gnu: aumix: Build with '-fcommon'.

* gnu/packages/linux.scm (aumix)[arguments]: New field.
author: Ludovic Courtès <ludo@gnu.org> 2021-10-17 00:34:27 +0200
committer: Ludovic Courtès <ludo@gnu.org> 2021-10-17 00:34:27 +0200
commit: 618ffc0ad52ae0f8a467561d16d6aab05739fca0 (patch)
tree: a22907965d0c8b0dc80510539fd5bdf2633f7e3f /tests/guix-daemon.sh
parent: 258bbc4fdcc8a0538c9b151d5a8e82a82092a3cb (diff)
download: guix-618ffc0ad52ae0f8a467561d16d6aab05739fca0.tar.gz
guix-618ffc0ad52ae0f8a467561d16d6aab05739fca0.zip
0 files changed, 0 insertions, 0 deletions
diff --git a/gnu/build/jami-service.scm b/gnu/build/jami-service.scm
index 0ceb03eb02..a00785f699 100644
--- a/gnu/build/jami-service.scm
+++ b/gnu/build/jami-service.scm
@@ -153,14 +153,11 @@ implementation detail used to identify the accounts in Jami."
         (error message username))))
 
 (define (account->username account)
-  "Return USERNAME, the registered username associated with ACCOUNT, else its
-public key fingerprint."
-  (or (assoc-ref account "Account.registeredName")
-      (assoc-ref account "Account.username")))
+  "Return the public key fingerprint of ACCOUNT."
+  (assoc-ref account "Account.username"))
 
 (define (id->username id)
-  "Return USERNAME, the registered username associated with ID, else its
-public key fingerprint, else #f."
+  "Return the public key fingerprint corresponding to account with ID, else #f."
   (account->username (id->account id)))
 
 (define (get-accounts)
diff --git a/gnu/build/linux-container.scm b/gnu/build/linux-container.scm
index a0c8174721..72e3a45422 100644
--- a/gnu/build/linux-container.scm
+++ b/gnu/build/linux-container.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 David Thompson <davet@gnu.org>
-;;; Copyright © 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2017-2019, 2022 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -233,7 +233,7 @@ that host UIDs (respectively GIDs) map to in the namespace."
   ;; The parent process must initialize the user namespace for the child
   ;; before it can boot.  To negotiate this, a pipe is used such that the
   ;; child process blocks until the parent writes to it.
-  (match (socketpair PF_UNIX SOCK_STREAM 0)
+  (match (socketpair PF_UNIX (logior SOCK_CLOEXEC SOCK_STREAM) 0)
     ((child . parent)
      (let ((flags (namespaces->bit-mask namespaces)))
        (match (clone flags)
@@ -442,6 +442,10 @@ return the exit status."
   "Like 'container-excursion', but return the return value of THUNK."
   (match (pipe)
     ((in . out)
+     ;; Make sure IN and OUT are not inherited if THUNK forks + execs.
+     (fcntl in F_SETFD FD_CLOEXEC)
+     (fcntl out F_SETFD FD_CLOEXEC)
+
      (match (container-excursion pid
               (lambda ()
                 (close-port in)
diff --git a/gnu/ci.scm b/gnu/ci.scm
index 2c51ea7387..19a48bdbf1 100644
--- a/gnu/ci.scm
+++ b/gnu/ci.scm
@@ -39,9 +39,10 @@
                 #:select (gpl3+ license? license-name))
   #:use-module ((guix utils) #:select (%current-system))
   #:use-module ((guix scripts pack)
-                #:select (lookup-compressor self-contained-tarball))
+                #:select (self-contained-tarball))
   #:use-module (gnu bootloader)
   #:use-module (gnu bootloader u-boot)
+  #:use-module (gnu compression)
   #:use-module (gnu image)
   #:use-module (gnu packages)
   #:use-module (gnu packages gcc)
diff --git a/gnu/compression.scm b/gnu/compression.scm
new file mode 100644
index 0000000000..0418e80a15
--- /dev/null
+++ b/gnu/compression.scm
@@ -0,0 +1,69 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2022 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 compression)
+  #:use-module (guix gexp)
+  #:use-module (guix ui)
+  #:use-module ((gnu packages compression) #:hide (zip))
+  #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-9)
+  #:use-module (ice-9 match)
+  #:export (compressor
+            compressor?
+            compressor-name
+            compressor-extension
+            compressor-command
+            %compressors
+            lookup-compressor))
+
+;; Type of a compression tool.
+(define-record-type <compressor>
+  (compressor name extension command)
+  compressor?
+  (name       compressor-name)      ;string (e.g., "gzip")
+  (extension  compressor-extension) ;string (e.g., ".lz")
+  (command    compressor-command))  ;gexp (e.g., #~(list "/gnu/store/…/gzip"
+                                    ;                    "-9n" ))
+
+(define %compressors
+  ;; Available compression tools.
+  (list (compressor "gzip"  ".gz"
+                    #~(list #+(file-append gzip "/bin/gzip") "-9n"))
+        (compressor "lzip"  ".lz"
+                    #~(list #+(file-append lzip "/bin/lzip") "-9"))
+        (compressor "xz"    ".xz"
+                    #~(append (list #+(file-append xz "/bin/xz")
+                                    "-e")
+                              (%xz-parallel-args)))
+        (compressor "bzip2" ".bz2"
+                    #~(list #+(file-append bzip2 "/bin/bzip2") "-9"))
+        (compressor "zstd" ".zst"
+                    ;; The default level 3 compresses better than gzip in a
+                    ;; fraction of the time, while the highest level 19
+                    ;; (de)compresses more slowly and worse than xz.
+                    #~(list #+(file-append zstd "/bin/zstd") "-3"))
+        (compressor "none" "" #f)))
+
+(define (lookup-compressor name)
+  "Return the compressor object called NAME.  Error out if it could not be
+found."
+  (or (find (match-lambda
+              (($ <compressor> name*)
+               (string=? name* name)))
+            %compressors)
+      (leave (G_ "~a: compressor not found~%") name)))
diff --git a/gnu/image.scm b/gnu/image.scm
index 4a0068934e..523653dd77 100644
--- a/gnu/image.scm
+++ b/gnu/image.scm
@@ -152,7 +152,7 @@ that is not in SET, mentioning FIELD in the error message."
 
 ;; The supported image formats.
 (define-set-sanitizer validate-image-format format
-  (disk-image compressed-qcow2 docker iso9660))
+  (disk-image compressed-qcow2 docker iso9660 tarball wsl2))
 
 ;; The supported partition table types.
 (define-set-sanitizer validate-partition-table-type partition-table-type
@@ -170,8 +170,7 @@ that is not in SET, mentioning FIELD in the error message."
   (size               image-size  ;size in bytes as integer
                       (default 'guess)
                       (sanitize validate-size))
-  (operating-system   image-operating-system  ;<operating-system>
-                      (default #f))
+  (operating-system   image-operating-system)  ;<operating-system>
   (partition-table-type image-partition-table-type ; 'mbr or 'gpt
                       (default 'mbr)
                       (sanitize validate-partition-table-type))
diff --git a/gnu/installer/newt/partition.scm b/gnu/installer/newt/partition.scm
index e7a97810ac..2adb4922b4 100644
--- a/gnu/installer/newt/partition.scm
+++ b/gnu/installer/newt/partition.scm
@@ -188,7 +188,7 @@ encryption of partition ~a (label: ~a).") file-name crypt-label)
                    (if (string=? password confirmation)
                        (user-partition
                         (inherit user-part)
-                        (crypt-password password))
+                        (crypt-password (make-secret password)))
                        (begin
                          (run-error-page
                           (G_ "Password mismatch, please try again.")
@@ -795,13 +795,13 @@ by pressing the Exit button.~%~%")))
          (user-partitions (run-page eligible-devices))
          (user-partitions-with-pass (prompt-luks-passwords
                                      user-partitions))
-         (form (draw-formatting-page user-partitions)))
+         (form (draw-formatting-page user-partitions-with-pass)))
     ;; Make sure the disks are not in use before proceeding to formatting.
     (free-parted eligible-devices)
     (format-user-partitions user-partitions-with-pass)
     (installer-log-line "formatted ~a user partitions"
             (length user-partitions-with-pass))
-    (installer-log-line "user-partitions: ~a" user-partitions)
+    (installer-log-line "user-partitions: ~a" user-partitions-with-pass)
 
     (destroy-form-and-pop form)
-    user-partitions))
+    user-partitions-with-pass))
diff --git a/gnu/installer/newt/services.scm b/gnu/installer/newt/services.scm
index 9951ad2212..b22024602c 100644
--- a/gnu/installer/newt/services.scm
+++ b/gnu/installer/newt/services.scm
@@ -99,10 +99,8 @@ non-graphical system.")
       #:item->text (compose G_ system-service-name)
       #:checkbox-tree-height 5
       #:exit-button-callback-procedure
-      (lambda ()
-        (raise
-          (condition
-            (&installer-step-abort)))))))
+      (lambda _
+        (abort-to-prompt 'installer-step 'abort)))))
 
 (define (run-network-management-page)
   "Run a page to select among several network management methods."
diff --git a/gnu/installer/parted.scm b/gnu/installer/parted.scm
index 84fdbe24fb..fcc936a391 100644
--- a/gnu/installer/parted.scm
+++ b/gnu/installer/parted.scm
@@ -148,7 +148,7 @@
                         (default #f))
   (crypt-label          user-partition-crypt-label
                         (default #f))
-  (crypt-password       user-partition-crypt-password
+  (crypt-password       user-partition-crypt-password ; <secret>
                         (default #f))
   (fs-type              user-partition-fs-type
                         (default 'ext4))
@@ -1183,7 +1183,7 @@ USER-PARTITION if it is encrypted, or the plain file-name otherwise."
   "Format and open the encrypted partition pointed by USER-PARTITION."
   (let* ((file-name (user-partition-file-name user-partition))
          (label (user-partition-crypt-label user-partition))
-         (password (user-partition-crypt-password user-partition)))
+         (password (secret-content (user-partition-crypt-password user-partition))))
     (call-with-luks-key-file
      password
      (lambda (key-file)
@@ -1194,6 +1194,20 @@ USER-PARTITION if it is encrypted, or the plain file-name otherwise."
        ((run-command-in-installer) "cryptsetup" "open" "--type" "luks"
         "--key-file" key-file file-name label)))))
 
+(define (luks-ensure-open user-partition)
+  "Ensure partition pointed by USER-PARTITION is opened."
+  (unless (file-exists? (user-partition-upper-file-name user-partition))
+    (let* ((file-name (user-partition-file-name user-partition))
+           (label (user-partition-crypt-label user-partition))
+           (password (secret-content (user-partition-crypt-password user-partition))))
+      (call-with-luks-key-file
+       password
+       (lambda (key-file)
+         (installer-log-line "opening LUKS entry ~s at ~s"
+                             label file-name)
+         ((run-command-in-installer) "cryptsetup" "open" "--type" "luks"
+          "--key-file" key-file file-name label))))))
+
 (define (luks-close user-partition)
   "Close the encrypted partition pointed by USER-PARTITION."
   (let ((label (user-partition-crypt-label user-partition)))
@@ -1278,6 +1292,8 @@ respective mount-points."
                         (user-fs-type->mount-type fs-type))
                        (file-name
                         (user-partition-upper-file-name user-partition)))
+                  (when crypt-label
+                    (luks-ensure-open user-partition))
                   (mkdir-p target)
                   (installer-log-line "mounting ~s on ~s" file-name target)
                   (mount file-name target mount-type)))
diff --git a/gnu/installer/tests.scm b/gnu/installer/tests.scm
index 3c049a1c85..8785cd9a9f 100644
--- a/gnu/installer/tests.scm
+++ b/gnu/installer/tests.scm
@@ -280,6 +280,10 @@ instrumented for further testing."
        exp)))
 
   (let ((content (call-with-input-file file read-expressions)))
+    ;; XXX: Remove the file before re-writing it, to be sure there are no
+    ;; leftovers.  We shouldn't have to do that as CALL-WITH-OUTPUT-FILE uses
+    ;; the O_TRUNC flag by default.
+    (delete-file file)
     (call-with-output-file file
       (lambda (port)
         (format port "\
diff --git a/gnu/installer/user.scm b/gnu/installer/user.scm
index 224040530c..2866e4520f 100644
--- a/gnu/installer/user.scm
+++ b/gnu/installer/user.scm
@@ -17,17 +17,13 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu installer user)
+  #:use-module (gnu installer utils)
   #:use-module (guix records)
   #:use-module (guix read-print)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-9)
   #:use-module (srfi srfi-9 gnu)
-  #:export (<secret>
-            secret?
-            make-secret
-            secret-content
-
-            <user>
+  #:export (<user>
             user
             make-user
             user-name
@@ -38,16 +34,6 @@
 
             users->configuration))
 
-(define-record-type <secret>
-  (make-secret content)
-  secret?
-  (content secret-content))
-
-(set-record-type-printer!
- <secret>
- (lambda (secret port)
-   (format port "<secret>")))
-
 (define-record-type* <user>
   user make-user
   user?
diff --git a/gnu/installer/utils.scm b/gnu/installer/utils.scm
index fb62fb8896..5fd2e2d425 100644
--- a/gnu/installer/utils.scm
+++ b/gnu/installer/utils.scm
@@ -23,6 +23,8 @@
   #:use-module (guix build utils)
   #:use-module (guix i18n)
   #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-9)
+  #:use-module (srfi srfi-9 gnu)
   #:use-module (srfi srfi-19)
   #:use-module (srfi srfi-34)
   #:use-module (srfi srfi-35)
@@ -33,7 +35,12 @@
   #:use-module (ice-9 regex)
   #:use-module (ice-9 format)
   #:use-module (ice-9 textual-ports)
-  #:export (read-lines
+  #:export (<secret>
+            secret?
+            make-secret
+            secret-content
+
+            read-lines
             read-all
             nearest-exact-integer
             read-percentage
@@ -58,6 +65,16 @@
 
             with-silent-shepherd))
 
+(define-record-type <secret>
+  (make-secret content)
+  secret?
+  (content secret-content))
+
+(set-record-type-printer!
+ <secret>
+ (lambda (secret port)
+   (format port "<secret>")))
+
 (define* (read-lines #:optional (port (current-input-port)))
   "Read lines from PORT and return them as a list."
   (let loop ((line (read-line port))
diff --git a/gnu/local.mk b/gnu/local.mk
index 297571c028..78bdc113ac 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -53,6 +53,7 @@
 # Copyright © 2022 John Kehayias <john.kehayias@protonmail.com>
 # Copyright © 2022 muradm <mail@muradm.net>
 # Copyright © 2022 Hilton Chain <hako@ultrarare.space>
+# Copyright © 2022 Alex Griffin <a@ajgrf.com>
 #
 # This file is part of GNU Guix.
 #
@@ -81,6 +82,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/bootloader/u-boot.scm                     \
   %D%/bootloader/depthcharge.scm                \
   %D%/ci.scm					\
+  %D%/compression.scm				\
   %D%/home.scm					\
   %D%/home/services.scm			\
   %D%/home/services/desktop.scm			\
@@ -682,6 +684,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/services/herd.scm				\
   %D%/services/pm.scm				\
   %D%/services/rsync.scm			\
+  %D%/services/samba.scm			\
   %D%/services/sddm.scm				\
   %D%/services/spice.scm				\
   %D%/services/ssh.scm				\
@@ -716,6 +719,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/system/images/pine64.scm			\
   %D%/system/images/pinebook-pro.scm		\
   %D%/system/images/rock64.scm			\
+  %D%/system/images/wsl2.scm			\
 						\
   %D%/machine.scm				\
 						\
@@ -761,6 +765,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/tests/package-management.scm		\
   %D%/tests/reconfigure.scm			\
   %D%/tests/rsync.scm				\
+  %D%/tests/samba.scm				\
   %D%/tests/security.scm			\
   %D%/tests/security-token.scm			\
   %D%/tests/singularity.scm			\
@@ -979,9 +984,12 @@ dist_patch_DATA =						\
   %D%/packages/patches/cmake-curl-certificates-3.24.patch	\
   %D%/packages/patches/coda-use-system-libs.patch		\
   %D%/packages/patches/collectd-5.11.0-noinstallvar.patch		\
-  %D%/packages/patches/containerd-create-pid-file.patch		\
   %D%/packages/patches/combinatorial-blas-awpm.patch		\
   %D%/packages/patches/combinatorial-blas-io-fix.patch		\
+  %D%/packages/patches/connman-CVE-2022-32292.patch		\
+  %D%/packages/patches/connman-CVE-2022-32293-pt1.patch	\
+  %D%/packages/patches/connman-CVE-2022-32293-pt2.patch	\
+  %D%/packages/patches/containerd-create-pid-file.patch	\
   %D%/packages/patches/cool-retro-term-wctype.patch		\
   %D%/packages/patches/coreutils-gnulib-tests.patch		\
   %D%/packages/patches/coq-fix-envvars.patch			\
@@ -1217,7 +1225,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/gnome-online-miners-tracker-3.patch	\
   %D%/packages/patches/gnome-settings-daemon-gc.patch		\
   %D%/packages/patches/gnome-session-support-elogind.patch	\
-  %D%/packages/patches/gnome-todo-libportal.patch		\
   %D%/packages/patches/gnome-tweaks-search-paths.patch		\
   %D%/packages/patches/gnupg-CVE-2022-34903.patch		\
   %D%/packages/patches/gnupg-default-pinentry.patch		\
@@ -1322,10 +1329,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/irrlicht-link-against-needed-libs.patch	\
   %D%/packages/patches/isl-0.11.1-aarch64-support.patch	\
   %D%/packages/patches/itk-snap-alt-glibc-compat.patch		\
-  %D%/packages/patches/jami-fix-esc-bug.patch			\
-  %D%/packages/patches/json-c-0.13-CVE-2020-12762.patch	\
-  %D%/packages/patches/json-c-0.12-CVE-2020-12762.patch	\
-  %D%/packages/patches/jsoncpp-pkg-config-version.patch		\
+  %D%/packages/patches/jami-fix-crash-on-block-contact.patch	\
   %D%/packages/patches/jamvm-1.5.1-aarch64-support.patch	\
   %D%/packages/patches/jamvm-1.5.1-armv7-support.patch	\
   %D%/packages/patches/jamvm-2.0.0-aarch64-support.patch	\
@@ -1347,6 +1351,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/jfsutils-add-sysmacros.patch		\
   %D%/packages/patches/jfsutils-gcc-compat.patch		\
   %D%/packages/patches/jfsutils-include-systypes.patch		\
+  %D%/packages/patches/json-c-0.13-CVE-2020-12762.patch	\
+  %D%/packages/patches/json-c-0.12-CVE-2020-12762.patch	\
+  %D%/packages/patches/jsoncpp-pkg-config-version.patch		\
   %D%/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch	\
   %D%/packages/patches/julia-tracker-16-compat.patch		\
   %D%/packages/patches/julia-allow-parallel-build.patch		\
@@ -1599,7 +1606,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/password-store-tree-compat.patch		\
   %D%/packages/patches/pciutils-hurd-configure.patch		\
   %D%/packages/patches/pciutils-hurd-fix.patch			\
-  %D%/packages/patches/pjproject-install-libpjsua2.patch	\
+  %D%/packages/patches/plasma-framework-fix-KF5PlasmaMacros.cmake.patch \
   %D%/packages/patches/pokerth-boost.patch			\
   %D%/packages/patches/ppsspp-disable-upgrade-and-gold.patch		\
   %D%/packages/patches/pthreadpool-system-libraries.patch	\
@@ -1733,6 +1740,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-werkzeug-tests.patch		\
   %D%/packages/patches/python-zeep-Fix-pytest_httpx-test-cases.patch	\
   %D%/packages/patches/qemu-build-info-manual.patch		\
+  %D%/packages/patches/qemu-disable-aarch64-migration-test.patch	\
   %D%/packages/patches/qemu-glibc-2.27.patch 			\
   %D%/packages/patches/qemu-glibc-2.30.patch 			\
   %D%/packages/patches/qemu-fix-agent-paths.patch 		\
@@ -1762,7 +1770,7 @@ dist_patch_DATA =						\
   %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-1.5.5-unvendor-libuv.patch	\
+  %D%/packages/patches/r-httpuv-1.6.6-unvendor-libuv.patch	\
   %D%/packages/patches/ri-li-modernize_cpp.patch		\
   %D%/packages/patches/ripperx-missing-file.patch		\
   %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
diff --git a/gnu/machine/ssh.scm b/gnu/machine/ssh.scm
index 550c989c34..60d127340a 100644
--- a/gnu/machine/ssh.scm
+++ b/gnu/machine/ssh.scm
@@ -339,9 +339,13 @@ by MACHINE."
   "Raise a '&message' error condition if it is clear that deploying MACHINE's
 'system' declaration would fail."
   (define assertions
-    (append (machine-check-file-system-availability machine)
-            (machine-check-initrd-modules machine)
-            (list (machine-check-forward-update machine))))
+    (parameterize ((%current-system
+                    (machine-ssh-configuration-system
+                     (machine-configuration machine)))
+                   (%current-target-system #f))
+      (append (machine-check-file-system-availability machine)
+              (machine-check-initrd-modules machine)
+              (list (machine-check-forward-update machine)))))
 
   (define aggregate-exp
     ;; Gather all the expressions so that a single round-trip is enough to
@@ -453,6 +457,10 @@ the 'should-roll-back' field set to SHOULD-ROLL-BACK?"
 (define (deploy-managed-host machine)
   "Internal implementation of 'deploy-machine' for MACHINE instances with an
 environment type of 'managed-host."
+  (define config (machine-configuration machine))
+  (define host   (machine-ssh-configuration-host-name config))
+  (define system (machine-ssh-configuration-system config))
+
   (maybe-raise-unsupported-configuration-error machine)
   (when (machine-ssh-configuration-authorize?
          (machine-configuration machine))
@@ -466,50 +474,54 @@ have you run 'guix archive --generate-key?'")
                                        (get-string-all port))))
                                   (machine-ssh-session machine)
                                   (machine-become-command machine)))
+
   (mlet %store-monad ((_ (check-deployment-sanity machine))
                       (boot-parameters (machine-boot-parameters machine)))
-    (let* ((os (machine-operating-system machine))
-           (host (machine-ssh-configuration-host-name
-                  (machine-configuration machine)))
-           (eval (cut machine-remote-eval machine <>))
-           (menu-entries (map boot-parameters->menu-entry boot-parameters))
-           (bootloader-configuration (operating-system-bootloader os))
-           (bootcfg (operating-system-bootcfg os menu-entries)))
-      (define-syntax-rule (eval/error-handling condition handler ...)
-        ;; Return a wrapper around EVAL such that HANDLER is evaluated if an
-        ;; exception is raised.
-        (lambda (exp)
-          (lambda (store)
-            (guard (condition ((inferior-exception? condition)
-                               (values (begin handler ...) store)))
-              (values (run-with-store store (eval exp))
-                      store)))))
-
-      (mbegin %store-monad
-        (with-roll-back #f
-          (switch-to-system (eval/error-handling c
-                              (raise (formatted-message
-                                      (G_ "\
+    ;; Make sure code that check %CURRENT-SYSTEM, such as
+    ;; %BASE-INITRD-MODULES, gets to see the right value.
+    (parameterize ((%current-system system)
+                   (%current-target-system #f))
+      (let* ((os (machine-operating-system machine))
+             (eval (cut machine-remote-eval machine <>))
+             (menu-entries (map boot-parameters->menu-entry boot-parameters))
+             (bootloader-configuration (operating-system-bootloader os))
+             (bootcfg (operating-system-bootcfg os menu-entries)))
+        (define-syntax-rule (eval/error-handling condition handler ...)
+          ;; Return a wrapper around EVAL such that HANDLER is evaluated if an
+          ;; exception is raised.
+          (lambda (exp)
+            (lambda (store)
+              (guard (condition ((inferior-exception? condition)
+                                 (values (begin handler ...) store)))
+                (values (run-with-store store (eval exp)
+                                        #:system system)
+                        store)))))
+
+        (mbegin %store-monad
+          (with-roll-back #f
+            (switch-to-system (eval/error-handling c
+                                (raise (formatted-message
+                                        (G_ "\
 failed to switch systems while deploying '~a':~%~{~s ~}")
-                                      host
-                                      (inferior-exception-arguments c))))
-                            os))
-        (with-roll-back #t
-          (mbegin %store-monad
-            (upgrade-shepherd-services (eval/error-handling c
-                                         (warning (G_ "\
+                                        host
+                                        (inferior-exception-arguments c))))
+                              os))
+          (with-roll-back #t
+            (mbegin %store-monad
+              (upgrade-shepherd-services (eval/error-handling c
+                                           (warning (G_ "\
 an error occurred while upgrading services on '~a':~%~{~s ~}~%")
-                                                  host
-                                                  (inferior-exception-arguments
-                                                   c)))
-                                       os)
-            (install-bootloader (eval/error-handling c
-                                  (raise (formatted-message
-                                          (G_ "\
+                                                    host
+                                                    (inferior-exception-arguments
+                                                     c)))
+                                         os)
+              (install-bootloader (eval/error-handling c
+                                    (raise (formatted-message
+                                            (G_ "\
 failed to install bootloader on '~a':~%~{~s ~}~%")
-                                          host
-                                          (inferior-exception-arguments c))))
-                                bootloader-configuration bootcfg)))))))
+                                            host
+                                            (inferior-exception-arguments c))))
+                                  bootloader-configuration bootcfg))))))))
 
 
 ;;;
diff --git a/gnu/packages/accessibility.scm b/gnu/packages/accessibility.scm
index 22e70b737a..499d79b8c8 100644
--- a/gnu/packages/accessibility.scm
+++ b/gnu/packages/accessibility.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2018, 2021, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Andrew Miloradovsky <andrew@interpretmath.pw>
 ;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2022 Hunter Jozwiak <hunter.t.joz@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,6 +29,7 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system glib-or-gtk)
+  #:use-module (guix build-system meson)
   #:use-module (gnu packages)
   #:use-module (gnu packages lisp)
   #:use-module (gnu packages ocaml)
@@ -316,3 +318,34 @@ works with every X Window System based GUI (depends only on libX11); or as an
 assistant for graphic designers, who need to select individual pixels.")
     ;; Licensed either under Expat or GPLv2+.
     (license (list license:expat license:gpl2+))))
+
+(define-public espeakup
+  (package
+    (name "espeakup")
+    (version "0.90")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/linux-speakup/espeakup")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0lmjwafvfxy07zn18v3dzjwwpnid2xffgvy2dzlwkbns8gb60ds2"))))
+    (build-system meson-build-system)
+    (native-inputs (list pkg-config))
+    (inputs (list espeak-ng alsa-lib))
+    (license license:gpl3+)
+    (synopsis "Bridge for espeak and speakup")
+    (description
+     "Espeakup is a bridge between the speakup driver implemented in
+the Linux kernel and the espeak-ng text to speach synthesizer.
+In order for this package to work, you need to have the following
+kernel modules built:
+@itemize @bullet
+@item
+CONFIG_SPEAKUP=m
+@item
+CONFIG_SPEAKUP_SOFT=m
+@end itemize")
+    (home-page "ttps://github.com/linux-speakup/espeakup")))
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 5fb621e027..668d710739 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -2506,20 +2506,24 @@ characters can be replaced as well, as can UTF-8 characters.")
 (define-public tree
   (package
     (name "tree")
-    (version "2.0.3")
+    (version "2.0.4")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "http://mama.indstate.edu/users/ice/tree/src/tree-"
+                    "https://mama.indstate.edu/users/ice/tree/src/tree-"
                     version ".tgz"))
               (sha256
-               (base32 "079vda37d5i3nfx12wx81z6r6bxynv2jww1z1hjziiwxbxxyf55s"))))
+               (base32 "0x7s9wxvf83fw4qah16kapswl2277pybw3d514zrlms9g0cr5smh"))))
     (build-system gnu-build-system)
     (arguments
      (list
        #:phases
        #~(modify-phases %standard-phases
-           (delete 'configure))         ; No configure script.
+           (delete 'configure)          ; No configure script.
+           (add-after 'unpack 'fix-manpage-version
+             (lambda _
+               (substitute* "doc/tree.1"
+                 (("Tree 2\\.0\\.0") (string-append "Tree " #$version))))))
        #:tests? #f                      ; No check target.
        #:make-flags
        #~(list (string-append "PREFIX=" #$output)
@@ -2529,7 +2533,7 @@ characters can be replaced as well, as can UTF-8 characters.")
      "Tree is a recursive directory listing command that produces a depth
 indented listing of files, which is colorized ala dircolors if the LS_COLORS
 environment variable is set and output is to tty.")
-    (home-page "http://mama.indstate.edu/users/ice/tree/")
+    (home-page "https://mama.indstate.edu/users/ice/tree/")
     (license license:gpl2+)))
 
 (define-public lr
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 87fcca746b..183d84c549 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -221,7 +221,7 @@ the real span of the lattice.")
 (define-public pari-gp
   (package
     (name "pari-gp")
-    (version "2.13.4")
+    (version "2.15.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -229,11 +229,10 @@ the real span of the lattice.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "11g1pkrj12dmggj1n6r00ijpnmk3f3dpqsf1h51q34hmmv79xpmw"))))
+                "11anfn2lmixi83208p8qxjhwkrrad9s2qqfrl3wy9m0n1lg8ax74"))))
     (build-system gnu-build-system)
-    (native-inputs
-     `(("texlive" ,(texlive-updmap.cfg
-                    (list texlive-amsfonts)))))
+    (native-inputs (list (texlive-updmap.cfg
+                          (list texlive-amsfonts))))
     (inputs (list gmp libx11 perl readline))
     (arguments
      '(#:make-flags '("all")
@@ -261,7 +260,7 @@ PARI is also available as a C library to allow for faster computations.")
 (define-public gp2c
   (package
    (name "gp2c")
-   (version "0.0.12")
+   (version "0.0.13")
    (source (origin
             (method url-fetch)
             (uri (string-append
@@ -269,7 +268,7 @@ PARI is also available as a C library to allow for faster computations.")
                   version ".tar.gz"))
             (sha256
               (base32
-                "039ip7qkwwv46wrcdrz7y12m30kazzkjr44kqbc0h137g4wzd7zf"))))
+                "0dlxlrwwvhmjljjzsq95fsm14j5n5353snd92b0pdg9ylzn784r6"))))
    (build-system gnu-build-system)
    (native-inputs (list perl))
    (inputs (list pari-gp))
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 29f1e6fc36..13ffdd74d3 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -29,6 +29,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages autotools)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
@@ -1054,6 +1055,29 @@ attempting to maintain ISTP compliance
 @end itemize\n")
     (license license:expat)))
 
+(define-public python-ephem
+  (package
+    (name "python-ephem")
+    (version "4.1.3")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "ephem" version))
+              (sha256
+               (base32
+                "0smmm3l8csnw9rrimh8mpyjrm80jaafjl184spnji98vk22qd8bz"))))
+    (build-system python-build-system)
+    (native-inputs (list tzdata))
+    (home-page "https://rhodesmill.org/pyephem/")
+    (synopsis "Compute positions of the planets and stars")
+    (description
+     "PyEphem provides an @code{ephem} Python package for performing
+high-precision astronomy computations.
+
+The name ephem is short for the word ephemeris, which is the traditional term
+for a table giving the position of a planet, asteroid, or comet for a series
+of dates.")
+    (license license:expat)))
+
 (define-public python-photutils
   (package
     (name "python-photutils")
@@ -1823,6 +1847,27 @@ N-Chilada and RAMSES AMR outputs.")
      (modify-inputs (package-inputs libsep)
        (prepend python-numpy)))))
 
+(define-public python-suntime
+  (package
+    (name "python-suntime")
+    (version "1.2.5")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "suntime" version))
+              (sha256
+               (base32
+                "0ja64w293wjx76q3z18ikx4rdihwkbj6pnjpbs82ycyyzhfnbpz4"))))
+    (build-system python-build-system)
+    (propagated-inputs (list python-dateutil))
+    (home-page "https://github.com/SatAgro/suntime")
+    (synopsis "Sunset and sunrise time calculation python library")
+    (description
+     "Python library doing sunrise and sunset time calculation.
+
+Takes a WGS84 (GPS) latitude/longitude as input as well as an UTC or local
+datetime object.")
+    (license license:lgpl3+)))
+
 (define-public python-asdf
   (package
     (name "python-asdf")
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 46278d326c..10b70bab06 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6313,14 +6313,14 @@ of gene-level counts.")
 (define-public r-valr
   (package
     (name "r-valr")
-    (version "0.6.4")
+    (version "0.6.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "valr" version))
        (sha256
         (base32
-         "0dd41irvibh6rwi52bw4zg4m7wpyihlp1kdkb8fdji3csw2fiz4k"))))
+         "1674sqclgi4l5r544pjjsblzl1ix2cy961jpkncb3ym47y6c1msw"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-broom
@@ -6993,14 +6993,14 @@ fitting of some classes of graphical Markov models.")
 (define-public r-perfmeas
   (package
     (name "r-perfmeas")
-    (version "1.2.1")
+    (version "1.2.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "PerfMeas" version))
        (sha256
         (base32
-         "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
+         "13yjk0kwpbsqwl056hzf0zj2br1mk4faqcn1whdfxmq348c14hjb"))))
     (properties `((upstream-name . "PerfMeas")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7976,14 +7976,14 @@ abnormal copy number.")
 (define-public r-htscluster
   (package
     (name "r-htscluster")
-    (version "2.0.8")
+    (version "2.0.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "HTSCluster" version))
        (sha256
         (base32
-         "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
+         "0scn4fsfmlkzxibfhsh6krm2cl9c8hsmyjgn48k9dyjf0ylyxg9n"))))
     (properties `((upstream-name . "HTSCluster")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13147,14 +13147,14 @@ rate} (FDR).")
 (define-public r-activedriverwgs
   (package
     (name "r-activedriverwgs")
-    (version "1.1.2")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ActiveDriverWGS" version))
        (sha256
         (base32
-         "13b5yazgv9kckcp6gck183mh1m0q8lc5ixagmcy9s8kv2wz7wq45"))))
+         "0xnplgwxd197a4d422bsxg753q158i12ils16awd1cw30wafdxkk"))))
     (properties
      `((upstream-name . "ActiveDriverWGS")))
     (build-system r-build-system)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4e9de568a0..a034bf134e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7273,6 +7273,228 @@ sequence.")
     (supported-systems '("i686-linux" "x86_64-linux"))
     (license license:bsd-3)))
 
+(define-public r-gutils
+  (let ((commit "10e36c7b580aacb2d952140a3fdd82418aaddea6")
+        (revision "1"))
+    (package
+      (name "r-gutils")
+      (version (git-version "0.2.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/mskilab/gUtils")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1wq9kd1afzy7ii510r20c4n9fkykj6p15q5c85ws27h1q5w4ghxy"))))
+      (properties `((upstream-name . "gUtils")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-biocgenerics
+             r-data-table
+             r-genomeinfodb
+             r-genomicranges
+             r-iranges
+             r-matrix
+             r-s4vectors
+             r-stringr))
+      (home-page "https://github.com/mskilab/gUtils")
+      (synopsis "Additional capabilities and speed for GenomicRanges operations")
+      (description
+       "This is an R package providing additional capabilities and speed for
+@code{GenomicRanges} operations.")
+      (license license:gpl2))))
+
+(define-public r-bamutils
+  (let ((commit "639dba901f16944fa1b7a8d7048701ba86a2cdb8")
+        (revision "1"))
+    (package
+      (name "r-bamutils")
+      (version (git-version "0.0.0.9000" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/mskilab/bamutils/")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0qwby2v5rydnipvf1iv1wz9nf02yq98k0xbc4inf9mqc54jwacs0"))))
+      (properties `((upstream-name . "bamUtils")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-abind
+             r-biocgenerics
+             r-data-table
+             r-genomicalignments
+             r-genomicranges
+             r-gutils
+             r-rsamtools
+             r-variantannotation))
+      (home-page "https://github.com/mskilab/bamutils/")
+      (synopsis "Utility functions for manipulating BAMs")
+      (description "This package provides utility functions for manipulating
+BAM files.")
+      (license license:gpl2))))
+
+(define-public r-gtrack
+  (let ((commit "a694fa36cedafca2658da79fc8e5b673535b15e5")
+        (revision "1"))
+    (package
+      (name "r-gtrack")
+      (version (git-version "0.1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/mskilab/gTrack/")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "070qlrbqsbj9max2vx740zigqh0ymvnw2pm1ia5la3wb4dbfwh2b"))))
+      (properties `((upstream-name . "gTrack")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-biocgenerics
+             r-data-table
+             r-genomeinfodb
+             r-genomicranges
+             r-gutils
+             r-iranges
+             r-matrix
+             r-rcolorbrewer
+             r-rcpp
+             r-rcurl
+             r-rtracklayer
+             r-s4vectors))
+      (home-page "https://github.com/mskilab/gTrack/")
+      (synopsis "Plot tracks of complex genomic data across multiple genomic windows")
+      (description
+       "This package provides an object for plotting GRanges, RleList, UCSC
+file formats, and ffTrack objects in multi-track panels.")
+      (license license:gpl2))))
+
+(define-public r-gchain
+  (let ((commit "dc393e8dd0d8efaf36270c04d7112db8553db36a")
+        (revision "1"))
+    (package
+      (name "r-gchain")
+      (version (git-version "0.2.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/mskilab/gChain/")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "105wgi5w2fhwq1grsvj6zjigwg0sny3z7zr577q8ki3qffjwdkj0"))))
+      (properties `((upstream-name . "gChain")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-bamutils
+             r-biostrings
+             r-data-table
+             r-genomicalignments
+             r-genomicranges
+             r-gtrack
+             r-gutils
+             r-matrix
+             r-rtracklayer))
+      (home-page "https://github.com/mskilab/gChain/")
+      (synopsis "Additional capabilities and speed for GenomicRanges operations")
+      (description
+       "This R package provides additional capabilities and speed for
+GenomicRanges operations.")
+      (license license:gpl2))))
+
+(define-public r-skitools
+  (let ((commit "22d107d32f063eb891eb5e7fb36996d1c0b0d2bc")
+        (revision "1"))
+    (package
+      (name "r-skitools")
+      (version (git-version "0.0.0.9000" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/mskilab/skitools/")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1977d9bkdk9l2n6niahfj9vksh9l1ga4g7c3b3x27lj1gc0qgr4z"))))
+      (properties `((upstream-name . "skitools")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-biostrings
+             r-complexheatmap
+             r-data-table
+             r-devtools
+             r-dt
+             r-gchain
+             r-genomeinfodb
+             r-genomicranges
+             r-ggplot2
+             r-gplots
+             r-gutils
+             r-htmlwidgets
+             r-hwriter
+             r-igraph
+             r-iranges
+             r-plotly
+             r-rcolorbrewer
+             r-reshape2
+             r-s4vectors
+             r-stringr
+             r-variantannotation))
+      (home-page "https://github.com/mskilab/skitools/")
+      (synopsis "Various mskilab R utilties")
+      (description
+       "This package provides R miscellaneous utilities for basic data
+manipulation, debugging, visualization, lsf management, and common mskilab
+tasks.")
+      (license license:expat))))
+
+(define-public r-chromunity
+  (let ((commit "09fce8bc12cb84b45a6ea25bf8db6e5b75113d4f")
+        (revision "1"))
+    (package
+      (name "r-chromunity")
+      (version (git-version "0.0.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/mskilab/chromunity")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0lp0h614k8fq6h9gpbylk4chh7q6w4qda8lx03ajrpppxmg7al2d"))))
+      (properties `((upstream-name . "chromunity")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-arrow
+             r-biocgenerics
+             r-data-table
+             r-gchain
+             r-genomicranges
+             r-gutils
+             r-igraph
+             r-magrittr
+             r-mass
+             r-matrix
+             r-pbmcapply
+             r-plyr
+             r-r6
+             r-skitools
+             r-zoo))
+      (home-page "https://github.com/mskilab/chromunity")
+      (synopsis "Discovery of communities in Pore-C concatemers")
+      (description "This is a package for the discovery of communities in
+Pore-C concatemers.")
+      (license license:gpl3))))
+
 (define-public r-presto
   (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad")
         (revision "0"))
@@ -12514,6 +12736,12 @@ fasta subsequences.")
              (substitute* '("requirements.txt"
                             "cooler.egg-info/requires.txt")
                (("cytoolz.*<.*0.11") "cytoolz"))))
+         ;; This version of flake8 just won't work with this version of
+         ;; pytest, because of dependency pinning.
+         (add-after 'unpack 'do-not-use-flake8
+           (lambda _
+             (substitute* "setup.cfg"
+               (("addopts = --flake8") "addopts = "))))
          (add-after 'unpack 'patch-tests
            (lambda _
              (substitute* "tests/test_create.py"
@@ -12522,10 +12750,13 @@ fasta subsequences.")
                                 "access to genome.ucsc.edu\")\n"
                                 "def test_roundtrip")))
              (substitute* "tests/test_util.py"
-              (("def test_fetch_chromsizes")
-                 (string-append "@pytest.mark.skip(reason=\"requires network "
-                                "access to genome.ucsc.edu\")\n"
-                                "def test_fetch_chromsizes")))
+               (("def test_fetch_chromsizes")
+                (string-append "@pytest.mark.skip(reason=\"requires network "
+                               "access to genome.ucsc.edu\")\n"
+                               "def test_fetch_chromsizes"))
+               ;; See https://github.com/open2c/cooler/issues/287
+               (("skipif\\(six.PY2, reason=\"Scipy on Py2 is too old\"")
+                "skip(reason=\"Scipy is too new\""))
              ;; This test depends on ipytree, which contains a lot of minified
              ;; JavaScript.
              (substitute* "tests/test_fileops.py"
@@ -15541,47 +15772,49 @@ for the analysis and visualization of raw nanopore signal.")
     (license license:mpl2.0)))
 
 (define-public python-pyvcf
-  (package
-    (name "python-pyvcf")
-    (version "0.6.8")
-    ;; Use git, because the PyPI tarballs lack test data.
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
+  (let ((commit "476169cd457ba0caa6b998b301a4d91e975251d9")
+        (revision "0"))
+    (package
+      (name "python-pyvcf")
+      (version (git-version "0.6.8" revision commit))
+      ;; Use git, because the PyPI tarballs lack test data.
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
                (url "https://github.com/jamescasbon/PyVCF.git")
                ;; Latest release is not tagged.
-               (commit "bfcedb9bad1a14074ac4526ffdb610611e073810")))
-        (file-name (git-file-name name version))
-        (sha256
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
           (base32
-            "0c7lsssns3zp8fh2ibllzzra003srg9vbxqzmq6654akbzdb7lrf"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-        (modify-phases %standard-phases
-          (add-after 'unpack 'patch-sample-script
-            (lambda _
-              ;; Add Python 3 compatibility to this sample script.
-              (substitute* "scripts/vcf_sample_filter.py"
-                (("print (.*)\n" _ arg)
-                 (string-append "print(" arg ")\n")))))
-          (add-after 'install 'remove-installed-tests
-            ;; Do not install test files.
-            (lambda* (#:key inputs outputs #:allow-other-keys)
-              (delete-file-recursively (string-append
+           "0qf9lwj7r2hjjp4bd4vc7nayrhblfm4qcqs4dbd43a6p4bj2jv5p"))))
+      (build-system python-build-system)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'patch-sample-script
+             (lambda _
+               ;; Add Python 3 compatibility to this sample script.
+               (substitute* "scripts/vcf_sample_filter.py"
+                 (("print (.*)\n" _ arg)
+                  (string-append "print(" arg ")\n")))))
+           (add-after 'install 'remove-installed-tests
+             ;; Do not install test files.
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (delete-file-recursively (string-append
                                          (site-packages inputs outputs)
                                          "/vcf/test")))))))
-    (native-inputs
-     ;; Older setuptools is needed for use_2to3.
-     (list python-cython python-setuptools))
-    (propagated-inputs
-     (list python-pysam python-rpy2))
-    (home-page "https://github.com/jamescasbon/PyVCF")
-    (synopsis "Variant Call Format parser for Python")
-    (description "This package provides a @acronym{VCF,Variant Call Format}
+      (native-inputs
+       ;; Older setuptools is needed for use_2to3.
+       (list python-cython python-setuptools-for-tensorflow))
+      (propagated-inputs
+       (list python-pysam python-rpy2))
+      (home-page "https://github.com/jamescasbon/PyVCF")
+      (synopsis "Variant Call Format parser for Python")
+      (description "This package provides a @acronym{VCF,Variant Call Format}
 parser for Python.")
-    (license license:expat)))
+      (license license:expat))))
 
 (define-public nanosv
   (package
@@ -15996,6 +16229,43 @@ BigWig files, as well as efficient region coverage summary over intervals from
 both types of files.")
     (license license:expat)))
 
+(define-public mudskipper
+  (package
+    (name "mudskipper")
+    (version "0.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "mudskipper" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1y7fnlz6irmxdmv6bxzm95w4ws4vzldlrh8npvgxmdnrz9pgb1dv"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #false    ;fail because the "mudskipper" crate cannot be found
+       #:cargo-inputs
+       (("rust-bio" ,rust-bio-0.39)
+        ("rust-bio-types" ,rust-bio-types-0.12)
+        ("rust-clap" ,rust-clap-2)
+        ("rust-coitrees" ,rust-coitrees-0.2)
+        ("rust-env-logger" ,rust-env-logger-0.9)
+        ("rust-fnv" ,rust-fnv-1)
+        ("rust-indicatif" ,rust-indicatif-0.16)
+        ("rust-libradicl" ,rust-libradicl-0.4)
+        ("rust-linecount" ,rust-linecount-0.1)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-num-cpus" ,rust-num-cpus-1)
+        ("rust-rust-htslib" ,rust-rust-htslib-0.38))))
+    (native-inputs
+     (list cmake pkg-config))
+    (inputs
+     (list zlib xz))
+    (home-page "https://github.com/OceanGenomics/mudskipper")
+    (synopsis "Convert genomic alignments to transcriptomic BAM/RAD files.")
+    (description "Mudskipper is a tool for projecting genomic alignments to
+transcriptomic coordinates.")
+    (license license:bsd-3)))
+
 (define-public r-ascat
   (package
    (name "r-ascat")
@@ -16155,6 +16425,29 @@ integration, exploration, and analysis of high-dimensional single-cell
 cytometry and imaging data.")
       (license license:expat))))
 
+(define-public r-compgenomrdata
+  (let ((commit "24484cb77631e1123ead6c329b9d62c160e600c6")
+        (revision "1"))
+    (package
+      (name "r-compgenomrdata")
+      (version (git-version "0.1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/compgenomr/compGenomRData")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "06gdvz4m4qlb1ylv10qfx09zv4c95cm7nps4y2s67m946kv8czv8"))))
+      (properties `((upstream-name . "compGenomRData")))
+      (build-system r-build-system)
+      (home-page "https://github.com/compgenomr/compGenomRData")
+      (synopsis "Data for Computational Genomics with R book")
+      (description "This package provides data for the book \"Computational
+Genomics with R\".")
+      (license license:gpl3))))
+
 (define-public r-cytonorm
   (let ((commit "e4b9d343ee65db3c422800f1db3e77c25abde987")
         (revision "1"))
diff --git a/gnu/packages/busybox.scm b/gnu/packages/busybox.scm
index 4468d71088..ccfe91257b 100644
--- a/gnu/packages/busybox.scm
+++ b/gnu/packages/busybox.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2014 John Darrington <jmd@gnu.org>
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018–2022 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2022 LuHui <luhux76@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -45,66 +46,74 @@
                 "0jfm9fik7nv4w21zqdg830pddgkdjmplmna9yjn9ck1lwn4vsps1"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (add-before 'configure 'disable-timestamps
-           (lambda _
-             (setenv "KCONFIG_NOTIMESTAMP" "1")))
-         (add-before 'configure 'disable-taskset
-           ;; This feature fails its tests in the build environment,
-           ;; was default 'n' until after 1.26.2.
-           (lambda _
-             (substitute* "util-linux/taskset.c"
-               (("default y") "default n"))))
-         (replace 'configure
-           (lambda* (#:key make-flags #:allow-other-keys)
-             (apply invoke "make" "defconfig" make-flags)))
-         (add-after 'configure 'dont-install-to-usr
-           (lambda _
-             (substitute* ".config"
-               (("# CONFIG_INSTALL_NO_USR is not set")
-                "CONFIG_INSTALL_NO_USR=y"))))
-         (replace 'check
-           (lambda* (#:key make-flags #:allow-other-keys)
-             (substitute* '("testsuite/du/du-s-works"
-                            "testsuite/du/du-works")
-               (("/bin") "/etc"))  ; there is no /bin but there is a /etc
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-before 'configure 'disable-timestamps
+                 (lambda _
+                   (setenv "KCONFIG_NOTIMESTAMP" "1")))
+               (add-before 'configure 'disable-taskset
+                 ;; This feature fails its tests in the build environment,
+                 ;; was default 'n' until after 1.26.2.
+                 (lambda _
+                   (substitute* "util-linux/taskset.c"
+                     (("default y") "default n"))))
+               (replace 'configure
+                 (lambda* (#:key make-flags #:allow-other-keys)
+                   (apply invoke "make" "defconfig" make-flags)))
+               (add-after 'configure 'dont-install-to-usr
+                 (lambda _
+                   (substitute* ".config"
+                     (("# CONFIG_INSTALL_NO_USR is not set")
+                      "CONFIG_INSTALL_NO_USR=y"))))
+               (replace 'check
+                 (lambda* (#:key tests? make-flags #:allow-other-keys)
+                   (substitute* '("testsuite/du/du-s-works"
+                                  "testsuite/du/du-works")
+                     (("/bin") "/etc")) ; there is no /bin but there is a /etc
 
-             ;; There is no /usr/bin or /bin - replace it with /gnu/store
-             (substitute* "testsuite/cpio.tests"
-               (("/usr/bin") (%store-directory))
-               (("usr") (car (filter (negate string-null?)
-                                     (string-split (%store-directory) #\/)))))
+                   ;; There is no /usr/bin or /bin - replace it with
+                   ;; /gnu/store.
+                   (substitute* "testsuite/cpio.tests"
+                     (("/usr/bin") (%store-directory))
+                     (("usr") (car (filter (negate string-null?)
+                                           (string-split (%store-directory) #\/)))))
 
-             (substitute* "testsuite/date/date-works-1"
-               (("/bin/date") (which "date")))
+                   (substitute* "testsuite/date/date-works-1"
+                     (("/bin/date") (which "date")))
 
-             (substitute* "testsuite/start-stop-daemon.tests"
-              (("/bin/false") (which "false")))
+                   (substitute* "testsuite/start-stop-daemon.tests"
+                     (("/bin/false") (which "false")))
 
-             ;; The pidof tests assume that pid 1 is called "init" but that is not
-             ;; true in guix build environment
-             (substitute* "testsuite/pidof.tests"
-               (("-s init") "-s $(cat /proc/1/comm)"))
+                   ;; The pidof tests assume that pid 1 is called "init" but
+                   ;; that is not 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.
-             (delete-file "testsuite/which/which-uses-default-path")
-             (rmdir "testsuite/which")
+                   ;; 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.
+                   (delete-file "testsuite/which/which-uses-default-path")
+                   (rmdir "testsuite/which")
 
-             (apply invoke "make"
-                     ;; "V=1"
-                     "SKIP_KNOWN_BUGS=1"
-                     "SKIP_INTERNET_TESTS=1"
-                     "check" make-flags)))
-         (replace 'install
-           (lambda* (#:key outputs make-flags #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (apply invoke "make"
-                       (string-append "CONFIG_PREFIX=" out)
-                       "install" make-flags)))))))
-    (native-inputs (list perl ; needed to generate the man pages (pod2man)
+                   (when tests?
+                     (apply invoke "make"
+                            ;; "V=1"
+                            "SKIP_KNOWN_BUGS=1"
+                            "SKIP_INTERNET_TESTS=1"
+                            "check" make-flags))))
+               (replace 'install
+                 (lambda* (#:key outputs make-flags #:allow-other-keys)
+                   (let ((out (assoc-ref outputs "out")))
+                     (apply invoke "make"
+                            (string-append "CONFIG_PREFIX=" out)
+                            "install" make-flags)))))
+           #:make-flags
+           #~(let ((target #$(%current-target-system)))
+               (if target
+                   (list (string-append "CROSS_COMPILE=" target "-"))
+                   '()))))
+    (native-inputs (list perl     ; needed to generate the man pages (pod2man)
                          ;; The following are needed by the tests.
                          inetutils
                          (@ (gnu packages base) which)
diff --git a/gnu/packages/calendar.scm b/gnu/packages/calendar.scm
index 715d158241..6583810277 100644
--- a/gnu/packages/calendar.scm
+++ b/gnu/packages/calendar.scm
@@ -401,7 +401,7 @@ traditional Chinese characters.")
     (license (list license:gpl2+ license:lgpl2.1+))))
 
 (define-public gsimplecal
-  (let ((version "2.2"))
+  (let ((version "2.4.1"))
     (package
       (name "gsimplecal")
       (version version)
@@ -411,16 +411,17 @@ traditional Chinese characters.")
                       (url "https://github.com/dmedvinsky/gsimplecal/")
                       (commit (string-append "v" version))))
                 (file-name (git-file-name name version))
-                (sha256 (base32
-                         "1qyf65l088dqsz25hm6s1cv18j52yaias0llqvpqwjfnvssa5cxg"))
+                (sha256
+                 (base32
+                  "0ypnq9q6v2l8jg0ah31d8502jig1rk2bz749ljj97wk0rg1rixpi"))
                 (modules '((guix build utils)))))
       (build-system gnu-build-system)
       (inputs (list gtk+))
-      (native-inputs
-       (list autoconf automake pkg-config))
+      (native-inputs (list autoconf automake pkg-config))
       (home-page "https://dmedvinsky.github.io/gsimplecal/")
       (synopsis "Lightweight calendar applet")
-      (description "@command{gsimplecal} is a lightweight calendar application
+      (description
+       "@command{gsimplecal} is a lightweight calendar application
 written in C++ using GTK.  Launched once, it pops up a small calendar applet,
 launched again it closes the running instance.  It can additionally be
 configured to show the current time in different timezones.")
diff --git a/gnu/packages/clojure.scm b/gnu/packages/clojure.scm
index 9876192f5f..622e43ac48 100644
--- a/gnu/packages/clojure.scm
+++ b/gnu/packages/clojure.scm
@@ -204,14 +204,14 @@ designs.")
 (define-public clojure-tools
   (package
     (name "clojure-tools")
-    (version "1.11.1.1149")
+    (version "1.11.1.1165")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://download.clojure.org/install/clojure-tools-"
                            version
                            ".tar.gz"))
-       (sha256 (base32 "196wl87br8zg3npfwpr5c1q0knxd1810vzgb0b6h195hyjf6i210"))
+       (sha256 (base32 "1lg97waqfcgzr3dz5426fbc4kqcsavpbqil2iyjm1dw3zrfa8ysi"))
        ;; Remove AOT compiled JAR.  The other JAR only contains uncompiled
        ;; Clojure source code.
        (snippet
diff --git a/gnu/packages/connman.scm b/gnu/packages/connman.scm
index f4e6e43ec8..80869f890e 100644
--- a/gnu/packages/connman.scm
+++ b/gnu/packages/connman.scm
@@ -53,7 +53,10 @@
         (uri (string-append "mirror://kernel.org/linux/network/connman/"
                             "connman-" version ".tar.xz"))
         (sha256
-         (base32 "12g5ilcnymx6i45z3359yds3cgd2dfqjyncfm92hqlymzps41yvr"))))
+         (base32 "12g5ilcnymx6i45z3359yds3cgd2dfqjyncfm92hqlymzps41yvr"))
+        (patches (search-patches "connman-CVE-2022-32292.patch"
+                                 "connman-CVE-2022-32293-pt1.patch"
+                                 "connman-CVE-2022-32293-pt2.patch"))))
     (build-system gnu-build-system)
     (arguments
      (list #:configure-flags
diff --git a/gnu/packages/containers.scm b/gnu/packages/containers.scm
index 029f0d4ba4..59eea423a1 100644
--- a/gnu/packages/containers.scm
+++ b/gnu/packages/containers.scm
@@ -274,7 +274,7 @@ configure network interfaces in Linux containers.")
 (define-public podman
   (package
     (name "podman")
-    (version "4.2.0")
+    (version "4.2.1")
     (source
      (origin
        (method git-fetch)
@@ -282,7 +282,7 @@ configure network interfaces in Linux containers.")
              (url "https://github.com/containers/podman")
              (commit (string-append "v" version))))
        (sha256
-        (base32 "00wyjppd11hznmals9ax4s2qjklj6p1vfz4jjkp50bk8q4blxfbj"))
+        (base32 "0ph8gf5gk9z1hm1v5kv924dipswvgrz0sgk23plnh2q0vbnh4wvv"))
        (file-name (git-file-name name version))))
 
     (build-system gnu-build-system)
diff --git a/gnu/packages/coq.scm b/gnu/packages/coq.scm
index bbb34df27d..60937af750 100644
--- a/gnu/packages/coq.scm
+++ b/gnu/packages/coq.scm
@@ -8,6 +8,7 @@
 ;;; Copyright © 2020 Robin Green <greenrd@greenrd.org>
 ;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz>
 ;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2022 Garek Dyszel <garekdyszel@disroot.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -43,6 +44,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system ocaml)
   #:use-module (guix download)
+  #:use-module (guix gexp)
   #:use-module (guix git-download)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
@@ -52,7 +54,7 @@
 (define-public coq-core
   (package
     (name "coq-core")
-    (version "8.15.2")
+    (version "8.16.0")
     (source
      (origin
        (method git-fetch)
@@ -62,7 +64,7 @@
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1m6dilfbp9q8j8sya4ap82q72m3a4mq6m96gzvi6vgv04cr6r33c"))
+         "1rp4m2yjldsz0kj7p2fsc312n740fr8kg99jlsk8aq3h524qz2h8"))
        (patches (search-patches "coq-fix-envvars.patch"))))
     (native-search-paths
      (list (search-path-specification
@@ -148,7 +150,7 @@ It is developed using Objective Caml and Camlp5.")
     (propagated-inputs
      (list coq coq-ide-server))
     (inputs
-     `(("lablgtk3" ,lablgtk3)))))
+     (list lablgtk3 ocaml-lablgtk3-sourceview3))))
 
 (define-public proof-general
   ;; The latest release is from 2016 and there has been more than 450 commits
@@ -240,7 +242,7 @@ provers.")
 (define-public coq-flocq
   (package
     (name "coq-flocq")
-    (version "4.0.0")
+    (version "4.1.0")
     (source
      (origin
        (method git-fetch)
@@ -250,7 +252,7 @@ provers.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "159ykkhxz7zms28r4v8jjccapl5vv00csdz29mfy83lwrv5b6rwk"))))
+         "1yscj1120wch6myakaia03j11qji416v78ylx842d23hrbaqwmw5"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf automake ocaml which coq))
@@ -287,7 +289,7 @@ inside Coq.")
 (define-public coq-gappa
   (package
     (name "coq-gappa")
-    (version "1.5.1")
+    (version "1.5.2")
     (source
      (origin
        (method git-fetch)
@@ -297,7 +299,7 @@ inside Coq.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "18y4mv44mcgyam77rf4xs7l06mg7pxx1qli3yvs0kklmnnvwa463"))))
+         "0l65ah81yj9vabgkwqh47c02qvscvl8nl60gqn1qrs47dx1pi80q"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf
@@ -315,7 +317,9 @@ inside Coq.")
     (arguments
      `(#:configure-flags
        (list (string-append "COQUSERCONTRIB=" (assoc-ref %outputs "out")
-                            "/lib/coq/user-contrib"))
+                            "/lib/coq/user-contrib")
+             (string-append "OCAMLFIND_DESTDIR=" (assoc-ref %outputs "out")
+                            "/lib/ocaml/site-lib"))
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'fix-remake
@@ -345,7 +349,7 @@ assistant.")
 (define-public coq-mathcomp
   (package
     (name "coq-mathcomp")
-    (version "1.14.0")
+    (version "1.15.0")
     (source
      (origin
        (method git-fetch)
@@ -354,7 +358,7 @@ assistant.")
              (commit (string-append "mathcomp-" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1rqg47dg84wr6d9v2pzna54dm62awcm8xdwx4dqwdwhf58fjxa9i"))))
+        (base32 "158zl36zbvi5qx2nqbfnrg00jpgp6hjr5hmls7d8d0421ar6b67i"))))
     (build-system gnu-build-system)
     (native-inputs
      (list ocaml which coq))
@@ -431,7 +435,7 @@ theorems between the two libraries.")
 (define-public coq-bignums
   (package
     (name "coq-bignums")
-    (version "8.15.0")
+    (version "8.16.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -440,7 +444,7 @@ theorems between the two libraries.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "093klwlhclgyrba1iv18dyz1qp5f0lwiaa7y0qwvgmai8rll5fns"))))
+                "07ndnm7pndmai3a2bkcmwjfjzfaqyq19c5an15hmhgmd0rdy4z8c"))))
     (build-system gnu-build-system)
     (native-inputs
      (list ocaml coq))
@@ -450,7 +454,9 @@ theorems between the two libraries.")
      `(#:tests? #f ; No test target.
        #:make-flags
        (list (string-append "COQLIBINSTALL=" (assoc-ref %outputs "out")
-                            "/lib/coq/user-contrib"))
+                            "/lib/coq/user-contrib")
+             (string-append "COQPLUGININSTALL=" (assoc-ref %outputs "out")
+                            "/lib/ocaml/site-lib/"))
        #:phases
        (modify-phases %standard-phases
          (delete 'configure))))
@@ -463,7 +469,7 @@ provides BigN, BigZ, BigQ that used to be part of Coq standard library.")
 (define-public coq-interval
   (package
     (name "coq-interval")
-    (version "4.4.0")
+    (version "4.5.2")
     (source
      (origin
        (method git-fetch)
@@ -473,7 +479,7 @@ provides BigN, BigZ, BigQ that used to be part of Coq standard library.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1rlcbv1nqm7zv60n63lca6nnxcq3c18akgzl72s1n3h89gvhs87z"))))
+         "138vgb0bq6wkygrhkahjgb9spwpzc6x6kkycj2qnf5naxx1z412w"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf automake ocaml which coq))
@@ -486,7 +492,9 @@ provides BigN, BigZ, BigQ that used to be part of Coq standard library.")
     (arguments
      `(#:configure-flags
        (list (string-append "COQUSERCONTRIB=" (assoc-ref %outputs "out")
-                            "/lib/coq/user-contrib"))
+                            "/lib/coq/user-contrib")
+             (string-append "OCAMLFIND_DESTDIR=" (assoc-ref %outputs "out")
+                            "/lib/ocaml/site-lib"))
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'fix-remake
@@ -557,11 +565,11 @@ uses Ltac to synthesize the substitution operation.")
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/mattam82/Coq-Equations")
-                    (commit (string-append "v" version "-8.15"))))
+                    (commit (string-append "v" version "-8.16"))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1vfcfpsp9zyj0sw0cwibk76nj6n0r6gwh8m1aa3lbvc0b1kbm32k"))))
+                "08f756vgdd1wklkarg0b93j4n5mhkqm5ixxrhyb23dcv2dwhc8yg"))))
     (build-system gnu-build-system)
     (native-inputs
      (list ocaml coq camlp5))
@@ -571,7 +579,10 @@ uses Ltac to synthesize the substitution operation.")
      `(#:test-target "test-suite"
        #:make-flags (list (string-append "COQLIBINSTALL="
                                          (assoc-ref %outputs "out")
-                                         "/lib/coq/user-contrib"))
+                                         "/lib/coq/user-contrib")
+                          (string-append "COQPLUGININSTALL="
+                                         (assoc-ref %outputs "out")
+                                         "/lib/ocaml/site-lib/"))
        #:phases
        (modify-phases %standard-phases
          (replace 'configure
@@ -685,3 +696,78 @@ for goals involving set operations.
 @end itemize")
     (home-page "https://gitlab.mpi-sws.org/iris/stdpp")
     (license license:bsd-3)))
+
+(define-public coq-mathcomp-finmap
+  (package
+    (name "coq-mathcomp-finmap")
+    (version "1.5.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/math-comp/finmap")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1k72wpp15xa5ag358jl8a71gschng0bgbaqjx0l5a0in6x5adafh"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(;; No tests supplied in Makefile.common.
+       ;; The project doesn't appear to have plans to include tests in
+       ;; the future.
+       #:tests? #f
+       #:make-flags (list (string-append "COQLIBINSTALL="
+                                         (assoc-ref %outputs "out")
+                                         "/lib/coq/user-contrib"))
+       #:phases (modify-phases %standard-phases
+                  (delete 'configure))))
+    (inputs (list coq coq-stdlib coq-mathcomp which))
+    (synopsis "Finite sets and finite types for coq-mathcomp")
+    (description
+     "This library is an extension of coq-mathcomp which supports finite sets
+and finite maps on choicetypes (rather than finite types).  This includes
+support for functions with finite support and multisets.  The library also
+contains a generic order and set libary, which will eventually be used to
+subsume notations for finite sets.")
+    (home-page "https://math-comp.github.io/")
+    (license license:cecill-b)))
+
+(define-public coq-mathcomp-bigenough
+  (package
+    (name "coq-mathcomp-bigenough")
+    (version "1.0.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/math-comp/bigenough")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "02f4dv4rz72liciwxb2k7acwx6lgqz4381mqyq5854p3nbyn06aw"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(;; No references to tests in Makefile.common.
+       ;; It doesn't appear as though tests will be included
+       ;; by the packaged project in the future.
+       #:tests? #f
+       #:make-flags ,#~(list (string-append "COQBIN="
+                                            #$(this-package-input "coq-core")
+                                            "/bin/")
+                             (string-append "COQMF_COQLIB="
+                                            (assoc-ref %outputs "out")
+                                            "/lib/ocaml/site-lib/coq")
+                             (string-append "COQLIBINSTALL="
+                                            (assoc-ref %outputs "out")
+                                            "/lib/coq/user-contrib"))
+       #:phases (modify-phases %standard-phases
+                  (delete 'configure))))
+    (propagated-inputs (list coq coq-core coq-mathcomp which))
+    (home-page "https://math-comp.github.io/")
+    (synopsis "Small library to do epsilon - N reasoning")
+    (description
+     "The package is used for reasoning with big enough objects (mostly
+natural numbers).  This package is essentially for backward compatibility
+purposes as @code{bigenough} will be subsumed by the near tactics.  The
+formalization is based on the Mathematical Components library.")
+    (license license:cecill-b)))
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5cdb37075e..da9482b1c0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -287,14 +287,14 @@ etc.")
 (define-public r-datawizard
   (package
     (name "r-datawizard")
-    (version "0.5.0")
+    (version "0.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "datawizard" version))
        (sha256
         (base32
-         "022bbfaszbpml3i281cal7z0y1i380i1zjnhk1ldy5r535vs9cgq"))))
+         "1r89h5npv8iwsvylkpazfpcadgh55zd336rz8hndbzp0w9dcmpli"))))
     (properties `((upstream-name . "datawizard")))
     (build-system r-build-system)
     (propagated-inputs
@@ -382,13 +382,13 @@ visualization of their differences.")
 (define-public r-dixontest
   (package
     (name "r-dixontest")
-    (version "1.0.3")
+    (version "1.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dixonTest" version))
        (sha256
-        (base32 "1a3yc30g5rbb0jhm2b0iir5i1dy4jyl67spkhx4yysg4snz131wv"))))
+        (base32 "0gz39s1z987bg56vwrpcs14wzyf7p07s7l7z9napz0i38564wsdq"))))
     (properties `((upstream-name . "dixonTest")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
@@ -603,14 +603,14 @@ pronounceable identifiers.")
 (define-public r-googlesheets4
   (package
     (name "r-googlesheets4")
-    (version "1.0.0")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "googlesheets4" version))
        (sha256
         (base32
-         "0yncqwv9l5knyrv88ys5gwcv44hl1j0mbklpins6v7f9m9v7s40a"))))
+         "14b5lzn6vjn72mw7vf3lzm2ppbjf0wr0n6sw0v5r6h4lk37cnki8"))))
     (properties `((upstream-name . "googlesheets4")))
     (build-system r-build-system)
     (propagated-inputs
@@ -692,14 +692,14 @@ easier.")
 (define-public r-rticles
   (package
     (name "r-rticles")
-    (version "0.23")
+    (version "0.24")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rticles" version))
        (sha256
         (base32
-         "1ipblw3rmkma22jl2hf1pyfm6l8k31zcmm3swmwii6k0x7khiav1"))))
+         "05idvyfjfa4f244km4sxripg8gndvganx5s0ch00xbi4cqnlr2pq"))))
     (properties `((upstream-name . "rticles")))
     (build-system r-build-system)
     (propagated-inputs
@@ -714,17 +714,24 @@ for authoring journal articles and conference submissions.")
 (define-public r-babelwhale
   (package
     (name "r-babelwhale")
-    (version "1.0.3")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "babelwhale" version))
        (sha256
-        (base32 "0ph825dwvr48fhamy1l5564linz7cj7b9sj511as77f1yqycv4a2"))))
+        (base32 "01l8vwyz3bx0iks6cjs5y9ifdsnc1p1yqp4i0kzqd1gjhycizv6y"))))
     (properties `((upstream-name . "babelwhale")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-crayon r-dplyr r-dynutils r-processx r-purrr))
+     (list r-crayon
+           r-digest
+           r-dplyr
+           r-dynutils
+           r-fs
+           r-glue
+           r-processx
+           r-purrr))
     (home-page "https://github.com/dynverse/babelwhale")
     (synopsis "Talking to Docker and Singularity containers")
     (description
@@ -1016,13 +1023,13 @@ known as Dynamic Linear Models.")
 (define-public r-zoo
   (package
     (name "r-zoo")
-    (version "1.8-10")
+    (version "1.8-11")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "zoo" version))
               (sha256
                (base32
-                "0izd66dywq6qd62hdp64apncainrrb9mgmm19wf6a8jc03c858n9"))))
+                "19cw09bhwj2qyd72765ym1cm2wmhh801ccif889nzq5gfpw513l4"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-lattice))
@@ -1259,14 +1266,14 @@ scale-sensitive information.")
 (define-public r-ggvenndiagram
   (package
     (name "r-ggvenndiagram")
-    (version "1.2.0")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggVennDiagram" version))
        (sha256
         (base32
-         "1mjs488npnxd53nsw936iw2vzv7z38h8d02pm4lwrz4i83jg3www"))))
+         "1l4cincm7c2q9x3djiv1lm9bvivaqk7kincx19b8f760wz9hp74k"))))
     (properties `((upstream-name . "ggVennDiagram")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1277,8 +1284,8 @@ scale-sensitive information.")
            r-purrr
            r-rvenn
            r-sf
-           r-stringr
-           r-tibble))
+           r-tibble
+           r-yulab-utils))
     (native-inputs (list r-knitr))
     (home-page "https://github.com/gaospecial/ggVennDiagram")
     (synopsis "Implementention of the Venn diagram using ggplot2")
@@ -1342,16 +1349,17 @@ axis} (SMA), and @dfn{ranged major axis} (RMA).")
 (define-public r-ggpmisc
   (package
     (name "r-ggpmisc")
-    (version "0.4.7")
+    (version "0.5.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "ggpmisc" version))
               (sha256
                (base32
-                "1z1ncnlbhy38ml2rdq43jbw33z7fmy0b6xp7wcwwqxy44c7y34zx"))))
+                "1i7cfmhmgih3hn0zr5yn33ziznfa3a4j8hkn237bv7jckwzpklxw"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-dplyr
+     (list r-confintr
+           r-dplyr
            r-generics
            r-ggplot2
            r-ggpp
@@ -1524,13 +1532,13 @@ available as companion packages.")
 (define-public r-scales
   (package
     (name "r-scales")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "scales" version))
        (sha256
-        (base32 "1pq2rrix6a5gsi8xw38viiydp1bsxxmcmyy7dv9q8gkb1qj50p8q"))))
+        (base32 "027daznawr9dy0z9s99lh64i4am691hdir01n7gr7vmgpmnkwiar"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-farver
@@ -1742,13 +1750,13 @@ excellent candidate for labeling of a polygon.")
 (define-public r-poorman
   (package
     (name "r-poorman")
-    (version "0.2.5")
+    (version "0.2.6")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "poorman" version))
               (sha256
                (base32
-                "05h7rjgri0b5a1jd0388p7lqvvg0y8z6g42f9bxc80jg1z730axr"))))
+                "0x1pk00ca7wjxnqfh1jphgsxcrq37s0c1nawv52yh5qgc4z0m3ij"))))
     (properties `((upstream-name . "poorman")))
     (build-system r-build-system)
     (native-inputs (list r-knitr))
@@ -2016,13 +2024,13 @@ read a protected key.")
 (define-public r-astsa
   (package
     (name "r-astsa")
-    (version "1.15")
+    (version "1.16")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "astsa" version))
        (sha256
-        (base32 "0mllsq0xdqkviyvs77lq565r1vznsj1qp9cnlj5p48k9v76d7arp"))))
+        (base32 "09872vkqb180cwprdfr3cn85jhazlc4vjdj6pjc70s06bh834f3w"))))
     (properties `((upstream-name . "astsa")))
     (build-system r-build-system)
     (home-page "https://github.com/nickpoison/astsa/")
@@ -2118,21 +2126,24 @@ single step.")
 (define-public r-rvest
   (package
     (name "r-rvest")
-    (version "1.0.2")
+    (version "1.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rvest" version))
        (sha256
-        (base32 "1905vxgnj3q09l1wf6rwxpbpydznp06nbkrclnc05j2415z4gfw9"))))
+        (base32 "07hws9infwchy19smrcd9m6c0jii0bdn335yxqk3ramgj5ryyrd4"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-httr
+     (list r-cli
+           r-glue
+           r-httr
            r-lifecycle
            r-magrittr
            r-rlang
            r-selectr
            r-tibble
+           r-withr
            r-xml2))
     (native-inputs
      (list r-knitr))
@@ -2170,14 +2181,14 @@ package is a port of the Python package @code{cssselect}.")
 (define-public r-reprex
   (package
     (name "r-reprex")
-    (version "2.0.1")
+    (version "2.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "reprex" version))
        (sha256
         (base32
-         "09k4rasp7mz6n796dsklcbc5l7prljiznrm7fra16qybr9kqcv8f"))))
+         "14khx09yzn97xhags48lvym1g37h1l2ymvw6r1jlldhjc7i1cnx8"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-callr
@@ -2186,6 +2197,7 @@ package is a port of the Python package @code{cssselect}.")
            r-fs
            r-glue
            r-knitr
+           r-lifecycle
            r-rlang
            r-rmarkdown
            r-rstudioapi
@@ -2226,14 +2238,14 @@ same time tries to group instances from the same class together.")
 (define-public r-callr
   (package
     (name "r-callr")
-    (version "3.7.1")
+    (version "3.7.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "callr" version))
        (sha256
         (base32
-         "1vc986d571nwmb5lw5rq3d38z4qw36lr94s3apz50c2v79xsbqrp"))))
+         "01q3b0w1cbrryvv1dwvnyd3j1f09xmhnwg1wskc51r3r4qhqmnhj"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-r6 r-processx))
@@ -2268,14 +2280,14 @@ mixture models.")
 (define-public r-readxl
   (package
     (name "r-readxl")
-    (version "1.4.0")
+    (version "1.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "readxl" version))
        (sha256
         (base32
-         "1xwi4k5si48hwkgfc59icfmp9dzlvfri59k5fsgn96zp9713k4mb"))))
+         "1ym11mldwj31lgk5av264v8b2zn7fmq5nd30rnm1pchgjizvpgpn"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cellranger r-cpp11 r-progress r-tibble))
@@ -2324,14 +2336,14 @@ the personalised models.")
 (define-public r-modelr
   (package
     (name "r-modelr")
-    (version "0.1.8")
+    (version "0.1.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "modelr" version))
        (sha256
         (base32
-         "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
+         "1jd9vxirj5ii4ac0ka07g0rcq1c8yqv06jg27nmvp5a6kvlgvs8h"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-broom
@@ -2393,16 +2405,16 @@ Zucchini.")
 (define-public r-httpuv
   (package
     (name "r-httpuv")
-    (version "1.6.5")
+    (version "1.6.6")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "httpuv" version))
               (sha256
                (base32
-                "0mlilxh2mlrsbbrncla2rg02crr8nnajv649d8whx7ayr8lkdxpm"))
+                "14qjf7bpl7pay89b7vi2vccl342q8xs6101a9x6qijy54k9myfa1"))
               ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
               ;; only contains fixes for building on Solaris.
-              (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch"))
+              (patches (search-patches "r-httpuv-1.6.6-unvendor-libuv.patch"))
               (modules '((guix build utils)))
               ;; Cannot unbundle http-parser, because it contains local
               ;; modifications.
@@ -3213,13 +3225,13 @@ application framework for R, making it easy to create attractive dashboards.")
 (define-public r-shinyfiles
   (package
     (name "r-shinyfiles")
-    (version "0.9.2")
+    (version "0.9.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shinyFiles" version))
        (sha256
-        (base32 "1l4a4v9ivxkj2vx6xw4z3pk7a8px23icppcgvgpybibq2j74pglg"))))
+        (base32 "11kjq0vw5c98lzrg80m9w917lkgw5im2h9wgk1b84vlaxrjy2wja"))))
     (properties `((upstream-name . "shinyFiles")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3868,14 +3880,14 @@ including functions for geolocation and routing.")
 (define-public r-haven
   (package
     (name "r-haven")
-    (version "2.5.0")
+    (version "2.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "haven" version))
        (sha256
         (base32
-         "1x5g6kjrzcyarbjz91f4aaspx7rb50qs6a9y29mzr3mjq4dk305m"))
+         "0w0aqm0z4h0rm1f7fylm1mbv79p43y2r795w64wczcd0jwh4ch4z"))
        (modules '((guix build utils)))
        (snippet
         ;; unvendor readstat
@@ -4037,13 +4049,13 @@ Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
 (define-public r-paletteer
   (package
     (name "r-paletteer")
-    (version "1.4.0")
+    (version "1.4.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "paletteer" version))
               (sha256
                (base32
-                "1m0h1p0cbmmi0rk157qyrgcz57pw0syadskrnfa4vs7hm1rndp3m"))))
+                "0vj945cgpfhmbd98mcj167mgshghv32dxh8m4ngxs6i4q4y5blm7"))))
     (properties `((upstream-name . "paletteer")))
     (build-system r-build-system)
     (propagated-inputs (list r-prismatic r-rematch2 r-rlang r-rstudioapi))
@@ -4059,14 +4071,14 @@ a streamlined API.")
 (define-public r-palmerpenguins
   (package
     (name "r-palmerpenguins")
-    (version "0.1.0")
+    (version "0.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "palmerpenguins" version))
        (sha256
         (base32
-         "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x"))))
+         "1d1h3bfx750is4qqj4w00rcigk9rrdy69bvd5bgqz5y7ls5x8h1a"))))
     (properties
      `((upstream-name . "palmerpenguins")))
     (build-system r-build-system)
@@ -4744,13 +4756,13 @@ curve to a data matrix in arbitrary dimensions.")
 (define-public r-prismatic
   (package
     (name "r-prismatic")
-    (version "1.1.0")
+    (version "1.1.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "prismatic" version))
               (sha256
                (base32
-                "1f6k11hcll33g2wbadjhm91pm5h4khg4zd8g9fzs3m9xlqpfaywh"))))
+                "013i0mq4n8s2zbzvfrz1vjcn2a6l98bamslkcv1a3cn70gpphja9"))))
     (properties `((upstream-name . "prismatic")))
     (build-system r-build-system)
     (propagated-inputs (list r-farver))
@@ -4785,13 +4797,13 @@ way.")
 (define-public r-restrserve
   (package
     (name "r-restrserve")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RestRserve" version))
        (sha256
-        (base32 "03mlzhs2k728kwy6csp60m7qy8n9ma5dd37j87rzh07fcdlx8wim"))))
+        (base32 "1xfcp0y9l31815g1jk33mnkb6z68qpjl0gb4fj7f4578kx3v1c8p"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-checkmate
@@ -5303,14 +5315,14 @@ topics for ecologists (ISBN 978-0-691-12522-0).")
 (define-public r-lpsolve
   (package
     (name "r-lpsolve")
-    (version "5.6.15")
+    (version "5.6.16")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lpSolve" version))
        (sha256
         (base32
-         "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
+         "0amvxki4l2sp60adcc6ra7kbqjrfv55gbn6kasq04klihi8ix88q"))))
     (properties `((upstream-name . "lpSolve")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/lpSolve")
@@ -5519,13 +5531,13 @@ available in a vignette.")
 (define-public r-progressr
   (package
     (name "r-progressr")
-    (version "0.10.1")
+    (version "0.11.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "progressr" version))
        (sha256
-        (base32 "1ldf7hqsz8vbjggz31990sqqyhrbiilzcnyla1krjlkg595h50wg"))))
+        (base32 "1nbc6vvsyqa1gvh1a1m4prnvng88wsa0r35i9fiwq84a6j18qrnq"))))
     (properties `((upstream-name . "progressr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5941,14 +5953,14 @@ by base R methods related to model fitting.")
 (define-public r-broom
   (package
     (name "r-broom")
-    (version "1.0.0")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "broom" version))
        (sha256
         (base32
-         "04hlwiqkj7c9cf357dgjfgg5a6mpicg6vzvwwcqjkq69nzbsr18n"))))
+         "14i8729m38nxf5q344isgq4006p3b50wi3q8jgckxqphhnj5lpjb"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-backports
@@ -6243,14 +6255,14 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.")
 (define-public r-jomo
   (package
     (name "r-jomo")
-    (version "2.7-3")
+    (version "2.7-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "jomo" version))
        (sha256
         (base32
-         "0qq03zspmh8x2c8w882ynsw7wshr9b0fyrpwnqx5yc1xlzrqffcx"))))
+         "1zck7p872k080hyfs0hibq7v13zmsry1jdlnq7k33ff1iljbq99d"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-lme4 r-mass r-ordinal r-survival r-tibble))
@@ -6739,14 +6751,14 @@ statistics, etc.")
 (define-public r-scatterplot3d
   (package
     (name "r-scatterplot3d")
-    (version "0.3-41")
+    (version "0.3-42")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "scatterplot3d" version))
        (sha256
         (base32
-         "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
+         "05jjdiam5w0znb114vc90zahclj22pqj1zzvr96nr10s1vkxvzm9"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
     (synopsis "3D scatter plot")
@@ -6802,17 +6814,15 @@ plots in @code{ggplot2}.")
 (define-public r-cli
   (package
     (name "r-cli")
-    (version "3.3.0")
+    (version "3.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cli" version))
        (sha256
         (base32
-         "0qqd4mscv8ndjbji7knprdlv2hhyk35gazagvapbjzq1p6yfpaf3"))))
+         "0mxsls49g8m5vrak64b9mpsgw3mh8hnb1xxn56skbn4qb1hppbff"))))
     (build-system r-build-system)
-    (propagated-inputs
-     (list r-glue))
     (home-page "https://github.com/r-lib/cli#readme")
     (synopsis "Helpers for developing command line interfaces")
     (description "This package provides a suite of tools designed to build
@@ -7030,13 +7040,13 @@ iVAT).")
 (define-public r-xfun
   (package
     (name "r-xfun")
-    (version "0.31")
+    (version "0.33")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xfun" version))
        (sha256
-        (base32 "0dgjkrlwl6rxmvdn6s1xrbiaa53hkfx2s7rqrbrc7c6shbkg6sfi"))))
+        (base32 "0v7f84gqsb94zff4x64478fssjg0sbis9m34vsxnjyw6ab9c5ys5"))))
     (build-system r-build-system)
     ;; knitr itself depends on xfun
     #;
@@ -7153,14 +7163,14 @@ estimated from a given sample.")
 (define-public r-pillar
   (package
     (name "r-pillar")
-    (version "1.8.0")
+    (version "1.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pillar" version))
        (sha256
         (base32
-         "0vxkg451s5kwkg0m8d9dnr8gl5s0pgi8mxcm39ry5vgdj8v47ijj"))))
+         "1v47dm2v4nlswd1gmgcx5c7yrgn1ksdfr9lqkc63jf2nkv6af1ig"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cli
@@ -7221,14 +7231,14 @@ packages that work with genomic data.")
 (define-public r-tinytex
   (package
     (name "r-tinytex")
-    (version "0.40")
+    (version "0.41")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tinytex" version))
        (sha256
         (base32
-         "13fqhg0yrzc28b39hpr4jip9w0q9yzhzxrczlf0q2yh45kdplpiz"))))
+         "1fhnh53fg8l4qyignvgz0nk5nqmljyykn8gpvq82nr7c051rfqaz"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-xfun))
@@ -7349,14 +7359,14 @@ vectors.")
 (define-public r-statnet-common
   (package
     (name "r-statnet-common")
-    (version "4.6.0")
+    (version "4.7.0")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "statnet.common" version))
         (sha256
           (base32
-            "07djgc6qbxahiy5v15lfayxbj4188lxsb8xcs7hnbm2hic953bfx"))))
+            "1cx1h1yzs8jjxk10y2h0wl69caspzgx5wdqp36dp4sxm0sk335xn"))))
     (properties
       `((upstream-name . "statnet.common")))
     (build-system r-build-system)
@@ -7923,14 +7933,14 @@ chaotic time series analysis.")
 (define-public r-urca
   (package
     (name "r-urca")
-    (version "1.3-0")
+    (version "1.3-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "urca" version))
        (sha256
         (base32
-         "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
+         "1wg9f691pif59xds43gnnw77mmzc9xpnhhvaksk2b0szffvaifj3"))))
     (build-system r-build-system)
     (propagated-inputs (list r-nlme))
     (native-inputs (list gfortran))
@@ -7944,14 +7954,14 @@ applied econometric analysis.")
 (define-public r-cubature
   (package
     (name "r-cubature")
-    (version "2.0.4.4")
+    (version "2.0.4.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cubature" version))
        (sha256
         (base32
-         "0sfmcy5xpa40w3qn0jbg7b802wksl5k8glz9jpx77n159wn3nyq8"))))
+         "08whkhvn218089r930spn97m91vv1njgh2amksia8l3rbf7127x8"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-rcpp))
@@ -8089,14 +8099,14 @@ creation and manipulation of WAVE audio files.")
 (define-public r-np
   (package
     (name "r-np")
-    (version "0.60-11")
+    (version "0.60-14")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "np" version))
        (sha256
         (base32
-         "1a9kzn37cddwfdki5zjmzanxp75pccdjnsvqfrh84hhcsy51pcx3"))))
+         "0v6mhcwdnqj5kjxwrzcqlff021ih2jdarwmikdm5bvjfwi8pyarl"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-boot r-cubature r-quadprog r-quantreg))
@@ -8392,14 +8402,14 @@ systems.")
 (define-public r-radiant-data
   (package
     (name "r-radiant-data")
-    (version "1.4.4")
+    (version "1.4.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "radiant.data" version))
        (sha256
         (base32
-         "1lj8zz9zg7kys9rkjxn9p5z6l944dk2bx6idlxal59yhy4ql2i4p"))
+         "1vas0bkpngwxybmpdcaimha2r008prnli4b3lgjbjfkzpgm966d1"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -8619,14 +8629,14 @@ specific S3-method.")
 (define-public r-vim
   (package
     (name "r-vim")
-    (version "6.1.1")
+    (version "6.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "VIM" version))
        (sha256
         (base32
-         "0fbpm6y3hhiw8srnbc38k19b859jcqzsh78ib8yvj86gck5av0bm"))))
+         "1r0myxcx8y1a3fkf9ssk882f09snn2j6zilsygpld32hahn4k9xg"))))
     (properties `((upstream-name . "VIM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8818,14 +8828,14 @@ evaluated by the @dfn{Akaike Information Criterion} (AIC).")
 (define-public r-arules
   (package
     (name "r-arules")
-    (version "1.7-3")
+    (version "1.7-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "arules" version))
        (sha256
         (base32
-         "05g6ik4z87g83nlicmb380331f84sqchvv1vch49zb7rq6v8gw6r"))))
+         "0pmikfq1phs73lmvhb4j9rlxj3z7kbp9wb619q2gqxpi9948raij"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-generics r-matrix))
@@ -8909,14 +8919,14 @@ misclassification probabilities of different models.")
 (define-public r-zip
   (package
     (name "r-zip")
-    (version "2.2.0")
+    (version "2.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "zip" version))
        (sha256
         (base32
-         "1n5ryjdj3i16b4mdp29wapgaklz3yzas5k8ffx7q6fa0jry9i5cz"))))
+         "08hl0sqiwh9my9ivkvkig044w7ppk8h8n38j3i0kjcc1fh43v1ql"))))
     (build-system r-build-system)
     (home-page "https://github.com/gaborcsardi/zip")
     (synopsis "Cross-platform Zip compression")
@@ -9294,14 +9304,14 @@ finance, conversion from and to JSON, and many other applications.")
 (define-public r-dtplyr
   (package
     (name "r-dtplyr")
-    (version "1.2.1")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dtplyr" version))
        (sha256
         (base32
-         "1wyhhn16mvdj55k2xsh7vy489l7xk4mkz7pjrw16z87awk6yjh16"))))
+         "1m72ac7461mlvanj1krpmfp2ljl3c2k5nw6zrahc66vhcgz2hngq"))))
     (properties `((upstream-name . "dtplyr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9574,14 +9584,14 @@ always locate the files relative to your project root.")
 (define-public r-reticulate
   (package
     (name "r-reticulate")
-    (version "1.25")
+    (version "1.26")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "reticulate" version))
        (sha256
         (base32
-         "0b1szzsqyc8wcfpkn5517bb1ds064vs2hky71my3p74kfngay991"))))
+         "1ibliic3qp597nskak2bfa6iyl721ssgcavwvfaf1c71plilimrz"))))
     (build-system r-build-system)
     (arguments
      (list
@@ -9887,14 +9897,14 @@ clustering.")
 (define-public r-factominer
   (package
     (name "r-factominer")
-    (version "2.4")
+    (version "2.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "FactoMineR" version))
        (sha256
         (base32
-         "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr"))))
+         "0xcg4vjs5v9k28hhxhkfkks7nvpxpp2cvim00kh67f4pq041c9l1"))))
     (properties `((upstream-name . "FactoMineR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9902,12 +9912,14 @@ clustering.")
            r-cluster
            r-dt
            r-ellipse
+           r-emmeans
            r-flashclust
            r-ggplot2
            r-ggrepel
            r-lattice
            r-leaps
            r-mass
+           r-multcompview
            r-scatterplot3d))
     (native-inputs
      (list r-knitr))
@@ -10003,14 +10015,14 @@ results to the user.")
 (define-public r-hdf5r
   (package
     (name "r-hdf5r")
-    (version "1.3.5")
+    (version "1.3.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hdf5r" version))
        (sha256
         (base32
-         "0bv2q4ir73sbk5ra2q4mc8wbcmiwkws8k0mjlnx9ysi2mdrm3dw7"))))
+         "16iin6krx2c50wm4d1id71v3kci6djvlari3ahic25vw1dg1k81l"))))
     (build-system r-build-system)
     (inputs
      (list hdf5 zlib))
@@ -10182,14 +10194,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
 (define-public r-rbibutils
   (package
     (name "r-rbibutils")
-    (version "2.2.8")
+    (version "2.2.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rbibutils" version))
        (sha256
         (base32
-         "0lnia2fk8zlvkkgnl7r7dyi1ip5vqlw448qrvqs2s14rpbpcvbpi"))))
+         "11pzbqykmn7m9gp5jspfcj6vij865wqf9ry6m3jkihvfj7zhfb5j"))))
     (properties `((upstream-name . "rbibutils")))
     (build-system r-build-system)
     (home-page "https://geobosh.github.io/rbibutils/")
@@ -10230,14 +10242,14 @@ references and Rd files.")
 (define-public r-officer
   (package
     (name "r-officer")
-    (version "0.4.3")
+    (version "0.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "officer" version))
        (sha256
         (base32
-         "1ksfmwqb91j8n8x4vchpqr848scvf817mgiknwac7n8lfz79synk"))))
+         "1h6fcqw4bg644lwr5jggphyxp2d0ycya9q869z8099a50gc6h03f"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-r6 r-uuid r-xml2 r-zip))
@@ -10466,14 +10478,14 @@ Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.")
 (define-public r-insight
   (package
     (name "r-insight")
-    (version "0.18.0")
+    (version "0.18.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "insight" version))
        (sha256
         (base32
-         "09gpkac882hqw84rk66h5dm94ljk08ydz13wz9fbjdxaffgw5ba1"))))
+         "1bj6dliin3draqb447zyy1w4z277n8rj5sdl3lnx468bq1yqc8h9"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -10602,14 +10614,14 @@ functions.")
 (define-public r-flextable
   (package
     (name "r-flextable")
-    (version "0.7.2")
+    (version "0.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "flextable" version))
        (sha256
         (base32
-         "03nxh9a9q0jgqz05i7kgp8zjncpq9m4f54dx3bvqgpds4hcqxli9"))))
+         "03l9wgsikg1n2i3hxkb850kprs49nlrawyrm46k1d95b83d2qq8s"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-base64enc
@@ -11335,13 +11347,13 @@ second male (P2) based on the best fit distribution.")
 (define-public r-abcrf
   (package
     (name "r-abcrf")
-    (version "1.8.1")
+    (version "1.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abcrf" version))
        (sha256
-        (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
+        (base32 "08mh1a6gxp0mfx6qnp1qzcrfx7xp64qj9kad4ziyswfx22ykdsxi"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-doparallel
@@ -11625,13 +11637,13 @@ subsequence} (LCS) using a dynamic programming algorithm.")
 (define-public r-mosaiccore
   (package
     (name "r-mosaiccore")
-    (version "0.9.0")
+    (version "0.9.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mosaicCore" version))
        (sha256
-        (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz"))))
+        (base32 "0mnizi1y7jn2z8v066b6kv08az7vss6avips740pjhgvi8frhsag"))))
     (properties `((upstream-name . "mosaicCore")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11645,14 +11657,14 @@ subsequence} (LCS) using a dynamic programming algorithm.")
 (define-public r-labelled
   (package
     (name "r-labelled")
-    (version "2.9.1")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "labelled" version))
        (sha256
         (base32
-         "0h7scbyzh7kr51gds222rkhld2b3k36s86hj8rrzpwv4bwj0pccy"))))
+         "02n4r4bizsysnlmxpw86w7zkiqi6aill9dq2nmrn43xzrffy54sy"))))
     (properties `((upstream-name . "labelled")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11676,13 +11688,13 @@ haven package.")
 (define-public r-ggformula
   (package
     (name "r-ggformula")
-    (version "0.10.1")
+    (version "0.10.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggformula" version))
        (sha256
-        (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp"))))
+        (base32 "0xb39gjn6q7va1d1fhvf2dw9428s1q13wasx4y3cz2f0lls1r2wl"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ggforce
@@ -11710,13 +11722,13 @@ while providing the intuitive capabilities of @code{r-ggplot2}.")
 (define-public r-mosaicdata
   (package
     (name "r-mosaicdata")
-    (version "0.20.2")
+    (version "0.20.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mosaicData" version))
        (sha256
-        (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4"))))
+        (base32 "1s97yq24z7yhzmx0dpspfadpd8hndyhn7aiw0nslwrhvilhwa409"))))
     (properties `((upstream-name . "mosaicData")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/mosaicData/")
@@ -11729,14 +11741,14 @@ used to teach mathematics, statistics, computation and modeling.")
 (define-public r-raster
   (package
     (name "r-raster")
-    (version "3.5-21")
+    (version "3.6-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "raster" version))
        (sha256
         (base32
-         "1alny43aw5ydlwc7157bf524r0dxp74bf5d0nkvm8qnni57z9bci"))))
+         "1in3n0hqzcdhibjl3y82nwn6m6wcv4k3l6s2jw57jn32qgvy01lz"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-rcpp r-sp r-terra))
@@ -11750,48 +11762,39 @@ Processing of very large files is supported.")
 
 (define-public r-mosaic
   (package
-   (name "r-mosaic")
-   (version "1.8.3")
-   (source
-    (origin
-     (method url-fetch)
-     (uri (cran-uri "mosaic" version))
-     (sha256
-      (base32 "1y0isqbva0vi5zlx1xvixbq87n4xp66ljh43qnd0cpzaz0mn21cg"))))
-   (build-system r-build-system)
-   (propagated-inputs
-    (list r-broom
-          r-dplyr
-          r-ggdendro
-          r-ggformula
-          r-ggplot2
-          r-ggrepel
-          r-ggridges
-          r-ggstance
-          r-glue
-          r-gridextra
-          r-lattice
-          r-latticeextra
-          r-leaflet
-          r-mass
-          r-matrix
-          r-mosaiccore
-          r-mosaicdata
-          r-readr
-          r-rlang
-          r-tidyr))
-   (native-inputs
-    (list r-knitr))
-   (home-page "https://github.com/ProjectMOSAIC/mosaic/")
-   (synopsis "Mathematics, statistics, and computation teaching utilities")
-   (description
-    "This package contain data sets and utilities from
+    (name "r-mosaic")
+    (version "1.8.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mosaic" version))
+       (sha256
+        (base32 "0ix9c4rpa1h7cya9mqzqph9ain1ng61px5v4wwvlaf76zdr51c0i"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-dplyr
+           r-ggformula
+           r-ggplot2
+           r-lattice
+           r-mass
+           r-matrix
+           r-mosaiccore
+           r-mosaicdata
+           r-purrr
+           r-rlang
+           r-tidyr))
+    (native-inputs
+     (list r-knitr))
+    (home-page "https://github.com/ProjectMOSAIC/mosaic/")
+    (synopsis "Mathematics, statistics, and computation teaching utilities")
+    (description
+     "This package contain data sets and utilities from
 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
 statistics, computation and modeling.  Project MOSAIC is a community of
 educators working to tie together aspects of quantitative work that students
 in science, technology, engineering and mathematics will need in their
 professional lives, but which are usually taught in isolation, if at all.")
-   (license license:gpl2+)))
+    (license license:gpl2+)))
 
 (define-public r-abd
   (package
@@ -11932,14 +11935,14 @@ genotypes as \"graphical genotypes\".")
 (define-public r-furrr
   (package
     (name "r-furrr")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "furrr" version))
        (sha256
         (base32
-         "117xj66l14r08macwghgyibzm282ljv1afpa133h952gc70irs9z"))))
+         "12z4q0fn7asxis17hisi82bvfabl5if1338lmfqmkrwv5rg7748d"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-future
@@ -12810,14 +12813,14 @@ the differences were not significantly different.")
 (define-public r-emmeans
   (package
     (name "r-emmeans")
-    (version "1.8.0")
+    (version "1.8.1-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "emmeans" version))
        (sha256
         (base32
-         "0xdvbjcywmwk6n8xbp55n92lmqz7wbc938gmv7lbg96hkf9kc993"))))
+         "0xv55v50v3fdg289mfqirfm4p644gn4ckqnvs0wb09sl4m25xz3r"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-estimability r-mvtnorm r-numderiv r-xtable))
@@ -12939,14 +12942,14 @@ Bayesian modeling.")
 (define-public r-tmb
   (package
     (name "r-tmb")
-    (version "1.9.0")
+    (version "1.9.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TMB" version))
        (sha256
         (base32
-         "1mr5vwamw6ag1fhd83jyy6015296908qwshwq0fcphhiv60x579c"))))
+         "03zv38gig31ir5gdhgw5j6j8xn1f4y91j2r87fv31gywmg1bhzl9"))))
     (properties `((upstream-name . "TMB")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13042,14 +13045,14 @@ differentiation.")
 (define-public r-bayestestr
   (package
     (name "r-bayestestr")
-    (version "0.12.1")
+    (version "0.13.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bayestestR" version))
        (sha256
         (base32
-         "1fbkpagc5zznrafy7h68nhx43a1yg4v7242pbqjkd0h2481c101z"))))
+         "1951zm88qlbmr4ragrzfzgw72awm7mqhh464s6kck0mcx7shas90"))))
     (properties `((upstream-name . "bayestestR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13069,14 +13072,14 @@ ROPE percentage and pd).")
 (define-public r-performance
   (package
     (name "r-performance")
-    (version "0.9.1")
+    (version "0.9.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "performance" version))
        (sha256
         (base32
-         "0xiqy9z070v5xzf2iq4x01licabhkygji5x6qfy7l08n43z4agny"))))
+         "0fdszf1dngqlbwcp7ynfdkzjgg0lang4d3b53ygjwsq7ph20xsw6"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-bayestestr r-datawizard r-insight))
@@ -13123,14 +13126,14 @@ results using @code{ggplot2}.")
 (define-public r-effectsize
   (package
     (name "r-effectsize")
-    (version "0.7.0")
+    (version "0.7.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "effectsize" version))
        (sha256
         (base32
-         "07dbj7n9vwjkb7xrdj224lzc3ppr3jjdgyyilkj7gpkvgjgfrqhz"))))
+         "0y8ng4wsms25qx2wmyrm97rbv5dgm5xyhh5ys99f0clr9lrcxr91"))))
     (properties `((upstream-name . "effectsize")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13252,14 +13255,14 @@ package works as intended.")
 (define-public r-gitcreds
   (package
     (name "r-gitcreds")
-    (version "0.1.1")
+    (version "0.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gitcreds" version))
        (sha256
         (base32
-         "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
+         "0pf70g4a2kxjcid5rc4ppmgcl3kpjhkszdgz4fqn4l33lp6apij1"))))
     (properties `((upstream-name . "gitcreds")))
     (build-system r-build-system)
     (inputs (list git-minimal))
@@ -13276,14 +13279,14 @@ repositories.")
 (define-public r-gh
   (package
     (name "r-gh")
-    (version "1.3.0")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gh" version))
        (sha256
         (base32
-         "077drbxz3rx7idv6w24ipj1p6jnzv86a3iyryab699cc9q2kjh54"))))
+         "1vqjhqlhvvqq8w2cqbgrkqphj0ga5s6fbl4zhcl3vc6fvsms5bpv"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cli r-gitcreds r-httr r-ini r-jsonlite))
@@ -13378,14 +13381,14 @@ user credentials.")
 (define-public r-gert
   (package
     (name "r-gert")
-    (version "1.7.0")
+    (version "1.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gert" version))
        (sha256
         (base32
-         "1pdqmnlrpbjkqwf9ns2232d3cgyqjkywyd2s8sqinaapnlh87y0x"))))
+         "1lb9rf4c8ip8cll9mycx88x8q774bcmd01j4bwjx9h0kx1hgahkb"))))
     (properties `((upstream-name . "gert")))
     (build-system r-build-system)
     (inputs
@@ -13702,14 +13705,14 @@ algorithms, clusterings, and individual clusters.")
 (define-public r-tweedie
   (package
     (name "r-tweedie")
-    (version "2.3.3")
+    (version "2.3.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tweedie" version))
        (sha256
         (base32
-         "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
+         "0ghwggdx6d391m7nay9n5li2xjqh3kmw416xx130sy2sxrgp8g4q"))))
     (build-system r-build-system)
     (native-inputs (list gfortran))
     (home-page "https://cran.r-project.org/web/packages/tweedie/")
@@ -13917,14 +13920,14 @@ parallel calculations across cluster nodes.")
 (define-public r-chk
   (package
     (name "r-chk")
-    (version "0.8.0")
+    (version "0.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "chk" version))
        (sha256
         (base32
-         "10gcv00mgi88vgxr9jrs0ar67crmdcdi4m9g86cm6pg3ly0v097y"))))
+         "0nw3aj8sbd2x8rsvpglsiavk7kivd330mgx676k46m7lhhj7nmpw"))))
     (properties `((upstream-name . "chk")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13966,13 +13969,13 @@ address a bug.")
 (define-public r-rcppalgos
   (package
     (name "r-rcppalgos")
-    (version "2.5.3")
+    (version "2.6.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppAlgos" version))
               (sha256
                (base32
-                "1ndibdf3k02bpcgackzviczramzkay9idn071nix3dhs5miq1ai8"))))
+                "11dvh0ba3chsqf3vw8g9h1754arxgwqryayavx3n6vm5daz2krqa"))))
     (properties `((upstream-name . "RcppAlgos")))
     (build-system r-build-system)
     (inputs (list gmp))
@@ -14269,14 +14272,14 @@ features (e.g. local modes).")
 (define-public r-arm
   (package
     (name "r-arm")
-    (version "1.12-2")
+    (version "1.13-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "arm" version))
        (sha256
         (base32
-         "0pagrc1vkaz460d0lvrgb4xj6gcd920f4mrc8zpzw07c3v1s2sw1"))))
+         "0dz9dnsky77da2mc198dr3600kz9vk75z1iihjarnsdrq68a4bf0"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-abind
@@ -14497,13 +14500,13 @@ Tabelow (2007) <DOI:10.18637/jss.v019.i01>.")
 (define-public r-admisc
   (package
     (name "r-admisc")
-    (version "0.29")
+    (version "0.30")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "admisc" version))
        (sha256
-        (base32 "02vl2k58ijqd30d7y01x0ap2b2vh1is3xg14g3cpvm5gflyxyinf"))))
+        (base32 "01b2qjxz0qicqjm1swvm04qkiwhr7zjn7lhqv26l6rj4yb43y339"))))
     (properties `((upstream-name . "admisc")))
     (build-system r-build-system)
     (home-page "https://github.com/dusadrian/admisc")
@@ -14709,14 +14712,14 @@ Processing.")
 (define-public r-waveslim
   (package
     (name "r-waveslim")
-    (version "1.8.3")
+    (version "1.8.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "waveslim" version))
        (sha256
         (base32
-         "0yxkwgdq1xqh027l2akwb4zji4li3sgpmyxlmfq1rhz15kjxr2wq"))))
+         "1510xpkgrhdw394m5anxccdczjikcxazyd09ix2z73i15akyx3j0"))))
     (build-system r-build-system)
     (native-inputs
      (list gfortran))
@@ -14779,13 +14782,13 @@ maps.")
 (define-public r-tidytree
   (package
     (name "r-tidytree")
-    (version "0.3.9")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidytree" version))
        (sha256
-        (base32 "1prfv2jy6z4zp4gyi9krzbysipsbnjrkxcccflm4nwsd9i7mshqj"))))
+        (base32 "0dm71zdrb1qwaja23jlzjpraa609b6yxl8bhksz8slgpfm1jgs00"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ape
@@ -14851,14 +14854,14 @@ giving it a description in the specific format.")
 (define-public r-sparsesvd
   (package
     (name "r-sparsesvd")
-    (version "0.2")
+    (version "0.2-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sparsesvd" version))
        (sha256
         (base32
-         "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
+         "0yz0mgayxriyrz6bbrd41cck0s56b916xvyh13hw86gydd6kpl5k"))))
     (build-system r-build-system)
     (propagated-inputs (list r-matrix))
     (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
@@ -15376,14 +15379,14 @@ conditional reporting based on the current \"output level\".")
 (define-public r-tractor-base
   (package
     (name "r-tractor-base")
-    (version "3.3.3.1")
+    (version "3.3.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tractor.base" version))
        (sha256
         (base32
-         "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p"))))
+         "0fxbzbhpi6l55m14nmww8y3kdxgchzj4mw1yf4xkm2y6s68phvgc"))))
     (properties `((upstream-name . "tractor.base")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15543,14 +15546,14 @@ Life Sciences\" by Ron Wehrens, Springer (2011).")
 (define-public r-als
   (package
     (name "r-als")
-    (version "0.0.6")
+    (version "0.0.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ALS" version))
        (sha256
         (base32
-         "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
+         "184d6xr4mgs78jvi7xa4njrq6p625i9sx69wak6mdn53qpl9b8ap"))))
     (properties `((upstream-name . "ALS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15640,14 +15643,14 @@ library.")
 (define-public r-ontologyindex
   (package
     (name "r-ontologyindex")
-    (version "2.7")
+    (version "2.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ontologyIndex" version))
        (sha256
         (base32
-         "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
+         "0hisb9scxyyqkxhxhvgsgwix54pkq0zma3xq3ywczyazvzcxd5f9"))))
     (properties `((upstream-name . "ontologyIndex")))
     (build-system r-build-system)
     (native-inputs
@@ -15662,14 +15665,14 @@ and manipulating sets of ontological terms.")
 (define-public r-gargle
   (package
     (name "r-gargle")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gargle" version))
        (sha256
         (base32
-         "0fypj70c1fjmvs57birik76wfx8a2fs4gzicbb52k57i6clwlijd"))))
+         "087hlbqpwjj7jnsg1ax2b12nc0h4zfj070q5hjp6fca05z4f4rzk"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cli
@@ -15728,14 +15731,14 @@ preparing, executing, and processing HTTP requests.")
 (define-public r-gmp
   (package
     (name "r-gmp")
-    (version "0.6-5")
+    (version "0.6-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gmp" version))
        (sha256
         (base32
-         "0llyd1wx606vpgvv7d61m0fv2a5yxsmisd38fhzanbjl2wynzrwa"))))
+         "14r7xlxjrwww6l726sispq6jhxy2yfwbcqrqgc9x4ma812l9byl7"))))
     (build-system r-build-system)
     (arguments
      '(#:phases
@@ -16242,13 +16245,13 @@ Differences with other sparse matrix packages are:
 (define-public r-fields
   (package
     (name "r-fields")
-    (version "14.0")
+    (version "14.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fields" version))
        (sha256
-        (base32 "0rjg2yx52f5s1fhg6jbk9lfv92qmjqwd6bwpz9rx1fkml9vy8zch"))))
+        (base32 "0d2lm4s9p3rv676z291fynpx3vdmi6cikcqlj23fxlj34icwbi2p"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-maps r-spam r-viridis))
@@ -16764,14 +16767,14 @@ subsetting.")
 (define-public r-globals
   (package
     (name "r-globals")
-    (version "0.16.0")
+    (version "0.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "globals" version))
        (sha256
         (base32
-         "0507lxykjz44yws4s4hb99zb3bn6kn6fy8m87lf2dsm431j40gy5"))))
+         "158y39qv99f1kc2i7w8d4lm2ls96plb43fzamz31im9xb9bkmxpp"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-codetools))
@@ -16816,14 +16819,14 @@ port-forwarding to your local computer.")
 (define-public r-future
   (package
     (name "r-future")
-    (version "1.27.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "future" version))
        (sha256
         (base32
-         "1ybhbdw158403n6plipgiwkw710pxpnq3mq8pdx5g8q3jibv93nh"))))
+         "1xhv0nf97yxxxsmxczyqqbnb4yn5sfn5vzvhm9dmw9csrmmadpbg"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -16851,14 +16854,14 @@ the local machine to, say, distributed processing on a remote compute cluster.")
 (define-public r-future-apply
   (package
     (name "r-future-apply")
-    (version "1.9.0")
+    (version "1.9.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "future.apply" version))
        (sha256
         (base32
-         "1xb7qj8izjwmy4aa92p5f4cdbhgp220hrly3b5879f9hrv2w2rk1"))))
+         "0cr141mamjxby79sww02493yal9lahslvp3a3ic7f856rbawq8jg"))))
     (properties `((upstream-name . "future.apply")))
     (build-system r-build-system)
     (arguments
@@ -16984,14 +16987,14 @@ chosen parallel environment and associated foreach backend.")
 (define-public r-blockmodeling
   (package
     (name "r-blockmodeling")
-    (version "1.0.5")
+    (version "1.1.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "blockmodeling" version))
        (sha256
         (base32
-         "1vc8gy4slsywcwxq532373i0dq73fhs5cac9mr6zz2pjaaxjghhq"))))
+         "19mxmxsnl6rrh85p0sak91vcaw4dz2cnm70hdzfwnvdrr695yw2z"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-matrix))
@@ -17315,13 +17318,13 @@ such software by imputing dropout events.")
 (define-public r-gamlss-dist
   (package
     (name "r-gamlss-dist")
-    (version "6.0-3")
+    (version "6.0-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gamlss.dist" version))
        (sha256
-        (base32 "1gqjr419v8z2ygh0h1xz7bipnsbp820njzwq7z3r9f41rn1ym47c"))))
+        (base32 "03m275qvrmpzmc10hs48277kxp503riz8sz6xk9pkpj8n7gsz20g"))))
     (properties `((upstream-name . "gamlss.dist")))
     (build-system r-build-system)
     (propagated-inputs (list r-mass))
@@ -18277,18 +18280,18 @@ univariate class intervals for mapping or other graphics purposes.")
 (define-public r-spdata
   (package
     (name "r-spdata")
-    (version "2.0.1")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spData" version))
        (sha256
         (base32
-         "1z4hp5ivwzyvl8mkp98j2ng1cl1xksqbjxv85vdlqfqjwpia6df6"))))
+         "07whxr039cxvk2nn65jada3i8vqqw34lgca9j17ah8chy9r0m73f"))))
     (properties `((upstream-name . "spData")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-raster r-sp))
+     (list r-sp))
     (home-page "https://github.com/Nowosad/spData")
     (synopsis "Datasets for spatial analysis")
     (description
@@ -18451,13 +18454,13 @@ datum transformations.")
 (define-public r-spdep
   (package
     (name "r-spdep")
-    (version "1.2-4")
+    (version "1.2-5")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "spdep" version))
               (sha256
                (base32
-                "0xx6k3rsvsz1hwj0ny8aqfi9ca54x38f8pz8sfya5cggaspxbx59"))
+                "1ib5jgahjgjpj2ajp5g71r4fw0q1zkddixgmywi1n73nqr39qwp2"))
               (snippet
                '(for-each delete-file '("inst/doc/CO69.html"
                                         "inst/doc/CO69.R"
@@ -18896,13 +18899,13 @@ SELECT or UPDATE queries to an end-point.")
 (define-public r-bookdown
   (package
     (name "r-bookdown")
-    (version "0.27")
+    (version "0.29")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "bookdown" version))
               (sha256
                (base32
-                "08wzi7hh3x1dfpmzpxhphrv5zb6a3p7rziaazisfpp1zwsxllwif"))))
+                "08zpky94bdbjsbhi90pymxpczpfkjxwbx7p1v7ip8raw9b23skjv"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-htmltools
@@ -19437,14 +19440,14 @@ packages with Rcpp.")
 (define-public r-tweenr
   (package
     (name "r-tweenr")
-    (version "1.0.2")
+    (version "2.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tweenr" version))
        (sha256
         (base32
-         "17znizh4yabh2zs9mzyr0sl6p0pw49961i61br7cl1b7v9sza18q"))))
+         "1wqzcsxlz1isb1j0v5g6dgvd40q3q9qlahvgcgiq0j4d87nzvfv4"))))
     (build-system r-build-system)
     (arguments
      (list
@@ -19456,7 +19459,7 @@ packages with Rcpp.")
                (("BASEDATETIME <- Sys.time.*")
                 "BASEDATETIME <- structure(0, class = c(\"POSIXct\", \"POSIXt\"))\n")))))))
     (propagated-inputs
-     (list r-farver r-magrittr r-rcpp r-rlang))
+     (list r-cpp11 r-farver r-magrittr r-rlang r-vctrs))
     (home-page "https://github.com/thomasp85/tweenr")
     (synopsis "Interpolate data for smooth animations")
     (description
@@ -19541,18 +19544,19 @@ sets of URLs.")
 (define-public r-ggforce
   (package
     (name "r-ggforce")
-    (version "0.3.3")
+    (version "0.3.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggforce" version))
        (sha256
         (base32
-         "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a"))))
+         "0lshvdb5kx0k5w36pc7fy653cs98w17spbw8f0jw36xb80sipiv2"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ggplot2
            r-gtable
+           r-lifecycle
            r-mass
            r-polyclip
            r-rcpp
@@ -19774,14 +19778,14 @@ graphics using Vega.")
 (define-public r-gbm
   (package
     (name "r-gbm")
-    (version "2.1.8")
+    (version "2.1.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gbm" version))
        (sha256
         (base32
-         "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
+         "02z85d7zp3i5x8r8q005hyw2rx1ck7lw81q7a3lqwraj8l95c94d"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-lattice r-survival))
@@ -19954,14 +19958,14 @@ function for computing a matrix of correlation p-values.")
 (define-public r-ggfun
   (package
     (name "r-ggfun")
-    (version "0.0.6")
+    (version "0.0.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggfun" version))
        (sha256
         (base32
-         "06si42b60hp8wprs5nbks93qlb9s269k9kw7akcirizwc399x62r"))))
+         "0x71p3mm0sw72hv92368wy2yiy7zv826p3kddpwndqv1bywmyfx8"))))
     (properties `((upstream-name . "ggfun")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19978,22 +19982,22 @@ each of the legends).")
 (define-public r-gridtext
   (package
     (name "r-gridtext")
-    (version "0.1.4")
+    (version "0.1.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gridtext" version))
        (sha256
         (base32
-         "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61"))))
+         "0f7i2qb8fawi8agy2iz2c173kfwj7cbb5ikjix64nmzqc5j7363d"))))
     (properties `((upstream-name . "gridtext")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-jpeg
+     (list r-curl
+           r-jpeg
            r-markdown
            r-png
            r-rcpp
-           r-rcurl
            r-rlang
            r-stringr
            r-xml2))
@@ -20009,14 +20013,14 @@ wrap.")
 (define-public r-ggtext
   (package
     (name "r-ggtext")
-    (version "0.1.1")
+    (version "0.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggtext" version))
        (sha256
         (base32
-         "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b"))))
+         "10vrrxviv4yp9lqsanqvwsvbj64vn66hwm1w7860x1g58hf1g0l7"))))
     (properties `((upstream-name . "ggtext")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20249,14 +20253,14 @@ external dependencies.  This package has is implemented purely in R.")
 (define-public r-aplot
   (package
     (name "r-aplot")
-    (version "0.1.6")
+    (version "0.1.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "aplot" version))
        (sha256
         (base32
-         "0310z9db2r8vr4053vy6w4rbcqhg5cv56p60rk7dh4y6ifbd2sbx"))))
+         "05l6pvhrl715xgdy7qmw6lyxigv9qn90ms3vf7awip8sdmghy9gn"))))
     (properties `((upstream-name . "aplot")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20324,14 +20328,14 @@ colored by the number of neighboring points.  This is useful to visualize the
 (define-public r-arrow
   (package
     (name "r-arrow")
-    (version "8.0.0")
+    (version "9.0.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "arrow" version))
        (sha256
         (base32
-         "1b85vc5ld7nibqgsdkl5kbzc0rm5jh5lqfdrssvrrcxpd26a16kc"))))
+         "1vbjny6v1d4fdf01rphg4wg8ljs0bzrjyxlsjwjq58pd6g2qcdgc"))))
     (properties `((upstream-name . "arrow")))
     (build-system r-build-system)
     (inputs
@@ -20438,14 +20442,14 @@ on, for a performance vs accuracy trade-off.")
 (define-public r-rsparse
   (package
     (name "r-rsparse")
-    (version "0.5.0")
+    (version "0.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rsparse" version))
        (sha256
         (base32
-         "0d05h47j29zipyxbkv9cwzv2dzj894z6hh9dqfhwswwjbv6ciwpq"))))
+         "15kdllm2lh6xdlv4j0ljyj5pczhx26s9d8cac7953zbb0sd45chz"))))
     (properties `((upstream-name . "rsparse")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20471,14 +20475,14 @@ Row} (CSR) format.")
 (define-public r-text2vec
   (package
     (name "r-text2vec")
-    (version "0.6.1")
+    (version "0.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "text2vec" version))
        (sha256
         (base32
-         "0bisr31051hnshw26rp9r4bm8ksr977dl9k1d3fb1x79pq5aa2pi"))))
+         "1as58w1hb6h0hpncwcr2nx9a8bj5fy6bfllx2a8ck8hal764iach"))))
     (properties `((upstream-name . "text2vec")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20580,14 +20584,14 @@ provides tools to compute this metric.")
 (define-public r-lintr
   (package
     (name "r-lintr")
-    (version "3.0.0")
+    (version "3.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lintr" version))
        (sha256
         (base32
-         "1d3pn6aarmpqyyzb2vawwcamrgrdvyqfdijk0ixp44c3fhld9cgf"))))
+         "18prww284sil98ck3gmkmfs6b4disn9nyfb00kfwwiwg7ay1df6g"))))
     (properties `((upstream-name . "lintr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20613,14 +20617,14 @@ code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
 (define-public r-sctransform
   (package
     (name "r-sctransform")
-    (version "0.3.3")
+    (version "0.3.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sctransform" version))
        (sha256
         (base32
-         "0aqbcarsvvzkh5h4i65f08y4b8dfcs3zi62hmvfy24gj81f15bw3"))))
+         "1nhmsbkrww74a55avln5zhd77g92f15p885j5q0khajw35iqnv0g"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-dplyr
@@ -20994,18 +20998,18 @@ and model output.")
 (define-public r-enrichr
   (package
     (name "r-enrichr")
-    (version "3.0")
+    (version "3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "enrichR" version))
        (sha256
         (base32
-         "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
+         "0ad7jp398prvmm2fym07268qhv40mg67dx55ml4ayqkwxwffr1i9"))))
     (properties `((upstream-name . "enrichR")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-ggplot2 r-httr r-rjson))
+     (list r-curl r-ggplot2 r-httr r-rjson))
     (native-inputs
      (list r-knitr))
     (home-page "https://cran.r-project.org/web/packages/enrichR/")
@@ -21167,14 +21171,14 @@ easily.")
 (define-public r-umap
   (package
     (name "r-umap")
-    (version "0.2.8.0")
+    (version "0.2.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "umap" version))
        (sha256
         (base32
-         "0aiarnzc8gl932gi8fxd9f9rshaiwh9vj570l135fkiaja3q2wap"))))
+         "1282v09kpds83mlr7kz06k8a40ji15hw85p30vrnp1g6w64w26sm"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-matrix r-openssl r-rcpp r-reticulate r-rspectra))
@@ -21191,14 +21195,14 @@ in R, including a translation of the original algorithm into R.")
 (define-public r-uwot
   (package
     (name "r-uwot")
-    (version "0.1.11")
+    (version "0.1.14")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "uwot" version))
        (sha256
         (base32
-         "06ylzxmdh8jipbrzgqaiivd2lnqmbcva41cyvc0iyals6vqr1ksg"))))
+         "1q4z98w3pkc51vrcpmwaibnwmlm17zjcnh0qlx660wky5ccyh5l0"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-dqrng
@@ -21207,8 +21211,7 @@ in R, including a translation of the original algorithm into R.")
            r-matrix
            r-rcpp
            r-rcppannoy
-           r-rcppprogress
-           r-rspectra))
+           r-rcppprogress))
     (home-page "https://github.com/jlmelville/uwot")
     (synopsis "Uniform manifold approximation and projection")
     (description
@@ -21351,14 +21354,14 @@ computed using the L1 (Manhattan, taxicab) metric.")
 (define-public r-leiden
   (package
     (name "r-leiden")
-    (version "0.4.2")
+    (version "0.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "leiden" version))
        (sha256
         (base32
-         "1gg24afwbz818041bhmswmdqgxv35zp5h1i1102p58aaiis8dkna"))))
+         "0f09k3mhb0di2cz1q95y6qd3rqh7xdybn0dpnd4ifqhfhr5lnika"))))
     (properties `((upstream-name . "leiden")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21377,14 +21380,14 @@ guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
 (define-public r-patchwork
   (package
     (name "r-patchwork")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "patchwork" version))
        (sha256
         (base32
-         "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg"))))
+         "0xw9mh1qakj131nw98icxrxwvdlwy2ngwvmagrqr3m84sz9dbffs"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ggplot2 r-gtable))
@@ -21520,13 +21523,13 @@ function and interfaces to external frameworks.")
 (define-public r-covr
   (package
     (name "r-covr")
-    (version "3.5.1")
+    (version "3.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "covr" version))
        (sha256
-        (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
+        (base32 "0mqiqmbwq5f083lda208nqd4ya0f912bkkya2i62fkqsii1ibgpz"))))
     (properties `((upstream-name . "covr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21582,14 +21585,14 @@ be used further by e.g. graphic devices.")
 (define-public r-graphlayouts
   (package
     (name "r-graphlayouts")
-    (version "0.8.0")
+    (version "0.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "graphlayouts" version))
        (sha256
         (base32
-         "1l7gkn0r1ijllv3w7cbwcbi0jggs7wlkq9b2lykprng4g1kjc96p"))))
+         "0yhg42p3jlz78kd712jd5525zm1h3n5gmjplfscjkgn342r3w92v"))))
     (properties `((upstream-name . "graphlayouts")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21607,14 +21610,14 @@ emphasize hidden group structures in networks or focus on specific nodes.")
 (define-public r-terra
   (package
     (name "r-terra")
-    (version "1.6-7")
+    (version "1.6-17")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "terra" version))
        (sha256
         (base32
-         "1p67797i9n4cjk1lp4a84h220428nxv940n1kjg1ysl3chrf0w1l"))))
+         "00mwigymvsqf7r3swbkdw8fwqzr05ddk84fhyhr16lfa4118z26v"))))
     (properties `((upstream-name . "terra")))
     (build-system r-build-system)
     (inputs
@@ -21641,14 +21644,14 @@ files is supported.")
 (define-public r-tidygraph
   (package
     (name "r-tidygraph")
-    (version "1.2.1")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidygraph" version))
        (sha256
         (base32
-         "0dmdff3bkg53xn0c51xd6k2d9c7l250x1lhl5z3libf533dw5g9g"))))
+         "0w34jfldjkynbkyinmi1vdrfjhjrs47hm599mbnx4sxmnpbclmfm"))))
     (properties `((upstream-name . "tidygraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21728,14 +21731,14 @@ in pipelines.")
 (define-public r-parameters
   (package
     (name "r-parameters")
-    (version "0.18.1")
+    (version "0.18.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "parameters" version))
        (sha256
         (base32
-         "0zcypf3fi745pa18vpqgx3q9izhkkmpcvcv1gv8pxawyq9mw8ag9"))))
+         "04swg19zb34y3nmclf94v19yskqlb2diqg93jflhgagrv9550az9"))))
     (properties `((upstream-name . "parameters")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21809,14 +21812,14 @@ atmospheric physics.")
 (define-public r-lifecycle
   (package
     (name "r-lifecycle")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lifecycle" version))
        (sha256
         (base32
-         "183v1z1h037pvsgrj6vakpwhnhsr29hsw8p16k59dgpi00f6x9qx"))))
+         "0qssl9lmfn94kmvcg1xpd4md17jx31i3sdbb77dwas60z673qgvv"))))
     (properties `((upstream-name . "lifecycle")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21916,13 +21919,13 @@ to ODEs by numerical differencing.")
 (define-public r-pmcmrplus
   (package
     (name "r-pmcmrplus")
-    (version "1.9.5")
+    (version "1.9.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "PMCMRplus" version))
        (sha256
-        (base32 "15xhwq231vgq9q7pk1r4z11wijn4hgdwcly1n9nxxa05w15x9q33"))))
+        (base32 "1mvj3cwrdkl3frk7fvh6l7v7yya5p3xm4z0qhc4fvykxdmb92ivz"))))
     (properties `((upstream-name . "PMCMRplus")))
     (build-system r-build-system)
     (inputs (list gmp))
@@ -22333,14 +22336,14 @@ cell free DNA} (cfDNA).")
 (define-public r-rintrojs
   (package
     (name "r-rintrojs")
-    (version "0.3.0")
+    (version "0.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rintrojs" version))
        (sha256
         (base32
-         "00l5mk80gj3xkbf3m1kip566ic98bhd88lh0bg69ybkpk4gifpyw"))
+         "19lpq421hrs1wc9bnimbwxx35p8bbzil3x1h9l28gjayn4djmjsh"))
        (snippet
         '(delete-file "inst/javascript/introjs/intro.min.js"))))
     (properties `((upstream-name . "rintrojs")))
@@ -22810,14 +22813,14 @@ and mixture of Gaussian models.")
 (define-public r-accsda
   (package
     (name "r-accsda")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "accSDA" version))
        (sha256
         (base32
-         "104xdz63mnibh6827xm0pfr9zbhbi2a7iw4m1x27xjqi7zqvbky6"))))
+         "0jf4x5j9y7a3mvf2ghjp6bxdq1s5jh2sx3x3ar6f3lyzzvrnls4v"))))
     (properties `((upstream-name . "accSDA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22912,14 +22915,14 @@ and prints vectorized images.")
 (define-public r-randtoolbox
   (package
     (name "r-randtoolbox")
-    (version "2.0.1")
+    (version "2.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "randtoolbox" version))
        (sha256
         (base32
-         "1p2jsn0hpihc49zk605z82mhhvma0ji2f5b94wa85g2xzriqkwn4"))))
+         "0mvafd2gm1jpg19gdn6bw8668pqghi0xmcb56rl4fwamg8jg09xn"))))
     (properties `((upstream-name . "randtoolbox")))
     (build-system r-build-system)
     (propagated-inputs
@@ -23805,20 +23808,21 @@ allowed.")
 (define-public r-gdina
   (package
     (name "r-gdina")
-    (version "2.8.8")
+    (version "2.9.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "GDINA" version))
        (sha256
         (base32
-         "1slq1npsq8s8aghnrpm6vvc6kxj4svz0kr2x0akblndrcr25wxjr"))))
+         "0bwg9sfsqs5nsqwhjnbb631fbhj0mx2dc4c185qkym9cjb5lfkm9"))))
     (properties `((upstream-name . "GDINA")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-alabama
            r-ggplot2
            r-mass
+           r-nloptr
            r-numderiv
            r-rcpp
            r-rcpparmadillo
@@ -24385,14 +24389,14 @@ it may be seen by an animal with less acute vision.")
 (define-public r-caret
   (package
     (name "r-caret")
-    (version "6.0-92")
+    (version "6.0-93")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "caret" version))
        (sha256
         (base32
-         "048mp325ndfl83a8p4dkd1b6zh5bws4gg9kxka5ss8qsj8m4m08x"))))
+         "01sa1h9pc3a062pwm0rxadvg9qxszwcylya7llv08fcxhy46n5ac"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-e1071
@@ -24523,31 +24527,35 @@ Visualizations are also available for most of these settings.")
 (define-public r-torch
   (package
     (name "r-torch")
-    (version "0.8.0")
+    (version "0.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "torch" version))
        (sha256
-        (base32 "0n2rmv2mwfp4y002x46fd278kssmhi54zcyj37558k4r1kazzfxp"))))
+        (base32 "1dncf5njdzw1hf98knlv94rxcxnc5gl3cmk2cvlbn1z8mri86rlc"))))
     (properties `((upstream-name . "torch")))
     (build-system r-build-system)
     (arguments
      (list
       #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'install 'link-libraries
-            (lambda* (#:key inputs #:allow-other-keys)
-              (let ((deps (string-append #$output "/site-library/torch/deps")))
-                (mkdir-p deps)
-                (symlink
-                 (search-input-file
-                  inputs "/lib/python3.9/site-packages/torch/lib/libtorch.so")
-                 (string-append deps "/libtorch.so"))
-                (symlink
-                 (search-input-file
-                  inputs "/lib/liblantern.so")
-                 (string-append deps "/liblantern.so"))))))))
+      (let ((python-version (version-major+minor (package-version python))))
+        #~(modify-phases %standard-phases
+            (add-after 'install 'link-libraries
+              (lambda* (#:key inputs #:allow-other-keys)
+                (let ((deps (string-append #$output "/site-library/torch/deps"))
+                      (site-packages (string-append "/lib/python"
+                                                    #$python-version
+                                                    "/site-packages")))
+                  (mkdir-p deps)
+                  (symlink
+                   (search-input-file
+                    inputs (string-append site-packages "/torch/lib/libtorch.so"))
+                   (string-append deps "/libtorch.so"))
+                  (symlink
+                   (search-input-file
+                    inputs "/lib/liblantern.so")
+                   (string-append deps "/liblantern.so")))))))))
     (inputs
      (list python-pytorch-for-r-torch
            liblantern))
@@ -24788,13 +24796,13 @@ statistical shape analysis and archetypal analysis.")
 (define-public r-anndata
   (package
     (name "r-anndata")
-    (version "0.7.5.3")
+    (version "0.7.5.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "anndata" version))
        (sha256
-        (base32 "115v7gdilayd18hd519vzkixp2s6rvvrd1inc1i6amn7d0spy8r1"))))
+        (base32 "0vn64b0rpnwbznn0h03b810mp8hcqxjzw69nzyjmndwa8r9ial2y"))))
     (properties `((upstream-name . "anndata")))
     (build-system r-build-system)
     (propagated-inputs (list r-assertthat r-matrix r-r6 r-reticulate))
@@ -24870,22 +24878,19 @@ finding peaks in spectra, converting humidity measures.")
 (define-public r-qqconf
   (package
     (name "r-qqconf")
-    (version "1.2.3")
+    (version "1.3.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "qqconf" version))
               (sha256
                (base32
-                "0qnfzq2zb776kmvbwmyj9di4nlzx7dg0nz4097hfcllfx9160nwv"))))
+                "11sh0q5bwmqdygqd1gspx7xc5mysj18whz11afnz6s1m820snhhw"))))
     (properties `((upstream-name . "qqconf")))
     (build-system r-build-system)
     (inputs (list fftw))
     (propagated-inputs
-     (list r-dplyr
-           r-magrittr
-           r-mass
+     (list r-mass
            r-rcpp
-           r-rlang
            r-robustbase))
     (native-inputs (list pkg-config r-knitr))
     (home-page "https://github.com/eweine/qqconf")
@@ -25491,14 +25496,14 @@ programming} (OOP) using R Reference Class.")
 (define-public r-proxyc
   (package
     (name "r-proxyc")
-    (version "0.3.0")
+    (version "0.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "proxyC" version))
        (sha256
         (base32
-         "0n3rjc64b3cbccwjajpzd9gr1frgji6rsylw67xswrr9qxkrm0fd"))))
+         "1nfl6nrzw2h7argn6mh3cyl1s9ynf6516fx4vgqrjvychnd98mkb"))))
     (properties `((upstream-name . "proxyC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -25605,14 +25610,14 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
 (define-public r-quanteda
   (package
     (name "r-quanteda")
-    (version "3.2.2")
+    (version "3.2.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "quanteda" version))
        (sha256
         (base32
-         "0qb5yl2bxh6mq4xnjviqv8hfy9fxnx4hmxf06icwldpgx15afa31"))))
+         "1blk9nhydvqyyz0kzhph7nh7ahcjzflmgyr4sv8fx5bpmn4hwjzk"))))
     (properties `((upstream-name . "quanteda")))
     (build-system r-build-system)
     (propagated-inputs
@@ -25805,14 +25810,14 @@ imputed data sets with the appropriate degree of sampling uncertainty.")
 (define-public r-matrixcalc
   (package
     (name "r-matrixcalc")
-    (version "1.0-5")
+    (version "1.0-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "matrixcalc" version))
        (sha256
         (base32
-         "1jkgl1v1q7cqpl1rf49qahdr9y0f33f0ldsbgby8xhfv0vpy21jr"))))
+         "09pk0ym6qzribxc6v18cpb6478i4r4kzxpkljjbb3n323zqx5iqb"))))
     (properties `((upstream-name . "matrixcalc")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
@@ -25827,13 +25832,13 @@ actuarial models such as pension mathematics.")
 (define-public r-matrixextra
   (package
     (name "r-matrixextra")
-    (version "0.1.11")
+    (version "0.1.13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MatrixExtra" version))
        (sha256
-        (base32 "0d32b8l28ds7162rgbwbg9g206hds1zzv1mqq7aa9m6f9gg8x3am"))))
+        (base32 "1s8y8zp9k7rsnyi1d8ghi4brjbbdwxijc9chhla24qm3fi6np33a"))))
     (properties `((upstream-name . "MatrixExtra")))
     (build-system r-build-system)
     (propagated-inputs
@@ -25916,14 +25921,14 @@ least squares.")
 (define-public r-regsem
   (package
     (name "r-regsem")
-    (version "1.8.0")
+    (version "1.9.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "regsem" version))
        (sha256
         (base32
-         "1v33wkrsawcvaa06cijp8ybwi82a0x34y59hdknwdbywplnirzr8"))))
+         "0vpizmdml55naxmhy9nfcm9ylhy15p9na7l0c6z3rvk29ck3g3sw"))))
     (properties `((upstream-name . "regsem")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26206,14 +26211,14 @@ model estimation.  See Epskamp et al. (2012)
 (define-public r-semplot
   (package
     (name "r-semplot")
-    (version "1.1.5")
+    (version "1.1.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "semPlot" version))
        (sha256
         (base32
-         "0d7v9yqc9nhx3hdrp444w1ah66zai3lg5y778m85r7ngh1prxlvc"))))
+         "0s9bp4pfsllg1k4x8a36yw82fw432dyz0xvmvi8dw9l12q3jkx8i"))))
     (properties `((upstream-name . "semPlot")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26244,14 +26249,14 @@ translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
 (define-public r-cdm
   (package
     (name "r-cdm")
-    (version "8.1-12")
+    (version "8.2-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "CDM" version))
        (sha256
         (base32
-         "1cnk19k09cj81ic43rwbvcalvczfca4ncdyy8r1gyc8fzf2glb0i"))))
+         "1lcq3i5rlyqkc12c26kj0x4fm2gh1jsisp6kbf59y3hjdkiqajhl"))))
     (properties `((upstream-name . "CDM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26275,14 +26280,14 @@ well as Ravand and Robitzsch (2015).")
 (define-public r-tam
   (package
     (name "r-tam")
-    (version "4.0-16")
+    (version "4.1-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TAM" version))
        (sha256
         (base32
-         "00ww277hsyci5rph4gb155h0y95dmjhqgn9amz6g8zbrjb2748dw"))))
+         "0b81d0g4j94yrfzj019jffxrk1aw24iscddp60kjbkrl5p7qy38g"))))
     (properties `((upstream-name . "TAM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26627,14 +26632,14 @@ techniques to average Bayesian predictive distributions.")
 (define-public r-rstan
   (package
     (name "r-rstan")
-    (version "2.21.5")
+    (version "2.21.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rstan" version))
        (sha256
         (base32
-         "1smr5cjrqvpdnkmjpjp73p96sy581x15mwrn4fqd1p4d5mbgxr46"))))
+         "0ibd3pj2pvd7658sdg95fa2yhfmxz9gy0cjwcrdr546k209j55a4"))))
     (properties `((upstream-name . "rstan")))
     (build-system r-build-system)
     (arguments
@@ -26895,14 +26900,14 @@ opponents' vessels.")
 (define-public r-zseq
   (package
     (name "r-zseq")
-    (version "0.2.0")
+    (version "0.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Zseq" version))
        (sha256
         (base32
-         "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
+         "0xp7qi5kjg8xmci9wrfvmygjmz8gbhq60fl9bvk8rnka6s4ppkrc"))))
     (properties `((upstream-name . "Zseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -27059,13 +27064,13 @@ appropriate dog and cat images for many status codes.")
 (define-public r-latex2exp
   (package
     (name "r-latex2exp")
-    (version "0.9.4")
+    (version "0.9.5")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "latex2exp" version))
               (sha256
                (base32
-                "0zbbrbgg524lpm733j8qsqk5ssg75c51s6dgzb18c6fk8byrx945"))))
+                "153br3xflvnnxqhkhm1wgwb2664bw08alhslgdcgjdk73clafhla"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-stringr r-magrittr))
@@ -27587,14 +27592,14 @@ here.")
 (define-public r-projpred
   (package
     (name "r-projpred")
-    (version "2.1.2")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "projpred" version))
        (sha256
         (base32
-         "1c6gnmknd3vb0fb5h6gd372dk27nzif90b4c1snql49wacg6b2m8"))))
+         "1a5hsqwcmn1w9lwjhsqw06av7cmqhwyxsil9zfrnv1396zfkpxhy"))))
     (properties `((upstream-name . "projpred")))
     (build-system r-build-system)
     (propagated-inputs
@@ -27624,20 +27629,19 @@ vignette for more information and examples.")
 (define-public r-distributional
   (package
     (name "r-distributional")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "distributional" version))
        (sha256
         (base32
-         "1mji8xlhwrw8msih5wdpbzwv4g59kly0xkdklhn8yzb18rrnrczs"))))
+         "0pr34yq6igb7ciqss2ldwa7gc55xvla040x8rkd8m2hcrz5mczkj"))))
     (properties
      `((upstream-name . "distributional")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-digest
-           r-ellipsis
            r-farver
            r-generics
            r-ggplot2
@@ -27661,14 +27665,14 @@ including means, variances, intervals, and highest density regions.")
 (define-public r-posterior
   (package
     (name "r-posterior")
-    (version "1.2.2")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "posterior" version))
        (sha256
         (base32
-         "0frm7p6cjkjfl4gviixaa7448qaac8n9ilkr5c02fa9vnisys5fn"))))
+         "0yjdjdr4ifssnml1niqyxs6jsqpci8rx8va0pinyhjx2j017h03h"))))
     (properties `((upstream-name . "posterior")))
     (build-system r-build-system)
     (propagated-inputs
@@ -27793,14 +27797,14 @@ multi-state models.")
 (define-public r-scatterpie
   (package
     (name "r-scatterpie")
-    (version "0.1.7")
+    (version "0.1.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "scatterpie" version))
        (sha256
         (base32
-         "1pmspv8a7k20zyd5xvmav2k9mnjrkfhdij3rr9k504zyki8hfy1z"))))
+         "183ji1q0wr8fswdrgaw161fvgh8y7j4x9xacf09s2gz6icxcdk56"))))
     (properties `((upstream-name . "scatterpie")))
     (build-system r-build-system)
     (propagated-inputs
@@ -28106,14 +28110,14 @@ incremented as outlined at @url{http://semver.org}.")
 (define-public r-binman
   (package
     (name "r-binman")
-    (version "0.1.2")
+    (version "0.1.3")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "binman" version))
         (sha256
           (base32
-            "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
+            "1xz9ky3axidm0fp518rj80ma6q14ybyvashil79hhkk3iqmx0lhw"))))
     (properties `((upstream-name . "binman")))
     (build-system r-build-system)
     (propagated-inputs
@@ -28137,14 +28141,14 @@ repositories to be added.")
 (define-public r-wdman
   (package
     (name "r-wdman")
-    (version "0.2.5")
+    (version "0.2.6")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "wdman" version))
         (sha256
           (base32
-            "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
+            "0n0wwb9ip6qc8qzdxn4dsqfbc8b3f607n8l6jigryd7g83ibnbp6"))))
     (properties `((upstream-name . "wdman")))
     (build-system r-build-system)
     (propagated-inputs
@@ -28166,23 +28170,20 @@ and to manage processes involving them.")
 (define-public r-rselenium
   (package
     (name "r-rselenium")
-    (version "1.7.7")
+    (version "1.7.9")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "RSelenium" version))
         (sha256
           (base32
-            "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
+            "18hd0gfpblg9ij99ik7ccc60q9dxha89n5rrwrrzx498c5sscjg2"))))
     (properties `((upstream-name . "RSelenium")))
     (build-system r-build-system)
     (propagated-inputs
-      (list r-binman
-            r-catools
-            r-httr
-            r-openssl
-            r-wdman
-            r-xml))
+     (list r-catools
+           r-httr
+           r-wdman))
     (native-inputs (list r-knitr))
     (home-page "https://docs.ropensci.org/RSelenium/")
     (synopsis "R bindings for Selenium WebDriver")
@@ -28201,14 +28202,14 @@ you can automate browsers locally or remotely.")
 (define-public r-conquer
   (package
     (name "r-conquer")
-    (version "1.3.0")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "conquer" version))
        (sha256
         (base32
-         "1ynmaf7lgqjb8grsifx5dzy29cd5kz4x3yh0abnl2vxdr4c4wddc"))))
+         "1mdwm0aanq4rx3042djvs0l2vkdx6zbzvrjfyfb9dhv0gfs8mhhl"))))
     (properties `((upstream-name . "conquer")))
     (build-system r-build-system)
     (propagated-inputs
@@ -28300,14 +28301,14 @@ simple interface for all functions.")
 (define-public r-iml
   (package
     (name "r-iml")
-    (version "0.11.0")
+    (version "0.11.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "iml" version))
        (sha256
         (base32
-         "1za7bjnp07i20vyb6vxz2ya5cr8g4p076w61n8m38wnz04lz5yz5"))))
+         "0fi37lv9czaxcc123f6r57607shqhs83ks96n2n0b93dl1qs0j52"))))
     (properties `((upstream-name . "iml")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29195,6 +29196,34 @@ function that determines the current environment and returns the appropriate
 value.")
     (license license:gpl3)))
 
+(define-public r-confintr
+  (package
+    (name "r-confintr")
+    (version "0.1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "confintr" version))
+              (sha256
+               (base32
+                "06c42jhqp7gp9062jf8f9py1lh34vx38q0g7b6l5kyf7a310ixr6"))))
+    (properties `((upstream-name . "confintr")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-boot))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/mayer79/confintr")
+    (synopsis "Confidence intervals")
+    (description
+     "This package calculates classic and/or bootstrap confidence intervals
+for many parameters such as the population mean, variance, @dfn{interquartile
+range} (IQR), @dfn{median absolute deviation} (MAD), skewness, kurtosis,
+Cramer's V, odds ratio, R-squared, quantiles (including median), proportions,
+different types of correlation measures, difference in means, quantiles and
+medians.  Many of the classic confidence intervals are described in Smithson,
+M. (2003, ISBN: 978-0761924999).  Bootstrap confidence intervals are
+calculated with the R package @code{boot}.  Both one- and two-sided intervals
+are supported.")
+    (license license:gpl2+)))
+
 (define-public r-adaptivesparsity
   (package
     (name "r-adaptivesparsity")
@@ -29398,14 +29427,14 @@ object sizes.")
 (define-public r-yardstick
   (package
     (name "r-yardstick")
-    (version "1.0.0")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "yardstick" version))
        (sha256
         (base32
-         "0mnpvwbzybxp47w4yibmjb7xppwinbjcqcyqfn8qn38l5liwy8yd"))))
+         "0bcirq9mp7c6kwx563nnsd4lk33xk0rfaakj1xj5r8pzmrcgbikj"))))
     (properties `((upstream-name . "yardstick")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29453,13 +29482,13 @@ observations.")
 (define-public r-scico
   (package
     (name "r-scico")
-    (version "1.3.0")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "scico" version))
        (sha256
-        (base32 "08grfbjd5s0vdw76ni37yjl2242rr8i2jy72sgpwgra282hpnji3"))))
+        (base32 "1f2czfhzdpi5dqjbxvbrrcnxjpylc5zzghj70ihlh2agq3n9hw5g"))))
     (properties `((upstream-name . "scico")))
     (build-system r-build-system)
     (propagated-inputs (list r-scales))
@@ -29778,14 +29807,14 @@ final SQL translation of the algorithm.  It currently supports @code{lm()},
 (define-public r-janeaustenr
   (package
     (name "r-janeaustenr")
-    (version "0.1.5")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "janeaustenr" version))
        (sha256
         (base32
-         "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
+         "1ap8p1lpbj2wz90mpf1vbyzhv2spzv03bi8lwzpsir2y77hjxhxl"))))
     (properties `((upstream-name . "janeaustenr")))
     (build-system r-build-system)
     (home-page "https://github.com/juliasilge/janeaustenr")
@@ -29870,14 +29899,14 @@ consistent interface, and the package is built on the @code{stringi} and
 (define-public r-hunspell
   (package
     (name "r-hunspell")
-    (version "3.0.1")
+    (version "3.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hunspell" version))
        (sha256
         (base32
-         "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z"))))
+         "0kij39rhsx7s4lfddy6745f1zjyi003srj14ckjpbhkcyxamk8jy"))))
     (properties `((upstream-name . "hunspell")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29904,14 +29933,14 @@ vignettes in all common formats.")
 (define-public r-tidytext
   (package
     (name "r-tidytext")
-    (version "0.3.3")
+    (version "0.3.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidytext" version))
        (sha256
         (base32
-         "0kljaxyhhzbcv9jkjdy0wn6gkamh25y2xfb9k11sqhz3lv72nfvm"))))
+         "0mk75wdiy4mixj1xlksw9ns4ajlj8ak90sgchjcg1zb90qp7gg56"))))
     (properties `((upstream-name . "tidytext")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29939,14 +29968,14 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
 (define-public r-parsnip
   (package
     (name "r-parsnip")
-    (version "1.0.0")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "parsnip" version))
        (sha256
         (base32
-         "0lwz95ff69arbl2mpmnkwjf24cgb866nr3frkb89va91gp1w9691"))))
+         "0pzr39jhlzjhm2nx1zcgd0mdxd4dxbdzhzc1qrvfsz05jwfb6xxy"))))
     (properties `((upstream-name . "parsnip")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29980,14 +30009,14 @@ functions or computational engines (e.g. R, Spark, Stan, etc).")
 (define-public r-infer
   (package
     (name "r-infer")
-    (version "1.0.2")
+    (version "1.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "infer" version))
        (sha256
         (base32
-         "0qfrxljvwpa8d1k66ii80irarlv593wr6rmcsmi4flc7adgydrnp"))))
+         "1m5srhcmkh8wq12pvy57g3g703wilkl8r3gmm5s7lbj103iz7v8b"))))
     (properties `((upstream-name . "infer")))
     (build-system r-build-system)
     (propagated-inputs
@@ -30014,14 +30043,14 @@ expressive statistical grammar that coheres with the Tidy design framework.")
 (define-public r-modeldata
   (package
     (name "r-modeldata")
-    (version "1.0.0")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "modeldata" version))
        (sha256
         (base32
-         "16ad8g86alahirgmp8bhb6v1ghayw965bdz5mrpnq7nnncazaqcm"))))
+         "0ik4r25l69brkf0l248bln1kicy7dpi6mziwn19by8rq3f8fylhy"))))
     (properties `((upstream-name . "modeldata")))
     (build-system r-build-system)
     (propagated-inputs
@@ -30164,14 +30193,14 @@ package also provides functions to visualize the observed data and the MLE.")
 (define-public r-metafor
   (package
     (name "r-metafor")
-    (version "3.4-0")
+    (version "3.8-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "metafor" version))
        (sha256
         (base32
-         "0vn244xfgq7yxwl6ykvadb305z360ssc9vzva7kbcdfiqhhvrqcj"))))
+         "05053cvk65fh2p4wrmygkvgqvrl73kz22rdbxsjxhi21jmzmg56n"))))
     (properties `((upstream-name . "metafor")))
     (build-system r-build-system)
     (propagated-inputs
@@ -30200,14 +30229,14 @@ phylogenetic relatedness) can also be conducted.")
 (define-public r-altmeta
   (package
     (name "r-altmeta")
-    (version "4.0")
+    (version "4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "altmeta" version))
        (sha256
         (base32
-         "17cyiydf4n5j64izj7jph2v43h4x9kfd5b0x6m0ik5ci2aw8xzr5"))))
+         "01v308389wqzp35icrp9ssb4y4gxwjzl600qw47c6rmm6s2mxzjh"))))
     (properties `((upstream-name . "altmeta")))
     (build-system r-build-system)
     (propagated-inputs
@@ -30379,14 +30408,14 @@ data to rasters.  It speeds up plotting of data with millions of points.")
 (define-public r-seuratobject
   (package
     (name "r-seuratobject")
-    (version "4.1.0")
+    (version "4.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "SeuratObject" version))
        (sha256
         (base32
-         "018anas8a9m3kh9jn5370v64d93k64z3iic13a75hp6r7g5hd94w"))))
+         "1h8b90vg9ysczk3p625n07bfrhmph3cxv9ymh896hqr7rn2qbwd6"))))
     (properties `((upstream-name . "SeuratObject")))
     (build-system r-build-system)
     (propagated-inputs
@@ -30558,17 +30587,18 @@ distributed as independent packages.")
 (define-public r-phangorn
   (package
     (name "r-phangorn")
-    (version "2.9.0")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "phangorn" version))
        (sha256
         (base32
-         "08ys4vgmsp070v3119wzl1nrgx359427gb6lcxj67p5y0bhdnqij"))))
+         "1kjxp352jdk1amxpk9jrql490d0qy79zm65y8szyxrm1adqghlyi"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ape
+           r-digest
            r-fastmatch
            r-generics
            r-igraph
@@ -30616,14 +30646,14 @@ rate speciation and extinction.")
 (define-public r-calculus
   (package
     (name "r-calculus")
-    (version "0.3.3")
+    (version "0.3.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "calculus" version))
        (sha256
         (base32
-         "1fhvr0l2mqik3d95v0vanafxmiab147g5a87q956g2i945wc5f22"))))
+         "0hpibnbxl3ngfgzxq8cp9hxsn1yv03dnxyycm3gkr5iv5gkbbpw9"))))
     (properties `((upstream-name . "calculus")))
     (build-system r-build-system)
     (propagated-inputs
@@ -30814,13 +30844,13 @@ Services (AWS) Simple Storage Service (S3) REST API.")
 (define-public r-lgr
   (package
     (name "r-lgr")
-    (version "0.4.3")
+    (version "0.4.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "lgr" version))
               (sha256
                (base32
-                "18s92qyakhvp336kk2777ydypwfrfwfz6a1gqkq812zy3kcb4mcc"))))
+                "09x1vw6cnc1c0p0ylcz1q1vcxyaf1kljhh7ni3gl5jm19zii2h4c"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-r6))
@@ -30931,8 +30961,8 @@ resampled, benchmarked, and tuned.")
     (license license:lgpl3)))
 
 (define-public r-mlr3ordinal
-  (let ((commit "9febac983b11b7b1f477e5cf0212e5999cd2ed44")
-        (revision "0"))
+  (let ((commit "736e3a39be6b7088b650297cc6d90208ec58c0d7")
+        (revision "1"))
     (package
       (name "r-mlr3ordinal")
       (version (git-version "0.1.0-9000" revision commit))
@@ -30944,7 +30974,7 @@ resampled, benchmarked, and tuned.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1icfhz1pjm0mlsn2y60gsrbk31b2p7xmpx3xsg7639rcgdb5f9gl"))))
+                  "0ipf6n4m6giicn0x7f3lrfmbqkhw8zkz32hzq2xf209wndkqhqm1"))))
       (build-system r-build-system)
       (propagated-inputs
        (list r-checkmate
@@ -30986,13 +31016,13 @@ implemented as @code{R6} classes.")
 (define-public r-mlr3
   (package
     (name "r-mlr3")
-    (version "0.13.4")
+    (version "0.14.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mlr3" version))
               (sha256
                (base32
-                "13g0krjry0da1yfm6hrdq63ga5rwag5lkgp375394michiipnbwk"))))
+                "0cnyby4947g1w0h45nd3ld5zr4k19xrwp565mq1hnqkjwmyjsgdj"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-r6
@@ -31023,13 +31053,13 @@ computational operations, add-on packages provide additional functionality.")
 (define-public r-mlr3learners
   (package
     (name "r-mlr3learners")
-    (version "0.5.3")
+    (version "0.5.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mlr3learners" version))
               (sha256
                (base32
-                "088i2piv7sgxsvc7jyr6mq53vqf8yjdlrysgqphsryq6k50i00zd"))))
+                "0sa2qjvhvjzsfssln9ah08zknzdcps1z28xzgkdfgi6dj25a0y3k"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-checkmate
@@ -31050,14 +31080,14 @@ vector machines, and gradient boosting.")
 (define-public r-bbotk
   (package
     (name "r-bbotk")
-    (version "0.5.3")
+    (version "0.5.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bbotk" version))
        (sha256
         (base32
-         "13qj8qysqismv9k9rfw770r7w8jdaw82n71k7sp3wsrlhxjxw734"))))
+         "02dp0b62dv02rvxsgj63mkmmcdzrlf06vxjr5gqy9rhq5s2mg4fa"))))
     (properties `((upstream-name . "bbotk")))
     (build-system r-build-system)
     (propagated-inputs
@@ -31080,13 +31110,13 @@ annealing.")
 (define-public r-mlr3tuning
   (package
     (name "r-mlr3tuning")
-    (version "0.13.1")
+    (version "0.14.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mlr3tuning" version))
               (sha256
                (base32
-                "0jfslx6pwk408ydn69grrvsp22jd7gsjmwvss0a1j0zav3q1pvks"))))
+                "10q4m37sg79y1v0gwk7bjrnc5b0a6sb80ramnza93mx9gx3vl99m"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-bbotk
@@ -32252,14 +32282,14 @@ BTM-WWW13.pdf}.")
 (define-public r-delaporte
   (package
     (name "r-delaporte")
-    (version "8.0.2")
+    (version "8.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Delaporte" version))
        (sha256
         (base32
-         "10xsmms2jfw7x4hmgpd35dv4n4azpjzmfid6585kg6qfh2zg23g5"))))
+         "1d1jkbxlwnqznh9pkjpkr7np2nmqzjvrdmlb210y1lb08mqmb73w"))))
     (properties `((upstream-name . "Delaporte")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
@@ -32507,14 +32537,14 @@ complex functions.")
 (define-public r-gganimate
   (package
     (name "r-gganimate")
-    (version "1.0.7")
+    (version "1.0.8")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "gganimate" version))
         (sha256
           (base32
-            "046v6j92xxgaghsnh88dy5h8x040qsfa8csvhp4dmsfmrrf0dz0f"))))
+            "1jabs9qr0319w508kdsk5nmzfhl6nzykpp1by7l639yfvrfqcbd1"))))
     (properties `((upstream-name . "gganimate")))
     (build-system r-build-system)
     (arguments
@@ -32531,7 +32561,6 @@ complex functions.")
     (propagated-inputs
       (list r-ggplot2
             r-glue
-            r-plyr
             r-progress
             r-rlang
             r-scales
@@ -32768,14 +32797,14 @@ Apache2.")
 (define-public r-exactextractr
   (package
     (name "r-exactextractr")
-    (version "0.8.2")
+    (version "0.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "exactextractr" version))
        (sha256
         (base32
-         "0x4axrq9iznvajqy07gcfcrvzniz5yj6wabchgksg0fqz0xancnc"))))
+         "13di9s0lv9kdv2p3hp9ksrr0rh98z6m998pj5a1xq9zl6iakankh"))))
     (properties `((upstream-name . "exactextractr")))
     (build-system r-build-system)
     (inputs (list geos))
@@ -32818,14 +32847,14 @@ the @code{raster} package that is suitable for extracting raster values using
 (define-public r-rapiserialize
   (package
     (name "r-rapiserialize")
-    (version "0.1.1")
+    (version "0.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RApiSerialize" version))
        (sha256
         (base32
-         "0gkix6s5hb7pdbb8miyz36hghx59hhwxql0slqnlr5nakh31klxp"))))
+         "02k0l8bi849b2102ysb102xky4p84i9v2r4w6fab7bgf32wvph4w"))))
     (properties `((upstream-name . "RApiSerialize")))
     (build-system r-build-system)
     (home-page
@@ -32842,14 +32871,14 @@ package.")
 (define-public r-qs
   (package
     (name "r-qs")
-    (version "0.25.3")
+    (version "0.25.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "qs" version))
        (sha256
         (base32
-         "0sxy497v5arjv6lwxng7chkbzrn703waqmgsxv77i7y12ahzdbai"))))
+         "0cx5k0mzn6bm8ff58yrqz3hjidxcawxgqbpijnynvin1m4395i4j"))))
     (properties `((upstream-name . "qs")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -32891,14 +32920,14 @@ C API for topology operations on geometries.")
 (define-public r-tfruns
   (package
     (name "r-tfruns")
-    (version "1.5.0")
+    (version "1.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tfruns" version))
        (sha256
         (base32
-         "04lfckg1if3kfwcl4s4fcc9aw04crwk4m1qr55ag22j2x2jlb2l9"))))
+         "1xk7dl51xd1h54798xwycvxmn77jv80in61hanm36zk0024wpxg8"))))
     (properties `((upstream-name . "tfruns")))
     (build-system r-build-system)
     (propagated-inputs
@@ -33252,18 +33281,24 @@ fully reproducible.")
 (define-public r-paws-common
   (package
     (name "r-paws-common")
-    (version "0.4.0")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "paws.common" version))
        (sha256
         (base32
-         "1zlv0ahv633z1fwx1syajzqg49zd9hs537df53gm2qch8b66y4bh"))))
+         "12dz3giv1xajdqq79s5gin9kw4x74w2iaw62ha6ssf8whrc3wmh5"))))
     (properties `((upstream-name . "paws.common")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-base64enc r-curl r-digest r-httr r-jsonlite r-xml2))
+     (list r-base64enc
+           r-curl
+           r-digest
+           r-httr
+           r-jsonlite
+           r-rcpp
+           r-xml2))
     (home-page "https://cran.r-project.org/package=paws.common")
     (synopsis "Paws low-level Amazon Web Services API")
     (description
@@ -33560,14 +33595,14 @@ services, including Simple Storage Service (S3).")
 (define-public r-paws-compute
   (package
     (name "r-paws-compute")
-    (version "0.1.12")
+    (version "0.1.13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "paws.compute" version))
        (sha256
         (base32
-         "1km6fng6il5fcjlrbbndahsw2dr2ql83hwac9wlpd67zm3wy9lky"))))
+         "1s7g4y2h763xf32p08drs3ygkfqb2zjikkgxb7yl91gk13zp7kjm"))))
     (properties `((upstream-name . "paws.compute")))
     (build-system r-build-system)
     (propagated-inputs
@@ -33673,14 +33708,14 @@ zoom/navigate any plot when called with any active plot.")
 (define-public r-zoolog
   (package
     (name "r-zoolog")
-    (version "1.0.1")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "zoolog" version))
        (sha256
         (base32
-         "00fi7czfwr0ll9070w3ijskd0xvilj02gy8wkgqzzrlilij8ah7p"))))
+         "06g44gjk9w73996n4h1a2q8kcd6q2mvm1vhx0iq0785gvrz18pj9"))))
     (properties `((upstream-name . "zoolog")))
     (build-system r-build-system)
     (propagated-inputs
@@ -33910,14 +33945,14 @@ neighborhood graphs, and relatives.")
 (define-public r-crul
   (package
     (name "r-crul")
-    (version "1.2.0")
+    (version "1.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "crul" version))
        (sha256
         (base32
-         "133g0skz4lifl8hm8pqdryd2m2drbrm6mdfzbbsrw8fg46di86my"))))
+         "0b8y12wb5kjylr8b4a2iarb5rpw1ydinw3lxp2ssq91pidyn2n40"))))
     (properties `((upstream-name . "crul")))
     (build-system r-build-system)
     (propagated-inputs
@@ -34071,14 +34106,14 @@ configuration of status code, short description, and verbose message.")
 (define-public r-webmockr
   (package
     (name "r-webmockr")
-    (version "0.8.0")
+    (version "0.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "webmockr" version))
        (sha256
         (base32
-         "0j40srwi0yasmllb9wsww4m6zkiyzqd549cis4dxd7c7p24hak8j"))))
+         "06lqv3v095i51xsac8bvkjgd58l6a5azamchiip8m2y7q0nm4iw9"))))
     (properties `((upstream-name . "webmockr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -34122,13 +34157,13 @@ parsing.")
 (define-public r-wordspace
   (package
     (name "r-wordspace")
-    (version "0.2-7")
+    (version "0.2-8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "wordspace" version))
        (sha256
-        (base32 "0hrjv5mag7gwl4wj7np248sdyns5i623wl37b11hlgalhbmlypyf"))))
+        (base32 "17fqd4zrsklv2ik3lg00x66yasfh1kyhs3k9ri6lrk56wwv6hzb2"))))
     (properties `((upstream-name . "wordspace")))
     (build-system r-build-system)
     (propagated-inputs
@@ -34389,18 +34424,24 @@ be efficient and easy to use.")
 (define-public r-ggh4x
   (package
     (name "r-ggh4x")
-    (version "0.2.1")
+    (version "0.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggh4x" version))
        (sha256
         (base32
-         "1r49yfm5fqv5s7jb92ad6rf8hd9plcry6f500czjhnhhrp16cqfp"))))
+         "11mskrby3gyjhkvnkcwl2ar1bdh4h45y48dfnm4kzgc7nwvdl3ia"))))
     (properties `((upstream-name . "ggh4x")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-ggplot2 r-gtable r-rlang r-scales r-vctrs))
+     (list r-cli
+           r-ggplot2
+           r-gtable
+           r-lifecycle
+           r-rlang
+           r-scales
+           r-vctrs))
     (native-inputs
      (list r-knitr))
     (home-page "https://github.com/teunbrand/ggh4x")
diff --git a/gnu/packages/crates-graphics.scm b/gnu/packages/crates-graphics.scm
index a8551c8f9f..19fc841b63 100644
--- a/gnu/packages/crates-graphics.scm
+++ b/gnu/packages/crates-graphics.scm
@@ -3282,7 +3282,10 @@ crate @code{rust-wayland-client} for usable bindings.")
         ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2)
         ("rust-web-sys" ,rust-web-sys-0.3)
         ("rust-winapi" ,rust-winapi-0.3)
-        ("rust-x11-dl" ,rust-x11-dl-2))))
+        ("rust-x11-dl" ,rust-x11-dl-2))
+       #:cargo-development-inputs
+       (("rust-console-log" ,rust-console-log-0.2)
+        ("rust-simple-logger" ,rust-simple-logger-1))))
     (inputs
      (list rust-wayland-client-0.29 rust-wayland-protocols-0.29))
     (home-page "https://github.com/rust-windowing/winit")
@@ -3338,7 +3341,10 @@ the platform-specific getters provided by winit, or another library.")
         ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2)
         ("rust-web-sys" ,rust-web-sys-0.3)
         ("rust-winapi" ,rust-winapi-0.3)
-        ("rust-x11-dl" ,rust-x11-dl-2))))
+        ("rust-x11-dl" ,rust-x11-dl-2))
+       #:cargo-development-inputs
+       (("rust-console-log" ,rust-console-log-0.2)
+        ("rust-simple-logger" ,rust-simple-logger-1))))
     (inputs
      (list rust-wayland-client-0.28))))
 
diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index f09ac91df5..538267c560 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
author	Ludovic Courtès <ludo@gnu.org>	2021-10-17 00:34:27 +0200
committer	Ludovic Courtès <ludo@gnu.org>	2021-10-17 00:34:27 +0200
commit	618ffc0ad52ae0f8a467561d16d6aab05739fca0 (patch)
tree	a22907965d0c8b0dc80510539fd5bdf2633f7e3f /tests/guix-daemon.sh
parent	258bbc4fdcc8a0538c9b151d5a8e82a82092a3cb (diff)
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