260,14 @@ functions.")
 (define-public r-flextable
   (package
     (name "r-flextable")
-    (version "0.5.10")
+    (version "0.5.11")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "flextable" version))
        (sha256
         (base32
-         "1j7yvjiavar21ywck6nyz0p6bd66fnj99bq8lljdz4rrl3314yb8"))))
+         "1yb872izzr9yja7q2vfqm0imcbcgs0fvi4b19arhdlwwa42figj4"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-base64enc" ,r-base64enc)
@@ -7913,18 +7915,17 @@ and coverage methods to tune the choice of threshold.")
 (define-public r-mosaiccore
   (package
     (name "r-mosaiccore")
-    (version "0.6.0")
+    (version "0.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mosaicCore" version))
        (sha256
-        (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
+        (base32 "00va6x1i8d3wkm1bgsms9dsjfn5a1l43prpl9pqirgq3zm85hrqj"))))
     (properties `((upstream-name . "mosaicCore")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
-       ("r-lazyeval" ,r-lazyeval)
        ("r-mass" ,r-mass)
        ("r-rlang" ,r-rlang)
        ("r-tidyr" ,r-tidyr)))
@@ -7966,13 +7967,13 @@ while providing the intuitive capabilities of @code{r-ggplot2}.")
 (define-public r-mosaicdata
   (package
     (name "r-mosaicdata")
-    (version "0.18.0")
+    (version "0.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mosaicData" version))
        (sha256
-        (base32 "0cx5dg26ha7nzkdyghkbbd6ikncj60qv1538az77lfgn2jylvkbz"))))
+        (base32 "05mrwvs7awhpv2gvk0jjva74gndfgh2cl17slxcjhwlpga8nmxji"))))
     (properties `((upstream-name . "mosaicData")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/mosaicData/")
@@ -9251,14 +9252,14 @@ ROPE percentage and pd).")
 (define-public r-performance
   (package
     (name "r-performance")
-    (version "0.4.8")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "performance" version))
        (sha256
         (base32
-         "1gl3m1pw0wrj9m9cgd0vzbj9swfwjg4aa40gpliplb9y7dcmgi4l"))))
+         "01csmn52d6rhlmcj7gi6ckc6v6a8pymnrpx9l729h13igxsnaf28"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bayestestr" ,r-bayestestr)
@@ -9278,14 +9279,14 @@ effects models and Bayesian models.")
 (define-public r-ggeffects
   (package
     (name "r-ggeffects")
-    (version "0.15.1")
+    (version "0.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggeffects" version))
        (sha256
         (base32
-         "12z58casz0yl1w7nfs64bz4miz0mmc300ap3rz4d2cc4z0rg0r47"))))
+         "0v8n8jmp6x1iagbyc5jgf1d29yz5hd3ibnyl9n9f73vqq5bzj0p5"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-insight" ,r-insight)
@@ -9970,14 +9971,14 @@ This package provides an R interface.")
 (define-public r-rcpphnsw
   (package
     (name "r-rcpphnsw")
-    (version "0.2.0")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RcppHNSW" version))
        (sha256
         (base32
-         "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
+         "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
     (properties `((upstream-name . "RcppHNSW")))
     (build-system r-build-system)
     (propagated-inputs `(("r-rcpp" ,r-rcpp)))
@@ -10124,14 +10125,14 @@ to colexicographical order.")
 (define-public r-misc3d
   (package
     (name "r-misc3d")
-    (version "0.8-4")
+    (version "0.9-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "misc3d" version))
        (sha256
         (base32
-         "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
+         "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/misc3d/")
     (synopsis "Miscellaneous 3D Plots")
@@ -10967,14 +10968,14 @@ Touzet and Varre (2007).")
 (define-public r-rnifti
   (package
     (name "r-rnifti")
-    (version "1.2.1")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RNifti" version))
        (sha256
         (base32
-         "1a5s75iwwngzmi7y69j7xkcrrfvjyjrfalv9ldpgwii4cwkbyf10"))))
+         "0h837jdspy071ckij8szqd8149bm113jpqwbclg87is4brsm5jzg"))))
     (properties `((upstream-name . "RNifti")))
     (build-system r-build-system)
     (propagated-inputs `(("r-rcpp" ,r-rcpp)))
@@ -11934,13 +11935,13 @@ Differences with other sparse matrix packages are:
 (define-public r-fields
   (package
     (name "r-fields")
-    (version "10.3")
+    (version "11.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fields" version))
        (sha256
-        (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
+        (base32 "0x8hbl0rn7gnhn7w45wd757g9in27884qr6vy30xrk150qaq941y"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-maps" ,r-maps)
@@ -12199,14 +12200,14 @@ JASA, 94:496-509.")
 (define-public r-etm
   (package
     (name "r-etm")
-    (version "1.1")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "etm" version))
        (sha256
         (base32
-         "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
+         "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-data-table" ,r-data-table)
@@ -12854,20 +12855,22 @@ transformation, respectively.")
 (define-public r-shinyjs
   (package
     (name "r-shinyjs")
-    (version "1.1")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shinyjs" version))
        (sha256
         (base32
-         "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
+         "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
        ("r-htmltools" ,r-htmltools)
        ("r-jsonlite" ,r-jsonlite)
        ("r-shiny" ,r-shiny)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://deanattali.com/shinyjs")
     (synopsis "Improve the user experience of your Shiny apps")
     (description
@@ -13888,14 +13891,14 @@ sampling.")
 (define-public r-deldir
   (package
     (name "r-deldir")
-    (version "0.1-28")
+    (version "0.1-29")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "deldir" version))
        (sha256
         (base32
-         "12ys8jdcrgzhf9m2yirlqfars397qb0q0pbypahmfa66lgr6wdx5"))))
+         "1vwh8c8zxspyls05q9kgzz5p85i8k8aax5ir45np2bmg0pjvh6kv"))))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
     (home-page "https://cran.r-project.org/web/packages/deldir")
@@ -13912,14 +13915,14 @@ tessellation.")
 (define-public r-sf
   (package
     (name "r-sf")
-    (version "0.9-5")
+    (version "0.9-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sf" version))
        (sha256
         (base32
-         "0c58asqrvz1pkdkb0lkzwz8cwb43pmxd39z0jp217hk7p7q3ngwf"))))
+         "01yqlnx9v7lzb6g4ywjlncz67cnkizszarnf2dmd4fi8abhw4zs9"))))
     (build-system r-build-system)
     (inputs
      `(("gdal" ,gdal)
@@ -14474,44 +14477,6 @@ authoring books and technical documents with R Markdown.")
 that accept short and long options.")
     (license license:gpl2+)))
 
-(define-public r-wgcna
-  (package
-    (name "r-wgcna")
-    (version "1.69")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "WGCNA" version))
-       (sha256
-        (base32
-         "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
-    (properties `((upstream-name . "WGCNA")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-doparallel" ,r-doparallel)
-       ("r-dynamictreecut" ,r-dynamictreecut)
-       ("r-fastcluster" ,r-fastcluster)
-       ("r-foreach" ,r-foreach)
-       ("r-go-db" ,r-go-db)
-       ("r-hmisc" ,r-hmisc)
-       ("r-impute" ,r-impute)
-       ("r-rcpp" ,r-rcpp)
-       ("r-survival" ,r-survival)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-preprocesscore" ,r-preprocesscore)))
-    (home-page
-     "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
-    (synopsis "Weighted correlation network analysis")
-    (description
-     "This package provides functions necessary to perform Weighted
-Correlation Network Analysis on high-dimensional data.  It includes functions
-for rudimentary data cleaning, construction and summarization of correlation
-networks, module identification and functions for relating both variables and
-modules to sample traits.  It also includes a number of utility functions for
-data manipulation and visualization.")
-    (license license:gpl2+)))
-
 (define-public r-kernlab
   (package
     (name "r-kernlab")
@@ -16097,14 +16062,14 @@ been used in the call to @code{aov}.")
 (define-public r-dalex
   (package
     (name "r-dalex")
-    (version "1.3.1.1")
+    (version "2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "DALEX" version))
        (sha256
         (base32
-         "0akw1yzhb3shpg6yb89vralqd2z80z5yk9azqaa55dx56as52kjs"))))
+         "1yn61cbqvyycn617pzhd7kgd34xsnmqvj3s10inn2ywycybk7byi"))))
     (properties `((upstream-name . "DALEX")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16532,7 +16497,7 @@ guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
      "The @code{ggplot2} package provides a strong API for sequentially
 building up a plot, but does not concern itself with composition of multiple
 plots.  Patchwork is a package that expands the API to allow for arbitrarily
-complex composition of plots by providing mathmatical operators for combining
+complex composition of plots by providing mathematical operators for combining
 multiple plots.")
     (license license:expat)))
 
@@ -16689,14 +16654,14 @@ both R code and compiled C/C++/FORTRAN code.")
 (define-public r-systemfonts
   (package
     (name "r-systemfonts")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "systemfonts" version))
        (sha256
         (base32
-         "16n25bin46r0vq59wjdskkb8631gzf7grwnp2wnk0zb9c2qr48ax"))))
+         "0ldxgcayyisp2gcbv4xw9zpb48bp4czi8016kq5nqdqhv1qb3sz0"))))
     (properties `((upstream-name . "systemfonts")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16837,14 +16802,14 @@ in pipelines.")
 (define-public r-parameters
   (package
     (name "r-parameters")
-    (version "0.8.2")
+    (version "0.8.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "parameters" version))
        (sha256
         (base32
-         "0kamszscywvdh4gikl5mmma7s5p7spmhirq3wrgf7x7f4gppbbmh"))))
+         "1vax5p1znq2ddbks2i614hbrnn2x6x71942xx49p813qk8dh284l"))))
     (properties `((upstream-name . "parameters")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18155,14 +18120,14 @@ models.")
 (define-public r-gamlss
   (package
     (name "r-gamlss")
-    (version "5.1-7")
+    (version "5.2-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gamlss" version))
        (sha256
         (base32
-         "0ywqwsp4k6jgnicp1gdsglji61l5cnackl52700v8kmkk83bq4c8"))))
+         "1q82md0439si0n7vqbbbdk45sjr0ad7i8mgrn3kwnr4h213pb4nk"))))
     (properties `((upstream-name . "gamlss")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19651,7 +19616,7 @@ on distances rather than on unit x variables.")
      "This package provides tools for depth functions methodology applied to
 multivariate analysis.  Besides allowing calculation of depth values and
 depth-based location estimators, the package includes functions or drawing
-contour plots and perspective plots of depth functions.  Euclidian and
+contour plots and perspective plots of depth functions.  Euclidean and
 spherical depths are supported.")
     (license license:gpl2)))
 
@@ -20304,14 +20269,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
 (define-public r-forecast
   (package
     (name "r-forecast")
-    (version "8.12")
+    (version "8.13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "forecast" version))
        (sha256
         (base32
-         "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
+         "0vrql5d4v28890np2m6ws1nr1fcl6frs1bz74vfkihkixcmkl3j9"))))
     (properties `((upstream-name . "forecast")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22478,14 +22443,14 @@ multi-state models.")
 (define-public r-scatterpie
   (package
     (name "r-scatterpie")
-    (version "0.1.4")
+    (version "0.1.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "scatterpie" version))
        (sha256
         (base32
-         "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb"))))
+         "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1"))))
     (properties `((upstream-name . "scatterpie")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22572,50 +22537,6 @@ Try a demo of the LSD by running @code{demotour()}.")
     ;; Either version
     (license (list license:gpl2 license:gpl3))))
 
-(define-public r-fourcseq
-  (package
-    (name "r-fourcseq")
-    (version "1.22.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "FourCSeq" version))
-       (sha256
-        (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
-    (properties `((upstream-name . "FourCSeq")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biostrings" ,r-biostrings)
-       ("r-deseq2" ,r-deseq2)
-       ("r-fda" ,r-fda)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggbio" ,r-ggbio)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gtools" ,r-gtools)
-       ("r-lsd" ,r-lsd)
-       ("r-matrix" ,r-matrix)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page
-     "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
-    (synopsis "Analysis of multiplexed 4C sequencing data")
-    (description
-     "This package is an R package dedicated to the analysis of (multiplexed)
-4C sequencing data.  @code{r-fourcseq} provides a pipeline to detect specific
-interactions between DNA elements and identify differential interactions
-between conditions.  The statistical analysis in R starts with individual bam
-files for each sample as inputs.  To obtain these files, the package contains
-a Python script to demultiplex libraries and trim off primer sequences.  With
-a standard alignment software the required bam files can be then be
-generated.")
-    (license license:gpl3+)))
-
 (define-public r-phylogram
   (package
     (name "r-phylogram")
@@ -23215,14 +23136,14 @@ aggregation for comparing different implementations in order to provide a
 (define-public r-rfast
   (package
     (name "r-rfast")
-    (version "2.0.0")
+    (version "2.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rfast" version))
        (sha256
         (base32
-         "010dm5h2vayvfbh0zny7i2c7fmn83r2b54849r0b4id3wjpmg3xy"))))
+         "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958"))))
     (properties `((upstream-name . "Rfast")))
     (build-system r-build-system)
     (propagated-inputs
@@ -24434,18 +24355,17 @@ as allowing spectra with different resolutions.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "3.2.0")
+    (version "3.2.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))
+                "0jipc4xpmx56jzc31w6nsl77ah8x8wq7jclg2mxhjql4ixkwmz54"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-ape" ,r-ape)
+     `(("r-cluster" ,r-cluster)
-       ("r-cluster" ,r-cluster)
        ("r-cowplot" ,r-cowplot)
        ("r-fitdistrplus" ,r-fitdistrplus)
        ("r-future" ,r-future)
@@ -24463,6 +24383,7 @@ as allowing spectra with different resolutions.")
        ("r-lmtest" ,r-lmtest)
        ("r-mass" ,r-mass)
        ("r-matrix" ,r-matrix)
+       ("r-matrixstats" ,r-matrixstats)
        ("r-miniui" ,r-miniui)
        ("r-patchwork" ,r-patchwork)
        ("r-pbapply" ,r-pbapply)
@@ -24527,14 +24448,14 @@ Maximum Parsimony, distance methods and Hadamard conjugation.")
 (define-public r-diversitree
   (package
     (name "r-diversitree")
-    (version "0.9-13")
+    (version "0.9-14")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "diversitree" version))
         (sha256
          (base32
-          "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
+          "0xkxw4n1rsagip51smh9k0h0lmnnvsajqcxma7yh95ifdkyrcyy4"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))

gnu/packages/crates-gtk.scm

@@ -0,0 +1,667 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages crates-gtk)
+  #:use-module (guix build-system cargo)
+  #:use-module (guix download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages crates-io)
+  #:use-module (gnu packages crates-graphics)
+  #:use-module (gnu packages glib)
+  #:use-module (gnu packages gtk))
+
+;;;
+;;; Please: Try to add new module packages in alphabetic order.
+;;;
+
+(define-public rust-cairo-rs-0.8
+  (package
+    (name "rust-cairo-rs")
+    (version "0.8.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cairo-rs" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "11303v1fv6hsc9n70ak380gknkf0098phpcxqdhkmahqjsx4jw0m"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-cairo-sys-rs" ,rust-cairo-sys-rs-0.9)
+        ("rust-glib" ,rust-glib-0.9)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2))
+       #:cargo-development-inputs
+       (("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1)
+        ("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("cairo" ,cairo)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "Rust bindings for the Cairo library")
+    (description
+     "Rust bindings for the Cairo library.")
+    (license license:expat)))
+
+(define-public rust-cairo-rs-0.7
+  (package
+    (inherit rust-cairo-rs-0.8)
+    (name "rust-cairo-rs")
+    (version "0.7.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cairo-rs" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "171m98g41avp5mmshqir4ka21napp7ma5fx45wi9mw5hwdyv8pg0"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-cairo-sys-rs" ,rust-cairo-sys-rs-0.9)
+        ("rust-glib" ,rust-glib-0.8)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-tempfile" ,rust-tempfile-3))))))
+
+(define-public rust-cairo-sys-rs-0.9
+  (package
+    (name "rust-cairo-sys-rs")
+    (version "0.9.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cairo-sys-rs" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0qsdy6s57yvscg2rfm7wdqrlhzbn1aq9lhk3dy1vw5f7r81blrgz"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-winapi" ,rust-winapi-0.3)
+        ("rust-x11" ,rust-x11-2)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))))
+    (inputs
+     `(("cairo" ,cairo)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "FFI bindings to libcairo")
+    (description "This package provides FFI bindings to libcairo.")
+    (license license:expat)))
+
+(define-public rust-gdk-pixbuf-0.8
+  (package
+    (name "rust-gdk-pixbuf")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gdk-pixbuf" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1mxxca0fkcw2rsd3kl3nvlb8ys4cgxqx4n5isjbv0adk8q624j72"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-gdk-pixbuf-sys" ,rust-gdk-pixbuf-sys-0.9)
+        ("rust-gio" ,rust-gio-0.8)
+        ("rust-gio-sys" ,rust-gio-sys-0.9)
+        ("rust-glib" ,rust-glib-0.9)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1))))
+    (inputs
+     `(("gdk-pixbuf" ,gdk-pixbuf)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "Rust bindings for the GdkPixbuf library")
+    (description
+     "Rust bindings for the GdkPixbuf library.")
+    (license license:expat)))
+
+(define-public rust-gdk-pixbuf-0.7
+  (package
+    (inherit rust-gdk-pixbuf-0.8)
+    (name "rust-gdk-pixbuf")
+    (version "0.7.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gdk-pixbuf" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1k2g3w2p57m68bi5sldvkmgjgslgqswrjsijjhqaibdvw67409lp"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-fragile" ,rust-fragile-0.3)
+        ("rust-futures-preview" ,rust-futures-preview-0.3)
+        ("rust-gdk-pixbuf-sys" ,rust-gdk-pixbuf-sys-0.9)
+        ("rust-gio" ,rust-gio-0.7)
+        ("rust-gio-sys" ,rust-gio-sys-0.9)
+        ("rust-glib" ,rust-glib-0.8)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1))))))
+
+(define-public rust-gdk-pixbuf-sys-0.9
+  (package
+    (name "rust-gdk-pixbuf-sys")
+    (version "0.9.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gdk-pixbuf-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1c2andpjb10y7bahh6nxnksh9m3g5qh4mgq9znx634cy1831p6fq"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f      ; tests not included in release
+       #:cargo-inputs
+       (("rust-gio-sys" ,rust-gio-sys-0.9)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))
+       #:cargo-development-inputs
+       (("rust-shell-words" ,rust-shell-words-0.1)
+        ("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("gdk-pixbuf" ,gdk-pixbuf)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "FFI bindings to libgdk_pixbuf-2.0")
+    (description "This package provides FFI bindings to @code{libgdk_pixbuf-2.0}.")
+    (license license:expat)))
+
+(define-public rust-gio-0.8
+  (package
+    (name "rust-gio")
+    (version "0.8.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gio" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "19cnla2ya0mi6wwaabd5mxbq2kzq46dg6jq2z19rpqyc2na0zl8c"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f  ; Not all files included in the tarball.
+       #:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-futures-channel" ,rust-futures-channel-0.3)
+        ("rust-futures-core" ,rust-futures-core-0.3)
+        ("rust-futures-io" ,rust-futures-io-0.3)
+        ("rust-futures-util" ,rust-futures-util-0.3)
+        ("rust-gio-sys" ,rust-gio-sys-0.9)
+        ("rust-glib" ,rust-glib-0.9)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1)
+        ("rust-serial-test" ,rust-serial-test-0.1)
+        ("rust-serial-test-derive" ,rust-serial-test-derive-0.1))))
+    (inputs
+     `(("glib" ,glib)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "Rust bindings for the Gio library")
+    (description "Rust bindings for the Gio library.")
+    (license license:expat)))
+
+(define-public rust-gio-0.7
+  (package
+    (inherit rust-gio-0.8)
+    (name "rust-gio")
+    (version "0.7.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gio" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1qv0wc1hqyb81c03h81s3xrl9jslrw23fr4yhygxbhih9k9vaqb2"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-fragile" ,rust-fragile-0.3)
+        ("rust-futures-preview" ,rust-futures-preview-0.3)
+        ("rust-gio-sys" ,rust-gio-sys-0.9)
+        ("rust-glib" ,rust-glib-0.8)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1))))))
+
+(define-public rust-gio-sys-0.9
+  (package
+    (name "rust-gio-sys")
+    (version "0.9.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gio-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "049rafihxp3maxg3fwj6062ni9dcfilvhfq6ibnfgsmr89925bag"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f      ; Some test libraries not included in release.
+       #:cargo-inputs
+       (("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))
+       #:cargo-development-inputs
+       (("rust-shell-words" ,rust-shell-words-0.1)
+        ("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("glib" ,glib)))
+    (home-page "http://gtk-rs.org/")
+    (synopsis "FFI bindings to libgio-2.0")
+    (description "This package provides FFI bindings to libgio-2.0.")
+    (license license:expat)))
+
+(define-public rust-gir-format-check-0.1
+  (package
+    (name "rust-gir-format-check")
+    (version "0.1.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gir-format-check" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0znl4qcgmg0656zk9vjkwdn9wj1zpkd0m0l5jnzmahd80ii7vf4b"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/gtk-rs/gir-format-check")
+    (synopsis "File format checker")
+    (description "File format checker in Rust.")
+    (license license:expat)))
+
+(define-public rust-glib-0.9
+  (package
+    (name "rust-glib")
+    (version "0.9.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "glib" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1h3100mf7kdfxibjz5na0sqzbd2mcsyd8pzivn3666w414x5gys0"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-futures-channel" ,rust-futures-channel-0.3)
+        ("rust-futures-core" ,rust-futures-core-0.3)
+        ("rust-futures-executor" ,rust-futures-executor-0.3)
+        ("rust-futures-preview" ,rust-futures-preview-0.3)
+        ("rust-futures-task" ,rust-futures-task-0.3)
+        ("rust-futures-util" ,rust-futures-util-0.3)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-libc" ,rust-libc-0.2))
+       #:cargo-development-inputs
+       (("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("glib" ,glib)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "Rust bindings for the GLib library")
+    (description
+     "Rust bindings for the GLib library.")
+    (license license:expat)))
+
+(define-public rust-glib-0.8
+  (package
+    (inherit rust-glib-0.9)
+    (name "rust-glib")
+    (version "0.8.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "glib" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0ysy87zrwyzhfpf3d8rkyyr3amwj85wky05fsl7kx95s84l269xy"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-futures-preview" ,rust-futures-preview-0.3)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-libc" ,rust-libc-0.2))
+       #:cargo-development-inputs
+       (("rust-tempfile" ,rust-tempfile-3))))))
+
+(define-public rust-glib-sys-0.9
+  (package
+    (name "rust-glib-sys")
+    (version "0.9.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "glib-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1qhnwfqqcp63mx4q9744rfkq78g6ky2j8ppsxxgw0ipl08w6z1cm"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f      ; Some test libraries not included in release.
+       #:cargo-inputs
+       (("rust-libc" ,rust-libc-0.2)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))
+       #:cargo-development-inputs
+       (("rust-shell-words" ,rust-shell-words-0.1)
+        ("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("glib" ,glib)))
+    (home-page "http://gtk-rs.org/")
+    (synopsis "FFI bindings to libglib-2.0")
+    (description "This package provides FFI bindings to libglib-2.0.")
+    (license license:expat)))
+
+(define-public rust-gobject-sys-0.9
+  (package
+    (name "rust-gobject-sys")
+    (version "0.9.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gobject-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1nakflbp3gjaas4fw7sn3p1p32khyfpcq1h06z7yqd10yq2ail9i"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f      ; Some test libraries not included in release.
+       #:cargo-inputs
+       (("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))
+       #:cargo-development-inputs
+       (("rust-shell-words" ,rust-shell-words-0.1)
+        ("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("glib" ,glib)))
+    (home-page "http://gtk-rs.org/")
+    (synopsis "FFI bindings to libgobject-2.0")
+    (description "This package provides FFI bindings to libgobject-2.0.")
+    (license license:expat)))
+
+(define-public rust-gtk-rs-lgpl-docs-0.1
+  (package
+    (name "rust-gtk-rs-lgpl-docs")
+    (version "0.1.15")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gtk-rs-lgpl-docs" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "06b1j64zg0xmhwfkyhzh3y0apclg6qihn3f7s1bd7kgjmkia4jlr"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-rustdoc-stripper" ,rust-rustdoc-stripper-0.1))))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "LGPL-licensed docs for Gtk-rs crates")
+    (description
+     "LGPL-licensed docs for Gtk-rs crates.")
+    (license license:lgpl2.0)))
+
+(define-public rust-pango-0.8
+  (package
+    (name "rust-pango")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pango" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0xq50950il3228grzs4xvc5s6phxcl5l50grz6syvs0vixr6p70y"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-glib" ,rust-glib-0.9)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pango-sys" ,rust-pango-sys-0.9)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1))))
+    (inputs
+     `(("pango" ,pango)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "Rust bindings for the Pango library")
+    (description
+     "Rust bindings for the Pango library.")
+    (license license:expat)))
+
+(define-public rust-pango-0.7
+  (package
+    (inherit rust-pango-0.8)
+    (name "rust-pango")
+    (version "0.7.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pango" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "11np7nxb69g3kid2l78b7k519x1wk1c3f9yy7swgzy24n5qs0grr"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-glib" ,rust-glib-0.8)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pango-sys" ,rust-pango-sys-0.9)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1))))))
+
+(define-public rust-pango-sys-0.9
+  (package
+    (name "rust-pango-sys")
+    (version "0.9.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pango-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0zdynikh6jrfa31fpmbrwnz46a57idci73zzkf0z0g3vj223vfc6"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f      ; Some test files not included in release.
+       #:cargo-inputs
+       (("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))
+       #:cargo-development-inputs
+       (("rust-shell-words" ,rust-shell-words-0.1)
+        ("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("pango" ,pango)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "FFI bindings to libpango-1.0")
+    (description "This package provides FFI bindings to @code{libpango-1.0}.")
+    (license license:expat)))
+
+(define-public rust-pangocairo-0.9
+  (package
+    (name "rust-pangocairo")
+    (version "0.9.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pangocairo" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0bap3h78hdqdyln58349qjjbcv45m8a0a16c4n9fprdj1my0gldx"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-cairo-rs" ,rust-cairo-rs-0.8)
+        ("rust-cairo-sys-rs" ,rust-cairo-sys-rs-0.9)
+        ("rust-glib" ,rust-glib-0.9)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pango" ,rust-pango-0.8)
+        ("rust-pango-sys" ,rust-pango-sys-0.9)
+        ("rust-pangocairo-sys" ,rust-pangocairo-sys-0.10)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1))))
+    (inputs
+     `(("gtk+" ,gtk+)))
+    (home-page "http://gtk-rs.org/")
+    (synopsis "Rust bindings for the PangoCairo library")
+    (description
+     "Rust bindings for the PangoCairo library.")
+    (license license:expat)))
+
+(define-public rust-pangocairo-0.8
+  (package
+    (inherit rust-pangocairo-0.9)
+    (name "rust-pangocairo")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pangocairo" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0qjiwsp73x3w0493dzycyjzxnzwq7ixwmf1ccr5r41pjhxbnk1kl"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-cairo-rs" ,rust-cairo-rs-0.7)
+        ("rust-cairo-sys-rs" ,rust-cairo-sys-rs-0.9)
+        ("rust-glib" ,rust-glib-0.8)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pango" ,rust-pango-0.7)
+        ("rust-pango-sys" ,rust-pango-sys-0.9)
+        ("rust-pangocairo-sys" ,rust-pangocairo-sys-0.10)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1))))))
+
+(define-public rust-pangocairo-sys-0.10
+  (package
+    (name "rust-pangocairo-sys")
+    (version "0.10.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pangocairo-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1zlyf5vajarnxg5034b8qa5w5zajv96lfvlgiki26svpmcqip4m3"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-cairo-sys-rs" ,rust-cairo-sys-rs-0.9)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pango-sys" ,rust-pango-sys-0.9)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))
+       #:cargo-development-inputs
+       (("rust-shell-words" ,rust-shell-words-0.1)
+        ("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("gtk+" ,gtk+)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "FFI bindings to libgtk-3")
+    (description "This package provides FFI bindings to libgtk-3.")
+    (license license:expat)))

gnu/packages/crypto.scm

@@ -143,7 +143,7 @@ communication, encryption, decryption, signatures, etc.")
 (define-public signify
   (package
     (name "signify")
-    (version "29")
+    (version "30")
     (home-page "https://github.com/aperezdc/signify")
     (source (origin
               (method url-fetch)
@@ -151,7 +151,7 @@ communication, encryption, decryption, signatures, etc.")
                                   "/download/v" version "/signify-" version ".tar.xz"))
               (sha256
                (base32
-                "1bzcax5kb4lr0rmpmrdpq5q0iq6b2dxzpl56li8aanbkck1c7hd9"))))
+                "11l67j04gyxnlw6zrzsygqs5cgsc1sww1rh0apl05yay131hd17n"))))
     (build-system gnu-build-system)
     ;; TODO Build with libwaive (described in README.md), to implement something
     ;; like OpenBSD's pledge().
@@ -359,10 +359,10 @@ secure operations. ")
           (base32
            "0lj38ldh8vzi11wp4ghw4k0fkwp0s04zv8k8d473p1snmbh7mx98"))))
       (inputs
-       `(("openssl" ,openssl))) ; It needs: openssl/{bn,pem,rsa,sha}.h
+       `(("openssl" ,openssl-1.0)))     ; for openssl/{bn,pem,rsa,sha}.h
       (build-system gnu-build-system)
       (arguments
-       `(#:make-flags (list "CC=gcc"
+       `(#:make-flags (list (string-append "CC=" ,(cc-for-target))
                             (string-append "PREFIX=" (assoc-ref %outputs "out"))
                             (string-append "INSTALL=" "install"))
          ;; XXX: make test would run a !VERY! long hashing of names with the use

gnu/packages/cryptsetup.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -35,7 +35,7 @@
 (define-public cryptsetup
   (package
    (name "cryptsetup")
-   (version "2.3.3")
+   (version "2.3.4")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://kernel.org/linux/utils/cryptsetup/v"
@@ -43,7 +43,7 @@
                                 "/cryptsetup-" version ".tar.xz"))
             (sha256
              (base32
-              "1pw2bq4nv2z3xyycckxkbp7dp9kkp2n6bspna3plryg277z4zjiv"))))
+              "0wrpz2fzbsszmsgxxbssxjgylpyiindh24z8g13m2fxmjsxyw5lx"))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags

gnu/packages/cups.scm

@@ -415,16 +415,17 @@ should only be used as part of the Guix cups-pk-helper service.")
 (define-public hplip
   (package
     (name "hplip")
-    (version "3.20.6")
+    (version "3.20.9")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/hplip/hplip/" version
                                   "/hplip-" version ".tar.gz"))
               (sha256
                (base32
-                "083w58wpvvm6sir6rf5dwx3r0rman9sv1zpl26chl0a88crjsjy6"))
+                "1prdbp410405xrfggjc7y34nzljg7jnbgjzalgv4khwwma4i299n"))
               (modules '((guix build utils)))
-              (patches (search-patches "hplip-remove-imageprocessor.patch"))
+              (patches (search-patches "hplip-fix-bug-1898438.patch"
+                                       "hplip-remove-imageprocessor.patch"))
               (snippet
                '(begin
                   ;; Delete non-free blobs: .so files, pre-compiled
@@ -465,10 +466,7 @@ should only be used as part of the Guix cups-pk-helper service.")
                          (assoc-ref %outputs "out") "/lib")
          ;; Disable until mime.types merging works (FIXME).
          "--disable-fax-build"
-         "--enable-hpcups-install"
          "--enable-new-hpcups"
-         "--enable-cups_ppd_install"
-         "--enable-cups_drv_install"
          ;; TODO add foomatic drv install eventually.
          ;; TODO --enable-policykit eventually.
          ,(string-append "--with-cupsfilterdir="
@@ -749,20 +747,19 @@ HP@tie{}LaserJet, and possibly other printers.  See @file{README} for details.")
 (define-public escpr
   (package
     (name "escpr")
-    (version "1.6.30")
+    (version "1.7.7")
     ;; XXX: This currently works.  But it will break as soon as a newer
     ;; version is available since the URLs for older versions are not
     ;; preserved.  An alternative source will be added as soon as
     ;; available.
-    (source (origin
+    (source
+     (origin
        (method url-fetch)
-              ;; The uri has to be chopped up in order to satisfy guix lint.
+       (uri (string-append "https://download3.ebz.epson.net/dsc/f/03/00/10/49/18/"
-              (uri (string-append "https://download3.ebz.epson.net/dsc/f/03/00/08/18/20/"
+                           "f3016be6120a7271a6d9cb64872f817bce1920b8/"
-                                  "e94de600e28e510c1cfa158929d8b2c0aadc8aa0/"
+                           "epson-inkjet-printer-escpr-1.7.7-1lsb3.2.tar.gz"))
-                                  "epson-inkjet-printer-escpr-1.6.30-1lsb3.2.tar.gz"))
        (sha256
-               (base32
+        (base32 "0khdf2a9iwh9aplj2gzyzl53yyfnfv0kszk3p018jnirl5l475ld"))))
-                "0m8pyfkixisp0vclwxj340isn15zzisal0v2xvv66kxfd68dzf12"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -771,13 +768,30 @@ HP@tie{}LaserJet, and possibly other printers.  See @file{README} for details.")
          ,(string-append "--with-cupsfilterdir="
                          (assoc-ref %outputs "out") "/lib/cups/filter")
          ,(string-append "--with-cupsppddir="
-                         (assoc-ref %outputs "out") "/share/ppd"))))
+                         (assoc-ref %outputs "out") "/share/cups/model"))
-    (inputs `(("cups" ,cups-minimal)))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-autotools-version-requirement
+           (lambda _
+             (substitute* "aclocal.m4"
+               (("1\\.15")
+                ,(package-version automake)))
+             (substitute* "configure"
+               (("^(ACLOCAL=).*" _ match)
+                (string-append match "aclocal"))
+               (("^(AUTOMAKE=).*" _ match)
+                (string-append match "automake")))
+             #t)))))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)))
+    (inputs
+     `(("cups" ,cups-minimal)))
     (synopsis "ESC/P-R printer driver")
     (description
-     "This package provides a filter for the Common UNIX Printing
+     "This package provides a filter for @acronym{CUPS, the Common UNIX Printing
-System (CUPS).  It offers high-quality printing with Seiko Epson color ink jet
+System} that offers high-quality printing with Seiko@tie{}Epson color ink jet
-printers.  It can only be used with printers that support the Epson ESC/P-R
+printers.  It can be used only with printers that support the Epson@tie{}ESC/P-R
 language.")
     (home-page "http://download.ebz.epson.net/dsc/search/01/search")
     (license license:gpl2+)))

gnu/packages/databases.scm

@@ -970,7 +970,7 @@ as a drop-in replacement of MySQL.")
 (define-public mariadb-connector-c
   (package
     (name "mariadb-connector-c")
-    (version "3.1.9")
+    (version "3.1.10")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -979,7 +979,7 @@ as a drop-in replacement of MySQL.")
                     version "-src.tar.gz"))
               (sha256
                (base32
-                "1izjzf7yzjqzlk8dkp327fa9lawsv2hnnlnr7g5lshyx5azrk38h"))))
+                "13v5z4w1cl890lnr2fbwbziw638lqw2aga45vdq1z0cyrc9mcgmg"))))
     (inputs
      `(("openssl" ,openssl)))
     (build-system cmake-build-system)
@@ -1343,7 +1343,7 @@ for example from a shell script.")
 (define-public sqitch
   (package
     (name "sqitch")
-    (version "1.0.0")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
@@ -1351,7 +1351,7 @@ for example from a shell script.")
              "mirror://cpan/authors/id/D/DW/DWHEELER/App-Sqitch-v"
              version ".tar.gz"))
        (sha256
-        (base32 "0p4wraqiscvwmmsvfqfy65blgsilwpvd9zj4d2zvm2xdx70ncr7l"))))
+        (base32 "1ayiwg9kh3w0nbacbcln7h944z94vq5vnnd5diz86033bpbnq57f"))))
     (build-system perl-build-system)
     (arguments
      '(#:phases
@@ -1383,6 +1383,7 @@ for example from a shell script.")
        ("perl-test-file" ,perl-test-file)
        ("perl-test-file-contents" ,perl-test-file-contents)
        ("perl-test-mockmodule" ,perl-test-mockmodule)
+       ("perl-test-mockobject" ,perl-test-mockobject)
        ("perl-test-nowarnings" ,perl-test-nowarnings)
        ("perl-test-warn" ,perl-test-warn)))
     (inputs
@@ -1391,7 +1392,9 @@ for example from a shell script.")
        ("perl-config-gitlike" ,perl-config-gitlike)
        ("perl-datetime" ,perl-datetime)
        ("perl-datetime-timezone" ,perl-datetime-timezone)
+       ("perl-dbd-mysql" ,perl-dbd-mysql)
        ("perl-dbd-pg" ,perl-dbd-pg)
+       ("perl-dbd-sqlite" ,perl-dbd-sqlite)
        ("perl-dbi" ,perl-dbi)
        ("perl-devel-stacktrace" ,perl-devel-stacktrace)
        ("perl-encode-locale" ,perl-encode-locale)
@@ -1738,7 +1741,7 @@ columns, primary keys, unique constraints and relationships.")
 (define-public perl-dbd-sqlite
   (package
     (name "perl-dbd-sqlite")
-    (version "1.64")
+    (version "1.66")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1746,7 +1749,7 @@ columns, primary keys, unique constraints and relationships.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "00gz5aw3xrr92lf9nfk0dhmy7a8jzmxhznddd9b0a8w4a1xqzbpl"))))
+                "1zljln5nh61gj3k22a1fv2vhx5l83waizmarwkh77hk6kzzmvrw9"))))
     (build-system perl-build-system)
     (inputs `(("sqlite" ,sqlite)))
     (propagated-inputs `(("perl-dbi" ,perl-dbi)))
@@ -1777,7 +1780,7 @@ module, and nothing else.")
     (synopsis "Parse and utilize MySQL's /etc/my.cnf and ~/.my.cnf files")
     (description
      "@code{MySQL::Config} emulates the @code{load_defaults} function from
-libmysqlclient.  It will fill an aray with long options, ready to be parsed by
+libmysqlclient.  It will fill an array with long options, ready to be parsed by
 @code{Getopt::Long}.")
     (license license:perl-license)))
 
@@ -2120,14 +2123,14 @@ database.")
 (define-public perl-db-file
  (package
   (name "perl-db-file")
-  (version "1.853")
+  (version "1.854")
   (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://cpan/authors/id/P/PM/PMQS/DB_File-"
                           version ".tar.gz"))
       (sha256
-        (base32 "1y967si45vj0skip1hnhicbv9da29fv6qcfwnsbnvj06n36mkj6h"))))
+        (base32 "0fv0any5am6vr6h1wcwhnraj70hd55fs4d8c2y7chsc9alf9di5y"))))
   (build-system perl-build-system)
   (inputs `(("bdb" ,bdb)))
   (native-inputs `(("perl-test-pod" ,perl-test-pod)))
@@ -2140,8 +2143,7 @@ database.")
                        (("/usr/local/BerkeleyDB") (assoc-ref inputs "bdb")))
                      #t)))))
   (home-page "https://metacpan.org/release/DB_File")
-  (synopsis
+  (synopsis "Perl5 access to Berkeley DB version 1.x")
-    "Perl5 access to Berkeley DB version 1.x")
   (description
     "The DB::File module provides Perl bindings to the Berkeley DB version 1.x.")
   (license license:perl-license)))
@@ -2450,13 +2452,13 @@ etc., and an SQL engine for performing simple SQL queries.")
 (define-public python-lmdb
   (package
     (name "python-lmdb")
-    (version "0.99")
+    (version "1.0.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "lmdb" version))
               (sha256
                (base32
-                "12fwlzfd82471ss9xzbqwcqc6f5miy51y72y2yya9j5cm9589szr"))
+                "1di1gj2agbxwqqwrpk4w58dpfah0kl10ha20s63dlqdd1bgzydj1"))
               (modules '((guix build utils)))
               (snippet
                ;; Delete bundled lmdb source files.
@@ -2475,6 +2477,7 @@ etc., and an SQL engine for performing simple SQL queries.")
          (add-before 'build 'use-system-lmdb
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((lmdb (assoc-ref inputs "lmdb")))
+               (setenv "LMDB_PURE" "set") ; don't apply env-copy-txn.patch
                (setenv "LMDB_FORCE_SYSTEM" "set")
                (setenv "LMDB_INCLUDEDIR" (string-append lmdb "/include"))
                (setenv "LMDB_LIBDIR" (string-append lmdb "/lib"))
@@ -2712,16 +2715,57 @@ You might also want to install the following optional dependencies:
 (define-public python2-sqlalchemy-utils
   (package-with-python2 python-sqlalchemy-utils))
 
+(define-public python-alchemy-mock
+  (package
+    (name "python-alchemy-mock")
+    (version "0.4.3")
+    (home-page "https://github.com/miki725/alchemy-mock")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "alchemy-mock" version))
+              (sha256
+               (base32
+                "0ylxygl3bcdapzz529n8wgk7vx9gjwb3ism564ypkpd7dbsw653r"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (replace 'check
+                    (lambda _
+                      ;; Create pytest.ini that adds doctest options to
+                      ;; prevent test failure.  Taken from tox.ini.
+                      (call-with-output-file "pytest.ini"
+                        (lambda (port)
+                          (format port "[pytest]
+doctest_optionflags=IGNORE_EXCEPTION_DETAIL
+")))
+                      (invoke "pytest" "-vv" "--doctest-modules"
+                              "alchemy_mock/"))))))
+    (native-inputs
+     `(("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)))
+    (propagated-inputs
+     `(("python-six" ,python-six)
+       ("python-sqlalchemy" ,python-sqlalchemy)))
+    (synopsis "Mock helpers for SQLAlchemy")
+    (description
+     "This package provides mock helpers for SQLAlchemy that makes it easy
+to mock an SQLAlchemy session while preserving the ability to do asserts.
+
+Normally Normally SQLAlchemy's expressions cannot be easily compared as
+comparison on binary expression produces yet another binary expression, but
+this library provides functions to facilitate such comparisons.")
+    (license license:expat)))
+
 (define-public python-alembic
   (package
     (name "python-alembic")
-    (version "1.4.2")
+    (version "1.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "alembic" version))
        (sha256
-        (base32 "1gsdrzx9h7wfva200qvvsc9sn4w79mk2vs0bbnzjhxi1jw2b0nh3"))))
+        (base32 "0if2dgb088clk738p26bwk50735h6jpd2kacdgc5capv2hiz6d2k"))))
     (build-system python-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases
@@ -2897,13 +2941,13 @@ designed to be easy and intuitive to use.")
 (define-public python-psycopg2
   (package
     (name "python-psycopg2")
-    (version "2.8.5")
+    (version "2.8.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "psycopg2" version))
        (sha256
-        (base32 "06081jk9srkd4ra9j8b93x9ld3a2yxsbsf5bbbcivbm1yx065m7p"))))
+        (base32 "0hzmk6b1hb5riqkljr5xics6p4zbvmis6knbczb7zhq7273zc8zv"))))
     (build-system python-build-system)
     (arguments
      ;; Tests would require a postgresql database "psycopg2_test"
@@ -2951,24 +2995,19 @@ database).")
 (define-public python-mysqlclient
   (package
     (name "python-mysqlclient")
-    (version "1.3.13")
+    (version "2.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "mysqlclient" version))
        (sha256
         (base32
-         "0kv4a1icwdav8jpl7qvnr931lw5h3v22ids6lwq6qpi1hjzf33pz"))))
+         "1rf5l8hazs3v18hmcrm90z3hi9wxv553ipwd5l6kj8j7l6p7abzv"))))
     (build-system python-build-system)
-    (native-inputs
+    (arguments '(#:tests? #f))          ;XXX: requires a live database
-     `(("nose" ,python-nose)
-       ("mock" ,python-mock)
-       ("py.test" ,python-pytest)))
     (inputs
      `(("mysql" ,mariadb "lib")
-       ("mysql-dev" ,mariadb "dev")
+       ("mysql-dev" ,mariadb "dev")))
-       ("libz" ,zlib)
-       ("openssl" ,openssl)))
     (home-page "https://github.com/PyMySQL/mysqlclient-python")
     (synopsis "MySQLdb is an interface to the popular MySQL database server for Python")
     (description "MySQLdb is an interface to the popular MySQL database server
@@ -2980,9 +3019,6 @@ for Python.  The design goals are:
 @end enumerate")
     (license license:gpl2)))
 
-(define-public python2-mysqlclient
-  (package-with-python2 python-mysqlclient))
-
 (define-public python-hiredis
   (package
     (name "python-hiredis")
@@ -3042,13 +3078,13 @@ reasonable substitute.")
 (define-public python-redis
   (package
     (name "python-redis")
-    (version "3.3.8")
+    (version "3.5.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "redis" version))
        (sha256
-        (base32 "0fyxzqax7lcwzwhvnz0i0q6v62hxyv1mv52ywx3bpff9a2vjz8lq"))))
+        (base32 "18h5b87g15x3j6pb1h2q27ri37p2qpvc9n2wgn5yl3b6m3y0qzhf"))))
     (build-system python-build-system)
     ;; Tests require a running Redis server.
     (arguments '(#:tests? #f))
@@ -3067,14 +3103,35 @@ reasonable substitute.")
 (define-public python-rq
   (package
     (name "python-rq")
-    (version "0.13.0")
+    (version "1.5.2")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (pypi-uri "rq" version))
+       (uri (git-reference
+             (url "https://github.com/rq/rq")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0xvapd2bxnyq480i48bdkddzlqmv2axbsq85rlfy8k3al8zxxxrf"))))
+        (base32 "0ikqmpq0g1qiqwd7ar1286l4hqjb6aj2wr844gihhb8ijzwhp8va"))))
     (build-system python-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (add-before 'check 'start-redis
+                    (lambda _
+                      (invoke "redis-server" "--daemonize" "yes")))
+                  (replace 'check
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      (let ((out (assoc-ref outputs "out")))
+                        ;; Drop test that needs the SDK for Sentry.io.
+                        (delete-file "tests/test_sentry.py")
+                        ;; Ensure 'rq' and 'rqworker' ends up on PATH.
+                        (setenv "PATH" (string-append out "/bin:"
+                                                      (getenv "PATH")))
+                        (invoke "pytest" "-vv")))))))
+    (native-inputs
+     `(("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)
+       ("redis" ,redis)))
     (propagated-inputs
      `(("python-click" ,python-click)
        ("python-redis" ,python-redis)))
@@ -3089,6 +3146,44 @@ is designed to have a low barrier to entry.")
 (define-public python2-rq
   (package-with-python2 python-rq))
 
+(define-public python-rq-scheduler
+  (package
+    (name "python-rq-scheduler")
+    (version "0.10.0")
+    (home-page "https://github.com/rq/rq-scheduler")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url home-page)
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0xg6yazqs5kbr2ayvhvljs1h5vgx5k5dds613fmhswln7gglf9hk"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (add-before 'check 'start-redis
+                    (lambda _
+                      (invoke "redis-server" "--daemonize" "yes")))
+                  (replace 'check
+                    (lambda _
+                      (substitute* "run_tests.py"
+                        (("/usr/bin/env")
+                         (which "env")))
+                      (invoke "./run_tests.py"))))))
+    (native-inputs
+     `(("redis" ,redis)
+       ("which" ,which)))
+    (propagated-inputs
+     `(("python-croniter" ,python-croniter)
+       ("python-rq" ,python-rq)))
+    (synopsis "Job scheduling capabilities for RQ (Redis Queue)")
+    (description
+     "This package provides job scheduling capabilities to @code{python-rq}
+(Redis Queue).")
+    (license license:expat)))
+
 (define-public python-trollius-redis
   (package
     (name "python-trollius-redis")

gnu/packages/datastructures.scm

@@ -37,14 +37,16 @@
     (name "gdsl")
     (version "1.8")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "http://download.gna.org/gdsl/"
+              (uri (git-reference
-                                  "gdsl-" version ".tar.gz"))
+                    (url "https://example.org") ;only hosted on Software Heritage
+                    (commit "6adb53be8b8f9f2e4bbfc92d357eedeefb4c7430")))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1v64jvlnj8jfpphphgjgb36p0kv50kwfyqncf0y12f16v8ydyiaw"))))
+                "0a52g12d9sf9hhcyvwfd7xdazj2a9i9jh97cnlqf2ymvwnvjk1g0"))))
     (build-system gnu-build-system)
-    (home-page "http://home.gna.org/gdsl/")
+    (home-page "https://web.archive.org/web/20170502005430/http://home.gna.org/gdsl/")
     (synopsis "Generic data structures library")
     (description "The Generic Data Structures Library (GDSL) is a collection
 of routines for generic data structures manipulation.  It is a re-entrant

gnu/packages/dico.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -39,14 +39,14 @@
 (define-public dico
   (package
     (name "dico")
-    (version "2.9")
+    (version "2.10")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/dico/dico-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "0i9xqhy3h5nlizcmav4mv5ay8ivdgn4l4k0k7fxix3fsc87nijyr"))))
+               "0qag47mzs00d53hnrmh381r0jay42766vp5xrffmzmsn2307x8vl"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags (list (string-append "--with-guile-site-dir=" %output

gnu/packages/dictionaries.scm

@@ -205,14 +205,14 @@ It comes with a German-English dictionary with approximately 270,000 entries.")
 (define-public grammalecte
   (package
     (name "grammalecte")
-    (version "1.12.0")
+    (version "1.12.2")
     (source
      (origin
        (method url-fetch/zipbomb)
        (uri (string-append "https://grammalecte.net/grammalecte/zip/"
                            "Grammalecte-fr-v" version ".zip"))
        (sha256
-        (base32 "1aifa7rj8zyxgk5cgmlgcws2hip7a7y6sr7kddjdnpfgdgy4jjgh"))))
+        (base32 "1qny2l5dr08pfj2dnzmvm5gmwqz8m879ryxfaw4k8dhaacrrrf62"))))
     (build-system python-build-system)
     (home-page "https://grammalecte.net")
     (synopsis "French spelling and grammar checker")

gnu/packages/disk.scm

@@ -1038,6 +1038,6 @@ of choice for all light thinking Unix addicts!")
     (home-page "https://savannah.nongnu.org/projects/hddtemp/")
     (synopsis "Report the temperature of hard drives from S.M.A.R.T. information")
     (description "@command{hddtemp} is a small utility that gives you the
-temperature of your hard drive by reading S.M.A.R.T. informations (for drives
+temperature of your hard drive by reading S.M.A.R.T. information (for drives
 that support this feature).")
     (license license:gpl2+)))

gnu/packages/dns.scm

@@ -313,7 +313,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
   (package
     (name "bind")
     ;; When updating, check whether isc-dhcp's bundled copy should be as well.
-    (version "9.16.6")
+    (version "9.16.7")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -321,7 +321,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
                     "/bind-" version ".tar.xz"))
               (sha256
                (base32
-                "1jvi6ms51vyrhpflx05xlb7gblyd59zsyj28b8s3pl3xnkrv0rxm"))))
+                "1l8lhgnkj3fnl1101bs3pzj5gv2x5m9ahvrbyscsc9mxxc91hzcz"))))
     (build-system gnu-build-system)
     (outputs `("out" "utils"))
     (inputs
@@ -756,16 +756,16 @@ served by AS112.  Stub and forward zones are supported.")
 (define-public yadifa
   (package
     (name "yadifa")
-    (version "2.3.9")
+    (version "2.3.10")
     (source
-     (let ((build "8497"))
+     (let ((build "9729"))
        (origin
          (method url-fetch)
          (uri
           (string-append "http://cdn.yadifa.eu/sites/default/files/releases/"
                          "yadifa-" version "-" build ".tar.gz"))
          (sha256
-          (base32 "0xvyr91sfgzkpw6g3h893ldbwnki3w2472n56rr18w67qghs1sa5")))))
+          (base32 "0azaignqmylfdzr4x02s8y3pkn4f0xkpz3d1pkiiz8mwk92zgybn")))))
     (build-system gnu-build-system)
     (native-inputs
      `(("which" ,which)))
@@ -803,37 +803,25 @@ Extensions} (DNSSEC).")
 (define-public knot
   (package
     (name "knot")
-    (version "2.9.6")
+    (version "3.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://secure.nic.cz/files/knot-dns/"
                            "knot-" version ".tar.xz"))
        (sha256
-        (base32 "1rxjjisr6rz1wa4279ghvj5zzhgyjhncmb9dkzqm8nw2qs1jhx5z"))
+        (base32 "1i76zflc49jbsaj3idxx7a6x87c0lzal294c3fdjyfl7dvznmjgi"))))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           ;; Delete bundled libraries.
-           (with-directory-excursion "src/contrib"
-             (delete-file-recursively "lmdb"))
-           #t))))
     (build-system gnu-build-system)
-    (native-inputs
-     `(("pkg-config" ,pkg-config)))
-    (inputs
-     `(("fstrm" ,fstrm)
-       ("gnutls" ,gnutls)
-       ("jansson" ,jansson)
-       ("libcap-ng" ,libcap-ng)
-       ("libedit" ,libedit)
-       ("libidn" ,libidn)
-       ("liburcu" ,liburcu)
-       ("lmdb" ,lmdb)
-       ("ncurses" ,ncurses)
-       ("protobuf-c" ,protobuf-c)))
     (arguments
-     `(#:phases
+     `(#:configure-flags
+       (list "--sysconfdir=/etc"
+             "--localstatedir=/var"
+             "--enable-dnstap"          ; let tools read/write capture files
+             "--with-module-dnstap=yes" ; detailed query capturing & logging
+             (string-append "--with-bash-completions="
+                            (assoc-ref %outputs "out")
+                            "/etc/bash_completion.d"))
+       #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'disable-directory-pre-creation
            (lambda _
@@ -848,15 +836,20 @@ Extensions} (DNSSEC).")
                     (etc (string-append doc "/examples/etc")))
                (invoke "make"
                        (string-append "config_dir=" etc)
-                       "install")))))
+                       "install")))))))
-       #:configure-flags
+    (native-inputs
-       (list "--sysconfdir=/etc"
+     `(("pkg-config" ,pkg-config)))
-             "--localstatedir=/var"
+    (inputs
-             "--enable-dnstap"          ; let tools read/write capture files
+     `(("fstrm" ,fstrm)
-             "--with-module-dnstap=yes" ; detailed query capturing & logging
+       ("gnutls" ,gnutls)
-             (string-append "--with-bash-completions="
+       ("jansson" ,jansson)
-                            (assoc-ref %outputs "out")
+       ("libcap-ng" ,libcap-ng)
-                            "/etc/bash_completion.d"))))
+       ("libedit" ,libedit)
+       ("libidn" ,libidn)
+       ("liburcu" ,liburcu)
+       ("lmdb" ,lmdb)
+       ("ncurses" ,ncurses)
+       ("protobuf-c" ,protobuf-c)))
     (home-page "https://www.knot-dns.cz/")
     (synopsis "Authoritative DNS name server")
     (description "Knot DNS is an authoritative name server for the @dfn{Domain
@@ -878,14 +871,14 @@ synthesis, and on-the-fly re-configuration.")
 (define-public knot-resolver
   (package
     (name "knot-resolver")
-    (version "4.3.0")
+    (version "5.1.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://secure.nic.cz/files/knot-resolver/"
                                   "knot-resolver-" version ".tar.xz"))
               (sha256
                (base32
-                "09ffmqx79lv5psr433x4n946njgsn071b9b7161pcb9bmrqz380c"))))
+                "12s5070nqqf599s1mb6rjas2as481rjf751qk5yrz6p34y885k90"))))
     (build-system meson-build-system)
     (arguments
      '(#:configure-flags '("-Ddoc=enabled")
@@ -932,11 +925,7 @@ synthesis, and on-the-fly re-configuration.")
        ("lmdb" ,lmdb)
        ("luajit" ,luajit)
        ;; TODO: Add optional lua modules: basexx and psl.
-       ("lua-bitop" ,lua5.1-bitop)
+       ("lua-bitop" ,lua5.1-bitop)))
-       ("lua-cqueues" ,lua5.1-cqueues)
-       ("lua-filesystem" ,lua5.1-filesystem)
-       ("lua-sec" ,lua5.1-sec)
-       ("lua-socket" ,lua5.1-socket)))
     (home-page "https://www.knot-resolver.cz/")
     (synopsis "Caching validating DNS resolver")
     (description

gnu/packages/docker.scm

@@ -5,6 +5,7 @@
 ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
 ;;; Copyright © 2020 Katherine Cox-Buday <cox.katherine.e@gmail.com>
+;;; Copyright © 2020 Jesse Dowell <jessedowell@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -48,6 +49,8 @@
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages virtualization))
 
+;; Note - when changing Docker versions it is important to update the versions
+;; of several associated packages (docker-libnetwork and go-sctp).
 (define %docker-version "19.03.12")
 
 (define-public python-docker
@@ -246,22 +249,25 @@ network attachments.")
 (define docker-libnetwork
   ;; There are no recent release for libnetwork, so choose the last commit of
   ;; the branch that Docker uses, as can be seen in the Docker source file
-  ;; 'hack/dockerfile/install/proxy.installer'.
+  ;; 'hack/dockerfile/install/proxy.installer'. NOTE - It is important that
-  (let ((commit "4725f2163fb214a6312f3beae5991f838ec36326")
+  ;; this version is kept in sync with the version of Docker being used.
-        (version "18.09")
+  ;; This commit is the "bump_19.03" branch, as mentioned in Docker's vendor.conf.
+  (let ((commit "026aabaa659832804b01754aaadd2c0f420c68b6")
+        (version (version-major+minor %docker-version))
         (revision "1"))
     (package
       (name "docker-libnetwork")
-      (version (git-version version "1" commit))
+      (version (git-version version revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
-                      (url "https://github.com/docker/libnetwork")
+                      ;; Redirected from github.com/docker/libnetwork.
+                      (url "https://github.com/moby/libnetwork")
                       (commit commit)))
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1zpnxki8qfzha6ljahpwd3vkzmjhsvkmf73w6crm4ilxxw5vnpfb"))
+                  "0bli21vn5v7bssw3ydym4jfdjsldhb47fld88kng7d138wl70lkw"))
                 ;; Delete bundled ("vendored") free software source code.
                 (modules '((guix build utils)))
                 (snippet '(begin
@@ -269,8 +275,8 @@ network attachments.")
                             #t))))
       (build-system go-build-system)
       (arguments
-       `(#:import-path "github.com/docker/libnetwork/"))
+       `(#:import-path "github.com/moby/libnetwork/"))
-      (home-page "https://github.com/docker/libnetwork/")
+      (home-page "https://github.com/moby/libnetwork/")
       (synopsis "Networking for containers")
       (description "Libnetwork provides a native Go implementation for
 connecting containers.  The goal of @code{libnetwork} is to deliver a robust
@@ -514,6 +520,7 @@ built-in registry server of Docker.")
              #t))
          (replace 'configure
            (lambda _
+             (setenv "DOCKER_BUILDTAGS" "seccomp")
              (setenv "DOCKER_GITCOMMIT" (string-append "v" ,%docker-version))
              (setenv "VERSION" (string-append ,%docker-version "-ce"))
              ;; Automatically use bundled dependencies.

gnu/packages/documentation.scm

@@ -273,7 +273,7 @@ and to some extent D.")
     (description
      "DOC++ is a documentation system for C, C++, IDL, and Java.  It can
 generate both TeX output for high-quality hardcopies or HTML output for online
-brwosing.  The documentation is extracted directly from the C/C++/IDL source
+browsing.  The documentation is extracted directly from the C/C++/IDL source
 or Java class files.")
     (license gpl2+)))
 

gnu/packages/easyrpg.scm

@@ -76,7 +76,7 @@ It can read and write LCF and XML files.")
 (define-public easyrpg-player
   (package
     (name "easyrpg-player")
-    (version "0.6.2.1")
+    (version "0.6.2.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -84,7 +84,7 @@ It can read and write LCF and XML files.")
                     "/easyrpg-player-" version ".tar.gz"))
               (sha256
                (base32
-                "1bai0mxjw1qvl2vcwgssycbyn0crk0b5l69ld9rawcs2nczb44s5"))))
+                "02nrqrb6klynwrq6z0639qnlhr2z900b0y94xr96i12icr7ihm5m"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags

gnu/packages/ebook.scm

@@ -4,8 +4,9 @@
 ;;; Copyright © 2016, 2017 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2017, 2019, 2020 Brendan Tildesley <mail@brendan.scot>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -26,26 +27,32 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix utils)
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system meson)
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages databases)
+  #:use-module (gnu packages file)
   #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages fribidi)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages gettext)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages glib)
+  #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages image)
   #:use-module (gnu packages javascript)
   #:use-module (gnu packages libusb)
   #:use-module (gnu packages libreoffice)
+  #:use-module (gnu packages music)
   #:use-module (gnu packages pdf)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
@@ -245,29 +252,7 @@
                      "--path-to-mathjax" (string-append
                                           (assoc-ref inputs "js-mathjax")
                                           "/share/javascript/mathjax"))
-             (invoke "python2" "setup.py" "rapydscript")))
+             (invoke "python2" "setup.py" "rapydscript")
-         (replace 'wrap
-           ;; Here we wrap PYTHONPATH exactly as it would be in
-           ;; python-build-system, plus the addition of
-           ;; QTWEBENGINEPROCESS_PATH, fixing a bug where Calibre would not
-           ;; find Qtwebengine.
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (bin (string-append out "/bin"))
-                    (python (assoc-ref inputs "python"))
-                    (site-packages
-                     (cons (string-append out "/lib/python"
-                                          (python-version python)
-                                          "/site-packages")
-                           (search-path-as-string->list (getenv "PYTHONPATH"))))
-                    (qtwebengineprocess
-                     (string-append (assoc-ref inputs "qtwebengine")
-                                    "/lib/qt5/libexec/QtWebEngineProcess")))
-               (for-each (lambda (program)
-                           (wrap-program program
-                                 `("QTWEBENGINEPROCESS_PATH" = (,qtwebengineprocess))
-                                 `("PYTHONPATH" prefix ,site-packages)))
-                         (find-files bin ".")))
              #t))
          (add-after 'install 'install-man-pages
            (lambda* (#:key outputs #:allow-other-keys)
@@ -285,6 +270,28 @@
                                             "/share/fonts/truetype")))
                (delete-file-recursively font-dest)
                (symlink font-src font-dest))
+             #t))
+         ;; Make run-time dependencies available to the binaries.
+         (add-after 'wrap 'wrap-program
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (qtwebengine (assoc-ref inputs "qtwebengine")))
+               (with-directory-excursion (string-append out "/bin")
+                 (for-each
+                  (lambda (binary)
+                    (wrap-program binary
+                      ;; Make QtWebEngineProcess available.
+                      `("QTWEBENGINEPROCESS_PATH" ":" =
+                        ,(list (string-append
+                                qtwebengine
+                                "/lib/qt5/libexec/QtWebEngineProcess")))))
+                  ;; Wrap all the binaries shipping with the package, except
+                  ;; for the wrappings created during the 'wrap standard
+                  ;; phase.  This extends existing .calibre-real wrappers
+                  ;; rather than create ..calibre-real-real-s.  For more
+                  ;; information see: https://issues.guix.gnu.org/43249.
+                  (find-files "." (lambda (file stat)
+                                    (not (wrapper? file)))))))
              #t)))))
     (home-page "https://calibre-ebook.com/")
     (synopsis "E-book library management software")
@@ -405,6 +412,105 @@ following formats:
 @end enumerate")
     (license license:gpl2+)))
 
+(define-public cozy
+  (package
+    (name "cozy")
+    (version "0.7.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/geigi/cozy")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0fmbddi4ga0bppwg3rm3yjmf7jgqc6zfslmavnr1pglbzkjhy9fs"))))
+    (build-system meson-build-system)
+    (arguments
+     `(#:glib-or-gtk? #t
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-desktop-file
+           (lambda _
+             (substitute* "data/com.github.geigi.cozy.desktop.in"
+               (("Exec=com.github.geigi.cozy") "Exec=cozy"))
+             #t))
+         (add-after 'install 'patch-executable-name
+           (lambda* (#:key outputs #:allow-other-keys)
+             (with-directory-excursion
+                 (string-append (assoc-ref outputs "out") "/bin")
+               (rename-file "com.github.geigi.cozy" "cozy"))
+             #t))
+         (add-after 'wrap 'wrap-libs
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out               (assoc-ref outputs "out"))
+                    (pylib             (string-append
+                                        out "/lib/python"
+                                        ,(version-major+minor
+                                          (package-version python))
+                                        "/site-packages"))
+                    (gi-typelib-path   (getenv "GI_TYPELIB_PATH"))
+                    (gst-plugin-path   (getenv "GST_PLUGIN_SYSTEM_PATH"))
+                    (libmagic-path     (string-append
+                                        (assoc-ref %build-inputs "file")
+                                        "/lib"))
+                    (python-path     (getenv "PYTHONPATH")))
+               (wrap-program (string-append out "/bin/cozy")
+                 `("LD_LIBRARY_PATH" ":" prefix (,libmagic-path))
+                 `("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path))
+                 `("GST_PLUGIN_SYSTEM_PATH" ":" prefix (,gst-plugin-path))
+                 `("PYTHONPATH" ":" prefix (,python-path ,pylib))))
+             #t)))))
+    (native-inputs
+     `(("desktop-file-utils" ,desktop-file-utils)
+       ("gettext" ,gettext-minimal)
+       ("glib:bin" ,glib "bin")
+       ("gobject-introspection" ,gobject-introspection)
+       ("gtk+:bin" ,gtk+ "bin")
+       ("pkg-config" ,pkg-config)
+       ("python" ,python-wrapper)))
+    (inputs
+     `(("file" ,file)
+       ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
+       ("gst-libav" ,gst-libav)
+       ("gst-plugins-bad" ,gst-plugins-bad)
+       ("gst-plugins-good" ,gst-plugins-good)
+       ("gst-plugins-ugly" ,gst-plugins-ugly)
+       ("gtk+" ,gtk+)
+       ("python-apsw" ,python-apsw)
+       ("python-distro" ,python-distro)
+       ("python-gst" ,python-gst)
+       ("python-mutagen" ,python-mutagen)
+       ("python-packaging" ,python-packaging)
+       ("python-peewee" ,python-peewee)
+       ("python-pycairo" ,python-pycairo)
+       ("python-pygobject" ,python-pygobject)
+       ("python-pytz" ,python-pytz)
+       ("python-requests" ,python-requests)))
+    (home-page "https://cozy.geigi.de/")
+    (synopsis "Modern audiobook player using GTK+")
+    (description
+     "Cozy is a modern audiobook player written in GTK+.
+
+Some of the current features:
+
+@itemize
+@item Import your audiobooks into Cozy to browse them comfortably
+@item Sort your audio books by author, reader & name
+@item Remembers your playback position
+@item Sleep timer
+@item Playback speed control
+@item Search your library
+@item Offline mode
+@item Add multiple storage locations
+@item Drag & Drop to import new audio books
+@item Support for DRM free mp3, m4a (aac, ALAC, …), flac, ogg, opus, wav files
+@item Mpris integration (Media keys & playback info for desktop environment)
+@end itemize")
+    ;; TODO: Unbundle python-inject.
+    (license (list license:gpl3+ ;cozy
+                   license:asl2.0)))) ;python-inject (bundled dependency)
+
 (define-public xchm
   (package
     (name "xchm")

gnu/packages/education.scm

@@ -275,7 +275,7 @@ easy.")
 (define-public snap
   (package
     (name "snap")
-    (version "6.1.4")
+    (version "6.2.1")
     (source
      (origin
        (method git-fetch)
@@ -284,7 +284,7 @@ easy.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0qvnm5jg2hlf32say531m8nmp3aib93mqnllw1g289s58fzk5li6"))))
+        (base32 "163pskgrssw0l6c73lrdx613fridnv0162lscl4xqx9sgg7hfaxh"))))
     (build-system trivial-build-system)
     (arguments
      `(#:modules ((guix build utils))
@@ -613,14 +613,14 @@ Portuguese, Spanish and Italian.")
 (define-public fet
   (package
     (name "fet")
-    (version "5.46.1")
+    (version "5.47.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.lalescu.ro/liviu/fet/download/"
                            "fet-" version ".tar.bz2"))
        (sha256
-        (base32 "1sakzizjsyjn6705zl283i81zxn1gxskg2i4jv7iq75vw3nzm6kv"))))
+        (base32 "1a4mzzd6qy7hpb3yvmf922dbrqrzacz60ld8dsds78m018jf9gaj"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/elixir.scm

@@ -27,7 +27,8 @@
   #:use-module (guix git-download)
   #:use-module (guix packages)
   #:use-module (gnu packages)
-  #:use-module (gnu packages erlang))
+  #:use-module (gnu packages erlang)
+  #:use-module (gnu packages version-control))
 
 (define-public elixir
   (package
@@ -99,7 +100,8 @@
              #t))
          (delete 'configure))))
     (inputs
-     `(("erlang" ,erlang)))
+     `(("erlang" ,erlang)
+       ("git" ,git)))
     (home-page "https://elixir-lang.org/")
     (synopsis "Elixir programming language")
     (description "Elixir is a dynamic, functional language used to build

gnu/packages/emacs-xyz.scm

@@ -78,6 +78,8 @@
 ;;; Copyright © 2020 Eric Bavier <bavier@posteo.net>
 ;;; Copyright © 2020 Morgan Smith <Morgan.J.Smith@outlook.com>
 ;;; Copyright © 2020 Peng Mei Yu <i@pengmeiyu.com>
+;;; Copyright © 2020 Niklas Eklund <niklas.eklund@posteo.net>
+;;; Copyright © 2020 Marco Grassi <marco.au.grassi98@protonmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -118,6 +120,7 @@
   #:use-module (gnu packages curl)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages dictionaries)
+  #:use-module (gnu packages djvu)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages gtk)
@@ -261,14 +264,14 @@ using geiser.")
 (define-public emacs-hyperbole
   (package
     (name "emacs-hyperbole")
-    (version "7.1.2")
+    (version "7.1.3")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/"
                            "hyperbole-" version ".tar"))
        (sha256
-        (base32 "1bspmqnbniwr9385wh823dsr5fgch5qnlkf45s4vi0nvg8jdccp1"))
+        (base32 "0bizibn4qgxqp89fyik6p47s9hss1g932mg8k7pznn3kkhj5c8rh"))
        (patches
         (search-patches "emacs-hyperbole-toggle-messaging.patch"))))
     (build-system emacs-build-system)
@@ -1723,14 +1726,14 @@ mode, Rmail, Gnus, MH-E, and VM).  BBDB is fully customizable.")
 (define-public emacs-bluetooth
   (package
     (name "emacs-bluetooth")
-    (version "0.1.2")
+    (version "0.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/"
                            "bluetooth-" version ".el"))
        (sha256
-        (base32 "1vp2vpyq0ybjni35ics1mg1kiwgvc7x12dlmvygy78sqp52sfkcv"))))
+        (base32 "1dq04p6ms0zx4awlypp4crkz7dzal4xg8ac7p8fqacz196rczssp"))))
     (build-system emacs-build-system)
     (inputs
      `(("bluez" ,bluez)))
@@ -1920,14 +1923,14 @@ as a library for other Emacs packages.")
 (define-public emacs-auctex
   (package
     (name "emacs-auctex")
-    (version "12.2.4")
+    (version "12.2.5")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/"
                            "auctex-" version ".tar"))
        (sha256
-        (base32 "1yz2h692mr35zgqwlxdq8rzv8n0jixhpaqmbiki00hlysm4zh9py"))))
+        (base32 "1288n0yna36g2h15gk34gvllifx4qms48355j8l2cafabvkffiph"))))
     (build-system emacs-build-system)
     ;; We use 'emacs' because AUCTeX requires dbus at compile time
     ;; ('emacs-minimal' does not provide dbus).
@@ -2315,24 +2318,27 @@ written in the Go programming language.")
     (license license:bsd-3)))
 
 (define-public emacs-google-maps
+  ;; There has been no new release tag since 2013.
+  (let ((commit "2eb16ff609f5a9f8d02c15238a111fbb7db6c146")
+        (revision "1"))
     (package
       (name "emacs-google-maps")
-    (version "1.0.0")
+      (version (git-version "1.0.0" revision commit))
-    (source (origin
+      (source
+       (origin
          (method git-fetch)
          (uri (git-reference
                (url "https://github.com/jd/google-maps.el")
-                    (commit version)))
+               (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-               (base32
+          (base32 "1bl0dnksbf14d0xcnvdy9qpvzc5c8jwkxpmfvgayj6djikxnw2md"))))
-                "183igr5lp20zcqi7rc01fk76sfxdhksd74i11v16gdsifdkjimd0"))))
       (build-system emacs-build-system)
       (home-page "https://github.com/jd/google-maps.el")
       (synopsis "Access Google Maps from Emacs")
-    (description "The @code{google-maps} package displays Google
+      (description "The @code{google-maps} package displays Google Maps
-Maps directly inside Emacs.")
+directly inside Emacs.  It requires a Google Map Static API key to function.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-graphviz-dot-mode
   (package
@@ -2479,13 +2485,30 @@ filters, new key bindings and faces.  It can be enabled by
        (sha256
         (base32 "0njgyx09q225hliacsnjk8wallg5i6xkz6bj501pb05nwqfbvfk7"))))
     (build-system emacs-build-system)
+    (inputs `(("djview" ,djview)
+              ("djvulibre" ,djvulibre)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'configure
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((file "djvu.el")
+                   (djview (assoc-ref inputs "djview"))
+                   (djvulibre (assoc-ref inputs "djvulibre")))
+               ;; Specify the absolute executable locations.
+               (chmod file #o644)
+               (substitute* file
+                 (("\"djvused\"") (string-append "\"" djvulibre "/bin/djvused\""))
+                 (("\"djvm\"") (string-append "\"" djvulibre "/bin/djvm\""))
+                 (("\"ddjvu\"") (string-append "\"" djvulibre "/bin/ddjvu\"")))
+               (emacs-substitute-variables file
+                 ("djvu-djview-command" (string-append djview "/bin/djview"))))
+             #t)))))
     (home-page "http://elpa.gnu.org/packages/djvu.html")
     (synopsis "Edit and view Djvu files via djvused")
     (description
      "This package is a front end for the command-line program djvused from
-DjVuLibre, see @url{http://djvu.sourceforge.net/}.  It assumes you have the
+DjVuLibre, see @url{http://djvu.sourceforge.net/}.")
-programs @command{djvused}, @command{djview}, @command{ddjvu}, and
-@command{djvm} installed.")
     (license license:gpl3+)))
 
 (define-public emacs-pabbrev
@@ -2513,18 +2536,22 @@ during idle time, while Emacs is doing nothing else.")
     (license license:gpl3+)))
 
 (define-public emacs-pdf-tools
+  ;; XXX: Development branch fixes an incompatibility with Emacs 27+.  See
+  ;; <https://github.com/politza/pdf-tools/issues/616>.
+  (let ((commit "c510442ab89c8a9e9881230eeb364f4663f59e76")
+        (revision "1"))
     (package
       (name "emacs-pdf-tools")
-    (version "0.90")
+      (version (git-version "0.90" revision commit))
-    (home-page "https://github.com/politza/pdf-tools")
+      (source
-    (source (origin
+       (origin
          (method git-fetch)
-              (uri (git-reference (url home-page)
+         (uri (git-reference
-                                  (commit (string-append "v" version))))
+               (url "https://github.com/politza/pdf-tools")
+               (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-               (base32
+          (base32 "17z3cpn76g9dp62drjrgrqpp1bgf4gl5k5gspylskpvd4kj4bq4d"))))
-                "0iv2g5kd14zk3r5dzdw7b7hk4b5w7qpbilcqkja46jgxbb6xnpl9"))))
       (build-system gnu-build-system)
       (arguments
        `(#:tests? #f                    ; there are no tests
@@ -2568,23 +2595,27 @@ during idle time, while Emacs is doing nothing else.")
              (assoc-ref emacs:%standard-phases 'build))
            (add-after 'emacs-install 'emacs-make-autoloads
              (assoc-ref emacs:%standard-phases 'make-autoloads)))))
-    (native-inputs `(("autoconf" ,autoconf)
+      (native-inputs
+       `(("autoconf" ,autoconf)
          ("automake" ,automake)
          ("pkg-config" ,pkg-config)
          ("emacs" ,emacs-minimal)))
-    (inputs `(("poppler" ,poppler)
+      (inputs
+       `(("poppler" ,poppler)
          ("cairo" ,cairo)
          ("glib" ,glib)
          ("libpng" ,libpng)
          ("zlib" ,zlib)))
-    (propagated-inputs `(("tablist" ,emacs-tablist)))
+      (propagated-inputs
+       `(("tablist" ,emacs-tablist)))
+      (home-page "https://github.com/politza/pdf-tools")
       (synopsis "Emacs support library for PDF files")
       (description
        "PDF Tools is, among other things, a replacement of DocView for PDF
 files.  The key difference is that pages are not pre-rendered by
 e.g. ghostscript and stored in the file-system, but rather created on-demand
 and stored in memory.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-dash
   (package
@@ -2774,7 +2805,7 @@ running Extempore process, and more.")
       (description "This package provides many, but not all of the editing
 primitives in the Kakoune editor.  Unlike Evil mode for Vim, this is a very
 shallow emulation, which seeks to do as little work as possible, leveraging
-Emacs native editing commmands and the work of other packages wherever
+Emacs native editing commands and the work of other packages wherever
 possible.")
       (license license:expat))))
 
@@ -2852,16 +2883,16 @@ a command.")
 (define-public emacs-olivetti
   (package
     (name "emacs-olivetti")
-    (version "1.8.1")
+    (version "1.11.1")
-    (source (origin
+    (source
+     (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/rnkn/olivetti")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-               (base32
+        (base32 "0rghxjdzyfykd4qc2zkavvbyf9xc899k1b8hbk890f1y3vakqvqz"))))
-                "1fbj9s49y5yx5i429awv9rybacfgvhwp7v5h0zw67bpgx4qs44pa"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/rnkn/olivetti")
     (synopsis "Emacs minor mode for a nice writing environment")
@@ -2959,6 +2990,27 @@ strings.")
 Stack Overflow, Super User, and other StackExchange sites.")
       (license license:gpl3+))))
 
+(define-public emacs-toc-org
+  (package
+    (name "emacs-toc-org")
+    (version "1.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/snosov1/toc-org")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0lk0rji85a1c0c5r9an0fdvsm4n4jyixsknmr8ywha3lfmc2p0l8"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/snosov1/toc-org")
+    (synopsis "Table of Contents generator for Emacs Org mode")
+    (description
+     "This package generates a table of contents when saving in Org and
+Markdown files.")
+    (license license:gpl2+)))
+
 (define-public emacs-toml-mode
   (let ((version "0.1.3")
         (revision "0")
@@ -3033,7 +3085,7 @@ files and directories.")
 (define-public emacs-fountain-mode
   (package
     (name "emacs-fountain-mode")
-    (version "3.2.2")
+    (version "3.3.0")
     (source
      (origin
        (method git-fetch)
@@ -3042,7 +3094,7 @@ files and directories.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0rwdwbw9cq8ljvbmgmz9izank8dqjki79l1bw127lli69fs72gyi"))))
+        (base32 "04jrv6i4ah3i8c9hcd9wyaw2vrxr46f50qb9qwna2v7qa5vaway3"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/rnkn/fountain-mode")
     (synopsis "Major mode for screenwriting in Fountain markup")
@@ -3766,6 +3818,30 @@ particular, the minor mode works quite well with Org or Markdown modes, or
 other markup language major modes.")
       (license license:gpl3+))))
 
+(define-public emacs-standard-dirs
+  (package
+    (name "emacs-standard-dirs")
+    (version "2.0.0")
+    (home-page "https://github.com/lafrenierejm/standard-dirs.el")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url home-page)
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0r814qcrhvx4qlx4sdzwdmrhiryslqclx0bnpp0qcrbx6g8qfl25"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-f" ,emacs-f)
+       ("emacs-s" ,emacs-s)))
+    (synopsis "Platform-specific paths for config, cache, and other data")
+    (description
+     "This package provides platform-specific paths for reading and writing
+configuration, cache, and other data.")
+    (license license:gpl3+)))
+
 (define-public emacs-string-inflection
   (package
     (name "emacs-string-inflection")
@@ -4069,6 +4145,30 @@ read from small to large monitors by using colors, a prefix feature, and smart
 truncation.")
     (license license:gpl2+)))
 
+(define-public emacs-sqlite
+  ;; XXX: There is no tagged commit.
+  (let ((commit "dad42b8bbca4994be1871343dd18fd6528ee5797")
+	(revision "0"))
+    (package
+      (name "emacs-sqlite")
+      (build-system emacs-build-system)
+      (version (git-version "1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+	       (url "https://gitlab.com/cnngimenez/sqlite.el")
+	       (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "06ln4vijl8kii3nzc5cscgsadx1fqgxksflijd3ain83bn8g4wrd"))))
+      (home-page "https://gitlab.com/cnngimenez/sqlite.el")
+      (synopsis "SQLite interface for Emacs Lisp")
+      (description "Emacs SQLite is a simple SQLite interface for connecting
+and retrieving information using the SQLite program through Elisp programming.
+It is not intended as a user interface.")
+      (license license:gpl3+))))
+
 (define-public emacs-sr-speedbar
   (let ((commit "77a83fb50f763a465c021eca7343243f465b4a47")
         (revision "0"))
@@ -4117,7 +4217,7 @@ the speedbar window.")
 (define-public emacs-shx
   (package
     (name "emacs-shx")
-    (version "1.4.0")
+    (version "1.5.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -4125,15 +4225,10 @@ the speedbar window.")
                     (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "0p9b621rgy34r1hl9xfzxh4xpx9gpsr3n330ypfxhlr0s5754j73"))))
+               (base32 "1cb5w6p9gnfxgh8qp7yj2f5ibpk1b4b5af3ynldaaj6yfpa8hqzn"))))
     (build-system emacs-build-system)
     (arguments
-     `(#:phases
+     `(#:tests? #t
-       (modify-phases %standard-phases
-         ;; A docstring provides examples of mapping hosts to programs in /bin.
-         ;; These examples are valid as-is.
-         (delete 'patch-el-files))
-       #:tests? #t
        #:test-command
        '("emacs" "--batch" "--quiet"
          "--script" "test/script.el")))
@@ -5249,6 +5344,29 @@ commands and highlighting.")
     ;; indicates GPL3.
     (license license:gpl3)))
 
+(define-public emacs-sbt-mode
+  (package
+    (name "emacs-sbt-mode")
+    (version "2.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/hvesalai/emacs-sbt-mode")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0lv9ridzk9x6rkf7lj21srnszypyq04vqg05vl10zhpz1yqlnbjd"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/hvesalai/emacs-sbt-mode")
+    (synopsis "Basic functionality for interacting with sbt inside Emacs")
+    (description
+     "This mode provides basic functionality required for successfully
+interacting with sbt inside Emacs.  The core functionality includes
+interacting with the sbt shell and Scala console, compiling code and
+navigation to errors.")
+    (license license:gpl3+)))
+
 (define-public emacs-scheme-complete
   (let ((commit "9b5cf224bf2a5994bc6d5b152ff487517f1a9bb5"))
     (package
@@ -6738,15 +6856,14 @@ line program.")
 (define-public emacs-rudel
   (package
     (name "emacs-rudel")
-    (version "0.3.1")
+    (version "0.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/rudel-"
                            version ".tar"))
        (sha256
-        (base32
+        (base32 "03hcvpp6ykavidwn5x48gs986w1i5icvh7ks6p74pdaagpgw4jmk"))))
-         "0glqa68g509p0s2vcc0i8kzlddnc9brd9jqhnm5rzxz4i050cvnz"))))
     (build-system emacs-build-system)
     (home-page "http://rudel.sourceforge.net/")
     (synopsis "Collaborative editing framework")
@@ -7335,7 +7452,7 @@ asynchronously, with Counsel and Ivy.  Simply call
 (define-public emacs-counsel-projectile
   (package
     (name "emacs-counsel-projectile")
-    (version "0.3.0")
+    (version "0.3.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -7344,7 +7461,7 @@ asynchronously, with Counsel and Ivy.  Simply call
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1inc4ndl0ysfwvxk4avbgpj4qi9rc93da6476a5c81xmwpsv8wmq"))))
+                "1k4n5lw6wwbgpwv0dg9dw0bjzi0hvbgkzrs1zmq36yhfz6y8gwnh"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-counsel" ,emacs-counsel)
@@ -7401,6 +7518,29 @@ be removed from the front.  This type of data structure is sometimes called an
 \"output-restricted deque\".")
     (license license:gpl3+)))
 
+(define-public emacs-quickrun
+  (package
+    (name "emacs-quickrun")
+    (version "2.3.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/emacsorphanage/quickrun")
+             (commit version)))
+       (sha256
+        (base32 "0a1n2v09h0n7d9p2izflqqang4ny0b46dlqvmxvkkik4bb6f4wcz"))
+       (file-name (git-file-name name version))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/emacsorphanage/quickrun")
+    (synopsis "Execute editing buffer and show its output quickly")
+    (description
+     "This package evaluates the content of a buffer, or region, and displays
+the result.  Quickrun executes not only script languages (Perl, Ruby, Python
+etc), but also compiling languages (C, C++, Go, Java etc) and markup
+languages.")
+    (license license:gpl3+)))
+
 (define-public emacs-pkg-info
   (package
     (name "emacs-pkg-info")
@@ -7788,7 +7928,7 @@ in Emacs.")
 (define-public emacs-edit-indirect
   (package
     (name "emacs-edit-indirect")
-    (version "0.1.5")
+    (version "0.1.6")
     (source
      (origin
        (method git-fetch)
@@ -7797,14 +7937,13 @@ in Emacs.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32
+        (base32 "189nvmlkki1jfszm9i0crbb1p4nzgmbly0wpvpg0i8vmw7vrpl40"))))
-         "0by1x53pji39fjrj5bd446kz831nv0vdgw2jqasbym4pc1p2947r"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/Fanael/edit-indirect")
     (synopsis "Edit regions in separate buffers")
     (description "This package allows you to edit regions in separate buffers,
 like @code{org-edit-src-code} but for arbitrary regions.")
-    (license license:gpl3+)))
+    (license license:bsd-2)))
 
 (define-public emacs-projectile
   (package
@@ -9586,14 +9725,14 @@ distribution, primarily targeting Clojure users")
 (define-public emacs-orgalist
   (package
     (name "emacs-orgalist")
-    (version "1.12")
+    (version "1.13")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/"
                            "orgalist-" version ".el"))
        (sha256
-        (base32 "1hwm7j0hbv2pg9w885ky1c9qga3grcfq8v216jv2ivkw8xzavysd"))))
+        (base32 "1wkxc5kcy1g4lx6pd78pa8znncjyl9zyhsvz7wpp56qmhq4hlav3"))))
     (build-system emacs-build-system)
     (home-page "https://elpa.gnu.org/packages/orgalist.html")
     (synopsis "Manage Org-like lists in non-Org buffers")
@@ -9651,13 +9790,13 @@ passive voice.")
     (name "emacs-org")
     ;; emacs-org-contrib inherits from this package.  Please update it as
     ;; well.
-    (version "9.3.8")
+    (version "9.4")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/org-" version ".tar"))
        (sha256
-        (base32 "1az00pi9rw3ibx4061jyqr6ll27kvs99yvd7nk5dckjh0ajd0gni"))))
+        (base32 "1awkrh3y90q7c0as3327rqj0zylf5cpjzr1pyvbzymli16irhwb6"))))
     (build-system emacs-build-system)
     (arguments
      `(#:phases
@@ -9682,14 +9821,14 @@ programming and reproducible research.")
   (package
     (inherit emacs-org)
     (name "emacs-org-contrib")
-    (version "20200907")
+    (version "20200914")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://orgmode.org/elpa/"
                            "org-plus-contrib-" version ".tar"))
        (sha256
-        (base32 "1rgk3pwhsmbmwlncg60ahwrrkm1ks4xpwy2wzv9q7myl1aihjj54"))))
+        (base32 "1naq25g4d95cx29axx428rnpc4m9hd0j7w1l0vqwkdjyr5qfj0ab"))))
     (arguments
      `(#:modules ((guix build emacs-build-system)
                   (guix build utils)
@@ -11037,7 +11176,7 @@ function to be used by other frontend programs.")
     (home-page "https://github.com/tumashu/pyim-basedict")
     (synopsis "Input method dictionary of pyim")
     (description "Pyim-basedict is the default pinyin input method dictionary,
-containing words from the rime project.")
+containing words from the Rime project.")
     (license license:gpl2+)))
 
 (define-public emacs-pyim
@@ -12906,7 +13045,7 @@ buffer.")
     (description "@code{eless} provides a combination of Bash script
 and a minimal Emacs view-mode.
 
-Feautures:
+Features:
 
 @itemize
 @item Independent of a user’s Emacs config.
@@ -14254,18 +14393,15 @@ timestamps by providing a @code{ts} struct.")
 (define-public emacs-peg
   (package
     (name "emacs-peg")
-    (version "0.6")
+    (version "1.0")
-    (source (origin
+    (source
-              (method git-fetch)
+     (origin
-              (uri (git-reference
+       (method url-fetch)
-                    (url "https://github.com/emacsmirror/peg")
+       (uri (string-append "https://elpa.gnu.org/packages/peg-" version ".tar"))
-                    (commit version)))
        (sha256
-               (base32
+        (base32 "0skr5dz9k34r409hisnj37n1b7n62l3md0glnfx578xkbmxlpcxl"))))
-                "0kjz7ch4bn0m4v9zgqyqcrsasnqc5c5drv2hp22j7rnbb7ny0q3n"))
-              (file-name (git-file-name name version))))
     (build-system emacs-build-system)
-    (home-page "https://github.com/emacsmirror/peg/")
+    (home-page "https://elpa.gnu.org/packages/peg.html")
     (synopsis "Parsing Expression Grammars in Elisp")
     (description "This package provides a macro that parses the current buffer
 according to a parsing expression grammar.")
@@ -15009,36 +15145,36 @@ macro takes a first argument (whose value must be an alist) and a body.")
     (license license:gpl3+)))
 
 (define-public emacs-esup
+  (let ((commit "0de8af8233d9ce1b67f05a50f25c481c4f1118d8")
+        (revision "1"))
     (package
       (name "emacs-esup")
-    (version "0.7")
+      (version (git-version "0.7.1" revision commit))
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
                (url "https://github.com/jschaf/esup")
-             (commit (string-append "v" version))))
+               (commit commit)))
          (file-name (git-file-name name version))
          (sha256
           (base32
-         "100w28n3qb3s5b18vvqpwmijdjnjazawn38i0pjbpxz5llhqgl1g"))))
+           "01khb3xyj0ylwib6ryzzvqmkh5wvzxiq2n3l0s3h9zv7wx849bzv"))))
       (build-system emacs-build-system)
       (native-inputs
        `(("emacs-noflet" ,emacs-noflet)
-       ("emacs-el-mock" ,emacs-el-mock)))
+         ("emacs-undercover" ,emacs-undercover)
+         ("emacs-buttercup" ,emacs-buttercup)))
+      (propagated-inputs
+       `(("emacs-dash" ,emacs-dash)))
       (arguments
-     `(#:phases
+     `(#:tests? #t
-       (modify-phases %standard-phases
+       #:test-command '("buttercup" "-L" ".")))
-         (add-before 'install 'check
-           (lambda* (#:key inputs #:allow-other-keys)
-             (invoke "emacs" "--batch" "-L" "."
-                     "-l" "test/esup-test.el"
-                     "-f" "ert-run-tests-batch-and-exit"))))))
       (home-page "https://github.com/jschaf/esup")
       (synopsis "Emacs start up profiler")
       (description "Benchmark Emacs Startup time without ever leaving
 your Emacs.")
-    (license license:gpl2+)))
+      (license license:gpl2+))))
 
 (define-public emacs-restart-emacs
   (let ((commit "9aa90d3df9e08bc420e1c9845ee3ff568e911bd9")
@@ -15225,7 +15361,7 @@ until the top-level form is no longer a macro call.")
 (define-public emacs-beginend
   (package
     (name "emacs-beginend")
-    (version "2.1.0")
+    (version "2.2.0")
     (source
      (origin
        (method git-fetch)
@@ -15234,7 +15370,7 @@ until the top-level form is no longer a macro call.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1ic5z3qb5sc3mjrjdlg0rqm2l59a43gwnakagns4cilln2a3xdg8"))))
+        (base32 "1r9033zlx2q2dk3bjz004flxdiw79qiswq0zqdjnlzwassvk0f35"))))
     ;; TODO: Run tests.
     (build-system emacs-build-system)
     (inputs
@@ -15714,18 +15850,21 @@ downloading manager for Emacs.")
       (license license:gpl3+))))
 
 (define-public emacs-helpful
+  (let ((version "0.17")
+        (commit "b0e937fff71dc0a5d34066bfd25310e76f284621")
+        (revision "1"))
     (package
       (name "emacs-helpful")
-    (version "0.17")
+      (version (git-version version revision commit))
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
                (url "https://github.com/Wilfred/helpful")
-             (commit version)))
+               (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-        (base32 "0v2y0x9pwi08y2mgjjiw5brfb5haa7pbmy4540glw904ffxxcblj"))))
+          (base32 "048qvlyj2vkgi872z8l07diwqnq21ziycv8slxzzy7rflw3wx0b2"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-elisp-refs" ,emacs-elisp-refs)
@@ -15760,7 +15899,7 @@ functions.
 @item Trace, disassemble functions from inside Helpful.  This is discoverable
 and doesn't require memorisation of commands.
 @end itemize\n")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-logview
   (package
@@ -15938,10 +16077,10 @@ Magit.")
     (license license:gpl3+)))
 
 (define-public emacs-lice-el
-  (let ((commit "4339929927c62bd636f89bb39ea999d18d269250"))
+  (let ((commit "482e58ab83fff86ed754b00be27b62a219597e7c"))
     (package
       (name "emacs-lice-el")
-      (version (git-version "0.2" "1" commit))
+      (version (git-version "0.2" "2" commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -15950,8 +16089,26 @@ Magit.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0879z761b7gajkhq176ps745xpdrivch349crransv8fnsc759yb"))))
+                  "0yxkjyhfk8kpr8yqz54gdx6xwkj4s8bnbz60162jh12crj0bs5n7"))))
       (build-system emacs-build-system)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'patch-template-directory
+             (lambda* (#:key outputs #:allow-other-keys)
+               (chmod "lice.el" #o666)
+               (emacs-substitute-variables "lice.el"
+                 ("lice:system-template-directory"
+                  (string-append (assoc-ref outputs "out")
+                                 "/share/emacs-lice-el/template")))
+               #t))
+           (add-after 'install 'install-templates
+             (lambda* (#:key outputs #:allow-other-keys)
+               (copy-recursively
+                "template"
+                (string-append (assoc-ref outputs "out")
+                               "/share/emacs-lice-el/template"))
+               #t)))))
       (home-page "https://github.com/buzztaiki/lice-el")
       (synopsis "License and header template for Emacs")
       (description "@code{lice.el} provides following features:
@@ -16898,6 +17055,27 @@ visiting the bookmark, a new @code{eshell} session will be opened in the
 appropriate directory if no @code{eshell} session is active.")
     (license license:gpl3+)))
 
+(define-public emacs-eshell-syntax-highlighting
+  (package
+    (name "emacs-eshell-syntax-highlighting")
+    (version "0.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/akreisher/eshell-syntax-highlighting")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0id27874wsb5y169030x8g1ldpa1mnskv1s2j3ygqiyh5fvpfash"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/akreisher/eshell-syntax-highlighting")
+    (synopsis "Add syntax highlighting to Eshell")
+    (description
+     "This package highlights user commands at the Eshell interactive prompt
+to provide feedback on the validity of commands and syntax.")
+    (license license:gpl3+)))
+
 (define-public emacs-eshell-z
   (package
     (name "emacs-eshell-z")
@@ -18436,7 +18614,7 @@ can be queued at any time.")
        ("emacs-esxml" ,emacs-esxml)
        ("emacs-s" ,emacs-s)))
     (inputs
-     `(("pandoc" ,ghc-pandoc)))
+     `(("pandoc" ,pandoc)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -19452,8 +19630,8 @@ stored playlists.")
 
 (define-public emacs-vterm
   (let ((version "0")
-        (revision "2")
+        (revision "3")
-        (commit "f41849c2c9c1899f22d1c3d4f871ec47c82627ce"))
+        (commit "14e4afdfc160b2e625c3e483d169786ac00cb4fe"))
     (package
       (name "emacs-vterm")
       (version (git-version version revision commit))
@@ -19465,7 +19643,7 @@ stored playlists.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1b5s1101n7a2lnpkbadm1h4k6z295fpijx0rdpmd05dkhyarax6n"))))
+                  "0wl613rxw493i3397n34qwqnd5fkyqrnn1fx3y2040xhvjl9rx70"))))
       (build-system emacs-build-system)
       (arguments
        `(#:modules ((guix build emacs-build-system)
@@ -21835,7 +22013,7 @@ it forcibly
 (define-public emacs-elpher
   (package
     (name "emacs-elpher")
-    (version "2.9.1")
+    (version "2.10.2")
     (source
      (origin
        (method git-fetch)
@@ -21844,7 +22022,7 @@ it forcibly
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0vyqmv7dycmad1726yb6yizd21x3kkz5cj33mca11r8nh38f1qzp"))))
+        (base32 "0xqiisirpvw4ka9417pq4r73x937wl3qbf8cpn2i03akm8d58smd"))))
     (build-system emacs-build-system)
     (native-inputs
      `(("texinfo" ,texinfo)))
@@ -21983,7 +22161,7 @@ format.")
                 "0iibxplgdp34bpq1yll2gmqjd8d8lnqn4mqjvx6cdf0y438yr4jz"))))
     (build-system emacs-build-system)
     (inputs
-     `(("pandoc" ,ghc-pandoc)))
+     `(("pandoc" ,pandoc)))
     (propagated-inputs
      `(("emacs-dash" ,emacs-dash)
        ("emacs-ht" ,emacs-ht)))
@@ -22880,6 +23058,52 @@ icon support, git integration, and several other utilities.")
     (home-page "https://github.com/seagle0128/doom-modeline/")
     (license license:gpl3+)))
 
+(define-public emacs-mood-line
+  (package
+    (name "emacs-mood-line")
+    (version "1.2.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/jessieh/mood-line")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0fh9j9fkgl433nykfzjnzap5labi4sdndfk1nv4f904ij69pmvxb"))))
+    (build-system emacs-build-system)
+    (home-page "https://gitlab.com/jessieh/mood-line")
+    (synopsis "Minimal mode-line for Emacs")
+    (description
+     "Mood-line is a minimal Emacs mode-line configuration that aims to
+replicate some of the features of the Doom modeline package.")
+    (license license:gpl2+)))
+
+(define-public emacs-frames-only-mode
+  (package
+    (name "emacs-frames-only-mode")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/davidshepherd7/frames-only-mode")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0y0sdjixaxvywrlp2sw51wnczhk51q1svl5aghbk9rkxpwv9ys9v"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-dash" ,emacs-dash)
+       ("emacs-s" ,emacs-s)))
+    (home-page "https://github.com/davidshepherd7/frames-only-mode")
+    (synopsis "Use frames instead of Emacs windows")
+    (description
+     "This is an Emacs global minor mode to use Emacs frames instead of Emacs'
+internal windowing system.  This combines particularly well with tiling window
+managers such as XMonad.")
+    (license license:gpl3+)))
+
 (define-public emacs-shrink-path
   (package
     (name "emacs-shrink-path")
@@ -23095,30 +23319,26 @@ interface.")
       (license license:gpl3+))))
 
 (define-public emacs-ivy-posframe
-  (let ((commit "ae9bafe94fe6b77b6fe45766ae6172646f6a5d50"))
   (package
     (name "emacs-ivy-posframe")
-      (version (git-version "0.1.0" "1" commit))
+    (version "0.2.0")
     (source
      (origin
-         (method git-fetch)
+       (method url-fetch)
-         (uri (git-reference
+       (uri (string-append "https://elpa.gnu.org/packages/"
-               (url "https://github.com/tumashu/ivy-posframe")
+                           "ivy-posframe-" version ".el"))
-               (commit commit)))
-         (file-name (git-file-name name version))
        (sha256
-          (base32
+        (base32 "0hr6bjlgflvz9rk5rnr55fcrd4873jxmksdr7r1zl1zcb8vdx7ks"))))
-           "1j6yns5d7lh2v1nfcznrirl7qicdli9csciqvfgj4gkh72a97pw1"))))
     (build-system emacs-build-system)
     (propagated-inputs
-       `(("emacs-posframe" ,emacs-posframe)
+     `(("emacs-ivy" ,emacs-ivy)
-         ("emacs-ivy" ,emacs-ivy)))
+       ("emacs-posframe" ,emacs-posframe)))
     (home-page "https://github.com/tumashu/ivy-posframe")
     (synopsis "Pop a posframe (a child frame) to show Ivy candidates")
     (description
      "This package provides an Emacs Ivy extension, which let Ivy use
 posframe to show its candidate menu.")
-      (license license:gpl3+))))
+    (license license:gpl3+)))
 
 (define-public emacs-shackle
   (let ((commit "7ccbe513852a1d1700b698547efca14b8940319d")
@@ -23757,7 +23977,7 @@ files and subdirectories when appropriate.")
 (define-public emacs-meson-mode
   (package
     (name "emacs-meson-mode")
-    (version "0.2")
+    (version "0.3")
     (source
      (origin
        (method git-fetch)
@@ -23766,7 +23986,7 @@ files and subdirectories when appropriate.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1720b3hpfqd989zrgcns51jbjrv4vzl9di9mccl55vkmkbqzfin0"))))
+        (base32 "0hlqvq3j4f6g16nj3bm2wbkncn8hv8c8iqd0sch3w80wwqnr622y"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/wentasah/meson-mode")
     (synopsis "Major mode for Meson build system files")
@@ -24523,7 +24743,7 @@ displayed for sharing.")
 buffer on an active webserver to which the user has SSH access.
 It is similar in purpose to services such as Gist or Pastebin,
 but is much simpler since it assumes the user has access to a
-publically-accessible HTTP server.")
+publicly-accessible HTTP server.")
       (license license:gpl3+))))
 
 (define-public emacs-company-reftex
@@ -24550,3 +24770,35 @@ publically-accessible HTTP server.")
 label references and citations in LaTeX.  It is based on RefTeX, which is
 included with Emacs.")
     (license license:gpl3+)))
+
+(define-public emacs-html-to-hiccup
+  ;; Package has no release.  Version is extracted from "Version:" keyword in
+  ;; main file.
+  (let ((commit "50a52e2b0d13d865187acdf775b8203d5003f2f1")
+        (revision "0"))
+    (package
+      (name "emacs-html-to-hiccup")
+      (version (git-version "1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/plexus/html-to-hiccup")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1qi092mw2n08v6yr0j6hlpx0pnlcnhxjqbsrlw9pn4yin6zk91yp"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("dash" ,emacs-dash)
+         ("s" ,emacs-s)))
+      (home-page "https://github.com/plexus/html-to-hiccup")
+      (synopsis "Turn HTML into Hiccup syntax")
+      (description
+       "This is an Emacs package that turns HTML into Hiccup syntax
+which is a popular notation to use when doing Clojure/ClojureScript
+web development.")
+      ;; There is a conflict between the repository official LICENSE
+      ;; file and the header of the main elisp file which indicates
+      ;; that it is licensed under the GPL version 3 or later.
+      (license (list license:mpl2.0 license:gpl3+)))))

gnu/packages/emacs.scm

@@ -196,11 +196,16 @@
            (lambda* (#:key outputs #:allow-other-keys)
              ;; Directly copy emacs-X.Y to emacs, so that it is not wrapped
              ;; twice.  This also fixes a minor issue, where WMs would not be
-             ;; able to track emacs back to emacs.desktop.
+             ;; able to track emacs back to emacs.desktop.  The version is
+             ;; accessed using using THIS-PACKAGE so it "just works" for
+             ;; inherited Emacs packages of different versions.
              (with-directory-excursion (assoc-ref outputs "out")
                (copy-file (string-append
                            "bin/emacs-"
-                           ,(version-major+minor (package-version emacs)))
+                           ,(let ((this-version (package-version this-package)))
+                              (or (false-if-exception
+                                   (version-major+minor+point this-version))
+                                  (version-major+minor this-version))))
                           "bin/emacs")
                #t)))
          (add-before 'reset-gzip-timestamps 'make-compressed-files-writable
@@ -279,11 +284,10 @@ languages.")
 
 (define-public emacs-next
   (let ((commit "2ea34662c20f71d35dd52a5ed996542c7386b9cb")
-        (revision "0")
+        (revision "0"))
-        (emacs-version "28.0.50.1"))
     (package/inherit emacs
       (name "emacs-next")
-      (version (git-version emacs-version revision commit))
+      (version (git-version "28.0.50" revision commit))
       (source
        (origin
          (inherit (package-source emacs))
@@ -295,24 +299,20 @@ languages.")
          (sha256
           (base32
            "0igjm9kwiswn2dpiy2k9xikbdfc7njs07ry48fqz70anljj8y7y3"))))
-      (arguments
-       (substitute-keyword-arguments (package-arguments emacs)
-         ((#:phases phases)
-          `(modify-phases ,phases
-             (replace 'strip-double-wrap
-               (lambda* (#:key outputs #:allow-other-keys)
-                 ;; Directly copy emacs-X.Y to emacs, so that it is not wrapped
-                 ;; twice.  This also fixes a minor issue, where WMs would not be
-                 ;; able to track emacs back to emacs.desktop.
-                 (with-directory-excursion (assoc-ref outputs "out")
-                   (copy-file (string-append
-                               "bin/emacs-"
-                               ,(version-major+minor+point (package-version emacs-next)))
-                              "bin/emacs")
-                   #t)))))))
       (native-inputs
        `(("autoconf" ,autoconf)
-         ,@(package-native-inputs emacs))))))
+         ,@(package-native-inputs emacs)))
+      (native-search-paths
+       (list (search-path-specification
+              (variable "EMACSLOADPATH")
+              ;; The versioned entry is for the Emacs' builtin libraries.
+              (files (list "share/emacs/site-lisp"
+                           (string-append "share/emacs/"
+                                          (version-major+minor+point version)
+                                          "/lisp"))))
+             (search-path-specification
+              (variable "INFOPATH")
+              (files '("share/info"))))))))
 
 (define-public emacs-minimal
   ;; This is the version that you should use as an input to packages that just

gnu/packages/emulators.scm

@@ -53,6 +53,7 @@
   #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
+  #:use-module (gnu packages fribidi)
   #:use-module (gnu packages game-development)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gettext)
@@ -1327,34 +1328,20 @@ multi-system game/emulator system.")
 (define-public scummvm
   (package
     (name "scummvm")
-    (version "2.1.2")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "http://www.scummvm.org/frs/scummvm/" version
                            "/scummvm-" version ".tar.xz"))
        (sha256
-        (base32 "1c4fz1nfg0nqnqx9iipayhzcsiqdmfxm2i95nw9dbhshhsdnrhf4"))))
+        (base32 "11vknasm5dna2vqr6gk343qynh7nhsq3kf60zayarn1vb5z6as8l"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                                 ;require "git"
        #:configure-flags (list "--enable-release") ;for optimizations
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'fix-build
-           ;; XXX: The following works around a build failure introduced when
-           ;; Fluidsynth was updated to version 2.1.  It has been applied
-           ;; upstream as 68758a879e0c8ecc0d40962516d4e808aa4e15e5 and can be
-           ;; removed once this commit makes it into a release.
-           (lambda _
-             (substitute* "audio/softsynth/fluidsynth.cpp"
-               (("#include <fluidsynth.h>") "")
-               (("#include \"common/scummsys.h\"") "#include \"config.h\"")
-               (("#include \"common/config-manager.h\"" line)
-                (string-append "#include <fluidsynth.h>\n"
-                               "#include \"common/scummsys.h\"\n"
-                               line)))
-             #t))
          (replace 'configure
            ;; configure does not work followed by both "SHELL=..." and
            ;; "CONFIG_SHELL=..."; set environment variables instead
@@ -1374,6 +1361,7 @@ multi-system game/emulator system.")
        ("faad2" ,faad2)
        ("fluidsynth" ,fluidsynth)
        ("freetype" ,freetype)
+       ("fribidi" ,fribidi)
        ("liba52" ,liba52)
        ("libflac" ,flac)
        ("libjpeg-turbo" ,libjpeg-turbo)
@@ -1397,7 +1385,7 @@ play them on systems for which they were never designed!")
 (define-public mame
   (package
     (name "mame")
-    (version "0.224")
+    (version "0.225")
     (source
      (origin
        (method git-fetch)
@@ -1406,7 +1394,7 @@ play them on systems for which they were never designed!")
              (commit (apply string-append "mame" (string-split version #\.)))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0dpg4hz2f1wlp0rmk5c5xq57fy0sblh97z3l66p814wkgzap4bhx"))
+        (base32 "1n61v1yqmc69399khcm8gdabqaz8rwwj822m8vm5mbyxnw92icqg"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled libraries.
@@ -1902,7 +1890,7 @@ framework based on QEMU.")
 (define-public ppsspp
   (package
     (name "ppsspp")
-    (version "1.10")
+    (version "1.10.3")
     (source
      (origin
        (method git-fetch)
@@ -1910,7 +1898,7 @@ framework based on QEMU.")
              (url "https://github.com/hrydgard/ppsspp")
              (commit (string-append "v" version))))
        (sha256
-        (base32 "02yx1w0ygclnmdl0imsvgj24lkzi55wvxkf47q617j0jgrqhy8yl"))
+        (base32 "0znxlbj6cfw7gn0naay0mzhc0k5saw8nrwpspcn7gap1023p06w2"))
        (file-name (git-file-name name version))
        (patches
         (search-patches "ppsspp-disable-upgrade-and-gold.patch"))
@@ -1961,7 +1949,7 @@ framework based on QEMU.")
                              " spirv-cross-reflect spirv-cross-util")))
            (substitute* "ext/CMakeLists.txt"
              (("add_subdirectory\\(glew\\)") "")
-             (("add_subdirectory\\(glslang\\)") "")
+             (("add_subdirectory\\(glslang( [A-Z_]*)*\\)") "")
              (("add_subdirectory\\(snappy\\)") "")
              (("add_subdirectory\\(SPIRV-Cross-build\\)") ""))
            ;; Finally, we can delete the bundled sources.
@@ -2004,14 +1992,14 @@ framework based on QEMU.")
        ;; TODO: unbundle armips.
        ("armips-source" ,(package-source armips))
        ("lang"
-        ,(let ((commit "d184ba2b607a03435be579406b816c90add334e6"))
+        ,(let ((commit "1c64b8fbd3cb6bd87935eb53f302f7de6f86e209"))
            (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/hrydgard/ppsspp-lang")
                    (commit commit)))
              (sha256
-              (base32 "0s003x6247nx09qd6a1jz1l2hsk5d6k1zmh8mg3m6hjjhvbvd9j9"))
+              (base32 "0rprn3yd8xfrvi0fm62sgpqa8n73jk7zmlscp8cp0h2fawqpiamd"))
              (file-name (git-file-name "ppsspp-lang" commit)))))
        ("tests"
         ,(let ((commit "328b839c7243e7f733f9eae88d059485e3d808e7"))

gnu/packages/engineering.scm

@@ -20,6 +20,7 @@
 ;;; Copyright © 2020 Ekaitz Zarraga <ekaitz@elenq.tech>
 ;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com>
 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020 Morgan Smith <Morgan.J.Smith@outlook.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -426,14 +427,14 @@ optimizer; and it can produce photorealistic and design review images.")
 (define-public pcb-rnd
   (package (inherit pcb)
     (name "pcb-rnd")
-    (version "2.2.3")
+    (version "2.2.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://repo.hu/projects/pcb-rnd/releases/"
                                   "pcb-rnd-" version ".tar.gz"))
               (sha256
                (base32
-                "0j650498d87b4xsggzc0xlk73k0hhj43wfy45qz2lcn0xc3bks1m"))))
+                "06ylc2rd4yvzp3krk62q9dbi13h0yq1x257fbjkh10vfjn0ga5c2"))))
     (arguments
      `(#:tests? #f                      ; no check target
        #:phases
@@ -1328,21 +1329,26 @@ developed at MIT to model electromagnetic systems.")
 (define-public adms
   (package
     (name "adms")
-    (version "2.3.6")
+    (version "2.3.7")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri
+              (uri (git-reference
-               (string-append
+                    (url "https://github.com/Qucs/ADMS")
-                "mirror://sourceforge/mot-adms/adms-source/"
+                    (commit (string-append "release-" version))))
-                (version-major+minor version) "/adms-" version ".tar.gz"))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1rn98l6jxcjhi6ai5f7p588khra9z80m0m0lql4n4sb7773fh1vk"))))
+                "0i37c9k6q1iglmzp9736rrgsnx7sw8xn3djqbbjw29zsyl3pf62c"))))
     (build-system gnu-build-system)
     (native-inputs
-     `(("flex" ,flex)
+     `(("autoconf" ,autoconf)
-       ("bison" ,bison)))
+       ("automake" ,automake)
-    (home-page "https://sourceforge.net/projects/mot-adms")
+       ("bison" ,bison)
+       ("flex" ,flex)
+       ("libtool" ,libtool)
+       ("perl" ,perl)
+       ("perl-xml-libxml" ,perl-xml-libxml)))
+    (home-page "https://github.com/Qucs/ADMS")
     (synopsis "Automatic device model synthesizer")
     (description
      "ADMS is a code generator that converts electrical compact device models

gnu/packages/enlightenment.scm

@@ -31,7 +31,6 @@
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
-  #:use-module (gnu packages avahi)
   #:use-module (gnu packages bittorrent)
   #:use-module (gnu packages check)
   #:use-module (gnu packages code)
@@ -69,7 +68,7 @@
 (define-public efl
   (package
     (name "efl")
-    (version "1.24.3")
+    (version "1.25.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -77,7 +76,7 @@
                     version ".tar.xz"))
               (sha256
                (base32
-                "0ajwc8lmay5ai7nsrp778g393h0p4h98p4c22gic2w61fgkcd5fy"))))
+                "0vlmf0rp2qxdl06pdmrd1xdfa10sdz30vnxzc98inpdg1n8iz52k"))))
     (build-system meson-build-system)
     (native-inputs
      `(("check" ,check-0.14)
@@ -115,8 +114,7 @@
     (propagated-inputs
      ;; All these inputs are in package config files in section
      ;; Requires.private.
-     `(("avahi" ,avahi)
+     `(("dbus" ,dbus)
-       ("dbus" ,dbus)
        ("elogind" ,elogind)
        ("eudev" ,eudev)
        ("fontconfig" ,fontconfig)
@@ -137,13 +135,9 @@
        ("wayland" ,wayland)
        ("zlib" ,zlib)))
     (arguments
-     `(#:configure-flags '("-Dsystemd=false"
+     `(#:configure-flags '("-Dembedded-lz4=false"
-                           "-Delogind=true"
-                           "-Dembedded-lz4=false"
-                           "-Devas-loaders-disabler=json"
                            "-Dbuild-examples=false"
                            "-Decore-imf-loaders-disabler=scim"
-                           "-Davahi=true"
                            "-Dglib=true"
                            "-Dmount-path=/run/setuid-programs/mount"
                            "-Dunmount-path=/run/setuid-programs/umount"
@@ -164,6 +158,7 @@
              (let ((curl    (assoc-ref inputs "curl"))
                    (pulse   (assoc-ref inputs "pulseaudio"))
                    (sndfile (assoc-ref inputs "libsndfile"))
+                   (elogind (assoc-ref inputs "elogind"))
                    (lib     "/lib/"))
                (substitute* "src/lib/ecore_con/ecore_con_url_curl.c"
                  (("libcurl.so.?" libcurl) ; libcurl.so.[45]
@@ -173,6 +168,9 @@
                   (string-append pulse lib libpulse))
                  (("libsndfile.so.1" libsnd)
                   (string-append sndfile lib libsnd)))
+               (substitute* "src/lib/elput/elput_logind.c"
+                 (("libelogind.so.0" libelogind)
+                  (string-append elogind "/lib/" libelogind)))
                #t)))
          (add-after 'unpack 'fix-install-paths
            (lambda _
@@ -566,19 +564,20 @@ directories.
 (define-public evisum
   (package
     (name "evisum")
-    (version "0.5.4")
+    (version "0.5.6")
     (source
       (origin
         (method url-fetch)
         (uri (string-append "https://download.enlightenment.org/rel/apps/"
                             "evisum/evisum-" version ".tar.xz"))
         (sha256
-         (base32 "1ip3w2d476g45sivqvm1madfyqmkni9q2i99qqxk53859jgs91pa"))))
+         (base32 "1l8pym7738kncvic5ga03sj9d5igigvmcxa9lbg47z2yvdjwzv97"))))
     (build-system meson-build-system)
     (arguments
      '(#:tests? #f))                    ; no tests
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     `(("gettext" ,gettext-minimal)
+       ("pkg-config" ,pkg-config)))
     (inputs
      `(("efl" ,efl)))
     (home-page "https://www.enlightenment.org")

gnu/packages/file-systems.scm

@@ -768,7 +768,7 @@ community.")
 (define-public mergerfs
   (package
     (name "mergerfs")
-    (version "2.29.0")
+    (version "2.31.0")
     (source
      (origin
        (method url-fetch)
@@ -776,7 +776,7 @@ community.")
                            version "/mergerfs-" version ".tar.gz"))
        (sha256
         (base32
-         "17gizw4vgbqqjd2ykkfpp276942jb5qclp0lkiwkmq1yjgyjqfmk"))))
+         "0k4asbg5n9dhy5jpjkw6simqqnr1zira2y4i71cq05091dfwm90p"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; No tests exist.
@@ -797,8 +797,9 @@ community.")
              ;; The Makefile does not allow overriding PREFIX via make variables.
              (substitute* '("Makefile" "libfuse/Makefile")
                (("= /usr/local") (string-append "= " (assoc-ref outputs "out")))
+               (("= /sbin") "= $(EXEC_PREFIX)/sbin")
                ;; cannot chown as build user
-               (("chown root:root") "true"))
+               (("chown root(:root)?") "true"))
              #t)))))
     ;; mergerfs bundles a heavily modified copy of libfuse.
     (inputs `(("util-linux" ,util-linux)))
@@ -813,8 +814,8 @@ is similar to mhddfs, unionfs, and aufs.")
               ))))
 
 (define-public mergerfs-tools
-  (let ((commit "c926779d87458d103f3b674603bf97801ae2486d")
+  (let ((commit "480296ed03d1c3c7909697d7ef96d35840ee26b8")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "mergerfs-tools")
       ;; No released version exists.
@@ -828,7 +829,7 @@ is similar to mhddfs, unionfs, and aufs.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "04hhwcib0xv4cf1mkj8zrp2aqpxkncml9iqg4m1mz6a5zhzsk0vm"))))
+           "0xr06gi4xcr832rzy0hkp5c1n231s7w5iq1nkjvx9kvm0dl7chpq"))))
       (build-system copy-build-system)
       (inputs
        `(("python" ,python)

gnu/packages/finance.scm

@@ -173,14 +173,14 @@ line client and a client based on Qt.")
 (define-public homebank
   (package
     (name "homebank")
-    (version "5.4.2")
+    (version "5.4.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://homebank.free.fr/public/homebank-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0bkjvd819kw9cwmr3macggbg8yil3yc8v2za8pjrl6g746s89kn6"))))
+                "02wd569viwy6ncy0144z9nxr3zmpl4shkqhz7zzwyky4gknxf8lj"))))
     (build-system glib-or-gtk-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
@@ -480,7 +480,7 @@ other machines/servers.  Electrum does not download the Bitcoin blockchain.")
 (define-public electron-cash
   (package
     (name "electron-cash")
-    (version "4.1.0")
+    (version "4.1.1")
     (source
      (origin
        (method git-fetch)
@@ -489,7 +489,7 @@ other machines/servers.  Electrum does not download the Bitcoin blockchain.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1ccfm6kkmbkvykfdzrisxvr0lx9kgq4l43ixk6v3xnvhnbfwz4s2"))))
+        (base32 "1fllz2s20lg4hrppzmnlgjy9mrq7gaq66l2apb3vz1avzvsjw3gm"))))
     (build-system python-build-system)
     (inputs
      `(("libevent" ,libevent)
@@ -555,7 +555,7 @@ other machines/servers.  Electroncash does not download the Bitcoin Cash blockch
   ;; the system's dynamically linked library.
   (package
     (name "monero")
-    (version "0.16.0.3")
+    (version "0.17.0.1")
     (source
      (origin
        (method git-fetch)
@@ -575,7 +575,7 @@ other machines/servers.  Electroncash does not download the Bitcoin Cash blockch
               "external/unbound"))
            #t))
        (sha256
-        (base32 "1r9x3712vhb24dxxirfiwj5f9x0h4m7x0ngiiavf5983dfdlgz33"))))
+        (base32 "1v0phvg5ralli4dr09a60nq032xqlci5d6v4zfq8304vgrn1ffgp"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("doxygen" ,doxygen)
@@ -605,7 +605,6 @@ other machines/servers.  Electroncash does not download the Bitcoin Cash blockch
        #:configure-flags
        (list "-DARCH=default"
              "-DBUILD_TESTS=ON"
-             "-DBUILD_GUI_DEPS=ON"
              (string-append "-DReadline_ROOT_DIR="
                             (assoc-ref %build-inputs "readline")))
        #:phases
@@ -651,17 +650,11 @@ other machines/servers.  Electroncash does not download the Bitcoin Cash blockch
                (invoke "tests/unit_tests/unit_tests"
                        (string-append "--gtest_filter=-"
                                       excluded-unit-tests)))))
-         (add-after 'install 'install-librandomx
+         (add-after 'install 'delete-unused-files
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
-               (install-file "external/randomx/librandomx.a" lib)
-               #t)))
-         (add-after 'install 'delete-dead-links
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((out (assoc-ref outputs "out")))
-               (delete-file (string-append out "/lib/libprotobuf.so"))
+               (delete-file-recursively (string-append out "/include")))
-               (delete-file (string-append out "/lib/libusb-1.0.so"))
+             #t)))))
-               #t))))))
     (home-page "https://web.getmonero.org/")
     (synopsis "Command-line interface to the Monero currency")
     (description
@@ -672,7 +665,7 @@ the Monero command line client and daemon.")
 (define-public monero-gui
   (package
     (name "monero-gui")
-    (version "0.16.0.3")
+    (version "0.17.0.1")
     (source
      (origin
        (method git-fetch)
@@ -681,21 +674,15 @@ the Monero command line client and daemon.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0iwjp8x5swy8i8pzrlm5v55awhm54cf48pm1vz98lcq361lhfzk6"))))
+        (base32 "1i9a3ampppyzsl4sllbqlr3w43sjpb3fdfxhb1j4n49p8g0jzmf3"))))
     (build-system qt-build-system)
     (native-inputs
-     `(("monero-source" ,(package-source monero))
+     `(,@(package-native-inputs monero)
-       ("pkg-config" ,pkg-config)
+       ("monero-source" ,(package-source monero))))
-       ("qttools" ,qttools)))
     (inputs
-     `(("boost" ,boost)
+     `(,@(package-inputs monero)
-       ("hidapi" ,hidapi)
        ("libgcrypt" ,libgcrypt)
-       ("libsodium" ,libsodium)
+       ("monero" ,monero)
-       ("libunwind" ,libunwind)
-       ("libusb" ,libusb)
-       ("openssl" ,openssl)
-       ("protobuf" ,protobuf)
        ("qtbase" ,qtbase)
        ("qtdeclarative" ,qtdeclarative)
        ("qtgraphicaleffects" ,qtgraphicaleffects)
@@ -704,78 +691,54 @@ the Monero command line client and daemon.")
        ("qtquickcontrols" ,qtquickcontrols)
        ("qtquickcontrols2",qtquickcontrols2)
        ("qtsvg" ,qtsvg)
-       ("qtxmlpatterns" ,qtxmlpatterns)
+       ("qtxmlpatterns" ,qtxmlpatterns)))
-       ("unbound" ,unbound)))
-    (propagated-inputs
-     `(("monero" ,monero)))
     (arguments
      `(#:tests? #f ; No tests
+       #:configure-flags
+       (list "-DARCH=default"
+             "-DENABLE_PASS_STRENGTH_METER=ON"
+             (string-append "-DReadline_ROOT_DIR="
+                            (assoc-ref %build-inputs "readline"))
+             "-DCMAKE_BUILD_TYPE=Release")
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'get-monero-extra-files
+         (add-after 'unpack 'extract-monero-sources
-           ;; Some headers and GnuPG public keys of the monero package source
+           ;; Some of the monero package source code is required
-           ;; code are required to build the GUI.
+           ;; to build the GUI.
            (lambda* (#:key inputs #:allow-other-keys)
-             (invoke "tar" "-xv" "--wildcards" "--strip-components=1"
+             (invoke "tar" "-xv" "--strip-components=1"
                      "-C" "monero"
-                     "-f" (assoc-ref inputs "monero-source")
+                     "-f" (assoc-ref inputs "monero-source"))
-                     "*.asc" "*.h")
              #t))
-         (add-after 'get-monero-extra-files 'fix-makefile-vars
+         (add-after 'extract-monero-sources 'fix-build
            (lambda _
+             (substitute* "monero/src/version.cpp.in"
+               (("@VERSION_IS_RELEASE@")
+                "false"))
+             (substitute* "src/version.js.in"
+               (("@VERSION_TAG_GUI@")
+                ,version))
              (substitute* "src/zxcvbn-c/makefile"
                (("\\?=") "="))
              #t))
-         (add-after 'fix-makefile-vars 'fix-paths
+         (add-before 'configure 'generate-zxcvbn-c-header
+           (lambda _
+             (invoke "make" "-C" "src/zxcvbn-c" "dict-src.h")))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+               (mkdir-p bin)
+               (install-file "../build/bin/monero-wallet-gui" bin))
+             #t))
+         (add-after 'qt-wrap 'install-monerod-link
+           ;; The monerod program must be available so that monero-wallet-gui
+           ;; can start a Monero daemon if necessary.
            (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let ((boost (assoc-ref inputs "boost"))
+             (symlink (string-append (assoc-ref inputs "monero")
-                   (monero (assoc-ref inputs "monero"))
+                                     "/bin/monerod")
-                   (openssl (assoc-ref inputs "openssl"))
+                      (string-append (assoc-ref outputs "out")
-                   (qttools (assoc-ref inputs "qttools"))
+                                     "/bin/monerod"))
-                   (out (assoc-ref outputs "out")))
+             #t)))))
-               (substitute* "monero-wallet-gui.pro"
-                 (("-L/usr/local/lib")
-                  "")
-                 (("-L/usr/local/opt/openssl/lib")
-                  (string-append "-L" openssl "/lib"))
-                 (("-L/usr/local/opt/boost/lib")
-                  (string-append "-L" boost "/lib"))
-                 (("\\$\\$\\[QT_INSTALL_BINS\\]/lrelease")
-                  (string-append qttools "/bin/lrelease"))
-                 (("\\$\\$\\[QT_INSTALL_BINS\\]/lupdate")
-                  (string-append qttools "/bin/lupdate")))
-               (substitute* "deployment.pri"
-                 (("/opt/\\$\\$\\{TARGET\\}/bin")
-                  (string-append out "/bin")))
-               (substitute* "src/daemon/DaemonManager.cpp"
-                 (("QApplication::applicationDirPath\\(\\) \\+ \"/monerod")
-                  (string-append "\"" monero "/bin/monerod")))
-               #t)))
-         (add-after 'fix-paths 'make-qt-deterministic
-           (lambda _
-             (setenv "QT_RCC_SOURCE_DATE_OVERRIDE" "1")
-             #t))
-         (add-after 'make-qt-deterministic 'fix-version
-           (lambda _
-             (substitute* "build.sh"
-               (("echo .*> version.js")
-                ""))
-             (with-output-to-file "version.js"
-               (lambda _
-                 (format #t
-                         "var GUI_VERSION = \"~a\"~@
-                          var GUI_MONERO_VERSION = \"~a\"~%"
-                         ,version
-                         ,(package-version monero))))
-             #t))
-         (replace 'configure
-           (lambda _
-             (mkdir-p "build")
-             (chdir "build")
-             (invoke "qmake" "../monero-wallet-gui.pro" "CONFIG+=release")))
-         (add-before 'build 'build-zxcvbn-c
-           (lambda _
-             (invoke "make" "-C" "../src/zxcvbn-c"))))))
     (home-page "https://web.getmonero.org/")
     (synopsis "Graphical user interface for the Monero currency")
     (description
@@ -1061,7 +1024,7 @@ amongst which a great number of VAT and other tax numbers,
 personal identity and company identification codes,
 international standard numbers (ISBN, IBAN, EAN, etc.)
 and various other formats.
-The module also inclused implementations of the Verhoeff,
+The module also includes implementations of the Verhoeff,
 Luhn and family of ISO/IEC 7064 check digit algorithms. ")
     (license license:lgpl2.1+)))
 
@@ -1399,7 +1362,7 @@ entity management.")
 (define-public bitcoin-unlimited
   (package
     (name "bitcoin-unlimited")
-    (version "1.9.0.0")
+    (version "1.9.0.1")
     (source
      (origin
        (method git-fetch)
@@ -1408,7 +1371,7 @@ entity management.")
              (commit (string-append "BCHunlimited" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1a64h7mcqdra4ahnw1nycp4ysx308ymgbl4yn5fj5jfaszdzvy0h"))))
+        (base32 "1pan24g3d5csa004d7zvlizj4mv58ly5i579341isp944phl3g5v"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -1443,32 +1406,20 @@ entity management.")
                        "/bin/lrelease")
         (string-append "ac_cv_path_LUPDATE="
                        (assoc-ref %build-inputs "qttools")
-                       "/bin/lupdate"))
+                       "/bin/lupdate")
+        "--disable-static")
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'fix-build
-           (lambda _
-             ;; The 'stack' header was not included in unlimited.cpp, which
-             ;; caused the build to fail.
-             (substitute* "src/unlimited.cpp"
-               (("#include <queue>" all)
-                (string-append all "\n#include <stack>")))
-             #t))
          (add-after 'unpack 'fix-tests
            (lambda _
-             ;; TODO: Find why txvalidationcache_tests fails and
+             ;; Disable utilprocess_tests because it never ends.
-             ;; utilprocess_tests never ends. Disable for now.
+             ;; It looks like it tries to start /bin/sleep and waits until it
+             ;; is in the list of running processes, but /bin/sleep doesn't
+             ;; exist.
              (substitute* "src/Makefile.test.include"
-               (("test/txvalidationcache_tests.cpp")
-                "")
                (("test/utilprocess_tests.cpp")
                 ""))
              #t))
-         (add-before 'configure 'make-qt-deterministic
-           (lambda _
-             ;; Make Qt deterministic.
-             (setenv "QT_RCC_SOURCE_DATE_OVERRIDE" "1")
-             #t))
          (add-before 'check 'set-home
            (lambda _
              (setenv "HOME" (getenv "TMPDIR")) ; tests write to $HOME

gnu/packages/fonts.scm

@@ -23,7 +23,7 @@
 ;;; Copyright © 2017 Mohammed Sadiq <sadiq@sadiqpk.org>
 ;;; Copyright © 2018 Charlie Ritter <chewzerita@posteo.net>
 ;;; Copyright © 2018 Gabriel Hondet <gabrielhondet@gmail.com>
-;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
+;;; Copyright © 2019, 2020 Jens Mølgaard <jens@zete.tk>
 ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2019 Baptiste Strazzulla <bstrazzull@hotmail.fr>
 ;;; Copyright © 2019 Alva <alva@skogen.is>
@@ -951,19 +951,16 @@ designed to work well in user interface environments.")
 (define-public font-adobe-source-sans-pro
   (package
     (name "font-adobe-source-sans-pro")
-    (version "2.040R-ro-1.090R-it")
+    (version "3.028R")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/adobe-fonts/source-sans-pro")
-             (commit (regexp-substitute/global
+             (commit version)))
-                      ;; The upstream tag uses "/" between the roman and italic
-                      ;; versions, so substitute our "-" separator here.
-                      #f "R-ro-" version 'pre "R-ro/" 'post))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1lzin2hfwidbvhps7shs201p1bpxy6220xmhhprv9fc8bknd4c45"))))
+        (base32 "0lgjqi4d5p1q1z00ad807v5qy4z54gmp7jpdaypc0rxk8czv6zq7"))))
     (build-system font-build-system)
     (home-page "https://github.com/adobe-fonts/source-sans-pro")
     (synopsis
@@ -976,19 +973,16 @@ work well in user interface (UI) environments.")
 (define-public font-adobe-source-serif-pro
   (package
     (name "font-adobe-source-serif-pro")
-    (version "2.007R-ro-1.007R-it")
+    (version "3.001R")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/adobe-fonts/source-serif-pro")
-             (commit (regexp-substitute/global
+             (commit version)))
-                      ;; The upstream tag uses "/" between the roman and italic
-                      ;; versions, so substitute our "-" separator here.
-                      #f "R-ro-" version 'pre "R-ro/" 'post))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1vvzfhjpi47m84bzkapylkd5fri8bdm8qng2hiylmmlw0wk4gpas"))))
+        (base32 "1z0pjvx0jpjwb8vzvc6l5gzlg0mqax4v9pizqcxx82l0ydlfh5bj"))))
     (build-system font-build-system)
     (home-page "https://github.com/adobe-fonts/source-serif-pro")
     (synopsis
@@ -1154,14 +1148,14 @@ later hand-tweaked with the gbdfed(1) editor:
 (define-public font-comic-neue
   (package
     (name "font-comic-neue")
-    (version "2.5")
+    (version "2.51")
     (source (origin
               (method url-fetch/zipbomb)
               (uri (string-append
                     "http://www.comicneue.com/comic-neue-" version ".zip"))
               (sha256
                (base32
-                "1ng0m0zs7qr91qy5ff0l01l27npr76961c6zfkxnhxf68zpwz5k4"))))
+                "0883542v915crz98v1ij6smgy40dg6gxwsid3j5nbmmqjf69kpal"))))
     (build-system font-build-system)
     (arguments
      `(#:phases
@@ -1742,7 +1736,7 @@ This package provides the TrueType fonts.")
 (define-public font-jetbrains-mono
   (package
     (name "font-jetbrains-mono")
-    (version "2.001")
+    (version "2.002")
     (source
      (origin
        (method url-fetch)
@@ -1750,17 +1744,16 @@ This package provides the TrueType fonts.")
         (string-append "https://download.jetbrains.com/fonts/"
                        "JetBrainsMono-" version ".zip"))
        (sha256
-        (base32 "0r3dk3kn536rik4mvpcjin9mwmifl3v8mawvb4a5l59pww0vcxzq"))))
+        (base32 "0lcsl718jhkqgld1xqll7fsv8j968jlf292541fkqxwm8i5g93sn"))))
     (build-system font-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (replace 'install-license-files
+         (add-before 'install-license-files 'change-directory-to-archive-root
-           (lambda* (#:key outputs #:allow-other-keys)
+           ;; Find the LICENSE file outside of the default subdirectory.
-             (let* ((out (assoc-ref outputs "out"))
+           (lambda _
-                    (doc (string-append out "/share/doc/" ,name "-" ,version)))
+             (chdir "..")
-               (install-file "../LICENSE" doc)
+             #t)))))
-               #t))))))
     (home-page "https://www.jetbrains.com/lp/mono/")
     (synopsis "Mono typeface for developers")
     (description

gnu/packages/fontutils.scm

@@ -303,7 +303,7 @@ work with most software requiring Type 1 fonts.")
     (inputs
      `(("brotli" ,google-brotli)))
     (synopsis "Libraries and tools for WOFF2 font format")
-    (description "WOFF2 provides libraires and tools to handle the Web Open
+    (description "WOFF2 provides libraries and tools to handle the Web Open
 Font Format (WOFF).")
     (home-page "https://w3c.github.io/woff/woff2/")
     (license license:expat)))
@@ -556,6 +556,7 @@ using the above tables.")
   (package
     (name "libspiro")
     (version "20190731")
+    (replacement libspiro-20200505)
     (source
      (origin
       (method url-fetch)
@@ -574,6 +575,19 @@ smooth contours with constant curvature at the spline joins.")
     (license license:gpl2+)
     (home-page "http://libspiro.sourceforge.net/")))
 
+(define libspiro-20200505
+  (package
+    (inherit libspiro)
+    (version "20200505")
+    (source
+     (origin
+      (method url-fetch)
+      (uri (string-append "https://github.com/fontforge/libspiro/releases"
+                          "/download/" version "/libspiro-dist-" version ".tar.gz"))
+      (sha256
+       (base32
+        "0j8fmyj4wz6mqk17dqs6f8jx0i52n68gv5px17qbrjnbilg9mih6"))))))
+
 (define-public libuninameslist
   (package
     (name "libuninameslist")

gnu/packages/freedesktop.scm

@@ -796,7 +796,7 @@ applications, X servers (rootless or fullscreen) or other display servers.")
 (define-public waylandpp
   (package
     (name "waylandpp")
-    (version "0.2.7")
+    (version "0.2.8")
     (home-page "https://github.com/NilsBrause/waylandpp")
     (source (origin
               (method git-fetch)
@@ -804,7 +804,7 @@ applications, X servers (rootless or fullscreen) or other display servers.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1r4m0xhvwpcqxrqvp3hz1bzlkxqj2jiymd5r6hj8xjzz536hyprz"))))
+                "1kxiqab48p0n97pwg8c2zx56wqq32m3rcq7qd2pjj33ipcanb3qq"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f))                    ; no tests
@@ -909,16 +909,14 @@ multiplexer to the KMS/DRM Linux kernel devices.")
     (license license:expat)))
 
 (define-public wev
-  ;; There simple tool has no version or release yet.
-  (let ((commit "cee3dfb2a8b40ee303611018c68ae182d84a7f46"))
   (package
     (name "wev")
-      (version (string-append "2020-02-06-" (string-take commit 8)))
+    (version "1.0.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://git.sr.ht/~sircmpwn/wev")
-                      (commit commit)))
+                    (commit version)))
               (file-name (git-file-name name version))
               (sha256
                (base32
@@ -943,7 +941,7 @@ multiplexer to the KMS/DRM Linux kernel devices.")
     (description "Wev is a tool that opens a window, printing all events
 sent to a Wayland window, such as key presses.  It is analogous to the X11 tool
 XEv.")
-      (license license:expat))))
+    (license license:expat)))
 
 (define-public exempi
   (package
@@ -1398,7 +1396,7 @@ wish to perform colour calibration.")
 (define-public libfprint
   (package
     (name "libfprint")
-    (version "1.90.1")
+    (version "1.90.3")
     (source
      (origin
        (method git-fetch)
@@ -1407,7 +1405,7 @@ wish to perform colour calibration.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0fdaak7qjr9b4482g7fhhqpyfdqpxq5kpmyzkp7f5i7qq2ynb78a"))))
+        (base32 "1fs0qrfrqnvc6kcsg81l5p89n8jnsx9dr1pzxpb8ghwas8c9v52i"))))
     (build-system meson-build-system)
     (arguments
      '(#:configure-flags

gnu/packages/game-development.scm

@@ -317,14 +317,13 @@ provide connectivity for client applications written in any language.")
 (define-public nml
   (package
     (name "nml")
-    (version "0.5.2")
+    (version "0.5.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "nml" version))
        (sha256
-        (base32
+        (base32 "0l5pfs8q7jrl3xscqq7pnwh5h5d17fsyjy7xspkc73sa0ayjm9jx"))))
-         "1lwf5sc5qqzrkxfx5wkkj3yh2j2nzh5r599ly5psy8yw92km24hy"))))
     (build-system python-build-system)
     ;; TODO: Fix test that fails with
     ;; "AttributeError: partially initialized module 'nml.nmlop' has no
@@ -581,7 +580,7 @@ sounds from presets such as \"explosion\" or \"powerup\".")
 (define-public surgescript
   (package
     (name "surgescript")
-    (version "0.5.4.3")
+    (version "0.5.4.4")
     (source
      (origin
        (method git-fetch)
@@ -590,7 +589,7 @@ sounds from presets such as \"explosion\" or \"powerup\".")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "13q81439zg1bn7gskligskjgcfq0rdapp6f3llmrlk48vnyq49s0"))))
+        (base32 "1vck1wk6r6jrrw5xzpqldplz601dfgpk5s5p45fam00nfsid0p7p"))))
      (build-system cmake-build-system)
      (arguments
       '(#:configure-flags
@@ -1528,7 +1527,7 @@ games.")
 (define-public godot
   (package
     (name "godot")
-    (version "3.2.2")
+    (version "3.2.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1537,7 +1536,7 @@ games.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1libz83mbyrkbbsmmi8z2rydv3ls0w9r4vb5v6diqqwn7ka8z804"))
+                "19vrp5lhyvxbm6wjxzn28sn3i0s8j08ca7nani8l1nrhvlc8wi0v"))
               (modules '((guix build utils)
                          (ice-9 ftw)
                          (srfi srfi-1)))

gnu/packages/games.scm

@@ -429,7 +429,9 @@ physics settings to tweak as well.")
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ;no test
-       #:configure-flags '("-DDATADIR=share/astromenace")
+       #:configure-flags (list (string-append "-DDATADIR="
+                                              (assoc-ref %outputs "out")
+                                              "/share/astromenace"))
        #:phases
        (modify-phases %standard-phases
          (replace 'install
@@ -1811,18 +1813,23 @@ Every puzzle has a complete solution, although there may be more than one.")
    (license license:gpl2+)))
 
 (define-public retux
+  (let ((release "1.4.1")
+        (revision 1))
     (package
       (name "retux")
-    (version "1.4")
+      (version (if (zero? revision)
+                   release
+                   (string-append release "-"
+                                  (number->string revision))))
       (source (origin
                 (method url-fetch)
                 (uri (string-append "https://github.com/retux-game/retux/"
                                     "releases/download/v"
-                                  (version-major+minor version) "/retux-"
+                                    version "/retux-"
-                                  version "-src.tar.gz"))
+                                    release "-src.tar.gz"))
                 (sha256
                  (base32
-                "1hxy1pvlxhk0ci3wh2i3mmr82faqdjnnxsiwwr5gcr93nfnw9w5f"))))
+                  "1vrldg2qh2gqfswj7vkpc589ldrrjd903j6cnfdik9zh0jhlq4h2"))))
       (build-system python-build-system)
       (arguments
        `(#:tests? #f                    ; no check target
@@ -1862,7 +1869,7 @@ utilizing the art assets from the @code{SuperTux} project.")
                      license:cc-by-sa3.0
                      license:cc-by-sa4.0
                      license:gpl2+
-                   license:gpl3+))))
+                     license:gpl3+)))))
 
 (define-public roguebox-adventures
   (package
@@ -2721,7 +2728,7 @@ interface or via an external visual interface such as GNU XBoard.")
                   (ftp-directory . "/chess")))
     (license license:gpl3+)))
 
-(define freedink-engine
+(define-public freedink-engine
   (package
     (name "freedink-engine")
     (version "109.6")
@@ -2751,7 +2758,16 @@ interface or via an external visual interface such as GNU XBoard.")
 	     (invoke "autoreconf")
 	     ;; Build fails when autom4te.cache exists.
 	     (delete-file-recursively "autom4te.cache")
-             #t)))))
+             #t))
+         (add-after 'install 'delete-freedinkedit-desktop
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+             ;; freedinkedit does not know where to find freedink data
+             ;; freedink data is read-only, so it cannot be edited anyway.
+             ;; TODO: fix freedink.desktop
+             (delete-file-recursively (string-append
+                            out "/share/applications"))
+             #t))))))
     (native-inputs `(("autoconf" ,autoconf)
                      ("automake" ,automake)
                      ("cxxtest" ,cxxtest)
@@ -2773,7 +2789,7 @@ game data files but it also supports user-produced game mods or \"D-Mods\".
 To that extent, it also includes a front-end for managing all of your D-Mods.")
     (license license:gpl3+)))
 
-(define freedink-data
+(define-public freedink-data
   (package
     (name "freedink-data")
     (version "1.08.20190120")
@@ -3459,15 +3475,15 @@ This game is based on the GPL version of the famous game TuxRacer.")
 (define-public supertuxkart
   (package
     (name "supertuxkart")
-    (version "1.1")
+    (version "1.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/supertuxkart/SuperTuxKart/"
-                           version "/supertuxkart-" version "-src.tar.xz"))
+                           version "/SuperTuxKart-" version "-src.tar.xz"))
        (sha256
         (base32
-         "1s0ai07g3sswck9mr0142989mrgzzq1njc1qxk5als5b245jpc79"))
+         "0dvx56hmy6wdhl7m9dw8zc1n3jqfp05gnxl6zs1rbfdyzl5dybh5"))
        (modules '((guix build utils)))
        (snippet
         ;; Delete bundled library sources
@@ -3475,12 +3491,9 @@ This game is based on the GPL version of the famous game TuxRacer.")
            ;; Supertuxkart uses modified versions of the Irrlicht engine
            ;; and the bullet library.  The developers gave an explanation
            ;; here: http://forum.freegamedev.net/viewtopic.php?f=17&t=3906
-           ;; FIXME: try to unbundle angelscript and libraqm
+           ;; FIXME: try to unbundle angelscript, libmcpp and libraqm
            (for-each delete-file-recursively
-                     '("lib/zlib"
+                     '("lib/glew"
-                       "lib/libpng"
-                       "lib/jpeglib"
-                       "lib/glew"
                        "lib/wiiuse"
                        "lib/enet"))
            #t))))
@@ -3489,34 +3502,31 @@ This game is based on the GPL version of the famous game TuxRacer.")
      `(#:tests? #f ; no check target
        #:configure-flags
        (list "-DUSE_WIIUSE=0"
-             ;; Do not use the bundled zlib, glew and enet.
-             "-DNO_IRR_COMPILE_WITH_ZLIB_=TRUE"
              "-DUSE_SYSTEM_GLEW=TRUE"
              "-DUSE_SYSTEM_ENET=TRUE"
              ;; In order to use the system ENet library, IPv6 support (added in
              ;; SuperTuxKart version 1.1) must be disabled.
              "-DUSE_IPV6=FALSE"
              ;; FIXME: needs libopenglrecorder
-             "-DBUILD_RECORDER=0"
+             "-DBUILD_RECORDER=0")))
-             ;; Irrlicht returns an integer instead of a boolean
-             "-DCMAKE_C_FLAGS=-fpermissive")))
     (inputs
-     `(("glew" ,glew)
+     `(("curl" ,curl)
-       ("zlib" ,zlib)
-       ("openal" ,openal)
-       ("libvorbis" ,libvorbis)
        ("freetype" ,freetype)
        ("fribidi" ,fribidi)
+       ("glew" ,glew)
        ("harfbuzz" ,harfbuzz)
-       ("mesa" ,mesa)
+       ("libvorbis" ,libvorbis)
        ("libx11" ,libx11)
        ("libxrandr" ,libxrandr)
-       ("curl" ,curl)
+       ("mesa" ,mesa)
+       ("openal" ,openal)
+       ("sdl2" ,sdl2)
+       ("zlib" ,zlib)
        ;; The following input is needed to build the bundled and modified
        ;; version of irrlicht.
+       ("enet" ,enet)
        ("libjpeg" ,libjpeg-turbo)
-       ("openssl" ,openssl)
+       ("openssl" ,openssl)))
-       ("enet" ,enet)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
     (home-page "https://supertuxkart.net/Main_Page")
@@ -3664,7 +3674,7 @@ falling, themeable graphics and sounds, and replays.")
 (define-public wesnoth
   (package
     (name "wesnoth")
-    (version "1.14.13")
+    (version "1.14.14")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/wesnoth/wesnoth-"
@@ -3673,7 +3683,7 @@ falling, themeable graphics and sounds, and replays.")
                                   "wesnoth-" version ".tar.bz2"))
               (sha256
                (base32
-                "1pmqj4rah0256qi9w394ksb9apid723i5f5agkg6x1lahb1ac91q"))))
+                "1l7mdxn4kw938qz824057rqh99b7y9439a54s64n1xz95w77lp0r"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f))                    ;no check target
@@ -3904,7 +3914,7 @@ engine.  When you start it you will be prompted to download a graphics set.")
     (home-page "http://dev.openttdcoop.org/projects/opengfx")
     (synopsis "Base graphics set for OpenTTD")
     (description
-     "The OpenGFX projects is an implementation of the OpenTTD base grahics
+     "The OpenGFX project is an implementation of the OpenTTD base graphics
 set that aims to ensure the best possible out-of-the-box experience.
 
 OpenGFX provides you with...
@@ -4785,7 +4795,7 @@ of war.  Widelands also offers an Artificial Intelligence to challenge you.")
 (define-public starfighter
   (package
     (name "starfighter")
-    (version "2.3.2")
+    (version "2.3.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -4794,7 +4804,7 @@ of war.  Widelands also offers an Artificial Intelligence to challenge you.")
                     version "-src.tar.gz"))
               (sha256
                (base32
-                "1nvi277cazsw36b6nhd5nmk0cjvm71rlxasy24mf18j7fsvq9vp8"))))
+                "0jz2lgvmp299nks6ajg2yxbx4xcaxlc4cpfr61861p7m7z2nv84y"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -7767,7 +7777,7 @@ their own levels.")
 (define-public libmanette
   (package
     (name "libmanette")
-    (version "0.2.4")
+    (version "0.2.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/libmanette/"
@@ -7775,7 +7785,7 @@ their own levels.")
                                   "libmanette-" version ".tar.xz"))
               (sha256
                (base32
-                "1xrc6rh73v5w3kbkflzv1yg8sbxk4wf06hfk95raxhxlssza9q2g"))))
+                "0awsl0d34k3w18jdiyh377r7qi00s4kmh5gc97vx9jy0h22f01l0"))))
     (build-system meson-build-system)
     (native-inputs
      `(("glib" ,glib "bin")             ; for glib-compile-resources

gnu/packages/gcc.scm

@@ -9,6 +9,7 @@
 ;;; Copyright © 2018, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2020 Joseph LaFreniere <joseph@lafreniere.xyz>
 ;;; Copyright © 2020 Guy Fleury Iteriteka <gfleury@disroot.org>
+;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -759,11 +760,26 @@ as the 'native-search-paths' field."
                (for-each delete-file
                          (find-files (string-append (assoc-ref outputs "out") "/bin")
                                      ".*(c\\+\\+|cpp|g\\+\\+|gcov|gcc|gcc-.*)"))
-               #t))))))))
+               #t))))))
+    (synopsis "GCC library generating machine code on-the-fly at runtime")
+    (description
+     "This package is part of the GNU Compiler Collection and provides an
+embeddable library for generating machine code on-the-fly at runtime.  This
+shared library can then be dynamically-linked into bytecode interpreters and
+other such programs that want to generate machine code on-the-fly at run-time.
+It can also be used for ahead-of-time code generation for building standalone
+compilers.  The just-in-time (jit) part of the name is now something of a
+misnomer.")))
 
 
 (define-public gccgo-4.9
-  (custom-gcc gcc-4.9 "gccgo" '("go")
+  (custom-gcc (package
+                (inherit gcc-4.9)
+                (synopsis "Go frontend to GCC")
+                (description
+                 "This package is part of the GNU Compiler Collection and
+provides the GNU compiler for the Go programming language."))
+              "gccgo" '("go")
               %generic-search-paths
               ;; Suppress the separate "lib" output, because otherwise the
               ;; "lib" and "out" outputs would refer to each other, creating

gnu/packages/geo.scm

@@ -12,6 +12,7 @@
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;; Copyright © 2019 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2020 Christopher Baines <mail@cbaines.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1276,7 +1277,7 @@ to the OSM opening hours specification.")
 (define-public josm
   (package
     (name "josm")
-    (version "16812")
+    (version "17013")
     (source (origin
               (method svn-fetch)
               (uri (svn-reference
@@ -1285,7 +1286,7 @@ to the OSM opening hours specification.")
                      (recursive? #f)))
               (sha256
                (base32
-                "131ly6ah9ygrah1wq1h2199v4hyzgflnh62ychs4jqvy9wz0dal6"))
+                "12mcqswjijvx2n7hz7lnx83i3vjr5ib58cazqin10hczcwnd778q"))
               (file-name (string-append name "-" version "-checkout"))
               (modules '((guix build utils)))
             (snippet
@@ -1339,7 +1340,8 @@ to the OSM opening hours specification.")
                        (filter
                          (lambda (s)
                            (let ((source (assoc-ref inputs "source")))
-                             (not (equal? (substring s 0 (string-length source)) source))))
+                             (not (equal? (substring s 0 (string-length source))
+                                          source))))
                          (string-split (getenv "CLASSPATH") #\:))
                        ":"))
              #t))
@@ -1386,6 +1388,19 @@ to the OSM opening hours specification.")
                                   "Is-Local-Build: true\n"
                                   "Build-Date: 1970-01-01 00:00:00 +0000\n"))))
              #t))
+         (add-after 'install 'install-share-directories
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out               (assoc-ref outputs "out"))
+                   (share-directories '("applications" "icons" "man" "menu"
+                                        "metainfo" "mime" "pixmaps")))
+               (for-each (lambda (directory)
+                           (copy-recursively (string-append
+                                              "native/linux/tested/usr/share/"
+                                              directory)
+                                             (string-append
+                                              out "/share/" directory)))
+                         share-directories))
+             #t))
          (add-after 'install 'install-bin
            (lambda* (#:key outputs inputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))

gnu/packages/gettext.scm

@@ -9,6 +9,7 @@
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Miguel <rosen644835@gmail.com>
+;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -34,6 +35,7 @@
   #:use-module (guix build-system perl)
   #:use-module (gnu packages docbook)
   #:use-module (gnu packages emacs)
+  #:use-module (gnu packages hurd)
   #:use-module (gnu packages libunistring)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
@@ -106,7 +108,11 @@
                #t)))))
 
        ;; When tests fail, we want to know the details.
-       #:make-flags '("VERBOSE=yes")))
+       #:make-flags '("VERBOSE=yes"
+                      ,@(if (hurd-target?)
+                            ;; Linking to libgettextlib.so makes test-raise fail
+                            '("XFAIL_TESTS=test-raise")
+                            '()))))
     (home-page "https://www.gnu.org/software/gettext/")
     (synopsis
      "Tools and documentation for translation (used to build other packages)")

gnu/packages/glib.scm

@@ -619,21 +619,6 @@ It also contains adaptor classes for connection of dissimilar callbacks and
 has an ease of use unmatched by other C++ callback libraries.")
     (license license:lgpl2.1+)))
 
-(define-public libsigc++-2
-  (package
-    (inherit libsigc++)
-    (name "libsigc++")
-    (version "2.10.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri
-        (string-append "mirror://gnome/sources/libsigc++/"
-                       (version-major+minor version) "/"
-                       name "-" version ".tar.xz"))
-       (sha256
-        (base32 "11j7j1jv4z58d9s7jvl42fnqa1dzl4idgil9r45cjv1w673dys0b"))))))
-
 (define glibmm
   (package
     (name "glibmm")
@@ -692,7 +677,7 @@ useful for C++.")
        (sha256
         (base32 "1v6lp23fr2qh4zshcnm28sn29j3nzgsvcqj2nhmrnvamipjq4lm7"))))
      (propagated-inputs
-      `(("libsigc++" ,libsigc++-2)
+      `(("libsigc++" ,libsigc++)
         ("glib" ,glib)))))
 
 (define-public python2-pygobject-2
@@ -950,7 +935,7 @@ programming language.  It also contains the utility
 (define-public appstream-glib
   (package
     (name "appstream-glib")
-    (version "0.7.17")
+    (version "0.7.18")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://people.freedesktop.org/~hughsient/"
@@ -958,7 +943,7 @@ programming language.  It also contains the utility
                                   "appstream-glib-" version ".tar.xz"))
               (sha256
                (base32
-                "0jg58m1p5xfrh8zkpqhhg00nqs727z5i1qy6sb0a3vyc98fyk9vw"))))
+                "00j0kkgf224nzmrha72g8pd72mymhph7vaisj35i4ffy7cpd47na"))))
     (build-system meson-build-system)
     (native-inputs
      `(("gettext" ,gettext-minimal)

gnu/packages/gnome-xyz.scm

@@ -234,7 +234,7 @@ some media players, are meant to run long-term in the background even after you
 close their window.  These applications remain accessible by adding an icon to
 the GNOME Shell Legacy Tray.  However, the Legacy Tray was removed in GNOME
 3.26.  TopIcons Redux brings those icons back into the top panel so that it's
-easier to keep track of apps running in the backround.")
+easier to keep track of applications running in the background.")
     (license license:gpl2+)))
 
 (define-public gnome-shell-extension-dash-to-dock

gnu/packages/gnome.scm

@@ -89,6 +89,8 @@
   #:use-module (gnu packages cmake)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages crates-io)
+  #:use-module (gnu packages crates-graphics)
+  #:use-module (gnu packages crates-gtk)
   #:use-module (gnu packages cups)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages cyrus-sasl)
@@ -105,6 +107,7 @@
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages game-development)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages gimp)
@@ -357,8 +360,8 @@ services.")
        ("libsoup" ,libsoup)
        ("libxml2" ,libxml2)))
     (synopsis "Glib library for feeds")
-    (description "LibGRSS is a Glib abstaction to handle feeds in RSS, Atom and
+    (description "LibGRSS is a Glib abstraction to handle feeds in RSS, Atom,
-other formats.")
+and other formats.")
     (home-page "https://wiki.gnome.org/Projects/Libgrss")
     (license license:lgpl3+)))
 
@@ -986,7 +989,7 @@ freedesktop.org desktop notification specification.")
 (define-public mm-common
   (package
     (name "mm-common")
-    (version "1.0.1")
+    (version "1.0.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/mm-common/"
@@ -994,7 +997,7 @@ freedesktop.org desktop notification specification.")
                                   "mm-common-" version ".tar.xz"))
               (sha256
                (base32
-                "1jasx9a9g7nqf7jcv3mrg4qh5cp9sq724jxjaz4wa1dzmxsxg8i8"))))
+                "07b4s5ckcz9q5gwx8vchim19mhfgl8wysqwi30pndks3m4zrzad2"))))
     (build-system meson-build-system)
     (arguments
      `(#:phases
@@ -1663,6 +1666,44 @@ uses duplicity as the backend, which supports incremental backups and storage
 either on a local, or remote machine via a number of methods.")
     (license license:gpl3+)))
 
+(define-public gnome-commander
+  (package
+    (name "gnome-commander")
+    (version "1.10.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://gnome/sources/" name "/"
+                           (version-major+minor version)  "/"
+                           "gnome-commander-" version ".tar.xz"))
+       (sha256
+        (base32 "0bis36awb73vhkncq8yr0qlnyaxynqkvmyqbg57ijqwd0m8hh4zg"))))
+    (build-system glib-or-gtk-build-system)
+    (native-inputs
+     `(("desktop-file-utils" ,desktop-file-utils)
+       ("gcc" ,gcc-8) ;required for -Wcast-function-type
+       ("gettext" ,gettext-minimal)
+       ("glib:bin" ,glib "bin")
+       ("gobject-introspection" ,gobject-introspection)
+       ("googletest" ,googletest)
+       ("intltool" ,intltool)
+       ("itstool" ,itstool)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("gconf" ,gconf)
+       ("gnome-vfs" ,gnome-vfs)
+       ("gtk+" ,gtk+-2)
+       ("libxml2" ,libxml2)))
+    (home-page "https://gcmd.github.io/")
+    (synopsis "Two-pane graphical file manager for the GNOME desktop")
+    (description
+     "GNOME Commander is a two-pane graphical file manager using GNOME
+libraries.  It aims to fulfill the demands of more advanced users who
+like to focus on file management, their work through special applications
+and running smart commands.")
+    (license license:gpl2+)))
+
 (define-public gnome-user-docs
   (package
    (name "gnome-user-docs")
@@ -2501,6 +2542,104 @@ on the GNOME Desktop with a single simple application.")
 for settings shared by various components of the GNOME desktop.")
     (license license:lgpl2.1+)))
 
+(define-public python-liblarch
+  (package
+    (name "python-liblarch")
+    (version "3.0.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/getting-things-gnome/liblarch")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0xv2mfvyzipbny3iz8vll77wsqxfwh28xj6bj1ff0l452waph45m"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'start-xserver
+           (lambda* (#:key inputs #:allow-other-keys)
+             (system (format #f "~a/bin/Xvfb :1 &"
+                             (assoc-ref inputs "xorg-server")))
+             (setenv "DISPLAY" ":1")
+             #t)))))
+    (native-inputs
+     `(("xorg-server" ,xorg-server-for-tests)))
+    (inputs
+     `(("gtk+" ,gtk+)))
+    (propagated-inputs
+     `(("python-pygobject" ,python-pygobject)))
+    (home-page "https://wiki.gnome.org/Projects/liblarch")
+    (synopsis "Library to easily handle complex data structures")
+    (description
+     "Liblarch is a Python library built to easily handle data structures such
+as lists, trees and acyclic graphs.  There's also a GTK binding that will
+allow you to use your data structure in a @code{Gtk.Treeview}.
+
+Liblarch support multiple views of one data structure and complex filtering.
+That way, you have a clear separation between your data themselves (Model)
+and how they are displayed (View).")
+    (license license:lgpl3+)))
+
+(define-public gtg
+  (package
+    (name "gtg")
+    (version "0.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/getting-things-gnome/gtg")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0r28vyr88rj3kd3cg4gj7sd29wadjchi92wzmbx67d4hlg25h8kk"))))
+    (build-system meson-build-system)
+    (arguments
+     `(#:glib-or-gtk? #t
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'glib-or-gtk-wrap 'python-and-gi-wrap
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((prog (string-append (assoc-ref outputs "out")
+                                        "/bin/gtg"))
+                   (pylib (string-append (assoc-ref outputs "out")
+                                         "/lib/python"
+                                         ,(version-major+minor
+                                           (package-version python))
+                                         "/site-packages")))
+               (wrap-program prog
+                 `("PYTHONPATH" = (,(getenv "PYTHONPATH") ,pylib))
+                 `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH"))))
+               #t))))))
+    (native-inputs
+     `(("desktop-file-utils" ,desktop-file-utils)
+       ("gettext" ,gettext-minimal)
+       ("glib:bin" ,glib "bin")
+       ("gobject-introspection" ,gobject-introspection)
+       ("gtk+:bin" ,gtk+ "bin")
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
+       ("gtk+" ,gtk+)
+       ("python-dbus" ,python-dbus)
+       ("python-liblarch" ,python-liblarch)
+       ("python-pycairo" ,python-pycairo)
+       ("python-pygobject" ,python-pygobject)
+       ("python-pyxdg" ,python-pyxdg)))
+    (home-page "https://wiki.gnome.org/Apps/GTG")
+    (synopsis "Personal organizer for the GNOME desktop")
+    (description
+     "Getting Things GNOME! (GTG) is a personal tasks and TODO list items
+organizer for the GNOME desktop environment inspired by the Getting Things
+Done (GTD) methodology.  GTG is designed with flexibility, adaptability,
+and ease of use in mind so it can be used as more than just GTD software.
+GTG is intended to help you track everything you need to do and need to
+know, from small tasks to large projects.")
+    (license license:gpl3+)))
+
 (define-public icon-naming-utils
   (package
     (name "icon-naming-utils")
@@ -2919,7 +3058,13 @@ API add-ons to make GTK+ widgets OpenGL-capable.")
     (description "Glade is a rapid application development (RAD) tool to
 enable quick & easy development of user interfaces for the GTK+ toolkit and
 the GNOME desktop environment.")
-    (license license:lgpl2.0+)))
+    (license license:lgpl2.0+)
+    (native-search-paths (list (search-path-specification
+                                (variable "GLADE_CATALOG_SEARCH_PATH")
+                                (files '("share/glade/catalogs")))
+                               (search-path-specification
+                                (variable "GLADE_MODULE_SEARCH_PATH")
+                                (files '("lib/glade/modules")))))))
 
 (define-public libcroco
   (package
@@ -3060,7 +3205,7 @@ library.")
 (define-public librsvg-next
   (package
     (name "librsvg")
-    (version "2.48.8")
+    (version "2.50.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/librsvg/"
@@ -3068,7 +3213,7 @@ library.")
                                   "librsvg-" version ".tar.xz"))
               (sha256
                (base32
-                "14i6xzghcidv64cyd3g0wdjbl82rph737yxn9s3x29nzpcjs707l"))
+                "02csvx2nzygh8kyal2qiy3y6xb7d52vszxxr37dzav704a9pkncv"))
               (modules '((guix build utils)))
               (snippet
                '(begin (delete-file-recursively "vendor")
@@ -3080,6 +3225,7 @@ library.")
        ((guix build cargo-build-system)
         (guix build utils)
         ((guix build gnu-build-system) #:prefix gnu:))
+       #:rust ,rust-1.40
        #:cargo-inputs
        (("rust-bitflags" ,rust-bitflags-1)
         ("rust-cairo-rs" ,rust-cairo-rs-0.8)
@@ -3087,9 +3233,8 @@ library.")
         ("rust-cast" ,rust-cast-0.2)
         ("rust-cssparser" ,rust-cssparser-0.27)
         ("rust-data-url" ,rust-data-url-0.1)
-        ("rust-downcast-rs" ,rust-downcast-rs-1.1)
         ("rust-encoding" ,rust-encoding-0.2)
-        ("rust-float-cmp" ,rust-float-cmp-0.6)
+        ("rust-float-cmp" ,rust-float-cmp-0.8)
         ("rust-gdk-pixbuf" ,rust-gdk-pixbuf-0.8)
         ("rust-gdk-pixbuf-sys" ,rust-gdk-pixbuf-sys-0.9)
         ("rust-gio" ,rust-gio-0.8)
@@ -3097,14 +3242,14 @@ library.")
         ("rust-glib" ,rust-glib-0.9)
         ("rust-glib-sys" ,rust-glib-sys-0.9)
         ("rust-gobject-sys" ,rust-gobject-sys-0.9)
-        ("rust-itertools" ,rust-itertools-0.8)
+        ("rust-itertools" ,rust-itertools-0.9)
         ("rust-language-tags" ,rust-language-tags-0.2)
         ("rust-libc" ,rust-libc-0.2)
         ("rust-locale-config" ,rust-locale-config-0.3)
         ("rust-markup5ever" ,rust-markup5ever-0.10)
-        ("rust-nalgebra" ,rust-nalgebra-0.19)
+        ("rust-nalgebra" ,rust-nalgebra-0.21)
         ("rust-num-traits" ,rust-num-traits-0.2)
-        ("rust-once-cell" ,rust-once-cell-1.2)
+        ("rust-once-cell" ,rust-once-cell-1)
         ("rust-pkg-config" ,rust-pkg-config-0.3)
         ("rust-pango" ,rust-pango-0.8)
         ("rust-pango-sys" ,rust-pango-sys-0.9)
@@ -3114,11 +3259,20 @@ library.")
         ("rust-rgb" ,rust-rgb-0.8)
         ("rust-regex" ,rust-regex-1)
         ("rust-selectors" ,rust-selectors-0.22)
+        ("rust-string-cache" ,rust-string-cache-0.8)
+        ("rust-tinyvec" ,rust-tinyvec-0.3)
         ("rust-url" ,rust-url-2.1)
         ("rust-xml5ever" ,rust-xml5ever-0.16))
        #:cargo-development-inputs
-       (("rust-cairo-rs" ,rust-cairo-rs-0.8)
+       (("rust-assert-cmd" ,rust-assert-cmd-1)
-        ("rust-criterion" ,rust-criterion-0.3))
+        ("rust-cairo-rs" ,rust-cairo-rs-0.8)
+        ("rust-chrono" ,rust-chrono-0.4)
+        ("rust-criterion" ,rust-criterion-0.3)
+        ("rust-float-cmp" ,rust-float-cmp-0.8)
+        ("rust-lopdf" ,rust-lopdf-0.25)
+        ("rust-png" ,rust-png-0.16)
+        ("rust-predicates" ,rust-predicates-1)
+        ("rust-tempfile" ,rust-tempfile-3))
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-docbook-xml
@@ -3171,6 +3325,31 @@ library.")
              #t))
          (replace 'build
            (assoc-ref gnu:%standard-phases 'build))
+         (add-before 'check 'ignore-failing-tests
+           ;; stderr=```/tmp/guix-build-.../librsvg-2.50.1/rsvg-convert: line 150: ls: command not found
+           (lambda _
+             (substitute* "tests/src/cmdline/rsvg_convert.rs"
+               (("fn background_color_option_invalid_color_yields_error" all)
+                (string-append "#[ignore] " all))
+               (("fn empty_input_yields_error" all)
+                (string-append "#[ignore] " all))
+               (("fn empty_svg_yields_error" all)
+                (string-append "#[ignore] " all))
+               (("fn env_source_data_epoch_empty" all)
+                (string-append "#[ignore] " all))
+               (("fn env_source_data_epoch_no_digits" all)
+                (string-append "#[ignore] " all))
+               (("fn env_source_data_epoch_trailing_garbage" all)
+                (string-append "#[ignore] " all))
+               (("fn export_id_option_error" all)
+                (string-append "#[ignore] " all))
+               (("fn huge_zoom_factor_yields_error" all)
+                (string-append "#[ignore] " all))
+               (("fn multiple_input_files_not_allowed_for_png_output" all)
+                (string-append "#[ignore] " all))
+               (("fn stylesheet_option_error" all)
+                (string-append "#[ignore] " all)))
+             #t))
          (replace 'check
            (lambda* args
              ((assoc-ref gnu:%standard-phases 'check)
@@ -3951,7 +4130,7 @@ engineering.")
 (define-public seahorse
   (package
     (name "seahorse")
-    (version "3.34")
+    (version "3.36")
     (source
      (origin
        (method url-fetch)
@@ -3960,7 +4139,7 @@ engineering.")
                            version ".tar.xz"))
        (sha256
         (base32
-         "16sfnqrdlr5xx6kixx2ln1mva7nngjlw1k3f5n454vyaigffjh2v"))))
+         "1nqn4a6dr4l1fpzj3mv4swhpnvhjcqlwsyhwm59sdzqgdfx4hbwr"))))
     (build-system meson-build-system)
     (arguments
      '(#:glib-or-gtk? #t
@@ -3980,6 +4159,7 @@ engineering.")
        ("openldap" ,openldap)
        ("openssh" ,openssh)
        ("avahi" ,avahi)
+       ("libhandy" ,libhandy-0.0)
        ("libpwquality" ,libpwquality)
        ("libsecret" ,libsecret)
        ("libsoup" ,libsoup)))
@@ -5114,7 +5294,8 @@ services for numerous locations.")
                            name "-" version ".tar.xz"))
        (sha256
         (base32
-         "07y1gbicz0pbxmdgwrdzyc4byy30wfwpbqgvnx27gnpqmc5s50cr"))))
+         "07y1gbicz0pbxmdgwrdzyc4byy30wfwpbqgvnx27gnpqmc5s50cr"))
+       (patches (search-patches "gnome-settings-daemon-gc.patch"))))
     (build-system meson-build-system)
     (arguments
      `(#:glib-or-gtk? #t
@@ -5127,6 +5308,21 @@ services for numerous locations.")
              (string-append "-Dc_link_args=-Wl,-rpath="
                             (assoc-ref %outputs "out")
                             "/lib/gnome-settings-daemon-3.0"))
+
+       #:phases (modify-phases %standard-phases
+                  (add-before 'configure 'set-baobab-file-name
+                    (lambda* (#:key inputs #:allow-other-keys)
+                      ;; Hard-code the file name of Baobab instead of looking
+                      ;; it up in $PATH.  This ensures users get the "Examine"
+                      ;; button in the low disk space notification of GDM even
+                      ;; if they don't have GNOME in their main profile.
+                      (let ((baobab (assoc-ref inputs "baobab")))
+                        (substitute* "plugins/housekeeping/gsd-disk-space.c"
+                          (("g_find_program_in_path \\(DISK_SPACE_ANALYZER\\)")
+                           (string-append "g_strdup (\"" baobab
+                                          "/bin/baobab\")")))
+                        #t))))
+
        ;; Color management test can't reach the colord system service.
        #:tests? #f))
     (native-inputs
@@ -5139,6 +5335,7 @@ services for numerous locations.")
        ("docbook-xsl" ,docbook-xsl)))
     (inputs
      `(("alsa-lib" ,alsa-lib)
+       ("baobab" ,baobab)
        ("colord" ,colord)
        ("libgudev" ,libgudev)
        ("upower" ,upower)
@@ -7895,7 +8092,7 @@ usage and information about running processes.")
 (define-public gnome-bluetooth
   (package
     (name "gnome-bluetooth")
-    (version "3.34.0")
+    (version "3.34.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -7903,7 +8100,7 @@ usage and information about running processes.")
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1bvbxcsjkyl0givy8nfm7112bq3c0vn1v89fdk2pip714dsfcrz8"))))
+                "0lmjvb49vgr4jjplrisv6pi29jsn1q42715i6c5a0p9ad3gawyyv"))))
     (build-system meson-build-system)
     (native-inputs
      `(("glib:bin" ,glib "bin") ; for gdbus-codegen, etc.
@@ -10006,7 +10203,7 @@ automatically and it can stream songs from online music services and charts.")
 (define-public gnome-video-effects
   (package
     (name "gnome-video-effects")
-    (version "0.4.3")
+    (version "0.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -10014,14 +10211,10 @@ automatically and it can stream songs from online music services and charts.")
                                   version ".tar.xz"))
               (sha256
                (base32
-                "06c2f1kihyhawap1s3zg5w7q7fypsybkp7xry4hxkdz4mpsy0zjs"))))
+                "1j6h98whgkcxrh30bwvnxvyqxrxchgpdgqhl0j71xz7x72dqxijd"))))
-    (build-system glib-or-gtk-build-system)
+    (build-system meson-build-system)
-    (arguments
-     `(#:out-of-source? #f))
     (native-inputs
-     `(("glib:bin" ,glib "bin")
+     `(("gettext" ,gettext-minimal)
-       ("intltool" ,intltool)
-       ("gettext" ,gettext-minimal)
        ("pkg-config" ,pkg-config)))
     (home-page "https://wiki.gnome.org/Projects/GnomeVideoEffects")
     (synopsis "Video effects for Cheese and other GNOME applications")
@@ -10033,7 +10226,7 @@ photo-booth-like software, such as Cheese.")
 (define-public cheese
   (package
     (name "cheese")
-    (version "3.34.0")
+    (version "3.38.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -10041,7 +10234,7 @@ photo-booth-like software, such as Cheese.")
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0wvyc9wb0avrprvm529m42y5fkv3lirdphqydc9jw0c8mh05d1ni"))))
+                "0vyim2avlgq3a48rgdfz5g21kqk11mfb53b2l883340v88mp7ll8"))))
     (arguments
      `(#:glib-or-gtk? #t
        ;; Tests require GDK.
@@ -10054,6 +10247,15 @@ photo-booth-like software, such as Cheese.")
              (substitute* "meson_post_install.py"
                (("gtk-update-icon-cache") (which "true")))
              #t))
+         (add-after 'unpack 'patch-docbook-xml
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; Avoid a network connection attempt during the build.
+             (substitute* '("docs/reference/cheese.xml"
+                            "docs/reference/cheese-docs.xml")
+               (("http://www.oasis-open.org/docbook/xml/4.3/docbookx.dtd")
+                (string-append (assoc-ref inputs "docbook-xml")
+                               "/xml/dtd/docbook/docbookx.dtd")))
+             #t))
          (add-after 'install 'wrap-cheese
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let ((out             (assoc-ref outputs "out"))
@@ -10064,6 +10266,7 @@ photo-booth-like software, such as Cheese.")
     (build-system meson-build-system)
     (native-inputs
      `(("docbook-xsl" ,docbook-xsl)
+       ("docbook-xml" ,docbook-xml-4.3)
        ("glib:bin" ,glib "bin")
        ("gtk-doc" ,gtk-doc)
        ("intltool" ,intltool)
@@ -10508,7 +10711,7 @@ advanced image management tool")
     (build-system meson-build-system)
     (arguments
      `(#:configure-flags
-       '("-Dglade_catalog=disabled"
+       '("-Dglade_catalog=enabled"
          "-Dgtk_doc=true")
        #:phases
        (modify-phases %standard-phases
@@ -10519,7 +10722,9 @@ advanced image management tool")
              (setenv "DISPLAY" ":1")
              #t)))))
     (inputs
-     `(("gtk+" ,gtk+)))
+     `(("gtk+" ,gtk+)
+       ("glade" ,glade3)
+       ("libxml2" ,libxml2)))
     (native-inputs
      `(("glib:bin" ,glib "bin")
        ("gobject-introspection" ,gobject-introspection) ; for g-ir-scanner
@@ -10550,7 +10755,11 @@ for usage on small and big screens.")
              (commit (string-append "v" version))))
        (file-name (git-file-name "libhandy" version))
        (sha256
-        (base32 "1y23k623sjkldfrdiwfarpchg5mg58smcy1pkgnwfwca15wm1ra5"))))))
+        (base32 "1y23k623sjkldfrdiwfarpchg5mg58smcy1pkgnwfwca15wm1ra5"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments libhandy)
+       ((#:configure-flags flags)
+        '(list "-Dglade_catalog=disabled" "-Dgtk_doc=true"))))))
 
 (define-public libgit2-glib
   (package
@@ -10763,6 +10972,44 @@ versions of Adwaita, Adwaita-dark and HighContrast themes.  It also provides
 index files needed for Adwaita to be used outside of GNOME.")
     (license license:lgpl2.1+)))
 
+(define-public gnote
+  (package
+    (name "gnote")
+    (version "3.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://gnome/sources/" name "/"
+                           (version-major+minor version)  "/"
+                           "gnote-" version ".tar.xz"))
+       (sha256
+        (base32 "1ingbaw4d8vpjn083xvzqw7kz8z0k2bx7msk78pbzd68bwgkadpx"))))
+    (build-system glib-or-gtk-build-system)
+    (native-inputs
+     `(("desktop-file-utils" ,desktop-file-utils)
+       ("glib:bin" ,glib "bin")
+       ("gobject-introspection" ,gobject-introspection)
+       ("intltool" ,intltool)
+       ("itstool" ,itstool)
+       ("pkg-config" ,pkg-config)
+       ("unittest-cpp" ,unittest-cpp))) ;FIXME: not found by pkg-config
+    (inputs
+     `(("glibmm" ,glibmm)
+       ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
+       ("gspell" ,gspell)
+       ("gtk+" ,gtk+)
+       ("gtkmm" ,gtkmm)
+       ("libsecret" ,libsecret)
+       ("libuuid" ,util-linux "lib")
+       ("libxml2" ,libxml2)
+       ("libxslt" ,libxslt)))
+    (synopsis "Note-taking application for the GNOME desktop")
+    (description
+     "Gnote is a note-taking application written for the GNOME desktop
+environment.")
+    (home-page "https://wiki.gnome.org/Apps/Gnote")
+    (license license:gpl3+)))
+
 (define-public polari
   (package
     (name "polari")
@@ -10998,6 +11245,49 @@ designed to work with various laser/ink-jet peel-off label and business
 card sheets that you’ll find at most office supply stores.")
     (license license:gpl3+)))
 
+;; Version 3.38.0 is out but requires tepl>=5 which requires glib>=2.64.
+(define-public gnome-latex
+  (package
+    (name "gnome-latex")
+    (version "3.36.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://gnome/sources/" name "/"
+                           (version-major+minor version)  "/"
+                           "gnome-latex-" version ".tar.xz"))
+       (sha256
+        (base32 "1869kr1zhcp04mzbi67lwgk497w840dbbc7427i9yh9b9s7j6mqn"))))
+    (build-system glib-or-gtk-build-system)
+    (native-inputs
+     `(("gettext" ,gettext-minimal)
+       ("glib:bin" ,glib "bin")
+       ("gobject-introspection" ,gobject-introspection)
+       ("gtk-doc" ,gtk-doc)
+       ("intltool" ,intltool)
+       ("itstool" ,itstool)
+       ("pkg-config" ,pkg-config)
+       ("vala" ,vala)))
+    (inputs
+     `(("amtk" ,amtk)
+       ("dconf" ,dconf)
+       ("glib" ,glib)
+       ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
+       ("gspell" ,gspell)
+       ("gtk+" ,gtk+)
+       ("gtksourceview" ,gtksourceview)
+       ("libgee" ,libgee)
+       ("tepl" ,tepl)
+       ("uchardet" ,uchardet)))
+    (home-page "https://wiki.gnome.org/Apps/GNOME-LaTeX")
+    (synopsis "LaTeX editor for the GNOME desktop")
+    (description
+     "GNOME LaTeX is a LaTeX editor for the GNOME desktop.  It has features
+such as build tools, completion of LaTeX commands, structure navigation,
+symbol tables, document templates, project management, spell-checking, menus
+and toolbars.")
+    (license license:gpl3+)))
+
 (define-public libratbag
   (package
     (name "libratbag")
@@ -11369,7 +11659,7 @@ integrated profiler via Sysprof, debugging support, and more.")
 (define-public komikku
   (package
     (name "komikku")
-    (version "0.19.0")
+    (version "0.21.1")
     (source
      (origin
        (method git-fetch)
@@ -11379,7 +11669,7 @@ integrated profiler via Sysprof, debugging support, and more.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "16d7k500nd9klnjqqcgk3glhv2sy78yndkz3n0x7lynvblsy45kk"))))
+         "17ss5k2hnymk6xyx1dy3q0y2pwcld78cw7d0cs9c0hnhskh5dirh"))))
     (build-system meson-build-system)
     (arguments
      `(#:glib-or-gtk? #t
@@ -11432,3 +11722,130 @@ integrated profiler via Sysprof, debugging support, and more.")
     (description "Komikku is an online/offline manga reader for GNOME,
 developed with the aim of being used with the Librem 5 phone.")
     (license license:gpl3+)))
+
+(define-public libgda
+  (package
+    (name "libgda")
+    (version "5.2.9")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.gnome.org/GNOME/libgda.git/")
+             (commit "LIBGDA_5_2_9")))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "122anbk15vj2dfxrw7s48b6zwlpp7cyppshxizynvf3zmc0ygw3j"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags '("--enable-vala")
+       ;; There's a race between check_cnc_lock and check_threaded_cnc
+       ;; in tests/multi-threading.
+       #:parallel-tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-glade-install
+           (lambda _
+             (substitute* "configure.ac"
+               (("`\\$PKG_CONFIG --variable=catalogdir gladeui-2\\.0`")
+                "${datadir}/glade/catalogs")
+               (("`\\$PKG_CONFIG --variable=pixmapdir gladeui-2\\.0`")
+                "${datadir}/glade/pixmaps"))
+             #t))
+         (add-before 'check 'pre-check
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; Tests require a running X server.
+             (system "Xvfb :1 &")
+             (setenv "DISPLAY" ":1")
+             #t))
+         (add-after 'install 'symlink-glade-module
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((shlib "libgda-ui-5.0.so")
+                    (out (assoc-ref outputs "out"))
+                    (out/lib (string-append out "/lib"))
+                    (moduledir (string-append out/lib "/glade/modules")))
+               (mkdir-p moduledir)
+               (symlink (string-append out/lib "/" shlib)
+                        (string-append moduledir "/" shlib))
+               #t))))))
+    (propagated-inputs
+     `(("libxml2" ,libxml2)))           ; required by libgda-5.0.pc
+    (inputs
+     `(("glib" ,glib)
+       ("glade" ,glade3)
+       ("gtk+" ,gtk+)
+       ("libsecret" ,libsecret)
+       ("libxslt" ,libxslt)
+       ("openssl" ,openssl)
+       ("vala" ,vala)))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("glib:bin" ,glib "bin")
+       ("gnome-common" ,gnome-common)
+       ("gobject-introspection" ,gobject-introspection)
+       ("gtk-doc" ,gtk-doc)
+       ("intltool" ,intltool)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)
+       ("vala" ,vala)
+       ("which" ,which)
+       ("xorg-server" ,xorg-server-for-tests)
+       ("yelp-tools" ,yelp-tools)))
+    (home-page "https://gitlab.gnome.org/GNOME/libgda")
+    (synopsis "Uniform data access")
+    (description
+     "GNU Data Access (GDA) is an attempt to provide uniform access to
+different kinds of data sources (databases, information servers, mail spools,
+etc).  It is a complete architecture that provides all you need to access
+your data.")
+    (license license:lgpl2.1+)))
+
+(define-public gtranslator
+  (package
+    (name "gtranslator")
+    (version "3.36.0")
+        (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://gnome/sources/" name "/"
+                                  (version-major+minor version) "/"
+                                  name "-" version ".tar.xz"))
+              (sha256
+               (base32
+                "1lxd2nkji4jk8g2xmyc1a1r3ww710ddk91zh9psmx8xlb4xivaid"))))
+    (build-system meson-build-system)
+    (inputs
+     `(("json-glib" ,json-glib)
+       ("jsonrpc-glib" ,jsonrpc-glib)
+       ("gettext" ,gettext-minimal)
+       ("glib" ,glib)
+       ("gtk+" ,gtk+)
+       ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
+       ("gspell" ,gspell)
+       ("libdazzle" ,libdazzle)
+       ("libgda" ,libgda)
+       ("libsoup" ,libsoup)))
+    (native-inputs
+     `(("glib:bin" ,glib "bin")
+       ("itstool" ,itstool)
+       ("pkg-config" ,pkg-config)))
+    (propagated-inputs
+     `(("gtksourceview" ,gtksourceview))) ; required for source view
+    (arguments
+     `(#:build-type "release"
+       #:phases
+       (modify-phases %standard-phases
+       (add-after 'unpack 'skip-gtk-update-icon-cache
+           (lambda _
+             (substitute* "build-aux/meson/meson_post_install.py"
+               (("gtk-update-icon-cache") (which "true")))
+             #t)))))
+    (home-page "https://wiki.gnome.org/Apps/Gtranslator")
+    (synopsis "Translation making program")
+    (description
+     "gtranslator is a quite comfortable gettext po/po.gz/(g)mo files editor
+for the GNOME 3.x platform with many features.  It aims to be a very complete
+editing environment for translation issues within the GNU gettext/GNOME desktop
+world.")
+    (license license:gpl3+)))

gnu/packages/gnu-pw-mgr.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2018, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,7 +30,7 @@
 (define-public gnu-pw-mgr
   (package
     (name "gnu-pw-mgr")
-    (version "2.4.2")
+    (version "2.7")
     (source
      (origin
       (method url-fetch)
@@ -38,7 +38,7 @@
                           version ".tar.xz"))
       (sha256
        (base32
-        "1yvdzc5w37qrjrkby5699ygj9bhkvgi3zk9k9jcjry1j6b7wdl17"))))
+        "1ra8in91qx6n8jydb8kwl2rnqaa2hix5pyawn6nvyqs815h9gx17"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -47,6 +47,12 @@
            (lambda _
              (substitute* "tests/dom.test"
                (("/usr/bin/printf") (which "printf")))
+             #t))
+         (add-before 'check 'pre-check
+           (lambda _
+             ;; In build environment, There is no /dev/tty
+             (substitute* "tests/base.test"
+               (("/dev/tty") "/dev/null"))
              #t)))))
     (native-inputs
      `(("which" ,which)))

gnu/packages/gnuzilla.scm

@@ -418,9 +418,9 @@ in C/C++.")
     (method hg-fetch)
     (uri (hg-reference
           (url "https://hg.mozilla.org/l10n/compare-locales/")
-          (changeset "RELEASE_3_3_0")))
+          (changeset "RELEASE_8_0_0")))
     (file-name "mozilla-compare-locales")
-    (sha256 (base32 "0biazbq7vbi99b99rfn4szwyx032dkpi09c9z4zs6f1br0f86iy1"))))
+    (sha256 (base32 "0052wq92sg4i776x407b5838jx9h3phl9xy69m2q34f31n3gdyk2"))))
 
 (define (mozilla-locale locale changeset hash-string)
   (origin
@@ -440,108 +440,102 @@ in C/C++.")
   (mozilla-locales
    ;;                      sha256                            changeset    locale
    ;;---------------------------------------------------------------------------
-   ("0pybx6j2ycbrr1xmv0spv19sd8a1dyzcs8kf6pzn71w8y6kiagcf" "35959cf2343c" "ach")
+   ("1q1p7nl97478hkf1msbbcdh98k6fn87xwqihbw8np00ll5gk9k4v" "97cf3c155484" "ach")
-   ("0dixmkha738w7fkx20nx95xkfyrqb9vczpy6m03qnqfvb76xaxj5" "e8dc1010f909" "af")
+   ("0sajpblp639l448xywx7xlybjr5dm0rfrzx511a8pa9wn7dma4mf" "46929b4dda4e" "af")
-   ("124j09va25gwfxdzyfixrli0skxv53c7niagjyp7g3a3kcv2lbhc" "4c67f6b96a7b" "an")
+   ("04s756aaf1yyli1dn1vfdjymgyjs1pz2n7jvz76j27x4nzdgss7l" "96ffd2b04ba3" "an")
-   ("0flgqll3xx0ym0zj0w9j2jw3fmhs6h9m4l5da6m0bpnk5ff80r06" "34cbea5f44a5" "ar")
+   ("16nw7slm7irsnjf81r6zl273kbzri8sdbimzgzxwm0vh6xr61rgs" "1c4231166ddf" "ar")
-   ("0kdb1yqfbfz508f4p77z3p1v6fwy190vs5ipj58hgdixjgbxkqay" "b4790b27633c" "ast")
+   ("0i0qrj4j8zjv55cisbmr21dp8mz933hc9wkpn3abz5k5pn84gpry" "bc4384b8be78" "ast")
-   ("1vm5xw6wg12pygswd3p0qpkaxyryah6nif5n15chb4sb42c1gqcm" "96d341bf49d4" "az")
+   ("1r77mmwg9x1jfa7g5lqa31rgyfrnix1zj80ibn5rq9gyhhsdrwbd" "dd56aead51fa" "az")
-   ("1j2qrrws51qij6haz5b77n5vzqhsxgs1ppqqw4mdrkacwvz4ciwh" "4adaede00646" "be")
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-   ("1vxkiwwni7470ywy99arxxa56ljkhjrhxslsp1l1l61g6gdbbspr" "49ec4f791806" "fr")
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-   ("0d8gwdcj0jpjv03nhjds8jrg86pg371xpylaibwri76wlyl7m54i" "faa761a5cfdc" "fy-NL")
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-   ("0nipbxx11a2sjadzhbi88vgknw5hzr4nqy2722q3kc1212jbi754" "5bd9466f9f9d" "ga-IE")
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-   ("0jj13i0ach85c975vaz2rr83mibs29ipssa7qsjkb0y2ch6xya1k" "c2d607e36cb5" "gn")
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-   ("1nhqbgzilcb0pr7941dxkhg079bf8v7ldikp1s5xli34wf9sabm2" "f34465d6ac1c" "gu-IN")
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-   ("11bh0541d996cfin1zy72l66753q94i4idgv2waf0h40h9g3z1bm" "c2ecb2762274" "he")
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-   ("1lslji7hh5lx5ig1xgfjh4cdindsgh3n2a7qlvzwz96gda43lvv4" "94d2bb10ee03" "hi-IN")
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-   ("1nx5yw00l25i3m3grdm29mi9mi7h0cy5qx02pypir754pk3hiwcc" "08df0d94edd5" "hr")
+   ("1b2jf83c500wm5wcdnijq0b7y4m8n6271smq8pygahn5nq17f0gq" "1a3039a52b8a" "hi-IN")
-   ("19yc9dk2pwqycynmx58d1ik6x4mnyfxscgr6sg676dpl613xd7nq" "21b614e77025" "hsb")
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-   ("0l3z64jlx6b6ivk1b5hwqyx9hm1m5721ywnb2m4zmg3g9fw4vn7f" "f82cad7170af" "hu")
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-   ("1sn0dxbbf2zwcpybwcw77qb4p0hf6fxapnsnn4avaab5g55dlgz4" "d94c30920396" "hy-AM")
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-   ("0c92cqxrhv4317kirmhpjk7mrq44yn6fp3v6syxnhz7xwxnhshjm" "6a5f176b0626" "ia")
+   ("0q0r076lq250d3vmnz9d92wj137c2v8i362c2avmkgp5zr3mcl0z" "2ea33335afdb" "hy-AM")
-   ("03gyg9gqsd6pwb9nydglhm46fi2wk2p2qygmhmrf8hnav3ba7n0r" "94e4302e0f85" "id")
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-   ("0ky8aaps92mn56rvkwn0i13wg8av8hzi1fvr0ahqhjcpj5sfgdwq" "eca348a59888" "is")
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-   ("01py0sfg7nljcsgpivryrvai4p4wzbcvhgc2ymr19r579nv1vw7g" "d541a6197359" "it")
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-   ("0iv7vmj43njmi7g1gjzsv68ax4j502d2wnkvbfz1rx11lrqs7yw1" "a5ab3a1d95b7" "ja")
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-   ("1sr9ccshcw6agbj4hbnpblxixb1jz0m36glas6f9ahxmi7m605si" "63763ffa5a94" "ja-JP-mac")
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-   ("1as33pzcsdkynrj16dv7w642vl6plbhk650am4l5djwm64f2rgms" "aa83e8555ddc" "ka")
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-   ("0cjfiwv0q5i8d7fpwb4m2w5ahq687dqjlwlicgpa443yi2zsxr4s" "33117723ceb1" "kk")
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-   ("0k5b56cv39aaxf9r0p9c27f3fp6yq2ffd4w6qmd0ibpl69sm629d" "aff7b2a7825e" "km")
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-   ("1a0zg96jgq4zn9cz0h2qwc0vv1fbkfzs5qrgabg62wqgz286jvvv" "ea91638cb1dd" "kn")
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-   ("0jhmv2n3yx55r6fg3myg7j1c1nhsv25g016m6lh2j023xbr723gp" "88821009b5b3" "ko")
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-   ("06bybgv4m4i7r9p0qld65j31vbrnljhsdj649dl93msv2r69ilif" "88685d5f07b3" "lij")
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-   ("1bzjf8smw6ngi88j5g3fawrg54m8fifbhshwjbgkpj7rnrpjgh4w" "e046c7ffa7d0" "lt")
+   ("0vagaiwy80bs1k3gkacshlzb5zchkcshx0ypwirvayc63sw4yl8l" "694b2a24e868" "lij")
-   ("18dmzmpavijb7fwzffas0j5nb6byqp8h6ki7hhf6qb35diqgfq6n" "c520ef4f576c" "lv")
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-   ("055zf7xj5h1h8mzxj1cjzhngpcvg2p5vs2dmffsa5zfprj02d0dm" "9e43723f18ad" "mk")
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-   ("1496fbyyzcl075gzcd3xy50h9jyhnzgb544k1scji56yhyfajacb" "ce615fef92c1" "mr")
+   ("0q8jxg1af22hs9wjdf0jd3bqk4rafxyzvsjl35k75am7l2y1fl3c" "9e482f6dd72c" "mk")
-   ("1wc1q8ksry181pvnysqsq4dhhsg5adw5vgqafmmq5sf6i2bwn2z0" "4fefe88cfaee" "ms")
+   ("1zsfzjrzbc58d30a9yz12h5vphywgpw8xg6y6zn3677a785dvr20" "1fd2763336a4" "mr")
-   ("0awf6mrdwdhy2yvxynssvp1zg1nc2fqbmg2d2bhjcib69zx944xw" "3987a06866fd" "my")
+   ("1rzygkkpn1a59daygd3hdaqph2np6sqvpgh68j0xr4il958ymnsm" "67ddab62dab4" "ms")
-   ("1hycvz7i4jd40hfs5abx6sgfdkafg0jhdgqih9b7lb08aqcl35pj" "2b3b8997d9a1" "nb-NO")
+   ("16jp6w5gizfxs7jvncg3ly13m59vqvh4rlmjd0q23m5g5ff9sklc" "3ed015b51bf3" "my")
-   ("048z1ib46izwryyy8l1x71kq4775n7l2ilbskhsyrbxqryma13k8" "f25324281615" "ne-NP")
+   ("1wfv023j67lb4iyf49fsknwm4z3xy0xqcf25b2nzanggxj26n01x" "d01801233a8f" "nb-NO")
-   ("1qkxqpyr4la9bn1bqsgc2h9869arglh9n2kwpkq6722jzdbynkz2" "04c7d32c57f6" "nl")
+   ("1946vfia58vbjfippb5pfsskbjj95w7hb340smn6ry2vmza99mxp" "582defb08fb2" "ne-NP")
-   ("08gnmdll55dbqj7qs63gq1kljbvg24nzns6q4m0av3sszsic0jv5" "5587520e5019" "nn-NO")
+   ("12w5ywh4c3s55y3zqc48cp1gcpwwjg444yfh1bghhhb9ni1xkh5i" "05f6359a29a6" "nl")
-   ("1yh2p4ipj5p2b7gh0xxj0n7ndvwn5bw2773ibrh7vz932mkzhhjn" "499386b02695" "oc")
+   ("17jb076320cgkw1ypwmws2vjxsqlv2ww8aaisa3j334vbrw1m4zx" "50b41a1ddded" "nn-NO")
-   ("0kjbnixjzv9hvyba4ll20gs76vx84pviy134fvpjp9lfjpnpib55" "31c01c325675" "pa-IN")
+   ("1y840j0v5zdgj94cbacy6j1snf44rynmzxq3yk8i26arcar62akl" "a6a138531a44" "oc")
-   ("0g61imvr4639bbydyi0kwc1il7l1gzlfij4ywx7hdcmq2x6vgb9v" "fb5f3b8dea09" "pl")
+   ("0jq1hq4xhqxpa26r8pb1bgbaljgfkhn9l6p5pbnslkllpbh70q6l" "e70a3afaef25" "pa-IN")
-   ("13n68d7z94d7943m6fwl4kizbqm3wp82xz69vng4w9vyqlvv7d41" "9a541cbdc748" "pt-BR")
+   ("1hih138skwy2gb8q10ngg6zalrk3aa3d549mg79gqzxbi5zy19fw" "e035f33389eb" "pl")
-   ("1j8afvrl1afmj2zixrp91rrhag5w4xw90raca1ic6mxyih9kvdi4" "edc959a685c2" "pt-PT")
+   ("1hhif4hx4k351wm1bzykzycfzb5q8msxmiwh5r1cy32rh8wkxwhh" "54098495f37f" "pt-BR")
-   ("0wf4a6q9nvcmam2g8ksbymjdnrz59pdr5nirfpjprfhifjmxx4nn" "d2699db715cd" "rm")
+   ("0gkjs12rxjml1m3mljskpz1gr6aph0c31nwpwdqybfg54w9qslib" "3fdf021f624e" "pt-PT")
-   ("1k9qalir5pbh490w1mxyq31yhy9hbxsyrrk11hwlwlgn6syp9nvp" "b5460a9017bc" "ro")
+   ("0anyvwd9v6mr8y3ww33s6qnxkawqn5lz65vrxx3m3kzky63ai1xk" "794f9374eb87" "rm")
-   ("1avy6wyfa5lbvy36wai6mwhhh6x1y8a0jyjk8hvjn52yfxj1gypk" "59ffa8ad047a" "ru")
+   ("1p4drj25gsfv7lwgm5saazh38iqrh53952n8i4bmxpn0nadbm2n5" "71ce18bcf6cc" "ro")
-   ("1cakhm4jxcw1ij0l1vhxw74hsp5wg68i3319dkdncyyc5a2s1qv9" "8b3c8a7ebdfa" "si")
+   ("17yssf4axd3zvncl4ka4wkfnwcn0z0arp3390vb9cps67na29p36" "3a9587227699" "ru")
-   ("0s534r09bqdfvw3q17y9b1035kzzlafjv656v73mqhyz3fkffsx5" "cb39dc77980e" "sk")
+   ("0xk6rksspcw1222v4rgk5a6gzrpx64k29hm7p9qkqwd70s34yj46" "c020582a72ce" "si")
-   ("1s58vgmnb9aiaiaqwwcivq3iyzpzj527w2aqh2nrh6xmaw7f43sr" "17d7969b1d9a" "sl")
+   ("1ax5ibydyn7sj208r66zcxlcr8dxdqrw28vqyjif4jx583rp4lfp" "745a699b7f51" "sk")
-   ("147qm7x5z8rkf24jpqvkdlqg0fjz1l3zwnaxvkh9y2jpzv7m0x7z" "c55b0e9ff99d" "son")
+   ("13rin7hm1dv8g0hbcv8mp2hiwpk1k5bhzvkqpqajkkik4lx523mc" "8e437e2351ef" "sl")
-   ("0nn4r1rxi8cy7x9nmn5ljd8gcsn2rjl2ma2j7waxkafkm4rs6n20" "2bb3808072da" "sq")
+   ("0yh5jkl5zw3f7x1w2w6zfj3dyvcl4wj1zv4di7qsq2nl2yyizf7x" "2d99e2eff94f" "son")
-   ("0jsb01b94z7qbm59yaj56nb7yx7a6hpgw8v6nzwhbvmnmcsird4p" "c323c0d02d61" "sr")
+   ("0vzq7s27jsdbw5k59wfykysg1kd8w229ab5d4zjdf30l59igkahh" "69bbdf07bd80" "sq")
-   ("1n7vv9y4sk3gig56rgfd2jk8jr2160grxk31bd1wkm7fvbndd259" "4220ce487cbc" "sv-SE")
+   ("1mwivvs8vrk6vjq6i33kwlrlisra7dy35521ayps9p2rz2dll4rr" "215df5c5125c" "sr")
-   ("06270mq7gajxfrsb8gqd25v2dac68ask5vvlh6kkkp3hrgy02vid" "6a1dbc2fe1d3" "ta")
+   ("0g97yz1rg5cfflj8vvq3sqliyvm06x818z9yldfh5rjg1y6n9fjd" "8be00a1a50d4" "sv-SE")
-   ("10az7pd3npa7n8wq0qywvsj2qrx9592i2wffs3rnc1fviv1i1q0y" "028505b5ecd1" "te")
+   ("0ii02jn3lh2i6d0s95whx9aj6w3x8axc7w1rlzj0lc2s9n52krz3" "170a84339dbe" "ta")
-   ("0yj0c3iyibb3jyypvyiyhbr9asxa48v0nq21kcf9gphi8fnyp5if" "e44d38b6a67b" "th")
+   ("1ss7symad2crapxjqc0xhc0n17l79r5vf7flvkgk7npjky4vb7nv" "72a79a304f7f" "te")
-   ("1qc4nvhw834lx7p304fxma0fjdr4xfj4lf69dhh6biqz795lx45p" "1e0771d95708" "tr")
+   ("11iqmg8zamgscnvs4n2xpw3g9azn6w38qs313wiwm86pyx6694ss" "8e91ce3064c5" "th")
-   ("1g4y2yq5xp61ncy7c08j7fqqr1jc0m1hjxmbg5659wzif3b3dkg4" "e3c96943e98f" "uk")
+   ("1zgkvn9flb8by62ip9r3gmpgxwgkww1zhml5mwa0djq3ppfdgi1c" "0f914d0cda56" "tl")
-   ("1zbi28z1c3p5il7ndixyjsv4nrimzq36zjvlmq10am38ycqr9df8" "f35da1b02691" "ur")
+   ("1filkhdak6dbrd83q602x1qw1703nlm53nm9gcyab8s16gsx6ylz" "62ca6a8eaeba" "tr")
-   ("1jrxjjj8k771y0wljqbadxdj4pasg0771jmg4l3hvpgs929i3j9g" "6fd2084b3efe" "uz")
+   ("0cgagdy0ixprk3knczdmkqxkmx4ybmshhh0956kxbd0iab0dfcf6" "f110ccac4cde" "trs")
-   ("1f8sqgxzgqmw6vzjv3f49lg43q09i3j62f471864vr71815agl8n" "33b5dfd0cd63" "vi")
+   ("1f1ghk67zwnwc5x3nk82vcv94nf8glngkfya1hg074q3088sj9pa" "56c0102d5f1c" "uk")
-   ("0ssnsbxw3q5k88fa081gkn1mbqn4j7bm6vb7yvz6h44j214xkz9x" "2d87c0740715" "xh")
+   ("0iyw1b2jjylkdwxv9sxvj4ikxl64sx612b2dvvmf1di8bw86w74r" "7d53bce5ae98" "ur")
-   ("0kd3mrvvgczhsmw4rvpxxxc71bb469ayr8r4azf7gc0y5nmlm950" "a2b6625688d3" "zh-CN")
+   ("1q83cp5pfgs8l03zirwi8r5qp8qyh4zvxdx1ilgaqqlyg42yql7c" "9b500e1a054d" "uz")
-   ("0qy1asyfplkyc89z3g3gfm7b32aka92350b3ayv9d9dcgwxmfdwz" "4d6e959a13d1" "zh-TW")))
+   ("1d4nkybz2hk64ay04k965b9lc5nhhpmzcs5ww3b6q4n93rf9c2z7" "2a000025928a" "vi")
-
+   ("1cnrsfnyl3sw3sxsggmjwydvphb2diy0vzknvxdhpnvq3ln18hga" "74724087c25b" "xh")
-(define (mozilla-patch file-name changeset hash)
+   ("1j6l66v1xw27z8w78mpsnmqgv8m277mf4r0hgqcrb4zx7xc2vqyy" "527e5e090608" "zh-CN")
-  "Return an origin for CHANGESET from the mozilla-esr60 repository."
+   ("1frwx35klpyz3sdwrkz7945ivb2dwaawhhyfnz4092h9hn7rc4ky" "6cd366ad2947" "zh-TW")))
-  (origin
-    (method url-fetch)
-    (uri (string-append "https://hg.mozilla.org/releases/mozilla-esr60/raw-rev/"
-                        changeset))
-    (sha256 (base32 hash))
-    (file-name file-name)))
 
 (define* (computed-origin-method gexp-promise hash-algo hash
                                  #:optional (name "source")
@@ -556,8 +550,8 @@ from forcing GEXP-PROMISE."
                       #:system system
                       #:guile-for-build guile)))
 
-(define %icecat-version "68.12.0-guix0-preview1")
+(define %icecat-version "78.3.1-guix0-preview1")
-(define %icecat-build-id "20200825000000") ;must be of the form YYYYMMDDhhmmss
+(define %icecat-build-id "20200926000000") ;must be of the form YYYYMMDDhhmmss
 
 ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball
 ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat'
@@ -579,11 +573,11 @@ from forcing GEXP-PROMISE."
                   "firefox-" upstream-firefox-version ".source.tar.xz"))
             (sha256
              (base32
-              "1k17pi4zh9hrvkzbw4rzzw879a15hpvwriylp75wl22rl7r2nsdf"))))
+              "1savwk91vhvg096w289xwpjvqbbd2ibfad90081hirlzd1kpvljz"))))
 
-         (upstream-icecat-base-version "68.12.0") ; maybe older than base-version
+         (upstream-icecat-base-version "78.3.1") ; maybe older than base-version
          ;;(gnuzilla-commit (string-append "v" upstream-icecat-base-version))
-         (gnuzilla-commit "15a7c3d991a670b6489d4f432b52a188358f4ca5")
+         (gnuzilla-commit "cd2af837fce69145effef83def6993d244887b03")
          (gnuzilla-source
           (origin
             (method git-fetch)
@@ -595,12 +589,12 @@ from forcing GEXP-PROMISE."
                                       (string-take gnuzilla-commit 8)))
             (sha256
              (base32
-              "0n7p067yay413iy0gzprz0xrdkcxj5f8ywhkcghhhzw1nwajckba"))))
+              "0266gp8vs4avlfdnr8dj7b47msxv1vkd0xpnifp04v4scvgj0yaj"))))
 
-         (makeicecat-patch
-          (local-file (search-patch "icecat-makeicecat.patch")))
          (gnuzilla-fixes-patch
-          (local-file (search-patch "icecat-use-older-reveal-hidden-html.patch"))))
+          (local-file (search-patch "icecat-use-older-reveal-hidden-html.patch")))
+         (makeicecat-patch
+          (local-file (search-patch "icecat-makeicecat.patch"))))
 
     (origin
       (method computed-origin-method)
@@ -644,10 +638,10 @@ from forcing GEXP-PROMISE."
 
                 (with-directory-excursion "/tmp/gnuzilla"
                   (make-file-writable "makeicecat")
-                  (invoke "patch" "--force" "--no-backup-if-mismatch"
-                          "-p1" "--input" #+makeicecat-patch)
                   (invoke "patch" "--force" "--no-backup-if-mismatch"
                           "-p1" "--input" #+gnuzilla-fixes-patch)
+                  (invoke "patch" "--force" "--no-backup-if-mismatch"
+                          "-p1" "--input" #+makeicecat-patch)
                   (patch-shebang "makeicecat")
                   (substitute* "makeicecat"
                     (("^FFMAJOR=(.*)" all ffmajor)
@@ -738,16 +732,16 @@ from forcing GEXP-PROMISE."
        ("glib" ,glib)
        ("gtk+" ,gtk+)
        ("gtk+-2" ,gtk+-2)
-       ("graphite2" ,graphite2)
+       ;; UNBUNDLE-ME! ("graphite2" ,graphite2)
        ("pango" ,pango)
        ("freetype" ,freetype)
-       ("harfbuzz" ,harfbuzz)
+       ;; UNBUNDLE-ME! ("harfbuzz" ,harfbuzz)
        ("libcanberra" ,libcanberra)
        ("libgnome" ,libgnome)
        ("libjpeg-turbo" ,libjpeg-turbo)
-       ("libogg" ,libogg)
+       ;; UNBUNDLE-ME! ("libogg" ,libogg)
-       ;; ("libtheora" ,libtheora) ; wants theora-1.2, not yet released
+       ;; UNBUNDLE-ME! ("libtheora" ,libtheora) ; wants theora-1.2, not yet released
-       ("libvorbis" ,libvorbis)
+       ;; UNBUNDLE-ME! ("libvorbis" ,libvorbis)
        ("libxft" ,libxft)
        ("libevent" ,libevent)
        ("libxinerama" ,libxinerama)
@@ -756,8 +750,8 @@ from forcing GEXP-PROMISE."
        ("libxt" ,libxt)
        ("libffi" ,libffi)
        ("ffmpeg" ,ffmpeg)
-       ("libvpx" ,libvpx)
+       ;; UNBUNDLE-ME! ("libvpx" ,libvpx)
-       ("icu4c" ,icu4c)
+       ("icu4c" ,icu4c-67)
        ("pixman" ,pixman)
        ("pulseaudio" ,pulseaudio)
        ("mesa" ,mesa)
@@ -767,11 +761,11 @@ from forcing GEXP-PROMISE."
        ;; UNBUNDLE-ME! ("nspr" ,nspr)
        ;; UNBUNDLE-ME! ("nss" ,nss)
        ("shared-mime-info" ,shared-mime-info)
-       ("sqlite" ,sqlite)
+       ;; UNBUNDLE-ME! ("sqlite" ,sqlite)
-       ("startup-notification" ,startup-notification)
        ("unzip" ,unzip)
        ("zip" ,zip)
-       ("zlib" ,zlib)))
+       ;; UNBUNDLE-ME! ("zlib" ,zlib)
+       ))
     (native-inputs
      ;; The following patches are specific to the Guix packaging of IceCat,
      ;; and therefore we prefer to leave them out of 'source', which should be
@@ -787,13 +781,13 @@ from forcing GEXP-PROMISE."
 
        ("patch" ,(canonical-package patch))
 
-       ("rust" ,rust)
+       ("rust" ,rust-1.41)
-       ("cargo" ,rust "cargo")
+       ("cargo" ,rust-1.41 "cargo")
-       ("rust-cbindgen" ,rust-cbindgen)
+       ("rust-cbindgen" ,rust-cbindgen-0.14)
        ("llvm" ,llvm)
        ("clang" ,clang)
        ("perl" ,perl)
-       ("node" ,node)
+       ("node" ,node-10.22)
        ("python" ,python)
        ("python-2" ,python-2)
        ("python2-pysqlite" ,python2-pysqlite)
@@ -812,22 +806,21 @@ from forcing GEXP-PROMISE."
        ;; practice somehow.  See <http://hydra.gnu.org/build/378133>.
        #:validate-runpath? #f
 
-       #:configure-flags `("--enable-default-toolkit=cairo-gtk3"
+       #:configure-flags `("--enable-default-toolkit=cairo-gtk3-wayland"
 
                            "--with-distribution-id=org.gnu"
 
-                           ;; Do not require addons in the global app
+                           ;; Do not require addons in the global app or
-                           ;; directory to be signed by Mozilla.
+                           ;; system directories to be signed by Mozilla.
-                           "--with-unsigned-addon-scopes=app"
+                           "--with-unsigned-addon-scopes=app,system"
+                           "--allow-addon-sideload"
 
-                           "--enable-startup-notification"
                            "--enable-pulseaudio"
 
                            "--disable-tests"
                            "--disable-updater"
                            "--disable-crashreporter"
                            "--disable-eme"
-                           "--disable-gconf"
 
                            ;; Building with debugging symbols takes ~5GiB, so
                            ;; disable it.
@@ -853,9 +846,9 @@ from forcing GEXP-PROMISE."
                            "--enable-official-branding"
 
                            ;; Avoid bundled libraries.
-                           "--with-system-zlib"
-                           "--with-system-bz2"
                            "--with-system-jpeg"        ; must be libjpeg-turbo
+                           ;; UNBUNDLE-ME! "--with-system-zlib"
+                           ;; UNBUNDLE-ME! "--with-system-bz2"
                            ;; UNBUNDLE-ME! "--with-system-libevent"
                            ;; UNBUNDLE-ME! "--with-system-ogg"
                            ;; UNBUNDLE-ME! "--with-system-vorbis"
@@ -951,8 +944,8 @@ from forcing GEXP-PROMISE."
                          ;;   * speex
                          ;;
                          "modules/freetype2"
-                         "modules/zlib"
                          ;; "media/libjpeg"  ; needed for now, because media/libjpeg/moz.build is referenced from config/external/moz.build
+                         ;; UNBUNDLE-ME! "modules/zlib"
                          ;; UNBUNDLE-ME! "ipc/chromium/src/third_party/libevent"
                          ;; UNBUNDLE-ME! "media/libvpx"
                          ;; UNBUNDLE-ME! "media/libogg"
@@ -1017,10 +1010,31 @@ from forcing GEXP-PROMISE."
            (lambda _
              (use-modules (guix build cargo-utils))
              (let ((null-hash "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"))
-               (substitute* '("Cargo.lock" "gfx/wr/Cargo.lock")
+               (for-each (lambda (file)
-                 (("(\"checksum .* = )\".*\"" all name)
+                           (format #t "patching checksums in ~a~%" file)
-                  (string-append name "\"" null-hash "\"")))
+                           (substitute* file
-               (generate-all-checksums "third_party/rust"))
+                             (("^checksum = \".*\"")
+                              (string-append "checksum = \"" null-hash "\""))))
+                         (find-files "." "Cargo.lock$"))
+               (for-each generate-all-checksums
+                         '("services"
+                           "js"
+                           "third_party/rust"
+                           "dom/media"
+                           "dom/webauthn"
+                           "toolkit"
+                           "gfx"
+                           "storage"
+                           "modules"
+                           "xpcom/rust"
+                           "media"
+                           "mozglue/static/rust"
+                           "netwerk"
+                           "remote"
+                           "intl"
+                           "servo"
+                           "security/manager/ssl"
+                           "build")))
              #t))
          (replace 'configure
            ;; configure does not work followed by both "SHELL=..." and
@@ -1120,6 +1134,10 @@ from forcing GEXP-PROMISE."
                     (libxscrnsaver-lib (string-append libxscrnsaver "/lib")))
                (wrap-program (car (find-files lib "^icecat$"))
                  `("XDG_DATA_DIRS" prefix (,gtk-share))
+                 ;; The following line is commented out because the icecat
+                 ;; package on guix has been observed to be unstable when
+                 ;; using wayland, and the bundled extensions stop working.
+                 ;;   `("MOZ_ENABLE_WAYLAND" = ("1"))
                  `("LD_LIBRARY_PATH" prefix (,pulseaudio-lib ,mesa-lib ,libxscrnsaver-lib)))
                #t))))))
     (home-page "https://www.gnu.org/software/gnuzilla/")
@@ -1129,7 +1147,7 @@ from forcing GEXP-PROMISE."
 software, which does not recommend non-free plugins and addons.  It also
 features built-in privacy-protecting features.
 
-WARNING: IceCat 68 has not yet been released by the upstream IceCat project.
+WARNING: IceCat 78 has not yet been released by the upstream IceCat project.
 This is a preview release, and does not currently meet the privacy-respecting
 standards of the IceCat project.")
     (license license:mpl2.0)     ;and others, see toolkit/content/license.html
@@ -1139,11 +1157,11 @@ standards of the IceCat project.")
        (cpe-version . ,(first (string-split version #\-)))))))
 
 ;; Update this together with icecat!
-(define %icedove-build-id "20200825000000") ;must be of the form YYYYMMDDhhmmss
+(define %icedove-build-id "20200926000000") ;must be of the form YYYYMMDDhhmmss
 (define-public icedove
   (package
     (name "icedove")
-    (version "68.12.0")
+    (version "78.3.1")
     (source icecat-source)
     (properties
      `((cpe-name . "thunderbird_esr")))
@@ -1169,10 +1187,15 @@ standards of the IceCat project.")
            (lambda _
              (use-modules (guix build cargo-utils))
              (let ((null-hash "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"))
-               (substitute* '("Cargo.lock" "gfx/wr/Cargo.lock")
+               (for-each (lambda (file)
-                 (("(\"checksum .* = )\".*\"" all name)
+                           (format #t "patching checksums in ~a~%" file)
-                  (string-append name "\"" null-hash "\"")))
+                           (substitute* file
-               (generate-all-checksums "third_party/rust"))
+                             (("^checksum = \".*\"")
+                              (string-append "checksum = \"" null-hash "\""))))
+                         (find-files "." "Cargo.lock$"))
+               (for-each generate-all-checksums
+                         '("third_party/rust"
+                           "toolkit/library/rust")))
              #t))
          ;; Fixes issue where each installation directory generates its own profile.
          ;; See e.g. https://trac.torproject.org/projects/tor/ticket/31457
@@ -1214,12 +1237,10 @@ standards of the IceCat project.")
                  (("mozilla.org") "guix.gnu.org")))
              ;; Remove other mentions of Thunderbird in user-visible text.
              (with-directory-excursion "comm/mail/base/content"
-               (substitute* '("newInstallPage.xhtml"
+               (substitute* '("overrides/app-license-name.html")
-                              "overrides/app-license-name.html"
-                              "newInstall.xul")
                  (("Thunderbird") "Icedove")))
              (with-directory-excursion "comm/mail/components/"
-               (substitute* '("mailGlue.js"
+               (substitute* '("MailGlue.jsm"
                               "extensions/schemas/addressBook.json"
                               "extensions/schemas/tabs.json"
                               "extensions/schemas/cloudFile.json"
@@ -1229,14 +1250,9 @@ standards of the IceCat project.")
                               "im/messages/mail/Info.plist"
                               "enterprisepolicies/moz.build"
                               "enterprisepolicies/helpers/moz.build"
-                              "enterprisepolicies/schemas/moz.build"
+                              "enterprisepolicies/schemas/moz.build")
-                              "preferences/chat.inc.xul")
                  (("Thunderbird") "Icedove")))
-             (substitute* "comm/calendar/lightning/lightning-packager.mk"
-               (("ifeq \\(thunderbird")
-                "ifeq (icedove"))
              (substitute* '("comm/mailnews/base/prefs/content/accountUtils.js"
-                            "comm/mailnews/extensions/newsblog/content/feed-subscriptions.js"
                             "comm/common/src/customizeToolbar.js")
                (("AppConstants.MOZ_APP_NAME (.)= \"thunderbird" _ e)
                 (format #f "AppConstants.MOZ_APP_NAME ~a= \"icedove" e)))
@@ -1309,8 +1325,7 @@ standards of the IceCat project.")
                      "ac_add_options --disable-debug\n"
                      "ac_add_options --disable-debug-symbols\n"
                      "ac_add_options --disable-elf-hack\n"
-                     "ac_add_options --disable-gconf\n"
+                     "ac_add_options --disable-jit\n"
-                     "ac_add_options --disable-ion\n"
                      "ac_add_options --disable-necko-wifi\n"
                      "ac_add_options --disable-official-branding\n"
                      "ac_add_options --disable-tests\n"
@@ -1318,16 +1333,13 @@ standards of the IceCat project.")
                      "ac_add_options --disable-webrtc\n"
                      "ac_add_options --enable-application=comm/mail\n"
                      "ac_add_options --enable-calendar\n"
-                     "ac_add_options --enable-content-sandbox\n"
                      "ac_add_options --enable-default-toolkit=\"cairo-gtk3\"\n"
                      "ac_add_options --enable-optimize\n"
                      "ac_add_options --enable-pulseaudio\n"
                      "ac_add_options --enable-release\n"
-                     "ac_add_options --enable-startup-notification\n"
                      "ac_add_options --enable-strip\n"
                      "ac_add_options --enable-system-ffi\n"
                      "ac_add_options --enable-system-pixman\n"
-                     "ac_add_options --enable-system-sqlite\n"
                      "ac_add_options --prefix=" out "\n"
                      "ac_add_options --with-clang-path=" (assoc-ref %build-inputs "clang") "/bin/clang\n"
                      "ac_add_options --with-distribution-id=org.gnu\n"
@@ -1398,7 +1410,7 @@ standards of the IceCat project.")
        ("gtk+" ,gtk+)
        ("gtk+-2" ,gtk+-2)
        ("hunspell" ,hunspell)
-       ("icu4c" ,icu4c)
+       ("icu4c" ,icu4c-67)
        ("libcanberra" ,libcanberra)
        ("libevent" ,libevent)
        ("libffi" ,libffi)
@@ -1414,7 +1426,7 @@ standards of the IceCat project.")
        ("mesa" ,mesa)
        ("mit-krb5" ,mit-krb5)
        ("nspr" ,nspr)
-       ("nss" ,nss)
+       ("nss" ,nss-3.57)
        ("pango" ,pango)
        ("pixman" ,pixman)
        ("pulseaudio" ,pulseaudio)
@@ -1429,28 +1441,28 @@ standards of the IceCat project.")
         ;; in the Thunderbird release tarball.  We don't use the release
         ;; tarball because it duplicates the Icecat sources and only adds the
         ;; "comm" directory, which is provided by this repository.
-        ,(let ((changeset "b41cdff70b185358d9c4c1d4a36cfad15a24f001"))
+        ,(let ((changeset "00912779d73faef4277c57fe99aa5259b11d244d"))
            (origin
              (method hg-fetch)
              (uri (hg-reference
-                   (url "https://hg.mozilla.org/releases/comm-esr68")
+                   (url "https://hg.mozilla.org/releases/comm-esr78")
                    (changeset changeset)))
              (file-name (string-append "thunderbird-" version "-checkout"))
              (sha256
               (base32
-               "1xvky8p5r41mxdyg9amydy94p51wmmdwdz0zq2vzspr9viixf7xm")))))
+               "12isvk6q8miwn81kimrgcmjh4vsmdbbx93q9pafgxlx3p92s5v8h")))))
        ("autoconf" ,autoconf-2.13)
-       ("cargo" ,rust "cargo")
+       ("cargo" ,rust-1.41 "cargo")
        ("clang" ,clang)
        ("llvm" ,llvm)
        ("nasm" ,nasm)
-       ("node" ,node)
+       ("node" ,node-10.22)
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)
        ("python" ,python)
        ("python2" ,python-2.7)
-       ("rust" ,rust)
+       ("rust" ,rust-1.41)
-       ("rust-cbindgen" ,rust-cbindgen)
+       ("rust-cbindgen" ,rust-cbindgen-0.14)
        ("which" ,which)
        ("yasm" ,yasm)))
     (home-page "https://www.thunderbird.net")

gnu/packages/golang.scm

@@ -559,6 +559,30 @@ per-goroutine.")
     (home-page "https://github.com/jtolds/gls")
     (license license:expat)))
 
+(define-public go-github-com-saracen-walker
+  (package
+    (name "go-github-com-saracen-walker")
+    (version "0.1.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/saracen/walker")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1rq1lrp99lx7k1ysbfznn4c1iagnxdhb4lnnklsadnnzi3gvygqz"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "github.com/saracen/walker"))
+    (inputs
+     `(("go-golang-org-x-sync" ,go-golang-org-x-sync)))
+    (home-page "https://github.com/saracen/walker")
+    (synopsis "Faster, parallel version of Go's filepath.Walk")
+    (license license:expat)
+    (description "The @code{walker} function is a faster, parallel version, of
+@code{filepath.Walk}")))
+
 (define-public go-github-com-tj-docopt
   (package
     (name "go-github-com-tj-docopt")
@@ -741,6 +765,36 @@ for the Go language.")
 processing.")
       (license license:bsd-3))))
 
+(define-public go-golang-org-x-sync
+  (let ((commit "6e8e738ad208923de99951fe0b48239bfd864f28")
+        (revision "1"))
+    (package
+      (name "go-golang-org-x-sync")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://go.googlesource.com/sync")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1avk27pszd5l5df6ff7j78wgla46ir1hhy2jwfl9a3c0ys602yx9"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "golang.org/x/sync"
+         #:tests? #f
+         ;; Source-only package
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'build))))
+      (synopsis "Additional Go concurrency primitives")
+      (description "This package provides Go concurrency primitives in addition
+to the ones provided by the language and “sync” and “sync/atomic”
+packages.")
+      (home-page "https://go.googlesource.com/sync/")
+      (license license:bsd-3))))
+
 (define-public go-golang-org-x-sys
   (let ((commit "c709ea063b76879dc9915358f55d4d77c16ab6d5")
         (revision "6"))
@@ -5238,9 +5292,9 @@ errors (warnings).")
      `(("go-gopkg-in-check-v1" ,go-gopkg-in-check-v1)))
     (home-page "https://github.com/go-git/go-billy/")
     (synopsis "File system abstraction for Go")
-    (description "Billy implements an interface based on the os standard
+    (description "Billy implements an interface based on the OS's standard
-library, allowing to develop applications without dependency on the underlying
+library to develop applications without depending on the underlying storage.
-storage.  Makes it virtually free to implement mocks and testing over
+This makes it virtually free to implement mocks and testing over
 file system operations.")
     (license license:asl2.0)))
 

gnu/packages/gps.scm

@@ -151,7 +151,7 @@ between two other data points.")
 (define-public gama
   (package
     (name "gama")
-    (version "2.09")
+    (version "2.10")
     (source
       (origin
         (method url-fetch)
@@ -159,7 +159,7 @@ between two other data points.")
                             version ".tar.gz"))
         (sha256
          (base32
-          "0c1b28frl6109arj09v4zr1xs859krn8871mkvis517g5pb55dc9"))))
+          "14im3ahh849rildvs4qsk009jywf9w84vcmh7w44ajmlwcw7xiys"))))
     (build-system gnu-build-system)
     (arguments '(#:parallel-tests? #f)) ; race condition
     (native-inputs

gnu/packages/graph.scm

@@ -121,34 +121,6 @@ more.")
     (home-page "https://pypi.org/project/python-igraph/")
     (synopsis "Python bindings for the igraph network analysis library")))
 
-(define-public r-rgraphviz
-  (package
-    (name "r-rgraphviz")
-    (version "2.32.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "Rgraphviz" version))
-       (sha256
-        (base32
-         "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
-    (properties `((upstream-name . "Rgraphviz")))
-    (build-system r-build-system)
-    ;; FIXME: Rgraphviz bundles the sources of an older variant of
-    ;; graphviz.  It does not build with the latest version of graphviz, so
-    ;; we do not add graphviz to the inputs.
-    (inputs `(("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-graph" ,r-graph)))
-    (native-inputs
-     `(("pkg-config" ,pkg-config)))
-    (home-page "https://bioconductor.org/packages/Rgraphviz")
-    (synopsis "Plotting capabilities for R graph objects")
-    (description
-     "This package interfaces R with the graphviz library for plotting R graph
-objects from the @code{graph} package.")
-    (license license:epl1.0)))
-
 (define-public r-rbiofabric
   (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
         (revision "1"))

gnu/packages/graphics.scm

@@ -22,6 +22,7 @@
 ;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2020 Raghav Gururajan <raghavgururajan@disroot.org>
 ;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2020 Gabriel Arazas <foo.dogsquared@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -614,6 +615,39 @@ NOTE: This older version of Blender is the last release that does not require
 OpenGL 3.  It is retained for use with older computers.")
     (license license:gpl2+)))
 
+(define-public goxel
+  (package
+    (name "goxel")
+    (version "0.10.6")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/guillaumechereau/goxel")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1wmxy5wfk1xrqgz0y0zcr4vkddylqc70cv4vzk117x6whjnldsm3"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f
+       #:phases (modify-phases %standard-phases (delete 'configure))
+       #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
+                          "release")))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("gtk3" ,gtk+)
+       ("glfw" ,glfw)
+       ("scons" ,scons)))
+    (home-page "https://goxel.xyz/")
+    (synopsis "Voxel editor")
+    (description
+     "Goxel is a voxel editor that features unlimited scene size, unlimited
+history buffer, 24-bit RGB colors, layers, procedural rendering, ray tracing,
+and export to various formats including the format used by Magicavoxel.")
+    (license license:gpl3+)))
+
 (define-public assimp
   (package
     (name "assimp")
@@ -1208,7 +1242,7 @@ realistic reflections, shading, perspective and other effects.")
        ("python" ,python-2)
        ("cython" ,python2-cython)))
     (native-inputs
-     `(("pandoc" ,ghc-pandoc)
+     `(("pandoc" ,pandoc)
        ("bison" ,bison)
        ("flex" ,flex)
        ("doxygen" ,doxygen)

gnu/packages/groff.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2019 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
@@ -191,17 +191,21 @@ is usually the formatter of \"man\" documentation pages.")
       (build-system gnu-build-system)
       (arguments
        `(#:test-target "test"
-         #:make-flags
-         (list (string-append "INSTALLDIR="
-                              (assoc-ref %outputs "out") "/bin"))
          #:phases
          (modify-phases %standard-phases
            (delete 'configure)
-           (add-before 'install 'pre-install
+           (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
-               (mkdir-p (string-append (assoc-ref outputs "out")
+               (let ((out (assoc-ref outputs "out")))
-                                       "/bin"))
+                 (install-file "roffit" (string-append out "/bin"))
-               #t)))))
+                 (install-file "roffit.1" (string-append out "/share/man/man1"))
+                 #t)))
+           (add-after 'install 'wrap-program
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((out (assoc-ref outputs "out")))
+                 (wrap-program (string-append out "/bin/roffit")
+                   `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB"))))
+                 #t))))))
       (native-inputs `(("html-tree" ,perl-html-tree))) ; for test
       (inputs
        `(("perl" ,perl)))

gnu/packages/gstreamer.scm

@@ -6,7 +6,7 @@
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2020 Leo Prikler <leo.prikler@student.tugraz.at>
 ;;;
@@ -360,14 +360,14 @@ http://www.tux.org/~ricdude/overview.html")
 (define-public orc
   (package
     (name "orc")
-    (version "0.4.31")
+    (version "0.4.32")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gstreamer.freedesktop.org/data/src/"
                                   "orc/orc-" version ".tar.xz"))
               (sha256
                (base32
-                "0xb0c7q3xv1ldmz5ipybazb01gy3cijj8622dcx7rbm9lq85zax0"))))
+                "1w0qmyj3v9sb2g7ff39pp38b9850y9hyy0bag26ifrby5f7ksvm6"))))
     (build-system meson-build-system)
     (arguments
      `(#:phases

gnu/packages/gtk.scm

@@ -1217,7 +1217,7 @@ library.")
         (base32 "1xlfl0fm5mgv53lr8xjv2kqsk3bz67qkk6qzvbrqmbvbvvbqp9wp"))))
     (propagated-inputs
      `(("cairo" ,cairo)
-       ("sigc++" ,libsigc++-2)))))
+       ("sigc++" ,libsigc++)))))
 
 (define-public pangomm
   (package

gnu/packages/guile-xyz.scm

@@ -1621,15 +1621,16 @@ The library is shipped with documentation in Info format and usage examples.")
 (define-public guile-wisp
   (package
     (name "guile-wisp")
-    (version "1.0.2")
+    (version "1.0.3")
     (source (origin
-              (method url-fetch)
+              (method hg-fetch)
-              (uri (string-append "https://bitbucket.org/ArneBab/"
+              (uri (hg-reference
-                                  "wisp/downloads/wisp-"
+                    (url "https://hg.sr.ht/~arnebab/wisp")
-                                  version ".tar.gz"))
+                    (changeset (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "03pz7pj9jyallynhflp5s7qax8dj1fs8la434wrfgz7g1kgjnvf6"))))
+                "10g97jz3ahpb5mg933ajsc3pa9jxlg14f42yf01qwx0dwq1b06d5"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((guix build gnu-build-system)
@@ -1643,11 +1644,9 @@ The library is shipped with documentation in Info format and usage examples.")
                            (guix build emacs-utils))
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'support-guile-3.0
+         (replace 'bootstrap
            (lambda _
-             (substitute* "configure"
+             (invoke "autoreconf" "-vif")
-               (("_guile_versions_to_search=\"2.2")
-                "_guile_versions_to_search=\"3.0 2.2"))
              #t))
          (add-before 'configure 'patch-/usr/bin/env
            (lambda _
@@ -1689,7 +1688,9 @@ The library is shipped with documentation in Info format and usage examples.")
     (inputs
      `(("guile" ,guile-3.0)))
     (native-inputs
-     `(("emacs" ,emacs-minimal)
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("emacs" ,emacs-minimal)
        ("python" ,python)
        ("pkg-config" ,pkg-config)))
     (synopsis "Whitespace to lisp syntax for Guile")

gnu/packages/guile.scm

@@ -420,11 +420,13 @@ GNU@tie{}Guile.  Use the @code{(ice-9 readline)} module and call its
   ;; A procedure that rewrites the dependency tree of the given package to use
   ;; GUILE-2.0 instead of GUILE-3.0.
   (package-input-rewriting `((,guile-3.0 . ,guile-2.0))
-                           (guile-variant-package-name "guile2.0")))
+                           (guile-variant-package-name "guile2.0")
+                           #:deep? #f))
 
 (define package-for-guile-2.2
   (package-input-rewriting `((,guile-3.0 . ,guile-2.2))
-                           (guile-variant-package-name "guile2.2")))
+                           (guile-variant-package-name "guile2.2")
+                           #:deep? #f))
 
 (define-syntax define-deprecated-guile3.0-package
   (lambda (s)
@@ -821,7 +823,7 @@ Guile's foreign function interface.")
 (define-public guile-lzlib
   (package
     (name "guile-lzlib")
-    (version "0.0.1")
+    (version "0.0.2")
     (source
      (origin
        (method url-fetch)
@@ -831,7 +833,7 @@ Guile's foreign function interface.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0rdmszn1qix085ci2mddwq5cypipc004fk7arrrkgn9bv39hazza"))))
+         "11sggvncyx08ssp1s5xii4d6nskh1qwqihnbpzzvkrs7sivxn8w6"))))
     (build-system gnu-build-system)
     (arguments
      '(#:make-flags

gnu/packages/haskell-apps.scm

@@ -775,7 +775,7 @@ too slow and you'll get wound up in the scroll and crushed.")
 (define-public shellcheck
   (package
     (name "shellcheck")
-    (version "0.7.0")
+    (version "0.7.1")
     (source
      (origin
        (method url-fetch)
@@ -783,7 +783,7 @@ too slow and you'll get wound up in the scroll and crushed.")
              "https://hackage.haskell.org/package/ShellCheck/ShellCheck-"
              version ".tar.gz"))
        (sha256
-        (base32 "1vx895cp5k5h0680xfwj74lk97m9y627n965x6srds0gfnbkzy9s"))
+        (base32 "06m4wh891nah3y0br4wh3adpsb16zawkb2ijgf1vcz61fznj6ps1"))
        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system haskell-build-system)
     (inputs