Merge branch 'master' into core-updates

Makefile.am

@@ -68,6 +68,7 @@ MODULES =					\
   guix/cpio.scm					\
   guix/deprecation.scm				\
   guix/docker.scm	   			\
+  guix/json.scm					\
   guix/records.scm				\
   guix/pki.scm					\
   guix/progress.scm				\
@@ -125,6 +126,7 @@ MODULES =					\
   guix/build-system/gnu.scm			\
   guix/build-system/guile.scm			\
   guix/build-system/haskell.scm			\
+  guix/build-system/julia.scm			\
   guix/build-system/linux-module.scm		\
   guix/build-system/node.scm			\
   guix/build-system/perl.scm			\
@@ -183,6 +185,7 @@ MODULES =					\
   guix/build/texlive-build-system.scm		\
   guix/build/waf-build-system.scm		\
   guix/build/haskell-build-system.scm		\
+  guix/build/julia-build-system.scm		\
   guix/build/linux-module-build-system.scm	\
   guix/build/store-copy.scm			\
   guix/build/json.scm				\

README

@@ -10,8 +10,8 @@ It provides [[https://www.gnu.org/software/guile/][Guile]] Scheme APIs, includin
 domain-specific languages (EDSLs) to describe how packages are to be
 built and composed.
 
-A user-land free software distribution for GNU/Linux comes as part of
+GNU Guix can be used on top of an already-installed GNU/Linux distribution, or
-Guix.
+it can be used standalone (we call that “Guix System”).
 
 Guix is based on the [[https://nixos.org/nix/][Nix]] package manager.
 
@@ -75,37 +75,17 @@ the promise of a build; it is stored as a text file under
 `derivation' primitive, as well as higher-level wrappers such as
 `build-expression->derivation'.
 
-Guix does remote procedure calls (RPCs) to the Guix or Nix daemon (the
+Guix does remote procedure calls (RPCs) to the build daemon (the =guix-daemon=
-=guix-daemon= or =nix-daemon= command), which in turn performs builds
+command), which in turn performs builds and accesses to the store on its
-and accesses to the Nix store on its behalf.  The RPCs are implemented
+behalf.  The RPCs are implemented in the (guix store) module.
-in the (guix store) module.
-
-* Installing Guix as non-root
-
-The Guix daemon allows software builds to be performed under alternate
-user accounts, which are normally created specifically for this
-purpose.  For instance, you may have a pool of accounts in the
-=guixbuild= group, and then you can instruct =guix-daemon= to use them
-like this:
-
-  $ guix-daemon --build-users-group=guixbuild
-
-However, unless it is run as root, =guix-daemon= cannot switch users.
-In that case, it falls back to using a setuid-root helper program call
-=nix-setuid-helper=.  That program is not setuid-root by default when
-you install it; instead you should run a command along these lines
-(assuming Guix is installed under /usr/local):
-
-  # chown root.root /usr/local/libexec/nix-setuid-helper
-  # chmod 4755 /usr/local/libexec/nix-setuid-helper
 
 * Contact
 
 GNU Guix is hosted at https://savannah.gnu.org/projects/guix/.
 
-Please email <bug-guix@gnu.org> for bug reports or questions regarding
+Please email <help-guix@gnu.org> for questions and <bug-guix@gnu.org> for bug
-Guix and its distribution; email <gnu-system-discuss@gnu.org> for
+reports; email <gnu-system-discuss@gnu.org> for general issues regarding the
-general issues regarding the GNU system.
+GNU system.
 
 Join #guix on irc.freenode.net.
 

doc/build.scm

@@ -34,6 +34,7 @@
              (gnu packages gawk)
              (gnu packages gettext)
              (gnu packages guile)
+             (gnu packages guile-xyz)
              (gnu packages iso-codes)
              (gnu packages texinfo)
              (gnu packages tex)
@@ -164,6 +165,115 @@ as well as images, OS examples, and translations."
   ;; Options passed to 'makeinfo --html'.
   '("--css-ref=https://www.gnu.org/software/gnulib/manual.css"))
 
+(define* (syntax-highlighted-html input
+                                  #:key
+                                  (name "highlighted-syntax")
+                                  (syntax-css-url
+                                   "/static/base/css/code.css"))
+  "Return a derivation called NAME that processes all the HTML files in INPUT
+to (1) add them a link to SYNTAX-CSS-URL, and (2) highlight the syntax of all
+its <pre class=\"lisp\"> blocks (as produced by 'makeinfo --html')."
+  (define build
+    (with-extensions (list guile-lib guile-syntax-highlight)
+      (with-imported-modules '((guix build utils))
+        #~(begin
+            (use-modules (htmlprag)
+                         (syntax-highlight)
+                         (syntax-highlight scheme)
+                         (syntax-highlight lexers)
+                         (guix build utils)
+                         (ice-9 match)
+                         (ice-9 threads))
+
+            (define entity->string
+              (match-lambda
+                ("rArr"   "⇒")
+                ("hellip" "…")
+                ("rsquo"  "’")
+                (e (pk 'unknown-entity e) (primitive-exit 2))))
+
+            (define (concatenate-snippets pieces)
+              ;; Concatenate PIECES, which contains strings and entities,
+              ;; replacing entities with their corresponding string.
+              (let loop ((pieces pieces)
+                         (strings '()))
+                (match pieces
+                  (()
+                   (string-concatenate-reverse strings))
+                  (((? string? str) . rest)
+                   (loop rest (cons str strings)))
+                  ((('*ENTITY* "additional" entity) . rest)
+                   (loop rest (cons (entity->string entity) strings)))
+                  ((('span _ lst ...) . rest)     ;for <span class="roman">
+                   (loop (append lst rest) strings))
+                  (something
+                   (pk 'unsupported-code-snippet something)
+                   (primitive-exit 1)))))
+
+            (define (syntax-highlight sxml)
+              ;; Recurse over SXML and syntax-highlight code snippets.
+              (match sxml
+                (('*TOP* decl body ...)
+                 `(*TOP* ,decl ,@(map syntax-highlight body)))
+                (('head things ...)
+                 `(head ,@things
+                        (link (@ (rel "stylesheet")
+                                 (type "text/css")
+                                 (href #$syntax-css-url)))))
+                (('pre ('@ ('class "lisp")) code-snippet ...)
+                 `(pre (@ (class "lisp"))
+                       ,(highlights->sxml
+                         (highlight lex-scheme
+                                    (concatenate-snippets code-snippet)))))
+                ((tag ('@ attributes ...) body ...)
+                 `(,tag (@ ,@attributes) ,@(map syntax-highlight body)))
+                ((tag body ...)
+                 `(,tag ,@(map syntax-highlight body)))
+                ((? string? str)
+                 str)))
+
+            (define (process-html file)
+              ;; Parse FILE and perform syntax highlighting for its Scheme
+              ;; snippets.  Install the result to #$output.
+              (format (current-error-port) "processing ~a...~%" file)
+              (let* ((shtml        (call-with-input-file file html->shtml))
+                     (highlighted  (syntax-highlight shtml))
+                     (base         (string-drop file (string-length #$input)))
+                     (target       (string-append #$output base)))
+                (mkdir-p (dirname target))
+                (call-with-output-file target
+                  (lambda (port)
+                    (write-shtml-as-html highlighted port)))))
+
+            (define (copy-as-is file)
+              ;; Copy FILE as is to #$output.
+              (let* ((base   (string-drop file (string-length #$input)))
+                     (target (string-append #$output base)))
+                (mkdir-p (dirname target))
+                (catch 'system-error
+                  (lambda ()
+                    (if (eq? 'symlink (stat:type (lstat file)))
+                        (symlink (readlink file) target)
+                        (link file target)))
+                  (lambda args
+                    (let ((errno (system-error-errno args)))
+                      (pk 'error-link file target (strerror errno))
+                      (primitive-exit 3))))))
+
+            ;; Install a UTF-8 locale so we can process UTF-8 files.
+            (setenv "GUIX_LOCPATH"
+                    #+(file-append glibc-utf8-locales "/lib/locale"))
+            (setlocale LC_ALL "en_US.utf8")
+
+            (n-par-for-each (parallel-job-count)
+                            (lambda (file)
+                              (if (string-suffix? ".html" file)
+                                  (process-html file)
+                                  (copy-as-is file)))
+                            (find-files #$input))))))
+
+  (computed-file name build))
+
 (define* (html-manual source #:key (languages %languages)
                       (version "0.0")
                       (manual "guix")
@@ -242,7 +352,10 @@ makeinfo OPTIONS."
                                                 "/html_node/images"))))
                     '#$languages))))
 
-  (computed-file (string-append manual "-html-manual") build))
+  (let* ((name   (string-append manual "-html-manual"))
+         (manual (computed-file name build)))
+    (syntax-highlighted-html manual
+                             #:name (string-append name "-highlighted"))))
 
 (define* (pdf-manual source #:key (languages %languages)
                      (version "0.0")

doc/guix.texi

@@ -5565,8 +5565,8 @@ specified in the @code{uri} field as a @code{git-reference} object; a
 
 @example
 (git-reference
-  (url "git://git.debian.org/git/pkg-shadow/shadow")
+  (url "https://git.savannah.gnu.org/git/hello.git")
-  (commit "v4.1.5.1"))
+  (commit "v2.10"))
 @end example
 @end table
 
@@ -6034,6 +6034,29 @@ Packages built with @code{guile-build-system} must provide a Guile package in
 their @code{native-inputs} field.
 @end defvr
 
+@defvr {Scheme Variable} julia-build-system
+This variable is exported by @code{(guix build-system julia)}.  It implements
+the build procedure used by @uref{https://julialang.org/, julia} packages,
+which essentially is similar to running @command{julia -e 'using Pkg;
+Pkg.add(package)'} in an environment where @code{JULIA_LOAD_PATH} contains the
+paths to all Julia package inputs.  Tests are run not run.
+
+Julia packages require the source @code{file-name} to be the real name of the
+package, correctly capitalized.
+
+For packages requiring shared library dependencies, you may need to write the
+@file{/deps/deps.jl} file manually. It's usually a line of @code{const
+variable = /gnu/store/libary.so} for each dependency, plus a void function
+@code{check_deps() = nothing}.
+
+Some older packages that aren't using @file{Package.toml} yet, will require
+this file to be created, too. The function @code{julia-create-package-toml}
+helps creating the file. You need to pass the outputs and the source of the
+package, it's name (the same as the @code{file-name} parameter), the package
+uuid, the package version, and a list of dependencies specified by their name
+and their uuid.
+@end defvr
+
 @defvr {Scheme Variable} minify-build-system
 This variable is exported by @code{(guix build-system minify)}.  It
 implements a minification procedure for simple JavaScript packages.
@@ -8509,8 +8532,13 @@ guix import @var{importer} @var{options}@dots{}
 
 @var{importer} specifies the source from which to import package
 metadata, and @var{options} specifies a package identifier and other
-options specific to @var{importer}.  Currently, the available
+options specific to @var{importer}.
-``importers'' are:
+
+Some of the importers rely on the ability to run the @command{gpgv} command.
+For these, GnuPG must be installed and in @code{$PATH}; run @code{guix install
+gnupg} if needed.
+
+Currently, the available ``importers'' are:
 
 @table @code
 @item gnu
@@ -8959,7 +8987,10 @@ update the version numbers and source tarball hashes of those package
 recipes (@pxref{Defining Packages}).  This is achieved by downloading
 each package's latest source tarball and its associated OpenPGP
 signature, authenticating the downloaded tarball against its signature
-using @command{gpg}, and finally computing its hash.  When the public
+using @command{gpgv}, and finally computing its hash---note that GnuPG must be
+installed and in @code{$PATH}; run @code{guix install gnupg} if needed.
+
+When the public
 key used to sign the tarball is missing from the user's keyring, an
 attempt is made to automatically retrieve it from a public key server;
 when this is successful, the key is added to the user's keyring; otherwise,
@@ -9241,6 +9272,31 @@ Parse the @code{source} URL to determine if a tarball from GitHub is
 autogenerated or if it is a release tarball.  Unfortunately GitHub's
 autogenerated tarballs are sometimes regenerated.
 
+@item archival
+@cindex Software Heritage, source code archive
+@cindex archival of source code, Software Heritage
+Checks whether the package's source code is archived at
+@uref{https://www.softwareheritage.org, Software Heritage}.
+
+When the source code that is not archived comes from a version-control system
+(VCS)---e.g., it's obtained with @code{git-fetch}, send Software Heritage a
+``save'' request so that it eventually archives it.  This ensures that the
+source will remain available in the long term, and that Guix can fall back to
+Software Heritage should the source code disappear from its original host.
+The status of recent ``save'' requests can be
+@uref{https://archive.softwareheritage.org/save/#requests, viewed on-line}.
+
+When source code is a tarball obtained with @code{url-fetch}, simply print a
+message when it is not archived.  As of this writing, Software Heritage does
+not allow requests to save arbitrary tarballs; we are working on ways to
+ensure that non-VCS source code is also archived.
+
+Software Heritage
+@uref{https://archive.softwareheritage.org/api/#rate-limiting, limits the
+request rate per IP address}.  When the limit is reached, @command{guix lint}
+prints a message and the @code{archival} checker stops doing anything until
+that limit has been reset.
+
 @item cve
 @cindex security vulnerabilities
 @cindex CVE, Common Vulnerabilities and Exposures
@@ -12620,13 +12676,14 @@ Either @code{#f} or a gexp to execute once the rotation has completed.
 @end deftp
 
 @defvr {Scheme Variable} %default-rotations
-Specifies weekly rotation of @var{%rotated-files} and
+Specifies weekly rotation of @var{%rotated-files} and of
-a couple of other files.
+@file{/var/log/guix-daemon.log}.
 @end defvr
 
 @defvr {Scheme Variable} %rotated-files
 The list of syslog-controlled files to be rotated.  By default it is:
-@code{'("/var/log/messages" "/var/log/secure")}.
+@code{'("/var/log/messages" "/var/log/secure" "/var/log/debug" \
+"/var/log/maillog")}.
 @end defvr
 
 @node Networking Services
@@ -14228,6 +14285,12 @@ programs.
 
 Defaults to @samp{"lp"}.
 @end deftypevr
+
+@deftypevr {@code{files-configuration} parameter} string set-env
+Set the specified environment variable to be passed to child processes.
+
+Defaults to @samp{"variable value"}.
+@end deftypevr
 @end deftypevr
 
 @deftypevr {@code{cups-configuration} parameter} access-log-level access-log-level
@@ -14248,6 +14311,14 @@ longer required for quotas.
 Defaults to @samp{#f}.
 @end deftypevr
 
+@deftypevr {@code{cups-configuration} parameter} comma-separated-string-list browse-dns-sd-sub-types
+Specifies a list of DNS-SD sub-types to advertise for each shared printer.
+For example, @samp{"_cups" "_print"} will tell network clients that both
+CUPS sharing and IPP Everywhere are supported.
+
+Defaults to @samp{"_cups"}.
+@end deftypevr
+
 @deftypevr {@code{cups-configuration} parameter} browse-local-protocols browse-local-protocols
 Specifies which protocols to use for local printer sharing.
 
@@ -14333,7 +14404,7 @@ Defaults to @samp{30}.
 Specifies what to do when an error occurs.  Possible values are
 @code{abort-job}, which will discard the failed print job;
 @code{retry-job}, which will retry the job at a later time;
-@code{retry-this-job}, which retries the failed job immediately; and
+@code{retry-current-job}, which retries the failed job immediately; and
 @code{stop-printer}, which stops the printer.
 
 Defaults to @samp{stop-printer}.
@@ -14747,12 +14818,6 @@ the output of the @code{uname} command.  @code{Full} reports @code{CUPS
 Defaults to @samp{Minimal}.
 @end deftypevr
 
-@deftypevr {@code{cups-configuration} parameter} string set-env
-Set the specified environment variable to be passed to child processes.
-
-Defaults to @samp{"variable value"}.
-@end deftypevr
-
 @deftypevr {@code{cups-configuration} parameter} multiline-string-list ssl-listen
 Listens on the specified interfaces for encrypted connections.  Valid
 values are of the form @var{address}:@var{port}, where @var{address} is
@@ -21369,12 +21434,12 @@ the @code{"custom-packages"} input, which is the equivalent of
                      (#:branch . "master")
                      (#:no-compile? . #t))
                     ((#:name . "config")
-                     (#:url . "git://git.example.org/config.git")
+                     (#:url . "https://git.example.org/config.git")
                      (#:load-path . ".")
                      (#:branch . "master")
                      (#:no-compile? . #t))
                     ((#:name . "custom-packages")
-                     (#:url . "git://git.example.org/custom-packages.git")
+                     (#:url . "https://git.example.org/custom-packages.git")
                      (#:load-path . ".")
                      (#:branch . "master")
                      (#:no-compile? . #t)))))))
@@ -25561,6 +25626,7 @@ evaluates to.  As an example, @var{file} might contain a definition like this:
        (environment managed-host-environment-type)
        (configuration (machine-ssh-configuration
                        (host-name "localhost")
+                       (system "x86_64-linux")
                        (user "alice")
                        (identity "./id_rsa")
                        (port 2222)))))

etc/guix-install.sh

@@ -345,6 +345,17 @@ sys_enable_guix_daemon()
             { cp "${ROOT_HOME}/.config/guix/current/lib/systemd/system/guix-daemon.service" \
                  /etc/systemd/system/;
               chmod 664 /etc/systemd/system/guix-daemon.service;
+
+	      # Work around <https://bugs.gnu.org/36074>, present in 1.0.1.
+	      sed -i /etc/systemd/system/guix-daemon.service \
+	          -e "s/GUIX_LOCPATH='/'GUIX_LOCPATH=/";
+
+	      # Work around <https://bugs.gnu.org/35671>, present in 1.0.1.
+	      if ! grep en_US /etc/systemd/system/guix-daemon.service >/dev/null;
+	      then sed -i /etc/systemd/system/guix-daemon.service \
+		       -e 's/^Environment=\(.*\)$/Environment=\1 LC_ALL=en_US.UTF-8';
+	      fi;
+
               systemctl daemon-reload &&
                   systemctl start guix-daemon &&
                   systemctl enable guix-daemon; } &&

gnu/bootloader.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2017 David Craven <david@craven.ch>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -23,6 +24,7 @@
   #:use-module (guix records)
   #:use-module (guix ui)
   #:use-module (srfi srfi-1)
+  #:use-module (ice-9 match)
   #:export (menu-entry
             menu-entry?
             menu-entry-label
@@ -32,6 +34,9 @@
             menu-entry-initrd
             menu-entry-device-mount-point
 
+            menu-entry->sexp
+            sexp->menu-entry
+
             bootloader
             bootloader?
             bootloader-name
@@ -76,6 +81,35 @@
                    (default '()))          ; list of string-valued gexps
   (initrd          menu-entry-initrd))     ; file name of the initrd as a gexp
 
+(define (menu-entry->sexp entry)
+  "Return ENTRY serialized as an sexp."
+  (match entry
+    (($ <menu-entry> label device mount-point linux linux-arguments initrd)
+     `(menu-entry (version 0)
+                  (label ,label)
+                  (device ,device)
+                  (device-mount-point ,mount-point)
+                  (linux ,linux)
+                  (linux-arguments ,linux-arguments)
+                  (initrd ,initrd)))))
+
+(define (sexp->menu-entry sexp)
+  "Turn SEXP, an sexp as returned by 'menu-entry->sexp', into a <menu-entry>
+record."
+  (match sexp
+    (('menu-entry ('version 0)
+                  ('label label) ('device device)
+                  ('device-mount-point mount-point)
+                  ('linux linux) ('linux-arguments linux-arguments)
+                  ('initrd initrd) _ ...)
+     (menu-entry
+      (label label)
+      (device device)
+      (device-mount-point mount-point)
+      (linux linux)
+      (linux-arguments linux-arguments)
+      (initrd initrd)))))
+
 
 ;;;
 ;;; Bootloader record.
@@ -108,7 +142,7 @@
   (bootloader         bootloader-configuration-bootloader) ;<bootloader>
   (target             bootloader-configuration-target      ;string
                       (default #f))
-  (menu-entries       bootloader-configuration-menu-entries ;list of <boot-parameters>
+  (menu-entries       bootloader-configuration-menu-entries ;list of <menu-entry>
                       (default '()))
   (default-entry      bootloader-configuration-default-entry ;integer
                       (default 0))

gnu/local.mk

@@ -1362,7 +1362,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/totem-meson-compat.patch			\
   %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		\
@@ -1420,7 +1419,6 @@ dist_patch_DATA =						\
   %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		\

gnu/packages/admin.scm

@@ -1500,7 +1500,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).")
 (define-public acpica
   (package
     (name "acpica")
-    (version "20190703")
+    (version "20190816")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1508,7 +1508,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).")
                     version ".tar.gz"))
               (sha256
                (base32
-                "0kp3ian3lffx9709ajrr3bp6b9cb6c6v1crjziyr8j8pp639jlwz"))))
+                "0lipy3jwl498lvgwzj6xcvmg61myl7hhilpallh1cf3ppgrq13l8"))))
     (build-system gnu-build-system)
     (native-inputs `(("flex" ,flex)
                      ("bison" ,bison)))

gnu/packages/agda.scm

@@ -22,9 +22,9 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages agda)
-  #:use-module (gnu packages haskell)
   #:use-module (gnu packages haskell-check)
   #:use-module (gnu packages haskell-web)
+  #:use-module (gnu packages haskell-xyz)
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system haskell)

gnu/packages/audio.scm

@@ -3693,7 +3693,7 @@ library.")
 (define-public faudio
   (package
     (name "faudio")
-    (version "19.08")
+    (version "19.09")
     (source
      (origin
        (method git-fetch)
@@ -3702,7 +3702,7 @@ library.")
              (commit version)))
        (file-name (string-append name "-" version "-checkout"))
        (sha256
-        (base32 "1v13kfhyr46241vb6a4dcb4gw5f149525sprwa9cj4rv6wlcqgm5"))))
+        (base32 "0fagik55jmy3qmb27nhg0zxash1ahfkxphx8m8gs0pimqqrdrd9d"))))
     (arguments
      '(#:tests? #f                      ; No tests.
        #:configure-flags '("-DFFMPEG=ON")))

gnu/packages/aux-files/chromium/master-preferences.json

@@ -17,9 +17,6 @@
     "alternate_error_pages": {
         "enabled": false
     },
-    "hardware": {
-        "audio_capture_enabled": false
-    },
     "default_apps": "noinstall",
     "hide_web_store_icon": true,
     "homepage": "https://www.gnu.org/software/guix/"

gnu/packages/aux-files/linux-libre/5.2-arm64.conf

@@ -8023,7 +8023,7 @@ CONFIG_VALIDATE_FS_PARSER=y
 CONFIG_FS_IOMAP=y
 # CONFIG_EXT2_FS is not set
 # CONFIG_EXT3_FS is not set
-CONFIG_EXT4_FS=m
+CONFIG_EXT4_FS=y
 CONFIG_EXT4_USE_FOR_EXT2=y
 CONFIG_EXT4_FS_POSIX_ACL=y
 CONFIG_EXT4_FS_SECURITY=y

gnu/packages/base.scm

@@ -1112,7 +1112,7 @@ to the @code{share/locale} sub-directory of this package.")
                                ;; tests---e.g., in Guile's i18n tests.
                                '("de_DE" "el_GR" "en_US" "fr_FR" "tr_TR"))
                      #t))))
-    (inputs `(("glibc" ,glibc)
+    (native-inputs `(("glibc" ,glibc)
                      ("gzip" ,gzip)))
     (synopsis "Small sample of UTF-8 locales")
     (description

gnu/packages/bioconductor.scm

@@ -31,7 +31,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages graph)
-  #:use-module (gnu packages haskell)
+  #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages image)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages netpbm)
@@ -532,6 +532,28 @@ annotations for the genome of the model mouse Mus musculus.")
 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-ensdb-hsapiens-v75
+  (package
+    (name "r-ensdb-hsapiens-v75")
+    (version "2.99.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
+       (sha256
+        (base32
+         "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
+    (properties
+     `((upstream-name . "EnsDb.Hsapiens.v75")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ensembldb" ,r-ensembldb)))
+    (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
+    (synopsis "Ensembl based annotation package")
+    (description
+     "This package exposes an annotation database generated from Ensembl.")
+    (license license:artistic2.0)))
+
 (define-public r-genelendatabase
   (package
     (name "r-genelendatabase")
@@ -686,6 +708,31 @@ the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
 based on the knownGene track.")
     (license license:artistic2.0)))
 
+(define-public r-txdb-celegans-ucsc-ce6-ensgene
+  (package
+    (name "r-txdb-celegans-ucsc-ce6-ensgene")
+    (version "3.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
+                              version 'annotation))
+       (sha256
+        (base32
+         "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
+    (properties
+     `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-genomicfeatures" ,r-genomicfeatures)))
+    (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
+    (synopsis "Annotation package for C elegans TxDb objects")
+    (description
+     "This package exposes a C elegans annotation database generated from UCSC
+by exposing these as TxDb objects.")
+    (license license:artistic2.0)))
+
 (define-public r-fdb-infiniummethylation-hg19
   (package
     (name "r-fdb-infiniummethylation-hg19")
@@ -2977,14 +3024,14 @@ phenotype of interest.")
 (define-public r-fgsea
   (package
     (name "r-fgsea")
-    (version "1.10.0")
+    (version "1.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fgsea" version))
        (sha256
         (base32
-         "07mvv1i690q80fm8sxgdqxchamn76409vn91ppgcck2xpi6b8q6c"))))
+         "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bh" ,r-bh)
@@ -5000,14 +5047,14 @@ self-organizing map clustering and minimal spanning trees.")
 (define-public r-mixomics
   (package
     (name "r-mixomics")
-    (version "6.8.0")
+    (version "6.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mixOmics" version))
        (sha256
         (base32
-         "1f08jx35amn3sfcmqb96mjxxsm6dnpzhff625z758x1992wj4zsk"))))
+         "0issfrhsgc102sr33q9v6w6jrrd32plig7szd1nm0n4r3yn4y2fc"))))
     (properties `((upstream-name . "mixOmics")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5230,3 +5277,192 @@ 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))))
+
+(define-public r-genie3
+  (package
+    (name "r-genie3")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "GENIE3" version))
+       (sha256
+        (base32
+         "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx"))))
+    (properties `((upstream-name . "GENIE3")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-reshape2" ,r-reshape2)))
+    (home-page "https://bioconductor.org/packages/GENIE3")
+    (synopsis "Gene network inference with ensemble of trees")
+    (description
+     "This package implements the GENIE3 algorithm for inferring gene
+regulatory networks from expression data.")
+    (license license:gpl2+)))
+
+(define-public r-roc
+  (package
+    (name "r-roc")
+    (version "1.60.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ROC" version))
+       (sha256
+        (base32
+         "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c"))))
+    (properties `((upstream-name . "ROC")))
+    (build-system r-build-system)
+    (home-page "https://www.bioconductor.org/packages/ROC/")
+    (synopsis "Utilities for ROC curves")
+    (description
+     "This package provides utilities for @dfn{Receiver Operating
+Characteristic} (ROC) curves, with a focus on micro arrays.")
+    (license license:artistic2.0)))
+
+(define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
+  (package
+    (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri
+             "IlluminaHumanMethylation450kanno.ilmn12.hg19"
+             version 'annotation))
+       (sha256
+        (base32
+         "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
+    (properties
+     `((upstream-name
+        . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-minfi" ,r-minfi)))
+    (home-page
+     "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
+    (synopsis "Annotation for Illumina's 450k methylation arrays")
+    (description
+     "This package provides manifests and annotation for Illumina's 450k array
+data.")
+    (license license:artistic2.0)))
+
+(define-public r-watermelon
+  (package
+    (name "r-watermelon")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "wateRmelon" version))
+       (sha256
+        (base32
+         "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z"))))
+    (properties `((upstream-name . "wateRmelon")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
+        ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
+       ("r-illuminaio" ,r-illuminaio)
+       ("r-limma" ,r-limma)
+       ("r-lumi" ,r-lumi)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-methylumi" ,r-methylumi)
+       ("r-roc" ,r-roc)))
+    (home-page "https://bioconductor.org/packages/wateRmelon/")
+    (synopsis "Illumina 450 methylation array normalization and metrics")
+    (description
+     "The standard index of DNA methylation (beta) is computed from methylated
+and unmethylated signal intensities.  Betas calculated from raw signal
+intensities perform well, but using 11 methylomic datasets we demonstrate that
+quantile normalization methods produce marked improvement.  The commonly used
+procedure of normalizing betas is inferior to the separate normalization of M
+and U, and it is also advantageous to normalize Type I and Type II assays
+separately.  This package provides 15 flavours of betas and three performance
+metrics, with methods for objects produced by the @code{methylumi} and
+@code{minfi} packages.")
+    (license license:gpl3)))
+
+(define-public r-gdsfmt
+  (package
+    (name "r-gdsfmt")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "gdsfmt" version))
+       (sha256
+        (base32
+         "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy"))
+       (modules '((guix build utils)))
+       ;; Remove bundled sources of zlib, lz4, and xz.  Don't attempt to build
+       ;; them and link with system libraries instead.
+       (snippet
+        '(begin
+           (for-each delete-file-recursively
+                     '("src/LZ4"
+                       "src/XZ"
+                       "src/ZLIB"))
+           (substitute* "src/Makevars"
+             (("all: \\$\\(SHLIB\\)") "all:")
+             (("\\$\\(SHLIB\\): liblzma.a") "")
+             (("(ZLIB|LZ4)/.*") "")
+             (("CoreArray/dVLIntGDS.cpp.*")
+              "CoreArray/dVLIntGDS.cpp")
+             (("CoreArray/dVLIntGDS.o.*")
+              "CoreArray/dVLIntGDS.o")
+             (("PKG_LIBS = ./liblzma.a")
+              "PKG_LIBS = -llz4"))
+           (substitute* "src/CoreArray/dStream.h"
+             (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
+              (string-append "include <" header ">")))
+           #t))))
+    (properties `((upstream-name . "gdsfmt")))
+    (build-system r-build-system)
+    (inputs
+     `(("lz4" ,lz4)
+       ("xz" ,xz)
+       ("zlib" ,zlib)))
+    (home-page "http://corearray.sourceforge.net/")
+    (synopsis
+     "R Interface to CoreArray Genomic Data Structure (GDS) Files")
+    (description
+     "This package provides a high-level R interface to CoreArray @dfn{Genomic
+Data Structure} (GDS) data files, which are portable across platforms with
+hierarchical structure to store multiple scalable array-oriented data sets
+with metadata information.  It is suited for large-scale datasets, especially
+for data which are much larger than the available random-access memory.  The
+@code{gdsfmt} package offers efficient operations specifically designed for
+integers of less than 8 bits, since a diploid genotype, like
+@dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
+byte.  Data compression and decompression are available with relatively
+efficient random access.  It is also allowed to read a GDS file in parallel
+with multiple R processes supported by the package @code{parallel}.")
+    (license license:lgpl3)))
+
+(define-public r-bigmelon
+  (package
+    (name "r-bigmelon")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "bigmelon" version))
+       (sha256
+        (base32
+         "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9"))))
+    (properties `((upstream-name . "bigmelon")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-gdsfmt" ,r-gdsfmt)
+       ("r-geoquery" ,r-geoquery)
+       ("r-methylumi" ,r-methylumi)
+       ("r-minfi" ,r-minfi)
+       ("r-watermelon" ,r-watermelon)))
+    (home-page "https://bioconductor.org/packages/bigmelon/")
+    (synopsis "Illumina methylation array analysis for large experiments")
+    (description
+     "This package provides methods for working with Illumina arrays using the
+@code{gdsfmt} package.")
+    (license license:gpl3)))

gnu/packages/bioinformatics.scm

@@ -77,9 +77,9 @@
   #:use-module (gnu packages groff)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages guile-xyz)
-  #:use-module (gnu packages haskell)
   #:use-module (gnu packages haskell-check)
   #:use-module (gnu packages haskell-web)
+  #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages java)
@@ -1758,8 +1758,8 @@ well as many of the command line options.")
          (add-after 'unpack 'keep-references-to-bwa
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "bwameth.py"
-               (("bwa mem")
+               (("bwa (mem|index)" _ command)
-                (string-append (which "bwa") " mem"))
+                (string-append (which "bwa") " " command))
                ;; There's an ill-advised check for "samtools" on PATH.
                (("^checkX.*") ""))
              #t)))))
@@ -2344,16 +2344,16 @@ other types of unwanted sequence from high-throughput sequencing reads.")
 (define-public libbigwig
   (package
     (name "libbigwig")
-    (version "0.4.2")
+    (version "0.4.4")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/dpryan79/libBigWig.git")
                     (commit version)))
-              (file-name (string-append name "-" version "-checkout"))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0h2smg24v5srdcqzrmz2g23cmlp4va465mgx8r2z571sfz8pv454"))))
+                "09693dmf1scdac5pyq6qyn8b4mcipvnmc370k9a5z41z81m3dcsj"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
@@ -7367,13 +7367,13 @@ S4Vectors package itself.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.18.1")
+    (version "2.18.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "1d64sh43pfc9vj2l7y7x6sb44l67wlnn3dzygp7ws0smn06mardq"))))
+                "0dc35844c1mfj07hvy6yn4wag6qdggbgl9gjcg3wpkh9hkm60a5n"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
@@ -7620,13 +7620,13 @@ on Bioconductor or which replace R functions.")
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.46.0")
+    (version "1.46.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "0lfq5668a6sq4kqhxx78hl3jcaqdsaaliiybl9xyya2scdk8c29c"))))
+                "13nanz4nzy0mcda8ljz2g8d81hpqfz6jky7ydz5hpk0g2264b9ga"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)
@@ -7647,13 +7647,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.40.3")
+    (version "2.40.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "022m1r44s00c5k9bmv0lr22lcn662nhc91aazvv0yyysxjamyf60"))))
+                "0dj51qkxm7bh24b3bs1di7lic6zgi7g5gf9iqkqhrwkbm7sqvn0v"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -7872,13 +7872,13 @@ alignments.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.44.2")
+    (version "1.44.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "03b4rfsbzjjf5kxcsjv7kq8hrsgcvz9rfzcn2v7fx3nr818pbb8s"))))
+                "091zydz1zpz519ha0jkbvzrhxjvw5r2963qz9grmvl2jd8girvcg"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -9446,13 +9446,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "3.0.2")
+    (version "3.1.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "016fgcmjz3sjfxdvam5hd7mdxpmpnc7f6p5zqlh97m21dgn5vpqn"))))
+                "0icxndnnkkmmr9hhd01dv3w8pih7x9r0rlp3fq9pk3qajp9gmlyq"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9469,6 +9469,7 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
        ("r-igraph" ,r-igraph)
        ("r-irlba" ,r-irlba)
        ("r-kernsmooth" ,r-kernsmooth)
+       ("r-leiden" ,r-leiden)
        ("r-lmtest" ,r-lmtest)
        ("r-mass" ,r-mass)
        ("r-matrix" ,r-matrix)
@@ -9479,6 +9480,7 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
        ("r-rann" ,r-rann)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-rcpp" ,r-rcpp)
+       ("r-rcppannoy" ,r-rcppannoy)
        ("r-rcppeigen" ,r-rcppeigen)
        ("r-rcppprogress" ,r-rcppprogress)
        ("r-reticulate" ,r-reticulate)
@@ -9489,7 +9491,8 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
        ("r-scales" ,r-scales)
        ("r-sctransform" ,r-sctransform)
        ("r-sdmtools" ,r-sdmtools)
-       ("r-tsne" ,r-tsne)))
+       ("r-tsne" ,r-tsne)
+       ("r-uwot" ,r-uwot)))
     (home-page "http://www.satijalab.org/seurat")
     (synopsis "Seurat is an R toolkit for single cell genomics")
     (description
@@ -10176,22 +10179,24 @@ by Ernst and Kellis.")
 (define-public r-ldblock
   (package
     (name "r-ldblock")
-    (version "1.14.0")
+    (version "1.14.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ldblock" version))
        (sha256
         (base32
-         "0lraxhq9ny3468534klrl64nx0dpaf9cbd5bir6m5qma8j7kfnyd"))))
+         "0xx04cghx6ads1ackwnw3z0gf72qv461nznzmcnkgmp7w5n9m2af"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-erma" ,r-erma)
+       ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
+       ("r-ensembldb" ,r-ensembldb)
        ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicfiles" ,r-genomicfiles)
        ("r-go-db" ,r-go-db)
        ("r-homo-sapiens" ,r-homo-sapiens)
+       ("r-httr" ,r-httr)
        ("r-matrix" ,r-matrix)
        ("r-rsamtools" ,r-rsamtools)
        ("r-snpstats" ,r-snpstats)
@@ -13412,8 +13417,7 @@ bgzipped text file that contains a pair of genomic coordinates per line.")
          "0y5zyjksj1rdglj601xd2bbni5abhdh622y3ck76chyzxz9z4rx8"))))
     (build-system python-build-system)
     (propagated-inputs
-     `(("python-setuptools" ,python-setuptools)
+     `(("python-six" ,python-six)))
-       ("python-six" ,python-six)))
     (home-page "http://mattshirley.com")
     (synopsis "Random access to fasta subsequences")
     (description
@@ -14653,16 +14657,14 @@ proximity within a reference genome.")
          "08y3vz1vcx09whmbsn722lcs6jl9wyrh9i4p3k8j4cb1i32bij4a"))))
     (build-system python-build-system)
     (inputs
-     `(("python-setuptools" ,python-setuptools)
+     `(("python-pandas" ,python-pandas)
-       ("python-pandas" ,python-pandas)
        ("python-future" ,python-future)
        ("python-scipy" ,python-scipy)
        ("python-matplotlib" ,python-matplotlib)
        ("python-regex" ,python-regex)
        ("python-pysam" ,python-pysam)))
     (native-inputs
-     `(("python-setuptools" ,python-setuptools)
+     `(("python-cython" ,python-cython)))
-       ("python-cython" ,python-cython)))
     (home-page "https://github.com/CGATOxford/UMI-tools")
     (synopsis "Tools for analyzing unique modular identifiers")
     (description "This package provides tools for dealing with @dfn{Unique
@@ -15215,3 +15217,37 @@ indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and
 complex events (composite insertion and substitution events) smaller than the
 length of a short-read sequencing alignment.")
       (license license:expat))))
+
+(define-public samblaster
+  (package
+    (name "samblaster")
+    (version "0.1.24")
+    (source (origin
+      (method git-fetch)
+      (uri (git-reference
+            (url "https://github.com/GregoryFaust/samblaster.git")
+            (commit (string-append "v." version))))
+      (file-name (git-file-name name version))
+      (sha256
+       (base32
+        "0iv2ddfw8363vb2x8gr3p8g88whb6mb9m0pf71i2cqsbv6jghap7"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; there are none
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure) ; There is no configure phase.
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (install-file "samblaster"
+                           (string-append (assoc-ref outputs "out") "/bin"))
+             #t)))))
+    (home-page "https://github.com/GregoryFaust/samblaster")
+    (synopsis "Mark duplicates in paired-end SAM files")
+    (description "Samblaster is a fast and flexible program for marking
+duplicates in read-id grouped paired-end SAM files.  It can also optionally
+output discordant read pairs and/or split read mappings to separate SAM files,
+and/or unmapped/clipped reads to a separate FASTQ file. When marking
+duplicates, samblaster will require approximately 20MB of memory per 1M read
+pairs.")
+    (license license:expat)))

gnu/packages/bootloaders.scm

@@ -99,7 +99,7 @@
        (list "PYTHON=true")
        #:phases (modify-phases %standard-phases
                   (add-after 'unpack 'patch-stuff
-                   (lambda* (#:key inputs #:allow-other-keys)
+                   (lambda* (#:key native-inputs inputs #:allow-other-keys)
                      (substitute* "grub-core/Makefile.in"
                        (("/bin/sh") (which "sh")))
 
@@ -114,7 +114,9 @@
                                        "/sbin/mdadm\"")))
 
                      ;; Make the font visible.
-                     (copy-file (assoc-ref inputs "unifont") "unifont.bdf.gz")
+                     (copy-file (assoc-ref (or native-inputs inputs)
+                                           "unifont")
+                                "unifont.bdf.gz")
                      (system* "gunzip" "unifont.bdf.gz")
 
                      ;; Give the absolute file name of 'ckbcomp'.

gnu/packages/cdrom.scm

@@ -884,7 +884,7 @@ CD data, and more.  It's mostly compatible with @code{cdrtools}.")
 (define-public libmirage
   (package
     (name "libmirage")
-    (version "3.2.2")
+    (version "3.2.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -892,7 +892,7 @@ CD data, and more.  It's mostly compatible with @code{cdrtools}.")
                     version ".tar.bz2"))
               (sha256
                (base32
-                "0gwrfia0fyhi0b3p2pfyyvrcfcb0qysfzgpdqsqjqbx4xaqx5wpi"))))
+                "08mfvqyk3833ksfd47i4j3ppmrw5ry219km6h7lywdh9hm9x14yf"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
@@ -913,7 +913,7 @@ the data stored in various image formats.")
 (define-public cdemu-daemon
   (package
     (name "cdemu-daemon")
-    (version "3.2.2")
+    (version "3.2.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -921,7 +921,7 @@ the data stored in various image formats.")
                     version ".tar.bz2"))
               (sha256
                (base32
-                "0himyrhhfjsr4ff5aci7240bpm9x34h20pid412ci8fm16nk929b"))))
+                "022xzgwmncswb9md71w3ly3mjkdfc93lbij2llp2jamq8grxjjxr"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
@@ -942,7 +942,7 @@ drive and disc (including CD-ROMs and DVD-ROMs).")
 (define-public cdemu-client
   (package
     (name "cdemu-client")
-    (version "3.2.1")
+    (version "3.2.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -950,7 +950,7 @@ drive and disc (including CD-ROMs and DVD-ROMs).")
                     version ".tar.bz2"))
               (sha256
                (base32
-                "1d8m24qvv62xcwafw5zs4yf39vs64kxl4idqcngd8yyjhrb2ykg5"))))
+                "1bvc2m63fx03rbp3ihgl2n7k24lwg5ydwkmr84gsjfcxp46q10zq"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)

gnu/packages/cedille.scm

@@ -21,6 +21,7 @@
   #:use-module (gnu packages agda)
   #:use-module (gnu packages emacs-xyz)
   #:use-module (gnu packages haskell)
+  #:use-module (gnu packages haskell-xyz)
   #:use-module (guix build-system emacs)
   #:use-module (guix git-download)
   #:use-module ((guix licenses) #:prefix license:)

gnu/packages/commencement.scm

@@ -2361,7 +2361,8 @@ exec ~a/bin/~a-~a -B~a/lib -Wl,-dynamic-linker -Wl,~a/~a \"$@\"~%"
   ;; function.)
   (package
     (inherit glibc-utf8-locales)
-    (inputs `(("glibc" ,glibc-final)
+    (native-inputs
+     `(("glibc" ,glibc-final)
        ("gzip"
         ,(package-with-explicit-inputs gzip %boot4-inputs
                                        (current-source-location)

gnu/packages/conky.scm

@@ -37,7 +37,7 @@
   (package
     (name "conky")
     (home-page "https://github.com/brndnmtthws/conky")
-    (version "1.11.3")
+    (version "1.11.5")
     (source
      (origin
        (method git-fetch)
@@ -46,7 +46,7 @@
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0pdl31xvmy8niagzqx9sd2b6hc6lzwfiaz66m4djf1gz9bksc8qv"))))
+        (base32 "1a75ss48mn9pknrxy33dh5rdgm67a5kpddsyqfhlcn1761kfzzyp"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ; there are no tests

gnu/packages/cran.scm

@@ -53,7 +53,7 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages graph)
   #:use-module (gnu packages gtk)
-  #:use-module (gnu packages haskell)
+  #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
@@ -166,14 +166,14 @@ objects.")
 (define-public r-sys
   (package
     (name "r-sys")
-    (version "3.2")
+    (version "3.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sys" version))
        (sha256
         (base32
-         "1k5vk5q9wa5sin0n226i05nymg469s24f6lx64yyhb7yc624j698"))))
+         "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
     (build-system r-build-system)
     (home-page "https://github.com/jeroen/sys")
     (synopsis "Powerful and reliable tools for running system commands in R")
@@ -212,14 +212,14 @@ read a protected key.")
 (define-public r-vegan
   (package
     (name "r-vegan")
-    (version "2.5-5")
+    (version "2.5-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vegan" version))
        (sha256
         (base32
-         "0wb90ng02gi13854bjq0b8a2vrknyhb0s0l1v3z38c4zy9k54sw7"))))
+         "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -872,14 +872,14 @@ well as file saving is available.")
 (define-public r-d3r
   (package
     (name "r-d3r")
-    (version "0.8.6")
+    (version "0.8.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "d3r" version))
        (sha256
         (base32
-         "0vcmiyhd000xyl28k6rm7ba50x5sz5b2cpllxnq36q13qhdnqw6k"))))
+         "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a"))))
     (build-system r-build-system)
     (arguments
      `(#:modules ((guix build utils)
@@ -1122,14 +1122,14 @@ coordinates.")
 (define-public r-rgooglemaps
   (package
     (name "r-rgooglemaps")
-    (version "1.4.3")
+    (version "1.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RgoogleMaps" version))
        (sha256
         (base32
-         "06ab3lg1rwm93hkshf1vxfm8mlxq5qsjan0wx43lhnrysay65js4"))))
+         "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x"))))
     (properties `((upstream-name . "RgoogleMaps")))
     (build-system r-build-system)
     (propagated-inputs `(("r-png" ,r-png)))
@@ -1441,14 +1441,14 @@ processes.  Most of its code is based on the @code{psutil} Python package.")
 (define-public r-pkgbuild
   (package
     (name "r-pkgbuild")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pkgbuild" version))
        (sha256
         (base32
-         "0prvx91dha5pvd0k4jca2arkngvi6vnfs2indmiy3kwwzyjyyd19"))))
+         "0y4i85axwajrk67h3w6fiqfm6wxmhn3dr240w5l2nvqg3ahpxc8q"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)
@@ -1649,14 +1649,14 @@ validation and filtering on the values, making options invisible or private.")
 (define-public r-circlize
   (package
     (name "r-circlize")
-    (version "0.4.6")
+    (version "0.4.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "circlize" version))
        (sha256
         (base32
-         "1yjnb88pnzk5c1p0vjxykc7cr3394ln5axviqcf12ajibvy8rj6f"))))
+         "07y1bchkslpz2wl43yg5j5h1nl9z0i425a07jdmfd5avrynd8p3m"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-colorspace" ,r-colorspace)
@@ -2663,14 +2663,14 @@ Optimization problems by using the simplex algorithm.")
 (define-public r-geometry
   (package
     (name "r-geometry")
-    (version "0.4.2")
+    (version "0.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "geometry" version))
        (sha256
         (base32
-         "0vq334115qi039vy198ggv1dsp6n1s6jwcm9ivipf5r8lbm287zz"))))
+         "0z4491mhfmrlbb8lazjvq55alrprx7k0abg2d39fj0lsj84cls1r"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-magic" ,r-magic)
@@ -3476,14 +3476,14 @@ of Eigenmatrices} (JADE).")
 (define-public r-dtw
   (package
     (name "r-dtw")
-    (version "1.20-1")
+    (version "1.21-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dtw" version))
        (sha256
         (base32
-         "1w301xwizncy5r8v9rwwdxfshydgp3l1pnjla1fjn6n8lx3imjj3"))))
+         "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-proxy" ,r-proxy)))
     (home-page "http://dtw.r-forge.r-project.org/")
@@ -3765,14 +3765,14 @@ Markdown documents.")
 (define-public r-seriation
   (package
     (name "r-seriation")
-    (version "1.2-7")
+    (version "1.2-8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "seriation" version))
        (sha256
         (base32
-         "0dbz5b5msy4fr2whhphyriqk1xc6305zpjq59rrwxyz3d7rzwpa6"))))
+         "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cluster" ,r-cluster)
@@ -3799,14 +3799,14 @@ iVAT).")
 (define-public r-xfun
   (package
     (name "r-xfun")
-    (version "0.8")
+    (version "0.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xfun" version))
        (sha256
         (base32
-         "05jlbi5byqpw0fkhmmxqglnaxh9gwbcigx77kcpw1pkxnpwfry62"))))
+         "1c3wmy6s4ck821mwl7i2g8cxd31g30llbpivbgq21g1rxs4zwlyl"))))
     (build-system r-build-system)
     (home-page "https://github.com/yihui/xfun")
     (synopsis "Miscellaneous functions")
@@ -4699,14 +4699,14 @@ systems.")
 (define-public r-radiant-data
   (package
     (name "r-radiant-data")
-    (version "1.0.0")
+    (version "1.0.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "radiant.data" version))
        (sha256
         (base32
-         "0b35jn4mcj10hqra18l8pi6s4pvj6fxipslbn6hkr4zza1z27gzw"))
+         "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -5064,14 +5064,14 @@ evaluated by the @dfn{Akaike Information Criterion} (AIC).")
 (define-public r-arules
   (package
     (name "r-arules")
-    (version "1.6-3")
+    (version "1.6-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "arules" version))
        (sha256
         (base32
-         "0dimrq1pz449z0mz9m87nhm5bpc0v789bcc3lghhh97wwi5zah9y"))))
+         "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)))
@@ -5161,14 +5161,14 @@ misclassification probabilities of different models.")
 (define-public r-zip
   (package
     (name "r-zip")
-    (version "2.0.3")
+    (version "2.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "zip" version))
        (sha256
         (base32
-         "0zii05jg9v9ljd0wd67g9x4bhlmpmsy5dzd093sbnc5n3vjbi32a"))))
+         "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
     (build-system r-build-system)
     (home-page "https://github.com/gaborcsardi/zip")
     (synopsis "Cross-platform Zip compression")
@@ -6921,14 +6921,14 @@ used to teach mathematics, statistics, computation and modeling.")
 (define-public r-raster
   (package
     (name "r-raster")
-    (version "2.9-23")
+    (version "3.0-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "raster" version))
        (sha256
         (base32
-         "1brqigic8ygr223bp2hgk5qjz3q03r4sfglrv4an0ghy7fgfralh"))))
+         "0z4qh3ag1iyly4zjvzi3x2namkndkqn3cjb3ac22xd11sq5gdgiz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)
@@ -7489,14 +7489,14 @@ multiple-imputation datasets.")
 (define-public r-magick
   (package
     (name "r-magick")
-    (version "2.1")
+    (version "2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "magick" version))
        (sha256
         (base32
-         "1pz71maz05gx4ds1wfw0alggc8nn2w75lj12dg1zr72s3kybhkzg"))))
+         "1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85"))))
     (build-system r-build-system)
     (inputs
      `(("imagemagick" ,imagemagick)
@@ -7927,14 +7927,14 @@ Cohen (1988).")
 (define-public r-libcoin
   (package
     (name "r-libcoin")
-    (version "1.0-4")
+    (version "1.0-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "libcoin" version))
        (sha256
         (base32
-         "1i893ij9vkmc4y721npw1s3prmmcs2da5vf3ajm0j8ccmfhbmp4i"))))
+         "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
     (home-page "https://cran.r-project.org/web/packages/libcoin")
@@ -7947,14 +7947,14 @@ and permutation inference in the framework of Strasser and Weber (1999).")
 (define-public r-coin
   (package
     (name "r-coin")
-    (version "1.3-0")
+    (version "1.3-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "coin" version))
        (sha256
         (base32
-         "1y0yl4mjaxca0jqz53sv1gcpdg89m099rq61iszxvpx7w0vvpkmd"))))
+         "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-libcoin" ,r-libcoin)
@@ -8518,14 +8518,14 @@ ways.")
 (define-public r-summarytools
   (package
     (name "r-summarytools")
-    (version "0.9.3")
+    (version "0.9.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "summarytools" version))
        (sha256
         (base32
-         "1wfbkgvicaic37zgpr6zcm4a58yx43p59h0sqggdj44ncqs7147f"))))
+         "1n695baz56mg4f13xjjadfq0xalw5xsn6xicil0yap5hgi8fsr3a"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-checkmate" ,r-checkmate)
@@ -8696,14 +8696,14 @@ analysing multivariate abundance data in community ecology.")
 (define-public r-afex
   (package
     (name "r-afex")
-    (version "0.24-1")
+    (version "0.25-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "afex" version))
        (sha256
         (base32
-         "14w7kcwr5hxmjcjmdm5ia9ka3bw1nl18pxlm1vpw62nmvicn3455"))))
+         "12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-car" ,r-car)
@@ -8930,14 +8930,14 @@ Bioconductor packages.")
 (define-public r-rgl
   (package
     (name "r-rgl")
-    (version "0.100.26")
+    (version "0.100.30")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rgl" version))
        (sha256
         (base32
-         "0h77akviwjd86j2qyx326xynbmwhypd6ydprzlwqnidd4ckrr271"))))
+         "0rzqzskcwf2ah4yr62x5rjwf7yh90d43h39gk7jmfc5lc08zaxc5"))))
     (build-system r-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -9325,6 +9325,51 @@ in-memory raw vectors.")
     ;; Either of these two license versions.
     (license (list license:gpl2 license:gpl3))))
 
+(define-public r-nlp
+  (package
+    (name "r-nlp")
+    (version "0.2-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "NLP" version))
+       (sha256
+        (base32
+         "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
+    (properties `((upstream-name . "NLP")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/NLP/")
+    (synopsis "Natural language processing infrastructure")
+    (description
+     "This package provides basic classes and methods for Natural Language
+Processing.")
+    (license license:gpl3)))
+
+(define-public r-tm
+  (package
+    (name "r-tm")
+    (version "0.7-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tm" version))
+       (sha256
+        (base32
+         "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r"))))
+    (properties `((upstream-name . "tm")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bh" ,r-bh)
+       ("r-nlp" ,r-nlp)
+       ("r-rcpp" ,r-rcpp)
+       ("r-slam" ,r-slam)
+       ("r-xml2" ,r-xml2)))
+    (home-page "http://tm.r-forge.r-project.org/")
+    (synopsis "Text mining package")
+    (description
+     "This package provides a framework for text mining applications within R.")
+    (license license:gpl3)))
+
 (define-public r-waveslim
   (package
     (name "r-waveslim")
@@ -9364,7 +9409,10 @@ pairs (Selesnick 2001, 2002).")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rcpp" ,r-rcpp)))
+       ("r-rcpp" ,r-rcpp)
+       ;; The "tm" package is only "suggested" according to CRAN, but the
+       ;; wordcloud package cannot be loaded without it.
+       ("r-tm" ,r-tm)))
     (home-page "https://cran.r-project.org/web/packages/wordcloud")
     (synopsis "Word clouds")
     (description
@@ -10749,14 +10797,14 @@ Differences with other sparse matrix packages are:
 (define-public r-fields
   (package
     (name "r-fields")
-    (version "9.8-3")
+    (version "9.8-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fields" version))
        (sha256
         (base32
-         "1q9x68dczjym56v7x90x4x5br59vj3dww6w8v42zd3yl17h7c1h1"))))
+         "07x95vk1idjfzi5ikn0ijal754mssdmgr1p4nswmx9w3i5ndcqaz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-maps" ,r-maps)
@@ -11786,14 +11834,14 @@ select colors to use in your R code.")
 (define-public r-ggextra
   (package
     (name "r-ggextra")
-    (version "0.8")
+    (version "0.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggExtra" version))
        (sha256
         (base32
-         "1m5zpn3l3p1y3d2692gyz50m63d58m2a3b7zb595kvcffdx2qr5b"))))
+         "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
     (properties `((upstream-name . "ggExtra")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11801,6 +11849,7 @@ select colors to use in your R code.")
        ("r-ggplot2" ,r-ggplot2)
        ("r-gtable" ,r-gtable)
        ("r-miniui" ,r-miniui)
+       ("r-r6" ,r-r6)
        ("r-scales" ,r-scales)
        ("r-shiny" ,r-shiny)
        ("r-shinyjs" ,r-shinyjs)))
@@ -11900,14 +11949,14 @@ probabilities from a standard bivariate normal CDF.")
 (define-public r-lavaan
   (package
     (name "r-lavaan")
-    (version "0.6-4")
+    (version "0.6-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lavaan" version))
        (sha256
         (base32
-         "1zf0sxpms35rhq2syb7r3sshhc8kjvc3pv97dk9x0gf4xl7pck4g"))))
+         "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)
@@ -12189,14 +12238,14 @@ network.")
 (define-public r-apcluster
   (package
     (name "r-apcluster")
-    (version "1.4.7")
+    (version "1.4.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "apcluster" version))
        (sha256
         (base32
-         "188hdfmwjjx3aic599nwmkzjqm9j9jighi5bly6qd43c1vj6ih2s"))))
+         "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)
@@ -12347,17 +12396,17 @@ extensions.")
 (define-public r-wgaim
   (package
     (name "r-wgaim")
-    (version "1.4-11")
+    (version "2.0-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "wgaim" version))
        (sha256
         (base32
-         "1jjyp100dcjjczp61xlvhmy48ynniqcys535vzbgswhr7fvijymg"))))
+         "0wnb10vibgq8h1ly6lq8kzymf30vx0j0g8fc2zidblbvwag9ka1g"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-lattice" ,r-lattice)
+     `(("r-ggplot2" ,r-ggplot2)
        ("r-qtl" ,r-qtl)))
     (home-page "https://cran.r-project.org/web/packages/wgaim")
     (synopsis "Whole genome average interval mapping for QTL detection")
@@ -12566,14 +12615,14 @@ utilities for sequence data management under the ACNUC system.")
 (define-public r-units
   (package
     (name "r-units")
-    (version "0.6-3")
+    (version "0.6-4")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "units" version))
         (sha256
           (base32
-            "0kx640h60s3zzkdr302asap7diap6vri6d41scnx507yvkcqiph3"))))
+            "1jz0mzd78sdfxkhqw041ji50hmhjk2ha55i31yjvz35nsw30lwi5"))))
     (build-system r-build-system)
     (inputs
      `(("udunits" ,udunits)))
@@ -13121,14 +13170,14 @@ exact test for Hardy-Weinberg equilibrium.")
 (define-public r-tdthap
   (package
     (name "r-tdthap")
-    (version "1.1-9")
+    (version "1.1-11")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tdthap" version))
        (sha256
         (base32
-         "0y01x0hcf0rw06cpn4pk17b0shf4v2c9was7vfs0zhsbq8qcwx7r"))))
+         "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/tdthap/")
     (synopsis "TDT tests for extended haplotypes")
@@ -13164,13 +13213,13 @@ SELECT or UPDATE queries to an end-point.")
 (define-public r-bookdown
   (package
     (name "r-bookdown")
-    (version "0.12")
+    (version "0.13")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "bookdown" version))
               (sha256
                (base32
-                "1c2v0rpa1rrpbx8yb66sfvrf4gf57f6a8x7ydjqqbkbwhxdlrsrq"))))
+                "15r9scgnq68hmfcfxvjk286hpbr825bib1d2kgh0lv3dgz2i2bg1"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-htmltools" ,r-htmltools)
@@ -13764,14 +13813,14 @@ sets of URLs.")
 (define-public r-ggforce
   (package
     (name "r-ggforce")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggforce" version))
        (sha256
         (base32
-         "118qyzy8h9kkkdpjd09667gxgw7xy1kbc8r87pswh54ixn8hymwk"))))
+         "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
@@ -14616,14 +14665,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
 (define-public r-dalex
   (package
     (name "r-dalex")
-    (version "0.4.4")
+    (version "0.4.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "DALEX" version))
        (sha256
         (base32
-         "04i17ni8g595jj8dxdfwr9vsxmdn2kkam90ab68vlwws3ywqjl6r"))))
+         "0iiwkf0pfdb90lf1xhv43qd32z3cjmkmf0ly9841n5lldkjazy3h"))))
     (properties `((upstream-name . "DALEX")))
     (build-system r-build-system)
     (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
@@ -14642,14 +14691,14 @@ and model output.")
 (define-public r-enrichr
   (package
     (name "r-enrichr")
-    (version "2.0")
+    (version "2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "enrichR" version))
        (sha256
         (base32
-         "056m6hksfss29fj7zvlk7pbh8g3gq84kjh3240isrsnhp9m1h9iz"))))
+         "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
     (properties `((upstream-name . "enrichR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14812,17 +14861,18 @@ easily.")
 (define-public r-umap
   (package
     (name "r-umap")
-    (version "0.2.2.0")
+    (version "0.2.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "umap" version))
        (sha256
         (base32
-         "1s82w9gy1387h7cprjfbhp49l89zbmn3gc9s0wzqb1s73nza9n31"))))
+         "0rzz1s029cn1w1bf5va2pav2lg9j1mq97ibwcln39drvm67kj76d"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-rcpp" ,r-rcpp)
+     `(("r-openssl" ,r-openssl)
+       ("r-rcpp" ,r-rcpp)
        ("r-reticulate" ,r-reticulate)
        ("r-rspectra" ,r-rspectra)))
     (home-page "https://github.com/tkonopka/umap")
@@ -14993,6 +15043,32 @@ radius searches and @code{bd} as well as @code{kd} trees.  The distance is
 computed using the L1 (Manhattan, taxicab) metric.")
     (license license:gpl3+)))
 
+(define-public r-leiden
+  (package
+    (name "r-leiden")
+    (version "0.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "leiden" version))
+       (sha256
+        (base32
+         "19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp"))))
+    (properties `((upstream-name . "leiden")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-igraph" ,r-igraph)
+       ("r-matrix" ,r-matrix)
+       ("r-reticulate" ,r-reticulate)))
+    (home-page "https://github.com/TomKellyGenetics/leiden")
+    (synopsis "R implementation of Leiden clustering algorithm")
+    (description
+     "This package implements the Python @code{leidenalg} module to be called
+in R.  It enables clustering using the Leiden algorithm for partitioning a
+graph into communities.  See also Traag et al (2018) \"From Louvain to Leiden:
+guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
+    (license license:gpl3)))
+
 (define-public r-patchwork
   ;; There has been no public release yet.
   (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242")

gnu/packages/cups.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2016 Danny Milosavljevic <dannym@scratchpost.org>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Mark H Weaver <mhw@netris.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.
 ;;;
@@ -48,6 +48,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python)
   #:use-module (guix download)
+  #:use-module (guix svn-download)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix utils)
@@ -418,14 +419,14 @@ should only be used as part of the Guix cups-pk-helper service.")
 (define-public hplip
   (package
     (name "hplip")
-    (version "3.18.9")
+    (version "3.19.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/hplip/hplip/" version
                                   "/hplip-" version ".tar.gz"))
               (sha256
                (base32
-                "0g3q5mm2crjyc1z4z6gv4lam6sc5d3diz704djrnpqadk4q3h290"))
+                "0cmshi5dkmc1n5yiahhp0cv5p94zg61018piiqa2sna10ahgx1d3"))
               (modules '((guix build utils)))
               (patches (search-patches "hplip-remove-imageprocessor.patch"))
               (snippet
@@ -438,10 +439,6 @@ should only be used as part of the Guix cups-pk-helper service.")
                                           (elf-file? file))))
                   (delete-file "prnt/hpcups/ImageProcessor.h")
 
-                  ;; Fix type mismatch.
-                  (substitute* "prnt/hpcups/genPCLm.cpp"
-                    (("boolean") "bool"))
-
                   ;; Install binaries under libexec/hplip instead of
                   ;; share/hplip; that'll at least ensure they get stripped.
                   ;; It's not even clear that they're of any use though...
@@ -740,6 +737,66 @@ language.")
     (home-page "http://download.ebz.epson.net/dsc/search/01/search")
     (license license:gpl2+)))
 
+(define-public splix
+  ;; The last release was in 2009.  The SVN repository contains 5 years of
+  ;; unreleased bug fixes and support for newer printer models.
+  (let ((revision 315))
+    (package
+      (name "splix")
+      (version (string-append "2.0.0-" (number->string revision)))
+      (source
+       (origin
+         (method svn-fetch)
+         (uri (svn-reference
+               (url "https://svn.code.sf.net/p/splix/code/splix/")
+               (revision revision)))
+         (file-name (string-append name "-" version "-checkout"))
+         (sha256
+          (base32 "16wbm4xnz35ca3mw2iggf5f4jaxpyna718ia190ka6y4ah932jxl"))))
+      (build-system gnu-build-system)
+      ;; 90% (3.8 MiB) of output are .ppd files.  Don't install them by default:
+      ;; CUPS has been able to read the .drv sources directly since version 1.2.
+      (outputs (list "out" "ppd"))
+      (arguments
+       '(#:make-flags
+         (list (string-append "CUPSDRV="
+                              (assoc-ref %outputs "out") "/share/cups/drv")
+               (string-append "CUPSFILTER="
+                              (assoc-ref %outputs "out") "/lib/cups/filter")
+               (string-append "CUPSPPD="
+                              (assoc-ref %outputs "ppd") "/share/cups/model")
+               "CACHESIZE=100"          ; pages in RAM, ±300 KiB each
+               "THREADS=4")             ; compress and print faster
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)          ; no configure script
+           (add-before 'build 'build-.drv-files
+             (lambda* (#:key make-flags #:allow-other-keys)
+               (apply invoke "make" "drv" make-flags)))
+           (add-after 'install 'install-.drv-files
+             (lambda* (#:key make-flags #:allow-other-keys)
+               (apply invoke "make" "install" "DRV_ONLY=1" make-flags))))
+         #:tests? #f))                  ; no test suite
+      (inputs
+       `(("cups" ,cups-minimal)
+         ("zlib" ,zlib)
+
+         ;; This dependency can be dropped by setting DISABLE_JBIG=1, but the
+         ;; result will not support some printers like the Samsung CLP-600.
+         ("jbigkit" ,jbigkit)))
+      (synopsis "QPDL (SPL2) printer driver")
+      (description
+       "SpliX is a set of CUPS drivers for printers that speak @acronym{QPDL,
+Quick Page Description Language}, also called @acronym{SPL2, Samsung Printer
+Language version 2}.  These include many laser printers sold by Samsung,
+Xerox, Lexmark, Toshiba, and Dell.
+
+Colour printers need colour profile files to get better results.  These
+@file{cms} files are provided by the printer's manufacturer and must be
+obtained and installed separately.")
+      (home-page "http://splix.ap2c.org/")
+      (license license:gpl2))))
+
 (define-public python-pycups
   (package
     (name "python-pycups")

gnu/packages/databases.scm

@@ -1264,14 +1264,14 @@ changes.")
 (define-public tdb
   (package
     (name "tdb")
-    (version "1.4.0")
+    (version "1.4.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.samba.org/ftp/tdb/tdb-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0d9d2f1c83gmmq30bkfs50yb8399mr9xjjzscma4kyq0ajf75861"))))
+                "0jh0iqbb6pkvqrqn033w5g6gwa4bdgkvp49z0qpkk3h2wk6b4h4h"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases

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 "1.2.1")
+    (version "1.3.0")
     (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
-         "1j2avdk8hcgcv0lahp029qzpdb2rnys38hc64jy30awzx64fa6i4"))))
+         "1knysfdd1rx4vc5cmmnry4jsza0cdjy26fv505m854yfmq6zrckd"))))
     (build-system python-build-system)
     (home-page "https://grammalecte.net")
     (synopsis  "French spelling and grammar checker")

gnu/packages/docker.scm

@@ -25,6 +25,7 @@
   #: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 (guix build-system go)
   #:use-module (guix build-system python)
@@ -368,7 +369,16 @@ built-in registry server of Docker.")
                (("StockRuntimeName = .*")
                 (string-append "StockRuntimeName = \""
                                (assoc-ref inputs "runc")
-                               "/sbin/runc\"\n")))
+                               "/sbin/runc\"\n"))
+               (("DefaultInitBinary = .*")
+                (string-append "DefaultInitBinary = \""
+                               (assoc-ref inputs "tini")
+                               "/bin/tini\"\n")))
+             (substitute* "daemon/config/config_common_unix_test.go"
+               (("expectedInitPath: \"docker-init\"")
+                (string-append "expectedInitPath: \""
+                               (assoc-ref inputs "tini")
+                               "/bin/tini\"")))
              (substitute* "vendor/github.com/moby/buildkit/executor/runcexecutor/executor.go"
                (("var defaultCommandCandidates = .*")
                 (string-append "var defaultCommandCandidates = []string{\""
@@ -541,6 +551,7 @@ built-in registry server of Docker.")
        ("runc" ,runc)
        ("util-linux" ,util-linux)
        ("lvm2" ,lvm2)
+       ("tini" ,tini)
        ("xfsprogs" ,xfsprogs)
        ("xz" ,xz)))
     (native-inputs
@@ -655,3 +666,36 @@ provisioning etc.")
 way to run commands in the current directory, but within a Docker container
 defined in a per-project configuration file.")
     (license license:gpl3+)))
+
+(define-public tini
+  (package
+    (name "tini")
+    (version "0.18.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/krallin/tini.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1h20i3wwlbd8x4jr2gz68hgklh0lb0jj7y5xk1wvr8y58fip1rdn"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f                    ;tests require a Docker daemon
+       #:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'disable-static-build
+                    ;; Disable the static build as it fails to install, with
+                    ;; the error: "No valid ELF RPATH or RUNPATH entry exists
+                    ;; in the file".
+                    (lambda _
+                      (substitute* "CMakeLists.txt"
+                        ((".*tini-static.*") ""))
+                      #t)))))
+    (home-page "https://github.com/krallin/tini")
+    (synopsis "Tiny but valid init for containers")
+    (description "Tini is an init program specifically designed for use with
+containers.  It manages a single child process and ensures that any zombie
+processes produced from it are reaped and that signals are properly forwarded.
+Tini is integrated with Docker.")
+    (license license:expat)))

gnu/packages/education.scm

@@ -251,7 +251,7 @@ easy.")
 (define-public snap
   (package
     (name "snap")
-    (version "5.0.8")
+    (version "5.1.0")
     (source
      (origin
        (method git-fetch)
@@ -261,7 +261,7 @@ easy.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0fwfssdgv3mfzyv8hw1a1z5ky1yn0p59kyl6l9fxsm4w2ckgyizd"))))
+         "11fqbbvrv4zqbdz176ahczb2d797inq5n7zg74335d96m377si3f"))))
     (build-system trivial-build-system)
     (arguments
      `(#:modules ((guix build utils))

gnu/packages/emacs-xyz.scm

@@ -137,7 +137,7 @@
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages video)
-  #:use-module (gnu packages haskell)
+  #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages wordnet)
   #:use-module (guix utils)
   #:use-module (srfi srfi-1)
@@ -2855,7 +2855,7 @@ mode-line.")
 (define-public emacs-robe
   (package
     (name "emacs-robe")
-    (version "0.8.1")
+    (version "0.8.2")
     (source
      (origin
        (method git-fetch)
@@ -2864,7 +2864,7 @@ mode-line.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0ll7ivxqnglfb0i70ly6qq2yfw9cyi3vq3lmj4s6h6c1c7rm3gcq"))))
+        (base32 "0qw18wi54yg971n4wnjqkd8lqj5lbs9ra8bvmngif2bzhqlfdsbn"))))
     (build-system emacs-build-system)
     (arguments
      '(#:include (cons "^lib\\/" %default-include)))
@@ -3091,7 +3091,10 @@ for Flow files.")
         (base32
          "0lybadq66bl4snkwph9i1y0qxln29wyfjn222ii3nfwany28cj66"))))
     (build-system emacs-build-system)
-    (arguments '(#:include '("\\.el$" "\\.org$")))
+    (arguments
+     `(#:include '("\\.el$" "\\.org$")
+       #:tests? #t
+       #:test-command '("make" "test")))
     (home-page "https://github.com/xuchunyang/elisp-demos/")
     (synopsis "Enhance @code{*Help*} buffers with additional examples")
     (description
@@ -3126,11 +3129,10 @@ completion of relevant keywords.")
 
 (define-public emacs-sudo-edit
   (let ((commit "cc3d478937b1accd38742bfceba92af02ee9357d")
-        (version "0.1.0")
         (revision "6"))
     (package
       (name "emacs-sudo-edit")
-      (version (git-version version revision commit))
+      (version (git-version "0.1.0" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -3142,6 +3144,18 @@ completion of relevant keywords.")
           (base32
            "1qv58x5j5a3v1s2ylhck1ykbfclq0mbi0gsvaql3nyv8cxazqlwl"))))
       (build-system emacs-build-system)
+      (native-inputs
+       `(("emacs-undercover" ,emacs-undercover)))
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-before 'check 'fix-makefile
+             (lambda _
+               (substitute* "Makefile"
+                 (("\\$\\(CASK\\) exec ") ""))
+               #t)))
+         #:tests? #t
+         #:test-command '("make" "test")))
       (home-page "https://github.com/nflath/sudo-edit/")
       (synopsis "Open files as another user")
       (description
@@ -4229,22 +4243,48 @@ number.")
     (license license:gpl3+)))
 
 (define-public emacs-org-pomodoro
+  ;; Last release version was from 2016.
+  (let ((commit "aa07c11318f91219336197e62c47bc7a3d090479")
+        (revision "1"))
     (package
       (name "emacs-org-pomodoro")
-    (version "2.1.0")
+      (version (git-version "2.1.0" revision commit))
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
-             (url "https://github.com/lolownia/org-pomodoro.git")
+               (url "https://github.com/marcinkoziej/org-pomodoro.git")
-             (commit version)))
+               (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-        (base32 "0r5shgikm34d66i2hblyknbblpg92lb2zc9x4bcb28xkh7m9d0xv"))))
+          (base32 "0nbprh2nhnmb7ngp9ndr6zr37ashcsvpi5slv7a37x1dl7j6w1k4"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-alert" ,emacs-alert)))
-    (home-page "https://github.com/lolownia/org-pomodoro")
+      (arguments
+       `(#:include (cons "^resources\\/" %default-include)
+         #:tests? #t
+         #:test-command '("emacs" "--batch"
+                          "-l" "org-pomodoro-tests.el"
+                          "-f" "ert-run-tests-batch-and-exit")
+         #:phases
+         (modify-phases %standard-phases
+           (add-before 'check 'make-tests-writable
+             (lambda _
+               (make-file-writable "org-pomodoro-tests.el")
+               #t))
+           (add-before 'check 'add-require
+             (lambda _
+               (emacs-batch-edit-file "org-pomodoro-tests.el"
+                 `(progn (progn (goto-char (point-min))
+                                (re-search-forward
+                                 "ert-deftest")
+                                (beginning-of-line)
+                                (forward-line -1)
+                                (insert "(require 'org-pomodoro)"))
+                         (basic-save-buffer)))
+               #t)))))
+      (home-page "https://github.com/marcinkoziej/org-pomodoro")
       (synopsis "Pomodoro technique for org-mode")
       (description "@code{emacs-org-pomodoro} adds very basic support for
 Pomodoro technique in Emacs org-mode.
@@ -4254,10 +4294,10 @@ last tasks that you clocked time for.  Each clocked-in pomodoro starts
 a timer of 25 minutes and after each pomodoro a break timer of 5
 minutes is started automatically.  Every 4 breaks a long break is
 started with 20 minutes.  All values are customizable.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-org-sidebar
-  (let ((commit "74ca98b9920f3de3f13d49866581435e1ec63ec5")
+  (let ((commit "ed951d1e0d8b7e65ed35797403fd3e8c88f507f5")
         (revision "1"))
     (package
       (name "emacs-org-sidebar")
@@ -4270,7 +4310,7 @@ started with 20 minutes.  All values are customizable.")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "03p1ndyw2qp2skib5hszc4xyh84w7p2mhkd4a9dy6qv8q47xpsqn"))))
+          (base32 "01sf8v53pjsy80fzwmj2n8rp2z5gsnpyld0fm6j3bdv213clp69y"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-dash" ,emacs-dash)
@@ -4316,6 +4356,30 @@ overview of tasks in a subtree.")
 organizer.")
     (license license:gpl3+)))
 
+(define-public emacs-org-tanglesync
+  (let ((commit "ab76a3eaaed263677d2e029d43f6c4de8fc21418")
+        (revision "1"))
+    (package
+      (name "emacs-org-tanglesync")
+      (version (git-version "0.6" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/mtekman/org-tanglesync.el.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "14ify3yirq2qmi9isk8kcbwx8pbclv1fyg49kraz4srhgf2fssgf"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-org" ,emacs-org)))
+      (home-page "https://github.com/mtekman/org-tanglesync.el")
+      (synopsis "Sync Org source blocks with tangled external files")
+      (description "This package automatically pulls changes from source code
+to their corresponding tangled blocks.")
+      (license license:gpl3+))))
+
 (define-public emacs-company-flow
   (let ((commit "76ef585c70d2a3206c2eadf24ba61e59124c3a16")
         (revision "1"))
@@ -4429,6 +4493,32 @@ variants.")
 package provides a light and a dark variant.")
     (license license:gpl3+)))
 
+(define-public emacs-poet-theme
+  (let ((commit "d84f7b259cc9b6ff8d442cf4c38bd6c7065ff8f4")
+        (revision "0"))
+    (package
+      (name "emacs-poet-theme")
+      (version (git-version "0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/kunalb/poet.git")
+               (commit commit)))
+         (sha256
+          (base32
+           "0a84jdaj619mb59a46dmkk2sfs42rylqk9ryl1drgs8d3lia79mz"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/kunalb/poet/")
+      (synopsis "Emacs theme for prose")
+      (description
+       "Emacs has very good support for multiple fonts in a single file.  Poet
+uses this support to make it much more convenient to write prose within Emacs,
+with particular attention paid to @code{org-mode} and @code{markdown-mode}.
+Code blocks, tables, etc are formatted in monospace text with the appropriate
+backgrounds.")
+      (license license:expat))))
+
 (define-public emacs-ahungry-theme
   (package
     (name "emacs-ahungry-theme")
@@ -6292,6 +6382,31 @@ not tied in the trap of backward compatibility.")
 for search-based navigation of buffers.")
     (license license:gpl2+)))
 
+(define-public emacs-helm-ag
+  (let ((commit "2fc02c4ead29bf0db06fd70740cc7c364cb650ac")
+        (revision "1"))
+    (package
+      (name "emacs-helm-ag")
+      (version "0.58")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/syohex/emacs-helm-ag.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1gnn0byywbld6afcq1vp92cjvy4wlag9d1wgymnqn86c3b1bcf21"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-helm" ,emacs-helm)))
+      (home-page "https://github.com/syohex/emacs-helm-ag")
+      (synopsis "Helm interface to the Silver Searcher")
+      (description
+       "This package provides a frontend for grepping tools like ag and ack,
+as well as features for editing search results.")
+      (license license:gpl3+))))
+
 (define-public emacs-helm-projectile
   (package
     (name "emacs-helm-projectile")
@@ -6316,6 +6431,86 @@ for search-based navigation of buffers.")
      "This Emacs library provides a Helm interface for Projectile.")
     (license license:gpl3+)))
 
+(define-public emacs-taskrunner
+  (let ((commit "3afd4a546d42339543d3d4e51b175fc3e82b3358")
+        (revision "1"))
+    (package
+      (name "emacs-taskrunner")
+      (version (git-version "0.6" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/emacs-taskrunner/emacs-taskrunner.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1lkdvmjn3alhqxq2i64sdr977sbw3g0b2670d9bwyzi67qh0jxrv"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-async" ,emacs-async)
+         ("emacs-projectile" ,emacs-projectile)))
+      (home-page "https://github.com/emacs-taskrunner/emacs-taskrunner")
+      (synopsis "Retrieve tasks from various build systems and task-runners")
+      (description "This package parses Makefiles and build-system files for
+multiple project types.")
+      (license license:gpl3+))))
+
+(define-public emacs-ivy-taskrunner
+  (let ((commit "75d8d67cfe3c29663fe0f5508a887adf40ed5162")
+        (revision "1"))
+    (package
+      (name "emacs-ivy-taskrunner")
+      (version (git-version "0.9" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/emacs-taskrunner/ivy-taskrunner.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1wf4s4k0ap21f7g5w6128an8nsvbja7f5n889vcml5b6gjz058db"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-ivy" ,emacs-ivy)
+         ("emacs-taskrunner" ,emacs-taskrunner)
+         ("emacs-projectile" ,emacs-projectile)))
+      (home-page "https://github.com/emacs-taskrunner/ivy-taskrunner")
+      (synopsis "Retrieve build-system tasks using Ivy")
+      (description "This package provides an Ivy interface for selecting
+Makefile targets.")
+      (license license:gpl3+))))
+
+(define-public emacs-helm-taskrunner
+  (let ((commit "1910dac19cbc7bd4fd08b0faf9affd455339fbea")
+        (revision "1"))
+    (package
+      (name "emacs-helm-taskrunner")
+      (version (git-version "0.9" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/emacs-taskrunner/helm-taskrunner.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "182lmr858fx6rdhp1fy7kv8dvrhzcnxzwfck1q22s6xs8x85d5q7"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-helm" ,emacs-helm)
+         ("emacs-taskrunner" ,emacs-taskrunner)
+         ("emacs-projectile" ,emacs-projectile)))
+      (home-page "https://github.com/emacs-taskrunner/helm-taskrunner")
+      (synopsis "Retrieve build-system tasks using Helm")
+      (description "This package provides a Helm interface for selecting
+Makefile targets.")
+      (license license:gpl3+))))
+
 (define-public emacs-helm-make
   (let ((commit "feae8df22bc4b20705ea08ac9adfc2b43bb348d0")
         (revision "1"))
@@ -6501,11 +6696,11 @@ extensions.")
     (license license:gpl3+)))
 
 (define-public emacs-evil-collection
-  (let ((commit "0748c695dfa89b79eb316da5060360de8c0f04da")
+  (let ((commit "986ca7eb0b75eccd843bdad2f7fdb48f4ca6ac22")
-        (revision "9"))
+        (revision "10"))
     (package
       (name "emacs-evil-collection")
-      (version (git-version "0.0.1" revision commit))
+      (version (git-version "0.0.2" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -6514,7 +6709,7 @@ extensions.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "17w8nh3q7ffc7776f3qzixk0c0g6vys3xybgw16ky1f416585kvb"))))
+                  "172sx5w50x5wrs5w0sb6rkbj3q22s7mmsnk4c6pwknhbz3vwlvwz"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-evil" ,emacs-evil)))
@@ -6581,8 +6776,8 @@ end of a line and increment or decrement it.")
       (license license:gpl3+))))
 
 (define-public emacs-evil-owl
-  (let ((commit "e8fe5b2f745e36db04cb71eb689bf91c5409614f")
+  (let ((commit "24c5f43df375194386344e69bc720ea3986c9510")
-        (revision "2"))
+        (revision "3"))
     (package
       (name "emacs-evil-owl")
       (version (git-version "0.0.1" revision commit))
@@ -6595,10 +6790,13 @@ end of a line and increment or decrement it.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "1g7kplna62f271135mnjdbvxk2ayx7m4gvd6l86d2394alx16nhq"))))
+           "0bqzch14whlmrcasakah3psrzswvkzd7mmi8hx5s64kfp29wbdhi"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-evil" ,emacs-evil)))
+      (arguments
+       `(#:tests? #t
+         #:test-command '("make" "test")))
       (home-page "https://github.com/mamapanda/evil-owl")
       (synopsis "Preview candidates when using Evil registers and marks")
       (description
@@ -6625,6 +6823,17 @@ a popup window for previewing candidates.")
            "0bjpn4yqig17ddym6wqq5fm1b294q74hzcbj9a6gs97fqiwf88xa"))))
       (build-system emacs-build-system)
       (propagated-inputs `(("emacs-evil" ,emacs-evil)))
+      (native-inputs `(("emacs-ert-runner" ,emacs-ert-runner)))
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-before 'check 'fix-makefile
+             (lambda _
+               (substitute* "Makefile"
+                 (("cask exec ") ""))
+               #t)))
+         #:tests? #t
+         #:test-command '("make" "test")))
       (home-page "https://github.com/Dewdrops/evil-exchange")
       (synopsis "Exchange text easily within Evil")
       (description
@@ -6754,6 +6963,9 @@ aligning text objects based on separators.")
            "0872ix682hkdz0k8pn6sb54rqkx00rz5fxpd5j2snx406yagpaxz"))))
       (build-system emacs-build-system)
       (propagated-inputs `(("emacs-evil" ,emacs-evil)))
+      (arguments
+       `(#:tests? #t
+         #:test-command '("make" "test")))
       (home-page "https://github.com/edkolev/evil-expat")
       (synopsis "Extra @code{ex} commands for @code{evil-mode}")
       (description
@@ -6924,14 +7136,14 @@ passive voice.")
     (name "emacs-org")
     ;; emacs-org-contrib inherits from this package.  Please update its sha256
     ;; checksum as well.
-    (version "9.2.5")
+    (version "9.2.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://elpa.gnu.org/packages/org-"
                                   version ".tar"))
               (sha256
                (base32
-                "1pid1sykgz83i4ry5n8f270finag6sm7ckqxn5lkikyya43wlzx1"))))
+                "0ikd78k4yw4sm5x7l3dsbvfcmvnv5qna2mxirr560gvcnzhr0zg4"))))
     (build-system emacs-build-system)
     (home-page "https://orgmode.org/")
     (synopsis "Outline-based notes management and organizer")
@@ -6945,14 +7157,14 @@ programming and reproducible research.")
   (package
     (inherit emacs-org)
     (name "emacs-org-contrib")
-    (version "20190805")
+    (version "20190904")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://orgmode.org/elpa/org-plus-contrib-"
+              (uri (string-append "https://orgmode.org/elpa/"
-                                  version ".tar"))
+                                  "org-plus-contrib-" version ".tar"))
               (sha256
                (base32
-                "1mw91hwbqyjq5pyz9hzdhvjlc2bphqpi23yqd3sdk1crpc87s40c"))))
+                "08s3fk3jim0y2v00l6ah8y08ba8wbcf29z6fxqzyaxj58a5sq81a"))))
     (arguments
      `(#:modules ((guix build emacs-build-system)
                   (guix build utils)
@@ -9503,6 +9715,75 @@ subsequent invocations can be readily customized.  Several recipes are
 included by default, and more can be readily added.")
       (license license:gpl3+))))
 
+(define-public emacs-unidecode
+  (let ((commit "5502ada9287b4012eabb879f12f5b0a9df52c5b7")
+        (revision "1"))
+    (package
+      (name "emacs-unidecode")
+      (version (git-version "0.2" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/sindikat/unidecode")
+               (commit commit)))
+         (sha256
+          (base32
+           "03x3nakbhmakwm977mwrf8jifvjnfwzpjv6wrwpizbqjnkgfchmn"))))
+      (build-system emacs-build-system)
+      (arguments
+       `(#:include (cons* "^tools/" "^data/" %default-include)
+         #:tests? #t
+         #:test-command '("emacs" "--batch"
+                          "-l" "unidecode-test.el"
+                          "-f" "ert-run-tests-batch-and-exit")
+         #:phases
+         (modify-phases %standard-phases
+           (add-before 'check 'make-tests-writable
+             (lambda _
+               (make-file-writable "unidecode-test.el")
+               #t))
+           (add-before 'check 'add-require
+             (lambda _
+               (emacs-batch-edit-file "unidecode-test.el"
+                 `(progn (progn (goto-char (point-min))
+                                (re-search-forward
+                                 "ert-deftest")
+                                (forward-line -1)
+                                (insert "(require 'unidecode)"))
+                         (basic-save-buffer)))
+               #t)))))
+      (home-page "https://github.com/sindikat/unidecode")
+      (synopsis "Transliterate Unicode text to ASCII")
+      (description "This package provides functions for converting Unicode to ASCII.")
+      (license license:gpl2+))))
+
+(define-public emacs-pubmed
+  (package
+    (name "emacs-pubmed")
+    (version "0.2.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/fvdbeek/emacs-pubmed.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "15bwjxc7g43m5pi8z17anaqqkvi209r7kk1chmf175477gvrv7c0"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-deferred" ,emacs-deferred)
+       ("emacs-esxml" ,emacs-esxml)
+       ("emacs-s" ,emacs-s)
+       ("emacs-unidecode" ,emacs-unidecode)))
+    (home-page "https://gitlab.com/fvdbeek/emacs-pubmed")
+    (synopsis "Interface to PubMed")
+    (description "This package provides an Emacs interface to the PubMed
+database of references on life sciences.")
+    (license license:gpl3+)))
+
 (define-public emacs-websocket
   (package
     (name "emacs-websocket")
@@ -11008,10 +11289,73 @@ into sections while preserving the structure imposed by any timestamps.")
 tables of contents.")
     (license license:gpl3+)))
 
+(define-public emacs-ts
+  (let ((commit "93c074f2895a204e003e8c7f3033c37d6486fac8")
+        (revision "1"))
+    (package
+      (name "emacs-ts")
+      (version (git-version "0.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/alphapapa/ts.el")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "0lpyv78k04vbp9glnv14dawcfgi3m49847wlgwfmkdq5cr3fn735"))
+                (file-name (git-file-name name version))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-s" ,emacs-s)
+         ("emacs-dash" ,emacs-dash)))
+      (arguments
+       ;; XXX: Three tests are failing because of a timezone-related issue
+       ;; with how they're written.  On my machine, all the failing test
+       ;; results are 18000 seconds (5 hours) off.
+
+       ;; The ts-parse-org function accepts a string without any timezone
+       ;; info, not assumed to be in Unix time, and converts it to a so-called
+       ;; ts struct.  The ts-unix function (accessor) accepts a ts struct,
+       ;; then seems to assume the struct's corresponding time is in terms of
+       ;; the user's current time zone, before returning a Unix time in
+       ;; seconds.
+
+       ;; The failing tests all have similar problems, but nothing else about
+       ;; the library seems particularly off.
+
+       `(#:tests? #t
+         #:test-command '("emacs" "--batch"
+                          "-l" "test/test.el"
+                          "-f" "ert-run-tests-batch-and-exit")
+         #:phases
+         (modify-phases %standard-phases
+           (add-before 'check 'make-tests-writable
+             (lambda _
+               (make-file-writable "test/test.el")
+               #t))
+           (add-before 'check 'delete-failing-tests
+             (lambda _
+               (emacs-batch-edit-file "test/test.el"
+                 `(progn (progn
+                          (goto-char (point-min))
+                          (dolist (test-regexp '("ert-deftest ts-format"
+                                                 "ert-deftest ts-parse-org\\_>"
+                                                 "ert-deftest ts-parse-org-element"))
+                                  (re-search-forward test-regexp)
+                                  (beginning-of-line)
+                                  (kill-sexp)))
+                         (basic-save-buffer)))
+               #t)))))
+      (home-page "https://github.com/alphapapa/ts.el")
+      (synopsis "Timestamp and date/time library")
+      (description "This package facilitates manipulating dates, times, and
+timestamps by providing a @code{ts} struct.")
+      (license license:gpl3+))))
+
 (define-public emacs-org-ql
   (package
     (name "emacs-org-ql")
-    (version "0.1")
+    (version "0.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -11019,12 +11363,19 @@ tables of contents.")
                     (commit version)))
               (sha256
                (base32
-                "1nvzirn1lmgmgl7irbsc1n391a2cw8gmvwm3pa228l2c1gcx8kd8"))
+                "0mq0aj0a3a5gi9nz0ncpzsh731d92n86b0iinvx1m45dcal06h9y"))
               (file-name (git-file-name name version))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-s" ,emacs-s)
+       ("emacs-ts" ,emacs-ts)
+       ("emacs-org" ,emacs-org)
        ("emacs-dash" ,emacs-dash)))
+    (native-inputs
+     `(("emacs-buttercup" ,emacs-buttercup)))
+    (arguments
+     `(#:tests? #t
+       #:test-command '("buttercup" "-L" ".")))
     (home-page "https://github.com/alphapapa/org-ql/")
     (synopsis "Query language for Org buffers")
     (description "This package provides a Lispy query language for Org
@@ -11906,12 +12257,11 @@ key again.")
     (license license:gpl3+)))
 
 (define-public emacs-mbsync
-  (let ((commit "42077e83ae2db778ce0f8e22f8357b40355526b3")
+  (let ((commit "f549eccde6033449d24cd5b6148599484850c403")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "emacs-mbsync")
-      (version (string-append "0.0.1" "-" revision "."
+      (version (git-version "0.1.2" revision commit))
-                              (string-take commit 7)))
       (source
        (origin
          (method git-fetch)
@@ -11921,7 +12271,7 @@ key again.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "0yj93y2mpxlir8x73znlg1slxlv4blm1vjv5h2w3j8lxg8bxvmn6"))))
+           "1pdj41rq3pq4jdb5pma5j495xj7w7jgn8pnz1z1zwg75pn7ydfp0"))))
       (build-system emacs-build-system)
       (home-page "https://github.com/dimitri/mbsync-el")
       (synopsis "Interface to mbsync for Emacs")
@@ -13530,28 +13880,31 @@ be changed by customizing the appropriate variables.")
     (license license:gpl3+)))
 
 (define-public emacs-org-caldav
+  (let ((commit "a563500c9884f38ce08793e2964f8274adde163d"))
     (package
       (name "emacs-org-caldav")
-    (version "20180403")
+      (version (git-version "0.0.0" "1" commit))
       (source
        (origin
-       (method url-fetch)
+         (method git-fetch)
-       (uri (string-append
+         (uri (git-reference
-             "https://github.com/dengste/org-caldav/raw/"
+               (url "https://github.com/dengste/org-caldav.git")
-             "8d3492c27a09f437d2d94f2736c56d7652e87aa0"
+               (commit commit)))
-             "/org-caldav.el"))
+         (file-name (git-file-name name version))
          (sha256
           (base32
-         "1fh4gh68ddj0is99z2ccyh97v6psnyda61n2dsadzqhcxn51amlc"))))
+           "18qi1iv5dc0gsvkv9ifal3cjpm568nlb907v8a53cnm4439x1l0l"))))
       (build-system emacs-build-system)
-    (propagated-inputs `(("emacs-org" ,emacs-org)))
+      (arguments
+       ;; Tests require to have two specific calendars on a test server.
+       `(#:exclude '("^org-caldav-testsuite\\.el")))
+      (propagated-inputs
+       `(("emacs-org" ,emacs-org)))
       (home-page "https://github.com/dengste/org-caldav")
-    (synopsis
+      (synopsis "Sync Org files with external calendars via the CalDAV protocol")
-     "Sync Org files with external calendars via the CalDAV protocol")
+      (description "Synchronize between events in Org files and a CalDAV
-    (description
+calendar.")
-     "Synchronize between events in Org-mode files and a CalDAV calendar.
+      (license license:gpl3+))))
-This code is still alpha.")
-    (license license:gpl3+)))
 
 (define-public emacs-zotxt
   (package
@@ -13632,6 +13985,18 @@ describing the key binding changes.")
     (propagated-inputs
      `(("emacs-evil" ,emacs-evil)
        ("emacs-iedit" ,emacs-iedit)))
+    (native-inputs
+     `(("emacs-ert-runner" ,emacs-ert-runner)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'fix-makefile
+           (lambda _
+             (substitute* "Makefile"
+               (("@cask exec ") ""))
+             #t)))
+       #:tests? #t
+       #:test-command '("make" "test")))
     (home-page
      "https://github.com/hlissner/evil-multiedit")
     (synopsis "Multiple cursors for Evil mode")
@@ -13861,7 +14226,7 @@ try completing.  See @code{fish-completion-fallback-on-bash-p}.")
                  ("gif-screencast-cropping-program"
                   (string-append imagemagick "/bin/mogrify"))
                  ("gif-screencast-optimize-program"
-                  (string-append imagemagick "/bin/gifsicle")))))))))
+                  (string-append gifsicle "/bin/gifsicle")))))))))
       (home-page
        "https://gitlab.com/Ambrevar/emacs-gif-screencast")
       (synopsis "One-frame-per-action GIF recording")
@@ -15514,6 +15879,31 @@ buffers, etc.  It also has plug-ins to help your Emacs life.")
 programs can use this table component for the application UI.")
       (license license:gpl3+))))
 
+(define-public emacs-leetcode
+  (let ((commit "8624496af9e105c3e07d88844b37ede87540d604")
+        (revision "1"))
+    (package
+      (name "emacs-leetcode")
+      (version (git-version "0" "1" commit))
+      (home-page "https://github.com/ginqi7/leetcode-emacs.git")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ginqi7/leetcode-emacs")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "11pp7ydlmwrv7djf9mwk4xzn295xbmdnj5x13bfj5yjpjr89p531"))
+                (file-name (git-file-name name version))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-names" ,emacs-names)
+         ("emacs-ctable" ,emacs-ctable)))
+      (synopsis "Solve and submit LeetCode problems from within Emacs")
+      (description "This package provides an Emacs interface to LeetCode
+allowing users to log in and solve problems of their choice using Emacs.")
+      (license license:unlicense))))
+
 (define-public emacs-epc
   (let ((commit "e1bfa5ca163273859336e3cc89b4b6460f7f8cda"))
     (package
@@ -15998,7 +16388,7 @@ the standard @code{Dockerfile} file format.")
 (define-public emacs-lsp-mode
   (package
     (name "emacs-lsp-mode")
-    (version "6.0")
+    (version "6.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -16007,12 +16397,13 @@ the standard @code{Dockerfile} file format.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1v1mq6ixzlgiazj8fmg4xaqhsqn3l89iqy74yndhvzh2rdf0pbkl"))))
+                "0jn5slhv9zfs446a5966bfg9dq144g22v79wnkx9hxq7if78p652"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-dash" ,emacs-dash)
        ("emacs-f" ,emacs-f)
        ("emacs-ht" ,emacs-ht)
+       ("emacs-markdown-mode" ,emacs-markdown-mode)
        ("emacs-spinner" ,emacs-spinner)))
     (home-page "https://github.com/emacs-lsp/lsp-mode")
     (synopsis "Emacs client and library for the Language Server Protocol")
@@ -16254,11 +16645,10 @@ unescaping of quotes.")
 
 (define-public emacs-flycheck-haskell
   (let ((commit "32ddff87165a7d3a35e7318bee997b5b4bd41278")
-        (version "0.8")
+        (revision "2"))
-        (revision "79"))
     (package
       (name "emacs-flycheck-haskell")
-      (version (git-version version revision commit))
+      (version (git-version "0.8" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -16276,6 +16666,8 @@ unescaping of quotes.")
          ("emacs-flycheck" ,emacs-flycheck)
          ("emacs-haskell-mode" ,emacs-haskell-mode)
          ("emacs-let-alist" ,emacs-let-alist)))
+      (arguments
+       `(#:include '("\\.el$" "\\.hs$")))
       (home-page "https://github.com/flycheck/flycheck-haskell")
       (synopsis "Flycheck for Haskell")
       (description "This package configures syntax-checking for Haskell
@@ -17257,6 +17649,17 @@ corresponding Evil keys.")
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-evil" ,emacs-evil)))
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'set-shell
+             ;; Setting the SHELL environment variable is required for the tests
+             ;; to find sh.
+             (lambda _
+               (setenv "SHELL" (which "sh"))
+               #t)))
+         #:tests? #t
+         #:test-command '("make" "test")))
       (home-page "https://github.com/mamapanda/evil-traces")
       (synopsis "Visual hints for @code{evil-ex}")
       (description "This package adds visual hints to certain @code{ex}

gnu/packages/emacs.scm

@@ -15,7 +15,7 @@
 ;;; Copyright © 2017 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Mathieu Othacehe <m.othacehe@gmail.com>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -68,14 +68,14 @@
 (define-public emacs
   (package
     (name "emacs")
-    (version "26.2")
+    (version "26.3")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/emacs/emacs-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "13n5m60i47k96mpv5pp6km2ph9rv2m5lmbpzj929v02vpsfyc70m"))
+               "119ldpk7sgn9jlpyngv5y4z3i7bb8q3xp4p0qqi7i5nq39syd42d"))
              (patches (search-patches "emacs-exec-path.patch"
                                       "emacs-fix-scheme-indent-function.patch"
                                       "emacs-source-date-epoch.patch"))

gnu/packages/emulators.scm

@@ -119,8 +119,8 @@
 
 ;; Building from recent Git because the official 5.0 release no longer builds.
 (define-public dolphin-emu
-  (let ((commit "24718c1a389e4f51db974575cd15c372485b92e2")
+  (let ((commit "a9745400ec5cea7e55d94955afbdc44d1a4982d1")
-        (revision "6"))
+        (revision "7"))
     (package
       (name "dolphin-emu")
       (version (git-version "5.0" revision commit))
@@ -140,13 +140,13 @@
                            (string-append "Externals/" dir)))
                        '("LZO" "OpenAL" "Qt" "SFML" "curl" "ffmpeg"
                          "gettext" "hidapi" "libpng" "libusb" "mbedtls"
-                         "miniupnpc" "zlib"))
+                         "miniupnpc" "MoltenVK" "zlib"))
              ;; Clean up source.
              (for-each delete-file (find-files "." ".*\\.(bin|dsy|exe|jar|rar)$"))
              #t))
          (sha256
           (base32
-           "1d92rhnw307j3m6swk6bycb8fyc7vw2hfgakd5hpsc4qw65vxfq8"))))
+           "0ic08ii4vlqlmk2wkfc99jiy6nji2wfq56r7slj23wgvhznnaabk"))))
       (build-system cmake-build-system)
       (arguments
        '(#:tests? #f
@@ -169,7 +169,11 @@
                  (copy-file "font_western.bin" "../Data/Sys/GC/font_western.bin")
                  (chdir "..")
                  (substitute* "Source/Core/VideoBackends/Vulkan/VulkanLoader.cpp"
-                              (("libvulkan.so") libvulkan))
+                              (("\"vulkan\", 1") (string-append "\"vulkan\"")))
+                 (substitute* "Source/Core/VideoBackends/Vulkan/VulkanLoader.cpp"
+                              (("\"vulkan\"") (string-append "\"" libvulkan "\"")))
+                 (substitute* "Source/Core/VideoBackends/Vulkan/VulkanLoader.cpp"
+                              (("Common::DynamicLibrary::GetVersionedFilename") ""))
                  #t))))
 
          ;; The FindGTK2 cmake script only checks hardcoded directories for
@@ -1053,7 +1057,7 @@ emulation community.  It provides highly accurate emulation.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0xxd9nhqiclpkdd9crymvba37fl0xs5mikwhya68nfzcgar7w480"))))
+        (base32 "0jwy5winrm87s6xa645fwa47x242r25m6i3rwf10x59448bd19r6"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no tests

gnu/packages/engineering.scm

@@ -12,6 +12,7 @@
 ;;; Copyright © 2018, 2019 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2019 Tim Stahel <swedneck@swedneck.xyz>
 ;;; Copyright © 2019 Jovany Leandro G.C <bit4bit@riseup.net>
+;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1940,7 +1941,7 @@ simulator backends @code{Qucsator}, @code{ngspice} and @code{Xyce}.")
 (define-public librepcb
   (package
     (name "librepcb")
-    (version "0.1.1")
+    (version "0.1.2")
     (source
      (origin
        (method url-fetch)
@@ -1948,7 +1949,7 @@ simulator backends @code{Qucsator}, @code{ngspice} and @code{Xyce}.")
                            version "/librepcb-" version "-source.zip"))
        (sha256
         (base32
-         "08lm95kr5gqyqyy4hcii0micqa6ryhbv0harvdndmpvi4ix1ggi8"))))
+         "1xgk0r3nxdd2cy7d1k165d005gsngnz1v2wbwivacw7gis0i8ip7"))))
     (build-system gnu-build-system)
     (inputs
      `(("qtbase" ,qtbase)
@@ -2109,3 +2110,38 @@ while keeping the user experience at mind.  Cutter is created by reverse
 engineers for reverse engineers.")
     (license (list license:cc-by-sa3.0  ;the "Iconic" icon set
                    license:gpl3+))))    ;everything else
+
+(define-public lib3mf
+  (package
+    (name "lib3mf")
+    (version "1.8.1")
+    (source
+     (origin
+      (method git-fetch)
+      (uri (git-reference (url "https://github.com/3MFConsortium/lib3mf.git")
+                          (commit (string-append "v" version))))
+      (file-name (git-file-name name version))
+      (sha256
+       (base32
+        "11wpk6n9ga2p57h1dcrp37w77mii0r7r6mlrgmykf7rvii1rzgqd"))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("googletest-source" ,(package-source googletest))))
+    (inputs
+     `(("libuuid" ,util-linux)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'unpack-googletest
+           (lambda* (#:key inputs #:allow-other-keys)
+             (copy-recursively (assoc-ref inputs "googletest-source")
+                               "UnitTests/googletest")
+             #t)))))
+    (synopsis "Implementation of the 3D Manufacturing Format (3MF) file standard")
+    (description
+     "Lib3MF is a C++ implementation of the 3D Manufacturing Format (3MF) file
+standard.  It offers a way to integrate 3MF reading and writing capabilities, as
+well as conversion and validation tools for input and output data.  The
+specification can be downloaded at @url{http://3mf.io/specification/}.")
+    (home-page "https://3mf.io/")
+    (license license:bsd-2)))

gnu/packages/enlightenment.scm

@@ -65,7 +65,7 @@
 (define-public efl
   (package
     (name "efl")
-    (version "1.22.3")
+    (version "1.22.4")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -73,7 +73,7 @@
                     version ".tar.xz"))
               (sha256
                (base32
-                "1j1i8cwq4ym9z34ikv35mdmv5q7q69hdp494mc6l03g9n6cl2yky"))))
+                "084ihxy6g86yczhln5vn1amxi4qzqhvk4lpz9005kx92i6wh4h25"))))
     (outputs '("out"       ; 53 MB
                "include")) ; 21 MB
     (build-system gnu-build-system)

gnu/packages/games.scm

@@ -112,6 +112,7 @@
   #:use-module (gnu packages guile)
   #:use-module (gnu packages haskell)
   #:use-module (gnu packages haskell-crypto)
+  #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)

gnu/packages/ghostscript.scm

@@ -275,7 +275,7 @@ output file formats and printers.")
     (home-page "https://www.ghostscript.com/")
     (license license:agpl3+)))
 
-(define-public ghostscript/fixed
+(define ghostscript/fixed
   ;; This adds the Freetype dependency (among other things), which fixes the
   ;; rendering issues described in <https://issues.guix.gnu.org/issue/34877>.
   (package/inherit

gnu/packages/gnome.scm

@@ -2534,24 +2534,40 @@ and objects.")
 (define-public libxklavier
   (package
     (name "libxklavier")
-    (version "5.3")
+    (version "5.4")
     (source (origin
-              (method url-fetch)
+              ;; Note: There's no tarball at ftp.gnome.org for this version.
-              (uri (string-append "mirror://gnome/sources/" name "/"
+              (method git-fetch)
-                                  version "/" name "-" version ".tar.xz"))
+              (uri (git-reference
+                    (url "https://anongit.freedesktop.org/git/libxklavier")
+                    (commit (string-append "libxklavier-" version))))
               (sha256
                (base32
-                "016lpdv35z0qsw1cprdc2k5qzkdi5waj6qmr0a2q6ljn9g2kpv7b"))))
+                "1w1x5mrgly2ldiw3q2r6y620zgd89gk7n90ja46775lhaswxzv7a"))
+              (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments
-     '(#:configure-flags
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'no-configure
+           (lambda* _
+            (setenv "NOCONFIGURE" "1")
+            #t)))
+       #:configure-flags
        (list (string-append "--with-xkb-base="
                             (assoc-ref %build-inputs "xkeyboard-config")
-                            "/share/X11/xkb"))))
+                            "/share/X11/xkb")
+             "--disable-xmodmap-support")))
     (native-inputs
      `(("glib:bin"              ,glib "bin") ; for glib-mkenums, etc.
        ("gobject-introspection" ,gobject-introspection)
-       ("pkg-config"            ,pkg-config)))
+       ("pkg-config"            ,pkg-config)
+       ("gtk-doc" ,gtk-doc)
+       ("intltool" ,intltool)
+       ("which" ,which)
+       ("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
     (propagated-inputs
      ;; Required by libxklavier.pc.
      `(("glib"    ,glib)
@@ -4337,15 +4353,15 @@ work and the interface is well tested.")
 (define-public eolie
   (package
     (name "eolie")
-    (version "0.9.62")
+    (version "0.9.63")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gitlab.gnome.org/World/eolie/"
-                                  "uploads/bb4aad19272cc636bd17f2f6602127fe/"
+                                  "uploads/d42b466752729a0d3fa828a721e25043/"
                                   "eolie-" version ".tar.xz"))
               (sha256
                (base32
-                "06v76hg87fnhw45dil5vvl20myvaa38n1jqsl0lmkkq6af4mk8wx"))))
+                "11pp8g0w22h1q0bbj9517l5838gcymvvp8fp9kh6h2dmgir2ssih"))))
     (build-system meson-build-system)
     (arguments
      `(#:glib-or-gtk? #t
@@ -8265,7 +8281,7 @@ advanced image management tool")
 (define-public libhandy
   (package
     (name "libhandy")
-    (version "0.0.10")
+    (version "0.0.11")
     (source
      (origin
        (method git-fetch)
@@ -8274,7 +8290,7 @@ advanced image management tool")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1702hbdqhfpgw0c4vj2ag08vgl83byiryrbngbq11b9azmj3jhzs"))))
+        (base32 "0622zp5wrvn5bvgardijxd11y76g1i54fs32y03dw9nrar7i6vb0"))))
     (build-system meson-build-system)
     (arguments
      `(#:configure-flags
@@ -8282,12 +8298,6 @@ advanced image management tool")
          "-Dgtk_doc=true")
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'disable-broken-test
-           (lambda _
-             ;; This test fails for unknown reasons
-             (substitute* "tests/meson.build"
-               (("'test-dialog',") ""))
-             #t))
          (add-before 'check 'pre-check
            (lambda _
              ;; Tests require a running X server.
@@ -8303,7 +8313,10 @@ advanced image management tool")
        ("gtk-doc" ,gtk-doc)
        ("pkg-config" ,pkg-config)
        ("gettext" ,gettext-minimal)
-       ("xorg-server" ,xorg-server)))
+       ("xorg-server" ,xorg-server)
+
+       ;; Test suite dependencies.
+       ("hicolor-icon-theme" ,hicolor-icon-theme)))
     (home-page "https://source.puri.sm/Librem5/libhandy")
     (synopsis "Library full of GTK+ widgets for mobile phones")
     (description "The aim of the handy library is to help with developing user

gnu/packages/gnucash.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2015 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Chris Marusich <cmmarusich@gmail.com>
-;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -231,17 +231,14 @@ to be read using the GNOME Yelp program.")
 (define-public gwenhywfar
   (package
     (name "gwenhywfar")
-    (version "4.20.0")
+    (version "4.20.2")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://www.aquamaniac.de/sites/download/"
+       (uri (string-append "https://www.aquamaniac.de/rdm/attachments/"
-                           "download.php?package=01&release=208&file=02&"
+                           "download/108/gwenhywfar-" version ".tar.gz"))
-                           "dummy=gwenhywfar-" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32
+        (base32 "0w1j7ppr1247kr3bpn4dqwyxp6cl8mfgr0m4782iz8f8a4ixjkqg"))))
-         "1c0g3f8jk6j693774ifslx2ds4ksabgbbalhhm9gk20kpamxm22s"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -271,17 +268,14 @@ applications and libraries.  It is used by AqBanking.")
 (define-public aqbanking
   (package
     (name "aqbanking")
-    (version "5.7.8")
+    (version "5.8.1")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://www.aquamaniac.de/sites/download/"
+       (uri (string-append "https://www.aquamaniac.de/rdm/attachments/"
-                           "download.php?package=03&release=217&file=02&"
+                           "download/105/aqbanking-" version ".tar.gz"))
-                           "dummy=aqbanking-" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32
+        (base32 "0m44n2hyxprxzq7ijkrd7rmhhl0r033s1k21ix9y67a0p9skl1mg"))))
-         "0s67mysskbiw1h1p0np4ph4351r7wq3nc873vylam7lsqi66xy0n"))))
     (build-system gnu-build-system)
     (arguments
      `(;; Parallel building fails because aqhbci is required before it's

gnu/packages/gnuzilla.scm

@@ -426,7 +426,7 @@ from forcing GEXP-PROMISE."
                       #:system system
                       #:guile-for-build guile)))
 
-(define %icecat-version "60.8.0-guix1")
+(define %icecat-version "60.9.0-guix1")
 
 ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball
 ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat'
@@ -448,7 +448,7 @@ from forcing GEXP-PROMISE."
                   "firefox-" upstream-firefox-version ".source.tar.xz"))
             (sha256
              (base32
-              "1gkz90clarbhgfxhq91s0is6lw6bfymyjb0xbyyswdg68kcqfcy1"))))
+              "0gy5x2rnnbkqmjd9sq93s3q5na9nkba68xwpizild7k6qn63qicz"))))
 
          (upstream-icecat-base-version "60.7.0") ; maybe older than base-version
          (upstream-icecat-gnu-version "1")

gnu/packages/golang.scm

@@ -3119,21 +3119,19 @@ as conversion to and from @command{net.Addr}.")
       (license license:expat))))
 
 (define-public go-github-com-urfave-cli
-  (let ((commit "693af58b4d51b8fcc7f9d89576da170765980581")
-        (revision "0"))
   (package
     (name "go-github-com-urfave-cli")
-      (version (git-version "1.20.0" revision commit))
+    (version "1.21.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/urfave/cli.git")
-               (commit commit)))
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
         (base32
-           "1krq752xgy658an1696vf4dc2zmp541clwjinhn11394sx2qksh6"))))
+         "104jldhxn6d97l5vsbsl0q8hgy1bxrahbr6dbfqrlppva51jmydd"))))
     (build-system go-build-system)
     (arguments
      '(#:import-path "github.com/urfave/cli"))
@@ -3142,7 +3140,7 @@ as conversion to and from @command{net.Addr}.")
     (description "@command{cli} is a simple, fast, and fun package for
 building command line apps in Go.  The goal is to enable developers to write
 fast and distributable command line applications in an expressive way.")
-      (license license:expat))))
+    (license license:expat)))
 
 (define-public go-github-com-whyrusleeping-json-filter
   (let ((commit "ff25329a9528f01c5175414f16cc0a6a162a5b8b")
@@ -3660,3 +3658,27 @@ and aid debugging.")
     (description "This package provides a cron library for Go.  It implements
 a cron spec parser and job runner.")
     (license license:expat)))
+
+(define-public go-github-com-shirou-gopsutil
+  (let ((commit "47ef3260b6bf6ead847e7c8fc4101b33c365e399")
+        (revision "0"))
+    (package
+      (name "go-github-com-shirou-gopsutil")
+      (version (git-version "v2.19.7" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/shirou/gopsutil")
+                       (commit commit))) ; XXX
+                (sha256
+                 (base32
+                  "0x1g4r32q4201nr2b754xnrrndmwsrhfr7zg37spya86qrmijnws"))))
+      (build-system go-build-system)
+      (arguments
+       '(#:import-path "github.com/shirou/gopsutil"))
+      (synopsis "Process and system monitoring in Go")
+      (description "This package provides a library for retrieving information
+on running processes and system utilization (CPU, memory, disks, network,
+sensors).")
+      (home-page "https://github.com/shirou/gopsutil")
+      (license license:bsd-3))))

gnu/packages/gps.scm

@@ -143,7 +143,7 @@ between two other data points.")
 (define-public gama
   (package
     (name "gama")
-    (version "2.06")
+    (version "2.07")
     (source
       (origin
         (method url-fetch)
@@ -151,7 +151,7 @@ between two other data points.")
                             version ".tar.gz"))
         (sha256
          (base32
-          "06xp3kj099b6m2fsmgcbzgj7xk4j0drsps52m4fr8vc6fglsh44p"))))
+          "0nmc6mkd55nryfffq5k9c09dhkbq6bfs06af8ammhbh5jzdn3s36"))))
     (build-system gnu-build-system)
     (arguments '(#:parallel-tests? #f)) ; race condition
     (native-inputs

gnu/packages/graphics.scm

@@ -49,7 +49,7 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages gtk)
-  #:use-module (gnu packages haskell)
+  #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages jemalloc)

gnu/packages/guile-wm.scm

@@ -172,7 +172,9 @@ dependencies.")
                                     Type=Application~%"
                              ,name ,synopsis %output))))
                #t)))))
-      (native-inputs `(("pkg-config" ,pkg-config)
+      (native-inputs `(("guile" ,guile-2.2)
+                       ("guile-xcb" ,guile-xcb)
+                       ("pkg-config" ,pkg-config)
                        ("texinfo" ,texinfo)))
       (inputs `(("guile" ,guile-2.2)
                 ("guile-xcb" ,guile-xcb)))

gnu/packages/guile-xyz.scm

@@ -2266,21 +2266,20 @@ list of components.  This module takes care of that for you.")
 (define-public guile-gi
   (package
     (name "guile-gi")
-    (version "0.0.2")
+    (version "0.2.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://lonelycactus.com/tarball/guile_gi-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0hs0viqzff7nzgcmyw721ima1jyymrlzrcycpgwrs6iprscxvqwn"))))
+                "1n4pbrmbrjkrx826a4m31ag5c35rgkj1sirqh4qalk7gg67cfb41"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:configure-flags '("--with-gnu-filesystem-hierarchy")
+     `(#:configure-flags '("--with-gnu-filesystem-hierarchy")))
-       ;; The atomic_int_set test does not actually fail.
-       #:make-flags '("XFAIL_TESTS=strjoinv.scm")))
     (native-inputs
      `(("gettext" ,gnu-gettext)
+       ("glib:bin" ,glib "bin") ; for glib-compile-resources
        ("libtool" ,libtool)
        ("pkg-config" ,pkg-config)))
     (propagated-inputs

gnu/packages/haskell-apps.scm

@@ -1,12 +1,16 @@
 ;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015 Siniša Biđin <sinisa@bidin.eu>
 ;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018 ng0 <ng0@n0.is>
+;;; Copyright © 2017 Danny Milosavljevic <dannym@scratchpost.org>
+;;; Copyright © 2017, 2018 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Timothy Sample <samplet@ngyro.com>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
 ;;; Copyright © 2019 Kyle Meyer <kyle@kyleam.com>
+;;; Copyright © 2015 John Soo <jsoo1@asu.edu>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,6 +29,7 @@
 
 (define-module (gnu packages haskell-apps)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix packages)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system haskell)
@@ -35,13 +40,110 @@
   #:use-module (gnu packages haskell-check)
   #:use-module (gnu packages haskell-crypto)
   #:use-module (gnu packages haskell-web)
+  #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages rsync)
-  #:use-module (gnu packages sdl)
   #:use-module (gnu packages version-control))
 
+(define-public cabal-install
+ (package
+  (name "cabal-install")
+   (version "2.2.0.0")
+   (source
+    (origin
+     (method url-fetch)
+      (uri (string-append
+            "https://hackage.haskell.org/package/cabal-install/cabal-install-"
+            version
+            ".tar.gz"))
+      (sha256
+       (base32 "1nd3ch7qr4dpfxhgkcq2lnhvszx2kjgnn1kwb44vk9y5jgfs4mn8"))))
+   (arguments `(#:tests? #f)) ; FIXME: testing libraries are missing.
+   (build-system haskell-build-system)
+   (inputs
+    `(("ghc-async" ,ghc-async)
+      ("ghc-base16-bytestring" ,ghc-base16-bytestring)
+      ("ghc-cryptohash-sha256" ,ghc-cryptohash-sha256)
+      ("ghc-echo" ,ghc-echo)
+      ("ghc-edit-distance" ,ghc-edit-distance)
+      ("ghc-hackage-security" ,ghc-hackage-security)
+      ("ghc-hashable" ,ghc-hashable)
+      ("ghc-http" ,ghc-http)
+      ("ghc-network-uri" ,ghc-network-uri)
+      ("ghc-network" ,ghc-network)
+      ("ghc-random" ,ghc-random)
+      ("ghc-resolv" ,ghc-resolv)
+      ("ghc-tar" ,ghc-tar)
+      ("ghc-zlib" ,ghc-zlib)))
+   (home-page "https://www.haskell.org/cabal/")
+   (synopsis "Command-line interface for Cabal and Hackage")
+   (description
+    "The cabal command-line program simplifies the process of managing
+Haskell software by automating the fetching, configuration, compilation and
+installation of Haskell libraries and programs.")
+   (license license:bsd-3)))
+
+(define-public corrode
+  (let ((commit "b6699fb2fa552a07c6091276285a44133e5c9789"))
+    (package
+      (name "corrode")
+      (version (string-append "0.0.1-" (string-take commit 7)))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/jameysharp/corrode.git")
+               (commit "b6699fb2fa552a07c6091276285a44133e5c9789")))
+         (file-name
+          (string-append name "-" version "-checkout"))
+         (sha256
+          (base32 "02v0yyj6sk4gpg2222wzsdqjxn8w66scbnf6b20x0kbmc69qcz4r"))))
+      (build-system haskell-build-system)
+      (inputs
+       `(("ghc-language-c" ,ghc-language-c)
+         ("ghc-markdown-unlit" ,ghc-markdown-unlit)))
+      (home-page "https://github.com/jameysharp/corrode")
+      (synopsis "Automatic semantics-preserving translation from C to Rust")
+      (description
+       "This program reads a C source file and prints an equivalent module in
+Rust syntax.  It is intended to be useful for two different purposes:
+
+@enumerate
+@item Partial automation for migrating legacy code that was implemented in C.
+@item A new, complementary approach to static analysis for C programs.
+@end enumerate\n")
+      (license license:gpl2+))))
+
+(define-public cpphs
+  (package
+    (name "cpphs")
+    (version "1.20.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/" name "/"
+             name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1bh524asqhk9v1s0wvipl0hgn7l63iy3js867yv0z3h5v2kn8vg5"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-polyparse" ,ghc-polyparse)
+       ("ghc-old-locale" ,ghc-old-locale)
+       ("ghc-old-time" ,ghc-old-time)))
+    (home-page "http://projects.haskell.org/cpphs/")
+    (synopsis "Liberalised re-implementation of cpp, the C pre-processor")
+    (description "Cpphs is a re-implementation of the C pre-processor that is
+both more compatible with Haskell, and itself written in Haskell so that it
+can be distributed with compilers.  This version of the C pre-processor is
+pretty-much feature-complete and compatible with traditional (K&R)
+pre-processors.  Additional features include: a plain-text mode; an option to
+unlit literate code files; and an option to turn off macro-expansion.")
+    (license (list license:lgpl2.1+ license:gpl3+))))
+
 ;; Darcs has no https support: http://irclog.perlgeek.de/darcs/2016-09-17
 ;; http://darcs.net/manual/Configuring_darcs.html#SECTION00440070000000000000
 ;; and results of search engines will show that if the protocol is http, https
@@ -276,93 +378,116 @@ used to keep a folder in sync between computers.")
     (license (list license:gpl3+
                    license:agpl3+))))
 
-(define-public ghc-sdl2
+(define-public hlint
   (package
-    (name "ghc-sdl2")
+    (name "hlint")
-    (version "2.4.1.0")
+    (version "2.1.10")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://hackage.haskell.org/package/"
+       (uri (string-append
-                           "sdl2/sdl2-" version ".tar.gz"))
+             "https://hackage.haskell.org/package/" name
+             "/" name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0p4b12fmxps0sbnkqdfy0qw19s355yrkw7fgw6xz53wzq706k991"))))
+         "19as2m9g75cr6n1agzvsij0cvqhb0wbjlk31w4y5d5mns87dki0w"))))
     (build-system haskell-build-system)
-    (arguments '(#:tests? #f)) ; tests require graphical environment
     (inputs
-     `(("ghc-exceptions" ,ghc-exceptions)
+     `(("cpphs" ,cpphs)
-       ("ghc-linear" ,ghc-linear)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
-       ("ghc-statevar" ,ghc-statevar)
+       ("ghc-yaml" ,ghc-yaml)
        ("ghc-vector" ,ghc-vector)
-       ("sdl2" ,sdl2)))
+       ("ghc-data-default" ,ghc-data-default)
-    (native-inputs
+       ("ghc-cmdargs" ,ghc-cmdargs)
-     `(("ghc-weigh" ,ghc-weigh)
+       ("ghc-haskell-src-exts" ,ghc-haskell-src-exts)
-       ("pkg-config" ,pkg-config)))
+       ("ghc-haskell-src-exts-util" ,ghc-haskell-src-exts-util)
-    (home-page "http://hackage.haskell.org/package/sdl2")
+       ("ghc-uniplate" ,ghc-uniplate)
-    (synopsis "High- and low-level bindings to the SDL library")
+       ("ghc-ansi-terminal" ,ghc-ansi-terminal)
-    (description
+       ("ghc-extra" ,ghc-extra)
-     "This package contains bindings to the SDL 2 library, in both high- and
+       ("ghc-refact" ,ghc-refact)
-low-level forms.  The @code{SDL} namespace contains high-level bindings, where
+       ("ghc-aeson" ,ghc-aeson)
-enumerations are split into sum types, and we perform automatic
+       ("hscolour" ,hscolour)))
-error-checking.  The @code{SDL.Raw} namespace contains an almost 1-1
+    (home-page "http://community.haskell.org/~ndm/hlint/")
-translation of the C API into Haskell FFI calls.  As such, this does not
+    (synopsis "Suggest improvements for Haskell source code")
-contain sum types nor error checking.  Thus this namespace is suitable for
+    (description "HLint reads Haskell programs and suggests changes that
-building your own abstraction over SDL, but is not recommended for day-to-day
+hopefully make them easier to read.  HLint also makes it easy to disable
-programming.")
+unwanted suggestions, and to add your own custom suggestions.")
     (license license:bsd-3)))
 
-(define-public ghc-sdl2-mixer
+(define-public hoogle
   (package
-    (name "ghc-sdl2-mixer")
+    (name "hoogle")
-    (version "1.1.0")
+    (version "5.0.17.3")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://hackage.haskell.org/package/sdl2-mixer/"
+       (uri
-                           "sdl2-mixer-" version ".tar.gz"))
+        (string-append
+         "https://hackage.haskell.org/package/hoogle/hoogle-"
+         version ".tar.gz"))
        (sha256
         (base32
-         "1k8avyccq5l9z7bwxigim312yaancxl1sr3q6a96bcm7pnhiak0g"))))
+         "174gp41v0krzj37m75pnr3aawyhkbk2wq4q6zk2z3zh0avvvmgk6"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-data-default-class" ,ghc-data-default-class)
+     `(("ghc-network-uri" ,ghc-network-uri)
-       ("ghc-lifted-base" ,ghc-lifted-base)
+       ("ghc-network" ,ghc-network)
-       ("ghc-monad-control" ,ghc-monad-control)
+       ("ghc-quickcheck" ,ghc-quickcheck)
-       ("ghc-sdl2" ,ghc-sdl2)
+       ("ghc-aeson" ,ghc-aeson)
+       ("ghc-cmdargs" ,ghc-cmdargs)
+       ("ghc-conduit" ,ghc-conduit)
+       ("ghc-conduit-extra" ,ghc-conduit-extra)
+       ("ghc-connection" ,ghc-connection)
+       ("ghc-extra" ,ghc-extra)
+       ("ghc-old-locale" ,ghc-old-locale)
+       ("ghc-haskell-src-exts" ,ghc-haskell-src-exts)
+       ("ghc-http-conduit" ,ghc-http-conduit)
+       ("ghc-http-types" ,ghc-http-types)
+       ("ghc-js-flot" ,ghc-js-flot)
+       ("ghc-js-jquery" ,ghc-js-jquery)
+       ("ghc-mmap" ,ghc-mmap)
+       ("ghc-process-extras" ,ghc-process-extras)
+       ("ghc-resourcet" ,ghc-resourcet)
+       ("ghc-storable-tuple" ,ghc-storable-tuple)
+       ("ghc-tar" ,ghc-tar)
+       ("ghc-uniplate" ,ghc-uniplate)
+       ("ghc-utf8-string" ,ghc-utf8-string)
        ("ghc-vector" ,ghc-vector)
-       ("sdl2-mixer" ,sdl2-mixer)))
+       ("ghc-wai" ,ghc-wai)
-    (native-inputs
+       ("ghc-wai-logger" ,ghc-wai-logger)
-     `(("pkg-config" ,pkg-config)))
+       ("ghc-warp" ,ghc-warp)
-    (home-page "http://hackage.haskell.org/package/sdl2-mixer")
+       ("ghc-warp-tls" ,ghc-warp-tls)
-    (synopsis "Bindings to SDL2 mixer")
+       ("ghc-zlib" ,ghc-zlib)))
-    (description "This package provides Haskell bindings to
+    (home-page "https://hoogle.haskell.org/")
-@code{SDL2_mixer}.")
+    (synopsis "Haskell API Search")
+    (description "Hoogle is a Haskell API search engine, which allows
+you to search many standard Haskell libraries by either function name,
+or by approximate type signature.")
     (license license:bsd-3)))
 
-(define-public ghc-sdl2-image
+(define-public hscolour
   (package
-    (name "ghc-sdl2-image")
+    (name "hscolour")
-    (version "2.0.0")
+    (version "1.24.4")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://hackage.haskell.org/package/sdl2-image/"
+       (uri (string-append
-                           "sdl2-image-" version ".tar.gz"))
+             "https://hackage.haskell.org/package/hscolour/hscolour-"
+             version
+             ".tar.gz"))
        (sha256
         (base32
-         "1pr6dkg73cy9z0w54lrkj9c5bhxj56nl92lxikjy8kz6nyr455rr"))))
+         "079jwph4bwllfp03yfr26s5zc6m6kw3nhb1cggrifh99haq34cr4"))))
     (build-system haskell-build-system)
-    (inputs
+    (home-page "https://hackage.haskell.org/package/hscolour")
-     `(("ghc-sdl2" ,ghc-sdl2)
+    (synopsis "Script to colourise Haskell code")
-       ("sdl2-image" ,sdl2-image)))
+    (description "HSColour is a small Haskell script to colourise Haskell
-    (native-inputs
+code.  It currently has six output formats: ANSI terminal codes (optionally
-     `(("pkg-config" ,pkg-config)))
+XTerm-256colour codes), HTML 3.2 with font tags, HTML 4.01 with CSS, HTML 4.01
-    (home-page "http://hackage.haskell.org/package/sdl2-image")
+with CSS and mouseover annotations, XHTML 1.0 with inline CSS styling, LaTeX,
-    (synopsis "Bindings to SDL2_image")
+and mIRC chat codes.")
-    (description "This package provides Haskell bindings to
+    (license license:bsd-3)))
-@code{SDL2_image}.")
-    (license license:expat)))
 
 (define-public raincat
   (package
@@ -405,3 +530,73 @@ play inspired from classics Lemmings and The Incredible Machine.  The project
 proved to be an excellent learning experience for the programmers.  Everything
 is programmed in Haskell.")
     (license license:bsd-3)))
+
+(define-public shellcheck
+  (package
+    (name "shellcheck")
+    (version "0.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/ShellCheck/ShellCheck-"
+             version ".tar.gz"))
+       (sha256
+        (base32 "1vx895cp5k5h0680xfwj74lk97m9y627n965x6srds0gfnbkzy9s"))
+       (file-name (string-append name "-" version ".tar.gz"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-aeson" ,ghc-aeson)
+       ("ghc-diff" ,ghc-diff)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-regex-tdfa" ,ghc-regex-tdfa)))
+    (home-page "https://github.com/koalaman/shellcheck")
+    (synopsis "Static analysis for shell scripts")
+    (description "@code{shellcheck} provides static analysis for
+@command{bash} and @command{sh} shell scripts.
+It gives warnings and suggestions in order to:
+
+@enumerate
+@item Point out and clarify typical beginner's syntax issues that cause
+a shell to give cryptic error messages.
+@item Point out and clarify typical intermediate level semantic problems
+that cause a shell to behave strangely and counter-intuitively.
+@item Point out subtle caveats, corner cases and pitfalls that may cause an
+advanced user's otherwise working script to fail under future circumstances.
+@end enumerate")
+    (license license:gpl3+)))
+
+(define-public stylish-haskell
+  (package
+    (name "stylish-haskell")
+    (version "0.9.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append
+         "mirror://hackage/package/stylish-haskell/"
+         "stylish-haskell-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1zs624xqp6j8vrl6pfv18dm8vz8hvz25grri65ximxhcizgwhnax"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-aeson" ,ghc-aeson)
+       ("ghc-file-embed" ,ghc-file-embed)
+       ("ghc-haskell-src-exts" ,ghc-haskell-src-exts)
+       ("ghc-semigroups" ,ghc-semigroups)
+       ("ghc-syb" ,ghc-syb)
+       ("ghc-yaml" ,ghc-yaml)
+       ("ghc-strict" ,ghc-strict)
+       ("ghc-optparse-applicative" ,ghc-optparse-applicative)
+       ("ghc-hunit" ,ghc-hunit)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)))
+    (home-page "https://github.com/jaspervdj/stylish-haskell")
+    (synopsis "Haskell code prettifier")
+    (description
+     "A simple Haskell code prettifier.  The goal is not to format all of the
+code in a file, just clean up import statements and a few other tedious
+items.  This tool tries to help where necessary without getting in the way.")
+    (license license:bsd-3)))

gnu/packages/haskell-check.scm

@@ -28,8 +28,8 @@
 
 (define-module (gnu packages haskell-check)
   #:use-module (gnu packages)
-  #:use-module (gnu packages haskell)
   #:use-module (gnu packages haskell-crypto)
+  #:use-module (gnu packages haskell-xyz)
   #:use-module (guix build-system haskell)
   #:use-module (guix download)
   #:use-module ((guix licenses) #:prefix license:)
@@ -837,3 +837,28 @@ of generated values by construction.
 To get started quickly, see the examples:
 @uref{https://github.com/hedgehogqa/haskell-hedgehog/tree/master/hedgehog-example}")
     (license license:bsd-3)))
+
+(define-public cabal-doctest
+  (package
+    (name "cabal-doctest")
+    (version "1.0.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "cabal-doctest/cabal-doctest-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0bgd4jdmzxq5y465r4sf4jv2ix73yvblnr4c9wyazazafddamjny"))))
+    (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("1" "1bk85avgc93yvcggwbk01fy8nvg6753wgmaanhkry0hz55h7mpld")))
+    (home-page "https://github.com/phadej/cabal-doctest")
+    (synopsis "Setup.hs helper for running doctests")
+    (description
+     "To properly work, the @code{doctest} package needs plenty of
+configuration.  This library provides the common bits for writing custom
+@file{Setup.hs} files.")
+    (license license:bsd-3)))

gnu/packages/haskell-web.scm

@@ -6,6 +6,7 @@
 ;;; Copyright © 2017 rsiddharth <s@ricketyspace.net>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Robert Vollmert <rob@vllmrt.net>
+;;; Copyright © 2019 John Soo <jsoo1@asu.edu>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1463,3 +1464,56 @@ Together with the snap-core library upon which it depends, it provides a
 clean and efficient Haskell programming interface to the HTTP
 protocol.")
     (license license:bsd-3)))
+
+(define-public ghc-js-jquery
+  (package
+    (name "ghc-js-jquery")
+    (version "3.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append
+         "https://hackage.haskell.org/package/js-jquery/js-jquery-"
+         version ".tar.gz"))
+       (sha256
+        (base32
+         "16q68jzbs7kp07dnq8cprdcc8fd41rim38039vg0w4x11lgniq70"))))
+    (build-system haskell-build-system)
+    (arguments `(#:tests? #f)) ; tests do network IO
+    (home-page "https://github.com/ndmitchell/js-jquery")
+    (synopsis "Obtain minified jQuery code")
+    (description "This package bundles the minified
+@url{http://jquery.com/, jQuery} code into a Haskell package, so it can
+be depended upon by Cabal packages.  The first three components of the
+version number match the upstream jQuery version.  The package is
+designed to meet the redistribution requirements of downstream
+users (e.g. Debian).")
+    (license license:expat)))
+
+(define-public ghc-js-flot
+  (package
+    (name "ghc-js-flot")
+    (version "0.8.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append
+         "https://hackage.haskell.org/package/js-flot/js-flot-"
+         version ".tar.gz"))
+       (sha256
+        (base32
+         "0yjyzqh3qzhy5h3nql1fckw0gcfb0f4wj9pm85nafpfqp2kg58hv"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-http" ,ghc-http)))
+    (home-page "https://github.com/ndmitchell/js-flot")
+    (synopsis "Obtain minified flot code")
+    (description "This package bundles the minified
+@url{http://www.flotcharts.org/, Flot} code (a jQuery plotting library)
+into a Haskell package, so it can be depended upon by Cabal packages.
+The first three components of the version number match the upstream flot
+version.  The package is designed to meet the redistribution
+requirements of downstream users (e.g. Debian).")
+    (license license:expat)))

gnu/packages/idris.scm

@@ -21,9 +21,9 @@
 
 (define-module (gnu packages idris)
   #:use-module (gnu packages)
-  #:use-module (gnu packages haskell)
   #:use-module (gnu packages haskell-check)
   #:use-module (gnu packages haskell-web)
+  #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages libffi)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ncurses)

gnu/packages/image.scm

@@ -625,6 +625,81 @@ work.")
     (home-page "https://jbig2dec.com")
     (license license:gpl2+)))
 
+(define-public jbigkit
+  (package
+    (name "jbigkit")
+    (version "2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://www.cl.cam.ac.uk/~mgk25/jbigkit/"
+                           "download/jbigkit-" version ".tar.gz"))
+       (sha256
+        (base32 "0cnrcdr1dwp7h7m0a56qw09bv08krb37mpf7cml5sjdgpyv0cwfy"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; Remove files without clear licence information.
+           (for-each delete-file-recursively
+                     (list "contrib" "examples"))
+           #t))))
+    (build-system gnu-build-system)
+    (outputs (list "out" "pbmtools"))
+    (arguments
+     `(#:modules ((srfi srfi-26)
+                  ,@%gnu-build-system-modules)
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)            ; no configure script
+         (replace 'install              ; no ‘make install’ target
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (lib (string-append out "/lib"))
+                    (include (string-append out "/include")))
+               (with-directory-excursion "libjbig"
+                 (for-each (cut install-file <> include)
+                           (find-files "." "\\.h$"))
+                 (for-each (cut install-file <> lib)
+                           (find-files "." "\\.a$")))
+               #t)))
+         (add-after 'install 'install-pbmtools
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "pbmtools"))
+                    (bin (string-append out "/bin"))
+                    (man1 (string-append out "/share/man/man1"))
+                    (man5 (string-append out "/share/man/man5")))
+               (with-directory-excursion "pbmtools"
+                 (for-each (cut install-file <> bin)
+                           (list "jbgtopbm" "jbgtopbm85"
+                                 "pbmtojbg" "pbmtojbg85"))
+
+                 (for-each (cut install-file <> man1)
+                           (find-files "." "\\.1$"))
+                 (for-each (cut install-file <> man5)
+                           (find-files "." "\\.5$"))
+                 #t)))))
+       #:test-target "test"
+       #:tests? #f))                    ; tests depend on examples/
+    (home-page "https://www.cl.cam.ac.uk/~mgk25/jbigkit/")
+    (synopsis "Lossless compression for bi-level high-resolution images")
+    (description
+     "JBIG-KIT implements the JBIG1 data compression standard (ITU-T T.82 and
+ISO/IEC 11544:1993), designed for bi-level (one bit per pixel) images such as
+black-and-white scanned documents.  It is widely used in fax products, printer
+firmware and drivers, document management systems, and imaging software.
+
+This package provides a static C library of (de)compression functions and some
+simple command-line converters similar to those provided by netpbm.
+
+Two JBIG1 variants are available.  One (@file{jbig.c}) implements nearly all
+options of the standard but has to keep the full uncompressed image in memory.
+The other (@file{jbig85.c}) implements just the ITU-T T.85 profile, with
+memory management optimized for embedded and fax applications.  It buffers
+only a few lines of the uncompressed image in memory and is able to stream
+images of initially unknown height.")
+    (license (list license:isc          ; pbmtools/p?m.5
+                   license:gpl2+))))    ; the rest
+
 (define-public openjpeg
   (package
     (name "openjpeg")
@@ -966,12 +1041,11 @@ multi-dimensional image processing.")
    (home-page "https://ukoethe.github.io/vigra/")))
 
 (define-public vigra-c
-  (let* ((commit "a2ff675f42079e2623318d8ff8b4288dbe7a7f06")
+  (let* ((commit "66ff4fa5a7d4a77415caa676a45c2c6ea16562e7")
-         (revision "0")
+         (revision "1"))
-         (version (git-version "0.0.0" revision commit)))
     (package
       (name "vigra-c")
-      (version version)
+      (version (git-version "0.0.0" revision commit))
       (home-page "https://github.com/BSeppke/vigra_c")
       (source (origin
                 (method git-fetch)
@@ -980,7 +1054,7 @@ multi-dimensional image processing.")
                       (commit commit)))
                 (sha256
                  (base32
-                  "1f1phmfbbz3dsq9330rd6bjmdg29hxskxi9l17cyx1f4mdqpgdgl"))
+                  "1pnd92s284dvsg8zp6md7p8ck55bmcsryz58gzic7jh6m72hg689"))
                 (file-name (git-file-name name version))))
       (build-system cmake-build-system)
       (arguments
@@ -990,6 +1064,7 @@ multi-dimensional image processing.")
       (inputs
        `(("fftw" ,fftw)
          ("fftwf" ,fftwf)
+         ("hdf5" ,hdf5)
          ("vigra" ,vigra)))
       (synopsis "C interface to the VIGRA computer vision library")
       (description

gnu/packages/julia.scm

@@ -482,6 +482,10 @@
        ("patchelf" ,patchelf)
        ("pkg-config" ,pkg-config)
        ("python" ,python-2)))
+    (native-search-paths
+     (list (search-path-specification
+            (variable "JULIA_LOAD_PATH")
+            (files (list "share/julia/packages/")))))
     ;; Julia is not officially released for ARM and MIPS.
     ;; See https://github.com/JuliaLang/julia/issues/10639
     (supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux"))

gnu/packages/libreoffice.scm

@@ -335,14 +335,14 @@ as Alfresco or Nuxeo.")
 (define-public libabw
   (package
     (name "libabw")
-    (version "0.1.2")
+    (version "0.1.3")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "https://dev-www.libreoffice.org/src/libabw/"
                           "libabw-" version ".tar.xz"))
       (sha256 (base32
-               "11949iscdb99f2jplxjd39282jxcrf2fw0sqbh5dl7gqb96r8whb"))))
+               "1vbfrmnvib3cym0yyyabnd8xpx4f7wp20vnn09s6dln347fajqz7"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("doxygen" ,doxygen)
@@ -354,9 +354,6 @@ as Alfresco or Nuxeo.")
        ("libxml2" ,libxml2)))
     (inputs
      `(("boost" ,boost)))
-    (arguments
-     ;; avoid triggering configure errors by simple inclusion of boost headers
-     `(#:configure-flags '("--disable-werror")))
     (home-page "https://wiki.documentfoundation.org/DLP/Libraries/libabw")
     (synopsis "Library for parsing the AbiWord format")
     (description "Libabw is a library that parses the file format of
@@ -585,14 +582,14 @@ created by PageMaker version 6.x and 7.")
 (define-public libvisio
   (package
     (name "libvisio")
-    (version "0.1.6")
+    (version "0.1.7")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "http://dev-www.libreoffice.org/src/libvisio/"
                           "libvisio-" version ".tar.xz"))
       (sha256 (base32
-               "1yahpfl13qk6178irv8jn5ppxdn7isafqisyqsdw0lqxcz9h447y"))))
+               "0k7adcbbf27l7n453cca1m6s9yj6qvb5j6bsg2db09ybf3w8vbwg"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("cppunit" ,cppunit)

gnu/packages/libusb.scm

@@ -51,15 +51,15 @@
 (define-public libusb
   (package
     (name "libusb")
-    (version "1.0.22")
+    (version "1.0.23")
     (source
      (origin
       (method url-fetch)
-      (uri (string-append "mirror://sourceforge/libusb/libusb-1.0/"
+      (uri (string-append "https://github.com/libusb/libusb/"
-                          "libusb-" version "/libusb-" version ".tar.bz2"))
+                          "releases/download/v" version
+                          "/libusb-" version ".tar.bz2"))
       (sha256
-       (base32
+       (base32 "13dd2a9x290d1q8nb1lqiaf36grcvns5ripk5k2xm0lajmpc04fv"))))
-        "0mw1a5ss4alg37m6bd4k44v35xwrcwp5qm4s686q1nsgkbavkbkm"))))
     (build-system gnu-build-system)
 
     ;; XXX: Enabling udev is now recommended, but eudev indirectly depends on
@@ -82,9 +82,9 @@ devices on various operating systems.")
      (origin
       (method url-fetch)
       (uri (string-append "mirror://sourceforge/libusb/"
-                          name "-" (version-major+minor version) "/"
+                          "libusb-compat-" (version-major+minor version) "/"
-                          name "-" version "/"
+                          "libusb-compat-" version "/"
-                          name "-" version ".tar.bz2"))
+                          "libusb-compat-" version ".tar.bz2"))
       (sha256
        (base32
         "0nn5icrfm9lkhzw1xjvaks9bq3w6mjg86ggv3fn7kgi4nfvg8kj0"))))

gnu/packages/linux.scm

@@ -349,42 +349,42 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
                         "linux-" version ".tar.xz"))
     (sha256 hash)))
 
-(define-public linux-libre-5.2-version "5.2.11")
+(define-public linux-libre-5.2-version "5.2.13")
 (define-public linux-libre-5.2-pristine-source
   (let ((version linux-libre-5.2-version)
-        (hash (base32 "1y9kn1zny3xpmbi5an3g7hbzywnycys8chfaw6laij1xk4gq6ahc")))
+        (hash (base32 "12hpph3iynr22mfwz7745lp01waf2kg579hr56d4pvhx4iahzdhp")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.2)))
 
-(define-public linux-libre-4.19-version "4.19.69")
+(define-public linux-libre-4.19-version "4.19.71")
 (define-public linux-libre-4.19-pristine-source
   (let ((version linux-libre-4.19-version)
-        (hash (base32 "11yrw8ixd5ni9rlpndqsz2ihx6k8qaf35a1lf164lkhaa85pd4f0")))
+        (hash (base32 "1bjwkb7k82l646ryyy0jbwsnygm2qsxgcwli8bdrj844skzynlqz")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.19)))
 
-(define-public linux-libre-4.14-version "4.14.141")
+(define-public linux-libre-4.14-version "4.14.142")
 (define-public linux-libre-4.14-pristine-source
   (let ((version linux-libre-4.14-version)
-        (hash (base32 "05rs411rw10hhnfzvaxmcik3pq20i1i05shvvra4bv164f0z1f8b")))
+        (hash (base32 "1wwhnm1n1b6yzsd2zzzf9i3n4hlvgnph70p67cwahw0ik4ssayz6")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.14)))
 
-(define-public linux-libre-4.9-version "4.9.190")
+(define-public linux-libre-4.9-version "4.9.191")
 (define-public linux-libre-4.9-pristine-source
   (let ((version linux-libre-4.9-version)
-        (hash (base32 "05ha3snfk0vdqk9i27icwpq2if0h2jvshavn69ldwqm4h2h1r2py")))
+        (hash (base32 "1g5p736p8zx5rmxaj56yw93jp768npl868jsn8973dny0rsbim6y")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.9)))
 
-(define-public linux-libre-4.4-version "4.4.190")
+(define-public linux-libre-4.4-version "4.4.191")
 (define-public linux-libre-4.4-pristine-source
   (let ((version linux-libre-4.4-version)
-        (hash (base32 "1rf28cjrrmj7mm8xqlfld6k20ddk15j4mmyarqibjx9pk9acij7y")))
+        (hash (base32 "0x3lnq4xyj5v6r1cz4jizm4vdspws1nb806f5qczwi3yil5nm6bh")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.4)))
@@ -664,6 +664,12 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration."
              #t))
          (replace 'configure
            (lambda* (#:key inputs native-inputs target #:allow-other-keys)
+             ;; Unset CROSS_CPATH to make sure that cross-libc is not
+             ;; found. Otherwise, some of its header would conflict with the
+             ;; one from linux (stdint.h and linux/types.h)
+             ,@(if (%current-target-system)
+                   '((unsetenv "CROSS_CPATH"))
+                   '())
              ;; Avoid introducing timestamps
              (setenv "KCONFIG_NOTIMESTAMP" "1")
              (setenv "KBUILD_BUILD_TIMESTAMP" (getenv "SOURCE_DATE_EPOCH"))
@@ -887,7 +893,7 @@ and should be used with caution, especially on untested models.")
 (define-public vhba-module
   (package
     (name "vhba-module")
-    (version "20190410")
+    (version "20190831")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -895,7 +901,7 @@ and should be used with caution, especially on untested models.")
                     version ".tar.bz2"))
               (sha256
                (base32
-                "1513hq130raxp9z5grj54cwfjfxj05apipxg425j0zicii59a60c"))))
+                "1ybbk6l06n0y11n5wnfmvdz0baizmq55l458ywimghdyz0n7g0ws"))))
     (build-system linux-module-build-system)
     (arguments
      ;; TODO: No tests?
@@ -1915,7 +1921,7 @@ transparently through a bridge.")
 (define-public libnl
   (package
     (name "libnl")
-    (version "3.4.0")
+    (version "3.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1924,7 +1930,7 @@ transparently through a bridge.")
                     "/libnl-" version ".tar.gz"))
               (sha256
                (base32
-                "1gzm444rnsib64dddv0cwlpzy1q4bycjqhp1i5pxpikimqvpca5p"))))
+                "1yh5bqmkivd78x378x34gzb28lvykn6b9k3hgvvpdnj5jpn3689m"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("bison" ,bison)
@@ -1939,7 +1945,7 @@ transparently through a bridge.")
                  (string-join (string-split version #\.) "_")
                  "/libnl-doc-" version ".tar.gz"))
            (sha256
-            (base32 "1m5cnzviv31gjnz6fz5rgyl6ah4dbp2akm49j9973sgwl36gs8jx"))))))
+            (base32 "19p5y8q3cm5wqvamqc4s5syxnnkvzxy3gw8ivxk6fv9ybn8jm35h"))))))
     (inputs
      `(("python-2" ,python-2)
        ("python-3" ,python-3)))
@@ -2308,15 +2314,15 @@ compressed, transparent to other programs, without decompressing them.")
 (define-public numactl
   (package
     (name "numactl")
-    (version "2.0.12")
+    (version "2.0.13")
     (source (origin
               (method url-fetch)
               (uri (string-append
                     "https://github.com/numactl/numactl/releases/download/v"
-                    version "/" name "-" version ".tar.gz"))
+                    version "/numactl-" version ".tar.gz"))
               (sha256
                (base32
-                "0ad7mpi3vacbfnx3aqxnvgsj64yp3mav9yxnaz8ancjv7wvdmfsm"))))
+                "16lcypvcmx1ydkpi2s82kqhg13kak7qhpbnj8hd9bdbyhr5ja7lr"))))
     (build-system gnu-build-system)
     (arguments
      '(;; There's a 'test' target, but it requires NUMA support in the kernel
@@ -2330,14 +2336,14 @@ compressed, transparent to other programs, without decompressing them.")
     (synopsis "Tools for non-uniform memory access (NUMA) machines")
     (description
      "NUMA stands for Non-Uniform Memory Access, in other words a system whose
-memory is not all in one place.  The numactl program allows you to run your
+memory is not all in one place.  The @command{numactl} program allows you to
-application program on specific CPU's and memory nodes.  It does this by
+run your application program on specific CPUs and memory nodes.  It does this
-supplying a NUMA memory policy to the operating system before running your
+by supplying a NUMA memory policy to the operating system before running your
 program.
 
-The package contains other commands, such as numademo, numastat and memhog.
+The package contains other commands, such as @command{numastat},
-The numademo command provides a quick overview of NUMA performance on your
+@command{memhog}, and @command{numademo} which provides a quick overview of
-system.")
+NUMA performance on your system.")
     (license (list license:gpl2                   ;programs
                    license:lgpl2.1))))            ;library
 

gnu/packages/lisp.scm

@@ -113,7 +113,7 @@
       (build-system gnu-build-system)
       (arguments
        `(#:parallel-build? #f  ; The build system seems not to be thread safe.
-         #:tests? #f  ; There does not seem to be make check or anything similar.
+         #:test-target "ansi-tests/test_results"
          #:configure-flags '("--enable-ansi") ; required for use by the maxima package
          #:make-flags (list
                        (string-append "GCL_CC=" (assoc-ref %build-inputs "gcc")
@@ -327,14 +327,14 @@ an interpreter, a compiler, a debugger, and much more.")
 (define-public sbcl
   (package
     (name "sbcl")
-    (version "1.5.5")
+    (version "1.5.6")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/sbcl/sbcl/" version "/sbcl-"
                            version "-source.tar.bz2"))
        (sha256
-        (base32 "1qmapk2hyxxqd3ajiqacz4isij0ibx7gn10n8dbmq33gm3kgliyb"))
+        (base32 "10z43dc29p7s8dl3jixklhmzqfp7gcm3fccjdfd36qqhyfxqxx3a"))
        (modules '((guix build utils)))
        (snippet
         ;; Add sbcl-bundle-systems to 'default-system-source-registry'.
@@ -353,11 +353,21 @@ an interpreter, a compiler, a debugger, and much more.")
      ;;       ABCL (recent versions only)
      ;;       CLISP (only some versions: 2.44.1 is OK, 2.47 is not)
      ;;       XCL
-     ;; CCL seems ideal then, but it unfortunately only builds reliably
+     ;;
-     ;; on some architectures.
+     ;; From NEWS:
+     ;;     * build enhancement: new host quirks mechanism, support for building under
+     ;;     ABCL and ECL (as well as CCL, CMUCL, CLISP and SBCL itself)
+     ;;
+     ;; CCL is not bootstrappable so it won't do.  CLISP 2.49 seems to work.
+     ;; ECL too.  ECL builds SBCL about 20% slower than CLISP.  As of
+     ;; 2019-09-05, ECL was last updated in 2016 while CLISP was last update
+     ;; in 2010.
+     ;;
+     ;; For now we stick to CLISP for all systems.  We keep the `match' in to
+     ;; make it easier to change the host compiler for various architectures.
      `(,@(match (%current-system)
            ((or "x86_64-linux" "i686-linux")
-            `(("ccl" ,ccl)))
+            `(("clisp" ,clisp)))
            (_
             `(("clisp" ,clisp))))
        ("which" ,which)
@@ -428,7 +438,7 @@ an interpreter, a compiler, a debugger, and much more.")
              (setenv "CC" "gcc")
              (invoke "sh" "make.sh" ,@(match (%current-system)
                                         ((or "x86_64-linux" "i686-linux")
-                                         `("ccl"))
+                                         `("clisp"))
                                         (_
                                          `("clisp")))
                      (string-append "--prefix="
@@ -488,6 +498,15 @@ statistical profiler, a code coverage tool, and many other extensions.")
                    (license:x11-style "file://src/code/loop.lisp")))))
 
 (define-public ccl
+  ;; Warning: according to upstream, CCL is not bootstrappable.
+  ;; See https://github.com/Clozure/ccl/issues/222 from 2019-09-02:
+  ;;
+  ;;     "As far as I know, there is no way to build CCL without an existing
+  ;;     running CCL image. It was bootstrapped back in 1986 or so as
+  ;;     Macintosh Common Lisp, by Gary Byers, I believe, who is no longer on
+  ;;     the planet to tell us the story. It SHOULD be possible to port the
+  ;;     CCL compiler to portable Common Lisp, so that ANY lisp could build
+  ;;     it, as is the case for SBCL, but I know of no attempt to do so."
   (package
     (name "ccl")
     (version "1.11.5")
@@ -710,10 +729,44 @@ portable between implementations.")
 (define-public ecl-alexandria
   (sbcl-package->ecl-package sbcl-alexandria))
 
+(define-public sbcl-net.didierverna.asdf-flv
+  (package
+    (name "sbcl-net.didierverna.asdf-flv")
+    (version "2.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/didierverna/asdf-flv")
+             (commit (string-append "version-" version))))
+       (file-name (git-file-name "asdf-flv" version))
+       (sha256
+        (base32 "1fi2y4baxan103jbg4idjddzihy03kwnj2mzbwrknw4d4x7xlgwj"))))
+    (build-system asdf-build-system/sbcl)
+    (synopsis "Common Lisp ASDF extension to provide support for file-local variables")
+    (description "ASDF-FLV provides support for file-local variables through
+ASDF.  A file-local variable behaves like @code{*PACKAGE*} and
+@code{*READTABLE*} with respect to @code{LOAD} and @code{COMPILE-FILE}: a new
+dynamic binding is created before processing the file, so that any
+modification to the variable becomes essentially file-local.
+
+In order to make one or several variables file-local, use the macros
+@code{SET-FILE-LOCAL-VARIABLE(S)}.")
+    (home-page "https://www.lrde.epita.fr/~didier/software/lisp/misc.php#asdf-flv")
+    (license (license:non-copyleft
+              "https://www.gnu.org/prep/maintain/html_node/License-Notices-for-Other-Files.html"
+              "GNU All-Permissive License"))))
+
+(define-public cl-net.didierverna.asdf-flv
+  (sbcl-package->cl-source-package sbcl-net.didierverna.asdf-flv))
+
+(define-public ecl-net.didierverna.asdf-flv
+  (sbcl-package->ecl-package sbcl-net.didierverna.asdf-flv))
+
 (define-public sbcl-fiveam
   (package
     (name "sbcl-fiveam")
-    (version "1.2")
+    (version "1.4.1")
     (source
      (origin
        (method git-fetch)
@@ -722,8 +775,11 @@ portable between implementations.")
              (commit (string-append "v" version))))
        (file-name (git-file-name "fiveam" version))
        (sha256
-        (base32 "1yx9716mk8pq9076q6cjx4c9lyax3amiccy37sh0913k2x8gsm4l"))))
+        (base32 "1q3d38pwafnwnw42clq0f8g5xw7pbzr287jl9jsqmb1vb0n1vrli"))))
-    (inputs `(("alexandria" ,sbcl-alexandria)))
+    (inputs
+     `(("alexandria" ,sbcl-alexandria)
+       ("net.didierverna.asdf-flv" ,sbcl-net.didierverna.asdf-flv)
+       ("trivial-backtrace" ,sbcl-trivial-backtrace)))
     (build-system asdf-build-system/sbcl)
     (synopsis "Common Lisp testing framework")
     (description "FiveAM is a simple (as far as writing and running tests
@@ -2175,7 +2231,7 @@ also be supported.")
 (define-public sbcl-ironclad
   (package
     (name "sbcl-ironclad")
-    (version "0.42")
+    (version "0.46")
     (source
      (origin
        (method git-fetch)
@@ -2184,14 +2240,15 @@ also be supported.")
              (commit (string-append "v" version))))
        (sha256
         (base32
-         "1wjcb9vpybxjrmch7f7s78a5abxmnknbd4fl49dl5lz8a3fc8vf0"))
+         "1s391awi2lsl7m1dbjirgpkm4p9p8wd076pakgvsvpn1rrznisnd"))
-       (file-name (string-append "ironblad" version "-checkout"))))
+       (file-name (git-file-name name version))))
     (build-system asdf-build-system/sbcl)
     (native-inputs
      ;; Tests only.
      `(("rt" ,sbcl-rt)))
     (inputs
-     `(("flexi-streams" ,sbcl-flexi-streams)
+     `(("bordeaux-threads" ,sbcl-bordeaux-threads)
+       ("flexi-streams" ,sbcl-flexi-streams)
        ("nibbles" ,sbcl-nibbles)))
     (synopsis "Cryptographic toolkit written in Common Lisp")
     (description
@@ -5337,17 +5394,18 @@ port within a range.")
 (define-public txr
   (package
     (name "txr")
-    (version "223")
+    (version "224")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "http://www.kylheku.com/cgit/txr/snapshot/txr-"
+       (uri (git-reference
-                           version
+             (url "http://www.kylheku.com/git/txr/")
-                           ".tar.bz2"))
+             (commit (string-append "txr-" version))))
+       (file-name (git-file-name name version))
        (patches (search-patches "txr-shell.patch"))
        (sha256
         (base32
-         "0109q8idqggba3kx58dpm5ccfpdrki68npkcxm18p5ga24611fcv"))))
+         "1036k71f6mffy9rjwzmhr5nnp1n0wzb0rqvilpzvb8jc5yxv0810"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("cc=gcc")
@@ -6740,3 +6798,66 @@ power of CXML is available when necessary.")
       (description "This is a Common Lisp library that allows to publish D-Bus
 objects as well as send and notify other objects connected to a bus.")
       (license license:bsd-2))))
+
+(define-public sbcl-cl-hooks
+  (let ((commit "5b638083f3b4f1221a52631d9c8a0a265565cac7")
+        (revision "1"))
+    (package
+      (name "sbcl-cl-hooks")
+      (build-system asdf-build-system/sbcl)
+      (version (git-version "0.2.1" revision commit))
+      (home-page "https://github.com/scymtym/architecture.hooks")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url home-page)
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0bg3l0a28lw5gqqjp6p6b5nhwqk46sgkb7184w5qbfngw1hk8x9y"))))
+      (inputs
+       `(("alexandria" ,sbcl-alexandria)
+         ("let-plus" ,sbcl-let-plus)
+         ("trivial-garbage" ,sbcl-trivial-garbage)
+         ("closer-mop" ,sbcl-closer-mop)))
+      (native-inputs
+       `(("fiveam" ,sbcl-fiveam)))
+      (synopsis "Hooks extension point mechanism (as in Emacs) for Common Lisp")
+      (description "A hook, in the present context, is a certain kind of
+extension point in a program that allows interleaving the execution of
+arbitrary code with the execution of a the program without introducing any
+coupling between the two.  Hooks are used extensively in the extensible editor
+Emacs.
+
+In the Common LISP Object System (CLOS), a similar kind of extensibility is
+possible using the flexible multi-method dispatch mechanism.  It may even seem
+that the concept of hooks does not provide any benefits over the possibilites
+of CLOS.  However, there are some differences:
+
+@itemize
+
+@item There can be only one method for each combination of specializers and
+qualifiers.  As a result this kind of extension point cannot be used by
+multiple extensions independently.
+@item Removing code previously attached via a @code{:before}, @code{:after} or
+@code{:around} method can be cumbersome.
+@item There could be other or even multiple extension points besides @code{:before}
+and @code{:after} in a single method.
+@item Attaching codes to individual objects using eql specializers can be
+cumbersome.
+@item Introspection of code attached a particular extension point is
+cumbersome since this requires enumerating and inspecting the methods of a
+generic function.
+@end itemize
+
+This library tries to complement some of these weaknesses of method-based
+extension-points via the concept of hooks.")
+      (license license:llgpl))))
+
+(define-public cl-hooks
+  (sbcl-package->cl-source-package sbcl-cl-hooks))
+
+(define-public ecl-cl-hooks
+  (sbcl-package->ecl-package sbcl-cl-hooks))

gnu/packages/mail.scm

@@ -1197,7 +1197,7 @@ delivery.")
 (define-public exim
   (package
     (name "exim")
-    (version "4.92.1")
+    (version "4.92.2")
     (source
      (origin
        (method url-fetch)
@@ -1206,7 +1206,7 @@ delivery.")
                   (string-append "https://ftp.exim.org/pub/exim/exim4/old/exim-"
                                  version ".tar.bz2")))
        (sha256
-        (base32 "132zmxgzz35xwi89g3crw6hd3y74rxj5zcpamakvrnlcn256amdp"))))
+        (base32 "1xnc5rdcg5mcrvjqp506a9frmcr89jwsh4c5vbks46awyz1rfzsm"))))
     (build-system gnu-build-system)
     (inputs
      `(("bdb" ,bdb-5.3) ; ‘#error Version 6 and later BDB API is not supported’

gnu/packages/maths.scm

@@ -31,6 +31,7 @@
 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
 ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -675,14 +676,14 @@ computations.")
 (define-public hdf4
   (package
     (name "hdf4")
-    (version "4.2.13")
+    (version "4.2.14")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
                            version "/src/hdf-" version ".tar.bz2"))
        (sha256
-        (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
+        (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l"))
        (patches (search-patches "hdf4-architectures.patch"
                                 "hdf4-reproducibility.patch"
                                 "hdf4-shared-fortran.patch"
@@ -5144,3 +5145,36 @@ algorithm, a parametric integer programming solver, and primitives for
 termination analysis via the automatic synthesis of linear ranking
 functions.")
     (license license:gpl3+)))
+
+(define-public speedcrunch
+  (package
+    (name "speedcrunch")
+    (version "0.12.0")
+    (source
+     (origin
+      (method git-fetch)
+      (uri (git-reference
+        (url "https://bitbucket.org/heldercorreia/speedcrunch.git")
+        (commit (string-append "release-" version))))
+      (file-name (git-file-name name version))
+      (sha256
+       (base32
+        "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
+    (build-system cmake-build-system)
+    (inputs `(("qtbase" ,qtbase)))
+    (native-inputs `(("qttools" ,qttools)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'chdir-to-src
+           (lambda _ (chdir "src") #t)))))
+    (synopsis "High-precision scientific calculator")
+    (description
+     "SpeedCrunch is a high-precision scientific calculator.  It features a
+syntax-highlighted scrollable display and is designed to be fully used via
+keyboard.  Some distinctive features are auto-completion of functions and
+variables, a formula book, and quick insertion of constants from various
+fields of knowledge.")
+    (home-page "http://speedcrunch.org/")
+    (license license:gpl2+)))
+

gnu/packages/mp3.scm

@@ -305,7 +305,7 @@ This package contains the binary.")
 (define-public mpg123
   (package
     (name "mpg123")
-    (version "1.25.10")
+    (version "1.25.12")
     (source (origin
               (method url-fetch)
               (uri (list (string-append "mirror://sourceforge/mpg123/mpg123/"
@@ -315,7 +315,7 @@ This package contains the binary.")
                           version ".tar.bz2")))
               (sha256
                (base32
-                "08vhp8lz7d9ybhxcmkq3adwfryhivfvp0745k4r9kgz4wap3f4vc"))))
+                "1l9iwwgqzw6yg5zk9pqmlbfyq6d8dqysbmj0j3m8dyrxd34wgzhz"))))
     (build-system gnu-build-system)
     (arguments '(#:configure-flags '("--with-default-audio=pulse")))
     (native-inputs `(("pkg-config" ,pkg-config)))

gnu/packages/music.scm

@@ -1999,14 +1999,14 @@ browser.")
 (define-public drumstick
   (package
     (name "drumstick")
-    (version "1.1.2")
+    (version "1.1.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/drumstick/"
                                   version "/drumstick-" version ".tar.bz2"))
               (sha256
                (base32
-                "0kljqyqj7s1i2z52i24x7ail1bywn6dcxxfbad5c59drm8wv94bp"))))
+                "1n9wvg79yvkygrkc8xd8pgrd3d7hqmr7gh24dccf0px23lla9b3m"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ; no test target
@@ -2042,6 +2042,52 @@ multiplatform realtime MIDI I/O library is also provided with various output
 backends, including ALSA, OSS, Network and FluidSynth.")
     (license license:gpl2+)))
 
+(define-public vmpk
+  (package
+    (name "vmpk")
+    (version "0.7.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/vmpk/vmpk/"
+                                  version "/vmpk-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "1i3hnvdgz46n4k5v0q4jhgh7nkh0s390ix4nqr69z0q3026yp0p6"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f  ; no test target
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'fix-docbook
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "cmake_admin/CreateManpages.cmake"
+               (("http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl")
+                (string-append (assoc-ref inputs "docbook-xsl")
+                               "/xml/xsl/docbook-xsl-"
+                               ,(package-version docbook-xsl)
+                               "/manpages/docbook.xsl")))
+             #t)))))
+    (inputs
+     `(("drumstick" ,drumstick)
+       ("qtbase" ,qtbase)
+       ("qtsvg" ,qtsvg)
+       ("qttools" ,qttools)
+       ("qtx11extras" ,qtx11extras)))
+    (native-inputs
+     `(("libxslt" ,libxslt) ;for xsltproc
+       ("docbook-xsl" ,docbook-xsl)
+       ("pkg-config" ,pkg-config)))
+    (home-page "http://vmpk.sourceforge.net")
+    (synopsis "Virtual MIDI piano keyboard")
+    (description
+     "Virtual MIDI Piano Keyboard is a MIDI events generator and receiver.  It
+doesn't produce any sound by itself, but can be used to drive a MIDI
+synthesizer (either hardware or software, internal or external).  You can use
+the computer's keyboard to play MIDI notes, and also the mouse.  You can use
+the Virtual MIDI Piano Keyboard to display the played MIDI notes from another
+instrument or MIDI file player.")
+    (license license:gpl3+)))
+
 (define-public zynaddsubfx
   (package
     (name "zynaddsubfx")
@@ -2091,7 +2137,7 @@ capabilities, custom envelopes, effects, etc.")
 (define-public yoshimi
   (package
     (name "yoshimi")
-    (version "1.5.10.2")
+    (version "1.6.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/yoshimi/"
@@ -2099,7 +2145,7 @@ capabilities, custom envelopes, effects, etc.")
                                   "/yoshimi-" version ".tar.bz2"))
               (sha256
                (base32
-                "1rr99qkq80s8l2iv3x4ccxan07m15dvmd5s9b10386bfjbwbya01"))))
+                "0bcc5spnq73yp1fmm367d1mxcswqkmzs3cnpb4cxr513ir98sa50"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ; there are no tests

gnu/packages/ocaml.scm

@@ -428,7 +428,7 @@ the opam file fomat.")
 (define-public opam
   (package
     (name "opam")
-    (version "2.0.4")
+    (version "2.0.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -437,7 +437,7 @@ the opam file fomat.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1yx5k8v5vnnc20fmz5zx8kqd242j48qcknlk6vmkr7rkq886ipq2"))))
+                "0pf2smq2sdcxryq5i87hz3dv05pb3zasb1is3kxq1pi1s4cn55mx"))))
     (build-system ocaml-build-system)
     (arguments
      `(#:configure-flags
@@ -1109,7 +1109,7 @@ files in these formats.")
 (define-public ocaml-zarith
   (package
     (name "ocaml-zarith")
-    (version "1.7")
+    (version "1.9.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1117,7 +1117,7 @@ files in these formats.")
                      (commit (string-append "release-" version))))
               (sha256
                (base32
-                "08x5xnamibhvxl50f1bb3jl9ym0hm6004hmc54xnrnrv7jxz9rvz"))))
+                "0hv5ywz1q2cgn8apfz490clwk5hcynr937g2v8i13x2ax4bnv0lz"))))
     (build-system ocaml-build-system)
     (native-inputs
      `(("perl" ,perl)))
@@ -1140,7 +1140,7 @@ for speed and space economy.")
 (define-public ocaml-frontc
   (package
     (name "ocaml-frontc")
-    (version "3.4.1")
+    (version "3.4.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1150,7 +1150,7 @@ for speed and space economy.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1dq5nks0c9gsbr1m8k39m1bniawr5hqcy1r8x5px7naa95ch06ak"))))
+                "0k7jk9hkglnkk27s62xl493jyqc017gyvwqb1lyc0ywbb001s102"))))
     (build-system ocaml-build-system)
     (arguments
      `(#:phases
@@ -1186,7 +1186,7 @@ GNU CC attributes.  It provides also a C pretty printer as an example of use.")
 (define-public ocaml-qcheck
   (package
     (name "ocaml-qcheck")
-    (version "0.9")
+    (version "0.10")
     (source
      (origin
        (method git-fetch)
@@ -1195,7 +1195,7 @@ GNU CC attributes.  It provides also a C pretty printer as an example of use.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0w83v9ylycsssyn47q8wnkfbvhn5vn10z6i35n5965i2m1r0mmcf"))))
+        (base32 "1i7axg7vmivrkzsahyg79my584myvzxv0922k4000bdwnhzd0kzh"))))
     (build-system dune-build-system)
     (arguments
      `(#:test-target "."))
@@ -1242,7 +1242,7 @@ to use -- to sophisticated random generation of test cases.")
 (define-public ocaml-stringext
   (package
     (name "ocaml-stringext")
-    (version "1.5.0")
+    (version "1.6.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1251,7 +1251,7 @@ to use -- to sophisticated random generation of test cases.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0035pyakk0r7pfhkrayvqncpv9mk6lssr455j3prmdcirh6s50d7"))))
+                "1m09cmn3vrk3gdm60fb730qsygcfyxsyv7gl9xfzck08q1x2x9qx"))))
     (build-system dune-build-system)
     (arguments
      `(#:test-target "."))
@@ -1317,14 +1317,16 @@ coverage information.")
 (define-public dune
   (package
     (name "dune")
-    (version "1.9.3")
+    (version "1.11.3")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/ocaml/dune/releases/"
+              (uri (git-reference
-                                  "download/" version "/dune-" version ".tbz"))
+                     (url "https://github.com/ocaml/dune")
+                     (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1jlhnx580v6i1d451z5cl8ibfd0m9qln963y2pp5v6s2winyqyri"))))
+                "0l4x0x2fz135pljv88zj8y6w1ninsqw0gn1mdxzprd6wbxbyn8wr"))))
     (build-system ocaml-build-system)
     (arguments
      `(#:tests? #f; require odoc
@@ -1347,7 +1349,7 @@ following a very simple s-expression syntax.")
 (define-public ocaml-migrate-parsetree
   (package
     (name "ocaml-migrate-parsetree")
-    (version "1.2.0")
+    (version "1.4.0")
     (home-page "https://github.com/ocaml-ppx/ocaml-migrate-parsetree")
     (source
      (origin
@@ -1358,7 +1360,7 @@ following a very simple s-expression syntax.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "16kas19iwm4afijv3yxd250s08absabmdcb4yj57wc8r4fmzv5dm"))))
+         "0sv1p4615l8gpbah4ya2c40yr6fbvahvv3ks7zhrsgcwcq2ljyr2"))))
     (build-system dune-build-system)
     (arguments
      `(#:tests? #f))
@@ -1376,16 +1378,16 @@ functions to the next and/or previous version.")
 (define-public ocaml-ppx-tools-versioned
   (package
     (name "ocaml-ppx-tools-versioned")
-    (version "5.2.1")
+    (version "5.2.3")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/ocaml-ppx/"
+              (uri (git-reference
-                                  "ppx_tools_versioned/archive/"
+                     (url "https://github.com/ocaml-ppx/ppx_tools_versioned")
-                                  version ".tar.gz"))
+                     (commit version)))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1x2xfjpkzbcz4rza1d7gh3ipliw6jqfcklbsln82v3561qgkqgmh"))))
+                "1hcmpnw26zf70a71r3d2c2c0mn8q084gdn1r36ynng6fv9hq6j0y"))))
     (build-system dune-build-system)
     (arguments
      `(#:test-target "."))
@@ -1435,7 +1437,7 @@ powerful.")
 (define-public ocaml-result
   (package
     (name "ocaml-result")
-    (version "1.3")
+    (version "1.4")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1444,7 +1446,7 @@ powerful.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "081ayblszn9pj2rqcif40x6cz2zda48vi45gy49rc2qfc4gszry3"))))
+                "0hir97k9i72nfkm6kncxnqpyk400wlsxysbldgcvk0fd9pjnsc3p"))))
     (build-system dune-build-system)
     (arguments
      `(#:test-target "."))
@@ -1798,7 +1800,7 @@ lets the client choose the concrete timeline.")
 (define-public ocaml-ssl
   (package
     (name "ocaml-ssl")
-    (version "0.5.7")
+    (version "0.5.9")
     (source
       (origin
         (method git-fetch)
@@ -1807,7 +1809,7 @@ lets the client choose the concrete timeline.")
               (commit version)))
         (file-name (git-file-name name version))
         (sha256 (base32
-                  "06zxqnwqkvf7pmj5s44jflkknv01czgbi4nbaac0ys1p7rv99y3x"))))
+                  "04h02rvzrwp886n5hsx84rnc9b150iggy38g5v1x1rwz3pkdnmf0"))))
     (build-system dune-build-system)
     (arguments
      `(#:test-target "."))
@@ -1868,15 +1870,16 @@ locks or other synchronization primitives.")
 (define-public ocaml-lwt-log
   (package
     (name "ocaml-lwt-log")
-    (version "1.1.0")
+    (version "1.1.1")
-    (source
+    (source (origin
-      (origin
+              (method git-fetch)
-        (method url-fetch)
+              (uri (git-reference
-        (uri (string-append "https://github.com/aantron/lwt_log/archive/" version
+                     (url "https://github.com/aantron/lwt_log")
-                            ".tar.gz"))
+                     (commit version)))
-        (file-name (string-append name "-" version ".tar.gz"))
+              (file-name (git-file-name name version))
-        (sha256 (base32
+              (sha256
-                  "1lr62j2266pbsi54xmzsfvl2z7fi7smhak7fp1ybl8hssxwi6in2"))))
+               (base32
+                "1n12i1rmn9cjn6p8yr6qn5dwbrwvym7ckr7bla04a1xnq8qlcyj7"))))
     (build-system dune-build-system)
     (arguments
      `(#:tests? #f; require lwt_ppx
@@ -2276,7 +2279,7 @@ many additional enhancements, including:
 (define-public ocaml-batteries
   (package
     (name "ocaml-batteries")
-    (version "2.9.0")
+    (version "2.10.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/ocaml-batteries-team/"
@@ -2284,7 +2287,7 @@ many additional enhancements, including:
                                   version "/batteries-" version ".tar.gz"))
               (sha256
                (base32
-                "0lkdmv2my5hirkswmci2cch341n6wkkj2q8apjhs83sg6528caxi"))))
+                "08ghw87d56h1a6y1nnh3x2wy9xj25jqfk5sp6ma9nsyd37babb0h"))))
     (build-system ocaml-build-system)
     (native-inputs
      `(("ocamlbuild" ,ocamlbuild)
@@ -2381,20 +2384,63 @@ language.")
 can match the question using a regular expression or a timeout.")
     (license license:lgpl2.1+))) ; with the OCaml static compilation exception
 
+(define-public ocaml-stdlib-shims
+  (package
+    (name "ocaml-stdlib-shims")
+    (version "0.1.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/ocaml/stdlib-shims")
+                     (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "007dwywsr5285z0np6a9nr0h8iqmyzfrlx6s5xaqcwj69zabsrjm"))))
+    (build-system dune-build-system)
+    (home-page "https://github.com/ocaml/stdlib-shims")
+    (synopsis "OCaml stdlib features backport to older OCaml compilers")
+    (description "This package backports some of the new stdlib features to
+older compilers, such as the Stdlib module.  This allows projects that require
+compatibility with older compiler to use these new features in their code.")
+    ;; with ocaml-linking exception
+    (license license:lgpl2.1+)))
+
 (define-public ocaml-fileutils
   (package
     (name "ocaml-fileutils")
-    (version "0.5.3")
+    (version "0.6.0")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (ocaml-forge-uri name version 1728))
+              (uri (git-reference
+                     (url "https://github.com/gildor478/ocaml-fileutils")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1rc4cqlvdhbs55i85zfbfhz938fsy4fj6kwlkfm3ra7bpwn8bmpd"))))
+                "06gxbqfssl16xc8y4d34wpm0mwfr0jgph4lmlwfmgazyggnmvc7m"))))
     (build-system ocaml-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'set-topfind
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; add the line #directory ".." at the top of each file
+             ;; using #use "topfind";; to be able to find topfind
+             (let* ((findlib-path (assoc-ref inputs "findlib"))
+                    (findlib-libdir
+                     (string-append findlib-path "/lib/ocaml/site-lib")))
+               (substitute* "setup.ml"
+                 (("#use \"topfind\";;" all)
+                  (string-append "#directory \"" findlib-libdir "\"\n"
+                                 all))))
+             #t)))))
+    (propagated-inputs
+     `(("ocaml-stdlib-shims" ,ocaml-stdlib-shims)))
     (native-inputs
      `(("ocamlbuild" ,ocamlbuild)
-       ("ounit" ,ocaml-ounit)))
+       ("ocaml-oasis" ,ocaml-oasis)
+       ("ocaml-ounit" ,ocaml-ounit)))
     (home-page "http://ocaml-fileutils.forge.ocamlcore.org")
     (synopsis "Pure OCaml functions to manipulate real file and filename")
     (description "Library to provide pure OCaml functions to manipulate real
@@ -2466,15 +2512,16 @@ from the oasis build log
 (define-public ocaml-cppo
   (package
     (name "ocaml-cppo")
-    (version "1.6.5")
+    (version "1.6.6")
     (source
       (origin
-        (method url-fetch)
+        (method git-fetch)
-        (uri (string-append "https://github.com/mjambon/cppo/archive/v" version
+        (uri (git-reference
-                            ".tar.gz"))
+               (url "https://github.com/mjambon/cppo")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
         (sha256 (base32
-                  "1dkm3d5h6h56y937gcdk2wixlpzl59vv5pmiafglr89p20kf7gqf"))
+                  "1smcc0l6fh2n0y6bp96c69j5nw755jja99w0b206wx3yb2m4w2hs"))))
-        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system dune-build-system)
     (arguments
      `(#:tests? #f
@@ -2706,19 +2753,28 @@ JSON.")
 (define-public ocaml-easy-format
   (package
     (name "ocaml-easy-format")
-    (version "1.3.1")
+    (version "1.3.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                      (url "https://github.com/mjambon/easy-format")
-                     (commit (string-append "v" version))))
+                     (commit version)))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0jfncci15b8sf1y72yrxfjlsmhs9aavcd14vwz4d7kj8k9w9c4qk"))))
+                "1fc95q2ypck6m6rv3kiawwilh5ac93v2hcp823mj608d5kj79xkb"))))
     (build-system dune-build-system)
     (arguments
-     `(#:jbuild? #t))
+     `(#:jbuild? #t
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'make-writable
+           (lambda _
+             (for-each
+               (lambda (file)
+                 (chmod file #o644))
+               (find-files "." "."))
+             #t)))))
     (home-page "https://github.com/mjambon/easy-format")
     (synopsis "Interface to the Format module")
     (description "Easy-format is a high-level and functional interface to the
@@ -2950,7 +3006,7 @@ the plugins facilitate extensibility, and the frontends serve as entry points.")
 (define-public ocaml-camomile
   (package
     (name "ocaml-camomile")
-    (version "1.0.1")
+    (version "1.0.2")
     (home-page "https://github.com/yoriyuki/Camomile")
     (source (origin
               (method url-fetch)
@@ -2958,18 +3014,19 @@ the plugins facilitate extensibility, and the frontends serve as entry points.")
                                   "/camomile-" version ".tbz"))
               (sha256
                (base32
-                "01ssjrqz41jvrqh27jxnh9cx7ywi9b5sgsykd00i7z9nrcwhlfy2"))))
+                "0chn7ldqb3wyf95yhmsxxq65cif56smgz1mhhc7m0dpwmyq1k97h"))))
     (build-system dune-build-system)
     (native-inputs
      `(("camlp4" ,camlp4)))
     (arguments
-     `(#:build-flags (list "--profile" "realease")
+     `(#:build-flags (list "--profile" "release")
        #:test-target "camomile-test"
+       #:tests? #f; Tests fail, see https://github.com/yoriyuki/Camomile/issues/82
        #:phases
        (modify-phases %standard-phases
          (add-before 'build 'fix-usr-share
            (lambda* (#:key outputs #:allow-other-keys)
-             (substitute* '("Camomile/jbuild" "configure.ml")
+             (substitute* '("Camomile/dune" "configure.ml")
                (("/usr/share") (string-append (assoc-ref outputs "out") "/share")))
              #t)))))
     (synopsis "Comprehensive Unicode library")
@@ -2980,10 +3037,34 @@ library is currently designed for Unicode Standard 3.2.")
     ;; with an exception for linked libraries to use a different license
     (license license:lgpl2.0+)))
 
+(define-public ocaml-charinfo-width
+  (package
+    (name "ocaml-charinfo-width")
+    (version "1.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri "https://bitbucket.org/zandoye/charinfo_width/get/1.1.0.tar.gz")
+              (sha256
+               (base32
+                "00bv4p1yqs8y0z4z07wd9w9yyv669dikp9b04dcjbwpiy2wy0086"))))
+    (build-system dune-build-system)
+    (propagated-inputs
+     `(("ocaml-result" ,ocaml-result)
+       ("ocaml-camomile" ,ocaml-camomile)))
+    (native-inputs
+     `(("ocaml-ppx-expect" ,ocaml-ppx-expect)))
+    (properties
+     `((upstream-name . "charInfo_width")))
+    (home-page "https://bitbucket.org/zandoye/charinfo_width/")
+    (synopsis "Determine column width for a character")
+    (description "This module is implements purely in OCaml a character width
+function that follows the prototype of POSIX's wcwidth.")
+    (license license:expat)))
+
 (define-public ocaml-zed
   (package
     (name "ocaml-zed")
-    (version "1.6")
+    (version "2.0.3")
     (source
      (origin
        (method git-fetch)
@@ -2992,14 +3073,15 @@ library is currently designed for Unicode Standard 3.2.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "00hhxcjf3bj3w2qm8nzs9x6vrqkadf4i0277s5whzy2rmiknj63v"))))
+        (base32 "0pa9awinqr0plp4b2az78dwpvh01pwaljnn5ydg8mc6hi7rmir55"))))
     (build-system dune-build-system)
     (arguments
      `(#:jbuild? #t
        #:test-target "."))
     (propagated-inputs
-     `(("camomile" ,ocaml-camomile)
+     `(("ocaml-camomile" ,ocaml-camomile)
-       ("react" ,ocaml-react)))
+       ("ocaml-charinfo-width" ,ocaml-charinfo-width)
+       ("ocaml-react" ,ocaml-react)))
     (home-page "https://github.com/diml/zed")
     (synopsis "Abstract engine for text editing in OCaml")
     (description "Zed is an abstract engine for text edition.  It can be used
@@ -3010,7 +3092,7 @@ connect an engine to your inputs and rendering functions to get an editor.")
 (define-public ocaml-lambda-term
   (package
     (name "ocaml-lambda-term")
-    (version "1.13")
+    (version "2.0.2")
     (source
      (origin
        (method git-fetch)
@@ -3019,7 +3101,7 @@ connect an engine to your inputs and rendering functions to get an editor.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0wwib20b2ir3h2g9zwhzn04cv160psb805skp8v23wqgyn5cnbh8"))))
+        (base32 "0zcjy6fvf0d3i2ssz96asl889n3r6bplyzk7xvb2s3dkxbgcisyy"))))
     (build-system dune-build-system)
     (arguments
      `(#:build-flags (list "--profile" "release")
@@ -3041,7 +3123,7 @@ instead of bindings to a C library.")
 (define-public ocaml-utop
   (package
     (name "ocaml-utop")
-    (version "2.3.0")
+    (version "2.4.1")
     (source
      (origin
        (method git-fetch)
@@ -3050,7 +3132,7 @@ instead of bindings to a C library.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0xvibb97vzzh7yabr5ajhilriwz8cg4c506lxq0bd7ss3aci9han"))))
+        (base32 "1jm3sagissbw8012mnppknsxl9dqd9514b891b64disqhdb5awg3"))))
     (build-system dune-build-system)
     (arguments
      `(#:jbuild? #t
@@ -3468,19 +3550,29 @@ than the first one.")
 (define-public ocaml-biniou
  (package
    (name "ocaml-biniou")
-   (version "1.2.0")
+   (version "1.2.1")
    (home-page "https://github.com/mjambon/biniou")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url (string-append home-page ".git"))
-             (commit (string-append "v" version))))
+             (commit version)))
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0mjpgwyfq2b2izjw0flmlpvdjgqpq8shs89hxj1np2r50csr8dcb"))))
+         "0x2kiy809n1j0yf32l7hj102y628jp5jdrkbi3z7ld8jq04h1790"))))
    (build-system dune-build-system)
+   (arguments
+    `(#:phases
+      (modify-phases %standard-phases
+        (add-before 'build 'make-writable
+          (lambda _
+            (for-each
+              (lambda (file)
+                (chmod file #o644))
+              (find-files "." "."))
+            #t)))))
    (inputs
     `(("ocaml-easy-format" ,ocaml-easy-format)))
    (native-inputs
@@ -4983,7 +5075,7 @@ the full Core is not available, such as in Javascript.")
 (define-public ocaml-markup
   (package
     (name "ocaml-markup")
-    (version "0.8.0")
+    (version "0.8.1")
     (home-page "https://github.com/aantron/markup.ml")
     (source
      (origin
@@ -4994,10 +5086,11 @@ the full Core is not available, such as in Javascript.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0aif4abvfmi9xc1pvw5n5rbm6rzkkpsxyvdn0lanr33rjpvkwdlm"))))
+         "0gzdjfnkv56vhmpvi9xpv1p05z50y55izhn156bkmb35s6izxds3"))))
     (build-system dune-build-system)
-    (inputs
+    (propagated-inputs
-     `(("ocaml-uchar" ,ocaml-uchar)
+     `(("ocaml-bisect-ppx" ,ocaml-bisect-ppx)
+       ("ocaml-uchar" ,ocaml-uchar)
        ("ocaml-uutf" ,ocaml-uutf)
        ("ocaml-lwt" ,ocaml-lwt)))
     (native-inputs `(("ocaml-ounit" ,ocaml-ounit)))
@@ -5072,10 +5165,22 @@ combinators.")
         (base32
          "1vp3qvrkz7q25nbmvd40vhsnz2k9aqh17bnd21i3q8q0xlr5hdag"))))
     (build-system dune-build-system)
-    (inputs
+    (propagated-inputs
      `(("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
        ("ocaml-ppx-tools-versioned" ,ocaml-ppx-tools-versioned)
        ("ocaml-ounit" ,ocaml-ounit)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'fix-deprecated
+           (lambda _
+             ;; Fixed upstream in 22dd1ad9a0c9629f60599c22d82c6488394d6d32, but
+             ;; not in a release yet.
+             (substitute* "src/ppx/instrument.ml"
+               (("module Ast = Ast_405")
+                "module Ast = Migrate_parsetree.Ast_405
+module Ast_405 = Ast"))
+             #t)))))
     (home-page "https://github.com/aantron/bisect_ppx")
     (synopsis "Code coverage for OCaml")
     (description "Bisect_ppx helps you test thoroughly.  It is a small
@@ -5090,7 +5195,7 @@ then run the Bisect_ppx report tool on the generated visitation files.")
 (define-public ocaml-odoc
   (package
     (name "ocaml-odoc")
-    (version "1.4.0")
+    (version "1.4.1")
     (source
      (origin
        (method git-fetch)
@@ -5100,7 +5205,7 @@ then run the Bisect_ppx report tool on the generated visitation files.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0br11cw6wa0mwafja4xdb45d2f8908l6nzdq5mw5lbfq2jnp68km"))))
+         "1i2j0krbzvb1n3dcic9h1pyyqxmf051ky82nrcyzx1nwqjb8zfh6"))))
     (build-system dune-build-system)
     (inputs
      `(("ocaml-alcotest" ,ocaml-alcotest)

gnu/packages/package-management.scm

@@ -544,7 +544,7 @@ transactions from C or Python.")
     (license license:gpl2+)))
 
 (define-public diffoscope
-  (let ((version "121"))
+  (let ((version "122"))
     (package
       (name "diffoscope")
       (version version)
@@ -556,7 +556,7 @@ transactions from C or Python.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1bw7s8qs1vnr93vhifl6pj6h6w6r6nrpc5anzhh9wx2gcaipkb3m"))))
+                  "1pwddknk8qyv88ba63why8vbnlc14b47434lv4ijx49m7ya3zfvg"))))
       (build-system python-build-system)
       (arguments
        `(#:phases (modify-phases %standard-phases
@@ -963,7 +963,7 @@ for packaging and deployment of cross-compiled Windows applications.")
 (define-public libostree
   (package
     (name "libostree")
-    (version "2018.9.1")
+    (version "2019.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -971,7 +971,7 @@ for packaging and deployment of cross-compiled Windows applications.")
                     (version-major+minor version) "/libostree-" version ".tar.xz"))
               (sha256
                (base32
-                "01mygpkbl9sk2vr3hjbpih6qlg8lwx0q5lklm09f7jfwfpnwyqzj"))))
+                "1r07yqbc9iiq0lzv1pryppd35fv695ym8r040msbfc93pmiy77y0"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -983,6 +983,7 @@ for packaging and deployment of cross-compiled Windows applications.")
              (setenv "TEST_TMPDIR" (getenv "TMPDIR"))
              #t)))
        ;; XXX: fails with:
+       ;;     tap-driver.sh: missing test plan
        ;;     tap-driver.sh: internal error getting exit status
        ;;     tap-driver.sh: fatal: I/O or internal error
        #:tests? #f))

gnu/packages/patches/twinkle-include-qregexpvalidator.patch

@@ -1,123 +0,0 @@
-Copied from upstream:
-
-https://github.com/LubosD/twinkle/commit/4b42755619011c117a76bdf98e417ebedc47e319
-
-From 4b42755619011c117a76bdf98e417ebedc47e319 Mon Sep 17 00:00:00 2001
-From: Michal Kubecek <mkubecek@suse.cz>
-Date: Wed, 6 Jun 2018 10:07:21 +0200
-Subject: [PATCH] Include <QRegExpValidator> explicitly
-
-Since Qt 5.11, generated ui_getprofilename.h no longer includes QHeaderView
-which breaks the chain that included qvalidator.h in getprofilename.cpp.
-As it feels rather fragile to rely on such indirect includes, let's include
-<QRegExpValidator> explicitly in each file using QRegExpValidator class.
----
- src/gui/diamondcardprofileform.cpp | 1 +
- src/gui/getprofilenameform.cpp     | 2 +-
- src/gui/inviteform.cpp             | 1 +
- src/gui/mphoneform.cpp             | 1 +
- src/gui/numberconversionform.cpp   | 1 +
- src/gui/syssettingsform.cpp        | 1 +
- src/gui/userprofileform.cpp        | 1 +
- src/gui/wizardform.cpp             | 1 +
- 8 files changed, 8 insertions(+), 1 deletion(-)
-
-diff --git a/src/gui/diamondcardprofileform.cpp b/src/gui/diamondcardprofileform.cpp
-index 6656909..517180b 100644
---- a/src/gui/diamondcardprofileform.cpp
-+++ b/src/gui/diamondcardprofileform.cpp
-@@ -21,6 +21,7 @@
- 
- #include <QRegExp>
- #include <QValidator>
-+#include <QRegExpValidator>
- #include "gui.h"
- #include "diamondcard.h"
- #include "getprofilenameform.h"
-diff --git a/src/gui/getprofilenameform.cpp b/src/gui/getprofilenameform.cpp
-index 1319e1d..89c715e 100644
---- a/src/gui/getprofilenameform.cpp
-+++ b/src/gui/getprofilenameform.cpp
-@@ -1,7 +1,7 @@
- #include "getprofilenameform.h"
--
- #include <QDir>
- #include <QMessageBox>
-+#include <QRegExpValidator>
- #include "user.h"
- #include "protocol.h"
- 
-diff --git a/src/gui/inviteform.cpp b/src/gui/inviteform.cpp
-index 433fb22..2a5b68d 100644
---- a/src/gui/inviteform.cpp
-+++ b/src/gui/inviteform.cpp
-@@ -7,6 +7,7 @@
- #include "sys_settings.h"
- #include <QRegExp>
- #include <QValidator>
-+#include <QRegExpValidator>
- 
- /*
-     Copyright (C) 2005-2009  Michel de Boer <michel@twinklephone.com>
-diff --git a/src/gui/mphoneform.cpp b/src/gui/mphoneform.cpp
-index 260fda7..c4e3c1d 100644
---- a/src/gui/mphoneform.cpp
-+++ b/src/gui/mphoneform.cpp
-@@ -54,6 +54,7 @@
- #include <QRegExp>
- #include <QValidator>
- #include <QSettings>
-+#include <QRegExpValidator>
- #include "buddyform.h"
- #include "diamondcardprofileform.h"
- #include "osd.h"
-diff --git a/src/gui/numberconversionform.cpp b/src/gui/numberconversionform.cpp
-index f8ae64c..8481a9b 100644
---- a/src/gui/numberconversionform.cpp
-+++ b/src/gui/numberconversionform.cpp
-@@ -1,5 +1,6 @@
- #include "numberconversionform.h"
- 
-+#include <QRegExpValidator>
- #include "gui.h"
- 
- /*
-diff --git a/src/gui/syssettingsform.cpp b/src/gui/syssettingsform.cpp
-index 216af54..355df59 100644
---- a/src/gui/syssettingsform.cpp
-+++ b/src/gui/syssettingsform.cpp
-@@ -28,6 +28,7 @@
- #include "twinkle_config.h"
- #include <QRegExp>
- #include <QValidator>
-+#include <QRegExpValidator>
- #include "syssettingsform.h"
- /*
-  *  Constructs a SysSettingsForm as a child of 'parent', with the
-diff --git a/src/gui/userprofileform.cpp b/src/gui/userprofileform.cpp
-index 28700a6..9ed9209 100644
---- a/src/gui/userprofileform.cpp
-+++ b/src/gui/userprofileform.cpp
-@@ -31,6 +31,7 @@
- #include <QStringList>
- #include "twinkle_config.h"
- #include <QListWidget>
-+#include <QRegExpValidator>
- #include "numberconversionform.h"
- #include "util.h"
- #include "userprofileform.h"
-diff --git a/src/gui/wizardform.cpp b/src/gui/wizardform.cpp
-index 777aa12..f925875 100644
---- a/src/gui/wizardform.cpp
-+++ b/src/gui/wizardform.cpp
-@@ -23,6 +23,7 @@
- #include <QTextStream>
- #include "gui.h"
- #include <QFile>
-+#include <QRegExpValidator>
- #include "wizardform.h"
- 
- #define PROV_NONE	QT_TRANSLATE_NOOP("WizardForm", "None (direct IP to IP calls)")
--- 
-2.17.0
-

gnu/packages/patches/xfce4-session-fix-xflock4.patch

@@ -1,31 +0,0 @@
-From cbb9c769316b4d32956a2c78aa01a38b473f0cfc Mon Sep 17 00:00:00 2001
-From: David Thompson <dthompson2@worcester.edu>
-Date: Fri, 30 Oct 2015 08:30:43 -0400
-Subject: [PATCH] xflock4: Do not override PATH with hardcoded value.
-
-The PATH "/bin:/usr/bin" may not be a valid search path on the user's
-machine.  The screen locking program may be in /usr/local/bin or
-elsewhere.  Distros that do not conform to the FHS, such as GuixSD and
-NixOS, will not have their executables in either location.  Thus, we
-simply leave PATH alone.
----
- scripts/xflock4 | 3 ---
- 1 file changed, 3 deletions(-)
-
-diff --git a/scripts/xflock4 b/scripts/xflock4
-index ec4d05d..e7981ac 100644
---- a/scripts/xflock4
-+++ b/scripts/xflock4
-@@ -21,9 +21,6 @@
- #  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- #
- 
--PATH=/bin:/usr/bin
--export PATH
--
- # Lock by xscreensaver or gnome-screensaver, if a respective daemon is running
- for lock_cmd in \
-     "xscreensaver-command -lock" \
--- 
-2.5.0
-

gnu/packages/photo.scm

@@ -70,14 +70,14 @@
 (define-public libraw
   (package
     (name "libraw")
-    (version "0.19.4")
+    (version "0.19.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.libraw.org/data/LibRaw-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "07wnzw9k3mwdq9dmpmg94al3ksc065kskfbxkknnmhvrsv2iri8k"))))
+                "1x827sh6vl8j3ll2ihkcr234y07f31hi1v7sl08jfw3irkbn58j0"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))

gnu/packages/php.scm

@@ -364,7 +364,7 @@
        ("libxpm" ,libxpm)
        ("libxslt" ,libxslt)
        ("libx11" ,libx11)
-       ("oniguruma" ,oniguruma-5)
+       ("oniguruma" ,oniguruma)
        ("openldap" ,openldap)
        ("openssl" ,openssl)
        ("pcre" ,pcre2)

gnu/packages/python-xyz.scm

@@ -4081,14 +4081,14 @@ operators such as union, intersection, and difference.")
 (define-public python-scipy
   (package
     (name "python-scipy")
-    (version "1.2.2")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "scipy" version))
        (sha256
         (base32
-         "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))
+         "1df113c9i6vazsn6y3n9wc22jh737z1g7dmx3mypkdwpdnscyhr6"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-numpy" ,python-numpy)
@@ -4184,9 +4184,19 @@ routines such as routines for numerical integration and optimization.")
     (properties `((python2-variant . ,(delay python2-scipy))))
     (license license:bsd-3)))
 
+;; Version 1.2.2 is the last version to support Python 2
 (define-public python2-scipy
-  (package-with-python2
+  (package
+    (inherit (package-with-python2
               (strip-python2-variant python-scipy)))
+    (version "1.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "scipy" version))
+       (sha256
+        (base32
+         "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
 
 (define-public python-socksipy-branch
   (package
@@ -14676,14 +14686,13 @@ working with iterables.")
 (define-public python-pybtex
   (package
     (name "python-pybtex")
-    (version "0.21")
+    (version "0.22.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pybtex" version))
        (sha256
-        (base32
+        (base32 "070wfcmxrd7xg1si421mi9150gmx2qwx431nwf69sq3hhmgnx080"))))
-         "00300j8dn5pxq4ndxmfmbmycg2znawkqs49val2x6jlmfiy6r2mg"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-nose" ,python-nose)))

gnu/packages/qt.scm

@@ -2219,6 +2219,12 @@ time Web content can be enhanced with native controls.")
     ;; Building QtWebKit takes around 13 hours on an AArch64 machine.  Give some
     ;; room for slower or busy hardware.
     (properties '((timeout . 64800)))   ;18 hours
+
+    ;; XXX: This consumes too much RAM to successfully build on AArch64 (e.g.,
+    ;; SoftIron OverDrive with 8 GiB of RAM), so instead of wasting resources,
+    ;; disable it on non-Intel platforms.
+    (supported-systems '("x86_64-linux" "i686-linux"))
+
     (license license:lgpl2.1+)))
 
 (define-public dotherside

gnu/packages/rust.scm

@@ -1070,7 +1070,7 @@ jemalloc = \"" jemalloc "/lib/libjemalloc_pic.a" "\"
                    (("bins::check") "//bins::check"))
                  #t)))))))))
 
-(define-public rust
+(define-public rust-1.36
   (let ((base-rust
          (rust-bootstrapped-package rust-1.35 "1.36.0"
            "06xv2p6zq03lidr0yaf029ii8wnjjqa894nkmrm6s0rx47by9i04")))
@@ -1081,3 +1081,20 @@ jemalloc = \"" jemalloc "/lib/libjemalloc_pic.a" "\"
          ((#:phases phases)
           `(modify-phases ,phases
              (delete 'patch-process-docs-rev-cmd))))))))
+
+(define-public rust
+  (let ((base-rust
+         (rust-bootstrapped-package rust-1.36 "1.37.0"
+           "1hrqprybhkhs6d9b5pjskfnc5z9v2l2gync7nb39qjb5s0h703hj")))
+    (package
+      (inherit base-rust)
+      (arguments
+       (substitute-keyword-arguments (package-arguments base-rust)
+         ((#:phases phases)
+          `(modify-phases ,phases
+             (add-before 'configure 'configure-cargo-home
+               (lambda _
+                 (let ((cargo-home (string-append (getcwd) "/.cargo")))
+                   (mkdir-p cargo-home)
+                   (setenv "CARGO_HOME" cargo-home)
+                   #t))))))))))

gnu/packages/samba.scm

@@ -154,14 +154,14 @@ anywhere.")
 (define-public samba
   (package
     (name "samba")
-    (version "4.10.6")
+    (version "4.10.8")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://download.samba.org/pub/samba/stable/"
                                  "samba-" version ".tar.gz"))
              (sha256
               (base32
-               "0hpgdqlyczj98pkh2ldglvvnkrb1q541r3qikdvxq0qjvd9fpywy"))))
+               "1x0hlhb674fndfkmimjicnzs543n3i8465a5ifcmjwvzavxha7y4"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -245,14 +245,14 @@ Desktops into Active Directory environments using the winbind daemon.")
 (define-public talloc
   (package
     (name "talloc")
-    (version "2.2.0")
+    (version "2.3.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.samba.org/ftp/talloc/talloc-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1g1fqa37xkjp9lp6lrwxrbfgashcink769ll505zvcwnxx2nlvsw"))))
+                "1iigk4a7n9k9qqq0h3a5vah67ycpqzvahvdhzy15lm428jrvrmbm"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -312,14 +312,14 @@ destructors.  It is the core memory allocator used in Samba.")
 (define-public tevent
   (package
     (name "tevent")
-    (version "0.10.0")
+    (version "0.10.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.samba.org/ftp/tevent/tevent-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1rm4d9245ya15wyrh9vqn1dnz14l2ic88mr46ykyc6kdrl99dwrk"))))
+                "1dhhd7fz6wyvlwrk1a6gj5m2mcjsc3ilx0mcv1qsr1lbndldm93r"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases

gnu/packages/statistics.scm

@@ -53,7 +53,7 @@
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages glib)
-  #:use-module (gnu packages haskell)
+  #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages image)
   #:use-module (gnu packages java)
@@ -1828,13 +1828,13 @@ and density estimation.")
 (define-public r-chron
   (package
     (name "r-chron")
-    (version "2.3-53")
+    (version "2.3-54")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "chron" version))
               (sha256
                (base32
-                "02bkywwsxwrxc035hv51dxgdm1fjxdm7dn19ivifln59dfs1862j"))))
+                "0vc7dxqwx0jqzwszax6di3091npsxnhnbvr7sy7rlip0jqzarwqd"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/chron")
     (synopsis "Chronological R objects which can handle dates and times")
@@ -2097,13 +2097,13 @@ previous R versions and their release dates.")
 (define-public r-whisker
   (package
     (name "r-whisker")
-    (version "0.3-2")
+    (version "0.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "whisker" version))
               (sha256
                (base32
-                "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
+                "1a7vz0dk95xfjvi38wbpw8vmf5qn3g8p490msz2rw0piwidmk1ks"))))
     (build-system r-build-system)
     (home-page "https://github.com/edwindj/whisker")
     (synopsis "Logicless mustache templating for R")
@@ -2490,14 +2490,14 @@ were originally a part of the r-devtools package.")
 (define-public r-hms
   (package
     (name "r-hms")
-    (version "0.5.0")
+    (version "0.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hms" version))
        (sha256
         (base32
-         "06snfqdczr0x0nbp7qnvwhlp2pw0wx9c2y3xb4gr1wrvbik74y58"))))
+         "1v4cxfpvp85la4gqla6b4q2bwx4jv1fxqwndcnjsibbnybz6wcvd"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rlang" ,r-rlang)
@@ -2696,14 +2696,14 @@ certain criterion, e.g., it contains a certain regular file.")
 (define-public r-rmarkdown
   (package
     (name "r-rmarkdown")
-    (version "1.14")
+    (version "1.15")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "rmarkdown" version))
         (sha256
           (base32
-            "0qfw5rkvwqpgix32g6qy9xrr50awmm146aqbm836xravih2b2dpn"))))
+            "0fkfzxkvakc6bb1s2lx7sxmnfff8q1m9isihynhiyqh4x8yikcmw"))))
     (properties `((upstream-name . "rmarkdown")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5028,14 +5028,14 @@ VGLMs can be loosely thought of as multivariate generalised linear models.")
 (define-public r-pbapply
   (package
     (name "r-pbapply")
-    (version "1.4-1")
+    (version "1.4-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pbapply" version))
        (sha256
         (base32
-         "1bbws9n90cqnnp5k58hp852jwmm6513jnhn4vzhl9f8x314k6qxk"))))
+         "1xmk4p006v8gij26rs6kp5prjyf2n32nqjxiyp8a6kvgyc4z46dc"))))
     (build-system r-build-system)
     (home-page "https://github.com/psolymos/pbapply")
     (synopsis "Adding progress bar to apply functions")

gnu/packages/sync.scm

@@ -264,19 +264,19 @@ over the Internet in an HTTP and CDN friendly way;
 (define-public rclone
   (package
     (name "rclone")
-    (version "1.48.0")
+    (version "1.49.1")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://github.com/ncw/rclone/releases/download/v"
+       (uri (string-append "https://github.com/rclone/rclone/releases/download/"
-                           version "/rclone-v" version ".tar.gz"))
+                           "v" version "/rclone-v" version ".tar.gz"))
        (sha256
-        (base32 "1r03rlsk0qpya1fl8xfhj5inccjywf2cqgkd8r6wfhf3w2qd1zlc"))))
+        (base32 "1d0qvj7fn5bx3zqlf6hzn1922nrmy4x341n760m1b6h9az32mc5x"))))
     ;; FIXME: Rclone bundles some libraries Guix already provides.  Need to
     ;; un-bundle them.
     (build-system go-build-system)
     (arguments
-     '(#:import-path "github.com/ncw/rclone"
+     '(#:import-path "github.com/rclone/rclone"
        #:install-source? #f))
     (synopsis "@code{rsync} for cloud storage")
     (description "@code{Rclone} is a command line program to sync files and

gnu/packages/syncthing.scm

@@ -30,7 +30,7 @@
 (define-public syncthing
   (package
     (name "syncthing")
-    (version "1.2.1")
+    (version "1.2.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/syncthing/syncthing"
@@ -38,7 +38,7 @@
                                   "/syncthing-source-v" version ".tar.gz"))
               (sha256
                (base32
-                "1b6fidpkwfa2bm6hlv4p0bzxa1ha6s88vajczhryhqi5vjfxafri"))
+                "1wdjh8xw09s1nfkpc95v04619gqa4dpbygp2y5l35ww4g916lv3s"))
               (modules '((guix build utils)))
               ;; Delete bundled ("vendored") free software source code.
               (snippet '(begin
@@ -55,7 +55,6 @@
      `(("go-github-com-audriusbutkevicius-go-nat-pmp"
         ,go-github-com-audriusbutkevicius-go-nat-pmp)
        ("go-github-com-bkaradzic-go-lz4" ,go-github-com-bkaradzic-go-lz4)
-       ("go-github-com-calmh-du" ,go-github-com-calmh-du)
        ("go-github-com-calmh-xdr" ,go-github-com-calmh-xdr)
        ("go-github-com-chmduquesne-rollinghash"
         ,go-github-com-chmduquesne-rollinghash)
@@ -84,6 +83,7 @@
         ,go-github-com-gogo-protobuf-protoc-gen-gogo)
        ("go-github-com-prometheus-client-golang-prometheus"
         ,go-github-com-prometheus-client-golang-prometheus)
+       ("go-github-com-shirou-gopsutil" ,go-github-com-shirou-gopsutil)
        ("go-golang-org-x-net-bpf" ,go-golang-org-x-net-bpf)
        ("go-golang-org-x-net-internal-iana" ,go-golang-org-x-net-internal-iana)
        ("go-golang-org-x-net-internal-socket"

gnu/packages/telephony.scm

@@ -491,22 +491,18 @@ Mumble consists of two applications for separate usage:
                    license:bsd-2))))
 
 (define-public twinkle
-  (let ((commit "02e1d1538af3337134bd7381dcd95f8d7775b30f")
-        (revision "1"))
   (package
     (name "twinkle")
-   (version (git-version "1.10.1" revision commit))
+    (version "1.10.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/LubosD/twinkle")
-                   (commit commit)))
+                    (commit (string-append "v" version))))
-             (patches
-              (search-patches "twinkle-include-qregexpvalidator.patch"))
               (file-name (git-file-name name version))
               (sha256
                (base32
-               "0ds4rp4vr1wagn4m4m7ldqbsx5vgmgbfcqqgyhn1wf6s1dm0020z"))))
+                "0s0gi03xwvzp02ah4q6j33r9jx9nbayr6dxlg2ck9pwbay1nq1hx"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                                ; no test target
@@ -551,7 +547,7 @@ Mumble consists of two applications for separate usage:
 messaging communcations using the SIP protocol.  You can use it for direct IP
 phone to IP phone communication or in a network using a SIP proxy to route your
 calls and messages")
-   (license license:gpl2+))))
+    (license license:gpl2+)))
 
 (define-public pjproject
   (package

gnu/packages/terminals.scm

@@ -955,7 +955,7 @@ tmux.")
 (define-public kitty
   (package
     (name "kitty")
-    (version "0.14.3")
+    (version "0.14.4")
     (home-page "https://sw.kovidgoyal.net/kitty/")
     (source
      (origin
@@ -966,7 +966,7 @@ tmux.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0wi6b6b1nyp16rcpcghk6by62wy6qsamv1xdymyn0zbqgd8h9n6b"))
+         "0z0y80wcbra3zfyaiim98afbqlfpkjkql430zfb8shx61rzzmn9i"))
        (modules '((guix build utils)))
        (snippet
         '(begin

gnu/packages/tex.scm

@@ -2885,19 +2885,31 @@ documents.  It comprises the packages color, graphics, graphicx, trig, epsfig,
 keyval, and lscape.")
     (license license:lppl1.3c+)))
 
-(define-public texlive-latex-xcolor
+(define-public texlive-xcolor
-  (package
+  (let ((template (simple-texlive-package
-    (name "texlive-latex-xcolor")
+                   "texlive-xcolor"
-    (version (number->string %texlive-revision))
+                   (list "/doc/latex/xcolor/"
-    (source (origin
+                         "/source/latex/xcolor/")
-              (method svn-fetch)
-              (uri (texlive-ref "latex" "xcolor"))
-              (file-name (string-append name "-" version "-checkout"))
-              (sha256
                    (base32
-                "01n613s7bcrd2n4jfawm0k4nn2ny3aaifp2jjfif3lz4sbv31494"))))
+                    "12q6spmpxg30alhvarjmxzigmz7lazapbrb0mc4vhbn6n1sdz7pp"))))
-    (build-system texlive-build-system)
+    (package
-    (arguments '(#:tex-directory "latex/xcolor"))
+      (inherit template)
+      (arguments
+       (substitute-keyword-arguments (package-arguments template)
+         ((#:tex-directory _ #t)
+          "latex/xcolor")
+         ((#:phases phases)
+          `(modify-phases ,phases
+             (add-after 'unpack 'chdir
+               (lambda _ (chdir "source/latex/xcolor") #t))
+             (add-after 'install 'move-files
+               (lambda* (#:key outputs #:allow-other-keys)
+                 (let ((share (string-append (assoc-ref outputs "out")
+                                             "/share/texmf-dist")))
+                   (mkdir-p (string-append share "/dvips/xcolor"))
+                   (rename-file (string-append share "/tex/latex/xcolor/xcolor.pro")
+                                (string-append share "/dvips/xcolor/xcolor.pro"))
+                   #t)))))))
       (home-page "https://www.ctan.org/pkg/xcolor")
       (synopsis "Driver-independent color extensions for LaTeX and pdfLaTeX")
       (description
@@ -2908,7 +2920,10 @@ document-wide target color model and offers complete tools for conversion
 between eight color models.  Additionally, there is a command for alternating
 row colors plus repeated non-aligned material (like horizontal lines) in
 tables.")
-    (license license:lppl1.2+)))
+      (license license:lppl1.2+))))
+
+(define-public texlive-latex-xcolor
+  (deprecated-package "texlive-latex-xcolor" texlive-xcolor))
 
 (define-public texlive-latex-hyperref
   (package
@@ -3969,31 +3984,6 @@ with a user specified LaTeX construction, properly aligned, scaled, and/or
 rotated.")
     (license (license:fsf-free "file://psfrag.dtx"))))
 
-(define-public texlive-latex-xkeyval
-  (package
-    (name "texlive-latex-xkeyval")
-    (version (number->string %texlive-revision))
-    (source (origin
-              (method svn-fetch)
-              (uri (texlive-ref "latex" "xkeyval"))
-              (file-name (string-append name "-" version "-checkout"))
-              (sha256
-               (base32
-                "0wancavix39j240pd8m9cgmwsijwx6jd6n54v8wg0x2rk5m44myp"))))
-    (build-system texlive-build-system)
-    (arguments '(#:tex-directory "latex/xkeyval"))
-    (home-page "https://www.ctan.org/pkg/xkeyval")
-    (synopsis "Macros for defining and setting keys")
-    (description
-     "This package is an extension of the @code{keyval} package and offers
-more flexible macros for defining and setting keys.  The package provides a
-pointer and a preset system.  Furthermore, it supplies macros to allow class
-and package options to contain options of the @code{key=value} form.  A LaTeX
-kernel patch is provided to avoid premature expansions of macros in class or
-package options.  A specialized system for setting @code{PSTricks} keys is
-provided by the @code{pst-xkey} package.")
-    (license license:lppl1.3+)))
-
 (define-public texlive-pstool
   (package
     (inherit (simple-texlive-package
@@ -7063,3 +7053,319 @@ the file to which it applies.")
      "This package helps LaTeX users to create PDF/X, PFD/A and other
 standards-compliant PDF documents with pdfTeX, LuaTeX and XeTeX.")
     (license license:lppl1.2+)))
+
+(define-public texlive-ydoc
+  (let ((template (simple-texlive-package
+                   "texlive-ydoc"
+                   (list "/doc/latex/ydoc/"
+                         "/source/latex/ydoc/")
+                   (base32
+                    "0ckcpy1b8v1fk3qc8qkxgiag2wc0qzxm6bgksv000m4m1hsi2g8b")
+                   #:trivial? #f)))
+    (package
+      (inherit template)
+      (outputs '("out" "doc"))
+      (arguments
+       (substitute-keyword-arguments (package-arguments template)
+         ((#:tex-directory _ #t)
+          "latex/ydoc")
+         ((#:build-targets _ #t)
+          ''("ydoc.dtx"))
+         ((#:phases phases)
+          `(modify-phases ,phases
+             (add-after 'unpack 'chdir
+               (lambda _ (chdir "source/latex/ydoc") #t))
+             (add-after 'copy-files 'move-files
+               (lambda* (#:key outputs #:allow-other-keys)
+                 (let* ((share (string-append (assoc-ref outputs "out")
+                                              "/share/texmf-dist"))
+                        (target (string-append share "/tex/generic/ydoc"))
+                        (doc (string-append (assoc-ref outputs "doc")
+                                            "/share/texmf-dist/doc") ))
+                   (mkdir-p target)
+                   (for-each
+                    (lambda (file)
+                      (rename-file (string-append share "/tex/latex/ydoc/" file)
+                                   (string-append target "/" file)))
+                    '("ydocincl.tex" "ydocstrip.tex"))
+                   (mkdir-p doc)
+                   (rename-file (string-append share "/doc") doc)
+                   #t)))))))
+      (home-page "http://www.ctan.org/pkg/ydoc")
+      (synopsis "Macros for documentation of LaTeX classes and packages")
+      (description "The package provides macros and environments to document
+LaTeX packages and classes.  It is an (as yet unfinished) alternative to the
+@code{ltxdoc} class and the @code{doc} or @code{xdoc} packages.  The aim is to
+provide a different layout and more modern styles (using the @code{xcolor},
+@code{hyperref} packages, etc.)  This is an alpha release, and should probably
+not (yet) be used with other packages, since the implementation might
+change.")
+      (license license:lppl1.3+))))
+
+(define-public texlive-pstricks
+  (let ((template (simple-texlive-package
+                   "texlive-pstricks"
+                   (list "/doc/generic/pstricks/"
+                         "/dvips/pstricks/"
+                         "/tex/generic/pstricks/"
+                         "/tex/latex/pstricks/")
+                   (base32
+                    "04566354c77claxl1sznc490cda0m5gaa5ck6ms4q7mm44rj3rzk")
+                   #:trivial? #t)))
+    (package
+      (inherit template)
+      (arguments
+       (substitute-keyword-arguments (package-arguments template)
+         ((#:phases phases)
+          `(modify-phases ,phases
+             (delete 'reset-gzip-timestamps)))))
+      (home-page "http://www.ctan.org/pkg/pstricks")
+      (synopsis "PostScript macros for TeX")
+      (description "PSTricks offers an extensive collection of macros for
+generating PostScript that is usable with most TeX macro formats, including
+Plain TeX, LaTeX, AMS-TeX, and AMS-LaTeX.  Included are macros for colour,
+graphics, pie charts, rotation, trees and overlays.  It has many special
+features, including a wide variety of graphics (picture drawing) macros, with
+a flexible interface and with colour support.  There are macros for colouring
+or shading the cells of tables.")
+      (license license:lppl1.3+))))
+
+(define-public texlive-pst-text
+  (let ((template (simple-texlive-package
+                   "texlive-pst-text"
+                   (list "/doc/generic/pst-text/"
+                         "/source/generic/pst-text/Makefile"
+                         "/dvips/pst-text/pst-text.pro"
+                         "/tex/generic/pst-text/"
+                         "/tex/latex/pst-text/")
+                   (base32
+                    "0s2bbkdfy0shqrrkjflrn0x0pnvxzbdc38pjbdfw46wnmnxrnasm")
+                   #:trivial? #t)))
+    (package
+      (inherit template)
+      (propagated-inputs
+       `(("texlive-pstricks" ,texlive-pstricks)))
+      (home-page "http://www.ctan.org/pkg/pst-text")
+      (synopsis "Text and character manipulation in PSTricks")
+      (description "Pst-text is a PSTricks based package for plotting text along
+a different path and manipulating characters.  It includes the functionality
+of the old package @code{pst-char}.")
+      (license license:lppl))))
+
+(define-public texlive-iftex
+  (let ((template (simple-texlive-package
+                   "texlive-iftex"
+                   (list "/doc/generic/iftex/"
+                         "/tex/generic/iftex/iftex.sty")
+                   (base32
+                    "089zvw31gby150n1k0zdk2c0q97pgbqs46phxydaqil64b55nnl7")
+                   #:trivial? #t)))
+    (package
+      (inherit template)
+      (home-page "http://www.ctan.org/pkg/iftex")
+      (synopsis "Determine the currently used TeX engine")
+      (description "This package, which works both for Plain TeX and for
+LaTeX, defines the @code{\\ifPDFTeX}, @code{\\ifXeTeX}, and @code{\\ifLuaTeX}
+conditionals for testing which engine is being used for typesetting.  The
+package also provides the @code{\\RequirePDFTeX}, @code{\\RequireXeTeX}, and
+@code{\\RequireLuaTeX} commands which throw an error if pdfTeX, XeTeX or
+LuaTeX (respectively) is not the engine in use.")
+      (license license:lppl1.3+))))
+
+(define-public texlive-tools
+  (let ((template (simple-texlive-package
+                   "texlive-tools"
+                   (list "/doc/latex/tools/"
+                         "/source/latex/tools/")
+                   (base32
+                    "0v3zqcpy0w5bzy1xdcv1wnxbmxrn1j6x03h3y2af7qmjggph2a09"))))
+    (package
+      (inherit template)
+      (arguments
+       (substitute-keyword-arguments (package-arguments template)
+         ((#:tex-directory _ '())
+          "latex/tools")
+         ((#:build-targets _ '())
+          ''("tools.ins"))
+         ((#:phases phases)
+          `(modify-phases ,phases
+             (add-after 'unpack 'chdir
+               (lambda _ (chdir "source/latex/tools") #t))))))
+      (home-page "https://www.ctan.org/tex-archive/macros/latex/required/tools/")
+      (synopsis "LaTeX standard tools bundle")
+      (description "This package provides a collection of simple tools that
+are part of the LaTeX required tools distribution, comprising the packages:
+@code{afterpage}, @code{array}, @code{bm}, @code{calc}, @code{dcolumn},
+@code{delarray}, @code{enumerate}, @code{fileerr}, @code{fontsmpl},
+@code{ftnright}, @code{hhline}, @code{indentfirst}, @code{layout},
+@code{longtable}, @code{multicol}, @code{rawfonts}, @code{showkeys},
+@code{somedefs}, @code{tabularx}, @code{theorem}, @code{trace},
+@code{varioref}, @code{verbatim}, @code{xr}, and @code{xspace}.")
+      (license license:lppl1.3+))))
+
+(define-public texlive-latex-xkeyval
+  (package
+    (name "texlive-latex-xkeyval")
+    (version (number->string %texlive-revision))
+    (source (origin
+              (method svn-fetch)
+              (uri (texlive-ref "latex" "xkeyval"))
+              (sha256
+               (base32
+                "0wancavix39j240pd8m9cgmwsijwx6jd6n54v8wg0x2rk5m44myp"))))
+    (build-system texlive-build-system)
+    (arguments
+     '(#:tex-directory "latex/xkeyval"
+       #:build-targets '("xkeyval.dtx")
+       #:tex-format "latex" ; won't build with luatex
+       #:phases
+       (modify-phases %standard-phases
+         ;; This package cannot be built out of tree as it expects to find
+         ;; built files in the working directory.
+         (add-before 'build 'fix-build
+           (lambda _
+             (setenv "TEXINPUTS"
+                     (string-append (getcwd) "/build:"))
+             (substitute* "xkeyval.dtx"
+               (("usepackage\\{xcolor\\}")
+                "usepackage[dvips]{xcolor}"))
+             #t))
+         ;; FIXME: We don't have a package for this font yet.
+         (add-after 'unpack 'remove-dependency-on-fourier
+           (lambda _
+             (substitute* "xkeyval.dtx"
+               (("\\\\usepackage\\{fourier\\}") ""))
+             #t))
+         (add-after 'install 'move-files
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (share (string-append out "/share/texmf-dist"))
+                    (source (string-append share "/tex/latex/xkeyval/"))
+                    (target (string-append share "/tex/generic/xkeyval/")))
+               (mkdir-p target)
+               (for-each (lambda (file)
+                           (rename-file (string-append source file)
+                                        (string-append target file)))
+                         '("keyval.tex"
+                           "pst-xkey.tex"
+                           "xkeyval.tex"
+                           "xkvex1.tex"
+                           "xkvex2.tex"
+                           "xkvex3.tex"
+                           "xkvex4.tex"
+                           "xkvtxhdr.tex"
+                           "xkvutils.tex"))
+               #t))))))
+    (native-inputs
+     `(("texlive-latex-base" ,texlive-latex-base)
+       ("texlive-cm" ,texlive-cm)
+       ("texlive-lm" ,texlive-lm)
+       ("texlive-url" ,texlive-url)
+       ("texlive-graphics-def" ,texlive-graphics-def)
+       ("texlive-xcolor" ,texlive-xcolor)
+       ("texlive-latex-footmisc" ,texlive-latex-footmisc)
+       ("texlive-latex-listings" ,texlive-latex-listings)
+       ("texlive-iftex" ,texlive-iftex)
+       ("texlive-pstricks" ,texlive-pstricks)
+       ("texlive-pst-text" ,texlive-pst-text)
+       ("texlive-tools" ,texlive-tools)
+       ("texlive-latex-pgf" ,texlive-latex-pgf)))
+    (home-page "http://www.ctan.org/pkg/xkeyval")
+    (synopsis "Extension of the keyval package")
+    (description
+     "This package is an extension of the keyval package and offers additional
+macros for setting keys and declaring and setting class or package options.
+The package allows the programmer to specify a prefix to the name of the
+macros it defines for keys, and to define families of key definitions; these
+all help use in documents where several packages define their own sets of
+keys.")
+    (license license:lppl1.3+)))
+
+(define-public texlive-standalone
+  (package
+    (name "texlive-standalone")
+    (version (number->string %texlive-revision))
+    (source
+     (origin
+       (method svn-fetch)
+       (uri (texlive-ref "latex" "standalone"))
+       (sha256
+        (base32
+         "192ydxcn8ir96q8qwvnppksmqf5i0p50i0wz6iqazbwmh3dqxpx4"))))
+    (build-system texlive-build-system)
+    (arguments '(#:tex-directory "latex/standalone"))
+    (propagated-inputs
+     `(("texlive-latex-xkeyval" ,texlive-latex-xkeyval)))
+    (native-inputs
+     `(("texlive-ydoc" ,texlive-ydoc)))
+    (home-page "http://www.ctan.org/pkg/standalone")
+    (synopsis "Compile TeX pictures stand-alone or as part of a document")
+    (description "A class and package is provided which allows TeX pictures or
+other TeX code to be compiled standalone or as part of a main document.
+Special support for pictures with beamer overlays is also provided.  The
+package is used in the main document and skips extra preambles in sub-files.
+The class may be used to simplify the preamble in sub-files.  By default the
+@code{preview} package is used to display the typeset code without margins.
+The behaviour in standalone mode may adjusted using a configuration file
+@code{standalone.cfg} to redefine the standalone environment.")
+    (license license:lppl1.3+)))
+
+(define-public texlive-siunitx
+  (package
+    (name "texlive-siunitx")
+    (version (number->string %texlive-revision))
+    (source (texlive-origin
+             name version
+             (list "/source/latex/siunitx/siunitx.dtx"
+                   "/doc/latex/siunitx/README.md")
+             (base32
+              "0dmljnxgv2bwl3mi74iil41q03swvrm1b0ziwxlhc4m9lx31b1q1")))
+    (build-system texlive-build-system)
+    (arguments
+     '(#:tex-directory "latex/siunitx"
+       #:build-targets '("siunitx.dtx")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'chdir
+           (lambda _ (chdir "source/latex/siunitx") #t)))))
+    (propagated-inputs
+     `(("texlive-latex-l3kernel" ,texlive-latex-l3kernel)
+       ("texlive-latex-l3packages" ,texlive-latex-l3packages)))
+    (home-page "http://www.ctan.org/pkg/siunitx")
+    (synopsis "Comprehensive SI units package")
+    (description
+     "Typesetting values with units requires care to ensure that the combined
+mathematical meaning of the value plus unit combination is clear.  In
+particular, the SI units system lays down a consistent set of units with rules
+on how they are to be used.  However, different countries and publishers have
+differing conventions on the exact appearance of numbers (and units).  A
+number of LaTeX packages have been developed to provide consistent application
+of the various rules.  The @code{siunitx} package takes the best from the
+existing packages, and adds new features and a consistent interface.  A number
+of new ideas have been incorporated, to fill gaps in the existing provision.
+The package also provides backward-compatibility with @code{SIunits},
+@code{sistyle}, @code{unitsdef} and @code{units}.  The aim is to have one
+package to handle all of the possible unit-related needs of LaTeX users.")
+    (license license:lppl1.3c)))
+
+(define-public texlive-booktabs
+  (package
+    (name "texlive-booktabs")
+    (version (number->string %texlive-revision))
+    (source
+     (origin
+       (method svn-fetch)
+       (uri (texlive-ref "latex" "booktabs"))
+       (sha256
+        (base32
+         "1dqid48vgh25wmw8xzmx6x3pfgz1y9f0r8aza1yxq2mjny5yf68x"))))
+    (build-system texlive-build-system)
+    (arguments '(#:tex-directory "latex/booktabs"))
+    (home-page "http://www.ctan.org/pkg/booktabs")
+    (synopsis "Publication quality tables in LaTeX")
+    (description
+     "This package enhances the quality of tables in LaTeX, providing extra
+commands as well as behind-the-scenes optimisation.  Guidelines are given as
+to what constitutes a good table in this context.  The package offers
+@code{longtable} compatibility.")
+    (license license:lppl1.3+)))

gnu/packages/textutils.scm

@@ -475,7 +475,7 @@ as existing hashing techniques, with provably negligible risk of collisions.")
 (define-public oniguruma
   (package
     (name "oniguruma")
-    (version "6.9.2")
+    (version "6.9.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/kkos/"
@@ -483,7 +483,7 @@ as existing hashing techniques, with provably negligible risk of collisions.")
                                   "/onig-" version ".tar.gz"))
               (sha256
                (base32
-                "0slp4hpw9qxk4xhn7abyw7065sd355xwkyfq72glxczcjsqxsynv"))))
+                "0pvj37r1rd5h5vw99mdk8z4k44gq1ldwrapkamdiicksdfkr4ndb"))))
     (build-system gnu-build-system)
     (home-page "https://github.com/kkos/oniguruma")
     (synopsis "Regular expression library")
@@ -492,20 +492,6 @@ characteristic of this library is that different character encoding for every
 regular expression object can be specified.")
     (license license:bsd-2)))
 
-;; PHP < 7.3.0 requires this old version.  Remove once no longer needed.
-(define-public oniguruma-5
-  (package
-    (inherit oniguruma)
-    (version "5.9.6")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/kkos/"
-                                  "oniguruma/releases/download/v" version
-                                  "/onig-" version ".tar.gz"))
-              (sha256
-               (base32
-                "19s79vsclqn170mw0ajwv7j37qsbn4f1yjz3yavnhvva6c820r6m"))))))
-
 (define-public antiword
   (package
     (name "antiword")

gnu/packages/upnp.scm

@@ -42,14 +42,14 @@
 (define-public miniupnpc
   (package
     (name "miniupnpc")
-    (version "2.1.20190625")
+    (version "2.1.20190824")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://miniupnp.tuxfamily.org/files/"
                            name "-" version ".tar.gz"))
        (sha256
-        (base32 "1yqp0d8x5ldjfma5x2vhpg1aaafdg0470ismccixww3rzpbza8w7"))))
+        (base32 "0rg1i51lnyq8zgflhcg981kq4348vgq03ndmbgiv7knd1vmfzb8z"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("python" ,python-2)))

gnu/packages/vim.scm

@@ -483,7 +483,7 @@ trouble using them, because you do not have to remember each snippet name.")
 (define-public vim-fugitive
   (package
     (name "vim-fugitive")
-    (version "2.5")
+    (version "3.0")
     (source
       (origin
         (method git-fetch)
@@ -493,7 +493,7 @@ trouble using them, because you do not have to remember each snippet name.")
         (file-name (git-file-name name version))
         (sha256
          (base32
-          "17yz7gxn7a49jzndr4z5vnk1y4a6c22qss3mwxzmq4m46fni0k8q"))))
+          "0ghh8a9xysc3njqql1khhl2dkhymz93snpwqp2apm7pka6l893bc"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f
@@ -508,11 +508,13 @@ trouble using them, because you do not have to remember each snippet name.")
                     (autoload (string-append vimfiles "/autoload"))
                     (doc      (string-append vimfiles "/doc"))
                     (ftdetect (string-append vimfiles "/ftdetect"))
-                    (plugin (string-append vimfiles "/plugin")))
+                    (plugin   (string-append vimfiles "/plugin"))
+                    (syntax   (string-append vimfiles "/syntax")))
                (copy-recursively "autoload" autoload)
                (copy-recursively "doc" doc)
                (copy-recursively "ftdetect" ftdetect)
                (copy-recursively "plugin" plugin)
+               (copy-recursively "syntax" syntax)
                #t))))))
     (home-page "https://github.com/tpope/vim-fugitive")
     (synopsis "Vim plugin to work with Git")

gnu/packages/web-browsers.scm

@@ -368,16 +368,18 @@ driven and does not detract you from your daily work.")
 (define next-gtk-webkit
   (package
     (name "next-gtk-webkit")
-    (version "1.3.0")
+    (version "1.3.1")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-             (url "https://source.atlas.engineer/public/next")
+             ;; TODO: Mirror seems to hang, let's fallback to GitHub for now.
+             ;; (url "https://source.atlas.engineer/public/next")
+             (url "https://github.com/atlas-engineer/next")
              (commit version)))
        (sha256
         (base32
-         "0ibq30xrf871pkpasi8p9krn0pmd86rsdzb3jqvz3wnp4wa3hl9d"))
+         "01fn1f080ydk0wj1bwkyakqz93bdq9xb5x8qz820jpl9id17bqgj"))
        (file-name (git-file-name "next" version))))
     (build-system glib-or-gtk-build-system)
     (arguments
@@ -413,7 +415,7 @@ features for productive professionals.")
     (arguments
      `(#:tests? #f                      ; Need online access.
        #:asd-file "next.asd"
-       #:asd-system-name "download-manager"))
+       #:asd-system-name "next/download-manager"))
     (inputs
      `(;; ASD libraries:
        ("trivial-features" ,sbcl-trivial-features)
@@ -501,8 +503,6 @@ features for productive professionals.")
          ("cl-markup" ,sbcl-cl-markup)
          ("cl-ppcre" ,sbcl-cl-ppcre)
          ("cl-ppcre-unicode" ,sbcl-cl-ppcre-unicode)
-         ("cl-string-match" ,sbcl-cl-string-match)
-         ("cl-strings" ,sbcl-cl-strings)
          ("closer-mop" ,sbcl-closer-mop)
          ("dbus" ,cl-dbus)
          ("dexador" ,sbcl-dexador)

gnu/packages/web.scm

@@ -208,14 +208,14 @@ Interface} specification.")
     ;; ’stable’ and recommends that “in general you deploy the NGINX mainline
     ;; branch at all times” (https://www.nginx.com/blog/nginx-1-6-1-7-released/)
     ;; Consider updating the nginx-documentation package together with this one.
-    (version "1.17.2")
+    (version "1.17.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://nginx.org/download/nginx-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1v39gslwbvpfhqqv74q0lkfrhrwsp59xc8pwhvxns7af8s3kccsy"))))
+                "0g0g9prwjy0rnv6n5smny5yl5dhnmflqdr3hwgyj5jpr5hfgx11v"))))
     (build-system gnu-build-system)
     (inputs `(("openssl" ,openssl)
               ("pcre" ,pcre)
@@ -4931,13 +4931,13 @@ deployments.")
   (package
     (name "varnish")
     (home-page "https://varnish-cache.org/")
-    (version "6.2.0")
+    (version "6.2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append home-page "_downloads/varnish-" version ".tgz"))
               (sha256
                (base32
-                "0lwfk2gq99c653h5f51fs3j37r0gh2pf0p4w5z986nm2mi9z6yn3"))))
+                "15qfvw3fp05bgyspcm6gbsnxhs430p4z3fwz5kkd1z68jb90b3pj"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags (list (string-append "LDFLAGS=-Wl,-rpath=" %output "/lib")

gnu/packages/wine.scm

@@ -318,7 +318,7 @@ integrate Windows applications into your desktop.")
 (define-public wine-staging-patchset-data
   (package
     (name "wine-staging-patchset-data")
-    (version "4.14")
+    (version "4.15")
     (source
      (origin
        (method git-fetch)
@@ -328,7 +328,7 @@ integrate Windows applications into your desktop.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1s17hcrp1aa0v99y5iav2s0lxdx2rzgm7z0c4zhxyydqxj399f5j"))))
+         "13g40h2ybcl6vab4zbl1ksqfqyly5hzxssza9dv8r5pmp8x54hgr"))))
     (build-system trivial-build-system)
     (native-inputs
      `(("bash" ,bash)
@@ -374,7 +374,7 @@ integrate Windows applications into your desktop.")
               (file-name (string-append name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1rl1a3k5sr0hyxc61d68kwandhxcnxwv6b77vh7x2rkl1h4nxmfs"))))
+                "0bfh4vd99zwj7f4108zvs80dfvmmnnsap7i6gmf21jgcly3paygq"))))
     (inputs `(("autoconf" ,autoconf) ; for autoreconf
               ("faudio" ,faudio)
               ("ffmpeg" ,ffmpeg)

gnu/packages/wm.scm

@@ -48,9 +48,9 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system python)
-  #:use-module (gnu packages haskell)
   #:use-module (gnu packages haskell-check)
   #:use-module (gnu packages haskell-web)
+  #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages gawk)
@@ -172,14 +172,14 @@ commands would.")
 (define-public i3-wm
   (package
     (name "i3-wm")
-    (version "4.17")
+    (version "4.17.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://i3wm.org/downloads/i3-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "1z8qmkkq9dhqmqy8sjw3rnpnmnb8v7lr456bs0qzp23bgpj17gjf"))))
+                "0iazv2i2rgmakzh95pgj6iapyzn7bdpcbcd35a79mhlml4ry33qy"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -1138,7 +1138,7 @@ functionality to display information about the most commonly used services.")
 (define-public wlroots
   (package
     (name "wlroots")
-    (version "0.6.0")
+    (version "0.7.0")
     (source
      (origin
        (method git-fetch)
@@ -1147,7 +1147,7 @@ functionality to display information about the most commonly used services.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1rdcmll5b8w242n6yfjpsaprq280ck2jmbz46dxndhignxgda7k4"))))
+        (base32 "0jzxa6psbc7ddxli7rbfqxmv1svxnis51l1vch4hb9fdixqm284a"))))
     (build-system meson-build-system)
     (arguments
      `(#:configure-flags '("-Dlogind-provider=elogind")

gnu/packages/xfce.scm

@@ -37,6 +37,7 @@
   #:use-module (guix build-system trivial)
   #:use-module (gnu artwork)
   #:use-module (gnu packages)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages calendar)
   #:use-module (gnu packages cdrom)
   #:use-module (gnu packages pkg-config)
@@ -54,6 +55,7 @@
   #:use-module (gnu packages pdf)
   #:use-module (gnu packages polkit)
   #:use-module (gnu packages gstreamer)
+  #:use-module (gnu packages libcanberra)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages photo)
   #:use-module (gnu packages pcre)
@@ -86,7 +88,7 @@
 (define-public libxfce4util
   (package
     (name "libxfce4util")
-    (version "4.12.1")
+    (version "4.14.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://archive.xfce.org/xfce/"
@@ -94,11 +96,13 @@
                                   "/src/" name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "07c8r3xwx5is298zk77m3r784gmr5y4mh8bbca5zdjqk5vxdwsw7"))))
+                "093338faqqsrlc8dkmzr7qv411ysxczg1wlg7s3gvhrfk6vpkb9j"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
-       ("intltool" ,intltool)))
+       ("gobject-introspection" ,gobject-introspection)
+       ("intltool" ,intltool)
+       ("vala" ,vala)))
     (propagated-inputs `(("glib" ,glib))) ; required by libxfce4util-1.0.pc
     (home-page "https://www.xfce.org/")
     (synopsis "Basic utility library for Xfce")
@@ -110,7 +114,7 @@ Xfce Desktop Environment.")
 (define-public xfconf
   (package
     (name "xfconf")
-    (version "4.12.1")
+    (version "4.14.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://archive.xfce.org/src/xfce/"
@@ -118,13 +122,13 @@ Xfce Desktop Environment.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "0dns190bwb615wy9ma2654sw4vz1d0rcv061zmaalkv9wmj8bx1m"))))
+                "0n8d55c98ff7wgwv3qa4g369sv4iasgm1w62zq10kq5f56iy14xq"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
        ;; Run check after install phase to test dbus activation.
        (modify-phases %standard-phases
-         (add-after 'install 'check
+         (add-after 'install 'custom-check
            (lambda _
              (setenv "HOME" (getenv "TMPDIR")) ; xfconfd requires a writable HOME
              ;; Run test-suite under a dbus session.
@@ -136,12 +140,14 @@ Xfce Desktop Environment.")
          (delete 'check))))
     (native-inputs
      `(("pkg-config" ,pkg-config)
-       ("intltool" ,intltool)))
+       ("intltool" ,intltool)
+       ("glib:bin" ,glib "bin") ;; for gdbus-codegen
+       ("gobject-introspection" ,gobject-introspection)
+       ("vala" ,vala)
+       ("dbus" ,dbus)))
     (propagated-inputs
      ;; libxfconf-0.pc refers to all these.
-     `(("glib" ,glib)
+     `(("glib" ,glib)))
-       ("dbus" ,dbus)
-       ("dbus-glib" ,dbus-glib)))
     (inputs
      `(("libxfce4util" ,libxfce4util)))
     (home-page "https://www.xfce.org/")
@@ -154,7 +160,7 @@ storage system.")
 (define-public libxfce4ui
   (package
     (name "libxfce4ui")
-    (version "4.12.1")
+    (version "4.14.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://archive.xfce.org/src/xfce/"
@@ -162,11 +168,15 @@ storage system.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "0hzzhiiwmqsrbv17nninhs2x1b8ck0ym85jck2xphx5ypw8rhq9x"))))
+                "1npjhznmnckhnylsv3l7p1zvhckhmp9d7vifs8w12kdfmrg0fjf4"))))
     (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags
+       (list "--with-vendor-info=GNU Guix")))
     (native-inputs
      `(("pkg-config" ,pkg-config)
-       ("intltool" ,intltool)))
+       ("intltool" ,intltool)
+       ("gobject-introspection" ,gobject-introspection)))
     (propagated-inputs
      `(("gtk+-3" ,gtk+)    ; required by libxfce4ui-2.pc
        ;; libxfce4kbd-private-2.pc refers to all these.
@@ -188,7 +198,7 @@ to share commonly used Xfce widgets among the Xfce applications.")
 (define-public exo
   (package
     (name "exo")
-    (version "0.12.6")
+    (version "0.12.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://archive.xfce.org/src/xfce/"
@@ -196,17 +206,19 @@ to share commonly used Xfce widgets among the Xfce applications.")
                                   "exo-" version ".tar.bz2"))
               (sha256
                (base32
-                "00qh8ihrf09jvd26kilybihkgvv6rvi0l1bvlldxc99jb7ygy5ql"))))
+                "1ppwi6n40aphh0dqsnfrk234zsp7pl4lkjnspqjxw7m49bka401l"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("intltool" ,intltool)))
     (propagated-inputs
-     ;; exo-1.pc refers to all these.
+     ;; exo-2.pc refers to all these.
-     `(("gtk+" ,gtk+-2)
+     `(("gtk+-3" ,gtk+)
        ("libxfce4util" ,libxfce4util)))
     (inputs
-     `(("libxfce4ui" ,libxfce4ui)
+     `(;; FIXME Refered to in exo-1.pc but conflict with gtk+-3
+       ("gtk+-2" ,gtk+-2)
+       ("libxfce4ui" ,libxfce4ui)
        ("perl-uri" ,perl-uri)))
     (home-page "https://www.xfce.org/")
     (synopsis "Extension library for Xfce")
@@ -220,7 +232,7 @@ development.")
 (define-public garcon
   (package
     (name "garcon")
-    (version "0.6.3")
+    (version "0.6.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://archive.xfce.org/src/xfce/"
@@ -228,16 +240,17 @@ development.")
                                   "garcon-" version ".tar.bz2"))
               (sha256
                (base32
-                "00c4g4gmbr8710k0yv1zybnm9s2gkc1rj63zfrg9qgin66jzxcbn"))))
+                "0bbngb4bn1m325j7y40gky36kn2nlsvqs6xp0wy76x3s0d9lfpnp"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("intltool" ,intltool)
        ("glib:bin" ,glib "bin")))
     (inputs
-     `(("gtk+" ,gtk+-2)))
+     `(("gtk+-2" ,gtk+-2))); required by garcon-gtk2-1.pc
     (propagated-inputs
-     `(("libxfce4ui" ,libxfce4ui))) ; required by garcon-gtk2-1.pc
+     `(("gtk+-3" ,gtk+)                 ; required by garcon-gtk3-1.pc
+       ("libxfce4ui" ,libxfce4ui))) ; required by garcon-gtk3-1.pc
     (home-page "https://www.xfce.org/")
     (synopsis "Implementation of the freedesktop.org menu specification")
     (description
@@ -250,7 +263,7 @@ merging features essential for loading menus modified with menu editors.")
 (define-public tumbler
   (package
     (name "tumbler")
-    (version "0.2.5")
+    (version "0.2.7")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://archive.xfce.org/src/xfce/"
@@ -258,7 +271,7 @@ merging features essential for loading menus modified with menu editors.")
                                   "tumbler-" version ".tar.bz2"))
               (sha256
                (base32
-                "0nfld1lvrdpsjfvm08y5487km45pm1mdr928hgqm8j0shrx6jiv4"))))
+                "1r0l0ghcrj71ax7yil1m4p7yjrfqm3icx0s8r7ivwv3i2rgw617p"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
@@ -286,7 +299,7 @@ management D-Bus specification.")
 (define-public xfce4-panel
   (package
     (name "xfce4-panel")
-    (version "4.12.2")
+    (version "4.14.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://archive.xfce.org/src/xfce/"
@@ -294,20 +307,32 @@ management D-Bus specification.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "1s8cvsrgmkmmm84g6mghpj2k4777gm22g5lrsf8pdy5qh6xql1a2"))
+                "1x3flv86jh9vqah7mr5mmfx2991mc6icsqjygsc3j88lgsyz7y6m"))
               (patches (search-patches "xfce4-panel-plugins.patch"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:configure-flags '("--enable-gtk3")))
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-tzdata-path
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* (string-append "plugins/clock/clock.c")
+               (("/usr/share/zoneinfo")
+                (string-append (assoc-ref inputs "tzdata") "/share/zoneinfo")))
+             #t)))))
     (native-inputs
      `(("pkg-config" ,pkg-config)
-       ("intltool" ,intltool)))
+       ("intltool" ,intltool)
+       ("glib:bin" ,glib "bin")))
     (propagated-inputs
-     `(("libxfce4util" ,libxfce4util))) ; required by libxfce4panel-1.0.pc
+     `(("gtk+-3" ,gtk+)                 ; required by libxfce4panel-2.0.pc
+       ("libxfce4util" ,libxfce4util))) ; required by libxfce4panel-2.0.pc
     (inputs
-     `(("exo" ,exo)
+     `(("tzdata" ,tzdata) ;; For fix-tzdata-path phase only.
+       ("exo" ,exo)
+       ("gtk+-2" ,gtk+-2)
+       ("xfconf" ,xfconf)
        ("garcon" ,garcon)
-       ("libwnck" ,libwnck-2)
+       ("libwnck" ,libwnck)
        ("libxfce4ui" ,libxfce4ui)))
     (native-search-paths
      (list (search-path-specification
@@ -324,7 +349,7 @@ applications menu, workspace switcher and more.")
 (define-public xfce4-battery-plugin
   (package
     (name "xfce4-battery-plugin")
-    (version "1.1.2")
+    (version "1.1.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://archive.xfce.org/src/panel-plugins/"
@@ -332,12 +357,12 @@ applications menu, workspace switcher and more.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "1nypi0zazrcrbbm5vb221yw64zxrk56v4fffkblxlyd9m6gk80fn"))))
+                "18s0s004nidii8cc3ldp5n3jajc18vwn9vhkhmhy3lbbs520mghj"))))
     (build-system gnu-build-system)
     (native-inputs `(("pkg-config" ,pkg-config)
                      ("intltool" ,intltool)))
     (inputs `(("glib" ,glib)
-              ("gtk+" ,gtk+-2)
+              ("gtk+" ,gtk+)
               ("libxfce4util" ,libxfce4util)
               ("libxfce4ui" ,libxfce4ui)
               ("xfce4-panel" ,xfce4-panel)))
@@ -384,7 +409,7 @@ matching them against regular expressions.")
 (define-public xfce4-pulseaudio-plugin
   (package
     (name "xfce4-pulseaudio-plugin")
-    (version "0.4.1")
+    (version "0.4.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://archive.xfce.org/src/panel-plugins/"
@@ -392,11 +417,26 @@ matching them against regular expressions.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "1w29y0a066y8as12xrkbfqcn7dpdsvx97idzw7028gmcvca87a3c"))))
+                "0851b0vs5xmy3cq899khcghmkqwvh9rnzwavi17msrsq4jyaxs2a"))))
     (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       ;; For dbus/dbus-glib.h in pulseaudio-config.h
+       (modify-phases %standard-phases
+         (add-after 'set-paths 'augment-cflags
+           (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "C_INCLUDE_PATH"
+                     (string-append (assoc-ref inputs "dbus-glib")
+                                    "/include/dbus-1.0" ":"
+                                    (assoc-ref inputs "dbus")
+                                    "/include/dbus-1.0" ":"
+                                    (getenv "C_INCLUDE_PATH")))
+             #t)))))
     (native-inputs
      `(("intltool" ,intltool)
-       ("pkg-config" ,pkg-config)))
+       ("pkg-config" ,pkg-config)
+       ("dbus-glib" ,dbus-glib)
+       ("dbus" ,dbus)))
     (inputs
      `(("exo" ,exo)
        ("libnotify" ,libnotify)
@@ -415,7 +455,7 @@ keys for controlling the audio volume.")
 (define-public xfce4-whiskermenu-plugin
   (package
     (name "xfce4-whiskermenu-plugin")
-    (version "2.3.1")
+    (version "2.3.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://archive.xfce.org/src/panel-plugins/"
@@ -423,7 +463,7 @@ keys for controlling the audio volume.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "1cnas2x7xi53v6ylq44040narhzd828dc0ysz8yk3qn2mmvp5yr2"))))
+                "0j0qmk372130avq8n07lfqrcm2al7n07l8gc06bbr1g6q57wrip0"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
@@ -432,7 +472,8 @@ keys for controlling the audio volume.")
      `(("xfce4-panel" ,xfce4-panel)
        ("garcon" ,garcon)
        ("exo" ,exo)
-       ("gtk+" ,gtk+-2)))
+       ("gtk+" ,gtk+)
+       ("libxfce4ui" ,libxfce4ui)))
     (arguments
       `(#:tests? #f)) ; no tests
     (home-page "https://goodies.xfce.org/projects/panel-plugins/xfce4-whiskermenu-plugin")
@@ -448,7 +489,7 @@ applications, and includes a search bar to search for applications.")
 (define-public xfce4-xkb-plugin
   (package
     (name "xfce4-xkb-plugin")
-    (version "0.7.1")
+    (version "0.8.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://archive.xfce.org/src/panel-plugins/"
@@ -456,7 +497,7 @@ applications, and includes a search bar to search for applications.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "10g65j5ia389ahhn3b9hr52ghpp0817fk0m60rfrv4wrzqrjxzk1"))))
+                "18b7cnaf3zxm598p2i47vim3kbbi8w923ia1hwabdph1c89cz7n1"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("intltool" ,intltool)
@@ -464,7 +505,7 @@ applications, and includes a search bar to search for applications.")
     (inputs
      `(("garcon" ,garcon)
        ("librsvg" ,librsvg)
-       ("libwnck" ,libwnck-2)
+       ("libwnck" ,libwnck)
        ("libx11" ,libx11)
        ("libxfce4ui" ,libxfce4ui)
        ("libxklavier" ,libxklavier)
@@ -486,7 +527,7 @@ per window.")
 (define-public xfce4-appfinder
   (package
     (name "xfce4-appfinder")
-    (version "4.12.0")
+    (version "4.14.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://archive.xfce.org/xfce/"
@@ -494,14 +535,14 @@ per window.")
                                   "/src/" name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "0ry5hin8xhgnkmm9vs7jq8blk1cnbyr0s18nm1j6nsm7360abm1a"))))
+                "162dibl6ipp72x0s35yhk7kkzxd4qimagg5zdkkv5kjgjpa7bhby"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("intltool" ,intltool)))
     (inputs
      `(("garcon" ,garcon)
-       ("gtk+" ,gtk+-2)
+       ("gtk+" ,gtk+)
        ("libxfce4ui" ,libxfce4ui)))
     (home-page "https://www.xfce.org/")
     (synopsis "Xfce application finder")
@@ -513,7 +554,7 @@ your system in categories, so you can quickly find and launch them.")
 (define-public xfce4-session
   (package
     (name "xfce4-session")
-    (version "4.12.1")
+    (version "4.14.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://archive.xfce.org/src/xfce/"
@@ -521,10 +562,7 @@ your system in categories, so you can quickly find and launch them.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "1z88klls3j161n5snpamz4l3p4823q4h87wdnqikczxgs2ig5mwp"))
+                "0gq4a8yiw58hb4d5dhvprxvzamqfg8qblmiqcw0b97mn9svnvyql"))
-              (patches
-               ;; See: https://bugzilla.xfce.org/show_bug.cgi?id=12282
-               (search-patches "xfce4-session-fix-xflock4.patch"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -549,7 +587,7 @@ your system in categories, so you can quickly find and launch them.")
        ("upower" ,upower)
        ("polkit" ,polkit)
        ("libsm" ,libsm)
-       ("libwnck" ,libwnck-2)
+       ("libwnck" ,libwnck)
        ("libxfce4ui" ,libxfce4ui)))
     (home-page "https://www.xfce.org/")
     (synopsis "Xfce session manager")
@@ -561,7 +599,7 @@ allows you to shutdown the computer from Xfce.")
 (define-public xfce4-settings
   (package
     (name "xfce4-settings")
-    (version "4.12.4")
+    (version "4.14.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://archive.xfce.org/src/xfce/"
@@ -569,9 +607,13 @@ allows you to shutdown the computer from Xfce.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "16vgidhhc19dz0p0i6fp5iiwxd53ky143j6h14a9b7mz92nlr872"))
+                "0g0ipkg2fyg8r1z95ynx0xjr78bp49c2dwh4mli05nmb4gb40c70"))
               (patches (search-patches "xfce4-settings-defaults.patch"))))
     (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags '("--enable-pluggable-dialogs"
+                           "--enable-sound-settings"
+                           "--enable-xrandr")))
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("intltool" ,intltool)))
@@ -659,7 +701,7 @@ and import the new pictures from your camera.")
 (define-public xfwm4
   (package
     (name "xfwm4")
-    (version "4.12.5")
+    (version "4.14.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://archive.xfce.org/src/xfce/"
@@ -667,14 +709,14 @@ and import the new pictures from your camera.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "1jnav0wcqlswl2v7nh61big9czg5hmnyvrvm6812sv362qic0xbp"))))
+                "05dn4a1i0nm6wm3nyj7qli5bvfalxghcl7x543qr5l33vkw2n65l"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("intltool" ,intltool)))
     (inputs
      `(("libdrm" ,libdrm)
-       ("libwnck" ,libwnck-2)
+       ("libwnck" ,libwnck)
        ("libxcomposite" ,libxcomposite)
        ("libxdamage" ,libxdamage)
        ("libxfce4ui" ,libxfce4ui)
@@ -689,7 +731,7 @@ on the screen.")
 (define-public xfdesktop
   (package
     (name "xfdesktop")
-    (version "4.12.4")
+    (version "4.14.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://archive.xfce.org/src/xfce/"
@@ -697,7 +739,7 @@ on the screen.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "1jzi851arljq5lza9inyq4ss513l62lbzbfm64a7x4320m8kb2h9"))
+                "10pqxgpj7b57wpcsh2k98sj4aavcgxbs1lc8qsq4mibf4hba01gp"))
               (modules '((guix build utils)))
               (snippet
                #~(begin
@@ -735,7 +777,7 @@ on the screen.")
      `(("exo" ,exo)
        ("garcon" ,garcon)
        ("libnotify" ,libnotify)
-       ("libwnck" ,libwnck-2)
+       ("libwnck" ,libwnck)
        ("libxfce4ui" ,libxfce4ui)
        ("thunar" ,thunar)))
     (home-page "https://www.xfce.org/")
@@ -749,7 +791,7 @@ devices and folders.")
 (define-public xfce4-terminal
   (package
     (name "xfce4-terminal")
-    (version "0.8.7.4")
+    (version "0.8.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://archive.xfce.org/src/apps/" name "/"
@@ -757,7 +799,7 @@ devices and folders.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "1as2dh5ccmv3hdvsbxm4b0xhmv2ky2q18zxxrzr988x79npri3x8"))))
+                "1zc7hkq77ajia099wxgh4wdvwifcg2zkcz5d2xsf1zm0sdh6mflg"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
@@ -831,7 +873,7 @@ system resources, while still being visually appealing and user friendly.")
 (define-public xfce4-power-manager
   (package
     (name "xfce4-power-manager")
-    (version "1.6.1")
+    (version "1.6.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://archive.xfce.org/src/xfce/"
@@ -839,16 +881,14 @@ system resources, while still being visually appealing and user friendly.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "0sv5927q8jxvdfx7b06f8s7qyq3qa1nqn0b8c1b9bf234d2jba0y"))))
+                "0x3s2bdwfhp65dz5yn3k43j99ywqlsvrpz3pqmgwm0dik5wbdb8h"))))
     (build-system gnu-build-system)
-    (arguments
-     '(#:configure-flags '("--enable-gtk3")))
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("intltool" ,intltool)))
     (inputs
-     `(("lbxrandr" ,libxrandr)
+     `(("libxrandr" ,libxrandr)
-       ("gtk+" ,gtk+-2)
+       ("gtk+" ,gtk+)
        ("upower" ,upower)
        ("libnotify" ,libnotify)
        ("libxfce4ui" ,libxfce4ui)))
@@ -913,7 +953,7 @@ the desktop wallpaper.")
      `(("intltool" ,intltool)
        ("pkg-config" ,pkg-config)))
     (inputs
-     `(("libwnck" ,libwnck-2)
+     `(("libwnck" ,libwnck)
        ("libxmu" ,libxmu)
        ("gtk+" ,gtk+)
        ;; FIXME: Remove libxext and libxt when libxmu propagates them.
@@ -961,7 +1001,7 @@ several different time zones.")
 (define-public xfce4-notifyd
   (package
     (name "xfce4-notifyd")
-    (version "0.4.3")
+    (version "0.4.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://archive.xfce.org/src/apps/"
@@ -969,7 +1009,7 @@ several different time zones.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "1h7avj149cafj9dabiza22y14i66vxgp5qj0wxx8i97w9h4dlg99"))))
+                "0m8vlbwdxiw9nmimaj5np9l5qm784gxpkdvc881k0hjcz6n72189"))))
     (build-system glib-or-gtk-build-system)
     (native-inputs
      `(("intltool" ,intltool)
@@ -1066,3 +1106,83 @@ of data to either CD/DVD/BD.")
     (description
      "Mousepad is a graphical text editor for Xfce based on Leafpad.")
     (license gpl2+)))
+
+(define-public xfce4-screenshooter
+  (package
+   (name "xfce4-screenshooter")
+   (version "1.9.5")
+   (source (origin
+            (method url-fetch)
+            (uri (string-append "http://archive.xfce.org/src/apps/"
+                                "xfce4-screenshooter/"
+                                (version-major+minor version)
+                                "/xfce4-screenshooter-"
+                                version ".tar.bz2"))
+            (sha256
+             (base32
+              "135kad07922jxjs05amn48sdgm2x1rh97wbzdmy9h85r5i1vaddz"))))
+   (build-system gnu-build-system)
+   (native-inputs
+    `(("pkg-config" ,pkg-config)
+      ("intltool" ,intltool)
+      ("glib:bin" ,glib "bin")))        ; glib-genmarshal
+   (inputs
+    `(("exo" ,exo)
+      ("libsoup" ,libsoup)
+      ("libxfce4ui" ,libxfce4ui)
+      ("xfce4-panel" ,xfce4-panel)))
+   (home-page "https://goodies.xfce.org/projects/applications/xfce4-screenshooter")
+   (synopsis "Xfce's application to take screenshots")
+   (description
+    "This application allows you to capture the entire screen, the active
+window or a selected region.  You can set the delay that elapses before the screenshot
+is taken and the action that will be done with the screenshot.
+A plugin for the Xfce panel is also available.")
+   (license gpl2+)))
+
+(define-public xfce4-screensaver
+  (package
+    (name "xfce4-screensaver")
+    (version "0.1.8")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://archive.xfce.org/src/apps/"
+                                  "xfce4-screensaver/"
+                                  (version-major+minor version)
+                                  "/xfce4-screensaver-"
+                                  version ".tar.bz2"))
+              (sha256
+               (base32
+                "1mv0r150yb29kji2rr2462g9p574bqjax1lb6bzcqgpxlmg08mj0"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-dbus-1-path
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (dbus-dir (string-append out "/share/dbus-1/services")))
+               (substitute* "configure"
+                 (("DBUS_SESSION_SERVICE_DIR=.*")
+                  (string-append "DBUS_SESSION_SERVICE_DIR="
+                                 dbus-dir)))))))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("intltool" ,intltool)
+       ("glib" ,glib)                             ; glib-compile-schemas
+       ("glib:bin" ,glib "bin")))                 ; glib-compile-schemas
+    (inputs
+     `(("dbus-glib" ,dbus-glib)
+       ("libux-pam" ,linux-pam)
+       ("elogind" ,elogind)
+       ("garcon" ,garcon)
+       ("libxklavier" ,libxklavier)
+       ("libwnxk" ,libwnck)
+       ("libxscrnsaver" ,libxscrnsaver)
+       ("xfconf" ,xfconf)))
+    (home-page "https://docs.xfce.org/apps/screensaver/start")
+    (synopsis "Screensaver for the Xfce desktop")
+    (description
+     "Xfce Screensaver is a screen saver and locker that aims to have simple,
+ sane, secure defaults and be well integrated with the Xfce desktop. ")
+    (license gpl2+)))

gnu/services/cups.scm

@@ -83,6 +83,14 @@
 (define (serialize-multiline-string-list field-name val)
   (for-each (lambda (str) (serialize-field field-name str)) val))
 
+(define (comma-separated-string-list? val)
+  (and (list? val)
+       (and-map (lambda (x)
+                  (and (string? x) (not (string-index x #\,))))
+                val)))
+(define (serialize-comma-separated-string-list field-name val)
+  (serialize-field field-name (string-join val ",")))
+
 (define (space-separated-string-list? val)
   (and (list? val)
        (and-map (lambda (x)
@@ -131,7 +139,7 @@
 (define-enumerated-field-type default-encryption
   (Never IfRequested Required))
 (define-enumerated-field-type error-policy
-  (abort-job retry-job retry-this-job stop-printer))
+  (abort-job retry-job retry-current-job stop-printer))
 (define-enumerated-field-type log-level
   (none emerg alert crit error warn notice info debug debug2))
 (define-enumerated-field-type log-time-format
@@ -450,7 +458,10 @@ or state files.")
   (user
    (string "lp")
    "Specifies the user name or ID that is used when running external
-programs."))
+programs.")
+  (set-env
+   (string "variable value")
+   "Set the specified environment variable to be passed to child processes."))
 
 (define (serialize-files-configuration field-name val)
   #f)
@@ -489,6 +500,11 @@ requests.")
    (boolean #f)
    "Specifies whether to purge job history data automatically when it is no
 longer required for quotas.")
+  (browse-dns-sd-sub-types
+   (comma-separated-string-list (list "_cups"))
+   "Specifies a list of DNS-SD sub-types to advertise for each shared printer.
+For example, @samp{\"_cups\" \"_print\"} will tell network clients that both
+CUPS sharing and IPP Everywhere are supported.")
   (browse-local-protocols
    (browse-local-protocols 'dnssd)
    "Specifies which protocols to use for local printer sharing.")
@@ -538,7 +554,7 @@ typically within a few milliseconds.")
    (error-policy 'stop-printer)
    "Specifies what to do when an error occurs.  Possible values are
 @code{abort-job}, which will discard the failed print job; @code{retry-job},
-which will retry the job at a later time; @code{retry-this-job}, which retries
+which will retry the job at a later time; @code{retry-current-job}, which retries
 the failed job immediately; and @code{stop-printer}, which stops the
 printer.")
   (filter-limit
@@ -798,9 +814,6 @@ reports @code{CUPS 2.0}.  @code{Minimal} reports @code{CUPS 2.0.0}.  @code{OS}
 reports @code{CUPS 2.0.0 (@var{uname})} where @var{uname} is the output of the
 @code{uname} command.  @code{Full} reports @code{CUPS 2.0.0 (@var{uname})
 IPP/2.0}.")
-  (set-env
-   (string "variable value")
-   "Set the specified environment variable to be passed to child processes.")
   (ssl-listen
    (multiline-string-list '())
    "Listens on the specified interfaces for encrypted connections.  Valid

gnu/services/web.scm

@@ -682,6 +682,7 @@ of index files."
        (system* (string-append #$nginx "/sbin/nginx")
                 "-c" #$(or file
                            (default-nginx-config config))
+                "-p" #$run-directory
                 "-t"))))
 
 (define (nginx-shepherd-service config)

gnu/system.scm

@@ -116,6 +116,7 @@
             boot-parameters-label
             boot-parameters-root-device
             boot-parameters-bootloader-name
+            boot-parameters-bootloader-menu-entries
             boot-parameters-store-device
             boot-parameters-store-mount-point
             boot-parameters-kernel
@@ -251,6 +252,8 @@ directly by the user."
   ;; OS's root file system, so it might be a device path like "/dev/sda3".
   (root-device      boot-parameters-root-device)
   (bootloader-name  boot-parameters-bootloader-name)
+  (bootloader-menu-entries                        ;list of <menu-entry>
+   boot-parameters-bootloader-menu-entries)
   (store-device     boot-parameters-store-device)
   (store-mount-point boot-parameters-store-mount-point)
   (kernel           boot-parameters-kernel)
@@ -297,6 +300,11 @@ file system labels."
          ((_ args) args)
          (#f       'grub))) ; for compatibility reasons.
 
+      (bootloader-menu-entries
+       (match (assq 'bootloader-menu-entries rest)
+         ((_ entries) (map sexp->menu-entry entries))
+         (#f          '())))
+
       ;; In the past, we would store the directory name of the kernel instead
       ;; of the absolute file name of its image.  Detect that and correct it.
       (kernel (if (string=? linux (direct-store-path linux))
@@ -1009,6 +1017,8 @@ such as '--root' and '--load' to <boot-parameters>."
           (operating-system-user-kernel-arguments os)))
      (initrd initrd)
      (bootloader-name bootloader-name)
+     (bootloader-menu-entries
+      (bootloader-configuration-menu-entries (operating-system-bootloader os)))
      (store-device (ensure-not-/dev (file-system-device store)))
      (store-mount-point (file-system-mount-point store)))))
 
@@ -1050,6 +1060,11 @@ being stored into the \"parameters\" file)."
                      #$(boot-parameters-kernel-arguments params))
                     (initrd #$(boot-parameters-initrd params))
                     (bootloader-name #$(boot-parameters-bootloader-name params))
+                    (bootloader-menu-entries
+                     #$(map menu-entry->sexp
+                            (or (and=> (operating-system-bootloader os)
+                                       bootloader-configuration-menu-entries)
+                                '())))
                     (store
                      (device
                       #$(device->sexp (boot-parameters-store-device params)))

gnu/system/linux-initrd.scm

@@ -99,7 +99,7 @@ the derivations referenced by EXP are automatically copied to the initrd."
                         #:init #$init
                         ;; Copy everything INIT refers to into the initrd.
                         #:references-graphs '("closure")
-                        #:gzip (string-append #$gzip "/bin/gzip")))))
+                        #:gzip (string-append #+gzip "/bin/gzip")))))
 
   (file-append (computed-file name builder
                               #:options

guix/build-system/cargo.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
@@ -35,12 +35,17 @@
   #:export (%cargo-build-system-modules
             %cargo-utils-modules
             cargo-build-system
+            %crate-base-url
             crate-url
             crate-url?
             crate-uri))
 
-(define crate-url "https://crates.io/api/v1/crates/")
+(define %crate-base-url
-(define crate-url? (cut string-prefix? crate-url <>))
+  (make-parameter "https://crates.io"))
+(define crate-url
+  (string-append (%crate-base-url) "/api/v1/crates/"))
+(define crate-url?
+  (cut string-prefix? crate-url <>))
 
 (define (crate-uri name version)
   "Return a URI string for the crate package hosted at crates.io corresponding

guix/build-system/julia.scm

@@ -0,0 +1,130 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2019 Nicolò Balzarotti <nicolo@nixo.xyz>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (guix build-system julia)
+  #:use-module (guix store)
+  #:use-module (guix utils)
+  #:use-module (guix packages)
+  #:use-module (guix derivations)
+  #:use-module (guix search-paths)
+  #:use-module (guix build-system)
+  #:use-module (guix build-system gnu)
+  #:use-module (ice-9 match)
+  #:use-module (srfi srfi-26)
+  #:export (%julia-build-system-modules
+            julia-build
+            julia-build-system))
+
+;; Commentary:
+;;
+;; Standard build procedure for Julia packages.
+;;
+;; Code:
+
+(define %julia-build-system-modules
+  ;; Build-side modules imported by default.
+  `((guix build julia-build-system)
+    ,@%gnu-build-system-modules))
+
+(define (default-julia)
+  "Return the default Julia package."
+  ;; Lazily resolve the binding to avoid a circular dependency.
+  (let ((julia-mod (resolve-interface '(gnu packages julia))))
+    (module-ref julia-mod 'julia)))
+
+(define* (lower name
+                #:key source inputs native-inputs outputs system target
+                (julia (default-julia))
+                #:allow-other-keys
+                #:rest arguments)
+  "Return a bag for NAME."
+  (define private-keywords
+    '(#:target #:julia #:inputs #:native-inputs))
+
+  (and (not target)                        ;XXX: no cross-compilation
+       (bag
+         (name name)
+         (system system)
+         (host-inputs `(,@(if source
+                              `(("source" ,source))
+                              '())
+                        ,@inputs
+                        
+                        ;; Keep the standard inputs of 'gnu-build-system'.
+                        ,@(standard-packages)))
+         (build-inputs `(("julia" ,julia)
+                         ,@native-inputs))
+         (outputs outputs)
+         (build julia-build)
+         (arguments (strip-keyword-arguments private-keywords arguments)))))
+
+(define* (julia-build store name inputs
+                      #:key source
+                      (tests? #f)
+                      (phases '(@ (guix build julia-build-system)
+                                  %standard-phases))
+                      (outputs '("out"))
+                      (search-paths '())
+                      (system (%current-system))
+                      (guile #f)
+                      (imported-modules %julia-build-system-modules)
+                      (modules '((guix build julia-build-system)
+                                 (guix build utils))))
+  "Build SOURCE using Julia, and with INPUTS."
+  (define builder
+    `(begin
+       (use-modules ,@modules)
+       (julia-build #:name ,name
+                    #:source ,(match (assoc-ref inputs "source")
+                                (((? derivation? source))
+                                 (derivation->output-path source))
+                                ((source)
+                                 source)
+                                (source
+                                 source))
+                    #:system ,system
+                    #:tests? ,tests?
+                    #:phases ,phases
+                    #:outputs %outputs
+                    #:search-paths ',(map search-path-specification->sexp
+                                          search-paths)
+                    #:inputs %build-inputs)))
+
+  (define guile-for-build
+    (match guile
+      ((? package?)
+       (package-derivation store guile system #:graft? #f))
+      (#f                                         ; the default
+       (let* ((distro (resolve-interface '(gnu packages commencement)))
+              (guile  (module-ref distro 'guile-final)))
+         (package-derivation store guile system #:graft? #f)))))
+
+  (build-expression->derivation store name builder
+                                #:inputs inputs
+                                #:system system
+                                #:modules imported-modules
+                                #:outputs outputs
+                                #:guile-for-build guile-for-build))
+
+(define julia-build-system
+  (build-system
+   (name 'julia)
+   (description "The build system for Julia packages")
+   (lower lower)))
+
+;;; julia.scm ends here

guix/build/cargo-build-system.scm

@@ -81,10 +81,10 @@ Cargo.toml file present at its root."
          ;; archive, but not nested anywhere else). We do this by cutting up
          ;; each output line and only looking at the second component. We then
          ;; check if it matches Cargo.toml exactly and short circuit if it does.
-         (zero? (apply system* (list "sh" "-c"
+         (apply invoke (list "sh" "-c"
                              (string-append "tar -tf " path
                                             " | cut -d/ -f2"
-                                                    " | grep -q '^Cargo.toml$'"))))))
+                                            " | grep -q '^Cargo.toml$'")))))
 
 (define* (configure #:key inputs
                     (vendor-dir "guix-vendor")
@@ -157,7 +157,7 @@ directory = '" port)
                 #:allow-other-keys)
   "Build a given Cargo package."
   (or skip-build?
-      (zero? (apply system* `("cargo" "build" ,@cargo-build-flags)))))
+      (apply invoke `("cargo" "build" ,@cargo-build-flags))))
 
 (define* (check #:key
                 tests?
@@ -165,7 +165,7 @@ directory = '" port)
                 #:allow-other-keys)
   "Run tests for a given Cargo package."
   (if tests?
-      (zero? (apply system* `("cargo" "test" ,@cargo-test-flags)))
+      (apply invoke `("cargo" "test" ,@cargo-test-flags))
       #t))
 
 (define (touch file-name)
@@ -184,7 +184,7 @@ directory = '" port)
     ;; otherwise cargo will raise an error.
     (or skip-build?
         (not (has-executable-target?))
-        (zero? (system* "cargo" "install" "--path" "." "--root" out)))))
+        (invoke "cargo" "install" "--path" "." "--root" out))))
 
 (define %standard-phases
   (modify-phases gnu:%standard-phases

guix/build/julia-build-system.scm

@@ -0,0 +1,135 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2019 Nicolò Balzarotti <nicolo@nixo.xyz>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+
+(define-module (guix build julia-build-system)
+  #:use-module ((guix build gnu-build-system) #:prefix gnu:)
+  #:use-module (guix build utils)
+  #:use-module (ice-9 match)
+  #:export (%standard-phases
+            julia-create-package-toml
+            julia-build))
+
+;; Commentary:
+;;
+;; Builder-side code of the standard build procedure for Julia packages.
+;;
+;; Code:
+
+(define (invoke-julia code)
+  (invoke "julia" "-e" code))
+
+;; subpath where we store the package content
+(define %package-path "/share/julia/packages/")
+
+(define (generate-load-path inputs outputs)
+  (string-append
+   (string-join (map (match-lambda
+                       ((_ . path)
+                        (string-append path %package-path)))
+                     ;; Restrict to inputs beginning with "julia-".
+                     (filter (match-lambda
+                               ((name . _)
+                                (string-prefix? "julia-" name)))
+                             inputs))
+                ":")
+   (string-append ":" (assoc-ref outputs "out") %package-path)
+   ;; stdlib is always required to find Julia's standard libraries.
+   ;; usually there are other two paths in this variable:
+   ;; "@" and "@v#.#"
+   ":@stdlib"))
+
+(define* (install #:key source inputs outputs #:allow-other-keys)
+  (let* ((out (assoc-ref outputs "out"))
+         (package-dir (string-append out %package-path
+                                     (string-append
+                                      (strip-store-file-name source)))))
+    (setenv "JULIA_LOAD_PATH" (generate-load-path inputs outputs))
+    (mkdir-p package-dir)
+    (copy-recursively source package-dir))
+  #t)
+
+;; TODO: Precompilation is working, but I don't know how to tell
+;; julia to use use it. If (on rantime) we set HOME to
+;; store path, julia tries to write files there (failing)
+(define* (precompile #:key source inputs outputs #:allow-other-keys)
+  (let* ((out (assoc-ref outputs "out"))
+         (builddir (string-append out "/share/julia/"))
+         (package (strip-store-file-name source)))
+    (mkdir-p builddir)
+    (setenv "JULIA_DEPOT_PATH" builddir)
+    (setenv "JULIA_LOAD_PATH" (generate-load-path inputs outputs))
+    ;; Actual precompilation
+    (invoke-julia (string-append "using " package)))
+  #t)
+
+(define* (check #:key source inputs outputs #:allow-other-keys)
+  (let* ((out (assoc-ref outputs "out"))
+         (package (strip-store-file-name source))
+         (builddir (string-append out "/share/julia/")))
+    (setenv "JULIA_DEPOT_PATH" builddir)
+    (setenv "JULIA_LOAD_PATH" (generate-load-path inputs outputs))
+    (invoke-julia (string-append "using Pkg;Pkg.test(\"" package "\")")))
+  #t)
+
+(define (julia-create-package-toml outputs source
+                                   name uuid version
+                                   deps)
+  "Some packages are not using the new Package.toml dependency specifications.
+Write this file manually, so that Julia can find its dependencies."
+  (let ((f (open-file
+            (string-append
+             (assoc-ref outputs "out")
+             %package-path
+             (string-append
+              name "/Project.toml"))
+            "w")))
+    (display (string-append
+              "
+name = \"" name "\"
+uuid = \"" uuid "\"
+version = \"" version "\"
+") f)
+    (when (not (null? deps))
+      (display "[deps]\n" f)
+      (for-each (lambda dep
+                  (display (string-append (car (car dep)) " = \"" (cdr (car dep)) "\"\n")
+                           f))
+                deps))
+    (close-port f))
+  #t)
+
+(define %standard-phases
+  (modify-phases gnu:%standard-phases
+    (delete 'check) ; tests must be run after installation
+    (replace 'install install)
+    (add-after 'install 'precompile precompile)
+    ;; (add-after 'install 'check check)
+    ;; TODO: In the future we could add a "system-image-generation" phase
+    ;; where we use PackageCompiler.jl to speed up package loading times
+    (delete 'configure)
+    (delete 'bootstrap)
+    (delete 'patch-usr-bin-file)
+    (delete 'build)))
+
+(define* (julia-build #:key inputs (phases %standard-phases)
+                      #:allow-other-keys #:rest args)
+  "Build the given Julia package, applying all of PHASES in order."
+  (apply gnu:gnu-build
+         #:inputs inputs #:phases phases
+         args))

guix/build/lisp-utils.scm

@@ -220,12 +220,19 @@ Also load TEST-ASD-FILE if necessary."
   "Return a lisp keyword for the concatenation of STRINGS."
   (string->symbol (apply string-append ":" strings)))
 
-(define (generate-executable-for-system type system)
+(define* (generate-executable-for-system type system #:key compress?)
   "Use LISP to generate an executable, whose TYPE can be 'asdf:image-op or
 'asdf:program-op.  The latter will always be standalone.  Depends on having
 created a \"SYSTEM-exec\" system which contains the entry program."
   (lisp-eval-program
    `((require :asdf)
+     ;; Only SBCL supports compression as of 2019-09-02.
+     ,(if (and compress? (string=? (%lisp-type) "sbcl"))
+          '(defmethod asdf:perform ((o asdf:image-op) (c asdf:system))
+                      (uiop:dump-image (asdf:output-file o c)
+                                       :executable t
+                                       :compression t))
+          '())
      (asdf:operate ',type ,(string-append system "-exec")))))
 
 (define (generate-executable-wrapper-system system dependencies)
@@ -339,6 +346,7 @@ which are not nested."
                         (dependency-prefixes (list (library-output outputs)))
                         (dependencies (list (basename program)))
                         entry-program
+                        compress?
                         #:allow-other-keys)
   "Generate an executable program containing all DEPENDENCIES, and which will
 execute ENTRY-PROGRAM.  The result is placed in PROGRAM.  When executed, it
@@ -350,6 +358,7 @@ retained."
                        #:dependencies dependencies
                        #:dependency-prefixes dependency-prefixes
                        #:entry-program entry-program
+                       #:compress? compress?
                        #:type 'asdf:program-op)
   (let* ((name (basename program))
          (bin-directory (dirname program)))
@@ -382,6 +391,7 @@ DEPENDENCY-PREFIXES to ensure references to those libraries are retained."
                               dependency-prefixes
                               entry-program
                               type
+                              compress?
                               #:allow-other-keys)
   "Generate an executable by using asdf operation TYPE, containing whithin the
 image all DEPENDENCIES, and running ENTRY-PROGRAM in the case of an
@@ -405,7 +415,7 @@ references to those libraries are retained."
                `(((,bin-directory :**/ :*.*.*)
                   (,bin-directory :**/ :*.*.*)))))))
 
-    (generate-executable-for-system type name)
+    (generate-executable-for-system type name #:compress? compress?)
 
     (let* ((after-store-prefix-index
             (string-index out-file #\/

guix/bzr-download.scm

@@ -75,6 +75,9 @@ HASH-ALGO (a symbol).  Use NAME as the file name, or a generic name if #f."
                       #:env-vars
                       `(("bzr url" . ,(bzr-reference-url ref))
                         ("bzr reference" . ,(bzr-reference-revision ref)))
+                      #:leaked-env-vars '("http_proxy" "https_proxy"
+                                          "LC_ALL" "LC_MESSAGES" "LANG"
+                                          "COLUMNS")
                       #:system system
                       #:local-build? #t  ;don't offload repo branching
                       #:hash-algo hash-algo

guix/ci.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -18,9 +18,10 @@
 
 (define-module (guix ci)
   #:use-module (guix http-client)
-  #:autoload   (json parser) (json->scm)
+  #:use-module (guix json)
+  #:use-module (json)
   #:use-module (srfi srfi-1)
-  #:use-module (srfi srfi-9)
+  #:use-module (ice-9 match)
   #:export (build?
             build-id
             build-derivation
@@ -42,7 +43,7 @@
             queued-builds
             latest-builds
             latest-evaluations
-            evaluation-for-commit))
+            evaluations-for-commit))
 
 ;;; Commentary:
 ;;;
@@ -51,28 +52,31 @@
 ;;;
 ;;; Code:
 
-(define-record-type <build>
+(define-json-mapping <build> make-build build?
-  (make-build id derivation system status timestamp)
+  json->build
-  build?
+  (id          build-id "id")                     ;integer
-  (id          build-id)                          ;integer
   (derivation  build-derivation)                  ;string | #f
   (system      build-system)                      ;string
-  (status      build-status)                      ;integer
+  (status      build-status "buildstatus" )       ;integer
   (timestamp   build-timestamp))                  ;integer
 
-(define-record-type <checkout>
+(define-json-mapping <checkout> make-checkout checkout?
-  (make-checkout commit input)
+  json->checkout
-  checkout?
   (commit      checkout-commit)                   ;string (SHA1)
   (input       checkout-input))                   ;string (name)
 
-(define-record-type <evaluation>
+(define-json-mapping <evaluation> make-evaluation evaluation?
-  (make-evaluation id spec complete? checkouts)
+  json->evaluation
-  evaluation?
   (id          evaluation-id)                     ;integer
   (spec        evaluation-spec)                   ;string
-  (complete?   evaluation-complete?)              ;Boolean
+  (complete?   evaluation-complete? "in-progress"
-  (checkouts   evaluation-checkouts))             ;<checkout>*
+               (match-lambda
+                 (0 #t)
+                 (_ #f)))                         ;Boolean
+  (checkouts   evaluation-checkouts "checkouts"   ;<checkout>*
+               (lambda (checkouts)
+                 (map json->checkout
+                      (vector->list checkouts)))))
 
 (define %query-limit
   ;; Max number of builds requested in queries.
@@ -84,18 +88,11 @@
     (close-port port)
     json))
 
-(define (json->build json)
-  (make-build (hash-ref json "id")
-              (hash-ref json "derivation")
-              (hash-ref json "system")
-              (hash-ref json "buildstatus")
-              (hash-ref json "timestamp")))
-
 (define* (queued-builds url #:optional (limit %query-limit))
   "Return the list of queued derivations on URL."
   (let ((queue (json-fetch (string-append url "/api/queue?nr="
                                           (number->string limit)))))
-    (map json->build queue)))
+    (map json->build (vector->list queue))))
 
 (define* (latest-builds url #:optional (limit %query-limit)
                         #:key evaluation system)
@@ -114,26 +111,15 @@ string such as \"x86_64-linux\"), restrict to builds for SYSTEM."
                                            (option "system" system)))))
     ;; Note: Hydra does not provide a "derivation" field for entries in
     ;; 'latestbuilds', but Cuirass does.
-    (map json->build latest)))
+    (map json->build (vector->list latest))))
-
-(define (json->checkout json)
-  (make-checkout (hash-ref json "commit")
-                 (hash-ref json "input")))
-
-(define (json->evaluation json)
-  (make-evaluation (hash-ref json "id")
-                   (hash-ref json "specification")
-                   (case (hash-ref json "in-progress")
-                     ((0) #t)
-                     (else #f))
-                   (map json->checkout (hash-ref json "checkouts"))))
 
 (define* (latest-evaluations url #:optional (limit %query-limit))
   "Return the latest evaluations performed by the CI server at URL."
   (map json->evaluation
+       (vector->list
         (json->scm
          (http-fetch (string-append url "/api/evaluations?nr="
-                                   (number->string limit))))))
+                                    (number->string limit)))))))
 
 
 (define* (evaluations-for-commit url commit #:optional (limit %query-limit))

guix/cvs-download.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2015, 2016, 2017, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014 Sree Harsha Totakura <sreeharsha@totakura.in>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;;
@@ -92,6 +92,9 @@ HASH-ALGO (a symbol).  Use NAME as the file name, or a generic name if #f."
 
   (mlet %store-monad ((guile (package->derivation guile system)))
     (gexp->derivation (or name "cvs-checkout") build
+                      #:leaked-env-vars '("http_proxy" "https_proxy"
+                                          "LC_ALL" "LC_MESSAGES" "LANG"
+                                          "COLUMNS")
                       #:system system
                       #:hash-algo hash-algo
                       #:hash hash

guix/git-download.scm

@@ -157,6 +157,9 @@ HASH-ALGO (a symbol).  Use NAME as the file name, or a generic name if #f."
                         ("git commit" . ,(git-reference-commit ref))
                         ("git recursive?" . ,(object->string
                                               (git-reference-recursive? ref))))
+                      #:leaked-env-vars '("http_proxy" "https_proxy"
+                                          "LC_ALL" "LC_MESSAGES" "LANG"
+                                          "COLUMNS")
 
                       #:system system
                       #:local-build? #t           ;don't offload repo cloning

guix/hg-download.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2015, 2016, 2017, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -92,6 +92,9 @@ HASH-ALGO (a symbol).  Use NAME as the file name, or a generic name if #f."
 
   (mlet %store-monad ((guile (package->derivation guile system)))
     (gexp->derivation (or name "hg-checkout") build
+                      #:leaked-env-vars '("http_proxy" "https_proxy"
+                                          "LC_ALL" "LC_MESSAGES" "LANG"
+                                          "COLUMNS")
                       #:system system
                       #:local-build? #t           ;don't offload repo cloning
                       #:hash-algo hash-algo

guix/import/cran.scm

@@ -230,6 +230,7 @@ from ~s: ~a (~s)~%"
                           (if (boolean? type) meta
                               (cons `(bioconductor-type . ,type) meta))))))))))
     ((git)
+     (and (string-prefix? "http" name)
           ;; Download the git repository at "NAME"
           (call-with-values
               (lambda () (download name #t))
@@ -239,7 +240,7 @@ from ~s: ~a (~s)~%"
                      (lambda (meta)
                        (cons* `(git . ,name)
                               `(git-commit . ,commit)
-                         meta))))))))
+                              meta)))))))))
 
 (define (listify meta field)
   "Look up FIELD in the alist META.  If FIELD contains a comma-separated
@@ -494,12 +495,16 @@ from the alist META, which was derived from the R package's DESCRIPTION file."
      "Fetch the metadata for PACKAGE-NAME from REPO and return the `package'
 s-expression corresponding to that package, or #f on failure."
      (let ((description (fetch-description repo package-name)))
-       (if (and (not description)
+       (if description
-                (eq? repo 'bioconductor))
+           (description->package repo description)
+           (case repo
+             ((git)
+              ;; Retry import from Bioconductor
+              (cran->guix-package package-name 'bioconductor))
+             ((bioconductor)
               ;; Retry import from CRAN
-           (cran->guix-package package-name 'cran)
+              (cran->guix-package package-name 'cran))
-           (and description
+             (else #f)))))))
-                (description->package repo description)))))))
 
 (define* (cran-recursive-import package-name #:optional (repo 'cran))
   (recursive-import package-name repo

guix/import/crate.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 David Craven <david@craven.ch>
+;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -22,6 +23,7 @@
   #:use-module ((guix download) #:prefix download:)
   #:use-module (gcrypt hash)
   #:use-module (guix http-client)
+  #:use-module (guix json)
   #:use-module (guix import json)
   #:use-module (guix import utils)
   #:use-module ((guix licenses) #:prefix license:)
@@ -30,7 +32,7 @@
   #:use-module (guix upstream)
   #:use-module (guix utils)
   #:use-module (ice-9 match)
-  #:use-module (ice-9 pretty-print) ; recursive
+  #:use-module (ice-9 regex)
   #:use-module (json)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-2)
@@ -39,46 +41,82 @@
             guix-package->crate-name
             %crate-updater))
 
-(define (crate-fetch crate-name callback)
+
-  "Fetch the metadata for CRATE-NAME from crates.io and call the callback."
+;;;
+;;; Interface to https://crates.io/api/v1.
+;;;
 
-  (define (crates->inputs crates)
+;; Crates.  A crate is essentially a "package".  It can have several
-    (sort (map (cut assoc-ref <> "crate_id") crates) string-ci<?))
+;; "versions", each of which has its own set of dependencies, license,
+;; etc.--see <crate-version> below.
+(define-json-mapping <crate> make-crate crate?
+  json->crate
+  (name          crate-name)                      ;string
+  (latest-version crate-latest-version "max_version") ;string
+  (home-page     crate-home-page "homepage")      ;string | #nil
+  (repository    crate-repository)                ;string
+  (description   crate-description)               ;string
+  (keywords      crate-keywords                   ;list of strings
+                 "keywords" vector->list)
+  (categories    crate-categories                 ;list of strings
+                 "categories" vector->list)
+  (versions      crate-versions "actual_versions" ;list of <crate-version>
+                 (lambda (vector)
+                   (map json->crate-version
+                        (vector->list vector))))
+  (links         crate-links))                    ;alist
 
-  (define (string->license string)
+;; Crate version.
-    (map spdx-string->license (string-split string #\/)))
+(define-json-mapping <crate-version> make-crate-version crate-version?
+  json->crate-version
+  (id            crate-version-id)                ;integer
+  (number        crate-version-number "num")      ;string
+  (download-path crate-version-download-path "dl_path") ;string
+  (readme-path   crate-version-readme-path "readme_path") ;string
+  (license       crate-version-license "license") ;string
+  (links         crate-version-links))            ;alist
 
-  (define (crate-kind-predicate kind)
+;; Crate dependency.  Each dependency (each edge in the graph) is annotated as
-    (lambda (dep) (string=? (assoc-ref dep "kind") kind)))
+;; being a "normal" dependency or a development dependency.  There also
+;; information about the minimum required version, such as "^0.0.41".
+(define-json-mapping <crate-dependency> make-crate-dependency
+  crate-dependency?
+  json->crate-dependency
+  (id            crate-dependency-id "crate_id")  ;string
+  (kind          crate-dependency-kind "kind"     ;'normal | 'dev
+                 string->symbol)
+  (requirement   crate-dependency-requirement "req")) ;string
 
-  (and-let* ((crate-json (json-fetch (string-append crate-url crate-name)))
+(define (lookup-crate name)
-             (crate (assoc-ref crate-json "crate"))
+  "Look up NAME on https://crates.io and return the corresopnding <crate>
-             (name (assoc-ref crate "name"))
+record or #f if it was not found."
-             (version (assoc-ref crate "max_version"))
+  (let ((json (json-fetch (string-append (%crate-base-url) "/api/v1/crates/"
-             (homepage (assoc-ref crate "homepage"))
+                                         name))))
-             (repository (assoc-ref crate "repository"))
+    (and=> (and json (assoc-ref json "crate"))
-             (synopsis (assoc-ref crate "description"))
+           (lambda (alist)
-             (description (assoc-ref crate "description"))
+             ;; The "versions" field of ALIST is simply a list of version IDs
-             (license (or (and=> (assoc-ref crate "license")
+             ;; (integers).  Here, we squeeze in the actual version
-                                 string->license)
+             ;; dictionaries that are not part of ALIST but are just more
-                          '()))                   ;missing license info
+             ;; convenient handled this way.
-             (path (string-append "/" version "/dependencies"))
+             (let ((versions (or (assoc-ref json "versions") '#())))
-             (deps-json (json-fetch (string-append crate-url name path)))
+               (json->crate `(,@alist
-             (deps (vector->list (assoc-ref deps-json "dependencies")))
+                              ("actual_versions" . ,versions))))))))
-             (dep-crates (filter (crate-kind-predicate "normal") deps))
+
-             (dev-dep-crates
+(define (crate-version-dependencies version)
-              (filter (lambda (dep)
+  "Return the list of <crate-dependency> records of VERSION, a
-                        (not ((crate-kind-predicate "normal") dep))) deps))
+<crate-version>."
-             (cargo-inputs (crates->inputs dep-crates))
+  (let* ((path (assoc-ref (crate-version-links version) "dependencies"))
-             (cargo-development-inputs (crates->inputs dev-dep-crates))
+         (url  (string-append (%crate-base-url) path)))
-             (home-page (match homepage
+    (match (assoc-ref (or (json-fetch url) '()) "dependencies")
-                          (() repository)
+      ((? vector? vector)
-                          (_ homepage))))
+       (map json->crate-dependency (vector->list vector)))
-    (callback #:name name #:version version
+      (_
-              #:cargo-inputs cargo-inputs
+       '()))))
-              #:cargo-development-inputs cargo-development-inputs
+
-              #:home-page home-page #:synopsis synopsis
+
-              #:description description #:license license)))
+;;;
+;;; Converting crates to Guix packages.
+;;;
 
 (define (maybe-cargo-inputs package-names)
   (match (package-names->package-inputs package-names)
@@ -138,10 +176,49 @@ and LICENSE."
          (close-port port)
          pkg))
 
+(define %dual-license-rx
+  ;; Dual licensing is represented by a string such as "MIT OR Apache-2.0".
+  ;; This regexp matches that.
+  (make-regexp "^(.*) OR (.*)$"))
+
 (define (crate->guix-package crate-name)
   "Fetch the metadata for CRATE-NAME from crates.io, and return the
 `package' s-expression corresponding to that package, or #f on failure."
-  (crate-fetch crate-name make-crate-sexp))
+  (define (string->license string)
+    (match (regexp-exec %dual-license-rx string)
+      (#f (list (spdx-string->license string)))
+      (m  (list (spdx-string->license (match:substring m 1))
+                (spdx-string->license (match:substring m 2))))))
+
+  (define (normal-dependency? dependency)
+    (eq? (crate-dependency-kind dependency) 'normal))
+
+  (define crate
+    (lookup-crate crate-name))
+
+  (and crate
+       (let* ((version        (find (lambda (version)
+                                      (string=? (crate-version-number version)
+                                                (crate-latest-version crate)))
+                                    (crate-versions crate)))
+              (dependencies   (crate-version-dependencies version))
+              (dep-crates     (filter normal-dependency? dependencies))
+              (dev-dep-crates (remove normal-dependency? dependencies))
+              (cargo-inputs   (sort (map crate-dependency-id dep-crates)
+                                    string-ci<?))
+              (cargo-development-inputs
+               (sort (map crate-dependency-id dev-dep-crates)
+                     string-ci<?)))
+         (make-crate-sexp #:name crate-name
+                          #:version (crate-version-number version)
+                          #:cargo-inputs cargo-inputs
+                          #:cargo-development-inputs cargo-development-inputs
+                          #:home-page (or (crate-home-page crate)
+                                          (crate-repository crate))
+                          #:synopsis (crate-description crate)
+                          #:description (crate-description crate)
+                          #:license (and=> (crate-version-license version)
+                                           string->license)))))
 
 (define (guix-package->crate-name package)
   "Return the crate name of PACKAGE."
@@ -157,6 +234,7 @@ and LICENSE."
 (define (crate-name->package-name name)
   (string-append "rust-" (string-join (string-split name #\_) "-")))
 
+
 ;;;
 ;;; Updater
 ;;;
@@ -175,8 +253,8 @@ and LICENSE."
 (define (latest-release package)
   "Return an <upstream-source> for the latest release of PACKAGE."
   (let* ((crate-name (guix-package->crate-name package))
-         (callback (lambda* (#:key version #:allow-other-keys) version))
+         (crate      (lookup-crate crate-name))
-         (version (crate-fetch crate-name callback))
+         (version    (crate-latest-version crate))
          (url        (crate-uri crate-name version)))
     (upstream-source
      (package (package-name package))

guix/import/opam.scm

@@ -238,7 +238,9 @@ path to the repository."
              (version (find-latest-version name repository))
              (file (string-append repository "/packages/" name "/" name "." version "/opam")))
     `(("metadata" ,@(get-metadata file))
-      ("version" . ,version))))
+      ("version" . ,(if (string-prefix? "v" version)
+                        (substring version 1)
+                        version)))))
 
 (define (opam->guix-package name)
   (and-let* ((opam-file (opam-fetch name))
@@ -283,7 +285,7 @@ path to the repository."
                                           'ocaml-build-system))
                        ,@(if (null? inputs)
                            '()
-                           `((inputs ,(list 'quasiquote inputs))))
+                           `((propagated-inputs ,(list 'quasiquote inputs))))
                        ,@(if (null? native-inputs)
                            '()
                            `((native-inputs ,(list 'quasiquote native-inputs))))

guix/json.scm

@@ -0,0 +1,62 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2018, 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 (guix json)
+  #:use-module (json)
+  #:use-module (srfi srfi-9)
+  #:export (define-json-mapping))
+
+;;; Commentary:
+;;;
+;;; Helpers to map JSON objects to SRFI-9 records.  Taken from (guix swh).
+;;;
+;;; Code:
+
+(define-syntax-rule (define-json-reader json->record ctor spec ...)
+  "Define JSON->RECORD as a procedure that converts a JSON representation,
+read from a port, string, or hash table, into a record created by CTOR and
+following SPEC, a series of field specifications."
+  (define (json->record input)
+    (let ((table (cond ((port? input)
+                        (json->scm input))
+                       ((string? input)
+                        (json-string->scm input))
+                       ((or (null? input) (pair? input))
+                        input))))
+      (let-syntax ((extract-field (syntax-rules ()
+                                    ((_ table (field key json->value))
+                                     (json->value (assoc-ref table key)))
+                                    ((_ table (field key))
+                                     (assoc-ref table key))
+                                    ((_ table (field))
+                                     (assoc-ref table
+                                                (symbol->string 'field))))))
+        (ctor (extract-field table spec) ...)))))
+
+(define-syntax-rule (define-json-mapping rtd ctor pred json->record
+                      (field getter spec ...) ...)
+  "Define RTD as a record type with the given FIELDs and GETTERs, à la SRFI-9,
+and define JSON->RECORD as a conversion from JSON to a record of this type."
+  (begin
+    (define-record-type rtd
+      (ctor field ...)
+      pred
+      (field getter) ...)
+
+    (define-json-reader json->record ctor
+      (field spec ...) ...)))