gnu: ntp: Update to 4.2.8p2.

* gnu/packages/ntp.scm (ntp): Update to 4.2.8p2.
author: Mark H Weaver <mhw@netris.org> 2015-04-18 02:27:30 -0400
committer: Mark H Weaver <mhw@netris.org> 2015-04-18 02:28:30 -0400
commit: 989a9fffa74f42a4c2a979b16fd01ae218cf0bb8 (patch)
tree: bae40dd8f474ee69bc0c2ee77ec6ee490c2e8217 /gnu/packages/gstreamer.scm
parent: ba42f54df6fede1ce6aec268e78784640ee642db (diff)
download: guix-989a9fffa74f42a4c2a979b16fd01ae218cf0bb8.tar.gz
guix-989a9fffa74f42a4c2a979b16fd01ae218cf0bb8.zip
0 files changed, 0 insertions, 0 deletions
diff --git a/Makefile.am b/Makefile.am
index 0371d92d7c..5422172e64 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -122,6 +122,7 @@ MODULES =					\
   guix/build-system/meson.scm			\
   guix/build-system/minify.scm			\
   guix/build-system/asdf.scm			\
+  guix/build-system/copy.scm			\
   guix/build-system/glib-or-gtk.scm		\
   guix/build-system/gnu.scm			\
   guix/build-system/guile.scm			\
@@ -169,6 +170,7 @@ MODULES =					\
   guix/build/go-build-system.scm		\
   guix/build/asdf-build-system.scm		\
   guix/build/bzr.scm				\
+  guix/build/copy-build-system.scm		\
   guix/build/git.scm				\
   guix/build/hg.scm				\
   guix/build/glib-or-gtk-build-system.scm	\
diff --git a/bootstrap b/bootstrap
index c9e7a084a1..a47269d87f 100755
--- a/bootstrap
+++ b/bootstrap
@@ -16,7 +16,7 @@ for lang in ${langs}; do
     fi
 done
 langs=`find po/doc -type f -name 'guix-cookbook*.po' \
-        | sed -e 's,guix-manual\.,,' \
+        | sed -e 's,guix-cookbook\.,,' \
         | xargs -n 1 -I{} basename {} .po`
 for lang in ${langs}; do
     if [ ! -e "doc/guix-cookbook.${lang}.texi" ]; then
diff --git a/build-aux/build-self.scm b/build-aux/build-self.scm
index fc13032b73..f2e785b7f1 100644
--- a/build-aux/build-self.scm
+++ b/build-aux/build-self.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -420,6 +420,7 @@ files."
                          ;; $GUILE_LOAD_PATH & co.
                          (with-clean-environment
                           (setenv "GUILE_WARN_DEPRECATED" "no") ;be quiet and drive
+                          (setenv "COLUMNS" "120") ;show wider backtraces
                           (when home
                             ;; Inherit HOME so that 'xdg-directory' works.
                             (setenv "HOME" home))
diff --git a/build-aux/git-authenticate.scm b/build-aux/git-authenticate.scm
index aa9103a372..640dedbff5 100644
--- a/build-aux/git-authenticate.scm
+++ b/build-aux/git-authenticate.scm
@@ -134,7 +134,8 @@
     ("lsl88"
      "2AE3 1395 932B E642 FC0E  D99C 9BED 6EDA 32E5 B0BC")
     ("mab"
-     "BE62 7373 8E61 6D6D 1B3A  08E8 A21A 0202 4881 6103")
+     ;; primary: "BE62 7373 8E61 6D6D 1B3A  08E8 A21A 0202 4881 6103"
+     "39B3 3C8D 9448 0D2D DCC2  A498 8B44 A0CD C7B9 56F2")
     ("marusich"
      "CBF5 9755 CBE7 E7EF EF18  3FB1 DD40 9A15 D822 469D")
     ("mbakke"
@@ -183,8 +184,6 @@
      "77DD AD2D 97F5 31BB C0F3  C7FD DFB5 EB09 AA62 5423")
     ("snape"
      "F494 72F4 7A59 00D5 C235  F212 89F9 6D48 08F3 59C7")
-    ("snape"
-     "F494 72F4 7A59 00D5 C235  F212 89F9 6D48 08F3 59C7")
     ("steap"
      "4E26 CCE9 578E 0828 9855  BDD4 1C79 95D2 D5A3 8336")
     ("taylanub"
@@ -192,7 +191,8 @@
 
     ;; https://lists.gnu.org/archive/html/guix-devel/2017-03/msg00826.html
     ("thomasd"
-     "1DD1 681F E285 E07F 11DC  0C59 2E15 A6BC D77D 54FD")
+     ;; primary: "1DD1 681F E285 E07F 11DC  0C59 2E15 A6BC D77D 54FD"
+     "3D2C DA58 819C 08C2 A649  D43D 5C3B 064C 724A 5726")
     ("thomasd (old)"
      "A5C5 92EA 606E 7106 A6A3  BC08 98B2 1575 91E1 2B08")
 
diff --git a/doc/contributing.texi b/doc/contributing.texi
index c6586a2adf..9d45becf86 100644
--- a/doc/contributing.texi
+++ b/doc/contributing.texi
@@ -274,6 +274,33 @@ trigger string @code{origin...}, which can be expanded further.  The
 @code{origin} snippet in turn may insert other trigger strings ending on
 @code{...}, which also can be expanded further.
 
+@cindex insert or update copyright
+@cindex @code{M-x guix-copyright}
+@cindex @code{M-x copyright-update}
+Additionaly we provide insertion and automatic update of a copyright in
+@file{etc/copyright.el}.  You may want to set your full name, mail, and
+load a file.
+
+@lisp
+(setq user-full-name "Alice Doe")
+(setq user-mail-address "alice@@mail.org")
+;; @r{Assuming the Guix checkout is in ~/src/guix.}
+(load-file "~/src/guix/etc/copyright.el")
+@end lisp
+
+To insert a copyright at the current line invoke @code{M-x guix-copyright}.
+
+To update a copyright you need to specify a @code{copyright-names-regexp}.
+
+@lisp
+(setq copyright-names-regexp
+      (format "%s <%s>" user-full-name user-mail-address))
+@end lisp
+
+You can check if your copyright is up to date by evaluating @code{M-x
+copyright-update}.  If you want to do it automatically after each buffer
+save then add @code{(add-hook 'after-save-hook 'copyright-update)} in
+Emacs.
 
 @node Packaging Guidelines
 @section Packaging Guidelines
@@ -347,6 +374,7 @@ needed is to review and apply the patch.
 * Python Modules::              A touch of British comedy.
 * Perl Modules::                Little pearls.
 * Java Packages::               Coffee break.
+* Rust Crates::                 Beware of oxidation.
 * Fonts::                       Fond of fonts.
 @end menu
 
@@ -685,6 +713,40 @@ dashes and prepend the prefix @code{java-}.  So the class
 @code{java-apache-commons-cli}.
 
 
+@node Rust Crates
+@subsection Rust Crates
+
+@cindex rust
+Rust programs standing for themselves are named as any other package, using the
+lowercase upstream name.
+
+To prevent namespace collisions we prefix all other Rust packages with the
+@code{rust-} prefix.  The name should be changed to lowercase as appropriate and
+dashes should remain in place.
+
+In the rust ecosystem it is common for multiple incompatible versions of a
+package to be used at any given time, so all packages should have a versioned
+suffix.  If a package has passed version 1.0.0 then just the major version
+number is sufficient (e.g.@: @code{rust-clap-2}), otherwise the version suffix
+should contain both the major and minor version (e.g.@: @code{rust-rand-0.6}).
+
+Because of the difficulty in reusing rust packages as pre-compiled inputs for
+other packages the Cargo build system (@pxref{Build Systems,
+@code{cargo-build-system}}) presents the @code{#:cargo-inputs} and
+@code{cargo-development-inputs} keywords as build system arguments.  It would be
+helpful to think of these as similar to @code{propagated-inputs} and
+@code{native-inputs}.  Rust @code{dependencies} and @code{build-dependencies}
+should go in @code{#:cargo-inputs}, and @code{dev-dependencies} should go in
+@code{#:cargo-development-inputs}.  If a Rust package links to other libraries
+then the standard placement in @code{inputs} and the like should be used.
+
+Care should be taken to ensure the correct version of dependencies are used; to
+this end we try to refrain from skipping the tests or using @code{#:skip-build?}
+when possible.  Of course this is not always possible, as the package may be
+developed for a different Operating System, depend on features from the Nightly
+Rust compiler, or the test suite may have atrophied since it was released.
+
+
 @node Fonts
 @subsection Fonts
 
diff --git a/doc/guix.texi b/doc/guix.texi
index 282f9578bf..fab9159530 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -73,6 +73,7 @@ Copyright @copyright{} 2020 Leo Prikler@*
 Copyright @copyright{} 2019, 2020 Simon Tournier@*
 Copyright @copyright{} 2020 Wiktor Żelazny@*
 Copyright @copyright{} 2020 Damien Cassou@*
+Copyright @copyright{} 2020 Jakub Kądziołka@*
 
 Permission is granted to copy, distribute and/or modify this document
 under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -771,11 +772,11 @@ The following dependencies are optional:
 
 @itemize
 @item
-@c Note: We need at least 0.10.2 for 'channel-send-eof'.
+@c Note: We need at least 0.12.0 for 'userauth-gssapi!'.
 Support for build offloading (@pxref{Daemon Offload Setup}) and
 @command{guix copy} (@pxref{Invoking guix copy}) depends on
 @uref{https://github.com/artyom-poptsov/guile-ssh, Guile-SSH},
-version 0.10.2 or later.
+version 0.12.0 or later.
 
 @item
 When @url{https://www.nongnu.org/lzip/lzlib.html, lzlib} is available, lzlib
@@ -2440,6 +2441,11 @@ your system includes the latest security updates (@pxref{Security Updates}).
 Note that @command{sudo guix} runs your user's @command{guix} command and
 @emph{not} root's, because @command{sudo} leaves @code{PATH} unchanged.  To
 explicitly run root's @command{guix}, type @command{sudo -i guix @dots{}}.
+
+The difference matters here, because @command{guix pull} updates
+the @command{guix} command and package definitions only for the user it is ran
+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
@@ -4230,7 +4236,7 @@ guix time-machine -- build hello
 @end example
 
 will thus build the package @code{hello} as defined in the master branch,
-which is in general a newer revison of Guix than you have installed.
+which is in general a newer revision of Guix than you have installed.
 Time travel works in both directions!
 
 Note that @command{guix time-machine} can trigger builds of channels and
@@ -4958,8 +4964,10 @@ shared and will change to the user's home directory within the container
 instead.  See also @code{--user}.
 
 @item --expose=@var{source}[=@var{target}]
-For containers, expose the file system @var{source} from the host system
-as the read-only file system @var{target} within the container.  If
+@itemx --share=@var{source}[=@var{target}]
+For containers, @code{--expose} (resp. @code{--share}) exposes the file
+system @var{source} from the host system as the read-only
+(resp. writable) file system @var{target} within the container.  If
 @var{target} is not specified, @var{source} is used as the target mount
 point in the container.
 
@@ -4971,19 +4979,6 @@ directory:
 guix environment --container --expose=$HOME=/exchange --ad-hoc guile -- guile
 @end example
 
-@item --share=@var{source}[=@var{target}]
-For containers, share the file system @var{source} from the host system
-as the writable file system @var{target} within the container.  If
-@var{target} is not specified, @var{source} is used as the target mount
-point in the container.
-
-The example below spawns a Guile REPL in a container in which the user's
-home directory is accessible for both reading and writing via the
-@file{/exchange} directory:
-
-@example
-guix environment --container --share=$HOME=/exchange --ad-hoc guile -- guile
-@end example
 @end table
 
 @command{guix environment}
@@ -6159,6 +6154,70 @@ parameters available to cargo.  It will also remove an included
 if they are defined by the crate.
 @end defvr
 
+
+@defvr {Scheme Variable} copy-build-system
+@cindex (copy build system)
+This variable is exported by @code{(guix build-system copy)}.  It
+supports builds of simple packages that don't require much compiling,
+mostly just moving files around.
+
+It adds much of the @code{gnu-build-system} packages to the set of
+inputs.  Because of this, the @code{copy-build-system} does not require
+all the boilerplate code often needed for the
+@code{trivial-build-system}.
+
+To further simplify the file installation process, an
+@code{#:install-plan} argument is exposed to let the packager specify
+which files go where.  The install plan is a list of @code{(@var{source}
+@var{target} [@var{filters}])}.  @var{filters} are optional.
+
+@itemize
+@item When @var{source} matches a file or directory without trailing slash, install it to @var{target}.
+@itemize
+@item If @var{target} has a trailing slash, install @var{source} basename beneath @var{target}.
+@item Otherwise install @var{source} as @var{target}.
+@end itemize
+
+@item When @var{source} is a directory with a trailing slash, or when @var{filters} are used,
+the trailing slash of @var{target} is implied with the same meaning
+as above.
+@itemize
+@item Without @var{filters}, install the full @var{source} @emph{content} to @var{target}.
+@item With @var{filters} among @code{#:include}, @code{#:include-regexp}, @code{#:exclude},
+@code{#:exclude-regexp}, only select files are installed depending on
+the filters.  Each filters is specified by a list of strings.
+@itemize
+@item With @code{#:include}, install all the files which the path suffix matches
+at least one of the elements in the given list.
+@item With @code{#:include-regexp}, install all the files which the
+subpaths match at least one of the regular expressions in the given
+list.
+@item The @code{#:exclude} and @code{#:exclude-regexp} filters
+are the complement of their inclusion counterpart.  Without @code{#:include} flags,
+install all files but those matching the exclusion filters.
+If both inclusions and exclusions are specified, the exclusions are done
+on top of the inclusions.
+@end itemize
+@end itemize
+In all cases, the paths relative to @var{source} are preserved within
+@var{target}.
+@end itemize
+
+Examples:
+
+@itemize
+@item @code{("foo/bar" "share/my-app/")}: Install @file{bar} to @file{share/my-app/bar}.
+@item @code{("foo/bar" "share/my-app/baz")}: Install @file{bar} to @file{share/my-app/baz}.
+@item @code{("foo/" "share/my-app")}: Install the content of @file{foo} inside @file{share/my-app},
+e.g., install @file{foo/sub/file} to @file{share/my-app/sub/file}.
+@item @code{("foo/" "share/my-app" #:include ("sub/file"))}: Install only @file{foo/sub/file} to
+@file{share/my-app/sub/file}.
+@item @code{("foo/sub" "share/my-app" #:include ("file"))}: Install @file{foo/sub/file} to
+@file{share/my-app/file}.
+@end itemize
+@end defvr
+
+
 @cindex Clojure (programming language)
 @cindex simple Clojure build system
 @defvr {Scheme Variable} clojure-build-system
@@ -6815,9 +6874,11 @@ instruct it to listen for TCP connections (@pxref{Invoking guix-daemon,
 
 @item ssh
 @cindex SSH access to build daemons
-These URIs allow you to connect to a remote daemon over
-SSH@footnote{This feature requires Guile-SSH (@pxref{Requirements}).}.
-A typical URL might look like this:
+These URIs allow you to connect to a remote daemon over SSH.  This
+feature requires Guile-SSH (@pxref{Requirements}) and a working
+@code{guile} binary in @code{PATH} on the destination machine.  It
+supports public key and GSSAPI authentication.  A typical URL might look
+like this:
 
 @example
 ssh://charlie@@guix.example.org:22
@@ -14037,7 +14098,7 @@ Each string gets on its own line.  See the @code{AcceptEnv} option in
 
 This example allows ssh-clients to export the @code{COLORTERM} variable.
 It is set by terminal emulators, which support colors.  You can use it in
-your shell's ressource file to enable colors for the prompt and commands
+your shell's resource file to enable colors for the prompt and commands
 if this variable is set.
 
 @lisp
@@ -14463,7 +14524,7 @@ Command to run when halting.
 Command to run when rebooting.
 
 @item @code{theme} (default "maldives")
-Theme to use. Default themes provided by SDDM are "elarun" or "maldives".
+Theme to use. Default themes provided by SDDM are "elarun", "maldives" or "maya".
 
 @item @code{themes-directory} (default "/run/current-system/profile/share/sddm/themes")
 Directory to look for themes.
@@ -14538,7 +14599,7 @@ Relogin after logout.
 @cindex X11 login
 @defvr {Scheme Variable} sddm-service-type
 This is the type of the service to run the
-@uref{https://github.com/sddm/sddm,SSDM display manager}.  Its value
+@uref{https://github.com/sddm/sddm,SDDM display manager}.  Its value
 must be a @code{sddm-configuration} record (see below).
 
 Here's an example use:
@@ -15560,7 +15621,7 @@ adding a service of type @code{mate-desktop-service-type} adds the MATE
 metapackage to the system profile.  ``Adding Enlightenment'' means that
 @code{dbus} is extended appropriately, and several of Enlightenment's binaries
 are set as setuid, allowing Enlightenment's screen locker and other
-functionality to work as expetected.
+functionality to work as expected.
 
 The desktop environments in Guix use the Xorg display server by
 default.  If you'd like to use the newer display server protocol
@@ -19987,7 +20048,7 @@ The @code{ServerName} in the configuration file, used to specify the
 request scheme, hostname and port that the server uses to identify
 itself.
 
-This doesn't need to be set in the server config, and can be specifyed
+This doesn't need to be set in the server config, and can be specified
 in virtual hosts. The default is @code{#f} to not specify a
 @code{ServerName}.
 
@@ -21143,7 +21204,7 @@ false, listed actions are allowed.
 @end deftp
 
 @deftp {Data Type} zone-entry
-Data type represnting a record entry in a zone file.
+Data type representing a record entry in a zone file.
 This type has the following parameters:
 
 @table @asis
@@ -21266,7 +21327,7 @@ The backend to store the keys in.  Can be @code{'pem} or @code{'pkcs11}.
 @item @code{config} (default: @code{"/var/lib/knot/keys/keys"})
 The configuration string of the backend.  An example for the PKCS#11 is:
 @code{"pkcs11:token=knot;pin-value=1234 /gnu/store/.../lib/pkcs11/libsofthsm2.so"}.
-For the pem backend, the string reprensents a path in the file system.
+For the pem backend, the string represents a path in the file system.
 
 @end table
 @end deftp
@@ -21799,6 +21860,13 @@ Defaults to @samp{#t}.
 
 @end deftypevr
 
+@deftypevr {@code{openvpn-client-configuration} parameter} boolean fast-io?
+(Experimental) Optimize TUN/TAP/UDP I/O writes by avoiding a call to
+poll/epoll/select prior to the write operation.
+
+Defaults to @samp{#f}.
+@end deftypevr
+
 @deftypevr {@code{openvpn-client-configuration} parameter} number verbosity
 Verbosity level.
 
@@ -21814,6 +21882,14 @@ Defaults to @samp{#f}.
 
 @end deftypevr
 
+@deftypevr {@code{openvpn-client-configuration} parameter} maybe-string auth-user-pass
+Authenticate with server using username/password.  The option is a file
+containing username/password on 2 lines.  Do not use a file-like object as it
+would be added to the store and readable by any user.
+
+Defaults to @samp{'disabled}.
+@end deftypevr
+
 @deftypevr {@code{openvpn-client-configuration} parameter} key-usage verify-key-usage?
 Whether to check the server certificate has server usage extension.
 
@@ -21935,6 +22011,13 @@ Defaults to @samp{#t}.
 
 @end deftypevr
 
+@deftypevr {@code{openvpn-server-configuration} parameter} boolean fast-io?
+(Experimental) Optimize TUN/TAP/UDP I/O writes by avoiding a call to
+poll/epoll/select prior to the write operation.
+
+Defaults to @samp{#f}.
+@end deftypevr
+
 @deftypevr {@code{openvpn-server-configuration} parameter} number verbosity
 Verbosity level.
 
@@ -24499,7 +24582,7 @@ Defaults to @samp{"a fast webinterface for the git dscm"}.
 
 @deftypevr {@code{cgit-configuration} parameter} string root-readme
 The content of the file specified with this option will be included
-verbatim below thef "about" link on the repository index page.
+verbatim below the "about" link on the repository index page.
 
 Defaults to @samp{""}.
 
@@ -25382,7 +25465,7 @@ of DICT server (@pxref{Dicod,,, dico, GNU Dico Manual}).
 
 The optional @var{config} argument specifies the configuration for
 @command{dicod}, which should be a @code{<dicod-configuration>} object, by
-default it serves the GNU Collaborative International Dictonary of English.
+default it serves the GNU Collaborative International Dictionary of English.
 
 You can add @command{open localhost} to your @file{~/.dico} file to make
 @code{localhost} the default server for @command{dico} client
@@ -26364,7 +26447,7 @@ Switch to an existing system generation.  This action atomically
 switches the system profile to the specified system generation.  It
 also rearranges the system's existing bootloader menu entries.  It
 makes the menu entry for the specified system generation the default,
-and it moves the entries for the other generatiors to a submenu, if
+and it moves the entries for the other generations to a submenu, if
 supported by the bootloader being used.  The next time the system
 boots, it will use the specified system generation.
 
diff --git a/doc/local.mk b/doc/local.mk
index a361f2388e..3805593172 100644
--- a/doc/local.mk
+++ b/doc/local.mk
@@ -27,7 +27,8 @@ info_TEXINFOS = %D%/guix.texi			\
   %D%/guix.fr.texi				\
   %D%/guix.ru.texi				\
   %D%/guix.zh_CN.texi				\
-  %D%/guix-cookbook.texi
+  %D%/guix-cookbook.texi			\
+  %D%/guix-cookbook.de.texi
 
 %C%_guix_TEXINFOS = \
   %D%/contributing.texi \
@@ -69,7 +70,8 @@ TRANSLATED_INFO =				\
   %D%/contributing.es.texi			\
   %D%/contributing.fr.texi			\
   %D%/contributing.ru.texi			\
-  %D%/contributing.zh_CN.texi
+  %D%/contributing.zh_CN.texi			\
+  %D%/guix-cookbook.de.texi
 
 # Bundle this file so that makeinfo finds it in out-of-source-tree builds.
 BUILT_SOURCES        += $(OS_CONFIG_EXAMPLES_TEXI) $(TRANSLATED_INFO)
diff --git a/etc/copyright.el b/etc/copyright.el
new file mode 100644
index 0000000000..f5ed723cea
--- /dev/null
+++ b/etc/copyright.el
@@ -0,0 +1,34 @@
+;;; copyright.el --- Insert a Guix copyright.
+
+;; Copyright © 2020 Oleg Pykhalov <go.wigust@gmail.com>
+
+;; This file is part of GNU Guix.
+
+;; GNU Guix is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation, either version 3 of the License, or
+;; (at your option) any later version.
+
+;; GNU Guix is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License
+;; along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+;;; Commentary:
+
+;; This package provides skeleton to insert a copyright with `guix-copyright'.
+
+;;; Code:
+
+(define-skeleton guix-copyright
+  "Insert a copyright by $USER notice at cursor."
+  "FULL_NAME <MAIL_ADDRESS>: "
+  comment-start
+  ";; Copyright © " `(format-time-string "%Y") " "
+  (or (format "%s <%s>" user-full-name user-mail-address) str)
+  comment-end)
+
+;;; copyright.el ends here
diff --git a/gnu/build/file-systems.scm b/gnu/build/file-systems.scm
index ee6375515f..902563b219 100644
--- a/gnu/build/file-systems.scm
+++ b/gnu/build/file-systems.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 David C. Trudgian <dave@trudgian.net>
+;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -581,6 +582,7 @@ were found."
      ((string-prefix? "btrfs" type) check-btrfs-file-system)
      ((string-suffix? "fat" type) check-fat-file-system)
      ((string-prefix? "jfs" type) check-jfs-file-system)
+     ((string-prefix? "nfs" type) (const 'pass))
      (else #f)))
 
   (if check-procedure
diff --git a/gnu/build/linux-boot.scm b/gnu/build/linux-boot.scm
index 3d40a7d05d..4fb711b8f2 100644
--- a/gnu/build/linux-boot.scm
+++ b/gnu/build/linux-boot.scm
@@ -362,12 +362,12 @@ the last argument of `mknod'."
   "Mount the root file system of type TYPE at device ROOT. If VOLATILE-ROOT? is
 true, mount ROOT read-only and make it an overlay with a writable tmpfs using
 the kernel built-in overlayfs. FLAGS and OPTIONS indicates the options to use
-to mount ROOT."
+to mount ROOT, and behave the same as for the `mount' procedure."
 
   (if volatile-root?
       (begin
         (mkdir-p "/real-root")
-        (mount root "/real-root" type MS_RDONLY options)
+        (mount root "/real-root" type (logior MS_RDONLY flags) options)
         (mkdir-p "/rw-root")
         (mount "none" "/rw-root" "tmpfs")
 
diff --git a/gnu/build/marionette.scm b/gnu/build/marionette.scm
index 1dbe385e89..fe754cd147 100644
--- a/gnu/build/marionette.scm
+++ b/gnu/build/marionette.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2018 Chris Marusich <cmmarusich@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -204,6 +204,7 @@ MARIONETTE.  Raise an error on failure."
                  (catch 'system-error
                    (lambda ()
                      (connect sock AF_INET INADDR_LOOPBACK ,port)
+                     (close-port sock)
                      'success)
                    (lambda args
                      (if (< i ,timeout)
@@ -227,6 +228,7 @@ accept connections in MARIONETTE.  Raise an error on failure."
                  (catch 'system-error
                    (lambda ()
                      (connect sock AF_UNIX ,file-name)
+                     (close-port sock)
                      'success)
                    (lambda args
                      (if (< i ,timeout)
@@ -315,8 +317,8 @@ PREDICATE, whichever comes first.  Raise an error when TIMEOUT is exceeded."
     (#\( . "shift-9")
     (#\) . "shift-0")
     (#\/ . "slash")
-    (#\< . "less")
-    (#\> . "shift-less")
+    (#\< . "shift-comma")
+    (#\> . "shift-dot")
     (#\. . "dot")
     (#\, . "comma")
     (#\; . "semicolon")
diff --git a/gnu/installer.scm b/gnu/installer.scm
index b93cebbc13..04f3dd5f26 100644
--- a/gnu/installer.scm
+++ b/gnu/installer.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018, 2020 Mathieu Othacehe <m.othacehe@gmail.com>
-;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -26,6 +26,7 @@
   #:use-module (guix utils)
   #:use-module (guix ui)
   #:use-module ((guix self) #:select (make-config.scm))
+  #:use-module (gnu installer utils)
   #:use-module (gnu packages admin)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
@@ -395,6 +396,8 @@ selected keymap."
                      #f)))
                 (const #f)
                 (lambda (key . args)
+                  (syslog "crashing due to uncaught exception: ~s ~s~%"
+                          key args)
                   (let ((error-file "/tmp/last-installer-error"))
                     (call-with-output-file error-file
                       (lambda (port)
diff --git a/gnu/installer/parted.scm b/gnu/installer/parted.scm
index c2b02c9281..6c805cc053 100644
--- a/gnu/installer/parted.scm
+++ b/gnu/installer/parted.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018, 2019 Mathieu Othacehe <m.othacehe@gmail.com>
-;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -1070,6 +1070,8 @@ USER-PARTITION if it is encrypted, or the plain file-name otherwise."
     (call-with-luks-key-file
      password
      (lambda (key-file)
+       (syslog "formatting and opening LUKS entry ~s at ~s~%"
+               label file-name)
        (system* "cryptsetup" "-q" "luksFormat" file-name key-file)
        (system* "cryptsetup" "open" "--type" "luks"
                 "--key-file" key-file file-name label)))))
@@ -1077,6 +1079,7 @@ USER-PARTITION if it is encrypted, or the plain file-name otherwise."
 (define (luks-close user-partition)
   "Close the encrypted partition pointed by USER-PARTITION."
   (let ((label (user-partition-crypt-label user-partition)))
+    (syslog "closing LUKS entry ~s~%" label)
     (system* "cryptsetup" "close" label)))
 
 (define (format-user-partitions user-partitions)
@@ -1150,6 +1153,7 @@ respective mount-points."
                        (file-name
                         (user-partition-upper-file-name user-partition)))
                   (mkdir-p target)
+                  (syslog "mounting ~s on ~s~%" file-name target)
                   (mount file-name target mount-type)))
               sorted-partitions)))
 
@@ -1165,6 +1169,7 @@ respective mount-points."
                        (target
                         (string-append (%installer-target-dir)
                                        mount-point)))
+                  (syslog "unmounting ~s~%" target)
                   (umount target)
                   (when crypt-label
                     (luks-close user-partition))))
diff --git a/gnu/installer/steps.scm b/gnu/installer/steps.scm
index 4e90f32f95..b2fc819d89 100644
--- a/gnu/installer/steps.scm
+++ b/gnu/installer/steps.scm
@@ -177,6 +177,7 @@ return the accumalated result so far."
                               #:done-steps '())))))
                  ((installer-step-break? c)
                   (reverse result)))
+         (syslog "running step '~a'~%" (installer-step-id step))
          (let* ((id (installer-step-id step))
                 (compute (installer-step-compute step))
                 (res (compute result done-steps)))
diff --git a/gnu/installer/utils.scm b/gnu/installer/utils.scm
index ddb96bc338..842bd02ced 100644
--- a/gnu/installer/utils.scm
+++ b/gnu/installer/utils.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Mathieu Othacehe <m.othacehe@gmail.com>
-;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -24,12 +24,16 @@
   #:use-module (srfi srfi-34)
   #:use-module (ice-9 rdelim)
   #:use-module (ice-9 regex)
+  #:use-module (ice-9 format)
   #:use-module (ice-9 textual-ports)
   #:export (read-lines
             read-all
             nearest-exact-integer
             read-percentage
-            run-shell-command))
+            run-shell-command
+
+            syslog-port
+            syslog))
 
 (define* (read-lines #:optional (port (current-input-port)))
   "Read lines from PORT and return them as a list."
@@ -85,9 +89,48 @@ COMMAND exited successfully, #f otherwise."
                 (format (current-error-port)
                         (G_ "Command failed with exit code ~a.~%")
                         (invoke-error-exit-status c))
+                (syslog "command ~s failed with exit code ~a"
+                        command (invoke-error-exit-status c))
                 (pause)
                 #f))
+       (syslog "running command ~s~%" command)
        (invoke "bash" "--init-file" file)
+       (syslog "command ~s succeeded~%" command)
        (newline)
        (pause)
        #t))))
+
+
+;;;
+;;; Logging.
+;;;
+
+(define (open-syslog-port)
+  "Return an open port (a socket) to /dev/log or #f if that wasn't possible."
+  (let ((sock (socket AF_UNIX SOCK_DGRAM 0)))
+    (catch 'system-error
+      (lambda ()
+        (connect sock AF_UNIX "/dev/log")
+        (setvbuf sock 'line)
+        sock)
+      (lambda args
+        (close-port sock)
+        #f))))
+
+(define syslog-port
+  (let ((port #f))
+    (lambda ()
+      "Return an output port to syslog."
+      (unless port
+        (set! port (open-syslog-port)))
+      (or port (%make-void-port "w")))))
+
+(define-syntax syslog
+  (lambda (s)
+    "Like 'format', but write to syslog."
+    (syntax-case s ()
+      ((_ fmt args ...)
+       (string? (syntax->datum #'fmt))
+       (with-syntax ((fmt (string-append "installer[~d]: "
+                                         (syntax->datum #'fmt))))
+         #'(format (syslog-port) fmt (getpid) args ...))))))
diff --git a/gnu/local.mk b/gnu/local.mk
index c6eccd7e4a..9b46ac5629 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -622,6 +622,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/tests.scm					\
   %D%/tests/audio.scm				\
   %D%/tests/base.scm				\
+  %D%/tests/cups.scm				\
   %D%/tests/databases.scm			\
   %D%/tests/desktop.scm				\
   %D%/tests/dict.scm				\
@@ -719,7 +720,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/antiword-CVE-2014-8123.patch			\
   %D%/packages/patches/antlr3-3_1-fix-java8-compilation.patch	\
   %D%/packages/patches/antlr3-3_3-fix-java8-compilation.patch	\
-  %D%/packages/patches/appstream-glib-2020.patch		\
   %D%/packages/patches/apr-skip-getservbyname-test.patch	\
   %D%/packages/patches/arm-trusted-firmware-disable-hdcp.patch	\
   %D%/packages/patches/aspell-default-dict-dir.patch		\
@@ -771,11 +771,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/catdoc-CVE-2017-11110.patch		\
   %D%/packages/patches/cdparanoia-fpic.patch			\
   %D%/packages/patches/cdrtools-3.01-mkisofs-isoinfo.patch 	\
-  %D%/packages/patches/ceph-boost-compat.patch			\
   %D%/packages/patches/ceph-disable-cpu-optimizations.patch	\
-  %D%/packages/patches/ceph-volume-respect-PATH.patch		\
   %D%/packages/patches/chmlib-inttypes.patch			\
-  %D%/packages/patches/choqok-Fix-building-under-Qt-5.13.patch	\
   %D%/packages/patches/clamav-config-llvm-libs.patch		\
   %D%/packages/patches/clamav-system-tomsfastmath.patch		\
   %D%/packages/patches/clang-3.5-libc-search-path.patch		\
@@ -783,6 +780,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/clang-3.8-libc-search-path.patch		\
   %D%/packages/patches/clang-6.0-libc-search-path.patch		\
   %D%/packages/patches/clang-7.0-libc-search-path.patch		\
+  %D%/packages/patches/clang-9.0-libc-search-path.patch		\
   %D%/packages/patches/clang-runtime-asan-build-fixes.patch	\
   %D%/packages/patches/clang-runtime-esan-build-fixes.patch	\
   %D%/packages/patches/classpath-aarch64-support.patch		\
@@ -795,6 +793,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/coda-use-system-libs.patch		\
   %D%/packages/patches/combinatorial-blas-awpm.patch		\
   %D%/packages/patches/combinatorial-blas-io-fix.patch		\
+  %D%/packages/patches/containerd-test-with-go1.13.patch		\
   %D%/packages/patches/cpufrequtils-fix-aclocal.patch		\
   %D%/packages/patches/crawl-upgrade-saves.patch		\
   %D%/packages/patches/crda-optional-gcrypt.patch		\
@@ -814,6 +813,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/debops-constants-for-external-program-names.patch \
   %D%/packages/patches/debops-debops-defaults-fall-back-to-less.patch \
   %D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch	\
+  %D%/packages/patches/desmume-gcc6-fixes.patch			\
+  %D%/packages/patches/desmume-gcc7-fixes.patch			\
   %D%/packages/patches/dfu-programmer-fix-libusb.patch		\
   %D%/packages/patches/diffutils-gets-undeclared.patch		\
   %D%/packages/patches/dkimproxy-add-ipv6-support.patch		\
@@ -1102,7 +1103,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/libexif-CVE-2018-20030.patch		\
   %D%/packages/patches/libextractor-exiv2.patch			\
   %D%/packages/patches/libgeotiff-adapt-test-script-for-proj-6.2.patch		\
-  %D%/packages/patches/libgit2-avoid-python.patch		\
   %D%/packages/patches/libgit2-mtime-0.patch			\
   %D%/packages/patches/libgnome-encoding.patch			\
   %D%/packages/patches/libgnomeui-utf8.patch			\
@@ -1357,6 +1357,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/qrcodegen-cpp-make-install.patch		\
   %D%/packages/patches/qt4-ldflags.patch			\
   %D%/packages/patches/qtbase-use-TZDIR.patch			\
+  %D%/packages/patches/qtbase-QTBUG-81715.patch			\
   %D%/packages/patches/qtscript-disable-tests.patch		\
   %D%/packages/patches/quagga-reproducible-build.patch          \
   %D%/packages/patches/quickswitch-fix-dmenu-check.patch	\
@@ -1468,7 +1469,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/ustr-fix-build-with-gcc-5.patch		\
   %D%/packages/patches/util-linux-tests.patch			\
   %D%/packages/patches/upower-builddir.patch			\
-  %D%/packages/patches/upx-fix-CVE-2017-15056.patch		\
   %D%/packages/patches/valgrind-enable-arm.patch		\
   %D%/packages/patches/vboot-utils-fix-format-load-address.patch	\
   %D%/packages/patches/vboot-utils-fix-tests-show-contents.patch	\
@@ -1514,7 +1514,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/xsane-fix-pdf-floats.patch		\
   %D%/packages/patches/xsane-fix-snprintf-buffer-length.patch	\
   %D%/packages/patches/xsane-support-ipv6.patch			\
-  %D%/packages/patches/xsane-tighten-default-umask.patch
+  %D%/packages/patches/xsane-tighten-default-umask.patch	\
+  %D%/packages/patches/zziplib-CVE-2018-16548.patch
 
 MISC_DISTRO_FILES =				\
-  %D%/packages/ld-wrapper.in
+  %D%/packages/ld-wrapper.in			\
+  %D%/packages/ld-wrapper-next.in
diff --git a/gnu/packages/abduco.scm b/gnu/packages/abduco.scm
index 3cb84f5fc8..37d2f37773 100644
--- a/gnu/packages/abduco.scm
+++ b/gnu/packages/abduco.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,7 +30,7 @@
    (source (origin
             (method url-fetch)
             (uri (string-append
-                  "http://www.brain-dump.org/projects/abduco/abduco-"
+                  "https://www.brain-dump.org/projects/abduco/abduco-"
                   version ".tar.gz"))
             (sha256
              (base32
@@ -45,5 +46,5 @@
    (description "abduco provides session management i.e. it allows programs to
 be run independently from their controlling terminal.  That is, programs can
 be detached---run in the background---and then later reattached.")
-   (home-page "http://www.brain-dump.org/projects/abduco/")
+   (home-page "https://www.brain-dump.org/projects/abduco/")
    (license isc)))
diff --git a/gnu/packages/acct.scm b/gnu/packages/acct.scm
index a0aac153b0..585a3c2184 100644
--- a/gnu/packages/acct.scm
+++ b/gnu/packages/acct.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
+;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -35,7 +36,7 @@
        (base32
         "0gv6m8giazshvgpvwbng98chpas09myyfw1zr2y7hqxib0mvy5ac"))))
     (build-system gnu-build-system)
-    (home-page "https://gnu.org/software/acct/")
+    (home-page "https://www.gnu.org/software/acct/")
     (synopsis "Standard login and process accounting utilities")
     (description
      "GNU acct provides a means for system administrators to determine
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 02fdb453b6..6fb342dfee 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
 ;;; Copyright © 2014, 2015, 2016, 2018, 2019 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
@@ -24,7 +24,7 @@
 ;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
-;;; Copyright © 2019 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
+;;; Copyright © 2019,2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2019 Jakob L. Kreuze <zerodaysfordays@sdf.org>
 ;;; Copyright © 2019 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2019 Alex Griffin <a@ajgrf.com>
@@ -196,14 +196,14 @@ and provides a \"top-like\" mode (monitoring).")
 (define-public shepherd
   (package
     (name "shepherd")
-    (version "0.6.1")
+    (version "0.7.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/shepherd/shepherd-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1xn6mb5bh8bpfgdrh09ja31jk0ln7bmxbbf0vjcqxkkixs2wl6sk"))))
+                "07j3vd0y8zab2nwbrwj0ahrfif1ldm5sjssn7m3dw4s307fsrfzx"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--localstatedir=/var")))
@@ -228,6 +228,16 @@ interface and is based on GNU Guile.")
     (license license:gpl3+)
     (home-page "https://www.gnu.org/software/shepherd/")))
 
+(define-public guile3.0-shepherd
+  (package
+    (inherit shepherd)
+    (name "guile3.0-shepherd")
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("guile" ,guile-next)))
+    (inputs
+     `(("guile" ,guile-next)))))
+
 (define-public cloud-utils
   (package
     (name "cloud-utils")
@@ -405,7 +415,7 @@ application (for console or X terminals) and requires ncurses.")
                           (("\"/bin/sh\"")
                            (string-append "\"" bash "/bin/sh\"")))
                         #t))))))
-    (home-page "https://www.gnu.org/software/pies/")
+    (home-page "https://www.gnu.org.ua/software/pies/")
     (synopsis "Program invocation and execution supervisor")
     (description
      "GNU pies is a program that supervises the invocation and execution of
@@ -1571,7 +1581,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).")
 (define-public acpica
   (package
     (name "acpica")
-    (version "20200110")
+    (version "20200214")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1579,7 +1589,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).")
                     version ".tar.gz"))
               (sha256
                (base32
-                "1hb4g6r7w8s4bhlkk36fmb4qxghnrwvad7f18cpn6zz0b4sjs7za"))))
+                "0jdasziq184l3iqyp5vhrsbi6g89n10wr0ssliiz0xi3dqwsxcqk"))))
     (build-system gnu-build-system)
     (native-inputs `(("flex" ,flex)
                      ("bison" ,bison)))
@@ -1774,7 +1784,7 @@ environment variable is set and output is to tty.")
                   (string-append "SHELL=" bash "/bin/sh")))
 
                #t))))))
-    (home-page "https://www.gnu.org/software/direvent/")
+    (home-page "https://www.gnu.org.ua/software/direvent/")
     (synopsis "Daemon to monitor directories for events such as file removal")
     (description
      "A daemon that monitors directories for events, such as creating,
@@ -1905,13 +1915,13 @@ of supported upstream metrics systems simultaneously.")
 (define-public ansible
   (package
     (name "ansible")
-    (version "2.8.5")
+    (version "2.9.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ansible" version))
        (sha256
-        (base32 "11k94ifp42psivzx147xwbmq1ak7qnjdgkb6c1xz53nfapkh754f"))))
+        (base32 "19fav6rs58zdc3gfhh1lxhki36jn4252183rrd769sv46b9m1bji"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-bcrypt" ,python-bcrypt)
@@ -2230,7 +2240,7 @@ displays a table of current bandwidth usage by pairs of hosts.")
 (define-public munge
   (package
     (name "munge")
-    (version "0.5.13")
+    (version "0.5.14")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/dun/munge/releases/"
@@ -2238,20 +2248,45 @@ displays a table of current bandwidth usage by pairs of hosts.")
                                   version ".tar.xz"))
               (sha256
                (base32
-                "1nj486bbg1adfg298zck96vgx57kchcypc1zdz1n7w540vyksxcr"))
+                "0h06sghb4rqvv1ywyd6mzsmbcgh712v6ygrff0gzm440y4ca41k6"))
               (modules '((guix build utils)))
               (snippet
                '(begin
                   ;; Don't insist on write access to /var.
                   (substitute* "src/etc/Makefile.in"
                     (("\\$\\(INSTALL\\)(.*)localstatedir" _ middle)
-                     (string-append "-$(INSTALL)" middle "localstatedir")))
+                     (string-append "-$(INSTALL)" middle "localstatedir"))
+                    (("\\$\\(MKDIR_P\\) .*(local|run)statedir.*")
+                     ""))
                   #t))))
     (inputs
      `(("openssl" ,openssl)
        ("libgcrypt" ,libgcrypt)))
     (build-system gnu-build-system)
-    (arguments '(#:configure-flags '("--localstatedir=/var")))
+    (arguments
+     '(#:configure-flags
+       (list "--localstatedir=/var"
+             (string-append "--with-pkgconfigdir="
+                            (assoc-ref %outputs "out") "/lib/pkgconfig"))
+       #:phases
+       (modify-phases %standard-phases
+         ;; XXX Many test series fail.  Some might be fixable, others do no-no
+         ;; things like invoking ‘sudo’.
+         (add-after 'unpack 'skip-failing-tests
+           (lambda _
+             (for-each (lambda (test)
+                         (substitute* "t/Makefile.in"
+                           (((string-append test "\\.t ")) "")))
+                       (list "0100-munged-lock"
+                             "0010-basic"
+                             "0011-munged-cmdline"
+                             "0012-munge-cmdline"
+                             "0013-unmunge-cmdline"
+                             "0101-munged-security-socket"
+                             "0102-munged-security-keyfile"
+                             "0103-munged-security-logfile"
+                             "0110-munged-origin-addr"))
+             #t)))))
     (home-page "https://dun.github.io/munge/")
     (synopsis "Cluster computing authentication service")
     (description
@@ -2500,7 +2535,7 @@ a new command using the matched rule, and runs it.")
              (setenv "prefix" (assoc-ref outputs "out"))
              #t)))
        #:make-flags (list "--environment-overrides")))
-    (home-page "https://www.gentoo.com/di/")
+    (home-page "https://gentoo.com/di/")
     (synopsis "Advanced df like disk information utility")
     (description
      "@code{di} is a disk information utility, displaying everything that your
@@ -2840,14 +2875,14 @@ Intel DRM Driver.")
 (define-public fabric
   (package
     (name "fabric")
-    (version "1.14.0")
+    (version "1.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Fabric" version))
        (sha256
         (base32
-         "13r0b0hllgf8j9rh6x1knmbgvingbdmx046aazv6vck2ll120mw1"))))
+         "1a3ndlpdw6bhn8fcw1jgznl117a8pnr84az9rb5fwnrypf1ph2b6"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2               ; Python 2 only
@@ -2871,7 +2906,7 @@ Intel DRM Driver.")
        ("python2-bcrypt" ,python2-bcrypt)))
     (propagated-inputs
      `(("python2-paramiko" ,python2-paramiko)))
-    (home-page "http://fabfile.org")
+    (home-page "https://www.fabfile.org/")
     (synopsis "Simple Pythonic remote execution and deployment tool")
     (description
      "Fabric is designed to upload files and run shell commands on a number of
@@ -3320,14 +3355,14 @@ support forum.  It runs with the @code{/exec} command in most IRC clients.")
 (define-public python-pyudev
   (package
     (name "python-pyudev")
-    (version "0.21.0")
+    (version "0.22.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "pyudev" version))
         (sha256
           (base32
-            "0arz0dqp75sszsmgm6vhg92n1lsx91ihddx3m944f4ah0487ljq9"))))
+            "0xmj6l08iih2js9skjqpv4w7y0dhxyg91zmrs6v5aa65gbmipfv9"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f ; Tests require /sys
@@ -3353,7 +3388,7 @@ support forum.  It runs with the @code{/exec} command in most IRC clients.")
        ("python-mock" ,python-mock)
        ("python-pytest" ,python-pytest)
        ("python-sphinx" ,python-sphinx)))
-    (home-page "http://pyudev.readthedocs.org/")
+    (home-page "https://pyudev.readthedocs.io/")
     (synopsis "Python udev binding")
     (description "This package provides @code{udev} bindings for Python.")
     (license license:lgpl2.1)))
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 08d209ec58..f71909090e 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2013, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016, 2017, 2018, 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2016, 2017, 2018, 2019, 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
@@ -92,7 +92,7 @@ implement the floating point approach to complex multiplication are
 implemented.  On the other hand, these comprise asymptotically fast
 multiplication routines such as Toom–Cook and the FFT.")
    (license license:lgpl3+)
-   (home-page "http://mpfrcx.multiprecision.org/")))
+   (home-page "http://www.multiprecision.org/mpfrcx/")))
 
 (define-public gf2x
   (package
@@ -141,7 +141,7 @@ multiplication via floating point approximations.  It consists of libraries
 that can be called from within a C program and of executable command
 line applications.")
    (license license:gpl3+)
-   (home-page "http://cm.multiprecision.org/")))
+   (home-page "http://www.multiprecision.org/cm/")))
 
 (define-public fplll
   (package
@@ -346,19 +346,19 @@ precision.")
 (define-public giac
   (package
     (name "giac")
-    (version "1.5.0-85")
-    (source (origin
-              (method url-fetch)
-              ;; "~parisse/giac" is not used because the maintainer regularly
-              ;; overwrites the release tarball there, introducing a checksum
-              ;; mismatch every time.  See
-              ;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README>
-              (uri (string-append "https://www-fourier.ujf-grenoble.fr/"
-                                  "~parisse/debian/dists/stable/main/"
-                                  "source/giac_" version ".tar.gz"))
-              (sha256
-               (base32
-                "03icgrfhb1xiy95cqmfgmcb1lw3775mr2ybnzandmyn44iycs6rh"))))
+    (version "1.5.0-87")
+    (source
+     (origin
+       (method url-fetch)
+       ;; "~parisse/giac" is not used because the maintainer regularly
+       ;; overwrites the release tarball there, introducing a checksum
+       ;; mismatch every time.  See
+       ;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README>
+       (uri (string-append "https://www-fourier.ujf-grenoble.fr/"
+                           "~parisse/debian/dists/stable/main/source/"
+                           "giac_" version ".tar.gz"))
+       (sha256
+        (base32 "1d0h1yb7qvh9x7wwv9yrzmcp712f49w1iljkxp4y6g9pzsmg1mmv"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)
@@ -1481,7 +1481,7 @@ cohomology ring of a Grassmann variety.  The software package also includes
 a program that performs fast computation of the more general multiplicative
 structure constants of Schubert polynomials.")
     (license license:gpl2+)
-    (home-page "http://sites.math.rutgers.edu/~asbuch/lrcalc/")))
+    (home-page "https://sites.math.rutgers.edu/~asbuch/lrcalc/")))
 
 (define-public iml
   (package
diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index 62a5466ed0..68bcb72e69 100644
--- a/gnu/packages/android.scm
+++ b/gnu/packages/android.scm
@@ -9,6 +9,7 @@
 ;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -716,7 +717,7 @@ to be passed to the @code{udev} service.")
 (define-public git-repo
   (package
     (name "git-repo")
-    (version "1.12.37")
+    (version "2.4.1")
     (source
      (origin
        (method git-fetch)
@@ -725,61 +726,66 @@ to be passed to the @code{udev} service.")
              (commit (string-append "v" version))))
        (file-name (string-append "git-repo-" version "-checkout"))
        (sha256
-        (base32 "0qp7jqhblv7xblfgpcq4n18dyjdv8shz7r60c3vnjxx2fngkj2jd"))))
+        (base32 "0khg1731927gvin73dcbw1657kbfq4k7agla5rpzqcnwkk5agzg3"))))
     (build-system python-build-system)
     (arguments
-     `(#:python ,python-2 ; code says: "Python 3 support is … experimental."
-       #:phases
+     `(#:phases
        (modify-phases %standard-phases
          (add-before 'build 'set-executable-paths
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (git (assoc-ref inputs "git"))
-                    (gpg (assoc-ref inputs "gnupg"))
                     (ssh (assoc-ref inputs "ssh")))
                (substitute* '("repo" "git_command.py")
-                 (("^GIT = 'git' ")
-                  (string-append "GIT = '" git "/bin/git' ")))
-               (substitute* "repo"
-                 ((" cmd = \\['gpg',")
-                  (string-append " cmd = ['" gpg "/bin/gpg',")))
+                 (("^GIT = 'git'")
+                  (string-append "GIT = '" git "/bin/git'")))
                (substitute* "git_config.py"
                  ((" command_base = \\['ssh',")
                   (string-append " command_base = ['" ssh "/bin/ssh',")))
                #t)))
-         (add-before 'build 'do-not-clone-this-source
+         (add-before 'build 'do-not-self-update
            (lambda* (#:key outputs #:allow-other-keys)
+             ;; Setting the REPO_MAIN variable to an absolute file name is
+             ;; enough to have _FindRepo return the store main.py file.  The
+             ;; self update mechanism is activated with the call to _Init() in
+             ;; main(), so we bypass it.
+
+             ;; Ticket requesting upstream to provide a mean to disable the
+             ;; self update mechanism:
+             ;; https://bugs.chromium.org/p/gerrit/issues/detail?id=12407.
              (let* ((out (assoc-ref outputs "out"))
-                    (repo-dir (string-append out "/share/" ,name)))
+                    (repo-main (string-append out "/share/git-repo/main.py")))
                (substitute* "repo"
-                 (("^def _FindRepo\\(\\):.*")
-                  (format #f "
-def _FindRepo():
-  '''Look for a repo installation, starting at the current directory.'''
-  # Use the installed version of git-repo.
-  repo_main = '~a/main.py'
-  curdir = os.getcwd()
-  olddir = None
-  while curdir != '/' and curdir != olddir:
-    dot_repo = os.path.join(curdir, repodir)
-    if os.path.isdir(dot_repo):
-      return (repo_main, dot_repo)
-    else:
-      olddir = curdir
-      curdir = os.path.dirname(curdir)
-  return None, ''
-
-  # The remaining of this function is dead code.  It was used to
-  # find a git-checked-out version in the local project.\n" repo-dir))
-                 ;; Neither clone, check out, nor verify the git repository
-                 (("(^\\s+)_Clone\\(.*\\)") "")
-                 (("(^\\s+)_Checkout\\(.*\\)") "")
-                 ((" rev = _Verify\\(.*\\)") " rev = None"))
-               #t)))
+                 (("^REPO_MAIN = .*")
+                  (format #f "REPO_MAIN = ~s~%" repo-main))
+                 ((" _Init\\(args, gitc_init=\\(cmd ==.*" all)
+                  (string-append "True #" all)))
+               ;; Prevent repo from trying to git describe its version from
+               ;; the (disabled) self updated copy.
+               (substitute* "git_command.py"
+                 (("ver = getattr\\(RepoSourceVersion.*")
+                  (format #f "ver = ~s~%" ,version)))
+               (substitute* "subcmds/version.py"
+                 (("rp_ver = .*")
+                  (format #f "rp_ver = ~s~%" ,version)))
+               ;; Prevent repo from adding its (disabled) self update copy to
+               ;; the list of projects to fetch when using 'repo sync'.
+               (substitute* "subcmds/sync.py"
+                 (("to_fetch\\.extend\\(all_projects\\).*" all)
+                  (string-append "#" all))
+                 (("self\\._Fetch\\(to_fetch")
+                  "self._Fetch(all_projects")
+                 (("_PostRepoFetch\\(rp, opt\\.repo_verify).*" all)
+                  (string-append "#" all))))))
          (delete 'build) ; nothing to build
+         (add-before 'check 'configure-git
+           (lambda _
+             (setenv "HOME" (getcwd))
+             (invoke "git" "config" "--global" "user.email" "you@example.com")
+             (invoke "git" "config" "--global" "user.name" "Your Name")))
          (replace 'check
            (lambda _
-             (invoke "python" "-m" "nose")))
+             (invoke "./run_tests")))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -795,10 +801,9 @@ def _FindRepo():
     (inputs
      ;; TODO: Add git-remote-persistent-https once it is available in guix
      `(("git" ,git)
-       ("gnupg" ,gnupg)
        ("ssh" ,openssh)))
     (native-inputs
-     `(("nose" ,python2-nose)))
+     `(("pytest" ,python-pytest)))
     (home-page "https://code.google.com/p/git-repo/")
     (synopsis "Helps to manage many Git repositories.")
     (description "Repo is a tool built on top of Git.  Repo helps manage many
diff --git a/gnu/packages/anthy.scm b/gnu/packages/anthy.scm
index d543cd85fd..0d86347e88 100644
--- a/gnu/packages/anthy.scm
+++ b/gnu/packages/anthy.scm
@@ -49,7 +49,7 @@
            (lambda _
              (with-directory-excursion "test"
                (invoke "./anthy" "--all")))))))
-    (home-page "http://anthy.osdn.jp/")
+    (home-page "https://anthy.osdn.jp/")
     (synopsis "Japanese input method")
     (description "Anthy is a Japanese input method for converting
 hiragana text to mixed kana and kanji.  It is written in the C
diff --git a/gnu/packages/aspell.scm b/gnu/packages/aspell.scm
index 0b9f0de9de..fecc9a89ae 100644
--- a/gnu/packages/aspell.scm
+++ b/gnu/packages/aspell.scm
@@ -174,11 +174,10 @@ dictionaries, including personal ones.")
 
 (define-public aspell-dict-da
   (aspell-dictionary "da" "Danish"
-                     #:version "1.4.42-1"
-                     #:prefix "aspell5-"
+                     #:version "1.6.36-11-0"
                      #:sha256
                      (base32
-                      "1hfkmiyhgrx5lgrb2mffjbdn1hivrm73wcg7x0iid74p2yb0fjpp")))
+                      "1xz2haayvwlxgss9jf1x2311a1ixbk75q2vgfprjhibsmb7cpinv")))
 
 (define-public aspell-dict-el
   (aspell-dictionary "el" "Greek"
diff --git a/gnu/packages/assembly.scm b/gnu/packages/assembly.scm
index a96b169d15..1ad49baf8e 100644
--- a/gnu/packages/assembly.scm
+++ b/gnu/packages/assembly.scm
@@ -148,14 +148,14 @@ to the clients.")
 (define-public fasm
   (package
     (name "fasm")
-    (version "1.73.21")
+    (version "1.73.22")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://flatassembler.net/fasm-"
                            version ".tgz"))
        (sha256
-        (base32 "143zh7x3q0r2kclshh8n5w4i5pw4lh60si7rspvc725xxjpjkvcv"))))
+        (base32 "1pb0rcfdsb0h89khjjrbikz5wjdllavj3ajim0rcyh7x12xr1hw5"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no tests exist
@@ -232,7 +232,7 @@ assembler, a C compiler and a linker.  The assembler uses Intel syntax
                 (uri (git-reference
                       (url "https://git.savannah.gnu.org/r/libjit.git")
                       (commit commit)))
-                (file-name (string-append name "-" version "-checkout"))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "0p6wklslkkp3s4aisj3w5a53bagqn5fy4m6088ppd4fcfxgqkrcd"))))
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 78d29e1c68..d0f55a96b8 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -322,7 +322,7 @@ namespace ARDOUR { const char* revision = \"" version "\" ; }"))
        ("itstool" ,itstool)
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)))
-    (home-page "http://ardour.org")
+    (home-page "https://ardour.org")
     (synopsis "Digital audio workstation")
     (description
      "Ardour is a multi-channel digital audio workstation, allowing users to
@@ -1193,7 +1193,7 @@ follower.")
 (define-public fluidsynth
   (package
     (name "fluidsynth")
-    (version "2.1.0")
+    (version "2.1.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1202,7 +1202,7 @@ follower.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0jhla1641rx77va4b6n4shn8srj87rpwvp170byj1bg8z8g89ji1"))))
+                "09jq04hrasidf6b5gkk4aba13fq55z3bmn7bq35rdaikz26xiij4"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f                      ; no check target
@@ -1812,14 +1812,14 @@ essential distortions.")
 (define-public liblo
   (package
     (name "liblo")
-    (version "0.30")
+    (version "0.31")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/liblo/liblo/" version
                                  "/liblo-" version ".tar.gz"))
              (sha256
               (base32
-               "06wdjzxjdshr6hyl4c94yvg3jixiylap8yjs8brdfpm297gck9rh"))))
+               "0l67rkdhfa8cffa0nynql3lh2xlbn1454h6qxhjddp1029p48krb"))))
     (build-system gnu-build-system)
     (arguments
      `(;; liblo test FAILED
@@ -1988,7 +1988,7 @@ software.")
      (list (search-path-specification
             (variable "LV2_PATH")
             (files '("lib/lv2")))))
-    (home-page "http://elephly.net/lv2/mdapiano.html")
+    (home-page "https://elephly.net/lv2/mdapiano.html")
     (synopsis "LV2 port of the mda Piano plugin")
     (description "An LV2 port of the mda Piano VSTi.")
     (license license:gpl3+)))
@@ -2002,7 +2002,7 @@ software.")
                      (string-append "PREFIX=" (assoc-ref %outputs "out")))
        #:tests? #f ; no check target
        #:phases (modify-phases %standard-phases (delete 'configure))))
-    (home-page "http://elephly.net/lv2/mdaepiano.html")
+    (home-page "https://elephly.net/lv2/mdaepiano.html")
     (synopsis "LV2 port of the mda EPiano plugin")
     (description "An LV2 port of the mda EPiano VSTi.")))
 
@@ -3391,7 +3391,7 @@ code, used in @code{libtoxcore}.")
      `(#:tests? #f))                   ; tests require access to ALSA devices.
     (inputs
      `(("alsa-lib" ,alsa-lib)))
-    (home-page "http://larsimmisch.github.io/pyalsaaudio/")
+    (home-page "https://larsimmisch.github.io/pyalsaaudio/")
     (synopsis "ALSA wrappers for Python")
     (description
      "This package contains wrappers for accessing the ALSA API from Python.
@@ -3516,7 +3516,7 @@ the Snd sources), Ruby, or Forth.")
 (define-public noise-repellent
   (package
     (name "noise-repellent")
-    (version "0.1.4")
+    (version "0.1.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -3525,16 +3525,12 @@ the Snd sources), Ruby, or Forth.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "0rd3dlmk3vivjmcr6x2x860y0j1d49c2j95j6ny50v184mwvn11j"))))
-    (build-system gnu-build-system)
+                "0hb89x9i2knzan46q4nwscf5zmnb2nwf4w13xl2c0y1mx1ls1mwl"))))
+    (build-system meson-build-system)
     (arguments
-     `(#:make-flags
-       (list "CC=gcc"
-             (string-append "PREFIX=" (assoc-ref %outputs "out")))
-       #:tests? #f ; there are none
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'configure))))
+     `(#:configure-flags
+       (list (string-append "--prefix=" (assoc-ref %outputs "out")
+                            "/lib/lv2"))))
     (inputs
      `(("lv2" ,lv2)
        ("fftwf" ,fftwf)))
diff --git a/gnu/packages/autotools.scm b/gnu/packages/autotools.scm
index 98f31f6bca..a011d8ee3d 100644
--- a/gnu/packages/autotools.scm
+++ b/gnu/packages/autotools.scm
@@ -61,8 +61,7 @@
     ;; XXX: testsuite: 209 and 279 failed. The latter is an impurity. It
     ;; should use our own "cpp" instead of "/lib/cpp".
     (arguments `(#:tests? #f))
-    (home-page
-     "http://www.gnu.org/software/autoconf/")
+    (home-page "https://www.gnu.org/software/autoconf/")
     (synopsis "Create source code configuration scripts")
     (description
      "Autoconf offers the developer a robust set of M4 macros which expand
diff --git a/gnu/packages/aux-files/emacs/guix-emacs.el b/gnu/packages/aux-files/emacs/guix-emacs.el
index 05fc9709b6..25a87ee52d 100644
--- a/gnu/packages/aux-files/emacs/guix-emacs.el
+++ b/gnu/packages/aux-files/emacs/guix-emacs.el
@@ -35,8 +35,9 @@
   "Return a list of Emacs 'autoloads' files in DIRECTORY.
 The files in the list do not have extensions (.el, .elc)."
   ;; `directory-files' doesn't honor group in regexp.
-  (mapcar #'file-name-sans-extension
-          (directory-files directory 'full-name guix-emacs-autoloads-regexp)))
+  (delete-dups (mapcar #'file-name-sans-extension
+                       (directory-files directory 'full-name
+                                        guix-emacs-autoloads-regexp))))
 
 ;;;###autoload
 (defun guix-emacs-autoload-packages ()
diff --git a/gnu/packages/avr.scm b/gnu/packages/avr.scm
index 1f99f636e0..608e487b93 100644
--- a/gnu/packages/avr.scm
+++ b/gnu/packages/avr.scm
@@ -63,7 +63,16 @@
           `(delete "--disable-multilib" ,flags))))
       (native-search-paths
        (list (search-path-specification
-              (variable "CROSS_CPATH")
+              (variable "CROSS_C_INCLUDE_PATH")
+              (files '("avr/include")))
+             (search-path-specification
+              (variable "CROSS_CPLUS_INCLUDE_PATH")
+              (files '("avr/include")))
+             (search-path-specification
+              (variable "CROSS_OBJC_INCLUDE_PATH")
+              (files '("avr/include")))
+             (search-path-specification
+              (variable "CROSS_OBJCPLUS_INCLUDE_PATH")
               (files '("avr/include")))
              (search-path-specification
               (variable "CROSS_LIBRARY_PATH")
@@ -76,7 +85,10 @@
   (package
     (inherit avr-gcc-4.9)
     (version (package-version gcc-5))
-    (source (package-source gcc-5))))
+    (source (origin
+              (inherit (package-source gcc-5))
+              (patches (append (origin-patches (package-source gcc-5))
+                               (search-patches "gcc-cross-environment-variables.patch")))))))
 
 (define (avr-libc avr-gcc)
   (package
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 5cdf3b9155..3e8161a63f 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -462,7 +462,7 @@ rdiff-backup is easy to use and settings have sensible defaults.")
     (inputs
      `(("perl" ,perl)
        ("rsync" ,rsync)))
-    (home-page "http://rsnapshot.org")
+    (home-page "https://rsnapshot.org")
     (synopsis "Deduplicating snapshot backup utility based on rsync")
     (description "rsnapshot is a file system snapshot utility based on rsync.
 rsnapshot makes it easy to make periodic snapshots of local machines, and
diff --git a/gnu/packages/bdw-gc.scm b/gnu/packages/bdw-gc.scm
index cc492105d1..73b0c073d9 100644
--- a/gnu/packages/bdw-gc.scm
+++ b/gnu/packages/bdw-gc.scm
@@ -87,13 +87,13 @@ simple collector interface.
 
 Alternatively, the garbage collector may be used as a leak detector for
 C or C++ programs, though that is not its primary goal.")
-   (home-page "http://www.hboehm.info/gc/")
+   (home-page "https://www.hboehm.info/gc/")
 
    (license (x11-style (string-append home-page "license.txt")))))
 
 (define-public libgc-8.0
-  (package/inherit
-   libgc
+  (package
+   (inherit libgc)
    (version "8.0.4")
    (source (origin
              (method url-fetch)
@@ -104,8 +104,8 @@ C or C++ programs, though that is not its primary goal.")
                "1798rp3mcfkgs38ynkbg2p47bq59pisrc6mn0l20pb5iczf0ssj3"))))))
 
 (define-public libgc/back-pointers
-  (package
-    (inherit libgc)
+  (package/inherit
+    libgc
     (name "libgc-back-pointers")
     (arguments
      `(#:make-flags
diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm
index 08478d3118..9ae30eefc8 100644
--- a/gnu/packages/benchmark.scm
+++ b/gnu/packages/benchmark.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2019 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2019 Gábor Boskovits <boskovits@gmail.com>
 ;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -35,6 +36,7 @@
   #:use-module (gnu packages linux)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
+  #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-xyz)
@@ -44,14 +46,14 @@
 (define-public fio
   (package
     (name "fio")
-    (version "3.17")
+    (version "3.18")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://brick.kernel.dk/snaps/"
                                   "fio-" version ".tar.bz2"))
               (sha256
                (base32
-                "1hvh8syjz6l0q9bm5p7rf0yrmpkfcx5zj5d47mf6335w1i0h5gqf"))))
+                "12wzi40hn0ylkdiqwjjljdjmiq78nhwsv3qqa0fad7h3x08w6w6b"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"
@@ -231,3 +233,28 @@ This can give a much better understanding of the command's performance.")
      "Benchmark is a library to benchmark code snippets,
 similar to unit tests.")
     (license license:asl2.0)))
+
+(define-public bonnie++
+  (package
+    (name "bonnie++")
+    (version "1.98")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://www.coker.com.au/bonnie++/bonnie++-"
+                                  version ".tgz"))
+              (sha256
+               (base32
+                "010bmlmi0nrlp3aq7p624sfaj5a65lswnyyxk3cnz1bqig0cn2vf"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("perl" ,perl)))
+    (arguments '(#:tests? #f)) ; there are no tests
+    (home-page "https://doc.coker.com.au/projects/bonnie/")
+    (synopsis "Hard drive and file system benchmark suite")
+    (description
+     "Bonnie++ is a benchmark suite that is aimed at performing a number of
+simple tests of hard drive and file system performance.  Bonnie++ allows you to
+benchmark how your file systems perform with respect to data read and write
+speed, the number of seeks that can be performed per second, and the number of
+file metadata operations that can be performed per second.")
+    (license license:gpl2)))   ;GPL 2 only, see copyright.txt
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a6e0c5a1e6..63687036fc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -224,6 +224,30 @@ Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by default.")
 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
     (license license:artistic2.0)))
 
+(define-public r-bsgenome-hsapiens-ncbi-grch38
+  (package
+    (name "r-bsgenome-hsapiens-ncbi-grch38")
+    (version "1.3.1000")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
+                              version 'annotation))
+       (sha256
+        (base32
+         "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
+    (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
+    (home-page
+     "https://bioconductor.org/packages/release/data/annotation/html/\
+BSgenome.Hsapiens.NCBI.GRCh38.html")
+    (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
+    (description
+     "This package provides full genome sequences for Homo sapiens (Human) as
+provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
+    (license license:artistic2.0)))
+
 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
   (package
     (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
@@ -594,14 +618,14 @@ database is exposed as a @code{TxDb} object.")
 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
   (package
     (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
-    (version "3.4.7")
+    (version "3.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
                                      version 'annotation))
               (sha256
                (base32
-                "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
+                "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
     (properties
      `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
     (build-system r-build-system)
@@ -722,6 +746,49 @@ the weighted combination of published signatures that, when summed, most
 closely reconstructs the mutational profile.")
     (license license:gpl2+)))
 
+;; This is a CRAN package, but it depends on Bioconductor packages.
+(define-public r-nmf
+  (package
+    (name "r-nmf")
+    (version "0.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "NMF" version))
+       (sha256
+        (base32
+         "0b2ls3x1nkrnam45hagpys624nzxj3v7kxnp0q216yakvx5h57cq"))))
+    (properties `((upstream-name . "NMF")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cluster" ,r-cluster)
+       ("r-biobase" ,r-biobase)
+       ("r-biocmanager" ,r-biocmanager)
+       ("r-bigmemory" ,r-bigmemory) ; suggested
+       ("r-synchronicity" ,r-synchronicity) ; suggested
+       ("r-colorspace" ,r-colorspace)
+       ("r-digest" ,r-digest)
+       ("r-doparallel" ,r-doparallel)
+       ("r-foreach" ,r-foreach)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridbase" ,r-gridbase)
+       ("r-pkgmaker" ,r-pkgmaker)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-registry" ,r-registry)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rngtools" ,r-rngtools)
+       ("r-stringr" ,r-stringr)))
+    (home-page "http://renozao.github.io/NMF")
+    (synopsis "Algorithms and framework for nonnegative matrix factorization")
+    (description
+     "This package provides a framework to perform Non-negative Matrix
+Factorization (NMF).  The package implements a set of already published
+algorithms and seeding methods, and provides a framework to test, develop and
+plug new or custom algorithms.  Most of the built-in algorithms have been
+optimized in C++, and the main interface function provides an easy way of
+performing parallel computations on multicore machines.")
+    (license license:gpl2+)))
+
 (define-public r-do-db
   (package
     (name "r-do-db")
@@ -1526,6 +1593,30 @@ expressed genes in DNA microarray experiments.")
      "This package implements some simple graph handling capabilities for R.")
     (license license:artistic2.0)))
 
+;; This is a CRAN package, but it depends on a Bioconductor package.
+(define-public r-ggm
+  (package
+    (name "r-ggm")
+    (version "2.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggm" version))
+       (sha256
+        (base32
+         "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
+    (properties `((upstream-name . "ggm")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-graph" ,r-graph)
+       ("r-igraph" ,r-igraph)))
+    (home-page "https://cran.r-project.org/package=ggm")
+    (synopsis "Functions for graphical Markov models")
+    (description
+     "This package provides functions and datasets for maximum likelihood
+fitting of some classes of graphical Markov models.")
+    (license license:gpl2+)))
+
 (define-public r-codedepends
   (package
     (name "r-codedepends")
@@ -1557,14 +1648,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.20.0")
+    (version "3.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "0hp3s3shnrb55cxvx9wrdl67wqw9f55gdgx7262s4mahpxjswfsa"))))
+         "0kmfha4vprbi0z6n7v9w28xfrqcx5qad7yfr0b316j5aj8v9f4hc"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1867,14 +1958,14 @@ experiments.")
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.20.0")
+    (version "1.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "10kwb70c9aq0bfqpq48h186lsbwgrg18m14r9z8x6n8l7cds5azc"))))
+         "140bp7c8p079xh5wwxmrq3a73pm6mdc9czq5w2gzjml7dgrca38a"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
@@ -2028,14 +2119,14 @@ genes or proteins in these datasets.")
 (define-public r-inspect
   (package
     (name "r-inspect")
-    (version "1.16.2")
+    (version "1.16.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "INSPEcT" version))
        (sha256
         (base32
-         "1g8la7k4pnyr2hvk4yjd1bwvjy6nqbbb0fwxrrh2ifgqf4h21x2p"))))
+         "0y4gpvrbmcipdnyz9lz9ywn0317xnpcriiisqvxygin05vgcpilp"))))
     (properties `((upstream-name . "INSPEcT")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2125,14 +2216,14 @@ samples.")
 (define-public r-biocneighbors
   (package
     (name "r-biocneighbors")
-    (version "1.4.1")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocNeighbors" version))
        (sha256
         (base32
-         "05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf"))))
+         "1bx7i5pifj8w89fnhfgcfgcar2ik2ad8wqs2rix7yks90vz185i6"))))
     (properties `((upstream-name . "BiocNeighbors")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2156,14 +2247,14 @@ achieved for all methods using the BiocParallel framework.")
 (define-public r-biocsingular
   (package
     (name "r-biocsingular")
-    (version "1.2.1")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSingular" version))
        (sha256
         (base32
-         "0fjfmmpda7pszsck2hm7bp4509pl3xaz02q2q03d5vla62h1h81k"))))
+         "1282fdwxrpga87y8xflr0sl8ajwawgn2i9i65my8mbg5vrixs407"))))
     (properties `((upstream-name . "BiocSingular")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3130,27 +3221,20 @@ surface of a flowcell.")
 (define-public r-gkmsvm
   (package
     (name "r-gkmsvm")
-    (version "0.79.0")
+    (version "0.80.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gkmSVM" version))
        (sha256
         (base32
-         "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
+         "0ljcga246ad0ql8x3drvrdsyp0f20mgp3p6lnl79xb76qgfdnm0p"))))
     (properties `((upstream-name . "gkmSVM")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-kernlab" ,r-kernlab)
+     `(("r-kernlab" ,r-kernlab)
        ("r-rcpp" ,r-rcpp)
        ("r-rocr" ,r-rocr)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
        ("r-seqinr" ,r-seqinr)))
     (home-page "https://cran.r-project.org/web/packages/gkmSVM")
     (synopsis "Gapped-kmer support vector machine")
@@ -3284,14 +3368,14 @@ gmapR.")
 (define-public r-heatplus
   (package
     (name "r-heatplus")
-    (version "2.32.0")
+    (version "2.32.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Heatplus" version))
        (sha256
         (base32
-         "0hx5gqgh4xrkx37ccprq7azj9jziff137bdk0gvrixcx52ws6h89"))))
+         "1ldxj2hasg6ysh70sc73mz2v4h3n8gf3lii09c3sqc4wmz5h7rp1"))))
     (properties `((upstream-name . "Heatplus")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3521,14 +3605,14 @@ profiles (GO and KEGG) of gene and gene clusters.")
 (define-public r-mlinterfaces
   (package
     (name "r-mlinterfaces")
-    (version "1.66.2")
+    (version "1.66.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MLInterfaces" version))
        (sha256
         (base32
-         "1wc280iw9vllg6f58vsdj895yaqs8w42kl7jk8sgii009gwlaj8d"))))
+         "19hlicdndy2p45y7w91gnwi3wgq5s465a646z3qqk8gmn5sn614q"))))
     (properties `((upstream-name . "MLInterfaces")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3942,14 +4026,14 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.10.1")
+    (version "1.10.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "12ix0bvwk50d48z85f3453k7szm1j27gk4qgw56az4fxra472rlh"))))
+         "0dzrizacy3br8fiy1vnsl5zf242lg1hqv9dyv5ayqh2n480is57f"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5305,14 +5389,14 @@ annotations.")
 (define-public r-rsubread
   (package
     (name "r-rsubread")
-    (version "2.0.0")
+    (version "2.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rsubread" version))
        (sha256
         (base32
-         "0l8q9y2a4m1di0w5nlxhq9jgliinhgr2fwjpm5ixnqx5j3iprlwd"))))
+         "0pdkx9mhvzw3a4ff725qvda9bxvs9vh2ppb29cc5jrivgjndv5cy"))))
     (properties `((upstream-name . "Rsubread")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -5817,14 +5901,14 @@ self-organizing map clustering and minimal spanning trees.")
 (define-public r-mixomics
   (package
     (name "r-mixomics")
-    (version "6.10.6")
+    (version "6.10.8")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mixOmics" version))
        (sha256
         (base32
-         "18jwrdyc4pnx917y1kskxz3fqvlrkyy4ny0xqrfcidz0j7p0b7wr"))))
+         "0307vhx9ck24rxqbvq15815ssxcc226sl2la060n204b51wi9jaa"))))
     (properties `((upstream-name . "mixOmics")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5859,14 +5943,14 @@ delete entire rows with missing data.")
 (define-public r-depecher
   (package
     (name "r-depecher")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DepecheR" version))
        (sha256
         (base32
-         "1f6zbc0fq7xjflh3mkjx1n83mpppw663dj22rlpxzwp1kpmf6wm5"))))
+         "08ja6ayvbax9m3x9w3xzi72z97miiha2nbsild1gp77n6sgn5i35"))))
     (properties `((upstream-name . "DepecheR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5937,14 +6021,14 @@ genes in the gene-set that are ranked above the leading edge).")
 (define-public r-cicero
   (package
     (name "r-cicero")
-    (version "1.4.0")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cicero" version))
        (sha256
         (base32
-         "0mmm7vvzq50b5fayid0bw82b5lar3xm9fwl2ya30q0p4db2y6wnz"))))
+         "154djqd32w87814ycfmfz27ikp17bnampvmvw5hzi5p2x9l3h82r"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -5966,6 +6050,7 @@ genes in the gene-set that are ranked above the leading edge).")
        ("r-s4vectors" ,r-s4vectors)
        ("r-stringr" ,r-stringr)
        ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)
        ("r-vgam" ,r-vgam)))
     (home-page "https://bioconductor.org/packages/cicero/")
     (synopsis "Predict cis-co-accessibility from single-cell data")
@@ -7205,14 +7290,14 @@ access.")
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
-    (version "1.12.2")
+    (version "1.12.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32
-         "0722f3jl1xq8k8w7vrv986jd16bgysqp3n07pgmdn0hh1zh2mcqc"))))
+         "1vf6l88j3n6109j6sd08wfqxqpj2k20dvr8ll9zl1szsn18b4gny"))))
     (properties
      `((upstream-name . "MultiAssayExperiment")))
     (build-system r-build-system)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 065555b37b..0c12e7c874 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -410,7 +410,7 @@ computational cluster.")
 (define-public bedtools
   (package
     (name "bedtools")
-    (version "2.27.1")
+    (version "2.29.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/arq5x/bedtools2/releases/"
@@ -418,7 +418,7 @@ computational cluster.")
                                   "bedtools-" version ".tar.gz"))
               (sha256
                (base32
-                "1ndg5yknrxl4djx8ddzgk12rrbiidfpmkkg5z3f95jzryfxarhn8"))))
+                "0m3hk6548846w83a9s5drsczvy67n2azx41kj71n03klb2gbzwg3"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"
@@ -427,7 +427,8 @@ computational cluster.")
        #:phases
        (modify-phases %standard-phases
          (delete 'configure))))
-    (native-inputs `(("python" ,python-2)))
+    (native-inputs
+     `(("python" ,python-wrapper)))
     (inputs
      `(("samtools" ,samtools)
        ("zlib" ,zlib)))
@@ -440,7 +441,7 @@ genome arithmetic: that is, set theory on the genome.  For example, bedtools
 allows one to intersect, merge, count, complement, and shuffle genomic
 intervals from multiple files in widely-used genomic file formats such as BAM,
 BED, GFF/GTF, VCF.")
-    (license license:gpl2)))
+    (license license:expat)))
 
 ;; Later releases of bedtools produce files with more columns than
 ;; what Ribotaper expects.
@@ -2272,23 +2273,23 @@ time.")
 (define-public crossmap
   (package
     (name "crossmap")
-    (version "0.2.9")
+    (version "0.3.8")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "CrossMap" version))
               (sha256
                (base32
-                "1byhclrqnqpvc1rqkfh4jwj6yhn0x9y7jk47i0qcjlhk0pjkw92p"))))
+                "1sb2f2qbxya4fzw3yjl09vbrs8vfmw22zrygrvz004sf9gb1vkan"))))
     (build-system python-build-system)
-    (arguments `(#:python ,python-2))
     (inputs
-     `(("python-bx-python" ,python2-bx-python)
-       ("python-numpy" ,python2-numpy)
-       ("python-pysam" ,python2-pysam)
+     `(("python-bx-python" ,python-bx-python)
+       ("python-numpy" ,python-numpy)
+       ("python-pybigwig" ,python-pybigwig)
+       ("python-pysam" ,python-pysam)
        ("zlib" ,zlib)))
     (native-inputs
-     `(("python-cython" ,python2-cython)
-       ("python-nose" ,python2-nose)))
+     `(("python-cython" ,python-cython)
+       ("python-nose" ,python-nose)))
     (home-page "http://crossmap.sourceforge.net/")
     (synopsis "Convert genome coordinates between assemblies")
     (description
@@ -2578,7 +2579,7 @@ accurately delineate genomic rearrangements throughout the genome.")
 (define-public diamond
   (package
     (name "diamond")
-    (version "0.9.22")
+    (version "0.9.30")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2587,7 +2588,7 @@ accurately delineate genomic rearrangements throughout the genome.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0bky78v79g3wmdpsd706cscckgw1v09fg8vdd0z8z0d5b97aj9zl"))))
+                "0k6f3kb6cniw11xw6763kkbs1sl0yack7xsy7q5fl5v170ssphq4"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; no "check" target
@@ -2744,7 +2745,7 @@ quantitative phenotypes.")
 (define-public edirect
   (package
     (name "edirect")
-    (version "12.1.20190819")
+    (version "12.1.20190829")
     (source (origin
               (method url-fetch)
               (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect"
@@ -2752,7 +2753,7 @@ quantitative phenotypes.")
                                   "/edirect-" version ".tar.gz"))
               (sha256
                (base32
-                "1i9s9mppcfqd60pfywpm8vdyz5vpnyslw22nd7dv0bhykrdnkz9g"))))
+                "1xb330z28dgp7slrvp8r7rgncsasv9lpcpqim571yg728dq7xdik"))))
     (build-system perl-build-system)
     (arguments
      `(#:phases
@@ -4274,19 +4275,30 @@ experiments.")
 (define-public macs
   (package
     (name "macs")
-    (version "2.1.1.20160309")
+    (version "2.2.6")
     (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "MACS2" version))
+              ;; The PyPi tarball does not contain tests.
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/taoliu/MACS.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "09ixspd1vcqmz1c81ih70xs4m7qml2iy5vyx1y74zww3iy1vl210"))))
+                "1c5gxr0mk6hkd4vclf0k00wvyvzw2vrmk52c85338p7aqjwg6n15"))))
     (build-system python-build-system)
     (arguments
-     `(#:python ,python-2 ; only compatible with Python 2.7
-       #:tests? #f)) ; no test target
+     `(#:phases
+       (modify-phases %standard-phases
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (invoke "pytest" "-v"))))))
     (inputs
-     `(("python-numpy" ,python2-numpy)))
+     `(("python-numpy" ,python-numpy)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
     (home-page "https://github.com/taoliu/MACS/")
     (synopsis "Model based analysis for ChIP-Seq data")
     (description
@@ -4910,20 +4922,26 @@ predicts the locations of structural units in the sequences.")
 (define-public proteinortho
   (package
     (name "proteinortho")
-    (version "5.16b")
-    (source
-     (origin
-      (method url-fetch)
-      (uri
-       (string-append
-        "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v"
-        version "_src.tar.gz"))
-      (sha256
-       (base32
-        "1wl0dawpssqwfjvr651r4wlww8hhjin8nba6xh71ks7sbypx886j"))))
+    (version "6.0.14")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://gitlab.com/paulklemm_PHD/proteinortho.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0pmy617zy2z2w6hjqxjhf3rzikf5n3mpia80ysq8233vfr7wrzff"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; remove pre-built scripts
+                  (delete-file-recursively "src/BUILD/")
+                  #t))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
+       #:make-flags '("CC=gcc")
        #:phases
        (modify-phases %standard-phases
          (replace 'configure
@@ -4941,15 +4959,23 @@ predicts the locations of structural units in the sequences.")
              #t))
          (add-after 'install 'wrap-programs
            (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let* ((path (getenv "PATH"))
-                    (out (assoc-ref outputs "out"))
-                    (binary (string-append out "/bin/proteinortho5.pl")))
-               (wrap-program binary `("PATH" ":" prefix (,path))))
+             (let ((path (getenv "PATH"))
+                   (out (assoc-ref outputs "out")))
+               (for-each (lambda (script)
+                           (wrap-script script `("PATH" ":" prefix (,path))))
+                         (cons (string-append out "/bin/proteinortho")
+                               (find-files out "\\.(pl|py)$"))))
              #t)))))
     (inputs
-     `(("perl" ,perl)
-       ("python" ,python-2)
-       ("blast+" ,blast+)))
+     `(("guile" ,guile-3.0) ; for wrap-script
+       ("diamond" ,diamond)
+       ("perl" ,perl)
+       ("python" ,python-wrapper)
+       ("blast+" ,blast+)
+       ("lapack" ,lapack)
+       ("openblas" ,openblas)))
+    (native-inputs
+     `(("which" ,which)))
     (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho")
     (synopsis "Detect orthologous genes across species")
     (description
@@ -4957,7 +4983,7 @@ predicts the locations of structural units in the sequences.")
 species.  For doing so, it compares similarities of given gene sequences and
 clusters them to find significant groups.  The algorithm was designed to handle
 large-scale data and can be applied to hundreds of species at once.")
-    (license license:gpl2+)))
+    (license license:gpl3+)))
 
 (define-public pyicoteo
   (package
@@ -5281,7 +5307,7 @@ BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
 (define-public rseqc
   (package
     (name "rseqc")
-    (version "2.6.1")
+    (version "3.0.1")
     (source
      (origin
        (method url-fetch)
@@ -5289,28 +5315,18 @@ BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
         (string-append "mirror://sourceforge/rseqc/"
                        "RSeQC-" version ".tar.gz"))
        (sha256
-        (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           ;; remove bundled copy of pysam
-           (delete-file-recursively "lib/pysam")
-           (substitute* "setup.py"
-             ;; remove dependency on outdated "distribute" module
-             (("^from distribute_setup import use_setuptools") "")
-             (("^use_setuptools\\(\\)") "")
-             ;; do not use bundled copy of pysam
-             (("^have_pysam = False") "have_pysam = True"))
-           #t))))
+        (base32
+         "0gbb9iyb7swiv5455fm5rg98r7l6qn27v564yllqjd574hncpx6m"))))
     (build-system python-build-system)
-    (arguments `(#:python ,python-2))
     (inputs
-     `(("python-cython" ,python2-cython)
-       ("python-pysam" ,python2-pysam)
-       ("python-numpy" ,python2-numpy)
+     `(("python-cython" ,python-cython)
+       ("python-bx-python" ,python-bx-python)
+       ("python-pybigwig" ,python-pybigwig)
+       ("python-pysam" ,python-pysam)
+       ("python-numpy" ,python-numpy)
        ("zlib" ,zlib)))
     (native-inputs
-     `(("python-nose" ,python2-nose)))
+     `(("python-nose" ,python-nose)))
     (home-page "http://rseqc.sourceforge.net/")
     (synopsis "RNA-seq quality control package")
     (description
@@ -6556,7 +6572,7 @@ profiles, and associated taxonomic information.")
 (define-public vcftools
   (package
     (name "vcftools")
-    (version "0.1.15")
+    (version "0.1.16")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -6564,7 +6580,7 @@ profiles, and associated taxonomic information.")
                     version "/vcftools-" version ".tar.gz"))
               (sha256
                (base32
-                "1qw30c45wihgy632rbz4rh3njnwj4msj46l1rsgdhyg6bgypmr1i"))))
+                "1qqlx7flfv7axrjwkaz6njkscsl1d0jw98ns8d8bh1n1hd1pgz6v"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no "check" target
@@ -6592,17 +6608,18 @@ data in the form of VCF files.")
 (define-public infernal
   (package
     (name "infernal")
-    (version "1.1.2")
+    (version "1.1.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://eddylab.org/software/infernal/"
                                   "infernal-" version ".tar.gz"))
               (sha256
                (base32
-                "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c"))))
+                "0pm8bm3s6nfa0av4x6m6h27lsg12b3lz3jm0fyh1mc77l2isd61v"))))
     (build-system gnu-build-system)
     (native-inputs
-     `(("perl" ,perl))) ; for tests
+     `(("perl" ,perl)
+       ("python" ,python))) ; for tests
     (home-page "http://eddylab.org/infernal/")
     (synopsis "Inference of RNA alignments")
     (description "Infernal (\"INFERence of RNA ALignment\") is a tool for
@@ -6613,7 +6630,7 @@ profile, but it scores a combination of sequence consensus and RNA secondary
 structure consensus, so in many cases, it is more capable of identifying RNA
 homologs that conserve their secondary structure more than their primary
 sequence.")
-    ;; Infernal 1.1.2 requires VMX or SSE capability for parallel instructions.
+    ;; Infernal 1.1.3 requires VMX or SSE capability for parallel instructions.
     (supported-systems '("i686-linux" "x86_64-linux"))
     (license license:bsd-3)))
 
@@ -6935,14 +6952,14 @@ testing and other simple calculations.")
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.44.1")
+    (version "1.44.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "1dh3q83hmi4l72vpif6dn51dzbi9ljrjgkq2zxg4sqy2jxv4vwza"))))
+         "0ykyrj4g6vc67d5s46sp4659qvar2iavflzhggm79w4p50hxia4s"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs
@@ -7465,13 +7482,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.28.0")
+    (version "3.28.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "1m7l6fbyik1b79v0h9qkmpa39svij1yiw24gxahbdqjg7fzsavh3"))))
+                "07dv99kl7jfa62nzcq705r56gcpb1hq7p4px48j71y2ddi1rqmr6"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7532,13 +7549,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.42.0")
+    (version "3.42.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "0cfynv6qbnar5rl7vjh5lvddd381g9wqx1zd6a7l130hf59mwswn"))))
+                "1nd01r7rd7jb5qz84vbgfnyrmgm9wiq7fsdji68537kjgvrzmm9z"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7751,13 +7768,13 @@ biological sequences or sets of sequences.")
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "2.2.1")
+    (version "2.2.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "0hpdc88prpq1gcja89n5s1ndcg81523qrkbkm9gbhm7rm8wmi8cl"))))
+                "1vj43acawqqkf9yval9fzxarpsf04fmn78m2hq4f083w1k0myhyr"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
@@ -7939,13 +7956,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.38.1")
+    (version "1.38.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "1c1x29f447dv0i1wi88paji645lfsgmg4ckn19hyhlra72smhzqc"))))
+                "0dd226kgks50jdx5w35f3wmg95hy8aibi4kcn8p5kmqp5i8j580b"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -8236,7 +8253,7 @@ throughput genetic sequencing data sets using regression methods.")
 (define-public r-qtl
  (package
   (name "r-qtl")
-  (version "1.44-9")
+  (version "1.45-11")
   (source
    (origin
     (method url-fetch)
@@ -8244,7 +8261,7 @@ throughput genetic sequencing data sets using regression methods.")
                         version ".tar.gz"))
     (sha256
      (base32
-      "03lmvydln8b7666b6w46qbryhf83vsd11d4y2v95rfgvqgq66l1i"))))
+      "1d6qgj602fm6zia3djl4hmca0ri4v57ffp3g93p2yc3cabx2hq90"))))
   (build-system r-build-system)
   (home-page "https://rqtl.org/")
   (synopsis "R package for analyzing QTL experiments in genetics")
@@ -8332,14 +8349,14 @@ secondary structure and comparative analysis in R.")
 (define-public r-rhtslib
   (package
     (name "r-rhtslib")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhtslib" version))
        (sha256
         (base32
-         "04inkq44lxwymqv51mxgaphasqjcdc9rl5p58imnrdm0kszs8prm"))))
+         "0gkbrmrcg55c9s5166ifljlx0v25rv4ijdyp4wf4c292xd6chy2l"))))
     (properties `((upstream-name . "Rhtslib")))
     (build-system r-build-system)
     ;; Without this a temporary directory ends up in the Rhtslib.so binary,
@@ -9122,14 +9139,14 @@ unmodeled, or latent sources of noise.")
 (define-public r-seqminer
   (package
     (name "r-seqminer")
-    (version "7.1")
+    (version "8.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "seqminer" version))
        (sha256
         (base32
-         "1jydcpkw4rwfp983j83kipvsvr10as9pb49zzn3c2v09k1gh3ymy"))))
+         "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
     (build-system r-build-system)
     (inputs
      `(("zlib" ,zlib)))
@@ -9504,13 +9521,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "3.1.2")
+    (version "3.1.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "0m1qi39snbmkkv1p07bzg1r7snc9x6a1y0dghvpk1nzgcfpmnsj4"))))
+                "0lhjbjhv1hnx5i3gkx41k68i8ykay3f24708h30wx9xywww9lsvi"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9533,6 +9550,7 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
        ("r-mass" ,r-mass)
        ("r-matrix" ,r-matrix)
        ("r-metap" ,r-metap)
+       ("r-patchwork" ,r-patchwork)
        ("r-pbapply" ,r-pbapply)
        ("r-plotly" ,r-plotly)
        ("r-png" ,r-png)
@@ -9549,7 +9567,6 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
        ("r-rtsne" ,r-rtsne)
        ("r-scales" ,r-scales)
        ("r-sctransform" ,r-sctransform)
-       ("r-sdmtools" ,r-sdmtools)
        ("r-tsne" ,r-tsne)
        ("r-uwot" ,r-uwot)))
     (home-page "http://www.satijalab.org/seurat")
@@ -10326,14 +10343,14 @@ family of feature/genome hypotheses.")
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.30.1")
+    (version "1.30.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "03jj193fzmhvkjw8f5zk6wgflkvm3phny0q38scawcplfsyb8z64"))))
+         "0c9i26h5czm60n1bxzmdxxpywcj0sig6wcj913pb41mr83bbgra3"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10478,14 +10495,14 @@ provided.")
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.14.1")
+    (version "1.14.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "04hd02zd5jix5p2zg10asmwjg1fynqgmclbhbmk7fb6arx5hm11f"))))
+         "1z153a7nxmlml72pl1saasj2il9g5ahpynkpv3mkhhsvl5kbwbh6"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (inputs
@@ -10675,14 +10692,14 @@ quality control.")
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.14.5")
+    (version "1.14.6")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "0ydy6gvpgpvrs4ryk1qvmmxp6cpaizs294jwg42jawxndkds1l3y"))))
+         "1y8wlgk5zbv7c7gcp0ahfpbh9lifab7y3zwf0093fzaw7vr1y6cr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
@@ -11072,8 +11089,8 @@ import matplotlib
 matplotlib.use('Agg')
 " line)))
                ;; Make sure GESS has all modules in its path
-               (wrap-program (string-append target "GESS.py")
-                 `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH"))))
+               (wrap-script (string-append target "GESS.py")
+                 `("PYTHONPATH" ":" = (,target ,(getenv "PYTHONPATH"))))
                (mkdir-p bin)
                (symlink (string-append target "GESS.py")
                         (string-append bin "GESS.py"))
@@ -11084,7 +11101,8 @@ matplotlib.use('Agg')
        ("python2-scipy" ,python2-scipy)
        ("python2-numpy" ,python2-numpy)
        ("python2-networkx" ,python2-networkx)
-       ("python2-biopython" ,python2-biopython)))
+       ("python2-biopython" ,python2-biopython)
+       ("guile" ,guile-3.0))) ; for the script wrapper
     (home-page "https://compbio.uthscsa.edu/GESS_Web/")
     (synopsis "Detect exon-skipping events from raw RNA-seq data")
     (description
@@ -12011,23 +12029,6 @@ graphs.  This library makes it easy to work with @file{.loom} files for
 single-cell RNA-seq data.")
     (license license:bsd-3)))
 
-;; pigx-scrnaseq does not work with the latest version of loompy.
-(define-public python-loompy-for-pigx-scrnaseq
-  (package (inherit python-loompy)
-    (name "python-loompy")
-    (version "2.0.3")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/linnarsson-lab/loompy.git")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "0pjyl532pl8sbv71yci6h0agchn0naw2qjcwj50n6afrsahbsag3"))))
-    ;; There are none.
-    (arguments '(#:tests? #f))))
-
 ;; We cannot use the latest commit because it requires Java 9.
 (define-public java-forester
   (let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6")
@@ -12771,7 +12772,7 @@ methylation and segmentation.")
 (define-public pigx-scrnaseq
   (package
     (name "pigx-scrnaseq")
-    (version "0.0.8")
+    (version "1.1.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
@@ -12779,27 +12780,21 @@ methylation and segmentation.")
                                   "/pigx_scrnaseq-" version ".tar.gz"))
               (sha256
                (base32
-                "0zv0sc5amivxhb95vx2gfx6l9bh7n80fh7h47dalnwxxnfvnzai4"))))
+                "0ga2jr4968qzwml6aycky4603q64lny3y7lzw6dmafch5pydl1qi"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:configure-flags
-       (list (string-append "PICARDJAR=" (assoc-ref %build-inputs "java-picard")
-			    "/share/java/picard.jar")
-	     (string-append "DROPSEQJAR=" (assoc-ref %build-inputs "dropseq-tools")
-			    "/share/java/dropseq.jar"))))
     (inputs
      `(("coreutils" ,coreutils)
        ("perl" ,perl)
-       ("dropseq-tools" ,dropseq-tools)
        ("fastqc" ,fastqc)
-       ("java-picard" ,java-picard-2.10.3) ; same as for dropseq
+       ("flexbar" ,flexbar)
        ("java" ,icedtea-8)
+       ("jellyfish" ,jellyfish)
        ("python-wrapper" ,python-wrapper)
        ("python-pyyaml" ,python-pyyaml)
        ("python-pandas" ,python-pandas)
        ("python-magic" ,python-magic)
        ("python-numpy" ,python-numpy)
-       ("python-loompy" ,python-loompy-for-pigx-scrnaseq)
+       ("python-loompy" ,python-loompy)
        ("ghc-pandoc" ,ghc-pandoc)
        ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
        ("samtools" ,samtools)
@@ -12826,6 +12821,7 @@ methylation and segmentation.")
        ("r-rtsne" ,r-rtsne)
        ("r-scater" ,r-scater)
        ("r-scran" ,r-scran)
+       ("r-seurat" ,r-seurat)
        ("r-singlecellexperiment" ,r-singlecellexperiment)
        ("r-stringr" ,r-stringr)
        ("r-yaml" ,r-yaml)))
@@ -13883,7 +13879,7 @@ absolute GSEA.")
 (define-public jamm
   (package
     (name "jamm")
-    (version "1.0.7.5")
+    (version "1.0.7.6")
     (source
      (origin
        (method git-fetch)
@@ -13893,7 +13889,7 @@ absolute GSEA.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0ls889jcma1ch9h21jjhnkadgszgqj41842hhcjh6cg88f85qf3i"))))
+         "0bsa5mf9n9q5jz7mmacrra41l7r8rac5vgsn6wv1fb52ya58b970"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; there are none
diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm
index 045fbe65ab..fa63c49920 100644
--- a/gnu/packages/bittorrent.scm
+++ b/gnu/packages/bittorrent.scm
@@ -380,7 +380,7 @@ and will take advantage of multiple processor cores where possible.")
 (define-public libtorrent-rasterbar
   (package
     (name "libtorrent-rasterbar")
-    (version "1.1.13")
+    (version "1.1.14")
     (source (origin
               (method url-fetch)
               (uri
@@ -390,7 +390,7 @@ and will take advantage of multiple processor cores where possible.")
                 "/libtorrent-rasterbar-" version ".tar.gz"))
               (sha256
                (base32
-                "1mza92ljjqvlz9582pmls3n45srqhxvw3q348xihcg4fhlchf11h"))))
+                "0sn3ingmk1lk9p56f9ifgdwhjg0qizcfgv15wyc9s71nm5fya7sc"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm
index e3d27874e8..425c0d53c9 100644
--- a/gnu/packages/bootloaders.scm
+++ b/gnu/packages/bootloaders.scm
@@ -670,7 +670,20 @@ it fits within common partitioning schemes.")
   (make-u-boot-sunxi64-package "pine64-lts" "aarch64-linux-gnu"))
 
 (define-public u-boot-pinebook
-  (make-u-boot-sunxi64-package "pinebook" "aarch64-linux-gnu"))
+  (let ((base (make-u-boot-sunxi64-package "pinebook" "aarch64-linux-gnu")))
+    (package
+      (inherit base)
+      (arguments
+       (substitute-keyword-arguments (package-arguments base)
+         ((#:phases phases)
+          `(modify-phases ,phases
+             (add-after 'unpack 'patch-pinebook-config
+               ;; Fix regression with LCD video output introduced in 2020.01
+               ;; https://patchwork.ozlabs.org/patch/1225130/
+               (lambda _
+                 (substitute* "configs/pinebook_defconfig"
+                   (("CONFIG_VIDEO_BRIDGE_ANALOGIX_ANX6345=y") "CONFIG_VIDEO_BRIDGE_ANALOGIX_ANX6345=y\nCONFIG_VIDEO_BPP32=y"))
+                 #t)))))))))
 
 (define-public u-boot-bananapi-m2-ultra
   (make-u-boot-package "Bananapi_M2_Ultra" "arm-linux-gnueabihf"))
diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm
index cfbcc0f318..7fbd1c472d 100644
--- a/gnu/packages/build-tools.scm
+++ b/gnu/packages/build-tools.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Corentin Bocquillon <corentin@nybble.fr>
-;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
 ;;; Copyright © 2018 Tomáš Čech <sleep_walker@gnu.org>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
@@ -80,7 +80,7 @@ makes a few sacrifices to acquire fast full and incremental build times.")
 (define-public bear
   (package
     (name "bear")
-    (version "2.4.2")
+    (version "2.4.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -89,7 +89,7 @@ makes a few sacrifices to acquire fast full and incremental build times.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1w1kyjzvvy5lj16kn3yyf7iil2cqlfkszi8kvagql7f5h5l6w9b1"))))
+                "19fk4flfykbzhb89ppmzqf0zlrkbjm6ajl9fsayndj9km5ys0041"))))
     (build-system cmake-build-system)
     (inputs
      `(("python" ,python-wrapper)))
diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm
index 921d473cd9..160f456f79 100644
--- a/gnu/packages/c.scm
+++ b/gnu/packages/c.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018, 2019 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
@@ -132,7 +132,7 @@ compiler while still keeping it small, simple, fast and understandable.")
 (define-public libbytesize
   (package
     (name "libbytesize")
-    (version "2.1")
+    (version "2.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -140,7 +140,7 @@ compiler while still keeping it small, simple, fast and understandable.")
                     "download/" version "/libbytesize-" version ".tar.gz"))
               (sha256
                (base32
-                "1bpz9cpb8s47kqplkkiz6ryfahas2ma95g9rh2axnfjp6w1d9ixc"))))
+                "1aivwypmnqcaj2230pifvf3jcgl5chja8rspkxf0j3480asm8g5r"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f))
diff --git a/gnu/packages/cedille.scm b/gnu/packages/cedille.scm
index 80ed7e9759..d3a6850f9f 100644
--- a/gnu/packages/cedille.scm
+++ b/gnu/packages/cedille.scm
@@ -30,7 +30,7 @@
 (define-public cedille
   (package
     (name "cedille")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
      (origin
        (method git-fetch)
@@ -40,7 +40,7 @@
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "07kv9wncyipfjf5w4ax8h2p35g70zb1qw6zc4afd7c225xia55wp"))))
+         "1h5s6ayh3s76z184jai3jidcs4cjk8s4nvkkv2am8dg4gfsybq22"))))
     (inputs
      `(("agda" ,agda)
        ("agda-ial" ,agda-ial)
diff --git a/gnu/packages/certs.scm b/gnu/packages/certs.scm
index 864fe5def1..24831db5e6 100644
--- a/gnu/packages/certs.scm
+++ b/gnu/packages/certs.scm
@@ -185,7 +185,7 @@ taken from the NSS package and thus ultimately from the Mozilla project.")
            (uri "https://letsencrypt.org/certs/isrgrootx1.pem")
            (sha256
             (base32
-             "0zycy85ff9ga53z1q03df89ka9iihb9p8bjhw056rq2y4rn3b6ac"))))
+             "1la36n2f31j9s03v847ig6ny9lr875q3g7smnq33dcsmf2i5gd92"))))
        ;; "Let’s Encrypt Authority X3", the active Let's Encrypt intermediate
        ;; certificate.
        ("letsencryptauthorityx3.pem"
@@ -194,7 +194,7 @@ taken from the NSS package and thus ultimately from the Mozilla project.")
            (uri "https://letsencrypt.org/certs/letsencryptauthorityx3.pem")
            (sha256
             (base32
-             "1kvac1dhm1d02bhrfj6l1cz1dpldz6ishb78zzvy8245zgvh7pdn"))))
+             "100lxxvqv4fj563bm03zzk5r36hq5jx9nnrajzs38g825c5k0cg2"))))
        ;; "Let’s Encrypt Authority X4", the backup Let's Encrypt intermediate
        ;; certificate.  This will be used for disaster recovery and will only be
        ;; used should Let's Encrypt lose the ability to issue with "Let’s
@@ -205,7 +205,7 @@ taken from the NSS package and thus ultimately from the Mozilla project.")
            (uri "https://letsencrypt.org/certs/letsencryptauthorityx4.pem")
            (sha256
             (base32
-             "0giiixknr0mls2ir6qqzb42mq7x9a7vz79gbn7fjszbf87pqhpzm"))))))
+             "0d5256gwf73drq6q6jala28rfzhrgbk5pjfq27vc40ly91pdyh8m"))))))
     (home-page "https://letsencrypt.org/certificates/")
     (synopsis "Let's Encrypt root and intermediate certificates")
     (description "This package provides a certificate store containing only the
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index e819ca72cd..692350cf5c 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -751,7 +751,7 @@ interfaces and processes.")
     (propagated-inputs
      `(("python-six" ,python-six)
        ("python-traceback2" ,python-traceback2)))
-    (home-page "http://pypi.python.org/pypi/unittest2")
+    (home-page "https://pypi.org/project/unittest2/")
     (synopsis "Python unit testing library")
     (description
      "Unittest2 is a replacement for the unittest module in the Python
@@ -1590,7 +1590,7 @@ the last py.test invocation.")
     (synopsis "Py.test plugin to test server connections locally")
     (description "Pytest-localserver is a plugin for the pytest testing
 framework which enables you to test server connections locally.")
-    (home-page "https://pypi.python.org/pypi/pytest-localserver")
+    (home-page "https://pypi.org/project/pytest-localserver/")
     (license license:expat)))
 
 (define-public python-pytest-xprocess
@@ -2052,7 +2052,7 @@ especially -cover-package.")
         (base32
          "0y8d0zwiqar51kxj8lzmkvwc3b8kazb04gk5zcb4nzg5k68zmhq5"))))
     (build-system python-build-system)
-    (home-page "http://pypi.python.org/pypi/discover/")
+    (home-page "https://pypi.org/project/discover/")
     (synopsis
      "Python test discovery for unittest")
     (description
diff --git a/gnu/packages/chicken.scm b/gnu/packages/chicken.scm
index 2034ca942a..7b86a58012 100644
--- a/gnu/packages/chicken.scm
+++ b/gnu/packages/chicken.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2020 Ekaitz Zarraga <ekaitz@elenq.tech>
+;;; Copyright © 2020 Evan Hanson <evhan@foldling.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,14 +29,14 @@
 (define-public chicken
   (package
     (name "chicken")
-    (version "5.1.0")
+    (version "5.2.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://code.call-cc.org/releases/"
                                   version "/chicken-" version ".tar.gz"))
               (sha256
                (base32
-                "0jsbp3kp0134f318j3wpd1n85gf8qzh034fn198gvazsv2l024aw"))))
+                "1yl0hxm9cirgcp8jgxp6vv29lpswfvaw3zfkh6rsj0vkrv44k4c1"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((guix build gnu-build-system)
@@ -59,7 +60,7 @@
        ;; Parallel builds are not supported, as noted in README.
        #:parallel-build? #f))
     (propagated-inputs `(("gcc-toolchain", gcc-toolchain)))
-    (home-page "http://www.call-cc.org/")
+    (home-page "https://www.call-cc.org/")
     (synopsis "R5RS Scheme implementation that compiles native code via C")
     (description
      "CHICKEN is a compiler for the Scheme programming language.  CHICKEN
diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm
index 49ad8de84c..0b3d19a428 100644
--- a/gnu/packages/chromium.scm
+++ b/gnu/packages/chromium.scm
@@ -37,7 +37,6 @@
   #:use-module (gnu packages curl)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
-  #:use-module (gnu packages gcc)
   #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages glib)
@@ -49,6 +48,7 @@
   #:use-module (gnu packages libevent)
   #:use-module (gnu packages libffi)
   #:use-module (gnu packages linux)
+  #:use-module (gnu packages llvm)
   #:use-module (gnu packages kerberos)
   #:use-module (gnu packages ninja)
   #:use-module (gnu packages node)
@@ -70,7 +70,8 @@
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages xorg)
-  #:use-module (ice-9 match))
+  #:use-module (ice-9 match)
+  #:use-module (srfi srfi-1))
 
 (define %preserved-third-party-files
   '("base/third_party/cityhash" ;Expat
@@ -106,10 +107,6 @@
     "third_party/blink" ;BSD-3, LGPL2+
     "third_party/boringssl" ;OpenSSL/ISC (Google additions are ISC)
     "third_party/boringssl/src/third_party/fiat" ;Expat
-    "third_party/boringssl/src/third_party/sike" ;Expat
-    ;; XXX: these files are generated by fp-$arch.pl in the above directory.
-    "third_party/boringssl/linux-aarch64/crypto/third_party/sike/asm/fp-armv8.S"
-    "third_party/boringssl/linux-x86_64/crypto/third_party/sike/asm/fp-x86_64.S"
     "third_party/breakpad" ;BSD-3
     "third_party/brotli" ;Expat
     "third_party/cacheinvalidation" ;ASL2.0
@@ -117,11 +114,14 @@
     "third_party/catapult/common/py_vulcanize/third_party/rcssmin" ;ASL2.0
     "third_party/catapult/common/py_vulcanize/third_party/rjsmin" ;ASL2.0
     "third_party/catapult/third_party/polymer" ;BSD-3
+    ;; XXX: This is a minified version of <https://d3js.org/>.
     "third_party/catapult/tracing/third_party/d3" ;BSD-3
     "third_party/catapult/tracing/third_party/gl-matrix" ;Expat
+    ;; XXX: Minified version of <https://github.com/Stuk/jszip>.
     "third_party/catapult/tracing/third_party/jszip" ;Expat or GPL3
     "third_party/catapult/tracing/third_party/mannwhitneyu" ;Expat
     "third_party/catapult/tracing/third_party/oboe" ;BSD-2
+    ;; XXX: Minified version of <https://github.com/nodeca/pako>.
     "third_party/catapult/tracing/third_party/pako" ;Expat
     "third_party/ced" ;BSD-3
     "third_party/cld_3" ;ASL2.0
@@ -134,6 +134,9 @@
     "third_party/dav1d" ;BSD-2
     "third_party/dawn" ;ASL2.0
     "third_party/depot_tools/owners.py" ;BSD-3
+    "third_party/devtools-frontend" ;BSD-3
+    "third_party/devtools-frontend/src/third_party/axe-core" ;MPL2.0
+    "third_party/devtools-frontend/src/third_party/pyjson5" ;ASL2.0
     "third_party/dom_distiller_js" ;BSD-3
     "third_party/emoji-segmenter" ;ASL2.0
     "third_party/flatbuffers" ;ASL2.0
@@ -154,6 +157,7 @@
     "third_party/libaom" ;BSD-2 or "Alliance for Open Media Patent License 1.0"
     "third_party/libaom/source/libaom/third_party/vector" ;Expat
     "third_party/libaom/source/libaom/third_party/x86inc" ;ISC
+    "third_party/libgifcodec" ;MPL1.1/GPL2+/LGPL2.1+, BSD-3, BSD-2
     "third_party/libjingle_xmpp" ;BSD-3
     "third_party/libphonenumber" ;ASL2.0
     "third_party/libsecret" ;LGPL2.1+
@@ -181,6 +185,7 @@
     "third_party/pdfium/third_party/bigint" ;Public domain, BSD-3
     "third_party/pdfium/third_party/skia_shared" ;BSD-3
     "third_party/pdfium/third_party/freetype/include/pstables.h" ;FreeType
+    "third_party/perfetto" ;ASL2.0
     "third_party/pffft" ;the "FFTPACK" license, similar to BSD-3
     "third_party/ply" ;BSD-3
     "third_party/polymer" ;BSD-3
@@ -194,7 +199,6 @@
     "third_party/sfntly" ;ASL2.0
     "third_party/skia" ;BSD-3
     "third_party/skia/include/third_party/skcms" ;BSD-3
-    "third_party/skia/third_party/gif" ;MPL1.1/GPL2+/LGPL2.1+
     "third_party/skia/third_party/skcms" ;BSD-3
     "third_party/skia/third_party/vulkanmemoryallocator" ;BSD-3, Expat
     "third_party/smhasher" ;Expat, public domain
@@ -243,9 +247,9 @@ from forcing GEXP-PROMISE."
                       #:system system
                       #:guile-for-build guile)))
 
-(define %chromium-version "79.0.3945.130")
-(define %ungoogled-revision "e2fae994d786b6716fb473a47b0c880bcfdc2497")
-(define %debian-revision "debian/79.0.3945.130-2")
+(define %chromium-version "80.0.3987.132")
+(define %ungoogled-revision "7e68f18f1d16a132fe7d913a176daf79897eaa58")
+(define %debian-revision "debian/80.0.3987.116-1")
 (define package-revision "0")
 (define %package-version (string-append %chromium-version "-"
                                         package-revision "."
@@ -259,7 +263,7 @@ from forcing GEXP-PROMISE."
                         %chromium-version ".tar.xz"))
     (sha256
      (base32
-      "183vz3lf1588cr9s5vlnj65qvbmz36s8cg8k7dvr64cxmcqk86an"))))
+      "00f2hpi2d0n15yw29dv3dli566cgi7qh55bfpziag9a6j02i401c"))))
 
 (define %ungoogled-origin
   (origin
@@ -270,7 +274,7 @@ from forcing GEXP-PROMISE."
                               (string-take %ungoogled-revision 7)))
     (sha256
      (base32
-      "15vmc07iba1zmzn4j7c5n2hyvyxzwwf9hc3kyym0m4jajlsyxr5f"))))
+      "196rr3nly42pzl2bap22vzw4d8x87yl3zy1wq2fla5z8iy4x8ym1"))))
 
 (define %debian-origin
   (origin
@@ -284,7 +288,7 @@ from forcing GEXP-PROMISE."
                                 (_ (string-take %debian-revision 7)))))
     (sha256
      (base32
-      "1rbzxcwfp7v0c6rkvn9jl9by7p363cnbdyqazwiak1z03kmw3nkz"))))
+      "1cc5sp566dd8f2grgr770xwbxgxf58dk1w7q3s8pmv4js5h3pwq8"))))
 
 ;; This is a "computed" origin that does the following:
 ;; *) Runs the Ungoogled scripts on a pristine Chromium tarball.
@@ -344,7 +348,7 @@ from forcing GEXP-PROMISE."
 
                    (with-directory-excursion chromium-dir
 
-                     (format #t "applying Debian patches...~%")
+                     (format #t "Applying Debian patches...~%")
                      (force-output)
                      (let* ((debian  #+debian-source)
                             (patches (string-append debian "/debian/patches"))
@@ -423,6 +427,18 @@ from forcing GEXP-PROMISE."
         `(cons "--enable-custom-modes"
                ,flags))))))
 
+;; Add a custom ld wrapper that supports quoted strings in response files.
+;; To be merged with 'ld-wrapper' in a future rebuild cycle.
+(define-public ld-wrapper-next
+  (let ((orig (car (assoc-ref (%final-inputs) "ld-wrapper"))))
+    (package
+      (inherit orig)
+      (name "ld-wrapper-next")
+      (inputs
+       `(("wrapper" ,(search-path %load-path
+                                  "gnu/packages/ld-wrapper-next.in"))
+         ,@(alist-delete "wrapper" (package-inputs orig)))))))
+
 (define-public ungoogled-chromium
   (package
     (name "ungoogled-chromium")
@@ -446,8 +462,10 @@ from forcing GEXP-PROMISE."
        ;; directory for an exhaustive list of supported flags.
        ;; (Note: The 'configure' phase will do that for you.)
        (list "is_debug=false"
+             "is_cfi=false"
              "use_gold=false"
              "use_lld=false"
+             "clang_use_chrome_plugins=false"
              "linux_use_bundled_binutils=false"
              "use_custom_libcxx=false"
              "use_sysroot=false"
@@ -477,18 +495,6 @@ from forcing GEXP-PROMISE."
              ;; friends from the environment.
              "custom_toolchain=\"//build/toolchain/linux/unbundle:default\""
              "host_toolchain=\"//build/toolchain/linux/unbundle:default\""
-             ;; Don't assume it's clang.
-             "is_clang=false"
-             ;; Disable debugging features to save space.  These are normally
-             ;; pulled in by "is_official_build", but that requires "is_clang".
-             "enable_iterator_debugging=false"
-             "exclude_unwind_tables=true"
-             ;; Optimize for building everything at once, as opposed to
-             ;; incrementally for development.  See "docs/jumbo.md".
-             "use_jumbo_build=true"
-             ;; The default file merge limit of 50 requires huge amounts of RAM.
-             ;; Cap it to make sure the build succeeds on commodity hardware.
-             "jumbo_file_merge_limit=8"
 
              ;; Prefer system libraries.
              "use_system_freetype=true"
@@ -584,6 +590,10 @@ from forcing GEXP-PROMISE."
              (substitute* "third_party/webrtc/rtc_base/strings/json.h"
                (("#include \"third_party/jsoncpp/") "#include \"json/"))
 
+             (substitute* "gpu/config/gpu_util.cc"
+               (("third_party/vulkan/include/")
+                ""))
+
              (substitute* '("components/viz/common/gpu/vulkan_context_provider.h"
                             "components/viz/common/resources/resource_format_utils.h")
                (("third_party/vulkan/include/") ""))
@@ -636,14 +646,19 @@ from forcing GEXP-PROMISE."
 
              ;; Make sure the right build tools are used.
              (setenv "AR" "ar") (setenv "NM" "nm")
-             (setenv "CC" "gcc") (setenv "CXX" "g++")
+             (setenv "CC" "clang") (setenv "CXX" "clang++")
 
-             ;; Prevent GCC from optimizing away null pointer safety checks.
+             ;; Do not optimize away null pointer safety checks.
              (setenv "CXXFLAGS" "-fno-delete-null-pointer-checks")
 
              ;; TODO: pre-compile instead. Avoids a race condition.
              (setenv "PYTHONDONTWRITEBYTECODE" "1")
 
+             (substitute*
+                 ;; From Debians 'system/node.patch'.
+                 "third_party/devtools-frontend/src/scripts/devtools_paths.py"
+               (("/usr/bin/nodejs") (which "node")))
+
              ;; XXX: How portable is this.
              (mkdir-p "third_party/node/linux/node-linux-x64")
              (symlink (string-append (assoc-ref inputs "node") "/bin")
@@ -748,9 +763,10 @@ from forcing GEXP-PROMISE."
                #t))))))
     (native-inputs
      `(("bison" ,bison)
-       ("gcc" ,gcc-8)
+       ("clang" ,clang-9)
        ("gn" ,gn)
        ("gperf" ,gperf)
+       ("ld-wrapper" ,ld-wrapper-next)
        ("ninja" ,ninja)
        ("node" ,node)
        ("pkg-config" ,pkg-config)
@@ -852,6 +868,16 @@ disabled in order to protect the users privacy.")
        ,@(package-inputs ungoogled-chromium)))
     (arguments
      (substitute-keyword-arguments (package-arguments ungoogled-chromium)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'unpack 'add-ozone-patch
+             (lambda _
+               ;; Add missing include statement required when using libstdc++,
+               ;; Clang and Ozone.  Fixed in M81.
+               (substitute* "ui/base/cursor/ozone/bitmap_cursor_factory_ozone.cc"
+                 (("#include \"base/logging\\.h" all)
+                  (string-append "#include <algorithm>\n" all)))
+               #t))))
        ((#:configure-flags flags)
         `(append (list "use_ozone=true"
                        "ozone_platform_wayland=true"
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 37da33908f..1f76f9ac1e 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
author	Mark H Weaver <mhw@netris.org>	2015-04-18 02:27:30 -0400
committer	Mark H Weaver <mhw@netris.org>	2015-04-18 02:28:30 -0400
commit	989a9fffa74f42a4c2a979b16fd01ae218cf0bb8 (patch)
tree	bae40dd8f474ee69bc0c2ee77ec6ee490c2e8217 /gnu/packages/gstreamer.scm
parent	ba42f54df6fede1ce6aec268e78784640ee642db (diff)
download	guix-989a9fffa74f42a4c2a979b16fd01ae218cf0bb8.tar.gz guix-989a9fffa74f42a4c2a979b16fd01ae218cf0bb8.zip