Merge branch 'master' into ungrafting

author: Marius Bakke <marius@gnu.org> 2020-12-13 01:10:06 +0100
committer: Marius Bakke <marius@gnu.org> 2020-12-13 01:10:06 +0100
commit: a7737f0ead2293536b9d0ba253de4673378a0ffa (patch)
tree: cf80318b0a9903aa56a69c316659a52f94abbe27
parent: ba47c83570b6d1824738ef5ff8580e7581990699 (diff)
parent: 1adeb744560af94687eb7c3780c7145c52674070 (diff)
download: guix-a7737f0ead2293536b9d0ba253de4673378a0ffa.tar.gz
105 files changed, 4901 insertions, 1921 deletions
diff --git a/Makefile.am b/Makefile.am
index 1a3ca227a4..9803ba5dc7 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -39,6 +39,7 @@ do_subst = $(SED)					\
   -e 's,[@]GUILE[@],$(GUILE),g'				\
   -e 's,[@]guilemoduledir[@],$(guilemoduledir),g'	\
   -e 's,[@]guileobjectdir[@],$(guileobjectdir),g'	\
+  -e 's,[@]abs_top_builddir[@],$(abs_top_builddir),g'	\
   -e 's,[@]localedir[@],$(localedir),g'
 
 scripts/guix: scripts/guix.in Makefile
diff --git a/config-daemon.ac b/config-daemon.ac
index 50ead355a8..85caee269b 100644
--- a/config-daemon.ac
+++ b/config-daemon.ac
@@ -13,7 +13,7 @@ if test "x$guix_build_daemon" = "xyes"; then
   GUIX_ASSERT_CXX11
 
   AC_PROG_RANLIB
-  AC_CONFIG_HEADER([nix/config.h])
+  AC_CONFIG_HEADERS([nix/config.h])
 
   dnl Use 64-bit file system calls so that we can support files > 2 GiB.
   AC_SYS_LARGEFILE
@@ -34,7 +34,6 @@ if test "x$guix_build_daemon" = "xyes"; then
   dnl Look for SQLite, a required dependency.
   PKG_CHECK_MODULES([SQLITE3], [sqlite3 >= 3.6.19])
 
-  AC_DEFINE([NIX_VERSION], ["0.0.0"], [Fake Nix version number.])
   AC_DEFINE_UNQUOTED([SYSTEM], ["$guix_system"],
     [Guix host system type--i.e., platform and OS kernel tuple.])
 
diff --git a/configure.ac b/configure.ac
index 942e84164a..a5bdf24e93 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,7 +1,7 @@
 #                                               -*- Autoconf -*-
 # Process this file with autoconf to produce a configure script.
 
-AC_PREREQ(2.68)
+AC_PREREQ([2.69])
 AC_INIT([GNU Guix],
   [m4_esyscmd([build-aux/git-version-gen .tarball-version])],
   [bug-guix@gnu.org], [guix],
@@ -29,35 +29,35 @@ GUIX_ASSERT_SUPPORTED_SYSTEM
 AM_CONDITIONAL([CROSS_COMPILING], [test "x$cross_compiling" = "xyes"])
 
 AC_ARG_WITH(store-dir,
-  AC_HELP_STRING([--with-store-dir=PATH],
+  AS_HELP_STRING([--with-store-dir=PATH],
     [file name of the store (defaults to /gnu/store)]),
   [storedir="$withval"],
   [storedir="/gnu/store"])
 AC_SUBST(storedir)
 
 AC_ARG_WITH([bash-completion-dir],
-  AC_HELP_STRING([--with-bash-completion-dir=DIR],
+  AS_HELP_STRING([--with-bash-completion-dir=DIR],
     [name of the Bash completion directory]),
   [bashcompletiondir="$withval"],
   [bashcompletiondir='${sysconfdir}/bash_completion.d'])
 AC_SUBST([bashcompletiondir])
 
 AC_ARG_WITH([zsh-completion-dir],
-  AC_HELP_STRING([--with-zsh-completion-dir=DIR],
+  AS_HELP_STRING([--with-zsh-completion-dir=DIR],
     [name of the Zsh completion directory]),
   [zshcompletiondir="$withval"],
   [zshcompletiondir='${datadir}/zsh/site-functions'])
 AC_SUBST([zshcompletiondir])
 
 AC_ARG_WITH([fish-completion-dir],
-  AC_HELP_STRING([--with-fish-completion-dir=DIR],
+  AS_HELP_STRING([--with-fish-completion-dir=DIR],
     [name of the Fish completion directory]),
   [fishcompletiondir="$withval"],
   [fishcompletiondir='${datadir}/fish/vendor_completions.d'])
 AC_SUBST([fishcompletiondir])
 
 AC_ARG_WITH([selinux-policy-dir],
-  AC_HELP_STRING([--with-selinux-policy-dir=DIR],
+  AS_HELP_STRING([--with-selinux-policy-dir=DIR],
     [name of the SELinux policy directory]),
   [selinux_policydir="$withval"],
   [selinux_policydir='${datadir}/selinux/'])
diff --git a/doc/guix.texi b/doc/guix.texi
index fc57f4f537..38927bc0b5 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -11291,6 +11291,25 @@ in Guix.
 @cindex OCaml
 Import metadata from the @uref{https://opam.ocaml.org/, OPAM} package
 repository used by the OCaml community.
+
+Additional options include:
+
+@table @code
+@item --recursive
+@itemx -r
+Traverse the dependency graph of the given upstream package recursively
+and generate package expressions for all those packages that are not yet
+in Guix.
+@item --repo
+Select the given repository (a repository name).  Possible values include:
+@itemize
+@item @code{opam}, the default opam repository,
+@item @code{coq} or @code{coq-released}, the stable repository for coq packages,
+@item @code{coq-core-dev}, the repository that contains development versions of coq,
+@item @code{coq-extra-dev}, the repository that contains development versions
+      of coq packages.
+@end itemize
+@end table
 @end table
 
 The structure of the @command{guix import} code is modular.  It would be
@@ -15334,6 +15353,14 @@ The TCP port to listen for connections.
 The host (and thus, network interface) to listen to.  Use
 @code{"0.0.0.0"} to listen on all the network interfaces.
 
+@item @code{advertise?} (default: @code{#f})
+When true, advertise the service on the local network @i{via} the DNS-SD
+protocol, using Avahi.
+
+This allows neighboring Guix devices with discovery on (see
+@code{guix-configuration} above) to discover this @command{guix publish}
+instance and to automatically download substitutes from it.
+
 @item @code{compression} (default: @code{'(("gzip" 3))})
 This is a list of compression method/level tuple used when compressing
 substitutes.  For example, to compress all substitutes with @emph{both} lzip
@@ -25695,6 +25722,9 @@ Owner's group of the @code{cuirass} process.
 Number of seconds between the poll of the repositories followed by the
 Cuirass jobs.
 
+@item @code{queue-size} (default: @code{1})
+Size of the database writer queue.
+
 @item @code{database} (default: @code{"/var/lib/cuirass/cuirass.db"})
 Location of sqlite database which contains the build results and previously
 added specifications.
diff --git a/etc/guix-daemon.cil.in b/etc/guix-daemon.cil.in
index cc8999d9a8..4f52157354 100644
--- a/etc/guix-daemon.cil.in
+++ b/etc/guix-daemon.cil.in
@@ -167,7 +167,9 @@
          (process (fork execmem setrlimit setpgid setsched)))
   (allow guix_daemon_t
          guix_daemon_exec_t
-         (file (execute execute_no_trans read open entrypoint map)))
+         (file (execute
+                execute_no_trans read write open entrypoint map
+                getattr link unlink)))
 
   ;; TODO: unknown
   (allow guix_daemon_t
diff --git a/etc/news.scm b/etc/news.scm
index 16bcd0450b..8cd1c89837 100644
--- a/etc/news.scm
+++ b/etc/news.scm
@@ -20,6 +20,7 @@
  (entry (commit "79f9dee3c4c0e6d21066f142116a537207ae7ba4")
         (title (en "Local substitute servers discovery is now supported")
                (de "Substitutserver können jetzt im lokalen Netz erkannt werden")
+               (es "Los servidores de sustituciones se pueden descubrir localmente")
                (fr "La découverte des serveurs de substituts locaux est désormais supportée"))
         (body
          (en "The @command{guix-daemon} can now discover local substitute
@@ -34,6 +35,12 @@ gefunden, die mit der Befehlszeilenoption @option{--advertise} gestartet
 wurden.  Die Ermittlung im Netzwerk verfügbarer Substitutserver baut auf den
 Protokollen mDNS und DNS-SD auf.  Derzeit wird dazu die Bibliothek Guile-Avahi
 benutzt.")
+         (es "El daemon @command{guix-daemon} ahora puede descubrir servidores
+de sustituciones locales cuando se le proporciona la opción
+@option{--discover}.  Únicamente se descubrirán los servidores de
+sustituciones que se hayan arrancado con la opción @option{--advertise}. La
+búsqueda en la red se basa en los protocolos mDNS y DNS-SD, actualmente
+mediante el uso de la biblioteca Guile-Avahi.")
          (fr "Le @command{guix-daemon} peut désormais découvrir les serveurs
 de substituts locaux lorsque l'option @option{--discover} est passée.  Seuls
 les serveurs de substituts démarrés avec l'option @option{--advertise} seront
@@ -42,7 +49,8 @@ l'instant grâce à la librairie Guile-Avahi.")))
 
  (entry (commit "a9a2fdaabcc78e7a54d9a6bcfa4ee3de308e9a90")
         (title (en "Logical Volume Manager (LVM) now supported on Guix System")
-               (de "Logical Volume Manager (LVM) wird jetzt auf Guix System unterstützt"))
+               (de "Logical Volume Manager (LVM) wird jetzt auf Guix System unterstützt")
+               (es "El sistema Guix ahora implementa también volúmenes lógicos LVM"))
         (body
          (en "On Guix System, the new @code{lvm-device-mapping} variable
 allows you to declare ``mapped devices'' for LVM, the Linux Logical Volume
@@ -70,7 +78,21 @@ Datenträgergruppe (Volume Group) „vg0“ wie folgt deklariert werden:
   (type lvm-device-mapping))
 @end lisp
 
-Siehe @command{info \"(guix.de) Zugeordnete Geräte\"} für nähere Informationen.")))
+Siehe @command{info \"(guix.de) Zugeordnete Geräte\"} für nähere Informationen.")
+         (es "En el sistema Guix, la nueva variable @code{lvm-device-mapping}
+le permite declarar «dispositivos traducidos» para LVM, el gestor de volúmenes
+lógicos de Linux. A continuación se muestra un ejemplo con la declaración de
+los volúmenes lógicos «alfa» y «beta» del grupo de volúmenes «vg0»:
+
+@lisp
+(mapped-device
+  (source \"vg0\")
+  (target (list \"vg0-alfa\" \"vg0-beta\"))
+  (type lvm-device-mapping))
+@end lisp
+
+Véase @command{info \"(guix.es) Dispositivos traducidos\"} para obtener más
+información.")))
 
  (entry (commit "3b6e4e5fd05e72b8a32ff1a2d5e21464260e21e6")
         (title (en "List of substitute keys is now declarative on Guix System")
diff --git a/gnu/installer.scm b/gnu/installer.scm
index f401b242f8..7863edbb67 100644
--- a/gnu/installer.scm
+++ b/gnu/installer.scm
@@ -266,6 +266,13 @@ selected keymap."
           (compute (lambda _
                      ((installer-network-page current-installer)))))
 
+         ;; Ask whether to enable substitute server discovery.
+         (installer-step
+          (id 'substitutes)
+          (description (G_ "Substitute server discovery"))
+          (compute (lambda _
+                     ((installer-substitutes-page current-installer)))))
+
          ;; Prompt for users (name, group and home directory).
          (installer-step
           (id 'user)
diff --git a/gnu/installer/newt.scm b/gnu/installer/newt.scm
index a1cbeca49a..4f7fc6f4dc 100644
--- a/gnu/installer/newt.scm
+++ b/gnu/installer/newt.scm
@@ -30,6 +30,7 @@
   #:use-module (gnu installer newt page)
   #:use-module (gnu installer newt partition)
   #:use-module (gnu installer newt services)
+  #:use-module (gnu installer newt substitutes)
   #:use-module (gnu installer newt timezone)
   #:use-module (gnu installer newt user)
   #:use-module (gnu installer newt utils)
@@ -101,6 +102,9 @@ problem. The backtrace is displayed below. Please report it by email to \
 (define (network-page)
   (run-network-page))
 
+(define (substitutes-page)
+  (run-substitutes-page))
+
 (define (hostname-page)
   (run-hostname-page))
 
@@ -130,6 +134,7 @@ problem. The backtrace is displayed below. Please report it by email to \
    (locale-page locale-page)
    (menu-page menu-page)
    (network-page network-page)
+   (substitutes-page substitutes-page)
    (timezone-page timezone-page)
    (hostname-page hostname-page)
    (user-page user-page)
diff --git a/gnu/installer/newt/substitutes.scm b/gnu/installer/newt/substitutes.scm
new file mode 100644
index 0000000000..938cb1a53b
--- /dev/null
+++ b/gnu/installer/newt/substitutes.scm
@@ -0,0 +1,43 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2020 Mathieu Othacehe <othacehe@gnu.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu installer newt substitutes)
+  #:use-module (gnu installer substitutes)
+  #:use-module (gnu installer utils)
+  #:use-module (guix i18n)
+  #:use-module (newt)
+  #:use-module (ice-9 match)
+  #:export (run-substitutes-page))
+
+(define* (run-substitutes-page)
+  (match (current-clients)
+    (()
+     (case (choice-window
+            (G_ "Substitute server discovery.")
+            (G_ "Enable") (G_ "Disable")
+            (G_ " By turning this option on, you allow Guix to fetch \
+substitutes (pre-built binaries) during installation from servers \
+discovered on your local area network (LAN) in addition to the official \
+server.  This can increase download throughput.
+
+ There are no security risks: only genuine substitutes may be retrieved from \
+those servers.  However, eavesdroppers on your LAN may be able to see what \
+software you are installing."))
+       ((1) (enable-discovery))
+       ((2) (disable-discovery))))
+    (_ #f)))
diff --git a/gnu/installer/proxy.scm b/gnu/installer/proxy.scm
index befaf3ab0a..86c827294e 100644
--- a/gnu/installer/proxy.scm
+++ b/gnu/installer/proxy.scm
@@ -17,15 +17,11 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu installer proxy)
+  #:use-module (gnu installer utils)
   #:use-module (gnu services herd)
   #:export (set-http-proxy
             clear-http-proxy))
 
-(define-syntax-rule (with-silent-shepherd exp ...)
-  (parameterize ((shepherd-message-port
-                  (%make-void-port "w")))
-    exp ...))
-
 (define (set-http-proxy proxy)
   (with-silent-shepherd
     (with-shepherd-action 'guix-daemon
diff --git a/gnu/installer/record.scm b/gnu/installer/record.scm
index 6ebd87f6a6..0b34318c45 100644
--- a/gnu/installer/record.scm
+++ b/gnu/installer/record.scm
@@ -33,6 +33,7 @@
             installer-locale-page
             installer-menu-page
             installer-network-page
+            installer-substitutes-page
             installer-timezone-page
             installer-hostname-page
             installer-user-page
@@ -73,6 +74,8 @@
   (menu-page installer-menu-page)
   ;; procedure void -> void
   (network-page installer-network-page)
+  ;; procedure void -> void
+  (substitutes-page installer-substitutes-page)
   ;; procedure (zonetab) -> posix-timezone
   (timezone-page installer-timezone-page)
   ;; procedure void -> void
diff --git a/gnu/installer/services.scm b/gnu/installer/services.scm
index 14a3bb9be6..ec5ea30594 100644
--- a/gnu/installer/services.scm
+++ b/gnu/installer/services.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Mathieu Othacehe <m.othacehe@gmail.com>
-;;; Copyright © 2019, 2020 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -93,11 +93,7 @@
      (system-service
       (name (G_ "OpenSSH secure shell daemon (sshd)"))
       (type 'networking)
-      (snippet '((service openssh-service-type
-                          (openssh-configuration
-                           ;; Currently the default is #t but it's considered
-                           ;; unsafe.  Explicitly pass #f.
-                           (password-authentication? #f))))))
+      (snippet '((service openssh-service-type))))
      (system-service
       (name (G_ "Tor anonymous network router"))
       (type 'networking)
diff --git a/gnu/installer/substitutes.scm b/gnu/installer/substitutes.scm
new file mode 100644
index 0000000000..c9a7418f89
--- /dev/null
+++ b/gnu/installer/substitutes.scm
@@ -0,0 +1,41 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2020 Mathieu Othacehe <m.othacehe@gmail.com>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu installer substitutes)
+  #:use-module (gnu installer utils)
+  #:use-module (gnu services herd)
+  #:export (enable-discovery
+            disable-discovery))
+
+(define (enable-discovery)
+  (with-silent-shepherd
+    (with-shepherd-action 'guix-daemon
+        ('discover "on")
+        result
+      result)))
+
+(define (disable-discovery)
+  (with-silent-shepherd
+    (with-shepherd-action 'guix-daemon
+        ('discover "off")
+        result
+      result)))
+
+;; Local Variables:
+;; eval: (put 'with-silent-shepherd 'scheme-indent-function 0)
+;; End:
diff --git a/gnu/installer/utils.scm b/gnu/installer/utils.scm
index a7fa66a199..bb97bc5560 100644
--- a/gnu/installer/utils.scm
+++ b/gnu/installer/utils.scm
@@ -18,6 +18,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu installer utils)
+  #:use-module (gnu services herd)
   #:use-module (guix utils)
   #:use-module (guix build utils)
   #:use-module (guix i18n)
@@ -43,7 +44,9 @@
             with-server-socket
             current-server-socket
             current-clients
-            send-to-clients))
+            send-to-clients
+
+            with-silent-shepherd))
 
 (define* (read-lines #:optional (port (current-input-port)))
   "Read lines from PORT and return them as a list."
@@ -233,3 +236,9 @@ accepting socket."
 
   (current-clients (reverse remainder))
   exp)
+
+(define-syntax-rule (with-silent-shepherd exp ...)
+  "Evaluate EXP while discarding shepherd messages."
+  (parameterize ((shepherd-message-port
+                  (%make-void-port "w")))
+    exp ...))
diff --git a/gnu/local.mk b/gnu/local.mk
index 6297c8e1d6..ee8aecf4a1 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -205,6 +205,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/erlang.scm			\
   %D%/packages/fabric-management.scm		\
   %D%/packages/fcitx.scm			\
+  %D%/packages/fcitx5.scm			\
   %D%/packages/figlet.scm			\
   %D%/packages/file.scm				\
   %D%/packages/file-systems.scm			\
@@ -716,6 +717,7 @@ INSTALLER_MODULES =                             \
   %D%/installer/record.scm		        \
   %D%/installer/services.scm			\
   %D%/installer/steps.scm			\
+  %D%/installer/substitutes.scm			\
   %D%/installer/tests.scm			\
   %D%/installer/timezone.scm			\
   %D%/installer/user.scm			\
@@ -732,6 +734,7 @@ INSTALLER_MODULES =                             \
   %D%/installer/newt/page.scm			\
   %D%/installer/newt/partition.scm		\
   %D%/installer/newt/services.scm		\
+  %D%/installer/newt/substitutes.scm		\
   %D%/installer/newt/timezone.scm		\
   %D%/installer/newt/user.scm			\
   %D%/installer/newt/utils.scm			\
@@ -856,7 +859,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/blender-2.79-python-3.7-fix.patch	\
   %D%/packages/patches/blender-2.79-python-3.8-fix.patch	\
   %D%/packages/patches/bpftrace-disable-bfd-disasm.patch	\
-  %D%/packages/patches/busybox-1.31.1-fix-build-with-glibc-2.31.patch \
   %D%/packages/patches/byobu-writable-status.patch		\
   %D%/packages/patches/calibre-no-updates-dialog.patch		\
   %D%/packages/patches/calibre-remove-test-sqlite.patch		\
@@ -1223,7 +1225,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/kmail-Fix-missing-link-libraries.patch \
   %D%/packages/patches/kmod-module-directory.patch		\
   %D%/packages/patches/kmscon-runtime-keymap-switch.patch	\
-  %D%/packages/patches/knot-resolver-fix-map-command-on-32-bit.patch	\
   %D%/packages/patches/kpackage-allow-external-paths.patch	\
   %D%/packages/patches/kpackage-fix-KF5PackageMacros.cmake.patch \
   %D%/packages/patches/kmplayer-aarch64.patch			\
@@ -1437,6 +1438,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/pam-krb5-CVE-2020-10595.patch		\
   %D%/packages/patches/pango-skip-libthai-test.patch		\
   %D%/packages/patches/pciutils-hurd-configure.patch		\
+  %D%/packages/patches/pciutils-hurd-fix.patch			\
   %D%/packages/patches/plasma-framework-fix-KF5PlasmaMacros.cmake.patch \
   %D%/packages/patches/ppsspp-disable-upgrade-and-gold.patch		\
   %D%/packages/patches/samba-fix-fcntl-hint-detection.patch		\
@@ -1571,6 +1573,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/rct-add-missing-headers.patch		\
   %D%/packages/patches/readline-link-ncurses.patch		\
   %D%/packages/patches/readline-6.2-CVE-2014-2524.patch		\
+  %D%/packages/patches/renpy-use-system-fribidi.patch		\
   %D%/packages/patches/reposurgeon-add-missing-docbook-files.patch	\
   %D%/packages/patches/r-httpuv-1.5.4-unvendor-libuv.patch	\
   %D%/packages/patches/ri-li-modernize_cpp.patch		\
@@ -1599,7 +1602,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/rust-openssl-sys-no-vendor.patch	\
   %D%/packages/patches/rxvt-unicode-escape-sequences.patch	\
   %D%/packages/patches/sbcl-clml-fix-types.patch		\
-  %D%/packages/patches/sbcl-geco-fix-organism-class.patch	\
   %D%/packages/patches/scalapack-blacs-mpi-deprecations.patch	\
   %D%/packages/patches/scheme48-tests.patch			\
   %D%/packages/patches/scotch-build-parallelism.patch		\
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 9df14b5ca0..d8083d6f7c 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -515,7 +515,7 @@ or via the @code{facter} Ruby library.")
 (define-public htop
   (package
     (name "htop")
-    (version "3.0.2")
+    (version "3.0.3")
     (source
      (origin
        (method git-fetch)
@@ -523,7 +523,7 @@ or via the @code{facter} Ruby library.")
              (url "https://github.com/htop-dev/htop")
              (commit version)))
        (sha256
-        (base32 "1qmqhbnc5yw4brd24yrp85k09770c1c00nl03mkv5pdz2bvqivk7"))
+        (base32 "0ylig6g2w4r3qfb16cf922iriqyn64frkzpk87vpga16kclvf08y"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (inputs
diff --git a/gnu/packages/autotools.scm b/gnu/packages/autotools.scm
index 775576ff5d..203f1bfb52 100644
--- a/gnu/packages/autotools.scm
+++ b/gnu/packages/autotools.scm
@@ -43,7 +43,7 @@
   #:use-module (ice-9 match)
   #:export (autoconf-wrapper))
 
-(define-public autoconf
+(define-public autoconf-2.69
   (package
     (name "autoconf")
     (version "2.69")
@@ -103,6 +103,39 @@ scripts are self-contained and portable, freeing the user from needing to
 know anything about Autoconf or M4.")
     (license gpl3+))) ; some files are under GPLv2+
 
+(define-public autoconf-2.70
+  (package
+    (inherit autoconf-2.69)
+    (version "2.70")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://gnu/autoconf/autoconf-"
+                           version ".tar.xz"))
+       (sha256
+        (base32
+         "1ipckz0wr2mvhj9n3ys54fmf2aksin6bhqvzl304bn6rc1w257ps"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments autoconf-2.69)
+       ((#:tests? _ #f)
+        ;; FIXME: To run the test suite, fix all the instances where scripts
+        ;; generates "#! /bin/sh" shebangs.
+        #f)
+       ((#:phases phases '%standard-phases)
+        `(modify-phases ,phases
+           (add-before 'check 'prepare-tests
+             (lambda _
+               (for-each patch-shebang
+                         (append (find-files "tests"
+                                             (lambda (file stat)
+                                               (executable-file? file)))
+                                 (find-files "bin"
+                                             (lambda (file stat)
+                                               (executable-file? file)))))
+               #t))))))))
+
+(define-public autoconf autoconf-2.69)
+
 (define-public autoconf-2.68
   (package (inherit autoconf)
     (version "2.68")
diff --git a/gnu/packages/aux-files/guile-launcher.c b/gnu/packages/aux-files/guile-launcher.c
index 886ede2846..1dd5d77e66 100644
--- a/gnu/packages/aux-files/guile-launcher.c
+++ b/gnu/packages/aux-files/guile-launcher.c
@@ -1,5 +1,5 @@
 /* GNU Guix --- Functional package management for GNU
-   Copyright 1996-1997,2000-2001,2006,2008,2011,2013,2018
+   Copyright 1996-1997,2000-2001,2006,2008,2011,2013,2018,2020
       Free Software Foundation, Inc.
    Copyright (C) 2020 Ludovic Courtès <ludo@gnu.org>
 
@@ -19,14 +19,47 @@
    along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.  */
 
 /* This file implements a variant of the 'guile' executable that does not
-   complain about locale issues.  */
+   complain about locale issues and arranges to reduce startup time by
+   ignoring GUILE_LOAD_PATH and GUILE_LOAD_COMPILED_PATH until it has
+   booted.  */
 
+#include <stdlib.h>
+#include <string.h>
 #include <locale.h>
 #include <libguile.h>
 
+/* Saved values of GUILE_LOAD_PATH and GUILE_LOAD_COMPILED_PATH.  */
+static const char *load_path, *load_compiled_path;
+
 static void
 inner_main (void *unused, int argc, char **argv)
 {
+  if (load_path != NULL)
+    {
+      setenv ("GUILE_LOAD_PATH", load_path, 1);
+      SCM load_path_var =
+	scm_c_public_lookup ("guile", "%load-path");
+      SCM addition =
+	scm_parse_path (scm_from_locale_string (load_path), SCM_EOL);
+      scm_variable_set_x (load_path_var,
+			  scm_append
+			  (scm_list_2 (scm_variable_ref (load_path_var),
+				       addition)));
+    }
+
+  if (load_compiled_path != NULL)
+    {
+      setenv ("GUILE_LOAD_COMPILED_PATH", load_compiled_path, 1);
+      SCM load_compiled_path_var =
+	scm_c_public_lookup ("guile", "%load-compiled-path");
+      SCM addition =
+	scm_parse_path (scm_from_locale_string (load_compiled_path), SCM_EOL);
+      scm_variable_set_x (load_compiled_path_var,
+			  scm_append
+			  (scm_list_2 (scm_variable_ref (load_compiled_path_var),
+				       addition)));
+    }
+
   scm_shell (argc, argv);
 }
 
@@ -40,6 +73,15 @@ main (int argc, char **argv)
        which is always preferable over the C locale.  */
     setlocale (LC_ALL, "en_US.utf8");
 
+  const char *str;
+  str = getenv ("GUILE_LOAD_PATH");
+  load_path = str != NULL ? strdup (str) : NULL;
+  str = getenv ("GUILE_LOAD_COMPILED_PATH");
+  load_compiled_path = str ? strdup (str) : NULL;
+
+  unsetenv ("GUILE_LOAD_PATH");
+  unsetenv ("GUILE_LOAD_COMPILED_PATH");
+
   scm_install_gmp_memory_functions = 1;
   scm_boot_guile (argc, argv, inner_main, 0);
   return 0; /* never reached */
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index a403224480..892b92dc2f 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -696,50 +696,6 @@ to not fully trusted targets.  Borg is a fork of Attic.")
     (home-page "https://www.borgbackup.org/")
     (license license:bsd-3)))
 
-(define-public attic
-  (package
-    (name "attic")
-    (version "0.16")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "Attic" version))
-              (sha256
-               (base32
-                "0b5skd36r4c0915lwpkqg5hxm49gls9pprs1b7hc40910wlcsl36"))))
-    (build-system python-build-system)
-    (arguments
-     `(;; The tests assume they are run as root:
-       ;; https://github.com/jborg/attic/issues/7
-       #:tests? #f
-       #:phases
-       (modify-phases %standard-phases
-         (add-before
-          'build 'set-openssl-prefix
-          (lambda* (#:key inputs #:allow-other-keys)
-            (setenv "ATTIC_OPENSSL_PREFIX" (assoc-ref inputs "openssl"))
-            #t)))))
-    (inputs
-     `(("acl" ,acl)
-       ("openssl" ,openssl)
-       ("python-msgpack" ,python-msgpack)
-
-       ;; Attic is probably incompatible with llfuse > 0.41.
-       ;; These links are to discussions of llfuse compatibility from
-       ;; the borg project. Borg is a recent fork of attic, and attic
-       ;; has not been updated since the fork, so it's likely that
-       ;; llfuse compatibility requirements are still the same.
-       ;; https://github.com/borgbackup/borg/issues/642
-       ;; https://github.com/borgbackup/borg/issues/643
-       ("python-llfuse" ,python-llfuse-0.41)))
-    (synopsis "Deduplicating backup program")
-    (description "Attic is a deduplicating backup program.  The main goal of
-Attic is to provide an efficient and secure way to backup data.  The data
-deduplication technique used makes Attic suitable for daily backups since only
-changes are stored.")
-    (home-page "https://attic-backup.org/")
-    (license license:bsd-3)
-    (properties `((superseded . ,borg)))))
-
 (define-public wimlib
   (package
     (name "wimlib")
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index eac9c074a9..85ee56c539 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2019, 2020 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>
@@ -72,6 +72,35 @@
 database, assembled using data from REACTOME.")
     (license license:cc-by4.0)))
 
+(define-public r-bluster
+  (package
+   (name "r-bluster")
+   (version "1.0.0")
+   (source (origin
+            (method url-fetch)
+            (uri (bioconductor-uri "bluster" version))
+            (sha256
+             (base32
+              "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61"))))
+   (properties `((upstream-name . "bluster")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-biocneighbors" ,r-biocneighbors)
+      ("r-biocparallel" ,r-biocparallel)
+      ("r-igraph" ,r-igraph)
+      ("r-matrix" ,r-matrix)
+      ("r-rcpp" ,r-rcpp)
+      ("r-s4vectors" ,r-s4vectors)))
+   (native-inputs
+    `(("r-knitr" ,r-knitr)))
+   (home-page "https://bioconductor.org/packages/bluster")
+   (synopsis "Clustering algorithms for Bioconductor")
+   (description"This package wraps common clustering algorithms in an easily
+extended S4 framework.  Backends are implemented for hierarchical, k-means
+and graph-based clustering.  Several utilities are also provided to compare
+and evaluate clustering results.")
+   (license license:gpl3)))
+
 (define-public r-bsgenome-celegans-ucsc-ce6
   (package
     (name "r-bsgenome-celegans-ucsc-ce6")
@@ -748,13 +777,13 @@ annotations.")
 (define-public r-ideoviz
   (package
     (name "r-ideoviz")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IdeoViz" version))
               (sha256
                (base32
-                "1ndj14qhpgidjb4qsga80ghqzz1x8kvy2gy1bvvgwlkfxa62rn50"))))
+                "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -1077,13 +1106,13 @@ package @code{affy}.")
 (define-public r-coverageview
   (package
     (name "r-coverageview")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "CoverageView" version))
               (sha256
                (base32
-                "1fcz7pkffz5l3jdxb9glji2zdmr6nx67h6vfpr2yi8n3slg2hrrj"))))
+                "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-s4vectors" ,r-s4vectors)
@@ -1104,13 +1133,13 @@ how the coverage distributed across the genome.")
 (define-public r-cummerbund
   (package
    (name "r-cummerbund")
-   (version "2.30.0")
+   (version "2.32.0")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "cummeRbund" version))
              (sha256
               (base32
-               "1av7yfxcq1wwbqfqcz7caiz5kf6kg5wq9qcg5v6yccihclzwvxjc"))))
+               "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
@@ -1170,14 +1199,14 @@ across the entire multi-'omics experiment.")
 (define-public r-biocversion
   (package
     (name "r-biocversion")
-    (version "3.11.1")
+    (version "3.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocVersion" version))
        (sha256
         (base32
-         "1rrzx3dqds0jlj1bmjc744wiamb2hssbh3jfxz1s9jp4cvnwrpmz"))))
+         "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk"))))
     (properties `((upstream-name . "BiocVersion")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BiocVersion/")
@@ -1190,13 +1219,13 @@ of Bioconductor.")
 (define-public r-biocgenerics
   (package
     (name "r-biocgenerics")
-    (version "0.34.0")
+    (version "0.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocGenerics" version))
               (sha256
                (base32
-                "15nvqyh2gx5zkn1krbs5c4rhw5642bijdfsf2rgic70gzr05cksk"))))
+                "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q"))))
     (properties
      `((upstream-name . "BiocGenerics")))
     (build-system r-build-system)
@@ -1210,14 +1239,14 @@ packages.")
 (define-public r-affycomp
   (package
     (name "r-affycomp")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycomp" version))
        (sha256
         (base32
-         "0zg8dshas5b2ny4pnxxxqihnr4l20666ivrgglb939a23mplgps0"))))
+         "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk"))))
     (properties `((upstream-name . "affycomp")))
     (build-system r-build-system)
     (propagated-inputs `(("r-biobase" ,r-biobase)))
@@ -1231,14 +1260,14 @@ measures for Affymetrix Oligonucleotide Arrays.")
 (define-public r-affycompatible
   (package
     (name "r-affycompatible")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AffyCompatible" version))
        (sha256
         (base32
-         "0394sr4spafhfypjsafwjr0y0zsgv52ajdcyvsmkdk7375898lqd"))))
+         "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x"))))
     (properties
      `((upstream-name . "AffyCompatible")))
     (build-system r-build-system)
@@ -1259,14 +1288,14 @@ Command Console} (AGCC)-compatible sample annotation files.")
 (define-public r-affycontam
   (package
     (name "r-affycontam")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyContam" version))
        (sha256
         (base32
-         "1dh5c3blk2dl9kg13y6snplnx61x2f9hvp5lc7jmg25xk916517i"))))
+         "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b"))))
     (properties `((upstream-name . "affyContam")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1284,14 +1313,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.")
 (define-public r-affycoretools
   (package
     (name "r-affycoretools")
-    (version "1.60.1")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycoretools" version))
        (sha256
         (base32
-         "0cnb54b3kmg9rnycvaz949bdali9n98qzrw7gwka6abmg1lv232s"))))
+         "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0"))))
     (properties `((upstream-name . "affycoretools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1326,14 +1355,14 @@ to streamline the more common analyses that a Biostatistician might see.")
 (define-public r-affxparser
   (package
     (name "r-affxparser")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affxparser" version))
        (sha256
         (base32
-         "0d4hq1w0a3dm4bg9qsv7wqrbv2y7b9gllxfmnqs9n2nnwmvgi8yq"))))
+         "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p"))))
     (properties `((upstream-name . "affxparser")))
     (build-system r-build-system)
     (home-page "https://github.com/HenrikBengtsson/affxparser")
@@ -1354,21 +1383,21 @@ structure.")
 (define-public r-annotate
   (package
     (name "r-annotate")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotate" version))
        (sha256
         (base32
-         "1ivszqknryq6n5a85z8zj12fvgcs6zz3zlza8q08pl6cs4m5rm4w"))))
+         "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
        ("r-dbi" ,r-dbi)
-       ("r-rcurl" ,r-rcurl)
+       ("r-httr" ,r-httr)
        ("r-xml" ,r-xml)
        ("r-xtable" ,r-xtable)))
     (home-page
@@ -1381,14 +1410,14 @@ microarrays.")
 (define-public r-hpar
   (package
     (name "r-hpar")
-    (version "1.30.0")
+    (version "1.32.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hpar" version))
        (sha256
         (base32
-         "1jq0qw7wq3426cp004divywjm3ryixkykcmwlhrri13agz6rx3r9"))))
+         "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -1401,14 +1430,14 @@ the Human Protein Atlas project.")
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.20.1")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "0bzjwzj5mvb49wgvs3gd3jfpm7s0zfkca763i65i7m994lgvz33c"))))
+         "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1432,14 +1461,14 @@ region sets and other genomic features.")
 (define-public r-reportingtools
   (package
     (name "r-reportingtools")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReportingTools" version))
        (sha256
         (base32
-         "1ig1h224silbdbdr0j9j9sysp9l9dzpcsjzn8jp57h3gh4pdqbfx"))))
+         "0gkshdhx44yjffqf1xmvik7j5hlhszp1n9ckanaws9ky3iia8j31"))))
     (properties
      `((upstream-name . "ReportingTools")))
     (build-system r-build-system)
@@ -1482,14 +1511,14 @@ browser.")
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geneplotter" version))
        (sha256
         (base32
-         "1y494da1llmrvn3qm7akwgwjazvpffabi8llw3fbday14cay1br5"))))
+         "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotate" ,r-annotate)
@@ -1507,14 +1536,14 @@ browser.")
 (define-public r-oligoclasses
   (package
     (name "r-oligoclasses")
-    (version "1.50.4")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligoClasses" version))
        (sha256
         (base32
-         "1d8c3i8v8kcm1afgpz6zc1iysip7993y8456cqxl37f7n6n0ax67"))))
+         "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy"))))
     (properties `((upstream-name . "oligoClasses")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1542,14 +1571,14 @@ packages.")
 (define-public r-oligo
   (package
     (name "r-oligo")
-    (version "1.52.1")
+    (version "1.54.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligo" version))
        (sha256
         (base32
-         "1gpvr33pwzz1glzajcipvjcplb7yxvjj00q0ybqcc3wa47bhfkwd"))))
+         "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3"))))
     (properties `((upstream-name . "oligo")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -1578,14 +1607,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
 (define-public r-qvalue
   (package
     (name "r-qvalue")
-    (version "2.20.0")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "qvalue" version))
        (sha256
         (base32
-         "1hndmdr9niagbr4ry0vbhffvjzjg9im27kdbn0sa774k6r5b4z3f"))))
+         "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
@@ -1606,32 +1635,110 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
     ;; Any version of the LGPL.
     (license license:lgpl3+)))
 
+(define r-rcppnumerical
+  (package
+   (name "r-rcppnumerical")
+   (version "0.4-0")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "RcppNumerical" version))
+            (sha256
+             (base32
+              "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
+   (properties `((upstream-name . "RcppNumerical")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-rcpp" ,r-rcpp)
+      ("r-rcppeigen" ,r-rcppeigen)))
+   (native-inputs
+    `(("r-knitr" ,r-knitr)))
+   (home-page "https://github.com/yixuan/RcppNumerical")
+   (synopsis "Rcpp integration for numerical computing libraries")
+   (description "This package provides a collection of open source libraries
+for numerical computing (numerical integration, optimization, etc.) and their
+integration with @code{Rcpp}.")
+   (license license:gpl2+)))
+
+(define-public r-apeglm
+  (package
+   (name "r-apeglm")
+   (version "1.12.0")
+   (source (origin
+            (method url-fetch)
+            (uri (bioconductor-uri "apeglm" version))
+            (sha256
+             (base32
+              "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2"))))
+   (properties `((upstream-name . "apeglm")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-emdbook" ,r-emdbook)
+      ("r-genomicranges" ,r-genomicranges)
+      ("r-rcpp" ,r-rcpp)
+      ("r-rcppeigen" ,r-rcppeigen)
+      ("r-rcppnumerical" ,r-rcppnumerical)
+      ("r-summarizedexperiment" ,r-summarizedexperiment)))
+   (native-inputs `(("r-knitr" ,r-knitr)))
+   (home-page "https://bioconductor.org/packages/apeglm")
+   (synopsis "Approximate posterior estimation for GLM coefficients")
+   (description "This package provides Bayesian shrinkage estimators for
+effect sizes for a variety of GLM models, using approximation of the
+posterior for individual coefficients.")
+   (license license:gpl2)))
+
+(define-public r-greylistchip
+  (package
+   (name "r-greylistchip")
+   (version "1.22.0")
+   (source (origin
+            (method url-fetch)
+            (uri (bioconductor-uri "GreyListChIP" version))
+            (sha256
+             (base32
+              "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6"))))
+   (properties `((upstream-name . "GreyListChIP")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-bsgenome" ,r-bsgenome)
+      ("r-genomeinfodb" ,r-genomeinfodb)
+      ("r-genomicalignments" ,r-genomicalignments)
+      ("r-genomicranges" ,r-genomicranges)
+      ("r-mass" ,r-mass)
+      ("r-rsamtools" ,r-rsamtools)
+      ("r-rtracklayer" ,r-rtracklayer)
+      ("r-summarizedexperiment" ,r-summarizedexperiment)))
+   (home-page "https://bioconductor.org/packages/GreyListChIP")
+   (synopsis "Greylist artefact regions based on ChIP inputs")
+   (description "This package identifies regions of ChIP experiments with high
+signal in the input, that lead to spurious peaks during peak calling.")
+   (license license:artistic2.0)))
+
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "2.16.2")
+    (version "3.0.8")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "11y9kigdikqcd0cnksh306nsaadak0kgivk7773mv3yszrxxwzj1"))))
+         "11svdfjp4faswrmzwkryzhd0ji2pl9vwsd35lvbfjgakbpxnyn8a"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
-    (inputs
-     `(("zlib" ,zlib)))
     (propagated-inputs
      `(("r-amap" ,r-amap)
+       ("r-apeglm" ,r-apeglm)
+       ("r-ashr" ,r-ashr)
        ("r-biocparallel" ,r-biocparallel)
        ("r-deseq2" ,r-deseq2)
        ("r-dplyr" ,r-dplyr)
-       ("r-edger" ,r-edger)
        ("r-genomicalignments" ,r-genomicalignments)
        ("r-genomicranges" ,r-genomicranges)
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggrepel" ,r-ggrepel)
        ("r-gplots" ,r-gplots)
+       ("r-greylistchip" ,r-greylistchip)
        ("r-iranges" ,r-iranges)
        ("r-lattice" ,r-lattice)
        ("r-limma" ,r-limma)
@@ -1687,14 +1794,14 @@ processing to visualization and annotation.")
 (define-public r-multtest
   (package
     (name "r-multtest")
-    (version "2.44.0")
+    (version "2.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "multtest" version))
        (sha256
         (base32
-         "12li7nzzygm3sjfx472095irqpawixk48d0k591wlnrms6sxchx2"))))
+         "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-survival" ,r-survival)
@@ -1725,13 +1832,13 @@ expressed genes in DNA microarray experiments.")
 (define-public r-graph
   (package
     (name "r-graph")
-    (version "1.66.0")
+    (version "1.68.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "graph" version))
               (sha256
                (base32
-                "15v0nx9gzpszmdn5lil1s1y8qfmsirlznh56wcyqq4sxwjbyjn9g"))))
+                "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)))
@@ -1823,36 +1930,31 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.22.4")
+    (version "3.24.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "0wxgjdikinkqj7jvs2725ak0291q6zhikyf1c93w8cngwvd9i1gq"))))
+         "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
        ("r-biomart" ,r-biomart)
        ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
        ("r-dbi" ,r-dbi)
-       ("r-delayedarray" ,r-delayedarray)
        ("r-ensembldb" ,r-ensembldb)
        ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicalignments" ,r-genomicalignments)
        ("r-genomicfeatures" ,r-genomicfeatures)
        ("r-genomicranges" ,r-genomicranges)
-       ("r-go-db" ,r-go-db)
+       ("r-ggplot2" ,r-ggplot2)
        ("r-graph" ,r-graph)
-       ("r-idr" ,r-idr)
        ("r-iranges" ,r-iranges)
-       ("r-limma" ,r-limma)
+       ("r-keggrest" ,r-keggrest)
        ("r-matrixstats" ,r-matrixstats)
        ("r-multtest" ,r-multtest)
        ("r-rbgl" ,r-rbgl)
@@ -1860,7 +1962,6 @@ determining dependencies between variables, code improvement suggestions.")
        ("r-rsamtools" ,r-rsamtools)
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)
-       ("r-seqinr" ,r-seqinr)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
        ("r-venndiagram" ,r-venndiagram)))
     (native-inputs
@@ -1878,15 +1979,42 @@ for finding the peaks with bi-directional promoters with summary statistics
 enrichedGO (addGeneIDs).")
     (license license:gpl2+)))
 
+(define-public r-matrixgenerics
+  (package
+   (name "r-matrixgenerics")
+   (version "1.2.0")
+   (source (origin
+            (method url-fetch)
+            (uri (bioconductor-uri "MatrixGenerics" version))
+            (sha256
+             (base32
+              "1a3sw79185d6rld3wlrynkzcbp754a7jkracrmvn0ra964ia8zvc"))))
+   (properties
+    `((upstream-name . "MatrixGenerics")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-matrixstats" ,r-matrixstats)))
+   (home-page "https://bioconductor.org/packages/MatrixGenerics")
+   (synopsis "S4 generic summary statistic functions for matrix-like objects")
+   (description
+    "This package provides S4 generic functions modeled after the
+@code{matrixStats} API for alternative matrix implementations.  Packages with
+alternative matrix implementation can depend on this package and implement the
+generic functions that are defined here for a useful set of row and column
+summary statistics.  Other package developers can import this package and
+handle a different matrix implementations without worrying about
+incompatibilities.")
+   (license license:artistic2.0)))
+
 (define-public r-marray
   (package
     (name "r-marray")
-    (version "1.66.0")
+    (version "1.68.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "marray" version))
               (sha256
-               (base32 "1sym3nis5qzg05b2in83xr019mvz8czy8qvispc0hzsq42yng6kd"))))
+               (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-limma" ,r-limma)))
@@ -1900,12 +2028,12 @@ normalization and quality checking.")
 (define-public r-cghbase
   (package
    (name "r-cghbase")
-   (version "1.48.0")
+   (version "1.50.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHbase" version))
             (sha256
-             (base32 "0gfqqa9rs5hid53ihlky88qndgrwxxz0s6j7s505f660dd5nzlkf"))))
+             (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4"))))
    (properties `((upstream-name . "CGHbase")))
    (build-system r-build-system)
    (propagated-inputs
@@ -1920,12 +2048,12 @@ the @code{arrayCGH} packages.")
 (define-public r-cghcall
   (package
    (name "r-cghcall")
-   (version "2.50.0")
+   (version "2.52.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHcall" version))
             (sha256
-             (base32 "1dz6sag8khl18vkb97b5w6fk6k9s7s9xxnc467dd3bmhmajlmrrg"))))
+             (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba"))))
    (properties `((upstream-name . "CGHcall")))
    (build-system r-build-system)
    (propagated-inputs
@@ -1943,12 +2071,12 @@ the @code{arrayCGH} packages.")
 (define-public r-qdnaseq
   (package
     (name "r-qdnaseq")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "QDNAseq" version))
               (sha256
-               (base32 "1ji9pl2r1idyj3qzggj7qd2kqx31i6b3igwk2hqjb8qzkyb37p86"))))
+               (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph"))))
     (properties `((upstream-name . "QDNAseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1976,14 +2104,14 @@ respectively.")
 (define-public r-bayseq
   (package
     (name "r-bayseq")
-    (version "2.22.0")
+    (version "2.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "baySeq" version))
        (sha256
         (base32
-         "1x0d34pqv9s15nmmxsfbw0ycxbf5348mi30ahycarjkjsyzycymj"))))
+         "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215"))))
     (properties `((upstream-name . "baySeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2002,14 +2130,14 @@ more complex hypotheses) via empirical Bayesian methods.")
 (define-public r-chipcomp
   (package
     (name "r-chipcomp")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPComp" version))
        (sha256
         (base32
-         "0780kj9vbzdhf2jkfb1my8m58pcdwk6jqw6zfng82g46jias98cp"))))
+         "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7"))))
     (properties `((upstream-name . "ChIPComp")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2036,14 +2164,14 @@ datasets.")
 (define-public r-riboprofiling
   (package
     (name "r-riboprofiling")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RiboProfiling" version))
        (sha256
         (base32
-         "0s30m96dbbrzbywz3wai5ar0nsshb16lq101nyl20w1bk7sk2bha"))))
+         "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg"))))
     (properties `((upstream-name . "RiboProfiling")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2077,14 +2205,14 @@ assessment, principal component analysis on codon coverage.")
 (define-public r-riboseqr
   (package
     (name "r-riboseqr")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "riboSeqR" version))
        (sha256
         (base32
-         "04a4dkmacd6xy55m84amxa0fspbc4kgg9r9k7bc3wrxswk77ccxk"))))
+         "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr"))))
     (properties `((upstream-name . "riboSeqR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2103,16 +2231,16 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
     (license license:gpl3)))
 
 (define-public r-interactionset
-  (package
+  (package                              ;BROKEN
     (name "r-interactionset")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "InteractionSet" version))
        (sha256
         (base32
-         "1nsivm9j0mzkfhwqsa2y9gxxdbaplg4z8vn5dfvls3nrihnqpk4v"))))
+         "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31"))))
     (properties
      `((upstream-name . "InteractionSet")))
     (build-system r-build-system)
@@ -2139,14 +2267,14 @@ experiments.")
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "0fg66v31nfajb40da6gxpigm2z11ywkdijs7npvc1mr62ynx9qmy"))))
+         "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
@@ -2180,14 +2308,14 @@ information and producing various plots and statistics.")
 (define-public r-ctc
   (package
     (name "r-ctc")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ctc" version))
        (sha256
         (base32
-         "0lv126xj092hps3f3dsv7hasdyy26wcx8npl9idq2l4h9addk6v6"))))
+         "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-amap" ,r-amap)))
     (home-page "https://bioconductor.org/packages/ctc/")
@@ -2200,14 +2328,14 @@ trees and clusters to other programs.")
 (define-public r-goseq
   (package
     (name "r-goseq")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "goseq" version))
        (sha256
         (base32
-         "1iyri4rrchzsn8p6wjxr4k30d3cqx3km5mnd9hkfm5d0s7fjzlym"))))
+         "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -2226,20 +2354,24 @@ defined categories which are over/under represented in RNA-seq data.")
 (define-public r-glimma
   (package
     (name "r-glimma")
-    (version "1.16.0")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Glimma" version))
        (sha256
         (base32
-         "1bxfgwjqb9p400a5a5q6p17kcnl3ddz090llihkfih9kyxii9n4y"))))
+         "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv"))))
     (properties `((upstream-name . "Glimma")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-edger" ,r-edger)
+     `(("r-deseq2" ,r-deseq2)
+       ("r-edger" ,r-edger)
+       ("r-htmlwidgets" ,r-htmlwidgets)
        ("r-jsonlite" ,r-jsonlite)
-       ("r-s4vectors" ,r-s4vectors)))
+       ("r-limma" ,r-limma)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/Shians/Glimma")
@@ -2255,14 +2387,14 @@ information.")
 (define-public r-rots
   (package
     (name "r-rots")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROTS" version))
        (sha256
         (base32
-         "1mqhi1rfiw7mhiyify7vm3w17p7sc76wjda3ak6690hrc3gsm3cm"))))
+         "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n"))))
     (properties `((upstream-name . "ROTS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2279,14 +2411,14 @@ in omics data.")
 (define-public r-plgem
   (package
     (name "r-plgem")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "plgem" version))
        (sha256
         (base32
-         "1fs5nbjnrm7x23y7d9krq56r1kzxka40ca1rs6sq70mn6syhj90a"))))
+         "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -2304,14 +2436,14 @@ genes or proteins in these datasets.")
 (define-public r-inspect
   (package
     (name "r-inspect")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "INSPEcT" version))
        (sha256
         (base32
-         "1yyglkdc3ww2jzswhcxk9g1imydfm39krl87as5l9fbm7mv3vd4z"))))
+         "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483"))))
     (properties `((upstream-name . "INSPEcT")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2351,14 +2483,14 @@ modeling the rates that determines changes in mature mRNA levels.")
 (define-public r-dnabarcodes
   (package
     (name "r-dnabarcodes")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNABarcodes" version))
        (sha256
         (base32
-         "03y39hjpkb05fnawy3k797bph1iydi1blmpgyy4244zjgk6rs5x7"))))
+         "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg"))))
     (properties `((upstream-name . "DNABarcodes")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2380,14 +2512,14 @@ demultiplexed, i.e. assigned to their original reference barcode.")
 (define-public r-ruvseq
   (package
     (name "r-ruvseq")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RUVSeq" version))
        (sha256
         (base32
-         "0yqs9xgyzw3cwb4l7zjl1cjgbsjp05qrqnwyvh7q81wdp7x5p55x"))))
+         "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh"))))
     (properties `((upstream-name . "RUVSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2408,21 +2540,20 @@ samples.")
 (define-public r-biocneighbors
   (package
     (name "r-biocneighbors")
-    (version "1.6.0")
+    (version "1.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocNeighbors" version))
        (sha256
         (base32
-         "14cyyrwxi82xm5wy6bb1176zg322ll67wjrw9vvi4fhfs1k4wqxy"))))
+         "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7"))))
     (properties `((upstream-name . "BiocNeighbors")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocparallel" ,r-biocparallel)
        ("r-matrix" ,r-matrix)
        ("r-rcpp" ,r-rcpp)
-       ("r-rcppannoy" ,r-rcppannoy)
        ("r-rcpphnsw" ,r-rcpphnsw)
        ("r-s4vectors" ,r-s4vectors)))
     (native-inputs
@@ -2441,14 +2572,14 @@ achieved for all methods using the BiocParallel framework.")
 (define-public r-biocsingular
   (package
     (name "r-biocsingular")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSingular" version))
        (sha256
         (base32
-         "0368a9xj4cvicqkxmhh12ln46q9gnxla70s1dqrxxfn3b6k525ih"))))
+         "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni"))))
     (properties `((upstream-name . "BiocSingular")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2475,14 +2606,14 @@ possible, parallelization is achieved using the BiocParallel framework.")
 (define-public r-destiny
   (package
     (name "r-destiny")
-    (version "3.2.0")
+    (version "3.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "destiny" version))
        (sha256
         (base32
-         "0ik5vwxz9cci3glwgb5ff03sfyr4sjcp8ckfymlgmlm6fz8cp21n"))))
+         "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -2493,7 +2624,6 @@ possible, parallelization is achieved using the BiocParallel framework.")
        ("r-irlba" ,r-irlba)
        ("r-knn-covertree" ,r-knn-covertree)
        ("r-matrix" ,r-matrix)
-       ("r-nbconvertr" ,r-nbconvertr)
        ("r-pcamethods" ,r-pcamethods)
        ("r-proxy" ,r-proxy)
        ("r-rcpp" ,r-rcpp)
@@ -2520,14 +2650,14 @@ maps.")
 (define-public r-savr
   (package
     (name "r-savr")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "savR" version))
        (sha256
         (base32
-         "17jdnr47ivblfspr4b32z9fds1fqiiwsi2z6r524g1v4944p8w5a"))))
+         "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic"))))
     (properties `((upstream-name . "savR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2546,14 +2676,14 @@ Viewer (SAV) files, access data, and generate QC plots.")
 (define-public r-chipexoqual
   (package
     (name "r-chipexoqual")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPexoQual" version))
        (sha256
         (base32
-         "02rsf1rvm0p6dn18zq2a4hpvpd9m2i5rziyi4zm8j43qvs8xhafp"))))
+         "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag"))))
     (properties `((upstream-name . "ChIPexoQual")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2586,13 +2716,13 @@ sequencing data.")
 (define-public r-copynumber
   (package
     (name "r-copynumber")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "copynumber" version))
               (sha256
                (base32
-                "1b7v6xijpi2mir49cf83gpadhxm5pnbs6d8q8qga7y06hn9jx6my"))))
+                "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-s4vectors" ,r-s4vectors)
@@ -2609,14 +2739,14 @@ penalized least squares regression method.")
 (define-public r-dnacopy
   (package
     (name "r-dnacopy")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNAcopy" version))
        (sha256
         (base32
-         "0jg8lr83drzfs5h73c7mk7x99vj99a2p2s1sqjc4gicn927xvhza"))))
+         "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc"))))
     (properties `((upstream-name . "DNAcopy")))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
@@ -2709,14 +2839,14 @@ and regression inferences from RNA-sequencing data.")
 (define-public r-ebseq
   (package
     (name "r-ebseq")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBSeq" version))
        (sha256
         (base32
-         "0s9r1xxpfm5794ipjm5a5c8gfxicc6arma6f74aaz8zi5y5q9x5f"))))
+         "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny"))))
     (properties `((upstream-name . "EBSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2733,13 +2863,13 @@ gene and isoform level using RNA-seq data")
 (define-public r-karyoploter
   (package
     (name "r-karyoploter")
-    (version "1.14.1")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "karyoploteR" version))
               (sha256
                (base32
-                "1wlnzkq58baqj9854nzf5rbglchb2xy4wsp3s0q8xfq8v0p3baxf"))))
+                "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -2771,14 +2901,14 @@ coordinates.")
 (define-public r-lpsymphony
   (package
     (name "r-lpsymphony")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lpsymphony" version))
        (sha256
         (base32
-         "072ikmd267n18hrj7dip4dp1vb5dinj82p3h95n2jaf04h9hwfn4"))))
+         "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9"))))
     (build-system r-build-system)
     (inputs
      `(("zlib" ,zlib)))
@@ -2801,14 +2931,14 @@ to install interface to SYMPHONY.")
 (define-public r-ihw
   (package
     (name "r-ihw")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IHW" version))
        (sha256
         (base32
-         "169ir0k1gygdh1wybwa0drdxnhrdrlyzzy0rkygi7jsirn69m74j"))))
+         "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0"))))
     (properties `((upstream-name . "IHW")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2833,14 +2963,14 @@ independent of the p-value under the null hypothesis.")
 (define-public r-icobra
   (package
     (name "r-icobra")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iCOBRA" version))
        (sha256
         (base32
-         "0cvklagby3i221dlhyb51cciv0b3ch4a8z0wpm67q5n6n3k0cil1"))))
+         "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s"))))
     (properties `((upstream-name . "iCOBRA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2869,14 +2999,14 @@ interactive exploration of results.")
 (define-public r-mast
   (package
     (name "r-mast")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MAST" version))
        (sha256
         (base32
-         "12d0q2fbq9d5jgyccmfv0cghv282s0j86wjfbnjpdf73fdrp6brr"))))
+         "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn"))))
     (properties `((upstream-name . "MAST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2904,14 +3034,14 @@ single cell assay data.")
 (define-public r-monocle
   (package
     (name "r-monocle")
-    (version "2.16.0")
+    (version "2.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "monocle" version))
        (sha256
         (base32
-         "1vziidavlyhixmx6j7lf29qx8xcjwrc9q3x2f63gcff41q3jf9xd"))))
+         "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -3023,14 +3153,14 @@ qPCR data, but could be used with other types as well.")
 (define-public r-noiseq
   (package
     (name "r-noiseq")
-    (version "2.31.0")
+    (version "2.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "NOISeq" version))
        (sha256
         (base32
-         "0lg3za0km6v9l6dxigbxx6nsx9y6m3dyzh9srngi53s8387vhj33"))))
+         "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f"))))
     (properties `((upstream-name . "NOISeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3050,14 +3180,14 @@ assumptions.")
 (define-public r-scdd
   (package
     (name "r-scdd")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scDD" version))
        (sha256
         (base32
-         "19q01jksxpv4p26wp2c6faa4fffkjnqlbcds2x955pk35jkqknxx"))))
+         "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g"))))
     (properties `((upstream-name . "scDD")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3088,14 +3218,14 @@ distributions.")
 (define-public r-scone
   (package
     (name "r-scone")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scone" version))
        (sha256
         (base32
-         "12hcmbpncm0l1yxhm3sgkqqfri7s5qc46ikv5qcj8pw5a42rkx3g"))))
+         "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-aroma-light" ,r-aroma-light)
@@ -3130,14 +3260,14 @@ high-throughput analyses.")
 (define-public r-geoquery
   (package
     (name "r-geoquery")
-    (version "2.56.0")
+    (version "2.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GEOquery" version))
        (sha256
         (base32
-         "0sap1dsa3k3qpv5z5y3cimxyhbm8qai87gqn3g1w3hwlcqsss92m"))))
+         "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4"))))
     (properties `((upstream-name . "GEOquery")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3163,14 +3293,14 @@ the bridge between GEO and BioConductor.")
 (define-public r-illuminaio
   (package
     (name "r-illuminaio")
-    (version "0.30.0")
+    (version "0.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "illuminaio" version))
        (sha256
         (base32
-         "0i587r1v5aa25w0jm1zvh7spc1gqmvza49i2kv00g1qzj8whq67c"))))
+         "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-base64" ,r-base64)))
@@ -3184,14 +3314,14 @@ files, including IDAT.")
 (define-public r-siggenes
   (package
     (name "r-siggenes")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "siggenes" version))
        (sha256
         (base32
-         "0i4y1hgq1ljxkf6sypb6c8yp412a8q5v5z68cx1zrgxnccvp0mfy"))))
+         "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -3210,14 +3340,14 @@ Bayes Analyses of Microarrays} (EBAM).")
 (define-public r-bumphunter
   (package
     (name "r-bumphunter")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bumphunter" version))
        (sha256
         (base32
-         "04y6spdx89j3bsq2xniqd3sbfmakwc0klbpzjlp1q2xs9kywr4dq"))))
+         "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -3244,14 +3374,14 @@ studies.")
 (define-public r-minfi
   (package
     (name "r-minfi")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "minfi" version))
        (sha256
         (base32
-         "0bl1sk9syy770d5wqa0k1y0wrs5x8sbj13px1v03v3693pdj081w"))))
+         "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beanplot" ,r-beanplot)
@@ -3295,14 +3425,14 @@ methylation arrays.")
 (define-public r-methylumi
   (package
     (name "r-methylumi")
-    (version "2.34.0")
+    (version "2.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "methylumi" version))
        (sha256
         (base32
-         "0phb2dyndnk9rv79nx246cn1sc9wbzdqqbgl6402knc7dgh799wr"))))
+         "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotate" ,r-annotate)
@@ -3341,14 +3471,14 @@ and Infinium HD arrays are also included.")
 (define-public r-lumi
   (package
     (name "r-lumi")
-    (version "2.40.0")
+    (version "2.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lumi" version))
        (sha256
         (base32
-         "196izc4mdh8j4f04fsf8cqm99w1inzpwy34kwvhz6zvxj2ywn1i9"))))
+         "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-affy" ,r-affy)
@@ -3380,14 +3510,14 @@ especially Illumina Infinium methylation microarrays.")
 (define-public r-linnorm
   (package
     (name "r-linnorm")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Linnorm" version))
        (sha256
         (base32
-         "143hdfswp5sda5al1igrm5gyn7a6mp1j7hjm5jsc300335lm3kgp"))))
+         "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3"))))
     (properties `((upstream-name . "Linnorm")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3441,14 +3571,14 @@ evaluation of DEG analysis methods.")
 (define-public r-ioniser
   (package
     (name "r-ioniser")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IONiseR" version))
        (sha256
         (base32
-         "05fndlblczabva60gn6h0dijqxyn0wknrv8a925fgc4bn415g31w"))))
+         "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx"))))
     (properties `((upstream-name . "IONiseR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3589,14 +3719,14 @@ peak definition in combination with known profile characteristics.")
 (define-public r-varianttools
   (package
     (name "r-varianttools")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantTools" version))
        (sha256
         (base32
-         "0g93rljlmhk1d53z0bgi84i2cn5c3r1dpm8id2pv0nk9ncdh3yxx"))))
+         "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89"))))
     (properties `((upstream-name . "VariantTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3629,14 +3759,14 @@ gmapR.")
 (define-public r-heatplus
   (package
     (name "r-heatplus")
-    (version "2.34.0")
+    (version "2.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Heatplus" version))
        (sha256
         (base32
-         "12nd0h8svx7qydv1shk0gdpvnbixf7qi6zh06881wsmxf5s970rw"))))
+         "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n"))))
     (properties `((upstream-name . "Heatplus")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3654,14 +3784,14 @@ information about samples and features can be added to the plot.")
 (define-public r-gosemsim
   (package
     (name "r-gosemsim")
-    (version "2.14.2")
+    (version "2.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOSemSim" version))
        (sha256
         (base32
-         "02r7m1x6g8bb7q8l0hpvakdzdv5v1nplhx5lbiy798a7c3xg895b"))))
+         "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs"))))
     (properties `((upstream-name . "GOSemSim")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3683,14 +3813,14 @@ sets of GO terms, gene products and gene clusters.")
 (define-public r-anota
   (package
     (name "r-anota")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "anota" version))
        (sha256
         (base32
-         "1ind5cyq85l63xpqmg2n9rg805s5amh48iiw05zqr8kih6hlilpm"))))
+         "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-multtest" ,r-multtest)
@@ -3714,14 +3844,14 @@ the data set is suitable for such analysis.")
 (define-public r-sigpathway
   (package
     (name "r-sigpathway")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "sigPathway" version))
         (sha256
           (base32
-            "0a79sdvag80p7xcdz8mp8wiby36yxmappzycfd2rp36v9drjk0h5"))))
+            "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l"))))
     (properties `((upstream-name . "sigPathway")))
     (build-system r-build-system)
     (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
@@ -3736,14 +3866,14 @@ phenotype of interest.")
 (define-public r-fgsea
   (package
     (name "r-fgsea")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fgsea" version))
        (sha256
         (base32
-         "0zbjj8al1ps7immxixsn5g8lvbmpmxvqwqbpdgsicxp00gb9bybc"))))
+         "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bh" ,r-bh)
@@ -3768,14 +3898,14 @@ to multiple hypothesis correction.")
 (define-public r-dose
   (package
     (name "r-dose")
-    (version "3.14.0")
+    (version "3.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DOSE" version))
        (sha256
         (base32
-         "1j0wcg7w2ns3ag9d272cqlg3j62ag2xnc5gfsjl6g2ij5xkvylb8"))))
+         "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4"))))
     (properties `((upstream-name . "DOSE")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3803,32 +3933,29 @@ data.")
 (define-public r-enrichplot
   (package
     (name "r-enrichplot")
-    (version "1.8.1")
+    (version "1.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "enrichplot" version))
        (sha256
         (base32
-         "01m3cp717ldfbz5w3yfywvjg6sfjzz7s3vlk7w268lmmcg6g6bz7"))))
+         "0h0455plh8bxnpizgfxij9625ff32rs1a51yzpnrf5hl27xbfkdd"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-cowplot" ,r-cowplot)
+     `(("r-cowplot" ,r-cowplot)
        ("r-dose" ,r-dose)
-       ("r-europepmc" ,r-europepmc)
        ("r-ggplot2" ,r-ggplot2)
-       ("r-ggplotify" ,r-ggplotify)
        ("r-ggraph" ,r-ggraph)
-       ("r-ggridges" ,r-ggridges)
        ("r-gosemsim" ,r-gosemsim)
-       ("r-gridextra" ,r-gridextra)
        ("r-igraph" ,r-igraph)
+       ("r-magrittr" ,r-magrittr)
        ("r-plyr" ,r-plyr)
        ("r-purrr" ,r-purrr)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-reshape2" ,r-reshape2)
-       ("r-scatterpie" ,r-scatterpie)))
+       ("r-scatterpie" ,r-scatterpie)
+       ("r-shadowtext" ,r-shadowtext)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/GuangchuangYu/enrichplot")
@@ -3842,14 +3969,14 @@ All the visualization methods are developed based on ggplot2 graphics.")
 (define-public r-clusterprofiler
   (package
     (name "r-clusterprofiler")
-    (version "3.16.1")
+    (version "3.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "clusterProfiler" version))
        (sha256
         (base32
-         "11zsgb8wbdv8r4c04iczz4aala4yw4ai7rz8igdzz87c0940nxkb"))))
+         "07xkc515gp9j4axg0qh39ni65mcbjgxmzjh5wxd86w64lz7xh8b9"))))
     (properties
      `((upstream-name . "clusterProfiler")))
     (build-system r-build-system)
@@ -3879,14 +4006,14 @@ profiles (GO and KEGG) of gene and gene clusters.")
 (define-public r-mlinterfaces
   (package
     (name "r-mlinterfaces")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MLInterfaces" version))
        (sha256
         (base32
-         "0x3mnvb5a6kri4q5w0wfmx02v79my08zhmkaik9pqlprd7y5wynq"))))
+         "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r"))))
     (properties `((upstream-name . "MLInterfaces")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3920,14 +4047,14 @@ data in R and Bioconductor containers.")
 (define-public r-annaffy
   (package
     (name "r-annaffy")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annaffy" version))
        (sha256
         (base32
-         "1rc9fb83by9jfgwfj2zhhbj93v296blwd8jl2rh7jj200mrpznn4"))))
+         "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -3956,19 +4083,21 @@ It allows searching of biological metadata using various criteria.")
 (define-public r-a4core
   (package
     (name "r-a4core")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Core" version))
        (sha256
         (base32
-         "1hn9lkaib1bx5n52as882f8zwsln8w40sx8hxbrnimjvgfxrbvnp"))))
+         "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2"))))
     (properties `((upstream-name . "a4Core")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
        ("r-glmnet" ,r-glmnet)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/a4Core")
     (synopsis "Automated Affymetrix array analysis core package")
     (description
@@ -3979,24 +4108,26 @@ arrays.")
 (define-public r-a4classif
   (package
     (name "r-a4classif")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Classif" version))
        (sha256
         (base32
-         "0bj8m4nprw3maahd1qx9jjdxfip9ihbbpydbzwjxn6dlgw2i8mcr"))))
+         "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz"))))
     (properties `((upstream-name . "a4Classif")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-a4core" ,r-a4core)
        ("r-a4preproc" ,r-a4preproc)
+       ("r-biobase" ,r-biobase)
        ("r-glmnet" ,r-glmnet)
-       ("r-mlinterfaces" ,r-mlinterfaces)
        ("r-pamr" ,r-pamr)
        ("r-rocr" ,r-rocr)
        ("r-varselrf" ,r-varselrf)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/a4Classif/")
     (synopsis "Automated Affymetrix array analysis classification package")
     (description
@@ -4007,18 +4138,21 @@ Affymetrix arrays.")
 (define-public r-a4preproc
   (package
     (name "r-a4preproc")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Preproc" version))
        (sha256
         (base32
-         "1hy3jvhdjyjzzmw5wkil3cs26hvqnb056r09x0p2bjg5sc9hh8b8"))))
+         "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i"))))
     (properties `((upstream-name . "a4Preproc")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)))
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/a4Preproc/")
     (synopsis "Automated Affymetrix array analysis preprocessing package")
     (description
@@ -4029,19 +4163,20 @@ is used for preprocessing the arrays.")
 (define-public r-a4reporting
   (package
     (name "r-a4reporting")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Reporting" version))
        (sha256
         (base32
-         "1jhlxqwfbgflcyzy9gyxznzcadj9zxchl3lfdlc4ffm0hwz5jl2f"))))
+         "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy"))))
     (properties `((upstream-name . "a4Reporting")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annaffy" ,r-annaffy)
-       ("r-xtable" ,r-xtable)))
+     `(("r-xtable" ,r-xtable)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/a4Reporting/")
     (synopsis "Automated Affymetrix array analysis reporting package")
     (description
@@ -4052,21 +4187,20 @@ provides reporting features.")
 (define-public r-a4base
   (package
     (name "r-a4base")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Base" version))
        (sha256
         (base32
-         "0b7fy1wcydb9z43wb1663skswvhivn7ji15g00gqcshwkkiq4x02"))))
+         "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp"))))
     (properties `((upstream-name . "a4Base")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-a4core" ,r-a4core)
        ("r-a4preproc" ,r-a4preproc)
        ("r-annaffy" ,r-annaffy)
-       ("r-annotationdbi" ,r-annotationdbi)
        ("r-biobase" ,r-biobase)
        ("r-genefilter" ,r-genefilter)
        ("r-glmnet" ,r-glmnet)
@@ -4084,14 +4218,14 @@ Affymetrix arrays.")
 (define-public r-a4
   (package
     (name "r-a4")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4" version))
        (sha256
         (base32
-         "1rzxg1h48jnlwqfjyyqzz6i3zlkfzc0i714rfplry7dyni6asgr7"))))
+         "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-a4base" ,r-a4base)
@@ -4109,19 +4243,18 @@ Affymetrix arrays.")
 (define-public r-abseqr
   (package
     (name "r-abseqr")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "abseqR" version))
        (sha256
         (base32
-         "0pzyfn0jv41rja6l4jbgwgsqy0q1d3kz23m9m6pc67p2a231i9c5"))))
+         "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f"))))
     (properties `((upstream-name . "abseqR")))
     (build-system r-build-system)
     (inputs
-     `(("pandoc" ,pandoc)
-       ("pandoc-citeproc" ,pandoc-citeproc)))
+     `(("pandoc" ,pandoc)))
     (propagated-inputs
      `(("r-biocparallel" ,r-biocparallel)
        ("r-biocstyle" ,r-biocstyle)
@@ -4158,14 +4291,14 @@ further downstream analysis on its output.")
 (define-public r-bacon
   (package
     (name "r-bacon")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bacon" version))
        (sha256
         (base32
-         "066b9vyp8ivnzm9741mb5z763a7z40ar9m8w31yw84fjiv01v3dl"))))
+         "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocparallel" ,r-biocparallel)
@@ -4185,14 +4318,14 @@ fitting a three-component normal mixture on z-scores.")
 (define-public r-rgadem
   (package
     (name "r-rgadem")
-    (version "2.36.0")
+    (version "2.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGADEM" version))
        (sha256
         (base32
-         "14mflbwhhj9f3b05zdlsdjwxmpb120r23fy306qkvxjprdqn4sz8"))))
+         "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw"))))
     (properties `((upstream-name . "rGADEM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4243,12 +4376,12 @@ distributions, modules and filter motifs.")
 (define-public r-motifdb
   (package
    (name "r-motifdb")
-   (version "1.30.0")
+   (version "1.32.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "MotifDb" version))
             (sha256
-             (base32 "0ixmdqp0s0xv9ar85n2wirbbssrzlk8a892wam55jdsf9y8aabkm"))))
+             (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5"))))
    (properties `((upstream-name . "MotifDb")))
    (build-system r-build-system)
    (propagated-inputs
@@ -4270,12 +4403,12 @@ frequency matrices from nine public sources, for multiple organisms.")
 (define-public r-motifbreakr
   (package
    (name "r-motifbreakr")
-   (version "2.2.0")
+   (version "2.4.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "motifbreakR" version))
             (sha256
-             (base32 "09czgmyjcycsvyvadpjddwwvqvxzd0ba3zhczh4mqc09gwa6vhlm"))))
+             (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7"))))
    (properties `((upstream-name . "motifbreakR")))
    (build-system r-build-system)
    (propagated-inputs
@@ -4321,24 +4454,21 @@ Bioconductor.")
 (define-public r-motifstack
   (package
     (name "r-motifstack")
-    (version "1.32.1")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifStack" version))
        (sha256
         (base32
-         "02vmkgn36n5xpmizy33znlzgmi3w5hnhsibgisbnhwwgxpkrwpcd"))))
+         "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb"))))
     (properties `((upstream-name . "motifStack")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ade4" ,r-ade4)
        ("r-biostrings" ,r-biostrings)
        ("r-ggplot2" ,r-ggplot2)
-       ("r-grimport2" ,r-grimport2)
        ("r-htmlwidgets" ,r-htmlwidgets)
-       ("r-motiv" ,r-motiv)
-       ("r-scales" ,r-scales)
        ("r-xml" ,r-xml)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -4355,20 +4485,22 @@ type and symbol colors.")
 (define-public r-genomicscores
   (package
     (name "r-genomicscores")
-    (version "2.0.0")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicScores" version))
        (sha256
         (base32
-         "0si2lgc37mkah4w990q1q2bf8xmshxj7cbx92bcrp0zaipjr96bb"))))
+         "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr"))))
     (properties `((upstream-name . "GenomicScores")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationhub" ,r-annotationhub)
        ("r-biobase" ,r-biobase)
+       ("r-biocfilecache" ,r-biocfilecache)
        ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocmanager" ,r-biocmanager)
        ("r-biostrings" ,r-biostrings)
        ("r-delayedarray" ,r-delayedarray)
        ("r-genomeinfodb" ,r-genomeinfodb)
@@ -4390,14 +4522,14 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.12.5")
+    (version "1.14.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "1103daz82k97vzmxjmf7jwm2nd3w8i0jwplrsi9996bkih11qwbf"))))
+         "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4437,14 +4569,14 @@ footprints.")
 (define-public r-gofuncr
   (package
     (name "r-gofuncr")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOfuncR" version))
        (sha256
         (base32
-         "1ixjkqb9wpwqfzxsg0h96c6fa63wrk72sfh6x4pq0kpyrcc0ind1"))))
+         "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq"))))
     (properties `((upstream-name . "GOfuncR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4486,14 +4618,14 @@ annotations and ontologies.")
 (define-public r-abaenrichment
   (package
     (name "r-abaenrichment")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ABAEnrichment" version))
        (sha256
         (base32
-         "09ihbgxrhpcz2q7svldhm710a0yrhiqk9p0q0myv11c2w50ymwkw"))))
+         "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c"))))
     (properties `((upstream-name . "ABAEnrichment")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4518,14 +4650,14 @@ the brain using an ontology, both provided by the Allen Brain Atlas project.")
 (define-public r-annotationfuncs
   (package
     (name "r-annotationfuncs")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationFuncs" version))
        (sha256
         (base32
-         "1yfsxzn7s1nlc3xz2yj39j6hmdfapc9qj9h0cd71gkaxj53ial7d"))))
+         "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
     (properties
      `((upstream-name . "AnnotationFuncs")))
     (build-system r-build-system)
@@ -4543,14 +4675,14 @@ different identifieres using the Biocore Data Team data-packages (e.g.
 (define-public r-annotationtools
   (package
     (name "r-annotationtools")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotationTools" version))
        (sha256
         (base32
-         "1b1yfnknr9vbn4y2mxdfyx57i5jbabhp9pwx8axlg2a7lawkfmdk"))))
+         "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224"))))
     (properties
      `((upstream-name . "annotationTools")))
     (build-system r-build-system)
@@ -4568,14 +4700,14 @@ text files).")
 (define-public r-allelicimbalance
   (package
     (name "r-allelicimbalance")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AllelicImbalance" version))
        (sha256
         (base32
-         "0irn4xdlvazdkv0055f45693y6zvqaz7j3vml5xscnh45ls6vmqr"))))
+         "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl"))))
     (properties
      `((upstream-name . "AllelicImbalance")))
     (build-system r-build-system)
@@ -4611,14 +4743,14 @@ investigation using RNA-seq data.")
 (define-public r-aucell
   (package
     (name "r-aucell")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AUCell" version))
        (sha256
         (base32
-         "0fgqkgjhf92vkljkwn44lm8cjvzq1lvk80nk6xhsp5q6s5isbmns"))))
+         "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx"))))
     (properties `((upstream-name . "AUCell")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4650,14 +4782,14 @@ needed.")
 (define-public r-ebimage
   (package
     (name "r-ebimage")
-    (version "4.30.0")
+    (version "4.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBImage" version))
        (sha256
         (base32
-         "13amrbh545hwk7sygndzyv7wpa0m2y0lzlwj89jm1xm62x577w9v"))))
+         "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww"))))
     (properties `((upstream-name . "EBImage")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4689,14 +4821,14 @@ visualization with image data.")
 (define-public r-yamss
   (package
     (name "r-yamss")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yamss" version))
        (sha256
         (base32
-         "00x2lnssgzbmhy5bb2m0f8rq2nsz3lb5xlp2vhkcagza39h3xb0c"))))
+         "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -4723,14 +4855,14 @@ analysis.")
 (define-public r-gtrellis
   (package
     (name "r-gtrellis")
-    (version "1.20.1")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gtrellis" version))
        (sha256
         (base32
-         "1v2l7r945xx4cf9s8m19csj7716n2ayxy05adkl8zqgxk0gxzqm1"))))
+         "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-circlize" ,r-circlize)
@@ -4752,14 +4884,14 @@ genomic categories and to add self-defined graphics in the plot.")
 (define-public r-somaticsignatures
   (package
     (name "r-somaticsignatures")
-    (version "2.24.0")
+    (version "2.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SomaticSignatures" version))
        (sha256
         (base32
-         "0d34mss73w1jdnmilk060a1fywlfmqbnlir089q9m3q1p3x0j4c1"))))
+         "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801"))))
     (properties
      `((upstream-name . "SomaticSignatures")))
     (build-system r-build-system)
@@ -4791,14 +4923,14 @@ decomposition algorithms.")
 (define-public r-yapsa
   (package
     (name "r-yapsa")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "YAPSA" version))
        (sha256
         (base32
-         "06lkf01vl4fyhj82srx8k870fhw76a1han0kp4jglh43b1c19c1k"))))
+         "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb"))))
     (properties `((upstream-name . "YAPSA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4818,7 +4950,7 @@ decomposition algorithms.")
        ("r-gridextra" ,r-gridextra)
        ("r-gtrellis" ,r-gtrellis)
        ("r-keggrest" ,r-keggrest)
-       ("r-lsei" ,r-lsei)
+       ("r-limsolve" ,r-limsolve)
        ("r-magrittr" ,r-magrittr)
        ("r-pmcmr" ,r-pmcmr)
        ("r-pracma" ,r-pracma)
@@ -4840,14 +4972,14 @@ provided.")
 (define-public r-gcrma
   (package
     (name "r-gcrma")
-    (version "2.60.0")
+    (version "2.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gcrma" version))
        (sha256
         (base32
-         "1klbnygc1i5ac1x00bsk0rjw5h5dn6pn65fa3y9r09q47gpy1c5g"))))
+         "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-affy" ,r-affy)
@@ -4876,14 +5008,14 @@ gene-specific binding is expected.")
 (define-public r-simpleaffy
   (package
     (name "r-simpleaffy")
-    (version "2.64.0")
+    (version "2.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "simpleaffy" version))
        (sha256
         (base32
-         "040043spblr8v67lkn3nnxhgfmfh2iwaizph4fnms1ik6qz662x7"))))
+         "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-affy" ,r-affy)
@@ -4904,14 +5036,14 @@ generating high resolution journal figures.")
 (define-public r-yaqcaffy
   (package
     (name "r-yaqcaffy")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yaqcaffy" version))
        (sha256
         (base32
-         "1l0cblh9sfrsil15bjya7d8kkas8bj6klj2w3c4384njdsjsjcf0"))))
+         "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-simpleaffy" ,r-simpleaffy)))
@@ -4926,14 +5058,14 @@ chips with the MAQC reference datasets.")
 (define-public r-quantro
   (package
     (name "r-quantro")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "quantro" version))
        (sha256
         (base32
-         "0ap9cl5z79wg44mnagjsk8py3kngb4f0ddnx85cbnwqkvb769zbz"))))
+         "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -4959,14 +5091,14 @@ groups.")
 (define-public r-yarn
   (package
     (name "r-yarn")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yarn" version))
        (sha256
         (base32
-         "1xdjwy1gkfg8lhgq4iwwmbi01903qljjs7yd96cvacmvgn8z6qvx"))))
+         "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -4996,14 +5128,14 @@ large RNA-seq experiments.")
 (define-public r-roar
   (package
     (name "r-roar")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "roar" version))
        (sha256
         (base32
-         "069g887migvk70n0377dqr0fk7wjbz3w0asgk42bwhp8xpjfym6f"))))
+         "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -5025,14 +5157,14 @@ sites and alignments obtained from standard RNA-seq experiments.")
 (define-public r-xbseq
   (package
     (name "r-xbseq")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "XBSeq" version))
        (sha256
         (base32
-         "13br7x1q6dg8daxahskwq24f09wbxr8kyszl1z7dhc26bid2pvy0"))))
+         "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
     (properties `((upstream-name . "XBSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5064,14 +5196,14 @@ genes.")
 (define-public r-massspecwavelet
   (package
     (name "r-massspecwavelet")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MassSpecWavelet" version))
        (sha256
         (base32
-         "0nv1r68g7f1rps6sqaccd4n4x0i19wklvyabhp4b03cdk22gl3nq"))))
+         "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3"))))
     (properties
      `((upstream-name . "MassSpecWavelet")))
     (build-system r-build-system)
@@ -5088,14 +5220,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
 (define-public r-xcms
   (package
     (name "r-xcms")
-    (version "3.10.2")
+    (version "3.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xcms" version))
        (sha256
         (base32
-         "0sk53jcl7sjrpw2ncdpl8sw1b1j9mizlrj517rinr1qrbm6lsn8f"))))
+         "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -5104,6 +5236,7 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
        ("r-iranges" ,r-iranges)
        ("r-lattice" ,r-lattice)
        ("r-massspecwavelet" ,r-massspecwavelet)
+       ("r-mscoreutils" ,r-mscoreutils)
        ("r-msnbase" ,r-msnbase)
        ("r-mzr" ,r-mzr)
        ("r-plyr" ,r-plyr)
@@ -5127,14 +5260,14 @@ data for high-throughput, untargeted analyte profiling.")
 (define-public r-wrench
   (package
     (name "r-wrench")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Wrench" version))
        (sha256
         (base32
-         "05dyk3yvbqrzvinv3ig8ad9wffwr14z715cicsbxwxpv5lq84wx6"))))
+         "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx"))))
     (properties `((upstream-name . "Wrench")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5153,14 +5286,14 @@ that arising from 16s metagenomic surveys.")
 (define-public r-wiggleplotr
   (package
     (name "r-wiggleplotr")
-    (version "1.12.1")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wiggleplotr" version))
        (sha256
         (base32
-         "1wknigh1md3w4h68caqlpq945maipdkpmw10hc2rlx4nbbpcnawp"))))
+         "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -5187,14 +5320,14 @@ visualization of exonic read coverage.")
 (define-public r-widgettools
   (package
     (name "r-widgettools")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "widgetTools" version))
        (sha256
         (base32
-         "0lrdpsgm9r7yfyyj5crvb7px4hrghxhmiic4iissz40slbfyvilx"))))
+         "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w"))))
     (properties `((upstream-name . "widgetTools")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/widgetTools/")
@@ -5208,14 +5341,14 @@ widgets in R.")
 (define-public r-webbioc
   (package
     (name "r-webbioc")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "webbioc" version))
        (sha256
         (base32
-         "16376ya5a5x2hwkl1v9y4r7np1drdwm912knnqg2dn90zmrdwr5f"))))
+         "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj"))))
     (build-system r-build-system)
     (inputs
      `(("netpbm" ,netpbm)
@@ -5241,14 +5374,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.")
 (define-public r-zfpkm
   (package
     (name "r-zfpkm")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zFPKM" version))
        (sha256
         (base32
-         "0scszhfqrgzhglz1a6kxfydq9dx8fqx28j3dypp91y5ah2w6mdys"))))
+         "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm"))))
     (properties `((upstream-name . "zFPKM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5270,14 +5403,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
 (define-public r-rbowtie2
   (package
     (name "r-rbowtie2")
-    (version "1.10.1")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie2" version))
        (sha256
         (base32
-         "19v7wfvrd53j618c1xbiqnlsf2kxw697myryx0vb9s2aspknyzz7"))))
+         "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5"))))
     (properties `((upstream-name . "Rbowtie2")))
     (build-system r-build-system)
     (inputs
@@ -5295,14 +5428,14 @@ rapid adapter trimming, identification, and read merging.")
 (define-public r-progeny
   (package
     (name "r-progeny")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "progeny" version))
        (sha256
         (base32
-         "09rq3nf9zm7w9djmx8xc8j3win3597p2v36zqgkhgkjwq5rkjgsh"))))
+         "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -5325,14 +5458,14 @@ expression\".")
 (define-public r-arrmnormalization
   (package
     (name "r-arrmnormalization")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ARRmNormalization" version))
        (sha256
         (base32
-         "0zhhvr051fmh6g0bqrl525mkf094j1jnc57j201jlzmvdpkydlpv"))))
+         "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95"))))
     (properties
      `((upstream-name . "ARRmNormalization")))
     (build-system r-build-system)
@@ -5348,14 +5481,14 @@ Infinium HumanMethylation 450k assay.")
 (define-public r-biocfilecache
   (package
     (name "r-biocfilecache")
-    (version "1.12.1")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocFileCache" version))
        (sha256
         (base32
-         "02yayjyliaqxcwqa0n2ccmsfflskqzf0gvdibh2r3nz5bi66imkf"))))
+         "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1"))))
     (properties `((upstream-name . "BiocFileCache")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5380,14 +5513,14 @@ and data files used across sessions.")
 (define-public r-iclusterplus
   (package
     (name "r-iclusterplus")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iClusterPlus" version))
        (sha256
         (base32
-         "0j987xvxixdz0wnhgp4kgfcgz5jffrcdhmldrgpgv582qmf4r94w"))))
+         "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q"))))
     (properties `((upstream-name . "iClusterPlus")))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
@@ -5410,14 +5543,14 @@ Gaussian distributions.")
 (define-public r-rbowtie
   (package
     (name "r-rbowtie")
-    (version "1.28.1")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie" version))
        (sha256
         (base32
-         "0589ggbfx6di42wvqyhnzgrhmb52swr3r5z22w6b8x0z2y7hl8b3"))))
+         "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507"))))
     (properties `((upstream-name . "Rbowtie")))
     (build-system r-build-system)
     (inputs
@@ -5435,14 +5568,14 @@ alignment tool.")
 (define-public r-sgseq
   (package
     (name "r-sgseq")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SGSeq" version))
        (sha256
         (base32
-         "11rxx7abjyga2sdcp4x4z3n8xjx6973sckyzmh9ax6r46kwhxq8c"))))
+         "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx"))))
     (properties `((upstream-name . "SGSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5478,14 +5611,14 @@ interpretation.")
 (define-public r-rhisat2
   (package
     (name "r-rhisat2")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhisat2" version))
        (sha256
         (base32
-         "0hhmcdnixkaqx9x9cl2vjaba3ri8m6wkbnbhxjmy51jwqzy2223a"))))
+         "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb"))))
     (properties `((upstream-name . "Rhisat2")))
     (build-system r-build-system)
     (arguments
@@ -5518,18 +5651,16 @@ index.")
 (define-public r-quasr
   (package
     (name "r-quasr")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "QuasR" version))
        (sha256
         (base32
-         "0d87ajaaq8a7xgzl820qx5bvxw86ppab8clqk77sj02rfijnvjn8"))))
+         "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8"))))
     (properties `((upstream-name . "QuasR")))
     (build-system r-build-system)
-    (inputs
-     `(("zlib" ,zlib)))
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-biobase" ,r-biobase)
@@ -5565,14 +5696,14 @@ quantification of genomic regions of interest.")
 (define-public r-rqc
   (package
     (name "r-rqc")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rqc" version))
        (sha256
         (base32
-         "1qsm9r6xfsplk8zpf7p0k7fi86l8a74nx963sna8gzig5qgrvnm3"))))
+         "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9"))))
     (properties `((upstream-name . "Rqc")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5608,14 +5739,14 @@ graphics.")
 (define-public r-birewire
   (package
     (name "r-birewire")
-    (version "3.20.0")
+    (version "3.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiRewire" version))
        (sha256
         (base32
-         "0y7jb1abnik2y4ivpyqrgfl77rml6fhz88isd54l646ghslwxj0g"))))
+         "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw"))))
     (properties `((upstream-name . "BiRewire")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5666,14 +5797,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.")
 (define-public r-multidataset
   (package
     (name "r-multidataset")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiDataSet" version))
        (sha256
         (base32
-         "0hjnj32m9wwlh2krdpdyl5jk1cakvlgki80z51mabhc62pajzf39"))))
+         "025gfgn83ancp0khdmq2y4lwm97v5zqnjksi79rr0w175syznx5w"))))
     (properties `((upstream-name . "MultiDataSet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5703,14 +5834,14 @@ packages.")
 (define-public r-ropls
   (package
     (name "r-ropls")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ropls" version))
        (sha256
         (base32
-         "1drww1mr0nira3qplyga6s3mljpjxshjgbn524kzxi0nrfbcvmnx"))))
+         "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -5741,14 +5872,14 @@ coefficients).")
 (define-public r-biosigner
   (package
     (name "r-biosigner")
-    (version "1.16.0")
+    (version "1.18.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biosigner" version))
        (sha256
         (base32
-         "1v760q7hzaybkf2q9230rmr4phi8hglm59qwsjzvncxrhs3dpj06"))))
+         "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -5774,14 +5905,14 @@ datasets.")
 (define-public r-annotatr
   (package
     (name "r-annotatr")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotatr" version))
        (sha256
         (base32
-         "0z3ydcybd81w543fw8fiblghndx5m28w8qsphh5vqj726i0nj8cl"))))
+         "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -5815,14 +5946,14 @@ annotations.")
 (define-public r-rsubread
   (package
     (name "r-rsubread")
-    (version "2.2.6")
+    (version "2.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rsubread" version))
        (sha256
         (base32
-         "04h79qhq93d8id0rr5xnj9vf82ygwxzdlnck78yv738xd0jjvnpm"))))
+         "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra"))))
     (properties `((upstream-name . "Rsubread")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -5841,14 +5972,14 @@ and to both short and long sequence reads.")
 (define-public r-flowutils
   (package
     (name "r-flowutils")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowUtils" version))
        (sha256
         (base32
-         "03jj4zyffm9kwzrg4vbsk6clc2v2m95wgalgqwzi31n9a2zyaza4"))))
+         "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09"))))
     (properties `((upstream-name . "flowUtils")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5867,14 +5998,14 @@ and to both short and long sequence reads.")
 (define-public r-consensusclusterplus
   (package
     (name "r-consensusclusterplus")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ConsensusClusterPlus" version))
        (sha256
         (base32
-         "06gq3a95h0km1hzbx1za8q0l7kla3jdzvn6cnfz43ijx4n3dzzcq"))))
+         "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp"))))
     (properties
      `((upstream-name . "ConsensusClusterPlus")))
     (build-system r-build-system)
@@ -5892,20 +6023,30 @@ cluster count and membership by stability evidence in unsupervised analysis.")
 (define-public r-cytolib
   (package
     (name "r-cytolib")
-    (version "2.0.3")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cytolib" version))
        (sha256
         (base32
-         "123d1wlymq8r8d83as380h1dgw6v4s317acyvp1lsg2cpfp3gslj"))))
+         "1wylzps7wbvm64k62w5bbi8l74gaqca96psfapxfg6mcac5yz4qw"))))
     (properties `((upstream-name . "cytolib")))
     (build-system r-build-system)
-    (inputs
-     `(("zlib" ,zlib)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-linking
+           (lambda _
+             (substitute* "src/Makevars.in"
+               ;; This is to avoid having a plain directory on the list of
+               ;; libraries to link.
+               (("\\(RHDF5_LIBS\\)" match)
+                (string-append match "/libhdf5.a")))
+             #t)))))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     `(("r-knitr" ,r-knitr)
+       ("pkg-config" ,pkg-config)))
     (propagated-inputs
      `(("r-bh" ,r-bh)
        ("r-rcpp" ,r-rcpp)
@@ -5923,14 +6064,14 @@ interact with gated cytometry data.")
 (define-public r-flowcore
   (package
     (name "r-flowcore")
-    (version "2.0.1")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowCore" version))
        (sha256
         (base32
-         "1xalndmfidfzqwlppdanx7cnm4ysznq21ingmykhxni86s42kd8p"))))
+         "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8"))))
     (properties `((upstream-name . "flowCore")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5941,7 +6082,8 @@ interact with gated cytometry data.")
        ("r-matrixstats" ,r-matrixstats)
        ("r-rcpp" ,r-rcpp)
        ("r-rcpparmadillo" ,r-rcpparmadillo)
-       ("r-rprotobuflib" ,r-rprotobuflib)))
+       ("r-rprotobuflib" ,r-rprotobuflib)
+       ("r-s4vectors" ,r-s4vectors)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/flowCore")
@@ -5954,14 +6096,14 @@ with flow cytometry data.")
 (define-public r-flowmeans
   (package
     (name "r-flowmeans")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowMeans" version))
        (sha256
         (base32
-         "1sv5vpwm3qdhkn1gdrk3n674harjcni91g63sqzfmybiwq8dlym7"))))
+         "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734"))))
     (properties `((upstream-name . "flowMeans")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5980,18 +6122,27 @@ change point detection.")
 (define-public r-ncdfflow
   (package
     (name "r-ncdfflow")
-    (version "2.34.0")
+    (version "2.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ncdfFlow" version))
        (sha256
         (base32
-         "0avxn2abh4fk1gkncrxz7jwzgvd90m3m0ly318q0z38cjhsw3j9f"))))
+         "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac"))))
     (properties `((upstream-name . "ncdfFlow")))
     (build-system r-build-system)
-    (inputs
-     `(("zlib" ,zlib)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-linking
+           (lambda _
+             (substitute* "src/Makevars"
+               ;; This is to avoid having a plain directory on the list of
+               ;; libraries to link.
+               (("\\(RHDF5_LIBS\\)" match)
+                (string-append match "/libhdf5.a")))
+             #t)))))
     (propagated-inputs
      `(("r-bh" ,r-bh)
        ("r-biobase" ,r-biobase)
@@ -6013,14 +6164,14 @@ manipulation of flow cytometry data.")
 (define-public r-ggcyto
   (package
     (name "r-ggcyto")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggcyto" version))
        (sha256
         (base32
-         "1ih6ggay7jjxnx8blc2sk95g8d40gkim145jllkk8sqwl02g44p0"))))
+         "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m"))))
     (properties `((upstream-name . "ggcyto")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6050,14 +6201,14 @@ statistics to the plot.")
 (define-public r-flowviz
   (package
     (name "r-flowviz")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowViz" version))
        (sha256
         (base32
-         "0f3jfwdmaq9wrgl737blk5gmpc29l9kb6nadqhxpvbjwqsnzx0yq"))))
+         "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k"))))
     (properties `((upstream-name . "flowViz")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6081,14 +6232,14 @@ statistics to the plot.")
 (define-public r-flowclust
   (package
     (name "r-flowclust")
-    (version "3.26.0")
+    (version "3.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowClust" version))
        (sha256
         (base32
-         "06mkq9y41jax07x4knhvhzgrkgqdvpvcw604bxdk6bv9wx3ipq5b"))))
+         "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq"))))
     (properties `((upstream-name . "flowClust")))
     (build-system r-build-system)
     (arguments
@@ -6121,14 +6272,14 @@ model with Box-Cox transformation.")
 (define-public r-rprotobuflib
   (package
     (name "r-rprotobuflib")
-    (version "2.0.0")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RProtoBufLib" version))
        (sha256
         (base32
-         "0kfinf9vzc1i5qxmaw832id557gr1vqdi1m8yiaxz83g37wh8vps"))))
+         "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz"))))
     (properties `((upstream-name . "RProtoBufLib")))
     (build-system r-build-system)
     (arguments
@@ -6151,18 +6302,31 @@ for other R packages to compile and link against.")
 (define-public r-flowworkspace
   (package
     (name "r-flowworkspace")
-    (version "4.0.6")
+    (version "4.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowWorkspace" version))
        (sha256
         (base32
-         "123ny8n3jjgmsnpghk1dafxkwmcyr513gxi8y4h4qszq4s6ai15v"))))
+         "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag"))))
     (properties `((upstream-name . "flowWorkspace")))
     (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-linking
+           (lambda _
+             (substitute* "src/Makevars"
+               ;; This is to avoid having a plain directory on the list of
+               ;; libraries to link.
+               (("\\{h5lib\\}" match)
+                (string-append match "/libhdf5.a")))
+             #t)))))
     (propagated-inputs
-     `(("r-bh" ,r-bh)
+     `(("r-aws-s3" ,r-aws-s3)
+       ("r-aws-signature" ,r-aws-signature)
+       ("r-bh" ,r-bh)
        ("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
        ("r-cytolib" ,r-cytolib)
@@ -6184,7 +6348,6 @@ for other R packages to compile and link against.")
        ("r-rhdf5lib" ,r-rhdf5lib)
        ("r-rprotobuflib" ,r-rprotobuflib)
        ("r-scales" ,r-scales)
-       ("r-stringr" ,r-stringr)
        ("r-xml" ,r-xml)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -6202,14 +6365,14 @@ matches the flowJo analysis.")
 (define-public r-flowstats
   (package
     (name "r-flowstats")
-    (version "4.0.0")
+    (version "4.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowStats" version))
        (sha256
         (base32
-         "1ygvxvd7y6jp907y0h3hycdwvw1fch16w84g06nk4f4g4kvrzdir"))))
+         "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x"))))
     (properties `((upstream-name . "flowStats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6238,14 +6401,14 @@ package.")
 (define-public r-opencyto
   (package
     (name "r-opencyto")
-    (version "2.0.0")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "openCyto" version))
        (sha256
         (base32
-         "10dyd6dddskv70vhpwfbsqdb8pb9i3ka0fgvl1h51wqlckbsj89m"))))
+         "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v"))))
     (properties `((upstream-name . "openCyto")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6282,16 +6445,27 @@ sequential way to mimic the manual gating strategy.")
 (define-public r-cytoml
   (package
     (name "r-cytoml")
-    (version "2.0.5")
+    (version "2.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CytoML" version))
        (sha256
         (base32
-         "174brv027mm90lydfg6hnhazwh8jy4vf6ial4hpsfalwa5jrz55n"))))
+         "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq"))))
     (properties `((upstream-name . "CytoML")))
     (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-linking
+           (lambda _
+             (substitute* "src/Makevars.in"
+               ;; This is to avoid having a plain directory on the list of
+               ;; libraries to link.
+               (("\\{h5lib\\}" match)
+                (string-append match "/libhdf5.a")))
+             #t)))))
     (inputs
      `(("libxml2" ,libxml2)))
     (propagated-inputs
@@ -6334,14 +6508,14 @@ standard to exchange gated cytometry data with other software platforms.")
 (define-public r-flowsom
   (package
     (name "r-flowsom")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "FlowSOM" version))
        (sha256
         (base32
-         "1p17jv4q1dbcc47jpjy9hbcvzpwrx8waq7qpcj778jsyz6z6jh78"))))
+         "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf"))))
     (properties `((upstream-name . "FlowSOM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6364,20 +6538,21 @@ self-organizing map clustering and minimal spanning trees.")
 (define-public r-mixomics
   (package
     (name "r-mixomics")
-    (version "6.12.2")
+    (version "6.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mixOmics" version))
        (sha256
         (base32
-         "1nkqlvm9j1f4vfj3f3kyxqgan38rpa9imimvl9pwivvsfl647vvc"))))
+         "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q"))))
     (properties `((upstream-name . "mixOmics")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-corpcor" ,r-corpcor)
        ("r-dplyr" ,r-dplyr)
        ("r-ellipse" ,r-ellipse)
+       ("r-ggrepel" ,r-ggrepel)
        ("r-ggplot2" ,r-ggplot2)
        ("r-gridextra" ,r-gridextra)
        ("r-igraph" ,r-igraph)
@@ -6406,16 +6581,16 @@ delete entire rows with missing data.")
     (license license:gpl2+)))
 
 (define-public r-depecher
-  (package
+  (package                              ;Source/Weave error
     (name "r-depecher")
-    (version "1.4.1")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DepecheR" version))
        (sha256
         (base32
-         "0dscfl6wxpl5538jzkrwisdwbr873d38rzd19vl6z5br71jvpv3v"))))
+         "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469"))))
     (properties `((upstream-name . "DepecheR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6425,6 +6600,7 @@ delete entire rows with missing data.")
        ("r-fnn" ,r-fnn)
        ("r-foreach" ,r-foreach)
        ("r-ggplot2" ,r-ggplot2)
+       ("r-gmodels" ,r-gmodels)
        ("r-gplots" ,r-gplots)
        ("r-mass" ,r-mass)
        ("r-matrixstats" ,r-matrixstats)
@@ -6453,14 +6629,14 @@ data, to only emphasize the data that actually matters.")
 (define-public r-rcistarget
   (package
     (name "r-rcistarget")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RcisTarget" version))
        (sha256
         (base32
-         "1lvi873dv0vhw53s1pmcilw8qwlywm9p2ybphcl168nzh6w31r4i"))))
+         "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf"))))
     (properties `((upstream-name . "RcisTarget")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6490,14 +6666,14 @@ genes in the gene-set that are ranked above the leading edge).")
 (define-public r-cicero
   (package
     (name "r-cicero")
-    (version "1.6.2")
+    (version "1.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cicero" version))
        (sha256
         (base32
-         "042ba6yfa7fksij2v7cwnp2sca3vmz7izn6fsxx9xswnncrkgcqh"))))
+         "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -6601,14 +6777,14 @@ cisTopics and explore the nature and regulatory proteins driving them.")
 (define-public r-genie3
   (package
     (name "r-genie3")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GENIE3" version))
        (sha256
         (base32
-         "1bsm0gxracsyg1wnaw3whvskghfpbgbm9navr8wdmxj2hjp3dqs7"))))
+         "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5"))))
     (properties `((upstream-name . "GENIE3")))
     (build-system r-build-system)
     (propagated-inputs `(("r-reshape2" ,r-reshape2)))
@@ -6624,14 +6800,14 @@ regulatory networks from expression data.")
 (define-public r-roc
   (package
     (name "r-roc")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROC" version))
        (sha256
         (base32
-         "0gmx3r77yl5fqrj5j2hamwynbis75qd62q28964kx16z33xfgx89"))))
+         "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9"))))
     (properties `((upstream-name . "ROC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6672,14 +6848,14 @@ data.")
 (define-public r-watermelon
   (package
     (name "r-watermelon")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wateRmelon" version))
        (sha256
         (base32
-         "1c3a6bq3ggmv8kmdfrgiar6nwgircgzjrbgd9z9dqiin7j13gxwn"))))
+         "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f"))))
     (properties `((upstream-name . "wateRmelon")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6709,14 +6885,14 @@ metrics, with methods for objects produced by the @code{methylumi} and
 (define-public r-gdsfmt
   (package
     (name "r-gdsfmt")
-    (version "1.24.1")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gdsfmt" version))
        (sha256
         (base32
-         "0ipf60wylbhvwk9q3mbnak0f1n6k7spfh90s1c1c0b47ryxsri67"))
+         "0x8ik179sf38ihx2y24cvsa9d8isdmx2z27sjhcwq0r3xpjxpz1a"))
        (modules '((guix build utils)))
        ;; Remove bundled sources of zlib, lz4, and xz.  Don't attempt to build
        ;; them and link with system libraries instead.
@@ -6768,14 +6944,14 @@ with multiple R processes supported by the package @code{parallel}.")
 (define-public r-bigmelon
   (package
     (name "r-bigmelon")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigmelon" version))
        (sha256
         (base32
-         "1cryjhbiacm45g097rpqgbva49hs5vdx4y4h5h2v1gw4k78hwb4y"))))
+         "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7"))))
     (properties `((upstream-name . "bigmelon")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6796,22 +6972,20 @@ with multiple R processes supported by the package @code{parallel}.")
 (define-public r-seqbias
   (package
     (name "r-seqbias")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqbias" version))
        (sha256
         (base32
-         "0sy2fv98x4qfz9llns28jh1n4bi991jj856y8a5fbzpx7y990lai"))))
+         "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2"))))
     (properties `((upstream-name . "seqbias")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biostrings" ,r-biostrings)
        ("r-genomicranges" ,r-genomicranges)
        ("r-rhtslib" ,r-rhtslib)))
-    (inputs
-     `(("zlib" ,zlib))) ; This comes from rhtslib.
     (home-page "https://bioconductor.org/packages/seqbias/")
     (synopsis "Estimation of per-position bias in high-throughput sequencing data")
     (description
@@ -6862,14 +7036,14 @@ injected in that sequence).")
 (define-public r-reqon
   (package
     (name "r-reqon")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReQON" version))
        (sha256
         (base32
-         "06m0hd4aqsxjyzhs8b1zys7lz8289qgwn7jp2dpln1j7cf02q4bz"))))
+         "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq"))))
     (properties `((upstream-name . "ReQON")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6887,14 +7061,14 @@ format.")
 (define-public r-wavcluster
   (package
     (name "r-wavcluster")
-    (version "2.22.0")
+    (version "2.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wavClusteR" version))
        (sha256
         (base32
-         "0204czqjmkwhd6gznwxzb0vj3dg3aif628g8c30085aa2jljn9bk"))))
+         "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi"))))
     (properties `((upstream-name . "wavClusteR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6911,8 +7085,7 @@ format.")
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)
        ("r-seqinr" ,r-seqinr)
-       ("r-stringr" ,r-stringr)
-       ("r-wmtsa" ,r-wmtsa)))
+       ("r-stringr" ,r-stringr)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/wavClusteR/")
@@ -6935,14 +7108,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).")
 (define-public r-timeseriesexperiment
   (package
     (name "r-timeseriesexperiment")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TimeSeriesExperiment" version))
        (sha256
         (base32
-         "1k0djvcsyjj1ayncvmi8nlqi3jdn5qp41y3fwsqg1cp0qsvx7zv3"))))
+         "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn"))))
     (properties
      `((upstream-name . "TimeSeriesExperiment")))
     (build-system r-build-system)
@@ -6976,14 +7149,14 @@ provides methods for retrieving enriched pathways.")
 (define-public r-variantfiltering
   (package
     (name "r-variantfiltering")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantFiltering" version))
        (sha256
         (base32
-         "0lsrnybsbm9siyjv4nal6bmprj8ynwgk4n1145f4h52g78wq3br4"))))
+         "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5"))))
     (properties
      `((upstream-name . "VariantFiltering")))
     (build-system r-build-system)
@@ -7082,14 +7255,14 @@ arrays based on fast wavelet-based functional models.")
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.18.3")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "1jrlhi2c5ibvq8a41g5hwdq4kk4rdd7m464rz5767zaaci7l2ay0"))))
+         "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah"))))
     (properties
      `((upstream-name . "variancePartition")))
     (build-system r-build-system)
@@ -7126,14 +7299,14 @@ measures.")
 (define-public r-htqpcr
   (package
     (name "r-htqpcr")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HTqPCR" version))
        (sha256
         (base32
-         "08bd5zkjdnz726s03bvvzv03va0xbrr818ipp6737z9g3nk9m81j"))))
+         "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji"))))
     (properties `((upstream-name . "HTqPCR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7160,14 +7333,14 @@ features (e.g.  genes, microRNAs).")
 (define-public r-unifiedwmwqpcr
   (package
     (name "r-unifiedwmwqpcr")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "unifiedWMWqPCR" version))
        (sha256
         (base32
-         "1l9gxq3askr3cz2a4bqsw7vjr1agivzvx651cblkygv57x08zf81"))))
+         "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv"))))
     (properties
      `((upstream-name . "unifiedWMWqPCR")))
     (build-system r-build-system)
@@ -7251,14 +7424,14 @@ cellular organization in health and disease.")
 (define-public r-bgmix
   (package
     (name "r-bgmix")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BGmix" version))
        (sha256
         (base32
-         "1pfi3hinjn6ymikadgj8dqm59h7mapf01wj86dbbvf8y1xqp8y8n"))))
+         "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50"))))
     (properties `((upstream-name . "BGmix")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7273,14 +7446,14 @@ gene expression.")
 (define-public r-bgx
   (package
     (name "r-bgx")
-    (version "1.54.1")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bgx" version))
        (sha256
         (base32
-         "0a10fg9n5p024jrmbis102gqpbz23sc6vdn1sal2697hlxikzb46"))))
+         "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im"))))
     (properties `((upstream-name . "bgx")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7298,14 +7471,14 @@ Affymetrix GeneChips.")
 (define-public r-bhc
   (package
     (name "r-bhc")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BHC" version))
        (sha256
         (base32
-         "06milqjg2nl3ra47sxi7a2p2d3mbrx3wk168pqgimvs8snldd2xr"))))
+         "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn"))))
     (properties `((upstream-name . "BHC")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BHC/")
@@ -7324,14 +7497,14 @@ algorithm which is more efficient for larger data sets.")
 (define-public r-bicare
   (package
     (name "r-bicare")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BicARE" version))
        (sha256
         (base32
-         "0llckbl3l26lf6wgjg7rxs8k1yrk043vvdhnkc6ncg33sydj383y"))))
+         "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k"))))
     (properties `((upstream-name . "BicARE")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7348,14 +7521,14 @@ results.")
 (define-public r-bifet
   (package
     (name "r-bifet")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiFET" version))
        (sha256
         (base32
-         "1v2dshs09iy2glzq0vwxmr83x867j844i1ixsfcamvfq33fwbbr5"))))
+         "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a"))))
     (properties `((upstream-name . "BiFET")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7378,14 +7551,14 @@ the read count and GC content bias.")
 (define-public r-rsbml
   (package
     (name "r-rsbml")
-    (version "2.46.0")
+    (version "2.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rsbml" version))
        (sha256
         (base32
-         "1i1izznnwzrc6m7s3hblfff466icfvxl2gjdqaln8qfg9v87rslx"))))
+         "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61"))))
     (properties `((upstream-name . "rsbml")))
     (build-system r-build-system)
     (inputs
@@ -7406,14 +7579,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
 (define-public r-hypergraph
   (package
     (name "r-hypergraph")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hypergraph" version))
        (sha256
         (base32
-         "1iq9b9rzy3ikx8xszsjiv3p8l702n2h2s9w33797wcmkg4apslb7"))))
+         "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97"))))
     (properties `((upstream-name . "hypergraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7428,14 +7601,14 @@ manipulating hypergraphs.")
 (define-public r-hyperdraw
   (package
     (name "r-hyperdraw")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hyperdraw" version))
        (sha256
         (base32
-         "1qzx5sqp7rpspk8g1j34p03ds1vmw0h7hpzb2ijpbvmsja5drzvf"))))
+         "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz"))))
     (properties `((upstream-name . "hyperdraw")))
     (build-system r-build-system)
     (inputs `(("graphviz" ,graphviz)))
@@ -7452,14 +7625,14 @@ manipulating hypergraphs.")
 (define-public r-biggr
   (package
     (name "r-biggr")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiGGR" version))
        (sha256
         (base32
-         "05afi6hsh1dv6lc6l0dfhvvi8k34wyzf1k1jimam7a6pbrhyy5dk"))))
+         "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y"))))
     (properties `((upstream-name . "BiGGR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7482,14 +7655,14 @@ networks and estimated fluxes can be visualized with hypergraphs.")
 (define-public r-bigmemoryextras
   (package
     (name "r-bigmemoryextras")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigmemoryExtras" version))
        (sha256
         (base32
-         "053bqcd3p4i7agj43ccjxfz40a1sxrymd49vdpfq8ypslkwk7g0g"))))
+         "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
     (properties
      `((upstream-name . "bigmemoryExtras")))
     (build-system r-build-system)
@@ -7516,14 +7689,14 @@ a file-backed matrix with factor properties.")
 (define-public r-bigpint
   (package
     (name "r-bigpint")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigPint" version))
        (sha256
         (base32
-         "1m92ngkzimcc37byf0ziphrby8wmjd5hfa53gvfphgaakyj9bjg8"))))
+         "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis"))))
     (properties `((upstream-name . "bigPint")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7559,14 +7732,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.")
 (define-public r-chemminer
   (package
     (name "r-chemminer")
-    (version "3.40.0")
+    (version "3.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChemmineR" version))
        (sha256
         (base32
-         "0cna5xsqflvhlp2k47asxyv3w4ympmz2wy2cwjyzlal6936fjikf"))))
+         "14q9zhhxgkx5skj424i2rbjdbp5j8jfkxspkhnkwv5i45cvkgh19"))))
     (properties `((upstream-name . "ChemmineR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7600,14 +7773,14 @@ structures.")
 (define-public r-bioassayr
   (package
     (name "r-bioassayr")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioassayR" version))
        (sha256
         (base32
-         "1n0gsnxcl0lplqk8rs5ygxrxpx389ddl6wv3ciyz9g2xry5biyfy"))))
+         "0vxnd8wnhjdfqh47nc6y1ffiy5r9a6n3g2hyk1r9bv6vhrd0ns3f"))))
     (properties `((upstream-name . "bioassayR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7635,14 +7808,14 @@ available bioactivity data.")
 (define-public r-biobroom
   (package
     (name "r-biobroom")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biobroom" version))
        (sha256
         (base32
-         "06qcrprn58kbrr5kyw1jl6z88b9w9g8xs6rkhrbnz8k7rv373fhf"))))
+         "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv"))))
     (properties `((upstream-name . "biobroom")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7667,14 +7840,14 @@ visualize bioinformatics analyses.")
 (define-public r-graphite
   (package
     (name "r-graphite")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "graphite" version))
        (sha256
         (base32
-         "0rc9cw3picz1y0lwhbzpk03ciij8kij74m15qgzh2ykla7zprb2p"))))
+         "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk"))))
     (properties `((upstream-name . "graphite")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7694,14 +7867,14 @@ symbols).")
 (define-public r-reactomepa
   (package
     (name "r-reactomepa")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReactomePA" version))
        (sha256
         (base32
-         "1ngilyn1mihwxs4sh5gk9y829xghdmh277cfw3vfgflz9sgwy21x"))))
+         "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m"))))
     (properties `((upstream-name . "ReactomePA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7726,14 +7899,14 @@ enrichment analysis and several functions for visualization.")
 (define-public r-ebarrays
   (package
     (name "r-ebarrays")
-    (version "2.52.0")
+    (version "2.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBarrays" version))
        (sha256
         (base32
-         "00ld26bld8xgin9zqwxybahvhmqbrvr09jfphg0yr4j4zck6sqgf"))))
+         "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd"))))
     (properties `((upstream-name . "EBarrays")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7750,14 +7923,14 @@ microarray data.")
 (define-public r-bioccasestudies
   (package
     (name "r-bioccasestudies")
-    (version "1.50.0")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocCaseStudies" version))
        (sha256
         (base32
-         "0fadck1dk1zavpn9yrcwx6zgfi18fw5xfs8svgzipns6bq41j8ix"))))
+         "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
     (properties
      `((upstream-name . "BiocCaseStudies")))
     (build-system r-build-system)
@@ -7772,14 +7945,14 @@ monograph.")
 (define-public r-biocgraph
   (package
     (name "r-biocgraph")
-    (version "1.50.0")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biocGraph" version))
        (sha256
         (base32
-         "1372bm4y3czqhpki10pnprxfkfncfcsy59zzvf8wj6q03acaavrj"))))
+         "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75"))))
     (properties `((upstream-name . "biocGraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7797,14 +7970,14 @@ different graph related packages produced by Bioconductor.")
 (define-public r-experimenthub
   (package
     (name "r-experimenthub")
-    (version "1.14.2")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ExperimentHub" version))
        (sha256
         (base32
-         "1kgvprchz1fg8pl1irj62mk2gyb4jcc9iimpypv4c2iccy5bp84x"))))
+         "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg"))))
     (properties `((upstream-name . "ExperimentHub")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7831,14 +8004,14 @@ access.")
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32
-         "0qlfnd86999jqv2nd0ikixi2sfd449dyg3ml4nbs8ycs57c2irgh"))))
+         "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs"))))
     (properties
      `((upstream-name . "MultiAssayExperiment")))
     (build-system r-build-system)
@@ -7866,14 +8039,14 @@ rownames.")
 (define-public r-bioconcotk
   (package
     (name "r-bioconcotk")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocOncoTK" version))
        (sha256
         (base32
-         "021qzygfwdnd3naz1iqq01zr3zxv3k7wm1lklik24vc7axshxbmk"))))
+         "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108"))))
     (properties `((upstream-name . "BiocOncoTK")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7911,14 +8084,14 @@ tools for genome-scale analysis of cancer studies.")
 (define-public r-biocor
   (package
     (name "r-biocor")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioCor" version))
        (sha256
         (base32
-         "1xghclfqv8d23g72g8914br5zjx4sz9zihzczwwmpl15lghpnqwy"))))
+         "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19"))))
     (properties `((upstream-name . "BioCor")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7940,14 +8113,14 @@ gene selection, testing relationships, and so on.")
 (define-public r-biocpkgtools
   (package
     (name "r-biocpkgtools")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocPkgTools" version))
        (sha256
         (base32
-         "0l5fvi1m4834n4h0iswbap135s9mpaiabw9czzn1r72ssz86vrcr"))))
+         "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m"))))
     (properties `((upstream-name . "BiocPkgTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7990,24 +8163,27 @@ analytics on packages.")
 (define-public r-biocset
   (package
     (name "r-biocset")
-    (version "1.2.2")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSet" version))
        (sha256
         (base32
-         "041hq3rp0kv7kjwcjjrksk8lw3sj6j1v3wdcr8z611k0g0z6p0cj"))))
+         "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg"))))
     (properties `((upstream-name . "BiocSet")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocio" ,r-biocio)
        ("r-dplyr" ,r-dplyr)
        ("r-keggrest" ,r-keggrest)
+       ("r-ontologyindex" ,r-ontologyindex)
        ("r-plyr" ,r-plyr)
        ("r-rlang" ,r-rlang)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-tibble" ,r-tibble)))
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page
@@ -8025,14 +8201,14 @@ accessing web references for elements/sets are also available in BiocSet.")
 (define-public r-biocworkflowtools
   (package
     (name "r-biocworkflowtools")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocWorkflowTools" version))
        (sha256
         (base32
-         "0p9r71ql67sdlgd5pv118lhz8b85pr5y4ijfwzcy8wrr8jwlbddy"))))
+         "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6"))))
     (properties
      `((upstream-name . "BiocWorkflowTools")))
     (build-system r-build-system)
@@ -8058,14 +8234,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
 (define-public r-biodist
   (package
     (name "r-biodist")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioDist" version))
        (sha256
         (base32
-         "17bvxk0anvsp29j5nbblvaymf8qgbj3sz4ir2l7wj8kb8jfi19cp"))))
+         "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap"))))
     (properties `((upstream-name . "bioDist")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8081,14 +8257,14 @@ distance measures.")
 (define-public r-pcatools
   (package
     (name "r-pcatools")
-    (version "2.0.0")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "PCAtools" version))
        (sha256
         (base32
-         "0mnwqrhm1hmhzwrpidf6z207w1ycpm572snvpp5swlg6hnxq6bnc"))))
+         "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb"))))
     (properties `((upstream-name . "PCAtools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8127,14 +8303,14 @@ dimensional mass cytometry data.")
 (define-public r-rgreat
   (package
     (name "r-rgreat")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGREAT" version))
        (sha256
         (base32
-         "0n8dw9ibb2klsczcxvvinpi9l53w8cs436i0c8w2jmramayl593v"))))
+         "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj"))))
     (properties `((upstream-name . "rGREAT")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8155,14 +8331,14 @@ user's input and automatically retrieving results from GREAT web server.")
 (define-public r-m3c
   (package
     (name "r-m3c")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "M3C" version))
        (sha256
         (base32
-         "0zq8lm4280p8h65i7myscwa4srs5ajh944xv6zni2f5sjyp7ij2y"))))
+         "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5"))))
     (properties `((upstream-name . "M3C")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8188,14 +8364,14 @@ hypothesis @code{K=1}.")
 (define-public r-icens
   (package
     (name "r-icens")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Icens" version))
        (sha256
         (base32
-         "0fh7wgkrw20f61p06i87nccnbig9wv4m0jcg7cx1rw7g2ndnabgp"))))
+         "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr"))))
     (properties `((upstream-name . "Icens")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8274,13 +8450,13 @@ with:
 (define-public r-fourcseq
   (package
     (name "r-fourcseq")
-    (version "1.22.1")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "FourCSeq" version))
        (sha256
-        (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
+        (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
     (properties `((upstream-name . "FourCSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8318,14 +8494,14 @@ generated.")
 (define-public r-preprocesscore
   (package
     (name "r-preprocesscore")
-    (version "1.50.0")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "preprocessCore" version))
        (sha256
         (base32
-         "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl"))))
+         "1i5ky3bfbkrz4lgfs72fkckr8q3wq48p38mp05cjmnmh1chmdw38"))))
     (properties
      `((upstream-name . "preprocessCore")))
     (build-system r-build-system)
@@ -8379,14 +8555,14 @@ data manipulation and visualization.")
 (define-public r-rgraphviz
   (package
     (name "r-rgraphviz")
-    (version "2.32.0")
+    (version "2.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rgraphviz" version))
        (sha256
         (base32
-         "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
+         "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77"))))
     (properties `((upstream-name . "Rgraphviz")))
     (build-system r-build-system)
     (arguments
@@ -8417,13 +8593,13 @@ objects from the @code{graph} package.")
 (define-public r-fithic
   (package
     (name "r-fithic")
-    (version "1.14.0")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "FitHiC" version))
               (sha256
                (base32
-                "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp"))))
+                "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2"))))
     (properties `((upstream-name . "FitHiC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8443,13 +8619,13 @@ assays such as Hi-C.")
 (define-public r-hitc
   (package
     (name "r-hitc")
-    (version "1.32.0")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "HiTC" version))
               (sha256
                (base32
-                "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy"))))
+                "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy"))))
     (properties `((upstream-name . "HiTC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8472,16 +8648,27 @@ provided.")
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.16.1")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn"))))
+         "1hr149q03p09y1cjnx8av854j53041wfyq66xpsjw4mypzjf6f28"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-linking
+           (lambda _
+             (substitute* "src/Makevars"
+               ;; This is to avoid having a plain directory on the list of
+               ;; libraries to link.
+               (("\\(RHDF5LIB_LIBS\\)" match)
+                (string-append match "/libhdf5.a")))
+             #t)))))
     (inputs
      `(("zlib" ,zlib)))
     (propagated-inputs
@@ -8502,14 +8689,14 @@ block processing.")
 (define-public r-rhdf5lib
   (package
     (name "r-rhdf5lib")
-    (version "1.10.1")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhdf5lib" version))
        (sha256
         (base32
-         "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
+         "0wia85a6dkgibsjcmpqas5068msck3h3bqpgw2x07bk189z4vay2"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -8544,6 +8731,8 @@ block processing.")
                  ;; Remove unnecessary store reference.
                  (("C Compiler:.*")
                   "C Compiler: GCC\n"))
+               (rename-file "hdf5/src/libhdf5.settings.in"
+                            "hdf5/src/libhdf5.settings")
                (rename-file "Makevars.in" "Makevars")
                (substitute* "Makevars"
                  (("@ZLIB_LIB@") "-lz")
@@ -8584,14 +8773,14 @@ packages.")
 (define-public r-beachmat
   (package
     (name "r-beachmat")
-    (version "2.4.0")
+    (version "2.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "beachmat" version))
        (sha256
         (base32
-         "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi"))))
+         "1yxm5andf4hsxxsmwrn5vl79707yfqkhzzajq6fvhsmaad3f97n7"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -8609,14 +8798,14 @@ matrices.")
 (define-public r-singlecellexperiment
   (package
     (name "r-singlecellexperiment")
-    (version "1.10.1")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SingleCellExperiment" version))
        (sha256
         (base32
-         "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp"))))
+         "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2"))))
     (properties
      `((upstream-name . "SingleCellExperiment")))
     (build-system r-build-system)
@@ -8635,20 +8824,54 @@ factors for each cell, along with the usual metadata for genes and
 libraries.")
     (license license:gpl3)))
 
+(define-public r-scuttle
+  (package
+    (name "r-scuttle")
+    (version "1.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "scuttle" version))
+       (sha256
+        (base32
+         "0l2r6fhyd33dllf2mc5a1pd5sawfvcin54pgh9l1nafqzg3sdv2m"))))
+    (properties `((upstream-name . "scuttle")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-beachmat" ,r-beachmat)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/scuttle")
+    (synopsis "Single-cell RNA-Seq analysis utilities")
+    (description
+     "This package provides basic utility functions for performing single-cell
+analyses, focusing on simple normalization, quality control and data
+transformations.  It also provides some helper functions to assist development
+of other packages.")
+    (license license:gpl3)))
+
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.16.2")
+    (version "1.18.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
+                "14f7yw277nykxmcm7wlhlsf3nizpwzz24hax1icx73lavfxmc535"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-beachmat" ,r-beachmat)
-       ("r-biocgenerics" ,r-biocgenerics)
+     `(("r-biocgenerics" ,r-biocgenerics)
        ("r-biocneighbors" ,r-biocneighbors)
        ("r-biocparallel" ,r-biocparallel)
        ("r-biocsingular" ,r-biocsingular)
@@ -8656,10 +8879,11 @@ libraries.")
        ("r-delayedmatrixstats" ,r-delayedmatrixstats)
        ("r-ggbeeswarm" ,r-ggbeeswarm)
        ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
        ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)
        ("r-rlang" ,r-rlang)
        ("r-s4vectors" ,r-s4vectors)
+       ("r-scuttle" ,r-scuttle)
        ("r-singlecellexperiment" ,r-singlecellexperiment)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
        ("r-viridis" ,r-viridis)))
@@ -8675,14 +8899,14 @@ quality control.")
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.16.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv"))))
+         "1zap12rm61z2hg6ykknbif478nr7g468v8mp50bj5hqgi69ywcww"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
@@ -8691,17 +8915,17 @@ quality control.")
        ("r-biocneighbors" ,r-biocneighbors)
        ("r-biocparallel" ,r-biocparallel)
        ("r-biocsingular" ,r-biocsingular)
+       ("r-bluster" ,r-bluster)
        ("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-scuttle" ,r-scuttle)
        ("r-singlecellexperiment" ,r-singlecellexperiment)
        ("r-statmod" ,r-statmod)
        ("r-summarizedexperiment" ,r-summarizedexperiment)))
@@ -8715,17 +8939,45 @@ cell-specific biases, assignment of cell cycle phase, and detection of highly
 variable and significantly correlated genes.")
     (license license:gpl3)))
 
+(define-public r-sparsematrixstats
+  (package
+    (name "r-sparsematrixstats")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "sparseMatrixStats" version))
+       (sha256
+        (base32
+         "0d1idbda1pzhdam9m0i5rn0c6pl7gwv0v3mcrv4wi5760v9qd5qh"))))
+    (properties
+     `((upstream-name . "sparseMatrixStats")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-matrix" ,r-matrix)
+       ("r-matrixgenerics" ,r-matrixgenerics)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-rcpp" ,r-rcpp)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
+    (synopsis "Summary statistics for rows and columns of sparse matrices")
+    (description
+     "This package provides high performance functions for row and column
+operations on sparse matrices.  Currently, the optimizations are limited to
+data in the column sparse format.")
+    (license license:expat)))
+
 (define-public r-delayedmatrixstats
   (package
     (name "r-delayedmatrixstats")
-    (version "1.10.1")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DelayedMatrixStats" version))
        (sha256
         (base32
-         "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx"))))
+         "1cyvj6ffl10vaiip146dldc1w8if854kpz9nhi50ndhpkmdb8sa0"))))
     (properties
      `((upstream-name . "DelayedMatrixStats")))
     (build-system r-build-system)
@@ -8735,8 +8987,10 @@ variable and significantly correlated genes.")
        ("r-hdf5array" ,r-hdf5array)
        ("r-iranges" ,r-iranges)
        ("r-matrix" ,r-matrix)
+       ("r-matrixgenerics" ,r-matrixgenerics)
        ("r-matrixstats" ,r-matrixstats)
-       ("r-s4vectors" ,r-s4vectors)))
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-sparsematrixstats" ,r-sparsematrixstats)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
@@ -8750,3 +9004,186 @@ contains high-performing functions operating on rows and columns of
 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-mscoreutils
+  (package
+    (name "r-mscoreutils")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MsCoreUtils" version))
+       (sha256
+        (base32
+         "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630"))))
+    (properties `((upstream-name . "MsCoreUtils")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)
+       ("r-rcpp" ,r-rcpp)
+       ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
+    (synopsis "Core utils for mass spectrometry data")
+    (description
+     "This package defines low-level functions for mass spectrometry data and
+is independent of any high-level data structures.  These functions include
+mass spectra processing functions (noise estimation, smoothing, binning),
+quantitative aggregation functions (median polish, robust summarisation,
+etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
+well as misc helper functions, that are used across high-level data structure
+within the R for Mass Spectrometry packages.")
+    (license license:artistic2.0)))
+
+(define-public r-biocio
+  (package
+    (name "r-biocio")
+    (version "1.0.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "BiocIO" version))
+        (sha256
+          (base32
+            "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18"))))
+    (properties `((upstream-name . "BiocIO")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-biocgenerics" ,r-biocgenerics)
+        ("r-genomicranges" ,r-genomicranges)
+        ("r-rcurl" ,r-rcurl)
+        ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/BiocIO")
+    (synopsis "Standard input and output for Bioconductor packages")
+    (description
+      "This package implements `import()` and `export()` standard generics for
+importing and exporting biological data formats. `import()` supports
+whole-file as well as chunk-wise iterative import.  The `import()` interface
+optionally provides a standard mechanism for 'lazy' access via `filter()` (on
+row or element-like components of the file resource), `select()` (on
+column-like components of the file resource) and `collect()`.  The `import()`
+interface optionally provides transparent access to remote (e.g.  via https)
+as well as local access.  Developers can register a file extension, e.g.,
+`.loom` for dispatch from character-based URIs to specific `import()` /
+`export()` methods based on classes representing file types, e.g.,
+`LoomFile()`.")
+    (license license:artistic2.0)))
+
+(define-public r-msmseda
+  (package
+    (name "r-msmseda")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "msmsEDA" version))
+       (sha256
+        (base32
+         "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx"))))
+    (properties `((upstream-name . "msmsEDA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-gplots" ,r-gplots)
+       ("r-mass" ,r-mass)
+       ("r-msnbase" ,r-msnbase)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+    (home-page
+     "https://bioconductor.org/packages/msmsEDA")
+    (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
+    (description
+     "Exploratory data analysis to assess the quality of a set of LC-MS/MS
+experiments, and visualize de influence of the involved factors.")
+    (license license:gpl2)))
+
+(define-public r-msmstests
+  (package
+    (name "r-msmstests")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "msmsTests" version))
+       (sha256
+        (base32
+         "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j"))))
+    (properties `((upstream-name . "msmsTests")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-edger" ,r-edger)
+       ("r-msmseda" ,r-msmseda)
+       ("r-msnbase" ,r-msnbase)
+       ("r-qvalue" ,r-qvalue)))
+    (home-page
+     "https://bioconductor.org/packages/msmsTests")
+    (synopsis "Differential LC-MS/MS expression tests")
+    (description
+     "This packages provides statistical tests for label-free LC-MS/MS data
+by spectral counts, to discover differentially expressed proteins between two
+biological conditions.  Three tests are available: Poisson GLM regression,
+quasi-likelihood GLM regression, and the negative binomial of the edgeR
+package.The three models admit blocking factors to control for nuissance
+variables.To assure a good level of reproducibility a post-test filter is
+available, where we may set the minimum effect size considered biologicaly
+relevant, and the minimum expression of the most abundant condition.")
+    (license license:gpl2)))
+
+(define-public r-catalyst
+  (package
+    (name "r-catalyst")
+    (version "1.14.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "CATALYST" version))
+        (sha256
+          (base32
+            "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh"))))
+    (properties `((upstream-name . "CATALYST")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-circlize" ,r-circlize)
+        ("r-complexheatmap" ,r-complexheatmap)
+        ("r-consensusclusterplus" ,r-consensusclusterplus)
+        ("r-cowplot" ,r-cowplot)
+        ("r-data-table" ,r-data-table)
+        ("r-dplyr" ,r-dplyr)
+        ("r-drc" ,r-drc)
+        ("r-flowcore" ,r-flowcore)
+        ("r-flowsom" ,r-flowsom)
+        ("r-ggplot2" ,r-ggplot2)
+        ("r-ggrepel" ,r-ggrepel)
+        ("r-ggridges" ,r-ggridges)
+        ("r-gridextra" ,r-gridextra)
+        ("r-magrittr" ,r-magrittr)
+        ("r-matrix" ,r-matrix)
+        ("r-matrixstats" ,r-matrixstats)
+        ("r-nnls" ,r-nnls)
+        ("r-purrr" ,r-purrr)
+        ("r-rcolorbrewer" ,r-rcolorbrewer)
+        ("r-reshape2" ,r-reshape2)
+        ("r-rtsne" ,r-rtsne)
+        ("r-s4vectors" ,r-s4vectors)
+        ("r-scales" ,r-scales)
+        ("r-scater" ,r-scater)
+        ("r-singlecellexperiment" ,r-singlecellexperiment)
+        ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page
+      "https://github.com/HelenaLC/CATALYST")
+    (synopsis "Cytometry data analysis tools")
+    (description
+      "This package is Cytometry dATa anALYSis Tools (CATALYST).  Mass
+cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as
+reporters to label antibodies, thereby substantially decreasing spectral
+overlap and allowing for examination of over 50 parameters at the single cell
+level.  While spectral overlap is significantly less pronounced in CyTOF than
+flow cytometry, spillover due to detection sensitivity, isotopic impurities,
+and oxide formation can impede data interpretability.  We designed
+CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for
+preprocessing of cytometry data, including i) normalization using bead
+standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
+    (license license:gpl2+)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5efcfdea11..172bb85791 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7142,14 +7142,14 @@ information as possible.")
 (define-public r-genefilter
   (package
     (name "r-genefilter")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "genefilter" version))
        (sha256
         (base32
-         "1sbbrnq6p90fri0ik6aq2zw26kasw63nyiy7xkzrj6vgyq7x258g"))))
+         "0929g6c4v2qhgipgrh1a5gv6444sm2dp52x9c3qbk03i8wzc6633"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)
@@ -7170,14 +7170,14 @@ high-throughput sequencing experiments.")
 (define-public r-deseq2
   (package
     (name "r-deseq2")
-    (version "1.28.1")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq2" version))
        (sha256
         (base32
-         "0xh12c2skr0bbv893p05gvbismkcnqw8zwh7yz4wmycgajfzg2pp"))))
+         "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp"))))
     (properties `((upstream-name . "DESeq2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7208,14 +7208,14 @@ distribution.")
 (define-public r-dexseq
   (package
     (name "r-dexseq")
-    (version "1.34.1")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DEXSeq" version))
        (sha256
         (base32
-         "1m03awaw06mfv5gszq23k5apsqqzjqa5rcwp20y4xbpl7bywpsyl"))))
+         "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
     (properties `((upstream-name . "DEXSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7253,14 +7253,14 @@ exploration of the results.")
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.30.1")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "1a2155jxbwc6qr3dcyvp850grhdr7czc7bs3s87ff4sgdl0jp3jw"))))
+         "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
@@ -7285,14 +7285,14 @@ databases.  Packages produced are intended to be used with AnnotationDbi.")
 (define-public r-rbgl
   (package
     (name "r-rbgl")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RBGL" version))
        (sha256
         (base32
-         "079599a6xn2i7snfn2vgshkw0c00rrfhj44pvi03ap8id29bkayy"))))
+         "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
     (properties `((upstream-name . "RBGL")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7308,14 +7308,14 @@ the graph algorithms contained in the Boost library.")
 (define-public r-gseabase
   (package
     (name "r-gseabase")
-    (version "1.50.1")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GSEABase" version))
        (sha256
         (base32
-         "1k4faj53cwvqijad8cf7fcghzxcv9shlbpl8n73bsncc8k192y2j"))))
+         "0lcxbxfg62zdf2nql49asn3555cqrrxpjm2xsxf7vlxv84dl6r44"))))
     (properties `((upstream-name . "GSEABase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7337,14 +7337,14 @@ Enrichment Analysis} (GSEA).")
 (define-public r-category
   (package
     (name "r-category")
-    (version "2.54.0")
+    (version "2.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Category" version))
        (sha256
         (base32
-         "1grspdzk5a4vidnxwcd1jmy1vcn494aydsp3vydx235yv7iqac1b"))))
+         "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr"))))
     (properties `((upstream-name . "Category")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7368,14 +7368,14 @@ analysis.")
 (define-public r-gostats
   (package
     (name "r-gostats")
-    (version "2.54.0")
+    (version "2.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOstats" version))
        (sha256
         (base32
-         "00q39cyv4l28r6s9gjnd0qhl7h80vmwp4lpmchisqzj44xzyics9"))))
+         "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j"))))
     (properties `((upstream-name . "GOstats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7399,14 +7399,14 @@ testing and other simple calculations.")
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "0l4kdln69y6yhln0xiv2jmpxg05fjcglln406p43a2bqvk2lr03d"))))
+         "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs
@@ -7419,6 +7419,7 @@ testing and other simple calculations.")
        ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicalignments" ,r-genomicalignments)
        ("r-genomicranges" ,r-genomicranges)
+       ("r-rhtslib" ,r-rhtslib)
        ("r-hwriter" ,r-hwriter)
        ("r-iranges" ,r-iranges)
        ("r-lattice" ,r-lattice)
@@ -7441,14 +7442,14 @@ ungapped alignment formats.")
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "1.22.0")
+    (version "1.24.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "01ilhlrvy28jfdyxjria4024yryj5zgympgqznw17g3y3az78kk2"))))
+         "0blvvci57q12sl18yvw07233rfnj47mfadzm0pdpig1ll5z6ld2j"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7464,6 +7465,7 @@ ungapped alignment formats.")
        ("r-ggplot2" ,r-ggplot2)
        ("r-go-db" ,r-go-db)
        ("r-gostats" ,r-gostats)
+       ("r-iranges" ,r-iranges)
        ("r-limma" ,r-limma)
        ("r-magrittr" ,r-magrittr)
        ("r-pheatmap" ,r-pheatmap)
@@ -7494,14 +7496,14 @@ annotation infrastructure.")
 (define-public r-grohmm
   (package
     (name "r-grohmm")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "groHMM" version))
        (sha256
         (base32
-         "04z9qq1xwdsaxbqhyld37w0ybvzly9pc1hcyrnwdbyjwd7n1fncb"))))
+         "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx"))))
     (properties `((upstream-name . "groHMM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7727,13 +7729,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.56.2")
+    (version "1.58.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "0kw0qfm1fw5yv2rbz6x23431rh0fnzj66f2bls7j285biyjmmx7w"))))
+                "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -7755,13 +7757,13 @@ also known as views, in a controlled vocabulary.")
 (define-public r-biocstyle
   (package
     (name "r-biocstyle")
-    (version "2.16.1")
+    (version "2.18.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocStyle" version))
               (sha256
                (base32
-                "09sz2bnbfbj8wz16k0q8xrvag9fldxqyp5vbg9pvd9skh28hv7c7"))))
+                "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp"))))
     (properties
      `((upstream-name . "BiocStyle")))
     (build-system r-build-system)
@@ -7783,13 +7785,13 @@ functionality.")
 (define-public r-bioccheck
   (package
     (name "r-bioccheck")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocCheck" version))
               (sha256
                (base32
-                "1p9ys18sn1crxw1iac2jdgqvwpb5hjd9nfxx0qn0ncrv0b550mny"))))
+                "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
     (properties
      `((upstream-name . "BiocCheck")))
     (build-system r-build-system)
@@ -7832,13 +7834,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.26.1")
+    (version "0.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "1ddr3ngyczx332zw9ai1a6h7442lgrbfcj8vrhvbkdkzqwj14xmb"))))
+                "0rfn46g2mfda01s75vpcfn5jc7xkp0jrl5v79gyd40jm37p4j1zv"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -7859,13 +7861,13 @@ S4Vectors package itself.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.22.2")
+    (version "2.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "1y24jw62806wp2afiyj1x6n00gj7d3323klqdypra9q43pg1w49d"))))
+                "1lfc8xz45v63y3q40im00i944hi0p9idwhx50w3nzkwdpk79315b"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
@@ -7911,13 +7913,13 @@ ID and species.  It is used by functions in the GenomeInfoDb package.")
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.24.2")
+    (version "1.26.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "1cqs53p4m5q1dr59war72bccphy01ilw4xra24fmngrv4x32rznd"))))
+                "092izc49maxjhf6m4b0qx21ad16dz7bmxy5pysp3vkyhdrfa2f7v"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
@@ -7941,13 +7943,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.30.3")
+    (version "3.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "1z9bkg08rgqn3jm2s4ndbj641w33wl8jd3j6m5if6h2nnw6011ic"))))
+                "0dkjd6li270icy1x5qbzpakk9bx712mdm5k32lrr3yrggq92jhjg"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7969,17 +7971,15 @@ CAGE.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.34.0")
+    (version "1.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "09y6ymwky839nb0y7y93w810hk9mvwqn7595q1276c28dkddiqvw"))))
+                "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
-    (inputs
-     `(("zlib" ,zlib)))
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-biobase" ,r-biobase)
@@ -7991,6 +7991,7 @@ CAGE.")
        ("r-genomicfeatures" ,r-genomicfeatures)
        ("r-genomicranges" ,r-genomicranges)
        ("r-iranges" ,r-iranges)
+       ("r-matrixgenerics" ,r-matrixgenerics)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
        ("r-rhtslib" ,r-rhtslib)
        ("r-rsamtools" ,r-rsamtools)
@@ -8008,13 +8009,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.44.3")
+    (version "3.46.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "09fnqxx4rzq5n447aqg2l6y0idfwgz2jxz99sifxsr2q8afzbcj6"))))
+                "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -8027,13 +8028,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-xvector
   (package
     (name "r-xvector")
-    (version "0.28.0")
+    (version "0.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "XVector" version))
               (sha256
                (base32
-                "11h1hszv4798q1gbx8r6zf8vlaqx4v9ql0lbh2xaxybp66a03pvc"))))
+                "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq"))))
     (properties
      `((upstream-name . "XVector")))
     (build-system r-build-system)
@@ -8063,13 +8064,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.40.0")
+    (version "1.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "0wn1zr2qq0rpv9z2wialgizn6xzdlcjg1w2kif67n53svz6vk2x1"))))
+                "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -8094,13 +8095,13 @@ manipulating genomic intervals and variables defined along a genome.")
 (define-public r-biobase
   (package
     (name "r-biobase")
-    (version "2.48.0")
+    (version "2.50.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biobase" version))
               (sha256
                (base32
-                "13p3kgnxm7hbn8cy289kbhaiyfa6rxx7l1pbvajwqzbay3cxznqp"))))
+                "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4"))))
     (properties
      `((upstream-name . "Biobase")))
     (build-system r-build-system)
@@ -8116,13 +8117,13 @@ on Bioconductor or which replace R functions.")
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.50.3")
+    (version "1.52.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "0qcxfn4pvaksna0nvxr74ysn2wzaxn732pkhd6ffrj8pwhkhy5p3"))))
+                "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)
@@ -8145,13 +8146,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.44.1")
+    (version "2.46.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "0np4nh3gj60mgb6312z7x0z9fg5bhrhw872sp3dzgmqc8q8b84iz"))))
+                "1zpdm8nw1d0m31pdmzw1dccbd6iczfhiklhm4d325zkzf3jrkvxf"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -8163,7 +8164,8 @@ annotation data packages using SQLite data storage.")
        ("r-progress" ,r-progress)
        ("r-rappdirs" ,r-rappdirs)
        ("r-stringr" ,r-stringr)
-       ("r-xml" ,r-xml)))
+       ("r-xml" ,r-xml)
+       ("r-xml2" ,r-xml2)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/biomaRt")
@@ -8182,13 +8184,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.22.0")
+    (version "1.24.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "1lsg5xm5j3ly5k60fidzhkgqc9jgscyfkqngjvd9qp6yfzvsb82g"))))
+                "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -8209,13 +8211,13 @@ objects.")
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.56.0")
+    (version "2.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "0imhfz7dg8b3l5qzipjranqqshdsg2x6zc49drlhn8sc7j40cvi8"))))
+                "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)
@@ -8236,13 +8238,13 @@ biological sequences or sets of sequences.")
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "2.4.0")
+    (version "2.6.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "0z01z0s71f941k7sns46nyabps28c69d6jxx6sppjpc6h4vrw0vq"))))
+                "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
@@ -8256,8 +8258,6 @@ biological sequences or sets of sequences.")
              (substitute* "NAMESPACE"
                (("import\\(zlibbioc\\)") ""))
              #t)))))
-    (inputs
-     `(("zlib" ,zlib)))
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-biocparallel" ,r-biocparallel)
@@ -8281,13 +8281,13 @@ tab-delimited (tabix) files.")
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-    (version "0.14.1")
+    (version "0.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DelayedArray" version))
               (sha256
                (base32
-                "0xi0i621hrl7k9rsc8x8nc3ib74sk8hxhbyr2lxqclw45pk95s7v"))))
+                "1564wnradxw15nsnv6w2wd3xngcs3xa1mlibbq3hygi5fcx4fk3g"))))
     (properties
      `((upstream-name . "DelayedArray")))
     (build-system r-build-system)
@@ -8296,7 +8296,7 @@ tab-delimited (tabix) files.")
        ("r-s4vectors" ,r-s4vectors)
        ("r-iranges" ,r-iranges)
        ("r-matrix" ,r-matrix)
-       ("r-matrixstats" ,r-matrixstats)))
+       ("r-matrixgenerics" ,r-matrixgenerics)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/DelayedArray")
@@ -8314,13 +8314,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.18.2")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "1raw5ycigr6gjgzn3kx3jls5hzww10fhnwd8c17c20hmhirf13rw"))))
+                "04x6d4mcsnvz6glkmf6k2cv3fs8zk03i9rvv0ahpl793n8l411ps"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
@@ -8332,6 +8332,7 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
        ("r-genomicranges" ,r-genomicranges)
        ("r-iranges" ,r-iranges)
        ("r-matrix" ,r-matrix)
+       ("r-matrixgenerics" ,r-matrixgenerics)
        ("r-s4vectors" ,r-s4vectors)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -8347,13 +8348,13 @@ samples.")
 (define-public r-genomicalignments
   (package
     (name "r-genomicalignments")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicAlignments" version))
               (sha256
                (base32
-                "0v8k6d7frm5p48cmk4zik78cw9abz4inx0zhl4zrmmx31ifyvk8d"))))
+                "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))
     (properties
      `((upstream-name . "GenomicAlignments")))
     (build-system r-build-system)
@@ -8380,13 +8381,13 @@ alignments.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.48.0")
+    (version "1.50.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "1zcgk92sidhy4y7ws9ms4nkkh2hnccfhfh53qgna0kma9jy4v5xf"))))
+                "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -8413,7 +8414,8 @@ alignments.")
        ("r-rsamtools" ,r-rsamtools)
        ("r-s4vectors" ,r-s4vectors)
        ("r-xml" ,r-xml)
-       ("r-xvector" ,r-xvector)))
+       ("r-xvector" ,r-xvector)
+       ("r-zlibbioc" ,r-zlibbioc)))
     (home-page "https://bioconductor.org/packages/rtracklayer")
     (synopsis "R interface to genome browsers and their annotation tracks")
     (description
@@ -8427,13 +8429,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.40.1")
+    (version "1.42.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "0zm7q957g952qyfqmvf27sldsnq6sqd0wlgnqzvmxayg9pxh0l0z"))))
+                "17dyd9hcw6pw16y353dh55wfhxmkxka99lbsxsp9xyrhffwrxi0s"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -8494,13 +8496,13 @@ information about the latest version of the Gene Ontologies.")
 (define-public r-topgo
   (package
     (name "r-topgo")
-    (version "2.40.0")
+    (version "2.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "topGO" version))
               (sha256
                (base32
-                "13rhbvn27sj75fklf1cnjaazacx8yyjlhqlnbp5zk157q6y5cwdr"))))
+                "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl"))))
     (properties
      `((upstream-name . "topGO")))
     (build-system r-build-system)
@@ -8527,13 +8529,13 @@ dependencies between GO terms can be implemented and applied.")
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
-    (version "1.56.0")
+    (version "1.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome" version))
               (sha256
                (base32
-                "1jw8r1qm9fpg2s1cw2y4np243jjxm65j2xdy2785h8fc1b02msf6"))))
+                "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq"))))
     (properties
      `((upstream-name . "BSgenome")))
     (build-system r-build-system)
@@ -8558,13 +8560,13 @@ genome data packages and support for efficient SNP representation.")
 (define-public r-impute
   (package
     (name "r-impute")
-    (version "1.62.0")
+    (version "1.64.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "impute" version))
               (sha256
                (base32
-                "161p6l1cp3wwdynkxwvg0yhrh6yv20brdlplw5w5mavn4hf1nm0h"))))
+                "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa"))))
     (native-inputs
      `(("gfortran" ,gfortran)))
     (build-system r-build-system)
@@ -8578,13 +8580,13 @@ microarray data, using nearest neighbor averaging.")
 (define-public r-seqpattern
   (package
     (name "r-seqpattern")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "seqPattern" version))
               (sha256
                (base32
-                "0f1yvx2ri1557rzjx08q5bgml1cvkm8hjl8xn1qi4rjs64sy6mci"))))
+                "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq"))))
     (properties
      `((upstream-name . "seqPattern")))
     (build-system r-build-system)
@@ -8605,13 +8607,13 @@ reference point and sorted by a user defined feature.")
 (define-public r-genomation
   (package
     (name "r-genomation")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "genomation" version))
               (sha256
                (base32
-                "1cy8kqwddiha5jy6nda1al956i4wncbgjkrxwijdb08cmka2sfwh"))))
+                "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biostrings" ,r-biostrings)
@@ -8653,7 +8655,7 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
 (define-public r-genomationdata
   (package
     (name "r-genomationdata")
-    (version "1.14.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8663,7 +8665,7 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
                                   "genomationData_" version ".tar.gz"))
               (sha256
                (base32
-                "10xyb8akjrhmak2i0mnv1agny2ipy364q9nlibyplpzc7vdb6bw7"))))
+                "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
     (build-system r-build-system)
     ;; As this package provides little more than large data files, it doesn't
     ;; make sense to build substitutes.
@@ -8681,16 +8683,18 @@ downloaded from Encode.")
 (define-public r-seqlogo
   (package
     (name "r-seqlogo")
-    (version "1.54.3")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqLogo" version))
        (sha256
         (base32
-         "09kkxir305fv8z2yyihvspkrzclxbw1cx5mvhfkrhl10rap6662j"))))
+         "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1"))))
     (properties `((upstream-name . "seqLogo")))
     (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/seqLogo")
     (synopsis "Sequence logos for DNA sequence alignments")
     (description
@@ -8729,13 +8733,13 @@ throughput genetic sequencing data sets using regression methods.")
 (define-public r-zlibbioc
   (package
     (name "r-zlibbioc")
-    (version "1.34.0")
+    (version "1.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "zlibbioc" version))
               (sha256
                (base32
-                "0j1l052jb2cwc1nifxzwknc9csagf4f2d092zs0i95dz0rma89l0"))))
+                "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg"))))
     (properties
      `((upstream-name . "zlibbioc")))
     (build-system r-build-system)
@@ -8771,14 +8775,14 @@ secondary structure and comparative analysis in R.")
 (define-public r-rhtslib
   (package
     (name "r-rhtslib")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhtslib" version))
        (sha256
         (base32
-         "186r7icrkzrni1c4n33ip7dlsfgys7hnqf0simvxrpl3yhh3ygdi"))))
+         "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4"))))
     (properties `((upstream-name . "Rhtslib")))
     (build-system r-build-system)
     ;; Without this a temporary directory ends up in the Rhtslib.so binary,
@@ -8786,9 +8790,8 @@ secondary structure and comparative analysis in R.")
     (arguments '(#:configure-flags '("--no-staged-install")))
     (propagated-inputs
      `(("curl" ,curl)
+       ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
        ("r-zlibbioc" ,r-zlibbioc)))
-    (inputs
-     `(("zlib" ,zlib)))
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("r-knitr" ,r-knitr)))
@@ -8803,14 +8806,14 @@ of other R packages who wish to make use of HTSlib.")
 (define-public r-bamsignals
   (package
     (name "r-bamsignals")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bamsignals" version))
        (sha256
         (base32
-         "0p858xxfv79yc8b3lq58zl9f00irvbn3czsd8wdi5040xg42m402"))))
+         "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -8819,8 +8822,6 @@ of other R packages who wish to make use of HTSlib.")
        ("r-rcpp" ,r-rcpp)
        ("r-rhtslib" ,r-rhtslib)
        ("r-zlibbioc" ,r-zlibbioc)))
-    (inputs
-     `(("zlib" ,zlib)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/bamsignals")
@@ -8835,13 +8836,13 @@ paired-end data.")
 (define-public r-rcas
   (package
     (name "r-rcas")
-    (version "1.14.0")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "RCAS" version))
               (sha256
                (base32
-                "0f812pgv3ys1zv4n9sqkgm01hj4cdd0i0h85dqbhkwd94zl6cavl"))))
+                "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m"))))
     (properties `((upstream-name . "RCAS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8935,33 +8936,40 @@ library implementing most of the pipeline's features.")
 (define-public r-mutationalpatterns
   (package
     (name "r-mutationalpatterns")
-    (version "2.0.0")
+    (version "3.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MutationalPatterns" version))
        (sha256
         (base32
-         "02lyjiabyhmifycksvpcx29a0pb7z9xjw0hgg8n0sd0dy3afqhcm"))))
+         "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35"))))
     (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
        ;; These two packages are suggested packages
        ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
        ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-genomicranges" ,r-genomicranges)
+       ("r-cowplot" ,r-cowplot)
+       ("r-dplyr" ,r-dplyr)
        ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggalluvial" ,r-ggalluvial)
+       ("r-ggdendro" ,r-ggdendro)
        ("r-ggplot2" ,r-ggplot2)
        ("r-iranges" ,r-iranges)
+       ("r-magrittr" ,r-magrittr)
        ("r-nmf" ,r-nmf)
-       ("r-plyr" ,r-plyr)
        ("r-pracma" ,r-pracma)
-       ("r-reshape2" ,r-reshape2)
-       ("r-cowplot" ,r-cowplot)
-       ("r-ggdendro" ,r-ggdendro)
+       ("r-purrr" ,r-purrr)
        ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)
        ("r-variantannotation" ,r-variantannotation)))
     (home-page "https://bioconductor.org/packages/MutationalPatterns/")
     (synopsis "Extract and visualize mutational patterns in genomic data")
@@ -9040,13 +9048,13 @@ factors bound at the specific regions.")
 (define-public r-tximport
   (package
     (name "r-tximport")
-    (version "1.16.1")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tximport" version))
               (sha256
                (base32
-                "1x9959lkjl2h869rgd1b30q1idxzjkr1fyqbpndqk3kbi4q2gr40"))))
+                "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -9061,21 +9069,57 @@ provided as a matrix which can be used as an offset for different expression
 of gene-level counts.")
     (license license:gpl2+)))
 
+(define-public r-rhdf5filters
+  (package
+    (name "r-rhdf5filters")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "rhdf5filters" version))
+       (sha256
+        (base32
+         "1jvnss44liapbc6hk93yg1gknv0ahd5x86dydqiwq9l65jd03psq"))))
+    (properties `((upstream-name . "rhdf5filters")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rhdf5lib" ,r-rhdf5lib)))
+    (inputs
+     `(("zlib" ,zlib)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/grimbough/rhdf5filters")
+    (synopsis "HDF5 compression filters")
+    (description
+     "This package provides a collection of compression filters for use with
+HDF5 datasets.")
+    (license license:bsd-2)))
+
 (define-public r-rhdf5
   (package
     (name "r-rhdf5")
-    (version "2.32.3")
+    (version "2.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rhdf5" version))
               (sha256
                (base32
-                "0fnx60dpf6s2qwq48lg98g18g8k7wgm66pw0kamlbb7l2hnwycvf"))))
+                "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi"))))
     (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-linking
+           (lambda _
+             (substitute* "src/Makevars"
+               ;; This is to avoid having a plain directory on the list of
+               ;; libraries to link.
+               (("\\(RHDF5_LIBS\\)" match)
+                (string-append match "/libhdf5.a")))
+             #t)))))
     (propagated-inputs
-     `(("r-rhdf5lib" ,r-rhdf5lib)))
-    (inputs
-     `(("zlib" ,zlib)))
+     `(("r-rhdf5filters" ,r-rhdf5filters)
+       ("r-rhdf5lib" ,r-rhdf5lib)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/rhdf5")
@@ -9093,13 +9137,13 @@ the available RAM.")
 (define-public r-annotationfilter
   (package
     (name "r-annotationfilter")
-    (version "1.12.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationFilter" version))
               (sha256
                (base32
-                "18kh1xrhpwb48s1qj4f1v8af3jmw49pnbp5afi2myn9894hxg0cs"))))
+                "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9"))))
     (properties
      `((upstream-name . "AnnotationFilter")))
     (build-system r-build-system)
@@ -9440,14 +9484,14 @@ manipulate and analyze genetic variants.")
 (define-public r-chipseq
   (package
     (name "r-chipseq")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chipseq" version))
        (sha256
         (base32
-         "0lh859s0aq73vac1phcgagf6n000qgq2xsk0bmfr61n5swifml2a"))))
+         "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -9492,14 +9536,14 @@ GenomicRanges Bioconductor package.")
 (define-public r-copywriter
   (package
     (name "r-copywriter")
-    (version "2.20.0")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CopywriteR" version))
        (sha256
         (base32
-         "0c36wpv0rygkbqpf3dwh5xmc3lr7p8lrdzsq2fbbpw04skl6i7m2"))))
+         "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f"))))
     (properties `((upstream-name . "CopywriteR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9532,13 +9576,13 @@ number detection tools.")
 (define-public r-methylkit
   (package
     (name "r-methylkit")
-    (version "1.14.2")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "methylKit" version))
               (sha256
                (base32
-                "1qr13d2712ypbn96ijic2z5adr5dsd61kzscx7shw6vyj360rlm5"))))
+                "11pmn191n0ga28x1w20cm2cmw8kddl29q6h2xfjjba5bspp2g613"))))
     (properties `((upstream-name . "methylKit")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9563,8 +9607,6 @@ number detection tools.")
        ("r-zlibbioc" ,r-zlibbioc)))
     (native-inputs
      `(("r-knitr" ,r-knitr))) ; for vignettes
-    (inputs
-     `(("zlib" ,zlib)))
     (home-page "https://github.com/al2na/methylKit")
     (synopsis
      "DNA methylation analysis from high-throughput bisulfite sequencing results")
@@ -9581,14 +9623,14 @@ TAB-Seq.")
 (define-public r-sva
   (package
     (name "r-sva")
-    (version "3.36.0")
+    (version "3.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "sva" version))
        (sha256
         (base32
-         "0xa1lm0k1a6nig90mab6xh4gln88rbs5l1cdr6ik6agg7jhs7ji4"))))
+         "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-edger" ,r-edger)
@@ -9644,14 +9686,14 @@ trait.")
 (define-public r-protgenerics
   (package
     (name "r-protgenerics")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ProtGenerics" version))
        (sha256
         (base32
-         "14xzdh7vxss8vmrw91hcwrszdn3ikm71mah8875b2lkrkrfzbl73"))))
+         "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz"))))
     (properties `((upstream-name . "ProtGenerics")))
     (build-system r-build-system)
     (home-page "https://github.com/lgatto/ProtGenerics")
@@ -9664,14 +9706,14 @@ proteomics packages.")
 (define-public r-mzr
   (package
     (name "r-mzr")
-    (version "2.22.0")
+    (version "2.24.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzR" version))
        (sha256
         (base32
-         "1r8j8yiz5lcan7j4h37sza2kwczl48dxvld3da3ghjjq67cdc2cm"))
+         "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -9686,14 +9728,19 @@ proteomics packages.")
            (lambda _
              (substitute* "src/Makevars"
                (("\\./boost/libs.*") "")
-               (("ARCH_OBJS=" line)
+               ;; This is to avoid having a plain directory on the list of
+               ;; libraries to link.
+               (("\\(RHDF5_LIBS\\)" match)
+                (string-append match "/libhdf5.a"))
+               (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
+               (("\\ARCH_OBJS=" line)
                 (string-append line
-                               "\nARCH_LIBS=-lboost_system -lboost_regex \
+                               "\nBOOST_LIBS=-lboost_system -lboost_regex \
 -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
              #t)))))
     (inputs
      `(;; Our default boost package won't work here, unfortunately, even with
-       ;; mzR version 2.22.0.
+       ;; mzR version 2.24.1.
        ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
        ("zlib" ,zlib)))
     (propagated-inputs
@@ -9720,14 +9767,14 @@ previously been used in XCMS.")
 (define-public r-affyio
   (package
     (name "r-affyio")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyio" version))
        (sha256
         (base32
-         "0j1f61409yq6hmkqrpzamfm7dx35rlq33ccs7wb1qcqx3d3nb75q"))))
+         "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-zlibbioc" ,r-zlibbioc)))
@@ -9744,14 +9791,14 @@ CDF file formats.")
 (define-public r-affy
   (package
     (name "r-affy")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affy" version))
        (sha256
         (base32
-         "0m6hkyjxmsf80n3anhwh9k26csxczv6v92fkb7klnchdski61pyc"))))
+         "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-affyio" ,r-affyio)
@@ -9772,14 +9819,14 @@ analysis.")
 (define-public r-vsn
   (package
     (name "r-vsn")
-    (version "3.56.0")
+    (version "3.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "vsn" version))
        (sha256
         (base32
-         "1k82dikrv1gcync5y1131wg7z1kxv2z2jl4nndg20bixc3398h58"))))
+         "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-affy" ,r-affy)
@@ -9808,14 +9855,14 @@ and specific in detecting differential transcription.")
 (define-public r-mzid
   (package
     (name "r-mzid")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzID" version))
        (sha256
         (base32
-         "0y50lzkdamkpz67f6r5whp246qsxpbammjil7g8vjprx0c4jk5n5"))))
+         "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2"))))
     (properties `((upstream-name . "mzID")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9824,7 +9871,6 @@ and specific in detecting differential transcription.")
        ("r-iterators" ,r-iterators)
        ("r-plyr" ,r-plyr)
        ("r-protgenerics" ,r-protgenerics)
-       ("r-rcpp" ,r-rcpp)
        ("r-xml" ,r-xml)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -9840,14 +9886,14 @@ specific parser.")
 (define-public r-pcamethods
   (package
     (name "r-pcamethods")
-    (version "1.80.0")
+    (version "1.82.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pcaMethods" version))
        (sha256
         (base32
-         "10cww4jxyynkwxbbsx804nwac31j0hh8dgisygld0q663gaxkgni"))))
+         "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0"))))
     (properties `((upstream-name . "pcaMethods")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9870,14 +9916,14 @@ structure (pcaRes) to provide a common interface to the PCA results.")
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.14.2")
+    (version "2.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "17vlv9gh41s1hp043b7j1jfqiw52alh1misjzy1kxl0g90rld00l"))))
+         "0cvcdmq1glifga5qwv9j3lgj31dcrcc6ql4kkk83jy4y43v2zxlx"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9915,30 +9961,43 @@ of mass spectrometry based proteomics data.")
 (define-public r-msnid
   (package
     (name "r-msnid")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnID" version))
        (sha256
         (base32
-         "0dwa6j2nqb3223a8g4f453aznjh69wngrpvdi12iy69j1psbbjcc"))))
+         "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d"))))
     (properties `((upstream-name . "MSnID")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationhub" ,r-annotationhub)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocstyle" ,r-biocstyle)
+       ("r-biostrings" ,r-biostrings)
        ("r-data-table" ,r-data-table)
        ("r-doparallel" ,r-doparallel)
        ("r-dplyr" ,r-dplyr)
        ("r-foreach" ,r-foreach)
+       ("r-ggplot2" ,r-ggplot2)
        ("r-iterators" ,r-iterators)
        ("r-msnbase" ,r-msnbase)
+       ("r-msmstests" ,r-msmstests)
        ("r-mzid" ,r-mzid)
        ("r-mzr" ,r-mzr)
        ("r-protgenerics" ,r-protgenerics)
+       ("r-purrr" ,r-purrr)
        ("r-r-cache" ,r-r-cache)
        ("r-rcpp" ,r-rcpp)
-       ("r-reshape2" ,r-reshape2)))
+       ("r-reshape2" ,r-reshape2)
+       ("r-rlang" ,r-rlang)
+       ("r-runit" ,r-runit)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
+       ("r-xtable" ,r-xtable)))
     (home-page "https://bioconductor.org/packages/MSnID")
     (synopsis "Utilities for LC-MSn proteomics identifications")
     (description
@@ -9954,14 +10013,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
-    (version "3.18.0")
+    (version "3.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "aroma.light" version))
        (sha256
         (base32
-         "19y5f2minx2pp73zdh43v1qkwpkaxygkl8cwlnwja15i46s0bcyc"))))
+         "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0"))))
     (properties `((upstream-name . "aroma.light")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10012,14 +10071,14 @@ distribution.")
 (define-public r-edaseq
   (package
     (name "r-edaseq")
-    (version "2.22.0")
+    (version "2.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EDASeq" version))
        (sha256
         (base32
-         "12gzxjh73qshlwvsf92lbrf4bi199kxg2snrkprh1z4yqf7bjfm4"))))
+         "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip"))))
     (properties `((upstream-name . "EDASeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10030,7 +10089,6 @@ distribution.")
        ("r-biocmanager" ,r-biocmanager)
        ("r-biomart" ,r-biomart)
        ("r-biostrings" ,r-biostrings)
-       ("r-deseq" ,r-deseq)
        ("r-genomicfeatures" ,r-genomicfeatures)
        ("r-genomicranges" ,r-genomicranges)
        ("r-iranges" ,r-iranges)
@@ -10053,14 +10111,14 @@ global-scaling and full-quantile normalization.")
 (define-public r-interactivedisplaybase
   (package
     (name "r-interactivedisplaybase")
-    (version "1.26.3")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "interactiveDisplayBase" version))
        (sha256
         (base32
-         "1x5vipqa4pgwpd62c1c58shnlpv3zyzzpf4wdwr00q1swkdb7wv3"))))
+         "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01"))))
     (properties
      `((upstream-name . "interactiveDisplayBase")))
     (build-system r-build-system)
@@ -10080,14 +10138,14 @@ Shiny-based display methods for Bioconductor objects.")
 (define-public r-annotationhub
   (package
     (name "r-annotationhub")
-    (version "2.20.2")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationHub" version))
        (sha256
         (base32
-         "04bz91m2wx1zm61rvpr0syyklz232fw74wrl73d965wi3x8fyda5"))))
+         "1950x654ffqx53b154kbph808zdh2xm5vmj9vzmc5nxc28fi2z5g"))))
     (properties `((upstream-name . "AnnotationHub")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10121,14 +10179,14 @@ by the user, helping with quick and reproducible access.")
 (define-public r-fastseg
   (package
     (name "r-fastseg")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fastseg" version))
        (sha256
         (base32
-         "1d48n245pzmvcpsz93lxb4frqh222gfhpmlvm0sb74skn16way63"))))
+         "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -10151,14 +10209,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-keggrest
   (package
     (name "r-keggrest")
-    (version "1.28.0")
+    (version "1.30.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGREST" version))
        (sha256
         (base32
-         "0q76w17fya2x0z7mvyhkk5kqh07flldgih13ma44vhcy1bdlm6j1"))))
+         "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s"))))
     (properties `((upstream-name . "KEGGREST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10177,14 +10235,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-gage
   (package
     (name "r-gage")
-    (version "2.38.3")
+    (version "2.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gage" version))
        (sha256
         (base32
-         "1bqmvjiya1df0b3h491lp1jxahiyidvaf9n094z0sk84x5y3xh2p"))))
+         "0xm50wgjjjymv71mbv1clnhx4m12nrd1pc6vfplpdqr5q49v3yd5"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -10208,14 +10266,14 @@ analysis using other methods.")
 (define-public r-genomicfiles
   (package
     (name "r-genomicfiles")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicFiles" version))
        (sha256
         (base32
-         "1k3824pzf9fdqvcv6cz2742q3mabpmncrc72hwa21ac8wy1b04n4"))))
+         "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz"))))
     (properties `((upstream-name . "GenomicFiles")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10225,6 +10283,7 @@ analysis using other methods.")
        ("r-genomicalignments" ,r-genomicalignments)
        ("r-genomicranges" ,r-genomicranges)
        ("r-iranges" ,r-iranges)
+       ("r-matrixgenerics" ,r-matrixgenerics)
        ("r-rsamtools" ,r-rsamtools)
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)
@@ -10241,25 +10300,30 @@ provide added flexibility for data combination and manipulation.")
 (define-public r-complexheatmap
   (package
     (name "r-complexheatmap")
-    (version "2.4.3")
+    (version "2.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ComplexHeatmap" version))
        (sha256
         (base32
-         "1gx0hzrkla92pgmfkrm2zp0ccnhizq6rs26zgzpi5x8a5lvghh5q"))))
+         "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x"))))
     (properties
      `((upstream-name . "ComplexHeatmap")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-circlize" ,r-circlize)
+     `(("r-cairo" ,r-cairo)
+       ("r-circlize" ,r-circlize)
        ("r-clue" ,r-clue)
        ("r-colorspace" ,r-colorspace)
+       ("r-digest" ,r-digest)
        ("r-getoptlong" ,r-getoptlong)
        ("r-globaloptions" ,r-globaloptions)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixstats" ,r-matrixstats)
        ("r-png" ,r-png)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-s4vectors" ,r-s4vectors)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page
@@ -10275,14 +10339,14 @@ self-defined annotation graphics.")
 (define-public r-dirichletmultinomial
   (package
     (name "r-dirichletmultinomial")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DirichletMultinomial" version))
        (sha256
         (base32
-         "1m9dsrddrllb2i88qzik1867iv9mggrgdkn0dlp8sq7gl69vmalb"))))
+         "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk"))))
     (properties
      `((upstream-name . "DirichletMultinomial")))
     (build-system r-build-system)
@@ -10304,14 +10368,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.12.1")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "1vvchc04nshxc768fp31rxb603aj3hmq8xlh5qabcwf2c3z9719g"))))
+         "04il99gcrqzakvc0bxchdp9gghkn1sp9lpiian0iz4y7r67z3wpy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -10349,14 +10413,14 @@ chromosome region or transcript models of lincRNA genes.")
 (define-public r-organismdbi
   (package
     (name "r-organismdbi")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "OrganismDbi" version))
        (sha256
         (base32
-         "194h5576inq44qr666snzq0ygnc77rk5ljkn9bn8zs6x6gb3cwaw"))))
+         "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw"))))
     (properties `((upstream-name . "OrganismDbi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10381,14 +10445,14 @@ the fact that each of these packages implements a select methods.")
 (define-public r-biovizbase
   (package
     (name "r-biovizbase")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biovizBase" version))
        (sha256
         (base32
-         "1vq2mxa2jkljgw75zqjdkyml0ppi5dspvwj4cznfhi31cq8ds0qh"))))
+         "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq"))))
     (properties `((upstream-name . "biovizBase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10423,14 +10487,14 @@ effort and encourages consistency.")
 (define-public r-ggbio
   (package
     (name "r-ggbio")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggbio" version))
        (sha256
         (base32
-         "11ggnqjq42fi2hm9xlvrrlr2xhy4kglvl1a0mycp1s4v67lxw5h5"))))
+         "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -10488,16 +10552,26 @@ interval to data view, mismatch pileup, and several splicing summaries.")
 (define-public r-gqtlbase
   (package
     (name "r-gqtlbase")
-    (version "1.20.4")
+    (version "1.21.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gQTLBase" version))
        (sha256
         (base32
-         "1ly14vhhqxjpbxjypi6ppd37dycabdhf4ny4nsvp9969k418zv41"))))
+         "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
     (properties `((upstream-name . "gQTLBase")))
     (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; This is an upstream bug.
+         (add-after 'unpack 'fix-imports
+           (lambda _
+             (substitute* "NAMESPACE"
+               ((".*maxffmode.*") "")
+               (("importFrom\\(ff,.*") "import(ff)\n"))
+             #t)))))
     (propagated-inputs
      `(("r-batchjobs" ,r-batchjobs)
        ("r-bbmisc" ,r-bbmisc)
@@ -10525,14 +10599,14 @@ and more.")
 (define-public r-snpstats
   (package
     (name "r-snpstats")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "snpStats" version))
        (sha256
         (base32
-         "1qv3nqqr30d3n66mawqd9dbl95dl89r4bcjvkc5iassy1yrwr8wq"))))
+         "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
     (properties `((upstream-name . "snpStats")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -10584,14 +10658,14 @@ several related annotation packages.")
 (define-public r-erma
   (package
     (name "r-erma")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "erma" version))
        (sha256
         (base32
-         "1ccfbq0r48sr3h8050w8zv8402h7nx09adr0xdyqlg7kwp9vd2l3"))))
+         "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -10624,14 +10698,14 @@ by Ernst and Kellis.")
 (define-public r-ldblock
   (package
     (name "r-ldblock")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ldblock" version))
        (sha256
         (base32
-         "0plw00n2zfgh029ab41dnydzgv2yxrapjp770147rx9pff4dngrv"))))
+         "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -10658,14 +10732,14 @@ defining LD blocks.")
 (define-public r-gqtlstats
   (package
     (name "r-gqtlstats")
-    (version "1.20.0")
+    (version "1.21.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gQTLstats" version))
        (sha256
         (base32
-         "1jjqfpjp93nmxjn757j5mzcax96bzcqdd1gr3rsdxg7ap008l2w7"))))
+         "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
     (properties `((upstream-name . "gQTLstats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10714,14 +10788,14 @@ family of feature/genome hypotheses.")
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "0cgkp0ciyy2qykqgh3vzp5mx9b4vsvacjh2jnsj3wldiapzlz08a"))))
+         "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10763,27 +10837,27 @@ with your data.")
 (define-public r-gwascat
   (package
     (name "r-gwascat")
-    (version "2.20.1")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gwascat" version))
        (sha256
         (base32
-         "1cq5cmdrf0a0arr841yvkh6d8drc15p7mif1afr215l1s3y2dwd4"))))
+         "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocfilecache" ,r-biocfilecache)
        ("r-biostrings" ,r-biostrings)
        ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicfeatures" ,r-genomicfeatures)
        ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
        ("r-iranges" ,r-iranges)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)))
+       ("r-readr" ,r-readr)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-snpstats" ,r-snpstats)
+       ("r-variantannotation" ,r-variantannotation)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/gwascat")
@@ -10796,13 +10870,13 @@ EMBL-EBI GWAS catalog.")
 (define-public r-sushi
   (package
     (name "r-sushi")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Sushi" version))
               (sha256
                (base32
-                "17j3d5qjq5nbv99by5mq8rwr0jgh2jyyfn2nwxmwgzlmk3lgi1rb"))))
+                "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
     (properties `((upstream-name . "Sushi")))
     (build-system r-build-system)
     (propagated-inputs
diff --git a/gnu/packages/busybox.scm b/gnu/packages/busybox.scm
index 0a93c6475e..7fc065f7ac 100644
--- a/gnu/packages/busybox.scm
+++ b/gnu/packages/busybox.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 John Darrington <jmd@gnu.org>
-;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -22,6 +22,7 @@
   #:use-module (guix licenses)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix utils)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages)
   #:use-module (gnu packages admin)
@@ -32,7 +33,7 @@
 (define-public busybox
   (package
     (name "busybox")
-    (version "1.31.1")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -40,10 +41,7 @@
                     version ".tar.bz2"))
               (sha256
                (base32
-                "1659aabzp8w4hayr4z8kcpbk2z1q2wqhw7i1yb0l72b45ykl1yfh"))
-              (patches
-               (search-patches
-                "busybox-1.31.1-fix-build-with-glibc-2.31.patch"))))
+                "12g63zsvzfz04wbyga8riyl8ils05riw4xf26cyiaasbs3qqfpf3"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -90,7 +88,7 @@
              ;; true in guix build environment
              (substitute* "testsuite/pidof.tests"
                (("-s init") "-s $(cat /proc/1/comm)"))
-  
+
              ;; This test cannot possibly pass.
              ;; It is trying to test that "which ls" returns "/bin/ls" when PATH is not set.
              ;; However, this relies on /bin/ls existing.  Which it does not in guix.
@@ -135,11 +133,11 @@ any small or embedded system.")
                 "00aw9d809wj1bqlb2fsssdgz7rj0363ya14py0gfdm0rkp98zcpa"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:phases
+     `(#:phases
        (modify-phases %standard-phases
          (add-before 'configure 'set-environment-variables
            (lambda _
-             (setenv "CC" (which "gcc"))
+             (setenv "CC" ,(cc-for-target))
              (setenv "HOSTCC" (which "gcc"))
              #t))
          (replace 'configure
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index 2fb9822fb5..161b45846e 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -68,8 +68,8 @@
                 (file-name (string-append name "-" version "-checkout")))))))
 
 (define-public cuirass
-  (let ((commit "fd432b8e8f449d691773e96e7d90f44761e01aa3")
-        (revision "55"))
+  (let ((commit "697fa14584551d9595cd042f1ffeba240e45a127")
+        (revision "56"))
     (package
       (name "cuirass")
       (version (git-version "0.0.1" revision commit))
@@ -81,7 +81,7 @@
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "10j3w3px0250avwry2x8wsa0m0plvm957g4qqgnajsbc9gvka554"))))
+                  "0gw9cja8fiyra9vnn3y384gwanvsqdq6gwjcvmz91sy5lvfwv34m"))))
       (build-system gnu-build-system)
       (arguments
        '(#:modules ((guix build utils)
@@ -94,7 +94,7 @@
          #:phases
          (modify-phases %standard-phases
            (add-after 'unpack 'disable-repo-tests
-             (λ _
+             (lambda _
                ;; Disable tests that use a connection to the Guix daemon.
                (substitute* "Makefile.am"
                  (("tests/repo.scm \\\\") "\\"))
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index adb1bf421b..45703792ed 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -31,6 +31,7 @@
 ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com>
+;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -95,21 +96,95 @@
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages tcl)
   #:use-module (gnu packages tls)
+  #:use-module (gnu packages version-control)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg))
 
+(define-public r-brio
+  (package
+    (name "r-brio")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "brio" version))
+       (sha256
+        (base32
+         "0f7amcd2cjm09aiq39209cz680l5d2gqpp6wwfhz24zagfsa7cvb"))))
+    (properties `((upstream-name . "brio")))
+    (build-system r-build-system)
+    (home-page "https://github.com/r-lib/brio")
+    (synopsis "Basic R input output")
+    (description
+     "This package provides functions to handle basic input output.  These
+functions always read and write UTF-8 (8-bit Unicode Transformation Format)
+files and provide more explicit control over line endings.")
+    (license license:expat)))
+
+(define-public r-diffobj
+  (package
+    (name "r-diffobj")
+    (version "0.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "diffobj" version))
+       (sha256
+        (base32
+         "0v18zz14g8ppzmj1d997rdmsfh327ml4wvpmfx168lravdsk5ym2"))))
+    (properties `((upstream-name . "diffobj")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-crayon" ,r-crayon)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/brodieG/diffobj")
+    (synopsis "Diffs for R objects")
+    (description
+     "Generate a colorized diff of two R objects for an intuitive
+visualization of their differences.")
+    (license license:gpl2+)))
+
+(define-public r-waldo
+  (package
+    (name "r-waldo")
+    (version "0.2.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "waldo" version))
+       (sha256
+        (base32
+         "0lsw8p4wiggqm9fvh5vgmf0ms0npcg3hcwyzlg5ahv5yx4pv5fhz"))))
+    (properties `((upstream-name . "waldo")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cli" ,r-cli)
+       ("r-diffobj" ,r-diffobj)
+       ("r-fansi" ,r-fansi)
+       ("r-glue" ,r-glue)
+       ("r-rematch2" ,r-rematch2)
+       ("r-rlang" ,r-rlang)
+       ("r-tibble" ,r-tibble)))
+    (home-page "https://github.com/r-lib/waldo")
+    (synopsis "Find differences between R objects")
+    (description
+     "Compare complex R objects and reveal the key differences.  This package
+was designed particularly for use in testing packages where being able to
+quickly isolate key differences makes understanding test failures much
+easier.")
+    (license license:expat)))
+
 (define-public r-rticles
   (package
     (name "r-rticles")
-    (version "0.16")
+    (version "0.17")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rticles" version))
        (sha256
         (base32
-         "1ca3k5sdy9mnm6frcimqwf5k18j14wn69x5iagjnjwhq711l8dv0"))))
+         "1wbwva5n88dw3vvhcrlzkr58cv03hyx0dqgfmxj7d0dgf4ichr3c"))))
     (properties `((upstream-name . "rticles")))
     (build-system r-build-system)
     (propagated-inputs
@@ -147,14 +222,14 @@ degree elevation and curve fitting.")
 (define-public r-v8
   (package
     (name "r-v8")
-    (version "3.3.1")
+    (version "3.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "V8" version))
        (sha256
         (base32
-         "1d2j9p1fsz9hp8n8lrywyrkwivhfa3qx5ha5f24vin8b6l04xy67"))))
+         "1g9z22pc8ydx1yhv57ww2d2jg5hvrl7ilwa79x89zgn17jha5j7m"))))
     (properties `((upstream-name . "V8")))
     (build-system r-build-system)
     (arguments
@@ -255,16 +330,45 @@ ordered indexed observations.  It is particularly aimed at irregular time
 series of numeric vectors/matrices and factors.")
     (license license:gpl2+)))
 
+(define-public r-ggalluvial
+  (package
+   (name "r-ggalluvial")
+   (version "0.12.3")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "ggalluvial" version))
+            (sha256
+             (base32
+              "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
+   (properties `((upstream-name . "ggalluvial")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-dplyr" ,r-dplyr)
+      ("r-ggplot2" ,r-ggplot2)
+      ("r-lazyeval" ,r-lazyeval)
+      ("r-rlang" ,r-rlang)
+      ("r-tidyr" ,r-tidyr)
+      ("r-tidyselect" ,r-tidyselect)))
+   (native-inputs
+    `(("r-knitr" ,r-knitr)))
+   (home-page "http://corybrunson.github.io/ggalluvial/")
+   (synopsis "Alluvial plots for ggplot2")
+   (description "This package provides alluvial plots for @code{ggplot2}.
+Alluvial plots use variable-width ribbons and stacked bar plots to represent
+multi-dimensional or repeated-measures data with categorical or ordinal
+variables.")
+   (license license:gpl3)))
+
 (define-public r-ggpmisc
   (package
     (name "r-ggpmisc")
-    (version "0.3.6")
+    (version "0.3.7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "ggpmisc" version))
               (sha256
                (base32
-                "05i81q9rg8zf35vgcxhn3yhkc9dlvcpwpxncq1q3zs0rxhfkf208"))))
+                "121s6c9k4fn3rcz2myc1kxczllq2826c8zllaii58q8lica7dsyn"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-broom" ,r-broom)
@@ -560,6 +664,30 @@ generalized linear, additive and interaction models to potentially
 high-dimensional data.")
    (license license:gpl2)))
 
+(define-public r-shadowtext
+  (package
+   (name "r-shadowtext")
+   (version "0.0.7")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "shadowtext" version))
+            (sha256
+             (base32
+              "1s1ip8zfr684a3ld7hvf524bhn2j31k6d1wbhh1ni0flsggv2ckf"))))
+   (properties `((upstream-name . "shadowtext")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-ggplot2" ,r-ggplot2)
+      ("r-scales" ,r-scales)))
+   (native-inputs
+    `(("r-knitr" ,r-knitr)))
+   (home-page "https://github.com/GuangchuangYu/shadowtext/")
+   (synopsis "Shadow text grob and layer")
+   (description "This package implements @code{shadowtextGrob()} for
+@code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
+These functions draw text grob with background shadow.")
+   (license license:artistic2.0)))
+
 (define-public r-sys
   (package
     (name "r-sys")
@@ -585,6 +713,34 @@ interrupts and timeouts.  This provides the basis for a sandboxing
 mechanism.")
     (license license:expat)))
 
+(define-public r-ashr
+  (package
+   (name "r-ashr")
+   (version "2.2-47")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "ashr" version))
+            (sha256
+             (base32
+              "1rqb5j30ylaf1h4l66x4jxyn5inrvhc42d90qd5mgkxsq0ghdlr4"))))
+   (properties `((upstream-name . "ashr")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-etrunct" ,r-etrunct)
+      ("r-invgamma" ,r-invgamma)
+      ("r-matrix" ,r-matrix)
+      ("r-mixsqp" ,r-mixsqp)
+      ("r-rcpp" ,r-rcpp)
+      ("r-squarem" ,r-squarem)
+      ("r-truncnorm" ,r-truncnorm)))
+   (native-inputs
+    `(("r-knitr" ,r-knitr)))
+   (home-page "https://github.com/stephens999/ashr")
+   (synopsis "Methods for adaptive shrinkage, using empirical bayes")
+   (description "This package implements an empirical Bayes approach for
+large-scale hypothesis testing and false discovery rate estimation.")
+   (license license:gpl3+)))
+
 (define-public r-askpass
   (package
     (name "r-askpass")
@@ -609,20 +765,20 @@ read a protected key.")
 (define-public r-vegan
   (package
     (name "r-vegan")
-    (version "2.5-6")
+    (version "2.5-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vegan" version))
        (sha256
         (base32
-         "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
+         "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6"))))
     (build-system r-build-system)
     (native-inputs
-     `(("gfortran" ,gfortran)))
+     `(("r-knitr" ,r-knitr)             ; needed for vignettes
+       ("gfortran" ,gfortran)))
     (propagated-inputs
      `(("r-cluster" ,r-cluster)
-       ("r-knitr" ,r-knitr)             ; needed for vignettes
        ("r-lattice" ,r-lattice)
        ("r-mass" ,r-mass)
        ("r-mgcv" ,r-mgcv)
@@ -1396,13 +1552,13 @@ application framework for R, making it easy to create attractive dashboards.")
 (define-public r-shinyfiles
   (package
     (name "r-shinyfiles")
-    (version "0.8.0")
+    (version "0.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shinyFiles" version))
        (sha256
-        (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
+        (base32 "0rsijlx16vd74r7bd8s9zipy71kgpw19v9s85kxj5bmwc6njmbai"))))
     (properties `((upstream-name . "shinyFiles")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1451,20 +1607,19 @@ Bootstrap themes, which are packaged for use with Shiny applications.")
 (define-public r-d3r
   (package
     (name "r-d3r")
-    (version "0.9.0")
+    (version "0.9.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "d3r" version))
        (sha256
         (base32
-         "0vd1qk8yr18xdfkv5ybhqvf0mmccpi721wqa7c881nzm9nnlzc4y"))))
+         "0kc82vvyfxhxvqfalngn36prn3sxdiinsx04rn99ha6zdc27zp5k"))))
     (build-system r-build-system)
     (arguments
      `(#:modules ((guix build utils)
                   (guix build r-build-system)
-                  (srfi srfi-1)
-                  (ice-9 popen))
+                  (srfi srfi-1))
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'process-javascript
@@ -1478,16 +1633,16 @@ Bootstrap themes, which are packaged for use with Shiny applications.")
                         (,(assoc-ref inputs "d3.v4.js")
                          "v4/dist/d3.min.js")
                         (,(assoc-ref inputs "d3.v5.js")
-                         "v5/dist/d3.min.js"))))
+                         "v5/dist/d3.min.js")
+                        (,(assoc-ref inputs "d3.v6.js")
+                         "v6/dist/d3.min.js"))))
                  (lambda (sources targets)
                    (for-each (lambda (source target)
                                (format #t "Processing ~a --> ~a~%"
                                        source target)
                                (delete-file target)
-                               (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
-                                 (call-with-output-file target
-                                   (lambda (port)
-                                     (dump-port minified port)))))
+                               (invoke "esbuild" source "--minify"
+                                       (string-append "--outfile=" target)))
                              sources targets))))
              #t)))))
     (propagated-inputs
@@ -1496,7 +1651,7 @@ Bootstrap themes, which are packaged for use with Shiny applications.")
        ("r-rlang" ,r-rlang)
        ("r-tidyr" ,r-tidyr)))
     (native-inputs
-     `(("uglify-js" ,uglify-js)
+     `(("esbuild" ,esbuild)
        ("d3.v3.js"
         ,(origin
            (method url-fetch)
@@ -1517,7 +1672,14 @@ Bootstrap themes, which are packaged for use with Shiny applications.")
            (uri "https://d3js.org/d3.v5.js")
            (sha256
             (base32
-             "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
+             "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
+       ("d3.v6.js"
+        ,(origin
+           (method url-fetch)
+           (uri "https://d3js.org/d3.v6.js")
+           (sha256
+            (base32
+             "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))))
     (home-page "https://github.com/timelyportfolio/d3r")
     (synopsis "d3.js utilities for R")
     (description
@@ -1912,14 +2074,16 @@ XML.  To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
 (define-public r-colorspace
   (package
     (name "r-colorspace")
-    (version "1.4-1")
+    (version "2.0-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "colorspace" version))
        (sha256
-        (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
+        (base32 "13h1hara0s6xn16bgkrbd0flszah1yiylwfwxwn2inqqk6pm6sjf"))))
     (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://cran.r-project.org/web/packages/colorspace")
     (synopsis "Color space manipulation")
     (description
@@ -2058,13 +2222,13 @@ print, summary, plot, update, etc.
 (define-public r-ps
   (package
     (name "r-ps")
-    (version "1.4.0")
+    (version "1.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ps" version))
        (sha256
-        (base32 "0yns03ffd2a2cs4b6dsjjlqhv46vq2g094m8psmhf3h9i52awyaz"))))
+        (base32 "15pyz94b0z6ibrjp25np5nd4z20whnnr35wsavdgwmsmynba2qbl"))))
     (build-system r-build-system)
     (home-page "https://ps.r-lib.org")
     (synopsis "List, query, and manipulate system processes")
@@ -2308,14 +2472,14 @@ validation and filtering on the values, making options invisible or private.")
 (define-public r-circlize
   (package
     (name "r-circlize")
-    (version "0.4.10")
+    (version "0.4.11")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "circlize" version))
        (sha256
         (base32
-         "1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk"))))
+         "1s84xl7kv3qc1261xxaq4aqh64gwywhacsf5nh6yf8djw0d1w42d"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-colorspace" ,r-colorspace)
@@ -2550,6 +2714,36 @@ quantities.")
 @code{melt} and @code{cast}.  This package provides them.")
     (license license:expat)))
 
+(define-public r-restrserve
+  (package
+    (name "r-restrserve")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RestRserve" version))
+       (sha256
+        (base32 "07mm65yxzpwlg6x3lsggj41v8nl4m6v9mszhqjpgj19v3yxvwgi0"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-checkmate" ,r-checkmate)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-mime" ,r-mime)
+       ("r-r6" ,r-r6)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rserve" ,r-rserve)
+       ("r-uuid" ,r-uuid)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://restrserve.org")
+    (synopsis "R web API framework")
+    (description
+     "RestRserve is an R web API framework for building high-performance AND
+robust microservices and app backends.  With Rserve backend on UNIX-like
+systems it is parallel by design.  It will handle incoming requests in
+parallel - each request in a separate fork.")
+    (license license:gpl2+)))
+
 (define-public r-progress
   (package
     (name "r-progress")
@@ -2751,14 +2945,14 @@ quantile mixture from L-moments and trimmed L-moments.")
 (define-public r-distillery
   (package
     (name "r-distillery")
-    (version "1.1")
+    (version "1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "distillery" version))
        (sha256
         (base32
-         "15qhvhg6wmvlxrvvw70sk8pv76z5pd04vyasgczvxa0599ih7bzh"))))
+         "10nhh9p0hp294pp4aav0y0zsmir2qbn05sf3k52rmzmm36q2kc8y"))))
     (build-system r-build-system)
     (home-page "https://ral.ucar.edu/staff/ericg/")
     (synopsis "Functions for confidence intervals and object information")
@@ -2769,17 +2963,36 @@ complex object; primarily used in common with the packages extRemes and
 SpatialVx.")
     (license license:gpl2+)))
 
+(define-public r-etrunct
+  (package
+   (name "r-etrunct")
+   (version "0.1")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "etrunct" version))
+            (sha256
+             (base32
+              "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
+   (properties `((upstream-name . "etrunct")))
+   (build-system r-build-system)
+   (home-page "https://cran.r-project.org/web/packages/etrunct")
+   (synopsis "Computes moments of univariate truncated T distribution")
+   (description "This package computes moments of univariate truncated
+T distribution.  There is only one exported function, @code{e_trunct},
+which should be seen for details.")
+   (license license:expat)))
+
 (define-public r-extremes
   (package
     (name "r-extremes")
-    (version "2.0-12")
+    (version "2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "extRemes" version))
        (sha256
         (base32
-         "0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2"))))
+         "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid"))))
     (properties `((upstream-name . "extRemes")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2841,13 +3054,13 @@ by Li, Brown, Huang, and Bickel")
 (define-public r-inline
   (package
     (name "r-inline")
-    (version "0.3.16")
+    (version "0.3.17")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "inline" version))
               (sha256
                (base32
-                "0x9m2hwin6anfhkf61cnsbqn4qp1pr2gy1pbwbdgbdz2cmns85nj"))))
+                "1wslsn60q959yrr27cwanba43qlpfaxzdli46i9dc26lxfr5fa3r"))))
     (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")
@@ -2878,6 +3091,24 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
 representation of intervals, including a method of coercing variables
 in data frames.")
     (license license:gpl2)))
+(define-public r-invgamma
+  (package
+   (name "r-invgamma")
+   (version "1.1")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "invgamma" version))
+            (sha256
+             (base32
+              "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
+   (properties `((upstream-name . "invgamma")))
+   (build-system r-build-system)
+   (home-page "https://github.com/dkahle/invgamma")
+   (synopsis "Inverse gamma distribution")
+   (description "This package provides a light weight implementation of the
+standard distribution functions for the inverse gamma distribution, wrapping
+those for the gamma distribution in the @code{stats} package.")
+   (license license:gpl2)))
 
 (define-public r-bdsmatrix
   (package
@@ -3013,14 +3244,14 @@ functions from LINPACK.")
 (define-public r-fitdistrplus
   (package
     (name "r-fitdistrplus")
-    (version "1.1-1")
+    (version "1.1-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fitdistrplus" version))
        (sha256
         (base32
-         "1rnfnwmxa495fql7q0h9018cnwygwhj8gfh6ryz1vbf474570vjl"))))
+         "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)
@@ -3178,14 +3409,14 @@ available in a vignette.")
 (define-public r-lava
   (package
     (name "r-lava")
-    (version "1.6.8")
+    (version "1.6.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lava" version))
        (sha256
         (base32
-         "0jdmjjs894mfncswmzz7sa6cy7hqbqii5fcvl3zqkmzpbadb2za2"))))
+         "1yiz8y3jhxkszgz9m9fialp9r27hy97xh0imfvs8ziv7dk43y93d"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-numderiv" ,r-numderiv)
@@ -3566,14 +3797,14 @@ created using basic graphics.")
 (define-public r-generics
   (package
     (name "r-generics")
-    (version "0.0.2")
+    (version "0.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "generics" version))
        (sha256
         (base32
-         "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
+         "0qw7r0d2qvlj1pvrlpv30d6akml624ydxkk19hv85iv6pfyx2wdb"))))
     (build-system r-build-system)
     (home-page "https://github.com/r-lib/generics")
     (synopsis "Common S3 generics not provided by base R methods")
@@ -3624,14 +3855,14 @@ provides a one-row summary of model-level statistics.")
 (define-public r-recipes
   (package
     (name "r-recipes")
-    (version "0.1.14")
+    (version "0.1.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "recipes" version))
        (sha256
         (base32
-         "0ix678aj71ml5cmfhy1j0b2ddhf5wlb1d74bjc9djr6r86xsqmcz"))))
+         "0xif0ak3w90xmfzlxvb5pnzc3scpfl1pyhrjffi3mq4asvsd52l0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
@@ -3915,21 +4146,23 @@ analysis of multiply imputed data sets.")
 (define-public r-mice
   (package
     (name "r-mice")
-    (version "3.11.0")
+    (version "3.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mice" version))
        (sha256
         (base32
-         "1gawccw32l00rcriyxys0mzbxh44x04rziy0cbycc3i1qm39d4fq"))))
+         "0i7i9r0ipn7fypzp5xv1dnr54l30b7kg38mmq1kcvj2z1mjrwpap"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-broom" ,r-broom)
+       ("r-cpp11" ,r-cpp11)
        ("r-dplyr" ,r-dplyr)
        ("r-generics" ,r-generics)
        ("r-lattice" ,r-lattice)
        ("r-rcpp" ,r-rcpp)
+       ("r-rlang" ,r-rlang)
        ("r-tidyr" ,r-tidyr)))
     (home-page "https://cran.r-project.org/web/packages/mice/")
     (synopsis "Multivariate imputation by chained equations")
@@ -3994,14 +4227,14 @@ programming} (SQP) based solver).")
 (define-public r-hardyweinberg
   (package
     (name "r-hardyweinberg")
-    (version "1.6.8")
+    (version "1.6.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "HardyWeinberg" version))
        (sha256
         (base32
-         "0b6j1mkpr7ck2nr9fmpnsjdv29jc6vg4b91cg50skmcgky1j0zi7"))))
+         "0l93r1hkr483hp4yd7rm7mdkgl5lp0nkvv0inahj3r1cplgfxpvs"))))
     (properties `((upstream-name . "HardyWeinberg")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4352,14 +4585,14 @@ plots in @code{ggplot2}.")
 (define-public r-cli
   (package
     (name "r-cli")
-    (version "2.1.0")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cli" version))
        (sha256
         (base32
-         "03zaq9yhz6gw49qdnhc66b3sw9i916ahkzyg2cgh17dhf31d2acq"))))
+         "1f20mk9pb9kqn0ni2z0sqsx8qj1apcbiw08pa4gwry142zv7m9rr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -4417,13 +4650,13 @@ constants, and control debugging of packages via environment variables.")
 (define-public r-processx
   (package
     (name "r-processx")
-    (version "3.4.4")
+    (version "3.4.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "processx" version))
        (sha256
-        (base32 "0as8lzfpbz5rcpcpczvrrgd67whngkmw12q33r2yn3k7lq80z95a"))))
+        (base32 "055v2gdrgqsfy8s672wsq79bqr44b4jjmcbqivx4p2d6lqx10s73"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ps" ,r-ps)
@@ -4627,14 +4860,14 @@ to variables on the left-hand side of the assignment.")
 (define-public r-vctrs
   (package
     (name "r-vctrs")
-    (version "0.3.4")
+    (version "0.3.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vctrs" version))
        (sha256
         (base32
-         "0xvqgc36zhd9y1xsm7kwrbr5sxwnd3jbr9qrb1gma2lqkqf42izb"))))
+         "1k1mcq7jkpc55dsm0wb4k8asc1irvmi5884v3ap4sabf22c5sq0i"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
@@ -4666,14 +4899,14 @@ to variables on the left-hand side of the assignment.")
 (define-public r-pillar
   (package
     (name "r-pillar")
-    (version "1.4.6")
+    (version "1.4.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pillar" version))
        (sha256
         (base32
-         "01ck8ziqzjc9ibbj3g88siz1iw263dgl8jx6ryw2v50rjrr3y7fj"))))
+         "167ji21fx04s2niw5pjq9vzxgagxzsg3gimh8dzr2kl5ljrb5vfd"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
@@ -4714,14 +4947,14 @@ terminals.")
 (define-public r-tinytex
   (package
     (name "r-tinytex")
-    (version "0.26")
+    (version "0.27")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tinytex" version))
        (sha256
         (base32
-         "02b0v8ydbfspma3rgsdpkf2cm6jl9qm3l9jsrl0xng482b06bb0q"))))
+         "10hbc9h1fsw91w5f4fjcaqy68b3n1wr6pml01fnkf3pdjiri5sj0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-xfun" ,r-xfun)))
@@ -4972,14 +5205,14 @@ provides some missing S-PLUS functionality in R.")
 (define-public r-ifultools
   (package
     (name "r-ifultools")
-    (version "2.0-5")
+    (version "2.0-22")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ifultools" version))
        (sha256
         (base32
-         "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
+         "0f95vqc47dgssqngznk0rclr72ndbyxc7gdq2cmbksvq7qpn3gg1"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)
@@ -5035,14 +5268,14 @@ Fisher's method), and Sidak correction.")
 (define-public r-quantmod
   (package
     (name "r-quantmod")
-    (version "0.4.17")
+    (version "0.4.18")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "quantmod" version))
        (sha256
         (base32
-         "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
+         "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-curl" ,r-curl)
@@ -5059,14 +5292,14 @@ financial trading strategies.")
 (define-public r-tseries
   (package
     (name "r-tseries")
-    (version "0.10-47")
+    (version "0.10-48")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tseries" version))
        (sha256
         (base32
-         "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
+         "0wa4rcf0igayi1yrwc6wak6d491560p0z89rz32haqlkiiq25gak"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-quadprog" ,r-quadprog)
@@ -5599,14 +5832,14 @@ systems.")
 (define-public r-radiant-data
   (package
     (name "r-radiant-data")
-    (version "1.3.10")
+    (version "1.3.12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "radiant.data" version))
        (sha256
         (base32
-         "09a3wn3gl1zjq5zsc5zaxyq71dg5qnpk57bmwd6qy8w99g2clm8c"))
+         "08bqqrfvpgyf613ikihwfnzb23l23f5nfs7zynnxbjxc1zfhbpny"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -6296,14 +6529,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
 (define-public r-renv
   (package
     (name "r-renv")
-    (version "0.12.0")
+    (version "0.12.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "renv" version))
        (sha256
         (base32
-         "1jwm1ik600xswb53i1swjsnfrjjdffmmyk5k9hjc7kc8nlfl0ay5"))))
+         "0k31x19gzpffb701c76p840cip10c0dh8yv3wcs30gqi0ag1g77l"))))
     (properties `((upstream-name . "renv")))
     (build-system r-build-system)
     (native-inputs
@@ -6864,17 +7097,16 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
 (define-public r-rbibutils
   (package
     (name "r-rbibutils")
-    (version "1.3")
+    (version "2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rbibutils" version))
        (sha256
         (base32
-         "1i000czyd059dczd2nn1cb0d4n0bjykrfh51rs85s8r2zlaydn6i"))))
+         "1vfg2188i4dyhrmvnwpsh2la8qkd4wkryz2fpj4cppi1wfz3ml83"))))
     (properties `((upstream-name . "rbibutils")))
     (build-system r-build-system)
-    (propagated-inputs `(("r-xml2" ,r-xml2)))
     (home-page "https://geobosh.github.io/rbibutils/")
     (synopsis "Convert between bibliography formats")
     (description
@@ -6887,14 +7119,14 @@ implemented in bibutils.")
 (define-public r-rdpack
   (package
     (name "r-rdpack")
-    (version "2.0")
+    (version "2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rdpack" version))
        (sha256
         (base32
-         "04gk68y3cxlqhfl1aarjwz2mvx934ka0yxfgzrnw03ykhvb47fpi"))))
+         "1kmz0kq2z1xl55w22paz98x9jpss06abvicmkslv4zq77kz99q16"))))
     (properties `((upstream-name . "Rdpack")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6914,14 +7146,14 @@ references and Rd files.")
 (define-public r-officer
   (package
     (name "r-officer")
-    (version "0.3.14")
+    (version "0.3.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "officer" version))
        (sha256
         (base32
-         "1nyv4710bcd2afh1l1qiy5zrspjcdvc7mrzz5189dwy9xvgxi31h"))))
+         "1s9hrkdx105c1plpxywv68bmp8hvvxbdizhwx81fxr79fhj62x5j"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-magrittr" ,r-magrittr)
@@ -7176,14 +7408,14 @@ other add-on packages.")
 (define-public r-insight
   (package
     (name "r-insight")
-    (version "0.10.0")
+    (version "0.11.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "insight" version))
        (sha256
         (base32
-         "1r4val3hvc43zailfmq6wcbg366s0bi0ysib476a49k1x6h8b6ji"))))
+         "1m95xfvai1kbzqxdggjvdbk6ax2dg4v2lrfpqn7v607g2n77n2k0"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -7310,14 +7542,14 @@ functions.")
 (define-public r-flextable
   (package
     (name "r-flextable")
-    (version "0.5.11")
+    (version "0.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "flextable" version))
        (sha256
         (base32
-         "1yb872izzr9yja7q2vfqm0imcbcgs0fvi4b19arhdlwwa42figj4"))))
+         "06nzyd2a9yaf9hmn740xrgxw0448z5dvlplcj3kizz9sm23aw9li"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-base64enc" ,r-base64enc)
@@ -7330,6 +7562,8 @@ functions.")
        ("r-rmarkdown" ,r-rmarkdown)
        ("r-uuid" ,r-uuid)
        ("r-xml2" ,r-xml2)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://davidgohel.github.io/flextable")
     (synopsis "Functions for tabular reporting")
     (description
@@ -7556,14 +7790,14 @@ the work.")
 (define-public r-doby
   (package
     (name "r-doby")
-    (version "4.6.7")
+    (version "4.6.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "doBy" version))
        (sha256
         (base32
-         "16vg1aa272sfzyqxfb63fyis9hv6g5m3nmxxa6mk1gy0irqnl3jk"))))
+         "0r97kwsj6g87m7shgnjc5c9y71jkhiq4xd9q0s2bxl0vl92qqwvg"))))
     (properties `((upstream-name . "doBy")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7642,14 +7876,14 @@ procedures to speed up calculations in R.")
 (define-public r-blockfest
   (package
     (name "r-blockfest")
-    (version "1.6")
+    (version "1.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "BlockFeST" version))
        (sha256
         (base32
-         "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
+         "12cbrmgqszlj729zrn9d1d7drbr0iay43knnmrzcxs6v7lfszsx5"))))
     (properties `((upstream-name . "BlockFeST")))
     (build-system r-build-system)
     (propagated-inputs `(("r-basix" ,r-basix)))
@@ -7749,13 +7983,13 @@ the analyzed items.")
 (define-public r-slam
   (package
     (name "r-slam")
-    (version "0.1-47")
+    (version "0.1-48")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "slam" version))
        (sha256
-        (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
+        (base32 "1ppsvkph4v1dffxgp12a4wnr9arj7pkmh4qv0and3f6nbz9k42qa"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/slam/")
     (synopsis "Sparse lightweight arrays and matrices")
@@ -8038,14 +8272,14 @@ used to teach mathematics, statistics, computation and modeling.")
 (define-public r-raster
   (package
     (name "r-raster")
-    (version "3.3-13")
+    (version "3.4-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "raster" version))
        (sha256
         (base32
-         "1s6457rq94qvm3s2lqscs2c2gn5kzcpxa13i8nhlgb1klx5kams7"))))
+         "19g4chd0nyhnz6hc2j0v9ahjcgz64vvja4y3mrj1pfis1dwhsqn6"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)
@@ -8599,17 +8833,48 @@ conveniently wrapped into a data frame.")
 multiple-imputation datasets.")
     (license license:gpl2)))
 
+(define-public r-mixsqp
+  (package
+   (name "r-mixsqp")
+   (version "0.3-43")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "mixsqp" version))
+            (sha256
+             (base32
+              "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
+   (properties `((upstream-name . "mixsqp")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-irlba" ,r-irlba)
+      ("r-rcpp" ,r-rcpp)
+      ("r-rcpparmadillo" ,r-rcpparmadillo)))
+   (native-inputs
+    `(("r-knitr" ,r-knitr)))
+   (home-page "https://github.com/stephenslab/mixsqp")
+   (synopsis
+    "Sequential quadratic programming for maximum-likelihood estimation")
+   (description
+    "This package provides an optimization method based on sequential
+quadratic programming for maximum likelihood estimation of the mixture
+proportions in a finite mixture model where the component densities are
+known.  The algorithm is expected to obtain solutions that are at least
+as accurate as the state-of-the-art MOSEK interior-point solver, and they
+are expected to arrive at solutions more quickly when the number of
+samples is large and the number of mixture components is not too large.")
+   (license license:expat)))
+
 (define-public r-magick
   (package
     (name "r-magick")
-    (version "2.5.0")
+    (version "2.5.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "magick" version))
        (sha256
         (base32
-         "1fhwr34xff6793ifbzqmij8b8qg7hrnr4birqpg33ib0mdd6flkf"))))
+         "0myvryya7b4bbw0hs4jqflrbdffmg78kz28gbybw3yc7zwc7sqxx"))))
     (build-system r-build-system)
     (inputs
      `(("imagemagick" ,imagemagick)
@@ -9016,14 +9281,14 @@ packages maintained by Torsten Hothorn.")
 (define-public r-multcomp
   (package
     (name "r-multcomp")
-    (version "1.4-14")
+    (version "1.4-15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "multcomp" version))
        (sha256
         (base32
-         "14a55isy1sp745s109nirlk5fryy144cri6dl8y9d9wjhfxz336a"))))
+         "1klvn4a1rlrzwhy1cjrkbbh6jspgzbrdm0jxsb1lmf1yzdz609wr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-codetools" ,r-codetools)
@@ -9280,14 +9545,14 @@ differentiation.")
 (define-public r-bayestestr
   (package
     (name "r-bayestestr")
-    (version "0.7.5")
+    (version "0.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bayestestR" version))
        (sha256
         (base32
-         "0l6q7v96m9asqa0p55k0gpzy8hddf8srkhc9r7zf4hv0dscbi9dv"))))
+         "11mxnpqc85y13wf8mnnrh0k8d3jqdsr99hkv4cgvwav38qpvjhhw"))))
     (properties `((upstream-name . "bayestestR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9307,14 +9572,14 @@ ROPE percentage and pd).")
 (define-public r-performance
   (package
     (name "r-performance")
-    (version "0.5.1")
+    (version "0.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "performance" version))
        (sha256
         (base32
-         "1vkc87vbhw7l626pdnpiravnpsa5j0iv73lbwy3m309lnfvv0cqx"))))
+         "0ai1pp6k0pmmjgpj7hc53s0h258c4mljln8lv3nd9r7kzrmic0gc"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bayestestr" ,r-bayestestr)
@@ -9334,14 +9599,14 @@ effects models and Bayesian models.")
 (define-public r-ggeffects
   (package
     (name "r-ggeffects")
-    (version "0.16.0")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggeffects" version))
        (sha256
         (base32
-         "0v8n8jmp6x1iagbyc5jgf1d29yz5hd3ibnyl9n9f73vqq5bzj0p5"))))
+         "18diwssc5vij5g7zh9mv0ppcv3xgfi2jqzfx9srxfahg05sr1xdq"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-insight" ,r-insight)
@@ -9364,14 +9629,14 @@ results using @code{ggplot2}.")
 (define-public r-effectsize
   (package
     (name "r-effectsize")
-    (version "0.4.0")
+    (version "0.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "effectsize" version))
        (sha256
         (base32
-         "0shx19ahw13wrn7jlyyvzvngqk66d6jiw9i51mx3psdn3hdnhy9s"))))
+         "1rbl63b1c7z9llznnwvclqrcgdd4hfmc7y66v7raqqf2a4nadqa5"))))
     (properties `((upstream-name . "effectsize")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9454,23 +9719,50 @@ files to an structured list.  Users can manipulate this resulting list with
 back to file after modifications.")
     (license license:gpl3)))
 
+(define-public r-gitcreds
+  (package
+    (name "r-gitcreds")
+    (version "0.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gitcreds" version))
+       (sha256
+        (base32
+         "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
+    (properties `((upstream-name . "gitcreds")))
+    (build-system r-build-system)
+    (inputs `(("git" ,git-minimal)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/r-lib/gitcreds")
+    (synopsis "Query git credentials from R")
+    (description
+     "Query, set, and delete credentials from the git credential store.
+Manage GitHub tokens and other git credentials.  This package is to be used by
+other packages that need to authenticate to GitHub and/or other git
+repositories.")
+    (license license:expat)))
+
 (define-public r-gh
   (package
     (name "r-gh")
-    (version "1.1.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gh" version))
        (sha256
         (base32
-         "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
+         "1zvy3ylxvni10lhvmbm9h14mg4wlsbdbzbzviwf28jxss8749219"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
+       ("r-gitcreds" ,r-gitcreds)
        ("r-httr" ,r-httr)
        ("r-ini" ,r-ini)
        ("r-jsonlite" ,r-jsonlite)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/r-lib/gh#readme")
     (synopsis "Access the GitHub API via R")
     (description
@@ -10001,14 +10293,14 @@ address a bug.")
 (define-public r-rcppannoy
   (package
     (name "r-rcppannoy")
-    (version "0.0.16")
+    (version "0.0.17")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RcppAnnoy" version))
        (sha256
         (base32
-         "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
+         "0z4dpvk2hmh817709l70jdl1vvnzn0vb9wlr5m8jza24sn9w14ac"))))
     (properties `((upstream-name . "RcppAnnoy")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10491,14 +10783,14 @@ redundant complex conjugate when the input is real data.")
 (define-public r-tiff
   (package
     (name "r-tiff")
-    (version "0.1-5")
+    (version "0.1-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tiff" version))
        (sha256
         (base32
-         "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
+         "1yy4im2lwzhjnnkfwxgkknsajvm83pcwaf370pkgfva2db0xjfv2"))))
     (build-system r-build-system)
     (inputs
      `(("libtiff" ,libtiff)
@@ -10536,14 +10828,14 @@ Processing.")
 (define-public r-tm
   (package
     (name "r-tm")
-    (version "0.7-7")
+    (version "0.7-8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tm" version))
        (sha256
         (base32
-         "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
+         "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
     (properties `((upstream-name . "tm")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10923,14 +11215,14 @@ diagnostics for controlling type-1 errors are also provided.")
 (define-public r-flare
   (package
     (name "r-flare")
-    (version "1.6.0.2")
+    (version "1.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "flare" version))
        (sha256
         (base32
-         "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
+         "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-igraph" ,r-igraph)
@@ -11023,14 +11315,14 @@ Touzet and Varre (2007).")
 (define-public r-rnifti
   (package
     (name "r-rnifti")
-    (version "1.2.3")
+    (version "1.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RNifti" version))
        (sha256
         (base32
-         "02jdxz3w423k9b5wldky4pnnq0cs2zlfi52jxjw1mk24z756j692"))))
+         "1zr0q79id62csmc30c7gs4hbmavk8n6p50a981sfz51dczhjj5ny"))))
     (properties `((upstream-name . "RNifti")))
     (build-system r-build-system)
     (propagated-inputs `(("r-rcpp" ,r-rcpp)))
@@ -11492,14 +11784,14 @@ limitations\" using the GNU Multiple Precision library.")
 (define-public r-rmpfr
   (package
     (name "r-rmpfr")
-    (version "0.8-1")
+    (version "0.8-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rmpfr" version))
        (sha256
         (base32
-         "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
+         "007pc7fpzl2mcg3qxa2vfjip6m2dr314qjsnybkj3kdj70bszxkl"))))
     (properties `((upstream-name . "Rmpfr")))
     (build-system r-build-system)
     (inputs
@@ -12281,19 +12573,20 @@ model with finite state space using the Aalen-Johansen estimator.")
 (define-public r-epi
   (package
     (name "r-epi")
-    (version "2.41")
+    (version "2.42")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Epi" version))
        (sha256
         (base32
-         "09miba6zk63bwc79n3030kgzlvy3whkq968pgqyghxnsjfh5ckp5"))))
+         "1vsyxlxl6n5y3wr8w7ji17hnhvbr0xsawqbdl1ajcfg5faizm9sl"))))
     (properties `((upstream-name . "Epi")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cmprsk" ,r-cmprsk)
        ("r-data-table" ,r-data-table)
+       ("r-dplyr" ,r-dplyr)
        ("r-etm" ,r-etm)
        ("r-mass" ,r-mass)
        ("r-matrix" ,r-matrix)
@@ -12439,14 +12732,14 @@ subsetting.")
 (define-public r-globals
   (package
     (name "r-globals")
-    (version "0.13.1")
+    (version "0.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "globals" version))
        (sha256
         (base32
-         "1ch9m7fxclfhfa38b743wcm7w1bkx9kmivc6l7phpbgs6h9jhrcc"))))
+         "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-codetools" ,r-codetools)))
@@ -12460,22 +12753,51 @@ simple as possible to identify global objects for the purpose of exporting
 them in distributed compute environments.")
     (license license:lgpl2.1+)))
 
+(define-public r-parallelly
+  (package
+    (name "r-parallelly")
+    (version "1.21.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "parallelly" version))
+       (sha256
+        (base32
+         "1hlr81khr7z4x9gprymdh19mdq3nw6wm8d2795sd2pa3ya6phnb0"))))
+    (properties `((upstream-name . "parallelly")))
+    (build-system r-build-system)
+    (home-page "https://github.com/HenrikBengtsson/parallelly")
+    (synopsis "Enhancements of the parallel package")
+    (description
+     "This package provides utility functions that enhance the @code{parallel}
+package and support the built-in parallel backends of the @code{future}
+package.  For example, @code{availableCores} gives the number of CPU cores
+available to your R process as given by R options and environment variables,
+including those set by job schedulers on high-performance compute clusters.
+If none is set, it will fall back to @code{parallel::detectCores}.  Another
+example is @code{makeClusterPSOCK}, which is backward compatible with
+@code{parallel::makePSOCKcluster} while doing a better job in setting up
+remote cluster workers without the need for configuring the firewall to do
+port-forwarding to your local computer.")
+    (license license:lgpl2.1+)))
+
 (define-public r-future
   (package
     (name "r-future")
-    (version "1.19.1")
+    (version "1.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "future" version))
        (sha256
         (base32
-         "12f483h7g172ygafbg7h43vykv0f7xz9miwqf5q8dyv7gpgqi5fl"))))
+         "14k00g8c9zgf77d6q7x2vibvlivzk2rzj7lwn7v7d9nr6prqzlb6"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
        ("r-globals" ,r-globals)
-       ("r-listenv" ,r-listenv)))
+       ("r-listenv" ,r-listenv)
+       ("r-parallelly" ,r-parallelly)))
     (native-inputs
      `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
     (home-page "https://github.com/HenrikBengtsson/future")
@@ -12761,14 +13083,14 @@ Coefficient Logit Models.")
 (define-public r-tensora
   (package
     (name "r-tensora")
-    (version "0.36.1")
+    (version "0.36.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tensorA" version))
        (sha256
         (base32
-         "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
+         "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
     (properties `((upstream-name . "tensorA")))
     (build-system r-build-system)
     (home-page "http://www.stat.boogaart.de/tensorA")
@@ -13947,14 +14269,14 @@ sampling.")
 (define-public r-deldir
   (package
     (name "r-deldir")
-    (version "0.1-29")
+    (version "0.2-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "deldir" version))
        (sha256
         (base32
-         "1vwh8c8zxspyls05q9kgzz5p85i8k8aax5ir45np2bmg0pjvh6kv"))))
+         "0kin1hsd6dj36kkg7n328mzp21wwn9jm69lvgg2rvbf6bq7q091d"))))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
     (home-page "https://cran.r-project.org/web/packages/deldir")
@@ -14211,13 +14533,13 @@ lspec, polyclass, and polymars.")
 (define-public r-rms
   (package
     (name "r-rms")
-    (version "6.0-1")
+    (version "6.1-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rms" version))
        (sha256
-        (base32 "1zkcsqcvldfj4kyn0346vi51igq951qrnpxlv2pfvap6n2v5wbxq"))))
+        (base32 "0llz519rgnc7v2jqhfrjgixkpkmmi5wi1a52hgz3n28s46ww77mq"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cluster" ,r-cluster)
@@ -15132,14 +15454,14 @@ databases, including ENA, PDB or ChEMBL are also accessible.")
 (define-public r-ggraph
   (package
     (name "r-ggraph")
-    (version "2.0.3")
+    (version "2.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggraph" version))
        (sha256
         (base32
-         "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq"))))
+         "1j3xf4fsv0i0gbppdrw4yprfyk53wx6s8nvnkipi2ywbm7cr4q4w"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
@@ -15155,7 +15477,8 @@ databases, including ENA, PDB or ChEMBL are also accessible.")
        ("r-rlang" ,r-rlang)
        ("r-scales" ,r-scales)
        ("r-tidygraph" ,r-tidygraph)
-       ("r-viridis" ,r-viridis)))
+       ("r-viridis" ,r-viridis)
+       ("r-withr" ,r-withr)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://cran.r-project.org/web/packages/ggraph/")
@@ -15240,22 +15563,22 @@ discriminant analysis for the purpose of classifying high dimensional data.")
 (define-public r-ggvis
   (package
     (name "r-ggvis")
-    (version "0.4.6")
+    (version "0.4.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggvis" version))
        (sha256
         (base32
-         "1k40mkfxj66qvwbsp849maihv6vxkdprhhzjkwffwn0lwl78lsz1"))))
+         "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
        ("r-dplyr" ,r-dplyr)
        ("r-htmltools" ,r-htmltools)
        ("r-jsonlite" ,r-jsonlite)
-       ("r-lazyeval" ,r-lazyeval)
        ("r-magrittr" ,r-magrittr)
+       ("r-rlang" ,r-rlang)
        ("r-shiny" ,r-shiny)))
     (home-page "https://ggvis.rstudio.com/")
     (synopsis "Interactive grammar of graphics")
@@ -15941,14 +16264,14 @@ experiments in a well-organized and reproducible way.")
 (define-public r-clue
   (package
     (name "r-clue")
-    (version "0.3-57")
+    (version "0.3-58")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "clue" version))
        (sha256
         (base32
-         "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
+         "1rwwxlnpl1k0n4k96vxc9zajw9kb4syqwzj76fvaf0qim8p6ddia"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-cluster" ,r-cluster)))
     (home-page "https://cran.r-project.org/web/packages/clue/")
@@ -16084,14 +16407,14 @@ classification and regression models.")
 (define-public r-dae
   (package
     (name "r-dae")
-    (version "3.1-27")
+    (version "3.1-32")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dae" version))
        (sha256
         (base32
-         "14q3cxhcz0zqjdkas0dl71k2bp5qwvb60gha47s78hdr38r46kml"))))
+         "126w1lb9pz8mb2ajl2vz5dj798nbifp0dypnzfgcwixif5g5bpqi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
@@ -16229,24 +16552,25 @@ results and plots in a unified style using the @code{ggplot2} package.")
 (define-public r-refmanager
   (package
     (name "r-refmanager")
-    (version "1.2.12")
+    (version "1.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RefManageR" version))
        (sha256
         (base32
-         "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
+         "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
     (properties `((upstream-name . "RefManageR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bibtex" ,r-bibtex)
-       ("r-httr" ,r-httr)
+     `(("r-httr" ,r-httr)
        ("r-jsonlite" ,r-jsonlite)
        ("r-lubridate" ,r-lubridate)
        ("r-plyr" ,r-plyr)
        ("r-stringr" ,r-stringr)
        ("r-xml2" ,r-xml2)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/ropensci/RefManageR/")
     (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
     (description
@@ -16326,14 +16650,14 @@ easily.")
 (define-public r-umap
   (package
     (name "r-umap")
-    (version "0.2.6.0")
+    (version "0.2.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "umap" version))
        (sha256
         (base32
-         "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f"))))
+         "191vpy84s0bar06y9z1qx43x2kc4qp7lmrcmd0cvz2pnzq722jab"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-openssl" ,r-openssl)
@@ -16353,14 +16677,14 @@ in R, including a translation of the original algorithm into R.")
 (define-public r-uwot
   (package
     (name "r-uwot")
-    (version "0.1.8")
+    (version "0.1.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "uwot" version))
        (sha256
         (base32
-         "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
+         "1iqvircvlxyd68n5279a0cwn5rc3pshxs7w1gqrns9c602xd6mhy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dqrng" ,r-dqrng)
@@ -16512,14 +16836,14 @@ computed using the L1 (Manhattan, taxicab) metric.")
 (define-public r-leiden
   (package
     (name "r-leiden")
-    (version "0.3.4")
+    (version "0.3.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "leiden" version))
        (sha256
         (base32
-         "0cj98s1d9771dahn2xwdb1hpkw51jsfmgvzpam34c7i57fj37hn2"))))
+         "1k1250bjgf2cb1whp2sl1r6b88156qwi2zkamw5iy2q1qhw6w2d7"))))
     (properties `((upstream-name . "leiden")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16540,14 +16864,14 @@ guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
 (define-public r-patchwork
   (package
     (name "r-patchwork")
-    (version "1.0.1")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "patchwork" version))
        (sha256
         (base32
-         "0wm93a40idrkzn5hpnykhznvh7hdbfqw0dkzzn0zk83qlwyc9g02"))))
+         "13vswvcfmadmjz7pw0qdqdr6x85zbza4gljx2nx3a39hldj71yck"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
@@ -16865,14 +17189,14 @@ in pipelines.")
 (define-public r-parameters
   (package
     (name "r-parameters")
-    (version "0.9.0")
+    (version "0.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "parameters" version))
        (sha256
         (base32
-         "17jjmy1qnx25ldvasrwhmal45nl1sr8qjxprbi8fcjwra9af6cr6"))))
+         "1xvjvsdd0hql209f7v2l1nw7gy8jkj5qp0699p5m2h55a01jl778"))))
     (properties `((upstream-name . "parameters")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17512,14 +17836,14 @@ server-side.")
 (define-public r-sysfonts
   (package
     (name "r-sysfonts")
-    (version "0.8.1")
+    (version "0.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sysfonts" version))
        (sha256
         (base32
-         "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994"))))
+         "1gapsiva0vjd2myxgm1avav6my5x00rmy2hx0qll7dm7v1isznbv"))))
     (properties `((upstream-name . "sysfonts")))
     (build-system r-build-system)
     (inputs
@@ -17560,14 +17884,14 @@ package.")
 (define-public r-showtext
   (package
     (name "r-showtext")
-    (version "0.9")
+    (version "0.9-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "showtext" version))
        (sha256
         (base32
-         "11fx2vv8jlvcnybh18y7v4bn2c67aqsqwfq7y8dpywbwr4zg8jid"))))
+         "1hq346k2lm7rv49hw7srn3ab5gcp6b0r4zc1kgsdmswyh3q1asra"))))
     (properties `((upstream-name . "showtext")))
     (build-system r-build-system)
     (inputs
@@ -17681,14 +18005,14 @@ regression models.")
 (define-public r-abtest
   (package
     (name "r-abtest")
-    (version "0.2.1")
+    (version "0.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abtest" version))
        (sha256
         (base32
-         "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
+         "1ak0m4jd1grriwg4pn3aqf1468qma6rjn5kqjh8izx7zl29jd07v"))))
     (properties `((upstream-name . "abtest")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18375,14 +18699,14 @@ the @code{aroma.affymetrix} package.")
 (define-public r-r-filesets
   (package
     (name "r-r-filesets")
-    (version "2.13.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "R.filesets" version))
        (sha256
         (base32
-         "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
+         "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh"))))
     (properties `((upstream-name . "R.filesets")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19028,21 +19352,124 @@ metrics to quantify time accumulation strategies based on minute level
 actigraphy-measured activity counts data.")
     (license license:gpl3)))
 
+(define-public r-ash
+  (package
+    (name "r-ash")
+    (version "1.0-15")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ash" version))
+       (sha256
+        (base32
+         "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
+    (properties `((upstream-name . "ash")))
+    (build-system r-build-system)
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/ash/")
+    (synopsis "David Scott's ASH routines")
+    (description
+     "This package provides David Scott's ASH routines ported from S-PLUS to
+R.")
+    (license license:gpl2+)))
+
+(define-public r-hdrcde
+  (package
+    (name "r-hdrcde")
+    (version "3.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "hdrcde" version))
+       (sha256
+        (base32
+         "0c2qbw4c3mq1cb068kjs72rxlbibz8svwcrx853jyr8ybs23z7ab"))))
+    (properties `((upstream-name . "hdrcde")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ash" ,r-ash)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-kernsmooth" ,r-kernsmooth)
+       ("r-ks" ,r-ks)
+       ("r-locfit" ,r-locfit)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "http://pkg.robjhyndman.com/hdrcde")
+    (synopsis "Highest density regions and conditional density estimation")
+    (description
+     "This is a package for the computation of highest density regions in one
+and two dimensions, kernel estimation of univariate density functions
+conditional on one covariate, and multimodal regression.")
+    (license license:gpl3)))
+
+(define-public r-rainbow
+  (package
+    (name "r-rainbow")
+    (version "3.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rainbow" version))
+       (sha256
+        (base32
+         "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
+    (properties `((upstream-name . "rainbow")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cluster" ,r-cluster)
+       ("r-colorspace" ,r-colorspace)
+       ("r-hdrcde" ,r-hdrcde)
+       ("r-ks" ,r-ks)
+       ("r-mass" ,r-mass)
+       ("r-pcapp" ,r-pcapp)))
+    (home-page "https://cran.r-project.org/web/packages/rainbow/")
+    (synopsis "Bagplots, boxplots and rainbow plots for functional data")
+    (description
+     "This is a package for visualizing functional data and identifying
+functional outliers with bagplots, boxplots and rainbow plots.")
+    (license license:gpl3)))
+
+(define-public r-fds
+  (package
+    (name "r-fds")
+    (version "1.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fds" version))
+       (sha256
+        (base32
+         "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
+    (properties `((upstream-name . "fds")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rainbow" ,r-rainbow)
+       ("r-rcurl" ,r-rcurl)))
+    (home-page "https://cran.r-project.org/web/packages/fds/")
+    (synopsis "Functional data sets")
+    (description "This package contains a list of functional time series,
+sliced functional time series, and functional data sets.  Functional time
+series is a special type of functional data observed over time.  Sliced
+functional time series is a special type of functional time series with a time
+variable observed over time.")
+    (license license:gpl2+)))
+
 (define-public r-fda
   (package
     (name "r-fda")
-    (version "5.1.5.1")
+    (version "5.1.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fda" version))
        (sha256
         (base32
-         "0zi001cw5536x6rgr4l0skva7fk53663zf6ggnsa8znml090sihm"))))
+         "1r8hfi6x1maw5zz8k95wfcr7v69lg4zl3mcj69cvvq2mkg4y3158"))))
     (properties `((upstream-name . "fda")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-matrix" ,r-matrix)))
+     `(("r-fds" ,r-fds)
+       ("r-matrix" ,r-matrix)))
     (home-page "https://www.functionaldata.org")
     (synopsis "Functional data analysis")
     (description
@@ -20418,14 +20845,14 @@ and Euclidean distance is particularly fast.")
 (define-public r-isocodes
   (package
     (name "r-isocodes")
-    (version "2020.03.16")
+    (version "2020.12.04")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ISOcodes" version))
        (sha256
         (base32
-         "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
+         "18373rkhmwm7y2drvfbhrxkqw9d23avf0ndvh0fg00z4djvddkjx"))))
     (properties `((upstream-name . "ISOcodes")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/package=ISOcodes")
@@ -20440,14 +20867,14 @@ character codes as well as the UN M.49 area codes.")
 (define-public r-stopwords
   (package
     (name "r-stopwords")
-    (version "2.0")
+    (version "2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stopwords" version))
        (sha256
         (base32
-         "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
+         "1g2p8gsj7xjck7idcwczgc7fmv72lzwjw00qarrj0cv44kypmiq8"))))
     (properties `((upstream-name . "stopwords")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21510,13 +21937,13 @@ recommendations for developers.")
 (define-public r-loo
   (package
     (name "r-loo")
-    (version "2.3.1")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "loo" version))
        (sha256
-        (base32 "12z0k8lhz0rxygs5lc7076nw6qhk0pda8nxf65hkinfrf4dy53fr"))))
+        (base32 "01a15ikfnyxhjhrgvy3ag929rg45dxp3wji1j38r4hg4q1yz4ma9"))))
     (properties `((upstream-name . "loo")))
     (build-system r-build-system)
     (inputs
@@ -21812,14 +22239,14 @@ Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
 (define-public r-isoband
   (package
     (name "r-isoband")
-    (version "0.2.2")
+    (version "0.2.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "isoband" version))
        (sha256
         (base32
-         "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx"))))
+         "1zkzdc39dpw2z59bjck27nimz9a2vskmw0f7wb17s53dvy7k3lzr"))))
     (properties `((upstream-name . "isoband")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22428,17 +22855,109 @@ connection, user authentication and file transfer.  A simple R client is
 included in this package as well.")
     (license license:gpl2)))
 
+(define-public r-gamm4
+  (package
+    (name "r-gamm4")
+    (version "0.2-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gamm4" version))
+       (sha256
+        (base32
+         "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
+    (properties `((upstream-name . "gamm4")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lme4" ,r-lme4)
+       ("r-matrix" ,r-matrix)
+       ("r-mgcv" ,r-mgcv)))
+    (home-page "https://cran.r-project.org/web/packages/gamm4/")
+    (synopsis "Generalized additive mixed models using mgcv and lme4")
+    (description
+     "Estimate generalized additive mixed models via a version of function
+@code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
+estimation.")
+    (license license:gpl2+)))
+
+(define-public r-optimx
+  (package
+    (name "r-optimx")
+    (version "2020-4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "optimx" version))
+       (sha256
+        (base32
+         "00bi2sr2hr7x6cfwlsn7hz2r56lcyv9naa8vmfcgr1r269fc50b3"))))
+    (properties `((upstream-name . "optimx")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-numderiv" ,r-numderiv)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://cran.r-project.org/web/packages/optimx/")
+    (synopsis "Expanded replacement and extension of the optim function")
+    (description
+     "This package provides a replacement and extension of the @code{optim}
+function to call to several function minimization codes in R in a single
+statement.  These methods handle smooth, possibly box constrained functions of
+several or many parameters.  Note that the function @code{optimr} was prepared
+to simplify the incorporation of minimization codes going forward.  This
+package also implements some utility codes and some extra solvers, including
+safeguarded Newton methods.  Many methods previously separate are now included
+here.")
+    (license license:gpl2)))
+
+(define-public r-projpred
+  (package
+    (name "r-projpred")
+    (version "2.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "projpred" version))
+       (sha256
+        (base32
+         "0nx514mrfh3gv854pr71w5x3zgdnn0kinf5nh7z90q3h7ysry2mg"))))
+    (properties `((upstream-name . "projpred")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-gamm4" ,r-gamm4)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-lme4" ,r-lme4)
+       ("r-loo" ,r-loo)
+       ("r-magrittr" ,r-magrittr)
+       ("r-mass" ,r-mass)
+       ("r-mgcv" ,r-mgcv)
+       ("r-optimx" ,r-optimx)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-rngtools" ,r-rngtools)
+       ("r-rstantools" ,r-rstantools)
+       ("r-tidyverse" ,r-tidyverse)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://mc-stan.org/projpred/")
+    (synopsis "Projection predictive feature selection")
+    (description
+     "This package performs projection predictive feature selection for
+generalized linear models and generalized linear and additive multilevel
+models.  The package is compatible with the @code{rstanarm} and @code{brms}
+packages, but other reference models can also be used.  See the package
+vignette for more information and examples.")
+    (license license:gpl3)))
+
 (define-public r-brms
   (package
     (name "r-brms")
-    (version "2.14.0")
+    (version "2.14.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "brms" version))
        (sha256
         (base32
-         "0s8dl1xm3bpivfv3hw94zv9cifjg8cgs5137yd8d755kc2v0fdmf"))))
+         "0mzwihhgmn405l6zq11a180q4k3chggj9qj0j7q838b9vrszg59j"))))
     (properties `((upstream-name . "brms")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22456,6 +22975,7 @@ included in this package as well.")
        ("r-mgcv" ,r-mgcv)
        ("r-nleqslv" ,r-nleqslv)
        ("r-nlme" ,r-nlme)
+       ("r-projpred" ,r-projpred)
        ("r-rcpp" ,r-rcpp)
        ("r-rstan" ,r-rstan)
        ("r-rstantools" ,r-rstantools)
@@ -22655,14 +23175,14 @@ counting and recursive k-means partitioning.")
 (define-public r-hardhat
   (package
     (name "r-hardhat")
-    (version "0.1.4")
+    (version "0.1.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hardhat" version))
        (sha256
         (base32
-         "0gaj4hr4dj27jaasp7v0hzaivipplvq746ajsyz4yd1in03hfjvs"))))
+         "1b7f9i9fy39j9n03g40vd6nzgq9fgq914xg3svf84najlknvjzly"))))
     (properties `((upstream-name . "hardhat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -23060,14 +23580,14 @@ which may also be useful for other purposes.")
 (define-public r-spatstat-data
   (package
     (name "r-spatstat-data")
-    (version "1.4-3")
+    (version "1.5-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.data" version))
        (sha256
         (base32
-         "18lfj5vkwxgf5w9qz0g5al3zy8y2yi3bnd13w24hszfc82nbcmc9"))))
+         "17vbf48g1mh8iigzzlaa9j4mw087hib7f1kkbl3c50xjcrr5iw6b"))))
     (properties `((upstream-name . "spatstat.data")))
     (build-system r-build-system)
     (propagated-inputs
@@ -23150,14 +23670,14 @@ for linear mixed models (AIREML).")
 (define-public r-cpp11
   (package
     (name "r-cpp11")
-    (version "0.2.3")
+    (version "0.2.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cpp11" version))
        (sha256
         (base32
-         "1avcip33bldzz0rhkl43b4sljrbb8i24684xxmr9il5bijcpyy97"))))
+         "08lrmpfkwh1w290a5ikhs9yn1vn32wbgvbzb4n3zb2indb8s5g69"))))
     (properties `((upstream-name . "cpp11")))
     (build-system r-build-system)
     (native-inputs `(("r-knitr" ,r-knitr)))
@@ -23964,27 +24484,26 @@ for creating, simulating, or validating values for such parameters.")
 (define-public r-tune
   (package
     (name "r-tune")
-    (version "0.1.1")
+    (version "0.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tune" version))
        (sha256
         (base32
-         "0293xkmv1nyvm72wxznnlm3qpf6475xzl2sf52mnrjxxr7i447p1"))))
+         "0ja7rjkjj88v3ngrc6izcz2qh9qv4s8abgcafmvx2ihgz99hds37"))))
     (properties `((upstream-name . "tune")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
-       ("r-crayon" ,r-crayon)
        ("r-dials" ,r-dials)
        ("r-dplyr" ,r-dplyr)
        ("r-foreach" ,r-foreach)
+       ("r-generics" ,r-generics)
        ("r-ggplot2" ,r-ggplot2)
        ("r-glue" ,r-glue)
        ("r-gpfit" ,r-gpfit)
        ("r-hardhat" ,r-hardhat)
-       ("r-lifecycle" ,r-lifecycle)
        ("r-parsnip" ,r-parsnip)
        ("r-purrr" ,r-purrr)
        ("r-recipes" ,r-recipes)
@@ -24286,20 +24805,19 @@ model-related packages.")
 (define-public r-tidymodels
   (package
     (name "r-tidymodels")
-    (version "0.1.1")
+    (version "0.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidymodels" version))
        (sha256
         (base32
-         "0w2xnr642klmqlflkw6rkvqcrgs01i8f34nk9wdax3fsl1yx2wi4"))))
+         "09njrl655sh82xrzckgg56a6ndfrjla5fy8675wj4jsj14jpv0fw"))))
     (properties `((upstream-name . "tidymodels")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-broom" ,r-broom)
        ("r-cli" ,r-cli)
-       ("r-crayon" ,r-crayon)
        ("r-dials" ,r-dials)
        ("r-dplyr" ,r-dplyr)
        ("r-ggplot2" ,r-ggplot2)
@@ -24573,14 +25091,14 @@ Maximum Parsimony, distance methods and Hadamard conjugation.")
 (define-public r-diversitree
   (package
     (name "r-diversitree")
-    (version "0.9-14")
+    (version "0.9-15")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "diversitree" version))
         (sha256
          (base32
-          "0xkxw4n1rsagip51smh9k0h0lmnnvsajqcxma7yh95ifdkyrcyy4"))))
+          "1sk3sgn5hi04978s5s7gy6pzp28g3v9rglmiamlgs96c9wyyyff7"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -24656,3 +25174,54 @@ orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
 parabolic or user defined by custom scale factors.")
     (license license:gpl3)))
 
+(define-public r-aws-signature
+  (package
+    (name "r-aws-signature")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "aws.signature" version))
+       (sha256
+        (base32
+         "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
+    (properties `((upstream-name . "aws.signature")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-base64enc" ,r-base64enc)
+       ("r-digest" ,r-digest)))
+    (home-page "https://github.com/cloudyr/aws.signature")
+    (synopsis "Amazon Web Services Request Signatures")
+    (description
+     "This package generates version 2 and 4 request signatures for Amazon Web
+Services (AWS) and provides a mechanism for retrieving credentials from
+environment variables, AWS credentials files, and EC2 instance metadata.  For
+use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
+    (license license:gpl2+)))
+
+(define-public r-aws-s3
+  (package
+    (name "r-aws-s3")
+    (version "0.3.21")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "aws.s3" version))
+       (sha256
+        (base32
+         "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
+    (properties `((upstream-name . "aws.s3")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-aws-signature" ,r-aws-signature)
+       ("r-base64enc" ,r-base64enc)
+       ("r-curl" ,r-curl)
+       ("r-digest" ,r-digest)
+       ("r-httr" ,r-httr)
+       ("r-xml2" ,r-xml2)))
+    (home-page "https://github.com/cloudyr/aws.s3")
+    (synopsis "AWS S3 Client Package")
+    (description
+     "This package provides a simple client package for the Amazon Web
+Services (AWS) Simple Storage Service (S3) REST API.")
+    (license license:gpl2+)))
diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index a0c31be751..6f71cf6398 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -1081,6 +1081,29 @@ standard library.")
     (description "Test CLI Applications.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-assert-cmd-0.9
+  (package
+    (inherit rust-assert-cmd-1)
+    (name "rust-assert-cmd")
+    (version "0.9.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "assert-cmd" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "02gq7j9qzjkbyq4hk18cih3kylk3dyxwa2gc5k7lah9kdwkhrdn5"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-escargot" ,rust-escargot-0.3)
+        ("rust-predicates" ,rust-predicates-0.9)
+        ("rust-predicates-core" ,rust-predicates-core-0.9)
+        ("rust-predicates-tree" ,rust-predicates-tree-0.9))
+       #:cargo-development-inputs
+       (("rust-docmatic" ,rust-docmatic-0.1))))))
+
 (define-public rust-assert-fs-0.11
   (package
     (name "rust-assert-fs")
@@ -1307,6 +1330,32 @@ methods.")
           "1chwgimpx5z7xbag7krr9d8asxfqbh683qhgl9kn3hxk2l0djj8x"))))
     (arguments '(#:skip-build? #t))))
 
+(define-public rust-automod-1
+  (package
+    (name "rust-automod")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "automod" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1z8kdbvvz0k8mfs45mvs16lr9xj59cdcp0sm45fawfh93gai4mhg"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1)
+        ("rust-quote" ,rust-quote-1)
+        ("rust-syn" ,rust-syn-1))
+       ;; Tests not included in tar.
+       #:tests? #f))
+    (home-page "https://github.com/dtolnay/automod")
+    (synopsis "Pull in every source file in a directory as a module")
+    (description "Pull in every source file in a directory as a module.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-average-0.10
   (package
     (name "rust-average")
@@ -1728,6 +1777,29 @@ tracebacks.")
 that uses Serde for transforming structs into bytes and vice versa!")
     (license license:expat)))
 
+(define-public rust-bincode-0.8
+  (package
+    (inherit rust-bincode-1)
+    (name "rust-bincode")
+    (version "0.8.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "bincode" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0nbj0lwykwa1a7sa4303rxgpng9p2hcz9s5d5qcrckrpmcxjsjkf"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-byteorder" ,rust-byteorder-1)
+        ("rust-num-traits" ,rust-num-traits-0.1)
+        ("rust-serde" ,rust-serde-1))
+       #:cargo-development-inputs
+       (("rust-serde-bytes" ,rust-serde-bytes-0.10)
+        ("rust-serde-derive" ,rust-serde-derive-1))))))
+
 (define-public rust-bindgen-0.55
   (package
     (name "rust-bindgen")
@@ -1967,6 +2039,41 @@ bindings to C and C++ libraries.")
         ("rust-diff" ,rust-diff-0.1)
         ("rust-shlex" ,rust-shlex-0.1))))))
 
+(define-public rust-bindgen-0.46
+  (package
+    (inherit rust-bindgen-0.50)
+    (name "rust-bindgen")
+    (version "0.46.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "bindgen" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1qclvj5pydn5camw396b0r3nz4nn3p5wpxg4fgg1favp043pyzwg"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-cexpr" ,rust-cexpr-0.3)
+        ("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-clang-sys" ,rust-clang-sys-0.26)
+        ("rust-clap" ,rust-clap-2)
+        ("rust-env-logger" ,rust-env-logger-0.6)
+        ("rust-hashbrown" ,rust-hashbrown-0.1)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-peeking-take-while" ,rust-peeking-take-while-0.1)
+        ("rust-proc-macro2" ,rust-proc-macro2-0.4)
+        ("rust-quote" ,rust-quote-0.6)
+        ("rust-regex" ,rust-regex-1)
+        ("rust-which" ,rust-which-2.0))
+       #:cargo-development-inputs
+       (("rust-clap" ,rust-clap-2)
+        ("rust-diff" ,rust-diff-0.1)
+        ("rust-shlex" ,rust-shlex-0.1))))) )
+
 (define-public rust-bindgen-0.37
   (package
     (inherit rust-bindgen-0.50)
@@ -3217,6 +3324,32 @@ exposed as Reader/Writer streams.")
      "The ChaCha family of stream ciphers.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-cachedir-0.1
+  (package
+    (name "rust-cachedir")
+    (version "0.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "cachedir" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1j18j73fxrr82marcdrn86123vr9v5n0fgyjkf9mi9pzyk8hjrf0"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-tempfile" ,rust-tempfile-3))
+       ;; Tests require a mutable home directory and access to /var/tmp.
+       #:tests? #f))
+    (home-page "https://github.com/lilianmoraru/cachedir")
+    (synopsis "Interact with cache directories and @file{CACHEDIR.TAG} files")
+    (description
+     "This package provides a library to help interacting with cache
+directories and @code{CACHEDIR.TAG} files.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-calloop-0.4
   (package
     (name "rust-calloop")
@@ -3599,6 +3732,32 @@ archive to be linked into Rustcode.")
        #:cargo-development-inputs
        (("rust-clang-sys" ,rust-clang-sys-0.11))))))
 
+(define-public rust-cfg-if-1
+  (package
+    (name "rust-cfg-if")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "cfg-if" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1za0vb97n4brpzpv8lsbnzmq5r8f2b0cpqqr0sy8h5bn751xxwds"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-compiler-builtins" ,rust-compiler-builtins-0.1)
+        ("rust-rustc-std-workspace-core" ,rust-rustc-std-workspace-core-1))))
+    (home-page "https://github.com/alexcrichton/cfg-if")
+    (synopsis "Define an item depending on parameters")
+    (description "This package provides a macro to ergonomically define an
+item depending on a large number of @code{#[cfg]} parameters.  Structured like
+an @code{if-else} chain, the first matching branch is the item that gets
+emitted.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-cfg-if-0.1
   (package
     (name "rust-cfg-if")
@@ -3627,7 +3786,7 @@ depending on a large number of #[cfg] parameters.  Structured like an
 (define-public rust-chrono-0.4
   (package
     (name "rust-chrono")
-    (version "0.4.13")
+    (version "0.4.19")
     (source
      (origin
        (method url-fetch)
@@ -3636,28 +3795,30 @@ depending on a large number of #[cfg] parameters.  Structured like an
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1dm0q1kmk2vq5djwhp1j9cm4aa38wr9vy1i1w19p2y0nj4188kf7"))))
+         "0wyfl6c00vhfl562spnfcna3zkw8jqvcp652m9iskhl8j26dc2k7"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t
-       #:cargo-inputs
-       (("rust-num-integer" ,rust-num-integer-0.1)
+     `(#:cargo-inputs
+       (("rust-js-sys" ,rust-js-sys-0.3)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-num-integer" ,rust-num-integer-0.1)
         ("rust-num-traits" ,rust-num-traits-0.2)
-        ("rust-js-sys" ,rust-js-sys-0.3)
+        ("rust-pure-rust-locales" ,rust-pure-rust-locales-0.5)
         ("rust-rustc-serialize" ,rust-rustc-serialize-0.3)
         ("rust-serde" ,rust-serde-1)
         ("rust-time" ,rust-time-0.1)
         ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2))
        #:cargo-development-inputs
-       (;("rust-bincode" ,rust-bincode-0.8)
-        ("rust-criterion" ,rust-criterion-0.2)
+       (("rust-bincode" ,rust-bincode-0.8)
+        ("rust-criterion" ,rust-criterion-0.3)
         ("rust-doc-comment" ,rust-doc-comment-0.3)
         ("rust-num-iter" ,rust-num-iter-0.1)
         ("rust-serde-derive" ,rust-serde-derive-1)
         ("rust-serde-json" ,rust-serde-json-1)
-        ("rust-wasm-bindgen-test" ,rust-wasm-bindgen-test-0.2))))
-    (home-page
-     "https://github.com/chronotope/chrono")
+        ("rust-wasm-bindgen-test" ,rust-wasm-bindgen-test-0.3))
+       #:features '("unstable-locales")
+       #:tests? #f))
+    (home-page "https://github.com/chronotope/chrono")
     (synopsis "Date and time library for Rust")
     (description "Date and time library for Rust.")
     (license (list license:expat license:asl2.0))))
@@ -6529,7 +6690,7 @@ error-chain.")
 (define-public rust-derive-more-0.99
   (package
     (name "rust-derive-more")
-    (version "0.99.9")
+    (version "0.99.11")
     (source
      (origin
        (method url-fetch)
@@ -6538,7 +6699,7 @@ error-chain.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0xizcpj39rx0474mbbx8m0xww98qh92zsg82gf52qnvbryqri299"))))
+         "131xrz5nmnh8zq3vcvv0wfpcaflypbxp3fin984fsqddc5hhxjs1"))))
     (build-system cargo-build-system)
     (arguments
      `(#:tests? #f  ; Some test files missing.
@@ -6896,6 +7057,28 @@ on Linux, the Known Folder API on Windows, and the Standard
 Directory guidelines on macOS.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-directories-next-1
+  (package
+    (inherit rust-directories-3)
+    (name "rust-directories-next")
+    (version "1.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "directories-next" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0mmym1h9vlyapwlzygfas3q9mx03mki8cnf5y1bmr713q7mwqa4a"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-cfg-if" ,rust-cfg-if-1)
+        ("rust-dirs-sys" ,rust-dirs-sys-next-0.1))
+       #:cargo-development-inputs
+       (("rust-bencher" ,rust-bencher-0.1))))
+    (home-page "https://github.com/xdg-rs/dirs/tree/master/directories")))
+
 (define-public rust-dirs-3
   (package
     (name "rust-dirs")
@@ -6955,6 +7138,28 @@ standard locations of directories for config, cache and other data.")
         ("rust-redox-users" ,rust-redox-users-0.3)
         ("rust-winapi" ,rust-winapi-0.3))))))
 
+(define-public rust-dirs-next-1
+  (package
+    (inherit rust-dirs-1.0)
+    (name "rust-dirs-next")
+    (version "1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "dirs-next" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1dl2dqzsrcb7qigfiwpdpakhdkpz0629pvylbj2ylyrkh1dfcdng"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-cfg-if" ,rust-cfg-if-1)
+        ("rust-dirs-sys" ,rust-dirs-sys-next-0.1))))
+    (home-page "https://github.com/xdg-rs/dirs")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-dirs-sys-0.3
   (package
     (name "rust-dirs-sys")
@@ -6983,6 +7188,27 @@ standard locations of directories for config, cache and other data.")
 and @code{directories} crates.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-dirs-sys-next-0.1
+  (package
+    (inherit rust-dirs-sys-0.3)
+    (name "rust-dirs-sys-next")
+    (version "0.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "dirs-sys-next" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0zgy7is3h2dyf1l4sa7k065w2kvx0l12l40my4rswm2mc1gkdplr"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-libc" ,rust-libc-0.2)
+        ("rust-redox-users" ,rust-redox-users-0.3)
+        ("rust-winapi" ,rust-winapi-0.3))))
+    (home-page "https://github.com/xdg-rs/dirs/tree/master/dirs-sys")))
+
 (define-public rust-discard-1.0
   (package
     (name "rust-discard")
@@ -8306,6 +8532,54 @@ variables.")
     (description "Cargo API written in Paris.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-escargot-0.3
+  (package
+    (inherit rust-escargot-0.5)
+    (name "rust-escargot")
+    (version "0.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "escargot" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "19fmn7bz1h6nlqy0mp825xwjwnrjn4xjdpwc06jl51j3fiz1znqr"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-serde" ,rust-serde-1)
+        ("rust-serde-json" ,rust-serde-json-1))))))
+
+(define-public rust-exitfailure-0.5
+  (package
+    (name "rust-exitfailure")
+    (version "0.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "exitfailure" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0585wix3b3pjjj90fkqj9x4ar46d24x82k8rdin3czzk5a1vvx9g"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-failure" ,rust-failure-0.1))
+       #:cargo-development-inputs
+       (("rust-assert-cmd" ,rust-assert-cmd-0.9)
+        ("rust-predicates" ,rust-predicates-0.9))
+       ;; Tests fail with "No such file or directory".
+       #:tests? #f))
+    (home-page "https://github.com/tismith/exitfailure")
+    (synopsis "Provide @code{newtype} wrappers for using @code{?} in @code{main}")
+    (description
+     "This package provides a basic @code{newtype} wrappers to help with using
+@code{?} in @code{main}.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-expat-sys-2.1
   (package
     (name "rust-expat-sys")
@@ -8843,6 +9117,21 @@ streams.")
          (base32
           "03hmx3n48hjm0x1ig84n1j87kzp75lzr6cj1sgi6a6pykgn4n8km"))))))
 
+(define-public rust-float-cmp-0.4
+  (package
+    (inherit rust-float-cmp-0.5)
+    (name "rust-float-cmp")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "float-cmp" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0036jb8ry4h83n319jb20b5yvyfyq8mx8dkxnyjm22nq8fl8yjhk"))))))
+
 (define-public rust-float-cmp-0.3
   (package
     (inherit rust-float-cmp-0.5)
@@ -11395,6 +11684,39 @@ hash map.")
         ("rust-rustc-hash" ,rust-rustc-hash-1)
         ("rust-serde-test" ,rust-serde-test-1))))))
 
+(define-public rust-hashbrown-0.1
+  (package
+    (inherit rust-hashbrown-0.5)
+    (name "rust-hashbrown")
+    (version "0.1.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "hashbrown" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1np350nrzysy021ndn2135q5vpzrp5nli78ywz114d1vcnv2kbiv"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           (substitute* "Cargo.toml"
+             (("~1.2") "1.2"))
+           #t))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-byteorder" ,rust-byteorder-1)
+        ("rust-rayon" ,rust-rayon-1)
+        ("rust-scopeguard" ,rust-scopeguard-0.3)
+        ("rust-serde" ,rust-serde-1))
+       #:cargo-development-inputs
+       (("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-rand" ,rust-rand-0.5)
+        ("rust-rayon" ,rust-rayon-1)
+        ("rust-rustc-hash" ,rust-rustc-hash-1)
+        ("rust-serde-test" ,rust-serde-test-1))))))
+
 (define-public rust-hashlink-0.6
   (package
     (name "rust-hashlink")
@@ -16959,6 +17281,21 @@ combinators library.")
 with all line endings.")
     (license license:asl2.0)))
 
+(define-public rust-normalize-line-endings-0.2
+  (package
+    (inherit rust-normalize-line-endings-0.3)
+    (name "rust-normalize-line-endings")
+    (version "0.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "normalize-line-endings" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1a1knz9j1w5a1pl2q6whmjphm3z6p64r5njnam7syp5rx8wil2if"))))))
+
 (define-public rust-notify-4
   (package
     (name "rust-notify")
@@ -20278,6 +20615,30 @@ dependency to expose a precomputed hash.")
 functions.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-predicates-0.9
+  (package
+    (inherit rust-predicates-1)
+    (name "rust-predicates")
+    (version "0.9.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "predicates" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "085ysw5iigw9l7fdy0pxqs7h165m9hxaxdknmkyq868izivpj7pk"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-difference" ,rust-difference-2)
+        ("rust-float-cmp" ,rust-float-cmp-0.4)
+        ("rust-normalize-line-endings" ,rust-normalize-line-endings-0.2)
+        ("rust-predicates-core" ,rust-predicates-core-0.9)
+        ("rust-regex" ,rust-regex-1))
+       #:cargo-development-inputs
+       (("rust-predicates-tree" ,rust-predicates-tree-0.9))))))
+
 (define-public rust-predicates-core-1
   (package
     (name "rust-predicates-core")
@@ -20299,6 +20660,21 @@ functions.")
      "An API for boolean-valued predicate functions.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-predicates-core-0.9
+  (package
+    (inherit rust-predicates-core-1)
+    (name "rust-predicates-core")
+    (version "0.9.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "predicates-core" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1ig5wi3j2faxss6kshv5xdwnchiwbkq2fgx6v962mh6ij31hpy45"))))))
+
 (define-public rust-predicates-tree-1
   (package
     (name "rust-predicates-tree")
@@ -20325,6 +20701,25 @@ functions.")
      "Render boolean-valued predicate functions results as a tree.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-predicates-tree-0.9
+  (package
+    (inherit rust-predicates-tree-1)
+    (name "rust-predicates-tree")
+    (version "0.9.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "predicates-tree" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1ga0yyfmqbwi28naxlr6cvpmiig0qnwx5adc858hmjxxh6dxz1if"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-predicates-core" ,rust-predicates-core-0.9)
+        ("rust-treeline" ,rust-treeline-0.1))))))
+
 (define-public rust-pretty-assertions-0.6
   (package
     (name "rust-pretty-assertions")
@@ -21132,6 +21527,31 @@ compliant email address validation.")
     (description "This package provides a library for async wake signals.")
     (license license:asl2.0)))
 
+(define-public rust-pure-rust-locales-0.5
+  (package
+    (name "rust-pure-rust-locales")
+    (version "0.5.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "pure-rust-locales" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0ryjj0gs4hfadqx9vl4sgi32zyb2dlvwpxca1m1kmrw9hk1g7gv5"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-itertools" ,rust-itertools-0.8)
+        ("rust-nom" ,rust-nom-5))))
+    (home-page "https://github.com/cecton/pure-rust-locales")
+    (synopsis "Pure Rust locales imported directly from the GNU C Library")
+    (description
+     "Pure Rust locales imported directly from the GNU C Library.
+@code{LC_COLLATE} and @code{LC_CTYPE} are not yet supported.")
+    (license license:expat)))
+
 (define-public rust-quantiles-0.7
   (package
     (name "rust-quantiles")
diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm
index a03888c72d..98fc6b3d63 100644
--- a/gnu/packages/curl.scm
+++ b/gnu/packages/curl.scm
@@ -54,6 +54,7 @@
   (package
    (name "curl")
    (version "7.73.0")
+   (replacement curl-7.74.0)
    (source (origin
              (method url-fetch)
              (uri (string-append "https://curl.haxx.se/download/curl-"
@@ -150,6 +151,19 @@ tunneling, and so on.")
     (name "curl-minimal")
     (inputs (alist-delete "openldap" (package-inputs curl))))))
 
+;; Replacement package to fix multiple security vulnerabilities.
+(define curl-7.74.0
+  (package
+    (inherit curl)
+    (version "7.74.0")
+    (source (origin
+              (inherit (package-source curl))
+              (uri (string-append "https://curl.haxx.se/download/curl-"
+                                  version ".tar.xz"))
+              (sha256
+               (base32
+                "12w7gskrglg6qrmp822j37fmbr0icrcxv7rib1fy5xiw80n5z7cr"))))))
+
 (define-public kurly
   (package
     (name "kurly")
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index bfa78556bc..4b1a1ff09d 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -1206,6 +1206,18 @@ pictures, sounds, or video.")
 
 (define-public postgresql-10 postgresql)
 
+(define-public postgresql-13
+  (package
+    (inherit postgresql)
+    (version "13.1")
+    (source (origin
+              (inherit (package-source postgresql))
+              (uri (string-append "https://ftp.postgresql.org/pub/source/v"
+                                  version "/postgresql-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "07z6zwr58dckaa97yl9ml240z83d1lhgaxw9aq49i8lsp21mqd0j"))))))
+
 (define-public postgresql-11
   (package
     (inherit postgresql)
diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm
index d59fe57ade..403ebd3d8b 100644
--- a/gnu/packages/dns.scm
+++ b/gnu/packages/dns.scm
@@ -937,17 +937,14 @@ synthesis, and on-the-fly re-configuration.")
 (define-public knot-resolver
   (package
     (name "knot-resolver")
-    (version "5.2.0")
+    (version "5.2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://secure.nic.cz/files/knot-resolver/"
                                   "knot-resolver-" version ".tar.xz"))
               (sha256
                (base32
-                "0cwlipib3x88dr6cijqv2aps13b4ijv524wc85ns07rkldy2c948"))
-               (patches
-                (search-patches
-                 "knot-resolver-fix-map-command-on-32-bit.patch"))))
+                "09jqy23q1pgj76y2qd1xfk72wwmypnyawm3span3gx00qi2bfdxa"))))
     (build-system meson-build-system)
     (outputs '("out" "doc"))
     (arguments
diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm
index a23c677880..f1e2bd49cb 100644
--- a/gnu/packages/ebook.scm
+++ b/gnu/packages/ebook.scm
@@ -7,6 +7,7 @@
 ;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020 Zheng Junjie <873216071@qq.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,6 +30,7 @@
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix git-download)
+  #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system python)
@@ -314,6 +316,32 @@ e-books for convenient reading.")
                    license:silofl1.1
                    license:cc-by-sa3.0))))
 
+(define-public ebook-tools
+  (package
+    (name "ebook-tools")
+    (version "0.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/ebook-tools/ebook-tools/"
+                           version "/ebook-tools-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1bi7wsz3p5slb43kj7lgb3r6lb91lvb6ldi556k4y50ix6b5khyb"))))
+    (arguments
+     `(#:tests? #f)) ; No 'test' target
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("libzip" ,libzip)
+       ("libxml2" ,libxml2)))
+    (home-page "http://ebook-tools.sourceforge.net")
+    (synopsis "Tools and library for dealing with various ebook file formats")
+    (description "This package provides command-line tools and a library for
+accessing and converting various ebook file formats.")
+    (license license:expat)))
+
 (define-public liblinebreak
   (package
     (name "liblinebreak")
diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index e2658b4547..ef2c891a27 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -1810,7 +1810,8 @@ mode, Rmail, Gnus, MH-E, and VM).  BBDB is fully customizable.")
         (base32 "1dq04p6ms0zx4awlypp4crkz7dzal4xg8ac7p8fqacz196rczssp"))))
     (build-system emacs-build-system)
     (inputs
-     `(("bluez" ,bluez)))
+     `(("bluez" ,bluez)
+       ("dbus" ,dbus)))
     (propagated-inputs
      `(("emacs-dash" ,emacs-dash)))
     (home-page "https://gitlab.com/rstocker/emacs-bluetooth")
@@ -2764,20 +2765,21 @@ type, for example: packages, buffers, files, etc.")
     (license license:gpl3+)))
 
 (define-public emacs-guix
-  (let ((commit "58a840d0671091e3064e36244790ef8839da87d6")
-        (revision "2"))
+  (let* ((commit "a694fdbcedb6edd2239a31d326e475c763ee32f8")
+         (revision "3"))
     (package
       (name "emacs-guix")
       (version (git-version "0.5.2" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
-                      (url "https://gitlab.com/emacs-guix/emacs-guix")
+                      ;; TODO: Use the official version when it has a new home
+                      (url "https://github.com/jsoo1/guix.el")
                       (commit commit)))
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1qnr5sixmvrhr9rinrhfy7sy20mikjvvwbdixwkbx30qpcdwgwj1"))))
+                  "1pqw7zbgxzwpig4xr0izc3z8h80c72i6bl5yi12br0d7aq6dbkvj"))))
       (build-system gnu-build-system)
       (native-inputs
        `(("autoconf" ,autoconf)
@@ -2786,7 +2788,8 @@ type, for example: packages, buffers, files, etc.")
          ("texinfo" ,texinfo)
          ("emacs" ,emacs-minimal)))
       (inputs
-       `(("guile" ,@(assoc-ref (package-native-inputs guix) "guile"))
+       `(("guile"
+          ,@(assoc-ref (package-native-inputs guix) "guile"))
          ("guix" ,guix)))
       (propagated-inputs
        `(("geiser" ,emacs-geiser)
@@ -3245,7 +3248,7 @@ files and directories.")
 (define-public emacs-fountain-mode
   (package
     (name "emacs-fountain-mode")
-    (version "3.3.0")
+    (version "3.3.3")
     (source
      (origin
        (method git-fetch)
@@ -3254,7 +3257,7 @@ files and directories.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "04jrv6i4ah3i8c9hcd9wyaw2vrxr46f50qb9qwna2v7qa5vaway3"))))
+        (base32 "095nrkg2bap6rcg9hy3bh0nis4v2f8w8d9hnahkzsa3njlpqa4ka"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/rnkn/fountain-mode")
     (synopsis "Major mode for screenwriting in Fountain markup")
@@ -4840,14 +4843,14 @@ source code using IPython.")
 (define-public emacs-debbugs
   (package
     (name "emacs-debbugs")
-    (version "0.26")
+    (version "0.27")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/debbugs-"
                            version ".tar"))
        (sha256
-        (base32 "14n2rrs3ccvlp8fhxs08awlqdfawxwbj8nq1xpa0wwlbfvxnf24c"))))
+        (base32 "1zn9p9vmfv5ihrp8d06b6abs48q225v42cgwa01s39hld6zg6wbv"))))
     (build-system emacs-build-system)
     (arguments '(#:include '("\\.el$" "\\.wsdl$" "\\.info$")))
     (propagated-inputs
@@ -6624,14 +6627,14 @@ board and goal value can be customized.")
 (define-public emacs-chess
   (package
     (name "emacs-chess")
-    (version "2.0.4")
+    (version "2.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/"
                            "chess-" version ".tar"))
        (sha256
-        (base32 "1sq1bjmp513vldfh7hc2bbfc54665abqiz0kqgqq3gijckaxn5js"))))
+        (base32 "1a4iwjdh6k348df6qywjws9z9f862d62m0b2sz57z4xhywiyxpr7"))))
     (build-system emacs-build-system)
     (arguments
      `(#:phases
@@ -10264,6 +10267,30 @@ lists, and project planning with a fast and effective plain-text system.
 This package is equivalent to org-plus-contrib, but only includes additional
 files that you would find in @file{contrib/} from the git repository.")))
 
+(define-public emacs-org-pretty-table
+  ;; There is no release yet.
+  (let ((commit "1331c600b83d95b28730b1bfcb48369ac1cf12ef")
+        (revision "0"))
+    (package
+      (name "emacs-org-pretty-table")
+      (version (git-version "0.0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/Fuco1/org-pretty-table")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0yvqxh66y400n2n5ykmb1zrzd80bakffpwn6nmf37728x4cj8krh"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/Fuco1/org-pretty-table")
+      (synopsis "Make tables in Org mode and OrgTbl mode prettier")
+      (description
+       "This package displays tables in Org mode and OrgTbl mode using Unicode
+characters.")
+      (license license:gpl3+))))
+
 (define-public emacs-ob-sclang
   (package
     (inherit emacs-org-contrib)
@@ -15235,6 +15262,14 @@ and @code{erc-send-modify-hook} to download and show images.")
        (sha256
         (base32 "07hbz2md52ccy95gv4d5n6szrfmpfqf3w4kwqdg2cf54c7kgf7hw"))))
     (build-system emacs-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-require-cl
+           (lambda _
+             (substitute* "list-utils.el"
+               (("\\(require 'cl\\)") "(require 'cl-lib)"))
+             #t)))))
     (home-page "https://github.com/rolandwalker/list-utils")
     (synopsis "List-manipulation utility functions")
     (description "This package provides a list manipulation library for Emacs.")
@@ -21011,31 +21046,29 @@ and code peeking.")
       (license license:gpl3+))))
 
 (define-public emacs-lsp-ivy
-  (let ((commit "caf1e1d7e22ed0b5fe18dd508d1a6f83dd163288")
-        (revision "2"))
-    (package
-      (name "emacs-lsp-ivy")
-      (version (git-version "0.1" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/emacs-lsp/lsp-ivy")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "084ds4qhzhivfnicy3h7z4mblxgcqx8pfnkbjr9qjrfng7cisy4z"))))
-      (build-system emacs-build-system)
-      (propagated-inputs
-       `(("emacs-ivy" ,emacs-ivy)
-         ("emacs-lsp-mode" ,emacs-lsp-mode)
-         ("emacs-dash" ,emacs-dash)))
-      (home-page "https://github.com/emacs-lsp/lsp-ivy")
-      (synopsis "Provide LSP-enhanced completion for symbols")
-      (description
-       "This package enhances @code{ivy} with completion for symbols from
+  (package
+    (name "emacs-lsp-ivy")
+    (version "0.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/emacs-lsp/lsp-ivy")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "08dpn0vcfdwwysijwdpnnj91m69yw0q464i0wmp51zpj3dyd4kb1"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-dash" ,emacs-dash)
+       ("emacs-ivy" ,emacs-ivy)
+       ("emacs-lsp-mode" ,emacs-lsp-mode)))
+    (home-page "https://github.com/emacs-lsp/lsp-ivy")
+    (synopsis "Provide LSP-enhanced completion for symbols")
+    (description
+     "This package enhances @code{ivy} with completion for symbols from
 workspaces with a LSP-compliant server running.")
-      (license license:gpl3+))))
+    (license license:gpl3+)))
 
 (define-public emacs-helm-lsp
   (let ((commit "3a58ca4cfd94b9ab1e15e819d3b16ef568e8889b")
@@ -21946,8 +21979,8 @@ copied into @code{org-mode} buffers.")
       (license license:gpl3+))))
 
 (define-public emacs-dash-docs
-  (let ((commit "111fd9b97001f1ad887b45e5308a14ddd68ce70a")
-        (revision "1"))
+  (let ((commit "dafc8fc9f1ddb2e4e39e0b8d066c42d5d7ce8d06")
+        (revision "2"))
     (package
       (name "emacs-dash-docs")
       (version (git-version "1.4.0" revision commit))
@@ -21960,7 +21993,7 @@ copied into @code{org-mode} buffers.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "0sckb7z0ylflva212bns7iq9mfnffgjghi0qspsbfwra35zb9xng"))))
+           "0n6d3mm43gj16v8kjjradcfik93wb89dsqnfcbskb28bvcamafid"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-async" ,emacs-async)))
@@ -22680,10 +22713,10 @@ it forcibly
            (lambda _
              (invoke "makeinfo" "elpher.texi"))))))
     (home-page "gopher://thelambdalab.xyz/1/projects/elpher/")
-    (synopsis "Gopher client for Emacs")
-    (description "Elpher is a full-featured gopher client for Emacs.  Its
-features include intuitive keyboard and mouse-driven browsing, out-of-the-box
-compatibility with evil-mode, clickable web and gopher links in plain text,
+    (synopsis "Gopher and gemini client for Emacs")
+    (description "Elpher is a full-featured gopher and gemini client for
+Emacs.  Its features include intuitive keyboard and mouse-driven browsing,
+out-of-the-box compatibility with evil-mode, clickable links in plain text,
 caching of visited sites, pleasant and configurable visualization of Gopher
 directories, direct visualisation of image files, jumping directly to links by
 name (with autocompletion), a simple bookmark management system and
@@ -23536,6 +23569,30 @@ Google guidelines.")
 fish-completion.  It can be used in both Eshell and M-x shell.")
     (license license:gpl3+)))
 
+(define-public emacs-helm-switch-to-repl
+  (package
+    (name "emacs-helm-switch-to-repl")
+    (version "0.1.0")
+    (home-page "https://github.com/emacs-helm/helm-switch-to-repl")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url home-page)
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0n19brymwnawhi0y10m54cas3qg64pmkqq1ajvjw1rfibmw3n6nk"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("helm" ,emacs-helm)))
+    (synopsis "Helm action to switch directory in Emacs REPLs")
+    (description "Helm \"Switch-to-REPL\" offers the
+@code{helm-switch-to-repl} action, a generalized and extensible version of
+@code{helm-ff-switch-to-shell}.  It can be added to @code{helm-find-files} and
+other @code{helm-type-file} sources such as @code{helm-locate}.")
+    (license license:gpl3+)))
+
 (define-public emacs-telega
   ;; This package has versions newer than indicated on MELPA.
   ;; Get the current version from `telega-version` in telega.el.
@@ -24816,7 +24873,7 @@ variables.")
 (define-public emacs-company-emoji
   (package
     (name "emacs-company-emoji")
-    (version "2.5.2")
+    (version "2.6.0")
     (source
      (origin
        (method git-fetch)
@@ -24825,7 +24882,7 @@ variables.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0r9zcbm3nb3zw5cwrkl098v5b49jbga5404bj7j55g6k4rwkjar2"))))
+        (base32 "0pa67yfcr8lrxdbvln8hs663gsxz38ggwpva7121ngascqgx42wp"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-company" ,emacs-company)))
@@ -25768,3 +25825,67 @@ anymore.  In this way, it's like a lightweight \"workspace\" manager, allowing
 you to easily restore one or more frames, including their windows, the
 windows' layout, and their buffers.")
     (license license:gpl3+)))
+
+(define-public emacs-smart-hungry-delete
+  (let ((commit "7c1d56a92481594e14d40b5fdf6c48657a0108a0"))
+    (package
+      (name "emacs-smart-hungry-delete")
+      (version "0.1")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/hrehfeld/emacs-smart-hungry-delete")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0mxaslx5823s68a8ggbbnmfk1jiswjvip5s4sg7ihfagnci72wni"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/hrehfeld/emacs-smart-hungry-delete")
+      (synopsis "Smart hungry deletion of whitespace")
+      (description "@code{emacs-smart-hungry-delete} hungrily deletes whitespace
+between cursor and next word, parenthesis or delimiter while honoring some
+rules about where space should be left to separate words and parentheses.")
+      (license license:gpl2+))))
+
+(define-public emacs-webpaste
+  (package
+    (name "emacs-webpaste")
+    (version "3.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/etu/webpaste.el")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "08545ihkzflw80rwklnxiswrpdrl8kr74xzxm5wsgrf36fkj9rn2"))))
+    (build-system emacs-build-system)
+    (arguments
+     `(#:tests? #t
+       #:test-command '("make" "unit" "integration")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-tests
+           (lambda _
+             ;; Do not use cask to run tests.
+             (substitute* "Makefile"
+               (("\\$\\{CASK\\} exec ") ""))
+             ;; Disable tests that need network access.
+             (substitute* (list "tests/unit/test-webpaste-provider-creation.el"
+                                "tests/integration/test-webpaste-providers.el")
+               (("describe") "xdescribe")))))))
+    (native-inputs
+     `(("emacs-buttercup" ,emacs-buttercup)))
+    (propagated-inputs
+     `(("emacs-request" ,emacs-request)))
+    (home-page "https://github.com/etu/webpaste.el")
+    (synopsis "Paste to pastebin-like services")
+    (description "This mode allows to paste whole buffers or parts of buffers
+to pastebin-like services.  It supports more than one service and will
+failover if one service fails.  More services can easily be added over time
+and prefered services can easily be configured.")
+    (license license:gpl3+)))
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index e436994492..7eb8bbf893 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -1133,22 +1133,23 @@ use on a given system.")
 (define-public libredwg
   (package
     (name "libredwg")
-    (version "0.11")
+    (version "0.11.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://gnu/libredwg/libredwg-"
              version ".tar.xz"))
        (sha256
-        (base32 "1vd7ii32k5447z7k4w9s005hv1ffpj6dyf1w40x6c53qksrblny2"))))
+        (base32 "1xx6y6ckm4mzqln8y8lqf5frcn2b32ypc0d0h9dzpz6363zh7pdn"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--disable-bindings")))
     (native-inputs
      `(("libxml2" ,libxml2)
        ("parallel" ,parallel)
+       ("perl" ,perl)
        ("pkg-config" ,pkg-config)
-       ("python" ,python)
+       ("python" ,python-wrapper)
        ("python-libxml2" ,python-libxml2)))
     (inputs
      `(("pcre2" ,pcre2)))
diff --git a/gnu/packages/fcitx5.scm b/gnu/packages/fcitx5.scm
new file mode 100644
index 0000000000..ed0d928fc7
--- /dev/null
+++ b/gnu/packages/fcitx5.scm
@@ -0,0 +1,450 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2020 Zhu Zihao <all_but_last@163.com>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages fcitx5)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system cmake)
+  #:use-module (guix build-system copy)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (gnu packages boost)
+  #:use-module (gnu packages curl)
+  #:use-module (gnu packages datastructures)
+  #:use-module (gnu packages enchant)
+  #:use-module (gnu packages freedesktop)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages gettext)
+  #:use-module (gnu packages glib)
+  #:use-module (gnu packages gtk)
+  #:use-module (gnu packages iso-codes)
+  #:use-module (gnu packages kde-frameworks)
+  #:use-module (gnu packages libevent)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages lua)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages pretty-print)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages qt)
+  #:use-module (gnu packages textutils)
+  #:use-module (gnu packages unicode)
+  #:use-module (gnu packages web)
+  #:use-module (gnu packages xdisorg)
+  #:use-module (gnu packages xml)
+  #:use-module (gnu packages xorg))
+
+(define-public xcb-imdkit
+  (package
+    (name "xcb-imdkit")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://download.fcitx-im.org/fcitx5/xcb-imdkit/xcb-imdkit-"
+             version ".tar.xz"))
+       (sha256
+        (base32 "1qgbbp8y8ci7haz99vgbrgpjsbrwwyjianyhdvxcirnbm5bybvmz"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; Remove bundled uthash.
+           (delete-file-recursively "uthash")
+           #t))))
+    (build-system cmake-build-system)
+    (inputs
+     `(("uthash" ,uthash)
+       ("libxcb" ,libxcb)
+       ("xcb-util" ,xcb-util)
+       ("xcb-util-keysyms" ,xcb-util-keysyms)))
+    (native-inputs
+     `(("extra-cmake-modules" ,extra-cmake-modules)
+       ("pkg-config" ,pkg-config)))
+    (home-page "https://github.com/fcitx/xcb-imdkit")
+    (synopsis "Input method development support for XCB")
+    (description "Xcb-imdkit is an implementation of xim protocol in XCB,
+comparing with the implementation of IMDkit with Xlib, and xim inside Xlib, it
+has less memory foot print, better performance, and safer on malformed
+client.")
+    (license license:lgpl2.1)))
+
+(define-public fcitx5
+  (package
+    (name "fcitx5")
+    (version "5.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://download.fcitx-im.org/fcitx5/fcitx5/fcitx5-"
+             version "_dict.tar.xz"))
+       (sha256
+        (base32 "06zkb33m2rnhg385iy79n3r4svz5jbav74di61xqa3lhbv7534s3"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "-DCLDR_DIR="
+                            (assoc-ref %build-inputs "unicode-cldr-common")
+                            "/share/unicode/cldr"))))
+    (inputs
+     `(("cairo" ,cairo)
+       ("cairo-xcb" ,cairo-xcb)
+       ("dbus" ,dbus)
+       ("enchant" ,enchant)
+       ("expat" ,expat)
+       ("fmt" ,fmt)
+       ("gdk-pixbuf" ,gdk-pixbuf)
+       ("gettext" ,gettext-minimal)
+       ("glib" ,glib)
+       ("iso-codes" ,iso-codes)
+       ("json-c" ,json-c)
+       ("libevent" ,libevent)
+       ("libpthread-stubs" ,libpthread-stubs)
+       ("libuuid" ,util-linux "lib")
+       ("libx11" ,libx11)
+       ("libxcb" ,libxcb)
+       ("libxfixes" ,libxfixes)
+       ("libxinerama" ,libxinerama)
+       ("libxkbcommon" ,libxkbcommon)
+       ("libxkbfile" ,libxkbfile)
+       ("pango" ,pango)
+       ("unicode-cldr-common" ,unicode-cldr-common)
+       ("wayland" ,wayland)
+       ("wayland-protocols" ,wayland-protocols)
+       ("xcb-imdkit" ,xcb-imdkit)
+       ("xcb-util" ,xcb-util)
+       ("xcb-util-keysyms" ,xcb-util-keysyms)
+       ("xcb-util-wm" ,xcb-util-wm)
+       ("xkeyboard-config" ,xkeyboard-config)))
+    (native-inputs
+     `(("extra-cmake-modules" ,extra-cmake-modules)
+       ("pkg-config" ,pkg-config)))
+    (native-search-paths
+     (list (search-path-specification
+            (variable "FCITX_ADDON_DIRS")
+            (files '("lib/fcitx5")))))
+    (home-page "https://github.com/fcitx/fcitx5")
+    (synopsis "Input method framework")
+    (description "Fcitx 5 is a generic input method framework.")
+    (license license:lgpl2.1+)))
+
+(define-public fcitx5-lua
+  (package
+    (name "fcitx5-lua")
+    (version "5.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://download.fcitx-im.org/fcitx5/fcitx5-lua/fcitx5-lua-"
+             version ".tar.xz"))
+       (sha256
+        (base32 "177mj56j8yrl79hvk7bbrifvm137np23pwalv83ibgk4l51z92hf"))))
+    (build-system cmake-build-system)
+    (inputs
+     `(("fcitx5" ,fcitx5)
+       ("lua" ,lua)
+       ("gettext" ,gettext-minimal)
+       ("libpthread-stubs" ,libpthread-stubs)))
+    (native-inputs
+     `(("extra-cmake-modules" ,extra-cmake-modules)))
+    (home-page "https://github.com/fcitx/fcitx5-lua")
+    (synopsis "Lua support for Fcitx 5")
+    (description "Fcitx5-lua allows writing Fcitx5 extension in Lua.")
+    (license license:lgpl2.1+)))
+
+(define-public libime
+  (package
+    (name "libime")
+    (version "1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://download.fcitx-im.org/fcitx5/libime/libime-"
+                           version "_dict.tar.xz"))
+       (sha256
+        (base32 "006pncby7p6h3rnicckzjwi6jzsrqiqbj6p9bpic80lanlllgw31"))))
+    (build-system cmake-build-system)
+    (inputs
+     `(("fcitx5" ,fcitx5)
+       ("boost" ,boost)))
+    (native-inputs
+     `(("gcc" ,gcc-9)                  ;for #include <filesystem> and ld support
+       ("extra-cmake-modules" ,extra-cmake-modules)
+       ("python" ,python)))             ;needed to run test
+    (home-page "https://github.com/fcitx/libime")
+    (synopsis "Library for implementing generic input method")
+    (description "Libime is a library for implmenting various input methods
+editors.")
+    (license license:lgpl2.1+)))
+
+(define-public fcitx5-gtk
+  (package
+    (name "fcitx5-gtk")
+    (version "5.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://download.fcitx-im.org/fcitx5"
+                           "/fcitx5-gtk/fcitx5-gtk-"
+                           version ".tar.xz"))
+       (sha256
+        (base32 "0h53liraqc5nz4nyi3ixdfdw3zzkdcsiff7j25acc3gmaa5gyij7"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f                      ;No test
+       #:configure-flags
+       (list (string-append "-DGOBJECT_INTROSPECTION_GIRDIR="
+                            %output "/share/gir-1.0")
+             (string-append "-DGOBJECT_INTROSPECTION_TYPELIBDIR="
+                            %output "/lib/girepository-1.0"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'patch-install-prefix
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (gtk2 (assoc-ref outputs "gtk2")))
+               ;; Install GTK+ 2 input method module to its own output.
+               (substitute* "gtk2/CMakeLists.txt"
+                 (("\\$\\{CMAKE_INSTALL_LIBDIR\\}")
+                  (string-append gtk2 "/lib")))))))))
+    (inputs
+     `(("fcitx5" ,fcitx5)
+       ("libxkbcommon" ,libxkbcommon)
+       ("gobject-introspection" ,gobject-introspection)
+       ("gtk2" ,gtk+-2)
+       ("gtk3" ,gtk+)
+       ("glib" ,glib)
+       ("libx11" ,libx11)
+       ("gettext" ,gettext-minimal)))
+    (native-inputs
+     `(("extra-cmake-modules" ,extra-cmake-modules)
+       ("pkg-config" ,pkg-config)
+       ("glib" ,glib "bin")))           ;for glib-genmarshal
+    ;; TODO: Add "lib" output to reduce the closure size of "gtk2".
+    (outputs '("out" "gtk2"))
+    (home-page "https://github.com/fcitx/fcitx5-gtk")
+    (synopsis "Glib based D-Bus client and GTK IM module for Fcitx 5")
+    (description "Fcitx5-gtk provides a Glib based D-Bus client and IM module
+for GTK+2/GTK+3 application.")
+    (license license:lgpl2.1+)))
+
+(define-public fcitx5-qt
+  (package
+    (name "fcitx5-qt")
+    (version "5.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://download.fcitx-im.org/fcitx5"
+                           "/fcitx5-qt/fcitx5-qt-"
+                           version ".tar.xz"))
+       (sha256
+        (base32 "0ilhb4yw9k3m1c4fidnv3nd5dgm9xxds11dgdys6gswjjnmcgqqm"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "-DCMAKE_INSTALL_QT5PLUGINDIR="
+                            %output "/lib/qt5/plugins")
+             "-DENABLE_QT4=Off")))
+    (inputs
+     `(("fcitx5" ,fcitx5)
+       ("libxcb" ,libxcb)
+       ("libxkbcommon" ,libxkbcommon)
+       ("qtbase" ,qtbase)
+       ("gettext" ,gettext-minimal)))
+    (native-inputs
+     `(("extra-cmake-modules" ,extra-cmake-modules)))
+    (home-page "https://github.com/fcitx/fcitx5-qt")
+    (synopsis "Qt library and IM module for Fcitx 5")
+    (description "Fcitx5-qt provides Qt library for development and IM module
+for Qt based application.")
+    (license (list license:lgpl2.1+
+                   ;; Files under qt4(Fcitx5Qt4DBusAddons), qt5/dbusaddons
+                   ;; and qt5/platforminputcontext.
+                   license:bsd-3))))
+
+(define-public fcitx5-chinese-addons
+  (package
+    (name "fcitx5-chinese-addons")
+    (version "5.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://download.fcitx-im.org/fcitx5"
+                           "/fcitx5-chinese-addons/fcitx5-chinese-addons-"
+                           version "_dict.tar.xz"))
+       (sha256
+        (base32 "0mf91gzwzhfci0jn6g3l516xjw8r4v40ginnbl70h1zx6vr24rfp"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'split-outputs
+           ;; Build with GUI supports requires Qt and increase package closure
+           ;; by 800M on x86_64, so place it under another output.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "gui/pinyindictmanager/CMakeLists.txt"
+               (("\\$\\{CMAKE_INSTALL_LIBDIR\\}" _)
+                (string-append (assoc-ref outputs "gui") "/lib"))))))))
+    (inputs
+     `(("fcitx5" ,fcitx5)
+       ("fcitx5-lua" ,fcitx5-lua)
+       ("boost" ,boost)
+       ("libime",libime)
+       ("curl" ,curl)
+       ("gettext" ,gettext-minimal)
+       ("fmt" ,fmt)
+       ("libpthread-stubs" ,libpthread-stubs)
+       ("opencc" ,opencc)
+       ("qtbase" ,qtbase)
+       ("fcitx5-qt" ,fcitx5-qt)
+       ("qtwebkit" ,qtwebkit)))
+    (native-inputs
+     `(("extra-cmake-modules" ,extra-cmake-modules)
+       ("pkg-config" ,pkg-config)))
+    (outputs '("out" "gui"))
+    (home-page "https://github.com/fcitx/fcitx5-chinese-addons")
+    (synopsis "Chinese related addons for Fcitx 5")
+    (description "Fcitx5-chinese-addons provides Chinese related addons,
+including input methods previous bundled inside Fcitx 4:
+
+@itemize
+@item Bingchan
+@item Cangjie
+@item Erbi
+@item Pinyin
+@item Shuangpin
+@item Wanfeng
+@item Wubi
+@item Wubi Pinyin
+@item Ziranma
+@end itemize\n")
+    (license (list license:lgpl2.1+
+                   license:gpl2+
+                   ;; im/pinyin/emoji.txt
+                   license:unicode))))
+
+(define-public fcitx5-configtool
+  (package
+   (name "fcitx5-configtool")
+   (version "5.0.1")
+   (source
+    (origin
+     (method url-fetch)
+     (uri (string-append
+           "https://download.fcitx-im.org/fcitx5"
+           "/fcitx5-configtool/fcitx5-configtool-" version ".tar.xz"))
+     (sha256
+      (base32 "0mrqhzvab41hkvhkz7vkb8d2mv5bgx4aqp9jpz4kf3kskwm1q14b"))))
+   (build-system cmake-build-system)
+   (arguments
+    `(#:configure-flags
+      ;; KDE is currently not working on Guix, KCM supports doesn't make sense.
+      '("-DENABLE_KCM=Off")))
+   (inputs
+    `(("fcitx5" ,fcitx5)
+      ("fcitx5-qt" ,fcitx5-qt)
+      ("qtbase" ,qtbase)
+      ("qtx11extras" ,qtx11extras)
+      ("kitemviews" ,kitemviews)
+      ("kwidgetsaddons" ,kwidgetsaddons)
+      ("libx11" ,libx11)
+      ("xkeyboard-config" ,xkeyboard-config)
+      ("libxkbfile" ,libxkbfile)
+      ("gettext" ,gettext-minimal)
+      ("iso-codes" ,iso-codes)))
+   (native-inputs
+    `(("gcc" ,gcc-9)
+      ("extra-cmake-modules" ,extra-cmake-modules)
+      ("pkg-config" ,pkg-config)))
+   (home-page "https://github.com/fcitx/fcitx5-configtool")
+   (synopsis "Graphical configuration tool for Fcitx 5")
+   (description "Fcitx5-configtool is a graphical configuration tool
+to manage different input methods in Fcitx 5.")
+   (license license:gpl2+)))
+
+(define-public fcitx5-material-color-theme
+  (package
+    (name "fcitx5-material-color-theme")
+    (version "0.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/hosxy/Fcitx5-Material-Color")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1mgc722521jmfx0xc3ibmiycd3q2w7xg2956xcpc07kz90gcdjaa"))))
+    (build-system copy-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (use-modules (srfi srfi-26))
+
+             (let* ((out (assoc-ref outputs "out"))
+                    (assets-dir (string-append
+                                 out "/share/fcitx5-material-color-theme"))
+                    (themes-prefix (string-append out "/share/fcitx5/themes")))
+
+               (define (install-theme-variant variant target)
+                 (let ((dir (string-append themes-prefix "/" target))
+                       (png (string-append "panel-" variant ".png"))
+                       (conf (string-append "theme-" variant ".conf")))
+                   (format #t "install: Installing color variant \"~a\" to ~a~%"
+                           variant dir)
+                   (substitute* conf
+                     (("^Name=.*")
+                      (string-append "Name=" target "\n")))
+                   (mkdir-p dir)
+                   (install-file png dir)
+                   (copy-file conf (string-append dir "/theme.conf"))
+                   (symlink (string-append assets-dir "/arrow.png")
+                            (string-append dir "/arrow.png"))))
+
+               (mkdir-p assets-dir)
+               (install-file "arrow.png" assets-dir)
+               (for-each
+                (lambda (x)
+                  (install-theme-variant
+                   x (string-append "Material-Color-" (string-capitalize x))))
+                '("black" "blue" "brown" "indigo"
+                  "orange" "pink" "red" "teal"))
+
+               (install-theme-variant
+                "deepPurple" "Material-Color-DeepPurple")))))))
+    (home-page "https://github.com/hosxy/Fcitx5-Material-Color")
+    (synopsis "Material Design for Fcitx 5")
+    (description "Fcitx5-material-color-theme is a Material Design theme
+for Fcitx 5 with following color variants:
+
+@itemize
+@item Black
+@item Blue
+@item Brown
+@item Indigo
+@item Orange
+@item Pink
+@item Red
+@item teal
+@item DeepPurple
+@end itemize\n")
+    (license license:asl2.0)))
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index df6d6fa424..579e060d26 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -625,7 +625,7 @@ other machines/servers.  Electroncash does not download the Bitcoin Cash blockch
   ;; the system's dynamically linked library.
   (package
     (name "monero")
-    (version "0.17.1.5")
+    (version "0.17.1.6")
     (source
      (origin
        (method git-fetch)
@@ -645,7 +645,7 @@ other machines/servers.  Electroncash does not download the Bitcoin Cash blockch
               "external/unbound"))
            #t))
        (sha256
-        (base32 "0yy9n2qng02j314h8fh5n0mcy6vpdks0yk4d8ifn8hj03f3g2c8b"))))
+        (base32 "0b6zyr3mzqvcxf48i2g45gr649x6nhppik5598jsvg0z7i2hxb9q"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("doxygen" ,doxygen)
@@ -735,7 +735,7 @@ the Monero command line client and daemon.")
 (define-public monero-gui
   (package
     (name "monero-gui")
-    (version "0.17.1.5")
+    (version "0.17.1.6")
     (source
      (origin
        (method git-fetch)
@@ -744,7 +744,7 @@ the Monero command line client and daemon.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0qlcqli0wvrjfy89mbgh1hpmk60dxgn5sws93h8lhgyfwx557iw0"))))
+        (base32 "0kn5wvx2psbdaqmy1cxlbf5l1mdpvh0b6hh9drah3s7nj3654a3r"))))
     (build-system qt-build-system)
     (native-inputs
      `(,@(package-native-inputs monero)
diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index c57ea5a908..21f7f7e880 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -1071,7 +1071,14 @@ to create fully featured games and multimedia programs in the python language.")
          (method url-fetch)
          (uri (string-append "https://www.renpy.org/dl/" renpy-version
                              "/pygame_sdl2-" version ".tar.gz"))
-         (sha256 (base32 "1bmr7j9mlsc4czpgw70ld15ymyp4wxrk9hdsqad40wjwdxvvg2dr"))))
+         (sha256 (base32 "1bmr7j9mlsc4czpgw70ld15ymyp4wxrk9hdsqad40wjwdxvvg2dr"))
+         (modules '((guix build utils)))
+         (snippet
+          '(begin
+             ;; drop generated sources
+             (delete-file-recursively "gen")
+             (delete-file-recursively "gen3")
+             #t))))
       (build-system python-build-system)
       (arguments
        `(#:tests? #f                ; tests require pygame to be installed first
@@ -1090,11 +1097,6 @@ to create fully featured games and multimedia programs in the python language.")
                                       "/lib -Wl,-rpath,"
                                       (assoc-ref inputs "sdl-union")
                                       "/lib -Wl,--enable-new-dtags -lSDL2"))
-               #t))
-           (add-before 'build 'drop-generated-files
-             (lambda args
-               (delete-file-recursively "gen")
-               (delete-file-recursively "gen3")
                #t)))))
       (inputs
        `(("sdl-union"
@@ -1118,7 +1120,18 @@ developed mainly for Ren'py.")
        (method url-fetch)
        (uri (string-append "https://www.renpy.org/dl/" version
                            "/renpy-" version "-source.tar.bz2"))
-       (sha256 (base32 "1anr5cfbvbsbik4v4rvrkdkciwhg700k4lydfbs4n85raimz9mw4"))))
+       (sha256 (base32 "1anr5cfbvbsbik4v4rvrkdkciwhg700k4lydfbs4n85raimz9mw4"))
+       (modules '((guix build utils)))
+       (patches
+        (search-patches
+         "renpy-use-system-fribidi.patch"))
+       (snippet
+        '(with-directory-excursion "module"
+           ;; drop generated sources
+           (delete-file-recursively "gen")
+           ;; drop fribidi sources
+           (delete-file-recursively "fribidi-src")
+           #t))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f ; Ren'py doesn't seem to package tests
@@ -1131,6 +1144,13 @@ developed mainly for Ren'py.")
                (("xdg-open")
                 (which "xdg-open")))
              #t))
+         (add-after 'unpack 'fix-include-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "module/setup.py"
+               (("/usr/include/fribidi")
+                (string-append (assoc-ref inputs "fribidi")
+                               "/include/fribidi")))
+             #t))
          (add-after 'set-paths 'set-build-vars
            (lambda* (#:key inputs #:allow-other-keys)
              (setenv "RENPY_CYTHON"
@@ -1168,6 +1188,7 @@ developed mainly for Ren'py.")
     (inputs
      `(("ffmpeg" ,ffmpeg)
        ("freetype" ,freetype)
+       ("fribidi" ,fribidi)
        ("glew" ,glew)
        ("libpng" ,libpng)
        ("python2-pygame" ,python2-pygame-sdl2)
diff --git a/gnu/packages/gimp.scm b/gnu/packages/gimp.scm
index a47de30ae4..da19939679 100644
--- a/gnu/packages/gimp.scm
+++ b/gnu/packages/gimp.scm
@@ -409,7 +409,7 @@ inverse fourier transform.")
 (define-public libmypaint
   (package
     (name "libmypaint")
-    (version "1.5.1")
+    (version "1.6.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/mypaint/libmypaint/"
@@ -417,7 +417,7 @@ inverse fourier transform.")
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0aqcv4fyscpfhknxgfpq0v84aj2nzigqvpi4zgv2zkl41h51by5f"))))
+                "0priwpmc7dizccqvn21ig6d649bprl3xl1hmjj7nddznjgr585vl"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("intltool" ,intltool)
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 623732d8bc..64fded105a 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -11504,7 +11504,7 @@ and toolbars.")
 (define-public setzer
   (package
     (name "setzer")
-    (version "0.3.6")
+    (version "0.3.8")
     (source
      (origin
        (method git-fetch)
@@ -11513,7 +11513,7 @@ and toolbars.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "118gip6bv4mcsq4nrai7kl0vmqqbyzpsd4ky9vhxb1x2cvg048s8"))))
+        (base32 "1f5qmkz4hzn54sh56z3hw8zrvg93xlz62ggzlzyg7vgsr83kpns9"))))
     (build-system meson-build-system)
     (arguments
      `(#:glib-or-gtk? #t
diff --git a/gnu/packages/gnucash.scm b/gnu/packages/gnucash.scm
index dcee4dc166..f71e8209fa 100644
--- a/gnu/packages/gnucash.scm
+++ b/gnu/packages/gnucash.scm
@@ -7,6 +7,7 @@
 ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2020 Prafulla Giri <pratheblackdiamond@gmail.com>
+;;; Copyright © 2020 Christopher Lam <christopher.lck@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -51,6 +52,7 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages swig)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web)
   #:use-module (gnu packages webkit)
@@ -61,25 +63,24 @@
   ;; directory.
   (package
     (name "gnucash")
-    (version "3.8")
+    (version "4.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/gnucash/gnucash%20%28stable%29/"
-                           version "/gnucash-" version "b" ".tar.bz2"))
+                           version "/gnucash-" version ".tar.bz2"))
        (sha256
         (base32
-         "0dvzm3bib7jcj685sklpzyy9mrak9mxyvih2k9fk4sl3v21wlphg"))))
+         "020k1mm909dcgs52ls4v7xx3yn8gqazi9awyr81l6y7pkq1spn2n"))))
     (build-system cmake-build-system)
     (inputs
-     `(("guile" ,guile-2.2)
+     `(("guile" ,guile-3.0)
        ("boost" ,boost)
        ("icu4c" ,icu4c)
        ("glib" ,glib)
        ("gtk" ,gtk+)
        ("libdbi" ,libdbi)
        ("libdbi-drivers" ,libdbi-drivers)
-       ("libgnomecanvas" ,libgnomecanvas)
        ("libofx" ,libofx)
        ("libxml2" ,libxml2)
        ("libxslt" ,libxslt)
@@ -95,6 +96,7 @@
        ("googlemock" ,(package-source googletest))
        ("googletest" ,googletest)
        ("gnucash-docs" ,gnucash-docs)
+       ("swig" ,swig)
        ("pkg-config" ,pkg-config)))
     (propagated-inputs
      ;; dconf is required at runtime according to README.dependencies.
@@ -134,8 +136,8 @@
          ;; execute them with perl, so execute them directly instead.
          (add-after 'unpack 'fix-finance-quote-check
            (lambda _
-             (substitute* "libgnucash/scm/price-quotes.scm"
-               (("\"perl\" \"-w\" ") ""))
+             (substitute* "gnucash/price-quotes.scm"
+                (("\"perl\" \"-w\" ") ""))
              #t))
          ;; The qof test requires the en_US, en_GB, and fr_FR locales.
          (add-before 'check 'install-locales
@@ -230,7 +232,7 @@ installed as well as Yelp, the Gnome help browser.")
                              version "/gnucash-docs-" version revision ".tar.gz"))
          (sha256
           (base32
-           "19v6kchda724xkkgwlw5rg21jcpirhch12j9sr6ibnv61sd4ql52"))))
+           "1p1rbv0gyi07nh5pzhk3xm46w66kjyaipb6rpaq9yb9gil1nl7q5"))))
       (build-system gnu-build-system)
       ;; These are native-inputs because they are only required for building the
       ;; documentation.
diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index bacb835dec..3b42bf3c8f 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -512,6 +512,35 @@ way of specifying command line options.")
     (home-page "https://github.com/jessevdk/go-flags")
     (license license:bsd-3)))
 
+(define-public go-github-com-aws-sdk
+  (package
+    (name "go-github-com-aws-sdk")
+    (version "1.35.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/aws/aws-sdk-go")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1ky5lw2s2zpslnnqcs6hgsrwvwbxwgflb5jwf16dd4aga3vrg10c"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/aws/aws-sdk-go/aws"
+       #:unpack-path "github.com/aws/aws-sdk-go"))
+    (propagated-inputs
+     `(("go-github-com-go-sql-driver-mysql" ,go-github-com-go-sql-driver-mysql)
+       ("go-github-com-jmespath-go-jmespath" ,go-github-com-jmespath-go-jmespath)
+       ("go-github-com-pkg-errors" ,go-github-com-pkg-errors)
+       ("go-golang-org-x-net" ,go-golang-org-x-net)))
+    (home-page "https://github.com/aws/aws-sdk-go")
+    (synopsis "Library to access Amazon Web Services (AWS)")
+    (description
+     "This is the official AWS SDK for the Go programming language.")
+    (license license:asl2.0)))
+
 (define-public go-gopkg.in-tomb.v2
   (let ((commit "d5d1b5820637886def9eef33e03a27a9f166942c")
         (revision "0"))
@@ -3582,6 +3611,31 @@ without requiring a real database connection.")
       (home-page "https://github.com/DATA-DOG/go-sqlmock")
       (license license:expat))))
 
+(define-public go-github-com-go-sql-driver-mysql
+  (package
+    (name "go-github-com-go-sql-driver-mysql")
+    (version "1.5.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/go-sql-driver/mysql")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "11x0m9yf3kdnf6981182r824psgxwfaqhn3x3in4yiidp0w0hk3v"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:tests? #f ;; tests require a network connection
+       #:import-path "github.com/go-sql-driver/mysql"))
+    (home-page "https://github.com/go-sql-driver/mysql")
+    (synopsis "MySQL driver for golang")
+    (description
+     "This is a pure Go implementaton of the MySQL API, compatible with
+golang's database/sql package.")
+    (license license:mpl2.0)))
+
 (define-public go-golang-org-colorful
   (package
     (name "go-golang-org-colorful")
@@ -5104,6 +5158,34 @@ the parse trees produced by the html package.")
 to jQuery to the Go language.")
     (license license:bsd-3)))
 
+(define-public go-github-com-jmespath-go-jmespath
+  (package
+    (name "go-github-com-jmespath-go-jmespath")
+    (version "0.4.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/jmespath/go-jmespath")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "18zyr9nlywmwp3wpzcjxrgq9s9d2mmc6zg6xhsna00m663nkyc3n"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/jmespath/go-jmespath"))
+    (native-inputs
+     `(("go-github-com-davecgh-go-spew" ,go-github-com-davecgh-go-spew)
+       ("go-github-com-pmezard-go-difflib" ,go-github-com-pmezard-go-difflib)
+       ("go-gopkg-in-yaml-v2" ,go-gopkg-in-yaml-v2)))
+    (home-page "https://github.com/jmespath/go-jmespath")
+    (synopsis "Golang implementation of JMESPath")
+    (description
+     "This package implements JMESPath, a query language for JSON.  It
+transforms one JSON document into another through a JMESPath expression.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-aymerick-douceur
   (package
     (name "go-github-com-aymerick-douceur")
diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm
index f49ddf9216..dfffbfc62f 100644
--- a/gnu/packages/guile-xyz.scm
+++ b/gnu/packages/guile-xyz.scm
@@ -32,6 +32,7 @@
 ;;; Copyright © 2020 Jesse Gibbons <jgibbons2357@gmail.com>
 ;;; Copyright © 2020 Mike Rosset <mike.rosset@gmail.com>
 ;;; Copyright © 2020 Leo Prikler <leo.prikler@student.tugraz.at>
+;;; Copyright © 2020 pukkamustard <pukkamustard@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -58,6 +59,7 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages crypto)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages disk)
   #:use-module (gnu packages emacs)
@@ -886,8 +888,8 @@ Vicare Scheme and IronScheme.  Right now it contains:
     (license license:bsd-3)))
 
 (define-public guile-prometheus
-  (let ((commit "2549c482fb04db84481d595f0bf99a1c8bb97c4c")
-        (revision "3"))
+  (let ((commit "35dc26c0ea44c3d70f1819f240d84e2cbb4b7b4c")
+        (revision "5"))
     (package
     (name "guile-prometheus")
     (version (git-version "0" revision commit))
@@ -898,7 +900,7 @@ Vicare Scheme and IronScheme.  Right now it contains:
                     (commit commit)))
               (sha256
                (base32
-                "0wfaspy3gvn2bkfzlvgx9ncz6114ldxxj25vnj4frcgbzqbdsair"))
+                "07822jj4appw37lf444kc4xlgl7nm64mgldag56072l55kwashgb"))
               (file-name (string-append name "-" version "-checkout"))))
     (build-system gnu-build-system)
     (native-inputs
@@ -966,8 +968,8 @@ convenient nested tree operations.")
     (license license:gpl3+)))
 
 (define-public guile-simple-zmq
-  (let ((commit "5fc3b7190d31c258ce969c2a5d2ad38c66a09d09")
-        (revision "4"))
+  (let ((commit "f8b7d81afb38525750f8818ed2956ca18c828ee8")
+        (revision "5"))
     (package
       (name "guile-simple-zmq")
       (version (git-version "0.0.0" revision commit))
@@ -979,7 +981,7 @@ convenient nested tree operations.")
                (commit commit)))
          (sha256
           (base32
-           "0inhvl5jssvbw3nd129wdahfwyvy1iciq403wzf0algbvl1fqs7z"))
+           "1gpzlpcq7bxw7sxyrg8zslwb3631vizw56lgg1aavw4gafh0hxb3"))
          (file-name (git-file-name name version))))
       (build-system guile-build-system)
       (arguments
@@ -4176,3 +4178,65 @@ recursively.  It also provides new versions of @code{open-output-file},
 directory of its argument if it does not exist.")
     (home-page "https://mkdir-p.divoplade.fr")
     (license license:asl2.0)))
+
+(define-public guile-sodium
+  (package
+    (name "guile-sodium")
+    (version "0.1.0")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://inqlab.net/git/guile-sodium.git")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256 (base32 "189jsj87hycs57a54x0b9lifwvhr63nypb9vfxdrq7rwrpcvi5f8"))))
+    (build-system gnu-build-system)
+    (arguments `())
+    (native-inputs
+      `(("autoconf" ,autoconf)
+        ("automake" ,automake)
+        ("pkg-config" ,pkg-config)
+        ("texinfo" ,texinfo)))
+    (inputs `(("guile" ,guile-3.0)))
+    (propagated-inputs `(("libsodium" ,libsodium)))
+    (synopsis "Guile bindings to the libsodium cryptographic library")
+    (description
+     "This package provides Guile bindings to the libsodium cryptographic library
+which provides core cryptographic primitives needed to build higher-level
+tools.")
+    (home-page "https://inqlab.net/git/guile-sodium.git")
+    (license license:gpl3+)))
+
+(define-public guile-eris
+  (package
+    (name "guile-eris")
+    (version "0.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://inqlab.net/git/eris.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256 (base32 "1ijglmwkdy1l87gj429qfjis0v8b1zlxhbyfhx5za8664h68nqka"))))
+    (build-system gnu-build-system)
+    (arguments '())
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("pkg-config" ,pkg-config)
+       ("texinfo" ,texinfo)
+       ;; test dependency
+       ("guile-srfi-180" ,guile-srfi-180)))
+    (inputs `(("guile" ,guile-3.0)))
+    (propagated-inputs
+     `(("guile-sodium" ,guile-sodium)))
+    (synopsis "Guile implementation of the Encoding for Robust Immutable Storage (ERIS)")
+    (description
+     "Guile-ERIS is the reference implementation of the Encoding for Robust
+Immutable Storage (ERIS).  ERIS allows arbirtary content to be encoded into
+uniformly sized, encrypted blocks that can be reassembled using a short
+read-capability.")
+    (home-page "https://inqlab.net/git/eris.git")
+    (license license:gpl3+)))
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index 195b49e5bc..dac1d654f6 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -59,8 +59,10 @@
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages ghostscript)
+  #:use-module (gnu packages gimp)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages glib)
+  #:use-module (gnu packages gnome)
   #:use-module (gnu packages graphics)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages lua)
@@ -76,6 +78,7 @@
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages swig)
   #:use-module (gnu packages textutils)
   #:use-module (gnu packages video)
   #:use-module (gnu packages web)
@@ -2150,6 +2153,66 @@ painting and palette manipulation tools.  It also handles JPEG, JPEG2000,
 GIF, TIFF, WEBP, BMP, PNG, XPM formats.")
     (license license:gpl3+)))
 
+(define-public mypaint
+  (package
+    (name "mypaint")
+    (version "2.0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/mypaint/mypaint/"
+                                  "releases/download/v" version "/mypaint-"
+                                  version ".tar.xz"))
+              (sha256
+               (base32
+                "05mvay73vb9d2sh1ckv4vny45n059dmsps1jcppjizfmrpbkgr7k"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:imported-modules ((guix build glib-or-gtk-build-system)
+                           ,@%python-build-system-modules)
+       #:modules ((guix build python-build-system)
+                  ((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:)
+                  (guix build utils))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'glib-or-gtk-wrap
+           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap))
+         (add-after 'install 'wrap-program
+           (lambda* (#:key outputs inputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (gdk-pixbuf (assoc-ref inputs "gdk-pixbuf"))
+                    (gtk+ (assoc-ref inputs "gtk+")))
+               (wrap-program (string-append out "/bin/mypaint")
+                 `("GI_TYPELIB_PATH" ":" prefix
+                   (,(getenv "GI_TYPELIB_PATH"))))
+               #t)))
+         (add-before 'check 'pre-check
+           (lambda _
+             ;; Tests need writing access
+             (setenv "HOME" "/tmp")
+             #t)))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("gobject-introspection" ,gobject-introspection)
+       ("swig" ,swig)
+       ("gettext" ,gettext-minimal)))
+    (inputs
+     `(("gtk+" ,gtk+)
+       ("gdk-pixbuf" ,gdk-pixbuf+svg)
+       ("hicolor-icon-theme" ,hicolor-icon-theme)
+       ("libmypaint" ,libmypaint)
+       ("mypaint-brushes" ,mypaint-brushes)
+       ("json-c" ,json-c)
+       ("lcms" ,lcms)
+       ("python-numpy" ,python-numpy)
+       ("python-pycairo" ,python-pycairo)
+       ("python-pygobject" ,python-pygobject)))
+    (home-page "http://mypaint.org/")
+    (synopsis "Fast and simple painting app for artists")
+    (description
+     "MyPaint is a simple drawing and painting program that works well with
+Wacom-style graphics tablets.")
+    (license license:gpl2+)))
+
 (define-public phockup
   (package
     (name "phockup")
diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index febdb1f4f0..951a2f8554 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -811,7 +811,7 @@ interfaces in the areas of colors, fonts, text, images, keyboard input.")
     (inputs
      `(("qtbase" ,qtbase)
        ("qtdeclarative" ,qtdeclarative)))
-    (home-page "https://cgit.kde.org/kholidays.git")
+    (home-page "https://invent.kde.org/frameworks/kholidays")
     (synopsis "Library for regional holiday information")
     (description "This library provides a C++ API that determines holiday and
 other special events for a geographical region.")
diff --git a/gnu/packages/kde-internet.scm b/gnu/packages/kde-internet.scm
index 4203ffbaec..617937002e 100644
--- a/gnu/packages/kde-internet.scm
+++ b/gnu/packages/kde-internet.scm
@@ -450,7 +450,7 @@ a full-featured client for BitTorrent.")
        ("qtbase" ,qtbase)))
     (arguments
      `(#:tests? #f)) ;; 2/7 tests fail (due to network issues?)
-    (home-page "https://cgit.kde.org/libgravatar.git")
+    (home-page "https://invent.kde.org/pim/libgravatar")
     (synopsis "Online avatar lookup library")
     (description "This library retrieves avatar images based on a
 hash from a person's email address, as well as local caching to avoid
@@ -484,7 +484,7 @@ unnecessary network operations.")
        ("qca" ,qca)
        ("qtbase" ,qtbase)
        ("solid" ,solid)))
-    (home-page "https://cgit.kde.org/libktorrent.git")
+    (home-page "https://invent.kde.org/network/libktorrent")
     (synopsis "BitTorrent protocol library for C++ / Qt 5 / KDE Frameworks")
     (description "The KTorrent library supports connectivity to HTTP and UDP
 trackers, mainline DHT and the new generation Micro Transport
diff --git a/gnu/packages/kde-multimedia.scm b/gnu/packages/kde-multimedia.scm
index 23417a982d..cc312b6c40 100644
--- a/gnu/packages/kde-multimedia.scm
+++ b/gnu/packages/kde-multimedia.scm
@@ -695,7 +695,7 @@ Its features include:
        ("qtbase" ,qtbase)))
     (arguments
      `(#:tests? #f)) ; Most tests require network
-    (home-page "https://cgit.kde.org/libkcddb.git")
+    (home-page "https://invent.kde.org/multimedia/libkcddb")
     (synopsis "CDDB library for KDE Platform (runtime)")
     (description "A library for retrieving and sending cddb information.")
     (license ;; GPL for programs, LGPL for libraries, FDL for documentation
@@ -722,7 +722,7 @@ Its features include:
        ("phonon" ,phonon)
        ("qtbase" ,qtbase)
        ("solid" ,solid)))
-    (home-page "https://cgit.kde.org/libkcompactdisc.git/")
+    (home-page "https://invent.kde.org/multimedia/libkcompactdisc")
     (synopsis "KDE library for playing & ripping CDs")
     (description "The KDE Compact Disc library provides an API for
 applications using the KDE Platform to interface with the CD drives for audio
diff --git a/gnu/packages/kde-pim.scm b/gnu/packages/kde-pim.scm
index 4ef49743fe..b0a2e565ed 100644
--- a/gnu/packages/kde-pim.scm
+++ b/gnu/packages/kde-pim.scm
@@ -391,7 +391,7 @@ Akonadi PIM data server.  It uses Xapian for indexing and querying.")
        ("kwallat" ,kwallet)
        ("libkdepim" ,libkdepim)
        ("qtbase" ,qtbase)))
-    (home-page "https://cgit.kde.org/incidenceeditor.git")
+    (home-page "https://invent.kde.org/pim/incidenceeditor")
     (synopsis "KDE PIM library for editing incidences")
     (description "This library provides an incidence editor for KDE PIM.")
     (license ;; GPL for programs, LGPL for libraries
@@ -518,7 +518,7 @@ calendar data.")
        ("qtbase" ,qtbase)
        ("syndication" ,syndication)))
     ;; Note: Some tests take up to 90 sec.
-    (home-page "https://cgit.kde.org/kblog.git")
+    (home-page "https://invent.kde.org/pim/kblog")
     (synopsis "Client-side support library for web application remote blogging
 APIs")
     (description "KBlog is a library for calling functions on Blogger 1.0,
@@ -634,7 +634,7 @@ functions for accessing calendar data using the kcalcore API.")
        ("kio" ,kio)
        ("qtbase" ,qtbase)
        ("qtxmlpatterns" ,qtxmlpatterns)))
-    (home-page "https://cgit.kde.org/kdav.git")
+    (home-page "https://invent.kde.org/frameworks/kdav")
     (synopsis "DAV protocol implementation with KJobs")
     (description "This is a DAV protocol implementation with KJobs.  Calendars
 and todos are supported, using either GroupDAV or CalDAV, and contacts are
@@ -679,7 +679,7 @@ supported using GroupDAV or CardDAV.")
        ("prison" ,prison)
        ("qgpgme" ,qgpgme)
        ("qtbase" ,qtbase)))
-    (home-page "https://cgit.kde.org/kdepim-apps-libs.git")
+    (home-page "https://invent.kde.org/pim/kdepim-apps-libs")
     (synopsis "KDE PIM mail related libraries and data files")
     (description "This package provides mail related libraries and data files
 for KDE PIM.")
@@ -761,7 +761,7 @@ for KDE PIM.")
                                              "/include/KF5:"
                                              (or (getenv "CPLUS_INCLUDE_PATH") "")))
                       #t)))))
-    (home-page "https://cgit.kde.org/kdepim-runtime.git")
+    (home-page "https://invent.kde.org/pim/kdepim-runtime")
     (synopsis "Runtime components for Akonadi KDE")
     (description "This package contains Akonadi agents written using KDE
 Development Platform libraries.  Any package that uses Akonadi should probably
@@ -816,7 +816,7 @@ package.")
        ("kxmlgui" ,kxmlgui)
        ("libkdepim" ,libkdepim)
        ("qtbase" ,qtbase)))
-    (home-page "https://cgit.kde.org/eventviews.git")
+    (home-page "https://invent.kde.org/pim/eventviews")
     (synopsis "KDE PIM library for creating events")
     (description "This library provides an event creator for KDE PIM.")
     (license ;; GPL for programs, LGPL for libraries
@@ -1180,7 +1180,7 @@ manager from KDE.")
        ("qtbase" ,qtbase)))
     (arguments
      `(#:tests? #f))  ;; TODO: 4/56 tests fail, even with "offscreen" and dbus
-    (home-page "https://cgit.kde.org/mailcommon.git")
+    (home-page "https://invent.kde.org/pim/mailcommon")
     (synopsis "KDE email utility library")
     (description "The mail common library provides utility functions for
 dealing with email.")
@@ -1219,7 +1219,7 @@ dealing with email.")
        ("kxmlgui" ,kxmlgui)
        ("libkdepim" ,libkdepim)
        ("qtbase" ,qtbase)))
-    (home-page "https://cgit.kde.org/mailimporter.git")
+    (home-page "https://invent.kde.org/pim/mailimporter")
     (synopsis "KDE mail importer library")
     (description "This package provides libraries for importing mails other
 e-mail client programs into KMail and KDE PIM.")
@@ -1373,7 +1373,7 @@ using a Qt/KMime C++ API.")
                                              "/include/KF5:"
                                              (or (getenv "CPLUS_INCLUDE_PATH") "")))
                       #t)))))
-    (home-page "https://cgit.kde.org/messagelib.git")
+    (home-page "https://invent.kde.org/pim/messagelib")
     (synopsis "KDE PIM messaging libraries")
     (description "This package provides several libraries for messages,
 e.g. a message list, a mime tree parse, a template parser and the
@@ -1701,7 +1701,7 @@ Virtual Contact File}) files to the KPeople contact management library.")
        ("qtwebengine" ,qtwebengine)))
     (arguments
      `(#:tests? #f)) ;; TODO tests hang
-    (home-page "https://cgit.kde.org/pimcommon.git")
+    (home-page "https://invent.kde.org/pim/pimcommon")
     (synopsis "Common libraries for KDE PIM")
     (description "This package provides common libraries for KDE PIM.")
     (license ;; GPL for programs, LGPL for libraries
@@ -1782,7 +1782,7 @@ text in the text edit to all kinds of markup, like HTML or BBCODE.")
                  _ prefix)
                 (string-append prefix "${KDE_INSTALL_TARGETS_DEFAULT_ARGS})")))
              #t)))))
-    (home-page "https://cgit.kde.org/ksmtp.git")
+    (home-page "https://invent.kde.org/pim/ksmtp")
     (synopsis "Library for sending email through an SMTP server")
     (description "This library provides an API for handling SMTP
 services.  SMTP (Simple Mail Transfer Protocol) is the most prevalent Internet
@@ -1863,7 +1863,7 @@ and allows one to view/extract message formatted text in Rich Text Format.")
        ("kwallet" ,kwallet)
        ("kwidgetsaddons" ,kwidgetsaddons)
        ("qtbase" ,qtbase)))
-    (home-page "https://cgit.kde.org/libkdepim.git")
+    (home-page "https://invent.kde.org/pim/libkdepim")
     (synopsis "Libraries for common KDE PIM apps")
     (description "This package provided libraries for common KDE PIM apps.")
     (license ;; GPL for programs, LGPL for libraries
@@ -1898,7 +1898,7 @@ and allows one to view/extract message formatted text in Rich Text Format.")
        ("qtwebengine" ,qtwebengine)))
     (arguments
      `(#:tests? #f)) ;; TODO 6/48 tests fail
-    (home-page "https://cgit.kde.org/libkgapi.git")
+    (home-page "https://invent.kde.org/pim/libkgapi")
     (synopsis "Library for accessing various Google services via their public
 API")
     (description "@code{LibKGAPI} is a C++ library that implements APIs for
@@ -1936,7 +1936,7 @@ various Google services.")
        ("kpimtextedit" ,kpimtextedit)
        ("qgpgme" ,qgpgme)
        ("qtbase" ,qtbase)))
-    (home-page "https://cgit.kde.org/libkleo.git/")
+    (home-page "https://invent.kde.org/pim/libkleo")
     (synopsis "KDE PIM cryptographic library")
     (description "@code{libkleo} is a library for Kleopatra and other parts of
 KDE using certificate-based crypto.")
@@ -1999,7 +1999,7 @@ KDE using certificate-based crypto.")
                ((".*sieveeditorgraphicalmodewidgettest\\.cpp.*")
                 ""))
              #t)))))
-    (home-page "https://cgit.kde.org/libksieve.git")
+    (home-page "https://invent.kde.org/pim/libksieve")
     (synopsis "KDE Sieve library")
     (description "Sieve is a language that can be used filter emails.  KSieve
 is a Sieve parser and interpreter library for KDE.")
diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm
index c53f6b29c7..e18d521ad2 100644
--- a/gnu/packages/kde-plasma.scm
+++ b/gnu/packages/kde-plasma.scm
@@ -52,7 +52,7 @@
     (inputs
      `(("ki18n" ,ki18n)
        ("qtbase" ,qtbase)))
-    (home-page "https://cgit.kde.org/kdecoration.git")
+    (home-page "https://invent.kde.org/plasma/kdecoration")
     (synopsis "Plugin based library to create window decorations")
     (description "KDecoration is a library to create window decorations.
 These window decorations can be used by for example an X11 based window
@@ -119,7 +119,7 @@ manager which re-parents a Client window to a window decoration frame.")
        ("solid" ,solid)
        ("wayland" ,wayland)
        ("xcb-util-keysyms" ,xcb-util-keysyms)))
-    (home-page "https://cgit.kde.org/kscreenlocker.git")
+    (home-page "https://invent.kde.org/plasma/kscreenlocker")
     (synopsis "Screen locking library")
     (description
      "@code{kscreenlocker} is a library for creating secure lock screens.")
diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm
index 1f747ecfd4..3a15aa6554 100644
--- a/gnu/packages/kde.scm
+++ b/gnu/packages/kde.scm
@@ -11,6 +11,7 @@
 ;;; Copyright © 2020 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
 ;;; Copyright © 2020 Prafulla Giri <pratheblackdiamond@gmail.com>
+;;; Copyright © 2020 Zheng Junjie <873216071@qq.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -130,7 +131,7 @@ This package contains GUI widgets for baloo.")
        ("kiconthemes" ,kiconthemes)
        ("knewstuff" ,knewstuff)
        ("qtbase" ,qtbase)))
-    (home-page "https://cgit.kde.org/grantleetheme.git")
+    (home-page "https://invent.kde.org/pim/grantleetheme")
     (synopsis "Library providing Grantlee theme support")
     (description "This library provides Grantlee theme support.")
     (license ;; LGPL for libraries, FDL for documentation
@@ -362,7 +363,7 @@ for some KDevelop language plugins (Ruby, PHP, CSS...).")
     (inputs
      `(("qtbase" ,qtbase)
        ("qtsvg" ,qtsvg)))
-    (home-page "https://cgit.kde.org/kdiagram.git/")
+    (home-page "https://invent.kde.org/graphics/kdiagram")
     (synopsis "Libraries for creating business diagrams")
     (description "This package provides libraries for integrating business
 diagrams in Qt-based applications.
@@ -765,6 +766,52 @@ Python, PHP, and Perl.")
     (description "Runtime library for kdegames")
     (license (list license:gpl2+  license:fdl1.2+))))
 
+(define-public kdegraphics-mobipocket
+  (package
+    (name "kdegraphics-mobipocket")
+    (version "20.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://kde/stable/release-service/" version
+                           "/src/" name "-" version ".tar.xz"))
+       (sha256
+        (base32 "0fm880lp9g60zgrkjyh4jxws6x0s77l9ia4f8pza3w8sxcbbswk5"))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("extra-cmake-modules" ,extra-cmake-modules)))
+    (inputs
+     `(("kio" ,kio)
+       ("qtbase" ,qtbase)))
+    (home-page "https://apps.kde.org/en/kdegraphics_mobipocket")
+    (synopsis "KDE thumbnailer for Mobipocket files")
+    (description "This package provides a KDE plugin that shows thumbnails of
+Mobipocket e-books in Dolphin and other KDE apps.")
+    (license license:gpl2+)))
+
+(define-public libkexiv2
+  (package
+    (name "libkexiv2")
+    (version "20.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://kde/stable/release-service/" version
+                           "/src/" name "-" version ".tar.xz"))
+       (sha256
+        (base32 "0k0iinf7s8qlk3fwvq7iic1b4zn2gm65rfd58q7d3wb1i1j2hjjk"))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("extra-cmake-modules" ,extra-cmake-modules)))
+    (inputs
+     `(("exiv2" ,exiv2)
+       ("qtbase" ,qtbase)))
+    (home-page "https://invent.kde.org/graphics/libkexiv2")
+    (synopsis "Manipulate the metadata of images")
+    (description "Libkexiv2 wraps the Exiv2 library, allowing to manipulate
+picture metadata as EXIF/IPTC and XMP.")
+    (license license:gpl2+)))
+
 (define-public zeroconf-ioslave
   (package
     (name "zeroconf-ioslave")
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 3d36468172..0e9932785d 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -352,7 +352,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 
 ;; The current "stable" kernel. That is, the most recently released major
 ;; version.
-(define-public linux-libre-5.9-version "5.9.12")
+(define-public linux-libre-5.9-version "5.9.14")
 (define deblob-scripts-5.9
   (linux-libre-deblob-scripts
    linux-libre-5.9-version
@@ -360,7 +360,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "0yb04a4j2wq3mwvks3cj7kcm2pscmfs29lrz3falkxpbvjxbbgq2")))
 (define-public linux-libre-5.9-pristine-source
   (let ((version linux-libre-5.9-version)
-        (hash (base32 "1gfrn3sz3h4cbsf3r8f9jxja400qsmbrk8sclk4cjx1l5qcmczyr")))
+        (hash (base32 "0jbb3rzbkh0l75zq9bnc60w55ryvrvcg7vw85fsbcwfzvi0zpz1r")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.9)))
@@ -368,7 +368,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 ;; The "longterm" kernels — the older releases with long-term upstream support.
 ;; Here are the support timelines:
 ;; <https://www.kernel.org/category/releases.html>
-(define-public linux-libre-5.4-version "5.4.81")
+(define-public linux-libre-5.4-version "5.4.83")
 (define deblob-scripts-5.4
   (linux-libre-deblob-scripts
    linux-libre-5.4-version
@@ -376,12 +376,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "167zcfkw62pm6nv1xdvvhxw0ca724sywcywnv3z00189f8f8p3vg")))
 (define-public linux-libre-5.4-pristine-source
   (let ((version linux-libre-5.4-version)
-        (hash (base32 "09w4bpr3v9rzcvxics5wddabplwbpk1mynl45lh9csbjfpjbsw4l")))
+        (hash (base32 "1ik14pfgynkn1sjhgyhgmxjvviq0mgvk0ygj76w8mplkpc5rgv5y")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.4)))
 
-(define-public linux-libre-4.19-version "4.19.161")
+(define-public linux-libre-4.19-version "4.19.163")
 (define deblob-scripts-4.19
   (linux-libre-deblob-scripts
    linux-libre-4.19-version
@@ -389,12 +389,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "1jiaw0as1ippkrjdpd52657w5mz9qczg3y2hlra7m9k0xawwiqlf")))
 (define-public linux-libre-4.19-pristine-source
   (let ((version linux-libre-4.19-version)
-        (hash (base32 "0h9wskmz9wridwnicnjlcmj1112qnlvqk01bhjkxv6b8jsajjh87")))
+        (hash (base32 "1z65iwwyx2b01fncygckmhpxirzs52qfqmv3agirn4laxgjw9viy")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.19)))
 
-(define-public linux-libre-4.14-version "4.14.210")
+(define-public linux-libre-4.14-version "4.14.212")
 (define deblob-scripts-4.14
   (linux-libre-deblob-scripts
    linux-libre-4.14-version
@@ -402,12 +402,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "1qij18inijj6c3ma8hv98yjagnzxdxyn134da9fd23ky8q6hbvky")))
 (define-public linux-libre-4.14-pristine-source
   (let ((version linux-libre-4.14-version)
-        (hash (base32 "067xqi6sgf50p7s3n6y77cgf5bj5062s3bz3kqpp6f9wnk85267r")))
+        (hash (base32 "0y8ck8pfxm8862wi4cz8qp9x9b18yl448i8m7bpbphs290nc66qf")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.14)))
 
-(define-public linux-libre-4.9-version "4.9.247")
+(define-public linux-libre-4.9-version "4.9.248")
 (define deblob-scripts-4.9
   (linux-libre-deblob-scripts
    linux-libre-4.9-version
@@ -415,12 +415,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "0fxajshb75siq39lj5h8xvhdj8lcmddkslwlyj65rhlwk6g2r4b2")))
 (define-public linux-libre-4.9-pristine-source
   (let ((version linux-libre-4.9-version)
-        (hash (base32 "1mngdbsq8pdzd0x9hif4715cc7wzc3ahgp1yrknnqk598q0fnfpp")))
+        (hash (base32 "1kzczy0lz3lnjkhvx90dgjmzn3d3y55qxlihiclkr4y9c602d1s6")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.9)))
 
-(define-public linux-libre-4.4-version "4.4.247")
+(define-public linux-libre-4.4-version "4.4.248")
 (define deblob-scripts-4.4
   (linux-libre-deblob-scripts
    linux-libre-4.4-version
@@ -428,7 +428,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "0hhin1jpfkd6nwrb6xqxjzl3hdxy4pn8a15hy2d3d83yw6pflbsf")))
 (define-public linux-libre-4.4-pristine-source
   (let ((version linux-libre-4.4-version)
-        (hash (base32 "1jh7vmyx55krk6y2r9v48liifs5wwkgns3gp8rs5sm4klfm36r2a")))
+        (hash (base32 "1z1xbkm0z0v6k3scszii5hi24pn391332g0li93p3n1rnv74jap5")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.4)))
@@ -4045,18 +4045,18 @@ thanks to the use of namespaces.")
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-references
            (lambda _
-             (substitute* "libexec/cli/build.exec"
-               (("if ! singularity_which mksquashfs") "if 0")
-               (("if ! mksquashfs")
-                (string-append "if ! " (which "mksquashfs"))))
-             (substitute* (list "libexec/cli/help.exec"
-                                "libexec/bootstrap-scripts/functions"
-                                "libexec/bootstrap-scripts/post.sh"
-                                "libexec/functions")
+             (substitute* "libexec/cli/build.exec.in"
+               (("-mksquashfs") (string-append "-" (which "mksquashfs"))))
+             (substitute* (append
+                            (find-files "libexec" "functions")
+                            (find-files "libexec/bootstrap-scripts" ".*sh$")
+                            (find-files "libexec/cli" ".*exec$"))
                (("\\| grep ")
                 (string-append "| " (which "grep") " "))
                (("egrep ")
-                (string-append (which "egrep") " ")))
+                (string-append (which "egrep") " "))
+               ((" sed ")
+                (string-append " " (which "sed") " ")))
              #t))
          (add-after 'install 'set-PATH
            (lambda* (#:key inputs outputs #:allow-other-keys)
@@ -4544,7 +4544,7 @@ arrays when needed.")
        ;; For tests.
        ("cmocka" ,cmocka)))
     (inputs
-     `(("json-c" ,json-c-0.13)
+     `(("json-c" ,json-c)
        ("libaio" ,libaio)
        ("liburcu" ,liburcu)
        ("lvm2" ,lvm2)
diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index 6fd4ec5b2d..f77e949fea 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -309,6 +309,45 @@ streams which are similar to string streams.")
 (define-public ecl-flexi-streams
   (sbcl-package->ecl-package sbcl-flexi-streams))
 
+(define-public sbcl-cl-abnf
+  ;; There are no releases
+  (let ((commit "ba1fbb104dedbdaddb1ef93d2e4da711bd96cd70")
+        (revision "1"))
+    (package
+     (name "sbcl-cl-abnf")
+     (version (git-version "0.0.0" revision commit))
+     (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+              (url "https://github.com/dimitri/cl-abnf")
+              (commit commit)))
+        (file-name (git-file-name "cl-abnf" version))
+        (sha256
+         (base32 "0f09nsndxa90acm71zd4qdnp40v705a4sqm04mnv9x76h6dlggmz"))))
+     (build-system asdf-build-system/sbcl)
+     (inputs
+      `(("cl-ppcre" ,sbcl-cl-ppcre)
+        ("esrap" ,sbcl-esrap)))
+     (arguments
+      `(#:asd-systems '("abnf")))
+     (home-page "https://github.com/dimitri/cl-abnf")
+     (synopsis "ABNF parser generator for Common Lisp")
+     (description "This Common Lisp library implements a parser generator for
+the ABNF grammar format as described in RFC2234.  The generated parser is a
+regular expression scanner provided by the cl-ppcre lib, which means that we
+can't parse recursive grammar definition.  One such definition is the ABNF
+definition as given by the RFC.  Fortunately, as you have this lib, you most
+probably don't need to generate another parser to handle that particular ABNF
+grammar.")
+     (license license:expat))))
+
+(define-public cl-abnf
+  (sbcl-package->cl-source-package sbcl-cl-abnf))
+
+(define-public ecl-cl-abnf
+  (sbcl-package->ecl-package sbcl-cl-abnf))
+
 (define-public sbcl-cl-ppcre
   (package
     (name "sbcl-cl-ppcre")
@@ -2725,7 +2764,11 @@ Lisp, featuring:
   (sbcl-package->cl-source-package sbcl-lparallel))
 
 (define-public ecl-lparallel
-  (sbcl-package->ecl-package sbcl-lparallel))
+  (package
+    (inherit (sbcl-package->ecl-package sbcl-lparallel))
+    (arguments
+     ;; TODO: Find why the tests get stuck forever; disable them for now.
+     `(#:tests? #f))))
 
 (define-public sbcl-cl-markup
   (let ((commit "e0eb7debf4bdff98d1f49d0f811321a6a637b390"))
@@ -5638,6 +5681,41 @@ extension-points via the concept of hooks.")
 (define-public ecl-cl-hooks
   (sbcl-package->ecl-package sbcl-cl-hooks))
 
+(define-public sbcl-cl-autowrap
+  (let ((revision "1")
+        (commit "ae846d6968fc0d000de0c541638929a157f3009e"))
+    ;; no taged branches
+    (package
+      (name "sbcl-cl-autowrap")
+      (version (git-version "1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/rpav/cl-autowrap")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1gisldp2zns92kdcaikghm7c38ldy2d884n8bfg0wcjvbz78p3ar"))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("alexandria" ,sbcl-alexandria)
+         ("cffi" ,sbcl-cffi)
+         ("cl-json" ,sbcl-cl-json)
+         ("cl-ppcre" ,sbcl-cl-ppcre)
+         ("defpackage-plus" ,sbcl-defpackage-plus)
+         ("trivial-features" ,sbcl-trivial-features)))
+      (home-page "https://github.com/rpav/cl-autowrap")
+      (synopsis "FFI wrapper generator for Common Lisp")
+      (description "This is a c2ffi-based wrapper generator for Common Lisp.")
+      (license license:bsd-2))))
+
+(define-public cl-autowrap
+  (sbcl-package->cl-source-package sbcl-cl-autowrap))
+
+(define-public ecl-cl-autowrap
+  (sbcl-package->ecl-package sbcl-cl-autowrap))
+
 (define-public sbcl-s-sysdeps
   ;; No release since 2013.
   (let ((commit "9aa23bbdceb24bcdbe0e7c39fa1901858f823106")
@@ -11234,17 +11312,18 @@ XML to Lisp structures or s-expressions and back.")
 (define-public sbcl-geco
   (package
     (name "sbcl-geco")
-    (version "2.01a")
+    (version "2.1.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://common-lisp.net/project/geco/download/"
-                           "geco-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/gpwwjr/GECO")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name "geco" version))
        (sha256
-        (base32 "0kk0bzr1019cfmf2b1jl1rk9shv3gx5z1znifxllg9mb98yqsgw0"))
-       (patches (search-patches "sbcl-geco-fix-organism-class.patch"))))
+        (base32 "1rc8a4mk40hjx5qy980hjylv6xxqdbq38hg8c4w30y93abfd519s"))))
     (build-system asdf-build-system/sbcl)
-    (home-page "https://common-lisp.net/project/geco/")
+    (home-page "http://hiwaay.net/~gpw/geco/geco.html")
     (synopsis "Genetic algorithm toolkit for Common Lisp")
     (description
      "GECO (Genetic Evolution through Combination of Objects) is an extensible,
@@ -12405,3 +12484,44 @@ Service (S3) and CloudFront service from Common Lisp.")
 
 (define-public ecl-zs3
   (sbcl-package->ecl-package sbcl-zs3))
+
+(define-public sbcl-simple-neural-network
+  (package
+    (name "sbcl-simple-neural-network")
+    (version "3.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/glv2/simple-neural-network")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name "simple-neural-network" version))
+       (sha256
+        (base32 "1jj1c90fr5clwka0jv32hv6xp1bkdlpa6x5jh19an13rhx8ll4zr"))))
+    (build-system asdf-build-system/sbcl)
+    (native-inputs
+     `(("chipz" ,sbcl-chipz)
+       ("fiveam" ,sbcl-fiveam)))
+    (inputs
+     `(("cl-store" ,sbcl-cl-store)
+       ("lparallel" ,sbcl-lparallel)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'check 'remove-test-data
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (for-each delete-file (find-files out "\\.gz$"))))))))
+    (synopsis "Simple neural network in Common Lisp")
+    (description
+     "@code{simple-neural-network} is a Common Lisp library for creating,
+training and using basic neural networks.  The networks created by this
+library are feedforward neural networks trained using backpropagation.")
+    (home-page "https://github.com/glv2/simple-neural-network")
+    (license license:gpl3+)))
+
+(define-public cl-simple-neural-network
+  (sbcl-package->cl-source-package sbcl-simple-neural-network))
+
+(define-public ecl-simple-neural-network
+  (sbcl-package->ecl-package sbcl-simple-neural-network))
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index f1d0922ef2..920b5d82ed 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -582,7 +582,7 @@ in terms of new algorithms.")
 (define-public python-onnx
   (package
     (name "python-onnx")
-    (version "1.7.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
@@ -591,7 +591,7 @@ in terms of new algorithms.")
        ;; to use googletest from Guix and enable tests by default.
        (patches (search-patches "python-onnx-use-system-googletest.patch"))
        (sha256
-        (base32 "0j6rgfbhsw3a8id8pyg18y93k68lbjbj1kq6qia36h69f6pvlyjy"))))
+        (base32 "0365zkikq6v3cl5hh2daa5z1alhij8xpn8rmlcny340jrv9pyy2z"))))
     (build-system python-build-system)
     (native-inputs
      `(("cmake" ,cmake)
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index a2d6b71377..f85713433e 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -39,6 +39,7 @@
 ;;; Copyright © 2020 Alexandru-Sergiu Marton <brown121407@posteo.ro>
 ;;; Copyright © 2020 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com>
+;;; Copyright © 2020 divoplade <d@divoplade.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1700,7 +1701,13 @@ delivery.")
                  (("(ZCAT_COMMAND=).*" all var)
                   (string-append var gzip "/bin/zcat\n"))
                  (("# (USE_GNUTLS(|_PC)=.*)" all line)
-                  (string-append line "\n")))
+                  (string-append line "\n"))
+                 (("# (AUTH_CRAM_MD5=yes)" all line) line)
+                 (("# (AUTH_DOVECOT=yes)" all line) line)
+                 (("# (AUTH_EXTERNAL=yes)" all line) line)
+                 (("# (AUTH_PLAINTEXT=yes)" all line) line)
+                 (("# (AUTH_SPA=yes)" all line) line)
+                 (("# (AUTH_TLS=yes)" all line) line))
                ;; This file has hard-coded relative file names for tools despite
                ;; the zcat configuration above.
                (substitute* '("src/exigrep.src")
@@ -1993,7 +2000,7 @@ hashing scheme (such as scrypt) plug-in for @code{Dovecot}.")
     (inputs
      `(("bdb" ,bdb)
        ("cyrus-sasl" ,cyrus-sasl)
-       ("openssl" ,openssl-1.0)
+       ("openssl" ,openssl)
        ("zlib" ,zlib)))
     (home-page "https://isync.sourceforge.io/")
     (synopsis "Mailbox synchronization program")
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 47cc8216dd..c118e9e25c 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -518,7 +518,7 @@ numbers.")
 (define-public sleef
   (package
     (name "sleef")
-    (version "3.4.1")
+    (version "3.5.1")
     (source
      (origin
        (method git-fetch)
@@ -527,7 +527,7 @@ numbers.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1gvf7cfvszmgjrsqivwmyy1jnp3hy80dmszxx827lhjz8yqq5019"))))
+        (base32 "1jybqrl2dvjxzg30xrhh847s375n2jr1pix644wi6hb5wh5mx3f7"))))
     (build-system cmake-build-system)
     (arguments
      '(#:configure-flags (list "-DCMAKE_BUILD_TYPE=Release"
@@ -2211,13 +2211,13 @@ ASCII text files using Gmsh's own scripting language.")
 (define-public veusz
   (package
     (name "veusz")
-    (version "3.2.1")
+    (version "3.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "veusz" version))
        (sha256
-        (base32 "00vmfpvyd6f33l5awlf02qdik3gmbhzyfizfwwbx7qnam2i9bbwy"))))
+        (base32 "1q7hi1qwwg4pgiz62isvv1pia85m13bspdpp1q3mrnwl11in0ag0"))))
     (build-system python-build-system)
     (arguments
      `(;; Tests will fail because they depend on optional packages like
@@ -4194,7 +4194,7 @@ revised simplex and the branch-and-bound methods.")
 (define-public dealii
   (package
     (name "dealii")
-    (version "9.1.1")
+    (version "9.2.0")
     (source
      (origin
        (method url-fetch)
@@ -4202,7 +4202,7 @@ revised simplex and the branch-and-bound methods.")
                            "download/v" version "/dealii-" version ".tar.gz"))
        (sha256
         (base32
-         "0xhjv0gzswpjbc43xbrpwfc5848g508l01855nszx3g5gwzlhnzw"))
+         "0fm4xzrnb7dfn4415j24d8v3jkh0lssi86250x2f5wgi83xq4nnh"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
diff --git a/gnu/packages/matrix.scm b/gnu/packages/matrix.scm
index 6a6cc628ca..426f26d1e1 100644
--- a/gnu/packages/matrix.scm
+++ b/gnu/packages/matrix.scm
@@ -61,13 +61,13 @@ an LDAP server.")
 (define-public synapse
   (package
     (name "synapse")
-    (version "1.22.1")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "matrix-synapse" version))
               (sha256
                (base32
-                "1pbxdqpfa7wzdz61p6x58x7841vng1g65qayxgcw73bn1shl50jb"))))
+                "0pmn8aqc7jj2xdrwljjz2vwg58hlyxp9axac471pcmg2vqais5yb"))))
     (build-system python-build-system)
     ;; TODO Run tests with ‘PYTHONPATH=. trial3 tests’.
     (propagated-inputs
diff --git a/gnu/packages/nfs.scm b/gnu/packages/nfs.scm
index ba50ca5e01..8370107939 100644
--- a/gnu/packages/nfs.scm
+++ b/gnu/packages/nfs.scm
@@ -117,10 +117,11 @@
      `(("keyutils" ,keyutils)
        ("libevent" ,libevent)
        ("libnfsidmap" ,libnfsidmap)
-       ("rpcsvc-proto" ,rpcsvc-proto) ;for 'rpcgen'
+       ("rpcsvc-proto" ,rpcsvc-proto)   ;for 'rpcgen'
        ("sqlite" ,sqlite)
        ("lvm2" ,lvm2)
-       ("util-linux" ,util-linux "lib")
+       ("util-linux" ,util-linux)           ; only for above substitutions
+       ("util-linux:lib" ,util-linux "lib") ; for libblkid
        ("mit-krb5" ,mit-krb5)
        ("libtirpc" ,libtirpc)
        ("python-wrapper" ,python-wrapper))) ;for the Python based tools
diff --git a/gnu/packages/ntp.scm b/gnu/packages/ntp.scm
index 95d784c62a..6d046eed1b 100644
--- a/gnu/packages/ntp.scm
+++ b/gnu/packages/ntp.scm
@@ -166,14 +166,14 @@ computers over a network.")
 (define-public openntpd
   (package
     (name "openntpd")
-    (version "6.2p3")
+    (version "6.8p1")
     (source (origin
               (method url-fetch)
               (uri (string-append
                     "mirror://openbsd/OpenNTPD/openntpd-" version ".tar.gz"))
               (sha256
                (base32
-                "0fn12i4kzsi0zkr4qp3dp9bycmirnfapajqvdfx02zhr4hanj0kv"))))
+                "0ijsylc7a4jlpxsqa0jq1w1c7333id8pcakzl7a5749ria1xp0l5"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags `( "--with-privsep-user=ntpd"
diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 369e819573..2bfda7307e 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -739,8 +739,7 @@ Emacs.")
 (define-public ocaml-menhir
   (package
     (name "ocaml-menhir")
-    ;; More recent versions can be built after we have dune >= 2.0
-    (version "20190626")
+    (version "20200211")
     (source
      (origin
        (method git-fetch)
@@ -749,19 +748,12 @@ Emacs.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0v8av4pw6rykzb7wx54xhbsx0jhh8xyb4x0k4yrxi0w5ylkck6mb"))))
-    (build-system ocaml-build-system)
+        (base32 "019izf51kdc7pzkw68zg8a2alc8lxw1gwdp7in970mr90n16b5zj"))))
+    (build-system dune-build-system)
     (inputs
      `(("ocaml" ,ocaml)))
-    (native-inputs
-     `(("ocamlbuild" ,ocamlbuild)))
     (arguments
-     `(#:make-flags `("USE_OCAMLFIND=true"
-                      ,(string-append "PREFIX=" (assoc-ref %outputs "out")))
-       #:tests? #f ; No check target
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'configure))))
+     `(#:tests? #f)) ; No check target
     (home-page "http://gallium.inria.fr/~fpottier/menhir/")
     (synopsis "Parser generator")
     (description "Menhir is a parser generator.  It turns high-level grammar
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index a76fc49b3e..f8a3a7771a 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -131,8 +131,8 @@
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
   (let ((version "1.2.0")
-        (commit "c952a9312a94bb236495ec654bf184685cf9fe79")
-        (revision 5))
+        (commit "799f066768bacb321ebad84c75b2bbfd269e7cd8")
+        (revision 6))
     (package
       (name "guix")
 
@@ -148,7 +148,7 @@
                       (commit commit)))
                 (sha256
                  (base32
-                  "1k32p37ikwls086mgxjhz9qhrbc7lgvfpbnk0ikfg4p40rxjp4w8"))
+                  "04k8q5yjmxazskl13ap210jki2zh73zlzd0xdx06v08liskgz10q"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments
diff --git a/gnu/packages/patches/busybox-1.31.1-fix-build-with-glibc-2.31.patch b/gnu/packages/patches/busybox-1.31.1-fix-build-with-glibc-2.31.patch
deleted file mode 100644
index 1518df067f..0000000000
--- a/gnu/packages/patches/busybox-1.31.1-fix-build-with-glibc-2.31.patch
+++ /dev/null
@@ -1,68 +0,0 @@
-See: https://bugs.gentoo.org/708350
-Author: Patrick McLean <patrick.mclean@sony.com>
-Date: 2020-02-06 23:06:22 +0000
-diff --git a/coreutils/date.c b/coreutils/date.c
-index 3414d38ae..4ade6abb4 100644
---- a/coreutils/date.c
-+++ b/coreutils/date.c
-@@ -279,6 +279,9 @@ int date_main(int argc UNUSED_PARAM, char **argv)
- 		time(&ts.tv_sec);
- #endif
- 	}
-+#if !ENABLE_FEATURE_DATE_NANO
-+	ts.tv_nsec = 0;
-+#endif
- 	localtime_r(&ts.tv_sec, &tm_time);
- 
- 	/* If date string is given, update tm_time, and maybe set date */
-@@ -301,9 +304,10 @@ int date_main(int argc UNUSED_PARAM, char **argv)
- 		if (date_str[0] != '@')
- 			tm_time.tm_isdst = -1;
- 		ts.tv_sec = validate_tm_time(date_str, &tm_time);
-+		ts.tv_nsec = 0;
- 
- 		/* if setting time, set it */
--		if ((opt & OPT_SET) && stime(&ts.tv_sec) < 0) {
-+		if ((opt & OPT_SET) && clock_settime(CLOCK_REALTIME, &ts) < 0) {
- 			bb_perror_msg("can't set date");
- 		}
- 	}
-diff --git a/libbb/missing_syscalls.c b/libbb/missing_syscalls.c
-index 87cf59b3d..dc40d9155 100644
---- a/libbb/missing_syscalls.c
-+++ b/libbb/missing_syscalls.c
-@@ -15,14 +15,6 @@ pid_t getsid(pid_t pid)
- 	return syscall(__NR_getsid, pid);
- }
- 
--int stime(const time_t *t)
--{
--	struct timeval tv;
--	tv.tv_sec = *t;
--	tv.tv_usec = 0;
--	return settimeofday(&tv, NULL);
--}
--
- int sethostname(const char *name, size_t len)
- {
- 	return syscall(__NR_sethostname, name, len);
-diff --git a/util-linux/rdate.c b/util-linux/rdate.c
-index 70f829e7f..878375d78 100644
---- a/util-linux/rdate.c
-+++ b/util-linux/rdate.c
-@@ -95,9 +95,13 @@ int rdate_main(int argc UNUSED_PARAM, char **argv)
- 	if (!(flags & 2)) { /* no -p (-s may be present) */
- 		if (time(NULL) == remote_time)
- 			bb_error_msg("current time matches remote time");
--		else
--			if (stime(&remote_time) < 0)
-+		else {
-+			struct timespec ts;
-+			ts.tv_sec = remote_time;
-+			ts.tv_nsec = 0;
-+			if (clock_settime(CLOCK_REALTIME, &ts) < 0)
- 				bb_perror_msg_and_die("can't set time of day");
-+		}
- 	}
- 
- 	if (flags != 1) /* not lone -s */
diff --git a/gnu/packages/patches/knot-resolver-fix-map-command-on-32-bit.patch b/gnu/packages/patches/knot-resolver-fix-map-command-on-32-bit.patch
deleted file mode 100644
index 02c0fbcb70..0000000000
--- a/gnu/packages/patches/knot-resolver-fix-map-command-on-32-bit.patch
+++ /dev/null
@@ -1,146 +0,0 @@
-commit e01979620025666633250b3e2d545fe59c629f73
-Author: Vladimír Čunát <vladimir.cunat@nic.cz>
-Date:   Fri Nov 13 14:16:32 2020 +0100
-
-    fix map() command on 32-bit platforms; regressed in 5.2.0
-    
-    LuaJIT FFI was using opendir() (etc.) variants with 32-bit inodes
-    but the C parts was using them as 64-bit inode variants.
-    Consequently the `struct dirent` layout didn't match and we were getting
-    filenames shifted by eight bytes.
-    
-    Now the whole dir-listing lua function is written in C.
-
-diff --git a/.luacheckrc b/.luacheckrc
-index 0cf0b884..67bc18f6 100644
---- a/.luacheckrc
-+++ b/.luacheckrc
-@@ -20,6 +20,7 @@ new_read_globals = {
- 	'user',
- 	'verbose',
- 	'worker',
-+	'kluautil_list_dir',
- 	-- Sandbox declarations
- 	'kB',
- 	'MB',
-diff --git a/NEWS b/NEWS
-index 2eae3082..9d8cde99 100644
---- a/NEWS
-+++ b/NEWS
-@@ -1,6 +1,10 @@
- Knot Resolver X.Y.X (yyyy-mm-dd)
- ================================
- 
-+Bugfixes
-+--------
-+- fix map() command on 32-bit platforms; regressed in 5.2.0 (!1093)
-+
- 
- Knot Resolver 5.2.0 (2020-11-11)
- ================================
-diff --git a/daemon/bindings/impl.c b/daemon/bindings/impl.c
-index d10f4525..d9ad0774 100644
---- a/daemon/bindings/impl.c
-+++ b/daemon/bindings/impl.c
-@@ -2,6 +2,7 @@
-  *  SPDX-License-Identifier: GPL-3.0-or-later
-  */
- 
-+#include <dirent.h>
- #include <lua.h>
- #include <lauxlib.h>
- #include <string.h>
-@@ -29,6 +30,29 @@ const char * lua_table_checkindices(lua_State *L, const char *keys[])
- 	return NULL;
- }
- 
-+/** Return table listing filenames in a given directory (ls -A). */
-+static int kluautil_list_dir(lua_State *L)
-+{
-+	lua_newtable(L); // empty table even on errors
-+
-+	const char *path = lua_tolstring(L, 1, NULL);
-+	if (!path) return 1;
-+	DIR *dir = opendir(path);
-+	if (!dir) return 1;
-+
-+	struct dirent *entry;
-+	int lua_i = 1;
-+	while ((entry = readdir(dir)) != NULL) {
-+		if (strcmp(entry->d_name, ".") && strcmp(entry->d_name, "..")) {
-+			lua_pushstring(L, entry->d_name);
-+			lua_rawseti(L, -2, lua_i++);
-+		}
-+	}
-+
-+	closedir(dir);
-+	return 1;
-+}
-+
- 
- /* Each of these just creates the correspondingly named lua table of functions. */
- int kr_bindings_cache   (lua_State *L); /* ./cache.c   */
-@@ -44,6 +68,9 @@ void kr_bindings_register(lua_State *L)
- 	kr_bindings_modules(L);
- 	kr_bindings_net(L);
- 	kr_bindings_worker(L);
-+
-+	/* Finally some lua utils *written in C*, not really a binding. */
-+	lua_register(L, "kluautil_list_dir", kluautil_list_dir);
- }
- 
- void lua_error_p(lua_State *L, const char *fmt, ...)
-diff --git a/daemon/lua/kluautil.lua b/daemon/lua/kluautil.lua
-index 57912e7b..e73e952c 100644
---- a/daemon/lua/kluautil.lua
-+++ b/daemon/lua/kluautil.lua
-@@ -1,6 +1,5 @@
- -- SPDX-License-Identifier: GPL-3.0-or-later
- 
--local ffi = require('ffi')
- local kluautil = {}
- 
- -- Get length of table
-@@ -28,14 +27,6 @@ function kluautil.kr_table_unpack(tab)
- 	return unpack(tab, 1, tab.n)
- end
- 
--ffi.cdef([[
--	typedef struct __dirstream DIR;
--	DIR *opendir(const char *name);
--	struct dirent *readdir(DIR *dirp);
--	int closedir(DIR *dirp);
--	char *strerror(int errnum);
--]])
--
- -- Fetch over HTTPS
- function kluautil.kr_https_fetch(url, out_file, ca_file)
- 	local http_ok, http_request = pcall(require, 'http.request')
-@@ -88,26 +79,6 @@ function kluautil.kr_https_fetch(url, out_file, ca_file)
- 	return true
- end
- 
---- List directory
--function kluautil.list_dir (path)
--	local results = {}
--	local dir = ffi.C.opendir(path)
--	if dir == nil then
--		return results
--	end
--
--	local entry = ffi.C.readdir(dir)
--	while entry ~= nil do
--		local entry_name = ffi.string(ffi.C.kr_dirent_name(entry))
--		if entry_name ~= '.' and entry_name ~= '..' then
--			table.insert(results, entry_name)
--		end
--		entry = ffi.C.readdir(dir)
--	end
--
--	ffi.C.closedir(dir)
--
--	return results
--end
-+kluautil.list_dir = kluautil_list_dir
- 
- return kluautil
diff --git a/gnu/packages/patches/pciutils-hurd-fix.patch b/gnu/packages/patches/pciutils-hurd-fix.patch
new file mode 100644
index 0000000000..f1979d4352
--- /dev/null
+++ b/gnu/packages/patches/pciutils-hurd-fix.patch
@@ -0,0 +1,23 @@
+Fix a build error on GNU/Hurd for pciutils 3.7.0.
+
+commit 053cf6c8b2acafadf828912828336d90fe9b8696
+Author: Martin Mares <mj@ucw.cz>
+Date:   Sun May 31 11:53:28 2020 +0200
+
+    HURD backend should compile again
+    
+    Fixes a bug introduced by commit 82c06b47dea5a38075ce9d56f743360bc47b4c78.
+
+diff --git a/lib/hurd.c b/lib/hurd.c
+index 7b3b2ae..ccd92f6 100644
+--- a/lib/hurd.c
++++ b/lib/hurd.c
+@@ -307,7 +307,6 @@ hurd_fill_regions(struct pci_dev *d)
+       d->base_addr[i] |= regions[i].is_64 << 2;
+       d->base_addr[i] |= regions[i].is_prefetchable << 3;
+ 
+-      if (flags & PCI_FILL_SIZES)
+-	d->size[i] = regions[i].size;
++      d->size[i] = regions[i].size;
+     }
+ }
diff --git a/gnu/packages/patches/renpy-use-system-fribidi.patch b/gnu/packages/patches/renpy-use-system-fribidi.patch
new file mode 100644
index 0000000000..1437274bcc
--- /dev/null
+++ b/gnu/packages/patches/renpy-use-system-fribidi.patch
@@ -0,0 +1,52 @@
+See also [Arch] and [Gentoo] for similar patches in other distros.
+[Arch] https://github.com/archlinux/svntogit-community/blob/packages/renpy/trunk/renpy-system-fribidi.patch
+[Gentoo] https://gitweb.gentoo.org/repo/gentoo.git/tree/games-engines/renpy/files/renpy-7.3.5-use-system-fribidi.patch
+
+Index: renpy-7.3.5-source/module/renpybidicore.c
+===================================================================
+--- renpy-7.3.5-source.orig/module/renpybidicore.c
++++ renpy-7.3.5-source/module/renpybidicore.c
+@@ -1,5 +1,5 @@
+ #include <Python.h>
+-#include <fribidi-src/lib/fribidi.h>
++#include <fribidi.h>
+ #include <stdlib.h>
+
+ #ifndef alloca
+Index: renpy-7.3.5-source/module/setup.py
+===================================================================
+--- renpy-7.3.5-source.orig/module/setup.py
++++ renpy-7.3.5-source/module/setup.py
+@@ -119,30 +119,13 @@ cython(
+     sdl + [ png, 'z', 'm' ])
+
+ FRIBIDI_SOURCES = """
+-fribidi-src/lib/fribidi.c
+-fribidi-src/lib/fribidi-arabic.c
+-fribidi-src/lib/fribidi-bidi.c
+-fribidi-src/lib/fribidi-bidi-types.c
+-fribidi-src/lib/fribidi-deprecated.c
+-fribidi-src/lib/fribidi-joining.c
+-fribidi-src/lib/fribidi-joining-types.c
+-fribidi-src/lib/fribidi-mem.c
+-fribidi-src/lib/fribidi-mirroring.c
+-fribidi-src/lib/fribidi-run.c
+-fribidi-src/lib/fribidi-shape.c
+ renpybidicore.c
+ """.split()
+ cython(
+     "_renpybidi",
+     FRIBIDI_SOURCES,
+-    includes=[
+-        BASE + "/fribidi-src/",
+-        BASE + "/fribidi-src/lib/",
+-        ],
+-    define_macros=[
+-        ("FRIBIDI_ENTRY", ""),
+-        ("HAVE_CONFIG_H", "1"),
+-        ])
++    includes=["/usr/include/fribidi"],
++    libs=["fribidi"])
+
+
+ cython("_renpysteam", language="c++", compile_if=steam_sdk, libs=["steam_api"])
diff --git a/gnu/packages/patches/sbcl-geco-fix-organism-class.patch b/gnu/packages/patches/sbcl-geco-fix-organism-class.patch
deleted file mode 100644
index 817596241e..0000000000
--- a/gnu/packages/patches/sbcl-geco-fix-organism-class.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Fix the ORGANISM class so that SBCL >= 2.0.9 can compile it without error.
-
---- a/classes.lisp	2020-10-28 12:11:10.725659464 +0100
-+++ b/classes.lisp	2020-10-31 17:34:36.822752447 +0100
-@@ -148,7 +148,7 @@
-     :accessor score
-     :initarg :score
-     :initform 'nil
--    :type number)
-+    :type (or number null))
-    (NORMALIZED-SCORE
-     :accessor normalized-score
-     :initarg :normalized-score
diff --git a/gnu/packages/pciutils.scm b/gnu/packages/pciutils.scm
index a5ed121c85..d7d224b292 100644
--- a/gnu/packages/pciutils.scm
+++ b/gnu/packages/pciutils.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2015, 2017, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
@@ -92,7 +92,15 @@
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              ;; Install the commands, library, and .pc files.
-             (invoke "make" "install" "install-lib"))))
+             (invoke "make" "install" "install-lib")))
+
+         ,@(if (hurd-target?)
+               '((add-after 'unpack 'apply-hurd-patch
+                   (lambda* (#:key inputs #:allow-other-keys)
+                     (let ((patch (assoc-ref inputs "hurd-patch")))
+                       (invoke "patch" "-p1" "--batch" "-i"
+                               patch)))))
+               '()))
 
        ;; Make sure programs have an RPATH so they can find libpciutils.so.
        #:make-flags (list (string-append "LDFLAGS=-Wl,-rpath="
@@ -109,6 +117,9 @@
                      (package-supported-systems kmod))
              `(("kmod" ,kmod))
              '())
+       ,@(if (hurd-target?)
+             `(("hurd-patch" ,(search-patch "pciutils-hurd-fix.patch")))
+             '())
        ("zlib" ,zlib)))
     (home-page "https://mj.ucw.cz/sw/pciutils/")
     (synopsis "Programs for inspecting and manipulating PCI devices")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 107f579ad6..9195b8328c 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -4989,7 +4989,7 @@ Some things HTTP Core does do:
 (define-public python-httpx
   (package
     (name "python-httpx")
-    (version "0.15.4")
+    (version "0.16.1")
     (source
      (origin
        ;; PyPI tarball does not contain tests.
@@ -4999,7 +4999,7 @@ Some things HTTP Core does do:
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1qr91xw6jxynvihmw953bi5446ssm9ffmb2c4nhfa77v7883sp21"))))
+        (base32 "00gmq45fckcqkj910bvd7pyqz1mvgsdvz4s0k7dzbnc5czzq1f4a"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d07c91121a..bfe005dc30 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -719,18 +719,6 @@ etc. ")
 (define-public python2-babel
   (package-with-python2 python-babel))
 
-;; Sphinx < 2.0 requires this version.  Remove once no longer needed.
-(define-public python2-babel-2.6
-  (package
-    (inherit python2-babel)
-    (version "2.6.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "Babel" version))
-              (sha256
-               (base32
-                "08rxmbx2s4irp0w0gmn498vns5xy0fagm0fg33xa772jiks51flc"))))))
-
 (define-public python2-backport-ssl-match-hostname
   (package
     (name "python2-backport-ssl-match-hostname")
@@ -2184,14 +2172,14 @@ backported for previous versions of Python from 2.4 to 3.3.")
 (define-public python-parse
   (package
     (name "python-parse")
-    (version "1.8.4")
+    (version "1.18.0")
     (source
      (origin
       (method url-fetch)
       (uri (pypi-uri "parse" version))
       (sha256
        (base32
-        "0f8997xr8nq2nq35iiviq8ningd1zvy59fg503xfpbi2dwhgdkf3"))))
+        "19063x4xdjpaf7rfxai6jpgm2k4yvkq7wha8aa8cagbjsqr60rli"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -8813,13 +8801,13 @@ third-party code.")
 (define-public python-llfuse
   (package
     (name "python-llfuse")
-    (version "1.3.6")
+    (version "1.3.8")
     (source (origin
               (method url-fetch)
-              (uri (pypi-uri "llfuse" version ".tar.bz2"))
+              (uri (pypi-uri "llfuse" version))
               (sha256
                (base32
-                "1j9fzxpgmb4rxxyl9jcf84zvznhgi3hnh4hg5vb0qaslxkvng8ii"))))
+                "1g2cdhdqrb6m7655qp61pn61pwj1ql61cdzhr2jvl3w4i8877ddr"))))
     (build-system python-build-system)
     (inputs
      `(("fuse" ,fuse)
@@ -8838,22 +8826,6 @@ third-party code.")
                  (strip-python2-variant python-llfuse)))
     (propagated-inputs `(("python2-contextlib2" ,python2-contextlib2)))))
 
-;; For attic-0.16
-(define-public python-llfuse-0.41
-  (package (inherit python-llfuse)
-    (version "0.41.1")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://bitbucket.org/nikratio/python-llfuse/downloads/"
-                    "llfuse-" version ".tar.bz2"))
-              (sha256
-               (base32
-                "1imlqw9b73086y97izr036f58pgc5akv4ihc2rrf8j5h75jbrlaa"))))
-    ;; Python-LLFUSE < 0.42 includes underscore.js, which is MIT (expat)
-    ;; licensed.  The rest of the package is licensed under LGPL2.0 or later.
-    (license (list license:expat license:lgpl2.0+))))
-
 (define-public python-msgpack
   (package
     (name "python-msgpack")
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index f48685be22..4c16f84099 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -228,7 +228,7 @@ a focus on simplicity and productivity.")
 (define-public mruby
   (package
     (name "mruby")
-    (version "2.0.0")
+    (version "2.1.2")
     (source
      (origin
        (method git-fetch)
@@ -238,7 +238,7 @@ a focus on simplicity and productivity.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1r6w1asjshff43ymdwa6xmrkggza99mi2kw88k7ic6ag2j81hcj5"))))
+         "0fhfv8pi7i8jn2vgk2n2rjnbnfa12nhj514v8i4k353n7q4pmkh3"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 314a11e429..c45544f52e 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -503,14 +503,14 @@ Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
 (define-public r-codetools
   (package
     (name "r-codetools")
-    (version "0.2-16")
+    (version "0.2-18")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "codetools" version))
        (sha256
         (base32
-         "00bmhzqprqfn3w6ghx7sakai6s7il8gbksfiawj8in5mbhbncypn"))))
+         "0a2c115glq8jxixwfigrpvjabhxchn9r4mc40y41dg9dg6wsd7hs"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/codetools")
     (synopsis "Code analysis tools for R")
@@ -889,14 +889,18 @@ algorithms.")
 (define-public r-magrittr
   (package
     (name "r-magrittr")
-    (version "1.5")
+    (version "2.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "magrittr" version))
        (sha256
-        (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
+        (base32 "0pxd99fvg406whqsk9wh756rayrwh84xn3h44zmlpcy23kanbhkm"))))
     (build-system r-build-system)
+    ;; knitr needs magrittr
+    #;
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
     (synopsis "A forward-pipe operator for R")
     (description
@@ -1579,26 +1583,36 @@ R packages that praise their users.")
 (define-public r-testthat
   (package
     (name "r-testthat")
-    (version "2.3.2")
+    (version "3.0.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "testthat" version))
               (sha256
                (base32
-                "0v70v2fs0f2ir962z9csbjlj8snrq9mbjfyhhb9dhz3zy26qs9hs"))))
+                "069ixg03r1s85my9dbc9c1261i4gz8fc1mv67whi2l6kpbp4cjzh"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-cli" ,r-cli)
+     `(("r-brio" ,r-brio)
+       ("r-callr" ,r-callr)
+       ("r-cli" ,r-cli)
        ("r-crayon" ,r-crayon)
+       ("r-desc" ,r-desc)
        ("r-digest" ,r-digest)
        ("r-ellipsis" ,r-ellipsis)
        ("r-evaluate" ,r-evaluate)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-lifecycle" ,r-lifecycle)
        ("r-magrittr" ,r-magrittr)
        ("r-pkgload" ,r-pkgload)
        ("r-praise" ,r-praise)
+       ("r-processx" ,r-processx)
+       ("r-ps" ,r-ps)
        ("r-r6" ,r-r6)
        ("r-rlang" ,r-rlang)
+       ("r-waldo" ,r-waldo)
        ("r-withr" ,r-withr)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/hadley/testthat")
     (synopsis "Unit testing for R")
     (description
@@ -1631,13 +1645,13 @@ defined in different packages.")
 (define-public r-rlang
   (package
     (name "r-rlang")
-    (version "0.4.8")
+    (version "0.4.9")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "rlang" version))
               (sha256
                (base32
-                "0z8hnwbzpwal66svwp04csjm49vdb9rmwzvn8hyqn93qy6pd9015"))))
+                "0qix6jigz3qqjx151fpv1k5hq2miqyakvm3jql2qqsyr9d1028yr"))))
     (build-system r-build-system)
     (home-page "http://rlang.tidyverse.org")
     (synopsis "Functions for base types, core R and Tidyverse features")
@@ -1717,14 +1731,14 @@ database.")
 (define-public r-dbplyr
   (package
     (name "r-dbplyr")
-    (version "1.4.4")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dbplyr" version))
        (sha256
         (base32
-         "1v0p0557n6bz84nq9jc4182k00mdd1hvz7h4w3bbg81z0fmpj0d8"))))
+         "0sa0ggirvfn8j9y4cvhj04z93h6979jm4knjzahdvyzyxhv1kmzc"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -1738,7 +1752,8 @@ database.")
        ("r-r6" ,r-r6)
        ("r-rlang" ,r-rlang)
        ("r-tibble" ,r-tibble)
-       ("r-tidyselect" ,r-tidyselect)))
+       ("r-tidyselect" ,r-tidyselect)
+       ("r-withr" ,r-withr)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/tidyverse/dbplyr")
@@ -1835,13 +1850,13 @@ times.")
 (define-public r-data-table
   (package
     (name "r-data-table")
-    (version "1.13.2")
+    (version "1.13.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "data.table" version))
               (sha256
                (base32
-                "011qsjfybvlpy2sjn9b6hfkcgwx2xrnpxlaqq3y3baps8n1lgnr7"))))
+                "0jrvl5b8qbzmiymhjgbj4l2nai87ijvv33aw24xvzjx0rkys9dv1"))))
     (build-system r-build-system)
     (inputs
      `(("zlib" ,zlib)))
@@ -2110,14 +2125,14 @@ limited to R.")
 (define-public r-backports
   (package
     (name "r-backports")
-    (version "1.1.10")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "backports" version))
        (sha256
         (base32
-         "1pq16bf40zx441ylmqqqilj3xp39r707h56kwqp5yqklq9yln2z1"))))
+         "1xgp4i6yxkh2viia96hlf004hn47yrhfivwf8wv63xdldqa8yj9v"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/backports")
     (synopsis "Reimplementations of functions introduced since R 3.0.0")
@@ -2418,14 +2433,16 @@ pure C implementation of the Git core methods.")
 (define-public r-rstudioapi
   (package
     (name "r-rstudioapi")
-    (version "0.11")
+    (version "0.13")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "rstudioapi" version))
               (sha256
                (base32
-                "0srh0m4mw4k6s7spwb84l4cx4xnn04cp5cjxi0fwza7bwavpzq0k"))))
+                "12vdfzzjc6mv4h105l8cp108j3hjk0mqmg23m6mqr3jarfymphxa"))))
     (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://cran.r-project.org/web/packages/rstudioapi")
     (synopsis "Safely access the RStudio API")
     (description
@@ -2613,13 +2630,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.10.1.0.0")
+    (version "0.10.1.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "0m0f4viw3r6zfk85b7v7h5dqydhdkjdacpl0bqxkmcndlzq8jnsb"))))
+                "0nzi6plhdijx3khavmywzw9wbch0hj8kygphw35wdlslm4cnqcj1"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2682,17 +2699,17 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.")
 (define-public r-rprojroot
   (package
     (name "r-rprojroot")
-    (version "1.3-2")
+    (version "2.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rprojroot" version))
        (sha256
         (base32
-         "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz"))))
+         "07wy07yhms8zln9qb0iwx69dq08h4lrdi8kavjcplfxcskq638az"))))
     (build-system r-build-system)
-    (propagated-inputs
-     `(("r-backports" ,r-backports)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/krlmlr/rprojroot")
     (synopsis "Finding files in project subdirectories")
     (description
@@ -2723,7 +2740,8 @@ certain criterion, e.g., it contains a certain regular file.")
        ("r-tinytex" ,r-tinytex)
        ("r-xfun" ,r-xfun)
        ("r-yaml" ,r-yaml)
-       ("pandoc" ,pandoc)))
+       ("pandoc" ,pandoc)
+       ("pandoc-citeproc" ,pandoc-citeproc)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://rmarkdown.rstudio.com")
@@ -4012,13 +4030,13 @@ package instead.")
 (define-public r-hmisc
   (package
     (name "r-hmisc")
-    (version "4.4-1")
+    (version "4.4-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Hmisc" version))
        (sha256
-        (base32 "0mm3r2kv0kgrhg7salk2hw0s37d4i2mghwk0l0qxaw2ny0w8w5z6"))))
+        (base32 "1j7vkckmahdh90ndcl646sjpxq82y4x55ngxqvkni22mv16wc2j9"))))
     (properties `((upstream-name . "Hmisc")))
     (build-system r-build-system)
     (native-inputs
@@ -4208,14 +4226,14 @@ including:
 (define-public r-gplots
   (package
     (name "r-gplots")
-    (version "3.1.0")
+    (version "3.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gplots" version))
        (sha256
         (base32
-         "05rislwgaw6v5dmhcwyvc04hi1fgaxrpb61f66kx483px45w6f24"))))
+         "0f8khaymz383w2ksnk80d4kpnvgmdk37pbycpsnl2vabaz11kbpr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-catools" ,r-catools)
@@ -4700,14 +4718,14 @@ models, generalized linear models and model-based clustering.")
 (define-public r-mclust
   (package
     (name "r-mclust")
-    (version "5.4.6")
+    (version "5.4.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mclust" version))
        (sha256
         (base32
-         "1z46qask09x3xpv0wzvhn09218vwyrip4f5jrhnx96khpwvczzyl"))))
+         "08scl72llpinfijiyx14yqvmx8lma9jvh8h92v9ynnzfr9kadxa5"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)
@@ -4919,14 +4937,14 @@ of the points.")
 (define-public r-fpc
   (package
     (name "r-fpc")
-    (version "2.2-8")
+    (version "2.2-9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fpc" version))
        (sha256
         (base32
-         "07a125pji1flmybn6iidcnizwnqyl6chnrckxa5jp4qxxfdqx658"))))
+         "0f7sfmpcycr9y7cy5gasyjm2ardxa62kglqms92mcr68jrp01c19"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-class" ,r-class)
@@ -5144,14 +5162,14 @@ algorithms.")
 (define-public r-lme4
   (package
     (name "r-lme4")
-    (version "1.1-25")
+    (version "1.1-26")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lme4" version))
        (sha256
         (base32
-         "0vvjac7hnn5lfbyl92zi8qxyc8kkjcwsg94z0p2s2q311in4gnp4"))))
+         "0ls2krph4pfjn45vf9fn3ln3x98s85wxrkvm5pnxyx55n1pnsjrn"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-boot" ,r-boot)
@@ -5480,14 +5498,14 @@ is supported.")
 (define-public r-lubridate
   (package
     (name "r-lubridate")
-    (version "1.7.9")
+    (version "1.7.9.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lubridate" version))
        (sha256
         (base32
-         "0wnjzvfkrgp2hkr8g5r5vcgcxmsq8bhdmkzkk0m93wr3fgh5xyfb"))))
+         "0yfvlgksasmia7rsp83lsipjpgvlly5qkldcfxj68lfaz9l2sspf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-generics" ,r-generics)
diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm
index 878cbb669d..749b93e29f 100644
--- a/gnu/packages/text-editors.scm
+++ b/gnu/packages/text-editors.scm
@@ -11,6 +11,7 @@
 ;;; Copyright © 2019, 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2020 Tom Zander <tomz@freedommail.ch>
+;;; Copyright © 2020 Mark Meyer <mark@ofosos.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -62,6 +63,7 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages regex)
@@ -1029,3 +1031,42 @@ files.  It was originally developed on the Amiga 3000T.")
 systems that displays its buffer(s) as a hex dump.  The user interface is kept
 similar to vi/ex.")
     (license license:bsd-3)))
+
+(define-public virtaal
+  (package
+    (name "virtaal")
+    (version "0.7.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/translate/Virtaal/"
+                                  version "/virtaal-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "0cyimjp3191qlmw6n0ipqdr9xr0cq4f6dqvz4rl9q31h6l3kywf9"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:use-setuptools? #f
+       #:tests? #f ;; Failing tests
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Set data file path to absolute store path.
+             (substitute* "virtaal/common/pan_app.py"
+               (("file_discovery\\.get_abs_data_filename.*")
+                (string-append "os.path.join('"
+                               (assoc-ref outputs "out")
+                               "/share', *path_parts)"))))))))
+    (inputs
+     `(("python2-lxml" ,python2-lxml)
+       ("python2-pygtk" ,python2-pygtk)
+       ("python2-simplejson" ,python2-simplejson)
+       ("python2-translate-toolkit" ,python2-translate-toolkit)
+       ("python2-pycurl" ,python2-pycurl)))
+    (synopsis "Graphical translation tool")
+    (description "Virtaal is a powerful yet simple translation tool with an
+uncluttered user interface.  It supports a multitude of translation formats
+provided by the Translate Toolkit, including XLIFF and PO.")
+    (home-page "https://virtaal.translatehouse.org/")
+    (license license:gpl2+)))
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 58703d3274..f4c7174c03 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -2190,14 +2190,14 @@ To load this plugin, specify the following option when starting mpv:
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2020.12.07")
+    (version "2020.12.12")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://youtube-dl.org/downloads/latest/"
                                   "youtube-dl-" version ".tar.gz"))
               (sha256
                (base32
-                "0sbrwak9c0pbacg15q2wj5fcsj5k5k1sx9jm7rcjwkjdhqcjqrsi"))))
+                "0iv4l78ylzx8q6myv4v7xq6r5y0hacz6l30bqk1szncfikvfc3cf"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion
diff --git a/gnu/packages/visidata.scm b/gnu/packages/visidata.scm
index 6ba2939b4f..db126eb4ff 100644
--- a/gnu/packages/visidata.scm
+++ b/gnu/packages/visidata.scm
@@ -31,14 +31,14 @@
 (define-public visidata
   (package
     (name "visidata")
-    (version "2.0.1")
+    (version "2.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "visidata" version))
        (sha256
         (base32
-         "1p4x9fz59ablyjvp18y50zdsapavhzx7w5hk2v8rsar5ill8947v"))))
+         "15y6yif0h610ill57ck85l8n5faw849caw6rhf95rd0x67hkikaa"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index 2763fba935..8628d9f4bb 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -14,6 +14,7 @@
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2020 Ryan Prior <rprior@protonmail.com>
 ;;; Copyright © 2020 Ivan Kozlov <kanichos@yandex.ru>
+;;; Copyright © 2020 David Dashyan <mail@davie.li>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -285,6 +286,34 @@ and probably others.")
    (license license:lgpl2.1)
    (home-page "https://www.infradead.org/openconnect/")))
 
+(define-public openfortivpn
+  (package
+    (name "openfortivpn")
+    (version "1.15.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/adrienverge/openfortivpn")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1qsfgpxg553s8rc9cyrc4k96z0pislxsdxb9wyhp8fdprkak2mw2"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("autotools" ,automake)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("openssl" ,openssl)
+       ("ppp" ,ppp)))
+    (home-page "https://github.com/adrienverge/openfortivpn")
+    (synopsis "Client for PPP+SSL VPN tunnel services")
+    (description "Openfortivpn is a client for PPP+SSL VPN tunnel services.  It
+spawns a pppd process and operates the communication between the gateway and
+this process.  It is compatible with Fortinet VPNs.")
+    (license license:gpl3+)))
+
 (define-public openvpn
   (package
     (name "openvpn")
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 17798c6c1d..041e24b53a 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -79,8 +79,10 @@
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
+  #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system python)
+  #:use-module (guix build-system qt)
   #:use-module (guix build-system scons)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
@@ -90,6 +92,7 @@
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bison)
+  #:use-module (gnu packages bittorrent)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
@@ -111,6 +114,7 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnu-doc)
+  #:use-module (gnu packages gnunet)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
   #:use-module (gnu packages gperf)
@@ -118,6 +122,7 @@
   #:use-module (gnu packages guile)
   #:use-module (gnu packages guile-xyz)
   #:use-module (gnu packages hurd)
+  #:use-module (gnu packages icu4c)
   #:use-module (gnu packages image)
   #:use-module (gnu packages java)
   #:use-module (gnu packages jemalloc)
@@ -152,6 +157,7 @@
   #:use-module (gnu packages qt)
   #:use-module (gnu packages re2c)
   #:use-module (gnu packages readline)
+  #:use-module (gnu packages search)
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages textutils)
@@ -1067,7 +1073,7 @@ instances, while JSON's objects will be mapped to @code{QVariantMap}.")
            (lambda* (#:key outputs #:allow-other-keys)
              (substitute* "src/src.pro"
                ;; Do not attempt to install the .prf file into qtbase
-               ;; "lib/mkspecs/features", ref <https://bugs.gnu.org/45301>.
+               ;; "lib/qt5/mkspecs/features", ref <https://bugs.gnu.org/45031>.
                (("\\$\\$\\[QMAKE_MKSPECS\\]")
                 (string-append (assoc-ref outputs "out") "/lib/qt5/mkspecs")))
              #t))
@@ -1470,7 +1476,7 @@ used to validate and fix HTML data.")
 (define-public esbuild
   (package
     (name "esbuild")
-    (version "0.8.19")
+    (version "0.8.21")
     (source
      (origin
        (method git-fetch)
@@ -1479,7 +1485,7 @@ used to validate and fix HTML data.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "19y4g0wjkvrqzl4ngnlkb1giqjyx35gwz4zfk8pw4szsy85z6mli"))
+        (base32 "1gkh3ka7gfdqvzymj6vh9w2d0cp7n2vih42y7ghg7y8x6ry4c6mi"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -7830,3 +7836,148 @@ solution for any project's interface needs:
       (description "gmnisrv is a simple Gemini protocol server written in C.")
       (license (list license:gpl3+
                      license:bsd-3))))) ;; for ini.c and ini.h
+
+(define-public libzim
+  (package
+    (name "libzim")
+    (version "6.2.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/openzim/libzim")
+                    (commit version)))
+              (sha256
+               (base32
+                "0p2317cp19lx0hw9n4fsb3nw2vc4hc1yyi98k3yrs41pkr840kwa"))
+              (file-name (git-file-name name version))))
+    (build-system meson-build-system)
+    (arguments
+     ;; TODO: Find out why tests fail.
+     '(#:tests? #f))
+    (inputs
+     `(("icu4c" ,icu4c)
+       ("liblzma" ,xz)
+       ("libuuid" ,util-linux "lib")
+       ("xapian" ,xapian)
+       ("zlib" ,zlib)
+       ("zstd" ,zstd "lib")))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("googletest" ,googletest)))
+    (home-page "https://wiki.openzim.org/wiki/Main_Page")
+    (synopsis "Reference implementation of the ZIM specification")
+    (description "The openZIM project proposes offline storage solutions for
+content coming from the Web.  The zimlib is the standard implementation of the
+ZIM specification.  It is a library which implements the read and write method
+for ZIM files.")
+    (license license:gpl2)))
+
+(define-public kiwix-lib
+  (package
+    (name "kiwix-lib")
+    (version "9.4.0")
+    (home-page "https://github.com/kiwix/kiwix-lib/")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url home-page)
+                    (commit version)))
+              (sha256
+               (base32
+                "0nsm4qgl0cb6wv983n0px1kf217k4kykb8q56b8j6ikp061lzamm"))
+              (file-name (git-file-name name version))))
+    (build-system meson-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'fix-paths-and-includes
+           (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "CPPFLAGS" (string-append "-I" (assoc-ref inputs "mustache")))
+             (substitute* "src/aria2.cpp"
+               (("ARIA2_CMD \"aria2c\"")
+                (string-append "ARIA2_CMD \""
+                               (assoc-ref inputs "aria2")
+                               "/bin/aria2c\"")))
+             #t)))))
+    (inputs
+     `(("aria2" ,aria2)
+       ("curl" ,curl)
+       ("icu4c" ,icu4c)
+       ("libmicrohttpd" ,libmicrohttpd)
+       ("libzim" ,libzim)
+       ("pugixml" ,pugixml)
+       ("xapian" ,xapian)
+       ("zlib" ,zlib)
+       ("zstd" ,zstd "lib")))
+    (native-inputs
+     `(("mustache" ,(origin
+                      (method git-fetch)
+                      (uri (git-reference
+                            (url "https://github.com/kainjow/Mustache")
+                            ;; XXX: Readme says to use version 3.  Can we use 3.2.1?
+                            (commit "v4.1")))
+                      (file-name (git-file-name "mustache" "4.1"))
+                      (sha256
+                       (base32
+                        "0r9rbk6v1wpld2ismfsk2lkhbyv3dkf0p03hkjivbj05qkfhvlbb"))))
+       ("pkg-config" ,pkg-config)))
+    (synopsis "Common code base for all Kiwix ports")
+    (description "The Kiwix library provides the Kiwix software suite core.
+It contains the code shared by all Kiwix ports.")
+    (license license:gpl3)))
+
+(define-public kiwix-desktop
+  (package
+    (name "kiwix-desktop")
+    (version "2.0.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://download.kiwix.org/release/kiwix-desktop/kiwix-desktop-"
+                    version
+                    ".tar.gz"))
+              (sha256
+               (base32
+                "1a9h4qmh6fkfscyp6lax0ri07dvvzw2wp4kr1sm86n0bdk3cwwha"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             (invoke "qmake"
+                     (string-append "PREFIX="
+                                    (assoc-ref outputs "out")))))
+         (add-before 'configrue 'enable-print-support
+           (lambda _
+             (substitute* "kiwix-desktop.pro"
+               (("webenginewidgets") "webenginewidgets printsupport"))
+             #t))
+         (add-before 'configure 'substitute-source
+           ;; Looks like .pro file is missing a feature.
+           ;; See https://github.com/kiwix/kiwix-desktop/issues/556.
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "kiwix-desktop.pro"
+               (("webenginewidgets" all) (string-append all " printsupport")))
+             #t)))))
+    (inputs
+     `(("curl" ,curl)
+       ("icu4c" ,icu4c)
+       ("kiwix-lib" ,kiwix-lib)
+       ("libzim" ,libzim)
+       ("pugixml" ,pugixml)
+       ("qtbase" ,qtbase)
+       ("qtdeclarative" ,qtdeclarative)
+       ("qtwebchannel" ,qtwebchannel)
+       ("qtwebengine" ,qtwebengine)
+       ("xapian" ,xapian)
+       ("zlib" ,zlib)
+       ("zstd" ,zstd "lib")))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("qmake" ,qtbase)))
+    (home-page "https://wiki.kiwix.org/wiki/Software")
+    (synopsis "Viewer and manager of ZIM files")
+    (description "Kiwix Desktop allows you to enjoy a lot of different content
+offline (such as Wikipedia), without any access to Internet.")
+    (license license:gpl3)))
diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index 653af37de7..6c4f2c6960 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -38,6 +38,9 @@
 ;;; Copyright © 2020 EuAndreh <eu@euandre.org>
 ;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
 ;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
+;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com>
+;; Copyright © 2020 Niklas Eklund <niklas.eklund@posteo.net>
+;;; Copyright © 2020 Robert Smith <robertsmith@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1557,6 +1560,27 @@ modules for building a Wayland compositor.")
 Wlroots based compositors.")
     (license license:expat))) ; MIT license
 
+(define-public wlr-randr
+  (package
+    (name "wlr-randr")
+    (version "0.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/emersion/wlr-randr")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "10c8zzp78s5bw34vvjhilipa28bsdx3jbyhnxgp8f8kawh3cvgsc"))))
+    (build-system meson-build-system)
+    (inputs `(("wayland" ,wayland)))
+    (native-inputs `(("pkg-config" ,pkg-config)))
+    (home-page "https://github.com/emersion/wlr-randr")
+    (synopsis "Utility to manage Wayland compositor outputs")
+    (description "wlr-randr is a utility to manage outputs of a Wayland compositor.")
+    (license license:expat))) ; MIT license
+
 (define-public mako
   (package
     (name "mako")
@@ -1679,6 +1703,7 @@ productive, customizable lisp based systems.")
              (lambda* (#:key inputs outputs #:allow-other-keys)
                (let* ((out (assoc-ref outputs "out"))
                       (program (string-append out "/bin/stumpwm")))
+                 (setenv "HOME" "/tmp")
                  (build-program program outputs
                                 #:entry-program '((stumpwm:stumpwm) 0)
                                 #:dependencies '("stumpwm" "slynk")
@@ -2029,6 +2054,52 @@ formatting, RandR and Xinerama support and EWMH compliance without
 wasting your precious memory.")
       (license license:x11))))
 
+(define-public lemonbar-xft
+  ;; Upstream v2.0 tag is several years behind HEAD
+  (let ((commit "481e12363e2a0fe0ddd2176a8e003392be90ed02"))
+    (package
+      (inherit lemonbar)
+      (name "lemonbar-xft")
+      (version (string-append "2.0." (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/drscream/lemonbar-xft")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0588g37h18lv50h7w8vfbwhvc3iajh7sdr53848spaif99nh3mh4"))))
+      (inputs
+       `(("freetype" ,freetype)
+         ("libxft" ,libxft)
+         ("libx11" ,libx11)
+         ,@(package-inputs lemonbar)))
+      (arguments
+       (substitute-keyword-arguments (package-arguments lemonbar)
+         ((#:make-flags make-flags)
+          `(append
+            ,make-flags
+            (list (string-append
+                   "CFLAGS="
+                   (string-join
+                    (list (string-append
+                           "-I" (assoc-ref %build-inputs "freetype")
+                           "/include/freetype2")
+                          (string-append
+                           "-D" "VERSION="
+                           (format #f "'~s'" ,version))))))))))
+      (home-page "https://github.com/drscream/lemonbar-xft")
+      (synopsis
+       (string-append
+        (package-synopsis lemonbar)
+        " with fontconfig support"))
+      (description
+       (string-append
+        (package-description lemonbar)
+        "This is a fork of the @code{lemonbar} package that adds fontconfig
+support, for easier unicode usage.")))))
+
 (define-public xclickroot
   (package
     (name "xclickroot")
diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index 7c4148c87f..93f23d6722 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -42,6 +42,7 @@
 ;;; Copyright © 2020 Gabriel Arazas <foo.dogsquared@gmail.com>
 ;;; Copyright © 2020 James Smith <jsubuntuxp@disroot.org>
 ;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com>
+;;; Copyright © 2020 Zheng Junjie <873216071@qq.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2618,3 +2619,43 @@ and execute @file{.desktop} files of the Application type.")
      "@command{sx} is a simple alternative to both @command{xinit} and
 @command{startx} for starting an Xorg server.")
     (license license:x11)))
+
+(define-public hsetroot
+  (package
+    (name "hsetroot")
+    (version "1.0.5")
+    (home-page "https://github.com/himdel/hsetroot")
+    (source (origin
+              (method git-fetch)
+              (file-name (git-file-name name version))
+              (uri (git-reference
+                    (url home-page)
+                    (commit version)))
+              (sha256
+               (base32
+                "1jbk5hlxm48zmjzkaq5946s58rqwg1v1ds2sdyd2ba029hmvr722"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f
+       #:make-flags
+       (list
+        "CC=gcc"
+        (string-append "PREFIX=" (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-before 'install 'mkdir-install-path
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (mkdir-p (string-append out "/bin"))))))))
+    (inputs
+     `(("libx11" ,libx11)
+       ("imlib2" ,imlib2)
+       ("libxinerama" ,libxinerama)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (synopsis "Imlib2-based wallpaper changer")
+    (description
+     "The @command{hsetroot} command composes wallpapers for X.
+This package is the fork of hsetroot by Hyriand.")
+    (license license:gpl2+)))
diff --git a/gnu/services/avahi.scm b/gnu/services/avahi.scm
index 54656708ca..7812191cb2 100644
--- a/gnu/services/avahi.scm
+++ b/gnu/services/avahi.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -130,7 +130,7 @@
     (list (shepherd-service
            (documentation "Run the Avahi mDNS/DNS-SD responder.")
            (provision '(avahi-daemon))
-           (requirement '(dbus-system networking))
+           (requirement '(user-processes dbus-system networking))
 
            (start #~(make-forkexec-constructor
                      (list #$(file-append avahi "/sbin/avahi-daemon")
diff --git a/gnu/services/base.scm b/gnu/services/base.scm
index 709d011f53..8449d924af 100644
--- a/gnu/services/base.scm
+++ b/gnu/services/base.scm
@@ -1825,7 +1825,9 @@ raise a deprecation warning if the 'compression-level' field was used."
           advertise?)
     (list (shepherd-service
            (provision '(guix-publish))
-           (requirement '(guix-daemon))
+           (requirement `(user-processes
+                          guix-daemon
+                          ,@(if advertise? '(avahi-daemon) '())))
            (start #~(make-forkexec-constructor
                      (list #$(file-append guix "/bin/guix")
                            "publish" "-u" "guix-publish"
diff --git a/gnu/services/cuirass.scm b/gnu/services/cuirass.scm
index a50f583807..7706ed41c6 100644
--- a/gnu/services/cuirass.scm
+++ b/gnu/services/cuirass.scm
@@ -69,6 +69,8 @@
                     (default "cuirass"))
   (interval         cuirass-configuration-interval ;integer (seconds)
                     (default 60))
+  (queue-size       cuirass-configuration-queue-size
+                    (default 1))
   (database         cuirass-configuration-database ;string (file-name)
                     (default "/var/lib/cuirass/cuirass.db"))
   (port             cuirass-configuration-port ;integer (port)
@@ -98,6 +100,7 @@
         (user             (cuirass-configuration-user config))
         (group            (cuirass-configuration-group config))
         (interval         (cuirass-configuration-interval config))
+        (queue-size       (cuirass-configuration-queue-size config))
         (database         (cuirass-configuration-database config))
         (ttl              (cuirass-configuration-ttl config))
         (port             (cuirass-configuration-port config))
@@ -119,6 +122,7 @@
                            "--database" #$database
                            "--ttl" #$(string-append (number->string ttl) "s")
                            "--interval" #$(number->string interval)
+                           "--queue-size" #$(number->string queue-size)
                            #$@(if queries-log-file
                                   (list (string-append "--log-queries="
                                                        queries-log-file))
diff --git a/gnu/services/science.scm b/gnu/services/science.scm
index 94ff0f36f2..6f7ac91154 100644
--- a/gnu/services/science.scm
+++ b/gnu/services/science.scm
@@ -1,3 +1,21 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
 (define-module (gnu services science)
   #:export (<rshiny-configuration>
             rshiny-configuration
diff --git a/gnu/services/security-token.scm b/gnu/services/security-token.scm
index 354549b33c..ec26006538 100644
--- a/gnu/services/security-token.scm
+++ b/gnu/services/security-token.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -57,7 +58,7 @@
         (modules '((gnu build shepherd)))
         (start #~(lambda _
                    (invoke #$(file-append pcsc-lite "/sbin/pcscd"))
-                   (call-with-input-file "/var/run/pcscd/pcscd.pid" read)))
+                   (call-with-input-file "/run/pcscd/pcscd.pid" read)))
         (stop #~(make-kill-destructor)))))))
 
 (define pcscd-activation
diff --git a/gnu/services/ssh.scm b/gnu/services/ssh.scm
index 1e45495e1b..1891db0487 100644
--- a/gnu/services/ssh.scm
+++ b/gnu/services/ssh.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2016 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
@@ -33,9 +33,6 @@
   #:use-module (guix gexp)
   #:use-module (guix records)
   #:use-module (guix modules)
-  #:use-module ((guix i18n) #:select (G_))
-  #:use-module ((guix diagnostics) #:select (warning source-properties->location))
-  #:use-module ((guix memoization) #:select (mlambda))
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-26)
   #:use-module (ice-9 match)
@@ -279,16 +276,6 @@ The other options should be self-descriptive."
 ;;; OpenSSH.
 ;;;
 
-(define true-but-soon-false
-  (mlambda (loc)
-    ;; The plan is to change the default 'password-authentication?' to #f in
-    ;; Guix 1.3.0 or so.  See <https://issues.guix.gnu.org/44808>.
-    (warning (source-properties->location loc)
-             (G_ "The default value of the 'password-authentication?'
-field of 'openssh-configuration' will change from #true to #false in the
-future.  Explicitly set it to #true to allow password authentication.~%"))
-    #t))
-
 (define-record-type* <openssh-configuration>
   openssh-configuration make-openssh-configuration
   openssh-configuration?
@@ -309,8 +296,7 @@ future.  Explicitly set it to #true to allow password authentication.~%"))
                           (default #f))
   ;; Boolean
   (password-authentication? openssh-configuration-password-authentication?
-                            (default (true-but-soon-false
-                                      (current-source-location))))
+                            (default #t))
   ;; Boolean
   (public-key-authentication? openssh-configuration-public-key-authentication?
                               (default #t))
diff --git a/gnu/system/install.scm b/gnu/system/install.scm
index 7701297411..a6b9e3d952 100644
--- a/gnu/system/install.scm
+++ b/gnu/system/install.scm
@@ -34,6 +34,7 @@
   #:use-module ((guix store) #:select (%store-prefix))
   #:use-module (gnu installer)
   #:use-module (gnu system locale)
+  #:use-module (gnu services avahi)
   #:use-module (gnu services dbus)
   #:use-module (gnu services networking)
   #:use-module (gnu services shepherd)
@@ -335,6 +336,10 @@ Access documentation at any time by pressing Alt-F2.\x1b[0m
           ;; The usual services.
           (syslog-service)
 
+          ;; Use the Avahi daemon to discover substitute servers on the local
+          ;; network.  It can be faster than fetching from remote servers.
+          (service avahi-service-type)
+
           ;; The build daemon.  Register the default substitute server key(s)
           ;; as trusted to allow the installation process to use substitutes by
           ;; default.
@@ -435,6 +440,7 @@ Access documentation at any time by pressing Alt-F2.\x1b[0m
     (host-name "gnu")
     (timezone "Europe/Paris")
     (locale "en_US.utf8")
+    (name-service-switch %mdns-host-lookup-nss)
     (bootloader (bootloader-configuration
                  (bootloader grub-bootloader)
                  (target "/dev/sda")))
diff --git a/guix/avahi.scm b/guix/avahi.scm
index 8a82fd3beb..aa90a5cdd4 100644
--- a/guix/avahi.scm
+++ b/guix/avahi.scm
@@ -92,6 +92,7 @@ when STOP-LOOP? procedure returns true."
 (define* (avahi-browse-service-thread proc
                                       #:key
                                       types
+                                      (ignore-local? #t)
                                       (family AF_INET)
                                       (stop-loop? (const #f))
                                       (timeout 100))
@@ -116,7 +117,9 @@ when STOP-LOOP? procedure returns true."
            ;; Add the service if the host is unknown.  This means that if a
            ;; service is available on multiple network interfaces for a single
            ;; host, only the first interface found will be considered.
-           (unless (hash-ref %known-hosts service-name)
+           (unless (or (hash-ref %known-hosts service-name)
+                       (and ignore-local?
+                            (member lookup-result-flag/local flags)))
              (let* ((address (inet-ntop family address))
                     (local-address (interface->ip-address interface))
                     (service* (avahi-service
@@ -144,8 +147,8 @@ when STOP-LOOP? procedure returns true."
      ((eq? event browser-event/remove)
       (let ((service (hash-ref %known-hosts service-name)))
         (when service
-            (proc 'remove-service service)
-            (hash-remove! %known-hosts service-name))))))
+          (proc 'remove-service service)
+          (hash-remove! %known-hosts service-name))))))
 
   (define client-callback
     (lambda (client state)
diff --git a/guix/build-system/r.scm b/guix/build-system/r.scm
index 5ef982d66a..e2bf41f18d 100644
--- a/guix/build-system/r.scm
+++ b/guix/build-system/r.scm
@@ -59,7 +59,7 @@ release corresponding to NAME and VERSION."
                          "/src/contrib/"
                          name "_" version ".tar.gz")
           ;; TODO: use %bioconductor-version from (guix import cran)
-          (string-append "https://bioconductor.org/packages/3.11"
+          (string-append "https://bioconductor.org/packages/3.12"
                          type-url-part
                          "/src/contrib/"
                          name "_" version ".tar.gz"))))
diff --git a/guix/download.scm b/guix/download.scm
index c24e0132c7..494825860e 100644
--- a/guix/download.scm
+++ b/guix/download.scm
@@ -248,22 +248,13 @@
       (imagemagick
        ;; from http://www.imagemagick.org/script/download.php
        ;; (without mirrors that are unavailable or not up to date)
-       ;; mirrors keeping old versions at the top level
-       "https://sunsite.icm.edu.pl/packages/ImageMagick/"
-       ;; mirrors moving old versions to "legacy"
-       "http://mirror.checkdomain.de/imagemagick/"
-       "http://ftp.surfnet.nl/pub/ImageMagick/"
-       "http://mirror.searchdaimon.com/ImageMagick"
-       "http://mirror.is.co.za/pub/imagemagick/"
-       "http://www.imagemagick.org/download/"
-       "ftp://mirror.aarnet.edu.au/pub/imagemagick/"
-       "ftp://ftp.kddlabs.co.jp/graphics/ImageMagick/"
-       "ftp://ftp.u-aizu.ac.jp/pub/graphics/image/ImageMagick/imagemagick.org/"
+       "https://sunsite.icm.edu.pl/packages/ImageMagick/releases"
+       "http://mirror.checkdomain.de/imagemagick/releases"
+       "ftp://ftp.u-aizu.ac.jp/pub/graphics/image/ImageMagick/imagemagick.org/releases"
        "ftp://ftp.nluug.nl/pub/ImageMagick/"
-       "ftp://ftp.tpnet.pl/pub/graphics/ImageMagick/"
-       "ftp://ftp.fifi.org/pub/ImageMagick/"
-       ;; one legacy location as a last resort
-       "http://www.imagemagick.org/download/legacy/")
+       "http://www.imagemagick.org/download/releases/"
+       ;; Try this if all else fails (normally contains just the latest version).
+       "http://www.imagemagick.org/download/")
       (debian
        "http://ftp.de.debian.org/debian/"
        "http://ftp.fr.debian.org/debian/"
diff --git a/guix/glob.scm b/guix/glob.scm
index a9fc744802..d73783cd30 100644
--- a/guix/glob.scm
+++ b/guix/glob.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2020 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -61,6 +62,11 @@ STR, a glob pattern such as \"foo*\" or \"foo??bar\"."
        (flatten (reverse (if (null? pending)
                              result
                              (cons-string pending result)))))
+      ((#\* #\* #\/ . rest)
+       (if (zero? brackets)
+           (loop rest '() 0
+                 (cons* '**/ (cons-string pending result)))
+           (loop rest (cons '**/ pending) brackets result)))
       (((and chr (or #\? #\*)) . rest)
        (let ((wildcard (match chr
                          (#\? '?)
@@ -121,6 +127,15 @@ STR, a glob pattern such as \"foo*\" or \"foo??bar\"."
       (string-null? str))
      (('*)
       #t)
+     (('**/)
+      #t)
+     (('**/ suffix . rest)
+      (let ((rest (if (eq? '* suffix) (cdr rest) rest))
+            (suffix (if (eq? '* suffix) (car rest) suffix)))
+        (match (string-contains str suffix)
+          (#f    #f)
+          (index (loop rest (string-drop str
+                                         (+ index (string-length suffix))))))))
      (('* suffix . rest)
       (match (string-contains str suffix)
         (#f    #f)
diff --git a/guix/http-client.scm b/guix/http-client.scm
index a767175d67..553640fe9e 100644
--- a/guix/http-client.scm
+++ b/guix/http-client.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2012, 2015 Free Software Foundation, Inc.
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -70,6 +70,7 @@
 
 
 (define* (http-fetch uri #:key port (text? #f) (buffered? #t)
+                     (keep-alive? #f)
                      (verify-certificate? #t)
                      (headers '((user-agent . "GNU Guile")))
                      timeout)
@@ -79,6 +80,9 @@ textual.  Follow any HTTP redirection.  When BUFFERED? is #f, return an
 unbuffered port, suitable for use in `filtered-port'.  HEADERS is an alist of
 extra HTTP headers.
 
+When KEEP-ALIVE? is true, the connection is marked as 'keep-alive' and PORT is
+not closed upon completion.
+
 When VERIFY-CERTIFICATE? is true, verify HTTPS server certificates.
 
 TIMEOUT specifies the timeout in seconds for connection establishment; when
@@ -104,11 +108,7 @@ Raise an '&http-get-error' condition if downloading fails."
         (setvbuf port 'none))
       (let*-values (((resp data)
                      (http-get uri #:streaming? #t #:port port
-                               ;; XXX: When #:keep-alive? is true, if DATA is
-                               ;; a chunked-encoding port, closing DATA won't
-                               ;; close PORT, leading to a file descriptor
-                               ;; leak.
-                               #:keep-alive? #f
+                               #:keep-alive? keep-alive?
                                #:headers headers))
                     ((code)
                      (response-code resp)))
diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index d6baa6b5e5..1d25a5125e 100644
--- a/guix/import/cran.scm
+++ b/guix/import/cran.scm
@@ -29,6 +29,7 @@
   #:use-module (srfi srfi-11)
   #:use-module (srfi srfi-26)
   #:use-module (srfi srfi-34)
+  #:use-module (srfi srfi-35)
   #:use-module (ice-9 receive)
   #:use-module (web uri)
   #:use-module (guix memoization)
@@ -142,9 +143,9 @@ package definition."
 (define %cran-url "https://cran.r-project.org/web/packages/")
 (define %bioconductor-url "https://bioconductor.org/packages/")
 
-;; The latest Bioconductor release is 3.11.  Bioconductor packages should be
+;; The latest Bioconductor release is 3.12.  Bioconductor packages should be
 ;; updated together.
-(define %bioconductor-version "3.11")
+(define %bioconductor-version "3.12")
 
 (define* (bioconductor-packages-list-url #:optional type)
   (string-append "https://bioconductor.org/packages/"
@@ -585,7 +586,10 @@ s-expression corresponding to that package, or #f on failure."
              ((bioconductor)
               ;; Retry import from CRAN
               (cran->guix-package package-name #:repo 'cran))
-             (else (values #f '()))))))))
+             (else
+              (raise (condition
+                      (&message
+                       (message "couldn't find meta-data for R package")))))))))))
 
 (define* (cran-recursive-import package-name #:key (repo 'cran))
   (recursive-import package-name
diff --git a/guix/import/opam.scm b/guix/import/opam.scm
index 867812124d..670973b193 100644
--- a/guix/import/opam.scm
+++ b/guix/import/opam.scm
@@ -120,12 +120,29 @@
 (define-peg-pattern condition-string all (and QUOTE (* STRCHR) QUOTE))
 (define-peg-pattern condition-var all (+ (or (range #\a #\z) "-" ":")))
 
-(define (get-opam-repository)
+(define* (get-opam-repository #:optional repo)
   "Update or fetch the latest version of the opam repository and return the
 path to the repository."
-  (receive (location commit _)
-    (update-cached-checkout "https://github.com/ocaml/opam-repository")
-    location))
+  (let ((url (cond
+               ((or (not repo) (equal? repo 'opam))
+                "https://github.com/ocaml/opam-repository")
+               ((string-prefix? "coq-" (symbol->string repo))
+                "https://github.com/coq/opam-coq-archive")
+               ((equal? repo 'coq) "https://github.com/coq/opam-coq-archive")
+               (else (throw 'unknown-repository repo)))))
+    (receive (location commit _)
+      (update-cached-checkout url)
+      (cond
+        ((or (not repo) (equal? repo 'opam))
+         location)
+        ((equal? repo 'coq)
+         (string-append location "/released"))
+        ((string-prefix? "coq-" (symbol->string repo))
+         (string-append location "/" (substring (symbol->string repo) 4)))
+        (else location)))))
+
+;; Prevent Guile 3 from inlining this procedure so we can mock it in tests.
+(set! get-opam-repository get-opam-repository)
 
 (define (latest-version versions)
   "Find the most recent version from a list of versions."
@@ -161,6 +178,7 @@ path to the repository."
   (substitute-char
     (cond
       ((equal? name "ocamlfind") "ocaml-findlib")
+      ((equal? name "coq") name)
       ((string-prefix? "ocaml" name) name)
       ((string-prefix? "conf-" name) (substring name 5))
       (else (string-append "ocaml-" name)))
@@ -235,12 +253,15 @@ path to the repository."
                      (equal? "ocaml" name))
                names)))
 
-(define (depends->inputs depends)
+(define (filter-dependencies depends)
+  "Remove implicit dependencies from the list of dependencies in @var{depends}."
   (filter (lambda (name)
-            (and (not (equal? "" name))
-                 (not (equal? "ocaml" name))
-                 (not (equal? "ocamlfind" name))))
-    (map dependency->input depends)))
+            (and (not (member name '("" "ocaml" "ocamlfind" "dune" "jbuilder")))
+                 (not (string-prefix? "base-" name))))
+          depends))
+
+(define (depends->inputs depends)
+  (filter-dependencies (map dependency->input depends)))
 
 (define (depends->native-inputs depends)
   (filter (lambda (name) (not (equal? "" name)))
@@ -261,18 +282,19 @@ path to the repository."
                         (substring version 1)
                         version)))))
 
-(define* (opam->guix-package name #:key (repository (get-opam-repository)) version)
+(define* (opam->guix-package name #:key (repo 'opam) version)
   "Import OPAM package NAME from REPOSITORY (a directory name) or, if
 REPOSITORY is #f, from the official OPAM repository.  Return a 'package' sexp
 or #f on failure."
-  (and-let* ((opam-file (opam-fetch name repository))
+  (and-let* ((opam-file (opam-fetch name (get-opam-repository repo)))
              (version (assoc-ref opam-file "version"))
-             (opam-content (pk (assoc-ref opam-file "metadata")))
+             (opam-content (assoc-ref opam-file "metadata"))
              (url-dict (metadata-ref opam-content "url"))
              (source-url (or (metadata-ref url-dict "src")
                              (metadata-ref url-dict "archive")))
              (requirements (metadata-ref opam-content "depends"))
-             (dependencies (dependency-list->names requirements))
+             (names (dependency-list->names requirements))
+             (dependencies (filter-dependencies names))
              (native-dependencies (depends->native-inputs requirements))
              (inputs (dependency-list->inputs (depends->inputs requirements)))
              (native-inputs (dependency-list->inputs
@@ -282,10 +304,7 @@ or #f on failure."
                                 (lambda (name)
                                   (not (member name '("dune" "jbuilder"))))
                                 native-dependencies))))
-        ;; If one of these are required at build time, it means we
-        ;; can use the much nicer dune-build-system.
-        (let ((use-dune? (or (member "dune" (append dependencies native-dependencies))
-                        (member "jbuilder" (append dependencies native-dependencies)))))
+        (let ((use-dune? (member "dune" names)))
           (call-with-temporary-output-file
             (lambda (temp port)
               (and (url-fetch source-url temp)
@@ -322,10 +341,11 @@ or #f on failure."
                         (not (member name '("dune" "jbuilder"))))
                       dependencies))))))))
 
-(define (opam-recursive-import package-name)
+(define* (opam-recursive-import package-name #:key repo)
   (recursive-import package-name
                     #:repo->guix-package opam->guix-package
-                    #:guix-name ocaml-name->guix-name))
+                    #:guix-name ocaml-name->guix-name
+                    #:repo repo))
 
 (define (guix-name->opam-name name)
   (if (string-prefix? "ocaml-" name)
diff --git a/guix/import/utils.scm b/guix/import/utils.scm
index 7de95349cd..e227c2e42d 100644
--- a/guix/import/utils.scm
+++ b/guix/import/utils.scm
@@ -275,9 +275,9 @@ version. If APPEND-VERSION?/string is a string, append this string."
                        (cond
                         ((string? append-version?/string)
                          (string-append name "-" append-version?/string))
-                        ((= append-version?/string #t)
+                        ((eq? append-version?/string #t)
                          (string-append name "-" (version-major+minor version)))
-                        ((#t) version)))
+                        (else name)))
         ,guix-package))))
 
 (define (build-system-modules)
diff --git a/guix/progress.scm b/guix/progress.scm
index fec65b424c..cd80ae620a 100644
--- a/guix/progress.scm
+++ b/guix/progress.scm
@@ -337,9 +337,10 @@ should be a <progress-reporter> object."
               (report total)
               (loop total (get-bytevector-n! in buffer 0 buffer-size))))))))
 
-(define (progress-report-port reporter port)
+(define* (progress-report-port reporter port #:key (close? #t))
   "Return a port that continuously reports the bytes read from PORT using
-REPORTER, which should be a <progress-reporter> object."
+REPORTER, which should be a <progress-reporter> object.  When CLOSE? is true,
+PORT is closed when the returned port is closed."
   (match reporter
     (($ <progress-reporter> start report stop)
      (let* ((total 0)
@@ -364,5 +365,6 @@ REPORTER, which should be a <progress-reporter> object."
                                         ;; trace.
                                         (unless (zero? total)
                                           (stop))
-                                        (close-port port)))))))
+                                        (when close?
+                                          (close-port port))))))))
 
diff --git a/guix/scripts/import/cran.scm b/guix/scripts/import/cran.scm
index 33944c4a3f..20e82ae2ca 100644
--- a/guix/scripts/import/cran.scm
+++ b/guix/scripts/import/cran.scm
@@ -97,10 +97,11 @@ Import and convert the CRAN package for PACKAGE-NAME.\n"))
       ((package-name)
        (if (assoc-ref opts 'recursive)
            ;; Recursive import
-           (map package->definition
-                (filter identity
-                        (cran-recursive-import package-name
-                                               #:repo (or (assoc-ref opts 'repo) 'cran))))
+           (with-error-handling
+             (map package->definition
+                  (filter identity
+                          (cran-recursive-import package-name
+                                                 #:repo (or (assoc-ref opts 'repo) 'cran)))))
            ;; Single import
            (let ((sexp (cran->guix-package package-name
                                            #:repo (or (assoc-ref opts 'repo) 'cran))))
diff --git a/guix/scripts/import/opam.scm b/guix/scripts/import/opam.scm
index 20da1437fe..da9392821c 100644
--- a/guix/scripts/import/opam.scm
+++ b/guix/scripts/import/opam.scm
@@ -45,6 +45,8 @@ Import and convert the opam package for PACKAGE-NAME.\n"))
   (display (G_ "
   -r, --recursive        import packages recursively"))
   (display (G_ "
+      --repo             import packages from this opam repository"))
+  (display (G_ "
   -V, --version          display version information and exit"))
   (newline)
   (show-bug-report-information))
@@ -58,6 +60,9 @@ Import and convert the opam package for PACKAGE-NAME.\n"))
          (option '(#\V "version") #f #f
                  (lambda args
                    (show-version-and-exit "guix import opam")))
+         (option '(#f "repo") #t #f
+                 (lambda (opt name arg result)
+                   (alist-cons 'repo arg result)))
          (option '(#\r "recursive") #f #f
                  (lambda (opt name arg result)
                    (alist-cons 'recursive #t result)))
@@ -79,6 +84,7 @@ Import and convert the opam package for PACKAGE-NAME.\n"))
                 %default-options))
 
   (let* ((opts (parse-options))
+         (repo (and=> (assoc-ref opts 'repo) string->symbol))
          (args (filter-map (match-lambda
                             (('argument . value)
                              value)
@@ -93,9 +99,9 @@ Import and convert the opam package for PACKAGE-NAME.\n"))
                    `(define-public ,(string->symbol name)
                       ,pkg))
                   (_ #f))
-                (opam-recursive-import package-name))
+                (opam-recursive-import package-name #:repo repo))
            ;; Single import
-           (let ((sexp (opam->guix-package package-name)))
+           (let ((sexp (opam->guix-package package-name #:repo repo)))
              (unless sexp
                (leave (G_ "failed to download meta-data for package '~a'~%")
                       package-name))
diff --git a/guix/scripts/substitute.scm b/guix/scripts/substitute.scm
index feae2df9cb..25075eedff 100755
--- a/guix/scripts/substitute.scm
+++ b/guix/scripts/substitute.scm
@@ -88,6 +88,7 @@
             write-narinfo
 
             %allow-unauthenticated-substitutes?
+            %error-to-file-descriptor-4?
 
             substitute-urls
             guix-substitute))
@@ -124,11 +125,7 @@ disabled!~%"))
   ;; purposes, and should be avoided otherwise.
   (make-parameter
    (and=> (getenv "GUIX_ALLOW_UNAUTHENTICATED_SUBSTITUTES")
-          (cut string-ci=? <> "yes"))
-   (lambda (value)
-     (when value
-       (warn-about-missing-authentication))
-     value)))
+          (cut string-ci=? <> "yes"))))
 
 (define %narinfo-ttl
   ;; Number of seconds during which cached narinfo lookups are considered
@@ -191,9 +188,14 @@ again."
         (sigaction SIGALRM SIG_DFL)
         (apply values result)))))
 
-(define* (fetch uri #:key (buffered? #t) (timeout? #t))
+(define* (fetch uri #:key (buffered? #t) (timeout? #t)
+                (keep-alive? #f) (port #f))
   "Return a binary input port to URI and the number of bytes it's expected to
-provide."
+provide.
+
+When PORT is true, use it as the underlying I/O port for HTTP transfers; when
+PORT is false, open a new connection for URI.  When KEEP-ALIVE? is true, the
+connection (typically PORT) is kept open once data has been fetched from URI."
   (case (uri-scheme uri)
     ((file)
      (let ((port (open-file (uri-path uri)
@@ -209,7 +211,7 @@ provide."
        ;;   sudo tc qdisc add dev eth0 root netem delay 1500ms
        ;; and then cancel with:
        ;;   sudo tc qdisc del dev eth0 root
-       (let ((port #f))
+       (let ((port port))
          (with-timeout (if timeout?
                            %fetch-timeout
                            0)
@@ -220,10 +222,11 @@ provide."
            (begin
              (when (or (not port) (port-closed? port))
                (set! port (guix:open-connection-for-uri
-                           uri #:verify-certificate? #f))
-               (unless (or buffered? (not (file-port? port)))
-                 (setvbuf port 'none)))
+                           uri #:verify-certificate? #f)))
+             (unless (or buffered? (not (file-port? port)))
+               (setvbuf port 'none))
              (http-fetch uri #:text? #f #:port port
+                         #:keep-alive? keep-alive?
                          #:verify-certificate? #f))))))
     (else
      (leave (G_ "unsupported substitute URI scheme: ~a~%")
@@ -481,17 +484,17 @@ indicates that PATH is unavailable at CACHE-URL."
     (build-request (string->uri url) #:method 'GET #:headers headers)))
 
 (define (at-most max-length lst)
-  "If LST is shorter than MAX-LENGTH, return it; otherwise return its
-MAX-LENGTH first elements."
+  "If LST is shorter than MAX-LENGTH, return it and the empty list; otherwise
+return its MAX-LENGTH first elements and its tail."
   (let loop ((len 0)
              (lst lst)
              (result '()))
     (match lst
       (()
-       (reverse result))
+       (values (reverse result) '()))
       ((head . tail)
        (if (>= len max-length)
-           (reverse result)
+           (values (reverse result) lst)
            (loop (+ 1 len) tail (cons head result)))))))
 
 (define* (http-multiple-get base-uri proc seed requests
@@ -893,6 +896,9 @@ authorized substitutes."
   (define (valid? obj)
     (valid-narinfo? obj acl))
 
+  (when (%allow-unauthenticated-substitutes?)
+    (warn-about-missing-authentication))
+
   (match (string-tokenize command)
     (("have" paths ..1)
      ;; Return the subset of PATHS available in CACHE-URLS.
@@ -962,6 +968,68 @@ the URI, its compression method (a string), and the compressed file size."
     (((uri compression file-size) _ ...)
      (values uri compression file-size))))
 
+(define %max-cached-connections
+  ;; Maximum number of connections kept in cache by
+  ;; 'open-connection-for-uri/cached'.
+  16)
+
+(define open-connection-for-uri/cached
+  (let ((cache '()))
+    (lambda* (uri #:key fresh?)
+      "Return a connection for URI, possibly reusing a cached connection.
+When FRESH? is true, delete any cached connections for URI and open a new
+one.  Return #f if URI's scheme is 'file' or #f."
+      (define host (uri-host uri))
+      (define scheme (uri-scheme uri))
+      (define key (list host scheme (uri-port uri)))
+
+      (and (not (memq scheme '(file #f)))
+           (match (assoc-ref cache key)
+             (#f
+              ;; Open a new connection to URI and evict old entries from
+              ;; CACHE, if any.
+              (let-values (((socket)
+                            (guix:open-connection-for-uri
+                             uri #:verify-certificate? #f))
+                           ((new-cache evicted)
+                            (at-most (- %max-cached-connections 1) cache)))
+                (for-each (match-lambda
+                            ((_ . port)
+                             (false-if-exception (close-port port))))
+                          evicted)
+                (set! cache (alist-cons key socket new-cache))
+                socket))
+             (socket
+              (if (or fresh? (port-closed? socket))
+                  (begin
+                    (false-if-exception (close-port socket))
+                    (set! cache (alist-delete key cache))
+                    (open-connection-for-uri/cached uri))
+                  (begin
+                    ;; Drain input left from the previous use.
+                    (drain-input socket)
+                    socket))))))))
+
+(define (call-with-cached-connection uri proc)
+  (let ((port (open-connection-for-uri/cached uri)))
+    (catch #t
+      (lambda ()
+        (proc port))
+      (lambda (key . args)
+        ;; If PORT was cached and the server closed the connection in the
+        ;; meantime, we get EPIPE.  In that case, open a fresh connection and
+        ;; retry.  We might also get 'bad-response or a similar exception from
+        ;; (web response) later on, once we've sent the request.
+        (if (or (and (eq? key 'system-error)
+                     (= EPIPE (system-error-errno `(,key ,@args))))
+                (memq key '(bad-response bad-header bad-header-component)))
+            (proc (open-connection-for-uri/cached uri #:fresh? #t))
+            (apply throw key args))))))
+
+(define-syntax-rule (with-cached-connection uri port exp ...)
+  "Bind PORT with EXP... to a socket connected to URI."
+  (call-with-cached-connection uri (lambda (port) exp ...)))
+
 (define* (process-substitution store-item destination
                                #:key cache-urls acl print-build-trace?)
   "Substitute STORE-ITEM (a store file name) from CACHE-URLS, and write it to
@@ -984,10 +1052,12 @@ DESTINATION as a nar file.  Verify the substitute against ACL."
               (G_ "Downloading ~a...~%") (uri->string uri)))
 
     (let*-values (((raw download-size)
-                   ;; Note that Hydra currently generates Nars on the fly
-                   ;; and doesn't specify a Content-Length, so
-                   ;; DOWNLOAD-SIZE is #f in practice.
-                   (fetch uri #:buffered? #f #:timeout? #f))
+                   ;; 'guix publish' without '--cache' doesn't specify a
+                   ;; Content-Length, so DOWNLOAD-SIZE is #f in this case.
+                   (with-cached-connection uri port
+                     (fetch uri #:buffered? #f #:timeout? #f
+                            #:port port
+                            #:keep-alive? #t)))
                   ((progress)
                    (let* ((dl-size  (or download-size
                                         (and (equal? compression "none")
@@ -1001,7 +1071,9 @@ DESTINATION as a nar file.  Verify the substitute against ACL."
                                          (uri->string uri) dl-size
                                          (current-error-port)
                                          #:abbreviation nar-uri-abbreviation))))
-                     (progress-report-port reporter raw)))
+                     ;; Keep RAW open upon completion so we can later reuse
+                     ;; the underlying connection.
+                     (progress-report-port reporter raw #:close? #f)))
                   ((input pids)
                    ;; NOTE: This 'progress' port of current process will be
                    ;; closed here, while the child process doing the
@@ -1017,7 +1089,10 @@ DESTINATION as a nar file.  Verify the substitute against ACL."
 
       ;; Skip a line after what 'progress-reporter/file' printed, and another
       ;; one to visually separate substitutions.
-      (display "\n\n" (current-error-port)))))
+      (display "\n\n" (current-error-port))
+
+      ;; Tell the daemon that we're done.
+      (display "success\n" (current-output-port)))))
 
 
 ;;;
@@ -1128,6 +1203,11 @@ default value."
   (unless (string->uri uri)
     (leave (G_ "~a: invalid URI~%") uri)))
 
+(define %error-to-file-descriptor-4?
+  ;; Whether to direct 'current-error-port' to file descriptor 4 like
+  ;; 'guix-daemon' expects.
+  (make-parameter #t))
+
 (define-command (guix-substitute . args)
   (category internal)
   (synopsis "implement the build daemon's substituter protocol")
@@ -1139,71 +1219,78 @@ default value."
       ((= string->number number) (> number 0))
       (_ #f)))
 
-  (mkdir-p %narinfo-cache-directory)
-  (maybe-remove-expired-cache-entries %narinfo-cache-directory
-                                      cached-narinfo-files
-                                      #:entry-expiration
-                                      cached-narinfo-expiration-time
-                                      #:cleanup-period
-                                      %narinfo-expired-cache-entry-removal-delay)
-  (check-acl-initialized)
-
-  ;; Starting from commit 22144afa in Nix, we are allowed to bail out directly
-  ;; when we know we cannot substitute, but we must emit a newline on stdout
-  ;; when everything is alright.
-  (when (null? (substitute-urls))
-    (exit 0))
-
-  ;; Say hello (see above.)
-  (newline)
-  (force-output (current-output-port))
-
-  ;; Sanity-check SUBSTITUTE-URLS so we can provide a meaningful error message.
-  (for-each validate-uri (substitute-urls))
-
-  ;; Attempt to install the client's locale so that messages are suitably
-  ;; translated.  LC_CTYPE must be a UTF-8 locale; it's the case by default so
-  ;; don't change it.
-  (match (or (find-daemon-option "untrusted-locale")
-             (find-daemon-option "locale"))
-    (#f     #f)
-    (locale (false-if-exception (setlocale LC_MESSAGES locale))))
-
-  (catch 'system-error
-    (lambda ()
-      (set-thread-name "guix substitute"))
-    (const #t))                                   ;GNU/Hurd lacks 'prctl'
-
-  (with-networking
-   (with-error-handling                           ; for signature errors
-     (match args
-       (("--query")
-        (let ((acl (current-acl)))
-          (let loop ((command (read-line)))
-            (or (eof-object? command)
-                (begin
-                  (process-query command
-                                 #:cache-urls (substitute-urls)
-                                 #:acl acl)
-                  (loop (read-line)))))))
-       (("--substitute" store-path destination)
-        ;; Download STORE-PATH and add store it as a Nar in file DESTINATION.
-        ;; Specify the number of columns of the terminal so the progress
-        ;; report displays nicely.
-        (parameterize ((current-terminal-columns (client-terminal-columns)))
-          (process-substitution store-path destination
-                                #:cache-urls (substitute-urls)
-                                #:acl (current-acl)
-                                #:print-build-trace? print-build-trace?)))
-       ((or ("-V") ("--version"))
-        (show-version-and-exit "guix substitute"))
-       (("--help")
-        (show-help))
-       (opts
-        (leave (G_ "~a: unrecognized options~%") opts))))))
+  ;; The daemon's agent code opens file descriptor 4 for us and this is where
+  ;; stderr should go.
+  (parameterize ((current-error-port (if (%error-to-file-descriptor-4?)
+                                         (fdopen 4 "wl")
+                                         (current-error-port))))
+    ;; Redirect diagnostics to file descriptor 4 as well.
+    (guix-warning-port (current-error-port))
+
+    (mkdir-p %narinfo-cache-directory)
+    (maybe-remove-expired-cache-entries %narinfo-cache-directory
+                                        cached-narinfo-files
+                                        #:entry-expiration
+                                        cached-narinfo-expiration-time
+                                        #:cleanup-period
+                                        %narinfo-expired-cache-entry-removal-delay)
+    (check-acl-initialized)
+
+    ;; Sanity-check SUBSTITUTE-URLS so we can provide a meaningful error
+    ;; message.
+    (for-each validate-uri (substitute-urls))
+
+    ;; Attempt to install the client's locale so that messages are suitably
+    ;; translated.  LC_CTYPE must be a UTF-8 locale; it's the case by default
+    ;; so don't change it.
+    (match (or (find-daemon-option "untrusted-locale")
+               (find-daemon-option "locale"))
+      (#f     #f)
+      (locale (false-if-exception (setlocale LC_MESSAGES locale))))
+
+    (catch 'system-error
+      (lambda ()
+        (set-thread-name "guix substitute"))
+      (const #t))                                 ;GNU/Hurd lacks 'prctl'
+
+    (with-networking
+     (with-error-handling                         ; for signature errors
+       (match args
+         (("--query")
+          (let ((acl (current-acl)))
+            (let loop ((command (read-line)))
+              (or (eof-object? command)
+                  (begin
+                    (process-query command
+                                   #:cache-urls (substitute-urls)
+                                   #:acl acl)
+                    (loop (read-line)))))))
+         (("--substitute")
+          ;; Download STORE-PATH and store it as a Nar in file DESTINATION.
+          ;; Specify the number of columns of the terminal so the progress
+          ;; report displays nicely.
+          (parameterize ((current-terminal-columns (client-terminal-columns)))
+            (let loop ()
+              (match (read-line)
+                ((? eof-object?)
+                 #t)
+                ((= string-tokenize ("substitute" store-path destination))
+                 (process-substitution store-path destination
+                                       #:cache-urls (substitute-urls)
+                                       #:acl (current-acl)
+                                       #:print-build-trace?
+                                       print-build-trace?)
+                 (loop))))))
+         ((or ("-V") ("--version"))
+          (show-version-and-exit "guix substitute"))
+         (("--help")
+          (show-help))
+         (opts
+          (leave (G_ "~a: unrecognized options~%") opts)))))))
 
 ;;; Local Variables:
 ;;; eval: (put 'with-timeout 'scheme-indent-function 1)
+;;; eval: (put 'with-cached-connection 'scheme-indent-function 2)
 ;;; End:
 
 ;;; substitute.scm ends here
diff --git a/guix/self.scm b/guix/self.scm
index c0de14b79a..7cda6656c9 100644
--- a/guix/self.scm
+++ b/guix/self.scm
@@ -649,18 +649,26 @@ load path."
 
   (program-file "guix-command"
                 #~(begin
+                    ;; Remove the empty extension from the search path.
+                    (set! %load-extensions '(".scm"))
+
                     (set! %load-path
-                      (cons (string-append #$module-directory
-                                           "/share/guile/site/"
-                                           (effective-version))
-                            %load-path))
+                      (append (list (string-append #$module-directory
+                                                   "/share/guile/site/"
+                                                   (effective-version))
+                                    (string-append #$guile "/share/guile/"
+                                                   (effective-version)))
+                              %load-path))
 
                     (set! %load-compiled-path
-                      (cons (string-append #$module-directory
-                                           "/lib/guile/"
-                                           (effective-version)
-                                           "/site-ccache")
-                            %load-compiled-path))
+                      (append (list (string-append #$module-directory
+                                                   "/lib/guile/"
+                                                   (effective-version)
+                                                   "/site-ccache")
+                                    (string-append #$guile "/lib/guile/"
+                                                   (effective-version)
+                                                   "/ccache"))
+                              %load-compiled-path))
 
                     ;; To maximize the chances that locales are set up right
                     ;; out-of-the-box, bundle "common" UTF-8 locales.
diff --git a/guix/store/database.scm b/guix/store/database.scm
index 2ea63b17aa..b36b127630 100644
--- a/guix/store/database.scm
+++ b/guix/store/database.scm
@@ -21,7 +21,6 @@
 (define-module (guix store database)
   #:use-module (sqlite3)
   #:use-module (guix config)
-  #:use-module (guix gexp)
   #:use-module (guix serialization)
   #:use-module (guix store deduplication)
   #:use-module (guix base16)
@@ -29,7 +28,6 @@
   #:use-module (guix build syscalls)
   #:use-module ((guix build utils)
                 #:select (mkdir-p executable-file?))
-  #:use-module (guix utils)
   #:use-module (guix build store-copy)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-11)
diff --git a/m4/guix.m4 b/m4/guix.m4
index 4fa7cdf737..f8eb5aaf51 100644
--- a/m4/guix.m4
+++ b/m4/guix.m4
@@ -26,7 +26,7 @@ AC_DEFUN([GUIX_SYSTEM_TYPE], [
   AC_REQUIRE([AC_CANONICAL_HOST])
   AC_PATH_PROG([SED], [sed])
 
-  AC_ARG_WITH(system, AC_HELP_STRING([--with-system=SYSTEM],
+  AC_ARG_WITH(system, AS_HELP_STRING([--with-system=SYSTEM],
     [Platform identifier (e.g., `i686-linux').]),
     [guix_system="$withval"],
     [case "$host_cpu" in
@@ -78,7 +78,7 @@ dnl Assert that this is a system to which the distro is ported.
 AC_DEFUN([GUIX_ASSERT_SUPPORTED_SYSTEM], [
   AC_REQUIRE([GUIX_SYSTEM_TYPE])
 
-  AC_ARG_WITH([courage], [AC_HELP_STRING([--with-courage],
+  AC_ARG_WITH([courage], [AS_HELP_STRING([--with-courage],
     [Assert that even if this platform is unsupported, you will be
 courageous and port the GNU System distribution to it (see
 "GNU Distribution" in the manual.)])],
diff --git a/nix/libstore/build.cc b/nix/libstore/build.cc
index 8413819114..b5551b87ae 100644
--- a/nix/libstore/build.cc
+++ b/nix/libstore/build.cc
@@ -262,6 +262,7 @@ public:
     LocalStore & store;
 
     std::shared_ptr<Agent> hook;
+    std::shared_ptr<Agent> substituter;
 
     Worker(LocalStore & store);
     ~Worker();
@@ -2773,15 +2774,6 @@ private:
     /* Path info returned by the substituter's query info operation. */
     SubstitutablePathInfo info;
 
-    /* Pipe for the substituter's standard output. */
-    Pipe outPipe;
-
-    /* Pipe for the substituter's standard error. */
-    Pipe logPipe;
-
-    /* The process ID of the builder. */
-    Pid pid;
-
     /* Lock on the store path. */
     std::shared_ptr<PathLocks> outputLock;
 
@@ -2795,6 +2787,17 @@ private:
     typedef void (SubstitutionGoal::*GoalState)();
     GoalState state;
 
+    /* The substituter. */
+    std::shared_ptr<Agent> substituter;
+
+    /* Either the empty string, or the expected hash as returned by the
+       substituter.  */
+    string expectedHashStr;
+
+    /* Either the empty string, or the status phrase returned by the
+       substituter.  */
+    string status;
+
     void tryNext();
 
 public:
@@ -2840,7 +2843,7 @@ SubstitutionGoal::SubstitutionGoal(const Path & storePath, Worker & worker, bool
 
 SubstitutionGoal::~SubstitutionGoal()
 {
-    if (pid != -1) worker.childTerminated(pid);
+    if (substituter) worker.childTerminated(substituter->pid);
 }
 
 
@@ -2848,9 +2851,9 @@ void SubstitutionGoal::timedOut()
 {
     if (settings.printBuildTrace)
         printMsg(lvlError, format("@ substituter-failed %1% timeout") % storePath);
-    if (pid != -1) {
-        pid_t savedPid = pid;
-        pid.kill();
+    if (substituter) {
+        pid_t savedPid = substituter->pid;
+	substituter.reset();
         worker.childTerminated(savedPid);
     }
     amDone(ecFailed);
@@ -2977,44 +2980,29 @@ void SubstitutionGoal::tryToRun()
 
     printMsg(lvlInfo, format("fetching path `%1%'...") % storePath);
 
-    outPipe.create();
-    logPipe.create();
-
     destPath = repair ? storePath + ".tmp" : storePath;
 
     /* Remove the (stale) output path if it exists. */
     if (pathExists(destPath))
         deletePath(destPath);
 
-    worker.store.setSubstituterEnv();
-
-    /* Fill in the arguments. */
-    Strings args;
-    args.push_back("guix");
-    args.push_back("substitute");
-    args.push_back("--substitute");
-    args.push_back(storePath);
-    args.push_back(destPath);
-
-    /* Fork the substitute program. */
-    pid = startProcess([&]() {
-
-        commonChildInit(logPipe);
-
-        if (dup2(outPipe.writeSide, STDOUT_FILENO) == -1)
-            throw SysError("cannot dup output pipe into stdout");
+    if (!worker.substituter) {
+	const Strings args = { "substitute", "--substitute" };
+	const std::map<string, string> env = { { "_NIX_OPTIONS", settings.pack() } };
+	worker.substituter = std::make_shared<Agent>(settings.guixProgram, args, env);
+    }
 
-        execv(settings.guixProgram.c_str(), stringsToCharPtrs(args).data());
+    /* Borrow the worker's substituter.  */
+    if (!substituter) substituter.swap(worker.substituter);
 
-        throw SysError(format("executing `%1% substitute'") % settings.guixProgram);
-    });
+    /* Send the request to the substituter.  */
+    writeLine(substituter->toAgent.writeSide,
+	      (format("substitute %1% %2%") % storePath % destPath).str());
 
-    pid.setSeparatePG(true);
-    pid.setKillSignal(SIGTERM);
-    outPipe.writeSide.close();
-    logPipe.writeSide.close();
-    worker.childStarted(shared_from_this(),
-        pid, singleton<set<int> >(logPipe.readSide), true, true);
+    set<int> fds;
+    fds.insert(substituter->fromAgent.readSide);
+    fds.insert(substituter->builderOut.readSide);
+    worker.childStarted(shared_from_this(), substituter->pid, fds, true, true);
 
     state = &SubstitutionGoal::finished;
 
@@ -3029,54 +3017,51 @@ void SubstitutionGoal::finished()
 {
     trace("substitute finished");
 
-    /* Since we got an EOF on the logger pipe, the substitute is
-       presumed to have terminated.  */
-    pid_t savedPid = pid;
-    int status = pid.wait(true);
-
-    /* So the child is gone now. */
-    worker.childTerminated(savedPid);
+    /* Remove the 'guix substitute' process from the list of children.  */
+    worker.childTerminated(substituter->pid);
 
-    /* Close the read side of the logger pipe. */
-    logPipe.readSide.close();
-
-    /* Get the hash info from stdout. */
-    string dummy = readLine(outPipe.readSide);
-    string expectedHashStr = statusOk(status) ? readLine(outPipe.readSide) : "";
-    outPipe.readSide.close();
+    /* If max-jobs > 1, the worker might have created a new 'substitute'
+       process in the meantime.  If that is the case, terminate ours;
+       otherwise, give it back to the worker.  */
+    if (worker.substituter) {
+	substituter.reset ();
+    } else {
+	worker.substituter.swap(substituter);
+    }
 
     /* Check the exit status and the build result. */
     HashResult hash;
     try {
 
-        if (!statusOk(status))
-            throw SubstError(format("fetching path `%1%' %2%")
-                % storePath % statusToString(status));
+        if (status != "success")
+            throw SubstError(format("fetching path `%1%' (status: '%2%')")
+                % storePath % status);
 
         if (!pathExists(destPath))
             throw SubstError(format("substitute did not produce path `%1%'") % destPath);
 
+	if (expectedHashStr == "")
+	    throw SubstError(format("substituter did not communicate hash for `%1'") % storePath);
+
         hash = hashPath(htSHA256, destPath);
 
         /* Verify the expected hash we got from the substituer. */
-        if (expectedHashStr != "") {
-            size_t n = expectedHashStr.find(':');
-            if (n == string::npos)
-                throw Error(format("bad hash from substituter: %1%") % expectedHashStr);
-            HashType hashType = parseHashType(string(expectedHashStr, 0, n));
-            if (hashType == htUnknown)
-                throw Error(format("unknown hash algorithm in `%1%'") % expectedHashStr);
-            Hash expectedHash = parseHash16or32(hashType, string(expectedHashStr, n + 1));
-            Hash actualHash = hashType == htSHA256 ? hash.first : hashPath(hashType, destPath).first;
-            if (expectedHash != actualHash) {
-		if (settings.printBuildTrace)
-		    printMsg(lvlError, format("@ hash-mismatch %1% %2% %3% %4%")
-			     % storePath % "sha256"
-			     % printHash16or32(expectedHash)
-			     % printHash16or32(actualHash));
-                throw SubstError(format("hash mismatch for substituted item `%1%'") % storePath);
-	    }
-        }
+	size_t n = expectedHashStr.find(':');
+	if (n == string::npos)
+	    throw Error(format("bad hash from substituter: %1%") % expectedHashStr);
+	HashType hashType = parseHashType(string(expectedHashStr, 0, n));
+	if (hashType == htUnknown)
+	    throw Error(format("unknown hash algorithm in `%1%'") % expectedHashStr);
+	Hash expectedHash = parseHash16or32(hashType, string(expectedHashStr, n + 1));
+	Hash actualHash = hashType == htSHA256 ? hash.first : hashPath(hashType, destPath).first;
+	if (expectedHash != actualHash) {
+	    if (settings.printBuildTrace)
+		printMsg(lvlError, format("@ hash-mismatch %1% %2% %3% %4%")
+			 % storePath % "sha256"
+			 % printHash16or32(expectedHash)
+			 % printHash16or32(actualHash));
+	    throw SubstError(format("hash mismatch for substituted item `%1%'") % storePath);
+	}
 
     } catch (SubstError & e) {
 
@@ -3122,16 +3107,40 @@ void SubstitutionGoal::finished()
 
 void SubstitutionGoal::handleChildOutput(int fd, const string & data)
 {
-    assert(fd == logPipe.readSide);
-    if (verbosity >= settings.buildVerbosity) writeToStderr(data);
-    /* Don't write substitution output to a log file for now.  We
-       probably should, though. */
+    if (verbosity >= settings.buildVerbosity
+	&& fd == substituter->builderOut.readSide) {
+	writeToStderr(data);
+	/* Don't write substitution output to a log file for now.  We
+	   probably should, though. */
+    }
+
+    if (fd == substituter->fromAgent.readSide) {
+	/* DATA may consist of several lines.  Process them one by one.  */
+	string input = data;
+	while (!input.empty()) {
+	    /* Process up to the first newline.  */
+	    size_t end = input.find_first_of("\n");
+	    string trimmed = (end != string::npos) ? input.substr(0, end) : input;
+
+	    /* Update the goal's state accordingly.  */
+	    if (expectedHashStr == "") {
+		expectedHashStr = trimmed;
+	    } else if (status == "") {
+		status = trimmed;
+		worker.wakeUp(shared_from_this());
+	    } else {
+		printMsg(lvlError, format("unexpected substituter message '%1%'") % input);
+	    }
+
+	    input = (end != string::npos) ? input.substr(end + 1) : "";
+	}
+    }
 }
 
 
 void SubstitutionGoal::handleEOF(int fd)
 {
-    if (fd == logPipe.readSide) worker.wakeUp(shared_from_this());
+    worker.wakeUp(shared_from_this());
 }
 
 
diff --git a/nix/libstore/local-store.cc b/nix/libstore/local-store.cc
index 8c479002ec..c304e2ddd1 100644
--- a/nix/libstore/local-store.cc
+++ b/nix/libstore/local-store.cc
@@ -57,7 +57,6 @@ void checkStoreNotSymlink()
 
 
 LocalStore::LocalStore(bool reserveSpace)
-    : didSetSubstituterEnv(false)
 {
     schemaPath = settings.nixDBPath + "/schema";
 
@@ -183,21 +182,6 @@ LocalStore::LocalStore(bool reserveSpace)
 LocalStore::~LocalStore()
 {
     try {
-	if (runningSubstituter) {
-	    RunningSubstituter &i = *runningSubstituter;
-            if (!i.disabled) {
-		i.to.close();
-		i.from.close();
-		i.error.close();
-		if (i.pid != -1)
-		    i.pid.wait(true);
-	    }
-        }
-    } catch (...) {
-        ignoreException();
-    }
-
-    try {
         if (fdTempRoots != -1) {
             fdTempRoots.close();
             unlink(fnTempRoots.c_str());
@@ -796,96 +780,31 @@ Path LocalStore::queryPathFromHashPart(const string & hashPart)
     });
 }
 
-
-void LocalStore::setSubstituterEnv()
-{
-    if (didSetSubstituterEnv) return;
-
-    /* Pass configuration options (including those overridden with
-       --option) to substituters. */
-    setenv("_NIX_OPTIONS", settings.pack().c_str(), 1);
-
-    didSetSubstituterEnv = true;
-}
-
-
-void LocalStore::startSubstituter(RunningSubstituter & run)
-{
-    if (run.disabled || run.pid != -1) return;
-
-    debug(format("starting substituter program `%1% substitute'")
-	  % settings.guixProgram);
-
-    Pipe toPipe, fromPipe, errorPipe;
-
-    toPipe.create();
-    fromPipe.create();
-    errorPipe.create();
-
-    setSubstituterEnv();
-
-    run.pid = startProcess([&]() {
-        if (dup2(toPipe.readSide, STDIN_FILENO) == -1)
-            throw SysError("dupping stdin");
-        if (dup2(fromPipe.writeSide, STDOUT_FILENO) == -1)
-            throw SysError("dupping stdout");
-        if (dup2(errorPipe.writeSide, STDERR_FILENO) == -1)
-            throw SysError("dupping stderr");
-        execl(settings.guixProgram.c_str(), "guix", "substitute", "--query", NULL);
-        throw SysError(format("executing `%1%'") % settings.guixProgram);
-    });
-
-    run.to = toPipe.writeSide.borrow();
-    run.from = run.fromBuf.fd = fromPipe.readSide.borrow();
-    run.error = errorPipe.readSide.borrow();
-
-    toPipe.readSide.close();
-    fromPipe.writeSide.close();
-    errorPipe.writeSide.close();
-
-    /* The substituter may exit right away if it's disabled in any way
-       (e.g. copy-from-other-stores.pl will exit if no other stores
-       are configured). */
-    try {
-        getLineFromSubstituter(run);
-    } catch (EndOfFile & e) {
-        run.to.close();
-        run.from.close();
-        run.error.close();
-        run.disabled = true;
-        if (run.pid.wait(true) != 0) throw;
-    }
-}
-
-
 /* Read a line from the substituter's stdout, while also processing
    its stderr. */
-string LocalStore::getLineFromSubstituter(RunningSubstituter & run)
+string LocalStore::getLineFromSubstituter(Agent & run)
 {
     string res, err;
 
-    /* We might have stdout data left over from the last time. */
-    if (run.fromBuf.hasData()) goto haveData;
-
     while (1) {
         checkInterrupt();
 
         fd_set fds;
         FD_ZERO(&fds);
-        FD_SET(run.from, &fds);
-        FD_SET(run.error, &fds);
+        FD_SET(run.fromAgent.readSide, &fds);
+        FD_SET(run.builderOut.readSide, &fds);
 
         /* Wait for data to appear on the substituter's stdout or
            stderr. */
-        if (select(run.from > run.error ? run.from + 1 : run.error + 1, &fds, 0, 0, 0) == -1) {
+        if (select(std::max(run.fromAgent.readSide, run.builderOut.readSide) + 1, &fds, 0, 0, 0) == -1) {
             if (errno == EINTR) continue;
             throw SysError("waiting for input from the substituter");
         }
 
         /* Completely drain stderr before dealing with stdout. */
-        if (FD_ISSET(run.error, &fds)) {
+        if (FD_ISSET(run.builderOut.readSide, &fds)) {
             char buf[4096];
-            ssize_t n = read(run.error, (unsigned char *) buf, sizeof(buf));
+            ssize_t n = read(run.builderOut.readSide, (unsigned char *) buf, sizeof(buf));
             if (n == -1) {
                 if (errno == EINTR) continue;
                 throw SysError("reading from substituter's stderr");
@@ -903,23 +822,20 @@ string LocalStore::getLineFromSubstituter(RunningSubstituter & run)
         }
 
         /* Read from stdout until we get a newline or the buffer is empty. */
-        else if (run.fromBuf.hasData() || FD_ISSET(run.from, &fds)) {
-        haveData:
-            do {
-                unsigned char c;
-                run.fromBuf(&c, 1);
-                if (c == '\n') {
-                    if (!err.empty()) printMsg(lvlError, "substitute: " + err);
-                    return res;
-                }
-                res += c;
-            } while (run.fromBuf.hasData());
+        else if (FD_ISSET(run.fromAgent.readSide, &fds)) {
+	    unsigned char c;
+	    readFull(run.fromAgent.readSide, (unsigned char *) &c, 1);
+	    if (c == '\n') {
+		if (!err.empty()) printMsg(lvlError, "substitute: " + err);
+		return res;
+	    }
+	    res += c;
         }
     }
 }
 
 
-template<class T> T LocalStore::getIntLineFromSubstituter(RunningSubstituter & run)
+template<class T> T LocalStore::getIntLineFromSubstituter(Agent & run)
 {
     string s = getLineFromSubstituter(run);
     T res;
@@ -934,51 +850,47 @@ PathSet LocalStore::querySubstitutablePaths(const PathSet & paths)
 
     if (!settings.useSubstitutes || paths.empty()) return res;
 
-    if (!runningSubstituter) {
-	std::unique_ptr<RunningSubstituter>fresh(new RunningSubstituter);
-	runningSubstituter.swap(fresh);
-    }
+    Agent & run = *substituter();
 
-    RunningSubstituter & run = *runningSubstituter;
-    startSubstituter(run);
-
-    if (!run.disabled) {
-	string s = "have ";
-	foreach (PathSet::const_iterator, j, paths)
-	    if (res.find(*j) == res.end()) { s += *j; s += " "; }
-	writeLine(run.to, s);
-	while (true) {
-	    /* FIXME: we only read stderr when an error occurs, so
-	       substituters should only write (short) messages to
-	       stderr when they fail.  I.e. they shouldn't write debug
-	       output. */
-	    Path path = getLineFromSubstituter(run);
-	    if (path == "") break;
-	    res.insert(path);
-	}
+    string s = "have ";
+    foreach (PathSet::const_iterator, j, paths)
+	if (res.find(*j) == res.end()) { s += *j; s += " "; }
+    writeLine(run.toAgent.writeSide, s);
+    while (true) {
+	/* FIXME: we only read stderr when an error occurs, so
+	   substituters should only write (short) messages to
+	   stderr when they fail.  I.e. they shouldn't write debug
+	   output. */
+	Path path = getLineFromSubstituter(run);
+	if (path == "") break;
+	res.insert(path);
     }
 
     return res;
 }
 
 
-void LocalStore::querySubstitutablePathInfos(PathSet & paths, SubstitutablePathInfos & infos)
+std::shared_ptr<Agent> LocalStore::substituter()
 {
-    if (!settings.useSubstitutes) return;
-
     if (!runningSubstituter) {
-	std::unique_ptr<RunningSubstituter>fresh(new RunningSubstituter);
-	runningSubstituter.swap(fresh);
+	const Strings args = { "substitute", "--query" };
+	const std::map<string, string> env = { { "_NIX_OPTIONS", settings.pack() } };
+	runningSubstituter = std::make_shared<Agent>(settings.guixProgram, args, env);
     }
 
-    RunningSubstituter & run = *runningSubstituter;
-    startSubstituter(run);
-    if (run.disabled) return;
+    return runningSubstituter;
+}
+
+void LocalStore::querySubstitutablePathInfos(PathSet & paths, SubstitutablePathInfos & infos)
+{
+    if (!settings.useSubstitutes) return;
+
+    Agent & run = *substituter();
 
     string s = "info ";
     foreach (PathSet::const_iterator, i, paths)
         if (infos.find(*i) == infos.end()) { s += *i; s += " "; }
-    writeLine(run.to, s);
+    writeLine(run.toAgent.writeSide, s);
 
     while (true) {
         Path path = getLineFromSubstituter(run);
diff --git a/nix/libstore/local-store.hh b/nix/libstore/local-store.hh
index 2e48cf03e6..9ba37219da 100644
--- a/nix/libstore/local-store.hh
+++ b/nix/libstore/local-store.hh
@@ -38,21 +38,14 @@ struct OptimiseStats
 };
 
 
-struct RunningSubstituter
-{
-    Pid pid;
-    AutoCloseFD to, from, error;
-    FdSource fromBuf;
-    bool disabled;
-    RunningSubstituter() : disabled(false) { };
-};
-
-
 class LocalStore : public StoreAPI
 {
 private:
     /* The currently running substituter or empty.  */
-    std::unique_ptr<RunningSubstituter> runningSubstituter;
+    std::shared_ptr<Agent> runningSubstituter;
+
+    /* Ensure the substituter is running and return it.  */
+    std::shared_ptr<Agent> substituter();
 
     Path linksDir;
 
@@ -178,8 +171,6 @@ public:
 
     void markContentsGood(const Path & path);
 
-    void setSubstituterEnv();
-
     void createUser(const std::string & userName, uid_t userId);
 
 private:
@@ -213,8 +204,6 @@ private:
     /* Cache for pathContentsGood(). */
     std::map<Path, bool> pathContentsGoodCache;
 
-    bool didSetSubstituterEnv;
-
     /* The file to which we write our temporary roots. */
     Path fnTempRoots;
     AutoCloseFD fdTempRoots;
@@ -262,11 +251,9 @@ private:
 
     void removeUnusedLinks(const GCState & state);
 
-    void startSubstituter(RunningSubstituter & runningSubstituter);
-
-    string getLineFromSubstituter(RunningSubstituter & run);
+    string getLineFromSubstituter(Agent & run);
 
-    template<class T> T getIntLineFromSubstituter(RunningSubstituter & run);
+    template<class T> T getIntLineFromSubstituter(Agent & run);
 
     Path createTempDirInStore();
 
diff --git a/nix/libutil/util.cc b/nix/libutil/util.cc
index 59a2981359..69f1c634a9 100644
--- a/nix/libutil/util.cc
+++ b/nix/libutil/util.cc
@@ -1173,7 +1173,7 @@ void commonChildInit(Pipe & logPipe)
 
 //////////////////////////////////////////////////////////////////////
 
-Agent::Agent(const string &command, const Strings &args)
+Agent::Agent(const string &command, const Strings &args, const std::map<string, string> &env)
 {
     debug(format("starting agent '%1%'") % command);
 
@@ -1191,6 +1191,10 @@ Agent::Agent(const string &command, const Strings &args)
 
         commonChildInit(fromAgent);
 
+	for (auto pair: env) {
+	    setenv(pair.first.c_str(), pair.second.c_str(), 1);
+	}
+
         if (chdir("/") == -1) throw SysError("changing into `/");
 
         /* Dup the communication pipes. */
diff --git a/nix/libutil/util.hh b/nix/libutil/util.hh
index 13cff44316..880b0e93b2 100644
--- a/nix/libutil/util.hh
+++ b/nix/libutil/util.hh
@@ -7,6 +7,7 @@
 #include <dirent.h>
 #include <unistd.h>
 #include <signal.h>
+#include <map>
 #include <functional>
 
 #include <cstdio>
@@ -281,8 +282,10 @@ struct Agent
     /* The process ID of the agent. */
     Pid pid;
 
-    /* The command and arguments passed to the agent.  */
-    Agent(const string &command, const Strings &args);
+    /* The command and arguments passed to the agent along with a list of
+       environment variable name/value pairs.  */
+    Agent(const string &command, const Strings &args,
+	  const std::map<string, string> &env = std::map<string, string>());
 
     ~Agent();
 };
diff --git a/po/guix/POTFILES.in b/po/guix/POTFILES.in
index 5afb13ffdb..1aec3bef3c 100644
--- a/po/guix/POTFILES.in
+++ b/po/guix/POTFILES.in
@@ -25,6 +25,7 @@ gnu/installer/newt/network.scm
 gnu/installer/newt/page.scm
 gnu/installer/newt/partition.scm
 gnu/installer/newt/services.scm
+gnu/installer/newt/substitutes.scm
 gnu/installer/newt/timezone.scm
 gnu/installer/newt/user.scm
 gnu/installer/newt/utils.scm
diff --git a/scripts/guix.in b/scripts/guix.in
index 0a3ab1f64d..e0194d6ea2 100644
--- a/scripts/guix.in
+++ b/scripts/guix.in
@@ -1,4 +1,4 @@
-#!@GUILE@ \
+#!@abs_top_builddir@/guile \
 --no-auto-compile -e main -s
 !#
 ;;; GNU Guix --- Functional package management for GNU
diff --git a/tests/glob.scm b/tests/glob.scm
index 3134069789..2a5a40c3c6 100644
--- a/tests/glob.scm
+++ b/tests/glob.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2020 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -53,7 +54,8 @@
  "foo[abc]bar" => '("foo" (set #\a #\b #\c) "bar")
  "foo[a[b]c]bar" => '("foo" (set #\a #\[ #\b #\] #\c) "bar")
  "[123]x" => '((set #\1 #\2 #\3) "x")
- "[a-z]" => '((range #\a #\z)))
+ "[a-z]" => '((range #\a #\z))
+ "**/*.scm" => '(**/ * ".scm"))
 
 (test-glob-match
  ("foo" matches "foo" (and not "foobar" "barfoo"))
@@ -64,6 +66,8 @@
  ("ab[0-9]c" matches "ab0c" "ab7c" "ab9c"
   (and not "ab-c" "ab00c" "ab3"))
  ("ab[cdefg]" matches "abc" "abd" "abg"
-  (and not "abh" "abcd" "ab[")))
+  (and not "abh" "abcd" "ab["))
+ ("foo/**/*.scm" matches "foo/bar/baz.scm" "foo/bar.scm" "foo/bar/baz/zab.scm"
+  (and not "foo/bar/baz.java" "foo/bar.smc")))
 
 (test-end "glob")
diff --git a/tests/opam.scm b/tests/opam.scm
index ec2a668307..11984b56a6 100644
--- a/tests/opam.scm
+++ b/tests/opam.scm
@@ -80,38 +80,41 @@ url {
                 (set! test-source-hash
                   (call-with-input-file file-name port-sha256))))
              (_ (error "Unexpected URL: " url)))))
-      (let ((my-package (string-append test-repo "/packages/foo/foo.1.0.0")))
-        (mkdir-p my-package)
-        (with-output-to-file (string-append my-package "/opam")
-          (lambda _
-            (format #t "~a" test-opam-file))))
-      (match (opam->guix-package "foo" #:repository test-repo)
-        (('package
-           ('name "ocaml-foo")
-           ('version "1.0.0")
-           ('source ('origin
-                      ('method 'url-fetch)
-                      ('uri "https://example.org/foo-1.0.0.tar.gz")
-                      ('sha256
-                       ('base32
-                        (? string? hash)))))
-           ('build-system 'ocaml-build-system)
-           ('propagated-inputs
-            ('quasiquote
-             (("ocaml-zarith" ('unquote 'ocaml-zarith)))))
-           ('native-inputs
-            ('quasiquote
-             (("ocaml-alcotest" ('unquote 'ocaml-alcotest))
-              ("ocamlbuild" ('unquote 'ocamlbuild)))))
-           ('home-page "https://example.org/")
-           ('synopsis "Some example package")
-           ('description "This package is just an example.")
-           ('license #f))
-         (string=? (bytevector->nix-base32-string
-                    test-source-hash)
-                   hash))
-        (x
-         (pk 'fail x #f)))))
+        (mock ((guix import opam) get-opam-repository
+               (const test-repo))
+              (let ((my-package (string-append test-repo
+                                               "/packages/foo/foo.1.0.0")))
+                (mkdir-p my-package)
+                (with-output-to-file (string-append my-package "/opam")
+                  (lambda _
+                    (format #t "~a" test-opam-file))))
+              (match (opam->guix-package "foo" #:repo test-repo)
+                (('package
+                   ('name "ocaml-foo")
+                   ('version "1.0.0")
+                   ('source ('origin
+                              ('method 'url-fetch)
+                              ('uri "https://example.org/foo-1.0.0.tar.gz")
+                              ('sha256
+                               ('base32
+                                (? string? hash)))))
+                   ('build-system 'ocaml-build-system)
+                   ('propagated-inputs
+                    ('quasiquote
+                     (("ocaml-zarith" ('unquote 'ocaml-zarith)))))
+                   ('native-inputs
+                    ('quasiquote
+                     (("ocaml-alcotest" ('unquote 'ocaml-alcotest))
+                      ("ocamlbuild" ('unquote 'ocamlbuild)))))
+                   ('home-page "https://example.org/")
+                   ('synopsis "Some example package")
+                   ('description "This package is just an example.")
+                   ('license #f))
+                 (string=? (bytevector->nix-base32-string
+                            test-source-hash)
+                           hash))
+                (x
+                 (pk 'fail x #f))))))
 
 ;; Test the opam file parser
 ;; We fold over some test cases. Each case is a pair of the string to parse and the
diff --git a/tests/substitute.scm b/tests/substitute.scm
index 6560612c40..b86ce09425 100644
--- a/tests/substitute.scm
+++ b/tests/substitute.scm
@@ -47,7 +47,8 @@ it writes to GUIX-WARNING-PORT a messages that matches ERROR-RX."
   (test-equal name
     '(1 #t)
     (let ((error-output (open-output-string)))
-      (parameterize ((guix-warning-port error-output))
+      (parameterize ((current-error-port error-output)
+                     (guix-warning-port error-output))
         (catch 'quit
           (lambda ()
             exp
@@ -57,6 +58,14 @@ it writes to GUIX-WARNING-PORT a messages that matches ERROR-RX."
                   (let ((message (get-output-string error-output)))
                     (->bool (string-match error-rx message))))))))))
 
+(define (request-substitution item destination)
+  "Run 'guix substitute --substitute' to fetch ITEM to DESTINATION."
+  (parameterize ((guix-warning-port (current-error-port)))
+    (with-input-from-string (string-append "substitute " item " "
+                                           destination "\n")
+      (lambda ()
+        (guix-substitute "--substitute")))))
+
 (define %public-key
   ;; This key is known to be in the ACL by default.
   (call-with-input-file (string-append %config-directory "/signing-key.pub")
@@ -183,6 +192,11 @@ a file for NARINFO."
 ;; Transmit these options to 'guix substitute'.
 (substitute-urls (list (getenv "GUIX_BINARY_SUBSTITUTE_URL")))
 
+;; Never use file descriptor 4, unlike what happens when invoked by the
+;; daemon.
+(%error-to-file-descriptor-4? #f)
+
+
 (test-equal "query narinfo without signature"
   ""                                              ; not substitutable
 
@@ -283,10 +297,12 @@ System: mips64el-linux\n")
 (test-quit "substitute, no signature"
     "no valid substitute"
   (with-narinfo %narinfo
-    (guix-substitute "--substitute"
-                     (string-append (%store-prefix)
-                                    "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
-                     "foo")))
+    (with-input-from-string (string-append "substitute "
+                                           (%store-prefix)
+                                           "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo"
+                                           " foo\n")
+      (lambda ()
+        (guix-substitute "--substitute")))))
 
 (test-quit "substitute, invalid hash"
     "no valid substitute"
@@ -294,10 +310,12 @@ System: mips64el-linux\n")
   (with-narinfo (string-append %narinfo "Signature: "
                                (signature-field "different body")
                                "\n")
-    (guix-substitute "--substitute"
-                     (string-append (%store-prefix)
-                                    "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
-                     "foo")))
+    (with-input-from-string (string-append "substitute "
+                                           (%store-prefix)
+                                           "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo"
+                                           " foo\n")
+      (lambda ()
+        (guix-substitute "--substitute")))))
 
 (test-quit "substitute, unauthorized key"
     "no valid substitute"
@@ -306,10 +324,12 @@ System: mips64el-linux\n")
                                 %narinfo
                                 #:public-key %wrong-public-key)
                                "\n")
-    (guix-substitute "--substitute"
-                     (string-append (%store-prefix)
-                                    "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
-                     "foo")))
+    (with-input-from-string (string-append "substitute "
+                                           (%store-prefix)
+                                           "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo"
+                                           " foo\n")
+      (lambda ()
+        (guix-substitute "--substitute")))))
 
 (test-equal "substitute, authorized key"
   "Substitutable data."
@@ -318,10 +338,9 @@ System: mips64el-linux\n")
     (dynamic-wind
       (const #t)
       (lambda ()
-        (guix-substitute "--substitute"
-                         (string-append (%store-prefix)
-                                        "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
-                         "substitute-retrieved")
+        (request-substitution (string-append (%store-prefix)
+                                             "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
+                              "substitute-retrieved")
         (call-with-input-file "substitute-retrieved" get-string-all))
       (lambda ()
         (false-if-exception (delete-file "substitute-retrieved"))))))
@@ -351,10 +370,9 @@ System: mips64el-linux\n")
                           (map (cut string-append "file://" <>)
                                (list %alternate-substitute-directory
                                      %main-substitute-directory))))
-            (guix-substitute "--substitute"
-                             (string-append (%store-prefix)
-                                            "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
-                             "substitute-retrieved"))
+            (request-substitution (string-append (%store-prefix)
+                                                 "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
+                                  "substitute-retrieved"))
           (call-with-input-file "substitute-retrieved" get-string-all))
         (lambda ()
           (false-if-exception (delete-file "substitute-retrieved")))))))
@@ -380,10 +398,9 @@ System: mips64el-linux\n")
                           (map (cut string-append "file://" <>)
                                (list %alternate-substitute-directory
                                      %main-substitute-directory))))
-            (guix-substitute "--substitute"
-                             (string-append (%store-prefix)
-                                            "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
-                             "substitute-retrieved"))
+            (request-substitution (string-append (%store-prefix)
+                                                 "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
+                                  "substitute-retrieved"))
           (call-with-input-file "substitute-retrieved" get-string-all))
         (lambda ()
           (false-if-exception (delete-file "substitute-retrieved")))))))
@@ -416,10 +433,9 @@ System: mips64el-linux\n")
                           (map (cut string-append "file://" <>)
                                (list %alternate-substitute-directory
                                      %main-substitute-directory))))
-            (guix-substitute "--substitute"
-                             (string-append (%store-prefix)
-                                            "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
-                             "substitute-retrieved"))
+            (request-substitution (string-append (%store-prefix)
+                                                 "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
+                                  "substitute-retrieved"))
           (call-with-input-file "substitute-retrieved" get-string-all))
         (lambda ()
           (false-if-exception (delete-file "substitute-retrieved")))))))
@@ -450,10 +466,9 @@ System: mips64el-linux\n")
                           (map (cut string-append "file://" <>)
                                (list %alternate-substitute-directory
                                      %main-substitute-directory))))
-            (guix-substitute "--substitute"
-                             (string-append (%store-prefix)
-                                            "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
-                             "substitute-retrieved"))
+            (request-substitution (string-append (%store-prefix)
+                                                 "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
+                                  "substitute-retrieved"))
           (call-with-input-file "substitute-retrieved" get-string-all))
         (lambda ()
           (false-if-exception (delete-file "substitute-retrieved")))))))
@@ -469,10 +484,12 @@ System: mips64el-linux\n")
                                    #:public-key %wrong-public-key))
         %main-substitute-directory
 
-      (guix-substitute "--substitute"
-                       (string-append (%store-prefix)
-                                      "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
-                       "substitute-retrieved"))))
+      (with-input-from-string (string-append "substitute "
+                                             (%store-prefix)
+                                             "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo"
+                                             " substitute-retrieved\n")
+        (lambda ()
+          (guix-substitute "--substitute"))))))
 
 (test-equal "substitute, narinfo with several URLs"
   "Substitutable data."
@@ -512,10 +529,9 @@ System: mips64el-linux\n")))
           (parameterize ((substitute-urls
                           (list (string-append "file://"
                                                %main-substitute-directory))))
-            (guix-substitute "--substitute"
-                             (string-append (%store-prefix)
-                                            "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
-                             "substitute-retrieved"))
+            (request-substitution (string-append (%store-prefix)
+                                                 "/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-foo")
+                                  "substitute-retrieved"))
           (call-with-input-file "substitute-retrieved" get-string-all))
         (lambda ()
           (false-if-exception (delete-file "substitute-retrieved")))))))
author	Marius Bakke <marius@gnu.org>	2020-12-13 01:10:06 +0100
committer	Marius Bakke <marius@gnu.org>	2020-12-13 01:10:06 +0100
commit	a7737f0ead2293536b9d0ba253de4673378a0ffa (patch)
tree	cf80318b0a9903aa56a69c316659a52f94abbe27
parent	ba47c83570b6d1824738ef5ff8580e7581990699 (diff)
parent	1adeb744560af94687eb7c3780c7145c52674070 (diff)
download	guix-a7737f0ead2293536b9d0ba253de4673378a0ffa.tar.gz