Merge branch 'master' into gnome-team

Change-Id: I62da840b7600f2d3d8541e666d09e2f2a1b7d8c4

Makefile.am

@@ -13,11 +13,12 @@
 # Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
 # Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
 # Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
-# Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
+# Copyright © 2019, 2023 Efraim Flashner <efraim@flashner.co.il>
 # Copyright © 2020, 2021, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 # Copyright © 2021 Chris Marusich <cmmarusich@gmail.com>
 # Copyright © 2021 Andrew Tropin <andrew@trop.in>
 # Copyright © 2023 Clément Lassieur <clement@lassieur.org>
+# Copyright © 2023 Wilko Meyer <w@wmeyer.eu>
 #
 # This file is part of GNU Guix.
 #
@@ -185,6 +186,7 @@ MODULES =					\
   guix/build-system/texlive.scm			\
   guix/build-system/tree-sitter.scm		\
   guix/build-system/trivial.scm			\
+  guix/build-system/vim.scm			\
   guix/build-system/zig.scm			\
   guix/ftp-client.scm				\
   guix/http-client.scm				\
@@ -243,6 +245,7 @@ MODULES =					\
   guix/build/scons-build-system.scm		\
   guix/build/texlive-build-system.scm		\
   guix/build/tree-sitter-build-system.scm	\
+  guix/build/vim-build-system.scm		\
   guix/build/waf-build-system.scm		\
   guix/build/haskell-build-system.scm		\
   guix/build/julia-build-system.scm		\
@@ -413,6 +416,10 @@ AUX_FILES =						\
   gnu/packages/aux-files/chromium/master-preferences.json		\
   gnu/packages/aux-files/emacs/guix-emacs.el		\
   gnu/packages/aux-files/guix.vim			\
+  gnu/packages/aux-files/linux-libre/6.6-arm.conf	\
+  gnu/packages/aux-files/linux-libre/6.6-arm64.conf	\
+  gnu/packages/aux-files/linux-libre/6.6-i686.conf	\
+  gnu/packages/aux-files/linux-libre/6.6-x86_64.conf	\
   gnu/packages/aux-files/linux-libre/6.5-arm.conf	\
   gnu/packages/aux-files/linux-libre/6.5-arm64.conf	\
   gnu/packages/aux-files/linux-libre/6.5-i686.conf	\

doc/contributing.texi

@@ -29,6 +29,7 @@ choice.
 * Submitting Patches::          Share your work.
 * Tracking Bugs and Changes::   Keeping it all organized.
 * Commit Access::               Pushing to the official repository.
+* Reviewing the Work of Others::  Some guidelines for sharing reviews.
 * Updating the Guix Package::   Updating the Guix package definition.
 * Writing Documentation::       Improving documentation in GNU Guix.
 * Translating Guix::            Make Guix speak your native language.
@@ -190,7 +191,7 @@ After updating the repository, @command{make} might fail with an error
 similar to the following example:
 
 @example
-error: failed to load 'gnu/packages/dunst.scm':
+error: failed to load 'gnu/packages/linux.scm':
 ice-9/eval.scm:293:34: In procedure abi-check: #<record-type <origin>>: record ABI mismatch; recompilation needed
 @end example
 
@@ -385,6 +386,7 @@ copyright-update}.  If you want to do it automatically after each buffer
 save then add @code{(add-hook 'after-save-hook 'copyright-update)} in
 Emacs.
 
+@node Viewing Bugs within Emacs
 @subsection Viewing Bugs within Emacs
 
 Emacs has a nice minor mode called @code{bug-reference}, which, when
@@ -452,6 +454,13 @@ configuration file:
           (group (zero-or-one "cgi/bugreport.cgi?bug="))
           (group-n 3 (one-or-more digit))
           line-end))
+
+;; Reduce the number of prompts with 'M-x debbugs-gnu'.
+(setq debbugs-gnu-default-packages '("guix" "guix-patches"))
+
+;; Show feature requests.
+(setq debbugs-gnu-default-severities
+ '("serious" "important" "normal" "minor" "wishlist"))
 @end lisp
 
 For more information, refer to @ref{Bug Reference,,, emacs, The GNU
@@ -1279,11 +1288,16 @@ implement low-level concepts, such as the @code{memoize} procedure.
 
 @node Modules
 @subsection Modules
-
+@cindex build-side modules
+@cindex host-side modules
 Guile modules that are meant to be used on the builder side must live in
 the @code{(guix build @dots{})} name space.  They must not refer to
 other Guix or GNU modules.  However, it is OK for a ``host-side'' module
-to use a build-side module.
+to use a build-side module.  As an example, the @code{(guix
+search-paths)} module should not be imported and used by a package since
+it isn't meant to be used as a ``build-side'' module.  It would also
+couple the module with the package's dependency graph, which is
+undesirable.
 
 Modules that deal with the broader GNU system should be in the
 @code{(gnu @dots{})} name space rather than @code{(guix @dots{})}.
@@ -1862,7 +1876,7 @@ browse issues:
 interface@footnote{The web interface at
 @url{https://issues.guix.gnu.org} is powered by Mumi, a nice piece of
 software written in Guile, and you can help!  See
-@url{https://git.elephly.net/gitweb.cgi?p=software/mumi.git}.} to browse
+@url{https://git.savannah.gnu.org/cgit/guix/mumi.git}.} to browse
 bug reports and patches, and to participate in discussions;
 @item
 @url{https://bugs.gnu.org/guix} lists bug reports;
@@ -1969,6 +1983,15 @@ For example, to list all open issues on @code{guix-patches}, hit:
 @kbd{C-u} @kbd{M-x} debbugs-gnu @kbd{RET} @kbd{RET} guix-patches @kbd{RET} n y
 @end example
 
+For a more convenient (shorter) way to access both the bugs and patches
+submissions, you may want to configure the
+@code{debbugs-gnu-default-packages} and
+@code{debbugs-gnu-default-severities} Emacs variables (@pxref{Viewing
+Bugs within Emacs}).
+
+To search for bugs, @samp{@kbd{M-x} debbugs-gnu-guix-search} can be
+used.
+
 @xref{Top,,, debbugs-ug, Debbugs User Guide}, for more information on
 this nifty tool!
 
@@ -1981,7 +2004,12 @@ Debbugs provides a feature called @dfn{usertags} that allows any user to
 tag any bug with an arbitrary label.  Bugs can be searched by usertag,
 so this is a handy way to organize bugs@footnote{The list of usertags is
 public information, and anyone can modify any user's list of usertags,
-so keep that in mind if you choose to use this feature.}.
+so keep that in mind if you choose to use this feature.}.  If you use
+Emacs Debbugs, the entry-point to consult existing usertags is the
+@samp{C-u M-x debbugs-gnu-usertags} procedure.  To set a usertag, press
+@samp{C} while consulting a bug within the *Guix-Patches* buffer opened
+with @samp{C-u M-x debbugs-gnu-bugs} buffer, then select @code{usertag}
+and follow the instructions.
 
 For example, to view all the bug reports (or patches, in the case of
 @code{guix-patches}) tagged with the usertag @code{powerpc64le-linux}
@@ -1994,9 +2022,9 @@ documentation for Debbugs or the documentation for whatever tool you use
 to interact with Debbugs.
 
 In Guix, we are experimenting with usertags to keep track of
-architecture-specific issues.  To facilitate collaboration, all our
+architecture-specific issues, as well as reviewed ones.  To facilitate
-usertags are associated with the single user @code{guix}.  The following
+collaboration, all our usertags are associated with the single user
-usertags currently exist for that user:
+@code{guix}.  The following usertags currently exist for that user:
 
 @table @code
 
@@ -2014,6 +2042,9 @@ For issues related to reproducibility.  For example, it would be
 appropriate to assign this usertag to a bug report for a package that
 fails to build reproducibly.
 
+@item reviewed-looks-good
+You have reviewed the series and it looks good to you (LGTM).
+
 @end table
 
 If you're a committer and you want to add a usertag, just start using it
@@ -2283,6 +2314,100 @@ only push their own awesome changes, but also offer some of their time
 you're welcome to use your expertise and commit rights to help other
 contributors, too!
 
+@node Reviewing the Work of Others
+@section Reviewing the Work of Others
+
+Perhaps the biggest action you can do to help GNU Guix grow as a project
+is to review the work contributed by others.  You do not need to be a
+committer to do so; applying, reading the source, building, linting and
+running other people's series and sharing your comments about your
+experience will give some confidence to committers.  Basically, you gmust
+ensure the check list found in the @ref{Submitting Patches} section has
+been correctly followed.  A reviewed patch series should give the best
+chances for the proposed change to be merged faster, so if a change you
+would like to see merged hasn't yet been reviewed, this is the most
+appropriate thing to do!
+
+@cindex reviewing, guidelines
+Review comments should be unambiguous; be as clear and explicit as you
+can about what you think should be changed, ensuring the author can take
+action on it.  Please try to keep the following guidelines in mind
+during review:
+
+@enumerate
+@item
+@emph{Be clear and explicit about changes you are suggesting}, ensuring
+the author can take action on it.  In particular, it is a good idea to
+explicitly ask for new revisions when you want it.
+
+@item
+@emph{Remain focused: do not change the scope of the work being
+reviewed.}  For example, if the contribution touches code that follows a
+pattern deemed unwieldy, it would be unfair to ask the submitter to fix
+all occurrences of that pattern in the code; to put it simply, if a
+problem unrelated to the patch at hand was already there, do not ask the
+submitter to fix it.
+
+@item
+@emph{Ensure progress.}  As they respond to review, submitters may
+submit new revisions of their changes; avoid requesting changes that you
+did not request in the previous round of comments.  Overall, the
+submitter should get a clear sense of progress; the number of items open
+for discussion should clearly decrease over time.
+
+@item
+@emph{Aim for finalization.}  Reviewing code is time-consuming.  Your
+goal as a reviewer is to put the process on a clear path towards
+integration, possibly with agreed-upon changes, or rejection, with a
+clear and mutually-understood reasoning.  Avoid leaving the review
+process in a lingering state with no clear way out.
+
+@item
+@emph{Review is a discussion.}  The submitter's and reviewer's views on
+how to achieve a particular change may not always be aligned.  To lead
+the discussion, remain focused, ensure progress and aim for
+finalization, spending time proportional to the stakes@footnote{The
+tendency to discuss minute details at length is often referred to as
+``bikeshedding'', where much time is spent discussing each one's
+preference for the color of the shed at the expense of progress made on
+the project to keep bikes dry.}.  As a reviewer, try hard to explain the
+rationale for suggestions you make, and to understand and take into
+account the submitter's motivation for doing things in a certain way.
+@end enumerate
+
+@cindex LGTM, Looks Good To Me
+@cindex review tags
+@cindex Reviewed-by, git trailer
+When you deem the proposed change adequate and ready for inclusion
+within Guix, the following well understood/codified
+@samp{Reviewed-by:@tie{}Your@tie{}Name<your-email@@example.com>}
+@footnote{The @samp{Reviewed-by} Git trailer is used by other projects
+such as Linux, and is understood by third-party tools such as the
+@samp{b4 am} sub-command, which is able to retrieve the complete
+submission email thread from a public-inbox instance and add the Git
+trailers found in replies to the commit patches.} line should be used to
+sign off as a reviewer, meaning you have reviewed the change and that it
+looks good to you:
+
+@itemize
+@item
+If the @emph{whole} series (containing multiple commits) looks good to
+you, reply with @samp{Reviewed-by:@tie{}Your@tie{}Name<your-email@@example.com>}
+to the cover page if it has one, or to the last patch of the series
+otherwise, adding another @samp{(for the whole series)} comment on the
+line below to explicit this fact.
+
+@item
+If you instead want to mark a @emph{single commit} as reviewed (but not
+the whole series), simply reply with
+@samp{Reviewed-by:@tie{}Your@tie{}Name<your-email@@example.com>} to that
+commit message.
+@end itemize
+
+If you are not a committer, you can help others find a @emph{series} you
+have reviewed more easily by adding a @code{reviewed-looks-good} usertag
+for the @code{guix} user (@pxref{Debbugs Usertags}).
+
 @node Updating the Guix Package
 @section Updating the Guix Package
 

doc/guix.texi

@@ -8375,6 +8375,13 @@ hash @var{hash} of type @var{hash-algo} (a symbol).  Use @var{name} as
 the file name, or a generic name if @code{#f}.
 @end deffn
 
+@deffn {Procedure} git-fetch/lfs ref hash-algo hash
+This is a variant of the @code{git-fetch} procedure that supports the
+Git @acronym{LFS, Large File Storage} extension.  This may be useful to
+pull some binary test data to run the test suite of a package, for
+example.
+@end deffn
+
 @deftp {Data Type} git-reference
 This data type represents a Git reference for @code{git-fetch} to
 retrieve.
@@ -9441,6 +9448,41 @@ e.g., install @file{foo/sub/file} to @file{share/my-app/sub/file}.
 @end itemize
 @end defvar
 
+@defvar vim-build-system
+This variable is exported by @code{(guix build-system vim)}.  It is an
+extension of the @code{copy-build-system}, installing Vim and Neovim plugins
+into locations where these two text editors know to find their plugins, using
+their packpaths.
+
+Packages which are prefixed with @code{vim-} will be installed in Vim's
+packpath, while those prefixed with @code{neovim-} will be installed in
+Neovim's packpath.  If there is a @code{doc} directory with the plugin then
+helptags will be generated automatically.
+
+There are a couple of keywords added with the @code{vim-build-system}:
+@itemize
+@item With @code{plugin-name} it is possible to set the name of the plugin.
+While by default this is set to the name and version of the package, it is
+often more helpful to set this to name which the upstream author calls their
+plugin.  This is the name used for @command{:packadd} from inside Vim.
+@item With @code{install-plan} it is possible to augment the built-in
+install-plan of the @code{vim-build-system}.  This is particularly helpful if
+you have files which should be installed in other locations.  For more
+information about using the @code{install-plan}, see the
+@code{copy-build-system} (@pxref{Build Systems, @code{copy-build-system}}).
+@item With @code{#:vim} it is possible to add this package to Vim's packpath,
+in addition to if it is added automatically because of the @code{vim-} prefix
+in the package's name.
+@item With @code{#:neovim} it is possible to add this package to Neovim's
+packpath, in addition to if it is added automatically because of the
+@code{neovim-} prefix in the package's name.
+@item With @code{#:mode} it is possible to adjust the path which the plugin is
+installed into.  By default the plugin is installed into @code{start} and other
+options are available, including @code{opt}.  Adding a plugin into @code{opt}
+will mean you will need to run, for example, @command{:packadd foo} to load the
+@code{foo} plugin from inside of Vim.
+@end itemize
+@end defvar
 
 @cindex Clojure (programming language)
 @cindex simple Clojure build system
@@ -44510,6 +44552,40 @@ The @code{(gnu home services desktop)} module provides services that you
 may find useful on ``desktop'' systems running a graphical user
 environment such as Xorg.
 
+@cindex X Window, for Guix Home services
+@cindex X11, in Guix Home
+@defvar home-x11-service-type
+This is the service type representing the X Window graphical display
+server (also referred to as ``X11'').
+
+X Window is necessarily started by a system service; on Guix System,
+starting it is the responsibility of @code{gdm-service-type} and similar
+services (@pxref{X Window}).  At the level of Guix Home, as an
+unprivileged user, we cannot start X Window; all we can do is check
+whether it is running.  This is what this service does.
+
+As a user, you probably don't need to worry or explicitly instantiate
+@code{home-x11-service-type}.  Services that require an X Window
+graphical display, such as @code{home-redshift-service-type} below,
+instantiate it and depend on its corresponding @code{x11-display}
+Shepherd service (@pxref{Shepherd Home Service}).
+
+When X Window is running, the @code{x11-display} Shepherd service starts
+and sets the @env{DISPLAY} environment variable of the
+@command{shepherd} process, using its original value if it was already
+set; otherwise, it fails to start.
+
+The service can also be forced to use a given value for @env{DISPLAY},
+like so:
+
+@example
+herd start x11-display :3
+@end example
+
+In the example above, @code{x11-display} is instructed to set
+@env{DISPLAY} to @code{:3}.
+@end defvar
+
 @defvar home-redshift-service-type
 This is the service type for @uref{https://github.com/jonls/redshift,
 Redshift}, a program that adjusts the display color temperature

etc/completion/fish/guix.fish

@@ -298,7 +298,7 @@ complete -f -c guix -n '__fish_guix_using_command publish' -l repl -d '[=PORT] s
 
 #### lint
 set -l remotecommands checkers list-checkers
-complete -f -c guix -n '__fish_guix_needs_command' -a lint -d 'Run a set of checkers on the specificied package.'
+complete -f -c guix -n '__fish_guix_needs_command' -a lint -d 'Run a set of checkers on the specified package.'
 complete -f -c guix -n '__fish_guix_using_command lint' -l list-checkers -d 'Display the list of available lint checkers.'
 complete -f -c guix -n '__fish_guix_using_command lint' -l checkers -d 'Only run the specified checkers.'
 complete -f -c guix -n '__fish_guix_using_command lint' -l description -d 'Validate package descriptions.'
@@ -327,7 +327,7 @@ complete -f -c guix -n '__fish_guix_using_command import; and not __fish_seen_su
 ##### import cpan
 complete -f -c guix -n '__fish_guix_using_command import; and not __fish_seen_subcommand_from $remotecommands' -a cpan -d 'Import and convert the CPAN package for PACKAGE-NAME.'
 ##### import hackage
-complete -f -c guix -n '__fish_guix_using_command import; and not __fish_seen_subcommand_from $remotecommands' -a hackage -d 'Import and convert the Hackage package for PACKAGE-NAME.  If PACKAGE-NAME includes a suffix constituted by a at-sign followed by a numerical version (as used with Guix packages), then a definition for the specified version of the package will be generated.  If no version suffix is pecified, then the generated package definition will correspond to the latest available version.'
+complete -f -c guix -n '__fish_guix_using_command import; and not __fish_seen_subcommand_from $remotecommands' -a hackage -d 'Import and convert the Hackage package for PACKAGE-NAME.  If PACKAGE-NAME includes a suffix constituted by a at-sign followed by a numerical version (as used with Guix packages), then a definition for the specified version of the package will be generated.  If no version suffix is specified, then the generated package definition will correspond to the latest available version.'
 complete -f -c guix -n '__fish_guix_using_command import; and __fish_seen_subcommand_from hackage' -s e -d 'ALIST specify environment for Cabal evaluation.'
 complete -f -c guix -n '__fish_guix_using_command import; and __fish_seen_subcommand_from hackage' -a "--cabal-environment=" -d 'ALIST specify environment for Cabal evaluation.'
 complete -f -c guix -n '__fish_guix_using_command import; and __fish_seen_subcommand_from hackage' -s s -l stdin -d 'Read from standard input.'

etc/git/gitconfig

@@ -16,3 +16,10 @@
         to = guix-patches@gnu.org
         headerCmd = etc/teams.scm cc-members-header-cmd
         thread = no
+
+[b4]
+        attestation-check-dkim = off
+        attestation-policy = off
+        linkmask = https://yhetil.org/guix/%s
+        linktrailermask = https://yhetil.org/guix/%s
+        midmask = https://yhetil.org/guix/%s

etc/teams.scm

@@ -529,6 +529,15 @@ GLib/GIO, GTK, GStreamer and Webkit."
         #:description "Audio related packages."
         #:scope (list "gnu/packages/audio.scm")))
 
+(define-team zig
+  (team 'zig
+        #:name "Zig team"
+        #:description "Zig, Zig packages, and the zig-build system"
+        #:scope (list "gnu/packages/zig.scm"
+                      "gnu/packages/zig-xyz.scm"
+                      "guix/build/zig-build-system.scm"
+                      "guix/build-system/zig.scm")))
+
 
 (define-member (person "Eric Bavier"
                        "bavier@posteo.net")
@@ -662,6 +671,10 @@ GLib/GIO, GTK, GStreamer and Webkit."
                        "gabriel@erlikon.ch")
   audio)
 
+(define-member (person "Ekaitz Zarraga"
+                       "ekaitz@elenq.tech")
+  bootstrap zig)
+
 
 (define (find-team name)
   (or (hash-ref %teams (string->symbol name))

gnu/home/services/desktop.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2022 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2022-2023 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2022 ( <paren@disroot.org>
 ;;; Copyright © 2023 conses <contact@conses.eu>
 ;;; Copyright © 2023 Janneke Nieuwenhuizen <janneke@gnu.org>
@@ -30,7 +30,9 @@
   #:use-module (guix gexp)
   #:use-module (srfi srfi-1)
   #:use-module (ice-9 match)
-  #:export (home-redshift-configuration
+  #:export (home-x11-service-type
+
+            home-redshift-configuration
             home-redshift-configuration?
             home-redshift-service-type
 
@@ -43,6 +45,79 @@
             home-xmodmap-configuration
             home-xmodmap-service-type))
 
+
+;;;
+;;; Waiting for X11.
+;;;
+
+(define (x11-shepherd-service delay)
+  (list (shepherd-service
+         (provision '(x11-display))
+         (modules '((ice-9 ftw)
+                    (ice-9 match)
+                    (srfi srfi-1)))
+         (start
+          #~(lambda* (#:optional (display (getenv "DISPLAY")))
+              (define x11-directory
+                "/tmp/.X11-unix")
+
+              (define (find-display delay)
+                ;; Wait for an accessible socket to show up in X11-DIRECTORY,
+                ;; up to DELAY seconds.
+                (let loop ((attempts delay))
+                  (define socket
+                    (find (match-lambda
+                            ((or "." "..") #f)
+                            (name
+                             (let ((name (in-vicinity x11-directory
+                                                      name)))
+                               (access? name O_RDWR))))
+                          (or (scandir x11-directory) '())))
+
+                  (if (and socket (string-prefix? "X" socket))
+                      (let ((display (string-append
+                                      ":" (string-drop socket 1))))
+                        (format #t "X11 display server found at ~s.~%"
+                                display)
+                        display)
+                      (if (zero? attempts)
+                          (begin
+                            (format (current-error-port)
+                                    "X11 display server did not show up; \
+giving up.\n")
+                            #f)
+                          (begin
+                            (sleep 1)
+                            (loop (- attempts 1)))))))
+
+              (let ((display (or display (find-display #$delay))))
+                (when display
+                  ;; Note: 'make-forkexec-constructor' calls take their
+                  ;; default #:environment-variables value before this service
+                  ;; is started and are thus unaffected by the 'setenv' call
+                  ;; below.  Users of this service have to explicitly query
+                  ;; its value.
+                  (setenv "DISPLAY" display))
+                display)))
+         (stop #~(lambda (_)
+                   (unsetenv "DISPLAY")
+                   #f))
+         (respawn? #f))))
+
+(define home-x11-service-type
+  (service-type
+   (name 'home-x11-display)
+   (extensions (list (service-extension home-shepherd-service-type
+                                        x11-shepherd-service)))
+   (default-value 10)
+   (description
+    "Create a @code{x11-display} Shepherd service that waits for the X
+Window (or ``X11'') graphical display server to be up and running, up to a
+configurable delay, and sets the @code{DISPLAY} environment variable of
+@command{shepherd} itself accordingly.  If no accessible X11 server shows up
+during that time, the @code{x11-display} service is marked as failing to
+start.")))
+
 
 ;;;
 ;;; Redshift.
@@ -169,11 +244,25 @@ format."))
   (list (shepherd-service
          (documentation "Redshift program.")
          (provision '(redshift))
-         ;; FIXME: This fails to start if Home is first activated from a
+
-         ;; non-X11 session.
+         ;; Depend on 'x11-display', which sets 'DISPLAY' if an X11 server is
-         (start #~(make-forkexec-constructor
+         ;; available, and fails to start otherwise.
-                   (list #$(file-append (home-redshift-configuration-redshift config) "/bin/redshift")
+         (requirement '(x11-display))
-                         "-c" #$config-file)))
+
+         (modules '((srfi srfi-1)
+                    (srfi srfi-26)))
+         (start #~(lambda _
+                    (fork+exec-command
+                     (list #$(file-append
+                              (home-redshift-configuration-redshift config)
+                              "/bin/redshift")
+                           "-c" #$config-file)
+
+                     ;; Inherit the 'DISPLAY' variable set by 'x11-display'.
+                     #:environment-variables
+                     (cons (string-append "DISPLAY=" (getenv "DISPLAY"))
+                           (remove (cut string-prefix? "DISPLAY=" <>)
+                                   (default-environment-variables))))))
          (stop #~(make-kill-destructor))
          (actions (list (shepherd-configuration-action config-file))))))
 
@@ -181,7 +270,11 @@ format."))
   (service-type
    (name 'home-redshift)
    (extensions (list (service-extension home-shepherd-service-type
-                                        redshift-shepherd-service)))
+                                        redshift-shepherd-service)
+                     ;; Ensure 'home-x11-service-type' is instantiated so we
+                     ;; can depend on the Shepherd 'x11-display' service.
+                     (service-extension home-x11-service-type
+                                        (const #t))))
    (default-value (home-redshift-configuration))
    (description
     "Run Redshift, a program that adjusts the color temperature of display

gnu/local.mk

@@ -235,7 +235,6 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/docbook.scm			\
   %D%/packages/docker.scm			\
   %D%/packages/documentation.scm		\
-  %D%/packages/dunst.scm			\
   %D%/packages/dvtm.scm				\
   %D%/packages/easyrpg.scm			\
   %D%/packages/ebook.scm			\
@@ -901,7 +900,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/aegisub-make43.patch			\
   %D%/packages/patches/agda-categories-remove-incompatible-flags.patch	\
   %D%/packages/patches/agda-categories-use-find.patch	\
+  %D%/packages/patches/agda-categories-use-stdlib-1.7.3.patch	\
   %D%/packages/patches/agda-libdirs-env-variable.patch	\
+  %D%/packages/patches/agda-use-sphinx-5.patch	\
   %D%/packages/patches/agda-stdlib-use-runhaskell.patch	\
   %D%/packages/patches/agg-am_c_prototype.patch			\
   %D%/packages/patches/agg-2.5-gcc8.patch			\
@@ -1020,6 +1021,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/clang-13.0-libc-search-path.patch	\
   %D%/packages/patches/clang-14.0-libc-search-path.patch	\
   %D%/packages/patches/clang-15.0-libc-search-path.patch	\
+  %D%/packages/patches/clang-16.0-libc-search-path.patch	\
+  %D%/packages/patches/clang-17.0-libc-search-path.patch	\
   %D%/packages/patches/clang-runtime-asan-build-fixes.patch	\
   %D%/packages/patches/clang-runtime-esan-build-fixes.patch	\
   %D%/packages/patches/clang-runtime-9-libsanitizer-mode-field.patch	\
@@ -1102,7 +1105,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/elm-reactor-static-files.patch		\
   %D%/packages/patches/elogind-fix-rpath.patch			\
   %D%/packages/patches/emacs-all-the-icons-remove-duplicate-rs.patch	\
-  %D%/packages/patches/emacs-debbugs-keep-patch-subject.patch	\
   %D%/packages/patches/emacs-deferred-fix-number-of-arguments.patch	\
   %D%/packages/patches/emacs-elpy-dup-test-name.patch		\
   %D%/packages/patches/emacs-exec-path.patch			\

gnu/packages/admin.scm

@@ -4432,6 +4432,9 @@ late.")
                      " *lmonpl = '\\0'"))
                   #t))))
     (build-system gnu-build-system)
+    (arguments
+     ;; GCC 11 defaults to c++17 but this package needs something older.
+     (list #:configure-flags #~'("CXXFLAGS=-std=c++14 -O2 -g")))
     (inputs
      (list openmpi
            munge
@@ -4439,7 +4442,7 @@ late.")
            libelf
            libgcrypt
            libgpg-error))
-    (synopsis "Infrastructue for large scale tool daemon launching")
+    (synopsis "Infrastructure for large-scale tool daemon launching")
     (description
      "LaunchMON is a software infrastructure that enables HPC run-time
 tools to co-locate tool daemons with a parallel job.  Its API allows a
@@ -4452,7 +4455,7 @@ launch daemons into the relevant nodes.")
 (define-public spindle
   (package
     (name "spindle")
-    (version "0.10")
+    (version "0.13")
     (source (origin
               ;; We use git checkout to avoid github auto-generated tarballs
               (method git-fetch)
@@ -4462,16 +4465,15 @@ launch daemons into the relevant nodes.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "15n3ay0qq81r5v7fif61q1vdjcq44pp2nynkh3fvbzc9fj3c39wd"))))
+                "1z594nhash1him9v00qmyqv9jvikzrs4wxqy1cvnfwqwnrrkp707"))))
     (build-system gnu-build-system)
     (arguments '(#:configure-flags '("--enable-sec-launchmon"
                                      "--enable-sec-munge"
-                                     "--enable-sec-none")))
+                                     "--enable-sec-none"
+                                     ;; Fails to build as c++17.
+                                     "CXXFLAGS=-std=c++14 -O2 -g")))
     (inputs
-     `(("mpi" ,openmpi)
+     (list openmpi munge launchmon libgcrypt))
-       ("munge" ,munge)
-       ("launchmon" ,launchmon)
-       ("libgcrypt" ,libgcrypt)))
     (synopsis "Scalable library loading in HPC environments")
     (description
      "Spindle is a tool for improving the performance of dynamic library and

gnu/packages/agda.scm

@@ -44,7 +44,7 @@
 (define-public agda
   (package
     (name "agda")
-    (version "2.6.3")
+    (version "2.6.4")
     (source
      (origin
        (method git-fetch)
@@ -53,12 +53,14 @@
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1s7zd01i8pmvi90ywx497kc07z50nah7h0fc2dn6jzb132k5sh1q"))
+        (base32 "0n4avd58j45rdcmnwgrmz5s0ril0z4n2z711mwwbahl50f7359ky"))
-       (patches (search-patches "agda-libdirs-env-variable.patch"))))
+       (patches (search-patches "agda-libdirs-env-variable.patch"
+                                "agda-use-sphinx-5.patch"))))
     (build-system haskell-build-system)
     (inputs
      (list ghc-aeson
            ghc-alex
+           ghc-ansi-terminal
            ghc-async
            ghc-blaze-html
            ghc-boxes
@@ -73,9 +75,11 @@
            ghc-monad-control
            ghc-murmur-hash
            ghc-parallel
+           ghc-peano
            ghc-regex-tdfa
            ghc-split
            ghc-strict
+           ghc-text-icu
            ghc-unordered-containers
            ghc-uri-encode
            ghc-vector-hashtables
@@ -91,6 +95,7 @@
                        (guix build utils)
                        (srfi srfi-26)
                        (ice-9 match))
+           #:configure-flags #~(list "-foptimise-heavily" "-fenable-cluster-counting")
            #:phases
            #~(modify-phases %standard-phases
                ;; This allows us to call the 'agda' binary before installing.
@@ -194,7 +199,7 @@ come from Agda's standard library.")
 (define-public agda-stdlib
   (package
     (name "agda-stdlib")
-    (version "1.7.2")
+    (version "1.7.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -203,7 +208,7 @@ come from Agda's standard library.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "065hf24xjpciwdrvk4isslgcgi01q0k93ql0y1sjqqvy5ryg5xmy"))))
+                "0y6rns64rrkh8hw7mamcf6797329pi4ravpak5zijpnkzdagmlmy"))))
     (build-system agda-build-system)
     (arguments
      (list
@@ -241,7 +246,8 @@ try agda-prelude instead.")
                (base32
                 "0xwgm2mfl2pxipsv31bin8p14y1yhd9n27lv3clvsxd4z9yc034m"))
               (patches (search-patches "agda-categories-remove-incompatible-flags.patch"
-                                       "agda-categories-use-find.patch"))))
+                                       "agda-categories-use-find.patch"
+                                       "agda-categories-use-stdlib-1.7.3.patch"))))
     (build-system agda-build-system)
     (arguments
      (list
@@ -259,12 +265,9 @@ try agda-prelude instead.")
     (license license:expat)))
 
 (define-public agda-cubical
-  ;; Upstream's HEAD follows the latest Agda release, but they don't release
-  ;; until a newer Agda release comes up, so their releases are always one
-  ;; version late.
   (package
     (name "agda-cubical")
-    (version "0.5")
+    (version "0.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -273,7 +276,7 @@ try agda-prelude instead.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0yfg7gr55n08ly1qgzpcp16s15k1abycppbcdi9lzg1hjryqxcg3"))))
+                "0zq0z328zcjmm43mrv2ks27i1dnbylcf8mhzja2hd4gvz1kq1ays"))))
     (build-system agda-build-system)
     (arguments
      (list
@@ -290,10 +293,10 @@ agda-stdlib but using cubical methods.")
     (license license:expat)))
 
 (define-public agda-1lab
-  ;; Upstream doesn't do releases (yet).  Use a commit that builds with 2.6.3,
+  ;; Upstream doesn't do releases (yet).  Use a commit that builds with 2.6.4,
   ;; since they use Agda HEAD.
-  (let* ((revision "1")
+  (let* ((revision "2")
-         (commit "47ca1d23640a6f49a3abe3c2fe27738bcc10c9c6"))
+         (commit "549fdb1c948a975e90e70f871993a4a4239aa280"))
     (package
       (name "agda-1lab")
       (version (git-version "0.0" revision commit))
@@ -306,10 +309,12 @@ agda-stdlib but using cubical methods.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "0j7mp6c0xd0849skdxzncklkxynxnyfrbpcjv4qp5p1xfn0dnfqx"))))
+           "1k4zj8dibyplakpxaw4a8hpsaqhakynjb83dqxrva4h4ssj6gkqj"))))
       (build-system agda-build-system)
       (arguments
-       (list #:plan '(("src/index\\.lagda\\.md$"))))
+       ;; Check files individually first, to avoid running out of heap :(
+       (list #:plan '(("src/.+/.+\\.lagda\\.md$")
+                      ("src/index\\.lagda\\.md$"))))
       (synopsis "Reference resource for mathematics done in Homotopy Type Theory")
       (description "A formalised, cross-linked reference resource for
 mathematics done in Homotopy Type Theory.  Unlike the HoTT book, the 1lab is

gnu/packages/astronomy.scm

@@ -589,13 +589,13 @@ mining in astronomy.")
 (define-public python-fitsio
   (package
     (name "python-fitsio")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "fitsio" version))
        (sha256
-        (base32 "04fbg1ffj7qrlzw50xzzkfnlk6qjjqq96j0im7phprmwb1rbvzzh"))
+        (base32 "19him5rcpjyz14ghkmifnd1xl3ivlyy84h45k6j2pyr5ixc60ky6"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove the bundled cfitsio. When update the package check the
@@ -703,7 +703,7 @@ for reading and writing.")
 (define-public erfa
   (package
     (name "erfa")
-    (version "2.0.0")
+    (version "2.0.1")
     (source
      (origin
        (method git-fetch)
@@ -712,7 +712,7 @@ for reading and writing.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0s9dpj0jdkqcg552f00jhd722czji4pffabmpys5pgi6djckq4f4"))))
+        (base32 "1hxjbcvdlq4871r17fphbaf3bd8dsjagp1rdb3j8v6kr4f1dil9n"))))
     (build-system gnu-build-system)
     (native-inputs
      (list automake autoconf libtool pkg-config))
@@ -923,7 +923,7 @@ astronomical image-processing packages like Drizzle, Swarp or SExtractor.")
            libtirpc
            qtbase-5
            zlib))
-    (home-page "https://projets.lam.fr/projects/unsio/wiki")
+    (home-page "https://projets.lam.fr/projects/glnemo2/wiki/Wiki")
     (synopsis "3D interactive visualization program for n-body like particles")
     (description
      "GLNEMO2 is an interactive 3D visualization program which displays
@@ -1121,7 +1121,7 @@ image formats.")
 (define-public splash
   (package
     (name "splash")
-    (version "3.8.4")
+    (version "3.9.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1129,7 +1129,7 @@ image formats.")
                     (commit (string-append "v" version))))
               (sha256
                (base32
-                "1l18sqz5mpab9wb5hlbfy18wfwq6fpijc3p9wa5bv6lrcymvpirp"))
+                "19r5j4jrxhp3gf865ns59vvfnn5a303dqgmb8y2kgcsx26fci1hs"))
               (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments
@@ -1385,7 +1385,7 @@ any arbitrary astrometric projection defined in the WCS standard.")
 (define-public celestia
   (package
     (name "celestia")
-    (version "1.6.3")
+    (version "1.6.4")
     (source
      (origin
        (method git-fetch)
@@ -1394,7 +1394,7 @@ any arbitrary astrometric projection defined in the WCS standard.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0dzci5n7gcnm1vq916gsn9zddkhbzhbsakqxrpnmvzibsqznn6c8"))))
+        (base32 "0nz9k5nd2zmrbwj1qhsfwmvqymqk8c4yjxpybck44isrild2ah9j"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -1466,13 +1466,13 @@ accurately in real time at any rate desired.")
 (define-public python-astropy
   (package
     (name "python-astropy")
-    (version "5.3.3")
+    (version "5.3.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
-        (base32 "1fwk7x4q1hgdf9m8q613c6q7045sam1g934vgqv588ksbngxyc03"))
+        (base32 "1n7iwvjari4xv37094cpiapmjhhm57b04hi4r40wqb5czbigg46l"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -1527,7 +1527,9 @@ accurately in real time at any rate desired.")
                              "not remote_data"
                              ;; XXX: Check why this tests failing.
                              " and not test_ignore_sigint"
-                             " and not test_parquet_filter"))))))))
+                             " and not test_parquet_filter"
+                             ;; See https://github.com/astropy/astropy/issues/15537
+                             " and not test_pvstar"))))))))
     (native-inputs
      (list pkg-config
            python-colorlog
@@ -1612,19 +1614,27 @@ astronomy and astrophysics.")
        (uri (pypi-uri "astroquery" version))
        (sha256
         (base32 "1vhkzsqlgn3ji5by2rdf2gwklhbyzvpzb1iglalhqjkkrdaaaz1h"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     (list #:phases
+     (list
+      #:test-flags
+      #~(list "--pyargs" "astroquery"
+              "-m" "not remote_data")
+      #:phases
       #~(modify-phases %standard-phases
-               (add-before 'check 'writable-home
+          (add-before 'check 'prepare-test-environment
-                 (lambda _              ; some tests need a writable home
+            (lambda _
-                   (setenv "HOME" (getcwd))))
+              (setenv "HOME" (getcwd)) ; some tests need a writable home
-               (replace 'check
+              ;; To solve pytest/conftest issue. Pytest tries to load all
-                 (lambda* (#:key tests? #:allow-other-keys)
+              ;; files with word 'test' in them.
-                   (when tests?
+              ;;
-                     (invoke "python" "-m" "pytest" "--pyargs" "astroquery"
+              ;; ImportError while loading conftest ...
-                             ;; Skip tests that require online data.
+              ;; _pytest.pathlib.ImportPathMismatchError: ...
-                             "-m" "not remote_data")))))))
+              ;;
+              (call-with-output-file "pytest.ini"
+                (lambda (port)
+                  (format port "[pytest]
+python_files = test_*.py"))))))))
     (propagated-inputs
      (list python-astropy
            python-beautifulsoup4
@@ -1634,12 +1644,13 @@ astronomy and astrophysics.")
            python-pyvo
            python-requests))
     (native-inputs
-     (list python-flask
+     (list python-astropy-healpix
-           python-jinja2
            python-matplotlib
+           ;; python-mocpy : Not packed yet, optional
            python-pytest-astropy
-           python-pytest-dependency))
+           python-pytest-dependency
-    (home-page "https://www.astropy.org/astroquery/")
+           python-regions))
+    (home-page "https://astroquery.readthedocs.io/en/latest/index.html")
     (synopsis "Access online astronomical data resources")
     (description "Astroquery is a package that contains a collection of tools
 to access online Astronomical data.  Each web service has its own sub-package.")
@@ -1724,13 +1735,13 @@ Herschel.")
 (define-public python-casa-formats-io
   (package
     (name "python-casa-formats-io")
-    (version "0.2.1")
+    (version "0.2.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "casa-formats-io" version))
               (sha256
                (base32
-                "07cchih2ws6jf6q1a4xhkv0jk96s3w08kzxx9l1911wzqk0pw9pj"))))
+                "16qwr6yq86qgdb0lvnmfm5mn6g2d29b1vrmfv26v77kxm6szxr8h"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -1784,7 +1795,7 @@ bad pixel tracking throughout the reduction process.")
 (define-public python-cdflib
   (package
     (name "python-cdflib")
-    (version "1.2.1")
+    (version "1.2.3")
     (source
      (origin
        (method git-fetch)   ; no tests in pypi archive
@@ -1793,7 +1804,7 @@ bad pixel tracking throughout the reduction process.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0v73fl69pxbk52ilhj2593zmn3qhqy4hrrwby8m9z2sq3fd5xk0v"))))
+        (base32 "0vpgcbc9pmx0qqfia1frnwq3jkgfp8y3ikqdnzs5bs1sr13p9p3w"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:phases
@@ -1833,13 +1844,13 @@ attempting to maintain ISTP compliance
 (define-public python-crds
   (package
     (name "python-crds")
-    (version "11.17.6")
+    (version "11.17.9")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "crds" version))
               (sha256
                (base32
-                "1sbfl45rx21g622vm8baqv0ydcdixf1jdjgydn07sxl7kn15fa4g"))))
+                "0ha7ibs5lmqs9pcr546jyxzgrmx1xyqps7fsp220rvlsbsisdgm0"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -1922,18 +1933,7 @@ Cesium.")
        (uri (pypi-uri "drms" version))
        (sha256
         (base32 "0mkrmr55fgca441z7hvsyri6x9cjsh0sfas3hrj0k1k10k8vszbw"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (replace 'check
-            (lambda* (#:key inputs outputs tests?
-                      #:allow-other-keys)
-              (when tests?
-                (add-installed-pythonpath inputs outputs)
-                (setenv "JSOC_EMAIL" "jsoc@sunpy.org")
-                (invoke "python" "-m" "pytest" "-vv")))))))
     (native-inputs
      (list python-astropy
            python-pytest-astropy
@@ -1994,13 +1994,13 @@ code to be greatly simplified.")
 (define-public python-ephem
   (package
     (name "python-ephem")
-    (version "4.1.4")
+    (version "4.1.5")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "ephem" version))
               (sha256
                (base32
-                "0q67z79lgwdylxagbsjm42xvsmk5jmgvghy36m2n5lb2446rz9bk"))))
+                "0ainqbnvw320pc61q5b6ad6f2mhn1pvrlnq489cwfx0m82mahr0c"))))
     (build-system python-build-system)
     (native-inputs (list tzdata))
     (home-page "https://rhodesmill.org/pyephem/")
@@ -2118,27 +2118,22 @@ of astronomical sources.")
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      #~(list "-m" "not remote_data"
+              ;; TODO: Review failing tests later when any upstream
+              ;; suggestions are provided:
+              ;; https://github.com/poliastro/poliastro/issues/1618
+              "-k" (string-append "not test_czml_add_trajectory"
+                                  " and not test_czml_custom_packet"
+                                  " and not test_czml_ground_station"
+                                  " and not test_czml_groundtrack"
+                                  " and not test_czml_preamble"))
       #:phases
       #~(modify-phases %standard-phases
           ;; NOTE: Tests take about 7-10 minutes to pass.
           (add-before 'check 'prepare-test-environment
             (lambda _
-              (setenv "HOME" "/tmp")
+              (setenv "HOME" "/tmp"))))))
-              ;; TODO: Review failing tests later when any upstream
-              ;; suggestions are provided:
-              ;; https://github.com/poliastro/poliastro/issues/1618
-              (substitute* "tests/test_czml.py"
-              (("def test_czml_add_trajectory") "def __off_test_czml_add_trajectory")
-              (("def test_czml_custom_packet") "def __off_test_czml_custom_packet")
-              (("def test_czml_ground_station") "def __off_test_czml_ground_station")
-              (("def test_czml_groundtrack") "def __off_test_czml_groundtrack")
-              (("def test_czml_preamble") "def __off_test_czml_preamble"))))
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                (invoke "python" "-m" "pytest"
-                        ;; Skip tests that need remote data.
-                        "-m" "not remote_data")))))))
     (native-inputs
      (list python-coverage
            python-hypothesis
@@ -2371,13 +2366,13 @@ changing the pixel resolution, orientation, coordinate system.")
 (define-public python-sgp4
   (package
     (name "python-sgp4")
-    (version "2.22")
+    (version "2.23")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sgp4" version))
        (sha256
-        (base32 "1yc6gcbhz80i875j0wf6ikx7rzs0m7m1qp72dmdhdjidmpma5w0p"))))
+        (base32 "0aalbmldks6ykgkcxwkvnp04q0avhv903m5zwvg8i7zvl99xrbfq"))))
     (build-system python-build-system)
     (propagated-inputs
      (list python-numpy))
@@ -2601,24 +2596,22 @@ of axis order, spatial projections, and spectral units that exist in the wild.
        (file-name (git-file-name name version))
        (sha256
         (base32 "0kzcncqir4v7nhk9lxj9gxr32p3krkaqa58y2i4kksgxxy24qw4z"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      (list
-      ;; NOTE: (Sharlatan-20220523T231348+0100): Tests depends on old Python2
+      ;; XXX: Disable one failing test
-      ;; libarry `sphere'
+      ;; See https://github.com/spacetelescope/spherical_geometry/issues/252
-      #:tests? #f
+      #:test-flags #~(list "-k" "not test_overlap")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'preparations
             (lambda _
-              ;; Fixing: setuptools-scm was unable to detect version for ...
+              (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
-              (substitute* "setup.py"
-                (("use_scm_version=True")
-                 (format #f "version=~s" #$version))
-                (("setup_requires=\\['setuptools_scm'\\],.*")
-                 ""))
               ;; Use our own libraries in place of bundles.
-              (setenv "USE_SYSTEM_QD" "1"))))))
+              (setenv "USE_SYSTEM_QD" "1")))
+          (add-before 'check 'build-extensions
+            (lambda _
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
      (list python-pytest
            python-setuptools-scm))
@@ -2674,7 +2667,7 @@ Science Institute} image array manipulation functions.")
               (sha256
                (base32
                 "14457izlbnks84dyza75ib3nvx2w8nhlqm9vc1zb7hbhknb5gjvw"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      (list #:tests? #f)) ;No tests
     (propagated-inputs (list python-numpy))
@@ -2702,11 +2695,23 @@ task}.")
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; XXX: Fix failing tests. There are errors to load test files.
+      #:phases
-      #:tests? #f))
+      #~(modify-phases %standard-phases
+          ;; Test steps are taken from GitHub Actions.
+          ;; See https://github.com/spacetelescope/stsci.stimage/issues/27
+          (replace 'check
+            (lambda _
+              (copy-file (string-append
+                #$(this-package-native-input "python-waf") "/bin/waf")
+               "waf")
+              (invoke "python" "waf" "configure" "build" "do_tests"))))))
     (propagated-inputs (list python-numpy))
-    (native-inputs (list python-codecov python-pytest python-pytest-cov
+    (native-inputs
-                         python-setuptools-scm))
+     (list python-codecov
+           python-pytest
+           python-pytest-cov
+           python-setuptools-scm
+           python-waf))
     (home-page "https://stscistimage.readthedocs.io/en/latest/")
     (synopsis "STScI image processing")
     (description "This package provides an astronomical Python package with
@@ -2974,22 +2979,18 @@ low quality ones")
     (license license:gpl3+)))
 
 (define-public libpasastro
-  ;; NOTE: (Sharlatan-20210122T215921+0000): the version tag has a build
-  ;; error on spice which is resolved with the latest commit.
-  (let ((commit "e3c218d1502a18cae858c83a9a8812ab197fcb60")
-        (revision "1"))
   (package
     (name "libpasastro")
-      (version (git-version "1.4.0" revision commit))
+    (version "1.4.1")
-      (source (origin
+    (source
+     (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/pchev/libpasastro")
-                      (commit commit)))
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-                 (base32
+        (base32 "1h92p9ph3zi4w8krny1azd9wgwna2nf07ims983jcky1chkfm0is"))))
-                  "0asp2sn34nds5va2ghppwc41vb6j3d1mf049j949rgrll817kx47"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f
@@ -3020,12 +3021,12 @@ standard astronomy libraries:
 @item @code{libpaswcs.so}: Interface with libwcs to work with FITS WCS.
 @item @code{libpasspice.so}: To work with NAIF/SPICE kernel.
 @end itemize\n")
-      (license license:gpl2+))))
+      (license license:gpl2+)))
 
 (define-public libxisf
   (package
     (name "libxisf")
-    (version "0.2.9")
+    (version "0.2.10")
     (source
      (origin
        (method git-fetch)
@@ -3034,7 +3035,7 @@ standard astronomy libraries:
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "02cxv86h0ng4kmvyjkf7cr2ak2i3vpf0q0ik7jg4nmqjsidcs796"))))
+        (base32 "0q5qipn8887yhrk9pmi4fksxxmqas3w2aw2p194yhzkjapxk2k9h"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags #~(list "-DUSE_BUNDLED_LIBS=OFF")))
@@ -3153,23 +3154,21 @@ Mercator, Mollweide, Peters, polyconic, orthographic and rectangular.")
        (sha256
         (base32 "0hwf97kng1zy8rxyglw04x89p0bg07zq30hgghm20yxiw2xc8ng7"))))
     (build-system gnu-build-system)
-    (native-inputs
-     `(("intltool" ,intltool)
-       ("gettext" ,gettext-minimal)
-       ("pkg-config" ,pkg-config)))
-    (inputs
-     (list curl glib goocanvas gtk+))
     (arguments
-     `(#:configure-flags '("CFLAGS=-O2 -g -fcommon")
+     (list
+      #:configure-flags #~(list "CFLAGS=-O2 -g -fcommon")
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
           (add-after 'unpack 'fix-tests
             (lambda _
               ;; Remove reference to non-existent file.
               (substitute* "po/POTFILES.in"
-               (("src/gtk-sat-tree\\.c")
+                (("src/gtk-sat-tree\\.c") "")))))))
-                ""))
+    (native-inputs
-             #t)))))
+     (list gettext-minimal intltool pkg-config))
+    (inputs
+     (list curl glib goocanvas gtk+))
+    (home-page "http://gpredict.oz9aec.net/index.php")
     (synopsis "Satellite tracking and orbit prediction application")
     (description
      "Gpredict is a real-time satellite tracking and orbit prediction
@@ -3177,7 +3176,6 @@ application.  It can track a large number of satellites and display their
 position and other data in lists, tables, maps, and polar plots (radar view).
 Gpredict can also predict the time of future passes for a satellite, and
 provide you with detailed information about each pass.")
-    (home-page "http://gpredict.oz9aec.net/index.php")
     (license license:gpl2+)))
 
 (define-public sgp4
@@ -3231,19 +3229,8 @@ It can be used to calculate the trajectory of satellites.")
         (base32 "0a6wb1a9adwd01dmy0r03xxp8iz9y7mvh30088ajilhj4lf90vxa"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:tests? #f                      ;no test provided
+     (list ;; No test provided
-       #:phases
+      #:tests? #f))
-       (modify-phases %standard-phases
-         (replace 'configure
-           (lambda* (#:key outputs #:allow-other-keys)
-             (mkdir-p "build")
-             (chdir "build")
-             (invoke
-              "cmake"
-              "-G" "Unix Makefiles"
-              "-DCMAKE_BUILD_TYPE=Release"
-              (string-append "-DCMAKE_INSTALL_PREFIX=" (assoc-ref outputs "out"))
-              ".."))))))
     (native-inputs
      (list boost pkg-config))
     (inputs
@@ -3404,13 +3391,13 @@ Moon position, etc.")
 (define-public python-jplephem
   (package
     (name "python-jplephem")
-    (version "2.19")
+    (version "2.20")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "jplephem" version))
        (sha256
-        (base32 "1kvdzwyh0invinvcnwfr14r9zbqzcwkdh0cpzw1m4vkdcm64aqn1"))))
+        (base32 "1yp1l3n07849411099f976ps0pyv8jk8k5l9da9nhv54ir86v65v"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -3435,13 +3422,13 @@ milliarcsecond).")
 (define-public python-jwst
   (package
     (name "python-jwst")
-    (version "1.12.3")
+    (version "1.12.5")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "jwst" version))
               (sha256
                (base32
-                "0bw7i0pmpdgk2zf47d57g45hm3yb4wbrf1p19z9vg555qv4f4kr5"))))
+                "0blrl00lz1snhcnr7j59nh05rnpqxdnfp8hhgagkr50h85q4smrn"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -3502,13 +3489,13 @@ exposures and high-level data products (mosaics, extracted spectra, etc.).")
 (define-public python-pyerfa
   (package
     (name "python-pyerfa")
-    (version "2.0.0.3")
+    (version "2.0.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyerfa" version))
        (sha256
-        (base32 "0f8zykzxjsiwv5ibdn5asla2ng2xl0xdkrcrrd61j31mb3xbnzyp"))
+        (base32 "0swsdkipnk73iflsa7qbaw89wahbnfyvplqaxwi0yfrxippp9b6v"))
        (modules '((guix build utils)))
        (snippet
         #~(begin
@@ -3519,6 +3506,7 @@ exposures and high-level data products (mosaics, extracted spectra, etc.).")
      (list
       ;; Disable only one failing test:
       ;; AttributeError: __warningregistry__
+      ;; See https://github.com/liberfa/pyerfa/issues/126
       #:test-flags #~(list "-k" "not test_errwarn_reporting")
       #:phases
       #~(modify-phases %standard-phases
@@ -3547,13 +3535,21 @@ functions, so that they can be called with scalar or array inputs.")
 (define-public python-pynbody
   (package
     (name "python-pynbody")
-    (version "1.3.1")
+    (version "1.4.2")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch) ;PyPi doesn't have not prebuit version.
-       (uri (pypi-uri "pynbody" version))
+       (uri (git-reference
+             (url "https://github.com/pynbody/pynbody")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1yp7ja66zqmbnh7bbwbyimxq1nkrmjrcif2rzfm1hswm0fp2fbga"))))
+        (base32 "1lwjs8vf3pc4a64c93fa5k6r276g1c60722swns2r10ig1s4wk0a"))
+       (modules '((guix build utils)))
+       (snippet
+        ;; Symlink goes to not existing directory.
+        #~(for-each delete-file '("docs/testdata"
+                                  "docs/tutorials/example_code/testdata")))))
     (build-system pyproject-build-system)
     (arguments
      (list #:test-flags #~(list
@@ -3584,7 +3580,12 @@ functions, so that they can be called with scalar or array inputs.")
                            "--ignore=tests/sph_smooth_test.py"
                            "--ignore=tests/subfind_test.py"
                            "--ignore=tests/subfindhdf_gadget4_test.py"
-                           "--ignore=tests/tipsy_test.py")))
+                           "--ignore=tests/tipsy_test.py")
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-before 'build 'set-compiler
+                 (lambda _
+                   (setenv "CC" #$(cc-for-target)))))))
     (native-inputs
      (list python-cython
            python-pandas
@@ -3723,9 +3724,21 @@ datetime object.")
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; XXX: Test needs more love to pass.
+      #:phases
-      ;; ERROR collecting synphot/tests/test_utils.py
+      #~(modify-phases %standard-phases
-      #:tests? #f))
+          (add-before 'check 'prepare-test-environment
+            (lambda _
+              (invoke "python" "setup.py" "build_ext" "--inplace")
+              ;; To solve pytest/conftest issue. Pytest tries to load all
+              ;; files with word 'test' in them.
+              ;;
+              ;; ImportError while loading conftest ...
+              ;; _pytest.pathlib.ImportPathMismatchError: ...
+              ;;
+              (call-with-output-file "pytest.ini"
+                (lambda (port)
+                  (format port "[pytest]
+python_files = test_*.py"))))))))
     (propagated-inputs (list python-astropy python-numpy python-scipy))
     (native-inputs (list python-pytest python-pytest-astropy
                          python-setuptools-scm))
@@ -3771,32 +3784,23 @@ between image and reference catalogs. Currently only aligning images with
 @code{FITS WCS} and @code{JWST gWCS} are supported.")
     (license license:bsd-3)))
 
-(define-public python-asdf
+(define-public python-asdf-3.0
   (package
     (name "python-asdf")
-    (version "2.15.0")
+    (version "3.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf" version))
        (sha256
-        (base32 "11s56797l5330kkhppkyz0bsvms016knmyswj4gx91zrxf8iqvv8"))))
+        (base32 "1jsk7b4mx04l0a08j832vnl309dba3gjnha9mbd61dzs9ridrfna"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list #:test-flags
-           #~(list "-k" (string-append
-                         "not test_overwrite"
-                         " and not test_tagging_scalars"
-                         " and not test_info_command"
-                         " and not test_array_inline_threshold_recursive"))))
     (native-inputs
-     (list python-astropy
+     (list python-fsspec
-           python-fsspec
            python-packaging
            python-psutil
            python-pytest
            python-pytest-doctestplus
-           python-pytest-openfiles
            python-pytest-remotedata
            python-semantic-version
            python-setuptools-scm))
@@ -3804,10 +3808,9 @@ between image and reference catalogs. Currently only aligning images with
      (list python-asdf-standard
            python-asdf-transform-schemas
            python-asdf-unit-schemas
+           python-attrs ;; for vendorized jsonschema
            python-importlib-metadata
-           python-importlib-resources
            python-jmespath
-           python-jsonschema
            python-lz4
            python-numpy
            python-pyyaml))
@@ -3819,6 +3822,34 @@ interchange format for scientific data.  This package contains the Python
 implementation of the ASDF Standard.")
     (license license:bsd-3)))
 
+(define-public python-asdf-2.15
+  (package
+    (inherit python-asdf-3.0)
+    (version "2.15.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "asdf" version))
+       (sha256
+        (base32 "11s56797l5330kkhppkyz0bsvms016knmyswj4gx91zrxf8iqvv8"))))
+    (arguments
+     (list #:test-flags
+           #~(list "-k" (string-append
+                         "not test_overwrite"
+                         " and not test_tagging_scalars"
+                         " and not test_info_command"
+                         " and not test_array_inline_threshold_recursive"))))
+    (native-inputs
+     (modify-inputs (package-native-inputs python-asdf-3.0)
+       (prepend python-astropy python-pytest-openfiles)))
+    (propagated-inputs
+     (modify-inputs (package-propagated-inputs python-asdf-3.0)
+       (prepend python-jsonschema python-importlib-resources)))))
+
+(define-public python-asdf
+  ;; Default version of ASDF..
+  python-asdf-2.15)
+
 (define-public python-asdf-standard
   (package
     (name "python-asdf-standard")
@@ -4101,13 +4132,13 @@ default) to world coordinates.")
 (define-public python-rad
   (package
     (name "python-rad")
-    (version "0.17.1")
+    (version "0.18.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "rad" version))
               (sha256
                (base32
-                "11jhh3qmd00g8sn6hcfshbpb2qy1rfj0xkxn30pd63lqazg4ra3p"))))
+                "1wgnbhldgq0j55yzg33y11vd5k5nzwckiccxywvmq518qh19pky5"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -4163,13 +4194,13 @@ channels
 (define-public python-roman-datamodels
   (package
     (name "python-roman-datamodels")
-    (version "0.17.1")
+    (version "0.18.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "roman_datamodels" version))
               (sha256
                (base32
-                "1y12cp8172i4a314gmhpi86jw6pfylz1adh0rzr5zqmvd3mrjqlj"))))
+                "0crlmd99p2nyqmrbykdqqng7v8zb4sibm8j9aqrq3ppak3r3r7q1"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -4207,7 +4238,7 @@ pipelines.")
 (define-public python-astroalign
   (package
     (name "python-astroalign")
-    (version "2.4.2")
+    (version "2.5.1")
     (source
      (origin
        ;; There are no tests in the PyPI tarball.
@@ -4217,7 +4248,7 @@ pipelines.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0hly20a65540hr3l1lsd1i4d90a0vdrbwnn6zx3z8s89ha9lq3pb"))))
+        (base32 "1kr5cszcxvrdbksy7mvv3ps1h1jzrn4yamfr6x7whkbi6bpqf7xp"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-astropy
@@ -4265,13 +4296,13 @@ orbit around the Earth.")
 (define-public python-wiimatch
   (package
     (name "python-wiimatch")
-    (version "0.3.1")
+    (version "0.3.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "wiimatch" version))
               (sha256
                (base32
-                "0x6p5z6a2cqinckwlpinjxagvmswl149s1jn6ihmdxk4k0h8rrz0"))))
+                "15kq7z30m9i286ncs9xvpaq3dq1p5fa47jz21prq146qwr7j6dm8"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-numpy python-scipy))
     (native-inputs (list python-codecov python-pytest python-pytest-cov

gnu/packages/aux-files/guix.vim

@@ -1,13 +1,8 @@
-" This appends all of the vim plugins to the end of Vim's runtimepath.
+" This appends all applicable vim paths to the end of packagepath.  Once we
+" have told vim the packagepath vim will add it to the runtimepath for us.
 for directory in ["/run/current-system/profile", $HOME . "/.guix-profile", $HOME ."/.guix-home/profile", $GUIX_PROFILE, $GUIX_ENVIRONMENT]
     let vimplugins = directory . "/share/vim/vimfiles"
     if isdirectory(vimplugins)
-        let &rtp = join([&rtp,vimplugins], ',')
+        let &pp = join([&pp,vimplugins], ',')
     endif
 endfor
-" Unconditionally add */after directories last, as intended by upstream
-" TODO: Remove duplicate */after directories
-for directory in [$VIM . "/vimfiles", $HOME ."/.vim"]
-    let vimplugins = directory . "/after"
-    let &rtp = join([&rtp,vimplugins], ',')
-endfor

gnu/packages/benchmark.scm

@@ -137,7 +137,7 @@ is to write a job file matching the I/O load one wants to simulate.")
 (define-public intel-mpi-benchmarks/openmpi
   (package
     (name "intel-mpi-benchmarks")
-    (version "2019.6")
+    (version "2021.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -146,7 +146,7 @@ is to write a job file matching the I/O load one wants to simulate.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "02hxbk9g9nl59bk5qcfl3djj7b58vsqys340m1xdbyqwcrbnahh9"))
+                "04kczch2hlfzbgk929vcxx480kc6raba8rbz246j7d26k1z1zh8h"))
               (modules '((guix build utils)))
               (snippet
                '(begin

gnu/packages/bioconductor.scm

@@ -68,6 +68,42 @@
 
 ;;; Annotations
 
+(define-public r-bsgenome-hsapiens-ucsc-hg38-masked
+  (package
+    (name "r-bsgenome-hsapiens-ucsc-hg38-masked")
+    (version "1.4.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38.masked" version
+                              'annotation))
+       (sha256
+        (base32 "0j71hdxqvvc0s8mc6jp6zk502mrf095qazj95yzzb4rm6sjvd20m"))))
+    (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38.masked")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg38
+                             r-genomeinfodb))
+    (home-page
+     "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38.masked")
+    (synopsis
+     "Full masked genomic sequences for Homo sapiens (UCSC version hg38)")
+    (description
+     "This package provides the complete genome sequences for Homo sapiens as
+provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31).
+The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each
+of them has the 4 following masks on top:
+
+@enumerate
+@item the mask of assembly gaps (AGAPS mask);
+@item the mask of intra-contig ambiguities (AMB mask);
+@item the mask of repeats from @code{RepeatMasker} (RM mask);
+@item the mask of repeats from Tandem Repeats Finder (TRF mask).
+@end enumerate
+
+Only the AGAPS and AMB masks are \"active\" by default.  The sequences are stored
+in @code{MaskedDNAString} objects.")
+    (license license:artistic2.0)))
+
 (define-public r-hpo-db
   (package
     (name "r-hpo-db")
@@ -507,6 +543,28 @@ Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by default.")
 as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-bsgenome-ecoli-ncbi-20080805
+  (package
+    (name "r-bsgenome-ecoli-ncbi-20080805")
+    (version "1.3.1000")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BSgenome.Ecoli.NCBI.20080805" version
+                              'annotation))
+       (sha256
+        (base32 "1l7mjyys1kaq4mbia9jamyw6sd0ij1wypwxvwy8aksan3gcfnh27"))))
+    (properties `((upstream-name . "BSgenome.Ecoli.NCBI.20080805")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-bsgenome))
+    (home-page
+     "https://bioconductor.org/packages/BSgenome.Ecoli.NCBI.20080805")
+    (synopsis "Escherichia coli full genomes")
+    (description
+     "This package provides Escherichia coli full genomes for several strains
+as provided by NCBI on 2008/08/05 and stored in Biostrings objects.")
+    (license license:artistic2.0)))
+
 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
   (package
     (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
@@ -1575,6 +1633,26 @@ biscuiteer.")
 demonstrate functionalities of the @code{breakpointR} package.")
     (license license:expat)))
 
+(define-public r-breastcancervdx
+  (package
+    (name "r-breastcancervdx")
+    (version "1.40.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "breastCancerVDX" version
+                              'experiment))
+       (sha256
+        (base32 "12r8zql30ssr0cxy8v1qawwsky54321c737ny19n2yrl7sm08gf0"))))
+    (properties `((upstream-name . "breastCancerVDX")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/breastCancerVDX")
+    (synopsis "Gene expression datasets")
+    (description
+     "This package is a collection of gene expression data from a breast
+cancer study published in Wang et al. 2005 and Minn et al 2007.")
+    (license license:artistic2.0)))
+
 (define-public r-celldex
   (package
     (name "r-celldex")
@@ -4165,6 +4243,27 @@ BaalChIP is able to account for copy number differences between the two
 alleles, a known phenotypical feature of cancer samples.")
     (license license:artistic2.0)))
 
+(define-public r-bags
+  (package
+    (name "r-bags")
+    (version "2.42.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BAGS" version))
+       (sha256
+        (base32 "0356ragpcldr48yycqj91sn3bcqvvfp5spv2z02r8g6hs0dndwdh"))))
+    (properties `((upstream-name . "BAGS")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase r-breastcancervdx))
+    (home-page "https://bioconductor.org/packages/BAGS")
+    (synopsis "Bayesian approach for geneset selection")
+    (description
+     "This R package is providing functions to perform geneset significance
+analysis over simple cross-sectional data between 2 and 5 phenotypes of
+interest.")
+    (license license:artistic2.0)))
+
 (define-public r-basespacer
   (package
     (name "r-basespacer")
@@ -8133,6 +8232,42 @@ nucleotide sequence analysis.  The package is primarily useful to developers
 of other R packages who wish to make use of HTSlib.")
     (license license:lgpl2.0+)))
 
+(define-public r-rnbeads
+  (package
+    (name "r-rnbeads")
+    (version "2.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "RnBeads" version))
+       (sha256
+        (base32 "15z7l4nmpy01xm19717l27nwf3rfsn6wjv211fn2y4ls40mz75qp"))))
+    (properties `((upstream-name . "RnBeads")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-cluster
+           r-ff
+           r-fields
+           r-genomicranges
+           r-ggplot2
+           r-gplots
+           r-gridextra
+           r-illuminaio
+           r-iranges
+           r-limma
+           r-mass
+           r-matrixstats
+           r-methylumi
+           r-plyr
+           r-s4vectors))
+    (home-page "https://bioconductor.org/packages/RnBeads")
+    (synopsis "RnBeads")
+    (description
+     "@code{RnBeads} facilitates comprehensive analysis of various types of DNA
+methylation data at the genome scale.")
+    (license license:gpl3)))
+
 (define-public r-impute
   (package
     (name "r-impute")
@@ -8637,6 +8772,44 @@ on the basis that cells of the same type should have more similar gene expressio
 profiles than cells of different types.")
     (license license:expat)))
 
+(define-public r-methylaid
+  (package
+    (name "r-methylaid")
+    (version "1.36.0")
+    (source
+    (origin
+      (method url-fetch)
+      (uri (bioconductor-uri "MethylAid" version))
+      (sha256
+        (base32 "0mzml9j6f7yycf9747ikkpfvxnwji07h8jhwa9a54ix2d0wyxk3d"))))
+    (properties `((upstream-name . "MethylAid")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-ggplot2
+           r-gridbase
+           r-hexbin
+           r-matrixstats
+           r-minfi
+           r-rcolorbrewer
+           r-shiny
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://git.bioconductor.org/packages/MethylAid")
+    (synopsis
+     "Quality control of large Illumina DNA Methylation array data sets")
+    (description
+     "This package provides a visual and interactive web application using
+RStudio's shiny package.  Bad quality samples are detected using sample-dependent
+and sample-independent controls present on the array and user adjustable
+thresholds.  In depth exploration of bad quality samples can be performed using
+several interactive diagnostic plots of the quality control probes present on
+the array.  Furthermore, the impact of any batch effect provided by the user can
+be explored.")
+    (license license:gpl2+)))
+
 (define-public r-methylkit
   (package
     (name "r-methylkit")
@@ -9419,6 +9592,37 @@ package contains functions for combining the results of multiple runs of gene
 set analyses.")
     (license license:gpl2+)))
 
+(define-public r-powertcr
+  (package
+    (name "r-powertcr")
+    (version "1.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "powerTCR" version))
+       (sha256
+        (base32 "06fmphdq95pjbbvm8m8h1wajbp3vhl0zj7ddbzks9fy7ankp1n3i"))))
+    (properties `((upstream-name . "powerTCR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-cubature
+           r-doparallel
+           r-evmix
+           r-foreach
+           r-magrittr
+           r-purrr
+           r-truncdist
+           r-vegan
+           r-vgam))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/powerTCR")
+    (synopsis "Model-based comparative analysis of the TCR repertoire")
+    (description
+     "This package provides a model for the clone size distribution of the
+@acronym{TCR, T-cell receptor} repertoire.  Further, it permits comparative
+analysis of TCR repertoire libraries based on theoretical model fits.")
+    (license license:artistic2.0)))
+
 ;; This is a CRAN package, but it depends on a Bioconductor package:
 ;; r-aroma-light, r-dnacopy..
 (define-public r-pscbs
@@ -10150,6 +10354,49 @@ a scRNA-seq experiment onto the cell-types or individual cells identified in a
 different experiment.")
     (license license:gpl3)))
 
+(define-public r-screpertoire
+  (package
+    (name "r-screpertoire")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "scRepertoire" version))
+       (sha256
+        (base32 "1wgs8dv5zl82iciy86w5ws1gq8v2piklcifbw7gmbw60kijyr2l1"))))
+    (properties `((upstream-name . "scRepertoire")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-doparallel
+           r-dplyr
+           r-ggalluvial
+           r-ggplot2
+           r-ggraph
+           r-igraph
+           r-plyr
+           r-powertcr
+           r-reshape2
+           r-rlang
+           r-seuratobject
+           r-singlecellexperiment
+           r-stringdist
+           r-stringr
+           r-summarizedexperiment
+           r-tidygraph
+           r-vegan))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/scRepertoire")
+    (synopsis "Toolkit for single-cell immune receptor profiling")
+    (description
+     "The scRepertoire package was built to process data derived from the 10x
+Genomics Chromium Immune Profiling for both @acronym{TCR, T-cell receptor} and
+@acronym{Ig, immunoglobulin} enrichment workflows and subsequently interacts with
+the popular Seurat and SingleCellExperiment R packages.  It also allows for
+general analysis of single-cell clonotype information without the use of
+expression information.  The package functions as a wrapper for Startrac and
+powerTCR R packages.")
+    (license license:gpl2)))
+
 (define-public r-scry
   (package
     (name "r-scry")
@@ -11956,13 +12203,13 @@ rectangular layout tree built by ggtree with the grammar of ggplot2.")
 (define-public r-ggpicrust2
   (package
     (name "r-ggpicrust2")
-    (version "1.7.2")
+    (version "1.7.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "ggpicrust2" version))
               (sha256
                (base32
-                "0yk62cc0vmv6dyfiwvvbgpsqlvp1cw61db60153xvzmcdvd077cl"))))
+                "0zjlsvzl2f74fvqw4ijnai23qwhlcpgd5p8z9dclnwnsgdbm6hcq"))))
     (properties `((upstream-name . "ggpicrust2")))
     (build-system r-build-system)
     (propagated-inputs (list r-aldex2
@@ -18780,14 +19027,14 @@ using whole genome sequencing data.")
 (define-public r-activepathways
   (package
     (name "r-activepathways")
-    (version "2.0.2")
+    (version "2.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ActivePathways" version))
        (sha256
         (base32
-         "1h0ih87pf6b5mdhmh65frv3nqx7v5adqv37wn2p3gkpszd6hwc79"))))
+         "0mgvxpqaq0jncr1kzmwhqkv3pajx2fz6vwhv5arw7fgla6w09p9h"))))
     (properties
      `((upstream-name . "ActivePathways")))
     (build-system r-build-system)
@@ -21782,14 +22029,14 @@ on the plot.")
 (define-public r-abn
   (package
     (name "r-abn")
-    (version "3.0.2")
+    (version "3.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abn" version))
        (sha256
         (base32
-         "06n69cbkdqpwpxks8276h43132c9v57n4hg33vsjjyxjifwbwxwh"))))
+         "1yh9nhfphalxh77132r0fkpp71mqsfhb8jk11is4d5nvlvr5316z"))))
     (build-system r-build-system)
     (inputs
      (list gsl))
@@ -22344,6 +22591,122 @@ within a certain time frame are deleted.  This aims to reduce disk usage by
 eliminating obsolete caches generated by old versions of packages.")
     (license license:gpl3)))
 
+(define-public r-basic4cseq
+  (package
+    (name "r-basic4cseq")
+    (version "1.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Basic4Cseq" version))
+       (sha256
+        (base32 "1vlrrkg885w77w34m2q8hngr95hhh5bkw9hrzyhnp39igjkcwqx4"))))
+    (properties `((upstream-name . "Basic4Cseq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biostrings
+           r-bsgenome-ecoli-ncbi-20080805
+           r-catools
+           r-genomicalignments
+           r-genomicranges
+           r-rcircos))
+    (home-page "https://bioconductor.org/packages/Basic4Cseq")
+    (synopsis "Analyzing 4C-seq data")
+    (description
+     "Basic4Cseq is an R package for basic filtering, analysis and subsequent
+visualization of @acronym{4C-seq, circular chromosome conformation capture
+sequencing} data.  Virtual fragment libraries can be created for any BSGenome
+package, and filter functions for both reads and fragments and basic quality
+controls are included.  Fragment data in the vicinity of the experiment's
+viewpoint can be visualized as a coverage plot based on a running median
+approach and a multi-scale contact profile.")
+    (license license:lgpl3)))
+
+(define-public r-basics
+  (package
+    (name "r-basics")
+    (version "2.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BASiCS" version))
+       (sha256
+        (base32 "0kf215n151sxphc5w9h4i2xsk7lmysi4abwcpyz4slbwhpki3ac8"))))
+    (properties `((upstream-name . "BASiCS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-assertthat
+           r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-coda
+           r-cowplot
+           r-ggextra
+           r-ggplot2
+           r-hexbin
+           r-mass
+           r-matrix
+           r-matrixstats
+           r-posterior
+           r-rcpp
+           r-rcpparmadillo
+           r-reshape2
+           r-s4vectors
+           r-scran
+           r-scuttle
+           r-singlecellexperiment
+           r-summarizedexperiment
+           r-viridis))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/catavallejos/BASiCS")
+    (synopsis "Bayesian analysis of single-cell sequencing data")
+    (description
+     "@acronym{BASiCS, Bayesian analysis of single-cell sequencing data} is an
+integrated Bayesian hierarchical model to perform statistical analyses of
+single-cell RNA sequencing datasets in the context of supervised experiments
+(where the groups of cells of interest are known a priori.  BASiCS performs
+built-in data normalisation (global scaling) and technical noise quantification
+(based on spike-in genes).  BASiCS provides an intuitive detection criterion
+for highly (or lowly) variable genes within a single group of cells.
+Additionally, BASiCS can compare gene expression patterns between two or more
+pre-specified groups of cells.")
+    (license license:gpl3)))
+
+(define-public r-basicstarrseq
+  (package
+    (name "r-basicstarrseq")
+    (version "1.30.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BasicSTARRseq" version))
+       (sha256
+        (base32 "1dw6bv1qk2bn0l3m458sqgvm3s1karh4n3431pl7r0jj2r3mr6xa"))))
+    (properties `((upstream-name . "BasicSTARRseq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-iranges
+           r-s4vectors))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/BasicSTARRseq")
+    (synopsis "Basic peak calling on STARR-seq data")
+    (description
+     "This package implements a method that aims to identify enhancers on
+large scale.  The STARR-seq data consists of two sequencing datasets of the
+same targets in a specifc genome.  The input sequences show which regions
+where tested for enhancers.  Significant enriched peaks i.e. a lot more
+sequences in one region than in the input where enhancers in the genomic DNA
+are, can be identified.  So the approach pursued is to call peak every region
+in which there is a lot more
+(significant in a binomial model) STARR-seq signal than input signal and
+propose an enhancer at that very same position.  Enhancers then are called
+weak or strong dependent of there degree of enrichment in comparison to
+input.")
+    (license license:lgpl3)))
+
 (define-public r-basilisk-utils
   (package
     (name "r-basilisk-utils")
@@ -22394,6 +22757,166 @@ Functions are also provided to enable smooth interoperability of multiple
 Python environments in a single R session.")
     (license license:gpl3)))
 
+(define-public r-bayesknockdown
+  (package
+    (name "r-bayesknockdown")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BayesKnockdown" version))
+       (sha256
+        (base32 "1argd4gfld2yb0vvpgb5k7m6agmi58712f6g5dj4gnb7kg4rp1l8"))))
+    (properties `((upstream-name . "BayesKnockdown")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase))
+    (home-page "https://bioconductor.org/packages/BayesKnockdown")
+    (synopsis "Posterior probabilities for edges from knockdown data")
+    (description
+     "This package provides a simple, fast Bayesian method for computing
+posterior probabilities for relationships between a single predictor variable
+and multiple potential outcome variables, incorporating prior probabilities of
+relationships.  In the context of knockdown experiments, the predictor
+variable is the knocked-down gene, while the other genes are potential
+targets.  It can also be used for differential expression/2-class data.")
+    (license license:gpl3)))
+
+(define-public r-bayesspace
+  (package
+    (name "r-bayesspace")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BayesSpace" version))
+       (sha256
+        (base32 "1mqgsylnrvf197cin5zzihjv31bm2q0m5a612ncbglys6n1jd105"))))
+    (properties `((upstream-name . "BayesSpace")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-assertthat
+           r-biocfilecache
+           r-biocsingular
+           r-coda
+           r-dirichletreg
+           r-ggplot2
+           r-matrix
+           r-mclust
+           r-purrr
+           r-rcpp
+           r-rcpparmadillo
+           r-rcppdist
+           r-rcppprogress
+           r-rcurl
+           r-rhdf5
+           r-s4vectors
+           r-scales
+           r-scater
+           r-scran
+           r-singlecellexperiment
+           r-summarizedexperiment
+           r-xgboost))
+    (native-inputs (list r-knitr))
+    (home-page "https://www.ezstatconsulting.com/BayesSpace/")
+    (synopsis "Clustering and resolution enhancement of spatial transcriptomes")
+    (description
+     "This package provides tools for clustering and enhancing the resolution
+of spatial gene expression experiments.  BayesSpace clusters a low-dimensional
+representation of the gene expression matrix, incorporating a spatial prior to
+encourage neighboring spots to cluster together.  The method can enhance the
+resolution of the low-dimensional representation into \"sub-spots\", for which
+features such as gene expression or cell type composition can be imputed.")
+    (license license:expat)))
+
+(define-public r-baynorm
+  (package
+    (name "r-baynorm")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "bayNorm" version))
+       (sha256
+        (base32 "01lv4w1x43x3f9sdrqikhsr1gdvkgqzrgcd9wnjj76qsljn57ifq"))))
+    (properties `((upstream-name . "bayNorm")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-bb
+           r-biocparallel
+           r-dosnow
+           r-fitdistrplus
+           r-foreach
+           r-iterators
+           r-locfit
+           r-mass
+           r-matrix
+           r-rcpp
+           r-rcpparmadillo
+           r-rcppprogress
+           r-singlecellexperiment
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/WT215/bayNorm")
+    (synopsis "Single-cell RNA sequencing data normalization")
+    (description
+     "The bayNorm package is used for normalizing single-cell RNA-seq data.
+The main function is @code{bayNorm}, which is a wrapper function for gene
+specific prior parameter estimation and normalization.  The input is a matrix
+of scRNA-seq data with rows different genes and coloums different cells.  The
+output is either point estimates from posterior (2D array) or samples from
+posterior (3D array).")
+    (license license:gpl2+)))
+
+(define-public r-bbcanalyzer
+  (package
+    (name "r-bbcanalyzer")
+    (version "1.32.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BBCAnalyzer" version))
+       (sha256
+        (base32 "108jcgsf5hyj348y17hcw8m3zcfjgzpx8nz4n5jgxp2lgxjyizy1"))))
+    (properties `((upstream-name . "BBCAnalyzer")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biostrings
+           r-genomicranges
+           r-iranges
+           r-rsamtools
+           r-summarizedexperiment
+           r-variantannotation))
+    (home-page "https://bioconductor.org/packages/BBCAnalyzer")
+    (synopsis "Visualizing base counts")
+    (description
+     "BBCAnalyzer is a package for visualizing the relative or absolute number
+of bases, deletions and insertions at defined positions in sequence alignment
+data available as bam files in comparison to the reference bases.  Markers for
+the relative base frequencies, the mean quality of the detected bases, known
+mutations or polymorphisms and variants called in the data may additionally be
+included in the plots.")
+    (license license:lgpl3)))
+
+(define-public r-bcrank
+  (package
+    (name "r-bcrank")
+    (version "1.64.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BCRANK" version))
+       (sha256
+        (base32 "1m1ccacryf8wjzp0d37n9n1kpa6734ddb8nvv1sy0sz5gplrars9"))))
+    (properties `((upstream-name . "BCRANK")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biostrings))
+    (home-page "https://bioconductor.org/packages/BCRANK")
+    (synopsis "Predicting binding site consensus from ranked DNA sequences")
+    (description
+     "This package provides functions and classes for de novo prediction of
+transcription factor binding consensus by heuristic search.")
+    (license license:gpl2)))
+
 (define-public r-biocthis
   (package
     (name "r-biocthis")

gnu/packages/bioinformatics.scm

@@ -876,6 +876,38 @@ attributes of microbiome data - zero-inflation and over-dispersion, are
 simultaneously considered.")
       (license license:gpl3))))
 
+(define-public r-ewastools
+  (let ((commit "f7646cacd73266708479b3fea5d625054d179f95")
+        (revision "1"))
+    (package
+      (name "r-ewastools")
+      (version (git-version "1.7.2" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/hhhh5/ewastools/")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0irarlnxfnasa755adxsn67rxsy01zwhjhw18g4cag08cqiyyw41"))))
+      (properties `((upstream-name . "ewastools")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-data-table
+             r-igraph
+             r-illuminaio
+             r-mblm
+             r-quadprog))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/hhhh5/ewastools/")
+      (synopsis
+       "Quality control toolset for the Illumina Infinium DNA methylation")
+      (description
+       "This package provides a collection of useful functions for working
+with DNA methylation micro-array data.")
+      (license license:unlicense))))
+
 (define-public r-numbat
   (let ((commit "4ab7752e7d267a3f443756675728521a9b0a7295")
         (revision "1"))
@@ -9891,6 +9923,51 @@ tasks.")
 Pore-C concatemers.")
       (license license:gpl3))))
 
+(define-public r-dnamcrosshyb
+  ;; There aren't any releases.
+  (let ((commit "fe8acb33667e81f00dcb84e0fa75c87ab2db5d8f")
+        (revision "1"))
+    (package
+      (name "r-dnamcrosshyb")
+      (version (git-version "0.0.0.9000" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/pjhop/DNAmCrosshyb")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "12j1xsiqpvny5rp23z1az0k4cj5ajbcwkg65z00s16vywi2rx6nb"))))
+      (properties `((upstream-name . "DNAmCrosshyb")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-biocgenerics
+             r-biocparallel
+             r-biostrings
+             r-bsgenome-hsapiens-ucsc-hg19-masked
+             r-bsgenome-hsapiens-ucsc-hg38-masked
+             r-dplyr
+             r-genomicranges
+             r-ggplot2
+             r-iranges
+             r-magrittr
+             r-minfi
+             r-purrr
+             r-s4vectors
+             r-shiny
+             r-stringi
+             r-stringr
+             r-tibble
+             r-tidyr
+             r-watermelon))
+      (home-page "https://github.com/pjhop/DNAmCrosshyb")
+      (synopsis "DNAmCrosshyb")
+      (description
+       "This package provides helper functions to detect cross-hybridization
+on Illumina DNAm arrays.")
+      (license license:gpl3))))
+
 (define-public r-doubletcollection
   (let ((commit "c0d62f1853942ee6a087eaf7b000d9e4261e2dfd")
         (revision "1"))
@@ -15580,6 +15657,41 @@ analysing cytometry data in R.")
 spatial single-cell expression data.")
       (license license:expat))))
 
+;; Variant of r-illuminahumanmethylationepicmanifest in the
+;; (gnu packages bioconductor) module.
+(define-public r-illuminahumanmethylationepicmanifest-latest
+  (let ((commit "a9ffbad36f5e496ece6c4c37b80e2f4f7e02d0c3")
+        (revision "1"))
+    (package
+      (name "r-illuminahumanmethylationepicmanifest")
+      (version (git-version "1.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url
+                "https://github.com/achilleasNP/IlluminaHumanMethylationEPICmanifest")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0v8f0hl0v8gwi61vgqw56rn5j09h95hj54rb8pzbn0znm162n4fc"))))
+      (properties `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
+      (build-system r-build-system)
+      (home-page
+       "https://github.com/achilleasNP/IlluminaHumanMethylationEPICmanifest")
+      (synopsis "Illumina Human Methylation Manifest 1.0 B5 for R and minfi")
+      (description
+       "This is a drop-in replacement for the
+@code{IlluminaHumanMethylationEPIC} package.  It utilizes a Manifest based on
+1.0B5 annotation.  As of version 0.3.0, the
+@code{IlluminaHumanMethylationEPIC} package still employs the 1.0B2 annotation
+manifest.  A corresponding annotation package,
+@code{IlluminaHumanMethylationEPICanno.ilm10b5.hg38}, is available to ensure
+proper annotation.  The decision to maintain the same name is due to
+complications in downstream processing caused by array name lookup in certain
+preprocessing options.")
+      (license license:artistic2.0))))
+
 (define-public r-illuminahumanmethylationepicanno-ilm10b5-hg38
   (let ((commit "3db06910e27f626e0cc8b335ff45cf9a4050a36a")
         (revision "1"))

gnu/packages/boost.scm

@@ -8,7 +8,7 @@
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018, 2019, 2021 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2018, 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2018, 2020, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2018, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2019, 2020 Giacomo Leidi <goodoldpaul@autistici.org>
@@ -44,6 +44,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
+  #:use-module (gnu packages autotools)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages llvm)
@@ -445,15 +446,18 @@ signals and slots system.")
 (define-public mdds
   (package
     (name "mdds")
-    (version "2.0.3")
+    (version "2.1.1")
     (source (origin
-             (method url-fetch)
+              (method git-fetch)
-             (uri (string-append "https://kohei.us/files/mdds/src/mdds-"
+              (uri (git-reference
-                                 version ".tar.xz"))
+                    (url "https://gitlab.com/mdds/mdds")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-               "1r68kxqppmhfg0dhz54d0hqzs5882cqrv1x6wpg7lak6gyyws0bc"))))
+                "0866020brc1kmiryh7dmhjamnywlsd56ks649hy87283k0p7d3bb"))))
     (build-system gnu-build-system)
+    (native-inputs (list autoconf automake))
     (propagated-inputs
       (list boost)) ; inclusion of header files
     (home-page "https://gitlab.com/mdds/mdds")

gnu/packages/browser-extensions.scm

@@ -57,8 +57,8 @@ supported content to the Kodi media center.")
   ;; Arbitrary commit of branch master,
   ;; Update when updating uBlockOrigin.
   (let* ((name "ublock-main-assets")
-         (commit "c8783488f377723165e3661062bd124ae6d57165")
+         (commit "d93605b8584df8cd47bcc91b3d932feecd9e3a2a")
-         (revision "0")
+         (revision "1")
          (version (git-version "0" revision commit)))
     (origin
       (method git-fetch)
@@ -67,14 +67,14 @@ supported content to the Kodi media center.")
             (commit commit)))
       (file-name (git-file-name name version))
       (sha256
-       (base32 "1b6a1m6s060r49vg563f32rsy057af6i4jcyprym4sdci3z90nls")))))
+       (base32 "1bbwxmb5rb1afh6i5a7m1ysaw0022wi5g091vpahi4h805p1s7a2")))))
 
 (define ublock-prod-assets
   ;; Arbitrary commit of branch gh-pages,
   ;; Update when updating uBlockOrigin.
   (let* ((name "ublock-prod-assets")
-         (commit "fbcfe9229ab6b865ef349c01a4eac73943be8418")
+         (commit "1d3df32ef6672763f44b27a95fd5cb3b5770d5e2")
-         (revision "0")
+         (revision "1")
          (version (git-version "0" revision commit)))
     (origin
       (method git-fetch)
@@ -83,12 +83,12 @@ supported content to the Kodi media center.")
             (commit commit)))
       (file-name (git-file-name name version))
       (sha256
-       (base32 "0s5rvaz8lc9lk44yfc8463vah8yppy1ybmag0dpd4m1hyj6165h0")))))
+       (base32 "1cbx7w1nzdcjq0z4z7j9nr8922i27nslprrw5dy03xcdqwc3x4l6")))))
 
 (define ublock-origin
   (package
     (name "ublock-origin")
-    (version "1.51.0")
+    (version "1.53.2")
     (home-page "https://github.com/gorhill/uBlock")
     (source (origin
               (method git-fetch)
@@ -98,7 +98,7 @@ supported content to the Kodi media center.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1i8rnij3sbwg6vj6znprrsca0n5xjzhmhppaa8v6jyxg6wrrfch1"))))
+                "0mz1k5ghyc25v51md02qx7chrbg4cxagvqi18bcbs4agq8ix6sp7"))))
     (build-system gnu-build-system)
     (outputs '("xpi" "firefox" "chromium"))
     (properties '((addon-id . "uBlock0@raymondhill.net")))

gnu/packages/c.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2016, 2017, 2018, 2019, 2021 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018, 2020–2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018, 2019 Pierre Neidhardt <mail@ambrevar.xyz>
-;;; Copyright © 2019, 2020, 2022 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2019, 2020, 2022, 2023 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2019, 2021 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
@@ -1198,7 +1198,7 @@ Telemetry Transport (MQTT) publish-subscribe messaging protocol.")
 (define-public mimalloc
   (package
     (name "mimalloc")
-    (version "2.0.9")
+    (version "2.1.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1207,10 +1207,13 @@ Telemetry Transport (MQTT) publish-subscribe messaging protocol.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "19w0i28p6knjd192rrcw1ayc3x0qp6rcm48cwkls4kwn8fng81fj"))))
+                "1pyf05snc1ib7zjjm9kspvbmynd8lmxqw72qcpz8lcyzyywmz24i"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:build-type "Release"))
+     `(#:build-type "Release"
+       ,@(if (target-ppc32?)
+           `(#:configure-flags '("-DMI_USE_LIBATOMIC=ON"))
+           '())))
     (synopsis "General purpose memory allocator")
     (description "@code{mimalloc} is a drop-in replacement for @code{malloc}.")
     (home-page "https://microsoft.github.io/mimalloc/")

gnu/packages/ccache.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015, 2016, 2018 Eric Bavier <bavier@member.fsf.org>
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2023 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2021, 2022 Greg Hogan <code@greghogan.com>
 ;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
@@ -62,7 +62,11 @@
                  ;; Tests require a writable HOME.
                  (lambda _
                    (setenv "HOME" (getenv "TMPDIR")))))))
-    (native-inputs (list perl ruby-asciidoctor which))
+    (native-inputs
+     (append (list perl which)
+             (if (supported-package? ruby-asciidoctor)
+               (list ruby-asciidoctor)
+               '())))
     (inputs (list zlib `(,zstd "lib")))
     (home-page "https://ccache.dev/")
     (synopsis "Compiler cache")

gnu/packages/check.scm

@@ -2551,7 +2551,7 @@ mypy plugins.")
 (define-public python-pytest-perf
   (package
     (name "python-pytest-perf")
-    (version "0.12.0")
+    (version "0.13.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2560,16 +2560,11 @@ mypy plugins.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "05mgknvrmyz1kmkgw8jzvisavc68wz1g2wxv69i6xvzgqxf17m9f"))))
+                "1hrccvrbccqwba04pqj749hdzn4sgldmbpg74nf3fzz7wyg6jxqk"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      (list
-      #:phases
+      #:test-flags '(list "-k"
-      #~(modify-phases %standard-phases
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                (invoke "pytest" "-k"
                           (string-append
                            ;; Do not test the myproject.toml build as it tries to pull
                            ;; dependencies from the internet.
@@ -2579,7 +2574,7 @@ mypy plugins.")
                            ;; network.
                            "and not BenchmarkRunner "
                            ;; The upstream_url test requires networking.
-                         "and not upstream_url"))))))))
+                           "and not upstream_url"))))
     (native-inputs
      (list python-pytest
            python-pytest-black

gnu/packages/cluster.scm

@@ -4,6 +4,7 @@
 ;;; Copyright © 2019 Andrew Miloradovsky <andrew@interpretmath.pw>
 ;;; Copyright © 2020, 2022 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2021 Dion Mendel <guix@dm9.info>
+;;; Copyright © 2023 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -74,7 +75,8 @@
     (arguments
      (list
       #:configure-flags
-      #~(list "--sysconfdir=/etc"
+      #~(append
+          (list "--sysconfdir=/etc"
                 "--localstatedir=/var"
                 ;; Do not install sysv or systemd init scripts.
                 "--with-initscripttype=none"
@@ -82,6 +84,9 @@
                 ;; Linux-Libre versions < 3.8.  8.4 is the latest
                 ;; kernel driver as of Linux 5.18.
                 "--without-83support")
+          #$(if (this-package-native-input "ruby-asciidoctor")
+               #~'()
+               #~(list "--without-manual")))
       #:test-target "test"
       #:make-flags #~(list "WANT_DRBD_REPRODUCIBLE_BUILD=yesplease")
       #:phases
@@ -126,16 +131,18 @@
                 (("\\$\\(DESTDIR\\)\\$\\(DRBD_LIB_DIR\\)")
                  "$(DESTDIR)$(prefix)$(DRBD_LIB_DIR)")))))))
     (native-inputs
-     (list clitest
+     (append (list clitest
                    eudev                        ;just to satisfy a configure check
-           flex
+                   flex)
              ;; For the documentation.
-           docbook-xml
+             (if (supported-package? ruby-asciidoctor)
+               (list docbook-xml
                      docbook-xml-4.4            ;used by documentation/ra2refentry.xsl
                      docbook-xsl
                      libxml2                    ;for XML_CATALOG_FILES
                      libxslt                    ;for xsltproc
-           ruby-asciidoctor))
+                     ruby-asciidoctor)
+               '())))
     (home-page "https://www.linbit.com/drbd/")
     (synopsis "Replicate block devices between machines")
     (description

gnu/packages/code.scm

@@ -237,8 +237,9 @@ highlighting your own code that seemed comprehensible when you wrote it.")
                  (lambda _
                    ;; Install the plugin files in the right place.
                    (let* ((data (string-append #$output "/share/gtags"))
-                          (vim  (string-append #$output
+                          (vim  (string-append
-                                               "/share/vim/vimfiles/plugin"))
+                                  #$output
+                                  "/share/vim/vimfiles/pack/guix/start/global/plugin"))
                           (lisp (string-append #$output "/share/emacs/site-lisp/"
                                                #$(package-name this-package) "-"
                                                #$(package-version this-package))))

gnu/packages/cpp.scm

@@ -31,7 +31,7 @@
 ;;; Copyright © 2022 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2022, 2023 David Elsing <david.elsing@posteo.net>
 ;;; Copyright © 2022, 2023 Zheng Junjie <873216071@qq.com>
-;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
 ;;; Copyright © 2023 Sughosha <Sughosha@proton.me>
 ;;; Copyright © 2023 Artyom V. Poptsov <poptsov.artyom@gmail.com>
@@ -609,6 +609,47 @@ container which uses the order in which keys were inserted to the container
 as ordering relation.")
     (license license:expat)))
 
+(define-public frozen
+  ;; The test suite fails to compile with the latest 1.1.1 release; use a
+  ;; newer commit (see:
+  ;; https://github.com/serge-sans-paille/frozen/issues/163).
+  (let ((commit "dd1f58c5f6c97fbf0832cc4e84676663839b913e")
+        (revision "0"))
+    (package
+      (name "frozen")
+      (version (git-version "1.1.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/serge-sans-paille/frozen")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "06i307a7v6alxfy24d47b1sjkz5f4mrqwl2vb4j8zx7wlgnrf08b"))))
+      (build-system cmake-build-system)
+      (home-page "https://github.com/serge-sans-paille/frozen")
+      (synopsis "C++ constexpr alternative header-only library")
+      (description "@code{frozen} is a header-only library that provides zero
+cost initialization for immutable containers, fixed-size containers, and
+various algorithms.  It provides features such as:
+@itemize
+@item
+immutable (also known as frozen), @code{constexpr}-compatible versions of
+{std::set}, {std::unordered_set}, {std::map} and {std::unordered_map}
+@item
+fixed-capacity, @code{constinit}-compatible versions of @code{std::map} and
+@code{std::unordered_map} with immutable, compile-time selected keys mapped to
+mutable values.
+@item
+zero cost initialization version of @code{std::search} for frozen needles
+using Boyer-Moore or Knuth-Morris-Pratt algorithms.
+@end itemize
+The @code{unordered_*} containers are guaranteed perfect (no hash
+collision) and the extra storage is linear with respect to the number of
+keys.")
+      (license license:asl2.0))))
+
 (define-public json-dto
   (package
     (name "json-dto")

gnu/packages/cran.scm

@@ -147,13 +147,13 @@ the vignette \"AER\" for a package overview.)")
 (define-public r-afpt
   (package
     (name "r-afpt")
-    (version "1.1.0.3")
+    (version "1.1.0.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "afpt" version))
               (sha256
                (base32
-                "18izncbr3ljckil97xx2w1y0y7qjykp06wm0ap8ismahqvia3xz3"))))
+                "15pa4p78p6r478l05481lzx6z4ahswj728s1sb3xp3pvn6rv4jfj"))))
     (properties `((upstream-name . "afpt")))
     (build-system r-build-system)
     (native-inputs (list r-knitr))
@@ -391,13 +391,13 @@ labels on the node can also be achieved.")
 (define-public r-collapse
   (package
     (name "r-collapse")
-    (version "2.0.3")
+    (version "2.0.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "collapse" version))
        (sha256
-        (base32 "16y4qxqr4k04690xn8s6c9fr3igpk34pgxygxkc41gc1na0ym37v"))))
+        (base32 "0azyl6667dzwns9knp3fplv6f9nav36wsrv42qzv90p5kzcaa872"))))
     (properties `((upstream-name . "collapse")))
     (build-system r-build-system)
     (propagated-inputs (list r-rcpp))
@@ -1490,14 +1490,14 @@ RUV-I, and RUV-III, along with various supporting algorithms.")
 (define-public r-waldo
   (package
     (name "r-waldo")
-    (version "0.5.1")
+    (version "0.5.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "waldo" version))
        (sha256
         (base32
-         "0inzdwna22axhjw0jdrk800g7zbkpcs7g1cmdi83r7j4zxn0ggs5"))))
+         "019fvypq36kwvr2znlr0fd9f2ihb08rgigf6ypdybry5n8daxkc2"))))
     (properties `((upstream-name . "waldo")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2201,14 +2201,14 @@ variables.")
 (define-public r-ggpp
   (package
     (name "r-ggpp")
-    (version "0.5.4")
+    (version "0.5.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggpp" version))
        (sha256
         (base32
-         "05w74003jp7kprxxbni0plr7ydzyc5hzw8g39kn0qd4p7dksjpwr"))))
+         "0nysan87vgy0pbcks3bychm84zcwx9pf4p250b45ghimhvxh5cvm"))))
     (properties `((upstream-name . "ggpp")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3223,6 +3223,27 @@ user-friendly output, and compatibility with tests implemented in R.")
 objects.")
     (license license:gpl3)))
 
+(define-public r-mblm
+  (package
+    (name "r-mblm")
+    (version "0.12.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mblm" version))
+       (sha256
+        (base32 "1fipb3bryaimr30lcxsxrn0ymv24z39swca7s4z7p9xcfg3ban1b"))))
+    (properties `((upstream-name . "mblm")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/mblm/index.html")
+    (synopsis "Median-based linear models")
+    (description
+     "This package provides linear models based on Theil-Sen single median and
+Siegel repeated medians.  They are very robust (29 or 50 percent breakdown
+point, respectively), and if no outliers are present, the estimators are very
+similar to OLS.")
+    (license license:gpl2+)))
+
 (define-public r-mboost
   (package
    (name "r-mboost")
@@ -4059,24 +4080,26 @@ particularly easy to create complete web applications using httpuv alone.")
 (define-public r-httr2
   (package
     (name "r-httr2")
-    (version "0.2.3")
+    (version "1.0.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "httr2" version))
               (sha256
                (base32
-                "0gabjyv2699p7fb4225jsr2kkbarx1w01kha8ipqzwhjjl13481m"))))
+                "0jaajfr1hr6bzb1vz2nw2csl2l09kbq619vsq5yrlchcarpjv1fb"))))
     (properties `((upstream-name . "httr2")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cli
            r-curl
            r-glue
+           r-lifecycle
            r-magrittr
            r-openssl
            r-r6
            r-rappdirs
            r-rlang
+           r-vctrs
            r-withr))
     (native-inputs (list r-knitr))
     (home-page "https://httr2.r-lib.org")
@@ -4206,13 +4229,13 @@ a list of p-values.")
 (define-public r-htmltools
   (package
     (name "r-htmltools")
-    (version "0.5.6.1")
+    (version "0.5.7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "htmltools" version))
               (sha256
                (base32
-                "0km08kvg0j2h1d0v6wpxf09yjadhp2srjjnmqwcahfyh37w4xf09"))))
+                "11mkk26pjck6r2w2nv6niy90c6l13g64zi01s3j4jgq634kdic7c"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-base64enc r-digest r-ellipsis r-fastmap r-rlang))
@@ -5202,14 +5225,14 @@ in R and Shiny via the D3 visualization library.")
 (define-public r-wesanderson
   (package
     (name "r-wesanderson")
-    (version "0.3.6")
+    (version "0.3.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "wesanderson" version))
        (sha256
         (base32
-         "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
+         "0kjyz5mrkrirg2glf57b0rhxj2fdp1m6q8zx947y0jg1w425cbn9"))))
     (properties `((upstream-name . "wesanderson")))
     (build-system r-build-system)
     (home-page "https://github.com/karthik/wesanderson")
@@ -5541,14 +5564,14 @@ and/or higher-resolution databases.")
 (define-public r-maps
   (package
     (name "r-maps")
-    (version "3.4.1")
+    (version "3.4.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "maps" version))
        (sha256
         (base32
-         "0034114pdakxcx480b45qy9j4vq1v5ss961ssy92w4nqiqhsb4z6"))))
+         "06l58919kgks9adwzgfir44q6gnx46j3c7ah9c6d4dn36xsld7fk"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/maps")
     (synopsis "Draw geographical maps")
@@ -5580,18 +5603,18 @@ coordinates.")
 (define-public r-rgooglemaps
   (package
     (name "r-rgooglemaps")
-    (version "1.4.5.3")
+    (version "1.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RgoogleMaps" version))
        (sha256
         (base32
-         "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
+         "197q5i2sky824dwq0x4hhrpkrsd1b6f9qg06mjlwb89mv4vnrzhl"))))
     (properties `((upstream-name . "RgoogleMaps")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-png r-sp))
+     (list r-png))
     (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
     (synopsis "Use Google Maps in R")
     (description "This package serves two purposes:
@@ -6185,6 +6208,30 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
 performs global optimization by differential evolution.")
     (license license:gpl2+)))
 
+(define-public r-rcppdist
+  (package
+    (name "r-rcppdist")
+    (version "0.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RcppDist" version))
+       (sha256
+        (base32 "02g57xwfipdcljv06krhm02dbqn9kfyj2km6rdg0a7vq9prwdz1x"))))
+    (properties `((upstream-name . "RcppDist")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-rcpp r-rcpparmadillo))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/duckmayr/RcppDist")
+    (synopsis "Integration of additional probability distributions")
+    (description
+     "RcppDist provides a header-only C++ library with functions for
+additional statistical distributions that can be called from C++ when writing
+code using Rcpp or RcppArmadillo.  Functions are available that return a
+@code{NumericVector} as well as doubles, and for multivariate or matrix
+distributions, Armadillo vectors and matrices.")
+    (license license:gpl2+)))
+
 (define-public r-rcppml
   (package
     (name "r-rcppml")
@@ -6295,6 +6342,27 @@ with Rcpp and retrieve an @code{XPtr} that can be passed to other C++
 components.")
     (license license:expat)))
 
+(define-public r-bb
+  (package
+    (name "r-bb")
+    (version "2019.10-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "BB" version))
+       (sha256
+        (base32 "0kf9sfsm3n036a8a8gjfpc9qdryvadb019kqjh80n1szdv7bdl04"))))
+    (properties `((upstream-name . "BB")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-quadprog))
+    (home-page "https://publichealth.jhu.edu/")
+    (synopsis "Solving and optimizing large-scale nonlinear systems")
+    (description
+     "This package implements Barzilai-Borwein spectral methods for solving
+nonlinear system of equations, and for optimizing nonlinear objective
+functions subject to simple constraints.")
+    (license license:gpl3)))
+
 (define-public r-bindr
   (package
     (name "r-bindr")
@@ -7122,13 +7190,13 @@ provides an interactive R manager and worker environment.")
 (define-public r-rmumps
   (package
     (name "r-rmumps")
-    (version "5.2.1-23")
+    (version "5.2.1-25")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rmumps" version))
        (sha256
-        (base32 "1mypmf9j9fzaldpv56bqng5yhyxfc55hvzd98d1dk6w1m1sncn09"))))
+        (base32 "15yn5i6v3xz90gimvaqgvp805cfpvr439y9wpckyvwn1iwp2745y"))))
     (properties `((upstream-name . "rmumps")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -7210,6 +7278,57 @@ T distribution.  There is only one exported function, @code{e_trunct},
 which should be seen for details.")
    (license license:expat)))
 
+(define-public r-evd
+  (package
+    (name "r-evd")
+    (version "2.3-6.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "evd" version))
+       (sha256
+        (base32 "0wc95hfj0gwkyghipdrhwd3s6q2agh9x2wy6y7dr6mjw7wnmjb36"))))
+    (properties `((upstream-name . "evd")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/package=evd")
+    (synopsis "Functions for extreme value distributions")
+    (description
+     "This package extends simulation, distribution, quantile and density
+functions to univariate and multivariate parametric extreme value distributions,
+and provides fitting functions which calculate maximum likelihood estimates for
+univariate and bivariate maxima models, and for univariate and bivariate
+threshold models.")
+    (license license:gpl3)))
+
+(define-public r-evmix
+  (package
+    (name "r-evmix")
+    (version "2.12")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "evmix" version))
+       (sha256
+        (base32 "02rabc9snci00s1x7h0svfr66lmw1wjcdg0149wc52mnccsdaivf"))))
+    (properties `((upstream-name . "evmix")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-gsl
+           r-mass
+           r-sparsem))
+    (home-page "http://www.math.canterbury.ac.nz/~c.scarrott/evmix.shtml")
+    (synopsis
+     "Extreme value threshold estimation and uncertainty quantification")
+    (description
+     "This package provides the usual distribution functions, maximum likelihood
+inference and model diagnostics for univariate stationary extreme value mixture
+models.  Also, there are provided kernel density estimation including various
+boundary corrected kernel density estimation methods and a wide choice of kernels,
+with cross-validation likelihood based bandwidth estimator.  Reasonable
+consistency with the base functions in the evd package is provided, so that users
+can safely interchange most code.")
+    (license license:gpl3)))
+
 (define-public r-excelr
   (package
     (name "r-excelr")
@@ -7825,14 +7944,14 @@ these progress updates.")
 (define-public r-lava
   (package
     (name "r-lava")
-    (version "1.7.2.1")
+    (version "1.7.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lava" version))
        (sha256
         (base32
-         "0bpg75w0ri1mkf7cw9gbw1fjpy4mh9h48k019y772xjfgrf1yayl"))))
+         "023av1mz4hr1lqv8cpbx0j1y3c7ljyns35rm838c618b6pqps22f"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-future-apply r-numderiv r-progressr r-squarem r-survival))
@@ -8932,6 +9051,30 @@ distribution with mean equal to @code{mean} and standard deviation equal to
 functions, as well as a random generation function.")
     (license license:gpl2)))
 
+(define-public r-truncdist
+  (package
+    (name "r-truncdist")
+    (version "1.0-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "truncdist" version))
+       (sha256
+        (base32 "02ihw4ixhadwr3sqm6r264i8vpcaz8pn69vkzabd8fwqvn5vcj5q"))))
+    (properties `((upstream-name . "truncdist")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-evd))
+    (home-page "https://cran.r-project.org/package=truncdist")
+    (synopsis "Truncated random variables")
+    (description
+     "This package provides a collection of tools to evaluate probability density
+functions, cumulative distribution functions, quantile functions and random
+numbers for truncated random variables.  These functions are provided to also
+compute the expected value and variance.  @acronym{Q-Q, quantile–quantile} plots
+can be produced.  All the probability functions in the stats, stats4 and evd
+packages are automatically available for truncation.")
+    (license license:gpl2+)))
+
 (define-public r-rsolnp
   (package
     (name "r-rsolnp")
@@ -9785,13 +9928,13 @@ iVAT).")
 (define-public r-xfun
   (package
     (name "r-xfun")
-    (version "0.40")
+    (version "0.41")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xfun" version))
        (sha256
-        (base32 "1xvngh0kbd87cl39bzmjx5i57pmxik9gw50li8dh42j438cnma8y"))))
+        (base32 "00ivgr557ja8l33lvawrivfhgj1xbjmdi4dj07zybwa1y6wc6x13"))))
     (build-system r-build-system)
     (properties
      ;; knitr itself depends on xfun
@@ -10353,13 +10496,13 @@ information between package updates.")
 (define-public r-leaflet
   (package
     (name "r-leaflet")
-    (version "2.2.0")
+    (version "2.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "leaflet" version))
        (sha256
-        (base32 "0k0zplbhmvld6q1id17s827z1230kvnz16c4hlvp6jn9g26yy0dq"))
+        (base32 "1gfsf7bsmp418zv4gpk5i1xg5vvgqwpdkznnvj5x0mk4rcqk1i81"))
        (snippet
         '(for-each
           delete-file
@@ -10750,13 +10893,13 @@ multivariate distributions.")
 (define-public r-fbasics
   (package
     (name "r-fbasics")
-    (version "4031.95")
+    (version "4032.96")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "fBasics" version))
               (sha256
                (base32
-                "1d1pbyidng68fcc6vrm98ybklz6yzrinqc2dhg8q6f1pg3kkx6bj"))))
+                "14461d6ac8hcn1x3srh45a4s5imafqb0xy8bn5l6d0qwhw4njmg1"))))
     (properties `((upstream-name . "fBasics")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12487,20 +12630,20 @@ JavaScript library) and interact with the igraph package.")
 (define-public r-data-tree
   (package
     (name "r-data-tree")
-    (version "1.0.0")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "data.tree" version))
        (sha256
         (base32
-         "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
+         "0qxd1g159phc6f18iddjljdg96sh09w63xqawjwbwyhg4blm9ddh"))))
     (properties `((upstream-name . "data.tree")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-r6 r-stringi))
     (native-inputs
-     (list r-knitr))
+     (list r-knitr r-rmarkdown))
     (home-page "https://github.com/gluc/data.tree")
     (synopsis "General purpose hierarchical data structure")
     (description
@@ -12547,14 +12690,14 @@ automatically translated to the equivalent, but usually much faster,
 (define-public r-collapsibletree
   (package
     (name "r-collapsibletree")
-    (version "0.1.7")
+    (version "0.1.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "collapsibleTree" version))
        (sha256
         (base32
-         "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
+         "1i5nmw5w7m8xdgxzim8z8n4w321f42isxbvvajl8ii59pg7drilq"))
        (snippet
         '(begin
            ;; Delete minified JavaScript file
@@ -12640,14 +12783,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
 (define-public r-rastervis
   (package
     (name "r-rastervis")
-    (version "0.51.5")
+    (version "0.51.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rasterVis" version))
        (sha256
         (base32
-         "18bsrw629p4pkyhrpjmiyhq73w882bhgpwmkih0gjnw3ywwgx7rs"))))
+         "12cl201gwah0bn14ji4nbygayd77w5fck9zkcikhrda5s0chvgb1"))))
     (properties `((upstream-name . "rasterVis")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13477,14 +13620,14 @@ implemented in bibutils.")
 (define-public r-rdpack
   (package
     (name "r-rdpack")
-    (version "2.5")
+    (version "2.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rdpack" version))
        (sha256
         (base32
-         "0xy8w3law1dn53f1gv4jd637pwssr928pvgchpbrpsqz8ghv4kad"))))
+         "02i21i85pb5aim529byjwhmyyz9jd82mi4j26a3kay0pcn6djxba"))))
     (properties `((upstream-name . "Rdpack")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14219,14 +14362,14 @@ the work.")
 (define-public r-doby
   (package
     (name "r-doby")
-    (version "4.6.19")
+    (version "4.6.20")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "doBy" version))
        (sha256
         (base32
-         "14hvbhf9zamqkjhr9jd8zjpm9xlc8hwqj04gy6ln32n2hzqqqr6v"))))
+         "08nsl9xzyi2k7xkwa9mn91fn77ji0z9z5lm388pfdmydbfmpy2ks"))))
     (properties `((upstream-name . "doBy")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14328,14 +14471,14 @@ containing one or more SNPs that evolved under directional selection.")
 (define-public r-proc
   (package
     (name "r-proc")
-    (version "1.18.4")
+    (version "1.18.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pROC" version))
        (sha256
         (base32
-         "0lqar1lbm461in4jb9rkdnpccl8lshrhig2qxr892m91mdxym46m"))))
+         "129cnh3kh9sr42nc7n9f14kr9svi3501834x40njynnzlr0wi4sm"))))
     (properties `((upstream-name . "pROC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15002,13 +15145,13 @@ subsequence} (LCS) using a dynamic programming algorithm.")
 (define-public r-mosaiccore
   (package
     (name "r-mosaiccore")
-    (version "0.9.2.1")
+    (version "0.9.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mosaicCore" version))
        (sha256
-        (base32 "1yns15yxr6215xf9qsxfvl24a9zvh1chw49n31dql7fy1zr1dkmp"))))
+        (base32 "0v3xhv6yfk1hc6a40jjgp6vvq102qa1l4n787pfywx6jhzbhamp2"))))
     (properties `((upstream-name . "mosaicCore")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15053,21 +15196,18 @@ haven package.")
 (define-public r-ggformula
   (package
     (name "r-ggformula")
-    (version "0.10.4")
+    (version "0.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggformula" version))
        (sha256
-        (base32 "07d9sq0dqi0g5x9h58icfk1f4hgg1xz4mhbp2z2rxg9qgs74fvdj"))))
+        (base32 "0vbpivyxms46px3wqkbl1wq199mqdxq94gsiplv4i7lz0lzghsfm"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-ggforce
+     (list r-ggplot2
-           r-ggplot2
            r-ggridges
-           r-ggstance
            r-labelled
-           r-magrittr
            r-mosaiccore
            r-rlang
            r-scales
@@ -15087,13 +15227,13 @@ while providing the intuitive capabilities of @code{r-ggplot2}.")
 (define-public r-mosaicdata
   (package
     (name "r-mosaicdata")
-    (version "0.20.3")
+    (version "0.20.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mosaicData" version))
        (sha256
-        (base32 "1s97yq24z7yhzmx0dpspfadpd8hndyhn7aiw0nslwrhvilhwa409"))))
+        (base32 "0y6ii234paknak0p8cm5wcjia4s4wh7iixjbbvdgp0w17c05dckh"))))
     (properties `((upstream-name . "mosaicData")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/mosaicData/")
@@ -15128,13 +15268,13 @@ Processing of very large files is supported.")
 (define-public r-mosaic
   (package
     (name "r-mosaic")
-    (version "1.8.4.2")
+    (version "1.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mosaic" version))
        (sha256
-        (base32 "12kpkb7vm54na9hjjkvzw6gm5plx0m6i0l9kihz2r30zanfx5jca"))))
+        (base32 "1dydqawljv5l9lmhdrhmr7wh3q1c2mnc61gc99jr0jbb1bmls327"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-dplyr
@@ -15147,6 +15287,7 @@ Processing of very large files is supported.")
            r-mosaicdata
            r-purrr
            r-rlang
+           r-tibble
            r-tidyr))
     (native-inputs
      (list r-knitr))
@@ -21838,14 +21979,14 @@ numbers from ZIP and ZINB distributions.")
 (define-public r-nor1mix
   (package
     (name "r-nor1mix")
-    (version "1.3-0")
+    (version "1.3-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nor1mix" version))
        (sha256
         (base32
-         "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
+         "0252kqhdsp374isc59pm1c6dmsb16jibpnsp1bpyh4k5mg73cdj6"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/nor1mix/")
     (synopsis "Normal (1-d) mixture models")
@@ -22149,14 +22290,14 @@ can be used with function approximation, eligibility traces (Singh & Sutton,
 (define-public r-lemon
   (package
     (name "r-lemon")
-    (version "0.4.6")
+    (version "0.4.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lemon" version))
        (sha256
         (base32
-         "0v1kbyk64yzsk92h6yq03kp9alc9632qprznsws61r8firiskim5"))))
+         "1r33n7bkfhjpyi23j7gsi387qvyazcy9b912dsd3vg2yqir8s26p"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ggplot2
@@ -24968,14 +25109,14 @@ Row} (CSR) format.")
 (define-public r-text2vec
   (package
     (name "r-text2vec")
-    (version "0.6.3")
+    (version "0.6.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "text2vec" version))
        (sha256
         (base32
-         "1hi7ydb7xkgbff4lwnnz1biyl8m90w16hn3x5rrzvscvm53sj4y7"))))
+         "0sjlvp4zhzwc0ai7626fpw3ws8xv0xhl8gv8mrk24lrpk5nhin2h"))))
     (properties `((upstream-name . "text2vec")))
     (build-system r-build-system)
     (propagated-inputs
@@ -25077,14 +25218,14 @@ provides tools to compute this metric.")
 (define-public r-lintr
   (package
     (name "r-lintr")
-    (version "3.1.0")
+    (version "3.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lintr" version))
        (sha256
         (base32
-         "1kb3jrzh1vn1fpj6phm2ni542yjgbbjmzgkn8w7khmh1sd9mj7pp"))))
+         "07c7h30nh1529wba8xkyg2sapj6r7jjckrxyzhrg2ssfwzs4dwdw"))))
     (properties `((upstream-name . "lintr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26348,13 +26489,13 @@ function and interfaces to external frameworks.")
 (define-public r-covr
   (package
     (name "r-covr")
-    (version "3.6.3")
+    (version "3.6.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "covr" version))
        (sha256
-        (base32 "17m2zzgfghr7gzcdgim21vsl12nd4714867dcp9xfb6ili31ikn0"))
+        (base32 "0al6n4gnnvgxk968skqnajpqpqyl6kpam3fmn782kihhcl1h8qib"))
        (modules '((guix build utils)))
        ;; TODO: still need to replace highlight.js/highlight.pack.js
        (snippet
@@ -26475,14 +26616,14 @@ be used further by e.g. graphic devices.")
 (define-public r-graphlayouts
   (package
     (name "r-graphlayouts")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "graphlayouts" version))
        (sha256
         (base32
-         "0x777ixw2vvj1z3dams0zmyk25v7cdm4sx8v6knlb2mfkkg2gcyk"))))
+         "1mg0j9kcjp8dbpd8fy9vr5f35pz41v18vxc7q4pyl986pj859jam"))))
     (properties `((upstream-name . "graphlayouts")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26626,14 +26767,14 @@ in pipelines.")
 (define-public r-parameters
   (package
     (name "r-parameters")
-    (version "0.21.2")
+    (version "0.21.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "parameters" version))
        (sha256
         (base32
-         "05ryyyibnm69hq1xa84r9n2gr1s1ifds70z4awmib2ch62098m43"))))
+         "091zpyq37v7xjicj4h4r4fqhrrc7d3hicgbdznsjn85sw4d7q595"))))
     (properties `((upstream-name . "parameters")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26711,14 +26852,14 @@ atmospheric physics.")
 (define-public r-lifecycle
   (package
     (name "r-lifecycle")
-    (version "1.0.3")
+    (version "1.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lifecycle" version))
        (sha256
         (base32
-         "1hk9mblhap429fk77qpgc4hv0j91q5wpahi0y76w118m471zsnb4"))))
+         "1k4ibf2x90xgmzaq47vf9wrsh6a2fp2lg1l8bq89632bx33x795d"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cli r-glue r-rlang))
@@ -26849,12 +26990,12 @@ to ODEs by numerical differencing.")
 (define-public r-pracma
   (package
     (name "r-pracma")
-    (version "2.4.2")
+    (version "2.4.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "pracma" version))
               (sha256
-               (base32 "05lwx2yx7f45cr5amzbjv3b2p6ibspjxl0aglq2dga6rvxzk6l0x"))))
+               (base32 "0zxsqr7f4pcr1nmbbzliihyldv091ykzajv1mbdrkycp46pz6khs"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/pracma/")
     (synopsis "Practical numerical math functions")
@@ -28856,14 +28997,14 @@ be conducted.  A graphical user interface is also provided.")
 (define-public r-actcd
   (package
     (name "r-actcd")
-    (version "1.2-0")
+    (version "1.3-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ACTCD" version))
        (sha256
         (base32
-         "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
+         "1a0gsznca5fv7i29xpcns4rkas5q88wv01rxvd4j66n64gw0ri4j"))))
     (properties `((upstream-name . "ACTCD")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29262,14 +29403,14 @@ API; see the package vignette for details.")
 (define-public r-actuar
   (package
     (name "r-actuar")
-    (version "3.3-3")
+    (version "3.3-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "actuar" version))
        (sha256
         (base32
-         "0ji5p19vqnr3i3vfrql2qndhzcjnr57jrh0szil6gaz6bm56afc4"))))
+         "06693w4cwcchi0z64vgg7khc4k4209nw6m2x441nwix4x6rk1zjs"))))
     (properties `((upstream-name . "actuar")))
     (build-system r-build-system)
     (propagated-inputs (list r-expint))
@@ -31191,14 +31332,14 @@ Complete access to optimized C functions is made available with
 (define-public r-openmx
   (package
     (name "r-openmx")
-    (version "2.21.8")
+    (version "2.21.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "OpenMx" version))
        (sha256
         (base32
-         "1vvlb9q3w6i6g7kf0r5jnrlmdxskh3rbfss90icand046rl37qdz"))))
+         "1kll5iim5l71dxkjd8y9ma1494818j369gp92qdsy3x6lxy244ym"))))
     (properties `((upstream-name . "OpenMx")))
     (build-system r-build-system)
     (propagated-inputs
@@ -31391,14 +31532,14 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.")
 (define-public r-qgraph
   (package
     (name "r-qgraph")
-    (version "1.9.5")
+    (version "1.9.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "qgraph" version))
        (sha256
         (base32
-         "1mi19bjx83zb42wmgb716a3l4gvwch3rmybdqmm8k3dl8xr2qnjc"))))
+         "1m019j5nxc0184p0r2zgdn457g555nxsp2s08maa053nydj1va0l"))))
     (properties `((upstream-name . "qgraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -34115,14 +34256,14 @@ aggregation for comparing different implementations in order to provide a
 (define-public r-rfast
   (package
     (name "r-rfast")
-    (version "2.0.9")
+    (version "2.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rfast" version))
        (sha256
         (base32
-         "12jl5kqjn571zcqh4n351d7nx86b3jh46ds8krqz92f0z6fjmkzz"))))
+         "1zqq4k85i0nbzndkh0iiq3k83ly0mpl3pn4wkka6qxfvk6n6rr7r"))))
     (properties `((upstream-name . "Rfast")))
     (build-system r-build-system)
     (propagated-inputs
@@ -35006,14 +35147,14 @@ and regression metrics (e.g., RMSE).")
 (define-public r-warp
   (package
     (name "r-warp")
-    (version "0.2.0")
+    (version "0.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "warp" version))
        (sha256
         (base32
-         "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
+         "1gj65kgs7x63f6y2vnv13k293b52k4afbmdlcam635h9vs8da2h2"))))
     (properties `((upstream-name . "warp")))
     (build-system r-build-system)
     (native-inputs (list r-knitr))
@@ -36067,21 +36208,23 @@ other R users.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "4.4.0")
+    (version "5.0.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "1pdlvjh5xs1fyj2zic98sfz9zazbb45qywfqnhfzqb34jyaxy5qg"))))
+                "1hvqxfskwpw06dxc9hc9zvxqb73wr7qjxgrqgyjklxaq1xhr335v"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cluster
            r-cowplot
+           r-fastdummies
            r-fitdistrplus
            r-future
            r-future-apply
+           r-generics
            r-ggplot2
            r-ggrepel
            r-ggridges
@@ -36092,6 +36235,7 @@ other R users.")
            r-jsonlite
            r-kernsmooth
            r-leiden
+           r-lifecycle
            r-lmtest
            r-mass
            r-matrix
@@ -36108,10 +36252,12 @@ other R users.")
            r-rcpp
            r-rcppannoy
            r-rcppeigen
+           r-rcpphnsw
            r-rcppprogress
            r-reticulate
            r-rlang
            r-rocr
+           r-rspectra
            r-rtsne
            r-scales
            r-scattermore
@@ -36867,14 +37013,14 @@ vector machines, and gradient boosting.")
 (define-public r-bbotk
   (package
     (name "r-bbotk")
-    (version "0.7.2")
+    (version "0.7.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bbotk" version))
        (sha256
         (base32
-         "1gw0rkbiv93ifl9110r9sr0p9g4vg7qc11mznmmjq0a5vzmqgpm9"))))
+         "1ddr5w7n68d3imcrm0ipgk1waml8zj4szi566dmmiqvlpzpgdr3p"))))
     (properties `((upstream-name . "bbotk")))
     (build-system r-build-system)
     (propagated-inputs
@@ -37128,14 +37274,14 @@ chunks.")
 (define-public r-clustree
   (package
     (name "r-clustree")
-    (version "0.5.0")
+    (version "0.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "clustree" version))
        (sha256
         (base32
-         "1haam13aifak8fladyxwa0gz56anj1zfczfjgs07gbw90kf6azx8"))))
+         "05yizn8hcf4nsibypxahp2mz64sy10vli776mi0d2gvfb5p4kwmm"))))
     (properties `((upstream-name . "clustree")))
     (build-system r-build-system)
     (propagated-inputs
@@ -39205,14 +39351,14 @@ fully reproducible.")
 (define-public r-paws-common
   (package
     (name "r-paws-common")
-    (version "0.6.2")
+    (version "0.6.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "paws.common" version))
        (sha256
         (base32
-         "1jgls5fks9s8m616qs6b7hvv0wf7nhzajyds15hnlasqwg387h3d"))))
+         "1pzgwljrk3maxcbmiy3yiccijm6c2ach8f9kzpqr7w5k5vkyhpvx"))))
     (properties `((upstream-name . "paws.common")))
     (build-system r-build-system)
     (propagated-inputs
@@ -40269,17 +40415,17 @@ formatting and delivering log messages with low overhead.")
 (define-public r-fasterize
   (package
     (name "r-fasterize")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "fasterize" version))
         (sha256
-          (base32 "1ckxi2iyxdahhgbliblcrkzziblfagzr54srjk27yp1lcgivvvs4"))))
+          (base32 "1d63q77hfbn2ly8cwsik4gaavdhidpi7idf7qj2y5bi9xhd10kyl"))))
     (properties `((upstream-name . "fasterize")))
     (build-system r-build-system)
     (propagated-inputs
-      (list r-raster r-rcpp r-rcpparmadillo r-sp))
+      (list r-raster r-rcpp r-rcpparmadillo r-wk))
     (native-inputs (list r-knitr))
     (home-page "https://github.com/ecohealthalliance/fasterize")
     (synopsis "Fast Polygon to Raster Conversion")

gnu/packages/crates-io.scm

@@ -8645,8 +8645,32 @@ streams in big-endian and little-endian formats.")
         ("rust-serde-test" ,rust-serde-test-1)
         ("rust-static-assertions" ,rust-static-assertions-1))))))
 
+(define-public rust-blake2-0.10
+  (package
+    (name "rust-blake2")
+    (version "0.10.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "blake2" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1zlf7w7gql12v61d9jcbbswa3dw8qxsjglylsiljp9f9b3a2ll26"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-digest" ,rust-digest-0.10))
+       #:cargo-development-inputs
+       (("rust-digest" ,rust-digest-0.10)
+        ("rust-hex-literal" ,rust-hex-literal-0.2))))
+    (home-page "https://github.com/RustCrypto/hashes")
+    (synopsis "BLAKE2 hash functions")
+    (description "This package provides BLAKE2 hash functions in Rust.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-blake2-0.9
   (package
+    (inherit rust-blake2-0.10)
     (name "rust-blake2")
     (version "0.9.2")
     (source
@@ -8656,7 +8680,6 @@ streams in big-endian and little-endian formats.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32 "0x7i67c0hn3bzcwny08rgjrrnarqnqw10qpmh2blbx9hd78kfkha"))))
-    (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-crypto-mac" ,rust-crypto-mac-0.8)
@@ -8665,14 +8688,11 @@ streams in big-endian and little-endian formats.")
        #:cargo-development-inputs
        (("rust-crypto-mac" ,rust-crypto-mac-0.8)
         ("rust-digest" ,rust-digest-0.9)
-        ("rust-hex-literal" ,rust-hex-literal-0.2))))
+        ("rust-hex-literal" ,rust-hex-literal-0.2))))))
-    (home-page "https://github.com/RustCrypto/hashes")
-    (synopsis "BLAKE2 hash functions")
-    (description "This package provides BLAKE2 hash functions in Rust.")
-    (license (list license:expat license:asl2.0))))
 
 (define-public rust-blake2-0.8
   (package
+    (inherit rust-blake2-0.10)
     (name "rust-blake2")
     (version "0.8.1")
     (source
@@ -8684,7 +8704,6 @@ streams in big-endian and little-endian formats.")
        (sha256
         (base32
          "0c4k11j04kqhkci6i9b7lz6p13kpcv228pdqixgrawvavaq0gjwl"))))
-    (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-byte-tools" ,rust-byte-tools-0.3)
@@ -8694,11 +8713,7 @@ streams in big-endian and little-endian formats.")
        #:cargo-development-inputs
        (("rust-crypto-mac" ,rust-crypto-mac-0.7)
         ("rust-digest" ,rust-digest-0.8)
-        ("rust-hex-literal" ,rust-hex-literal-0.1))))
+        ("rust-hex-literal" ,rust-hex-literal-0.1))))))
-    (home-page "https://github.com/RustCrypto/hashes")
-    (synopsis "BLAKE2 hash functions")
-    (description "This package provides BLAKE2 hash functions in Rust.")
-    (license (list license:expat license:asl2.0))))
 
 (define-public rust-blake2b-simd-1
   (package

gnu/packages/databases.scm

@@ -5001,7 +5001,9 @@ The drivers officially supported by @code{libdbi} are:
      `(#:configure-flags
        ;; C++11 (-DSOCI_CXX11) is OFF by default.  hyperledger-iroha needs it.
        (list "-DCMAKE_CXX_STANDARD=17"
-             "-DSOCI_LIBDIR=lib")
+             "-DSOCI_LIBDIR=lib"
+             ;; This is for relocation when linking statically
+             "-DCMAKE_CXX_FLAGS=-fPIE")
        #:tests? #f))         ; may require running database management systems
     (synopsis "C++ Database Access Library")
     (description

gnu/packages/dezyne.scm

@@ -32,14 +32,14 @@
 (define-public dezyne
   (package
     (name "dezyne")
-    (version "2.17.7")
+    (version "2.17.8")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://dezyne.org/download/dezyne/"
                            name "-" version ".tar.gz"))
        (sha256
-        (base32 "09w2rl2ghm8z6fv3iflxnikcj2q98119imvlgvkmkhch5cplx7ny"))))
+        (base32 "0m5cnymcyg7k1jhp4xjpvpay7ia72xdzyjnjg0spsr4p7fy7yql4"))))
     (inputs (list bash-minimal
                   guile-3.0-latest
                   guile-json-4

gnu/packages/dunst.scm

@@ -1,89 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2017, 2018 Alex Kost <alezost@gmail.com>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2019, 2023 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
-;;; Copyright © 2021 Alexandru-Sergiu Marton <brown121407@posteo.ro>
-;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
-;;; Copyright © 2022 Jai Vetrivelan <jaivetrivelan@gmail.com>
-;;;
-;;; This file is part of GNU Guix.
-;;;
-;;; GNU Guix is free software; you can redistribute it and/or modify it
-;;; under the terms of the GNU General Public License as published by
-;;; the Free Software Foundation; either version 3 of the License, or (at
-;;; your option) any later version.
-;;;
-;;; GNU Guix is distributed in the hope that it will be useful, but
-;;; WITHOUT ANY WARRANTY; without even the implied warranty of
-;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;;; GNU General Public License for more details.
-;;;
-;;; You should have received a copy of the GNU General Public License
-;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
-
-(define-module (gnu packages dunst)
-  #:use-module (guix packages)
-  #:use-module (guix git-download)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix utils)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (gnu packages)
-  #:use-module (gnu packages base)
-  #:use-module (gnu packages freedesktop)
-  #:use-module (gnu packages glib)
-  #:use-module (gnu packages gnome)
-  #:use-module (gnu packages gtk)
-  #:use-module (gnu packages perl)
-  #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages xorg))
-
-(define-public dunst
-  (package
-    (name "dunst")
-    (version "1.9.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/dunst-project/dunst")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1nfxf2rahngxpy606yrizrz16d0pswl5sa9jfzpv7h19x6xy24vx"))))
-    (build-system gnu-build-system)
-    (arguments
-     `(#:tests? #f                      ; no check target
-       #:make-flags (list (string-append "CC=" ,(cc-for-target))
-                          (string-append "PREFIX=" %output)
-                          (string-append "SYSCONFDIR=" %output "/etc")
-                          ;; Otherwise it tries to install service file
-                          ;; to "dbus" store directory.
-                          (string-append "SERVICEDIR_DBUS=" %output
-                                         "/share/dbus-1/services")
-                          "dunstify")
-       #:phases (modify-phases %standard-phases
-                  (delete 'configure))))
-    (native-inputs
-     (list pkg-config perl ; for pod2man
-           which))
-    (inputs
-     (list dbus
-           (librsvg-for-system) ; for svg support
-           glib
-           cairo
-           pango
-           libnotify ; for dunstify
-           libx11
-           libxscrnsaver
-           libxinerama
-           libxrandr
-           libxdg-basedir
-           wayland))           ; for wayland support
-    (home-page "https://dunst-project.org/")
-    (synopsis "Customizable and lightweight notification daemon")
-    (description
-     "Dunst is a highly configurable and minimalistic notification daemon.
-It provides @code{org.freedesktop.Notifications} D-Bus service, so it is
-started automatically on the first call via D-Bus.")
-    (license license:bsd-3)))

gnu/packages/engineering.scm

@@ -1092,7 +1092,7 @@ Emacs).")
 (define-public kicad
   (package
     (name "kicad")
-    (version "7.0.8")
+    (version "7.0.9")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1100,7 +1100,7 @@ Emacs).")
                     (commit version)))
               (sha256
                (base32
-                "1gaj833hm3avyb7gyjnl4jk9cckcmj8084y6q45ysjvh283rxsy4"))
+                "1hq9rba1gcks14zwbr8nbicpsil4imslgfch6ll33fhizbks3fq4"))
               (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (arguments
@@ -1200,7 +1200,7 @@ electrical diagrams), gerbview (viewing Gerber files) and others.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1ya9kwcbsh8cqbinjr1hr14sd0g6rls1awmvw8hwd7715f97x8fg"))))
+                "14dg99fvl6av9sn6gig6d6k1sdcf2svxy4fipqcz994z2khhz1sj"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags (list "-DBUILD_FORMATS=html")
@@ -1234,7 +1234,7 @@ electrical diagrams), gerbview (viewing Gerber files) and others.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "176zb7df25vz3wbhs94plmpabcgzxsnzbqmpdyssqr7m2wb2424a"))))
+                "0ynsnjq3z126cjkgm1fjbjvdvpc0walnr42ya9dv46l27kxy2j77"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f))                    ; no tests exist
@@ -1263,7 +1263,7 @@ libraries.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1560m5mwwq0jrjhr8zdh2xrm1w7pgr250p81xzhdc4wj7zsb0rrp"))))
+                "16a4c2xs4i8wbm01a901yxabxk0qdsjkzlccfawddv82bkh4b87h"))))
     (synopsis "Official KiCad footprint libraries")
     (description "This package contains the official KiCad footprint libraries.")))
 
@@ -1280,7 +1280,7 @@ libraries.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1ypy2nzs1x8i98jr5kmlxfd6y592qs22aq73yl8nq0s6640fc4kk"))))
+                "1cly28vc07i54v487zbb8d1h70nrd3naxvq146b0xnbrjwnd2q28"))))
     (synopsis "Official KiCad 3D model libraries")
     (description "This package contains the official KiCad 3D model libraries.")))
 

gnu/packages/fabric-management.scm

@@ -46,7 +46,7 @@
 (define-public opensm
   (package
     (name "opensm")
-    (version "3.3.22")
+    (version "3.3.24")
     (source
      (origin
        (method url-fetch)
@@ -54,7 +54,7 @@
         (string-append "https://github.com/linux-rdma/opensm/releases/download/"
                        version "/opensm-" version ".tar.gz"))
        (sha256
-        (base32 "19scwwpwqhqsyq4hbr5cflcmypss828lalxxd36yby7mbimca38y"))))
+        (base32 "0q74sx8y23h7picdzb4g5r84wcvc9hr9vzsdawkl812b38vmwcx3"))))
     (build-system gnu-build-system)
     (native-inputs
      (list bison
@@ -66,18 +66,20 @@
     (inputs
      (list rdma-core))
     (arguments
-     `(#:configure-flags '("--disable-static")
+     (list
+      #:configure-flags #~'("--disable-static")
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
           (add-after 'install 'install-doc
             (lambda* (#:key outputs #:allow-other-keys)
               (let* ((base (assoc-ref outputs "out"))
                      (doc (string-append base "/share/doc/"
-                                         ,name "-" ,version)))
+                                         #$(package-name this-package)
+                                         "-"
+                                         #$(package-version this-package))))
                 (for-each (lambda (file)
                             (install-file file doc))
-                         (find-files "doc"))
+                          (find-files "doc"))))))))
-               #t))))))
     (home-page "https://www.openfabrics.org/")
     (synopsis "OpenIB InfiniBand Subnet Manager and management utilities")
     (description "\
@@ -183,7 +185,7 @@ testing InfiniBand networks.")
 (define-public ucx
   (package
     (name "ucx")
-    (version "1.14.0")
+    (version "1.15.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -193,7 +195,7 @@ testing InfiniBand networks.")
               (patches (search-patches "ucx-tcp-iface-ioctl.patch"))
               (sha256
                (base32
-                "0ki2r768wqm92qv06wxrh3kv2nl2yj4ds9fz0s0b5rr2ycjiw9ir"))))
+                "1mk46vyfp8hsivk88s8gv0nf458jfs59fczpf66wwa3a9yp324jp"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/fonts.scm

@@ -1015,15 +1015,16 @@ utilities to ease adding new glyphs to the font.")
 (define-public font-google-noto
   (package
     (name "font-google-noto")
-    (version "20171025")
+    (version "23.11.1")
     (source
      (origin
-       (method url-fetch/zipbomb)
+       (method git-fetch)
-       (uri (string-append "https://noto-website-2.storage.googleapis.com/"
+       (uri (git-reference
-                           "pkgs/Noto-hinted.zip"))
+             (url "https://github.com/notofonts/notofonts.github.io")
-       (file-name (string-append name "-" version ".zip"))
+             (commit (string-append "noto-monthly-release-" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1bp42whyin7xcgmrbnfvz3rvd98xmxaz3ywqybbjmqzwaa9llyw3"))))
+        (base32 "0vvxhky35l4i0ha60yw0gj26f3v33hpf2zax17yyj16mww4cn4d8"))))
     (build-system font-build-system)
     (home-page "https://www.google.com/get/noto/")
     (synopsis "Fonts to cover all languages")

gnu/packages/geo.scm

@@ -1940,7 +1940,7 @@ to the OSM opening hours specification.")
 (define-public josm
   (package
     (name "josm")
-    (version "18646")
+    (version "18822")
     (source (origin
               (method svn-fetch)
               (uri (svn-reference
@@ -1949,7 +1949,7 @@ to the OSM opening hours specification.")
                      (recursive? #f)))
               (sha256
                (base32
-                "0zr3p1i39wi0f29lgb3xrnv6lijrq5ia8jxn4wnq1yz0xdlbg98i"))
+                "0b4q6n3jbqrh7dsfmcf2g0xdd1wjj62sjq8lwvggvrpqlk1fyn1b"))
               (file-name (string-append name "-" version "-checkout"))
               (modules '((guix build utils)))
             (snippet
@@ -1963,17 +1963,18 @@ to the OSM opening hours specification.")
      (list java-commons-jcs
            java-commons-compress
            java-jmapviewer
-           java-jsonp-api
+           java-jakarta-json
-           java-jsonp-impl ; runtime dependency
            java-jsr305
            java-metadata-extractor
            java-opening-hours-parser
            java-openjfx-media
+           java-parsson ; runtime dependency
            java-signpost-core
            java-svg-salamander))
     (arguments
      `(#:tests? #f
        #:jar-name "josm.jar"
+       #:jdk ,openjdk11
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'rm-build.xml

gnu/packages/gnuzilla.scm

@@ -1058,10 +1058,12 @@ variable defined below.  It requires guile-json to be installed."
             (lambda* (#:key (make-flags '()) (parallel-build? #t)
                       #:allow-other-keys)
               (apply invoke "./mach" "build"
-                     ;; mach will use parallel build if possible by default
+                     ;; mach will use a wide parallel build if possible by
-                     `(,@(if parallel-build?
+                     ;; default, so reign it in if requested.
-                             '()
+                     `(,(string-append
-                             '("-j1"))
+                         "-j" (number->string (if parallel-build?
+                                                  (parallel-job-count)
+                                                  1)))
                        ,@make-flags))))
           (add-after 'build 'neutralise-store-references
             (lambda _

gnu/packages/guile-xyz.scm

@@ -1284,8 +1284,8 @@ works with Guile 1.4.x to 2.0.x.")
     (license license:gpl3+)))
 
 (define-public guile-prometheus
-  (let ((commit "35dc26c0ea44c3d70f1819f240d84e2cbb4b7b4c")
+  (let ((commit "4aaf902eb45b3a4c1003f854bda56c516fdf4f5b")
-        (revision "5"))
+        (revision "6"))
     (package
     (name "guile-prometheus")
     (version (git-version "0" revision commit))
@@ -1296,7 +1296,7 @@ works with Guile 1.4.x to 2.0.x.")
                     (commit commit)))
               (sha256
                (base32
-                "07822jj4appw37lf444kc4xlgl7nm64mgldag56072l55kwashgb"))
+                "03sr7wgksi9ys6jyzsnwanl2qqa8csi8jzcgrc3wfzp17vcc16yi"))
               (file-name (string-append name "-" version "-checkout"))))
     (build-system gnu-build-system)
     (native-inputs

gnu/packages/hardware.scm

@@ -1089,11 +1089,17 @@ technology, such as head mounted displays with built in head tracking.")
                  (("dependencies/json")
                   (string-append #$(this-package-input "nlohmann-json")
                                  "/include/nlohmann")))))
+           (add-after 'unpack 'patch-chmod
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* "scripts/build-udev-rules.sh"
+                (("/bin/chmod") (string-append (assoc-ref inputs "coreutils")
+                                               "/bin/chmod")))))
            ;; Call qmake instead of configure to create a Makefile.
            (replace 'configure
              (lambda _ (invoke "qmake" "PREFIX=/" "OpenRGB.pro"))))))
     (inputs
-     (list hidapi
+     (list coreutils
+           hidapi
            hueplusplus
            nlohmann-json
            libusb

gnu/packages/haskell-xyz.scm

@@ -65,6 +65,7 @@
   #:use-module (gnu packages haskell-check)
   #:use-module (gnu packages haskell-crypto)
   #:use-module (gnu packages haskell-web)
+  #:use-module (gnu packages icu4c)
   #:use-module (gnu packages libffi)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages llvm)
@@ -8352,6 +8353,46 @@ require aeson
     (description "Safe conversions between textual types")
     (license license:isc)))
 
+(define-public ghc-text-icu
+  (package
+    (name "ghc-text-icu")
+    (version "0.8.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (hackage-uri "text-icu" version))
+       (sha256
+        (base32 "1yj0jdjrsx12sy6lj1gizb2ys5likp9rcv8ryc6sjf2dw74097rd"))))
+    (build-system haskell-build-system)
+    (properties '((upstream-name . "text-icu")))
+    (inputs (list icu4c))
+    (native-inputs (list ghc-hunit
+                         ghc-quickcheck
+                         ghc-random
+                         ghc-test-framework
+                         ghc-test-framework-hunit
+                         ghc-test-framework-quickcheck2
+                         pkg-config))
+    (home-page "https://github.com/haskell/text-icu")
+    (synopsis "Bindings to the ICU library")
+    (description
+     "Haskell bindings to the International Components for Unicode (ICU) libraries.
+These libraries provide robust and full-featured Unicode services on a wide
+variety of platforms. .  Features include: . * Both pure and impure bindings, to
+allow for fine control over efficiency and ease of use. . * Breaking of strings
+on character, word, sentence, and line boundaries. . * Access to the Unicode
+Character Database (UCD) of character metadata. . * String collation functions,
+for locales where the conventions for lexicographic ordering differ from the
+simple numeric ordering of character codes. . * Character set conversion
+functions, allowing conversion between Unicode and over 220 character encodings.
+. * Unicode normalization. (When implementations keep strings in a normalized
+form, they can be assured that equivalent strings have a unique binary
+representation.) . * Regular expression search and replace. . * Security checks
+for visually confusable (spoofable) strings. . * Bidirectional Unicode algorithm
+. * Calendar objects holding dates and times. . * Number and calendar
+formatting.")
+    (license license:bsd-3)))
+
 (define-public ghc-text-short
   (package
     (name "ghc-text-short")

gnu/packages/image-processing.scm

@@ -1412,7 +1412,12 @@ combine the information contained in both.")
        (uri (string-append "mirror://sourceforge/itk/itk/4.12/"
                            "InsightToolkit-" version ".tar.xz"))
        (sha256
-        (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))))
+        (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments insight-toolkit-4)
+       ((#:configure-flags cf #~'())
+        ;; error: ISO C++17 does not allow dynamic exception specifications
+        #~(cons* "-DCMAKE_CXX_FLAGS=-std=c++14" #$cf))))))
 
 (define-public itk-snap
   (package

gnu/packages/java.scm

@@ -518,6 +518,8 @@
                                                    "/lib/arm")
                                                   ("aarch64-linux"
                                                    "/lib/aarch64")
+                                                  ("powerpc-linux"
+                                                   "/lib/ppc")
                                                   ;; We need a catch-all, dropping
                                                   ;; '-linux' works in most cases.
                                                   (_
@@ -878,7 +880,14 @@ new Date();"))
     (build-system gnu-build-system)
     (outputs '("out" "jdk" "doc"))
     (arguments
-     `(#:tests? #f; require jtreg
+     `(#:imported-modules
+       ((guix build ant-build-system)
+        ,@%gnu-build-system-modules)
+       #:modules
+       ((guix build utils)
+        (guix build gnu-build-system)
+        (ice-9 popen))
+       #:tests? #f; require jtreg
        #:make-flags '("all")
        #:disallowed-references ,(list (gexp-input icedtea-8)
                                       (gexp-input icedtea-8 "jdk"))
@@ -971,6 +980,80 @@ new Date();"))
                 (find-files "."
                             "\\.c$|\\.h$"))
                #t)))
+           ;; By default OpenJDK only generates an empty keystore.  In order to
+           ;; be able to use certificates in Java programs we need to generate a
+           ;; keystore from a set of certificates.  For convenience we use the
+           ;; certificates from the nss-certs package.
+           (add-after 'install 'install-keystore
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (use-modules (ice-9 rdelim))
+               (let* ((keystore  "cacerts")
+                      (certs-dir (search-input-directory inputs
+                                                         "etc/ssl/certs"))
+                      (keytool   (string-append (assoc-ref outputs "jdk")
+                                                "/bin/keytool")))
+                 (define (extract-cert file target)
+                   (call-with-input-file file
+                     (lambda (in)
+                       (call-with-output-file target
+                         (lambda (out)
+                           (let loop ((line (read-line in 'concat))
+                                      (copying? #f))
+                             (cond
+                              ((eof-object? line) #t)
+                              ((string-prefix? "-----BEGIN" line)
+                               (display line out)
+                               (loop (read-line in 'concat) #t))
+                              ((string-prefix? "-----END" line)
+                               (display line out)
+                               #t)
+                              (else
+                               (when copying? (display line out))
+                               (loop (read-line in 'concat) copying?)))))))))
+                 (define (import-cert cert)
+                   (format #t "Importing certificate ~a\n" (basename cert))
+                   (let ((temp "tmpcert"))
+                     (extract-cert cert temp)
+                     (let ((port (open-pipe* OPEN_WRITE keytool
+                                             "-import"
+                                             "-alias" (basename cert)
+                                             "-keystore" keystore
+                                             "-storepass" "changeit"
+                                             "-file" temp)))
+                       (display "yes\n" port)
+                       (when (not (zero? (status:exit-val (close-pipe port))))
+                         (format #t "failed to import ~a\n" cert)))
+                     (delete-file temp)))
+
+                 ;; This is necessary because the certificate directory contains
+                 ;; files with non-ASCII characters in their names.
+                 (setlocale LC_ALL "en_US.utf8")
+                 (setenv "LC_ALL" "en_US.utf8")
+
+                 (copy-file (string-append (assoc-ref outputs "out")
+                                           "/lib/security/cacerts")
+                            keystore)
+                 (chmod keystore #o644)
+                 (for-each import-cert (find-files certs-dir "\\.pem$"))
+                 (mkdir-p (string-append (assoc-ref outputs "out")
+                                         "/lib/security"))
+                 (mkdir-p (string-append (assoc-ref outputs "jdk")
+                                         "/lib/security"))
+
+                 ;; The cacerts files we are going to overwrite are chmod'ed as
+                 ;; read-only (444) in icedtea-8 (which derives from this
+                 ;; package).  We have to change this so we can overwrite them.
+                 (chmod (string-append (assoc-ref outputs "out")
+                                       "/lib/security/" keystore) #o644)
+                 (chmod (string-append (assoc-ref outputs "jdk")
+                                       "/lib/security/" keystore) #o644)
+
+                 (install-file keystore
+                               (string-append (assoc-ref outputs "out")
+                                              "/lib/security"))
+                 (install-file keystore
+                               (string-append (assoc-ref outputs "jdk")
+                                              "/lib/security")))))
          ;; Some of the libraries in the lib/ folder link to libjvm.so.
          ;; But that shared object is located in the server/ folder, so it
          ;; cannot be found.  This phase creates a symbolic link in the
@@ -1044,6 +1127,7 @@ new Date();"))
        ("icedtea-8:jdk" ,icedtea-8 "jdk")
        ;; XXX: The build system fails with newer versions of GNU Make.
        ("make@4.2" ,gnu-make-4.2)
+       ("nss-certs" ,nss-certs)
        ("unzip" ,unzip)
        ("which" ,which)
        ("zip" ,zip)))
@@ -1126,6 +1210,7 @@ new Date();"))
      `(("openjdk9" ,openjdk9)
        ("openjdk9:jdk" ,openjdk9 "jdk")
        ("make@4.2" ,gnu-make-4.2)
+       ("nss-certs" ,nss-certs)
        ("unzip" ,unzip)
        ("which" ,which)
        ("zip" ,zip)))))
@@ -1152,6 +1237,7 @@ new Date();"))
       #:modules `((guix build gnu-build-system)
                   (guix build utils)
                   (ice-9 match)
+                  (ice-9 popen)
                   (srfi srfi-1)
                   (srfi srfi-26))
       #:disallowed-references (list (gexp-input openjdk10)
@@ -1394,6 +1480,7 @@ new Date();"))
            openjdk10
            `(,openjdk10 "jdk")
            gnu-make-4.2
+           nss-certs
            pkg-config
            unzip
            which
@@ -13568,6 +13655,70 @@ and allows building a Java object model for JSON text using API classes
 parse, generate, transform and query) JSON messages.  This package contains
 a reference implementation of that API.")))
 
+(define-public java-jakarta-json
+  (package
+    (name "java-jakarta-json")
+    (version "2.1.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/jakartaee/jsonp-api")
+                     (commit (string-append version "-RELEASE"))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1q600harqfhlf763l75j4fx7ai7ybp7ga06aiky2a2hg8mhz0s5f"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "jakarta-json.jar"
+       #:source-dir "api/src/main/java"
+       #:tests? #f; no tests
+       #:jdk ,openjdk11))
+    (home-page "https://github.com/jakartaee/jsonp-api")
+    (synopsis "Portable API for JSON handling in Java")
+    (description "This project contains API and Compatible Implementation of
+Jakarta JSON Processing specification.  Jakarta JSON Processing provides
+portable APIs to parse, generate, transform, and query JSON documents.")
+    ;; with classpath exception
+    (license license:epl2.0)))
+
+(define-public java-parsson
+  (package
+    (name "java-parsson")
+    (version "1.1.5")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/eclipse-ee4j/parsson")
+                     (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "06vvr6qv1ihnk212gdxg4x0sd61lgxk7wf062s7gym5k2h7fms0p"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "parsson.jar"
+       #:source-dir "impl/src/main/java"
+       #:test-dir "impl/src/test"
+       #:use-java-modules? #t
+       #:jdk ,openjdk11
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'copy-resources
+           (lambda _
+             (copy-recursively "impl/src/main/resources"
+                               "build/classes"))))))
+    (inputs
+      (list java-jakarta-json))
+    (native-inputs
+      (list java-junit))
+    (home-page "https://github.com/eclipse-ee4j/parsson")
+    (synopsis "Implementation of Jakarta JSON API")
+    (description "Eclipse Parsson is an implementation of the Jakarta JSON
+Processing specification.")
+    ;; with classpath exception
+    (license license:epl2.0)))
+
 (define-public java-xmp
   (package
     (name "java-xmp")

gnu/packages/libreoffice.scm

@@ -14,6 +14,7 @@
 ;;; Copyright © 2019 Chris Marusich <cmmarusich@gmail.com>
 ;;; Copyright © 2020 Marcin Karpezo <sirmacik@wioo.waw.pl>
 ;;; Copyright © 2023 Nicolas Graves <ngraves@ngraves.fr>
+;;; Copyright © 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -50,6 +51,7 @@
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages cpp)
   #:use-module (gnu packages cups)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages cyrus-sasl)
@@ -92,20 +94,19 @@
 (define-public ixion
   (package
     (name "ixion")
-    (version "0.17.0")
+    (version "0.19.0")
-    (source
+    (source (origin
-     (origin
+              (method git-fetch)
-       (method url-fetch)
+              (uri (git-reference
-       (uri (string-append "http://kohei.us/files/ixion/src/libixion-"
+                    (url "https://gitlab.com/ixion/ixion")
-                           version ".tar.xz"))
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-         "07hhqkvns4da8xv990gr1smqz1zf40m531lg95nphfrz48wp3jak"))))
+                "0nycbs3765wkaw9ff7aflm56ayxkn15dlfl5pbbb9b5i2rcv3dq6"))))
     (build-system gnu-build-system)
-    (native-inputs
+    (native-inputs (list autoconf automake libtool pkg-config))
-     (list pkg-config))
+    (inputs (list mdds python spdlog))
-    (inputs
-     (list mdds python spdlog))
     (home-page "https://gitlab.com/ixion/ixion")
     (synopsis "General purpose formula parser and interpreter")
     (description "Ixion is a library for calculating the results of formula
@@ -117,22 +118,22 @@ their dependencies automatically upon calculation.")
 (define-public orcus
   (package
     (name "orcus")
-    (version "0.17.2")
+    (version "0.19.0")
-    (source
+    (source (origin
-     (origin
+              ;; The test suite requires data files store with Git Large
-       (method url-fetch)
+              ;; File Storage.
-       (uri (string-append "http://kohei.us/files/orcus/src/lib"
+              (method git-fetch/lfs)
-                           "orcus-" version ".tar.xz"))
+              (uri (git-reference
+                    (url "https://gitlab.com/orcus/orcus")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-         "1as04qb74jnlnwy4wh5jwaw2nnzgn2s3230ymvh3kx1w9r0rsl1h"))))
+                "02prj6kgph56fkr89k8wlqarrmx65cq92863i4rrny5sqr8c2llr"))))
     (build-system gnu-build-system)
-    (arguments
+    (arguments (list #:configure-flags #~(list "--disable-static")))
-     `(#:configure-flags '("--disable-static")))
+    (native-inputs (list autoconf automake libtool pkg-config))
-    (native-inputs
+    (inputs (list ixion mdds python zlib))
-     (list pkg-config))
-    (inputs
-     (list ixion mdds python zlib))
     (home-page "https://gitlab.com/orcus/orcus")
     (synopsis "File import filter library for spreadsheet documents")
     (description "Orcus is a library that provides a collection of standalone
@@ -353,7 +354,7 @@ working with graphics in the WPG (WordPerfect Graphics) format.")
     (name "libcmis")
     ;; Note: Use an unreleased version because libreoffice requires it and
     ;; is the only user (see <https://github.com/tdf/libcmis/pull/43>).
-    (version "0.5.2-46-gf264a61")
+    (version "0.6.0")
     (home-page "https://github.com/tdf/libcmis")
     (source
      (origin
@@ -363,7 +364,7 @@ working with graphics in the WPG (WordPerfect Graphics) format.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "06ff5vw0xrymvvna18wlaayyk20755sk2541i1gh7zpbmncs2ni6"))))
+         "17jx9fb7nmyp6jhz9nlmb3wcp8k03vhcv7sqql6a7jhsjnw3hq0k"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf automake libtool cppunit pkg-config))
@@ -897,7 +898,7 @@ commonly called @code{ftoa} or @code{dtoa}.")
 (define-public libreoffice
   (package
     (name "libreoffice")
-    (version "7.5.4.2")
+    (version "7.6.3.1")
     (source
      (origin
        (method url-fetch)
@@ -906,7 +907,7 @@ commonly called @code{ftoa} or @code{dtoa}.")
          "https://download.documentfoundation.org/libreoffice/src/"
          (version-prefix version 3) "/libreoffice-" version ".tar.xz"))
        (sha256
-        (base32 "1s3592ick745kl60yjlv7ki3p7nnwswj0mgjh3nk6k7skyvx3fv8"))))
+        (base32 "148084acq370483y0xwvcvck30kxhr78cnmibp5lks17xqp5f9q7"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      (list
@@ -1088,6 +1089,7 @@ commonly called @code{ftoa} or @code{dtoa}.")
      (list bison
            cppunit
            flex
+           frozen                       ;header-only library
            pkg-config
            python-wrapper
            which

gnu/packages/linux.scm

@@ -493,7 +493,22 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 ;; The current "stable" kernels. That is, the most recently released major
 ;; versions that are still supported upstream.
 
-(define-public linux-libre-6.5-version "6.5.9")
+(define-public linux-libre-6.6-version "6.6.1")
+(define-public linux-libre-6.6-gnu-revision "gnu")
+(define deblob-scripts-6.6
+  (linux-libre-deblob-scripts
+   linux-libre-6.6-version
+   linux-libre-6.6-gnu-revision
+   (base32 "0g8m0rb15b0231dv8ji456s75a67szsaim71may3yprplycz6pav")
+   (base32 "1hg3ck1j8288fhlhcvhgs1zzwh3i62nfvphw7x3vsaqr75kiwbjp")))
+(define-public linux-libre-6.6-pristine-source
+  (let ((version linux-libre-6.6-version)
+        (hash (base32 "0d42b1hbvv9w3y3q4wydr6il0g5a823n54a06p4p5vcpgkadf7ns")))
+   (make-linux-libre-source version
+                            (%upstream-linux-source version hash)
+                            deblob-scripts-6.6)))
+
+(define-public linux-libre-6.5-version "6.5.11")
 (define-public linux-libre-6.5-gnu-revision "gnu")
 (define deblob-scripts-6.5
   (linux-libre-deblob-scripts
@@ -503,7 +518,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "066z5lw5vrfayhv23hpfcm6fh6b7zmn2v13kfv1g3z3jl1wblhfh")))
 (define-public linux-libre-6.5-pristine-source
   (let ((version linux-libre-6.5-version)
-        (hash (base32 "1mcg0lpxr832mwyqlbn0s5gssvsk2nn2xhq9w0qbymizf5j2yrn6")))
+        (hash (base32 "06dmb4hbwrms0lp4axphwgj8wbnzsym70sx55lxr501b53wlmqif")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.5)))
@@ -511,52 +526,52 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 ;; The "longterm" kernels — the older releases with long-term upstream support.
 ;; Here are the support timelines:
 ;; <https://www.kernel.org/category/releases.html>
-(define-public linux-libre-6.1-version "6.1.60")
+(define-public linux-libre-6.1-version "6.1.62")
 (define-public linux-libre-6.1-gnu-revision "gnu")
 (define deblob-scripts-6.1
   (linux-libre-deblob-scripts
    linux-libre-6.1-version
    linux-libre-6.1-gnu-revision
    (base32 "1sf80f2i4vf888xjcn84ymn4w5ynn30ib9033zwmv7f09yvfhapy")
-   (base32 "1c73516nbhnz0cxjz38b5794dxygb8sznv9idiibw7ablmjbhd11")))
+   (base32 "1hdibv43xbn1lv83i6qjgfmf1bvqxvq17fryfsq4r4sjgs9212js")))
 (define-public linux-libre-6.1-pristine-source
   (let ((version linux-libre-6.1-version)
-        (hash (base32 "02pvymr1dgd36mp7yikxqqv0sfrpwi1grnvxvx6jbbx6wmx0wljq")))
+        (hash (base32 "1v453q4sf0j8708ivs1zmdf645hgimqvxfc8xz7czgnnmipn3zdr")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.1)))
 
-(define-public linux-libre-5.15-version "5.15.137")
+(define-public linux-libre-5.15-version "5.15.138")
 (define-public linux-libre-5.15-gnu-revision "gnu")
 (define deblob-scripts-5.15
   (linux-libre-deblob-scripts
    linux-libre-5.15-version
    linux-libre-5.15-gnu-revision
    (base32 "18ac30kxg2mf2f6gk3p935hzhz2qs110jy4xwk21kblnnkskbxj8")
-   (base32 "1c3lm0j401lv2lk39dmr4mlf5ic173snm7cc0cckl6czyvxr5ysy")))
+   (base32 "1idjrn2w8jrixj8ifkk1awxyyq5042nc4p2mld4rda96azlnp948")))
 (define-public linux-libre-5.15-pristine-source
   (let ((version linux-libre-5.15-version)
-        (hash (base32 "1xxjbxldrhmnh2q6rykpxyfbj8xqgl82q30n8sfavrzr14bb4jcp")))
+        (hash (base32 "1ajaxy97gx0c9cdxiyxa49ykfsykir22i9abfrcizh71ci0yb15g")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.15)))
 
-(define-public linux-libre-5.10-version "5.10.199")
+(define-public linux-libre-5.10-version "5.10.200")
 (define-public linux-libre-5.10-gnu-revision "gnu1")
 (define deblob-scripts-5.10
   (linux-libre-deblob-scripts
    linux-libre-5.10-version
    linux-libre-5.10-gnu-revision
    (base32 "1b33rkn32b923025iiz4xzxiy8y5ii9j5qk4021mg575890rl4ch")
-   (base32 "0nnp46mn32yk436swd2qh34igmzinfgkwvbzp3lqyy45f06hbc2j")))
+   (base32 "0xrrnmb5kcc5r21bdm24aq0fnkk1imn367c1cxlj78b6l6gigx4b")))
 (define-public linux-libre-5.10-pristine-source
   (let ((version linux-libre-5.10-version)
-        (hash (base32 "1h944syk7n6c4j1djlx19n77alzwbxcdza77c9ykicgfynhpgsm0")))
+        (hash (base32 "012i41bj8rcqn0vhfxrwq3gg82nb6pp2cwq8n146wj47pwgrcbcx")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.10)))
 
-(define-public linux-libre-5.4-version "5.4.259")
+(define-public linux-libre-5.4-version "5.4.260")
 (define-public linux-libre-5.4-gnu-revision "gnu1")
 (define deblob-scripts-5.4
   (linux-libre-deblob-scripts
@@ -566,27 +581,27 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "0sw67b2pk3lng4y67diqqnhxaggnp3nbkx8dxc5fs27rinfxr4m1")))
 (define-public linux-libre-5.4-pristine-source
   (let ((version linux-libre-5.4-version)
-        (hash (base32 "195v4fidavzm637glj6580006mrcaygnbj4za874imb62bxf9rpz")))
+        (hash (base32 "1zpbaipd2j3idj8h9iznlj0ywcq5nkhwj707a1f9ixf82h3q4c4q")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.4)))
 
-(define-public linux-libre-4.19-version "4.19.297")
+(define-public linux-libre-4.19-version "4.19.298")
 (define-public linux-libre-4.19-gnu-revision "gnu1")
 (define deblob-scripts-4.19
   (linux-libre-deblob-scripts
    linux-libre-4.19-version
    linux-libre-4.19-gnu-revision
-   (base32 "0ghdizzs6969872rnjcv9p6sl9rcbs29v3ismk125yyvjaczd428")
+   (base32 "0pjal2cc2f99cvw8r4icb4l24j41k48jkj6bqk7pcahzcgx33ycb")
    (base32 "1425mhkfxn18vxn05bb4h3li7x1jl7l1hf1zi8xhnqv3wa31h9wl")))
 (define-public linux-libre-4.19-pristine-source
   (let ((version linux-libre-4.19-version)
-        (hash (base32 "0c9xxqgv2i36hrr06dwz7f3idc04xpv0a5pxg08xdh03cnyf12cx")))
+        (hash (base32 "0mhgq6hdcls1af7nj999x1mds5b37s7vwin8nsb4q0lnx2y1da4x")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.19)))
 
-(define-public linux-libre-4.14-version "4.14.328")
+(define-public linux-libre-4.14-version "4.14.329")
 (define-public linux-libre-4.14-gnu-revision "gnu1")
 (define deblob-scripts-4.14
   (linux-libre-deblob-scripts
@@ -596,7 +611,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "1faagsj4i31z2bp83hflx3q9vrddjnn37a3ah2b47iaplva7z1nd")))
 (define-public linux-libre-4.14-pristine-source
   (let ((version linux-libre-4.14-version)
-        (hash (base32 "1igcpvnhwwrczfdsafmszvi0456k7f6j4cgpfw6v6afw09p95d8x")))
+        (hash (base32 "1dvb4xf0b7snabznl7bg7gga7ffdmywy8vr8q65pzl9yf6fnhdny")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.14)))
@@ -629,6 +644,11 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
     (patches (append (origin-patches source)
                      patches))))
 
+(define-public linux-libre-6.6-source
+  (source-with-patches linux-libre-6.6-pristine-source
+                       (list %boot-logo-patch
+                             %linux-libre-arm-export-__sync_icache_dcache-patch)))
+
 (define-public linux-libre-6.5-source
   (source-with-patches linux-libre-6.5-pristine-source
                        (list %boot-logo-patch
@@ -748,6 +768,11 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
     (description "Headers of the Linux-Libre kernel.")
     (license license:gpl2)))
 
+(define-public linux-libre-headers-6.6
+  (make-linux-libre-headers* linux-libre-6.6-version
+                             linux-libre-6.6-gnu-revision
+                             linux-libre-6.6-source))
+
 (define-public linux-libre-headers-6.5
   (make-linux-libre-headers* linux-libre-6.5-version
                              linux-libre-6.5-gnu-revision
@@ -1092,6 +1117,14 @@ Linux kernel.  It has been modified to remove all non-free binary blobs.")
 ;;; Generic kernel packages.
 ;;;
 
+(define-public linux-libre-6.6
+  (make-linux-libre* linux-libre-6.6-version
+                     linux-libre-6.6-gnu-revision
+                     linux-libre-6.6-source
+                     '("x86_64-linux" "i686-linux" "armhf-linux"
+                       "aarch64-linux" "powerpc64le-linux" "riscv64-linux")
+                     #:configuration-file kernel-config))
+
 (define-public linux-libre-6.5
   (make-linux-libre* linux-libre-6.5-version
                      linux-libre-6.5-gnu-revision
@@ -6739,7 +6772,7 @@ from the ntfs-3g package.  It is meant to be used in initrds.")
 (define-public rdma-core
   (package
     (name "rdma-core")
-    (version "44.0")
+    (version "48.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/linux-rdma/rdma-core"
@@ -6747,7 +6780,7 @@ from the ntfs-3g package.  It is meant to be used in initrds.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "12w5v74wz1akac09frw7qk1yd06b00239zh7bvbvqyzjc0g61mi5"))))
+                "0h281dw2yph8pzfsr1wblqy6pb8nd9yj1pdf5c62zwc1l9b2fa3q"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ;no tests
@@ -8562,7 +8595,7 @@ comparing system environments.")
 (define-public libfabric
   (package
     (name "libfabric")
-    (version "1.11.2")
+    (version "1.19.0")
     (source
      (origin
        (method url-fetch)
@@ -8570,7 +8603,7 @@ comparing system environments.")
         (string-append "https://github.com/ofiwg/libfabric/releases/download/v"
                        version "/libfabric-" version ".tar.bz2"))
        (sha256
-        (base32 "1nnpfkwxhim2nqjkb1vwrb4wj4j3l6w6yvvy69fqam2snlhshazz"))))
+        (base32 "17pg0fb4fa77r1bmp0xk535m8n8fadpfdg93cb280ghhx55pck7i"))))
     (build-system gnu-build-system)
     (inputs `(("rdma-core" ,rdma-core)
               ,@(match (%current-system)
@@ -8851,16 +8884,17 @@ privileges.")
 (define-public psm2
   (package
     (name "psm2")
-    (version "11.2.230")
+    (version "12.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/intel/opa-psm2")
-                    (commit (string-append "PSM2_" version))))
+                    ;; tag 'psm-v12.0' = commit ad5dd1b
+                    (commit (string-append "psm-v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1bm7ndhi8qzmd0plnggj2h52yb34bab4k38530nsnkmv9smwdivl"))))
+                "04nar65ac11qqx41vkfs7iip8kfiah0zms7l4rmsxncpiz2iqfik"))))
     (build-system gnu-build-system)
     (arguments
      (list #:make-flags

gnu/packages/lisp-check.scm

@@ -356,11 +356,11 @@ experience.")
   (sbcl-package->ecl-package sbcl-clunit))
 
 (define-public sbcl-clunit2
-  (let ((commit "c3159275a6c5af166e60b592c3b7e22eaa69c048")
+  (let ((commit "b24c56851ee6ee6c4a9dc3725a634c06b604f207")
         (revision "2"))
     (package
       (name "sbcl-clunit2")
-      (version (git-version "0.5.2" revision commit))
+      (version (git-version "0.6.1" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -369,7 +369,7 @@ experience.")
                (commit commit)))
          (file-name (git-file-name "cl-clunit2" version))
          (sha256
-          (base32 "0n92z98dqfik3kfp25nz7yqycx4bpxlqbn69i5skcdnrj2ywmv01"))))
+          (base32 "03k4wc2zz31wcqcxy8fhq095i8xzcaxrzgrlrn2va10lcjs4v51b"))))
       (build-system asdf-build-system/sbcl)
       (synopsis "Unit testing framework for Common Lisp")
       (description
@@ -625,8 +625,8 @@ to make test code more informative.
   (sbcl-package->cl-source-package sbcl-kaputt))
 
 (define-public sbcl-lift
-  (let ((commit "2594160d6ca3a77d8750110dfa63214256aab852")
+  (let ((commit "a7941845a9de72be60e66ea941aa34cbee35bf23")
-        (revision "2"))
+        (revision "3"))
     (package
       (name "sbcl-lift")
       (version (git-version "1.7.1" revision commit))
@@ -634,10 +634,10 @@ to make test code more informative.
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/gwkkwg/lift")
+               (url "https://github.com/hraban/lift")
                (commit commit)))
          (sha256
-          (base32 "01xvz9sl5l5lai4h9dabmcjnm659wf5zllaxqbs55lffskp6jwq3"))
+          (base32 "1513n46fkqw8rnvz69s7xnwj476qm8ibdlwsr63qj9yh0mib0q6x"))
          (file-name (git-file-name "lift" version))
          (modules '((guix build utils)))
          (snippet

gnu/packages/lisp-xyz.scm

@@ -1247,8 +1247,8 @@ and Gopher website hosting.")
               (delete 'build-program))))))))
 
 (define-public sbcl-trivial-timeout
-  (let ((commit "feb869357f40f5e109570fb40abad215fb370c6c")
+  (let ((commit "e70d9b4f7caeab83ea6ac50d724470fe49561e66")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "sbcl-trivial-timeout")
       (version (git-version "0.1.5" revision commit))
@@ -1256,19 +1256,15 @@ and Gopher website hosting.")
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/gwkkwg/trivial-timeout/")
+               (url "https://github.com/hraban/trivial-timeout")
                (commit commit)))
          (file-name (git-file-name "trivial-timeout" version))
          (sha256
-          (base32 "1kninxwvvih9nhh7a9y8lfgi7pdr76675y1clw4ss17vz8fbim5p"))))
+          (base32 "0s8z9aj6b3kv21yiyk13cjylzf5zlnw9v86vcff477m1gk9yddjs"))))
       (build-system asdf-build-system/sbcl)
       (native-inputs
        (list sbcl-lift))
-      (arguments
+      (home-page "https://github.com/hraban/trivial-timeout")
-       ;; NOTE: (Sharlatan-20210202T231437+0000): Due to the age of this library
-       ;; tests use some deprecated functionality and keep failing.
-       `(#:tests? #f))
-      (home-page "https://github.com/gwkkwg/trivial-timeout/")
       (synopsis "Timeout library for Common Lisp")
       (description
        "This library provides an OS and implementation independent access to
@@ -2260,8 +2256,9 @@ antialiased TrueType font rendering using CLX and XRender extension.")
   (sbcl-package->ecl-package sbcl-clx-truetype))
 
 (define-public sbcl-slynk
-  (let ((commit "df62abae73bd511885c9c7ec0ea7ea1469a00923")
+  ;; Update together with emacs-sly.
-        (revision "8"))
+  (let ((commit "9c43bf65b967e12cef1996f1af5f0671d8aecbf4")
+        (revision "9"))
     (package
       (name "sbcl-slynk")
       (version (git-version "1.0.43" revision commit))
@@ -2273,7 +2270,7 @@ antialiased TrueType font rendering using CLX and XRender extension.")
            (url "https://github.com/joaotavora/sly")
            (commit commit)))
          (sha256
-          (base32 "1nxijv52bja6la2i3asq7kklpj5li25454n52sgsc6xnnfvakbsv"))
+          (base32 "15nyr02ykkws4q79jcmxcawddg8sgq9v5l8k7jv7gg3hnpzxjlb2"))
          (file-name (git-file-name "cl-slynk" version))))
       (build-system asdf-build-system/sbcl)
       (outputs '("out" "image"))
@@ -2708,8 +2705,8 @@ arbitrary Lisp data.")
   (sbcl-package->ecl-package sbcl-cl-dot))
 
 (define-public sbcl-cl-graph
-  (let ((commit "3cb786797b24883d784b7350e7372e8b1e743508")
+  (let ((commit "c617de35390cb02db88bc5b5febffafdb8947ae8")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "sbcl-cl-graph")
       (version (git-version "0.10.2" revision commit))
@@ -2717,11 +2714,11 @@ arbitrary Lisp data.")
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/gwkkwg/cl-graph")
+               (url "https://github.com/hraban/cl-graph")
                (commit commit)))
          (file-name (git-file-name "cl-graph" version))
          (sha256
-          (base32 "1748rj52f2jmd5jvsy9jwhn0zf73sjzjhwhnljvq6yi2kdqr30kl"))))
+          (base32 "0g1abkph9zb0m9zz6q2471ml9q9acdhwyapk8ra3bisqpwlxvpyf"))))
       (build-system asdf-build-system/sbcl)
       (arguments
        ;; TODO: (Sharlatan-20221118T215839+0000): Tests failed
@@ -3610,8 +3607,8 @@ writing code that contains string literals that contain code themselves.")
   (sbcl-package->ecl-package sbcl-pythonic-string-reader))
 
 (define-public sbcl-slime-swank
-  (let ((commit "0cc2e736112a0bc2a048ef6efd11dd67e3fbf7ad")
+  (let ((commit "735258a26bb97e85d25f39e4bef83c1f80c12f5d")
-        (revision "0"))
+        (revision "1"))
     (package
       (name "sbcl-slime-swank")
       (version (git-version "2.28" revision commit))
@@ -3623,7 +3620,7 @@ writing code that contains string literals that contain code themselves.")
                (url "https://github.com/slime/slime/")
                (commit commit)))
          (sha256
-          (base32 "0iq9r4007rrnabj290y79i926x2m4j20j6b0x701pkywz926sn02"))
+          (base32 "0prskgzfqjmn8sc7p9nklnd0n1plwcvh40slgh23km31raplmzk7"))
          (modules '((guix build utils)))
          (snippet
           ;; The doc folder drags `gawk' into the closure.  Doc is already
@@ -5044,7 +5041,7 @@ is a library for creating graphical user interfaces.")
 (define-public sbcl-cl-webkit
   (package
     (name "sbcl-cl-webkit")
-    (version "3.5.9")
+    (version "3.5.10")
     (source
      (origin
        (method git-fetch)
@@ -5054,7 +5051,7 @@ is a library for creating graphical user interfaces.")
        (file-name (git-file-name "cl-webkit" version))
        (sha256
         (base32
-         "00h61p5mrvvbycp703isy0wvgqlfb7k0cidw4vg75y7s29m3k6k0"))))
+         "0bn8idvbi58kg0g76lanvjzkgnkcy41yn9vbp7f80q9fa7w892rq"))))
     (build-system asdf-build-system/sbcl)
     (inputs
      `(("cffi" ,sbcl-cffi)
@@ -5601,8 +5598,8 @@ client and server.")
   (sbcl-package->ecl-package sbcl-trivial-clipboard))
 
 (define-public sbcl-trivial-backtrace
-  (let ((commit "6eb65bde7229413040c81d42ea22f0e4c9c8cfc9")
+  (let ((commit "7f90b4a4144775cca0728791e4b92ac2557b07a1")
-        (revision "1"))
+        (revision "2"))
     (package
      (name "sbcl-trivial-backtrace")
      (version (git-version "1.1.0" revision commit))
@@ -5610,11 +5607,11 @@ client and server.")
       (origin
        (method git-fetch)
        (uri (git-reference
-             (url "https://github.com/gwkkwg/trivial-backtrace")
+             (url "https://github.com/hraban/trivial-backtrace")
              (commit commit)))
        (file-name (git-file-name "trivial-backtrace" version))
        (sha256
-        (base32 "1mbaqiwj5034iw6jzw30jyhwzp1pvhnz1zcy0lns0z5j2h9ldapw"))))
+        (base32 "11j0p3vgmnn5q84xw7sacr5p3cvff2hfhsh2is8xpm2iwxc723kn"))))
      (build-system asdf-build-system/sbcl)
      (native-inputs
       (list sbcl-lift))
@@ -7730,8 +7727,8 @@ CPython implementation of Python) and Common Lisp.")
   (sbcl-package->ecl-package sbcl-burgled-batteries3))
 
 (define-public sbcl-metabang-bind
-  (let ((commit "c93b7f7e1c18c954c2283efd6a7fdab36746ab5e")
+  (let ((commit "08196426cb099db0623e6cae2aeca566e0b788b2")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "sbcl-metabang-bind")
       (version (git-version "0.8.0" revision commit))
@@ -7739,12 +7736,12 @@ CPython implementation of Python) and Common Lisp.")
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/gwkkwg/metabang-bind")
+               (url "https://github.com/hraban/metabang-bind")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "0hd0kr91795v77akpbcyqiss9p0p7ypa9dznrllincnmgvsxlmf0"))))
+           "14g7k3zhm8cd6bssc5mm5h6iq1dv5lfhiq33aimcmj5a6vbiq47d"))))
       (build-system asdf-build-system/sbcl)
       (native-inputs
        (list sbcl-lift))
@@ -9220,8 +9217,8 @@ discontiguous ranges of time.")
   (sbcl-package->ecl-package sbcl-periods))
 
 (define-public sbcl-metatilities-base
-  (let ((commit "6eaa9e3ff0939a93a92109dd0fcd218de85417d5")
+  (let ((commit "ef04337759972fd622c9b27b53149f3d594a841f")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "sbcl-metatilities-base")
       (version (git-version "0.6.6" revision commit))
@@ -9229,12 +9226,12 @@ discontiguous ranges of time.")
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/gwkkwg/metatilities-base")
+               (url "https://github.com/hraban/metatilities-base")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "0xpa86pdzlnf4v5g64j3ifaplx71sx2ha8b7vvakswi652679ma0"))))
+           "069rk5ncwvjnnzvvky6xiriynl72yzvjpnzl6jw9jf3b8na14zrk"))))
       (build-system asdf-build-system/sbcl)
       (native-inputs
        (list sbcl-lift))
@@ -9252,8 +9249,8 @@ which implements a set of utilities.")
   (sbcl-package->ecl-package sbcl-metatilities-base))
 
 (define-public sbcl-cl-containers
-  (let ((commit "3d1df53c22403121bffb5d553cf7acb1503850e7")
+  (let ((commit "781ebfe0888bae46f07c018f7d473898b1bd4f5f")
-        (revision "3"))
+        (revision "4"))
     (package
       (name "sbcl-cl-containers")
       (version (git-version "0.12.1" revision commit))
@@ -9261,12 +9258,12 @@ which implements a set of utilities.")
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/gwkkwg/cl-containers")
+               (url "https://github.com/hraban/cl-containers")
                (commit commit)))
          (file-name (git-file-name "cl-containers" version))
          (sha256
           (base32
-           "18s6jfq11n8nv9k4biz32pm1s7y9zl054ry1gmdbcf39nisy377y"))))
+           "1nrql8s1j123v5gscy99lxvhlzp0ijig9x94w30v3lwfa58hf90l"))))
       (build-system asdf-build-system/sbcl)
       (native-inputs
        (list sbcl-lift))
@@ -12135,6 +12132,50 @@ for reading and writing JPEG image files.")
 (define-public ecl-cl-jpeg
   (sbcl-package->ecl-package sbcl-cl-jpeg))
 
+(define-public sbcl-jpeg-turbo
+  (let ((commit "f79c646cc266c107bdace53572a31664754c6e0c")
+        (revision "1"))
+    (package
+      (name "sbcl-jpeg-turbo")
+      (version (git-version "1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/shamazmazum/jpeg-turbo/")
+               (commit commit)))
+         (file-name (git-file-name "cl-jpeg-turbo" version))
+         (sha256
+          (base32 "1andd1ibbk3224idnpsnrn96flr5d1wm9ja3di57fs04wn577sag"))))
+      (build-system asdf-build-system/sbcl)
+      (arguments
+       (list #:phases
+             #~(modify-phases %standard-phases
+                 (add-after 'unpack 'fix-lib-paths
+                   (lambda* (#:key inputs #:allow-other-keys)
+                     (substitute* "src/jpeg-turbo.lisp"
+                       (("\"libturbojpeg\\.so\\.0\"")
+                        (string-append "\""
+                                       (search-input-file inputs
+                                                          "/lib/libturbojpeg.so")
+                                       "\""))))))))
+      (native-inputs
+       (list sbcl-fiveam))
+      (inputs
+       (list libjpeg-turbo sbcl-cffi))
+      (synopsis "Common Lisp wrapper for libjpeg-turbo")
+      (description
+       "This is a Common Lisp wrapper for libjpeg-turbo library which provides
+TurboJPEG API for compressing and decompressing JPEG images.")
+      (home-page "https://github.com/shamazmazum/jpeg-turbo/")
+      (license license:bsd-2))))
+
+(define-public cl-jpeg-turbo
+  (sbcl-package->cl-source-package sbcl-jpeg-turbo))
+
+(define-public ecl-cl-jpeg-turbo
+  (sbcl-package->ecl-package sbcl-jpeg-turbo))
+
 (define-public sbcl-png
   (let ((commit "11b965fe378fd0561abe3616b18ff03af5179648")
         (revision "1"))
@@ -17097,12 +17138,21 @@ not so easy to copy (ssyntax, argument destructuring, etc.).")
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/gwkkwg/trivial-shell")
+               (url "https://github.com/hraban/trivial-shell")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
           (base32 "08mpkl5ij5sjfsyn8pq2kvsvpvyvr7ha1r8g1224fa667b8k2q85"))))
       (build-system asdf-build-system/sbcl)
+      (arguments
+       (list
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-after 'unpack 'fix-paths
+              (lambda _
+                (substitute* "dev/definitions.lisp"
+                  (("/bin/sh")
+                   (which "sh"))))))))
       (native-inputs
        (list sbcl-lift))
       (home-page "https://common-lisp.net/project/trivial-shell/")
@@ -17687,18 +17737,20 @@ It aims to be implementation-agnostic and to climb the syntax trees.")
   (sbcl-package->ecl-package sbcl-agnostic-lizard))
 
 (define-public sbcl-dynamic-classes
+  (let ((commit "ebd7405603f67b16e8f2bc08ce8e2bcfcf439501")
+        (revision "0"))
     (package
       (name "sbcl-dynamic-classes")
-    (version "1.0.2")
+      (version (git-version "1.0.2" revision commit))
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
-             (url "https://github.com/gwkkwg/dynamic-classes")
+               (url "https://github.com/hraban/dynamic-classes")
-             (commit (string-append "version-" version))))
+               (commit commit)))
          (file-name (git-file-name "dynamic-classes" version))
          (sha256
-        (base32 "1z3ag6w4ff0v6715xa9zhvwjqnp4i6zrjfmxdz8m115sklbwgm6c"))))
+          (base32 "1k9lkchwyi2xhygp2v8ifq3kg1l3wcnihhzgr06jrivjxgdqpc1a"))))
       (build-system asdf-build-system/sbcl)
       (inputs
        `(("metatilities-base" ,sbcl-metatilities-base)))
@@ -17706,12 +17758,13 @@ It aims to be implementation-agnostic and to climb the syntax trees.")
        ;; NOTE: (Sharlatan-20210106222900+0000) Circular dependencies and failing
        ;; test suites. lift-standard.config contains referances to deprecated
        ;; functionality.
+       ;; See https://github.com/hraban/dynamic-classes/issues/2
        `(#:tests? #f))
       (home-page "https://common-lisp.net/project/dynamic-classes/")
       (synopsis "Dynamic class definition for Common Lisp")
       (description "Dynamic-Classes helps to ease the prototyping process by
 bringing dynamism to class definition.")
-    (license license:expat)))
+      (license license:expat))))
 
 (define-public ecl-dynamic-classes
   (sbcl-package->ecl-package sbcl-dynamic-classes))
@@ -17720,41 +17773,47 @@ bringing dynamism to class definition.")
   (sbcl-package->cl-source-package sbcl-dynamic-classes))
 
 (define-public sbcl-cl-markdown
-  ;; NOTE: (Sharlatan-20210106214629+0000) latest version tag
+  ;; The latest changes with fixes are not released yet, see
-  ;; "version-0.10.6_version-0.10.6" is failing to build due to missing system
+  ;; https://github.com/hraban/cl-markdown/issues/9
-  ;; #:container-dynamic-classes
+  (let ((commit "3788802199228b49d0e06c3feb80c1c22af05cfc")
+        (revision "0"))
     (package
       (name "sbcl-cl-markdown")
-    (version "0.10.4")
+      (version (git-version "0.10.6" revision commit))
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
-             (url "https://github.com/gwkkwg/cl-markdown")
+               (url "https://github.com/hraban/cl-markdown")
-             (commit (string-append "version-" version))))
+               (commit commit)))
          (file-name (git-file-name "cl-markdown" version))
          (sha256
-        (base32 "1wdjbdd1zyskxf7zlilcp6fmwkivybj0wjp64vvzb265d5xi7p8p"))))
+          (base32 "1algqwmafipyf194cx9wfhg0pdx1ppx6s444p1pm8yaycbsyla1v"))))
       (build-system asdf-build-system/sbcl)
+      (native-inputs
+       (list sbcl-lift sbcl-trivial-shell))
       (inputs
-     `(("anaphora" ,sbcl-anaphora)
+       (list sbcl-anaphora
-       ("cl-containers" ,sbcl-cl-containers)
+             sbcl-cl-containers
-       ("cl-ppcre" ,sbcl-cl-ppcre)
+             sbcl-cl-ppcre
-       ("dynamic-classes" ,sbcl-dynamic-classes)
+             sbcl-dynamic-classes
-       ("metabang-bind" ,sbcl-metabang-bind)
+             sbcl-metabang-bind
-       ("metatilities-base" ,sbcl-metatilities-base)))
+             sbcl-metatilities-base))
-    (arguments
-     ;; NOTE: (Sharlatan-20210107213629+0000) Tests depend on too many not
-     ;; available systems, which  themself are abandoned.
-     `(#:tests? #f))
       (home-page "https://common-lisp.net/project/cl-markdown/")
       (synopsis "Common Lisp rewrite of Markdown")
       (description
        "This is an implementation of a Markdown parser in Common Lisp.")
-    (license license:expat)))
+      (license license:expat))))
 
 (define-public ecl-cl-markdown
-  (sbcl-package->ecl-package sbcl-cl-markdown))
+  (let ((pkg (sbcl-package->ecl-package sbcl-cl-markdown)))
+    (package
+      (inherit pkg)
+      (arguments
+       ;; XXX: Tests fail with "The function LIFT::GET-BACKTRACE-AS-STRING is
+       ;; undefined" on ECL.
+       ;; See https://github.com/hraban/cl-markdown/issues/11
+       '(#:tests? #f)))))
 
 (define-public cl-markdown
   (sbcl-package->cl-source-package sbcl-cl-markdown))
@@ -18832,7 +18891,7 @@ HTML documents.")
   (sbcl-package->cl-source-package sbcl-cl-html-diff))
 
 (define-public sbcl-tooter
-  (let ((commit "2e1b22f0993419c1e7e6d10ead45d7bcafb5b6cb")
+  (let ((commit "2dcc2facddcacd79d0cce545a8c4b73c35826fc1")
         (revision "4"))
     (package
       (name "sbcl-tooter")
@@ -18845,10 +18904,13 @@ HTML documents.")
                (commit commit)))
          (file-name (git-file-name "cl-tooter" version))
          (sha256
-          (base32 "02ys58gzasvk7r84jmz6k522qcw2hkbgv8p0ax5i8dggjhr04cz2"))))
+          (base32 "1zisrmslj4rnibm02vxh7hbas2cfsjh6iizs2nfdg3a3pn7bhf6h"))))
       (build-system asdf-build-system/sbcl)
       (inputs
-       (list sbcl-cl-ppcre sbcl-documentation-utils sbcl-drakma
+       (list sbcl-alexandria
+             sbcl-cl-ppcre
+             sbcl-documentation-utils
+             sbcl-drakma
              sbcl-yason))
       (synopsis "Common Lisp client library for Mastodon instances")
       (description
@@ -18866,7 +18928,7 @@ protocol for Mastodon.")
 (define-public sbcl-croatoan
   (package
     (name "sbcl-croatoan")
-    (version "0.1")
+    (version "0.2")
     (source
      (origin
        (method git-fetch)
@@ -18875,7 +18937,7 @@ protocol for Mastodon.")
              (commit (string-append "v" version))))
        (file-name (git-file-name "cl-croatoan" version))
        (sha256
-        (base32 "1whbvwc4df7zz0002xy3aczrpf4s3vk6kmyh9wydgwl112h060pd"))))
+        (base32 "0x2rlckyn8kn5mqy0fib8piggz694g3naarz2dvha1hsy4jhb1wg"))))
     (build-system asdf-build-system/sbcl)
     (arguments
      '(#:phases
@@ -19481,7 +19543,7 @@ immediately loaded.")
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/gwkkwg/cl-mathstats")
+               (url "https://github.com/hraban/cl-mathstats")
                (commit commit)))
          (file-name (git-file-name "cl-mathstats" version))
          (sha256
@@ -19491,7 +19553,7 @@ immediately loaded.")
        (list sbcl-lift))
       (inputs
        (list sbcl-cl-containers sbcl-metatilities-base))
-      (home-page "https://github.com/gwkkwg/cl-mathstats")
+      (home-page "https://github.com/hraban/cl-mathstats")
       (synopsis "Common Lisp collection of mathematical routines")
       (description
        "This package provides Common Lisp math and statistics routines.")
@@ -21219,8 +21281,8 @@ running into parallelism problems when having to change directory.")
   (sbcl-package->cl-source-package sbcl-simple-inferiors))
 
 (define-public sbcl-metacopy
-  (let ((commit "1b5bf443206cc1dea7801ae23d1167bd02122d30")
+  (let ((commit "df7856f2a43fa91124fe780ef22f792040bc130c")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "sbcl-metacopy")
       (version (git-version "0.2.0" revision commit))
@@ -21228,27 +21290,27 @@ running into parallelism problems when having to change directory.")
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/gwkkwg/metacopy")
+               ;; Upstream changed the maintaner.
+               ;; legacy https://github.com/gwkkwg/metacopy
+               (url "https://github.com/hraban/metacopy")
                (commit commit)))
          (file-name (git-file-name "cl-metacopy" version))
          (sha256
-          (base32 "1rzp112djgw5n76s6hy2aq92bc43p0zd5bgzvqwvgvws4pls42s9"))))
+          (base32 "0l5ryg8pvqz9sn9s8bsvd0plvcnm7crsx86iqk5wxblkialaizip"))))
       (build-system asdf-build-system/sbcl)
       (native-inputs
        (list sbcl-asdf-system-connections sbcl-lift))
       (inputs
        (list sbcl-contextl sbcl-moptilities))
-      (home-page "https://github.com/gwkkwg/metacopy")
+      (home-page "https://github.com/hraban/metacopy")
       (synopsis "Flexible Common Lisp shallow/deep copy mechanism")
       (description
        "This package provides a flexible shallow/deep copy mechanism for
 Common Lisp.")
       (license license:expat))))
 
-;; NOTE: (Sharlatan-20221112T214131+0000): There is no ecl-moptilities variable
+(define-public ecl-metacopy
-;; required for tests.
+  (sbcl-package->ecl-package sbcl-metacopy))
-;;
-;; ecl-metacopy
 
 (define-public cl-metacopy
   (sbcl-package->cl-source-package sbcl-metacopy))

gnu/packages/lisp.scm

@@ -1061,8 +1061,9 @@ the HTML documentation of TXR.")
                                '("txr-manpage.html" "txr-manpage.pdf")))))
                (add-after 'install 'install-vim-files
                  (lambda _
-                   (let ((syntax (string-append #$output
+                   (let ((syntax (string-append
-                                                "/share/vim/vimfiles/syntax")))
+                                   #$output
+                                   "/share/vim/vimfiles/pack/guix/start/txr/syntax")))
                      (install-file "tl.vim" syntax)
                      (install-file "txr.vim" syntax)))))))
     (native-inputs

gnu/packages/llvm.scm

@@ -26,6 +26,7 @@
 ;;; Copyright © 2022 John Kehayias <john.kehayias@protonmail.com>
 ;;; Copyright © 2022 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2022 Zhu Zihao <all_but_last@163.com>
+;;; Copyright © 2023 Hilton Chain <hako@ultrarare.space>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -139,9 +140,19 @@ as \"x86_64-linux\"."
            (patches (map search-patch patches)))
          (llvm-monorepo (package-version llvm))))
     (build-system cmake-build-system)
-    (native-inputs (package-native-inputs llvm))
+    (native-inputs
+     (if (version>=? version "15")
+         ;; TODO: Remove this when GCC 12 is the default.
+         ;; libfuzzer fails to build with GCC 11
+         (modify-inputs (package-native-inputs llvm)
+           (prepend gcc-12))
+         (package-native-inputs llvm)))
     (inputs
-     (list llvm))
+     (append
+      (list llvm)
+      (if (version>=? version "15")
+          (list libffi)
+          '())))
     (arguments
      `(;; Don't use '-g' during the build to save space.
        #:build-type "Release"
@@ -150,6 +161,11 @@ as \"x86_64-linux\"."
                   (ice-9 match)
                   ,@%cmake-build-system-modules)
        #:phases (modify-phases (@ (guix build cmake-build-system) %standard-phases)
+                  ,@(if hash
+                        '()
+                        '((add-after 'unpack 'change-directory
+                            (lambda _
+                              (chdir "compiler-rt")))))
                   (add-after 'set-paths 'hide-glibc
                     ;; Work around https://issues.guix.info/issue/36882.  We need to
                     ;; remove glibc from CPLUS_INCLUDE_PATH so that the one hardcoded
@@ -342,6 +358,15 @@ until LLVM/Clang 14."
                                 (("@GLIBC_LIBDIR@")
                                  (string-append libc "/lib"))))))
                         #t)))
+                  ,@(if (version>=? version "17")
+                        '((add-after 'unpack 'include-test-runner
+                            (lambda _
+                              (substitute* "CMakeLists.txt"
+                                ((".*llvm_gtest" line)
+                                 (string-append
+                                  "add_subdirectory(${LLVM_THIRD_PARTY_DIR}/uni\
+ttest third-party/unittest)\n" line))))))
+                        '())
                   ;; Awkwardly, multiple phases added after the same phase,
                   ;; e.g. unpack, get applied in the reverse order.  In other
                   ;; words, adding 'change-directory last means it occurs
@@ -574,11 +599,15 @@ output), and Binutils.")
 
 (define %llvm-monorepo-hashes
   '(("14.0.6" . "14f8nlvnmdkp9a9a79wv67jbmafvabczhah8rwnqrgd5g3hfxxxx")
-    ("15.0.7" . "12sggw15sxq1krh1mfk3c1f07h895jlxbcifpwk3pznh4m1rjfy2")))
+    ("15.0.7" . "12sggw15sxq1krh1mfk3c1f07h895jlxbcifpwk3pznh4m1rjfy2")
+    ("16.0.6" . "0jxmapg7shwkl88m4mqgfjv4ziqdmnppxhjz6vz51ycp2x4nmjky")
+    ("17.0.3" . "1fhrnsv87if7kbqmrsxy2r7ykx3gnr9lmbmvkhvycc91ii4ihybx")))
 
 (define %llvm-patches
   '(("14.0.6" . ("clang-14.0-libc-search-path.patch"))
-    ("15.0.7" . ("clang-15.0-libc-search-path.patch"))))
+    ("15.0.7" . ("clang-15.0-libc-search-path.patch"))
+    ("16.0.6" . ("clang-16.0-libc-search-path.patch"))
+    ("17.0.3" . ("clang-17.0-libc-search-path.patch"))))
 
 (define (llvm-monorepo version)
   (origin
@@ -703,34 +732,10 @@ of programming tools as well as libraries with equivalent functionality.")
        ("perl"   ,perl)))))
 
 (define-public clang-runtime-15
-  (let ((template (clang-runtime-from-llvm llvm-15)))
+  (clang-runtime-from-llvm llvm-15))
-    (package
-      (inherit template)
-      (arguments
-       (substitute-keyword-arguments (package-arguments template)
-         ((#:phases phases '(@ (guix build cmake-build-system) %standard-phases))
-          #~(modify-phases #$phases
-              (add-after 'unpack 'change-directory
-                (lambda _
-                  (chdir "compiler-rt")))))))
-      (native-inputs
-       (modify-inputs (package-native-inputs template)
-         (prepend gcc-12)))             ;libfuzzer fails to build with GCC 11
-      (inputs
-       (modify-inputs (package-inputs template)
-         (append libffi))))))
 
 (define-public clang-runtime-14
-  (let ((template (clang-runtime-from-llvm llvm-14)))
+  (clang-runtime-from-llvm llvm-14))
-    (package
-      (inherit template)
-      (arguments
-       (substitute-keyword-arguments (package-arguments template)
-         ((#:phases phases '(@ (guix build cmake-build-system) %standard-phases))
-          #~(modify-phases #$phases
-              (add-after 'unpack 'change-directory
-                (lambda _
-                  (chdir "compiler-rt"))))))))))
 
 (define-public clang-15
   (clang-from-llvm
@@ -1458,6 +1463,74 @@ Library.")
                    #:legacy-build-shared-libs? #t
                    #:patches '("clang-3.5-libc-search-path.patch")))
 
+(define-public llvm-16
+  (package
+    (inherit llvm-15)
+    (version "16.0.6")
+    (source (llvm-monorepo version))))
+
+(define-public clang-runtime-16
+  (clang-runtime-from-llvm llvm-16))
+
+(define-public clang-16
+  (clang-from-llvm
+   llvm-16 clang-runtime-16
+   #:tools-extra
+   (origin
+     (method url-fetch)
+     (uri (llvm-uri "clang-tools-extra"
+                    (package-version llvm-16)))
+     (sha256
+      (base32
+       "0cbgffciql06a1i0ybyyqbnkkr4g7x8cxaar5a5v3415vd27hk0p")))))
+
+(define-public libomp-16
+  (package
+    (inherit libomp-15)
+    (version (package-version llvm-16))
+    (source (llvm-monorepo version))
+    (native-inputs
+     (modify-inputs (package-native-inputs libomp-15)
+       (replace "clang" clang-16)
+       (replace "llvm" llvm-16)))))
+
+(define-public clang-toolchain-16
+  (make-clang-toolchain clang-16 libomp-16))
+
+(define-public llvm-17
+  (package
+    (inherit llvm-15)
+    (version "17.0.3")
+    (source (llvm-monorepo version))))
+
+(define-public clang-runtime-17
+  (clang-runtime-from-llvm llvm-17))
+
+(define-public clang-17
+  (clang-from-llvm
+   llvm-17 clang-runtime-17
+   #:tools-extra
+   (origin
+     (method url-fetch)
+     (uri (llvm-uri "clang-tools-extra"
+                    (package-version llvm-17)))
+     (sha256
+      (base32
+       "0an16xdc8rgrdf0dcq3sdg82ajyb00h4bff9n0gm7gqf48ds0da8")))))
+
+(define-public libomp-17
+  (package
+    (inherit libomp-15)
+    (version (package-version llvm-17))
+    (source (llvm-monorepo version))
+    (native-inputs
+     (modify-inputs (package-native-inputs libomp-15)
+       (replace "clang" clang-17)
+       (replace "llvm" llvm-17)))))
+
+(define-public clang-toolchain-17
+  (make-clang-toolchain clang-17 libomp-17))
+
 ;; Default LLVM and Clang version.
 (define-public libomp libomp-13)
 (define-public llvm llvm-13)
@@ -1602,6 +1675,20 @@ components which highly leverage existing libraries in the larger LLVM Project."
     (inputs (modify-inputs (package-inputs lld)
               (replace "llvm" llvm-11)))))
 
+(define-public lld-16
+  (package
+    (inherit lld-15)
+    (version (package-version llvm-16))
+    (source (llvm-monorepo version))
+    (inputs (list llvm-16))))
+
+(define-public lld-17
+  (package
+    (inherit lld-15)
+    (version (package-version llvm-17))
+    (source (llvm-monorepo version))
+    (inputs (list llvm-17))))
+
 (define-public lld lld-14)
 
 (define* (make-lld-wrapper lld #:key lld-as-ld?)

gnu/packages/mail.scm

@@ -1867,7 +1867,8 @@ addons which can add many functionalities to the base client.")
                       (doc (string-append out "/share/doc/msmtp"))
                       (msmtpq "scripts/msmtpq")
                       (msmtpqueue "scripts/msmtpqueue")
-                      (vimfiles (string-append out "/share/vim/vimfiles/syntax")))
+                      (vimfiles (string-append
+                                  out "/share/vim/vimfiles/pack/guix/start/msmtp/syntax")))
                  (install-file (string-append msmtpq "/msmtpq") bin)
                  (install-file (string-append msmtpq "/msmtp-queue") bin)
                  (install-file (string-append msmtpqueue "/msmtp-enqueue.sh") bin)

gnu/packages/markup.scm

@@ -125,20 +125,17 @@ convert it to structurally valid XHTML (or HTML).")
                                    "See License.text in the distribution."))))
 
 (define-public lowdown
-  (let ((commit "1de10c1d71bfb4348ae0beaec8b1547d5e114969")
-        (revision "1"))
   (package
     (name "lowdown")
-      (version (git-version "0.10.0" revision commit))
+    (version "1.1.0")
     (source
      (origin
-         (method git-fetch)
+       (method url-fetch)
-         (uri (git-reference
+       (uri (string-append
-               (url "https://github.com/kristapsdz/lowdown")
+             "https://kristaps.bsd.lv/lowdown/snapshots/lowdown-"
-               (commit commit)))
+             version ".tar.gz"))
-         (file-name (git-file-name name version))
        (sha256
-          (base32 "1wh07nkiihvp1m79sj4qlnqklnn0rfp3hwls8sqcp0bfd96wpa1h"))))
+        (base32 "0y88gffrg1zrin0y53j4gbkmpia0r8p0kyklj501wavkqi83j7pk"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -149,15 +146,18 @@ convert it to structurally valid XHTML (or HTML).")
             (lambda _
               (invoke "./configure"
                       (string-append "PREFIX=" #$output)
-                        (string-append "MANDIR=" #$output "/share/man")))))
+                      (string-append "MANDIR=" #$output "/share/man"))))
+          (replace 'install
+            (lambda _
+              (invoke "make" "install" "install_libs"))))
       #:make-flags #~(list "CFLAGS=-fPIC")))
     (native-inputs
      (list which))
     (home-page "https://kristaps.bsd.lv/lowdown/")
     (synopsis "Simple Markdown translator")
-      (description "Lowdown is a Markdown translator producing HTML5,
+    (description "Lowdown is a Markdown translator producing HTML5, roff
-roff documents in the ms and man formats, LaTeX, gemini, and terminal output.")
+documents in the ms and man formats, LaTeX, gemini, and terminal output.")
-      (license license:isc))))
+    (license license:isc)))
 
 (define-public discount
   (package

gnu/packages/mastodon.scm

@@ -119,6 +119,7 @@ Features include:
      (list gdk-pixbuf ; so pixbuf loader cache (for webp) is generated
            gettext-minimal
            `(,glib "bin") ; for glib-compile-resources
+           gsettings-desktop-schemas    ; for the org.gnome.system.proxy schema
            pkg-config))
     (inputs
      (list gst-plugins-bad

gnu/packages/maths.scm

@@ -7594,60 +7594,65 @@ symmetric matrices.")
     (synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
 
 (define-public elemental
+  ;; The build of 0.87.7 is failed for a long time due to new version of GCC. The
+  ;; latest commit has fixes.
+  ;; See https://github.com/elemental/Elemental/issues/254
+  (let ((commit "6eb15a0da2a4998bf1cf971ae231b78e06d989d9")
+        (revision "0"))
     (package
       (name "elemental")
-    (version "0.87.7")
+      (version (git-version "0.87.7" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
                       (url "https://github.com/elemental/Elemental")
-                     (commit (string-append "v" version))))
+                      (commit commit)))
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
+                  "06xcs4ic60ndcf2hq19gr8yjwdsnphpcyhapab41rkw726z4lm7p"))))
       (build-system cmake-build-system)
-    (home-page "https://github.com/elemental/Elemental")
-    (native-inputs
-     (list gfortran))
-    (inputs
-     `(("blas" ,openblas)
-       ("gfortran:lib" ,gfortran "lib")
-       ("gmp" ,gmp)
-       ("lapack" ,lapack)
-       ("metis" ,metis)
-       ("mpc" ,mpc)
-       ("mpfr" ,mpfr)
-       ("mpi" ,openmpi)
-       ("qd" ,qd)))
       (arguments
-     `(#:build-type "Release"           ;default RelWithDebInfo not supported
+       (list
-       #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
+        #:build-type "Release" ;default RelWithDebInfo not supported
+        #:configure-flags
+        #~(list "-DEL_DISABLE_PARMETIS:BOOL=YES"
                 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
                 "-DEL_CACHE_WARNINGS:BOOL=YES"
                 "-DEL_TESTS:BOOL=YES"
                 "-DCMAKE_INSTALL_LIBDIR=lib"
                 "-DGFORTRAN_LIB=gfortran")
-       #:phases (modify-phases %standard-phases
+        #:phases
+        #~(modify-phases %standard-phases
             (add-before 'check 'mpi-setup
-                    ,%openmpi-setup)
+                 #$%openmpi-setup)
             (add-before 'check 'setup-tests
-                    (lambda _
+              (lambda _                ;; Parallelism is done at the MPI layer.
-                      ;; Parallelism is done at the MPI layer.
+                (setenv "OMP_NUM_THREADS" "1")))
-                      (setenv "OMP_NUM_THREADS" "1")
-                      #t))
             (add-after 'install 'remove-tests
-                    (lambda* (#:key outputs #:allow-other-keys)
+              (lambda _
                 ;; Tests are installed, with no easy configuration
                 ;; switch to prevent this, so delete them.
                 (delete-file-recursively
-                        (string-append (assoc-ref outputs "out") "/bin"))
+                 (string-append  #$output "/bin/test")))))))
-                      #t)))))
+      (native-inputs
+       (list gfortran))
+      (inputs
+       (list `(,gfortran "lib")
+             gmp
+             lapack
+             metis
+             mpc
+             mpfr
+             openmpi
+             qd
+             openblas))
+      (home-page "https://github.com/elemental/Elemental")
       (synopsis "Dense and sparse-direct linear algebra and optimization")
       (description "Elemental is a modern C++ library for distributed-memory
 dense and sparse-direct linear algebra, conic optimization, and lattice
 reduction.")
-    (license license:bsd-2)))
+      (license license:bsd-2))))
 
 (define-public mcrl2
   (package

gnu/packages/mes.scm

@@ -33,6 +33,7 @@
   #:use-module (gnu packages texinfo)
   #:use-module (guix build-system gnu)
   #:use-module (guix download)
+  #:use-module (guix gexp)
   #:use-module (guix git-download)
   #:use-module (guix licenses)
   #:use-module (guix packages)
@@ -153,15 +154,16 @@ parsers to allow execution with Guile as extension languages.")))
 (define-public mes
   (package
     (name "mes")
-    (version "0.24.2")
+    (version "0.25")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/mes/"
                                   "mes-" version ".tar.gz"))
               (sha256
                (base32
-                "0vp8v88zszh1imm3dvdfi3m8cywshdj7xcrsq4cgmss69s2y1nkx"))))
+                "0h49h85m1jkppfsv95zdxdrrw1q1mwswhq81lwxj1nbyasrm0lij"))))
-    (supported-systems '("armhf-linux" "i686-linux" "x86_64-linux"))
+    (supported-systems '("aarch64-linux" "armhf-linux" "i686-linux"
+                         "x86_64-linux" "riscv64-linux"))
     (propagated-inputs (list mescc-tools nyacc-1.00.2))
     (native-inputs
      (append (list guile-3.0)
@@ -173,6 +175,11 @@ parsers to allow execution with Guile as extension languages.")))
              ;; MesCC 64 bit .go files installed ready for use with Guile.
              (list (cross-binutils "i686-unknown-linux-gnu")
                    (cross-gcc "i686-unknown-linux-gnu")))
+         ((string-prefix? "aarch64-linux" target-system)
+          ;; Use cross-compiler rather than #:system "armhf-linux" to get
+          ;; MesCC 64 bit .go files installed ready for use with Guile.
+          (let ((triplet "arm-linux-gnueabihf"))
+            (list (cross-binutils triplet) (cross-gcc triplet))))
          (else
           '())))
        (list graphviz help2man
@@ -206,26 +213,28 @@ Guile.")
 (define-public mescc-tools
   (package
     (name "mescc-tools")
-    (version "1.4.0")
+    (version "1.5.0")
     (source (origin
-              (method git-fetch)
+              (method url-fetch)
-              (uri (git-reference
+              (uri (string-append "mirror://savannah/" name "/"
-                    (url "https://git.savannah.nongnu.org/r/mescc-tools.git")
+                                  name "-" version ".tar.gz"))
-                    (commit (string-append "Release_" version))
-                    (recursive? #t)))             ;for M2libc
-              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0z2ni2qn2np1walcaqlxz8sinzb78d4hiq9glddzf26wxc226hs4"))))
+                "1vjczlajyrbjcx9ld35vhdqbxfdwwy3axg0jray3iwnrf70qr700"))))
     (build-system gnu-build-system)
     (supported-systems '("i686-linux" "x86_64-linux"
                          "armhf-linux" "aarch64-linux"
                          "riscv64-linux"))
     (arguments
-     `(#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
+     (list
+      #:make-flags #~(list (string-append "PREFIX=" #$output))
       #:test-target "test"
-       #:phases (modify-phases %standard-phases
+      #:phases #~(modify-phases %standard-phases
-                  (delete 'configure))))
+                   (delete 'configure)
+                   (add-after 'unpack 'patch-Kaem/test.sh
+                     (lambda _
+                       (substitute* "Kaem/test.sh"
+                         (("#/usr/") "#! /usr")))))))
     (native-inputs (list which))
     (synopsis "Tools for the full source bootstrapping process")
     (description
@@ -239,19 +248,20 @@ get_machine.")
 (define-public m2-planet
   (package
     (name "m2-planet")
-    (version "1.9.0")
+    (version "1.11.0")
     (source (origin
-              (method git-fetch)
+              (method url-fetch)
-              (uri (git-reference
+              (uri (string-append
-                    (url "https://github.com/oriansj/m2-planet")
+                    "https://github.com/oriansj/M2-Planet/releases/download/"
-                    (commit (string-append "Release_" version))
+                    "Release_" version "/" name "-" version ".tar.gz"))
-                    (recursive? #t)))             ;for M2libc
-              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0cgvvq91cbxxm93k8ayyvhpaf3c2lv10qw4wyqwn3hc1qb1cfyvr"))))
+                "1c510p55amxjyvjlx9jpa30gixlgmf6mmfnaqcs46412krymwg38"))))
     (native-inputs (list mescc-tools))
     (build-system gnu-build-system)
+    (supported-systems '("i686-linux" "x86_64-linux"
+                         "armhf-linux" "aarch64-linux"
+                         "riscv32-linux" "riscv64-linux"))
     (arguments
      `(#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
                           ,(string-append "CC=" (cc-for-target)))
@@ -269,3 +279,4 @@ built as Phase-5 of the full source bootstrapping process and is capable of
 building GNU Mes.")
     (home-page "https://github.com/oriansj/m2-planet")
     (license gpl3+)))
+

gnu/packages/messaging.scm

@@ -2636,11 +2636,11 @@ replacement.")
     (license license:gpl2+)))
 
 (define-public tdlib
-  (let ((commit "4d1d22d6f477d61f6ff2b8f6e49de1847092c5b4")
+  (let ((commit "4ed0b23c9c99868ab4d2d28e8ff244687f7b3144")
         (revision "0"))
     (package
       (name "tdlib")
-      (version (git-version "1.8.16" revision commit))
+      (version (git-version "1.8.20" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -2648,7 +2648,7 @@ replacement.")
                (url "https://github.com/tdlib/td")
                (commit commit)))
          (sha256
-          (base32 "0nv921k795kq0l993rxzd5pm5v3l3mnwbaxb7d7d0m0506l4w9fk"))
+          (base32 "16kprlcnphi89yfwgnlaxjwwb1xx24az8xd710rx8cslb4zv00qw"))
          (file-name (git-file-name name version))))
       (build-system cmake-build-system)
       (arguments

gnu/packages/mold.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2023 Zhu Zihao <all_but_last@163.com>
+;;; Copyright © 2023 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -34,7 +35,7 @@
 (define-public mold
   (package
     (name "mold")
-    (version "1.10.1")
+    (version "2.3.2")
     (source
      (origin
        (method git-fetch)
@@ -43,10 +44,22 @@
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1bqv1a93n3nks38k8fdc5i7v7ca2sav8n4xxaph0ikaqw1mkjcg7"))
+        (base32 "1p6w92caysy9h0vkl26iv3viv0lvwzvbd357yykls0p13hnzlzkr"))
        (modules '((guix build utils)))
        (snippet
         #~(begin
+            ;; Fix detection of i686 systems.
+            ;; This can be removed with the next release of mold.
+            (substitute* "test/elf/common.inc"
+              (("echo i386") "echo i686"))
+            (substitute* '("test/elf/common.inc"
+                           "test/elf/global-offset-table.sh"
+                           "test/elf/i386_tls-module-base.sh"
+                           "test/elf/large-alignment-dso.sh"
+                           "test/elf/large-alignment.sh"
+                           "test/elf/nocopyreloc.sh"
+                           "test/elf/range-extension-thunk.sh")
+              (("MACHINE = i386") "MACHINE = i686"))
             (for-each
              (lambda (x)
                (delete-file-recursively (string-append "third-party/" x)))
@@ -55,7 +68,8 @@
     (arguments
      (list
       #:configure-flags #~(list "-DMOLD_USE_SYSTEM_MIMALLOC=ON"
-                                "-DMOLD_USE_SYSTEM_TBB=ON")
+                                "-DMOLD_USE_SYSTEM_TBB=ON"
+                                "-DBUILD_TESTING=ON")
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'configure 'force-system-xxhash
@@ -69,6 +83,10 @@
                 (("CC=\"\\$\\{TEST_CC:-cc\\}\"") "CC=gcc")
                 (("CXX=\"\\$\\{TEST_CXX:-c\\+\\+\\}\"")
                  "CXX=g++"))))
+          (add-before 'configure 'skip-tbb-lto-test
+            (lambda _
+              ;; This test needs tbb 2021.9.0 or newer
+              (delete-file "test/elf/lto-version-script.sh")))
           (add-before 'configure 'disable-rpath-test
             (lambda _
               ;; This test fails because mold expect the RUNPATH as-is,

gnu/packages/mpi.scm

@@ -141,7 +141,7 @@ bind processes, and much more.")
 (define-public hwloc-2
   (package
     (inherit hwloc-1)
-    (version "2.9.2")
+    (version "2.9.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://download.open-mpi.org/release/hwloc/v"
@@ -149,7 +149,7 @@ bind processes, and much more.")
                                   "/hwloc-" version ".tar.bz2"))
               (sha256
                (base32
-                "1kv0n3b9knb8aawf0hxaxn9wc9bbpwh676r2gmb0pc7qfzvgv1qa"))))
+                "1v0dzzgzp40slakdwdb8vy0hy4m2ff3gnzqpzi8k8vbgap764h2w"))))
 
     ;; libnuma is no longer needed.
     (inputs (modify-inputs (package-inputs hwloc-1)
@@ -184,7 +184,7 @@ bind processes, and much more.")
 (define-public openmpi
   (package
     (name "openmpi")
-    (version "4.1.5")
+    (version "4.1.6")
     (source
      (origin
        (method url-fetch)
@@ -192,7 +192,7 @@ bind processes, and much more.")
                            (version-major+minor version)
                            "/downloads/openmpi-" version ".tar.bz2"))
        (sha256
-        (base32 "1qyvc77diyrxmviirdwqpibgm32c4vkdlvw8g79rsf2pq9mrhh56"))
+        (base32 "05g4245v0pdqcyjmgn50519ry5v5q8ig26iinmiynvaihm29jh7p"))
        (patches (search-patches "openmpi-mtl-priorities.patch"))))
 
     (properties

gnu/packages/multiprecision.scm

@@ -10,6 +10,7 @@
 ;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2023 Janneke Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -251,24 +252,23 @@ error.  Additionally, iRRAM uses the concept of multi-valued functions.")
 (define-public qd
   (package
     (name "qd")
-    (version "2.3.23")
+    (version "2.3.24")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://crd-legacy.lbl.gov/~dhbailey/mpdist/qd-"
                            version ".tar.gz"))
        (sha256
-        (base32 "09pfd77rmy370hy7qdqw84z21y9zpl3fcwzf93rhiv0kwhfg9smk"))))
+        (base32 "0f0fwsyh23p5zfyrj6n16q7b56g213fnhdc8dbl22r3fz1rnqyx4"))))
     (build-system gnu-build-system)
-    (native-inputs
+    (native-inputs (list automake autoconf gfortran))
-     (list gfortran))
     (arguments
-     `(#:configure-flags `("--disable-enable_fma" ;weird :/
+     (list
+      #:configure-flags
+      #~(list "--disable-enable_fma" ;weird :/
               "--disable-static"
               "--enable-shared"
-                           ,,@(if (string-prefix? "aarch64"
+              #$@(if (target-aarch64?)
-                                                  (or (%current-target-system)
-                                                      (%current-system)))
                      ;; XXX: The qd_test test fails numerical
                      ;; accuracy checks for 'dd_real::exp()' on
                      ;; aarch64 with GCC 5.4 at -O2.  Disabling

gnu/packages/music.scm

@@ -4982,7 +4982,7 @@ includes LV2 plugins and a JACK standalone client.")
 (define-public musescore
   (package
     (name "musescore")
-    (version "4.0.2")
+    (version "4.1.1")
     (source
      (origin
        (method git-fetch)
@@ -4991,14 +4991,11 @@ includes LV2 plugins and a JACK standalone client.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1yri94xs4xw0lsvmk5q7bqnpgmdadchfn08r7bb2y07jsi8qgm6w"))
+        (base32 "12h26k9qnsq027gdpch579nchwrqva1ymwm2fj5xmlh0aayrwy4d"))
        (modules '((guix build utils)))
        (snippet
         '(begin
-           ;; Remove unused libraries...
+           ;; Delete precompiled binaries.
-           (for-each delete-file-recursively
-                     '("thirdparty/freetype"))
-           ;; ... and precompiled binaries.
            (delete-file-recursively "src/diagnostics/crashpad_handler")
            (substitute* "src/diagnostics/CMakeLists.txt"
              (("install") "#install"))))))

gnu/packages/networking.scm

@@ -154,7 +154,6 @@
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages readline)
-  #:use-module (gnu packages ruby)
   #:use-module (gnu packages samba)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages shells)
@@ -867,25 +866,9 @@ publish/subscribe, RPC-style request/reply, or service discovery.")
        (sha256
         (base32 "01ddfzjlkf2dgijrmm3j3j8irccsnbgfvjcnwslsfaxnrmrq5s64"))))
     (build-system cmake-build-system)
-    (outputs '("out" "doc"))
     (arguments
      `(#:configure-flags
-       (list
+       (list "-DNN_ENABLE_COVERAGE=ON")))
-        "-DNN_ENABLE_COVERAGE=ON")
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'install 'move-docs
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (doc (assoc-ref outputs "doc")))
-               (mkdir-p (string-append doc "/share/doc"))
-               (rename-file
-                (string-append out "/share/doc/nanomsg")
-                (string-append doc "/share/doc/nanomsg"))
-               #t))))))
-    (native-inputs
-     `(("asciidoctor" ,ruby-asciidoctor)
-       ("pkg-config" ,pkg-config)))
     (synopsis "Scalable socket library")
     (description "Nanomsg is a socket library that provides several common
 communication patterns.  It aims to make the networking layer fast, scalable,
@@ -4415,6 +4398,27 @@ client and server.  It allows you to use remote block devices over a TCP/IP
 network.")
     (license license:gpl2)))
 
+(define-public ngtcp2
+  (package
+    (name "ngtcp2")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/ngtcp2/ngtcp2/"
+                           "releases/download/v" version "/"
+                           "ngtcp2-" version ".tar.xz"))
+       (sha256
+        (base32 "0l84hnj9n4bfxjizgmqsqbz71jx7m00a7l1z43fg5ls3apx9ij11"))))
+    (build-system gnu-build-system)
+    (native-inputs (list cunit))
+    (home-page "https://nghttp2.org/ngtcp2/")
+    (synopsis "QUIC protocol implementation")
+    (description
+     "The ngtcp2 project is an effort to implement the RFC9000 (IETF)
+QUIC protocol.")
+    (license license:expat)))
+
 (define-public yggdrasil
   (package
     (name "yggdrasil")
@@ -4540,7 +4544,7 @@ on hub/switched networks.  It is based on @acronym{ARP} packets, it will send
 (define-public phantomsocks
   (package
     (name "phantomsocks")
-    (version "0.0.0-20230829023258-013a0002abe2")
+    (version "0.0.0-20231031033204-8b0ac27fc450")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -4549,10 +4553,11 @@ on hub/switched networks.  It is based on @acronym{ARP} packets, it will send
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0pqq4mh6dr7fb7i001wggwkxpvavxq0ps9h2cmm4gv8ygh4v6f10"))))
+                "1q4i8pgj6hzry9wzlczx729dmmgqdqfb26rfaim2ngmp1dyy9drl"))))
     (build-system go-build-system)
     (arguments
-     (list #:install-source? #f
+     (list #:go go-1.20
+           #:install-source? #f
            #:import-path "github.com/macronut/phantomsocks"
            #:build-flags #~'("-tags" #$(if (target-linux?)
                                            "rawsocket"

gnu/packages/node.scm

@@ -738,14 +738,14 @@ source files.")
 (define-public node-lts
   (package
     (inherit node)
-    (version "18.17.1")
+    (version "18.18.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://nodejs.org/dist/v" version
                                   "/node-v" version ".tar.gz"))
               (sha256
                (base32
-                "0dachvhf5jxrb1av8mn2dikbhwklxsgc9y2zg4h50fcwh5d54mqi"))
+                "0ci1faxjsbp0lv05kskh5anfljn6zawqcf7dawiby5d5qg7x572h"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -903,7 +903,26 @@ source files.")
                                           "/lib/node_modules/npm/node_modules"
                                           "/tar/lib/write-entry.js")))
                  (substitute* file
-                   (("this.stat.nlink > 1") "false")))))))))
+                   (("this.stat.nlink > 1") "false")))))
+           (add-after 'install 'install-node-gyp-wrapper
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (dir (string-append out "/lib/node_modules/npm/bin/node-gyp-bin"))
+                      (file (string-append dir "/node-gyp")))
+                 (mkdir-p dir)
+                 ;; See https://github.com/npm/cli/issues/6842
+                 (call-with-output-file file
+                   (lambda (port)
+                     (format port "#!~a/bin/sh
+if [ \"x$npm_config_node_gyp\" = \"x\" ]; then
+  ~a/bin/node \"~a/lib/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js\" \"$@\"
+else
+  \"$npm_config_node_gyp\" \"$@\"
+fi"
+                             (assoc-ref inputs "bash")
+                             out
+                             out)))
+                 (chmod file #o555))))))))
     (native-inputs
      (list ;; Runtime dependencies for binaries used as a bootstrap.
            c-ares-for-node

gnu/packages/package-management.scm

@@ -174,8 +174,8 @@
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
   (let ((version "1.4.0")
-        (commit "e863274e67e2242b970845783172c9f4e49405ca")
+        (commit "a60ff4611a8814d1f33d64af07401762afbcc597")
-        (revision 13))
+        (revision 14))
     (package
       (name "guix")
 
@@ -191,7 +191,7 @@
                       (commit commit)))
                 (sha256
                  (base32
-                  "0g8p0w9qrqbzz3b4fzbvvqpdfgwhlxpz75n3ysa6haima5s19mp3"))
+                  "08czk2789y21cydg1xwwrmah8hjaprdnzvb993n7d7d70ccxk5kz"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments
@@ -1754,8 +1754,8 @@ in an isolated environment, in separate namespaces.")
     (license license:gpl3+)))
 
 (define-public nar-herder
-  (let ((commit "53682fac7e00cd2801406edbd014922c1720c347")
+  (let ((commit "bf539aa08edfe8010606a31c00e0296c3d400319")
-        (revision "21"))
+        (revision "22"))
     (package
       (name "nar-herder")
       (version (git-version "0" revision commit))
@@ -1766,7 +1766,7 @@ in an isolated environment, in separate namespaces.")
                       (commit commit)))
                 (sha256
                  (base32
-                  "18mzrpc5ni8d6xbp1bg0nzdj0brmnji4jm1gyiq77dm17c118zyz"))
+                  "1i9q7ys26r6y2xa4qqy21bcxlqiynxp3p1wl5gmyj33jnb9ryjby"))
                 (file-name (string-append name "-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments

gnu/packages/parallel.scm

@@ -9,7 +9,7 @@
 ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018–2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
-;;; Copyright © 2019-2022 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2019-2023 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2020 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2021 Stefan Reichör <stefan@xsteve.at>
 ;;;
@@ -185,7 +185,7 @@ when jobs finish.")
 (define-public slurm
   (package
     (name "slurm")
-    (version "22.05.1")
+    (version "23.02.6")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -193,7 +193,7 @@ when jobs finish.")
                     version ".tar.bz2"))
               (sha256
                (base32
-                "0f3hhlki8g7slllsnyj1qikbsvr62i0hig85lcdcfnmsagzlhbyi"))
+                "08rz3r1rlnb3pmfdnbh542gm44ja0fdy8rkj4vm4lclc48cvqp2a"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -281,6 +281,20 @@ by managing a queue of pending work.")
 ;; As noted in the link, YY.MM is the release scheme, and the 'maintenance'
 ;; digit does not introduce incompatibilities.
 
+(define-public slurm-22.05
+  (package
+    (inherit slurm)
+    (version "22.05.1")
+    (source (origin
+              (inherit (package-source slurm))
+              (method url-fetch)
+              (uri (string-append
+                    "https://download.schedmd.com/slurm/slurm-"
+                    version ".tar.bz2"))
+              (sha256
+               (base32
+                "0f3hhlki8g7slllsnyj1qikbsvr62i0hig85lcdcfnmsagzlhbyi"))))))
+
 (define-public slurm-21.08
   (package
     (inherit slurm)

gnu/packages/patches/agda-categories-use-stdlib-1.7.3.patch

@@ -0,0 +1,28 @@
+From 76d3863a5e6e7b9ee948f10a3faec3420a2020f1 Mon Sep 17 00:00:00 2001
+Message-ID: <76d3863a5e6e7b9ee948f10a3faec3420a2020f1.1698265016.git.dev@jpoiret.xyz>
+From: Josselin Poiret <dev@jpoiret.xyz>
+Date: Wed, 25 Oct 2023 22:15:43 +0200
+Subject: [PATCH] Bump stdlib to 1.7.3
+
+From: Josselin Poiret <dev@jpoiret.xyz>
+
+---
+ agda-categories.agda-lib | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/agda-categories.agda-lib b/agda-categories.agda-lib
+index 5b19c405..4d63d415 100644
+--- a/agda-categories.agda-lib
++++ b/agda-categories.agda-lib
+@@ -1,3 +1,3 @@
+ name: agda-categories
+-depend: standard-library-1.7.2
++depend: standard-library-1.7.3
+ include: src/
+
+base-commit: 9d61106740147a67fa2cae0a89ac066897b24a51
+prerequisite-patch-id: 508dabd923ba9ac1ee4d8dab6697432b4bd8ba18
+prerequisite-patch-id: b5f39b4fc9e4c9993ab31300de041ed2c7eb696b
+-- 
+2.41.0
+

gnu/packages/patches/agda-use-sphinx-5.patch

@@ -0,0 +1,51 @@
+From 99ed1b59ef73fd35053810f6a09e034e1513caee Mon Sep 17 00:00:00 2001
+Message-ID: <99ed1b59ef73fd35053810f6a09e034e1513caee.1698243851.git.dev@jpoiret.xyz>
+From: Josselin Poiret <dev@jpoiret.xyz>
+Date: Wed, 25 Oct 2023 16:23:32 +0200
+Subject: [PATCH] Revert "Docs: bump Sphinx to 6.0.0"
+
+From: Josselin Poiret <dev@jpoiret.xyz>
+
+This reverts commit 40dd42eaa7c04e134fa38cb4f958414a76df27a7.
+---
+ doc/user-manual/conf.py          | 5 ++---
+ doc/user-manual/requirements.txt | 4 ++--
+ 2 files changed, 4 insertions(+), 5 deletions(-)
+
+diff --git a/doc/user-manual/conf.py b/doc/user-manual/conf.py
+index 127f6582dc..d737ede19b 100644
+--- a/doc/user-manual/conf.py
++++ b/doc/user-manual/conf.py
+@@ -35,7 +35,7 @@ release = version
+ #
+ # If your change the version here also change it in the
+ # `requirements.txt` file [Issue #1936].
+-needs_sphinx = '6.0.0'
++needs_sphinx = '5.0.0'
+ 
+ # Add any Sphinx extension module names here, as strings. They can be
+ # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+@@ -43,8 +43,7 @@ needs_sphinx = '6.0.0'
+ extensions = [
+     'sphinx.ext.imgmath',
+     'sphinx.ext.ifconfig',
+-    'sphinx.ext.imgconverter',
+-    'sphinxcontrib.jquery'
++    'sphinx.ext.imgconverter'
+ ]
+ 
+ # Add any paths that contain templates here, relative to this directory.
+diff --git a/doc/user-manual/requirements.txt b/doc/user-manual/requirements.txt
+index 384b1466b4..656e6c9ac0 100644
+--- a/doc/user-manual/requirements.txt
++++ b/doc/user-manual/requirements.txt
+@@ -1,2 +1,2 @@
+-Sphinx           >= 7.2.5
+-sphinx_rtd_theme >= 1.3.0
++Sphinx           >= 5.0.0, != 5.2.0.post0
++sphinx_rtd_theme >= 1.0
+
+base-commit: 08b79a684d712ba3dc4b26e5052ec49f49f5ff6c
+-- 
+2.41.0
+

gnu/packages/patches/clang-16.0-libc-search-path.patch

@@ -0,0 +1,95 @@
+Clang attempts to guess file names based on the OS and distro (yes!),
+but unfortunately, that doesn't work for us.
+
+This patch makes it easy to insert libc's $libdir so that Clang passes the
+correct absolute file name of crt1.o etc. to 'ld'.  It also disables all
+the distro-specific stuff and removes the hard-coded FHS directory names
+to make sure Clang also works on foreign distros.
+
+diff --git a/clang/lib/Driver/Distro.cpp b/clang/lib/Driver/Distro.cpp
+index 87a0c5a58511..86ea82eda4b5 100644
+--- a/clang/lib/Driver/Distro.cpp
++++ b/clang/lib/Driver/Distro.cpp
+@@ -98,6 +98,10 @@ static Distro::DistroType DetectLsbRelease(llvm::vfs::FileSystem &VFS) {
+ }
+ 
+ static Distro::DistroType DetectDistro(llvm::vfs::FileSystem &VFS) {
++  // The compiler should always behave the same, even when used via Guix on a
++  // foreign distro.
++  return Distro::UnknownDistro;
++
+   Distro::DistroType Version = Distro::UnknownDistro;
+ 
+   // Newer freedesktop.org's compilant systemd-based systems
+diff --git a/clang/lib/Driver/ToolChains/Cuda.cpp b/clang/lib/Driver/ToolChains/Cuda.cpp
+index aa125bb308e8..8b86e144054c 100644
+--- a/clang/lib/Driver/ToolChains/Cuda.cpp
++++ b/clang/lib/Driver/ToolChains/Cuda.cpp
+@@ -124,6 +124,9 @@ CudaInstallationDetector::CudaInstallationDetector(
+     const Driver &D, const llvm::Triple &HostTriple,
+     const llvm::opt::ArgList &Args)
+     : D(D) {
++  // Don't look for CUDA in /usr.
++  return;
++
+   struct Candidate {
+     std::string Path;
+     bool StrictChecking;
+diff --git a/clang/lib/Driver/ToolChains/Linux.cpp b/clang/lib/Driver/ToolChains/Linux.cpp
+index c6fb290ffdb4..4736f4bb3392 100644
+--- a/clang/lib/Driver/ToolChains/Linux.cpp
++++ b/clang/lib/Driver/ToolChains/Linux.cpp
+@@ -189,6 +189,10 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+ 
+   Generic_GCC::PushPPaths(PPaths);
+ 
++  // Comment out the distro-specific tweaks so that they don't bite when
++  // using Guix on a foreign distro.
++#if 0
++
+   Distro Distro(D.getVFS(), Triple);
+ 
+   if (Distro.IsAlpineLinux() || Triple.isAndroid()) {
+@@ -249,6 +253,7 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+ 
+ #ifdef ENABLE_LINKER_BUILD_ID
+   ExtraOpts.push_back("--build-id");
++#endif
+ #endif
+ 
+   // The selection of paths to try here is designed to match the patterns which
+@@ -270,6 +275,7 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+   }
+   Generic_GCC::AddMultilibPaths(D, SysRoot, OSLibDir, MultiarchTriple, Paths);
+ 
++#if 0
+   addPathIfExists(D, concat(SysRoot, "/lib", MultiarchTriple), Paths);
+   addPathIfExists(D, concat(SysRoot, "/lib/..", OSLibDir), Paths);
+ 
+@@ -298,9 +304,11 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+     addPathIfExists(D, concat(SysRoot, "/", OSLibDir, ABIName), Paths);
+     addPathIfExists(D, concat(SysRoot, "/usr", OSLibDir, ABIName), Paths);
+   }
++#endif
+ 
+   Generic_GCC::AddMultiarchPaths(D, SysRoot, OSLibDir, Paths);
+ 
++#if 0
+   // The deprecated -DLLVM_ENABLE_PROJECTS=libcxx configuration installs
+   // libc++.so in D.Dir+"/../lib/". Detect this path.
+   // TODO Remove once LLVM_ENABLE_PROJECTS=libcxx is unsupported.
+@@ -310,6 +318,14 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+ 
+   addPathIfExists(D, concat(SysRoot, "/lib"), Paths);
+   addPathIfExists(D, concat(SysRoot, "/usr/lib"), Paths);
++#endif
++
++  // Add libc's lib/ directory to the search path, so that crt1.o, crti.o,
++  // and friends can be found.
++  addPathIfExists(D, "@GLIBC_LIBDIR@", Paths);
++
++  // Add GCC's lib/ directory so libstdc++.so can be found.
++  addPathIfExists(D, GCCInstallation.getParentLibPath(), Paths);
+ }
+ 
+ ToolChain::RuntimeLibType Linux::GetDefaultRuntimeLibType() const {

gnu/packages/patches/clang-17.0-libc-search-path.patch

@@ -0,0 +1,90 @@
+Clang attempts to guess file names based on the OS and distro (yes!),
+but unfortunately, that doesn't work for us.
+
+This patch makes it easy to insert libc's $libdir so that Clang passes the
+correct absolute file name of crt1.o etc. to 'ld'.  It also disables all
+the distro-specific stuff and removes the hard-coded FHS directory names
+to make sure Clang also works on foreign distros.
+
+diff --git a/clang/lib/Driver/Distro.cpp b/clang/lib/Driver/Distro.cpp
+index 6e0087565941..c0a3ba7d7702 100644
+--- a/clang/lib/Driver/Distro.cpp
++++ b/clang/lib/Driver/Distro.cpp
+@@ -99,6 +99,10 @@ static Distro::DistroType DetectLsbRelease(llvm::vfs::FileSystem &VFS) {
+ }
+ 
+ static Distro::DistroType DetectDistro(llvm::vfs::FileSystem &VFS) {
++  // The compiler should always behave the same, even when used via Guix on a
++  // foreign distro.
++  return Distro::UnknownDistro;
++
+   Distro::DistroType Version = Distro::UnknownDistro;
+ 
+   // Newer freedesktop.org's compilant systemd-based systems
+diff --git a/clang/lib/Driver/ToolChains/Cuda.cpp b/clang/lib/Driver/ToolChains/Cuda.cpp
+index 3a577650eb08..ca3373edc127 100644
+--- a/clang/lib/Driver/ToolChains/Cuda.cpp
++++ b/clang/lib/Driver/ToolChains/Cuda.cpp
+@@ -128,6 +128,9 @@ CudaInstallationDetector::CudaInstallationDetector(
+     const Driver &D, const llvm::Triple &HostTriple,
+     const llvm::opt::ArgList &Args)
+     : D(D) {
++  // Don't look for CUDA in /usr.
++  return;
++
+   struct Candidate {
+     std::string Path;
+     bool StrictChecking;
+diff --git a/clang/lib/Driver/ToolChains/Linux.cpp b/clang/lib/Driver/ToolChains/Linux.cpp
+index 1ba222bf83b1..28766c5ab792 100644
+--- a/clang/lib/Driver/ToolChains/Linux.cpp
++++ b/clang/lib/Driver/ToolChains/Linux.cpp
+@@ -220,6 +220,10 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+ 
+   Generic_GCC::PushPPaths(PPaths);
+ 
++  // Comment out the distro-specific tweaks so that they don't bite when
++  // using Guix on a foreign distro.
++#if 0
++
+   Distro Distro(D.getVFS(), Triple);
+ 
+   if (Distro.IsAlpineLinux() || Triple.isAndroid()) {
+@@ -280,6 +284,7 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+ 
+ #ifdef ENABLE_LINKER_BUILD_ID
+   ExtraOpts.push_back("--build-id");
++#endif
+ #endif
+ 
+   // The selection of paths to try here is designed to match the patterns which
+@@ -301,6 +306,7 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+   }
+   Generic_GCC::AddMultilibPaths(D, SysRoot, OSLibDir, MultiarchTriple, Paths);
+ 
++#if 0
+   addPathIfExists(D, concat(SysRoot, "/lib", MultiarchTriple), Paths);
+   addPathIfExists(D, concat(SysRoot, "/lib/..", OSLibDir), Paths);
+ 
+@@ -329,11 +335,21 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+     addPathIfExists(D, concat(SysRoot, "/", OSLibDir, ABIName), Paths);
+     addPathIfExists(D, concat(SysRoot, "/usr", OSLibDir, ABIName), Paths);
+   }
++#endif
+ 
+   Generic_GCC::AddMultiarchPaths(D, SysRoot, OSLibDir, Paths);
+ 
++#if 0
+   addPathIfExists(D, concat(SysRoot, "/lib"), Paths);
+   addPathIfExists(D, concat(SysRoot, "/usr/lib"), Paths);
++#endif
++
++  // Add libc's lib/ directory to the search path, so that crt1.o, crti.o,
++  // and friends can be found.
++  addPathIfExists(D, "@GLIBC_LIBDIR@", Paths);
++
++  // Add GCC's lib/ directory so libstdc++.so can be found.
++  addPathIfExists(D, GCCInstallation.getParentLibPath(), Paths);
+ }
+ 
+ ToolChain::RuntimeLibType Linux::GetDefaultRuntimeLibType() const {

gnu/packages/patches/emacs-debbugs-keep-patch-subject.patch

@@ -1,29 +0,0 @@
-Preserve subject when replying to patch threads.
-Upstream status: likely to be in the next release (bug#66330)
-
-diff --git a/debbugs-gnu.el b/debbugs-gnu.el
-index f366fba11d..cd549e364d 100644
---- a/debbugs-gnu.el
-+++ b/debbugs-gnu.el
-@@ -1747,6 +1747,12 @@ MERGED is the list of bugs merged with this one."
- 	 (format "Re: bug#%d: %s" id (alist-get 'subject status)))
-     (debbugs-gnu-summary-mode 1)))
-
-+(defcustom debbugs-gnu-summary-keep-subject
-+  (rx "[PATCH" (? (0+ (not (any digit "/]"))) (1+ digit) "/" (1+ digit)) "]")
-+  "Regular expression which keeps the original message subject in replies."
-+  :version "29.1"
-+  :type 'regexp)
-+
- (defvar debbugs-gnu-summary-mode-map
-   (let ((map (make-sparse-keymap)))
-     (define-key map "C" #'debbugs-gnu-send-control-message)
-@@ -1778,6 +1784,8 @@ MERGED is the list of bugs merged with this one."
- 			    (cons new new))
- 			address))))))
- 	  ,@(and debbugs-gnu-subject
-+                 (not (string-match-p debbugs-gnu-summary-keep-subject
-+                                      debbugs-gnu-subject))
- 		 `((subject ,debbugs-gnu-subject)))))))
-
- (defun debbugs-gnu-guess-current-id ()

gnu/packages/patches/ucx-tcp-iface-ioctl.patch

@@ -3,89 +3,108 @@ TCP network interfaces cannot be obtained via /sys/class/net.  This patch
 provides alternative code that uses the SIOCGIFCONF ioctl to get the
 names of the available TCP network interfaces.
 
+Initially submitted at <https://github.com/openucx/ucx/pull/4462>.
+
 diff --git a/src/uct/tcp/tcp_iface.c b/src/uct/tcp/tcp_iface.c
-index cad4a2709..7c1d2c9de 100644
+index 6a6cd34fa..af32bb2e9 100644
 --- a/src/uct/tcp/tcp_iface.c
 +++ b/src/uct/tcp/tcp_iface.c
-@@ -17,6 +17,8 @@
+@@ -18,6 +18,8 @@
- #include <sys/poll.h>
  #include <netinet/tcp.h>
  #include <dirent.h>
+ #include <float.h>
 +#include <net/if.h>
 +#include <sys/ioctl.h>
  
+ #define UCT_TCP_IFACE_NETDEV_DIR "/sys/class/net"
  
- extern ucs_class_t UCS_CLASS_DECL_NAME(uct_tcp_iface_t);
+@@ -875,6 +877,85 @@ static UCS_CLASS_DEFINE_NEW_FUNC(uct_tcp_iface_t, uct_iface_t, uct_md_h,
-@@ -586,6 +588,68 @@ static UCS_CLASS_DEFINE_NEW_FUNC(uct_tcp_iface_t, uct_iface_t, uct_md_h,
                                   uct_worker_h, const uct_iface_params_t*,
                                   const uct_iface_config_t*);
  
 +/* Fetch information about available network devices through an ioctl.  */
-+static ucs_status_t query_devices_ioctl(uct_md_h md,
++static ucs_status_t uct_tcp_query_devices_ioctl(uct_md_h md,
-+					uct_tl_device_resource_t **tl_devices_p,
++                                                uct_tl_device_resource_t **devices_p,
-+					unsigned *num_tl_devices_p)
++                                                unsigned *num_devices_p)
 +{
 +    int sock, err, i;
-+    uct_tl_device_resource_t *resources, *tmp;
++    uct_tl_device_resource_t *devices, *tmp;
-+    unsigned num_resources;
++    unsigned num_devices;
 +    ucs_status_t status;
 +    struct ifconf conf;
-+    struct ifreq reqs[10];
 +
-+    conf.ifc_len = sizeof reqs;
++    conf.ifc_len = 0;
-+    conf.ifc_req = reqs;
++    conf.ifc_req = NULL;
 +
-+    sock = socket(SOCK_STREAM, AF_INET, 0);
++    status = ucs_socket_create(AF_INET, SOCK_STREAM, &sock);
-+    if (sock < 0) {
++    if (status != UCS_OK) {
-+	ucs_error("socket(2) failed: %m");
-+	status = UCS_ERR_IO_ERROR;
 +        goto out;
 +    }
 +
 +    err = ioctl(sock, SIOCGIFCONF, &conf);
 +    if (err < 0) {
-+	ucs_error("SIOCGIFCONF ioctl failed: %m");
++        ucs_error("ioctl(SIOCGIFCONF) failed: %m");
 +        status = UCS_ERR_IO_ERROR;
 +        goto out;
 +    }
 +
-+    resources     = NULL;
++    conf.ifc_req = ucs_calloc(1, conf.ifc_len, "ifreq");
-+    num_resources = 0;
++    if (conf.ifc_req == NULL) {
-+    for (i = 0; i < conf.ifc_len / sizeof(struct ifreq); i++) {
++        ucs_error("memory alocation failed");
-+	const char *name = reqs[i].ifr_name;
-+
-+        if (!ucs_netif_is_active(name, AF_INET)) {
-+            continue;
-+        }
-+
-+        tmp = ucs_realloc(resources, sizeof(*resources) * (num_resources + 1),
-+                          "tcp resources");
-+        if (tmp == NULL) {
-+            ucs_free(resources);
 +        status = UCS_ERR_NO_MEMORY;
 +        goto out;
 +    }
-+        resources = tmp;
 +
-+        ucs_snprintf_zero(resources[i].name, sizeof(resources[i].name),
++    err = ioctl(sock, SIOCGIFCONF, &conf);
-+                          "%s", name);
++    if (err < 0) {
-+        resources[i].type = UCT_DEVICE_TYPE_NET;
++        ucs_error("ioctl(SIOCGIFCONF) failed: %m");
-+        ++num_resources;
++        status = UCS_ERR_IO_ERROR;
++        goto out_free;
 +    }
 +
-+    *num_tl_devices_p = num_resources;
++    devices     = NULL;
-+    *tl_devices_p     = resources;
++    num_devices = 0;
++    for (i = 0; i < (conf.ifc_len / sizeof(struct ifreq)); i++) {
++        const char *name = conf.ifc_req[i].ifr_name;
++	sa_family_t family = conf.ifc_req[i].ifr_addr.sa_family;
++
++        if (!ucs_netif_is_active(name, family)) {
++            continue;
++        }
++
++        tmp = ucs_realloc(devices, sizeof(*devices) * (num_devices + 1),
++                          "tcp devices");
++        if (tmp == NULL) {
++            ucs_free(devices);
++            status = UCS_ERR_NO_MEMORY;
++            goto out_free;
++        }
++        devices = tmp;
++
++        ucs_snprintf_zero(devices[num_devices].name,
++                          sizeof(devices[num_devices].name),
++                          "%s", name);
++        devices[num_devices].type = UCT_DEVICE_TYPE_NET;
++        ++num_devices;
++    }
++
++    *num_devices_p = num_devices;
++    *devices_p     = devices;
 +    status         = UCS_OK;
 +
++out_free:
++    ucs_free(conf.ifc_req);
 +out:
-+    if (sock >= 0) close(sock);
++    if (sock >= 0) {
++        close(sock);
++    }
 +    return status;
 +}
 +
  ucs_status_t uct_tcp_query_devices(uct_md_h md,
                                     uct_tl_device_resource_t **devices_p,
                                     unsigned *num_devices_p)
-@@ -599,9 +663,9 @@ ucs_status_t uct_tcp_query_devices(uct_md_h md,
+@@ -893,9 +974,9 @@ ucs_status_t uct_tcp_query_devices(uct_md_h md,
  
      dir = opendir(UCT_TCP_IFACE_NETDEV_DIR);
      if (dir == NULL) {
@@ -94,11 +113,11 @@ index cad4a2709..7c1d2c9de 100644
 -        goto out;
 +        /* When /sys is unavailable, as can be the case in a container,
 +         * resort to a good old 'ioctl'.  */
-+	return query_devices_ioctl(md, devices_p, num_devices_p);
++        return uct_tcp_query_devices_ioctl(md, devices_p, num_devices_p);
      }
  
      devices     = NULL;
-@@ -655,7 +719,6 @@ ucs_status_t uct_tcp_query_devices(uct_md_h md,
+@@ -963,7 +1044,6 @@ ucs_status_t uct_tcp_query_devices(uct_md_h md,
  
  out_closedir:
      closedir(dir);

gnu/packages/pdf.scm

@@ -117,7 +117,7 @@
 (define-public capypdf
   (package
     (name "capypdf")
-    (version "0.5.0")
+    (version "0.6.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -125,7 +125,7 @@
                     (commit version)))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "1mb3i0jq04gg5cm1l07mn9kal5s748miql97j6fpaf1x1j2lcrsx"))))
+               (base32 "15l8zwc83l65xh739s0qddlv5qv537wnx74s8fcwlm1r8y7kf2x4"))))
     (build-system meson-build-system)
     (arguments
      (list #:meson meson/newer

gnu/packages/python-check.scm

@@ -528,13 +528,13 @@ Astropy project, but is optimized for use with astropy-related projects.")
 (define-public python-pytest-astropy
   (package
     (name "python-pytest-astropy")
-    (version "0.10.0")
+    (version "0.11.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-astropy" version))
        (sha256
-        (base32 "04g2rh261s3s6ym8mwi4iv2a6anbgwvwzcvkyilfck6yxrncdqw5"))))
+        (base32 "1d9rcxnc57rjp96xag1gq725pwl11b3k5hdaz7c3w5lixncsmbjf"))))
     (build-system python-build-system)
     (arguments (list #:tests? #f)) ; there are no tests
     (native-inputs
@@ -586,13 +586,13 @@ are too large to conveniently hard-code them in the tests.")
 (define-public python-pytest-doctestplus
   (package
     (name "python-pytest-doctestplus")
-    (version "0.12.1")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-doctestplus" version))
        (sha256
-        (base32 "10ciqylgziihxwxryxvxgmkqgws51pqcarn0gbh1d4cxx55rx5vs"))))
+        (base32 "17ylfnrcvvp6sd13bfj40jl40paqmjsbywysszb3xqgdr86l8l7n"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:test-flags
@@ -753,13 +753,13 @@ were inadvertently left open at the end of a unit test.")
 (define-public python-pytest-remotedata
   (package
     (name "python-pytest-remotedata")
-    (version "0.4.0")
+    (version "0.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-remotedata" version))
        (sha256
-        (base32 "1j5106j331cfdyfcwzrbs3yby84mq1b0kddfysq12z2dwdcca8dy"))))
+        (base32 "0ndvnj9zghfj17haphrygiri9iy38wb8lwq1xdkfvlfd73v8ph05"))))
     (build-system pyproject-build-system)
     (arguments
      (list

gnu/packages/python-science.scm

@@ -22,6 +22,7 @@
 ;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
 ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
 ;;; Copyright © 2022 jgart <jgart@dismail.de>
+;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -349,6 +350,38 @@ implements several methods for sequential model-based optimization.
 @code{skopt} aims to be accessible and easy to use in many contexts.")
     (license license:bsd-3)))
 
+(define-public python-tdda
+  (package
+    (name "python-tdda")
+    (version "2.0.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "tdda" version))
+       (sha256
+        (base32 "1xs91s8b7cshjcqw88qsrjh10xly799k5rf2ycawqfz2mw8sy3br"))))
+    (build-system pyproject-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'relax-requirements
+                    (lambda _
+                      (substitute* "setup.py"
+                        (("pandas>=1.5.2")
+                         "pandas"))))
+                  (replace 'check
+                    (lambda* (#:key tests? #:allow-other-keys)
+                      (when tests?
+                        (invoke "tdda" "test")))))))
+    (native-inputs (list python-numpy python-pandas))
+    (home-page "https://www.stochasticsolutions.com")
+    (synopsis "Test-driven data analysis library for Python")
+    (description
+     "The TDDA Python module provides command-line and Python API support
+for the overall process of data analysis, through tools that peform
+reference testing, constraint discovery for data, automatic inference
+of regular expressions from text data and automatic test generation.")
+    (license license:expat))) ; MIT License
+
 (define-public python-trimesh
   (package
     (name "python-trimesh")

gnu/packages/python-web.scm

@@ -5204,54 +5204,29 @@ with oauthlib.")
 (define-public whoogle-search
   (package
     (name "whoogle-search")
-    (version "0.8.2")
+    (version "0.8.3")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "whoogle-search" version))
               (sha256
                (base32
-                "1r6ymainwc3b8aar90b74mpnx3rsfscgzh0llwvsb03fbhiypw5g"))))
+                "09b9k97jflajvrs0npyz994rj8xkk400s98jw63b6vpsgw9q9nk4"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       ;; The tests need network access
       #:tests? #f))
     (propagated-inputs
-     (list python-attrs
+     (list python-beautifulsoup4
-           python-beautifulsoup4
-           python-cachelib
-           python-certifi
-           python-cffi
            python-brotli
-           python-chardet
-           python-click
            python-cryptography
            python-cssutils
            python-defusedxml
            python-flask
-           python-flask-session
+           python-dotenv
-           python-idna
-           python-itsdangerous
-           python-jinja2
-           python-markupsafe
-           python-more-itertools
-           python-packaging
-           python-pluggy
-           python-py
-           python-pycodestyle
-           python-pycparser
-           python-pyopenssl
-           python-pyparsing
-           python-pysocks
-           python-dateutil
            python-requests
-           python-soupsieve
            python-stem
-           python-urllib3
+           python-waitress))
-           python-waitress
-           python-wcwidth
-           python-werkzeug
-           python-dotenv))
     (home-page "https://github.com/benbusby/whoogle-search")
     (synopsis "Self-hosted, ad-free, privacy-respecting metasearch engine")
     (description

gnu/packages/python-xyz.scm

@@ -8726,6 +8726,7 @@ retrieve text and metadata from PDFs as well as merge entire files together.")
            python-attrs
            python-coverage
            python-hypothesis
+           python-setuptools-scm
            python-psutil
            python-pytest
            python-pytest-cov
@@ -32572,13 +32573,13 @@ collection.")
 (define-public python-types-pytz
   (package
     (name "python-types-pytz")
-    (version "2021.3.6")
+    (version "2023.3.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "types-pytz" version))
        (sha256
-        (base32 "14yr5hg2ww8s4a0mz2bkd549fv8qgm538fnzxvqv92ld1pcpym3l"))))
+        (base32 "16mbinqac2fjjh4gqw2940q8ysjqwj0hrvj4p9mqz76l5hcx08yc"))))
     (build-system python-build-system)
     (home-page "https://github.com/python/typeshed")
     (synopsis "Typing stubs for pytz")

gnu/packages/radio.scm

@@ -13,6 +13,7 @@
 ;;; Copyright © 2022 Greg Hogan <code@greghogan.com>
 ;;; Copyright © 2022 Ryan Tolboom <ryan@using.tech>
 ;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2023 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -218,21 +219,18 @@ mathematical operations, and much more.")
     (license license:expat)))
 
 (define-public rtl-sdr
-  ;; No tagged release since 2018
-  (let ((commit "5e73f90f1d85d8db2e583f3dbf1cff052d71d59b")
-        (revision "1"))
   (package
     (name "rtl-sdr")
-      (version (git-version "0.6.0" revision commit))
+    (version "2.0.1")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://git.osmocom.org/rtl-sdr/")
-               (commit commit)))
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-          (base32 "106fwzyr7cba952f3p3wm3hdqzm9zvm0v3gcz4aks2n7fnvrgrvn"))))
+        (base32 "0z8dn0gdava894fb9fs9gcwvmik31fcj6ldkggylc0mhgw5145pr"))))
     (build-system cmake-build-system)
     (inputs
      (list libusb))
@@ -275,7 +273,7 @@ system configuration:
 
 To install the rtl-sdr udev rules, you must extend 'udev-service-type' with
 this package.  E.g.: @code{(udev-rules-service 'rtl-sdr rtl-sdr)}")
-      (license license:gpl2+))))
+    (license license:gpl2+)))
 
 (define-public airspy
   (let ((commit "6f92f47146aa8a8fce59b60927cf8c53da6851b3")
@@ -1662,13 +1660,19 @@ instances over the network, and general QSO and DXpedition logging.")
         (base32 "1lqd77v9xm58k9g9kfwxva3mmzm1yyk1v27nws5j1a293zfg2hkw"))))
     (build-system qt-build-system)
     (arguments
-     (list #:tests? #f)) ; No test suite
+     (list #:tests? #f   ; No test suite
+           #:configure-flags
+           (if (this-package-native-input "ruby-asciidoctor")
+             #~'()
+             #~(list "-DWSJT_GENERATE_DOCS=OFF"))))
     (native-inputs
-     (list asciidoc
+     (append (list asciidoc
                    gfortran
                    pkg-config
-           qttools-5
+                   qttools-5)
-           ruby-asciidoctor))
+             (if (supported-package? ruby-asciidoctor)
+               (list ruby-asciidoctor)
+               '())))
     (inputs
      (list boost
            fftw
@@ -1914,7 +1918,7 @@ from devices on the 433 MHz, 868 MHz, 315 MHz, 345 MHz and 915 MHz ISM bands.")
 (define-public multimon-ng
   (package
     (name "multimon-ng")
-    (version "1.2.0")
+    (version "1.3.0")
     (source
      (origin
        (method git-fetch)
@@ -1923,7 +1927,7 @@ from devices on the 433 MHz, 868 MHz, 315 MHz, 345 MHz and 915 MHz ISM bands.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0hm7391z1iz2sk4xkwfphqz8qvihqjzsh45csz14gb4jfs1p6ks2"))))
+        (base32 "1gd3kxb1w2fc6waa8g7af036yicjbg4a7hs0dgdci4d3aqwyz690"))))
     (build-system cmake-build-system)
     (inputs
      (list libx11 pulseaudio))
@@ -2569,7 +2573,7 @@ voice formats.")
 (define-public sdrangel
   (package
     (name "sdrangel")
-    (version "7.16.0")
+    (version "7.17.0")
     (source
      (origin
        (method git-fetch)
@@ -2578,7 +2582,7 @@ voice formats.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1c2pdxw2a3pysqlmr42gghg0ga33afwdp6wc97h7s6gwc5km6zlk"))))
+        (base32 "16hpnfzccpj8a3i24ryli870ym6kjih981sjapcqdc8va0q14qdz"))))
     (build-system qt-build-system)
     (native-inputs
      (list doxygen graphviz pkg-config))

gnu/packages/ruby.scm

@@ -34,6 +34,7 @@
 ;;; Copyright © 2023 Yovan Naumovski <yovan@gorski.stream>
 ;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
 ;;; Copyright © 2023 Janneke Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -130,7 +131,13 @@
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
-       #:configure-flags '("--enable-shared") ; dynamic linking
+       #:configure-flags
+       ,(if (%current-target-system)
+            '(list (string-append
+                    "LDFLAGS=-Wl,-rpath="
+                    (assoc-ref %outputs "out") "/lib")
+                   "--enable-shared")
+            ''("--enable-shared")) ; dynamic linking
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'replace-bin-sh-and-remove-libffi
@@ -148,6 +155,9 @@
                             "tool/rbinstall.rb")
                (("/bin/sh") (which "sh")))
              #t)))))
+    (native-inputs (if (%current-target-system)
+                       (list this-package)
+                       '()))
     (inputs
      (list readline openssl-1.1 libffi gdbm))
     (propagated-inputs
@@ -178,7 +188,13 @@ a focus on simplicity and productivity.")
          "042xrdk7hsv4072bayz3f8ffqh61i8zlhvck10nfshllq063n877"))))
     (arguments
      `(#:test-target "test"
-       #:configure-flags '("--enable-shared") ; dynamic linking
+       #:configure-flags
+       ,(if (%current-target-system)
+            '(list (string-append
+                    "LDFLAGS=-Wl,-rpath="
+                    (assoc-ref %outputs "out") "/lib")
+                   "--enable-shared")
+            ''("--enable-shared")) ; dynamic linking
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'replace-bin-sh-and-remove-libffi
@@ -205,7 +221,10 @@ a focus on simplicity and productivity.")
                      (delete-file "test/ruby/test_io.rb"))))
                '()))))
     (native-inputs
-     (list autoconf))))
+     (append (if (%current-target-system)
+                 (list this-package)
+                 '())
+             (list autoconf)))))
 
 (define ruby-2.7-fixed
   (package

gnu/packages/rust-apps.scm

@@ -2206,7 +2206,8 @@ consecutive lines and since program start.")
                      (bin (string-append out "/bin"))
                      (share (string-append out "/share"))
                      (man (string-append out "/share/man"))
-                     (vimfiles (string-append share "/vim/vimfiles/plugin"))
+                     (vimfiles (string-append
+                                 share "/vim/vimfiles/pack/guix/start/skim/plugin"))
                      (bash-completion
                       (string-append share "/bash-completions/completions"))
                      (zsh-site (string-append share "/zsh/site-functions"))

gnu/packages/statistics.scm

@@ -672,14 +672,14 @@ also flexible enough to handle most nonstandard requirements.")
 (define-public r-matrix
   (package
     (name "r-matrix")
-    (version "1.6-1.1")
+    (version "1.6-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Matrix" version))
        (sha256
         (base32
-         "1hlcxr38p4ybb67n25cc1ssh2q2r8cj0flc59lid8hclzvqv27ik"))))
+         "094n9qf5j7bzi4cyxhm276qx2b2qp676ad8w9gql0qhzhfc889li"))))
     (properties `((upstream-name . "Matrix")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1178,14 +1178,14 @@ solution for sending email, including attachments, from within R.")
 (define-public r-stringi
   (package
     (name "r-stringi")
-    (version "1.7.12")
+    (version "1.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stringi" version))
        (sha256
         (base32
-         "02g0464sbprrbjlacx727p9ad1s5nbxl2mnvfmm9h7q000lsrs7g"))))
+         "0jm2f5wh231dzs46g7ic2k4633x9v9bd2a03dlpmq5rr46j299ay"))))
     (build-system r-build-system)
     (inputs (list icu4c))
     (native-inputs (list pkg-config))
@@ -1204,13 +1204,13 @@ transliteration, concatenation, date-time formatting and parsing, etc.")
 (define-public r-stringr
   (package
     (name "r-stringr")
-    (version "1.5.0")
+    (version "1.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stringr" version))
        (sha256
-        (base32 "0fk34ql5ak57f06l10ai300kxay6r7kkkyfanh8r24qaf3bmkcaj"))))
+        (base32 "1pj5xwg8kq2jllmszgkw96qj37wlb0x0vx4f3m5j211zpd8yrbd4"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cli r-glue r-lifecycle r-magrittr r-rlang r-stringi r-vctrs))
@@ -1448,13 +1448,13 @@ for template use among CRAN packages.")
 (define-public r-evaluate
   (package
     (name "r-evaluate")
-    (version "0.22")
+    (version "0.23")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "evaluate" version))
               (sha256
                (base32
-                "0sz4zimz4brbd9sawdazfgipkmfzzdmdq01b5m8pnrql5xrxhiwh"))))
+                "0p540jl6sixpgk08cp2h9470d28p7n66pfafiskvz3rba0vrrky9"))))
     (build-system r-build-system)
     (home-page "https://github.com/hadley/evaluate")
     (synopsis "Parsing and evaluation tools for R")
@@ -1782,13 +1782,13 @@ defined in different packages.")
 (define-public r-rlang
   (package
     (name "r-rlang")
-    (version "1.1.1")
+    (version "1.1.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "rlang" version))
               (sha256
                (base32
-                "16fsibxbh4fy62x6fw358qbniw085qs1wjyr75n22xv9g6kwjpjy"))))
+                "14l0dz36wav2jbz0dd3w34va68lrhr7fgd9dqf1v4nawdvff23ia"))))
     (build-system r-build-system)
     (home-page "http://rlang.tidyverse.org")
     (synopsis "Functions for base types, core R and Tidyverse features")
@@ -3063,13 +3063,13 @@ disk (or a connection).")
 (define-public r-plotrix
   (package
     (name "r-plotrix")
-    (version "3.8-2")
+    (version "3.8-4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "plotrix" version))
               (sha256
                (base32
-                "07xwq3505qb2yak7pfda22yqwifj6m78f8b5rm0ym74808qrawmv"))))
+                "1mp8mb79prgf5fzlaix4fvslr4q67hrzxqdv3kr7mik1mf9jv8p6"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/plotrix")
     (synopsis "Various plotting functions")
@@ -3126,13 +3126,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.12.6.4.0")
+    (version "0.12.6.6.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "1k7xq2yl4pkc7krz1bcdnx5kfj6n4zjmnm40nly2da2ji87agv49"))))
+                "171yflg07xi6570ich5gxhzsqqs7k3rxyhwg96amlkm1qn8v2pnk"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3195,14 +3195,14 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.")
 (define-public r-rprojroot
   (package
     (name "r-rprojroot")
-    (version "2.0.3")
+    (version "2.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rprojroot" version))
        (sha256
         (base32
-         "15zq606s544wmbvk5dw13xq0sspr9dsxyxlvzvn0r48f8x3l4q2h"))))
+         "16bf6ga5fgm83j3m67plw5i54az2vdbvw5m99ixaqkd24pxn7x5m"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -3340,13 +3340,13 @@ a column in data frame.")
 (define-public r-rsqlite
   (package
     (name "r-rsqlite")
-    (version "2.3.2")
+    (version "2.3.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RSQLite" version))
               (sha256
                (base32
-                "09vbx3akqws8a07ai6qbp3jn1w05qsmazl79wl2dyvvjpzs8b62x"))))
+                "0i1cjhqcclglv62j4dclxraaj5jmqdwyj4bs3qfbd8jd8v5d1c9j"))))
     (properties `((upstream-name . "RSQLite")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3370,13 +3370,13 @@ engine (version 3.8.8.2) is included.")
 (define-public r-rcurl
   (package
     (name "r-rcurl")
-    (version "1.98-1.12")
+    (version "1.98-1.13")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RCurl" version))
               (sha256
                (base32
-                "1ci6lsxm0f13yzw712gcbq23syl54x5llvhs2w1b8wwm9vqgx0qs"))))
+                "01pkmip1sllislmp34c25i9m9mlrid9b48xfjbf93sml55ijz985"))))
     (properties `((upstream-name . "RCurl")))
     (build-system r-build-system)
     (arguments
@@ -3412,13 +3412,13 @@ ldap, and also supports cookies, redirects, authentication, etc.")
 (define-public r-xml
   (package
     (name "r-xml")
-    (version "3.99-0.14")
+    (version "3.99-0.15")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "XML" version))
               (sha256
                (base32
-                "1ygi65ddgbsamxw2rm0p2clfak1xj44xyisgk48y72cd9ldaddic"))))
+                "0giv03bixc4kcq4dmcwzra7gp01i41hfr1710fd1v2hacya4d8cq"))))
     (properties
      `((upstream-name . "XML")))
     (build-system r-build-system)
@@ -4543,13 +4543,13 @@ t-probabilities, quantiles, random deviates and densities.")
 (define-public r-matrixstats
   (package
     (name "r-matrixstats")
-    (version "1.0.0")
+    (version "1.1.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "matrixStats" version))
               (sha256
                (base32
-                "0vxd7g1fm4x0f72bs1xfik1d4yklvpjdyg1hpx86pl8fwr86i1wl"))))
+                "0h85hjvsmc8s3hyjdj83fykb2vl8jc7pb9ynp2xsl0q9v1sihrxl"))))
     (properties `((upstream-name . "matrixStats")))
     (build-system r-build-system)
     (arguments
@@ -6014,18 +6014,18 @@ based on an interface to Fortran implementations by M. J. D. Powell.")
 (define-public r-rcppeigen
   (package
     (name "r-rcppeigen")
-    (version "0.3.3.9.3")
+    (version "0.3.3.9.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RcppEigen" version))
        (sha256
         (base32
-         "0xhwgn77166ir7qnzl25mj0byskkqr0b36hihrpr2zaqsrzs8wsq"))))
+         "1faz1phvg7g14bchi88vizn5mfhgiwmsjg7jzkyf1yjg0f6vpsj1"))))
     (properties `((upstream-name . "RcppEigen")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-rcpp r-matrix))
+     (list r-rcpp))
     (home-page "http://eigen.tuxfamily.org")
     (synopsis "Rcpp integration for the Eigen templated linear algebra library")
     (description
@@ -6060,14 +6060,14 @@ metrics for evaluating models.")
 (define-public r-matrixmodels
   (package
     (name "r-matrixmodels")
-    (version "0.5-2")
+    (version "0.5-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MatrixModels" version))
        (sha256
         (base32
-         "0ap3mfzb2psjwlksfjzs2ycl5598bllwzx5hfmf9db4yjsydn1hw"))))
+         "03zjfxjk4l2dl1117slz163w0ky675d23sjfni4d7fdhqq359ny2"))))
     (properties `((upstream-name . "MatrixModels")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6142,14 +6142,14 @@ algorithms.")
 (define-public r-lme4
   (package
     (name "r-lme4")
-    (version "1.1-34")
+    (version "1.1-35.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lme4" version))
        (sha256
         (base32
-         "1bbaxkrd5m3d40y6jdyrdr4vsjyzkfixbqjwj6c8inmks98f2wp8"))))
+         "0nzv1a22pfsf2ryw91h16ic4cb8y8g6wh0gx3msr7gv8dwwi3974"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-boot
@@ -6395,14 +6395,14 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
 (define-public r-ranger
   (package
     (name "r-ranger")
-    (version "0.15.1")
+    (version "0.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ranger" version))
        (sha256
         (base32
-         "0bibv9xf6w8k8nsc13f2yd4kx99aq0i758h3wfh089szgkpdjrad"))))
+         "12c52gqqwaaid5b062gad18ir1vala1z3a0z5j4af1xqzlxgk583"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-rcpp r-matrix r-rcppeigen))

gnu/packages/tbb.scm

@@ -52,7 +52,19 @@
        '(,@(if (target-riscv64?)
             '("-DTBB_TEST_LINK_FLAGS=-latomic")
             `())
-         "-DTBB_STRICT=OFF"))) ;; Don't fail on warnings
+         ,@(if (target-arm32?)
+             '("-DTBB_TEST_COMPILE_FLAGS=-DTBB_TEST_LOW_WORKLOAD")
+             `())
+         "-DTBB_STRICT=OFF")   ;; Don't fail on warnings
+       #:phases
+       (modify-phases %standard-phases
+         ,@(if (target-arm32?)
+             `((add-after 'unpack 'adjust-test-suite
+                 (lambda _
+                   (substitute* "test/CMakeLists.txt"
+                     ;; Bus error, skipped on mips.
+                     ((".*test_malloc_pools.*") "")))))
+             '()))))
     (home-page "https://www.threadingbuildingblocks.org")
     (synopsis "C++ library for parallel programming")
     (description

gnu/packages/tor.scm

@@ -63,14 +63,14 @@
 (define-public tor
   (package
     (name "tor")
-    (version "0.4.8.7")
+    (version "0.4.8.9")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://dist.torproject.org/tor-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "14blalf96240dg6crpmgyf2bdcj109dyx47h0w6a0a6vfjf2n3dj"))))
+               "0rfgn88izn74nh6gy42ggwmiicnylp73skrlwm61n4znj247vfsr"))))
     (build-system gnu-build-system)
     (arguments
      (list #:configure-flags

gnu/packages/version-control.scm

@@ -3188,7 +3188,9 @@ will reconstruct the object along its delta-base chain and return it.")
                #$(file-append (this-package-input "go-golang-org-x-net")
                               "/src/golang.org/x/net/publicsuffix/data")
                "src/golang.org/x/net/publicsuffix/data")))
-          (add-before 'build 'man-gen
+          ;; Only build the man pages if ruby-asciidoctor is available.
+          #$@(if (this-package-native-input "ruby-asciidoctor")
+               #~((add-before 'build 'man-gen
                     ;; Without this, the binary generated in 'build
                     ;; phase won't have any embedded usage-text.
                     (lambda _
@@ -3205,9 +3207,14 @@ will reconstruct the object along its delta-base chain and return it.")
                          (lambda (manpage)
                            (install-file manpage
                                          (string-append #$output "/share/man/man1")))
-                 (find-files "." "^git-lfs.*\\.1$"))))))))
+                         (find-files "." "^git-lfs.*\\.1$"))))))
+               #~()))))
     ;; make `ronn` available during build for man page generation
-    (native-inputs (list ronn-ng git-minimal ruby-asciidoctor))
+    (native-inputs
+     (append (list git-minimal)
+             (if (supported-package? ruby-asciidoctor)
+               (list ronn-ng ruby-asciidoctor)
+               '())))
     (propagated-inputs
      (list go-github-com-xeipuuv-gojsonschema
            go-github-com-xeipuuv-gojsonreference

gnu/packages/video.scm

@@ -179,6 +179,7 @@
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-build)
+  #:use-module (gnu packages python-check)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
@@ -1782,14 +1783,14 @@ audio/video codec library.")
 (define-public ffmpeg-5
   (package
     (inherit ffmpeg)
-    (version "5.1.3")
+    (version "5.1.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0biil32xnshg1b4lwzbdc5rxv1g7lpfsr5gdgaz96wlhzy9ka48v"))))))
+                "0qwhyhil805hns7yksdxagnrcc90h60al7lz1rc65kd1j2w3nf2l"))))))
 
 (define-public ffmpeg-4
   (package
@@ -1812,14 +1813,14 @@ audio/video codec library.")
 (define-public ffmpeg-3.4
   (package
     (inherit ffmpeg-4)
-    (version "3.4.11")
+    (version "3.4.13")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "1rijdvcx8xjqwh084qchwz91vcj8wsvb4diax0g8miywpir00ccw"))))
+               "0np0yalqdrm7rn7iykgfzz3ly4vbgigrajg48c1l6n7qrzqvfszv"))))
     (arguments
      (substitute-keyword-arguments (package-arguments ffmpeg-4)
        ((#:modules modules %gnu-build-system-modules)
@@ -1837,14 +1838,14 @@ audio/video codec library.")
 (define-public ffmpeg-2.8
   (package
     (inherit ffmpeg-3.4)
-    (version "2.8.20")
+    (version "2.8.22")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "1ivnfqmfnp3zmn1q2dxy4p85427y3r6d3jbnl5kprr7lqckf6rl5"))))
+                "0c8m4hhv2k5fybha908wzrpnf3wqkq52hayl658jq4bah0igdfqz"))))
     (arguments
      `(#:tests? #f               ; XXX: Enable them later, if required
        #:configure-flags
@@ -2430,7 +2431,7 @@ images and image hosting sites.")
 (define-public mpv-mpris
   (package
     (name "mpv-mpris")
-    (version "1.0")
+    (version "1.1")
     (source
       (origin
         (method git-fetch)
@@ -2439,7 +2440,7 @@ images and image hosting sites.")
                (commit version)))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "1vpx4kzyg4pssn1hql2ci4s9x08sdx2v0kphw4aryywnz04yjhzf"))))
+         (base32 "1384y8n3l0xk8hbad1nsj9ljzb1h02g3ln3jysd8bd6shbl0x4mx"))))
     (build-system copy-build-system)
     (arguments
      '(#:install-plan
@@ -2453,7 +2454,7 @@ images and image hosting sites.")
     (native-inputs
      (list pkg-config))
     (inputs
-     (list glib mpv))
+     (list ffmpeg glib mpv))
     (home-page "https://github.com/hoyon/mpv-mpris")
     (synopsis "MPRIS plugin for mpv")
     (description "This package provides an @dfn{MPRIS} (Media Player Remote
@@ -3272,33 +3273,45 @@ and custom quantization matrices.")
 (define-public streamlink
   (package
     (name "streamlink")
-    (version "3.2.0")
+    (version "6.3.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "streamlink" version))
         (sha256
          (base32
-          "09nrspga15svzi0hmakcarbciav0nzf30hg1ff53gia473cd4w4p"))))
+          "0i2qym2plm4gpcq50vl67j69m8a4zz9mb8gi2xryx28pbnpdzh4k"))
+        (snippet
+         #~(begin (use-modules (guix build utils))
+                  (substitute* "pyproject.toml"
+                    (("trio >=0\\.22") "trio >=0.21"))))))
     (build-system python-build-system)
     (arguments
-     `(#:phases (modify-phases %standard-phases
+     `(#:phases
+       (modify-phases %standard-phases
          (replace 'check
           (lambda* (#:key tests? #:allow-other-keys)
               (when tests?
                   (invoke "python" "-m" "pytest")))))))
     (native-inputs
-     (list python-freezegun python-mock python-pytest
+     (list python-freezegun
-           python-requests-mock))
+           python-requests-mock
+           python-pytest
+           python-pytest-asyncio
+           python-pytest-trio))
     (propagated-inputs
-     (list python-pysocks
+     (list python-certifi
-           python-websocket-client
            python-isodate
            python-lxml
            python-pycountry
            python-pycryptodome
+           python-pysocks
            python-requests
-           python-urllib3))
+           python-trio
+           python-trio-websocket
+           python-typing-extensions
+           python-urllib3
+           python-websocket-client))
     (home-page "https://github.com/streamlink/streamlink")
     (synopsis "Extract streams from various services")
     (description "Streamlink is command-line utility that extracts streams

gnu/packages/vim.scm

@@ -38,10 +38,10 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system cmake)
-  #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system vim)
   #:use-module (gnu packages)
   #:use-module (gnu packages acl)
   #:use-module (gnu packages admin) ; For GNU hostname
@@ -299,12 +299,9 @@ written in the Python 3, Perl, Ruby, Tcl, and Lua programming languages.")))
        (sha256
         (base32
          "1h6sci5mhdfg6sjsjpi8l5li02hg858zcayiwl60y9j2gqnd18lv"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     (list #:plugin-name "neocomplete"))
-       '(("autoload" "share/vim/vimfiles/")
-         ("doc" "share/vim/vimfiles/")
-         ("plugin" "share/vim/vimfiles/"))))
     (synopsis "Next generation completion framework for Vim")
     (description
      "@code{neocomplete}, an abbreviation of 'neo-completion with cache',
@@ -332,10 +329,9 @@ features than Vim's built-in completion.")
          (sha256
           (base32
            "151wpvbj6jb9jdkbhj3b77f5sq7y328spvwfbqyj1y32rg4ifmc6"))))
-      (build-system copy-build-system)
+      (build-system vim-build-system)
       (arguments
-       '(#:install-plan
+       (list #:plugin-name "neosnippet"))   ; Extends neosnippet
-         '(("neosnippets" "share/vim/vimfiles/"))))
     (synopsis "Snippets for neosnippet")
     (description
      "@code{neosnippet-snippets} provides standard snippets for the Vim plugin
@@ -361,17 +357,9 @@ you can fill in on the fly.")
        (sha256
         (base32
          "0k80syscmpnj38ks1fq02ds59g0r4jlg9ll7z4qc048mgi35alw5"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     (list #:plugin-name "neosnippet"))
-       '(("autoload" "share/vim/vimfiles/")
-         ("doc" "share/vim/vimfiles/")
-         ("ftdetect" "share/vim/vimfiles/")
-         ("ftplugin" "share/vim/vimfiles/")
-         ("indent" "share/vim/vimfiles/")
-         ("plugin" "share/vim/vimfiles/")
-         ("rplugin" "share/vim/vimfiles/")
-         ("syntax" "share/vim/vimfiles/"))))
     (synopsis "Snippet support for Vim")
     (description
      "@code{neosnippet}, is a plugin for Vim which adds snippet support to Vim.
@@ -400,12 +388,9 @@ trouble using them, because you do not have to remember each snippet name.")
          (sha256
           (base32
            "04h946vr4f8wxap3wzqs69y2v8n50g2zbk22jsg2kxr4c01z5cbw"))))
-      (build-system copy-build-system)
+      (build-system vim-build-system)
       (arguments
-       '(#:install-plan
+       (list #:plugin-name "vim-scheme"))
-         '(("ftplugin" "share/vim/vimfiles/")
-           ("indent" "share/vim/vimfiles/")
-           ("syntax" "share/vim/vimfiles/"))))
       (synopsis "Scheme syntax for Vim")
       (description
        "@code{vim-scheme} provides Scheme support for Vim (R7RS and CHICKEN).")
@@ -428,10 +413,9 @@ trouble using them, because you do not have to remember each snippet name.")
          (sha256
           (base32
            "0ka3qbhsh8lix1vyj4678j7dnchkd8khhirrnn3aylxxf8fpqyg8"))))
-      (build-system copy-build-system)
+      (build-system vim-build-system)
       (arguments
-       '(#:install-plan
+       (list #:plugin-name "luna"))
-         '(("colors" "share/vim/vimfiles/"))))
       (synopsis "Dark color theme for Vim")
       (description
        "@code{vim-luna} is a dark color theme for Vim.")
@@ -455,11 +439,9 @@ trouble using them, because you do not have to remember each snippet name.")
          (sha256
           (base32
            "0alvrfhmd91zkd9h83s8wvgyq4iakcf6rybsyjd369qbgpcqky89"))))
-      (build-system copy-build-system)
+      (build-system vim-build-system)
       (arguments
-       '(#:install-plan
+       (list #:plugin-name "context_filetype"))
-         '(("doc" "share/vim/vimfiles/")
-           ("autoload" "share/vim/vimfiles/"))))
       (synopsis "Context filetype library for Vim")
       (description
        "@code{vim-context-filetype} is context filetype library for Vim script.")
@@ -479,15 +461,9 @@ trouble using them, because you do not have to remember each snippet name.")
         (file-name (git-file-name name version))
         (sha256
          (base32 "138290g2aph1jjhaza6biky5qi4ka6435s01bwxivllgb53g3irc"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     (list #:plugin-name "fugitive"))
-       '(("autoload" "share/vim/vimfiles/")
-         ("doc" "share/vim/vimfiles/")
-         ("ftdetect" "share/vim/vimfiles/")
-         ("ftplugin" "share/vim/vimfiles/")
-         ("plugin" "share/vim/vimfiles/")
-         ("syntax" "share/vim/vimfiles/"))))
     (home-page "https://github.com/tpope/vim-fugitive")
     (synopsis "Vim plugin to work with Git")
     (description "Vim-fugitive is a wrapper for Vim that complements the
@@ -509,12 +485,9 @@ commit or run any Git arbitrary command.")
        (sha256
         (base32
          "1aksmr73648pvyc75pfdz28k2d4ky52rn7xiwcv7lz87q3vqld7k"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     (list #:plugin-name "airline"))
-       '(("autoload" "share/vim/vimfiles/")
-         ("doc" "share/vim/vimfiles/")
-         ("plugin" "share/vim/vimfiles/"))))
     (synopsis "Statusline for Vim")
     (description
      "@code{vim-airline} is an extensible statusline for Vim.
@@ -540,12 +513,9 @@ and powerline symbols, etc.")
          (sha256
           (base32
            "1sb7nb7j7bz0pv1c9bgdy0smhr0jk2b1vbdv9yzghg5lrknpsbr6"))))
-      (build-system copy-build-system)
+      (build-system vim-build-system)
       (arguments
-       '(#:install-plan
+       (list #:plugin-name "airline-themes"))
-         '(("autoload" "share/vim/vimfiles/")
-           ("doc" "share/vim/vimfiles/")
-           ("plugin" "share/vim/vimfiles/"))))
       (synopsis "Collection of themes for Vim-airline")
       (description
        "@code{vim-airline-themes} is a collection of themes for @code{vim-airline}.")
@@ -565,13 +535,9 @@ and powerline symbols, etc.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "0j91f72jaz1s6aw1hpjiz30vk2ds2aqd9gisk91grsldy6nz6hhz"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     (list #:plugin-name "syntastic"))
-       '(("autoload" "share/vim/vimfiles/")
-         ("doc" "share/vim/vimfiles/")
-         ("plugin" "share/vim/vimfiles/")
-         ("syntax_checkers" "share/vim/vimfiles/"))))
     (synopsis "Syntax checking plugin for Vim")
     (description
      "Vim-syntastic is a syntax checking plugin for Vim.  It runs files through
@@ -581,6 +547,17 @@ are detected, the user is notified.")
     (home-page "https://github.com/vim-syntastic/syntastic")
     (license license:wtfpl2)))
 
+(define-public neovim-syntastic
+  (package
+    (inherit vim-syntastic)
+    (name "neovim-syntastic")
+    (synopsis "Syntax checking plugin for Neovim")
+    (description
+     "Vim-syntastic is a syntax checking plugin for Neovim.  It runs files through
+external syntax checkers and displays any resulting errors to the user.  This
+can be done on demand, or automatically as files are saved.  If syntax errors
+are detected, the user is notified.")))
+
 (define-public vim-solarized
   (let ((commit "62f656a02f93c5190a8753159e34b385588d5ff3")
         (revision "1"))
@@ -596,11 +573,15 @@ are detected, the user is notified.")
          (file-name (git-file-name name version))
          (sha256
           (base32 "0001mz5v3a8zvi3gzmxhi3yrsb6hs7qf6i497arsngnvj2cwn61d"))))
-      (build-system copy-build-system)
+      (build-system vim-build-system)
       (arguments
-       '(#:install-plan
+       (list
-         '(("vim-colors-solarized/colors" "share/vim/vimfiles/")
+         #:plugin-name "solarized"
-           ("vim-colors-solarized/doc" "share/vim/vimfiles/"))))
+         #:phases
+         #~(modify-phases %standard-phases
+             (add-after 'unpack 'chdir
+               (lambda _
+                 (chdir "vim-colors-solarized"))))))
       (home-page "https://github.com/altercation/vim-colors-solarized")
       (synopsis "Solarized color scheme for Vim")
       (description
@@ -631,9 +612,16 @@ switching between the light and dark background modes.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "1jya8wwlkmgs89hndrq6gsaskhk9g0fh62wdib8v9vz2x5g3738z"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan '(("opt" "share/vim/vimfiles/pack/rainbow/"))))
+     (list
+       #:plugin-name "rainbow"
+       #:mode "opt"
+       #:phases
+       #~(modify-phases %standard-phases
+           (add-after 'unpack 'chdir
+             (lambda _
+               (chdir "opt/rainbow"))))))
     (home-page "https://github.com/mason1920/rainbow")
     (synopsis "Rainbow Parentheses Improved")
     (description
@@ -656,12 +644,11 @@ codes by showing different levels of parentheses in different colors.")
         (sha256
          (base32
           "0mp80bi2m56bb93szw87vy6q5s85yk9g91sl4pr51316rgdv5kkv"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     (list
-       '(("autoload" "share/vim/vimfiles/")
+       #:plugin-name "editorconfig"
-         ("doc" "share/vim/vimfiles/")
+       #:vim? #t))
-         ("plugin" "share/vim/vimfiles/"))))
     (home-page "https://editorconfig.org/")
     (synopsis "EditorConfig plugin for Vim")
     (description "EditorConfig makes it easy to maintain the correct coding
@@ -686,11 +673,9 @@ editors.")
                 (sha256
                  (base32
                   "1xn08z3a21mgfvp5i1nv57jnldwxwnl5nkryiff3zc99b1mizigp"))))
-      (build-system copy-build-system)
+      (build-system vim-build-system)
       (arguments
-       (list #:install-plan
+       (list #:plugin-name "packer.nvim"))
-             #~'(("lua" "share/nvim/site/pack/guix/start/packer.nvim/")
-                 ("doc" "share/nvim/site/pack/guix/start/packer.nvim/"))))
       (home-page "https://github.com/wbthomason/packer.nvim")
       (synopsis "Plugin manager for Neovim")
       (description
@@ -699,23 +684,6 @@ editors.")
 is based on Vim's builtin plugin support.")
       (license license:expat))))
 
-(define-public neovim-syntastic
-  (package
-    (inherit vim-syntastic)
-    (name "neovim-syntastic")
-    (arguments
-     '(#:install-plan
-       '(("autoload" "share/nvim/site/")
-         ("doc" "share/nvim/site/")
-         ("plugin" "share/nvim/site/")
-         ("syntax_checkers" "share/nvim/site/"))))
-    (synopsis "Syntax checking plugin for Neovim")
-    (description
-     "Vim-syntastic is a syntax checking plugin for Neovim.  It runs files through
-external syntax checkers and displays any resulting errors to the user.  This
-can be done on demand, or automatically as files are saved.  If syntax errors
-are detected, the user is notified.")))
-
 (define-public neovim
   (package
     (name "neovim")
@@ -889,12 +857,12 @@ and support for fonts with ligatures.")
             (lambda* (#:key outputs #:allow-other-keys)
               (let* ((out (assoc-ref outputs "out"))
                      (vifm (string-append out "/share/vifm"))
-                     (vimfiles (string-append out "/share/vim/vimfiles")))
+                     (vimfiles (string-append
+                                 out "/share/vim/vimfiles/pack/guix/start/vifm")))
                 (copy-recursively (string-append vifm "/colors")
                                   (string-append vimfiles "/colors"))
                 (copy-recursively (string-append vifm "/vim")
                                   vimfiles)
-                (delete-file-recursively (string-append vifm "/colors"))
                 (delete-file-recursively (string-append vifm "/vim"))))))))
     (native-inputs
      (list groff)) ; for the documentation
@@ -986,17 +954,9 @@ a nested nvim process.")
               (sha256
                (base32
                 "013yn2n2nsspk12bldkc9xn4z4kjx9rvracbllc8i1nngldckxd0"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     (list #:plugin-name "guix"))
-       '(("autoload" "share/vim/vimfiles/")
-         ("compiler" "share/vim/vimfiles/")
-         ("doc" "share/vim/vimfiles/")
-         ("indent" "share/vim/vimfiles/")
-         ("ftdetect" "share/vim/vimfiles/")
-         ("ftplugin" "share/vim/vimfiles/")
-         ("plugin" "share/vim/vimfiles/")
-         ("syntax" "share/vim/vimfiles/"))))
     (home-page "https://git.sr.ht/~efraim/guix.vim")
     (synopsis "Guix integration in Vim")
     (description "This package provides support for GNU Guix in Vim.")
@@ -1015,11 +975,10 @@ a nested nvim process.")
               (sha256
                (base32
                 "11zcw0sll6qg6ha0rr6n1cw5v73azvf7ycwn9lgiwa5cj7rrqjf4"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     (list
-       '(("plugin" "share/vim/vimfiles/")
+       #:plugin-name "asyncrun"))
-         ("doc/" "share/vim/vimfiles/doc" #:include ("asyncrun.txt")))))
     (home-page "https://github.com/skywind3000/asyncrun.vim")
     (synopsis "Run Async Shell Commands in Vim")
     (description "This plugin takes the advantage of new APIs in Vim 8 (and
@@ -1041,12 +1000,9 @@ quickfix window in realtime.")
         (sha256
          (base32
           "1m8b5mn2zqlphzs6xfwykwmghf6p0wabrhpjmh7vav35jgcxc4wl"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     (list #:plugin-name "dispatch"))
-       '(("autoload" "share/vim/vimfiles/")
-         ("doc" "share/vim/vimfiles/")
-         ("plugin" "share/vim/vimfiles/"))))
     (home-page "https://github.com/tpope/vim-dispatch")
     (synopsis "Asynchronous build and test dispatcher")
     (description "Leverage the power of Vim's compiler plugins without being
@@ -1071,11 +1027,9 @@ the job completes, errors will be loaded and parsed automatically.")
           (file-name (git-file-name name version))
           (sha256
            (base32 "05ffhhfahjqwxyrqmsinsahrs15wknzl2qbj8mznyv319mn2civ2"))))
-      (build-system copy-build-system)
+      (build-system vim-build-system)
       (arguments
-       `(#:install-plan
+       (list #:plugin-name "gemini"))
-         '(("ftdetect" "share/vim/vimfiles/")
-           ("syntax" "share/vim/vimfiles/"))))
       (home-page "https://git.sr.ht/~torresjrjr/gemini.vim")
       (synopsis "Vim syntax highlighting plugin for Gemini")
       (description "This Vim plugin provides a Vim syntax highlighting plugin
@@ -1099,11 +1053,9 @@ specification.")
           (sha256
            (base32
             "1xadb22kd40swmww0qxmmkcpcq6viy8l167pjck5q32hfngll5d3"))))
-      (build-system copy-build-system)
+      (build-system vim-build-system)
       (arguments
-       '(#:install-plan
+       (list #:plugin-name "eunuch"))
-         '(("doc" "share/vim/vimfiles/")
-           ("plugin" "share/vim/vimfiles/"))))
       (home-page "https://github.com/tpope/vim-eunuch")
       (synopsis "Vim sugar for the UNIX shell commands")
       (description "Vim sugar for the UNIX shell commands that need it the most.
@@ -1127,13 +1079,9 @@ help working on Vim buffers and the files they reference with one command.")
           (file-name (git-file-name name version))
           (sha256
            (base32 "0k4b629jn6xlxyjxdl3cgm06v9dmx967rqnslv5m82c9kscwpyh4"))))
-      (build-system copy-build-system)
+      (build-system vim-build-system)
       (arguments
-       `(#:install-plan
+       (list #:plugin-name "vim-slime"))
-         '(("autoload" "share/vim/vimfiles/")
-           ("doc" "share/vim/vimfiles/")
-           ("ftplugin" "share/vim/vimfiles/")
-           ("plugin" "share/vim/vimfiles/"))))
       (home-page "https://technotales.wordpress.com/2007/10/03/like-slime-for-vim/")
       (synopsis "Vim plugin to give you some slime")
       (description "SLIME is an Emacs plugin to turn Emacs into a Lisp IDE.  You
@@ -1159,28 +1107,29 @@ to Lisp.")
        (sha256
         (base32 "1dfc1wyjsgkckrklkzvk4whaz3ahaka59rvm7rc724mabmk83pmp"))
        (file-name (git-file-name name version))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     '(#:plugin-name "vlime"
-       '(("vim/autoload" "share/vim/vimfiles/")
-         ("vim/doc" "share/vim/vimfiles/")
-         ("vim/ftplugin" "share/vim/vimfiles/")
-         ("vim/syntax" "share/vim/vimfiles/")
-         ("vim/test" "share/vim/vimfiles/")
-         ;; This is so the Vimscript part of Vlime can find the lisp files.
-         ("lisp" "share/vim/")
-         ;; This is so lisp can load Vlime without the Vim part.
-         ("lisp" "share/common-lisp/source/vlime"))
        #:phases
        (modify-phases %standard-phases
+         (add-after 'symlink-files 'install-lisp-files
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (common-lisp (string-append out "/share/common-lisp")))
                ;; Create a symbolic link to the .asd file so that
                ;; (asdf:load-system "vlime") finds the system.
-         (add-after 'install 'link-asd
+               (copy-recursively "lisp" (string-append common-lisp "/source/vlime"))
-           (lambda* (#:key outputs #:allow-other-keys)
+               (mkdir-p (string-append common-lisp "/systems/"))
-             (let ((out (assoc-ref outputs "out")))
+               (symlink (string-append common-lisp "/source/vlime/vlime.asd")
-               (mkdir-p (string-append out "/share/common-lisp/systems/"))
+                        (string-append common-lisp "/systems/vlime.asd")))))
-               (symlink (string-append out "/share/common-lisp/source/vlime/vlime.asd")
+         (add-after 'install 'symlink-files
-                        (string-append out "/share/common-lisp/systems/vlime.asd"))))))))
+           (lambda* (#:key outputs plugin-name mode #:allow-other-keys)
+             (with-directory-excursion
+               (string-append (assoc-ref outputs "out")
+                              "/share/vim/vimfiles/pack/guix/" mode "/" plugin-name)
+               (for-each (lambda (dir)
+                           (symlink (string-append "./vim/" dir) dir))
+                         (list "after" "autoload" "doc" "ftplugin" "syntax"))))))))
     (propagated-inputs
      (list cl-alexandria
            cl-slime-swank
@@ -1211,11 +1160,9 @@ to aid you in your glorious Common Lisp hacking quest.")
           (file-name (git-file-name name version))
           (sha256
            (base32 "07d5s20r0ssd7rir45vy0fqlci44gha1a81rcilgar227f3nw328"))))
-      (build-system copy-build-system)
+      (build-system vim-build-system)
       (arguments
-       '(#:install-plan
+       (list #:plugin-name "paredit"))
-         '(("doc" "share/vim/vimfiles/")
-           ("plugin" "share/vim/vimfiles/"))))
       (home-page "https://github.com/kovisoft/paredit")
       (synopsis "Vim plugin for structured editing of Lisp S-expressions")
       (description
@@ -1237,11 +1184,9 @@ to aid you in your glorious Common Lisp hacking quest.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "1b0bd5m5lv1p4d299mrwjfs2gk0zqwyaqdaid9hs9yqlxnr8s5nf"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     (list #:plugin-name "surround"))
-       '(("doc" "share/vim/vimfiles/")
-         ("plugin" "share/vim/vimfiles/"))))
     (home-page "https://github.com/tpope/vim-surround")
     (synopsis "Vim plugin for easy quoting and parenthesizing")
     (description
@@ -1262,12 +1207,9 @@ change and add such surroundings in pairs.")
                            "/vim-gnupg-v" version ".tar.gz"))
        (sha256
         (base32 "02w8lgyyh7wgxysvmmcf9ja5c06vrbyh3alzvv97x8cfhrp0skn7"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     (list #:plugin-name "vim-gnupg"))
-       '(("autoload" "share/vim/vimfiles/")
-         ("doc" "share/vim/vimfiles/")
-         ("plugin" "share/vim/vimfiles/"))))
     (home-page "https://www.vim.org/scripts/script.php?script_id=3645")
     (synopsis "Vim plugin for transparent editing of gpg encrypted files")
     (description
@@ -1293,12 +1235,9 @@ swapfile, and undofile when editing encrypted files to increase security.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "0n68hg59h4rjn0ziqbsh5pr03l3kr98zk54659ny6vq107af1w96"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     (list #:plugin-name "ctrlp.vim"))
-       '(("autoload" "share/vim/vimfiles/")
-         ("doc" "share/vim/vimfiles/")
-         ("plugin" "share/vim/vimfiles/"))))
     (home-page "https://ctrlpvim.github.io/ctrlp.vim/")
     (synopsis "Fuzzy file, buffer, mru, tag, etc. finder for Vim")
     (description
@@ -1330,12 +1269,9 @@ anything).
        (file-name (git-file-name name version))
        (sha256
         (base32 "054g80n09mmxxlh8xaic29bn8bgn3clvv732rymljdyvbj1mlhwd"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     (list #:plugin-name "MUcomplete"))
-       '(("autoload" "share/vim/vimfiles/")
-         ("doc" "share/vim/vimfiles/")
-         ("plugin" "share/vim/vimfiles/"))))
     (home-page "https://github.com/lifepillar/vim-mucomplete")
     (synopsis "MUcomplete is a minimalist autocompletion plugin for Vim")
     (description
@@ -1359,12 +1295,9 @@ result is returned.")
          (file-name (git-file-name name version))
          (sha256
           (base32 "0zpa7cs59a8sq0k3frlf9flpf30jcn239yrpmv40r7nqvxzglbpl"))))
-      (build-system copy-build-system)
+      (build-system vim-build-system)
       (arguments
-       '(#:install-plan
+       (list #:plugin-name "gitgutter"))
-         '(("autoload" "share/vim/vimfiles/")
-           ("doc" "share/vim/vimfiles/")
-           ("plugin" "share/vim/vimfiles/"))))
       (synopsis "Vim plugin which shows a git diff in the sign column")
       (description
        "A Vim plugin which shows a git diff in the sign column.  It shows which
@@ -1388,12 +1321,9 @@ buffer.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "0ppsbsd696ih40d9f76mdl9sd9y7p2pvm65qmvq4b2zhkv4xbpxz"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     (list #:plugin-name "characterize"))
-       '(("autoload" "share/vim/vimfiles/")
-         ("doc" "share/vim/vimfiles/")
-         ("plugin" "share/vim/vimfiles/"))))
     (home-page "https://github.com/tpope/vim-characterize")
     (synopsis "Vim plugin for showing Unicode character metadata")
     (description
@@ -1422,13 +1352,9 @@ additions:
        (file-name (git-file-name name version))
        (sha256
         (base32 "1fqfs8msmr6d4kpvxqp14sdjvp5fj52q5w5kz71myzcd4kqzmirp"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     '(#:plugin-name "tagbar"
-       '(("autoload" "share/vim/vimfiles/")
-         ("doc" "share/vim/vimfiles/")
-         ("plugin" "share/vim/vimfiles/")
-         ("syntax" "share/vim/vimfiles/"))
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'link-universal-ctags
@@ -1463,15 +1389,9 @@ the class they are defined in.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "1si8qla86ng8cffbmfrk9gss0i3912yw0f1ph4bsiq0kk837lccp"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     '(#:install-plan
+     (list #:plugin-name "nerdtree"))
-       '(("autoload" "share/vim/vimfiles/")
-         ("doc" "share/vim/vimfiles/")
-         ("lib" "share/vim/vimfiles/")
-         ("nerdtree_plugin" "share/vim/vimfiles/")
-         ("plugin" "share/vim/vimfiles/")
-         ("syntax" "share/vim/vimfiles/"))))
     (home-page "https://github.com/preservim/nerdtree")
     (synopsis "Tree explorer plugin for Vim")
     (description
@@ -1493,13 +1413,9 @@ files for reading or editing, and perform basic file system operations.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "1ka2rqn7rby55aps3iblh1dcqxm7m7qx72mpkz6y2aaj8mkj0zyd"))))
-    (build-system copy-build-system)
+    (build-system vim-build-system)
     (arguments
-     (list
+     (list #:plugin-name "nerdcommenter"))
-      #:install-plan
-      #~`(("autoload" "share/vim/vimfiles/")
-          ("doc" "share/vim/vimfiles/")
-          ("plugin" "share/vim/vimfiles/"))))
     (home-page "https://github.com/preservim/nerdcommenter")
     (synopsis "Vim plugin for easy commenting of code")
     (description

gnu/packages/web-browsers.scm

@@ -586,7 +586,7 @@ driven and does not detract you from your daily work.")
 (define-public nyxt
   (package
     (name "nyxt")
-    (version "3.9.1")
+    (version "3.9.2")
     (source
      (origin
        (method git-fetch)
@@ -595,7 +595,7 @@ driven and does not detract you from your daily work.")
              (commit version)))
        (sha256
         (base32
-         "1x7ia43yh024hwwsh2a6g2daznkzgjlisnxvjfcb9sgvfqfa368i"))
+         "1v85jn46d9vacjig6n9z797fch88fw6vzwbfdzlqdkm86vvm8dwn"))
        (file-name (git-file-name "nyxt" version))
        (modules '((guix build utils)))
        (snippet

gnu/packages/web.scm

@@ -64,6 +64,7 @@
 ;;; Copyright © 2023 David Thompson <dthompson2@worcester.edu>
 ;;; Copyright © 2023 Christopher Howard <christopher@librehacker.com>
 ;;; Copyright © 2023 Felix Lechner <felix.lechner@lease-up.com>
+;;; Copyright © 2023 Evgeny Pisemsky <evgeny@pisemsky.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1004,7 +1005,7 @@ similar to live activity monitoring provided with NGINX plus.")
 (define-public lighttpd
   (package
     (name "lighttpd")
-    (version "1.4.72")
+    (version "1.4.73")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://download.lighttpd.net/lighttpd/"
@@ -1012,7 +1013,7 @@ similar to live activity monitoring provided with NGINX plus.")
                                   "lighttpd-" version ".tar.xz"))
               (sha256
                (base32
-                "1v2m9vavrg3ibbl0kfq3rjlnqicbrlrkqih1iisa0m5pd56xxjpp"))))
+                "1a2cx3di07wf8qii7dpk4yr5wvaz8c9na1x7523smc0lng81d241"))))
     (build-system gnu-build-system)
     (arguments
      (list #:configure-flags
@@ -4955,8 +4956,8 @@ Cloud.")
     (license license:expat)))
 
 (define-public guix-data-service
-  (let ((commit "1c7539418743e0dfe3a9cad22c414fd732daef8f")
+  (let ((commit "37a07c2d6e8285877ad0440a7e4ae286b7b65177")
-        (revision "42"))
+        (revision "43"))
     (package
       (name "guix-data-service")
       (version (string-append "0.0.1-" revision "." (string-take commit 7)))
@@ -4968,7 +4969,7 @@ Cloud.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1gp4mhjssxky0jjjz916rfgz4w2f327wfd5ixb6lb00ydlfh5mws"))))
+                  "0h83j10bq7dyda2idbqh5y6dcvmbl3xgc147yq4pk6bkh10y29y6"))))
       (build-system gnu-build-system)
       (arguments
        (list
@@ -7910,6 +7911,35 @@ features include:
 @end enumerate\n")
     (license license:expat)))
 
+(define-public monsterid
+  (let ((commit "5597f177b473343ff5cad9a6e0e5b255312c6096")
+        (revision "0"))
+    (package
+      (name "monsterid")
+      (version (git-version "0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/splitbrain/monsterID")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0ixyrrcbw96plcdna2rx1pqwisqy9hnr57kvamgj13lzlv2whdb3"))))
+      (build-system copy-build-system)
+      (arguments
+       '(#:install-plan '(("monsterid.php" "share/web/monsterid/")
+                          ("parts/" "share/web/monsterid/parts/"
+                           #:include-regexp ("\\.png$")))))
+      (home-page "https://www.splitbrain.org/projects/monsterid")
+      (synopsis "The original MonsterID implementation")
+      (description
+       "MonsterID is a method to generate a unique monster image based upon a
+certain identifier (IP address, email address, whatever).  It can be
+used to automatically provide personal avatar images in blog comments
+or other community services.")
+      (license license:expat))))
+
 (define-public cat-avatar-generator
   (let ((commit "9360ea33f79d1dad3e43494b09878b5e3f6b41fa")
         (revision "1"))

gnu/packages/wm.scm

@@ -64,6 +64,7 @@
 ;;; Copyright © 2023 Jonathan Brielamier <jonathan.brielmaier@web.de>
 ;;; Copyright © 2023 Vessel Wave <vesselwave@disroot.org>
 ;;; Copyright © 2023 Nicolas Graves <ngraves@ngraves.fr>
+;;; Copyright © 2023 Jaeme Sifat <jaeme@runbox.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -786,7 +787,7 @@ desktop environment.")
 (define-public icewm
   (package
     (name "icewm")
-    (version "3.4.3")
+    (version "3.4.4")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -794,7 +795,7 @@ desktop environment.")
                     version "/icewm-" version ".tar.lz"))
               (sha256
                (base32
-                "1r2x7acjahq4666mds1di46zc32sl80592wllghqcp5800jpjcjm"))))
+                "0cdsb2d45dwcr2dm4jfh0z5g6pkb0ghd4jaybxqiz74mbw5rmjhv"))))
     (build-system gnu-build-system)
     (native-inputs (list pkg-config))
     (inputs (list fontconfig
@@ -1083,7 +1084,8 @@ drags, snap-to-border support, and virtual desktops.")
          (add-after 'install 'install-vim-files
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
-                    (syntax (string-append out "/share/vim/vimfiles/syntax")))
+                    (syntax (string-append
+                              out "/share/vim/vimfiles/pack/guix/start/fluxbox/syntax")))
                (copy-recursively "3rd/vim/vim/syntax" syntax)
                #t)))
          (add-after 'install 'install-xsession
@@ -1490,6 +1492,56 @@ It is inspired by Xmonad and dwm.  Its major features include:
 project derived from the original Calm Window Manager.")
     (license license:isc)))
 
+(define-public dunst
+  (package
+    (name "dunst")
+    (version "1.9.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/dunst-project/dunst")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "17zrw7jrnlyln81pxw7p4jgvl7j1w1gf488nfskhns6j6dcz90gh"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f ;no check target
+      #:make-flags #~(list (string-append "CC="
+                                          #$(cc-for-target))
+                           (string-append "PREFIX=" %output)
+                           (string-append "SYSCONFDIR=" %output "/etc")
+                           ;; Otherwise it tries to install service file
+                           ;; to "dbus" store directory.
+                           (string-append "SERVICEDIR_DBUS=" %output
+                                          "/share/dbus-1/services")
+                           "dunstify")
+      #:phases #~(modify-phases %standard-phases
+                   (delete 'configure))))
+    (native-inputs (list pkg-config perl ;for pod2man
+                         which))
+    (inputs (list dbus
+                  (librsvg-for-system) ;for svg support
+                  glib
+                  cairo
+                  pango
+                  libnotify ;for dunstify
+                  libx11
+                  libxscrnsaver
+                  libxinerama
+                  libxrandr
+                  libxdg-basedir
+                  wayland)) ;for wayland support
+    (home-page "https://dunst-project.org/")
+    (synopsis "Customizable and lightweight notification daemon")
+    (description
+     "Dunst is a highly configurable and minimalistic notification daemon.
+It provides @code{org.freedesktop.Notifications} D-Bus service, so it is
+started automatically on the first call via D-Bus.")
+    (license license:bsd-3)))
+
 (define-public dwl
   (package
     (name "dwl")

gnu/tests.scm

@@ -33,6 +33,10 @@
   #:use-module (gnu services base)
   #:use-module (gnu services shepherd)
   #:use-module (guix discovery)
+  #:use-module (guix monads)
+  #:use-module ((guix store) #:select (%store-monad))
+  #:use-module ((guix utils)
+                #:select (%current-system %current-target-system))
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-9 gnu)
   #:use-module (ice-9 match)
@@ -284,8 +288,9 @@ the system under test."
 (define-gexp-compiler (compile-system-test (test <system-test>)
                                            system target)
   "Compile TEST to a derivation."
-  ;; XXX: SYSTEM and TARGET are ignored.
+  (mparameterize %store-monad ((%current-system system)
-  (system-test-value test))
+                               (%current-target-system target))
+    (system-test-value test)))
 
 (define (test-modules)
   "Return the list of modules that define system tests."

gnu/tests/networking.scm

@@ -349,9 +349,8 @@ port 7, and a dict service on port 2628."
 
           ;; Make sure the PID file is created.
           (test-assert "PID file"
-            (marionette-eval
+            (wait-for-file "/var/run/inetd.pid" marionette
-             '(file-exists? "/var/run/inetd.pid")
+                           #:timeout 30))
-             marionette))
 
           ;; Test the echo service.
           (test-equal "echo response"

guix/build-system/ant.scm

@@ -103,6 +103,7 @@
                     (build-target "jar")
                     (jar-name #f)
                     (main-class #f)
+                    (use-java-modules? #f)
                     (test-include (list "**/*Test.java"))
                     (test-exclude (list "**/Abstract*.java"))
                     (source-dir "src")
@@ -131,6 +132,7 @@
                      #:build-target #$build-target
                      #:jar-name #$jar-name
                      #:main-class #$main-class
+                     #:use-java-modules? #$use-java-modules?
                      #:test-include (list #$@test-include)
                      #:test-exclude (list #$@test-exclude)
                      #:source-dir #$source-dir

guix/build-system/vim.scm

@@ -0,0 +1,157 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2022 Jonathan Scoresby <me@jonscoresby.com>
+;;; Copyright © 2023 Efraim Flashner <efraim@flashner.co.il>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (guix build-system vim)
+  #:use-module (guix store)
+  #:use-module (guix utils)
+  #:use-module (guix gexp)
+  #:use-module (guix monads)
+  #:use-module (guix packages)
+  #:use-module (guix search-paths)
+  #:use-module (guix build-system)
+  #:use-module (guix build-system copy)
+  #:use-module (guix build-system gnu)
+  #:export (%vim-build-system-modules vim-build vim-build-system))
+
+;; Commentary:
+;;
+;; Standard package installer for vim and neovim plugins.
+;; This is implemented as an extension of the `copy-build-system'
+;; and takes advantage of vim and neovim's built-in package manager.
+;; It extends the installation procedure from the copy-build-system
+;; to put files in the correct place and then generates help tags.
+;;
+;; Code:
+
+(define %vim-build-system-modules
+  ;; Build-side modules imported by default.
+  `((guix build vim-build-system)
+    ,@%copy-build-system-modules))
+
+(define (default-vim)
+  "Return the default Vim package."
+  ;; Lazily resolve the binding to avoid a circular dependency.
+  (let ((vim (resolve-interface '(gnu packages vim))))
+    (module-ref vim 'vim)))
+
+(define (default-neovim)
+  "Return the default Neovim package."
+  (let ((vim (resolve-interface '(gnu packages vim))))
+    (module-ref vim 'neovim)))
+
+(define* (lower name
+                #:key source
+                inputs
+                native-inputs
+                outputs
+                system
+                target
+                (vim? #f)
+                (neovim? #f)
+                (plugin-name name)
+                (vim (default-vim))
+                (neovim (default-neovim))
+                #:allow-other-keys #:rest arguments)
+  "Return a bag for NAME."
+  (let* ((private-keywords '(#:target #:vim #:neovim #:inputs #:native-inputs))
+         (vim? (or (string-prefix? "vim-" name)
+                   vim?))
+         (neovim? (or (string-prefix? "neovim-" name)
+                      neovim?))
+         (vim-inputs (append (if vim?
+                                 `(("vim" ,vim))
+                                 '())
+                             (if neovim?
+                                 `(("neovim" ,neovim))
+                                 '())))
+         (vim-arguments (append arguments
+                                `(#:vim? ,vim?
+                                  #:neovim? ,neovim?))))
+    (bag (name name)
+         (system system)
+         (host-inputs `(,@(if source
+                              `(("source" ,source))
+                              '()) ,@inputs
+
+                        ;; Keep the standard inputs of 'gnu-build-system'.
+                        ,@(standard-packages)))
+         (build-inputs `(,@vim-inputs ,@native-inputs))
+         (outputs outputs)
+         (build vim-build)
+         (arguments (strip-keyword-arguments private-keywords vim-arguments)))))
+
+(define* (vim-build name inputs
+                    #:key guile
+                    source
+                    (vim? #f)
+                    (neovim? #f)
+                    (mode "start")
+                    (plugin-name name)
+                    (install-plan ''())
+                    (phases '(@ (guix build vim-build-system) %standard-phases))
+                    (outputs '("out"))
+                    (search-paths '())
+                    (system (%current-system))
+                    (substitutable? #t)
+                    (imported-modules %vim-build-system-modules)
+                    (modules '((guix build vim-build-system)
+                               (guix build utils))))
+
+  (define build
+    (with-imported-modules imported-modules
+      #~(begin
+          (use-modules #$@modules)
+          #$(with-build-variables inputs outputs
+              #~(vim-build #:name #$name
+                           #:vim? #$vim?
+                           #:neovim? #$neovim?
+                           #:mode #$mode
+                           #:plugin-name #$plugin-name
+                           #:install-plan #$(if (pair? install-plan)
+                                                (sexp->gexp install-plan)
+                                                install-plan)
+                           #:source #+source
+                           #:system #$system
+                           #:phases #$(if (pair? phases)
+                                          (sexp->gexp phases)
+                                          phases)
+                           #:outputs %outputs
+                           #:search-paths '#$(sexp->gexp
+                                               (map search-path-specification->sexp
+                                                    search-paths))
+                           #:inputs
+                           %build-inputs)))))
+
+  (mlet %store-monad
+        ((guile (package->derivation (or guile (default-guile))
+                                     system #:graft? #f)))
+        (gexp->derivation name
+                          build
+                          #:system system
+                          #:target #f
+                          #:graft? #f
+                          #:substitutable? substitutable?
+                          #:guile-for-build guile)))
+
+(define vim-build-system
+  (build-system (name 'vim)
+                (description "The standard Vim build system")
+                (lower lower)))
+
+;;; vim.scm ends here

guix/build/ant-build-system.scm

@@ -37,6 +37,7 @@
 
 (define* (default-build.xml jar-name prefix #:optional
                             (source-dir ".") (test-dir "./test") (main-class #f)
+                            (use-java-modules? #f)
                             (test-include '("**/*Test.java"))
                             (test-exclude '("**/Abstract*Test.java")))
   "Create a simple build.xml with standard targets for Ant."
@@ -65,7 +66,7 @@
                               (value "first")))
                  (property (@ (environment "env")))
                  (path (@ (id "classpath"))
-                       (pathelement (@ (location "${env.CLASSPATH}"))))
+                       (pathelement (@ (path "${env.CLASSPATH}"))))
 
                  (target (@ (name "manifest"))
                          (mkdir (@ (dir "${manifest.dir}")))
@@ -79,14 +80,26 @@
                          (mkdir (@ (dir "${classes.dir}")))
                          (javac (@ (includeantruntime "false")
                                    (srcdir ,source-dir)
-                                   (destdir "${classes.dir}")
+                                   (destdir "${classes.dir}"))
-                                   (classpath (@ (refid "classpath"))))))
+                          ,(if use-java-modules?
+                             `((modulepath (@ (refid "classpath"))))
+                             '())
+                          (classpath (@ (refid "classpath")))))
 
                  (target (@ (name "compile-tests"))
                          (mkdir (@ (dir "${test.classes.dir}")))
                          (javac (@ (includeantruntime "false")
                                    (srcdir ,test-dir)
                                    (destdir "${test.classes.dir}"))
+                           ,(if use-java-modules?
+                                `((classpath
+                                    (pathelement
+                                      (@ (path "${env.CLASSPATH}")))
+                                    (pathelement
+                                      (@ (location "${classes.dir}")))
+                                    (pathelement
+                                      (@ (location "${test.classes.dir}")))))
+                                '())
                            (classpath
                             (pathelement (@ (path "${env.CLASSPATH}")))
                             (pathelement (@ (location "${classes.dir}")))
@@ -156,13 +169,15 @@ to the default GNU unpack strategy."
                     (source-dir "src")
                     (test-dir "src/test")
                     (main-class #f)
+                    (use-java-modules? #f)
                     (test-include '("**/*Test.java"))
                     (test-exclude '("**/Abstract*.java")) #:allow-other-keys)
   (when jar-name
     (default-build.xml jar-name
                        (string-append (assoc-ref outputs "out")
                                       "/share/java")
-                       source-dir test-dir main-class test-include test-exclude))
+                       source-dir test-dir main-class use-java-modules?
+                       test-include test-exclude))
   (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
   (setenv "CLASSPATH" (generate-classpath inputs))
   #t)

guix/build/git.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2016, 2019, 2023 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -33,10 +34,13 @@
 ;;; Code:
 
 (define* (git-fetch url commit directory
-                    #:key (git-command "git") recursive?)
+                    #:key (git-command "git")
+                    lfs? recursive?)
   "Fetch COMMIT from URL into DIRECTORY.  COMMIT must be a valid Git commit
-identifier.  When RECURSIVE? is true, all the sub-modules of URL are fetched,
+identifier.  When LFS? is true, configure Git to also fetch Large File
-recursively.  Return #t on success, #f otherwise."
+Storage (LFS) files; it assumes that the @code{git-lfs} extension is available
+in the environment.  When RECURSIVE? is true, all the sub-modules of URL are
+fetched, recursively.  Return #t on success, #f otherwise."
 
   ;; Disable TLS certificate verification.  The hash of the checkout is known
   ;; in advance anyway.
@@ -57,6 +61,11 @@ recursively.  Return #t on success, #f otherwise."
     (with-directory-excursion directory
       (invoke git-command "init" "--initial-branch=main")
       (invoke git-command "remote" "add" "origin" url)
+
+      (when lfs?
+        (setenv "HOME" "/tmp")
+        (invoke git-command "lfs" "install"))
+
       (if (zero? (system* git-command "fetch" "--depth" "1" "origin" commit))
           (invoke git-command "checkout" "FETCH_HEAD")
           (begin
@@ -81,11 +90,13 @@ recursively.  Return #t on success, #f otherwise."
 
 
 (define* (git-fetch-with-fallback url commit directory
-                                  #:key (git-command "git") recursive?)
+                                  #:key (git-command "git")
+                                  lfs? recursive?)
   "Like 'git-fetch', fetch COMMIT from URL into DIRECTORY, but fall back to
 alternative methods when fetching from URL fails: attempt to download a nar,
 and if that also fails, download from the Software Heritage archive."
   (or (git-fetch url commit directory
+                 #:lfs? lfs?
                  #:recursive? recursive?
                  #:git-command git-command)
       (download-nar directory)

guix/build/guile-build-system.scm

@@ -28,6 +28,7 @@
   #:use-module (ice-9 format)
   #:use-module (guix build utils)
   #:export (target-guile-effective-version
+            target-guile-scm+go
             %standard-phases
             guile-build))
 
@@ -44,6 +45,16 @@ Return #false if it cannot be determined."
          (string? line)
          line)))
 
+(define* (target-guile-scm+go output #:optional guile)
+  "Return paths under `output' for scm and go files for effective version of
+GUILE or whichever `guile' is in $PATH.  Raises an error if they cannot be
+determined."
+  (let* ((version (or (target-guile-effective-version guile)
+                      (error "Cannot determine the effective target guile version.")))
+         (scm (string-append output "/share/guile/site/" version))
+         (go (string-append output "/lib/guile/" version "/site-ccache")))
+    (values scm go)))
+
 (define (file-sans-extension file)      ;TODO: factorize
   "Return the substring of FILE without its extension, if any."
   (let ((dot (string-rindex file #\.)))

guix/build/minetest-build-system.scm

@@ -126,7 +126,8 @@ If it is unknown, make an educated guess."
                    (/ total-old-size (expt 1024 2))
                    (/ total-new-size (expt 1024 2)))))))
 
-(define name-regexp (make-regexp "^name[ ]*=(.+)$"))
+(define name-regexp
+  (make-regexp "^name[[:space:]]*=[[:space:]]*([[:graph:]]+)[[:space:]]*$"))
 
 (define* (read-mod-name mod.conf #:optional not-found)
   "Read the name of a mod from MOD.CONF.  If MOD.CONF

guix/build/syscalls.scm

@@ -192,6 +192,7 @@
             terminal-window-size
             terminal-columns
             terminal-rows
+            terminal-string-width
             openpty
             login-tty
 
@@ -2336,6 +2337,20 @@ PORT, trying to guess a reasonable value if all else fails.  The result is
 always a positive integer."
   (terminal-dimension window-size-rows port (const 25)))
 
+(define terminal-string-width
+  (let ((mbstowcs (syscall->procedure int "mbstowcs" (list '* '* size_t)))
+        (wcswidth (syscall->procedure int "wcswidth" (list '* size_t))))
+    (lambda (str)
+      "Return the width of a string as it would be printed on the terminal.
+This procedure accounts for characters that have a different width than 1, such
+as CJK double-width characters."
+      (let ((wchar (make-bytevector (* (+ (string-length str) 1) 4))))
+        (mbstowcs (bytevector->pointer wchar)
+                  (string->pointer str)
+                  (string-length str))
+        (wcswidth (bytevector->pointer wchar)
+                  (string-length str))))))
+
 (define openpty
   (let ((proc (syscall->procedure int "openpty" '(* * * * *)
                                   #:library "libutil")))

guix/build/vim-build-system.scm

@@ -0,0 +1,119 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2022 Jonathan Scoresby <me@jonscoresby.com>
+;;; Copyright © 2023 Efraim Flashner <efraim@flashner.co.il>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (guix build vim-build-system)
+  #:use-module ((guix build copy-build-system)
+                #:prefix copy:)
+  #:use-module (guix build utils)
+  #:use-module (ice-9 match)
+  #:use-module (ice-9 ftw)
+  #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-26)
+  #:export (%standard-phases vim-build))
+
+;; Commentary:
+;;
+;; System for installing vim and neovim plugins.  It downloads
+;; the source and copies the appropriate files to vim and nvim
+;; packpaths.  It then generates helptags.
+;;
+;; Code:
+
+(define copy:install
+  (assoc-ref copy:%standard-phases 'install))
+
+(define vim-path
+  "/share/vim/vimfiles/pack/guix/")
+(define nvim-path
+  "/share/nvim/site/pack/guix/")
+
+(define* (install #:key plugin-name
+                  install-plan
+                  neovim?
+                  vim?
+                  mode
+                  outputs
+                  #:allow-other-keys)
+
+  (let* ((include-regexp '(".*\\/.*\\/.*"))
+         (exclude-regexp '("^scripts/.*"
+                           "tests?/.*" "^t/.*"
+                           "assets/.*"
+                           ".*\\/\\..*"))
+         (vim-install
+           (if vim?
+             `(("." ,(string-append vim-path mode "/" plugin-name "/")
+                #:include-regexp ,include-regexp
+                #:exclude-regexp ,exclude-regexp))
+             '()))
+         (neovim-install
+           (if neovim?
+             `(("." ,(string-append nvim-path mode "/" plugin-name "/")
+                #:include-regexp ,include-regexp
+                #:exclude-regexp ,exclude-regexp))
+             '())))
+    (copy:install #:outputs outputs
+                  #:install-plan (append vim-install
+                                         neovim-install
+                                         install-plan))))
+
+(define* (generate-helptags #:key plugin-name
+                            neovim?
+                            vim?
+                            mode
+                            outputs
+                            #:allow-other-keys)
+
+  (define (vim-generate-helptags output)
+    (invoke "vim" "--clean" "-en" "--cmd"
+            (string-append "helptags "
+                           output vim-path mode "/" plugin-name "/doc")
+            "--cmd" "q"))
+
+  (define (neovim-generate-helptags output)
+    (invoke "nvim" "--clean" "--headless" "-en" "--cmd"
+            (string-append "helptags "
+                           output nvim-path mode "/" plugin-name "/doc")
+            "--cmd" "q"))
+
+  (when (scandir "./doc")
+    (let ((out (assoc-ref outputs "out")))
+      (when vim?
+            (vim-generate-helptags out))
+      (when neovim?
+            (neovim-generate-helptags out)))))
+
+(define %standard-phases
+  ;; Everything is as with the Copy Build System except for
+  ;; the addition of the generate-helptags phase and a few
+  ;; custom actions are added to the install phase
+  (modify-phases copy:%standard-phases
+    (replace 'install install)
+    (add-after 'install 'generate-helptags generate-helptags)))
+
+(define* (vim-build #:key inputs
+                    (phases %standard-phases)
+                    #:allow-other-keys #:rest args)
+  "Build the given package, applying all of PHASES in order."
+  (apply copy:copy-build
+         #:inputs inputs
+         #:phases phases
+         args))
+
+;;; vim-build-system.scm ends here

guix/download.scm

@@ -129,7 +129,7 @@
        "ftp://ftp.hu.netfilter.org/"
        "ftp://www.lt.netfilter.org/pub/")
       (kernel.org
-       "http://linux-kernel.uio.no/pub/"
+       "https://cdn.kernel.org/pub/"
        "http://ftp.be.debian.org/pub/"
        "https://mirrors.edge.kernel.org/pub/"
        "ftp://ftp.funet.fi/pub/mirrors/ftp.kernel.org/pub/")

guix/git-download.scm

@@ -4,6 +4,7 @@
 ;;; Copyright © 2017 Christopher Baines <mail@cbaines.net>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2023 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -54,6 +55,7 @@
             git-reference-recursive?
 
             git-fetch
+            git-fetch/lfs
             git-version
             git-file-name
             git-predicate))
@@ -79,30 +81,36 @@
   (let ((distro (resolve-interface '(gnu packages version-control))))
     (module-ref distro 'git-minimal)))
 
-(define* (git-fetch/in-band ref hash-algo hash
+(define (git-lfs-package)
+  "Return the default 'git-lfs' package."
+  (let ((distro (resolve-interface '(gnu packages version-control))))
+    (module-ref distro 'git-lfs)))
+
+(define* (git-fetch/in-band* ref hash-algo hash
                              #:optional name
                              #:key (system (%current-system))
                              (guile (default-guile))
-                            (git (git-package)))
+                             (git (git-package))
-  "Return a fixed-output derivation that performs a Git checkout of REF, using
+                             git-lfs)
-GIT and GUILE (thus, said derivation depends on GIT and GUILE).
+  "Shared implementation code for git-fetch/in-band & friends.  Refer to their
-
+respective documentation."
-This method is deprecated in favor of the \"builtin:git-download\" builder.
-It will be removed when versions of guix-daemon implementing
-\"builtin:git-download\" will be sufficiently widespread."
   (define inputs
-    `(("git" ,(or git (git-package)))
+    `(,(or git (git-package))
-
+      ,@(if git-lfs
-      ;; When doing 'git clone --recursive', we need sed, grep, etc. to be
+            (list git-lfs)
-      ;; available so that 'git submodule' works.
+            '())
       ,@(if (git-reference-recursive? ref)
-            (standard-packages)
+            ;; TODO: remove (standard-packages) after
+            ;; 48e528a26f9c019eeaccf5e3de3126aa02c98d3b is merged into master;
+            ;; currently when doing 'git clone --recursive', we need sed, grep,
+            ;; etc. to be available so that 'git submodule' works.
+            (map second (standard-packages))
 
             ;; The 'swh-download' procedure requires tar and gzip.
-            `(("gzip" ,(module-ref (resolve-interface '(gnu packages compression))
+            (list (module-ref (resolve-interface '(gnu packages compression))
-                                   'gzip))
+                              'gzip)
-              ("tar" ,(module-ref (resolve-interface '(gnu packages base))
+                  (module-ref (resolve-interface '(gnu packages base))
-                                  'tar))))))
+                              'tar)))))
 
   (define guile-json
     (module-ref (resolve-interface '(gnu packages guile)) 'guile-json-4))
@@ -134,6 +142,9 @@ It will be removed when versions of guix-daemon implementing
                           #:select (set-path-environment-variable))
                          (ice-9 match))
 
+            (define lfs?
+              (call-with-input-string (getenv "git lfs?") read))
+
             (define recursive?
               (call-with-input-string (getenv "git recursive?") read))
 
@@ -144,18 +155,17 @@ It will be removed when versions of guix-daemon implementing
                     #+(file-append glibc-locales "/lib/locale"))
             (setlocale LC_ALL "en_US.utf8")
 
-            ;; The 'git submodule' commands expects Coreutils, sed,
+            ;; The 'git submodule' commands expects Coreutils, sed, grep,
-            ;; grep, etc. to be in $PATH.
+            ;; etc. to be in $PATH.  This also ensures that git extensions are
-            (set-path-environment-variable "PATH" '("bin")
+            ;; found.
-                                           (match '#+inputs
+            (set-path-environment-variable "PATH" '("bin") '#+inputs)
-                                             (((names dirs outputs ...) ...)
-                                              dirs)))
 
             (setvbuf (current-output-port) 'line)
             (setvbuf (current-error-port) 'line)
 
             (git-fetch-with-fallback (getenv "git url") (getenv "git commit")
                                      #$output
+                                     #:lfs? lfs?
                                      #:recursive? recursive?
                                      #:git-command "git")))))
 
@@ -175,7 +185,8 @@ It will be removed when versions of guix-daemon implementing
                                          (git-reference-url ref))))
                         ("git commit" . ,(git-reference-commit ref))
                         ("git recursive?" . ,(object->string
-                                              (git-reference-recursive? ref))))
+                                              (git-reference-recursive? ref)))
+                        ("git lfs?" . ,(if git-lfs "#t" "#f")))
                       #:leaked-env-vars '("http_proxy" "https_proxy"
                                           "LC_ALL" "LC_MESSAGES" "LANG"
                                           "COLUMNS")
@@ -187,6 +198,36 @@ It will be removed when versions of guix-daemon implementing
                       #:recursive? #t
                       #:guile-for-build guile)))
 
+(define* (git-fetch/in-band ref hash-algo hash
+                             #:optional name
+                             #:key (system (%current-system))
+                             (guile (default-guile))
+                             (git (git-package)))
+  "Return a fixed-output derivation that performs a Git checkout of REF, using
+GIT and GUILE (thus, said derivation depends on GIT and GUILE).
+
+This method is deprecated in favor of the \"builtin:git-download\" builder.
+It will be removed when versions of guix-daemon implementing
+\"builtin:git-download\" will be sufficiently widespread."
+  (git-fetch/in-band* ref hash-algo hash name
+                      #:system system
+                      #:guile guile
+                      #:git git))
+
+(define* (git-fetch/lfs ref hash-algo hash
+                        #:optional name
+                        #:key (system (%current-system))
+                        (guile (default-guile))
+                        (git (git-package))
+                        (git-lfs (git-lfs-package)))
+  "Like git-fetch/in-band, but with support for the Git Large File
+Storage (LFS) extension."
+  (git-fetch/in-band* ref hash-algo hash name
+                      #:system system
+                      #:guile guile
+                      #:git git
+                      #:git-lfs git-lfs))
+
 (define* (git-fetch/built-in ref hash-algo hash
                              #:optional name
                              #:key (system (%current-system)))

guix/git.scm

@@ -33,6 +33,8 @@
   #:use-module (guix store)
   #:use-module (guix utils)
   #:use-module (guix records)
+  #:use-module ((guix build syscalls)
+                #:select (terminal-string-width))
   #:use-module (guix gexp)
   #:autoload   (guix git-download)
   (git-reference-url git-reference-commit git-reference-recursive?)
@@ -154,7 +156,7 @@ the 'SSL_CERT_FILE' and 'SSL_CERT_DIR' environment variables."
   ;; TODO: Both should be handled & exposed by the PROGRESS-BAR API instead.
   (define width
     (max (- (current-terminal-columns)
-            (string-length label) 7)
+            (terminal-string-width label) 7)
          3))
 
   (define grain

guix/inferior.scm

@@ -872,14 +872,17 @@ prefix, resolve it; and if 'commit' is unset, fetch CHANNEL's branch tip."
                                   (authenticate? #t)
                                   (cache-directory (%inferior-cache-directory))
                                   (ttl (* 3600 24 30))
-                                  validate-channels)
+                                  (reference-channels '())
+                                  (validate-channels (const #t)))
   "Return a directory containing a guix filetree defined by CHANNELS, a list of channels.
 The directory is a subdirectory of CACHE-DIRECTORY, where entries can be
 reclaimed after TTL seconds.  This procedure opens a new connection to the
 build daemon.  AUTHENTICATE? determines whether CHANNELS are authenticated.
-VALIDATE-CHANNELS, if specified, must be a one argument procedure accepting a
+
-list of channels that can be used to validate the channels; it should raise an
+VALIDATE-CHANNELS must be a four-argument procedure used to validate channel
-exception in case of problems."
+instances against REFERENCE-CHANNELS; it is passed as #:validate-pull to
+'latest-channel-instances' and should raise an exception in case a target
+channel commit is deemed \"invalid\"."
   (define commits
     ;; Since computing the instances of CHANNELS is I/O-intensive, use a
     ;; cheaper way to get the commit list of CHANNELS.  This limits overhead
@@ -927,14 +930,15 @@ exception in case of problems."
 
   (if (file-exists? cached)
       cached
-      (begin
-        (when (procedure? validate-channels)
-          (validate-channels channels))
       (run-with-store store
         (mlet* %store-monad ((instances
                               -> (latest-channel-instances store channels
                                                            #:authenticate?
-                                                             authenticate?))
+                                                           authenticate?
+                                                           #:current-channels
+                                                           reference-channels
+                                                           #:validate-pull
+                                                           validate-channels))
                              (profile
                               (channel-instances->derivation instances)))
           (mbegin %store-monad
@@ -950,7 +954,7 @@ exception in case of problems."
                   (return cached))
                 (mbegin %store-monad
                   (add-temp-root* (derivation->output-path profile))
-                    (return (derivation->output-path profile))))))))))
+                  (return (derivation->output-path profile)))))))))
 
 (define* (inferior-for-channels channels
                                 #:key