Merge branch 'staging' into core-updates

Makefile.am

@@ -661,17 +661,17 @@ SUPPORTED_SYSTEMS ?= x86_64-linux i686-linux armhf-linux aarch64-linux
 BINARY_TARBALLS =							\
   $(foreach system,$(SUPPORTED_SYSTEMS),guix-binary.$(system).tar.xz)
 
-# Systems supported by GuixSD.
+# Systems supported by Guix System.
-GUIXSD_SUPPORTED_SYSTEMS ?= x86_64-linux i686-linux
+GUIX_SYSTEM_SUPPORTED_SYSTEMS ?= x86_64-linux i686-linux
 
-# Systems for which we build GuixSD VMs.
+# Systems for which we build Guix VMs.
-GUIXSD_VM_SYSTEMS ?= x86_64-linux
+GUIX_SYSTEM_VM_SYSTEMS ?= x86_64-linux
 
-# Prefix of the GuixSD installation image file name.
+# Prefix of the Guix installation image file name.
-GUIXSD_IMAGE_BASE = guixsd-install-$(PACKAGE_VERSION)
+GUIX_SYSTEM_IMAGE_BASE = guix-system-install-$(PACKAGE_VERSION)
 
-# Prefix of the GuixSD VM image file name.
+# Prefix of the Guix VM image file name.
-GUIXSD_VM_IMAGE_BASE = guixsd-vm-image-$(PACKAGE_VERSION)
+GUIX_SYSTEM_VM_IMAGE_BASE = guix-system-vm-image-$(PACKAGE_VERSION)
 
 # The release process works in several phases:
 #
@@ -680,7 +680,7 @@ GUIXSD_VM_IMAGE_BASE = guixsd-vm-image-$(PACKAGE_VERSION)
 #   2. Update the 'guix' package so that it corresponds to the 'vX.Y' tag.
 #   3. Build the binary tarballs for that 'guix' package.
 #   4. Update the 'guix' package again.
-#   5. Build the GuixSD installation images.  The images will run 'guix'
+#   5. Build the installation images.  The images will run 'guix'
 #      corresponding to 'vX.Y' + 1 commit, and they will install 'vX.Y'.
 #
 # This 'release' target takes care of everything and copies the resulting
@@ -713,32 +713,32 @@ release: dist
 	   "`git rev-parse HEAD`"
 	git add $(top_srcdir)/gnu/packages/package-management.scm
 	git commit -m "gnu: guix: Update to `git rev-parse HEAD | cut -c1-7`."
-	for system in $(GUIXSD_SUPPORTED_SYSTEMS) ; do					\
+	for system in $(GUIX_SYSTEM_SUPPORTED_SYSTEMS) ; do				\
 	  image=`$(top_builddir)/pre-inst-env						\
 	    guix system disk-image							\
 	    --file-system-type=iso9660							\
             --system=$$system								\
 	    gnu/system/install.scm` ;							\
 	  if [ ! -f "$$image" ] ; then							\
-	    echo "failed to produced GuixSD installation image for $$system" >&2 ;	\
+	    echo "failed to produced Guix installation image for $$system" >&2 ;	\
 	    exit 1 ;									\
 	  fi ;										\
-	  xz < "$$image" > "$(releasedir)/$(GUIXSD_IMAGE_BASE).$$system.iso.xz.tmp" ;	\
+	  xz < "$$image" > "$(releasedir)/$(GUIX_SYSTEM_IMAGE_BASE).$$system.iso.xz.tmp" ;	\
-	  mv "$(releasedir)/$(GUIXSD_IMAGE_BASE).$$system.iso.xz.tmp"			\
+	  mv "$(releasedir)/$(GUIX_SYSTEM_IMAGE_BASE).$$system.iso.xz.tmp"		\
-	     "$(releasedir)/$(GUIXSD_IMAGE_BASE).$$system.iso.xz" ;			\
+	     "$(releasedir)/$(GUIX_SYSTEM_IMAGE_BASE).$$system.iso.xz" ;		\
 	done
-	for system in $(GUIXSD_VM_SYSTEMS) ; do						\
+	for system in $(GUIX_SYSTEM_VM_SYSTEMS) ; do					\
 	  image=`$(top_builddir)/pre-inst-env						\
 	    guix system vm-image							\
 	    --system=$$system								\
 	    gnu/system/examples/vm-image.tmpl` ;					\
 	  if [ ! -f "$$image" ] ; then							\
-	    echo "failed to produced GuixSD VM image for $$system" >&2 ;		\
+	    echo "failed to produced Guix VM image for $$system" >&2 ;			\
 	    exit 1 ;									\
 	  fi ;										\
-	  xz < "$$image" > "$(releasedir)/$(GUIXSD_VM_IMAGE_BASE).$$system.xz.tmp" ;	\
+	  xz < "$$image" > "$(releasedir)/$(GUIX_SYSTEM_VM_IMAGE_BASE).$$system.xz.tmp" ;	\
-	  mv "$(releasedir)/$(GUIXSD_VM_IMAGE_BASE).$$system.xz.tmp"			\
+	  mv "$(releasedir)/$(GUIX_SYSTEM_VM_IMAGE_BASE).$$system.xz.tmp"			\
-	     "$(releasedir)/$(GUIXSD_VM_IMAGE_BASE).$$system.xz" ;			\
+	     "$(releasedir)/$(GUIX_SYSTEM_VM_IMAGE_BASE).$$system.xz" ;			\
 	done
 	@echo
 	@echo "Congratulations!  All the release files are now in $(releasedir)."

doc/contributing.de.texi

@@ -27,6 +27,7 @@ beliebigen Namen oder ein Pseudonym ihrer Wahl verwenden.
 * Erstellung aus dem Git::   Das Neueste und Beste.
 * Guix vor der Installation ausführen::  Hacker-Tricks.
 * Perfekt eingerichtet::     Die richtigen Werkzeuge.
+* Paketrichtlinien::         Die Distribution wachsen lassen.
 * Code-Stil::                Wie Mitwirkende hygienisch arbeiten.
 * Einreichen von Patches::   Teilen Sie Ihre Arbeit.
 @end menu
@@ -114,15 +115,17 @@ lokalen Quellbaum vorgenommenen Änderungen zunächst zu testen, ohne sie
 tatsächlich zu installieren. So können Sie zwischen Ihrem
 Endnutzer-»Straßenanzug« und Ihrem »Faschingskostüm« unterscheiden.
 
-To that end, all the command-line tools can be used even if you have not run
+Zu diesem Zweck können alle Befehlszeilenwerkzeuge auch schon benutzt
-@code{make install}.  To do that, you first need to have an environment with
+werden, ohne dass Sie @code{make install} laufen lassen.  Dazu müssen Sie
-all the dependencies available (@pxref{Erstellung aus dem Git}), and then simply
+sich in einer Umgebung befinden, in der alle Abhängigkeiten von Guix
-prefix each command with @command{./pre-inst-env} (the @file{pre-inst-env}
+verfügbar sind (@pxref{Erstellung aus dem Git}) und darin einfach vor jeden
-script lives in the top build tree of Guix; it is generated by
+Befehl @command{./pre-inst-env} schreiben (das Skript @file{pre-inst-env}
-@command{./configure}), as in@footnote{The @option{-E} flag to
+befindet sich auf oberster Ebene im Verzeichnis, wo Guix erstellt wird, wo
-@command{sudo} guarantees that @code{GUILE_LOAD_PATH} is correctly set such
+es durch @command{./configure} erzeugt wird), zum Beispiel so@footnote{Die
-that @command{guix-daemon} and the tools it uses can find the Guile modules
+Befehlszeilenoption @option{-E} von @command{sudo} stellt sicher, dass
-they need.}:
+@code{GUILE_LOAD_PATH} richtig gesetzt wird, damit @command{guix-daemon} und
+die davon benutzten Werkzeuge die von ihnen benötigten Guile-Module finden
+können.}:
 
 @example
 $ sudo -E ./pre-inst-env guix-daemon --build-users-group=guixbuild
@@ -164,21 +167,25 @@ Das @command{pre-inst-env}-Skript richtet alle Umgebungsvariablen ein, die
 nötig sind, um dies zu ermöglichen, einschließlich @env{PATH} und
 @env{GUILE_LOAD_PATH}.
 
-Note that @command{./pre-inst-env guix pull} does @emph{not} upgrade the
+Beachten Sie, dass @command{./pre-inst-env guix pull} den lokalen Quellbaum
-local source tree; it simply updates the @file{~/.config/guix/current}
+@emph{nicht} aktualisiert; es aktualisiert lediglich die symbolische
-symlink (@pxref{Aufruf von guix pull}).  Run @command{git pull} instead if you
+Verknüpfung @file{~/.config/guix/current} (@pxref{Aufruf von guix pull}).  Um
-want to upgrade your local source tree.
+Ihren lokalen Quellbaum zu aktualisieren, müssen Sie stattdessen
+@command{git pull} benutzen.
 
 
 @node Perfekt eingerichtet
 @section Perfekt eingerichtet
 
-Um perfekt für das Hacken an Guix eingerichtet zu sein, brauchen Sie an sich
+The Perfect Setup to hack on Guix is basically the perfect setup used for
-dasselbe wie um perfekt für das Hacken mit Guile (@pxref{Using Guile in
+Guile hacking (@pxref{Using Guile in Emacs,,, guile, Guile Reference
-Emacs,,, guile, Guile Reference Manual}).  Zunächst brauchen Sie mehr als
+Manual}).  First, you need more than an editor, you need
-ein Textverarbeitungsprogramm, Sie brauchen
+@url{http://www.gnu.org/software/emacs, Emacs}, empowered by the wonderful
-@url{http://www.gnu.org/software/emacs, Emacs}, ermächtigt vom wunderbaren
+@url{http://nongnu.org/geiser/, Geiser}.  To set that up, run:
-@url{http://nongnu.org/geiser/, Geiser}.
+
+@example
+guix package -i emacs guile emacs-geiser
+@end example
 
 Geiser ermöglicht interaktive und inkrementelle Entwicklung aus Emacs
 heraus: Code kann in Puffern kompiliert und ausgewertet werden. Zugang zu
@@ -218,12 +225,14 @@ umzuschreiben. Vielleicht möchten Sie das Schnipselverzeichnis zu Ihrer
   (add-to-list 'yas-snippet-dirs "~/src/guix/etc/snippets"))
 @end lisp
 
-The commit message snippets depend on @url{https://magit.vc/, Magit} to
+Die Schnipsel für Commit-Nachrichten setzen @url{https://magit.vc/, Magit}
-display staged files.  When editing a commit message type @code{add}
+voraus, um zum Commit vorgemerkte Dateien anzuzeigen. Wenn Sie eine
-followed by @kbd{TAB} to insert a commit message template for adding a
+Commit-Nachricht bearbeiten, können Sie @code{add} gefolgt von @kbd{TAB}
-package; type @code{update} followed by @kbd{TAB} to insert a template for
+eintippen, um eine Commit-Nachrichten-Vorlage für das Hinzufügen eines
-updating a package; type @code{https} followed by @kbd{TAB} to insert a
+Pakets zu erhalten; tippen Sie @code{update} gefolgt von @kbd{TAB} ein, um
-template for changing the home page URI of a package to HTTPS.
+eine Vorlage zum Aktualisieren eines Pakets zu bekommen; tippen Sie
+@code{https} gefolgt von @kbd{TAB} ein, um eine Vorlage zum Ändern der
+Homepage-URI eines Pakets auf HTTPS einzufügen.
 
 Das Hauptschnipsel für @code{scheme-mode} wird ausgelöst, indem Sie
 @code{package...} gefolgt von @kbd{TAB} eintippen. Dieses Snippet fügt auch
@@ -233,6 +242,445 @@ Auslöse-Zeichenketten einfügen, die alle auf @code{...} enden, was selbst
 wieder weiter umgeschrieben werden kann.
 
 
+@node Paketrichtlinien
+@section Paketrichtlinien
+
+@cindex packages, creating
+The GNU distribution is nascent and may well lack some of your favorite
+packages.  This section describes how you can help make the distribution
+grow.
+
+Free software packages are usually distributed in the form of @dfn{source
+code tarballs}---typically @file{tar.gz} files that contain all the source
+files.  Adding a package to the distribution means essentially two things:
+adding a @dfn{recipe} that describes how to build the package, including a
+list of other packages required to build it, and adding @dfn{package
+metadata} along with that recipe, such as a description and licensing
+information.
+
+In Guix all this information is embodied in @dfn{package definitions}.
+Package definitions provide a high-level view of the package.  They are
+written using the syntax of the Scheme programming language; in fact, for
+each package we define a variable bound to the package definition, and
+export that variable from a module (@pxref{Paketmodule}).  However,
+in-depth Scheme knowledge is @emph{not} a prerequisite for creating
+packages.  For more information on package definitions, @pxref{Pakete definieren}.
+
+Once a package definition is in place, stored in a file in the Guix source
+tree, it can be tested using the @command{guix build} command
+(@pxref{Aufruf von guix build}).  For example, assuming the new package is
+called @code{gnew}, you may run this command from the Guix build tree
+(@pxref{Guix vor der Installation ausführen}):
+
+@example
+./pre-inst-env guix build gnew --keep-failed
+@end example
+
+Using @code{--keep-failed} makes it easier to debug build failures since it
+provides access to the failed build tree.  Another useful command-line
+option when debugging is @code{--log-file}, to access the build log.
+
+If the package is unknown to the @command{guix} command, it may be that the
+source file contains a syntax error, or lacks a @code{define-public} clause
+to export the package variable.  To figure it out, you may load the module
+from Guile to get more information about the actual error:
+
+@example
+./pre-inst-env guile -c '(use-modules (gnu packages gnew))'
+@end example
+
+Once your package builds correctly, please send us a patch
+(@pxref{Einreichen von Patches}).  Well, if you need help, we will be happy to
+help you too.  Once the patch is committed in the Guix repository, the new
+package automatically gets built on the supported platforms by
+@url{http://hydra.gnu.org/jobset/gnu/master, our continuous integration
+system}.
+
+@cindex substituter
+Users can obtain the new package definition simply by running @command{guix
+pull} (@pxref{Aufruf von guix pull}).  When @code{@value{SUBSTITUTE-SERVER}}
+is done building the package, installing the package automatically downloads
+binaries from there (@pxref{Substitute}).  The only place where human
+intervention is needed is to review and apply the patch.
+
+
+@menu
+* Software-Freiheit::        Was in die Distribution aufgenommen werden 
+                               darf.
+* Paketbenennung::           Was macht einen Namen aus?
+* Versionsnummern::          Wenn der Name noch nicht genug ist.
+* Zusammenfassungen und Beschreibungen::  Den Nutzern helfen, das richtige 
+                                            Paket zu finden.
+* Python-Module::            Ein Touch britischer Comedy.
+* Perl-Module::              Kleine Perlen.
+* Java-Pakete::              Kaffeepause.
+* Schriftarten::             Schriften verschriftlicht.
+@end menu
+
+@node Software-Freiheit
+@subsection Software-Freiheit
+
+@c ===========================================================================
+@c
+@c This file was generated with po4a. Translate the source file.
+@c
+@c ===========================================================================
+@c Adapted from http://www.gnu.org/philosophy/philosophy.html.
+@cindex free software
+The GNU operating system has been developed so that users can have freedom
+in their computing.  GNU is @dfn{free software}, meaning that users have the
+@url{http://www.gnu.org/philosophy/free-sw.html,four essential freedoms}: to
+run the program, to study and change the program in source code form, to
+redistribute exact copies, and to distribute modified versions.  Packages
+found in the GNU distribution provide only software that conveys these four
+freedoms.
+
+In addition, the GNU distribution follow the
+@url{http://www.gnu.org/distros/free-system-distribution-guidelines.html,free
+software distribution guidelines}.  Among other things, these guidelines
+reject non-free firmware, recommendations of non-free software, and discuss
+ways to deal with trademarks and patents.
+
+Some otherwise free upstream package sources contain a small and optional
+subset that violates the above guidelines, for instance because this subset
+is itself non-free code.  When that happens, the offending items are removed
+with appropriate patches or code snippets in the @code{origin} form of the
+package (@pxref{Pakete definieren}).  This way, @code{guix build --source}
+returns the ``freed'' source rather than the unmodified upstream source.
+
+
+@node Paketbenennung
+@subsection Paketbenennung
+
+@cindex package name
+A package has actually two names associated with it: First, there is the
+name of the @emph{Scheme variable}, the one following @code{define-public}.
+By this name, the package can be made known in the Scheme code, for instance
+as input to another package.  Second, there is the string in the @code{name}
+field of a package definition.  This name is used by package management
+commands such as @command{guix package} and @command{guix build}.
+
+Both are usually the same and correspond to the lowercase conversion of the
+project name chosen upstream, with underscores replaced with hyphens.  For
+instance, GNUnet is available as @code{gnunet}, and SDL_net as
+@code{sdl-net}.
+
+We do not add @code{lib} prefixes for library packages, unless these are
+already part of the official project name.  But @pxref{Python-Module} and
+@ref{Perl-Module} for special rules concerning modules for the Python and
+Perl languages.
+
+Font package names are handled differently, @pxref{Schriftarten}.
+
+
+@node Versionsnummern
+@subsection Versionsnummern
+
+@cindex package version
+We usually package only the latest version of a given free software
+project.  But sometimes, for instance for incompatible library versions, two
+(or more) versions of the same package are needed.  These require different
+Scheme variable names.  We use the name as defined in @ref{Paketbenennung}
+for the most recent version; previous versions use the same name, suffixed
+by @code{-} and the smallest prefix of the version number that may
+distinguish the two versions.
+
+The name inside the package definition is the same for all versions of a
+package and does not contain any version number.
+
+Zum Beispiel können für GTK in den Versionen 2.24.20 und 3.9.12 Pakete wie
+folgt geschrieben werden:
+
+@example
+(define-public gtk+
+  (package
+    (name "gtk+")
+    (version "3.9.12")
+    ...))
+(define-public gtk+-2
+  (package
+    (name "gtk+")
+    (version "2.24.20")
+    ...))
+@end example
+Wenn wir auch GTK 3.8.2 wollten, würden wir das Paket schreiben als
+@example
+(define-public gtk+-3.8
+  (package
+    (name "gtk+")
+    (version "3.8.2")
+    ...))
+@end example
+
+@c See <https://lists.gnu.org/archive/html/guix-devel/2016-01/msg00425.html>,
+@c for a discussion of what follows.
+@cindex version number, for VCS snapshots
+Occasionally, we package snapshots of upstream's version control system
+(VCS) instead of formal releases.  This should remain exceptional, because
+it is up to upstream developers to clarify what the stable release is.  Yet,
+it is sometimes necessary.  So, what should we put in the @code{version}
+field?
+
+Clearly, we need to make the commit identifier of the VCS snapshot visible
+in the version string, but we also need to make sure that the version string
+is monotonically increasing so that @command{guix package --upgrade} can
+determine which version is newer.  Since commit identifiers, notably with
+Git, are not monotonically increasing, we add a revision number that we
+increase each time we upgrade to a newer snapshot.  The resulting version
+string looks like this:
+
+@example
+2.0.11-3.cabba9e
+  ^    ^    ^
+  |    |    `-- upstream commit ID
+  |    |
+  |    `--- Guix package revision
+  |
+latest upstream version
+@end example
+
+It is a good idea to strip commit identifiers in the @code{version} field
+to, say, 7 digits.  It avoids an aesthetic annoyance (assuming aesthetics
+have a role to play here) as well as problems related to OS limits such as
+the maximum shebang length (127 bytes for the Linux kernel.)  It is best to
+use the full commit identifiers in @code{origin}s, though, to avoid
+ambiguities.  A typical package definition may look like this:
+
+@example
+(define my-package
+  (let ((commit "c3f29bc928d5900971f65965feaae59e1272a3f7")
+        (revision "1"))          ;Guix package revision
+    (package
+      (version (git-version "0.9" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "git://example.org/my-package.git")
+                      (commit commit)))
+                (sha256 (base32 "1mbikn@dots{}"))
+                (file-name (git-file-name name version))))
+      ;; @dots{}
+      )))
+@end example
+
+@node Zusammenfassungen und Beschreibungen
+@subsection Zusammenfassungen und Beschreibungen
+
+@cindex package description
+@cindex package synopsis
+As we have seen before, each package in GNU@tie{}Guix includes a synopsis
+and a description (@pxref{Pakete definieren}).  Synopses and descriptions
+are important: They are what @command{guix package --search} searches, and a
+crucial piece of information to help users determine whether a given package
+suits their needs.  Consequently, packagers should pay attention to what
+goes into them.
+
+Synopses must start with a capital letter and must not end with a period.
+They must not start with ``a'' or ``the'', which usually does not bring
+anything; for instance, prefer ``File-frobbing tool'' over ``A tool that
+frobs files''.  The synopsis should say what the package is---e.g., ``Core
+GNU utilities (file, text, shell)''---or what it is used for---e.g., the
+synopsis for GNU@tie{}grep is ``Print lines matching a pattern''.
+
+Keep in mind that the synopsis must be meaningful for a very wide audience.
+For example, ``Manipulate alignments in the SAM format'' might make sense
+for a seasoned bioinformatics researcher, but might be fairly unhelpful or
+even misleading to a non-specialized audience.  It is a good idea to come up
+with a synopsis that gives an idea of the application domain of the
+package.  In this example, this might give something like ``Manipulate
+nucleotide sequence alignments'', which hopefully gives the user a better
+idea of whether this is what they are looking for.
+
+Descriptions should take between five and ten lines.  Use full sentences,
+and avoid using acronyms without first introducing them.  Please avoid
+marketing phrases such as ``world-leading'', ``industrial-strength'', and
+``next-generation'', and avoid superlatives like ``the most
+advanced''---they are not helpful to users looking for a package and may
+even sound suspicious.  Instead, try to be factual, mentioning use cases and
+features.
+
+@cindex Texinfo markup, in package descriptions
+Descriptions can include Texinfo markup, which is useful to introduce
+ornaments such as @code{@@code} or @code{@@dfn}, bullet lists, or hyperlinks
+(@pxref{Overview,,, texinfo, GNU Texinfo}).  However you should be careful
+when using some characters for example @samp{@@} and curly braces which are
+the basic special characters in Texinfo (@pxref{Special Characters,,,
+texinfo, GNU Texinfo}).  User interfaces such as @command{guix package
+--show} take care of rendering it appropriately.
+
+Synopses and descriptions are translated by volunteers
+@uref{http://translationproject.org/domain/guix-packages.html, at the
+Translation Project} so that as many users as possible can read them in
+their native language.  User interfaces search them and display them in the
+language specified by the current locale.
+
+To allow @command{xgettext} to extract them as translatable strings,
+synopses and descriptions @emph{must be literal strings}.  This means that
+you cannot use @code{string-append} or @code{format} to construct these
+strings:
+
+@lisp
+(package
+  ;; @dots{}
+  (synopsis "This is translatable")
+  (description (string-append "This is " "*not*" " translatable.")))
+@end lisp
+
+Translation is a lot of work so, as a packager, please pay even more
+attention to your synopses and descriptions as every change may entail
+additional work for translators.  In order to help them, it is possible to
+make recommendations or instructions visible to them by inserting special
+comments like this (@pxref{xgettext Invocation,,, gettext, GNU Gettext}):
+
+@example
+;; TRANSLATORS: "X11 resize-and-rotate" should not be translated.
+(description "ARandR is designed to provide a simple visual front end
+for the X11 resize-and-rotate (RandR) extension. @dots{}")
+@end example
+
+
+@node Python-Module
+@subsection Python-Module
+
+@cindex python
+We currently package Python 2 and Python 3, under the Scheme variable names
+@code{python-2} and @code{python} as explained in @ref{Versionsnummern}.  To
+avoid confusion and naming clashes with other programming languages, it
+seems desirable that the name of a package for a Python module contains the
+word @code{python}.
+
+Some modules are compatible with only one version of Python, others with
+both.  If the package Foo compiles only with Python 3, we name it
+@code{python-foo}; if it compiles only with Python 2, we name it
+@code{python2-foo}. If it is compatible with both versions, we create two
+packages with the corresponding names.
+
+If a project already contains the word @code{python}, we drop this; for
+instance, the module python-dateutil is packaged under the names
+@code{python-dateutil} and @code{python2-dateutil}.  If the project name
+starts with @code{py} (e.g.@: @code{pytz}), we keep it and prefix it as
+described above.
+
+@subsubsection Specifying Dependencies
+@cindex inputs, for Python packages
+
+Dependency information for Python packages is usually available in the
+package source tree, with varying degrees of accuracy: in the
+@file{setup.py} file, in @file{requirements.txt}, or in @file{tox.ini}.
+
+Your mission, when writing a recipe for a Python package, is to map these
+dependencies to the appropriate type of ``input'' (@pxref{»package«-Referenz,
+inputs}).  Although the @code{pypi} importer normally does a good job
+(@pxref{Aufruf von guix import}), you may want to check the following check
+list to determine which dependency goes where.
+
+@itemize
+
+@item
+We currently package Python 2 with @code{setuptools} and @code{pip}
+installed like Python 3.4 has per default.  Thus you don't need to specify
+either of these as an input.  @command{guix lint} will warn you if you do.
+
+@item
+Python dependencies required at run time go into @code{propagated-inputs}.
+They are typically defined with the @code{install_requires} keyword in
+@file{setup.py}, or in the @file{requirements.txt} file.
+
+@item
+Python packages required only at build time---e.g., those listed with the
+@code{setup_requires} keyword in @file{setup.py}---or only for
+testing---e.g., those in @code{tests_require}---go into
+@code{native-inputs}.  The rationale is that (1) they do not need to be
+propagated because they are not needed at run time, and (2) in a
+cross-compilation context, it's the ``native'' input that we'd want.
+
+Examples are the @code{pytest}, @code{mock}, and @code{nose} test
+frameworks.  Of course if any of these packages is also required at
+run-time, it needs to go to @code{propagated-inputs}.
+
+@item
+Anything that does not fall in the previous categories goes to
+@code{inputs}, for example programs or C libraries required for building
+Python packages containing C extensions.
+
+@item
+If a Python package has optional dependencies (@code{extras_require}), it is
+up to you to decide whether to add them or not, based on their
+usefulness/overhead ratio (@pxref{Einreichen von Patches, @command{guix size}}).
+
+@end itemize
+
+
+@node Perl-Module
+@subsection Perl-Module
+
+@cindex perl
+Perl programs standing for themselves are named as any other package, using
+the lowercase upstream name.  For Perl packages containing a single class,
+we use the lowercase class name, replace all occurrences of @code{::} by
+dashes and prepend the prefix @code{perl-}.  So the class @code{XML::Parser}
+becomes @code{perl-xml-parser}.  Modules containing several classes keep
+their lowercase upstream name and are also prepended by @code{perl-}.  Such
+modules tend to have the word @code{perl} somewhere in their name, which
+gets dropped in favor of the prefix.  For instance, @code{libwww-perl}
+becomes @code{perl-libwww}.
+
+
+@node Java-Pakete
+@subsection Java-Pakete
+
+@cindex java
+Java programs standing for themselves are named as any other package, using
+the lowercase upstream name.
+
+To avoid confusion and naming clashes with other programming languages, it
+is desirable that the name of a package for a Java package is prefixed with
+@code{java-}.  If a project already contains the word @code{java}, we drop
+this; for instance, the package @code{ngsjava} is packaged under the name
+@code{java-ngs}.
+
+For Java packages containing a single class or a small class hierarchy, we
+use the lowercase class name, replace all occurrences of @code{.} by dashes
+and prepend the prefix @code{java-}.  So the class @code{apache.commons.cli}
+becomes package @code{java-apache-commons-cli}.
+
+
+@node Schriftarten
+@subsection Schriftarten
+
+@cindex Schriftarten
+For fonts that are in general not installed by a user for typesetting
+purposes, or that are distributed as part of a larger software package, we
+rely on the general packaging rules for software; for instance, this applies
+to the fonts delivered as part of the X.Org system or fonts that are part of
+TeX Live.
+
+To make it easier for a user to search for fonts, names for other packages
+containing only fonts are constructed as follows, independently of the
+upstream package name.
+
+The name of a package containing only one font family starts with
+@code{font-}; it is followed by the foundry name and a dash @code{-} if the
+foundry is known, and the font family name, in which spaces are replaced by
+dashes (and as usual, all upper case letters are transformed to lower
+case).  For example, the Gentium font family by SIL is packaged under the
+name @code{font-sil-gentium}.
+
+For a package containing several font families, the name of the collection
+is used in the place of the font family name.  For instance, the Liberation
+fonts consist of three families, Liberation Sans, Liberation Serif and
+Liberation Mono.  These could be packaged separately under the names
+@code{font-liberation-sans} and so on; but as they are distributed together
+under a common name, we prefer to package them together as
+@code{font-liberation}.
+
+In the case where several formats of the same font family or font collection
+are packaged separately, a short form of the format, prepended by a dash, is
+added to the package name.  We use @code{-ttf} for TrueType fonts,
+@code{-otf} for OpenType fonts and @code{-type1} for PostScript Type 1
+fonts.
+
+
 @node Code-Stil
 @section Code-Stil
 
@@ -382,6 +830,33 @@ geänderte Paket bezeichnet, und beheben Sie alle gemeldeten Fehler
 Stellen Sie sicher, dass das Paket auf Ihrer Plattform erstellt werden kann,
 indem Sie @code{guix build @var{Paket}} ausführen.
 
+@item
+We recommend you also try building the package on other supported
+platforms.  As you may not have access to actual hardware platforms, we
+recommend using the @code{qemu-binfmt-service-type} to emulate them.  In
+order to enable it, add the following service to the list of services in
+your @code{operating-system} configuration:
+
+@example
+(service qemu-binfmt-service-type
+ (qemu-binfmt-configuration
+   (platforms (lookup-qemu-platforms "arm" "aarch64" "ppc" "mips64el"))
+   (guix-support? #t)))
+@end example
+
+Then reconfigure your system.
+
+You can then build packages for different platforms by specifying the
+@code{--system} option.  For example, to build the "hello" package for the
+armhf, aarch64, powerpc, or mips64 architectures, you would run the
+following commands, respectively:
+@example
+guix build --system=armhf-linux --rounds=2 hello
+guix build --system=aarch64-linux --rounds=2 hello
+guix build --system=powerpc-linux --rounds=2 hello
+guix build --system=mips64el-linux --rounds=2 hello
+@end example
+
 @item
 @cindex gebündelt
 Achten Sie darauf, dass im Paket keine Software gebündelt mitgeliefert wird,
@@ -399,22 +874,18 @@ einzuspielen, die aber das gesamte System betreffen — gebündelt
 mitgelieferte Kopien würden dies verhindern.
 
 @item
-Schauen Sie sich das von @command{guix size} ausgegebene Profil an
+Take a look at the profile reported by @command{guix size} (@pxref{Aufruf von guix size}).  This will allow you to notice references to other packages
-(@pxref{Aufruf von guix size}). Dadurch können Sie Referenzen auf andere
+unwillingly retained.  It may also help determine whether to split the
-Pakete finden, die ungewollt vorhanden sind. Dies kann auch dabei helfen, zu
+package (@pxref{Pakete mit mehreren Ausgaben.}), and which optional
-entscheiden, ob das Paket aufgespalten werden sollte (@pxref{Pakete mit mehreren Ausgaben.}) und welche optionalen Abhängigkeiten verwendet werden
+dependencies should be used.  In particular, avoid adding @code{texlive} as
-sollten.
+a dependency: because of its extreme size, use @code{texlive-tiny} or
+@code{texlive-union} instead.
 
 @item
 Achten Sie bei wichtigen Änderungen darauf, dass abhängige Pakete (falls
 vorhanden) nicht von der Änderung beeinträchtigt werden; @code{guix refresh
 --list-dependent @var{Paket}} hilft Ihnen dabei (@pxref{Aufruf von guix refresh}).
 
-@c ===========================================================================
-@c
-@c This file was generated with po4a. Translate the source file.
-@c
-@c ===========================================================================
 @c See <https://lists.gnu.org/archive/html/guix-devel/2016-10/msg00933.html>.
 @cindex Branching-Strategie
 @cindex Neuerstellungs-Zeitplan
@@ -438,17 +909,20 @@ beeinträchtigende Änderungen umfassen). Dieser Branch wird planmäßig in
 @code{master} alle 2,5 Monate oder so gemerget.
 @end table
 
-All these branches are @uref{https://hydra.gnu.org/project/gnu, tracked by
+All diese Branches werden kontinuierlich
-our build farm} and merged into @code{master} once everything has been
+@uref{https://hydra.gnu.org/project/gnu, auf unserer Build-Farm} erstellt
-successfully built.  This allows us to fix issues before they hit users, and
+und in @code{master} gemerget, sobald alles erfolgreich erstellt worden
-to reduce the window during which pre-built binaries are not available.
+ist. Dadurch können wir Probleme beheben, bevor sie bei Nutzern auftreten,
+und zudem das Zeitfenster, während dessen noch keine vorerstellten
+Binärdateien verfügbar sind, verkürzen.
 
 @c TODO: It would be good with badges on the website that tracks these
 @c branches.  Or maybe even a status page.
-Generally, branches other than @code{master} are considered @emph{frozen} if
+Im Allgemeinen werden Branches außer @code{master} als @emph{unveränderlich}
-there has been a recent evaluation, or there is a corresponding @code{-next}
+angesehen, wenn sie kürzlich ausgewertet wurden oder ein entsprechender
-branch.  Please ask on the mailing list or IRC if unsure where to place a
+@code{-next}-Branch existiert. Bitte fragen Sie auf der Mailing-Liste oder
-patch.
+IRC, wenn Sie sich nicht sicher sind, wo ein Patch eingespielt werden
+sollte.
 
 @item
 @cindex Determinismus, von Erstellungsprozessen
@@ -468,16 +942,14 @@ Dies reicht aus, um eine ganze Klasse häufiger Ursachen von
 Nichtdeterminismus zu finden, wie zum Beispiel Zeitstempel oder
 zufallsgenerierte Ausgaben im Ergebnis der Erstellung.
 
-Eine weitere Möglichkeit ist, @command{guix challenge} (@pxref{Aufruf von guix challenge}) zu benutzen. Sie können es ausführen, sobald ein Paket commitet
+Another option is to use @command{guix challenge} (@pxref{Aufruf von guix challenge}).  You may run it once the package has been committed and built
-und von @code{hydra.gnu.org} erstellt wurde, um zu sehen, ob dort dasselbe
+by @code{@value{SUBSTITUTE-SERVER}} to check whether it obtains the same
-Ergebnis wie bei Ihnen geliefert wurde. Noch besser: Finden Sie eine andere
+result as you did.  Better yet: Find another machine that can build it and
-Maschine, die das Paket erstellen kann, und führen Sie @command{guix
+run @command{guix publish}.  Since the remote build machine is likely
-publish} aus. Da sich die entfernte Erstellungsmaschine wahrscheinlich von
+different from yours, this can catch non-determinism issues related to the
-Ihrer unterscheidet, können Sie auf diese Weise Probleme durch
+hardware---e.g., use of different instruction set extensions---or to the
-Nichtdeterminismus erkennen, die mit der Hardware zu tun haben — zum
+operating system kernel---e.g., reliance on @code{uname} or @file{/proc}
-Beispiel die Nutzung anderer Befehlssatzerweiterungen — oder mit dem
+files.
-Betriebssystem-Kernel — zum Beispiel, indem @code{uname} oder
-@file{/proc}-Dateien verwendet werden.
 
 @item
 Beim Schreiben von Dokumentation achten Sie bitte auf eine
@@ -500,11 +972,13 @@ wollen Sie dies automatisch tun lassen durch das Skript
 @command{etc/indent-code.el} (@pxref{Formatierung von Code}).
 
 @item
-When possible, use mirrors in the source URL (@pxref{Aufruf von guix download}).  Use reliable URLs, not generated ones.  For instance, GitHub
+Benutzen Sie, wenn möglich, Spiegelserver (Mirrors) in der Quell-URL
-archives are not necessarily identical from one generation to the next, so
+(@pxref{Aufruf von guix download}). Verwenden Sie verlässliche URLs, keine
-in this case it's often better to clone the repository.  Don't use the
+automatisch generierten. Zum Beispiel sind Archive von GitHub nicht immer
-@command{name} field in the URL: it is not very useful and if the name
+identisch von einer Generation auf die nächste, daher ist es in diesem Fall
-changes, the URL will probably be wrong.
+besser, als Quelle einen Klon des Repositorys zu verwenden. Benutzen Sie
+@emph{nicht} das @command{name}-Feld beim Angeben der URL; er hilft nicht
+wirklich und wenn sich der Name ändert, stimmt die URL nicht mehr.
 
 @end enumerate
 

doc/guix.texi

@@ -165,10 +165,17 @@ System Installation
 * Hardware Considerations::     Supported hardware.
 * USB Stick and DVD Installation::  Preparing the installation medium.
 * Preparing for Installation::  Networking, partitioning, etc.
-* Proceeding with the Installation::  The real thing.
+* Guided Graphical Installation::  Easy graphical installation.
+* Manual Installation::         Manual installation for wizards.
+* After System Installation::   When installation succeeded.
 * Installing Guix in a VM::     Guix System playground.
 * Building the Installation Image::  How this comes to be.
 
+Manual Installation
+
+* Keyboard Layout and Networking and Partitioning:: Initial setup.
+* Proceeding with the Installation::  Installing.
+
 Package Management
 
 * Features::                    How Guix will make your life brighter.
@@ -1777,7 +1784,9 @@ available.
 * Hardware Considerations::     Supported hardware.
 * USB Stick and DVD Installation::  Preparing the installation medium.
 * Preparing for Installation::  Networking, partitioning, etc.
-* Proceeding with the Installation::  The real thing.
+* Guided Graphical Installation::  Easy graphical installation.
+* Manual Installation::         Manual installation for wizards.
+* After System Installation::   When installation succeeded.
 * Installing Guix in a VM::     Guix System playground.
 * Building the Installation Image::  How this comes to be.
 @end menu
@@ -1866,7 +1875,7 @@ about their support in GNU/Linux.
 
 An ISO-9660 installation image that can be written to a USB stick or
 burnt to a DVD can be downloaded from
-@indicateurl{https://alpha.gnu.org/gnu/guix/guixsd-install-@value{VERSION}.@var{system}.iso.xz},
+@indicateurl{https://alpha.gnu.org/gnu/guix/guix-system-install-@value{VERSION}.@var{system}.iso.xz},
 where @var{system} is one of:
 
 @table @code
@@ -1882,8 +1891,8 @@ Make sure to download the associated @file{.sig} file and to verify the
 authenticity of the image against it, along these lines:
 
 @example
-$ wget https://alpha.gnu.org/gnu/guix/guixsd-install-@value{VERSION}.@var{system}.iso.xz.sig
+$ wget https://alpha.gnu.org/gnu/guix/guix-system-install-@value{VERSION}.@var{system}.iso.xz.sig
-$ gpg --verify guixsd-install-@value{VERSION}.@var{system}.iso.xz.sig
+$ gpg --verify guix-system-install-@value{VERSION}.@var{system}.iso.xz.sig
 @end example
 
 If that command fails because you do not have the required public key,
@@ -1910,7 +1919,7 @@ To copy the image to a USB stick, follow these steps:
 Decompress the image using the @command{xz} command:
 
 @example
-xz -d guixsd-install-@value{VERSION}.@var{system}.iso.xz
+xz -d guix-system-install-@value{VERSION}.@var{system}.iso.xz
 @end example
 
 @item
@@ -1919,7 +1928,7 @@ its device name.  Assuming that the USB stick is known as @file{/dev/sdX},
 copy the image with:
 
 @example
-dd if=guixsd-install-@value{VERSION}.@var{system}.iso of=/dev/sdX
+dd if=guix-system-install-@value{VERSION}.@var{system}.iso of=/dev/sdX
 sync
 @end example
 
@@ -1935,7 +1944,7 @@ To copy the image to a DVD, follow these steps:
 Decompress the image using the @command{xz} command:
 
 @example
-xz -d guixsd-install-@value{VERSION}.@var{system}.iso.xz
+xz -d guix-system-install-@value{VERSION}.@var{system}.iso.xz
 @end example
 
 @item
@@ -1944,7 +1953,7 @@ its device name.  Assuming that the DVD drive is known as @file{/dev/srX},
 copy the image with:
 
 @example
-growisofs -dvd-compat -Z /dev/srX=guixsd-install-@value{VERSION}.@var{system}.iso
+growisofs -dvd-compat -Z /dev/srX=guix-system-install-@value{VERSION}.@var{system}.iso
 @end example
 
 Access to @file{/dev/srX} usually requires root privileges.
@@ -1963,21 +1972,19 @@ Guix System in a virtual machine (VM).
 @node Preparing for Installation
 @section Preparing for Installation
 
-Once you have successfully booted your computer using the installation medium,
+Once you have booted, you can use the guided graphical installer, which makes
-you should end up with the welcome page of the graphical installer.  The
+it easy to get started (@pxref{Guided Graphical Installation}).  Alternately,
-graphical installer is a text-based user interface built upon the newt
+if you are already familiar with GNU/Linux and if you want more control than
-library.  It shall guide you through all the different steps needed to install
+what the graphical installer provides, you can choose the ``manual''
-GNU@tie{}Guix System.  However, as the graphical installer is still under heavy
+installation process (@pxref{Manual Installation}).
-development, you might want to fallback to the original, shell based install
-process, by switching to TTYs 3 to 6 with the shortcuts CTRL-ALT-F[3-6]. The
-following sections describe the installation procedure assuming you're using
-one of those TTYs. They are configured and can be used to run commands as
-root.
 
-TTY2 shows this documentation, browsable using the Info reader commands
+The graphical installer is available on TTY1.  You can obtain root shells on
-(@pxref{Top,,, info-stnd, Stand-alone GNU Info}).  The installation system
+TTYs 3 to 6 by hitting @kbd{ctrl-alt-f3}, @kbd{ctrl-alt-f4}, etc.  TTY2 shows
-runs the GPM mouse daemon, which allows you to select text with the left mouse
+this documentation and you can reach it with @kbd{ctrl-alt-f2}.  Documentation
-button and to paste it with the middle button.
+is browsable using the Info reader commands (@pxref{Top,,, info-stnd,
+Stand-alone GNU Info}).  The installation system runs the GPM mouse daemon,
+which allows you to select text with the left mouse button and to paste it
+with the middle button.
 
 @quotation Note
 Installation requires access to the Internet so that any missing
@@ -1985,12 +1992,65 @@ dependencies of your system configuration can be downloaded.  See the
 ``Networking'' section below.
 @end quotation
 
-The installation system includes many common tools needed for this task.
+@node Guided Graphical Installation
-But it is also a full-blown Guix System, which means that you can
+@section Guided Graphical Installation
-install additional packages, should you need it, using @command{guix
-package} (@pxref{Invoking guix package}).
 
-@subsection Keyboard Layout
+The graphical installer is a text-based user interface.  It will guide you,
+with dialog boxes, through the steps needed to install GNU@tie{}Guix System.
+
+The first dialog boxes allow you to set up the system as you use it during the
+installation: you can choose the language, keyboard layout, and set up
+networking, which will be used during the installation.  The image below shows
+the networking dialog.
+
+@image{images/installer-network,5in,, networking setup with the graphical installer}
+
+Later steps allow you to partition your hard disk, as shown in the image
+below, to choose whether or not to use encrypted file systems, to enter the
+host name and root password, and to create an additional account, among other
+things.
+
+@image{images/installer-partitions,5in,, partitioning with the graphical installer}
+
+Note that, at any time, the installer allows you to exit the current
+installation step and resume at a previous step, as show in the image below.
+
+@image{images/installer-resume,5in,, resuming the installation process}
+
+Once you're done, the installer produces an operating system configuration and
+displays it (@pxref{Using the Configuration System}).  At that point you can
+hit ``OK'' and installation will proceed.  On success, you can reboot into the
+new system and enjoy.  @xref{After System Installation}, for what's next!
+
+
+@node Manual Installation
+@section Manual Installation
+
+This section describes how you would ``manually'' install GNU@tie{}Guix System
+on your machine.  This option requires familiarity with GNU/Linux, with the
+shell, and with common administration tools.  If you think this is not for
+you, consider using the guided graphical installer (@pxref{Guided Graphical
+Installation}).
+
+The installation system provides root shells on TTYs 3 to 6; press
+@kbd{ctrl-alt-f3}, @kbd{ctrl-alt-f4}, and so on to reach them.  It includes
+many common tools needed to install the system.  But it is also a full-blown
+Guix System, which means that you can install additional packages, should you
+need it, using @command{guix package} (@pxref{Invoking guix package}).
+
+@menu
+* Keyboard Layout and Networking and Partitioning:: Initial setup.
+* Proceeding with the Installation::  Installing.
+@end menu
+
+@node Keyboard Layout and Networking and Partitioning
+@subsection Keyboard Layout, Networking, and Partitioning
+
+Before you can install the system, you may want to adjust the keyboard layout,
+set up networking, and partition your target hard disk.  This section will
+guide you through this.
+
+@subsubsection Keyboard Layout
 
 @cindex keyboard layout
 The installation image uses the US qwerty keyboard layout.  If you want
@@ -2005,7 +2065,7 @@ See the files under @file{/run/current-system/profile/share/keymaps} for
 a list of available keyboard layouts.  Run @command{man loadkeys} for
 more information.
 
-@subsection Networking
+@subsubsection Networking
 
 Run the following command to see what your network interfaces are called:
 
@@ -2098,7 +2158,7 @@ herd start ssh-daemon
 Make sure to either set a password with @command{passwd}, or configure
 OpenSSH public key authentication before logging in.
 
-@subsection Disk Partitioning
+@subsubsection Disk Partitioning
 
 Unless this has already been done, the next step is to partition, and
 then format the target partition(s).
@@ -2219,7 +2279,7 @@ file in its file system as described above, then the encryption also
 protects the swap file, just like any other file in that file system.
 
 @node Proceeding with the Installation
-@section Proceeding with the Installation
+@subsection Proceeding with the Installation
 
 With the target partitions ready and the target root mounted on
 @file{/mnt}, we're ready to go.  First, run:
@@ -2303,9 +2363,14 @@ in the new system is initially empty; other users' passwords need to be
 initialized by running the @command{passwd} command as @code{root},
 unless your configuration specifies otherwise
 (@pxref{user-account-password, user account passwords}).
+@xref{After System Installation}, for what's next!
 
-@cindex upgrading Guix System
+
-From then on, you can update the system whenever you want by running, say:
+@node After System Installation
+@section After System Installation
+
+Success, you've now booted into Guix System!  From then on, you can update the
+system whenever you want by running, say:
 
 @example
 guix pull
@@ -2326,8 +2391,8 @@ explicitly run root's @command{guix}, type @command{sudo -i guix @dots{}}.
 @end quotation
 
 Join us on @code{#guix} on the Freenode IRC network or on
-@email{guix-devel@@gnu.org} to share your experience---good or not so
+@email{guix-devel@@gnu.org} to share your experience!
-good.
+
 
 @node Installing Guix in a VM
 @section Installing Guix in a Virtual Machine
@@ -2364,7 +2429,7 @@ Boot the USB installation image in an VM:
 @example
 qemu-system-x86_64 -m 1024 -smp 1 \
   -net user -net nic,model=virtio -boot menu=on \
-  -drive file=guixsd-install-@value{VERSION}.@var{system}.iso \
+  -drive file=guix-system-install-@value{VERSION}.@var{system}.iso \
   -drive file=guixsd.img
 @end example
 
@@ -14165,7 +14230,7 @@ field of an @code{operating-system} declaration (@pxref{operating-system
 Reference, @code{services}}).
 
 Additionally, the @code{gnome-desktop-service},
-@code{xfce-desktop-service}, @code{mate-desktop-service} and
+@code{xfce-desktop-service}, @code{mate-desktop-service-type} and
 @code{enlightenment-desktop-service-type} procedures can add GNOME, XFCE, MATE
 and/or Enlightenment to a system.  To ``add GNOME'' means that system-level
 services like the backlight adjustment helpers and the power management
@@ -14181,8 +14246,8 @@ administrator's password via the standard polkit graphical interface.
 To ``add MATE'' means that @code{polkit} and @code{dbus} are extended
 appropriately, allowing MATE to operate with elevated privileges on a
 limited number of special-purpose system interfaces.  Additionally,
-adding a service made by @code{mate-desktop-service} adds the MATE
+adding a service of type @code{mate-desktop-service-type} adds the MATE
-metapackage to the system profile.  ``Adding ENLIGHTENMENT'' means that
+metapackage to the system profile.  ``Adding Enlightenment'' means that
 @code{dbus} is extended appropriately, and several of Enlightenment's binaries
 are set as setuid, allowing Enlightenment's screen locker and other
 functionality to work as expetected.
@@ -14209,13 +14274,26 @@ file system as root from within a user session, after the user has
 authenticated with the administrator's password.
 @end deffn
 
-@deffn {Scheme Procedure} mate-desktop-service
+@deffn {Scheme Variable} mate-desktop-service-type
-Return a service that adds the @code{mate} package to the system
+This is the type of the service that runs the @uref{https://mate-desktop.org/,
+MATE desktop environment}.  Its value is a @code{mate-desktop-configuration}
+object (see below.)
+
+This service adds the @code{mate} package to the system
 profile, and extends polkit with the actions from
 @code{mate-settings-daemon}.
 @end deffn
 
-@deffn {Scheme Procedure} enlightenment-desktop-service-type
+@deftp {Data Type} mate-desktop-configuration
+Configuration record for the MATE desktop environment.
+
+@table @asis
+@item @code{mate} (default @code{mate})
+The MATE package to use.
+@end table
+@end deftp
+
+@deffn {Scheme Variable} enlightenment-desktop-service-type
 Return a service that adds the @code{enlightenment} package to the system
 profile, and extends dbus with actions from @code{efl}.
 @end deffn
@@ -16471,7 +16549,7 @@ Defaults to @samp{"internal_plain"}.
 
 @deftypevr {@code{prosody-configuration} parameter} maybe-string log
 Set logging options.  Advanced logging configuration is not yet supported
-by the Guix Prosody Service.  See @url{https://prosody.im/doc/logging}.
+by the Prosody service.  See @url{https://prosody.im/doc/logging}.
 Defaults to @samp{"*syslog"}.
 @end deftypevr
 
@@ -23347,7 +23425,7 @@ system configuration file.  You can then load the image and launch a
 Docker container using commands like the following:
 
 @example
-image_id="$(docker load < guixsd-docker-image.tar.gz)"
+image_id="$(docker load < guix-system-docker-image.tar.gz)"
 docker run -e GUIX_NEW_SYSTEM=/var/guix/profiles/system \\
     --entrypoint /var/guix/profiles/system/profile/bin/guile \\
     $image_id /var/guix/profiles/system/boot
@@ -23533,7 +23611,7 @@ example graph.
 @cindex virtual machine
 To run Guix in a virtual machine (VM), one can either use the
 pre-built Guix VM image distributed at
-@indicateurl{https://alpha.gnu.org/gnu/guix/guixsd-vm-image-@value{VERSION}.@var{system}.xz}
+@indicateurl{https://alpha.gnu.org/gnu/guix/guix-system-vm-image-@value{VERSION}.@var{system}.xz}
 , or build their own virtual machine image using @command{guix system
 vm-image} (@pxref{Invoking guix system}).  The returned image is in
 qcow2 format, which the @uref{http://qemu.org/, QEMU emulator} can

doc/local.mk

@@ -1,6 +1,6 @@
 # GNU Guix --- Functional package management for GNU
 # Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
-# Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+# Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 # Copyright © 2013 Andreas Enge <andreas@enge.fr>
 # Copyright © 2016 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 # Copyright © 2016, 2018 Mathieu Lirzin <mthl@gnu.org>
@@ -112,7 +112,10 @@ $(srcdir)/%D%/contributing.%.texi: po/doc/guix-manual.%.po
 infoimagedir = $(infodir)/images
 dist_infoimage_DATA =				\
   $(DOT_FILES:%.dot=%.png)			\
-  %D%/images/coreutils-size-map.png
+  %D%/images/coreutils-size-map.png		\
+  %D%/images/installer-network.png		\
+  %D%/images/installer-partitions.png		\
+  %D%/images/installer-resume.png
 
 # Try hard to obtain an image size and aspect that's reasonable for inclusion
 # in an Info or PDF document.

gnu/bootloader/extlinux.scm

@@ -57,10 +57,10 @@ corresponding to old generations of the system."
     #~(call-with-output-file #$output
         (lambda (port)
           (let ((timeout #$(bootloader-configuration-timeout config)))
-            (format port "# This file was generated from your GuixSD configuration.  Any changes
+            (format port "# This file was generated from your Guix configuration.  Any changes
 # will be lost upon reconfiguration.
 UI menu.c32
-MENU TITLE GuixSD Boot Options
+MENU TITLE GNU Guix Boot Options
 PROMPT ~a
 TIMEOUT ~a~%"
                     (if (> timeout 0) 1 0)

gnu/bootloader/grub.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Chris Marusich <cmmarusich@gmail.com>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
@@ -334,7 +334,7 @@ entries corresponding to old generations of the system."
     #~(call-with-output-file #$output
         (lambda (port)
           (format port
-                  "# This file was generated from your GuixSD configuration.  Any changes
+                  "# This file was generated from your Guix configuration.  Any changes
 # will be lost upon reconfiguration.
 ")
           #$sugar
@@ -380,7 +380,7 @@ submenu \"GNU system, old configurations...\" {~%")
       ;; system whose root is mounted at MOUNT-POINT.
       (let ((grub-install (string-append bootloader "/sbin/grub-install"))
             (install-dir (string-append mount-point "/boot"))
-            ;; When installing GuixSD, it's common to mount EFI-DIR below
+            ;; When installing Guix, it's common to mount EFI-DIR below
             ;; MOUNT-POINT rather than /boot/efi on the live image.
             (target-esp (if (file-exists? (string-append mount-point efi-dir))
                             (string-append mount-point efi-dir)
@@ -389,7 +389,7 @@ submenu \"GNU system, old configurations...\" {~%")
         ;; root partition.
         (setenv "GRUB_ENABLE_CRYPTODISK" "y")
         (unless (zero? (system* grub-install "--boot-directory" install-dir
-                                "--bootloader-id=GuixSD"
+                                "--bootloader-id=Guix"
                                 "--efi-directory" target-esp))
           (error "failed to install GRUB (EFI)")))))
 

gnu/build/linux-modules.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2016, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2016, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -47,7 +47,8 @@
 
             device-module-aliases
             known-module-aliases
-            matching-modules))
+            matching-modules
+            missing-modules))
 
 ;;; Commentary:
 ;;;
@@ -463,4 +464,26 @@ ALIAS is a string like \"scsi:t-0x00\" as returned by
                       module)))
               known-aliases))
 
+(define* (missing-modules device modules-provided)
+  "Assuming MODULES-PROVIDED lists kernel modules that are already
+provided--e.g., in the initrd, return the list of missing kernel modules that
+are required to access DEVICE."
+  (define aliases
+    ;; Attempt to load 'modules.alias' from the current kernel, assuming we're
+    ;; on Guix System, and assuming that corresponds to the kernel we'll be
+    ;; installing.
+    (known-module-aliases))
+
+  (if aliases
+      (let* ((modules  (delete-duplicates
+                        (append-map (cut matching-modules <> aliases)
+                                    (device-module-aliases device))))
+
+             ;; Module names (not file names) are supposed to use underscores
+             ;; instead of hyphens.  MODULES is a list of module names, whereas
+             ;; LINUX-MODULES is file names without '.ko', so normalize them.
+             (provided (map file-name->module-name modules-provided)))
+        (remove (cut member <> provided) modules))
+      '()))
+
 ;;; linux-modules.scm ends here

gnu/build/vm.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
@@ -422,7 +422,7 @@ SYSTEM-DIRECTORY is the name of the directory of the 'system' derivation."
             (string-append "boot/grub/grub.cfg=" config-file))))
 
 (define* (make-iso9660-image grub config-file os-drv target
-                             #:key (volume-id "GuixSD_image") (volume-uuid #f)
+                             #:key (volume-id "Guix_image") (volume-uuid #f)
                              register-closures? (closures '()))
   "Given a GRUB package, creates an iso image as TARGET, using CONFIG-FILE as
 GRUB configuration and OS-DRV as the stuff in it."
@@ -550,7 +550,7 @@ passing it a directory name where it is mounted."
           (lambda (port)
             (format port
                     "insmod part_msdos~@
-                    search --set=root --label GuixSD_image~@
+                    search --set=root --label Guix_image~@
                     configfile /boot/grub/grub.cfg~%")))
 
         (display "creating EFI firmware image...")

gnu/ci.scm

@@ -235,7 +235,7 @@ system.")
             (system-test-value test))))
 
       `((derivation . ,(derivation-file-name drv))
-        (description . ,(format #f "GuixSD '~a' system test"
+        (description . ,(format #f "Guix '~a' system test"
                                 (system-test-name test)))
         (long-description . ,(system-test-description test))
         (license . ,(license-name gpl3+))
@@ -270,7 +270,7 @@ system.")
     `((derivation . ,(derivation-file-name drv))
       (description . "Stand-alone binary Guix tarball")
       (long-description . "This is a tarball containing binaries of Guix and
-all its dependencies, and ready to be installed on non-GuixSD distributions.")
+all its dependencies, and ready to be installed on \"foreign\" distributions.")
       (license . ,(license-name gpl3+))
       (home-page . ,%guix-home-page-url)
       (maintainers . ("bug-guix@gnu.org"))))

gnu/installer/newt/network.scm

@@ -113,7 +113,7 @@ FULL-VALUE tentatives, spaced by 1 second."
   (let* ((full-value 5))
     (run-scale-page
      #:title (G_ "Checking connectivity")
-     #:info-text (G_ "Waiting internet access is established.")
+     #:info-text (G_ "Waiting for Internet access establishment...")
      #:scale-full-value full-value
      #:scale-update-proc
      (lambda (value)
@@ -123,8 +123,8 @@ FULL-VALUE tentatives, spaced by 1 second."
            (+ value 1))))
     (unless (connman-online?)
       (run-error-page
-       (G_ "The selected network does not provide an Internet \
+       (G_ "The selected network does not provide access to the \
-access, please try again.")
+Internet, please try again.")
        (G_ "Connection error"))
       (raise
        (condition

gnu/installer/newt/welcome.scm

@@ -92,8 +92,8 @@ we want this page to occupy all the screen space available."
 the page. Ask the user to choose between manual installation, graphical
 installation and reboot."
   (run-menu-page
-   (G_ "GNU GuixSD install")
+   (G_ "GNU Guix install")
-   (G_ "Welcome to GNU GuixSD installer!
+   (G_ "Welcome to GNU Guix system installer!
 
 Please note that the present graphical installer is still under heavy \
 development, so you might want to prefer using the shell based process. \

gnu/local.mk

@@ -1155,6 +1155,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/psm-arch.patch				\
   %D%/packages/patches/psm-ldflags.patch			\
   %D%/packages/patches/psm-repro.patch				\
+  %D%/packages/patches/pugixml-versioned-libdir.patch		\
   %D%/packages/patches/pulseaudio-fix-mult-test.patch		\
   %D%/packages/patches/pulseaudio-longer-test-timeout.patch	\
   %D%/packages/patches/pybugz-encode-error.patch		\

gnu/packages.scm

@@ -159,23 +159,26 @@ flags."
   ;; Search path for package modules.  Each item must be either a directory
   ;; name or a pair whose car is a directory and whose cdr is a sub-directory
   ;; to narrow the search.
-  (let* ((not-colon   (char-set-complement (char-set #\:)))
+  (let*-values (((not-colon)
-         (environment (string-tokenize (or (getenv "GUIX_PACKAGE_PATH") "")
+                 (char-set-complement (char-set #\:)))
-                                       not-colon))
+                ((environment)
-         (channels    (package-path-entries)))
+                 (string-tokenize (or (getenv "GUIX_PACKAGE_PATH") "")
+                                  not-colon))
+                ((channels-scm channels-go)
+                 (package-path-entries)))
     ;; Automatically add channels and items from $GUIX_PACKAGE_PATH to Guile's
     ;; search path.  For historical reasons, $GUIX_PACKAGE_PATH goes to the
     ;; front; channels go to the back so that they don't override Guix' own
     ;; modules.
     (set! %load-path
-      (append environment %load-path channels))
+      (append environment %load-path channels-scm))
     (set! %load-compiled-path
-      (append environment %load-compiled-path channels))
+      (append environment %load-compiled-path channels-go))
 
     (make-parameter
      (append environment
              %default-package-module-path
-             channels))))
+             channels-scm))))
 
 (define %patch-path
   ;; Define it after '%package-module-path' so that '%load-path' contains user

gnu/packages/admin.scm

@@ -113,14 +113,14 @@
 (define-public aide
   (package
     (name "aide")
-    (version "0.16")
+    (version "0.16.1")
-    (source (origin
+    (source
-              (method url-fetch)
+     (origin
-              (uri (string-append "mirror://sourceforge/aide/aide/"
+       (method url-fetch)
-                                  version "/aide-" version ".tar.gz"))
+       (uri (string-append "https://github.com/aide/aide/releases/download/v"
-              (sha256
+                           version "/aide-" version ".tar.gz"))
-               (base32
+       (sha256
-                "0ibkv4z2gk14fn014kq13rp2ysiq6nn2cflv2q5i7zf466hm6758"))))
+        (base32 "1dqhc0c24wa4zid06pfy61k357yvzh28ij86bk9jf6hcqzn7qaqg"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("bison" ,bison)
@@ -141,7 +141,7 @@ that it finds from its configuration files.  Once this database is initialized
 it can be used to verify the integrity of the files.  It has several message
 digest algorithms that are used to check the integrity of files.  All of the
 usual file attributes can be checked for inconsistencies.")
-    (home-page "http://aide.sourceforge.net/")
+    (home-page "https://aide.github.io/")
     (license license:gpl2+)))
 
 (define-public progress
@@ -1598,14 +1598,13 @@ of supported upstream metrics systems simultaneously.")
 (define-public ansible
   (package
     (name "ansible")
-    (version "2.7.7")
+    (version "2.7.8")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ansible" version))
        (sha256
-        (base32
+        (base32 "11yx7vd0mp5gkq428af141dwnrwf8f9cp3f65243qbs9icjxnrrx"))))
-         "0l4id24jqi578xmybvwrz10sm2jhs90gk9gs1y04gfarz4vcj304"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-bcrypt" ,python-bcrypt)
@@ -2700,16 +2699,16 @@ Python loading in HPC environments.")
   (let ((real-name "inxi"))
     (package
       (name "inxi-minimal")
-      (version "3.0.20-1")
+      (version "3.0.22-1")
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
                (url "https://github.com/smxi/inxi")
                (commit version)))
+         (file-name (git-file-name real-name version))
          (sha256
-          (base32
+          (base32 "1br392s3xc2nwqmfx4nwb3i97wjwasvkq8ayr8jq72mi5qzsgizn"))))
-           "1k9148xnfznch1443niaa3w1kmsw4vp0xpwna6npgmi7zqg06ymy"))))
       (build-system trivial-build-system)
       (inputs
        `(("bash" ,bash-minimal)

gnu/packages/aspell.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2016, 2017, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Christopher Andersson <christopher@8bits.nu>
 ;;; Copyright © 2016 Theodoros Foradis <theodoros@foradis.org>
-;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2016, 2017, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -198,11 +198,25 @@ dictionaries, including personal ones.")
                       "13bhbghx5b8g0119g3wxd4n8mlf707y41vlf59irxjj0kynankfn")))
 
 (define-public aspell-dict-it
-  (aspell-dictionary "it" "Italian"
+  (let ((version "2.4-20070901-0")
-                     #:version "2.2_20050523-0"
+        (sha256
-                     #:sha256
+         (base32 "0d6ypii3jblprpibazb6ypady536jz62rwxlss1x1raq07rhvvqn")))
-                     (base32
+    (package
-                      "1gdf7bc1a0kmxsmphdqq8pl01h667mjsj6hihy6kqy14k5qdq69v")))
+      (inherit (aspell-dictionary "it" "Italian"
+                                  #:version version
+                                  #:sha256 sha256))
+
+      ;; The version hosted at <https://ftp.gnu.org/gnu/aspell/dict> is even
+      ;; more out of date.
+      (source
+       (origin
+         (method url-fetch)
+         (uri (string-append "mirror://sourceforge/linguistico/"
+                             "Dizionario%20italiano%20per%20Aspell/" version "/"
+                             "aspell6-it-" version ".tar.bz2"))
+         (sha256 sha256)))
+       (home-page
+        "http://linguistico.sourceforge.net/pages/dizionario_italiano.html"))))
 
 (define-public aspell-dict-nl
   (aspell-dictionary "nl" "Dutch"

gnu/packages/audio.scm

@@ -2270,7 +2270,7 @@ for experimenting with sound synthesis and algorithmic composition.
 SuperCollider requires jackd to be installed in your user profile and your
 user must be allowed to access the realtime features of the kernel.  Search
 for \"realtime\" in the index of the Guix manual to learn how to achieve this
-using GuixSD.")
+using Guix System.")
     (license license:gpl2+)))
 
 (define-public raul
@@ -2834,7 +2834,26 @@ portions of LAME.")
        ("automake" ,automake)
        ("libtool" ,libtool)
        ("pkg-config" ,pkg-config)))
-    (arguments '(#:tests? #f))                    ;no 'check' target
+    (arguments
+     '(#:tests? #f                    ;no 'check' target
+       #:configure-flags '("--with-pic")
+       #:phases
+       (modify-phases %standard-phases
+         ;; This is needed for linking the static libraries
+         (add-after 'unpack 'build-only-position-independent-code
+           (lambda _
+             (substitute* "configure.in"
+               (("AC_PROG_LIBTOOL" m)
+                (string-append m "\nAM_PROG_AR\nLT_INIT([pic-only])")))
+             (delete-file "configure")
+             #t))
+         ;; Some headers are not installed by default, but are needed by
+         ;; packages like Kaldi.
+         (add-after 'install 'install-missing-headers
+           (lambda* (#:key outputs #:allow-other-keys)
+             (install-file "src/common/pa_ringbuffer.h"
+                           (string-append (assoc-ref outputs "out") "/include"))
+             #t)))))
     (home-page "http://www.portaudio.com/")
     (synopsis "Audio I/O library")
     (description
@@ -3361,14 +3380,14 @@ on the ALSA software PCM plugin.")
 (define-public snd
   (package
     (name "snd")
-    (version "17.7")
+    (version "19.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "ftp://ccrma-ftp.stanford.edu/pub/Lisp/"
                                   "snd-" version ".tar.gz"))
               (sha256
                (base32
-                "1vm0dy5qlycqkima7y5ajzvazyjybifa803fabjcpncjz08c26vp"))))
+                "1a6ls2hyvggss12idca22hq5vsq4jw2xkwrx22dx29i9926gdr6h"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      `(#:tests? #f                      ; no tests

gnu/packages/bioconductor.scm

@@ -30,9 +30,13 @@
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages graph)
   #:use-module (gnu packages maths)
+  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages web))
 
+
+;;; Annotations
+
 (define-public r-bsgenome-celegans-ucsc-ce6
   (package
     (name "r-bsgenome-celegans-ucsc-ce6")
@@ -646,7 +650,103 @@ 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-fdb-infiniummethylation-hg19
+  (package
+    (name "r-fdb-infiniummethylation-hg19")
+    (version "2.2.0")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/annotation/" instead of "bioc/".
+              (uri (string-append "https://www.bioconductor.org/packages/"
+                                  "release/data/annotation/src/contrib/"
+                                  "FDb.InfiniumMethylation.hg19_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
+    (properties
+     `((upstream-name . "FDb.InfiniumMethylation.hg19")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biostrings" ,r-biostrings)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-annotationdbi" ,r-annotationdbi)
+       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
+       ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
+    (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
+    (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
+    (description
+     "This is an annotation package for Illumina Infinium DNA methylation
+probes.  It contains the compiled HumanMethylation27 and HumanMethylation450
+annotations.")
+    (license license:artistic2.0)))
+
+(define-public r-illuminahumanmethylationepicmanifest
+  (package
+    (name "r-illuminahumanmethylationepicmanifest")
+    (version "0.3.0")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/annotation/" instead of "bioc/".
+              (uri (string-append "https://www.bioconductor.org/packages/"
+                                  "release/data/annotation/src/contrib/"
+                                  "IlluminaHumanMethylationEPICmanifest_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
+    (properties
+     `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-minfi" ,r-minfi)))
+    (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
+    (synopsis "Manifest for Illumina's EPIC methylation arrays")
+    (description
+     "This is a manifest package for Illumina's EPIC methylation arrays.")
+    (license license:artistic2.0)))
+
 
+;;; Experiment data
+
+(define-public r-hsmmsinglecell
+  (package
+    (name "r-hsmmsinglecell")
+    (version "1.2.0")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/experiment/" instead of "bioc/".
+              (uri (string-append "https://www.bioconductor.org/packages/"
+                                  "release/data/experiment/src/contrib/"
+                                  "HSMMSingleCell_" version ".tar.gz"))
+              (sha256
+               (base32
+                "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
+    (properties
+     `((upstream-name . "HSMMSingleCell")))
+    (build-system r-build-system)
+    (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
+    (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
+    (description
+     "Skeletal myoblasts undergo a well-characterized sequence of
+morphological and transcriptional changes during differentiation.  In this
+experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
+under high mitogen conditions (GM) and then differentiated by switching to
+low-mitogen media (DM).  RNA-Seq libraries were sequenced from each of several
+hundred cells taken over a time-course of serum-induced differentiation.
+Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
+72 hours) following serum switch using the Fluidigm C1 microfluidic system.
+RNA from each cell was isolated and used to construct mRNA-Seq libraries,
+which were then sequenced to a depth of ~4 million reads per library,
+resulting in a complete gene expression profile for each cell.")
+    (license license:artistic2.0)))
+
+
+;;; Packages
+
 (define-public r-biocgenerics
   (package
     (name "r-biocgenerics")
@@ -766,6 +866,35 @@ region sets and other genomic features.")
      "This package provides functions for plotting genomic data.")
     (license license:artistic2.0)))
 
+(define-public r-qvalue
+  (package
+    (name "r-qvalue")
+    (version "2.14.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "qvalue" version))
+       (sha256
+        (base32
+         "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-reshape2" ,r-reshape2)))
+    (home-page "http://github.com/jdstorey/qvalue")
+    (synopsis "Q-value estimation for false discovery rate control")
+    (description
+     "This package takes a list of p-values resulting from the simultaneous
+testing of many hypotheses and estimates their q-values and local @dfn{false
+discovery rate} (FDR) values.  The q-value of a test measures the proportion
+of false positives incurred when that particular test is called significant.
+The local FDR measures the posterior probability the null hypothesis is true
+given the test's p-value.  Various plots are automatically generated, allowing
+one to make sensible significance cut-offs.  The software can be applied to
+problems in genomics, brain imaging, astrophysics, and data mining.")
+    ;; Any version of the LGPL.
+    (license license:lgpl3+)))
+
 (define-public r-diffbind
   (package
     (name "r-diffbind")
@@ -1694,3 +1823,663 @@ estimation is performed using either the EM or CEM algorithm, and the slope
 heuristics are used for model selection (i.e., to choose the number of
 clusters).")
     (license license:gpl3+)))
+
+(define-public r-deds
+  (package
+    (name "r-deds")
+    (version "1.56.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DEDS" version))
+       (sha256
+        (base32
+         "1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c"))))
+    (properties `((upstream-name . "DEDS")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/DEDS/")
+    (synopsis "Differential expression via distance summary for microarray data")
+    (description
+     "This library contains functions that calculate various statistics of
+differential expression for microarray data, including t statistics, fold
+change, F statistics, SAM, moderated t and F statistics and B statistics.  It
+also implements a new methodology called DEDS (Differential Expression via
+Distance Summary), which selects differentially expressed genes by integrating
+and summarizing a set of statistics using a weighted distance approach.")
+    ;; Any version of the LGPL.
+    (license license:lgpl3+)))
+
+;; This is a CRAN package, but since it depends on a Bioconductor package we
+;; put it here.
+(define-public r-nbpseq
+  (package
+    (name "r-nbpseq")
+    (version "0.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "NBPSeq" version))
+       (sha256
+        (base32
+         "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
+    (properties `((upstream-name . "NBPSeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-qvalue" ,r-qvalue)))
+    (home-page "https://cran.r-project.org/web/packages/NBPSeq")
+    (synopsis "Negative binomial models for RNA-Seq data")
+    (description
+     "This package provides negative binomial models for two-group comparisons
+and regression inferences from RNA-sequencing data.")
+    (license license:gpl2)))
+
+(define-public r-ebseq
+  (package
+    (name "r-ebseq")
+    (version "1.22.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "EBSeq" version))
+       (sha256
+        (base32
+         "1gzbk1hbwdan0j131ah88yryfvsiq0wqjnb09qbr4qaczpgvbad0"))))
+    (properties `((upstream-name . "EBSeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-blockmodeling" ,r-blockmodeling)
+       ("r-gplots" ,r-gplots)
+       ("r-testthat" ,r-testthat)))
+    (home-page "https://bioconductor.org/packages/EBSeq")
+    (synopsis "Differential expression analysis of RNA-seq data")
+    (description
+     "This package provides tools for differential expression analysis at both
+gene and isoform level using RNA-seq data")
+    (license license:artistic2.0)))
+
+(define-public r-lpsymphony
+  (package
+    (name "r-lpsymphony")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "lpsymphony" version))
+       (sha256
+        (base32
+         "0vnsf5x6gvd1k8h89al7r6xbgbxsjbxphr675czzwggz79zbvq7y"))))
+    (build-system r-build-system)
+    (inputs
+     `(("gfortran" ,gfortran)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://r-forge.r-project.org/projects/rsymphony")
+    (synopsis "Symphony integer linear programming solver in R")
+    (description
+     "This package was derived from Rsymphony.  The package provides an R
+interface to SYMPHONY, a linear programming solver written in C++.  The main
+difference between this package and Rsymphony is that it includes the solver
+source code, while Rsymphony expects to find header and library files on the
+users' system.  Thus the intention of @code{lpsymphony} is to provide an easy
+to install interface to SYMPHONY.")
+    ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
+    ;; lpsimphony is released under the same terms.
+    (license license:epl1.0)))
+
+(define-public r-ihw
+  (package
+    (name "r-ihw")
+    (version "1.10.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "IHW" version))
+       (sha256
+        (base32
+         "10wqasl8k2j3y5qvak3xr2xj6symk656xww1y5n2l22nz832j19n"))))
+    (properties `((upstream-name . "IHW")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-fdrtool" ,r-fdrtool)
+       ("r-lpsymphony" ,r-lpsymphony)
+       ("r-slam" ,r-slam)))
+    (home-page "https://bioconductor.org/packages/IHW")
+    (synopsis "Independent hypothesis weighting")
+    (description
+     "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
+procedure that increases power compared to the method of Benjamini and
+Hochberg by assigning data-driven weights to each hypothesis.  The input to
+IHW is a two-column table of p-values and covariates.  The covariate can be
+any continuous-valued or categorical variable that is thought to be
+informative on the statistical properties of each hypothesis test, while it is
+independent of the p-value under the null hypothesis.")
+    (license license:artistic2.0)))
+
+(define-public r-icobra
+  (package
+    (name "r-icobra")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "iCOBRA" version))
+       (sha256
+        (base32
+         "0i1swrm31g0zffi5pm48bfvdfqpd32d0zdchkbyipz96al46jnld"))))
+    (properties `((upstream-name . "iCOBRA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-dt" ,r-dt)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-limma" ,r-limma)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rocr" ,r-rocr)
+       ("r-scales" ,r-scales)
+       ("r-shiny" ,r-shiny)
+       ("r-shinybs" ,r-shinybs)
+       ("r-shinydashboard" ,r-shinydashboard)
+       ("r-upsetr" ,r-upsetr)))
+    (home-page "https://bioconductor.org/packages/iCOBRA")
+    (synopsis "Comparison and visualization of ranking and assignment methods")
+    (description
+     "This package provides functions for calculation and visualization of
+performance metrics for evaluation of ranking and binary
+classification (assignment) methods.  It also contains a Shiny application for
+interactive exploration of results.")
+    (license license:gpl2+)))
+
+(define-public r-mast
+  (package
+    (name "r-mast")
+    (version "1.8.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MAST" version))
+       (sha256
+        (base32
+         "0rhx655dza0m6yg9jcfz2nmxqahvxx2l91kqgyp7qai0bzz9d9ix"))))
+    (properties `((upstream-name . "MAST")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-abind" ,r-abind)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-data-table" ,r-data-table)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-plyr" ,r-plyr)
+       ("r-progress" ,r-progress)
+       ("r-reshape2" ,r-reshape2)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-stringr" ,r-stringr)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://github.com/RGLab/MAST/")
+    (synopsis "Model-based analysis of single cell transcriptomics")
+    (description
+     "This package provides methods and models for handling zero-inflated
+single cell assay data.")
+    (license license:gpl2+)))
+
+(define-public r-monocle
+  (package
+    (name "r-monocle")
+    (version "2.10.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "monocle" version))
+       (sha256
+        (base32
+         "0shwkgqs93j2l5h36yyvb1lf724107cfjrmzp5fxfj1lqc0y61lf"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocviews" ,r-biocviews)
+       ("r-cluster" ,r-cluster)
+       ("r-combinat" ,r-combinat)
+       ("r-ddrtree" ,r-ddrtree)
+       ("r-densityclust" ,r-densityclust)
+       ("r-dplyr" ,r-dplyr)
+       ("r-fastica" ,r-fastica)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-hsmmsinglecell" ,r-hsmmsinglecell)
+       ("r-igraph" ,r-igraph)
+       ("r-irlba" ,r-irlba)
+       ("r-limma" ,r-limma)
+       ("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-pheatmap" ,r-pheatmap)
+       ("r-plyr" ,r-plyr)
+       ("r-proxy" ,r-proxy)
+       ("r-qlcmatrix" ,r-qlcmatrix)
+       ("r-rann" ,r-rann)
+       ("r-rcpp" ,r-rcpp)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rtsne" ,r-rtsne)
+       ("r-slam" ,r-slam)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
+       ("r-vgam" ,r-vgam)
+       ("r-viridis" ,r-viridis)))
+    (home-page "https://bioconductor.org/packages/monocle")
+    (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
+    (description
+     "Monocle performs differential expression and time-series analysis for
+single-cell expression experiments.  It orders individual cells according to
+progress through a biological process, without knowing ahead of time which
+genes define progress through that process.  Monocle also performs
+differential expression analysis, clustering, visualization, and other useful
+tasks on single cell expression data.  It is designed to work with RNA-Seq and
+qPCR data, but could be used with other types as well.")
+    (license license:artistic2.0)))
+
+(define-public r-noiseq
+  (package
+    (name "r-noiseq")
+    (version "2.26.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "NOISeq" version))
+       (sha256
+        (base32
+         "1wyhhi9ydlbjlz427093mdp5ppby77n37w5c2iyxlpsdk2m2nqsn"))))
+    (properties `((upstream-name . "NOISeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-matrix" ,r-matrix)))
+    (home-page "https://bioconductor.org/packages/NOISeq")
+    (synopsis "Exploratory analysis and differential expression for RNA-seq data")
+    (description
+     "This package provides tools to support the analysis of RNA-seq
+expression data or other similar kind of data.  It provides exploratory plots
+to evaluate saturation, count distribution, expression per chromosome, type of
+detected features, features length, etc.  It also supports the analysis of
+differential expression between two experimental conditions with no parametric
+assumptions.")
+    (license license:artistic2.0)))
+
+(define-public r-scdd
+  (package
+    (name "r-scdd")
+    (version "1.6.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "scDD" version))
+       (sha256
+        (base32
+         "0dp2awajd5281dwpbs0wb8ij2pq9l60p0b80xhxrb41m5qybcri8"))))
+    (properties `((upstream-name . "scDD")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-arm" ,r-arm)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-ebseq" ,r-ebseq)
+       ("r-fields" ,r-fields)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-mclust" ,r-mclust)
+       ("r-outliers" ,r-outliers)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scran" ,r-scran)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://github.com/kdkorthauer/scDD")
+    (synopsis "Mixture modeling of single-cell RNA-seq data")
+    (description
+     "This package implements a method to analyze single-cell RNA-seq data
+utilizing flexible Dirichlet Process mixture models.  Genes with differential
+distributions of expression are classified into several interesting patterns
+of differences between two conditions.  The package also includes functions
+for simulating data with these patterns from negative binomial
+distributions.")
+    (license license:gpl2)))
+
+(define-public r-scone
+  (package
+    (name "r-scone")
+    (version "1.6.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "scone" version))
+       (sha256
+        (base32
+         "0l1x4cjnfjbpx6k55sjqx03555daa6v63rq0rg6b7jpz8xxzwa7p"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-aroma-light" ,r-aroma-light)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-boot" ,r-boot)
+       ("r-class" ,r-class)
+       ("r-cluster" ,r-cluster)
+       ("r-compositions" ,r-compositions)
+       ("r-diptest" ,r-diptest)
+       ("r-edger" ,r-edger)
+       ("r-fpc" ,r-fpc)
+       ("r-gplots" ,r-gplots)
+       ("r-hexbin" ,r-hexbin)
+       ("r-limma" ,r-limma)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-mixtools" ,r-mixtools)
+       ("r-rarpack" ,r-rarpack)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rhdf5" ,r-rhdf5)
+       ("r-ruvseq" ,r-ruvseq)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://bioconductor.org/packages/scone")
+    (synopsis "Single cell overview of normalized expression data")
+    (description
+     "SCONE is an R package for comparing and ranking the performance of
+different normalization schemes for single-cell RNA-seq and other
+high-throughput analyses.")
+    (license license:artistic2.0)))
+
+(define-public r-geoquery
+  (package
+    (name "r-geoquery")
+    (version "2.50.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "GEOquery" version))
+       (sha256
+        (base32
+         "074dl00c8yi1ihpjkw7vl9vy2hggvipib0jn0hli0wrw7x1h9hg6"))))
+    (properties `((upstream-name . "GEOquery")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-dplyr" ,r-dplyr)
+       ("r-httr" ,r-httr)
+       ("r-limma" ,r-limma)
+       ("r-magrittr" ,r-magrittr)
+       ("r-readr" ,r-readr)
+       ("r-tidyr" ,r-tidyr)
+       ("r-xml2" ,r-xml2)))
+    (home-page "https://github.com/seandavi/GEOquery/")
+    (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
+    (description
+     "The NCBI Gene Expression Omnibus (GEO) is a public repository of
+microarray data.  Given the rich and varied nature of this resource, it is
+only natural to want to apply BioConductor tools to these data.  GEOquery is
+the bridge between GEO and BioConductor.")
+    (license license:gpl2)))
+
+(define-public r-illuminaio
+  (package
+    (name "r-illuminaio")
+    (version "0.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "illuminaio" version))
+       (sha256
+        (base32
+         "1rdp9b4xlv91yzba7pd7k50s3nkljfxmdmyz5jl0j8ybhmpl6rns"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-base64" ,r-base64)))
+    (home-page "https://github.com/HenrikBengtsson/illuminaio/")
+    (synopsis "Parse Illumina microarray output files")
+    (description
+     "This package provides tools for parsing Illumina's microarray output
+files, including IDAT.")
+    (license license:gpl2)))
+
+(define-public r-siggenes
+  (package
+    (name "r-siggenes")
+    (version "1.56.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "siggenes" version))
+       (sha256
+        (base32
+         "0cjlb5r04x15xkhk00i3wvpx21kj0k29pn0mj3whwqk31zznnk1b"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-multtest" ,r-multtest)))
+    (home-page "https://bioconductor.org/packages/siggenes/")
+    (synopsis
+     "Multiple testing using SAM and Efron's empirical Bayes approaches")
+    (description
+     "This package provides tools for the identification of differentially
+expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
+both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
+Bayes Analyses of Microarrays} (EBAM).")
+    (license license:lgpl2.0+)))
+
+(define-public r-bumphunter
+  (package
+    (name "r-bumphunter")
+    (version "1.24.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "bumphunter" version))
+       (sha256
+        (base32
+         "1f9vk3srffbx8jpza40nd18a4y0p0z8q40mx55dlcnddkwrqi19b"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-dorng" ,r-dorng)
+       ("r-foreach" ,r-foreach)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-iterators" ,r-iterators)
+       ("r-limma" ,r-limma)
+       ("r-locfit" ,r-locfit)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://github.com/ririzarr/bumphunter")
+    (synopsis "Find bumps in genomic data")
+    (description
+     "This package provides tools for finding bumps in genomic data in order
+to identify differentially methylated regions in epigenetic epidemiology
+studies.")
+    (license license:artistic2.0)))
+
+(define-public r-minfi
+  (package
+    (name "r-minfi")
+    (version "1.28.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "minfi" version))
+       (sha256
+        (base32
+         "1sjwwqb0syngvj75saaky9y06hbxsawhhcmfvavzkhicxipafv7r"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-beanplot" ,r-beanplot)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biostrings" ,r-biostrings)
+       ("r-bumphunter" ,r-bumphunter)
+       ("r-data-table" ,r-data-table)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+       ("r-genefilter" ,r-genefilter)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-geoquery" ,r-geoquery)
+       ("r-hdf5array" ,r-hdf5array)
+       ("r-illuminaio" ,r-illuminaio)
+       ("r-iranges" ,r-iranges)
+       ("r-lattice" ,r-lattice)
+       ("r-limma" ,r-limma)
+       ("r-mass" ,r-mass)
+       ("r-mclust" ,r-mclust)
+       ("r-nlme" ,r-nlme)
+       ("r-nor1mix" ,r-nor1mix)
+       ("r-preprocesscore" ,r-preprocesscore)
+       ("r-quadprog" ,r-quadprog)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-reshape" ,r-reshape)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-siggenes" ,r-siggenes)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://github.com/hansenlab/minfi")
+    (synopsis "Analyze Illumina Infinium DNA methylation arrays")
+    (description
+     "This package provides tools to analyze and visualize Illumina Infinium
+methylation arrays.")
+    (license license:artistic2.0)))
+
+(define-public r-methylumi
+  (package
+    (name "r-methylumi")
+    (version "2.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "methylumi" version))
+       (sha256
+        (base32
+         "14p2qi18cprfvb2gxng1vm48c7zwh23h88q9qjgipj9xl5axsgw2"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotate" ,r-annotate)
+       ("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
+       ("r-genefilter" ,r-genefilter)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-illuminaio" ,r-illuminaio)
+       ("r-iranges" ,r-iranges)
+       ("r-lattice" ,r-lattice)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-minfi" ,r-minfi)
+       ("r-reshape2" ,r-reshape2)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scales" ,r-scales)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://bioconductor.org/packages/methylumi")
+    (synopsis "Handle Illumina methylation data")
+    (description
+     "This package provides classes for holding and manipulating Illumina
+methylation data.  Based on eSet, it can contain MIAME information, sample
+information, feature information, and multiple matrices of data.  An
+\"intelligent\" import function, methylumiR can read the Illumina text files
+and create a MethyLumiSet.  methylumIDAT can directly read raw IDAT files from
+HumanMethylation27 and HumanMethylation450 microarrays.  Normalization,
+background correction, and quality control features for GoldenGate, Infinium,
+and Infinium HD arrays are also included.")
+    (license license:gpl2)))
+
+(define-public r-lumi
+  (package
+    (name "r-lumi")
+    (version "2.34.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "lumi" version))
+       (sha256
+        (base32
+         "1fpmjpgcy5n0hx9whn9m3jhjmciqq0l59nvy5addbq0a4wnjhx8q"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-affy" ,r-affy)
+       ("r-annotate" ,r-annotate)
+       ("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-dbi" ,r-dbi)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-kernsmooth" ,r-kernsmooth)
+       ("r-lattice" ,r-lattice)
+       ("r-mass" ,r-mass)
+       ("r-methylumi" ,r-methylumi)
+       ("r-mgcv" ,r-mgcv)
+       ("r-nleqslv" ,r-nleqslv)
+       ("r-preprocesscore" ,r-preprocesscore)
+       ("r-rsqlite" ,r-rsqlite)))
+    (home-page "https://bioconductor.org/packages/lumi")
+    (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
+    (description
+     "The lumi package provides an integrated solution for the Illumina
+microarray data analysis.  It includes functions of Illumina
+BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
+variance stabilization, normalization and gene annotation at the probe level.
+It also includes the functions of processing Illumina methylation microarrays,
+especially Illumina Infinium methylation microarrays.")
+    (license license:lgpl2.0+)))
+
+(define-public r-linnorm
+  (package
+    (name "r-linnorm")
+    (version "2.6.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Linnorm" version))
+       (sha256
+        (base32
+         "1qgk8m5kc409flqxs3vnf228v3z0112q8py9hgfgyiwvi6yzdbp6"))))
+    (properties `((upstream-name . "Linnorm")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-amap" ,r-amap)
+       ("r-apcluster" ,r-apcluster)
+       ("r-ellipse" ,r-ellipse)
+       ("r-fastcluster" ,r-fastcluster)
+       ("r-fpc" ,r-fpc)
+       ("r-ggdendro" ,r-ggdendro)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gmodels" ,r-gmodels)
+       ("r-igraph" ,r-igraph)
+       ("r-limma" ,r-limma)
+       ("r-mass" ,r-mass)
+       ("r-mclust" ,r-mclust)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-rtsne" ,r-rtsne)
+       ("r-statmod" ,r-statmod)
+       ("r-vegan" ,r-vegan)
+       ("r-zoo" ,r-zoo)))
+    (home-page "http://www.jjwanglab.org/Linnorm/")
+    (synopsis "Linear model and normality based transformation method")
+    (description
+     "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
+count data or any large scale count data.  It transforms such datasets for
+parametric tests.  In addition to the transformtion function (@code{Linnorm}),
+the following pipelines are implemented:
+
+@enumerate
+@item Library size/batch effect normalization (@code{Linnorm.Norm})
+@item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
+  clustering or hierarchical clustering (@code{Linnorm.tSNE},
+  @code{Linnorm.PCA}, @code{Linnorm.HClust})
+@item Differential expression analysis or differential peak detection using
+  limma (@code{Linnorm.limma})
+@item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
+@item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
+@item Stable gene selection for scRNA-seq data; for users without or who do
+  not want to rely on spike-in genes (@code{Linnorm.SGenes})
+@item Data imputation (@code{Linnorm.DataImput}).
+@end enumerate
+
+Linnorm can work with raw count, CPM, RPKM, FPKM and TPM.  Additionally, the
+@code{RnaXSim} function is included for simulating RNA-seq data for the
+evaluation of DEG analysis methods.")
+    (license license:expat)))

gnu/packages/bioinformatics.scm

@@ -1752,6 +1752,72 @@ high-throughput sequencing data – with an emphasis on simplicity.")
 (define-public python2-plastid
   (package-with-python2 python-plastid))
 
+(define-public tetoolkit
+  (package
+    (name "tetoolkit")
+    (version "2.0.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/mhammell-laboratory/tetoolkit.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1yzi0kfpzip8zpjb82x1ik6h22yzfyjiz2dv85v6as2awwqvk807"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2               ; not guaranteed to work with Python 3
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'make-writable
+           (lambda _
+             (for-each make-file-writable (find-files "."))
+             #t))
+         (add-after 'unpack 'patch-invocations
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* '("bin/TEtranscripts"
+                            "bin/TEcount")
+               (("'sort ")
+                (string-append "'" (which "sort") " "))
+               (("'rm -f ")
+                (string-append "'" (which "rm") " -f "))
+               (("'Rscript'") (string-append "'" (which "Rscript") "'")))
+             (substitute* "TEToolkit/IO/ReadInputs.py"
+               (("BamToBED") (which "bamToBed")))
+             (substitute* "TEToolkit/Normalization.py"
+               (("\"Rscript\"")
+                (string-append "\"" (which "Rscript") "\"")))
+             #t))
+         (add-after 'install 'wrap-program
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Make sure the executables find R packages.
+             (let ((out (assoc-ref outputs "out")))
+               (for-each
+                (lambda (script)
+                  (wrap-program (string-append out "/bin/" script)
+                    `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
+                '("TEtranscripts"
+                  "TEcount")))
+             #t)))))
+    (inputs
+     `(("coreutils" ,coreutils)
+       ("bedtools" ,bedtools)
+       ("python-argparse" ,python2-argparse)
+       ("python-pysam" ,python2-pysam)
+       ("r-minimal" ,r-minimal)
+       ("r-deseq2" ,r-deseq2)))
+    (home-page "https://github.com/mhammell-laboratory/tetoolkit")
+    (synopsis "Transposable elements in differential enrichment analysis")
+    (description
+     "This is package for including transposable elements in differential
+enrichment analysis of sequencing datasets.  TEtranscripts and TEcount take
+RNA-seq (and similar data) and annotates reads to both genes and transposable
+elements.  TEtranscripts then performs differential analysis using DESeq2.
+Note that TEtranscripts and TEcount rely on specially curated GTF files, which
+are not included due to their size.")
+    (license license:gpl3+)))
+
 (define-public cd-hit
   (package
     (name "cd-hit")
@@ -10293,35 +10359,6 @@ quality controls, normalization, visualization, and further analysis are also
 provided.")
     (license license:artistic2.0)))
 
-(define-public r-qvalue
-  (package
-    (name "r-qvalue")
-    (version "2.14.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "qvalue" version))
-       (sha256
-        (base32
-         "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-ggplot2" ,r-ggplot2)
-       ("r-reshape2" ,r-reshape2)))
-    (home-page "http://github.com/jdstorey/qvalue")
-    (synopsis "Q-value estimation for false discovery rate control")
-    (description
-     "This package takes a list of p-values resulting from the simultaneous
-testing of many hypotheses and estimates their q-values and local @dfn{false
-discovery rate} (FDR) values.  The q-value of a test measures the proportion
-of false positives incurred when that particular test is called significant.
-The local FDR measures the posterior probability the null hypothesis is true
-given the test's p-value.  Various plots are automatically generated, allowing
-one to make sensible significance cut-offs.  The software can be applied to
-problems in genomics, brain imaging, astrophysics, and data mining.")
-    ;; Any version of the LGPL.
-    (license license:lgpl3+)))
-
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
@@ -11908,21 +11945,35 @@ variational inference.")
 (define-public python-loompy
   (package
     (name "python-loompy")
-    (version "2.0.2")
+    (version "2.0.17")
-    (source
+    ;; The tarball on Pypi does not include the tests.
-     (origin
+    (source (origin
-       (method url-fetch)
+              (method git-fetch)
-       (uri (pypi-uri "loompy" version))
+              (uri (git-reference
-       (sha256
+                    (url "https://github.com/linnarsson-lab/loompy.git")
-        (base32
+                    (commit version)))
-         "1drgv8j1hxqzzpnfg272x9djb6j8qr798w1pc2x8ikmfgyd9gh51"))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "12a5kjgiikapv93wahfw0frszx1lblnppyz3vs5gy8fgmgngra07"))))
     (build-system python-build-system)
-    ;; There are no tests
+    (arguments
-    (arguments '(#:tests? #f))
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (setenv "PYTHONPATH"
+                     (string-append (getcwd) ":"
+                                    (getenv "PYTHONPATH")))
+             (invoke "pytest" "tests")
+             #t)))))
     (propagated-inputs
      `(("python-h5py" ,python-h5py)
        ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
        ("python-scipy" ,python-scipy)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
     (home-page "https://github.com/linnarsson-lab/loompy")
     (synopsis "Work with .loom files for single-cell RNA-seq data")
     (description "The loom file format is an efficient format for very large
@@ -14158,3 +14209,34 @@ short read sequences, removes errors then produces high quality unique
 contigs.  It then uses paired read information, if available, to retrieve the
 repeated areas between contigs.")
     (license license:gpl2+)))
+
+(define-public python-velocyto
+  (package
+    (name "python-velocyto")
+    (version "0.17.17")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "velocyto" version))
+       (sha256
+        (base32
+         "0fgygyzqgrq32dv6a00biq1p1cwi6kbl5iqblxq1kklj6b2mzmhs"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-click" ,python-click)
+       ("python-cython" ,python-cython)
+       ("python-h5py" ,python-h5py)
+       ("python-loompy" ,python-loompy)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-numba" ,python-numba)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-pysam" ,python-pysam)
+       ("python-scikit-learn" ,python-scikit-learn)
+       ("python-scipy" ,python-scipy)))
+    (home-page "https://github.com/velocyto-team/velocyto.py")
+    (synopsis "RNA velocity analysis for single cell RNA-seq data")
+    (description
+     "Velocyto is a library for the analysis of RNA velocity.  Velocyto
+includes a command line tool and an analysis pipeline.")
+    (license license:bsd-2)))

gnu/packages/bootloaders.scm

@@ -340,7 +340,7 @@ menu to select one of the installed operating systems.")
 (define-public dtc
   (package
     (name "dtc")
-    (version "1.4.7")
+    (version "1.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -348,11 +348,13 @@ menu to select one of the installed operating systems.")
                     "dtc-" version ".tar.xz"))
               (sha256
                (base32
-                "1rydi5jvhlhsr110h6n0pavv3daqa0cb4m5vcps50qzq1zqfhhv6"))))
+                "0wh10p42hf5403ipvs0dsxddb6kzfyk2sq4fgid9zqzpr51y8wn6"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("bison" ,bison)
        ("flex" ,flex)
+       ("libyaml" ,libyaml)
+       ("pkg-config" ,pkg-config)
        ("swig" ,swig)
        ("valgrind" ,valgrind)))
     (inputs

gnu/packages/compression.scm

@@ -1587,14 +1587,14 @@ recreates the stored directory structure by default.")
 (define-public libzip
   (package
     (name "libzip")
-    (version "1.5.1")
+    (version "1.5.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "https://libzip.org/download/" name "-" version ".tar.xz"))
+                    "https://libzip.org/download/libzip-" version ".tar.xz"))
               (sha256
                (base32
-                "0wnkkvkq90wyawj9221i77sf3nix1vj3ygzdy59k8yvcjnv3bsh4"))))
+                "1d53shcy7nvls5db573bbdlm25lfz1iw2zshng5f00cssi5lvpmk"))))
     (native-inputs
      `(("perl" ,perl)))
     (inputs

gnu/packages/cran.scm

@@ -14,6 +14,7 @@
 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net>
+;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -58,9 +59,11 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages multiprecision)
+  #:use-module (gnu packages networking)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web)
@@ -10839,3 +10842,900 @@ using @code{S3}.")
 for model selection.  The calibration methods available are based on the slope
 heuristics.")
     (license license:gpl2+)))
+
+(define-public r-dorng
+  (package
+    (name "r-dorng")
+    (version "1.7.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "doRNG" version))
+       (sha256
+        (base32
+         "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
+    (properties `((upstream-name . "doRNG")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-foreach" ,r-foreach)
+       ("r-iterators" ,r-iterators)
+       ("r-pkgmaker" ,r-pkgmaker)
+       ("r-rngtools" ,r-rngtools)))
+    (home-page "https://renozao.github.io/doRNG/")
+    (synopsis "Generic reproducible parallel backend for foreach loops")
+    (description
+     "This package provides functions to perform reproducible parallel
+@code{foreach} loops, using independent random streams as generated by
+L'Ecuyer's combined multiple-recursive generator.  It enables to easily
+convert standard @code{%dopar%} loops into fully reproducible loops,
+independently of the number of workers, the task scheduling strategy, or the
+chosen parallel environment and associated foreach backend.")
+    (license license:gpl2+)))
+
+(define-public r-blockmodeling
+  (package
+    (name "r-blockmodeling")
+    (version "0.3.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "blockmodeling" version))
+       (sha256
+        (base32
+         "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-doparallel" ,r-doparallel)
+       ("r-dorng" ,r-dorng)
+       ("r-foreach" ,r-foreach)
+       ("r-matrix" ,r-matrix)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/blockmodeling")
+    (synopsis "Generalized and classical blockmodeling of valued networks")
+    (description
+     "This package is primarily meant as an implementation of generalized
+blockmodeling for valued networks.  In addition, measures of similarity or
+dissimilarity based on structural equivalence and regular equivalence (REGE
+algorithms) can be computed and partitioned matrices can be plotted.")
+    (license license:gpl2+)))
+
+(define-public r-upsetr
+  (package
+    (name "r-upsetr")
+    (version "1.3.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "UpSetR" version))
+       (sha256
+        (base32
+         "08vj7l92b8fpqyqwxshll2mhk3yhgyr74axvr2lf29z78bapymhz"))))
+    (properties `((upstream-name . "UpSetR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-plyr" ,r-plyr)
+       ("r-scales" ,r-scales)))
+    (home-page "https://github.com/hms-dbmi/UpSetR")
+    (synopsis "Visualize intersecting sets")
+    (description
+     "This package provides a more scalable alternative to Venn and Euler
+diagrams for visualizing intersecting sets.  Create visualizations of
+intersecting sets using a novel matrix design, along with visualizations of
+several common set, element and attribute related tasks.")
+    (license license:expat)))
+
+;; This package includes a JavaScript file, which is not minified.  When
+;; upgrading please check that there are no new minified JavaScript files.
+(define-public r-shinybs
+  (package
+    (name "r-shinybs")
+    (version "0.61")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "shinyBS" version))
+       (sha256
+        (base32
+         "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
+    (properties `((upstream-name . "shinyBS")))
+    (build-system r-build-system)
+    ;; The tests spawn Shiny browser apps.  They cannot be run
+    ;; non-interactively.
+    (arguments '(#:tests? #f))
+    (propagated-inputs
+     `(("r-htmltools" ,r-htmltools)
+       ("r-shiny" ,r-shiny)))
+    (home-page "https://ebailey78.github.io/shinyBS/")
+    (synopsis "Twitter Bootstrap components for Shiny")
+    (description
+     "This package adds additional Twitter Bootstrap components to Shiny.")
+    (license license:gpl3)))
+
+(define-public r-outliers
+  (package
+    (name "r-outliers")
+    (version "0.14")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "outliers" version))
+       (sha256
+        (base32
+         "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
+    (synopsis "Tests for outliers")
+    (description
+     "This package provides a collection of some tests commonly used for
+identifying outliers.")
+    (license license:gpl2+)))
+
+(define-public r-bayesm
+  (package
+    (name "r-bayesm")
+    (version "3.1-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "bayesm" version))
+       (sha256
+        (base32
+         "0y30cza92s6kgvmxjpr6f5g0qbcck7hslqp89ncprarhxiym2m28"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page "http://www.perossi.org/home/bsm-1")
+    (synopsis "Bayesian inference for marketing/micro-econometrics")
+    (description
+     "This package covers many important models used in marketing and
+micro-econometrics applications, including Bayes Regression (univariate or
+multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
+Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
+Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
+Mixtures of Normals (including clustering), Dirichlet Process Prior Density
+Estimation with normal base, Hierarchical Linear Models with normal prior and
+covariates, Hierarchical Linear Models with a mixture of normals prior and
+covariates, Hierarchical Multinomial Logits with a mixture of normals prior
+and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
+and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
+analysis of choice-based conjoint data, Bayesian treatment of linear
+instrumental variables models, Analysis of Multivariate Ordinal survey data
+with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
+Coefficient Logit Models.")
+    (license license:gpl2+)))
+
+(define-public r-tensora
+  (package
+    (name "r-tensora")
+    (version "0.36.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tensorA" version))
+       (sha256
+        (base32
+         "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
+    (properties `((upstream-name . "tensorA")))
+    (build-system r-build-system)
+    (home-page "http://www.stat.boogaart.de/tensorA")
+    (synopsis "Advanced tensor arithmetic with named indices")
+    (description
+     "This package provides convenience functions for advanced linear algebra
+with tensors and computation with datasets of tensors on a higher level
+abstraction.  It includes Einstein and Riemann summing conventions, dragging,
+co- and contravariate indices, and parallel computations on sequences of
+tensors.")
+    (license license:gpl2+)))
+
+(define-public r-rarpack
+  (package
+    (name "r-rarpack")
+    (version "0.11-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rARPACK" version))
+       (sha256
+        (base32
+         "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
+    (properties `((upstream-name . "rARPACK")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-rspectra" ,r-rspectra)))
+    (home-page "https://github.com/yixuan/rARPACK")
+    (synopsis "Solvers for large scale eigenvalue and SVD problems")
+    (description
+     "This package was previously an R wrapper of the ARPACK library, and now
+a shell of the R package RSpectra, an R interface to the Spectra library for
+solving large scale eigenvalue/vector problems.  The current version of
+rARPACK simply imports and exports the functions provided by RSpectra.  New
+users of rARPACK are advised to switch to the RSpectra package.")
+    (license license:bsd-3)))
+
+(define-public r-compositions
+  (package
+    (name "r-compositions")
+    (version "1.40-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "compositions" version))
+       (sha256
+        (base32
+         "12mp05yi7jkdqg9iwh6bc9sx6sdxagcnrirznxy9hq8502p7238i"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bayesm" ,r-bayesm)
+       ("r-energy" ,r-energy)
+       ("r-robustbase" ,r-robustbase)
+       ("r-tensora" ,r-tensora)))
+    (home-page "http://www.stat.boogaart.de/compositions")
+    (synopsis "Compositional data analysis")
+    (description
+     "This package provides functions for the consistent analysis of
+compositional data (e.g. portions of substances) and positive
+numbers (e.g. concentrations).")
+    (license license:gpl2+)))
+
+(define-public r-cobs
+  (package
+    (name "r-cobs")
+    (version "1.3-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "cobs" version))
+       (sha256
+        (base32
+         "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-quantreg" ,r-quantreg)
+       ("r-sparsem" ,r-sparsem)))
+    (home-page "https://cran.r-project.org/web/packages/cobs")
+    (synopsis "Constrained B-Splines (sparse matrix based)")
+    (description
+     "This package provides qualitatively constrained (regression) smoothing
+splines via linear programming and sparse matrices.")
+    (license license:gpl2+)))
+
+(define-public r-drimpute
+  (package
+    (name "r-drimpute")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "DrImpute" version))
+       (sha256
+        (base32
+         "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
+    (properties `((upstream-name . "DrImpute")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page "https://github.com/ikwak2/DrImpute")
+    (synopsis "Imputing dropout events in single-cell RNA-Seq data")
+    (description
+     "This is an R package for imputing dropout events.  Many statistical
+methods in cell type identification, visualization and lineage reconstruction
+do not account for dropout events.  DrImpute can improve the performance of
+such software by imputing dropout events.")
+    (license license:gpl3)))
+
+(define-public r-gamlss-dist
+  (package
+    (name "r-gamlss-dist")
+    (version "5.1-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gamlss.dist" version))
+       (sha256
+        (base32
+         "1cd0vl9klcb849i8xwyjm8ihb1da92631j1rxdbnflgffkzrkya4"))))
+    (properties `((upstream-name . "gamlss.dist")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-mass" ,r-mass)))
+    (home-page "http://www.gamlss.org/")
+    (synopsis "Distributions for Generalized Additive Models for location scale and shape")
+    (description
+     "This package provides a set of distributions which can be used for
+modelling the response variables in Generalized Additive Models for Location
+Scale and Shape.  The distributions can be continuous, discrete or mixed
+distributions.  Extra distributions can be created, by transforming, any
+continuous distribution defined on the real line, to a distribution defined on
+ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
+transformation, respectively.")
+    ;; Either version of the GPL.
+    (license (list license:gpl2 license:gpl3))))
+
+;; This package includes JavaScript files, which are not minified.  When
+;; upgrading please check that there are no new minified JavaScript files.
+(define-public r-shinyjs
+  (package
+    (name "r-shinyjs")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "shinyjs" version))
+       (sha256
+        (base32
+         "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-digest" ,r-digest)
+       ("r-htmltools" ,r-htmltools)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-shiny" ,r-shiny)))
+    (home-page "https://deanattali.com/shinyjs")
+    (synopsis "Improve the user experience of your Shiny apps")
+    (description
+     "Perform common useful JavaScript operations in Shiny apps that will
+greatly improve your apps without having to know any JavaScript.  Examples
+include: hiding an element, disabling an input, resetting an input back to its
+original value, delaying code execution by a few seconds, and many more useful
+functions for both the end user and the developer.  Shinyjs can also be used
+to easily call your own custom JavaScript functions from R.")
+    (license license:agpl3+)))
+
+;; This package includes minified JavaScript files.  When upgrading please
+;; check that there are no new minified JavaScript files.
+(define-public r-colourpicker
+  (package
+    (name "r-colourpicker")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "colourpicker" version))
+       (sha256
+        (base32
+         "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
+    (build-system r-build-system)
+    (arguments
+     `(#:modules ((guix build utils)
+                  (guix build r-build-system)
+                  (srfi srfi-1)
+                  (ice-9 popen))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'process-javascript
+           (lambda* (#:key inputs #:allow-other-keys)
+             (with-directory-excursion "inst"
+               (call-with-values
+                   (lambda ()
+                     (unzip2
+                      `((,(assoc-ref inputs "js-salvattore")
+                         "examples/colourInput/www/salvattore.min.js")
+                        (,(assoc-ref inputs "js-jquery")
+                         "htmlwidgets/lib/jquery/jquery.min.js")
+                        ("www/shared/colourpicker/js/colourpicker.js"
+                         "www/shared/colourpicker/js/colourpicker.min.js"))))
+                 (lambda (sources targets)
+                   (for-each (lambda (source target)
+                               (format #t "Processing ~a --> ~a~%"
+                                       source target)
+                               (delete-file target)
+                               (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
+                                 (call-with-output-file target
+                                   (lambda (port)
+                                     (dump-port minified port)))))
+                             sources targets))))
+             #t)))))
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-htmltools" ,r-htmltools)
+       ("r-htmlwidgets" ,r-htmlwidgets)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-miniui" ,r-miniui)
+       ("r-shiny" ,r-shiny)
+       ("r-shinyjs" ,r-shinyjs)))
+    (native-inputs
+     `(("uglify-js" ,uglify-js)
+       ("js-jquery"
+        ,(origin
+           (method url-fetch)
+           (uri "https://code.jquery.com/jquery-3.3.1.js")
+           (sha256
+            (base32
+             "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
+       ("js-salvattore"
+        ,(origin
+           (method url-fetch)
+           (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
+           (sha256
+            (base32
+             "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
+    (home-page "https://github.com/daattali/colourpicker")
+    (synopsis "Color picker tool for Shiny and for selecting colors in plots")
+    (description
+     "This package provides a color picker that can be used as an input in
+Shiny apps or Rmarkdown documents.  The color picker supports alpha opacity,
+custom color palettes, and many more options.  A plot color helper tool is
+available as an RStudio Addin, which helps you pick colors to use in your
+plots.  A more generic color picker RStudio Addin is also provided to let you
+select colors to use in your R code.")
+    (license license:expat)))
+
+(define-public r-ggextra
+  (package
+    (name "r-ggextra")
+    (version "0.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggExtra" version))
+       (sha256
+        (base32
+         "1m5zpn3l3p1y3d2692gyz50m63d58m2a3b7zb595kvcffdx2qr5b"))))
+    (properties `((upstream-name . "ggExtra")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-colourpicker" ,r-colourpicker)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gtable" ,r-gtable)
+       ("r-miniui" ,r-miniui)
+       ("r-scales" ,r-scales)
+       ("r-shiny" ,r-shiny)
+       ("r-shinyjs" ,r-shinyjs)))
+    (home-page "https://github.com/daattali/ggExtra")
+    (synopsis "Marginal histograms for ggplot2 and other enhancements")
+    (description
+     "This package is a collection of functions and layers to enhance ggplot2.
+The flagship function is @code{ggMarginal()}, which can be used to add
+marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
+    (license license:expat)))
+
+(define-public r-minpack-lm
+  (package
+    (name "r-minpack-lm")
+    (version "1.2-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "minpack.lm" version))
+       (sha256
+        (base32
+         "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
+    (properties `((upstream-name . "minpack.lm")))
+    (build-system r-build-system)
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/minpack.lm")
+    (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
+    (description
+     "The @code{nls.lm} function provides an R interface to @code{lmder} and
+@code{lmdif} from the MINPACK library, for solving nonlinear least-squares
+problems by a modification of the Levenberg-Marquardt algorithm, with support
+for lower and upper parameter bounds.  The implementation can be used via
+@code{nls}-like calls using the @code{nlsLM} function.")
+    (license license:gpl3)))
+
+(define-public r-moments
+  (package
+    (name "r-moments")
+    (version "0.14")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "moments" version))
+       (sha256
+        (base32
+         "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/moments")
+    (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
+    (description
+     "This package provides functions to calculate: moments, Pearson's
+kurtosis, Geary's kurtosis and skewness; it also includes tests related to
+them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
+    (license license:gpl2+)))
+
+(define-public r-msir
+  (package
+    (name "r-msir")
+    (version "1.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "msir" version))
+       (sha256
+        (base32
+         "1ipzgdffsqly3dp91pw7yp3h5cwn08l9qsj7cdmrykd42jc98950"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mclust" ,r-mclust)
+       ("r-rgl" ,r-rgl)))
+    (home-page "https://cran.r-project.org/web/packages/msir")
+    (synopsis "Model-based sliced inverse regression")
+    (description
+     "This is an R package for dimension reduction based on finite Gaussian
+mixture modeling of inverse regression.")
+    (license license:gpl2+)))
+
+(define-public r-pbivnorm
+  (package
+    (name "r-pbivnorm")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pbivnorm" version))
+       (sha256
+        (base32
+         "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
+    (build-system r-build-system)
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://github.com/brentonk/pbivnorm")
+    (synopsis "Vectorized bivariate normal CDF")
+    (description
+     "This package provides a vectorized R function for calculating
+probabilities from a standard bivariate normal CDF.")
+    (license license:gpl2+)))
+
+(define-public r-lavaan
+  (package
+    (name "r-lavaan")
+    (version "0.6-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "lavaan" version))
+       (sha256
+        (base32
+         "0hw856kv11zqn6nd4216rh19i6xbnc1rh044r7jvvxkhzgbqkyxz"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)
+       ("r-mnormt" ,r-mnormt)
+       ("r-numderiv" ,r-numderiv)
+       ("r-pbivnorm" ,r-pbivnorm)))
+    (home-page "http://lavaan.ugent.be")
+    (synopsis "Latent variable analysis")
+    (description
+     "This package provides tools to fit a variety of latent variable models,
+including confirmatory factor analysis, structural equation modeling and
+latent growth curve models.")
+    (license license:gpl2+)))
+
+(define-public r-nonnest2
+  (package
+    (name "r-nonnest2")
+    (version "0.5-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "nonnest2" version))
+       (sha256
+        (base32
+         "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-compquadform" ,r-compquadform)
+       ("r-lavaan" ,r-lavaan)
+       ("r-mvtnorm" ,r-mvtnorm)
+       ("r-sandwich" ,r-sandwich)))
+    (home-page "https://cran.r-project.org/web/packages/nonnest2/")
+    (synopsis "Tests of non-nested models")
+    (description
+     "This package allows for testing of non-nested models.  It includes tests
+of model distinguishability and of model fit that can be applied to both
+nested and non-nested models.  The package also includes functionality to
+obtain confidence intervals associated with AIC and BIC.")
+    ;; Either version of the GPL.
+    (license (list license:gpl2 license:gpl3))))
+
+(define-public r-penalized
+  (package
+    (name "r-penalized")
+    (version "0.9-51")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "penalized" version))
+       (sha256
+        (base32
+         "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-survival" ,r-survival)))
+    (home-page "https://cran.r-project.org/web/packages/penalized/")
+    (synopsis "Penalized estimation in GLMs and in the Cox model")
+    (description
+     "This package provides tools for fitting possibly high dimensional
+penalized regression models.  The penalty structure can be any combination of
+an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
+constraint on the regression coefficients.  The supported regression models
+are linear, logistic and Poisson regression and the Cox Proportional Hazards
+model.  Cross-validation routines allow optimization of the tuning
+parameters.")
+    (license license:gpl2+)))
+
+(define-public r-zim
+  (package
+    (name "r-zim")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ZIM" version))
+       (sha256
+        (base32
+         "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
+    (properties `((upstream-name . "ZIM")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-mass" ,r-mass)))
+    (home-page "https://github.com/biostatstudio/ZIM")
+    (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
+    (description
+     "Analyze count time series with excess zeros.  Two types of statistical
+models are supported: Markov regression and state-space models.  They are also
+known as observation-driven and parameter-driven models respectively in the
+time series literature.  The functions used for Markov regression or
+observation-driven models can also be used to fit ordinary regression models
+with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
+negative binomial (ZINB) assumption.  The package also contains miscellaneous
+functions to compute density, distribution, quantile, and generate random
+numbers from ZIP and ZINB distributions.")
+    (license license:gpl3)))
+
+(define-public r-nor1mix
+  (package
+    (name "r-nor1mix")
+    (version "1.2-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "nor1mix" version))
+       (sha256
+        (base32
+         "1bvk888qml9qr7q703s7qzgm0sqfchcjdjqwqllm5vrjx0cnapj3"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/nor1mix/")
+    (synopsis "Normal (1-d) mixture models")
+    (description
+     "This package provides S3 classes and methods for one-dimensional normal
+mixture models, for, e.g., density estimation or clustering algorithms
+research and teaching; it provides the widely used Marron-Wand densities.  It
+also provides tools for efficient random number generation and graphics.")
+    (license license:gpl2+)))
+
+(define-public r-beanplot
+  (package
+    (name "r-beanplot")
+    (version "1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "beanplot" version))
+       (sha256
+        (base32
+         "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/beanplot/")
+    (synopsis "Visualization via beanplots")
+    (description
+     "This package provides beanplots, an alternative to
+boxplot/stripchart/violin plots.  It can be used to plot univariate comparison
+graphs.")
+    (license license:gpl2)))
+
+(define-public r-pbdzmq
+  (package
+    (name "r-pbdzmq")
+    (version "0.3-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pbdZMQ" version))
+       (sha256
+        (base32
+         "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
+    (properties `((upstream-name . "pbdZMQ")))
+    (build-system r-build-system)
+    (inputs
+     `(("zeromq" ,zeromq)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "https://pbdr.org/")
+    (synopsis "R interface to ZeroMQ")
+    (description
+     "ZeroMQ is a well-known library for high-performance asynchronous
+messaging in scalable, distributed applications.  This package provides high
+level R wrapper functions to easily utilize ZeroMQ.  The main focus is on
+interactive client/server programming frameworks.  A few wrapper functions
+compatible with @code{rzmq} are also provided.")
+    (license license:gpl3)))
+
+(define-public r-repr
+  (package
+    (name "r-repr")
+    (version "0.19.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "repr" version))
+       (sha256
+        (base32
+         "1mhhzakkagb8z568yx3p2ixs8fcifm7f8l2yq285zrz8jmnpckfx"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-base64enc" ,r-base64enc)
+       ("r-htmltools" ,r-htmltools)
+       ("r-jsonlite" ,r-jsonlite)))
+    (home-page "https://cran.r-project.org/web/packages/repr/")
+    (synopsis "Serializable representations")
+    (description
+     "This package provides string and binary representations of objects for
+several formats and MIME types.")
+    (license license:gpl3)))
+
+(define-public r-irdisplay
+  (package
+    (name "r-irdisplay")
+    (version "0.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "IRdisplay" version))
+       (sha256
+        (base32
+         "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
+    (properties `((upstream-name . "IRdisplay")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-repr" ,r-repr)))
+    (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
+    (synopsis "Jupyter display machinery")
+    (description
+     "This package provides an interface to the rich display capabilities of
+Jupyter front-ends (e.g. Jupyter Notebook).  It is designed to be used from a
+running IRkernel session.")
+    (license license:expat)))
+
+(define-public r-irkernel
+  (package
+    (name "r-irkernel")
+    (version "0.8.15")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "IRkernel" version))
+       (sha256
+        (base32
+         "1n0nc3paij8fgbp7l2b4405zk9k4y3gdi2bz6z8x6j0h5mi6k6a6"))))
+    (properties `((upstream-name . "IRkernel")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'install-kernelspec
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (setenv "HOME" "/tmp")
+               (invoke "jupyter" "kernelspec" "install"
+                       "--name" "ir"
+                       "--prefix" out
+                       (string-append out "/site-library/IRkernel/kernelspec"))
+               #t))))))
+    (inputs
+     `(("jupyter" ,jupyter)))
+    (propagated-inputs
+     `(("r-crayon" ,r-crayon)
+       ("r-digest" ,r-digest)
+       ("r-evaluate" ,r-evaluate)
+       ("r-irdisplay" ,r-irdisplay)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-pbdzmq" ,r-pbdzmq)
+       ("r-repr" ,r-repr)
+       ("r-uuid" ,r-uuid)))
+    (home-page "https://cran.r-project.org/web/packages/IRkernel/")
+    (synopsis "Native R kernel for Jupyter")
+    (description
+     "The R kernel for the Jupyter environment executes R code which the
+front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
+network.")
+    (license license:expat)))
+
+(define-public r-gmodels
+  (package
+    (name "r-gmodels")
+    (version "2.18.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gmodels" version))
+       (sha256
+        (base32
+         "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-gdata" ,r-gdata)
+       ("r-mass" ,r-mass)))
+    (home-page "https://cran.r-project.org/web/packages/gmodels/")
+    (synopsis "Various R programming tools for model fitting")
+    (description
+     "This package provides various R programming tools for model fitting.")
+    (license license:gpl2)))
+
+(define-public r-apcluster
+  (package
+    (name "r-apcluster")
+    (version "1.4.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "apcluster" version))
+       (sha256
+        (base32
+         "188hdfmwjjx3aic599nwmkzjqm9j9jighi5bly6qd43c1vj6ih2s"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://cran.r-project.org/web/packages/apcluster/")
+    (synopsis "Affinity propagation clustering")
+    (description
+     "This package implements affinity propagation clustering introduced by
+Frey and Dueck (2007).  The package further provides leveraged affinity
+propagation and an algorithm for exemplar-based agglomerative clustering that
+can also be used to join clusters obtained from affinity propagation.  Various
+plotting functions are available for analyzing clustering results.")
+    (license license:gpl2+)))
+
+(define-public r-valr
+  (package
+    (name "r-valr")
+    (version "0.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "valr" version))
+       (sha256
+        (base32
+         "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-broom" ,r-broom)
+       ("r-dplyr" ,r-dplyr)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-rcpp" ,r-rcpp)
+       ("r-readr" ,r-readr)
+       ("r-rlang" ,r-rlang)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)))
+    (home-page "http://github.com/rnabioco/valr")
+    (synopsis "Genome interval arithmetic in R")
+    (description
+     "This package enables you to read and manipulate genome intervals and
+signals.  It provides functionality similar to command-line tool suites within
+R, enabling interactive analysis and visualization of genome-scale data.")
+    (license license:expat)))
+
+(define-public r-rematch2
+  (package
+    (name "r-rematch2")
+    (version "2.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rematch2" version))
+       (sha256
+        (base32
+         "16k0i5p7fa3qfxv59ijyn638wpz8n4jrkrnilqmh5g9l8f8bn4h6"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-tibble" ,r-tibble)))
+    (home-page "https://github.com/r-lib/rematch2")
+    (synopsis "Tidy output from regular expression matching")
+    (description
+     "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
+return the match results in tidy data frames.")
+    (license license:expat)))

gnu/packages/curl.scm

@@ -107,7 +107,7 @@
              (("/bin/sh") (which "sh")))
 
            ;; XXX FIXME: Test #1510 seems to work on some machines and not
-           ;; others, possibly based on the kernel version.  It works on GuixSD
+           ;; others, possibly based on the kernel version.  It works on Guix System
            ;; on x86_64 with linux-libre-4.1, but fails on Hydra for both i686
            ;; and x86_64 with the following error:
            ;;

gnu/packages/databases.scm

@@ -1275,15 +1275,14 @@ columns, primary keys, unique constraints and relationships.")
 (define-public perl-dbd-mysql
   (package
     (name "perl-dbd-mysql")
-    (version "4.048")
+    (version "4.050")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://cpan/authors/id/M/MI/MICHIELB/"
+       (uri (string-append "mirror://cpan/authors/id/D/DV/DVEEDEN/"
                            "DBD-mysql-" version ".tar.gz"))
        (sha256
-        (base32
+        (base32 "0y4djb048i09dk19av7mzfb3khr72vw11p3ayw2p82jsy4gm8j2g"))))
-         "1zqmch6c9gq06z90mkmk1skajk2kaggriw19ym5w04l7wv5gydqp"))))
     (build-system perl-build-system)
     (arguments
      `(#:phases
@@ -1313,7 +1312,7 @@ columns, primary keys, unique constraints and relationships.")
 (define-public perl-dbd-sqlite
   (package
     (name "perl-dbd-sqlite")
-    (version "1.58")
+    (version "1.62")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1321,7 +1320,7 @@ columns, primary keys, unique constraints and relationships.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "0fqx386jgs9mmrknr7smmzapf07izgivza7x08lfm39ks2cxs83i"))))
+                "0p78ri1q6xpc1i98i6mlriv8n66iz8r5r11dlsknjm4y58rfz0mx"))))
     (build-system perl-build-system)
     (inputs `(("sqlite" ,sqlite)))
     (propagated-inputs `(("perl-dbi" ,perl-dbi)))
@@ -1336,15 +1335,14 @@ module, and nothing else.")
 (define-public perl-sql-abstract
   (package
     (name "perl-sql-abstract")
-    (version "1.85")
+    (version "1.86")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://cpan/authors/id/I/IL/ILMARI/"
                            "SQL-Abstract-" version ".tar.gz"))
        (sha256
-        (base32
+        (base32 "1pwcm8hwxcgidyyrak37lx69d85q728jxsb0b14jz93gbvdgg9z7"))))
-         "1aycggrvppy2zgkwwn85jkdz93n5gsx4dambrjk67k5067hayi4z"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-module-install" ,perl-module-install)
@@ -1847,14 +1845,13 @@ for ODBC.")
 (define-public python-pyodbc
   (package
     (name "python-pyodbc")
-    (version "4.0.24")
+    (version "4.0.25")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyodbc" version))
        (sha256
-        (base32
+        (base32 "1bbwrb812w5i0x56jfn0l86mxc2ck904hl8y87mziay96znwia0f"))
-         "1m311vi7vpay1j7rkq71fpsk0gb7454k4lldk5b63hyy6yvsn9j3"))
        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system python-build-system)
     (inputs
@@ -2095,25 +2092,24 @@ Database API 2.0T.")
 (define-public python-sqlalchemy
   (package
     (name "python-sqlalchemy")
-    (version "1.2.11")
+    (version "1.3.1")
     (source
      (origin
       (method url-fetch)
       (uri (pypi-uri "SQLAlchemy" version))
       (sha256
-       (base32
+       (base32 "12sr36646sipf9ac3n2xh8z0w5pz4d3dvw5qjv2kzvcls6wvf7vq"))))
-        "094mmbs4igrxplfyqd59j90jb83ixpbbzqc0w49yw81m82nnjrgg"))))
     (build-system python-build-system)
     (native-inputs
-     `(("python-cython" ,python-cython) ;for c extensions
+     `(("python-cython" ,python-cython) ; for C extensions
        ("python-pytest" ,python-pytest)
-       ("python-mock"   ,python-mock))) ;for tests
+       ("python-mock"   ,python-mock))) ; for tests
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
            (lambda _ (invoke "py.test"))))))
-    (home-page "http://www.sqlalchemy.org")
+    (home-page "https://www.sqlalchemy.org")
     (synopsis "Database abstraction library")
     (description
      "SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that
@@ -2335,14 +2331,13 @@ designed to be easy and intuitive to use.")
 (define-public python-psycopg2
   (package
     (name "python-psycopg2")
-    (version "2.7.5")
+    (version "2.7.7")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "psycopg2" version))
        (sha256
-        (base32
+        (base32 "0zjbabb4qjx9dm07imhf8y5a9rpa06d5zah80myiimgdi83nslpl"))))
-         "17klx964gw8z0znl0raz3by8vdc7cq5gxj4pdcrfcina84nrdkzc"))))
     (build-system python-build-system)
     (arguments
      ;; Tests would require a postgresql database "psycopg2_test"
@@ -2580,14 +2575,13 @@ provides support for parsing, splitting and formatting SQL statements.")
 (define-public python-sql
   (package
     (name "python-sql")
-    (version "0.9")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "python-sql" version))
        (sha256
-        (base32
+        (base32 "05ni936y0ia9xmryl7mlhbj9i80nnvq1bi4zxhb96rv7yvpb3fqb"))))
-         "0p6kaqj02vz0habmdx37zjk6hjxdfm8aw737zs059vvpr70ird87"))))
     (build-system python-build-system)
     (home-page "https://python-sql.tryton.org/")
     (synopsis "Library to write SQL queries in a pythonic way")

gnu/packages/education.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -41,6 +41,7 @@
   #:use-module (gnu packages sdl)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages texinfo)
+  #:use-module (gnu packages tls)
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages xml)
   #:use-module ((guix licenses) #:prefix license:)
@@ -116,16 +117,15 @@ of categories with some of the activities available in that category.
 (define-public gcompris-qt
   (package
     (name "gcompris-qt")
-    (version "0.95")
+    (version "0.96")
     (source
-      (origin
+     (origin
-        (method url-fetch)
+       (method url-fetch)
-        (uri (string-append
+       (uri (string-append
-               "https://gcompris.net/download/qt/src/gcompris-qt-"
+             "https://gcompris.net/download/qt/src/gcompris-qt-"
-               version ".tar.xz"))
+             version ".tar.xz"))
-        (sha256
+       (sha256
-         (base32
+        (base32 "06483il59l46ny2w771sg45dgzjwv1ph7vidzzbj0wb8wbk2rg52"))))
-          "1aaijjx2b7k1cyx59jhs64hlp1sppw1faa81qxl5lxc79vifrlrl"))))
     (build-system cmake-build-system)
     (arguments
      `(#:phases
@@ -162,7 +162,8 @@ of categories with some of the activities available in that category.
        ("qttools" ,qttools)
        ("xorg-server" ,xorg-server)))
     (inputs
-     `(("python-2" ,python-2)
+     `(("openssl" ,openssl)
+       ("python-2" ,python-2)
        ("qtbase" ,qtbase)
        ("qtdeclarative" ,qtdeclarative)
        ("qtgraphicaleffects" ,qtgraphicaleffects)

gnu/packages/emacs-xyz.scm

@@ -26,7 +26,7 @@
 ;;; Copyright © 2017 George Clemmer <myglc2@gmail.com>
 ;;; Copyright © 2017, 2018 Feng Shu <tumashu@163.com>
 ;;; Copyright © 2017 Jan Nieuwenhuizen <janneke@gnu.org>
-;;; Copyright © 2017, 2018 Oleg Pykhalov <go.wigust@gmail.com>
+;;; Copyright © 2017, 2018, 2019 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2017 Mekeor Melire <mekeor.melire@gmail.com>
 ;;; Copyright © 2017 Peter Mikkelsen <petermikkelsen10@gmail.com>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -278,7 +278,12 @@ on stdout instead of using a socket as the Emacsclient does.")
        ("magit-popup" ,emacs-magit-popup)
        ("with-editor" ,emacs-with-editor)))
     (arguments
-     `(#:test-target "test"
+     `(#:modules ((guix build gnu-build-system)
+                  (guix build utils)
+                  (guix build emacs-utils))
+       #:imported-modules (,@%gnu-build-system-modules
+                           (guix build emacs-utils))
+       #:test-target "test"
        #:tests? #f               ; tests are not included in the release
 
        #:make-flags
@@ -317,8 +322,9 @@ on stdout instead of using a socket as the Emacsclient does.")
           'build 'patch-exec-paths
           (lambda* (#:key inputs #:allow-other-keys)
             (let ((perl (assoc-ref inputs "perl")))
-              (substitute* "lisp/magit-sequence.el"
+              (make-file-writable "lisp/magit-sequence.el")
-                (("perl") (string-append perl "/bin/perl")))
+              (emacs-substitute-variables "lisp/magit-sequence.el"
+                ("magit-perl-executable" (string-append perl "/bin/perl")))
               #t))))))
     (home-page "https://magit.vc/")
     (synopsis "Emacs interface for the Git version control system")
@@ -1610,7 +1616,7 @@ and stored in memory.")
 (define-public emacs-dash
   (package
     (name "emacs-dash")
-    (version "2.14.1")
+    (version "2.15.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1619,7 +1625,7 @@ and stored in memory.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1kzijmjxjxgr7p8clphzvmm47vczckbs8mza9an77c25bn627ywl"))))
+                "0dx8q3jr8fh73cfl7mqi5dq0012ambpvc74d2c71fsv9rfw85693"))))
     (build-system emacs-build-system)
     (arguments
      `(#:tests? #t
@@ -4951,7 +4957,7 @@ ack, ag, helm and pt.")
 (define-public emacs-helm
   (package
     (name "emacs-helm")
-    (version "3.0")
+    (version "3.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -4960,7 +4966,7 @@ ack, ag, helm and pt.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0k2r0ccppaqfjvyszaxa16vf7g2qzj1clhfr6v646ncsy17laciw"))))
+                "0ymykcsbcgq2kskqc0ddigg0kfznxx3j02mkd5r3c3n8gn3kgz84"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-async" ,emacs-async)
@@ -7032,7 +7038,19 @@ running a customisable handler command (@code{ignore} by default). ")
        ("ert-runner" ,emacs-ert-runner)))
     (arguments
      `(#:tests? #t
-       #:test-command '("ert-runner")))
+       #:test-command '("ert-runner")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'delete-json-objects-order-test
+           (lambda _
+             (emacs-batch-edit-file "test/json-reformat-test.el"
+               `(progn (progn (goto-char (point-min))
+                              (re-search-forward
+                               "ert-deftest json-reformat-test:json-reformat-region")
+                              (beginning-of-line)
+                              (kill-sexp))
+                       (basic-save-buffer)))
+             #t)))))
     (home-page "https://github.com/gongo/json-reformat")
     (synopsis "Reformatting tool for JSON")
     (description "@code{json-reformat} provides a reformatting tool for
@@ -10143,23 +10161,26 @@ and doesn't require memorisation of commands.
 (define-public emacs-suggest
   (package
     (name "emacs-suggest")
-    (version "0.4")
+    (version "0.7")
+    (home-page "https://github.com/Wilfred/suggest.el")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/Wilfred/suggest.el/archive/"
+       (uri (git-reference
-                           version ".tar.gz"))
+             (url home-page)
-       (file-name (string-append name "-" version ".tar.gz"))
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1760fm3j19w8xxcawq6s859h86q1rdg69pg9yz48n76kwfk3vlgp"))))
+         "01v8plska5d3g19sb1m4ph1i3ayprfzk8mi6mpabjy6zad397xjl"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-loop" ,emacs-loop)
        ("emacs-dash" ,emacs-dash)
        ("emacs-s" ,emacs-s)
-       ("emacs-f" ,emacs-f)))
+       ("emacs-f" ,emacs-f)
-    (home-page "https://github.com/Wilfred/suggest.el")
+       ("emacs-spinner" ,emacs-spinner)
+       ("emacs-shut-up" ,emacs-shut-up)))
     (synopsis "Suggest Elisp functions that give the output requested")
     (description "Suggest.el will find functions that give the output
 requested.  It's a great way of exploring list, string and arithmetic
@@ -11155,6 +11176,29 @@ systems.")
 filters, highlighting of regexp group levels, and more.")
       (license license:gpl2+))))
 
+(define-public emacs-eshell-bookmark
+  (package
+    (name "emacs-eshell-bookmark")
+    (version "2.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Fuco1/eshell-bookmark")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "14dmsnixf9vqdhsixw693sml0fn80zcf0b37z049fb40cmppqxdw"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/Fuco1/eshell-bookmark")
+    (synopsis "Provide @file{bookmark.el} integration for @code{eshell}")
+    (description
+     "This package allows for bookmarking @code{eshell} buffers.  Upon
+visiting the bookmark, a new @code{eshell} session will be opened in the
+appropriate directory if no @code{eshell} session is active.")
+    (license license:gpl3+)))
+
 (define-public emacs-esh-autosuggest
   (package
     (name "emacs-esh-autosuggest")
@@ -11358,6 +11402,56 @@ Org-mode.  It features:
 @end itemize\n")
       (license license:gpl3+))))
 
+(define-public emacs-debpaste
+  (package
+    (name "emacs-debpaste")
+    (version "0.1.5")
+    (home-page "https://github.com/alezost/debpaste.el")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference (url home-page)
+                           (commit (string-append "v" version))))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1wi70r56pd5z0x4dp4m58p9asq03j74kdm4fi9vai83vsl2z9amq"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-xml-rpc" ,emacs-xml-rpc)))
+    (synopsis "Manipulate pastes from the Debian Pastezone")
+    (description "Debpaste is an Emacs interface for the Debian Pastezone,
+allowing you to receive, post, and delete pastes.  It communicates with the
+server using XML-RPC.")
+    (license license:gpl3+)))
+
+(define-public emacs-xml-rpc
+  (let ((commit "8f624f8b964e9145acb504e4457c9510e87dd93c")
+        (revision "1"))
+    (package
+      (name "emacs-xml-rpc")
+      (version (git-version "1.6.12" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/hexmode/xml-rpc-el")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0xa54z52rsfl3n0xgmbycj4zazp8ksgdwcq56swzs6wp72zlalmj"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/hexmode/xml-rpc-el")
+      (synopsis "XML-RPC client for Emacs")
+      (description "This package provides an XML-RPC client for Emacs capable
+of both synchronous and asynchronous method calls using the @code{url}
+package's async retrieval functionality.  @file{xml-rpc.el} represents XML-RPC
+datatypes as Lisp values, automatically converting to and from the XML
+datastructures as needed, both for method parameters and return values, making
+using XML-RPC methods fairly transparent to the Lisp code.")
+      (license license:gpl3+))))
+
 (define-public emacs-fish-completion
   (package
     (name "emacs-fish-completion")
@@ -13235,3 +13329,180 @@ provides several enhancements over the ordinary
 in the completion list and showing keyboard shortcuts, and it supports several
 completion systems for selecting commands, such as ido and ivy.")
     (license license:gpl3+)))
+
+(define-public emacs-lorem-ipsum
+  (let ((commit "4b39f6fed455d67f635b3837cf5668bf74d0f6cd"))
+    (package
+      (name "emacs-lorem-ipsum")
+      (version (git-version "0.2" "1" commit))
+      (home-page "https://github.com/jschaf/emacs-lorem-ipsum/")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url home-page)
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0a3b18p3vdjci89prsgdzjnfxsl8p67vjhf8ai4qdng7zvh50lir"))))
+      (build-system emacs-build-system)
+      (synopsis "Insert dummy pseudo Latin text in Emacs")
+      (description "This package provides convenience functions to insert
+dummy Latin text into a buffer.  This can be useful if you need to produce
+paragraphs or pages of text for testing purposes.")
+      (license license:gpl3+))))
+
+(define-public emacs-lisp-extra-font-lock
+  (let ((commit "4605eccbe1a7fcbd3cacf5b71249435413b4db4f"))
+    (package
+      (name "emacs-lisp-extra-font-lock")
+      (version (git-version "0.0.6" "1" commit))
+      (home-page "https://github.com/Lindydancer/lisp-extra-font-lock")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url home-page)
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "152vcp3mdlv33jf5va4rinl1d0k960gnfhbrqqrafazgx9j3ya8w"))))
+      (build-system emacs-build-system)
+      (synopsis "Highlight bound variables and quoted expressions in Emacs")
+      (description "This package highlight the location where local variables
+is created (bound, for example, by let) as well as quoted and backquoted
+constant expressions.")
+      (license license:gpl3+))))
+
+(define-public emacs-docker-tramp
+  (package
+    (name "emacs-docker-tramp")
+    (version "0.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/emacs-pe/docker-tramp.el")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0lxvzmfg52fhxrhbvp92zwp7cv4i1rlxnkyyzgngj3sjm7y60yvg"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/emacs-pe/docker-tramp.el")
+    (synopsis "TRAMP integration for docker containers")
+    (description
+     "This package provides a TRAMP method for Docker containers.")
+    (license license:gpl3+)))
+
+(define-public emacs-docker
+  (package
+    (name "emacs-docker")
+    (version "1.2.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/Silex/docker.el")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "15kd86kaq1x6giz855q9w6zvnyc742j309j0pmm86rwx398g4rq1"))))
+    (inputs
+     `(("emacs-undercover" ,emacs-undercover)))
+    (propagated-inputs
+     `(("emacs-dash" ,emacs-dash)
+       ("emacs-docker-tramp" ,emacs-docker-tramp)
+       ("emacs-magit-popup" ,emacs-magit-popup)
+       ("emacs-s" ,emacs-s)
+       ("emacs-tablist" ,emacs-tablist)
+       ("emacs-json-mode" ,emacs-json-mode)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (delete 'check)))) ;no tests
+    (build-system emacs-build-system)
+    (home-page "https://github.com/Silex/docker.el")
+    (synopsis "Manage docker from Emacs")
+    (description "This package provides an Emacs interface for Docker.")
+    (license license:gpl3+)))
+
+(define-public emacs-dockerfile-mode
+  ;; Latest upstream release is too old.
+  (let ((commit "7223d92718f78fa3ab15667cdb2ed90cfeb579e7"))
+    (package
+      (name "emacs-dockerfile-mode")
+      (version (git-version "1.2" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/spotify/dockerfile-mode.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0hmipgl4rk6aih11i8mnspwdijjiwk2y0wns6lzs8bgkvy3c064r"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-s" ,emacs-s)))
+      (home-page "https://github.com/spotify/dockerfile-mode")
+      (synopsis "Major mode for editing Dockerfile")
+      (description
+       "This package provides a major mode @code{dockerfile-mode} for use with
+the standard @code{Dockerfile} file format.")
+      (license license:asl2.0))))
+
+(define-public emacs-lsp-mode
+  (package
+    (name "emacs-lsp-mode")
+    (version "6.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/emacs-lsp/lsp-mode.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1v1mq6ixzlgiazj8fmg4xaqhsqn3l89iqy74yndhvzh2rdf0pbkl"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-dash" ,emacs-dash)
+       ("emacs-f" ,emacs-f)
+       ("emacs-ht" ,emacs-ht)
+       ("emacs-spinner" ,emacs-spinner)))
+    (home-page "https://github.com/emacs-lsp/lsp-mode")
+    (synopsis "Emacs client and library for the Language Server Protocol")
+    (description "@code{LSP-mode} is a client and library implmentation for
+the Language Server Protocol.  This mode aims to provide an IDE-like
+experience by providing optional integration with other popular Emacs packages
+like @code{company}, @code{flycheck}, and @code{projectile}.")
+    (license license:gpl3+)))
+
+(define-public emacs-lsp-ui
+  (package
+    (name "emacs-lsp-ui")
+    (version "6.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/emacs-lsp/lsp-ui.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1r4327fd8cvjxfwkddp5c4bdskyncbs4sx9m3z2w4d773y2jrakc"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-dash" ,emacs-dash)
+       ("emacs-lsp-mode" ,emacs-lsp-mode)
+       ("emacs-markdown-mode" ,emacs-markdown-mode)
+       ("emacs-flycheck" ,emacs-flycheck)))
+    (home-page "https://github.com/emacs-lsp/lsp-ui")
+    (synopsis "User interface extensions for @code{lsp-mode}")
+    (description
+     "@code{LSP-ui} contains several enhancements and integrations for
+@code{lsp-mode}, such as visual flychecking, displaying references in-line,
+and code peeking.")
+    (license license:gpl3+)))

gnu/packages/emacs.scm

@@ -92,7 +92,7 @@
                                    '("eshell/esh-groups.el")))
 
                  ;; Make sure Tramp looks for binaries in the right places on
-                 ;; remote GuixSD machines, where 'getconf PATH' returns
+                 ;; remote Guix System machines, where 'getconf PATH' returns
                  ;; something bogus.
                  (substitute* "net/tramp-sh.el"
                    ;; Patch the line after "(defcustom tramp-remote-path".

gnu/packages/emulators.scm

@@ -1333,7 +1333,6 @@ play them on systems for which they were never designed!")
                #t))))))
     (native-inputs
      `(("pkg-config" ,pkg-config)
-       ("pugixml" ,pugixml)
        ("python-sphinx" ,python-sphinx)
        ("texinfo" ,texinfo)))
     (inputs
@@ -1348,6 +1347,7 @@ play them on systems for which they were never designed!")
        ("lua" ,lua)
        ("portaudio" ,portaudio)
        ("portmidi" ,portmidi)
+       ("pugixml" ,pugixml)
        ("python-wrapper" ,python-wrapper)
        ("qtbase" ,qtbase)
        ("rapidjson" ,rapidjson)

gnu/packages/engineering.scm

@@ -734,16 +734,16 @@ language.")
 (define-public kicad
     (package
       (name "kicad")
-      (version "5.0.0")
+      (version "5.0.2")
       (source
        (origin
          (method url-fetch)
          (file-name (string-append name "-" version ".tar.xz"))
          (uri (string-append
                 "https://launchpad.net/kicad/" (version-major+minor version)
-                "/" version "/+download/" name "-" version ".tar.xz"))
+                "/" version "/+download/kicad-" version ".tar.xz"))
          (sha256
-          (base32 "17nqjszyvd25wi6550j981whlnb1wxzmlanljdjihiki53j84x9p"))))
+          (base32 "10605rr10x0353n6yk2z095ydnkd1i6j1ncbq64pfxdn5vkhcd1g"))))
       (build-system cmake-build-system)
       (arguments
        `(#:out-of-source? #t
@@ -888,16 +888,16 @@ render model libraries.")
 (define-public kicad-symbols
   (package
     (name "kicad-symbols")
-    (version "5.0.1")
+    (version "5.0.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/KiCad/kicad-symbols.git")
                     (commit version)))
-              (file-name (string-append "kicad-symbols-" version "-checkout"))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "18z5vpdq7hy2mpvm5vz1dz3ra3a5iybavvlzi8q2bmmdb6gsvf64"))))
+                "1rjh2pjcrc3bhcgyyskj5pssm7vffrjk0ymwr70fb7sjpmk96yjk"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f)) ; No tests exist

gnu/packages/fpga.scm

@@ -301,14 +301,14 @@ Includes the actual FTDI connector.")
 (define-public gtkwave
   (package
     (name "gtkwave")
-    (version "3.3.91")
+    (version "3.3.99")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://gtkwave.sourceforge.net/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1vp9qj3wyfwm36jk3pajvi09xvc1m1crf3d4gphfbs6nkyx2z942"))))
+                "0lc4y2vizrbxldjk5yw2i4y7pyprjdjqx3iafzjfnin694zp2630"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("gperf" ,gperf)

gnu/packages/freedesktop.scm

@@ -8,7 +8,7 @@
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2017, 2018 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2017, 2018, 2019 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2017 Brendan Tildesley <brendan.tildesley@openmailbox.org>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -36,6 +36,7 @@
   #: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 meson)
   #:use-module (guix build-system perl)
@@ -152,7 +153,7 @@ freedesktop.org project.")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://freedesktop.org/software/libinput/"
-                                  name "-" version ".tar.xz"))
+                                  "libinput-" version ".tar.xz"))
               (sha256
                (base32
                 "0pgla0mc6mvyr1ljy10mcqvfz8i5z6yp7dbx2bcd70y67wx05d0j"))))
@@ -452,6 +453,33 @@ applications, X servers (rootless or fullscreen) or other display servers.")
     (home-page "https://wayland.freedesktop.org")
     (license license:expat)))
 
+(define-public waylandpp
+  (package
+    (name "waylandpp")
+    (version "0.2.5")
+    (home-page "https://github.com/NilsBrause/waylandpp")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference (url home-page) (commit version)))
+              (sha256
+               (base32
+                "16h57hzd688664qcyznzhjp3hxipdkzgv46x82yhkww24av8b55n"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f))                    ;no tests
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("mesa" ,mesa)
+       ("pugixml" ,pugixml)))
+    (propagated-inputs
+     `(;; In Requires of the .pc files.
+       ("wayland" ,wayland)))
+    (synopsis "Wayland C++ bindings")
+    (description
+     "This package provides C++ bindings for the Wayland display protocol.")
+    (license license:bsd-2)))
+
 (define-public weston
   (package
     (name "weston")

gnu/packages/ftp.scm

@@ -209,14 +209,14 @@ output.
 (define-public filezilla
   (package
     (name "filezilla")
-    (version "3.40.0")
+    (version "3.41.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://download.filezilla-project.org/client/"
                            "FileZilla_" version "_src.tar.bz2"))
        (sha256
-        (base32 "11b0410fcwrahq5dd7ph10bc09m62sxra4bjp0kj5gph822s0v63"))))
+        (base32 "0mlv21054fk11rspbnig0q4gph1iqsqm4rpya3wl5is50p33vg5w"))))
     (build-system gnu-build-system)
     (arguments
       ;; Don't let filezilla phone home to check for updates.
@@ -224,7 +224,6 @@ output.
     (native-inputs
      `(("gettext" ,gettext-minimal)
        ("pkg-config" ,pkg-config)
-       ("pugixml" ,pugixml)
        ("xdg-utils" ,xdg-utils)))
     (inputs
      `(("dbus" ,dbus)
@@ -233,6 +232,7 @@ output.
        ("libfilezilla" ,libfilezilla)
        ("libidn" ,libidn)
        ("nettle" ,nettle)
+       ("pugixml" ,pugixml)
        ("sqlite" ,sqlite)
        ("wxwidgets" ,wxwidgets)))
     (home-page "https://filezilla-project.org")

gnu/packages/games.scm

@@ -1403,14 +1403,14 @@ interface or via an external visual interface such as GNU XBoard.")
 (define freedink-engine
   (package
     (name "freedink-engine")
-    (version "109.4")
+    (version "109.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/freedink/freedink-" version
                                   ".tar.gz"))
               (sha256
                (base32
-                "0iaagwnyfgm3mqzkj550q60hrsjr13gykg5vfn2nz2ia520bb52g"))))
+                "00hhk1bjdrc1np2qz44sa5n1mb62qzwxbvsnws3vpms6iyn3a2sy"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--disable-embedded-resources")
@@ -4437,12 +4437,17 @@ fish.  The whole game is accompanied by quiet, comforting music.")
        ("python-pyyaml" ,python-pyyaml)
        ("pkg-config" ,pkg-config)))
     (arguments
-     '(#:make-flags
+     `(#:make-flags
        (let* ((sqlite (assoc-ref %build-inputs "sqlite"))
               (out (assoc-ref %outputs "out")))
          (list (string-append "SQLITE_INCLUDE_DIR=" sqlite "/include")
                (string-append "prefix=" out)
                "SAVEDIR=~/.crawl"
+               ;; Don't compile with SSE on systems which don't use it
+               ,@(match (%current-system)
+                   ((or "i686-linux" "x86_64-linux")
+                    '())
+                   (_ '("NOSSE=TRUE")))
                ;; don't build any bundled dependencies
                "BUILD_LUA="
                "BUILD_SQLITE="
@@ -4450,11 +4455,6 @@ fish.  The whole game is accompanied by quiet, comforting music.")
                "-Csource"))
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'patch-flags
-           (lambda _
-             (substitute* "source/Makefile"
-               (("-mfpmath=sse -msse2") ""))
-             #t))
          (add-after 'unpack 'find-SDL-image
            (lambda _
              (substitute* "source/windowmanager-sdl.cc"
@@ -5860,7 +5860,7 @@ when packaged in Blorb container files or optionally from individual files.")
 (define-public libmanette
   (package
     (name "libmanette")
-    (version "0.2.1")
+    (version "0.2.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -5868,7 +5868,7 @@ when packaged in Blorb container files or optionally from individual files.")
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "14vqz30p4693yy3yxs0gj858x25sl2kawib1g9lj8g5frgl0hd82"))))
+                "1lpprk2qz1lsqf9xj6kj2ciyc1zmjhj5lwd584qkh7jgz2x9y6wb"))))
     (build-system meson-build-system)
     (native-inputs
      `(("glib" ,glib "bin")             ; for glib-compile-resources

gnu/packages/geo.scm

@@ -63,7 +63,7 @@
 (define-public geos
   (package
     (name "geos")
-    (version "3.7.0")
+    (version "3.7.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://download.osgeo.org/geos/geos-"
@@ -71,7 +71,7 @@
                                   ".tar.bz2"))
               (sha256
                (base32
-                "1mrz778m6bd1x9k6sha5kld43kalhq79h2lynlx2jx7xjakl3gsg"))))
+                "1312m02xk4sp6f1xdpb9w0ic0zbxg90p5y66qnwidl5fksscf1h0"))))
     (build-system gnu-build-system)
     (arguments `(#:phases
                  (modify-phases %standard-phases

gnu/packages/gnome.scm

@@ -2596,7 +2596,7 @@ libxml to ease remote use of the RESTful API.")
 (define-public libsoup
   (package
     (name "libsoup")
-    (version "2.64.2")
+    (version "2.66.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/libsoup/"
@@ -2604,38 +2604,23 @@ libxml to ease remote use of the RESTful API.")
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1il6lyrmfi0hfh3ysw8w1qzc1rdz0igkb7dv6d8g5mmilnac3pbm"))))
+                "08c9kkdhzy504gv23pfdm4sq3dd3j20sikwz6gv0qrwcdjnw5bai"))))
-    (build-system gnu-build-system)
+    (build-system meson-build-system)
     (outputs '("out" "doc"))
     (arguments
      `(#:modules ((guix build utils)
-                  (guix build gnu-build-system)
+                  (guix build meson-build-system)
                   (ice-9 popen))
 
-       #:configure-flags
+       #:configure-flags '("-Ddoc=true")
-       (list (string-append "--with-html-dir="
-                            (assoc-ref %outputs "doc")
-                            "/share/gtk-doc/html")
-             (string-append "--with-apache-module-dir="
-                            (assoc-ref %build-inputs "httpd")
-                            "/modules"))
        #:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'disable-unconnected-socket-test
+         (add-after 'unpack 'adjust-tests
-           ;; This test fails due to missing /etc/nsswitch.conf
-           ;; in the build environment.
            (lambda _
+             ;; This test fails due to missing /etc/nsswitch.conf
+             ;; in the build environment.
              (substitute* "tests/socket-test.c"
                ((".*/sockets/unconnected.*") ""))
-             #t))
-         (add-before 'check 'pre-check
-           (lambda _
-             ;; The 'check-local' target runs 'env LANG=C sort -u',
-             ;; unset 'LC_ALL' to make 'LANG' working.
-             (unsetenv "LC_ALL")
-             ;; HTTPD in Guix uses mod_event and does not build prefork.
-             (substitute* "tests/httpd.conf"
-               (("^LoadModule mpm_prefork_module.*$") "\n"))
 
              ;; Generate a self-signed certificate that has "localhost" as its
              ;; 'dnsName'.  Failing to do that, and starting with GnuTLS
@@ -2681,16 +2666,19 @@ libxml to ease remote use of the RESTful API.")
                            ))
                (close-pipe pipe))
              #t))
-         (replace 'install
+         (add-after 'install 'move-doc
-           (lambda _
+           (lambda* (#:key outputs #:allow-other-keys)
-             (invoke "make"
+             (let ((out (assoc-ref outputs "out"))
-                     ;; Install vala bindings into $out.
+                   (doc (assoc-ref outputs "doc")))
-                     (string-append "vapidir=" %output
+               (mkdir-p (string-append doc "/share"))
-                                    "/share/vala/vapi")
+               (copy-recursively (string-append out "/share/gtk-doc")
-                     "install"))))))
+                                 (string-append doc "/share/gtk-doc"))
+               (delete-file-recursively (string-append out "/share/gtk-doc"))
+               #t))))))
     (native-inputs
      `(("glib:bin" ,glib "bin")                   ; for glib-mkenums
        ("gobject-introspection" ,gobject-introspection)
+       ("gtk-doc" ,gtk-doc)
        ("intltool" ,intltool)
        ("pkg-config" ,pkg-config)
        ("python" ,python-wrapper)
@@ -2703,11 +2691,12 @@ libxml to ease remote use of the RESTful API.")
     (propagated-inputs
      ;; libsoup-2.4.pc refers to all these.
      `(("glib" ,glib)
-       ("libxml2" ,libxml2)))
+       ("libpsl" ,libpsl)
+       ("libxml2" ,libxml2)
+       ("sqlite" ,sqlite)))
     (inputs
      `(("glib-networking" ,glib-networking)
-       ("libpsl" ,libpsl)
+       ("mit-krb5" ,mit-krb5)))
-       ("sqlite" ,sqlite)))
     (home-page "https://live.gnome.org/LibSoup/")
     (synopsis "GLib-based HTTP Library")
     (description
@@ -5212,7 +5201,7 @@ users.")
              (doc      (assoc-ref %outputs "doc"))
              (dhclient (string-append (assoc-ref %build-inputs "isc-dhcp")
                                       "/sbin/dhclient")))
-         (list "--with-systemd-logind=yes" ;In GuixSD, this is provided by elogind.
+         (list "--with-systemd-logind=yes" ;In Guix System, this is provided by elogind.
                "--with-consolekit=no"
                "--with-crypto=gnutls"
                "--disable-config-plugin-ibft"
@@ -5763,10 +5752,9 @@ properties, screen resolution, and other GNOME parameters.")
                    (copy-file #$(file-append %artwork-repository
                                              "/slim/0.x/background.png")
                               "data/theme/guix-background.png")
-                   (invoke #+(file-append inkscape "/bin/inkscape")
+                   (copy-file #$(file-append %artwork-repository
-                           "--export-png=data/theme/guix-logo.png"
+                                             "/logo/Guix-horizontal-white.svg")
-                           #$(file-append %artwork-repository
+                              "data/theme/guix-logo.svg")
-                                          "/logo/Guix-horizontal-white.svg"))
                    #t))))
     (build-system meson-build-system)
     (arguments
@@ -5788,6 +5776,11 @@ properties, screen resolution, and other GNOME parameters.")
                  (("keysdir =.*")
                   (string-append "keysdir = '" keysdir "'\n")))
                #t)))
+         (add-before 'configure 'convert-logo-to-png
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; Convert the logo from SVG to PNG.
+             (invoke "inkscape" "--export-png=data/theme/guix-logo.png"
+                     "data/theme/guix-logo.svg")))
          (add-before 'check 'pre-check
            (lambda* (#:key inputs #:allow-other-keys)
              ;; Tests require a running X server.
@@ -5819,6 +5812,7 @@ properties, screen resolution, and other GNOME parameters.")
      `(("glib:bin" ,glib "bin") ; for glib-compile-schemas, etc.
        ("desktop-file-utils" ,desktop-file-utils) ; for update-desktop-database
        ("gobject-introspection" ,gobject-introspection)
+       ("inkscape" ,inkscape)
        ("intltool" ,intltool)
        ("pkg-config" ,pkg-config)
        ("python" ,python)

gnu/packages/gtk.scm

@@ -731,7 +731,7 @@ application suites.")
    (name "gtk+")
    ;; NOTE: When updating the version of 'gtk+', the hash of 'mate-themes' in
    ;;       mate.scm will also need to be updated.
-   (version "3.24.5")
+   (version "3.24.7")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnome/sources/" name "/"
@@ -739,7 +739,7 @@ application suites.")
                                 name "-" version ".tar.xz"))
             (sha256
              (base32
-              "0bxhvnixc1hjxbzx063lghmix0wmv282khsqmckdxhrb606zpr8b"))
+              "080m925dyhiidlhsxqzx040l4iha2gg38pzbfpnsnjyzl92124jj"))
             (patches (search-patches "gtk3-respect-GUIX_GTK3_PATH.patch"
                                      "gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch"))
             (modules '((guix build utils)))

gnu/packages/guile-xyz.scm

@@ -605,18 +605,19 @@ using Guile's foreign function interface.")
   (package
     (name "guile-colorized")
     (version "0.1")
-    (source (origin
+    (source
-              (method url-fetch)
+     (origin
-              (uri (string-append "https://github.com/NalaGinrut/guile-colorized/"
+       (method git-fetch)
-                                  "archive/v" version ".tar.gz"))
+       (uri (git-reference
-              (file-name (string-append name "-" version ".tar.gz"))
+             (url "https://gitlab.com/NalaGinrut/guile-colorized.git")
-              (sha256
+             (commit (string-append "v" version))))
-               (base32
+       (file-name (git-file-name name version))
-                "16xhc3an6aglnca8xl3mvgi8hsqzqn68vsl5ga4bz8bvbap5fn4p"))))
+       (sha256
+        (base32 "10mv8c63159r3qvwwdvsgnsvdg7nc2ghak85zapwqpv4ywrqp9zc"))))
     (build-system guile-build-system)
     (native-inputs
      `(("guile" ,guile-2.2)))
-    (home-page "https://github.com/NalaGinrut/guile-colorized")
+    (home-page "https://gitlab.com/NalaGinrut/guile-colorized")
     (synopsis "Colorized REPL for Guile")
     (description
      "Guile-colorized provides you with a colorized REPL for GNU Guile.")
@@ -2069,6 +2070,7 @@ completion, a simple mode line, etc.")
                 (uri (git-reference
                       (url "https://gitlab.com/tampe/stis-parser")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "0v4hvq7rlpbra1ni73lf8k6sdmjlflr50yi3p1f24g85h77pc7c0"))))
@@ -2079,6 +2081,11 @@ completion, a simple mode line, etc.")
          (modify-phases %standard-phases
            (add-after 'unpack 'chdir
              (lambda _ (chdir "modules") #t))
+           (add-after 'chdir 'use-canonical-directory-for-go-files
+             (lambda _
+               (substitute* "Makefile.am"
+                 (("/ccache") "/site-ccache"))
+               #t))
            (add-after 'chdir 'delete-broken-symlink
              (lambda _
                (delete-file "parser/stis-parser/lang/.#calc.scm")
@@ -2097,3 +2104,103 @@ supports backtracking and a small logical framework. The idea is to build up
 chunks that are memoized and there is no clear scanner/parser separation,
 chunks can be expressions as well as simple tokens.")
       (license license:lgpl2.0+))))
+
+(define-public guile-persist
+  (let ((commit "b14927b0368af51c024560aee5f55724aee35233")
+        (revision "1"))
+    (package
+      (name "guile-persist")
+      (version (git-version "0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://gitlab.com/tampe/guile-persist")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0z5nf377wh8yj6n3sx2ddn4bdx1qrqnw899dlqjhg0q69qzil522"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'patch-prefix
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (substitute* "src/Makefile.am"
+                 (("/usr/local/lib/guile")
+                  (string-append (assoc-ref outputs "out") "/lib/guile"))
+                 (("/usr/local/include/guile")
+                  (string-append (assoc-ref inputs "guile") "/include/guile"))
+                 (("-L/usr/local/lib")
+                  (string-append "-L" (assoc-ref inputs "guile") "/lib"))
+                 ;; Use canonical directory for go files.
+                 (("/ccache") "/site-ccache"))
+               #t))
+           (add-after 'unpack 'patch-library-reference
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((out (assoc-ref outputs "out")))
+                 (substitute* "persist/persistance.scm"
+                   (("\"libguile-persist\"")
+                    (format #f "\"~a/lib/guile/2.2/extensions/libguile-persist\"" out)))
+                 #t))))))
+      (inputs
+       `(("guile" ,guile-2.2)))
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("libtool" ,libtool)
+         ("pkg-config" ,pkg-config)))
+      (home-page "https://gitlab.com/tampe/guile-persist")
+      (synopsis "Persistance programming framework for Guile")
+      (description
+       "This is a serialization library for serializing objects like classes
+and objects, closures and structs.  This currently does not support
+serializing continuations or delimited continuations.")
+      (license license:lgpl2.0+))))
+
+(define-public python-on-guile
+  (let ((commit "0cb7c2b2fff4338ca6153473f3f5c409a818f293")
+        (revision "1"))
+    (package
+      (name "python-on-guile")
+      (version (git-version "0.1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://gitlab.com/python-on-guile/python-on-guile.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0kpz08rrp5mwcf5ksc4flgrw992syham9x49dn9wq9w31bpcpnby"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:parallel-build? #f ; not supported
+         #:make-flags
+         '("GUILE_AUTO_COMPILE=0")        ; to prevent guild errors
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'chdir
+             (lambda _ (chdir "modules") #t))
+           (add-after 'chdir 'use-canonical-directory-for-go-files
+             (lambda _
+               (substitute* "Makefile.am"
+                 (("/ccache") "/site-ccache"))
+               #t)))))
+      (inputs
+       `(("guile" ,guile-2.2)))
+      (propagated-inputs
+       `(("guile-persist" ,guile-persist)
+         ("guile-readline" ,guile-readline)
+         ("guile-stis-parser" ,guile-stis-parser)))
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("libtool" ,libtool)
+         ("pkg-config" ,pkg-config)))
+      (home-page "https://gitlab.com/python-on-guile/python-on-guile/")
+      (synopsis "Python implementation in Guile")
+      (description
+       "This package allows you to compile a Guile Python file to any target
+from @code{tree-il}.")
+      (license license:lgpl2.0+))))

gnu/packages/guile.scm

@@ -391,7 +391,7 @@ GNU@tie{}Guile.  Use the @code{(ice-9 readline)} module and call its
 (define package-for-guile-2.0
   ;; A procedure that rewrites the dependency tree of the given package to use
   ;; GUILE-2.0 instead of GUILE-2.2.
-  (package-input-rewriting (delay `((,guile-2.2 . ,guile-2.0)))
+  (package-input-rewriting `((,guile-2.2 . ,guile-2.0))
                            (guile-variant-package-name "guile2.0")))
 
 (define-public guile-for-guile-emacs

gnu/packages/image.scm

@@ -1101,7 +1101,7 @@ convert, manipulate, filter and display a wide variety of image formats.")
 (define-public jasper
   (package
     (name "jasper")
-    (version "2.0.14")
+    (version "2.0.16")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1110,7 +1110,7 @@ convert, manipulate, filter and display a wide variety of image formats.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0aarg8nbik9wrm7fx0451sbm5ypfdfr6i169pxzi354mpdp8gg7f"))))
+                "05l75yd1zsxwv25ykwwwjs8961szv7iywf16nc6vc6qpby27ckv6"))))
     (build-system cmake-build-system)
     (inputs `(("libjpeg" ,libjpeg)))
     (synopsis "JPEG-2000 library")

gnu/packages/julia.scm

@@ -148,7 +148,7 @@
             (use-modules (ice-9 match))
             (substitute* "src/runtime_ccall.cpp"
               ;; Patch out invocations of '/sbin/ldconfig' to avoid getting
-              ;; error messages about missing '/sbin/ldconfig' on GuixSD.
+              ;; error messages about missing '/sbin/ldconfig' on Guix System.
               (("popen\\(.*ldconfig.*\\);")
                "NULL;\n")
 

gnu/packages/kde-frameworks.scm

@@ -3487,7 +3487,7 @@ workspace.")
        ("qtsvg" ,qtsvg)
        ("qttools" ,qttools)
        ("qtx11extras" ,qtx11extras)))
-    ;; FIXME: Use GuixSD ca-bundle.crt in etc/xdg/ksslcalist and
+    ;; FIXME: Use Guix ca-bundle.crt in etc/xdg/ksslcalist and
     ;; share/kf5/kssl/ca-bundle.crt
     ;; TODO: NixOS has nix-kde-include-dir.patch to change std-dir "include"
     ;; into "@dev@/include/". Think about whether this is needed for us, too.

gnu/packages/kodi.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 David Thompson <davet@gnu.org>
-;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2017, 2019 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
@@ -43,6 +43,7 @@
   #:use-module (gnu packages databases)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages fontutils)
+  #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages fribidi)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages ghostscript)
@@ -462,6 +463,23 @@ plug-in system.")
                    license:bsd-3                  ;misc, gtest
                    license:bsd-2))))              ;xbmc/freebsd
 
+(define-public kodi/wayland
+  (package/inherit kodi
+    (name "kodi-wayland")
+    (arguments
+     (substitute-keyword-arguments (package-arguments kodi)
+       ((#:configure-flags flags)
+        `(append '("-DCORE_PLATFORM_NAME=wayland"
+                   "-DWAYLAND_RENDER_SYSTEM=gl")
+                   ,flags))))
+    (inputs
+     `(("libinput" ,libinput)
+       ("libxkbcommon" ,libxkbcommon)
+       ("waylandpp" ,waylandpp)
+       ("waylandp-protocols" ,wayland-protocols)
+       ,@(package-inputs kodi)))
+    (synopsis "Kodi with Wayland rendering backend")))
+
 (define-public kodi-cli
   (let ((commit "104dc23b2a993c8e6db8c46f4f8bec24b146549b") ; Add support for
         (revision "1"))                                     ; `$HOME/.kodirc'.

gnu/packages/libevent.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2016 David Thompson <davet@gnu.org>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -170,14 +170,14 @@ resolution, asynchronous file system operations, and threading primitives.")
 (define-public perl-anyevent
   (package
     (name "perl-anyevent")
-    (version "7.14")
+    (version "7.15")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cpan/authors/id/M/ML/MLEHMANN/"
                                   "AnyEvent-" version ".tar.gz"))
               (sha256
                (base32
-                "0akxr9y0q9yjkl614x4clbiiayvh5a67y8gmci54plxs4p95i4sk"))))
+                "0m73r67ah9xmcwzxs50jxf8ncd8h71mi4wf2mvnqkxvibhrv478i"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-canary-stability" ,perl-canary-stability)))

gnu/packages/linux.scm

@@ -405,8 +405,8 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration."
 It has been modified to remove all non-free binary blobs.")
     (license license:gpl2)))
 
-(define %linux-libre-version "5.0")
+(define %linux-libre-version "5.0.1")
-(define %linux-libre-hash "18gs0kl5xvbmh725m7crg6iyqw3p8qq421aql7z0nlk035fh5xbx")
+(define %linux-libre-hash "0izbdpml170g5jg87ccnf2q1hc01gsyiy1gqxnqzzi3pri00dfyz")
 
 (define %linux-libre-5.0-patches
   (list %boot-logo-patch
@@ -419,8 +419,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:patches %linux-libre-5.0-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.19-version "4.19.27")
+(define %linux-libre-4.19-version "4.19.28")
-(define %linux-libre-4.19-hash "055n4s4yrkcrwkdsxbf1q1zyxmpabf7kba8d0phpfadian3wr4s0")
+(define %linux-libre-4.19-hash "0j65gp9z3qrygx67mkhm4ri3pj1pz0gdwcdlds2ypg53rh12jc0a")
 
 (define %linux-libre-4.19-patches
   (list %boot-logo-patch
@@ -1110,7 +1110,7 @@ MIDI functionality to the Linux-based operating system.")
     (outputs '("out" "pulseaudio" "jack"))
     (arguments
      `(#:configure-flags '(;; Do not install a "local" configuration targeted
-                           ;; for /etc/alsa.  On GuixSD plugins are loaded from
+                           ;; for /etc/alsa.  On Guix System plugins are loaded from
                            ;; the ALSA service, and other distributions likely
                            ;; won't use these files.
                            "--with-alsalconfdir=/tmp/noop")
@@ -1577,7 +1577,7 @@ devices.  It replaces @code{iwconfig}, which is deprecated.")
      '(#:phases
        (modify-phases %standard-phases
          ;; TODO: Patch some hardcoded "wlan0" in calibrate/calibrate.cpp to
-         ;; allow calibrating the network interface in GuixSD.
+         ;; allow calibrating the network interface in Guix System.
          (add-after 'unpack 'patch-absolute-file-names
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((kmod (assoc-ref inputs "kmod")))
@@ -2377,7 +2377,7 @@ compliance.")
        #:tests? #f                                ;no tests
        #:make-flags (let ((out (assoc-ref %outputs "out")))
                       (list (string-append "PREFIX=" out)
-                            (string-append "LSB_ID=GuixSD")
+                            (string-append "LSB_ID=Guix")
                             (string-append "DISTRO_PUBKEY=/dev/null")
                             (string-append "DISTRO_PRIVKEY=/dev/null")
                             (string-append "REGDB_PUBKEY=/dev/null")

gnu/packages/llvm.scm

@@ -451,14 +451,14 @@ use with Clang, targeting C++11, C++14 and above.")
 (define-public python-llvmlite
   (package
     (name "python-llvmlite")
-    (version "0.24.0")
+    (version "0.27.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "llvmlite" version))
        (sha256
         (base32
-         "01zwjlc3c5mhrwmv4b73zgbskwqps9ly0nrh54bbj1f1l72f839j"))))
+         "1aq003zbyjnz4q1118h6qx5lfimc8s5fvgskl75j12gxd6pc78a8"))))
     (build-system python-build-system)
     (inputs
      `(("llvm"
@@ -472,10 +472,10 @@ use with Clang, targeting C++11, C++14 and above.")
                          (method url-fetch)
                          (uri (string-append "https://raw.githubusercontent.com/numba/"
                                              "llvmlite/v" version "/conda-recipes/"
-                                             "D47188-svml.patch"))
+                                             "D47188-svml-VF.patch"))
                          (sha256
                           (base32
-                           "0mrj24jvkv3hjcmyg98zmvmyl1znlh2j63rdr69f6g7s96d2pfv1")))
+                           "0wxhgb61k17f0zg2m0726sf3hppm41f8jar2kkg2n8sl5cnjj9mr")))
                        (origin
                          (method url-fetch)
                          (uri (string-append "https://raw.githubusercontent.com/numba/"

gnu/packages/machine-learning.scm

@@ -40,14 +40,19 @@
   #:use-module (guix git-download)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
+  #:use-module (gnu packages audio)
   #:use-module (gnu packages autotools)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cran)
   #:use-module (gnu packages dejagnu)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages glib)
+  #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages linux)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages ocaml)
@@ -924,3 +929,101 @@ interactive learning.")
 Models, is a program for performing both single-SNP and SNP-set genome-wide
 association studies (GWAS) on extremely large data sets.")
     (license license:asl2.0)))
+
+;; There have been no proper releases yet.
+(define-public kaldi
+  (let ((commit "2f95609f0bb085bd3a1dc5eb0a39f3edea59e606")
+        (revision "1"))
+    (package
+      (name "kaldi")
+      (version (git-version "0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/kaldi-asr/kaldi.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "082qh3pfi7hvncylp4xsmkfahbd7gb0whdfa4rwrx7fxk9rdh3kz"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:test-target "test"
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'chdir
+             (lambda _ (chdir "src") #t))
+           (replace 'configure
+             (lambda* (#:key build system inputs outputs #:allow-other-keys)
+               (when (not (or (string-prefix? "x86_64" system)
+                              (string-prefix? "i686" system)))
+                 (substitute* "makefiles/linux_openblas.mk"
+                   (("-msse -msse2") "")))
+               (substitute* "makefiles/default_rules.mk"
+                 (("/bin/bash") (which "bash")))
+               (substitute* "Makefile"
+                 (("ext_depend: check_portaudio")
+                  "ext_depend:"))
+               (substitute* '("online/Makefile"
+                              "onlinebin/Makefile"
+                              "gst-plugin/Makefile")
+                 (("../../tools/portaudio/install")
+                  (assoc-ref inputs "portaudio")))
+
+               ;; This `configure' script doesn't support variables passed as
+               ;; arguments, nor does it support "prefix".
+               (let ((out (assoc-ref outputs "out"))
+                     (openblas (assoc-ref inputs "openblas"))
+                     (openfst (assoc-ref inputs "openfst")))
+                 (substitute* "configure"
+                   (("check_for_slow_expf;") "")
+                   ;; This affects the RPATH and also serves as the installation
+                   ;; directory.
+                   (("KALDILIBDIR=`pwd`/lib")
+                    (string-append "KALDILIBDIR=" out "/lib")))
+                 (mkdir-p out) ; must exist
+                 (setenv "CONFIG_SHELL" (which "bash"))
+                 (setenv "OPENFST_VER" ,(package-version openfst))
+                 (invoke "./configure"
+                         "--use-cuda=no"
+                         "--shared"
+                         (string-append "--openblas-root=" openblas)
+                         (string-append "--fst-root=" openfst)))))
+           (add-after 'build 'build-ext-and-gstreamer-plugin
+             (lambda _
+               (invoke "make" "-C" "online" "depend")
+               (invoke "make" "-C" "online")
+               (invoke "make" "-C" "onlinebin" "depend")
+               (invoke "make" "-C" "onlinebin")
+               (invoke "make" "-C" "gst-plugin" "depend")
+               (invoke "make" "-C" "gst-plugin")
+               #t))
+           ;; TODO: also install the executables.
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (lib (string-append out "/lib")))
+                 (mkdir-p lib)
+                 (install-file "gst-plugin/libgstonlinegmmdecodefaster.so" lib)
+                 #t))))))
+      (inputs
+       `(("alsa-lib" ,alsa-lib)
+         ("gfortran" ,gfortran "lib")
+         ("glib" ,glib)
+         ("gstreamer" ,gstreamer)
+         ("jack" ,jack-1)
+         ("openblas" ,openblas)
+         ("openfst" ,openfst)
+         ("portaudio" ,portaudio)
+         ("python" ,python)))
+      (native-inputs
+       `(("glib" ,glib "bin")             ; glib-genmarshal
+         ("grep" ,grep)
+         ("sed" ,sed)
+         ("pkg-config" ,pkg-config)
+         ("which" ,which)))
+      (home-page "https://kaldi-asr.org/")
+      (synopsis "Speech recognition toolkit")
+      (description "Kaldi is an extensible toolkit for speech recognition
+written in C++.")
+      (license license:asl2.0))))

gnu/packages/maths.scm

@@ -324,7 +324,7 @@ enough to be used effectively as a scientific calculator.")
 (define-public double-conversion
   (package
     (name "double-conversion")
-    (version "3.1.3")
+    (version "3.1.4")
     (home-page "https://github.com/google/double-conversion")
     (source (origin
               (method git-fetch)
@@ -333,7 +333,7 @@ enough to be used effectively as a scientific calculator.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "082w15xq8f4c422a71phvcahgc8vmqrig97av9g9628q5n2ybbgg"))))
+                "13xwcqk2c0q8c1siw566clxcpvp0xrxvb72mra42wa3nvq9wlsv6"))))
     (build-system cmake-build-system)
     (arguments
      '(#:test-target "test"

gnu/packages/music.scm

@@ -3667,7 +3667,7 @@ audio samples and various soft sythesizers.  It can receive input from a MIDI ke
 (define-public musescore
   (package
     (name "musescore")
-    (version "3.0.4")
+    (version "3.0.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -3676,7 +3676,7 @@ audio samples and various soft sythesizers.  It can receive input from a MIDI ke
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "05cn4j5f7xr438lgl0by3lrc7wckdgicdn4jrvxfqic8hv81sca7"))
+                "1inf6zdyh6yspjv1i7g6rw9wn90vki1s2qgilkp0j4aphayj4mic"))
               (modules '((guix build utils)))
               (snippet
                ;; Un-bundle OpenSSL and remove unused libraries.
@@ -3835,7 +3835,7 @@ specification and header.")
 (define-public rosegarden
   (package
     (name "rosegarden")
-    (version "18.06")
+    (version "18.12")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3843,10 +3843,10 @@ specification and header.")
                     version "/rosegarden-" version ".tar.bz2"))
               (sha256
                (base32
-                "04qc80sqb2ji42pq3mayhvqqn39hlxzymsywpbpzfpchr19chxx7"))))
+                "15i9fm0vkn3wsgahaxqi1j5zs0wc0j3wdwml0x49084gk2p328vb"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:configure-flags '("-DUSE_QT5=1") ; "-DCMAKE_BUILD_TYPE=Release"
+     `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release")
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-tests

gnu/packages/networking.scm

@@ -591,7 +591,7 @@ of the same name.")
 (define-public wireshark
   (package
     (name "wireshark")
-    (version "2.6.6")
+    (version "3.0.0")
     (source
      (origin
        (method url-fetch)
@@ -599,59 +599,58 @@ of the same name.")
                            version ".tar.xz"))
        (sha256
         (base32
-         "0qz8a1ays63712pq1v7nnw7c57zlqkcifq7himfv5nsv0zm36ya8"))))
+         "17h0ixq7yr6scscjkidaj3dh5x6dfd3f97ggdxlklkz9nbsk0kxw"))))
-    (build-system gnu-build-system)
+    (build-system cmake-build-system)
-    (inputs `(("c-ares" ,c-ares)
-              ("glib" ,glib)
-              ("gnutls" ,gnutls)
-              ("libcap" ,libcap)
-              ("libgcrypt" ,libgcrypt)
-              ("libnl" ,libnl)
-              ("libpcap" ,libpcap)
-              ("libssh" ,libssh)
-              ("libxml2" ,libxml2)
-              ("lz4" ,lz4)
-              ("lua" ,lua-5.2)          ;Lua 5.3 unsupported
-              ("krb5" ,mit-krb5)
-              ("portaudio" ,portaudio)
-              ("qtbase" ,qtbase)
-              ("qtmultimedia" ,qtmultimedia)
-              ("sbc" ,sbc)
-              ("snappy" ,snappy)
-              ("zlib" ,zlib)))
-    (native-inputs `(("perl" ,perl)
-                     ("pkg-config" ,pkg-config)
-                     ("python" ,python-wrapper)
-                     ("qttools" ,qttools)))
     (arguments
-     `(#:configure-flags
+     `(#:phases
-       (list (string-append "--with-c-ares=" (assoc-ref %build-inputs "c-ares"))
-             (string-append "--with-krb5=" (assoc-ref %build-inputs "krb5"))
-             (string-append "--with-libcap=" (assoc-ref %build-inputs "libcap"))
-             (string-append "--with-libssh=" (assoc-ref %build-inputs "libssh"))
-             (string-append "--with-lua=" (assoc-ref %build-inputs "lua"))
-             (string-append "--with-lz4=" (assoc-ref %build-inputs "lz4"))
-             (string-append "--with-pcap=" (assoc-ref %build-inputs "libpcap"))
-             (string-append "--with-portaudio="
-                            (assoc-ref %build-inputs "portaudio"))
-             (string-append "--with-sbc=" (assoc-ref %build-inputs "sbc"))
-             (string-append "--with-snappy=" (assoc-ref %build-inputs "snappy"))
-             (string-append "--with-zlib=" (assoc-ref %build-inputs "zlib")))
-       #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'patch-source
+         (add-after 'unpack 'remove-failing-test
+           ;; Test 31/32 fails with errors like "Program reassemble_test is
+           ;; not available".  Skipping it for now.
            (lambda _
-             ;; Fix build against Qt 5.11.
+             (substitute* "CMakeLists.txt"
-             (substitute* "ui/qt/packet_format_group_box.cpp"
+               (("suite_unittests" all) (string-append "# " all)))
-               (("#include <QStyle>") "#include <QStyle>
+             #t)))
-#include <QStyleOption>"))
+       ;; Build process chokes during `validate-runpath' phase.
-             (substitute* "ui/qt/time_shift_dialog.cpp"
+       ;;
-               (("#include <ui/time_shift.h>") "#include <ui/time_shift.h>
+       ;; Errors are like the following:
-#include <QStyleOption>"))
+       ;; "/gnu/store/...wireshark-3.0.0/lib/wireshark/plugins/3.0/epan/ethercat.so:
-             (substitute* "ui/qt/wireless_frame.cpp"
+       ;; error: depends on 'libwireshark.so.12', which cannot be found in
-               (("#include <QProcess>") "#include <QProcess>
+       ;; RUNPATH".  That is, "/gnu/store/...wireshark-3.0.0./lib" doesn't
-#include <QAbstractItemView>"))
+       ;; belong to RUNPATH.
-             #t)))))
+       ;;
+       ;; That’s not a problem in practice because "ethercat.so" is a plugin,
+       ;; so it’s dlopen’d by a process that already provides "libwireshark".
+       ;; For now, we disable this phase.
+       #:validate-runpath? #f))
+    (inputs
+     `(("c-ares" ,c-ares)
+       ("glib" ,glib)
+       ("gnutls" ,gnutls)
+       ("libcap" ,libcap)
+       ("libgcrypt" ,libgcrypt)
+       ("libnl" ,libnl)
+       ("libpcap" ,libpcap)
+       ("libssh" ,libssh)
+       ("libxml2" ,libxml2)
+       ("lz4" ,lz4)
+       ("lua" ,lua-5.2)                 ;Lua 5.3 unsupported
+       ("krb5" ,mit-krb5)
+       ("qtbase" ,qtbase)
+       ("qtmultimedia" ,qtmultimedia)
+       ("qtsvg" ,qtsvg)
+       ("sbc" ,sbc)
+       ("snappy" ,snappy)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("bison" ,bison)
+       ("doxygen" ,doxygen)
+       ("flex" ,flex)
+       ("gettext" ,gettext-minimal)
+       ("perl" ,perl)
+       ("pkg-config" ,pkg-config)
+       ("python" ,python-wrapper)
+       ("qttools" ,qttools)))
     (synopsis "Network traffic analyzer")
     (description "Wireshark is a network protocol analyzer, or @dfn{packet
 sniffer}, that lets you capture and interactively browse the contents of

gnu/packages/package-management.scm

@@ -142,8 +142,8 @@
 
                             ;; Set 'DOT_USER_PROGRAM' to the empty string so
                             ;; we don't keep a reference to Graphviz, whose
-                            ;; closure is pretty big (too big for the GuixSD
+                            ;; closure is pretty big (too big for the Guix
-                            ;; installation image.)
+                            ;; system installation image.)
                             "ac_cv_path_DOT_USER_PROGRAM=dot"
 
                             ;; To avoid problems with the length of shebangs,

gnu/packages/patches/pugixml-versioned-libdir.patch

@@ -0,0 +1,61 @@
+This patch makes pugixml install its headers to a standard location when
+built as a shared library.
+
+Taken from this upstream commit:
+https://github.com/zeux/pugixml/commit/daeb8013b20f9c47e85730faaa4131064a1f9c2e
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 90fa6793..d7bc1b20 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -4,7 +4,7 @@ project(pugixml)
+ 
+ option(BUILD_SHARED_LIBS "Build shared instead of static library" OFF)
+ option(BUILD_TESTS "Build tests" OFF)
+-option(BUILD_PKGCONFIG "Build in PKGCONFIG mode" OFF)
++option(USE_VERSIONED_LIBDIR "Use a private subdirectory to install the headers and libs" OFF)
+ 
+ set(BUILD_DEFINES "" CACHE STRING "Build defines")
+ 
+@@ -55,7 +55,7 @@ endif()
+ set_target_properties(pugixml PROPERTIES VERSION 1.9 SOVERSION 1)
+ get_target_property(PUGIXML_VERSION_STRING pugixml VERSION)
+ 
+-if(BUILD_PKGCONFIG)
++if(USE_VERSIONED_LIBDIR)
+ 	# Install library into its own directory under LIBDIR
+ 	set(INSTALL_SUFFIX /pugixml-${PUGIXML_VERSION_STRING})
+ endif()
+@@ -71,10 +71,8 @@ install(TARGETS pugixml EXPORT pugixml-config
+ install(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}${INSTALL_SUFFIX})
+ install(EXPORT pugixml-config DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/pugixml)
+ 
+-if(BUILD_PKGCONFIG)
+-	configure_file(scripts/pugixml.pc.in ${PROJECT_BINARY_DIR}/pugixml.pc @ONLY)
+-	install(FILES ${PROJECT_BINARY_DIR}/pugixml.pc DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/pkgconfig)
+-endif()
++configure_file(scripts/pugixml.pc.in ${PROJECT_BINARY_DIR}/pugixml.pc @ONLY)
++install(FILES ${PROJECT_BINARY_DIR}/pugixml.pc DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/pkgconfig)
+ 
+ if(BUILD_TESTS)
+ 	file(GLOB TEST_SOURCES tests/*.cpp)
+diff --git a/scripts/pugixml.pc.in b/scripts/pugixml.pc.in
+index 3c97c28d..804c4d38 100644
+--- a/scripts/pugixml.pc.in
++++ b/scripts/pugixml.pc.in
+@@ -1,11 +1,11 @@
+ prefix=@CMAKE_INSTALL_PREFIX@
+ exec_prefix=${prefix}
+-includedir=${prefix}/include/pugixml-@PUGIXML_VERSION_STRING@
+-libdir=${exec_prefix}/lib/pugixml-@PUGIXML_VERSION_STRING@
++includedir=${prefix}/include@INSTALL_SUFFIX@
++libdir=${exec_prefix}/lib@INSTALL_SUFFIX@
+ 
+ Name: pugixml
+ Description: Light-weight, simple and fast XML parser for C++ with XPath support.
+ URL: http://pugixml.org/
+ Version: @PUGIXML_VERSION_STRING@
+ Cflags: -I${includedir}
+-Libs: -L${libdir} -lpugixml
+\ No newline at end of file
++Libs: -L${libdir} -lpugixml

gnu/packages/photo.scm

@@ -207,15 +207,18 @@ MTP, and much more.")
 (define-public perl-image-exiftool
   (package
     (name "perl-image-exiftool")
-    (version "11.11")
+    (version "11.31")
-    (source (origin
+    (source
-              (method url-fetch)
+     (origin
-              (uri (string-append
+       (method url-fetch)
-                    "mirror://cpan/authors/id/E/EX/EXIFTOOL/Image-ExifTool-"
+       (uri (list
-                    version ".tar.gz"))
+             (string-append "mirror://cpan/authors/id/E/EX/EXIFTOOL/"
-              (sha256
+                            "Image-ExifTool-" version ".tar.gz")
-               (base32
+             ;; New releases may take a while to hit CPAN.
-                "1szg1k82nz88pp5n7lg71ja7q3hh5i5f9bcbb7m482dwrmsywkp6"))))
+             (string-append "https://www.sno.phy.queensu.ca/~phil/exiftool/"
+                            "Image-ExifTool-" version ".tar.gz")))
+       (sha256
+        (base32 "1kplb7hvhrhqxkr4ddc44q7a3fs0r8svv2jlh325nwkfi7aa5kz5"))))
     (build-system perl-build-system)
     (arguments
      '(#:phases

gnu/packages/polkit.scm

@@ -73,7 +73,7 @@
                  (substitute* "src/polkitbackend/polkitbackendjsauthority.cpp"
                    (("systemd") "elogind"))
 
-                 ;; GuixSD's polkit service stores actions under
+                 ;; Guix System's polkit service stores actions under
                  ;; /etc/polkit-1/actions.
                  (substitute* "src/polkitbackend/polkitbackendinteractiveauthority.c"
                    (("PACKAGE_DATA_DIR \"/polkit-1/actions\"")

gnu/packages/python-xyz.scm

@@ -3224,26 +3224,19 @@ color scales, and color space conversion easy.  It has support for:
 (define-public python-pygit2
   (package
     (name "python-pygit2")
-    (version "0.27.3")
+    (version "0.27.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pygit2" version))
        (sha256
         (base32
-         "046ahvsb7a20sgvscqfm3cb32sp3sii4gim9vz7zzrkf7yz16xlv"))))
+         "15c1mhwwjc7nr8hn5gm21hcfhw61jmwb0vngpjhlm3y5565wg2pz"))))
     (build-system python-build-system)
     (arguments
-     '(#:phases
+     '(#:tests? #f; tests don't run correctly in our environment
+       #:phases
        (modify-phases %standard-phases
-         ;; Remove after the next update. See:
-         ;; https://github.com/libgit2/pygit2/pull/851
-         (add-after 'unpack 'compile-with-cffi
-           (lambda _
-             (substitute* "setup.py"
-               (("install_requires")
-                "setup_requires=['cffi'],\n      install_requires"))
-             #t))
          (add-after 'unpack 'fix-dependency-versioning
            (lambda _
              (substitute* "setup.py"
@@ -8976,14 +8969,14 @@ to occurrences in strings and comments.")
 (define-public python-py3status
   (package
     (name "python-py3status")
-    (version "3.7")
+    (version "3.16")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "py3status" version))
        (sha256
         (base32
-         "0shxcfz4wcczj0mhwp4w0dvwd2fdd9bgprq8slim1519iiqzgwhq"))))
+         "1xrfph277bgjln3jbpzpgkhxad04fjvj7s3xfil42q1sxi4s3q3g"))))
     (build-system python-build-system)
     (inputs
      `(("file" ,file)))
@@ -11620,6 +11613,27 @@ applications in seconds while maintaining all the flexibility.")
 (define-public python2-mando
   (package-with-python2 python-mando))
 
+(define-public python2-argparse
+  (package
+    (name "python2-argparse")
+    (version "1.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "argparse" version))
+       (sha256
+        (base32
+         "1r6nznp64j68ih1k537wms7h57nvppq0szmwsaf99n71bfjqkc32"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2))
+    (home-page "https://github.com/ThomasWaldmann/argparse/")
+    (synopsis "Python command-line parsing library")
+    (description
+     "This package is mostly for people who want to have @code{argparse} on
+older Pythons because it was not part of the standard library back then.")
+    (license license:psfl)))
+
 (define-public python-fudge
   (package
     (name "python-fudge")
@@ -14331,14 +14345,14 @@ validation testing and application logic.")
 (define-public python-numba
   (package
     (name "python-numba")
-    (version "0.39.0")
+    (version "0.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "numba" version))
        (sha256
         (base32
-         "1bibvkwga1v8293i9ivl469d8bzgabn3vgr2ig7c1i68v8frsx07"))))
+         "03rqdfx0512lcri2bcpngx5k3jwfbqnanqj3n19c7d6h6hqxvq9x"))))
     (build-system python-build-system)
     (arguments
      `(#:modules ((guix build utils)

gnu/packages/samba.scm

@@ -151,14 +151,14 @@ anywhere.")
 (define-public samba
   (package
     (name "samba")
-    (version "4.9.4")
+    (version "4.9.5")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://download.samba.org/pub/samba/stable/"
                                  "samba-" version ".tar.gz"))
              (sha256
               (base32
-               "0kqbzywlnh1skg6g78qilyn12qv7wri66h5v9f77igncpkcai63d"))))
+               "001p896z609vb0qs196bgl362j7y3qibgm5gcl9028lfv795d287"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/shells.scm

@@ -91,7 +91,7 @@ direct descendant of NetBSD's Almquist Shell (@command{ash}).")
 (define-public fish
   (package
     (name "fish")
-    (version "3.0.0")
+    (version "3.0.2")
     (source
      (origin
        (method url-fetch)
@@ -99,7 +99,7 @@ direct descendant of NetBSD's Almquist Shell (@command{ash}).")
                            "releases/download/" version "/"
                            name "-" version ".tar.gz"))
        (sha256
-        (base32 "1kzjd0n0sfslkd36lzrvvvgy3qwkd9y466bkrqlnhd5h9dhx77ga"))))
+        (base32 "03j3jl9jzlnhq4p86zj8wqsh5sx45j1d1fvfa80ks1cfdg68qwhl"))))
     (build-system gnu-build-system)
     (inputs
      `(("fish-foreign-env" ,fish-foreign-env)

gnu/packages/skarnet.scm

@@ -29,15 +29,14 @@
 (define-public skalibs
   (package
     (name "skalibs")
-    (version "2.7.0.0")
+    (version "2.8.0.1")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "http://skarnet.org/software/skalibs/skalibs-"
                           version ".tar.gz"))
       (sha256
-       (base32
+       (base32 "00mh15jx3p4xzhkslxzpgi1c0xglywck1ik7ffi0hfwcq092wla7"))))
-        "0mnprdf4w4ami0db22rwd111m037cdmn2p8xa4i8cbwxcrv4sjcn"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f                      ; no tests exist
@@ -62,15 +61,14 @@ and file system operations.  It is used by all skarnet.org software.")
 (define-public execline
   (package
     (name "execline")
-    (version "2.5.0.1")
+    (version "2.5.1.0")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "http://skarnet.org/software/execline/execline-"
                           version ".tar.gz"))
       (sha256
-       (base32
+       (base32 "0xr6yb50wm6amj1wc7jmxyv7hvlx2ypbnww1vc288j275625d9xi"))))
-        "0j8hwdw8wn0rv8njdza8fbgmvyjg7hqp3qlbw00i7fwskr7d21wd"))))
     (build-system gnu-build-system)
     (inputs `(("skalibs" ,skalibs)))
     (arguments
@@ -105,15 +103,14 @@ complexity.")))
 (define-public s6
   (package
    (name "s6")
-   (version "2.7.2.2")
+   (version "2.8.0.0")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "http://skarnet.org/software/s6/s6-"
                          version ".tar.gz"))
      (sha256
-      (base32
+      (base32 "01milx5shixvniaxxmanfzz54vcymjfi86433w62rk5ypvc94ir8"))))
-       "0psjmfidjdciswakw9agzzniqfmhrr21765m0q77kwxg7iisgpsq"))))
    (build-system gnu-build-system)
    (inputs `(("skalibs" ,skalibs)
              ("execline" ,execline)))
@@ -144,15 +141,14 @@ functionality with a very small amount of code.")))
 (define-public s6-dns
   (package
    (name "s6-dns")
-   (version "2.3.0.1")
+   (version "2.3.0.2")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "http://skarnet.org/software/s6-dns/s6-dns-"
                          version ".tar.gz"))
      (sha256
-      (base32
+      (base32 "1y9bhvx8bqsb2xq5lmlfnc1hw2b3jyqg11i9r4lj0n6vvaqwh1j8"))))
-       "16ymalc4yxbwc0kapwmissxlw2bdk4sx3b33zp1gwx3n6hkcgh8c"))))
     (build-system gnu-build-system)
     (inputs `(("skalibs" ,skalibs)))
     (arguments
@@ -174,15 +170,14 @@ as an alternative to the BIND, djbdns or other DNS clients.")))
 (define-public s6-networking
   (package
    (name "s6-networking")
-   (version "2.3.0.3")
+   (version "2.3.0.4")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "http://skarnet.org/software/s6-networking/s6-networking-"
                          version ".tar.gz"))
      (sha256
-      (base32
+      (base32 "00kqp0mcp8c7f0z5s4399rd1haxasxkqgd6ds0j0607hvi56mqqa"))))
-       "1kfjl7da6wkmyq1mvq9irkbzk2wbi0axjfbcw5cym5y11mqswsjs"))))
     (build-system gnu-build-system)
     (inputs `(("skalibs" ,skalibs)
               ("execline" ,execline)
@@ -218,15 +213,14 @@ clock synchronization.")))
 (define-public s6-rc
   (package
    (name "s6-rc")
-   (version "0.4.1.0")
+   (version "0.5.0.0")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "http://skarnet.org/software/s6-rc/s6-rc-"
                          version ".tar.gz"))
      (sha256
-      (base32
+      (base32 "0p97p49i8m44lfiffycgn7xi08yzxkrs5dyb03svdhd6clwh6zyb"))))
-       "1xl37xi509pcm5chcvn8l7gb952sr5mkpxhpkbsxhsllj791bfa2"))))
     (build-system gnu-build-system)
     (inputs `(("skalibs" ,skalibs)
               ("execline" ,execline)
@@ -260,7 +254,7 @@ environment.")))
 (define-public s6-portable-utils
   (package
    (name "s6-portable-utils")
-   (version "2.2.1.2")
+   (version "2.2.1.3")
    (source
     (origin
      (method url-fetch)
@@ -268,8 +262,7 @@ environment.")))
            "http://skarnet.org/software/s6-portable-utils/s6-portable-utils-"
            version ".tar.gz"))
      (sha256
-      (base32
+      (base32 "1ibjns1slyg1p7jl9irzlrjz8b01f506iw87g3s7db5arhf17vv2"))))
-       "0if77z07rfygd1yk9d2abxkdbx3dg52vcjhb20isb8kvqxhkg8ih"))))
     (build-system gnu-build-system)
     (inputs `(("skalibs" ,skalibs)))
     (arguments
@@ -293,7 +286,7 @@ systems and other constrained environments, but they work everywhere.")))
 (define-public s6-linux-init
   (package
    (name "s6-linux-init")
-   (version "0.4.0.0")
+   (version "0.4.0.1")
    (source
     (origin
      (method url-fetch)
@@ -301,8 +294,7 @@ systems and other constrained environments, but they work everywhere.")))
            "http://skarnet.org/software/s6-linux-init/s6-linux-init-"
            version ".tar.gz"))
      (sha256
-      (base32
+      (base32 "0i79b0r3amhsf1xqr9k9v9bxmm4imlakfpsybviwhlj8dlawldxm"))))
-       "0zpd6n30cf8847240f658gw40sh64lm1mbaxr19q6rryvs5rpb6l"))))
     (build-system gnu-build-system)
     (inputs
      `(("skalibs" ,skalibs)))
@@ -331,7 +323,7 @@ all the details.")))
 (define-public s6-linux-utils
   (package
    (name "s6-linux-utils")
-   (version "2.5.0.0")
+   (version "2.5.0.1")
    (source
     (origin
      (method url-fetch)
@@ -339,8 +331,7 @@ all the details.")))
            "http://skarnet.org/software/s6-linux-utils/s6-linux-utils-"
            version ".tar.gz"))
      (sha256
-      (base32
+      (base32 "0bpcaah3rbz4i013bkarr7wxmfvisjyxg0z78xg5zfbgajpgjxx1"))))
-       "04q2z71dkzahd2ppga2zikclz2qk014c23gm7rigqxjc8rs1amvq"))))
     (build-system gnu-build-system)
     (inputs `(("skalibs" ,skalibs)))
     (arguments

gnu/packages/statistics.scm

@@ -177,7 +177,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
 (define r-with-tests
   (package
     (name "r-with-tests")
-    (version "3.5.1")
+    (version "3.5.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
@@ -185,7 +185,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1vap2k8kj5icy9naw61f9zyphf4rs0c9rxvil0zxkwx0xvsvyqq4"))))
+                "1337irx9y0r3jm1rcq1dcwnxsgfhnvgjs5wadcyh17vhpnvkgyib"))))
     (build-system gnu-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)

gnu/packages/terminals.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Mckinley Olsen <mck.olsen@gmail.com>
 ;;; Copyright © 2016, 2017 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
@@ -44,6 +44,7 @@
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages crypto)
   #:use-module (gnu packages docbook)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
@@ -60,6 +61,8 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages perl-check)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages popt)
+  #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
@@ -338,7 +341,7 @@ combining, and so on, with a simple interface.")
 (define-public picocom
   (package
     (name "picocom")
-    (version "2.2")
+    (version "3.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -347,15 +350,16 @@ combining, and so on, with a simple interface.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "06b2ic34dnxc73cprc5imi3iamlhsv623sbg9vj5h5rvs586dwjx"))))
+                "1vvjydqf0ax47nvdyyl67jafw5b3sfsav00xid6qpgia1gs2r72n"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags '("CC=gcc")
-       #:tests? #f ; No tests
+       #:tests? #f                      ; no tests
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure)
+         (delete 'configure)            ; no configure script
          (replace 'install
+           ;; The Makefile lacks an ‘install’ target.
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (bin (string-append out "/bin"))
@@ -363,11 +367,12 @@ combining, and so on, with a simple interface.")
                (install-file "picocom" bin)
                (install-file "picocom.1" man)))))))
     (home-page "https://github.com/npat-efault/picocom")
-    (synopsis "Minimal dumb-terminal emulation program")
+    (synopsis "Minimal dumb-terminal emulator")
-    (description "It was designed to serve as a simple, manual, modem
+    (description
-configuration, testing, and debugging tool.  It has also serves well
+     "Picocom is a minimal dumb-terminal emulation program.  It was designed to
-as a low-tech serial communications program to allow access to all
+serve as a simple and manual modem configuration, testing, and debugging tool.
-types of devices that provide serial consoles.")
+It also serves well as a low-tech serial communications program to allow access
+to all types of devices that provide serial consoles.")
     (license license:gpl2+)))
 
 (define-public beep
@@ -1015,3 +1020,50 @@ arbitrary programs of your choice.  This is useful for browsing the history
 comfortably in a pager or editor.
 @end itemize")
     (license license:gpl3+)))
+
+(define-public eternalterminal
+  (package
+    (name "eternalterminal")
+    (version "5.1.9")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/MisterTea/EternalTerminal.git")
+               (commit (string-append "et-v" version))))
+        (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "07ynkcnk3z6wafdlnzdxcd308cw1rzabxyq47ybj79lyji3wsgk7"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:configure-flags '("-DBUILD_TEST=ON")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'insert-googletests
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((tests (assoc-ref inputs "googletest")))
+               (invoke "tar" "xvf" tests "-C" "external/googletest"
+                       "--strip-components=1"))))
+         (add-after 'install 'dont-provide-gtest-libraries
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (delete-file-recursively (string-append out "/include"))
+               (delete-file-recursively (string-append out "/lib")))
+             #t)))))
+    (inputs
+     `(("gflags" ,gflags)
+       ("libsodium" ,libsodium)
+       ("protobuf" ,protobuf)))
+    (native-inputs
+     `(("googletest" ,(package-source googletest))))
+    (home-page "https://mistertea.github.io/EternalTerminal/")
+    (synopsis "Remote shell that reconnects without interrupting the session")
+    (description "@dfn{Eternal Terminal} (ET) is a remote shell that
+automatically reconnects without interrupting the session.  ET uses SSH to
+initialize a secure connection.  Unlike SSH sessions, which must be killed and
+reconnected after a network outage an ET session will survive network outages
+and IP roaming.  ET provides the same core functionality as @command{mosh},
+while also supporting native scrolling and @command{tmux} control mode
+(@code{tmux -CC}).")
+    (license license:asl2.0)))

gnu/packages/tex.scm

@@ -9,7 +9,7 @@
 ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Danny Milosavljevic <dannym+a@scratchpost.org>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;;
@@ -185,7 +185,7 @@
           ;; ps2eps.pl uses the "gswin32c" ghostscript executable on Windows,
           ;; and the "gs" ghostscript executable on Unix. It detects Unix by
           ;; checking for the existence of the /usr/bin directory. Since
-          ;; GuixSD does not have /usr/bin, it is also detected as Windows.
+          ;; Guix System does not have /usr/bin, it is also detected as Windows.
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "utils/ps2eps/ps2eps-src/bin/ps2eps.pl"
               (("gswin32c") "gs"))
@@ -5466,14 +5466,14 @@ PDF documents.")
 (define-public texmaker
   (package
     (name "texmaker")
-    (version "5.0.2")
+    (version "5.0.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://www.xm1math.net/texmaker/texmaker-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "0y81mjm89b99pr9svcwpaf4iz2q9pc9hjas5kiwd1pbgl5vqskm9"))))
+                "0vrj9w5lk3vf6138n5bz8phmy3xp5kv4dq1rgirghcf4hbxdyx30"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/tls.scm

@@ -497,13 +497,13 @@ netcat implementation that supports TLS.")
   (package
     (name "python-acme")
     ;; Remember to update the hash of certbot when updating python-acme.
-    (version "0.31.0")
+    (version "0.32.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "acme" version))
               (sha256
                (base32
-                "1gxjv09c695lj8swspa390nch117i60qkrgy135383vfk00jsp3y"))))
+                "1v0skyrjnbxq0lfmia5k6jy29iig4sxbi9j9q367xsw0g25wxvqf"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -554,7 +554,7 @@ netcat implementation that supports TLS.")
               (uri (pypi-uri name version))
               (sha256
                (base32
-                "0wq4jgyzli684h154w26xplp0fzyks2vlrnmhafhyb0h1bw9cc8c"))))
+                "1j63i0j019q0d3l5rx14fv4nxy01nplhk7q2k2fq10vxl0jlxff0"))))
     (build-system python-build-system)
     (arguments
      `(,@(substitute-keyword-arguments (package-arguments python-acme)
@@ -572,8 +572,8 @@ netcat implementation that supports TLS.")
                     #t))))))))
     ;; TODO: Add optional inputs for testing.
     (native-inputs
-     `(("python-nose" ,python-nose)
+     `(("python-mock" ,python-mock)
-       ("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)
        ;; For documentation
        ("python-sphinx" ,python-sphinx)
        ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme)
@@ -582,6 +582,7 @@ netcat implementation that supports TLS.")
        ("texinfo" ,texinfo)))
     (propagated-inputs
      `(("python-acme" ,python-acme)
+       ("python-cryptography" ,python-cryptography)
        ("python-zope-interface" ,python-zope-interface)
        ("python-pyrfc3339" ,python-pyrfc3339)
        ("python-pyopenssl" ,python-pyopenssl)

gnu/packages/tmux.scm

@@ -5,6 +5,7 @@
 ;;; Copyright © 2017 Vasile Dumitrascu <va511e@yahoo.com>
 ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019 Oleg Pykhalov <go.wigust@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,7 +28,9 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
+  #:use-module (gnu packages bash)
   #:use-module (gnu packages libevent)
   #:use-module (gnu packages ncurses))
 
@@ -134,3 +137,50 @@ continue running in the background, then later reattached.")
 command and helper commands provided by tmuxifier to manage Tmux sessions and
 windows.")
     (license expat)))
+
+(define-public tmux-xpanes
+  (package
+    (name "tmux-xpanes")
+    (version "4.0.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/greymd/tmux-xpanes.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0px164ikhnzfls6dld4xhiyd9j5jp2rbmwfg11b1pxzm9mp7qk6r"))))
+    (build-system trivial-build-system)
+    (inputs
+     `(("bash" ,bash)))
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (setenv "PATH" (string-append (assoc-ref %build-inputs "bash") "/bin"))
+         (copy-recursively (assoc-ref %build-inputs "source") ".")
+         (substitute* "bin/xpanes"
+           (("/bin/bash") (which "bash")))
+         (install-file "bin/xpanes" (string-append %output "/bin"))
+         (install-file "man/xpanes.1" (string-append %output "/man/man1"))
+         #t)))
+    (home-page "https://github.com/greymd/tmux-xpanes")
+    (synopsis "Tmux based terminal divider")
+    (description "This package provides tmux-based terminal divider.
+
+@code{xpanes} or @code{tmux-xpanes} (alias of @code{xpanes}) commands have
+following features:
+
+@itemize
+@item Split tmux window into multiple panes.
+@item Build command lines & execute them on the panes.
+@item Runnable from outside of tmux session.
+@item Runnable from inside of tmux session.
+@item Record operation log.
+@item Flexible layout arrangement for panes.
+@item Display pane title on each pane.
+@item Generate command lines from standard input (Pipe mode).
+@end itemize")
+    (license expat)))

gnu/packages/video.scm

@@ -1412,7 +1412,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2019.03.01")
+    (version "2019.03.09")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/rg3/youtube-dl/releases/"
@@ -1420,7 +1420,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0bxk6adyppdv50jnp5cika8wc6wfgd6d8zbg1njgmcs1pxskllmf"))))
+                "1g46mrmzr31b2r6x0g6wmg3j00qc8l6cbzmdik0l5vwjfcrdvghf"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion
@@ -1531,7 +1531,7 @@ other site that youtube-dl supports.")
 (define-public you-get
   (package
     (name "you-get")
-    (version "0.4.1256")
+    (version "0.4.1270")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1540,7 +1540,7 @@ other site that youtube-dl supports.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1hzr7ha1jvbc0v2bwl7s08ymwdmvb0f2jz4xp1fi6agq5y3ca1iv"))))
+                "123g6x8sh32v4yn4ss55lfw7j79hgl3l6aiwgrk4ndq7dzhnz46q"))))
     (build-system python-build-system)
     (inputs
      `(("ffmpeg" ,ffmpeg)))             ; for multi-part and >=1080p videos
@@ -1816,15 +1816,15 @@ for use with HTML5 video.")
 (define-public avidemux
   (package
     (name "avidemux")
-    (version "2.7.1")
+    (version "2.7.2")
     (source (origin
              (method url-fetch)
              (uri (string-append
-                   "mirror://sourceforge/" name "/" name "/" version "/"
+                   "mirror://sourceforge/avidemux/avidemux/" version "/"
-                   name "_" version ".tar.gz"))
+                   "avidemux_" version ".tar.gz"))
              (sha256
               (base32
-               "15g9h791qbnmycabbbl7s2b3n3xpvygm88qrfk35g2cw6957ik9w"))
+               "07fdz3y4iln7cizikdjj96dqvp2f8zzhs31ncxxwzdkngn5v8138"))
              (patches (search-patches "avidemux-install-to-lib.patch"))))
     (build-system cmake-build-system)
     (native-inputs
@@ -1857,73 +1857,74 @@ for use with HTML5 video.")
        #:phases
        ;; Make sure files inside the included ffmpeg tarball are
        ;; patch-shebanged.
-       (modify-phases %standard-phases
+       (let ((ffmpeg "ffmpeg-4.1.1"))
-       (add-before 'patch-source-shebangs 'unpack-ffmpeg
+         (modify-phases %standard-phases
-         (lambda _
+           (add-before 'patch-source-shebangs 'unpack-ffmpeg
-           (with-directory-excursion "avidemux_core/ffmpeg_package"
+             (lambda _
-             (invoke "tar" "xf" "ffmpeg-3.3.7.tar.bz2")
+               (with-directory-excursion "avidemux_core/ffmpeg_package"
-             (delete-file "ffmpeg-3.3.7.tar.bz2"))
+                 (invoke "tar" "xf" (string-append ffmpeg ".tar.bz2"))
-           #t))
+                 (delete-file (string-append ffmpeg ".tar.bz2")))
-       (add-after 'patch-source-shebangs 'repack-ffmpeg
+               #t))
-         (lambda _
+           (add-after 'patch-source-shebangs 'repack-ffmpeg
-           (with-directory-excursion "avidemux_core/ffmpeg_package"
+             (lambda _
-             (substitute* "ffmpeg-3.3.7/configure"
+               (with-directory-excursion "avidemux_core/ffmpeg_package"
-               (("#! /bin/sh") (string-append "#!" (which "sh"))))
+                 (substitute* (string-append ffmpeg "/configure")
-             (invoke "tar" "cjf" "ffmpeg-3.3.7.tar.bz2" "ffmpeg-3.3.7"
+                   (("#! /bin/sh") (string-append "#!" (which "sh"))))
-                     ;; avoid non-determinism in the archive
+                 (invoke "tar" "cjf" (string-append ffmpeg ".tar.bz2") ffmpeg
-                     "--sort=name" "--mtime=@0"
+                         ;; avoid non-determinism in the archive
-                     "--owner=root:0" "--group=root:0")
+                         "--sort=name" "--mtime=@0"
-             (delete-file-recursively "ffmpeg-3.3.7"))
+                         "--owner=root:0" "--group=root:0")
-           #t))
+                 (delete-file-recursively ffmpeg))
-       (replace 'configure
+               #t))
-         (lambda _
+           (replace 'configure
-           ;; Copy-paste settings from the cmake build system.
+             (lambda _
-           (setenv "CMAKE_LIBRARY_PATH" (getenv "LIBRARY_PATH"))
+               ;; Copy-paste settings from the cmake build system.
-           (setenv "CMAKE_INCLUDE_PATH" (getenv "C_INCLUDE_PATH"))
+               (setenv "CMAKE_LIBRARY_PATH" (getenv "LIBRARY_PATH"))
-           #t))
+               (setenv "CMAKE_INCLUDE_PATH" (getenv "C_INCLUDE_PATH"))
-       (replace 'build
+               #t))
-         (lambda* (#:key inputs outputs #:allow-other-keys)
+           (replace 'build
-           (let* ((out (assoc-ref outputs "out"))
+             (lambda* (#:key inputs outputs #:allow-other-keys)
-                  (lib (string-append out "/lib"))
+               (let* ((out (assoc-ref outputs "out"))
-                  (top (getcwd))
+                      (lib (string-append out "/lib"))
-                  (sdl (assoc-ref inputs "sdl"))
+                      (top (getcwd))
-                  (build_component
+                      (sdl (assoc-ref inputs "sdl"))
-                   (lambda* (component srcdir #:optional (args '()))
+                      (build_component
-                     (let ((builddir (string-append "build_" component)))
+                       (lambda* (component srcdir #:optional (args '()))
-                       (mkdir builddir)
+                         (let ((builddir (string-append "build_" component)))
-                       (with-directory-excursion builddir
+                           (mkdir builddir)
-                         (apply invoke "cmake"
+                           (with-directory-excursion builddir
-                                "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE"
+                             (apply invoke "cmake"
-                                (string-append "-DCMAKE_INSTALL_PREFIX=" out)
+                                    "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE"
-                                (string-append "-DCMAKE_INSTALL_RPATH=" lib)
+                                    (string-append "-DCMAKE_INSTALL_PREFIX=" out)
-                                (string-append "-DCMAKE_SHARED_LINKER_FLAGS="
+                                    (string-append "-DCMAKE_INSTALL_RPATH=" lib)
-                                               "\"-Wl,-rpath=" lib "\"")
+                                    (string-append "-DCMAKE_SHARED_LINKER_FLAGS="
-                                (string-append "-DAVIDEMUX_SOURCE_DIR=" top)
+                                                   "\"-Wl,-rpath=" lib "\"")
-                                (string-append "-DSDL_INCLUDE_DIR="
+                                    (string-append "-DAVIDEMUX_SOURCE_DIR=" top)
-                                               sdl "/include/SDL")
+                                    (string-append "-DSDL_INCLUDE_DIR="
-                                (string-append "../" srcdir)
+                                                   sdl "/include/SDL")
-                                "-DENABLE_QT5=True"
+                                    (string-append "../" srcdir)
-                                args)
+                                    "-DENABLE_QT5=True"
-                         (invoke "make" "-j"
+                                    args)
-                                 (number->string (parallel-job-count)))
+                             (invoke "make" "-j"
-                         (invoke "make" "install"))))))
+                                     (number->string (parallel-job-count)))
-             (mkdir out)
+                             (invoke "make" "install"))))))
-             (build_component "core" "avidemux_core")
+                 (mkdir out)
-             (build_component "cli" "avidemux/cli")
+                 (build_component "core" "avidemux_core")
-             (build_component "qt4" "avidemux/qt4")
+                 (build_component "cli" "avidemux/cli")
-             (build_component "plugins_common" "avidemux_plugins"
+                 (build_component "qt4" "avidemux/qt4")
-                              '("-DPLUGIN_UI=COMMON"))
+                 (build_component "plugins_common" "avidemux_plugins"
-             (build_component "plugins_cli" "avidemux_plugins"
+                                  '("-DPLUGIN_UI=COMMON"))
-                              '("-DPLUGIN_UI=CLI"))
+                 (build_component "plugins_cli" "avidemux_plugins"
-             (build_component "plugins_qt4" "avidemux_plugins"
+                                  '("-DPLUGIN_UI=CLI"))
-                              '("-DPLUGIN_UI=QT4"))
+                 (build_component "plugins_qt4" "avidemux_plugins"
-             (build_component "plugins_settings" "avidemux_plugins"
+                                  '("-DPLUGIN_UI=QT4"))
-                              '("-DPLUGIN_UI=SETTINGS"))
+                 (build_component "plugins_settings" "avidemux_plugins"
-             ;; Remove .exe and .dll file.
+                                  '("-DPLUGIN_UI=SETTINGS"))
-             (delete-file-recursively
+                 ;; Remove .exe and .dll file.
-              (string-append out "/share/ADM6_addons"))
+                 (delete-file-recursively
-             #t)))
+                  (string-append out "/share/ADM6_addons"))
-       (delete 'install))))
+                 #t)))
+           (delete 'install)))))
     (home-page "http://fixounet.free.fr/avidemux/")
     (synopsis "Video editor")
     (description "Avidemux is a video editor designed for simple cutting,
@@ -1983,7 +1984,7 @@ format changes.")
 (define-public xvid
   (package
     (name "xvid")
-    (version "1.3.4")
+    (version "1.3.5")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1991,7 +1992,7 @@ format changes.")
                     version ".tar.bz2"))
               (sha256
                (base32
-                "1xwbmp9wqshc0ckm970zdpi0yvgqxlqg0s8bkz98mnr8p2067bsz"))))
+                "1d0hy1w9sn6491a3vhyf3vmhq4xkn6yd4ralx1191s6qz5wz483w"))))
     (build-system gnu-build-system)
     (native-inputs `(("yasm" ,yasm)))
     (arguments

gnu/packages/vulkan.scm

@@ -163,7 +163,7 @@ interpretation of the specifications for these languages.")
 (define-public vulkan-headers
   (package
     (name "vulkan-headers")
-    (version "1.1.102")
+    (version "1.1.103")
     (source
      (origin
        (method git-fetch)
@@ -173,7 +173,7 @@ interpretation of the specifications for these languages.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1dkjg48l7dfpq16bq1w9c3y9dwpj2hhv7b3njvj52lpgpa14s0f9"))))
+         "1q3c79rf3mma0vqmwnxwps588pnyzap4nn49hk41m39k79vniaz8"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f))                    ; No tests.
@@ -187,7 +187,7 @@ interpretation of the specifications for these languages.")
 (define-public vulkan-loader
   (package
     (name "vulkan-loader")
-    (version (package-version vulkan-headers))
+    (version "1.1.102")
     (source
      (origin
        (method git-fetch)
@@ -244,7 +244,7 @@ and the ICD.")
 (define-public vulkan-tools
   (package
     (name "vulkan-tools")
-    (version (package-version vulkan-headers))
+    (version "1.1.102")
     (source
      (origin
        (method git-fetch)

gnu/packages/w3m.scm

@@ -39,7 +39,7 @@
 (define-public w3m
   (package
     (name "w3m")
-    (version "0.5.3+git20180125")
+    (version "0.5.3+git20190105")
     (source (origin
               (method git-fetch)
               ;; Debian's fork of w3m is the only one that is still maintained.
@@ -49,7 +49,7 @@
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0dafdfx1yhrvhbqzslkcapj09dvf64m2jadz3wl2icni0k4msq90"))))
+                "1fbg2p8qh2gvi3g4iz4q6vc0k70pf248r4yndi5lcn2m3mzvjx0i"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f  ; no check target

gnu/packages/web.scm

@@ -194,16 +194,18 @@ Interface} specification.")
 (define-public nginx
   (package
     (name "nginx")
-    ;; Consider updating the nginx-documentation package if the nginx package is
+    ;; Track the ‘mainline’ branch.  Upstream considers it more reliable than
-    ;; updated.
+    ;; ’stable’ and recommends that “in general you deploy the NGINX mainline
-    (version "1.14.2")
+    ;; 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 "1.15.9")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://nginx.org/download/nginx-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "15wppq12qmq8acjs35xfj61czhf9cdc0drnl5mm8hcg3aihryb80"))))
+                "0hxfsz1117r91b9fb5hjddyrf1czvb36lh1z7zalqqdskfcbmkz4"))))
     (build-system gnu-build-system)
     (inputs `(("openssl" ,openssl)
               ("pcre" ,pcre)
@@ -327,13 +329,13 @@ documentation.")
       (license l:bsd-2))))
 
 (define-public nginx-documentation
-  ;; This documentation should be relevant for nginx@1.13.11.
+  ;; This documentation should be relevant for nginx@1.15.9.
-  (let ((revision 2131)
+  (let ((revision 2345)
-        (changeset "dbaf3950f8e9"))
+        (changeset "7ef11708457e"))
     (package
       (name "nginx-documentation")
       (version
-       (simple-format #f "2018-04-04-~A-~A" revision changeset))
+       (simple-format #f "2019-03-01-~A-~A" revision changeset))
       (source
        (origin (method hg-fetch)
                (uri (hg-reference
@@ -342,7 +344,7 @@ documentation.")
                (file-name (string-append name "-" version))
                (sha256
                 (base32
-                 "0acdjsdaqixzh9g9s6db552v4pan4nqrllyqapay9ns9yzh1hrp7"))))
+                 "15975jvh53mnsgi4hhgrwdwy3by23v4kxnhy2vnkziq8v7wkmy4y"))))
       (build-system gnu-build-system)
       (arguments
        '(#:tests? #f                    ; no test suite
@@ -360,8 +362,7 @@ documentation.")
                  ;; banner.
                  (substitute* "xslt/style.xslt"
                    (("#banner           \\{ background:     black;")
-                    "#banner           { background:     black;
+                    "#banner           { display:        none;"))
-                            display:     none;"))
                  (invoke "make")
                  #t)))
            (replace 'install
@@ -750,7 +751,7 @@ current version of any major web browser.")
     (source (origin
              (method git-fetch)
              (uri (git-reference
-                   (url "https://github.com/miloyip/rapidjson.git")
+                   (url "https://github.com/Tencent/rapidjson.git")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
@@ -775,7 +776,7 @@ current version of any major web browser.")
                      (("native") "armv8-a"))
                    #t))))
            '())))
-    (home-page "https://github.com/miloyip/rapidjson")
+    (home-page "https://github.com/Tencent/rapidjson")
     (synopsis "JSON parser/generator for C++ with both SAX/DOM style API")
     (description
      "RapidJSON is a fast JSON parser/generator for C++ with both SAX/DOM
@@ -4763,15 +4764,14 @@ tools like SSH (Secure Shell) to reach the outside world.")
 (define-public stunnel
   (package
   (name "stunnel")
-  (version "5.48")
+  (version "5.50")
   (source
     (origin
       (method url-fetch)
       (uri (string-append "https://www.stunnel.org/downloads/stunnel-"
                           version ".tar.gz"))
       (sha256
-       (base32
+       (base32 "0j811iakljjxw39qchmqf235jdkwixb0i4xxjyi55f08558947cm"))))
-        "1pxqn9ixl80nrhfq12igyi874653jclji56hh9w24snf0aixa48h"))))
   (build-system gnu-build-system)
   (native-inputs
    ;; For tests.

gnu/packages/webkit.scm

@@ -59,14 +59,14 @@
 (define-public webkitgtk
   (package
     (name "webkitgtk")
-    (version "2.22.7")
+    (version "2.24.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.webkitgtk.org/releases/"
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1zrhmz90sn30zgyflj4i86fsscws10xsi2kfs87nj2nd0pbggrjb"))))
+                "01s446lmjk7y8il4snjm32vpxws2rp4hmxrwm2swx0p47x8d2jif"))))
     (build-system cmake-build-system)
     (outputs '("out" "doc"))
     (arguments
@@ -147,6 +147,7 @@
        ("libxslt" ,libxslt)
        ("libxt" ,libxt)
        ("mesa" ,mesa)
+       ("openjpeg" ,openjpeg)
        ("sqlite" ,sqlite)))
     (home-page "https://www.webkitgtk.org/")
     (synopsis "Web content engine for GTK+")

gnu/packages/wm.scm

@@ -18,6 +18,7 @@
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <contact@parouby.fr>
 ;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
+;;; Copyright © 2019 Rutger Helling <rhelling@mykolab.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -42,6 +43,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system haskell)
+  #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system python)
   #:use-module (gnu packages haskell)
@@ -77,6 +79,10 @@
   #:use-module (gnu packages linux)
   #:use-module (gnu packages suckless)
   #:use-module (gnu packages mpd)
+  #:use-module (gnu packages gl)
+  #:use-module (gnu packages video)
+  #:use-module (gnu packages version-control)
+  #:use-module (gnu packages man)
   #:use-module (guix download)
   #:use-module (guix git-download))
 
@@ -1102,3 +1108,145 @@ its size
 customizable status bars for their desktop environment.  It has built-in
 functionality to display information about the most commonly used services.")
     (license license:expat)))
+
+(define-public wlroots
+  (package
+    (name "wlroots")
+    (version "0.5.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/swaywm/wlroots.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1phiidyddzgaxy4gbqwmykxn0y8za6y5mp66l9dpd9i6fml153yq"))))
+    (build-system meson-build-system)
+    (arguments
+     `(#:configure-flags '("-Dlogind-provider=elogind")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'hardcode-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "xwayland/xwayland.c"
+               (("Xwayland") (string-append (assoc-ref inputs
+                                                       "xorg-server-xwayland")
+                                            "/bin/Xwayland")))
+             #t)))))
+    (inputs `(("elogind" ,elogind)
+              ("eudev" ,eudev)
+              ("libinput" ,libinput)
+              ("libxkbcommon" ,libxkbcommon)
+              ("mesa" ,mesa)
+              ("pixman" ,pixman)
+              ("wayland" ,wayland)
+              ("xorg-server-xwayland" ,xorg-server-xwayland)))
+    (native-inputs `(("ffmpeg" ,ffmpeg)
+                     ("libcap" ,libcap)
+                     ("libpng" ,libpng)
+                     ("pkg-config" ,pkg-config)
+                     ("wayland-protocols" ,wayland-protocols)))
+    (home-page "https://github.com/swaywm/wlroots")
+    (synopsis "Pluggable, composable, unopinionated modules for building a
+Wayland compositor")
+    (description "wlroots is a set of pluggable, composable, unopinionated
+modules for building a Wayland compositor.")
+    (license license:expat)))  ; MIT license
+
+(define-public sway
+  (package
+    (name "sway")
+    (version "1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/swaywm/sway.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "09cndc2nl39d3l7g5634xp0pxcz60pvc5277mfw89r22mh0j78rx"))))
+    (build-system meson-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'hardcode-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "meson.build"
+               (("scdoc.get_pkgconfig_variable..scdoc..")
+                (string-append "'" (assoc-ref inputs "scdoc")
+                               "/bin/scdoc'")))
+             #t)))))
+    (inputs `(("cairo" ,cairo)
+              ("elogind" ,elogind)
+              ("gdk-pixbuf" ,gdk-pixbuf)
+              ("json-c" ,json-c)
+              ("libinput" ,libinput)
+              ("libxkbcommon" ,libxkbcommon)
+              ("pango" ,pango)
+              ("wayland" ,wayland)
+              ("wlroots" ,wlroots)))
+    (native-inputs `(("git" ,git)
+                     ("libcap" ,libcap)
+                     ("linux-pam" ,linux-pam)
+                     ("mesa" ,mesa)
+                     ("pkg-config" ,pkg-config)
+                     ("scdoc" ,scdoc)
+                     ("wayland-protocols" ,wayland-protocols)))
+    (home-page "https://github.com/swaywm/sway")
+    (synopsis "Wayland compositor compatible with i3")
+    (description "Sway is a i3-compatible Wayland compositor.")
+    (license license:expat)))       ; MIT license
+
+(define-public swayidle
+  (package
+    (name "swayidle")
+    (version "1.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/swaywm/swayidle.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0b65flajwn2i6k2kdxxgw25w7ikzzmm595f4j5x1wac1rb0yah9w"))))
+    (build-system meson-build-system)
+    (inputs `(("wayland" ,wayland)))
+    (native-inputs `(("pkg-config" ,pkg-config)
+                     ("scdoc" ,scdoc)
+                     ("wayland-protocols" ,wayland-protocols)))
+    (home-page "https://github.com/swaywm/sway")
+    (synopsis "Idle management daemon for Wayland compositors")
+    (description "Swayidle is a idle management daemon for Wayland compositors.")
+    (license license:expat))) ; MIT license
+
+(define-public swaylock
+  (package
+    (name "swaylock")
+    (version "1.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/swaywm/swaylock.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "093nv1y9wyg48rfxhd36qdljjry57v1vkzrlc38mkf6zvsq8j7wb"))))
+    (build-system meson-build-system)
+    (inputs `(("cairo" ,cairo)
+              ("gdk-pixbuf" ,gdk-pixbuf)
+              ("libxkbcommon" ,libxkbcommon)
+              ;("linux-pam" ,linux-pam) ; FIXME: Doesn't work.
+              ("wayland" ,wayland)))
+    (native-inputs `(("git" ,git)
+                     ("pango" ,pango)
+                     ("pkg-config" ,pkg-config)
+                     ("scdoc" ,scdoc)
+                     ("wayland-protocols" ,wayland-protocols)))
+    (home-page "https://github.com/swaywm/sway")
+    (synopsis "Screen locking utility for Wayland compositors")
+    (description "Swaylock is a screen locking utility for Wayland compositors.")
+    (license license:expat))) ; MIT license

gnu/packages/xml.scm

@@ -867,14 +867,16 @@ the form of functions.")
       (method url-fetch)
       (uri (string-append "https://github.com/zeux/pugixml/releases/download/v"
                           version "/pugixml-" version ".tar.gz"))
+      (patches (search-patches "pugixml-versioned-libdir.patch"))
       (sha256
        (base32
         "19nv3zhik3djp4blc4vrjwrl8dfhzmal8b21sq7y907nhddx6mni"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:configure-flags '("-DCMAKE_CXX_FLAGS=-shared -fPIC"
+     `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")
-                           "-DCMAKE_C_FLAGS=-shared -fPIC")
+       #:tests? #f))                     ;no tests
-       #:tests? #f))                    ; no tests
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
     (home-page "https://pugixml.org")
     (synopsis "Light-weight, simple and fast XML parser for C++ with XPath support")
     (description

gnu/packages/xorg.scm

@@ -1271,7 +1271,7 @@ with the Cygwin XWin server when running X11 in a rootless mode.")
 (define-public libxcomposite
   (package
     (name "libxcomposite")
-    (version "0.4.4")
+    (version "0.4.5")
     (source
       (origin
         (method url-fetch)
@@ -1281,7 +1281,7 @@ with the Cygwin XWin server when running X11 in a rootless mode.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0y21nfpa5s8qmx0srdlilyndas3sgl0c6rc26d5fx2vx436m1qpd"))))
+            "13sfcglvz87vl58hd9rszwr73z0z4nwga3c12rfh7f5s2ln8l8dk"))))
     (build-system gnu-build-system)
     (propagated-inputs
      ;; xcomposite.pc refers to all these.
@@ -2636,17 +2636,14 @@ as USB mice.")
 (define-public xf86-video-amdgpu
   (package
     (name "xf86-video-amdgpu")
-    (version "18.1.0")
+    (version "19.0.0")
     (source
-      (origin
+     (origin
-        (method url-fetch)
+       (method url-fetch)
-        (uri (string-append
+       (uri (string-append "mirror://xorg/individual/driver/"
-               "mirror://xorg/individual/driver/xf86-video-amdgpu-"
+                           "xf86-video-amdgpu-" version ".tar.bz2"))
-               version
+       (sha256
-               ".tar.bz2"))
+        (base32 "0lag9jxd752ja7m7ngz3dmqffb5wbx4crdwjw74qx42m8xyi8dl8"))))
-        (sha256
-          (base32
-           "0wlnb929l3yqj4hdkzyxyhbaph13ac4villajgmbh66pa6xja7z1"))))
     (build-system gnu-build-system)
     (inputs `(("xorg-server" ,xorg-server)))
     (native-inputs `(("pkg-config" ,pkg-config)))
@@ -2706,17 +2703,14 @@ X server.")
 (define-public xf86-video-ati
   (package
     (name "xf86-video-ati")
-    (version "18.0.1")
+    (version "19.0.0")
     (source
-      (origin
+     (origin
-        (method url-fetch)
+       (method url-fetch)
-        (uri (string-append
+       (uri (string-append "mirror://xorg/individual/driver/"
-               "mirror://xorg/individual/driver/xf86-video-ati-"
+                           "xf86-video-ati-" version ".tar.bz2"))
-               version
+       (sha256
-               ".tar.bz2"))
+        (base32 "0mzl7yp3qkvankh22758sgpaw9mg6jxsfbg6wy0nxfw4i0qpv46x"))))
-        (sha256
-          (base32
-            "180l2yw8c63cbcs3zk729vx439aig1d7yicpyxj0nmfl4y0kpskj"))))
     (build-system gnu-build-system)
     (inputs `(("mesa" ,mesa)
               ("xorgproto" ,xorgproto)
@@ -5291,7 +5285,7 @@ draggable titlebars and borders.")
 (define-public libxcursor
   (package
     (name "libxcursor")
-    (version "1.1.15")
+    (version "1.2.0")
     (source
       (origin
         (method url-fetch)
@@ -5301,7 +5295,7 @@ draggable titlebars and borders.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0syzlfvh29037p0vnlc8f3jxz8nl55k65blswsakklkwsc6nfki9"))))
+            "10l7c9fm0jmpkm9ab9dz8r6m1pr87vvgqjnbx1psz50h4pwfklrs"))))
     (build-system gnu-build-system)
     (propagated-inputs
       `(("libx11" ,libx11)
@@ -6373,7 +6367,7 @@ output.")
 (define-public console-setup
   (package
     (name "console-setup")
-    (version "1.189")
+    (version "1.190")
     (source
      (origin
        (method git-fetch)
@@ -6381,7 +6375,7 @@ output.")
              (url "https://salsa.debian.org/installer-team/console-setup.git")
              (commit version)))
        (sha256
-        (base32 "09rfnnhwjm98im711v6jrgl49iy5n1b26x12zzk5rw6g1667mz86"))
+        (base32 "0qklm9ww1wap2bs7hp31xkfjyhdrirg2mk4hiv7h6fiqckzmdwvd"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments

gnu/services/base.scm

@@ -43,6 +43,7 @@
                 #:select (canonical-package glibc glibc-utf8-locales))
   #:use-module (gnu packages bash)
   #:use-module (gnu packages package-management)
+  #:use-module ((gnu packages gnupg) #:select (guile-gcrypt))
   #:use-module (gnu packages linux)
   #:use-module (gnu packages terminals)
   #:use-module ((gnu build file-systems)
@@ -50,6 +51,7 @@
   #:use-module (guix gexp)
   #:use-module (guix records)
   #:use-module (guix modules)
+  #:use-module ((guix self) #:select (make-config.scm))
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-26)
   #:use-module (ice-9 match)
@@ -329,7 +331,7 @@ seconds after @code{SIGTERM} has been sent are terminated with
   `(("fstab" ,(plain-file "fstab"
                           (string-append
                            "\
-# This file was generated from your GuixSD configuration.  Any changes
+# This file was generated from your Guix configuration.  Any changes
 # will be lost upon reboot or reconfiguration.\n\n"
                            (string-join (map file-system->fstab-entry
                                              file-systems)
@@ -1481,16 +1483,14 @@ pam-limits-entry specified in LIMITS via pam_limits.so."
 
 (define* (guix-build-accounts count #:key
                               (group "guixbuild")
-                              (first-uid 30001)
                               (shadow shadow))
-  "Return a list of COUNT user accounts for Guix build users, with UIDs
+  "Return a list of COUNT user accounts for Guix build users with the given
-starting at FIRST-UID, and under GID."
+GID."
   (unfold (cut > <> count)
           (lambda (n)
             (user-account
              (name (format #f "guixbuilder~2,'0d" n))
              (system? #t)
-             (uid (+ first-uid n -1))
              (group group)
 
              ;; guix-daemon expects GROUP to be listed as a
@@ -1504,27 +1504,58 @@ starting at FIRST-UID, and under GID."
           1+
           1))
 
+(define not-config?
+  ;; Select (guix …) and (gnu …) modules, except (guix config).
+  (match-lambda
+    (('guix 'config) #f)
+    (('guix rest ...) #t)
+    (('gnu rest ...) #t)
+    (rest #f)))
+
 (define (hydra-key-authorization keys guix)
   "Return a gexp with code to register KEYS, a list of files containing 'guix
 archive' public keys, with GUIX."
-  #~(unless (file-exists? "/etc/guix/acl")
+  (define aaa
-      (for-each (lambda (key)
+    ;; XXX: Terrible hack to work around <https://bugs.gnu.org/15602>: this
-                  (let ((pid (primitive-fork)))
+    ;; forces (guix config) and (guix utils) to be loaded upfront, so that
-                    (case pid
+    ;; their run-time symbols are defined.
-                      ((0)
+    (scheme-file "aaa.scm"
-                       (let* ((port (open-file key "r0b")))
+                 #~(define-module (guix aaa)
-                         (format #t "registering public key '~a'...~%" key)
+                     #:use-module (guix config)
-                         (close-port (current-input-port))
+                     #:use-module (guix memoization))))
-                         (dup port 0)
+
-                         (execl #$(file-append guix "/bin/guix")
+  (define default-acl
-                                "guix" "archive" "--authorize")
+    (with-extensions (list guile-gcrypt)
-                         (primitive-exit 1)))
+      (with-imported-modules `(((guix config) => ,(make-config.scm))
-                      (else
+                               ((guix aaa) => ,aaa)
-                       (let ((status (cdr (waitpid pid))))
+                               ,@(source-module-closure '((guix pki))
-                         (unless (zero? status)
+                                                        #:select? not-config?))
-                           (format (current-error-port) "warning: \
+        (computed-file "acl"
-failed to register public key '~a': ~a~%" key status)))))))
+                       #~(begin
-                '(#$@keys))))
+                           (use-modules (guix pki)
+                                        (gcrypt pk-crypto)
+                                        (ice-9 rdelim))
+
+                           (define keys
+                             (map (lambda (file)
+                                    (call-with-input-file file
+                                      (compose string->canonical-sexp
+                                               read-string)))
+                                  '(#$@keys)))
+
+                           (call-with-output-file #$output
+                             (lambda (port)
+                               (write-acl (public-keys->acl keys)
+                                          port))))))))
+
+  (with-imported-modules '((guix build utils))
+    #~(begin
+        (use-modules (guix build utils))
+
+        (unless (file-exists? "/etc/guix/acl")
+          (mkdir-p "/etc/guix")
+          (copy-file #+default-acl "/etc/guix/acl")
+          (chmod "/etc/guix/acl" #o600)))))
 
 (define %default-authorized-guix-keys
   ;; List of authorized substitute keys.

gnu/services/configuration.scm

@@ -22,6 +22,7 @@
   #:use-module (guix packages)
   #:use-module (guix records)
   #:use-module (guix gexp)
+  #:use-module ((guix utils) #:select (source-properties->location))
   #:autoload   (texinfo) (texi-fragment->stexi)
   #:autoload   (texinfo serialize) (stexi->texi)
   #:use-module (ice-9 match)
@@ -129,6 +130,10 @@
                  #,(id #'stem #'% #'stem)
                  #,(id #'stem #'make- #'stem)
                  #,(id #'stem #'stem #'?)
+                 (%location #,(id #'stem #'-location)
+                            (default (and=> (current-source-location)
+                                            source-properties->location))
+                            (innate))
                  (field field-getter (default def))
                  ...)
                (define #,(id #'stem #'stem #'-fields)

gnu/services/cups.scm

@@ -862,7 +862,7 @@ IPP specifications.")
         (define* (create-self-signed-certificate-if-absent
                   #:key private-key public-key (owner (getpwnam "root"))
                   (common-name (gethostname))
-                  (organization-name "GuixSD")
+                  (organization-name "Guix")
                   (organization-unit-name "Default Self-Signed Certificate")
                   (subject-parameters `(("CN" . ,common-name)
                                         ("O" . ,organization-name)

gnu/services/desktop.scm

@@ -906,9 +906,13 @@ and extends polkit with the actions from @code{gnome-settings-daemon}."
           (service-extension profile-service-type
                              (compose list
                                       mate-package))))
+   (default-value (mate-desktop-configuration))
    (description "Run the MATE desktop environment.")))
 
-(define* (mate-desktop-service #:key (config (mate-desktop-configuration)))
+(define-deprecated (mate-desktop-service #:key
+                                         (config
+                                          (mate-desktop-configuration)))
+  mate-desktop-service-type
   "Return a service that adds the @code{mate} package to the system profile,
 and extends polkit with the actions from @code{mate-settings-daemon}."
   (service mate-desktop-service-type config))

gnu/services/mail.scm

@@ -1485,7 +1485,7 @@ greyed out, instead of only later giving \"not selectable\" popup error.
         (define* (create-self-signed-certificate-if-absent
                   #:key private-key public-key (owner (getpwnam "root"))
                   (common-name (gethostname))
-                  (organization-name "GuixSD")
+                  (organization-name "Guix")
                   (organization-unit-name "Default Self-Signed Certificate")
                   (subject-parameters `(("CN" . ,common-name)
                                         ("O" . ,organization-name)

gnu/services/messaging.scm

@@ -461,7 +461,7 @@ about using the hashed backend.  See also
     (log
      (maybe-string "*syslog")
      "Set logging options.  Advanced logging configuration is not yet supported
-by the GuixSD Prosody Service.  See @url{https://prosody.im/doc/logging}."
+by the Prosody service.  See @url{https://prosody.im/doc/logging}."
      common)
 
     (pidfile

gnu/services/monitoring.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Sou Bunnbu <iyzsong@member.fsf.org>
 ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
-;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
+;;; Copyright © 2018, 2019 Oleg Pykhalov <go.wigust@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,7 +29,8 @@
   #:use-module (guix gexp)
   #:use-module (guix packages)
   #:use-module (guix records)
-  #:use-module ((guix ui) #:select (display-hint))
+  #:use-module (guix utils)
+  #:use-module ((guix ui) #:select (display-hint G_))
   #:use-module (ice-9 match)
   #:use-module (ice-9 rdelim)
   #:use-module (srfi srfi-26)
@@ -509,13 +510,12 @@ create it manually.")
    (number 10051)
    "Zabbix server port."))
 
-(define zabbix-front-end-config
+(define (zabbix-front-end-config config)
-  (match-lambda
+  (match-record config <zabbix-front-end-configuration>
-    (($ <zabbix-front-end-configuration>
+    (%location db-host db-port db-name db-user db-password db-secret-file
-        _ db-host db-port db-name db-user db-password db-secret-file
+               zabbix-host zabbix-port)
-        zabbix-host zabbix-port)
+    (mixed-text-file "zabbix.conf.php"
-     (mixed-text-file "zabbix.conf.php"
+                     "\
-                      "\
 <?php
 // Zabbix GUI configuration file.
 global $DB;
@@ -525,20 +525,29 @@ $DB['SERVER']   = '" db-host "';
 $DB['PORT']     = '" (number->string db-port) "';
 $DB['DATABASE'] = '" db-name "';
 $DB['USER']     = '" db-user "';
-$DB['PASSWORD'] = '" (if (string-null? db-password)
+$DB['PASSWORD'] = '" (let ((file (location-file %location))
-                         (if (string-null? db-secret-file)
+                           (line (location-line %location))
-                             (raise (condition
+                           (column (location-column %location)))
-                                     (&message
+                       (if (string-null? db-password)
-                                      (message "\
+                           (if (string-null? db-secret-file)
-you must provide either 'db-secret-file' or 'db-password'"))))
+                               (raise (make-compound-condition
-                             (string-trim-both
+                                       (condition
-                              (with-input-from-file db-secret-file
+                                        (&message
-                                read-string)))
+                                         (message
-                         (begin
+                                          (format #f "no '~A' or '~A' field in your '~A' record"
-                           (display-hint "\
+                                                  'db-secret-file 'db-password
-Consider using @code{db-secret-file} instead of @code{db-password} and unset
+                                                  'zabbix-front-end-configuration))))
-@code{db-password} for security in @code{zabbix-front-end-configuration}.")
+                                       (condition
-                           db-password)) "';
+                                        (&error-location
+                                         (location %location)))))
+                               (string-trim-both
+                                (with-input-from-file db-secret-file
+                                  read-string)))
+                           (begin
+                             (display-hint (format #f (G_ "~a:~a:~a: ~a:
+Consider using @code{db-secret-file} instead of @code{db-password} for better
+security.") file line column 'zabbix-front-end-configuration))
+                             db-password))) "';
 
 // Schema name. Used for IBM DB2 and PostgreSQL.
 $DB['SCHEMA'] = '';
@@ -548,7 +557,7 @@ $ZBX_SERVER_PORT = '" (number->string zabbix-port) "';
 $ZBX_SERVER_NAME = '';
 
 $IMAGE_FORMAT_DEFAULT = IMAGE_FORMAT_PNG;
-"))))
+")))
 
 (define %maintenance.inc.php
   ;; Empty php file to allow us move zabbix-frontend configs to ‘/etc/zabbix’

gnu/system/examples/vm-image.tmpl

@@ -8,7 +8,7 @@
 (define vm-image-motd (plain-file "motd" "
 This is the GNU system.  Welcome!
 
-This instance of GuixSD is a bare-bones template for virtualized environments.
+This instance of Guix System is a bare-bones template for virtualized environments.
 
 You will probably want to do these things first if you booted in a virtual
 private server (VPS):

gnu/system/install.scm

@@ -353,7 +353,7 @@ You have been warned.  Thanks for being so brave.\x1b[0m
      ;; the appropriate one.
      (cons* (file-system
               (mount-point "/")
-              (device (file-system-label "GuixSD_image"))
+              (device (file-system-label "Guix_image"))
               (type "ext4"))
 
             ;; Make /tmp a tmpfs instead of keeping the overlayfs.  This

gnu/system/linux-container.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 David Thompson <davet@gnu.org>
-;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,6 +28,7 @@
   #:use-module (guix modules)
   #:use-module (gnu build linux-container)
   #:use-module (gnu services)
+  #:use-module (gnu services base)
   #:use-module (gnu system)
   #:use-module (gnu system file-systems)
   #:export (system-container
@@ -54,8 +55,19 @@ containerized OS."
     (file-system (inherit (file-system-mapping->bind-mount fs))
       (needed-for-boot? #t)))
 
+  (define useless-services
+    ;; Services that make no sense in a container.  Those that attempt to
+    ;; access /dev/tty[0-9] in particular cannot work in a container.
+    (list console-font-service-type
+          mingetty-service-type
+          agetty-service-type))
+
   (operating-system (inherit os)
     (swap-devices '()) ; disable swap
+    (services (remove (lambda (service)
+                        (memq (service-kind service)
+                              useless-services))
+                      (operating-system-user-services os)))
     (file-systems (append (map mapping->fs (cons %store-mapping mappings))
                           %container-file-systems
                           user-file-systems))))

gnu/system/mapped-devices.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2017, 2018 Mark H Weaver <mhw@netris.org>
 ;;;
@@ -32,8 +32,7 @@
   #:use-module (gnu system uuid)
   #:autoload   (gnu build file-systems) (find-partition-by-luks-uuid)
   #:autoload   (gnu build linux-modules)
-                 (device-module-aliases matching-modules known-module-aliases
+                 (missing-modules)
-                  normalize-module-name file-name->module-name)
   #:autoload   (gnu packages cryptsetup) (cryptsetup-static)
   #:autoload   (gnu packages linux) (mdadm-static)
   #:use-module (srfi srfi-1)
@@ -118,37 +117,27 @@
 (define (check-device-initrd-modules device linux-modules location)
   "Raise an error if DEVICE needs modules beyond LINUX-MODULES to operate.
 DEVICE must be a \"/dev\" file name."
-  (define aliases
+  (define missing
-    ;; Attempt to load 'modules.alias' from the current kernel, assuming we're
+    ;; Attempt to determine missing modules.
-    ;; on GuixSD, and assuming that corresponds to the kernel we'll be
-    ;; installing.  Skip the whole thing if that file cannot be read.
     (catch 'system-error
       (lambda ()
-        (known-module-aliases))
+        (missing-modules device linux-modules))
-      (const #f)))
 
-  (when aliases
+      ;; If we can't do that (e.g., EPERM), skip the whole thing.
-    (let* ((modules  (delete-duplicates
+      (const '())))
-                      (append-map (cut matching-modules <> aliases)
-                                  (device-module-aliases device))))
 
-           ;; Module names (not file names) are supposed to use underscores
+  (unless (null? missing)
-           ;; instead of hyphens.  MODULES is a list of module names, whereas
+    ;; Note: What we suggest here is a list of module names (e.g.,
-           ;; LINUX-MODULES is file names without '.ko', so normalize them.
+    ;; "usb_storage"), not file names (e.g., "usb-storage.ko").  This is
-           (provided (map file-name->module-name linux-modules))
+    ;; OK because we have machinery that accepts both the hyphen and the
-           (missing  (remove (cut member <> provided) modules)))
+    ;; underscore version.
-      (unless (null? missing)
+    (raise (condition
-        ;; Note: What we suggest here is a list of module names (e.g.,
+            (&message
-        ;; "usb_storage"), not file names (e.g., "usb-storage.ko").  This is
+             (message (format #f (G_ "you may need these modules \
-        ;; OK because we have machinery that accepts both the hyphen and the
-        ;; underscore version.
-        (raise (condition
-                (&message
-                 (message (format #f (G_ "you may need these modules \
 in the initrd for ~a:~{ ~a~}")
-                                  device missing)))
+                              device missing)))
-                (&fix-hint
+            (&fix-hint
-                 (hint (format #f (G_ "Try adding them to the
+             (hint (format #f (G_ "Try adding them to the
 @code{initrd-modules} field of your @code{operating-system} declaration, along
 these lines:
 
@@ -161,9 +150,9 @@ these lines:
 
 If you think this diagnostic is inaccurate, use the @option{--skip-checks}
 option of @command{guix system}.\n")
-                               missing)))
+                           missing)))
-                (&error-location
+            (&error-location
-                 (location (source-properties->location location)))))))))
+             (location (source-properties->location location)))))))
 
 
 ;;;

gnu/system/vm.scm

@@ -463,8 +463,8 @@ the image."
   "Build a docker image.  OS is the desired <operating-system>.  NAME is the
 base name to use for the output file.  When REGISTER-CLOSURES? is not #f,
 register the closure of OS with Guix in the resulting Docker image.  This only
-makes sense when you want to build a GuixSD Docker image that has Guix
+makes sense when you want to build a Guix System Docker image that has Guix
-installed inside of it.  If you don't need Guix (e.g., your GuixSD Docker
+installed inside of it.  If you don't need Guix (e.g., your Docker
 image just contains a web server that is started by the Shepherd), then you
 should set REGISTER-CLOSURES? to #f."
   (define schema
@@ -610,7 +610,7 @@ to USB sticks meant to be read-only."
 
   (define root-label
     ;; Volume name of the root file system.
-    (normalize-label "GuixSD_image"))
+    (normalize-label "Guix_image"))
 
   (define root-uuid
     ;; UUID of the root file system, computed in a deterministic fashion.

gnu/tests/install.scm

@@ -47,7 +47,7 @@
 
 ;;; Commentary:
 ;;;
-;;; Test the installation of GuixSD using the documented approach at the
+;;; Test the installation of Guix using the documented approach at the
 ;;; command line.
 ;;;
 ;;; Code:
@@ -204,7 +204,7 @@ reboot\n")
                                                 (guix combinators))))
                       (installation-disk-image-file-system-type "ext4")
                       (target-size (* 2200 MiB)))
-  "Run SCRIPT (a shell script following the GuixSD installation procedure) in
+  "Run SCRIPT (a shell script following the system installation procedure) in
 OS to install TARGET-OS.  Return a VM image of TARGET-SIZE bytes containing
 the installed system.  The packages specified in PACKAGES will be appended to
 packages defined in installation-os."

guix/describe.scm

@@ -65,19 +65,28 @@ lives in, or #f if this is not applicable."
        (let ((manifest (profile-manifest profile)))
          (manifest-entries manifest))))))
 
-(define package-path-entries
+(define current-channel-entries
   (mlambda ()
-    "Return a list of package path entries to be added to the package search
+    "Return manifest entries corresponding to extra channels--i.e., not the
-path.  These entries are taken from the 'guix pull' profile the calling
+'guix' channel."
-process lives in, when applicable."
+    (remove (lambda (entry)
-    ;; Filter out Guix itself.
+              (string=? (manifest-entry-name entry) "guix"))
-    (filter-map (lambda (entry)
+            (current-profile-entries))))
-                  (and (not (string=? (manifest-entry-name entry)
+
-                                      "guix"))
+(define (package-path-entries)
-                       (string-append (manifest-entry-item entry)
+  "Return two values: the list of package path entries to be added to the
+package search path, and the list to be added to %LOAD-COMPILED-PATH.  These
+entries are taken from the 'guix pull' profile the calling process lives in,
+when applicable."
+  ;; Filter out Guix itself.
+  (unzip2 (map (lambda (entry)
+                 (list (string-append (manifest-entry-item entry)
                                       "/share/guile/site/"
-                                      (effective-version))))
+                                      (effective-version))
-                (current-profile-entries))))
+                       (string-append (manifest-entry-item entry)
+                                      "/lib/guile/" (effective-version)
+                                      "/site-ccache")))
+               (current-channel-entries))))
 
 (define (package-provenance package)
   "Return the provenance of PACKAGE as an sexp for use as the 'provenance'

guix/modules.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -112,7 +112,7 @@ depends on."
                  ".scm"))
 
 (define (guix-module-name? name)
-  "Return true if NAME (a list of symbols) denotes a Guix or GuixSD module."
+  "Return true if NAME (a list of symbols) denotes a Guix module."
   (match name
     (('guix _ ...) #t)
     (('gnu _ ...) #t)

guix/packages.scm

@@ -857,27 +857,19 @@ when CUT? returns true for a given package."
                                   #:optional (rewrite-name identity))
   "Return a procedure that, when passed a package, replaces its direct and
 indirect dependencies (but not its implicit inputs) according to REPLACEMENTS.
-REPLACEMENTS is a list of package pairs or a promise thereof; the first
+REPLACEMENTS is a list of package pairs; the first element of each pair is the
-element of each pair is the package to replace, and the second one is the
+package to replace, and the second one is the replacement.
-replacement.
 
 Optionally, REWRITE-NAME is a one-argument procedure that takes the name of a
 package and returns its new name after rewrite."
   (define (rewrite p)
-    (match (assq-ref (if (promise? replacements)
+    (match (assq-ref replacements p)
-                         (force replacements)
-                         replacements)
-                     p)
       (#f  (package
              (inherit p)
              (name (rewrite-name (package-name p)))))
       (new new)))
 
-  (package-mapping rewrite
+  (package-mapping rewrite (cut assq <> replacements)))
-                   (lambda (package)
-                     (assq package (if (promise? replacements)
-                                       (force replacements)
-                                       replacements)))))
 
 (define-syntax-rule (package/inherit p overrides ...)
   "Like (package (inherit P) OVERRIDES ...), except that the same

nix/libstore/optimise-store.cc

@@ -114,7 +114,7 @@ void LocalStore::optimisePath_(OptimiseStats & stats, const Path & path, InodeHa
 
     /* Sometimes SNAFUs can cause files in the store to be
        modified, in particular when running programs as root under
-       GuixSD (example: $fontconfig/var/cache being modified).  Skip
+       Guix System (example: $fontconfig/var/cache being modified).  Skip
        those files.  FIXME: check the modification time. */
     if (S_ISREG(st.st_mode) && (st.st_mode & S_IWUSR)) {
         printMsg(lvlError, format("skipping suspicious writable file `%1%'") % path);