Merge remote-tracking branch 'origin/master' into core-updates

.dir-locals.el

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

Makefile.am

@@ -68,7 +68,6 @@ MODULES =					\
   guix/cpio.scm					\
   guix/deprecation.scm				\
   guix/docker.scm	   			\
-  guix/json.scm					\
   guix/records.scm				\
   guix/openpgp.scm				\
   guix/pki.scm					\
@@ -80,6 +79,7 @@ MODULES =					\
   guix/modules.scm				\
   guix/download.scm				\
   guix/discovery.scm				\
+  guix/android-repo-download.scm		\
   guix/bzr-download.scm            		\
   guix/git-download.scm				\
   guix/hg-download.scm				\
@@ -170,6 +170,7 @@ MODULES =					\
   guix/build/minify-build-system.scm		\
   guix/build/font-build-system.scm		\
   guix/build/go-build-system.scm		\
+  guix/build/android-repo.scm			\
   guix/build/asdf-build-system.scm		\
   guix/build/bzr.scm				\
   guix/build/copy-build-system.scm		\
@@ -335,10 +336,6 @@ AUX_FILES =						\
   gnu/packages/aux-files/linux-libre/5.8-arm64.conf     \
   gnu/packages/aux-files/linux-libre/5.8-i686.conf      \
   gnu/packages/aux-files/linux-libre/5.8-x86_64.conf    \
-  gnu/packages/aux-files/linux-libre/5.7-arm.conf	\
-  gnu/packages/aux-files/linux-libre/5.7-arm64.conf	\
-  gnu/packages/aux-files/linux-libre/5.7-i686.conf	\
-  gnu/packages/aux-files/linux-libre/5.7-x86_64.conf	\
   gnu/packages/aux-files/linux-libre/5.4-arm.conf	\
   gnu/packages/aux-files/linux-libre/5.4-arm64.conf	\
   gnu/packages/aux-files/linux-libre/5.4-i686.conf	\
@@ -838,6 +835,7 @@ release: dist-with-updated-version
 	  image=`$(top_builddir)/pre-inst-env						\
 	    guix system disk-image							\
 	    --file-system-type=iso9660							\
+	    --label="GUIX_$${system}_$(VERSION)"						\
             --system=$$system --fallback						\
 	    gnu/system/install.scm` ;							\
 	  if [ ! -f "$$image" ] ; then							\

build-aux/pre-inst-env.in

@@ -1,7 +1,7 @@
 #!/bin/sh
 
 # GNU Guix --- Functional package management for GNU
-# Copyright © 2012, 2013, 2014, 2015, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
+# Copyright © 2012, 2013, 2014, 2015, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 # Copyright © 2017 Eric Bavier <bavier@cray.com>
 #
 # This file is part of GNU Guix.
@@ -46,13 +46,6 @@ export PATH
 GUIX="$abs_top_builddir/scripts/guix"
 export GUIX
 
-# The following variables need only be defined when compiling Guix
-# modules, but we define them to be on the safe side in case of
-# auto-compilation.
-
-NIX_HASH="@NIX_HASH@"
-export NIX_HASH
-
 # Define $GUIX_UNINSTALLED to prevent `guix' from
 # prepending @guilemoduledir@ to the Guile load paths.
 

configure.ac

@@ -171,10 +171,6 @@ AM_CONDITIONAL([ENABLE_INSTALLER],
 dnl Make sure we have a full-fledged Guile.
 GUIX_ASSERT_GUILE_FEATURES([regex posix socket net-db threads])
 
-dnl Make sure we don't suffer from the bug in 'equal?' wrt. syntax objects
-dnl found in 2.2.1.  See <https://bugs.gnu.org/29903>.
-GUIX_ASSERT_SYNTAX_OBJECT_EQUAL
-
 AC_PROG_SED
 
 dnl Decompressors, for use by the substituter and other modules.
@@ -198,11 +194,6 @@ AC_ARG_WITH([nix-prefix],
    esac],
   [])
 
-AC_PATH_PROG([NIX_HASH], [nix-hash])
-if test "x$guix_build_daemon$NIX_HASH" = "xno"; then
-   AC_MSG_ERROR([Nix programs not found; please install Nix or use `--with-nix-prefix'.])
-fi
-
 AC_ARG_WITH([nixpkgs],
   [AS_HELP_STRING([--with-nixpkgs=DIR],
     [search for Nixpkgs in DIR (for testing purposes only)])],

doc/build.scm

@@ -310,6 +310,8 @@ its <pre class=\"lisp\"> blocks (as produced by 'makeinfo --html')."
                    (loop rest (cons (entity->string entity) strings)))
                   ((('span _ lst ...) . rest)     ;for <span class="roman">
                    (loop (append lst rest) strings))
+                  ((('var name) . rest)           ;for @var{name} within @lisp
+                   (loop rest (cons name strings))) ;XXX: losing formatting
                   (something
                    (pk 'unsupported-code-snippet something)
                    (primitive-exit 1)))))

doc/contributing.texi

@@ -42,13 +42,14 @@ git clone https://git.savannah.gnu.org/git/guix.git
 
 @cindex authentication, of a Guix checkout
 How do you ensure that you obtained a genuine copy of the repository?
-To do that, run @command{guix git authenticate}, passing if the commit
+To do that, run @command{guix git authenticate}, passing it the commit
 and OpenPGP fingerprint of the @dfn{channel introduction}
 (@pxref{Invoking guix git authenticate}):
 
 @c The commit and fingerprint below must match those of the channel
 @c introduction in '%default-channels'.
 @example
+git fetch origin keyring:keyring
 guix git authenticate 9edb3f66fd807b096b48283debdcddccfea34bad \
   "BBB0 2DDF 2CEA F6A8 0D1D  E643 A2A0 6DF2 A33A 54FA"
 @end example
@@ -368,6 +369,7 @@ needed is to review and apply the patch.
 * Package Naming::              What's in a name?
 * Version Numbers::             When the name is not enough.
 * Synopses and Descriptions::   Helping users find the right package.
+* Snippets versus Phases::      Whether to use a snippet, or a build phase.
 * Python Modules::              A touch of British comedy.
 * Perl Modules::                Little pearls.
 * Java Packages::               Coffee break.
@@ -598,6 +600,20 @@ Gettext}):
 for the X11 resize-and-rotate (RandR) extension. @dots{}")
 @end example
 
+@node Snippets versus Phases
+@subsection Snippets versus Phases
+
+@cindex snippets, when to use
+The boundary between using an origin snippet versus a build phase to
+modify the sources of a package can be elusive.  Origin snippets are
+typically used to remove unwanted files such as bundled libraries,
+nonfree sources, or to apply simple substitutions.  The source derived
+from an origin should produce a source that can be used to build the
+package on any system that the upstream package supports (i.e., act as
+the corresponding source).  In particular, origin snippets must not
+embed store items in the sources; such patching should rather be done
+using build phases.  Refer to the @code{origin} record documentation for
+more information (@pxref{origin Reference}).
 
 @node Python Modules
 @subsection Python Modules

doc/guix-cookbook.texi

@@ -16,6 +16,7 @@ Copyright @copyright{} 2020 Matthew Brooks@*
 Copyright @copyright{} 2020 Marcin Karpezo@*
 Copyright @copyright{} 2020 Brice Waegeneire@*
 Copyright @copyright{} 2020 André Batista@*
+Copyright @copyright{} 2020 Christopher Lemmer Webber
 
 Permission is granted to copy, distribute and/or modify this document
 under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -1348,6 +1349,7 @@ reference.
 * Customizing the Kernel::       Creating and using a custom Linux kernel on 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
 * 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.
 @end menu
@@ -1760,6 +1762,246 @@ your screen but not suspend it, it's a good idea to notify xss-lock about this s
 confusion occurs. This can be done by executing @code{xset s activate} immediately
 before you execute slock.
 
+@node Running Guix on a Linode Server
+@section Running Guix on a Linode Server
+@cindex linode, Linode
+
+To run Guix on a server hosted by @uref{https://www.linode.com, Linode},
+start with a recommended Debian server.  We recommend using the default
+distro as a way to bootstrap Guix. Create your SSH keys.
+
+@example
+ssh-keygen
+@end example
+
+Be sure to add your SSH key for easy login to the remote server.
+This is trivially done via Linode's graphical interface for adding
+SSH keys.  Go to your profile and click add SSH Key.
+Copy into it the output of:
+
+@example
+cat ~/.ssh/<username>_rsa.pub
+@end example
+
+Power the Linode down. In the Linode's Disks/Configurations tab, resize
+the Debian disk to be smaller. 30 GB is recommended.
+
+In the Linode settings, "Add a disk", with the following:
+@itemize @bullet
+@item
+Label: "Guix"
+
+@item
+Filesystem: ext4
+
+@item
+Set it to the remaining size
+@end itemize
+
+On the "configuration" field that comes with the default image, press
+"..." and select "Edit", then on that menu add to @file{/dev/sdc} the "Guix"
+label.
+
+Now "Add a Configuration", with the following:
+@itemize @bullet
+@item
+Label: Guix
+
+@item
+Kernel:GRUB 2 (it's at the bottom!  This step is @b{IMPORTANT!})
+
+@item
+Block device assignment:
+
+@item
+@file{/dev/sda}: Guix
+
+@item
+@file{/dev/sdb}: swap
+
+@item
+Root device: @file{/dev/sda}
+
+@item
+Turn off all the filesystem/boot helpers
+@end itemize
+
+Now power it back up, picking the Debian configuration.  Once it's
+booted up, ssh in your server via @code{ssh
+root@@@var{<your-server-IP-here>}}. (You can find your server IP address in
+your Linode Summary section.) Now you can run the "install guix from
+@pxref{Binary Installation,,, guix, GNU Guix}" steps:
+
+@example
+sudo apt-get install gpg
+wget https://sv.gnu.org/people/viewgpg.php?user_id=15145 -qO - | gpg --import -
+wget https://git.savannah.gnu.org/cgit/guix.git/plain/etc/guix-install.sh
+chmod +x guix-install.sh
+./guix-install.sh
+guix pull
+@end example
+
+Now it's time to write out a config for the server.  The key information
+is below. Save the resulting file as @file{guix-config.scm}.
+
+@lisp
+(use-modules (gnu)
+             (guix modules))
+(use-service-modules networking
+                     ssh)
+(use-package-modules admin
+                     certs
+                     package-management
+                     ssh
+                     tls)
+
+(operating-system
+  (host-name "my-server")
+  (timezone "America/New_York")
+  (locale "en_US.UTF-8")
+  ;; This goofy code will generate the grub.cfg
+  ;; without installing the grub bootloader on disk.
+  (bootloader (bootloader-configuration
+               (bootloader
+                (bootloader
+                 (inherit grub-bootloader)
+                 (installer #~(const #t))))))
+  (file-systems (cons (file-system
+                        (device "/dev/sda")
+                        (mount-point "/")
+                        (type "ext4"))
+                      %base-file-systems))
+
+
+  (swap-devices (list "/dev/sdb"))
+
+
+  (initrd-modules (cons "virtio_scsi"    ; Needed to find the disk
+                        %base-initrd-modules))
+
+  (users (cons (user-account
+                (name "janedoe")
+                (group "users")
+                ;; Adding the account to the "wheel" group
+                ;; makes it a sudoer.
+                (supplementary-groups '("wheel"))
+                (home-directory "/home/janedoe"))
+               %base-user-accounts))
+
+  (packages (cons* nss-certs            ;for HTTPS access
+                   openssh-sans-x
+                   %base-packages))
+
+  (services (cons*
+             (service dhcp-client-service-type)
+             (service openssh-service-type
+                      (openssh-configuration
+                       (openssh openssh-sans-x)
+                       (password-authentication? #f)
+                       (authorized-keys
+                        `(("janedoe" ,(local-file "janedoe_rsa.pub"))
+                          ("root" ,(local-file "janedoe_rsa.pub"))))))
+             %base-services)))
+@end lisp
+
+Replace the following fields in the above configuration:
+@lisp
+(host-name "my-server")       ; replace with your server name
+; if you chose a linode server outside the U.S., then
+; use tzselect to find a correct timezone string
+(timezone "America/New_York") ; if needed replace timezone
+(name "janedoe")              ; replace with your username
+("janedoe" ,(local-file "janedoe_rsa.pub")) ; replace with your ssh key
+("root" ,(local-file "janedoe_rsa.pub")) ; replace with your ssh key
+@end lisp
+
+The last line in the above example lets you log into the server as root
+and set the initial root password.  After you have done this, you may
+delete that line from your configuration and reconfigure to prevent root
+login.
+
+Save your ssh public key (eg: @file{~/.ssh/id_rsa.pub}) as
+@file{@var{<your-username-here>}_rsa.pub} and your
+@file{guix-config.scm} in the same directory.  In a new terminal run
+these commands.
+
+@example
+sftp root@@<remote server ip address>
+put /home/<username>/ssh/id_rsa.pub .
+put /path/to/linode/guix-config.scm .
+@end example
+
+In your first terminal, mount the guix drive:
+
+@example
+mkdir /mnt/guix
+mount /dev/sdc /mnt/guix
+@end example
+
+Due to the way we set things up above, we do not install GRUB
+completely.  Instead we install only our grub configuration file.  So we
+need to copy over some of the other GRUB stuff that is already there:
+
+@example
+mkdir -p /mnt/guix/boot/grub
+cp -r /boot/grub/* /mnt/guix/boot/grub/
+@end example
+
+Now initialize the Guix installation:
+
+@example
+guix system init guix-config.scm /mnt/guix
+@end example
+
+Ok, power it down!
+Now from the Linode console, select boot and select "Guix".
+
+Once it boots, you should be able to log in via SSH!  (The server config
+will have changed though.)  You may encounter an error like:
+
+@example
+$ ssh root@@<server ip address>
+@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+@    WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED!     @
+@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
+Someone could be eavesdropping on you right now (man-in-the-middle attack)!
+It is also possible that a host key has just been changed.
+The fingerprint for the ECDSA key sent by the remote host is
+SHA256:0B+wp33w57AnKQuHCvQP0+ZdKaqYrI/kyU7CfVbS7R4.
+Please contact your system administrator.
+Add correct host key in /home/joshua/.ssh/known_hosts to get rid of this message.
+Offending ECDSA key in /home/joshua/.ssh/known_hosts:3
+ECDSA host key for 198.58.98.76 has changed and you have requested strict checking.
+Host key verification failed.
+@end example
+
+Either delete @file{~/.ssh/known_hosts} file, or delete the offending line
+starting with your server IP address.
+
+Be sure to set your password and root's password.
+
+@example
+ssh root@@<remote ip address>
+passwd  ; for the root password
+passwd <username> ; for the user password
+@end example
+
+You may not be able to run the above commands at this point.  If you
+have issues remotely logging into your linode box via SSH, then you may
+still need to set your root and user password initially by clicking on
+the ``Launch Console'' option in your linode.  Choose the ``Glish''
+instead of ``Weblish''.  Now you should be able to ssh into the machine.
+
+Horray!  At this point you can shut down the server, delete the
+Debian disk, and resize the Guix to the rest of the size.
+Congratulations!
+
+By the way, if you save it as a disk image right at this point, you'll
+have an easy time spinning up new Guix images!  You may need to
+down-size the Guix image to 6144MB, to save it as an image.  Then you
+can resize it again to the max size.
+
 @node Setting up a bind mount
 @section Setting up a bind mount
 

doc/guix.texi

@@ -144,6 +144,7 @@ Project}.
 * Introduction::                What is Guix about?
 * Installation::                Installing Guix.
 * System Installation::         Installing the whole operating system.
+* Getting Started::             Your first steps.
 * Package Management::          Package installation, upgrade, etc.
 * Development::                 Guix-aided software development.
 * Programming Interface::       Using Guix in Scheme.
@@ -196,6 +197,8 @@ System Installation
 * Installing Guix in a VM::     Guix System playground.
 * Building the Installation Image::  How this comes to be.
 
+Getting Started
+
 Manual Installation
 
 * Keyboard Layout and Networking and Partitioning:: Initial setup.
@@ -562,6 +565,9 @@ wget https://git.savannah.gnu.org/cgit/guix.git/plain/etc/guix-install.sh
 chmod +x guix-install.sh
 ./guix-install.sh
 @end example
+
+When you're done, @pxref{Application Setup} for extra configuration you
+might need, and @ref{Getting Started} for your first steps!
 @end quotation
 
 Installing goes along these lines:
@@ -784,7 +790,8 @@ or later;
 @c FIXME: Specify a version number once a release has been made.
 @uref{https://gitlab.com/guile-git/guile-git, Guile-Git}, from August
 2017 or later;
-@item @uref{https://savannah.nongnu.org/projects/guile-json/, Guile-JSON} 3.x;
+@item @uref{https://savannah.nongnu.org/projects/guile-json/, Guile-JSON}
+4.3.0 or later;
 @item @url{https://www.gnu.org/software/make/, GNU Make}.
 @end itemize
 
@@ -2476,7 +2483,8 @@ as.  This means that if you choose to use @command{guix system reconfigure} in
 root's login shell, you'll need to @command{guix pull} separately.
 @end quotation
 
-Join us on @code{#guix} on the Freenode IRC network or on
+Now, @pxref{Getting Started}, and
+join us on @code{#guix} on the Freenode IRC network or on
 @email{guix-devel@@gnu.org} to share your experience!
 
 
@@ -2563,6 +2571,210 @@ guix system disk-image --system=armhf-linux -e '((@@ (gnu system install) os-wit
 @code{A20-OLinuXino-Lime2} is the name of the board.  If you specify an invalid
 board, a list of possible boards will be printed.
 
+@c *********************************************************************
+@node Getting Started
+@chapter Getting Started
+
+Presumably, you've reached this section because either you have
+installed Guix on top of another distribution (@pxref{Installation}), or
+you've installed the standalone Guix System (@pxref{System
+Installation}).  It's time for you to get started using Guix and this
+section aims to help you do that and give you a feel of what it's like.
+
+Guix is about installing software, so probably the first thing you'll
+want to do is to actually look for software.  Let's say you're looking
+for a text editor, you can run:
+
+@example
+guix search text editor
+@end example
+
+This command shows you a number of matching @dfn{packages}, each time
+showing the package's name, version, a description, and additional info.
+Once you've found out the one you want to use, let's say Emacs (ah ha!),
+you can go ahead and install it (run this command as a regular user,
+@emph{no need for root privileges}!):
+
+@example
+guix install emacs
+@end example
+
+You've installed your first package, congrats!  In the process, you've
+probably noticed that Guix downloaded pre-built binaries; or, if you
+explicitly chose to @emph{not} use pre-built binaries, then probably
+Guix is still building software (@pxref{Substitutes}, for more info).
+
+Unless you're using Guix System, the @command{guix install} command must
+have printed this hint:
+
+@example
+hint: Consider setting the necessary environment variables by running:
+
+     GUIX_PROFILE="$HOME/.guix-profile"
+     . "$GUIX_PROFILE/etc/profile"
+
+Alternately, see `guix package --search-paths -p "$HOME/.guix-profile"'.
+@end example
+
+Indeed, you must now tell your shell where @command{emacs} and other
+programs installed with Guix are to be found.  Pasting the two lines
+above will do just that: it will add
+@code{$HOME/.guix-profile/bin}---which is where the installed package
+is---to the @code{PATH} environment variable.  You can paste these two
+lines in your shell so they take effect right away, but more importantly
+you should add them to @file{~/.bash_profile} (or equivalent file if you
+do not use Bash) so that environment variables are set next time you
+spawn a shell.  You only need to do this once and other search paths
+environment variables will be taken care of similarly---e.g., if you
+eventually install @code{python} and Python libraries, @code{PYTHONPATH}
+will be defined.
+
+You can go on installing packages at your will.  To list installed
+packages, run:
+
+@example
+guix package --list-installed
+@end example
+
+To remove a package, you would unsurprisingly run @command{guix remove}.
+A distinguishing feature is the ability to @dfn{roll back} any operation
+you made---installation, removal, upgrade---by simply typing:
+
+@example
+guix package --roll-back
+@end example
+
+This is because each operation is in fact a @dfn{transaction} that
+creates a new @dfn{generation}.  These generations and the difference
+between them can be displayed by running:
+
+@example
+guix package --list-generations
+@end example
+
+Now you know the basics of package management!
+
+@quotation Going further
+@xref{Package Management}, for more about package management.  You may
+like @dfn{declarative} package management with @command{guix package
+--manifest}, managing separate @dfn{profiles} with @option{--profile},
+deleting old generations, collecting garbage, and other nifty features
+that will come in handy as you become more familiar with Guix.  If you
+are a developer, @pxref{Development} for additional tools.  And if
+you're curious, @pxref{Features}, to peek under the hood.
+@end quotation
+
+Once you've installed a set of packages, you will want to periodically
+@emph{upgrade} them to the latest and greatest version.  To do that, you
+will first pull the latest revision of Guix and its package collection:
+
+@example
+guix pull
+@end example
+
+The end result is a new @command{guix} command, under
+@file{~/.config/guix/current/bin}.  Unless you're on Guix System, the
+first time you run @command{guix pull}, be sure to follow the hint that
+the command prints and, similar to what we saw above, paste these two
+lines in your terminal and @file{.bash_profile}:
+
+@example
+GUIX_PROFILE="$HOME/.config/guix/current/etc/profile"
+. "$GUIX_PROFILE/etc/profile"
+@end example
+
+@noindent
+You must also instruct your shell to point to this new @command{guix}:
+
+@example
+hash guix
+@end example
+
+At this point, you're running a brand new Guix.  You can thus go ahead
+and actually upgrade all the packages you previously installed:
+
+@example
+guix upgrade
+@end example
+
+As you run this command, you will see that binaries are downloaded (or
+perhaps some packages are built), and eventually you end up with the
+upgraded packages.  Should one of these upgraded packages not be to your
+liking, remember you can always roll back!
+
+You can display the exact revision of Guix you're currently using by
+running:
+
+@example
+guix describe
+@end example
+
+The information it displays is @emph{all it takes to reproduce the exact
+same Guix}, be it at a different point in time or on a different
+machine.
+
+@quotation Going further
+@xref{Invoking guix pull}, for more information.  @xref{Channels}, on
+how to specify additional @dfn{channels} to pull packages from, how to
+replicate Guix, and more.  You may also find @command{time-machine}
+handy (@pxref{Invoking guix time-machine}).
+@end quotation
+
+If you installed Guix System, one of the first things you'll want to do
+is to upgrade your system.  Once you've run @command{guix pull} to get
+the latest Guix, you can upgrade the system like this:
+
+@example
+sudo guix system reconfigure /etc/config.scm
+@end example
+
+Upon completion, the system runs the latest versions of its software
+packages.  When you eventually reboot, you'll notice a sub-menu in the
+bootloader that reads ``Old system generations'': it's what allows you
+to boot @emph{an older generation of your system}, should the latest
+generation be ``broken'' or otherwise unsatisfying.  Just like for
+packages, you can always @emph{roll back} to a previous generation
+@emph{of the whole system}:
+
+@example
+sudo guix system roll-back
+@end example
+
+There are many things you'll probably want to tweak on your system:
+adding new user accounts, adding new system services, fiddling with the
+configuration of those services, etc.  The system configuration is
+@emph{entirely} described in the @file{/etc/config.scm} file.
+@xref{Using the Configuration System}, to learn how to change it.
+
+Now you know enough to get started!
+
+@quotation Resources
+The rest of this manual provides a reference for all things Guix.  Here
+are some additional resources you may find useful:
+
+@itemize
+@item
+@xref{Top,,, guix-cookbook, The GNU Guix Cookbook}, for a list of
+``how-to'' style of recipes for a variety of applications.
+
+@item
+The @uref{https://guix.gnu.org/guix-refcard.pdf, GNU Guix Reference
+Card} lists in two pages most of the commands and options you'll ever
+need.
+
+@item
+The web site contains @uref{https://guix.gnu.org/en/videos/,
+instructional videos} covering topics such as everyday use of Guix, how
+to get help, and how to become a contributor.
+
+@item
+@xref{Documentation}, to learn how to access documentation on your
+computer.
+@end itemize
+
+We hope you will enjoy Guix as much as the community enjoys building it!
+@end quotation
+
 @c *********************************************************************
 @node Package Management
 @chapter Package Management
@@ -2602,6 +2814,10 @@ guix install emacs-guix
 @node Features
 @section Features
 
+Here we assume you've already made your first steps with Guix
+(@pxref{Getting Started}) and would like to get an overview about what's
+going on under the hood.
+
 When using Guix, each package ends up in the @dfn{package store}, in its
 own directory---something that resembles
 @file{/gnu/store/xxx-package-1.2}, where @code{xxx} is a base32 string.
@@ -4774,7 +4990,13 @@ what you should use in this case (@pxref{Invoking guix copy}).
 
 @cindex nar, archive format
 @cindex normalized archive (nar)
-Archives are stored in the ``normalized archive'' or ``nar'' format, which is
+@cindex nar bundle, archive format
+Each store item is written in the @dfn{normalized archive} or @dfn{nar}
+format (described below), and the output of @command{guix archive
+--export} (and input of @command{guix archive --import}) is a @dfn{nar
+bundle}.
+
+The nar format is
 comparable in spirit to `tar', but with differences
 that make it more appropriate for our purposes.  First, rather than
 recording all Unix metadata for each file, the nar format only mentions
@@ -4784,6 +5006,10 @@ entries are stored always follows the order of file names according to
 the C locale collation order.  This makes archive production fully
 deterministic.
 
+That nar bundle format is essentially the concatenation of zero or more
+nars along with metadata for each store item it contains: its file name,
+references, corresponding derivation, and a digital signature.
+
 When exporting, the daemon digitally signs the contents of the archive,
 and that digital signature is appended.  When importing, the daemon
 verifies the signature and rejects the import in case of an invalid
@@ -8334,10 +8560,12 @@ This is the declarative counterpart of @code{text-file}.
 @end deffn
 
 @deffn {Scheme Procedure} computed-file @var{name} @var{gexp} @
-          [#:options '(#:local-build? #t)]
+          [#:local-build? #t]
+          [#:options '()]
 Return an object representing the store item @var{name}, a file or
-directory computed by @var{gexp}.  @var{options}
+directory computed by @var{gexp}.  When @var{local-build?} is true (the
-is a list of additional arguments to pass to @code{gexp->derivation}.
+default), the derivation is built locally.  @var{options} is a list of
+additional arguments to pass to @code{gexp->derivation}.
 
 This is the declarative counterpart of @code{gexp->derivation}.
 @end deffn
@@ -12203,6 +12431,19 @@ example for an encrypted partition (@pxref{Mapped Devices}).
 @end table
 @end deftp
 
+@deffn {Scheme Procedure} file-system-label @var{str}
+This procedure returns an opaque file system label from @var{str}, a
+string:
+
+@lisp
+(file-system-label "home")
+@result{} #<file-system-label "home">
+@end lisp
+
+File system labels are used to refer to file systems by label rather
+than by device name.  See above for examples.
+@end deffn
+
 The @code{(gnu system file-systems)} exports the following useful
 variables.
 
@@ -12249,6 +12490,29 @@ and unmount user-space FUSE file systems.  This requires the
 @code{fuse.ko} kernel module to be loaded.
 @end defvr
 
+The @code{(gnu system uuid)} module provides tools to deal with file
+system ``unique identifiers'' (UUIDs).
+
+@deffn {Scheme Procedure} uuid @var{str} [@var{type}]
+Return an opaque UUID (unique identifier) object of the given @var{type}
+(a symbol) by parsing @var{str} (a string):
+
+@lisp
+(uuid "4dab5feb-d176-45de-b287-9b0a6e4c01cb")
+@result{} #<<uuid> type: dce bv: @dots{}>
+
+(uuid "1234-ABCD" 'fat)
+@result{} #<<uuid> type: fat bv: @dots{}>
+@end lisp
+
+@var{type} may be one of @code{dce}, @code{iso9660}, @code{fat},
+@code{ntfs}, or one of the commonly found synonyms for these.
+
+UUIDs are another way to unambiguously refer to file systems in
+operating system configuration.  See the examples above.
+@end deffn
+
+
 @node Btrfs file system
 @subsection Btrfs file system
 
@@ -21943,6 +22207,31 @@ Can be set to @code{#f} to disable logging.
 @item @code{file} (default @code{#f})
 An optional override of the whole configuration.
 You can use the @code{mixed-text-file} function or an absolute filepath for it.
+@item @code{php-ini-file} (default @code{#f})
+An optional override of the default php settings.
+It may be any ``file-like'' object (@pxref{G-Expressions, file-like objects}).
+You can use the @code{mixed-text-file} function or an absolute filepath for it.
+
+For local development it is useful to set a higher timeout and memory
+limit for spawned php processes.  This be accomplished with the
+following operating system configuration snippet:
+@lisp
+(define %local-php-ini
+  (plain-file "php.ini"
+              "memory_limit = 2G
+max_execution_time = 1800"))
+
+(operating-system
+  ;; @dots{}
+  (services (cons (service php-fpm-service-type
+                           (php-fpm-configuration
+                            (php-ini-file %local-php-ini)))
+                  %base-services)))
+@end lisp
+
+Consult the @url{https://www.php.net/manual/en/ini.core.php,core php.ini
+directives} for comprehensive documentation on the acceptable
+@file{php.ini} directives.
 @end table
 @end deftp
 
@@ -22196,9 +22485,10 @@ A list of @code{certificates-configuration}s for which to generate
 certificates and request signatures.  Each certificate has a @code{name}
 and several @code{domains}.
 
-@item @code{email}
+@item @code{email} (default: @code{#f})
-Mandatory email used for registration, recovery contact, and important
+Optional email address used for registration and recovery contact.
-account notifications.
+Setting this is encouraged as it allows you to receive important
+notifications about the account and issued certificates.
 
 @item @code{server} (default: @code{#f})
 Optional URL of ACME server.  Setting this overrides certbot's default,
@@ -25126,6 +25416,7 @@ Return the name of @var{platform}---a string such as @code{"arm"}.
 
 @cindex @code{hurd}
 @cindex the Hurd
+@cindex childhurd
 
 Service @code{hurd-vm} provides support for running GNU/Hurd in a
 virtual machine (VM), a so-called ``Childhurd''.  The virtual machine is
@@ -25198,15 +25489,41 @@ By default, it produces
 @lisp
 '("--device" "rtl8139,netdev=net0"
   "--netdev" "user,id=net0\
+              ,hostfwd=tcp:127.0.0.1:<secrets-port>-:1004\
               ,hostfwd=tcp:127.0.0.1:<ssh-port>-:2222\
               ,hostfwd=tcp:127.0.0.1:<vnc-port>-:5900")
 @end lisp
 with forwarded ports
 @example
+<ssh-port>: @code{(+ 11004 (* 1000 @var{ID}))}
 <ssh-port>: @code{(+ 10022 (* 1000 @var{ID}))}
 <vnc-port>: @code{(+ 15900 (* 1000 @var{ID}))}
 @end example
 
+@item @code{secret-root} (default: @file{/etc/childhurd})
+The root directory with out-of-band secrets to be installed into the
+childhurd once it runs.  Childhurds are volatile which means that on
+every startup, secrets such as the SSH host keys and Guix signing key
+are recreated.
+
+If the @file{/etc/childhurd} directory does not exist, the
+@code{secret-service} running in the Childhurd will be sent an empty
+list of secrets.
+
+Typical use to populate @file{"/etc/childhurd"} with a tree of
+non-volatile secrets, like so
+
+@example
+/etc/childhurd/etc/guix/signing-key.pub
+/etc/childhurd/etc/guix/signing-key.sec
+/etc/childhurd/etc/ssh/ssh_host_ed25519_key
+/etc/childhurd/etc/ssh/ssh_host_ecdsa_key
+/etc/childhurd/etc/ssh/ssh_host_ed25519_key.pub
+/etc/childhurd/etc/ssh/ssh_host_ecdsa_key.pub
+@end example
+
+to be sent to the Childhurd, including permissions.
+
 @end table
 @end deftp
 
@@ -27688,7 +28005,7 @@ The Containerd package to use.
 @item @code{proxy} (default @var{docker-libnetwork-cmd-proxy})
 The Docker user-land networking proxy package to use.
 
-@item @code{enable-proxy?} (default @code{#f})
+@item @code{enable-proxy?} (default @code{#t})
 Enable or disable the use of the Docker user-land networking proxy.
 
 @item @code{debug?} (default @code{#f})
@@ -27799,7 +28116,7 @@ The common way to create this file is as follows:
        (app       (string-append out "/bin/" ,name))
        (Rbin      (string-append (assoc-ref %build-inputs "r-min")
                                  "/bin/Rscript")))
-@dots{}
+  ;; @dots{}
   (mkdir-p (string-append out "/bin"))
   (call-with-output-file app
     (lambda (port)
@@ -27808,8 +28125,7 @@ The common way to create this file is as follows:
 library(shiny)
 setwd(\"~a\")
 runApp(launch.browser=0, port=4202)~%\n"
-      Rbin targetdir)))
+      Rbin targetdir))))
-@dots{}
 @end lisp
 
 @end table
@@ -28843,7 +29159,9 @@ the @option{--image-size} option is ignored in the case of
 @code{docker-image}.
 
 You can specify the root file system type by using the
-@option{--file-system-type} option.  It defaults to @code{ext4}.
+@option{--file-system-type} option.  It defaults to @code{ext4}.  When its
+value is @code{iso9660}, the @option{--label} option can be used to specify
+a volume ID with @code{disk-image}.
 
 When using @code{vm-image}, the returned image is in qcow2 format, which
 the QEMU emulator can efficiently use. @xref{Running Guix in a VM},
@@ -29777,6 +30095,23 @@ calls it, passing it the initial value of the service as the first
 argument and the result of applying @code{compose} to the extension
 values as the second argument.  It must return a value that is a valid
 parameter value for the service instance.
+
+@item @code{description}
+This is a string, possibly using Texinfo markup, describing in a couple
+of sentences what the service is about.  This string allows users to
+find about the service through @command{guix system search}
+(@pxref{Invoking guix system}).
+
+@item @code{default-value} (default: @code{&no-default-value})
+The default value associated for instances of this service type.  This
+allows users to use the @code{service} form without its second argument:
+
+@lisp
+(service @var{type})
+@end lisp
+
+The returned service in this case has the default value specified by
+@var{type}.
 @end table
 
 @xref{Service Types and Services}, for examples.

etc/completion/bash/guix

@@ -19,6 +19,19 @@
 # Bash completion for Guix commands.
 
 declare _guix_available_packages
+declare _guix_commands
+
+_guix_complete_command ()
+{
+    local word_at_point="${COMP_WORDS[$COMP_CWORD]}"
+    if [ -z "$_guix_commands" ]
+    then
+	# Cache the list of commands to speed things up.
+	_guix_commands="$(guix --help 2> /dev/null \
+                                     | grep '^  ' | cut -c 2-)"
+    fi
+    COMPREPLY=($(compgen -W "$_guix_commands" -- "$word_at_point"))
+}
 
 _guix_complete_subcommand ()
 {
@@ -146,19 +159,6 @@ _guix_complete_pid ()
     COMPREPLY=($(compgen -W "$pids" -- "$1"))
 }
 
-declare _guix_subcommands
-
-_guix_complete_subcommand ()
-{
-    if [ -z "$_guix_subcommands" ]
-    then
-	# Cache the list of subcommands to speed things up.
-	_guix_subcommands="$(guix --help 2> /dev/null \
-                                     | grep '^  ' | cut -c 2-)"
-    fi
-    COMPREPLY=($(compgen -W "$_guix_subcommands" -- "$word_at_point"))
-}
-
 _guix_complete ()
 {
     local word_count=${#COMP_WORDS[*]}
@@ -176,7 +176,7 @@ _guix_complete ()
 
     case $COMP_CWORD in
 	1)
-	    _guix_complete_subcommand
+	    _guix_complete_command
 	    ;;
 	*)
 	    if _guix_is_command "package"
@@ -251,7 +251,7 @@ _guix_complete ()
                 then
                     _guix_complete_file
 		else
-		    _guix_complete_subcommand
+		    _guix_complete_command
                 fi
 	    elif _guix_is_command "container"
 	    then

etc/guix-install.sh

@@ -111,7 +111,7 @@ chk_gpg_keyring()
     # systems where gpg has never been used, causing errors and confusion.
     gpg --dry-run --list-keys ${OPENPGP_SIGNING_KEY_ID} >/dev/null 2>&1 || (
         _err "${ERR}Missing OpenPGP public key.  Fetch it with this command:"
-        echo "  wget https://sv.gnu.org/people/viewgpg.php?user_id=15145 -qO - | sudo -i gpg --import -"
+        echo "  wget 'https://sv.gnu.org/people/viewgpg.php?user_id=15145' -qO - | sudo -i gpg --import -"
         exit 1
     )
 }

gnu/bootloader/grub.scm

@@ -295,6 +295,33 @@ code."
         ((? file-system-label? label)
          (format #f "search --label --set ~a"
                  (file-system-label->string label)))
+        ((? (lambda (device)
+              (and (string? device) (string-contains device ":/"))) nfs-uri)
+         ;; This assumes that if your root file system is on NFS, then
+         ;; you also want to load your grub extra files, kernel and initrd
+         ;; from there.
+         ;;
+         ;; We explicitly set "root=(tftp)" here even though if grub.cfg
+         ;; had been loaded via TFTP, Grub would have set "root=(tftp)"
+         ;; automatically anyway.  The reason is if you have a system that
+         ;; used to be on NFS but now is local, root would be set to local
+         ;; disk.  If you then selected an older system generation that is
+         ;; supposed to boot from network in the Grub boot menu, Grub still
+         ;; wouldn't load those files from network otherwise.
+         ;;
+         ;; TFTP is preferred to HTTP because it is used more widely and
+         ;; specified in standards more widely--especially BOOTP/DHCPv4
+         ;; defines a TFTP server for DHCP option 66, but not HTTP.
+         ;;
+         ;; Note: DHCPv6 specifies option 59 to contain a boot-file-url,
+         ;; which can contain a HTTP or TFTP URL.
+         ;;
+         ;; Note: It is assumed that the file paths are of a similar
+         ;; setup on both the TFTP server and the NFS server (it is
+         ;; not possible to search for files on TFTP).
+         ;;
+         ;; TODO: Allow HTTP.
+         "set root=(tftp)")
         ((or #f (? string?))
          #~(format #f "search --file --set ~a" #$file)))))
 
@@ -506,6 +533,10 @@ fi~%"))))
 ;;;
 ;;; Bootloader definitions.
 ;;;
+;;; For all these grub-bootloader variables the path to /boot/grub/grub.cfg
+;;; is fixed.  Inheriting and overwriting the field 'configuration-file' will
+;;; break 'guix system delete-generations', 'guix system switch-generation',
+;;; and 'guix system roll-back'.
 
 (define grub-bootloader
   (bootloader
@@ -516,12 +547,12 @@ fi~%"))))
    (configuration-file "/boot/grub/grub.cfg")
    (configuration-file-generator grub-configuration-file)))
 
-(define* grub-minimal-bootloader
+(define grub-minimal-bootloader
   (bootloader
    (inherit grub-bootloader)
    (package grub-minimal)))
 
-(define* grub-efi-bootloader
+(define grub-efi-bootloader
   (bootloader
    (inherit grub-bootloader)
    (installer install-grub-efi)
@@ -529,7 +560,7 @@ fi~%"))))
    (name 'grub-efi)
    (package grub-efi)))
 
-(define* grub-mkrescue-bootloader
+(define grub-mkrescue-bootloader
   (bootloader
    (inherit grub-efi-bootloader)
    (package grub-hybrid)))

gnu/build/file-systems.scm

@@ -675,7 +675,8 @@ were found."
 
 (define (canonicalize-device-spec spec)
   "Return the device name corresponding to SPEC, which can be a <uuid>, a
-<file-system-label>, or a string (typically a /dev file name)."
+<file-system-label>, or a string (typically a /dev file name or an nfs-root
+containing ':/')."
   (define max-trials
     ;; Number of times we retry partition label resolution, 1 second per
     ;; trial.  Note: somebody reported a delay of 16 seconds (!) before their

gnu/build/install.scm

@@ -18,6 +18,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu build install)
+  #:use-module (guix build syscalls)
   #:use-module (guix build utils)
   #:use-module (guix build store-copy)
   #:use-module (srfi srfi-26)
@@ -26,7 +27,9 @@
             evaluate-populate-directive
             populate-root-file-system
             install-database-and-gc-roots
-            populate-single-profile-directory))
+            populate-single-profile-directory
+            mount-cow-store
+            unmount-cow-store))
 
 ;;; Commentary:
 ;;;
@@ -229,4 +232,43 @@ This is used to create the self-contained tarballs with 'guix pack'."
     (_
      #t)))
 
+(define (mount-cow-store target backing-directory)
+  "Make the store copy-on-write, using TARGET as the backing store.  This is
+useful when TARGET is on a hard disk, whereas the current store is on a RAM
+disk."
+  (define (set-store-permissions directory)
+    "Set the right perms on DIRECTORY to use it as the store."
+    (chown directory 0 30000)      ;use the fixed 'guixbuild' GID
+    (chmod directory #o1775))
+
+  (let ((tmpdir (string-append target "/tmp")))
+    (mkdir-p tmpdir)
+    (mount tmpdir "/tmp" "none" MS_BIND))
+
+  (let* ((rw-dir (string-append target backing-directory))
+         (work-dir (string-append rw-dir "/../.overlayfs-workdir")))
+    (mkdir-p rw-dir)
+    (mkdir-p work-dir)
+    (mkdir-p "/.rw-store")
+    (set-store-permissions rw-dir)
+    (set-store-permissions "/.rw-store")
+
+    ;; Mount the overlay, then atomically make it the store.
+    (mount "none" "/.rw-store" "overlay" 0
+           (string-append "lowerdir=" (%store-directory) ","
+                          "upperdir=" rw-dir ","
+                          "workdir=" work-dir))
+    (mount "/.rw-store" (%store-directory) "" MS_MOVE)
+    (rmdir "/.rw-store")))
+
+(define (unmount-cow-store target backing-directory)
+  "Unmount copy-on-write store."
+  (let ((tmp-dir "/remove"))
+    (mkdir-p tmp-dir)
+    (mount (%store-directory) tmp-dir "" MS_MOVE)
+    (umount tmp-dir)
+    (rmdir tmp-dir)
+    (delete-file-recursively
+     (string-append target backing-directory))))
+
 ;;; install.scm ends here

gnu/build/linux-boot.scm

@@ -469,9 +469,10 @@ upon error."
 
   (define (device-string->file-system-device device-string)
     ;; The "--root=SPEC" kernel command-line option always provides a
-    ;; string, but the string can represent a device, a UUID, or a
+    ;; string, but the string can represent a device, an nfs-root, a UUID, or a
-    ;; label.  So check for all three.
+    ;; label.  So check for all four.
     (cond ((string-prefix? "/" device-string) device-string)
+          ((string-contains device-string ":/") device-string) ; nfs-root
           ((uuid device-string) => identity)
           (else (file-system-label device-string))))
 

gnu/build/linux-container.scm

@@ -243,7 +243,8 @@ that host UIDs (respectively GIDs) map to in the namespace."
              (match (read child)
                ('ready
                 (purify-environment)
-                (when (memq 'mnt namespaces)
+                (when (and (memq 'mnt namespaces)
+                           (not (string=? root "/")))
                   (catch #t
                     (lambda ()
                       (mount-file-systems root mounts

gnu/build/secret-service.scm

@@ -0,0 +1,137 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2020 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu build secret-service)
+  #:use-module (guix build utils)
+
+  #:use-module (srfi srfi-26)
+  #:use-module (rnrs bytevectors)
+  #:use-module (ice-9 binary-ports)
+  #:use-module (ice-9 match)
+  #:use-module (ice-9 rdelim)
+
+  #:export (secret-service-receive-secrets
+            secret-service-send-secrets))
+
+;;; Commentary:
+;;;
+;;; Utility procedures for copying secrets into a VM.
+;;;
+;;; Code:
+
+(define* (secret-service-send-secrets port secret-root #:key (retry 60))
+  "Copy all files under SECRET-ROOT using TCP to secret-service listening at
+local PORT.  If connect fails, sleep 1s and retry RETRY times."
+
+  (define (file->file+size+mode file-name)
+    (let ((stat (stat file-name))
+          (target (substring file-name (string-length secret-root))))
+      (list target (stat:size stat) (stat:mode stat))))
+
+  (format (current-error-port) "sending secrets to ~a~%" port)
+  (let ((sock (socket AF_INET SOCK_STREAM 0))
+        (addr (make-socket-address AF_INET INADDR_LOOPBACK port)))
+    ;; connect to wait for port
+    (let loop ((retry retry))
+      (catch 'system-error
+        (cute connect sock addr)
+        (lambda (key . args)
+          (when (zero? retry)
+            (apply throw key args))
+          (format (current-error-port) "retrying connection~%")
+          (sleep 1)
+          (loop (1- retry)))))
+
+    (format (current-error-port) "connected!  sending files in ~s %~"
+            secret-root)
+    (let* ((files (if secret-root (find-files secret-root) '()))
+           (files-sizes-modes (map file->file+size+mode files))
+           (secrets `(secrets
+                      (version 0)
+                      (files ,files-sizes-modes))))
+      (write secrets sock)
+      (for-each (compose (cute dump-port <> sock)
+                         (cute open-input-file <>))
+                files))))
+
+(define (secret-service-receive-secrets port)
+  "Listen to local PORT and wait for a secret service client to send secrets.
+Write them to the file system."
+
+  (define (wait-for-client port)
+    ;; Wait for a TCP connection on PORT.  Note: We cannot use the
+    ;; virtio-serial ports, which would be safer, because they are
+    ;; (presumably) unsupported on GNU/Hurd.
+    (let ((sock (socket AF_INET SOCK_STREAM 0)))
+      (bind sock AF_INET INADDR_ANY port)
+      (listen sock 1)
+      (format (current-error-port)
+              "waiting for secrets on port ~a...~%"
+              port)
+      (match (accept sock)
+        ((client . address)
+         (format (current-error-port) "client connection from ~a~%"
+                 (inet-ntop (sockaddr:fam address)
+                            (sockaddr:addr address)))
+         (close-port sock)
+         client))))
+
+  ;; TODO: Remove when (@ (guix build utils) dump-port) has a 'size'
+  ;; parameter.
+  (define (dump in out size)
+    ;; Copy SIZE bytes from IN to OUT.
+    (define buf-size 65536)
+    (define buf (make-bytevector buf-size))
+
+    (let loop ((left size))
+      (if (<= left 0)
+          0
+          (let ((read (get-bytevector-n! in buf 0 (min left buf-size))))
+            (if (eof-object? read)
+                left
+                (begin
+                  (put-bytevector out buf 0 read)
+                  (loop (- left read))))))))
+
+  (define (read-secrets port)
+    ;; Read secret files from PORT and install them.
+    (match (false-if-exception (read port))
+      (('secrets ('version 0)
+                 ('files ((files sizes modes) ...)))
+       (for-each (lambda (file size mode)
+                   (format (current-error-port)
+                           "installing file '~a' (~a bytes)...~%"
+                           file size)
+                   (mkdir-p (dirname file))
+                   (call-with-output-file file
+                     (lambda (output)
+                       (dump port output size)
+                       (chmod file mode))))
+                 files sizes modes))
+      (_
+       (format (current-error-port)
+               "invalid secrets received~%")
+       #f)))
+
+  (let* ((port (wait-for-client port))
+         (result (read-secrets port)))
+    (close-port port)
+    result))
+
+;;; secret-service.scm ends here

gnu/build/shepherd.scm

@@ -20,10 +20,12 @@
   #:use-module (gnu system file-systems)
   #:use-module (gnu build linux-container)
   #:use-module (guix build utils)
+  #:use-module (guix utils)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-26)
   #:use-module (ice-9 match)
-  #:export (make-forkexec-constructor/container))
+  #:export (make-forkexec-constructor/container
+            fork+exec-command/container))
 
 ;;; Commentary:
 ;;;
@@ -93,7 +95,8 @@
 ;; XXX: Lazy-bind the Shepherd to avoid a compile-time dependency.
 (module-autoload! (current-module)
                   '(shepherd service)
-                  '(read-pid-file exec-command %precious-signals))
+                  '(fork+exec-command read-pid-file exec-command
+                    %precious-signals))
 (module-autoload! (current-module)
                   '(shepherd system) '(unblock-signals))
 
@@ -188,6 +191,17 @@ namespace, in addition to essential bind-mounts such /proc."
               (read-pid-file pid-file #:max-delay pid-file-timeout))
           pid))))
 
+(define* (fork+exec-command/container command
+                                      #:key pid
+                                      #:allow-other-keys
+                                      #:rest args)
+  "This is a variant of 'fork+exec-command' procedure, that joins the
+namespaces of process PID beforehand."
+  (container-excursion* pid
+    (lambda ()
+      (apply fork+exec-command command
+             (strip-keyword-arguments '(#:pid) args)))))
+
 ;; Local Variables:
 ;; eval: (put 'container-excursion* 'scheme-indent-function 1)
 ;; End:

gnu/ci.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2018, 2019 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2020 Julien Lepiller <julien@lepiller.eu>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,6 +26,7 @@
   #:use-module (guix profiles)
   #:use-module (guix packages)
   #:use-module (guix channels)
+  #:use-module (guix config)
   #:use-module (guix derivations)
   #:use-module (guix build-system)
   #:use-module (guix monads)
@@ -116,7 +118,7 @@ SYSTEM."
   ;; Note: Don't put the '-final' package variants because (1) that's
   ;; implicit, and (2) they cannot be cross-built (due to the explicit input
   ;; chain.)
-  (list gcc-4.8 gcc-4.9 gcc-5 glibc binutils
+  (list gcc-7 gcc-8 gcc-9 gcc-10 glibc binutils
         gmp mpfr mpc coreutils findutils diffutils patch sed grep
         gawk gnu-gettext hello guile-2.0 guile-2.2 zlib gzip xz
         %bootstrap-binaries-tarball
@@ -233,7 +235,12 @@ system.")
         ,(->job 'iso9660-image
                 (build-image
                  (image
-                  (inherit iso9660-image)
+                  (inherit (image-with-label
+                             iso9660-image
+                             (string-append "GUIX_" system "_"
+                                            (if (> (string-length %guix-version) 7)
+                                                (substring %guix-version 0 7)
+                                                %guix-version))))
                   (operating-system installation-os))))
         ;; Only cross-compile Guix System images from x86_64-linux for now.
         ,@(if (string=? system "x86_64-linux")

gnu/installer/final.scm

@@ -26,6 +26,8 @@
   #:use-module (guix build syscalls)
   #:use-module (guix build utils)
   #:use-module (gnu build accounts)
+  #:use-module (gnu build install)
+  #:use-module (gnu build linux-container)
   #:use-module ((gnu system shadow) #:prefix sys:)
   #:use-module (rnrs io ports)
   #:use-module (srfi srfi-1)
@@ -133,49 +135,32 @@ USERS."
                        (_ #f))))))
               pids)))
 
-(define (umount-cow-store)
+(define (call-with-mnt-container thunk)
-  "Remove the store overlay and the bind-mount on /tmp created by the
+  "This is a variant of call-with-container. Run THUNK in a new container
-cow-store service.  This procedure is very fragile and a better approach would
+process, within a separate MNT namespace. The container is not jailed so that
-be much appreciated."
+it can interact with the rest of the system."
-  (catch #t
+  (let ((pid (run-container "/" '() '(mnt) 1 thunk)))
-    (lambda ()
+    ;; Catch SIGINT and kill the container process.
-      (let ((tmp-dir "/remove"))
+    (sigaction SIGINT
-        (syslog "Unmounting cow-store.~%")
+      (lambda (signum)
+        (false-if-exception
+         (kill pid SIGKILL))))
 
-        (mkdir-p tmp-dir)
+    (match (waitpid pid)
-        (mount (%store-directory) tmp-dir "" MS_MOVE)
+      ((_ . status) status))))
-
-        ;; The guix-daemon has possibly opened files from the cow-store,
-        ;; restart it.
-        (restart-service 'guix-daemon)
-
-        (syslog "Killing cow users.")
-
-        ;; Kill all processes started while the cow-store was active (logins
-        ;; on other TTYs for instance).
-        (kill-cow-users tmp-dir)
-
-        ;; Try to umount the store overlay. Some process such as udevd
-        ;; workers might still be active, so do some retries.
-        (let loop ((try 5))
-          (syslog "Umount try ~a~%" (- 5 try))
-          (sleep 1)
-          (let ((umounted? (false-if-exception (umount tmp-dir))))
-            (if (and (not umounted?) (> try 0))
-                (loop (- try 1))
-                (if umounted?
-                    (syslog "Umounted ~a successfully.~%" tmp-dir)
-                    (syslog "Failed to umount ~a.~%" tmp-dir)))))
-
-        (umount "/tmp")))
-    (lambda args
-      (syslog "~a~%" args))))
 
 (define* (install-system locale #:key (users '()))
   "Create /etc/shadow and /etc/passwd on the installation target for USERS.
 Start COW-STORE service on target directory and launch guix install command in
 a subshell.  LOCALE must be the locale name under which that command will run,
 or #f.  Return #t on success and #f on failure."
+  (define backing-directory
+    ;; Sub-directory used as the backing store for copy-on-write.
+    "/tmp/guix-inst")
+
+  (define (assert-exit x)
+    (primitive-exit (if x 0 1)))
+
   (let* ((options         (catch 'system-error
                             (lambda ()
                               ;; If this file exists, it can provide
@@ -188,7 +173,11 @@ or #f.  Return #t on success and #f on failure."
                                         "--fallback")
                                   options
                                   (list (%installer-configuration-file)
-                                        (%installer-target-dir)))))
+                                        (%installer-target-dir))))
+         (database-dir    "/var/guix/db")
+         (database-file   (string-append database-dir "/db.sqlite"))
+         (saved-database  (string-append database-dir "/db.save"))
+         (ret             #f))
     (mkdir-p (%installer-target-dir))
 
     ;; We want to initialize user passwords but we don't want to store them in
@@ -198,27 +187,49 @@ or #f.  Return #t on success and #f on failure."
     ;; passwords that we've put in there.
     (create-user-database users (%installer-target-dir))
 
+    ;; When the store overlay is mounted, other processes such as kmscon, udev
+    ;; and guix-daemon may open files from the store, preventing the
+    ;; underlying install support from being umounted. See:
+    ;; https://lists.gnu.org/archive/html/guix-devel/2018-12/msg00161.html.
+    ;;
+    ;; To avoid this situation, mount the store overlay inside a container,
+    ;; and run the installation from within that container.
+    (zero?
+     (call-with-mnt-container
+       (lambda ()
          (dynamic-wind
            (lambda ()
-        (start-service 'cow-store (list (%installer-target-dir))))
+             ;; Save the database, so that it can be restored once the
+             ;; cow-store is umounted.
+             (copy-file database-file saved-database)
+             (mount-cow-store (%installer-target-dir) backing-directory))
            (lambda ()
+             ;; We need to drag the guix-daemon to the container MNT
+             ;; namespace, so that it can operate on the cow-store.
+             (stop-service 'guix-daemon)
+             (start-service 'guix-daemon (list (number->string (getpid))))
+
+             (setvbuf (current-output-port) 'none)
+             (setvbuf (current-error-port) 'none)
+
              ;; If there are any connected clients, assume that we are running
              ;; installation tests. In that case, dump the standard and error
              ;; outputs to syslog.
+             (set! ret
                    (if (not (null? (current-clients)))
                        (with-output-to-file "/dev/console"
                          (lambda ()
                            (with-error-to-file "/dev/console"
                              (lambda ()
-                    (setvbuf (current-output-port) 'none)
+                               (run-command install-command
-                    (setvbuf (current-error-port) 'none)
+                                            #:locale locale)))))
-                    (run-command install-command #:locale locale)))))
+                       (run-command install-command #:locale locale))))
-            (run-command install-command #:locale locale)))
            (lambda ()
-        (stop-service 'cow-store)
+             ;; Restart guix-daemon so that it does no keep the MNT namespace
-        ;; Remove the store overlay created at cow-store service start.
+             ;; alive.
-        ;; Failing to do that will result in further umount calls to fail
+             (restart-service 'guix-daemon)
-        ;; because the target device is seen as busy. See:
+             (copy-file saved-database database-file)
-        ;; https://lists.gnu.org/archive/html/guix-devel/2018-12/msg00161.html.
+
-        (umount-cow-store)
+             ;; Finally umount the cow-store and exit the container.
-        #f))))
+             (unmount-cow-store (%installer-target-dir) backing-directory)
+             (assert-exit ret))))))))

gnu/installer/newt/final.scm

@@ -102,13 +102,6 @@ a specific step, or restart the installer."))
                             #:key (users '()))
   (clear-screen)
   (newt-suspend)
-  ;; XXX: Force loading 'bold' font files before mouting the
-  ;; cow-store. Otherwise, if the file is loaded by kmscon after the cow-store
-  ;; in mounted, it will be necessary to kill kmscon to umount to cow-store.
-  (display
-   (colorize-string
-    (format #f (G_ "Installing Guix System ...~%"))
-    (color BOLD)))
   (let ((install-ok? (install-system locale #:users users)))
     (newt-resume)
     install-ok?))

gnu/local.mk

@@ -36,6 +36,7 @@
 # Copyright © 2020 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
 # Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 # Copyright © 2020 Tanguy Le Carrour <tanguy@bioneland.org>
+# Copyright © 2020 Martin Becze <mjbecze@riseup.net>
 #
 # This file is part of GNU Guix.
 #
@@ -342,6 +343,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/lout.scm				\
   %D%/packages/logging.scm			\
   %D%/packages/logo.scm				\
+  %D%/packages/loko.scm				\
   %D%/packages/lolcode.scm                      \
   %D%/packages/lsof.scm				\
   %D%/packages/lua.scm				\
@@ -414,6 +416,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/package-management.scm		\
   %D%/packages/pantheon.scm			\
   %D%/packages/parallel.scm			\
+  %D%/packages/pascal.scm			\
   %D%/packages/password-utils.scm		\
   %D%/packages/patchutils.scm			\
   %D%/packages/pciutils.scm			\
@@ -429,6 +432,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/photo.scm			\
   %D%/packages/phabricator.scm 			\
   %D%/packages/php.scm				\
+  %D%/packages/piet.scm			\
   %D%/packages/pkg-config.scm			\
   %D%/packages/plotutils.scm			\
   %D%/packages/poedit.scm				\
@@ -658,6 +662,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/build/linux-initrd.scm			\
   %D%/build/linux-modules.scm			\
   %D%/build/marionette.scm			\
+  %D%/build/secret-service.scm			\
   %D%/build/vm.scm				\
 						\
   %D%/tests.scm					\
@@ -919,7 +924,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/elixir-path-length.patch			\
   %D%/packages/patches/elm-compiler-disable-reactor.patch	\
   %D%/packages/patches/elm-compiler-fix-map-key.patch		\
-  %D%/packages/patches/emacs27-exec-path.patch			\
   %D%/packages/patches/emacs-exec-path.patch			\
   %D%/packages/patches/emacs-exwm-fix-fullscreen-states.patch	\
   %D%/packages/patches/emacs-fix-scheme-indent-function.patch	\
@@ -964,6 +968,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/foomatic-filters-CVE-2015-8327.patch	\
   %D%/packages/patches/foomatic-filters-CVE-2015-8560.patch	\
   %D%/packages/patches/fontconfig-hurd-path-max.patch		\
+  %D%/packages/patches/fpc-reproducibility.patch		\
   %D%/packages/patches/freedink-engine-fix-sdl-hints.patch	\
   %D%/packages/patches/freeimage-unbundle.patch		\
   %D%/packages/patches/fuse-overlapping-headers.patch				\
@@ -1015,6 +1020,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gd-brect-bounds.patch			\
   %D%/packages/patches/gdb-hurd.patch				\
   %D%/packages/patches/gdm-default-session.patch		\
+  %D%/packages/patches/genimage-signedness.patch		\
   %D%/packages/patches/geoclue-config.patch			\
   %D%/packages/patches/ghc-8.0-fall-back-to-madv_dontneed.patch	\
   %D%/packages/patches/ghc-testsuite-dlopen-pie.patch		\
@@ -1073,6 +1079,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gobject-introspection-girepository.patch	\
   %D%/packages/patches/go-skip-gc-test.patch			\
   %D%/packages/patches/gpm-glibc-2.26.patch			\
+  %D%/packages/patches/gpodder-disable-updater.patch		\
   %D%/packages/patches/gpsbabel-minizip.patch     		\
   %D%/packages/patches/gpsbabel-qstring.patch     		\
   %D%/packages/patches/grantlee-merge-theme-dirs.patch		\
@@ -1521,6 +1528,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/readline-link-ncurses.patch		\
   %D%/packages/patches/readline-6.2-CVE-2014-2524.patch		\
   %D%/packages/patches/reposurgeon-add-missing-docbook-files.patch	\
+  %D%/packages/patches/r-httpuv-1.5.4-unvendor-libuv.patch	\
   %D%/packages/patches/ri-li-modernize_cpp.patch		\
   %D%/packages/patches/ripperx-missing-file.patch		\
   %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
@@ -1566,9 +1574,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/slim-login.patch				\
   %D%/packages/patches/slim-display.patch			\
   %D%/packages/patches/snappy-add-O2-flag-in-CmakeLists.txt.patch	\
-  %D%/packages/patches/sooperlooper-build-with-wx-30.patch 	\
   %D%/packages/patches/sphinxbase-fix-doxygen.patch		\
   %D%/packages/patches/sssd-fix-samba.patch			\
+  %D%/packages/patches/sssd-system-directories.patch		\
   %D%/packages/patches/steghide-fixes.patch			\
   %D%/packages/patches/suitesparse-mongoose-cmake.patch		\
   %D%/packages/patches/superlu-dist-awpm-grid.patch		\
@@ -1608,7 +1616,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/tk-find-library.patch			\
   %D%/packages/patches/transcode-ffmpeg.patch	\
   %D%/packages/patches/ttf2eot-cstddef.patch			\
-  %D%/packages/patches/ttfautohint-source-date-epoch.patch	\
   %D%/packages/patches/tomb-fix-errors-on-open.patch		\
   %D%/packages/patches/tup-unbundle-dependencies.patch		\
   %D%/packages/patches/tuxpaint-stamps-path.patch		\
@@ -1638,6 +1645,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/vboot-utils-fix-format-load-address.patch	\
   %D%/packages/patches/vboot-utils-fix-tests-show-contents.patch	\
   %D%/packages/patches/vboot-utils-skip-test-workbuf.patch	\
+  %D%/packages/patches/vcflib-use-shared-libraries.patch	\
   %D%/packages/patches/vigra-python-compat.patch		\
   %D%/packages/patches/vinagre-newer-freerdp.patch             \
   %D%/packages/patches/vinagre-newer-rdp-parameters.patch      \
@@ -1653,6 +1661,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/webkitgtk-share-store.patch		\
   %D%/packages/patches/webkitgtk-bind-all-fonts.patch		\
   %D%/packages/patches/websocketpp-fix-for-cmake-3.15.patch	\
+  %D%/packages/patches/wgetpaste-update-bpaste.patch		\
   %D%/packages/patches/wicd-bitrate-none-fix.patch		\
   %D%/packages/patches/wicd-get-selected-profile-fix.patch	\
   %D%/packages/patches/wicd-urwid-1.3.patch			\
@@ -1668,12 +1677,11 @@ dist_patch_DATA =						\
   %D%/packages/patches/xf86-video-mach64-glibc-2.20.patch	\
   %D%/packages/patches/xf86-video-savage-xorg-compat.patch 	\
   %D%/packages/patches/xf86-video-siliconmotion-fix-ftbfs.patch \
-  %D%/packages/patches/xf86-video-sis-xorg-compat.patch 	\
   %D%/packages/patches/xf86-video-tga-remove-mibstore.patch	\
   %D%/packages/patches/xf86-video-voodoo-pcitag.patch		\
   %D%/packages/patches/xfce4-panel-plugins.patch		\
   %D%/packages/patches/xfce4-settings-defaults.patch		\
-  %D%/packages/patches/xorg-server-CVE-2020-14347.patch		\
+  %D%/packages/patches/xmonad-dynamic-linking.patch		\
   %D%/packages/patches/xplanet-1.3.1-cxx11-eof.patch		\
   %D%/packages/patches/xplanet-1.3.1-libdisplay_DisplayOutput.cpp.patch	\
   %D%/packages/patches/xplanet-1.3.1-libimage_gif.c.patch	\

gnu/machine/ssh.scm

@@ -172,6 +172,8 @@ exist on the machine."
               (and (file-system-mount? fs)
                    (not (member (file-system-type fs)
                                 %pseudo-file-system-types))
+                   ;; Don't try to validate network file systems.
+                   (not (string-prefix? "nfs" (file-system-type fs)))
                    (not (memq 'bind-mount (file-system-flags fs)))))
             (operating-system-file-systems (machine-operating-system machine))))
 

gnu/packages/admin.scm

@@ -443,7 +443,7 @@ graphs and can export its output to different formats.")
 (define-public facter
   (package
     (name "facter")
-    (version "4.0.34")
+    (version "4.0.35")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -452,7 +452,7 @@ graphs and can export its output to different formats.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "19lcmmcnxkbirvh5bn5xa9a99z48zmb1b8845cp5r598y019gxqp"))))
+                "1f203g2hp96cp8w4x1myhqdj5j09z9s23kylwkrxr69fjhn0vhnb"))))
     (build-system ruby-build-system)
     (arguments
      `(#:phases
@@ -514,20 +514,24 @@ or via the @code{facter} Ruby library.")
 (define-public htop
   (package
     (name "htop")
-    (version "2.2.0")
+    (version "3.0.1")
-    (source (origin
+    (source
-              (method url-fetch)
+     (origin
-              (uri (string-append "http://hisham.hm/htop/releases/"
+       (method git-fetch)
-                                  version "/htop-" version ".tar.gz"))
+       (uri (git-reference
+             (url "https://github.com/htop-dev/htop")
+             (commit version)))
        (sha256
-               (base32
+        (base32 "0kjlphdvwwbj91kk91s4ksc954d3c2bznddzx2223jmb1bn9rcsa"))
-                "0mrwpb3cpn3ai7ar33m31yklj64c3pp576vh1naqff6f21pq5mnr"))))
+       (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (inputs
      `(("ncurses" ,ncurses)))
     (native-inputs
-     `(("python" ,python-wrapper)))     ;for scripts/MakeHeader.py
+     `(("autoconf" ,autoconf)
-    (home-page "https://hisham.hm/htop/")
+       ("automake" ,automake)
+       ("python" ,python-wrapper)))     ; for scripts/MakeHeader.py
+    (home-page "https://htop.dev")
     (synopsis "Interactive process viewer")
     (description
      "This is htop, an interactive process viewer.  It is a text-mode
@@ -1048,10 +1052,10 @@ connection alive.")
                ;; if finds all the programs it needs.
                (let* ((out       (assoc-ref outputs "out"))
                       (libexec   (string-append out "/libexec"))
-                      (coreutils (assoc-ref inputs "coreutils"))
+                      (coreutils (assoc-ref inputs "coreutils*"))
                       (inetutils (assoc-ref inputs "inetutils"))
                       (net-tools (assoc-ref inputs "net-tools"))
-                      (sed       (assoc-ref inputs "sed")))
+                      (sed       (assoc-ref inputs "sed*")))
                  (substitute* "client/scripts/linux"
                    (("/sbin/ip")
                     (string-append (assoc-ref inputs "iproute")
@@ -1091,12 +1095,8 @@ connection alive.")
                      (base32
                       "1j9a4r83a77mp8k1y8z524c9rzdqgd8rzwczd6zwmw86a00xiimg"))))
 
-                ;; When cross-compiling, we need the cross Coreutils and sed.
+                ("coreutils*" ,coreutils)
-                ;; Otherwise just use those from %FINAL-INPUTS.
+                ("sed*" ,sed)))
-                ,@(if (%current-target-system)
-                      `(("coreutils" ,coreutils)
-                        ("sed" ,sed))
-                      '())))
 
       (home-page "https://www.isc.org/products/DHCP/")
       (synopsis "Dynamic Host Configuration Protocol (DHCP) tools")
@@ -1375,10 +1375,11 @@ at once based on a Perl regular expression.")
                          "packdir=\"/var/log\""))
                       #t))
                   (add-before 'install 'tweak-rc-weekly
-                    (lambda _
+                    (lambda* (#:key inputs #:allow-other-keys)
                       (substitute* "rc/weekly"
                         (("/bin/kill")
-                         (which "kill"))
+                         (string-append (assoc-ref inputs "coreutils*")
+                                        "/bin/kill"))
                         (("syslogd\\.pid")
                          ;; The file is called 'syslog.pid' (no 'd').
                          "syslog.pid"))
@@ -1389,6 +1390,7 @@ at once based on a Perl regular expression.")
     (native-inputs `(("texinfo" ,texinfo)
                      ("automake" ,automake)
                      ("util-linux" ,util-linux))) ; for 'cal'
+    (inputs `(("coreutils*" ,coreutils)))
     (home-page "https://www.gnu.org/software/rottlog/")
     (synopsis "Log rotation and management")
     (description
@@ -2085,7 +2087,7 @@ track changes in important system configuration files.")
 (define-public libcap-ng
   (package
     (name "libcap-ng")
-    (version "0.7.11")
+    (version "0.8")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2093,7 +2095,7 @@ track changes in important system configuration files.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "1s8akhnnazk0b5c6z5i3x54rjb26p8pz2wdl1m21ml3231qmr0c5"))))
+                "08cy59iassiwbmfxa5v0kb374r80290vv32f5q1mnip11av26kgi"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -2137,24 +2139,19 @@ degradation and failure.")
 (define-public fdupes
   (package
     (name "fdupes")
-    (version "1.6.1")
+    (version "2.1.2")
     (source
      (origin
-       (method git-fetch)
+       (method url-fetch)
-       (uri (git-reference
+       (uri (string-append "https://github.com/adrianlopezroche/fdupes/"
-             (url "https://github.com/adrianlopezroche/fdupes")
+                           "releases/download/v" version "/"
-             (commit (string-append "v" version))))
+                           "fdupes-" version ".tar.gz"))
-       (file-name (git-file-name name version))
        (sha256
-        (base32 "19b6vqblddaw8ccw4sn0qsqzbswlhrz8ia6n4m3hymvcxn8skpz9"))))
+        (base32 "1g9p50xhi2sp0hqxml4w2k0kq9jv988q2yxm347z5349dlxvap6d"))))
     (build-system gnu-build-system)
-    (arguments
+    (inputs
-     '(#:phases (modify-phases %standard-phases
+     `(("ncurses" ,ncurses)
-                  (delete 'configure))
+       ("pcre2" ,pcre2)))
-       #:tests? #f ; no 'check' target
-       #:make-flags (list "CC=gcc"
-                          (string-append "PREFIX="
-                                         (assoc-ref %outputs "out")))))
     (home-page "https://github.com/adrianlopezroche/fdupes")
     (synopsis "Identify duplicate files")
     (description
@@ -3598,7 +3595,7 @@ Python loading in HPC environments.")
   (let ((real-name "inxi"))
     (package
       (name "inxi-minimal")
-      (version "3.1.05-2")
+      (version "3.1.06-1")
       (source
        (origin
          (method git-fetch)
@@ -3607,7 +3604,7 @@ Python loading in HPC environments.")
                (commit version)))
          (file-name (git-file-name real-name version))
          (sha256
-          (base32 "1a7nl2wk49yz5hcrph692xh5phv1mdg1m5cbvgv3ya12c6r32pa2"))))
+          (base32 "0h65n03q9kdsv0i1q5f88i11iv79ca7fqq97rdkzkmiqb4whhnm2"))))
       (build-system trivial-build-system)
       (inputs
        `(("bash" ,bash-minimal)

gnu/packages/algebra.scm

@@ -1118,17 +1118,17 @@ xtensor provides:
 (define-public gap
   (package
     (name "gap")
-    (version "4.10.2")
+    (version "4.11.0")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://www.gap-system.org/pub/gap/gap-"
+       (uri (string-append "https://files.gap-system.org/gap-"
                            (version-major+minor version)
                            "/tar.bz2/gap-"
                            version
                            ".tar.bz2"))
        (sha256
-        (base32 "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94"))
+        (base32 "00l6hvy4iggnlrib4vp805sxdm3j7n3hzpv5zs9hbiiavh80l1xz"))
        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
        (snippet
         '(begin
@@ -1140,41 +1140,46 @@ xtensor provides:
            ;; FIXME: This might be fixed in the next release, see
            ;; https://github.com/gap-system/gap/issues/3292
            (delete-file "tst/testinstall/dir.tst")
-           ;; Delete all packages except for a fixed list.
+           ;; Delete all packages except for a fixed list,
+           ;; given by their names up to version numbers.
            (with-directory-excursion "pkg"
              (for-each delete-file-recursively
-               (lset-difference string=? (scandir ".")
+               (lset-difference
+                 (lambda (all keep) (string-prefix? keep all))
+                 (scandir ".")
                  '("." ".."
                    ;; Necessary packages.
-                   "GAPDoc-1.6.2"
+                   "GAPDoc-"
-                   "primgrp-3.3.2"
+                   "primgrp-"
-                   "SmallGrp-1.3"    ; artistic2.0
+                   "SmallGrp-"   ; artistic2.0
                    "transgrp"    ; artistic2.0 for data,
                                  ; gpl2 or gpl3 for code
-                   ;; Recommanded package.
+                   ;; Recommended package.
-                   "io-4.5.4"        ; gpl3+
+                   "io-"         ; gpl3+
                    ;; Optional packages, searched for at start,
                    ;; and their depedencies.
-                   "alnuth-3.1.0"
+                   "alnuth-"
-                   "autpgrp-1.10"
+                   "autpgrp-"
-                   "crisp-1.4.4"     ; bsd-2
+                   "crisp-"      ; bsd-2
-                   "ctbllib"       ; gpl3+ according to doc/chap0.txt
+                   "ctbllib"     ; gpl3+, clarified in the next release;
-                   "FactInt-1.6.2"
+                                 ; see
+                                 ; http://www.math.rwth-aachen.de/~Thomas.Breuer/ctbllib/README.md
+                   "FactInt-"
                    "fga"
-                   "irredsol-1.4"    ; bsd-2
+                   "irredsol-"   ; bsd-2
-                   "laguna-3.9.2"
+                   "laguna-"
-                   "polenta-1.3.8"
+                   "polenta-"
-                   "polycyclic-2.14"
+                   "polycyclic-"
-                   "radiroot-2.8"
+                   "radiroot-"
-                   "resclasses-4.7.1"
+                   "resclasses-"
-                   "sophus-1.24"
+                   "sophus-"
-                   "tomlib-1.2.7"  ; gpl2+, clarified in the git repository
+                   "tomlib-"
-                                   ; and the next release
+                   "utils-"))))
-                   "utils-0.59"))))
            #t))))
     (build-system gnu-build-system)
     (inputs
      `(("gmp" ,gmp)
+       ("readline" ,readline)
        ("zlib" ,zlib)))
     (arguments
      `(#:modules ((ice-9 ftw)
@@ -1201,15 +1206,14 @@ xtensor provides:
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (bin (string-append out "/bin"))
-                    (lib (string-append out "/lib"))
                     (prog (string-append bin "/gap"))
                     (prog-real (string-append bin "/.gap-real"))
-                    (share (string-append out "/share/gap"))
+                    (share (string-append out "/share/gap")))
-                    (include (string-append out "/include/gap"))
-                    (include-hpc (string-append include "/hpc")))
                ;; Install only the gap binary; the gac compiler is left
                ;; for maybe later. "Wrap" it in a shell script that calls
                ;; the binary with the correct parameter.
+               ;; The make target install-bin is supposed to do that, but
+               ;; is not currently working.
                (mkdir-p bin)
                (copy-file "gap" prog-real)
                (call-with-output-file prog
@@ -1220,52 +1224,18 @@ xtensor provides:
                            prog-real
                            share)))
                (chmod prog #o755)
-               ;; Install the headers, which are needed by Sage. The
+               ;; Install the headers and library, which are needed by Sage.
-               ;; Makefile target "install-headers" was available in
+               (invoke "make" "install-headers")
-               ;; gap-4.10.0, but has been commented out in gap-4.10.1.
+               (invoke "make" "install-libgap")
-               (mkdir-p include-hpc)
-               (install-file "gen/config.h" include)
-               (let ((file-name-predicate-without-stat
-                       (lambda (regex)
-                         (cut (file-name-predicate regex) <> #f))))
-                 (with-directory-excursion "src"
-                   (for-each
-                     (cut install-file <> include)
-                     (scandir "."
-                              (file-name-predicate-without-stat ".*\\.h$"))))
-                 (with-directory-excursion "src/hpc"
-                   (for-each
-                     (cut install-file <> include-hpc)
-                     (scandir "."
-                              (file-name-predicate-without-stat ".*\\.h$")))))
-               ;; Install the library, which is needed by Sage. The
-               ;; Makefile target "install-libgap" was available in
-               ;; gap-4.10.0, but has been commented out in gap-4.10.1.
-               ;; Compared to the Makefile, which used libtool, the
-               ;; following approach of copying files and making symlinks
-               ;; is rather pedestrian. There is hope that some later
-               ;; version of gap reinstates and completes the install
-               ;; targets.
-               (invoke "make" "libgap.la")
-               (install-file "libgap.la" lib)
-               (install-file ".libs/libgap.so.0.0.0" lib)
-               (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so")) 
-               (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0"))
-               ;; Install a certain number of files and directories to
-               ;; SHARE, where the wrapped shell script expects them.
                ;; Remove information on the build directory from sysinfo.gap.
                (substitute* "sysinfo.gap"
                  (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
                  (("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"")
                  (("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\""))
-               (install-file "sysinfo.gap" share)
+               (invoke "make" "install-gaproot")
-               (copy-recursively "grp" (string-append share "/grp"))
+               ;; Copy the directory of compiled packages; the make target
-               (copy-recursively "pkg" (string-append share "/pkg"))
+               ;; install-pkg is currently empty.
-               ;; The following is not the C library libgap.so, but a
+               (copy-recursively "pkg" (string-append share "/pkg")))
-               ;; library of GAP code.
-               (copy-recursively "lib" (string-append share "/lib"))
-               ;; The gap binary looks for documentation inside SHARE.
-               (copy-recursively "doc" (string-append share "/doc")))
              #t)))))
     (home-page "https://www.gap-system.org/")
     (synopsis

gnu/packages/android.scm

@@ -7,9 +7,10 @@
 ;;; Copyright © 2017 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2019, 2020 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2020 Sergey Trofimov <sarg@sarg.org.ru>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,8 +31,9 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
-  #:use-module (guix build-system gnu)
   #:use-module (guix build-system android-ndk)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system go)
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module ((guix licenses) #:prefix license:)
@@ -41,6 +43,7 @@
   #:use-module (gnu packages docker)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gnupg)
+  #:use-module (gnu packages golang)
   #:use-module (gnu packages java)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages pcre)
@@ -916,14 +919,14 @@ useful for reverse engineering, analysis of Android applications and more.")
 (define-public fdroidserver
   (package
     (name "fdroidserver")
-    (version "1.1.1")
+    (version "1.1.9")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "fdroidserver" version))
         (sha256
          (base32
-          "0fp7q8faicx6i6wxm717qqaham3jpilb23mvynpz6v73z7hm6wcg"))))
+          "0m07f791z45w7r2dzx4yb6s54b3c3wykm3w9hn25p2jcyax082a2"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -931,14 +934,20 @@ useful for reverse engineering, analysis of Android applications and more.")
          (add-after 'unpack 'fix-versioning
            (lambda _
              (substitute* "setup.py"
-               (("0.2.1") ,(package-version python-pyasn1-modules)))
+               (("0.2.1") ,(package-version python-pyasn1-modules))
+               ;; The dependency on docker has been removed upstream by
+               ;; a fairly large patch:
+               ;; https://gitlab.com/fdroid/fdroidserver/-/commit/89614851250c79a05db84070feca6dea033af334
+               ;; that is not in a release yet. It appears we can compile with
+               ;; a newer version.
+               (("docker-py >= 1.9, < 2.0") "docker >= 1.9"))
              #t)))))
     (propagated-inputs
      `(("python-androguard" ,python-androguard)
        ("python-apache-libcloud" ,python-apache-libcloud)
        ("python-clint" ,python-clint)
        ("python-defusedxml" ,python-defusedxml)
-       ("python-docker-py" ,python-docker-py)
+       ("python-docker" ,python-docker)
        ("python-gitpython" ,python-gitpython)
        ("python-mwclient" ,python-mwclient)
        ("python-paramiko" ,python-paramiko)
@@ -966,6 +975,36 @@ publishing, or to assist in creating, testing and submitting metadata to the
 main repository.")
     (license license:agpl3+)))
 
+(define-public fdroidcl
+  (package
+    (name "fdroidcl")
+    (version "0.5.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/mvdan/fdroidcl")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32 "1rxcdyy2j34z0ql9d62w7ivsch9xihjnpb1z9kgy9q46vl8zhhy0"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "mvdan.cc/fdroidcl"
+       #:tests? #f  ; TODO: Inputs missing.
+       #:install-source? #f))
+    (inputs
+     `(("go-github-com-kr-pretty" ,go-github-com-kr-pretty)))
+    ;(native-inputs
+    ; `(("go-github-com-rogpeppe-go-internal-testscript"
+    ;    ,go-github-com-rogpeppe-go-internal-testscript)))
+    (synopsis "F-Droid desktop client")
+    (description
+     "While the Android client integrates with the system with regular update
+checks and notifications, this is a simple command line client that talks to
+connected devices via ADB.")
+    (home-page "https://github.com/mvdan/fdroidcl")
+    (license license:bsd-3)))
+
 (define-public enjarify
   (package
     (name "enjarify")

gnu/packages/assembly.scm

@@ -151,14 +151,14 @@ to the clients.")
 (define-public fasm
   (package
     (name "fasm")
-    (version "1.73.24")
+    (version "1.73.25")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://flatassembler.net/fasm-"
                            version ".tgz"))
        (sha256
-        (base32 "142vxhs8mh8isvlzq7ir0asmqda410phzxmk9gk9b43dldskkj7k"))))
+        (base32 "0k3h61mfwslyb34kf4dnapfwl8jxlmrp4dv666wc057hkj047knn"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no tests exist

gnu/packages/astronomy.scm

@@ -128,7 +128,7 @@ header.")
 (define-public gnuastro
   (package
     (name "gnuastro")
-    (version "0.12")
+    (version "0.13")
     (source
      (origin
        (method url-fetch)
@@ -136,7 +136,7 @@ header.")
                            version ".tar.lz"))
        (sha256
         (base32
-         "0ypk1c72q778cixfa52vjxzbd5m4qc6hfjgnipy16sfa7mnspmyf"))))
+         "07di6zx2irc5q0zyymx2951ydzxdfjmzd3az5qnk67ncf3hknvj5"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--disable-static")))

gnu/packages/audio.scm

@@ -108,6 +108,7 @@
   #:use-module (gnu packages valgrind)
   #:use-module (gnu packages video)
   #:use-module (gnu packages vim) ;xxd
+  #:use-module (gnu packages web)
   #:use-module (gnu packages webkit)
   #:use-module (gnu packages wxwidgets)
   #:use-module (gnu packages xiph)
@@ -298,7 +299,7 @@ Linux kernel.")
 (define-public libopenmpt
   (package
     (name "libopenmpt")
-    (version "0.5.1")
+    (version "0.5.2")
     (source
      (origin
        (method url-fetch)
@@ -306,8 +307,20 @@ Linux kernel.")
         (string-append "https://download.openmpt.org/archive/libopenmpt/src/"
                        "libopenmpt-" version "+release.autotools.tar.gz"))
        (sha256
-        (base32 "1vpalfsrkbx4vyrh1qy564lr91jwdxlbjivv5gzf8zcywxasf0xa"))))
+        (base32 "1cwpc4j90dpxa2siia68rg9qwwm2xk6bhxnslfjj364507jy6s4l"))))
     (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "--docdir=" (assoc-ref %outputs "out")
+                            "/share/doc/" ,name "-" ,version))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'delete-static-libraries
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (lib (string-append out "/lib")))
+               (for-each delete-file (find-files lib "\\.a$"))
+               #t))))))
     (native-inputs
      `(("doxygen" ,doxygen)
        ("perl" ,perl)
@@ -1810,7 +1823,7 @@ patches that can be used with softsynths such as Timidity and WildMidi.")
 (define-public guitarix
   (package
     (name "guitarix")
-    (version "0.38.1")
+    (version "0.41.0")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -1818,28 +1831,14 @@ patches that can be used with softsynths such as Timidity and WildMidi.")
                    version ".tar.xz"))
              (sha256
               (base32
-               "0bw7xnrx062nwb1bfj9x660h7069ncmz77szcs8icpqxrvhs7z80"))))
+               "0qsfbyrrpb3bbdyq68k28mjql7kglxh8nqcw9jvja28x6x9ik5a0"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f ; no "check" target
-       #:python ,python-2
        #:configure-flags
        (list
         ;; Add the output lib directory to the RUNPATH.
-        (string-append "--ldflags=-Wl,-rpath=" %output "/lib"))
+        (string-append "--ldflags=-Wl,-rpath=" %output "/lib"))))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-boost-includes
-           (lambda _
-             (substitute* "src/headers/gx_internal_plugins.h"
-               (("namespace gx_jack" m)
-                (string-append "#include <boost/noncopyable.hpp>\n" m)))
-             (substitute* '("src/headers/gx_system.h"
-                            "src/headers/gx_parameter.h"
-                            "src/headers/gx_json.h")
-               (("namespace gx_system" m)
-                (string-append "#include <boost/noncopyable.hpp>\n" m)))
-             #t)))))
     (inputs
      `(("libsndfile" ,libsndfile)
        ("boost" ,boost)
@@ -1850,8 +1849,8 @@ patches that can be used with softsynths such as Timidity and WildMidi.")
        ("lilv" ,lilv)
        ("ladspa" ,ladspa)
        ("jack" ,jack-1)
-       ("gtkmm" ,gtkmm-2)
+       ("gtkmm" ,gtkmm)
-       ("gtk+" ,gtk+-2)
+       ("gtk+" ,gtk+)
        ("fftwf" ,fftwf)
        ("lrdf" ,lrdf)
        ("zita-resampler" ,zita-resampler)
@@ -1861,7 +1860,8 @@ patches that can be used with softsynths such as Timidity and WildMidi.")
        ("faust" ,faust)
        ("intltool" ,intltool)
        ("gettext" ,gettext-minimal)
-       ("pkg-config" ,pkg-config)))
+       ("pkg-config" ,pkg-config)
+       ("sassc" ,sassc)))
     (native-search-paths
      (list (search-path-specification
             (variable "LV2_PATH")
@@ -4013,14 +4013,14 @@ on the ALSA software PCM plugin.")
 (define-public snd
   (package
     (name "snd")
-    (version "20.6")
+    (version "20.7")
     (source (origin
               (method url-fetch)
               (uri (string-append "ftp://ccrma-ftp.stanford.edu/pub/Lisp/"
                                   "snd-" version ".tar.gz"))
               (sha256
                (base32
-                "1h4dsq5xcvwjbnayhn719cln0lg199w3xm59sl9d2jz8bq78gqgj"))))
+                "1kd422krz8ln4m8g3p14wfplcq8lgpzly9297rpbvyc94dc6sdwj"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      `(#:tests? #f                      ; no tests
@@ -4467,7 +4467,7 @@ supports both of ID3v1/v2 and APEv2 tags.")
 (define-public redkite
   (package
     (name "redkite")
-    (version "0.8.1")
+    (version "1.0.3")
     (source
      (origin
        (method git-fetch)
@@ -4476,7 +4476,7 @@ supports both of ID3v1/v2 and APEv2 tags.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "17kv2jc4jvn3sdicz3sf8dnf25wbvv7ijzkr0mm0sbrrjz6vrwz0"))))
+        (base32 "1m2db7c791fi33snkjwnvlxapmf879g5r8azlkx7sr6vp2s0jq2k"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f))                    ;no tests included
@@ -4610,7 +4610,7 @@ in the package.")
 (define-public libaudec
   (package
     (name "libaudec")
-    (version "0.2.2")
+    (version "0.2.3")
     (source
       (origin
         (method git-fetch)
@@ -4620,14 +4620,14 @@ in the package.")
         (file-name (git-file-name name version))
         (sha256
           (base32
-            "04mpmfmqc43asw0m3zxhb6jj4qms7x4jw7mx4xb1d3lh16xllniz"))))
+            "04hw61db8wscj28qjyiaiafx8xl87njgmvqszxyhs4gmg8xgjip7"))))
    (build-system meson-build-system)
    (arguments
-    `(#:configure-flags `("-Denable_tests=true -Denable_ffmpeg=true")))
+     ;; Compile tests.
+    `(#:configure-flags `("-Dtests=true")))
    (inputs
     `(("libsamplerate" ,libsamplerate)
-      ("libsndfile" ,libsndfile)
+      ("libsndfile" ,libsndfile)))
-      ("ffmpeg" ,ffmpeg)))
    (native-inputs
      `(("pkg-config", pkg-config)))
    (synopsis "Library for reading and resampling audio files")
@@ -4640,7 +4640,7 @@ libsamplerate for reading and resampling audio files, based on Robin Gareus'
 (define-public lv2lint
   (package
     (name "lv2lint")
-    (version "0.4.0")
+    (version "0.8.0")
     (source
       (origin
         (method git-fetch)
@@ -4650,7 +4650,7 @@ libsamplerate for reading and resampling audio files, based on Robin Gareus'
         (file-name (git-file-name name version))
         (sha256
           (base32
-            "1pspwqpzl2dw1hd9ra9yr53arqbbqjn7d7j0f7p9g3iqa76vblpi"))))
+            "1jrka0hsn4n1clri7zfkcl3c2vi52144lkpjm81l51ff8rqy8ks1"))))
     (build-system meson-build-system)
     (arguments
      `(#:configure-flags
@@ -4778,6 +4778,37 @@ edited, converted, compressed and saved.")
        ,@(package-inputs ztoolkit)))
     (synopsis "ZToolkit with SVG support")))
 
+(define-public lsp-dsp-lib
+  (package
+    (name "lsp-dsp-lib")
+    (version "0.5.8")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://github.com/sadko4u/lsp-dsp-lib/"
+                            "releases/download/lsp-dsp-lib-" version
+                            "/lsp-dsp-lib-" version "-src.tar.gz"))
+        (sha256
+         (base32
+          "07w3d2i0z0xmvi1ngcgs7lc5a0da8jvf7rv4dnjk01md43b7fkh1"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; no tests
+       #:make-flags
+       (list (string-append "CC=" ,(cc-for-target)))
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             (invoke "make" "config"
+                     (string-append "PREFIX=" (assoc-ref outputs "out"))))))))
+    (home-page "https://github.com/sadko4u/lsp-dsp-lib")
+    (synopsis "Digital signal processing library")
+    (description "The LSP DSP library provides a set of functions that perform
+SIMD-optimized computing on several hardware architectures.  All functions
+currently operate on IEEE-754 single-precision floating-point numbers.")
+    (license license:lgpl3+)))
+
 (define-public codec2
   (package
     (name "codec2")

gnu/packages/aux-files/linux-libre/4.14-arm.conf

@@ -305,7 +305,9 @@ CONFIG_MODULE_FORCE_UNLOAD=y
 CONFIG_MODVERSIONS=y
 # CONFIG_MODULE_SRCVERSION_ALL is not set
 # CONFIG_MODULE_SIG is not set
-# CONFIG_MODULE_COMPRESS is not set
+CONFIG_MODULE_COMPRESS=y
+CONFIG_MODULE_COMPRESS_GZIP=y
+# CONFIG_MODULE_COMPRESS_XZ is not set
 # CONFIG_TRIM_UNUSED_KSYMS is not set
 CONFIG_MODULES_TREE_LOOKUP=y
 CONFIG_BLOCK=y

gnu/packages/aux-files/linux-libre/4.14-i686.conf

@@ -350,7 +350,9 @@ CONFIG_MODULE_UNLOAD=y
 CONFIG_MODVERSIONS=y
 CONFIG_MODULE_SRCVERSION_ALL=y
 # CONFIG_MODULE_SIG is not set
-# CONFIG_MODULE_COMPRESS is not set
+CONFIG_MODULE_COMPRESS=y
+CONFIG_MODULE_COMPRESS_GZIP=y
+# CONFIG_MODULE_COMPRESS_XZ is not set
 CONFIG_MODULES_TREE_LOOKUP=y
 CONFIG_BLOCK=y
 CONFIG_LBDAF=y

gnu/packages/aux-files/linux-libre/4.14-x86_64.conf

@@ -370,7 +370,9 @@ CONFIG_MODULE_UNLOAD=y
 CONFIG_MODVERSIONS=y
 CONFIG_MODULE_SRCVERSION_ALL=y
 # CONFIG_MODULE_SIG is not set
-# CONFIG_MODULE_COMPRESS is not set
+CONFIG_MODULE_COMPRESS=y
+CONFIG_MODULE_COMPRESS_GZIP=y
+# CONFIG_MODULE_COMPRESS_XZ is not set
 CONFIG_MODULES_TREE_LOOKUP=y
 CONFIG_BLOCK=y
 CONFIG_BLK_SCSI_REQUEST=y

gnu/packages/aux-files/linux-libre/4.19-arm.conf

@@ -876,7 +876,9 @@ CONFIG_MODULE_FORCE_UNLOAD=y
 CONFIG_MODVERSIONS=y
 # CONFIG_MODULE_SRCVERSION_ALL is not set
 # CONFIG_MODULE_SIG is not set
-# CONFIG_MODULE_COMPRESS is not set
+CONFIG_MODULE_COMPRESS=y
+CONFIG_MODULE_COMPRESS_GZIP=y
+# CONFIG_MODULE_COMPRESS_XZ is not set
 # CONFIG_TRIM_UNUSED_KSYMS is not set
 CONFIG_MODULES_TREE_LOOKUP=y
 CONFIG_BLOCK=y

gnu/packages/aux-files/linux-libre/4.19-arm64.conf

@@ -750,7 +750,9 @@ CONFIG_MODULE_FORCE_UNLOAD=y
 CONFIG_MODVERSIONS=y
 # CONFIG_MODULE_SRCVERSION_ALL is not set
 # CONFIG_MODULE_SIG is not set
-# CONFIG_MODULE_COMPRESS is not set
+CONFIG_MODULE_COMPRESS=y
+CONFIG_MODULE_COMPRESS_GZIP=y
+# CONFIG_MODULE_COMPRESS_XZ is not set
 # CONFIG_TRIM_UNUSED_KSYMS is not set
 CONFIG_MODULES_TREE_LOOKUP=y
 CONFIG_BLOCK=y

gnu/packages/aux-files/linux-libre/4.19-i686.conf

@@ -881,7 +881,9 @@ CONFIG_MODULE_UNLOAD=y
 CONFIG_MODVERSIONS=y
 CONFIG_MODULE_SRCVERSION_ALL=y
 # CONFIG_MODULE_SIG is not set
-# CONFIG_MODULE_COMPRESS is not set
+CONFIG_MODULE_COMPRESS=y
+CONFIG_MODULE_COMPRESS_GZIP=y
+# CONFIG_MODULE_COMPRESS_XZ is not set
 CONFIG_MODULES_TREE_LOOKUP=y
 CONFIG_BLOCK=y
 CONFIG_LBDAF=y

gnu/packages/aux-files/linux-libre/4.19-x86_64.conf

@@ -872,7 +872,9 @@ CONFIG_MODULE_UNLOAD=y
 CONFIG_MODVERSIONS=y
 CONFIG_MODULE_SRCVERSION_ALL=y
 # CONFIG_MODULE_SIG is not set
-# CONFIG_MODULE_COMPRESS is not set
+CONFIG_MODULE_COMPRESS=y
+CONFIG_MODULE_COMPRESS_GZIP=y
+# CONFIG_MODULE_COMPRESS_XZ is not set
 CONFIG_MODULES_TREE_LOOKUP=y
 CONFIG_BLOCK=y
 CONFIG_BLK_SCSI_REQUEST=y

gnu/packages/aux-files/linux-libre/4.4-i686.conf

@@ -302,7 +302,9 @@ CONFIG_MODULE_UNLOAD=y
 CONFIG_MODVERSIONS=y
 CONFIG_MODULE_SRCVERSION_ALL=y
 # CONFIG_MODULE_SIG is not set
-# CONFIG_MODULE_COMPRESS is not set
+CONFIG_MODULE_COMPRESS=y
+CONFIG_MODULE_COMPRESS_GZIP=y
+# CONFIG_MODULE_COMPRESS_XZ is not set
 CONFIG_MODULES_TREE_LOOKUP=y
 CONFIG_BLOCK=y
 CONFIG_LBDAF=y

gnu/packages/aux-files/linux-libre/4.4-x86_64.conf

@@ -315,7 +315,9 @@ CONFIG_MODULE_UNLOAD=y
 CONFIG_MODVERSIONS=y
 CONFIG_MODULE_SRCVERSION_ALL=y
 # CONFIG_MODULE_SIG is not set
-# CONFIG_MODULE_COMPRESS is not set
+CONFIG_MODULE_COMPRESS=y
+CONFIG_MODULE_COMPRESS_GZIP=y
+# CONFIG_MODULE_COMPRESS_XZ is not set
 CONFIG_MODULES_TREE_LOOKUP=y
 CONFIG_BLOCK=y
 CONFIG_BLK_DEV_BSG=y

gnu/packages/aux-files/linux-libre/4.9-i686.conf

@@ -322,7 +322,9 @@ CONFIG_MODULE_UNLOAD=y
 CONFIG_MODVERSIONS=y
 CONFIG_MODULE_SRCVERSION_ALL=y
 # CONFIG_MODULE_SIG is not set
-# CONFIG_MODULE_COMPRESS is not set
+CONFIG_MODULE_COMPRESS=y
+CONFIG_MODULE_COMPRESS_GZIP=y
+# CONFIG_MODULE_COMPRESS_XZ is not set
 CONFIG_MODULES_TREE_LOOKUP=y
 CONFIG_BLOCK=y
 CONFIG_LBDAF=y

gnu/packages/aux-files/linux-libre/4.9-x86_64.conf

@@ -339,7 +339,9 @@ CONFIG_MODULE_UNLOAD=y
 CONFIG_MODVERSIONS=y
 CONFIG_MODULE_SRCVERSION_ALL=y
 # CONFIG_MODULE_SIG is not set
-# CONFIG_MODULE_COMPRESS is not set
+CONFIG_MODULE_COMPRESS=y
+CONFIG_MODULE_COMPRESS_GZIP=y
+# CONFIG_MODULE_COMPRESS_XZ is not set
 CONFIG_MODULES_TREE_LOOKUP=y
 CONFIG_BLOCK=y
 CONFIG_BLK_DEV_BSG=y

gnu/packages/aux-files/linux-libre/5.4-arm.conf

@@ -880,7 +880,9 @@ CONFIG_MODULE_FORCE_UNLOAD=y
 CONFIG_MODVERSIONS=y
 # CONFIG_MODULE_SRCVERSION_ALL is not set
 # CONFIG_MODULE_SIG is not set
-# CONFIG_MODULE_COMPRESS is not set
+CONFIG_MODULE_COMPRESS=y
+CONFIG_MODULE_COMPRESS_GZIP=y
+# CONFIG_MODULE_COMPRESS_XZ is not set
 # CONFIG_MODULE_ALLOW_MISSING_NAMESPACE_IMPORTS is not set
 # CONFIG_UNUSED_SYMBOLS is not set
 # CONFIG_TRIM_UNUSED_KSYMS is not set

gnu/packages/aux-files/linux-libre/5.4-arm64.conf

@@ -781,7 +781,9 @@ CONFIG_MODVERSIONS=y
 CONFIG_ASM_MODVERSIONS=y
 # CONFIG_MODULE_SRCVERSION_ALL is not set
 # CONFIG_MODULE_SIG is not set
-# CONFIG_MODULE_COMPRESS is not set
+CONFIG_MODULE_COMPRESS=y
+CONFIG_MODULE_COMPRESS_GZIP=y
+# CONFIG_MODULE_COMPRESS_XZ is not set
 # CONFIG_MODULE_ALLOW_MISSING_NAMESPACE_IMPORTS is not set
 # CONFIG_UNUSED_SYMBOLS is not set
 # CONFIG_TRIM_UNUSED_KSYMS is not set

gnu/packages/aux-files/linux-libre/5.4-i686.conf

@@ -850,7 +850,9 @@ CONFIG_MODVERSIONS=y
 CONFIG_ASM_MODVERSIONS=y
 CONFIG_MODULE_SRCVERSION_ALL=y
 # CONFIG_MODULE_SIG is not set
-# CONFIG_MODULE_COMPRESS is not set
+CONFIG_MODULE_COMPRESS=y
+CONFIG_MODULE_COMPRESS_GZIP=y
+# CONFIG_MODULE_COMPRESS_XZ is not set
 # CONFIG_MODULE_ALLOW_MISSING_NAMESPACE_IMPORTS is not set
 CONFIG_UNUSED_SYMBOLS=y
 CONFIG_MODULES_TREE_LOOKUP=y

gnu/packages/aux-files/linux-libre/5.4-x86_64.conf

@@ -849,7 +849,9 @@ CONFIG_MODVERSIONS=y
 CONFIG_ASM_MODVERSIONS=y
 CONFIG_MODULE_SRCVERSION_ALL=y
 # CONFIG_MODULE_SIG is not set
-# CONFIG_MODULE_COMPRESS is not set
+CONFIG_MODULE_COMPRESS=y
+CONFIG_MODULE_COMPRESS_GZIP=y
+# CONFIG_MODULE_COMPRESS_XZ is not set
 # CONFIG_MODULE_ALLOW_MISSING_NAMESPACE_IMPORTS is not set
 CONFIG_UNUSED_SYMBOLS=y
 CONFIG_MODULES_TREE_LOOKUP=y

gnu/packages/aux-files/run-in-namespace.c

@@ -405,6 +405,23 @@ relocated_search_path (const char *path[], const char *store)
   return new_path;
 }
 
+/* Concatenate PATH1 and PATH2 with a colon in between.  The result is
+   potentially malloc'd.  */
+static char *
+concat_paths (const char *path1, const char *path2)
+{
+  if (path1[0] == '\0')
+    return (char *) path2;
+  else
+    {
+      char *result = xmalloc (strlen (path1) + strlen (path2) + 2);
+      strcpy (result, path1);
+      strcat (result, ":");
+      strcat (result, path2);
+      return result;
+    }
+}
+
 /* Execute the wrapped program by invoking the loader (ld.so) directly,
    passing it the audit module and preloading libfakechroot.so.  */
 static void
@@ -421,9 +438,12 @@ exec_with_loader (const char *store, int argc, char *argv[])
   loader_argv[2] = concat (store,
 			   LOADER_AUDIT_MODULE + sizeof original_store);
 
-  /* The audit module depends on libc.so and libgcc_s.so.  */
+  /* The audit module depends on libc.so and libgcc_s.so so honor
+     AUDIT_LIBRARY_PATH.  Additionally, honor $LD_LIBRARY_PATH if set.  */
   loader_argv[3] = "--library-path";
-  loader_argv[4] = relocated_search_path (audit_library_path, store);
+  loader_argv[4] =
+    concat_paths (getenv ("LD_LIBRARY_PATH") ?: "",
+		  relocated_search_path (audit_library_path, store));
 
   loader_argv[5] = "--preload";
   loader_argv[6] = concat (store,

gnu/packages/backup.scm

@@ -1072,7 +1072,7 @@ interractive mode.")
 (define-public burp
   (package
     (name "burp")
-    (version "2.3.32")
+    (version "2.3.34")
     (source
      (origin
        (method git-fetch)
@@ -1080,7 +1080,7 @@ interractive mode.")
              (url "https://github.com/grke/burp")
              (commit version)))
        (sha256
-        (base32 "0cxxf9ni34c9662ffmr2qc8xmh4g9pmg3swqvhn49mqgr5ra6k2g"))
+        (base32 "0ri62xshcjrk5vgyx8s11vsllab132mk1pcy4xxl9kzijdsjhdpy"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments

gnu/packages/bioconductor.scm

@@ -3,6 +3,7 @@
 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1762,6 +1763,7 @@ expressed genes in DNA microarray experiments.")
 fitting of some classes of graphical Markov models.")
     (license license:gpl2+)))
 
+;; This is a CRAN package, but it depends on a Bioconductor package.
 (define-public r-codedepends
   (package
     (name "r-codedepends")
@@ -1793,14 +1795,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.22.2")
+    (version "3.22.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "199mlg0gwjy39afyk0ah6lzcm759bzxla4hgcajj0ay9jiibjqpa"))))
+         "0q3f55hh0a2hl96272js6gagmgps9cxs8s13pf6fii64rzaz5m7y"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3452,14 +3454,14 @@ surface of a flowcell.")
 (define-public r-gkmsvm
   (package
     (name "r-gkmsvm")
-    (version "0.80.0")
+    (version "0.81.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gkmSVM" version))
        (sha256
         (base32
-         "0ljcga246ad0ql8x3drvrdsyp0f20mgp3p6lnl79xb76qgfdnm0p"))))
+         "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
     (properties `((upstream-name . "gkmSVM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4360,14 +4362,14 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.12.3")
+    (version "1.12.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "12710c4024pndwwqiiqr6dhrd360z26fc8r3fxhs739gyd0ddk9r"))))
+         "1gs9862hhh4gr1akij6ykhcj29s9dzg1vnj87hqrm19dfgl43qbh"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6334,14 +6336,14 @@ self-organizing map clustering and minimal spanning trees.")
 (define-public r-mixomics
   (package
     (name "r-mixomics")
-    (version "6.12.1")
+    (version "6.12.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mixOmics" version))
        (sha256
         (base32
-         "13kq9l5xwhwp30y5gfqfh5f11n63vn8rk195mb2y2mww4cwi6lv4"))))
+         "1nkqlvm9j1f4vfj3f3kyxqgan38rpa9imimvl9pwivvsfl647vvc"))))
     (properties `((upstream-name . "mixOmics")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6460,14 +6462,14 @@ genes in the gene-set that are ranked above the leading edge).")
 (define-public r-cicero
   (package
     (name "r-cicero")
-    (version "1.6.1")
+    (version "1.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cicero" version))
        (sha256
         (base32
-         "0nf9yqg5krj26n4n82iyx3rsr84d46b17i9zfk35sh12l4xssbii"))))
+         "042ba6yfa7fksij2v7cwnp2sca3vmz7izn6fsxx9xswnncrkgcqh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -7157,14 +7159,14 @@ data.")
 (define-public r-activedriverwgs
   (package
     (name "r-activedriverwgs")
-    (version "1.0.1")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ActiveDriverWGS" version))
        (sha256
         (base32
-         "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1"))))
+         "0l6h0f54zjvcx19ngq3kp01dypsjqf28vssjm8yzccmpyacfypag"))))
     (properties
      `((upstream-name . "ActiveDriverWGS")))
     (build-system r-build-system)
@@ -7175,8 +7177,9 @@ data.")
        ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicranges" ,r-genomicranges)
        ("r-iranges" ,r-iranges)
-       ("r-plyr" ,r-plyr)
        ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
     (synopsis "Driver discovery tool for cancer whole genomes")
     (description
@@ -8153,3 +8156,89 @@ user's input and automatically retrieving results from GREAT web server.")
 simulation to eliminate overestimation of @code{K} and can reject the null
 hypothesis @code{K=1}.")
     (license license:agpl3+)))
+
+(define-public r-icens
+  (package
+    (name "r-icens")
+    (version "1.60.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Icens" version))
+       (sha256
+        (base32
+         "0fh7wgkrw20f61p06i87nccnbig9wv4m0jcg7cx1rw7g2ndnabgp"))))
+    (properties `((upstream-name . "Icens")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-survival" ,r-survival)))
+    (home-page "https://bioconductor.org/packages/Icens")
+    (synopsis "NPMLE for censored and truncated data")
+    (description
+     "This package provides many functions for computing the
+@dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
+truncated data.")
+    (license license:artistic2.0)))
+
+;; This is a CRAN package but it depends on r-icens, which is published on
+;; Bioconductor.
+(define-public r-interval
+  (package
+    (name "r-interval")
+    (version "1.1-0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "interval" version))
+       (sha256
+        (base32
+         "1lln9jkli28i4wivwzqrsxvv2n15560f7msjy5gssrm45vxrxms8"))))
+    (properties `((upstream-name . "interval")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-icens" ,r-icens)
+       ("r-mlecens" ,r-mlecens)
+       ("r-perm" ,r-perm)
+       ("r-survival" ,r-survival)))
+    (home-page "https://cran.r-project.org/web/packages/interval/")
+    (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
+    (description
+     "This package provides functions to fit nonparametric survival curves,
+plot them, and perform logrank or Wilcoxon type tests.")
+    (license license:gpl2+)))
+
+;; This is a CRAN package, but it depends on r-interval, which depends on a
+;; Bioconductor package.
+(define-public r-fhtest
+  (package
+    (name "r-fhtest")
+    (version "1.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "FHtest" version))
+       (sha256
+        (base32
+         "1wsn0j9ydpp9nfswiqg21p09kgkvaq8fh0y0h8syqgizah7i8vs2"))))
+    (properties `((upstream-name . "FHtest")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-interval" ,r-interval)
+       ("r-kmsurv" ,r-kmsurv)
+       ("r-mass" ,r-mass)
+       ("r-perm" ,r-perm)
+       ("r-survival" ,r-survival)))
+    (home-page "https://cran.r-project.org/web/packages/FHtest/")
+    (synopsis "Tests for survival data based on the Fleming-Harrington class")
+    (description
+     "This package provides functions to compare two or more survival curves
+with:
+
+@itemize
+@item The Fleming-Harrington test for right-censored data based on
+  permutations and on counting processes.
+@item An extension of the Fleming-Harrington test for interval-censored data
+  based on a permutation distribution and on a score vector distribution.
+@end itemize
+")
+    (license license:gpl2+)))

gnu/packages/bioinformatics.scm

@@ -2620,7 +2620,7 @@ with Python.")
 (define-public delly
   (package
     (name "delly")
-    (version "0.7.9")
+    (version "0.8.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2628,7 +2628,7 @@ with Python.")
                     (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z"))
+               (base32 "1ibnplgfzj96w8glkx17v7sld3pm402fr5ybmf3h0rlcryabxrqy"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -2652,9 +2652,9 @@ with Python.")
                #t))))))
     (inputs
      `(("boost" ,boost)
+       ("bzip2" ,bzip2)
        ("htslib" ,htslib)
-       ("zlib" ,zlib)
+       ("zlib" ,zlib)))
-       ("bzip2" ,bzip2)))
     (home-page "https://github.com/dellytools/delly")
     (synopsis "Integrated structural variant prediction method")
     (description "Delly is an integrated structural variant prediction method
@@ -6357,14 +6357,14 @@ bioinformatics file formats, sequence alignment, and more.")
 (define-public seqmagick
   (package
     (name "seqmagick")
-    (version "0.7.0")
+    (version "0.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "seqmagick" version))
        (sha256
         (base32
-         "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
+         "0pf98da7i59q47gwrbx0wjk6xlvbybiwphw80w7h4ydjj0579a2b"))))
     (build-system python-build-system)
     (inputs
      `(("python-biopython" ,python-biopython)))
@@ -8510,57 +8510,6 @@ Stephens (1990).")
 throughput genetic sequencing data sets using regression methods.")
     (license license:artistic2.0)))
 
-(define-public r-qtl
- (package
-  (name "r-qtl")
-  (version "1.46-2")
-  (source
-   (origin
-    (method url-fetch)
-    (uri (string-append "mirror://cran/src/contrib/qtl_"
-                        version ".tar.gz"))
-    (sha256
-     (base32
-      "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
-  (build-system r-build-system)
-  (home-page "https://rqtl.org/")
-  (synopsis "R package for analyzing QTL experiments in genetics")
-  (description "R/qtl is an extension library for the R statistics
-system.  It is used to analyze experimental crosses for identifying
-genes contributing to variation in quantitative traits (so-called
-quantitative trait loci, QTLs).
-
-Using a hidden Markov model, R/qtl estimates genetic maps, to
-identify genotyping errors, and to perform single-QTL and two-QTL,
-two-dimensional genome scans.")
-  (license license:gpl3)))
-
-(define-public r-qtl2
-  (package
-    (name "r-qtl2")
-    (version "0.22-11")
-    (source (origin
-              (method url-fetch)
-              (uri (cran-uri "qtl2" version))
-              (sha256
-               (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-data-table" ,r-data-table)
-       ("r-jsonlite" ,r-jsonlite)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcppeigen" ,r-rcppeigen)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-yaml" ,r-yaml)))
-    (home-page "https://kbroman.org/qtl2/")
-    (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
-    (description
-     "This package provides a set of tools to perform @dfn{Quantitative Trait
-Locus} (QTL) analysis in experimental crosses.  It is a reimplementation of the
-@code{R/qtl} package to better handle high-dimensional data and complex cross
-designs.  Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
-    (license license:gpl3)))
-
 (define-public r-zlibbioc
   (package
     (name "r-zlibbioc")
@@ -9444,28 +9393,6 @@ imaging data that can be used in subsequent analyses to adjust for unknown,
 unmodeled, or latent sources of noise.")
     (license license:artistic2.0)))
 
-(define-public r-seqminer
-  (package
-    (name "r-seqminer")
-    (version "8.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "seqminer" version))
-       (sha256
-        (base32
-         "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
-    (build-system r-build-system)
-    (inputs
-     `(("zlib" ,zlib)))
-    (home-page "http://seqminer.genomic.codes")
-    (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
-    (description
-     "This package provides tools to integrate nucleotide sequencing
-data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
-    ;; Any version of the GPL is acceptable
-    (license (list license:gpl2+ license:gpl3+))))
-
 (define-public r-raremetals2
   (package
     (name "r-raremetals2")
@@ -9498,32 +9425,6 @@ for analyzing gene-level association tests in meta-analyses for binary
 trait.")
     (license license:gpl3)))
 
-(define-public r-maldiquant
-  (package
-    (name "r-maldiquant")
-    (version "1.19.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "MALDIquant" version))
-       (sha256
-        (base32
-         "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
-    (properties `((upstream-name . "MALDIquant")))
-    (build-system r-build-system)
-    (home-page "https://cran.r-project.org/web/packages/MALDIquant")
-    (synopsis "Quantitative analysis of mass spectrometry data")
-    (description
-     "This package provides a complete analysis pipeline for matrix-assisted
-laser desorption/ionization-time-of-flight (MALDI-TOF) and other
-two-dimensional mass spectrometry data.  In addition to commonly used plotting
-and processing methods it includes distinctive features, namely baseline
-subtraction methods such as morphological filters (TopHat) or the
-statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
-alignment using warping functions, handling of replicated measurements as well
-as allowing spectra with different resolutions.")
-    (license license:gpl3+)))
-
 (define-public r-protgenerics
   (package
     (name "r-protgenerics")
@@ -9834,71 +9735,6 @@ contains a number of utilities to explore the MS/MS results and assess missed
 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
     (license license:artistic2.0)))
 
-(define-public r-seurat
-  (package
-    (name "r-seurat")
-    (version "3.2.0")
-    (source (origin
-              (method url-fetch)
-              (uri (cran-uri "Seurat" version))
-              (sha256
-               (base32
-                "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))
-    (properties `((upstream-name . "Seurat")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-ape" ,r-ape)
-       ("r-cluster" ,r-cluster)
-       ("r-cowplot" ,r-cowplot)
-       ("r-fitdistrplus" ,r-fitdistrplus)
-       ("r-future" ,r-future)
-       ("r-future-apply" ,r-future-apply)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggrepel" ,r-ggrepel)
-       ("r-ggridges" ,r-ggridges)
-       ("r-httr" ,r-httr)
-       ("r-ica" ,r-ica)
-       ("r-igraph" ,r-igraph)
-       ("r-irlba" ,r-irlba)
-       ("r-jsonlite" ,r-jsonlite)
-       ("r-kernsmooth" ,r-kernsmooth)
-       ("r-leiden" ,r-leiden)
-       ("r-lmtest" ,r-lmtest)
-       ("r-mass" ,r-mass)
-       ("r-matrix" ,r-matrix)
-       ("r-miniui" ,r-miniui)
-       ("r-patchwork" ,r-patchwork)
-       ("r-pbapply" ,r-pbapply)
-       ("r-plotly" ,r-plotly)
-       ("r-png" ,r-png)
-       ("r-rann" ,r-rann)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcppannoy" ,r-rcppannoy)
-       ("r-rcppeigen" ,r-rcppeigen)
-       ("r-rcppprogress" ,r-rcppprogress)
-       ("r-reticulate" ,r-reticulate)
-       ("r-rlang" ,r-rlang)
-       ("r-rocr" ,r-rocr)
-       ("r-rsvd" ,r-rsvd)
-       ("r-rtsne" ,r-rtsne)
-       ("r-scales" ,r-scales)
-       ("r-sctransform" ,r-sctransform)
-       ("r-shiny" ,r-shiny)
-       ("r-spatstat" ,r-spatstat)
-       ("r-tibble" ,r-tibble)
-       ("r-uwot" ,r-uwot)))
-    (home-page "http://www.satijalab.org/seurat")
-    (synopsis "Seurat is an R toolkit for single cell genomics")
-    (description
-     "This package is an R package designed for QC, analysis, and
-exploration of single cell RNA-seq data.  It easily enables widely-used
-analytical techniques, including the identification of highly variable genes,
-dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
-algorithms; density clustering, hierarchical clustering, k-means, and the
-discovery of differentially expressed genes and markers.")
-    (license license:gpl3)))
-
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
@@ -11100,34 +10936,6 @@ are optimized per data type and for subsetted calculations such that both
 memory usage and processing time is minimized.")
     (license license:expat)))
 
-(define-public r-phangorn
-  (package
-    (name "r-phangorn")
-    (version "2.5.5")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "phangorn" version))
-       (sha256
-        (base32
-         "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-ape" ,r-ape)
-       ("r-fastmatch" ,r-fastmatch)
-       ("r-igraph" ,r-igraph)
-       ("r-magrittr" ,r-magrittr)
-       ("r-matrix" ,r-matrix)
-       ("r-quadprog" ,r-quadprog)
-       ("r-rcpp" ,r-rcpp)))
-    (home-page "https://github.com/KlausVigo/phangorn")
-    (synopsis "Phylogenetic analysis in R")
-    (description
-     "Phangorn is a package for phylogenetic analysis in R.  It supports
-estimation of phylogenetic trees and networks using Maximum Likelihood,
-Maximum Parsimony, distance methods and Hadamard conjugation.")
-    (license license:gpl2+)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
@@ -13276,37 +13084,6 @@ analyses in addition to large-scale sequence-level searches.")
       (supported-systems '("x86_64-linux"))
       (license license:bsd-3))))
 
-(define-public r-diversitree
-  (package
-    (name "r-diversitree")
-    (version "0.9-13")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (cran-uri "diversitree" version))
-        (sha256
-         (base32
-          "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
-    (build-system r-build-system)
-    (native-inputs
-     `(("gfortran" ,gfortran)))
-    (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
-    (propagated-inputs
-     `(("r-ape" ,r-ape)
-       ("r-desolve" ,r-desolve)
-       ("r-rcpp" ,r-rcpp)
-       ("r-subplex" ,r-subplex)))
-    (home-page "https://www.zoology.ubc.ca/prog/diversitree")
-    (synopsis "Comparative 'phylogenetic' analyses of diversification")
-    (description "This package contains a number of comparative \"phylogenetic\"
-methods, mostly focusing on analysing diversification and character evolution.
-Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
-and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
-Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
-include Markov models of discrete and continuous trait evolution and constant
-rate speciation and extinction.")
-    (license license:gpl2+)))
-
 (define-public sjcount
   ;; There is no tag for version 3.2, nor is there a release archive.
   (let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5")
@@ -14306,33 +14083,6 @@ downstream analysis.  Poretools operates directly on the native FAST5, a variant
 of the Hierarchical Data Format (HDF5) standard.")
       (license license:expat))))
 
-(define-public r-absfiltergsea
-  (package
-    (name "r-absfiltergsea")
-    (version "1.5.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "AbsFilterGSEA" version))
-       (sha256
-        (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
-    (properties `((upstream-name . "AbsFilterGSEA")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-deseq" ,r-deseq)
-       ("r-limma" ,r-limma)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)))
-    (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
-    (synopsis "Improved false positive control of gene-permuting with absolute filtering")
-    (description
-     "This package provides a function that performs gene-permuting of a gene-set
-enrichment analysis (GSEA) calculation with or without the absolute filtering.
-  Without filtering, users can perform (original) two-tailed or one-tailed
-absolute GSEA.")
-    (license license:gpl2)))
-
 (define-public jamm
   (package
     (name "jamm")
@@ -15400,12 +15150,34 @@ mutations from scRNA-Seq data.")
                       (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
                       (string-append "INCLUDES= -I" htslib-ref "/include/htslib")
                       "HTS_HEADERS="    ; No need to check for headers here.
-                      (string-append "LIBPATH=-L. -L" htslib-ref "/include")))))
+                      (string-append "LIBPATH=-L. -L" htslib-ref "/include"))
+              (invoke "g++" "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts")
+              (invoke "ar" "rcs" "libtabixpp.a" "tabix.o"))))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
-            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+            (let* ((out (assoc-ref outputs "out"))
-              (install-file "tabix++" bin))
+                   (lib (string-append out "/lib"))
-            #t)))))
+                   (bin (string-append out "/bin")))
+              (install-file "tabix++" bin)
+              (install-file "libtabixpp.so" lib)
+              (install-file "libtabixpp.a" lib)
+              (install-file "tabix.hpp" (string-append out "/include"))
+              (mkdir-p (string-append lib "/pkgconfig"))
+              (with-output-to-file (string-append lib "/pkgconfig/tabixpp.pc")
+                (lambda _
+                  (format #t "prefix=~a~@
+                          exec_prefix=${prefix}~@
+                          libdir=${exec_prefix}/lib~@
+                          includedir=${prefix}/include~@
+                          ~@
+                          ~@
+                          Name: libtabixpp~@
+                          Version: ~a~@
+                          Description: C++ wrapper around tabix project~@
+                          Libs: -L${libdir} -ltabixpp~@
+                          Cflags: -I${includedir}~%"
+                          out ,version)))
+              #t))))))
    (home-page "https://github.com/ekg/tabixpp")
    (synopsis "C++ wrapper around tabix project")
    (description "This is a C++ wrapper around the Tabix project which abstracts
@@ -15432,13 +15204,45 @@ some of the details of opening and jumping in tabix-indexed files.")
          #:phases
          (modify-phases %standard-phases
            (delete 'configure) ; There is no configure phase.
+           (add-after 'unpack 'patch-source
+             (lambda _
+               (substitute* "Makefile"
+                 (("-c ") "-c -fPIC "))
+               #t))
+           (add-after 'build 'build-dynamic
+             (lambda _
+               (invoke "g++"
+                       "-shared" "-o" "libsmithwaterman.so"
+                       "smithwaterman.o" "SmithWatermanGotoh.o"
+                       "disorder.o" "BandedSmithWaterman.o"
+                       "LeftAlign.o" "Repeats.o" "IndelAllele.o")))
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
                (let* ((out (assoc-ref outputs "out"))
                       (bin (string-append out "/bin"))
                       (lib (string-append out "/lib")))
                  (install-file "smithwaterman" bin)
-                 (install-file "libsw.a" lib))
+                 (for-each
+                   (lambda (file)
+                     (install-file file (string-append out "/include/smithwaterman")))
+                   (find-files "." "\\.h$"))
+                 (install-file "libsmithwaterman.so" lib)
+                 (install-file "libsw.a" lib)
+                 (mkdir-p (string-append lib "/pkgconfig"))
+                 (with-output-to-file (string-append lib "/pkgconfig/smithwaterman.pc")
+                   (lambda _
+                     (format #t "prefix=~a~@
+                             exec_prefix=${prefix}~@
+                             libdir=${exec_prefix}/lib~@
+                             includedir=${prefix}/include/smithwaterman~@
+                             ~@
+                             ~@
+                             Name: smithwaterman~@
+                             Version: ~a~@
+                             Description: smith-waterman-gotoh alignment algorithm~@
+                             Libs: -L${libdir} -lsmithwaterman~@
+                             Cflags: -I${includedir}~%"
+                             out ,version))))
                #t)))))
       (home-page "https://github.com/ekg/smithwaterman")
       (synopsis "Implementation of the Smith-Waterman algorithm")
@@ -15528,10 +15332,43 @@ neural networks.")
        #:phases
        (modify-phases %standard-phases
          (delete 'configure) ; There is no configure phase.
+           (add-after 'unpack 'patch-source
+             (lambda _
+               (substitute* "Makefile"
+                 (("-c ") "-c -fPIC "))
+               #t))
+         (add-after 'build 'build-dynamic
+           (lambda _
+             (invoke "g++"
+                     "-shared" "-o" "libfastahack.so"
+                     "Fasta.o" "FastaHack.o" "split.o" "disorder.o")))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
-             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+             (let* ((out (assoc-ref outputs "out"))
-               (install-file "fastahack" bin))
+                    (lib (string-append out "/lib"))
+                    (bin (string-append out "/bin")))
+               (mkdir-p (string-append out "/include/fastahack"))
+               (for-each
+                 (lambda (file)
+                   (install-file file (string-append out "/include/fastahack")))
+                 (find-files "." "\\.h$"))
+               (install-file "fastahack" bin)
+               (install-file "libfastahack.so" lib)
+               (mkdir-p (string-append lib "/pkgconfig"))
+               (with-output-to-file (string-append lib "/pkgconfig/fastahack.pc")
+                 (lambda _
+                   (format #t "prefix=~a~@
+                           exec_prefix=${prefix}~@
+                           libdir=${exec_prefix}/lib~@
+                           includedir=${prefix}/include/fastahack~@
+                           ~@
+                           ~@
+                           Name: fastahack~@
+                           Version: ~a~@
+                           Description: Indexing and sequence extraction from FASTA files~@
+                           Libs: -L${libdir} -lfastahack~@
+                           Cflags: -I${includedir}~%"
+                           out ,version))))
              #t)))))
     (home-page "https://github.com/ekg/fastahack")
     (synopsis "Indexing and sequence extraction from FASTA files")
@@ -15554,9 +15391,16 @@ library automatically handles index file generation and use.")
                            "/vcflib-" version "-src.tar.gz"))
        (sha256
         (base32 "14zzrg8hg8cq9cvq2wdvp21j7nmxxkjrbagw2apd2yqv2kyx42lm"))
+       (patches (search-patches "vcflib-use-shared-libraries.patch"))
        (modules '((guix build utils)))
        (snippet
         `(begin
+           (substitute* (find-files "." "\\.(h|c)(pp)?$")
+             (("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>")
+             (("\"convert.h\"") "<smithwaterman/convert.h>")
+             (("\"disorder.h\"") "<smithwaterman/disorder.h>")
+             (("\"tabix.hpp\"") "<tabix.hpp>")
+             (("\"Fasta.h\"") "<fastahack/Fasta.h>"))
            (for-each delete-file-recursively
                      '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree"
                        "libVCFH" "multichoose" "smithwaterman" "tabixpp"))
@@ -15564,34 +15408,34 @@ library automatically handles index file generation and use.")
     (build-system gnu-build-system)
     (inputs
      `(("htslib" ,htslib)
+       ("fastahack" ,fastahack)
        ("perl" ,perl)
        ("python" ,python)
+       ("smithwaterman" ,smithwaterman)
+       ("tabixpp" ,tabixpp)
+       ("xz" ,xz)
        ("zlib" ,zlib)))
     (native-inputs
-     `(;; Submodules.
+     `(("pkg-config" ,pkg-config)
+       ;; Submodules.
        ;; This package builds against the .o files so we need to extract the source.
-       ("fastahack-src" ,(package-source fastahack))
        ("filevercmp-src" ,(package-source filevercmp))
-       ("fsom-src" ,(package-source fsom))
        ("intervaltree-src" ,(package-source intervaltree))
-       ("multichoose-src" ,(package-source multichoose))
+       ("multichoose-src" ,(package-source multichoose))))
-       ("smithwaterman-src" ,(package-source smithwaterman))
-       ("tabixpp-src" ,(package-source tabixpp))))
     (arguments
      `(#:tests? #f ; no tests
-       #:make-flags (list (string-append "HTS_LIB="
-                                         (assoc-ref %build-inputs "htslib")
-                                         "/lib/libhts.a")
-                          (string-append "HTS_INCLUDES= -I"
-                                         (assoc-ref %build-inputs "htslib")
-                                         "/include/htslib")
-                          (string-append "HTS_LDFLAGS= -L"
-                                         (assoc-ref %build-inputs "htslib")
-                                         "/include/htslib" " -lhts"))
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'set-flags
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "Makefile"
+               (("LDFLAGS =")
+                (string-append "LDFLAGS = -Wl,-rpath="
+                               (assoc-ref outputs "out") "/lib ")))
+             (substitute* "filevercmp/Makefile"
+               (("-c") "-c -fPIC"))
+             #t))
          (delete 'configure)
-         (delete 'check)
          (add-after 'unpack 'unpack-submodule-sources
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((unpack (lambda (source target)
@@ -15603,34 +15447,39 @@ library automatically handles index file generation and use.")
                                            (assoc-ref inputs source)
                                            "--strip-components=1"))))))
                (and
-                (unpack "fastahack-src" "fastahack")
                 (unpack "filevercmp-src" "filevercmp")
-                (unpack "fsom-src" "fsom")
                 (unpack "intervaltree-src" "intervaltree")
-                (unpack "multichoose-src" "multichoose")
+                (unpack "multichoose-src" "multichoose")))))
-                (unpack "smithwaterman-src" "smithwaterman")
-                (unpack "tabixpp-src" "tabixpp")))))
-         (replace 'build
-           (lambda* (#:key inputs make-flags #:allow-other-keys)
-             (let ((htslib (assoc-ref inputs "htslib")))
-               (with-directory-excursion "tabixpp"
-                 (substitute* "Makefile"
-                   (("-Ihtslib") (string-append "-I" htslib "/include/htslib"))
-                   (("-Lhtslib") (string-append "-L" htslib "/lib/htslib"))
-                   (("htslib/htslib") (string-append htslib "/include/htslib")))
-                 (invoke "make"
-                         (string-append "HTS_LIB=" htslib "/lib/libhts.a")))
-               (apply invoke "make" "CC=gcc" "CFLAGS=-Itabixpp" make-flags))))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
-             (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+             (let* ((out (assoc-ref outputs "out"))
-                   (lib (string-append (assoc-ref outputs "out") "/lib")))
+                    (bin (string-append out "/bin"))
+                    (lib (string-append out "/lib")))
                (for-each (lambda (file)
                            (install-file file bin))
                          (find-files "bin" ".*"))
-               ;; The header files in src/ do not interface libvcflib,
+               (install-file "libvcflib.so" lib)
-               ;; therefore they are left out.
+               (install-file "libvcflib.a" lib)
-               (install-file "libvcflib.a" lib))
+               (for-each
+                 (lambda (file)
+                   (install-file file (string-append out "/include")))
+                 (find-files "include" "\\.h(pp)?$"))
+               (mkdir-p (string-append lib "/pkgconfig"))
+               (with-output-to-file (string-append lib "/pkgconfig/vcflib.pc")
+                 (lambda _
+                   (format #t "prefix=~a~@
+                           exec_prefix=${prefix}~@
+                           libdir=${exec_prefix}/lib~@
+                           includedir=${prefix}/include~@
+                           ~@
+                           ~@
+                           Name: libvcflib~@
+                           Version: ~a~@
+                           Requires: smithwaterman, fastahack~@
+                           Description: C++ library for parsing and manipulating VCF files~@
+                           Libs: -L${libdir} -lvcflib~@
+                           Cflags: -I${includedir}~%"
+                           out ,version))))
              #t)))))
     (home-page "https://github.com/vcflib/vcflib/")
     (synopsis "Library for parsing and manipulating VCF files")

gnu/packages/bittorrent.scm

@@ -34,6 +34,7 @@
   #:use-module (guix build-system python)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module ((guix licenses) #:prefix l:)
+  #:use-module (guix utils)
   #:use-module (gnu packages)
   #:use-module (gnu packages adns)
   #:use-module (gnu packages boost)
@@ -55,6 +56,7 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-crypto)
+  #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages sqlite)
@@ -465,29 +467,65 @@ features.")
 (define-public deluge
   (package
     (name "deluge")
-    (version "1.3.15")
+    (version "2.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
-             "http://download.deluge-torrent.org/source/deluge-"
+             "https://ftp.osuosl.org/pub/deluge/source/"
-             version ".tar.xz"))
+             (version-major+minor version) "/deluge-" version ".tar.xz"))
        (sha256
         (base32
-         "0b7rri4x0wrcj7rjghrnw1kfrsd5i7i6aq85dsg5dg1w1qa0ar59"))))
+         "14d8kn2pvr1qv8mwqrxmj85jycr73vwfqz12hzag0ararbkfhyky"))))
     (build-system python-build-system)
-    (inputs
+    (propagated-inputs
-     `(("libtorrent" ,libtorrent-rasterbar)
+     `(("gtk+" ,gtk+)
-       ("python2-chardet" ,python2-chardet)
+       ("librsvg" ,librsvg)
-       ("python2-pygtk" ,python2-pygtk)
+       ("libtorrent" ,libtorrent-rasterbar)
-       ("python2-pyopenssl" ,python2-pyopenssl)
+       ("python-pycairo" ,python-pycairo)
-       ("python2-pyxdg" ,python2-pyxdg)
+       ("python-chardet" ,python-chardet)
-       ("python2-service-identity" ,python2-service-identity)
+       ("python-dbus" ,python-dbus)
-       ("python2-twisted" ,python2-twisted)))
+       ("python-mako" ,python-mako)
+       ("python-pygobject" ,python-pygobject)
+       ("python-pillow" ,python-pillow)
+       ("python-pyopenssl" ,python-pyopenssl)
+       ("python-pyxdg" ,python-pyxdg)
+       ("python-rencode" ,python-rencode)
+       ("python-service-identity" ,python-service-identity)
+       ("python-setproctitle" ,python-setproctitle)
+       ("python-six" ,python-six)
+       ("python-twisted" ,python-twisted)
+       ("python-zope-interface" ,python-zope-interface)))
     (native-inputs
-     `(("intltool" ,intltool)))
+     `(("intltool" ,intltool)
+       ("python-wheel" ,python-wheel)))
+    ;; TODO: Enable tests.
+    ;; After "pytest-twisted" is packaged, HOME is set, and an X server is
+    ;; started, some of the tests still fail.  There are likely some tests
+    ;; that require a network connection.
     (arguments
-     `(#:python ,python-2))
+     `(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         ;; Remove this phase when upgrading to version 2.0.4 or beyond, as
+         ;; the issue is fixed upstream.
+         (add-after 'unpack 'fix-gettext-warning
+           (lambda _
+             (substitute* "deluge/i18n/util.py"
+               (("names='ngettext'") "names=['ngettext']"))
+             #t))
+         (add-after 'install 'wrap
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out               (assoc-ref outputs "out"))
+                   (gi-typelib-path   (getenv "GI_TYPELIB_PATH")))
+               (for-each
+                (lambda (program)
+                  (wrap-program program
+                    `("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path))))
+                (map (lambda (name)
+                       (string-append out "/bin/" name))
+                     '("deluge" "deluge-gtk"))))
+             #t)))))
     (home-page "https://www.deluge-torrent.org/")
     (synopsis  "Fully-featured cross-platform ​BitTorrent client")
     (description

gnu/packages/build-tools.scm

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

gnu/packages/chez.scm

@@ -240,7 +240,9 @@ and 32-bit PowerPC architectures.")
      `(("chez-scheme" ,chez-scheme)))
     (arguments
      `(#:make-flags (let ((out (assoc-ref %outputs "out")))
-                      (list (string-append "PREFIX=" out)))
+                      (list (string-append "PREFIX=" out)
+                            "CHEZ=chez-scheme --libdirs ./"
+                            (string-append "chezversion=" ,(package-version chez-scheme))))
        #:test-target "test"
        #:phases (modify-phases %standard-phases
                   (delete 'configure))))
@@ -414,7 +416,11 @@ Chez Scheme.")
 ;; files.
 (define (chez-make-flags name version)
   `(let ((out (assoc-ref %outputs "out")))
-     (list (string-append "PREFIX=" out)
+     (list
+      ;; Set 'chezversion' so that libraries are installed in
+      ;; 'lib/csvX.Y.Z-site' like Chez's 'native-search-paths' expects.
+      (string-append "chezversion=" ,(package-version chez-scheme))
+      (string-append "PREFIX=" out)
       (string-append "DOCDIR=" out "/share/doc/"
                      ,name "-" ,version))))
 

gnu/packages/ci.scm

@@ -47,8 +47,8 @@
   #:use-module (guix build-system gnu))
 
 (define-public cuirass
-  (let ((commit "f2984c7230f69a6e50810edc5e9d36bd671801f9")
+  (let ((commit "cf11b73db00678b45b70108768138d0fb74d9506")
-        (revision "43"))
+        (revision "45"))
     (package
       (name "cuirass")
       (version (git-version "0.0.1" revision commit))
@@ -60,7 +60,7 @@
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1p9mlmhv4kz8wixgywh1ffm3140p4mkgz92n7ry3n5s9w5n7fpjl"))))
+                  "1f7jqnscy8vjqrpgl4cyynrvbx6zp3slsd82fykap6qvvwwn7xj8"))))
       (build-system gnu-build-system)
       (arguments
        '(#:modules ((guix build utils)

gnu/packages/code.scm

@@ -125,14 +125,14 @@ highlighting your own code that seemed comprehensible when you wrote it.")
 (define-public global                             ; a global variable
   (package
     (name "global")
-    (version "6.6.4")
+    (version "6.6.5")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/global/global-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "1515642wsjz7x3rsgaqk4sc7n0z2znl7idsk8jz8wgy5aswqqzlq"))))
+               "10vvsgx8v54whb4j9mk5qqyb5h3rdd9da0il3wir8pcpksyk0dww"))))
     (build-system gnu-build-system)
     (inputs `(("ncurses" ,ncurses)
               ("libltdl" ,libltdl)

gnu/packages/commencement.scm

@@ -3851,7 +3851,8 @@ COREUTILS-FINAL vs. COREUTILS, etc."
       (description
        "This package provides a complete GCC tool chain for C/C++ development to
 be installed in user profiles.  This includes GCC, as well as libc (headers and
-binaries, plus debugging symbols in the @code{debug} output), and Binutils.")
+binaries, plus debugging symbols in the @code{debug} output), and Binutils.  GCC
+is the GNU Compiler Collection.")
       (home-page "https://gcc.gnu.org/")
       (outputs '("out" "debug" "static"))
 
@@ -3892,6 +3893,12 @@ binaries, plus debugging symbols in the @code{debug} output), and Binutils.")
 (define-public gcc-toolchain-10
   (make-gcc-toolchain gcc-10))
 
+(define-public gcc-toolchain-aka-gcc
+  ;; It's natural for users to try "guix install gcc".  This package
+  ;; automatically "redirects" them to 'gcc-toolchain'.
+  (deprecated-package "gcc" gcc-toolchain-10))
+
+
 (define-public gdc-toolchain-10
   (package (inherit (make-gcc-toolchain gdc-10))
     (synopsis "Complete GCC tool chain for D lang development")

gnu/packages/coq.scm

@@ -4,6 +4,8 @@
 ;;; Copyright © 2019 Dan Frumin <dfrumin@cs.ru.nl>
 ;;; Copyright © 2020 Brett Gilio <brettg@gnu.org>
 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
+;;; Copyright © 2020 raingloom <raingloom@riseup.net>
+;;; Copyright © 2020 Robin Green <greenrd@greenrd.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -33,6 +35,7 @@
   #:use-module (gnu packages ocaml)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages rsync)
   #:use-module (gnu packages texinfo)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system ocaml)
@@ -46,7 +49,7 @@
 (define-public coq
   (package
     (name "coq")
-    (version "8.10.2")
+    (version "8.11.2")
     (source
      (origin
        (method git-fetch)
@@ -56,7 +59,7 @@
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0ji2rzd70b3hcwfw97qk7rv3m2977ylqnq82l1555dp3njr8nm3q"))))
+         "1gia82dkmzqspw2w3s4gjyh39ghbmw4i41i4hyzc91g7mza17nbz"))))
     (native-search-paths
      (list (search-path-specification
             (variable "COQPATH")
@@ -69,7 +72,9 @@
        ("camlp5" ,camlp5)
        ("ocaml-num" ,ocaml-num)))
     (native-inputs
-     `(("ocaml-ounit" ,ocaml-ounit)))
+     `(("ocaml-ounit" ,ocaml-ounit)
+       ("rsync" ,rsync)
+       ("which" ,which)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -96,11 +101,18 @@
          (add-after 'install 'remove-duplicate
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
-                    (bin (string-append out "/bin")))
+                    (bin (string-append out "/bin"))
+                    (coqtop (string-append bin "/coqtop"))
+                    (coqidetop (string-append bin "/coqidetop"))
+                    (coqtop.opt (string-append coqtop ".opt"))
+                    (coqidetop.opt (string-append coqidetop ".opt")))
                ;; These files are exact copies without `.opt` extension.
                ;; Removing these saves 35 MiB in the resulting package.
-               (delete-file (string-append bin "/coqtop.opt"))
+               ;; Unfortunately, completely deleting them breaks coqide.
-               (delete-file (string-append bin "/coqidetop.opt")))
+               (delete-file coqtop.opt)
+               (delete-file coqidetop.opt)
+               (symlink coqtop coqtop.opt)
+               (symlink coqidetop coqidetop.opt))
              #t))
          (add-after 'install 'install-ide
            (lambda* (#:key outputs #:allow-other-keys)
@@ -117,7 +129,7 @@
                ;; Fails because the output is not formatted as expected.
                (delete-file-recursively "coq-makefile/timing")
                ;; Fails because we didn't build coqtop.byte.
-               (delete-file-recursively "coq-makefile/findlib-package")
+               (delete-file "misc/printers.sh")
                (invoke "make")))))))
     (home-page "https://coq.inria.fr")
     (synopsis "Proof assistant for higher-order logic")
@@ -207,7 +219,7 @@ provers.")
 (define-public coq-flocq
   (package
     (name "coq-flocq")
-    (version "3.2.0")
+    (version "3.3.1")
     (source
      (origin
        (method git-fetch)
@@ -217,7 +229,7 @@ provers.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "15bi36x7zj0glsb3s2gwqd4wswhfzh36rbp7imbyff53a7nna95l"))))
+         "01gdykva0lcw6y3dm8j0djxayb87szfg9vn0mxd6z3pks644misl"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -264,7 +276,7 @@ inside Coq.")
 (define-public coq-gappa
   (package
     (name "coq-gappa")
-    (version "1.4.2")
+    (version "1.4.4")
     (source
      (origin
        (method git-fetch)
@@ -274,7 +286,7 @@ inside Coq.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0r7jwp5xssdfzivs2flp7mzrscqhgl63mryhhf1cvndpgzqwfk2f"))))
+         "0f3g3wjkvfkm961l4jpckhsqd43jnvm7f5qqk78qc32zh1fg339n"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -324,7 +336,7 @@ assistant.")
 (define-public coq-mathcomp
   (package
     (name "coq-mathcomp")
-    (version "1.10.0")
+    (version "1.11.0")
     (source
      (origin
        (method git-fetch)
@@ -333,7 +345,7 @@ assistant.")
              (commit (string-append "mathcomp-" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1h5h1c2025r1ms5qryvwy6pikxmpmmjav6yl127xpzmqdi6w732d"))))
+        (base32 "1axywpa1jcpnidd86irpd1gdbbg2sfbwc652675xisq5wnmfmf6f"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("ocaml" ,ocaml)
@@ -366,7 +378,7 @@ part of the distribution.")
 (define-public coq-coquelicot
   (package
     (name "coq-coquelicot")
-    (version "3.0.3")
+    (version "3.1.0")
     (source
      (origin
        (method git-fetch)
@@ -376,7 +388,7 @@ part of the distribution.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0m5wbr2s8lnf8b7cfwv15hyzsmbcaz6hgdn7aazcrkxnwr87vgkp"))))
+         "0mz3pxan1237fr5fi79c66y7b9z7bmi0sc45kwrmkczsjm5462jm"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -419,7 +431,7 @@ theorems between the two libraries.")
 (define-public coq-bignums
   (package
     (name "coq-bignums")
-    (version "8.10.0")
+    (version "8.11.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -428,7 +440,7 @@ theorems between the two libraries.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0bpb4flckn4nqxbs3wjiznyx1k7r8k93qdigp3qwmikp2lxvcbw5"))))
+                "1xcd7c7qlvs0narfba6px34zq0mz8rffnhxw0kzhhg6i4iw115dp"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("ocaml" ,ocaml)
@@ -452,7 +464,7 @@ provides BigN, BigZ, BigQ that used to be part of Coq standard library.")
 (define-public coq-interval
   (package
     (name "coq-interval")
-    (version "3.4.1")
+    (version "4.0.0")
     (source
      (origin
        (method git-fetch)
@@ -462,7 +474,7 @@ provides BigN, BigZ, BigQ that used to be part of Coq standard library.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "03q3dfqi3r3f7aji5s06ig4aav9ajcwswwdzi5lrgr69z0m487k4"))))
+         "01iz6qmnsm6b9s1vmdjs79vjx9xgwzn5rwyjp6bvs8hg3zlmhpip"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -548,16 +560,16 @@ uses Ltac to synthesize the substitution operation.")
 (define-public coq-equations
   (package
     (name "coq-equations")
-    (version "1.2.1")
+    (version "1.2.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/mattam82/Coq-Equations")
-                    (commit (string-append "v" version "-8.10"))))
+                    (commit (string-append "v" version "-8.11"))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "023q5dww3drw35dm9bi9p9d0wrj9k7vax7hfdsprf8l340pb4s0k"))))
+                "1srxz1rws8jsh7402g2x2vcqgjbbsr64dxxj5d2zs48pmhb20csf"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("ocaml"  ,ocaml)
@@ -588,7 +600,7 @@ kernel.")
 (define-public coq-stdpp
   (package
     (name "coq-stdpp")
-    (version "1.2.1")
+    (version "1.4.0")
     (synopsis "Alternative Coq standard library std++")
     (source (origin
               (method git-fetch)
@@ -598,7 +610,7 @@ kernel.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1lczybg1jq9drbi8nzrlb0k199x4n07aawjwfzrl3qqc0w8kmvdz"))))
+                "1m6c7ibwc99jd4cv14v3r327spnfvdf3x2mnq51f9rz99rffk68r"))))
     (build-system gnu-build-system)
     (inputs
      `(("coq" ,coq)))

gnu/packages/cpp.scm

@@ -13,6 +13,7 @@
 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2020 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
+;;; Copyright © 2020 Alexandros Theodotou <alex@zrythm.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -360,7 +361,7 @@ intuitive syntax and trivial integration.")
 (define-public xtl
   (package
     (name "xtl")
-    (version "0.6.16")
+    (version "0.6.18")
     (source (origin
               (method git-fetch)
               (uri
@@ -369,7 +370,7 @@ intuitive syntax and trivial integration.")
                 (commit version)))
               (sha256
                (base32
-                "0hkz01l7fc1m79s02hz86cl9nb4rwdvg255r6aj82gnsx5qvxy2l"))
+                "0s9gnv1wq0cmpw878dmx0lnci86895hhdrwyc9x8lfbc1hr7ypnh"))
               (file-name (git-file-name name version))))
     (native-inputs
      `(("googletest" ,googletest)
@@ -493,6 +494,36 @@ it's own version of the tool, this is a fork that aims to be more responsive
 and make @code{cpplint} usable in wider contexts.")
     (license license:bsd-3)))
 
+(define-public reproc
+  (package
+    (name "reproc")
+    (version "14.1.0")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/DaanDeMeyer/reproc")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+          (base32
+            "1n71wb50qv2dmhjgw7azx5gigbrp19l2n3d41g9p05l5l0y1qg0q"))))
+   (build-system cmake-build-system)
+   (arguments
+      ;; No tests.
+    `(#:tests? #f
+      ;; Enable building of shared library.
+      #:configure-flags `("-DBUILD_SHARED_LIBS=1")))
+   (native-inputs
+    `(("pkg-config" ,pkg-config)))
+   (synopsis "Process IO library")
+   (description "reproc (Redirected Process) is a C/C++ library that
+simplifies starting, stopping and communicating with external programs.  The
+main use case is executing command line applications directly from C or C++
+code and retrieving their output.")
+   (home-page "https://github.com/DaanDeMeyer/reproc")
+   (license license:expat)))
+
 (define-public sobjectizer
   (package
     (name "sobjectizer")

gnu/packages/crates-io.scm

@@ -293,8 +293,7 @@ the Rust programming language.")
          (base32
           "19f8v503ibvlyr824g5ynicrh1lsmp2i0zmpszr8lqay0qw3vkl1"))))
     (arguments
-     `(#:skip-build? #t
+     `(#:cargo-inputs
-       #:cargo-inputs
        (("rust-memchr" ,rust-memchr-2))
        #:cargo-development-inputs
        (("rust-csv" ,rust-csv-1.1)
@@ -1031,7 +1030,7 @@ Mac, and Unix.")
 (define-public rust-autocfg-1.0
   (package
     (name "rust-autocfg")
-    (version "1.0.0")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
@@ -1040,7 +1039,7 @@ Mac, and Unix.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "17cv6pwb4q08s0ynpr4n8hv5299hcmhdgvdchzixfpw8y5qcgapq"))))
+         "0jj6i9zn4gjl03kjvziqdji6rwx8ykz8zk2ngpc331z2g3fk3c6d"))))
     (build-system cargo-build-system)
     (home-page "https://github.com/cuviper/autocfg")
     (synopsis
@@ -1172,7 +1171,7 @@ trace (backtrace) at runtime in a Rust program.")
 (define-public rust-backtrace-sys-0.1
   (package
     (name "rust-backtrace-sys")
-    (version "0.1.35")
+    (version "0.1.37")
     (source
       (origin
         (method url-fetch)
@@ -1180,7 +1179,7 @@ trace (backtrace) at runtime in a Rust program.")
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "066iviphi72mx9hd3njzsplk5v45jhi10mrccbbyij391ahsps3x"))))
+          "16a3igz22q9lnnjjr77f4k8ci48v8zdwrs67khx3h7wx3jzfpyqq"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -2315,7 +2314,7 @@ in a byte slice, fast.")
 (define-public rust-bytemuck-1
   (package
     (name "rust-bytemuck")
-    (version "1.3.1")
+    (version "1.4.0")
     (source
       (origin
         (method url-fetch)
@@ -2324,14 +2323,45 @@ in a byte slice, fast.")
          (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-          "1scaac5xbfynzbpvz9yjbmg9ag2jalxfijapwlqh7xldf4li0ynv"))))
+          "071043n73hwi55z9c55ga4v52v8a7ri56gqja8r98clkdyxns14j"))))
     (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bytemuck-derive" ,rust-bytemuck-derive-1))))
     (home-page "https://github.com/Lokathor/bytemuck")
     (synopsis "Crate for mucking around with piles of bytes")
     (description
      "This package provides a crate for mucking around with piles of bytes.")
     (license license:zlib)))
 
+(define-public rust-bytemuck-derive-1
+  (package
+    (name "rust-bytemuck-derive")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bytemuck-derive" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1k59b6g2d87nf32qwhp73vng3al0zklxg64iiwf0pkxy74xf5ni8"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1)
+        ("rust-quote" ,rust-quote-1)
+        ("rust-syn" ,rust-syn-1))
+       #:cargo-development-inputs
+       (("rust-bytemuck" ,rust-bytemuck-1))))
+    (home-page "https://github.com/Lokathor/bytemuck")
+    (synopsis "Derive proc-macros for @code{bytemuck}")
+    (description
+     "This package derives proc-macros for the @code{bytemuck} crate.")
+    (license
+      (list license:zlib license:asl2.0 license:expat))))
+
 (define-public rust-byteorder-1.3
   (package
     (name "rust-byteorder")
@@ -2481,7 +2511,7 @@ exposed as Reader/Writer streams.")
 (define-public rust-bzip2-sys-0.1
   (package
     (name "rust-bzip2-sys")
-    (version "0.1.7")
+    (version "0.1.9+1.0.8")
     (source
      (origin
        (method url-fetch)
@@ -2490,11 +2520,11 @@ exposed as Reader/Writer streams.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0pz2mdhkk8yphiqdh2kghdxb60kqyd10lfrjym3r4k5dylvam135"))
+         "0pi8lxzb1104q9cpvv1jgnk909cggqh2zcdhywqwlbq6c2i3jfxd"))
         (modules '((guix build utils)))
         (snippet
          '(begin
-            (delete-file-recursively "bzip2-1.0.6")
+            (delete-file-recursively "bzip2-1.0.8")
             (delete-file "build.rs")
             ;; Inspired by Debian's patch.
             (with-output-to-file "build.rs"
@@ -2507,7 +2537,8 @@ exposed as Reader/Writer streams.")
     (arguments
      `(#:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
-        ("rust-cc" ,rust-cc-1))))
+        ("rust-cc" ,rust-cc-1)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))))
     (home-page "https://github.com/alexcrichton/bzip2-rs")
     (synopsis "Rust bindings to libbzip2")
     (description
@@ -5049,7 +5080,7 @@ Transparency logs for use with sct crate.")
      `(#:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
         ("rust-libnghttp2-sys" ,rust-libnghttp2-sys-0.1)
-        ("rust-libz-sys" ,rust-libz-sys-1.0)
+        ("rust-libz-sys" ,rust-libz-sys-1)
         ("rust-openssl-sys" ,rust-openssl-sys-0.9)
         ("rust-winapi" ,rust-winapi-0.3)
         ("rust-cc" ,rust-cc-1)
@@ -7408,7 +7439,7 @@ cross platform API.")
         ("rust-crc32fast" ,rust-crc32fast-1.2)
         ("rust-futures" ,rust-futures-0.1)
         ("rust-libc" ,rust-libc-0.2)
-        ("rust-libz-sys" ,rust-libz-sys-1.0)
+        ("rust-libz-sys" ,rust-libz-sys-1)
         ("rust-miniz-sys" ,rust-miniz-sys-0.1)
         ("rust-miniz-oxide" ,rust-miniz-oxide-0.3)
         ("rust-tokio-io" ,rust-tokio-io-0.1))
@@ -7790,7 +7821,7 @@ values to other threads.")
     (arguments
      `(#:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
-        ("rust-libz-sys" ,rust-libz-sys-1.0)
+        ("rust-libz-sys" ,rust-libz-sys-1)
         ("rust-pkg-config" ,rust-pkg-config-0.3))))
     (inputs
      `(("freetype" ,freetype)
@@ -8966,6 +8997,37 @@ retrieving random data from system source.")
     (description "This package provides raw FFI bindings for GNU Gettext.")
     (license license:expat)))
 
+(define-public rust-gfa-0.6
+  (package
+    (name "rust-gfa")
+    (version "0.6.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gfa" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0ghmy4r0324s6vvmj9nmh326346nkwm7nybnpcpswnjvf02b85gw"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bstr" ,rust-bstr-0.2)
+        ("rust-bytemuck" ,rust-bytemuck-1)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-nom" ,rust-nom-5)
+        ("rust-regex" ,rust-regex-1)
+        ("rust-serde" ,rust-serde-1))
+       #:cargo-development-inputs
+       (("rust-criterion" ,rust-criterion-0.3))))
+    (home-page "https://github.com/chfi/rs-gfa")
+    (synopsis "Library for graphs in the GFA (Graphical Fragment Assembly) format")
+    (description
+     "This package provides a library for working with graphs in the
+@acronym{GFA, Graphical Fragment Assembly} format.")
+    (license license:expat)))
+
 (define-public rust-gfx-0.18
   (package
     (name "rust-gfx")
@@ -12455,7 +12517,7 @@ macros on libc without stdlib.")
     (arguments
      `(#:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
-        ("rust-libz-sys" ,rust-libz-sys-1.0)
+        ("rust-libz-sys" ,rust-libz-sys-1)
         ("rust-libssh2-sys" ,rust-libssh2-sys-0.2)
         ("rust-openssl-sys" ,rust-openssl-sys-0.9)
         ;; Build dependencies:
@@ -12518,7 +12580,7 @@ macros on libc without stdlib.")
        (("rust-curl-sys" ,rust-curl-sys-0.4)
         ("rust-libc" ,rust-libc-0.2)
         ("rust-libssh2-sys" ,rust-libssh2-sys-0.2)
-        ("rust-libz-sys" ,rust-libz-sys-1.0)
+        ("rust-libz-sys" ,rust-libz-sys-1)
         ("rust-openssl-sys" ,rust-openssl-sys-0.9)
         ("rust-cc" ,rust-cc-1)
         ("rust-pkg-config" ,rust-pkg-config-0.3))))))
@@ -12615,7 +12677,7 @@ functions and static variables these libraries contain.")
 (define-public rust-libnghttp2-sys-0.1
   (package
     (name "rust-libnghttp2-sys")
-    (version "0.1.2")
+    (version "0.1.4+1.41.0")
     (source
       (origin
         (method url-fetch)
@@ -12623,18 +12685,30 @@ functions and static variables these libraries contain.")
         (file-name (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-          "0qr4lyh7righx9n22c7amlcpk906rn1jnb2zd6gdfpa3yi24s982"))
+          "1wcd93a8cw1h9y25834160y6ng982fi0qcd277hpjvhnvz34wqh3"))
         (modules '((guix build utils)))
         (snippet
-         '(begin (delete-file-recursively "nghttp2") #t))))
+         '(begin
+            (delete-file-recursively "nghttp2")
+            (substitute* "Cargo.toml"
+              (("false")
+               "false\n[build-dependencies.pkg-config]\nversion = \"0.3\"\n"))
+            (delete-file "build.rs")
+            (with-output-to-file "build.rs"
+              (lambda _
+                (format #t "fn main() {~@
+                        println!(\"cargo:rustc-link-lib=nghttp2\");~@
+                        }~%")))
+                 #t))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t     ; Uses unstable features
+     `(#:cargo-inputs
-       #:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
-        ("rust-cc" ,rust-cc-1))))
+        ("rust-cc" ,rust-cc-1)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))))
     (inputs
-     `(("nghttp2" ,nghttp2)))
+     `(("nghttp2" ,nghttp2 "lib")
+       ("pkg-config" ,pkg-config)))
     (home-page "https://github.com/alexcrichton/nghttp2-rs")
     (synopsis "FFI bindings for libnghttp2 (nghttp2)")
     (description
@@ -12668,10 +12742,10 @@ functions and static variables these libraries contain.")
     (description "Native bindings to the libsqlite3 library")
     (license license:expat)))
 
-(define-public rust-libz-sys-1.0
+(define-public rust-libz-sys-1
   (package
     (name "rust-libz-sys")
-    (version "1.0.25")
+    (version "1.1.1")
     (source
       (origin
         (method url-fetch)
@@ -12679,16 +12753,19 @@ functions and static variables these libraries contain.")
         (file-name (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-          "1gjycyl2283525abks98bhxa4r259m617xfm5z52p3p3c8ry9d9f"))
+          "1q25cb8vs113si7q2p0innhi8jk0wpq37hqi2wcc219hcmw43cr3"))
         (modules '((guix build utils)))
         (snippet
-         '(begin (delete-file-recursively "src/zlib") #t))))
+         '(begin (delete-file-recursively "src/zlib")
+                 (delete-file-recursively "src/zlib-ng")
+                 #t))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
         ;; Build dependencies:
         ("rust-cc" ,rust-cc-1)
+        ("rust-cmake" ,rust-cmake-0.1)
         ("rust-pkg-config" ,rust-pkg-config-0.3)
         ("rust-vcpkg" ,rust-vcpkg-0.2))))
     (native-inputs
@@ -12830,7 +12907,7 @@ pairs in insertion order.")
 (define-public rust-libssh2-sys-0.2
   (package
     (name "rust-libssh2-sys")
-    (version "0.2.14")
+    (version "0.2.19")
     (source
       (origin
         (method url-fetch)
@@ -12838,7 +12915,7 @@ pairs in insertion order.")
         (file-name (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-          "042gsgbvxgm5by4mk906j3zm4qdvzcfhjxrb55is1lrr6f0nxain"))
+          "0mkhw4pksbz7gldj8hia7k6npc479n1x09i8r0pm275sac424ina"))
         (modules '((guix build utils)))
         (snippet
          '(begin (delete-file-recursively "libssh2") #t))))
@@ -12846,7 +12923,7 @@ pairs in insertion order.")
     (arguments
      `(#:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
-        ("rust-libz-sys" ,rust-libz-sys-1.0)
+        ("rust-libz-sys" ,rust-libz-sys-1)
         ("rust-openssl-sys" ,rust-openssl-sys-0.9)
         ;; Build dependencies:
         ("rust-cc" ,rust-cc-1)
@@ -16008,21 +16085,21 @@ system for OpenSSL.")
 (define-public rust-openssl-sys-0.9
   (package
     (name "rust-openssl-sys")
-    (version "0.9.53")
+    (version "0.9.58")
     (source
       (origin
         (method url-fetch)
         (uri (crate-uri "openssl-sys" version))
         (file-name (string-append name "-" version ".tar.gz"))
         (sha256
-         (base32 "0vvk8vzrc73y8n5rf4yj3x8ygyxjaz7wxrbxiwqi7qy0gyp1cpa6"))
+         (base32 "1pkq3x8w16kqvkg75g4w7nny56w9clssww0ibpzg015n153xnhm8"))
         (patches (search-patches "rust-openssl-sys-no-vendor.patch"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
         ;; Build dependencies:
-        ("rust-autocfg" ,rust-autocfg-0.1)
+        ("rust-autocfg" ,rust-autocfg-1.0)
         ("rust-cc" ,rust-cc-1)
         ("rust-pkg-config" ,rust-pkg-config-0.3)
         ("rust-vcpkg" ,rust-vcpkg-0.2))
@@ -17040,7 +17117,7 @@ in pure Rust.")
 (define-public rust-pcre2-sys-0.2
   (package
     (name "rust-pcre2-sys")
-    (version "0.2.2")
+    (version "0.2.5")
     (source
      (origin
        (method url-fetch)
@@ -17049,7 +17126,7 @@ in pure Rust.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0nwdvc43dkb89qmm5q8gw1zyll0wsfqw7kczpn23mljra3874v47"))
+         "08mp6yxrvadplwd0drdydzskvzapr6dri9fyy7xvhzn3krg0xhyy"))
        (modules '((guix build utils)))
        (snippet
         '(begin (delete-file-recursively "pcre2") #t))))

gnu/packages/crypto.scm

@@ -518,7 +518,7 @@ user's graphical desktop.")
 (define-public scrypt
   (package
     (name "scrypt")
-    (version "1.2.1")
+    (version "1.3.1")
     (source
       (origin
         (method url-fetch)
@@ -526,20 +526,24 @@ user's graphical desktop.")
                             version ".tgz"))
         (sha256
          (base32
-          "0xy5yhrwwv13skv9im9vm76rybh9f29j2dh4hlh2x01gvbkza8a6"))))
+          "1hnl0r6pmyxiy4dmafmqk1db7wpc0x9rqpzqcwr9d2cmghcj6byz"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:phases (modify-phases %standard-phases
+     `(#:license-file-regexp "COPYRIGHT"
-        (add-after 'unpack 'patch-command-invocations
+       #:phases (modify-phases %standard-phases
+        (add-after 'unpack 'patch-$PATH-assumptions
           (lambda _
+            (substitute* "configure"
+              (("\\{POSIX_PATH\\}")
+               "{PATH}"))
             (substitute* "Makefile.in"
               (("command -p") ""))
             #t))
         (add-after 'install 'install-docs
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref %outputs "out"))
-                   (misc (string-append out "/share/doc/scrypt")))
+                   (doc (string-append out "/share/doc/" ,name "-" ,version)))
-              (install-file "FORMAT" misc)
+              (install-file "FORMAT" doc)
               #t))))))
     (inputs
      `(("openssl" ,openssl)))
@@ -765,7 +769,7 @@ data on your platform, so the seed itself will be as random as possible.
                      "libdir=" out "/lib\n"
                      "includedir=" out "/include\n\n"
                      "Name: libcrypto++-" ,version "\n"
-                     "Description: Class library of cryptographic schemes"
+                     "Description: Class library of cryptographic schemes\n"
                      "Version: " ,version "\n"
                      "Libs: -L${libdir} -lcryptopp\n"
                      "Cflags: -I${includedir}\n"))
@@ -1057,6 +1061,58 @@ Features:
       (home-page "https://github.com/bitcoin-core/secp256k1")
       (license license:unlicense))))
 
+(define-public libsecp256k1-bitcoin-cash
+  (package
+    (name "libsecp256k1-bitcoin-cash")
+    (version "0.22.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Bitcoin-ABC/secp256k1")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1rnif3iny6pz1r3g69bagzr342mm3x0v66b60csnmm1rg44bd5v1"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (arguments
+     '(#:configure-flags '("--enable-module-recovery"
+                           "--enable-experimental"
+                           "--enable-module-ecdh"
+                           "--disable-jni"
+                           "--with-bignum=no"
+                           "--enable-module-schnorr"
+                           "--disable-static"
+                           "--enable-shared")))
+    (synopsis "Optimized C library for EC operations on curve secp256k1")
+    (description
+     "Optimized C library for cryptographic operations on curve secp256k1.
+
+This library is used for consensus critical cryptographic operations on the
+Bitcoin Cash network.
+
+Features:
+
+@itemize
+@item secp256k1 ECDSA signing/verification and key generation.
+@item secp256k1 Schnorr signing/verification (Bitcoin Cash Schnorr variant).
+@item Additive and multiplicative tweaking of secret/public keys.
+@item Serialization/parsing of secret keys, public keys, signatures.
+@item Constant time, constant memory access signing and pubkey generation.
+@item Derandomized ECDSA (via RFC6979 or with a caller provided function).
+@item Very efficient implementation.
+@item Suitable for embedded systems.
+@item Optional module for public key recovery.
+@item Optional module for ECDH key exchange (experimental).
+@item Optional module for multiset hash (experimental).
+@end itemize\n")
+    (home-page "https://github.com/Bitcoin-ABC/secp256k1")
+    (license license:expat)))
+
 (define-public stoken
   (package
     (name "stoken")

gnu/packages/datastructures.scm

@@ -2,7 +2,7 @@
 ;;; Copyright © 2015, 2016, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
-;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2020 Mark H Weaver <mhw@netris.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -236,14 +236,34 @@ to the structure and choosing one or more fields to act as the key.")
                           "0m542xpys54bni29zibgrfpgpd0zgyny4h131virxsanixsbz52z")))))))
     (build-system cmake-build-system)
     (arguments
-     '(#:phases
+     `(#:phases
        (modify-phases %standard-phases
          (add-after 'install 'install-static-library
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((out (assoc-ref outputs "out")))
                (copy-file "lib/libsdsl_static.a"
                           (string-append out "/lib/libsdsl.a")))
-             #t)))))
+             #t))
+        (add-after 'install 'install-pkgconfig-file
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let* ((out (assoc-ref outputs "out"))
+                   (lib (string-append out "/lib")))
+              (mkdir-p (string-append lib "/pkgconfig"))
+              (with-output-to-file (string-append lib "/pkgconfig/sdsl-lite.pc")
+                (lambda _
+                  (format #t "prefix=~a~@
+                          exec_prefix=${prefix}~@
+                          libdir=${exec_prefix}/lib~@
+                          includedir=${prefix}/include~@
+                          ~@
+                          ~@
+                          Name: sdsl~@
+                          Version: ~a~@
+                          Description: SDSL: Succinct Data Structure Library~@
+                          Libs: -L${libdir} -lsdsl -ldivsufsort -ldivsufsort64~@
+                          Cflags: -I${includedir}~%"
+                          out ,version)))
+              #t))))))
     (native-inputs
      `(("libdivsufsort" ,libdivsufsort)))
     (home-page "https://github.com/simongog/sdsl-lite")

gnu/packages/dav.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2015, 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -23,29 +24,45 @@
   #:use-module (guix download)
   #:use-module (guix licenses)
   #:use-module (guix packages)
+  #:use-module (guix git-download)
   #:use-module (gnu packages)
   #:use-module (gnu packages check)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-check)
+  #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
-  #:use-module (gnu packages sphinx))
+  #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages time)
+  #:use-module (gnu packages xml))
 
 (define-public radicale
   (package
     (name "radicale")
-    (version "1.1.6")
+    (version "3.0.4")
-    (source (origin
+    (source
-             (method url-fetch)
+     (origin
-             (uri (pypi-uri "Radicale" version))
+       ;; There are no tests in the PyPI tarball.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Kozea/Radicale")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-              (base32
+        (base32 "0hj9mmhrj32mzhxlnjcfijb7768cyjsn603nalp54clgb2gkmvw8"))))
-               "0ay90nj6fmr2aq8imi0mbjl4m2rzq7a83ikj8qs9gxsylj71j1y0"))))
     (build-system python-build-system)
-    (arguments
+    (native-inputs
-     '(#:tests? #f)) ; The tests are not distributed in the PyPi release.
+     `(("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-flake8" ,python-pytest-flake8)
+       ("python-pytest-isort" ,python-pytest-isort)
+       ("python-pytest-runner" ,python-pytest-runner)
+       ("python-waitress" ,python-waitress)))
     (propagated-inputs
-      ;; TODO: Add python-pam
+     `(("python-dateutil" ,python-dateutil)
-     `(("python-requests" ,python-requests)))
+       ("python-defusedxml" ,python-defusedxml)
+       ("python-passlib" ,python-passlib)
+       ("python-vobject" ,python-vobject)))
     (synopsis "Basic CalDAV and CardDAV server")
     (description "Radicale is a CalDAV and CardDAV server for UNIX-like
 platforms.  Calendars and address books are available for both local and remote
@@ -58,6 +75,44 @@ clients.")
     (home-page "https://radicale.org/")
     (license gpl3+)))
 
+(define-public xandikos
+  (package
+    (name "xandikos")
+    (version "0.2.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "xandikos" version))
+       (sha256
+        (base32 "13ikmcja9p42azb5ccqj2bw98zybna6zlflj10hqy0kvbib70l94"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-aiohttp" ,python-aiohttp)
+       ("python-defusedxml" ,python-defusedxml)
+       ("python-dulwich" ,python-dulwich)
+       ("python-icalendar" ,python-icalendar)
+       ("python-jinja2" ,python-jinja2)
+       ("python-multidict" ,python-multidict)))
+    (home-page "https://www.xandikos.org/")
+    (synopsis "Lightweight CalDAV/CardDAV server")
+    (description
+     "Xandikos is a lightweight yet complete CardDAV/CalDAV server that backs
+onto a Git repository.
+
+Features:
+
+@itemize
+@item Easy to set up
+@item Share calendars (events, todo items, journal entries) via CalDAV and
+contacts (vCard) via CardDAV
+@item Automatically keep history and back up changes in Git
+@item Supports synchronization extensions for CalDAV/CardDAV for quick and
+efficient syncing
+@item Automatically keep history and back up
+@item Works with all tested CalDAV and CardDAV clients
+@end itemize")
+    (license gpl3+)))
+
 (define-public vdirsyncer
   (package
     (name "vdirsyncer")

gnu/packages/debian.scm

@@ -202,7 +202,7 @@ unpacking them into a directory which can eventually be chrooted into.")
 (define-public debianutils
   (package
     (name "debianutils")
-    (version "4.11")
+    (version "4.11.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -211,7 +211,7 @@ unpacking them into a directory which can eventually be chrooted into.")
               (file-name (git-file-name "debianutils" version))
               (sha256
                (base32
-                "1fmhzvymajack7kh8g4qjbwd9mq85z6rxl1psd1sm67s5695i9rc"))))
+                "18ypb7fivch53wwrdf73yhf1fhkwn9kvw1kfdc1m450241d6191w"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases

gnu/packages/disk.scm

@@ -689,7 +689,7 @@ passphrases.")
 (define-public ndctl
   (package
     (name "ndctl")
-    (version "68")
+    (version "69")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -698,7 +698,7 @@ passphrases.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0xmim7z4qp6x2ggndnbwd940c73pa1qlf3hxyn3qh5pyr69nh9y8"))))
+                "1l7p0ycj27d4z07gf9qp796xpg16kfsg3rwx6plhilbhip1as4w7"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("asciidoc" ,asciidoc)

gnu/packages/dns.scm

@@ -803,14 +803,14 @@ Extensions} (DNSSEC).")
 (define-public knot
   (package
     (name "knot")
-    (version "2.9.5")
+    (version "2.9.6")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://secure.nic.cz/files/knot-dns/"
                            "knot-" version ".tar.xz"))
        (sha256
-        (base32 "0xmzmhd2m9rb24clrrd9k058harsq67nyjplpbyxvy1g46xah28i"))
+        (base32 "1rxjjisr6rz1wa4279ghvj5zzhgyjhncmb9dkzqm8nw2qs1jhx5z"))
        (modules '((guix build utils)))
        (snippet
         '(begin

gnu/packages/docker.scm

@@ -50,9 +50,9 @@
 
 (define %docker-version "19.03.12")
 
-(define-public python-docker-py
+(define-public python-docker
   (package
-    (name "python-docker-py")
+    (name "python-docker")
     (version "3.7.3")
     (source
      (origin
@@ -116,7 +116,7 @@ client.")
     (inputs
      `(("python-cached-property"
         ,python-cached-property)
-       ("python-docker-py" ,python-docker-py)
+       ("python-docker" ,python-docker)
        ("python-dockerpty" ,python-dockerpty)
        ("python-docopt" ,python-docopt)
        ("python-jsonschema" ,python-jsonschema)

gnu/packages/dunst.scm

@@ -36,7 +36,7 @@
 (define-public dunst
   (package
     (name "dunst")
-    (version "1.4.1")
+    (version "1.5.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -45,7 +45,7 @@
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0xjj1f2jr1ja5grj6wrx5jjz1sx5fpqnvkw7nqi4452j3nc4p4l2"))))
+                "0irwkqcgwkqaylcpvqgh25gn2ysbdm2kydipxfzcq1ddj9ns6f9c"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f                      ; no check target

gnu/packages/ebook.scm

@@ -246,6 +246,29 @@
                                           (assoc-ref inputs "js-mathjax")
                                           "/share/javascript/mathjax"))
              (invoke "python2" "setup.py" "rapydscript")))
+         (replace 'wrap
+           ;; Here we wrap PYTHONPATH exactly as it would be in
+           ;; python-build-system, plus the addition of
+           ;; QTWEBENGINEPROCESS_PATH, fixing a bug where Calibre would not
+           ;; find Qtwebengine.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (python (assoc-ref inputs "python"))
+                    (site-packages
+                     (cons (string-append out "/lib/python"
+                                          (python-version python)
+                                          "/site-packages")
+                           (search-path-as-string->list (getenv "PYTHONPATH"))))
+                    (qtwebengineprocess
+                     (string-append (assoc-ref inputs "qtwebengine")
+                                    "/lib/qt5/libexec/QtWebEngineProcess")))
+               (for-each (lambda (program)
+                           (wrap-program program
+                                 `("QTWEBENGINEPROCESS_PATH" = (,qtwebengineprocess))
+                                 `("PYTHONPATH" prefix ,site-packages)))
+                         (find-files bin ".")))
+             #t))
          (add-after 'install 'install-man-pages
            (lambda* (#:key outputs #:allow-other-keys)
              (copy-recursively

gnu/packages/education.scm

@@ -8,6 +8,7 @@
 ;;; Copyright © 2020 Robert Smith <robertsmith@posteo.net>
 ;;; Copyright © 2020 Guy Fleury Iteriteka <gfleury@disroot.org>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
+;;; Copyright © 2020 Prafulla Giri <pratheblackdiamond@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -486,7 +487,7 @@ specialized device.")
                             Comment[ca]=Conjunt de jocs educatius per a xiquets~@
                             Comment[es]=Conjunto de juegos educativos para niños~@
                             Comment[de]=Sammlung mit lehrreichen Spielen für kleine Kinder~@
-                            Exec=~a/bin/childsplay.py~@
+                            Exec=~a/bin/childsplay~@
                             Terminal=false~@
                             Icon=logo_cp.svg~@
                             Type=Application~@
@@ -612,14 +613,14 @@ Portuguese, Spanish and Italian.")
 (define-public fet
   (package
     (name "fet")
-    (version "5.46.0")
+    (version "5.46.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.lalescu.ro/liviu/fet/download/"
                            "fet-" version ".tar.bz2"))
        (sha256
-        (base32 "1vcsm12lqf84mz9ppw2knjyv5ss2ws0dblbp418hll91dry7m49a"))))
+        (base32 "1sakzizjsyjn6705zl283i81zxn1gxskg2i4jv7iq75vw3nzm6kv"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/emacs-xyz.scm

@@ -118,6 +118,7 @@
   #:use-module (gnu packages curl)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages dictionaries)
+  #:use-module (gnu packages djvu)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages gtk)
@@ -175,6 +176,7 @@
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages shells)
   #:use-module (gnu packages sqlite)
+  #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages video)
   #:use-module (gnu packages haskell-xyz)
@@ -681,6 +683,30 @@ Alternatively the menu can be bound globally, for example:
 @code{(global-set-key [S-down-mouse-3] 'minions-minor-modes-menu)}.")
     (license license:gpl3+)))
 
+(define-public emacs-moody
+  (package
+    (name "emacs-moody")
+    (version "0.5.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/tarsius/moody")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1xyw4l42053595r76lj8safsx6pj25as0107wd96by3h7dg9m586"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/tarsius/moody")
+    (synopsis "Tabs and ribbons for Emacs mode-line")
+    (description
+     "@code{emacs-moody} provides utilities for displaying elements of
+the mode line as tabs and ribbons.  It also provides replacements for a few
+built-in elements.  The biggest difference to similar packages is that
+this one is much simpler and much more consistent.  When using this package,
+then only the color of the mode line changes when a window becomes in-/active.")
+    (license license:gpl3+)))
+
 (define-public emacs-treepy
   (package
     (name "emacs-treepy")
@@ -959,8 +985,13 @@ replacement.")
            ;; native input.
            (lambda _
              (with-directory-excursion "tests"
+               ;; File `haskell-indent-tests.el' fails with
+               ;; `haskell-indent-put-region-in-literate-2'
+               ;; on Emacs 27.1+
+               ;; XXX: https://github.com/haskell/haskell-mode/issues/1714
                (for-each delete-file
-                         '("haskell-customize-tests.el"
+                         '("haskell-indent-tests.el"
+                           "haskell-customize-tests.el"
                            "inferior-haskell-tests.el")))
              #t))
          (replace 'install
@@ -1307,8 +1338,6 @@ regexp-like arguments to @code{skip-chars-forward} and
           (base32
            "134fj493sdn93pyyac8rpz1fzahzmayvphsrmqp3wvgysmfqm38l"))))
       (build-system emacs-build-system)
-      (propagated-inputs
-       `(("emacs-seq" ,emacs-seq)))
       (home-page "https://github.com/Malabarba/elisp-bug-hunter")
       (synopsis "Hunt down errors by bisecting elisp files")
       (description
@@ -1909,6 +1938,21 @@ as a library for other Emacs packages.")
        #:exclude '("^tests/" "^latex/README")
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'configure
+           (lambda* (#:key inputs #:allow-other-keys)
+             (emacs-substitute-variables "preview.el"
+               ("preview-gs-command"
+                (string-append (assoc-ref inputs "ghostscript") "/bin/gs")))
+             (substitute* "preview.el"
+               (("\"dvipng ")
+                (string-append "\"" (assoc-ref inputs "texlive")
+                               "/bin/dvipng "))
+               (("\"dvips ")
+                (string-append "\"" (assoc-ref inputs "texlive")
+                               "/bin/dvips "))
+               (("\"pdf2dsc ")
+                (string-append "\"" (assoc-ref inputs "ghostscript")
+                               "/bin/pdf2dsc ")))))
          (add-after 'install 'install-doc
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -1923,7 +1967,8 @@ as a library for other Emacs packages.")
     (native-inputs
      `(("perl" ,perl)))
     (inputs
-     `(("texlive" ,(texlive-union (list texlive-amsfonts)))))
+     `(("ghostscript" ,ghostscript)
+       ("texlive" ,(texlive-union (list texlive-amsfonts)))))
     (home-page "https://www.gnu.org/software/auctex/")
     (synopsis "Integrated environment for TeX")
     (description
@@ -2058,7 +2103,7 @@ Lock key.")
 (define-public emacs-chronometrist
   (package
     (name "emacs-chronometrist")
-    (version "0.5.3")
+    (version "0.5.5")
     (source
      (origin
        (method git-fetch)
@@ -2067,7 +2112,7 @@ Lock key.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0jz35972m372kx9x8mgf42zhzdw2w9wv2ri52chfb2fin4bh1biy"))))
+        (base32 "1zccyfpgq68ixrcl8jq2r38165ngkqrb42y2hkyab6gxhvh4wkpl"))))
     (build-system emacs-build-system)
     (arguments
      `(#:phases
@@ -2091,7 +2136,8 @@ Lock key.")
                                   (find-files "." "\\.md$")))))
              #t)))))
     (propagated-inputs
-     `(("emacs-dash" ,emacs-dash)
+     `(("emacs-anaphora" ,emacs-anaphora)
+       ("emacs-dash" ,emacs-dash)
        ("emacs-s" ,emacs-s)
        ("emacs-ts" ,emacs-ts)))
     (home-page "https://github.com/contrapunctus-1/chronometrist")
@@ -2113,7 +2159,7 @@ Its features are:
 (define-public emacs-direnv
   (package
     (name "emacs-direnv")
-    (version "2.0.0")
+    (version "2.1.0")
     (source
      (origin
        (method git-fetch)
@@ -2122,8 +2168,7 @@ Its features are:
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32
+        (base32 "0xkqn4604k2imas6azy1www56br8ls4iv9a44pxcd8h94j1fp44d"))))
-         "005ibyzsx1fdyrl5iyhqpb1bg83mphzahq7zvw58x00syyqi2z49"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("dash" ,emacs-dash)
@@ -2435,13 +2480,30 @@ filters, new key bindings and faces.  It can be enabled by
        (sha256
         (base32 "0njgyx09q225hliacsnjk8wallg5i6xkz6bj501pb05nwqfbvfk7"))))
     (build-system emacs-build-system)
+    (inputs `(("djview" ,djview)
+              ("djvulibre" ,djvulibre)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'configure
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((file "djvu.el")
+                   (djview (assoc-ref inputs "djview"))
+                   (djvulibre (assoc-ref inputs "djvulibre")))
+               ;; Specify the absolute executable locations.
+               (chmod file #o644)
+               (substitute* file
+                 (("\"djvused\"") (string-append "\"" djvulibre "/bin/djvused\""))
+                 (("\"djvm\"") (string-append "\"" djvulibre "/bin/djvm\""))
+                 (("\"ddjvu\"") (string-append "\"" djvulibre "/bin/ddjvu\"")))
+               (emacs-substitute-variables file
+                 ("djvu-djview-command" (string-append djview "/bin/djview"))))
+             #t)))))
     (home-page "http://elpa.gnu.org/packages/djvu.html")
     (synopsis "Edit and view Djvu files via djvused")
     (description
      "This package is a front end for the command-line program djvused from
-DjVuLibre, see @url{http://djvu.sourceforge.net/}.  It assumes you have the
+DjVuLibre, see @url{http://djvu.sourceforge.net/}.")
-programs @command{djvused}, @command{djview}, @command{ddjvu}, and
-@command{djvm} installed.")
     (license license:gpl3+)))
 
 (define-public emacs-pabbrev
@@ -2469,18 +2531,22 @@ during idle time, while Emacs is doing nothing else.")
     (license license:gpl3+)))
 
 (define-public emacs-pdf-tools
+  ;; XXX: Development branch fixes an incompatibility with Emacs 27+.  See
+  ;; <https://github.com/politza/pdf-tools/issues/616>.
+  (let ((commit "c510442ab89c8a9e9881230eeb364f4663f59e76")
+        (revision "1"))
     (package
       (name "emacs-pdf-tools")
-    (version "0.90")
+      (version (git-version "0.90" revision commit))
-    (home-page "https://github.com/politza/pdf-tools")
+      (source
-    (source (origin
+       (origin
          (method git-fetch)
-              (uri (git-reference (url home-page)
+         (uri (git-reference
-                                  (commit (string-append "v" version))))
+               (url "https://github.com/politza/pdf-tools")
+               (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-               (base32
+          (base32 "17z3cpn76g9dp62drjrgrqpp1bgf4gl5k5gspylskpvd4kj4bq4d"))))
-                "0iv2g5kd14zk3r5dzdw7b7hk4b5w7qpbilcqkja46jgxbb6xnpl9"))))
       (build-system gnu-build-system)
       (arguments
        `(#:tests? #f                    ; there are no tests
@@ -2524,23 +2590,27 @@ during idle time, while Emacs is doing nothing else.")
              (assoc-ref emacs:%standard-phases 'build))
            (add-after 'emacs-install 'emacs-make-autoloads
              (assoc-ref emacs:%standard-phases 'make-autoloads)))))
-    (native-inputs `(("autoconf" ,autoconf)
+      (native-inputs
+       `(("autoconf" ,autoconf)
          ("automake" ,automake)
          ("pkg-config" ,pkg-config)
          ("emacs" ,emacs-minimal)))
-    (inputs `(("poppler" ,poppler)
+      (inputs
+       `(("poppler" ,poppler)
          ("cairo" ,cairo)
          ("glib" ,glib)
          ("libpng" ,libpng)
          ("zlib" ,zlib)))
-    (propagated-inputs `(("tablist" ,emacs-tablist)))
+      (propagated-inputs
+       `(("tablist" ,emacs-tablist)))
+      (home-page "https://github.com/politza/pdf-tools")
       (synopsis "Emacs support library for PDF files")
       (description
        "PDF Tools is, among other things, a replacement of DocView for PDF
 files.  The key difference is that pages are not pre-rendered by
 e.g. ghostscript and stored in the file-system, but rather created on-demand
 and stored in memory.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-dash
   (package
@@ -2989,7 +3059,7 @@ files and directories.")
 (define-public emacs-fountain-mode
   (package
     (name "emacs-fountain-mode")
-    (version "3.1.0")
+    (version "3.2.2")
     (source
      (origin
        (method git-fetch)
@@ -2998,7 +3068,7 @@ files and directories.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "08giwg0jwk8zzj2i4cm08322qr6znrnv9a49za7c6j47bykpwj6s"))))
+        (base32 "0rwdwbw9cq8ljvbmgmz9izank8dqjki79l1bw127lli69fs72gyi"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/rnkn/fountain-mode")
     (synopsis "Major mode for screenwriting in Fountain markup")
@@ -3188,6 +3258,29 @@ project.
 This package also includes relevant snippets for yasnippet.")
       (license license:expat))))
 
+(define-public emacs-gdscript-mode
+  (package
+    (name "emacs-gdscript-mode")
+    (version "1.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/godotengine/emacs-gdscript-mode")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "02by4bvdayldbjlz6jkp36m5rgcy2h5bwhqx2cj7wma6xf6cw3lf"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/godotengine/emacs-gdscript-mode")
+    (synopsis "GDScript support and syntax highlighting in Emacs")
+    (description
+     "This package adds support for the GDScript programming language from the
+Godot game engine in Emacs. It features all the essentials, e.g., syntax
+highlighting, code folding, indentation, automatic pairing, auto-completion,
+and code formatting.")
+    (license license:gpl3+)))
+
 (define-public emacs-el-mock
   (package
     (name "emacs-el-mock")
@@ -3338,8 +3431,9 @@ keep pressing the key until it selects what you want.  There's also
          ;; byte-compilation is finished
          #:parallel-tests? #f))
       (home-page "https://github.com/lastquestion/explain-pause-mode")
-      (synopsis "Provides a top like interface to determine why Emacs paused")
+      (synopsis "Top-like interface to determine why Emacs paused")
-      (description "Monitors Emacs function calls and records their execution
+      (description
+       "This package monitors Emacs function calls and records their execution
 time.  This information can be reviewed to determine what is causing the user
 interface to pause.")
       (license license:gpl3+))))
@@ -3501,7 +3595,6 @@ IRC bouncer with ERC.")
          (sha256
           (base32 "1hwlhzgx03z8891sblz56zdp8zj0izh72kxykgcnz5rrkyc3vfi3"))))
       (build-system emacs-build-system)
-      (propagated-inputs `(("emacs-seq" ,emacs-seq)))
       (home-page "https://github.com/drewbarbs/erc-status-sidebar")
       (synopsis "Hexchat-like activity overview for ERC channels")
       (description
@@ -6460,7 +6553,7 @@ regexp that matches all known keywords.")
 (define-public emacs-perspective
   (package
     (name "emacs-perspective")
-    (version "2.10")
+    (version "2.11")
     (source
      (origin
        (method git-fetch)
@@ -6470,7 +6563,7 @@ regexp that matches all known keywords.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1xfcm69nd6f9chwlqfz5vd8nnyl5mwharxjrn1m515568dqrk62x"))))
+         "0nka5z6226r174ligja023qx2bb1pfyjbanafxprbyxkr17b2794"))))
     (build-system emacs-build-system)
     (arguments
      `(#:tests? #t
@@ -7183,7 +7276,17 @@ allowing unprefixed keys to insert their respective characters as expected.")
        ("emacs-s" ,emacs-s)))
     (arguments
      `(#:tests? #t
-       #:test-command '("buttercup")))
+       #:test-command '("buttercup")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'fix-tests
+           ;; See: https://github.com/clojure-emacs/clojure-mode/issues/568
+           (lambda _
+             (substitute* "clojure-mode.el"
+               (("\\(list \\(cdr project\\)\\)" line)
+                (string-append "\"Return the list of directory roots of the PROJECT.\"\n"
+                               line)))
+             #t)))))
     (home-page "https://github.com/clojure-emacs/clojure-mode")
     (synopsis "Major mode for Clojure code")
     (description
@@ -7510,18 +7613,20 @@ to all the other commands, too.")
     (license license:gpl3+)))
 
 (define-public emacs-js2-mode
+  (let ((commit "40aab27581279d0fdbfeb9afeb85f39d401a927f")
+        (revision "1"))
     (package
       (name "emacs-js2-mode")
-    (version "20190219")
+      (version (git-version "20190219" revision commit))
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
                (url "https://github.com/mooz/js2-mode")
-             (commit version)))
+               (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-        (base32 "0766bbr4piia9vfr4ivd2gwi8dxah654adv6h28ylz4q8xmfzm1b"))))
+          (base32 "0ysd0ji3vvk2zpjcg1wl7b2hva8471vq0ypib4h6spnpjdr43vzk"))))
       (build-system emacs-build-system)
       (arguments
        `(#:tests? #t
@@ -7534,7 +7639,7 @@ advanced than the built-in javascript-mode.  Features include accurate syntax
 highlighting using a recursive-descent parser, on-the-fly reporting of syntax
 errors and strict-mode warnings, smart line-wrapping within comments and
 strings, and code folding.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-nodejs-repl
   (package
@@ -8449,7 +8554,7 @@ ack, ag, helm and pt.")
 (define-public emacs-helm
   (package
     (name "emacs-helm")
-    (version "3.6.4")
+    (version "3.6.5")
     (source
      (origin
        (method git-fetch)
@@ -8458,7 +8563,7 @@ ack, ag, helm and pt.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0cl5awhq5py872qx9s30sfgfpfwjivwbsi18mgar8lj6lvs4s8zz"))))
+        (base32 "0yzpb84346v42ig4h0rsnvzmln58ilhc0gsq0ggc7038ypqkdw4d"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-async" ,emacs-async)
@@ -8679,7 +8784,7 @@ target will call @code{compile} on it.")
 (define-public emacs-cider
   (package
     (name "emacs-cider")
-    (version "0.26.0")
+    (version "0.26.1")
     (source
      (origin
        (method git-fetch)
@@ -8688,7 +8793,7 @@ target will call @code{compile} on it.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1qwizvmm9ln75ph1jg2rfqv3hd9p4zaz8kp2i6yr3vq99c3a00i7"))))
+        (base32 "0m77jbxl380dp1wyj12m82bb06r80js8yxl530ryp1mwvy74f00d"))))
     (build-system emacs-build-system)
     (arguments
      '(#:exclude                        ;don't exclude 'cider-test.el'
@@ -8719,9 +8824,9 @@ CIDER).")
 ;; There hasn't been a tag or release since 2016, so we take the latest
 ;; commit.
 (define-public emacs-sly
-  (let ((commit "6a2f543cb21f14104c2253af5a1427b884a987ae")
+  (let ((commit "8e22c1f62667434ec1acd1e0c6b7ec1c22dc0958")
         ;; Update together with sbcl-slynk-boot0.
-        (revision "5"))
+        (revision "6"))
     (package
       (name "emacs-sly")
       (version (git-version "1.0.0" revision commit))
@@ -8734,7 +8839,7 @@ CIDER).")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "0wbpg9p9yg2hd62l15pvy50fk3hndq5zzyqlyyf04g368s895144"))))
+           "09wyqixsn7k889i54amf8bwjg6iyirp89xmcrgfwal010kh1ixcl"))))
       (build-system emacs-build-system)
       (native-inputs
        `(("texinfo" ,texinfo)))
@@ -8890,8 +8995,8 @@ file.")
       (license license:gpl3+))))
 
 (define-public emacs-sly-macrostep
-  (let ((commit "be2d24545092d164be1a91031d8881afd29c9ec0")
+  (let ((commit "5113e4e926cd752b1d0bcc1508b3ebad5def5fad")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "emacs-sly-macrostep")
       (version (git-version "0.1" revision commit))
@@ -8905,7 +9010,7 @@ file.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "0v8m3zkccpqd2l8m9340y672l2mm3mrry8422nva5kfvpcwdayqb"))))
+           "1nxf28gn4f3n0wnv7nb5sgl36fz175y470zs9hig4kq8cp0yal0r"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-sly" ,emacs-sly)
@@ -9572,13 +9677,13 @@ passive voice.")
     (name "emacs-org")
     ;; emacs-org-contrib inherits from this package.  Please update it as
     ;; well.
-    (version "9.3.6")
+    (version "9.3.8")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/org-" version ".tar"))
        (sha256
-        (base32 "0jwpgfzjvf1hd3mx582pw86hysdryaqzp69hk6azi9kmq4bzk87d"))))
+        (base32 "1az00pi9rw3ibx4061jyqr6ll27kvs99yvd7nk5dckjh0ajd0gni"))))
     (build-system emacs-build-system)
     (arguments
      `(#:phases
@@ -9603,14 +9708,14 @@ programming and reproducible research.")
   (package
     (inherit emacs-org)
     (name "emacs-org-contrib")
-    (version "20200213")
+    (version "20200907")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://orgmode.org/elpa/"
                            "org-plus-contrib-" version ".tar"))
        (sha256
-        (base32 "0g6rrrwplrifz4ip0jg638m4kvpvdg03hwnyghd813w0lm935mh5"))))
+        (base32 "1rgk3pwhsmbmwlncg60ahwrrkm1ks4xpwy2wzv9q7myl1aihjj54"))))
     (arguments
      `(#:modules ((guix build emacs-build-system)
                   (guix build utils)
@@ -9646,6 +9751,29 @@ lists, and project planning with a fast and effective plain-text system.
 This package is equivalent to org-plus-contrib, but only includes additional
 files that you would find in @file{contrib/} from the git repository.")))
 
+(define-public emacs-org-edna
+  (package
+    (name "emacs-org-edna")
+    (version "1.1.2")
+    (source (origin
+              (method bzr-fetch)
+              (uri (bzr-reference
+                    (url "bzr://bzr.savannah.nongnu.org/org-edna-el")
+                    (revision version)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "01dblddgx0yid5hrgl4swbr4grhv057kfbdy122wihzqpsrgq86n"))))
+    (build-system emacs-build-system)
+    (home-page "https://savannah.nongnu.org/projects/org-edna-el/")
+    (synopsis "Manage Org task dependencies")
+    (description "This package provides an extensible means of specifying
+conditions which must be fulfilled before a task can be completed and actions
+to take once it is.  Org Edna runs when either the BLOCKER or TRIGGER
+properties are set on a heading, and when it is changing from a TODO state to
+a DONE state.")
+    (license license:gpl3+)))
+
 (define-public emacs-flx
   (package
     (name "emacs-flx")
@@ -11864,7 +11992,7 @@ or @code{treemacs}, but leveraging @code{Dired} to do the job of display.")
 (define-public emacs-which-key
   (package
     (name "emacs-which-key")
-    (version "3.4.0")
+    (version "3.5.0")
     (source
      (origin
        (method git-fetch)
@@ -11873,7 +12001,7 @@ or @code{treemacs}, but leveraging @code{Dired} to do the job of display.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1ahgb7dqdc75farkl0fg0a6hvx2067gdvjq99cd3z2dz56km0p05"))))
+        (base32 "13lgjsm9pwgjsxg7lzc1c9sw2bzssxikfj6grnshqfll8kz8yr4r"))))
     (build-system emacs-build-system)
     (arguments
      `(#:tests? #t
@@ -12453,14 +12581,14 @@ write applications that use WebSockets, and is not useful by itself.")
 (define-public emacs-oauth2
   (package
     (name "emacs-oauth2")
-    (version "0.13")
+    (version "0.15")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/"
                            "oauth2-" version ".el"))
        (sha256
-        (base32 "0y5nbdwxz2hfr09xgsqgyv60vgx0rsaisibcpkz00klvgg26w33r"))))
+        (base32 "0ij17g6i8d4cyzc8v6sy2qglwhzd767331gavll6d507krdh3ca3"))))
     (build-system emacs-build-system)
     (home-page "https://elpa.gnu.org/packages/oauth2.html")
     (synopsis "OAuth 2.0 authorization protocol implementation")
@@ -12474,6 +12602,28 @@ needs to be refreshed, the code handles it automatically and stores the new
 value of the access token.")
     (license license:gpl3+)))
 
+(define-public emacs-auth-source-xoauth2
+  (package
+    (name "emacs-auth-source-xoauth2")
+    (version "1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ccrusius/auth-source-xoauth2")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0nl859csl8xcd6ybpjj15ph8l8fxwkwf45kbylss68alkyf1rl3v"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/ccrusius/auth-source-xoauth2")
+    (synopsis "XOAuth2 authentication capabilities for Emacs auth-source")
+    (description
+     "This package adds XOAuth2 authentication capabilities to Emacs
+auth-source.  This integration requires some preliminary work on the users’
+part, which includes creating tokens.")
+    (license license:asl2.0)))
+
 (define-public emacs-circe
   (package
     (name "emacs-circe")
@@ -13521,8 +13671,7 @@ and can be consulted and modified.")
          ("emacs-dash" ,emacs-dash)
          ("emacs-flycheck" ,emacs-flycheck)
          ("emacs-let-alist" ,emacs-let-alist)
-         ("emacs-s" ,emacs-s)
+         ("emacs-s" ,emacs-s)))
-         ("emacs-seq" ,emacs-seq)))
       (home-page "https://github.com/purescript-emacs/psc-ide-emacs")
       (synopsis "Emacs integration for PureScript's psc-ide tool")
       (description
@@ -14282,8 +14431,7 @@ with (La)TeX mode, Org mode and other Emacs editing modes.")
         (base32 "1gxjind6r235az59dr8liv03d8994mqb8a7m28j3c12q7p70aziz"))))
     (build-system emacs-build-system)
     (propagated-inputs
-     `(("emacs-seq" ,emacs-seq)
+     `(("emacs-dash" ,emacs-dash)
-       ("emacs-dash" ,emacs-dash)
        ("emacs-let-alist" ,emacs-let-alist)))
     (home-page "https://github.com/cpitclaudel/biblio.el")
     (synopsis "Browse and import bibliographic references")
@@ -14691,24 +14839,6 @@ timestamps and date-time format strings library for Emacs.")
      "@code{npm-mode} provides a minor mode to work with @code{npm} projects.")
     (license license:gpl3+)))
 
-(define-public emacs-seq
-  (package
-    (name "emacs-seq")
-    (version "2.20")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://elpa.gnu.org/packages/seq-" version ".tar"))
-       (sha256
-        (base32
-         "0vrpx6nnyjb0gsypknzagimlhvcvi5y1rcdkpxyqr42415zr8d0n"))))
-    (build-system emacs-build-system)
-    (home-page "https://elpa.gnu.org/packages/seq.html")
-    (synopsis "Sequence manipulation functions")
-    (description "Sequence-manipulation functions that complement basic
-functions provided by @file{subr.el}.")
-    (license license:gpl3+)))
-
 (define-public emacs-itail
   (let ((commit "6e43c20da03be3b9c6ece93b7dc3495975ec1888")
         (revision "1"))
@@ -14788,7 +14918,17 @@ continue.")
        ("emacs-undercover" ,emacs-undercover)))
     (arguments
      `(#:tests? #t
-       #:test-command '("ert-runner")))
+       #:test-command '("ert-runner")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'disable-refs-next-match-test
+           ;; Hack to disable the failing test for emacs27
+           ;; https://github.com/Wilfred/elisp-refs/issues/29
+           (lambda _
+             (substitute* "test/unit-test.el"
+               (("ert-deftest elisp-refs-next-match")
+                "defun elisp-refs-next-match"))
+             #t)))))
     (home-page "https://github.com/Wilfred/elisp-refs")
     (synopsis "Find callers of elisp functions or macros")
     (description "Find references to functions, macros or variables.  Unlike a
@@ -14895,36 +15035,36 @@ macro takes a first argument (whose value must be an alist) and a body.")
     (license license:gpl3+)))
 
 (define-public emacs-esup
+  (let ((commit "0de8af8233d9ce1b67f05a50f25c481c4f1118d8")
+        (revision "1"))
     (package
       (name "emacs-esup")
-    (version "0.7")
+      (version (git-version "0.7.1" revision commit))
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
                (url "https://github.com/jschaf/esup")
-             (commit (string-append "v" version))))
+               (commit commit)))
          (file-name (git-file-name name version))
          (sha256
           (base32
-         "100w28n3qb3s5b18vvqpwmijdjnjazawn38i0pjbpxz5llhqgl1g"))))
+           "01khb3xyj0ylwib6ryzzvqmkh5wvzxiq2n3l0s3h9zv7wx849bzv"))))
       (build-system emacs-build-system)
       (native-inputs
        `(("emacs-noflet" ,emacs-noflet)
-       ("emacs-el-mock" ,emacs-el-mock)))
+         ("emacs-undercover" ,emacs-undercover)
+         ("emacs-buttercup" ,emacs-buttercup)))
+      (propagated-inputs
+       `(("emacs-dash" ,emacs-dash)))
       (arguments
-     `(#:phases
+     `(#:tests? #t
-       (modify-phases %standard-phases
+       #:test-command '("buttercup" "-L" ".")))
-         (add-before 'install 'check
-           (lambda* (#:key inputs #:allow-other-keys)
-             (invoke "emacs" "--batch" "-L" "."
-                     "-l" "test/esup-test.el"
-                     "-f" "ert-run-tests-batch-and-exit"))))))
       (home-page "https://github.com/jschaf/esup")
       (synopsis "Emacs start up profiler")
       (description "Benchmark Emacs Startup time without ever leaving
 your Emacs.")
-    (license license:gpl2+)))
+      (license license:gpl2+))))
 
 (define-public emacs-restart-emacs
   (let ((commit "9aa90d3df9e08bc420e1c9845ee3ff568e911bd9")
@@ -16531,20 +16671,18 @@ scroll up to read the function name and then scroll down to original position.")
       (license license:gpl3+))))
 
 (define-public emacs-git-auto-commit-mode
-  (let ((commit "23abaff792c0459e51e596d3fecd5513617e8cb1")
-        (revision "1"))
   (package
     (name "emacs-git-auto-commit-mode")
-      (version (git-version "4.6.0" revision commit))
+    (version "4.7.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/ryuslash/git-auto-commit-mode")
-               (commit commit)))
+             (commit version)))
        (file-name (git-file-name name version))
        (sha256
-          (base32 "0hqj34q8z4jg86zz2lwfvj6xk07b4g1222h9y1zqs83qgivwpk1l"))))
+        (base32 "0gpib57f7xza04g3iyihw5v15hb7pncqsmvyggib902yvcxlkvqf"))))
     (build-system emacs-build-system)
     (native-inputs
      `(("emacs-buttercup" ,emacs-buttercup)
@@ -16557,9 +16695,9 @@ scroll up to read the function name and then scroll down to original position.")
     (description "@code{git-auto-commit-mode} is an Emacs minor mode that
 tries to commit changes to a file after every save.
 
-When @code{gac-automatically-push-p} is non-nil, it also tries to push to
+When @code{gac-automatically-push-p} is non-nil, it also tries to push to the
-the current upstream.")
+current upstream.")
-      (license license:gpl3+))))
+    (license license:gpl3+)))
 
 (define-public emacs-scroll-on-drag
   (let ((commit "888abd04c34753b1fc4b2fe541bc004ebec5c996")
@@ -18324,7 +18462,7 @@ can be queued at any time.")
        ("emacs-esxml" ,emacs-esxml)
        ("emacs-s" ,emacs-s)))
     (inputs
-     `(("pandoc" ,ghc-pandoc)))
+     `(("pandoc" ,pandoc)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -20411,7 +20549,6 @@ unescaping of quotes.")
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-dash" ,emacs-dash)
-         ("emacs-seq" ,emacs-seq)
          ("emacs-flycheck" ,emacs-flycheck)
          ("emacs-haskell-mode" ,emacs-haskell-mode)
          ("emacs-let-alist" ,emacs-let-alist)))
@@ -21110,7 +21247,7 @@ through Dash docsets.")
 (define-public emacs-calibredb
   (package
     (name "emacs-calibredb")
-    (version "2.5.0")
+    (version "2.6.0")
     (source
      (origin
        (method git-fetch)
@@ -21119,11 +21256,10 @@ through Dash docsets.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "11m9d015fnjf89qg6wpy0vs1vhvak5q753m4dzqrdw3jgm9zsnmv"))))
+        (base32 "132afbbh4km2cbll46i6bpksvin0ncgfy782g4nkfjmwjaqh3d5l"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-dash" ,emacs-dash)
-       ("emacs-org" ,emacs-org)
        ("emacs-s" ,emacs-s)
        ("emacs-transient" ,emacs-transient)))
     (home-page "https://github.com/chenyanming/calibredb.el")
@@ -21232,14 +21368,14 @@ well as an option for visually flashing evaluated s-expressions.")
 (define-public emacs-tramp
   (package
     (name "emacs-tramp")
-    (version "2.4.4.1")
+    (version "2.4.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/"
                            "tramp-" version ".tar"))
        (sha256
-        (base32 "0jayd75yscaqvg6y0m6g2mgbjswyj5gqdij2az9g0j18vm5vbqy3"))))
+        (base32 "16c8x5d803hjql0z88lidyx3zrhxlpjphdpzn3ppzz3wrsxsv8rf"))))
     (build-system emacs-build-system)
     (arguments
      `(#:emacs ,emacs                   ;need D-Bus
@@ -21873,7 +22009,7 @@ format.")
                 "0iibxplgdp34bpq1yll2gmqjd8d8lnqn4mqjvx6cdf0y438yr4jz"))))
     (build-system emacs-build-system)
     (inputs
-     `(("pandoc" ,ghc-pandoc)))
+     `(("pandoc" ,pandoc)))
     (propagated-inputs
      `(("emacs-dash" ,emacs-dash)
        ("emacs-ht" ,emacs-ht)))
@@ -21942,14 +22078,14 @@ federated microblogging social network.")
 (define-public emacs-ebdb
   (package
     (name "emacs-ebdb")
-    (version "0.6.18")
+    (version "0.6.19")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/"
                            "ebdb-" version ".tar"))
        (sha256
-        (base32 "0znbv3c7wdgak1f1zb051vg4r29fksqh53k1j77jfmqcvwkpz2mw"))))
+        (base32 "0ch5vzhxa8h5v75lg3blsmrln497lr3ylivx6w28aiyb6cv5016l"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/girzel/ebdb")
     (synopsis "EIEIO port of BBDB, Emacs's contact-management package")
@@ -22270,14 +22406,14 @@ Emacs that integrate with major modes like Org-mode.")
 (define-public emacs-modus-operandi-theme
   (package
     (name "emacs-modus-operandi-theme")
-    (version "0.11.0")
+    (version "0.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/"
                            "modus-operandi-theme-" version ".el"))
        (sha256
-        (base32 "11sq105vpp8rmyayfb7h8gz099kfdr7nb8n4pg81iby4fllj1kgd"))))
+        (base32 "1mllyysn701qfnglxs7n2f6mrzrz55v9hcwspvafc6fl2blr393y"))))
     (build-system emacs-build-system)
     (home-page "https://gitlab.com/protesilaos/modus-themes")
     (synopsis "Accessible light theme (WCAG AAA)")
@@ -22291,14 +22427,14 @@ standard.  This is the highest standard of its kind.")
 (define-public emacs-modus-vivendi-theme
   (package
     (name "emacs-modus-vivendi-theme")
-    (version "0.11.0")
+    (version "0.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/"
                            "modus-vivendi-theme-" version ".el"))
        (sha256
-        (base32 "14ky9cxg9cpvhgg24ra0xla2dapqjlf948470q7v0m402x1r2iif"))))
+        (base32 "01f6z5xjnmki1k9m83jwva42lxidb31pdpwm4wpxjzxqmb96picn"))))
     (build-system emacs-build-system)
     (home-page "https://gitlab.com/protesilaos/modus-themes")
     (synopsis "Accessible dark theme (WCAG AAA)")
@@ -22569,7 +22705,7 @@ Google guidelines.")
 (define-public emacs-helm-fish-completion
   (package
     (name "emacs-helm-fish-completion")
-    (version "0.5")
+    (version "0.6")
     (home-page "https://github.com/emacs-helm/helm-fish-completion")
     (source
      (origin
@@ -22579,7 +22715,7 @@ Google guidelines.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0hpsm39kx8vpz2zmarjrkvy1capkk5lwpsmdg2xnklsck6xsn922"))))
+        (base32 "1j2vfngq3512naaayv9kx0d1q2zg1xgs69l8afc7swg72h0l0imw"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("helm" ,emacs-helm)
@@ -24349,3 +24485,94 @@ applying highlighting to any face in GNU Emacs.  The functionality
 of this library depends on overlays, which by default are not
 picked up when copy-pasting text from buffer to buffer.")
       (license license:gpl2+))))
+
+(define-public emacs-org-webring
+  (package
+    (name "emacs-org-webring")
+    (version "1.6")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://git.sr.ht/~brettgilio/org-webring")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "00d7jqsbfa08rhyv3ry87rgy9ikv233spn4rz0d3riy0bp7b7j6b"))))
+    (build-system emacs-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'install-assets
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (assets
+                     (string-append out "/share/emacs/org-webring-assets")))
+               (mkdir-p assets)
+               (copy-recursively "assets" assets)
+               #t))))))
+    (propagated-inputs
+     `(("emacs-xmlgen" ,emacs-xmlgen)))
+    (home-page "https://sr.ht/~brettgilio/org-webring")
+    (synopsis "Generate webrings for Org-based sites / blogs")
+    (description "Org-webring is an alternative implementation of a
+feed-based webring, taking inspiration from openring by Drew DeVault.
+Intended to integrate with Org-based websites and blogs (either
+directly, or indirectly, as in ox-hugo), it will fetch a given list of
+web feed files and correctly parse and format the elements to be
+displayed for sharing.")
+    (license license:gpl3+)))
+
+(define-public emacs-scpaste
+  (let ((commit "cd4fa0aafecd839736e0b6cba68b4fc4d7045472")
+        (revision "0"))
+    (package
+      (name "emacs-scpaste")
+      (version "0.6.5")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://git.sr.ht/~technomancy/scpaste")
+               (commit commit)))
+         (file-name (git-file-name name commit))
+         (sha256
+          (base32
+           "1nvwbwl26z03963g9c82b3ggm39r95z1vp7c9qsa9mjm46dyq27w"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-htmlize" ,emacs-htmlize)))
+      (home-page "https://git.sr.ht/~technomancy/scpaste")
+      (synopsis "Emacs-based static HTML pastebin")
+      (description "This library will place an HTML copy of a
+buffer on an active webserver to which the user has SSH access.
+It is similar in purpose to services such as Gist or Pastebin,
+but is much simpler since it assumes the user has access to a
+publically-accessible HTTP server.")
+      (license license:gpl3+))))
+
+(define-public emacs-company-reftex
+  (package
+    (name "emacs-company-reftex")
+    (version "0.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/TheBB/company-reftex")
+             (commit "275ef708f08d3bf0eb30632148e5c6184eeaacdb")))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "118cgw5lsffqdqz95mnkw36mmnsbg9m52r2np4m7v14mjjwr9fby"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-company" ,emacs-company)
+       ("emacs-s" ,emacs-s)))
+    (home-page "https://github.com/TheBB/company-reftex")
+    (synopsis "RefTeX backends for company-mode")
+    (description "This package provides company-mode backends for completing
+label references and citations in LaTeX.  It is based on RefTeX, which is
+included with Emacs.")
+    (license license:gpl3+)))

gnu/packages/emacs.scm

@@ -2,7 +2,7 @@
 ;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com>
-;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014, 2015, 2016, 2017 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2016, 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2016 Federico Beffa <beffa@fbengineering.ch>
@@ -21,6 +21,7 @@
 ;;; Copyright © 2019 Leo Prikler <leo.prikler@student.tugraz.at>
 ;;; Copyright © 2019 Amin Bandali <bandali@gnu.org>
 ;;; Copyright © 2020 Jack Hill <jackhill@jackhill.us>
+;;; Copyright © 2020 Morgan Smith <Morgan.J.Smith@outlook.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -61,6 +62,7 @@
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages linux)     ; alsa-lib
   #:use-module (gnu packages mail)      ; for mailutils
+  #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages texinfo)
@@ -75,14 +77,14 @@
 (define-public emacs
   (package
     (name "emacs")
-    (version "26.3")
+    (version "27.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/emacs/emacs-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "119ldpk7sgn9jlpyngv5y4z3i7bb8q3xp4p0qqi7i5nq39syd42d"))
+                "0h9f2wpmp6rb5rfwvqwv1ia1nw86h74p7hnz3vb3gjazj67i4k2a"))
               (patches (search-patches "emacs-exec-path.patch"
                                        "emacs-fix-scheme-indent-function.patch"
                                        "emacs-ignore-empty-xim-styles.patch"
@@ -95,15 +97,7 @@
                   (for-each delete-file
                             (append (find-files "." "\\.elc$")
                                     (find-files "." "loaddefs\\.el$")
-                                    ;; This is the only "autoloads" file that
+                                    (find-files "eshell" "^esh-groups\\.el$")))
-                                    ;; does not have "*loaddefs.el" name.
-                                    ;; TODO: Next time changing this package,
-                                    ;; replace the following with a call to
-                                    ;; `find-files', so that `delete-file'
-                                    ;; wouldn't error out when the file is
-                                    ;; missing, making the entire snippet field
-                                    ;; reusable as-is for `emacs-next' below.
-                                    '("eshell/esh-groups.el")))
 
                   ;; Make sure Tramp looks for binaries in the right places on
                   ;; remote Guix System machines, where 'getconf PATH' returns
@@ -130,6 +124,7 @@
     (arguments
      `(#:tests? #f                      ; no check target
        #:configure-flags (list "--with-modules"
+                               "--with-cairo"
                                "--disable-build-details")
        #:phases
        (modify-phases %standard-phases
@@ -180,7 +175,42 @@
                ;; which leads to conflicts.
                (delete-file (string-append lisp-dir "/subdirs.el"))
                ;; Byte compile the site-start files.
-               (emacs-byte-compile-directory lisp-dir)))))))
+               (emacs-byte-compile-directory lisp-dir))
+             #t))
+         (add-after 'glib-or-gtk-wrap 'restore-emacs-pdmp
+           ;; restore the dump file that Emacs installs somewhere in
+           ;; libexec/ to its original state
+           (lambda* (#:key outputs target #:allow-other-keys)
+             (let* ((libexec (string-append (assoc-ref outputs "out")
+                                            "/libexec"))
+                    ;; each of these find-files should return one file
+                    (pdmp (find-files libexec "^emacs\\.pdmp$"))
+                    (pdmp-real (find-files libexec
+                                           "^\\.emacs\\.pdmp-real$")))
+               (for-each (lambda (wrapper real)
+                           (delete-file wrapper)
+                           (rename-file real wrapper))
+                         pdmp pdmp-real))
+             #t))
+         (add-after 'glib-or-gtk-wrap 'strip-double-wrap
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Directly copy emacs-X.Y to emacs, so that it is not wrapped
+             ;; twice.  This also fixes a minor issue, where WMs would not be
+             ;; able to track emacs back to emacs.desktop.
+             (with-directory-excursion (assoc-ref outputs "out")
+               (copy-file (string-append
+                           "bin/emacs-"
+                           ,(version-major+minor (package-version emacs)))
+                          "bin/emacs")
+               #t)))
+         (add-before 'reset-gzip-timestamps 'make-compressed-files-writable
+           ;; The 'reset-gzip-timestamps phase will throw a permission error
+           ;; if gzip files aren't writable then.  This phase is needed when
+           ;; building from a git checkout.
+           (lambda _
+             (for-each make-file-writable
+                       (find-files %output ".*\\.t?gz$"))
+             #t)))))
     (inputs
      `(("gnutls" ,gnutls)
        ("ncurses" ,ncurses)
@@ -192,12 +222,16 @@
        ;; TODO: Add the optional dependencies.
        ("libx11" ,libx11)
        ("gtk+" ,gtk+)
+       ("cairo" ,cairo)
+       ("pango" ,pango)
+       ("harfbuzz" ,harfbuzz)
        ("libxft" ,libxft)
        ("libtiff" ,libtiff)
        ("giflib" ,giflib)
        ("libjpeg" ,libjpeg-turbo)
-       ("imagemagick" ,imagemagick)
        ("acl" ,acl)
+       ("jansson" ,jansson)
+       ("gmp" ,gmp)
 
        ;; When looking for libpng `configure' links with `-lpng -lz', so we
        ;; must also provide zlib as an input.
@@ -244,118 +278,57 @@ languages.")
     (license license:gpl3+)))
 
 (define-public emacs-next
-  (let ((commit "c36c5a3dedbb2e0349be1b6c3b7567ea7b594f1c")
+  (let ((commit "2ea34662c20f71d35dd52a5ed996542c7386b9cb")
         (revision "0")
-        (emacs-version "27.0.91"))
+        (emacs-version "28.0.50.1"))
-    (package
+    (package/inherit emacs
-      (inherit emacs)
       (name "emacs-next")
       (version (git-version emacs-version revision commit))
       (source
        (origin
+         (inherit (package-source emacs))
          (method git-fetch)
          (uri (git-reference
-               (url "https://git.savannah.gnu.org/git/emacs.git")
+               (url "https://git.savannah.gnu.org/git/emacs.git/")
                (commit commit)))
-         (sha256
-          (base32 "0mlrg2npy1r79laahkgzhxd1qassfcdz8qk1cpw7mqgf6y5x505h"))
          (file-name (git-file-name name version))
-         (patches (search-patches "emacs27-exec-path.patch"
+         (sha256
-                                  "emacs-fix-scheme-indent-function.patch"
+          (base32
-                                  "emacs-ignore-empty-xim-styles.patch"
+           "0igjm9kwiswn2dpiy2k9xikbdfc7njs07ry48fqz70anljj8y7y3"))))
-                                  "emacs-source-date-epoch.patch"))
-         (modules (origin-modules (package-source emacs)))
-         ;; TODO: once the snippet for `emacs' is changed to not fail when
-         ;; eshell/esh-groups.el does not exist, replace this snippet with
-         ;; (snippet (origin-snippet (package-source emacs))))).
-         (snippet
-          '(with-directory-excursion "lisp"
-             ;; Make sure Tramp looks for binaries in the right places on
-             ;; remote Guix System machines, where 'getconf PATH' returns
-             ;; something bogus.
-             (substitute* "net/tramp-sh.el"
-               ;; Patch the line after "(defcustom tramp-remote-path".
-               (("\\(tramp-default-remote-path")
-                (format #f "(tramp-default-remote-path ~s ~s ~s ~s "
-                        "~/.guix-profile/bin" "~/.guix-profile/sbin"
-                        "/run/current-system/profile/bin"
-                        "/run/current-system/profile/sbin")))
-
-             ;; Make sure Man looks for C header files in the right
-             ;; places.
-             (substitute* "man.el"
-               (("\"/usr/local/include\"" line)
-                (string-join
-                 (list line
-                       "\"~/.guix-profile/include\""
-                       "\"/var/guix/profiles/system/profile/include\"")
-                 " ")))
-             #t))))
       (arguments
        (substitute-keyword-arguments (package-arguments emacs)
-         ((#:configure-flags flags)
-          `(cons* "--with-harfbuzz" ,flags))
          ((#:phases phases)
           `(modify-phases ,phases
-             ;; The 'reset-gzip-timestamps phase will throw a
+             (replace 'strip-double-wrap
-             ;; permission error if gzip files aren't writable then
+               (lambda* (#:key outputs #:allow-other-keys)
-             (add-before
+                 ;; Directly copy emacs-X.Y to emacs, so that it is not wrapped
-                 'reset-gzip-timestamps
+                 ;; twice.  This also fixes a minor issue, where WMs would not be
-                 'make-compressed-files-writable
+                 ;; able to track emacs back to emacs.desktop.
-               (lambda _
+                 (with-directory-excursion (assoc-ref outputs "out")
-                 (for-each make-file-writable
+                   (copy-file (string-append
-                           (find-files %output ".*\\.t?gz$"))
+                               "bin/emacs-"
-                 #t))
+                               ,(version-major+minor+point (package-version emacs-next)))
-             ;; restore the dump file that Emacs installs somewhere in
+                              "bin/emacs")
-             ;; libexec/ to its original state
-             (add-after 'glib-or-gtk-wrap 'restore-emacs-pdmp
-               (lambda* (#:key outputs target #:allow-other-keys)
-                 (let* ((libexec (string-append (assoc-ref outputs "out")
-                                                "/libexec"))
-                        ;; each of these find-files should return one file
-                        (pdmp (find-files libexec "^emacs\\.pdmp$"))
-                        (pdmp-real (find-files libexec
-                                               "^\\.emacs\\.pdmp-real$")))
-                   (for-each (lambda (wrapper real)
-                               (delete-file wrapper)
-                               (rename-file real wrapper))
-                             pdmp pdmp-real)
                    #t)))))))
-      (inputs
-       `(("jansson" ,jansson)
-         ("harfbuzz" ,harfbuzz)
-         ;; Emacs no longer uses ImageMagick by default
-         ;; https://git.savannah.gnu.org/cgit/emacs.git/tree/etc/NEWS?h=emacs-27.0.91&id=c36c5a3dedbb2e0349be1b6c3b7567ea7b594f1c#n102
-         ,@(alist-delete "imagemagick" (package-inputs emacs))))
       (native-inputs
-       `(("autoconf" ,autoconf)      ; needed when building from trunk
+       `(("autoconf" ,autoconf)
-         ,@(package-native-inputs emacs)))
+         ,@(package-native-inputs emacs))))))
-
-      ;; TODO: consider changing `emacs' to use a more robust way of
-      ;; specifying version for "EMACSLOADPATH", so as to avoid having to
-      ;; duplicate native-search-paths here.
-      (native-search-paths
-       (list (search-path-specification
-              (variable "EMACSLOADPATH")
-              ;; The versioned entry is for the Emacs' builtin libraries.
-              (files
-               (list "share/emacs/site-lisp"
-                     (string-append "share/emacs/" emacs-version "/lisp"))))
-             (search-path-specification
-              (variable "INFOPATH")
-              (files '("share/info"))))))))
 
 (define-public emacs-minimal
   ;; This is the version that you should use as an input to packages that just
   ;; need to byte-compile .el files.
-  (package (inherit emacs)
+  (package/inherit emacs
     (name "emacs-minimal")
     (synopsis "The extensible text editor (used only for byte-compilation)")
     (build-system gnu-build-system)
     (arguments
      (substitute-keyword-arguments (package-arguments emacs)
        ((#:configure-flags flags ''())
-        `(list "--with-gnutls=no" "--disable-build-details"))))
+        `(list "--with-gnutls=no" "--disable-build-details"))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (delete 'restore-emacs-pdmp)
+           (delete 'strip-double-wrap)))))
     (inputs
      `(("guix-emacs.el" ,(search-auxiliary-file "emacs/guix-emacs.el"))
        ("ncurses" ,ncurses)))
@@ -363,8 +336,7 @@ languages.")
      `(("pkg-config" ,pkg-config)))))
 
 (define-public emacs-xwidgets
-  (package
+  (package/inherit emacs
-    (inherit emacs)
     (name "emacs-xwidgets")
     (synopsis "The extensible, customizable, self-documenting text
 editor (with xwidgets support)")
@@ -372,14 +344,18 @@ editor (with xwidgets support)")
     (arguments
      (substitute-keyword-arguments (package-arguments emacs)
        ((#:configure-flags flags ''())
-        `(cons "--with-xwidgets" ,flags))))
+        `(cons "--with-xwidgets" ,flags))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (delete 'restore-emacs-pdmp)
+           (delete 'strip-double-wrap)))))
     (inputs
      `(("webkitgtk" ,webkitgtk)
        ("libxcomposite" ,libxcomposite)
        ,@(package-inputs emacs)))))
 
 (define-public emacs-no-x
-  (package (inherit emacs)
+  (package/inherit emacs
     (name "emacs-no-x")
     (synopsis "The extensible, customizable, self-documenting text
 editor (console only)")
@@ -388,13 +364,21 @@ editor (console only)")
                   (package-inputs emacs)
                   '("libx11" "gtk+" "libxft" "libtiff" "giflib" "libjpeg"
                     "imagemagick" "libpng" "librsvg" "libxpm" "libice"
-                    "libsm"
+                    "libsm" "cairo" "pango" "harfbuzz"
 
                     ;; These depend on libx11, so remove them as well.
-                    "libotf" "m17n-lib" "dbus")))))
+                    "libotf" "m17n-lib" "dbus")))
+    (arguments
+     (substitute-keyword-arguments (package-arguments emacs)
+       ((#:configure-flags flags ''())
+        `(delete "--with-cairo" ,flags))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (delete 'restore-emacs-pdmp)
+           (delete 'strip-double-wrap)))))))
 
 (define-public emacs-no-x-toolkit
-  (package (inherit emacs)
+  (package/inherit emacs
     (name "emacs-no-x-toolkit")
     (synopsis "The extensible, customizable, self-documenting text
 editor (without an X toolkit)" )
@@ -402,13 +386,16 @@ editor (without an X toolkit)" )
     (inputs (append `(("inotify-tools" ,inotify-tools))
                     (alist-delete "gtk+" (package-inputs emacs))))
     (arguments
-     `(,@(substitute-keyword-arguments (package-arguments emacs)
+     (substitute-keyword-arguments (package-arguments emacs)
-           ((#:configure-flags cf)
+       ((#:configure-flags flags ''())
-            `(cons "--with-x-toolkit=no" ,cf)))))))
+        `(cons "--with-x-toolkit=no" ,flags))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (delete 'restore-emacs-pdmp)
+           (delete 'strip-double-wrap)))))))
 
 (define-public emacs-wide-int
-  (package
+  (package/inherit emacs
-    (inherit emacs)
     (name "emacs-wide-int")
     (synopsis "The extensible, customizable, self-documenting text
 editor (with wide ints)" )
@@ -420,7 +407,7 @@ editor (with wide ints)" )
 (define-public guile-emacs
   (let ((commit "41120e0f595b16387eebfbf731fff70481de1b4b")
         (revision "0"))
-    (package (inherit emacs)
+    (package/inherit emacs
       (name "guile-emacs")
       (version (git-version "0.0.0" revision commit))
       (source (origin
@@ -444,6 +431,8 @@ editor (with wide ints)" )
                                        ;; Tests aren't passing for now.
                                        #:tests? #f
                                        ,@(package-arguments emacs))
+         ((#:configure-flags flags ''())
+          `(delete "--with-cairo" ,flags))
          ((#:phases phases)
           `(modify-phases ,phases
              (add-after 'unpack 'autogen
@@ -452,7 +441,9 @@ editor (with wide ints)" )
              ;; Build sometimes fails: deps/dispnew.d: No such file or directory
              (add-before 'build 'make-deps-dir
                (lambda _
-                 (invoke "mkdir" "-p" "src/deps"))))))))))
+                 (invoke "mkdir" "-p" "src/deps")))
+             (delete 'restore-emacs-pdmp)
+             (delete 'strip-double-wrap))))))))
 
 (define-public m17n-db
   (package

gnu/packages/embedded.scm

@@ -47,6 +47,7 @@
   #:use-module (gnu packages guile)
   #:use-module (gnu packages libftdi)
   #:use-module (gnu packages libusb)
+  #:use-module (gnu packages messaging)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
@@ -1357,3 +1358,51 @@ simplifies configuration and is also pluggable: you can write your own west
 this feature to provide conveniences for building applications, flashing and
 debugging them, and more.")
     (license license:expat)))
+
+(define-public ebusd
+  (package
+    (name "ebusd")
+    (version "3.4")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/john30/ebusd.git")
+                     (commit (string-append "v" version))))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "0iva70bam7wdx60bpd3an9kxr28zxlvp3vprivgqshwwdhqa0hzp"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'install-config
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((config-destination
+                    (string-append (assoc-ref outputs "out")
+                                   "/share/ebusd")))
+               (copy-recursively (string-append (assoc-ref inputs "config")
+                                                "/ebusd-2.1.x")
+                                 config-destination)
+               #t))))))
+    (inputs
+     `(("mosquitto" ,mosquitto)))
+    (native-inputs
+     `(("automake" ,automake)
+       ("autoconf" ,autoconf)
+       ("config"
+        ,(origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/john30/ebusd-configuration.git")
+                     (commit "666c0f6b9c4d7545eff7f43ab28a1c7baeab7913")))
+              (file-name "config-checkout")
+              (sha256
+               (base32
+                "0yxnx8p4lbk614l16854r9s9d8s9c7ixgczfs8mph94xz0wkda7x"))))))
+    (synopsis "Daemon for communicating with eBUS devices")
+    (description "This package provides @command{ebusd}, a daemon for
+handling communication with eBUS devices connected to a 2-wire bus system
+(\"energy bus\" used by numerous heating systems).")
+    (home-page "https://ebusd.eu/")
+    (license license:gpl3+)))

gnu/packages/emulators.scm

@@ -1397,7 +1397,7 @@ play them on systems for which they were never designed!")
 (define-public mame
   (package
     (name "mame")
-    (version "0.223")
+    (version "0.224")
     (source
      (origin
        (method git-fetch)
@@ -1406,7 +1406,7 @@ play them on systems for which they were never designed!")
              (commit (apply string-append "mame" (string-split version #\.)))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0fmf9ygbic4lw84vifhpz8wq2736dj8zsi1cqhb1m0fjq3dvn0vm"))
+        (base32 "0dpg4hz2f1wlp0rmk5c5xq57fy0sblh97z3l66p814wkgzap4bhx"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled libraries.

gnu/packages/engineering.scm

@@ -795,6 +795,51 @@ language.")
       (license (list license:mpl2.0               ;library
                      license:gpl2+)))))           ;Guile bindings and GUI
 
+(define-public inspekt3d
+  (let ((commit "703f52ccbfedad2bf5240bf8183d1b573c9d54ef")
+        (revision "0"))
+    (package
+      (name "inspekt3d")
+      (version (git-version "0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://gitlab.com/kavalogic-inc/inspekt3d.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0lan6930g5a9z4ack9jj0zdd0mb2s6q2xzpiwcjdc3pvl9b1nbw4"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'patch-libfive-guile-location
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* "inspekt3d/library.scm"
+                 (("\"libfive-guile")
+                  (string-append "\""
+                                 (assoc-ref inputs "libfive")
+                                 "/lib/libfive-guile")))
+               #t)))))
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("pkg-config" ,pkg-config)))
+      (inputs
+       `(("mesa" ,mesa)
+         ("guile" ,guile-2.2)))
+      (propagated-inputs
+       `(("libfive" ,libfive)
+         ("guile-opengl" ,guile-opengl)))
+      (home-page "https://gitlab.com/kavalogic-inc/inspekt3d/")
+      (synopsis "Lightweight 3D viewer for Libfive written in Guile Scheme")
+      (description
+       "Inspekt3d is a lightweight 3D viewer for Libfive written in Guile Scheme.
+The viewer can be used interactively with a REPL (for example Geiser in
+Emacs).")
+      (license license:gpl3+))))
+
 ;; TODO Add doc https://gitlab.com/kicad/services/kicad-doc/-/tree/master
 (define-public kicad
   (package

gnu/packages/enlightenment.scm

@@ -32,7 +32,6 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages avahi)
-  #:use-module (gnu packages bash)
   #:use-module (gnu packages bittorrent)
   #:use-module (gnu packages check)
   #:use-module (gnu packages code)
@@ -304,6 +303,7 @@ Libraries with some extra bells and whistles.")
        (let ((efl (assoc-ref %build-inputs "efl")))
          (list "-Dsystemd=false"
                "-Dpackagekit=false"
+               "-Dwl=true"
                (string-append "-Dedje-cc=" efl "/bin/edje_cc")
                (string-append "-Deldbus-codegen=" efl "/bin/eldbus-codegen")
                (string-append "-Deet=" efl "/bin/eet")))
@@ -315,7 +315,6 @@ Libraries with some extra bells and whistles.")
              (setenv "HOME" "/tmp")
              (let ((xkeyboard (assoc-ref inputs "xkeyboard-config"))
                    (setxkbmap (assoc-ref inputs "setxkbmap"))
-                   (utils     (assoc-ref inputs "util-linux"))
                    (libc      (assoc-ref inputs "libc"))
                    (bc        (assoc-ref inputs "bc"))
                    (efl       (assoc-ref inputs "efl")))
@@ -346,20 +345,18 @@ Libraries with some extra bells and whistles.")
                (substitute* "data/etc/meson.build"
                  (("/bin/mount") "/run/setuid-programs/mount")
                  (("/bin/umount") "/run/setuid-programs/umount")
-                 (("/usr/bin/eject") (string-append utils "/bin/eject")))
+                 (("/usr/bin/eject") "/run/current-system/profile/bin/eject"))
                (substitute* "src/bin/system/e_system_power.c"
                  (("systemctl") "loginctl"))
                #t))))))
     (native-inputs
      `(("gettext" ,gettext-minimal)
-       ("pkg-config" ,pkg-config)
+       ("pkg-config" ,pkg-config)))
-       ("util-linux" ,util-linux)))
     (inputs
      `(("alsa-lib" ,alsa-lib)
        ("bc" ,bc)
        ("bluez" ,bluez)
        ("dbus" ,dbus)
-       ("efl" ,efl)
        ("freetype" ,freetype)
        ("libxcb" ,libxcb)
        ("libxext" ,libxext)
@@ -367,7 +364,12 @@ Libraries with some extra bells and whistles.")
        ("puleseaudio" ,pulseaudio)
        ("setxkbmap" ,setxkbmap)
        ("xcb-util-keysyms" ,xcb-util-keysyms)
-       ("xkeyboard-config" ,xkeyboard-config)))
+       ("xkeyboard-config" ,xkeyboard-config)
+       ("xorg-server-xwayland" ,xorg-server-xwayland)))
+    (propagated-inputs
+     `(("efl" ,efl)
+       ("libxkbcommon" ,libxkbcommon)
+       ("wayland-protocols" ,wayland-protocols)))
     (home-page "https://www.enlightenment.org/about-enlightenment")
     (synopsis "Lightweight desktop environment")
     (description
@@ -378,17 +380,7 @@ embedded systems.")
     (license license:bsd-2)))
 
 (define-public enlightenment-wayland
-  (package
+  (deprecated-package "enlightenment-wayland" enlightenment))
-    (inherit enlightenment)
-    (name "enlightenment-wayland")
-    (arguments
-     (substitute-keyword-arguments (package-arguments enlightenment)
-       ((#:configure-flags flags)
-        `(cons* "-Dwl=true" ,flags))))
-    (inputs
-     `(("wayland-protocols" ,wayland-protocols)
-       ("xorg-server-xwayland" ,xorg-server-xwayland)
-       ,@(package-inputs enlightenment)))))
 
 (define-public python-efl
   (package
@@ -406,11 +398,13 @@ embedded systems.")
         ;; Remove files generated by Cython
         (snippet
          '(begin
-             (copy-file "efl/dbus_mainloop/e_dbus.c" "efl/dbus_mainloop/e_dbus.q")
+            (for-each (lambda (file)
-             (for-each delete-file (find-files "efl" ".*\\.c$"))
+                        (let ((generated-file
+                                (string-append (string-drop-right file 3) "c")))
+                          (when (file-exists? generated-file)
+                            (delete-file generated-file))))
+                      (find-files "efl" "\\.pyx$"))
             (delete-file "efl/eo/efl.eo_api.h")
-             (copy-file "efl/dbus_mainloop/e_dbus.q" "efl/dbus_mainloop/e_dbus.c")
-             (delete-file "efl/dbus_mainloop/e_dbus.q")
             #t))))
     (build-system python-build-system)
     (arguments
@@ -572,14 +566,14 @@ directories.
 (define-public evisum
   (package
     (name "evisum")
-    (version "0.5.3")
+    (version "0.5.4")
     (source
       (origin
         (method url-fetch)
         (uri (string-append "https://download.enlightenment.org/rel/apps/"
                             "evisum/evisum-" version ".tar.xz"))
         (sha256
-         (base32 "06ws75qfid0xizasw2aqpdhvxl4c31bn66fqa8aq4w0rykzs2r46"))))
+         (base32 "1ip3w2d476g45sivqvm1madfyqmkni9q2i99qqxk53859jgs91pa"))))
     (build-system meson-build-system)
     (arguments
      '(#:tests? #f))                    ; no tests

gnu/packages/finance.scm

@@ -480,7 +480,7 @@ other machines/servers.  Electrum does not download the Bitcoin blockchain.")
 (define-public electron-cash
   (package
     (name "electron-cash")
-    (version "4.0.15")
+    (version "4.1.0")
     (source
      (origin
        (method git-fetch)
@@ -489,11 +489,11 @@ other machines/servers.  Electrum does not download the Bitcoin blockchain.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0bvj64fdxpi0dbivhgv509kqq503zjp7r7xckl8q5c48j5h1zik2"))))
+        (base32 "1ccfm6kkmbkvykfdzrisxvr0lx9kgq4l43ixk6v3xnvhnbfwz4s2"))))
     (build-system python-build-system)
     (inputs
      `(("libevent" ,libevent)
-       ("libsecp256k1", libsecp256k1)
+       ("libsecp256k1", libsecp256k1-bitcoin-cash)
        ("openssl" ,openssl)
        ("python-cython" ,python-cython)
        ("python-dateutil", python-dateutil)
@@ -530,7 +530,9 @@ other machines/servers.  Electrum does not download the Bitcoin blockchain.")
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "lib/secp256k1.py"
                (("library_paths = .* 'libsecp256k1.so.0'.")
-                (string-append "library_paths = ('" (assoc-ref inputs "libsecp256k1") "/lib/libsecp256k1.so.0'")))
+                (string-append "library_paths = ('"
+                               (assoc-ref inputs "libsecp256k1")
+                               "/lib/libsecp256k1.so.0'")))
              #t))
          (add-after 'install 'wrap-qt
            (lambda* (#:key outputs #:allow-other-keys)
@@ -1397,7 +1399,7 @@ entity management.")
 (define-public bitcoin-unlimited
   (package
     (name "bitcoin-unlimited")
-    (version "1.8.0.0")
+    (version "1.9.0.0")
     (source
      (origin
        (method git-fetch)
@@ -1406,7 +1408,7 @@ entity management.")
              (commit (string-append "BCHunlimited" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1ivkig6q7i4n389dg1zv06cmfki20bjq0slmshx0p5a1aavkqj7k"))))
+        (base32 "1a64h7mcqdra4ahnw1nycp4ysx308ymgbl4yn5fj5jfaszdzvy0h"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)

gnu/packages/fonts.scm

@@ -1203,7 +1203,7 @@ typeface, by mimicking Comic Sans while fixing its most obvious shortcomings.")
   (package
     (name "font-iosevka")
     ;; When updating, also update the hash of the Iosevka variant(s) below.
-    (version "3.2.2")
+    (version "3.4.7")
     (source
      (origin
        (method url-fetch/zipbomb)
@@ -1211,7 +1211,7 @@ typeface, by mimicking Comic Sans while fixing its most obvious shortcomings.")
                            "/releases/download/v" version
                            "/ttc-iosevka-" version ".zip"))
        (sha256
-        (base32 "16iqr4zjlshrgzcs3sjp3gz777gpi069r7p7scqi6vap9acqjvph"))))
+        (base32 "178xyxz57ncigv715db0898d5arcx1l7qi73a8prb2fdlb7x2yx6"))))
     (build-system font-build-system)
     (home-page "https://be5invis.github.io/Iosevka/")
     (synopsis "Coders' typeface, built from code")
@@ -1234,7 +1234,7 @@ programming.  Iosevka is completely generated from its source code.")
                            "/releases/download/v" version
                            "/ttc-iosevka-slab-" version ".zip"))
        (sha256
-        (base32 "0knsb1b0wqv50r7f9128xvq344x7hnvgm7kh1dxaahlck910z62x"))))))
+        (base32 "1zqgly4ymmmz3ckfsc2vdxw6d62axcyl79fq3gi630c4951nfikz"))))))
 
 (define-public font-iosevka-term
   (package
@@ -1249,7 +1249,7 @@ programming.  Iosevka is completely generated from its source code.")
                            "/ttf-iosevka-term-" version ".zip"))
        (sha256
         (base32
-         "0nyq6iq9xjn9nqwh1fh4v0pvblycmm8ssw7y3vcjv1ymbkdqfqhr"))))
+         "0nfwxhxgrgz3hhhrvr759263bm88zbh0zsavpnmphxwg9kykjq39"))))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -1271,7 +1271,7 @@ programming.  Iosevka is completely generated from its source code.")
                            "/ttf-iosevka-term-slab-" version ".zip"))
        (sha256
         (base32
-         "1blhhbnk2hyaxjrz88icd2gwyniq5idxd0h6rqx6vjcack6094z0"))))
+         "01ynnwlfq3294p8v0656xw6wcfmqklf0yqwkqh3sh2wmj7rrs7wi"))))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -1292,7 +1292,7 @@ programming.  Iosevka is completely generated from its source code.")
                            "/releases/download/v" version
                            "/ttc-iosevka-aile-" version ".zip"))
        (sha256
-        (base32 "1zg0gn4gcf3w8n8jzf93y9ninyn3bci31c5zss3mxzz1lzfm8zd5"))))))
+        (base32 "0h4wzjyw3h5zbxzfb71z7aj5xwp8r1hd93qim6zicxfk9dgczgw5"))))))
 
 (define-public font-iosevka-etoile
   (package
@@ -1306,7 +1306,7 @@ programming.  Iosevka is completely generated from its source code.")
                            "/releases/download/v" version
                            "/ttc-iosevka-etoile-" version ".zip"))
        (sha256
-        (base32 "1061yaf35f19dcym4k552q1yzbsbc98r3glm9frslirra9f33sl2"))))))
+        (base32 "1n1jy7g0q0kd4ihsyka1v02s7xgpg80rf9sml1yhxkqw5pq62972"))))))
 
 (define-public font-iosevka-sparkle
   (package
@@ -1320,7 +1320,7 @@ programming.  Iosevka is completely generated from its source code.")
                            "/releases/download/v" version
                            "/ttc-iosevka-sparkle-" version ".zip"))
        (sha256
-        (base32 "1c1s9j6qgyhn4md0kql0x2201nbs5jx3612jf8q020gm484xqq03"))))))
+        (base32 "0chl6x3xy6alq64sax71psvpq6f6fgw6pbn04f5j5skgrbqkk292"))))))
 
 (define-public font-sarasa-gothic
   (package

gnu/packages/fontutils.scm

@@ -2,7 +2,7 @@
 ;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014, 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Rene Saavedra <rennes@openmailbox.org>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Nikita <nikita@n0.is>
@@ -100,7 +100,7 @@ anti-aliased glyph bitmap generation with 256 gray levels.")
 (define-public ttfautohint
   (package
     (name "ttfautohint")
-    (version "1.5")
+    (version "1.8.3")
     (source
      (origin
        (method url-fetch)
@@ -108,8 +108,7 @@ anti-aliased glyph bitmap generation with 256 gray levels.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "1lgghck46p33z3hg8dnl76jryig4fh6d8rhzms837zp7x4hyfkv4"))
+         "0zpqgihn3yh3v51ynxwr8asqrijvs4gv686clwv7bm8sawr4kfw7"))))
-       (patches (list (search-patch "ttfautohint-source-date-epoch.patch")))))
     (build-system gnu-build-system)
     (native-inputs
      `(("flex" ,flex)
@@ -119,7 +118,8 @@ anti-aliased glyph bitmap generation with 256 gray levels.")
      `(("freetype" ,freetype)
        ("harfbuzz" ,harfbuzz)))
     (arguments
-     `(#:configure-flags '("--with-qt=no"))) ;no gui
+     `(#:configure-flags '("--disable-static"
+                           "--with-qt=no"))) ;no gui
     (synopsis "Automated font hinting")
     (description
      "ttfautohint provides a 99% automated hinting process and a platform for

gnu/packages/freedesktop.scm

@@ -1717,14 +1717,14 @@ their MIME type.
 (define-public uchardet
   (package
     (name "uchardet")
-    (version "0.0.6")
+    (version "0.0.7")
     (source
       (origin
         (method url-fetch)
         (uri (string-append "https://www.freedesktop.org/software/"
                             name "/releases/" name "-" version ".tar.xz"))
         (sha256
-          (base32 "0q9c02b6nmw41yfsiqsnphgc3f0yg3fj31wkccp47cmwvy634lc3"))))
+          (base32 "1ca51sryhryqz82v4d0graaiqqq5w2f33a9gj83b910xmq499irz"))))
     (build-system cmake-build-system)
     (home-page "https://www.freedesktop.org/wiki/Software/uchardet/")
     (synopsis "Encoding detector library")

gnu/packages/freeipmi.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015, 2016, 2017, 2020 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,14 +28,14 @@
 (define-public freeipmi
   (package
     (name "freeipmi")
-    (version "1.6.5")
+    (version "1.6.6")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/freeipmi/freeipmi-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "1ncf1s84752xaq07h36wrxa5ww1167s2bizkww0igxv8djyddwk1"))))
+               "1ava5s0babfwx6dqi87phzyzjjgyah7avhljrxrjwn2cniwh38yg"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--disable-static")))

gnu/packages/game-development.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2015, 2018 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2015, 2016, 2017 David Thompson <davet@gnu.org>
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2016, 2017 Kei Kebreau <kkebreau@posteo.net>
+;;; Copyright © 2016, 2017, 2020 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2016, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018 Julian Graham <joolean@gmail.com>
 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -342,26 +342,22 @@ compiling NML files (along with their associated language, sound and graphic
 files) into @file{.grf} and/or @file{.nfo} files.")
     (license license:gpl2+)))
 
-(define-public python-sge-pygame
+(define-public python-sge
   (package
-    (name "python-sge-pygame")
+    (name "python-sge")
-    (version "1.5.1")
+    (version "1.7")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://savannah/stellarengine/"
+       (uri (pypi-uri "sge" version))
-                           (version-major+minor version) "/sge-pygame-"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1rl3xjzh78sl0sq3xl8rl7cgp9v9v3h7s2pfwn7nj1vrmffzkcpd"))))
+         "02fn6v6bxk3sngwd4kd3mglrp0jlnhx7x6h8nnkik6wdv150a0wv"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-pygame" ,python-pygame)
-       ("python-six" ,python-six)
        ("python-uniseg" ,python-uniseg)))
-    (home-page "http://stellarengine.nongnu.org")
+    (home-page "https://python-sge.github.io/")
     (synopsis "2D game engine for Python")
     (description
      "The SGE Game Engine (\"SGE\", pronounced like \"Sage\") is a
@@ -370,8 +366,8 @@ you can focus on the game itself.  This makes more rapid game development
 possible, and it also makes the SGE easy to learn.")
     (license license:lgpl3+)))
 
-(define-public python2-sge-pygame
+(define-public python-sge-pygame
-  (package-with-python2 python-sge-pygame))
+  (deprecated-package "python-sge-pygame" python-sge))
 
 (define-public python-tmx
   (package
@@ -412,14 +408,15 @@ levels.")
 (define-public python-xsge
   (package
     (name "python-xsge")
-    (version "2018.02.26")
+    (version "2020.09.07")
     (source (origin
               (method url-fetch)
-              (uri (string-append "mirror://savannah/xsge/xsge/xsge-"
+              (uri (string-append "https://github.com/python-sge/xsge"
-                                  version ".tar.gz"))
+                                  "/releases/download/v" version
+                                  "/xsge-" version ".zip"))
               (sha256
                (base32
-                "0bx93hgf7cgdw2gsygbh59y8vpw37pgsa279rajw3fkdpl8vrc40"))))
+                "136xgy3f9vw636wxpqbha022avk0wyxw63mm3a2dvwhh90s716f9"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
@@ -432,12 +429,11 @@ levels.")
                      (string-append "--prefix=" (assoc-ref outputs "out"))
                      "--root=/"))))
        #:tests? #f)) ; no check target
+    (native-inputs
+     `(("unzip" ,unzip)))
     (propagated-inputs
-     `(("python-sge-pygame" ,python-sge-pygame)
+     `(("python-sge" ,python-sge)))
-       ("python-pygame" ,python-pygame)
+    (home-page "https://python-sge.github.io/")
-       ("python-six" ,python-six)
-       ("python-tmx" ,python-tmx)))
-    (home-page "http://xsge.nongnu.org")
     (synopsis "Extensions for the SGE Game Engine")
     (description
      "xSGE is a collection of modules that make doing certain tasks with the SGE
@@ -446,9 +442,6 @@ GUI toolkit, lighting and physics frameworks and @code{Tiled} TMX format
 support.")
     (license license:gpl3+)))
 
-(define-public python2-xsge
-  (package-with-python2 python-xsge))
-
 (define-public tiled
   (package
     (name "tiled")

gnu/packages/games.scm

@@ -17,7 +17,7 @@
 ;;; Copyright © 2016, 2017 Rodger Fox <thylakoid@openmailbox.org>
 ;;; Copyright © 2016, 2017, 2018 Nikita <nikita@n0.is>
 ;;; Copyright © 2016 Albin Söderqvist <albin@fripost.org>
-;;; Copyright © 2016, 2017, 2018, 2019 Kei Kebreau <kkebreau@posteo.net>
+;;; Copyright © 2016, 2017, 2018, 2019, 2020 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
@@ -385,15 +385,17 @@ The game includes a built-in editor so you can design and share your own maps.")
 (define-public armagetronad
   (package
     (name "armagetronad")
-    (version "0.2.8.3.5")
+    (version "0.2.9.0.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/armagetronad/stable/"
-                                  version "/armagetronad-" version ".src.tar.gz"))
+                                  version "/armagetronad-" version ".tbz"))
               (sha256
                (base32
-                "1z266haq22n5b0733h7qsg1rpzhz8lvm82f7wd06r008iiar7jdl"))))
+                "19rfhlg4gp0r7k1j8v4iw20325ciy156nmzax4xikmw22c6nmxcz"))))
     (build-system gnu-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
     (inputs
      `(("libxml2" ,libxml2)
        ("sdl" ,sdl)
@@ -1811,15 +1813,16 @@ Every puzzle has a complete solution, although there may be more than one.")
 (define-public retux
   (package
     (name "retux")
-    (version "1.3.6")
+    (version "1.4")
     (source (origin
               (method url-fetch)
-              (uri (string-append "mirror://savannah/retux/"
+              (uri (string-append "https://github.com/retux-game/retux/"
+                                  "releases/download/v"
                                   (version-major+minor version) "/retux-"
                                   version "-src.tar.gz"))
               (sha256
                (base32
-                "01bidh4zisjp3nc436x0g85v60dvwb3ig37i7y01sa71j8fm4fmb"))))
+                "1hxy1pvlxhk0ci3wh2i3mmr82faqdjnnxsiwwr5gcr93nfnw9w5f"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f ; no check target
@@ -1831,28 +1834,22 @@ Every puzzle has a complete solution, although there may be more than one.")
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out    (assoc-ref outputs "out"))
                     (bin    (string-append out "/bin"))
-                    (data   (string-append out "/share/retux"))
+                    (data   (string-append out "/share/retux")))
-                    (doc    (string-append out "/share/doc/retux")))
                (mkdir-p bin)
 
                (substitute* "retux.py"
                  ;; Use the correct data directory.
                  (("os\\.path\\.join\\(os\\.path\\.dirname\\(__file__\\), \"data\"\\),")
-                  (string-append "\"" data "\","))
+                  (string-append "\"" data "\",")))
-                 ;; Use Python 3 so the patch-shebangs phase works properly.
-                 ((".*python2.*") "#!/usr/bin/python3"))
 
                (copy-file "retux.py" (string-append bin "/retux"))
-
                (copy-recursively "data" data)
-
-               (install-file "COPYING" doc)
                #t))))))
     (inputs
      `(("python-sge-pygame" ,python-sge-pygame)
        ("python-six" ,python-six)
        ("python-xsge" ,python-xsge)))
-    (home-page "http://retux.nongnu.org")
+    (home-page "https://retux-game.github.io/")
     (synopsis "Action platformer game")
     (description
      "ReTux is an action platformer loosely inspired by the Mario games,
@@ -3667,7 +3664,7 @@ falling, themeable graphics and sounds, and replays.")
 (define-public wesnoth
   (package
     (name "wesnoth")
-    (version "1.14.13")
+    (version "1.14.14")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/wesnoth/wesnoth-"
@@ -3676,7 +3673,7 @@ falling, themeable graphics and sounds, and replays.")
                                   "wesnoth-" version ".tar.bz2"))
               (sha256
                (base32
-                "1pmqj4rah0256qi9w394ksb9apid723i5f5agkg6x1lahb1ac91q"))))
+                "1l7mdxn4kw938qz824057rqh99b7y9439a54s64n1xz95w77lp0r"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f))                    ;no check target
@@ -4788,7 +4785,7 @@ of war.  Widelands also offers an Artificial Intelligence to challenge you.")
 (define-public starfighter
   (package
     (name "starfighter")
-    (version "2.3.1")
+    (version "2.3.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -4797,7 +4794,7 @@ of war.  Widelands also offers an Artificial Intelligence to challenge you.")
                     version "-src.tar.gz"))
               (sha256
                (base32
-                "13396hvsj4cswlrw52kwqn37dadxps00vhr0hrqgm87fl4ih5yyx"))))
+                "1nvi277cazsw36b6nhd5nmk0cjvm71rlxasy24mf18j7fsvq9vp8"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -7048,7 +7045,7 @@ Strife, Chex Quest, and fan-created games like Harmony, Hacx and Freedoom.")
 (define-public odamex
   (package
     (name "odamex")
-    (version "0.8.1")
+    (version "0.8.3")
     (source
      (origin
        (method url-fetch)
@@ -7056,7 +7053,7 @@ Strife, Chex Quest, and fan-created games like Harmony, Hacx and Freedoom.")
              "mirror://sourceforge/odamex/Odamex/" version "/"
              "odamex-src-" version ".tar.gz"))
        (sha256
-        (base32 "1ywbqkfacc9fc5di3dn95y5ah2ys9i241j64q3f37a73x92llw1i"))))
+        (base32 "0f887g87bmcq4dpcga7xc2mpxs947dkbc934ir9xs55gz6z13q96"))))
     (build-system cmake-build-system)
     (arguments `(#:tests? #f))          ; no tests
     (inputs
@@ -8848,7 +8845,8 @@ play with up to four players simultaneously.  It has network support.")
      ;; XXX: Engine is built as Pascal source code, requiring Free Pascal
      ;; Compiler, which we haven't packaged yet.  With the flag below, we use
      ;; a Pascal to C translator and Clang instead.
-     `(#:configure-flags (list "-DBUILD_ENGINE_C=ON")
+     `(#:configure-flags (list "-DBUILD_ENGINE_C=ON"
+                               "-Dhaskell_flags=-dynamic;-fPIC")
        #:phases
        (modify-phases %standard-phases
          (replace 'check

gnu/packages/gcc.scm

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

gnu/packages/genimage.scm

@@ -50,7 +50,9 @@
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "15jmh17lvm3jw9c92bjarly7iwhmnfl322d91mprfv10ppb9ip54"))))
+                "15jmh17lvm3jw9c92bjarly7iwhmnfl322d91mprfv10ppb9ip54"))
+              ;; will be shipped with release 14
+              (patches (search-patches "genimage-signedness.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -169,7 +171,6 @@
        ("automake" ,automake)
        ;;; Note: cramfs is obsolete.
        ("dtc" ,dtc) ; for the tests
-       ("fdisk" ,fdisk) ; for the tests
        ("pkg-config" ,pkg-config)
        ("util-linux" ,util-linux))) ; for the tests
     (inputs

gnu/packages/geo.scm

@@ -12,6 +12,7 @@
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;; Copyright © 2019 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2020 Christopher Baines <mail@cbaines.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1339,7 +1340,8 @@ to the OSM opening hours specification.")
                        (filter
                          (lambda (s)
                            (let ((source (assoc-ref inputs "source")))
-                             (not (equal? (substring s 0 (string-length source)) source))))
+                             (not (equal? (substring s 0 (string-length source))
+                                          source))))
                          (string-split (getenv "CLASSPATH") #\:))
                        ":"))
              #t))
@@ -1386,6 +1388,19 @@ to the OSM opening hours specification.")
                                   "Is-Local-Build: true\n"
                                   "Build-Date: 1970-01-01 00:00:00 +0000\n"))))
              #t))
+         (add-after 'install 'install-share-directories
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out               (assoc-ref outputs "out"))
+                   (share-directories '("applications" "icons" "man" "menu"
+                                        "metainfo" "mime" "pixmaps")))
+               (for-each (lambda (directory)
+                           (copy-recursively (string-append
+                                              "native/linux/tested/usr/share/"
+                                              directory)
+                                             (string-append
+                                              out "/share/" directory)))
+                         share-directories))
+             #t))
          (add-after 'install 'install-bin
            (lambda* (#:key outputs inputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))

gnu/packages/gnome.scm

@@ -155,6 +155,7 @@
   #:use-module (gnu packages polkit)
   #:use-module (gnu packages popt)
   #:use-module (gnu packages pretty-print)
+  #:use-module (gnu packages protobuf)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-crypto)
@@ -1028,7 +1029,7 @@ Library reference documentation.")
 (define-public phodav
   (package
    (name "phodav")
-   (version "2.4")
+   (version "2.5")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnome/sources/" name "/"
@@ -1036,10 +1037,21 @@ Library reference documentation.")
                                 name "-" version ".tar.xz"))
             (sha256
              (base32
-              "1hxq8c5qfah3w7mxcyy3yhzdgswplll31a69p5mqdl04bsvw5pbx"))))
+              "045rdzf8isqmzix12lkz6z073b5qvcqq6ad028advm5gf36skw3i"))))
    (build-system meson-build-system)
+   (arguments
+    `(#:phases
+      (modify-phases %standard-phases
+        (add-before 'check 'start-virtual-dir-server
+          ;; The same server when started by tests/virtual-dir returns an
+          ;; unexpected status (4 instead of 200) and fails a test.  It is
+          ;; unclear why starting it manually here makes it pass.
+          (lambda _
+            (system "tests/virtual-dir-server &")
+            #t)))))
    (native-inputs
-    `(("gettext" ,gettext-minimal)
+    `(("docbook-xml" ,docbook-xml-4.3)
+      ("gettext" ,gettext-minimal)
       ("glib:bin" ,glib "bin")
       ("gtk-doc" ,gtk-doc)
       ("pkg-config" ,pkg-config)))
@@ -2907,7 +2919,13 @@ API add-ons to make GTK+ widgets OpenGL-capable.")
     (description "Glade is a rapid application development (RAD) tool to
 enable quick & easy development of user interfaces for the GTK+ toolkit and
 the GNOME desktop environment.")
-    (license license:lgpl2.0+)))
+    (license license:lgpl2.0+)
+    (native-search-paths (list (search-path-specification
+                                (variable "GLADE_CATALOG_SEARCH_PATH")
+                                (files '("share/glade/catalogs")))
+                               (search-path-specification
+                                (variable "GLADE_MODULE_SEARCH_PATH")
+                                (files '("lib/glade/modules")))))))
 
 (define-public libcroco
   (package
@@ -4033,7 +4051,7 @@ libraries written in C.")
 (define-public vala-0.48
   (package
     (inherit vala)
-    (version "0.48.7")
+    (version "0.48.9")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/vala/"
@@ -4041,7 +4059,7 @@ libraries written in C.")
                                   "vala-" version ".tar.xz"))
               (sha256
                (base32
-                "0lswkb7gj0chas9n3l3dbrm9l71hs77adhvm2v600id2ipi37pi8"))))))
+                "1agyrvslv2yh9ikiw7k5nw6j6il1l2zrzfan0pzdpb9xpg9idslw"))))))
 
 (define-public vte
   (package
@@ -4635,7 +4653,7 @@ and other secrets.  It communicates with the \"Secret Service\" using DBus.")
 (define-public gnome-mines
   (package
     (name "gnome-mines")
-    (version "3.34.0")
+    (version "3.36.1")
     (source
      (origin
        (method url-fetch)
@@ -4643,8 +4661,7 @@ and other secrets.  It communicates with the \"Secret Service\" using DBus.")
                            (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
-        (base32
+        (base32 "0m2680r94nk61imym4x73j03jwfjd8cxm592m5ybiqdfdw6i723i"))))
-         "1spxa6qr1y8s5rrsvpciywpvhk812ngn95s1apaxaigwy2g1iw54"))))
     (build-system meson-build-system)
     (arguments
      '(#:glib-or-gtk? #t
@@ -5158,7 +5175,7 @@ settings, themes, mouse settings, and startup of other daemons.")
 (define-public totem-pl-parser
  (package
    (name "totem-pl-parser")
-   (version "3.26.3")
+   (version "3.26.5")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnome/sources/totem-pl-parser/"
@@ -5166,7 +5183,7 @@ settings, themes, mouse settings, and startup of other daemons.")
                                 "totem-pl-parser-" version ".tar.xz"))
             (sha256
              (base32
-              "13a45py2j1r9967zgww8kd24bn2fhycd4m3kzr90sxx9l2w03z8f"))))
+              "132jihnf51zs98yjkc6jxyqib4f3dawpjm17g4bj4j78y93dww2k"))))
    (build-system meson-build-system)
    (arguments
     ;; FIXME: Tests require gvfs.
@@ -5646,16 +5663,15 @@ as possible!")
 (define-public grilo
   (package
     (name "grilo")
-    (version "0.3.10")
+    (version "0.3.12")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://gnome/sources/" name "/"
+       (uri (string-append "mirror://gnome/sources/grilo/"
                            (version-major+minor version) "/"
-                           name "-" version ".tar.xz"))
+                           "grilo-" version ".tar.xz"))
        (sha256
-        (base32
+        (base32 "0w8sq5g6g1rg85h53vbll8va70fcp6082mlpmy98aa03444ddyyv"))))
-         "1s7ilyywf18q26aj5c4709kfizqywjlnacp4jzmj9v9i9kkv4i3y"))))
     (build-system meson-build-system)
     (native-inputs
      `(("glib:bin" ,glib "bin")         ; for glib-mkenums and glib-genmarshal
@@ -5687,7 +5703,7 @@ for application developers.")
 (define-public grilo-plugins
   (package
     (name "grilo-plugins")
-    (version "0.3.10")
+    (version "0.3.11")
     (source
      (origin
        (method url-fetch)
@@ -5695,8 +5711,7 @@ for application developers.")
                            (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
-        (base32
+        (base32 "0wyd3n5mn7b77hxylkc3f62v01mlavh96901pz342hwrn42ydqnx"))))
-         "0jldaixc4kzycn5v8ixkjld1n0z3dp0l1p3vchgdwpvdvc7kcfw0"))))
     (build-system meson-build-system)
     (native-inputs
      `(("gettext" ,gettext-minimal)
@@ -6169,7 +6184,7 @@ USB transfers with your high-level application or system daemon.")
 (define-public simple-scan
   (package
     (name "simple-scan")
-    (version "3.36.4")
+    (version "3.36.6")
     (source
      (origin
        (method url-fetch)
@@ -6177,7 +6192,7 @@ USB transfers with your high-level application or system daemon.")
                            (version-major+minor version) "/"
                            "simple-scan-" version ".tar.xz"))
        (sha256
-        (base32 "09gmzrlljdqkj3w6wa1c27wypy6j8z9dw3jzv9izfqvp38liibsn"))))
+        (base32 "0x9hzqnji5l966yy2k5gppl8hqasn3sd5an4sr8srjmncxcs80ys"))))
     (build-system meson-build-system)
     ;; TODO: Fix icons in home screen, About dialogue, and scan menu.
     (arguments
@@ -8263,7 +8278,7 @@ easy, safe, and automatic.")
 (define-public tracker
   (package
     (name "tracker")
-    (version "2.3.4")
+    (version "2.3.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/tracker/"
@@ -8271,7 +8286,7 @@ easy, safe, and automatic.")
                                   "tracker-" version ".tar.xz"))
               (sha256
                (base32
-                "0vai0qz9jn3z5dlzysynwhbbmslp84ygdql81f5wfxxr98j54yap"))))
+                "1ixxyqjlv7pnl4j8g6b72fkbjvzfspza8y71ppkncry8i6xkr223"))))
     (build-system meson-build-system)
     (arguments
      `(#:glib-or-gtk? #t
@@ -8333,7 +8348,7 @@ endpoint and it understands SPARQL. ")
 (define-public tracker-miners
   (package
     (name "tracker-miners")
-    (version "2.3.3")
+    (version "2.3.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/tracker-miners/"
@@ -8341,7 +8356,7 @@ endpoint and it understands SPARQL. ")
                                   "/tracker-miners-" version ".tar.xz"))
               (sha256
                (base32
-                "06abxrnrz7xayykrabn135rpsm6z0fqw7gibrb9j09l6swlalwkl"))))
+                "10wy8d8ski52k809p7s6lbw72qmg05bbmhnl00vx4qrbzqyxvc0b"))))
     (build-system meson-build-system)
     (arguments
      `(#:glib-or-gtk? #t
@@ -9159,7 +9174,7 @@ existing databases over the internet.")
        ("gtk+" ,gtk+)
        ("gobject-introspection" ,gobject-introspection)
        ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
-       ("libhandy" ,libhandy)
+       ("libhandy" ,libhandy-0.0)
        ("libnotify" ,libnotify)
        ("libsoup" ,libsoup)
        ("nautilus" ,nautilus)
@@ -10268,7 +10283,7 @@ hexadecimal or ASCII.  It is useful for editing binary files in general.")
 (define-public libdazzle
   (package
     (name "libdazzle")
-    (version "3.34.1")
+    (version "3.37.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/libdazzle/"
@@ -10276,7 +10291,7 @@ hexadecimal or ASCII.  It is useful for editing binary files in general.")
                                   "libdazzle-" version ".tar.xz"))
               (sha256
                (base32
-                "01cmcrd75b7ns7j2b4p6h7pv68vjhkcl9zbvzzx7pf4vknxir61x"))))
+                "03r5cr11dc031qa3694bpgm3lajrhiiln67kvl7vjj4q0scf7w7x"))))
     (build-system meson-build-system)
     (arguments
      `(#:phases
@@ -10480,20 +10495,20 @@ advanced image management tool")
 (define-public libhandy
   (package
     (name "libhandy")
-    (version "0.0.12")
+    (version "1.0.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-             (url "https://source.puri.sm/Librem5/libhandy")
+             (url "https://gitlab.gnome.org/GNOME/libhandy")
-             (commit (string-append "v" version))))
+             (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "09wlknarzsbk9hr5ws6s7x5kibkhx9ayrbhshfqib4zkhq2f76hw"))))
+        (base32 "193y09yy0302x8fkyrnq591m805xp68bkd93fl5qggxi52k8pj0v"))))
     (build-system meson-build-system)
     (arguments
      `(#:configure-flags
-       '("-Dglade_catalog=disabled"
+       '("-Dglade_catalog=enabled"
          "-Dgtk_doc=true")
        #:phases
        (modify-phases %standard-phases
@@ -10504,7 +10519,9 @@ advanced image management tool")
              (setenv "DISPLAY" ":1")
              #t)))))
     (inputs
-     `(("gtk+" ,gtk+)))
+     `(("gtk+" ,gtk+)
+       ("glade" ,glade3)
+       ("libxml2" ,libxml2)))
     (native-inputs
      `(("glib:bin" ,glib "bin")
        ("gobject-introspection" ,gobject-introspection) ; for g-ir-scanner
@@ -10523,6 +10540,24 @@ interfaces for mobile devices using GTK+.  It provides responsive GTK+ widgets
 for usage on small and big screens.")
     (license license:lgpl2.1+)))
 
+(define-public libhandy-0.0
+  (package
+    (inherit libhandy)
+    (version "0.0.13")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.gnome.org/GNOME/libhandy")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name "libhandy" version))
+       (sha256
+        (base32 "1y23k623sjkldfrdiwfarpchg5mg58smcy1pkgnwfwca15wm1ra5"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments libhandy)
+       ((#:configure-flags flags)
+        '(list "-Dglade_catalog=disabled" "-Dgtk_doc=true"))))))
+
 (define-public libgit2-glib
   (package
     (name "libgit2-glib")
@@ -10897,7 +10932,7 @@ join_paths\\('build-aux', 'post_install.py'\\)\\)")
        ("json-glib" ,json-glib)
        ("libcanberra" ,libcanberra)
        ("libgee" ,libgee)
-       ("libhandy" ,libhandy)
+       ("libhandy" ,libhandy-0.0)
        ("libpeas" ,libpeas)
        ("libsecret" ,libsecret)
        ("libunwind" ,libunwind)
@@ -11336,3 +11371,70 @@ environment (IDE) for writing GNOME-based software.  It features fuzzy search,
 auto-completion, a mini code map, documentation browsing, Git integration, an
 integrated profiler via Sysprof, debugging support, and more.")
     (license license:gpl3+)))
+
+(define-public komikku
+  (package
+    (name "komikku")
+    (version "0.19.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/valos/Komikku/")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "16d7k500nd9klnjqqcgk3glhv2sy78yndkz3n0x7lynvblsy45kk"))))
+    (build-system meson-build-system)
+    (arguments
+     `(#:glib-or-gtk? #t
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-sources
+           (lambda _
+             (substitute* "komikku/utils.py"
+               (("from komikku\\.servers import get_servers_list")
+                ;; code following that line should migrate old databases
+                ;; but the line itself results in an import error
+                "return data_dir_path"))))
+         (add-after 'unpack 'skip-gtk-update-icon-cache
+           (lambda _
+             (substitute* "meson_post_install.py"
+               (("gtk-update-icon-cache") (which "true")))
+             #t))
+         (add-after 'glib-or-gtk-wrap 'python-and-gi-wrap
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let ((prog (string-append (assoc-ref outputs "out")
+                                       "/bin/komikku")))
+              (wrap-program prog
+                `("PYTHONPATH" = (,(getenv "PYTHONPATH")))
+                `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH"))))
+              #t))))))
+    (inputs
+     `(("gtk+" ,gtk+)
+       ("libhandy" ,libhandy)
+       ("libnotify" ,libnotify)
+       ("libsecret" ,libsecret)
+       ("python-beautifulsoup4" ,python-beautifulsoup4)
+       ("python-cloudscraper" ,python-cloudscraper)
+       ("python-dateparser" ,python-dateparser)
+       ("python-keyring" ,python-keyring)
+       ("python-lxml" ,python-lxml)
+       ("python-magic" ,python-magic)
+       ("python-pillow" ,python-pillow)
+       ("python-pure-protobuf" ,python-pure-protobuf)
+       ("python-pycairo" ,python-pycairo)
+       ("python-pygobject" ,python-pygobject)
+       ("python-unidecode" ,python-unidecode)))
+    (native-inputs
+     `(("desktop-file-utils" ,desktop-file-utils)
+       ("gettext" ,gettext-minimal)
+       ("glib:bin" ,glib "bin")
+       ("gobject-introspection" ,gobject-introspection)
+       ("pkg-config" ,pkg-config)))
+    (home-page "https://gitlab.com/valos/Komikku")
+    (synopsis "Manga reader for GNOME")
+    (description "Komikku is an online/offline manga reader for GNOME,
+developed with the aim of being used with the Librem 5 phone.")
+    (license license:gpl3+)))

gnu/packages/gnupg.scm

@@ -2,7 +2,7 @@
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013, 2015, 2018 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014, 2018 Eric Bavier <bavier@member.fsf.org>
-;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2014, 2015, 2016, 2020 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015, 2016, 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
@@ -254,7 +254,7 @@ compatible to GNU Pth.")
 (define-public gnupg
   (package
     (name "gnupg")
-    (version "2.2.20")
+    (version "2.2.23")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnupg/gnupg/gnupg-" version
@@ -262,7 +262,7 @@ compatible to GNU Pth.")
               (patches (search-patches "gnupg-default-pinentry.patch"))
               (sha256
                (base32
-                "0c6a4v9p6qzhsw1pfcwc459bxpc8hma0w9z8iqb9khvligack9q4"))))
+                "0p6ss4f3vlkf91pmp27bmvfr5bdxxi0pb3dmxpqljglbsx4mxd8h"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -400,23 +400,14 @@ libskba (working with X.509 certificates and CMS data).")
 (define-public gpgme
   (package
     (name "gpgme")
-    (version "1.13.1")
+    (version "1.14.0")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "mirror://gnupg/gpgme/gpgme-" version ".tar.bz2"))
       (sha256
-       (base32 "0imyjfryvvjdbai454p70zcr95m94j9xnzywrlilqdw2fqi0pqy4"))))
+       (base32 "01s3rlspykbm9vmi5rfbdm3d20ip6yni69r48idqzlmhlq8ggwff"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-before 'check 'disable-failing-test
-           ;; XXX gnupg@2.2.20 breaks the expected JSON response for this test.
-           (lambda _
-             (substitute* "tests/json/t-json.c"
-               (("\"t-keylist-secret\", ") ""))
-             #t)))))
     (native-inputs
      `(("gnupg" ,gnupg)))
     (propagated-inputs
@@ -877,6 +868,8 @@ enter a passphrase when required by @code{gpg} or other software.")))
   (package
     (inherit pinentry-tty)
     (name "pinentry-gtk2")
+    (arguments
+     `(#:configure-flags '("--enable-fallback-curses")))
     (inputs
      `(("gtk+" ,gtk+-2)
        ("glib" ,glib)
@@ -895,7 +888,8 @@ passphrase when @code{gpg} is run and needs it.")))
        ("glib" ,glib)
        ,@(package-inputs pinentry-tty)))
     (arguments
-     `(#:configure-flags '("--enable-pinentry-gnome3")))
+     `(#:configure-flags '("--enable-pinentry-gnome3"
+                           "--enable-fallback-curses")))
     (description
      "Pinentry provides a console and a GUI designed for use with GNOME@tie{}3
 that allows users to enter a passphrase when required by @code{gpg} or other
@@ -905,6 +899,8 @@ software.")))
   (package
     (inherit pinentry-tty)
     (name "pinentry-qt")
+    (arguments
+     `(#:configure-flags '("--enable-fallback-curses")))
     (inputs
      `(("qtbase" ,qtbase)
        ,@(package-inputs pinentry-tty)))
@@ -921,7 +917,8 @@ passphrase when @code{gpg} is run and needs it.")))
         (inherit (package-source pinentry-tty))
         (patches (search-patches "pinentry-efl.patch"))))
     (arguments
-     '(#:configure-flags '("--enable-pinentry-efl")
+     '(#:configure-flags '("--enable-pinentry-efl"
+                           "--enable-fallback-curses")
        #:phases
        (modify-phases %standard-phases
          (replace 'bootstrap

gnu/packages/gnuzilla.scm

@@ -1139,11 +1139,11 @@ standards of the IceCat project.")
        (cpe-version . ,(first (string-split version #\-)))))))
 
 ;; Update this together with icecat!
-(define %icedove-build-id "20200726000000") ;must be of the form YYYYMMDDhhmmss
+(define %icedove-build-id "20200825000000") ;must be of the form YYYYMMDDhhmmss
 (define-public icedove
   (package
     (name "icedove")
-    (version "68.11.0")
+    (version "68.12.0")
     (source icecat-source)
     (properties
      `((cpe-name . "thunderbird_esr")))
@@ -1429,7 +1429,7 @@ standards of the IceCat project.")
         ;; in the Thunderbird release tarball.  We don't use the release
         ;; tarball because it duplicates the Icecat sources and only adds the
         ;; "comm" directory, which is provided by this repository.
-        ,(let ((changeset "a247645d951bcedb356a0d9f273e878a7d4d2180"))
+        ,(let ((changeset "b41cdff70b185358d9c4c1d4a36cfad15a24f001"))
            (origin
              (method hg-fetch)
              (uri (hg-reference
@@ -1438,7 +1438,7 @@ standards of the IceCat project.")
              (file-name (string-append "thunderbird-" version "-checkout"))
              (sha256
               (base32
-               "0nf7ic1sw7yawnwrxwm3b4yl2cn4hp8szzh0xd462s1hjm59ksjl")))))
+               "1xvky8p5r41mxdyg9amydy94p51wmmdwdz0zq2vzspr9viixf7xm")))))
        ("autoconf" ,autoconf-2.13)
        ("cargo" ,rust "cargo")
        ("clang" ,clang)

gnu/packages/golang.scm

@@ -18,6 +18,7 @@
 ;;; Copyright © 2019, 2020 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2020 Jack Hill <jackhill@jackhill.us>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
+;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1047,6 +1048,30 @@ Features include:
 optimized for performance yet simple to use.")
       (license license:expat))))
 
+(define-public go-github-com-tv42-httpunix
+  (let ((commit "2ba4b9c3382c77e7b9ea89d00746e6111d142a22")
+        (revision "0"))
+    (package
+      (name "go-github-com-tv42-httpunix")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/tv42/httpunix.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0xbwpip2hsfhd2kd878jn5ndl8y1i9658lggha4x3xb5m1rsds9w"))))
+      (build-system go-build-system)
+      (arguments
+       '(#:import-path "github.com/tv42/httpunix"))
+      (home-page "https://github.com/tv42/httpunix")
+      (synopsis "Go library to talk HTTP over Unix domain sockets")
+      (description "This package is a Go library to talk HTTP over Unix domain
+sockets.")
+      (license license:expat))))
+
 (define-public go-github-com-blang-semver
   (let ((commit "60ec3488bfea7cca02b021d106d9911120d25fe9")
         (revision "0"))
@@ -4180,7 +4205,7 @@ data serialization format.")
 (define-public go-github-com-mattn-go-zglob
   (package
     (name "go-github-com-mattn-go-zglob")
-    (version "0.0.1")
+    (version "0.0.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -4189,7 +4214,7 @@ data serialization format.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1sncdyq5fbd42al4amyy91h7vlzm3wm6c9vl8za2pjgfgsd581fz"))))
+                "1923lvakm66mzy62jmngdvcmbmiqclinsvnghs3907rgygnx1qc1"))))
     (build-system go-build-system)
     (arguments
      `(#:import-path "github.com/mattn/go-zglob"))

gnu/packages/gpodder.scm

@@ -38,7 +38,7 @@
 (define-public gpodder
   (package
     (name "gpodder")
-    (version "3.10.15")
+    (version "3.10.16")
     (source
      (origin
        (method git-fetch)
@@ -47,8 +47,9 @@
              (commit version)))
        (sha256
         (base32
-         "0ghbanj142n0hgydzfjmnkdgri2kswsjal3mn10c723kih4ir4yr"))
+         "0pbpaasd7kj6y25nm45y1qyb9sxd4570f7g6zkfcpf6pa3nx7qkq"))
-       (file-name (git-file-name name version))))
+       (file-name (git-file-name name version))
+       (patches (search-patches "gpodder-disable-updater.patch"))))
     (build-system python-build-system)
     (native-inputs
      `(("intltool" ,intltool)

gnu/packages/graph.scm

@@ -121,63 +121,6 @@ more.")
     (home-page "https://pypi.org/project/python-igraph/")
     (synopsis "Python bindings for the igraph network analysis library")))
 
-(define-public r-igraph
-  (package
-    (name "r-igraph")
-    (version "1.2.5")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "igraph" version))
-       (sha256
-        (base32
-         "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c"))))
-    (build-system r-build-system)
-    (native-inputs
-     `(("gfortran" ,gfortran)))
-    (inputs
-     `(("gmp" ,gmp)
-       ("glpk" ,glpk)
-       ("libxml2" ,libxml2)
-       ("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-magrittr" ,r-magrittr)
-       ("r-matrix" ,r-matrix)
-       ("r-pkgconfig" ,r-pkgconfig)))
-    (home-page "https://igraph.org")
-    (synopsis "Network analysis and visualization")
-    (description
-     "This package provides routines for simple graphs and network analysis.
-It can handle large graphs very well and provides functions for generating
-random and regular graphs, graph visualization, centrality methods and much
-more.")
-    (license license:gpl2+)))
-
-(define-public r-diffusionmap
-  (package
-    (name "r-diffusionmap")
-    (version "1.2.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "diffusionMap" version))
-       (sha256
-        (base32
-         "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
-    (properties `((upstream-name . "diffusionMap")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-igraph" ,r-igraph)
-       ("r-matrix" ,r-matrix)
-       ("r-scatterplot3d" ,r-scatterplot3d)))
-    (home-page "https://www.r-project.org")
-    (synopsis "Diffusion map")
-    (description "This package implements the diffusion map method of data
-parametrization, including creation and visualization of diffusion maps,
-clustering with diffusion K-means and regression using the adaptive regression
-model.")
-    (license license:gpl2)))
-
 (define-public r-rgraphviz
   (package
     (name "r-rgraphviz")

gnu/packages/graphics.scm

@@ -824,7 +824,7 @@ other vector formats such as:
 (define-public ogre
   (package
     (name "ogre")
-    (version "1.12.5")
+    (version "1.12.6")
     (source
      (origin
        (method git-fetch)
@@ -834,7 +834,7 @@ other vector formats such as:
              (recursive? #t)))          ;for Dear ImGui submodule
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1sx0jsw4kmb4ycf62bgx3ygwv8k1cgjx52y47d7dk07z6gk6wpyj"))))
+        (base32 "1ap3krrl55hswv1n2r3ijf3xrb3kf9dnqvwyrc0fgnc7j7vd45sk"))))
     (build-system cmake-build-system)
     (arguments
      '(#:phases
@@ -1208,7 +1208,7 @@ realistic reflections, shading, perspective and other effects.")
        ("python" ,python-2)
        ("cython" ,python2-cython)))
     (native-inputs
-     `(("pandoc" ,ghc-pandoc)
+     `(("pandoc" ,pandoc)
        ("bison" ,bison)
        ("flex" ,flex)
        ("doxygen" ,doxygen)

gnu/packages/gtk.scm

@@ -229,7 +229,7 @@ affine transformation (scale, rotation, shear, etc.).")
 (define-public libdatrie
   (package
     (name "libdatrie")
-    (version "0.2.11")
+    (version "0.2.12")
     (source
      (origin
        (method url-fetch)
@@ -237,7 +237,7 @@ affine transformation (scale, rotation, shear, etc.).")
         (string-append "https://linux.thai.net/pub/ThaiLinux/software/"
                        "libthai/libdatrie-" version ".tar.xz"))
        (sha256
-        (base32 "0jz9k0dd8jim4iyk5xrhkkdm4zq2ly6aw317ydjss44ymg97nz2l"))))
+        (base32 "0jdi01pcxv0b24zbjy7zahawsqqqw4mv94f2yy01zh4n796wqba5"))))
     (build-system gnu-build-system)
     (outputs '("out" "doc"))
     (arguments
@@ -916,14 +916,14 @@ application suites.")
 (define-public guile-cairo
   (package
     (name "guile-cairo")
-    (version "1.10.0")
+    (version "1.11.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://savannah/guile-cairo/guile-cairo-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0p6xrhf2k6n5dybn88050za7h90gnd7534n62l53vsca187pwgdf"))
+                "1gc642r9ndsjhhmh9bl5cbd3dwvy4dpxwhr0zpsw43y9nmz37xpl"))
               (modules '((guix build utils)))
               (snippet
                (begin
@@ -945,7 +945,8 @@ application suites.")
     (arguments
      ;; Uses of 'scm_t_uint8' & co. are deprecated; don't stop the build
      ;; because of them.
-     '(#:configure-flags '("--disable-Werror")))
+     '(#:configure-flags '("--disable-Werror")
+       #:make-flags '("GUILE_AUTO_COMPILE=0")))     ; to prevent guild warnings
     (inputs
      `(("guile-lib" ,guile-lib)
        ("expat" ,expat)

gnu/packages/guile-xyz.scm

@@ -798,6 +798,7 @@ using Guile's foreign function interface.")
     (build-system guile-build-system)
     (arguments
      '(#:source-directory "src"
+       #:compile-flags '("--r6rs" "-Wunbound-variable" "-Warity-mismatch")
        #:phases (modify-phases %standard-phases
                   (add-after 'unpack 'move-files-around
                     (lambda _
@@ -806,8 +807,7 @@ using Guile's foreign function interface.")
                       (mkdir-p "src/pfds")
                       (for-each (lambda (file)
                                   (rename-file file
-                                               (string-append "src/pfds/"
+                                    (string-append "src/pfds/" file)))
-                                                              file)))
                                 '("bbtrees.sls"
                                   "deques"
                                   "deques.sls"
@@ -821,15 +821,6 @@ using Guile's foreign function interface.")
                                   "queues.sls"
                                   "sequences.sls"
                                   "sets.sls"))
-
-                      ;; In Guile <= 2.2.4, there's no way to tell 'guild
-                      ;; compile' to accept the ".sls" extension.  So...
-                      (for-each (lambda (file)
-                                  (rename-file file
-                                               (string-append
-                                                (string-drop-right file 4)
-                                                ".scm")))
-                                (find-files "." "\\.sls$"))
                       #t)))))
     (native-inputs
      `(("guile" ,guile-3.0)))
@@ -853,6 +844,36 @@ Vicare Scheme and IronScheme.  Right now it contains:
 @end itemize\n")
     (license license:bsd-3)))
 
+(define-public guile-prometheus
+  (let ((commit "cbc6e1b03512443a03d66414c426adb8470b5f2b")
+        (revision "0"))
+    (package
+    (name "guile-prometheus")
+    (version (git-version "0" revision commit))
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://git.cbaines.net/git/guile/prometheus")
+                    (commit commit)))
+              (sha256
+               (base32
+                "1k1qg4ia87w2ipnf8cpikdc67lxi5bmahkhgk2x0i9ibdyvqb7np"))
+              (file-name (string-append name "-" version "-checkout"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("autoconf" ,autoconf)
+       ("automake" ,automake)))
+    (inputs
+     `(("guile" ,guile-3.0)))
+    (home-page "https://git.cbaines.net/guile/prometheus")
+    (synopsis "Prometheus client library for Guile")
+    (description
+     "This Guile library provides instrumentation code intended to be used
+with the Prometheus time series service.  Counter, gauge and histogram metric
+types are supported.")
+    (license license:gpl3+))))
+
 (define-public guile2.2-pfds
   (package
     (inherit guile-pfds)
@@ -862,7 +883,18 @@ Vicare Scheme and IronScheme.  Right now it contains:
      (substitute-keyword-arguments (package-arguments guile-pfds)
        ((#:phases phases)
         `(modify-phases ,phases
-           (delete 'work-around-guile-bug)))))))
+           (delete 'work-around-guile-bug)
+           (add-after 'move-files-around 'sls->scm
+             (lambda _
+               ;; In Guile <= 2.2.4, there's no way to tell 'guild
+               ;; compile' to accept the ".sls" extension.  So...
+               (for-each (lambda (file)
+                           (rename-file file
+                                        (string-append
+                                         (string-drop-right file 4)
+                                         ".scm")))
+                         (find-files "." "\\.sls$"))
+               #t))))))))
 
 (define-public guile3.0-pfds
   (deprecated-package "guile3.0-pfds" guile-pfds))
@@ -1729,19 +1761,20 @@ capabilities.")
     (license license:gpl3+)))
 
 (define-public g-golf
-  (let ((commit "5d2903afb4b6b65c22f587835d8fdff91916e5ee"))
+  (let ((commit   "84e894eb7945c3bcdf7f8d5135c1be3efa524c92")
+        (revision "822"))
     (package
       (name "g-golf")
-      (version (git-version "1" "804" commit))
+      (version (git-version "0.1.0" revision commit))
-      (source (origin
+      (source
+       (origin
          (method git-fetch)
          (uri (git-reference
                (url "https://git.savannah.gnu.org/git/g-golf.git")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-                 (base32
+          (base32 "1pkcij65zy2lkip5yrfzj85nq17pp9mrf0d4sk6hpjqr4kd0bxd5"))))
-                  "1xkb6a5d3i9s8lpb5cf06bd64p5srqnnhn5l0b2f5csbvyz8hmmh"))))
       (build-system gnu-build-system)
       (native-inputs
        `(("autoconf" ,autoconf)
@@ -2437,11 +2470,11 @@ The picture values can directly be displayed in Geiser.")
                       guile-picture-language))
 
 (define-public guile-studio
-  (let ((commit "d24d59a68e3f1fa9477e3430fc48a2efe97b805d")
+  (let ((commit "5c05b03e8a5c450f7358ceec7ea602f29c49d54e")
         (revision "1"))
     (package
       (name "guile-studio")
-      (version (git-version "0.0.2" revision commit))
+      (version (git-version "0.0.3" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -2450,7 +2483,7 @@ The picture values can directly be displayed in Geiser.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0kqi0q8a7si65n21b7gn8vbninwcg0fqy5hmvy3l1bi6iync20zr"))))
+                  "11wyf6x7mhyhimv0cd57pl39zgav9hc9ljqi3g2g35b264hylpnx"))))
       (build-system gnu-build-system)
       (arguments
        `(#:modules
@@ -2487,6 +2520,7 @@ The picture values can directly be displayed in Geiser.")
          ("emacs-geiser" ,emacs-geiser)
          ("emacs-company" ,emacs-company)
          ("emacs-flycheck" ,emacs-flycheck)
+         ("emacs-flycheck-guile" ,emacs-flycheck-guile)
          ("emacs-smart-mode-line" ,emacs-smart-mode-line)
          ("emacs-paren-face" ,emacs-paren-face)
          ("adwaita-icon-theme" ,adwaita-icon-theme)))
@@ -2827,6 +2861,36 @@ parameters, which  define* and lambda* special forms")
 denote the invalidity of certain code paths in a Scheme program.")
     (license license:gpl3+)))
 
+(define-public guile-srfi-158
+  (package
+    (name "guile-srfi-158")
+    (version "0.0.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/mjbecze/guile-srfi-158.git")
+             (commit version)))
+       (sha256
+        (base32
+         "0b8hlv1bldbcwkcxi9y8mm6xp5gbgpg7b15bwqxv70iynl9d9a7c"))
+       (file-name (git-file-name name version))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("guile" ,guile-3.0)))
+    (home-page "https://gitlab.com/samplet/guile-srfi-158")
+    (synopsis "SRFI 158 (Generators and Accumulators) for Guile")
+    (description "This package provides an implementation of SRFI 158
+for Guile.  SRFI 158 defines utility procedures that create,
+transform, and consume generators.  It also defines procedures that
+return accumulators.  It is implemented by wrapping the sample
+implementation in a thin Guile compatibility layer.")
+    (license license:gpl3+)))
+
 (define-public guile-srfi-159
   (let ((commit "1bd98abda2ae4ef8f36761a167903e55c6bda7bb")
         (revision "0"))
@@ -2857,6 +2921,45 @@ formatting combinators specified by
 more expressive and flexible than the traditional @code{format} procedure.")
       (license license:bsd-3))))
 
+(define-public guile-srfi-180
+  (let ((commit "9188bf9724c6d320ef804579d222e855b007b193")
+        (revision "0"))
+    (package
+      (name "guile-srfi-180")
+      (version (git-version "0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/scheme-requests-for-implementation/srfi-180.git")
+               (commit commit)))
+         (sha256
+          (base32
+           "08lf70rsak8mwfij55xc37pg9zg7c87fizmhz7ln46skzj68sl3y"))
+         (modules '((guix build utils)))
+         (snippet
+          '(begin
+             (delete-file-recursively "srfi/files")
+             (delete-file "srfi/run-r7rs-checks.guile.scm")
+             (delete-file "srfi/run-r7rs-checks.scm")
+             (delete-file "srfi/check.scm")
+             #t))
+         (file-name (git-file-name name version))))
+      (build-system guile-build-system)
+      (arguments
+       '(#:not-compiled-file-regexp "body\\.scm$"))
+      (native-inputs
+       `(("guile" ,guile-3.0)))
+      (propagated-inputs
+       `(("guile-srfi-145" ,guile-srfi-145)))
+      (home-page "https://srfi.schemers.org/srfi-180/")
+      (synopsis "JSON parser and printer for Guile")
+      (description
+       "This library implements a JavaScript Object Notation (JSON) parser and printer.
+It also supports parsing JSON objects that may be bigger than memory with a streaming
+API.")
+      (license license:expat))))
+
 (define-public emacsy
   (package
     (name "emacsy")
@@ -2939,20 +3042,20 @@ in C using Gtk+-3 and WebKitGtk.")
     (license license:gpl3+)))
 
 (define-public emacsy-minimal
-  (let ((commit "v0.4.1-28-gd459ca1"))
+  (let ((commit "v0.4.1-31-g415d96f"))
     (package
       (inherit emacsy)
       (name "emacsy-minimal")
       (version (string-drop commit 1))
-      (source (origin
+      (source
+       (origin
          (method git-fetch)
          (uri (git-reference
                (url "https://git.savannah.gnu.org/git/emacsy.git")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-                 (base32
+          (base32 "1cs1i1hxwrv0a512j54yrvfh743nci1chx6qjgp4jyzq98ncvxgg"))))
-                  "1ps15w8cxj9kc18gmvys9jv9xa1qqa7m43ismv34l3cmhddrn0sr"))))
       (build-system gnu-build-system)
       (inputs
        `(("guile" ,guile-2.2)
@@ -3005,16 +3108,16 @@ perform geometrical transforms on JPEG images.")
 (define-public nomad
   (package
     (name "nomad")
-    (version "0.2.0-alpha")
+    (version "0.2.0-alpha-100-g6a565d3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://git.savannah.gnu.org/git/nomad.git")
+                    (url "https://git.savannah.gnu.org/git/nomad.git/")
                     (commit version)))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1z2z5x37v1qrk2vb8qlz2yj030iirzzd0maa9fjxzlqkrg6krbaj"))))
+                "0anmprm63a88kii251rl296v1g4iq62r6n4nssx5jbc0hzkknanz"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -3025,36 +3128,35 @@ perform geometrical transforms on JPEG images.")
        ("guile" ,guile-2.2)
        ("glib:bin" ,glib "bin")
        ("texinfo" ,texinfo)
+       ("gettext" ,gnu-gettext)
        ("perl" ,perl)))
     (inputs
-     `(("guile" ,guile-2.2)
+     `(;; Guile
+       ("guile" ,guile-2.2)
        ("guile-lib" ,guile2.2-lib)
        ("guile-readline" ,guile2.2-readline)
        ("guile-gcrypt" ,guile2.2-gcrypt)
        ("gnutls" ,gnutls)
+       ("g-golf" ,g-golf)
        ("shroud" ,shroud)
        ("emacsy" ,emacsy-minimal)
+       ;; Gtk
        ("glib" ,glib)
        ("dbus-glib" ,dbus-glib)
+       ("glib-networking" ,glib-networking)
        ("gtk+" ,gtk+)
        ("gtk+:bin" ,gtk+ "bin")
-       ("gtksourceview" ,gtksourceview)
        ("webkitgtk" ,webkitgtk)
-       ("g-golf" ,g-golf)
+       ("gtksourceview" ,gtksourceview)
-       ("xorg-server" ,xorg-server)))
+       ("vte" ,vte)
-    (propagated-inputs
+       ;; Gstreamer
-     `(("glib" ,glib)
-       ("glib-networking" ,glib-networking)
        ("gstreamer" ,gstreamer)
        ("gst-plugins-base" ,gst-plugins-base)
        ("gst-plugins-good" ,gst-plugins-good)
        ("gst-plugins-bad" ,gst-plugins-bad)
        ("gst-plugins-ugly" ,gst-plugins-ugly)
-       ("gtk+" ,gtk+)
+       ;; Util
-       ("gtksourceview" ,gtksourceview)
+       ("xorg-server" ,xorg-server)))
-       ("vte" ,vte)
-       ("webkitgtk" ,webkitgtk)
-       ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)))
     (arguments
      `(#:modules ((guix build gnu-build-system)
                   (guix build utils)
@@ -3073,48 +3175,39 @@ perform geometrical transforms on JPEG images.")
          (add-after 'install 'wrap-binaries
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((out        (assoc-ref outputs "out"))
-                    (gio-deps (map (cut assoc-ref inputs <>)
-                                   '("glib-networking"
-                                     "glib"
-                                     "gstreamer"
-                                     "gst-plugins-base"
-                                     "gst-plugins-good"
-                                     "gst-plugins-bad"
-                                     "gst-plugins-ugly")))
-                    (gio-mod-path (map (cut string-append <>
-                                            "/lib/gio/modules")
-                                       gio-deps))
                     (effective  (read-line (open-pipe*
                                             OPEN_READ
                                             "guile" "-c"
                                             "(display (effective-version))")))
-                    (deps (map (cut assoc-ref inputs <>)
+                    (gst-plugins (map (lambda (i)
-                               '("emacsy" "guile-lib" "guile-readline"
+                                        (string-append (assoc-ref inputs i)
-                                 "g-golf" "shroud")))
+                                                       "/lib/gstreamer-1.0"))
-                    (scm-path (map (cut string-append <>
+                                      `("gstreamer"
-                                        "/share/guile/site/" effective)
+                                        "gst-plugins-base"
-                                   `(,out ,@deps)))
+                                        "gst-plugins-good"
-                    (go-path (map (cut string-append <>
+                                        "gst-plugins-bad"
-                                       "/lib/guile/" effective "/site-ccache")
+                                        "gst-plugins-ugly")))
-                                  `(,out ,@deps)))
+                    (out-append (lambda (. args)
-                    (progs (map (cut string-append out "/bin/" <>)
+                                  (apply string-append out args)))
-                                '("nomad"))))
+                    (gi-path    (out-append "/lib/girepository-1.0"))
-               (map (cut wrap-program <>
+                    (load-path  (out-append "/share/guile/site/" effective))
-                         `("GIO_EXTRA_MODULES" ":" prefix ,gio-mod-path)
+                    (comp-path  (out-append "/lib/guile/"
-                         `("GUILE_LOAD_PATH" ":" prefix ,scm-path)
+                                            effective "/site-ccache"))
-                         `("GUILE_LOAD_COMPILED_PATH" ":"
+                    (ext-path   (out-append "/libexec/nomad")))
-                           prefix ,go-path))
+               (wrap-program (string-append out "/bin/nomad")
-                    progs)
+                 `("GUILE_LOAD_PATH" ":" prefix
+                   (,load-path
+                    ,(getenv "GUILE_LOAD_PATH")))
+                 `("GUILE_LOAD_COMPILED_PATH" ":" prefix
+                   (,comp-path
+                    ,(getenv "GUILE_LOAD_COMPILED_PATH")))
+                 `("GI_TYPELIB_PATH" ":" prefix
+                   (,gi-path ,(getenv "GI_TYPELIB_PATH")))
+                 `("GIO_EXTRA_MODULES" ":" prefix
+                   (,(getenv "GIO_EXTRA_MODULES")))
+                 `("GST_PLUGIN_SYSTEM_PATH" ":" prefix ,gst-plugins)
+                 `("NOMAD_WEB_EXTENSION_DIR" ":" prefix (,ext-path)))
                #t))))))
-    (native-search-paths
-     (list (search-path-specification
-            (variable "GI_TYPELIB_PATH")
-            (separator ":")
-            (files '("lib/girepository-1.0")))
-           (search-path-specification
-            (variable "NOMAD_WEB_EXTENSION_DIR")
-            (separator ":")
-            (files '("libexec/nomad")))))
     (home-page "https://savannah.nongnu.org/projects/nomad/")
     (synopsis "Extensible Web Browser in Guile Scheme")
     (description "Nomad is a Emacs-like web browser that consists of a modular
@@ -3774,3 +3867,141 @@ between data, in a way that is very similar to WikiData or RDF for instance.
 An object can have relations (in the form of an IRI) that relates it to one or
 more objects or strings, represented by a Json object or an IRI.")
     (license license:gpl3+)))
+
+(define-public guile-struct-pack
+  (package
+    (name "guile-struct-pack")
+    (version "1.1.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/weinholt/struct-pack")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0hd72m821pahjphzyjn26i55542v8makr55xzjll2cycja4wsbc1"))))
+    (build-system guile-build-system)
+    (arguments
+     `(#:compile-flags '("--r6rs" "-Wunbound-variable" "-Warity-mismatch")
+       #:modules ((guix build guile-build-system)
+                  (guix build utils)
+                  (srfi srfi-26)
+                  (ice-9 ftw))
+       #:phases (modify-phases %standard-phases
+                  (add-before 'build 'move-sls-files
+                    (lambda _
+                      ;; Move files under a struct/ directory to reflect the
+                      ;; module hierarchy.
+                      (define dst-folder "struct")
+                      (define (target file)
+                        (string-append dst-folder "/" file))
+                      (define files
+                        (scandir "." (negate (cut member <> '("." "..")))))
+                      (mkdir dst-folder)
+                      (for-each (lambda (file)
+                                  (rename-file file (target file)))
+                                files)
+                      #t)))))
+    (native-inputs
+     `(("guile" ,guile-3.0)))
+    (home-page "https://github.com/weinholt/struct-pack")
+    (synopsis "R6RS library for working with packed byte structures")
+    (description
+     "This is an R6RS library for working with packed byte structures.  It is
+similar to struct in Python or pack and unpack in Perl.")
+    (license license:expat)))
+
+(define-public guile-machine-code
+  (package
+    (name "guile-machine-code")
+    (version "2.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/weinholt/machine-code")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0wzj3caj2jypzyjqfkfqkvr3kkbjabsnhldv9kvnx9w9qnria5yd"))))
+    (build-system guile-build-system)
+    (arguments
+     `(#:compile-flags '("--r6rs" "-Wunbound-variable" "-Warity-mismatch")
+       #:modules ((guix build guile-build-system)
+                  (guix build utils)
+                  (srfi srfi-26)
+                  (ice-9 ftw))
+       #:phases (modify-phases %standard-phases
+                  (add-before 'build 'move-sls-files
+                    (lambda _
+                      ;; Move files under a struct/ directory to reflect the
+                      ;; module hierarchy.
+                      (define dst-folder "machine-code")
+                      (define (target file)
+                        (string-append dst-folder "/" file))
+                      (define files
+                        (scandir "." (negate (cut member <> '("." "..")))))
+                      (mkdir dst-folder)
+                      (for-each (lambda (file)
+                                  (rename-file file (target file)))
+                                files)
+                      #t)))))
+    (native-inputs
+     `(("guile" ,guile-3.0)))
+    (propagated-inputs
+     `(("guile-struct-pack" ,guile-struct-pack)))
+    (home-page "https://github.com/weinholt/machine-code")
+    (synopsis "Tools that relate to machine code and object formats")
+    (description
+     "This project is about the development of tools that relate to machine
+code and object formats; for all architectures.  Here you'll find libraries
+for working with binary code: assembly, disassembly, instruction tables,
+object formats and related areas.")
+    (license license:expat)))
+
+(define-public guile-laesare
+  (package
+    (name "guile-laesare")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/weinholt/laesare")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "15q619gzw717r8r1ql23zfdaibpnp9qqs96032vdc3rj74msxc92"))))
+    (build-system guile-build-system)
+    (arguments
+     `(#:compile-flags '("--r6rs" "-Wunbound-variable" "-Warity-mismatch")
+       #:modules ((guix build guile-build-system)
+                  (guix build utils)
+                  (srfi srfi-26)
+                  (ice-9 ftw))
+       #:phases (modify-phases %standard-phases
+                  (add-before 'build 'move-sls-files
+                    (lambda _
+                      ;; Move files under a laesare directory to reflect
+                      ;; the module hierarchy.
+                      (define dst-folder "laesare")
+                      (define (target file)
+                        (string-append dst-folder "/" file))
+                      (define files
+                        (scandir "." (negate (cut member <> '("." "..")))))
+                      (mkdir dst-folder)
+                      (for-each (lambda (file)
+                                  (rename-file file (target file)))
+                                files)
+                      #t)))))
+    (native-inputs
+     `(("guile" ,guile-3.0)))
+    (home-page "https://github.com/weinholt/laesare")
+    (synopsis "R6RS Scheme library that provides a reader")
+    (description
+     "This is an R6RS Scheme library that provides a reader with some extra
+features not found in the standard read procedure such as a compatible mode
+with support for other RnRS standards and a tolerant mode that continues on
+errors.")
+    (license license:expat)))

gnu/packages/haskell-apps.scm

@@ -12,7 +12,7 @@
 ;;; Copyright © 2019, 2020 Kyle Meyer <kyle@kyleam.com>
 ;;; Copyright © 2015 John Soo <jsoo1@asu.edu>
 ;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2019 Alex Griffin <a@ajgrf.com>
+;;; Copyright © 2019, 2020 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2020 Alexandru-Sergiu Marton <brown121407@member.fsf.org>
 ;;; Copyright © 2020 Brian Leung <bkleung89@gmail.com>
 ;;;
@@ -339,18 +339,18 @@ to @code{cabal repl}).")
 (define-public git-annex
   (package
     (name "git-annex")
-    (version "8.20200810")
+    (version "8.20200908")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://hackage.haskell.org/package/"
                            "git-annex/git-annex-" version ".tar.gz"))
        (sha256
-        (base32 "1wy6ckcf5f6m94gakg1504h1zryail3mmj85sglq03s45vawjcg6"))))
+        (base32 "1113inl10f4m0699ba2zglaqlfqvwhqjkqg6r6m1d5rqv5brswb1"))))
     (build-system haskell-build-system)
     (arguments
      `(#:configure-flags
-       '("--flags=-Android -Assistant -Pairing -Webapp -WebDAV")
+       '("--flags=-Android -Assistant -Pairing -Webapp")
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'patch-shell-for-tests
@@ -448,6 +448,7 @@ to @code{cabal repl}).")
        ("ghc-crypto-api" ,ghc-crypto-api)
        ("ghc-cryptonite" ,ghc-cryptonite)
        ("ghc-data-default" ,ghc-data-default)
+       ("ghc-dav" ,ghc-dav)
        ("ghc-disk-free-space" ,ghc-disk-free-space)
        ("ghc-dlist" ,ghc-dlist)
        ("ghc-edit-distance" ,ghc-edit-distance)
@@ -627,7 +628,7 @@ and mIRC chat codes.")
 (define-public kmonad
   (package
     (name "kmonad")
-    (version "0.3.0")
+    (version "0.4.0")
     (source
      (origin
        (method git-fetch)
@@ -636,7 +637,7 @@ and mIRC chat codes.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1g40nkpldih6h1rlxjx5yf9iavr3qs1f2b6j0gd8135p5hkg8d8n"))))
+        (base32 "064gnzzcm6fnxfiildbjmgbdxkhqvp61zrl6qhkl1pgbn27j1mll"))))
     (build-system haskell-build-system)
     (arguments
      `(#:phases
@@ -661,7 +662,7 @@ and mIRC chat codes.")
                     (doc (string-append out "/share/doc/kmonad-" ,version)))
                (install-file "README.md" doc)
                (copy-recursively "doc" doc)
-               (copy-recursively "example" (string-append doc "/example"))
+               (copy-recursively "keymap" (string-append doc "/keymap"))
                #t))))))
     (inputs
      `(("ghc-cereal" ,ghc-cereal)
@@ -670,6 +671,8 @@ and mIRC chat codes.")
        ("ghc-lens" ,ghc-lens)
        ("ghc-megaparsec" ,ghc-megaparsec)
        ("ghc-optparse-applicative" ,ghc-optparse-applicative)
+       ("ghc-resourcet" ,ghc-resourcet)
+       ("ghc-rio" ,ghc-rio)
        ("ghc-unagi-chan" ,ghc-unagi-chan)
        ("ghc-unliftio" ,ghc-unliftio)
        ("ghc-unordered-containers" ,ghc-unordered-containers)))
@@ -772,7 +775,7 @@ too slow and you'll get wound up in the scroll and crushed.")
 (define-public shellcheck
   (package
     (name "shellcheck")
-    (version "0.7.0")
+    (version "0.7.1")
     (source
      (origin
        (method url-fetch)
@@ -780,7 +783,7 @@ too slow and you'll get wound up in the scroll and crushed.")
              "https://hackage.haskell.org/package/ShellCheck/ShellCheck-"
              version ".tar.gz"))
        (sha256
-        (base32 "1vx895cp5k5h0680xfwj74lk97m9y627n965x6srds0gfnbkzy9s"))
+        (base32 "06m4wh891nah3y0br4wh3adpsb16zawkb2ijgf1vcz61fznj6ps1"))
        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system haskell-build-system)
     (inputs

gnu/packages/haskell-web.scm

@@ -9,6 +9,7 @@
 ;;; Copyright © 2019 John Soo <jsoo1@asu.edu>
 ;;; Copyright © 2020 Alexandru-Sergiu Marton <brown121407@gmail.com>
 ;;; Copyright © 2020 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2020 Kyle Meyer <kyle@kyleam.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1945,3 +1946,38 @@ as frontend to hjsmin.")
      "This package provides a data type and ToJSON/FromJSON instances for
 Bower's package manifest file, bower.json.")
     (license license:expat)))
+
+(define-public ghc-dav
+  (package
+    (name "ghc-dav")
+    (version "1.3.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/DAV/DAV-"
+                           version ".tar.gz"))
+       (sha256
+        (base32 "1isvi4fahq70lzxfz23as7qzkc01g7kba568l6flrgd0j1984fsy"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-case-insensitive" ,ghc-case-insensitive)
+       ("ghc-data-default" ,ghc-data-default)
+       ("ghc-exceptions" ,ghc-exceptions)
+       ("ghc-http-client" ,ghc-http-client)
+       ("ghc-http-client-tls" ,ghc-http-client-tls)
+       ("ghc-http-types" ,ghc-http-types)
+       ("ghc-lens" ,ghc-lens)
+       ("ghc-transformers-base" ,ghc-transformers-base)
+       ("ghc-transformers-compat" ,ghc-transformers-compat)
+       ("ghc-utf8-string" ,ghc-utf8-string)
+       ("ghc-xml-conduit" ,ghc-xml-conduit)
+       ("ghc-xml-hamlet" ,ghc-xml-hamlet)
+       ("ghc-network" ,ghc-network)
+       ("ghc-network-uri" ,ghc-network-uri)
+       ("ghc-optparse-applicative" ,ghc-optparse-applicative)))
+    (home-page "http://floss.scru.org/hDAV")
+    (synopsis "RFC 4918 WebDAV support")
+    (description "This package provides a library for the Web Distributed
+Authoring and Versioning (WebDAV) extensions to HTTP as well an executable,
+@command{hdav}, for command-line operation.")
+    (license license:gpl3)))

gnu/packages/haskell-xyz.scm

@@ -20,7 +20,7 @@
 ;;; Copyright © 2019 Robert Vollmert <rob@vllmrt.net>
 ;;; Copyright © 2019 Jacob MacDonald <jaccarmac@gmail.com>
 ;;; Copyright © 2019,2020 John Soo <jsoo1@asu.edu>
-;;; Copyright © 2019 Kyle Meyer <kyle@kyleam.com>
+;;; Copyright © 2019, 2020 Kyle Meyer <kyle@kyleam.com>
 ;;; Copyright © 2019 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2020 Brett Gilio <brettg@gnu.org>
 ;;; Copyright © 2020 JoJo <jo@jo.zone>
@@ -14712,6 +14712,30 @@ the @code{conduit} package.")
 documents.")
     (license license:expat)))
 
+(define-public ghc-xml-hamlet
+  (package
+    (name "ghc-xml-hamlet")
+    (version "0.5.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/xml-hamlet/"
+                           "xml-hamlet-" version ".tar.gz"))
+       (sha256
+        (base32 "0jrhcjy7ww59dafg857f2g2df1fw2jmbwcs1q379ph0pc5rxj3lj"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-shakespeare" ,ghc-shakespeare)
+       ("ghc-xml-conduit" ,ghc-xml-conduit)))
+    (native-inputs
+     `(("ghc-hspec" ,ghc-hspec)
+       ("ghc-hunit" ,ghc-hunit)))
+    (home-page "https://www.yesodweb.com/")
+    (synopsis "Hamlet-style quasiquoter for XML content")
+    (description "This package provides a type-safe tool for generating XML
+code via quasi-quoting built on top of @code{ghc-shakespeare}.")
+    (license license:bsd-3)))
+
 (define-public ghc-yaml
   (package
     (name "ghc-yaml")

gnu/packages/hexedit.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2017 Gábor Boskovits <boskovits@gmail.com>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -34,7 +34,7 @@
 (define-public hexedit
   (package
     (name "hexedit")
-    (version "1.4.2")
+    (version "1.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -43,7 +43,7 @@
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1xsxa5mip892jkvz9jshj73y6c7j3mgp8y393ciihqlyf2nmfs67"))))
+                "1sfa4i374n1xrz2ivvzcd8jzc296ly11x1713s4bplvszcqpw6dv"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no check target