Merge branch 'master' into core-updates

.dir-locals.el

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

Makefile.am

@@ -144,6 +144,7 @@ MODULES =					\
   guix/svn-download.scm				\
   guix/colors.scm				\
   guix/i18n.scm					\
+  guix/diagnostics.scm				\
   guix/ui.scm					\
   guix/status.scm				\
   guix/build/android-ndk-build-system.scm	\

doc/guix.texi

@@ -64,6 +64,7 @@ Copyright @copyright{} 2018 Laura Lazzati@*
 Copyright @copyright{} 2018 Alex Vong@*
 Copyright @copyright{} 2019 Josh Holland@*
 Copyright @copyright{} 2019 Diego Nicola Barbato@*
+Copyright @copyright{} 2019 Ivan Petkov@*
 
 Permission is granted to copy, distribute and/or modify this document
 under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -569,7 +570,7 @@ you may have to run @code{su -} or @code{sudo -i}.  As @code{root}, run:
 @example
 # cd /tmp
 # tar --warning=no-timestamp -xf \
-     guix-binary-@value{VERSION}.@var{system}.tar.xz
+     /path/to/guix-binary-@value{VERSION}.@var{system}.tar.xz
 # mv var/guix /var/ && mv gnu /
 @end example
 
@@ -757,6 +758,11 @@ Support for build offloading (@pxref{Daemon Offload Setup}) and
 @uref{https://github.com/artyom-poptsov/guile-ssh, Guile-SSH},
 version 0.10.2 or later.
 
+@item
+When @url{https://www.nongnu.org/lzip/lzlib.html, lzlib} is available, lzlib
+substitutes can be used and @command{guix publish} can compress substitutes
+with lzlib.
+
 @item
 When @url{http://www.bzip.org, libbz2} is available,
 @command{guix-daemon} can use it to compress build logs.
@@ -4214,7 +4220,7 @@ to another like this:
 
 @example
 guix archive --export -r $(readlink -f ~/.guix-profile) | \
-  ssh the-machine guix-archive --import
+  ssh the-machine guix archive --import
 @end example
 
 @noindent
@@ -4861,6 +4867,29 @@ advantage to work without requiring special kernel support, but it incurs
 run-time overhead every time a system call is made.
 @end quotation
 
+@cindex entry point, for Docker images
+@item --entry-point=@var{command}
+Use @var{command} as the @dfn{entry point} of the resulting pack, if the pack
+format supports it---currently @code{docker} and @code{squashfs} (Singularity)
+support it.  @var{command} must be relative to the profile contained in the
+pack.
+
+The entry point specifies the command that tools like @code{docker run} or
+@code{singularity run} automatically start by default.  For example, you can
+do:
+
+@example
+guix pack -f docker --entry-point=bin/guile guile
+@end example
+
+The resulting pack can easily be loaded and @code{docker run} with no extra
+arguments will spawn @code{bin/guile}:
+
+@example
+docker load -i pack.tar.gz
+docker run @var{image-id}
+@end example
+
 @item --expression=@var{expr}
 @itemx -e @var{expr}
 Consider the package @var{expr} evaluates to.
@@ -5786,10 +5815,21 @@ This variable is exported by @code{(guix build-system cargo)}.  It
 supports builds of packages using Cargo, the build tool of the
 @uref{https://www.rust-lang.org, Rust programming language}.
 
-In its @code{configure} phase, this build system replaces dependencies
+It adds @code{rustc} and @code{cargo} to the set of inputs.
-specified in the @file{Cargo.toml} file with inputs to the Guix package.
+A different Rust package can be specified with the @code{#:rust} parameter.
-The @code{install} phase installs the binaries, and it also installs the
+
-source code and @file{Cargo.toml} file.
+Regular cargo dependencies should be added to the package definition via the
+@code{#:cargo-inputs} parameter as a list of name and spec pairs, where the
+spec can be a package or a source definition.  Note that the spec must
+evaluate to a path to a gzipped tarball which includes a @code{Cargo.toml}
+file at its root, or it will be ignored.  Similarly, cargo dev-dependencies
+should be added to the package definition via the
+@code{#:cargo-development-inputs} parameter.
+
+In its @code{configure} phase, this build system will make any source inputs
+specified in the @code{#:cargo-inputs} and @code{#:cargo-development-inputs}
+parameters available to cargo.  The @code{install} phase installs any crate
+the binaries if they are defined by the crate.
 @end defvr
 
 @cindex Clojure (programming language)
@@ -6438,10 +6478,11 @@ path.  @var{references} is the list of store paths referred to by the
 resulting store path.
 @end deffn
 
-@deffn {Scheme Procedure} build-derivations @var{server} @var{derivations}
+@deffn {Scheme Procedure} build-derivations @var{store} @var{derivations} @
-Build @var{derivations} (a list of @code{<derivation>} objects or
+  [@var{mode}]
-derivation paths), and return when the worker is done building them.
+Build @var{derivations}, a list of @code{<derivation>} objects, @file{.drv}
-Return @code{#t} on success.
+file names, or derivation/output pairs, using the specified
+@var{mode}---@code{(build-mode normal)} by default.
 @end deffn
 
 Note that the @code{(guix monads)} module provides a monad as well as
@@ -9656,12 +9697,20 @@ accept connections from any interface.
 Change privileges to @var{user} as soon as possible---i.e., once the
 server socket is open and the signing key has been read.
 
-@item --compression[=@var{level}]
+@item --compression[=@var{method}[:@var{level}]]
-@itemx -C [@var{level}]
+@itemx -C [@var{method}[:@var{level}]]
-Compress data using the given @var{level}.  When @var{level} is zero,
+Compress data using the given @var{method} and @var{level}.  @var{method} is
-disable compression.  The range 1 to 9 corresponds to different gzip
+one of @code{lzip} and @code{gzip}; when @var{method} is omitted, @code{gzip}
-compression levels: 1 is the fastest, and 9 is the best (CPU-intensive).
+is used.
-The default is 3.
+
+When @var{level} is zero, disable compression.  The range 1 to 9 corresponds
+to different compression levels: 1 is the fastest, and 9 is the best
+(CPU-intensive).  The default is 3.
+
+Usually, @code{lzip} compresses noticeably better than @code{gzip} for a small
+increase in CPU usage; see
+@uref{https://nongnu.org/lzip/lzip_benchmark.html,benchmarks on the lzip Web
+page}.
 
 Unless @option{--cache} is used, compression occurs on the fly and
 the compressed streams are not
@@ -9672,6 +9721,11 @@ run @command{guix publish} behind a caching proxy, or to use
 allows @command{guix publish} to add @code{Content-Length} HTTP header
 to its responses.
 
+This option can be repeated, in which case every substitute gets compressed
+using all the selected methods, and all of them are advertised.  This is
+useful when users may not support all the compression methods: they can select
+the one they support.
+
 @item --cache=@var{directory}
 @itemx -c @var{directory}
 Cache archives and meta-data (@code{.narinfo} URLs) to @var{directory}
@@ -12214,10 +12268,19 @@ The TCP port to listen for connections.
 The host (and thus, network interface) to listen to.  Use
 @code{"0.0.0.0"} to listen on all the network interfaces.
 
-@item @code{compression-level} (default: @code{3})
+@item @code{compression} (default: @code{'(("gzip" 3))})
-The gzip compression level at which substitutes are compressed.  Use
+This is a list of compression method/level tuple used when compressing
-@code{0} to disable compression altogether, and @code{9} to get the best
+substitutes.  For example, to compress all substitutes with @emph{both} lzip
-compression ratio at the expense of increased CPU usage.
+at level 7 and gzip at level 9, write:
+
+@example
+'(("lzip" 7) ("gzip" 9))
+@end example
+
+Level 9 achieves the best compression ratio at the expense of increased CPU
+usage, whereas level 1 achieves fast compression.
+
+An empty list disables compression altogether.
 
 @item @code{nar-path} (default: @code{"nar"})
 The URL path at which ``nars'' can be fetched.  @xref{Invoking guix
@@ -13623,11 +13686,11 @@ Directory to look for faces.
 @item @code{default-path} (default "/run/current-system/profile/bin")
 Default PATH to use.
 
-@item @code{minimum-uid} (default 1000)
+@item @code{minimum-uid} (default: 1000)
-Minimum UID to display in SDDM.
+Minimum UID displayed in SDDM and allowed for log-in.
 
-@item @code{maximum-uid} (default 2000)
+@item @code{maximum-uid} (default: 2000)
-Maximum UID to display in SDDM
+Maximum UID to display in SDDM.
 
 @item @code{remember-last-user?} (default #t)
 Remember last user.
@@ -16703,6 +16766,297 @@ variables.
 @end table
 @end deftp
 
+@subsubheading Getmail service
+
+@cindex IMAP
+@cindex POP
+
+@deffn {Scheme Variable} getmail-service-type
+This is the type of the @uref{http://pyropus.ca/software/getmail/, Getmail}
+mail retriever, whose value should be an @code{getmail-configuration}.
+@end deffn
+
+Available @code{getmail-configuration} fields are:
+
+@deftypevr {@code{getmail-configuration} parameter} symbol name
+A symbol to identify the getmail service.
+
+Defaults to @samp{"unset"}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-configuration} parameter} package package
+The getmail package to use.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-configuration} parameter} string user
+The user to run getmail as.
+
+Defaults to @samp{"getmail"}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-configuration} parameter} string group
+The group to run getmail as.
+
+Defaults to @samp{"getmail"}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-configuration} parameter} string directory
+The getmail directory to use.
+
+Defaults to @samp{"/var/lib/getmail/default"}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-configuration} parameter} getmail-configuration-file rcfile
+The getmail configuration file to use.
+
+Available @code{getmail-configuration-file} fields are:
+
+@deftypevr {@code{getmail-configuration-file} parameter} getmail-retriever-configuration retriever
+What mail account to retrieve mail from, and how to access that account.
+
+Available @code{getmail-retriever-configuration} fields are:
+
+@deftypevr {@code{getmail-retriever-configuration} parameter} string type
+The type of mail retriever to use.  Valid values include @samp{passwd}
+and @samp{static}.
+
+Defaults to @samp{"SimpleIMAPSSLRetriever"}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-retriever-configuration} parameter} string server
+Space separated list of arguments to the userdb driver.
+
+Defaults to @samp{unset}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-retriever-configuration} parameter} string username
+Space separated list of arguments to the userdb driver.
+
+Defaults to @samp{unset}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-retriever-configuration} parameter} non-negative-integer port
+Space separated list of arguments to the userdb driver.
+
+Defaults to @samp{#f}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-retriever-configuration} parameter} string password
+Override fields from passwd.
+
+Defaults to @samp{""}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-retriever-configuration} parameter} list password-command
+Override fields from passwd.
+
+Defaults to @samp{()}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-retriever-configuration} parameter} string keyfile
+PEM-formatted key file to use for the TLS negotiation
+
+Defaults to @samp{""}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-retriever-configuration} parameter} string certfile
+PEM-formatted certificate file to use for the TLS negotiation
+
+Defaults to @samp{""}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-retriever-configuration} parameter} string ca-certs
+CA certificates to use
+
+Defaults to @samp{""}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-retriever-configuration} parameter} parameter-alist extra-parameters
+Extra retriever parameters
+
+Defaults to @samp{()}.
+
+@end deftypevr
+
+@end deftypevr
+
+@deftypevr {@code{getmail-configuration-file} parameter} getmail-destination-configuration destination
+What to do with retrieved messages.
+
+Available @code{getmail-destination-configuration} fields are:
+
+@deftypevr {@code{getmail-destination-configuration} parameter} string type
+The type of mail destination.  Valid values include @samp{Maildir},
+@samp{Mboxrd} and @samp{MDA_external}.
+
+Defaults to @samp{unset}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-destination-configuration} parameter} string-or-filelike path
+The path option for the mail destination.  The behaviour depends on the
+chosen type.
+
+Defaults to @samp{""}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-destination-configuration} parameter} parameter-alist extra-parameters
+Extra destination parameters
+
+Defaults to @samp{()}.
+
+@end deftypevr
+
+@end deftypevr
+
+@deftypevr {@code{getmail-configuration-file} parameter} getmail-options-configuration options
+Configure getmail.
+
+Available @code{getmail-options-configuration} fields are:
+
+@deftypevr {@code{getmail-options-configuration} parameter} non-negative-integer verbose
+If set to @samp{0}, getmail will only print warnings and errors.  A
+value of @samp{1} means that messages will be printed about retrieving
+and deleting messages.  If set to @samp{2}, getmail will print messages
+about each of it's actions.
+
+Defaults to @samp{1}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-options-configuration} parameter} boolean read-all
+If true, getmail will retrieve all available messages.  Otherwise it
+will only retrieve messages it hasn't seen previously.
+
+Defaults to @samp{#t}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-options-configuration} parameter} boolean delete
+If set to true, messages will be deleted from the server after
+retrieving and successfully delivering them.  Otherwise, messages will
+be left on the server.
+
+Defaults to @samp{#f}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-options-configuration} parameter} non-negative-integer delete-after
+Getmail will delete messages this number of days after seeing them, if
+they have not been delivered.  This means messages will be left on the
+server this number of days after delivering them.  A value of @samp{0}
+disabled this feature.
+
+Defaults to @samp{0}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-options-configuration} parameter} non-negative-integer delete-bigger-than
+Delete messages larger than this of bytes after retrieving them, even if
+the delete and delete-after options are disabled.  A value of @samp{0}
+disables this feature.
+
+Defaults to @samp{0}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-options-configuration} parameter} non-negative-integer max-bytes-per-session
+Retrieve messages totalling up to this number of bytes before closing
+the session with the server.  A value of @samp{0} disables this feature.
+
+Defaults to @samp{0}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-options-configuration} parameter} non-negative-integer max-message-size
+Don't retrieve messages larger than this number of bytes.  A value of
+@samp{0} disables this feature.
+
+Defaults to @samp{0}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-options-configuration} parameter} boolean delivered-to
+If true, getmail will add a Delivered-To header to messages.
+
+Defaults to @samp{#t}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-options-configuration} parameter} boolean received
+If set, getmail adds a Received header to the messages.
+
+Defaults to @samp{#t}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-options-configuration} parameter} string message-log
+Getmail will record a log of its actions to the named file.  A value of
+@samp{""} disables this feature.
+
+Defaults to @samp{""}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-options-configuration} parameter} boolean message-log-syslog
+If true, getmail will record a log of its actions using the system
+logger.
+
+Defaults to @samp{#t}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-options-configuration} parameter} boolean message-log-verbose
+If true, getmail will log information about messages not retrieved and
+the reason for not retrieving them, as well as starting and ending
+information lines.
+
+Defaults to @samp{#t}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-options-configuration} parameter} parameter-alist extra-parameters
+Extra options to include.
+
+Defaults to @samp{()}.
+
+@end deftypevr
+
+@end deftypevr
+
+@end deftypevr
+
+@deftypevr {@code{getmail-configuration} parameter} list idle
+A list of mailboxes that getmail should wait on the server for new mail
+notifications.  This depends on the server supporting the IDLE
+extension.
+
+Defaults to @samp{()}.
+
+@end deftypevr
+
+@deftypevr {@code{getmail-configuration} parameter} list environment-variables
+Environment variables to set for getmail.
+
+Defaults to @samp{()}.
+
+@end deftypevr
+
 @subsubheading Mail Aliases Service
 
 @cindex email aliases
@@ -19085,6 +19439,180 @@ Additional arguments to pass to the @command{varnishd} process.
 @end table
 @end deftp
 
+@subsubheading Patchwork
+@cindex Patchwork
+Patchwork is a patch tracking system.  It can collect patches sent to a
+mailing list, and display them in a web interface.
+
+@defvr {Scheme Variable} patchwork-service-type
+Service type for Patchwork.
+@end defvr
+
+The following example is an example of a minimal service for Patchwork, for
+the @code{patchwork.example.com} domain.
+
+@example
+(service patchwork-service-type
+         (patchwork-configuration
+          (domain "patchwork.example.com")
+          (settings-module
+           (patchwork-settings-module
+            (allowed-hosts (list domain))
+            (default-from-email "patchwork@@patchwork.example.com")))
+          (getmail-retriever-config
+           (getmail-retriever-configuration
+            (type "SimpleIMAPSSLRetriever")
+            (server "imap.example.com")
+            (port 993)
+            (username "patchwork")
+            (password-command
+             (list (file-append coreutils "/bin/cat")
+                   "/etc/getmail-patchwork-imap-password"))
+            (extra-parameters
+            '((mailboxes . ("Patches"))))))))
+
+@end example
+
+There are three records for configuring the Patchwork service.  The
+@code{<patchwork-configuration>} relates to the configuration for Patchwork
+within the HTTPD service.
+
+The @code{settings-module} field within the @code{<patchwork-configuration>}
+record can be populated with the @code{<patchwork-settings-module>} record,
+which describes a settings module that is generated within the Guix store.
+
+For the @code{database-configuration} field within the
+@code{<patchwork-settings-module>}, the
+@code{<patchwork-database-configuration>} must be used.
+
+@deftp {Data Type} patchwork-configuration
+Data type representing the Patchwork service configuration.  This type has the
+following parameters:
+
+@table @asis
+@item @code{patchwork} (default: @code{patchwork})
+The Patchwork package to use.
+
+@item @code{domain}
+The domain to use for Patchwork, this is used in the HTTPD service virtual
+host.
+
+@item @code{settings-module}
+The settings module to use for Patchwork. As a Django application, Patchwork
+is configured with a Python module containing the settings. This can either be
+an instance of the @code{<patchwork-settings-module>} record, any other record
+that represents the settings in the store, or a directory outside of the
+store.
+
+@item @code{static-path}  (default: @code{"/static/"})
+The path under which the HTTPD service should serve the static files.
+
+@item @code{getmail-retriever-config}
+The getmail-retriever-configuration record value to use with
+Patchwork. Getmail will be configured with this value, the messages will be
+delivered to Patchwork.
+
+@end table
+@end deftp
+
+@deftp {Data Type} patchwork-settings-module
+Data type representing a settings module for Patchwork.  Some of these
+settings relate directly to Patchwork, but others relate to Django, the web
+framework used by Patchwork, or the Django Rest Framework library.  This type
+has the following parameters:
+
+@table @asis
+@item @code{database-configuration} (default: @code{(patchwork-database-configuration)})
+The database connection settings used for Patchwork.  See the
+@code{<patchwork-database-configuration>} record type for more information.
+
+@item @code{secret-key-file} (default: @code{"/etc/patchwork/django-secret-key"})
+Patchwork, as a Django web application uses a secret key for cryptographically
+signing values.  This file should contain a unique unpredictable value.
+
+If this file does not exist, it will be created and populated with a random
+value by the patchwork-setup shepherd service.
+
+This setting relates to Django.
+
+@item @code{allowed-hosts}
+A list of valid hosts for this Patchwork service. This should at least include
+the domain specified in the @code{<patchwork-configuration>} record.
+
+This is a Django setting.
+
+@item @code{default-from-email}
+The email address from which Patchwork should send email by default.
+
+This is a Patchwork setting.
+
+@item @code{static-url} (default: @code{#f})
+The URL to use when serving static assets. It can be part of a URL, or a full
+URL, but must end in a @code{/}.
+
+If the default value is used, the @code{static-path} value from the
+@code{<patchwork-configuration>} record will be used.
+
+This is a Django setting.
+
+@item @code{admins} (default: @code{'()})
+Email addresses to send the details of errors that occur.  Each value should
+be a list containing two elements, the name and then the email address.
+
+This is a Django setting.
+
+@item @code{debug?} (default: @code{#f})
+Whether to run Patchwork in debug mode.  If set to @code{#t}, detailed error
+messages will be shown.
+
+This is a Django setting.
+
+@item @code{enable-rest-api?} (default: @code{#t})
+Whether to enable the Patchwork REST API.
+
+This is a Patchwork setting.
+
+@item @code{enable-xmlrpc?} (default: @code{#t})
+Whether to enable the XML RPC API.
+
+This is a Patchwork setting.
+
+@item @code{force-https-links?} (default: @code{#t})
+Whether to use HTTPS links on Patchwork pages.
+
+This is a Patchwork setting.
+
+@item @code{extra-settings} (default: @code{""})
+Extra code to place at the end of the Patchwork settings module.
+
+@end table
+@end deftp
+
+@deftp {Data Type} patchwork-database-configuration
+Data type representing the database configuration for Patchwork.
+
+@table @asis
+@item @code{engine} (default: @code{"django.db.backends.postgresql_psycopg2"})
+The database engine to use.
+
+@item @code{name} (default: @code{"patchwork"})
+The name of the database to use.
+
+@item @code{user} (default: @code{"httpd"})
+The user to connect to the database as.
+
+@item @code{password} (default: @code{""})
+The password to use when connecting to the database.
+
+@item @code{host} (default: @code{""})
+The host to make the database connection to.
+
+@item @code{port} (default: @code{""})
+The port on which to connect to the database.
+
+@end table
+@end deftp
+
 @subsubheading FastCGI
 @cindex fastcgi
 @cindex fcgiwrap
@@ -22208,10 +22736,10 @@ Extra options will be passed to @code{git daemon}, please run
 @end deftp
 
 The @code{git://} protocol lacks authentication.  When you pull from a
-repository fetched via @code{git://}, you don't know that the data you
+repository fetched via @code{git://}, you don't know whether the data you
-receive was modified is really coming from the specified host, and you
+receive was modified or is even coming from the specified host, and your
-have your connection is subject to eavesdropping.  It's better to use an
+connection is subject to eavesdropping.  It's better to use an authenticated
-authenticated and encrypted transport, such as @code{https}.  Although Git allows you
+and encrypted transport, such as @code{https}.  Although Git allows you
 to serve repositories using unsophisticated file-based web servers,
 there is a faster protocol implemented by the @code{git-http-backend}
 program.  This program is the back-end of a proper Git web service.  It
@@ -23598,7 +24126,7 @@ The following is an example @code{dicod-service} configuration.
 @cindex Docker
 @subsubheading Docker Service
 
-The @code{(gnu services docker)} module provides the following service.
+The @code{(gnu services docker)} module provides the following services.
 
 @defvr {Scheme Variable} docker-service-type
 
@@ -23622,6 +24150,107 @@ The Containerd package to use.
 @end table
 @end deftp
 
+@cindex Audit
+@subsubheading Auditd Service
+
+The @code{(gnu services auditd)} module provides the following service.
+
+@defvr {Scheme Variable} auditd-service-type
+
+This is the type of the service that runs
+@url{https://people.redhat.com/sgrubb/audit/,auditd},
+a daemon that tracks security-relevant information on your system.
+
+Examples of things that can be tracked:
+
+@enumerate
+@item
+File accesses
+@item
+System calls
+@item
+Invoked commands
+@item
+Failed login attempts
+@item
+Firewall filtering
+@item
+Network access
+@end enumerate
+
+@command{auditctl} from the @code{audit} package can be used in order
+to add or remove events to be tracked (until the next reboot).
+In order to permanently track events, put the command line arguments
+of auditctl into @file{/etc/audit/audit.rules}.
+@command{aureport} from the @code{audit} package can be used in order
+to view a report of all recorded events.
+The audit daemon usually logs into the directory @file{/var/log/audit}.
+
+@end defvr
+
+@deftp {Data Type} auditd-configuration
+This is the data type representing the configuration of auditd.
+
+@table @asis
+
+@item @code{audit} (default: @code{audit})
+The audit package to use.
+
+@end table
+@end deftp
+
+@defvr {Scheme Variable} singularity-service-type
+This is the type of the service that allows you to run
+@url{https://www.sylabs.io/singularity/, Singularity}, a Docker-style tool to
+create and run application bundles (aka. ``containers'').  The value for this
+service is the Singularity package to use.
+
+The service does not install a daemon; instead, it installs helper programs as
+setuid-root (@pxref{Setuid Programs}) such that unprivileged users can invoke
+@command{singularity run} and similar commands.
+@end defvr
+
+@cindex Nix
+@subsubheading Nix service
+
+The @code{(gnu services nix)} module provides the following service.
+
+@defvr {Scheme Variable} nix-service-type
+
+This is the type of the service that runs build daemon of the
+@url{https://nixos.org/nix/, Nix} package manager.  Here is an example showing
+how to use it:
+
+@example
+(use-modules (gnu))
+(use-service-modules nix)
+(use-package-modules package-management)
+
+(operating-system
+  ;; @dots{}
+  (packages (append (list nix)
+                    %base-packages))
+
+  (services (append (list (service nix-service-type))
+                    %base-services)))
+@end example
+
+After @command{guix system reconfigure} configure Nix for your user:
+
+@itemize
+@item Add a Nix channel and update it.  See
+@url{https://nixos.org/nix/manual/, Nix Package Manager Guide}.
+
+@item Create a symlink to your profile and activate Nix profile:
+@end itemize
+
+@example
+$ ln -s "/nix/var/nix/profiles/per-user/$USER/profile" ~/.nix-profile
+$ source /run/current-system/profile/etc/profile.d/nix.sh
+@end example
+
+@end defvr
+
 @node Setuid Programs
 @section Setuid Programs
 
@@ -24132,7 +24761,7 @@ The bootloader theme object describing the theme to use.  If no theme
 is provided, some bootloaders might use a default theme, that's true
 for GRUB.
 
-@item @code{terminal-outputs} (default: @code{'gfxterm})
+@item @code{terminal-outputs} (default: @code{'(gfxterm)})
 The output terminals used for the bootloader boot menu, as a list of
 symbols.  GRUB accepts the values: @code{console}, @code{serial},
 @code{serial_@{0-3@}}, @code{gfxterm}, @code{vga_text},

etc/guix-daemon.service.in

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

etc/guix-publish.service.in

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

gnu/artwork.scm

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

gnu/build/accounts.scm

@@ -19,6 +19,7 @@
 (define-module (gnu build accounts)
   #:use-module (guix records)
   #:use-module (guix combinators)
+  #:use-module ((guix build syscalls) #:select (fdatasync))
   #:use-module (gnu system accounts)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-11)
@@ -51,6 +52,7 @@
             group-entry-gid
             group-entry-members
 
+            %password-lock-file
             write-group
             write-passwd
             write-shadow
@@ -224,6 +226,19 @@ each field."
                    (serialization list->comma-separated comma-separated->list)
                    (default '())))
 
+(define %password-lock-file
+  ;; The password database lock file used by libc's 'lckpwdf'.  Users should
+  ;; grab this lock with 'with-file-lock' when they access the databases.
+  "/etc/.pwd.lock")
+
+(define-syntax-rule (catch-ENOSYS exp)
+  (catch 'system-error
+    (lambda () exp)
+    (lambda args
+      (if (= ENOSYS (system-error-errno args))
+          #f
+          (apply throw args)))))
+
 (define (database-writer file mode entry->string)
   (lambda* (entries #:optional (file-or-port file))
     "Write ENTRIES to FILE-OR-PORT.  When FILE-OR-PORT is a file name, write
@@ -243,9 +258,16 @@ to it atomically and set the appropriate permissions."
             (lambda ()
               (chmod port mode)
               (write-entries port)
+
+              ;; XXX: When booting with the statically-linked Guile,
+              ;; 'fdatasync' is unavailable.
+              (catch-ENOSYS (fdatasync port))
+
+              (close-port port)
               (rename-file template file-or-port))
             (lambda ()
-              (close-port port)
+              (unless (port-closed? port)
+                (close-port port))
               (when (file-exists? template)
                 (delete-file template))))))))
 

gnu/build/activation.scm

@@ -22,6 +22,7 @@
   #:use-module (gnu build accounts)
   #:use-module (gnu build linux-boot)
   #:use-module (guix build utils)
+  #:use-module ((guix build syscalls) #:select (with-file-lock))
   #:use-module (ice-9 ftw)
   #:use-module (ice-9 match)
   #:use-module (ice-9 vlist)
@@ -129,11 +130,15 @@ group records) are all available."
   ;; Allow home directories to be created under /var/lib.
   (mkdir-p "/var/lib")
 
+  ;; Take same lock as libc's 'lckpwdf' (but without a timeout) while we read
+  ;; and write the databases.  This ensures there's no race condition with
+  ;; other tools that might be accessing it at the same time.
+  (with-file-lock %password-lock-file
     (let-values (((groups passwd shadow)
                   (user+group-databases users groups)))
       (write-group groups)
       (write-passwd passwd)
-    (write-shadow shadow)
+      (write-shadow shadow)))
 
   ;; Home directories of non-system accounts are created by
   ;; 'activate-user-home'.
@@ -144,7 +149,7 @@ group records) are all available."
   (for-each (lambda (directory)
               (chown directory 0 0)
               (chmod directory #o555))
-              (duplicates (map user-account-home-directory system-accounts)))))
+            (duplicates (map user-account-home-directory system-accounts))))
 
 (define (activate-user-home users)
   "Create and populate the home directory of USERS, a list of tuples, unless

gnu/build/linux-boot.scm

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

gnu/build/locale.scm

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

gnu/installer/connman.scm

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

gnu/installer/locale.scm

@@ -19,6 +19,7 @@
 
 (define-module (gnu installer locale)
   #:use-module (gnu installer utils)
+  #:use-module ((gnu build locale) #:select (normalize-codeset))
   #:use-module (guix records)
   #:use-module (json)
   #:use-module (srfi srfi-1)
@@ -71,24 +72,6 @@ optionally, CODESET."
       (codeset   . ,(or codeset (match:substring matches 5)))
       (modifier  . ,(match:substring matches 7)))))
 
-(define (normalize-codeset codeset)
-  "Compute the \"normalized\" variant of CODESET."
-  ;; info "(libc) Using gettextized software", for the algorithm used to
-  ;; compute the normalized codeset.
-  (letrec-syntax ((-> (syntax-rules ()
-                        ((_ proc value)
-                         (proc value))
-                        ((_ proc rest ...)
-                         (proc (-> rest ...))))))
-    (-> (lambda (str)
-          (if (string-every char-set:digit str)
-              (string-append "iso" str)
-              str))
-        string-downcase
-        (lambda (str)
-          (string-filter char-set:letter+digit str))
-        codeset)))
-
 (define (locale->locale-string locale)
   "Reverse operation of locale-string->locale."
   (let ((language (locale-language locale))

gnu/installer/newt/network.scm

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

gnu/installer/newt/wifi.scm

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

gnu/installer/parted.scm

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

gnu/installer/services.scm

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

gnu/local.mk

@@ -17,7 +17,7 @@
 # Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 # Copyright © 2017, 2018 Gábor Boskovits <boskovits@gmail.com>
 # Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
-# Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
+# Copyright © 2018, 2019 Oleg Pykhalov <go.wigust@gmail.com>
 # Copyright © 2018 Stefan Stefanović <stefanx2ovic@gmail.com>
 # Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 #
@@ -121,6 +121,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/cpp.scm 				\
   %D%/packages/cppi.scm				\
   %D%/packages/cran.scm				\
+  %D%/packages/crates-io.scm			\
   %D%/packages/cross-base.scm			\
   %D%/packages/crypto.scm			\
   %D%/packages/cryptsetup.scm			\
@@ -261,6 +262,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/jrnl.scm				\
   %D%/packages/jose.scm				\
   %D%/packages/julia.scm			\
+  %D%/packages/kawa.scm				\
   %D%/packages/kde.scm				\
   %D%/packages/kde-frameworks.scm		\
   %D%/packages/kde-plasma.scm			\
@@ -468,6 +470,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/uml.scm				\
   %D%/packages/unrtf.scm			\
   %D%/packages/upnp.scm				\
+  %D%/packages/usb-modeswitch.scm		\
   %D%/packages/uucp.scm				\
   %D%/packages/valgrind.scm			\
   %D%/packages/version-control.scm		\
@@ -501,6 +504,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/services.scm				\
   %D%/services/admin.scm			\
   %D%/services/audio.scm                        \
+  %D%/services/auditd.scm			\
   %D%/services/avahi.scm			\
   %D%/services/base.scm				\
   %D%/services/certbot.scm			\
@@ -516,6 +520,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/services/docker.scm			\
   %D%/services/authentication.scm		\
   %D%/services/games.scm			\
+  %D%/services/getmail.scm				\
   %D%/services/kerberos.scm			\
   %D%/services/lirc.scm				\
   %D%/services/virtualization.scm		\
@@ -524,6 +529,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/services/messaging.scm			\
   %D%/services/monitoring.scm			\
   %D%/services/networking.scm			\
+  %D%/services/nix.scm				\
   %D%/services/nfs.scm			\
   %D%/services/security-token.scm		\
   %D%/services/shepherd.scm			\
@@ -585,6 +591,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/tests/networking.scm			\
   %D%/tests/rsync.scm				\
   %D%/tests/security-token.scm			\
+  %D%/tests/singularity.scm			\
   %D%/tests/ssh.scm				\
   %D%/tests/version-control.scm			\
   %D%/tests/virtualization.scm			\
@@ -636,6 +643,7 @@ dist_installer_DATA =				\
 
 # Modules that do not need to be compiled.
 MODULES_NOT_COMPILED +=				\
+  %D%/build/locale.scm				\
   %D%/build/shepherd.scm			\
   %D%/build/svg.scm
 
@@ -688,7 +696,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/blender-2.79-newer-ffmpeg.patch		\
   %D%/packages/patches/blender-2.79-python-3.7-fix.patch	\
   %D%/packages/patches/boost-fix-icu-build.patch		\
-  %D%/packages/patches/borg-fix-hard-link-preloading.patch	\
   %D%/packages/patches/byobu-writable-status.patch		\
   %D%/packages/patches/calibre-no-updates-dialog.patch		\
   %D%/packages/patches/calibre-remove-test-bs4.patch		\
@@ -754,7 +761,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/emacs-highlight-stages-add-gexp.patch	\
   %D%/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch	\
   %D%/packages/patches/emacs-source-date-epoch.patch		\
-  %D%/packages/patches/emacs-realgud-fix-configure-ac.patch	\
   %D%/packages/patches/emacs-undohist-ignored.patch	\
   %D%/packages/patches/emacs-wordnut-require-adaptive-wrap.patch	\
   %D%/packages/patches/emacs-zones-called-interactively.patch	\
@@ -869,7 +875,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/gmp-faulty-test.patch			\
   %D%/packages/patches/gnome-shell-theme.patch			\
   %D%/packages/patches/gnome-tweaks-search-paths.patch		\
-  %D%/packages/patches/gnucash-fix-test-transaction-failure.patch \
   %D%/packages/patches/gnutls-skip-trust-store-test.patch	\
   %D%/packages/patches/gobject-introspection-absolute-shlib-path.patch \
   %D%/packages/patches/gobject-introspection-cc.patch		\
@@ -899,6 +904,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gtk3-respect-GUIX_GTK3_PATH.patch	\
   %D%/packages/patches/gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch \
   %D%/packages/patches/gtkglext-disable-disable-deprecated.patch \
+  %D%/packages/patches/gtksourceview-2-add-default-directory.patch \
   %D%/packages/patches/gzdoom-search-in-installed-share.patch	\
   %D%/packages/patches/handbrake-opt-in-nvenc.patch		\
   %D%/packages/patches/haskell-mode-unused-variables.patch	\
@@ -985,13 +991,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/libcroco-CVE-2017-7960.patch		\
   %D%/packages/patches/libcroco-CVE-2017-7961.patch		\
   %D%/packages/patches/libdrm-symbol-check.patch		\
-  %D%/packages/patches/libevent-dns-tests.patch			\
-  %D%/packages/patches/libevent-2.0-CVE-2016-10195.patch	\
-  %D%/packages/patches/libevent-2.0-CVE-2016-10196.patch	\
-  %D%/packages/patches/libevent-2.0-CVE-2016-10197.patch	\
-  %D%/packages/patches/libevent-2.0-evbuffer-add-use-last-with-datap.patch	\
-  %D%/packages/patches/libevent-2.1-dns-tests.patch		\
-  %D%/packages/patches/libevent-2.1-skip-failing-test.patch	\
   %D%/packages/patches/libexif-CVE-2016-6328.patch		\
   %D%/packages/patches/libexif-CVE-2017-7544.patch		\
   %D%/packages/patches/libgpg-error-gawk-compat.patch		\
@@ -1172,7 +1171,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/plink-endian-detection.patch		\
   %D%/packages/patches/plotutils-libpng-jmpbuf.patch		\
   %D%/packages/patches/podofo-cmake-3.12.patch			\
-  %D%/packages/patches/polkit-CVE-2018-19788.patch		\
   %D%/packages/patches/portaudio-audacity-compat.patch		\
   %D%/packages/patches/portmidi-modular-build.patch		\
   %D%/packages/patches/postgresql-disable-resolve_symlinks.patch	\
@@ -1283,6 +1281,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/superlu-dist-awpm-grid.patch		\
   %D%/packages/patches/superlu-dist-fix-mpi-deprecations.patch	\
   %D%/packages/patches/superlu-dist-scotchmetis.patch		\
+  %D%/packages/patches/supertux-fix-build-with-gcc5.patch	\
+  %D%/packages/patches/supertux-unbundle-squirrel.patch		\
   %D%/packages/patches/swig-guile-gc.patch			\
   %D%/packages/patches/swish-e-search.patch			\
   %D%/packages/patches/swish-e-format-security.patch		\
@@ -1317,6 +1317,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/totem-meson-easy-codec.patch		\
   %D%/packages/patches/tuxpaint-stamps-path.patch		\
   %D%/packages/patches/twinkle-include-qregexpvalidator.patch	\
+  %D%/packages/patches/txr-shell.patch				\
   %D%/packages/patches/u-boot-fix-mkimage-header-verification.patch	\
   %D%/packages/patches/unzip-CVE-2014-8139.patch		\
   %D%/packages/patches/unzip-CVE-2014-8140.patch		\
@@ -1335,6 +1336,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/util-linux-tests.patch			\
   %D%/packages/patches/upower-builddir.patch			\
   %D%/packages/patches/upx-fix-CVE-2017-15056.patch		\
+  %D%/packages/patches/usb-modeswitch-accept-config-arg.patch	\
   %D%/packages/patches/valgrind-enable-arm.patch		\
   %D%/packages/patches/vboot-utils-fix-format-load-address.patch	\
   %D%/packages/patches/vboot-utils-fix-tests-show-contents.patch	\

gnu/packages/admin.scm

@@ -115,14 +115,14 @@
 (define-public aide
   (package
     (name "aide")
-    (version "0.16.1")
+    (version "0.16.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/aide/aide/releases/download/v"
                            version "/aide-" version ".tar.gz"))
        (sha256
-        (base32 "1dqhc0c24wa4zid06pfy61k357yvzh28ij86bk9jf6hcqzn7qaqg"))))
+        (base32 "15xp47sz7kk1ciffw3f5xw2jg2mb2lqrbr3q6p4bkbz5dap9iy8p"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("bison" ,bison)
@@ -1734,13 +1734,13 @@ of supported upstream metrics systems simultaneously.")
 (define-public ansible
   (package
     (name "ansible")
-    (version "2.7.10")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ansible" version))
        (sha256
-        (base32 "15721d0bxymghxnlnknq43lszlxg3ybbcp2p5v424hhw6wg2v944"))))
+        (base32 "1bpk5r5x6vdgn839n74yv2chd2ja10yfrhav0fzwa38mi5yxsd3j"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-bcrypt" ,python-bcrypt)
@@ -2124,25 +2124,36 @@ results (ndiff), and a packet generation and response analysis tool (nping).")
 (define-public dstat
   (package
     (name "dstat")
-    (version "0.7.3")
+    (version "0.7.4")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/dagwieers/dstat.git")
-             (commit version)))
+             (commit (string-append "v" version))))
        (file-name (git-file-name "dstat" version))
        (sha256
-        (base32 "0sbpna531034gr40w4g9cwz35s2fpf9h654paznsxw9fih91rfa5"))))
+        (base32 "1qnmkhqmjd1m3if05jj29dvr5hn6kayq9bkkkh881w472c0zhp8v"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no make check
        #:make-flags (let ((out (assoc-ref %outputs "out")))
                       (list (string-append "DESTDIR=" out)
                             "prefix=/"))
-       ;; No configure script.
+       #:phases
-       #:phases (modify-phases %standard-phases (delete 'configure))))
+       (modify-phases %standard-phases
-    (inputs `(("python-2" ,python-2)))
+         (delete 'configure)            ; no configure script
+         (add-after 'install 'wrap
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/bin/dstat")
+                 `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH"))))
+               #t))))))
+    (inputs
+     ;; Python 3 is supposedly supported but prints a DeprecationWarning.
+     ;; Upstream is dead.  See <https://github.com/dagwieers/dstat/releases>.
+     `(("python" ,python-wrapper)
+       ("python-six" ,python-six)))
     (synopsis "Versatile resource statistics tool")
     (description "Dstat is a versatile replacement for @command{vmstat},
 @command{iostat}, @command{netstat}, and @command{ifstat}.  Dstat overcomes
@@ -2160,7 +2171,7 @@ throughput (in the same interval).")
 (define-public thefuck
   (package
     (name "thefuck")
-    (version "3.28")
+    (version "3.29")
     (source
      (origin
        (method git-fetch)
@@ -2169,7 +2180,7 @@ throughput (in the same interval).")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "070b2sx8r0b4hry6xg97psxlikxghmz91zicg2cm6kc1yhgz4agc"))
+        (base32 "1qhxwjjgrzpqrqjv7l2847ywpln76lyd6j8bl9gz2r6kl0fx2fqs"))
        (patches (search-patches "thefuck-test-environ.patch"))))
     (build-system python-build-system)
     (arguments
@@ -2849,7 +2860,7 @@ Python loading in HPC environments.")
   (let ((real-name "inxi"))
     (package
       (name "inxi-minimal")
-      (version "3.0.33-1")
+      (version "3.0.34-1")
       (source
        (origin
          (method git-fetch)
@@ -2858,7 +2869,7 @@ Python loading in HPC environments.")
                (commit version)))
          (file-name (git-file-name real-name version))
          (sha256
-          (base32 "19bfdid4zp39irsdq3m6yyqf2336c30da35qgslrzcr2vh815g8c"))))
+          (base32 "0x2s40lwsan2pk292nspjgyw00f9f5fdfmwfvl50924pxhyxn2fh"))))
       (build-system trivial-build-system)
       (inputs
        `(("bash" ,bash-minimal)

gnu/packages/aidc.scm

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

gnu/packages/algebra.scm

@@ -251,7 +251,7 @@ precision.")
 (define-public giac
   (package
     (name "giac")
-    (version "1.5.0-49")
+    (version "1.5.0-57")
     (source (origin
               (method url-fetch)
               ;; "~parisse/giac" is not used because the maintainer regularly
@@ -263,7 +263,7 @@ precision.")
                                   "source/giac_" version ".tar.gz"))
               (sha256
                (base32
-                "0f4pkand9vmqfayw18jm5qxbhcwi1405qfd7ibzh9lwzz6amkm3l"))))
+                "08c93knsisbk9dkyyrignw0wvqbr1sa5czlvk5l307ahxbbmqncf"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)

gnu/packages/animation.scm

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

gnu/packages/aspell.scm

@@ -6,6 +6,7 @@
 ;;; Copyright © 2016 Christopher Andersson <christopher@8bits.nu>
 ;;; Copyright © 2016 Theodoros Foradis <theodoros@foradis.org>
 ;;; Copyright © 2016, 2017, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -31,7 +32,8 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages perl))
+  #:use-module (gnu packages perl)
+  #:use-module (ice-9 match))
 
 (define-public aspell
   (package
@@ -102,7 +104,14 @@ dictionaries, including personal ones.")
 (define* (aspell-dictionary dict-name full-name
                             #:key version sha256 (prefix "aspell6-"))
   (package
-    (name (string-append "aspell-dict-" dict-name))
+    (name (string-append
+           "aspell-dict-"
+           ;; Downcase and replace underscore in package names
+           ;; to follow Guix naming conventions.
+           (string-map (match-lambda
+                         (#\_ #\-)
+                         (chr chr))
+           (string-downcase dict-name))))
     (version version)
     (source (origin
               (method url-fetch)
@@ -132,6 +141,22 @@ dictionaries, including personal ones.")
     (home-page "http://aspell.net/")))
 
 
+(define-public aspell-dict-ar
+  (aspell-dictionary "ar" "Arabic"
+                     #:version "1.2-0"
+		     #:prefix "aspell6-"
+                     #:sha256
+                     (base32
+                      "1avw40bp8yi5bnkq64ihm2rldgw34lk89yz281q9bmndh95a47h4")))
+
+(define-public aspell-dict-be
+  (aspell-dictionary "be" "Belarusian"
+                     #:version "0.01"
+                     #:prefix "aspell5-"
+                     #:sha256
+                     (base32
+                      "1svls9p7rsfi3hs0afh0cssj006qb4v1ik2yzqgj8hm10c6as2sm")))
+
 (define-public aspell-dict-ca
   (aspell-dictionary "ca" "Catalan"
                      #:version "2.1.5-1"
@@ -146,6 +171,14 @@ dictionaries, including personal ones.")
                      (base32
                       "01p92qj66cqb346gk7hjfynaap5sbcn85xz07kjfdq623ghr8v5s")))
 
+(define-public aspell-dict-da
+  (aspell-dictionary "da" "Danish"
+                     #:version "1.4.42-1"
+                     #:prefix "aspell5-"
+                     #:sha256
+                     (base32
+                      "1hfkmiyhgrx5lgrb2mffjbdn1hivrm73wcg7x0iid74p2yb0fjpp")))
+
 (define-public aspell-dict-el
   (aspell-dictionary "el" "Greek"
                      #:version "0.08-0"
@@ -175,6 +208,14 @@ dictionaries, including personal ones.")
                      (base32
                       "1k5g328ac1hdpp6fsg57d8md6i0aqcwlszp3gbmp5706wyhpydmd")))
 
+(define-public aspell-dict-fi
+  (aspell-dictionary "fi" "Finnish"
+                     #:version "0.7-0"
+                     #:prefix "aspell6-"
+                     #:sha256
+                     (base32
+                      "07d5s08ba4dd89cmwy9icc01i6fjdykxlb9ravmhdrhi8mxz1mzq")))
+
 (define-public aspell-dict-fr
   (aspell-dictionary "fr" "French"
                      #:version "0.50-3"
@@ -197,6 +238,14 @@ dictionaries, including personal ones.")
                      (base32
                       "13bhbghx5b8g0119g3wxd4n8mlf707y41vlf59irxjj0kynankfn")))
 
+(define-public aspell-dict-hi
+  (aspell-dictionary "hi" "Hindi"
+                     #:version "0.02-0"
+                     #:prefix "aspell6-"
+                     #:sha256
+                     (base32
+                      "0drs374qz4419zx1lf2k281ydxf2750jk5ailafj1x0ncz27h1ys")))
+
 (define-public aspell-dict-it
   (let ((version "2.4-20070901-0")
         (sha256
@@ -218,6 +267,13 @@ dictionaries, including personal ones.")
        (home-page
         "http://linguistico.sourceforge.net/pages/dizionario_italiano.html"))))
 
+(define-public aspell-dict-mi
+  (aspell-dictionary "mi" "Maori"
+                     #:version "0.50-0"
+                     #:sha256
+                     (base32
+                      "12bxplpd348yx8d2q8qvahi9dlp7qf28qmanzhziwc7np8rixvmy")))
+
 (define-public aspell-dict-nl
   (aspell-dictionary "nl" "Dutch"
                      #:version "0.50-2"
@@ -226,14 +282,29 @@ dictionaries, including personal ones.")
                      (base32
                       "0ffb87yjsh211hllpc4b9khqqrblial4pzi1h9r3v465z1yhn3j4")))
 
+(define-public aspell-dict-nn
+  (aspell-dictionary "nn" "Norwegian Nynorsk"
+                     #:version "0.50.1-1"
+                     #:sha256
+                     (base32
+                      "0w2k5l5rbqpliripgqwiqixz5ghnjf7i9ggbrc4ly4vy1ia10rmc")))
+
 (define-public aspell-dict-pt-br
-  (aspell-dictionary "pt-br" "Brazilian Portuguese"
+  (aspell-dictionary "pt_BR" "Brazilian Portuguese"
                      #:version "20090702-0"
                      #:prefix "aspell6-"
                      #:sha256
                      (base32
                       "1y09lx9zf2rnp55r16b2vgj953l3538z1vaqgflg9mdvm555bz3p")))
 
+(define-public aspell-dict-pt-pt
+  (aspell-dictionary "pt_PT" "Portuguese"
+                     #:version "20070510-0"
+                     #:prefix "aspell6-"
+                     #:sha256
+                     (base32
+                      "1mnr994cwlag6shy8865ky99lymysiln07mbldcncahg90dagdxq")))
+
 (define-public aspell-dict-ru
   (aspell-dictionary "ru" "Russian"
                      #:version "0.99f7-1"
@@ -249,6 +320,13 @@ dictionaries, including personal ones.")
                      (base32
                       "02jwkjhr32kvyibnyzgx3smbnm576jwdzg3avdf6zxwckhy5fw4v")))
 
+(define-public aspell-dict-uk
+  (aspell-dictionary "uk" "Ukrainian"
+                     #:version "1.4.0-0"
+                     #:sha256
+                     (base32
+                      "137i4njvnslab6l4s291s11xijr5jsy75lbdph32f9y183lagy9m")))
+
 
 ;;;
 ;;; Hunspell packages made from the Aspell word lists.

gnu/packages/astronomy.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 John Darrington <jmd@gnu.org>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -37,15 +37,15 @@
 (define-public cfitsio
   (package
     (name "cfitsio")
-    (version "3.450")
+    (version "3.47")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
              "http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/"
-             name (string-replace-substring version "." "") ".tar.gz"))
+             name "-" version ".tar.gz"))
        (sha256
-        (base32 "0bmrkw6w65zb0k3mszaaqy1f4zjm2hl7njww74nb5v38wvdi4q5z"))))
+        (base32 "1vzlxnrjckz78p2wf148v2z3krkwnykfqvlj42sz3q711vqid1a1"))))
     (build-system gnu-build-system)
     ;; XXX Building with curl currently breaks wcslib.  It doesn't use
     ;; pkg-config and hence won't link with -lcurl.

gnu/packages/audio.scm

@@ -174,14 +174,14 @@ Filter) modules follow the convention of 1V / Octave.")
         "--enable-jack"
         "--enable-sndfile"
         "--enable-samplerate"
-        ;; TODO: enable compilation with avcodec once available.
+        "--enable-avcodec")
-        "--disable-avcodec")
        #:python ,python-2))
     (inputs
      `(("jack" ,jack-1)
        ("libsndfile" ,libsndfile)
        ("libsamplerate" ,libsamplerate)
-       ("fftwf" ,fftwf)))
+       ("fftwf" ,fftwf)
+       ("ffmpeg" ,ffmpeg))) ; for libavcodec
     (native-inputs
      `(("pkg-config" ,pkg-config)))
     (home-page "https://aubio.org/")
@@ -2120,14 +2120,14 @@ different audio devices such as ALSA or PulseAudio.")
 (define-public qjackctl
   (package
     (name "qjackctl")
-    (version "0.5.7")
+    (version "0.5.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/qjackctl/qjackctl/"
                                   version "/qjackctl-" version ".tar.gz"))
               (sha256
                (base32
-                "1g6a5j74p45yisl28bw4fcc9nr6b710ikk459p4mp6djh9gs8v95"))))
+                "1r5hf3hcr20n93jrrm7xk2zf6yx264pcr4d10cpybhrancxh602n"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f))                    ; no check target
@@ -3701,7 +3701,7 @@ library.")
 (define-public faudio
   (package
     (name "faudio")
-    (version "19.05")
+    (version "19.06.07")
     (source
      (origin
        (method git-fetch)
@@ -3710,7 +3710,7 @@ library.")
              (commit version)))
        (file-name (string-append name "-" version "-checkout"))
        (sha256
-        (base32 "1dja2ykixk1ycqda116cg9fy4qg364dqj88amfln0r9pnsj2kbxk"))))
+        (base32 "1w37qp279lgpyvslwz3wlb4fp0i68ncd411rqdlk5s71b1zz466n"))))
     (arguments
      '(#:tests? #f                      ; No tests.
        #:configure-flags '("-DFFMPEG=ON")))

gnu/packages/backup.scm

@@ -73,7 +73,7 @@
 (define-public duplicity
   (package
     (name "duplicity")
-    (version "0.7.18.2")
+    (version "0.7.19")
     (source
      (origin
       (method url-fetch)
@@ -82,7 +82,7 @@
                           "-series/" version "/+download/duplicity-"
                           version ".tar.gz"))
       (sha256
-       (base32 "0j37dgyji36hvb5dbzlmh5rj83jwhni02yq16g6rd3hj8f7qhdn2"))))
+       (base32 "0ag9dknslxlasslwfjhqgcqbkb1mvzzx93ry7lch2lfzcdd91am6"))))
     (build-system python-build-system)
     (native-inputs
      `(("util-linux" ,util-linux)       ; setsid command, for the tests
@@ -495,15 +495,13 @@ detection, and lossless compression.")
 (define-public borg
   (package
     (name "borg")
-    (version "1.1.9")
+    (version "1.1.10")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "borgbackup" version))
        (sha256
-        (base32
+        (base32 "1pp70p4n5kamvcbl4d8021ggrxhyykmg9isjg4yd3wags8b19d7g"))
-         "0x95nhv4h34m8cxycbwc4xdz350saaxlgh727b23bgn4ci7gh3vx"))
-       (patches (search-patches "borg-fix-hard-link-preloading.patch"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -525,7 +523,12 @@ detection, and lossless compression.")
            ;; Remove bundled shared libraries.
            (with-directory-excursion "src/borg/algorithms"
              (for-each delete-file-recursively
-                       (list "blake2" "lz4" "zstd")))
+                       (list "blake2" "lz4" "msgpack" "zstd")))
+           ;; Purge some msgpack references from setup.py or the resulting
+           ;; sources will be unbuildable.
+           (substitute* "setup.py"
+             ((".*Extension\\('borg\\.algorithms\\.msgpack\\..*") "")
+             (("msgpack_packer_source, msgpack_unpacker_source") ""))
            #t))))
     (build-system python-build-system)
     (arguments
@@ -549,6 +552,12 @@ detection, and lossless compression.")
                ;; HOME=/homeless-shelter.
                (setenv "HOME" "/tmp")
                #t)))
+         (add-after 'unpack 'use-system-msgpack
+           (lambda _
+             (substitute* "src/borg/helpers.py"
+               (("prefer_system_msgpack = False")
+                "prefer_system_msgpack = True"))
+             #t))
          ;; The tests need to be run after Borg is installed.
          (delete 'check)
          (add-after 'install 'check

gnu/packages/base.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2019 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org>
 ;;; Copyright © 2014, 2015, 2016, 2018 Mark H Weaver <mhw@netris.org>
@@ -992,12 +992,47 @@ to the @code{share/locale} sub-directory of this package.")
      (let ((args `(#:tests? #f #:strip-binaries? #f
                    ,@(package-arguments glibc))))
        (substitute-keyword-arguments args
+         ((#:modules modules '((guix build utils)
+                               (guix build gnu-build-system)))
+          `((srfi srfi-11)
+            (gnu build locale)
+            ,@modules))
+         ((#:imported-modules modules '())
+          `((gnu build locale)
+            ,@%gnu-build-system-modules))
          ((#:phases phases)
           `(modify-phases ,phases
              (replace 'build
                (lambda _
                  (invoke "make" "localedata/install-locales"
                          "-j" (number->string (parallel-job-count)))))
+             (add-after 'build 'symlink-normalized-codesets
+               (lambda* (#:key outputs #:allow-other-keys)
+                 ;; The above phase does not install locales with names using
+                 ;; the "normalized codeset."  Thus, create symlinks like:
+                 ;;   en_US.utf8 -> en_US.UTF-8
+                 (define (locale-directory? file stat)
+                   (and (file-is-directory? file)
+                        (string-index (basename file) #\_)
+                        (string-rindex (basename file) #\.)))
+
+                 (let* ((out (assoc-ref outputs "out"))
+                        (locales (find-files out locale-directory?
+                                             #:directories? #t)))
+                   (for-each (lambda (directory)
+                               (let*-values (((base)
+                                              (basename directory))
+                                             ((name codeset)
+                                              (locale->name+codeset base))
+                                             ((normalized)
+                                              (normalize-codeset codeset)))
+                                 (unless (string=? codeset normalized)
+                                   (symlink base
+                                            (string-append (dirname directory)
+                                                           "/" name "."
+                                                           normalized)))))
+                             locales)
+                   #t)))
              (delete 'install)
              (delete 'move-static-libs)))
          ((#:configure-flags flags)

gnu/packages/benchmark.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Dave Love <fx@gnu.org>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019 Eric Bavier <bavier@member.fsf.org>
 ;;;
@@ -38,14 +38,14 @@
 (define-public fio
   (package
     (name "fio")
-    (version "3.13")
+    (version "3.14")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://brick.kernel.dk/snaps/"
                                   "fio-" version ".tar.bz2"))
               (sha256
                (base32
-                "0ddj7zm04jqlna3w61qyp4qvwnv0r2lc1hzpwrgbvv4fq581w7d2"))))
+                "047y53nyhnmnxcrsfbsf0gcpxw7bli3n19ycscpxy9974j0fck0v"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"

gnu/packages/bioconductor.scm

@@ -590,6 +590,35 @@ data.  It is derived from the UCSC hg19 genome and based on the \"knownGene\"
 track.  The database is exposed as a @code{TxDb} object.")
     (license license:artistic2.0)))
 
+(define-public r-txdb-hsapiens-ucsc-hg38-knowngene
+  (package
+    (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
+    (version "3.4.6")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/annotation/" instead of "bioc/".
+              (uri (string-append "https://bioconductor.org/packages/"
+                                  "release/data/annotation/src/contrib"
+                                  "/TxDb.Hsapiens.UCSC.hg38.knownGene_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
+    (properties
+     `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genomicfeatures" ,r-genomicfeatures)))
+    (home-page
+     "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
+    (synopsis "Annotation package for human genome in TxDb format")
+    (description
+     "This package provides an annotation database of Homo sapiens genome
+data.  It is derived from the UCSC hg38 genome and based on the \"knownGene\"
+track.  The database is exposed as a @code{TxDb} object.")
+    (license license:artistic2.0)))
+
 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
   (package
     (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
@@ -1153,14 +1182,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.18.0")
+    (version "3.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "089v16mm5m0rlyyyd0d6rz8gwb852zf3bcdrrw70wanlfjn258q7"))))
+         "1mwi5s600c3jxy8f1azfrndc3g06qvhbmrp9wqac9nwjbfx1kfji"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2086,14 +2115,14 @@ independent of the p-value under the null hypothesis.")
 (define-public r-icobra
   (package
     (name "r-icobra")
-    (version "1.12.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iCOBRA" version))
        (sha256
         (base32
-         "1w9frnczgypzc2czbwrvlizqcqhbp6cdpyws7vkmnn9k0ggzxvfc"))))
+         "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
     (properties `((upstream-name . "iCOBRA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2886,14 +2915,14 @@ to multiple hypothesis correction.")
 (define-public r-dose
   (package
     (name "r-dose")
-    (version "3.10.0")
+    (version "3.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DOSE" version))
        (sha256
         (base32
-         "0dvhnfhzhhzcxm8zhdwrkif7sak4p888sjqfd3a0p77h0hs6g8pv"))))
+         "0ab7mgj42fg6608qkciyqivr1n8s8r5ibvp0z3jfclrnyx6cl0w1"))))
     (properties `((upstream-name . "DOSE")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3408,14 +3437,14 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.8.0")
+    (version "1.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "03f130vcd6hd3fv2pg60id0ddd6qkwsyx73gm907xaayf42ar2pj"))))
+         "0h5j3724hnd86w22vy3whqx6gkf0nf2dxd2clgzdvjzblbcd5s69"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3621,14 +3650,14 @@ investigation using RNA-seq data.")
 (define-public r-aucell
   (package
     (name "r-aucell")
-    (version "1.6.0")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AUCell" version))
        (sha256
         (base32
-         "025q1as9pifbxa7hidlz634q6d7l73zx8mqy4rjbfrk7d5615xvm"))))
+         "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
     (properties `((upstream-name . "AUCell")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4438,14 +4467,14 @@ interpretation.")
 (define-public r-rhisat2
   (package
     (name "r-rhisat2")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhisat2" version))
        (sha256
         (base32
-         "01jhj5vvfl4n2d0nl3nd1iw9nii85mgw2adnrmxb8wwlxgy240vr"))))
+         "1y3zqvk1vbcb10r1myh6f5yzjvf7bhwhpiq78bs1k6spli4bzj0q"))))
     (properties `((upstream-name . "Rhisat2")))
     (build-system r-build-system)
     (native-inputs
@@ -4548,3 +4577,171 @@ high-throughput sequencing data.  It performs parallel processing of entire
 files and produces a report which contains a set of high-resolution
 graphics.")
     (license license:gpl2+)))
+
+(define-public r-birewire
+  (package
+    (name "r-birewire")
+    (version "3.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BiRewire" version))
+       (sha256
+        (base32
+         "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518"))))
+    (properties `((upstream-name . "BiRewire")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-igraph" ,r-igraph)
+       ("r-matrix" ,r-matrix)
+       ("r-slam" ,r-slam)
+       ("r-tsne" ,r-tsne)))
+    (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
+    (synopsis "Tools for randomization of bipartite graphs")
+    (description
+     "This package provides functions for bipartite network rewiring through N
+consecutive switching steps and for the computation of the minimal number of
+switching steps to be performed in order to maximise the dissimilarity with
+respect to the original network.  It includes functions for the analysis of
+the introduced randomness across the switching steps and several other
+routines to analyse the resulting networks and their natural projections.")
+    (license license:gpl3)))
+
+(define-public r-birta
+  (package
+    (name "r-birta")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "birta" version))
+       (sha256
+        (base32
+         "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-limma" ,r-limma)
+       ("r-mass" ,r-mass)))
+    (home-page "https://bioconductor.org/packages/birta")
+    (synopsis "Bayesian inference of regulation of transcriptional activity")
+    (description
+     "Expression levels of mRNA molecules are regulated by different
+processes, comprising inhibition or activation by transcription factors and
+post-transcriptional degradation by microRNAs.  @dfn{birta} (Bayesian
+Inference of Regulation of Transcriptional Activity) uses the regulatory
+networks of transcription factors and miRNAs together with mRNA and miRNA
+expression data to predict switches in regulatory activity between two
+conditions.  A Bayesian network is used to model the regulatory structure and
+Markov-Chain-Monte-Carlo is applied to sample the activity states.")
+    (license license:gpl2+)))
+
+(define-public r-ropls
+  (package
+    (name "r-ropls")
+    (version "1.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ropls" version))
+       (sha256
+        (base32
+         "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-biobase" ,r-biobase)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr))) ; for vignettes
+    (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
+    (synopsis "Multivariate analysis and feature selection of omics data")
+    (description
+     "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
+and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
+regression, classification, and feature selection of omics data where the
+number of variables exceeds the number of samples and with multicollinearity
+among variables.  @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
+separately model the variation correlated (predictive) to the factor of
+interest and the uncorrelated (orthogonal) variation.  While performing
+similarly to PLS, OPLS facilitates interpretation.
+
+This package provides imlementations of PCA, PLS, and OPLS for multivariate
+analysis and feature selection of omics data.  In addition to scores, loadings
+and weights plots, the package provides metrics and graphics to determine the
+optimal number of components (e.g. with the R2 and Q2 coefficients), check the
+validity of the model by permutation testing, detect outliers, and perform
+feature selection (e.g. with Variable Importance in Projection or regression
+coefficients).")
+    (license license:cecill)))
+
+(define-public r-biosigner
+  (package
+    (name "r-biosigner")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "biosigner" version))
+       (sha256
+        (base32
+         "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-e1071" ,r-e1071)
+       ("r-randomforest" ,r-randomforest)
+       ("r-ropls" ,r-ropls)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("pandoc" ,ghc-pandoc)
+       ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
+    (home-page "https://bioconductor.org/packages/biosigner/")
+    (synopsis "Signature discovery from omics data")
+    (description
+     "Feature selection is critical in omics data analysis to extract
+restricted and meaningful molecular signatures from complex and high-dimension
+data, and to build robust classifiers.  This package implements a method to
+assess the relevance of the variables for the prediction performances of the
+classifier.  The approach can be run in parallel with the PLS-DA, Random
+Forest, and SVM binary classifiers.  The signatures and the corresponding
+'restricted' models are returned, enabling future predictions on new
+datasets.")
+    (license license:cecill)))
+
+(define-public r-annotatr
+  (package
+    (name "r-annotatr")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "annotatr" version))
+       (sha256
+        (base32
+         "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationhub" ,r-annotationhub)
+       ("r-dplyr" ,r-dplyr)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-iranges" ,r-iranges)
+       ("r-readr" ,r-readr)
+       ("r-regioner" ,r-regioner)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/annotatr/")
+    (synopsis "Annotation of genomic regions to genomic annotations")
+    (description
+     "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
+differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
+to investigate the intersecting genomic annotations.  Such annotations include
+those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
+CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
+enhancers.  The annotatr package provides an easy way to summarize and
+visualize the intersection of genomic sites/regions with genomic
+annotations.")
+    (license license:gpl3)))

gnu/packages/bioinformatics.scm

@@ -7245,18 +7245,19 @@ Bioconductor, CRAN, and Github.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.52.0")
+    (version "1.52.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "1wc7a953n6qrlh9azzg1q68rk99h3xkbs82wq0yk6h2vb2c5r3zk"))))
+                "0qwrsd9fcpkv7hhzy1scnj7ahdxi6cjary28kqk6b36gkzmnrw4r"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
+       ("r-biocmanager" ,r-biocmanager)
        ("r-graph" ,r-graph)
        ("r-rbgl" ,r-rbgl)
        ("r-rcurl" ,r-rcurl)
@@ -7372,13 +7373,13 @@ S4Vectors package itself.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.18.0")
+    (version "2.18.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "0g06y6xlm2q7p7g7phfc8qj14pqpgbb0mkyjzkfgsrwjmzvpwy6m"))))
+                "1d64sh43pfc9vj2l7y7x6sb44l67wlnn3dzygp7ws0smn06mardq"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
@@ -7452,13 +7453,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.26.3")
+    (version "3.26.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "12889lwcray2cw0skzy1xp1y3siiz6n5cwx8ni86m7r671p6zmb2"))))
+                "013glavk6a1wpyq3q35k343bdp6rf27w30q59i4kf47rp3i37g15"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7480,13 +7481,13 @@ CAGE.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.30.0")
+    (version "1.30.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "1sd01yv1hnwc16412ilncrrph4gxsr9ds0nqg1czl69fqaixjn1i"))))
+                "144x3d3b9a3q5jy4aqrk1nf2yavwjhwlf71s7qyr4x3ms3wmvf8i"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (inputs
@@ -7924,13 +7925,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.36.0")
+    (version "1.36.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "17jy7lrpdaafd8g5v6j70xsypi0lqljdqmhv9f2r1xpyg3yjd84p"))))
+                "02psq3jfgghdydwbydb1j792lvfg44l5npb44mx8d54ckr8658dd"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -9040,14 +9041,14 @@ TAB-Seq.")
 (define-public r-sva
   (package
     (name "r-sva")
-    (version "3.32.0")
+    (version "3.32.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "sva" version))
        (sha256
         (base32
-         "100jwi43y4xdqb5lldx1ld58jg9icdjgz6c7ylx95gspipnkbgjp"))))
+         "0jj6klfha5v5qmx2sjblf1an6s2zqd7mmgsp7sfmh4k2jpqi3jm9"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-genefilter" ,r-genefilter)
@@ -9369,14 +9370,14 @@ structure (pcaRes) to provide a common interface to the PCA results.")
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.10.0")
+    (version "2.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "1lqdlyvs2c9g55zf8gnw142ps4jid644fhfvclnax7sjjwrqdjzv"))))
+         "0z63yqazkycq0zbbarq9ida6al35hv3g7g9g7s7bss4gh0hk7lhd"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10568,13 +10569,13 @@ libraries.")
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.12.1")
+    (version "1.12.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "0k4jc0xc2n49saylcjrg7laxq4mchg4nv06nrbc6cp4vzpf33jh5"))))
+                "16a17161xlhh6qpna9qxph3anlc7ydgyrczmy4alfiw8si7pzmxa"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
@@ -10603,14 +10604,14 @@ quality control.")
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.12.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "19cyjjzgmhswni6js4bhbj5djp976sl9n648kk7viazgkspql884"))))
+         "17mknpkvs7mgnlbf2hv9k7rwbx2vlg60yrwfyb8nn3nxsb6vm7yn"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
@@ -12535,15 +12536,15 @@ once.  This package provides tools to perform Drop-seq analyses.")
 (define-public pigx-rnaseq
   (package
     (name "pigx-rnaseq")
-    (version "0.0.5")
+    (version "0.0.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
-                                  "releases/download/v" version
+                                  "releases/download/v." version
                                   "/pigx_rnaseq-" version ".tar.gz"))
               (sha256
                (base32
-                "05gn658zpj9xki5dbs728z9zxq1mcm25hkwr5vzwqxsfi15l5f2l"))))
+                "1w7cwbbz1sbvbyqh5c60iqcjfs3qsppmdgxqa1i0w5wwb9mkh27m"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-tests? #f             ; not supported
@@ -12566,7 +12567,6 @@ once.  This package provides tools to perform Drop-seq analyses.")
        ("trim-galore" ,trim-galore)
        ("htseq" ,htseq)
        ("samtools" ,samtools)
-       ("bedtools" ,bedtools)
        ("r-minimal" ,r-minimal)
        ("r-rmarkdown" ,r-rmarkdown)
        ("r-ggplot2" ,r-ggplot2)
@@ -12603,7 +12603,7 @@ expression report comparing samples in an easily configurable manner.")
 (define-public pigx-chipseq
   (package
     (name "pigx-chipseq")
-    (version "0.0.40")
+    (version "0.0.41")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
@@ -12611,7 +12611,7 @@ expression report comparing samples in an easily configurable manner.")
                                   "/pigx_chipseq-" version ".tar.gz"))
               (sha256
                (base32
-                "0y9x62cfwzhsp82imnawyamxp58bcb00yjxdy44spylqnjdlsaj8"))))
+                "0akbxdmsjsq5fzbwaap04hqjpsfgv1l6yrc2pwgbya1xgqvcq6vy"))))
     (build-system gnu-build-system)
     ;; parts of the tests rely on access to the network
     (arguments '(#:tests? #f))
@@ -14754,3 +14754,34 @@ ATAC-seq results.  It was written to make it easier to spot differences that
 might be caused by ATAC-seq library prep or sequencing.  The main program,
 @code{ataqv}, examines aligned reads and reports some basic metrics.")
     (license license:gpl3+)))
+
+(define-public r-psiplot
+  (package
+    (name "r-psiplot")
+    (version "2.3.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/kcha/psiplot.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "08438h16cfry5kqh3y9hs8q1b1a8bxhblsm75knviz5r6q0n1jxh"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)
+       ("r-dplyr" ,r-dplyr)
+       ("r-tidyr" ,r-tidyr)
+       ("r-purrr" ,r-purrr)
+       ("r-readr" ,r-readr)
+       ("r-magrittr" ,r-magrittr)
+       ("r-ggplot2" ,r-ggplot2)))
+    (home-page "https://github.com/kcha/psiplot")
+    (synopsis "Plot percent spliced-in values of alternatively-spliced exons")
+    (description
+     "PSIplot is an R package for generating plots of @dfn{percent
+spliced-in} (PSI) values of alternatively-spliced exons that were computed by
+vast-tools, an RNA-Seq pipeline for alternative splicing analysis.  The plots
+are generated using @code{ggplot2}.")
+    (license license:expat)))

gnu/packages/bootstrap.scm

@@ -184,6 +184,7 @@ or false to signal an error."
         ((string=? system "powerpc64le-linux") "/lib/ld64.so.2")
         ((string=? system "alpha-linux") "/lib/ld-linux.so.2")
         ((string=? system "s390x-linux") "/lib/ld64.so.1")
+        ((string=? system "riscv64-linux") "/lib/ld-linux-riscv64-lp64d.so.1")
 
         ;; XXX: This one is used bare-bones, without a libc, so add a case
         ;; here just so we can keep going.

gnu/packages/build-tools.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Corentin Bocquillon <corentin@nybble.fr>
-;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
 ;;; Copyright © 2018 Tomáš Čech <sleep_walker@gnu.org>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
@@ -242,7 +242,7 @@ other lower-level build files.")
 (define-public osc
   (package
     (name "osc")
-    (version "0.165.0")
+    (version "0.165.1")
     (source
      (origin
        (method git-fetch)
@@ -251,8 +251,7 @@ other lower-level build files.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32
+        (base32 "16p4z34ziy4z2w7mfpclk13x1w2p69wivkdwp0224x18r2fwj67v"))))
-         "0l6iw8a040l60ixxdms9rxajm38vqfdwgij2bm7ahgv1akza64jk"))))
     (build-system python-build-system)
     (arguments
      `(#:phases

gnu/packages/busybox.scm

@@ -108,7 +108,7 @@ any small or embedded system.")
 (define-public toybox
   (package
     (name "toybox")
-    (version "0.8.0")
+    (version "0.8.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -116,7 +116,7 @@ any small or embedded system.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "0mirj977zxsxnfaiqndwgsn9calgg312d817fi1hkfbd8kcyrk73"))))
+                "1czxzvyggm157z8wgxbk8k0n675p1gig9xvrcijsplh9p1i1xi0s"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases

gnu/packages/chromium.scm

@@ -98,6 +98,7 @@
     "third_party/angle/third_party/vulkan-tools" ;ASL2.0
     "third_party/angle/third_party/vulkan-validation-layers" ;ASL2.0
     "third_party/apple_apsl" ;APSL2.0
+    "third_party/axe-core" ;MPL2.0
     "third_party/blink" ;BSD-3, LGPL2+
     "third_party/boringssl" ;OpenSSL/ISC (Google additions are ISC)
     "third_party/boringssl/src/third_party/fiat" ;Expat
@@ -117,13 +118,14 @@
     "third_party/ced" ;BSD-3
     "third_party/cld_3" ;ASL2.0
     "third_party/crashpad" ;ASL2.0
+    "third_party/crashpad/crashpad/third_party/lss" ;ASL2.0
     "third_party/crashpad/crashpad/third_party/zlib/zlib_crashpad.h" ;Zlib
     "third_party/crc32c" ;BSD-3
     "third_party/cros_system_api" ;BSD-3
     "third_party/dav1d" ;BSD-2
+    "third_party/dawn" ;ASL2.0
     "third_party/dom_distiller_js" ;BSD-3
     "third_party/emoji-segmenter" ;ASL2.0
-    "third_party/fips181" ;BSD-3
     "third_party/flatbuffers" ;ASL2.0
     "third_party/glslang" ;BSD-3, Expat, ASL2.0
     "third_party/google_input_tools" ;ASL2.0
@@ -166,6 +168,7 @@
     "third_party/pdfium/third_party/bigint" ;Public domain, BSD-3
     "third_party/pdfium/third_party/skia_shared" ;BSD-3
     "third_party/pdfium/third_party/freetype/include/pstables.h" ;FreeType
+    "third_party/pffft" ;the "FFTPACK" license, similar to BSD-3
     "third_party/ply" ;BSD-3
     "third_party/polymer" ;BSD-3
     "third_party/protobuf" ;BSD-3
@@ -223,22 +226,15 @@ from forcing GEXP-PROMISE."
                       #:system system
                       #:guile-for-build guile)))
 
-(define %chromium-version "74.0.3729.169")
+(define %chromium-version "75.0.3770.80")
-(define %ungoogled-revision "d2beaeff47a6e97b8909163147ad6b4058238f36")
+(define %ungoogled-revision "5d8abc38b43a62f379615a0dc972b29d9aebb4b4")
-(define %debian-revision "debian/74.0.3729.108-1")
+(define %debian-revision "debian/75.0.3770.80-1")
 (define package-revision "0")
-
 (define %package-version (string-append %chromium-version "-"
                                         package-revision "."
                                         (string-take %ungoogled-revision 7)))
 
-;; This is a "computed" origin that does the following:
+(define %chromium-origin
-;; *) Runs the Ungoogled scripts on a pristine Chromium tarball.
-;; *) Applies Debians Chromium patches, for their unbundling and GCC work.
-;; *) Prunes all third_party directories that are not explicitly preserved.
-;; *) Adjusts "GN" build files such that system libraries are preferred.
-(define ungoogled-chromium-source
-  (let ((chromium-source
   (origin
     (method url-fetch)
     (uri (string-append "https://commondatastorage.googleapis.com"
@@ -246,8 +242,9 @@ from forcing GEXP-PROMISE."
                         %chromium-version ".tar.xz"))
     (sha256
      (base32
-             "1d0c3asfhqh6wlzngajcl0v2wn573m1jd1zqci9bcm3z048043q7"))))
+      "1mk6gb3iif8i6zq41wjn3lhqqlqp1syzpav1nj0170l7v348p0ns"))))
-        (ungoogled-source
+
+(define %ungoogled-origin
   (origin
     (method git-fetch)
     (uri (git-reference (url "https://github.com/Eloston/ungoogled-chromium")
@@ -256,8 +253,9 @@ from forcing GEXP-PROMISE."
                               (string-take %ungoogled-revision 7)))
     (sha256
      (base32
-             "04schaaqhnkrgh0p1p0wyjd5aybpxmj3kfnyipwy5nh7d39afymc"))))
+      "1vk8jzzsn20ysn4nlz84mwwhfa9nnywzd1lrahlhcky9pf6xzpwa"))))
-        (debian-source
+
+(define %debian-origin
   (origin
     (method git-fetch)
     (uri (git-reference
@@ -269,8 +267,17 @@ from forcing GEXP-PROMISE."
                                   (string-take %debian-revision 7))))
     (sha256
      (base32
-             "1bn0c86sxkkxgdz0i88y0zh4zr39l6379r2rhgk3b3qbvwz25s3j")))))
+      "16z4bncc2q1d5bymywq8291bzkcvba447ql3vsq20rwcdjckyimx"))))
 
+;; This is a "computed" origin that does the following:
+;; *) Runs the Ungoogled scripts on a pristine Chromium tarball.
+;; *) Applies Debians Chromium patches, for their unbundling and GCC work.
+;; *) Prunes all third_party directories that are not explicitly preserved.
+;; *) Adjusts "GN" build files such that system libraries are preferred.
+(define ungoogled-chromium-source
+  (let ((chromium-source %chromium-origin)
+        (ungoogled-source %ungoogled-origin)
+        (debian-source %debian-origin))
     (origin
       (method computed-origin-method)
       (file-name (string-append "ungoogled-chromium-" %package-version ".tar.xz"))
@@ -335,7 +342,6 @@ from forcing GEXP-PROMISE."
                                (when (and (> (string-length line) 1)
                                           ;; Skip the Debian-specific ones.
                                           (not (string-prefix? "debianization/" line))
-                                          (not (string-prefix? "gcc6/" line))
                                           ;; And those that conflict with Ungoogled.
                                           (not (any (cute string-suffix? <> line)
                                                     '("widevine-buildflag.patch"
@@ -434,6 +440,7 @@ from forcing GEXP-PROMISE."
              "enable_reporting=false"
              "enable_service_discovery=false"
              "enable_swiftshader=false"
+             "enable_vr=false"
              "enable_widevine=false"
              ;; Disable type-checking for the Web UI to avoid a Java dependency.
              "closure_compile=false"

gnu/packages/compression.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2017, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
@@ -128,7 +128,16 @@ in compression.")
      `(#:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'enter-source
-           (lambda _ (chdir "contrib/minizip") #t)))))
+           (lambda _ (chdir "contrib/minizip") #t))
+         (add-after 'install 'remove-crypt-h
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Remove <minizip/crypt.h> because it interferes with libc's
+             ;; <crypt.h> given that 'minizip.pc' says "-I…/include/minizip".
+             ;; Fedora does the same:
+             ;; <https://src.fedoraproject.org/rpms/zlib/c/4d2785ec3116947872f6f32dc4104e6d36d8a7a4?branch=master>.
+             (let ((out (assoc-ref outputs "out")))
+               (delete-file (string-append out "/include/minizip/crypt.h"))
+               #t))))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)

gnu/packages/coq.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Dan Frumin <dfrumin@cs.ru.nl>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -43,7 +43,7 @@
 (define-public coq
   (package
     (name "coq")
-    (version "8.9.0")
+    (version "8.9.1")
     (source
      (origin
        (method git-fetch)
@@ -52,7 +52,7 @@
              (commit (string-append "V" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "01ad7az6f95w16xya7979lk32agy22lf4bqgqf5qpnarpkpxhbw8"))))
+        (base32 "1p4z967s18wkblayv12ygqsrqlyk5ax1pz40yf4kag8pva6gblhk"))))
     (native-search-paths
      (list (search-path-specification
             (variable "COQPATH")
@@ -499,7 +499,7 @@ uses Ltac to synthesize the substitution operation.")
 (define-public coq-equations
   (package
     (name "coq-equations")
-    (version "1.2-beta2")
+    (version "1.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -508,7 +508,7 @@ uses Ltac to synthesize the substitution operation.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0y2zwv7jxs1crprj5qvg46h0v9wyfn99ln40yskq91y9h1lj5h3j"))))
+                "1q3wvicr43bgy7xn1diwh4j43mnrhprrc2xd22qlbz9cl6bhf8bj"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("ocaml"  ,ocaml)

gnu/packages/cpp.scm

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

gnu/packages/cran.scm

@@ -738,6 +738,8 @@ and vice-versa.")
        ("js-strftime" ,js-strftime)
        ("js-highlight" ,js-highlight)
        ("js-es5-shim" ,js-es5-shim)))
+    (native-inputs
+     `(("uglify-js" ,uglify-js)))
     (home-page "http://shiny.rstudio.com")
     (synopsis "Easy interactive web applications with R")
     (description
@@ -983,14 +985,14 @@ coordinates.")
 (define-public r-geosphere
   (package
     (name "r-geosphere")
-    (version "1.5-7")
+    (version "1.5-10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "geosphere" version))
        (sha256
         (base32
-         "186qdm5niq7v3d4w4rngx71znsgi44hnam7698bsx9ar5mg5b6wx"))))
+         "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-sp" ,r-sp)))
     (home-page "https://cran.r-project.org/web/packages/geosphere")
@@ -2066,14 +2068,14 @@ topics for ecologists (ISBN 978-0-691-12522-0).")
 (define-public r-lpsolve
   (package
     (name "r-lpsolve")
-    (version "5.6.13")
+    (version "5.6.13.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lpSolve" version))
        (sha256
         (base32
-         "13a9ry8xf5j1f2j6imqrxdgxqz3nqp9sj9b4ivyx9sid459irm6m"))))
+         "1f10ywlaaldgjj84vs108ly0nsbkrdgbn5d6qj7nk93j1x1xrn3a"))))
     (properties `((upstream-name . "lpSolve")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/lpSolve")
@@ -2204,14 +2206,14 @@ George Marsaglia are included.")
 (define-public r-ksamples
   (package
     (name "r-ksamples")
-    (version "1.2-8")
+    (version "1.2-9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "kSamples" version))
        (sha256
         (base32
-         "15d5q5vpp4wx5rk5kjxjdxpwc8mkq5sbdz8gi07iscrvhzb5rzfr"))))
+         "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
     (properties `((upstream-name . "kSamples")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2817,14 +2819,14 @@ color labels, layout, etc.")
 (define-public r-stringdist
   (package
     (name "r-stringdist")
-    (version "0.9.5.1")
+    (version "0.9.5.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stringdist" version))
        (sha256
         (base32
-         "0gap1g9xwhp0zxqsznkc2carpvi80z03prr4q8m528684lznx2xa"))))
+         "0nw8c317qkfq63pr0prl0hx522ddfq4cbgixb5r4pq3fxk9z303l"))))
     (build-system r-build-system)
     (home-page "https://github.com/markvanderloo/stringdist")
     (synopsis "Approximate string matching and string distance functions")
@@ -2892,14 +2894,14 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.")
 (define-public r-jomo
   (package
     (name "r-jomo")
-    (version "2.6-7")
+    (version "2.6-8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "jomo" version))
        (sha256
         (base32
-         "0lyvi32aikkvwdj0y2hc13kmmi0cw1icg8z9lcw10l8326sxm0vf"))))
+         "097zfdcqc3a45ay8xxbraqh8xsfyivskkdmc2b4ca4n979lx8vyb"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lme4" ,r-lme4)
@@ -3494,14 +3496,14 @@ timeout.  It can also poll several processes at once.")
 (define-public r-tsp
   (package
     (name "r-tsp")
-    (version "1.1-6")
+    (version "1.1-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TSP" version))
        (sha256
         (base32
-         "1ym97xl2icjpfkrici0wig29w06bb704hp51v7h5liygjlwpkhlc"))))
+         "0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb"))))
     (properties `((upstream-name . "TSP")))
     (build-system r-build-system)
     (propagated-inputs `(("r-foreach" ,r-foreach)))
@@ -3581,14 +3583,14 @@ Markdown documents.")
 (define-public r-seriation
   (package
     (name "r-seriation")
-    (version "1.2-3")
+    (version "1.2-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "seriation" version))
        (sha256
         (base32
-         "1q6hw4hjw224b4y0dc0j630v2pgj6sn455nwkilb70w8k31hpk92"))))
+         "0dbz5b5msy4fr2whhphyriqk1xc6305zpjq59rrwxyz3d7rzwpa6"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cluster" ,r-cluster)
@@ -3713,14 +3715,14 @@ to variables on the left-hand side of the assignment.")
 (define-public r-pillar
   (package
     (name "r-pillar")
-    (version "1.4.0")
+    (version "1.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pillar" version))
        (sha256
         (base32
-         "1c8rwwh677vc92f4k6qj4mxl3acran1iqdv5dj6r1dyv7fvmcvfx"))))
+         "0mcc09caxm69pghhz6b8vawj9ni63aijv5qba53pg4ph7rxclwgm"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
@@ -3831,14 +3833,14 @@ supports arbitrary vertex/edge/graph attributes.")
 (define-public r-statnet-common
   (package
     (name "r-statnet-common")
-    (version "4.2.0")
+    (version "4.3.0")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "statnet.common" version))
         (sha256
           (base32
-            "0q942g6kqmqxfss1cxb3yg8y5r1k1h5cyy99s1cfisrn6hqc6xhi"))))
+            "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
     (properties
       `((upstream-name . "statnet.common")))
     (build-system r-build-system)
@@ -4031,14 +4033,14 @@ financial trading strategies.")
 (define-public r-tseries
   (package
     (name "r-tseries")
-    (version "0.10-46")
+    (version "0.10-47")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tseries" version))
        (sha256
         (base32
-         "08kjw0bfj5gfcrxpblwqxwna8a5g9gnr7ya61qb02r263pyhm50j"))))
+         "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-quadprog" ,r-quadprog)
@@ -4995,14 +4997,14 @@ additional external tools on any platform.")
 (define-public r-openxlsx
   (package
     (name "r-openxlsx")
-    (version "4.1.0")
+    (version "4.1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "openxlsx" version))
        (sha256
         (base32
-         "1n7z22pm78xa77fvn77kdn68az6xzxk36y11sqf0w6h6adri4yxb"))))
+         "1lflygpi1z4rlb1c6g6wsmi334maiiy7jhpg6ph4sw8lpvg12w4b"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)
@@ -5859,14 +5861,14 @@ intervals.")
 (define-public r-snakecase
   (package
     (name "r-snakecase")
-    (version "0.10.0")
+    (version "0.11.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "snakecase" version))
        (sha256
         (base32
-         "0325zkpyqa15lx7biq2cbimr2773332bp4jvcvnl00bjx41ia2fm"))))
+         "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-stringi" ,r-stringi)
@@ -5931,22 +5933,22 @@ information are missing.")
 (define-public r-sjlabelled
   (package
     (name "r-sjlabelled")
-    (version "1.0.17")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sjlabelled" version))
        (sha256
         (base32
-         "00c0c22ynpihgf2bvmcfnkvqwqvxax2zzb7wldsmg2f7z5a32aa6"))))
+         "0rnmlwpp41h04dzfjd5ncvzjzs43slaimb4v2in1axznv3haafyc"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-dplyr" ,r-dplyr)
+     `(("r-haven" ,r-haven)
-       ("r-haven" ,r-haven)
        ("r-insight" ,r-insight)
        ("r-magrittr" ,r-magrittr)
        ("r-purrr" ,r-purrr)
-       ("r-rlang" ,r-rlang)))
+       ("r-rlang" ,r-rlang)
+       ("r-tidyselect" ,r-tidyselect)))
     (home-page "https://github.com/strengejacke/sjlabelled")
     (synopsis "Labelled data utility functions")
     (description
@@ -6290,14 +6292,14 @@ Group (Non-)Overlap considerations.")
 (define-public r-refgenome
   (package
     (name "r-refgenome")
-    (version "1.7.3.1")
+    (version "1.7.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "refGenome" version))
        (sha256
         (base32
-         "1s4lxv5pqk6d0f0a9iclgv88yl346fwvzgraxh0gwpbym1yhh787"))))
+         "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
     (properties `((upstream-name . "refGenome")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6362,14 +6364,14 @@ containing one or more SNPs that evolved under directional selection.")
 (define-public r-proc
   (package
     (name "r-proc")
-    (version "1.14.0")
+    (version "1.15.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pROC" version))
        (sha256
         (base32
-         "0ki1pvj5iaki81crapvwqllg5avn5qlvv62axnsdkdcmv9xc3wg0"))))
+         "1dxxkwdhxfnj2znq4c5ggrr9m5klh5pmfxg17rz59vr2hfb73m24"))))
     (properties `((upstream-name . "pROC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7786,14 +7788,14 @@ correlation, censored, ordered and multivariate problems.")
 (define-public r-bayesplot
   (package
     (name "r-bayesplot")
-    (version "1.6.0")
+    (version "1.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bayesplot" version))
        (sha256
         (base32
-         "0in9cq2ybpa7njrwqx4l6nc8i01cjswsvzwlyiw465pi74aapr57"))))
+         "0h23sbfny2hcipvvfhq5aiwdh1vanizn7f8lpb9kffypxhcd7v7w"))))
     (build-system r-build-system)
     (inputs
      `(("pandoc" ,ghc-pandoc)
@@ -7802,8 +7804,11 @@ correlation, censored, ordered and multivariate problems.")
      `(("r-dplyr" ,r-dplyr)
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggridges" ,r-ggridges)
+       ("r-glue" ,r-glue)
        ("r-reshape2" ,r-reshape2)
-       ("r-rlang" ,r-rlang)))
+       ("r-rlang" ,r-rlang)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyselect" ,r-tidyselect)))
     (home-page "http://mc-stan.org/bayesplot")
     (synopsis "Plotting for Bayesian models")
     (description
@@ -7845,25 +7850,26 @@ detection, parallelism through BLAS and parallel user templates.")
 (define-public r-sjstats
   (package
     (name "r-sjstats")
-    (version "0.17.4")
+    (version "0.17.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sjstats" version))
        (sha256
         (base32
-         "012hp9m17xzjnsfvjjz2wdfgxm3irsrfx0zmahfnfmgdrwxd5vk5"))))
+         "1x9ybvz84vgaabmqp4z6crbv5q6kqjg6msk1spbr11zx9dbj06ca"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-broom" ,r-broom)
+     `(("r-bayestestr" ,r-bayestestr)
+       ("r-broom" ,r-broom)
        ("r-dplyr" ,r-dplyr)
        ("r-emmeans" ,r-emmeans)
        ("r-insight" ,r-insight)
        ("r-lme4" ,r-lme4)
        ("r-magrittr" ,r-magrittr)
        ("r-mass" ,r-mass)
-       ("r-matrix" ,r-matrix)
        ("r-modelr" ,r-modelr)
+       ("r-performance" ,r-performance)
        ("r-purrr" ,r-purrr)
        ("r-rlang" ,r-rlang)
        ("r-sjlabelled" ,r-sjlabelled)
@@ -7918,14 +7924,14 @@ differentiation.")
 (define-public r-bayestestr
   (package
     (name "r-bayestestr")
-    (version "0.1.0")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bayestestR" version))
        (sha256
         (base32
-         "1m6gj55z3shm3m3mgqj8nk73wij67y617sl04rbj400wz9qrhfva"))))
+         "0729j4fdxkkvmh99nmny38dywidzgmipdjqbi2ljxygsn4jg7ysy"))))
     (properties `((upstream-name . "bayestestR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7943,14 +7949,14 @@ ROPE percentage and pd).")
 (define-public r-performance
   (package
     (name "r-performance")
-    (version "0.1.0")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "performance" version))
        (sha256
         (base32
-         "19lfx25hkavzbycrh6hq4v24a0dz4s60ryq6jyihjlxgrb9g7cnw"))))
+         "1pzd6z7i1jxr2xi1shg3d0bxlbpmjl7kpmwgjnfys6syv57znd1z"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bayestestr" ,r-bayestestr)
@@ -8797,14 +8803,14 @@ isosurfaces.")
 (define-public r-ks
   (package
     (name "r-ks")
-    (version "1.11.4")
+    (version "1.11.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ks" version))
        (sha256
         (base32
-         "0d5i8458s8ri9pcx2jm003z1ajk7ha3pmw1sr6lgn6a8d7wgmvqb"))))
+         "06ymx244yknmpl6935l4pafqbm4gcbpnhqg7rinql6rrfr9mcrag"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-fnn" ,r-fnn)
@@ -9761,14 +9767,14 @@ the combination of non-negative and non-positive constraints.")
 (define-public r-iso
   (package
     (name "r-iso")
-    (version "0.0-17")
+    (version "0.0-18")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Iso" version))
        (sha256
         (base32
-         "0lljc99sdzdqj6d56qbsggibr6pkdwkh821bj70ianikyvmdc1y0"))))
+         "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
     (properties `((upstream-name . "Iso")))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
@@ -10481,14 +10487,14 @@ Differences with other sparse matrix packages are:
 (define-public r-fields
   (package
     (name "r-fields")
-    (version "9.8-1")
+    (version "9.8-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fields" version))
        (sha256
         (base32
-         "1zb44bm9mwbnld2q915nxxji3hqa025cmlaar7da35lyqlrjl30v"))))
+         "1q9x68dczjym56v7x90x4x5br59vj3dww6w8v42zd3yl17h7c1h1"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-maps" ,r-maps)
@@ -10724,14 +10730,14 @@ But it can also be used to do data analysis for small scale data sets.")
 (define-public r-cmprsk
   (package
     (name "r-cmprsk")
-    (version "2.2-7")
+    (version "2.2-8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cmprsk" version))
        (sha256
         (base32
-         "1imr3wpnj4g57n2x4ryahl4lk8lvq9y2r7319zv3k82mznha8bcm"))))
+         "1nacbzx950ygaqgnj0949skhwpzar5i3xlscd44jsimk2gsppx6z"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-survival" ,r-survival)))
@@ -10751,14 +10757,14 @@ JASA, 94:496-509.")
 (define-public r-etm
   (package
     (name "r-etm")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "etm" version))
        (sha256
         (base32
-         "0ws103b3pmli0z4xbyfxkly2wnnnxnnwc0r66qjjqjrlvm7pffl1"))))
+         "1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-data-table" ,r-data-table)
@@ -10777,14 +10783,14 @@ model with finite state space using the Aalen-Johansen estimator.")
 (define-public r-epi
   (package
     (name "r-epi")
-    (version "2.35")
+    (version "2.37")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Epi" version))
        (sha256
         (base32
-         "1z3959761ryv54y6vsrxxvhrwzz50xrxn55pqh5y7lrxh91zdsvl"))))
+         "1lanr9x0c6w22406p56j7cwk6wck8njq6pscb4gzc613d68zj1lk"))))
     (properties `((upstream-name . "Epi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11020,14 +11026,14 @@ machine or distributed on a compute cluster.")
 (define-public r-rsvd
   (package
     (name "r-rsvd")
-    (version "1.0.0")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rsvd" version))
        (sha256
         (base32
-         "0vjhrvnkl9rmvl8sv2kac5sd10z3fgxymb676ynxzc2pmhydy3an"))))
+         "1faskhf5j2bj9f971qljsmh182g3rnyilj1wwijz530a6skxidzz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)))
@@ -11155,14 +11161,14 @@ algorithms) can be computed and partitioned matrices can be plotted.")
 (define-public r-upsetr
   (package
     (name "r-upsetr")
-    (version "1.3.3")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "UpSetR" version))
        (sha256
         (base32
-         "08vj7l92b8fpqyqwxshll2mhk3yhgyr74axvr2lf29z78bapymhz"))))
+         "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
     (properties `((upstream-name . "UpSetR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12895,21 +12901,21 @@ SELECT or UPDATE queries to an end-point.")
 (define-public r-bookdown
   (package
     (name "r-bookdown")
-    (version "0.10")
+    (version "0.11")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "bookdown" version))
               (sha256
                (base32
-                "0xk57p9iyj7rqrwb89q3pm8p29ca615fj1h9blf5yb3zhga4bjk3"))))
+                "0w4fkv5fqiaqgkx44p0s161imf29zir9742126xkz1pl1j25jn1r"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-htmltools" ,r-htmltools)
        ("r-knitr" ,r-knitr)
        ("r-rmarkdown" ,r-rmarkdown)
        ("r-tinytex" ,r-tinytex)
-       ("r-yaml" ,r-yaml)
+       ("r-xfun" ,r-xfun)
-       ("r-xfun" ,r-xfun)))
+       ("pandoc" ,ghc-pandoc)))
     (home-page "https://github.com/rstudio/bookdown")
     (synopsis "Authoring books and technical documents with R markdown")
     (description "This package provides output formats and utilities for
@@ -12941,14 +12947,14 @@ that accept short and long options.")
 (define-public r-wgcna
   (package
     (name "r-wgcna")
-    (version "1.67")
+    (version "1.68")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "WGCNA" version))
        (sha256
         (base32
-         "09387w85lxvwr8ax2i2h602b4dgfv4wbvsl9aj1q0b1vfs4rkk69"))))
+         "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a"))))
     (properties `((upstream-name . "WGCNA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14398,14 +14404,14 @@ includes data sets from oceanography.")
 (define-public r-ggfortify
   (package
     (name "r-ggfortify")
-    (version "0.4.6")
+    (version "0.4.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggfortify" version))
        (sha256
         (base32
-         "1clyha9f9ygma64xbgi78lxsp1203f2ashqhhdpm71nr6w91bm88"))))
+         "1wk9j0xg5hj9i1vf62qjiphv8cbsgq7y6baay3pfl3wyb2dwgci0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)

gnu/packages/crates-io.scm

@@ -0,0 +1,92 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2019 Ivan Petkov <ivanppetkov@gmail.com>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages crates-io)
+  #:use-module (guix build-system cargo)
+  #:use-module (guix download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages))
+
+(define-public rust-unicode-xid
+  (package
+    (name "rust-unicode-xid")
+    (version "0.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "unicode-xid" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1z57lqh4s18rr4x0j4fw4fmp9hf9346h0kmdgqsqx0fhjr3k0wpw"))))
+    (build-system cargo-build-system)
+    (home-page
+      "https://github.com/unicode-rs/unicode-xid")
+    (synopsis "Determine Unicode XID related properties")
+    (description "Determine whether characters have the XID_Start
+or XID_Continue properties according to Unicode Standard Annex #31.")
+    ;; Dual licensed.
+    (license (list license:asl2.0 license:expat))))
+
+(define-public rust-proc-macro2
+  (package
+    (name "rust-proc-macro2")
+    (version "0.4.27")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "proc-macro2" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "05c92v787snyaq4ss16vxc9mdv6zndfgsdq8k3hnnyffmsf7ycad"))))
+    (build-system cargo-build-system)
+    (arguments
+      `(#:cargo-inputs (("rust-unicode-xid" ,rust-unicode-xid))
+        #:cargo-development-inputs (("rust-quote" ,rust-quote))))
+    (home-page "https://github.com/alexcrichton/proc-macro2")
+    (synopsis "Stable implementation of the upcoming new `proc_macro` API")
+    (description "This package provides a stable implementation of the upcoming new
+`proc_macro` API.  Comes with an option, off by default, to also reimplement itself
+in terms of the upstream unstable API.")
+    ;; Dual licensed.
+    (license (list license:asl2.0 license:expat))))
+
+(define-public rust-quote
+  (package
+    (name "rust-quote")
+    (version "0.6.12")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "quote" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1nw0klza45hf127kfyrpxsxd5jw2l6h21qxalil3hkr7bnf7kx7s"))))
+    (build-system cargo-build-system)
+    (arguments
+      `(#:cargo-inputs (("rust-proc-macro2" ,rust-proc-macro2))))
+    (home-page "https://github.com/dtolnay/quote")
+    (synopsis "Quasi-quoting macro quote!(...)")
+    (description "Quasi-quoting macro quote!(...)")
+    ;; Dual licensed.
+    (license (list license:asl2.0 license:expat))))

gnu/packages/cross-base.scm

@@ -40,7 +40,8 @@
   #:export (cross-binutils
             cross-libc
             cross-gcc
-            cross-newlib?))
+            cross-newlib?
+            cross-kernel-headers))
 
 (define-syntax %xgcc
   ;; GCC package used as the basis for cross-compilation.  It doesn't have to
@@ -286,18 +287,19 @@ target that libc."
 
 (define* (cross-kernel-headers target
                                #:optional
+                               (linux-headers linux-libre-headers)
                                (xgcc (cross-gcc target))
                                (xbinutils (cross-binutils target)))
   "Return headers depending on TARGET."
 
   (define xlinux-headers
-    (package (inherit linux-libre-headers)
+    (package (inherit linux-headers)
-      (name (string-append (package-name linux-libre-headers)
+      (name (string-append (package-name linux-headers)
                            "-cross-" target))
       (arguments
        (substitute-keyword-arguments
            `(#:implicit-cross-inputs? #f
-             ,@(package-arguments linux-libre-headers))
+             ,@(package-arguments linux-headers))
          ((#:phases phases)
           `(alist-replace
             'build
@@ -310,7 +312,7 @@ target that libc."
             ,phases))))
       (native-inputs `(("cross-gcc" ,xgcc)
                        ("cross-binutils" ,xbinutils)
-                       ,@(package-native-inputs linux-libre-headers)))))
+                       ,@(package-native-inputs linux-headers)))))
 
   (define xgnumach-headers
     (package (inherit gnumach-headers)

gnu/packages/crypto.scm

@@ -75,7 +75,7 @@
 (define-public libsodium
   (package
     (name "libsodium")
-    (version "1.0.17")
+    (version "1.0.18")
     (source (origin
             (method url-fetch)
             (uri (list (string-append
@@ -86,7 +86,7 @@
                         "releases/old/libsodium-" version ".tar.gz")))
             (sha256
              (base32
-              "1cf2d9v1gylz1qcy2zappbf526qfmph6gd6fnn3w2b347vixmhqc"))))
+              "1h9ncvj23qbbni958knzsli8dvybcswcjbx0qjjgi922nf848l3g"))))
     (build-system gnu-build-system)
     (synopsis "Portable NaCl-based crypto library")
     (description

gnu/packages/databases.scm

@@ -33,6 +33,7 @@
 ;;; Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019 Jack Hill <jackhill@jackhill.us>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -108,6 +109,7 @@
   #:use-module (guix download)
   #:use-module (guix bzr-download)
   #:use-module (guix git-download)
+  #:use-module (guix build-system emacs)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system perl)
@@ -928,8 +930,7 @@ organized in a hash table or B+ tree.")
                                       (assoc-ref %build-inputs "bash:include")
                                       "/include/bash"))))
 
-    (native-inputs `(("emacs" ,emacs-minimal)
+    (native-inputs `(("bc" ,bc)
-                     ("bc" ,bc)
                      ("bash:include" ,bash "include")
                      ("check" ,check)
                      ("libuuid" ,util-linux)
@@ -948,6 +949,26 @@ types are supported, as is encryption.")
     (license license:gpl3+)
     (home-page "https://www.gnu.org/software/recutils/")))
 
+(define-public emacs-recutils
+  (package
+    (inherit recutils)
+    (name "emacs-recutils")
+    (build-system emacs-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'change-directory
+           (lambda _
+             (chdir "etc")
+             #t)))))
+    (native-inputs '())
+    (inputs '())
+    (synopsis "Emacs mode for working with recutils database files")
+    (description "This package provides an Emacs major mode @code{rec-mode}
+for working with GNU Recutils text-based, human-editable databases.  It
+supports editing, navigation, and querying of recutils database files
+including field and record folding.")))
+
 (define-public rocksdb
   (package
     (name "rocksdb")
@@ -2398,14 +2419,14 @@ You might also want to install the following optional dependencies:
 (define-public python-alembic
   (package
     (name "python-alembic")
-    (version "1.0.2")
+    (version "1.0.10")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "alembic" version))
        (sha256
         (base32
-         "0asqz9mwc4w8bsar1icv3ik9jslxrj3gv3yxgmhc6nc6r9qbkg04"))))
+         "1dwl0264r6ri2jyrjr68am04x538ab26xwy4crqjnnhm4alwm3c2"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-mock" ,python-mock)

gnu/packages/datastructures.scm

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

gnu/packages/debian.scm

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

gnu/packages/dictionaries.scm

@@ -218,7 +218,7 @@ It comes with a German-English dictionary with approximately 270,000 entries.")
 (define-public grammalecte
   (package
     (name "grammalecte")
-    (version "1.1")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch/zipbomb)
@@ -226,7 +226,7 @@ It comes with a German-English dictionary with approximately 270,000 entries.")
                            "Grammalecte-fr-v" version ".zip"))
        (sha256
         (base32
-         "031d6cn1wn7ps3j38vx6s8z2gjp9nqgiypqm3bfbhxqcammyhian"))))
+         "1al4c3976wgxijxghxqb1banarj82hwad51kln87xj2r5kwcfm05"))))
     (build-system python-build-system)
     (home-page "https://grammalecte.net")
     (synopsis  "French spelling and grammar checker")

gnu/packages/disk.scm

@@ -13,6 +13,7 @@
 ;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018, 2019 Pierre Neidhardt <mail@ambrevar.xyz>
+;;; Copyright © 2019 Leo Famulari <leo@famulari.name>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -341,32 +342,31 @@ and can dramatically shorten the lifespan of the drive if left unchecked.")
 (define-public gparted
   (package
     (name "gparted")
-    (version "0.33.0")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/gparted/gparted/gparted-"
                            version "/gparted-" version ".tar.gz"))
        (sha256
-        (base32 "1ml1ky3s75lbxr91p608q3prsdh9x899mw7nbgk252pqhg4vh8sh"))))
+        (base32
+         "0mdvn85jvy72ff7nds3dakx9kzknh8gx1z8i0w2sf970q03qp2z4"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f                      ; tests require a network connection
+      ;; Tests require access to paths outside the build container, such
-       #:configure-flags '("--disable-scrollkeeper")))
+      ;; as '/dev/disk/by-id'
+     `(#:tests? #f))
     (inputs
      `(("util-linux" ,util-linux)
        ("parted" ,parted)
        ("glib" ,glib)
-       ("gtkmm" ,gtkmm-2)
+       ("gtkmm" ,gtkmm)
        ("libxml2" ,libxml2)
-       ("libxslt" ,libxslt)
+       ("yelp-tools" ,yelp-tools)
-       ("gnome-doc-utils" ,gnome-doc-utils)
+       ("itstool" ,itstool)))
-       ("docbook-xml" ,docbook-xml-4.2)
-       ("python" ,python-2)
-       ("python-libxml2" ,python2-libxml2)
-       ("which" ,which)))
     (native-inputs
      `(("intltool" ,intltool)
+       ("lvm2" ,lvm2) ; for tests
        ("pkg-config" ,pkg-config)))
     (home-page "https://gparted.org/")
     (synopsis "Partition editor to graphically manage disk partitions")

gnu/packages/display-managers.scm

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

gnu/packages/django.scm

@@ -41,13 +41,13 @@
 (define-public python-django
   (package
     (name "python-django")
-    (version "1.11.20")
+    (version "1.11.21")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "Django" version))
               (sha256
                (base32
-                "0h90kdq8r4y8wa73hdxmyy5psnwlg61dcq3qsa098cpfiyh9vaa3"))))
+                "0adhcw8sx2mgwk9y2j760y96pqbip1ni3sf2v2ls5zxc9x93wwms"))))
     (build-system python-build-system)
     (arguments
      '(#:modules ((srfi srfi-1)

gnu/packages/education.scm

@@ -27,7 +27,10 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages databases)
+  #:use-module (gnu packages fonts)
   #:use-module (gnu packages freedesktop)
+  #:use-module (gnu packages game-development)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
@@ -373,3 +376,107 @@ keyboard is also available if the child does not have any other
 specialized device.")
     (home-page "https://bipede.fr/contrib/")
     (license license:gpl3)))
+
+(define-public childsplay
+  (package
+    (name "childsplay")
+    (version "3.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://sourceforge/schoolsplay/"
+                    "childsplay-" version ".tgz"))
+              (sha256
+               (base32
+                "0z7yp2swjnbz51vn2zyfnjn40jq38l5mbh15yafmx1z3vn2z1m77"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'unbundle-dejavu-font
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let* ((dejavu-dir
+                     (string-append (assoc-ref inputs "font-dejavu")
+                                    "/share/fonts/truetype"))
+                    (dejavu-font
+                     (string-append dejavu-dir
+                                    "/DejaVuSansCondensed-Bold.ttf")))
+               (substitute* "SPConstants.py"
+                 (("^(TTF(BOLD)? = ).*" _ prefix)
+                  (string-append prefix "'" dejavu-font "'\n")))
+               (for-each (lambda (f) (delete-file f))
+                         (find-files "lib/SPData" "DejaVu"))
+               #t)))
+         (delete 'build)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (pixmaps (string-append out "/share/pixmaps"))
+                    (share (string-append out "/share/childsplay"))
+                    (doc (string-append out "/share/doc/" ,name "-",version)))
+               ;; Install icon.
+               (install-file "lib/SPData/themes/childsplay/logo_cp.svg" pixmaps)
+               ;; Install data.
+               (mkdir-p share)
+               (for-each (lambda (f)
+                           (copy-recursively f (string-append share "/" f)))
+                         '("alphabet-sounds" "lib" "locale" "SPWidgets"))
+               (for-each (lambda (f) (install-file f share))
+                         (find-files "." "\\.(py|dev|db)$"))
+               ;; Install documentation.
+               (mkdir-p doc)
+               (copy-recursively "docs" doc)
+               #t)))
+         (add-after 'install 'create-executable
+           (lambda* (#:key outputs inputs #:allow-other-keys)
+             (let* ((python (string-append (assoc-ref inputs "python")
+                                           "/bin/python"))
+                    (out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (executable (string-append bin "/childsplay")))
+               (mkdir-p bin)
+               (call-with-output-file executable
+                 (lambda (file)
+                   (format file
+                           "~a ~a"
+                           python
+                           (string-append out "/share/childsplay/childsplay.py"))))
+               (chmod executable #o555)
+               #t)))
+         (add-after 'install 'create-desktop-file
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (applications (string-append out "/share/applications")))
+               (mkdir-p applications)
+               (call-with-output-file
+                   (string-append applications "/childsplay.desktop")
+                 (lambda (file)
+                   (format file
+                           "[Desktop Entry]~@
+                            Name=Childsplay~@
+                            Comment=Suite of educational games for young children~@
+                            Comment[ca]=Conjunt de jocs educatius per a xiquets~@
+                            Comment[es]=Conjunto de juegos educativos para niños~@
+                            Comment[de]=Sammlung mit lehrreichen Spielen für kleine Kinder~@
+                            Exec=~a/bin/childsplay.py~@
+                            Terminal=false~@
+                            Icon=logo_cp.svg~@
+                            Type=Application~@
+                            Categories=Application;Game;Education;KidsGame;~@
+                            Keywords=suite;children;games;young;educational;~%"
+                           out)))
+               #t))))))
+    (inputs
+     `(("font-dejavu" ,font-dejavu)
+       ("pygame" ,python2-pygame)
+       ("sqlalchemy" ,python2-sqlalchemy)))
+    (synopsis "Suite of educational games for young children")
+    (description "Childsplay is a collection of educational activities
+for young children.  Childsplay can be used at home, kindergartens and
+pre-schools.  Childsplay is a fun and safe way to let young children
+use the computer and at the same time teach them a little math,
+letters of the alphabet, spelling, eye-hand coordination, etc.")
+    (home-page "http://www.schoolsplay.org")
+    (license license:gpl3+)))

gnu/packages/elf.scm

@@ -160,10 +160,16 @@ static analysis of the ELF binaries at hand.")
   (package
     (name "libelf")
     (version "0.8.13")
-    (source (origin
+    (source
+     (origin
        (method url-fetch)
-             (uri (string-append "http://www.mr511.de/software/libelf-"
+       (uri (list
-                                 version ".tar.gz"))
+             ;; As of May 2019, the original URL at mr511.de redirects to a
+             ;; domain that doesn't resolve.  Use these two mirrors instead.
+             (string-append "https://fossies.org/linux/misc/old/"
+                            "libelf-" version ".tar.gz")
+             (string-append "https://ftp.osuosl.org/pub/blfs/conglomeration/"
+                            "libelf/libelf-" version ".tar.gz")))
        (sha256
         (base32
          "0vf7s9dwk2xkmhb79aigqm0x0yfbw1j0b9ksm51207qwr179n6jr"))))
@@ -183,7 +189,8 @@ static analysis of the ELF binaries at hand.")
                                        (%current-system))
                              '("--host=aarch64-unknown-linux-gnu")
                              '()))))))))
-    (home-page "http://www.mr511.de/software/english.html")
+    (home-page (string-append "https://web.archive.org/web/20181111033959/"
+                              "http://www.mr511.de/software/english.html"))
     (synopsis "ELF object file access library")
     (description "Libelf is a C library to access ELF object files.")
     (license lgpl2.0+)))

gnu/packages/emacs-xyz.scm

@@ -33,7 +33,7 @@
 ;;; Copyright © 2017 Mike Gerwitz <mtg@gnu.org>
 ;;; Copyright © 2017, 2018, 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2018 Sohom Bhattacharjee <soham.bhattacharjee15@gmail.com>
-;;; Copyright © 2018 Mathieu Lirzin <mthl@gnu.org>
+;;; Copyright © 2018, 2019 Mathieu Lirzin <mthl@gnu.org>
 ;;; Copyright © 2018, 2019 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2018, 2019 Tim Gesthuizen <tim.gesthuizen@yahoo.de>
 ;;; Copyright © 2018, 2019 Jack Hill <jackhill@jackhill.us>
@@ -47,6 +47,7 @@
 ;;; Copyright © 2019 mikadoZero <mikadozero@yandex.com>
 ;;; Copyright © 2019 Gabriel Hondet <gabrielhondet@gmail.com>
 ;;; Copyright © 2019 LaFreniere, Joseph <joseph@lafreniere.xyz>
+;;; Copyright © 2019 Amar Singh <nly@disroot.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -545,6 +546,35 @@ handful of functions that are not resource-specific.")
 for editing Racket's Scribble documentation syntax in Emacs.")
       (license license:gpl3+))))
 
+(define-public emacs-shroud
+  (package
+    (name "emacs-shroud")
+    (version "1.15.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/o-nly/emacs-shroud.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0wvm4lxqcc1p8v7rpqal3bnqgnpk1gs7v18i83f6cvi5d88jkgdg"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-bui" ,emacs-bui)
+       ("emacs-dash" ,emacs-dash)
+       ("emacs-f" ,emacs-f)
+       ("emacs-s" ,emacs-s)
+       ("gnupg" ,gnupg)
+       ("shroud" ,shroud)))
+    (home-page "https://github.com/o-nly/emacs-shroud")
+    (synopsis "Emacs interface to the Shroud password manager")
+    (description
+     "This package provides an Emacs interface to the Shroud password manager,
+using the Buffers User Interface library.  You can view, copy, and edit secrets
+from within Emacs.")
+    (license license:gpl3+)))
+
 (define-public emacs-unpackaged-el
   (let ((commit "f4df7f8dfea715e893b2223adda32545803f5cce")
         (revision "1"))
@@ -667,6 +697,37 @@ programs.")
 (define-public haskell-mode
   (deprecated-package "haskell-mode" emacs-haskell-mode))
 
+(define-public emacs-dante
+  (let ((commit "149dded24ca9cdff09a3d859e4b62638db4aadda")
+        (revision "1"))
+    (package
+      (name "emacs-dante")
+      (version (git-version "1.5" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/jyp/dante")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "0i7kj3d6pfys6si9va5f36qzifyac9mahdl0qh40rya9m0syrkla"))
+                (file-name (git-file-name name version))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-dash" ,emacs-dash)
+         ("emacs-f" ,emacs-f)
+         ("emacs-flycheck" ,emacs-flycheck)
+         ("emacs-haskell-mode" ,emacs-haskell-mode)
+         ("emacs-s" ,emacs-s)
+         ("emacs-company" ,emacs-company)
+         ("emacs-lcr" ,emacs-lcr)))
+      (home-page "https://github.com/jyp/dante")
+      (synopsis "Minor mode for interactive Haskell")
+      (description
+       "This package provides a minor mode for Haskell development that
+supports type hints, definition-jumping, completion, and more.")
+      (license license:gpl3+))))
+
 (define-public emacs-flycheck
   (package
     (name "emacs-flycheck")
@@ -777,7 +838,7 @@ in certain cases.  It also enables recursion for anonymous functions.")
 (define-public emacs-xr
   (package
     (name "emacs-xr")
-    (version "1.11")
+    (version "1.12")
     (source
      (origin
        (method url-fetch)
@@ -785,7 +846,7 @@ in certain cases.  It also enables recursion for anonymous functions.")
              "https://elpa.gnu.org/packages/xr-" version ".tar"))
        (sha256
         (base32
-         "0xwfs2mkmgf63sfp5jwmw0ybc8pa0rlxh5aqwb348ddgmclv322f"))))
+         "1vv87h0h8ldc1mbsn45w5z1m6jq8j2js4xz23a9ixdby06g60y3g"))))
     (build-system emacs-build-system)
     (home-page "http://elpa.gnu.org/packages/xr.html")
     (synopsis "Convert string regexp to rx notation")
@@ -804,10 +865,33 @@ skip set strings, which are arguments to @code{skip-chars-forward} and
 @code{skip-chars-backward}.")
     (license license:gpl3+)))
 
+(define-public emacs-reformatter
+  (package
+    (name "emacs-reformatter")
+    (version "0.4")
+    (source
+     (origin
+      (method git-fetch)
+      (uri (git-reference
+            (url "https://github.com/purcell/reformatter.el.git")
+            (commit version)))
+      (file-name (git-file-name name version))
+      (sha256
+       (base32
+        "0hhy6x1bkwlhdlarsgm06g3am4yh02yqv8qs34szpzgy53x84qah"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/purcell/reformatter.el")
+    (synopsis "Define commands which run reformatters on the current buffer")
+    (description
+     "This library lets elisp authors easily define an idiomatic command to
+reformat the current buffer using a command-line program, together with an
+optional minor mode which can apply this command automatically on save.")
+    (license license:gpl3+)))
+
 (define-public emacs-relint
   (package
     (name "emacs-relint")
-    (version "1.7")
+    (version "1.8")
     (source
      (origin
        (method url-fetch)
@@ -815,7 +899,7 @@ skip set strings, which are arguments to @code{skip-chars-forward} and
              "https://elpa.gnu.org/packages/relint-" version ".el"))
        (sha256
         (base32
-         "0h9nc84yv5lmbaa8any6i3bqcn6xn1gy6cv6kqaywn0nnqrm17i1"))))
+         "1bl6m2h7131acbmr0kqfnjjpv2syiv2mxfnm61g874ynnvkmmkm3"))))
     (build-system emacs-build-system)
     (propagated-inputs `(("emacs-xr" ,emacs-xr)))
     (home-page "https://github.com/mattiase/relint")
@@ -2500,6 +2584,28 @@ evaluated in the browser, just like Emacs does with an inferior Lisp process
 in Lisp modes.")
     (license license:unlicense)))
 
+(define-public emacs-litable
+  (let ((commit "b0278f3f8dcff424bfbdfdefb545b1fbff33206f"))
+    (package
+      (name "emacs-litable")
+      (version (git-version "0.1" "0" commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/Fuco1/litable.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0bny40hv9a024n01clxns351cs4j4ifhgcc7m4743xncqf612p7g"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-dash" ,emacs-dash)))
+      (home-page "https://github.com/Fuco1/litable/")
+      (synopsis "Dynamic evaluation replacement with Emacs")
+      (description "This packages provides dynamic evaluation in Emacs.")
+      (license license:gpl3+))))
+
 (define-public emacs-string-inflection
   (package
     (name "emacs-string-inflection")
@@ -4074,20 +4180,26 @@ well as completely new features.")
     (license license:gpl3+)))
 
 (define-public emacs-highlight-symbol
+  ;; We prefer a more recent commit that provides an option to squelch
+  ;; echo-area alerts that can drown out useful information like eldoc
+  ;; messages.
+  (let ((commit "7a789c779648c55b16e43278e51be5898c121b3a")
+        (version "1.3")
+        (revision "1"))
     (package
       (name "emacs-highlight-symbol")
-    (version "1.3")
+      (version (git-version version revision commit))
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
                (url "https://github.com/nschum/highlight-symbol.el.git")
-             (commit version)))
+               (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-        (base32 "09z13kv2g21kjjkkm3iyaz93sdjmdy2d563r8n7r7ng94acrn7f6"))))
+          (base32 "19cgyk0sh8nsmf3jbi92i8qsdx4l4yilfq5jj9zfdbj9p5gvwx96"))))
       (build-system emacs-build-system)
-    (home-page "https://nschum.de/src/emacs/highlight-symbol")
+      (home-page "https://nschum.de/src/emacs/highlight-symbol/")
       (synopsis "Automatic and manual symbol highlighting for Emacs")
       (description
        "Use @code{highlight-symbol} to toggle highlighting of the symbol at
@@ -4103,7 +4215,7 @@ bindings @code{M-p} and @code{M-p} for navigation.  When
 regardless of @code{highlight-symbol-idle-delay}.
 
 @code{highlight-symbol-query-replace} can be used to replace the symbol. ")
-    (license license:gpl2+)))
+      (license license:gpl2+))))
 
 (define-public emacs-hl-todo
   (package
@@ -4131,16 +4243,17 @@ regexp that matches all known keywords.")
 (define-public emacs-perspective
   (package
     (name "emacs-perspective")
-    (version "1.12")
+    (version "2.2")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/nex3/perspective-el/"
+       (uri (git-reference
-                           "archive/" version ".tar.gz"))
+             (url "https://github.com/nex3/perspective-el.git")
-       (file-name (string-append name "-" version ".tar.gz"))
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "078ahh0kmhdylq5ib9c81c76kz1n02xwc83pm729d00i84ibviic"))))
+         "0pd5sqrrz6y3md20yh6ffy32jdcgb1gc9b4j14pm6r54bqxik68h"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/nex3/perspective-el")
     (synopsis "Switch between named \"perspectives\"")
@@ -4223,19 +4336,17 @@ after buffer changes.")
 (define-public emacs-realgud
   (package
     (name "emacs-realgud")
-    (version "1.4.5")
+    (version "1.5.0")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://elpa.gnu.org/packages/realgud-"
+       (uri (git-reference
-                           version ".tar"))
+             (url "https://github.com/realgud/realgud/")
+             (commit version)))
        (sha256
         (base32
-         "108wgxg7fb4byaiasgvbxv2hq7b00biq9f0mh9hy6vw4160y5w24"))
+         "0xnick9016wxrgi8v0lycvxhyz8l2k4nfvdpjc5yq476vwrjfzbz"))
-       (patches
+       (file-name (git-file-name name version))))
-        ;; Patch awaiting inclusion upstream (see:
-        ;; https://github.com/realgud/realgud/pull/226).
-        (search-patches "emacs-realgud-fix-configure-ac.patch"))))
     (build-system emacs-build-system)
     (arguments
      `(#:tests? #t
@@ -4254,11 +4365,6 @@ after buffer changes.")
              (setenv "HOME" (getenv "TMPDIR"))))
          (add-before 'patch-el-files 'remove-realgud-pkg.el
            (lambda _
-             ;; XXX: This file is auto-generated at some point and causes
-             ;; substitute* to crash during the `patch-el-files' phase with:
-             ;; ERROR: In procedure stat: No such file or directory:
-             ;; "./realgud-pkg.el"
-             (delete-file "./realgud-pkg.el")
              ;; FIXME: `patch-el-files' crashes on this file with error:
              ;; unable to locate "bashdb".
              (delete-file "./test/test-regexp-bashdb.el"))))
@@ -4397,6 +4503,33 @@ splitting the input text by spaces and re-building it into a regular
 expression.")
     (license license:gpl3+)))
 
+(define-public emacs-ivy-pass
+  (let ((commit "5b523de1151f2109fdd6a8114d0af12eef83d3c5")
+        (revision "1"))
+    (package
+      (name "emacs-ivy-pass")
+      (version (git-version "0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/ecraven/ivy-pass.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "18crb4zh2pjf0cmv3b913m9vfng27girjwfqc3mk7vqd1r5a49yk"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-ivy" ,emacs-ivy)
+         ("emacs-password-store" ,emacs-password-store)
+         ("password-store" ,password-store)))
+      (home-page "https://github.com/ecraven/ivy-pass")
+      (synopsis "Ivy interface for password store (pass)")
+      (description "This package provides an Ivy interface for working with
+the password store @code{pass}.")
+      (license license:gpl3))))
+
 (define-public emacs-ivy-yasnippet
   (let ((commit "32580b4fd23ebf9ca7dde96704f7d53df6e253cd")
         (revision "2"))
@@ -4455,7 +4588,7 @@ show icons as well.")
 (define-public emacs-avy
   (package
     (name "emacs-avy")
-    (version "0.4.0")
+    (version "0.5.0")
     (source
      (origin
        (method git-fetch)
@@ -4464,7 +4597,7 @@ show icons as well.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0rq9ab264565z83cly743nbhrd9m967apmnlhqr1gy8dm4hcy7nm"))))
+        (base32 "09qdni1s74i5pv8741szl5g4ynj8fxn0x65qmwa9rmfkbimnc0fs"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/abo-abo/avy")
     (synopsis "Tree-based completion for Emacs")
@@ -4554,20 +4687,18 @@ navigate code in a tree-like fashion.")
       (license license:gpl3+))))
 
 (define-public emacs-lispy
-  ;; Release 0.26.0 was almost 3 years ago, and there have been ~772 commits
-  ;; since.
-  (let ((commit "f94cfc6b8f9c3afe7d028c366928049c011023de")
-        (revision "1"))
   (package
     (name "emacs-lispy")
-      (version (git-version "0.26.0" revision commit))
+    (version "0.27.0")
     (home-page "https://github.com/abo-abo/lispy")
     (source (origin
               (method git-fetch)
-                (uri (git-reference (url home-page) (commit commit)))
+              (uri (git-reference
+                    (url "https://github.com/abo-abo/lispy")
+                    (commit version)))
               (sha256
                (base32
-                  "1bm2cpwizg1qfpm377gpx1af1hm5maw69if1csnk5vwaphmv8c4g"))
+                "1cm7f4pyl73f3vhkb7ah6bbbrj2sa7n0p31g09k7dy4zgx04bgw6"))
               (file-name (git-file-name name version))))
     (build-system emacs-build-system)
     (propagated-inputs
@@ -4584,7 +4715,7 @@ unprefixed printable characters can be used to call commands when the point is
 at one of these special locations.  Lispy provides unprefixed keybindings for
 S-expression editing when point is at the beginning or end of an
 S-expression.")
-      (license license:gpl3+))))
+    (license license:gpl3+)))
 
 (define-public emacs-lispyville
   (let ((commit "d28b937f0cabd8ce61e2020fe9a733ca80d82c74")
@@ -5554,7 +5685,7 @@ ack, ag, helm and pt.")
 (define-public emacs-helm
   (package
     (name "emacs-helm")
-    (version "3.1")
+    (version "3.2")
     (source
      (origin
        (method git-fetch)
@@ -5563,7 +5694,7 @@ ack, ag, helm and pt.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1x3nv8zvp8vvl30bm2d83hd7zxb0ca64pc8kwb81ml9al6r3mm01"))))
+        (base32 "12yyprpgh2by2pd41i4z9gz55fxg0f90x03bfrsf791xwbhf6931"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-async" ,emacs-async)
@@ -6915,7 +7046,7 @@ highlights quasi-quoted expressions.")
 (define-public emacspeak
   (package
     (name "emacspeak")
-    (version "49.0")
+    (version "50.0")
     (source
      (origin
        (method url-fetch)
@@ -6924,7 +7055,7 @@ highlights quasi-quoted expressions.")
              version "/emacspeak-" version ".tar.bz2"))
        (sha256
         (base32
-         "1smf26m7201z0bk49lzbw9zhbjfi6wylidfjixb8ylp6g0wnh8dx"))))
+         "0rsj7rzfyqmyidfsjrhjnxi2d43axx6r3gac1fhv5xkkbiiqzqkb"))))
     (build-system gnu-build-system)
     (arguments
      '(#:make-flags (list (string-append "prefix="
@@ -6932,13 +7063,10 @@ highlights quasi-quoted expressions.")
        #:phases
        (modify-phases %standard-phases
          (replace 'configure
-           (lambda* (#:key outputs #:allow-other-keys)
+           (lambda _
-             (let* ((out (assoc-ref outputs "out"))
-                    (lisp (string-append out
-                                         "/share/emacs/site-lisp/emacspeak")))
              (setenv "SHELL" (which "sh"))
              ;; Configure Emacspeak according to etc/install.org.
-               (invoke "make" "config"))))
+             (invoke "make" "config")))
          (add-after 'build 'build-espeak
            (lambda _
              (invoke "make" "espeak")))
@@ -6955,7 +7083,7 @@ highlights quasi-quoted expressions.")
                (for-each
                 (lambda (file)
                   (copy-recursively file (string-append lisp "/" file)))
-                '("etc" "info" "js" "lisp" "media" "scapes" "servers" "sounds"
+                '("etc" "info" "js" "lisp" "media" "servers" "sounds"
                   "stumpwm" "xsl"))
                ;; Make sure emacspeak is loaded from the correct directory.
                (substitute* "etc/emacspeak.sh"
@@ -7021,15 +7149,16 @@ actually changing the buffer's text.")
 (define-public emacs-diff-hl
   (package
     (name "emacs-diff-hl")
-  (version "1.8.5")
+    (version "1.8.6")
     (source
      (origin
-      (method url-fetch)
+       (method git-fetch)
-      (uri (string-append "https://elpa.gnu.org/packages/diff-hl-"
+       (uri (git-reference
-                          version ".tar"))
+             (url "https://github.com/dgutov/diff-hl")
+             (commit version)))
        (sha256
         (base32
-          "1vxc7z7c2qs0mx7l5sa4sybi5qbzv0s79flj74p1ynw8dl3qxg3d"))))
+         "1xlsg728mz3cwhrsqvisa0aidic67nymd9g7h4c1h3q63j39yb2s"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/dgutov/diff-hl")
     (synopsis
@@ -7994,6 +8123,30 @@ from within Emacs.  Restclient runs queries from a plan-text query sheet,
 displays results pretty-printed in XML or JSON with @code{restclient-mode}")
       (license license:public-domain))))
 
+(define-public emacs-whitespace-cleanup-mode
+  (let ((commit "72427144b054b0238a86e1348c45d986b8830d9d")
+        (revision "1"))
+    (package
+      (name "emacs-whitespace-cleanup-mode")
+      (version (git-version "0.10" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/purcell/whitespace-cleanup-mode")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1zlk534jbwrsabcg3kqlzk4h4hwya60lh6q2n1v4yn4rpf5ghsag"))
+                (file-name (git-file-name name version))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/purcell/whitespace-cleanup-mode")
+      (synopsis "Intelligently call @code{whitespace-cleanup} on save")
+      (description
+       "This package provides a minor mode that calls
+@code{whitespace-cleanup} before saving the current buffer only if the
+whitespace in the buffer was initially clean.")
+      (license license:gpl3+))))
+
 (define-public emacs-eimp
   (let ((version "1.4.0")
         (commit "2e7536fe6d8f7faf1bad7a8ae37faba0162c3b4f")
@@ -8225,6 +8378,56 @@ multiplexer.")
 editing RPM spec files.")
     (license license:gpl2+)))
 
+(define-public emacs-lcr
+  (package
+    (name "emacs-lcr")
+    (version "1.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/jyp/lcr")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0mc55icihxqpf8b05990q1lc2nj2792wcgyr73xsiqx0963sjaj8"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-dash" ,emacs-dash)))
+    (home-page "https://github.com/jyp/lcr")
+    (synopsis "Lightweight coroutines in Emacs Lisp")
+    (description "This package provides macros that can translate code into
+equivalent continuation-passing code, as well as miscellaneous utility
+functions written in continuation-passing style.")
+    (license license:gpl3+)))
+
+(define-public emacs-attrap
+  (let ((commit "3b092bb8f6755a97e6ecb7623b9d2dde58beba4a")
+        (revision "1"))
+    (package
+      (name "emacs-attrap")
+      (version (git-version "1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/jyp/attrap")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "05d32980saji8ja1pcv65l0s3dq7w0n5hpikbf246hciy1x067pp"))
+                (file-name (git-file-name name version))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-dash" ,emacs-dash)
+         ("emacs-f" ,emacs-f)
+         ("emacs-flycheck" ,emacs-flycheck)
+         ("emacs-s" ,emacs-s)))
+      (home-page "https://github.com/jyp/attrap")
+      (synopsis "Fix coding error at point")
+      (description "This package provides a command to fix the Flycheck error
+at point.")
+      (license license:gpl3+))))
+
 (define-public emacs-git-messenger
   (package
     (name "emacs-git-messenger")
@@ -8355,18 +8558,21 @@ key.  Optionally, a mouse pop-up can be added by binding
     (license license:gpl3+)))
 
 (define-public emacs-idris-mode
+  (let ((commit "acc8835449475d7cd205aba213fdd3d41c38ba40")
+        (revision "0"))
     (package
       (name "emacs-idris-mode")
-    (version "0.9.19")
+      (version (git-version "0.9.19" revision commit))
       (source
        (origin
-       (method url-fetch)
+         (method git-fetch)
-       (uri (string-append
+         (uri (git-reference
-             "http://stable.melpa.org/packages/idris-mode-"
+               (url "https://github.com/idris-hackers/idris-mode.git")
-             version ".tar"))
+               (commit commit)))
+         (file-name (git-file-name name commit))
          (sha256
           (base32
-         "16hl2s22l3wc9drnwzw6hn7xrm49ml9lii0s6k218dgahdgsncmf"))))
+           "0n9xbknc68id0mf8hbfmawi8qpvrs47ix807sk9ffv2g3ik32kk6"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-prop-menu" ,emacs-prop-menu)))
@@ -8377,7 +8583,7 @@ key.  Optionally, a mouse pop-up can be added by binding
        "This is an Emacs mode for editing Idris code.  It requires the latest
 version of Idris, and some features may rely on the latest Git version of
 Idris.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-browse-at-remote
   (package
@@ -9223,16 +9429,16 @@ functionality is inherited from @code{hcl-mode}.")
 (define-public emacs-exec-path-from-shell
   (package
     (name "emacs-exec-path-from-shell")
-    (version "1.11")
+    (version "1.12")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append
+       (uri (git-reference
-             "https://stable.melpa.org/packages/exec-path-from-shell-"
+             (url "https://github.com/purcell/exec-path-from-shell")
-             version ".el"))
+             (commit version)))
        (sha256
         (base32
-         "03qjgb81cq1l3j54lvlf98r75vmmgd06mj6qh5wa6mz4xzp4w26r"))))
+         "1ga8bpxngd3ph2hdiik92c612ki71qxw818i6rgx6f6a5r0sbf3p"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/purcell/exec-path-from-shell")
     (synopsis "Get environment variables such as @var{PATH} from the shell")
@@ -11752,7 +11958,7 @@ Emacs minor mode to escape sequences in code.")
 (define-public emacs-dashboard
   (package
     (name "emacs-dashboard")
-    (version "1.2.4")
+    (version "1.5.0")
     (source
      (origin
        (method git-fetch)
@@ -11761,11 +11967,22 @@ Emacs minor mode to escape sequences in code.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1hhh1kfsz87qfmh45wjf2r93rz79rq0vbyxlfrsl02092zjbl1zr"))))
+        (base32 "0ihpcagwgc9qy70lf2y3dvx2bm5h9lnqh4sx6643cr8pp06ysbvq"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-page-break-lines" ,emacs-page-break-lines)))
-    (arguments '(#:include '("\\.el$" "\\.txt$" "\\.png$")))
+    (arguments
+     '(#:include '("\\.el$" "\\.txt$" "\\.png$")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-dashboard-widgets
+           ;; This phase fixes compilation error.
+           (lambda _
+             (chmod "dashboard-widgets.el" #o666)
+             (emacs-substitute-variables "dashboard-widgets.el"
+               ("dashboard-init-info"
+                '(format "Loaded in %s" (emacs-init-time))))
+             #t)))))
     (home-page "https://github.com/rakanalh/emacs-dashboard")
     (synopsis "Startup screen extracted from Spacemacs")
     (description "This package provides an extensible Emacs dashboard, with
@@ -12467,16 +12684,17 @@ the GIF result.")
 (define-public emacs-google-translate
   (package
     (name "emacs-google-translate")
-    (version "0.11.16")
+    (version "0.11.17")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/atykhonov/google-translate/"
+       (uri (git-reference
-                           "archive/v" version ".tar.gz"))
+             (url "https://github.com/atykhonov/google-translate/")
-       (file-name (string-append name "-" version ".tar.gz"))
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "01n9spj1d0gjfj39x526rl3m9c28wnx9afipmf5s8y77cx3mfwhl"))))
+         "05ljjw7kbnszygw3w085kv57swfiiqxri2b5xvsf5dw3pc3g7j3c"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/atykhonov/google-translate")
     (synopsis "Emacs interface to Google Translate")
@@ -13405,7 +13623,7 @@ backends, including the @command{wordnet} offline backend.")
 (define-public emacs-editorconfig
   (package
     (name "emacs-editorconfig")
-    (version "0.7.14")
+    (version "0.8.0")
     (source
      (origin
        (method git-fetch)
@@ -13415,7 +13633,7 @@ backends, including the @command{wordnet} offline backend.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "19j2428ij7sqvrqs7rqg1mcnv9109y6drqba40dkv3vrkk5d2yia"))))
+         "1b2cpqz75pivl323bs60j5rszwi787x6vy68csycikqz9mhpmjn9"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/editorconfig/editorconfig-emacs")
     (synopsis "Define and maintain consistent coding styles between different
@@ -15346,7 +15564,7 @@ well as an option for visually flashing evaluated s-expressions.")
 (define-public emacs-counsel-tramp
   (package
     (name "emacs-counsel-tramp")
-    (version "0.6.2")
+    (version "0.6.3")
     (source
      (origin
        (method git-fetch)
@@ -15356,7 +15574,7 @@ well as an option for visually flashing evaluated s-expressions.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0nz0733x2b9b5nkwivvhv5c8747dng451na1sdfbkx5x9fjs5gc7"))))
+         "1qy9lf7cyv6hp9mmpwh92cpdcffbxzyzchx6878d5pmk9qh6xy92"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-ivy" ,emacs-ivy)))
@@ -15616,3 +15834,26 @@ verb commands which would are normally destructive (such as deletion) are
 provided.  Those alternative commands are and bound by default to their
 corresponding Evil keys.")
       (license license:expat))))
+
+(define-public emacs-xterm-color
+  (let ((commit "a452ab38a7cfae97078062ff8885b5d74fd1e5a6")
+        (version "1.8")
+        (revision "1"))
+    (package
+      (name "emacs-xterm-color")
+      (version (git-version version revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/atomontage/xterm-color.git")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "02kpajb993yshhjhsizpfcbrcndyzkf4dqfipifhxxng50dhp95i"))
+                (file-name (git-file-name name version))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/atomontage/xterm-color")
+      (synopsis "ANSI & xterm-256 color text property translator for Emacs")
+      (description "@code{xterm-color.el} is an ANSI control sequence to
+text-property translator.")
+      (license license:bsd-2))))

gnu/packages/emulators.scm

@@ -401,7 +401,7 @@ Super Game Boy, BS-X Satellaview, and Sufami Turbo.")
 (define-public mgba
   (package
     (name "mgba")
-    (version "0.7.1")
+    (version "0.7.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -410,7 +410,7 @@ Super Game Boy, BS-X Satellaview, and Sufami Turbo.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0q0yg2zna7gjbvpaswyykbg3lr9k3c8l8fydqa407xrgq77lahq4"))
+                "0g0xa1mzvan0sl1p5c784j2g5mcw9kd2b7wiahy06gy0c1nmbcnp"))
               (modules '((guix build utils)))
               (snippet
                ;; Make sure we don't use the bundled software.
@@ -1185,7 +1185,7 @@ play them on systems for which they were never designed!")
 (define-public mame
   (package
     (name "mame")
-    (version "0.209")
+    (version "0.210")
     (source
      (origin
        (method git-fetch)
@@ -1195,7 +1195,7 @@ play them on systems for which they were never designed!")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "08qvwmx8wbfkqxiccmcff86dsrlq6wjxf6blnhhrsbzic1ji99bh"))
+         "08c62mc8aajzh44q36qvmrcq404hdzh3i8wwdfnvn0c4w8dbf486"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled libraries.
@@ -1344,6 +1344,7 @@ play them on systems for which they were never designed!")
        ("fontconfig" ,fontconfig)
        ("glm" ,glm)
        ("libjpeg" ,libjpeg-8)    ;jpeg_read_header argument error in libjpeg-9
+       ("libxi" ,libxi)
        ("libxinerama" ,libxinerama)
        ("lua" ,lua)
        ("portaudio" ,portaudio)

gnu/packages/enlightenment.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2015 Daniel Pimentel <d4n1@member.fsf.org>
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 ng0 <ng0@n0.is>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Timo Eisenmann <eisenmann@fn.de>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -184,7 +184,7 @@ removable devices or support for multimedia.")
 (define-public terminology
   (package
     (name "terminology")
-    (version "1.4.0")
+    (version "1.4.1")
     (source (origin
               (method url-fetch)
               (uri
@@ -192,7 +192,7 @@ removable devices or support for multimedia.")
                               "terminology/terminology-" version ".tar.xz"))
               (sha256
                (base32
-                "0q1y7fadj42n23aspx9y8hm4w4xlc316wc3415wnf75ibsx08ngd"))
+                "0mm9v5a94369is3kaarnr3a28wy42wslzi1mcisaidlcldgv7f6p"))
               (modules '((guix build utils)))
               ;; Remove the bundled fonts.
               (snippet

gnu/packages/finance.scm

@@ -345,7 +345,7 @@ do so.")
 (define-public electrum
   (package
     (name "electrum")
-    (version "3.3.5")
+    (version "3.3.6")
     (source
      (origin
        (method url-fetch)
@@ -353,7 +353,7 @@ do so.")
                            version "/Electrum-"
                            version ".tar.gz"))
        (sha256
-        (base32 "1csj0n96zlajnrs39wsazfj5lmy7v7n77cdz56lr8nkmchh6k9z1"))
+        (base32 "0am5ki3z0yvhrz16vp2jjy5fkxxqph0mj9qqpbw3kpql65shykwz"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -742,14 +742,14 @@ Ledger Blue/Nano S.")
 (define-public python-trezor
   (package
     (name "python-trezor")
-    (version "0.11.2")
+    (version "0.11.3")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "trezor" version))
         (sha256
           (base32
-            "1f0zfki12mnhidkfxpx2lpq1xim8f35i2d64bx9lf4m26xxv9x56"))))
+            "0211m027vlvyqy83kwbjjjxalb04xgf1klv0h0y0f0yhj07516n7"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -770,12 +770,13 @@ Ledger Blue/Nano S.")
        ("python-requests" ,python-requests)
        ("python-typing-extensions" ,python-typing-extensions)))
     (native-inputs
-     `(("protobuf" ,protobuf) ; Tests
+     ;; For tests.
-       ("python-black" ,python-black) ; Tests
+     `(("protobuf" ,protobuf)
-       ("python-protobuf" ,python-protobuf) ; Tests
+       ("python-black" ,python-black)
-       ("python-isort" ,python-isort) ; Tests
+       ("python-protobuf" ,python-protobuf)
-       ("python-pyqt" ,python-pyqt) ; Tests
+       ("python-isort" ,python-isort)
-       ("python-pytest" ,python-pytest))) ; Tests
+       ("python-pyqt" ,python-pyqt)
+       ("python-pytest" ,python-pytest)))
     (home-page "https://github.com/trezor/python-trezor")
     (synopsis "Python library for communicating with TREZOR Hardware Wallet")
     (description "@code{trezor} is a Python library for communicating with

gnu/packages/fonts.scm

@@ -616,15 +616,17 @@ languages, plus Greek and Cyrillic.")
 (define-public font-gnu-unifont
   (package
     (name "font-gnu-unifont")
-    (version "12.0.01")
+    (version "12.1.02")
-    (source (origin
+    (source
+     (origin
        (method url-fetch)
-              (uri (string-append
+       (uri (list
-                    "mirror://gnu/unifont/unifont-" version "/unifont-"
+             (string-append "http://unifoundry.com/pub/unifont/unifont-"
-                    version ".tar.gz"))
+                            version "/unifont-" version ".tar.gz")
+             (string-append "mirror://gnu/unifont/unifont-"
+                            version "/unifont-" version ".tar.gz")))
        (sha256
-               (base32
+        (base32 "12wdxnlyz5gl5d7h6pazcz8d7h81fwkng1xrayxsgrzh6bqdq4p8"))))
-                "059j82z6z4wqyy3261ns0zg2b2vh2wvxxfbsa9hra9xasism49vb"))))
     (build-system gnu-build-system)
     (outputs '("out"   ; TrueType version
                "pcf"   ; PCF (bitmap) version

gnu/packages/fpga.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Danny Milosavljevic <dannym@scratchpost.org>
 ;;; Copyright © 2016, 2017 Theodoros Foradis <theodoros@foradis.org>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Amin Bandali <bandali@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -301,14 +301,14 @@ Includes the actual FTDI connector.")
 (define-public gtkwave
   (package
     (name "gtkwave")
-    (version "3.3.100")
+    (version "3.3.101")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://gtkwave.sourceforge.net/"
                                   "gtkwave-" version ".tar.gz"))
               (sha256
                (base32
-                "1z60i5nh8dz8j9ii63fwaw7k0p3x0scp91478cxmdv4xhp4njlxa"))))
+                "1j6capxwgi8aj3sgqg1r7161icni9y8y93g1rl3bzd3s40jcyhsz"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("gperf" ,gperf)

gnu/packages/game-development.scm

@@ -435,7 +435,7 @@ support.")
 (define-public tiled
   (package
     (name "tiled")
-    (version "1.2.3")
+    (version "1.2.4")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -444,7 +444,7 @@ support.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1nfyigfkl10n9r82p1qxhpr09jn2kwalh9n5r209bcaj8dxspph8"))))
+                "04v738h298pvcwb70mwd1r2yj7578f6gkfzs0165j9fqy7avwm18"))))
     (build-system gnu-build-system)
     (inputs
      `(("qtbase" ,qtbase)
@@ -465,7 +465,7 @@ support.")
              (let ((out (assoc-ref outputs "out")))
                (invoke "qmake"
                        (string-append "PREFIX=" out))))))))
-    (home-page "http://www.mapeditor.org/")
+    (home-page "https://www.mapeditor.org/")
     (synopsis "Tile map editor")
     (description
      "Tiled is a general purpose tile map editor.  It is meant to be used for
@@ -684,17 +684,15 @@ etc.")
 (define-public allegro
   (package
     (name "allegro")
-    (version "5.2.4.0")
+    (version "5.2.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/liballeg/allegro5/releases"
                                   "/download/" version "/allegro-"
                                   version ".tar.gz"))
-              (patches (search-patches
-                        "allegro-mesa-18.2.5-and-later.patch"))
               (sha256
                (base32
-                "1w9a5yqi5q03b2qvmx5ff90paz0xbr9cy7i7f0xiqa65ava66q9l"))))
+                "06dpkfnac8w3pq36834nn2iij3ajz6prladqd0w92lq39aiqv5jr"))))
     (build-system cmake-build-system)
     (arguments `(#:tests? #f))          ; there are no tests
     (inputs
@@ -1321,24 +1319,15 @@ a 2D editor view.")
 (define-public guile-chickadee
   (package
     (name "guile-chickadee")
-    (version "0.3.0")
+    (version "0.4.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://files.dthompson.us/chickadee/"
                                   "chickadee-" version ".tar.gz"))
               (sha256
                (base32
-                "0jl223dybsj5gvs7z4q60gnafj1b7kgi5mx0kj58m5knrp8qwg5h"))))
+                "1fdicsgls5cp0yffcm5vjmav67gv9bxhz1s3jvdvinspxb485x7l"))))
     (build-system gnu-build-system)
-    (arguments
-     '(#:make-flags '("GUILE_AUTO_COMPILE=0")
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'configure 'patch-godir
-           (lambda _
-             ;; Install compiled '.go' files into the site directory.
-             (substitute* "Makefile.in"
-               (("/ccache") "/site-ccache")))))))
     (propagated-inputs
      `(("guile-opengl" ,guile-opengl)
        ("guile-sdl2" ,guile-sdl2)))
@@ -1521,5 +1510,4 @@ the original, ioquake3 has been cleaned up, bugs have been fixed and features
 added.  The permanent goal is to create the open source Quake 3 distribution
 upon which people base their games, ports to new platforms, and other
 projects.")
-      (supported-systems '("x86_64-linux" "i686-linux"))
       (license license:gpl2))))

gnu/packages/games.scm

@@ -40,6 +40,7 @@
 ;;; Copyright © 2019 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
 ;;; Copyright © 2019 Julien Lepiller <julien@lepiller.eu>
+;;; Copyright © 2019 Jesse Gibbons <jgibbons2357+guix@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -141,6 +142,7 @@
   #:use-module (gnu packages sdl)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sqlite)
+  #:use-module (gnu packages squirrel)
   #:use-module (gnu packages swig)
   #:use-module (gnu packages tcl)
   #:use-module (gnu packages terminals)
@@ -3490,19 +3492,36 @@ with the \"Stamp\" tool within Tux Paint.")
 (define-public supertux
   (package
    (name "supertux")
-   (version "0.5.1")
+   (version "0.6.0")
    (source (origin
             (method url-fetch)
             (uri (string-append "https://github.com/SuperTux/supertux/"
                                 "releases/download/v" version "/SuperTux-v"
                                 version "-Source.tar.gz"))
+            (file-name (string-append name "-" version ".tar.gz"))
             (sha256
              (base32
-              "1i8avad7w7ikj870z519j383ldy29r6f956bs38cbr8wk513pp69"))))
+              "1h1s4abirkdv4ag22zvyk6zkk64skqbjmcnnba67ps4hdzxfbhy4"))
+            (patches
+             (search-patches "supertux-fix-build-with-gcc5.patch"
+                             "supertux-unbundle-squirrel.patch"))))
    (arguments
     '(#:tests? #f
       #:configure-flags '("-DINSTALL_SUBDIR_BIN=bin"
-                          "-DENABLE_BOOST_STATIC_LIBS=OFF")))
+                          "-DENABLE_BOOST_STATIC_LIBS=OFF"
+                          "-DUSE_SYSTEM_PHYSFS=ON")
+      #:phases
+      (modify-phases %standard-phases
+        (add-after 'unpack 'patch-squirrel-path
+          (lambda* (#:key inputs #:allow-other-keys)
+            (let ((squirrel (assoc-ref inputs "squirrel")))
+              (substitute* "CMakeLists.txt"
+                (("set\\(SQUIRREL_PREFIX.*")
+                 (string-append "set(SQUIRREL_PREFIX " squirrel ")"))
+                (("add_dependencies\\(supertux2_lib squirrel\\)") "")
+                (("\\$\\{SQUIRREL_PREFIX\\}/include")
+                 (string-append "${SQUIRREL_PREFIX}/include/squirrel"))))
+            #t)))))
    (build-system cmake-build-system)
    (inputs `(("sdl2" ,sdl2)
              ("sdl2-image" ,sdl2-image)
@@ -3514,7 +3533,9 @@ with the \"Stamp\" tool within Tux Paint.")
              ("libogg" ,libogg)
              ("physfs" ,physfs)
              ("curl" ,curl)
-             ("boost" ,boost)))
+             ("boost" ,boost)
+             ("freetype" ,freetype)
+             ("squirrel" ,squirrel)))
    (native-inputs `(("pkg-config" ,pkg-config)))
    (synopsis "2D platformer game")
    (description "SuperTux is a free classic 2D jump'n run sidescroller game
@@ -7312,3 +7333,51 @@ Unfortunately, Hacker is not aware of Drascula's real ambitions: DOMINATING
 the World and demonstrating that he is even more evil than his brother Vlad.")
     ;; Drascula uses a BSD-like license.
     (license (license:non-copyleft "file:///readme.txt"))))
+
+(define-public gnurobots
+  (package
+    (name "gnurobots")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://gnu/gnurobots/gnurobots-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "07gi3lsmbzzsjambgixj6xy79lh22km84z7bnzgwzxdy806lyvwb"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("glib" ,glib)
+       ("gtk+" ,gtk+-2)
+       ("vte" ,vte/gtk+-2)
+       ("readline" ,readline)
+       ("guile" ,guile-1.8)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (arguments
+     `(#:make-flags
+       (list
+        ;; Do not abort build on "deprecated-declarations" warnings.
+        "CFLAGS=-Wno-error=deprecated-declarations"
+        ;; Find readline headers in sub-directory.
+        (string-append "READLINE_CFLAGS=-I"
+                       (assoc-ref %build-inputs "readline")
+                       "/include/readline/"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'install-doc
+           (lambda* (#:key outputs #:allow-other-keys)
+             (install-file "doc/Robots-HOWTO"
+                           (string-append (assoc-ref outputs "out")
+                                          "/share/doc/gnurobots-"
+                                          ,version))
+             #t)))))
+    (home-page "https://www.gnu.org/software/gnurobots/")
+    (synopsis "Program a little robot and watch it explore a world")
+    (description
+     "GNU Robots is a game in which you program a robot to explore a world
+full of enemies that can hurt it, obstacles and food to be eaten.  The goal of
+the game is to stay alive and collect prizes.  The robot program conveniently
+may be written in a plain text file in the Scheme programming language.")
+    (license license:gpl3+)))

gnu/packages/geo.scm

@@ -7,6 +7,7 @@
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
+;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -36,6 +37,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix utils)
+  #:use-module (gnu packages autotools)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
@@ -840,3 +842,30 @@ map, geocoding with Nominatim, or general analysis.")
 the texture and density of features is visible at every zoom level, instead of
 dropping features at lower levels.")
     (license license:bsd-2)))
+
+(define-public osmctools
+  (package
+    (name "osmctools")
+    (version "0.9")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/osm-c-tools/osmctools")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1m8d3r1q1v05pkr8k9czrmb4xjszw6hvgsf3kn9pf0v14gpn4r8f"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)))
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://gitlab.com/osm-c-tools/osmctools")
+    (synopsis "Tools to convert, filter and update OpenStreetMap data files")
+    (description "This project contains a few tools which are used in the
+OpenStreetMap project.  They can be used to convert, filter and update
+OpenStreetMap data files.")
+    (license license:agpl3)))

gnu/packages/gettext.scm

@@ -176,14 +176,14 @@ color, font attributes (weight, posture), or underlining.")
 (define-public po4a
   (package
     (name "po4a")
-    (version "0.55")
+    (version "0.56")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/mquinson/po4a/releases/download/v"
                                   version "/po4a-" version ".tar.gz"))
               (sha256
                (base32
-                "1qss4q5df3nsydsbggb7gg50bn0kdxq5wn8riqm9zwkiq6a4bifg"))))
+                "0kyhww0yw4q0m4vj8vil2wsf6sn4hidh8mqz2gjrq7gpdf83cmnr"))))
     (build-system perl-build-system)
     (arguments
      `(#:phases

gnu/packages/gimp.scm

@@ -49,7 +49,7 @@
 (define-public babl
   (package
     (name "babl")
-    (version "0.1.62")
+    (version "0.1.66")
     (source (origin
               (method url-fetch)
               (uri (list (string-append "https://download.gimp.org/pub/babl/"
@@ -63,7 +63,7 @@
                                         "/babl-" version ".tar.bz2")))
               (sha256
                (base32
-                "047msfzj8v4sfl61a2xhd69r9rh2pjq4lzpk3j10ijyv9qbry9yw"))))
+                "0qx1dwbinxihwl2lmxi60qiqi402jlrdcnixx14kk6j88n9xi79n"))))
     (build-system gnu-build-system)
     (home-page "http://gegl.org/babl/")
     (synopsis "Image pixel format conversion library")
@@ -118,7 +118,7 @@ buffers.")
 (define-public gimp
   (package
     (name "gimp")
-    (version "2.10.10")
+    (version "2.10.12")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://download.gimp.org/pub/gimp/v"
@@ -126,7 +126,7 @@ buffers.")
                                   "/gimp-" version ".tar.bz2"))
               (sha256
                (base32
-                "0xwck5nbpb945s1cyij3kfqw1pchbhx8i5vf5hgywyjw4r1z5l8j"))))
+                "0wdcr8d2ink4swn5r4v13bsiya6s3xm4ya97sdbhs4l40y7bb03x"))))
     (build-system gnu-build-system)
     (outputs '("out"
                "doc"))                            ; 9 MiB of gtk-doc HTML

gnu/packages/gl.scm

@@ -447,7 +447,7 @@ from software emulation to complete hardware acceleration for modern GPUs.")
                '("src/xdemos/glxdemo" "src/xdemos/glxgears"
                  "src/xdemos/glxinfo" "src/xdemos/glxheads"))
               #t))))))
-    (home-page "http://mesa3d.org/")
+    (home-page "https://mesa3d.org/")
     (synopsis "Utility tools for Mesa")
     (description
      "The mesa-utils package contains several utility tools for Mesa: glxdemo,
@@ -619,7 +619,7 @@ OpenGL graphics API.")
      `(("unzip" ,unzip)))
     (inputs
      `(("mesa" ,mesa)))
-    (home-page "http://www.lonesock.net/soil.html")
+    (home-page "https://www.lonesock.net/soil.html")
     (synopsis "OpenGL texture loading library")
     (description
      "SOIL is a tiny C library used primarily for uploading textures into
@@ -724,7 +724,7 @@ mixed vector/bitmap output.")
 (define-public virtualgl
   (package
     (name "virtualgl")
-    (version "2.6.1")
+    (version "2.6.2")
     (source
      (origin
        (method git-fetch)
@@ -733,7 +733,7 @@ mixed vector/bitmap output.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "04fdwm6mz76lw4iwd5m7yxjfhpa0rpxd357bv5smk5lclnlbz1bv"))))
+        (base32 "0yyc553xsb5n0rx7jp9p4wdbd7md07b3qrkf3ssyjavqqg908qg9"))))
     (arguments
      `(#:tests? #f                      ; no tests are available
        #:configure-flags (list

gnu/packages/gnome.scm

@@ -162,6 +162,7 @@
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (guix download)
   #:use-module (guix git-download)
@@ -2114,7 +2115,7 @@ Hints specification (EWMH).")
 (define-public gnumeric
   (package
     (name "gnumeric")
-    (version "1.12.44")
+    (version "1.12.45")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/gnumeric/"
@@ -2122,7 +2123,7 @@ Hints specification (EWMH).")
                                   "gnumeric-" version ".tar.xz"))
               (sha256
                (base32
-                "0147962c6ybdsj57rz95nla0rls7g545wc2n7pz59zmzyd5pksk0"))))
+                "0c8dl1kvnj3g32qy3s92qpqpqfy0in59cx005gjvvzsflahav61h"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      `(;; The gnumeric developers don't worry much about failing tests.
@@ -3940,26 +3941,15 @@ which can read a large number of file formats.")
 (define-public rhythmbox
  (package
    (name "rhythmbox")
-   (version "3.4.2")
+   (version "3.4.3")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnome/sources/" name "/"
                                 (version-major+minor version) "/"
                                 name "-" version ".tar.xz"))
-            (patches
-             (list
-              ;; fmradio: Fix build with GStreamer master
-              (origin
-                (method url-fetch)
-                (uri (string-append
-                      "https://gitlab.gnome.org/GNOME/rhythmbox/commit/"
-                      "b182c6b9e1d09e601bac0b703cc5f8b159ebbc3a.patch"))
             (sha256
              (base32
-                  "06n87xgf927djmv1vshal84nqx7g8nwgljza3g2vydhy7g2n1csq")))))
+              "1yx3n7p9vmv23jsv98fxwq95n78awdxqm8idhyhxx2d6vk4w1hgx"))))
-            (sha256
-             (base32
-              "0hzcns8gf5yb0rm4ss8jd8qzarcaplp5cylk6plwilsqfvxj4xn2"))))
    (build-system glib-or-gtk-build-system)
    (arguments
     `(#:configure-flags
@@ -4319,15 +4309,15 @@ work and the interface is well tested.")
 (define-public eolie
   (package
     (name "eolie")
-    (version "0.9.60")
+    (version "0.9.62")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gitlab.gnome.org/World/eolie/"
-                                  "uploads/3b2ceb7eb15860587db6886bfdd8a91e/"
+                                  "uploads/bb4aad19272cc636bd17f2f6602127fe/"
                                   "eolie-" version ".tar.xz"))
               (sha256
                (base32
-                "1s9gkzxa6457v6bh0q8n1ijq1chd2jwgvhk5kppsnya7kxvsx8qh"))))
+                "06v76hg87fnhw45dil5vvl20myvaa38n1jqsl0lmkkq6af4mk8wx"))))
     (build-system meson-build-system)
     (arguments
      `(#:glib-or-gtk? #t
@@ -4441,7 +4431,7 @@ principles are simplicity and standards compliance.")
 (define-public d-feet
   (package
     (name "d-feet")
-    (version "0.3.11")
+    (version "0.3.14")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -4449,7 +4439,7 @@ principles are simplicity and standards compliance.")
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1hmrijm4d9vwzx2r8qzzsy8ccpj79l1y6cc569n9jjzqcq699p53"))))
+                "1m8lwiwl5jhi0x7y6x5zmd3hjplgvdjrb8a8jg74rvkygslj1p7f"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      '(#:out-of-source? #f ; tests need to run in the source directory.
@@ -4488,6 +4478,7 @@ principles are simplicity and standards compliance.")
      `(("gobject-introspection" ,gobject-introspection)
        ("gtk+" ,gtk+)
        ("python" ,python-wrapper)
+       ("hicolor-icon-theme" ,hicolor-icon-theme)
        ("python-pygobject" ,python-pygobject)))
     (home-page "https://wiki.gnome.org/Apps/DFeet")
     (synopsis "D-Bus debugger")
@@ -5473,7 +5464,7 @@ to virtual private networks (VPNs) via OpenVPN.")
 (define-public mobile-broadband-provider-info
   (package
     (name "mobile-broadband-provider-info")
-    (version "20170310")
+    (version "20190116")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -5482,10 +5473,10 @@ to virtual private networks (VPNs) via OpenVPN.")
                     "mobile-broadband-provider-info-" version ".tar.xz"))
               (sha256
                (base32
-                "0fxm11x8k9hxjg8l5inaldfmmjnwkay3ibjv899jra03bv4h6kql"))))
+                "16y5lc7pfdvai9c8xwb825zc3v46039gghbip13fqslf5gw11fic"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f)) ; No tests
+     `(#:tests? #f))                    ; no tests
     (home-page "https://wiki.gnome.org/Projects/NetworkManager")
     (synopsis "Database of broadband connection configuration")
     (description "Database of broadband connection configuration.")
@@ -5876,6 +5867,9 @@ devices using the GNOME desktop.")
                  (("\"nm-connection-editor")
                   (string-append "\"" nm-applet
                                  "/bin/nm-connection-editor")))
+               (substitute* '("panels/user-accounts/run-passwd.c")
+                 (("/usr/bin/passwd")
+                  "/run/setuid-programs/passwd"))
                #t))))))
     (native-inputs
      `(("glib:bin" ,glib "bin") ; for glib-mkenums, etc.
@@ -7970,3 +7964,95 @@ functionality.")
     (license (list license:lgpl2.1 license:lgpl3 ; either one of these
                    license:openldap2.8 ; addressbook/gui/component/openldap-extract.h
                    license:lgpl2.1+))))  ; smime/lib/*
+
+(define-public gthumb
+  (package
+    (name "gthumb")
+    (version "3.8.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://gnome/sources/gthumb/"
+                                  (version-major+minor version) "/"
+                                  "gthumb-" version ".tar.xz"))
+              (sha256
+               (base32
+                "1l2s1facq1r6yvqjqc34aqfzlvb3nhkhn79xisxbbdlgrrxdq52f"))))
+    (build-system meson-build-system)
+    (arguments
+     `(#:glib-or-gtk? #t
+       #:configure-flags
+       ;; Ensure the RUNPATH contains all installed library locations.
+       (list (string-append "-Dc_link_args=-Wl,-rpath="
+                            (assoc-ref %outputs "out")
+                            "/lib/gthumb/extensions")
+             (string-append "-Dcpp_link_args=-Wl,-rpath="
+                            (assoc-ref %outputs "out")
+                            "/lib/gthumb/extensions"))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("glib:bin" ,glib "bin")                   ; for glib-compile-resources
+       ("gtk+:bin" ,gtk+ "bin")                   ; for gtk-update-icon-cache
+       ("desktop-file-utils" ,desktop-file-utils) ; for update-desktop-database
+       ("intltool" ,intltool)
+       ("itstool" ,itstool)))
+    (inputs
+     `(("exiv2" ,exiv2)
+       ("gtk" ,gtk+)
+       ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
+       ("gstreamer" ,gstreamer)
+       ("clutter" ,clutter)
+       ("clutter-gst" ,clutter-gst)
+       ("clutter-gtk" ,clutter-gtk)
+       ("libjpeg" ,libjpeg)
+       ("libtiff" ,libtiff)
+       ("libraw" ,libraw)))
+    (home-page "https://wiki.gnome.org/Apps/Gthumb")
+    (synopsis "GNOME image viewer and browser")
+    (description "GThumb is an image viewer, browser, organizer, editor and
+advanced image management tool")
+    (license license:gpl2+)))
+
+(define-public terminator
+  (package
+    (name "terminator")
+    (version "1.91")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://launchpad.net/" name "/"
+                                  "gtk3/" version "/" "+download/"
+                                  name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0sdyqwydmdnh7j6mn74vrywz35m416kqsbxbrqcnv5ak08y6xxwm"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("intltool" ,intltool)
+       ("glib:bin" ,glib "bin")                   ; for glib-compile-resources
+       ("gettext" ,gettext-minimal)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("cairo" ,cairo)
+       ("gobject-introspection" ,gobject-introspection)
+       ("python2-pycairo" ,python2-pycairo)
+       ("python2-pygobject" ,python2-pygobject)
+       ("python2-psutil" ,python2-psutil)
+       ("vte" ,vte)))
+    (arguments
+     `(#:python ,python-2                          ;Python 3 not supported
+       #:phases
+       (modify-phases %standard-phases
+         (add-after
+          'install 'wrap-program
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let ((prog (string-append (assoc-ref outputs "out")
+                                       "/bin/terminator")))
+              (wrap-program prog
+                `("PYTHONPATH" = (,(getenv "PYTHONPATH")))
+                `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH"))))
+              #t))))))
+    (home-page "https://gnometerminator.blogspot.com/")
+    (synopsis "Store and run multiple GNOME terminals in one window")
+    (description
+     "Terminator allows you to run multiple GNOME terminals in a grid and
++tabs, and it supports drag and drop re-ordering of terminals.")
+    (license license:gpl2)))

gnu/packages/gnucash.scm

@@ -54,7 +54,7 @@
   ;; directory.
   (package
     (name "gnucash")
-    (version "3.4")
+    (version "3.5")
     (source
      (origin
        (method url-fetch)
@@ -62,8 +62,7 @@
                            version "/gnucash-" version ".tar.bz2"))
        (sha256
         (base32
-         "1ms2wg4sh5gq3rpjmmnp85rh5nc9ahca1imxkvhz4d3yiwy8hm52"))
+         "0ibp7g6aknvnkwkin97kv04ipksy3l18dsz9qysjb7h2nr8hnvbp"))))
-       (patches (search-patches "gnucash-fix-test-transaction-failure.patch"))))
     (build-system cmake-build-system)
     (inputs
      `(("guile" ,guile-2.2)
@@ -197,7 +196,7 @@ installed as well as Yelp, the Gnome help browser.")
 ;; This package is not public, since we use it to build the "doc" output of
 ;; the gnucash package (see above).  It would be confusing if it were public.
 (define gnucash-docs
-  (let ((revision "a"))              ;set to the empty string when no revision
+  (let ((revision ""))              ;set to the empty string when no revision
     (package
       (name "gnucash-docs")
       (version (package-version gnucash))
@@ -208,7 +207,7 @@ installed as well as Yelp, the Gnome help browser.")
                              version "/gnucash-docs-" version revision ".tar.gz"))
          (sha256
           (base32
-           "0bgjxpxgk7hy8ihn1kvd8p6vv191q5md2hz6jb9mqc4aykpvdlq7"))))
+           "0gjndyms413vilf5nqh39frs1691sxib8l7y9mbvcyirj1f8285k"))))
       (build-system gnu-build-system)
       ;; These are native-inputs because they are only required for building the
       ;; documentation.

gnu/packages/gnupg.scm

@@ -232,14 +232,14 @@ compatible to GNU Pth.")
 (define-public gnupg
   (package
     (name "gnupg")
-    (version "2.2.15")
+    (version "2.2.16")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnupg/gnupg/gnupg-" version
                                   ".tar.bz2"))
               (sha256
                (base32
-                "0m6lyphbb20i84isdxzfhcbzyc682hdrdv4aqkzmhrdksycf536b"))))
+                "1jqlzp9b3kpfp1dkjqskm67jjrhvf9nh3lzf45321p7m9d2qvgkc"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))

gnu/packages/gnuzilla.scm

@@ -426,7 +426,7 @@ from forcing GEXP-PROMISE."
                       #:system system
                       #:guile-for-build guile)))
 
-(define %icecat-version "60.7.0-guix1")
+(define %icecat-version "60.7.0-guix2")
 
 ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball
 ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat'
@@ -450,7 +450,7 @@ from forcing GEXP-PROMISE."
              (base32
               "08x0nijh0ja5jza95a8y030ibk756bn7zlw3a3c4750yilfhqpqa"))))
 
-         (upstream-icecat-base-version "60.3.0") ; maybe older than base-version
+         (upstream-icecat-base-version "60.7.0") ; maybe older than base-version
          (upstream-icecat-gnu-version "1")
          (upstream-icecat-version (string-append upstream-icecat-base-version
                                                  "-gnu"
@@ -463,7 +463,7 @@ from forcing GEXP-PROMISE."
                   "/icecat-" upstream-icecat-version ".tar.bz2"))
             (sha256
              (base32
-              "0icnl64nxcyf7dprpdpygxhabsvyhps8c3ixysj9bcdlj9q34ib1"))))
+              "09xqdfd8rwbn2n6m7n059qf1psbrj5v5kfzm7gg5xng22ddxawv8"))))
 
          (gnuzilla-commit (string-append "v" upstream-icecat-base-version))
          (gnuzilla-source
@@ -475,7 +475,7 @@ from forcing GEXP-PROMISE."
             (file-name (git-file-name "gnuzilla" upstream-icecat-base-version))
             (sha256
              (base32
-              "19wal7hkbb4wvk40hs6d7a5paal2bfday08hwssm02srcbv48fj0"))))
+              "1vqhb0py28hnwcynbaad304ziciz1kn5bv1qg2q4f7g13js3b1hf"))))
 
          (makeicecat-patch
           (local-file (search-patch "icecat-makeicecat.patch"))))
@@ -545,10 +545,6 @@ from forcing GEXP-PROMISE."
                                     #$upstream-icecat-gnu-version "\n"))
                     (("^DATA=.*")
                      "DATA=/tmp/gnuzilla/data\n")
-                    (("^sed .* debian/" all)
-                     (string-append "echo warning: skipped: " all))
-                    (("^debian/rules " all)
-                     (string-append "echo warning: skipped: " all))
                     (("^find extensions/gnu/ ")
                      "find extensions/gnu/ | sort ")
                     (("/bin/sed")
@@ -560,21 +556,19 @@ from forcing GEXP-PROMISE."
                 (rename-file firefox-dir icecat-dir)
 
                 (with-directory-excursion icecat-dir
-                  (for-each mkdir-p '("l10n" "debian/config"))
+                  (mkdir "l10n")
-                  (call-with-output-file "debian/control" (const #t))
                   (format #t "Running makeicecat script...~%")
                   (force-output)
                   (invoke "bash" "/tmp/gnuzilla/makeicecat")
-                  (for-each delete-file-recursively '("l10n" "debian")))
+                  (delete-file-recursively "l10n"))
 
-                (format #t (string-append "Unpacking l10n/* and debian/* from"
+                (format #t (string-append "Unpacking l10n/* from"
                                           " upstream IceCat tarball...~%"))
                 (force-output)
                 (unless (string=? icecat-dir old-icecat-dir)
                   (symlink icecat-dir old-icecat-dir))
                 (invoke "tar" "xf" #+upstream-icecat-source
-                        (string-append old-icecat-dir "/l10n")
+                        (string-append old-icecat-dir "/l10n"))
-                        (string-append old-icecat-dir "/debian"))
 
                 (format #t "Packing new IceCat tarball...~%")
                 (force-output)
@@ -899,43 +893,16 @@ from forcing GEXP-PROMISE."
          (add-before 'configure 'install-desktop-entry
            (lambda* (#:key outputs #:allow-other-keys)
              ;; Install the '.desktop' file.
-             (define (swallow-%%-directives input output)
+             (let* ((desktop-file "taskcluster/docker/icecat-snap/icecat.desktop")
-               ;; Interpret '%%ifdef' directives found in the '.desktop' file.
+                    (out          (assoc-ref outputs "out"))
-               (let loop ((state 'top))
-                 (match (read-line input 'concat)
-                   ((? eof-object?)
-                    #t)
-                   ((? string? line)
-                    (cond ((string-prefix? "%%ifdef" line)
-                           (loop 'ifdef))
-                          ((string-prefix? "%%else" line)
-                           (loop 'else))
-                          ((string-prefix? "%%endif" line)
-                           (loop 'top))
-                          (else
-                           (case state
-                             ((top else)
-                              (display line output)
-                              (loop state))
-                             (else
-                              (loop state)))))))))
-
-             (let* ((out (assoc-ref outputs "out"))
                     (applications (string-append out "/share/applications")))
-               (call-with-input-file "debian/icecat.desktop.in"
+               (substitute* desktop-file
-                 (lambda (input)
+                 (("^Exec=icecat")     (string-append "Exec=" out "/bin/icecat"))
-                   (call-with-output-file "debian/icecat.desktop"
+                 (("IceCat")           "GNU IceCat")
-                     (lambda (output)
+                 (("Icon=.*")          "Icon=icecat\n")
-                       (swallow-%%-directives input output)))))
+                 (("NewWindow")        "new-window")
-
+                 (("NewPrivateWindow") "new-private-window"))
-               (substitute* "debian/icecat.desktop"
+               (install-file desktop-file applications)
-                 (("@MOZ_DISPLAY_NAME@")
-                  "GNU IceCat")
-                 (("^Exec=@MOZ_APP_NAME@")
-                  (string-append "Exec=" out "/bin/icecat"))
-                 (("@MOZ_APP_NAME@")
-                  "icecat"))
-               (install-file "debian/icecat.desktop" applications)
                #t)))
          (add-after 'install-desktop-entry 'install-icons
            (lambda* (#:key outputs #:allow-other-keys)

gnu/packages/golang.scm

@@ -14,6 +14,7 @@
 ;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright @ 2018, 2019 Katherine Cox-Buday <cox.katherine.e@gmail.com>
 ;;; Copyright @ 2019 Giovanni Biscuolo <g@xelera.eu>
+;;; Copyright @ 2019 Alex Griffin <a@ajgrf.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -61,14 +62,16 @@
 (define-public go-1.4
   (package
     (name "go")
-    (version "1.4.3")
+    ;; The C-language bootstrap of Go:
+    ;; https://golang.org/doc/install/source#go14
+    (version "1.4-bootstrap-20171003")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://storage.googleapis.com/golang/"
-                                  name version ".src.tar.gz"))
+                                  name version ".tar.gz"))
               (sha256
                (base32
-                "0na9yqilzpvq0bjndbibfp07wr796gf252y471cip10bbdqgqiwr"))))
+                "0liybk5z00hizsb5ypkbhqcawnwwa6mkwgvjjg4y3jm3ndg5pzzl"))))
     (build-system gnu-build-system)
     (outputs '("out"
                "doc"
@@ -135,13 +138,6 @@
                   ("os/os_test.go" "(.+)(TestHostname.+)")
                   ("time/format_test.go" "(.+)(TestParseInSydney.+)")
 
-                  ;; Tzdata 2016g changed the name of the time zone used in this
-                  ;; test, and the patch for Go 1.7 does not work for 1.4.3:
-                  ;; https://github.com/golang/go/issues/17545
-                  ;; https://github.com/golang/go/issues/17276
-                  ("time/time_test.go" "(.+)(TestLoadFixed.+)")
-                  ("time/format_test.go" "(.+)(TestParseInLocation.+)")
-
                   ("os/exec/exec_test.go" "(.+)(TestEcho.+)")
                   ("os/exec/exec_test.go" "(.+)(TestCommandRelativeName.+)")
                   ("os/exec/exec_test.go" "(.+)(TestCatStdin.+)")
@@ -168,9 +164,7 @@
                (setenv "GOOS" "linux")
                (setenv "GOROOT" (dirname (getcwd)))
                (setenv "GOROOT_FINAL" output)
-               ;; Go 1.4's cgo will not work with binutils >= 2.27:
+               (setenv "GO14TESTS" "1")
-               ;; https://github.com/golang/go/issues/16906
-               (setenv "CGO_ENABLED" "0")
                (invoke "sh" "all.bash"))))
 
          (replace 'install
@@ -1920,7 +1914,7 @@ values.")
 (define-public go-github-com-mattn-go-isatty
   (package
     (name "go-github-com-mattn-go-isatty")
-    (version "0.0.4")
+    (version "0.0.7")
     (source
      (origin
        (method git-fetch)
@@ -1930,8 +1924,10 @@ values.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0zs92j2cqaw9j8qx1sdxpv3ap0rgbs0vrvi72m40mg8aa36gd39w"))))
+         "1i77aq4gf9as03m8fpfh8fq49n4z9j7548blrcsidm1xhslzk5xd"))))
     (build-system go-build-system)
+    (propagated-inputs
+     `(("go-golang-org-x-sys-unix" ,go-golang-org-x-sys-unix)))
     (arguments
      '(#:import-path "github.com/mattn/go-isatty"))
     (home-page "https://github.com/mattn/go-isatty")

gnu/packages/gpodder.scm

@@ -36,7 +36,7 @@
 (define-public gpodder
   (package
     (name "gpodder")
-    (version "3.10.7")
+    (version "3.10.9")
     (source
      (origin
        (method git-fetch)
@@ -45,7 +45,7 @@
              (commit version)))
        (sha256
         (base32
-         "0sx9rj6dpvd2xz7lak2yi0zlgr3lp2ng1fw23s39la9ly4g1835j"))
+         "1sdmr1sq1d4p492zp9kq3npl7p56yr0pr470z9r6xxcylax5mhfq"))
        (file-name (git-file-name name version))))
     (build-system python-build-system)
     (native-inputs
@@ -81,12 +81,12 @@
              (for-each
                (lambda (f)
                  (chmod f #o664))
-               (find-files "po"))))
+               (find-files "po"))
+             #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (setenv "PREFIX" (assoc-ref outputs "out"))
-             (invoke "make" "install")
+             (invoke "make" "install")))
-             #t))
          (add-after 'install 'wrap-gpodder
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((out (assoc-ref outputs "out"))

gnu/packages/gps.scm

@@ -175,16 +175,16 @@ coordinates as well as partial support for adjustments in global coordinate syst
 (define-public gpxsee
   (package
     (name "gpxsee")
-    (version "4.19")
+    (version "7.8")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri
+              (uri (git-reference
-               (string-append "https://github.com/tumic0/GPXSee/archive/"
+                    (url "https://github.com/tumic0/GPXSee")
-                              version ".tar.gz"))
+                    (commit version)))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "00j0gjldw1kn3i45dppld1pz8r4s1g7lw89k7gfvvqbjjyjih1wg"))))
+                "1ymqz4wrl9ghkyyqi2vrnlyvz3fc84s3p8a1dkiqlvyvj360ck9j"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -195,27 +195,16 @@ coordinates as well as partial support for adjustments in global coordinate syst
              (for-each (lambda (file)
                          (invoke "lrelease" file))
                        (find-files "lang" "\\.ts"))
-             (substitute* "src/config.h"
-               (("/usr/share/gpxsee")
-                (string-append
-                 (assoc-ref outputs "out") "/share/gpxsee")))
              (invoke "qmake"
                      (string-append "PREFIX="
-                                    (assoc-ref outputs "out")))))
+                                    (assoc-ref outputs "out"))))))))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (share (string-append out "/share/gpxsee/")))
-               (install-file "GPXSee" (string-append out "/bin/GPXSee"))
-               (install-file "pkg/maps.txt" share))
-             #t)))))
     (inputs
      `(("qtbase" ,qtbase)))
     (native-inputs
      `(("qttools" ,qttools)))
-    (home-page "http://www.gpxsee.org")
+    (home-page "https://www.gpxsee.org")
-    (synopsis "GPX file viewer and analyzer")
+    (synopsis "GPS log file viewer and analyzer")
     (description
-     "GPXSee is a Qt-based GPS log file viewer and analyzer that supports GPX,
+     "GPXSee is a Qt-based GPS log file viewer and analyzer that supports
-TCX, KML, FIT, IGC and NMEA files.")
+all common GPS log file formats.")
     (license license:gpl3)))

gnu/packages/gtk.scm

@@ -348,7 +348,10 @@ diagrams.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "07hrabhpl6n8ajz10s0d960jdwndxs87szxyn428mpxi8cvpg1f5"))))
+                "07hrabhpl6n8ajz10s0d960jdwndxs87szxyn428mpxi8cvpg1f5"))
+              (patches
+                (search-patches
+                  "gtksourceview-2-add-default-directory.patch"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("intltool" ,intltool)

gnu/packages/guile-xyz.scm

@@ -9,7 +9,7 @@
 ;;; Copyright © 2016, 2017 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2016, 2017 Adonay "adfeno" Felipe Nogueira <https://libreplanet.org/wiki/User:Adfeno> <adfeno@openmailbox.org>
 ;;; Copyright © 2016 Amirouche <amirouche@hypermove.net>
-;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2016, 2019 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2017 Andy Wingo <wingo@igalia.com>
 ;;; Copyright © 2017 David Thompson <davet@gnu.org>
 ;;; Copyright © 2017, 2018 Mathieu Othacehe <m.othacehe@gmail.com>
@@ -53,8 +53,10 @@
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gl)
+  #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gperf)
+  #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages hurd)
   #:use-module (gnu packages image)
@@ -66,6 +68,7 @@
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages networking)
+  #:use-module (gnu packages noweb)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
@@ -73,14 +76,17 @@
   #:use-module (gnu packages sdl)
   #:use-module (gnu packages slang)
   #:use-module (gnu packages sqlite)
+  #:use-module (gnu packages tex)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages version-control)
+  #:use-module (gnu packages webkit)
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages xorg)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
+  #:use-module (guix hg-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system guile)
   #:use-module (guix utils)
@@ -2232,3 +2238,150 @@ slashes are present and accounted for, resolving @code{.} and @code{..}, etc).
 Inevitably, you have to break the string up into chunks and operate on that
 list of components.  This module takes care of that for you.")
     (license license:lgpl3+)))
+
+(define-public guile-gi
+  (let ((commit "26e885219ae6b31a83766564a2ecfe8c4532346f")
+        (revision "1"))
+    (package
+      (name "guile-gi")
+      (version (string-append "0.0.1-" revision "." (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/spk121/guile-gi.git")
+                      (commit commit)))
+                (file-name (string-append name "-" version))
+                (sha256
+                 (base32
+                  "1prbzhr4sqqihb34l6yfrz6sd8nghwd3q9wvbm36jnl2n3z2nxj8"))))
+      (build-system gnu-build-system)
+      (native-inputs `(("autoconf" ,autoconf)
+                       ("automake" ,automake)
+                       ("gettext" ,gnu-gettext)
+                       ("libtool" ,libtool)
+                       ("pkg-config" ,pkg-config)
+                       ("texinfo" ,texinfo)))
+      (propagated-inputs `(("glib" ,glib)
+                           ("gobject-introspection" ,gobject-introspection)
+                           ("gssettings-desktop-schemas" ,gsettings-desktop-schemas)
+                           ("gtk+" ,gtk+)
+                           ("guile-lib" ,guile-lib)
+                           ("webkitgtk" ,webkitgtk)))
+      (inputs `(("guile" ,guile-2.2)))
+      (arguments
+       `(#:configure-flags '("--with-gnu-filesystem-hierarchy")))
+      (home-page "https://github.com/spk121/guile-gi")
+      (synopsis "GObject bindings for Guile")
+      (description
+       "Guile-GI is a library for Guile that allows using GObject-based
+libraries, such as GTK+3.  Its README comes with the disclaimer: This is
+pre-alpha code.")
+      (license license:gpl3+))))
+
+(define-public guile-srfi-159
+  (let ((commit "1bd98abda2ae4ef8f36761a167903e55c6bda7bb")
+        (revision "0"))
+    (package
+      (name "guile-srfi-159")
+      (version (git-version "0" revision commit))
+      (home-page "https://bitbucket.org/bjoli/guile-srfi-159")
+      (source (origin
+                (method hg-fetch)
+                (uri (hg-reference (changeset commit)
+                                   (url home-page)))
+                (sha256
+                 (base32
+                  "1zw6cmcy7xdbfiz3nz9arqnn7l2daidaps6ixkcrc9b6k51fdv3p"))
+                (file-name (git-file-name name version))))
+      (build-system guile-build-system)
+      (arguments
+       ;; The *-impl.scm files are actually included from module files; they
+       ;; should not be compiled separately, but they must be installed.
+       '(#:not-compiled-file-regexp "-impl\\.scm$"))
+      (inputs
+       `(("guile" ,guile-2.2)))
+      (synopsis "Formatting combinators for Guile")
+      (description
+       "The @code{(srfi-159)} module and its sub-modules implement the
+formatting combinators specified by
+@uref{https://srfi.schemers.org/srfi-159/srfi-159.html, SRFI-159}.  These are
+more expressive and flexible than the traditional @code{format} procedure.")
+      (license license:bsd-3))))
+
+(define-public emacsy
+  (let ((commit "7d49cc1425d5d209bdb82cac0d8ea0694b8b3784")
+        (revision "4"))
+    (package
+      (name "emacsy")
+      (version (string-append "0.1.2-" revision "." (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://gitlab.com/janneke/emacsy.git")
+                      (commit commit)))
+                (file-name (string-append name "-" version))
+                (sha256
+                 (base32
+                  "0k9yns1v8zn135w60sx96nqs2bm2p2dvcvlm987hkw4lbff9ii6i"))))
+      (build-system gnu-build-system)
+      (native-inputs
+       `(("emacsy-webkit-gtk"
+          ,(origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://gitlab.com/janneke/emacsy-webkit-gtk.git")
+                   (commit "35ded1b3e997fd779a17e0c4a2c73741718562d9")))
+             (file-name (string-append "emacsy-webkit-gtk" "-" version))
+             (sha256
+              (base32
+               "1gp0li2rbp6in926r3hrww6cnh864pp46v1din2pgmd7vzzl7kg0"))))
+         ("hello-emacsy"
+          ,(origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://gitlab.com/janneke/hello-emacsy.git")
+                   (commit "2c117e5286a261be4ff24938f3ae1d348396c538")))
+             (file-name (string-append "hello-emacsy" "-" version))
+             (sha256
+              (base32
+               "15ykd7s8axcy8ym4v71fgal4x28fxnim0pv0jmpi3dnhizr63zqn"))))
+         ("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("bzip2" ,bzip2)
+         ("guile" ,guile-2.2)
+         ("gettext" ,gnu-gettext)
+         ("libtool" ,libtool)
+         ("noweb" ,noweb)
+         ("perl" ,perl)
+         ("pkg-config" ,pkg-config)
+         ("texinfo" ,texinfo)
+         ("texlive" ,texlive)))
+      (propagated-inputs
+       `(("guile-lib" ,guile-lib)
+         ("guile-readline" ,guile-readline)
+         ("freeglut" ,freeglut)
+         ("gssettings-desktop-schemas" ,gsettings-desktop-schemas)
+         ("webkitgtk" ,webkitgtk)))
+      (inputs `(("guile" ,guile-2.2)))
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'unpack-examples
+             (lambda _
+               (copy-recursively (assoc-ref %build-inputs "emacsy-webkit-gtk")
+                                 "example/emacsy-webkit-gtk")
+               (copy-recursively (assoc-ref %build-inputs "hello-emacsy")
+                                 "example/hello-emacsy")))
+           (add-before 'configure 'setenv
+             (lambda _
+               (setenv "GUILE_AUTO_COMPILE" "0"))))))
+      (home-page "https://github.com/shanecelis/emacsy/")
+      (synopsis "Embeddable GNU Emacs-like library using Guile")
+      (description
+       "Emacsy is an embeddable GNU Emacs-like library that uses GNU Guile
+as extension language.  Emacsy can give a C program an Emacsy feel with
+keymaps, minibuffer, recordable macros, history, tab completion, major
+and minor modes, etc., and can also be used as a pure Guile library.  It
+comes with a simple counter example using GLUT and browser examples in C
+using gtk+-3 and webkitgtk.")
+      (license license:gpl3+))))

gnu/packages/haskell-web.scm

@@ -5,6 +5,7 @@
 ;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 rsiddharth <s@ricketyspace.net>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019 Robert Vollmert <rob@vllmrt.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -118,7 +119,7 @@ requests, and the library is intended for implementing Ajax APIs.")
 (define-public ghc-http-types
   (package
     (name "ghc-http-types")
-    (version "0.12.1")
+    (version "0.12.3")
     (source
      (origin
        (method url-fetch)
@@ -126,7 +127,7 @@ requests, and the library is intended for implementing Ajax APIs.")
                            "http-types-" version ".tar.gz"))
        (sha256
         (base32
-         "1wv9k6nlvkdsxwlr7gaynphvzmvi5211gvwq96mbcxgk51a739rz"))))
+         "05j00b9nqmwh9zaq9y9x50k81v2pd3j7a71kd91zlnbl8xk4m2jf"))))
     (build-system haskell-build-system)
     (native-inputs
      `(("ghc-doctest" ,ghc-doctest)
@@ -136,7 +137,6 @@ requests, and the library is intended for implementing Ajax APIs.")
        ("hspec-discover" ,hspec-discover)))
     (inputs
      `(("ghc-case-insensitive" ,ghc-case-insensitive)
-       ("ghc-blaze-builder" ,ghc-blaze-builder)
        ("ghc-text" ,ghc-text)))
     (home-page "https://github.com/aristidb/http-types")
     (synopsis "Generic HTTP types for Haskell")
@@ -550,7 +550,7 @@ transfers.")
 (define-public ghc-warp
   (package
     (name "ghc-warp")
-    (version "3.2.23")
+    (version "3.2.27")
     (source
      (origin
        (method url-fetch)
@@ -558,8 +558,7 @@ transfers.")
                            "warp-" version "/" "warp-" version
                            ".tar.gz"))
        (sha256
-        (base32
+        (base32 "0p2w88q0zd55ms20qylipbi0qzbf324i9r8b9qqxyds5yc1anq76"))))
-         "12v9qhi4hyp0sb90yddsax16jj7x47nmqwn53sv7b5nszcxgzam0"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-async" ,ghc-async)

gnu/packages/haskell.scm

@@ -17,6 +17,7 @@
 ;;; Copyright © 2018, 2019 Timothy Sample <samplet@ngyro.com>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018, 2019 Gabriel Hondet <gabrielhondet@gmail.com>
+;;; Copyright © 2019 Robert Vollmert <rob@vllmrt.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1325,6 +1326,16 @@ postfix notation.  For more information on stack based languages, see
         (base32
          "138xpxdb7x62lpmgmb6b3v3vgdqqvqn4273jaap3mjmc2gla709y"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'skip-test-issue93
+           (lambda _
+             ;; Tests run out of memory on a system with 2GB of available RAM,
+             ;; in 'issue93.a.hs' and 'issue93.n.hs'.
+             (substitute* "tests/Makefile"
+               ((" issue93.y ") " "))
+             #t)))))
     (home-page "https://hackage.haskell.org/package/happy")
     (synopsis "Parser generator for Haskell")
     (description "Happy is a parser generator for Haskell.  Given a grammar
@@ -1794,7 +1805,7 @@ version 1.3).")
 (define-public ghc-streaming-commons
   (package
     (name "ghc-streaming-commons")
-    (version "0.2.1.0")
+    (version "0.2.1.1")
     (source
      (origin
        (method url-fetch)
@@ -1803,7 +1814,7 @@ version 1.3).")
                            version ".tar.gz"))
        (sha256
         (base32
-         "13fn6qmpiggwpn8lczyydgp77cyzfypwds7wxskrwir4i5cgxlfq"))))
+         "1lmyx3wkjsayhy5yilzvy0kf8qwmycwlk26r1d8f3cxbfhkr7s52"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-async" ,ghc-async)
@@ -6941,7 +6952,7 @@ upon it.")
 (define-public ghc-conduit-extra
   (package
     (name "ghc-conduit-extra")
-    (version "1.3.0")
+    (version "1.3.1.1")
     (source
      (origin
        (method url-fetch)
@@ -6950,7 +6961,7 @@ upon it.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "1bi2b6kdzy5f9glq46jzsk02has95jkxqz0cchpbmnakzhjwjh9c"))))
+         "0jaj350vv6mbb26gdwcqz4gwzfzrjydv5pis2da49wz1npbakcfw"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-conduit" ,ghc-conduit)

gnu/packages/image-viewers.scm

@@ -9,6 +9,7 @@
 ;;; Copyright © 2017 nee <nee-git@hidamari.blue>
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -429,3 +430,50 @@ imaging.  It supports several HDR and LDR image formats, and it can:
 a comic and manga reader.  It supports a variety of container formats
 including CBZ, CB7, CBT, LHA.")
     (license license:gpl2+)))
+
+(define-public qview
+  (package
+    (name "qview")
+    (version "2.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/jurplel/qView.git")
+                    (commit version)))
+              (sha256
+               (base32
+                "1s29hz44rb5dwzq8d4i4bfg77dr0v3ywpvidpa6xzg7hnnv3mhi5"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda _
+             (invoke "qmake")))
+         ;; Installation process hard-codes "/usr/bin", possibly
+         ;; prefixed.
+         (add-after 'configure 'fix-install-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (substitute* "Makefile"
+                 (("\\$\\(INSTALL_ROOT\\)/usr") out))
+               #t)))
+         ;; Don't phone home or show "Checking for updates..." in the
+         ;; About menu.
+         (add-before 'build 'disable-auto-update
+           (lambda _
+             (substitute* "src/qvaboutdialog.cpp"
+               (("ui->updateLabel->setText\\(updateText\\);") "")
+               (("requestUpdates\\(\\);") ""))
+             #t)))))
+    (inputs
+     `(("qtbase" ,qtbase)
+       ("qtsvg" ,qtsvg)
+       ("qtimageformats" ,qtimageformats)))
+    (home-page "https://interversehq.com/qview/")
+    (synopsis "Convenient and minimal image viewer")
+    (description "qView is a Qt image viewer designed with visually
+minimalism and usability in mind.  Its features include animated GIF
+controls, file history, rotation/mirroring, and multithreaded
+preloading.")
+    (license license:gpl3+)))

gnu/packages/image.scm

@@ -1553,7 +1553,7 @@ identical visual appearance.")
 (define-public grim
   (package
    (name "grim")
-   (version "1.1")
+   (version "1.2.0")
    (source
     (origin
      (method git-fetch)
@@ -1562,7 +1562,7 @@ identical visual appearance.")
            (commit (string-append "v" version))))
      (file-name (git-file-name name version))
      (sha256
-      (base32 "1bcvkggqszcwy6hg8g4mch3yr25ic0baafbd90af5s5mrhrjxxxz"))))
+      (base32 "0brljl4zfbn5mh9hkfrfkvd27c5y9vdkgap9r1hrfy9r1x20sskn"))))
    (build-system meson-build-system)
    (native-inputs `(("pkg-config" ,pkg-config)))
    (inputs `(("cairo" ,cairo)
@@ -1579,7 +1579,7 @@ identical visual appearance.")
 (define-public slurp
   (package
    (name "slurp")
-   (version "1.0.1")
+   (version "1.2.0")
    (source
     (origin
      (method git-fetch)
@@ -1588,7 +1588,7 @@ identical visual appearance.")
            (commit (string-append "v" version))))
      (file-name (git-file-name name version))
      (sha256
-      (base32 "072lkwhpvr753wfqzmd994bnhbrgfavxcgqcyml7abab28sdhs1y"))))
+      (base32 "0580m6kaiilgsrcj608r837r37sl6a25y7w21p7d6ij20fs3gvg1"))))
    (build-system meson-build-system)
    (native-inputs `(("pkg-config" ,pkg-config)))
    (inputs `(("cairo" ,cairo)

gnu/packages/kawa.scm

@@ -0,0 +1,53 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2019 Carlo Zancanaro <carlo@zancanaro.id.au>
+;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages kawa)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix build-system gnu)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (gnu packages java))
+
+(define-public kawa
+  (package
+    (name "kawa")
+    (version "3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://gnu/kawa/kawa-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1k9qpydc64ar4aqyg3q7jmmxy503ayj85227qfhc5n6ngchqavhy"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:parallel-build? #f
+       #:parallel-tests? #f))
+    (inputs
+     `(("icedtea" ,icedtea-8 "jdk")))
+    (home-page "https://www.gnu.org/software/kawa/")
+    (synopsis "Java framework and implementation of Scheme, Elisp, and more")
+    (description
+     "GNU Kawa is an implementation of the Scheme programming language that
+is built on top of the Java platform.  It is thus conveniently integrated
+with Java and benefits from this by having a compiler, optional static
+typing, and so on.  Kawa also serves as a framework for implementing other
+programming languages on the Java platform.  Included in Kawa is qexo, a
+partial implementation of XQuery in Java.")
+    (license license:expat)))

gnu/packages/libevent.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2015, 2017 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
 ;;; Copyright © 2016 David Thompson <davet@gnu.org>
-;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2017, 2019 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
@@ -41,7 +41,7 @@
 (define-public libevent
   (package
     (name "libevent")
-    (version "2.1.8")
+    (version "2.1.10")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -49,11 +49,7 @@
                    version "-stable/libevent-" version "-stable.tar.gz"))
              (sha256
               (base32
-               "1hhxnxlr0fsdv7bdmzsnhdz16fxf3jg2r6vyljcl3kj6pflcap4n"))
+               "1c25928gdv495clxk2v1d4gkr5py7ack4gx2n7d13frnld0syr78"))))
-             (patches (search-patches "libevent-2.1-dns-tests.patch"
-                                      ;; XXX: Try removing this for > 2.1.8.
-                                      ;; https://github.com/libevent/libevent/issues/452
-                                      "libevent-2.1-skip-failing-test.patch"))))
     (build-system gnu-build-system)
     (arguments
       ;; This skips some of the tests which fail on armhf and aarch64.
@@ -62,7 +58,7 @@
      `(("python" ,python-2)))           ; for 'event_rpcgen.py'
     (native-inputs
      `(("which" ,which)))
-    (home-page "http://libevent.org/")
+    (home-page "https://libevent.org/")
     (synopsis "Event notification library")
     (description
      "The libevent API provides a mechanism to execute a callback
@@ -76,27 +72,6 @@ then add or remove events dynamically without having to change the event
 loop.")
     (license bsd-3)))
 
-(define-public libevent-2.0
-  (package
-    (inherit libevent)
-    (version "2.0.22")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/libevent/libevent/releases/download/release-"
-                    version "-stable/libevent-" version "-stable.tar.gz"))
-              (sha256
-               (base32
-                "18qz9qfwrkakmazdlwxvjmw8p76g70n3faikwvdwznns1agw9hki"))
-              (patches
-               (search-patches
-                "libevent-dns-tests.patch"
-                "libevent-2.0-CVE-2016-10195.patch"
-                "libevent-2.0-CVE-2016-10196.patch"
-                "libevent-2.0-CVE-2016-10197.patch"
-                "libevent-2.0-evbuffer-add-use-last-with-datap.patch"))))
-    (arguments '())))
-
 (define-public libev
   (package
     (name "libev")
@@ -154,19 +129,6 @@ resolution, asynchronous file system operations, and threading primitives.")
     ;; details.  Documentation is CC-BY 4.0 as of 1.12.0; see 'LICENSE-docs'.
     (license (list expat cc-by4.0))))
 
-;; This version is required for Node versions < 10.
-(define-public libuv-1.19
-  (package
-    (inherit libuv)
-    (version "1.19.2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://dist.libuv.org/dist/v" version
-                                  "/libuv-v" version ".tar.gz"))
-              (sha256
-               (base32
-                "1msk9ac1z69whww88ibrwjqkd1apdla6l77cm2fwy5kigq0z5g3w"))))))
-
 (define-public perl-anyevent
   (package
     (name "perl-anyevent")

gnu/packages/linux.scm

@@ -34,6 +34,7 @@
 ;;; Copyright © 2018 Vasile Dumitrascu <va511e@yahoo.com>
 ;;; Copyright © 2019 Tim Gesthuizen <tim.gesthuizen@yahoo.de>
 ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019 Stefan Stefanović <stefanx2ovic@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -143,6 +144,7 @@
           ((string-prefix? "alpha" arch) "alpha")
           ((string-prefix? "powerpc" arch) "powerpc") ;including "powerpc64le"
           ((string-prefix? "s390" arch) "s390")
+          ((string-prefix? "riscv" arch) "riscv")
           (else arch))))
 
 (define-public (system->defconfig system)
@@ -169,18 +171,20 @@ defconfig.  Return the appropriate make target if applicable, otherwise return
          "mirror://gnu/linux-libre/" version "-gnu/linux-libre-"
          version "-gnu.tar.xz")))
 
-(define-public linux-libre-headers
+(define (make-linux-libre-headers version hash)
   (package
     (name "linux-libre-headers")
-    (version "4.14.67")
+    (version version)
     (source (origin
              (method url-fetch)
              (uri (linux-libre-urls version))
-             (sha256
+             (sha256 (base32 hash))))
-              (base32
-               "050zvdxjy6sc64q75pr1gxsmh49chwav2pwxz8xlif39bvahnrpg"))))
     (build-system gnu-build-system)
-    (native-inputs `(("perl" ,perl)))
+    (native-inputs `(("perl" ,perl)
+                     ,@(if (version>=? version "4.16")
+                           `(("flex" ,flex)
+                             ("bison" ,bison))
+                           '())))
     (arguments
      `(#:modules ((guix build gnu-build-system)
                   (guix build utils)
@@ -246,7 +250,7 @@ defconfig.  Return the appropriate make target if applicable, otherwise return
           "/raw/34a7d9011fcfcfa38b68282fd2b1a8797e6834f0"
           "/debian/patches/bugfix/arm/"
           "arm-mm-export-__sync_icache_dcache-for-xen-privcmd.patch"))
-    (file-name "linux-libre-4.19-arm-export-__sync_icache_dcache.patch")
+    (file-name "linux-libre-arm-export-__sync_icache_dcache.patch")
     (sha256
      (base32 "1ifnfhpakzffn4b8n7x7w5cps9mzjxlkcfz9zqak2vaw8nzvl39f"))))
 
@@ -417,22 +421,26 @@ 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 "5.1.4")
+(define %linux-libre-version "5.1.9")
-(define %linux-libre-hash "02pzad29w2apcqsk4r4fq93539z3by8kvk1f59lb8xnl0gvhdi5v")
+(define %linux-libre-hash "1l1nhq3giqyv7zir1sl8m32xbbpmqhsw8dgf90kf4qcnh6bvjin1")
 
 (define %linux-libre-5.1-patches
   (list %boot-logo-patch
         %linux-libre-arm-export-__sync_icache_dcache-patch))
 
-(define-public linux-libre
+(define-public linux-libre-5.1
   (make-linux-libre %linux-libre-version
                     %linux-libre-hash
                     '("x86_64-linux" "i686-linux" "armhf-linux" "aarch64-linux")
                     #:patches %linux-libre-5.1-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.19-version "4.19.45")
+(define-public linux-libre-headers-5.1
-(define %linux-libre-4.19-hash "1wiy8vzpzzml4k76nv3ycjx7ky55x7dqx3mgpjqbh73mj2gcr5bx")
+  (make-linux-libre-headers %linux-libre-version
+                            %linux-libre-hash))
+
+(define %linux-libre-4.19-version "4.19.50")
+(define %linux-libre-4.19-hash "0j1p459al3y77cv2xwjx7ppghc8ixs3wm3w9a10sc3ckbq1hw8ly")
 
 (define %linux-libre-4.19-patches
   (list %boot-logo-patch
@@ -445,8 +453,12 @@ It has been modified to remove all non-free binary blobs.")
                     #:patches %linux-libre-4.19-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.121")
+(define-public linux-libre-headers-4.19
-(define %linux-libre-4.14-hash "1g7gyjmp056pasf9m34dqs8pa15my6hqasdd551jw8mgkbhsfnxg")
+  (make-linux-libre-headers %linux-libre-4.19-version
+                            %linux-libre-4.19-hash))
+
+(define %linux-libre-4.14-version "4.14.125")
+(define %linux-libre-4.14-hash "1ms7ai7c6xspq8r2amgjfsdyl87x10dc4b1c3iacrhrxaqqmab01")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
@@ -454,15 +466,19 @@ It has been modified to remove all non-free binary blobs.")
                     '("x86_64-linux" "i686-linux" "armhf-linux")
                     #:configuration-file kernel-config))
 
+(define-public linux-libre-headers-4.14
+  (make-linux-libre-headers %linux-libre-4.14-version
+                            %linux-libre-4.14-hash))
+
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.178"
+  (make-linux-libre "4.9.181"
-                    "1ridlkymf382qnkc6hi07pkghrrxfv2avx55snjnkfcpdccvsmrb"
+                    "0fdqfd6z73q00nracrixliw0i0b60f4z352jmzabcwy431wszar5"
                     '("x86_64-linux" "i686-linux")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.180"
+  (make-linux-libre "4.4.181"
-                    "157kfs4slii86q9yrspvqdynpiv6rff80hrrn569v6h4nkc4b7ag"
+                    "1ird78a3pg8k6h60258g56ka86jpgiaj0q9r2jws770qgrmy324l"
                     '("x86_64-linux" "i686-linux")
                     #:configuration-file kernel-config
                     #:extra-options
@@ -472,14 +488,6 @@ It has been modified to remove all non-free binary blobs.")
                        ("CONFIG_DEVPTS_MULTIPLE_INSTANCES" . #t))
                      %default-extra-linux-options)))
 
-(define-public linux-libre-arm-generic
-  (make-linux-libre %linux-libre-version
-                    %linux-libre-hash
-                    '("armhf-linux")
-                    #:patches %linux-libre-5.1-patches
-                    #:defconfig "multi_v7_defconfig"
-                    #:extra-version "arm-generic"))
-
 (define-public linux-libre-arm-veyron
   (make-linux-libre %linux-libre-version
                     %linux-libre-hash
@@ -488,6 +496,21 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config-veyron
                     #:extra-version "arm-veyron"))
 
+(define-public linux-libre-headers-4.14.67
+  (make-linux-libre-headers "4.14.67"
+                            "050zvdxjy6sc64q75pr1gxsmh49chwav2pwxz8xlif39bvahnrpg"))
+
+(define-public linux-libre-headers linux-libre-headers-4.14.67)
+(define-public linux-libre linux-libre-5.1)
+
+(define-public linux-libre-arm-generic
+  (make-linux-libre %linux-libre-version
+                    %linux-libre-hash
+                    '("armhf-linux")
+                    #:patches %linux-libre-5.1-patches
+                    #:defconfig "multi_v7_defconfig"
+                    #:extra-version "arm-generic"))
+
 (define-public linux-libre-arm-generic-4.19
   (make-linux-libre %linux-libre-4.19-version
                     %linux-libre-4.19-hash
@@ -526,28 +549,6 @@ It has been modified to remove all non-free binary blobs.")
                     #:defconfig "omap2plus_defconfig"
                     #:extra-version "arm-omap2plus"))
 
-(define-public vhba-module
-  (package
-    (name "vhba-module")
-    (version "20190410")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "http://downloads.sourceforge.net/cdemu/vhba-module/vhba-module-"
-                    version ".tar.bz2"))
-              (sha256
-               (base32
-                "1513hq130raxp9z5grj54cwfjfxj05apipxg425j0zicii59a60c"))))
-    (build-system linux-module-build-system)
-    (arguments
-     ;; TODO: No tests?
-     `(#:tests? #f))
-    (home-page "https://cdemu.sourceforge.io/")
-    (synopsis "Kernel module that emulates SCSI devices")
-    (description "VHBA module provides a Virtual (SCSI) HBA, which is the link
-between the CDemu userspace daemon and linux kernel.")
-    (license license:gpl2+)))
-
 
 ;;;
 ;;; Linux kernel modules.
@@ -933,7 +934,7 @@ slabtop, and skill.")
 (define-public e2fsprogs
   (package
     (name "e2fsprogs")
-    (version "1.44.5")
+    (version "1.45.2")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -942,7 +943,7 @@ slabtop, and skill.")
                    name "-" version ".tar.xz"))
              (sha256
               (base32
-               "1ff56h6h1h17sj2zvlddv5c88nmbx46p1fcbh6b0s5k9kl3b6pms"))))
+               "02g0cm72sgz709s9pkg4mvj56m7bgs7rwnyc2cp7cvg3j6pcjlj9"))))
     (build-system gnu-build-system)
     (inputs `(("util-linux" ,util-linux)))
     (native-inputs `(("pkg-config" ,pkg-config)
@@ -2535,7 +2536,7 @@ compliance.")
 (define-public wireless-regdb
   (package
     (name "wireless-regdb")
-    (version "2017.03.07")
+    (version "2019.06.03")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2543,7 +2544,7 @@ compliance.")
                     "wireless-regdb-" version ".tar.xz"))
               (sha256
                (base32
-                "1f9mcp78sdd4sci6v32vxfcl1rfjpv205jisz1p93kkfnaisy7ip"))
+                "1gslvh0aqdkv48jyr2ddq153mw28i7qz2ybrjj9qvkk3dgc7x4fd"))
 
               ;; We're building 'regulatory.bin' by ourselves.
               (snippet '(begin
@@ -2551,13 +2552,25 @@ compliance.")
                           #t))))
     (build-system gnu-build-system)
     (arguments
-     '(#:phases (modify-phases %standard-phases
+     '(#:phases
+       (modify-phases %standard-phases
          (add-after 'unpack 'gzip-determinism
            (lambda _
              (substitute* "Makefile"
                (("gzip") "gzip --no-name"))
              #t))
-                  (delete 'configure))
+         (add-after 'unpack 'omit-signature
+           (lambda _
+             (substitute* "Makefile"
+               ;; Signing requires a REGDB_PUBCERT and REGDB_PRIVKEY which we
+               ;; don't provide (see below).  Disable it.
+               ((" regulatory\\.db\\.p7s") "")
+               ;; regulatory.db is built as a dependency of regulatory.db.p7s,
+               ;; but ‘make install’ depends only on the latter while installing
+               ;; both (and failing).  Depend on it explicitly.
+               (("^install: " all) (string-append all "regulatory.db ")))
+             #t))
+         (delete 'configure))  ; no configure script
 
        ;; The 'all' target of the makefile depends on $(REGDB_CHANGED), which
        ;; is computed and can be equal to 'maintainer-clean'; when that
@@ -2566,18 +2579,21 @@ compliance.")
        #:parallel-build? #f
 
        #:tests? #f                      ; no tests
-       #:make-flags (let ((out (assoc-ref %outputs "out")))
+       #:make-flags
+       (let ((out (assoc-ref %outputs "out")))
          (list (string-append "PREFIX=" out)
-                            (string-append "LSB_ID=Guix")
+               (string-append "FIRMWARE_PATH=$(PREFIX)/lib/firmware")
-                            (string-append "DISTRO_PUBKEY=/dev/null")
-                            (string-append "DISTRO_PRIVKEY=/dev/null")
-                            (string-append "REGDB_PUBKEY=/dev/null")
 
-                            ;; Leave that empty so that db2bin.py doesn't try
+               ;; Leave this empty so that db2bin.py doesn't try to sign
-                            ;; to sign 'regulatory.bin'.  This allows us to
+               ;; ‘regulatory.bin’.  This allows us to avoid managing a key
-                            ;; avoid managing a key pair for the whole distro.
+               ;; pair for the whole distribution.
-                            (string-append "REGDB_PRIVKEY=")))))
+               (string-append "REGDB_PRIVKEY=")
-    (native-inputs `(("python" ,python-2)))
+               ;; Don't generate a public key for the same reason.  These are
+               ;; used as Makefile targets and can't be the empty string.
+               (string-append "REGDB_PUBCERT=/dev/null")
+               (string-append "REGDB_PUBKEY=/dev/null")))))
+    (native-inputs
+     `(("python" ,python-wrapper)))
     (home-page
      "https://wireless.wiki.kernel.org/en/developers/regulatory/wireless-regdb")
     (synopsis "Wireless regulatory database")
@@ -2860,12 +2876,16 @@ thanks to the use of namespaces.")
                   (substitute* "bin/singularity.in"
                     (("^PATH=.*" all)
                      (string-append "#" all "\n")))
+
+                  (substitute* (find-files "libexec/cli" "\\.exec$")
+                    (("\\$SINGULARITY_libexecdir/singularity/bin/([a-z]+)-suid"
+                      _ program)
+                     (string-append "/run/setuid-programs/singularity-"
+                                    program "-helper")))
                   #t))))
     (build-system gnu-build-system)
     (arguments
-     `(#:configure-flags
+     `(#:configure-flags '("--localstatedir=/var")
-       (list "--disable-suid"
-             "--localstatedir=/var")
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-reference-to-squashfs-tools
@@ -4052,6 +4072,39 @@ Linux kernel to retrieve and control processor features related to power saving,
 such as frequency and voltage scaling.")
     (license license:gpl2)))
 
+(define-public x86-energy-perf-policy
+  (package
+    (name "x86-energy-perf-policy")
+    (version (package-version linux-libre))
+    (source (package-source linux-libre))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'enter-subdirectory
+           (lambda _
+             (chdir "tools/power/x86/x86_energy_perf_policy")
+             #t))
+         (delete 'configure)
+         (add-before 'build 'fix-makefile
+           (lambda _
+             (substitute* "Makefile" (("/usr") ""))
+             #t)))
+       #:make-flags
+       (let ((out (assoc-ref %outputs "out")))
+         (list (string-append "DESTDIR=" out)
+               (string-append "LDFLAGS=-Wl,-rpath=" out "/lib")))))
+    (supported-systems '("i686-linux" "x86_64-linux"))
+    (home-page (package-home-page linux-libre))
+    (synopsis "Display and update Intel-CPU energy-performance policy")
+    (description
+     "@command{x86_energy_perf_policy} displays and updates energy-performance
+policy settings specific to Intel Architecture Processors.  Settings are
+accessed via Model Specific Register (MSR) updates, no matter if the Linux
+cpufreq sub-system is enabled or not.")
+    (license license:gpl2)))
+
 (define-public haveged
   (package
     (name "haveged")
@@ -4329,15 +4382,16 @@ developers.")
 (define-public radeontop
   (package
     (name "radeontop")
-    (version "1.1")
+    (version "1.2")
-    (home-page "https://github.com/clbr/radeontop/")
+    (source
-    (source (origin
+     (origin
-              (method url-fetch)
+       (method git-fetch)
-              (uri (string-append home-page "archive/v" version ".tar.gz"))
+       (uri (git-reference
-              (file-name (string-append name "-" version ".tar.gz"))
+             (url "https://github.com/clbr/radeontop.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-               (base32
+        (base32 "1b1m30r2nfwqkajqw6m01xmfhlq83z1qylyijxg7962mp9x2k0gw"))))
-                "1fv06j5c99imvzkac3j40lgjhr5b2i77fnyffhlvj92bli1fm1c6"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
@@ -4361,6 +4415,7 @@ developers.")
        ("libpciaccess" ,libpciaccess)
        ("libxcb" ,libxcb)
        ("ncurses" ,ncurses)))
+    (home-page "https://github.com/clbr/radeontop/")
     (synopsis "Usage monitor for AMD Radeon graphics")
     (description "RadeonTop monitors resource consumption on supported AMD
 Radeon Graphics Processing Units (GPUs), either in real time as bar graphs on
@@ -4592,10 +4647,19 @@ interface in sysfs, which can be accomplished with the included udev rules.")
               ("sed" ,sed)
               ("usbutils" ,usbutils)
               ("util-linux" ,util-linux)
-              ("wireless-tools" ,wireless-tools)))
+              ("wireless-tools" ,wireless-tools)
+              ,@(if (let ((system (or (%current-target-system)
+                                      (%current-system))))
+                      (or (string-prefix? "i686-" system)
+                          (string-prefix? "x86_64-" system)))
+                    `(("x86-energy-perf-policy" ,x86-energy-perf-policy))
+                    '())))
     (build-system gnu-build-system)
     (arguments
-     `(#:phases
+     `(#:modules ((guix build gnu-build-system)
+                  (guix build utils)
+                  (srfi srfi-1))
+       #:phases
        (modify-phases %standard-phases
          (delete 'configure)            ; no configure script
          (add-before 'build 'setenv
@@ -4633,14 +4697,16 @@ interface in sysfs, which can be accomplished with the included udev rules.")
              (let* ((bin (string-append (assoc-ref outputs "out") "/bin"))
                     (bin-files (find-files bin ".*")))
                (define (bin-directory input-name)
-                 (string-append (assoc-ref inputs input-name) "/bin"))
+                 (let ((p (assoc-ref inputs input-name)))
+                   (and p (string-append p "/bin"))))
                (define (sbin-directory input-name)
                  (string-append (assoc-ref inputs input-name) "/sbin"))
                (for-each (lambda (program)
                            (wrap-program program
                              `("PATH" ":" prefix
                                ,(append
-                                 (map bin-directory '("bash"
+                                 (filter-map bin-directory
+                                             '("bash"
                                                "coreutils"
                                                "dbus"
                                                "eudev"
@@ -4650,8 +4716,10 @@ interface in sysfs, which can be accomplished with the included udev rules.")
                                                "perl"
                                                "sed"
                                                "usbutils"
-                                                      "util-linux"))
+                                               "util-linux"
-                                 (map sbin-directory '("ethtool"
+                                               "x86-energy-perf-policy"))
+                                 (filter-map sbin-directory
+                                             '("ethtool"
                                                "hdparm"
                                                "iw"
                                                "pciutils"

gnu/packages/lisp.scm

@@ -14,6 +14,7 @@
 ;;; Copyright © 2018 Pierre Langlois <pierre.langlois@gmx.com>
 ;;; Copyright © 2019 Katherine Cox-Buday <cox.katherine.e@gmail.com>
 ;;; Copyright © 2019 Jesse Gildersleve <jessejohngildersleve@protonmail.com>
+;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -45,8 +46,10 @@
   #:use-module (gnu packages admin)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bdw-gc)
+  #:use-module (gnu packages bison)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages ed)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gettext)
@@ -5321,3 +5324,48 @@ port within a range.")
 
 (define-public ecl-find-port
   (sbcl-package->ecl-package sbcl-find-port))
+
+(define-public txr
+  (package
+    (name "txr")
+    (version "216")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://www.kylheku.com/cgit/txr/snapshot/txr-"
+                           version
+                           ".tar.bz2"))
+       (patches (search-patches "txr-shell.patch"))
+       (sha256
+        (base32
+         "07cxdpc9zsqd0c2668g00dqjpd6zc4mfdn74aarr6d2hpzdhh937"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:configure-flags '("cc=gcc")
+       #:phases (modify-phases %standard-phases
+                  (add-after 'configure 'fix-tests
+                    (lambda _
+                      (substitute* "tests/017/realpath.tl"
+                        (("/usr/bin") "/"))
+                      (substitute* "tests/017/realpath.expected"
+                        (("/usr/bin") "/"))
+                      #t))
+                  (replace 'check
+                    (lambda _
+                      (zero? (system* "make" "tests")))))))
+    (native-inputs
+     `(("bison" ,bison)
+       ("flex" ,flex)))
+    (inputs
+     `(("libffi" ,libffi)))
+    (synopsis "General-purpose, multi-paradigm programming language")
+    (description
+     "TXR is a general-purpose, multi-paradigm programming language.  It
+comprises two languages integrated into a single tool: a text scanning and
+extraction language referred to as the TXR Pattern Language (sometimes just
+\"TXR\"), and a general-purpose dialect of Lisp called TXR Lisp.  TXR can be
+used for everything from \"one liner\" data transformation tasks at the
+command line, to data scanning and extracting scripts, to full application
+development in a wide-range of areas.")
+    (home-page "https://nongnu.org/txr/")
+    (license license:bsd-2)))

gnu/packages/machine-learning.scm

@@ -573,16 +573,16 @@ in terms of new algorithms.")
 (define-public rxcpp
   (package
     (name "rxcpp")
-    (version "4.0.0")
+    (version "4.1.0")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/ReactiveX/RxCpp/archive/v"
+       (uri (git-reference
-                           version ".tar.gz"))
+             (url "https://github.com/ReactiveX/RxCpp.git")
+             (commit (string-append "v" version))))
        (sha256
-        (base32
+        (base32 "1rdpa3jlc181jd08nk437aar085h28i45s6nzrv65apb3xyyz0ij"))
-         "0y2isr8dy2n1yjr9c5570kpc9lvdlch6jv0jvw000amwn5d3krsh"))
+       (file-name (git-file-name name version))))
-       (file-name (string-append name "-" version ".tar.gz"))))
     (build-system cmake-build-system)
     (arguments
      `(#:phases

gnu/packages/mail.scm

@@ -351,14 +351,14 @@ aliasing facilities to work just as they would on normal mail.")
 (define-public mutt
   (package
     (name "mutt")
-    (version "1.11.4")
+    (version "1.12.0")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://bitbucket.org/mutt/mutt/downloads/"
                                  "mutt-" version ".tar.gz"))
              (sha256
               (base32
-               "0098pr4anmq2a0id8wfi2vci3cgcfwf9k4q411w22xn8lrz3aldn"))
+               "13zr2fpql33sdbsjsiaa952js5bvphc1x4lqsj36qyzdhj3l84na"))
              (patches (search-patches "mutt-store-references.patch"))))
     (build-system gnu-build-system)
     (inputs
@@ -581,7 +581,7 @@ and corrections.  It is based on a Bayesian filter.")
 (define-public offlineimap
   (package
     (name "offlineimap")
-    (version "7.2.3")
+    (version "7.2.4")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -590,7 +590,7 @@ and corrections.  It is based on a Bayesian filter.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "18sdnhjldn8zs03bgqy1qa3ikmlfvyxcvwp3nbnv1a74biccqbpa"))))
+                "0h5q5nk2p2vx86w6rrbs7v70h81dpqqr68x6l3klzl3m0yj9agb1"))))
     (build-system python-build-system)
     (native-inputs
      `(("asciidoc" ,asciidoc)))
@@ -847,14 +847,14 @@ invoking @command{notifymuch} from the post-new hook.")
 (define-public notmuch
   (package
     (name "notmuch")
-    (version "0.28.4")
+    (version "0.29")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://notmuchmail.org/releases/notmuch-"
-                                  version ".tar.gz"))
+                                  version ".tar.xz"))
               (sha256
                (base32
-                "1jjnhs4xs4gksvg0a9qn68rxrj41im5bh58snka2pkj20nxwmcds"))))
+                "0rg4jp0wlsham76rx9fmlpmcbv3n9vsd81vrzqvh6jrwlnmjds88"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((guix build gnu-build-system)

gnu/packages/mate.scm

@@ -79,8 +79,7 @@
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -136,10 +135,10 @@ actions.")
   (package
     (name "mate-icon-theme")
     (version "1.22.0")
-    (source (origin
+    (source
+     (origin
        (method url-fetch)
-              (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                                  (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -159,10 +158,10 @@ actions.")
   (package
     (name "mate-icon-theme-faenza")
     (version "1.20.0")
-    (source (origin
+    (source
+     (origin
        (method url-fetch)
-              (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                                  (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -197,11 +196,11 @@ from Mint-X-F and Faenza-Fresh icon packs.")
   (package
     (name "mate-themes")
     (version "3.22.19")
-    (source (origin
+    (source
+     (origin
        (method url-fetch)
-              (uri (string-append "https://pub.mate-desktop.org/releases/themes/"
+       (uri (string-append "mirror://mate/themes/" (version-major+minor version)
-                                  (version-major+minor version) "/mate-themes-"
+                           "/mate-themes-" version ".tar.xz"))
-                                  version ".tar.xz"))
               (sha256
                (base32
                 "1ycb8b8r0s8d1h1477135mynr53s5781gdb2ap8xlvj2g58492wq"))))
@@ -225,10 +224,10 @@ themes for both gtk+-2 and gtk+-3.")
   (package
     (name "mate-desktop")
     (version "1.22.0")
-    (source (origin
+    (source
+     (origin
        (method url-fetch)
-              (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                                  (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -259,10 +258,10 @@ desktop and the mate-about program.")
   (package
     (name "libmateweather")
     (version "1.22.0")
-    (source (origin
+    (source
+     (origin
        (method url-fetch)
-              (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                                  (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -308,8 +307,7 @@ the MATE desktop environment.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -349,8 +347,7 @@ configurations (profiles).")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -417,8 +414,7 @@ configuration program to choose applications starting on login.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -460,8 +456,7 @@ configuration program to choose applications starting on login.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -490,8 +485,7 @@ sound systems.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -519,10 +513,10 @@ MATE desktop environment.")
   (package
     (name "mate-menus")
     (version "1.22.0")
-    (source (origin
+    (source
+     (origin
        (method url-fetch)
-              (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                                  (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -563,8 +557,7 @@ assorted menu related utility programs.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -637,8 +630,7 @@ Interactive Weather Information Network (IWIN).
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -674,8 +666,7 @@ mate-volume-control, a MATE volume control application and applet.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -748,8 +739,7 @@ infamous 'Wanda the Fish'.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -852,8 +842,7 @@ infamous 'Wanda the Fish'.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -911,8 +900,7 @@ icons on the MATE desktop.  It works on local and remote file systems.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -966,8 +954,7 @@ icons on the MATE desktop.  It works on local and remote file systems.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -1026,8 +1013,7 @@ of various aspects of your desktop.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -1077,8 +1063,7 @@ for use with MATE or as a standalone window manager.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -1117,8 +1102,7 @@ sessions, panels, menus, file management, and preferences.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -1149,8 +1133,7 @@ sessions, panels, menus, file management, and preferences.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -1172,8 +1155,7 @@ can be used as backgrounds in the MATE Desktop environment.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -1214,8 +1196,7 @@ Re-decorates windows on un-maximise.
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -1286,8 +1267,7 @@ can be used as backgrounds in the MATE Desktop environment.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -1339,8 +1319,7 @@ can be used as backgrounds in the MATE Desktop environment.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -1390,8 +1369,7 @@ can be used as backgrounds in the MATE Desktop environment.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -1444,8 +1422,7 @@ can be used as backgrounds in the MATE Desktop environment.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -1495,8 +1472,7 @@ can be used as backgrounds in the MATE Desktop environment.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32
@@ -1536,8 +1512,7 @@ MATE Desktop to monitor your system resources and usage.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pub.mate-desktop.org/releases/"
+       (uri (string-append "mirror://mate/" (version-major+minor version) "/"
-                           (version-major+minor version) "/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32

gnu/packages/maths.scm

@@ -1692,7 +1692,7 @@ September 2004}")
 (define-public petsc
   (package
     (name "petsc")
-    (version "3.10.4")
+    (version "3.11.2")
     (source
      (origin
       (method url-fetch)
@@ -1700,7 +1700,7 @@ September 2004}")
       (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
                           "petsc-lite-" version ".tar.gz"))
       (sha256
-       (base32 "0fk16944zh3473ra198kdkxdn08rq7b6ap838hxy1mh1i0hb488r"))))
+       (base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
     (outputs '("out"                    ; libraries and headers
                "examples"))             ; ~30MiB of examples
     (build-system gnu-build-system)
@@ -1845,7 +1845,11 @@ scientific applications modeled by partial differential equations.")
         ``("--with-mpiexec=mpirun"
            ,(string-append "--with-mpi-dir="
                            (assoc-ref %build-inputs "openmpi"))
-           ,@(delete "--with-mpi=0" ,cf)))))
+           ,@(delete "--with-mpi=0" ,cf)))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-before 'configure 'mpi-setup
+             ,%openmpi-setup)))))
     (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
 
 (define-public python-petsc4py
@@ -1910,7 +1914,7 @@ savings are consistently > 5x.")
 (define-public slepc
   (package
     (name "slepc")
-    (version "3.10.1")
+    (version "3.11.1")
     (source
      (origin
        (method url-fetch)
@@ -1918,10 +1922,11 @@ savings are consistently > 5x.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "188j1a133q91h8pivpnzwcf78kz8dvz2nzf6ndnjygdbqb48fizn"))))
+         "1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
     (build-system gnu-build-system)
     (native-inputs
-     `(("python" ,python-2)))
+     `(("python" ,python-2)
+       ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
     (inputs
      `(("arpack" ,arpack-ng)
        ("gfortran" ,gfortran)))
@@ -1933,7 +1938,10 @@ savings are consistently > 5x.")
        `(,(string-append "--with-arpack-dir="
                          (assoc-ref %build-inputs "arpack") "/lib"))
        #:make-flags                     ;honor (parallel-job-count)
-       `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
+       `(,(format #f "MAKE_NP=~a" (parallel-job-count))
+         ,(string-append "PETSCCONFIGDIR="
+                         (assoc-ref %build-inputs "petsc:examples")
+                         "/share/petsc/examples/config"))
        #:phases
        (modify-phases %standard-phases
          (replace 'configure
@@ -2752,7 +2760,7 @@ to BMP, JPEG or PNG image formats.")
 (define-public maxima
   (package
     (name "maxima")
-    (version "5.42.2")
+    (version "5.43.0")
     (source
      (origin
        (method url-fetch)
@@ -2760,7 +2768,7 @@ to BMP, JPEG or PNG image formats.")
                            version "-source/" name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0kdncy6137sg3rradirxzj10mkcvafxd892zlclwhr9sa7b12zhn"))
+         "0xyahp4c6509haxh4n1swiqm3421gplkdisa0zypclh3252sbzfw"))
        (patches (search-patches "maxima-defsystem-mkdir.patch"))))
     (build-system gnu-build-system)
     (inputs
@@ -2794,11 +2802,18 @@ to BMP, JPEG or PNG image formats.")
              (let* ((sed (string-append (assoc-ref inputs "sed") "/bin/sed"))
                     (coreutils (assoc-ref inputs "coreutils"))
                     (dirname (string-append coreutils "/bin/dirname"))
-                    (head (string-append coreutils "/bin/head")))
+                    (head (string-append coreutils "/bin/head"))
+                    (perl (string-append (assoc-ref inputs "perl") "/bin/perl"))
+                    (python (string-append (assoc-ref inputs "python")
+                                           "/bin/python3")))
                (substitute* "src/maxima.in"
                  (("sed ") (string-append sed " "))
                  (("dirname") dirname)
                  (("head") head))
+               (substitute* "doc/info/Makefile.in"
+                 (("/usr/bin/env perl") perl))
+               (substitute* "doc/info/build_html.sh.in"
+                 (("python") python))
                #t)))
          (add-before 'check 'pre-check
            (lambda _
@@ -2829,9 +2844,6 @@ to BMP, JPEG or PNG image formats.")
                (with-directory-excursion out
                  (mkdir-p "share/emacs")
                  (mkdir-p "share/doc")
-                 (symlink
-                  (string-append datadir "/emacs/")
-                  (string-append out "/share/emacs/site-lisp"))
                  (symlink
                   (string-append datadir "/doc/")
                   (string-append out "/share/doc/maxima"))
@@ -2863,7 +2875,7 @@ point numbers.")
 (define-public wxmaxima
   (package
     (name "wxmaxima")
-    (version "19.03.1")
+    (version "19.05.7")
     (source
      (origin
        (method git-fetch)
@@ -2873,7 +2885,7 @@ point numbers.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1qkf4jg86xnn3wk3782ffmfz12axb92dkjagcz3ffzw2wi1rclml"))))
+         "0zaz71fh156b9inrxf86scnix247al5pl9v18cxhjxcm0lanqxdp"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("gettext" ,gettext-minimal)))
@@ -3553,6 +3565,7 @@ in finite element programs.")
     (inputs
      `(("mpi" ,openmpi)
        ;;Supported only with MPI:
+       ("hdf5" ,hdf5-parallel-openmpi)  ;TODO: have petsc-openmpi propagate?
        ("p4est" ,p4est-openmpi)
        ("petsc" ,petsc-openmpi)
        ("slepc" ,slepc-openmpi)

gnu/packages/mes.scm

@@ -28,6 +28,7 @@
   #:use-module (gnu packages man)
   #:use-module (gnu packages package-management)
   #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages texinfo)
   #:use-module (guix build-system gnu)
   #:use-module (guix download)
@@ -35,7 +36,7 @@
   #:use-module (guix licenses)
   #:use-module (guix packages))
 
-(define-public nyacc
+(define-public nyacc-0.86
   (package
     (name "nyacc")
     (version "0.86.0")
@@ -58,6 +59,37 @@ extensive examples, including parsers for the Javascript and C99 languages.")
     (home-page "https://savannah.nongnu.org/projects/nyacc")
     (license (list gpl3+ lgpl3+))))
 
+(define-public nyacc
+  (package
+    (inherit nyacc-0.86)
+    (version "0.94.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://savannah/nyacc/nyacc-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "12qnzwm1n3j8z7hbr9hy2wka9a1aasm2rvnpnvdxkjcsbdzj8fn4"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (substitute* (find-files "." "^Makefile\\.in$")
+                    (("^SITE_SCM_DIR =.*")
+                     "SITE_SCM_DIR = \
+@prefix@/share/guile/site/@GUILE_EFFECTIVE_VERSION@\n")
+                    (("^SITE_SCM_GO_DIR =.*")
+                     "SITE_SCM_GO_DIR = \
+@prefix@/lib/guile/@GUILE_EFFECTIVE_VERSION@/site-ccache\n")
+                    (("^INFODIR =.*")
+                     "INFODIR = @prefix@/share/info\n")
+                    (("^DOCDIR =.*")
+                     "DOCDIR = @prefix@/share/doc/$(PACKAGE_TARNAME)\n"))
+                  #t))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("guile" ,guile-2.2)))))
+
 (define-public mes
   (package
     (name "mes")
@@ -73,7 +105,10 @@ extensive examples, including parsers for the Javascript and C99 languages.")
     (supported-systems '("i686-linux" "x86_64-linux"))
     (propagated-inputs
      `(("mescc-tools" ,mescc-tools)
-       ("nyacc" ,nyacc)))
+
+       ;; XXX: MesCC appears to enter an infinite loop (?) while building
+       ;; crt1.o when we switch to nyacc 0.94.
+       ("nyacc" ,nyacc-0.86)))
     (native-inputs
      `(("guile" ,guile-2.2)
        ,@(let ((target-system (or (%current-target-system)

gnu/packages/messaging.scm

@@ -371,15 +371,14 @@ authentication.")
 (define-public pidgin
   (package
     (name "pidgin")
-    (version "2.12.0")
+    (version "2.13.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/pidgin/Pidgin/"
-                           version "/" name "-" version ".tar.bz2"))
+                           version "/pidgin-" version ".tar.bz2"))
        (sha256
-        (base32
+        (base32 "13vdqj70315p9rzgnbxjp9c51mdzf1l4jg1kvnylc4bidw61air7"))
-         "1y5p2mq3bfw35b66jsafmbva0w5gg1k99y9z8fyp3jfksqv3agcc"))
        (patches (search-patches "pidgin-add-search-path.patch"))))
     (build-system glib-or-gtk-build-system)
     (native-inputs
@@ -403,13 +402,13 @@ authentication.")
        ;; TODO: gstreamer: patches needed to support gstreamer-1.0 or later
        ;; TODO: farstream
        ;; TODO: meanwhile
-       ;; TODO: network-manager
        ;; TODO: gtkspell
        ;; TODO: libxephyr
        ;; TODO: libgadu
        ("libxslt" ,libxslt)
        ("avahi" ,avahi)
        ("ncurses" ,ncurses)
+       ("network-manager" ,network-manager)
        ("sqlite" ,sqlite)
        ("libice" ,libice)
        ("libsm" ,libsm)
@@ -420,7 +419,6 @@ authentication.")
        (list "--disable-gtkspell"
              "--disable-tcl"
              "--disable-meanwhile"
-             "--disable-nm"  ; XXX remove when we have network-manager
              "--disable-vv"  ; XXX remove when we have farstream and gstreamer
              "--disable-gstreamer" ; XXX patches needed to support gstreamer-1.0
              "--enable-cyrus-sasl"
@@ -433,7 +431,7 @@ authentication.")
             (files (list (string-append "lib/purple-"
                                         (version-major version))
                          "lib/pidgin")))))
-    (home-page "http://www.pidgin.im/")
+    (home-page "https://www.pidgin.im/")
     (synopsis "Graphical multi-protocol instant messaging client")
     (description
      "Pidgin is a modular instant messaging client that supports many popular

gnu/packages/mpd.scm

@@ -91,7 +91,7 @@ interfacing MPD in the C, C++ & Objective C languages.")
 (define-public mpd
   (package
     (name "mpd")
-    (version "0.21.8")
+    (version "0.21.9")
     (source (origin
               (method url-fetch)
               (uri
@@ -100,7 +100,7 @@ interfacing MPD in the C, C++ & Objective C languages.")
                               "/mpd-" version ".tar.xz"))
               (sha256
                (base32
-                "0mwpkbjsljj1khlnnjanvw3pgxbhsdl0bh2k9bxnpijn2gqq7q13"))))
+                "0ghda8g9q0bi6nrvl6n756d8f45spqpblkh77mnb4k9gmiv57qir"))))
     (build-system meson-build-system)
     (arguments
      `(#:configure-flags '("-Ddocumentation=true"))) ;the default is 'false'...

gnu/packages/music.scm

@@ -1315,16 +1315,16 @@ Editor.  It is compatible with Power Tab Editor 1.7 and Guitar Pro.")
 (define-public jalv-select
   (package
     (name "jalv-select")
-    (version "0.8")
+    (version "1.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/brummer10/jalv_select.git")
-                    (commit (string-append "V" version))))
+                    (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0gqh768sbvn9ffyx1vqg9i57py9x9v4l65bk6wjsvgga4d7m83k1"))))
+                "15yanq1wra0hyh6x72ji7pk562iddg476g3vksj495x91zhnl6vm"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
@@ -1337,8 +1337,6 @@ Editor.  It is compatible with Power Tab Editor 1.7 and Guitar Pro.")
              (substitute* "jalv.select.cpp"
                (("echo \\$PATH.*tr ':'.*xargs ls")
                 (string-append "ls -1 " (assoc-ref inputs "jalv") "/bin")))
-             (substitute* "jalv.select.h"
-               (("gtkmm.h") "gtkmm-2.4/gtkmm.h"))
              #t))
          (add-before 'reset-gzip-timestamps 'make-manpages-writable
            (lambda* (#:key outputs #:allow-other-keys)
@@ -3727,7 +3725,7 @@ audio samples and various soft sythesizers.  It can receive input from a MIDI ke
 (define-public musescore
   (package
     (name "musescore")
-    (version "3.0.5")
+    (version "3.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -3736,7 +3734,7 @@ audio samples and various soft sythesizers.  It can receive input from a MIDI ke
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1inf6zdyh6yspjv1i7g6rw9wn90vki1s2qgilkp0j4aphayj4mic"))
+                "07xkn8gnnqzhj9cn1li5qpm2rfm86bmxbbfd76i1jx4v999icn0j"))
               (modules '((guix build utils)))
               (snippet
                ;; Un-bundle OpenSSL and remove unused libraries.

gnu/packages/networking.scm

@@ -1485,15 +1485,15 @@ procedure calls (RPCs).")
 (define-public openvswitch
   (package
     (name "openvswitch")
-    (version "2.10.1")
+    (version "2.11.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "http://openvswitch.org/releases/openvswitch-"
+                    "https://www.openvswitch.org/releases/openvswitch-"
                     version ".tar.gz"))
               (sha256
                (base32
-                "103wi6k8xal0z1pyy680gms56skagh6jawa2ja588ljr55jcg4sg"))))
+                "1p5mv44jaslvrr1ym15smqna19y0gi4vqcsyj58625vv9bj6laf1"))))
     (build-system gnu-build-system)
     (arguments
      '(;; FIXME: many tests fail with:
@@ -1529,7 +1529,7 @@ procedure calls (RPCs).")
      `(("libcap-ng" ,libcap-ng)
        ("openssl" ,openssl)))
     (synopsis "Virtual network switch")
-    (home-page "http://www.openvswitch.org/")
+    (home-page "https://www.openvswitch.org/")
     (description
      "Open vSwitch is a multilayer virtual switch.  It is designed to enable
 massive network automation through programmatic extension, while still

gnu/packages/node.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Mike Gerwitz <mtg@gnu.org>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018, 2019 Marius Bakke <mbakke@fastmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -45,14 +45,14 @@
 (define-public node
   (package
     (name "node")
-    (version "9.11.1")
+    (version "10.15.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://nodejs.org/dist/v" version
-                                  "/node-v" version ".tar.gz"))
+                                  "/node-v" version ".tar.xz"))
               (sha256
                (base32
-                "1vjh9zvw7wkdz6b0l99ya7mqjk0l8lbg9isr1q8rxwp400dhkk32"))
+                "1mcijznh481s44i59p571a38bfvcxm9f8x2l0l1005aly0kdj8jf"))
               (modules '((guix build utils)))
               (snippet
                `(begin
@@ -83,18 +83,14 @@
                            "--shared-zlib"
                            "--without-snapshot"
                            "--with-intl=system-icu")
+       ;; Run only the CI tests.  The default test target requires additional
+       ;; add-ons from NPM that are not distributed with the source.
+       #:test-target "test-ci-js"
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'patch-files
            (lambda* (#:key inputs #:allow-other-keys)
 
-             ;; This phase is inherited by Node LTS, which does not have all
-             ;; the files listed here.  Use this helper for convenience.
-             (define (delete-if-exists file)
-               (if (file-exists? file)
-                   (delete-file file)
-                   '()))
-
              ;; Fix hardcoded /bin/sh references.
              (substitute* '("lib/child_process.js"
                             "lib/internal/v8_prof_polyfill.js"
@@ -110,17 +106,9 @@
                (("'/usr/bin/env'")
                 (string-append "'" (which "env") "'")))
 
-             ;; FIXME: These tests depend on being able to install eslint.
-             ;; See https://github.com/nodejs/node/issues/17098.
-             (for-each delete-if-exists
-                       '("test/parallel/test-eslint-alphabetize-errors.js"
-                         "test/parallel/test-eslint-buffer-constructor.js"
-                         "test/parallel/test-eslint-documented-errors.js"
-                         "test/parallel/test-eslint-inspector-check.js"))
-
              ;; FIXME: These tests fail in the build container, but they don't
              ;; seem to be indicative of real problems in practice.
-             (for-each delete-if-exists
+             (for-each delete-file
                        '("test/async-hooks/test-ttywrap.readstream.js"
                          "test/parallel/test-util-inspect.js"
                          "test/parallel/test-v8-serdes.js"
@@ -132,14 +120,13 @@
                          "test/parallel/test-net-listen-after-destroying-stdin.js"
                          "test/parallel/test-npm-install.js"
                          "test/sequential/test-child-process-emfile.js"
-                         "test/sequential/test-benchmark-child-process.js"
                          "test/sequential/test-http-regr-gh-2928.js"))
 
              ;; These tests have an expiry date: they depend on the validity of
              ;; TLS certificates that are bundled with the source.  We want this
              ;; package to be reproducible forever, so remove those.
              ;; TODO: Regenerate certs instead.
-             (for-each delete-if-exists
+             (for-each delete-file
                        '("test/parallel/test-tls-passphrase.js"
                          "test/parallel/test-tls-server-verify.js"))
              #t))
@@ -184,9 +171,9 @@
      `(("c-ares" ,c-ares)
        ("http-parser" ,http-parser)
        ("icu4c" ,icu4c)
-       ("libuv" ,libuv-1.19)
+       ("libuv" ,libuv)
        ("nghttp2" ,nghttp2 "lib")
-       ("openssl" ,openssl-1.0)
+       ("openssl" ,openssl)
        ("zlib" ,zlib)))
     (synopsis "Evented I/O for V8 JavaScript")
     (description "Node.js is a platform built on Chrome's JavaScript runtime
@@ -197,16 +184,3 @@ devices.")
     (home-page "https://nodejs.org/")
     (license expat)
     (properties '((timeout . 3600))))) ; 1 h
-
-(define-public node-lts
-  (package
-    (inherit node)
-    (name "node-lts")
-    (version "8.12.0")
-    (source (origin
-              (inherit (package-source node))
-              (uri (string-append "https://nodejs.org/dist/v" version
-                                  "/node-v" version ".tar.xz"))
-              (sha256
-               (base32
-                "16j1rrxkhmvpcw689ndw1raql1gz4jqn7n82z55zn63c05cgz7as"))))))

gnu/packages/ocaml.scm

@@ -697,7 +697,8 @@ written in Objective Caml.")
            (lambda* (#:key outputs #:allow-other-keys)
              (format #t "~a~%" (find-files "." ".*.so"))
              (let ((stubdir (string-append (assoc-ref outputs "out")
-                                           "/lib/ocaml/site-lib")))
+                                           "/lib/ocaml/site-lib/stublibs")))
+               (delete-file stubdir)
                (mkdir-p stubdir)
                (install-file "src/dllnums.so" stubdir))
              #t)))))
@@ -1626,7 +1627,13 @@ spans without being subject to operating system calendar time adjustments.")
                                          "/lib/ocaml/site-lib/cmdliner"))
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure))))
+         (delete 'configure)
+         (add-before 'build 'fix-source-file-order
+           (lambda _
+             (substitute* "build.ml"
+               (("Sys.readdir dir")
+                "let a = Sys.readdir dir in Array.sort String.compare a; a"))
+             #t)))))
     (home-page "http://erratique.ch/software/cmdliner")
     (synopsis "Declarative definition of command line interfaces for OCaml")
     (description "Cmdliner is a module for the declarative definition of command
@@ -2290,6 +2297,12 @@ many additional enhancements, including:
      `(#:phases
        (modify-phases %standard-phases
          (delete 'check) ; tests are run by the build phase
+         (add-before 'build 'fix-nondeterminism
+           (lambda _
+             (substitute* "setup.ml"
+               (("Sys.readdir dirname")
+                "let a = Sys.readdir dirname in Array.sort String.compare a; a"))
+             #t))
          (replace 'build
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let ((files

gnu/packages/package-management.scm

@@ -111,8 +111,8 @@
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
   (let ((version "1.0.1")
-        (commit "820429517f9cc8333704a839b4346ac4b02468c4")
+        (commit "4a54ed774913480c0f8dad3caf0cd627e4fa8ebf")
-        (revision 1))
+        (revision 3))
     (package
       (name "guix")
 
@@ -128,7 +128,7 @@
                       (commit commit)))
                 (sha256
                  (base32
-                  "1vfp7ps1k1cwn8p0gsgarlxcy982hzyvb7zqnj66jqd258a1qfgh"))
+                  "14m4a4bn0d5hav6mrks5d7r223knx9dpswgbsc875wgr2921na2h"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments
@@ -272,6 +272,7 @@
        `(("bzip2" ,bzip2)
          ("gzip" ,gzip)
          ("zlib" ,zlib)                           ;for 'guix publish'
+         ("lzlib" ,lzlib)            ;for 'guix publish' and 'guix substitute'
 
          ("sqlite" ,sqlite)
          ("libgcrypt" ,libgcrypt)
@@ -547,13 +548,16 @@ transactions from C or Python.")
 (define-public diffoscope
   (package
     (name "diffoscope")
-    (version "114")
+    (version (git-version "115" "1" "7f3416ffd12572b42c814e43ac15cee44ef48155"))
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (pypi-uri name version))
+              (uri (git-reference
+                    (url "https://salsa.debian.org/reproducible-builds/diffoscope.git")
+                    (commit "7f3416ffd12572b42c814e43ac15cee44ef48155")))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "07sma4izcqxdv0zi1s5fnsybvkc47c3vbpm372sg83q8l7rhizzp"))))
+                "1pn2rwlz5shdx7s63798wx2v7029bl5if6dlq3i2r6zsnpp0laki"))))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
@@ -589,7 +593,8 @@ transactions from C or Python.")
                       #t))
                   (add-before 'check 'delete-failing-test
                     (lambda _
-                      (delete-file "tests/test_tools.py") ;this requires /sbin to be on the path
+                      ;; this requires /sbin to be on the path
+                      (delete-file "tests/test_tools.py")
                       #t)))))
     (inputs `(("rpm" ,rpm)                        ;for rpm-python
               ("python-file" ,python-file)
@@ -598,10 +603,9 @@ transactions from C or Python.")
               ("python-tlsh" ,python-tlsh)
               ("acl" ,acl)                        ;for getfacl
               ("colordiff" ,colordiff)
-              ("xxd" ,xxd)
+              ("xxd" ,xxd)))
-
     ;; Below are modules used for tests.
-              ("python-pytest" ,python-pytest)
+    (native-inputs `(("python-pytest" ,python-pytest)
                      ("python-chardet" ,python-chardet)))
     (home-page "https://diffoscope.org/")
     (synopsis "Compare files, archives, and directories in depth")

gnu/packages/password-utils.scm

@@ -108,7 +108,7 @@ human.")
 (define-public keepassxc
   (package
     (name "keepassxc")
-    (version "2.4.1")
+    (version "2.4.2")
     (source
      (origin
        (method url-fetch)
@@ -117,7 +117,7 @@ human.")
                            version "-src.tar.xz"))
        (sha256
         (base32
-         "1aw9airx9z846p0xc0qjgy5hg35b8cxp57rvlq39n6wx4z8ppa8d"))))
+         "0f31lmpbkw0wrhq0qa4yw5b51bjv7vqp3ikr355qcm905456vyhm"))))
     (build-system cmake-build-system)
     (arguments
      '(#:configure-flags '("-DWITH_XC_NETWORKING=YES"
@@ -310,6 +310,15 @@ and vice versa.")
        (sha256
         (base32 "1rimpjsdnmw8f5b7k558cic41p2qy2n2yrlqp5vh7mp4162hk0py"))))
     (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'install-dict
+           (lambda* (#:key make-flags #:allow-other-keys)
+             (begin
+               (chmod (string-append "util/cracklib-format") #o755)
+               (apply invoke "make" "dict" make-flags)
+               #t))))))
     (synopsis "Password checking library")
     (home-page "https://github.com/cracklib/cracklib")
     (description

gnu/packages/patches/borg-fix-hard-link-preloading.patch

@@ -1,157 +0,0 @@
-Fix a bug that would cause the test suite to hang:
-
-https://github.com/borgbackup/borg/issues/4350
-
-Patch copied from upstream source repository:
-
-https://github.com/borgbackup/borg/commit/18242ab9e2f26c450b8507aa1d5eceadab8ad027
-
-From 18242ab9e2f26c450b8507aa1d5eceadab8ad027 Mon Sep 17 00:00:00 2001
-From: Thomas Waldmann <tw@waldmann-edv.de>
-Date: Thu, 2 May 2019 21:02:26 +0200
-Subject: [PATCH] preload chunks for hardlink slaves w/o preloaded master,
- fixes #4350
-
-also split the hardlink extraction test into 2 tests.
-
-(cherry picked from commit f33f318d816505161d1449a02ddfdeb97d6fe80a)
----
- src/borg/archive.py            | 42 +++++++++++++++++++++++++++++-----
- src/borg/archiver.py           |  5 ++--
- src/borg/testsuite/archiver.py | 20 +++++++++-------
- 3 files changed, 51 insertions(+), 16 deletions(-)
-
-diff --git a/src/borg/archive.py b/src/borg/archive.py
-index adc1f42c..0793672a 100644
---- a/src/borg/archive.py
-+++ b/src/borg/archive.py
-@@ -192,7 +192,7 @@ def __init__(self, repository, key):
-         self.repository = repository
-         self.key = key
- 
--    def unpack_many(self, ids, filter=None, preload=False):
-+    def unpack_many(self, ids, filter=None, partial_extract=False, preload=False, hardlink_masters=None):
-         """
-         Return iterator of items.
- 
-@@ -209,12 +209,40 @@ def unpack_many(self, ids, filter=None, preload=False):
-             for item in items:
-                 if 'chunks' in item:
-                     item.chunks = [ChunkListEntry(*e) for e in item.chunks]
-+
-+            def preload(chunks):
-+                self.repository.preload([c.id for c in chunks])
-+
-             if filter:
-                 items = [item for item in items if filter(item)]
-+
-             if preload:
--                for item in items:
--                    if 'chunks' in item:
--                        self.repository.preload([c.id for c in item.chunks])
-+                if filter and partial_extract:
-+                    # if we do only a partial extraction, it gets a bit
-+                    # complicated with computing the preload items: if a hardlink master item is not
-+                    # selected (== not extracted), we will still need to preload its chunks if a
-+                    # corresponding hardlink slave is selected (== is extracted).
-+                    # due to a side effect of the filter() call, we now have hardlink_masters dict populated.
-+                    masters_preloaded = set()
-+                    for item in items:
-+                        if 'chunks' in item:  # regular file, maybe a hardlink master
-+                            preload(item.chunks)
-+                            # if this is a hardlink master, remember that we already preloaded it:
-+                            if 'source' not in item and hardlinkable(item.mode) and item.get('hardlink_master', True):
-+                                masters_preloaded.add(item.path)
-+                        elif 'source' in item and hardlinkable(item.mode):  # hardlink slave
-+                            source = item.source
-+                            if source not in masters_preloaded:
-+                                # we only need to preload *once* (for the 1st selected slave)
-+                                chunks, _ = hardlink_masters[source]
-+                                preload(chunks)
-+                                masters_preloaded.add(source)
-+                else:
-+                    # easy: we do not have a filter, thus all items are selected, thus we need to preload all chunks.
-+                    for item in items:
-+                        if 'chunks' in item:
-+                            preload(item.chunks)
-+
-             for item in items:
-                 yield item
- 
-@@ -433,8 +461,10 @@ def item_filter(self, item, filter=None):
-             return False
-         return filter(item) if filter else True
- 
--    def iter_items(self, filter=None, preload=False):
--        for item in self.pipeline.unpack_many(self.metadata.items, preload=preload,
-+    def iter_items(self, filter=None, partial_extract=False, preload=False, hardlink_masters=None):
-+        assert not (filter and partial_extract and preload) or hardlink_masters is not None
-+        for item in self.pipeline.unpack_many(self.metadata.items, partial_extract=partial_extract,
-+                                              preload=preload, hardlink_masters=hardlink_masters,
-                                               filter=lambda item: self.item_filter(item, filter)):
-             yield item
- 
-diff --git a/src/borg/archiver.py b/src/borg/archiver.py
-index 957959d6..dcc20455 100644
---- a/src/borg/archiver.py
-+++ b/src/borg/archiver.py
-@@ -755,7 +755,8 @@ def peek_and_store_hardlink_masters(item, matched):
-         else:
-             pi = None
- 
--        for item in archive.iter_items(filter, preload=True):
-+        for item in archive.iter_items(filter, partial_extract=partial_extract,
-+                                       preload=True, hardlink_masters=hardlink_masters):
-             orig_path = item.path
-             if strip_components:
-                 item.path = os.sep.join(orig_path.split(os.sep)[strip_components:])
-@@ -997,7 +998,7 @@ def item_to_tarinfo(item, original_path):
-                 return None, stream
-             return tarinfo, stream
- 
--        for item in archive.iter_items(filter, preload=True):
-+        for item in archive.iter_items(filter, preload=True, hardlink_masters=hardlink_masters):
-             orig_path = item.path
-             if strip_components:
-                 item.path = os.sep.join(orig_path.split(os.sep)[strip_components:])
-diff --git a/src/borg/testsuite/archiver.py b/src/borg/testsuite/archiver.py
-index c35ad800..935b3d79 100644
---- a/src/borg/testsuite/archiver.py
-+++ b/src/borg/testsuite/archiver.py
-@@ -823,7 +823,18 @@ def test_mount_hardlinks(self):
-             assert open('input/dir1/subdir/hardlink', 'rb').read() == b'123456'
- 
-     @requires_hardlinks
--    def test_extract_hardlinks(self):
-+    def test_extract_hardlinks1(self):
-+        self._extract_hardlinks_setup()
-+        with changedir('output'):
-+            self.cmd('extract', self.repository_location + '::test')
-+            assert os.stat('input/source').st_nlink == 4
-+            assert os.stat('input/abba').st_nlink == 4
-+            assert os.stat('input/dir1/hardlink').st_nlink == 4
-+            assert os.stat('input/dir1/subdir/hardlink').st_nlink == 4
-+            assert open('input/dir1/subdir/hardlink', 'rb').read() == b'123456'
-+
-+    @requires_hardlinks
-+    def test_extract_hardlinks2(self):
-         self._extract_hardlinks_setup()
-         with changedir('output'):
-             self.cmd('extract', self.repository_location + '::test', '--strip-components', '2')
-@@ -839,13 +850,6 @@ def test_extract_hardlinks(self):
-             assert open('input/dir1/subdir/hardlink', 'rb').read() == b'123456'
-             assert os.stat('input/dir1/aaaa').st_nlink == 2
-             assert os.stat('input/dir1/source2').st_nlink == 2
--        with changedir('output'):
--            self.cmd('extract', self.repository_location + '::test')
--            assert os.stat('input/source').st_nlink == 4
--            assert os.stat('input/abba').st_nlink == 4
--            assert os.stat('input/dir1/hardlink').st_nlink == 4
--            assert os.stat('input/dir1/subdir/hardlink').st_nlink == 4
--            assert open('input/dir1/subdir/hardlink', 'rb').read() == b'123456'
- 
-     def test_extract_include_exclude(self):
-         self.cmd('init', '--encryption=repokey', self.repository_location)
--- 
-2.21.0
-

gnu/packages/patches/emacs-realgud-fix-configure-ac.patch

@@ -1,27 +0,0 @@
-From a293690f29407ac54a218d6d20c2142e1a0319d1 Mon Sep 17 00:00:00 2001
-From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
-Date: Wed, 31 Oct 2018 00:08:34 -0400
-Subject: [PATCH] configure.ac: Fix NO_CHECK_EMACS_PACKAGES elisp.
-
-Remove the extraneous trailing parenthesis.
----
- configure.ac | 3 +--
- 1 file changed, 1 insertion(+), 2 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index de0d932..69bcea7 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -25,8 +25,7 @@ AC_MSG_NOTICE("Checking prerequiste packages")
- $EMACS -batch -q --no-site-file -eval \
-   '(dolist (package
-          (quote (cl-lib loc-changes load-relative test-simple)))
--        (require package))
--   )'
-+        (require package))'
- fi
- if test $? -ne 0 ; then
-     AC_MSG_ERROR([Can't continue until above error is corrected.])
--- 
-2.19.0
-

gnu/packages/patches/gnucash-fix-test-transaction-failure.patch

@@ -1,54 +0,0 @@
-# This patch was submitted upstream to: https://bugs.gnucash.org/show_bug.cgi?id=797008.
-From c20d74bebca516d0e391724202aad511967fe109 Mon Sep 17 00:00:00 2001
-From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
-Date: Wed, 2 Jan 2019 14:46:28 -0500
-Subject: [PATCH] tests: Fix a test failure in test-transaction.scm.
-
-With the New Year upon us, a test which was hard-coded to use 2018 now
-failed.
-
-Fixes issue #797008 (see:
-https://bugs.gnucash.org/show_bug.cgi?id=797008).
-
-* gnucash/report/standard-reports/test/test-transaction.scm:
-(trep-tests): Use the current year in the test string instead of a
-static one.
----
- gnucash/report/standard-reports/test/test-transaction.scm | 7 +++++--
- 1 file changed, 5 insertions(+), 2 deletions(-)
-
-diff --git a/gnucash/report/standard-reports/test/test-transaction.scm b/gnucash/report/standard-reports/test/test-transaction.scm
-index 755aba298..ae3fbd5c1 100644
---- a/gnucash/report/standard-reports/test/test-transaction.scm
-+++ b/gnucash/report/standard-reports/test/test-transaction.scm
-@@ -5,6 +5,7 @@
- (use-modules (gnucash report stylesheets))
- (use-modules (gnucash report report-system))
- (use-modules (gnucash report report-system test test-extras))
-+(use-modules (srfi srfi-19))
- (use-modules (srfi srfi-64))
- (use-modules (gnucash engine test srfi64-extras))
- (use-modules (sxml simple))
-@@ -643,7 +644,8 @@
-       (set-option! options "General" "Show original currency amount" #t)
-       (set-option! options "Sorting" "Primary Key" 'date)
-       (set-option! options "Sorting" "Primary Subtotal for Date Key" 'none)
--      (let* ((sxml (options->sxml options "dual columns")))
-+      (let* ((sxml (options->sxml options "dual columns"))
-+	     (current-year (date->string (current-date) "~y")))
-         (test-equal "dual amount column, with original currency headers"
-           (list "Date" "Num" "Description" "Memo/Notes" "Account"
-                 "Debit (USD)" "Credit (USD)" "Debit" "Credit")
-@@ -652,7 +654,8 @@
-           (list "Grand Total" "$2,280.00" "$2,280.00")
-           (get-row-col sxml -1 #f))
-         (test-equal "dual amount column, first transaction correct"
--          (list "01/03/18" "$103 income" "Root.Asset.Bank" "$103.00" "$103.00")
-+          (list (string-append "01/03/" current-year) "$103 income"
-+		"Root.Asset.Bank" "$103.00" "$103.00")
-           (get-row-col sxml 1 #f)))
-       )
- 
--- 
-2.19.0
-

gnu/packages/patches/gtksourceview-2-add-default-directory.patch

@@ -0,0 +1,33 @@
+From fc401acb15f15d487c942437b6fb429289dd3c67 Mon Sep 17 00:00:00 2001
+From: Julien Lepiller <julien@lepiller.eu>
+Date: Fri, 31 May 2019 13:22:25 +0200
+Subject: [PATCH] Add installation directory as a default directory.
+
+In Guix, this library is installed in a separate directory in the store,
+and it's typically not installed system-wide in a fixed directory. Add
+the store path to the set of default directories so dependents can find
+default langs and source highlighting scheme.
+---
+ gtksourceview/gtksourceview-utils.c | 6 ++++++
+ 1 file changed, 6 insertions(+)
+
+diff --git a/gtksourceview/gtksourceview-utils.c b/gtksourceview/gtksourceview-utils.c
+index 6f06bab..c3467d5 100644
+--- a/gtksourceview/gtksourceview-utils.c
++++ b/gtksourceview/gtksourceview-utils.c
+@@ -66,6 +66,12 @@ _gtk_source_view_get_default_dirs (const char *basename,
+ 							 basename,
+ 							 NULL));
+ 
++    /* installed dir */
++    g_ptr_array_add (dirs, g_build_filename (DATADIR,
++						 SOURCEVIEW_DIR,
++						 basename,
++						 NULL));
++
+ 	g_ptr_array_add (dirs, NULL);
+ 
+ 	return (gchar**) g_ptr_array_free (dirs, FALSE);
+-- 
+2.21.0
+

gnu/packages/patches/icecat-makeicecat.patch

@@ -3,10 +3,10 @@ in a snippet without network access.  After this patch is applied, some
 additional changes will be made using 'substitute*'.
 
 diff --git a/makeicecat b/makeicecat
-index aa46b94..db27a86 100644
+index 5a4390b..fcfa143 100644
 --- a/makeicecat
 +++ b/makeicecat
-@@ -36,75 +36,75 @@ export DEBFULLNAME="Ruben Rodriguez"
+@@ -29,55 +29,55 @@ SOURCEDIR=icecat-$FFVERSION
  
  DATA="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"/data
  
@@ -25,6 +25,7 @@ index aa46b94..db27a86 100644
 -wget -N https://ftp.mozilla.org/pub/mozilla.org/firefox/releases/${FFVERSION}esr/source/firefox-${FFVERSION}esr.source.tar.xz.asc
 -gpg --recv-keys --keyserver keyserver.ubuntu.com 24C6F355
 -gpg --verify firefox-${FFVERSION}esr.source.tar.xz.asc
+-echo -n 0a5f0c1d8d1e9443d85083d37fec32e5cc15c1001ea992d49745490065b4a023 firefox-${FFVERSION}esr.source.tar.xz |sha256sum -c -
 -
 -echo Extracting Firefox tarball
 -tar -xf firefox-${FFVERSION}esr.source.tar.xz
@@ -36,49 +37,13 @@ index aa46b94..db27a86 100644
 +# wget -N https://ftp.mozilla.org/pub/mozilla.org/firefox/releases/${FFVERSION}esr/source/firefox-${FFVERSION}esr.source.tar.xz.asc
 +# gpg --recv-keys --keyserver keyserver.ubuntu.com 24C6F355
 +# gpg --verify firefox-${FFVERSION}esr.source.tar.xz.asc
++# echo -n 0a5f0c1d8d1e9443d85083d37fec32e5cc15c1001ea992d49745490065b4a023 firefox-${FFVERSION}esr.source.tar.xz |sha256sum -c -
 +# 
 +# echo Extracting Firefox tarball
 +# tar -xf firefox-${FFVERSION}esr.source.tar.xz
 +# 
 +# mv firefox-${FFVERSION} $SOURCEDIR
  
- ###############################################################################
- # Retrieve /debian from Ubuntu
- ###############################################################################
- 
--rm -rf firefox.$CODENAME
--bzr branch https://code.launchpad.net/~mozillateam/firefox/firefox.$CODENAME
--cd firefox.$CODENAME
--bzr revert -r$REVISION
--echo '3.0 (native)' > debian/source/format
--
--for PATCH in ubuntu-bookmarks.patch ubuntu-ua-string-changes.patch unity-menubar.patch ubuntu-search-defaults.patch fix-make-package-tests-without-webrtc.patch revert-upstream-search-engine-changes.patch
--do
--  rm debian/patches/$PATCH
--  sed "/$PATCH/d" -i debian/patches/series
--done
--sed "/test-/d" -i debian/patches/series
--cd ..
--
--mv firefox.$CODENAME/debian $SOURCEDIR
--rm -rf firefox.$CODENAME
-+# rm -rf firefox.$CODENAME
-+# bzr branch https://code.launchpad.net/~mozillateam/firefox/firefox.$CODENAME
-+# cd firefox.$CODENAME
-+# bzr revert -r$REVISION
-+# echo '3.0 (native)' > debian/source/format
-+# 
-+# for PATCH in ubuntu-bookmarks.patch ubuntu-ua-string-changes.patch unity-menubar.patch ubuntu-search-defaults.patch fix-make-package-tests-without-webrtc.patch revert-upstream-search-engine-changes.patch
-+# do
-+#   rm debian/patches/$PATCH
-+#   sed "/$PATCH/d" -i debian/patches/series
-+# done
-+# sed "/test-/d" -i debian/patches/series
-+# cd ..
-+# 
-+# mv firefox.$CODENAME/debian $SOURCEDIR
-+# rm -rf firefox.$CODENAME
- 
  ###############################################################################
  # Retrieve l10n
  ###############################################################################
@@ -133,19 +98,10 @@ index aa46b94..db27a86 100644
  
  #for patch in $DATA/patches/*; do
  #    echo Patching with file: $patch
-@@ -720,7 +720,7 @@ debian/rules debian/control
+@@ -590,6 +590,6 @@ sed 's/777/755/;' -i toolkit/crashreporter/google-breakpad/Makefile.in
- touch -d "yesterday" debian/control
+ # Fix CVE-2012-3386
- debian/rules debian/control
- 
--echo | dch -b -D stable -v "$ICECATVERSION"  "Converted into IceCat (http://www.gnu.org/software/gnuzilla/)"
-+# echo | dch -b -D stable -v "$ICECATVERSION"  "Converted into IceCat (http://www.gnu.org/software/gnuzilla/)"
- sed "1s/firefox/icecat/" -i debian/changelog
- 
- touch configure js/src/configure
-@@ -734,6 +734,6 @@ sed 's/777/755/;' -i toolkit/crashreporter/google-breakpad/Makefile.in
  /bin/sed 's/chmod a+w/chmod u+w/' -i ./js/src/ctypes/libffi/Makefile.in ./toolkit/crashreporter/google-breakpad/Makefile.in ./toolkit/crashreporter/google-breakpad/src/third_party/glog/Makefile.in || true
  
- 
 -cd ..
 -echo Packaging tarball
 -tar cfj icecat-$ICECATVERSION.tar.bz2 $SOURCEDIR

gnu/packages/patches/libevent-2.0-CVE-2016-10195.patch

@@ -1,41 +0,0 @@
-Fix CVE-2016-10195 (buffer overread in libevent's DNS code):
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-10195
-https://github.com/libevent/libevent/issues/317
-
-Patch copied from upstream source repository:
-
-https://github.com/libevent/libevent/commit/96f64a022014a208105ead6c8a7066018449d86d
-
-From 3c570970516f48da35f42fef98276531fcc0abaa Mon Sep 17 00:00:00 2001
-From: Azat Khuzhin <a3at.mail@gmail.com>
-Date: Mon, 1 Feb 2016 17:32:09 +0300
-Subject: [PATCH] evdns: name_parse(): fix remote stack overread
-
----
- evdns.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/evdns.c b/evdns.c
-index 60b10485..137c24ea 100644
---- a/evdns.c
-+++ b/evdns.c
-@@ -960,7 +960,6 @@ name_parse(u8 *packet, int length, int *idx, char *name_out, int name_out_len) {
- 
- 	for (;;) {
- 		u8 label_len;
--		if (j >= length) return -1;
- 		GET8(label_len);
- 		if (!label_len) break;
- 		if (label_len & 0xc0) {
-@@ -981,6 +980,7 @@ name_parse(u8 *packet, int length, int *idx, char *name_out, int name_out_len) {
- 			*cp++ = '.';
- 		}
- 		if (cp + label_len >= end) return -1;
-+		if (j + label_len > length) return -1;
- 		memcpy(cp, packet + j, label_len);
- 		cp += label_len;
- 		j += label_len;
--- 
-2.11.0
-

gnu/packages/patches/libevent-2.0-CVE-2016-10196.patch

@@ -1,41 +0,0 @@
-Fix CVE-2016-10196 (buffer overflow in evutil):
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-10196
-https://github.com/libevent/libevent/issues/318
-
-Patch copied from upstream source repository:
-
-https://github.com/libevent/libevent/commit/329acc18a0768c21ba22522f01a5c7f46cacc4d5
-
-From 28bdc2f3f62259d21ccaf7be2b60ef0a53e6f342 Mon Sep 17 00:00:00 2001
-From: Azat Khuzhin <a3at.mail@gmail.com>
-Date: Sun, 31 Jan 2016 00:57:16 +0300
-Subject: [PATCH] evutil_parse_sockaddr_port(): fix buffer overflow
-
----
- evutil.c | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/evutil.c b/evutil.c
-index 33445170..e2dfe6e4 100644
---- a/evutil.c
-+++ b/evutil.c
-@@ -1808,12 +1808,12 @@ evutil_parse_sockaddr_port(const char *ip_as_string, struct sockaddr *out, int *
- 
- 	cp = strchr(ip_as_string, ':');
- 	if (*ip_as_string == '[') {
--		int len;
-+		size_t len;
- 		if (!(cp = strchr(ip_as_string, ']'))) {
- 			return -1;
- 		}
--		len = (int) ( cp-(ip_as_string + 1) );
--		if (len > (int)sizeof(buf)-1) {
-+		len = ( cp-(ip_as_string + 1) );
-+		if (len > sizeof(buf)-1) {
- 			return -1;
- 		}
- 		memcpy(buf, ip_as_string+1, len);
--- 
-2.11.0
-

gnu/packages/patches/libevent-2.0-CVE-2016-10197.patch

@@ -1,39 +0,0 @@
-Fix CVE-2016-10197 (out of bounds read on empty hostnames in evdns):
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-10197
-https://github.com/libevent/libevent/issues/332
-
-Patch copied from upstream source repository:
-
-https://github.com/libevent/libevent/commit/ec65c42052d95d2c23d1d837136d1cf1d9ecef9e
-
-From a0305cec166a5bc89f1eb362510cc4cd25ecc0bc Mon Sep 17 00:00:00 2001
-From: Azat Khuzhin <a3at.mail@gmail.com>
-Date: Fri, 25 Mar 2016 00:33:47 +0300
-Subject: [PATCH] evdns: fix searching empty hostnames
-
----
- evdns.c | 5 ++++-
- 1 file changed, 4 insertions(+), 1 deletion(-)
-
-diff --git a/evdns.c b/evdns.c
-index 137c24ea..6191c677 100644
---- a/evdns.c
-+++ b/evdns.c
-@@ -3122,9 +3122,12 @@ search_set_from_hostname(struct evdns_base *base) {
- static char *
- search_make_new(const struct search_state *const state, int n, const char *const base_name) {
- 	const size_t base_len = strlen(base_name);
--	const char need_to_append_dot = base_name[base_len - 1] == '.' ? 0 : 1;
-+	char need_to_append_dot;
- 	struct search_domain *dom;
- 
-+	if (!base_len) return NULL;
-+	need_to_append_dot = base_name[base_len - 1] == '.' ? 0 : 1;
-+
- 	for (dom = state->head; dom; dom = dom->next) {
- 		if (!n--) {
- 			/* this is the postfix we want */
--- 
-2.11.0
-

gnu/packages/patches/libevent-2.0-evbuffer-add-use-last-with-datap.patch

@@ -1,38 +0,0 @@
-From a8769ef12d7e223e33fc47bed03fba2bfa2f3536 Mon Sep 17 00:00:00 2001
-From: Marcus Sundberg <marcus@marcussundberg.com>
-Date: Sat, 26 Mar 2016 20:11:43 +0100
-Subject: [PATCH] evbuffer_add: Use last_with_datap if set, not last.
-
-evbuffer_add() would always put data in the last chain, even if there
-was available space in a previous chain, and in doing so it also
-failed to update last_with_datap, causing subsequent calls to other
-functions that do look at last_with_datap to add data in the middle
-of the evbuffer instead of at the end.
-
-Fixes the evbuffer_add() part of issue #335, and the evbuffer/add2 and
-evbuffer/add3 tests, and also prevents wasting space available in the
-chain pointed to by last_with_datap.
----
- buffer.c | 6 +++++-
- 1 file changed, 5 insertions(+), 1 deletion(-)
-
-diff --git a/buffer.c b/buffer.c
-index 7cca0e8a..f378b731 100644
---- a/buffer.c
-+++ b/buffer.c
-@@ -1732,7 +1732,11 @@ evbuffer_add(struct evbuffer *buf, const void *data_in, size_t datlen)
- 		goto done;
- 	}
- 
--	chain = buf->last;
-+	if (*buf->last_with_datap == NULL) {
-+		chain = buf->last;
-+	} else {
-+		chain = *buf->last_with_datap;
-+	}
- 
- 	/* If there are no chains allocated for this buffer, allocate one
- 	 * big enough to hold all the data. */
--- 
-2.12.0
-