Merge branch 'master' into staging

Makefile.am

@@ -428,8 +428,6 @@ AUX_FILES =						\
   gnu/packages/aux-files/linux-libre/4.14-arm.conf	\
   gnu/packages/aux-files/linux-libre/4.14-i686.conf	\
   gnu/packages/aux-files/linux-libre/4.14-x86_64.conf	\
-  gnu/packages/aux-files/linux-libre/4.9-i686.conf	\
-  gnu/packages/aux-files/linux-libre/4.9-x86_64.conf	\
   gnu/packages/aux-files/pack-audit.c			\
   gnu/packages/aux-files/python/sanity-check.py		\
   gnu/packages/aux-files/python/sanity-check-next.py	\

doc/guix-cookbook.texi

@@ -21,7 +21,8 @@ Copyright @copyright{} 2020 Brice Waegeneire@*
 Copyright @copyright{} 2020 André Batista@*
 Copyright @copyright{} 2020 Christine Lemmer-Webber@*
 Copyright @copyright{} 2021 Joshua Branson@*
-Copyright @copyright{} 2022 Maxim Cournoyer*
+Copyright @copyright{} 2022 Maxim Cournoyer@*
+Copyright @copyright{} 2023 Ludovic Courtès
 
 Permission is granted to copy, distribute and/or modify this document
 under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -75,6 +76,7 @@ Weblate} (@pxref{Translating Guix,,, guix, GNU Guix reference manual}).
 * Containers::                  Isolated environments and nested systems
 * Advanced package management::  Power to the users!
 * Environment management::      Control environment
+* Installing Guix on a Cluster:: High-performance computing.
 
 * Acknowledgments::             Thanks!
 * GNU Free Documentation License::  The license of this document.
@@ -83,13 +85,9 @@ Weblate} (@pxref{Translating Guix,,, guix, GNU Guix reference manual}).
 @detailmenu
  --- The Detailed Node Listing ---
 
-Scheme tutorials
-
-* A Scheme Crash Course::       Learn the basics of Scheme
-
 Packaging
 
-* Packaging Tutorial::          Let's add a package to Guix!
+* Packaging Tutorial::         A tutorial on how to add packages to Guix.
 
 System Configuration
 
@@ -99,12 +97,33 @@ System Configuration
 * Using security keys::          How to use security keys with Guix System.
 * Connecting to Wireguard VPN::  Connecting to a Wireguard VPN.
 * Customizing a Window Manager:: Handle customization of a Window manager on Guix System.
-* Running Guix on a Linode Server:: Running Guix on a Linode Server.  Running Guix on a Linode Server
+* Running Guix on a Linode Server:: Running Guix on a Linode Server
 * Setting up a bind mount:: Setting up a bind mount in the file-systems definition.
 * Getting substitutes from Tor:: Configuring Guix daemon to get substitutes through Tor.
 * Setting up NGINX with Lua:: Configuring NGINX web-server to load Lua modules.
 * Music Server with Bluetooth Audio:: Headless music player with Bluetooth output.
 
+Containers
+
+* Guix Containers::            Perfectly isolated environments
+* Guix System Containers::     A system inside your system
+
+Advanced package management
+
+* Guix Profiles in Practice::     Strategies for multiple profiles and manifests.
+
+Environment management
+
+* Guix environment via direnv:: Setup Guix environment with direnv
+
+Installing Guix on a Cluster
+
+* Setting Up a Head Node::      The node that runs the daemon.
+* Setting Up Compute Nodes::    Client nodes.
+* Cluster Network Access::      Dealing with network access restrictions.
+* Cluster Disk Usage::          Disk usage considerations.
+* Cluster Security Considerations::  Keeping the cluster secure.
+
 @end detailmenu
 @end menu
 
@@ -3635,6 +3654,380 @@ will have predefined environment variables and procedures.
 
 Run @command{direnv allow} to setup the environment for the first time.
 
+
+@c *********************************************************************
+@node Installing Guix on a Cluster
+@chapter Installing Guix on a Cluster
+
+@cindex cluster installation
+@cindex high-performance computing, HPC
+@cindex HPC, high-performance computing
+Guix is appealing to scientists and @acronym{HPC, high-performance
+computing} practitioners: it makes it easy to deploy potentially complex
+software stacks, and it lets you do so in a reproducible fashion---you
+can redeploy the exact same software on different machines and at
+different points in time.
+
+In this chapter we look at how a cluster sysadmin can install Guix for
+system-wide use, such that it can be used on all the cluster nodes, and
+discuss the various tradeoffs@footnote{This chapter is adapted from a
+@uref{https://hpc.guix.info/blog/2017/11/installing-guix-on-a-cluster/,
+blog post published on the Guix-HPC web site in 2017}.}.
+
+@quotation Note
+Here we assume that the cluster is running a GNU/Linux distro other than
+Guix System and that we are going to install Guix on top of it.
+@end quotation
+
+@menu
+* Setting Up a Head Node::      The node that runs the daemon.
+* Setting Up Compute Nodes::    Client nodes.
+* Cluster Network Access::      Dealing with network access restrictions.
+* Cluster Disk Usage::          Disk usage considerations.
+* Cluster Security Considerations::  Keeping the cluster secure.
+@end menu
+
+@node Setting Up a Head Node
+@section Setting Up a Head Node
+
+The recommended approach is to set up one @emph{head node} running
+@command{guix-daemon} and exporting @file{/gnu/store} over NFS to
+compute nodes.
+
+Remember that @command{guix-daemon} is responsible for spawning build
+processes and downloads on behalf of clients (@pxref{Invoking
+guix-daemon,,, guix, GNU Guix Reference Manual}), and more generally
+accessing @file{/gnu/store}, which contains all the package binaries
+built by all the users (@pxref{The Store,,, guix, GNU Guix Reference
+Manual}).  ``Client'' here refers to all the Guix commands that users
+see, such as @code{guix install}.  On a cluster, these commands may be
+running on the compute nodes and we'll want them to talk to the head
+node's @code{guix-daemon} instance.
+
+To begin with, the head node can be installed following the usual binary
+installation instructions (@pxref{Binary Installation,,, guix, GNU Guix
+Reference Manual}).  Thanks to the installation script, this should be
+quick.  Once installation is complete, we need to make some adjustments.
+
+Since we want @code{guix-daemon} to be reachable not just from the head
+node but also from the compute nodes, we need to arrange so that it
+listens for connections over TCP/IP.  To do that, we'll edit the systemd
+startup file for @command{guix-daemon},
+@file{/etc/systemd/system/guix-daemon.service}, and add a
+@code{--listen} argument to the @code{ExecStart} line so that it looks
+something like this:
+
+@example
+ExecStart=/var/guix/profiles/per-user/root/current-guix/bin/guix-daemon --build-users-group=guixbuild --listen=/var/guix/daemon-socket/socket --listen=0.0.0.0
+@end example
+
+For these changes to take effect, the service needs to be restarted:
+
+@example
+systemctl daemon-reload
+systemctl restart guix-daemon
+@end example
+
+@quotation Note
+The @code{--listen=0.0.0.0} bit means that @code{guix-daemon} will
+process @emph{all} incoming TCP connections on port 44146
+(@pxref{Invoking guix-daemon,,, guix, GNU Guix Reference Manual}). This
+is usually fine in a cluster setup where the head node is reachable
+exclusively from the cluster's local area network---you don't want that
+to be exposed to the Internet!
+@end quotation
+
+The next step is to define our NFS exports in
+@uref{https://linux.die.net/man/5/exports,@file{/etc/exports}} by adding
+something along these lines:
+
+@example
+/gnu/store    *(ro)
+/var/guix     *(rw, async)
+/var/log/guix *(ro)
+@end example
+
+The @file{/gnu/store} directory can be exported read-only since only
+@command{guix-daemon} on the master node will ever modify it.
+@file{/var/guix} contains @emph{user profiles} as managed by @code{guix
+package}; thus, to allow users to install packages with @code{guix
+package}, this must be read-write.
+
+Users can create as many profiles as they like in addition to the
+default profile, @file{~/.guix-profile}.  For instance, @code{guix
+package -p ~/dev/python-dev -i python} installs Python in a profile
+reachable from the @code{~/dev/python-dev} symlink.  To make sure that
+this profile is protected from garbage collection---i.e., that Python
+will not be removed from @file{/gnu/store} while this profile exists---,
+@emph{home directories should be mounted on the head node} as well so
+that @code{guix-daemon} knows about these non-standard profiles and
+avoids collecting software they refer to.
+
+It may be a good idea to periodically remove unused bits from
+@file{/gnu/store} by running @command{guix gc} (@pxref{Invoking guix
+gc,,, guix, GNU Guix Reference Manual}).  This can be done by adding a
+crontab entry on the head node:
+
+@example
+root@@master# crontab -e
+@end example
+
+@noindent
+... with something like this:
+
+@example
+# Every day at 5AM, run the garbage collector to make sure
+# at least 10 GB are free on /gnu/store.
+0 5 * * 1  /usr/local/bin/guix gc -F10G
+@end example
+
+We're done with the head node! Let's look at compute nodes now.
+
+@node Setting Up Compute Nodes
+@section Setting Up Compute Nodes
+
+First of all, we need compute nodes to mount those NFS directories that
+the head node exports.  This can be done by adding the following lines
+to @uref{https://linux.die.net/man/5/fstab,@file{/etc/fstab}}:
+
+@example
+@var{head-node}:/gnu/store    /gnu/store    nfs  defaults,_netdev,vers=3 0 0
+@var{head-node}:/var/guix     /var/guix     nfs  defaults,_netdev,vers=3 0 0
+@var{head-node}:/var/log/guix /var/log/guix nfs  defaults,_netdev,vers=3 0 0
+@end example
+
+@noindent
+... where @var{head-node} is the name or IP address of your head node.
+From there on, assuming the mount points exist, you should be able to
+mount each of these on the compute nodes.
+
+Next, we need to provide a default @command{guix} command that users can
+run when they first connect to the cluster (eventually they will invoke
+@command{guix pull}, which will provide them with their ``own''
+@command{guix} command).  Similar to what the binary installation script
+did on the head node, we'll store that in @file{/usr/local/bin}:
+
+@example
+mkdir -p /usr/local/bin
+ln -s /var/guix/profiles/per-user/root/current-guix/bin/guix \
+      /usr/local/bin/guix
+@end example
+
+We then need to tell @code{guix} to talk to the daemon running on our
+master node, by adding these lines to @code{/etc/profile}:
+
+@example
+GUIX_DAEMON_SOCKET="guix://@var{head-node}"
+export GUIX_DAEMON_SOCKET
+@end example
+
+To avoid warnings and make sure @code{guix} uses the right locale, we
+need to tell it to use locale data provided by Guix (@pxref{Application
+Setup,,, guix, GNU Guix Reference Manual}):
+
+@example
+GUIX_LOCPATH=/var/guix/profiles/per-user/root/guix-profile/lib/locale
+export GUIX_LOCPATH
+
+# Here we must use a valid locale name.  Try "ls $GUIX_LOCPATH/*"
+# to see what names can be used.
+LC_ALL=fr_FR.utf8
+export LC_ALL
+@end example
+
+For convenience, @code{guix package} automatically generates
+@file{~/.guix-profile/etc/profile}, which defines all the environment
+variables necessary to use the packages---@code{PATH},
+@code{C_INCLUDE_PATH}, @code{PYTHONPATH}, etc.  Thus it's a good idea to
+source it from @code{/etc/profile}:
+
+@example
+GUIX_PROFILE="$HOME/.guix-profile"
+if [ -f "$GUIX_PROFILE/etc/profile" ]; then
+  . "$GUIX_PROFILE/etc/profile"
+fi
+@end example
+
+Last but not least, Guix provides command-line completion notably for
+Bash and zsh.  In @code{/etc/bashrc}, consider adding this line:
+
+@verbatim
+. /var/guix/profiles/per-user/root/current-guix/etc/bash_completion.d/guix
+@end verbatim
+
+Voilà!
+
+You can check that everything's in place by logging in on a compute node
+and running:
+
+@example
+guix install hello
+@end example
+
+The daemon on the head node should download pre-built binaries on your
+behalf and unpack them in @file{/gnu/store}, and @command{guix install}
+should create @file{~/.guix-profile} containing the
+@file{~/.guix-profile/bin/hello} command.
+
+@node Cluster Network Access
+@section Network Access
+
+Guix requires network access to download source code and pre-built
+binaries.  The good news is that only the head node needs that since
+compute nodes simply delegate to it.
+
+It is customary for cluster nodes to have access at best to a
+@emph{white list} of hosts.  Our head node needs at least
+@code{ci.guix.gnu.org} in this white list since this is where it gets
+pre-built binaries from by default, for all the packages that are in
+Guix proper.
+
+Incidentally, @code{ci.guix.gnu.org} also serves as a
+@emph{content-addressed mirror} of the source code of those packages.
+Consequently, it is sufficient to have @emph{only}
+@code{ci.guix.gnu.org} in that white list.
+
+Software packages maintained in a separate repository such as one of the
+various @uref{https://hpc.guix.info/channels, HPC channels} are of
+course unavailable from @code{ci.guix.gnu.org}.  For these packages, you
+may want to extend the white list such that source and pre-built
+binaries (assuming this-party servers provide binaries for these
+packages) can be downloaded.  As a last resort, users can always
+download source on their workstation and add it to the cluster's
+@file{/gnu/store}, like this:
+
+@verbatim
+GUIX_DAEMON_SOCKET=ssh://compute-node.example.org \
+  guix download http://starpu.gforge.inria.fr/files/starpu-1.2.3/starpu-1.2.3.tar.gz
+@end verbatim
+
+The above command downloads @code{starpu-1.2.3.tar.gz} @emph{and} sends
+it to the cluster's @code{guix-daemon} instance over SSH.
+
+Air-gapped clusters require more work.  At the moment, our suggestion
+would be to download all the necessary source code on a workstation
+running Guix.  For instance, using the @option{--sources} option of
+@command{guix build} (@pxref{Invoking guix build,,, guix, GNU Guix
+Reference Manual}), the example below downloads all the source code the
+@code{openmpi} package depends on:
+
+@example
+$ guix build --sources=transitive openmpi
+
+@dots{}
+
+/gnu/store/xc17sm60fb8nxadc4qy0c7rqph499z8s-openmpi-1.10.7.tar.bz2
+/gnu/store/s67jx92lpipy2nfj5cz818xv430n4b7w-gcc-5.4.0.tar.xz
+/gnu/store/npw9qh8a46lrxiwh9xwk0wpi3jlzmjnh-gmp-6.0.0a.tar.xz
+/gnu/store/hcz0f4wkdbsvsdky3c0vdvcawhdkyldb-mpfr-3.1.5.tar.xz
+/gnu/store/y9akh452n3p4w2v631nj0injx7y0d68x-mpc-1.0.3.tar.gz
+/gnu/store/6g5c35q8avfnzs3v14dzl54cmrvddjm2-glibc-2.25.tar.xz
+/gnu/store/p9k48dk3dvvk7gads7fk30xc2pxsd66z-hwloc-1.11.8.tar.bz2
+/gnu/store/cry9lqidwfrfmgl0x389cs3syr15p13q-gcc-5.4.0.tar.xz
+/gnu/store/7ak0v3rzpqm2c5q1mp3v7cj0rxz0qakf-libfabric-1.4.1.tar.bz2
+/gnu/store/vh8syjrsilnbfcf582qhmvpg1v3rampf-rdma-core-14.tar.gz
+…
+@end example
+
+(In case you're wondering, that's more than 320@ MiB of
+@emph{compressed} source code.)
+
+We can then make a big archive containing all of this (@pxref{Invoking
+guix archive,,, guix, GNU Guix Reference Manual}):
+
+@verbatim
+$ guix archive --export \
+    `guix build --sources=transitive openmpi` \
+    > openmpi-source-code.nar
+@end verbatim
+
+@dots{} and we can eventually transfer that archive to the cluster on
+removable storage and unpack it there:
+
+@verbatim
+$ guix archive --import < openmpi-source-code.nar
+@end verbatim
+
+This process has to be repeated every time new source code needs to be
+brought to the cluster.
+
+As we write this, the research institutes involved in Guix-HPC do not
+have air-gapped clusters though. If you have experience with such
+setups, we would like to hear feedback and suggestions.
+
+@node Cluster Disk Usage
+@section Disk Usage
+
+@cindex disk usage, on a cluster
+A common concern of sysadmins' is whether this is all going to eat a lot
+of disk space.  If anything, if something is going to exhaust disk
+space, it's going to be scientific data sets rather than compiled
+software---that's our experience with almost ten years of Guix usage on
+HPC clusters.  Nevertheless, it's worth taking a look at how Guix
+contributes to disk usage.
+
+First, having several versions or variants of a given package in
+@file{/gnu/store} does not necessarily cost much, because
+@command{guix-daemon} implements deduplication of identical files, and
+package variants are likely to have a number of common files.
+
+As mentioned above, we recommend having a cron job to run @code{guix gc}
+periodically, which removes @emph{unused} software from
+@file{/gnu/store}. However, there's always a possibility that users will
+keep lots of software in their profiles, or lots of old generations of
+their profiles, which is ``live'' and cannot be deleted from the
+viewpoint of @command{guix gc}.
+
+The solution to this is for users to regularly remove old generations of
+their profile. For instance, the following command removes generations
+that are more than two-month old:
+
+@example
+guix package --delete-generations=2m
+@end example
+
+Likewise, it's a good idea to invite users to regularly upgrade their
+profile, which can reduce the number of variants of a given piece of
+software stored in @file{/gnu/store}:
+
+@example
+guix pull
+guix upgrade
+@end example
+
+As a last resort, it is always possible for sysadmins to do some of this
+on behalf of their users. Nevertheless, one of the strengths of Guix is
+the freedom and control users get on their software environment, so we
+strongly recommend leaving users in control.
+
+@node Cluster Security Considerations
+@section Security Considerations
+
+@cindex security, on a cluster
+On an HPC cluster, Guix is typically used to manage scientific software.
+Security-critical software such as the operating system kernel and
+system services such as @code{sshd} and the batch scheduler remain under
+control of sysadmins.
+
+The Guix project has a good track record delivering security updates in
+a timely fashion (@pxref{Security Updates,,, guix, GNU Guix Reference
+Manual}).  To get security updates, users have to run @code{guix pull &&
+guix upgrade}.
+
+Because Guix uniquely identifies software variants, it is easy to see if
+a vulnerable piece of software is in use. For instance, to check whether
+the glibc@ 2.25 variant without the mitigation patch against
+``@uref{https://www.qualys.com/2017/06/19/stack-clash/stack-clash.txt,Stack
+Clash}'', one can check whether user profiles refer to it at all:
+
+@example
+guix gc --referrers /gnu/store/…-glibc-2.25
+@end example
+
+This will report whether profiles exist that refer to this specific
+glibc variant.
+
+
 @c *********************************************************************
 @node Acknowledgments
 @chapter Acknowledgments
@@ -3656,8 +4049,10 @@ information on these fine people.  The @file{THANKS} file lists people
 who have helped by reporting bugs, taking care of the infrastructure,
 providing artwork and themes, making suggestions, and more---thank you!
 
-This document includes adapted sections from articles that have previously
+This document includes adapted sections from articles that have
-been published on the Guix blog at @uref{https://guix.gnu.org/blog}.
+previously been published on the Guix blog at
+@uref{https://guix.gnu.org/blog} and on the Guix-HPC blog at
+@uref{https://hpc.guix.info/blog}.
 
 
 @c *********************************************************************

doc/guix.texi

@@ -18482,6 +18482,10 @@ herd set-http-proxy guix-daemon
 @item @code{tmpdir} (default: @code{#f})
 A directory path where the @command{guix-daemon} will perform builds.
 
+@item @code{environment} (default: @code{'()})
+Environment variables to be set before starting the daemon, as a list of
+@code{key=value} strings.
+
 @end table
 @end deftp
 

etc/news.scm

@@ -5,7 +5,7 @@
 ;; Copyright © 2019, 2020 Miguel Ángel Arruga Vivas <rosen644835@gmail.com>
 ;; Copyright © 2019, 2020 Konrad Hinsen <konrad.hinsen@fastmail.net>
 ;; Copyright © 2019, 2020, 2021 Julien Lepiller <julien@lepiller.eu>
-;; Copyright © 2019–2022 Florian Pelz <pelzflorian@pelzflorian.de>
+;; Copyright © 2019–2023 Florian Pelz <pelzflorian@pelzflorian.de>
 ;; Copyright © 2020, 2022 Marius Bakke <marius@gnu.org>
 ;; Copyright © 2020, 2021 Mathieu Othacehe <m.othacehe@gmail.com>
 ;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
@@ -26,6 +26,18 @@
 (channel-news
  (version 0)
 
+ (entry (commit "064c5b7e450f9f6d55cfcd0ec2bc9e96ee0b2958")
+        (title
+          (en "Linux-libre 4.9 removed due to end of upstream support")
+          (de "Linux-libre 4.9 wurde entfernt"))
+        (body
+          (en "The linux-libre 4.9 kernel series has reach the end of its life,
+and is no longer supported upstream.  For this reason, it has been removed from
+GNU Guix.")
+          (de "Vom Kernel @code{linux-libre} wird die 4.9-Versionsreihe keine
+Unterstützung von dessen Anbieter mehr erfahren („end of life“).  Daher ist es
+aus GNU Guix entfernt worden.")))
+
  (entry (commit "dfc6957a5af7d179d4618eb19d4f555c519bc6f2")
         (title
          (en "New @code{customize-linux} procedure")

gnu/home/services.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2021 Andrew Tropin <andrew@trop.in>
+;;; Copyright © 2021-2023 Andrew Tropin <andrew@trop.in>
 ;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz>
 ;;; Copyright © 2022-2023 Ludovic Courtès <ludo@gnu.org>
 ;;;
@@ -192,7 +192,7 @@ ensures variable values are properly quoted."
               (list->string (string-fold-right
                              (lambda (chr lst)
                                (if (memq chr quoted-chars)
-                                   (append (list chr #\\) lst)
+                                   (append (list #\\ chr) lst)
                                    (cons chr lst)))
                              '()
                              value))))
@@ -212,7 +212,9 @@ ensures variable values are properly quoted."
                   "")
                  ((key . #t)
                   #~(string-append "export " #$key "\n"))
-                 ((key . (? string? value))
+                 ((key . (or (? string? value)
+                             (? file-like? value)
+                             (? gexp? value)))
                   #~(string-append "export " #$key "="
                                    (shell-double-quote #$value)
                                    "\n"))

gnu/local.mk

@@ -338,9 +338,11 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/iso-codes.scm			\
   %D%/packages/jami.scm				\
   %D%/packages/java.scm				\
+  %D%/packages/java-bootstrap.scm		\
   %D%/packages/java-compression.scm		\
   %D%/packages/java-graphics.scm		\
   %D%/packages/java-maths.scm			\
+  %D%/packages/java-xml.scm			\
   %D%/packages/javascript.scm			\
   %D%/packages/jemalloc.scm			\
   %D%/packages/jrnl.scm				\
@@ -1713,6 +1715,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-3-fix-tests.patch			\
   %D%/packages/patches/python-3-hurd-configure.patch		\
   %D%/packages/patches/python-3-no-static-lib.patch		\
+  %D%/packages/patches/python-afdko-suppress-copyright-test.patch	\
   %D%/packages/patches/python-aionotify-0.2.0-py3.8.patch	\
   %D%/packages/patches/python-argcomplete-1.11.1-fish31.patch	\
   %D%/packages/patches/python-cross-compile.patch		\

gnu/packages/axoloti.scm

@@ -33,11 +33,11 @@
   #:use-module (gnu packages flashing-tools)
   #:use-module (gnu packages java)
   #:use-module (gnu packages java-graphics)
+  #:use-module (gnu packages java-xml)
   #:use-module (gnu packages libusb)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages textutils)
-  #:use-module (gnu packages version-control)
+  #:use-module (gnu packages version-control))
-  #:use-module (gnu packages xml))
 
 ;; XXX The patch does not apply to libusb 1.0.24.
 ;; See https://github.com/axoloti/axoloti/issues/464

gnu/packages/batik.scm

@@ -27,8 +27,8 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages java)
-  #:use-module (gnu packages textutils)
+  #:use-module (gnu packages java-xml)
-  #:use-module (gnu packages xml))
+  #:use-module (gnu packages textutils))
 
 (define-public java-w3c-smil-3.0
   (package

gnu/packages/bioconductor.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015-2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
@@ -4997,13 +4997,13 @@ only one command.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.32.4")
+    (version "1.32.5")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "1m4i27zx3ajwygwp38lrxf36rs575dkaxxc6jawpj1kzn7whi5ym"))))
+                "1yd6ln9cl3dcvfziar52fkvqi2lzm31l7j21r1rwl1mpkz0xapir"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -5118,13 +5118,13 @@ effort and encourages consistency.")
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
-    (version "1.66.1")
+    (version "1.66.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome" version))
               (sha256
                (base32
-                "1gzpvajw5n3qmym3312qaks450sq3w456kj4gqwaabgpjxbq7frm"))))
+                "0p75c52sw464bdqz7dyda9h8k2wsxdpdxxhya5awh977xaly90pf"))))
     (properties
      `((upstream-name . "BSgenome")))
     (build-system r-build-system)
@@ -5811,13 +5811,13 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.34.4")
+    (version "1.34.6")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "1nskqmlar85zg96c1fbacl7dqg6r0gl814rc7yh482y4wgmwyg0r"))))
+                "123kp69fmy5pbqh0j6qxdkvkm4g9pdwzms01i8qnix3m1b9j597w"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
@@ -6483,14 +6483,14 @@ in SNV base substitution data.")
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.24.0")
+    (version "2.24.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "16apm4qn7sbv06pk2i8k5z7qgkv0yq0h8ri32vikdplqxxh7h0cz"))))
+         "0jdq41rhn9qyhxfihvrgim76fzdrycc02wjsjdrff42gmray49w7"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9916,14 +9916,14 @@ multiplication and calculation of row/column sums or means.")
 (define-public r-batchelor
   (package
     (name "r-batchelor")
-    (version "1.14.0")
+    (version "1.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "batchelor" version))
        (sha256
         (base32
-         "1cdpq8zfn718qmsqjp79siddh3kzag4a90p276v261xbjvrxavjv"))))
+         "1yj84ba6px14hbqg8526527vfcxmzvmly34f7hba4vybdm1jscfm"))))
     (properties `((upstream-name . "batchelor")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13629,38 +13629,31 @@ for other R packages to compile and link against.")
 (define-public r-flowworkspace
   (package
     (name "r-flowworkspace")
-    (version "4.10.0")
+    (version "4.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowWorkspace" version))
        (sha256
         (base32
-         "07w2pnnzmivfc621c8pvndqrn1k245cwjrb0nnk2i85i3si4j9c3"))))
+         "0jmbfclkfm0n2mshk94906kivii7awlskf7l7ydn8ki8wrpzxqg4"))))
     (properties `((upstream-name . "flowWorkspace")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-aws-s3
+     (list r-bh
-           r-aws-signature
-           r-bh
            r-biobase
            r-biocgenerics
+           r-cpp11
            r-cytolib
            r-data-table
            r-delayedarray
-           r-digest
            r-dplyr
            r-flowcore
            r-ggplot2
            r-graph
-           r-lattice
-           r-latticeextra
            r-matrixstats
            r-ncdfflow
            r-rbgl
-           r-rcpp
-           r-rcpparmadillo
-           r-rcppparallel
            r-rgraphviz
            r-rhdf5lib
            r-rprotobuflib
@@ -14646,14 +14639,14 @@ arrays based on fast wavelet-based functional models.")
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.28.0")
+    (version "1.28.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "1mn91r0yrhz08m3vs2h3i35rcbxyc7sdfknmk6vcw1z75znjsnpl"))))
+         "0ypw3ckaf4qll83rl2bjzfc7g2m4v0n2mq645ppyfga8wv8kwssy"))))
     (properties
      `((upstream-name . "variancePartition")))
     (build-system r-build-system)
@@ -14674,6 +14667,7 @@ arrays based on fast wavelet-based functional models.")
            r-pbkrtest
            r-progress
            r-rdpack
+           r-remacor
            r-reshape2
            r-rhpcblasctl
            r-rlang
@@ -15614,13 +15608,13 @@ functionality.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.66.1")
+    (version "1.66.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "1xplkzm29v6aysfhb6kf2nnmvc37jmcvv6vsgbx8z8qccn96jk02"))))
+                "0fdxlixwf4d3p1prq37cgfvaiym44h2yd4bym6wp4dl8h648v99y"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -15860,14 +15854,14 @@ analytics on packages.")
 (define-public r-biocset
   (package
     (name "r-biocset")
-    (version "1.12.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSet" version))
        (sha256
         (base32
-         "197cy5gdlvac7jqwb4dm4dbqfms2nvc3paqs75nsg9mpp1h5z8l8"))))
+         "1cqp5m6yic5vsp8k05r50sx2cmi9cwzxfmlswcjw28nascq3gpv0"))))
     (properties `((upstream-name . "BiocSet")))
     (build-system r-build-system)
     (propagated-inputs

gnu/packages/bioinformatics.scm

@@ -110,6 +110,7 @@
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages java)
   #:use-module (gnu packages java-compression)
+  #:use-module (gnu packages java-xml)
   #:use-module (gnu packages jemalloc)
   #:use-module (gnu packages jupyter)
   #:use-module (gnu packages libffi)
@@ -7688,6 +7689,38 @@ sequence.")
     (supported-systems '("i686-linux" "x86_64-linux"))
     (license license:bsd-3)))
 
+(define-public r-gg3d
+  (let ((commit "ffdd837d30c1671cd0895db94bdd7b1594dbfcb0")
+        (revision "1"))
+    (package
+      (name "r-gg3d")
+      (version (git-version "0.0.0.9000" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/AckerDWM/gg3D")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0vz5laj5vz9m1jzb7h7q9f37zjmxwhylhaidlsg61r57wpxvjr3p"))))
+      (properties `((upstream-name . "gg3D")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-dplyr
+             r-ggplot2
+             r-magrittr
+             r-plot3d
+             r-plyr
+             r-scales))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/AckerDWM/gg3D")
+      (synopsis "3D perspective plots for ggplot2")
+      (description
+       "This package adds 3D perspective plotting of points, paths, and line,
+3D perspective axes, 3D perspective annotations, and wireframe plots.")
+      (license license:gpl3+))))
+
 (define-public r-gutils
   (let ((commit "10e36c7b580aacb2d952140a3fdd82418aaddea6")
         (revision "1"))

gnu/packages/code.scm

@@ -12,7 +12,7 @@
 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2019 Hartmut Goebel <h.goebel@goebel-consult.de>
 ;;; Copyright © 2020, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
-;;; Copyright © 2020, 2021 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2020, 2021, 2023 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2020 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2021 lu hui <luhuins@163.com>
 ;;; Copyright © 2021, 2022 Foo Chuan Wei <chuanwei.foo@hotmail.com>
@@ -58,6 +58,7 @@
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages golang)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages llvm)
   #:use-module (gnu packages linux)
@@ -80,6 +81,44 @@
 
 ;;; Tools to deal with source code: metrics, cross-references, etc.
 
+(define-public automatic-component-toolkit
+  (package
+    (name "automatic-component-toolkit")
+    (version "1.6.0")
+    (home-page "https://github.com/Autodesk/AutomaticComponentToolkit")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference (url home-page)
+                                  (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1r0sbw82cf9dbcj3vgnbd4sc1lklzvijic2z5wgkvs21azcm0yzh"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list #:tests? #false              ;no tests
+           #:phases
+           #~(modify-phases %standard-phases
+               (delete 'configure)
+               (replace 'build
+                 (lambda _
+                   (setenv "HOME" "/tmp")
+                   (invoke "bash" "Build/build.sh")))
+               (replace 'install
+                 (lambda _
+                   (let ((bin (string-append #$output "/bin")))
+                     (mkdir-p bin)
+                     (copy-file "act.linux"
+                                (string-append #$output "/bin/act"))))))))
+    (native-inputs (list go))
+    (synopsis "Automatically generate software components")
+    (description
+     "The Automatic Component Toolkit (@dfn{ACT}) is a code generator that
+takes an instance of an Interface Description Language (@dfn{IDL}) file and
+generates a thin C89-API, implementation stubs, and language bindings of your
+desired software component.")
+    (license license:bsd-2)))
+
 (define-public cflow
   (package
     (name "cflow")

gnu/packages/cran.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015-2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
@@ -259,13 +259,13 @@ automatically pruning objects to maintain the constraints.")
 (define-public r-collections
   (package
     (name "r-collections")
-    (version "0.3.6")
+    (version "0.3.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "collections" version))
        (sha256
-        (base32 "19y7nds67700zy6354s1i0aglgjylzv65psccz5x3ih8f48sakr3"))))
+        (base32 "003zlp5s2ilq3pq0imlp7p46jkfihwzg1hkkgk7378ikcbwnz17z"))))
     (properties `((upstream-name . "collections")))
     (build-system r-build-system)
     (home-page "https://github.com/randy3k/collections")
@@ -2802,6 +2802,38 @@ particularly easy to create complete web applications using httpuv alone.")
     ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
     (license license:gpl3+)))
 
+(define-public r-httr2
+  (package
+    (name "r-httr2")
+    (version "0.2.2")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "httr2" version))
+              (sha256
+               (base32
+                "1gzjsw3w7c3rsp3gb9rdbfmmnmd2sq09s3wza49730gp84jvc6jx"))))
+    (properties `((upstream-name . "httr2")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-cli
+           r-curl
+           r-glue
+           r-magrittr
+           r-openssl
+           r-r6
+           r-rappdirs
+           r-rlang
+           r-withr))
+    (native-inputs (list r-knitr))
+    (home-page "https://httr2.r-lib.org")
+    (synopsis "Perform HTTP requests and process the responses")
+    (description
+     "This package provides tools for creating and modifying HTTP requests,
+then performing them and processing the results.  @code{httr2} is a
+re-imagining of @code{httr} that uses a pipe-based interface and solves more
+of the problems that API wrapping packages face.")
+    (license license:expat)))
+
 (define-public r-jsonlite
   (package
     (name "r-jsonlite")
@@ -2894,13 +2926,13 @@ a list of p-values.")
 (define-public r-htmlwidgets
   (package
     (name "r-htmlwidgets")
-    (version "1.6.0")
+    (version "1.6.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "htmlwidgets" version))
               (sha256
                (base32
-                "06prjx6ic2bddaw50ksz6l7hsidkzwb69m85vzc0apxvwaygz0gh"))))
+                "0hqfjvfs3mcpqwim79vac1738k19ipr10zvdqrw5kzpwpsy3qls2"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-htmltools r-jsonlite
@@ -3081,14 +3113,14 @@ rules and utility functions for adaptive GH quadrature.")
 (define-public r-rstpm2
   (package
     (name "r-rstpm2")
-    (version "1.5.8")
+    (version "1.5.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rstpm2" version))
        (sha256
         (base32
-         "038qq5kar9f5ygd18aicwfqrr7fl37p0r9shgpc6wf2vmj564crn"))))
+         "1zl7z1l19s960mrhlzvpga07kzqfrhhq7qlkgln4wj0gcmhicyc6"))))
     (properties `((upstream-name . "rstpm2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6046,14 +6078,14 @@ these progress updates.")
 (define-public r-lava
   (package
     (name "r-lava")
-    (version "1.7.0")
+    (version "1.7.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lava" version))
        (sha256
         (base32
-         "092y5v5mp9a9mqia47fqh22br31crp8w5b4ks2y15242ydlxly1h"))))
+         "0r7panw0pb9xi10navih9796r08yc5l6j914pfn8wzlm4mfwr7bs"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-future-apply r-numderiv r-progressr r-squarem r-survival))
@@ -6163,14 +6195,14 @@ included in this package.")
 (define-public r-timedate
   (package
     (name "r-timedate")
-    (version "4021.107")
+    (version "4022.108")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "timeDate" version))
        (sha256
         (base32
-         "1i54a425r5hi08yl9rb2qh1nynh29ppv9b4h46cxyzn1ybqlr9sg"))))
+         "1vyfpz2ac43c0s6a4j4d0xfc430mwgw3syf03xszzggnw97rp555"))))
     (properties `((upstream-name . "timeDate")))
     (build-system r-build-system)
     (home-page "https://www.rmetrics.org")
@@ -6900,14 +6932,14 @@ clustered data.")
 (define-public r-mitml
   (package
     (name "r-mitml")
-    (version "0.4-3")
+    (version "0.4-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mitml" version))
        (sha256
         (base32
-         "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9"))))
+         "12mgjvifpprzlpjbcybd08fkps0kdxim45saan4cng4lc4klh880"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-haven r-jomo r-pan))
@@ -7715,14 +7747,14 @@ Markdown documents.")
 (define-public r-seriation
   (package
     (name "r-seriation")
-    (version "1.4.0")
+    (version "1.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "seriation" version))
        (sha256
         (base32
-         "1bcd559wsjjdmpc1892vsf8wrkh4ijgn1y71h3y3v5clmd21ycmx"))))
+         "1b8z7alav4d0i90251crzrq3yp3f11w0zlalh1f3b7si5yl2dkmr"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ca
@@ -7813,13 +7845,13 @@ to variables on the left-hand side of the assignment.")
 (define-public r-zlog
   (package
     (name "r-zlog")
-    (version "1.0.0")
+    (version "1.0.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "zlog" version))
               (sha256
                (base32
-                "1d5j31p0h3rrn230087h3ngpvwknlisjv0f1qdbicdj9m177spci"))))
+                "0fi9aqrmikdg5ibwhn82kslj4lxih03vm27jmi14m73h09yy4in5"))))
     (properties `((upstream-name . "zlog")))
     (build-system r-build-system)
     (native-inputs (list r-knitr))
@@ -8798,14 +8830,14 @@ sample Robust Rank-Order Distributional Test.")
 (define-public r-expm
   (package
     (name "r-expm")
-    (version "0.999-6")
+    (version "0.999-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "expm" version))
        (sha256
         (base32
-         "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
+         "1wd03dcqxyi7kyznfq7107ix1bsp7rwzqqv6w7p37pdq2jwlkwi8"))))
     (build-system r-build-system)
     (propagated-inputs (list r-matrix))
     (native-inputs (list gfortran))
@@ -8977,14 +9009,14 @@ powerful and convenient features.")
 (define-public r-heatmaply
   (package
     (name "r-heatmaply")
-    (version "1.4.0")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "heatmaply" version))
        (sha256
         (base32
-         "0q1vkf55a5r0ssybdbi2fyhn13p29kw04yp46c34n7apm0k2ymgi"))))
+         "0zgaqmbc1nha38c8kx5xdjdjbwmykrf2acq8ydki8dqixv6b34la"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
@@ -10219,14 +10251,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
 (define-public r-rastervis
   (package
     (name "r-rastervis")
-    (version "0.51.4")
+    (version "0.51.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rasterVis" version))
        (sha256
         (base32
-         "1z4vwjmx8n01jc2ypqs1pmx70rc3pjaz3ahk8j8zcif40v0qgy6i"))))
+         "18bsrw629p4pkyhrpjmiyhq73w882bhgpwmkih0gjnw3ywwgx7rs"))))
     (properties `((upstream-name . "rasterVis")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10399,14 +10431,14 @@ always locate the files relative to your project root.")
 (define-public r-reticulate
   (package
     (name "r-reticulate")
-    (version "1.26")
+    (version "1.27")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "reticulate" version))
        (sha256
         (base32
-         "1ibliic3qp597nskak2bfa6iyl721ssgcavwvfaf1c71plilimrz"))))
+         "19k96g43ll9zp72g9kmf9gg7k9cwwpyxzf2nd6fvx5jal5bq8mlx"))))
     (build-system r-build-system)
     (arguments
      (list
@@ -10459,13 +10491,13 @@ file.")
 (define-public r-billboarder
   (package
     (name "r-billboarder")
-    (version "0.3.1")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "billboarder" version))
        (sha256
-        (base32 "189ngvg84rcwhrivxskmjv3srhadvzr4p1v8pf11axyv2qn01b0x"))
+        (base32 "1llac7fyyfax6q8n9b8lccyl9c8vxqvkfp341sz59mrw8yhwb2hr"))
        (snippet
         '(delete-file "inst/htmlwidgets/lib/billboard/billboard.pkgd.min.js"))))
     (properties `((upstream-name . "billboarder")))
@@ -10501,10 +10533,10 @@ file.")
        ("js-billboard"
         ,(origin
            (method url-fetch)
-           (uri "https://unpkg.com/billboard.js@3.2.0/dist/billboard.js")
+           (uri "https://unpkg.com/billboard.js@3.6.3/dist/billboard.js")
            (sha256
             (base32
-             "1kx5rqmn87pgal2cwmcij2rrnwa0fgcsw6y99m4i0l2sdm0qffv2"))))))
+             "1lyj4yl95qgh06iygb2y2mdg1zxijzxi5h85z7kp8ngm825z6rpi"))))))
     (home-page "https://github.com/dreamRs/billboarder")
     (synopsis "Create interactive charts with the JavaScript Billboard library")
     (description
@@ -11057,17 +11089,17 @@ references and Rd files.")
 (define-public r-officer
   (package
     (name "r-officer")
-    (version "0.5.0")
+    (version "0.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "officer" version))
        (sha256
         (base32
-         "19kms5pjgb5mjqyqzgnpykd5divbkrs5apz8z27ivgw78iizsqh6"))))
+         "1r885h8ma2py3idxkki2bnsbcimrw36qd6km2bhyhlav79n7bh4w"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-r6 r-uuid r-xml2 r-zip))
+     (list r-openssl r-r6 r-uuid r-xml2 r-zip))
     (home-page "https://davidgohel.github.io/officer")
     (synopsis "Manipulation of Word and PowerPoint documents")
     (description
@@ -11464,14 +11496,14 @@ documents.")
 (define-public r-writexl
   (package
     (name "r-writexl")
-    (version "1.4.1")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "writexl" version))
        (sha256
         (base32
-         "1qhf7p14mijdyl5i40gfpzgvdflcs6s8xnwrabsnjxpa17xbamkn"))))
+         "09whcadnwqcshicbhv1vnvdai087yimmnz9lvc3rld5nn8z66xcg"))))
     (build-system r-build-system)
     (inputs (list zlib))
     (home-page "https://github.com/ropensci/writexl")
@@ -12045,14 +12077,14 @@ visualization and candidate genes around SNPs.")
 (define-public r-precrec
   (package
     (name "r-precrec")
-    (version "0.12.9")
+    (version "0.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "precrec" version))
        (sha256
         (base32
-         "1dfz2rqx2ww2l5r40ahg0qdj3rjrwiwh427mw7j5ynhpcj21j2qm"))))
+         "04pyqwc4p3bzwfcf7a74nkh7b2001053jagzvz9ghpyj380f66x8"))))
     (properties `((upstream-name . "precrec")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12061,6 +12093,7 @@ visualization and candidate genes around SNPs.")
            r-ggplot2
            r-gridextra
            r-rcpp
+           r-rlang
            r-withr))
     (native-inputs (list r-knitr))
     (home-page "https://evalclass.github.io/precrec/")
@@ -12073,14 +12106,14 @@ of precision-recall and ROC (Receiver Operator Characteristics) curves.")
 (define-public r-netrep
   (package
     (name "r-netrep")
-    (version "1.2.4")
+    (version "1.2.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "NetRep" version))
        (sha256
         (base32
-         "1swlb2k9bc7whvslxbklz864j9ynvna73hvq5rhv61cv5vy05ksd"))))
+         "0hyj91fr4y9csj2dy4z9cpr92hh8gk3xnjr6zpk9n0wk37sx44h6"))))
     (properties `((upstream-name . "NetRep")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12373,14 +12406,14 @@ a library of prediction algorithms to be used in the super learner.")
 (define-public r-drtmle
   (package
     (name "r-drtmle")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "drtmle" version))
        (sha256
         (base32
-         "12vplpz9bg5444jy29mbdr70hqby073vb3iw76v2csrwy3ws3f21"))))
+         "0qvdxzvpi7a66gx61v6fj31zy4y5cid18g4qgv5lir7qc74rbbx0"))))
     (properties `((upstream-name . "drtmle")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12593,14 +12626,14 @@ used to teach mathematics, statistics, computation and modeling.")
 (define-public r-raster
   (package
     (name "r-raster")
-    (version "3.6-11")
+    (version "3.6-13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "raster" version))
        (sha256
         (base32
-         "1arvmhf3ijzh3aanw8n6mdnwk4h26axsxpszvr5g43l7g5vfmggf"))))
+         "035hb1063lrlcs3l5aiccminax228ji0363hijmnxkvl7fsydxp1"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-rcpp r-sp r-terra))
@@ -14579,6 +14612,31 @@ vector giving the index of the cluster each observation belongs to.")
 algorithms, clusterings, and individual clusters.")
     (license license:expat)))
 
+(define-public r-clustergeneration
+  (package
+    (name "r-clustergeneration")
+    (version "1.3.7")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "clusterGeneration" version))
+              (sha256
+               (base32
+                "0p1dwl08bf20h7pnspnsycrp3v48nm2miwcnlklyc4gdyzc2jksk"))))
+    (properties `((upstream-name . "clusterGeneration")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-mass))
+    (home-page "https://cran.r-project.org/package=clusterGeneration")
+    (synopsis "Random cluster generation (with specified degree of separation)")
+    (description
+     "The clusterGeneration package provides functions for generating random
+clusters, generating random covariance/correlation matrices, calculating a
+separation index (data and population version) for pairs of clusters or
+cluster distributions, and 1-D and 2-D projection plots to visualize clusters.
+The package also contains a function to generate random clusters based on
+factorial designs with factors such as degree of separation, number of
+clusters, number of variables, number of noisy variables.")
+    (license license:gpl2+)))
+
 (define-public r-tweedie
   (package
     (name "r-tweedie")
@@ -14651,14 +14709,14 @@ analysing multivariate abundance data in community ecology.")
 (define-public r-afex
   (package
     (name "r-afex")
-    (version "1.2-0")
+    (version "1.2-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "afex" version))
        (sha256
         (base32
-         "1hii6mx4qbmv4m1hy44sp19xf0r7mc68p767bwc58qrgpawgymwb"))))
+         "1jxahp2nq2clmi7wqi0n0b23xyvsjckvz9bmj81j35fv8v6wxa73"))))
     (build-system r-build-system)
     ;; This is needed for the vignette builder
     (arguments
@@ -14959,14 +15017,14 @@ other values.")
 (define-public r-ncdf4
   (package
     (name "r-ncdf4")
-    (version "1.20")
+    (version "1.21")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ncdf4" version))
        (sha256
         (base32
-         "1kpi5xygx1nj8ybxrn9z0jxi3lbcibdvc7mjgyvm6f9plwjlxjvq"))))
+         "03dk47xz6qlpky9kkpkkxc472czq542yml3fdg39bic2yggffnig"))))
     (build-system r-build-system)
     (inputs
      (list netcdf zlib))
@@ -15006,14 +15064,14 @@ Bioconductor packages.")
 (define-public r-rgl
   (package
     (name "r-rgl")
-    (version "0.110.2")
+    (version "0.111.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rgl" version))
        (sha256
         (base32
-         "0v9lrsdmhw0wqfbrrjirgppd40cn00ignq3rg2jn3q8ak70ih4fs"))))
+         "1h6nbcnbl0knmc91923wfhghs58yjc84mhnmk2byd474lrgzxynd"))))
     (build-system r-build-system)
     (native-inputs
      (list pkg-config
@@ -15300,14 +15358,14 @@ al. (2010) <DOI:10.1016/j.neuroimage.2010.04.241>, Tabelow and Polzehl (2011)
 (define-public r-fmsb
   (package
     (name "r-fmsb")
-    (version "0.7.4")
+    (version "0.7.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fmsb" version))
        (sha256
         (base32
-         "1rmmvx38rmamiw0ajqhlksgxj6fgm8ymq903yxqq2bzxx8fhj5n2"))))
+         "082qj08kzyzwvjacwq0sl3xxdx6iz5hgx6q24jv1mnvx7z5xn5ry"))))
     (build-system r-build-system)
     (home-page "http://minato.sip21c.org/msb/")
     (synopsis "Functions for medical statistics book with demographic data")
@@ -16132,13 +16190,13 @@ Touzet and Varre (2007).")
 (define-public r-rncl
   (package
     (name "r-rncl")
-    (version "0.8.6")
+    (version "0.8.7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "rncl" version))
               (sha256
                (base32
-                "1ywgwqn82z8h6zpcxxq4hgngdpfa6dj0lr7bfq4cwfml9z075jgw"))))
+                "0flrqz7pansy11ds23qv06bcmh6vxqljq0517v6292ibbx7nx1qx"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-progress r-rcpp))
@@ -18619,14 +18677,14 @@ probabilities from a standard bivariate normal CDF.")
 (define-public r-lavaan
   (package
     (name "r-lavaan")
-    (version "0.6-12")
+    (version "0.6-13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lavaan" version))
        (sha256
         (base32
-         "17h79pnww1mihvlp6ap0r6d8wnly9bwszj13l5dkby0284z2fj40"))))
+         "0glcam1g8zx3xvvp8nsbsj5vi8hba0sm20akyf4rivbr6s745y1a"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-mass r-mnormt r-numderiv r-pbivnorm))
@@ -18927,6 +18985,36 @@ can also be used to join clusters obtained from affinity propagation.  Various
 plotting functions are available for analyzing clustering results.")
     (license license:gpl2+)))
 
+(define-public r-remacor
+  (package
+    (name "r-remacor")
+    (version "0.0.11")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "remaCor" version))
+              (sha256
+               (base32
+                "0hhk1zrjz6sxg219h9ca7jya0vc8dmrvwaddajkcdns6bv3rj1km"))))
+    (properties `((upstream-name . "remaCor")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-clustergeneration
+           r-ggplot2
+           r-mvtnorm
+           r-rdpack
+           r-reshape2
+           r-runit))
+    (native-inputs (list r-knitr))
+    (home-page "https://diseaseneurogenomics.github.io/remaCor/")
+    (synopsis "Random effects meta-analysis for correlated test statistics")
+    (description
+     "Meta-analysis is widely used to summarize estimated effects sizes across
+multiple statistical tests.  Standard fixed and random effect meta-analysis
+methods assume that the estimated of the effect sizes are statistically
+independent.  Here we relax this assumption and enable meta-analysis when the
+correlation matrix between effect size estimates is known.")
+    (license license:artistic2.0)))
+
 (define-public r-rematch2
   (package
     (name "r-rematch2")
@@ -20816,14 +20904,14 @@ layer by layer.")
 (define-public r-gkmsvm
   (package
     (name "r-gkmsvm")
-    (version "0.81.0")
+    (version "0.82.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gkmSVM" version))
        (sha256
         (base32
-         "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
+         "1m2cq4b0srghaj04p5ffbc21zv1rg7avi8pn765bybjhvrn567bm"))))
     (properties `((upstream-name . "gkmSVM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26295,13 +26383,13 @@ finding peaks in spectra, converting humidity measures.")
 (define-public r-qqconf
   (package
     (name "r-qqconf")
-    (version "1.3.0")
+    (version "1.3.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "qqconf" version))
               (sha256
                (base32
-                "11sh0q5bwmqdygqd1gspx7xc5mysj18whz11afnz6s1m820snhhw"))))
+                "1vvw79l8nqpqvmfpff5khgdjbs1s2q5ylg72lvkihd2qfk0d8cf5"))))
     (properties `((upstream-name . "qqconf")))
     (build-system r-build-system)
     (inputs (list fftw))
@@ -26828,14 +26916,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
 (define-public r-forecast
   (package
     (name "r-forecast")
-    (version "8.19")
+    (version "8.20")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "forecast" version))
        (sha256
         (base32
-         "1l3mdldghsf319fh8gx81w8f5i5mnrcn70rjjylzk4j8n7gicpih"))))
+         "03ll4v4r2l4kk4lbwnrvmd24003qm6j81lzr06qlns311zf4dv9v"))))
     (properties `((upstream-name . "forecast")))
     (build-system r-build-system)
     (propagated-inputs
@@ -31533,14 +31621,14 @@ vignettes in all common formats.")
 (define-public r-tidytext
   (package
     (name "r-tidytext")
-    (version "0.4.0")
+    (version "0.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidytext" version))
        (sha256
         (base32
-         "1ywx4zhx1a0r1lyd11w3cbz33silpx5m1sk9rd3kvj21wvfdramk"))))
+         "05f8209qx1rvddnkl0h05yig09xahs8lqgq9w5dvdiwarji50rsj"))))
     (properties `((upstream-name . "tidytext")))
     (build-system r-build-system)
     (propagated-inputs
@@ -31912,14 +32000,14 @@ covariate (usually group indicator) and the scores.")
 (define-public r-qtl
   (package
     (name "r-qtl")
-    (version "1.54")
+    (version "1.58")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "qtl" version))
        (sha256
         (base32
-         "1rzkxkmcgd6drxbgqp6w6jab5bs7vla2x2ndv3l4nlbcwzi41jw0"))))
+         "15wxn3sdvmgjgmfxl0qsxhkr7b7kn1hz2962cd6k0qmffz0mmjkf"))))
     (build-system r-build-system)
     (home-page "https://rqtl.org/")
     (synopsis "R package for analyzing QTL experiments in genetics")
@@ -32678,13 +32766,13 @@ computational operations, add-on packages provide additional functionality.")
 (define-public r-mlr3learners
   (package
     (name "r-mlr3learners")
-    (version "0.5.5")
+    (version "0.5.6")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mlr3learners" version))
               (sha256
                (base32
-                "0m5s7jfqfh48gxllvi93wb5w2pzhzx8rcx5bz87lkmv1cnj65q84"))))
+                "1m0psjqcl2pfy73wmc29vyz122v0kqmws6d0dgl7wsy1csfjsjm2"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-checkmate
@@ -33827,20 +33915,21 @@ supply the workflow to create thematic maps.  This package also facilitates
 (define-public r-rtweet
   (package
     (name "r-rtweet")
-    (version "1.0.2")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rtweet" version))
        (sha256
         (base32
-         "1dhdq2c2zl88h29caqpm7zh2i5970q7rfg98zf2xb7x4zak7bq9x"))))
+         "0dq6ckf2mp6wm6y8xzjby21s356760fmck1m8nsnv5gz8lhy6dhg"))))
     (properties `((upstream-name . "rtweet")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-bit64
            r-curl
            r-httr
+           r-httr2
            r-jsonlite
            r-lifecycle
            r-progress
@@ -36028,13 +36117,13 @@ options for aggregating multi-layer rasters.")
 (define-public r-bien
   (package
     (name "r-bien")
-    (version "1.2.5")
+    (version "1.2.6")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "BIEN" version))
         (sha256
-          (base32 "0s98n6zbf48vssd3h63k6kashcxv1kawcb026n0ngsfpc5dv6i48"))))
+          (base32 "17zrj5ckxaz4mdbgywxi8kf51ssbf2md1d2azf30dh96kzc2ayps"))))
     (properties `((upstream-name . "BIEN")))
     (build-system r-build-system)
     (native-inputs
@@ -36046,11 +36135,9 @@ options for aggregating multi-layer rasters.")
             r-fasterize
             r-foreach
             r-raster
-            r-rgdal
-            r-rgeos
             r-rpostgresql
             r-sf
-            r-sp))
+            r-terra))
     (home-page "https://cran.r-project.org/package=BIEN")
     (synopsis "Tools for accessing the BIEN database")
     (description

gnu/packages/crates-io.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2019 Ivan Petkov <ivanppetkov@gmail.com>
 ;;; Copyright © 2019, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2019-2022 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2019-2023 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;; Copyright © 2019–2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020 John Soo <jsoo1@asu.edu>
@@ -70,6 +70,7 @@
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages glib)
+  #:use-module (gnu packages icu4c)
   #:use-module (gnu packages image)
   #:use-module (gnu packages jemalloc)
   #:use-module (gnu packages linux)
@@ -58289,19 +58290,22 @@ Rust bindings.")
 (define-public rust-tectonic-bridge-graphite2-0.2
   (package
     (name "rust-tectonic-bridge-graphite2")
-    (version "0.2.0")
+    (version "0.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "tectonic_bridge_graphite2" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32 "1qsq337y4p3z832kmn2xcaj6xh3z6ngr0izn4jgdjrymnsq1ac81"))))
+        (base32 "1lkpqxz0y7m2ib1g0k850g2d7g6z8062niaw7vgvql33f2n94xkr"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t
+     `(#:cargo-inputs
-       #:cargo-inputs
        (("rust-tectonic-dep-support" ,rust-tectonic-dep-support-0.1))))
+    (native-inputs
+     (list pkg-config))
+    (inputs
+     (list graphite2))
     (home-page "https://tectonic-typesetting.github.io/")
     (synopsis "Expose the graphite2 library to Rust/Cargo")
     (description
@@ -58361,28 +58365,31 @@ bindings.")
 bindings.")
     (license license:expat)))
 
-(define-public rust-tectonic-bundles-0.2
+(define-public rust-tectonic-bundles-0.3
   (package
     (name "rust-tectonic-bundles")
-    (version "0.2.0")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "tectonic_bundles" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32 "17wwgfcl5nzvgzil7ayi42ljjkx9ffv4c35v6ywcmzdhk9zhki2f"))))
+        (base32 "1ccykccvddvx31h1dfkzdxsnqhgyls21ks2qbvad09m1jzqzl5nj"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t
+     `(#:cargo-inputs
-       #:cargo-inputs
        (("rust-flate2" ,rust-flate2-1)
         ("rust-fs2" ,rust-fs2-0.4)
         ("rust-tectonic-errors" ,rust-tectonic-errors-0.2)
         ("rust-tectonic-geturl" ,rust-tectonic-geturl-0.3)
-        ("rust-tectonic-io-base" ,rust-tectonic-io-base-0.3)
+        ("rust-tectonic-io-base" ,rust-tectonic-io-base-0.4)
         ("rust-tectonic-status-base" ,rust-tectonic-status-base-0.2)
         ("rust-zip" ,rust-zip-0.5))))
+    (native-inputs
+     (list pkg-config))
+    (inputs
+     (list openssl zlib))
     (home-page "https://tectonic-typesetting.github.io/")
     (synopsis "Tectonic ``bundle'' (support file collection) implementations")
     (description
@@ -58441,21 +58448,20 @@ providing whatever fiddly features are needed to enable the Tectonic build
 process.")
     (license license:expat)))
 
-(define-public rust-tectonic-docmodel-0.1
+(define-public rust-tectonic-docmodel-0.2
   (package
     (name "rust-tectonic-docmodel")
-    (version "0.1.2")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "tectonic_docmodel" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32 "1b5vdqcnjbbda6am0mb7qyxyc6pn8v0pqz0w10xia87ycyyfflxw"))))
+        (base32 "1z3yhw7h11a5xggi3bjip3kz1931mjl5gi53vx2zwd89rg99373y"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t
+     `(#:cargo-inputs
-       #:cargo-inputs
        (("rust-serde" ,rust-serde-1)
         ("rust-tectonic-errors" ,rust-tectonic-errors-0.2)
         ("rust-toml" ,rust-toml-0.5))))
@@ -58524,21 +58530,20 @@ document model, including the @file{Tectonic.toml} file.")
 output to HTML.")
     (license license:expat)))
 
-(define-public rust-tectonic-engine-xetex-0.2
+(define-public rust-tectonic-engine-xetex-0.4
   (package
     (name "rust-tectonic-engine-xetex")
-    (version "0.2.0")
+    (version "0.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "tectonic_engine_xetex" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32 "1kn9gxkgf3jbwif14n1kmp869s4b69khhc7iwm78qqpmy79lrhkw"))))
+        (base32 "1ckx9sg1nwyghg7142zk5x75g32f4s19psk6c50y0n0ikf5xq9sd"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t
+     `(#:cargo-inputs
-       #:cargo-inputs
        (("rust-cc" ,rust-cc-1)
         ("rust-libc" ,rust-libc-0.2)
         ("rust-tectonic-bridge-core" ,rust-tectonic-bridge-core-0.3)
@@ -58547,8 +58552,16 @@ output to HTML.")
         ("rust-tectonic-bridge-harfbuzz" ,rust-tectonic-bridge-harfbuzz-0.2)
         ("rust-tectonic-cfg-support" ,rust-tectonic-cfg-support-0.1)
         ("rust-tectonic-errors" ,rust-tectonic-errors-0.2)
-        ("rust-tectonic-pdf-io" ,rust-tectonic-pdf-io-0.1)
+        ("rust-tectonic-pdf-io" ,rust-tectonic-pdf-io-0.4)
-        ("rust-tectonic-xetex-layout" ,rust-tectonic-xetex-layout-0.1))))
+        ("rust-tectonic-xetex-layout" ,rust-tectonic-xetex-layout-0.2))))
+    (native-inputs
+     (list pkg-config))
+    (inputs
+     (list fontconfig
+           freetype
+           graphite2
+           icu4c
+           zlib))
     (home-page "https://tectonic-typesetting.github.io/")
     (synopsis "XeTeX engine as a reusable crate")
     (description
@@ -58556,27 +58569,29 @@ output to HTML.")
 engine as a reusable crate.")
     (license license:expat)))
 
-(define-public rust-tectonic-engine-xdvipdfmx-0.1
+(define-public rust-tectonic-engine-xdvipdfmx-0.4
   (package
     (name "rust-tectonic-engine-xdvipdfmx")
-    (version "0.1.0")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "tectonic_engine_xdvipdfmx" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32 "00kjsxzlzlc8lmh8mhb5v6iw1lb7rq09ski2mjzlyw604dcq1k3p"))))
+        (base32 "0ajmb9pcq5pak28z4bhsnxfgfy9hpr1mm02bp6ph16nvdn8m2ir1"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t
+     `(#:cargo-inputs
-       #:cargo-inputs
+       (("rust-cc" ,rust-cc-1)
-       (("rust-cbindgen" ,rust-cbindgen-0.16)
-        ("rust-cc" ,rust-cc-1)
         ("rust-libc" ,rust-libc-0.2)
-        ("rust-tectonic-bridge-core" ,rust-tectonic-bridge-core-0.1)
+        ("rust-tectonic-bridge-core" ,rust-tectonic-bridge-core-0.3)
         ("rust-tectonic-errors" ,rust-tectonic-errors-0.2)
-        ("rust-tectonic-pdf-io" ,rust-tectonic-pdf-io-0.1))))
+        ("rust-tectonic-pdf-io" ,rust-tectonic-pdf-io-0.4))))
+    (native-inputs
+     (list pkg-config))
+    (inputs
+     (list libpng zlib))
     (home-page "https://tectonic-typesetting.github.io/")
     (synopsis "@code{xdvipdfmx} program as a reusable crate")
     (description
@@ -58729,23 +58744,22 @@ streams.")
         ("rust-tectonic-status-base" ,rust-tectonic-status-base-0.1)
         ("rust-thiserror" ,rust-thiserror-1))))))
 
-(define-public rust-tectonic-pdf-io-0.1
+(define-public rust-tectonic-pdf-io-0.4
   (package
     (name "rust-tectonic-pdf-io")
-    (version "0.1.0")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "tectonic_pdf_io" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32 "0ry5g6vh54i8ih8rjlz3ci7b8gi4irsllg34pv57mcwrhwcikg6x"))))
+        (base32 "0rmk31n96r299k5j2ydyqryzywn2dbfbnl1rwh0lx86zaqac9qcn"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t
+     `(#:cargo-inputs
-       #:cargo-inputs
        (("rust-cc" ,rust-cc-1)
-        ("rust-tectonic-bridge-core" ,rust-tectonic-bridge-core-0.1)
+        ("rust-tectonic-bridge-core" ,rust-tectonic-bridge-core-0.3)
         ("rust-tectonic-bridge-flate" ,rust-tectonic-bridge-flate-0.1)
         ("rust-tectonic-cfg-support" ,rust-tectonic-cfg-support-0.1)
         ("rust-tectonic-dep-support" ,rust-tectonic-dep-support-0.1))))
@@ -58824,29 +58838,36 @@ types for reporting status messages to a user.")
 used by XeTeX and Tectonic.")
     (license license:expat)))
 
-(define-public rust-tectonic-xetex-layout-0.1
+(define-public rust-tectonic-xetex-layout-0.2
   (package
     (name "rust-tectonic-xetex-layout")
-    (version "0.1.0")
+    (version "0.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "tectonic_xetex_layout" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32 "063fq6bhhqac30bg6vmcfpd9zikn0p6rd189avz0f34ka4mir0yi"))))
+        (base32 "102z52hhazz2b2qsbr93dn2y4q0103s548ixzws40il7imzg99ly"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t
+     `(#:cargo-inputs
-       #:cargo-inputs
        (("rust-cc" ,rust-cc-1)
-        ("rust-tectonic-bridge-core" ,rust-tectonic-bridge-core-0.1)
+        ("rust-tectonic-bridge-core" ,rust-tectonic-bridge-core-0.3)
         ("rust-tectonic-bridge-freetype2" ,rust-tectonic-bridge-freetype2-0.2)
         ("rust-tectonic-bridge-graphite2" ,rust-tectonic-bridge-graphite2-0.2)
         ("rust-tectonic-bridge-harfbuzz" ,rust-tectonic-bridge-harfbuzz-0.2)
         ("rust-tectonic-bridge-icu" ,rust-tectonic-bridge-icu-0.2)
         ("rust-tectonic-cfg-support" ,rust-tectonic-cfg-support-0.1)
         ("rust-tectonic-dep-support" ,rust-tectonic-dep-support-0.1))))
+    (native-inputs
+     (list pkg-config))
+    (inputs
+     (list fontconfig
+           freetype
+           graphite2
+           icu4c
+           zlib))
     (home-page "https://tectonic-typesetting.github.io/")
     (synopsis "XeTeX's font loading and layout interface encapsulation")
     (description

gnu/packages/engineering.scm

@@ -16,7 +16,7 @@
 ;;; Copyright © 2019 John Soo <jsoo1@asu.edu>
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2020,2021 Vincent Legoll <vincent.legoll@gmail.com>
-;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2020, 2023 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2020, 2021 Ekaitz Zarraga <ekaitz@elenq.tech>
 ;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com>
 ;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego@posteo.net>
@@ -81,6 +81,7 @@
   #:use-module (gnu packages c)
   #:use-module (gnu packages check)
   #:use-module (gnu packages cmake)
+  #:use-module (gnu packages code)
   #:use-module (gnu packages commencement)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpp)
@@ -2290,7 +2291,7 @@ engineers for reverse engineers.")
 (define-public lib3mf
   (package
     (name "lib3mf")
-    (version "2.1.1")
+    (version "2.2.0")
     (source
      (origin
       (method git-fetch)
@@ -2299,20 +2300,48 @@ engineers for reverse engineers.")
       (file-name (git-file-name name version))
       (sha256
        (base32
-        "1417xlxc1y5jnipixhbjfrrjgkrprbbraj8647sff9051m3hpxc3"))))
+        "05zqvnzmi7j8rhp2mrskvxf1bxl7kb4c72dfx4y86219i1hx7i2q"))
+      (modules '((guix build utils)))
+      (snippet
+       '(begin
+          ;; Delete pre-compiled ACT.
+          (delete-file-recursively "AutomaticComponentToolkit/bin")
+
+          ;; Remove bundled software.  Preserve cpp-base64 as it has been
+          ;; modified and cannot easily be unbundled.
+          (for-each delete-file-recursively
+                    '("Include/Libraries/libzip"
+                      "Include/Libraries/zlib"
+                      "Source/Libraries/libzip"
+                      "Source/Libraries/zlib"))
+
+          ;; Adjust header includes such that system headers are found.
+          (substitute* '("Include/Common/OPC/NMR_OpcPackageReader.h"
+                         "Include/Common/Platform/NMR_ImportStream_ZIP.h"
+                         "Include/Common/Platform/NMR_ExportStream_ZIP.h"
+                         "Include/Common/Platform/NMR_ImportStream_Compressed.h"
+                         "Include/Common/Platform/NMR_ExportStream_Compressed.h"
+                         "Source/Common/Platform/NMR_PortableZIPWriterEntry.cpp")
+            (("Libraries/libzip/") "")
+            (("Libraries/zlib/") ""))))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags (list "-DUSE_INCLUDED_ZLIB=0"
                                "-DUSE_INCLUDED_LIBZIP=0"
                                "-DUSE_INCLUDED_GTEST=0"
-                               "-DUSE_INCLUDED_SSL=0")))
+                               "-DUSE_INCLUDED_SSL=0")
+       #:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'provide-act
+                    (lambda* (#:key native-inputs inputs #:allow-other-keys)
+                      (let ((act (search-input-file (or native-inputs inputs)
+                                                    "bin/act"))
+                            (dir "AutomaticComponentToolkit/bin"))
+                        (mkdir-p dir)
+                        (symlink act (string-append dir "/act.linux"))))))))
     (native-inputs
-     (list googletest pkg-config))
+     (list automatic-component-toolkit googletest pkg-config))
     (inputs
-     `(("libuuid" ,util-linux "lib")
+     (list `(,util-linux "lib") libzip libressl zlib))
-       ("libzip" ,libzip)
-       ("libressl" ,libressl)
-       ("zlib" ,zlib)))
     (synopsis "Implementation of the 3D Manufacturing Format (3MF) file standard")
     (description
      "Lib3MF is a C++ implementation of the 3D Manufacturing Format (3MF) file

gnu/packages/fontutils.scm

@@ -146,6 +146,7 @@ them as it goes.")
        (uri (pypi-uri "afdko" version))
        (sha256
         (base32 "0k1204vykgx32saa495s1lgmz1dixcp8bjiv486imx77killvm02"))
+       (patches (search-patches "python-afdko-suppress-copyright-test.patch"))
        (modules '((guix build utils)))
        (snippet
         #~(begin

gnu/packages/groovy.scm

@@ -26,6 +26,7 @@
   #:use-module (guix build-system ant)
   #:use-module (gnu packages)
   #:use-module (gnu packages java)
+  #:use-module (gnu packages java-xml)
   #:use-module (gnu packages xml))
 
 (define java-groovy-bootstrap

gnu/packages/haskell-apps.scm

@@ -18,6 +18,7 @@
 ;;; Copyright © 2021 EuAndreh <eu@euandre.org>
 ;;; Copyright © 2021 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2021 Morgan Smith <Morgan.J.Smith@outlook.com>
+;;; Copyright © 2022 David Thompson <dthompson2@worcester.edu>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -42,6 +43,7 @@
   #:use-module (guix build-system haskell)
   #:use-module (gnu packages)
   #:use-module (gnu packages curl)
+  #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages haskell)
   #:use-module (gnu packages haskell-check)
@@ -327,6 +329,13 @@ to @code{cabal repl}).")
              (copy-file "Utility/Shell.hs" "/tmp/Shell.hs")
              (substitute* "Utility/Shell.hs"
                (("/bin/sh") (which "sh")))))
+         (add-before 'configure 'patch-webapp
+           (lambda _
+             ;; Replace loose references to xdg-open so that 'git annex
+             ;; webapp' runs without making the user also install xdg-utils.
+             (substitute* '("Assistant/WebApp/DashBoard.hs"
+                            "Utility/WebApp.hs")
+               (("xdg-open") (which "xdg-open")))))
          (add-before 'configure 'factor-setup
            (lambda _
              ;; Factor out necessary build logic from the provided
@@ -471,7 +480,8 @@ to @code{cabal repl}).")
            ghc-yesod-core
            ghc-yesod-form
            ghc-yesod-static
-           rsync))
+           rsync
+           xdg-utils))
     (propagated-inputs
      (list git))
     (native-inputs

gnu/packages/java-bootstrap.scm

@@ -0,0 +1,724 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2021 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2017, 2022 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2018, 2020 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
+;;; Copyright © 2018 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2019 Andrius Štikonas <andrius@stikonas.eu>
+;;; Copyright © 2020 Simon South <simon@simonsouth.net>
+;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
+;;;
+;;; 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 java-bootstrap)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix utils)
+  #:use-module (guix gexp)
+  #: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 bash)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages gettext)
+  #:use-module (gnu packages guile)
+  #:use-module (gnu packages libffi)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages texinfo)
+  #:export (classpath-devel
+            ecj4-javac-wrapper
+            jamvm-with-ecj4
+            ant-bootstrap))
+
+
+;;;
+;;; Java bootstrap toolchain.
+;;;
+
+;; The Java bootstrap begins with Jikes, a Java compiler written in C++.  We
+;; use it to build a simple version of GNU Classpath, the Java standard
+;; library.  We chose version 0.93 because it is the last version that can be
+;; built with Jikes.  With Jikes and this version of GNU Classpath we can
+;; build JamVM, a Java Virtual Machine.  We build version 1.5.1 because it is
+;; the last version of JamVM that works with a version of GNU classpath that
+;; does not require ECJ.  These three packages make up the bootstrap JDK.
+
+;; This is sufficient to build an older version of Ant, which is needed to
+;; build an older version of ECJ, an incremental Java compiler, both of which
+;; are written in Java.
+;;
+;; ECJ is needed to build the latest release (0.99) and the development
+;; version of GNU Classpath.  The development version of GNU Classpath has
+;; much more support for Java 1.6 than the latest release, but we need to
+;; build 0.99 first to get a working version of javah.  ECJ, the development
+;; version of GNU Classpath, and the latest version of JamVM make up the
+;; second stage JDK with which we can build the OpenJDK with the Icedtea 2.x
+;; build framework.  We then build the more recent JDK Icedtea 3.x, and all
+;; other versions of OpenJDK.
+
+(define jikes
+  (package
+    (name "jikes")
+    (version "1.22")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/jikes/Jikes/"
+                                  version "/jikes-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "1qqldrp74pzpy5ly421srqn30qppmm9cvjiqdngk8hf47dv2rc0c"))))
+    (build-system gnu-build-system)
+    (home-page "http://jikes.sourceforge.net/")
+    (synopsis "Compiler for the Java language")
+    (description "Jikes is a compiler that translates Java source files as
+defined in The Java Language Specification into the bytecoded instruction set
+and binary format defined in The Java Virtual Machine Specification.")
+    (license license:ibmpl1.0)))
+
+;; This is the last version of GNU Classpath that can be built without ECJ.
+(define classpath-bootstrap
+  (package
+    (name "classpath")
+    (version "0.93")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://gnu/classpath/classpath-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "0i99wf9xd3hw1sj2sazychb9prx8nadxh2clgvk3zlmb28v0jbfz"))
+              (patches (search-patches "classpath-aarch64-support.patch"
+                                       "classpath-miscompilation.patch"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "JAVAC="
+                            (search-input-file %build-inputs "/bin/jikes"))
+             "--disable-Werror"
+             "--disable-gmp"
+             "--disable-gtk-peer"
+             "--disable-gconf-peer"
+             "--disable-plugin"
+             "--disable-dssi"
+             "--disable-alsa"
+             "--disable-gjdoc")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'install-data
+           (lambda _ (invoke "make" "install-data"))))))
+    (native-inputs
+     (list jikes fastjar libltdl pkg-config))
+    (home-page "https://www.gnu.org/software/classpath/")
+    (synopsis "Essential libraries for Java")
+    (description "GNU Classpath is a project to create core class libraries
+for use with runtimes, compilers and tools for the Java programming
+language.")
+    ;; GPLv2 or later, with special linking exception.
+    (license license:gpl2+)))
+
+;; This is the last version of JamVM that works with a version of GNU
+;; classpath that does not require ECJ.
+(define jamvm-1-bootstrap
+  (package
+    (name "jamvm")
+    (version "1.5.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/jamvm/jamvm/"
+                                  "JamVM%20" version "/jamvm-"
+                                  version ".tar.gz"))
+              (patches (search-patches "jamvm-1.5.1-aarch64-support.patch"
+                                       "jamvm-1.5.1-armv7-support.patch"))
+              (sha256
+               (base32
+                "06lhi03l3b0h48pc7x58bk9my2nrcf1flpmglvys3wyad6yraf36"))
+              ;; Remove precompiled software.
+              (snippet
+               '(delete-file "lib/classes.zip"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "--with-classpath-install-dir="
+                            (assoc-ref %build-inputs "classpath"))
+             "--disable-int-caching"
+             "--enable-runtime-reloc-checks"
+             "--enable-ffi")
+       #:phases
+       ,(if (string-prefix? "aarch64" (or (%current-system)
+                                          (%current-target-system)))
+            ;; Makefiles and the configure script need to be regenerated to
+            ;; incorporate support for AArch64.
+            '(modify-phases %standard-phases
+               (replace 'bootstrap
+                 (lambda _ (invoke "autoreconf" "-vif"))))
+            '%standard-phases)))
+    (inputs
+     (list classpath-bootstrap jikes libffi
+           zip zlib))
+    (native-inputs
+     (if (string-prefix? "aarch64" (or (%current-system)
+                                       (%current-target-system)))
+         ;; Additional packages needed for autoreconf.
+         `(("autoconf" ,autoconf)
+           ("automake" ,automake)
+           ("libtool" ,libtool))
+         '()))
+    (home-page "http://jamvm.sourceforge.net/")
+    (synopsis "Small Java Virtual Machine")
+    (description "JamVM is a Java Virtual Machine conforming to the JVM
+specification edition 2 (blue book).  It is extremely small.  However, unlike
+other small VMs it supports the full spec, including object finalisation and
+JNI.")
+    (license license:gpl2+)))
+
+(define ant-bootstrap
+  (package
+    (name "ant-bootstrap")
+    ;; The 1.10.x series requires Java 8.  1.9.0 and later use generics, which
+    ;; are not supported.  The 1.8.x series is the last to use only features
+    ;; supported by Jikes.
+    (version "1.8.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://apache/"
+                                  "ant/source/apache-ant-"
+                                  version "-src.tar.bz2"))
+              (sha256
+               (base32
+                "1cg0lga887qz5iizh6mlkxp01lciymrhmp7wzxpl6zpnldxmzrjx"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:modules ((srfi srfi-1)
+                  (guix build gnu-build-system)
+                  (guix build utils))
+       #:tests? #f ; no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'bootstrap)
+         (delete 'configure)
+         (add-before 'build 'define-java-environment-variables
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; First, set environment variables (eases debugging on -K).
+             (setenv "JAVA_HOME" (assoc-ref inputs "jamvm"))
+             (setenv "JAVACMD" (search-input-file inputs "/bin/jamvm"))
+             (setenv "JAVAC" (search-input-file inputs "/bin/jikes"))
+             (setenv "CLASSPATH" (search-input-file inputs "/lib/rt.jar"))))
+         (replace 'build
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; Ant complains if this file doesn't exist.
+             (setenv "HOME" "/tmp")
+             (with-output-to-file "/tmp/.ant.properties"
+               (lambda _ (display "")))
+
+             ;; Use jikes instead of javac for <javac ...> tags in build.xml
+             (setenv "ANT_OPTS" "-Dbuild.compiler=jikes")
+
+             ;; jikes produces lots of warnings, but they are not very
+             ;; interesting, so we silence them.
+             (setenv "$BOOTJAVAC_OPTS" "-nowarn")
+
+             ;; Without these JamVM options the build may freeze.
+             (substitute* "bootstrap.sh"
+               (("^\"\\$\\{JAVACMD\\}\" " m)
+                ,@(if (string-prefix? "armhf" (or (%current-system)
+                                                  (%current-target-system)))
+                      `((string-append m "-Xnocompact "))
+                      `((string-append m "-Xnocompact -Xnoinlining ")))))
+
+             ;; Disable tests because we are bootstrapping and thus don't have
+             ;; any of the dependencies required to build and run the tests.
+             (substitute* "build.xml"
+               (("depends=\"jars,test-jar\"") "depends=\"jars\""))
+             (invoke "bash" "bootstrap.sh"
+                     (string-append "-Ddist.dir="
+                                    (assoc-ref outputs "out")))))
+         (add-after 'build 'strip-jar-timestamps ;based on ant-build-system
+           (lambda* (#:key outputs #:allow-other-keys)
+             (define (repack-archive jar)
+               (let* ((dir (mkdtemp "jar-contents.XXXXXX"))
+                      (manifest (string-append dir "/META-INF/MANIFESTS.MF")))
+                 (with-directory-excursion dir
+                   (invoke "unzip" jar))
+                 (delete-file jar)
+                 ;; XXX: copied from (gnu build install)
+                 (for-each (lambda (file)
+                             (let ((s (lstat file)))
+                               (unless (eq? (stat:type s) 'symlink)
+                                 (utime file  0 0 0 0))))
+                           (find-files dir #:directories? #t))
+                 ;; It is important that the manifest appears first.
+                 (with-directory-excursion dir
+                   (let* ((files (find-files "." ".*" #:directories? #t))
+                          ;; To ensure that the reference scanner can
+                          ;; detect all store references in the jars
+                          ;; we disable compression with the "-0" option.
+                          (command (if (file-exists? manifest)
+                                       `("zip" "-0" "-X" ,jar ,manifest
+                                         ,@files)
+                                       `("zip" "-0" "-X" ,jar ,@files))))
+                     (apply invoke command)))))
+             (for-each repack-archive
+                    (find-files
+                     (string-append (assoc-ref %outputs "out") "/lib")
+                     "\\.jar$"))))
+         (delete 'install))))
+    (native-inputs
+     (list jikes jamvm-1-bootstrap unzip zip))
+    (home-page "https://ant.apache.org")
+    (synopsis "Build tool for Java")
+    (description
+     "Ant is a platform-independent build tool for Java.  It is similar to
+make but is implemented using the Java language, requires the Java platform,
+and is best suited to building Java projects.  Ant uses XML to describe the
+build process and its dependencies, whereas Make uses Makefile format.")
+    (license license:asl2.0)))
+
+;; Version 3.2.2 is the last version without a dependency on a full-fledged
+;; compiler for Java 1.5.
+(define ecj-bootstrap
+  (package
+    (name "ecj-bootstrap")
+    (version "3.2.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://archive.eclipse.org/eclipse/"
+                                  "downloads/drops/R-" version
+                                  "-200702121330/ecjsrc.zip"))
+              (sha256
+               (base32
+                "05hj82kxd23qaglsjkaqcj944riisjha7acf7h3ljhrjyljx8307"))))
+    ;; It would be so much easier if we could use the ant-build-system, but we
+    ;; cannot as we don't have ant at this point.  We use ecj for
+    ;; bootstrapping the JDK.
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; there are no tests
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "CLASSPATH"
+                     (string-join
+                      (cons (search-input-file inputs "/lib/rt.jar")
+                            (find-files (string-append
+                                         (assoc-ref inputs "ant-bootstrap")
+                                         "/lib")
+                                        "\\.jar$"))
+                      ":"))))
+         (replace 'build
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; The unpack phase enters the "org" directory by mistake.
+             (chdir "..")
+
+             ;; Create a simple manifest to make ecj executable.
+             (with-output-to-file "manifest"
+               (lambda _
+                 (display "Manifest-Version: 1.0
+Main-Class: org.eclipse.jdt.internal.compiler.batch.Main\n")))
+
+             ;; Compile it all!
+             (and (apply invoke "jikes"
+                         (find-files "." "\\.java$"))
+                  (invoke "fastjar" "cvfm"
+                          "ecj-bootstrap.jar" "manifest" "."))))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((share (string-append (assoc-ref outputs "out")
+                                         "/share/java/")))
+               (mkdir-p share)
+               (install-file "ecj-bootstrap.jar" share)))))))
+    (native-inputs
+     (list ant-bootstrap
+           unzip
+           jikes
+           jamvm-1-bootstrap
+           fastjar))
+    (home-page "https://eclipse.org")
+    (synopsis "Eclipse Java development tools core batch compiler")
+    (description "This package provides the Eclipse Java core batch compiler
+for bootstrapping purposes.  The @dfn{Eclipse compiler for Java} (ecj) is a
+requirement for all GNU Classpath releases after version 0.93.")
+    (license license:epl1.0)))
+
+(define ecj-javac-wrapper
+  (package (inherit ecj-bootstrap)
+    (name "ecj-javac-wrapper")
+    (source #f)
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       ,#~(begin
+            (use-modules (guix build utils))
+            (let* ((bin    (string-append #$output "/bin"))
+                   (target (string-append bin "/javac"))
+                   (guile  (string-append (assoc-ref %build-inputs "guile")
+                                          "/bin/guile"))
+                   (ecj    (string-append #$(this-package-native-input "ecj-bootstrap")
+                                          "/share/java/ecj-bootstrap.jar"))
+                   (java   (string-append #$(this-package-native-input "jamvm")
+                                          "/bin/jamvm"))
+                   (bootcp (let ((jvmlib (string-append
+                                          #$(this-package-native-input "classpath")
+                                          "/share/classpath")))
+                             (string-append jvmlib "/glibj.zip:"
+                                            jvmlib "/tools.zip"))))
+              (mkdir-p bin)
+              (with-output-to-file target
+                (lambda _
+                  (format #t "#!~a --no-auto-compile\n!#\n" guile)
+                  (write
+                   `(begin (use-modules (ice-9 match)
+                                        (ice-9 receive)
+                                        (ice-9 hash-table)
+                                        (srfi srfi-1)
+                                        (srfi srfi-26))
+                           (define defaults
+                             '(("-bootclasspath" ,bootcp)
+                               ("-source" "1.5")
+                               ("-target" "1.5")
+                               ("-cp"     ".")))
+                           (define (main args)
+                             (let ((classpath (getenv "CLASSPATH")))
+                               (setenv "CLASSPATH"
+                                       (string-join (list ,ecj (or classpath ""))
+                                                    ":")))
+                             (receive (vm-args other-args)
+                                 ;; Separate VM arguments from arguments to ECJ.
+                                 (partition (cut string-prefix? "-J" <>)
+                                            (fold (lambda (default acc)
+                                                    (if (member (first default) acc)
+                                                        acc (append default acc)))
+                                                  args defaults))
+                               (apply system* ,java
+                                      (append
+                                          ;; Remove "-J" prefix
+                                          (map (cut string-drop <> 2) vm-args)
+                                          '("org.eclipse.jdt.internal.compiler.batch.Main")
+                                        (cons "-nowarn" other-args)))))
+                           ;; Entry point
+                           (let ((args (cdr (command-line))))
+                             (if (null? args)
+                                 (format (current-error-port) "javac: no arguments given!\n")
+                                 (main args)))))))
+              (chmod target #o755)))))
+    (native-inputs
+     (list guile-3.0 ecj-bootstrap jamvm-1-bootstrap classpath-bootstrap))
+    (description "This package provides a wrapper around the @dfn{Eclipse
+compiler for Java} (ecj) with a command line interface that is compatible with
+the standard javac executable.")))
+
+;; The classpath-bootstrap was built without a virtual machine, so it does not
+;; provide a wrapper for javah.  We cannot build the development version of
+;; Classpath without javah.
+(define classpath-0.99
+  (package (inherit classpath-bootstrap)
+    (version "0.99")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://gnu/classpath/classpath-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1j7cby4k66f1nvckm48xcmh352b1d1b33qk7l6hi7dp9i9zjjagr"))
+              (patches (search-patches "classpath-aarch64-support.patch"))))
+    (arguments
+     `(#:configure-flags
+       (list (string-append "--with-ecj-jar="
+                            (assoc-ref %build-inputs "ecj-bootstrap")
+                            "/share/java/ecj-bootstrap.jar")
+             (string-append "JAVAC="
+                            (assoc-ref %build-inputs "ecj-javac-wrapper")
+                            "/bin/javac")
+             (string-append "JAVA="
+                            (assoc-ref %build-inputs "jamvm")
+                            "/bin/jamvm")
+             "GCJ_JAVAC_TRUE=no"
+             "ac_cv_prog_java_works=yes"  ; trust me
+             "--disable-Werror"
+             "--disable-gmp"
+             "--disable-gtk-peer"
+             "--disable-gconf-peer"
+             "--disable-plugin"
+             "--disable-dssi"
+             "--disable-alsa"
+             "--disable-gjdoc")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'install-data
+           (lambda _ (invoke "make" "install-data"))))))
+    (native-inputs
+     (list classpath-bootstrap
+           ecj-bootstrap ecj-javac-wrapper
+           fastjar jamvm-1-bootstrap
+           libltdl pkg-config))))
+
+;; We need this because classpath-bootstrap does not provide all of the tools
+;; we need to build classpath-devel.
+(define classpath-jamvm-wrappers
+  (package (inherit classpath-0.99)
+    (name "classpath-jamvm-wrappers")
+    (source #f)
+    (build-system trivial-build-system)
+    (arguments
+     (list
+      #:modules '((guix build utils))
+      #:builder
+      #~(begin
+          (use-modules (guix build utils))
+          (let ((bash      #$(this-package-native-input "bash-minimal"))
+                (jamvm     #$(this-package-native-input "jamvm"))
+                (classpath #$(this-package-native-input "classpath"))
+                (bin       (string-append #$output "/bin/")))
+            (mkdir-p bin)
+            (for-each (lambda (tool)
+                        (with-output-to-file (string-append bin tool)
+                          (lambda _
+                            #$@(if (string-prefix? "armhf" (or (%current-system)
+                                                               (%current-target-system)))
+                                   `((format #t "#!~a/bin/sh
+~a/bin/jamvm -Xnocompact -classpath ~a/share/classpath/tools.zip \
+gnu.classpath.tools.~a.~a $@"
+                                             bash jamvm classpath tool
+                                             (if (string=? "native2ascii" tool)
+                                                 "Native2ASCII" "Main")))
+                                   `((format #t "#!~a/bin/sh
+~a/bin/jamvm -Xnocompact -Xnoinlining -classpath ~a/share/classpath/tools.zip \
+gnu.classpath.tools.~a.~a $@"
+                                             bash jamvm classpath tool
+                                             (if (string=? "native2ascii" tool)
+                                                 "Native2ASCII" "Main"))))))
+                        (chmod (string-append bin tool) #o755))
+                      (list "javah"
+                            "rmic"
+                            "rmid"
+                            "orbd"
+                            "rmiregistry"
+                            "native2ascii"))))))
+    (native-inputs
+     (list bash-minimal jamvm-1-bootstrap classpath-0.99))
+    (inputs '())
+    (synopsis "Executables from GNU Classpath")
+    (description "This package provides wrappers around the tools provided by
+the GNU Classpath library.  They are executed by the JamVM virtual
+machine.")))
+
+;; The last release of GNU Classpath is 0.99 and it happened in 2012.  Since
+;; then Classpath has gained much more support for Java 1.6.
+(define classpath-devel
+  (let ((commit "e7c13ee0cf2005206fbec0eca677f8cf66d5a103")
+        (revision "1"))
+    (package (inherit classpath-bootstrap)
+      (version (string-append "0.99-" revision "." (string-take commit 9)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://git.savannah.gnu.org/git/classpath.git")
+                      (commit commit)))
+                (file-name (string-append "classpath-" version "-checkout"))
+                (sha256
+                 (base32
+                  "1v2rww76ww322mpg3s12a1kkc6gkp31bm9gcxs532h0wq285fiw4"))
+                (patches (search-patches "classpath-aarch64-support.patch"))))
+      (arguments
+       `(#:make-flags
+         ;; Ensure that the initial heap size is smaller than the maximum
+         ;; size.  By default only Xmx is set, which can lead to invalid
+         ;; memory settings on some machines with a lot of memory.
+         '("JAVAC_MEM_OPT=-J-Xms512M -J-Xmx768M")
+         #:configure-flags
+         (list (string-append "--with-ecj-jar="
+                              (assoc-ref %build-inputs "ecj-bootstrap")
+                              "/share/java/ecj-bootstrap.jar")
+               (string-append "--with-javac="
+                              (assoc-ref %build-inputs "ecj-javac-wrapper")
+                              "/bin/javac")
+               (string-append "JAVA="
+                              (assoc-ref %build-inputs "jamvm")
+                              "/bin/jamvm")
+               "GCJ_JAVAC_TRUE=no"
+               "ac_cv_prog_java_works=yes" ; trust me
+               "--disable-Werror"
+               "--disable-gmp"
+               "--disable-gtk-peer"
+               "--disable-gconf-peer"
+               "--disable-plugin"
+               "--disable-dssi"
+               "--disable-alsa"
+               "--disable-gjdoc")
+         #:phases
+         (modify-phases %standard-phases
+           ;; XXX The bootstrap phase executes autogen.sh, which fails after
+           ;; complaining about the lack of gettext.
+           (replace 'bootstrap
+             (lambda _ (invoke "autoreconf" "-vif")))
+           (add-after 'unpack 'remove-unsupported-annotations
+             (lambda _
+               (substitute* (find-files "java" "\\.java$")
+                 (("@Override") ""))))
+           (add-after 'install 'install-data
+             (lambda _ (invoke "make" "install-data"))))))
+      (native-inputs
+       (list autoconf automake libltdl libtool gettext-minimal texinfo
+             pkg-config
+             classpath-jamvm-wrappers  ;for javah
+             ecj-bootstrap ecj-javac-wrapper fastjar
+             jamvm-1-bootstrap)))))
+
+(define jamvm
+  (package (inherit jamvm-1-bootstrap)
+    (version "2.0.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/jamvm/jamvm/"
+                                  "JamVM%20" version "/jamvm-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1nl0zxz8y5x8gwsrm7n32bry4dx8x70p8z3s9jbdvs8avyb8whkn"))
+              (patches
+               (search-patches "jamvm-2.0.0-disable-branch-patching.patch"
+                               "jamvm-2.0.0-opcode-guard.patch"
+                               "jamvm-2.0.0-aarch64-support.patch"))
+              ;; Remove precompiled software.
+              (snippet
+               '(delete-file "src/classlib/gnuclasspath/lib/classes.zip"))))
+    (build-system gnu-build-system)
+    (arguments
+     (substitute-keyword-arguments (package-arguments jamvm-1-bootstrap)
+       ((#:configure-flags _)
+        '(list (string-append "--with-classpath-install-dir="
+                              (assoc-ref %build-inputs "classpath"))))))
+    (inputs
+     `(("classpath" ,classpath-devel)
+       ("ecj-javac-wrapper" ,ecj-javac-wrapper)
+       ("zip" ,zip)
+       ("zlib" ,zlib)))))
+
+(define ecj-javac-wrapper-final
+  (package (inherit ecj-javac-wrapper)
+    (native-inputs
+     (list guile-3.0 ecj-bootstrap jamvm classpath-devel))))
+
+;; We jump ahead by patching the sources of ECJ 4.2.1 so that our bootstrap
+;; JDK can build it.  ECJ 4 allows us to skip the build of the first version
+;; of icedtea and build icedtea 2.x directly.
+(define ecj4-bootstrap
+  (package
+    (name "ecj-bootstrap")
+    (version "4.2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://archive.eclipse.org/eclipse/"
+                                  "downloads/drops4/R-" version
+                                  "-201209141800/ecjsrc-" version ".jar"))
+              (sha256
+               (base32
+                "1x281p87m14zylvinkiz6gc23ss7pzlx419qjbql11jriwav4qfj"))))
+    ;; It would be so much easier if we could use the ant-build-system, but we
+    ;; cannot as we don't have ant at this point.  We use ecj for
+    ;; bootstrapping the JDK.
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ; there are no tests
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'unpack
+           (lambda* (#:key source #:allow-other-keys)
+             (mkdir "src")
+             (with-directory-excursion "src"
+               (invoke "gjar" "-xf" source))
+             (chdir "src")))
+         (replace 'configure
+           (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "CLASSPATH"
+                     (string-join
+                      (cons (search-input-file inputs "/lib/rt.jar")
+                            (find-files (string-append
+                                         (assoc-ref inputs "ant-bootstrap")
+                                         "/lib")
+                                        "\\.jar$"))
+                      ":"))
+             ;; This directive is not supported by our simple bootstrap JDK.
+             (substitute* (find-files "." "\\.java$")
+               (("@Override") ""))))
+         (replace 'build
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; We can't compile these yet, but we don't need them at this
+             ;; point anyway.
+             (delete-file "org/eclipse/jdt/core/JDTCompilerAdapter.java")
+             (delete-file-recursively "org/eclipse/jdt/internal/antadapter")
+
+             ;; Create a simple manifest to make ecj executable.
+             (mkdir-p "META-INF")
+             (with-output-to-file "META-INF/MANIFESTS.MF"
+               (lambda _
+                 (display "Manifest-Version: 1.0
+Main-Class: org.eclipse.jdt.internal.compiler.batch.Main\n")))
+
+             ;; Compile it all!
+             (apply invoke "javac"
+                    (find-files "." "\\.java$"))
+
+             ;; Pack it all up!  We don't use "jar" here, because
+             ;; it doesn't produce reproducible zip archives.
+             ;; XXX: copied from (gnu build install)
+             (for-each (lambda (file)
+                         (let ((s (lstat file)))
+                           (unless (eq? (stat:type s) 'symlink)
+                             (utime file  0 0 0 0))))
+                       (find-files "." #:directories? #t))
+
+             ;; It is important that the manifest appears first.
+             (apply invoke "zip" "-0" "-X" "ecj-bootstrap.jar"
+                    "META-INF/MANIFESTS.MF"
+                    (delete "./META-INF/MANIFESTS.MF"
+                            (find-files "." ".*" #:directories? #t)))))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((share (string-append (assoc-ref outputs "out")
+                                         "/share/java/")))
+               (mkdir-p share)
+               (install-file "ecj-bootstrap.jar" share)))))))
+    (native-inputs
+     (list ant-bootstrap classpath-devel ecj-javac-wrapper-final jamvm
+           unzip zip))
+    (home-page "https://eclipse.org")
+    (synopsis "Eclipse Java development tools core batch compiler")
+    (description "This package provides the Eclipse Java core batch compiler
+for bootstrapping purposes.  The @dfn{Eclipse compiler for Java} (ecj) is a
+requirement for all GNU Classpath releases after version 0.93.  This version
+supports sufficient parts of Java 7 to build Icedtea 2.x.")
+    (license license:epl1.0)))
+
+(define ecj4-javac-wrapper
+  (package
+    (inherit ecj-javac-wrapper)
+    (native-inputs
+     (list guile-3.0 ecj4-bootstrap jamvm classpath-devel))))
+
+(define jamvm-with-ecj4
+  (package
+    (inherit jamvm)
+    (inputs
+     (modify-inputs (package-inputs jamvm)
+       (replace "ecj-javac-wrapper" ecj4-javac-wrapper)))))
+

gnu/packages/java-xml.scm

@@ -0,0 +1,688 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2017, 2021, 2023 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2018, 2021 Julien Lepiller <julien@lepiller.eu>
+;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
+;;; Copyright © 2019, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
+;;; Copyright © 2021 Léo Le Bouter <lle-bout@zaclys.net>
+;;; Copyright © 2022 Christopher Baines <mail@cbaines.net>
+;;;
+;;; 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 java-xml)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages check)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages gtk)
+  #:use-module (gnu packages java)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix gexp)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system ant)
+  #:use-module (guix utils))
+
+(define-public java-simple-xml
+  (package
+    (name "java-simple-xml")
+    (version "2.7.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/simple/simple-xml-"
+                                  version ".zip"))
+              (sha256
+               (base32
+                "0w19k1awslmihpwsxwjbg89hv0vjhk4k3i0vrfchy3mqknd988y5"))
+              (patches (search-patches "java-simple-xml-fix-tests.patch"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:build-target "build"
+       #:test-target "test"
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'install (install-jars "jar"))
+         (add-before 'check 'disable-failing-test
+           (lambda _
+             ;; This test sometimes fails with an out of memory exception
+             (delete-file
+              "test/src/org/simpleframework/xml/core/NoAnnotationsRequiredTest.java"))))))
+    (native-inputs
+     (list unzip))
+    (home-page "http://simple.sourceforge.net/")
+    (synopsis "XML serialization framework for Java")
+    (description "Simple is a high performance XML serialization and
+configuration framework for Java.  Its goal is to provide an XML framework
+that enables rapid development of XML configuration and communication systems.
+This framework aids the development of XML systems with minimal effort and
+reduced errors.  It offers full object serialization and deserialization,
+maintaining each reference encountered.")
+    (license license:asl2.0)))
+
+;; TODO: Debian builds several jars out of this: jaxp-1.4.jar,
+;; xml-apis.jar and xml-apis-1.4.01.jar.
+(define-public java-jaxp
+  (package
+    (name "java-jaxp")
+    (version "1.4.01")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://apache/xerces/xml-commons/source/"
+                           "xml-commons-external-" version "-src.tar.gz"))
+       (sha256
+        (base32 "0rhq32a7dl9yik7zx9h0naz2iz068qgcdiayak91wp4wr26xhjyk"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "jaxp.jar"
+       #:jdk ,icedtea-8
+       #:source-dir ".."
+       #:tests? #f)); no tests
+    (home-page "http://xerces.apache.org/xml-commons/")
+    (synopsis "Java XML parser and transformer APIs (DOM, SAX, JAXP, TrAX)")
+    (description "Jaxp from the Apache XML Commons project is used by
+the Xerces-J XML parser and Xalan-J XSLT processor and specifies these APIs:
+
+@itemize
+@item Document Object Model (DOM)
+@item Simple API for XML (SAX)
+@item Java APIs for XML Processing (JAXP)
+@item Transformation API for XML (TrAX)
+@item Document Object Model (DOM) Load and Save
+@item JSR 206 Java API for XML Processing
+@end itemize")
+    (license (list license:asl2.0
+                   license:w3c ;; Files under org.w3c
+                   license:public-domain)))) ;; org.xml.sax
+
+(define-public java-apache-xml-commons-resolver
+  (package
+    (name "java-apache-xml-commons-resolver")
+    (version "1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://apache/xerces/xml-commons/"
+                           "xml-commons-resolver-" version ".tar.gz"))
+       (sha256
+        (base32 "1zhy4anc3fg9f8y348bj88vmab15aavrg6nf419ifb25asyygnsm"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           (for-each delete-file (find-files "." ".*\\.(jar|zip)"))
+           #t))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name (string-append "xml-resolver.jar")
+       #:tests? #f)); no tests
+    (inputs
+     (list java-junit))
+    (home-page "http://xerces.apache.org/xml-commons/")
+    (synopsis "Catalog-based entity and URI resolution")
+    (description "The resolver class implements the full semantics of OASIS Technical
+Resolution 9401:1997 (Amendment 2 to TR 9401) catalogs and the 06 Aug
+2001 Committee Specification of OASIS XML Catalogs.
+
+It also includes a framework of classes designed to read catalog files
+in a number of formats:
+
+@itemize
+@item The plain-text flavor described by TR9401.
+@item The XCatalog XML format defined by John Cowan
+@item The XML Catalog format defined by the OASIS Entity Resolution
+      Technical Committee.
+@end itemize")
+    (license license:asl2.0)))
+
+;; Jaxen requires java-dom4j and java-xom that in turn require jaxen.
+;; This package is a bootstrap version without dependencies on dom4j and xom.
+(define java-jaxen-bootstrap
+  (package
+    (name "java-jaxen-bootstrap")
+    (version "1.1.6")
+    (source (origin
+              (method url-fetch)
+              ;; No release on github
+              (uri (string-append "https://repo1.maven.org/maven2/jaxen/jaxen/"
+                                  version "/jaxen-" version "-sources.jar"))
+              (sha256
+               (base32
+                "18pa8mks3gfhazmkyil8wsp6j1g1x7rggqxfv4k2mnixkrj5x1kx"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "jaxen.jar"
+       #:source-dir "src"
+       #:tests? #f; no tests
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'remove-dom4j
+           (lambda _
+             (delete-file-recursively "src/org/jaxen/dom4j")
+             (delete-file-recursively "src/org/jaxen/xom")
+             #t)))))
+    (inputs
+     `(("java-jdom" ,java-jdom)))
+    (home-page "https://github.com/jaxen-xpath/jaxen")
+    (synopsis "XPath library")
+    (description "Jaxen is an XPath library written in Java.  It is adaptable
+to many different object models, including DOM, XOM, dom4j, and JDOM.  It is
+also possible to write adapters that treat non-XML trees such as compiled
+Java byte code or Java beans as XML, thus enabling you to query these trees
+with XPath too.")
+    (license license:bsd-3)))
+
+(define-public java-jaxen
+  (package
+    (inherit java-jaxen-bootstrap)
+    (name "java-jaxen")
+    (inputs
+     (list java-jdom java-xom java-dom4j))))
+
+(define-public java-xom
+  (package
+    (name "java-xom")
+    (version "127")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/elharo/xom")
+                    (commit (string-append "XOM_" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1jh6y03g5zzdhsb5jm6ms1xnamr460qmn96y3w6aw0ikfwqlg0bq"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (for-each delete-file
+                            (find-files "." "\\.jar$"))
+                  #t))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "xom.jar"
+       #:jdk ,icedtea-8
+       #:tests? #f                      ; no tests
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'make-git-checkout-writable
+           (lambda _
+             (for-each make-file-writable (find-files "."))
+             #t))
+         (add-before 'configure 'fix-tagsoup-dep
+           (lambda _
+             ;; FIXME: Where is tagsoup source?
+             (delete-file "src/nu/xom/tools/XHTMLJavaDoc.java")
+             #t)))))
+    (inputs
+     (list java-jdom java-junit java-classpathx-servletapi
+           java-jaxen-bootstrap java-xerces))
+    (home-page "https://xom.nu/")
+    (synopsis "XML Object Model")
+    (description "XOM is a new XML Object Model for processing XML with Java 
+that strives for correctness and simplicity.")
+    ;; 2.1 only
+    (license license:lgpl2.1)))
+
+(define-public java-xsdlib
+  (package
+    (name "java-xsdlib")
+    (version "2013.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://repo1.maven.org/maven2/com/sun/msv/"
+                                  "datatype/xsd/xsdlib/" version "/xsdlib-"
+                                  version "-sources.jar"))
+              (sha256
+               (base32
+                "185i48p1xp09wbq03i9zgfl701qa262rq46yf4cajzmk3336kqim"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:tests? #f; no tests
+       #:jar-name "xsdlib.jar"
+       #:jdk ,icedtea-8))
+    (inputs
+     (list java-xerces))
+    (home-page (string-append "https://web.archive.org/web/20161127144537/"
+                              "https://msv.java.net//"))
+    (synopsis "Sun Multi-Schema Validator")
+    (description "Xsdlib contains an implementation of sun.com.msv, an XML
+validator.")
+    (license license:bsd-2)))
+
+(define-public java-xpp3
+  (package
+    (name "java-xpp3")
+    (version "1.1.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://ci.guix.gnu.org/file/"
+                    "xpp3-1.1.4_src.tgz"
+                    "/sha256/"
+                    "1b99zrhyij5qwyhilyjdl1ykxvhk902vsvflh6gx4fir8hfvdl5p"))
+              (file-name (string-append name "-" version "_src.tgz"))
+              (sha256
+               (base32
+                "1b99zrhyij5qwyhilyjdl1ykxvhk902vsvflh6gx4fir8hfvdl5p"))
+              (modules '((guix build utils)))
+              (snippet
+                '(begin ;; Delete bundled jar archives.
+                   (for-each delete-file (find-files "." ".*\\.jar"))
+                   #t))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:tests? #f; no tests
+       #:build-target "jar"
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'install (install-jars "build")))))
+    (home-page "http://www.extreme.indiana.edu/xgws/xsoap/xpp/")
+    (synopsis "Streaming pull XML parser")
+    (description "Xml Pull Parser (in short XPP) is a streaming pull XML
+parser and should be used when there is a need to process quickly and
+efficiently all input elements (for example in SOAP processors). This
+package is a stable XmlPull parsing engine that is based on ideas from XPP
+and in particular XPP2 but completely revised and rewritten to take the best
+advantage of JIT JVMs.")
+    (license (license:non-copyleft "file://LICENSE.txt"))))
+
+(define-public java-xmlpull2
+  (package
+    (name "java-xmlpull2")
+    (version "2.1.10")
+    (source (origin
+              (method url-fetch)
+              ;; Unfortunately, archive.org does not have a copy of this file.
+              (uri (string-append "https://ftp.fau.de/gentoo/distfiles/"
+                                  "PullParser" version ".tgz"))
+              (sha256
+               (base32
+                "1kw9nhyqb7bzhn2zjbwlpi5vp5rzj89amzi3hadw2acyh2dmd0md"))
+              (modules '((guix build utils)))
+              (snippet
+                '(begin ;; Delete bundled jar archives.
+                   (for-each delete-file (find-files "." ".*\\.jar"))
+                   #t))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:tests? #f; no tests
+       #:build-target "impl"
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'install (install-jars "build/lib")))))
+    (home-page (string-append "https://web.archive.org/web/20210225153105/"
+                              "https://www.extreme.indiana.edu/"))
+    (synopsis "Streaming pull XML parser")
+    (description "Xml Pull Parser (in short XPP) is a streaming pull XML
+parser and should be used when there is a need to process quickly and
+efficiently all input elements (for example in SOAP processors).  This
+package is in maintenance mode.")
+    (license (license:non-copyleft "file:///LICENSE.txt"))))
+
+(define-public java-xmlpull-api-v1
+  (package
+    (name "java-xmlpull-api-v1")
+    (version "1.1.3.4b")
+    (source (origin
+              ;; The package is originally from Extreme! Lab, but the website
+              ;; is now gone.  This repositories contains the sources of the
+              ;; latest version.
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/aslom/xmlpull-api-v1")
+                     ;; No releases, this is the latest commit
+                     (commit "abeaa4aa87b2625af70c32f658f44e11355fe568")))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "15bdqxfncnakskna4m9gsh4f9iczxy83qxn2anqiqd15z406a5ih"))
+              (modules '((guix build utils)))
+              (snippet
+               `(begin
+                  (delete-file-recursively "lib")
+                  (mkdir-p "lib")
+                  ;; prevents a failure in "dist_lite"
+                  (substitute* "build.xml"
+                    (("README.html") "README.md"))))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:test-target "junit"
+       #:build-target "dist"
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (doc (string-append out "/share/doc/" ,name "-" ,version))
+                    (java (string-append out "/share/java"))
+                    (project (string-append
+                               "xmlpull_"
+                               ,(string-join (string-split version #\.) "_"))))
+               (mkdir-p doc)
+               (copy-recursively (string-append "build/dist/" project "/doc/")
+                                 doc)
+               (mkdir-p java)
+               (copy-file (string-append "build/dist/" project "/" project ".jar")
+                          (string-append java "/" project ".jar")))
+             )))))
+    (home-page "https://github.com/aslom/xmlpull-api-v1")
+    (synopsis "XML pull parsing API")
+    (description "XmlPull v1 API is a simple to use XML pull parsing API.  XML
+pull parsing allows incremental (sometimes called streaming) parsing of XML
+where application is in control - the parsing can be interrupted at any given
+moment and resumed when application is ready to consume more input.")
+    (license license:public-domain)))
+
+(define-public java-dom4j
+  (package
+    (name "java-dom4j")
+    (version "2.1.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/dom4j/dom4j")
+                    (commit (string-append "version-" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0q907srj9v4hwicpcrn4slyld5npf2jv7hzchsgrg29q2xmbwkdl"))
+              (modules '((guix build utils)))
+              (snippet
+                '(begin ;; Delete bundled jar archives.
+                   (for-each delete-file (find-files "." ".*\\.jar"))
+                   #t))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "dom4j.jar"
+       #:jdk ,icedtea-8
+       #:source-dir "src/main/java"
+       ;; FIXME: Requires xalan, but xalan depends on java-cup which has a
+       ;; dependency on itself through jflex.
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-jaxen-sources
+           ;; java-jaxen-bootstrap is not enough. These files have a circular
+           ;; dependency and there is no subset of dom4j that would allow
+           ;; breaking the circle.
+           (lambda* (#:key inputs #:allow-other-keys)
+             (mkdir-p "jaxen-sources")
+             (with-directory-excursion "jaxen-sources"
+               (system* "jar" "xf" (assoc-ref inputs "java-jaxen-sources")))
+             (mkdir-p "src/main/java/org/jaxen/dom4j")
+             (copy-file "jaxen-sources/org/jaxen/dom4j/DocumentNavigator.java"
+                        "src/main/java/org/jaxen/dom4j/DocumentNavigator.java")
+             (copy-file "jaxen-sources/org/jaxen/dom4j/Dom4jXPath.java"
+                        "src/main/java/org/jaxen/dom4j/Dom4jXPath.java")
+             #t))
+         (add-before 'build 'fix-old-xpp2
+           (lambda _
+             ;; This package normally depends on xpp2 2.0, but version 2.1.10
+             ;; is the only version whose source code is published.
+             (substitute* "src/main/java/org/dom4j/xpp/ProxyXmlStartTag.java"
+               (("public void resetStartTag")
+                "public boolean removeAttributeByRawName(String name) {\n
+  return false;\n
+}\n
+public boolean removeAttributeByName(String name, String name2) {\n
+  return false;\n
+}\n\npublic void resetStartTag")
+               (("Atttribute") "Attribute"))
+             #t)))))
+    (inputs
+     `(("java-jaxen-bootstrap" ,java-jaxen-bootstrap)
+       ("java-jaxen-sources" ,(package-source java-jaxen-bootstrap))
+       ("java-xmlpull2" ,java-xmlpull2)
+       ("java-xpp3" ,java-xpp3)
+       ("java-xsdlib" ,java-xsdlib)))
+    (native-inputs
+     (list java-testng java-xerces))
+    (home-page "https://dom4j.github.io/")
+    (synopsis "Flexible XML framework for Java")
+    (description "Dom4j is a flexible XML framework for Java.  DOM4J works
+with DOM, SAX, XPath, and XSLT.  It can parse large XML documents with very
+low memory footprint.")
+    ;; some BSD-like 5-clause license
+    (license (license:non-copyleft "file://LICENSE"))))
+
+(define-public java-kxml2
+  (package
+    (name "java-kxml2")
+    (version "2.4.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/stefanhaustein/kxml2")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0g6d8c9r9sh3x04sf4wdpgwvhkqvk11k3kq9skx91i60h4vn01hg"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "kxml2.jar"
+       #:source-dir "src/main/java"
+       #:test-include (list "TestWb.java")
+       ;; Test failure: it was expected to get an XML entity but got the
+       ;; equivalent Unicode character instead.
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'make-git-checkout-writable
+           (lambda _
+             (for-each make-file-writable (find-files "."))
+             #t))
+         (add-before 'build 'copy-resources
+           (lambda _
+             (copy-recursively "src/main/resources" "build/classes")
+             #t)))))
+    (inputs
+     (list java-xpp3))
+    (native-inputs
+     (list java-junit))
+    (home-page "http://kxml.org")
+    (synopsis "XML pull parser")
+    (description "kXML is a small XML pull parser, specially designed for
+constrained environments such as Applets, Personal Java or devices compliant
+with the Mobile Information Device Profile (MIDP).")
+    (license license:expat)))
+
+(define-public java-stax
+  (package
+    (name "java-stax")
+    (version "1.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://repo1.maven.org/maven2/stax/stax/"
+                                  version "/stax-" version "-sources.jar"))
+              (sha256
+               (base32
+                "04ba4qvbrps45j8bldbakxq31k7gjlsay9pppa9yn13fr00q586z"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "stax.jar"
+       #:tests? #f; no tests
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'fix-utf8
+           (lambda _
+             ;; This file is ISO-8859-1 but java expects UTF-8.
+             ;; Remove special characters in comments.
+             (with-fluids ((%default-port-encoding "ISO-8859-1"))
+               (substitute* "src/com/wutka/dtd/Scanner.java"
+                 (("//.*") "\n")))
+             #t)))))
+    (home-page "https://repo1.maven.org/maven2/stax/stax/")
+    (synopsis "Streaming API for XML")
+    (description "This package provides the reference implementation of the
+@dfn{Streaming API for XML} (StAX).  It is used for streaming XML data to
+and from a Java application.  It provides a standard pull parser interface.")
+    (license license:asl2.0)))
+
+(define-public java-jettison
+  (package
+    (name "java-jettison")
+    (version "1.3.7")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/codehaus/jettison")
+                    (commit (string-append "jettison-" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "15sydmi5chdh4126qc7v8bsrp7fp4ldaya8a05iby4pq2324q0qw"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "jettison.jar"
+       #:source-dir "src/main/java"
+       #:test-exclude (list "**/Abstract*.java"
+                            ;; Abstract classes
+                            "**/DOMTest.java"
+                            "**/BadgerFishDOMTest.java"
+                            "**/MappedDOMTest.java")))
+    (native-inputs
+     (list java-junit))
+    (home-page "https://github.com/codehaus/jettison")
+    (synopsis "StAX implementation for JSON")
+    (description "Jettison is a Java library for converting XML to JSON and
+vice-versa with the help of the @dfn{Streaming API for XML} (StAX).  It
+implements @code{XMLStreamWriter} and @code{XMLStreamReader} and supports
+@code{Mapped} and @code{BadgerFish} conventions.")
+    (license license:asl2.0)))
+
+(define-public java-jdom2
+  (package
+    (name "java-jdom")
+    (version "2.0.6.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/hunterhacker/jdom")
+                    (commit (string-append "JDOM-" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1r4pwl0z7hm45v9l2wbq3fjmqi13zmwzbrggyqizrwv31kghhx56"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:build-target "package"
+       #:tests? #f                ; tests are run as part of the build process
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'install
+           (install-jars "build")))))
+    (home-page "http://jdom.org/")
+    (synopsis "Access, manipulate, and output XML data")
+    (description "Jdom is a Java-based solution for accessing, manipulating, and
+outputting XML data from Java code.")
+    (license license:bsd-4)))
+
+(define-public java-xstream
+  (package
+    (name "java-xstream")
+    (version "1.4.16")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/x-stream/xstream")
+             (commit (string-append
+                      "XSTREAM_"
+                      (string-map (lambda (x) (if (eq? x #\.) #\_ x))
+                                  version)))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "16k2mc63h2fw7lxv74qmhg4p8q9hfrw114daa6nxwnpv08cnq755"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "xstream.jar"
+       ;; FIXME: Tests are not in a java subdirectory as assumed by ant-build-system.
+       #:tests? #f
+       #:jdk ,icedtea-8
+       #:source-dir "xstream/src/java"))
+    (inputs
+     `(("java-jdom" ,java-jdom)
+       ("java-jdom2" ,java-jdom2)
+       ("java-cglib" ,java-cglib)
+       ("java-joda-time" ,java-joda-time)
+       ("java-jettison" ,java-jettison)
+       ("java-xom" ,java-xom)
+       ("java-mxparser" ,java-mxparser)
+       ("java-xpp3" ,java-xpp3)
+       ("java-dom4j" ,java-dom4j)
+       ("java-stax2-api" ,java-stax2-api)
+       ("java-woodstox-core" ,java-woodstox-core)
+       ("java-kxml2" ,java-kxml2)
+       ("java-stax" ,java-stax)))
+    (home-page "https://x-stream.github.io")
+    (synopsis "XML serialization library")
+    (description "XStream is a simple library to serialize Java objects to XML
+and back again.")
+    (license license:bsd-3)))
+
+(define-public java-mxparser
+  (package
+    (name "java-mxparser")
+    (version "1.2.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/x-stream/mxparser")
+              (commit (string-append "v-" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0i3jrjbz4hgf62fm1ix7nlcmhi4kcv4flqsfvh7a3l2v7nsp5ryb"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "mxparser.jar"
+       #:source-dir "src/main/java"
+       #:test-dir "src/test"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (copy-recursively "src/main/resources" "build/classes")
+             #t)))))
+    (propagated-inputs
+     (list java-xmlpull-api-v1))
+    (native-inputs
+     (list java-junit))
+    (home-page "https://github.com/x-stream/mxparser")
+    (synopsis "Streaming pull XML parser forked from @code{java-xpp3}")
+    (description "Xml Pull Parser (in short XPP) is a streaming pull XML
+parser and should be used when there is a need to process quickly and
+efficiently all input elements (for example in SOAP processors). This
+package is a stable XmlPull parsing engine that is based on ideas from XPP
+and in particular XPP2 but completely revised and rewritten to take the best
+advantage of JIT JVMs.
+
+MXParser is a fork of xpp3_min 1.1.7 containing only the parser with merged
+changes of the Plexus fork. It is an implementation of the XMLPULL V1 API
+(parser only).")
+    (license (license:non-copyleft "file://LICENSE.txt"))))
+
+
+
+
+
+
+
+
+
+

gnu/packages/linux.scm

@@ -15,7 +15,7 @@
 ;;; Copyright © 2016, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2016 John Darrington <jmd@gnu.org>
-;;; Copyright © 2016-2022 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2016-2023 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2016, 2018 Rene Saavedra <pacoon@protonmail.com>
 ;;; Copyright © 2016 Carlos Sánchez de La Lama <csanchezdll@gmail.com>
 ;;; Copyright © 2016, 2017 Nikita <nikita@n0.is>
@@ -588,21 +588,6 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.14)))
 
-(define-public linux-libre-4.9-version "4.9.337")
-(define-public linux-libre-4.9-gnu-revision "gnu1")
-(define deblob-scripts-4.9
-  (linux-libre-deblob-scripts
-   linux-libre-4.9-version
-   linux-libre-4.9-gnu-revision
-   (base32 "0nai5m4rbh37qaj1xf2qj7656l2gacfh0847q5d07y22b048fq5n")
-   (base32 "0bib3641dbcqdkx3anna3caxnsg3nw9cnmhcklq0s93g3m57041h")))
-(define-public linux-libre-4.9-pristine-source
-  (let ((version linux-libre-4.9-version)
-        (hash (base32 "1imkn3dbxsr35br79sp9s2r9hy1xqvsm652icbsf6rn7apnam1ak")))
-    (make-linux-libre-source version
-                             (%upstream-linux-source version hash)
-                             deblob-scripts-4.9)))
-
 (define %boot-logo-patch
   ;; Linux-Libre boot logo featuring Freedo and a gnu.
   (origin
@@ -671,10 +656,6 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (source-with-patches linux-libre-4.14-pristine-source
                        (list %boot-logo-patch)))
 
-(define-public linux-libre-4.9-source
-  (source-with-patches linux-libre-4.9-pristine-source
-                       (list %boot-logo-patch)))
-
 
 ;;;
 ;;; Kernel headers.
@@ -787,11 +768,6 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
                              linux-libre-4.14-gnu-revision
                              linux-libre-4.14-source))
 
-(define-public linux-libre-headers-4.9
-  (make-linux-libre-headers* linux-libre-4.9-version
-                             linux-libre-4.9-gnu-revision
-                             linux-libre-4.9-source))
-
 ;; The following package is used in the early bootstrap, and thus must be kept
 ;; stable and with minimal build requirements.
 (define-public linux-libre-headers-5.10.35
@@ -1159,13 +1135,6 @@ Linux kernel.  It has been modified to remove all non-free binary blobs.")
                        "powerpc64le-linux")
                      #:configuration-file kernel-config))
 
-(define-public linux-libre-4.9
-  (make-linux-libre* linux-libre-4.9-version
-                     linux-libre-4.9-gnu-revision
-                     linux-libre-4.9-source
-                     '("x86_64-linux" "i686-linux" "powerpc64le-linux")
-                     #:configuration-file kernel-config))
-
 ;; Linux-Libre-LTS points to the *newest* released long-term support version of
 ;; Linux-Libre.
 ;; Reference: https://jxself.org/linux-libre/
@@ -6594,30 +6563,20 @@ The following service daemons are also provided:
 (define-public perftest
   (package
     (name "perftest")
-    (version "4.4-0.4")
+    (version "4.5-0.20")
-    (source
+    (home-page "https://github.com/linux-rdma/perftest")
-     (origin
+    (source (origin
-       (method url-fetch)
+              (method git-fetch)
-       (uri (string-append "https://github.com/linux-rdma/perftest/releases/download/v"
+              (uri (git-reference (url home-page)
-                           version "/perftest-" version ".g0927198.tar.gz"))
+                                  (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
-        (base32 "11ix4h0rrmqqyi84y55a9xnkvwsmwq0sywr46hvxzm4rqz4ma8vq"))))
+               (base32
+                "1hrpzmkz1kq4jwpy6b5fl8073iy7dllcq2hfzdw6waaf5920vd64"))))
     (build-system gnu-build-system)
-    (arguments
+    (native-inputs
-     `(#:phases
+     (list autoconf automake libtool))
-       (modify-phases %standard-phases
+    (inputs (list pciutils rdma-core))
-         (add-after 'unpack 'patch-header-paths
-           (lambda _
-             (substitute* '("src/raw_ethernet_fs_rate.c"
-                            "src/raw_ethernet_resources.c"
-                            "src/raw_ethernet_resources.h"
-                            "src/raw_ethernet_send_burst_lat.c"
-                            "src/raw_ethernet_send_bw.c"
-                            "src/raw_ethernet_send_lat.c")
-               (("/usr/include/netinet/ip.h") "netinet/ip.h"))
-             #t)))))
-    (inputs (list rdma-core))
-    (home-page "https://github.com/linux-rdma/perftest/")
     (synopsis "Open Fabrics Enterprise Distribution (OFED) Performance Tests")
     (description "This is a collection of tests written over uverbs intended for
 use as a performance micro-benchmark. The tests may be used for hardware or

gnu/packages/llvm.scm

@@ -562,11 +562,11 @@ output), and Binutils.")
 
 (define %llvm-monorepo-hashes
   '(("14.0.6" . "14f8nlvnmdkp9a9a79wv67jbmafvabczhah8rwnqrgd5g3hfxxxx")
-    ("15.0.5" . "1z2szqlanksdmj91590wnxqav5z437mpasg00ghb610xkam2v34m")))
+    ("15.0.6" . "13vj0q6if5095a3awq8d97l17qdsc7fks6avkai9k80kl0kzxpv6")))
 
 (define %llvm-patches
   '(("14.0.6" . ("clang-14.0-libc-search-path.patch"))
-    ("15.0.5" . ("clang-15.0-libc-search-path.patch"))))
+    ("15.0.6" . ("clang-15.0-libc-search-path.patch"))))
 
 (define (llvm-monorepo version)
   (origin
@@ -582,7 +582,7 @@ output), and Binutils.")
 (define-public llvm-15
   (package
     (name "llvm")
-    (version "15.0.5")
+    (version "15.0.6")
     (source (llvm-monorepo version))
     (build-system cmake-build-system)
     (outputs '("out" "opt-viewer"))
@@ -739,7 +739,7 @@ of programming tools as well as libraries with equivalent functionality.")
                     (package-version llvm-15)))
      (sha256
       (base32
-       "0sa6si9v7ddsa9vmg6s3918xx969rvck2v1a0g7hb0fp9jk9j4r1")))))
+       "099v2yqg11h0h8qqddzkny6b77pafcr7vy5ksc33kqggji173ccj")))))
 
 (define-public clang-14
   (clang-from-llvm

gnu/packages/maven.scm

@@ -32,9 +32,9 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages java)
+  #:use-module (gnu packages java-xml)
   #:use-module (gnu packages maven-parent-pom)
   #:use-module (gnu packages web)
-  #:use-module (gnu packages xml)
   #:use-module (ice-9 match))
 
 (define-public maven-resolver-api

gnu/packages/minetest.scm

@@ -472,6 +472,31 @@ bunnies, chickens, cows, kittens, rats, sheep, warthogs, penguins and pandas.")
     (license (list license:cc0 license:expat))
     (properties `((upstream-name . "TenPlus1/mobs_animal")))))
 
+(define-public minetest-mobs-monster
+  (package
+    (name "minetest-mobs-monster")
+    ;; Upstream does not use version numbers, so use the release title
+    ;; from ContentDB instead;
+    (version "2022-12-10")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://notabug.org/TenPlus1/mobs_monster")
+             (commit "1b197f9ae136179a764ef45824464b667ade52e6")))
+       (sha256
+        (base32 "15g8acrzvsiccxchfmgjhyf2lmkbrpdjqv3v7hmqz7xqypi8wm3h"))
+       (file-name (git-file-name name version))))
+    (build-system minetest-mod-build-system)
+    (propagated-inputs (list minetest-mobs))
+    (home-page "https://notabug.org/TenPlus1/mobs_monster")
+    (synopsis "Add monsters with Mobs Redo on minetest")
+    (description
+     "This Minetest mod adds many types of monsters to Minetest, that live on the
+surface or deep underground.")
+    (license license:expat)
+    (properties `((upstream-name . "TenPlus1/mobs_monster")))))
+
 (define-public minetest-pipeworks
   (package
     (name "minetest-pipeworks")
@@ -769,3 +794,25 @@ build your island in the sky.  Every 30 seconds you will receive a random
 block or item from the oneblock to expand the island!")
     (license license:gpl3+)
     (properties `((upstream-name . "NO11/oneblock")))))
+
+(define-public minetest-wielded-light
+  (package
+    (name "minetest-wielded-light")
+    (version "2022-06-24")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/minetest-mods/wielded_light")
+                    (commit "b5236562af9772dff8522fe2bda5b5f738e81b88")))
+              (sha256
+               (base32
+                "0m5rf8wkc9iq04xppjfva9d83qmhlnx8fibdbi2d3pkwwl6p2y5c"))
+              (file-name (git-file-name name version))))
+    (build-system minetest-mod-build-system)
+    (home-page (minetest-topic 19378))
+    (synopsis "Adds shining for wielded and dropped items")
+    (description
+     "With this Minetest extension, all bright nodes lighten the player
+environment if wielded.")
+    (license license:gpl3+)
+    (properties `((upstream-name . "bell07/wielded_light")))))

gnu/packages/patches/python-afdko-suppress-copyright-test.patch

@@ -0,0 +1,20 @@
+Supress copyright check in tests which can differ based on current year.
+
+  https://github.com/adobe-type-tools/afdko/issues/1589
+
+Adapted from upstream:
+
+  https://github.com/adobe-type-tools/afdko/commit/feebd77d9b6507a0b32f837535511be3c94d9c6f
+
+diff --git a/tests/tx_test.py b/tests/tx_test.py
+--- a/tests/tx_test.py
++++ b/tests/tx_test.py
+@@ -1246,7 +1246,7 @@ def test_ufo_fontinfo_parsing(file, msg, ret_code):
+     if (ret_code == 0):
+         expected_path = generate_ps_dump(expected_path)
+         output_path = generate_ps_dump(output_path)
+-        assert differ([expected_path, output_path])
++        assert differ([expected_path, output_path, '-s'] + PFA_SKIP)
+     else:
+         arg = [TOOL, '-t1', '-f', ufo_input_path]
+         assert subprocess.call(arg) == 6

gnu/packages/rust-apps.scm

@@ -6,7 +6,7 @@
 ;;; Copyright © 2020 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2020 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2020 Gabriel Arazas <foo.dogsquared@gmail.com>
-;;; Copyright © 2020-2022 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2020-2023 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.ccom>
@@ -1314,14 +1314,14 @@ of the project is to be runnable on untrusted networks without crashing.")
 (define-public tectonic
   (package
     (name "tectonic")
-    (version "0.8.2")
+    (version "0.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "tectonic" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32 "041v887a3aybrkn5fnrjwy95wxfk4npl6lj8ar8dnidjmfh92bka"))))
+        (base32 "1q4mz2c32gfypx33zlzgd1q9h4322jrk13fzvsf8h676ylclqzpc"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-build-flags '("--release" "--features" "external-harfbuzz")
@@ -1341,18 +1341,17 @@ of the project is to be runnable on untrusted networks without crashing.")
         ("rust-sha2" ,rust-sha2-0.9)
         ("rust-structopt" ,rust-structopt-0.3)
         ("rust-tectonic-bridge-core" ,rust-tectonic-bridge-core-0.3)
-        ("rust-tectonic-bundles" ,rust-tectonic-bundles-0.2)
+        ("rust-tectonic-bundles" ,rust-tectonic-bundles-0.3)
-        ("rust-tectonic-docmodel" ,rust-tectonic-docmodel-0.1)
+        ("rust-tectonic-docmodel" ,rust-tectonic-docmodel-0.2)
         ("rust-tectonic-engine-bibtex" ,rust-tectonic-engine-bibtex-0.1)
         ("rust-tectonic-engine-spx2html" ,rust-tectonic-engine-spx2html-0.1)
-        ("rust-tectonic-engine-xdvipdfmx" ,rust-tectonic-engine-xdvipdfmx-0.1)
+        ("rust-tectonic-engine-xdvipdfmx" ,rust-tectonic-engine-xdvipdfmx-0.4)
-        ("rust-tectonic-engine-xetex" ,rust-tectonic-engine-xetex-0.2)
+        ("rust-tectonic-engine-xetex" ,rust-tectonic-engine-xetex-0.4)
         ("rust-tectonic-errors" ,rust-tectonic-errors-0.2)
         ("rust-tectonic-geturl" ,rust-tectonic-geturl-0.3)
         ("rust-tectonic-io-base" ,rust-tectonic-io-base-0.4)
         ("rust-tectonic-status-base" ,rust-tectonic-status-base-0.2)
         ("rust-tectonic-xdv" ,rust-tectonic-xdv-0.2)
-        ("rust-tectonic-xetex-layout" ,rust-tectonic-xetex-layout-0.1)
         ("rust-tempfile" ,rust-tempfile-3)
         ("rust-termcolor" ,rust-termcolor-1)
         ("rust-toml" ,rust-toml-0.5)

gnu/packages/statistics.scm

@@ -1138,14 +1138,14 @@ designed by Cynthia Brewer as described at http://colorbrewer2.org")
 (define-public r-sendmailr
   (package
     (name "r-sendmailr")
-    (version "1.3-1")
+    (version "1.3-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sendmailR" version))
        (sha256
         (base32
-         "1vxs9pdz1qbm7gzzigmvn5ybglakj4fska8dfj94azdvpkijs6hx"))))
+         "0yyxxzhm88xipk68vzqxcckcpjgl9lajnqyxxbkp1i29jcpfgdfa"))))
     (properties `((upstream-name . "sendmailR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5038,13 +5038,13 @@ Wall Street Journal, among others.  This package also provides
 (define-public r-statmod
   (package
     (name "r-statmod")
-    (version "1.4.37")
+    (version "1.5.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "statmod" version))
               (sha256
                (base32
-                "04v9nynv3lakhnd7b17v5syrlnscrxml71jnd3r93chckskwillh"))))
+                "1jbf07h0mnncn2qp4wcw5bnbvsw3lizpd3cg0cpb8mcxn3wkw76n"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/statmod")
     (native-inputs
@@ -5521,14 +5521,14 @@ of the points.")
 (define-public r-fpc
   (package
     (name "r-fpc")
-    (version "2.2-9")
+    (version "2.2-10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fpc" version))
        (sha256
         (base32
-         "0f7sfmpcycr9y7cy5gasyjm2ardxa62kglqms92mcr68jrp01c19"))))
+         "1lj7j74yx747iic1hcngzbym0sqxppja8bxw64m0j6na5s7m9d4r"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-class

gnu/packages/web.scm

@@ -19,7 +19,7 @@
 ;;; Copyright © 2016–2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016 Bake Timmons <b3timmons@speedymail.org>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
-;;; Copyright © 2017, 2018, 2020, 2021, 2022 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2017-2018, 2020-2023 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2017 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2017 Petter <petter@mykolab.ch>
 ;;; Copyright © 2017, 2021 Pierre Langlois <pierre.langlois@gmx.com>
@@ -5230,28 +5230,34 @@ NetSurf project.")
                          (find-files bin))
                #t))))))
     (native-inputs
-     `(("which" ,which)
+     (list which
-       ("gettext" ,gettext-minimal)
+           gettext-minimal
-       ("subversion" ,subversion)
+           subversion
-       ("git" ,git)
+           git
-       ("bazaar" ,bazaar)
+           bazaar
-       ("cvs" ,cvs)
+           cvs
-       ("mercurial" ,mercurial)))
+           mercurial))
     (inputs
-     `(("python" ,python-wrapper)
+     (list python-wrapper
-       ("perl-authen-passphrase" ,perl-authen-passphrase)
+           perl-authen-passphrase
-       ("perl-cgi-simple" ,perl-cgi-simple)
+           perl-cgi-simple
-       ("perl-db-file" ,perl-db-file)
+           perl-db-file
-       ("perl-file-mimeinfo" ,perl-file-mimeinfo)
+           perl-file-mimeinfo
-       ("perl-html-tagset" ,perl-html-tagset)
+           perl-html-tagset
-       ("perl-image-magick" ,perl-image-magick)
+           perl-image-magick
-       ("perl-ipc-run" ,perl-ipc-run)
+           perl-ipc-run
-       ("perl-lwpx-paranoidagent" ,perl-lwpx-paranoidagent)
+           perl-lwpx-paranoidagent
-       ("perl-xml-feed" ,perl-xml-feed)
+           perl-xml-feed
-       ("perl-xml-sax" ,perl-xml-sax)
+           perl-xml-sax
-       ("perl-xml-twig" ,perl-xml-twig)
+           perl-xml-twig
-       ("perl-yaml-tiny" ,perl-yaml-tiny)
+           perl-yaml-tiny
-       ("po4a" ,po4a)))
+
+           ;; Ikiwiki loads po4a as a library, and thus needs the po4a dependencies
+           ;; available.  Duplicate them here.
+           ;; XXX: It would be ideal to hard code these in po4a somehow.
+           perl-syntax-keyword-try
+           perl-xs-parse-keyword
+           po4a))
     (propagated-inputs
      (list perl-cgi-formbuilder
            perl-cgi-session

gnu/packages/xml.scm

@@ -64,7 +64,6 @@
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages gtk)
-  #:use-module (gnu packages java)
   #:use-module (gnu packages nss)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages perl-check)
@@ -76,7 +75,6 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
-  #:use-module (guix build-system ant)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
@@ -1544,42 +1542,6 @@ Excel(TM) since version 2007.")
     (home-page "https://github.com/brechtsanders/xlsxio")
     (license license:expat)))
 
-(define-public java-simple-xml
-  (package
-    (name "java-simple-xml")
-    (version "2.7.1")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://sourceforge/simple/simple-xml-"
-                                  version ".zip"))
-              (sha256
-               (base32
-                "0w19k1awslmihpwsxwjbg89hv0vjhk4k3i0vrfchy3mqknd988y5"))
-              (patches (search-patches "java-simple-xml-fix-tests.patch"))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:build-target "build"
-       #:test-target "test"
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'install (install-jars "jar"))
-         (add-before 'check 'disable-failing-test
-           (lambda _
-             ;; This test sometimes fails with an out of memory exception
-             (delete-file
-              "test/src/org/simpleframework/xml/core/NoAnnotationsRequiredTest.java"))))))
-    (native-inputs
-     (list unzip))
-    (home-page "http://simple.sourceforge.net/")
-    (synopsis "XML serialization framework for Java")
-    (description "Simple is a high performance XML serialization and
-configuration framework for Java.  Its goal is to provide an XML framework
-that enables rapid development of XML configuration and communication systems.
-This framework aids the development of XML systems with minimal effort and
-reduced errors.  It offers full object serialization and deserialization,
-maintaining each reference encountered.")
-    (license license:asl2.0)))
-
 (define-public perl-xml-xpathengine
   (package
     (name "perl-xml-xpathengine")
@@ -1735,610 +1697,6 @@ XML), full XPath support (unless you use @code{XML::Twig::XPath}), nor DOM
 support.")
     (license license:perl-license)))
 
-;; TODO: Debian builds several jars out of this: jaxp-1.4.jar,
-;; xml-apis.jar and xml-apis-1.4.01.jar.
-(define-public java-jaxp
-  (package
-    (name "java-jaxp")
-    (version "1.4.01")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "mirror://apache/xerces/xml-commons/source/"
-                           "xml-commons-external-" version "-src.tar.gz"))
-       (sha256
-        (base32 "0rhq32a7dl9yik7zx9h0naz2iz068qgcdiayak91wp4wr26xhjyk"))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:jar-name "jaxp.jar"
-       #:jdk ,icedtea-8
-       #:source-dir ".."
-       #:tests? #f)); no tests
-    (home-page "http://xerces.apache.org/xml-commons/")
-    (synopsis "Java XML parser and transformer APIs (DOM, SAX, JAXP, TrAX)")
-    (description "Jaxp from the Apache XML Commons project is used by
-the Xerces-J XML parser and Xalan-J XSLT processor and specifies these APIs:
-
-@itemize
-@item Document Object Model (DOM)
-@item Simple API for XML (SAX)
-@item Java APIs for XML Processing (JAXP)
-@item Transformation API for XML (TrAX)
-@item Document Object Model (DOM) Load and Save
-@item JSR 206 Java API for XML Processing
-@end itemize")
-    (license (list license:asl2.0
-                   license:w3c ;; Files under org.w3c
-                   license:public-domain)))) ;; org.xml.sax
-
-(define-public java-apache-xml-commons-resolver
-  (package
-    (name "java-apache-xml-commons-resolver")
-    (version "1.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "mirror://apache/xerces/xml-commons/"
-                           "xml-commons-resolver-" version ".tar.gz"))
-       (sha256
-        (base32 "1zhy4anc3fg9f8y348bj88vmab15aavrg6nf419ifb25asyygnsm"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           (for-each delete-file (find-files "." ".*\\.(jar|zip)"))
-           #t))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:jar-name (string-append "xml-resolver.jar")
-       #:tests? #f)); no tests
-    (inputs
-     (list java-junit))
-    (home-page "http://xerces.apache.org/xml-commons/")
-    (synopsis "Catalog-based entity and URI resolution")
-    (description "The resolver class implements the full semantics of OASIS Technical
-Resolution 9401:1997 (Amendment 2 to TR 9401) catalogs and the 06 Aug
-2001 Committee Specification of OASIS XML Catalogs.
-
-It also includes a framework of classes designed to read catalog files
-in a number of formats:
-
-@itemize
-@item The plain-text flavor described by TR9401.
-@item The XCatalog XML format defined by John Cowan
-@item The XML Catalog format defined by the OASIS Entity Resolution
-      Technical Committee.
-@end itemize")
-    (license license:asl2.0)))
-
-;; Jaxen requires java-dom4j and java-xom that in turn require jaxen.
-;; This package is a bootstrap version without dependencies on dom4j and xom.
-(define java-jaxen-bootstrap
-  (package
-    (name "java-jaxen-bootstrap")
-    (version "1.1.6")
-    (source (origin
-              (method url-fetch)
-              ;; No release on github
-              (uri (string-append "https://repo1.maven.org/maven2/jaxen/jaxen/"
-                                  version "/jaxen-" version "-sources.jar"))
-              (sha256
-               (base32
-                "18pa8mks3gfhazmkyil8wsp6j1g1x7rggqxfv4k2mnixkrj5x1kx"))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:jar-name "jaxen.jar"
-       #:source-dir "src"
-       #:tests? #f; no tests
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'remove-dom4j
-           (lambda _
-             (delete-file-recursively "src/org/jaxen/dom4j")
-             (delete-file-recursively "src/org/jaxen/xom")
-             #t)))))
-    (inputs
-     `(("java-jdom" ,java-jdom)))
-    (home-page "https://github.com/jaxen-xpath/jaxen")
-    (synopsis "XPath library")
-    (description "Jaxen is an XPath library written in Java.  It is adaptable
-to many different object models, including DOM, XOM, dom4j, and JDOM.  It is
-also possible to write adapters that treat non-XML trees such as compiled
-Java byte code or Java beans as XML, thus enabling you to query these trees
-with XPath too.")
-    (license license:bsd-3)))
-
-(define-public java-jaxen
-  (package
-    (inherit java-jaxen-bootstrap)
-    (name "java-jaxen")
-    (inputs
-     (list java-jdom java-xom java-dom4j))))
-
-(define-public java-xom
-  (package
-    (name "java-xom")
-    (version "127")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/elharo/xom")
-                    (commit (string-append "XOM_" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1jh6y03g5zzdhsb5jm6ms1xnamr460qmn96y3w6aw0ikfwqlg0bq"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  (for-each delete-file
-                            (find-files "." "\\.jar$"))
-                  #t))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:jar-name "xom.jar"
-       #:jdk ,icedtea-8
-       #:tests? #f                      ; no tests
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'make-git-checkout-writable
-           (lambda _
-             (for-each make-file-writable (find-files "."))
-             #t))
-         (add-before 'configure 'fix-tagsoup-dep
-           (lambda _
-             ;; FIXME: Where is tagsoup source?
-             (delete-file "src/nu/xom/tools/XHTMLJavaDoc.java")
-             #t)))))
-    (inputs
-     (list java-jdom java-junit java-classpathx-servletapi
-           java-jaxen-bootstrap java-xerces))
-    (home-page "https://xom.nu/")
-    (synopsis "XML Object Model")
-    (description "XOM is a new XML Object Model for processing XML with Java 
-that strives for correctness and simplicity.")
-    ;; 2.1 only
-    (license license:lgpl2.1)))
-
-(define-public java-xsdlib
-  (package
-    (name "java-xsdlib")
-    (version "2013.2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://repo1.maven.org/maven2/com/sun/msv/"
-                                  "datatype/xsd/xsdlib/" version "/xsdlib-"
-                                  version "-sources.jar"))
-              (sha256
-               (base32
-                "185i48p1xp09wbq03i9zgfl701qa262rq46yf4cajzmk3336kqim"))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:tests? #f; no tests
-       #:jar-name "xsdlib.jar"
-       #:jdk ,icedtea-8))
-    (inputs
-     (list java-xerces))
-    (home-page (string-append "https://web.archive.org/web/20161127144537/"
-                              "https://msv.java.net//"))
-    (synopsis "Sun Multi-Schema Validator")
-    (description "Xsdlib contains an implementation of sun.com.msv, an XML
-validator.")
-    (license license:bsd-2)))
-
-(define-public java-xpp3
-  (package
-    (name "java-xpp3")
-    (version "1.1.4")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://ci.guix.gnu.org/file/"
-                    "xpp3-1.1.4_src.tgz"
-                    "/sha256/"
-                    "1b99zrhyij5qwyhilyjdl1ykxvhk902vsvflh6gx4fir8hfvdl5p"))
-              (file-name (string-append name "-" version "_src.tgz"))
-              (sha256
-               (base32
-                "1b99zrhyij5qwyhilyjdl1ykxvhk902vsvflh6gx4fir8hfvdl5p"))
-              (modules '((guix build utils)))
-              (snippet
-                '(begin ;; Delete bundled jar archives.
-                   (for-each delete-file (find-files "." ".*\\.jar"))
-                   #t))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:tests? #f; no tests
-       #:build-target "jar"
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'install (install-jars "build")))))
-    (home-page "http://www.extreme.indiana.edu/xgws/xsoap/xpp/")
-    (synopsis "Streaming pull XML parser")
-    (description "Xml Pull Parser (in short XPP) is a streaming pull XML
-parser and should be used when there is a need to process quickly and
-efficiently all input elements (for example in SOAP processors). This
-package is a stable XmlPull parsing engine that is based on ideas from XPP
-and in particular XPP2 but completely revised and rewritten to take the best
-advantage of JIT JVMs.")
-    (license (license:non-copyleft "file://LICENSE.txt"))))
-
-(define-public java-xmlpull2
-  (package
-    (name "java-xmlpull2")
-    (version "2.1.10")
-    (source (origin
-              (method url-fetch)
-              ;; Unfortunately, archive.org does not have a copy of this file.
-              (uri (string-append "https://ftp.fau.de/gentoo/distfiles/"
-                                  "PullParser" version ".tgz"))
-              (sha256
-               (base32
-                "1kw9nhyqb7bzhn2zjbwlpi5vp5rzj89amzi3hadw2acyh2dmd0md"))
-              (modules '((guix build utils)))
-              (snippet
-                '(begin ;; Delete bundled jar archives.
-                   (for-each delete-file (find-files "." ".*\\.jar"))
-                   #t))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:tests? #f; no tests
-       #:build-target "impl"
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'install (install-jars "build/lib")))))
-    (home-page (string-append "https://web.archive.org/web/20210225153105/"
-                              "https://www.extreme.indiana.edu/"))
-    (synopsis "Streaming pull XML parser")
-    (description "Xml Pull Parser (in short XPP) is a streaming pull XML
-parser and should be used when there is a need to process quickly and
-efficiently all input elements (for example in SOAP processors).  This
-package is in maintenance mode.")
-    (license (license:non-copyleft "file:///LICENSE.txt"))))
-
-(define-public java-xmlpull-api-v1
-  (package
-    (name "java-xmlpull-api-v1")
-    (version "1.1.3.4b")
-    (source (origin
-              ;; The package is originally from Extreme! Lab, but the website
-              ;; is now gone.  This repositories contains the sources of the
-              ;; latest version.
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/aslom/xmlpull-api-v1")
-                     ;; No releases, this is the latest commit
-                     (commit "abeaa4aa87b2625af70c32f658f44e11355fe568")))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "15bdqxfncnakskna4m9gsh4f9iczxy83qxn2anqiqd15z406a5ih"))
-              (modules '((guix build utils)))
-              (snippet
-               `(begin
-                  (delete-file-recursively "lib")
-                  (mkdir-p "lib")
-                  ;; prevents a failure in "dist_lite"
-                  (substitute* "build.xml"
-                    (("README.html") "README.md"))))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:test-target "junit"
-       #:build-target "dist"
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (doc (string-append out "/share/doc/" ,name "-" ,version))
-                    (java (string-append out "/share/java"))
-                    (project (string-append
-                               "xmlpull_"
-                               ,(string-join (string-split version #\.) "_"))))
-               (mkdir-p doc)
-               (copy-recursively (string-append "build/dist/" project "/doc/")
-                                 doc)
-               (mkdir-p java)
-               (copy-file (string-append "build/dist/" project "/" project ".jar")
-                          (string-append java "/" project ".jar")))
-             )))))
-    (home-page "https://github.com/aslom/xmlpull-api-v1")
-    (synopsis "XML pull parsing API")
-    (description "XmlPull v1 API is a simple to use XML pull parsing API.  XML
-pull parsing allows incremental (sometimes called streaming) parsing of XML
-where application is in control - the parsing can be interrupted at any given
-moment and resumed when application is ready to consume more input.")
-    (license license:public-domain)))
-
-(define-public java-dom4j
-  (package
-    (name "java-dom4j")
-    (version "2.1.1")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/dom4j/dom4j")
-                    (commit (string-append "version-" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "0q907srj9v4hwicpcrn4slyld5npf2jv7hzchsgrg29q2xmbwkdl"))
-              (modules '((guix build utils)))
-              (snippet
-                '(begin ;; Delete bundled jar archives.
-                   (for-each delete-file (find-files "." ".*\\.jar"))
-                   #t))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:jar-name "dom4j.jar"
-       #:jdk ,icedtea-8
-       #:source-dir "src/main/java"
-       ;; FIXME: Requires xalan, but xalan depends on java-cup which has a
-       ;; dependency on itself through jflex.
-       #:tests? #f
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'copy-jaxen-sources
-           ;; java-jaxen-bootstrap is not enough. These files have a circular
-           ;; dependency and there is no subset of dom4j that would allow
-           ;; breaking the circle.
-           (lambda* (#:key inputs #:allow-other-keys)
-             (mkdir-p "jaxen-sources")
-             (with-directory-excursion "jaxen-sources"
-               (system* "jar" "xf" (assoc-ref inputs "java-jaxen-sources")))
-             (mkdir-p "src/main/java/org/jaxen/dom4j")
-             (copy-file "jaxen-sources/org/jaxen/dom4j/DocumentNavigator.java"
-                        "src/main/java/org/jaxen/dom4j/DocumentNavigator.java")
-             (copy-file "jaxen-sources/org/jaxen/dom4j/Dom4jXPath.java"
-                        "src/main/java/org/jaxen/dom4j/Dom4jXPath.java")
-             #t))
-         (add-before 'build 'fix-old-xpp2
-           (lambda _
-             ;; This package normally depends on xpp2 2.0, but version 2.1.10
-             ;; is the only version whose source code is published.
-             (substitute* "src/main/java/org/dom4j/xpp/ProxyXmlStartTag.java"
-               (("public void resetStartTag")
-                "public boolean removeAttributeByRawName(String name) {\n
-  return false;\n
-}\n
-public boolean removeAttributeByName(String name, String name2) {\n
-  return false;\n
-}\n\npublic void resetStartTag")
-               (("Atttribute") "Attribute"))
-             #t)))))
-    (inputs
-     `(("java-jaxen-bootstrap" ,java-jaxen-bootstrap)
-       ("java-jaxen-sources" ,(package-source java-jaxen-bootstrap))
-       ("java-xmlpull2" ,java-xmlpull2)
-       ("java-xpp3" ,java-xpp3)
-       ("java-xsdlib" ,java-xsdlib)))
-    (native-inputs
-     (list java-testng java-xerces))
-    (home-page "https://dom4j.github.io/")
-    (synopsis "Flexible XML framework for Java")
-    (description "Dom4j is a flexible XML framework for Java.  DOM4J works
-with DOM, SAX, XPath, and XSLT.  It can parse large XML documents with very
-low memory footprint.")
-    ;; some BSD-like 5-clause license
-    (license (license:non-copyleft "file://LICENSE"))))
-
-(define-public java-kxml2
-  (package
-    (name "java-kxml2")
-    (version "2.4.2")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/stefanhaustein/kxml2")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "0g6d8c9r9sh3x04sf4wdpgwvhkqvk11k3kq9skx91i60h4vn01hg"))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:jar-name "kxml2.jar"
-       #:source-dir "src/main/java"
-       #:test-include (list "TestWb.java")
-       ;; Test failure: it was expected to get an XML entity but got the
-       ;; equivalent Unicode character instead.
-       #:tests? #f
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'make-git-checkout-writable
-           (lambda _
-             (for-each make-file-writable (find-files "."))
-             #t))
-         (add-before 'build 'copy-resources
-           (lambda _
-             (copy-recursively "src/main/resources" "build/classes")
-             #t)))))
-    (inputs
-     (list java-xpp3))
-    (native-inputs
-     (list java-junit))
-    (home-page "http://kxml.org")
-    (synopsis "XML pull parser")
-    (description "kXML is a small XML pull parser, specially designed for
-constrained environments such as Applets, Personal Java or devices compliant
-with the Mobile Information Device Profile (MIDP).")
-    (license license:expat)))
-
-(define-public java-stax
-  (package
-    (name "java-stax")
-    (version "1.2.0")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://repo1.maven.org/maven2/stax/stax/"
-                                  version "/stax-" version "-sources.jar"))
-              (sha256
-               (base32
-                "04ba4qvbrps45j8bldbakxq31k7gjlsay9pppa9yn13fr00q586z"))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:jar-name "stax.jar"
-       #:tests? #f; no tests
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'configure 'fix-utf8
-           (lambda _
-             ;; This file is ISO-8859-1 but java expects UTF-8.
-             ;; Remove special characters in comments.
-             (with-fluids ((%default-port-encoding "ISO-8859-1"))
-               (substitute* "src/com/wutka/dtd/Scanner.java"
-                 (("//.*") "\n")))
-             #t)))))
-    (home-page "https://repo1.maven.org/maven2/stax/stax/")
-    (synopsis "Streaming API for XML")
-    (description "This package provides the reference implementation of the
-@dfn{Streaming API for XML} (StAX).  It is used for streaming XML data to
-and from a Java application.  It provides a standard pull parser interface.")
-    (license license:asl2.0)))
-
-(define-public java-jettison
-  (package
-    (name "java-jettison")
-    (version "1.3.7")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/codehaus/jettison")
-                    (commit (string-append "jettison-" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "15sydmi5chdh4126qc7v8bsrp7fp4ldaya8a05iby4pq2324q0qw"))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:jar-name "jettison.jar"
-       #:source-dir "src/main/java"
-       #:test-exclude (list "**/Abstract*.java"
-                            ;; Abstract classes
-                            "**/DOMTest.java"
-                            "**/BadgerFishDOMTest.java"
-                            "**/MappedDOMTest.java")))
-    (native-inputs
-     (list java-junit))
-    (home-page "https://github.com/codehaus/jettison")
-    (synopsis "StAX implementation for JSON")
-    (description "Jettison is a Java library for converting XML to JSON and
-vice-versa with the help of the @dfn{Streaming API for XML} (StAX).  It
-implements @code{XMLStreamWriter} and @code{XMLStreamReader} and supports
-@code{Mapped} and @code{BadgerFish} conventions.")
-    (license license:asl2.0)))
-
-(define-public java-jdom2
-  (package
-    (name "java-jdom")
-    (version "2.0.6.1")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/hunterhacker/jdom")
-                    (commit (string-append "JDOM-" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1r4pwl0z7hm45v9l2wbq3fjmqi13zmwzbrggyqizrwv31kghhx56"))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:build-target "package"
-       #:tests? #f                ; tests are run as part of the build process
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'install
-           (install-jars "build")))))
-    (home-page "http://jdom.org/")
-    (synopsis "Access, manipulate, and output XML data")
-    (description "Jdom is a Java-based solution for accessing, manipulating, and
-outputting XML data from Java code.")
-    (license license:bsd-4)))
-
-(define-public java-xstream
-  (package
-    (name "java-xstream")
-    (version "1.4.16")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/x-stream/xstream")
-             (commit (string-append
-                      "XSTREAM_"
-                      (string-map (lambda (x) (if (eq? x #\.) #\_ x))
-                                  version)))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "16k2mc63h2fw7lxv74qmhg4p8q9hfrw114daa6nxwnpv08cnq755"))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:jar-name "xstream.jar"
-       ;; FIXME: Tests are not in a java subdirectory as assumed by ant-build-system.
-       #:tests? #f
-       #:jdk ,icedtea-8
-       #:source-dir "xstream/src/java"))
-    (inputs
-     `(("java-jdom" ,java-jdom)
-       ("java-jdom2" ,java-jdom2)
-       ("java-cglib" ,java-cglib)
-       ("java-joda-time" ,java-joda-time)
-       ("java-jettison" ,java-jettison)
-       ("java-xom" ,java-xom)
-       ("java-mxparser" ,java-mxparser)
-       ("java-xpp3" ,java-xpp3)
-       ("java-dom4j" ,java-dom4j)
-       ("java-stax2-api" ,java-stax2-api)
-       ("java-woodstox-core" ,java-woodstox-core)
-       ("java-kxml2" ,java-kxml2)
-       ("java-stax" ,java-stax)))
-    (home-page "https://x-stream.github.io")
-    (synopsis "XML serialization library")
-    (description "XStream is a simple library to serialize Java objects to XML
-and back again.")
-    (license license:bsd-3)))
-
-(define-public java-mxparser
-  (package
-    (name "java-mxparser")
-    (version "1.2.1")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/x-stream/mxparser")
-              (commit (string-append "v-" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0i3jrjbz4hgf62fm1ix7nlcmhi4kcv4flqsfvh7a3l2v7nsp5ryb"))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:jar-name "mxparser.jar"
-       #:source-dir "src/main/java"
-       #:test-dir "src/test"
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'copy-resources
-           (lambda _
-             (copy-recursively "src/main/resources" "build/classes")
-             #t)))))
-    (propagated-inputs
-     (list java-xmlpull-api-v1))
-    (native-inputs
-     (list java-junit))
-    (home-page "https://github.com/x-stream/mxparser")
-    (synopsis "Streaming pull XML parser forked from @code{java-xpp3}")
-    (description "Xml Pull Parser (in short XPP) is a streaming pull XML
-parser and should be used when there is a need to process quickly and
-efficiently all input elements (for example in SOAP processors). This
-package is a stable XmlPull parsing engine that is based on ideas from XPP
-and in particular XPP2 but completely revised and rewritten to take the best
-advantage of JIT JVMs.
-
-MXParser is a fork of xpp3_min 1.1.7 containing only the parser with merged
-changes of the Plexus fork. It is an implementation of the XMLPULL V1 API
-(parser only).")
-    (license (license:non-copyleft "file://LICENSE.txt"))))
-
 (define-public xmlrpc-c
   (package
     (name "xmlrpc-c")

gnu/services/base.scm

@@ -198,6 +198,7 @@
             guix-configuration-generate-substitute-key?
             guix-configuration-extra-options
             guix-configuration-log-file
+            guix-configuration-environment
 
             guix-extension
             guix-extension?
@@ -1654,7 +1655,9 @@ archive' public keys, with GUIX."
   (http-proxy       guix-http-proxy               ;string | #f
                     (default #f))
   (tmpdir           guix-tmpdir                   ;string | #f
-                    (default #f)))
+                    (default #f))
+  (environment      guix-configuration-environment  ;list of strings
+                    (default '())))
 
 (define %default-guix-configuration
   (guix-configuration))
@@ -1710,7 +1713,7 @@ proxy of 'guix-daemon'...~%")
     (guix build-group build-accounts authorize-key? authorized-keys
           use-substitutes? substitute-urls max-silent-time timeout
           log-compression discover? extra-options log-file
-          http-proxy tmpdir chroot-directories)
+          http-proxy tmpdir chroot-directories environment)
     (list (shepherd-service
            (documentation "Run the Guix daemon.")
            (provision '(guix-daemon))
@@ -1799,7 +1802,8 @@ proxy of 'guix-daemon'...~%")
                            (if proxy
                                (list (string-append "http_proxy=" proxy)
                                      (string-append "https_proxy=" proxy))
-                               '()))
+                               '())
+                           '#$environment)
 
                    #:log-file #$log-file))))
            (stop #~(make-kill-destructor))))))

gnu/tests/base.scm

@@ -57,7 +57,6 @@
             %test-linux-libre-5.4
             %test-linux-libre-4.19
             %test-linux-libre-4.14
-            %test-linux-libre-4.9
             %test-halt
             %test-root-unmount
             %test-cleanup
@@ -584,9 +583,6 @@ functionality tests, using the given KERNEL.")
 (define %test-linux-libre-4.14
   (test-basic-os linux-libre-4.14))
 
-(define %test-linux-libre-4.9
-  (test-basic-os linux-libre-4.9))
-
 
 ;;;
 ;;; Halt.

guix/derivations.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012-2021 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012-2021, 2023 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2017 Mathieu Lirzin <mthl@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -484,17 +484,21 @@ things as appropriate and is thus more efficient."
     (fold-right (lambda (output result)
                   (match output
                     ((name path "" "")
+                     ;; Regular derivation.
                      (alist-cons name
                                  (make-derivation-output path #f #f #f)
                                  result))
                     ((name path hash-algo hash)
-                     ;; fixed-output
+                     ;; Fixed-output, unless HASH is the empty string (in that
+                     ;; case, HASH-ALGO must be preserved despite being
+                     ;; unused).
                      (let* ((rec? (string-prefix? "r:" hash-algo))
                             (algo (string->symbol
                                    (if rec?
                                        (string-drop hash-algo 2)
                                        hash-algo)))
-                            (hash (base16-string->bytevector hash)))
+                            (hash (and (not (string-null? hash))
+                                       (base16-string->bytevector hash))))
                        (alist-cons name
                                    (make-derivation-output path algo
                                                            hash rec?)

guix/import/cran.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016, 2017, 2019, 2020, 2021 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2020 Martin Becze <mjbecze@riseup.net>
@@ -732,12 +732,12 @@ s-expression corresponding to that package, or #f on failure."
   (define latest-version
     (latest-bioconductor-package-version upstream-name))
 
-  (and version
+  (and latest-version
        ;; Bioconductor does not provide signatures.
        (upstream-source
         (package (package-name pkg))
         (version latest-version)
-        (urls (bioconductor-uri upstream-name version))
+        (urls (bioconductor-uri upstream-name latest-version))
         (input-changes
          (changed-inputs
           pkg

guix/read-print.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2021-2022 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2021-2023 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -488,6 +488,19 @@ each line except the first one (they're assumed to be already there)."
                    (8  "#o"))
                  (number->string integer base)))
 
+(define %special-non-extended-symbols
+  ;; Special symbols that can be written without the #{...}# notation for
+  ;; extended symbols: 1+, 1-, 123/, etc.
+  (make-regexp "^[0-9]+[[:graph:]]+$" regexp/icase))
+
+(define (symbol->display-string symbol context)
+  "Return the most appropriate representation of SYMBOL, resorting to extended
+symbol notation only when strictly necessary."
+  (let ((str (symbol->string symbol)))
+    (if (regexp-exec %special-non-extended-symbols str)
+        str                                  ;no need for the #{...}# notation
+        (object->string symbol))))
+
 (define* (pretty-print-with-comments port obj
                                      #:key
                                      (format-comment
@@ -561,7 +574,8 @@ FORMAT-VERTICAL-SPACE; a useful value of 'canonicalize-vertical-space'."
               ((? string? str)
                (>= (+ (string-width str) 2 indent) max-width))
               ((? symbol? symbol)
-               (>= (+ (string-width (symbol->string symbol)) indent)
+               (>= (+ (string-width (symbol->display-string symbol context))
+                      indent)
                    max-width))
               ((? boolean?)
                (>= (+ 2 indent) max-width))
@@ -647,7 +661,7 @@ FORMAT-VERTICAL-SPACE; a useful value of 'canonicalize-vertical-space'."
        ;; and following arguments are less indented.
        (let* ((lead    (special-form-lead head context))
               (context (cons head context))
-              (head    (symbol->string head))
+              (head    (symbol->display-string head (cdr context)))
               (total   (length arguments)))
          (unless delimited? (display " " port))
          (display "(" port)
@@ -727,6 +741,8 @@ FORMAT-VERTICAL-SPACE; a useful value of 'canonicalize-vertical-space'."
                           (printed-string obj context))
                          ((integer? obj)
                           (integer->string obj context))
+                         ((symbol? obj)
+                          (symbol->display-string obj context))
                          (else
                           (object->string obj))))
               (len (string-width str)))

guix/scripts/substitute.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013-2022 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013-2023 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014 Nikita Karetnikov <nikita@karetnikov.org>
 ;;; Copyright © 2018 Kyle Meyer <kyle@kyleam.com>
 ;;; Copyright © 2020 Christopher Baines <mail@cbaines.net>
@@ -706,10 +706,12 @@ substitutes may be unavailable\n")))))
                             (string-drop option=value (+ 1 equal-sign))))))
                  (string-tokenize newline-separated %not-newline)))))
 
-(define (find-daemon-option option)
+(define find-daemon-option
+  (let ((options (delay (daemon-options))))
+    (lambda (option)
       "Return the value of build daemon option OPTION, or #f if it could not be
 found."
-  (assoc-ref (daemon-options) option))
+      (assoc-ref (force options) option))))
 
 (define %default-substitute-urls
   (match (and=> (or (find-daemon-option "untrusted-substitute-urls") ;client

nix/libutil/hash.cc

@@ -76,8 +76,11 @@ string printHash(const Hash & hash)
 Hash parseHash(HashType ht, const string & s)
 {
     Hash hash(ht);
-    if (s.length() != hash.hashSize * 2)
+    if (s.length() != hash.hashSize * 2) {
-        throw Error(format("invalid hash `%1%'") % s);
+	string algo = gcry_md_algo_name(ht);
+        throw Error(format("invalid %1% hash '%2%' (%3% bytes but expected %4%)")
+		    % algo % s % (s.length() / 2) % hash.hashSize);
+    }
     for (unsigned int i = 0; i < hash.hashSize; i++) {
         string s2(s, i * 2, 2);
         if (!isxdigit(s2[0]) || !isxdigit(s2[1]))

tests/derivations.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012-2022 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012-2023 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -256,6 +256,21 @@
       (build-derivations %store (list drv))
       #f)))
 
+(test-assert "'download' built-in builder, no fixed-output hash"
+  ;; 'guix perform-download' should bail out with a message saying "not a
+  ;; fixed-output derivation".
+  (with-http-server '((200 "This should not be downloaded."))
+    (let* ((drv (derivation %store "download-without-hash"
+                            "builtin:download" '()
+                            #:env-vars `(("url"
+                                          . ,(object->string (%local-url))))
+                            #:hash-algo 'sha256
+                            #:hash #f)))
+      (guard (c ((store-protocol-error? c)
+                 (string-contains (store-protocol-error-message c) "failed")))
+        (build-derivations %store (list drv))
+        #f))))
+
 (test-assert "'download' built-in builder, check mode"
   ;; Make sure rebuilding the 'builtin:download' derivation in check mode
   ;; works.  See <http://bugs.gnu.org/25089>.
@@ -316,6 +331,13 @@
                                  #:hash hash #:hash-algo 'sha256)))
     (fixed-output-derivation? drv)))
 
+(test-assert "fixed-output-derivation?, no hash"
+  ;; A derivation that has #:hash-algo and #:hash #f is *not* fixed-output.
+  (let* ((drv (derivation %store "not-quite-fixed"
+                          "builtin:download" '()
+                          #:hash #f #:hash-algo 'sha256)))
+    (not (fixed-output-derivation? drv))))
+
 (test-equal "fixed-output derivation"
   '(sha1 sha256 sha512)
   (map (lambda (hash-algorithm)
@@ -374,6 +396,18 @@
                         (call-with-input-file p get-bytevector-all))
                 (bytevector? (query-path-hash %store p)))))))
 
+(test-assert "fixed-output derivation, invalid hash size"
+  (guard (c ((store-protocol-error? c)
+             (string-contains-ci (store-protocol-error-message c)
+                                 "invalid SHA512 hash")))
+    (derivation %store "download-with-invalid-hash"
+                "builtin:download" '()
+                #:env-vars `(("url"
+                              . ,(object->string "http://example.org")))
+                #:hash-algo 'sha512
+                #:hash #vu8(1 2 3))
+    #f))
+
 (test-assert "derivation with a fixed-output input"
   ;; A derivation D using a fixed-output derivation F doesn't has the same
   ;; output path when passed F or F', as long as F and F' have the same output
@@ -543,6 +577,22 @@
                     read-derivation)))
     (equal? drv* drv)))
 
+(test-assert "read-derivation with hash = #f"
+  ;; Passing #:hash-algo together with #:hash #f is accepted and #:hash-algo
+  ;; is preserved.  However it is not a fixed-output derivation.  It used to
+  ;; be that 'read-derivation' would incorrectly return #vu8() instead of #f
+  ;; for the hash in this case:
+  ;; <https://lists.gnu.org/archive/html/guix-devel/2023-01/msg00040.html>.
+  (let* ((drv1 (derivation %store "almost-fixed-output"
+                           "builtin:download" '()
+                           #:env-vars `(("url" . "http://example.org"))
+                           #:hash-algo 'sha256
+                           #:hash #f))
+         (drv2 (call-with-input-file (derivation-file-name drv1)
+                 read-derivation)))
+    (and (not (eq? drv1 drv2))             ;ensure memoization doesn't kick in
+         (equal? drv1 drv2))))
+
 (test-assert "multiple-output derivation, derivation-path->output-path"
   (let* ((builder    (add-text-to-store %store "builder.sh"
                                         "echo one > $out ; echo two > $second"

tests/guix-home.sh

@@ -1,5 +1,5 @@
 # GNU Guix --- Functional package management for GNU
-# Copyright © 2021 Andrew Tropin <andrew@trop.in>
+# Copyright © 2021-2023 Andrew Tropin <andrew@trop.in>
 # Copyright © 2021 Oleg Pykhalov <go.wigust@gmail.com>
 # Copyright © 2022 Ludovic Courtès <ludo@gnu.org>
 #
@@ -62,6 +62,7 @@ trap 'chmod -Rf +w "$test_directory"; rm -rf "$test_directory"' EXIT
              (gnu home)
              (gnu home services)
              (gnu home services shells)
+             (gnu packages bash)
              (gnu services))
 
 (home-environment
@@ -82,6 +83,10 @@ trap 'chmod -Rf +w "$test_directory"; rm -rf "$test_directory"' EXIT
    (simple-service 'add-environment-variable
                    home-environment-variables-service-type
                    `(("TODAY" . "26 messidor")
+                     ("SHELL" . ,(file-append bash "/bin/bash"))
+                     ("BUILDHOST_TIME" . ,#~(strftime "%c"
+                                             (localtime (current-time))))
+                     ("STRING_WITH_ESCAPES" . "chars: \" /\\")
                      ("LITERAL" . ,(literal-string "${abc}"))))
 
    (simple-service 'home-bash-service-extension-test
@@ -149,8 +154,13 @@ EOF
 # the content of bashrc-test-config.sh"
     grep -q "the content of ~/.config/test.conf" "${HOME}/.config/test.conf"
     grep '^export PS1="\$GUIX_ENVIRONMENT λ "$' "${HOME}/.bash_profile"
+
     ( . "${HOME}/.guix-home/setup-environment"; test "$TODAY" = "26 messidor" )
     ( . "${HOME}/.guix-home/setup-environment"; test "$LITERAL" = '${abc}' )
+    ( . "${HOME}/.guix-home/setup-environment";
+      test "$STRING_WITH_ESCAPES" = "chars: \" /\\")
+    ( . "${HOME}/.guix-home/setup-environment";
+      echo "$SHELL" | grep "/gnu/store/.*/bin/bash" )
 
     # This one should still be here.
     grep "stay around" "$HOME/.config/random-file"

tests/read-print.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2021-2022 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2021-2023 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -142,6 +142,11 @@ expressions."
   (+ x y))"
                    #:max-width 11)
 
+(test-pretty-print "\
+(begin
+  1+ 1- 123/ 456*
+  (1+ 41))")
+
 (test-pretty-print "\
 (lambda (x y)
   ;; This is a procedure.