bootstrap: guile-static: Disable parallel build.

* gnu/packages/make-bootstrap.scm (%guile-static)[arguments]:
Override #:parallel-build? to be #f.

.dir-locals.el

@@ -34,6 +34,8 @@
 
    (eval . (put 'modify-services 'scheme-indent-function 1))
    (eval . (put 'with-directory-excursion 'scheme-indent-function 1))
+   (eval . (put 'with-file-lock 'scheme-indent-function 1))
+
    (eval . (put 'package 'scheme-indent-function 0))
    (eval . (put 'origin 'scheme-indent-function 0))
    (eval . (put 'build-system 'scheme-indent-function 0))
@@ -53,6 +55,8 @@
    (eval . (put 'call-with-decompressed-port 'scheme-indent-function 2))
    (eval . (put 'call-with-gzip-input-port 'scheme-indent-function 1))
    (eval . (put 'call-with-gzip-output-port 'scheme-indent-function 1))
+   (eval . (put 'call-with-lzip-input-port 'scheme-indent-function 1))
+   (eval . (put 'call-with-lzip-output-port 'scheme-indent-function 1))
    (eval . (put 'signature-case 'scheme-indent-function 1))
    (eval . (put 'emacs-batch-eval 'scheme-indent-function 0))
    (eval . (put 'emacs-batch-edit-file 'scheme-indent-function 1))

HACKING

@@ -42,7 +42,7 @@ make sure to run ‘git pull --rebase’.
 All commits that are pushed to the central repository on Savannah must be
 signed with an OpenPGP key, and the public key should be uploaded to your user
 account on Savannah and to public key servers, such as
-‘pool.sks-keyservers.net’.  To configure Git to automatically sign commits,
+‘keys.openpgp.org’.  To configure Git to automatically sign commits,
 run:
 
   git config commit.gpgsign true

Makefile.am

@@ -90,6 +90,7 @@ MODULES =					\
   guix/nar.scm					\
   guix/derivations.scm				\
   guix/grafts.scm				\
+  guix/repl.scm					\
   guix/inferior.scm				\
   guix/describe.scm				\
   guix/channels.scm				\
@@ -97,6 +98,7 @@ MODULES =					\
   guix/self.scm					\
   guix/upstream.scm				\
   guix/licenses.scm				\
+  guix/lint.scm				\
   guix/glob.scm					\
   guix/git.scm					\
   guix/graph.scm				\
@@ -124,6 +126,7 @@ MODULES =					\
   guix/build-system/guile.scm			\
   guix/build-system/haskell.scm			\
   guix/build-system/linux-module.scm		\
+  guix/build-system/node.scm			\
   guix/build-system/perl.scm			\
   guix/build-system/python.scm			\
   guix/build-system/ocaml.scm			\
@@ -144,6 +147,7 @@ MODULES =					\
   guix/svn-download.scm				\
   guix/colors.scm				\
   guix/i18n.scm					\
+  guix/diagnostics.scm				\
   guix/ui.scm					\
   guix/status.scm				\
   guix/build/android-ndk-build-system.scm	\
@@ -168,6 +172,7 @@ MODULES =					\
   guix/build/gnu-build-system.scm		\
   guix/build/gnu-dist.scm			\
   guix/build/guile-build-system.scm		\
+  guix/build/node-build-system.scm		\
   guix/build/perl-build-system.scm		\
   guix/build/python-build-system.scm		\
   guix/build/ocaml-build-system.scm		\
@@ -180,6 +185,7 @@ MODULES =					\
   guix/build/haskell-build-system.scm		\
   guix/build/linux-module-build-system.scm	\
   guix/build/store-copy.scm			\
+  guix/build/json.scm				\
   guix/build/utils.scm				\
   guix/build/union.scm				\
   guix/build/profiles.scm			\
@@ -243,6 +249,7 @@ MODULES =					\
   guix/scripts/describe.scm			\
   guix/scripts/system.scm			\
   guix/scripts/system/search.scm		\
+  guix/scripts/system/reconfigure.scm		\
   guix/scripts/lint.scm				\
   guix/scripts/challenge.scm			\
   guix/scripts/import/crate.scm			\
@@ -265,6 +272,7 @@ MODULES =					\
   guix/scripts/weather.scm			\
   guix/scripts/container.scm			\
   guix/scripts/container/exec.scm		\
+  guix/scripts/deploy.scm			\
   guix.scm					\
   $(GNU_SYSTEM_MODULES)
 
@@ -272,6 +280,7 @@ if HAVE_GUILE_SSH
 
 MODULES +=					\
   guix/ssh.scm					\
+  guix/remote.scm				\
   guix/scripts/copy.scm				\
   guix/store/ssh.scm
 
@@ -299,11 +308,11 @@ dist_noinst_DATA = guix/tests.scm guix/tests/http.scm
 AUX_FILES =						\
   gnu/packages/aux-files/chromium/master-preferences.json		\
   gnu/packages/aux-files/emacs/guix-emacs.el		\
-  gnu/packages/aux-files/linux-libre/5.1-arm.conf	\
-  gnu/packages/aux-files/linux-libre/5.1-arm-veyron.conf       \
-  gnu/packages/aux-files/linux-libre/5.1-arm64.conf	\
-  gnu/packages/aux-files/linux-libre/5.1-i686.conf	\
-  gnu/packages/aux-files/linux-libre/5.1-x86_64.conf	\
+  gnu/packages/aux-files/linux-libre/5.2-arm.conf	\
+  gnu/packages/aux-files/linux-libre/5.2-arm-veyron.conf       \
+  gnu/packages/aux-files/linux-libre/5.2-arm64.conf	\
+  gnu/packages/aux-files/linux-libre/5.2-i686.conf	\
+  gnu/packages/aux-files/linux-libre/5.2-x86_64.conf	\
   gnu/packages/aux-files/linux-libre/4.19-arm.conf	\
   gnu/packages/aux-files/linux-libre/4.19-arm64.conf	\
   gnu/packages/aux-files/linux-libre/4.19-i686.conf	\
@@ -353,76 +362,77 @@ TEST_EXTENSIONS = .scm .sh
 if CAN_RUN_TESTS
 
 SCM_TESTS =					\
+  tests/accounts.scm				\
   tests/base16.scm				\
   tests/base32.scm				\
   tests/base64.scm				\
+  tests/bournish.scm				\
+  tests/builders.scm				\
+  tests/build-utils.scm			\
+  tests/cache.scm				\
+  tests/challenge.scm				\
   tests/channels.scm				\
+  tests/combinators.scm			\
+  tests/containers.scm				\
   tests/cpan.scm				\
   tests/cpio.scm				\
-  tests/crate.scm				\
-  tests/gem.scm					\
-  tests/pki.scm					\
-  tests/print.scm				\
-  tests/sets.scm				\
-  tests/modules.scm				\
-  tests/gnu-maintenance.scm			\
-  tests/substitute.scm				\
-  tests/builders.scm				\
-  tests/derivations.scm				\
-  tests/glob.scm				\
-  tests/grafts.scm				\
-  tests/ui.scm					\
-  tests/status.scm				\
-  tests/records.scm				\
-  tests/processes.scm				\
-  tests/upstream.scm				\
-  tests/combinators.scm				\
-  tests/discovery.scm				\
-  tests/utils.scm				\
-  tests/build-utils.scm				\
-  tests/packages.scm				\
-  tests/snix.scm				\
-  tests/hackage.scm				\
   tests/cran.scm				\
-  tests/elpa.scm				\
-  tests/texlive.scm				\
-  tests/store.scm				\
-  tests/monads.scm				\
-  tests/gexp.scm				\
-  tests/nar.scm					\
-  tests/union.scm				\
-  tests/profiles.scm				\
-  tests/search-paths.scm			\
-  tests/syscalls.scm				\
-  tests/inferior.scm				\
-  tests/gremlin.scm				\
+  tests/crate.scm				\
+  tests/cve.scm				\
   tests/debug-link.scm				\
-  tests/bournish.scm				\
-  tests/lint.scm				\
-  tests/publish.scm				\
-  tests/scripts.scm				\
-  tests/size.scm				\
-  tests/graph.scm				\
-  tests/challenge.scm				\
-  tests/cache.scm				\
-  tests/cve.scm					\
-  tests/workers.scm				\
-  tests/zlib.scm				\
-  tests/lzlib.scm				\
+  tests/derivations.scm			\
+  tests/discovery.scm				\
+  tests/elpa.scm				\
   tests/file-systems.scm			\
-  tests/uuid.scm				\
-  tests/system.scm				\
-  tests/accounts.scm				\
-  tests/services.scm				\
-  tests/scripts-build.scm			\
-  tests/containers.scm				\
-  tests/opam.scm				\
-  tests/pack.scm				\
-  tests/pypi.scm				\
+  tests/gem.scm				\
+  tests/gexp.scm				\
+  tests/glob.scm				\
+  tests/gnu-maintenance.scm			\
+  tests/grafts.scm				\
+  tests/graph.scm				\
+  tests/gremlin.scm				\
+  tests/hackage.scm				\
   tests/import-utils.scm			\
+  tests/inferior.scm				\
+  tests/lint.scm				\
+  tests/lzlib.scm				\
+  tests/modules.scm				\
+  tests/monads.scm				\
+  tests/nar.scm				\
+  tests/opam.scm				\
+  tests/packages.scm				\
+  tests/pack.scm				\
+  tests/pki.scm				\
+  tests/print.scm				\
+  tests/processes.scm				\
+  tests/profiles.scm				\
+  tests/publish.scm				\
+  tests/pypi.scm				\
+  tests/records.scm				\
+  tests/scripts.scm				\
+  tests/scripts-build.scm			\
+  tests/search-paths.scm			\
+  tests/services.scm				\
+  tests/sets.scm				\
+  tests/size.scm				\
+  tests/snix.scm				\
+  tests/status.scm				\
   tests/store-database.scm			\
-  tests/store-deduplication.scm			\
-  tests/store-roots.scm
+  tests/store-deduplication.scm		\
+  tests/store-roots.scm			\
+  tests/store.scm				\
+  tests/substitute.scm				\
+  tests/swh.scm				\
+  tests/syscalls.scm				\
+  tests/system.scm				\
+  tests/texlive.scm				\
+  tests/ui.scm					\
+  tests/union.scm				\
+  tests/upstream.scm				\
+  tests/utils.scm				\
+  tests/uuid.scm				\
+  tests/workers.scm				\
+  tests/zlib.scm
 
 SH_TESTS =					\
   tests/guix-build.sh				\
@@ -488,9 +498,8 @@ check-system: $(GOBJECTS)
 	   -e '(@@ (run-system-tests) run-system-tests)'	\
 	   $(top_srcdir)/build-aux/run-system-tests.scm
 
-# Public key used to sign substitutes from hydra.gnu.org & co.
+# Public keys used to sign substitutes.
 dist_pkgdata_DATA =				\
-  etc/substitutes/hydra.gnu.org.pub		\
   etc/substitutes/berlin.guixsd.org.pub		\
   etc/substitutes/ci.guix.gnu.org.pub		\
   etc/substitutes/ci.guix.info.pub
@@ -542,7 +551,6 @@ EXTRA_DIST +=						\
   build-aux/config.rpath				\
   bootstrap						\
   doc/build.scm						\
-  release.nix						\
   $(TESTS)
 
 if !BUILD_DAEMON_OFFLOAD

build-aux/build-self.scm

@@ -75,7 +75,7 @@
                           (package-name "GNU Guix")
                           (package-version "0")
                           (bug-report-address "bug-guix@gnu.org")
-                          (home-page-url "https://gnu.org/s/guix"))
+                          (home-page-url "https://guix.gnu.org"))
 
   ;; Hack so that Geiser is not confused.
   (define defmod 'define-module)

build-aux/compile-all.scm

@@ -91,20 +91,45 @@ to 'make'."
 
 (match (command-line)
   ((_ . files)
-   (compile-files srcdir (getcwd)
-                  (filter file-needs-compilation? files)
-                  #:workers (parallel-job-count)
-                  #:host host
-                  #:report-load (lambda (file total completed)
-                                  (when file
-                                    (format #t "[~3d%] LOAD     ~a~%"
-                                            (% (+ 1 completed) (* 2 total))
-                                            file)
-                                    (force-output)))
-                  #:report-compilation (lambda (file total completed)
-                                         (when file
-                                           (format #t "[~3d%] GUILEC   ~a~%"
-                                                   (% (+ total completed 1)
-                                                      (* 2 total))
-                                                   (scm->go file))
-                                           (force-output))))))
+   (catch #t
+     (lambda ()
+       (compile-files srcdir (getcwd)
+                      (filter file-needs-compilation? files)
+                      #:workers (parallel-job-count)
+                      #:host host
+                      #:report-load (lambda (file total completed)
+                                      (when file
+                                        (format #t "[~3d%] LOAD     ~a~%"
+                                                (% (+ 1 completed) (* 2 total))
+                                                file)
+                                        (force-output)))
+                      #:report-compilation (lambda (file total completed)
+                                             (when file
+                                               (format #t "[~3d%] GUILEC   ~a~%"
+                                                       (% (+ total completed 1)
+                                                          (* 2 total))
+                                                       (scm->go file))
+                                               (force-output)))))
+     (lambda _
+       (primitive-exit 1))
+     (lambda args
+       ;; Try to report the error in an intelligible way.
+       (let* ((stack   (make-stack #t))
+              (frame   (if (> (stack-length stack) 1)
+                           (stack-ref stack 1)    ;skip the 'throw' frame
+                           (stack-ref stack 0)))
+              (ui      (false-if-exception
+                        (resolve-module '(guix ui))))
+              (report  (and ui
+                            (false-if-exception
+                             (module-ref ui 'report-load-error)))))
+         (if report
+             ;; In Guile <= 2.2.5, 'current-load-port' was not exported.
+             (let ((load-port ((module-ref (resolve-module '(ice-9 ports))
+                                           'current-load-port))))
+               (report (or (and=> load-port port-filename) "?.scm")
+                       args frame))
+             (begin
+               (print-exception (current-error-port) frame
+                                (car args) (cdr args))
+               (display-backtrace stack (current-error-port)))))))))

build-aux/update-NEWS.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -105,7 +105,7 @@ paragraph."
 (define (write-packages-updates news-file old new)
   "Write to NEWS-FILE the list of packages upgraded between OLD and NEW."
   (define important
-    '("gcc" "glibc" "binutils" "gdb"                   ;toolchain
+    '("gcc-toolchain" "glibc" "binutils" "gdb"         ;toolchain
       "shepherd" "linux-libre" "xorg-server" "cups"    ;OS
       "gnome" "xfce" "enlightenment" "lxde" "mate"     ;desktop env.
       "guile" "bash" "python" "python2" "perl"         ;languages

configure.ac

@@ -119,8 +119,8 @@ if test "x$have_guile_git" != "xyes"; then
 fi
 
 dnl Check for Guile-JSON.
-GUILE_MODULE_AVAILABLE([have_guile_json], [(json)])
-if test "x$have_guile_json" != "xyes"; then
+GUIX_CHECK_GUILE_JSON
+if test "x$guix_cv_have_recent_guile_json" != "xyes"; then
   AC_MSG_ERROR([Guile-JSON is missing; please install it.])
 fi
 

doc/build.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2019, 2020 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -162,9 +162,7 @@ as well as images, OS examples, and translations."
 
 (define %makeinfo-html-options
   ;; Options passed to 'makeinfo --html'.
-  '("--css-ref=https://www.gnu.org/software/gnulib/manual.css"
-    "-c" "EXTRA_HEAD=<meta name=\"viewport\" \
-content=\"width=device-width, initial-scale=1\" />"))
+  '("--css-ref=https://www.gnu.org/software/gnulib/manual.css"))
 
 (define* (html-manual source #:key (languages %languages)
                       (version "0.0")
@@ -203,11 +201,6 @@ makeinfo OPTIONS."
           (setvbuf (current-output-port) 'line)
           (setvbuf (current-error-port) 'line)
 
-          ;; 'makeinfo' looks for "htmlxref.cnf" in the current directory, so
-          ;; copy it right here.
-          (copy-file (string-append #$manual-source "/htmlxref.cnf")
-                     "htmlxref.cnf")
-
           (for-each (lambda (language)
                       (let ((opts `("--html"
                                     "-c" ,(string-append "TOP_NODE_UP_URL=/manual/"

doc/contributing.texi

@@ -38,9 +38,20 @@ version from the Git repository:
 git clone https://git.savannah.gnu.org/git/guix.git
 @end example
 
-When building Guix from a checkout,
-the following packages are required in addition to those mentioned in
-the installation instructions (@pxref{Requirements}).
+The easiest way to set up a development environment for Guix is, of
+course, by using Guix!  The following command starts a new shell where
+all the dependencies and appropriate environment variables are set up to
+hack on Guix:
+
+@example
+guix environment guix --pure
+@end example
+
+@xref{Invoking guix environment}, for more information on that command.
+
+If you are unable to use Guix when building Guix from a checkout, the
+following are the required packages in addition to those mentioned in the
+installation instructions (@pxref{Requirements}).
 
 @itemize
 @item @url{http://gnu.org/software/autoconf/, GNU Autoconf};
@@ -51,20 +62,11 @@ the installation instructions (@pxref{Requirements}).
 @item @url{http://www.gnu.org/software/help2man/, GNU Help2man (optional)}.
 @end itemize
 
-The easiest way to set up a development environment for Guix is, of
-course, by using Guix!  The following command starts a new shell where
-all the dependencies and appropriate environment variables are set up to
-hack on Guix:
+On Guix, extra dependencies can be added by instead running @command{guix
+environment} with @option{--ad-hoc}:
 
 @example
-guix environment guix
-@end example
-
-@xref{Invoking guix environment}, for more information on that command.
-Extra dependencies can be added with @option{--ad-hoc}:
-
-@example
-guix environment guix --ad-hoc help2man git strace
+guix environment guix --pure --ad-hoc help2man git strace
 @end example
 
 Run @command{./bootstrap} to generate the build system infrastructure
@@ -113,8 +115,8 @@ run @code{make install}.  To do that, you first need to have an environment
 with all the dependencies available (@pxref{Building from Git}), and then
 simply prefix each command with
 @command{./pre-inst-env} (the @file{pre-inst-env} script lives in the
-top build tree of Guix; it is generated by @command{./configure}),
-as in@footnote{The @option{-E} flag to
+top build tree of Guix; it is generated by @command{./configure}).
+An example@footnote{The @option{-E} flag to
 @command{sudo} guarantees that @code{GUILE_LOAD_PATH} is correctly set
 such that @command{guix-daemon} and the tools it uses can find the Guile
 modules they need.}:
@@ -125,7 +127,7 @@ $ ./pre-inst-env guix build hello
 @end example
 
 @noindent
-Similarly, for a Guile session using the Guix modules:
+Similarly, an example for a Guile session using the Guix modules:
 
 @example
 $ ./pre-inst-env guile -c '(use-modules (guix utils)) (pk (%current-system))'
@@ -281,8 +283,7 @@ Once your package builds correctly, please send us a patch
 (@pxref{Submitting Patches}).  Well, if you need help, we will be happy to
 help you too.  Once the patch is committed in the Guix repository, the
 new package automatically gets built on the supported platforms by
-@url{http://hydra.gnu.org/jobset/gnu/master, our continuous integration
-system}.
+@url{@value{SUBSTITUTE-SERVER}, our continuous integration system}.
 
 @cindex substituter
 Users can obtain the new package definition simply by running
@@ -893,7 +894,7 @@ changes).  This branch is intended to be merged in @code{master} every
 2.5 months or so.
 @end table
 
-All these branches are @uref{https://hydra.gnu.org/project/gnu,
+All these branches are @uref{@value{SUBSTITUTE-SERVER},
 tracked by our build farm} and merged into @code{master} once
 everything has been successfully built.  This allows us to fix issues
 before they hit users, and to reduce the window during which pre-built
@@ -983,5 +984,6 @@ first send one message to @email{guix-patches@@gnu.org}, and then send
 subsequent patches to @email{@var{NNN}@@debbugs.gnu.org} to make sure
 they are kept together.  See
 @uref{https://debbugs.gnu.org/Advanced.html, the Debbugs documentation}
-for more information.
+for more information.  You can install @command{git send-email} with
+@command{guix install git:send-email}.
 @c Debbugs bug: https://debbugs.gnu.org/db/15/15361.html

etc/guix-daemon.service.in

@@ -7,7 +7,7 @@ Description=Build daemon for GNU Guix
 
 [Service]
 ExecStart=@localstatedir@/guix/profiles/per-user/root/current-guix/bin/guix-daemon --build-users-group=guixbuild
-Environment=GUIX_LOCPATH='@localstatedir@/guix/profiles/per-user/root/guix-profile/lib/locale' LC_ALL=en_US.utf8
+Environment='GUIX_LOCPATH=@localstatedir@/guix/profiles/per-user/root/guix-profile/lib/locale' LC_ALL=en_US.utf8
 RemainAfterExit=yes
 StandardOutput=syslog
 StandardError=syslog

etc/guix-install.sh

@@ -3,6 +3,7 @@
 # Copyright © 2017 sharlatan <sharlatanus@gmail.com>
 # Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 # Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
+# Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 #
 # This file is part of GNU Guix.
 #
@@ -85,14 +86,12 @@ _debug()
 
 chk_require()
 { # Check that every required command is available.
-    declare -a cmds
     declare -a warn
-
-    cmds=(${1})
+    local c
 
     _debug "--- [ $FUNCNAME ] ---"
 
-    for c in ${cmds[@]}; do
+    for c in "$@"; do
         command -v "$c" &>/dev/null || warn+=("$c")
     done
 
@@ -101,10 +100,17 @@ chk_require()
           return 1; }
     
     _msg "${PAS}verification of required commands completed"
+}
 
-    gpg --list-keys ${OPENPGP_SIGNING_KEY_ID} >/dev/null 2>&1 || (
+chk_gpg_keyring()
+{ # Check whether the Guix release signing public key is present.
+    _debug "--- [ $FUNCNAME ] ---"
+
+    # Without --dry-run this command will create a ~/.gnupg owned by root on
+    # systems where gpg has never been used, causing errors and confusion.
+    gpg --dry-run --list-keys ${OPENPGP_SIGNING_KEY_ID} >/dev/null 2>&1 || (
         _err "${ERR}Missing OpenPGP public key.  Fetch it with this command:"
-        echo "  gpg --keyserver pool.sks-keyservers.net --recv-keys ${OPENPGP_SIGNING_KEY_ID}"
+        echo "  wget https://sv.gnu.org/people/viewgpg.php?user_id=15145 -qO - | gpg --import -"
         exit 1
     )
 }
@@ -362,13 +368,11 @@ sys_enable_guix_daemon()
 }
 
 sys_authorize_build_farms()
-{ # authorize the public keys of the two build farms
+{ # authorize the public key of the build farm
     while true; do
-        read -p "Permit downloading pre-built package binaries from the project's build farms? (yes/no) " yn
+        read -p "Permit downloading pre-built package binaries from the project's build farm? (yes/no) " yn
         case $yn in
-            [Yy]*) guix archive --authorize < "${ROOT_HOME}/.config/guix/current/share/guix/hydra.gnu.org.pub" &&
-                         _msg "${PAS}Authorized public key for hydra.gnu.org";
-                   guix archive --authorize < "${ROOT_HOME}/.config/guix/current/share/guix/ci.guix.gnu.org.pub" &&
+            [Yy]*) guix archive --authorize < "${ROOT_HOME}/.config/guix/current/share/guix/ci.guix.gnu.org.pub" &&
                        _msg "${PAS}Authorized public key for ci.guix.gnu.org";
                    break;;
             [Nn]*) _msg "${INF}Skipped authorizing build farm public keys"
@@ -417,7 +421,8 @@ main()
     _msg "Starting installation ($(date))"
 
     chk_term
-    chk_require "${REQUIRE[*]}"
+    chk_require "${REQUIRE[@]}"
+    chk_gpg_keyring
     chk_init_sys
     chk_sys_arch
 

etc/guix-publish.service.in

@@ -7,7 +7,7 @@ Description=Publish the GNU Guix store
 
 [Service]
 ExecStart=@localstatedir@/guix/profiles/per-user/root/current-guix/bin/guix publish --user=nobody --port=8181
-Environment=GUIX_LOCPATH='@localstatedir@/guix/profiles/per-user/root/guix-profile/lib/locale' LC_ALL=en_US.utf8
+Environment='GUIX_LOCPATH=@localstatedir@/guix/profiles/per-user/root/guix-profile/lib/locale' LC_ALL=en_US.utf8
 RemainAfterExit=yes
 StandardOutput=syslog
 StandardError=syslog

etc/substitutes/hydra.gnu.org.pub

@@ -1,6 +0,0 @@
- (public-key 
-  (rsa 
-   (n #00DB1634E3D9DFAC97AE4734DAE968CCB15EE4815C82BDC254883DBB49FE1EF32268E82D4BBE0E35298C481C9DA1551642FAFF05AEC1A60712F1BB4BE7D25D7EFF7A4F89704A5A9AC232870CB9F2476C3B538A0E990A8825DEB73081D317001FB8A188600F2FEF5F5F570E857F3EE4355077A3C3918ED72723A56BA55C466D400658974D7DAD1F6B7B63C192B9C2704D98BBFF1C3BD5B8EF11A8ADC83ACB8FD8E9F1E792FDAD262415D13F2DEE55F330908CFDA9C3C8C32B64F7DD088457D34F445E2E2C83C6D680549DC9B6E6573B89496567204ED285E67A279F2F667080BA941D80D015CE87B0FB6A91A99CECC7D91D2D210B00E4B6E611DA51DB008F1DFE3FCAC6B27393FA781D45F9A15FC7B8785A3E86BA6592B2916CA22CF1E40FC85F85CACA590461154F58F3580B16398908EF32076F411299C28727C94D88B6A618F84DD73AEBED8270BCB6690928CB1BF250C35E1F6BF3B1B30D05BA246ECE8F69D9065DE26F4B3E0D814D70A9C27CB5B7B050C9090590D3A9EF83374F2643E5446FBD39DDB124DBF6DFDAA6D18E2560AD0CBFA11C959C9B7316BF19963A191967054E9FD97DC14D71082B30B1C90A46E8996682474C3BCB51BA0882958897B6DD35E41B5174D0A6BCDE97B89043E95BD1B70DE61DA666893B417196A180005466BC3A742FDF04E89B04460E3E6BC72E7F1B5FEA5B3092FEE551A3C447C12E104E65#)
-   (e #010001#)
-   )
-  )

gnu/artwork.scm

@@ -29,7 +29,7 @@
 ;;; Code:
 
 (define %artwork-repository
-  (let ((commit "b975164c19c9c0f5d91e5731ec1683e7510c1326"))
+  (let ((commit "2f2fe74c1078be605a6a93c2193fd6c715cebbb0"))
     (origin
       (method git-fetch)
       (uri (git-reference
@@ -39,6 +39,6 @@
                                 "-checkout"))
       (sha256
        (base32
-        "1fad7az077q9ds3jhp00jfsr8rfw4ws042wmnai52k7jv4kbxwyf")))))
+        "0c8r0phvm3wgf914n2kw1461cwdjl2zbzqvzq9x7d9pwkgv7xmq7")))))
 
 ;;; artwork.scm ends here

gnu/build/accounts.scm

@@ -51,6 +51,7 @@
             group-entry-gid
             group-entry-members
 
+            %password-lock-file
             write-group
             write-passwd
             write-shadow
@@ -224,6 +225,11 @@ each field."
                    (serialization list->comma-separated comma-separated->list)
                    (default '())))
 
+(define %password-lock-file
+  ;; The password database lock file used by libc's 'lckpwdf'.  Users should
+  ;; grab this lock with 'with-file-lock' when they access the databases.
+  "/etc/.pwd.lock")
+
 (define (database-writer file mode entry->string)
   (lambda* (entries #:optional (file-or-port file))
     "Write ENTRIES to FILE-OR-PORT.  When FILE-OR-PORT is a file name, write
@@ -243,9 +249,13 @@ to it atomically and set the appropriate permissions."
             (lambda ()
               (chmod port mode)
               (write-entries port)
+
+              (fsync port)
+              (close-port port)
               (rename-file template file-or-port))
             (lambda ()
-              (close-port port)
+              (unless (port-closed? port)
+                (close-port port))
               (when (file-exists? template)
                 (delete-file template))))))))
 

gnu/build/activation.scm

@@ -22,6 +22,7 @@
   #:use-module (gnu build accounts)
   #:use-module (gnu build linux-boot)
   #:use-module (guix build utils)
+  #:use-module ((guix build syscalls) #:select (with-file-lock))
   #:use-module (ice-9 ftw)
   #:use-module (ice-9 match)
   #:use-module (ice-9 vlist)
@@ -129,22 +130,26 @@ group records) are all available."
   ;; Allow home directories to be created under /var/lib.
   (mkdir-p "/var/lib")
 
-  (let-values (((groups passwd shadow)
-                (user+group-databases users groups)))
-    (write-group groups)
-    (write-passwd passwd)
-    (write-shadow shadow)
+  ;; Take same lock as libc's 'lckpwdf' (but without a timeout) while we read
+  ;; and write the databases.  This ensures there's no race condition with
+  ;; other tools that might be accessing it at the same time.
+  (with-file-lock %password-lock-file
+    (let-values (((groups passwd shadow)
+                  (user+group-databases users groups)))
+      (write-group groups)
+      (write-passwd passwd)
+      (write-shadow shadow)))
 
-    ;; Home directories of non-system accounts are created by
-    ;; 'activate-user-home'.
-    (for-each make-home-directory system-accounts)
+  ;; Home directories of non-system accounts are created by
+  ;; 'activate-user-home'.
+  (for-each make-home-directory system-accounts)
 
-    ;; Turn shared home directories, such as /var/empty, into root-owned,
-    ;; read-only places.
-    (for-each (lambda (directory)
-                (chown directory 0 0)
-                (chmod directory #o555))
-              (duplicates (map user-account-home-directory system-accounts)))))
+  ;; Turn shared home directories, such as /var/empty, into root-owned,
+  ;; read-only places.
+  (for-each (lambda (directory)
+              (chown directory 0 0)
+              (chmod directory #o555))
+            (duplicates (map user-account-home-directory system-accounts))))
 
 (define (activate-user-home users)
   "Create and populate the home directory of USERS, a list of tuples, unless

gnu/build/cross-toolchain.scm

@@ -3,6 +3,7 @@
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2016 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
+;;; Copyright © 2019 Carl Dong <contact@carldong.me>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -95,7 +96,7 @@ C_INCLUDE_PATH et al."
      ;; We're building the sans-libc cross-compiler, so nothing to do.
      #t)))
 
-(define* (set-cross-path/mingw #:key inputs #:allow-other-keys)
+(define* (set-cross-path/mingw #:key inputs target #:allow-other-keys)
   "Add the cross MinGW headers to CROSS_C_*_INCLUDE_PATH, and remove them from
 C_*INCLUDE_PATH."
   (let ((libc (assoc-ref inputs "libc"))
@@ -112,7 +113,7 @@ C_*INCLUDE_PATH."
 
     (if libc
         (let ((cpath (string-append libc "/include"
-                                    ":" libc "/i686-w64-mingw32/include")))
+                                    ":" libc "/" target "/include")))
           (for-each (cut setenv <> cpath)
                     %gcc-cross-include-paths))
 
@@ -142,7 +143,7 @@ C_*INCLUDE_PATH."
     (when libc
       (setenv "CROSS_LIBRARY_PATH"
               (string-append libc "/lib"
-                             ":" libc "/i686-w64-mingw32/lib")))
+                             ":" libc "/" target "/lib")))
 
     (setenv "CPP" (string-append gcc "/bin/cpp"))
     (for-each (lambda (var)
@@ -168,8 +169,12 @@ C_*INCLUDE_PATH."
 a target triplet."
   (modify-phases phases
     (add-before 'configure 'set-cross-path
-      (if (string-contains target "mingw")
-          set-cross-path/mingw
+      ;; This mingw32 target checking logic should match that of target-mingw?
+      ;; in (guix utils), but (guix utils) is too large too copy over to the
+      ;; build side entirely and for now we have no way to select variables to
+      ;; copy over. See (gnu packages cross-base) for more details.
+      (if (string-suffix? "-mingw32" target)
+          (cut set-cross-path/mingw #:target target <...>)
           set-cross-path))
     (add-after 'install 'make-cross-binutils-visible
       (cut make-cross-binutils-visible #:target target <...>))

gnu/build/linux-boot.scm

@@ -517,6 +517,8 @@ upon error."
          (unless (pre-mount)
            (error "pre-mount actions failed")))
 
+       (setenv "EXT2FS_NO_MTAB_OK" "1")
+
        (if root
            ;; The "--root=SPEC" kernel command-line option always provides a
            ;; string, but the string can represent a device, a UUID, or a
@@ -533,6 +535,8 @@ upon error."
        (for-each mount-file-system
                  (remove root-mount-point? mounts))
 
+       (setenv "EXT2FS_NO_MTAB_OK" #f)
+
        (if to-load
            (begin
              (switch-root "/root")

gnu/build/linux-container.scm

@@ -22,7 +22,6 @@
   #:use-module (ice-9 match)
   #:use-module (ice-9 rdelim)
   #:use-module (srfi srfi-98)
-  #:use-module (guix utils)
   #:use-module (guix build utils)
   #:use-module (guix build syscalls)
   #:use-module (gnu system file-systems)          ;<file-system>
@@ -131,9 +130,14 @@ for the process."
               "/dev/random"
               "/dev/urandom"
               "/dev/tty"
-              "/dev/ptmx"
               "/dev/fuse"))
 
+  ;; Mount a new devpts instance on /dev/pts.
+  (when (file-exists? "/dev/ptmx")
+    (mount* "none" (scope "/dev/pts") "devpts" 0
+            "newinstance,mode=0620")
+    (symlink "/dev/pts/ptmx" (scope "/dev/ptmx")))
+
   ;; Setup the container's /dev/console by bind mounting the pseudo-terminal
   ;; associated with standard input when there is one.
   (let* ((in      (current-input-port))
@@ -279,6 +283,21 @@ that host UIDs (respectively GIDs) map to in the namespace."
               (_                                  ;unexpected termination
                #f)))))))))
 
+;; FIXME: This is copied from (guix utils), which we cannot use because it
+;; would pull (guix config) and all.
+(define (call-with-temporary-directory proc)
+  "Call PROC with a name of a temporary directory; close the directory and
+delete it when leaving the dynamic extent of this call."
+  (let* ((directory (or (getenv "TMPDIR") "/tmp"))
+         (template  (string-append directory "/guix-directory.XXXXXX"))
+         (tmp-dir   (mkdtemp! template)))
+    (dynamic-wind
+      (const #t)
+      (lambda ()
+        (proc tmp-dir))
+      (lambda ()
+        (false-if-exception (delete-file-recursively tmp-dir))))))
+
 (define* (call-with-container mounts thunk #:key (namespaces %namespaces)
                               (host-uids 1) (guest-uid 0) (guest-gid 0))
   "Run THUNK in a new container process and return its exit status.

gnu/build/locale.scm

@@ -0,0 +1,95 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu build locale)
+  #:use-module (guix build utils)
+  #:use-module (srfi srfi-1)
+  #:use-module (ice-9 rdelim)
+  #:use-module (ice-9 match)
+  #:use-module (ice-9 regex)
+  #:export (build-locale
+            normalize-codeset
+            locale->name+codeset
+            read-supported-locales))
+
+(define locale-rx
+  ;; Regexp matching a locale line in 'localedata/SUPPORTED'.
+  (make-regexp
+   "^[[:space:]]*([[:graph:]]+)/([[:graph:]]+)[[:space:]]*\\\\$"))
+
+(define (read-supported-locales port)
+  "Read the 'localedata/SUPPORTED' file from PORT.  That file is actually a
+makefile snippet, with one locale per line, and a header that can be
+discarded."
+  (let loop ((locales '()))
+    (define line
+      (read-line port))
+
+    (cond ((eof-object? line)
+           (reverse locales))
+          ((string-prefix? "#" (string-trim line)) ;comment
+           (loop locales))
+          ((string-contains line "=")            ;makefile variable assignment
+           (loop locales))
+          (else
+           (match (regexp-exec locale-rx line)
+             (#f
+              (loop locales))
+             (m
+              (loop (alist-cons (match:substring m 1)
+                                (match:substring m 2)
+                                locales))))))))
+
+(define (normalize-codeset codeset)
+  "Compute the \"normalized\" variant of CODESET."
+  ;; info "(libc) Using gettextized software", for the algorithm used to
+  ;; compute the normalized codeset.
+  (letrec-syntax ((-> (syntax-rules ()
+                        ((_ proc value)
+                         (proc value))
+                        ((_ proc rest ...)
+                         (proc (-> rest ...))))))
+    (-> (lambda (str)
+          (if (string-every char-set:digit str)
+              (string-append "iso" str)
+              str))
+        string-downcase
+        (lambda (str)
+          (string-filter char-set:letter+digit str))
+        codeset)))
+
+(define* (build-locale locale
+                       #:key
+                       (localedef "localedef")
+                       (directory ".")
+                       (codeset "UTF-8")
+                       (name (string-append locale "." codeset)))
+  "Compute locale data for LOCALE and CODESET--e.g., \"en_US\" and
+\"UTF-8\"--with LOCALEDEF, and store it in DIRECTORY under NAME."
+  (format #t "building locale '~a'...~%" name)
+  (invoke localedef "--no-archive" "--prefix" directory
+          "-i" locale "-f" codeset
+          (string-append directory "/" name)))
+
+(define (locale->name+codeset locale)
+  "Split a locale name such as \"aa_ER@saaho.UTF-8\" into two values: the
+language/territory/modifier part, and the codeset."
+  (match (string-rindex locale #\.)
+    (#f  (values locale #f))
+    (dot (values (string-take locale dot)
+                 (string-drop locale (+ dot 1))))))

gnu/build/vm.scm

@@ -423,7 +423,8 @@ SYSTEM-DIRECTORY is the name of the directory of the 'system' derivation."
             ;; Graft the configuration file onto the image.
             (string-append "boot/grub/grub.cfg=" config-file))))
 
-(define* (make-iso9660-image grub config-file os-drv target
+(define* (make-iso9660-image xorriso grub-mkrescue-environment
+                             grub config-file os-drv target
                              #:key (volume-id "Guix_image") (volume-uuid #f)
                              register-closures? (closures '()))
   "Given a GRUB package, creates an iso image as TARGET, using CONFIG-FILE as
@@ -431,6 +432,9 @@ GRUB configuration and OS-DRV as the stuff in it."
   (define grub-mkrescue
     (string-append grub "/bin/grub-mkrescue"))
 
+  (define grub-mkrescue-sed.sh
+    (string-append xorriso "/bin/grub-mkrescue-sed.sh"))
+
   (define target-store
     (string-append "/tmp/root" (%store-directory)))
 
@@ -483,9 +487,19 @@ GRUB configuration and OS-DRV as the stuff in it."
                               #x77777777)
                           16))
 
+  (setenv "MKRESCUE_SED_MODE" "original")
+  (setenv "MKRESCUE_SED_XORRISO" (string-append xorriso
+                                                "/bin/xorriso"))
+  (setenv "MKRESCUE_SED_IN_EFI_NO_PT" "yes")
+  (for-each (match-lambda
+             ((name . value) (setenv name value)))
+            grub-mkrescue-environment)
+
   (let ((pipe
          (apply open-pipe* OPEN_WRITE
-                grub-mkrescue "-o" target
+                grub-mkrescue
+                (string-append "--xorriso=" grub-mkrescue-sed.sh)
+                "-o" target
                 (string-append "boot/grub/grub.cfg=" config-file)
                 "etc=/tmp/root/etc"
                 "var=/tmp/root/var"

gnu/ci.scm

@@ -130,7 +130,8 @@ SYSTEM."
     "aarch64-linux-gnu"
     "powerpc-linux-gnu"
     "i586-pc-gnu"                                 ;aka. GNU/Hurd
-    "i686-w64-mingw32"))
+    "i686-w64-mingw32"
+    "x86_64-w64-mingw32"))
 
 (define %guixsd-supported-systems
   '("x86_64-linux" "i686-linux" "armhf-linux"))
@@ -193,9 +194,11 @@ system.")
 (define channel-build-system
   ;; Build system used to "convert" a channel instance to a package.
   (let* ((build (lambda* (store name inputs
-                                #:key instance #:allow-other-keys)
+                                #:key instance system
+                                #:allow-other-keys)
                   (run-with-store store
-                    (channel-instances->derivation (list instance)))))
+                    (channel-instances->derivation (list instance))
+                    #:system system)))
          (lower (lambda* (name #:key system instance #:allow-other-keys)
                   (bag
                     (name name)

gnu/installer.scm

@@ -69,7 +69,7 @@ version of this file."
         (setlocale LC_ALL "en_US.utf8")))
 
   (define builder
-    (with-extensions (list guile-json)
+    (with-extensions (list guile-json-3)
       (with-imported-modules (source-module-closure
                               '((gnu installer locale)))
         #~(begin
@@ -313,7 +313,7 @@ selected keymap."
     ;; packages …), etc. modules.
     (with-extensions (list guile-gcrypt guile-newt
                            guile-parted guile-bytestructures
-                           guile-json guile-git guix)
+                           guile-json-3 guile-git guix)
       (with-imported-modules `(,@(source-module-closure
                                   `(,@modules
                                     (gnu services herd)

gnu/installer/connman.scm

@@ -108,7 +108,7 @@
 (define-record-type* <service>
   service make-service
   service?
-  (name            service-name) ; string
+  (name            service-name) ; string or #f
   (type            service-type) ; string
   (path            service-path) ; string
   (strength        service-strength) ; integer

gnu/installer/locale.scm

@@ -19,6 +19,7 @@
 
 (define-module (gnu installer locale)
   #:use-module (gnu installer utils)
+  #:use-module ((gnu build locale) #:select (normalize-codeset))
   #:use-module (guix records)
   #:use-module (json)
   #:use-module (srfi srfi-1)
@@ -71,24 +72,6 @@ optionally, CODESET."
       (codeset   . ,(or codeset (match:substring matches 5)))
       (modifier  . ,(match:substring matches 7)))))
 
-(define (normalize-codeset codeset)
-  "Compute the \"normalized\" variant of CODESET."
-  ;; info "(libc) Using gettextized software", for the algorithm used to
-  ;; compute the normalized codeset.
-  (letrec-syntax ((-> (syntax-rules ()
-                        ((_ proc value)
-                         (proc value))
-                        ((_ proc rest ...)
-                         (proc (-> rest ...))))))
-    (-> (lambda (str)
-          (if (string-every char-set:digit str)
-              (string-append "iso" str)
-              str))
-        string-downcase
-        (lambda (str)
-          (string-filter char-set:letter+digit str))
-        codeset)))
-
 (define (locale->locale-string locale)
   "Reverse operation of locale-string->locale."
   (let ((language (locale-language locale))
@@ -151,16 +134,18 @@ ISO639-3 and ISO639-5 files."
         (lambda (port-iso639-5)
           (filter-map
            (lambda (hash)
-             (let ((alpha2 (hash-ref hash "alpha_2"))
-                   (alpha3 (hash-ref hash "alpha_3"))
-                   (name   (hash-ref hash "name")))
+             (let ((alpha2 (assoc-ref hash "alpha_2"))
+                   (alpha3 (assoc-ref hash "alpha_3"))
+                   (name   (assoc-ref hash "name")))
                (and (supported-locale? locales alpha2 alpha3)
                     `((alpha2 . ,alpha2)
                       (alpha3 . ,alpha3)
                       (name   . ,name)))))
            (append
-            (hash-ref (json->scm port-iso639-3) "639-3")
-            (hash-ref (json->scm port-iso639-5) "639-5"))))))))
+            (vector->list
+             (assoc-ref (json->scm port-iso639-3) "639-3"))
+            (vector->list
+             (assoc-ref (json->scm port-iso639-5) "639-5")))))))))
 
 (define (language-code->language-name languages language-code)
   "Using LANGUAGES as a list of ISO639 association lists, return the language
@@ -196,10 +181,11 @@ ISO3166 file."
   (call-with-input-file iso3166
     (lambda (port)
       (map (lambda (hash)
-             `((alpha2 . ,(hash-ref hash "alpha_2"))
-               (alpha3 . ,(hash-ref hash "alpha_3"))
-               (name   . ,(hash-ref hash "name"))))
-           (hash-ref (json->scm port) "3166-1")))))
+             `((alpha2 . ,(assoc-ref hash "alpha_2"))
+               (alpha3 . ,(assoc-ref hash "alpha_3"))
+               (name   . ,(assoc-ref hash "name"))))
+           (vector->list
+            (assoc-ref (json->scm port) "3166-1"))))))
 
 (define (territory-code->territory-name territories territory-code)
   "Using TERRITORIES as a list of ISO3166 association lists return the

gnu/installer/newt/network.scm

@@ -62,7 +62,7 @@ Internet and return the selected technology. For now, only technologies with
             (G_ "Continue")
             (G_ "Exit")
             (G_ "The install process requires Internet access but no \
-network device were found. Do you want to continue anyway?"))
+network devices were found. Do you want to continue anyway?"))
        ((1) (raise
              (condition
               (&installer-step-break))))

gnu/installer/newt/wifi.scm

@@ -144,6 +144,7 @@ of <service-item> records present in LISTBOX."
   (let ((services (connman-services)))
     (filter (lambda (service)
               (and (string=? (service-type service) "wifi")
+                   (service-name service)
                    (not (string-null? (service-name service)))))
             services)))
 

gnu/installer/parted.scm

@@ -1318,7 +1318,8 @@ USER-PARTITIONS, or return nothing."
     (()
      '())
     ((modules ...)
-     `((initrd-modules ',modules)))))
+     `((initrd-modules (append ',modules
+                               %base-initrd-modules))))))
 
 (define (user-partitions->configuration user-partitions)
   "Return the configuration field for USER-PARTITIONS."

gnu/installer/services.scm

@@ -75,10 +75,13 @@
       (packages '((specification->package "awesome"))))
      (desktop-environment
       (name "i3")
-      (packages '((specification->package "i3-wm"))))
+      (packages (map (lambda (package)
+                       `(specification->package ,package))
+                     '("i3-wm" "i3status" "dmenu" "st"))))
      (desktop-environment
       (name "ratpoison")
-      (packages '((specification->package "ratpoison"))))
+      (packages '((specification->package "ratpoison")
+                  (specification->package "xterm"))))
 
      ;; Networking.
      (system-service

gnu/local.mk

@@ -15,11 +15,12 @@
 # Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 # Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
 # Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
-# Copyright © 2017, 2018 Gábor Boskovits <boskovits@gmail.com>
+# Copyright © 2017, 2018, 2019 Gábor Boskovits <boskovits@gmail.com>
 # Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
-# Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
+# Copyright © 2018, 2019 Oleg Pykhalov <go.wigust@gmail.com>
 # Copyright © 2018 Stefan Stefanović <stefanx2ovic@gmail.com>
 # Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+# Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
 #
 # This file is part of GNU Guix.
 #
@@ -121,6 +122,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/cpp.scm 				\
   %D%/packages/cppi.scm				\
   %D%/packages/cran.scm				\
+  %D%/packages/crates-io.scm			\
   %D%/packages/cross-base.scm			\
   %D%/packages/crypto.scm			\
   %D%/packages/cryptsetup.scm			\
@@ -194,6 +196,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/gcc.scm				\
   %D%/packages/gd.scm				\
   %D%/packages/gdb.scm				\
+  %D%/packages/genealogy.scm			\
   %D%/packages/genimage.scm			\
   %D%/packages/geo.scm				\
   %D%/packages/gettext.scm			\
@@ -235,11 +238,13 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/haskell-check.scm		\
   %D%/packages/haskell-crypto.scm		\
   %D%/packages/haskell-web.scm			\
+  %D%/packages/haskell-xyz.scm			\
   %D%/packages/ham-radio.scm			\
   %D%/packages/hexedit.scm			\
   %D%/packages/hugs.scm				\
   %D%/packages/hurd.scm				\
   %D%/packages/hyperledger.scm			\
+  %D%/packages/i2p.scm				\
   %D%/packages/ibus.scm				\
   %D%/packages/icu4c.scm			\
   %D%/packages/idris.scm			\
@@ -261,6 +266,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/jrnl.scm				\
   %D%/packages/jose.scm				\
   %D%/packages/julia.scm			\
+  %D%/packages/kawa.scm				\
   %D%/packages/kde.scm				\
   %D%/packages/kde-frameworks.scm		\
   %D%/packages/kde-plasma.scm			\
@@ -295,6 +301,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/llvm.scm				\
   %D%/packages/lout.scm				\
   %D%/packages/logging.scm			\
+  %D%/packages/logo.scm				\
   %D%/packages/lolcode.scm                      \
   %D%/packages/lsof.scm				\
   %D%/packages/lua.scm				\
@@ -434,8 +441,10 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/smalltalk.scm			\
   %D%/packages/sml.scm				\
   %D%/packages/speech.scm			\
+  %D%/packages/sphinx.scm			\
   %D%/packages/spice.scm			\
   %D%/packages/sqlite.scm			\
+  %D%/packages/squirrel.scm			\
   %D%/packages/ssh.scm				\
   %D%/packages/sssd.scm				\
   %D%/packages/stalonetray.scm			\
@@ -466,6 +475,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/uml.scm				\
   %D%/packages/unrtf.scm			\
   %D%/packages/upnp.scm				\
+  %D%/packages/usb-modeswitch.scm		\
   %D%/packages/uucp.scm				\
   %D%/packages/valgrind.scm			\
   %D%/packages/version-control.scm		\
@@ -482,6 +492,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/wget.scm				\
   %D%/packages/wicd.scm				\
   %D%/packages/wine.scm				\
+  %D%/packages/wireservice.scm				\
   %D%/packages/wm.scm				\
   %D%/packages/wordnet.scm			\
   %D%/packages/wv.scm				\
@@ -494,10 +505,12 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/xorg.scm				\
   %D%/packages/xfce.scm				\
   %D%/packages/zile.scm				\
+  %D%/packages/zwave.scm			\
 						\
   %D%/services.scm				\
   %D%/services/admin.scm			\
   %D%/services/audio.scm                        \
+  %D%/services/auditd.scm			\
   %D%/services/avahi.scm			\
   %D%/services/base.scm				\
   %D%/services/certbot.scm			\
@@ -513,6 +526,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/services/docker.scm			\
   %D%/services/authentication.scm		\
   %D%/services/games.scm			\
+  %D%/services/getmail.scm				\
   %D%/services/kerberos.scm			\
   %D%/services/lirc.scm				\
   %D%/services/virtualization.scm		\
@@ -521,6 +535,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/services/messaging.scm			\
   %D%/services/monitoring.scm			\
   %D%/services/networking.scm			\
+  %D%/services/nix.scm				\
   %D%/services/nfs.scm			\
   %D%/services/security-token.scm		\
   %D%/services/shepherd.scm			\
@@ -553,6 +568,9 @@ GNU_SYSTEM_MODULES =				\
   %D%/system/uuid.scm				\
   %D%/system/vm.scm				\
 						\
+  %D%/machine.scm				\
+  %D%/machine/ssh.scm				\
+						\
   %D%/build/accounts.scm			\
   %D%/build/activation.scm			\
   %D%/build/bootloader.scm			\
@@ -580,8 +598,10 @@ GNU_SYSTEM_MODULES =				\
   %D%/tests/mail.scm				\
   %D%/tests/messaging.scm			\
   %D%/tests/networking.scm			\
+  %D%/tests/reconfigure.scm			\
   %D%/tests/rsync.scm				\
   %D%/tests/security-token.scm			\
+  %D%/tests/singularity.scm			\
   %D%/tests/ssh.scm				\
   %D%/tests/version-control.scm			\
   %D%/tests/virtualization.scm			\
@@ -617,7 +637,7 @@ INSTALLER_MODULES =                             \
   %D%/installer/newt/user.scm			\
   %D%/installer/newt/utils.scm			\
   %D%/installer/newt/welcome.scm		\
-  %D%/installer/newt/wifi.scm	
+  %D%/installer/newt/wifi.scm
 
 # Always ship the installer modules but compile them only when
 # ENABLE_INSTALLER is true.
@@ -633,6 +653,7 @@ dist_installer_DATA =				\
 
 # Modules that do not need to be compiled.
 MODULES_NOT_COMPILED +=				\
+  %D%/build/locale.scm				\
   %D%/build/shepherd.scm			\
   %D%/build/svg.scm
 
@@ -642,6 +663,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/4store-unset-preprocessor-directive.patch	\
   %D%/packages/patches/a2ps-CVE-2001-1593.patch	\
   %D%/packages/patches/a2ps-CVE-2014-0466.patch	\
+  %D%/packages/patches/a2ps-CVE-2015-8107.patch	\
   %D%/packages/patches/abiword-explictly-cast-bools.patch	\
   %D%/packages/patches/abiword-black-drawing-with-gtk322.patch	\
   %D%/packages/patches/acl-fix-perl-regex.patch		\
@@ -663,7 +685,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/apr-skip-getservbyname-test.patch	\
   %D%/packages/patches/aria2-CVE-2019-3500.patch		\
   %D%/packages/patches/aspell-default-dict-dir.patch		\
-  %D%/packages/patches/at-spi2-core-meson-compat.patch		\
   %D%/packages/patches/ath9k-htc-firmware-binutils.patch	\
   %D%/packages/patches/ath9k-htc-firmware-gcc.patch		\
   %D%/packages/patches/ath9k-htc-firmware-objcopy.patch		\
@@ -676,13 +697,14 @@ dist_patch_DATA =						\
   %D%/packages/patches/avidemux-install-to-lib.patch		\
   %D%/packages/patches/awesome-reproducible-png.patch		\
   %D%/packages/patches/azr3.patch				\
+  %D%/packages/patches/bash-4.4-linux-pgrp-pipe.patch		\
   %D%/packages/patches/bash-completion-directories.patch	\
   %D%/packages/patches/bastet-change-source-of-unordered_set.patch	\
   %D%/packages/patches/bazaar-CVE-2017-14176.patch		\
   %D%/packages/patches/beets-python-3.7-fix.patch		\
   %D%/packages/patches/beignet-correct-file-names.patch		\
+  %D%/packages/patches/benchmark-unbundle-googletest.patch	\
   %D%/packages/patches/biber-fix-encoding-write.patch		\
-  %D%/packages/patches/bind-fix-unused-pk11-ecc-constants.patch	\
   %D%/packages/patches/binutils-loongson-workaround.patch	\
   %D%/packages/patches/blender-2.79-newer-ffmpeg.patch		\
   %D%/packages/patches/blender-2.79-python-3.7-fix.patch	\
@@ -717,7 +739,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/clementine-use-openssl.patch		\
   %D%/packages/patches/clisp-remove-failing-test.patch		\
   %D%/packages/patches/clucene-pkgconfig.patch			\
-  %D%/packages/patches/clx-remove-demo.patch			\
   %D%/packages/patches/coda-use-system-libs.patch		\
   %D%/packages/patches/combinatorial-blas-awpm.patch		\
   %D%/packages/patches/combinatorial-blas-io-fix.patch		\
@@ -725,16 +746,20 @@ dist_patch_DATA =						\
   %D%/packages/patches/cpufrequtils-fix-aclocal.patch		\
   %D%/packages/patches/crawl-upgrade-saves.patch		\
   %D%/packages/patches/crda-optional-gcrypt.patch		\
+  %D%/packages/patches/csvkit-fix-tests.patch			\
   %D%/packages/patches/clucene-contribs-lib.patch               \
   %D%/packages/patches/cube-nocheck.patch			\
   %D%/packages/patches/cursynth-wave-rand.patch			\
-  %D%/packages/patches/cvs-2017-12836.patch			\
+  %D%/packages/patches/cvs-CVE-2017-12836.patch		\
+  %D%/packages/patches/darkice-workaround-fpermissive-error.patch	\
   %D%/packages/patches/dbus-helper-search-path.patch		\
+  %D%/packages/patches/dbus-CVE-2019-12749.patch		\
   %D%/packages/patches/dealii-mpi-deprecations.patch		\
   %D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch	\
   %D%/packages/patches/dfu-programmer-fix-libusb.patch		\
   %D%/packages/patches/diffutils-gets-undeclared.patch		\
   %D%/packages/patches/diffutils-getopt.patch			\
+  %D%/packages/patches/dkimproxy-add-ipv6-support.patch		\
   %D%/packages/patches/docbook-xsl-nonrecursive-string-subst.patch	\
   %D%/packages/patches/doc++-include-directives.patch		\
   %D%/packages/patches/doc++-segfault-fix.patch			\
@@ -743,17 +768,20 @@ dist_patch_DATA =						\
   %D%/packages/patches/docker-use-fewer-modprobes.patch		\
   %D%/packages/patches/dovecot-trees-support-dovecot-2.3.patch	\
   %D%/packages/patches/doxygen-test.patch			\
+  %D%/packages/patches/dstat-fix-crash-when-specifying-delay.patch	\
+  %D%/packages/patches/dstat-skip-devices-without-io.patch	\
   %D%/packages/patches/dvd+rw-tools-add-include.patch 		\
   %D%/packages/patches/elfutils-tests-ptrace.patch		\
   %D%/packages/patches/elixir-path-length.patch			\
   %D%/packages/patches/einstein-build.patch			\
+  %D%/packages/patches/emacs-dired-toggle-sudo-emacs-26.patch   \
   %D%/packages/patches/emacs-exec-path.patch			\
   %D%/packages/patches/emacs-fix-scheme-indent-function.patch	\
   %D%/packages/patches/emacs-json-reformat-fix-tests.patch	\
   %D%/packages/patches/emacs-highlight-stages-add-gexp.patch	\
   %D%/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch	\
   %D%/packages/patches/emacs-source-date-epoch.patch		\
-  %D%/packages/patches/emacs-realgud-fix-configure-ac.patch	\
+  %D%/packages/patches/emacs-unpackaged-req.patch		\
   %D%/packages/patches/emacs-undohist-ignored.patch	\
   %D%/packages/patches/emacs-wordnut-require-adaptive-wrap.patch	\
   %D%/packages/patches/emacs-zones-called-interactively.patch	\
@@ -763,6 +791,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/evilwm-lost-focus-bug.patch		\
   %D%/packages/patches/exiv2-CVE-2017-14860.patch		\
   %D%/packages/patches/exiv2-CVE-2017-14859-14862-14864.patch	\
+  %D%/packages/patches/expat-CVE-2018-20843.patch		\
   %D%/packages/patches/extundelete-e2fsprogs-1.44.patch		\
   %D%/packages/patches/fastcap-mulGlobal.patch			\
   %D%/packages/patches/fastcap-mulSetup.patch			\
@@ -781,7 +810,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/findutils-localstatedir.patch		\
   %D%/packages/patches/findutils-makedev.patch			\
   %D%/packages/patches/findutils-test-xargs.patch		\
-  %D%/packages/patches/flac-CVE-2017-6888.patch		\
   %D%/packages/patches/flann-cmake-3.11.patch			\
   %D%/packages/patches/flint-ldconfig.patch			\
   %D%/packages/patches/foomatic-filters-CVE-2015-8327.patch	\
@@ -857,12 +885,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/glibc-2.27-git-fixes.patch		\
   %D%/packages/patches/glibc-2.28-git-fixes.patch		\
   %D%/packages/patches/glusterfs-use-PATH-instead-of-hardcodes.patch		\
-  %D%/packages/patches/glog-gcc-5-demangling.patch		\
   %D%/packages/patches/gmp-arm-asm-nothumb.patch		\
   %D%/packages/patches/gmp-faulty-test.patch			\
   %D%/packages/patches/gnome-shell-theme.patch			\
   %D%/packages/patches/gnome-tweaks-search-paths.patch		\
-  %D%/packages/patches/gnucash-fix-test-transaction-failure.patch \
   %D%/packages/patches/gnutls-skip-trust-store-test.patch	\
   %D%/packages/patches/gobject-introspection-absolute-shlib-path.patch \
   %D%/packages/patches/gobject-introspection-cc.patch		\
@@ -873,12 +899,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/grep-timing-sensitive-test.patch		\
   %D%/packages/patches/groff-source-date-epoch.patch		\
   %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch	\
-  %D%/packages/patches/grub-binutils-compat.patch		\
-  %D%/packages/patches/grub-check-error-efibootmgr.patch	\
   %D%/packages/patches/grub-efi-fat-serial-number.patch		\
   %D%/packages/patches/gsl-test-i686.patch			\
   %D%/packages/patches/gspell-dash-test.patch			\
-  %D%/packages/patches/gst-plugins-good-libvpx-compat.patch	\
   %D%/packages/patches/guile-1.8-cpp-4.5.patch			\
   %D%/packages/patches/guile-2.2-default-utf8.patch		\
   %D%/packages/patches/guile-default-utf8.patch			\
@@ -888,12 +911,14 @@ dist_patch_DATA =						\
   %D%/packages/patches/guile-relocatable.patch			\
   %D%/packages/patches/guile-rsvg-pkgconfig.patch		\
   %D%/packages/patches/guile-emacs-fix-configure.patch		\
+  %D%/packages/patches/gstreamer-buffer-reset-offset.patch	\
   %D%/packages/patches/gtk2-respect-GUIX_GTK2_PATH.patch	\
   %D%/packages/patches/gtk2-respect-GUIX_GTK2_IM_MODULE_FILE.patch \
   %D%/packages/patches/gtk2-theme-paths.patch			\
   %D%/packages/patches/gtk3-respect-GUIX_GTK3_PATH.patch	\
   %D%/packages/patches/gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch \
   %D%/packages/patches/gtkglext-disable-disable-deprecated.patch \
+  %D%/packages/patches/gtksourceview-2-add-default-directory.patch \
   %D%/packages/patches/gzdoom-search-in-installed-share.patch	\
   %D%/packages/patches/haskell-mode-unused-variables.patch	\
   %D%/packages/patches/haskell-mode-make-check.patch		\
@@ -924,9 +949,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/id3lib-CVE-2007-4460.patch			\
   %D%/packages/patches/idris-test-no-node.patch			\
   %D%/packages/patches/ilmbase-fix-tests.patch			\
-  %D%/packages/patches/inkscape-poppler-compat3.patch		\
   %D%/packages/patches/intltool-perl-compatibility.patch	\
   %D%/packages/patches/irrlicht-use-system-libs.patch		\
+  %D%/packages/patches/isc-dhcp-4.4.1-fixes-for-newer-bind.patch	\
   %D%/packages/patches/isl-0.11.1-aarch64-support.patch	\
   %D%/packages/patches/jacal-fix-texinfo.patch			\
   %D%/packages/patches/jamvm-arm.patch				\
@@ -940,7 +965,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/java-xerces-xjavac_taskdef.patch	\
   %D%/packages/patches/jbig2dec-ignore-testtest.patch		\
   %D%/packages/patches/kdbusaddons-kinit-file-name.patch	\
-  %D%/packages/patches/khmer-use-libraries.patch                \
   %D%/packages/patches/libziparchive-add-includes.patch		\
   %D%/packages/patches/localed-xorg-keyboard.patch		\
   %D%/packages/patches/kiki-level-selection-crash.patch		\
@@ -962,9 +986,14 @@ dist_patch_DATA =						\
   %D%/packages/patches/kodi-set-libcurl-ssl-parameters.patch		\
   %D%/packages/patches/kodi-skip-test-449.patch		\
   %D%/packages/patches/laby-make-install.patch			\
+  %D%/packages/patches/lcalc-default-parameters-1.patch		\
+  %D%/packages/patches/lcalc-default-parameters-2.patch		\
+  %D%/packages/patches/lcalc-lcommon-h.patch    		\
+  %D%/packages/patches/lcalc-using-namespace-std.patch 		\
   %D%/packages/patches/lcms-CVE-2018-16435.patch		\
   %D%/packages/patches/ldc-bootstrap-disable-tests.patch	\
   %D%/packages/patches/ldc-disable-phobos-tests.patch		\
+  %D%/packages/patches/leela-zero-gtest.patch			\
   %D%/packages/patches/liba52-enable-pic.patch			\
   %D%/packages/patches/liba52-link-with-libm.patch		\
   %D%/packages/patches/liba52-set-soname.patch			\
@@ -981,15 +1010,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/libcroco-CVE-2017-7960.patch		\
   %D%/packages/patches/libcroco-CVE-2017-7961.patch		\
   %D%/packages/patches/libdrm-symbol-check.patch		\
-  %D%/packages/patches/libevent-dns-tests.patch			\
-  %D%/packages/patches/libevent-2.0-CVE-2016-10195.patch	\
-  %D%/packages/patches/libevent-2.0-CVE-2016-10196.patch	\
-  %D%/packages/patches/libevent-2.0-CVE-2016-10197.patch	\
-  %D%/packages/patches/libevent-2.0-evbuffer-add-use-last-with-datap.patch	\
-  %D%/packages/patches/libevent-2.1-dns-tests.patch		\
-  %D%/packages/patches/libevent-2.1-skip-failing-test.patch	\
   %D%/packages/patches/libexif-CVE-2016-6328.patch		\
   %D%/packages/patches/libexif-CVE-2017-7544.patch		\
+  %D%/packages/patches/libexif-CVE-2018-20030.patch		\
   %D%/packages/patches/libgcrypt-make-yat2m-reproducible.patch	\
   %D%/packages/patches/libgit2-avoid-python.patch		\
   %D%/packages/patches/libgit2-mtime-0.patch			\
@@ -1003,7 +1026,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/libotr-test-auth-fix.patch		\
   %D%/packages/patches/libmad-armv7-thumb-pt1.patch		\
   %D%/packages/patches/libmad-armv7-thumb-pt2.patch		\
-  %D%/packages/patches/libmad-frame-length.patch		\
+  %D%/packages/patches/libmad-length-check.patch		\
+  %D%/packages/patches/libmad-md_size.patch			\
   %D%/packages/patches/libmad-mips-newgcc.patch			\
   %D%/packages/patches/libmygpo-qt-fix-qt-5.11.patch		\
   %D%/packages/patches/libmygpo-qt-missing-qt5-modules.patch	\
@@ -1040,6 +1064,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/llvm-3.5-fix-clang-build-with-gcc5.patch	\
   %D%/packages/patches/llvm-for-extempore.patch			\
   %D%/packages/patches/lm-sensors-hwmon-attrs.patch		\
+  %D%/packages/patches/lrcalc-includes.patch    		\
   %D%/packages/patches/lrzip-CVE-2017-8842.patch		\
   %D%/packages/patches/lua-CVE-2014-5461.patch                      \
   %D%/packages/patches/lua-pkgconfig.patch                      \
@@ -1053,6 +1078,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/lxsession-use-gapplication.patch         \
   %D%/packages/patches/make-glibc-compat.patch			\
   %D%/packages/patches/make-impure-dirs.patch			\
+  %D%/packages/patches/mame-rapidjson-fix.patch			\
   %D%/packages/patches/mariadb-client-test-32bit.patch		\
   %D%/packages/patches/mars-install.patch			\
   %D%/packages/patches/mars-sfml-2.3.patch			\
@@ -1097,6 +1123,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/netsurf-longer-test-timeout.patch	\
   %D%/packages/patches/nfs-utils-missing-headers.patch		\
   %D%/packages/patches/ngircd-handle-zombies.patch		\
+  %D%/packages/patches/nm-plugin-path.patch			\
+  %D%/packages/patches/nss-freebl-stubs.patch			\
   %D%/packages/patches/nss-increase-test-timeout.patch		\
   %D%/packages/patches/nss-pkgconfig.patch			\
   %D%/packages/patches/ntfs-3g-CVE-2019-9755.patch		\
@@ -1128,6 +1156,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/openssl-1.1-c-rehash-in.patch		\
   %D%/packages/patches/openssl-c-rehash-in.patch		\
   %D%/packages/patches/openssl-CVE-2019-1559.patch		\
+  %D%/packages/patches/open-zwave-hidapi.patch			\
   %D%/packages/patches/orpheus-cast-errors-and-includes.patch	\
   %D%/packages/patches/osip-CVE-2017-7853.patch			\
   %D%/packages/patches/ots-no-include-missing-file.patch	\
@@ -1141,6 +1170,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/patchelf-rework-for-arm.patch		\
   %D%/packages/patches/patchutils-test-perms.patch		\
   %D%/packages/patches/patch-hurd-path-max.patch		\
+  %D%/packages/patches/pcre2-fix-jit_match-crash.patch		\
   %D%/packages/patches/perl-autosplit-default-time.patch	\
   %D%/packages/patches/perl-deterministic-ordering.patch	\
   %D%/packages/patches/perl-finance-quote-unuse-mozilla-ca.patch \
@@ -1165,9 +1195,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/pixman-CVE-2016-5296.patch		\
   %D%/packages/patches/plink-1.07-unclobber-i.patch		\
   %D%/packages/patches/plink-endian-detection.patch		\
+  %D%/packages/patches/plib-CVE-2011-4620.patch		\
+  %D%/packages/patches/plib-CVE-2012-4552.patch		\
   %D%/packages/patches/plotutils-libpng-jmpbuf.patch		\
   %D%/packages/patches/podofo-cmake-3.12.patch			\
-  %D%/packages/patches/polkit-CVE-2018-19788.patch		\
   %D%/packages/patches/portaudio-audacity-compat.patch		\
   %D%/packages/patches/portmidi-modular-build.patch		\
   %D%/packages/patches/postgresql-disable-resolve_symlinks.patch	\
@@ -1210,10 +1241,12 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-mox3-python3.6-compat.patch	\
   %D%/packages/patches/python-testtools.patch			\
   %D%/packages/patches/python-paste-remove-timing-test.patch	\
+  %D%/packages/patches/python-pyatspi-python-37.patch	\
   %D%/packages/patches/python-pycrypto-CVE-2013-7459.patch	\
   %D%/packages/patches/python2-pygobject-2-gi-info-type-error-domain.patch \
   %D%/packages/patches/python-pygpgme-fix-pinentry-tests.patch	\
   %D%/packages/patches/python-robotframework-honor-source-date-epoch.patch \
+  %D%/packages/patches/python-slugify-depend-on-unidecode.patch	\
   %D%/packages/patches/python2-subprocess32-disable-input-test.patch	\
   %D%/packages/patches/python-unittest2-python3-compat.patch	\
   %D%/packages/patches/python-unittest2-remove-argparse.patch	\
@@ -1231,6 +1264,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/randomjungle-disable-static-build.patch	\
   %D%/packages/patches/rapicorn-isnan.patch			\
   %D%/packages/patches/raptor2-heap-overflow.patch		\
+  %D%/packages/patches/ratpoints-sturm_and_rp_private.patch	\
   %D%/packages/patches/ratpoison-shell.patch			\
   %D%/packages/patches/rcs-5.9.4-noreturn.patch			\
   %D%/packages/patches/rct-add-missing-headers.patch		\
@@ -1238,6 +1272,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/readline-6.2-CVE-2014-2524.patch		\
   %D%/packages/patches/red-eclipse-remove-gamma-name-hack.patch	\
   %D%/packages/patches/reposurgeon-add-missing-docbook-files.patch	\
+  %D%/packages/patches/ri-li-modernize_cpp.patch		\
   %D%/packages/patches/ripperx-missing-file.patch		\
   %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
   %D%/packages/patches/rtags-separate-rct.patch			\
@@ -1253,14 +1288,12 @@ dist_patch_DATA =						\
   %D%/packages/patches/rust-1.25-accept-more-detailed-gdb-lines.patch \
   %D%/packages/patches/rust-bootstrap-stage0-test.patch		\
   %D%/packages/patches/rust-coresimd-doctest.patch		\
-  %D%/packages/patches/rust-1.30-gdb-llvm.patch			\
   %D%/packages/patches/rust-reproducible-builds.patch		 \
   %D%/packages/patches/rxvt-unicode-escape-sequences.patch	\
   %D%/packages/patches/scalapack-blacs-mpi-deprecations.patch	\
   %D%/packages/patches/scheme48-tests.patch			\
   %D%/packages/patches/scotch-build-parallelism.patch		\
   %D%/packages/patches/scotch-integer-declarations.patch	\
-  %D%/packages/patches/scribus-poppler.patch			\
   %D%/packages/patches/sdl-libx11-1.6.patch			\
   %D%/packages/patches/seq24-rename-mutex.patch			\
   %D%/packages/patches/sharutils-CVE-2018-1000097.patch		\
@@ -1276,14 +1309,21 @@ dist_patch_DATA =						\
   %D%/packages/patches/soundconverter-remove-gconf-dependency.patch	\
   %D%/packages/patches/sssd-curl-compat.patch			\
   %D%/packages/patches/steghide-fixes.patch			\
+  %D%/packages/patches/strace-ipc-tests.patch			\
   %D%/packages/patches/streamlink-update-test.patch		\
+  %D%/packages/patches/stumpwm-fix-broken-read-one-line.patch	\
   %D%/packages/patches/superlu-dist-awpm-grid.patch		\
   %D%/packages/patches/superlu-dist-fix-mpi-deprecations.patch	\
   %D%/packages/patches/superlu-dist-scotchmetis.patch		\
+  %D%/packages/patches/supertux-fix-build-with-gcc5.patch	\
+  %D%/packages/patches/supertux-unbundle-squirrel.patch		\
   %D%/packages/patches/swig-guile-gc.patch			\
   %D%/packages/patches/swish-e-search.patch			\
   %D%/packages/patches/swish-e-format-security.patch		\
-  %D%/packages/patches/stumpwm-fix-broken-read-one-line.patch	\
+  %D%/packages/patches/symmetrica-bruch.patch			\
+  %D%/packages/patches/symmetrica-int32.patch			\
+  %D%/packages/patches/symmetrica-return_values.patch 		\
+  %D%/packages/patches/symmetrica-sort_sum_rename.patch 	\
   %D%/packages/patches/t1lib-CVE-2010-2642.patch		\
   %D%/packages/patches/t1lib-CVE-2011-0764.patch		\
   %D%/packages/patches/t1lib-CVE-2011-1552+.patch		\
@@ -1314,6 +1354,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/totem-meson-easy-codec.patch		\
   %D%/packages/patches/tuxpaint-stamps-path.patch		\
   %D%/packages/patches/twinkle-include-qregexpvalidator.patch	\
+  %D%/packages/patches/txr-shell.patch				\
   %D%/packages/patches/u-boot-fix-mkimage-header-verification.patch	\
   %D%/packages/patches/unzip-CVE-2014-8139.patch		\
   %D%/packages/patches/unzip-CVE-2014-8140.patch		\
@@ -1332,6 +1373,7 @@ dist_patch_DATA =						\
   %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/usb-modeswitch-accept-config-arg.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	\
@@ -1348,7 +1390,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/wavpack-CVE-2018-6767.patch		\
   %D%/packages/patches/wavpack-CVE-2018-7253.patch		\
   %D%/packages/patches/wavpack-CVE-2018-7254.patch		\
-  %D%/packages/patches/webkitgtk-sse2.patch			\
   %D%/packages/patches/weechat-python.patch			\
   %D%/packages/patches/wicd-bitrate-none-fix.patch		\
   %D%/packages/patches/wicd-get-selected-profile-fix.patch	\
@@ -1368,11 +1409,14 @@ dist_patch_DATA =						\
   %D%/packages/patches/xf86-video-siliconmotion-fix-ftbfs.patch \
   %D%/packages/patches/xf86-video-sis-xorg-compat.patch 	\
   %D%/packages/patches/xf86-video-tga-remove-mibstore.patch	\
+  %D%/packages/patches/xf86-video-voodoo-pcitag.patch		\
   %D%/packages/patches/xfce4-panel-plugins.patch		\
   %D%/packages/patches/xfce4-session-fix-xflock4.patch		\
   %D%/packages/patches/xfce4-settings-defaults.patch		\
   %D%/packages/patches/xinetd-fix-fd-leak.patch			\
-  %D%/packages/patches/xinetd-CVE-2013-4342.patch
+  %D%/packages/patches/xinetd-CVE-2013-4342.patch		\
+  %D%/packages/patches/xorriso-no-partition-table-in-inner-efi.patch \
+  %D%/packages/patches/xorriso-no-mbr-in-inner-efi.patch
 
 MISC_DISTRO_FILES =				\
   %D%/packages/ld-wrapper.in

gnu/machine.scm

@@ -0,0 +1,132 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2019 David Thompson <davet@gnu.org>
+;;; Copyright © 2019 Jakob L. Kreuze <zerodaysfordays@sdf.lonestar.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu machine)
+  #:use-module (gnu system)
+  #:use-module (guix derivations)
+  #:use-module (guix monads)
+  #:use-module (guix records)
+  #:use-module (guix store)
+  #:use-module ((guix utils) #:select (source-properties->location))
+  #:use-module (srfi srfi-35)
+  #:export (environment-type
+            environment-type?
+            environment-type-name
+            environment-type-description
+            environment-type-location
+
+            machine
+            machine?
+            this-machine
+
+            machine-operating-system
+            machine-environment
+            machine-configuration
+            machine-display-name
+
+            deploy-machine
+            roll-back-machine
+            machine-remote-eval
+
+            &deploy-error
+            deploy-error?
+            deploy-error-should-roll-back
+            deploy-error-captured-args))
+
+;;; Commentary:
+;;;
+;;; This module provides the types used to declare individual machines in a
+;;; heterogeneous Guix deployment. The interface allows users of specify system
+;;; configurations and the means by which resources should be provisioned on a
+;;; per-host basis.
+;;;
+;;; Code:
+
+
+;;;
+;;; Declarations for resources that can be provisioned.
+;;;
+
+(define-record-type* <environment-type> environment-type
+  make-environment-type
+  environment-type?
+
+  ;; Interface to the environment type's deployment code. Each procedure
+  ;; should take the same arguments as the top-level procedure of this file
+  ;; that shares the same name. For example, 'machine-remote-eval' should be
+  ;; of the form '(machine-remote-eval machine exp)'.
+  (machine-remote-eval environment-type-machine-remote-eval) ; procedure
+  (deploy-machine      environment-type-deploy-machine)      ; procedure
+  (roll-back-machine   environment-type-roll-back-machine)   ; procedure
+
+  ;; Metadata.
+  (name        environment-type-name)       ; symbol
+  (description environment-type-description ; string
+               (default #f))
+  (location    environment-type-location    ; <location>
+               (default (and=> (current-source-location)
+                               source-properties->location))
+               (innate)))
+
+
+;;;
+;;; Declarations for machines in a deployment.
+;;;
+
+(define-record-type* <machine> machine
+  make-machine
+  machine?
+  this-machine
+  (operating-system machine-operating-system) ; <operating-system>
+  (environment      machine-environment)      ; symbol
+  (configuration    machine-configuration     ; configuration object
+                    (default #f)))            ; specific to environment
+
+(define (machine-display-name machine)
+  "Return the host-name identifying MACHINE."
+  (operating-system-host-name (machine-operating-system machine)))
+
+(define (machine-remote-eval machine exp)
+  "Evaluate EXP, a gexp, on MACHINE. Ensure that all the elements EXP refers to
+are built and deployed to MACHINE beforehand."
+  (let ((environment (machine-environment machine)))
+    ((environment-type-machine-remote-eval environment) machine exp)))
+
+(define (deploy-machine machine)
+  "Monadic procedure transferring the new system's OS closure to the remote
+MACHINE, activating it on MACHINE and switching MACHINE to the new generation."
+  (let ((environment (machine-environment machine)))
+    ((environment-type-deploy-machine environment) machine)))
+
+(define (roll-back-machine machine)
+  "Monadic procedure rolling back to the previous system generation on
+MACHINE. Return the number of the generation that was current before switching
+and the new generation number."
+  (let ((environment (machine-environment machine)))
+    ((environment-type-roll-back-machine environment) machine)))
+
+
+;;;
+;;; Error types.
+;;;
+
+(define-condition-type &deploy-error &error
+  deploy-error?
+  (should-roll-back deploy-error-should-roll-back)
+  (captured-args deploy-error-captured-args))

gnu/machine/ssh.scm

@@ -0,0 +1,470 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2019 Jakob L. Kreuze <zerodaysfordays@sdf.lonestar.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu machine ssh)
+  #:use-module (gnu bootloader)
+  #:use-module (gnu machine)
+  #:autoload   (gnu packages gnupg) (guile-gcrypt)
+  #:use-module (gnu system)
+  #:use-module (gnu system file-systems)
+  #:use-module (gnu system uuid)
+  #:use-module (guix diagnostics)
+  #:use-module (guix gexp)
+  #:use-module (guix i18n)
+  #:use-module (guix modules)
+  #:use-module (guix monads)
+  #:use-module (guix pki)
+  #:use-module (guix records)
+  #:use-module (guix remote)
+  #:use-module (guix scripts system reconfigure)
+  #:use-module (guix ssh)
+  #:use-module (guix store)
+  #:use-module (guix utils)
+  #:use-module (gcrypt pk-crypto)
+  #:use-module (ice-9 match)
+  #:use-module (ice-9 textual-ports)
+  #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-19)
+  #:use-module (srfi srfi-26)
+  #:use-module (srfi srfi-34)
+  #:use-module (srfi srfi-35)
+  #:export (managed-host-environment-type
+
+            machine-ssh-configuration
+            machine-ssh-configuration?
+            machine-ssh-configuration
+
+            machine-ssh-configuration-host-name
+            machine-ssh-configuration-build-locally?
+            machine-ssh-configuration-authorize?
+            machine-ssh-configuration-port
+            machine-ssh-configuration-user
+            machine-ssh-configuration-session))
+
+;;; Commentary:
+;;;
+;;; This module implements remote evaluation and system deployment for
+;;; machines that are accessible over SSH and have a known host-name. In the
+;;; sense of the broader "machine" interface, we describe the environment for
+;;; such machines as 'managed-host.
+;;;
+;;; Code:
+
+
+;;;
+;;; Parameters for the SSH client.
+;;;
+
+(define-record-type* <machine-ssh-configuration> machine-ssh-configuration
+  make-machine-ssh-configuration
+  machine-ssh-configuration?
+  this-machine-ssh-configuration
+  (host-name      machine-ssh-configuration-host-name)     ; string
+  (system         machine-ssh-configuration-system)        ; string
+  (build-locally? machine-ssh-configuration-build-locally? ; boolean
+                  (default #t))
+  (authorize?     machine-ssh-configuration-authorize?     ; boolean
+                  (default #t))
+  (port           machine-ssh-configuration-port           ; integer
+                  (default 22))
+  (user           machine-ssh-configuration-user           ; string
+                  (default "root"))
+  (identity       machine-ssh-configuration-identity       ; path to a private key
+                  (default #f))
+  (session        machine-ssh-configuration-session        ; session
+                  (default #f)))
+
+(define (machine-ssh-session machine)
+  "Return the SSH session that was given in MACHINE's configuration, or create
+one from the configuration's parameters if one was not provided."
+  (maybe-raise-unsupported-configuration-error machine)
+  (let ((config (machine-configuration machine)))
+    (or (machine-ssh-configuration-session config)
+        (let ((host-name (machine-ssh-configuration-host-name config))
+              (user (machine-ssh-configuration-user config))
+              (port (machine-ssh-configuration-port config))
+              (identity (machine-ssh-configuration-identity config)))
+          (open-ssh-session host-name
+                            #:user user
+                            #:port port
+                            #:identity identity)))))
+
+
+;;;
+;;; Remote evaluation.
+;;;
+
+(define (machine-become-command machine)
+  "Return as a list of strings the program and arguments necessary to run a
+shell command with escalated privileges for MACHINE's configuration."
+  (if (string= "root" (machine-ssh-configuration-user
+                       (machine-configuration machine)))
+      '()
+      '("/run/setuid-programs/sudo" "-n" "--")))
+
+(define (managed-host-remote-eval machine exp)
+  "Internal implementation of 'machine-remote-eval' for MACHINE instances with
+an environment type of 'managed-host."
+  (maybe-raise-unsupported-configuration-error machine)
+  (let ((config (machine-configuration machine)))
+    (remote-eval exp (machine-ssh-session machine)
+                 #:build-locally?
+                 (machine-ssh-configuration-build-locally? config)
+                 #:system
+                 (machine-ssh-configuration-system config))))
+
+
+;;;
+;;; Safety checks.
+;;;
+
+(define (machine-check-file-system-availability machine)
+  "Raise a '&message' error condition if any of the file-systems specified in
+MACHINE's 'system' declaration do not exist on the machine."
+  (define file-systems
+    (filter (lambda (fs)
+              (and (file-system-mount? fs)
+                   (not (member (file-system-type fs)
+                                %pseudo-file-system-types))
+                   (not (memq 'bind-mount (file-system-flags fs)))))
+            (operating-system-file-systems (machine-operating-system machine))))
+
+  (define (check-literal-file-system fs)
+    (define remote-exp
+      #~(catch 'system-error
+          (lambda ()
+            (stat #$(file-system-device fs))
+            #t)
+          (lambda args
+            (system-error-errno args))))
+
+    (mlet %store-monad ((errno (machine-remote-eval machine remote-exp)))
+      (when (number? errno)
+        (raise (condition
+                (&message
+                 (message (format #f (G_ "device '~a' not found: ~a")
+                                  (file-system-device fs)
+                                  (strerror errno)))))))
+      (return #t)))
+
+  (define (check-labeled-file-system fs)
+    (define remote-exp
+      (with-imported-modules '((gnu build file-systems))
+        #~(begin
+            (use-modules (gnu build file-systems))
+            (find-partition-by-label #$(file-system-label->string
+                                        (file-system-device fs))))))
+
+    (mlet %store-monad ((result (machine-remote-eval machine remote-exp)))
+      (unless result
+        (raise (condition
+                (&message
+                 (message (format #f (G_ "no file system with label '~a'")
+                                  (file-system-label->string
+                                   (file-system-device fs))))))))
+      (return #t)))
+
+  (define (check-uuid-file-system fs)
+    (define remote-exp
+      (with-imported-modules (source-module-closure
+                              '((gnu build file-systems)
+                                (gnu system uuid)))
+        #~(begin
+            (use-modules (gnu build file-systems)
+                         (gnu system uuid))
+
+            (define uuid
+              (string->uuid #$(uuid->string (file-system-device fs))))
+
+            (find-partition-by-uuid uuid))))
+
+    (mlet %store-monad ((result (machine-remote-eval machine remote-exp)))
+      (unless result
+        (raise (condition
+                (&message
+                 (message (format #f (G_ "no file system with UUID '~a'")
+                                  (uuid->string (file-system-device fs))))))))
+      (return #t)))
+
+  (mbegin %store-monad
+    (mapm %store-monad check-literal-file-system
+          (filter (lambda (fs)
+                    (string? (file-system-device fs)))
+                  file-systems))
+    (mapm %store-monad check-labeled-file-system
+          (filter (lambda (fs)
+                    (file-system-label? (file-system-device fs)))
+                  file-systems))
+    (mapm %store-monad check-uuid-file-system
+          (filter (lambda (fs)
+              (uuid? (file-system-device fs)))
+                  file-systems))))
+
+(define (machine-check-initrd-modules machine)
+  "Raise a '&message' error condition if any of the modules needed by
+'needed-for-boot' file systems in MACHINE are not available in the initrd."
+  (define file-systems
+    (filter file-system-needed-for-boot?
+            (operating-system-file-systems (machine-operating-system machine))))
+
+  (define (missing-modules fs)
+    (define remote-exp
+      (let ((device (file-system-device fs)))
+        (with-imported-modules (source-module-closure
+                                '((gnu build file-systems)
+                                  (gnu build linux-modules)
+                                  (gnu system uuid)))
+          #~(begin
+              (use-modules (gnu build file-systems)
+                           (gnu build linux-modules)
+                           (gnu system uuid))
+
+              (define dev
+                #$(cond ((string? device) device)
+                        ((uuid? device) #~(find-partition-by-uuid
+                                           (string->uuid
+                                            #$(uuid->string device))))
+                        ((file-system-label? device)
+                         #~(find-partition-by-label
+                            (file-system-label->string #$device)))))
+
+              (missing-modules dev '#$(operating-system-initrd-modules
+                                       (machine-operating-system machine)))))))
+    (mlet %store-monad ((missing (machine-remote-eval machine remote-exp)))
+      (return (list fs missing))))
+
+  (mlet %store-monad ((device (mapm %store-monad missing-modules file-systems)))
+    (for-each (match-lambda
+                ((fs missing)
+                 (unless (null? missing)
+                   (raise (condition
+                           (&message
+                            (message (format #f (G_ "~a missing modules ~{ ~a~}~%")
+                                             (file-system-device fs)
+                                             missing))))))))
+              device)
+    (return #t)))
+
+(define (machine-check-building-for-appropriate-system machine)
+  "Raise a '&message' error condition if MACHINE is configured to be built
+locally and the 'system' field does not match the '%current-system' reported
+by MACHINE."
+  (let ((config (machine-configuration machine))
+        (system (remote-system (machine-ssh-session machine))))
+    (when (and (machine-ssh-configuration-build-locally? config)
+               (not (string= system (machine-ssh-configuration-system config))))
+      (raise (condition
+              (&message
+               (message (format #f (G_ "incorrect target system \
+('~a' was given, while the system reports that it is '~a')~%")
+                                (machine-ssh-configuration-system config)
+                                system)))))))
+  (with-monad %store-monad (return #t)))
+
+(define (check-deployment-sanity machine)
+  "Raise a '&message' error condition if it is clear that deploying MACHINE's
+'system' declaration would fail."
+  ;; Order is important here -- an incorrect value for 'system' will cause
+  ;; invocations of 'remote-eval' to fail.
+  (mbegin %store-monad
+    (machine-check-building-for-appropriate-system machine)
+    (machine-check-file-system-availability machine)
+    (machine-check-initrd-modules machine)))
+
+
+;;;
+;;; System deployment.
+;;;
+
+(define (machine-boot-parameters machine)
+  "Monadic procedure returning a list of 'boot-parameters' for the generations
+of MACHINE's system profile, ordered from most recent to oldest."
+  (define bootable-kernel-arguments
+    (@@ (gnu system) bootable-kernel-arguments))
+
+  (define remote-exp
+    (with-extensions (list guile-gcrypt)
+      (with-imported-modules (source-module-closure '((guix config)
+                                                      (guix profiles)))
+        #~(begin
+            (use-modules (guix config)
+                         (guix profiles)
+                         (ice-9 textual-ports))
+
+            (define %system-profile
+              (string-append %state-directory "/profiles/system"))
+
+            (define (read-file path)
+              (call-with-input-file path
+                (lambda (port)
+                  (get-string-all port))))
+
+            (map (lambda (generation)
+                   (let* ((system-path (generation-file-name %system-profile
+                                                             generation))
+                          (boot-parameters-path (string-append system-path
+                                                               "/parameters"))
+                          (time (stat:mtime (lstat system-path))))
+                     (list generation
+                           system-path
+                           time
+                           (read-file boot-parameters-path))))
+                 (reverse (generation-numbers %system-profile)))))))
+
+  (mlet* %store-monad ((generations (machine-remote-eval machine remote-exp)))
+    (return
+     (map (lambda (generation)
+            (match generation
+              ((generation system-path time serialized-params)
+               (let* ((params (call-with-input-string serialized-params
+                                read-boot-parameters))
+                      (root (boot-parameters-root-device params))
+                      (label (boot-parameters-label params)))
+                 (boot-parameters
+                  (inherit params)
+                  (label
+                   (string-append label " (#"
+                                  (number->string generation) ", "
+                                  (let ((time (make-time time-utc 0 time)))
+                                    (date->string (time-utc->date time)
+                                                  "~Y-~m-~d ~H:~M"))
+                                  ")"))
+                  (kernel-arguments
+                   (append (bootable-kernel-arguments system-path root)
+                           (boot-parameters-kernel-arguments params))))))))
+          generations))))
+
+(define-syntax-rule (with-roll-back should-roll-back? mbody ...)
+  "Catch exceptions that arise when binding MBODY, a monadic expression in
+%STORE-MONAD, and collect their arguments in a &deploy-error condition, with
+the 'should-roll-back' field set to SHOULD-ROLL-BACK?"
+  (catch #t
+    (lambda ()
+      mbody ...)
+    (lambda args
+      (raise (condition (&deploy-error
+                         (should-roll-back should-roll-back?)
+                         (captured-args args)))))))
+
+(define (deploy-managed-host machine)
+  "Internal implementation of 'deploy-machine' for MACHINE instances with an
+environment type of 'managed-host."
+  (maybe-raise-unsupported-configuration-error machine)
+  (when (machine-ssh-configuration-authorize?
+         (machine-configuration machine))
+    (unless (file-exists? %public-key-file)
+      (raise (condition
+              (&message
+               (message (format #f (G_ "no signing key '~a'. \
+have you run 'guix archive --generate-key?'")
+                                %public-key-file))))))
+    (remote-authorize-signing-key (call-with-input-file %public-key-file
+                                    (lambda (port)
+                                      (string->canonical-sexp
+                                       (get-string-all port))))
+                                  (machine-ssh-session machine)))
+  (mlet %store-monad ((_ (check-deployment-sanity machine))
+                      (boot-parameters (machine-boot-parameters machine)))
+    (let* ((os (machine-operating-system machine))
+           (eval (cut machine-remote-eval machine <>))
+           (menu-entries (map boot-parameters->menu-entry boot-parameters))
+           (bootloader-configuration (operating-system-bootloader os))
+           (bootcfg (operating-system-bootcfg os menu-entries)))
+      (mbegin %store-monad
+        (with-roll-back #f
+          (switch-to-system eval os))
+        (with-roll-back #t
+          (mbegin %store-monad
+            (upgrade-shepherd-services eval os)
+            (install-bootloader eval bootloader-configuration bootcfg)))))))
+
+
+;;;
+;;; Roll-back.
+;;;
+
+(define (roll-back-managed-host machine)
+  "Internal implementation of 'roll-back-machine' for MACHINE instances with
+an environment type of 'managed-host."
+  (define remote-exp
+    (with-extensions (list guile-gcrypt)
+      (with-imported-modules (source-module-closure '((guix config)
+                                                      (guix profiles)))
+        #~(begin
+            (use-modules (guix config)
+                         (guix profiles))
+
+            (define %system-profile
+              (string-append %state-directory "/profiles/system"))
+
+            (define target-generation
+              (relative-generation %system-profile -1))
+
+            (if target-generation
+                (switch-to-generation %system-profile target-generation)
+                'error)))))
+
+  (define roll-back-failure
+    (condition (&message (message (G_ "could not roll-back machine")))))
+
+  (mlet* %store-monad ((boot-parameters (machine-boot-parameters machine))
+                       (_ -> (if (< (length boot-parameters) 2)
+                                 (raise roll-back-failure)))
+                       (entries -> (map boot-parameters->menu-entry
+                                        (list (second boot-parameters))))
+                       (old-entries -> (map boot-parameters->menu-entry
+                                            (drop boot-parameters 2)))
+                       (bootloader -> (operating-system-bootloader
+                                       (machine-operating-system machine)))
+                       (bootcfg (lower-object
+                                 ((bootloader-configuration-file-generator
+                                   (bootloader-configuration-bootloader
+                                    bootloader))
+                                  bootloader entries
+                                  #:old-entries old-entries)))
+                       (remote-result (machine-remote-eval machine remote-exp)))
+    (when (eqv? 'error remote-result)
+      (raise roll-back-failure))))
+
+
+;;;
+;;; Environment type.
+;;;
+
+(define managed-host-environment-type
+  (environment-type
+   (machine-remote-eval managed-host-remote-eval)
+   (deploy-machine      deploy-managed-host)
+   (roll-back-machine   roll-back-managed-host)
+   (name                'managed-host-environment-type)
+   (description         "Provisioning for machines that are accessible over SSH
+and have a known host-name. This entails little more than maintaining an SSH
+connection to the host.")))
+
+(define (maybe-raise-unsupported-configuration-error machine)
+  "Raise an error if MACHINE's configuration is not an instance of
+<machine-ssh-configuration>."
+  (let ((config (machine-configuration machine))
+        (environment (environment-type-name (machine-environment machine))))
+    (unless (and config (machine-ssh-configuration? config))
+      (raise (condition
+              (&message
+               (message (format #f (G_ "unsupported machine configuration '~a'
+for environment of type '~a'")
+                                config
+                                environment))))))))

gnu/packages.scm

@@ -534,14 +534,18 @@ optionally contain a version number and an output name, as in these examples:
   guile@2.0.9:debug
 
 If SPEC does not specify a version number, return the preferred newest
-version; if SPEC does not specify an output, return OUTPUT."
+version; if SPEC does not specify an output, return OUTPUT.
+
+When OUTPUT is false and SPEC does not specify any output, return #f as the
+output."
   (let-values (((name version sub-drv)
                 (package-specification->name+version+output spec output)))
     (match (%find-package spec name version)
       (#f
        (values #f #f))
       (package
-       (if (member sub-drv (package-outputs package))
+       (if (or (and (not output) (not sub-drv))
+               (member sub-drv (package-outputs package)))
            (values package sub-drv)
            (leave (G_ "package `~a' lacks output `~a'~%")
                   (package-full-name package)

gnu/packages/admin.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
-;;; Copyright © 2014, 2015, 2016, 2018 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2014, 2015, 2016, 2018, 2019 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015, 2016 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015 Alex Sassmannshausen <alex.sassmannshausen@gmail.com>
@@ -90,6 +90,7 @@
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt)
+  #:use-module (gnu packages sphinx)
   #:use-module (gnu packages terminals)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages groff)
@@ -114,14 +115,14 @@
 (define-public aide
   (package
     (name "aide")
-    (version "0.16.1")
+    (version "0.16.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/aide/aide/releases/download/v"
                            version "/aide-" version ".tar.gz"))
        (sha256
-        (base32 "1dqhc0c24wa4zid06pfy61k357yvzh28ij86bk9jf6hcqzn7qaqg"))))
+        (base32 "15xp47sz7kk1ciffw3f5xw2jg2mb2lqrbr3q6p4bkbz5dap9iy8p"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("bison" ,bison)
@@ -370,7 +371,7 @@ application (for console or X terminals) and requires ncurses.")
 (define-public pies
   (package
     (name "pies")
-    (version "1.3")
+    (version "1.4")
     (source
      (origin
        (method url-fetch)
@@ -378,7 +379,7 @@ application (for console or X terminals) and requires ncurses.")
                            version ".tar.bz2"))
        (sha256
         (base32
-         "12r7rjjyibjdj08dvwbp0iflfpzl4s0zhn6cr6zj3hwf9gbzgl1g"))))
+         "14jb4pa4zs26d5j2skxbaypnwhsx2lw8jgj1irrgs03c2dnf7gp6"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases
@@ -387,7 +388,7 @@ application (for console or X terminals) and requires ncurses.")
                       ;; Use the right shell when executing user-provided
                       ;; shell commands.
                       (let ((bash (assoc-ref inputs "bash")))
-                        (substitute* "src/progman.c"
+                        (substitute* '("src/progman.c" "src/comp.c")
                           (("\"/bin/sh\"")
                            (string-append "\"" bash "/bin/sh\"")))
                         #t))))))
@@ -437,7 +438,7 @@ hostname.")
 (define-public shadow
   (package
     (name "shadow")
-    (version "4.6")
+    (version "4.7")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -445,7 +446,7 @@ hostname.")
                     "download/" version "/shadow-" version ".tar.xz"))
               (sha256
                (base32
-                "10smy01km2bqjjvsd2jz17zvrxbzj89qczyb1amk38j28bcci609"))))
+                "0v71474rx38lg9kidrm4xbk35sg3icv3s5pk2b42icp3lyj9dqg5"))))
     (build-system gnu-build-system)
     (arguments
      `(;; Assume System V `setpgrp (void)', which is the default on GNU
@@ -481,7 +482,7 @@ hostname.")
                                   "-linux")
                  `(("linux-pam" ,linux-pam))
                  '()))
-    (home-page "http://pkg-shadow.alioth.debian.org/")
+    (home-page "https://github.com/shadow-maint/shadow")
     (synopsis "Authentication-related tools such as passwd, su, and login")
     (description
      "Shadow provides a number of authentication-related tools, including:
@@ -683,9 +684,9 @@ connection alive.")
 (define-public isc-dhcp
   (let* ((bind-major-version "9")
          (bind-minor-version "11")
-         (bind-patch-version "4")
-         (bind-release-type "-P")         ; for patch release, use "-P"
-         (bind-release-version "2")      ; for patch release, e.g. "6"
+         (bind-patch-version "9")
+         (bind-release-type "")         ; for patch release, use "-P"
+         (bind-release-version "")      ; for patch release, e.g. "6"
          (bind-version (string-append bind-major-version
                                       "."
                                       bind-minor-version
@@ -709,7 +710,18 @@ connection alive.")
          #:phases
          (modify-phases %standard-phases
            (add-after 'unpack 'replace-bundled-bind
-             (lambda* (#:key inputs #:allow-other-keys)
+             (lambda* (#:key inputs native-inputs #:allow-other-keys)
+               ;; XXX TODO: Remove the following invocation of 'patch' when
+               ;; isc-dhcp is updated.  It should be needed only for 4.4.1.
+               (let ((patch (string-append (assoc-ref (or native-inputs inputs)
+                                                      "patch")
+                                           "/bin/patch"))
+                     (the-patch (assoc-ref (or native-inputs inputs)
+                                           "fixes-for-newer-bind.patch")))
+                 (format #t "applying '~a'...~%" the-patch)
+                 (invoke patch "--force" "--no-backup-if-mismatch"
+                         "-p1" "--input" the-patch))
+
                (delete-file "bind/bind.tar.gz")
                (copy-file (assoc-ref inputs "bind-source-tarball")
                           "bind/bind.tar.gz")
@@ -742,15 +754,18 @@ connection alive.")
                ;; shell is used.
                (with-directory-excursion "bind"
                  (substitute* "Makefile"
-                   (("\\./configure")
+                   (("\\./configure ")
                     (let ((sh (which "sh")))
                       (string-append "./configure CONFIG_SHELL="
-                                     sh " SHELL=" sh))))
+                                     sh " SHELL=" sh " "))))
 
                  (let ((bind-directory (string-append "bind-" ,bind-version)))
                    (invoke "tar" "xf" "bind.tar.gz")
                    (for-each patch-shebang
                              (find-files bind-directory ".*"))
+                   (substitute* (string-append bind-directory "/configure")
+                     (("/usr/bin/file")
+                      (which "file")))
                    (invoke "tar" "cf" "bind.tar.gz"
                            bind-directory
                            ;; avoid non-determinism in the archive
@@ -786,7 +801,15 @@ connection alive.")
                            (list inetutils net-tools coreutils sed))))
                  #t))))))
 
-      (native-inputs `(("perl" ,perl)))
+      (native-inputs
+       `(("perl" ,perl)
+         ("file" ,file)
+
+         ;; XXX TODO: Remove the following patch, and also the 'patch'
+         ;; program, when isc-dhcp is updated.
+         ("fixes-for-newer-bind.patch"
+          ,(search-patch "isc-dhcp-4.4.1-fixes-for-newer-bind.patch"))
+         ("patch" ,patch)))
 
       (inputs `(("inetutils" ,inetutils)
                 ("net-tools" ,net-tools)
@@ -802,7 +825,7 @@ connection alive.")
                                         "/bind-" bind-version ".tar.gz"))
                     (sha256
                      (base32
-                      "04fq17zksd2b3w6w6padps5n7b6s2lasxpksbhl4378h56vgfnm8"))))
+                      "03n57as73ygw6g3lqsmq2idkykajpbskzgixixdvi5a76m4g0fwn"))))
 
                 ;; When cross-compiling, we need the cross Coreutils and sed.
                 ;; Otherwise just use those from %FINAL-INPUTS.
@@ -912,6 +935,51 @@ by bandwidth they use.")
                (base32
                 "0rmk2p3f2wz1h092anidjclh212rv3gxyk0c641qk3frlrjnw6mp"))))
     (build-system perl-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'refer-to-inputs
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* (list "lib/App/ClusterSSH/Config.pm"
+                                "t/15config.t")
+               (("xterm")
+                (which "xterm")))
+             #t))
+         (add-before 'check 'delete-failing-tests
+           (lambda _
+             ;; This checks whether all code is nicely formatted.  The above
+             ;; ‘refer-to-inputs’ phase breaks this pedantry, so disable it.
+             (delete-file "t/perltidy.t")
+             ;; Update the manifest so t/manifest.t happily passes.
+             (substitute* "MANIFEST"
+               (("t/perltidy.t\n") ""))
+             #t))
+         (add-after 'install 'augment-library-path
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin")))
+               (with-directory-excursion bin
+                 (for-each
+                  (lambda (program)
+                    (wrap-program program
+                      `("PERL5LIB" ":" prefix
+                        ,(map (lambda (file-name)
+                                (string-append file-name
+                                               "/lib/perl5/site_perl"))
+                              (cons out
+                                    (map (lambda (input)
+                                           (assoc-ref inputs input))
+                                         ;; These may be propagated and hence
+                                         ;; not explicitly listed as inputs.
+                                         (list "perl-class-data-inheritable"
+                                               "perl-devel-stacktrace"
+                                               "perl-exception-class"
+                                               "perl-tk"
+                                               "perl-try-tiny"
+                                               "perl-x11-protocol"
+                                               "perl-x11-protocol-other")))))))
+                  (find-files "." ".*")))
+               #t))))))
     (native-inputs
      `(("perl-cpan-changes" ,perl-cpan-changes)
        ("perl-file-slurp" ,perl-file-slurp)
@@ -925,13 +993,14 @@ by bandwidth they use.")
        ("perl-test-pod-coverage" ,perl-test-pod-coverage)
        ("perl-test-trap" ,perl-test-trap)
        ("perltidy" ,perltidy)))
-    (propagated-inputs
-     `(("xterm" ,xterm)
-       ("perl-exception-class" ,perl-exception-class)
+    (inputs
+     `(("perl-exception-class" ,perl-exception-class)
+       ("perl-sort-naturally" ,perl-sort-naturally)
        ("perl-tk" ,perl-tk)
        ("perl-try-tiny" ,perl-try-tiny)
        ("perl-x11-protocol" ,perl-x11-protocol)
-       ("perl-x11-protocol-other" ,perl-x11-protocol-other)))
+       ("perl-x11-protocol-other" ,perl-x11-protocol-other)
+       ("xterm" ,xterm)))
     ;; The clusterssh.sourceforge.net address requires login to view
     (home-page "https://sourceforge.net/projects/clusterssh/")
     (synopsis "Secure concurrent multi-server terminal control")
@@ -1134,7 +1203,7 @@ commands and their arguments.")
 (define-public wpa-supplicant-minimal
   (package
     (name "wpa-supplicant-minimal")
-    (version "2.8")
+    (version "2.9")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1142,7 +1211,7 @@ commands and their arguments.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "15ixzm347n8w6gdvi3j3yks3i15qmp6by9ayvswm34d929m372d6"))
+                "05qzak1mssnxcgdrafifxh9w86a4ha69qabkg4bsigk499xyxggw"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -1421,7 +1490,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).")
 (define-public acpica
   (package
     (name "acpica")
-    (version "20190509")
+    (version "20190703")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1429,7 +1498,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).")
                     version ".tar.gz"))
               (sha256
                (base32
-                "17cf5jhcy9wqla5c9s08khqg0pxhar2nmwdcja2jf2srl2a5y2w6"))))
+                "0kp3ian3lffx9709ajrr3bp6b9cb6c6v1crjziyr8j8pp639jlwz"))))
     (build-system gnu-build-system)
     (native-inputs `(("flex" ,flex)
                      ("bison" ,bison)))
@@ -1452,6 +1521,28 @@ tables.  This package contains only the user-space tools needed for ACPI table
 development, not the kernel implementation of ACPI.")
     (license license:gpl2)))            ; dual GPLv2/ACPICA Licence
 
+(define-public s-tui
+  (package
+    (name "s-tui")
+    (version "0.8.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "s-tui" version))
+       (sha256
+        (base32
+         "00lsh2v4i8rwfyjyxx5lijd6rnk9smcfffhzg5sv94ijpcnh216m"))))
+    (build-system python-build-system)
+    (inputs
+     `(("python-psutil" ,python-psutil)
+       ("python-urwid" ,python-urwid)))
+    (home-page "https://github.com/amanusk/s-tui")
+    (synopsis "Interactive terminal stress test and monitoring tool")
+    (description
+     "The Stress Terminal UI displays graphs of the CPU frequency,
+utilization, temperature and power.")
+    (license license:gpl2+)))
+
 (define-public stress
   (package
     (name "stress")
@@ -1516,20 +1607,20 @@ characters can be replaced as well, as can UTF-8 characters.")
 (define-public testdisk
   (package
     (name "testdisk")
-    (version "7.0")
+    (version "7.1")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://www.cgsecurity.org/testdisk-"
+              (uri (string-append "https://www.cgsecurity.org/testdisk-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "0ba4wfz2qrf60vwvb1qsq9l6j0pgg81qgf7fh22siaz649mkpfq0"))))
+                "1zlh44w67py416hkvw6nrfmjickc2d43v51vcli5p374d5sw84ql"))))
     (build-system gnu-build-system)
     (inputs
      `(("ntfs-3g" ,ntfs-3g)
        ("util-linux" ,util-linux)
        ("openssl" ,openssl)
-       ;; FIXME: add reiserfs
+       ;; FIXME: add reiserfs.
        ("zlib" ,zlib)
        ("e2fsprogs" ,e2fsprogs)
        ("libjpeg" ,libjpeg)
@@ -1569,14 +1660,14 @@ environment variable is set and output is to tty.")
 (define-public direvent
   (package
     (name "direvent")
-    (version "5.1")
+    (version "5.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/direvent/direvent-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1nwvjmx7kb14ni34c0b8x9a3791pc20gvhj7xaj66d8q4h6n0qf4"))
+                "0m9vi01b1km0cpknflyzsjnknbava0s1n6393b2bpjwyvb6j5613"))
               (modules '((guix build utils)))
               (snippet '(begin
                           (substitute* "tests/testsuite"
@@ -1733,13 +1824,13 @@ of supported upstream metrics systems simultaneously.")
 (define-public ansible
   (package
     (name "ansible")
-    (version "2.7.10")
+    (version "2.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ansible" version))
        (sha256
-        (base32 "15721d0bxymghxnlnknq43lszlxg3ybbcp2p5v424hhw6wg2v944"))))
+        (base32 "0ia4x17ywym3r1m96ar4h0wc2xlylhbjp6x4wzwkh4p2i0x1vmg1"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-bcrypt" ,python-bcrypt)
@@ -2123,25 +2214,41 @@ results (ndiff), and a packet generation and response analysis tool (nping).")
 (define-public dstat
   (package
     (name "dstat")
-    (version "0.7.3")
+    (version "0.7.4")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/dagwieers/dstat.git")
-             (commit version)))
+             (commit (string-append "v" version))))
        (file-name (git-file-name "dstat" version))
        (sha256
-        (base32 "0sbpna531034gr40w4g9cwz35s2fpf9h654paznsxw9fih91rfa5"))))
+        (base32 "1qnmkhqmjd1m3if05jj29dvr5hn6kayq9bkkkh881w472c0zhp8v"))
+       (patches (search-patches "dstat-fix-crash-when-specifying-delay.patch"
+                                "dstat-skip-devices-without-io.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no make check
        #:make-flags (let ((out (assoc-ref %outputs "out")))
                       (list (string-append "DESTDIR=" out)
                             "prefix=/"))
-       ;; No configure script.
-       #:phases (modify-phases %standard-phases (delete 'configure))))
-    (inputs `(("python-2" ,python-2)))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-python3-DeprecationWarning
+           (lambda _
+             (substitute* "dstat"
+               (("collections") "collections.abc"))
+             #t))
+         (delete 'configure)            ; no configure script
+         (add-after 'install 'wrap
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/bin/dstat")
+                 `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH"))))
+               #t))))))
+    (inputs
+     `(("python" ,python-wrapper)
+       ("python-six" ,python-six)))
     (synopsis "Versatile resource statistics tool")
     (description "Dstat is a versatile replacement for @command{vmstat},
 @command{iostat}, @command{netstat}, and @command{ifstat}.  Dstat overcomes
@@ -2159,7 +2266,7 @@ throughput (in the same interval).")
 (define-public thefuck
   (package
     (name "thefuck")
-    (version "3.28")
+    (version "3.29")
     (source
      (origin
        (method git-fetch)
@@ -2168,7 +2275,7 @@ throughput (in the same interval).")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "070b2sx8r0b4hry6xg97psxlikxghmz91zicg2cm6kc1yhgz4agc"))
+        (base32 "1qhxwjjgrzpqrqjv7l2847ywpln76lyd6j8bl9gz2r6kl0fx2fqs"))
        (patches (search-patches "thefuck-test-environ.patch"))))
     (build-system python-build-system)
     (arguments
@@ -2203,19 +2310,19 @@ a new command using the matched rule, and runs it.")
 (define-public di
   (package
     (name "di")
-    (version "4.47")
+    (version "4.47.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://gentoo.com/di/di-" version ".tar.gz"))
        (sha256
-        (base32 "0zlapxlzjizwzwa8xwrwibhcbkh0wx7n74gvjpp6wlwq7cgiq0xm"))))
+        (base32 "1bdbl9k3gqf4h6g21difqc0w17pjid6r587y19wi37vx36aava7f"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f                      ; obscure test failures.
+     `(#:tests? #f                      ; obscure test failures
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure)
+         (delete 'configure)            ; no configure script
          (add-before 'build 'setup-environment
            (lambda* (#:key outputs #:allow-other-keys)
              (setenv "CC" "gcc")
@@ -2234,7 +2341,7 @@ produce uniform output across heterogeneous networks.")
 (define-public cbatticon
   (package
     (name "cbatticon")
-    (version "1.6.8")
+    (version "1.6.9")
     (source
      (origin
        (method git-fetch)
@@ -2242,7 +2349,7 @@ produce uniform output across heterogeneous networks.")
              (url "https://github.com/valr/cbatticon.git")
              (commit version)))
        (sha256
-        (base32 "16g26vin1693dbdr9qsnw36fdchx394lp79gvp7gcbw0w1ny9av6"))
+        (base32 "0kw09d678sd3m18fmi4380sl4a2m5lkfmq0kps16cdmq7z80rvaf"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments
@@ -2445,7 +2552,7 @@ in order to be able to find it.
 (define-public sedsed
   (package
     (name "sedsed")
-    (version "1.0")
+    (version "1.1")
     (source
      (origin
        (method git-fetch)
@@ -2454,11 +2561,10 @@ in order to be able to find it.
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0009lsjsxhqmgaklpwq15hhd94hpiy7r4va69yy0ig3mxi6zbg2z"))))
+        (base32 "05cl35mwljdb9ynbbsfa8zx6ig8r0xncbg2cir9vwn5manndjj18"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f                      ; no tests
-       #:python ,python-2
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-sed-in
@@ -2475,29 +2581,30 @@ in order to be able to find it.
                ;; Just one file to copy around
                (install-file "sedsed.py" bin)
                #t)))
-         (add-after 'install 'symlink
+         (add-after 'wrap 'symlink
            ;; Create 'sedsed' symlink to "sedsed.py".
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (bin (string-append out "/bin"))
                     (sed (string-append bin "/sedsed"))
                     (sedpy (string-append bin "/sedsed.py")))
-               (symlink  sedpy sed)
+               (symlink sedpy sed)
                #t))))))
-    (home-page "http://aurelio.net/projects/sedsed")
+    (home-page "https://aurelio.net/projects/sedsed")
     (synopsis "Sed sed scripts")
     (description
-     "@code{sedsed} can debug, indent, tokenize and HTMLize your sed(1) script.
+     "@code{sedsed} can debug, indent, tokenize and HTMLize your @command{sed}
+script.
 
-In debug mode it reads your script and add extra commands to it.  When
+In debug mode, it reads your script and adds extra commands to it.  When
 executed you can see the data flow between the commands, revealing all the
-magic sed does on its internal buffers.
+magic sed performs on its internal buffers.
 
-In indent mode your script is reformatted with standard spacing.
+In indent mode, your script is reformatted with standard spacing.
 
-In tokenize mode you can see the elements of every command you use.
+In tokenize mode, you can see the elements of every command you use.
 
-In HTMLize mode your script is converted to a beautiful colored HTML file,
+In HTMLize mode, your script is converted to a beautiful colored HTML file,
 with all the commands and parameters identified for your viewing pleasure.
 
 With sedsed you can master any sed script.  No more secrets, no more hidden
@@ -2521,7 +2628,7 @@ buffers.")
      `(#:tests? #f              ; many of the tests try to load kernel modules
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
+         (replace 'bootstrap
            (lambda _
              ;; Don't run configure in this phase.
              (setenv "NOCONFIGURE" "1")
@@ -2848,7 +2955,7 @@ Python loading in HPC environments.")
   (let ((real-name "inxi"))
     (package
       (name "inxi-minimal")
-      (version "3.0.33-1")
+      (version "3.0.34-1")
       (source
        (origin
          (method git-fetch)
@@ -2857,7 +2964,7 @@ Python loading in HPC environments.")
                (commit version)))
          (file-name (git-file-name real-name version))
          (sha256
-          (base32 "19bfdid4zp39irsdq3m6yyqf2336c30da35qgslrzcr2vh815g8c"))))
+          (base32 "0x2s40lwsan2pk292nspjgyw00f9f5fdfmwfvl50924pxhyxn2fh"))))
       (build-system trivial-build-system)
       (inputs
        `(("bash" ,bash-minimal)

gnu/packages/agda.scm

@@ -64,9 +64,7 @@
        ("ghc-uri-encode" ,ghc-uri-encode)
        ("ghc-parallel" ,ghc-parallel)
        ("ghc-regex-tdfa" ,ghc-regex-tdfa)
-       ("ghc-stm" ,ghc-stm)
        ("ghc-strict" ,ghc-strict)
-       ("ghc-text" ,ghc-text)
        ("ghc-unordered-containers" ,ghc-unordered-containers)
        ("ghc-zlib" ,ghc-zlib)))
     (arguments

gnu/packages/aidc.scm

@@ -3,6 +3,7 @@
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -26,8 +27,15 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (gnu packages autotools)
-  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages imagemagick)
+  #:use-module (gnu packages glib)
+  #:use-module (gnu packages gtk)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages qt)
+  #:use-module (gnu packages video)
   #:use-module (guix build-system gnu))
 
 
@@ -102,3 +110,48 @@ characters, and is highly robust.")
 barcodes of the modern ECC200 variety.  libdmtx is a shared library, allowing
 C/C++ programs to use its capabilities without restrictions or overhead.")
     (license license:bsd-3)))
+
+(define-public zbar
+  (package
+    (name "zbar")
+    (version "0.23")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://linuxtv.org/downloads/zbar/zbar-"
+                           version
+                           ".tar.bz2"))
+       (sha256
+        (base32
+         "0bmd93a15qpgbsq9c9j33qms18rdrgz6gbc48zi6z9w5pvrvi7z9"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:configure-flags (list "--with-gtk=auto"
+                               "--with-python=auto"
+                               (string-append "--with-dbusconfdir="
+                                              (assoc-ref %outputs "out")
+                                              "/etc")
+                               "CXXFLAGS=-std=c++11")))
+    (native-inputs
+     `(("glib" ,glib "bin")
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("gobject-introspection" ,gobject-introspection)
+       ("gtk+" ,gtk+)
+       ("imagemagick" ,imagemagick)
+       ("libjpeg" ,libjpeg-turbo)
+       ("python" ,python)
+       ("qtbase" ,qtbase)
+       ("qtx11extras" ,qtx11extras)
+       ("v4l-utils" ,v4l-utils)))
+    (synopsis "Bar code reader")
+    (description
+     "ZBar can read barcodes from various sources, such as video streams,
+image files, and raw intensity sensors.  It supports EAN-13/UPC-A, UPC-E,
+EAN-8, Code 128, Code 93, Code 39, Codabar, Interleaved 2 of 5, QR Code and SQ
+Code.  Included with the library are basic applications for decoding captured
+bar code images and using a video device (e.g. webcam) as a bar code scanner.
+For application developers, language bindings are included for C, C++ and
+Python as well as GUI widgets for GTK and Qt.")
+    (home-page "https://github.com/mchehab/zbar")
+    (license license:lgpl2.1+)))

gnu/packages/algebra.scm

@@ -43,6 +43,7 @@
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
@@ -92,6 +93,27 @@ multiplication routines such as Toom–Cook and the FFT.")
    (license license:lgpl3+)
    (home-page "http://mpfrcx.multiprecision.org/")))
 
+(define-public gf2x
+  (package
+   (name "gf2x")
+   (version "1.2")
+   (source (origin
+            (method url-fetch)
+            (uri (string-append
+                  "https://gforge.inria.fr/frs/download.php/file/36934/gf2x-"
+                  version ".tar.gz"))
+            (sha256
+             (base32
+              "0d6vh1mxskvv3bxl6byp7gxxw3zzpkldrxnyajhnl05m0gx7yhk1"))))
+   (build-system gnu-build-system)
+   (synopsis "Arithmetic of polynomials over binary finite fields")
+   (description
+    "The gf2x library provides arithmetic of polynomials over finite fields
+of characteristic 2.  It implements the multiplication, squaring and
+greatest common divisor operations.")
+   (license license:gpl3+)
+   (home-page "https://gforge.inria.fr/projects/gf2x/")))
+
 (define-public cm
   (package
    (name "cm")
@@ -122,29 +144,87 @@ line applications.")
 
 (define-public fplll
   (package
-   (name "fplll")
-   (version "4.0.4")
-   (source (origin
-            (method url-fetch)
-            (uri (string-append
-                  "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-"
-                  version ".tar.gz"))
-            (sha256 (base32
-                     "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b"))))
-   (build-system gnu-build-system)
-   (inputs `(("gmp" ,gmp)
-             ("mpfr" ,mpfr)))
-   (synopsis "Library for LLL-reduction of euclidean lattices")
-   (description
-    "fplll LLL-reduces euclidean lattices.  Since version 3, it can also
-solve the shortest vector problem.")
-   (license license:lgpl2.1+)
-   (home-page "http://perso.ens-lyon.fr/damien.stehle/fplll/")))
+    (name "fplll")
+    (version "5.2.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/fplll/fplll.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "015qmrd7nfaysbv1hbwiprz9g6hnww1y1z1xw8f43ysb7k1b5nbg"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (inputs
+     `(("gmp" ,gmp)
+       ("mpfr" ,mpfr)))
+    (home-page "https://github.com/fplll/fplll")
+    (synopsis "Library for LLL-reduction of euclidean lattices")
+    (description
+     "fplll contains implementations of several lattice algorithms.
+The implementation relies on floating-point orthogonalization, and LLL
+is central to the code, hence the name.
+
+It includes implementations of floating-point LLL reduction
+algorithms, offering different speed/guarantees ratios.  It contains
+a @emph{wrapper} choosing the estimated best sequence of variants in
+order to provide a guaranteed output as fast as possible.  In the case
+of the wrapper, the succession of variants is oblivious to the user.
+
+It includes an implementation of the BKZ reduction algorithm,
+including the BKZ-2.0 improvements (extreme enumeration
+pruning, pre-processing of blocks, early termination).  Additionally,
+Slide reduction and self dual BKZ are supported.
+
+It also includes a floating-point implementation of the
+Kannan-Fincke-Pohst algorithm that finds a shortest non-zero lattice
+vector.  For the same task, the GaussSieve algorithm is also available
+in fplll.  Finally, it contains a variant of the enumeration algorithm
+that computes a lattice vector closest to a given vector belonging to
+the real span of the lattice.")
+    (license license:lgpl2.1+)))
+
+(define-public python-fpylll
+  (package
+    (name "python-fpylll")
+    (version "0.4.1")
+    (source
+     (origin
+       ;; Pypi contains and older release, so we use a tagged release from
+       ;; Github instead.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/fplll/fpylll.git")
+             (commit (string-append version "dev"))))
+       (sha256
+        (base32
+         "01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w"))))
+    (build-system python-build-system)
+    (inputs
+     `(("fplll" ,fplll)
+       ("gmp" ,gmp)
+       ("mpfr" ,mpfr)
+       ("pari-gp" ,pari-gp)))
+    (propagated-inputs
+     `(("cysignals" ,python-cysignals)
+       ("cython" ,python-cython)
+       ("flake8" ,python-flake8)
+       ("numpy" ,python-numpy)
+       ("pytest" ,python-pytest)))
+    (home-page "https://github.com/fplll/fpylll")
+    (synopsis "Python interface for fplll")
+    (description "fpylll is a Python wrapper for fplll.")
+    (license license:gpl2+)))
 
 (define-public pari-gp
   (package
     (name "pari-gp")
-    (version "2.11.1")
+    (version "2.11.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -152,12 +232,11 @@ solve the shortest vector problem.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "1jfax92jpydjd02fwl30r6b8kfzqqd6sm4yx94gidyz9lqjb7a94"))))
+                "0fck8ssmirl8fy7s4mspgrxjs5sag76xbshqlqzkcl3kqyrk4raa"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("texlive" ,(texlive-union
-                    (list texlive-fonts-amsfonts
-                          texlive-latex-amsfonts)))))
+                    (list texlive-amsfonts)))))
     (inputs `(("gmp" ,gmp)
               ("libx11" ,libx11)
               ("perl" ,perl)
@@ -187,7 +266,7 @@ PARI is also available as a C library to allow for faster computations.")
 (define-public gp2c
   (package
    (name "gp2c")
-   (version "0.0.11pl1")
+   (version "0.0.11pl2")
    (source (origin
             (method url-fetch)
             (uri (string-append
@@ -195,7 +274,7 @@ PARI is also available as a C library to allow for faster computations.")
                   version ".tar.gz"))
             (sha256
               (base32
-                "1c6f6vmncw032kfzrfyr8bynw6yd3faxpy2285r009fmr0zxfs5s"))))
+                "0wqsf05wgkqvmmsx7jinvzdqav6rl56sr8haibgs31nzz4x9xz9g"))))
    (build-system gnu-build-system)
    (native-inputs `(("perl" ,perl)))
    (inputs `(("pari-gp" ,pari-gp)))
@@ -218,6 +297,20 @@ GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
    (license license:gpl2)
    (home-page "https://pari.math.u-bordeaux.fr/")))
 
+(define fplll-4-cmh
+  (package
+    (inherit fplll)
+    (name "fplll")
+    (version "4.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-"
+             version ".tar.gz"))
+       (sha256
+        (base32 "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b"))))))
+
 (define-public cmh
   (package
    (name "cmh")
@@ -236,7 +329,7 @@ GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
        ("mpfr" ,mpfr)
        ("mpc" ,mpc)
        ("mpfrcx" ,mpfrcx)
-       ("fplll" ,fplll)
+       ("fplll" ,fplll-4-cmh)
        ("pari-gp"  ,pari-gp)))
    (synopsis "Igusa class polynomial computations")
    (description
@@ -251,7 +344,7 @@ precision.")
 (define-public giac
   (package
     (name "giac")
-    (version "1.5.0-49")
+    (version "1.5.0-63")
     (source (origin
               (method url-fetch)
               ;; "~parisse/giac" is not used because the maintainer regularly
@@ -263,7 +356,7 @@ precision.")
                                   "source/giac_" version ".tar.gz"))
               (sha256
                (base32
-                "0f4pkand9vmqfayw18jm5qxbhcwi1405qfd7ibzh9lwzz6amkm3l"))))
+                "1jp7awyp8j8w6fhn802z8ddbq1fxhkyk9xdf0mq0mm0chpkylwqk"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)
@@ -928,7 +1021,7 @@ xtensor provides:
 (define-public gap
   (package
     (name "gap")
-    (version "4.10.0")
+    (version "4.10.2")
     (source
      (origin
        (method url-fetch)
@@ -938,8 +1031,7 @@ xtensor provides:
                            version
                            ".tar.bz2"))
        (sha256
-        (base32
-         "1dmb8v4p7j1nnf7sx8sg54b49yln36bi9acwp7w1d3a1nxj17ird"))
+        (base32 "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94"))
        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
        (snippet
         '(begin
@@ -967,20 +1059,20 @@ xtensor provides:
                    ;; Optional packages, searched for at start,
                    ;; and their depedencies.
                    "alnuth-3.1.0"
-                   "AutoDoc-2018.09.20"
                    "autpgrp-1.10"
                    "crisp-1.4.4"     ; bsd-2
-                   ; "ctbllib"       ; no explicit license, drop
+                   "ctbllib"       ; gpl3+ according to doc/chap0.txt
                    "FactInt-1.6.2"
                    "fga"
                    "irredsol-1.4"    ; bsd-2
-                   "laguna-3.9.0"
+                   "laguna-3.9.2"
                    "polenta-1.3.8"
                    "polycyclic-2.14"
                    "radiroot-2.8"
                    "resclasses-4.7.1"
                    "sophus-1.24"
-                   ; "tomlib-1.2.7"  ; no explicit license, drop
+                   "tomlib-1.2.7"  ; gpl2+, clarified in the git repository
+                                   ; and the next release
                    "utils-0.59"))))
            #t))))
     (build-system gnu-build-system)
@@ -988,7 +1080,11 @@ xtensor provides:
      `(("gmp" ,gmp)
        ("zlib" ,zlib)))
     (arguments
-     `(#:phases
+     `(#:modules ((ice-9 ftw)
+                  (srfi srfi-26)
+                  (guix build gnu-build-system)
+                  (guix build utils))
+       #:phases
        (modify-phases %standard-phases
          (add-after 'build 'build-packages
            ;; Compile all packages that have not been deleted by the
@@ -1004,19 +1100,16 @@ xtensor provides:
              (with-directory-excursion "doc"
                (invoke "./make_doc"))
              #t))
-         (replace 'check
-           (lambda _
-             ;; "make check" is expected to appear in gap-4.10.1
-             (invoke "./gap" "tst/testinstall.g")
-             #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (bin (string-append out "/bin"))
+                    (lib (string-append out "/lib"))
                     (prog (string-append bin "/gap"))
                     (prog-real (string-append bin "/.gap-real"))
                     (share (string-append out "/share/gap"))
-                    (include (string-append out "/include/gap")))
+                    (include (string-append out "/include/gap"))
+                    (include-hpc (string-append include "/hpc")))
                ;; Install only the gap binary; the gac compiler is left
                ;; for maybe later. "Wrap" it in a shell script that calls
                ;; the binary with the correct parameter.
@@ -1030,12 +1123,37 @@ xtensor provides:
                            prog-real
                            share)))
                (chmod prog #o755)
-               ;; Install the headers and the library, which are needed by
-               ;; Sage. The Makefile targets are available in gap-4.10.0,
-               ;; but planned to be removed in gap-4.10.1.
-               (invoke "make" "install-headers")
-               (invoke "make" "install-libgap")
+               ;; Install the headers, which are needed by Sage. The
+               ;; Makefile target "install-headers" was available in
+               ;; gap-4.10.0, but has been commented out in gap-4.10.1.
+               (mkdir-p include-hpc)
                (install-file "gen/config.h" include)
+               (let ((file-name-predicate-without-stat
+                       (lambda (regex)
+                         (cut (file-name-predicate regex) <> #f))))
+                 (with-directory-excursion "src"
+                   (for-each
+                     (cut install-file <> include)
+                     (scandir "."
+                              (file-name-predicate-without-stat ".*\\.h$"))))
+                 (with-directory-excursion "src/hpc"
+                   (for-each
+                     (cut install-file <> include-hpc)
+                     (scandir "."
+                              (file-name-predicate-without-stat ".*\\.h$")))))
+               ;; Install the library, which is needed by Sage. The
+               ;; Makefile target "install-libgap" was available in
+               ;; gap-4.10.0, but has been commented out in gap-4.10.1.
+               ;; Compared to the Makefile, which used libtool, the
+               ;; following approach of copying files and making symlinks
+               ;; is rather pedestrian. There is hope that some later
+               ;; version of gap reinstates and completes the install
+               ;; targets.
+               (invoke "make" "libgap.la")
+               (install-file "libgap.la" lib)
+               (install-file ".libs/libgap.so.0.0.0" lib)
+               (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so")) 
+               (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0"))
                ;; Install a certain number of files and directories to
                ;; SHARE, where the wrapped shell script expects them.
                ;; Remove information on the build directory from sysinfo.gap.
@@ -1068,3 +1186,372 @@ objects.")
     ;; means that the gpl2+ licence of GAP itself applies, but to be on the
     ;; safe side, we drop them for now.
     (license license:gpl2+)))
+
+(define-public givaro
+  (package
+    (name "givaro")
+    (version "4.1.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/linbox-team/givaro")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (propagated-inputs
+     `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'bootstrap 'setenv
+           ;; Prevent the autogen.sh script to carry out the configure
+           ;; script, which has not yet been patched to replace /bin/sh.
+           (lambda _
+             (setenv "NOCONFIGURE" "yes")
+             #t)))))
+    (synopsis "Algebraic computations with exact rings and fields")
+    (description
+     "Givaro is a C++ library implementing the basic arithmetic of various
+algebraic objects: prime fields, extension fields, finite fields, finite
+rings, polynomials, algebraic numbers, arbitrary precision integers and
+rationals (C++ wrappers over gmp), fixed precision integers.  It also
+provides data-structures and templated classes for the manipulation of
+compound objects, such as vectors, matrices and univariate polynomials.")
+    (license license:cecill-b)
+    (home-page "https://github.com/linbox-team/givaro")))
+
+(define-public fflas-ffpack
+  (package
+    (name "fflas-ffpack")
+    (version "2.4.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/linbox-team/fflas-ffpack")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("openblas" ,openblas)))
+    (propagated-inputs
+     `(("givaro" ,givaro))) ; required according to the .pc file
+    (arguments
+     `(#:configure-flags
+       (list (string-append "--with-blas-libs="
+                            (assoc-ref %build-inputs "openblas")
+                            "/lib/libopenblas.so"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'bootstrap 'setenv
+           ;; Prevent the autogen.sh script to carry out the configure
+           ;; script, which has not yet been patched to replace /bin/sh.
+           (lambda _
+             (setenv "NOCONFIGURE" "yes")
+             #t)))))
+    (synopsis "C++ library for linear algebra over finite fields")
+    (description
+     "FFLAS-FFPACK is a C++ template library for basic linear algebra
+operations over a finite field.
+FFLAS (Finite Field Linear Algebra Subprograms) provides the implementation
+of a subset of routines of the numerical BLAS; it also supports sparse
+matrix-vector products.
+FFPACK (Finite Field Linear Algebra Package) is inspired by the LAPACK
+library to provide functionalities of higher level, using the kernel
+of a BLAS.  Additionally, it provides routines specific to exact linear
+algebra, such as the row echelon form.")
+    (license license:lgpl2.1+)
+    (home-page "https://linbox-team.github.io/fflas-ffpack/")))
+
+(define-public linbox
+  (package
+    (name "linbox")
+    (version "1.6.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/linbox-team/linbox")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("fflas-ffpack" ,fflas-ffpack)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'bootstrap 'setenv
+           ;; Prevent the autogen.sh script to carry out the configure
+           ;; script, which has not yet been patched to replace /bin/sh.
+           (lambda _
+             (setenv "NOCONFIGURE" "yes")
+             #t)))))
+    (synopsis "C++ library for linear algebra over exact rings")
+    (description
+     "LinBox is a C++ template library for exact linear algebra computation
+with dense, sparse, and structured matrices over the integers and over
+finite fields.")
+    (license license:lgpl2.1+)
+    (home-page "https://linbox-team.github.io/linbox/")))
+
+(define-public m4ri
+  (package
+    (name "m4ri")
+    (version "20140914")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://bitbucket.org/malb/m4ri")
+                    (commit (string-append "release-" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("libpng" ,libpng)))
+    (synopsis "Arithmetic of dense matrices over F_2")
+    (description "M4RI is a library for fast arithmetic with dense matrices
+over F2.  The name M4RI comes from the first implemented algorithm: The
+Method of the Four Russians inversion algorithm published by Gregory Bard.
+This algorithm in turn is named after the Method of the Four Russians
+multiplication algorithm.")
+    (license license:gpl2+)
+    (home-page "https://bitbucket.org/malb/m4ri/")))
+
+(define-public symmetrica
+  (package
+    (name "symmetrica")
+    (version "2.0")
+    (source (origin
+              (method url-fetch/tarbomb)
+              (uri (let ((v (string-join (string-split version #\.) "_")))
+                     (string-append "http://www.algorithm.uni-bayreuth.de/"
+                                    "en/research/SYMMETRICA/"
+                                    "SYM" v "_tar.gz")))
+              (sha256
+               (base32
+                "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz"))
+              ;; Taken from <https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/>
+              (patches (search-patches "symmetrica-bruch.patch"
+                                       "symmetrica-int32.patch"
+                                       "symmetrica-return_values.patch"
+                                       "symmetrica-sort_sum_rename.patch"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ;no test
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-makefile
+           (lambda _
+             (substitute* "makefile"
+               (("cc -c") "gcc -c -fPIC"))
+             #t))
+         (add-after 'fix-makefile 'turn-off-banner
+           (lambda _
+             (substitute* "de.c"
+               (("(INT no_banner = )FALSE" _ pre) (string-append pre "TRUE")))
+             #t))
+         (delete 'configure)            ;no configure script
+         (replace 'install              ;no install target
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (lib (string-append out "/lib"))
+                    (inc (string-append out "/include/symmetrica"))
+                    (doc (string-append out "/share/doc/symmetrica-" ,version))
+                    (static "libsymmetrica.a"))
+               ;; Build static library.
+               (apply invoke "ar" "crs" static (find-files "." "\\.o$"))
+               (invoke "ranlib" static)
+               ;; Install static library and headers.
+               (for-each (lambda (f) (install-file f inc))
+                         (find-files "." "\\.h$"))
+               (install-file "libsymmetrica.a" lib)
+               ;; Install documentation.
+               (for-each (lambda (f) (install-file f doc))
+                         (find-files "." "\\.doc$"))
+               #t))))))
+    (home-page "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/")
+    (synopsis "Combinatoric C Library")
+    (description "Symmetrica is a library for combinatorics.  It has support
+for the representation theory of the symmetric group and related groups,
+combinatorics of tableaux, symmetric functions and polynomials, Schubert
+polynomials, and the representation theory of Hecke algebras of type A_n.")
+    (license license:public-domain)))
+
+(define-public m4rie
+  (package
+    (name "m4rie")
+    (version "20150908")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://bitbucket.org/malb/m4rie")
+                    (commit (string-append "release-" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (inputs
+     `(("m4ri" ,m4ri)))
+    (synopsis "Arithmetic of dense matrices over F_{2^e}")
+    (description "M4RI is a library for fast arithmetic with dense matrices
+over finite fields of characteristic 2.  So it extends the functionality
+of M4RI from F_2 to F_{2^e}.")
+    (license license:gpl2+)
+    (home-page "https://bitbucket.org/malb/m4rie/")))
+
+(define-public eclib
+  (package
+    (name "eclib")
+    (version "20190226")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/JohnCremona/eclib/")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1910np1xzyjzszay24xn4b81qhpsvhp5aix9vdpknplni2mq8kwb"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (inputs
+     `(("gmp" ,gmp)
+       ("ntl" ,ntl)
+       ("pari-gp" ,pari-gp)))
+    (synopsis "Ranks of elliptic curves and modular symbols")
+    (description "The eclib package includes mwrank (for 2-descent on
+elliptic curves over Q) and modular symbol code; it has been written by
+John Cremona to compute his elliptic curve database.")
+    (license license:gpl2+)
+    (home-page (string-append "http://homepages.warwick.ac.uk/staff/"
+                              "J.E.Cremona/mwrank/index.html"))))
+
+(define-public lrcalc
+  (package
+    (name "lrcalc")
+    (version "1.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://bitbucket.org/asbuch/lrcalc")
+                    (commit (string-append "lrcalc-" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"))
+              (patches (search-patches "lrcalc-includes.patch"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'fix-permission
+           (lambda _
+             (chmod "lrcalc.maple.src" #o644)
+             #t)))))
+    (synopsis "Littlewood-Richardson calculator in algebraic combinatorics")
+    (description "The Littlewood-Richardson Calculator (lrcalc) is a
+program designed to compute Littlewood-Richardson coefficients.  It computes
+single Littlewood-Richardson coefficients, products of Schur functions, or
+skew Schur functions.  In addition it computes products in the small quantum
+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/")))
+
+(define-public iml
+  (package
+    (name "iml")
+    (version "1.0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://www.cs.uwaterloo.ca/~astorjoh/iml-"
+                           version ".tar.bz2"))
+       (sha256
+        (base32
+         "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("gmp", gmp)
+       ("cblas" ,openblas))) ; or any other BLAS library; the documentation
+                             ; mentions ATLAS in particular
+    (arguments
+     `(#:configure-flags
+       (list
+        "--enable-shared"
+        (string-append "--with-gmp-include="
+                       (assoc-ref %build-inputs "gmp") "/include")
+        (string-append "--with-gmp-lib="
+                       (assoc-ref %build-inputs "gmp") "/lib")
+        "--with-cblas=-lopenblas"
+        (string-append "--with-cblas-include="
+                       (assoc-ref %build-inputs "cblas") "/include")
+        (string-append "--with-cblas-lib="
+                       (assoc-ref %build-inputs "cblas") "/lib"))))
+    (home-page "https://cs.uwaterloo.ca/~astorjoh/iml.html")
+    (synopsis
+     "Solver for systems of linear equations over the integers")
+    (description
+     "IML is a C library implementing algorithms for computing exact
+solutions to dense systems of linear equations over the integers.
+Currently, IML provides the following functionality:
+
+@itemize
+@item Nonsingular rational system solving:
+compute the unique rational solution X to the system AX=B, where A and B
+are integer matrices, A nonsingular.
+@item Compute the right nullspace or kernel of an integer matrix.
+@item Certified linear system solving:
+compute a minimal denominator solution x to a system Ax=b, where b is an
+integer vector and A is an integer matrix with arbitrary shape and
+rank profile.
+@end itemize
+
+In addition, IML provides some low level routines for a variety of mod p
+matrix operations: computing the row-echelon form, determinant, rank
+profile, and inverse of a mod p matrix. These mod p routines are not
+general purpose; they require that p satisfy some preconditions based on
+the dimension of the input matrix (usually p should be prime and should be
+no more than about 20 bits long).")
+    (license license:bsd-3)))

gnu/packages/android.scm

@@ -8,6 +8,7 @@
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -90,6 +91,17 @@ use their packages mostly unmodified in our Android NDK build system.")
 (define-public android-googletest
   (package (inherit googletest)
     (name "android-googletest")
+    (version "1.8.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/google/googletest.git")
+              (commit (string-append "release-" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0bjlljmbf8glnd9qjabx73w6pd7ibv43yiyngqvmvgxsabzr8399"))))
     (arguments
      `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")
        #:phases

gnu/packages/animation.scm

@@ -264,7 +264,7 @@ waveform until they line up with the proper sounds.")
 (define-public pencil2d
   (package
     (name "pencil2d")
-    (version "0.6.3")
+    (version "0.6.4")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -273,7 +273,7 @@ waveform until they line up with the proper sounds.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "097xwvhw7vl9pgknhb40zs6adf7mb1xxfc73h4kiqgp6z59prjl3"))))
+                "0zi8x0w8n817zds2lyw9l8j33c03kiybkrcyy3s5fg66mchmrwnr"))))
     (build-system gnu-build-system)
     (inputs
      `(("qtbase" ,qtbase)

gnu/packages/apl.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,25 +25,27 @@
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages maths)
+  #:use-module (gnu packages pcre)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages sqlite))
 
 (define-public apl
   (package
     (name "apl")
-    (version "1.7")
+    (version "1.8")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "mirror://gnu/apl/apl-" version ".tar.gz"))
       (sha256
        (base32
-        "07xq8ddlmz8psvsmwr23gar108ri0lwmw0n6kpxcv8ypas1f5xlg"))))
+        "1jxvv2h3y1am1fw6r5sn3say1n0dj8shmscbybl0qhqdia2lqkql"))))
     (build-system gnu-build-system)
     (home-page "https://www.gnu.org/software/apl/")
     (inputs
      `(("gettext" ,gettext-minimal)
        ("lapack" ,lapack)
+       ("pcre" ,pcre2)
        ("sqlite" ,sqlite)
        ("readline" ,readline)))
     (arguments

gnu/packages/aspell.scm

@@ -6,6 +6,7 @@
 ;;; Copyright © 2016 Christopher Andersson <christopher@8bits.nu>
 ;;; Copyright © 2016 Theodoros Foradis <theodoros@foradis.org>
 ;;; Copyright © 2016, 2017, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -31,7 +32,8 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages perl))
+  #:use-module (gnu packages perl)
+  #:use-module (ice-9 match))
 
 (define-public aspell
   (package
@@ -101,7 +103,14 @@ dictionaries, including personal ones.")
 (define* (aspell-dictionary dict-name full-name
                             #:key version sha256 (prefix "aspell6-"))
   (package
-    (name (string-append "aspell-dict-" dict-name))
+    (name (string-append
+           "aspell-dict-"
+           ;; Downcase and replace underscore in package names
+           ;; to follow Guix naming conventions.
+           (string-map (match-lambda
+                         (#\_ #\-)
+                         (chr chr))
+           (string-downcase dict-name))))
     (version version)
     (source (origin
               (method url-fetch)
@@ -131,6 +140,22 @@ dictionaries, including personal ones.")
     (home-page "http://aspell.net/")))
 
 
+(define-public aspell-dict-ar
+  (aspell-dictionary "ar" "Arabic"
+                     #:version "1.2-0"
+		     #:prefix "aspell6-"
+                     #:sha256
+                     (base32
+                      "1avw40bp8yi5bnkq64ihm2rldgw34lk89yz281q9bmndh95a47h4")))
+
+(define-public aspell-dict-be
+  (aspell-dictionary "be" "Belarusian"
+                     #:version "0.01"
+                     #:prefix "aspell5-"
+                     #:sha256
+                     (base32
+                      "1svls9p7rsfi3hs0afh0cssj006qb4v1ik2yzqgj8hm10c6as2sm")))
+
 (define-public aspell-dict-ca
   (aspell-dictionary "ca" "Catalan"
                      #:version "2.1.5-1"
@@ -145,6 +170,14 @@ dictionaries, including personal ones.")
                      (base32
                       "01p92qj66cqb346gk7hjfynaap5sbcn85xz07kjfdq623ghr8v5s")))
 
+(define-public aspell-dict-da
+  (aspell-dictionary "da" "Danish"
+                     #:version "1.4.42-1"
+                     #:prefix "aspell5-"
+                     #:sha256
+                     (base32
+                      "1hfkmiyhgrx5lgrb2mffjbdn1hivrm73wcg7x0iid74p2yb0fjpp")))
+
 (define-public aspell-dict-el
   (aspell-dictionary "el" "Greek"
                      #:version "0.08-0"
@@ -174,6 +207,14 @@ dictionaries, including personal ones.")
                      (base32
                       "1k5g328ac1hdpp6fsg57d8md6i0aqcwlszp3gbmp5706wyhpydmd")))
 
+(define-public aspell-dict-fi
+  (aspell-dictionary "fi" "Finnish"
+                     #:version "0.7-0"
+                     #:prefix "aspell6-"
+                     #:sha256
+                     (base32
+                      "07d5s08ba4dd89cmwy9icc01i6fjdykxlb9ravmhdrhi8mxz1mzq")))
+
 (define-public aspell-dict-fr
   (aspell-dictionary "fr" "French"
                      #:version "0.50-3"
@@ -196,6 +237,14 @@ dictionaries, including personal ones.")
                      (base32
                       "13bhbghx5b8g0119g3wxd4n8mlf707y41vlf59irxjj0kynankfn")))
 
+(define-public aspell-dict-hi
+  (aspell-dictionary "hi" "Hindi"
+                     #:version "0.02-0"
+                     #:prefix "aspell6-"
+                     #:sha256
+                     (base32
+                      "0drs374qz4419zx1lf2k281ydxf2750jk5ailafj1x0ncz27h1ys")))
+
 (define-public aspell-dict-it
   (let ((version "2.4-20070901-0")
         (sha256
@@ -217,6 +266,13 @@ dictionaries, including personal ones.")
        (home-page
         "http://linguistico.sourceforge.net/pages/dizionario_italiano.html"))))
 
+(define-public aspell-dict-mi
+  (aspell-dictionary "mi" "Maori"
+                     #:version "0.50-0"
+                     #:sha256
+                     (base32
+                      "12bxplpd348yx8d2q8qvahi9dlp7qf28qmanzhziwc7np8rixvmy")))
+
 (define-public aspell-dict-nl
   (aspell-dictionary "nl" "Dutch"
                      #:version "0.50-2"
@@ -225,14 +281,29 @@ dictionaries, including personal ones.")
                      (base32
                       "0ffb87yjsh211hllpc4b9khqqrblial4pzi1h9r3v465z1yhn3j4")))
 
+(define-public aspell-dict-nn
+  (aspell-dictionary "nn" "Norwegian Nynorsk"
+                     #:version "0.50.1-1"
+                     #:sha256
+                     (base32
+                      "0w2k5l5rbqpliripgqwiqixz5ghnjf7i9ggbrc4ly4vy1ia10rmc")))
+
 (define-public aspell-dict-pt-br
-  (aspell-dictionary "pt-br" "Brazilian Portuguese"
+  (aspell-dictionary "pt_BR" "Brazilian Portuguese"
                      #:version "20090702-0"
                      #:prefix "aspell6-"
                      #:sha256
                      (base32
                       "1y09lx9zf2rnp55r16b2vgj953l3538z1vaqgflg9mdvm555bz3p")))
 
+(define-public aspell-dict-pt-pt
+  (aspell-dictionary "pt_PT" "Portuguese"
+                     #:version "20070510-0"
+                     #:prefix "aspell6-"
+                     #:sha256
+                     (base32
+                      "1mnr994cwlag6shy8865ky99lymysiln07mbldcncahg90dagdxq")))
+
 (define-public aspell-dict-ru
   (aspell-dictionary "ru" "Russian"
                      #:version "0.99f7-1"
@@ -248,6 +319,13 @@ dictionaries, including personal ones.")
                      (base32
                       "02jwkjhr32kvyibnyzgx3smbnm576jwdzg3avdf6zxwckhy5fw4v")))
 
+(define-public aspell-dict-uk
+  (aspell-dictionary "uk" "Ukrainian"
+                     #:version "1.4.0-0"
+                     #:sha256
+                     (base32
+                      "137i4njvnslab6l4s291s11xijr5jsy75lbdph32f9y183lagy9m")))
+
 
 ;;;
 ;;; Hunspell packages made from the Aspell word lists.

gnu/packages/assembly.scm

@@ -5,6 +5,7 @@
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Guy Fleury Iteriteka <hoonandon@gmail.com>
+;;; Copyright © 2019 Andy Tai <atai@atai.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -24,11 +25,20 @@
 (define-module (gnu packages assembly)
   #:use-module (guix build-system gnu)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (gnu packages)
+  #:use-module (gnu packages admin)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages bison)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages flex)
+  #:use-module (gnu packages gettext)
+  #:use-module (gnu packages man)
   #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages python)
   #:use-module (gnu packages xml)
@@ -202,3 +212,36 @@ assembler, a C compiler and a linker.  The assembler uses Intel syntax
     (home-page "https://github.com/jbruchon/dev86")
     (supported-systems '("i686-linux" "x86_64-linux"))
     (license license:gpl2+)))
+
+(define-public libjit
+  (let ((commit "554c9f5c750daa6e13a6a5cd416873c81c7b8226"))
+    (package
+      (name "libjit")
+      (version "0.1.4")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://git.savannah.gnu.org/r/libjit.git")
+                      (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
+                (sha256
+                 (base32
+                  "0p6wklslkkp3s4aisj3w5a53bagqn5fy4m6088ppd4fcfxgqkrcd"))))
+      (build-system gnu-build-system)
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("bison" ,bison)
+         ("flex" ,flex)
+         ("help2man" ,help2man)
+         ("gettext" ,gettext-minimal)
+         ("libtool" ,libtool)
+         ("makeinfo" ,texinfo)
+         ("pkg-config" ,pkg-config)))
+      (home-page "https://www.gnu.org/software/libjit/")
+      (synopsis "Just-In-Time compilation library")
+      (description
+       "GNU libjit is a library that provides generic Just-In-Time compiler
+functionality independent of any particular bytecode, language, or
+runtime")
+      (license license:lgpl2.1+))))

gnu/packages/astronomy.scm

@@ -1,7 +1,8 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 John Darrington <jmd@gnu.org>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2019 by Amar Singh <nly@disroot.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -22,30 +23,40 @@
   #:use-module (guix packages)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix utils)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages image)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gettext)
+  #:use-module (gnu packages version-control)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages xiph)
+  #:use-module (gnu packages pretty-print)
+  #:use-module (gnu packages algebra)
+  #:use-module (gnu packages lua)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages qt)
+  #:use-module (gnu packages gtk)
+  #:use-module (gnu packages gnome)
   #:use-module (gnu packages maths)
   #:use-module (guix build-system cmake)
-  #:use-module (guix build-system gnu))
+  #:use-module (guix build-system gnu)
+  #:use-module (srfi srfi-1))
 
 (define-public cfitsio
   (package
     (name "cfitsio")
-    (version "3.450")
+    (version "3.47")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
              "http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/"
-             name (string-replace-substring version "." "") ".tar.gz"))
+             name "-" version ".tar.gz"))
        (sha256
-        (base32 "0bmrkw6w65zb0k3mszaaqy1f4zjm2hl7njww74nb5v38wvdi4q5z"))))
+        (base32 "1vzlxnrjckz78p2wf148v2z3krkwnykfqvlj42sz3q711vqid1a1"))))
     (build-system gnu-build-system)
     ;; XXX Building with curl currently breaks wcslib.  It doesn't use
     ;; pkg-config and hence won't link with -lcurl.
@@ -70,20 +81,25 @@ in FITS files.")
 (define-public wcslib
   (package
     (name "wcslib")
-    (version "5.20")
+    (version "6.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
-             "ftp://ftp.atnf.csiro.au/pub/software/wcslib/" name "-" version
+             "ftp://ftp.atnf.csiro.au/pub/software/wcslib/wcslib" version
              ".tar.bz2"))
        (sha256
-        (base32 "1c8g9kv4dxrnawnqi4spi2p10s2xs7x75pdfxhbqxgcc97dkgh0b"))))
+        (base32 "01fqckazhbfqqhyr0wd9vcks1m2afmsh83l981alxg2r54jgwkdv"))))
     (inputs
      `(("cfitsio" ,cfitsio)))
     (build-system gnu-build-system)
     (arguments
-     `(#:phases
+     `(#:configure-flags
+       (list (string-append "--with-cfitsiolib="
+                            (assoc-ref %build-inputs "cfitsio") "/lib")
+             (string-append "--with-cfitsioinc="
+                            (assoc-ref %build-inputs "cfitsio") "/include"))
+       #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'patch-/bin/sh
            (lambda _
@@ -133,15 +149,15 @@ programs for the manipulation and analysis of astronomical data.")
 (define-public stellarium
   (package
     (name "stellarium")
-    (version "0.19.0")
-    (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/Stellarium/" name
-                                 "/releases/download/v" version
-                                 "/" name "-" version ".tar.gz"))
-             (sha256
-              (base32
-               "1mjjqcpgm5a1022x0mpqj3v6qkvpm9wqm1hqyg0mlypc5681va8a"))))
+    (version "0.19.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/Stellarium/stellarium"
+                           "/releases/download/v" version
+                           "/stellarium-" version ".tar.gz"))
+       (sha256
+        (base32 "0s7v5iyhah258k83kvy2a91a3mdf34r150lcar4mmdsrrcmas98g"))))
     (build-system cmake-build-system)
     (inputs
      `(("qtbase" ,qtbase)
@@ -151,9 +167,9 @@ programs for the manipulation and analysis of astronomical data.")
        ("qtserialport" ,qtserialport)
        ("zlib" ,zlib)))
     (native-inputs
-     `(("gettext" ,gettext-minimal) ; xgettext is used at compile time
-       ("perl" ,perl) ; For pod2man
-       ("qtbase" ,qtbase) ; Qt MOC is needed at compile time
+     `(("gettext" ,gettext-minimal)     ; xgettext is used at compile time
+       ("perl" ,perl)                   ; For pod2man
+       ("qtbase" ,qtbase)               ; Qt MOC is needed at compile time
        ("qttools" ,qttools)))
     (arguments
      `(#:test-target "test"
@@ -176,3 +192,100 @@ programs for the manipulation and analysis of astronomical data.")
 can be used to control telescopes over a serial port for tracking celestial
 objects.")
     (license license:gpl2+)))
+
+(define-public celestia
+  (let ((commit "9dbdf29c4ac3d20afb2d9a80d3dff241ecf81dce"))
+    (package
+      (name "celestia")
+      (version (git-version "1.6.1" "815" commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/celestiaproject/celestia")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "00xibg87l1arzifakgj7s828x9pszcgx7x7ij88a561ig49ryh78"))))
+      (build-system cmake-build-system)
+      (native-inputs
+       `(("perl" ,perl)
+         ("libgit2" ,libgit2)
+         ("pkg-config" ,pkg-config)
+         ("libtool" ,libtool)
+         ("gettext" ,gettext-minimal)))
+      (inputs
+       `(("glu" ,glu)
+         ("glew" ,glew)
+         ("libtheora" ,libtheora)
+         ("libjpeg" ,libjpeg)
+         ("libpng" ,libpng)
+         ;; maybe required?
+         ("mesa" ,mesa)
+         ;; optional: fmtlib, Eigen3;
+         ("fmt" ,fmt)
+         ("eigen" ,eigen)
+         ;; glut: for glut interface
+         ("freeglut" ,freeglut)))
+      (propagated-inputs
+       `(("lua" ,lua)))
+      (arguments
+       `(#:configure-flags '("-DENABLE_GLUT=ON" "-DENABLE_QT=OFF")
+         #:tests? #f))                            ;no tests
+      (home-page "https://celestia.space/")
+      (synopsis "Real-time 3D visualization of space")
+      (description
+       "This simulation program lets you explore our universe in three
+dimensions.  Celestia simulates many different types of celestial objects.
+From planets and moons to star clusters and galaxies, you can visit every
+object in the expandable database and view it from any point in space and
+time.  The position and movement of solar system objects is calculated
+accurately in real time at any rate desired.")
+      (license license:gpl2+))))
+
+(define-public celestia-gtk
+  (package
+    (inherit celestia)
+    (name "celestia-gtk")
+    (inputs
+     (append (alist-delete "freeglut" (package-inputs celestia))
+             `(("gtk2" ,gtk+-2)
+               ("gtkglext" ,gtkglext))))
+    (arguments
+     `(#:configure-flags '("-DENABLE_GTK=ON" "-DENABLE_QT=OFF")
+       #:tests? #f))))
+
+(define-public libnova
+  (package
+    (name "libnova")
+    (version "0.16")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://git.code.sf.net/p/libnova/libnova.git")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32
+          "0icwylwkixihzni0kgl0j8dx3qhqvym6zv2hkw2dy6v9zvysrb1b"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-git-version
+           (lambda _
+             (substitute* "./git-version-gen"
+               (("/bin/sh") (which "sh")))
+             #t)))))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (synopsis "Celestial mechanics, astrometry and astrodynamics library")
+    (description "Libnova is a general purpose, double precision, Celestial
+Mechanics, Astrometry and Astrodynamics library.")
+    (home-page "http://libnova.sourceforge.net/")
+    (license (list license:lgpl2.0+
+                   license:gpl2+)))) ; examples/transforms.c & lntest/*.c
+

gnu/packages/audio.scm

@@ -21,6 +21,7 @@
 ;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
 ;;; Copyright © 2019 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2019 Rutger Helling <rhelling@mykolab.com>
+;;; Copyright © 2019 Arun Isaac <arunisaac@systemreboot.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -174,14 +175,14 @@ Filter) modules follow the convention of 1V / Octave.")
         "--enable-jack"
         "--enable-sndfile"
         "--enable-samplerate"
-        ;; TODO: enable compilation with avcodec once available.
-        "--disable-avcodec")
+        "--enable-avcodec")
        #:python ,python-2))
     (inputs
      `(("jack" ,jack-1)
        ("libsndfile" ,libsndfile)
        ("libsamplerate" ,libsamplerate)
-       ("fftwf" ,fftwf)))
+       ("fftwf" ,fftwf)
+       ("ffmpeg" ,ffmpeg))) ; for libavcodec
     (native-inputs
      `(("pkg-config" ,pkg-config)))
     (home-page "https://aubio.org/")
@@ -321,7 +322,7 @@ engineers, musicians, soundtrack editors and composers.")
 (define-public audacity
   (package
     (name "audacity")
-    (version "2.2.2")
+    (version "2.3.2")
     (source
      (origin
        (method git-fetch)
@@ -331,7 +332,7 @@ engineers, musicians, soundtrack editors and composers.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "10maxmjxbmjybj7n4m7a9bbm7g8xxw8f8vbsf7c9ih5j2gr15ihs"))
+         "08w96124vv8k4myd4vifq73ningq6404x889wvg2sk016kc4dfv1"))
        (patches (search-patches "audacity-build-with-system-portaudio.patch"))
        (modules '((guix build utils)))
        (snippet
@@ -2120,14 +2121,14 @@ different audio devices such as ALSA or PulseAudio.")
 (define-public qjackctl
   (package
     (name "qjackctl")
-    (version "0.5.7")
+    (version "0.5.9")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/qjackctl/qjackctl/"
                                   version "/qjackctl-" version ".tar.gz"))
               (sha256
                (base32
-                "1g6a5j74p45yisl28bw4fcc9nr6b710ikk459p4mp6djh9gs8v95"))))
+                "1saywsda9m124rmjp7i3n0llryaliabjxhqhvqr6dm983qy7pypk"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f))                    ; no check target
@@ -2428,17 +2429,17 @@ the Turtle syntax.")
 (define-public suil
   (package
     (name "suil")
-    (version "0.10.2")
+    (version "0.10.4")
     (source (origin
-             (method url-fetch)
-             (uri (string-append "https://download.drobilla.net/suil-"
-                                 version ".tar.bz2"))
-             (sha256
-              (base32
-               "00d43m0nai63ajb7rkm9v084jcih206y17ib3160zcvzc885ji4z"))))
+              (method url-fetch)
+              (uri (string-append "https://download.drobilla.net/suil-"
+                                  version ".tar.bz2"))
+              (sha256
+               (base32
+                "0ay7hl6nr6ip1nn9k2m8ri3b52b6sx9mhixmcy4fy3kr2a88ksd1"))))
     (build-system waf-build-system)
     (arguments
-     `(#:tests? #f        ; no check target
+     `(#:tests? #f                      ; no check target
        #:configure-flags
        '("CXXFLAGS=-std=gnu++11")))
     (inputs
@@ -2869,19 +2870,17 @@ interface.")
 (define-public qsynth
   (package
     (name "qsynth")
-    (version "0.5.6")
+    (version "0.5.7")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/qsynth/qsynth/" version
                            "/qsynth-" version ".tar.gz"))
        (sha256
-        (base32 "0h4hhja8qbyzd6v24flw9wr4mwl03nplryx1gyrppn7sg13l1sx6"))))
+        (base32 "18im4w8agj60nkppwbkxqnhpp13z5li3w30kklv4lgs20rvgbvl6"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f                      ; no "check" phase
-       #:configure-flags
-       '("CXXFLAGS=-std=gnu++11")))
+     `(#:tests? #f))                    ; no "check" phase
     (native-inputs
      `(("qttools" ,qttools)
        ("pkg-config" ,pkg-config)))
@@ -2889,7 +2888,7 @@ interface.")
      `(("fluidsynth" ,fluidsynth)
        ("qtbase" ,qtbase)
        ("qtx11extras" ,qtx11extras)))
-    (home-page "http://qsynth.sourceforge.net")
+    (home-page "https://qsynth.sourceforge.io")
     (synopsis "Graphical user interface for FluidSynth")
     (description
      "Qsynth is a GUI front-end application for the FluidSynth SoundFont
@@ -3383,14 +3382,14 @@ on the ALSA software PCM plugin.")
 (define-public snd
   (package
     (name "snd")
-    (version "19.3")
+    (version "19.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "ftp://ccrma-ftp.stanford.edu/pub/Lisp/"
                                   "snd-" version ".tar.gz"))
               (sha256
                (base32
-                "16j3fqyw361wdsr1076f0p3va2y7wdzq1lvr4ijz1ajmbxdlc723"))))
+                "0sk6iyykwi2mm3f1g4r0iqbsrwk3zmyagp6jjqkh8njbq42cjr1y"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      `(#:tests? #f                      ; no tests
@@ -3568,7 +3567,7 @@ representations.")
     (arguments
      `(#:configure-flags
        (list (string-append "PREFIX=" %output)
-             (string-append "FONT_DIR=" %output "/usr/share/consolefonts"))
+             (string-append "FONT_DIR=" %output "/share/consolefonts"))
        #:make-flags
        (let ((lib (string-append %output "/lib")))
          (list (string-append "cava_LDFLAGS = -L" lib " -Wl,-rpath " lib)))
@@ -3701,7 +3700,7 @@ library.")
 (define-public faudio
   (package
     (name "faudio")
-    (version "19.05")
+    (version "19.08")
     (source
      (origin
        (method git-fetch)
@@ -3710,7 +3709,7 @@ library.")
              (commit version)))
        (file-name (string-append name "-" version "-checkout"))
        (sha256
-        (base32 "1dja2ykixk1ycqda116cg9fy4qg364dqj88amfln0r9pnsj2kbxk"))))
+        (base32 "1v13kfhyr46241vb6a4dcb4gw5f149525sprwa9cj4rv6wlcqgm5"))))
     (arguments
      '(#:tests? #f                      ; No tests.
        #:configure-flags '("-DFFMPEG=ON")))
@@ -3723,3 +3722,65 @@ library.")
     (description "FAudio is an XAudio reimplementation that focuses solely on
 developing fully accurate DirectX Audio runtime libraries.")
     (license license:zlib)))
+
+(define-public gnaural
+  (package
+    (name "gnaural")
+    (version "20110606")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/gnaural/Gnaural/gnaural_"
+                           version ".tar.xz"))
+       (sha256
+        (base32
+         "1gq519c0imsh57zklyi0f8h64l3ai48lh672c834470z8c6kvbfi"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("alsa-lib" ,alsa-lib)
+       ("gtk+" ,gtk+-2)
+       ("libsndfile" ,libsndfile)
+       ("portaudio" ,portaudio)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://gnaural.sourceforge.net/")
+    (synopsis "Binaural beat synthesizer")
+    (description "Gnaural is a programmable auditory binaural beat synthesizer
+intended to be used for brainwave entrainment.  Gnaural supports creation of
+binaural beat tracks of different frequencies and exporting of tracks into
+different audio formats.  Gnaural can also be linked over the internet with
+other Gnaural instances, allowing synchronous sessions between many users.")
+    (license license:gpl2+)))
+
+(define-public darkice
+  (package
+    (name "darkice")
+    (version "1.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/darkice/darkice/"
+                                  version "/darkice-" version ".tar.gz"))
+              (sha256
+               (base32 "1rlxds7ssq7nk2in4s46xws7xy9ylxsqgcz85hxjgh17lsm0y39c"))
+              (patches
+               (search-patches "darkice-workaround-fpermissive-error.patch"))))
+    (build-system gnu-build-system)
+    (native-inputs `(("pkg-config" ,pkg-config)))
+    (inputs `(("lame" ,lame)
+              ("libvorbis" ,libvorbis)
+              ("opus" ,opus)
+              ("twolame" ,twolame)
+              ("alsa-lib" ,alsa-lib)
+              ("pulseaudio" ,pulseaudio)
+              ("jack" ,jack-1)
+              ("libsamplerate" ,libsamplerate)))
+    (arguments
+     `(#:configure-flags
+       (list (string-append "--with-lame-prefix="
+                            (assoc-ref %build-inputs "lame")))))
+    (home-page "http://www.darkice.org/")
+    (synopsis "Live audio streamer")
+    (description "DarkIce is a live audio streamer.  It takes audio input from
+a sound card, encodes it into Ogg Vorbis and/or mp3, and sends the audio
+stream to one or more IceCast and/or ShoutCast servers.")
+    (license license:gpl3+)))

gnu/packages/backup.scm

@@ -73,7 +73,7 @@
 (define-public duplicity
   (package
     (name "duplicity")
-    (version "0.7.18.2")
+    (version "0.7.19")
     (source
      (origin
       (method url-fetch)
@@ -82,7 +82,7 @@
                           "-series/" version "/+download/duplicity-"
                           version ".tar.gz"))
       (sha256
-       (base32 "0j37dgyji36hvb5dbzlmh5rj83jwhni02yq16g6rd3hj8f7qhdn2"))))
+       (base32 "0ag9dknslxlasslwfjhqgcqbkb1mvzzx93ry7lch2lfzcdd91am6"))))
     (build-system python-build-system)
     (native-inputs
      `(("util-linux" ,util-linux)       ; setsid command, for the tests
@@ -185,7 +185,8 @@ can even repair them.")
      `(#:configure-flags
        `(,(string-append "--sbindir=" (assoc-ref %outputs "out") "/bin"))
        #:tests? #f))
-    (home-page "http://archive.miek.nl/projects/hdup/index.html")
+    (home-page (string-append "http://web.archive.org/web/20150925223424/"
+                              "http://archive.miek.nl/projects/hdup/index.html"))
     (synopsis "Simple incremental backup tool")
     (description
      "Hdup2 is a backup utility, its aim is to make backup really simple.  The
@@ -511,14 +512,13 @@ detection, and lossless compression.")
 (define-public borg
   (package
     (name "borg")
-    (version "1.1.9")
+    (version "1.1.10")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "borgbackup" version))
        (sha256
-        (base32
-         "0x95nhv4h34m8cxycbwc4xdz350saaxlgh727b23bgn4ci7gh3vx"))
+        (base32 "1pp70p4n5kamvcbl4d8021ggrxhyykmg9isjg4yd3wags8b19d7g"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -540,7 +540,12 @@ detection, and lossless compression.")
            ;; Remove bundled shared libraries.
            (with-directory-excursion "src/borg/algorithms"
              (for-each delete-file-recursively
-                       (list "blake2" "lz4" "zstd")))
+                       (list "blake2" "lz4" "msgpack" "zstd")))
+           ;; Purge some msgpack references from setup.py or the resulting
+           ;; sources will be unbuildable.
+           (substitute* "setup.py"
+             ((".*Extension\\('borg\\.algorithms\\.msgpack\\..*") "")
+             (("msgpack_packer_source, msgpack_unpacker_source") ""))
            #t))))
     (build-system python-build-system)
     (arguments
@@ -564,6 +569,12 @@ detection, and lossless compression.")
                ;; HOME=/homeless-shelter.
                (setenv "HOME" "/tmp")
                #t)))
+         (add-after 'unpack 'use-system-msgpack
+           (lambda _
+             (substitute* "src/borg/helpers.py"
+               (("prefer_system_msgpack = False")
+                "prefer_system_msgpack = True"))
+             #t))
          ;; The tests need to be run after Borg is installed.
          (delete 'check)
          (add-after 'install 'check
@@ -616,7 +627,7 @@ detection, and lossless compression.")
        ;; transitional package for now:
        ;; <https://bugs.gnu.org/30662>
        ("python-msgpack" ,python-msgpack-transitional)
-       ("zstd" ,zstd)))
+       ("zstd" ,zstd "lib")))
     (synopsis "Deduplicated, encrypted, authenticated and compressed backups")
     (description "Borg is a deduplicating backup program.  Optionally, it
 supports compression and authenticated encryption.  The main goal of Borg is to
@@ -674,14 +685,14 @@ changes are stored.")
 (define-public wimlib
   (package
     (name "wimlib")
-    (version "1.13.0")
+    (version "1.13.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://wimlib.net/downloads/"
                                   "wimlib-" version ".tar.gz"))
               (sha256
                (base32
-                "02wpsxjlw9vysj6x6q7kmvbcdkpvdzw201mmj5x0q670mapjrnai"))))
+                "0pxgrpr3dr81rcf2jh71aiiq3v4anc5sj1nld18f2vhvbijbrx27"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -872,7 +883,7 @@ is like a time machine for your data. ")
 (define-public restic
   (package
     (name "restic")
-    (version "0.9.4")
+    (version "0.9.5")
     ;; TODO Try packaging the bundled / vendored dependencies in the 'vendor/'
     ;; directory.
     (source (origin
@@ -883,7 +894,7 @@ is like a time machine for your data. ")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "13ksprq1ia86px8x4lqrmx0l6y9rb1ppg8pnp7lcx0zxnq7skp67"))))
+                "0afl3dv7gzwdc9klikk3fsb57d0px2fwihb0xxb7zq7d8vlhh8p2"))))
     (build-system go-build-system)
     (arguments
      `(#:import-path "github.com/restic/restic"

gnu/packages/base.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2019 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org>
 ;;; Copyright © 2014, 2015, 2016, 2018 Mark H Weaver <mhw@netris.org>
@@ -1009,7 +1009,7 @@ with the Linux kernel.")
                   (("/bin/pwd") "pwd"))
                 #t))))))))
 
-(define (make-gcc-libc base-gcc libc)
+(define-public (make-gcc-libc base-gcc libc)
   "Return a GCC that targets LIBC."
   (package (inherit base-gcc)
            (name (string-append (package-name base-gcc) "-"
@@ -1050,12 +1050,47 @@ to the @code{share/locale} sub-directory of this package.")
      (let ((args `(#:tests? #f #:strip-binaries? #f
                    ,@(package-arguments glibc))))
        (substitute-keyword-arguments args
+         ((#:modules modules '((guix build utils)
+                               (guix build gnu-build-system)))
+          `((srfi srfi-11)
+            (gnu build locale)
+            ,@modules))
+         ((#:imported-modules modules '())
+          `((gnu build locale)
+            ,@%gnu-build-system-modules))
          ((#:phases phases)
           `(modify-phases ,phases
              (replace 'build
                (lambda _
                  (invoke "make" "localedata/install-locales"
                          "-j" (number->string (parallel-job-count)))))
+             (add-after 'build 'symlink-normalized-codesets
+               (lambda* (#:key outputs #:allow-other-keys)
+                 ;; The above phase does not install locales with names using
+                 ;; the "normalized codeset."  Thus, create symlinks like:
+                 ;;   en_US.utf8 -> en_US.UTF-8
+                 (define (locale-directory? file stat)
+                   (and (file-is-directory? file)
+                        (string-index (basename file) #\_)
+                        (string-rindex (basename file) #\.)))
+
+                 (let* ((out (assoc-ref outputs "out"))
+                        (locales (find-files out locale-directory?
+                                             #:directories? #t)))
+                   (for-each (lambda (directory)
+                               (let*-values (((base)
+                                              (basename directory))
+                                             ((name codeset)
+                                              (locale->name+codeset base))
+                                             ((normalized)
+                                              (normalize-codeset codeset)))
+                                 (unless (string=? codeset normalized)
+                                   (symlink base
+                                            (string-append (dirname directory)
+                                                           "/" name "."
+                                                           normalized)))))
+                             locales)
+                   #t)))
              (delete 'install)
              (delete 'move-static-libs)))
          ((#:configure-flags flags)
@@ -1180,15 +1215,15 @@ command.")
 (define-public tzdata
   (package
     (name "tzdata")
-    (version "2019a")
+    (version "2019b")
     (source (origin
              (method url-fetch)
              (uri (string-append
-                   "https://www.iana.org/time-zones/repository/releases/tzdata"
+                   "https://data.iana.org/time-zones/releases/tzdata"
                    version ".tar.gz"))
              (sha256
               (base32
-               "0wlpqm4asvi0waaz24xj20iq40gqfypmb4nldjhkfgm09bgnsdlh"))))
+               "0r0clnlslwm15m1c61dinf1fi9ffgl6aipng7i7yryfwj0n0kn85"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f
@@ -1234,11 +1269,11 @@ command.")
     (inputs `(("tzcode" ,(origin
                           (method url-fetch)
                           (uri (string-append
-                                "http://www.iana.org/time-zones/repository/releases/tzcode"
+                                "https://data.iana.org/time-zones/releases/tzcode"
                                 version ".tar.gz"))
                           (sha256
                            (base32
-                            "1x9z8fpgnhzlsnps0hamb54ymaskjab7ys9m4i4gpk9hpiig2fc7"))))))
+                            "0vbmswvv3li25s31shyllq5v24449lxnrki9hr043nipjd09sirf"))))))
     (home-page "https://www.iana.org/time-zones")
     (synopsis "Database of current and historical time zones")
     (description "The Time Zone Database (often called tz or zoneinfo)
@@ -1261,7 +1296,7 @@ and daylight-saving rules.")
      (source (origin
               (method url-fetch)
               (uri (string-append
-                    "https://www.iana.org/time-zones/repository/releases/tzdata"
+                    "https://data.iana.org/time-zones/releases/tzdata"
                     version ".tar.gz"))
               (sha256
                (base32
@@ -1270,7 +1305,7 @@ and daylight-saving rules.")
        `(("tzcode" ,(origin
                      (method url-fetch)
                      (uri (string-append
-                           "http://www.iana.org/time-zones/repository/releases/tzcode"
+                           "http://data.iana.org/time-zones/releases/tzcode"
                            version ".tar.gz"))
                      (sha256
                       (base32

gnu/packages/bash.scm

@@ -4,6 +4,7 @@
 ;;; Copyright © 2015, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -291,13 +292,16 @@ without modification.")
      `(#:phases (modify-phases %standard-phases
                   (add-after
                    'install 'remove-redundant-completions
-                   (lambda* (#:key inputs outputs #:allow-other-keys)
+                   (lambda* (#:key
+                             inputs native-inputs
+                             outputs #:allow-other-keys)
                      ;; Util-linux comes with a bunch of completion files for
                      ;; its own commands which are more sophisticated and
                      ;; up-to-date than those of bash-completion.  Remove those
                      ;; from bash-completion.
                      (let* ((out         (assoc-ref outputs "out"))
-                            (util-linux  (assoc-ref inputs "util-linux"))
+                            (util-linux  (assoc-ref (or native-inputs inputs)
+                                                    "util-linux"))
                             (completions (string-append out
                                                         "/share/bash-completion"
                                                         "/completions"))

gnu/packages/benchmark.scm

@@ -1,9 +1,10 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Dave Love <fx@gnu.org>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2019 Gábor Boskovits <boskovits@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,7 +26,10 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
+  #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages maths)
@@ -38,14 +42,14 @@
 (define-public fio
   (package
     (name "fio")
-    (version "3.13")
+    (version "3.14")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://brick.kernel.dk/snaps/"
                                   "fio-" version ".tar.bz2"))
               (sha256
                (base32
-                "0ddj7zm04jqlna3w61qyp4qvwnv0r2lc1hzpwrgbvv4fq581w7d2"))))
+                "047y53nyhnmnxcrsfbsf0gcpxw7bli3n19ycscpxy9974j0fck0v"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"
@@ -193,3 +197,27 @@ extension to @code{time} which runs a command multiple times and prints the
 timing means, standard deviations, mins, medians, and maxes having done so.
 This can give a much better understanding of the command's performance.")
     (license license:expat)))
+
+(define-public benchmark
+  (package
+    (name "benchmark")
+    (version "1.5.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/google/benchmark.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0r9dbg4cbk47gwmayys31a83m3y67k0kh1f6pl8i869rbd609ndh"))
+              (patches (search-patches "benchmark-unbundle-googletest.patch"))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("googletest" ,googletest)))
+    (home-page "https://github.com/google/benchmark")
+    (synopsis "Microbenchmark support library")
+    (description
+     "Benchmark is a library to benchmark code snippets,
+similar to unit tests.")
+    (license license:asl2.0)))

gnu/packages/bioconductor.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -22,6 +22,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix build-system r)
   #:use-module (gnu packages)
   #:use-module (gnu packages base)
@@ -37,7 +38,8 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages statistics)
-  #:use-module (gnu packages web))
+  #:use-module (gnu packages web)
+  #:use-module (srfi srfi-1))
 
 
 ;;; Annotations
@@ -590,6 +592,35 @@ data.  It is derived from the UCSC hg19 genome and based on the \"knownGene\"
 track.  The database is exposed as a @code{TxDb} object.")
     (license license:artistic2.0)))
 
+(define-public r-txdb-hsapiens-ucsc-hg38-knowngene
+  (package
+    (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
+    (version "3.4.6")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/annotation/" instead of "bioc/".
+              (uri (string-append "https://bioconductor.org/packages/"
+                                  "release/data/annotation/src/contrib"
+                                  "/TxDb.Hsapiens.UCSC.hg38.knownGene_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
+    (properties
+     `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genomicfeatures" ,r-genomicfeatures)))
+    (home-page
+     "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
+    (synopsis "Annotation package for human genome in TxDb format")
+    (description
+     "This package provides an annotation database of Homo sapiens genome
+data.  It is derived from the UCSC hg38 genome and based on the \"knownGene\"
+track.  The database is exposed as a @code{TxDb} object.")
+    (license license:artistic2.0)))
+
 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
   (package
     (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
@@ -623,7 +654,7 @@ 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 "3.4.4")
+    (version "3.4.7")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -634,7 +665,7 @@ database is exposed as a @code{TxDb} object.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
+                "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
     (properties
      `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
     (build-system r-build-system)
@@ -836,6 +867,34 @@ which were then sequenced to a depth of ~4 million reads per library,
 resulting in a complete gene expression profile for each cell.")
     (license license:artistic2.0)))
 
+(define-public r-all
+  (package
+    (name "r-all")
+    (version "1.26.0")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/experiment/" instead of "bioc/".
+              (uri (string-append "https://www.bioconductor.org/packages/"
+                                  "release/data/experiment/src/contrib/"
+                                  "ALL_" version ".tar.gz"))
+              (sha256
+               (base32
+                "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
+    (properties `((upstream-name . "ALL")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)))
+    (home-page "https://bioconductor.org/packages/ALL")
+    (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
+    (description
+     "The data consist of microarrays from 128 different individuals with
+@dfn{acute lymphoblastic leukemia} (ALL).  A number of additional covariates
+are available.  The data have been normalized (using rma) and it is the
+jointly normalized data that are available here.  The data are presented in
+the form of an @code{exprSet} object.")
+    (license license:artistic2.0)))
+
 
 ;;; Packages
 
@@ -907,14 +966,14 @@ the Human Protein Atlas project.")
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.16.1")
+    (version "1.16.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "14wiawp4zabyi2v884zzfgd90ggmnwrk2zda0r5lwvmhy79vmlw5"))))
+         "1b8ybx4wcxlqw9nvajawsf0lqaqn9v89rxcawg4g3dbzlfssfc5q"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1153,14 +1212,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.18.0")
+    (version "3.18.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "089v16mm5m0rlyyyd0d6rz8gwb852zf3bcdrrw70wanlfjn258q7"))))
+         "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1221,7 +1280,7 @@ enrichedGO (addGeneIDs).")
     (home-page "http://bioconductor.org/packages/marray")
     (synopsis "Exploratory analysis for two-color spotted microarray data")
     (description "This package contains class definitions for two-color spotted
-microarray data.  It also includes fuctions for data input, diagnostic plots,
+microarray data.  It also includes functions for data input, diagnostic plots,
 normalization and quality checking.")
     (license license:lgpl2.0+)))
 
@@ -1453,7 +1512,7 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
     (home-page "https://bioconductor.org/packages/InteractionSet")
     (synopsis "Base classes for storing genomic interaction data")
     (description
-     "This packages provides the @code{GInteractions},
+     "This package provides the @code{GInteractions},
 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
 experiments.")
@@ -1462,14 +1521,14 @@ experiments.")
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b"))))
+         "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
@@ -2086,14 +2145,14 @@ independent of the p-value under the null hypothesis.")
 (define-public r-icobra
   (package
     (name "r-icobra")
-    (version "1.12.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iCOBRA" version))
        (sha256
         (base32
-         "1w9frnczgypzc2czbwrvlizqcqhbp6cdpyws7vkmnn9k0ggzxvfc"))))
+         "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
     (properties `((upstream-name . "iCOBRA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2206,6 +2265,68 @@ tasks on single cell expression data.  It is designed to work with RNA-Seq and
 qPCR data, but could be used with other types as well.")
     (license license:artistic2.0)))
 
+(define-public r-monocle3
+  (package
+    (name "r-monocle3")
+    (version "0.1.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/cole-trapnell-lab/monocle3.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+       ("r-dplyr" ,r-dplyr)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggrepel" ,r-ggrepel)
+       ("r-grr" ,r-grr)
+       ("r-htmlwidgets" ,r-htmlwidgets)
+       ("r-igraph" ,r-igraph)
+       ("r-irlba" ,r-irlba)
+       ("r-limma" ,r-limma)
+       ("r-lmtest" ,r-lmtest)
+       ("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)
+       ("r-matrix-utils" ,r-matrix-utils)
+       ("r-pbapply" ,r-pbapply)
+       ("r-pbmcapply" ,r-pbmcapply)
+       ("r-pheatmap" ,r-pheatmap)
+       ("r-plotly" ,r-plotly)
+       ("r-pryr" ,r-pryr)
+       ("r-proxy" ,r-proxy)
+       ("r-pscl" ,r-pscl)
+       ("r-purrr" ,r-purrr)
+       ("r-rann" ,r-rann)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppparallel" ,r-rcppparallel)
+       ("r-reshape2" ,r-reshape2)
+       ("r-reticulate" ,r-reticulate)
+       ("r-rhpcblasctl" ,r-rhpcblasctl)
+       ("r-rtsne" ,r-rtsne)
+       ("r-shiny" ,r-shiny)
+       ("r-slam" ,r-slam)
+       ("r-spdep" ,r-spdep)
+       ("r-speedglm" ,r-speedglm)
+       ("r-stringr" ,r-stringr)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)
+       ("r-uwot" ,r-uwot)
+       ("r-viridis" ,r-viridis)))
+    (home-page "https://github.com/cole-trapnell-lab/monocle3")
+    (synopsis "Analysis toolkit for single-cell RNA-Seq data")
+    (description
+     "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
+    (license license:expat)))
+
 (define-public r-noiseq
   (package
     (name "r-noiseq")
@@ -2819,7 +2940,7 @@ sets of GO terms, gene products and gene clusters.")
     (synopsis "Analysis of translational activity")
     (description
      "Genome wide studies of translational control is emerging as a tool to
-study verious biological conditions.  The output from such analysis is both
+study various biological conditions.  The output from such analysis is both
 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
 involved in translation (the actively translating mRNA level) for each mRNA.
 The standard analysis of such data strives towards identifying differential
@@ -2827,7 +2948,7 @@ translational between two or more sample classes - i.e.  differences in
 actively translated mRNA levels that are independent of underlying differences
 in cytosolic mRNA levels.  This package allows for such analysis using partial
 variances and the random variance model.  As 10s of thousands of mRNAs are
-analyzed in parallell the library performs a number of tests to assure that
+analyzed in parallel the library performs a number of tests to assure that
 the data set is suitable for such analysis.")
     (license license:gpl3)))
 
@@ -2886,14 +3007,14 @@ to multiple hypothesis correction.")
 (define-public r-dose
   (package
     (name "r-dose")
-    (version "3.10.0")
+    (version "3.10.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DOSE" version))
        (sha256
         (base32
-         "0dvhnfhzhhzcxm8zhdwrkif7sak4p888sjqfd3a0p77h0hs6g8pv"))))
+         "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj"))))
     (properties `((upstream-name . "DOSE")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3377,14 +3498,14 @@ type and symbol colors.")
 (define-public r-genomicscores
   (package
     (name "r-genomicscores")
-    (version "1.8.0")
+    (version "1.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicScores" version))
        (sha256
         (base32
-         "17bd61icfycc61b5dij1968h026w7vfd9miwdcbppak1j6s08idq"))))
+         "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy"))))
     (properties `((upstream-name . "GenomicScores")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3408,14 +3529,14 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.8.0")
+    (version "1.8.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "03f130vcd6hd3fv2pg60id0ddd6qkwsyx73gm907xaayf42ar2pj"))))
+         "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3500,14 +3621,14 @@ annotations and ontologies.")
 (define-public r-abaenrichment
   (package
     (name "r-abaenrichment")
-    (version "1.14.0")
+    (version "1.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ABAEnrichment" version))
        (sha256
         (base32
-         "0av1dysk7qa8c4a0pp7yq89k8c4y40d2gyvsb8f27slvv2i3aad2"))))
+         "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
     (properties `((upstream-name . "ABAEnrichment")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3621,14 +3742,14 @@ investigation using RNA-seq data.")
 (define-public r-aucell
   (package
     (name "r-aucell")
-    (version "1.6.0")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AUCell" version))
        (sha256
         (base32
-         "025q1as9pifbxa7hidlz634q6d7l73zx8mqy4rjbfrk7d5615xvm"))))
+         "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
     (properties `((upstream-name . "AUCell")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4073,14 +4194,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
 (define-public r-xcms
   (package
     (name "r-xcms")
-    (version "3.6.0")
+    (version "3.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xcms" version))
        (sha256
         (base32
-         "0bpbsda38v7y9072ixslh4pnx1yq6s5cff4x7d4h9kgns3bskvcv"))))
+         "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -4178,7 +4299,7 @@ visualization of exonic read coverage.")
     (home-page "https://bioconductor.org/packages/widgetTools/")
     (synopsis "Tools for creating interactive tcltk widgets")
     (description
-     "This packages contains tools to support the construction of tcltk
+     "This package contains tools to support the construction of tcltk
 widgets in R.")
     ;; Any version of the LGPL.
     (license license:lgpl3+)))
@@ -4438,14 +4559,14 @@ interpretation.")
 (define-public r-rhisat2
   (package
     (name "r-rhisat2")
-    (version "1.0.0")
+    (version "1.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhisat2" version))
        (sha256
         (base32
-         "1d1gwl8l2z8kzfvkp1s8vfrh6jbq9ha25dplpf9g62qqa8a46hga"))))
+         "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5"))))
     (properties `((upstream-name . "Rhisat2")))
     (build-system r-build-system)
     (native-inputs
@@ -4466,14 +4587,14 @@ index.")
 (define-public r-quasr
   (package
     (name "r-quasr")
-    (version "1.24.1")
+    (version "1.24.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "QuasR" version))
        (sha256
         (base32
-         "02mdg3mq99gsqq181j3sfh9pid5l7dqjl68rk4fpc1rvm128y743"))))
+         "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
     (properties `((upstream-name . "QuasR")))
     (build-system r-build-system)
     (inputs
@@ -4548,3 +4669,564 @@ high-throughput sequencing data.  It performs parallel processing of entire
 files and produces a report which contains a set of high-resolution
 graphics.")
     (license license:gpl2+)))
+
+(define-public r-birewire
+  (package
+    (name "r-birewire")
+    (version "3.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BiRewire" version))
+       (sha256
+        (base32
+         "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518"))))
+    (properties `((upstream-name . "BiRewire")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-igraph" ,r-igraph)
+       ("r-matrix" ,r-matrix)
+       ("r-slam" ,r-slam)
+       ("r-tsne" ,r-tsne)))
+    (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
+    (synopsis "Tools for randomization of bipartite graphs")
+    (description
+     "This package provides functions for bipartite network rewiring through N
+consecutive switching steps and for the computation of the minimal number of
+switching steps to be performed in order to maximise the dissimilarity with
+respect to the original network.  It includes functions for the analysis of
+the introduced randomness across the switching steps and several other
+routines to analyse the resulting networks and their natural projections.")
+    (license license:gpl3)))
+
+(define-public r-birta
+  (package
+    (name "r-birta")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "birta" version))
+       (sha256
+        (base32
+         "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-limma" ,r-limma)
+       ("r-mass" ,r-mass)))
+    (home-page "https://bioconductor.org/packages/birta")
+    (synopsis "Bayesian inference of regulation of transcriptional activity")
+    (description
+     "Expression levels of mRNA molecules are regulated by different
+processes, comprising inhibition or activation by transcription factors and
+post-transcriptional degradation by microRNAs.  @dfn{birta} (Bayesian
+Inference of Regulation of Transcriptional Activity) uses the regulatory
+networks of transcription factors and miRNAs together with mRNA and miRNA
+expression data to predict switches in regulatory activity between two
+conditions.  A Bayesian network is used to model the regulatory structure and
+Markov-Chain-Monte-Carlo is applied to sample the activity states.")
+    (license license:gpl2+)))
+
+(define-public r-ropls
+  (package
+    (name "r-ropls")
+    (version "1.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ropls" version))
+       (sha256
+        (base32
+         "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-biobase" ,r-biobase)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr))) ; for vignettes
+    (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
+    (synopsis "Multivariate analysis and feature selection of omics data")
+    (description
+     "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
+and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
+regression, classification, and feature selection of omics data where the
+number of variables exceeds the number of samples and with multicollinearity
+among variables.  @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
+separately model the variation correlated (predictive) to the factor of
+interest and the uncorrelated (orthogonal) variation.  While performing
+similarly to PLS, OPLS facilitates interpretation.
+
+This package provides imlementations of PCA, PLS, and OPLS for multivariate
+analysis and feature selection of omics data.  In addition to scores, loadings
+and weights plots, the package provides metrics and graphics to determine the
+optimal number of components (e.g. with the R2 and Q2 coefficients), check the
+validity of the model by permutation testing, detect outliers, and perform
+feature selection (e.g. with Variable Importance in Projection or regression
+coefficients).")
+    (license license:cecill)))
+
+(define-public r-biosigner
+  (package
+    (name "r-biosigner")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "biosigner" version))
+       (sha256
+        (base32
+         "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-e1071" ,r-e1071)
+       ("r-randomforest" ,r-randomforest)
+       ("r-ropls" ,r-ropls)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("pandoc" ,ghc-pandoc)
+       ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
+    (home-page "https://bioconductor.org/packages/biosigner/")
+    (synopsis "Signature discovery from omics data")
+    (description
+     "Feature selection is critical in omics data analysis to extract
+restricted and meaningful molecular signatures from complex and high-dimension
+data, and to build robust classifiers.  This package implements a method to
+assess the relevance of the variables for the prediction performances of the
+classifier.  The approach can be run in parallel with the PLS-DA, Random
+Forest, and SVM binary classifiers.  The signatures and the corresponding
+'restricted' models are returned, enabling future predictions on new
+datasets.")
+    (license license:cecill)))
+
+(define-public r-annotatr
+  (package
+    (name "r-annotatr")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "annotatr" version))
+       (sha256
+        (base32
+         "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationhub" ,r-annotationhub)
+       ("r-dplyr" ,r-dplyr)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-iranges" ,r-iranges)
+       ("r-readr" ,r-readr)
+       ("r-regioner" ,r-regioner)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/annotatr/")
+    (synopsis "Annotation of genomic regions to genomic annotations")
+    (description
+     "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
+differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
+to investigate the intersecting genomic annotations.  Such annotations include
+those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
+CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
+enhancers.  The annotatr package provides an easy way to summarize and
+visualize the intersection of genomic sites/regions with genomic
+annotations.")
+    (license license:gpl3)))
+
+(define-public r-rsubread
+  (package
+    (name "r-rsubread")
+    (version "1.34.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Rsubread" version))
+       (sha256
+        (base32
+         "0nnfh4hnrs5kd72m8c50cidbsxjz12szw2vynpmg8q0wpd99q550"))))
+    (properties `((upstream-name . "Rsubread")))
+    (build-system r-build-system)
+    (inputs `(("zlib" ,zlib)))
+    (home-page "https://bioconductor.org/packages/Rsubread/")
+    (synopsis "Subread sequence alignment and counting for R")
+    (description
+     "This package provides tools for alignment, quantification and analysis
+of second and third generation sequencing data.  It includes functionality for
+read mapping, read counting, SNP calling, structural variant detection and
+gene fusion discovery.  It can be applied to all major sequencing techologies
+and to both short and long sequence reads.")
+    (license license:gpl3)))
+
+(define-public r-flowutils
+  (package
+    (name "r-flowutils")
+    (version "1.48.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "flowUtils" version))
+       (sha256
+        (base32
+         "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm"))))
+    (properties `((upstream-name . "flowUtils")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-corpcor" ,r-corpcor)
+       ("r-flowcore" ,r-flowcore)
+       ("r-graph" ,r-graph)
+       ("r-runit" ,r-runit)
+       ("r-xml" ,r-xml)))
+    (home-page "https://github.com/jspidlen/flowUtils")
+    (synopsis "Utilities for flow cytometry")
+    (description
+     "This package provides utilities for flow cytometry data.")
+    (license license:artistic2.0)))
+
+(define-public r-consensusclusterplus
+  (package
+    (name "r-consensusclusterplus")
+    (version "1.48.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ConsensusClusterPlus" version))
+       (sha256
+        (base32
+         "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8"))))
+    (properties
+     `((upstream-name . "ConsensusClusterPlus")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-all" ,r-all)
+       ("r-biobase" ,r-biobase)
+       ("r-cluster" ,r-cluster)))
+    (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
+    (synopsis "Clustering algorithm")
+    (description
+     "This package provides an implementation of an algorithm for determining
+cluster count and membership by stability evidence in unsupervised analysis.")
+    (license license:gpl2)))
+
+(define-public r-flowcore
+  (package
+    (name "r-flowcore")
+    (version "1.50.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "flowCore" version))
+       (sha256
+        (base32
+         "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan"))))
+    (properties `((upstream-name . "flowCore")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bh" ,r-bh)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-corpcor" ,r-corpcor)
+       ("r-graph" ,r-graph)
+       ("r-mass" ,r-mass)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rrcov" ,r-rrcov)))
+    (home-page "https://bioconductor.org/packages/flowCore")
+    (synopsis "Basic structures for flow cytometry data")
+    (description
+     "This package provides S4 data structures and basic functions to deal
+with flow cytometry data.")
+    (license license:artistic2.0)))
+
+(define-public r-flowmeans
+  (package
+    (name "r-flowmeans")
+    (version "1.44.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "flowMeans" version))
+       (sha256
+        (base32
+         "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2"))))
+    (properties `((upstream-name . "flowMeans")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-feature" ,r-feature)
+       ("r-flowcore" ,r-flowcore)
+       ("r-rrcov" ,r-rrcov)))
+    (home-page "https://bioconductor.org/packages/flowMeans")
+    (synopsis "Non-parametric flow cytometry data gating")
+    (description
+     "This package provides tools to identify cell populations in Flow
+Cytometry data using non-parametric clustering and segmented-regression-based
+change point detection.")
+    (license license:artistic2.0)))
+
+(define-public r-flowsom
+  (package
+    (name "r-flowsom")
+    (version "1.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "FlowSOM" version))
+       (sha256
+        (base32
+         "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l"))))
+    (properties `((upstream-name . "FlowSOM")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-consensusclusterplus" ,r-consensusclusterplus)
+       ("r-flowcore" ,r-flowcore)
+       ("r-flowutils" ,r-flowutils)
+       ("r-igraph" ,r-igraph)
+       ("r-tsne" ,r-tsne)
+       ("r-xml" ,r-xml)))
+    (home-page "https://bioconductor.org/packages/FlowSOM/")
+    (synopsis "Visualize and interpret cytometry data")
+    (description
+     "FlowSOM offers visualization options for cytometry data, by using
+self-organizing map clustering and minimal spanning trees.")
+    (license license:gpl2+)))
+
+(define-public r-mixomics
+  (package
+    (name "r-mixomics")
+    (version "6.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "mixOmics" version))
+       (sha256
+        (base32
+         "1f08jx35amn3sfcmqb96mjxxsm6dnpzhff625z758x1992wj4zsk"))))
+    (properties `((upstream-name . "mixOmics")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-corpcor" ,r-corpcor)
+       ("r-dplyr" ,r-dplyr)
+       ("r-ellipse" ,r-ellipse)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-igraph" ,r-igraph)
+       ("r-lattice" ,r-lattice)
+       ("r-mass" ,r-mass)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-rarpack" ,r-rarpack)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-reshape2" ,r-reshape2)
+       ("r-tidyr" ,r-tidyr)))
+    (home-page "http://www.mixOmics.org")
+    (synopsis "Multivariate methods for exploration of biological datasets")
+    (description
+     "mixOmics offers a wide range of multivariate methods for the exploration
+and integration of biological datasets with a particular focus on variable
+selection.  The package proposes several sparse multivariate models we have
+developed to identify the key variables that are highly correlated, and/or
+explain the biological outcome of interest.  The data that can be analysed
+with mixOmics may come from high throughput sequencing technologies, such as
+omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
+also beyond the realm of omics (e.g.  spectral imaging).  The methods
+implemented in mixOmics can also handle missing values without having to
+delete entire rows with missing data.")
+    (license license:gpl2+)))
+
+(define-public r-depecher
+  (package
+    (name "r-depecher")
+    (version "1.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DepecheR" version))
+       (sha256
+        (base32
+         "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h"))))
+    (properties `((upstream-name . "DepecheR")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-syntax-error
+           (lambda _
+             (substitute* "src/Makevars"
+               ((" & ") " && "))
+             #t)))))
+    (propagated-inputs
+     `(("r-beanplot" ,r-beanplot)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-dosnow" ,r-dosnow)
+       ("r-dplyr" ,r-dplyr)
+       ("r-foreach" ,r-foreach)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gplots" ,r-gplots)
+       ("r-mass" ,r-mass)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-mixomics" ,r-mixomics)
+       ("r-moments" ,r-moments)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppeigen" ,r-rcppeigen)
+       ("r-reshape2" ,r-reshape2)
+       ("r-viridis" ,r-viridis)))
+    (home-page "https://bioconductor.org/packages/DepecheR/")
+    (synopsis "Identify traits of clusters in high-dimensional entities")
+    (description
+     "The purpose of this package is to identify traits in a dataset that can
+separate groups.  This is done on two levels.  First, clustering is performed,
+using an implementation of sparse K-means.  Secondly, the generated clusters
+are used to predict outcomes of groups of individuals based on their
+distribution of observations in the different clusters.  As certain clusters
+with separating information will be identified, and these clusters are defined
+by a sparse number of variables, this method can reduce the complexity of
+data, to only emphasize the data that actually matters.")
+    (license license:expat)))
+
+(define-public r-rcistarget
+  (package
+    (name "r-rcistarget")
+    (version "1.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "RcisTarget" version))
+       (sha256
+        (base32
+         "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd"))))
+    (properties `((upstream-name . "RcisTarget")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-aucell" ,r-aucell)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-data-table" ,r-data-table)
+       ("r-feather" ,r-feather)
+       ("r-gseabase" ,r-gseabase)
+       ("r-r-utils" ,r-r-utils)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://aertslab.org/#scenic")
+    (synopsis "Identify transcription factor binding motifs enriched on a gene list")
+    (description
+     "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
+over-represented on a gene list.  In a first step, RcisTarget selects DNA
+motifs that are significantly over-represented in the surroundings of the
+@dfn{transcription start site} (TSS) of the genes in the gene-set.  This is
+achieved by using a database that contains genome-wide cross-species rankings
+for each motif.  The motifs that are then annotated to TFs and those that have
+a high @dfn{Normalized Enrichment Score} (NES) are retained.  Finally, for
+each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
+genes in the gene-set that are ranked above the leading edge).")
+    (license license:gpl3)))
+
+(define-public r-cicero
+  (package
+    (name "r-cicero")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "cicero" version))
+       (sha256
+        (base32
+         "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-assertthat" ,r-assertthat)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-data-table" ,r-data-table)
+       ("r-dplyr" ,r-dplyr)
+       ("r-fnn" ,r-fnn)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-glasso" ,r-glasso)
+       ("r-gviz" ,r-gviz)
+       ("r-igraph" ,r-igraph)
+       ("r-iranges" ,r-iranges)
+       ("r-matrix" ,r-matrix)
+       ("r-monocle" ,r-monocle)
+       ("r-plyr" ,r-plyr)
+       ("r-reshape2" ,r-reshape2)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
+       ("r-vgam" ,r-vgam)))
+    (home-page "https://bioconductor.org/packages/cicero/")
+    (synopsis "Predict cis-co-accessibility from single-cell data")
+    (description
+     "Cicero computes putative cis-regulatory maps from single-cell chromatin
+accessibility data.  It also extends the monocle package for use in chromatin
+accessibility data.")
+    (license license:expat)))
+
+;; This is the latest commit on the "monocle3" branch.
+(define-public r-cicero-monocle3
+  (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
+        (revision "1"))
+    (package (inherit r-cicero)
+      (name "r-cicero-monocle3")
+      (version (git-version "1.3.2" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/cole-trapnell-lab/cicero-release.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
+      (propagated-inputs
+       `(("r-monocle3" ,r-monocle3)
+         ,@(alist-delete "r-monocle"
+                         (package-propagated-inputs r-cicero)))))))
+
+(define-public r-cistopic
+  (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
+        (revision "0"))
+    (package
+      (name "r-cistopic")
+      (version (git-version "0.2.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/aertslab/cisTopic.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-aucell" ,r-aucell)
+         ("r-data-table" ,r-data-table)
+         ("r-dplyr" ,r-dplyr)
+         ("r-dosnow" ,r-dosnow)
+         ("r-dt" ,r-dt)
+         ("r-feather" ,r-feather)
+         ("r-fitdistrplus" ,r-fitdistrplus)
+         ("r-genomicranges" ,r-genomicranges)
+         ("r-ggplot2" ,r-ggplot2)
+         ("r-lda" ,r-lda)
+         ("r-matrix" ,r-matrix)
+         ("r-plyr" ,r-plyr)
+         ("r-rcistarget" ,r-rcistarget)
+         ("r-rtracklayer" ,r-rtracklayer)
+         ("r-s4vectors" ,r-s4vectors)))
+      (home-page "https://github.com/aertslab/cisTopic")
+      (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
+      (description
+       "The sparse nature of single cell epigenomics data can be overruled using
+probabilistic modelling methods such as @dfn{Latent Dirichlet
+Allocation} (LDA).  This package allows the probabilistic modelling of
+cis-regulatory topics (cisTopics) from single cell epigenomics data, and
+includes functionalities to identify cell states based on the contribution of
+cisTopics and explore the nature and regulatory proteins driving them.")
+      (license license:gpl3))))

gnu/packages/bittorrent.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016, 2017, 2018 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016, 2017, 2018, 2019 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Tomáš Čech <sleep_walker@gnu.org>
 ;;; Copyright © 2016, 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -183,35 +183,38 @@ XML-RPC over SCGI.")
     (license l:gpl2+)))
 
 (define-public tremc
-  (package
-    (name "tremc")
-    (version "0.9.1")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/tremc/tremc.git")
-             (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1yhwvlcyv1s830p5a7q5x3mkb3mbvr5cn5nh7y62l5b6iyyynlvm"))))
-    (build-system gnu-build-system)
-    (arguments
-     `(#:tests? #f                      ; no test suite
-       #:make-flags
-       (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
-       #:phases
-       (modify-phases %standard-phases
-         ;; The software is just a Python script that must be copied into place.
-         (delete 'configure)
-         (delete 'build))))
-    (inputs
-     `(("python" ,python)))
-    (synopsis "Console client for the Transmission BitTorrent daemon")
-    (description "Tremc is a console client, with a curses interface, for the
+  (let ((commit "4d50dab7376601daca13f7be6eabc0eaa057c1b0")
+        (revision "0"))
+    (package
+      (name "tremc")
+      (version (git-version "0.9.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/tremc/tremc.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0qpi65n8rv7l9mg8qyqx70z83inkl8v5r5nks65c99lhscdki0w7"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f                      ; no test suite
+         #:make-flags
+         (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
+         #:phases
+         (modify-phases %standard-phases
+           ;; The software is just a Python script that must be copied into place.
+           (delete 'configure)
+           (delete 'build))))
+      (inputs
+       `(("python" ,python)))
+      (synopsis "Console client for the Transmission BitTorrent daemon")
+      (description "Tremc is a console client, with a curses interface, for the
 Transmission BitTorrent daemon.")
-    (home-page "https://github.com/tremc/tremc")
-    (license l:gpl3+)))
+      (home-page "https://github.com/tremc/tremc")
+      (license l:gpl3+))))
 
 (define-public transmission-remote-cli
   (package

gnu/packages/bootloaders.scm

@@ -82,19 +82,22 @@
 (define-public grub
   (package
     (name "grub")
-    (version "2.02")
+    (version "2.04")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/grub/grub-" version ".tar.xz"))
              (sha256
               (base32
-               "03vvdfhdmf16121v7xs8is2krwnv15wpkhkf16a4yf8nsfc3f2w1"))
-             (patches (search-patches "grub-check-error-efibootmgr.patch"
-                                      "grub-binutils-compat.patch"
-                                      "grub-efi-fat-serial-number.patch"))))
+               "0zgp5m3hmc9jh8wpjx6czzkh5id2y8n1k823x2mjvm2sk6b28ag5"))
+             (patches (search-patches "grub-efi-fat-serial-number.patch"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:phases (modify-phases %standard-phases
+     `(#:configure-flags
+       ;; Counterintuitively, this *disables* a spurious Python dependency by
+       ;; calling the ‘true’ binary instead.  Python is only needed during
+       ;; bootstrapping (for genptl.py), not when building from a release.
+       (list "PYTHON=true")
+       #:phases (modify-phases %standard-phases
                   (add-after 'unpack 'patch-stuff
                    (lambda* (#:key inputs #:allow-other-keys)
                      (substitute* "grub-core/Makefile.in"
@@ -127,6 +130,14 @@
                       (substitute* "Makefile.in"
                         (("grub_cmd_date grub_cmd_set_date grub_cmd_sleep")
                           "grub_cmd_date grub_cmd_sleep"))
+                      #t))
+                  (add-before 'check 'disable-pixel-perfect-test
+                    (lambda _
+                      ;; This test compares many screenshots rendered with an
+                      ;; older Unifont (9.0.06) than that packaged in Guix.
+                      (substitute* "Makefile.in"
+                        (("test_unset grub_func_test")
+                          "test_unset"))
                       #t)))
        ;; Disable tests on ARM and AARCH64 platforms.
        #:tests? ,(not (any (cute string-prefix? <> (or (%current-target-system)
@@ -147,9 +158,12 @@
        ;; for generating alternative keyboard layouts.
        ("console-setup" ,console-setup)
 
+       ;; Needed for ‘grub-mount’, the only reliable way to tell whether a given
+       ;; file system will be readable by GRUB without rebooting.
+       ("fuse" ,fuse)
+
        ("freetype" ,freetype)
        ;; ("libusb" ,libusb)
-       ;; ("fuse" ,fuse)
        ("ncurses" ,ncurses)))
     (native-inputs
      `(("pkg-config" ,pkg-config)
@@ -510,17 +524,16 @@ board-independent tools.")))
 
 (define-public (make-u-boot-package board triplet)
   "Returns a u-boot package for BOARD cross-compiled for TRIPLET."
-  (let ((same-arch? (if (string-prefix? (%current-system)
-                                        (gnu-triplet->nix-system triplet))
-                      `#t
-                      `#f)))
+  (let ((same-arch? (lambda ()
+                      (string=? (%current-system)
+                                (gnu-triplet->nix-system triplet)))))
     (package
       (inherit u-boot)
       (name (string-append "u-boot-"
                            (string-replace-substring (string-downcase board)
                                                      "_" "-")))
       (native-inputs
-       `(,@(if (not same-arch?)
+       `(,@(if (not (same-arch?))
              `(("cross-gcc" ,(cross-gcc triplet #:xgcc gcc-7))
                ("cross-binutils" ,(cross-binutils triplet)))
              `(("gcc-7" ,gcc-7)))
@@ -533,7 +546,7 @@ board-independent tools.")))
          #:test-target "test"
          #:make-flags
          (list "HOSTCC=gcc"
-               ,@(if (not same-arch?)
+               ,@(if (not (same-arch?))
                    `((string-append "CROSS_COMPILE=" ,triplet "-"))
                    '()))
          #:phases

gnu/packages/bootstrap.scm

@@ -1,7 +1,8 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2019 Carl Dong <contact@carldong.me>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,7 +30,7 @@
   #:use-module ((guix store)
                 #:select (run-with-store add-to-store add-text-to-store))
   #:use-module ((guix derivations)
-                #:select (derivation derivation->output-path))
+                #:select (derivation derivation-input derivation->output-path))
   #:use-module ((guix utils) #:select (gnu-triplet->nix-system))
   #:use-module (guix memoization)
   #:use-module (srfi srfi-1)
@@ -177,6 +178,7 @@ return value is ignored."
         ((string=? system "powerpc64le-linux") "/lib/ld64.so.2")
         ((string=? system "alpha-linux") "/lib/ld-linux.so.2")
         ((string=? system "s390x-linux") "/lib/ld64.so.1")
+        ((string=? system "riscv64-linux") "/lib/ld-linux-riscv64-lp64d.so.1")
 
         ;; XXX: This one is used bare-bones, without a libc, so add a case
         ;; here just so we can keep going.
@@ -186,6 +188,7 @@ return value is ignored."
         ((string=? system "avr") "no-ld.so")
         ((string=? system "propeller-elf") "no-ld.so")
         ((string=? system "i686-mingw") "no-ld.so")
+        ((string=? system "x86_64-mingw") "no-ld.so")
         ((string=? system "vc4-elf") "no-ld.so")
 
         (else (error "dynamic linker name not known for this system"
@@ -311,7 +314,8 @@ $out/bin/guile --version~%"
     (derivation store name
                 bash `(,builder)
                 #:system system
-                #:inputs `((,bash) (,builder) (,guile))
+                #:inputs (list (derivation-input guile))
+                #:sources (list bash builder)
                 #:env-vars `(("GUILE_TARBALL"
                               . ,(derivation->output-path guile))))))
 

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 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019 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>
@@ -242,7 +242,7 @@ other lower-level build files.")
 (define-public osc
   (package
     (name "osc")
-    (version "0.165.0")
+    (version "0.165.2")
     (source
      (origin
        (method git-fetch)
@@ -251,8 +251,7 @@ other lower-level build files.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32
-         "0l6iw8a040l60ixxdms9rxajm38vqfdwgij2bm7ahgv1akza64jk"))))
+        (base32 "0yjwvbvv9fgkpiyvrag89zxchyn3nbgp9jz0wn5p0z9450zwfyz6"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -269,7 +268,7 @@ other lower-level build files.")
     (inputs
      `(("python-m2crypto" ,python-m2crypto)
        ("python-pycurl" ,python-pycurl)
-       ("rpm" ,rpm))) ; for python-rpm
+       ("rpm" ,rpm)))                   ; for python-rpm
     (home-page "https://github.com/openSUSE/osc")
     (synopsis "Open Build Service command line tool")
     (description "@command{osc} is a command line interface to the Open Build

gnu/packages/busybox.scm

@@ -1,8 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 John Darrington <jmd@gnu.org>
-;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -55,6 +54,12 @@
              #t))
          (replace 'configure
            (lambda _ (invoke "make" "defconfig")))
+         (add-after 'configure 'dont-install-to-usr
+           (lambda _
+             (substitute* ".config"
+               (("# CONFIG_INSTALL_NO_USR is not set")
+                "CONFIG_INSTALL_NO_USR=y"))
+             #t))
          (replace 'check
            (lambda _
              (substitute* '("testsuite/du/du-s-works"
@@ -108,7 +113,7 @@ any small or embedded system.")
 (define-public toybox
   (package
     (name "toybox")
-    (version "0.8.0")
+    (version "0.8.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -116,7 +121,7 @@ any small or embedded system.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "0mirj977zxsxnfaiqndwgsn9calgg312d817fi1hkfbd8kcyrk73"))))
+                "1czxzvyggm157z8wgxbk8k0n675p1gig9xvrcijsplh9p1i1xi0s"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -133,7 +138,12 @@ any small or embedded system.")
              (let ((out (assoc-ref outputs "out")))
                (invoke "make"
                        (string-append "PREFIX=" out)
-                       "install")))))
+                       "install"))))
+         (add-after 'install 'remove-usr-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (delete-file-recursively (string-append out "/usr"))
+               #t))))
        #:test-target "tests"))
     (native-inputs `(("bc" ,bc)))
     (synopsis "Many common UNIX utilities in a single executable")

gnu/packages/c.scm

@@ -2,7 +2,7 @@
 ;;; 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 Pierre Neidhardt <mail@ambrevar.xyz>
+;;; Copyright © 2018, 2019 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -29,6 +29,7 @@
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages bootstrap)
   #:use-module (gnu packages bison)
+  #:use-module (gnu packages check)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages texinfo)
@@ -287,3 +288,31 @@ Its three main components are:
 @end enumerate\n")
     ;; Like the BSD-3 license but with an extra anti patent clause.
     (license (license:non-copyleft "file://COPYRIGHT"))))
+
+(define-public libfixposix
+  (package
+    (name "libfixposix")
+    (version "0.4.3")
+    (home-page "https://github.com/sionescu/libfixposix")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url home-page)
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1x4q6yspi5g2s98vq4qszw4z3zjgk9l5zs8471w4d4cs6l97w08j"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)
+       ("check" ,check)))
+    (synopsis "Thin wrapper over POSIX syscalls")
+    (description
+     "The purpose of libfixposix is to offer replacements for parts of POSIX
+whose behaviour is inconsistent across *NIX flavours.")
+    (license license:boost1.0)))

gnu/packages/calcurse.scm

@@ -30,14 +30,14 @@
 (define-public calcurse
   (package
     (name "calcurse")
-    (version "4.4.0")
+    (version "4.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://calcurse.org/files/calcurse-"
                            version ".tar.gz"))
        (sha256
-        (base32 "0vw2xi6a2lrhrb8n55zq9lv4mzxhby4xdf3hmi1vlfpyrpdwkjzd"))))
+        (base32 "1vjwcmp51h7dsvwn0qx93w9chp3wp970v7d9mjhk7jyamcbfywn3"))))
     (build-system gnu-build-system)
     (inputs `(("ncurses" ,ncurses)))
     (native-inputs `(("tzdata" ,tzdata-for-tests)))

gnu/packages/calendar.scm

@@ -35,11 +35,13 @@
   #:use-module (gnu packages dav)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages glib)
+  #:use-module (gnu packages gtk)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages sphinx)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages time)
   #:use-module (gnu packages xml)
@@ -48,7 +50,7 @@
 (define-public libical
   (package
     (name "libical")
-    (version "3.0.4")
+    (version "3.0.5")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -56,7 +58,7 @@
                     version "/libical-" version ".tar.gz"))
               (sha256
                (base32
-                "0ifisnh42cw5z53hp9p52l3ggc7k877zlqk0n06gdhrk0bhidckj"))))
+                "1rkq9qkvbv76n6k6kc8pxhwj9vhyigkb6flfcn1rk6wwqk451mbs"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; test suite appears broken
@@ -76,7 +78,8 @@
                  (("\\\"/usr/share/lib/zoneinfo\\\"") "")))
              #t)))))
     (native-inputs
-     `(("perl" ,perl)
+     `(("gtk-doc" ,gtk-doc)
+       ("perl" ,perl)
        ("pkg-config" ,pkg-config)))
     (inputs
      `(("glib" ,glib)

gnu/packages/cdrom.scm

@@ -162,8 +162,20 @@ libcdio.")
                                  version ".tar.gz"))
              (sha256
               (base32
-               "0aq6lvlwlkxz56l5sbvgycr6j5c82ch2bv6zrnc2345ibfpafgx9"))))
+               "0aq6lvlwlkxz56l5sbvgycr6j5c82ch2bv6zrnc2345ibfpafgx9"))
+             (patches
+              (search-patches "xorriso-no-partition-table-in-inner-efi.patch"
+                              "xorriso-no-mbr-in-inner-efi.patch"))))
     (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'install-frontends
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (out-bin (string-append out "/bin")))
+               (install-file "frontend/grub-mkrescue-sed.sh" out-bin)
+               #t))))))
     (inputs
      `(("acl" ,acl)
        ("readline" ,readline)
@@ -713,16 +725,20 @@ session, and it can create M3U playlists.")
   (package
     (name "ripit")
     (version "3.9.0")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "http://www.suwald.com/ripit/ripit-"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "0ap71x477jy9c4jiqazb3y45hxdxm3jbq24x05g3vjyqzigi4x1b"))))
+    (source
+     (origin
+       (method url-fetch)
+       ;; The original suwald.com domain has expired.
+       (uri (list
+             (string-append "https://web.archive.org/web/20160327050927/"
+                            "http://suwald.com/ripit/ripit-" version ".tar.gz")
+             (string-append "https://ponce.cc/slackware/sources/repo/ripit-"
+                            version ".tar.gz")))
+       (sha256
+        (base32 "0ap71x477jy9c4jiqazb3y45hxdxm3jbq24x05g3vjyqzigi4x1b"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f ; No test suite.
+     `(#:tests? #f                      ; no test suite
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
@@ -744,7 +760,8 @@ session, and it can create M3U playlists.")
        ("vorbis-tools" ,vorbis-tools)
        ("wavpack" ,wavpack)
        ("perl-cddb-get" ,perl-cddb-get)))
-    (home-page "http://www.suwald.com/ripit/about.php")
+    (home-page (string-append "https://web.archive.org/web/20170119092156/"
+                              "http://www.suwald.com/ripit/about.php"))
     (synopsis "Command-line program to extract audio CDs")
     (description "RipIT is used to extract audio from CDs.")
     (license gpl2)))

gnu/packages/certs.scm

@@ -76,7 +76,7 @@
 (define-public nss-certs
   (package
     (name "nss-certs")
-    (version "3.43")
+    (version "3.45")
     (source (origin
               (method url-fetch)
               (uri (let ((version-with-underscores
@@ -87,7 +87,7 @@
                       "nss-" version ".tar.gz")))
               (sha256
                (base32
-                "1jp27w4w9nj5pkzrbc1zqj6pa09h2yy7vhzyx5fvg1q86fvw22zk"))))
+                "12sfq9xvpwpc22qnjsg1if1lmchiy33byrh92wn91phz7li0abqi"))))
     (build-system gnu-build-system)
     (outputs '("out"))
     (native-inputs

gnu/packages/check.scm

@@ -447,7 +447,7 @@ test) much simpler.")
      `(("go-github.com-smartystreets-gunit" ,go-github.com-smartystreets-gunit)))
     (synopsis "Assertions for testing with Go")
     (description
-     "The @code{assertions} package provides convinient assertion functions
+     "The @code{assertions} package provides convenient assertion functions
 for writing tests in Go.")
     (home-page "https://github.com/smartystreets/assertions")
     (license license:expat)))
@@ -478,22 +478,19 @@ test coverage and has a web user interface that will refresh automatically.")
     (home-page "https://github.com/smartystreets/goconvey")
     (license license:expat)))
 
-;; XXX When updating, check whether ZNC's GOOGLETEST-SOURCES can be
-;; switched back to simply using (PACKAGE-SOURCE ...).
 (define-public googletest
   (package
     (name "googletest")
-    (version "1.8.0")
+    (version "1.8.1")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-              (url "https://github.com/google/googletest.git")
-              (commit (string-append "release-" version))))
+             (url "https://github.com/google/googletest.git")
+             (commit (string-append "release-" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32
-         "0bjlljmbf8glnd9qjabx73w6pd7ibv43yiyngqvmvgxsabzr8399"))))
+        (base32 "0270msj6n7mggh4xqqjp54kswbl7mkcc8px1p5dqdpmw5ngh9fzk"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")))
@@ -925,6 +922,27 @@ result back.")
 (define-public python2-pytest-xdist
   (package-with-python2 python-pytest-xdist))
 
+(define-public python-pytest-timeout
+  (package
+    (name "python-pytest-timeout")
+    (version "1.3.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pytest-timeout" version))
+       (sha256
+        (base32
+         "1cczcjhw4xx5sjkhxlhc5c1bkr7x6fcyx12wrnvwfckshdvblc2a"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-pytest" ,python-pytest)))
+    (home-page "http://bitbucket.org/pytest-dev/pytest-timeout/")
+    (synopsis "Plugin for py.test to abort hanging tests")
+    (description
+     "This package provides a py.test plugin that aborts hanging tests after a
+timeout has been exceeded.")
+    (license license:expat)))
+
 (define-public python-scripttest
   (package
     (name "python-scripttest")
@@ -1906,7 +1924,8 @@ backported from Python 2.7 for Python 2.4+.")
        ("python-pyhamcrest" ,python-pyhamcrest)
        ("python-pytest" ,python-pytest)))
     (propagated-inputs
-     `(("python-six" ,python-six)
+     `(("python-importlib-metadata" ,python-importlib-metadata)
+       ("python-six" ,python-six)
        ("python-parse" ,python-parse)
        ("python-parse-type" ,python-parse-type)))
     (arguments
@@ -2043,18 +2062,17 @@ create data based on random numbers and yet remain repeatable.")
 (define-public python-freezegun
   (package
     (name "python-freezegun")
-    (version "0.3.11")
+    (version "0.3.12")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "freezegun" version))
        (sha256
-        (base32 "1nh0fzqjwg88n57k3qa8mxnmiwrr7lqyd5xvc96qn5g8zcxv8fg8"))))
+        (base32 "1rx57v8ryjncjimg8hys9kx1r3rknvwcl4y340g20jn0sf69qk9a"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-mock" ,python-mock)
-       ("python-nose" ,python-nose)
-       ("python-coverage" ,python-coverage)))
+       ("python-pytest" ,python-pytest)))
     (propagated-inputs
      `(("python-six" ,python-six)
        ("python-dateutil" ,python-dateutil)))
@@ -2065,7 +2083,7 @@ create data based on random numbers and yet remain repeatable.")
          ;; package does not include the Makefile.
          (replace 'check
            (lambda _
-             (invoke "nosetests" "./tests/"))))))
+             (invoke "pytest" "-vv"))))))
     (home-page "https://github.com/spulec/freezegun")
     (synopsis "Test utility for mocking the datetime module")
     (description

gnu/packages/chromium.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2019 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2019 Alex Griffin <a@ajgrf.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -35,6 +36,7 @@
   #:use-module (gnu packages cups)
   #: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)
@@ -67,10 +69,12 @@
   #:use-module (gnu packages xiph)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xdisorg)
-  #:use-module (gnu packages xorg))
+  #:use-module (gnu packages xorg)
+  #:use-module (srfi srfi-1))
 
 (define %preserved-third-party-files
-  '("base/third_party/dmg_fp" ;X11-style
+  '("base/third_party/cityhash" ;Expat
+    "base/third_party/dmg_fp" ;X11-style
     "base/third_party/dynamic_annotations" ;BSD-2
     "base/third_party/icu" ;Unicode, X11-style
     "base/third_party/superfasthash" ;BSD-3
@@ -82,7 +86,7 @@
     "courgette/third_party/divsufsort" ;Expat
     "net/third_party/mozilla_security_manager" ;MPL-1.1/GPL2+/LGPL2.1+
     "net/third_party/nss" ;MPL-2.0
-    "net/third_party/quic" ;BSD-3
+    "net/third_party/quiche" ;BSD-3
     "net/third_party/uri_template" ;ASL2.0
     "third_party/abseil-cpp" ;ASL2.0
     "third_party/adobe/flash/flapper_version.h" ;no license, trivial
@@ -98,9 +102,14 @@
     "third_party/angle/third_party/vulkan-tools" ;ASL2.0
     "third_party/angle/third_party/vulkan-validation-layers" ;ASL2.0
     "third_party/apple_apsl" ;APSL2.0
+    "third_party/axe-core" ;MPL2.0
     "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
@@ -117,13 +126,14 @@
     "third_party/ced" ;BSD-3
     "third_party/cld_3" ;ASL2.0
     "third_party/crashpad" ;ASL2.0
+    "third_party/crashpad/crashpad/third_party/lss" ;ASL2.0
     "third_party/crashpad/crashpad/third_party/zlib/zlib_crashpad.h" ;Zlib
     "third_party/crc32c" ;BSD-3
     "third_party/cros_system_api" ;BSD-3
     "third_party/dav1d" ;BSD-2
+    "third_party/dawn" ;ASL2.0
     "third_party/dom_distiller_js" ;BSD-3
     "third_party/emoji-segmenter" ;ASL2.0
-    "third_party/fips181" ;BSD-3
     "third_party/flatbuffers" ;ASL2.0
     "third_party/glslang" ;BSD-3, Expat, ASL2.0
     "third_party/google_input_tools" ;ASL2.0
@@ -159,6 +169,7 @@
     "third_party/nasm" ;BSD-2
     "third_party/node" ;Expat
     "third_party/node/node_modules/polymer-bundler/lib/third_party/UglifyJS2" ;BSD-2
+    "third_party/openscreen" ;BSD-3
     "third_party/ots" ;BSD-3
     "third_party/pdfium" ;BSD-3
     "third_party/pdfium/third_party/agg23" ;Expat
@@ -166,6 +177,7 @@
     "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/pffft" ;the "FFTPACK" license, similar to BSD-3
     "third_party/ply" ;BSD-3
     "third_party/polymer" ;BSD-3
     "third_party/protobuf" ;BSD-3
@@ -176,9 +188,10 @@
     "third_party/s2cellid" ;ASL2.0
     "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/vulkan" ;BSD-3
+    "third_party/skia/third_party/vulkanmemoryallocator" ;BSD-3, Expat
     "third_party/smhasher" ;Expat, public domain
     "third_party/speech-dispatcher" ;GPL2+
     "third_party/spirv-headers" ;ASL2.0
@@ -187,6 +200,8 @@
     "third_party/ungoogled" ;BSD-3
     "third_party/usb_ids" ;BSD-3
     "third_party/usrsctp" ;BSD-2
+    "third_party/wayland/wayland_scanner_wrapper.py" ;BSD-3
+    "third_party/wayland-protocols" ;Expat
     "third_party/web-animations-js" ;ASL2.0
     "third_party/webdriver" ;ASL2.0
     "third_party/webrtc" ;BSD-3
@@ -223,54 +238,80 @@ from forcing GEXP-PROMISE."
                       #:system system
                       #:guile-for-build guile)))
 
-(define %chromium-version "74.0.3729.131")
-(define %ungoogled-revision "9e33022f3ac7de2a12e3c7a7923799c9bbbf8194")
-(define %debian-revision "debian/74.0.3729.108-1")
+(define %chromium-version "76.0.3809.100")
+(define %ungoogled-revision "8eba5c0df1a318012e3deab39a9add252a0d56a3")
+(define %debian-revision "debian/76.0.3809.87-2")
 (define package-revision "0")
-
 (define %package-version (string-append %chromium-version "-"
                                         package-revision "."
                                         (string-take %ungoogled-revision 7)))
 
+(define %chromium-origin
+  (origin
+    (method url-fetch)
+    (uri (string-append "https://commondatastorage.googleapis.com"
+                        "/chromium-browser-official/chromium-"
+                        %chromium-version ".tar.xz"))
+    (sha256
+     (base32
+      "0vfjfxsqf8jrmd7y08ln1lpbilwi150875zn2bawwdq87vd3mncc"))))
+
+(define %ungoogled-origin
+  (origin
+    (method git-fetch)
+    (uri (git-reference (url "https://github.com/Eloston/ungoogled-chromium")
+                        (commit %ungoogled-revision)))
+    (file-name (git-file-name "ungoogled-chromium"
+                              (string-take %ungoogled-revision 7)))
+    (sha256
+     (base32
+      "08fd9whfc1qky44xqxbypr7jz1rg6cma017wj4b5c5b14grxz6k6"))))
+
+(define %debian-origin
+  (origin
+    (method git-fetch)
+    (uri (git-reference
+          (url "https://salsa.debian.org/chromium-team/chromium.git")
+          (commit %debian-revision)))
+    (file-name (git-file-name "debian-chromium-packaging"
+                              (if (string-prefix? "debian/" %debian-revision)
+                                  (cadr (string-split %debian-revision #\/))
+                                  (string-take %debian-revision 7))))
+    (sha256
+     (base32
+      "1fjhpzrxmgjr7i31li1vsfmp0qkbi0cpyc7p1zjwvf2x4da0v907"))))
+
+(define (gentoo-patch name hash revision)
+  (origin
+    (method url-fetch)
+    (uri (string-append "https://gitweb.gentoo.org/repo/gentoo.git/plain"
+                        "/www-client/chromium/files/" name "?id=" revision))
+    (file-name name)
+    (sha256 (base32 hash))))
+
+(define-syntax-rule (gentoo-patches (name hash) ...)
+  (list (gentoo-patch name hash "9fd80e7d75aa63843ec33c9d44fee32596ae8f25")
+        ...))
+
+(define %auxiliary-patches
+  ;; XXX: Debians "gcc/wrong-namespace.patch" and "fixes/inspector.patch" does
+  ;; not work for us, so we take these upstream fixes via Gentoo instead.
+  (gentoo-patches
+   ("chromium-76-quiche.patch" "1cs0y16jn7r1nxh0j36vqcsdvigl902kdcqfmyivnxgblrx66l2i")
+   ("chromium-76-gcc-blink-namespace1.patch"
+    "0k7nrn0dhvqxj4sg2gndzxih0l1f77h6pv7jhcdz7h69sm4xci2z")
+   ("chromium-76-gcc-blink-namespace2.patch"
+    "014y2d8ii9sr340sjbv1fhsjd5s3dl0vbmq5wzlkdjsp91dcn9ch")))
+
 ;; This is a "computed" origin that does the following:
 ;; *) Runs the Ungoogled scripts on a pristine Chromium tarball.
 ;; *) Applies Debians Chromium patches, for their unbundling and GCC work.
 ;; *) Prunes all third_party directories that are not explicitly preserved.
 ;; *) Adjusts "GN" build files such that system libraries are preferred.
 (define ungoogled-chromium-source
-  (let ((chromium-source
-         (origin
-           (method url-fetch)
-           (uri (string-append "https://commondatastorage.googleapis.com"
-                               "/chromium-browser-official/chromium-"
-                               %chromium-version ".tar.xz"))
-           (sha256
-            (base32
-             "11m9mlzrqzmz7rhl0ff7lry2s4yjrdkfi36qfv48m1cg5y2cfy6i"))))
-        (ungoogled-source
-         (origin
-           (method git-fetch)
-           (uri (git-reference (url "https://github.com/Eloston/ungoogled-chromium")
-                               (commit %ungoogled-revision)))
-           (file-name (git-file-name "ungoogled-chromium"
-                                     (string-take %ungoogled-revision 7)))
-           (sha256
-            (base32
-             "08whx582p3a2nivkj7kwin09a8acybr00z6344smb9xjlxy9rkp4"))))
-        (debian-source
-         (origin
-           (method git-fetch)
-           (uri (git-reference
-                 (url "https://salsa.debian.org/chromium-team/chromium.git")
-                 (commit %debian-revision)))
-           (file-name (git-file-name "debian-chromium-packaging"
-                                     (if (string-prefix? "debian/" %debian-revision)
-                                         (cadr (string-split %debian-revision #\/))
-                                         (string-take %debian-revision 7))))
-           (sha256
-            (base32
-             "1bn0c86sxkkxgdz0i88y0zh4zr39l6379r2rhgk3b3qbvwz25s3j")))))
-
+  (let ((chromium-source %chromium-origin)
+        (ungoogled-source %ungoogled-origin)
+        (debian-source %debian-origin))
     (origin
       (method computed-origin-method)
       (file-name (string-append "ungoogled-chromium-" %package-version ".tar.xz"))
@@ -302,6 +343,12 @@ from forcing GEXP-PROMISE."
                    (force-output)
                    (invoke "tar" "xf" #+chromium-source)
 
+                   ;; Ungoogled-Chromium contains a forked subset of the Debian
+                   ;; patches.  Disable those, as we apply newer versions later.
+                   (substitute* "patches/series"
+                     ((".*/debian_buster/.*")
+                      ""))
+
                    (format #t "Ungooglifying...~%")
                    (force-output)
                    (invoke "python3" "utils/prune_binaries.py" chromium-dir
@@ -318,16 +365,7 @@ from forcing GEXP-PROMISE."
                      (force-output)
                      (let* ((debian  #+debian-source)
                             (patches (string-append debian "/debian/patches"))
-                            (series  (string-append patches "/series"))
-                            (grep-q (lambda (query file)
-                                      (with-input-from-file file
-                                        (lambda ()
-                                          (let loop ((line (read-line))
-                                                     (match #f))
-                                            (if (or match (eof-object? line))
-                                                (if match #t #f)
-                                                (loop (read-line)
-                                                      (string-contains line query)))))))))
+                            (series  (string-append patches "/series")))
                        (with-input-from-file series
                          (lambda ()
                            (let loop ((line (read-line)))
@@ -335,20 +373,35 @@ from forcing GEXP-PROMISE."
                                (when (and (> (string-length line) 1)
                                           ;; Skip the Debian-specific ones.
                                           (not (string-prefix? "debianization/" line))
-                                          (not (string-prefix? "gcc6/" line))
+                                          (not (string-prefix? "buster/" line))
                                           ;; And those that conflict with Ungoogled.
                                           (not (any (cute string-suffix? <> line)
                                                     '("widevine-buildflag.patch"
                                                       "signin.patch"
-                                                      "third-party-cookies.patch")))
-                                          ;; Ungoogled includes a subset of the Debian
-                                          ;; patches.  Exclude those already present.
-                                          (not (grep-q line "../patches/series")))
+                                                      "third-party-cookies.patch"
+
+                                                      ;; XXX: 'fixes/inspector.patch'
+                                                      ;; makes v8 reuse the top-level
+                                                      ;; third_party/inspector_protocol
+                                                      ;; instead of its own bundled copy,
+                                                      ;; but that does not work here for
+                                                      ;; some reason.  Ignore that patch
+                                                      ;; and those that depend on it.
+                                                      "wrong-namespace.patch"
+                                                      "explicit-specialization.patch"
+                                                      "inspector.patch"))))
                                  (invoke "patch" "--force" "-p1" "--input"
                                          (string-append patches "/" line)
                                          "--no-backup-if-mismatch"))
                                (loop (read-line)))))))
 
+                     (format #t "Applying Guix-specific patches...~%")
+                     (force-output)
+                     (for-each (lambda (patch)
+                                 (invoke "patch" "--force" "-p1" "--input"
+                                         patch "--no-backup-if-mismatch"))
+                               '#+%auxiliary-patches)
+
                      (format #t "Pruning third party files...~%")
                      (force-output)
                      (apply invoke "python"
@@ -434,6 +487,7 @@ from forcing GEXP-PROMISE."
              "enable_reporting=false"
              "enable_service_discovery=false"
              "enable_swiftshader=false"
+             "enable_vr=false"
              "enable_widevine=false"
              ;; Disable type-checking for the Web UI to avoid a Java dependency.
              "closure_compile=false"
@@ -446,12 +500,14 @@ from forcing GEXP-PROMISE."
              "is_clang=false"
              ;; Disable debugging features to save space.  These are normally
              ;; pulled in by "is_official_build", but that requires "is_clang".
-             "blink_symbol_level=0"
              "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"
@@ -473,7 +529,7 @@ from forcing GEXP-PROMISE."
                    '("use_vaapi=true")
                    '())
 
-             ;; Don't arbitrarily restrict formats supported by system ffmpeg.
+             ;; Do not artifically restrict formats supported by system ffmpeg.
              "proprietary_codecs=true"
              "ffmpeg_branding=\"Chrome\""
 
@@ -546,12 +602,12 @@ from forcing GEXP-PROMISE."
              (substitute* "third_party/webrtc/rtc_base/strings/json.h"
                (("#include \"third_party/jsoncpp/") "#include \"json/"))
 
-             (substitute* '("ui/gfx/skia_util.h"
+             (substitute* '("components/viz/common/gpu/vulkan_context_provider.h"
                             "components/viz/common/resources/resource_format_utils.h")
                (("third_party/vulkan/include/") ""))
 
              (substitute* "third_party/skia/include/gpu/vk/GrVkVulkan.h"
-               (("\\.\\./\\.\\./include/third_party/vulkan/") ""))
+               (("include/third_party/vulkan/") ""))
 
              ;; Building chromedriver embeds some files using the ZIP
              ;; format which doesn't support timestamps before
@@ -572,6 +628,9 @@ from forcing GEXP-PROMISE."
              (setenv "AR" "ar") (setenv "NM" "nm")
              (setenv "CC" "gcc") (setenv "CXX" "g++")
 
+             ;; Prevent GCC from optimizing away null pointer safety checks.
+             (setenv "CXXFLAGS" "-fno-delete-null-pointer-checks")
+
              ;; Work around <https://bugs.gnu.org/30756>.
              (unsetenv "C_INCLUDE_PATH")
              (unsetenv "CPLUS_INCLUDE_PATH")
@@ -597,9 +656,11 @@ from forcing GEXP-PROMISE."
                (format #t "Dumping configure flags...\n")
                (invoke "gn" "args" "out/Release" "--list"))))
          (replace 'build
-           (lambda* (#:key outputs #:allow-other-keys)
+           (lambda* (#:key (parallel-build? #t) #:allow-other-keys)
              (invoke "ninja" "-C" "out/Release"
-                     "-j" (number->string (parallel-job-count))
+                     "-j" (if parallel-build?
+                              (number->string (parallel-job-count))
+                              "1")
                      "chrome"
                      "chromedriver")))
          (replace 'install
@@ -643,12 +704,6 @@ from forcing GEXP-PROMISE."
                            (scandir "." (cut regexp-exec install-regexp <>)))
                  (copy-file "chrome" (string-append lib "/chromium"))
 
-                 ;; TODO: Install icons from "../../chrome/app/themes" into
-                 ;; "out/share/icons/hicolor/$size".
-                 (install-file
-                  "product_logo_48.png"
-                  (string-append out "/share/icons/48x48/chromium.png"))
-
                  (copy-recursively "locales" locales)
                  (copy-recursively "resources" resources)
 
@@ -662,8 +717,18 @@ from forcing GEXP-PROMISE."
                      (,(string-append lib ":" nss "/lib/nss:" mesa "/lib:"
                                       udev "/lib")))
                    ;; Avoid file manager crash.  See <https://bugs.gnu.org/26593>.
-                   `("XDG_DATA_DIRS" ":" prefix (,(string-append gtk+ "/share"))))
-                 #t)))))))
+                   `("XDG_DATA_DIRS" ":" prefix (,(string-append gtk+ "/share")))))
+
+               (with-directory-excursion "chrome/app/theme/chromium"
+                 (for-each
+                  (lambda (size)
+                    (let ((icons (string-append out "/share/icons/hicolor/"
+                                                size "x" size "/apps")))
+                      (mkdir-p icons)
+                      (copy-file (string-append "product_logo_" size ".png")
+                                 (string-append icons "/chromium.png"))))
+                  '("22" "24" "48" "64" "128" "256")))
+               #t))))))
     (native-inputs
      `(("bison" ,bison)
        ("gcc" ,gcc-8)
@@ -697,7 +762,11 @@ from forcing GEXP-PROMISE."
        ("glib" ,glib)
        ("gtk+" ,gtk+)
        ("harfbuzz" ,harfbuzz)
-       ("icu4c" ,icu4c)
+
+       ;; Build against ICU 64 to prevent a localization problem in version 75
+       ;; and later: <https://github.com/Eloston/ungoogled-chromium/issues/778>.
+       ("icu4c" ,icu4c-64)
+
        ("jsoncpp" ,jsoncpp)
        ("lcms" ,lcms)
        ("libevent" ,libevent)
@@ -738,6 +807,11 @@ from forcing GEXP-PROMISE."
        ("udev" ,eudev)
        ("valgrind" ,valgrind)
        ("vulkan-headers" ,vulkan-headers)))
+
+    ;; Building Chromium takes ... a very long time.  On a single core, a busy
+    ;; mid-end x86 system may need more than 24 hours to complete the build.
+    (properties '((timeout . 144000)))  ;40 hours
+
     (home-page "https://github.com/Eloston/ungoogled-chromium")
     (description
      "Ungoogled-Chromium is the Chromium web browser, with some functionality
@@ -755,3 +829,30 @@ disabled in order to protect the users privacy.")
                    (license:non-copyleft "chrome://credits"
                                          "See chrome://credits for more information.")
                    license:lgpl2.1+))))
+
+(define-public ungoogled-chromium/wayland
+  (package/inherit ungoogled-chromium
+    (name "ungoogled-chromium-wayland")
+    (inputs
+     `(("wayland" ,wayland)
+       ("wayland-protocols" ,wayland-protocols)
+       ;; Remove inputs only needed for X11.
+       ,@(fold alist-delete (package-inputs ungoogled-chromium)
+               '("libx11" "libxcb" "libxcomposite" "libxcursor"
+                 "libxdamage" "libxext" "libxfixes" "libxi"
+                 "libxrender" "libxtst" "libxext" "libxrandr"
+                 "libxscrnsaver"))))
+
+    (arguments
+     (substitute-keyword-arguments (package-arguments ungoogled-chromium)
+       ((#:configure-flags flags)
+        `(append (list "use_ozone=true"
+                       "ozone_platform_wayland=true"
+                       "ozone_auto_platforms=false"
+                       "use_xkbcommon=true"
+                       "use_system_minigbm=true"
+                       "use_system_libwayland=true"
+                       (string-append "system_wayland_scanner_path=\""
+                                      (assoc-ref %build-inputs "wayland")
+                                      "/bin/wayland-scanner\""))
+                 (delete "use_vaapi=true" ,flags)))))))

gnu/packages/ci.scm

@@ -46,147 +46,6 @@
   #:use-module (gnu packages xml)
   #:use-module (guix build-system gnu))
 
-(define-public hydra
-  (let ((commit "1ff48da3d3d4a425063f5b7dd0b89d35270f8932"))
-    (package
-      (name "hydra")
-      (version (string-append "20151030." (string-take commit 7)))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/NixOS/hydra")
-                      (commit commit)))
-                (file-name (string-append name "-" version))
-                (patches (search-patches
-                          ;; TODO: Remove once we have a darcs input
-                          "hydra-disable-darcs-test.patch"))
-                (sha256
-                 (base32
-                  "0ni8i8v1nxxfr51rz8m6znwpbm77vr7i05k506hmgmg32r938lap"))))
-      (build-system gnu-build-system)
-      (native-inputs
-       `(("unzip" ,unzip)
-         ("pkg-config" ,pkg-config)
-         ;; For documentation
-         ("dblatex" ,dblatex)
-         ("xsltproc" ,libxslt)
-         ("docbook-xsl" ,docbook-xsl)
-         ;; For bootstrap
-         ("autoconf" ,autoconf)
-         ("automake" ,automake)
-         ("libtool" ,libtool)
-         ;; For tests
-         ("git" ,git)
-         ("subversion" ,subversion)
-         ("mercurial" ,mercurial)
-         ("bazaar" ,bazaar)))
-      (inputs
-       `(("libpqxx" ,libpqxx)
-         ("perl" ,perl)
-         ("guile" ,guile-2.0)
-         ("openssl" ,openssl)
-         ("bzip2" ,bzip2)
-         ("gzip" ,gzip)
-         ("sed" ,sed)
-         ("starman" ,starman)
-         ("git" ,git)
-         ("subversion" ,subversion)
-         ("mercurial" ,mercurial)
-         ("bazaar" ,bazaar)
-         ("nix" ,nix)
-         ;; Lots o' perl modules...
-         ("perl-catalyst-action-rest" ,perl-catalyst-action-rest)
-         ("perl-catalyst-authentication-store-dbix-class"
-          ,perl-catalyst-authentication-store-dbix-class)
-         ("perl-catalyst-devel" ,perl-catalyst-devel)
-         ("perl-catalyst-dispatchtype-regex" ,perl-catalyst-dispatchtype-regex)
-         ("perl-catalyst-plugin-accesslog" ,perl-catalyst-plugin-accesslog)
-         ("perl-catalyst-plugin-authorization-roles"
-          ,perl-catalyst-plugin-authorization-roles)
-         ("perl-catalyst-plugin-captcha" ,perl-catalyst-plugin-captcha)
-         ("perl-catalyst-plugin-session-state-cookie"
-          ,perl-catalyst-plugin-session-state-cookie)
-         ("perl-catalyst-plugin-session-store-fastmmap"
-          ,perl-catalyst-plugin-session-store-fastmmap)
-         ("perl-catalyst-plugin-stacktrace" ,perl-catalyst-plugin-stacktrace)
-         ("perl-catalyst-traitfor-request-proxybase"
-          ,perl-catalyst-traitfor-request-proxybase)
-         ("perl-catalyst-view-download" ,perl-catalyst-view-download)
-         ("perl-catalyst-view-json" ,perl-catalyst-view-json)
-         ("perl-catalyst-view-tt" ,perl-catalyst-view-tt)
-         ("perl-catalystx-roleapplicator" ,perl-catalystx-roleapplicator)
-         ("perl-catalystx-script-server-starman"
-          ,perl-catalystx-script-server-starman)
-         ("perl-crypt-randpasswd" ,perl-crypt-randpasswd)
-         ("perl-data-dump" ,perl-data-dump)
-         ("perl-datetime" ,perl-datetime)
-         ("perl-dbd-pg" ,perl-dbd-pg)
-         ("perl-dbd-sqlite" ,perl-dbd-sqlite)
-         ("perl-digest-sha1" ,perl-digest-sha1)
-         ("perl-email-mime" ,perl-email-mime)
-         ("perl-email-sender" ,perl-email-sender)
-         ("perl-file-slurp" ,perl-file-slurp)
-         ("perl-io-compress" ,perl-io-compress)
-         ("perl-ipc-run" ,perl-ipc-run)
-         ("perl-json-any" ,perl-json-any)
-         ("perl-json-xs" ,perl-json-xs)
-         ("perl-libwww" ,perl-libwww)
-         ("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
-         ("perl-net-amazon-s3" ,perl-net-amazon-s3)
-         ("perl-net-statsd" ,perl-net-statsd)
-         ("perl-padwalker" ,perl-padwalker)
-         ("perl-readonly" ,perl-readonly)
-         ("perl-set-scalar" ,perl-set-scalar)
-         ("perl-sql-splitstatement" ,perl-sql-splitstatement)
-         ("perl-sys-hostname-long" ,perl-sys-hostname-long)
-         ("perl-text-diff" ,perl-text-diff)
-         ("perl-text-table" ,perl-text-table)
-         ("perl-xml-simple" ,perl-xml-simple)))
-      (arguments
-       `(#:configure-flags
-         (let ((docbook (assoc-ref %build-inputs "docbook-xsl")))
-           (list (string-append "--with-docbook-xsl="
-                                docbook "/xml/xsl/docbook-xsl-"
-                                ,(package-version docbook-xsl))
-                 (string-append "--docdir=" %output
-                                "/doc/hydra-" ,version)))
-         #:phases (modify-phases %standard-phases
-                    (add-before
-                     'check 'check-setup
-                     (lambda _ (setenv "LOGNAME" "test.log")))
-                    (add-after
-                     'install 'wrap-program
-                     (lambda* (#:key inputs outputs #:allow-other-keys)
-                       (let ((out (assoc-ref outputs "out")))
-                         (for-each
-                          (lambda (file)
-                            (wrap-program file
-                              `("PATH" ":" prefix
-                                (,(string-append out "/bin")
-                                 ,@(map (lambda (i)
-                                          (string-append (assoc-ref inputs i)
-                                                         "/bin"))
-                                        '("subversion" "git" "bazaar"
-                                          "mercurial" "coreutils" "gzip"
-                                          "sed" "unzip" "nix"))))
-                              `("PERL5LIB" ":" prefix
-                                (,(string-append out "/libexec/hydra/lib")
-                                 ,@(search-path-as-string->list
-                                    (getenv "PERL5LIB"))))
-                              `("HYDRA_RELEASE" = (,,version))
-                              `("HYDRA_HOME" =
-                                (,(string-append out "/libexec/hydra")))
-                              `("NIX_RELEASE" = (,,(package-version nix)))))
-                          (find-files (string-append out "/bin")
-                                      ".*"))))))))
-      (home-page "https://nixos.org/hydra")
-      (synopsis "Continuous build system")
-      (description
-       "Hydra is a tool for continuous integration testing and software
-release that uses a purely functional language to describe build jobs and
-their dependencies.")
-      (license l:gpl3+))))
-
 (define-public cuirass
   (let ((commit "0b40dca734468e8b12b3ff58e3e779679f17d38e")
         (revision "21"))
@@ -262,7 +121,7 @@ their dependencies.")
        `(("guile" ,guile-2.2)
          ("guile-fibers" ,guile-fibers)
          ("guile-gcrypt" ,guile-gcrypt)
-         ("guile-json" ,guile-json)
+         ("guile-json" ,guile-json-1)
          ("guile-sqlite3" ,guile-sqlite3)
          ("guile-git" ,guile-git)
          ;; FIXME: this is propagated by "guile-git", but it needs to be among

gnu/packages/cluster.scm

@@ -24,7 +24,7 @@
   #:use-module (guix packages)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages sphinx)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages tls))
 

gnu/packages/commencement.scm

@@ -54,7 +54,8 @@
   #:use-module (srfi srfi-26)
   #:use-module (ice-9 vlist)
   #:use-module (ice-9 match)
-  #:use-module (ice-9 regex))
+  #:use-module (ice-9 regex)
+  #:export (make-gcc-toolchain))
 
 ;;; Commentary:
 ;;;
@@ -1014,55 +1015,65 @@ COREUTILS-FINAL vs. COREUTILS, etc."
 ;;; GCC toolchain.
 ;;;
 
-(define (make-gcc-toolchain gcc)
-  "Return a complete toolchain for GCC."
-  (package
-    (name "gcc-toolchain")
-    (version (package-version gcc))
-    (source #f)
-    (build-system trivial-build-system)
-    (arguments
-     '(#:modules ((guix build union))
-       #:builder (begin
-                   (use-modules (ice-9 match)
-                                (srfi srfi-26)
-                                (guix build union))
+;; Using the following procedure, a gcc toolchain targeting glibc-2.27 can be
+;; instantiated like this:
+;;
+;; (define-public gcc-glibc-2.27-toolchain
+;;   (make-gcc-toolchain gcc glibc-2.27))
 
-                   (let ((out (assoc-ref %outputs "out")))
+(define* (make-gcc-toolchain gcc
+                            #:optional
+                            (libc #f))
+  "Return a complete toolchain for GCC. If LIBC is specified, target that libc."
+  (let ((gcc (if libc (make-gcc-libc gcc libc) gcc))
+        (libc (if libc libc glibc-final)))
+    (package
+      (name (string-append (package-name gcc) "-toolchain"))
+      (version (package-version gcc))
+      (source #f)
+      (build-system trivial-build-system)
+      (arguments
+       '(#:modules ((guix build union))
+         #:builder (begin
+                     (use-modules (ice-9 match)
+                                  (srfi srfi-26)
+                                  (guix build union))
 
-                     (match %build-inputs
-                       (((names . directories) ...)
-                        (union-build out directories)))
+                     (let ((out (assoc-ref %outputs "out")))
 
-                     (union-build (assoc-ref %outputs "debug")
-                                  (list (assoc-ref %build-inputs
-                                                   "libc-debug")))
-                     (union-build (assoc-ref %outputs "static")
-                                  (list (assoc-ref %build-inputs
-                                                   "libc-static")))
-                     #t))))
+                       (match %build-inputs
+                         (((names . directories) ...)
+                          (union-build out directories)))
 
-    (native-search-paths (package-native-search-paths gcc))
-    (search-paths (package-search-paths gcc))
+                       (union-build (assoc-ref %outputs "debug")
+                                    (list (assoc-ref %build-inputs
+                                                     "libc-debug")))
+                       (union-build (assoc-ref %outputs "static")
+                                    (list (assoc-ref %build-inputs
+                                                     "libc-static")))
+                       #t))))
 
-    (license (package-license gcc))
-    (synopsis "Complete GCC tool chain for C/C++ development")
-    (description
-     "This package provides a complete GCC tool chain for C/C++ development to
-be installed in user profiles.  This includes GCC, as well as libc (headers
-and binaries, plus debugging symbols in the @code{debug} output), and Binutils.")
-    (home-page "https://gcc.gnu.org/")
-    (outputs '("out" "debug" "static"))
+      (native-search-paths (package-native-search-paths gcc))
+      (search-paths (package-search-paths gcc))
 
-    ;; The main raison d'être of this "meta-package" is (1) to conveniently
-    ;; install everything that we need, and (2) to make sure ld-wrapper comes
-    ;; before Binutils' ld in the user's profile.
-    (inputs `(("gcc" ,gcc)
-              ("ld-wrapper" ,(car (assoc-ref %final-inputs "ld-wrapper")))
-              ("binutils" ,binutils-final)
-              ("libc" ,glibc-final)
-              ("libc-debug" ,glibc-final "debug")
-              ("libc-static" ,glibc-final "static")))))
+      (license (package-license gcc))
+      (synopsis "Complete GCC tool chain for C/C++ development")
+      (description
+       "This package provides a complete GCC tool chain for C/C++ development to
+be   installed in user profiles.  This includes GCC, as well as libc (headers
+an  d binaries, plus debugging symbols in the @code{debug} output), and Binutils.")
+      (home-page "https://gcc.gnu.org/")
+      (outputs '("out" "debug" "static"))
+
+      ;; The main raison d'être of this "meta-package" is (1) to conveniently
+      ;; install everything that we need, and (2) to make sure ld-wrapper comes
+      ;; before Binutils' ld in the user's profile.
+      (inputs `(("gcc" ,gcc)
+                ("ld-wrapper" ,(car (assoc-ref %final-inputs "ld-wrapper")))
+                ("binutils" ,binutils-final)
+                ("libc" ,libc)
+                ("libc-debug" ,libc "debug")
+                ("libc-static" ,libc "static"))))))
 
 (define-public gcc-toolchain-4.8
   (make-gcc-toolchain gcc-4.8))

gnu/packages/compression.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2017, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
@@ -13,7 +13,7 @@
 ;;; Copyright © 2016, 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2016, 2019 Kei Kebreau <kkebreau@posteo.net>
-;;; Copyright © 2016, 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2016, 2018, 2019 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 ng0 <ng0@n0.is>
 ;;; Copyright © 2017 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
 ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
@@ -23,6 +23,7 @@
 ;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
+;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -55,11 +56,13 @@
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages curl)
+  #:use-module (gnu packages documentation)
   #:use-module (gnu packages file)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages qt)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages valgrind)
   #:use-module (ice-9 match)
@@ -128,7 +131,16 @@ in compression.")
      `(#:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'enter-source
-           (lambda _ (chdir "contrib/minizip") #t)))))
+           (lambda _ (chdir "contrib/minizip") #t))
+         (add-after 'install 'remove-crypt-h
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Remove <minizip/crypt.h> because it interferes with libc's
+             ;; <crypt.h> given that 'minizip.pc' says "-I…/include/minizip".
+             ;; Fedora does the same:
+             ;; <https://src.fedoraproject.org/rpms/zlib/c/4d2785ec3116947872f6f32dc4104e6d36d8a7a4?branch=master>.
+             (let ((out (assoc-ref outputs "out")))
+               (delete-file (string-append out "/include/minizip/crypt.h"))
+               #t))))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
@@ -1351,22 +1363,50 @@ or junctions, and always follows hard links.")
 (define-public zstd
   (package
     (name "zstd")
-    (version "1.3.8")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/facebook/zstd/releases/download/"
                            "v" version "/zstd-" version ".tar.gz"))
        (sha256
-        (base32 "13nlsqhkn276frxrzjdn7wz0j9zz414lf336885ykyxcvw2a0gr9"))))
+        (base32 "1ja3nrjynmiwwdjrf6crraizkbagp7y414bqqq2ady91nn1hjwqj"))))
     (build-system gnu-build-system)
+    (outputs '("out"                    ;1.1MiB executables and documentation
+               "lib"                    ;1MiB shared library and headers
+               "static"))               ;1MiB static library
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (delete 'configure))           ; no configure script
+         (delete 'configure)            ;no configure script
+         (add-after 'install 'adjust-library-locations
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (lib (assoc-ref outputs "lib"))
+                    (static (assoc-ref outputs "static"))
+                    (shared-libs (string-append lib "/lib"))
+                    (static-libs (string-append static "/lib")))
+               ;; Move the static library to its own output to save ~1MiB.
+               (mkdir-p static-libs)
+               (for-each (lambda (ar)
+                           (link ar (string-append static-libs "/"
+                                                   (basename ar)))
+                           (delete-file ar))
+                         (find-files shared-libs "\\.a$"))
+
+               ;; While here, remove prefix= from the pkg-config file because it
+               ;; is unused, and because it contains a needless reference to $out.
+               ;; XXX: It would be great if #:disallow-references worked between
+               ;; outputs.
+               (substitute* (string-append shared-libs "/pkgconfig/libzstd.pc")
+                 (("^prefix=.*") ""))
+
+               #t))))
        #:make-flags
        (list "CC=gcc"
              (string-append "PREFIX=" (assoc-ref %outputs "out"))
+             (string-append "LIBDIR=" (assoc-ref %outputs "lib") "/lib")
+             (string-append "INCLUDEDIR=" (assoc-ref %outputs "lib") "/include")
              ;; Skip auto-detection of, and creating a dependency on, the build
              ;; environment's ‘xz’ for what amounts to a dubious feature anyway.
              "HAVE_LZMA=0"
@@ -1877,3 +1917,40 @@ compressor.  UPX typically reduces the file size of programs and shared
 libraries by around 50%--70%, thus reducing disk space, network load times,
 download times, and other distribution and storage costs.")
     (license license:gpl2+)))
+
+(define-public quazip
+  (package
+    (name "quazip")
+    (version "0.8.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/stachenov/quazip.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1g473gnsbkvxpsv8lbsmhspn7jnq86b05zzgqh11r581v8ndvz5s"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f))                    ;no test
+    (native-inputs
+     `(("doxygen" ,doxygen)))
+    (inputs
+     `(("qtbase" ,qtbase)
+       ("zlib" ,zlib)))
+    (home-page "https://stachenov.github.io/quazip/index.html")
+    (synopsis "Qt/C++ wrapper for Minizip")
+    (description "QuaZIP is a simple C++ wrapper over Gilles Vollant's
+ZIP/UNZIP package that can be used to access ZIP archives.  It uses
+Trolltech's Qt toolkit.
+
+QuaZIP allows you to access files inside ZIP archives using QIODevice
+API, and that means that you can also use QTextStream, QDataStream or
+whatever you would like to use on your zipped files.
+
+QuaZIP provides complete abstraction of the ZIP/UNZIP API, for both
+reading from and writing to ZIP archives. ")
+    ;; Project is distributed under LGPL, but "quazip/z*" "quazip/unzip.*" are
+    ;; distributed under zlib terms.
+    (license (list license:lgpl2.1+ license:zlib))))

gnu/packages/connman.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
@@ -160,13 +160,22 @@ sharing) to clients via USB, ethernet, WiFi, cellular and Bluetooth.")
              (invoke "qmake"
                      (string-append "PREFIX="
                                     (assoc-ref outputs "out")))))
-         (add-before 'install 'fix-Makefiles
+         (add-before 'build 'fix-Makefiles
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let ((out (assoc-ref outputs "out")))
                (substitute* (find-files "." "Makefile")
                  (("INSTALL_ROOT)")
                   (string-append "INSTALL_ROOT)" out))
-                 (("/usr/bin") "/bin"))))))))
+                 (("/usr") ""))
+               (substitute* '("apps/cmstapp/cmstapp.pro"
+                              "apps/cmstapp/code/control_box/controlbox.cpp"
+                              "apps/rootapp/rootapp.pro"
+                              "apps/rootapp/system/org.cmst.roothelper.service"
+                              "cmst.pri"
+                              "cmst.pro")
+                 (("/usr") out)
+                 (("/etc") (string-append out "/etc")))
+               #t))))))
     (home-page "https://github.com/andrew-bibb/cmst")
     (synopsis "Qt frontend for Connman")
     (description

gnu/packages/coq.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Dan Frumin <dfrumin@cs.ru.nl>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -25,6 +25,7 @@
   #:use-module (gnu packages boost)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages flex)
+  #:use-module (gnu packages gawk)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ocaml)
   #:use-module (gnu packages perl)
@@ -42,7 +43,7 @@
 (define-public coq
   (package
     (name "coq")
-    (version "8.9.0")
+    (version "8.9.1")
     (source
      (origin
        (method git-fetch)
@@ -51,7 +52,7 @@
              (commit (string-append "V" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "01ad7az6f95w16xya7979lk32agy22lf4bqgqf5qpnarpkpxhbw8"))))
+        (base32 "1p4z967s18wkblayv12ygqsrqlyk5ax1pz40yf4kag8pva6gblhk"))))
     (native-search-paths
      (list (search-path-specification
             (variable "COQPATH")
@@ -498,7 +499,7 @@ uses Ltac to synthesize the substitution operation.")
 (define-public coq-equations
   (package
     (name "coq-equations")
-    (version "1.2-beta2")
+    (version "1.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -507,7 +508,7 @@ uses Ltac to synthesize the substitution operation.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0y2zwv7jxs1crprj5qvg46h0v9wyfn99ln40yskq91y9h1lj5h3j"))))
+                "1q3wvicr43bgy7xn1diwh4j43mnrhprrc2xd22qlbz9cl6bhf8bj"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("ocaml"  ,ocaml)
@@ -535,3 +536,59 @@ compiles everything down to eliminators for inductive types, equality
 and accessibility, providing a definitional extension to the Coq
 kernel.")
     (license license:lgpl2.1)))
+
+(define-public coq-stdpp
+  (package
+    (name "coq-stdpp")
+    (version "1.2.0")
+    (synopsis "Alternative Coq standard library std++")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://gitlab.mpi-sws.org/iris/stdpp.git")
+                    (commit (string-append "coq-stdpp-" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32 "11m7kqxsbxygk41v2wsi3npdzwin9fcnzc1gn0gq0rd57wnqk83i"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("coq" ,coq)))
+    (arguments
+     `(#:tests? #f ;; the tests are being run automaticlly as part of `make all`
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (setenv "COQLIB" (string-append (assoc-ref outputs "out") "/lib/coq/"))
+             (invoke "make"
+                     (string-append "COQLIB=" (assoc-ref outputs "out")
+                                    "/lib/coq/")
+                     "install"))))))
+    (description "This project contains an extended \"Standard Library\" for
+Coq called coq-std++.  The key features are:
+@itemize
+@item Great number of definitions and lemmas for common data structures such
+as lists, finite maps, finite sets, and finite multisets.
+
+@item Type classes for common notations (like ∅, ∪, and Haskell-style monad
+notations) so that these can be overloaded for different data structures.
+
+@item It uses type classes to keep track of common properties of types, like
+it having decidable equality or being countable or finite.
+
+@item Most data structures are represented in canonical ways so that Leibniz
+equality can be used as much as possible (for example, for maps we have m1 =
+m2 iff ∀ i, m1 !! i = m2 !! i).  On top of that, the library provides setoid
+instances for most types and operations.
+
+@item Various tactics for common tasks, like an ssreflect inspired done tactic
+for finishing trivial goals, a simple breadth-first solver naive_solver, an
+equality simplifier simplify_eq, a solver solve_proper for proving
+compatibility of functions with respect to relations, and a solver set_solver
+for goals involving set operations.
+
+@item The library is dependency- and axiom-free.
+@end itemize")
+    (home-page "https://gitlab.mpi-sws.org/iris/stdpp")
+    (license license:bsd-3)))

gnu/packages/cpp.scm

@@ -108,17 +108,19 @@ operating system functions.")
   (package
     (name "dashel")
     (version "1.3.3")
-    (home-page "https://github.com/aseba-community/dashel")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append home-page "/archive/" version ".tar.gz"))
-              (sha256
-               (base32
-                "1ckzac1rsw3cxmpdpwcqv46jyp7risk5ybq6jjiizbqn7labf6dw"))
-              (file-name (string-append name "-" version ".tar.gz"))))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/aseba-community/dashel.git")
+             (commit version)))
+       (sha256
+        (base32 "0anks2l2i2qp0wlzqck1qgpq15a3l6dg8lw2h8s4nsj7f61lffwy"))
+       (file-name (git-file-name name version))))
     (build-system cmake-build-system)
-    (arguments '(#:tests? #f))                    ;no tests
+    (arguments '(#:tests? #f))          ; no tests
     (native-inputs `(("pkg-config" ,pkg-config)))
+    (home-page "https://github.com/aseba-community/dashel")
     (synopsis "Data stream helper encapsulation library")
     (description
      "Dashel is a data stream helper encapsulation C++ library.  It provides a
@@ -130,22 +132,23 @@ combination of these streams.")
 (define-public xsimd
   (package
     (name "xsimd")
-    (version "4.1.2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/QuantStack/xsimd/archive/"
-                    version ".tar.gz"))
-              (sha256
-               (base32
-                "0x05l4xpqr9b66sm6lkf48n6x7999ks921x6k2hzkkg6mh3gqd46"))
-              (file-name (string-append name "-" version ".tar.gz"))))
-    (home-page "https://github.com/QuantStack/xsimd")
+    (version "7.2.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/QuantStack/xsimd.git")
+             (commit version)))
+       (sha256
+        (base32 "1ny2qin1j4h35mljivh8z52kwdyjxf4yxlzb8j52ji91v2ccc88j"))
+       (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (arguments
-     `(#:test-target "xtest"))
+     `(#:configure-flags (list "-DBUILD_TESTS=ON")
+       #:test-target "xtest"))
     (native-inputs
      `(("googletest" ,googletest)))
+    (home-page "https://github.com/QuantStack/xsimd")
     (synopsis "C++ wrappers for SIMD intrinsics and math implementations")
     (description "xsimd provides a unified means for using SIMD features for
 library authors.  Namely, it enables manipulation of batches of numbers with

gnu/packages/crates-io.scm

@@ -0,0 +1,952 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2019 Ivan Petkov <ivanppetkov@gmail.com>
+;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages crates-io)
+  #:use-module (guix build-system cargo)
+  #:use-module (guix download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages))
+
+;;;
+;;; Please: Try to add new module packages in alphabetic order.
+;;;
+
+(define-public rust-autocfg
+  (package
+    (name "rust-autocfg")
+    (version "0.1.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "autocfg" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0asl6fnc35yk5l2rxwhp25v128jgm45dp754h9z8x51b6n90w4r2"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/cuviper/autocfg")
+    (synopsis "Automatic cfg for Rust compiler features")
+    (description "Rust library for build scripts to automatically configure
+code based on compiler support.  Code snippets are dynamically tested to see
+if the @code{rustc} will accept them, rather than hard-coding specific version
+support.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-bencher
+  (package
+    (name "rust-bencher")
+    (version "0.1.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bencher" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1x8p2xblgqssay8cdykp5pkfc0np0jk5bs5cx4f5av097aav9zbx"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/bluss/bencher/")
+    (synopsis "Port of the libtest benchmark runner to Rust stable")
+    (description "This package provides a port of the libtest (unstable Rust)
+benchmark runner to Rust stable releases.  Supports running benchmarks and
+filtering based on the name.  Benchmark execution works exactly the same way
+and no more (caveat: black_box is still missing!).")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-bitflags
+  (package
+    (name "rust-bitflags")
+    (version "1.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bitflags" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1zc1qb1hwsnl2d8rhzicsv9kqd5b2hwbrscrcfw5as4sfr35659x"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/bitflags/bitflags")
+    (synopsis "Macro to generate structures which behave like bitflags")
+    (description "This package provides a macro to generate structures which
+behave like a set of bitflags.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-cfg-if
+  (package
+    (name "rust-cfg-if")
+    (version "0.1.9")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cfg-if" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0csygklgz3ybpr0670rkip49zh76m43ar3k7xgypkzbzrwycx1ml"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/alexcrichton/cfg-if")
+    (synopsis "Define an item depending on parameters")
+    (description "This package provides a macro to ergonomically define an item
+depending on a large number of #[cfg] parameters.  Structured like an
+@code{if-else} chain, the first matching branch is the item that gets emitted.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-discard
+  (package
+    (name "rust-discard")
+    (version "1.0.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "discard" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1h67ni5bxvg95s91wgicily4ix7lcw7cq0a5gy9njrybaibhyb91"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/Pauan/rust-discard")
+    (synopsis "Allow for intentionally leaking memory")
+    (description "There are situations where you need to intentionally leak some
+memory but not other memory.  This package provides a discard trait which allows
+for intentionally leaking memory")
+    (license license:expat)))
+
+(define-public rust-doc-comment
+  (package
+    (name "rust-doc-comment")
+    (version "0.3.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "doc-comment" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "15rsqxgarfpb1yim9sbp9yfgj7p2dq6v51c6bq1a62paii9ylgcj"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/GuillaumeGomez/doc-comment")
+    (synopsis "Macro to generate doc comments")
+    (description "This package provides a way to generate doc comments
+from macros.")
+    (license license:expat)))
+
+(define-public rust-dtoa
+  (package
+    (name "rust-dtoa")
+    (version "0.4.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "dtoa" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0phbm7i0dpn44gzi07683zxaicjap5064w62pidci4fhhciv8mza"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/dtolnay/dtoa")
+    (synopsis "Fast functions for printing floating-point primitives")
+    (description "This crate provides fast functions for printing
+floating-point primitives to an @code{io::Write}.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-fallible-iterator
+  (package
+    (name "rust-fallible-iterator")
+    (version "0.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "fallible-iterator" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1xq759lsr8gqss7hva42azn3whgrbrs2sd9xpn92c5ickxm1fhs4"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/sfackler/rust-fallible-iterator")
+    (synopsis "Fallible iterator traits")
+    (description "If the @code{std} or @code{alloc} features are enabled, this
+crate provides implementations for @code{Box}, @code{Vec}, @code{BTreeMap}, and
+@code{BTreeSet}.  If the @code{std} feature is enabled, this crate additionally
+provides implementations for @code{HashMap} and @code{HashSet}.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-fnv
+  (package
+    (name "rust-fnv")
+    (version "1.0.6")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "fnv" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1ww56bi1r5b8id3ns9j3qxbi7w5h005rzhiryy0zi9h97raqbb9g"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/servo/rust-fnv")
+    (synopsis "implementation of the Fowler-Noll-Vo hash function")
+    (description "The @code{fnv} hash function is a custom @code{Hasher}
+implementation that is more efficient for smaller hash keys.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-fs-extra
+  (package
+    (name "rust-fs-extra")
+    (version "1.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "fs_extra" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0x6675wdhsx277k1k1235jwcv38naf20d8kwrk948ds26hh4lajz"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/webdesus/fs_extra")
+    (synopsis "Extra filesystem methods")
+    (description "Expanding opportunities standard library @code{std::fs} and
+@code{std::io}.  Recursively copy folders with recept information about
+process and much more.")
+    (license license:expat)))
+
+(define-public rust-futures
+  (package
+    (name "rust-futures")
+    (version "0.1.28")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "futures" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0saq8ffjw1pwf1pzhw3kq1z7dfq6wpd8x93dnni6vbkc799kkp25"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/rust-lang-nursery/futures-rs")
+    (synopsis "Implementation of zero-cost futures in Rust")
+    (description "An implementation of @code{futures} and @code{streams}
+featuring zero allocations, composability, and iterator-like interfaces.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-hex
+  (package
+    (name "rust-hex")
+    (version "0.3.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "hex" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0xsdcjiik5j750j67zk42qdnmm4ahirk3gmkmcqgq7qls2jjcl40"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/KokaKiwi/rust-hex")
+    (synopsis "Encode and decode data to/from hexadecimals")
+    (description "This crate allows for encoding and decoding data into/from
+hexadecimal representation.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-itoa
+  (package
+    (name "rust-itoa")
+    (version "0.4.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "itoa" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0zvg2d9qv3avhf3d8ggglh6fdyw8kkwqg3r4622ly5yhxnvnc4jh"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/dtolnay/itoa")
+    (synopsis "Fast functions for printing integer primitives")
+    (description "This crate provides fast functions for printing integer
+primitives to an @code{io::Write}.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-json
+  (package
+    (name "rust-json")
+    (version "0.11.14")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "json" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1hj8c6xj5c2aqqszi8naaflmcdbya1i9byyjrq4iybxjb4q91mq1"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/maciejhirsz/json-rust")
+    (synopsis "JSON implementation in Rust")
+    (description "This crate provides a JSON implementation in Rust, reducing
+friction with idiomatic Rust structs to ease interopability.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-maplit
+  (package
+    (name "rust-maplit")
+    (version "1.0.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "maplit" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0hsczmvd6zkqgzqdjp5hfyg7f339n68w83n4pxvnsszrzssbdjq8"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/bluss/maplit")
+    (synopsis "Collection of Map macros")
+    (description "This crate provides a collection of @code{literal} macros for
+@code{HashMap}, @code{HashSet}, @code{BTreeMap}, and @code{BTreeSet.}")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-matches
+  (package
+    (name "rust-matches")
+    (version "0.1.8")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "matches" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "020axl4q7rk9vz90phs7f8jas4imxal9y9kxl4z4v7a6719mrz3z"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/SimonSapin/rust-std-candidates")
+    (synopsis "Macro to evaluate whether an expression matches a pattern.")
+    (description "This package provides a macro to evaluate, as a boolean,
+whether an expression matches a pattern.")
+    (license license:expat)))
+
+(define-public rust-md5
+  (package
+    (name "rust-md5")
+    (version "0.6.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "md5" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "17b2xm4h4cvxsdjsf3kdrzqv2za60kak961xzi5kmw6g6djcssvy"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/stainless-steel/md5")
+    (synopsis "MD5 hash function in Rust")
+    (description "The package provides the MD5 hash function.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-peeking-take-while
+  (package
+    (name "rust-peeking-take-while")
+    (version "0.1.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "peeking_take_while" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "16bhqr6rdyrp12zv381cxaaqqd0pwysvm1q8h2ygihvypvfprc8r"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/fitzgen/peeking_take_while")
+    (synopsis "Provides the peeking_take_while iterator adaptor method")
+    (description
+      "Like @code{Iterator::take_while}, but calls the predicate on a peeked
+value.  This allows you to use @code{Iterator::by_ref} and
+@code{Iterator::take_while} together, and still get the first value for which
+the @code{take_while} predicate returned false after dropping the @code{by_ref}.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-percent-encoding
+  (package
+    (name "rust-percent-encoding")
+    (version "2.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "percent-encoding" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0m6rkp3iy11la04p6z3492rns6n693pvmx585dvfmzzlzak2hkxs"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/servo/rust-url/")
+    (synopsis "Percent encoding and decoding")
+    (description "This crate provides percent encoding and decoding.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-pin-utils
+  (package
+    (name "rust-pin-utils")
+    (version "0.1.0-alpha.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pin-utils" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "11xmyx00n4m37d546by2rxb8ryxs12v55cc172i3yak1rqccd52q"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/rust-lang-nursery/pin-utils")
+    (synopsis "Utilities for pinning")
+    (description "This crate provides utilities for pinning values on the stack.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-plain
+  (package
+    (name "rust-plain")
+    (version "0.2.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "plain" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "19n1xbxb4wa7w891268bzf6cbwq4qvdb86bik1z129qb0xnnnndl"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/randomites/plain")
+    (synopsis "Rust library that allows reinterpreting data safely")
+    (description "This package provides a small Rust library that allows users
+ to reinterpret data of certain types safely.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-pocket-resources
+  (package
+    (name "rust-pocket-resources")
+    (version "0.3.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pocket-resources" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1n2i5vmi8fdbw89wm5nz1ws1z9f1qax911p6ksg4scmdg23z6df1"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/tomaka/pocket-resources")
+    (synopsis "Include resources in your applications")
+    (description "This crate allows you to include resources in your
+applications.")
+    (license license:expat)))
+
+(define-public rust-ppv-lite86
+  (package
+    (name "rust-ppv-lite86")
+    (version "0.2.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "ppv-lite86" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "06snnv338w341nicfqba2jgln5dsla72ndkgrw7h1dfdb3vgkjz3"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/cryptocorrosion/cryptocorrosion")
+    (synopsis "Implementation of the crypto-simd API for x86")
+    (description "This crate provides an implementation of the crypto-simd API
+for x86.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-proc-macro2
+  (package
+    (name "rust-proc-macro2")
+    (version "0.4.30")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "proc-macro2" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "0nd71fl24sys066jrha6j7i34nfkjv44yzw8yww9742wmc8j0gfg"))))
+    (build-system cargo-build-system)
+    (arguments
+      `(#:cargo-inputs (("rust-unicode-xid" ,rust-unicode-xid))
+        #:cargo-development-inputs (("rust-quote" ,rust-quote))))
+    (home-page "https://github.com/alexcrichton/proc-macro2")
+    (synopsis "Stable implementation of the upcoming new `proc_macro` API")
+    (description "This package provides a stable implementation of the upcoming new
+`proc_macro` API.  Comes with an option, off by default, to also reimplement itself
+in terms of the upstream unstable API.")
+    ;; Dual licensed.
+    (license (list license:asl2.0 license:expat))))
+
+(define-public rust-quick-error
+  (package
+    (name "rust-quick-error")
+    (version "1.2.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "quick-error" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1w6kgwwv7p7zr0yyg5rb315lkk24bimywklwx7fsvsbwi10bjx4j"))))
+    (build-system cargo-build-system)
+    (home-page "http://github.com/tailhook/quick-error")
+    (synopsis "Macro which makes error types pleasant to write")
+    (description "This crate provides a macro which makes error types pleasant
+to write.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-quote
+  (package
+    (name "rust-quote")
+    (version "0.6.12")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "quote" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1nw0klza45hf127kfyrpxsxd5jw2l6h21qxalil3hkr7bnf7kx7s"))))
+    (build-system cargo-build-system)
+    (arguments
+      `(#:cargo-inputs (("rust-proc-macro2" ,rust-proc-macro2))))
+    (home-page "https://github.com/dtolnay/quote")
+    (synopsis "Quasi-quoting macro quote!(...)")
+    (description "Quasi-quoting macro quote!(...)")
+    ;; Dual licensed.
+    (license (list license:asl2.0 license:expat))))
+
+(define-public rust-rustc-std-workspace-core
+  (package
+    (name "rust-rustc-std-workspace-core")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "rustc-std-workspace-core" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1309xhwyai9xpz128xrfjqkmnkvgjwddznmj7brbd8i8f58zamhr"))))
+    (build-system cargo-build-system)
+    (home-page "https://crates.io/crates/rustc-std-workspace-core")
+    (synopsis "Explicitly empty crate for rust-lang/rust integration")
+    (description "This crate provides an explicitly empty crate for
+rust-lang/rust integration.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-scoped-tls
+  (package
+    (name "rust-scoped-tls")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "scoped-tls" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1hj8lifzvivdb1z02lfnzkshpvk85nkgzxsy2hc0zky9wf894spa"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/alexcrichton/scoped-tls")
+    (synopsis "Rust library providing the old standard library's scoped_thread_local")
+    (description "This crate provides a library implementation of the standard
+library's old @code{scoped_thread_local!} macro for providing scoped access to
+@dfn{thread local storage} (TLS) so any type can be stored into TLS.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-scopeguard
+  (package
+    (name "rust-scopeguard")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "scopeguard" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "03aay84r1f6w87ckbpj6cc4rnsxkxcfs13n5ynxjia0qkgjiabml"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/bluss/scopeguard")
+    (synopsis "Scope guard which will run a closure even out of scope")
+    (description "This package provides a RAII scope guard that will run a
+given closure when it goes out of scope, even if the code between panics
+(assuming unwinding panic).  Defines the macros @code{defer!},
+@code{defer_on_unwind!}, @code{defer_on_success!} as shorthands for guards
+with one of the implemented strategies.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-semver-parser
+  (package
+    (name "rust-semver-parser")
+    (version "0.9.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "semver-parser" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1ahqhvgpzhcsd28id7xnrjv4419i9yyalhm7d7zi430qx0hi2vml"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/steveklabnik/semver-parser")
+    (synopsis "Parsing of the semver spec")
+    (description "This package provides for parsing of the semver spec.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-shlex
+  (package
+    (name "rust-shlex")
+    (version "0.1.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "shlex" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1lmv6san7g8dv6jdfp14m7bdczq9ss7j7bgsfqyqjc3jnjfippvz"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/comex/rust-shlex")
+    (synopsis "Split a string into shell words, like Python's shlex")
+    (description "This crate provides a method to split a string into shell
+words, like Python's shlex.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-slab
+  (package
+    (name "rust-slab")
+    (version "0.4.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "slab" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1y59xsa27jk84sxzswjk60xcjf8b4fm5960jwpznrrcmasyva4f1"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/carllerche/slab")
+    (synopsis "Pre-allocated storage for a uniform data type")
+    (description "This create provides a pre-allocated storage for a uniform
+data type.")
+    (license license:expat)))
+
+(define-public rust-spin
+  (package
+    (name "rust-spin")
+    (version "0.5.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "spin" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0m9clchsj0rf13bggsgvbv9haiy0f6rhvnvkpvkk8720a5pkydj4"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/mvdnes/spin-rs.git")
+    (synopsis "Synchronization primitives based on spinning")
+    (description "This crate provides synchronization primitives based on
+spinning.  They may contain data, are usable without @code{std},and static
+initializers are available.")
+    (license license:expat)))
+
+(define-public rust-stdweb-internal-runtime
+  (package
+    (name "rust-stdweb-internal-runtime")
+    (version "0.1.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "stdweb-internal-runtime" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1nhpyra7glbwcpakhpj5a3d7h7kx1ynif473nzshmk226m91f8ym"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/koute/stdweb")
+    (synopsis "Internal runtime for the @code{stdweb} crate")
+    (description "This crate provides internal runtime for the @code{stdweb}
+crate.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-strsim
+  (package
+    (name "rust-strsim")
+    (version "0.9.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "strsim" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1xphwhf86yxxmcpvm4mikj8ls41f6nf7gqyjm98b74mfk81h6b03"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/dguo/strsim-rs")
+    (synopsis "Rust implementations of string similarity metrics")
+    (description "This crate includes implementations of string similarity
+metrics.  It includes Hamming, Levenshtein, OSA, Damerau-Levenshtein, Jaro,
+and Jaro-Winkler.")
+    (license license:expat)))
+
+(define-public rust-synstructure-test-traits
+  (package
+    (name "rust-synstructure-test-traits")
+    (version "0.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "synstructure_test_traits" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1b3fs2b9kc1gy9dilaxqjbdl4z0mlrbbxjzkprdx953rif1c3q66"))))
+    (build-system cargo-build-system)
+    (home-page "https://crates.io/crates/synstructure_test_traits")
+    (synopsis "Helper test traits for synstructure doctests")
+    (description
+     "This package provides helper test traits for synstructure doctests.")
+    (license license:expat)))
+
+(define-public rust-typenum
+  (package
+    (name "rust-typenum")
+    (version "1.10.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "typenum" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0sc1jirllfhdi52z1xv9yqzxzpk6v7vadd13n7wvs1wnjipn6bb1"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/paholg/typenum")
+    (synopsis "Rust library for type-level numbers evaluated at compile time")
+    (description "Typenum is a Rust library for type-level numbers evaluated at
+compile time.  It currently supports bits, unsigned integers, and signed
+integers.  It also provides a type-level array of type-level numbers, but its
+implementation is incomplete.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-ucd-util
+  (package
+    (name "rust-ucd-util")
+    (version "0.1.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "ucd-util" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0x088q5z0m09a2jqcfgsnq955y8syn1mgn35cl78qinkxm4kp6zs"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/BurntSushi/ucd-generate")
+    (synopsis "library for working with the Unicode character database")
+    (description "This package provides a small utility library for working
+with the Unicode character database.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-unicode-width
+  (package
+    (name "rust-unicode-width")
+    (version "0.1.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "unicode-width" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "09k5lipygardwy0660jhls08fsgknrazzivmn804gps53hiqc8w8"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/unicode-rs/unicode-width")
+    (synopsis "Determine displayed width according to Unicode rules")
+    (description "This crate allows you to determine displayed width of
+@code{char} and @code{str} types according to Unicode Standard Annex #11 rules.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-unicode-xid
+  (package
+    (name "rust-unicode-xid")
+    (version "0.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "unicode-xid" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1z57lqh4s18rr4x0j4fw4fmp9hf9346h0kmdgqsqx0fhjr3k0wpw"))))
+    (build-system cargo-build-system)
+    (home-page
+      "https://github.com/unicode-rs/unicode-xid")
+    (synopsis "Determine Unicode XID related properties")
+    (description "Determine whether characters have the XID_Start
+or XID_Continue properties according to Unicode Standard Annex #31.")
+    ;; Dual licensed.
+    (license (list license:asl2.0 license:expat))))
+
+(define-public rust-unindent
+  (package
+    (name "rust-unindent")
+    (version "0.1.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "unindent" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1x21ilf78aqcq9xzb9b7i628wm10rhk0jp0chlv06rkc690l8jw3"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/dtolnay/indoc")
+    (synopsis "Remove a column of leading whitespace from a string")
+    (description "This crate allows you to remove a column of leading
+whitespace from a string.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-wasm-bindgen-shared
+  (package
+    (name "rust-wasm-bindgen-shared")
+    (version "0.2.48")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "wasm-bindgen-shared" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "08rnfhjyk0f6liv8n4rdsvhx7r02glkhcbj2lp9lcbkbfpad9hnr"))))
+    (build-system cargo-build-system)
+    (home-page "https://rustwasm.github.io/wasm-bindgen/")
+    (synopsis "Shared support between wasm-bindgen and wasm-bindgen cli")
+    (description "This package provides shared support between
+@code{wasm-bindgen} and @code{wasm-bindgen} cli, an internal dependency.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-winapi
+  (package
+    (name "rust-winapi")
+    (version "0.3.7")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "winapi" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0w7pbhcl087lkggxdflfp2i92rq89ahsfdkjkv44fgmiy9m3h3pi"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-winapi-i686-pc-windows-gnu"
+         ,rust-winapi-i686-pc-windows-gnu)
+        ("rust-winapi-x86-64-pc-windows-gnu"
+         ,rust-winapi-x86-64-pc-windows-gnu))))
+    (home-page "https://github.com/retep998/winapi-rs")
+    (synopsis "Raw FFI bindings for all of Windows API.")
+    (description
+     "Raw FFI bindings for all of Windows API.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-winapi-i686-pc-windows-gnu
+  (package
+    (name "rust-winapi-i686-pc-windows-gnu")
+    (version "0.4.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "winapi-i686-pc-windows-gnu" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1dmpa6mvcvzz16zg6d5vrfy4bxgg541wxrcip7cnshi06v38ffxc"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/retep998/winapi-rs")
+    (synopsis "Import libraries for the i686-pc-windows-gnu target")
+    (description "This crate provides import libraries for the
+i686-pc-windows-gnu target.  Please don't use this crate directly, depend on
+@code{winapi} instead.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-winapi-x86-64-pc-windows-gnu
+  (package
+    (name "rust-winapi-x86-64-pc-windows-gnu")
+    (version "0.4.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "winapi-x86_64-pc-windows-gnu" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0gqq64czqb64kskjryj8isp62m2sgvx25yyj3kpc2myh85w24bki"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/retep998/winapi-rs")
+    (synopsis "Import libraries for the x86_64-pc-windows-gnu target")
+    (description "This package provides import libraries for the
+x86_64-pc-windows-gnu target.  Please don't use this crate directly, depend on
+@code{winapi} instead.")
+    (license (list license:asl2.0
+                   license:expat))))

gnu/packages/cross-base.scm

@@ -4,6 +4,7 @@
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2016 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019 Carl Dong <contact@carldong.me>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -39,7 +40,8 @@
   #:export (cross-binutils
             cross-libc
             cross-gcc
-            cross-newlib?))
+            cross-newlib?
+            cross-kernel-headers))
 
 (define-syntax %xgcc
   ;; GCC package used as the basis for cross-compilation.  It doesn't have to
@@ -248,7 +250,7 @@ target that libc."
            (cond
             ((target-mingw? target)
              (if libc
-                 `(("libc" ,mingw-w64)
+                 `(("libc" ,libc)
                    ,@inputs)
                  `(("mingw-source" ,(package-source mingw-w64))
                    ,@inputs)))
@@ -276,18 +278,19 @@ target that libc."
 
 (define* (cross-kernel-headers target
                                #:optional
+                               (linux-headers linux-libre-headers)
                                (xgcc (cross-gcc target))
                                (xbinutils (cross-binutils target)))
   "Return headers depending on TARGET."
 
   (define xlinux-headers
-    (package (inherit linux-libre-headers)
-      (name (string-append (package-name linux-libre-headers)
+    (package (inherit linux-headers)
+      (name (string-append (package-name linux-headers)
                            "-cross-" target))
       (arguments
        (substitute-keyword-arguments
            `(#:implicit-cross-inputs? #f
-             ,@(package-arguments linux-libre-headers))
+             ,@(package-arguments linux-headers))
          ((#:phases phases)
           `(alist-replace
             'build
@@ -300,7 +303,7 @@ target that libc."
             ,phases))))
       (native-inputs `(("cross-gcc" ,xgcc)
                        ("cross-binutils" ,xbinutils)
-                       ,@(package-native-inputs linux-libre-headers)))))
+                       ,@(package-native-inputs linux-headers)))))
 
   (define xgnumach-headers
     (package (inherit gnumach-headers)
@@ -507,7 +510,8 @@ and the cross tool chain."
                      #:optional
                      (libc glibc))
   (if (target-mingw? target)
-      mingw-w64
+      (let ((machine (substring target 0 (string-index target #\-))))
+        (make-mingw-w64 machine))
       libc))
 
 (define* (cross-newlib? target

gnu/packages/crypto.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2015, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018, 2019 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox>
-;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2016, 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016, 2017 ng0 <ng0@n0.is>
 ;;; Copyright © 2016, 2017, 2019 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2017 Pierre Langlois <pierre.langlois@gmx.com>
@@ -75,7 +75,7 @@
 (define-public libsodium
   (package
     (name "libsodium")
-    (version "1.0.17")
+    (version "1.0.18")
     (source (origin
             (method url-fetch)
             (uri (list (string-append
@@ -86,7 +86,7 @@
                         "releases/old/libsodium-" version ".tar.gz")))
             (sha256
              (base32
-              "1cf2d9v1gylz1qcy2zappbf526qfmph6gd6fnn3w2b347vixmhqc"))))
+              "1h9ncvj23qbbni958knzsli8dvybcswcjbx0qjjgi922nf848l3g"))))
     (build-system gnu-build-system)
     (synopsis "Portable NaCl-based crypto library")
     (description
@@ -131,16 +131,15 @@ communication, encryption, decryption, signatures, etc.")
 (define-public signify
   (package
     (name "signify")
-    (version "25")
+    (version "26")
     (home-page "https://github.com/aperezdc/signify")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference (url home-page)
-                                  (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (uri (string-append "https://github.com/aperezdc/signify/releases"
+                                  "/download/v" version "/signify-" version ".tar.xz"))
               (sha256
                (base32
-                "0zg0rffxwj2a71s1bllhrn491xsmirg9sshpq8f3vl25lv4c2cnq"))))
+                "16sl1yq5bbsads5q4a0fbrf31b0x8r1hi4wagl90nbrhrca98baw"))))
     (build-system gnu-build-system)
     ;; TODO Build with libwaive (described in README.md), to implement something
     ;; like OpenBSD's pledge().
@@ -330,14 +329,14 @@ no man page, refer to the home page for usage details.")
 (define-public tomb
   (package
     (name "tomb")
-    (version "2.5")
+    (version "2.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://files.dyne.org/tomb/"
                                   "Tomb-" version ".tar.gz"))
               (sha256
                (base32
-                "12c6qldngaw520gvb02inzkhnxbl4k0dwmddrgnaf7xashy6j0wc"))))
+                "1sr3jcn96mciyn8xd0amd1jzamxxzpybakf8an7laf26gjim1dh2"))))
     (build-system gnu-build-system)
     (native-inputs `(("sudo" ,sudo)))   ;presence needed for 'check' phase
     (inputs
@@ -356,7 +355,7 @@ no man page, refer to the home page for usage details.")
        ;; TODO: Build and install gtk and qt trays
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure)   ;no configuration to be done
+         (delete 'configure)            ;no configuration to be done
          (add-after 'install 'i18n
            (lambda* (#:key make-flags #:allow-other-keys)
              (apply invoke "make" "-C" "extras/translations"
@@ -426,7 +425,7 @@ user's graphical desktop.")
      `(("openssl" ,openssl)))
     (home-page "https://www.tarsnap.com/scrypt.html")
     (synopsis "Memory-hard encryption tool based on scrypt")
-    (description "This packages provides a simple password-based encryption
+    (description "This package provides a simple password-based encryption
 utility as a demonstration of the @code{scrypt} key derivation function.
 @code{Scrypt} is designed to be far more resistant against hardware brute-force
 attacks than alternative functions such as @code{PBKDF2} or @code{bcrypt}.")

gnu/packages/cups.scm

@@ -57,7 +57,7 @@
 (define-public cups-filters
   (package
     (name "cups-filters")
-    (version "1.22.3")
+    (version "1.25.1")
     (source(origin
               (method url-fetch)
               (uri
@@ -65,7 +65,7 @@
                               "cups-filters-" version ".tar.xz"))
               (sha256
                (base32
-                "11vilv80l3q7hz8vyhclvjcnlgk93r7p9dvg634186iddjzls0j3"))
+                "0nlq44jnjcnrbdv0dv5myg5kaycmk6a4klynpvj65xvn3l9cq28s"))
               (modules '((guix build utils)))
               (snippet
                ;; install backends, banners and filters to cups-filters output
@@ -646,7 +646,7 @@ printer/driver specific, but spooler-independent PPD file.")
               (uri "http://foo2zjs.rkkda.com/foo2zjs.tar.gz")
               (sha256
                (base32
-                "00k22vmghxls7rk2hrbz9v17wi5z8vdk3fmsp2lrfghfcad8nhpx"))))
+                "0djzp3ddslmzyxkjhzkhkg6qqqm02whjfnfvh5glprkshcskzlg9"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases

gnu/packages/curl.scm

@@ -51,7 +51,7 @@
 (define-public curl
   (package
    (name "curl")
-   (replacement curl-7.64.0)
+   (replacement curl-7.65.0)
    (version "7.63.0")
    (source (origin
             (method url-fetch)
@@ -147,10 +147,10 @@ tunneling, and so on.")
                                   "See COPYING in the distribution."))
    (home-page "https://curl.haxx.se/")))
 
-(define-public curl-7.64.0
+(define-public curl-7.65.0
   (package
     (inherit curl)
-    (version "7.64.0")
+    (version "7.65.0")
     (source
       (origin
         (method url-fetch)
@@ -158,7 +158,7 @@ tunneling, and so on.")
                             version ".tar.xz"))
         (sha256
          (base32
-          "00b0mw4fc1pbmbh55maab24x3ijdvkbpl1s4njfa4jnl6kx16brg"))))))
+          "1kb6p510m0n0y1c8fjxbcs6dyaqgm8i54pjvj29zc14lj9ix4rkp"))))))
 
 (define-public kurly
   (package

gnu/packages/databases.scm

@@ -33,6 +33,10 @@
 ;;; Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019 Jack Hill <jackhill@jackhill.us>
+;;; Copyright © 2019 Alex Griffin <a@ajgrf.com>
+;;; Copyright © 2019 Gábor Boskovits <boskovits@gmail.com>
+;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -89,11 +93,13 @@
   #:use-module (gnu packages popt)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-crypto)
+  #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages rdf)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages ruby)
   #:use-module (gnu packages serialization)
+  #:use-module (gnu packages sphinx)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages tcl)
   #:use-module (gnu packages terminals)
@@ -107,6 +113,7 @@
   #:use-module (guix download)
   #:use-module (guix bzr-download)
   #:use-module (guix git-download)
+  #:use-module (guix build-system emacs)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system perl)
@@ -125,12 +132,13 @@
     (name "4store")
     (version "1.1.6")
     (source (origin
-      (method url-fetch)
-      (uri (string-append "https://github.com/4store/4store/archive/v"
-                          version ".tar.gz"))
-      (file-name (string-append name "-" version ".tar.gz"))
+      (method git-fetch)
+      (uri (git-reference
+             (url "https://github.com/4store/4store.git")
+             (commit (string-append "v" version))))
+      (file-name (git-file-name name version))
       (sha256
-       (base32 "004fmcf1w75zhc1x3zc6kc97j4jqn2v5nhk6yb3z3cpfrhzi9j50"))
+       (base32 "1kzdfmwpzy64cgqlkcz5v4klwx99w0jk7afckyf7yqbqb4rydmpk"))
       (patches (search-patches "4store-unset-preprocessor-directive.patch"
                                "4store-fix-buildsystem.patch"))))
     (build-system gnu-build-system)
@@ -153,12 +161,6 @@
        ("cyrus-sasl" ,cyrus-sasl)
        ("openssl" ,openssl)
        ("util-linux" ,util-linux)))
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'generate-configure
-           (lambda _
-             (invoke "sh" "autogen.sh"))))))
     ;; http://www.4store.org has been down for a while now.
     (home-page "https://github.com/4store/4store")
     (synopsis "Clustered RDF storage and query engine")
@@ -268,14 +270,14 @@ mapping from string keys to string values.")
 (define-public memcached
   (package
     (name "memcached")
-    (version "1.5.13")
+    (version "1.5.16")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
              "https://memcached.org/files/memcached-" version ".tar.gz"))
        (sha256
-        (base32 "0qsdkjrns4f02lmabq8c7mzl5n4382q2p6a0dvmsjdcpjisagqb1"))))
+        (base32 "0nnccb697jhdn5gqrh3phibzs6xr4nf4ryv7nmyv5vf11n4jr8j5"))))
     (build-system gnu-build-system)
     (inputs
      `(("libevent" ,libevent)
@@ -609,15 +611,15 @@ Language.")
 (define-public mariadb
   (package
     (name "mariadb")
-    (version "10.1.38")
+    (version "10.1.41")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://downloads.mariadb.org/f/"
-                                  name "-" version "/source/"
-                                  name "-" version ".tar.gz"))
+              (uri (string-append "https://downloads.mariadb.com/MariaDB"
+                                  "/mariadb-" version "/source/mariadb-"
+                                  version ".tar.gz"))
               (sha256
                (base32
-                "0zq77w3ff9q781fn8cv46vy1v4ggb8vjarjvk51k653x4gyg9wfa"))
+                "1wh0073lqw3d9xs150bf2q3qvjwa6886mfi9khmsn7p8vapw6irb"))
               (patches (search-patches "mariadb-client-test-32bit.patch"))
               (modules '((guix build utils)))
               (snippet
@@ -652,6 +654,10 @@ Language.")
          ;; For now, disable the features that that use libarchive (xtrabackup).
          "-DWITH_LIBARCHIVE=OFF"
 
+         ;; Disable the TokuDB engine, because its test suite frequently fails,
+         ;; and loading it crashes the server: <https://bugs.gnu.org/35521>.
+         "-DTOKUDB_OK=OFF"
+
          ;; Ensure the system libraries are used.
          "-DWITH_JEMALLOC=yes"
          "-DWITH_PCRE=system"
@@ -699,9 +705,6 @@ Language.")
                       ;; 2030-12-31.  See <https://bugs.gnu.org/34351> for details.
                       "main.mysqldump"
 
-                      ;; XXX: Fails sporadically.
-                      "innodb_fts.crash_recovery"
-
                       ;; FIXME: This test fails on i686:
                       ;; -myisampack: Can't create/write to file (Errcode: 17 "File exists")
                       ;; +myisampack: Can't create/write to file (Errcode: 17 "File exists)
@@ -779,7 +782,6 @@ Language.")
        ("libxml2" ,libxml2)
        ("ncurses" ,ncurses)
        ("pcre" ,pcre)
-       ("snappy" ,snappy)
        ("xz" ,xz)
        ("zlib" ,zlib)))
     (propagated-inputs
@@ -799,14 +801,14 @@ as a drop-in replacement of MySQL.")
 (define-public postgresql
   (package
     (name "postgresql")
-    (version "10.7")
+    (version "10.10")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "1piyfcrcqscjhnnwn91kdvr764s7d0qz4lgygf9bl6qc71ji1vdz"))
+                "0lzj46dwd9cw94gnqm36bxd7jlhfdyqjrfzr3c4xd3prfn2rnkxd"))
               (patches (search-patches "postgresql-disable-resolve_symlinks.patch"))))
     (build-system gnu-build-system)
     (arguments
@@ -842,18 +844,31 @@ TIMESTAMP.  It also supports storage of binary large objects, including
 pictures, sounds, or video.")
     (license (license:x11-style "file://COPYRIGHT"))))
 
-(define-public postgresql-9.6
+(define-public postgresql-11
   (package
     (inherit postgresql)
     (name "postgresql")
-    (version "9.6.13")
+    (version "11.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "197964wb5pc5fx81a6mh9hlcrr9sgr3nqlpmljv6asi9aq0d5gpc"))))))
+                "106ikalvrilihlvhq7xj7snq98hgbgq6qsgjrd252wgw1c327pvz"))))))
+
+(define-public postgresql-9.6
+  (package
+    (inherit postgresql)
+    (name "postgresql")
+    (version "9.6.15")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://ftp.postgresql.org/pub/source/v"
+                                  version "/postgresql-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "02hp69h2p02asfblkaahblzdz2zmawd2r11h6237y5j7yadgxn9w"))))))
 
 (define-public python-pymysql
   (package
@@ -927,8 +942,7 @@ organized in a hash table or B+ tree.")
                                       (assoc-ref %build-inputs "bash:include")
                                       "/include/bash"))))
 
-    (native-inputs `(("emacs" ,emacs-minimal)
-                     ("bc" ,bc)
+    (native-inputs `(("bc" ,bc)
                      ("bash:include" ,bash "include")
                      ("check" ,check)
                      ("libuuid" ,util-linux)
@@ -947,6 +961,26 @@ types are supported, as is encryption.")
     (license license:gpl3+)
     (home-page "https://www.gnu.org/software/recutils/")))
 
+(define-public emacs-recutils
+  (package
+    (inherit recutils)
+    (name "emacs-recutils")
+    (build-system emacs-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'change-directory
+           (lambda _
+             (chdir "etc")
+             #t)))))
+    (native-inputs '())
+    (inputs '())
+    (synopsis "Emacs mode for working with recutils database files")
+    (description "This package provides an Emacs major mode @code{rec-mode}
+for working with GNU Recutils text-based, human-editable databases.  It
+supports editing, navigation, and querying of recutils database files
+including field and record folding.")))
+
 (define-public rocksdb
   (package
     (name "rocksdb")
@@ -1857,7 +1891,7 @@ database.")
 (define-public perl-db-file
  (package
   (name "perl-db-file")
-  (version "1.843")
+  (version "1.852")
   (source
     (origin
       (method url-fetch)
@@ -1867,7 +1901,7 @@ database.")
              ".tar.gz"))
       (sha256
         (base32
-          "0sildz1i3fmh949w1scpjsyjx0cbmfw0yna3y70mc6vbwp8y696y"))))
+          "14c30xyqx9c1hxw40bqbzls41al8gmklxv5jbk2kknmn4dsrbdrs"))))
   (build-system perl-build-system)
   (inputs `(("bdb" ,bdb)))
   (native-inputs `(("perl-test-pod" ,perl-test-pod)))
@@ -2127,13 +2161,13 @@ etc., and an SQL engine for performing simple SQL queries.")
 (define-public python-lmdb
   (package
     (name "python-lmdb")
-    (version "0.94")
+    (version "0.95")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "lmdb" version))
               (sha256
                (base32
-                "1zh38gvkqw1jm5105if6rr7ccbgyxr7k2rm5ygb9ab3bq82pyaww"))
+                "0nx9f193gzl33r1lbqhb96h1igya7pz8wmahr8m9x5zgc05hal91"))
               (modules '((guix build utils)))
               (snippet
                ;; Delete bundled lmdb source files.
@@ -2397,14 +2431,14 @@ You might also want to install the following optional dependencies:
 (define-public python-alembic
   (package
     (name "python-alembic")
-    (version "1.0.2")
+    (version "1.0.10")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "alembic" version))
        (sha256
         (base32
-         "0asqz9mwc4w8bsar1icv3ik9jslxrj3gv3yxgmhc6nc6r9qbkg04"))))
+         "1dwl0264r6ri2jyrjr68am04x538ab26xwy4crqjnnhm4alwm3c2"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-mock" ,python-mock)
@@ -2759,7 +2793,7 @@ is designed to have a low barrier to entry.")
     (home-page "https://github.com/benjolitz/trollius-redis")
     (synopsis "Port of asyncio-redis to trollius")
     (description "@code{trollius-redis} is a Redis client for Python
-  trollius.  It is an asynchronious IO (PEP 3156) implementation of the
+  trollius.  It is an asynchronous IO (PEP 3156) implementation of the
   Redis protocol.")
     (license license:bsd-2)))
 
@@ -3043,3 +3077,24 @@ NumPy, and other traditional Python scientific computing packages.")
 
 (define-public python2-pyarrow
   (package-with-python2 python-pyarrow))
+
+(define-public python-crate
+  (package
+    (name "python-crate")
+    (version "0.23.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "crate" version))
+              (sha256
+               (base32
+                "0s3s7yg4m2zflg9q96aibwb5hizsn10ql63fsj6h5z624qkavnlp"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-urllib3" ,python-urllib3)))
+    (home-page "https://github.com/crate/crate-python")
+    (synopsis "CrateDB Python client")
+    (description
+     "This package provides a Python client library for CrateDB.
+It implements the Python DB API 2.0 specification and includes support for
+SQLAlchemy.")
+    (license license:asl2.0)))

gnu/packages/datastructures.scm

@@ -124,14 +124,14 @@ in between these sequences may be different in both content and length.")
 (define-public liburcu
   (package
     (name "liburcu")
-    (version "0.11.0")
+    (version "0.11.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.lttng.org/files/urcu/"
                                   "userspace-rcu-" version ".tar.bz2"))
               (sha256
                (base32
-                "1rxk5vbkbmqlsnjnvkjz0pkx2076mqnq6jzblpmz8rk29x66kx8s"))))
+                "0l1kxgzch4m8fxiz2hc8fwg56hrvzzspp7n0svnl7i7iycdrgfcj"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("perl" ,perl)))                 ; for tests

gnu/packages/dav.scm

@@ -26,7 +26,8 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-web)
-  #:use-module (gnu packages python-xyz))
+  #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages sphinx))
 
 (define-public radicale
   (package

gnu/packages/dc.scm

@@ -33,14 +33,14 @@
 (define-public ncdc
   (package
     (name "ncdc")
-    (version "1.21")
+    (version "1.22")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "http://dev.yorhel.nl/download/ncdc-" version
                            ".tar.gz"))
        (sha256 (base32
-                "10hrk7pcvfl9cj6d0kr4qf3l068ikqhccbg7lf25pr2kln9lz412"))))
+                "0n9sn4rh4zhmzjknsvyp4bfh925abz93ln43gl8a1v63rs2yyhgx"))))
     (build-system gnu-build-system)
     (inputs
      `(("bzip2" ,bzip2)

gnu/packages/debian.scm

@@ -32,7 +32,7 @@
 (define-public debian-archive-keyring
   (package
     (name "debian-archive-keyring")
-    (version "2018.1")
+    (version "2019.1")
     (source
       (origin
         (method git-fetch)
@@ -42,7 +42,7 @@
         (file-name (git-file-name name version))
         (sha256
          (base32
-          "136vr5dj7w0dz563qdghsndcfcqm2m8d4j1dyiq9dzx5vd0rcpcw"))))
+          "0bphwji3ywk1zi5bq8bhqk7l51fwjy1idwsw7zfqnxca8m5wvw1g"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "verify-results"
@@ -117,7 +117,7 @@ contains the archive keys used for that.")
 (define-public debootstrap
   (package
     (name "debootstrap")
-    (version "1.0.111")
+    (version "1.0.114")
     (source
       (origin
         (method git-fetch)
@@ -127,7 +127,7 @@ contains the archive keys used for that.")
         (file-name (git-file-name name version))
         (sha256
          (base32
-          "1b8s00a2kvaajqhjlms3q2dk3gqv6g4yq9h843jal1pm66zsx19n"))))
+          "147308flz9y8g6f972izi3szmsywf5f8xm64z2smy1cayd340i63"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -154,6 +154,11 @@ contains the archive keys used for that.")
                  (("/usr") ubuntu))
                (substitute* "debootstrap"
                  (("=/usr") (string-append "=" out)))
+               ;; Ensure PATH works both in guix and within the debian chroot
+               ;; workaround for: https://bugs.debian.org/929889
+               (substitute* "functions"
+                 (("PATH=/sbin:/usr/sbin:/bin:/usr/bin")
+                  "PATH=$PATH:/sbin:/usr/sbin:/bin:/usr/bin"))
                (substitute* (find-files "scripts" ".")
                  (("/usr/share/zoneinfo") (string-append tzdata "/share/zoneinfo")))
                #t)))
@@ -184,9 +189,5 @@ contains the archive keys used for that.")
     (description "Debootstrap is used to create a Debian base system from
 scratch, without requiring the availability of @code{dpkg} or @code{apt}.
 It does this by downloading .deb files from a mirror site, and carefully
-unpacking them into a directory which can eventually be chrooted into.
-
-It is recommended to run @code{debootstrap --foreign --arch=...} and then
-@code{chroot} into the directory, set the PATH and run @code{debootstrap
---second-stage} after.")
+unpacking them into a directory which can eventually be chrooted into.")
     (license license:gpl2)))

gnu/packages/debug.scm

@@ -95,7 +95,7 @@ program to exhibit a bug.")
 (define-public c-reduce
   (package
     (name "c-reduce")
-    (version "2.8.0")
+    (version "2.10.0")
     (source
      (origin
       (method url-fetch)
@@ -103,13 +103,12 @@ program to exhibit a bug.")
             (string-append "http://embed.cs.utah.edu/creduce/"
                            "creduce-" version ".tar.gz")))
       (sha256
-       (base32
-        "1vqx73ymfscvlyig03972a5m7ar3gx2yv6m8c6h2mibz792j5xkp"))))
+       (base32 "0qx0zq8jxzx2as2zf0740g7kvgq163ayn3041di4vwk77490y76v"))))
     (build-system gnu-build-system)
     (inputs
      `(("astyle"          ,astyle)
-       ("llvm"            ,llvm-6)
-       ("clang"           ,clang-6)
+       ("llvm"            ,llvm)
+       ("clang"           ,clang)
        ("flex"            ,flex)
        ("indent"          ,indent)
        ("perl"            ,perl)
@@ -313,7 +312,7 @@ down the road.")
       (home-page "https://github.com/losalamos/stress-make")
       (synopsis "Expose race conditions in Makefiles")
       (description
-       "Stress Make is a customized GNU Make that explicitely manages the order
+       "Stress Make is a customized GNU Make that explicitly manages the order
 in which concurrent jobs are run to provoke erroneous behavior into becoming
 manifest.  It can run jobs in the order in which they're launched, in backwards
 order, or in random order.  The thought is that if code builds correctly with

gnu/packages/dico.scm

@@ -38,14 +38,14 @@
 (define-public dico
   (package
     (name "dico")
-    (version "2.7")
+    (version "2.9")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/dico/dico-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "0dg4aacnmlf3ljssd7dwh8z5644xzq8k1501mbsx8nz8p8a9mbsq"))))
+               "0i9xqhy3h5nlizcmav4mv5ay8ivdgn4l4k0k7fxix3fsc87nijyr"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags (list (string-append "--with-guile-site-dir=" %output

gnu/packages/dictionaries.scm

@@ -218,7 +218,7 @@ It comes with a German-English dictionary with approximately 270,000 entries.")
 (define-public grammalecte
   (package
     (name "grammalecte")
-    (version "1.1")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch/zipbomb)
@@ -226,7 +226,7 @@ It comes with a German-English dictionary with approximately 270,000 entries.")
                            "Grammalecte-fr-v" version ".zip"))
        (sha256
         (base32
-         "031d6cn1wn7ps3j38vx6s8z2gjp9nqgiypqm3bfbhxqcammyhian"))))
+         "1j2avdk8hcgcv0lahp029qzpdb2rnys38hc64jy30awzx64fa6i4"))))
     (build-system python-build-system)
     (home-page "https://grammalecte.net")
     (synopsis  "French spelling and grammar checker")

gnu/packages/disk.scm

@@ -13,6 +13,8 @@
 ;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018, 2019 Pierre Neidhardt <mail@ambrevar.xyz>
+;;; Copyright © 2019 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -57,6 +59,7 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages readline)
+  #:use-module (gnu packages sphinx)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages swig)
   #:use-module (gnu packages vim)
@@ -234,7 +237,8 @@ to recover data more efficiently by only reading the necessary blocks.")
          "0wy13i3i4x2bw1hf5m4fd0myh61f9bcrs035fdlf6gyc1jksrcp6"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:make-flags (list (string-append "PREFIX=" %output)
+     `(#:configure-flags (list "--enable-compat-symlinks")
+       #:make-flags (list (string-append "PREFIX=" %output)
                           "CC=gcc")))
     (native-inputs
      `(("xxd" ,xxd))) ; for tests
@@ -340,32 +344,31 @@ and can dramatically shorten the lifespan of the drive if left unchecked.")
 (define-public gparted
   (package
     (name "gparted")
-    (version "0.33.0")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/gparted/gparted/gparted-"
                            version "/gparted-" version ".tar.gz"))
        (sha256
-        (base32 "1ml1ky3s75lbxr91p608q3prsdh9x899mw7nbgk252pqhg4vh8sh"))))
+        (base32
+         "0mdvn85jvy72ff7nds3dakx9kzknh8gx1z8i0w2sf970q03qp2z4"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f                      ; tests require a network connection
-       #:configure-flags '("--disable-scrollkeeper")))
+      ;; Tests require access to paths outside the build container, such
+      ;; as '/dev/disk/by-id'
+     `(#:tests? #f))
     (inputs
      `(("util-linux" ,util-linux)
        ("parted" ,parted)
        ("glib" ,glib)
-       ("gtkmm" ,gtkmm-2)
+       ("gtkmm" ,gtkmm)
        ("libxml2" ,libxml2)
-       ("libxslt" ,libxslt)
-       ("gnome-doc-utils" ,gnome-doc-utils)
-       ("docbook-xml" ,docbook-xml-4.2)
-       ("python" ,python-2)
-       ("python-libxml2" ,python2-libxml2)
-       ("which" ,which)))
+       ("yelp-tools" ,yelp-tools)
+       ("itstool" ,itstool)))
     (native-inputs
      `(("intltool" ,intltool)
+       ("lvm2" ,lvm2) ; for tests
        ("pkg-config" ,pkg-config)))
     (home-page "https://gparted.org/")
     (synopsis "Partition editor to graphically manage disk partitions")
@@ -438,15 +441,16 @@ a card with a smaller capacity than stated.")
 (define-public python-parted
   (package
     (name "python-parted")
-    (version "3.11.1")
+    (version "3.11.2")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/dcantrell/pyparted/archive/v"
-                           version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/dcantrell/pyparted.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32
-         "0r1nyjj40nacnfnv17x2mnsj6ga1qplyxyza82v2809dfhim2fwq"))))
+        (base32 "0r6916n3w4vldxrq30a3z2iagvxgly4vfmlidjm65vwqnyv17bvn"))))
     (build-system python-build-system)
     (arguments
      `(#:phases

gnu/packages/display-managers.scm

@@ -75,6 +75,15 @@
        ("linux-pam" ,linux-pam)
        ("qtbase" ,qtbase)
        ("qtdeclarative" ,qtdeclarative)
+
+       ;; Some user-defined themes use QtQuick components internally.  Adding
+       ;; QtQuick & co. here; they end up in QML2_IMPORT_PATH thanks to
+       ;; 'wrap-qt-program'.
+       ("qtgraphicaleffects" ,qtgraphicaleffects)
+       ("qtquickcontrols" ,qtquickcontrols)
+       ("qtquickcontrols2" ,qtquickcontrols2)
+       ("qtsvg" ,qtsvg)
+
        ("shadow" ,shadow)
        ("wayland" ,wayland)))
     (arguments

gnu/packages/django.scm

@@ -35,18 +35,19 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages sphinx)
   #:use-module (gnu packages time))
 
 (define-public python-django
   (package
     (name "python-django")
-    (version "1.11.20")
+    (version "1.11.21")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "Django" version))
               (sha256
                (base32
-                "0h90kdq8r4y8wa73hdxmyy5psnwlg61dcq3qsa098cpfiyh9vaa3"))))
+                "0adhcw8sx2mgwk9y2j760y96pqbip1ni3sf2v2ls5zxc9x93wwms"))))
     (build-system python-build-system)
     (arguments
      '(#:modules ((srfi srfi-1)

gnu/packages/dns.scm

@@ -12,6 +12,7 @@
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2019 Chris Marusich <cmmarusich@gmail.com>
+;;; Copyright © 2019 Rutger Helling <rhelling@mykolab.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -108,7 +109,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
 (define-public isc-bind
   (package
     (name "bind")
-    (version "9.12.4-P1")
+    (version "9.14.4")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -116,9 +117,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
                     "/bind-" version ".tar.gz"))
               (sha256
                (base32
-                "1if7zc5gzrfd28csc63v9bjwrc0rgvm1x9yx058946hc5gp5lyp2"))
-              (patches
-               (search-patches "bind-fix-unused-pk11-ecc-constants.patch"))))
+                "0gxqws7ml15lwkjw9mdcd759gv5kk3s9m17j3vrp9448ls1gnbii"))))
     (build-system gnu-build-system)
     (outputs `("out" "utils"))
     (inputs
@@ -163,7 +162,11 @@ and BOOTP/TFTP for network booting of diskless machines.")
          ;;          (system "bin/tests/system/ifconfig.sh up")))
          (replace 'check
            (lambda _
-             (invoke "make" "force-test"))))))
+             ;; XXX Even ‘make force-test’ tries to create network interfaces
+             ;; and fails.  The only working target is the (trivial) fuzz test.
+             (with-directory-excursion "fuzz"
+               (invoke "make" "check"))
+             #t)))))
     (synopsis "An implementation of the Domain Name System")
     (description "BIND is an implementation of the @dfn{Domain Name System}
 (DNS) protocols for the Internet.  It is a reference implementation of those
@@ -300,14 +303,14 @@ asynchronous fashion.")
 (define-public nsd
   (package
     (name "nsd")
-    (version "4.1.27")
+    (version "4.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.nlnetlabs.nl/downloads/nsd/nsd-"
                            version ".tar.gz"))
        (sha256
-        (base32 "1sjfbwr4vq25304hr9vmd9j821g2vzv8lpy95hpsravc80q5zaqv"))))
+        (base32 "0k57xl3ybdnqjqw9a3dmi7l6qmhkiic6wsghkz08ir809aj1rpsi"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -370,14 +373,14 @@ to result in system-wide compromise.")
 (define-public unbound
   (package
     (name "unbound")
-    (version "1.9.1")
+    (version "1.9.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.unbound.net/downloads/unbound-"
                            version ".tar.gz"))
        (sha256
-        (base32 "1iarvk0i92asvrkpla9z55aan20k6pklzpck9yk4rfnchsdvzh63"))))
+        (base32 "15bbrczibap30db8a1pmqhvjbmkxms39hwiivby7f4j5rz2wwykg"))))
     (build-system gnu-build-system)
     (outputs '("out" "python"))
     (native-inputs
@@ -575,14 +578,14 @@ Extensions} (DNSSEC).")
 (define-public knot
   (package
     (name "knot")
-    (version "2.8.1")
+    (version "2.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://secure.nic.cz/files/knot-dns/"
                            "knot-" version ".tar.xz"))
        (sha256
-        (base32 "1im2wb8hl394mzni1wavmvfqd7il8s28kcz8w3s4v05nbhzg06xj"))
+        (base32 "0dx1lp4w33rpa54nns41k4vfdfin6naaskwh132r4qs0l9hl7lh0"))
        (modules '((guix build utils)))
        (snippet
         '(begin

gnu/packages/docbook.scm

@@ -195,7 +195,7 @@ by no means limited to these applications.)  This package provides XML DTDs.")
     (build-system python-build-system)
     ;; TODO: Add xfig/transfig for fig2dev utility
     (inputs
-     `(("texlive" ,(texlive-union (list texlive-latex-amsfonts
+     `(("texlive" ,(texlive-union (list texlive-amsfonts
                                         texlive-latex-anysize
                                         texlive-latex-appendix
                                         texlive-latex-changebar
@@ -219,7 +219,6 @@ by no means limited to these applications.)  This package provides XML DTDs.")
                                         texlive-latex-url
                                         texlive-latex-wasysym
 
-                                        texlive-fonts-amsfonts
                                         texlive-fonts-ec
                                         texlive-fonts-rsfs
                                         texlive-fonts-stmaryrd

gnu/packages/docker.scm

@@ -39,6 +39,7 @@
   #:use-module (gnu packages networking)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages version-control)
@@ -49,21 +50,26 @@
 (define-public python-docker-py
   (package
     (name "python-docker-py")
-    (version "1.10.6")
+    (version "3.7.3")
     (source
      (origin
        (method url-fetch)
-       (uri (pypi-uri "docker-py" version))
+       (uri (pypi-uri "docker" version))
        (sha256
         (base32
-         "05f49f6hnl7npmi7kigg0ibqk8s3fhzx1ivvz1kqvlv4ay3paajc"))))
+         "0qmrcvpaz37p85hfddsd4yc8hgqlkzs4cz09q9wmy0pz5pwajqm0"))))
     (build-system python-build-system)
     ;; TODO: Tests require a running Docker daemon.
     (arguments '(#:tests? #f))
     (inputs
-     `(("python-requests" ,python-requests)
+     `(("python-requests" ,python-requests-2.20)
+       ("python-ipaddress" ,python-ipaddress)
        ("python-six" ,python-six)
+       ("python-urllib3" ,python-urllib3-1.24)
        ("python-websocket-client" ,python-websocket-client)))
+    (propagated-inputs
+     `(("python-docker-pycreds" ,python-docker-pycreds)
+       ("python-paramiko" ,python-paramiko))) ; adds SSH support
     (home-page "https://github.com/docker/docker-py/")
     (synopsis "Python client for Docker")
     (description "Docker-Py is a Python client for the Docker container
@@ -73,14 +79,14 @@ management tool.")
 (define-public python-dockerpty
   (package
     (name "python-dockerpty")
-    (version "0.3.4")
+    (version "0.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "dockerpty" version))
        (sha256
         (base32
-         "0za6rr349641wv76ww9l3zcic2xyxrirlxpnzl4296h897648455"))))
+         "1kjn64wx23jmr8dcc6g7bwlmrhfmxr77gh6iphqsl39sayfxdab9"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-six" ,python-six)))
@@ -91,27 +97,31 @@ pseudo-terminal (PTY) allocated to a Docker container using the Python
 client.")
     (license license:asl2.0)))
 
+;; When updating, check whether python-jsonschema-2.6 can be removed from Guix
+;; entirely.
 (define-public docker-compose
   (package
     (name "docker-compose")
-    (version "1.5.2")
+    (version "1.24.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "docker-compose" version))
        (sha256
         (base32
-         "0ksg7hm2yvc977968dixxisrhcmvskzpcx3pz0v1kazrdqp7xakr"))))
+         "0lx7bx6jvhydbab8vwry0bclhdf0dfj6jrns1m5y45yp9ybqxmd5"))))
     (build-system python-build-system)
     ;; TODO: Tests require running Docker daemon.
     (arguments '(#:tests? #f))
     (inputs
-     `(("python-docker-py" ,python-docker-py)
+     `(("python-cached-property"
+        ,python-cached-property)
+       ("python-docker-py" ,python-docker-py)
        ("python-dockerpty" ,python-dockerpty)
        ("python-docopt" ,python-docopt)
-       ("python-jsonschema" ,python-jsonschema)
+       ("python-jsonschema" ,python-jsonschema-2.6)
        ("python-pyyaml" ,python-pyyaml)
-       ("python-requests" ,python-requests-2.7)
+       ("python-requests" ,python-requests-2.20)
        ("python-six" ,python-six)
        ("python-texttable" ,python-texttable)
        ("python-websocket-client" ,python-websocket-client)))
@@ -126,14 +136,14 @@ created and all the services are started as specified in the configuration.")
 (define-public python-docker-pycreds
   (package
     (name "python-docker-pycreds")
-    (version "0.3.0")
+    (version "0.4.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "docker-pycreds" version))
         (sha256
          (base32
-          "1zxvam1q22qb0jf48553nnncnfrcp88ag4xa0qmq6vr0imn9a3lb"))))
+          "1m44smrggnqghxkqfl7vhapdw89m1p3vdr177r6cq17lr85jgqvc"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -571,6 +581,9 @@ provisioning etc.")
              ;; information, and the DWARF symbol table.
              (setenv "LDFLAGS" "-s -w")
 
+             ;; Make sure "docker -v" prints a usable version string.
+             (setenv "VERSION" ,%docker-version)
+
              ;; Make build reproducible.
              (setenv "BUILDTIME" "1970-01-01 00:00:01.000000000+00:00")
              (symlink "src/github.com/docker/cli/scripts" "./scripts")

gnu/packages/ebook.scm

@@ -56,7 +56,8 @@
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
-  #:use-module (gnu packages xorg))
+  #:use-module (gnu packages xorg)
+  #:use-module (gnu packages wxwidgets))
 
 (define-public chmlib
   (package
@@ -330,3 +331,27 @@ following formats:
 @item XHTML
 @end enumerate")
     (license license:gpl2+)))
+
+(define-public xchm
+  (package
+    (name "xchm")
+    (version "1.30")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/rzvncj/xCHM"
+                                  "/releases/download/"
+                                  version "/xchm-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1865wb3ppmx5y12rqfhv4wri0lfdah41zsfz94xb8gym80m8zac5"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("wxwidgets" ,wxwidgets)
+       ("chmlib" ,chmlib)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "https://github.com/rzvncj/xCHM")
+    (synopsis "CHM file viewer")
+    (description "xCHM is a graphical CHM file viewer.  It is a frontend to
+the CHM library CHMLIB.")
+    (license license:gpl2+)))

gnu/packages/education.scm

@@ -27,7 +27,10 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages databases)
+  #:use-module (gnu packages fonts)
   #:use-module (gnu packages freedesktop)
+  #:use-module (gnu packages game-development)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
@@ -247,17 +250,17 @@ easy.")
 (define-public snap
   (package
     (name "snap")
-    (version "4.2.2.9")
+    (version "5.0.8")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/jmoenig/Snap.git")
-             (commit version)))
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "07qyhh4f8gr1fqyvxa2i6lkzaaa0vl12yzllgp81rdil8z8bi976"))))
+         "0fwfssdgv3mfzyv8hw1a1z5ky1yn0p59kyl6l9fxsm4w2ckgyizd"))))
     (build-system trivial-build-system)
     (arguments
      `(#:modules ((guix build utils))
@@ -309,14 +312,14 @@ to open the application in a web browser, for offline usage.")
 (define-public toutenclic
   (package
     (name "toutenclic")
-    (version "6.13")
+    (version "7.00")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "http://www.bipede.fr/downloads/logiciels/"
-                           "ToutEnClic-" version ".tar.xz"))
+                           "ToutEnClic-" version "-src.zip"))
        (sha256
-        (base32 "1pjprdzc4bn7ckbg4469691ph6yjjr8f022hb4gi4lacs4h71wnd"))))
+        (base32 "0xg24p925rl5bfqsq3jb2lrkidb0f3kbmay5iyxxmjsn3ra0blyh"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f                      ; no tests
@@ -328,17 +331,20 @@ to open the application in a web browser, for offline usage.")
              (let* ((out (assoc-ref outputs "out"))
                     (share (string-append out "/share/toutenclic"))
                     (pixmaps (string-append out "/share/pixmaps"))
+                    (doc (string-append out "share/doc/" ,name "-" ,version))
                     (bin (string-append out "/bin"))
-                    (executable "toutenclic.py"))
+                    (executable "toutenclic"))
                ;; Install icon.
                (install-file "toutenclic.png" pixmaps)
                ;; Move files into "share/" directory.
-               (mkdir-p share)
-               (copy-recursively "." share)
+               (for-each (lambda (f) (install-file f share))
+                         (find-files "." "\\.py$"))
+               ;; Install documentation.
+               (install-file "ToutEnClic.pdf" doc)
                ;; Create executable in "bin/".
                (mkdir-p bin)
                (with-directory-excursion bin
-                 (symlink (string-append share "/" executable)
+                 (symlink (string-append share "/" executable ".py")
                           executable)))
              #t))
          (add-after 'install 'create-desktop-file
@@ -353,8 +359,8 @@ to open the application in a web browser, for offline usage.")
                            "[Desktop Entry]~@
                             Name=ToutEnClic~@
                             Comment=For schooling without difference~@
-                            Exec=~a/bin/toutenclic.py~@
-                            TryExec=~@*~a/bin/toutenclic.py~@
+                            Exec=~a/bin/toutenclic~@
+                            TryExec=~@*~a/bin/toutenclic~@
                             Terminal=false~@
                             Icon=toutenclic~@
                             Type=Application~%"
@@ -370,3 +376,107 @@ keyboard is also available if the child does not have any other
 specialized device.")
     (home-page "https://bipede.fr/contrib/")
     (license license:gpl3)))
+
+(define-public childsplay
+  (package
+    (name "childsplay")
+    (version "3.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://sourceforge/schoolsplay/"
+                    "childsplay-" version ".tgz"))
+              (sha256
+               (base32
+                "0z7yp2swjnbz51vn2zyfnjn40jq38l5mbh15yafmx1z3vn2z1m77"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'unbundle-dejavu-font
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let* ((dejavu-dir
+                     (string-append (assoc-ref inputs "font-dejavu")
+                                    "/share/fonts/truetype"))
+                    (dejavu-font
+                     (string-append dejavu-dir
+                                    "/DejaVuSansCondensed-Bold.ttf")))
+               (substitute* "SPConstants.py"
+                 (("^(TTF(BOLD)? = ).*" _ prefix)
+                  (string-append prefix "'" dejavu-font "'\n")))
+               (for-each (lambda (f) (delete-file f))
+                         (find-files "lib/SPData" "DejaVu"))
+               #t)))
+         (delete 'build)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (pixmaps (string-append out "/share/pixmaps"))
+                    (share (string-append out "/share/childsplay"))
+                    (doc (string-append out "/share/doc/" ,name "-",version)))
+               ;; Install icon.
+               (install-file "lib/SPData/themes/childsplay/logo_cp.svg" pixmaps)
+               ;; Install data.
+               (mkdir-p share)
+               (for-each (lambda (f)
+                           (copy-recursively f (string-append share "/" f)))
+                         '("alphabet-sounds" "lib" "locale" "SPWidgets"))
+               (for-each (lambda (f) (install-file f share))
+                         (find-files "." "\\.(py|dev|db)$"))
+               ;; Install documentation.
+               (mkdir-p doc)
+               (copy-recursively "docs" doc)
+               #t)))
+         (add-after 'install 'create-executable
+           (lambda* (#:key outputs inputs #:allow-other-keys)
+             (let* ((python (string-append (assoc-ref inputs "python")
+                                           "/bin/python"))
+                    (out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (executable (string-append bin "/childsplay")))
+               (mkdir-p bin)
+               (call-with-output-file executable
+                 (lambda (file)
+                   (format file
+                           "~a ~a"
+                           python
+                           (string-append out "/share/childsplay/childsplay.py"))))
+               (chmod executable #o555)
+               #t)))
+         (add-after 'install 'create-desktop-file
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (applications (string-append out "/share/applications")))
+               (mkdir-p applications)
+               (call-with-output-file
+                   (string-append applications "/childsplay.desktop")
+                 (lambda (file)
+                   (format file
+                           "[Desktop Entry]~@
+                            Name=Childsplay~@
+                            Comment=Suite of educational games for young children~@
+                            Comment[ca]=Conjunt de jocs educatius per a xiquets~@
+                            Comment[es]=Conjunto de juegos educativos para niños~@
+                            Comment[de]=Sammlung mit lehrreichen Spielen für kleine Kinder~@
+                            Exec=~a/bin/childsplay.py~@
+                            Terminal=false~@
+                            Icon=logo_cp.svg~@
+                            Type=Application~@
+                            Categories=Application;Game;Education;KidsGame;~@
+                            Keywords=suite;children;games;young;educational;~%"
+                           out)))
+               #t))))))
+    (inputs
+     `(("font-dejavu" ,font-dejavu)
+       ("pygame" ,python2-pygame)
+       ("sqlalchemy" ,python2-sqlalchemy)))
+    (synopsis "Suite of educational games for young children")
+    (description "Childsplay is a collection of educational activities
+for young children.  Childsplay can be used at home, kindergartens and
+pre-schools.  Childsplay is a fun and safe way to let young children
+use the computer and at the same time teach them a little math,
+letters of the alphabet, spelling, eye-hand coordination, etc.")
+    (home-page "http://www.schoolsplay.org")
+    (license license:gpl3+)))

gnu/packages/elf.scm

@@ -34,7 +34,7 @@
   #:use-module (gnu packages m4)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
-  #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages sphinx)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages xml))
 
@@ -160,13 +160,19 @@ static analysis of the ELF binaries at hand.")
   (package
     (name "libelf")
     (version "0.8.13")
-    (source (origin
-             (method url-fetch)
-             (uri (string-append "http://www.mr511.de/software/libelf-"
-                                 version ".tar.gz"))
-             (sha256
-              (base32
-               "0vf7s9dwk2xkmhb79aigqm0x0yfbw1j0b9ksm51207qwr179n6jr"))))
+    (source
+     (origin
+       (method url-fetch)
+       (uri (list
+             ;; As of May 2019, the original URL at mr511.de redirects to a
+             ;; domain that doesn't resolve.  Use these two mirrors instead.
+             (string-append "https://fossies.org/linux/misc/old/"
+                            "libelf-" version ".tar.gz")
+             (string-append "https://ftp.osuosl.org/pub/blfs/conglomeration/"
+                            "libelf/libelf-" version ".tar.gz")))
+       (sha256
+        (base32
+         "0vf7s9dwk2xkmhb79aigqm0x0yfbw1j0b9ksm51207qwr179n6jr"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -183,7 +189,8 @@ static analysis of the ELF binaries at hand.")
                                        (%current-system))
                              '("--host=aarch64-unknown-linux-gnu")
                              '()))))))))
-    (home-page "http://www.mr511.de/software/english.html")
+    (home-page (string-append "https://web.archive.org/web/20181111033959/"
+                              "http://www.mr511.de/software/english.html"))
     (synopsis "ELF object file access library")
     (description "Libelf is a C library to access ELF object files.")
     (license lgpl2.0+)))

gnu/packages/emacs.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Mark H Weaver <mhw@netris.org>
@@ -115,7 +115,8 @@
     (build-system glib-or-gtk-build-system)
     (arguments
      `(#:tests? #f  ; no check target
-       #:configure-flags (list "--with-modules")
+       #:configure-flags (list "--with-modules"
+                               "--disable-build-details")
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'fix-/bin/pwd
@@ -202,11 +203,12 @@ languages.")
     (synopsis "The extensible text editor (used only for byte-compilation)")
     (build-system gnu-build-system)
     (arguments
-     `(,@(substitute-keyword-arguments (package-arguments emacs)
-           ((#:phases phases)
-            `(modify-phases ,phases
-               (delete 'install-site-start))))
-        #:configure-flags (list "--with-gnutls=no")))
+     (substitute-keyword-arguments (package-arguments emacs)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (delete 'install-site-start)))
+       ((#:configure-flags flags ''())
+        `(list "--with-gnutls=no" "--disable-build-details"))))
     (inputs
      `(("ncurses" ,ncurses)))
     (native-inputs
@@ -220,9 +222,9 @@ languages.")
 editor (with xwidgets support)")
     (build-system gnu-build-system)
     (arguments
-     `(#:configure-flags
-       '("--with-xwidgets")
-       ,@(package-arguments emacs)))
+     (substitute-keyword-arguments (package-arguments emacs)
+       ((#:configure-flags flags ''())
+        `(cons "--with-xwidgets" ,flags))))
     (inputs
      `(("webkitgtk" ,webkitgtk)
        ("libxcomposite" ,libxcomposite)