Merge branch 'master' into core-updates

Makefile.am

@@ -34,7 +34,8 @@ nodist_noinst_SCRIPTS =				\
 
 # Modules that are not compiled but are installed nonetheless, such as
 # build-side modules with unusual dependencies.
-MODULES_NOT_COMPILED =
+MODULES_NOT_COMPILED =				\
+  guix/man-db.scm
 
 include gnu/local.mk
 
@@ -102,6 +103,7 @@ MODULES =					\
   guix/http-client.scm				\
   guix/gnupg.scm				\
   guix/elf.scm					\
+  guix/profiling.scm				\
   guix/store.scm				\
   guix/cvs-download.scm				\
   guix/svn-download.scm				\
@@ -252,6 +254,7 @@ AUX_FILES =						\
 # Templates, examples.
 EXAMPLES =					\
   gnu/system/examples/bare-bones.tmpl		\
+  gnu/system/examples/beaglebone-black.tmpl	\
   gnu/system/examples/desktop.tmpl		\
   gnu/system/examples/lightweight-desktop.tmpl	\
   gnu/system/examples/vm-image.tmpl

build-aux/build-self.scm

@@ -267,6 +267,7 @@ Please upgrade to an intermediate version first, for instance with:
                                   ;; Closure of (guix modules).
                                   (guix modules)
                                   (guix memoization)
+                                  (guix profiling)
                                   (guix sets))
 
                       ;; Arrange so that our own (guix build …) modules are

build-aux/hydra/gnu-system.scm

@@ -22,12 +22,14 @@
 ;;; tool.
 ;;;
 
-;; Attempt to use our very own Guix modules.
+(use-modules (system base compile))
+
 (eval-when (compile load eval)
 
-  ;; Ignore any available .go, and force recompilation.  This is because our
+  ;; Pre-load the compiler so we don't end up auto-compiling it.
-  ;; checkout in the store has mtime set to the epoch, and thus .go files look
+  (compile #t)
-  ;; newer, even though they may not correspond.
+
+  ;; Use our very own Guix modules.
   (set! %fresh-auto-compile #t)
 
   (and=> (assoc-ref (current-source-location) 'filename)
@@ -334,6 +336,13 @@ valid."
   (parameterize ((%graft? #f))
     ;; Return one job for each package, except bootstrap packages.
     (append-map (lambda (system)
+                  (format (current-error-port)
+                          "evaluating for '~a' (heap size: ~a MiB)...~%"
+                          system
+                          (round
+                           (/ (assoc-ref (gc-stats) 'heap-size)
+                              (expt 2. 20))))
+                  (invalidate-derivation-caches!)
                   (case subset
                     ((all)
                      ;; Build everything, including replacements.

doc/contributing.texi

@@ -193,6 +193,34 @@ facilities to directly operate on the syntax tree, such as raising an
 s-expression or wrapping it, swallowing or rejecting the following
 s-expression, etc.
 
+@cindex code snippets
+@cindex templates
+@cindex reducing boilerplate
+We also provide templates for common git commit messages and package
+definitions in the @file{etc/snippets} directory.  These templates can
+be used with @url{http://joaotavora.github.io/yasnippet/, YASnippet} to
+expand short trigger strings to interactive text snippets.  You may want
+to add the snippets directory to the @var{yas-snippet-dirs} variable in
+Emacs.
+
+@lisp
+;; @r{Assuming the Guix checkout is in ~/src/guix.}
+(with-eval-after-load 'yasnippet
+  (add-to-list 'yas-snippet-dirs "~/src/guix/etc/snippets"))
+@end lisp
+
+The commit message snippets depend on @url{https://magit.vc/, Magit} to
+display staged files.  When editing a commit message type @code{add}
+followed by @kbd{TAB} to insert a commit message template for adding a
+package; type @code{update} followed by @kbd{TAB} to insert a template
+for updating a package.
+
+The main snippet for @code{scheme-mode} is triggered by typing
+@code{package...} followed by @kbd{TAB}.  This snippet also inserts the
+trigger string @code{origin...}, which can be expanded further.  The
+@code{origin} snippet in turn may insert other trigger strings ending on
+@code{...}, which also can be expanded further.
+
 
 @node Coding Style
 @section Coding Style

doc/guix.texi

@@ -43,7 +43,8 @@ Copyright @copyright{} 2017 Maxim Cournoyer@*
 Copyright @copyright{} 2017 Tobias Geerinckx-Rice@*
 Copyright @copyright{} 2017 George Clemmer@*
 Copyright @copyright{} 2017 Andy Wingo@*
-Copyright @copyright{} 2017 Arun Isaac
+Copyright @copyright{} 2017 Arun Isaac@*
+Copyright @copyright{} 2017 nee
 
 Permission is granted to copy, distribute and/or modify this document
 under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -1065,6 +1066,15 @@ regular expression like this:
 # guix offload test machines.scm '\.gnu\.org$'
 @end example
 
+@cindex offload status
+To display the current load of all build hosts, run this command on the
+main node:
+
+@example
+# guix offload status
+@end example
+
+
 @node Invoking guix-daemon
 @section Invoking @command{guix-daemon}
 
@@ -1550,7 +1560,7 @@ features.
 This chapter describes the main features of Guix, as well as the
 package management tools it provides.  Along with the command-line
 interface described below (@pxref{Invoking guix package, @code{guix
-package}}), you may also use Emacs Interface (@pxref{Top,,,
+package}}), you may also use the Emacs-Guix interface (@pxref{Top,,,
 emacs-guix, The Emacs-Guix Reference Manual}), after installing
 @code{emacs-guix} package (run @kbd{M-x guix-help} command to start
 with it):
@@ -8690,6 +8700,9 @@ also specified.  @xref{Mapped Devices} and @ref{File Systems}.
 @itemx @code{groups} (default: @var{%base-groups})
 List of user accounts and groups.  @xref{User Accounts}.
 
+If the @code{users} list lacks a user account with UID@tie{}0, a
+``root'' account with UID@tie{}0 is automatically added.
+
 @item @code{skeletons} (default: @code{(default-skeletons)})
 A list target file name/file-like object tuples (@pxref{G-Expressions,
 file-like objects}).  These are the skeleton files that will be added to
@@ -14813,10 +14826,7 @@ A simple example configuration is given below.
            (server-blocks
              (list (nginx-server-configuration
                      (server-name '("www.example.com"))
-                     (root "/srv/http/www.example.com")
+                     (root "/srv/http/www.example.com"))))))
-                     (https-port #f)
-                     (ssl-certificate #f)
-                     (ssl-certificate-key #f))))))
 @end example
 
 In addition to adding server blocks to the service configuration
@@ -14826,9 +14836,6 @@ blocks, as in this example:
 @example
 (simple-service 'my-extra-server nginx-service-type
                 (list (nginx-server-configuration
-                        (https-port #f)
-                        (ssl-certificate #f)
-                        (ssl-certificate-key #f)
                         (root "/srv/http/extra-website")
                         (try-files (list "$uri" "$uri/index.html")))))
 @end example
@@ -14873,10 +14880,7 @@ HTTPS.
            (server-blocks
              (list (nginx-server-configuration
                      (server-name '("www.example.com"))
-                     (root "/srv/http/www.example.com")
+                     (root "/srv/http/www.example.com"))))))
-                     (https-port #f)
-                     (ssl-certificate #f)
-                     (ssl-certificate-key #f))))))
 @end example
 
 @item @code{upstream-blocks} (default: @code{'()})
@@ -14899,9 +14903,6 @@ requests with two servers.
       (list (nginx-server-configuration
               (server-name '("www.example.com"))
               (root "/srv/http/www.example.com")
-              (https-port #f)
-              (ssl-certificate #f)
-              (ssl-certificate-key #f)
               (locations
                 (list
                   (nginx-location-configuration
@@ -14925,6 +14926,13 @@ This can be useful if you have an existing configuration file, or it's
 not possible to do what is required through the other parts of the
 nginx-configuration record.
 
+@item @code{server-names-hash-bucket-size} (default: @code{#f})
+Bucket size for the server names hash tables, defaults to @code{#f} to
+use the size of the processors cache line.
+
+@item @code{server-names-hash-bucket-max-size} (default: @code{#f})
+Maximum bucket size for the server names hash tables.
+
 @end table
 @end deffn
 
@@ -14933,17 +14941,15 @@ Data type representing the configuration of an nginx server block.
 This type has the following parameters:
 
 @table @asis
-@item @code{http-port} (default: @code{80})
+@item @code{listen} (default: @code{'("80" "443 ssl")})
-Nginx will listen for HTTP connection on this port.  Set it at @code{#f} if
+Each @code{listen} directive sets the address and port for IP, or the
-nginx should not listen for HTTP (non secure) connection for this
+path for a UNIX-domain socket on which the server will accept requests.
-@dfn{server block}.
+Both address and port, or only address or only port can be specified.
+An address may also be a hostname, for example:
 
-@item @code{https-port} (default: @code{443})
+@example
-Nginx will listen for HTTPS connection on this port.  Set it at @code{#f} if
+'("127.0.0.1:8000" "127.0.0.1" "8000" "*:8000" "localhost:8000")
-nginx should not listen for HTTPS (secure) connection for this @dfn{server block}.
+@end example
-
-Note that nginx can listen for HTTP and HTTPS connections in the same
-@dfn{server block}.
 
 @item @code{server-name} (default: @code{(list 'default)})
 A list of server names this server represents. @code{'default} represents the
@@ -14965,17 +14971,20 @@ Nginx will send the list of files in the directory.
 A list of files whose existence is checked in the specified order.
 @code{nginx} will use the first file it finds to process the request.
 
-@item @code{ssl-certificate} (default: @code{"/etc/nginx/cert.pem"})
+@item @code{ssl-certificate} (default: @code{#f})
 Where to find the certificate for secure connections.  Set it to @code{#f} if
 you don't have a certificate or you don't want to use HTTPS.
 
-@item @code{ssl-certificate-key} (default: @code{"/etc/nginx/key.pem"})
+@item @code{ssl-certificate-key} (default: @code{#f})
 Where to find the private key for secure connections.  Set it to @code{#f} if
 you don't have a key or you don't want to use HTTPS.
 
 @item @code{server-tokens?} (default: @code{#f})
 Whether the server should add its configuration to response.
 
+@item @code{raw-content} (default: @code{'()})
+A list of raw lines added to the server block.
+
 @end table
 @end deftp
 
@@ -15086,6 +15095,145 @@ capability also has to be configured on the front-end as well.
 @end table
 @end deftp
 
+@cindex php-fpm
+PHP-FPM (FastCGI Process Manager) is an alternative PHP FastCGI implementation
+with some additional features useful for sites of any size.
+
+These features include:
+@itemize @bullet
+@item Adaptive process spawning
+@item Basic statistics (similar to Apache's mod_status)
+@item Advanced process management with graceful stop/start
+@item Ability to start workers with different uid/gid/chroot/environment
+and different php.ini (replaces safe_mode)
+@item Stdout & stderr logging
+@item Emergency restart in case of accidental opcode cache destruction
+@item Accelerated upload support
+@item Support for a "slowlog"
+@item Enhancements to FastCGI, such as fastcgi_finish_request() -
+a special function to finish request & flush all data while continuing to do
+something time-consuming (video converting, stats processing, etc.)
+@end itemize
+... and much more.
+
+@defvr {Scheme Variable} php-fpm-service-type
+A Service type for @code{php-fpm}.
+@end defvr
+
+@deftp {Data Type} php-fpm-configuration
+Data Type for php-fpm service configuration.
+@table @asis
+@item @code{php} (default: @code{php})
+The php package to use.
+@item @code{socket} (default: @code{(string-append "/var/run/php" (version-major (package-version php)) "-fpm.sock")})
+The address on which to accept FastCGI requests.  Valid syntaxes are:
+@table @asis
+@item @code{"ip.add.re.ss:port"}
+Listen on a TCP socket to a specific address on a specific port.
+@item @code{"port"}
+Listen on a TCP socket to all addresses on a specific port.
+@item @code{"/path/to/unix/socket"}
+Listen on a unix socket.
+@end table
+
+@item @code{user} (default: @code{php-fpm})
+User who will own the php worker processes.
+@item @code{group} (default: @code{php-fpm})
+Group of the worker processes.
+@item @code{socket-user} (default: @code{php-fpm})
+User who can speak to the php-fpm socket.
+@item @code{socket-group} (default: @code{php-fpm})
+Group that can speak to the php-fpm socket.
+@item @code{pid-file} (default: @code{(string-append "/var/run/php" (version-major (package-version php)) "-fpm.pid")})
+The process id of the php-fpm process is written to this file
+once the service has started.
+@item @code{log-file} (default: @code{(string-append "/var/log/php" (version-major (package-version php)) "-fpm.log")})
+Log for the php-fpm master process.
+@item @code{process-manager} (default: @code{(php-fpm-dynamic-process-manager-configuration)})
+Detailed settings for the php-fpm process manager.
+Must be either:
+@table @asis
+@item @code{<php-fpm-dynamic-process-manager-configuration>}
+@item @code{<php-fpm-static-process-manager-configuration>}
+@item @code{<php-fpm-on-demand-process-manager-configuration>}
+@end table
+@item @code{display-errors} (default @code{#f})
+Determines wether php errors and warning should be sent to clients
+and displayed in their browsers.
+This is useful for local php development, but a security risk for public sites,
+as error messages can reveal passwords and personal data.
+@item @code{workers-logfile} (default @code{(string-append "/var/log/php" (version-major (package-version php)) "-fpm.www.log")})
+This file will log the @code{stderr} outputs of php worker processes.
+Can be set to @code{#f} to disable logging.
+@item @code{file} (default @code{#f})
+An optional override of the whole configuration.
+You can use the @code{mixed-text-file} function or an absolute filepath for it.
+@end table
+@end deftp
+
+@deftp {Data type} php-fpm-dynamic-process-manager-configuration
+Data Type for the @code{dynamic} php-fpm process manager.  With the
+@code{dynamic} process manager, spare worker processes are kept around
+based on it's configured limits.
+@table @asis
+@item @code{max-children} (default: @code{5})
+Maximum of worker processes.
+@item @code{start-servers} (default: @code{2})
+How many worker processes should be started on start-up.
+@item @code{min-spare-servers} (default: @code{1})
+How many spare worker processes should be kept around at minimum.
+@item @code{max-spare-servers} (default: @code{3})
+How many spare worker processes should be kept around at maximum.
+@end table
+@end deftp
+
+@deftp {Data type} php-fpm-static-process-manager-configuration
+Data Type for the @code{static} php-fpm process manager.  With the
+@code{static} process manager, an unchanging number of worker processes
+are created.
+@table @asis
+@item @code{max-children} (default: @code{5})
+Maximum of worker processes.
+@end table
+@end deftp
+
+@deftp {Data type} php-fpm-on-demand-process-manager-configuration
+Data Type for the @code{on-demand} php-fpm process manager.  With the
+@code{on-demand} process manager, worker processes are only created as
+requests arrive.
+@table @asis
+@item @code{max-children} (default: @code{5})
+Maximum of worker processes.
+@item @code{process-idle-timeout} (default: @code{10})
+The time in seconds after which a process with no requests is killed.
+@end table
+@end deftp
+
+
+@deffn {Scheme Procedure} nginx-php-fpm-location @
+       [#:nginx-package nginx] @
+       [socket (string-append "/var/run/php" @
+                              (version-major (package-version php)) @
+                              "-fpm.sock")]
+A helper function to quickly add php to an @code{nginx-server-configuration}.
+@end deffn
+
+A simple services setup for nginx with php can look like this:
+@example
+(services (cons* (dhcp-client-service)
+                 (service php-fpm-service-type)
+                 (service nginx-service-type
+                          (nginx-server-configuration
+                           (server-name '("example.com"))
+                           (root "/srv/http/")
+                           (locations
+                            (list (nginx-php-location)))
+                           (https-port #f)
+                           (ssl-certificate #f)
+                           (ssl-certificate-key #f)))
+                 %base-services))
+@end example
+
 @node Certificate Services
 @subsubsection Certificate Services
 
@@ -15206,7 +15354,7 @@ and one slave, is:
 (operating-system
   ;; ...
   (services (cons* (service knot-service-type
-                     (knot-confifguration
+                     (knot-configuration
                        (remotes (list plop-master))
                        (zones (list master-zone slave-zone))))
                    ;; ...
@@ -17545,7 +17693,7 @@ serve the default @file{/srv/git} over HTTPS might be:
           (server-blocks
            (list
             (nginx-server-configuration
-             (http-port #f)
+             (listen '("443 ssl"))
              (server-name "git.my-host.org")
              (ssl-certificate
               "/etc/letsencrypt/live/git.my-host.org/fullchain.pem")
@@ -18228,7 +18376,6 @@ system.
 A possibly empty list of @code{menu-entry} objects (see below), denoting
 entries to appear in the bootloader menu, in addition to the current
 system entry and the entry pointing to previous system generations.
-generations.
 
 @item @code{default-entry} (default: @code{0})
 The index of the default boot menu entry.  Index 0 is for the entry of the
@@ -18609,6 +18756,14 @@ Build Options}).  In addition, @var{options} can contain one of the
 following:
 
 @table @option
+@item --expression=@var{expr}
+@itemx -e @var{expr}
+Consider the operating-system @var{expr} evaluates to.
+This is an alternative to specifying a file which evaluates to an
+operating system.
+This is used to generate the GuixSD installer @pxref{Building the
+Installation Image}).
+
 @item --system=@var{system}
 @itemx -s @var{system}
 Attempt to build for @var{system} instead of the host system type.

etc/snippets/scheme-mode/guix-cvs-reference

@@ -0,0 +1,8 @@
+# -*- mode: snippet -*-
+# name: guix-cvs-reference
+# key: cvs-reference...
+# --
+(cvs-reference
+  (root-directory "${1:root-directory}")
+  (module "${2:module}")
+  (revision "${3:revision}"))

etc/snippets/scheme-mode/guix-git-reference

@@ -0,0 +1,7 @@
+# -*- mode: snippet -*-
+# name: guix-git-reference
+# key: git-reference...
+# --
+(git-reference
+  (url "$1")
+  (commit ${2:commit}))

etc/snippets/scheme-mode/guix-hg-reference

@@ -0,0 +1,7 @@
+# -*- mode: snippet -*-
+# name: guix-hg-reference
+# key: hg-reference...
+# --
+(hg-reference
+  (url "$1")
+  (changeset ${2:changeset}))

etc/snippets/scheme-mode/guix-origin

@@ -0,0 +1,23 @@
+# -*- mode: snippet -*-
+# name: guix-origin
+# key: origin...
+# --
+(origin
+ (method ${1:$$(yas-choose-value "url-fetch"
+                                 "url-fetch/tarbomb"
+                                 "url-fetch/zipbomb"
+                                 "cvs-fetch"
+                                 "git-fetch"
+                                 "hg-fetch"
+                                 "svn-fetch")})
+ (uri ${1:$(cond ((equal yas-text "git-fetch") "git-reference...")
+                 ((equal yas-text "svn-fetch") "svn-reference...")
+                 ((equal yas-text "hg-fetch")  "hg-reference...")
+                 ((equal yas-text "cvs-fetch") "cvs-reference...")
+                 (t "(string-append \\"https://\\" version \\".tar.gz\\")"))}$0)
+ ${1:$(cond ((member yas-text '("git-fetch" "svn-fetch" "hg-fetch" "cvs-fetch"))
+             "(file-name (string-append name \\"-\\" version \\"-checkout\\"))")
+            (t ""))}
+ (sha256
+  (base32
+    "$2")))

etc/snippets/scheme-mode/guix-package

@@ -0,0 +1,34 @@
+# -*- mode: snippet -*-
+# name: guix-package
+# key: package...
+# --
+(define-public $1
+  (package
+    (name "$1")
+    (version "$2")
+    (source origin...$0)
+    (build-system ${3:$$(yas-choose-value "ant-build-system"
+                                          "asdf-build-system"
+                                          "cargo-build-system"
+                                          "cmake-build-system"
+                                          "dub-build-system"
+                                          "emacs-build-system"
+                                          "font-build-system"
+                                          "glib-or-gtk-build-system"
+                                          "gnu-build-system"
+                                          "go-build-system"
+                                          "haskell-build-system"
+                                          "meson-build-system"
+                                          "minify-build-system"
+                                          "ocaml-build-system"
+                                          "perl-build-system"
+                                          "python-build-system"
+                                          "r-build-system"
+                                          "ruby-build-system"
+                                          "texlive-build-system"
+                                          "trivial-build-system"
+                                          "waf-build-system")})
+    (home-page "$4")
+    (synopsis "$5")
+    (description "$6")
+    (license $7)))

etc/snippets/scheme-mode/guix-svn-reference

@@ -0,0 +1,7 @@
+# -*- mode: snippet -*-
+# name: guix-svn-reference
+# key: svn-reference...
+# --
+(svn-reference
+  (url "$1")
+  (revision ${2:svn-revision}))

etc/snippets/text-mode/guix-commit-message-add-package

@@ -0,0 +1,8 @@
+# -*- mode: snippet -*-
+# name: guix-commit-message-add-package
+# key: add
+# condition: git-commit-mode
+# --
+gnu: Add $1.
+
+* `(car (magit-staged-files))` ($1): New variable.

etc/snippets/text-mode/guix-commit-message-update-package

@@ -0,0 +1,9 @@
+# -*- mode: snippet -*-
+# name: guix-commit-message-update-package
+# key: update
+# condition: git-commit-mode
+# --
+gnu: $1: Update to $2.
+
+* `(car (magit-staged-files))` ($1): Update to $2.$0
+`(mapconcat (lambda (file) (concat "* " file)) (cdr (magit-staged-files)) "\n")`

gnu/bootloader/extlinux.scm

@@ -20,6 +20,7 @@
 (define-module (gnu bootloader extlinux)
   #:use-module (gnu bootloader)
   #:use-module (gnu system)
+  #:use-module (gnu build bootloader)
   #:use-module (gnu packages bootloaders)
   #:use-module (guix gexp)
   #:use-module (guix monads)
@@ -95,13 +96,8 @@ TIMEOUT ~a~%"
                   (find-files syslinux-dir "\\.c32$"))
         (unless
             (and (zero? (system* extlinux "--install" install-dir))
-                 (call-with-input-file (string-append syslinux-dir "/" #$mbr)
+                 (write-file-on-device
-                   (lambda (input)
+                  (string-append syslinux-dir "/" #$mbr) 440 device 0))
-                     (let ((bv (get-bytevector-n input 440)))
-                       (call-with-output-file device
-                         (lambda (output)
-                           (put-bytevector output bv))
-                         #:binary #t)))))
           (error "failed to install SYSLINUX")))))
 
 (define install-extlinux-mbr

gnu/bootloader/u-boot.scm

@@ -21,18 +21,35 @@
   #:use-module (gnu bootloader extlinux)
   #:use-module (gnu bootloader)
   #:use-module (gnu system)
+  #:use-module (gnu build bootloader)
   #:use-module (gnu packages bootloaders)
   #:use-module (guix gexp)
   #:use-module (guix monads)
   #:use-module (guix records)
   #:use-module (guix utils)
-  #:export (u-boot-bootloader))
+  #:export (u-boot-bootloader
+            u-boot-beaglebone-black-bootloader))
 
 (define install-u-boot
   #~(lambda (bootloader device mount-point)
       (if bootloader
         (error "Failed to install U-Boot"))))
 
+(define install-beaglebone-black-u-boot
+  ;; http://wiki.beyondlogic.org/index.php?title=BeagleBoneBlack_Upgrading_uBoot
+  ;; This first stage bootloader called MLO (U-Boot SPL) is expected at
+  ;; 0x20000 by BBB ROM code. The second stage bootloader will be loaded by
+  ;; the MLO and is expected at 0x60000.  Write both first stage ("MLO") and
+  ;; second stage ("u-boot.img") images, read in BOOTLOADER directory, to the
+  ;; specified DEVICE.
+  #~(lambda (bootloader device mount-point)
+      (let ((mlo (string-append bootloader "/libexec/MLO"))
+            (u-boot (string-append bootloader "/libexec/u-boot.img")))
+        (write-file-on-device mlo (* 256 512)
+                              device (* 256 512))
+        (write-file-on-device u-boot (* 1024 512)
+                              device (* 768 512)))))
+
 
 
 ;;;
@@ -45,3 +62,9 @@
    (name 'u-boot)
    (package #f)
    (installer install-u-boot)))
+
+(define u-boot-beaglebone-black-bootloader
+  (bootloader
+   (inherit u-boot-bootloader)
+   (package u-boot-beagle-bone-black)
+   (installer install-beaglebone-black-u-boot)))

gnu/build/bootloader.scm

@@ -0,0 +1,37 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@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 build bootloader)
+  #:use-module (ice-9 binary-ports)
+  #:export (write-file-on-device))
+
+
+;;;
+;;; Writing utils.
+;;;
+
+(define (write-file-on-device file size device offset)
+  "Write SIZE bytes from FILE to DEVICE starting at OFFSET."
+  (call-with-input-file file
+    (lambda (input)
+      (let ((bv (get-bytevector-n input size)))
+        (call-with-output-file device
+          (lambda (output)
+            (seek output offset SEEK_SET)
+            (put-bytevector output bv))
+          #:binary #t)))))

gnu/build/linux-boot.scm

@@ -22,8 +22,11 @@
   #:use-module (system repl error-handling)
   #:autoload   (system repl repl) (start-repl)
   #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-9)
   #:use-module (srfi srfi-26)
   #:use-module (ice-9 match)
+  #:use-module (ice-9 rdelim)
+  #:use-module (ice-9 regex)
   #:use-module (ice-9 ftw)
   #:use-module (guix build utils)
   #:use-module ((guix build syscalls)
@@ -35,6 +38,7 @@
             linux-command-line
             find-long-option
             make-essential-device-nodes
+            make-static-device-nodes
             configure-qemu-networking
 
             bind-mount
@@ -105,6 +109,109 @@ with the given MAJOR number, starting with MINOR."
              'block-special #o644 (device-number major (+ minor i)))
       (loop (+ i 1)))))
 
+;; Representation of a /dev node.
+(define-record-type <device-node>
+  (device-node name type major minor module)
+  device-node?
+  (name device-node-name)
+  (type device-node-type)
+  (major device-node-major)
+  (minor device-node-minor)
+  (module device-node-module))
+
+(define (read-static-device-nodes port)
+  "Read from PORT a list of <device-node> written in the format used by
+/lib/modules/*/*.devname files."
+  (let loop ((line (read-line port)))
+    (if (eof-object? line)
+      '()
+      (match (string-split line #\space)
+       (((? (cut string-prefix? "#" <>)) _ ...)
+        (loop (read-line port)))
+       ((module-name device-name device-spec)
+        (let* ((device-parts
+               (string-match "([bc])([0-9][0-9]*):([0-9][0-9]*)"
+                             device-spec))
+               (type-string (match:substring device-parts 1))
+               (type (match type-string
+                      ("c" 'char-special)
+                      ("b" 'block-special)))
+               (major-string (match:substring device-parts 2))
+               (major (string->number major-string 10))
+               (minor-string (match:substring device-parts 3))
+               (minor (string->number minor-string 10)))
+          (cons (device-node device-name type major minor module-name)
+                (loop (read-line port)))))
+       (_
+        (begin
+          (format (current-error-port)
+                  "read-static-device-nodes: ignored devname line '~a'~%" line)
+          (loop (read-line port))))))))
+
+(define* (mkdir-p* dir #:optional (mode #o755))
+  "This is a variant of 'mkdir-p' that works around
+<http://bugs.gnu.org/24659> by passing MODE explicitly in each 'mkdir' call."
+  (define absolute?
+    (string-prefix? "/" dir))
+
+  (define not-slash
+    (char-set-complement (char-set #\/)))
+
+  (let loop ((components (string-tokenize dir not-slash))
+             (root       (if absolute?
+                             ""
+                             ".")))
+    (match components
+      ((head tail ...)
+       (let ((path (string-append root "/" head)))
+         (catch 'system-error
+           (lambda ()
+             (mkdir path mode)
+             (loop tail path))
+           (lambda args
+             (if (= EEXIST (system-error-errno args))
+                 (loop tail path)
+                 (apply throw args))))))
+      (() #t))))
+
+(define (report-system-error name . args)
+  "Report a system error for the file NAME."
+  (let ((errno (system-error-errno args)))
+    (format (current-error-port) "could not create '~a': ~a~%" name
+            (strerror errno))))
+
+;; Catch a system-error, log it and don't die from it.
+(define-syntax-rule (catch-system-error name exp)
+  (catch 'system-error
+    (lambda ()
+      exp)
+    (lambda args
+      (apply report-system-error name args))))
+
+;; Create a device node like the <device-node> passed here on the filesystem.
+(define create-device-node
+  (match-lambda
+    (($ <device-node> xname type major minor module)
+     (let ((name (string-append "/dev/" xname)))
+       (mkdir-p* (dirname name))
+       (catch-system-error name
+         (mknod name type #o600 (device-number major minor)))))))
+
+(define* (make-static-device-nodes linux-release-module-directory)
+  "Create static device nodes required by the given Linux release.
+This is required in order to solve a chicken-or-egg problem:
+The Linux kernel has a feature to autoload modules when a device is first
+accessed.
+And udev has a feature to set the permissions of static nodes correctly
+when it is starting up and also to automatically create nodes when hardware
+is hotplugged. That leaves universal device files which are not linked to
+one specific hardware device. These we have to create."
+  (let ((devname-name (string-append linux-release-module-directory "/"
+                                     "modules.devname")))
+    (for-each create-device-node
+              (call-with-input-file devname-name
+                                    read-static-device-nodes))))
+
 (define* (make-essential-device-nodes #:key (root "/"))
   "Make essential device nodes under ROOT/dev."
   ;; The hand-made devtmpfs/udev!

gnu/build/vm.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
-;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;;
@@ -77,6 +77,7 @@
                            linux initrd
                            make-disk-image?
                            single-file-output?
+                           target-arm32?
                            (disk-image-size (* 100 (expt 2 20)))
                            (disk-image-format "qcow2")
                            (references-graphs '()))
@@ -91,6 +92,31 @@ access it via /dev/hda.
 
 REFERENCES-GRAPHS can specify a list of reference-graph files as produced by
 the #:references-graphs parameter of 'derivation'."
+
+  (define arch-specific-flags
+    `(;; On ARM, a machine has to be specified. Use "virt" machine to avoid
+      ;; hardware limits imposed by other machines.
+      ,@(if target-arm32? '("-M" "virt") '())
+
+      ;; Only enable kvm if we see /dev/kvm exists.  This allows users without
+      ;; hardware virtualization to still use these commands.  KVM support is
+      ;; still buggy on some ARM32 boards. Do not use it even if available.
+      ,@(if (and (file-exists? "/dev/kvm")
+                 (not target-arm32?))
+            '("-enable-kvm")
+            '())
+      "-append"
+      ;; The serial port name differs between emulated architectures/machines.
+      ,@(if target-arm32?
+            `(,(string-append "console=ttyAMA0 --load=" builder))
+            `(,(string-append "console=ttyS0 --load=" builder)))
+      ;; NIC is not supported on ARM "virt" machine, so use a user mode
+      ;; network stack instead.
+      ,@(if target-arm32?
+            '("-device" "virtio-net-pci,netdev=mynet"
+              "-netdev" "user,id=mynet")
+            '("-net" "nic,model=virtio"))))
+
   (when make-disk-image?
     (format #t "creating ~a image of ~,2f MiB...~%"
             disk-image-format (/ disk-image-size (expt 2 20)))
@@ -113,7 +139,8 @@ the #:references-graphs parameter of 'derivation'."
   (unless (zero?
            (apply system* qemu "-nographic" "-no-reboot"
                   "-m" (number->string memory-size)
-                  "-net" "nic,model=virtio"
+                  "-object" "rng-random,filename=/dev/urandom,id=guixsd-vm-rng"
+                  "-device" "virtio-rng-pci,rng=guixsd-vm-rng"
                   "-virtfs"
                   (string-append "local,id=store_dev,path="
                                  (%store-directory)
@@ -127,15 +154,12 @@ the #:references-graphs parameter of 'derivation'."
                                            builder)
                   (append
                    (if make-disk-image?
-                       `("-drive" ,(string-append "file=" output
+                       `("-device" "virtio-blk,drive=myhd"
-                                                  ",if=virtio"))
+                         "-drive" ,(string-append "if=none,file=" output
+                                                  ",format=" disk-image-format
+                                                  ",id=myhd"))
                        '())
-                   ;; Only enable kvm if we see /dev/kvm exists.
+                   arch-specific-flags)))
-                   ;; This allows users without hardware virtualization to still
-                   ;; use these commands.
-                   (if (file-exists? "/dev/kvm")
-                       '("-enable-kvm")
-                       '()))))
     (error "qemu failed" qemu))
 
   ;; When MAKE-DISK-IMAGE? is true, the image is in OUTPUT already.

gnu/local.mk

@@ -490,6 +490,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/system/vm.scm				\
 						\
   %D%/build/activation.scm			\
+  %D%/build/bootloader.scm			\
   %D%/build/cross-toolchain.scm			\
   %D%/build/file-systems.scm			\
   %D%/build/install.scm				\
@@ -557,6 +558,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/binutils-ld-new-dtags.patch		\
   %D%/packages/patches/binutils-loongson-workaround.patch	\
   %D%/packages/patches/blast+-fix-makefile.patch		\
+  %D%/packages/patches/borg-fix-archive-corruption-bug.patch	\
   %D%/packages/patches/byobu-writable-status.patch		\
   %D%/packages/patches/cairo-CVE-2016-9082.patch			\
   %D%/packages/patches/calibre-no-updates-dialog.patch		\
@@ -607,6 +609,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/dtc-format-modifier.patch		\
   %D%/packages/patches/dtc-32-bits-check.patch			\
   %D%/packages/patches/dvd+rw-tools-add-include.patch 		\
+  %D%/packages/patches/eigen-arm-neon-fixes.patch		\
   %D%/packages/patches/elfutils-tests-ptrace.patch		\
   %D%/packages/patches/elixir-disable-failing-tests.patch	\
   %D%/packages/patches/einstein-build.patch			\
@@ -701,15 +704,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/gobject-introspection-absolute-shlib-path.patch \
   %D%/packages/patches/gobject-introspection-cc.patch		\
   %D%/packages/patches/gobject-introspection-girepository.patch	\
-  %D%/packages/patches/graphicsmagick-CVE-2017-11403+CVE-2017-14103.patch	\
-  %D%/packages/patches/graphicsmagick-CVE-2017-12935.patch	\
-  %D%/packages/patches/graphicsmagick-CVE-2017-12936.patch	\
-  %D%/packages/patches/graphicsmagick-CVE-2017-12937.patch	\
-  %D%/packages/patches/graphicsmagick-CVE-2017-13775.patch	\
-  %D%/packages/patches/graphicsmagick-CVE-2017-13776+CVE-2017-13777.patch	\
-  %D%/packages/patches/graphicsmagick-CVE-2017-14042.patch	\
-  %D%/packages/patches/graphicsmagick-CVE-2017-14165.patch	\
-  %D%/packages/patches/graphicsmagick-CVE-2017-14649.patch	\
   %D%/packages/patches/graphite2-ffloat-store.patch		\
   %D%/packages/patches/grep-timing-sensitive-test.patch		\
   %D%/packages/patches/groff-source-date-epoch.patch		\
@@ -760,6 +754,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/isl-0.11.1-aarch64-support.patch	\
   %D%/packages/patches/jacal-fix-texinfo.patch			\
   %D%/packages/patches/java-powermock-fix-java-files.patch		\
+  %D%/packages/patches/jemalloc-arm-address-bits.patch		\
   %D%/packages/patches/jbig2dec-ignore-testtest.patch		\
   %D%/packages/patches/jq-CVE-2015-8863.patch			\
   %D%/packages/patches/kdbusaddons-kinit-file-name.patch	\
@@ -826,6 +821,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/libtool-skip-tests2.patch		\
   %D%/packages/patches/libusb-0.1-disable-tests.patch		\
   %D%/packages/patches/libusb-for-axoloti.patch			\
+  %D%/packages/patches/libvdpau-va-gl-unbundle.patch		\
   %D%/packages/patches/libvpx-CVE-2016-2818.patch		\
   %D%/packages/patches/libxcb-python-3.5-compat.patch		\
   %D%/packages/patches/libxslt-generated-ids.patch		\
@@ -942,6 +938,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/perl-module-pluggable-search.patch	\
   %D%/packages/patches/perl-reproducible-build-date.patch	\
   %D%/packages/patches/perl-www-curl-remove-symbol.patch	\
+  %D%/packages/patches/picprog-non-intel-support.patch		\
   %D%/packages/patches/pidgin-add-search-path.patch		\
   %D%/packages/patches/pinball-const-fix.patch			\
   %D%/packages/patches/pinball-cstddef.patch			\
@@ -994,6 +991,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-parse-too-many-fields.patch	\
   %D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch	\
   %D%/packages/patches/python-statsmodels-fix-tests.patch	\
+  %D%/packages/patches/python-scikit-learn-fix-test-non-determinism.patch	\
   %D%/packages/patches/python-configobj-setuptools.patch	\
   %D%/packages/patches/python-faker-fix-build-32bit.patch	\
   %D%/packages/patches/python-pandas-skip-failing-tests.patch	\
@@ -1008,9 +1006,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-unittest2-python3-compat.patch	\
   %D%/packages/patches/python-unittest2-remove-argparse.patch	\
   %D%/packages/patches/qemu-CVE-2017-15038.patch		\
-  %D%/packages/patches/qemu-CVE-2017-15118.patch		\
-  %D%/packages/patches/qemu-CVE-2017-15119.patch		\
-  %D%/packages/patches/qemu-CVE-2017-15268.patch		\
   %D%/packages/patches/qemu-CVE-2017-15289.patch		\
   %D%/packages/patches/qt4-ldflags.patch			\
   %D%/packages/patches/qtscript-disable-tests.patch		\
@@ -1028,6 +1023,11 @@ dist_patch_DATA =						\
   %D%/packages/patches/ripperx-missing-file.patch		\
   %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
   %D%/packages/patches/rsem-makefile.patch			\
+  %D%/packages/patches/rsync-CVE-2017-16548.patch			\
+  %D%/packages/patches/rsync-CVE-2017-17433.patch			\
+  %D%/packages/patches/rsync-CVE-2017-17433-fix-tests.patch			\
+  %D%/packages/patches/rsync-CVE-2017-17434-pt1.patch			\
+  %D%/packages/patches/rsync-CVE-2017-17434-pt2.patch			\
   %D%/packages/patches/ruby-concurrent-ignore-broken-test.patch	\
   %D%/packages/patches/ruby-concurrent-test-arm.patch		\
   %D%/packages/patches/ruby-rack-ignore-failing-test.patch      \
@@ -1053,7 +1053,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/synfigstudio-fix-ui-with-gtk3.patch 	\
   %D%/packages/patches/t1lib-CVE-2010-2642.patch		\
   %D%/packages/patches/t1lib-CVE-2011-0764.patch		\
-  %D%/packages/patches/t1lib-CVE-2011-1552+CVE-2011-1553+CVE-2011-1554.patch		\
+  %D%/packages/patches/t1lib-CVE-2011-1552+.patch		\
   %D%/packages/patches/tar-CVE-2016-6321.patch			\
   %D%/packages/patches/tar-skip-unreliable-tests.patch		\
   %D%/packages/patches/tclxml-3.2-install.patch			\

gnu/packages/algebra.scm

@@ -7,6 +7,7 @@
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -577,27 +578,34 @@ cosine/ sine transforms or DCT/DST).")
 (define-public eigen
   (package
     (name "eigen")
-    (version "3.2.9")
+    (version "3.3.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://bitbucket.org/eigen/eigen/get/"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "1zs5b210mq7nyanky07li6456rrd0xv2nxf6sl2lhkzdq5p067jd"))
+                "19m4406jvqnwh7kpcvx1lfx2vdc5zwia5q9ayv89bimg1gmln9fx"))
               (file-name (string-append name "-" version ".tar.bz2"))
+	      (patches (search-patches "eigen-arm-neon-fixes.patch"))
               (modules '((guix build utils)))
               (snippet
                ;; There are 3 test failures in the "unsupported" directory,
                ;; but maintainers say it's a known issue and it's unsupported
                ;; anyway, so just skip them.
-               '(substitute* "CMakeLists.txt"
+               '(begin
-                  (("add_subdirectory\\(unsupported\\)")
+		  (substitute* "CMakeLists.txt"
-                   "# Do not build the tests for unsupported features.\n")
+                    (("add_subdirectory\\(unsupported\\)")
-                  ;; Work around
+                     "# Do not build the tests for unsupported features.\n")
-                  ;; <http://eigen.tuxfamily.org/bz/show_bug.cgi?id=1114>.
+                    ;; Work around
-                  (("\"include/eigen3\"")
+                    ;; <http://eigen.tuxfamily.org/bz/show_bug.cgi?id=1114>.
-                   "\"${CMAKE_INSTALL_PREFIX}/include/eigen3\"")))))
+                    (("\"include/eigen3\"")
+                     "\"${CMAKE_INSTALL_PREFIX}/include/eigen3\""))
+		  (substitute* "test/bdcsvd.cpp"
+                    ;; See
+                    ;; https://bitbucket.org/eigen/eigen/commits/ea8c22ce6920e982d15245ee41d0531a46a28e5d
+                    ((".*svd_preallocate[^\n]*" &)
+                     (string-append "//" & " // Not supported by BDCSVD")))))))
     (build-system cmake-build-system)
     (arguments
      '(;; Turn off debugging symbols to save space.
@@ -608,6 +616,7 @@ cosine/ sine transforms or DCT/DST).")
                     (lambda _
                       (let* ((cores  (parallel-job-count))
                              (dash-j (format #f "-j~a" cores)))
+			(setenv "EIGEN_SEED" "1") ;for reproducibility
                         ;; First build the tests, in parallel.  See
                         ;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
                         (and (zero? (system* "make" "buildtests" dash-j))

gnu/packages/aspell.scm

@@ -2,7 +2,7 @@
 ;;; Copyright © 2013, 2014, 2015, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015, 2016 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2016 John Darrington <jmd@gnu.org>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Christopher Andersson <christopher@8bits.nu>
 ;;; Copyright © 2016 Theodoros Foradis <theodoros@foradis.org>
 ;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -130,12 +130,20 @@ dictionaries, including personal ones.")
                      (base32
                       "01p92qj66cqb346gk7hjfynaap5sbcn85xz07kjfdq623ghr8v5s")))
 
-(define-public aspell-dict-en
+(define-public aspell-dict-el
-  (aspell-dictionary "en" "English"
+  (aspell-dictionary "el" "Greek"
-                     #:version "2017.01.22-0"
+                     #:version "0.08-0"
+                     #:prefix "aspell6-"
                      #:sha256
                      (base32
-                      "1qamzpw1fsnn5n9jpsnnnzqj1a0m0xvsikmkdp5a6pmb7sp3ziwk")))
+                      "1ljcc30zg2v2h3w5h5jr5im41mw8jbsgvvhdd2cii2yzi8d0zxja")))
+
+(define-public aspell-dict-en
+  (aspell-dictionary "en" "English"
+                     #:version "2017.08.24-0"
+                     #:sha256
+                     (base32
+                      "0z2vvm1by485cm0sna21cmw6zb771c2l2lnn676zmrwm46q65d89")))
 
 (define-public aspell-dict-eo
   (aspell-dictionary "eo" "Esperanto"
@@ -159,12 +167,19 @@ dictionaries, including personal ones.")
                      (base32
                       "14ffy9mn5jqqpp437kannc3559bfdrpk7r36ljkzjalxa53i0hpr")))
 
-(define-public aspell-dict-ru
+(define-public aspell-dict-grc
-  (aspell-dictionary "ru" "Russian"
+  (aspell-dictionary "grc" "Ancient Greek"
-                     #:version "0.99f7-1"
+                     #:version "0.02-0"
                      #:sha256
                      (base32
-                      "0ip6nq43hcr7vvzbv4lwwmlwgfa60hrhsldh9xy3zg2prv6bcaaw")))
+                      "1zxr8958v37v260fkqd4pg37ns5h5kyqm54hn1hg70wq5cz8h512")))
+
+(define-public aspell-dict-he
+  (aspell-dictionary "he" "Hebrew"
+                     #:version "1.0-0"
+                     #:sha256
+                     (base32
+                      "13bhbghx5b8g0119g3wxd4n8mlf707y41vlf59irxjj0kynankfn")))
 
 (define-public aspell-dict-it
   (aspell-dictionary "it" "Italian"
@@ -181,12 +196,20 @@ dictionaries, including personal ones.")
                      (base32
                       "0ffb87yjsh211hllpc4b9khqqrblial4pzi1h9r3v465z1yhn3j4")))
 
-(define-public aspell-dict-he
+(define-public aspell-dict-pt-br
-  (aspell-dictionary "he" "Hebrew"
+  (aspell-dictionary "pt-br" "Brazilian Portuguese"
-                     #:version "1.0-0"
+                     #:version "20090702-0"
+                     #:prefix "aspell6-"
                      #:sha256
                      (base32
-                      "13bhbghx5b8g0119g3wxd4n8mlf707y41vlf59irxjj0kynankfn")))
+                      "1y09lx9zf2rnp55r16b2vgj953l3538z1vaqgflg9mdvm555bz3p")))
+
+(define-public aspell-dict-ru
+  (aspell-dictionary "ru" "Russian"
+                     #:version "0.99f7-1"
+                     #:sha256
+                     (base32
+                      "0ip6nq43hcr7vvzbv4lwwmlwgfa60hrhsldh9xy3zg2prv6bcaaw")))
 
 (define-public aspell-dict-sv
   (aspell-dictionary "sv" "Swedish"
@@ -196,29 +219,6 @@ dictionaries, including personal ones.")
                      (base32
                       "02jwkjhr32kvyibnyzgx3smbnm576jwdzg3avdf6zxwckhy5fw4v")))
 
-(define-public aspell-dict-el
-  (aspell-dictionary "el" "Greek"
-                     #:version "0.08-0"
-                     #:prefix "aspell6-"
-                     #:sha256
-                     (base32
-                      "1ljcc30zg2v2h3w5h5jr5im41mw8jbsgvvhdd2cii2yzi8d0zxja")))
-
-(define-public aspell-dict-grc
-  (aspell-dictionary "grc" "Ancient Greek"
-                     #:version "0.02-0"
-                     #:sha256
-                     (base32
-                      "1zxr8958v37v260fkqd4pg37ns5h5kyqm54hn1hg70wq5cz8h512")))
-
-(define-public aspell-dict-pt-br
-  (aspell-dictionary "pt-br" "Brazilian Portuguese"
-                     #:version "20090702-0"
-                     #:prefix "aspell6-"
-                     #:sha256
-                     (base32
-                      "1y09lx9zf2rnp55r16b2vgj953l3538z1vaqgflg9mdvm555bz3p")))
-
 
 ;;;
 ;;; Hunspell packages made from the Aspell word lists.

gnu/packages/audio.scm

@@ -222,7 +222,7 @@ namespace ARDOUR { const char* revision = \"" version "\" ; }")))))
        (modify-phases %standard-phases
          (add-after
           'unpack 'set-rpath-in-LDFLAGS
-          ,(ardour-rpath-phase (version-prefix version 1))))
+          ,(ardour-rpath-phase (version-major version))))
        #:test-target "test"
        #:python ,python-2))
     (inputs
@@ -1993,6 +1993,38 @@ and ALSA.")
 into various outputs and to start, stop and configure jackd")
     (license license:gpl2+)))
 
+(define-public qjackrcd
+  (package
+    (name "qjackrcd")
+    (version "1.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/qjackrcd/stable/"
+                                  "qjackrcd-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0xpnhzbwg5c60n5dhwln5p7qm191nvmf23la88zxfqx1jv0mmxxb"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             (zero? (system* "qmake"
+                             (string-append "PREFIX="
+                                            (assoc-ref outputs "out")))))))))
+    (native-inputs
+     `(("qtbase" ,qtbase))) ; for qmake
+    (inputs
+     `(("jack" ,jack-1)
+       ("libsndfile" ,libsndfile)
+       ("qtbase" ,qtbase)))
+    (home-page "https://sourceforge.net/projects/qjackrcd/")
+    (synopsis "Stereo audio recorder for JACK")
+    (description "QJackRcd is a simple graphical stereo recorder for JACK
+supporting silence processing for automatic pause, file splitting, and
+background file post-processing.")
+    (license license:gpl2+)))
 
 (define-public raul
   (package
@@ -3136,3 +3168,106 @@ on the ALSA software PCM plugin.")
 customized and extended using either the s7 Scheme implementation (included in
 the Snd sources), Ruby, or Forth.")
     (license (license:non-copyleft "file://COPYING"))))
+
+(define-public noise-repellent
+  (package
+    (name "noise-repellent")
+    (version "0.1.4")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/lucianodato/noise-repellent.git")
+                    (commit version)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "0rd3dlmk3vivjmcr6x2x860y0j1d49c2j95j6ny50v184mwvn11j"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:make-flags
+       (list "CC=gcc"
+             (string-append "PREFIX=" (assoc-ref %outputs "out")))
+       #:tests? #f ; there are none
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure))))
+    (inputs
+     `(("lv2" ,lv2)
+       ("fftwf" ,fftwf)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "https://github.com/lucianodato/noise-repellent")
+    (synopsis "LV2 plugin for broadband noise reduction")
+    (description "Noise Repellent is an LV2 plugin to reduce noise.  It has
+the following features:
+
+@enumerate
+@item Spectral gating and spectral subtraction suppression rule
+@item Adaptive and manual noise thresholds estimation
+@item Adjustable noise floor
+@item Adjustable offset of thresholds to perform over-subtraction
+@item Time smoothing and a masking estimation to reduce artifacts
+@item Basic onset detector to avoid transients suppression
+@item Whitening of the noise floor to mask artifacts and to recover higher
+  frequencies
+@item Option to listen to the residual signal
+@item Soft bypass
+@item Noise profile saved with the session
+@end enumerate
+")
+    (license license:lgpl3+)))
+
+(define-public cli-visualizer
+  (package
+    (name "cli-visualizer")
+    (version "1.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/dpayne/cli-visualizer/archive/"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "07zkm87f2fr8kc6531zrkya7q81sdanm6813y2f54mg13g41y6hi"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("which" ,which)))
+    (inputs
+     `(("fftw" ,fftw)
+       ("googletest" ,googletest)
+       ("ncurses" ,ncurses)
+       ("pulseaudio" ,pulseaudio)))
+    (arguments
+     '(#:test-target "test"
+       #:make-flags
+       (list (string-append "PREFIX=" %output "/bin/") "ENABLE_PULSE=1")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'remove-sudo
+           (lambda _
+             (substitute* "install.sh" (("sudo") ""))
+             #t))
+         (add-before 'check 'set-check-environment
+           (lambda _
+             (setenv "CXX" "g++")
+             (setenv "CC" "gcc")
+             #t))
+         (add-before 'install 'make-prefix
+           (lambda _
+             (mkdir-p (string-append (assoc-ref %outputs "out") "/bin"))
+             #t))
+         (add-after 'install 'data
+           (lambda _
+             (for-each (lambda (file)
+                         (install-file file
+                                       (string-append (assoc-ref %outputs "out")
+                                                      "/share/doc")))
+                       (find-files "examples"))
+             #t)))))
+    (home-page "https://github.com/dpayne/cli-visualizer/")
+    (synopsis "Command-line audio visualizer")
+    (description "@code{cli-visualizer} displays fast-Fourier
+transforms (FFTs) of the sound being played, as well as other graphical
+representations.")
+    (license license:expat)))

gnu/packages/axoloti.scm

@@ -189,7 +189,7 @@
      `(("chibios"
         ,(origin
            (method url-fetch)
-           (uri "mirror://sourceforge/chibios/ChibiOS_RT%20stable/Version%202.6.9/ChibiOS_2.6.9.zip")
+           (uri "mirror://sourceforge/chibios/ChibiOS%20GPL3/Version%202.6.9/ChibiOS_2.6.9.zip")
            (sha256
             (base32
              "0lb5s8pkj80mqhsy47mmq0lqk34s2a2m3xagzihalvabwd0frhlj"))))

gnu/packages/backup.scm

@@ -456,6 +456,7 @@ detection, and lossless compression.")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "borgbackup" version))
+              (patches (search-patches "borg-fix-archive-corruption-bug.patch"))
               (sha256
                (base32
                 "1rvn8b6clzd1r317r9jkvk34r31risi0dxfjc7jffhnwasck4anc"))

gnu/packages/bioinformatics.scm

@@ -421,7 +421,7 @@ computational cluster.")
 (define-public bedtools
   (package
     (name "bedtools")
-    (version "2.27.0")
+    (version "2.27.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/arq5x/bedtools2/releases/"
@@ -429,7 +429,7 @@ computational cluster.")
                                   "bedtools-" version ".tar.gz"))
               (sha256
                (base32
-                "0q6fsiz4s52yzxs6h2vxwq95fsi3n64wkpinkk05mfh4dmhybw74"))))
+                "1ndg5yknrxl4djx8ddzgk12rrbiidfpmkkg5z3f95jzryfxarhn8"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"
@@ -466,7 +466,19 @@ BED, GFF/GTF, VCF.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf"))))))
+                "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf"))))
+    (arguments
+     '(#:test-target "test"
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+               (for-each (lambda (file)
+                           (install-file file bin))
+                         (find-files "bin" ".*")))
+             #t)))))))
 
 (define-public ribotaper
   (package
@@ -2061,7 +2073,7 @@ identify enrichments with functional annotations of the genome.")
 (define-public diamond
   (package
     (name "diamond")
-    (version "0.9.13")
+    (version "0.9.14")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2070,7 +2082,7 @@ identify enrichments with functional annotations of the genome.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1pi5ncqwmynqpmmp3j3lhnqrjhj34sr6wpmsgrpkv3wyxx22fv86"))))
+                "07li3chjdna0wjyh680j3bhwiqh1fbfq9dy9jxxs82mc0rw0m1yy"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; no "check" target
@@ -2905,7 +2917,7 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
        (method url-fetch)
        (uri (string-append
              "http://eddylab.org/software/hmmer"
-             (version-prefix version 1) "/"
+             (version-major version) "/"
              version "/hmmer-" version ".tar.gz"))
        (sha256
         (base32
@@ -9385,83 +9397,89 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
     (license license:artistic2.0)))
 
 (define-public r-seurat
-  ;; Source releases are only made for new x.0 versions.  All newer versions
+  (package
-  ;; are only released as pre-built binaries.  At the time of this writing the
+    (name "r-seurat")
-  ;; latest binary release is 1.4.0.12, which is equivalent to this commit.
+    (version "2.1.0")
-  (let ((commit "fccb77d1452c35ee47e47ebf8e87bddb59f3b08d")
+    (source (origin
-        (revision "1"))
+              (method url-fetch)
-    (package
+              (uri (cran-uri "Seurat" version))
-      (name "r-seurat")
+              (sha256
-      (version (string-append "1.4.0.12-" revision "." (string-take commit 7)))
+               (base32
-      (source (origin
+                "1hqaq6bciikrsyw157w8fn4jw885air7xbkxrmism93rp4qx483x"))
-                (method git-fetch)
+              ;; Delete pre-built jar.
-                (uri (git-reference
+              (snippet
-                      (url "https://github.com/satijalab/seurat")
+               '(begin (delete-file "inst/java/ModularityOptimizer.jar")
-                      (commit commit)))
+                       #t))))
-                (file-name (string-append name "-" version "-checkout"))
+    (properties `((upstream-name . "Seurat")))
-                (sha256
+    (build-system r-build-system)
-                 (base32
+    (arguments
-                  "101wq3aqrdmbfi3lqmq4iivk9iwbf10d4z216ss25hf7n9091cyl"))
+     `(#:phases
-                ;; Delete pre-built jar.
+       (modify-phases %standard-phases
-                (snippet
+         (add-after 'unpack 'build-jar
-                 '(begin (delete-file "inst/java/ModularityOptimizer.jar")
+           (lambda* (#:key inputs #:allow-other-keys)
-                         #t))))
+             (let ((classesdir "tmp-classes"))
-      (build-system r-build-system)
+               (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
-      (arguments
+               (mkdir classesdir)
-       `(#:phases
+               (with-output-to-file "manifest"
-         (modify-phases %standard-phases
+                 (lambda _
-           (add-after 'unpack 'build-jar
+                   (display "Manifest-Version: 1.0
-             (lambda* (#:key inputs #:allow-other-keys)
+Main-Class: ModularityOptimizer\n")))
-               (let ((classesdir "tmp-classes"))
+               (and (zero? (apply system* `("javac" "-d" ,classesdir
-                 (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
+                                            ,@(find-files "java" "\\.java$"))))
-                 (mkdir classesdir)
+                    (zero? (system* "jar"
-                 (and (zero? (apply system* `("javac" "-d" ,classesdir
+                                    "-cmf" "manifest"
-                                              ,@(find-files "java" "\\.java$"))))
+                                    "inst/java/ModularityOptimizer.jar"
-                      (zero? (system* "jar"
+                                    "-C" classesdir  ".")))))))))
-                                      "-cf" "inst/java/ModularityOptimizer.jar"
+    (native-inputs
-                                      "-C" classesdir ".")))))))))
+     `(("jdk" ,icedtea "jdk")))
-      (native-inputs
+    (propagated-inputs
-       `(("jdk" ,icedtea "jdk")))
+     `(("r-ape" ,r-ape)
-      (propagated-inputs
+       ("r-caret" ,r-caret)
-       `(("r-ape" ,r-ape)
+       ("r-cowplot" ,r-cowplot)
-         ("r-caret" ,r-caret)
+       ("r-diffusionmap" ,r-diffusionmap)
-         ("r-cowplot" ,r-cowplot)
+       ("r-dplyr" ,r-dplyr)
-         ("r-dplyr" ,r-dplyr)
+       ("r-dtw" ,r-dtw)
-         ("r-fastica" ,r-fastica)
+       ("r-fnn" ,r-fnn)
-         ("r-fnn" ,r-fnn)
+       ("r-fpc" ,r-fpc)
-         ("r-fpc" ,r-fpc)
+       ("r-gdata" ,r-gdata)
-         ("r-gdata" ,r-gdata)
+       ("r-ggjoy" ,r-ggjoy)
-         ("r-ggplot2" ,r-ggplot2)
+       ("r-ggplot2" ,r-ggplot2)
-         ("r-gplots" ,r-gplots)
+       ("r-gplots" ,r-gplots)
-         ("r-gridextra" ,r-gridextra)
+       ("r-gridextra" ,r-gridextra)
-         ("r-igraph" ,r-igraph)
+       ("r-hmisc" ,r-hmisc)
-         ("r-irlba" ,r-irlba)
+       ("r-ica" ,r-ica)
-         ("r-lars" ,r-lars)
+       ("r-igraph" ,r-igraph)
-         ("r-mixtools" ,r-mixtools)
+       ("r-irlba" ,r-irlba)
-         ("r-pbapply" ,r-pbapply)
+       ("r-lars" ,r-lars)
-         ("r-plyr" ,r-plyr)
+       ("r-mass" ,r-mass)
-         ("r-ranger" ,r-ranger)
+       ("r-matrix" ,r-matrix)
-         ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-mixtools" ,r-mixtools)
-         ("r-rcpp" ,r-rcpp)
+       ("r-nmf" ,r-nmf)
-         ("r-rcppeigen" ,r-rcppeigen)
+       ("r-pbapply" ,r-pbapply)
-         ("r-rcppprogress" ,r-rcppprogress)
+       ("r-plotly" ,r-plotly)
-         ("r-reshape2" ,r-reshape2)
+       ("r-ranger" ,r-ranger)
-         ("r-rocr" ,r-rocr)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
-         ("r-rtsne" ,r-rtsne)
+       ("r-rcpp" ,r-rcpp)
-         ("r-stringr" ,r-stringr)
+       ("r-rcppprogress" ,r-rcppprogress)
-         ("r-tclust" ,r-tclust)
+       ("r-reshape2" ,r-reshape2)
-         ("r-tsne" ,r-tsne)
+       ("r-rocr" ,r-rocr)
-         ("r-vgam" ,r-vgam)))
+       ("r-rtsne" ,r-rtsne)
-      (home-page "http://www.satijalab.org/seurat")
+       ("r-sdmtools" ,r-sdmtools)
-      (synopsis "Seurat is an R toolkit for single cell genomics")
+       ("r-stringr" ,r-stringr)
-      (description
+       ("r-tclust" ,r-tclust)
-       "This package is an R package designed for QC, analysis, and
+       ("r-tidyr" ,r-tidyr)
+       ("r-tsne" ,r-tsne)
+       ("r-vgam" ,r-vgam)))
+    (home-page "http://www.satijalab.org/seurat")
+    (synopsis "Seurat is an R toolkit for single cell genomics")
+    (description
+     "This package is an R package designed for QC, analysis, and
 exploration of single cell RNA-seq data.  It easily enables widely-used
 analytical techniques, including the identification of highly variable genes,
 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
 algorithms; density clustering, hierarchical clustering, k-means, and the
 discovery of differentially expressed genes and markers.")
-      (license license:gpl3))))
+    (license license:gpl3)))
 
 (define-public r-aroma-light
   (package

gnu/packages/build-tools.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Corentin Bocquillon <corentin@nybble.fr>
+;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -70,7 +71,7 @@ makes a few sacrifices to acquire fast full and incremental build times.")
 (define-public meson
   (package
     (name "meson")
-    (version "0.43.0")
+    (version "0.44.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/mesonbuild/meson/"
@@ -78,7 +79,7 @@ makes a few sacrifices to acquire fast full and incremental build times.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0h3k0m45004ay1hzz9r66fkl1kwizaigxahyrlabyw0d1slyq4y5"))))
+                "06r8limj38mv884s5riiz6lpzw37cvhbf9jd0smzcbi7fwmv3yah"))))
     (build-system python-build-system)
     (inputs `(("ninja", ninja)))
     (propagated-inputs `(("python" ,python)))

gnu/packages/chez.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -61,14 +62,14 @@
 (define-public chez-scheme
   (package
     (name "chez-scheme")
-    (version "9.4")
+    (version "9.5")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/cisco/ChezScheme/archive/"
                            "v" version ".tar.gz"))
        (sha256
-        (base32 "0lprmpsjg2plc6ykgkz482zyvhkzv6gd0vnar71ph21h6zknyklz"))
+        (base32 "135991hspq0grf26pvl2lkwhp92yz204h6rgiwyym0x6v0xzknd1"))
        (file-name (string-append "chez-scheme-" version ".tar.gz"))))
     (build-system gnu-build-system)
     (inputs
@@ -104,7 +105,15 @@
          (add-after 'unpack 'patch-processor-detection
            (lambda _ (substitute* "configure"
                        (("uname -a") "uname -m"))
-             #t))
+                   #t))
+         (add-after 'unpack 'patch-broken-documentation
+           (lambda _
+             ;; Work around an oversight in the 9.5 release tarball that causes
+             ;; building the documentation to fail. This should be fixed in the
+             ;; next one; see <https://github.com/cisco/ChezScheme/issues/209>.
+             (substitute* "csug/copyright.stex"
+               (("\\\\INSERTREVISIONMONTHSPACEYEAR" )
+                "October 2017"))))     ; tarball release date
          ;; Adapt the custom 'configure' script.
          (replace 'configure
            (lambda* (#:key inputs outputs #:allow-other-keys)

gnu/packages/code.scm

@@ -2,7 +2,7 @@
 ;;; Copyright © 2013, 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 Andy Wingo <wingo@igalia.com>
@@ -99,14 +99,14 @@ highlighting your own code that seemed comprehensible when you wrote it.")
 (define-public global                             ; a global variable
   (package
     (name "global")
-    (version "6.5.7")
+    (version "6.6.1")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/global/global-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "0cnd7a7d1pl46yk15q6mnr9i9w3xi8pxgchw4ia9njgr4jjqzh6r"))))
+               "1r2r6z41lmgbszzwx7h3jqhwnqb9jj32pndzhr3lb0id710c8gcl"))))
     (build-system gnu-build-system)
     (inputs `(("ncurses" ,ncurses)
               ("libltdl" ,libltdl)

gnu/packages/compression.scm

@@ -661,7 +661,7 @@ compression library.")
 (define-public perl-compress-raw-zlib
   (package
     (name "perl-compress-raw-zlib")
-    (version "2.074")
+    (version "2.076")
     (source
      (origin
        (method url-fetch)
@@ -669,7 +669,7 @@ compression library.")
                            "Compress-Raw-Zlib-" version ".tar.gz"))
        (sha256
         (base32
-         "08bpx9v6i40n54rdcj6invlj294z20amrl8wvwf9b83aldwdwsd3"))))
+         "1al2h0i6mspldmlf5c09fy5a4j8swsxd31v6zi8zx9iyqk1lw7in"))))
     (build-system perl-build-system)
     (inputs
      `(("zlib" ,zlib)))

gnu/packages/cran.scm

@@ -1642,3 +1642,134 @@ originally inspired by the book \"Visualizing Categorical Data\" by Michael
 Friendly and is now the main support package for a new book, \"Discrete Data
 Analysis with R\" by Michael Friendly and David Meyer (2015).")
     (license license:gpl2)))
+
+(define-public r-ica
+  (package
+    (name "r-ica")
+    (version "1.0-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ica" version))
+       (sha256
+        (base32
+         "1bkl4a72l0k6gm82l3jxnib898z20cw17zg81jj39l9dn65rlmcq"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/ica/")
+    (synopsis "Independent component analysis")
+    (description "This package provides tools for @dfn{Independent Component
+Analysis} (ICA) using various algorithms: FastICA,
+Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
+of Eigenmatrices} (JADE).")
+    (license license:gpl2+)))
+
+(define-public r-dtw
+  (package
+    (name "r-dtw")
+    (version "1.18-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "dtw" version))
+       (sha256
+        (base32
+         "1b91vahba09cqlb8b1ry4dlv4rbldb4s2p6w52gmyw31vxdv5nnr"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-proxy" ,r-proxy)))
+    (home-page "http://dtw.r-forge.r-project.org/")
+    (synopsis "Dynamic Time Warping Algorithms")
+    (description "This package provides a comprehensive implementation of
+@dfn{dynamic time warping} (DTW) algorithms in R.  DTW computes the
+optimal (least cumulative distance) alignment between points of two time
+series.  Common DTW variants covered include local (slope) and global (window)
+constraints, subsequence matches, arbitrary distance definitions,
+normalizations, minimum variance matching, and so on.")
+    (license license:gpl2+)))
+
+(define-public r-sdmtools
+  (package
+    (name "r-sdmtools")
+    (version "1.1-221")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "SDMTools" version))
+       (sha256
+        (base32
+         "1kacrpamshv7wz83yn45sfbw4m9c44xrrngzcklnwx8gcxx2knm6"))))
+    (properties `((upstream-name . "SDMTools")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-r-utils" ,r-r-utils)))
+    (home-page "http://www.rforge.net/SDMTools/")
+    (synopsis "Species distribution modelling tools")
+    (description "This packages provides a set of tools for post processing
+the outcomes of species distribution modeling exercises.  It includes novel
+methods for comparing models and tracking changes in distributions through
+time.  It further includes methods for visualizing outcomes, selecting
+thresholds, calculating measures of accuracy and landscape fragmentation
+statistics, etc.")
+    (license license:gpl3+)))
+
+(define-public r-scatterplot3d
+  (package
+    (name "r-scatterplot3d")
+    (version "0.3-40")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "scatterplot3d" version))
+       (sha256
+        (base32
+         "0ababcj87kx7860mica9y2ydlhskxmgj9n46crx036cila512jc2"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/scatterplot3d/")
+    (synopsis "3D scatter plot")
+    (description "This package provides an implementation of scatter plots for
+plotting.  a three dimensional point cloud.")
+    (license license:gpl2)))
+
+(define-public r-ggridges
+  (package
+    (name "r-ggridges")
+    (version "0.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggridges" version))
+       (sha256
+        (base32
+         "0kfa3icqdalqdg1klxjrhfl7if35d3wnsiyl86bprw5dyqyh3lh3"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-plyr" ,r-plyr)
+       ("r-scales" ,r-scales)))
+    (home-page "https://github.com/clauswilke/ggridges")
+    (synopsis "Ridgeline plots in ggplot2")
+    (description
+     "Ridgeline plots provide a convenient way of visualizing changes in
+distributions over time or space.  This package enables the creation of such
+plots in @code{ggplot2}.")
+    (license license:gpl2)))
+
+(define-public r-ggjoy
+  (package
+    (name "r-ggjoy")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggjoy" version))
+       (sha256
+        (base32
+         "1s24zn7gmk52bvjjhanxby7rxbnc2yfl0nx5nv7x7z0zja8gg7nb"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-ggridges" ,r-ggridges)))
+    (home-page "https://github.com/clauswilke/ggjoy")
+    (synopsis "Joyplots in ggplot2")
+    (description "Joyplots provide a convenient way of visualizing changes in
+distributions over time or space.  This package enables the creation of such
+plots in @code{ggplot2}.")
+    (license license:gpl2)))

gnu/packages/crypto.scm

@@ -61,7 +61,7 @@
 (define-public libsodium
   (package
     (name "libsodium")
-    (version "1.0.15")
+    (version "1.0.16")
     (source (origin
             (method url-fetch)
             (uri (list (string-append
@@ -72,7 +72,7 @@
                         "releases/old/libsodium-" version ".tar.gz")))
             (sha256
              (base32
-              "1x3qw7lsz44vcxpcn1dvwig410phg6gmv31jwj94arrgka3rwspv"))))
+              "0cq5pn7qcib7q70mm1lgjwj75xdxix27v0xl1xl0kvxww7hwgbgf"))))
     (build-system gnu-build-system)
     (synopsis "Portable NaCl-based crypto library")
     (description

gnu/packages/cups.scm

@@ -370,14 +370,19 @@ device-specific programs to convert and print many types of files.")
 (define-public hplip
   (package
     (name "hplip")
-    (version "3.17.10")
+    (version "3.17.11")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/hplip/hplip/" version
                                   "/hplip-" version ".tar.gz"))
               (sha256
                (base32
-                "0v27hg856b5z2rilczcbfgz8ksxn0n810g1glac3mxkj8qbl8wqg"))))
+                "0xda7x7xxjvzn1l0adlvbwcw21crq1r3r79bkf94q3m5i6abx49g"))
+              (modules '((guix build utils)))
+              (snippet
+               ;; Fix type mismatch.
+               '(substitute* "prnt/hpcups/genPCLm.cpp"
+                  (("boolean") "bool")))))
     (build-system gnu-build-system)
     (home-page "http://hplipopensource.com/")
     (synopsis "HP Printer Drivers")
@@ -437,11 +442,11 @@ device-specific programs to convert and print many types of files.")
                           (("/usr/include/libusb-1.0")
                            (string-append (assoc-ref inputs "libusb")
                                           "/include/libusb-1.0"))
-                          (("^\tinstall-dist_hplip_stateDATA")
+                          (("hplip_statedir =.*$")
-                           ;; Remove dependencies on
+                           ;; Don't bail out while trying to create
-                           ;; 'install-dist_hplip_stateDATA' so we don't bail
+                           ;; /var/lib/hplip.  We can safely change its value
-                           ;; out while trying to create /var/lib/hplip.
+                           ;; here because it's hard-coded in the code anyway.
-                           "\t")
+                           "hplip_statedir = $(prefix)\n")
                           (("hplip_confdir = /etc/hp")
                            ;; This is only used for installing the default config.
                            (string-append "hplip_confdir = " out
@@ -470,12 +475,14 @@ device-specific programs to convert and print many types of files.")
               ("cups-minimal" ,cups-minimal)
               ("libusb" ,libusb)
               ("sane-backends" ,sane-backends-minimal)
+              ("zlib" ,zlib)
               ("dbus" ,dbus)
               ("python-wrapper" ,python-wrapper)
               ("python" ,python)
               ;; TODO: Make hp-setup find python-dbus.
               ("python-dbus" ,python-dbus)))
-    (native-inputs `(("pkg-config" ,pkg-config)))))
+    (native-inputs `(("pkg-config" ,pkg-config)
+                     ("perl" ,perl)))))
 
 (define-public foomatic-filters
   (package

gnu/packages/databases.scm

@@ -1280,7 +1280,7 @@ module, and nothing else.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://cpan/authors/id/R/RI/RIBASUSHI/"
+       (uri (string-append "mirror://cpan/authors/id/I/IL/ILMARI/"
                            "SQL-Abstract-" version ".tar.gz"))
        (sha256
         (base32

gnu/packages/datastructures.scm

@@ -116,3 +116,58 @@ with the number of cores.  liburcu-cds provides efficient data structures
 based on RCU and lock-free algorithms.  These structures include hash tables,
 queues, stacks, and doubly-linked lists.")
     (license license:lgpl2.1+)))
+
+(define-public uthash
+  (package
+    (name "uthash")
+    (version "2.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (file-name (string-append name "-" version ".tar.gz"))
+       (uri (string-append "https://github.com/troydhanson/uthash/archive/v"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1la82gdlyl7m8ahdjirigwfh7zjgkc24cvydrqcri0vsvm8iv8rl"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("perl" ,perl)))
+    (arguments
+     `(#:make-flags
+       (list "CC=gcc")
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)            ; nothing to configure
+         (delete 'build)                ; nothing to build
+         (replace 'check
+           (lambda* (#:key make-flags #:allow-other-keys)
+             (with-directory-excursion "tests"
+               (zero? (apply system* "make"
+                             make-flags)))))
+         (replace 'install
+           ;; There is no top-level Makefile to do this for us.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (doc (string-append out "/share/doc/" ,name))
+                    (include (string-append out "/include")))
+               ;; Don't install HTML files: they're just the below .txt files
+               ;; dolled up, can be stale, and regeneration requires asciidoc.
+               (for-each (λ (file) (install-file file doc))
+                         (find-files "doc" "\\.txt$"))
+               (for-each (λ (file) (install-file file include))
+                         (find-files "src" "\\.h$"))
+               #t))))))
+    (home-page "https://troydhanson.github.io/uthash/")
+    (synopsis
+     "Hash tables, lists, and other data structures implemented as C macros")
+    (description
+     "uthash implements a hash table and a few other basic data structures
+as C preprocessor macros.  It aims to be minimalistic and efficient: it's
+around 1,000 lines of code which, being macros, inline automatically.
+
+Unlike function calls with fixed prototypes, macros operate on untyped
+arguments.  Thus, they are able to work with any type of structure and key.
+Any C structure can be stored in a hash table by adding @code{UT_hash_handle}
+to the structure and choosing one or more fields to act as the key.")
+    (license license:bsd-2)))

gnu/packages/dictionaries.scm

@@ -23,6 +23,7 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages base)
   #:use-module (gnu packages curl)
@@ -206,6 +207,45 @@ It comes with a German-English dictionary with approximately 270,000 entries.")
     (home-page  "http://www-user.tu-chemnitz.de/~fri/ding/")
     (license gpl2+)))
 
+(define-public grammalecte
+  (package
+    (name "grammalecte")
+    (version "0.6.1")
+    (source
+     (origin
+       (method url-fetch/zipbomb)
+       (uri (string-append "https://www.dicollecte.org/grammalecte/zip/"
+                           "Grammalecte-fr-v" version ".zip"))
+       (sha256
+        (base32
+         "0bl342i7nqbg8swk3fxashg9liyp3jdnix59pndhy41cpm1xln4i"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-setup.py
+           ;; FIXME: "setup.py" contains a typo in 0.6.1 release. The
+           ;; issue was reported and fixed upstream
+           ;; (https://dicollecte.org/thread.php?prj=fr&t=674). This
+           ;; phase can be removed in next release.
+           (lambda _
+             (substitute* "setup.py"
+               (("server_options\\.") "grammalecte-server-options."))
+             #t)))))
+    (home-page "https://www.dicollecte.org")
+    (synopsis  "French spelling and grammar checker")
+    (description "Grammalecte is a grammar checker dedicated to the French
+language, derived from Lightproof.
+
+Grammalecte aims at helping to write a proper French without distracting users
+with false positives.  This grammar checker follows the principle: the less
+false positives, the better; if it cannot know with a good chance if
+a dubious expression is wrong, it will keep silent.
+
+The package provides the command line interface, along with a server
+and a Python library.")
+    (license gpl3+)))
+
 (define-public translate-shell
   (package
     (name "translate-shell")

gnu/packages/emacs.scm

@@ -31,6 +31,7 @@
 ;;; Copyright © 2017 Peter Mikkelsen <petermikkelsen10@gmail.com>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Mike Gerwitz <mtg@gnu.org>
+;;; Copyright © 2017 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -377,7 +378,7 @@ when typing parentheses directly or commenting out code line by line.")
 
 (define-public git-modes
   (package
-    (name "git-modes")
+    (name "emacs-git-modes")
     (version "1.2.6")
     (source (origin
               (method url-fetch)
@@ -396,6 +397,9 @@ when typing parentheses directly or commenting out code line by line.")
 configuration files, such as .gitattributes, .gitignore, and .git/config.")
     (license license:gpl3+)))
 
+(define-public git-modes/old-name
+  (deprecated-package "git-modes" git-modes))
+
 (define-public emacs-with-editor
   (package
     (name "emacs-with-editor")
@@ -1972,6 +1976,26 @@ keep pressing the key until it selects what you want.  There's also
 column by drawing a thin line down the length of the editing window.")
     (license license:gpl3+)))
 
+(define-public emacs-grep-a-lot
+  (package
+    (name "emacs-grep-a-lot")
+    (version "1.0.7")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ZungBang/emacs-grep-a-lot.git")
+                    (commit "9f9f645b9e308a0d887b66864ff97d0fca1ba4ad")))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "1f8262mrlinzgnn4m49hbj1hm3c1mvzza24py4b37sasn49546lw"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/ZungBang/emacs-grep-a-lot")
+    (synopsis "Enables multiple grep buffers in Emacs")
+    (description
+     "This Emacs package allows managing multiple grep buffers.")
+    (license license:gpl3+)))
+
 (define-public emacs-inf-ruby
   (package
     (name "emacs-inf-ruby")
@@ -2153,6 +2177,43 @@ evaluated in the browser, just like Emacs does with an inferior Lisp process
 in Lisp modes.")
     (license license:unlicense)))
 
+(define-public emacs-string-inflection
+  (package
+    (name "emacs-string-inflection")
+    (version "1.0.6")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/akicho8/string-inflection")
+                    (commit "a150e7bdda60b7824d3a936750ce23f73b0e4edd")))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "1k0sm552iawi49v4zis6dbb81d1rzgky9v0dpv7nj31gnb7bmy7k"))))
+    (build-system emacs-build-system)
+    (native-inputs
+     `(("ert-runner" ,ert-runner)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'install 'check
+           (lambda _
+             (zero? (system* "ert-runner")))))))
+    (home-page "https://github.com/akicho8/string-inflection")
+    (synopsis "Convert symbol names between different naming conventions")
+    (description
+     "This Emacs package provides convenient methods for manipulating the
+naming style of a symbol.  It supports different naming conventions such as:
+
+@enumerate
+@item camel case
+@item Pascal case
+@item all upper case
+@item lower case separated by underscore
+@item etc...
+@end enumerate\n")
+    (license license:gpl2+)))
+
 (define-public emacs-stripe-buffer
   (package
     (name "emacs-stripe-buffer")
@@ -2195,6 +2256,31 @@ tables.")
 mode-line.")
     (license license:gpl2+)))
 
+(define-public emacs-robe
+  (package
+    (name "emacs-robe")
+    (version "0.8.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/dgutov/robe/"
+                           "archive/" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1vp45y99fwj88z04ah4yppz4z568qcib646az6m9az5ar0f203br"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-inf-ruby" ,emacs-inf-ruby)))
+    (home-page "https://github.com/dgutov/robe")
+    (synopsis "Ruby code assistance tool for Emacs")
+    (description
+     "Robe can provide information on loaded classes and modules in Ruby code,
+as well as where methods are defined.  This allows the user to jump to method
+definitions, modules and classes, display method documentation and provide
+method and constant name completion.")
+    (license license:gpl3+)))
+
 (define-public emacs-rspec
   (package
     (name "emacs-rspec")
@@ -2969,7 +3055,7 @@ single theme but a set of guidelines with numerous implementations.")
 (define-public emacs-smartparens
   (package
     (name "emacs-smartparens")
-    (version "1.10.1")
+    (version "1.11.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2978,7 +3064,7 @@ single theme but a set of guidelines with numerous implementations.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1nwsi6fbbxjq3r22r6knmx71la3g0lmwfb95i9q4k138gn0m2l3i"))))
+                "0q5as813xs8y29i3v2rm97phd6m7xsmmw6hwbvx57gwmi8i1c409"))))
     (build-system emacs-build-system)
     (propagated-inputs `(("emacs-dash" ,emacs-dash)))
     (home-page "https://github.com/Fuco1/smartparens")
@@ -4897,7 +4983,7 @@ highlights quasi-quoted expressions.")
 (define-public emacspeak
   (package
     (name "emacspeak")
-    (version "46.0")
+    (version "47.0")
     (source
      (origin
        (method url-fetch)
@@ -4906,11 +4992,7 @@ highlights quasi-quoted expressions.")
              version "/emacspeak-" version ".tar.bz2"))
        (sha256
         (base32
-         "15x4yfp3wl2fxm1nkx6pz3clw6zyw3argcsqxgcx6pa28sivlg2n"))
+         "0xbcc266x752y68s3g096m161irzvsqym3axzqn8rb276a8x55n7"))))
-       (modules '((guix build utils)))
-       (snippet
-        ;; Delete the bundled byte-compiled elisp files.
-        '(for-each delete-file (find-files "lisp" "\\.elc$")))))
     (build-system gnu-build-system)
     (arguments
      '(#:make-flags (list (string-append "prefix="
@@ -4920,6 +5002,7 @@ highlights quasi-quoted expressions.")
          (replace 'configure
            (lambda _
              ;; Configure Emacspeak according to etc/install.org.
+             (setenv "SHELL" (which "sh"))
              (zero? (system* "make" "config"))))
          (add-after 'build 'build-espeak
            (lambda _
@@ -4998,6 +5081,28 @@ you'd get with @kbd{M-q} using @code{adaptive-fill-mode}, but without
 actually changing the buffer's text.")
     (license license:gpl3+)))
 
+(define-public emacs-diff-hl
+ (package
+  (name "emacs-diff-hl")
+  (version "1.8.4")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (string-append "http://elpa.gnu.org/packages/diff-hl-"
+                          version ".tar"))
+      (sha256
+        (base32
+          "0axhidc3cym7a2x4rpxf4745qss9s9ajyg4s9h5b4zn7v7fyp71n"))))
+  (build-system emacs-build-system)
+  (home-page "https://github.com/dgutov/diff-hl")
+  (synopsis
+    "Highlight uncommitted changes using VC")
+  (description
+    "@code{diff-hl-mode} highlights uncommitted changes on the side of the
+window (using the fringe, by default), allows you to jump between
+the hunks and revert them selectively.")
+  (license license:gpl3+)))
+
 (define-public emacs-diminish
   (package
     (name "emacs-diminish")
@@ -5386,7 +5491,7 @@ It should enable you to implement low-level X11 applications.")
 (define-public emacs-exwm
   (package
     (name "emacs-exwm")
-    (version "0.15")
+    (version "0.16")
     (synopsis "Emacs X window manager")
     (source (origin
               (method url-fetch)
@@ -5394,7 +5499,7 @@ It should enable you to implement low-level X11 applications.")
                                   version ".tar"))
               (sha256
                (base32
-                "1y7nqry9y0a99bsdqkk9f554vczfw4sz6raadw3138835qy697jg"))))
+                "0c4w5k9lzqj8yzhdqipdb4fs7ld2qklc6s137104jnfdvmrwcv2i"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-xelb" ,emacs-xelb)))
@@ -5930,6 +6035,35 @@ available key bindings that follow C-x (or as many as space allows given your
 settings).")
     (license license:gpl3+)))
 
+(define-public emacs-ws-butler
+  (package
+    (name "emacs-ws-butler")
+    (version "0.6")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/lewang/ws-butler.git")
+                    (commit "323b651dd70ee40a25accc940b8f80c3a3185205")))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "1a4b0lsmwq84qfx51c5xy4fryhb1ysld4fhgw2vr37izf53379sb"))))
+    (build-system emacs-build-system)
+    (native-inputs
+     `(("ert-runner" ,ert-runner)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'install 'check
+           (lambda _
+             (zero? (system* "ert-runner" "tests")))))))
+    (home-page "https://github.com/lewang/ws-butler")
+    (synopsis "Trim spaces from end of lines")
+    (description
+     "This Emacs package automatically and unobtrusively trims whitespace
+characters from end of lines.")
+    (license license:gpl3+)))
+
 (define-public emacs-org-edit-latex
   (package
     (name "emacs-org-edit-latex")
@@ -6272,6 +6406,28 @@ and shell-command prompts that are based on bash completion.")
 let users kill or mark things easily.")
     (license license:gpl3+)))
 
+(define-public emacs-csv-mode
+  (package
+    (name "emacs-csv-mode")
+    (version "1.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://elpa.gnu.org/packages/csv-mode-"
+                           version ".el"))
+       (sha256
+        (base32
+         "0r4bip0w3h55i8h6sxh06czf294mrhavybz0zypzrjw91m1bi7z6"))))
+    (build-system emacs-build-system)
+    (home-page
+     "http://elpa.gnu.org/packages/csv-mode.html")
+    (synopsis
+     "Major mode for editing comma/char separated values")
+    (description
+     "This Emacs package implements CSV mode, a major mode for editing records
+in a generalized CSV (character-separated values) format.")
+    (license license:gpl3+)))
+
 (define-public emacs-transmission
   (package
     (name "emacs-transmission")

gnu/packages/embedded.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017 Theodoros Foradis <theodoros@foradis.org>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
+;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -932,3 +933,40 @@ int fast_build_block_buffer"))
 MPSSE (Multi-Protocol Synchronous Serial Engine) adapter by FTDI that can do
 SPI, I2C, JTAG.")
     (license license:gpl2+)))
+
+(define-public picprog
+  (package
+    (name "picprog")
+    (version "1.9.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://www.iki.fi/hyvatti/pic/picprog-"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1r04hg1n3v2jf915qr05la3q9cxy7a5jnh9cc98j04lh6c9p4x85"))
+              (patches (search-patches "picprog-non-intel-support.patch"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ; No tests exist.
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-paths
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "Makefile"
+               (("/usr/local") (assoc-ref outputs "out"))
+               ((" -o 0 -g 0 ") " ")
+               (("testport") ""))
+             #t))
+         (add-before 'install 'mkdir
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (mkdir-p (string-append out "/bin"))
+               (mkdir-p (string-append out "/man/man1"))
+               #t)))
+         (delete 'configure))))
+    (synopsis "Programs Microchip's PIC microcontrollers")
+    (description "This program programs Microchip's PIC microcontrollers.")
+    (home-page "http://hyvatti.iki.fi/~jaakko/pic/picprog.html")
+    (license license:gpl3+)))

gnu/packages/erlang.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Steve Sprang <scs@stevesprang.com>
-;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2017 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -23,6 +23,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix download)
   #:use-module (guix packages)
+  #:use-module (guix utils)
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages fontutils)
@@ -35,7 +36,7 @@
 (define-public erlang
   (package
     (name "erlang")
-    (version "20.1")
+    (version "20.1.7")
     (source (origin
               (method url-fetch)
               ;; The tarball from http://erlang.org/download contains many
@@ -46,7 +47,7 @@
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0r4g8ag7nlpw06y4c39fgcyccykj2sbyhv5jgp4qmrjci2ydgns8"))
+                "00pmngdyh1h088anmx6fbk085i93ajgk92rz7qsyhfc0lx0sm0a9"))
               (patches (search-patches "erlang-man-path.patch"))))
     (build-system gnu-build-system)
     (native-inputs
@@ -59,7 +60,7 @@
         ,(origin
            (method url-fetch)
            (uri (string-append "http://erlang.org/download/otp_doc_man_"
-                               version ".tar.gz"))
+                               (version-major+minor version) ".tar.gz"))
            (sha256
             (base32
              "0ikvdpn4z7az6szg176l1r2yxhgs3msa3wgb3gmy45jkz0pzik05"))))))

gnu/packages/fontutils.scm

@@ -297,9 +297,13 @@ high quality, anti-aliased and subpixel rendered text on a display.")
             (sha256 (base32
                      "0nbvjpnmcznib1nlgg8xckrmsw3haa154byds2h90y2g0nsjh4w2"))
             (patches (search-patches
-                       "t1lib-CVE-2010-2642.patch"
+                       "t1lib-CVE-2010-2642.patch" ; 2011-0443, 2011-5244
                        "t1lib-CVE-2011-0764.patch"
-                       "t1lib-CVE-2011-1552+CVE-2011-1553+CVE-2011-1554.patch"))))
+                       "t1lib-CVE-2011-1552+.patch")))) ; 2011-1553, 2011-1554
+   (properties `((lint-hidden-cve . ("CVE-2011-0433"
+                                     "CVE-2011-1553"
+                                     "CVE-2011-1554"
+                                     "CVE-2011-5244"))))
    (build-system gnu-build-system)
    (arguments
     ;; Making the documentation requires latex, but t1lib is also an input

gnu/packages/fvwm.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017 ng0 <ng0@infotropique.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -34,16 +35,15 @@
 (define-public fvwm
   (package
     (name "fvwm")
-    (version "2.6.6")
+    (version "2.6.7")
     (source (origin
               (method url-fetch)
               (uri (string-append
                     "https://github.com/fvwmorg/fvwm/releases/download/"
-                    "version-" (string-join (string-split version #\.) "_")
+                    version "/" name "-" version ".tar.gz"))
-                    "/" name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0b6w0vk6cpqaz0ws3vl4by0mycv33r42a0m806j2h8avy9ghipn5"))))
+                "0wzghjgy65pkn31rgl14fngizw7nbkzbxsfa670xmrndpmd4sr81"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("perl" ,perl)

gnu/packages/game-development.scm

@@ -12,6 +12,7 @@
 ;;; Copyright © 2017 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
 ;;; Copyright © 2017 Peter Mikkelsen <petermikkelsen10@gmail.com>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -111,7 +112,7 @@ is used in some video games and movies.")
 (define-public deutex
   (package
    (name "deutex")
-   (version "5.0.0")
+   (version "5.1.0")
    (source (origin
             (method url-fetch)
             (uri (string-append "https://github.com/Doom-Utils/" name
@@ -119,7 +120,7 @@ is used in some video games and movies.")
                                 name "-" version ".tar.xz"))
             (sha256
              (base32
-              "1jvffcpq64hk3jysz4q6zi9hqkksy151ci9553h8q7wrrkbw0i9z"))))
+              "0hwkm0q2w16ddmiwh7x3jcfp58zjb40a5dh7c3sybwm9bar37pn1"))))
    (build-system gnu-build-system)
    (native-inputs `(("asciidoc" ,asciidoc)))
    (home-page "https://github.com/Doom-Utils/deutex")
@@ -1014,7 +1015,7 @@ of use.")
 (define-public openmw
   (package
     (name "openmw")
-    (version "0.42.0")
+    (version "0.43.0")
     (source
      (origin
        (method url-fetch)
@@ -1023,7 +1024,7 @@ of use.")
                        name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1pla8016lpbg8cgm9kia318a860f26dmiayc72p3zl35mqrc7g7w"))))
+         "11phjx7b3mv4n295xgq25lkcwq0mgr35i5k05hf1h77y6n6jbw64"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ; No test target

gnu/packages/games.scm

@@ -355,6 +355,47 @@ played.  Freedoom complements the Doom engine with free levels, artwork, sound
 effects and music to make a completely free game.")
    (license license:bsd-3)))
 
+(define-public knights
+  (package
+    (name "knights")
+    (version "025")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://www.knightsgame.org.uk/files/knights_"
+                                  version "_src.tar.gz"))
+              (sha256
+               (base32
+                "18vp2ygvn0s0jz8rm585jqf6hjqkam1ximq81k0r9hpmfj7wb88f"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:make-flags
+       (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         ;; No configure script.
+         (delete 'configure))
+       #:tests? #f)) ;; No check target.
+    (inputs
+     `(("boost" ,boost)
+       ("sdl-union" ,(sdl-union (list sdl sdl-image sdl-mixer)))
+       ("freetype" ,freetype)
+       ("fontconfig" ,fontconfig)
+       ("curl" ,curl)))
+    (home-page "http://www.knightsgame.org.uk/")
+    (synopsis "Multiplayer dungeon game involving knights and quests")
+    (description "Knights is a multiplayer game involving several knights who
+must run around a dungeon and complete various quests.  Each game revolves
+around a quest – for example, you might have to find some items and carry them
+back to your starting point.  This may sound easy, but as there are only
+enough items in the dungeon for one player to win, you may end up having to
+kill your opponents to get their stuff!  Other quests involve escaping from
+the dungeon, fighting a duel to the death against the enemy knights, or
+destroying an ancient book using a special wand.")
+    ;; This package includes modified sources of lua (X11), enet (Expat), and
+    ;; guichan (BSD-3).  The "Coercri" library is released under the Boost
+    ;; license.  The whole package is released under GPLv3+.
+    (license license:gpl3+)))
+
 (define-public gnubg
   (package
     (name "gnubg")
@@ -2737,6 +2778,9 @@ Transport Tycoon Deluxe.")
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ;; no tests available
+       #:configure-flags
+        (list (string-append "-DCMAKE_INSTALL_LIBDIR="
+                       (assoc-ref %outputs "out") "/lib"))
        #:phases
         (modify-phases %standard-phases
           (add-after 'unpack 'fix-usr-share-paths

gnu/packages/gl.scm

@@ -8,6 +8,7 @@
 ;;; Copyright © 2016 David Thompson <davet@gnu.org>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -41,6 +42,7 @@
   #:use-module (gnu packages llvm)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages tls)
   #:use-module (gnu packages video)
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages xml)
@@ -724,3 +726,36 @@ mixed vector/bitmap output.")
     (license (list license:lgpl2.0+
                    (license:fsf-free "http://www.geuz.org/gl2ps/COPYING.GL2PS"
                                      "GPL-incompatible copyleft license")))))
+
+(define-public virtualgl
+  (package
+    (name "virtualgl")
+    (version "2.5.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/VirtualGL/virtualgl/archive/"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0rnid3hwrry9d5d4m7sygq00xxx976rgk00a3557m9r5kxbmy476"))))
+    (arguments
+     `(#:tests? #f ;; no tests are available
+       #:configure-flags (list "-DVGL_USESSL=1" ;; use OpenSSL
+                          (string-append "-DCMAKE_INSTALL_LIBDIR="
+                                         (assoc-ref %outputs "out") "/lib"))))
+    (build-system cmake-build-system)
+    (inputs `(("glu" ,glu)
+              ("libjpeg-turbo" ,libjpeg-turbo)
+              ("mesa" ,mesa)
+              ("openssl" ,openssl)))
+    (native-inputs `(("pkg-config", pkg-config)))
+    (home-page "https://www.virtualgl.org")
+    (synopsis "Redirects 3D commands from an OpenGL application onto a 3D
+graphics card")
+    (description "VirtualGL redirects the 3D rendering commands from OpenGL
+applications to 3D accelerator hardware in a dedicated server and displays the
+rendered output interactively to a thin client located elsewhere on the
+network.")
+    (license license:wxwindows3.1+)))

gnu/packages/gnome.scm

@@ -4061,7 +4061,7 @@ work and the interface is well tested.")
 (define-public eolie
   (package
     (name "eolie")
-    (version "0.9.13")
+    (version "0.9.15")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/gnumdk/eolie/"
@@ -4069,7 +4069,7 @@ work and the interface is well tested.")
                                   "/eolie-" version ".tar.xz"))
               (sha256
                (base32
-                "1khpc6x40y5gm0a3p5fxiva9p1djijxmsh74xinigddnyqbjqw69"))))
+                "0glydxp1xh85gfidk1l9miqn6qxdbvvk5s3iy0pjlv8nrs3263jd"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      `(#:phases
@@ -6638,7 +6638,7 @@ basically a text box in which notes can be written.")
        (sha256
         (base32
          "0c1q9w5vql0vvg6g0knxfnv4ap19fg5cdrwndi1cj9lsym92c78j"))))
-    (build-system gnu-build-system)
+    (build-system glib-or-gtk-build-system)
     (native-inputs
      `(("desktop-file-utils" ,desktop-file-utils)
        ("glib:bin" ,glib "bin") ; for glib-compile-resources.

gnu/packages/gnunet.scm

@@ -144,14 +144,14 @@ tool to extract metadata from a file and print the results.")
 (define-public libmicrohttpd
   (package
    (name "libmicrohttpd")
-   (version "0.9.57")
+   (version "0.9.58")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnu/libmicrohttpd/libmicrohttpd-"
                                 version ".tar.gz"))
             (sha256
              (base32
-              "0kmgkk9sjg1n3q7rbzw5y4qmgh51zn5qi2j69gbqmr6phxjaghfy"))))
+              "1wq17qvizis7bsyvyw1gnfycvivssncngziddnyrbzv2dhvy24bs"))))
    (build-system gnu-build-system)
    (inputs
     `(("curl" ,curl)
@@ -188,11 +188,10 @@ authentication and support for SSL3 and TLS.")
    (version "7.57.0")
    (source (origin
             (method url-fetch)
-            (uri (string-append "https://gnunet.org/sites/default/files/"
+            (uri (string-append "mirror://gnu/gnunet/" name "-" version ".tar.xz"))
-                                name "-" version ".tar.bz2"))
             (sha256
              (base32
-              "1dykh12mc241jnxcd8q5pm1yw9ras53ywyba9f9dy5cq39j2mk9c"))))
+              "0cl2x1jddnhn1z8gd75w6k7lb6pymn5rf2vqgl2vdkbxsz677z07"))))
    (build-system gnu-build-system)
    (outputs '("out"
               "doc"))                             ; 1.5 MiB of man3 pages

gnu/packages/gnupg.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013, 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
@@ -736,7 +736,10 @@ including tools for signing keys, keyring analysis, and party preparation.
     (description
      "Pinentry provides a console that allows users to enter a passphrase when
 @code{gpg} is run and needs it.")
-    (license license:gpl2+)))
+    (license license:gpl2+)
+    (properties '((ftp-server . "ftp.gnupg.org")
+                  (ftp-directory . "/gcrypt/pinentry")
+                  (upstream-name . "pinentry")))))
 
 (define-public pinentry-gtk2
   (package

gnu/packages/gnuzilla.scm

@@ -481,7 +481,8 @@ security standards.")
         (mozilla-patch "icecat-bug-1047098-pt3.patch"    "36bd15d14c5a" "0cb3l3hpsgk674f08kfamxhqfga3ah5v904gpxq9ag006vzd2cxz")
         (mozilla-patch "icecat-bug-1404105.patch"        "2909ba991f31" "126vssj57dc800347f075wlnjzcwamnxxmgxl9w78jpb0hj9gf16")
         (search-patch  "icecat-bug-1415133.patch")
-        (mozilla-patch "icecat-bug-1355576.patch"        "cf34a0574e58" "1z7sa1d12hypgivm5xxn32s58afpjcij97jvnafcgnfvxywrgr1m")))
+        (mozilla-patch "icecat-bug-1355576.patch"        "cf34a0574e58" "1z7sa1d12hypgivm5xxn32s58afpjcij97jvnafcgnfvxywrgr1m")
+        (mozilla-patch "icecat-CVE-2017-7843.patch"      "f6216ea8b8fc" "0jnhdkj0ch9mj01mzlvhjgf8zsxlbg6m7yvpq99qr7xmg0pzbgwl")))
       (modules '((guix build utils)))
       (snippet
        '(begin

gnu/packages/graph.scm

@@ -27,6 +27,7 @@
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages bioinformatics)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages cran)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages multiprecision)
@@ -119,6 +120,31 @@ random and regular graphs, graph visualization, centrality methods and much
 more.")
     (license license:gpl2+)))
 
+(define-public r-diffusionmap
+  (package
+    (name "r-diffusionmap")
+    (version "1.1-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "diffusionMap" version))
+       (sha256
+        (base32
+         "1l985q2hfc8ss5afajik4p25dx628yikvhdimz5s0pql800q2yv3"))))
+    (properties `((upstream-name . "diffusionMap")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-igraph" ,r-igraph)
+       ("r-matrix" ,r-matrix)
+       ("r-scatterplot3d" ,r-scatterplot3d)))
+    (home-page "http://www.r-project.org")
+    (synopsis "Diffusion map")
+    (description "This package implements the diffusion map method of data
+parametrization, including creation and visualization of diffusion maps,
+clustering with diffusion K-means and regression using the adaptive regression
+model.")
+    (license license:gpl2)))
+
 (define-public r-rgraphviz
   (package
     (name "r-rgraphviz")

gnu/packages/gstreamer.scm

@@ -100,7 +100,7 @@ arrays of data.")
 (define-public gstreamer
   (package
     (name "gstreamer")
-    (version "1.12.3")
+    (version "1.12.4")
     (source
      (origin
       (method url-fetch)
@@ -109,7 +109,7 @@ arrays of data.")
             version ".tar.xz"))
       (sha256
        (base32
-        "0vi1g8rmmsnd630ds3jwv2iph46ll8y07fzf04mz15q88j9g926k"))))
+        "0x06jxmc5fhlz7cr1pl5lp0hm1jgz519jjic37d09srf9jm091ss"))))
     (build-system gnu-build-system)
     (outputs '("out" "doc"))
     (arguments
@@ -148,7 +148,7 @@ This package provides the core library and elements.")
 (define-public gst-plugins-base
   (package
     (name "gst-plugins-base")
-    (version "1.12.3")
+    (version "1.12.4")
     (source
      (origin
       (method url-fetch)
@@ -156,7 +156,7 @@ This package provides the core library and elements.")
                           name "-" version ".tar.xz"))
       (sha256
        (base32
-        "19ffwdch7m777ragmwpy6prqmfb742ym1n3ki40s0zyki627plyk"))))
+        "10i255q7i8an1hxz3szb36x1jcs9nfdy511pj2wg24h2vw1nnc2c"))))
     (build-system gnu-build-system)
     (outputs '("out" "doc"))
     (propagated-inputs
@@ -203,7 +203,7 @@ for the GStreamer multimedia library.")
 (define-public gst-plugins-good
   (package
     (name "gst-plugins-good")
-    (version "1.12.3")
+    (version "1.12.4")
     (source
      (origin
       (method url-fetch)
@@ -212,7 +212,7 @@ for the GStreamer multimedia library.")
             name "-" version ".tar.xz"))
       (sha256
        (base32
-        "00sznj1sl97fqpn6j8ngps04clvxp8h8yhw6lvszx4b855wz9rqk"))))
+        "0mxrbrqrfq1946gn9im19maj7ivld4k946vkwrzd94h8qsz4k7v4"))))
     (build-system gnu-build-system)
     (inputs
      `(("aalib" ,aalib)
@@ -262,14 +262,14 @@ developers consider to have good quality code and correct functionality.")
 (define-public gst-plugins-bad
   (package
     (name "gst-plugins-bad")
-    (version "1.12.3")
+    (version "1.12.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gstreamer.freedesktop.org/src/"
                                   name "/" name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1v5z3i5ha20gmbb3r9dwsaaspv5fm1jfzlzwlzqx1gjj31v5kl1n"))))
+                "021d3q81m968lpnah517sfclagadcqwd6jz3lqdmqvb82sz5fy0c"))))
     (outputs '("out" "doc"))
     (build-system gnu-build-system)
     (arguments
@@ -277,16 +277,7 @@ developers consider to have good quality code and correct functionality.")
        #:configure-flags
        (list (string-append "--with-html-dir="
                             (assoc-ref %outputs "doc")
-                            "/share/gtk-doc/html"))
+                            "/share/gtk-doc/html"))))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'patch-openjpeg-reference
-           (lambda _
-             ;; Remove hard-coded openjpeg-2.2 path. 2.3 is API- and
-             ;; ABI-compatible.
-             (substitute* "ext/openjpeg/gstopenjpeg.h"
-               (("<openjpeg-2\\.2/") "<openjpeg-2.3/"))
-             #t)))))
     (propagated-inputs
      `(("gst-plugins-base" ,gst-plugins-base)))
     (native-inputs
@@ -347,7 +338,7 @@ par compared to the rest.")
 (define-public gst-plugins-ugly
   (package
     (name "gst-plugins-ugly")
-    (version "1.12.3")
+    (version "1.12.4")
     (source
      (origin
        (method url-fetch)
@@ -355,7 +346,7 @@ par compared to the rest.")
                            name "/" name "-" version ".tar.xz"))
        (sha256
         (base32
-         "0lh00rg26iy5lr5al23lxsyncjqkgzph1bzkrgp8x9sfr62ab378"))))
+         "08p5kggk1szvr76cdbx3q3yfc235w1przb76v2n51lwfi26mn5hw"))))
     (build-system gnu-build-system)
     (inputs
      `(("gst-plugins-base" ,gst-plugins-base)
@@ -386,7 +377,7 @@ distribution problems in some jurisdictions, e.g. due to patent threats.")
 (define-public gst-libav
   (package
     (name "gst-libav")
-    (version "1.12.3")
+    (version "1.12.4")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -394,7 +385,7 @@ distribution problems in some jurisdictions, e.g. due to patent threats.")
                     name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0l4nc6ikdx49l7bdrk3bd9p3pzry8a328r22zg48gyzpnv5ghph1"))))
+                "0qly3lgamm36xql9q7wg5751gi6j2d3ifzz1pkr15ncc5mfslmia"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--with-system-libav")
@@ -411,7 +402,7 @@ distribution problems in some jurisdictions, e.g. due to patent threats.")
        ("python" ,python)))
     (inputs
      `(("gst-plugins-base" ,gst-plugins-base)
-       ("ffmpeg" ,ffmpeg-3.3)
+       ("ffmpeg" ,ffmpeg)
        ("orc" ,orc)
        ("zlib" ,zlib)))
     (home-page "http://gstreamer.freedesktop.org/")
@@ -424,7 +415,7 @@ compression formats through the use of the libav library.")
 (define-public python-gst
   (package
     (name "python-gst")
-    (version "1.12.3")
+    (version "1.12.4")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -432,7 +423,7 @@ compression formats through the use of the libav library.")
                     "gst-python-" version ".tar.xz"))
               (sha256
                (base32
-                "19rb06x2m7103zwfm0plxx95gb8bp01ng04h4q9k6ii9q7g2kxf3"))))
+                "1sm3dy10klf6i3w6a6mz0rnm29l2lxci5hr8346496jwc7v6mki0"))))
     (build-system gnu-build-system)
     (arguments
      ;; XXX: Factorize python-sitedir with python-build-system.

gnu/packages/gtk.scm

@@ -15,6 +15,7 @@
 ;;; Copyright © 2016 Patrick Hetu <patrick.hetu@auf.org>
 ;;; Coypright © 2016 ng0 <ng0@we.make.ritual.n0.is>
 ;;; Coypright © 2017 Roel Janssen <roel@gnu.org>
+;;; Coypright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -380,7 +381,7 @@ printing and other features typical of a source code editor.")
 (define-public gtksourceview
  (package
    (name "gtksourceview")
-   (version "3.24.4")
+   (version "3.24.6")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnome/sources/" name "/"
@@ -388,7 +389,7 @@ printing and other features typical of a source code editor.")
                                  name "-" version ".tar.xz"))
              (sha256
               (base32
-               "14x738xrz9q8qz13xd7dys748ryxyq2srbqyaa9r7n47h2av2zr0"))))
+               "1261fwjpwn3qizmvjns9z3k3a264j3ql5anyvmisfwywpkzbv9ks"))))
    (build-system gnu-build-system)
    (arguments
     '(#:phases

gnu/packages/guile.scm

@@ -15,6 +15,7 @@
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
 ;;; Copyright © 2017 ng0 <ng0@infotropique.org>
+;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1117,13 +1118,16 @@ inspired by the SCSH regular expression system.")
                 (compile-file
                  (lambda (in-file out-file)
                    (system* guild "compile" "-o" out-file in-file))))
-           ;; Make installation directories.
-           (mkdir-p module-dir)
-           (mkdir-p doc)
-
            ;; Switch directory for compiling and installing
            (chdir source)
 
+           ;; Install the documentation.
+           (install-file "README.md" doc)
+           (copy-recursively "examples" (string-append doc "/examples"))
+
+           ;; Make installation directories.
+           (mkdir-p module-dir)
+
            ;; copy the source
            (copy-file "gdbm.scm" gdbm.scm-dest)
 
@@ -1136,7 +1140,7 @@ inspired by the SCSH regular expression system.")
            ;; compile to the destination
            (compile-file gdbm.scm-dest gdbm.go-dest)))))
     (inputs
-     `(("guile" ,guile-2.0)))
+     `(("guile" ,guile-2.2)))
     (propagated-inputs
      `(("gdbm" ,gdbm)))
     (home-page "https://github.com/ijp/guile-gdbm")
@@ -1146,8 +1150,11 @@ inspired by the SCSH regular expression system.")
 Guile's foreign function interface.")
     (license license:gpl3+)))
 
+(define-public guile2.0-gdbm-ffi
+  (package-for-guile-2.0 guile-gdbm-ffi))
+
 (define-public guile2.2-gdbm-ffi
-  (package-for-guile-2.2 guile-gdbm-ffi))
+  (deprecated-package "guile2.2-gdbm-ffi" guile-gdbm-ffi))
 
 (define-public guile-sqlite3
   (let ((commit "607721fe1174a299e45d457acacf94eefb964071"))

gnu/packages/haskell.scm

@@ -1292,7 +1292,7 @@ unlit literate code files; and an option to turn off macro-expansion.")
 (define-public ghc-reflection
   (package
     (name "ghc-reflection")
-    (version "2.1")
+    (version "2.1.2")
     (source
      (origin
        (method url-fetch)
@@ -1302,7 +1302,7 @@ unlit literate code files; and an option to turn off macro-expansion.")
              ".tar.gz"))
        (sha256
         (base32
-         "10w3m6v3g6am203wbrikdbp57x9vw6b4jsh7bxdzsss4nmpm81zg"))))
+         "0f9w0akbm6p8h7kzgcd2f6nnpw1wy84pqn45vfz1ch5j0hn8h2d9"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-tagged" ,ghc-tagged)))
     (home-page "https://github.com/ekmett/reflection")

gnu/packages/image.scm

@@ -1112,14 +1112,14 @@ PNG, and performs PNG integrity checks and corrections.")
 (define-public libjpeg-turbo
   (package
     (name "libjpeg-turbo")
-    (version "1.5.2")
+    (version "1.5.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/" name "/" version "/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0a5m0psfp5952y5vrcs0nbdz1y9wqzg2ms0xwrx752034wxr964h"))))
+                "08r5b5mywwrxv4axvq80dm31cklz81grczlzlxr2xqa6pgi90j5j"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("nasm" ,nasm)))

gnu/packages/imagemagick.scm

@@ -164,7 +164,7 @@ script.")
 (define-public graphicsmagick
   (package
     (name "graphicsmagick")
-    (version "1.3.26")
+    (version "1.3.27")
     (source (origin
               (method url-fetch)
               (uri
@@ -176,17 +176,7 @@ script.")
                                  "/GraphicsMagick-" version ".tar.xz")))
               (sha256
                (base32
-                "122zgs96dqrys62mnh8x5yvfff6km4d3yrnvaxzg3mg5sprib87v"))
+                "0rq35p3rml10cxz2z4s7xcfsilhhk19mmy094g3ivz0fg797hcnh"))))
-              (patches
-               (search-patches "graphicsmagick-CVE-2017-11403+CVE-2017-14103.patch"
-                               "graphicsmagick-CVE-2017-12935.patch"
-                               "graphicsmagick-CVE-2017-12936.patch"
-                               "graphicsmagick-CVE-2017-12937.patch"
-                               "graphicsmagick-CVE-2017-13775.patch"
-                               "graphicsmagick-CVE-2017-13776+CVE-2017-13777.patch"
-                               "graphicsmagick-CVE-2017-14042.patch"
-                               "graphicsmagick-CVE-2017-14165.patch"
-                               "graphicsmagick-CVE-2017-14649.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags

gnu/packages/jemalloc.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -23,6 +24,8 @@
   #:use-module ((guix licenses) #:select (bsd-2))
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix utils)
+  #:use-module (gnu packages)
   #:use-module (gnu packages perl)
   #:use-module (guix build-system gnu))
 
@@ -37,7 +40,8 @@
                     version "/jemalloc-" version ".tar.bz2"))
               (sha256
                (base32
-                "1sf3lzgb0y8nnyzmp4zrca3sngdxw3kfh20sna9z03jv74fph528"))))
+                "1sf3lzgb0y8nnyzmp4zrca3sngdxw3kfh20sna9z03jv74fph528"))
+              (patches (search-patches "jemalloc-arm-address-bits.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -62,3 +66,17 @@
      "This library providing a malloc(3) implementation that emphasizes
 fragmentation avoidance and scalable concurrency support.")
     (license bsd-2)))
+
+(define-public jemalloc-4.5.0
+  (package
+    (inherit jemalloc)
+    (version "4.5.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/jemalloc/jemalloc/releases/download/"
+                    version "/jemalloc-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"))))
+    (inputs '())))

gnu/packages/kde.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
+;;; Copyright © 2017 Mark Meyer <mark@ofosos.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -23,18 +24,29 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix utils)
+  #:use-module (gnu packages algebra)
   #:use-module (gnu packages apr)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages curl)
   #:use-module (gnu packages documentation)
+  #:use-module (gnu packages gettext)
+  #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages gnome)
+  #:use-module (gnu packages graphics)
+  #:use-module (gnu packages image)
   #:use-module (gnu packages kde-frameworks)
   #:use-module (gnu packages llvm)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages pdf)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages photo)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages qt)
-  #:use-module (gnu packages version-control))
+  #:use-module (gnu packages version-control)
+  #:use-module (gnu packages xorg))
 
 (define-public kdevelop
   (package
@@ -220,6 +232,86 @@ for some KDevelop language plugins (Ruby, PHP, CSS...).")
 plugins, as well as code to create plugins, or complete applications.")
     (license license:gpl3+)))
 
+(define-public krita
+  (package
+    (name "krita")
+    (version "3.3.2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://kde/stable/krita/"
+                    "3.3.2/" name "-" version ".tar.xz"))
+              (sha256
+               (base32
+                "0i3l27cfi1h486m74xf4ynk0pwx32xaqraa91a0g1bpj1jxf2mg5"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f
+       #:configure-flags
+       (list "-DBUILD_TESTING=OFF" "-DKDE4_BUILD_TESTS=OFF"
+             (string-append "-DWITH_FFTW3="
+                            (assoc-ref %build-inputs "fftw"))
+             (string-append "-DWITH_GSL="
+                            (assoc-ref %build-inputs "gsl"))
+             (string-append "-DWITH_LibRaw="
+                            (assoc-ref %build-inputs "libraw"))
+             (string-append "-DWITH_TIFF="
+                            (assoc-ref %build-inputs "libtiff"))
+             (string-append "-DCMAKE_CXX_FLAGS=-I"
+                            (assoc-ref %build-inputs "ilmbase")
+                            "/include/OpenEXR"))))
+    (native-inputs
+     `(("curl" ,curl)
+       ("eigen" ,eigen)
+       ("extra-cmake-modules" ,extra-cmake-modules)
+       ("gettext-minimal" ,gettext-minimal)
+       ("kitemmodels" ,kitemmodels)
+       ("qwt" ,qwt)
+       ("vc" ,vc)))
+    (inputs
+     `(("qtbase" ,qtbase)
+       ("qtdeclarative" ,qtdeclarative)
+       ("qtmultimedia" ,qtmultimedia)
+       ("qtx11extras" ,qtx11extras)
+       ("qtsvg" ,qtsvg)
+       ("karchive" ,karchive)
+       ("kcompletion" ,kcompletion)
+       ("kconfig" ,kconfig)
+       ("kcoreaddons" ,kcoreaddons)
+       ("kcrash" ,kcrash)
+       ("kguiaddons" ,kguiaddons)
+       ("ki18n" ,ki18n)
+       ("kiconthemes" ,kiconthemes)
+       ("kio" ,kio)
+       ("kitemviews" ,kitemviews)
+       ("kwidgetsaddons" ,kwidgetsaddons)
+       ("kwindowsystem" ,kwindowsystem)
+       ("kxmlgui" ,kxmlgui)
+       ("boost" ,boost)
+       ("exiv2" ,exiv2)
+       ("lcms" ,lcms)
+       ("libpng" ,libpng)
+       ("libjpeg-turbo" ,libjpeg-turbo)
+       ("zlib" ,zlib)
+       ("libx11" ,libx11)
+       ("libxcb" ,libxcb)
+       ("libxi" ,libxi)
+       ("fftw" ,fftw)
+       ("gsl" ,gsl)
+       ("poppler-qt5" ,poppler-qt5)
+       ("libraw" ,libraw)
+       ("libtiff" ,libtiff)
+       ("perl" ,perl)
+       ("ilmbase" ,ilmbase)
+       ("openexr" ,openexr)))
+    (home-page "https://krita.org")
+    (synopsis "Digital painting application")
+    (description
+     "Krita is a professional painting tool designed for concept artists,
+illustrators, matte and texture artists, and the VFX industry.  Notable
+features include brush stabilizers, brush engines and wrap-around mode.")
+    (license license:gpl2+)))
+
 (define-public libkomparediff2
   (package
     (name "libkomparediff2")

gnu/packages/language.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -51,7 +52,7 @@ manipulating such numbers.")
 (define-public perl-lingua-en-inflect
   (package
     (name "perl-lingua-en-inflect")
-    (version "1.901")
+    (version "1.903")
     (source
      (origin
        (method url-fetch)
@@ -59,7 +60,7 @@ manipulating such numbers.")
                            "Lingua-EN-Inflect-" version ".tar.gz"))
        (sha256
         (base32
-         "0mcwlgf6hkh4zm3s1x899f25xj4hyzrc2vssiwfxysqja36yf5ys"))))
+         "0j8d1f1wvmgc11d71pc8xp8fv5a1nb2yfw1dgd19xhscn1klpvzw"))))
     (build-system perl-build-system)
     (native-inputs `(("perl-module-build" ,perl-module-build)))
     (home-page "http://search.cpan.org/dist/Lingua-EN-Inflect")
@@ -284,15 +285,15 @@ parameters, returning the stemmed Italian word.")
 (define-public perl-lingua-stem-ru
   (package
     (name "perl-lingua-stem-ru")
-    (version "0.01")
+    (version "0.04")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://cpan/authors/id/A/AL/ALGDR/"
+       (uri (string-append "mirror://cpan/authors/id/N/NE/NEILB/"
                            "Lingua-Stem-Ru-" version ".tar.gz"))
        (sha256
         (base32
-         "0pqgg442fkf12ayh9fgmpa8q9x0iqx6s96181r52yn7s7pcs61h6"))))
+         "0a2jmdz7jn32qj5hyiw5kbv8fvlpmws8i00a6xcbkzb48yvwww0j"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/Lingua-Stem-Ru")
     (synopsis "Porter's stemming algorithm for Russian")

gnu/packages/linux.scm

@@ -78,6 +78,7 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages netpbm)
   #:use-module (gnu packages networking)
   #:use-module (gnu packages ninja)
   #:use-module (gnu packages perl)
@@ -369,8 +370,8 @@ It has been modified to remove all non-free binary blobs.")
 (define %intel-compatible-systems '("x86_64-linux" "i686-linux"))
 (define %linux-compatible-systems '("x86_64-linux" "i686-linux" "armhf-linux"))
 
-(define %linux-libre-version "4.14.4")
+(define %linux-libre-version "4.14.6")
-(define %linux-libre-hash "1hl4n1jpqd05b7qnxbwjmbl2l5cgrh2spqsjq1fnihphmawjd3li")
+(define %linux-libre-hash "0q6dl2shkj5dkf0wgzgfyaq0axk97w05j618xi619y9xqph4ql79")
 
 ;; linux-libre configuration for armhf-linux is derived from Debian armmp.  It
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
@@ -383,20 +384,20 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.67"
+  (make-linux-libre "4.9.69"
-                    "1fr8h4g3j4ns0x33i36kgsgb175cdz9v530gx8sxcrbkd10i9i07"
+                    "0xkqbh8fpx47appszjbxzljr6vr0wyk0fphlkynpcrmingk4b98j"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.104"
+  (make-linux-libre "4.4.105"
-                    "1971hphyqbzh80frkbidbqwhgk21r5p2a42bihjcd5kh3pssn4zl"
+                    "177qvci7wfrc23vi11bnyayfivxf6d8hankgrzv26jr3z6j0rall"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.1
-  (make-linux-libre "4.1.46"
+  (make-linux-libre "4.1.48"
-                    "0bg1vplfksgsnxqdxdp2n0b5lv2j299nv52s8hpja5ckp396jkhk"
+                    "13ii6ixcm46hzk1ns6n4hrrv4dyc0n3wvj2qhmxi178akdcgbn8a"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
@@ -4333,10 +4334,11 @@ libraries, which are often integrated directly into libfabric.")
   (package
     (name "psm")
     (version "3.3.20170428")
+    (home-page "https://github.com/intel/psm")
     (source
      (origin
        (method git-fetch)
-       (uri (git-reference (url "http://github.com/01org/psm")
+       (uri (git-reference (url home-page)
                            (commit "604758e76dc31e68d1de736ccf5ddf16cb22355b")))
        (file-name (string-append "psm-" version ".tar.gz"))
        (sha256
@@ -4362,7 +4364,6 @@ libraries, which are often integrated directly into libfabric.")
                       (substitute* "Makefile"
                         (("/lib64") "/lib"))
                       #t)))))
-    (home-page "https://github.com/01org/psm")
     (synopsis "Intel Performance Scaled Messaging (PSM) Libraries")
     (description
      "The PSM Messaging API, or PSM API, is Intel's low-level user-level
@@ -4372,3 +4373,119 @@ interfaces in parallel environments.")
     ;; Only Intel-compatable processors are supported.
     (supported-systems '("i686-linux" "x86_64-linux"))
     (license (list license:bsd-2 license:gpl2)))) ;dual
+
+(define-public snapscreenshot
+  (package
+    (name "snapscreenshot")
+    (version "1.0.14.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://bisqwit.iki.fi/src/arch/"
+                           name "-" version ".tar.bz2"))
+       (sha256
+        (base32 "0gzvqsbf6a2sbd1mqvj1lbm57i2bm5k0cr6ncr821d1f32gw03mk"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:make-flags
+       (let ((out (assoc-ref %outputs "out")))
+         (list (string-append "BINDIR=" out "/bin")
+               (string-append "MANDIR=" out "/share/man")))
+       #:tests? #f                      ; no test suite
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)            ; ./configure is a snarky no-op
+         (add-before 'install 'fix-ownership
+           ;; Install binaries owned by ‘root’ instead of the nonexistent ‘bin’.
+           (lambda _
+             (substitute* "depfun.mak"
+               ((" -o bin -g bin ") " "))
+             #t))
+         (add-before 'install 'create-output-directories
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (mkdir-p (string-append out "/share/man/man1"))
+               #t))))))
+    (home-page "http://bisqwit.iki.fi/source/snapscreenshot.html")
+    (synopsis "Take screenshots of one or more Linux text consoles")
+    (description
+     "snapscreenshot saves a screenshot of one or more Linux text consoles as a
+Targa (@dfn{.tga}) image.  It can be used by anyone with read access to the
+relevant @file{/dev/vcs*} file(s).")
+    (license license:gpl2)))
+
+(define-public fbcat
+  (package
+    (name "fbcat")
+    (version "0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/jwilk/fbcat/releases/download/"
+                           version "/" name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1dla1na3nf3s4xy0p6w0v54zipg1x8c14yqsw8w9qjzhchr4caxw"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     ;; For building the man pages.
+     `(("docbook-xml" ,docbook-xml)
+       ("docbook-xsl" ,docbook-xsl)
+       ("xsltproc" ,libxslt)))
+    (inputs
+     ;; The ‘fbgrab’ wrapper can use one of several PPM-to-PNG converters.  We
+     ;; choose netpbm simply because it's the smallest.  It still adds ~94 MiB
+     ;; to an otherwise tiny package, so we put ‘fbgrab’ in its own output.
+     `(("pnmtopng" ,netpbm)))
+    (outputs (list "out" "fbgrab"))
+    (arguments
+     `(#:make-flags (list "CC=gcc")
+       #:tests? #f                      ; no tests
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-docbook-location
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "doc/Makefile"
+               (("http://docbook.sourceforge.net/release/xsl/current")
+                (string-append (assoc-ref inputs "docbook-xsl")
+                               "/xml/xsl/docbook-xsl-"
+                               ,(package-version docbook-xsl))))
+             #t))
+         (delete 'configure)            ; no configure script
+         (add-after 'build 'build-documentation
+           (lambda* (#:key make-flags #:allow-other-keys)
+             (zero? (apply system* "make" "-C" "doc"
+                           make-flags))))
+         (add-after 'build 'qualify-references
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((pnmtopng (assoc-ref inputs "pnmtopng"))
+                    (out (assoc-ref outputs "out")))
+               (substitute* "fbgrab"
+                 (("fbcat" all)
+                  (string-append out "/bin/" all))
+                 (("pnmtopng" all)
+                  (string-append pnmtopng "/bin/" all)))
+               #t)))
+         (replace 'install
+           ;; The Makefile lacks an ‘install’ target.  Install files manually.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (out:fbgrab (assoc-ref outputs "fbgrab")))
+               (install-file "fbcat" (string-append out "/bin"))
+               (install-file "doc/fbcat.1"
+                             (string-append out "/share/man/man1"))
+               (install-file "fbgrab" (string-append out:fbgrab "/bin"))
+               (install-file "doc/fbgrab.1"
+                             (string-append out:fbgrab "/share/man/man1"))
+               #t))))))
+    (home-page "https://jwilk.net/software/fbcat")
+    (synopsis "Take a screenshot of the contents of the Linux framebuffer")
+    (description
+     "fbcat saves the contents of the Linux framebuffer (@file{/dev/fb*}), or
+a dump therof.  It supports a wide range of drivers and pixel formats.
+@command{fbcat} can take screenshots of virtually any application that can be
+made to write its output to the framebuffer, including (but not limited to)
+text-mode or graphical applications that don't use a display server.
+
+Also included is @command{fbgrab}, a wrapper around @command{fbcat} that
+emulates the behaviour of Gunnar Monell's older fbgrab utility.")
+    (license license:gpl2)))

gnu/packages/machine-learning.scm

@@ -621,7 +621,9 @@ computing environments.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "18n8775kyfwbvcjjjzda9c5sqy4737c0hrmj6qj1ps2jmlqzair9"))))
+         "18n8775kyfwbvcjjjzda9c5sqy4737c0hrmj6qj1ps2jmlqzair9"))
+       (patches (search-patches
+                "python-scikit-learn-fix-test-non-determinism.patch"))))
     (build-system python-build-system)
     (arguments
      `(#:phases

gnu/packages/mail.scm

@@ -15,7 +15,7 @@
 ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org>
 ;;; Copyright © 2016 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2016, 2017 Troy Sankey <sankeytms@gmail.com>
-;;; Copyright © 2016, 2017 ng0 <ng0@infotropique.org>
+;;; Copyright © 2016, 2017 ng0 <ng0@n0.is>
 ;;; Copyright © 2016 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2016, 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2016 John Darrington <jmd@gnu.org>
@@ -240,14 +240,14 @@ aliasing facilities to work just as they would on normal mail.")
 (define-public mutt
   (package
     (name "mutt")
-    (version "1.9.1")
+    (version "1.9.2")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://bitbucket.org/mutt/mutt/downloads/"
                                  "mutt-" version ".tar.gz"))
              (sha256
               (base32
-               "1c8vv4anl555a03pbnwf8wnf0d8pcnd4p35y3q8f5ikkcflq76vl"))
+               "15kqxpx8bykqbyw4q33hkz0j2f65v6cl21sl5li2vw5vaaim5qd2"))
              (patches (search-patches "mutt-store-references.patch"))))
     (build-system gnu-build-system)
     (inputs
@@ -279,7 +279,7 @@ operating systems.")
 (define-public neomutt
   (package
     (name "neomutt")
-    (version "20171027")
+    (version "20171208")
     (source
      (origin
        (method url-fetch)
@@ -287,7 +287,7 @@ operating systems.")
                            "/archive/" name "-" version ".tar.gz"))
        (sha256
         (base32
-         "10z523cy3s6syh0mwpsncl87wrvyzsk99y7nzicwvx6y3hmdw01d"))))
+         "0dfp7m794ws6vg029zx7wrrjrscrnmi8cvbzqzgxafl97bbjipwz"))))
     (build-system gnu-build-system)
     (inputs
      `(("cyrus-sasl" ,cyrus-sasl)
@@ -693,17 +693,23 @@ invoking @command{notifymuch} from the post-new hook.")
 (define-public notmuch
   (package
     (name "notmuch")
-    (version "0.25.2")
+    (version "0.25.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://notmuchmail.org/releases/notmuch-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0ai6vbs9wzwfz7jcphgqsqpcbq137l34xhmcli4h5c8n82fvmdp4"))))
+                "1fyx20rjpwbf2j1v5fpa5s0rjnwhcgvijzh2qyinp8rlbh1qxmab"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:make-flags (list "V=1") ; Verbose test output.
+     `(#:modules ((guix build gnu-build-system)
+                  ((guix build emacs-build-system) #:prefix emacs:)
+                  (guix build utils))
+       #:imported-modules (,@%gnu-build-system-modules
+                           (guix build emacs-build-system)
+                           (guix build emacs-utils))
+       #:make-flags (list "V=1") ; Verbose test output.
        #:phases (modify-phases %standard-phases
                   (add-after 'unpack 'patch-notmuch-lib.el
                     (lambda _
@@ -715,16 +721,25 @@ invoking @command{notifymuch} from the post-new hook.")
                       (setenv "CC" "gcc")
                       (setenv "CONFIG_SHELL" (which "sh"))
 
-                      (let ((out (assoc-ref outputs "out")))
+                      (let* ((out (assoc-ref outputs "out"))
-                        (zero? (system* "./configure"
+                             (elisp
-                                        (string-append "--prefix=" out))))))
+                              (string-append out "/share/emacs/site-lisp/guix.d/"
+                                             ,name "-" ,version)))
+                        (zero?
+                         (system*
+                          "./configure"
+                          (string-append "--prefix=" out)
+                          (string-append "--emacslispdir=" elisp)
+                          (string-append "--emacsetcdir=" elisp))))))
                   (add-before 'check 'prepare-test-environment
                     (lambda _
                       (setenv "TEST_CC" "gcc")
                       ;; Patch various inline shell invocations.
                       (substitute* (find-files "test" "\\.sh$")
                         (("/bin/sh") (which "sh")))
-                      #t)))))
+                      #t))
+                  (add-after 'install 'make-autoloads
+                    (assoc-ref emacs:%standard-phases 'make-autoloads)))))
     (native-inputs
      `(("bash-completion" ,bash-completion)
        ("emacs" ,emacs-no-x) ; Minimal lacks libxml, needed for some tests.
@@ -928,7 +943,7 @@ compresses it.")
 (define-public claws-mail
   (package
     (name "claws-mail")
-    (version "3.15.1")
+    (version "3.16.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -936,7 +951,7 @@ compresses it.")
                     ".tar.xz"))
               (sha256
                (base32
-                "0hlm2jipyr4z6izlrpvabpz4ivh49i13avnm848kr1nv68pkq2cd"))))
+                "1awpr3s7n8bq8p3w10a4j6lg5bizjxyiqp4rqzc2j8cn7lyi64n2"))))
     (build-system gnu-build-system)
     (native-inputs `(("pkg-config" ,pkg-config)))
     (inputs `(("bogofilter" ,bogofilter)
@@ -2181,7 +2196,7 @@ to access GNU Mailman.")
 (define-public blists
   (package
     (name "blists")
-    (version "1.0")
+    (version "2.0")
     (source
      (origin
        (method url-fetch)
@@ -2189,7 +2204,7 @@ to access GNU Mailman.")
                            "blists/blists-" version ".tar.gz"))
        (sha256
         (base32
-         "1gp51kmb8yv8d693wcpdslmwlbw5w2kgz4kxhrcaf7y89w8wy4qd"))))
+         "1xll5wn7py3bbncbwrj172f56nz75c9gwfsa80rwd96ss9gfmp3c"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; No tests
@@ -2381,3 +2396,28 @@ the GNOME desktop.  It supports both POP3 and IMAP servers as well as the
 mbox, maildir and mh local mailbox formats.  Balsa also supports SMTP and/or
 the use of a local MTA such as Sendmail.")
     (license gpl3+)))
+
+(define-public afew
+  (package
+    (name "afew")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "afew" version))
+       (sha256
+        (base32
+         "121w7bd53xyibllxxbfykjj76n81kn1vgjqd22izyh67y8qyyk5r"))))
+    (build-system python-build-system)
+    (inputs
+     `(("python-chardet" ,python-chardet)
+       ("python-notmuch" ,python-notmuch)))
+    (native-inputs
+     `(("python-setuptools-scm" ,python-setuptools-scm)))
+    (home-page "https://github.com/afewmail/afew")
+    (synopsis "Initial tagging script for notmuch mail")
+    (description "afew is an initial tagging script for notmuch mail.  It
+provides automatic tagging each time new mail is registered with notmuch.  It
+can add tags based on email headers or Maildir folders and can handle spam and
+killed threads.")
+    (license isc)))

gnu/packages/maths.scm

@@ -335,7 +335,7 @@ the OCaml language.")
 (define-public glpk
   (package
     (name "glpk")
-    (version "4.63")
+    (version "4.64")
     (source
      (origin
       (method url-fetch)
@@ -343,7 +343,7 @@ the OCaml language.")
                           version ".tar.gz"))
       (sha256
        (base32
-        "1xp7nclmp8inp20968bvvfcwmz3mz03sbm0v3yjz8aqwlpqjfkci"))))
+        "096cqgjc7vkq6wd8znhcxjbs1s2rym3qf753fqxrrq531vs6g4jk"))))
     (build-system gnu-build-system)
     (inputs
      `(("gmp" ,gmp)))
@@ -1230,7 +1230,7 @@ interfaces.")
 (define-public ceres
   (package
     (name "ceres-solver")
-    (version "1.11.0")
+    (version "1.13.0")
     (home-page "http://ceres-solver.org/")
     (source (origin
               (method url-fetch)
@@ -1238,7 +1238,7 @@ interfaces.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0i7qkbf8g6pd8arxzldppga26ckv93y8zldsfz6wbd4n6b1nqrjd"))))
+                "1kbxgab3q1vgyq7hjqasr1lji4b2sgn7ss351amklkb3jyhr1x0x"))))
     (build-system cmake-build-system)
     (arguments
      ;; TODO: Build HTML user documentation and install separately.

gnu/packages/messaging.scm

@@ -387,7 +387,7 @@ authentication.")
      (list (search-path-specification
             (variable "PURPLE_PLUGIN_PATH")
             (files (list (string-append "lib/purple-"
-                                        (version-prefix version 1))
+                                        (version-major version))
                          "lib/pidgin")))))
     (home-page "http://www.pidgin.im/")
     (synopsis "Graphical multi-protocol instant messaging client")

gnu/packages/mpd.scm

@@ -76,7 +76,7 @@ interfacing MPD in the C, C++ & Objective C languages.")
 (define-public mpd
   (package
     (name "mpd")
-    (version "0.20.11")
+    (version "0.20.12")
     (source (origin
               (method url-fetch)
               (uri
@@ -85,7 +85,7 @@ interfacing MPD in the C, C++ & Objective C languages.")
                               "/mpd-" version ".tar.xz"))
               (sha256
                (base32
-                "1g0lwm8p98q2hxa9vd6jx61s7d3r665s2bmz6ipkv9ijmyfps8p9"))))
+                "02gpfkki61c24hphaas9pb29wpvd0pbmwdqrpn8wi1gv103aqng1"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/music.scm

@@ -40,6 +40,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system python)
   #:use-module (guix build-system scons)
+  #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system waf)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
@@ -469,6 +470,75 @@ background while you work.")
 enable professional yet simple and intuitive pattern-based drum programming.")
     (license license:gpl2+)))
 
+(define-public easytag
+  (package
+    (name "easytag")
+    (version "2.4.3")
+    (source (origin
+             (method url-fetch)
+              (uri (string-append "mirror://gnome/sources/easytag/2.4/easytag-"
+                     version ".tar.xz"))
+             (sha256
+              (base32
+               "1mbxnqrw1fwcgraa1bgik25vdzvf97vma5pzknbwbqq5ly9fwlgw"))))
+    (build-system glib-or-gtk-build-system)
+    (native-inputs
+     `(("desktop-file-utils" ,desktop-file-utils)
+       ("glib" ,glib "bin")
+       ("intltool" ,intltool)
+       ("itstool" ,itstool)
+       ("pkg-config" ,pkg-config)
+       ("xmllint" ,libxml2)))
+    (inputs
+     `(("flac" ,flac)
+       ("gtk+" ,gtk+)
+       ("id3lib" ,id3lib)
+       ("libid3tag" ,libid3tag)
+       ("libvorbis" ,libvorbis)
+       ("opusfile" ,opusfile)
+       ("speex" ,speex)
+       ("taglib" ,taglib)
+       ("wavpack" ,wavpack)
+       ("yelp" ,yelp)))
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'configure-libid3tag
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; libid3tag does not provide a .pc file and EasyTAG's configure
+             ;; script healivy relies on pkg-config.  Providing a temporary
+             ;; local .pc file is easier than patching the configure script.
+             (let* ((libid3tag (assoc-ref inputs "libid3tag")))
+               (mkdir-p "pkgconfig")
+               (with-output-to-file
+                 "pkgconfig/id3tag.pc"
+                 (lambda _
+                   (format #t
+                     "prefix=~@*~a~@
+                      libdir=${prefix}/lib~@
+                      includedir=${prefix}/include~@
+                      Libs: -L${libdir} -lid3tag -lz~@
+                      Cflags: -I${includedir}~%"
+                     libid3tag)))
+               (setenv "PKG_CONFIG_PATH"
+                 (string-append (getenv "PKG_CONFIG_PATH")
+                   ":" (getcwd) "/pkgconfig")))))
+         (add-after 'unpack 'patch-makefile
+           (lambda _
+             (substitute* "Makefile.in"
+               ;; The Makefile generates a test-desktop-file-validate.sh
+               ;; script with /bin/sh hard-coded.
+               (("/bin/sh") (which "sh"))
+               ;; Don't create 'icon-theme.cache'.
+               (("gtk-update-icon-cache") "true")))))))
+    (home-page "https://wiki.gnome.org/Apps/EasyTAG")
+    (synopsis "Simple application for viewing and editing tags in audio files")
+    (description
+      "EasyTAG is an application for viewing and editing tags in audio files.
+It supports MP3, MP2, MP4/AAC, FLAC, Ogg Opus, Ogg Speex, Ogg Vorbis,
+MusePack, Monkey's Audio, and WavPack files.")
+    (license license:gpl2+)))
+
 (define-public extempore
   (package
     (name "extempore")
@@ -1857,7 +1927,7 @@ capabilities, custom envelopes, effects, etc.")
 (define-public yoshimi
   (package
     (name "yoshimi")
-    (version "1.5.3")
+    (version "1.5.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/yoshimi/"
@@ -1865,7 +1935,7 @@ capabilities, custom envelopes, effects, etc.")
                                   "/yoshimi-" version ".tar.bz2"))
               (sha256
                (base32
-                "0sns35pyw2f74xrv1fxiyf9g9415kvh2rrbdjd60hsiv584nlari"))))
+                "0h71x9742bswifwll7bma1fz648fd5xd0yfp7byvsczy6zhjz5pf"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ; there are no tests
@@ -1975,6 +2045,43 @@ on the library.")
 allows you to send JACK MIDI events (i.e. play) using your PC keyboard.")
     (license license:bsd-2)))
 
+(define-public jack-capture
+  (package
+    (name "jack-capture")
+    (version "0.9.73")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/kmatheussen/jack_capture.git")
+                    (commit version)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "0jcqky96q8xgya6wqv1p8pj9fkf2wh7ynl67ah7x5bn3basgfclf"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:make-flags
+       (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
+       #:tests? #f ; there are none
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("which" ,which)))
+    (inputs
+     `(("gtk+" ,gtk+-2)
+       ("jack" ,jack-1)
+       ("libogg" ,libogg)
+       ("liblo" ,liblo)
+       ("lame" ,lame)
+       ("libsndfile" ,libsndfile)))
+    (home-page "https://github.com/kmatheussen/jack_capture")
+    (synopsis "Program for recording sound files with JACK")
+    (description "This is a program for recording sound files with JACK.  It
+can connect to any JACK port and record the output into a stereo WAV file.")
+    (license license:gpl2+)))
+
 (define-public cursynth
   (package
     (name "cursynth")
@@ -2001,6 +2108,34 @@ synthesis engine.  Notes and parameter changes may be entered via MIDI or the
 computer's keyboard.")
     (license license:gpl3+)))
 
+(define-public aj-snapshot
+  (package
+    (name "aj-snapshot")
+    (version "0.9.7")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/aj-snapshot/"
+                                  "aj-snapshot-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "0yxccgp9qw2cyqv719wlbq8wfsr5ga8czvwa7bmb8dh5s11n3rn8"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("minixml" ,minixml)
+       ("jack" ,jack-1)
+       ("alsa-lib" ,alsa-lib)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://aj-snapshot.sourceforge.net/")
+    (synopsis "Snapshot connections between ALSA and JACK clients")
+    (description "Aj-snapshot is a small program that can be used to make
+snapshots of the connections made between JACK and/or ALSA clients.  Because
+JACK can provide both audio and MIDI support to programs, aj-snapshot can
+store both types of connections for JACK.  ALSA, on the other hand, only
+provides routing facilities for MIDI clients.  Aj-snapshot is meant to be used
+from the command line.")
+    (license license:gpl3+)))
+
 (define-public qtractor
   (package
     (name "qtractor")
@@ -2607,13 +2742,14 @@ standard MIDI file with the csvmidi program.")
     (name "gx-guvnor-lv2")
     (version "0.1")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/brummer10/GxGuvnor.lv2/"
+              (uri (git-reference
-                                  "archive/v" version ".tar.gz"))
+                    (url "https://github.com/brummer10/GxGuvnor.lv2.git")
-              (file-name (string-append name "-" version ".tar.gz"))
+                    (commit (string-append "v" version))))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "0rnfvrvs8qmmldyfmx4llyly33zp68448gx40ywdwj42x0mam92p"))))
+                "1wa5070j40p7f0b3kr259pzm99xb6cf2badr2capayjvgayd6gnm"))))
     (build-system gnu-build-system)
     (arguments
      `(;; The check target is used only to output a warning.
@@ -2625,7 +2761,8 @@ standard MIDI file with the csvmidi program.")
          (replace 'configure
            (lambda _
              (substitute* "Makefile"
-               (("INSTALL_DIR = .*") "INSTALL_DIR=/lib/lv2\n"))
+               (("INSTALL_DIR = .*") "INSTALL_DIR=/lib/lv2\n")
+               (("install : all") "install :"))
              #t)))))
     (inputs
      `(("lv2" ,lv2)))
@@ -2634,12 +2771,13 @@ standard MIDI file with the csvmidi program.")
     (description "This package provides the LV2 plugin \"GxGuvnor\", a
 simulation of an overdrive or distortion pedal for guitars.")
     ;; The LICENSE file says GPLv3 but the license headers in the files say
-    ;; GPLv2 or later.
+    ;; GPLv2 or later.  The whole project is released under GPLv3 or later
-    (license license:gpl2+)))
+    ;; according to https://github.com/brummer10/GxGuvnor.lv2/issues/1
+    (license license:gpl3+)))
 
 (define-public gx-vbass-preamp-lv2
-  (let ((commit "0e599abab10c7669dd444e5d06f671c2fc1b9c6c")
+  (let ((commit "eb999b0ca0ef4da40a59e458a9ab6e7042b96c99")
-        (revision "1"))
+        (revision "2"))
     (package (inherit gx-guvnor-lv2)
       (name "gx-vbass-preamp-lv2")
       (version (string-append "0-" revision "." (string-take commit 9)))
@@ -2650,18 +2788,13 @@ simulation of an overdrive or distortion pedal for guitars.")
                       (commit commit)))
                 (sha256
                  (base32
-                  "1dzksdfrva666gpi62fd2ni9rhf18sl917f1894qr0b17pbdh9k1"))
+                  "0firap073ldw4nrykkd7jvyyj0jbl1nslxyzjj4kswazp99x7d9h"))
                 (file-name (string-append name "-" version "-checkout"))))
-      (arguments
+      (inputs
-       (substitute-keyword-arguments (package-arguments gx-guvnor-lv2)
+       `(("lv2" ,lv2)
-         ((#:phases phases)
+         ("gtk+" ,gtk+-2)))
-          `(modify-phases ,phases
+      (native-inputs
-             (replace 'configure
+       `(("pkg-config" ,pkg-config)))
-               (lambda _
-                 (substitute* "Makefile"
-                   (("INSTALL_DIR = .*") "INSTALL_DIR=/lib/lv2\n")
-                   (("install : all") "install :"))
-                 #t))))))
       (home-page "https://github.com/brummer10/GxVBassPreAmp.lv2")
       (synopsis "Simulation of the Vox Venue Bass 100 Pre Amp Section")
       (description "This package provides the LV2 plugin \"GxVBassPreAmp\", a
@@ -2671,7 +2804,7 @@ Section."))))
 (define-public gx-overdriver-lv2
   (let ((commit "ed71801987449414bf3adaa0dbfac68e8775f1ce")
         (revision "1"))
-    (package (inherit gx-vbass-preamp-lv2)
+    (package (inherit gx-guvnor-lv2)
       (name "gx-overdriver-lv2")
       (version (string-append "0-" revision "." (string-take commit 9)))
       (source (origin
@@ -2691,7 +2824,7 @@ overdrive effect."))))
 (define-public gx-tone-mender-lv2
   (let ((commit "b6780b4a3e4782b3ed0e5882d6788f178aed138f")
         (revision "1"))
-    (package (inherit gx-vbass-preamp-lv2)
+    (package (inherit gx-guvnor-lv2)
       (name "gx-tone-mender-lv2")
       (version (string-append "0-" revision "." (string-take commit 9)))
       (source (origin
@@ -2711,7 +2844,7 @@ clean boost effect with a 3-knob tonestack."))))
 (define-public gx-push-pull-lv2
   (let ((commit "7f76ae2068498643ac8671ee0930b13ee3fd8eb5")
         (revision "1"))
-    (package (inherit gx-vbass-preamp-lv2)
+    (package (inherit gx-guvnor-lv2)
       (name "gx-push-pull-lv2")
       (version (string-append "0-" revision "." (string-take commit 9)))
       (source (origin
@@ -2733,14 +2866,14 @@ simulation of a push pull transistor fuzz effect with added high octave."))))
     (name "gx-suppa-tone-bender-lv2")
     (version "0.1")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/brummer10/"
+              (uri (git-reference
-                                  "GxSuppaToneBender.lv2/archive/v"
+                    (url "https://github.com/brummer10/GxSuppaToneBender.lv2.git")
-                                  version ".tar.gz"))
+                    (commit (string-append "v" version))))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "1j90fns87035sfr6bxs4cvqxbyy3pqjhihx1nis8xajn202nl1hx"))
+                "01x6bjmllkmvxfzc5xwdix7w021j26js71awv728cxsmkxgqw0zy"))))
-              (file-name (string-append name "-" version ".tar.gz"))))
     (home-page "https://github.com/brummer10/GxSuppaToneBender.lv2")
     (synopsis "Simulation of the Vox Suppa Tone Bender pedal")
     (description "This package provides the LV2 plugin
@@ -2748,8 +2881,8 @@ simulation of a push pull transistor fuzz effect with added high octave."))))
 pedal.")))
 
 (define-public gx-saturator-lv2
-  (let ((commit "0b581ac85c515325b9f16e51937cae6e1bf81a0a")
+  (let ((commit "605330f432c94b6eb3f8203cbe472befae959532")
-        (revision "2"))
+        (revision "3"))
     (package (inherit gx-vbass-preamp-lv2)
       (name "gx-saturator-lv2")
       (version (string-append "0-" revision "." (string-take commit 9)))
@@ -2760,7 +2893,7 @@ pedal.")))
                       (commit commit)))
                 (sha256
                  (base32
-                  "1cl785pzq8zk55m1rnhfd6qsabci6kpf4pf002gwr91vagyq246z"))
+                  "1w4nvh0rmxrv3s3hmh4fs74f3hc0jn31v00j769j7v68mqr7kawy"))
                 (file-name (string-append name "-" version "-checkout"))))
       (home-page "https://github.com/brummer10/GxSaturator.lv2")
       (synopsis "Saturation effect")
@@ -2772,14 +2905,14 @@ saturation effect."))))
     (name "gx-hyperion-lv2")
     (version "0.1")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/brummer10/"
+              (uri (git-reference
-                                  "GxHyperion.lv2/archive/v"
+                    (url "https://github.com/brummer10/GxHyperion.lv2.git")
-                                  version ".tar.gz"))
+                    (commit (string-append "v" version))))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "1pd7l33a14kq73wavgqq7csw4n3mwjz9d5rxaj0jgsyxd3llp3wh"))
+                "1vx79s6s9if117y2g0ppdja2sv2wcny6xcfl3j1z4cipahnildxf"))))
-              (file-name (string-append name "-" version ".tar.gz"))))
     (home-page "https://github.com/brummer10/GxHyperion.lv2")
     (synopsis "Simulation of the Hyperion Fuzz pedal")
     (description "This package provides the LV2 plugin \"GxHyperion\", a
@@ -2790,14 +2923,14 @@ simulation of the Hyperion Fuzz pedal.")))
     (name "gx-voodoo-fuzz-lv2")
     (version "0.1")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/brummer10/"
+              (uri (git-reference
-                                  "GxVoodoFuzz.lv2/archive/v"
+                    (url "https://github.com/brummer10/GxVoodoFuzz.lv2.git")
-                                  version ".tar.gz"))
+                    (commit (string-append "v" version))))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "0cc8sg7q493bs6pcq4ipqp6czpxv04nh9yvn8kq2x65ni2208n2f"))
+                "1v0scphivri1fk4hl20j13f92i48mnx1zsil4hgnadsmm4nsfw43"))))
-              (file-name (string-append name "-" version ".tar.gz"))))
     (home-page "https://github.com/brummer10/GxVoodoFuzz.lv2")
     (synopsis "Fuzz effect modelled after the Voodoo Lab SuperFuzz")
     (description "This package provides the LV2 plugin \"GxVoodooFuzz\", a
@@ -2810,14 +2943,14 @@ parallel with a DarkBooster, followed by a volume control.")))
     (name "gx-super-fuzz-lv2")
     (version "0.1")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/brummer10/"
+              (uri (git-reference
-                                  "GxSuperFuzz.lv2/archive/v"
+                    (url "https://github.com/brummer10/GxSuperFuzz.lv2.git")
-                                  version ".tar.gz"))
+                    (commit (string-append "v" version))))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "0pnivq05f1kji8c5jxsqdzhdfk3xn422v2d1x20x3jfsxnaf115x"))
+                "1jlljd9hlgfflbiizq47lv1xbbgjyx3v835mf24zmh1q5zsw4np4"))))
-              (file-name (string-append name "-" version ".tar.gz"))))
     (home-page "https://github.com/brummer10/GxSuperFuzz.lv2")
     (synopsis "Fuzz effect modelled after the UniVox SuperFuzz")
     (description "This package provides the LV2 plugin \"GxSuperFuzz\", an
@@ -2830,22 +2963,22 @@ adjusts the amount of harmonics.")))
     (name "gx-vintage-fuzz-master-lv2")
     (version "0.1")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/brummer10/"
+              (uri (git-reference
-                                  "GxVintageFuzzMaster.lv2/archive/v"
+                    (url "https://github.com/brummer10/GxVintageFuzzMaster.lv2.git")
-                                  version ".tar.gz"))
+                    (commit (string-append "v" version))))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "0bdkfj6xi2g4izfw3pmr4i0nqzg8jnkdwc23x9ifxwc6p1kbayzk"))
+                "02jb211z8rw2qr5r1z5mdxlqgiw6cbc319xpqplvn6k21c59mskv"))))
-              (file-name (string-append name "-" version ".tar.gz"))))
     (home-page "https://github.com/brummer10/GxVintageFuzzMaster.lv2")
     (synopsis "Fuzz effect simulation of the vintage Fuzz Master")
     (description "This package provides the LV2 plugin
 \"GxVintageFuzzMaster\", a simulation of the vintage Fuzz Master pedal.")))
 
 (define-public gx-slow-gear-lv2
-  (let ((commit "cb852e0426f4e6fe077e7f1ede73a4da335cfc5e")
+  (let ((commit "5d37e775b0feef1d82feee94e2a7a2d7e57efe2d")
-        (revision "2"))
+        (revision "3"))
     (package (inherit gx-vbass-preamp-lv2)
       (name "gx-slow-gear-lv2")
       (version (string-append "0-" revision "." (string-take commit 9)))
@@ -2856,7 +2989,7 @@ adjusts the amount of harmonics.")))
                       (commit commit)))
                 (sha256
                  (base32
-                  "0dp7afi1r3kzciiyn1hrkz6arsq47ys9sx5g4b7xa9k1dv92ishp"))
+                  "141mz69zkhk3lm54bb6wgpnghb92zm1ig7fv07240cmhydqji1q1"))
                 (file-name (string-append name "-" version "-checkout"))))
       (home-page "https://github.com/brummer10/GxSlowGear.lv2")
       (synopsis "Slow gear audio effect")
@@ -2866,7 +2999,7 @@ slow gear audio effect to produce volume swells."))))
 (define-public gx-switchless-wah-lv2
   (let ((commit "7b08691203314612999f0ce2328cdc1161cd6665")
         (revision "2"))
-    (package (inherit gx-vbass-preamp-lv2)
+    (package (inherit gx-guvnor-lv2)
       (name "gx-switchless-wah-lv2")
       (version (string-append "0-" revision "." (string-take commit 9)))
       (source (origin
@@ -2884,8 +3017,8 @@ slow gear audio effect to produce volume swells."))))
 a simulation of an analog Wah pedal with switchless activation."))))
 
 (define-public mod-utilities
-  (let ((commit "7cdeeac26ae682730740105ece121d4dddb8ba3f")
+  (let ((commit "80ea3ea9f52fab7f191671f4810bf90fc955a046")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "mod-utilities")
       (version (string-append "0-" revision "." (string-take commit 9)))
@@ -2894,17 +3027,19 @@ a simulation of an analog Wah pedal with switchless activation."))))
                 (uri (git-reference
                       (url "https://github.com/moddevices/mod-utilities.git")
                       (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "1ilnkbrmwrszxvc21qlb86h29yz7cnc6rcp0jmna1y693ny2qhf4"))
+                  "1v55zmzmlg0ka7341x5lsvb44amy17vk27s669ps1basd1bk5s5v"))))
-                (file-name (string-append name "-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments
        `(#:tests? #f ; there are no tests
          #:make-flags
          (list (string-append "INSTALL_PATH="
                               (assoc-ref %outputs "out")
-                              "/lib/lv2"))
+                              "/lib/lv2")
+               (string-append "PREFIX=" (assoc-ref %outputs "out"))
+               "CC=gcc")
          #:phases
          (modify-phases %standard-phases
            (delete 'configure))))
@@ -3005,14 +3140,14 @@ develop custom plugins for use in other applications without programming.")
 (define-public qmidiarp
   (package
     (name "qmidiarp")
-    (version "0.6.4")
+    (version "0.6.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/qmidiarp/qmidiarp/"
                                   version "/qmidiarp-" version ".tar.bz2"))
               (sha256
                (base32
-                "1gkfv8ajgf86kbn6j5ilfc1zlz17gdi9yxzywqd6jwff4xlm75hx"))))
+                "043yh1p0rrbj1v840y27529m9260g55gvh1km8az4jxy7mns58r2"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -3548,3 +3683,71 @@ by The Echo Nest.")
 @url{https://gpodder.net} APIs.  It allows applications to discover, manage
 and track podcasts.")
     (license license:lgpl2.1+)))
+
+(define-public sonivox-eas
+  (package
+    (name "sonivox-eas")
+    (version "1.1.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/pedrolcl/Linux-SonivoxEas.git")
+                    (commit (string-append "v" version))))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "0l9gs00p5g4k4qy6i7nv1mfi2n2wnsycwjrgrh9hxzam4irf2mw2"))))
+    (build-system cmake-build-system)
+    (arguments '(#:tests? #f)) ; there are no tests
+    (inputs
+     `(("alsa-lib" ,alsa-lib)
+       ("drumstick" ,drumstick)
+       ("pulseaudio" ,pulseaudio)
+       ("qtbase" ,qtbase)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "https://github.com/pedrolcl/Linux-SonivoxEas")
+    (synopsis "MIDI synthesizer library")
+    (description "This project is a real time General MIDI synthesizer based
+on the Sonivox EAS Synthesizer by Google.  It does not need external
+soundfonts, using embedded samples instead.")
+    ;; Sonivox is released under the ASL2.0; the rest of the code is under
+    ;; GPLv2+.
+    (license (list license:gpl2+ license:asl2.0))))
+
+(define-public whysynth
+  (package
+    (name "whysynth")
+    (version "20170701")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://smbolton.com/whysynth/whysynth-"
+                                  version ".tar.bz2"))
+              (sha256
+               (base32
+                "02qbn0hbvn1iym4zxv35b201blg31yjpgh71h8db0j5zls2xc0m6"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("dssi" ,dssi)
+       ("liblo" ,liblo)
+       ("fftwf" ,fftwf)
+       ("gtk+" ,gtk+-2)
+       ("ladspa" ,ladspa)
+       ("alsa-lib" ,alsa-lib)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://smbolton.com/whysynth.html")
+    (synopsis "DSSI software synthesizer")
+    (description "WhySynth is a versatile softsynth which operates as a plugin
+for the DSSI Soft Synth Interface.  A brief list of features:
+
+@enumerate
+@item 4 oscillators, 2 filters, 3 LFOs, and 5 envelope generators per voice.
+@item 11 oscillator modes: minBLEP, wavecycle, chorused wavecycle,
+  asynchronous granular, three FM modes, waveshaper, noise, PADsynth, and phase
+  distortion.
+@item 10 filter modes.
+@item flexible modulation and mixdown options, plus effects.
+@end enumerate
+")
+    (license license:gpl2+)))

gnu/packages/networking.scm

@@ -450,7 +450,7 @@ and up to 1 Mbit/s downstream.")
 (define-public whois
   (package
     (name "whois")
-    (version "5.2.18")
+    (version "5.2.19")
     (source
      (origin
        (method url-fetch)
@@ -458,7 +458,7 @@ and up to 1 Mbit/s downstream.")
                            name "_" version ".tar.xz"))
        (sha256
         (base32
-         "1mcpgj18n1xppvlhjqzpj05yr5z48bym9bd88k10fwgkmwk0spf3"))))
+         "0b16w48c17k35lhd95qcl2kjq2rahk8znkg3w467rf3kzmsa4fbc"))))
     (build-system gnu-build-system)
     ;; TODO: unbundle mkpasswd binary + its po files.
     (arguments
@@ -471,13 +471,14 @@ and up to 1 Mbit/s downstream.")
          (add-before 'build 'setenv
            (lambda _
              (setenv "HAVE_ICONV" "1")
-             (setenv "HAVE_LIBIDN" "1")
              #t)))))
     (inputs
+     ;; TODO: Switch to libidn2 when >= 2.0.3 is ungrafted in master.
      `(("libidn" ,libidn)))
     (native-inputs
      `(("gettext" ,gettext-minimal)
-       ("perl" ,perl)))
+       ("perl" ,perl)
+       ("pkg-config" ,pkg-config)))
     (synopsis "Improved whois client")
     (description "This whois client is intelligent and can
 automatically select the appropriate whois server for most queries.
@@ -710,7 +711,7 @@ allows for heavy scripting.")
 (define-public perl-net-dns
  (package
   (name "perl-net-dns")
-  (version "1.13")
+  (version "1.14")
   (source
     (origin
       (method url-fetch)
@@ -720,7 +721,7 @@ allows for heavy scripting.")
              ".tar.gz"))
       (sha256
         (base32
-          "0dlca65l45mqs7l58fg838bj3as5kmnbs1zy8vg9cbsz6rindivy"))))
+          "1z4r092qv0ify033dld5jayk8gs0bc7pl130dvb8ab7b9rcqmhw3"))))
   (build-system perl-build-system)
   (inputs
     `(("perl-digest-hmac" ,perl-digest-hmac)))

gnu/packages/nutrition.scm

@@ -52,11 +52,18 @@
     (inputs
      `(("pygtk"             ,python2-pygtk)
        ("sqlalchemy"        ,python2-sqlalchemy)
+       ("python-lxml"       ,python2-lxml)
        ("python-pillow"     ,python2-pillow)
        ("elib.intl"         ,python2-elib.intl)))
     (arguments
      `(#:python ,python-2               ;exception and print syntax
-       #:tests? #f))                    ;tests look bitrotted
+       #:tests? #f                      ;tests look bitrotted
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'install
+           (lambda* (#:key make-flags #:allow-other-keys)
+             (zero? (system* "python" "setup.py" "install" "--prefix"
+                             (assoc-ref %outputs "out"))))))))
     (home-page "http://thinkle.github.io/gourmet/")
     (synopsis "Recipe organizer")
     (description

gnu/packages/package-management.scm

@@ -87,8 +87,8 @@
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
   (let ((version "0.14.0")
-        (commit "ad4953bc0ec1684c49c0934304c7ec200a0cd280")
+        (commit "02345c963e1e8a45afcdf5acb80fca4538244b36")
-        (revision 1))
+        (revision 2))
     (package
       (name "guix")
 
@@ -104,7 +104,7 @@
                       (commit commit)))
                 (sha256
                  (base32
-                  "0ngra4cb1kf3kwccslmhnvlr116drsnbqrsjniq1hrg5mqf6vf1b"))
+                  "0f33makasj14zf0zfv1w7k04bkcpdy5grx5b904vv5ygi5bak7nx"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments

gnu/packages/password-utils.scm

@@ -14,6 +14,7 @@
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2017 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2017 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
+;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -98,6 +99,10 @@ human.")
         (base32
          "0wrl8kxb16wzdgfjj057yv18cfg0b8z8lxp1fl2q8fkdgr7phm9g"))))
     (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "-DCMAKE_INSTALL_LIBDIR="
+                            (assoc-ref %outputs "out") "/lib"))))
     (inputs
      `(("libgcrypt" ,libgcrypt)
        ("libxi" ,libxi)

gnu/packages/patches/borg-fix-archive-corruption-bug.patch

@@ -0,0 +1,68 @@
+Fix a bug in `borg check --repair` that corrupts existing archives:
+
+https://github.com/borgbackup/borg/issues/3444
+
+Patches copied from upstream source repository:
+
+https://github.com/borgbackup/borg/commit/e09892caec8a63d59e909518c4e9c230dbd69774
+https://github.com/borgbackup/borg/commit/a68d28bfa4db30561150c83eb6a0dca5efa4d9e8
+
+From a68d28bfa4db30561150c83eb6a0dca5efa4d9e8 Mon Sep 17 00:00:00 2001
+From: Thomas Waldmann <tw@waldmann-edv.de>
+Date: Sat, 16 Dec 2017 01:11:40 +0100
+Subject: [PATCH 1/2] modify borg check unit test so it "hangs", see #3444
+
+it doesn't infinitely hang, but slows down considerably.
+---
+ src/borg/testsuite/archiver.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/borg/testsuite/archiver.py b/src/borg/testsuite/archiver.py
+index c7def2c7..b3383e97 100644
+--- a/src/borg/testsuite/archiver.py
++++ b/src/borg/testsuite/archiver.py
+@@ -3006,7 +3006,7 @@ def test_missing_file_chunk(self):
+     def test_missing_archive_item_chunk(self):
+         archive, repository = self.open_archive('archive1')
+         with repository:
+-            repository.delete(archive.metadata.items[-5])
++            repository.delete(archive.metadata.items[0])
+             repository.commit()
+         self.cmd('check', self.repository_location, exit_code=1)
+         self.cmd('check', '--repair', self.repository_location, exit_code=0)
+-- 
+2.15.1
+
+
+From e09892caec8a63d59e909518c4e9c230dbd69774 Mon Sep 17 00:00:00 2001
+From: Thomas Waldmann <tw@waldmann-edv.de>
+Date: Sat, 16 Dec 2017 01:16:05 +0100
+Subject: [PATCH 2/2] check --repair: fix malfunctioning validator, fixes #3444
+
+the major problem was the ('path' in item) expression.
+the dict has bytes-typed keys there, so it never succeeded as it
+looked for a str key. this is a 1.1 regression, 1.0 was fine.
+
+the dict -> StableDict change is just for being more specific,
+the check triggered correctly as StableDict subclasses dict,
+it was just a bit too general.
+---
+ src/borg/archive.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/borg/archive.py b/src/borg/archive.py
+index 239d00b7..be086800 100644
+--- a/src/borg/archive.py
++++ b/src/borg/archive.py
+@@ -1457,7 +1457,7 @@ def robust_iterator(archive):
+             """
+             item_keys = frozenset(key.encode() for key in self.manifest.item_keys)
+             required_item_keys = frozenset(key.encode() for key in REQUIRED_ITEM_KEYS)
+-            unpacker = RobustUnpacker(lambda item: isinstance(item, dict) and 'path' in item,
++            unpacker = RobustUnpacker(lambda item: isinstance(item, StableDict) and b'path' in item,
+                                       self.manifest.item_keys)
+             _state = 0
+ 
+-- 
+2.15.1
+

gnu/packages/patches/eigen-arm-neon-fixes.patch

@@ -0,0 +1,245 @@
+# HG changeset patch
+# User Gael Guennebaud <g.gael@free.fr>
+# Date 1497514590 -7200
+# Node ID d781c1de98342c5ca29c2fe719d8d3c96a35dcd4
+# Parent  48cd83b2b459aa9f3f5dca135d38760fe0b02a2f
+Bug 1436: fix compilation of Jacobi rotations with ARM NEON, some specializations of internal::conj_helper were missing.
+
+diff --git a/Eigen/Core b/Eigen/Core
+--- a/Eigen/Core
++++ b/Eigen/Core
+@@ -371,6 +371,7 @@
+ #include "src/Core/MathFunctions.h"
+ #include "src/Core/GenericPacketMath.h"
+ #include "src/Core/MathFunctionsImpl.h"
++#include "src/Core/arch/Default/ConjHelper.h"
+ 
+ #if defined EIGEN_VECTORIZE_AVX512
+   #include "src/Core/arch/SSE/PacketMath.h"
+diff --git a/Eigen/src/Core/arch/AVX/Complex.h b/Eigen/src/Core/arch/AVX/Complex.h
+--- a/Eigen/src/Core/arch/AVX/Complex.h
++++ b/Eigen/src/Core/arch/AVX/Complex.h
+@@ -204,23 +204,7 @@
+   }
+ };
+ 
+-template<> struct conj_helper<Packet8f, Packet4cf, false,false>
+-{
+-  EIGEN_STRONG_INLINE Packet4cf pmadd(const Packet8f& x, const Packet4cf& y, const Packet4cf& c) const
+-  { return padd(c, pmul(x,y)); }
+-
+-  EIGEN_STRONG_INLINE Packet4cf pmul(const Packet8f& x, const Packet4cf& y) const
+-  { return Packet4cf(Eigen::internal::pmul(x, y.v)); }
+-};
+-
+-template<> struct conj_helper<Packet4cf, Packet8f, false,false>
+-{
+-  EIGEN_STRONG_INLINE Packet4cf pmadd(const Packet4cf& x, const Packet8f& y, const Packet4cf& c) const
+-  { return padd(c, pmul(x,y)); }
+-
+-  EIGEN_STRONG_INLINE Packet4cf pmul(const Packet4cf& x, const Packet8f& y) const
+-  { return Packet4cf(Eigen::internal::pmul(x.v, y)); }
+-};
++EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet4cf,Packet8f)
+ 
+ template<> EIGEN_STRONG_INLINE Packet4cf pdiv<Packet4cf>(const Packet4cf& a, const Packet4cf& b)
+ {
+@@ -400,23 +384,7 @@
+   }
+ };
+ 
+-template<> struct conj_helper<Packet4d, Packet2cd, false,false>
+-{
+-  EIGEN_STRONG_INLINE Packet2cd pmadd(const Packet4d& x, const Packet2cd& y, const Packet2cd& c) const
+-  { return padd(c, pmul(x,y)); }
+-
+-  EIGEN_STRONG_INLINE Packet2cd pmul(const Packet4d& x, const Packet2cd& y) const
+-  { return Packet2cd(Eigen::internal::pmul(x, y.v)); }
+-};
+-
+-template<> struct conj_helper<Packet2cd, Packet4d, false,false>
+-{
+-  EIGEN_STRONG_INLINE Packet2cd pmadd(const Packet2cd& x, const Packet4d& y, const Packet2cd& c) const
+-  { return padd(c, pmul(x,y)); }
+-
+-  EIGEN_STRONG_INLINE Packet2cd pmul(const Packet2cd& x, const Packet4d& y) const
+-  { return Packet2cd(Eigen::internal::pmul(x.v, y)); }
+-};
++EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cd,Packet4d)
+ 
+ template<> EIGEN_STRONG_INLINE Packet2cd pdiv<Packet2cd>(const Packet2cd& a, const Packet2cd& b)
+ {
+diff --git a/Eigen/src/Core/arch/AltiVec/Complex.h b/Eigen/src/Core/arch/AltiVec/Complex.h
+--- a/Eigen/src/Core/arch/AltiVec/Complex.h
++++ b/Eigen/src/Core/arch/AltiVec/Complex.h
+@@ -224,23 +224,7 @@
+   }
+ };
+ 
+-template<> struct conj_helper<Packet4f, Packet2cf, false,false>
+-{
+-  EIGEN_STRONG_INLINE Packet2cf pmadd(const Packet4f& x, const Packet2cf& y, const Packet2cf& c) const
+-  { return padd(c, pmul(x,y)); }
+-
+-  EIGEN_STRONG_INLINE Packet2cf pmul(const Packet4f& x, const Packet2cf& y) const
+-  { return Packet2cf(internal::pmul<Packet4f>(x, y.v)); }
+-};
+-
+-template<> struct conj_helper<Packet2cf, Packet4f, false,false>
+-{
+-  EIGEN_STRONG_INLINE Packet2cf pmadd(const Packet2cf& x, const Packet4f& y, const Packet2cf& c) const
+-  { return padd(c, pmul(x,y)); }
+-
+-  EIGEN_STRONG_INLINE Packet2cf pmul(const Packet2cf& x, const Packet4f& y) const
+-  { return Packet2cf(internal::pmul<Packet4f>(x.v, y)); }
+-};
++EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
+ 
+ template<> EIGEN_STRONG_INLINE Packet2cf pdiv<Packet2cf>(const Packet2cf& a, const Packet2cf& b)
+ {
+@@ -416,23 +400,8 @@
+     return pconj(internal::pmul(a, b));
+   }
+ };
+-template<> struct conj_helper<Packet2d, Packet1cd, false,false>
+-{
+-  EIGEN_STRONG_INLINE Packet1cd pmadd(const Packet2d& x, const Packet1cd& y, const Packet1cd& c) const
+-  { return padd(c, pmul(x,y)); }
+ 
+-  EIGEN_STRONG_INLINE Packet1cd pmul(const Packet2d& x, const Packet1cd& y) const
+-  { return Packet1cd(internal::pmul<Packet2d>(x, y.v)); }
+-};
+-
+-template<> struct conj_helper<Packet1cd, Packet2d, false,false>
+-{
+-  EIGEN_STRONG_INLINE Packet1cd pmadd(const Packet1cd& x, const Packet2d& y, const Packet1cd& c) const
+-  { return padd(c, pmul(x,y)); }
+-
+-  EIGEN_STRONG_INLINE Packet1cd pmul(const Packet1cd& x, const Packet2d& y) const
+-  { return Packet1cd(internal::pmul<Packet2d>(x.v, y)); }
+-};
++EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
+ 
+ template<> EIGEN_STRONG_INLINE Packet1cd pdiv<Packet1cd>(const Packet1cd& a, const Packet1cd& b)
+ {
+diff --git a/Eigen/src/Core/arch/Default/ConjHelper.h b/Eigen/src/Core/arch/Default/ConjHelper.h
+new file mode 100644
+--- /dev/null
++++ b/Eigen/src/Core/arch/Default/ConjHelper.h
+@@ -0,0 +1,29 @@
++
++// This file is part of Eigen, a lightweight C++ template library
++// for linear algebra.
++//
++// Copyright (C) 2017 Gael Guennebaud <gael.guennebaud@inria.fr>
++//
++// This Source Code Form is subject to the terms of the Mozilla
++// Public License v. 2.0. If a copy of the MPL was not distributed
++// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
++
++#ifndef EIGEN_ARCH_CONJ_HELPER_H
++#define EIGEN_ARCH_CONJ_HELPER_H
++
++#define EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(PACKET_CPLX, PACKET_REAL)                                                          \
++  template<> struct conj_helper<PACKET_REAL, PACKET_CPLX, false,false> {                                          \
++    EIGEN_STRONG_INLINE PACKET_CPLX pmadd(const PACKET_REAL& x, const PACKET_CPLX& y, const PACKET_CPLX& c) const \
++    { return padd(c, pmul(x,y)); }                                                                                \
++    EIGEN_STRONG_INLINE PACKET_CPLX pmul(const PACKET_REAL& x, const PACKET_CPLX& y) const                        \
++    { return PACKET_CPLX(Eigen::internal::pmul<PACKET_REAL>(x, y.v)); }                                           \
++  };                                                                                                              \
++                                                                                                                  \
++  template<> struct conj_helper<PACKET_CPLX, PACKET_REAL, false,false> {                                          \
++    EIGEN_STRONG_INLINE PACKET_CPLX pmadd(const PACKET_CPLX& x, const PACKET_REAL& y, const PACKET_CPLX& c) const \
++    { return padd(c, pmul(x,y)); }                                                                                \
++    EIGEN_STRONG_INLINE PACKET_CPLX pmul(const PACKET_CPLX& x, const PACKET_REAL& y) const                        \
++    { return PACKET_CPLX(Eigen::internal::pmul<PACKET_REAL>(x.v, y)); }                                           \
++  };
++
++#endif // EIGEN_ARCH_CONJ_HELPER_H
+diff --git a/Eigen/src/Core/arch/NEON/Complex.h b/Eigen/src/Core/arch/NEON/Complex.h
+--- a/Eigen/src/Core/arch/NEON/Complex.h
++++ b/Eigen/src/Core/arch/NEON/Complex.h
+@@ -265,6 +265,8 @@
+   }
+ };
+ 
++EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
++
+ template<> EIGEN_STRONG_INLINE Packet2cf pdiv<Packet2cf>(const Packet2cf& a, const Packet2cf& b)
+ {
+   // TODO optimize it for NEON
+@@ -456,6 +458,8 @@
+   }
+ };
+ 
++EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
++
+ template<> EIGEN_STRONG_INLINE Packet1cd pdiv<Packet1cd>(const Packet1cd& a, const Packet1cd& b)
+ {
+   // TODO optimize it for NEON
+diff --git a/Eigen/src/Core/arch/SSE/Complex.h b/Eigen/src/Core/arch/SSE/Complex.h
+--- a/Eigen/src/Core/arch/SSE/Complex.h
++++ b/Eigen/src/Core/arch/SSE/Complex.h
+@@ -229,23 +229,7 @@
+   }
+ };
+ 
+-template<> struct conj_helper<Packet4f, Packet2cf, false,false>
+-{
+-  EIGEN_STRONG_INLINE Packet2cf pmadd(const Packet4f& x, const Packet2cf& y, const Packet2cf& c) const
+-  { return padd(c, pmul(x,y)); }
+-
+-  EIGEN_STRONG_INLINE Packet2cf pmul(const Packet4f& x, const Packet2cf& y) const
+-  { return Packet2cf(Eigen::internal::pmul<Packet4f>(x, y.v)); }
+-};
+-
+-template<> struct conj_helper<Packet2cf, Packet4f, false,false>
+-{
+-  EIGEN_STRONG_INLINE Packet2cf pmadd(const Packet2cf& x, const Packet4f& y, const Packet2cf& c) const
+-  { return padd(c, pmul(x,y)); }
+-
+-  EIGEN_STRONG_INLINE Packet2cf pmul(const Packet2cf& x, const Packet4f& y) const
+-  { return Packet2cf(Eigen::internal::pmul<Packet4f>(x.v, y)); }
+-};
++EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
+ 
+ template<> EIGEN_STRONG_INLINE Packet2cf pdiv<Packet2cf>(const Packet2cf& a, const Packet2cf& b)
+ {
+@@ -430,23 +414,7 @@
+   }
+ };
+ 
+-template<> struct conj_helper<Packet2d, Packet1cd, false,false>
+-{
+-  EIGEN_STRONG_INLINE Packet1cd pmadd(const Packet2d& x, const Packet1cd& y, const Packet1cd& c) const
+-  { return padd(c, pmul(x,y)); }
+-
+-  EIGEN_STRONG_INLINE Packet1cd pmul(const Packet2d& x, const Packet1cd& y) const
+-  { return Packet1cd(Eigen::internal::pmul<Packet2d>(x, y.v)); }
+-};
+-
+-template<> struct conj_helper<Packet1cd, Packet2d, false,false>
+-{
+-  EIGEN_STRONG_INLINE Packet1cd pmadd(const Packet1cd& x, const Packet2d& y, const Packet1cd& c) const
+-  { return padd(c, pmul(x,y)); }
+-
+-  EIGEN_STRONG_INLINE Packet1cd pmul(const Packet1cd& x, const Packet2d& y) const
+-  { return Packet1cd(Eigen::internal::pmul<Packet2d>(x.v, y)); }
+-};
++EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
+ 
+ template<> EIGEN_STRONG_INLINE Packet1cd pdiv<Packet1cd>(const Packet1cd& a, const Packet1cd& b)
+ {
+diff --git a/Eigen/src/Core/arch/ZVector/Complex.h b/Eigen/src/Core/arch/ZVector/Complex.h
+--- a/Eigen/src/Core/arch/ZVector/Complex.h
++++ b/Eigen/src/Core/arch/ZVector/Complex.h
+@@ -336,6 +336,9 @@
+   }
+ };
+ 
++EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
++EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
++
+ template<> EIGEN_STRONG_INLINE Packet1cd pdiv<Packet1cd>(const Packet1cd& a, const Packet1cd& b)
+ {
+   // TODO optimize it for AltiVec

gnu/packages/patches/graphicsmagick-CVE-2017-11403+CVE-2017-14103.patch

@@ -1,137 +0,0 @@
-http://www.openwall.com/lists/oss-security/2017/09/01/6
-
-CVE-2017-11403:
-http://hg.code.sf.net/p/graphicsmagick/code/rev/d0a76868ca37
-
-CVE-2017-14103:
-http://hg.code.sf.net/p/graphicsmagick/code/rev/98721124e51f
-
-some changes were made to make the patch apply
-
-# HG changeset patch
-# User Glenn Randers-Pehrson <glennrp+bmo@gmail.com>
-# Date 1503875721 14400
-# Node ID 98721124e51fd5ec0c6fba64bce2e218869632d2
-# Parent  f0f2ea85a2930f3b6dcd72352719adb9660f2aad
-Attempt to fix Issue 440.
-
-diff -ru a/coders/png.c b/coders/png.c
---- a/coders/png.c	1969-12-31 19:00:00.000000000 -0500
-+++ b/coders/png.c	2017-09-10 11:31:56.543194173 -0400
-@@ -3106,7 +3106,9 @@
-       if (length > PNG_MAX_UINT || count == 0)
-         {
-           DestroyJNGInfo(color_image_info,alpha_image_info);
--          ThrowReaderException(CorruptImageError,CorruptImage,image);
-+          (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+              "chunk length (%lu) > PNG_MAX_UINT",length);
-+          return ((Image*)NULL);
-         }
-
-       chunk=(unsigned char *) NULL;
-@@ -3117,13 +3119,16 @@
-           if (chunk == (unsigned char *) NULL)
-             {
-               DestroyJNGInfo(color_image_info,alpha_image_info);
--              ThrowReaderException(ResourceLimitError,MemoryAllocationFailed,
--                                   image);
-+              (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                  "    Could not allocate chunk memory");
-+              return ((Image*)NULL);
-             }
-           if (ReadBlob(image,length,chunk) < length)
-             {
-               DestroyJNGInfo(color_image_info,alpha_image_info);
--              ThrowReaderException(CorruptImageError,CorruptImage,image);
-+              (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                  "    chunk reading was incomplete");
-+              return ((Image*)NULL);
-             }
-           p=chunk;
-         }
-@@ -3198,7 +3203,7 @@
-                   jng_width, jng_height);
-               MagickFreeMemory(chunk);
-               DestroyJNGInfo(color_image_info,alpha_image_info);
--              ThrowReaderException(CorruptImageError,ImproperImageHeader,image);
-+              return ((Image *)NULL);
-             }
-
-           /* Temporarily set width and height resources to match JHDR */
-@@ -3233,8 +3238,9 @@
-           if (color_image == (Image *) NULL)
-             {
-               DestroyJNGInfo(color_image_info,alpha_image_info);
--              ThrowReaderException(ResourceLimitError,MemoryAllocationFailed,
--                                   image);
-+              (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                  "    could not open color_image blob");
-+              return ((Image *)NULL);
-             }
-           if (logging)
-             (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-@@ -3245,7 +3251,9 @@
-           if (status == MagickFalse)
-             {
-               DestroyJNGInfo(color_image_info,alpha_image_info);
--              ThrowReaderException(CoderError,UnableToOpenBlob,color_image);
-+              (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                  "    could not open color_image blob");
-+              return ((Image *)NULL);
-             }
-
-           if (!image_info->ping && jng_color_type >= 12)
-@@ -3255,17 +3263,18 @@
-               if (alpha_image_info == (ImageInfo *) NULL)
-                 {
-                   DestroyJNGInfo(color_image_info,alpha_image_info);
--                  ThrowReaderException(ResourceLimitError,
--                                       MemoryAllocationFailed, image);
-+                  (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                      "    could not allocate alpha_image_info",length);
-+                  return ((Image *)NULL);
-                 }
-               GetImageInfo(alpha_image_info);
-               alpha_image=AllocateImage(alpha_image_info);
-               if (alpha_image == (Image *) NULL)
-                 {
-                   DestroyJNGInfo(color_image_info,alpha_image_info);
--                  ThrowReaderException(ResourceLimitError,
--                                       MemoryAllocationFailed,
--                                       alpha_image);
-+                  (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                      "    could not allocate alpha_image");
-+                  return ((Image *)NULL);
-                 }
-               if (logging)
-                 (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-@@ -3277,7 +3286,9 @@
-                 {
-                   DestroyJNGInfo(color_image_info,alpha_image_info);
-                   DestroyImage(alpha_image);
--                  ThrowReaderException(CoderError,UnableToOpenBlob,image);
-+                  (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                      "    could not allocate alpha_image blob");
-+                  return ((Image *)NULL);
-                 }
-               if (jng_alpha_compression_method == 0)
-                 {
-@@ -3613,6 +3624,8 @@
-               alpha_image = (Image *)NULL;
-               DestroyImageInfo(alpha_image_info);
-               alpha_image_info = (ImageInfo *)NULL;
-+              (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                  " Destroy the JNG image");
-               DestroyImage(jng_image);
-               jng_image = (Image *)NULL;
-             }
-@@ -5146,8 +5159,8 @@
-
-       if (image == (Image *) NULL)
-         {
--          DestroyImageList(previous);
-           CloseBlob(previous);
-+          DestroyImageList(previous);
-           MngInfoFreeStruct(mng_info,&have_mng_structure);
-           return((Image *) NULL);
-         }

gnu/packages/patches/graphicsmagick-CVE-2017-12935.patch

@@ -1,28 +0,0 @@
-This patch comes from http://hg.code.sf.net/p/graphicsmagick/code/rev/cd699a44f188.
-
-diff -ur a/coders/png.c b/coders/png.c
---- a/coders/png.c	2017-07-04 17:32:08.000000000 -0400
-+++ b/coders/png.c	2017-08-19 11:16:20.933969362 -0400
-@@ -4101,11 +4101,17 @@
-                   mng_info->image=image;
-                 }
- 
--              if ((mng_info->mng_width > 65535L) || (mng_info->mng_height
--                                                     > 65535L))
--                (void) ThrowException(&image->exception,ImageError,
--                                      WidthOrHeightExceedsLimit,
--                                      image->filename);
-+              if ((mng_info->mng_width > 65535L) ||
-+                  (mng_info->mng_height > 65535L))
-+                {
-+                  (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                      "  MNG width or height is too large: %lu, %lu",
-+                      mng_info->mng_width,mng_info->mng_height);
-+                  MagickFreeMemory(chunk);
-+                  ThrowReaderException(CorruptImageError,
-+                     ImproperImageHeader,image);
-+                }
-+
-               FormatString(page_geometry,"%lux%lu+0+0",mng_info->mng_width,
-                            mng_info->mng_height);
-               mng_info->frame.left=0;

gnu/packages/patches/graphicsmagick-CVE-2017-12936.patch

@@ -1,16 +0,0 @@
-This patch comes from http://hg.code.sf.net/p/graphicsmagick/code/rev/be898b7c97bd.
-
-diff -ur a/coders/wmf.c b/coders/wmf.c
---- a/coders/wmf.c	2016-09-05 15:20:23.000000000 -0400
-+++ b/coders/wmf.c	2017-08-19 10:38:08.984187264 -0400
-@@ -2719,8 +2719,8 @@
-   if(image->exception.severity != UndefinedException)
-     ThrowException2(exception,
-                    CoderWarning,
--                   ddata->image->exception.reason,
--                   ddata->image->exception.description);
-+                   image->exception.reason,
-+                   image->exception.description);
- 
-   if(logging)
-     (void) LogMagickEvent(CoderEvent,GetMagickModule(),"leave ReadWMFImage()");

gnu/packages/patches/graphicsmagick-CVE-2017-12937.patch

@@ -1,28 +0,0 @@
-This patch comes from http://hg.code.sf.net/p/graphicsmagick/code/rev/95d00d55e978.
-
-diff -ur a/coders/sun.c b/coders/sun.c
---- a/coders/sun.c	2016-05-30 13:19:54.000000000 -0400
-+++ b/coders/sun.c	2017-08-18 18:00:00.191023610 -0400
-@@ -1,5 +1,5 @@
- /*
--% Copyright (C) 2003-2015 GraphicsMagick Group
-+% Copyright (C) 2003-2017 GraphicsMagick Group
- % Copyright (C) 2002 ImageMagick Studio
- % Copyright 1991-1999 E. I. du Pont de Nemours and Company
- %
-@@ -577,6 +577,7 @@
-           for (bit=7; bit >= 0; bit--)
-             {
-               index=((*p) & (0x01 << bit) ? 0x01 : 0x00);
-+              VerifyColormapIndex(image,index);
-               indexes[x+7-bit]=index;
-               q[x+7-bit]=image->colormap[index];
-             }
-@@ -587,6 +588,7 @@
-             for (bit=7; bit >= (long) (8-(image->columns % 8)); bit--)
-               {
-                 index=((*p) & (0x01 << bit) ? 0x01 : 0x00);
-+                VerifyColormapIndex(image,index);
-                 indexes[x+7-bit]=index;
-                 q[x+7-bit]=image->colormap[index];
-               }

gnu/packages/patches/graphicsmagick-CVE-2017-13775.patch

@@ -1,195 +0,0 @@
-http://openwall.com/lists/oss-security/2017/08/31/3
-http://hg.code.sf.net/p/graphicsmagick/code/raw-rev/b037d79b6ccd
-
-some changes were made to make the patch apply
-
-# HG changeset patch
-# User Bob Friesenhahn <bfriesen@GraphicsMagick.org>
-# Date 1503774853 18000
-# Node ID b037d79b6ccd0cfba7ba9ce09b454ed46d688036
-# Parent  198ea602ea7cc767dc3022bbcf887bcd4534158d
-JNX: Fix DOS issues
-
-diff -r 198ea602ea7c -r b037d79b6ccd coders/jnx.c
---- a/coders/jnx.c	Tue Aug 22 08:08:30 2017 -0500
-+++ b/coders/jnx.c	Sat Aug 26 14:14:13 2017 -0500
-@@ -1,5 +1,5 @@
- /*
--% Copyright (C) 2012-2015 GraphicsMagick Group
-+% Copyright (C) 2012-2017 GraphicsMagick Group
- %
- % This program is covered by multiple licenses, which are described in
- % Copyright.txt. You should have received a copy of Copyright.txt with this
-@@ -100,6 +100,7 @@
- 
-   char img_label_str[MaxTextExtent];
- 
-+
-   alloc_size = TileInfo->PicSize + 2;
- 
-   if (image->logging)
-@@ -242,6 +243,9 @@
-     total_tiles,
-     current_tile;
- 
-+  magick_off_t
-+    file_size;
-+
-   /* Open image file. */
-   assert(image_info != (const ImageInfo *) NULL);
-   assert(image_info->signature == MagickSignature);
-@@ -254,9 +258,8 @@
-   if (status == False)
-     ThrowReaderException(FileOpenError, UnableToOpenFile, image);
- 
--  memset(JNXLevelInfo, 0, sizeof(JNXLevelInfo));
--
-   /* Read JNX image header. */
-+  (void) memset(&JNXHeader, 0, sizeof(JNXHeader));
-   JNXHeader.Version = ReadBlobLSBLong(image);
-   if (JNXHeader.Version > 4)
-     ThrowReaderException(CorruptImageError, ImproperImageHeader, image);
-@@ -266,8 +269,6 @@
-   JNXHeader.MapBounds.SouthWest.lat = ReadBlobLSBLong(image);
-   JNXHeader.MapBounds.SouthWest.lon = ReadBlobLSBLong(image);
-   JNXHeader.Levels = ReadBlobLSBLong(image);
--  if (JNXHeader.Levels > 20)
--    ThrowReaderException(CorruptImageError, ImproperImageHeader, image);
-   JNXHeader.Expiration = ReadBlobLSBLong(image);
-   JNXHeader.ProductID = ReadBlobLSBLong(image);
-   JNXHeader.CRC = ReadBlobLSBLong(image);
-@@ -279,7 +280,41 @@
-   if (EOFBlob(image))
-     ThrowReaderException(CorruptImageError,UnexpectedEndOfFile,image);
- 
-+  file_size = GetBlobSize(image);
-+
-+  (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                        "JNX Header:\n"
-+                        "    Version:    %u\n"
-+                        "    DeviceSN:   %u\n"
-+                        "    MapBounds:\n"
-+                        "      NorthEast: lat = %u, lon = %u\n"
-+                        "      SouthWest: lat = %u, lon = %u\n"
-+                        "    Levels:     %u\n"
-+                        "    Expiration: %u\n"
-+                        "    ProductID:  %u\n"
-+                        "    CRC:        %u\n"
-+                        "    SigVersion: %u\n"
-+                        "    SigOffset:  %u\n"
-+                        "    ZOrder:     %u",
-+                        JNXHeader.Version,
-+                        JNXHeader.DeviceSN,
-+                        JNXHeader.MapBounds.NorthEast.lat,
-+                        JNXHeader.MapBounds.NorthEast.lon,
-+                        JNXHeader.MapBounds.SouthWest.lat,
-+                        JNXHeader.MapBounds.SouthWest.lon,
-+                        JNXHeader.Levels,
-+                        JNXHeader.Expiration,
-+                        JNXHeader.ProductID,
-+                        JNXHeader.CRC,
-+                        JNXHeader.SigVersion,
-+                        JNXHeader.SigOffset,
-+                        JNXHeader.ZOrder);
-+
-+  if (JNXHeader.Levels > 20)
-+    ThrowReaderException(CorruptImageError, ImproperImageHeader, image);
-+
-   /* Read JNX image level info. */
-+  memset(JNXLevelInfo, 0, sizeof(JNXLevelInfo));
-   total_tiles = 0;
-   current_tile = 0;
-   for (i = 0; i < JNXHeader.Levels; i++)
-@@ -302,11 +337,23 @@
-         {
-           JNXLevelInfo[i].Copyright = NULL;
-         }
-+
-+      if (EOFBlob(image))
-+        ThrowReaderException(CorruptImageError,UnexpectedEndOfFile,image);
-+
-+      if (image->logging)
-+        (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                              "Level[%u] Info:"
-+                              "  TileCount: %4u"
-+                              "  TilesOffset: %6u"
-+                              "  Scale: %04u",
-+                              i,
-+                              JNXLevelInfo[i].TileCount,
-+                              JNXLevelInfo[i].TilesOffset,
-+                              JNXLevelInfo[i].Scale
-+                              );
-     }
- 
--  if (EOFBlob(image))
--    ThrowReaderException(CorruptImageError,UnexpectedEndOfFile,image);
--
-   /* Get the current limit */
-   SaveLimit = GetMagickResourceLimit(MapResource);
- 
-@@ -316,11 +363,32 @@
-   /* Read JNX image data. */
-   for (i = 0; i < JNXHeader.Levels; i++)
-     {
-+      /*
-+        Validate TileCount against remaining file data
-+      */
-+      const magick_off_t current_offset = TellBlob(image);
-+      const size_t pos_list_entry_size =
-+        sizeof(magick_uint32_t) + sizeof(magick_uint32_t) + sizeof(magick_uint32_t) +
-+        sizeof(magick_uint32_t) + sizeof(magick_uint16_t) + sizeof(magick_uint16_t) +
-+        sizeof(magick_uint32_t) + sizeof(magick_uint32_t);
-+      const magick_off_t remaining = file_size-current_offset;
-+      const size_t needed = MagickArraySize(pos_list_entry_size,JNXLevelInfo[i].TileCount);
-+
-+      if ((needed == 0U) || (remaining <= 0) || (remaining < (magick_off_t) needed))
-+        {
-+          (void) SetMagickResourceLimit(MapResource, SaveLimit);
-+          ThrowReaderException(CorruptImageError,UnexpectedEndOfFile,image);
-+        }
-+
-       PositionList = MagickAllocateArray(TJNXTileInfo *,
-                                          JNXLevelInfo[i].TileCount,
-                                          sizeof(TJNXTileInfo));
-       if (PositionList == NULL)
--        continue;
-+        {
-+          (void) SetMagickResourceLimit(MapResource, SaveLimit);
-+          ThrowReaderException(ResourceLimitError,MemoryAllocationFailed,
-+                               image);
-+        }
- 
-       (void) SeekBlob(image, JNXLevelInfo[i].TilesOffset, SEEK_SET);
-       for (j = 0; j < JNXLevelInfo[i].TileCount; j++)
-@@ -333,12 +401,15 @@
-           PositionList[j].PicHeight = ReadBlobLSBShort(image);
-           PositionList[j].PicSize = ReadBlobLSBLong(image);
-           PositionList[j].PicOffset = ReadBlobLSBLong(image);
--        }
- 
--      if (EOFBlob(image))
--        {
--          MagickFreeMemory(PositionList);
--          ThrowReaderException(CorruptImageError,UnexpectedEndOfFile,image);
-+          if (EOFBlob(image) ||
-+              ((magick_off_t) PositionList[j].PicOffset +
-+               PositionList[j].PicSize > file_size))
-+            {
-+              (void) SetMagickResourceLimit(MapResource, SaveLimit);
-+              MagickFreeMemory(PositionList);
-+              ThrowReaderException(CorruptImageError,UnexpectedEndOfFile,image);
-+            }
-         }
- 
-       for (j = 0; j < JNXLevelInfo[i].TileCount; j++)
-@@ -351,6 +422,9 @@
-           image = ExtractTileJPG(image, image_info, PositionList+j, exception);
-           (void) SetMonitorHandler(previous_handler);
- 
-+          if (exception->severity >= ErrorException)
-+            break;
-+
-           current_tile++;
-           if (QuantumTick(current_tile,total_tiles))
-             if (!MagickMonitorFormatted(current_tile,total_tiles,exception,
-

gnu/packages/patches/graphicsmagick-CVE-2017-13776+CVE-2017-13777.patch

@@ -1,179 +0,0 @@
-http://openwall.com/lists/oss-security/2017/08/31/1
-http://openwall.com/lists/oss-security/2017/08/31/2
-http://hg.code.sf.net/p/graphicsmagick/code/raw-rev/233a720bfd5e
-
-some changes were made to make the patch apply
-
-# HG changeset patch
-# User Bob Friesenhahn <bfriesen@GraphicsMagick.org>
-# Date 1503779175 18000
-# Node ID 233a720bfd5efd378f133a776507ed41230da617
-# Parent  b037d79b6ccd0cfba7ba9ce09b454ed46d688036
-XBM: Fix DOS issues.
-
-diff -r b037d79b6ccd -r 233a720bfd5e coders/xbm.c
---- a/coders/xbm.c	Sat Aug 26 14:14:13 2017 -0500
-+++ b/coders/xbm.c	Sat Aug 26 15:26:15 2017 -0500
-@@ -1,5 +1,5 @@
- /*
--% Copyright (C) 2003 -2012 GraphicsMagick Group
-+% Copyright (C) 2003-2017 GraphicsMagick Group
- % Copyright (C) 2002 ImageMagick Studio
- % Copyright 1991-1999 E. I. du Pont de Nemours and Company
- %
-@@ -121,13 +121,15 @@
- 
- static int XBMInteger(Image *image,short int *hex_digits)
- {
-+  unsigned int
-+    flag;
-+
-   int
-     c,
--    flag,
-     value;
- 
-   value=0;
--  flag=0;
-+  flag=0U;
-   for ( ; ; )
-   {
-     c=ReadBlobByte(image);
-@@ -158,18 +160,14 @@
-   Image
-     *image;
- 
--  int
--    bit;
--
--  long
--    y;
--
-   register IndexPacket
-     *indexes;
- 
--  register long
-+  register size_t
-+    bytes_per_line,
-     i,
--    x;
-+    x,
-+    y;
- 
-   register PixelPacket
-     *q;
-@@ -177,22 +175,24 @@
-   register unsigned char
-     *p;
- 
--  short int
--    hex_digits[256];
--
-   unsigned char
-     *data;
- 
-   unsigned int
-+    bit,
-+    byte,
-+    padding,
-+    version;
-+
-+  int
-+    value;
-+
-+  short int
-+    hex_digits[256];
-+
-+  MagickPassFail
-     status;
- 
--  unsigned long
--    byte,
--    bytes_per_line,
--    padding,
--    value,
--    version;
--
-   /*
-     Open image file.
-   */
-@@ -207,6 +207,8 @@
-   /*
-     Read X bitmap header.
-   */
-+  (void) memset(buffer,0,sizeof(buffer));
-+  name[0]='\0';
-   while (ReadBlobString(image,buffer) != (char *) NULL)
-     if (sscanf(buffer,"#define %s %lu",name,&image->columns) == 2)
-       if ((strlen(name) >= 6) &&
-@@ -278,6 +280,8 @@
-   /*
-     Initialize hex values.
-   */
-+  for (i = 0; i < sizeof(hex_digits)/sizeof(hex_digits[0]); i++)
-+    hex_digits[i]=(-1);
-   hex_digits['0']=0;
-   hex_digits['1']=1;
-   hex_digits['2']=2;
-@@ -311,40 +315,50 @@
-   */
-   p=data;
-   if (version == 10)
--    for (i=0; i < (long) (bytes_per_line*image->rows); (i+=2))
-+    for (i=0; i < (bytes_per_line*image->rows); (i+=2))
-     {
-       value=XBMInteger(image,hex_digits);
-+      if (value < 0)
-+        {
-+          MagickFreeMemory(data);
-+          ThrowReaderException(CorruptImageError,ImproperImageHeader,image);
-+        }
-       *p++=(unsigned char) value;
-       if (!padding || ((i+2) % bytes_per_line))
-         *p++=(unsigned char) (value >> 8);
-     }
-   else
--    for (i=0; i < (long) (bytes_per_line*image->rows); i++)
-+    for (i=0; i < (bytes_per_line*image->rows); i++)
-     {
-       value=XBMInteger(image,hex_digits);
-+      if (value < 0)
-+        {
-+          MagickFreeMemory(data);
-+          ThrowReaderException(CorruptImageError,ImproperImageHeader,image);
-+        }
-       *p++=(unsigned char) value;
-     }
-   /*
-     Convert X bitmap image to pixel packets.
-   */
-   p=data;
--  for (y=0; y < (long) image->rows; y++)
-+  for (y=0; y < image->rows; y++)
-   {
-     q=SetImagePixels(image,0,y,image->columns,1);
-     if (q == (PixelPacket *) NULL)
-       break;
-     indexes=AccessMutableIndexes(image);
--    bit=0;
--    byte=0;
--    for (x=0; x < (long) image->columns; x++)
-+    bit=0U;
-+    byte=0U;
-+    for (x=0; x < image->columns; x++)
-     {
--      if (bit == 0)
-+      if (bit == 0U)
-         byte=(*p++);
-       indexes[x]=byte & 0x01 ? 0x01 : 0x00;
-       bit++;
--      byte>>=1;
--      if (bit == 8)
--        bit=0;
-+      byte>>=1U;
-+      if (bit == 8U)
-+        bit=0U;
-     }
-     if (!SyncImagePixels(image))
-       break;
-

gnu/packages/patches/graphicsmagick-CVE-2017-14042.patch

@@ -1,80 +0,0 @@
-http://openwall.com/lists/oss-security/2017/08/28/5
-http://hg.code.sf.net/p/graphicsmagick/code/rev/3bbf7a13643d
-
-some changes were made to make the patch apply
-
-# HG changeset patch
-# User Bob Friesenhahn <bfriesen@GraphicsMagick.org>
-# Date 1503268616 18000
-# Node ID 3bbf7a13643df3be76b0e19088a6cc632eea2072
-# Parent  83a5b946180835f260bcb91e3d06327a8e2577e3
-PNM: For binary formats, verify sufficient backing file data before memory request.
-
-diff -r 83a5b9461808 -r 3bbf7a13643d coders/pnm.c
---- a/coders/pnm.c	Sun Aug 20 17:31:35 2017 -0500
-+++ b/coders/pnm.c	Sun Aug 20 17:36:56 2017 -0500
-@@ -569,7 +569,7 @@
-           (void) LogMagickEvent(CoderEvent,GetMagickModule(),"Colors: %u",
-                                 image->colors);
-         }
--      number_pixels=image->columns*image->rows;
-+      number_pixels=MagickArraySize(image->columns,image->rows);
-       if (number_pixels == 0)
-         ThrowReaderException(CorruptImageError,NegativeOrZeroImageSize,image);
-       if (image->storage_class == PseudoClass)
-@@ -858,14 +858,14 @@
-		if (1 == bits_per_sample)
-		  {
-		    /* PBM */
--		    bytes_per_row=((image->columns+7) >> 3);
-+		    bytes_per_row=((image->columns+7U) >> 3);
-		    import_options.grayscale_miniswhite=MagickTrue;
-		    quantum_type=GrayQuantum;
-		  }
-		else
-		  {
-		    /* PGM & XV_332 */
--		    bytes_per_row=((bits_per_sample+7)/8)*image->columns;
-+		    bytes_per_row=MagickArraySize(((bits_per_sample+7U)/8U),image->columns);
-		    if (XV_332_Format == format)
-		      {
-			quantum_type=IndexQuantum;
-@@ -878,7 +878,8 @@
-	      }
-	    else
-	      {
--		bytes_per_row=(((bits_per_sample+7)/8)*samples_per_pixel)*image->columns;
-+		bytes_per_row=MagickArraySize((((bits_per_sample+7)/8)*samples_per_pixel),
-+                                              image->columns);
-		if (3 == samples_per_pixel)
-		  {
-		    /* PPM */
-@@ -915,6 +916,28 @@
-		    is_monochrome=MagickFalse;
-		  }
-	      }
-+
-+            /* Validate file size before allocating memory */
-+            if (BlobIsSeekable(image))
-+              {
-+                const magick_off_t file_size = GetBlobSize(image);
-+                const magick_off_t current_offset = TellBlob(image);
-+                if ((file_size > 0) &&
-+                    (current_offset > 0) &&
-+                    (file_size > current_offset))
-+                  {
-+                    const magick_off_t remaining = file_size-current_offset;
-+                    const magick_off_t needed = (magick_off_t) image->rows *
-+                      (magick_off_t) bytes_per_row;
-+                    if ((remaining < (magick_off_t) bytes_per_row) ||
-+                        (remaining < needed))
-+                      {
-+                        ThrowException(exception,CorruptImageError,UnexpectedEndOfFile,
-+                                       image->filename);
-+                        break;
-+                      }
-+                  }
-+              }
-
-             scanline_set=AllocateThreadViewDataArray(image,exception,bytes_per_row,1);
-             if (scanline_set == (ThreadViewDataSet *) NULL)

gnu/packages/patches/graphicsmagick-CVE-2017-14165.patch

@@ -1,72 +0,0 @@
-http://hg.code.sf.net/p/graphicsmagick/code/raw-rev/493da54370aa
-http://openwall.com/lists/oss-security/2017/09/06/4
-
-some changes were made to make the patch apply
-
-# HG changeset patch
-# User Bob Friesenhahn <bfriesen@GraphicsMagick.org>
-# Date 1503257388 18000
-# Node ID 493da54370aa42cb430c52a69eb75db0001a5589
-# Parent  f8724674907902b7bc37c04f252fe30fbdd88e6f
-SUN: Verify that file header data length, and file length are sufficient for claimed image dimensions.
-
-diff -r f87246749079 -r 493da54370aa coders/sun.c
---- a/coders/sun.c	Sun Aug 20 12:21:03 2017 +0200
-+++ b/coders/sun.c	Sun Aug 20 14:29:48 2017 -0500
-@@ -498,6 +498,12 @@
-     if (sun_info.depth < 8)
-       image->depth=sun_info.depth;
- 
-+    if (image_info->ping)
-+      {
-+        CloseBlob(image);
-+        return(image);
-+      }
-+
-     /*
-       Compute bytes per line and bytes per image for an unencoded
-       image.
-@@ -522,15 +528,37 @@
-       if (bytes_per_image > sun_info.length)
-         ThrowReaderException(CorruptImageError,ImproperImageHeader,image);
- 
--    if (image_info->ping)
--      {
--        CloseBlob(image);
--        return(image);
--      }
-     if (sun_info.type == RT_ENCODED)
-       sun_data_length=(size_t) sun_info.length;
-     else
-       sun_data_length=bytes_per_image;
-+
-+    /*
-+      Verify that data length claimed by header is supported by file size
-+    */
-+    if (sun_info.type == RT_ENCODED)
-+      {
-+        if (sun_data_length < bytes_per_image/255U)
-+          {
-+            ThrowReaderException(CorruptImageError,ImproperImageHeader,image);
-+          }
-+      }
-+    if (BlobIsSeekable(image))
-+      {
-+        const magick_off_t file_size = GetBlobSize(image);
-+        const magick_off_t current_offset = TellBlob(image);
-+        if ((file_size > 0) &&
-+            (current_offset > 0) &&
-+            (file_size > current_offset))
-+        {
-+          const magick_off_t remaining = file_size-current_offset;
-+          if (remaining < (magick_off_t) sun_data_length)
-+            {
-+              ThrowReaderException(CorruptImageError,UnexpectedEndOfFile,image);
-+            }
-+        }
-+      }
-+
-     sun_data=MagickAllocateMemory(unsigned char *,sun_data_length);
-     if (sun_data == (unsigned char *) NULL)
-       ThrowReaderException(ResourceLimitError,MemoryAllocationFailed,image);
-

gnu/packages/patches/graphicsmagick-CVE-2017-14649.patch

@@ -1,210 +0,0 @@
-http://hg.code.sf.net/p/graphicsmagick/code/rev/358608a46f0a
-http://www.openwall.com/lists/oss-security/2017/09/22/2
-
-Some changes were made to make the patch apply.
-
-Notably, the DestroyJNG() function in the upstream diff has been replaced by
-its equivalent, a series of calls to MagickFreeMemory(), DestroyImageInfo(),
-and DestroyImage(). See
-http://hg.code.sf.net/p/graphicsmagick/code/rev/d445af60a8d5.
-
-# HG changeset patch
-# User Glenn Randers-Pehrson <glennrp+bmo@gmail.com>
-# Date 1504014487 14400
-# Node ID 358608a46f0a9c55e9bb8b37d09bf1ac9bc87f06
-# Parent  38c362f0ae5e7a914c3fe822284c6953f8e6eee2
-Fix Issue 439
-
-diff -ru a/coders/png.c b/coders/png.c
---- a/coders/png.c	1969-12-31 19:00:00.000000000 -0500
-+++ b/coders/png.c	2017-09-30 08:20:16.218944991 -0400
-@@ -1176,15 +1176,15 @@
-   /* allocate space */
-   if (length == 0)
-     {
--      (void) ThrowException2(&image->exception,CoderWarning,
--                             "invalid profile length",(char *) NULL);
-+      (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+          "invalid profile length");
-       return (MagickFail);
-     }
-   info=MagickAllocateMemory(unsigned char *,length);
-   if (info == (unsigned char *) NULL)
-     {
--      (void) ThrowException2(&image->exception,CoderWarning,
--                             "unable to copy profile",(char *) NULL);
-+      (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+          "Unable to copy profile");
-       return (MagickFail);
-     }
-   /* copy profile, skipping white space and column 1 "=" signs */
-@@ -1197,8 +1197,8 @@
-           if (*sp == '\0')
-             {
-               MagickFreeMemory(info);
--              (void) ThrowException2(&image->exception,CoderWarning,
--                                     "ran out of profile data",(char *) NULL);
-+              (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                  "ran out of profile data");
-               return (MagickFail);
-             }
-           sp++;
-@@ -1234,8 +1234,9 @@
-   if(SetImageProfile(image,profile_name,info,length) == MagickFail)
-     {
-       MagickFreeMemory(info);
--      (void) ThrowException(&image->exception,ResourceLimitError,
--                            MemoryAllocationFailed,"unable to copy profile");
-+      (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+           "unable to copy profile");
-+      return MagickFail;
-     }
-   MagickFreeMemory(info);
-   return MagickTrue;
-@@ -3285,7 +3286,6 @@
-               if (status == MagickFalse)
-                 {
-                   DestroyJNGInfo(color_image_info,alpha_image_info);
--                  DestroyImage(alpha_image);
-                   (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-                       "    could not allocate alpha_image blob");
-                   return ((Image *)NULL);
-@@ -3534,7 +3534,7 @@
-       CloseBlob(color_image);
-       if (logging)
-         (void) LogMagickEvent(CoderEvent,GetMagickModule(),
--                              "    Reading jng_image from color_blob.");
-+            "    Reading jng_image from color_blob.");
-
-       FormatString(color_image_info->filename,"%.1024s",color_image->filename);
-
-@@ -3558,13 +3558,18 @@
-
-       if (logging)
-         (void) LogMagickEvent(CoderEvent,GetMagickModule(),
--                              "    Copying jng_image pixels to main image.");
-+            "    Copying jng_image pixels to main image.");
-       image->rows=jng_height;
-       image->columns=jng_width;
-       length=image->columns*sizeof(PixelPacket);
-+      if ((jng_height == 0 || jng_width == 0) && logging)
-+        (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+            "    jng_width=%lu jng_height=%lu",
-+            (unsigned long)jng_width,(unsigned long)jng_height);
-       for (y=0; y < (long) image->rows; y++)
-         {
--          s=AcquireImagePixels(jng_image,0,y,image->columns,1,&image->exception);
-+          s=AcquireImagePixels(jng_image,0,y,image->columns,1,
-+             &image->exception);
-           q=SetImagePixels(image,0,y,image->columns,1);
-           (void) memcpy(q,s,length);
-           if (!SyncImagePixels(image))
-@@ -3589,45 +3594,79 @@
-               CloseBlob(alpha_image);
-               if (logging)
-                 (void) LogMagickEvent(CoderEvent,GetMagickModule(),
--                                      "    Reading opacity from alpha_blob.");
-+                     "    Reading opacity from alpha_blob.");
-
-               FormatString(alpha_image_info->filename,"%.1024s",
-                            alpha_image->filename);
-
-               jng_image=ReadImage(alpha_image_info,exception);
-
--              for (y=0; y < (long) image->rows; y++)
-+              if (jng_image == (Image *)NULL)
-                 {
--                  s=AcquireImagePixels(jng_image,0,y,image->columns,1,
--                                       &image->exception);
--                  if (image->matte)
--                    {
--                      q=SetImagePixels(image,0,y,image->columns,1);
--                      for (x=(long) image->columns; x > 0; x--,q++,s++)
--                        q->opacity=(Quantum) MaxRGB-s->red;
--                    }
--                  else
-+                  (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                       "    jng_image is NULL.");
-+                  if (color_image_info)
-+                    DestroyImageInfo(color_image_info);
-+                  if (alpha_image_info)
-+                    DestroyImageInfo(alpha_image_info);
-+                  if (color_image)
-+                    DestroyImage(color_image);
-+                  if (alpha_image)
-+                    DestroyImage(alpha_image);
-+                }
-+              else
-+                {
-+
-+                  if (logging)
-                     {
--                      q=SetImagePixels(image,0,y,image->columns,1);
--                      for (x=(long) image->columns; x > 0; x--,q++,s++)
--                        {
--                          q->opacity=(Quantum) MaxRGB-s->red;
--                          if (q->opacity != OpaqueOpacity)
--                            image->matte=MagickTrue;
--                        }
-+                      (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                          "    Read jng_image.");
-+                      (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                          "      jng_image->width=%lu, jng_image->height=%lu",
-+                          (unsigned long)jng_width,(unsigned long)jng_height);
-+                      (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                          "      image->rows=%lu, image->columns=%lu",
-+                         (unsigned long)image->rows,
-+                         (unsigned long)image->columns);
-                     }
--                  if (!SyncImagePixels(image))
--                    break;
--                }
--              (void) LiberateUniqueFileResource(alpha_image->filename);
--              DestroyImage(alpha_image);
--              alpha_image = (Image *)NULL;
--              DestroyImageInfo(alpha_image_info);
--              alpha_image_info = (ImageInfo *)NULL;
--              (void) LogMagickEvent(CoderEvent,GetMagickModule(),
--                  " Destroy the JNG image");
--              DestroyImage(jng_image);
--              jng_image = (Image *)NULL;
-+
-+                  for (y=0; y < (long) image->rows; y++)
-+                   {
-+                     s=AcquireImagePixels(jng_image,0,y,image->columns,1,
-+                                          &image->exception);
-+                     if (image->matte)
-+                       {
-+                         q=SetImagePixels(image,0,y,image->columns,1);
-+                         for (x=(long) image->columns; x > 0; x--,q++,s++)
-+                           q->opacity=(Quantum) MaxRGB-s->red;
-+                       }
-+                     else
-+                       {
-+                         q=SetImagePixels(image,0,y,image->columns,1);
-+                         for (x=(long) image->columns; x > 0; x--,q++,s++)
-+                           {
-+                             q->opacity=(Quantum) MaxRGB-s->red;
-+                             if (q->opacity != OpaqueOpacity)
-+                               image->matte=MagickTrue;
-+                           }
-+                       }
-+                     if (!SyncImagePixels(image))
-+                       break;
-+                   }
-+                 (void) LiberateUniqueFileResource(alpha_image->filename);
-+                 if (color_image_info)
-+                   DestroyImageInfo(color_image_info);
-+                 if (alpha_image_info)
-+                   DestroyImageInfo(alpha_image_info);
-+                 if (color_image)
-+                   DestroyImage(color_image);
-+                 if (alpha_image)
-+                   DestroyImage(alpha_image);
-+                 (void) LogMagickEvent(CoderEvent,GetMagickModule(),
-+                     " Destroy the JNG image");
-+                 DestroyImage(jng_image);
-+                 jng_image = (Image *)NULL;
-+               }
-             }
-         }

gnu/packages/patches/jemalloc-arm-address-bits.patch

@@ -0,0 +1,39 @@
+From 8cfc9dec37b312a2686f602bbcdd102ca07cca99 Mon Sep 17 00:00:00 2001
+From: David Goldblatt <davidgoldblatt@fb.com>
+Date: Fri, 29 Sep 2017 13:54:08 -0700
+Subject: [PATCH] ARM: Don't extend bit LG_VADDR to compute high address bits.
+
+In userspace ARM on Linux, zero-ing the high bits is the correct way to do this.
+This doesn't fix the fact that we currently set LG_VADDR to 48 on ARM, when in
+fact larger virtual address sizes are coming soon.  We'll cross that bridge when
+we come to it.
+---
+ include/jemalloc/internal/rtree.h | 12 ++++++++++++
+ 1 file changed, 12 insertions(+)
+
+diff --git a/include/jemalloc/internal/rtree.h b/include/jemalloc/internal/rtree.h
+index b5d4db39..4563db23 100644
+--- a/include/jemalloc/internal/rtree.h
++++ b/include/jemalloc/internal/rtree.h
+@@ -178,9 +178,21 @@ rtree_leaf_elm_bits_read(tsdn_t *tsdn, rtree_t *rtree, rtree_leaf_elm_t *elm,
+ 
+ JEMALLOC_ALWAYS_INLINE extent_t *
+ rtree_leaf_elm_bits_extent_get(uintptr_t bits) {
++#    ifdef __aarch64__
++	/*
++	 * aarch64 doesn't sign extend the highest virtual address bit to set
++	 * the higher ones.  Instead, the high bits gets zeroed.
++	 */
++	uintptr_t high_bit_mask = ((uintptr_t)1 << LG_VADDR) - 1;
++	/* Mask off the slab bit. */
++	uintptr_t low_bit_mask = ~(uintptr_t)1;
++	uintptr_t mask = high_bit_mask & low_bit_mask;
++	return (extent_t *)(bits & mask);
++#    else
+ 	/* Restore sign-extended high bits, mask slab bit. */
+ 	return (extent_t *)((uintptr_t)((intptr_t)(bits << RTREE_NHIB) >>
+ 	    RTREE_NHIB) & ~((uintptr_t)0x1));
++#    endif
+ }
+ 
+ JEMALLOC_ALWAYS_INLINE szind_t

gnu/packages/patches/libvdpau-va-gl-unbundle.patch

@@ -0,0 +1,35 @@
+From 18e3ff648356cf06a39372aa4a4bbf2732d9d0f4 Mon Sep 17 00:00:00 2001
+From: Efraim Flashner <efraim@flashner.co.il>
+Date: Tue, 12 Dec 2017 21:36:44 +0200
+Subject: [PATCH] don't use bundled libvdpau headers
+
+---
+ CMakeLists.txt | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 0484179..e950707 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -9,16 +9,17 @@ find_package(PkgConfig REQUIRED)
+ find_package(X11 REQUIRED)
+ pkg_check_modules(LIBVA      libva-x11  REQUIRED)
+ pkg_check_modules(LIBGL      gl         REQUIRED)
++pkg_check_modules(LIBVDPAU   vdpau      REQUIRED)
+ 
+ set(DRIVER_NAME "vdpau_va_gl" CACHE STRING "driver name")
+ set(LIB_SUFFIX "" CACHE STRING "library path suffix (if needed)")
+ set(LIB_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}/vdpau" CACHE PATH "library installation path")
+ 
+ include_directories (
+-    3rdparty
+     ${X11_INCLUDE_DIRS}
+     ${LIBVA_INCLUDE_DIRS}
+     ${LIBGL_INCLUDE_DIRS}
++    ${LIBVDPAU_INCLUDE_DIRS}
+     ${GENERATED_INCLUDE_DIRS}
+     ${CMAKE_BINARY_DIR}
+ )
+-- 
+2.15.1
+

gnu/packages/patches/picprog-non-intel-support.patch

@@ -0,0 +1,74 @@
+https://sources.debian.org/data/main/p/picprog/1.9.1-3/debian/patches/20_iopl.patch
+
+Description: Avoid some functions in some architectures
+ Upstream uses iopl() function and other architecture-dependent
+ codes. This patch adds building switches to avoid them in
+ some architectures.
+Author: Koichi Akabe <vbkaisetsu@gmail.com>
+Last-Update: 2011-11-30
+
+--- picprog-1.9.1.orig/picport.cc
++++ picprog-1.9.1/picport.cc
+@@ -38,7 +38,12 @@
+ #include <ctime>
+ 
+ #include <sys/ioctl.h>
+-#include <sys/io.h>
++
++#if defined(__i386__) || defined(__x86_64__)
++  #include <sys/io.h>
++  #define HAVE_IOPL
++#endif
++
+ #include <fcntl.h>
+ #include <sys/time.h>
+ #include <unistd.h>
+@@ -160,8 +165,12 @@
+     // Not root.  Cannot use realtime scheduling.
+     use_nanosleep = 0;
+   }
++#ifdef HAVE_IOPL
+   if (iopl (3))
+     disable_interrupts = 0;
++#else
++  disable_interrupts = 0;
++#endif
+ 
+ #ifdef CPU_SETSIZE
+   // When computing the delay loops, we do not want the cpu's to change.
+@@ -403,13 +412,17 @@
+ {
+   struct timeval tv1, tv2;
+   gettimeofday (&tv1, 0);
++#if defined(__i386__) or defined(__x86_64__)
+   if (tsc_1000ns > 1 && disable_interrupts)
+     asm volatile("pushf; cli");
++#endif
+   set_clock_data (1, b); // set data, clock up
+   delay (cable_delay);
+   set_clock_data (0, b); // clock down
++#if defined(__i386__) or defined(__x86_64__)
+   if (tsc_1000ns > 1 && disable_interrupts)
+     asm volatile("popf");
++#endif
+   gettimeofday (&tv2, 0);
+ 
+   // We may have spent a long time in an interrupt or in another task
+@@ -428,13 +441,17 @@
+ {
+   struct timeval tv1, tv2;
+   gettimeofday (&tv1, 0);
++#if defined(__i386__) or defined(__x86_64__)
+   if (tsc_1000ns > 1 && disable_interrupts)
+     asm volatile("pushf; cli");
++#endif
+   set_clock_data (1, 1); // clock up
+   delay (cable_delay);
+   set_clock_data (0, 1); // set data up, clock down
++#if defined(__i386__) or defined(__x86_64__)
+   if (tsc_1000ns > 1 && disable_interrupts)
+     asm volatile("popf");
++#endif
+   gettimeofday (&tv2, 0);
+ 
+   // We may have spent a long time in an interrupt or in another task

gnu/packages/patches/python-scikit-learn-fix-test-non-determinism.patch

@@ -0,0 +1,25 @@
+This patch stops a test sometimes failing because of non-determinism.  See
+https://github.com/scikit-learn/scikit-learn/pull/9542
+
+From ff9f6db6e8b59c2b3528c8137ed4054f57c1d7c4 Mon Sep 17 00:00:00 2001
+From: Hanmin Qin <qinhanmin2005@sina.com>
+Date: Sun, 13 Aug 2017 22:13:49 +0800
+Subject: [PATCH] add random_state
+
+---
+ sklearn/tests/test_kernel_ridge.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/sklearn/tests/test_kernel_ridge.py b/sklearn/tests/test_kernel_ridge.py
+index 4750a096ac6..979875870b6 100644
+--- a/sklearn/tests/test_kernel_ridge.py
++++ b/sklearn/tests/test_kernel_ridge.py
+@@ -10,7 +10,7 @@
+ from sklearn.utils.testing import assert_array_almost_equal
+ 
+ 
+-X, y = make_regression(n_features=10)
++X, y = make_regression(n_features=10, random_state=0)
+ Xcsr = sp.csr_matrix(X)
+ Xcsc = sp.csc_matrix(X)
+ Y = np.array([y, y]).T

gnu/packages/patches/qemu-CVE-2017-15118.patch

@@ -1,58 +0,0 @@
-Fix CVE-2017-15118:
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-15118
-https://bugzilla.redhat.com/show_bug.cgi?id=1516922
-
-Patch copied from upstream source repository:
-
-https://git.qemu.org/?p=qemu.git;a=commitdiff;h=51ae4f8455c9e32c54770c4ebc25bf86a8128183
-
-From 51ae4f8455c9e32c54770c4ebc25bf86a8128183 Mon Sep 17 00:00:00 2001
-From: Eric Blake <eblake@redhat.com>
-Date: Wed, 22 Nov 2017 15:07:22 -0600
-Subject: [PATCH] nbd/server: CVE-2017-15118 Stack smash on large export name
-
-Introduced in commit f37708f6b8 (2.10).  The NBD spec says a client
-can request export names up to 4096 bytes in length, even though
-they should not expect success on names longer than 256.  However,
-qemu hard-codes the limit of 256, and fails to filter out a client
-that probes for a longer name; the result is a stack smash that can
-potentially give an attacker arbitrary control over the qemu
-process.
-
-The smash can be easily demonstrated with this client:
-$ qemu-io f raw nbd://localhost:10809/$(printf %3000d 1 | tr ' ' a)
-
-If the qemu NBD server binary (whether the standalone qemu-nbd, or
-the builtin server of QMP nbd-server-start) was compiled with
--fstack-protector-strong, the ability to exploit the stack smash
-into arbitrary execution is a lot more difficult (but still
-theoretically possible to a determined attacker, perhaps in
-combination with other CVEs).  Still, crashing a running qemu (and
-losing the VM) is bad enough, even if the attacker did not obtain
-full execution control.
-
-CC: qemu-stable@nongnu.org
-Signed-off-by: Eric Blake <eblake@redhat.com>
----
- nbd/server.c | 4 ++++
- 1 file changed, 4 insertions(+)
-
-diff --git a/nbd/server.c b/nbd/server.c
-index a81801e3bc..92c0fdd03b 100644
---- a/nbd/server.c
-+++ b/nbd/server.c
-@@ -386,6 +386,10 @@ static int nbd_negotiate_handle_info(NBDClient *client, uint32_t length,
-         msg = "name length is incorrect";
-         goto invalid;
-     }
-+    if (namelen >= sizeof(name)) {
-+        msg = "name too long for qemu";
-+        goto invalid;
-+    }
-     if (nbd_read(client->ioc, name, namelen, errp) < 0) {
-         return -EIO;
-     }
--- 
-2.15.0
-

gnu/packages/patches/qemu-CVE-2017-15119.patch

@@ -1,68 +0,0 @@
-Fix CVE-2017-15119:
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-15119
-https://bugzilla.redhat.com/show_bug.cgi?id=1516925
-
-Patch copied from upstream source repository:
-
-https://git.qemu.org/?p=qemu.git;a=commitdiff;h=fdad35ef6c5839d50dfc14073364ac893afebc30
-
-From fdad35ef6c5839d50dfc14073364ac893afebc30 Mon Sep 17 00:00:00 2001
-From: Eric Blake <eblake@redhat.com>
-Date: Wed, 22 Nov 2017 16:25:16 -0600
-Subject: [PATCH] nbd/server: CVE-2017-15119 Reject options larger than 32M
-
-The NBD spec gives us permission to abruptly disconnect on clients
-that send outrageously large option requests, rather than having
-to spend the time reading to the end of the option.  No real
-option request requires that much data anyways; and meanwhile, we
-already have the practice of abruptly dropping the connection on
-any client that sends NBD_CMD_WRITE with a payload larger than 32M.
-
-For comparison, nbdkit drops the connection on any request with
-more than 4096 bytes; however, that limit is probably too low
-(as the NBD spec states an export name can theoretically be up
-to 4096 bytes, which means a valid NBD_OPT_INFO could be even
-longer) - even if qemu doesn't permit exports longer than 256
-bytes.
-
-It could be argued that a malicious client trying to get us to
-read nearly 4G of data on a bad request is a form of denial of
-service.  In particular, if the server requires TLS, but a client
-that does not know the TLS credentials sends any option (other
-than NBD_OPT_STARTTLS or NBD_OPT_EXPORT_NAME) with a stated
-payload of nearly 4G, then the server was keeping the connection
-alive trying to read all the payload, tying up resources that it
-would rather be spending on a client that can get past the TLS
-handshake.  Hence, this warranted a CVE.
-
-Present since at least 2.5 when handling known options, and made
-worse in 2.6 when fixing support for NBD_FLAG_C_FIXED_NEWSTYLE
-to handle unknown options.
-
-CC: qemu-stable@nongnu.org
-Signed-off-by: Eric Blake <eblake@redhat.com>
----
- nbd/server.c | 6 ++++++
- 1 file changed, 6 insertions(+)
-
-diff --git a/nbd/server.c b/nbd/server.c
-index 7d6801b427..a81801e3bc 100644
---- a/nbd/server.c
-+++ b/nbd/server.c
-@@ -673,6 +673,12 @@ static int nbd_negotiate_options(NBDClient *client, uint16_t myflags,
-         }
-         length = be32_to_cpu(length);
- 
-+        if (length > NBD_MAX_BUFFER_SIZE) {
-+            error_setg(errp, "len (%" PRIu32" ) is larger than max len (%u)",
-+                       length, NBD_MAX_BUFFER_SIZE);
-+            return -EINVAL;
-+        }
-+
-         trace_nbd_negotiate_options_check_option(option,
-                                                  nbd_opt_lookup(option));
-         if (client->tlscreds &&
--- 
-2.15.0
-

gnu/packages/patches/qemu-CVE-2017-15268.patch

@@ -1,62 +0,0 @@
-Fix CVE-2017-15268:
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-15268
-
-Patch copied from upstream source repository:
-
-https://git.qemu.org/?p=qemu.git;a=commitdiff;h=a7b20a8efa28e5f22c26c06cd06c2f12bc863493
-
-From a7b20a8efa28e5f22c26c06cd06c2f12bc863493 Mon Sep 17 00:00:00 2001
-From: "Daniel P. Berrange" <berrange@redhat.com>
-Date: Mon, 9 Oct 2017 14:43:42 +0100
-Subject: [PATCH] io: monitor encoutput buffer size from websocket GSource
-
-The websocket GSource is monitoring the size of the rawoutput
-buffer to determine if the channel can accepts more writes.
-The rawoutput buffer, however, is merely a temporary staging
-buffer before data is copied into the encoutput buffer. Thus
-its size will always be zero when the GSource runs.
-
-This flaw causes the encoutput buffer to grow without bound
-if the other end of the underlying data channel doesn't
-read data being sent. This can be seen with VNC if a client
-is on a slow WAN link and the guest OS is sending many screen
-updates. A malicious VNC client can act like it is on a slow
-link by playing a video in the guest and then reading data
-very slowly, causing QEMU host memory to expand arbitrarily.
-
-This issue is assigned CVE-2017-15268, publically reported in
-
-  https://bugs.launchpad.net/qemu/+bug/1718964
-
-Reviewed-by: Eric Blake <eblake@redhat.com>
-Signed-off-by: Daniel P. Berrange <berrange@redhat.com>
----
- io/channel-websock.c | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/io/channel-websock.c b/io/channel-websock.c
-index d1d471f86e..04bcc059cd 100644
---- a/io/channel-websock.c
-+++ b/io/channel-websock.c
-@@ -28,7 +28,7 @@
- #include <time.h>
- 
- 
--/* Max amount to allow in rawinput/rawoutput buffers */
-+/* Max amount to allow in rawinput/encoutput buffers */
- #define QIO_CHANNEL_WEBSOCK_MAX_BUFFER 8192
- 
- #define QIO_CHANNEL_WEBSOCK_CLIENT_KEY_LEN 24
-@@ -1208,7 +1208,7 @@ qio_channel_websock_source_check(GSource *source)
-     if (wsource->wioc->rawinput.offset || wsource->wioc->io_eof) {
-         cond |= G_IO_IN;
-     }
--    if (wsource->wioc->rawoutput.offset < QIO_CHANNEL_WEBSOCK_MAX_BUFFER) {
-+    if (wsource->wioc->encoutput.offset < QIO_CHANNEL_WEBSOCK_MAX_BUFFER) {
-         cond |= G_IO_OUT;
-     }
- 
--- 
-2.15.0
-

gnu/packages/patches/rsync-CVE-2017-16548.patch

@@ -0,0 +1,31 @@
+https://bugzilla.samba.org/show_bug.cgi?id=13112
+https://git.samba.org/rsync.git/?p=rsync.git;a=patch;h=47a63d90e71d3e19e0e96052bb8c6b9cb140ecc1
+
+From 47a63d90e71d3e19e0e96052bb8c6b9cb140ecc1 Mon Sep 17 00:00:00 2001
+From: Wayne Davison <wayned@samba.org>
+Date: Sun, 5 Nov 2017 11:33:15 -0800
+Subject: [PATCH] Enforce trailing \0 when receiving xattr name values. Fixes
+ bug 13112.
+
+---
+ xattrs.c | 4 ++++
+ 1 file changed, 4 insertions(+)
+
+diff --git a/xattrs.c b/xattrs.c
+index 68305d7..4867e6f 100644
+--- a/xattrs.c
++++ b/xattrs.c
+@@ -824,6 +824,10 @@ void receive_xattr(int f, struct file_struct *file)
+ 			out_of_memory("receive_xattr");
+ 		name = ptr + dget_len + extra_len;
+ 		read_buf(f, name, name_len);
++		if (name_len < 1 || name[name_len-1] != '\0') {
++			rprintf(FERROR, "Invalid xattr name received (missing trailing \\0).\n");
++			exit_cleanup(RERR_FILEIO);
++		}
+ 		if (dget_len == datum_len)
+ 			read_buf(f, ptr, dget_len);
+ 		else {
+-- 
+1.9.1
+

gnu/packages/patches/rsync-CVE-2017-17433-fix-tests.patch

@@ -0,0 +1,42 @@
+https://git.samba.org/?p=rsync.git;a=patch;h=f5e8a17e093065fb20fea00a29540fe2c7896441
+minor edits were made to get the patch to apply
+
+From f5e8a17e093065fb20fea00a29540fe2c7896441 Mon Sep 17 00:00:00 2001
+From: Wayne Davison <wayned@samba.org>
+Date: Sun, 3 Dec 2017 15:49:56 -0800
+Subject: [PATCH] Fix issue with earlier path-check (fixes "make check") and
+ make a BOOL more explicit.
+
+---
+ checksum.c |  2 +-
+ receiver.c | 10 +++++-----
+ 2 files changed, 6 insertions(+), 6 deletions(-)
+
+diff --git a/receiver.c b/receiver.c
+index 9c46242..75cb00d 100644
+--- a/receiver.c
++++ b/receiver.c
+@@ -574,15 +574,15 @@ int recv_files(int f_in, int f_out, char *local_name)
+ 			file = dir_flist->files[cur_flist->parent_ndx];
+ 		fname = local_name ? local_name : f_name(file, fbuf);
+ 
+-		if (daemon_filter_list.head
+-		    && check_filter(&daemon_filter_list, FLOG, fname, 0) < 0) {
++		if (DEBUG_GTE(RECV, 1))
++			rprintf(FINFO, "recv_files(%s)\n", fname);
++
++		if (daemon_filter_list.head && (*fname != '.' || fname[1] != '\0')
++		 && check_filter(&daemon_filter_list, FLOG, fname, 0) < 0) {
+ 			rprintf(FERROR, "attempt to hack rsync failed.\n");
+ 			exit_cleanup(RERR_PROTOCOL);
+ 		}
+ 
+-		if (DEBUG_GTE(RECV, 1))
+-			rprintf(FINFO, "recv_files(%s)\n", fname);
+-
+ #ifdef SUPPORT_XATTRS
+ 		if (preserve_xattrs && iflags & ITEM_REPORT_XATTR && do_xfers
+ 		 && !(want_xattr_optim && BITS_SET(iflags, ITEM_XNAME_FOLLOWS|ITEM_LOCAL_CHANGE)))
+-- 
+1.9.1
+

gnu/packages/patches/rsync-CVE-2017-17433.patch

@@ -0,0 +1,45 @@
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-17433
+https://git.samba.org/?p=rsync.git;a=patch;h=3e06d40029cfdce9d0f73d87cfd4edaf54be9c51
+
+From 3e06d40029cfdce9d0f73d87cfd4edaf54be9c51 Mon Sep 17 00:00:00 2001
+From: Jeriko One <jeriko.one@gmx.us>
+Date: Thu, 2 Nov 2017 23:44:19 -0700
+Subject: [PATCH] Check fname in recv_files sooner.
+
+---
+ receiver.c | 12 ++++++------
+ 1 file changed, 6 insertions(+), 6 deletions(-)
+
+diff --git a/receiver.c b/receiver.c
+index baae3a9..9fdafa1 100644
+--- a/receiver.c
++++ b/receiver.c
+@@ -574,6 +574,12 @@ int recv_files(int f_in, int f_out, char *local_name)
+ 			file = dir_flist->files[cur_flist->parent_ndx];
+ 		fname = local_name ? local_name : f_name(file, fbuf);
+ 
++		if (daemon_filter_list.head
++		    && check_filter(&daemon_filter_list, FLOG, fname, 0) < 0) {
++			rprintf(FERROR, "attempt to hack rsync failed.\n");
++			exit_cleanup(RERR_PROTOCOL);
++		}
++
+ 		if (DEBUG_GTE(RECV, 1))
+ 			rprintf(FINFO, "recv_files(%s)\n", fname);
+ 
+@@ -645,12 +651,6 @@ int recv_files(int f_in, int f_out, char *local_name)
+ 
+ 		cleanup_got_literal = 0;
+ 
+-		if (daemon_filter_list.head
+-		    && check_filter(&daemon_filter_list, FLOG, fname, 0) < 0) {
+-			rprintf(FERROR, "attempt to hack rsync failed.\n");
+-			exit_cleanup(RERR_PROTOCOL);
+-		}
+-
+ 		if (read_batch) {
+ 			int wanted = redoing
+ 				   ? we_want_redo(ndx)
+-- 
+1.9.1
+

gnu/packages/patches/rsync-CVE-2017-17434-pt1.patch

@@ -0,0 +1,28 @@
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-17434
+https://git.samba.org/?p=rsync.git;a=patch;h=5509597decdbd7b91994210f700329d8a35e70a1
+
+From 5509597decdbd7b91994210f700329d8a35e70a1 Mon Sep 17 00:00:00 2001
+From: Jeriko One <jeriko.one@gmx.us>
+Date: Thu, 16 Nov 2017 17:26:03 -0800
+Subject: [PATCH] Check daemon filter against fnamecmp in recv_files().
+
+---
+ receiver.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/receiver.c b/receiver.c
+index 9fdafa1..9c46242 100644
+--- a/receiver.c
++++ b/receiver.c
+@@ -722,7 +722,7 @@ int recv_files(int f_in, int f_out, char *local_name)
+ 				break;
+ 			}
+ 			if (!fnamecmp || (daemon_filter_list.head
+-			  && check_filter(&daemon_filter_list, FLOG, fname, 0) < 0)) {
++			  && check_filter(&daemon_filter_list, FLOG, fnamecmp, 0) < 0)) {
+ 				fnamecmp = fname;
+ 				fnamecmp_type = FNAMECMP_FNAME;
+ 			}
+-- 
+1.9.1
+

gnu/packages/patches/rsync-CVE-2017-17434-pt2.patch

@@ -0,0 +1,39 @@
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-17434
+https://git.samba.org/?p=rsync.git;a=patch;h=70aeb5fddd1b2f8e143276f8d5a085db16c593b9
+
+From 70aeb5fddd1b2f8e143276f8d5a085db16c593b9 Mon Sep 17 00:00:00 2001
+From: Jeriko One <jeriko.one@gmx.us>
+Date: Thu, 16 Nov 2017 17:05:42 -0800
+Subject: [PATCH] Sanitize xname in read_ndx_and_attrs.
+
+---
+ rsync.c | 6 ++++++
+ 1 file changed, 6 insertions(+)
+
+diff --git a/rsync.c b/rsync.c
+index b82e598..a0945ba 100644
+--- a/rsync.c
++++ b/rsync.c
+@@ -49,6 +49,7 @@ extern int flist_eof;
+ extern int file_old_total;
+ extern int keep_dirlinks;
+ extern int make_backups;
++extern int sanitize_paths;
+ extern struct file_list *cur_flist, *first_flist, *dir_flist;
+ extern struct chmod_mode_struct *daemon_chmod_modes;
+ #ifdef ICONV_OPTION
+@@ -396,6 +397,11 @@ int read_ndx_and_attrs(int f_in, int f_out, int *iflag_ptr, uchar *type_ptr,
+ 	if (iflags & ITEM_XNAME_FOLLOWS) {
+ 		if ((len = read_vstring(f_in, buf, MAXPATHLEN)) < 0)
+ 			exit_cleanup(RERR_PROTOCOL);
++
++		if (sanitize_paths) {
++			sanitize_path(buf, buf, "", 0, SP_DEFAULT);
++			len = strlen(buf);
++		}
+ 	} else {
+ 		*buf = '\0';
+ 		len = -1;
+-- 
+1.9.1
+

gnu/packages/perl-check.scm

@@ -10,6 +10,7 @@
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Christopher Baines <mail@cbaines.net>
 ;;; Copyright © 2017 Petter <petter@mykolab.ch>
+;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -637,7 +638,7 @@ the behavior, just the input and the output.")
 (define-public perl-test-mocktime
   (package
     (name "perl-test-mocktime")
-    (version "0.13")
+    (version "0.15")
     (source
      (origin
        (method url-fetch)
@@ -645,7 +646,9 @@ the behavior, just the input and the output.")
                            "Test-MockTime-" version ".tar.gz"))
        (sha256
         (base32
-         "0yrqmjg33akannwz2f99rfm7dvvxpzsdj23lsvlvfi4qslrlqfvw"))))
+         "0j6cxmkj52i5xkwg8dg6klm0dh386fzc5v80n5nbdalpvq0h48c8"))))
+    (propagated-inputs
+     `(("perl-time-piece" ,perl-time-piece)))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/Test-MockTime/")
     (synopsis "Replaces actual time with simulated time")
@@ -659,7 +662,7 @@ to gmtime,time or localtime.")
 (define-public perl-test-most
   (package
     (name "perl-test-most")
-    (version "0.34")
+    (version "0.35")
     (source
      (origin
        (method url-fetch)
@@ -667,7 +670,7 @@ to gmtime,time or localtime.")
                            "Test-Most-" version ".tar.gz"))
        (sha256
         (base32
-         "0i72aih3pakm8gh73wx1n4dwq8lbx6dvxhla46gsapszws6hr0n2"))))
+         "0zv5dyzq55r28plffibcr7wd00abap0h2zh4s4p8snaiszsad5wq"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-test-differences" ,perl-test-differences)
@@ -809,15 +812,15 @@ as flexible as possible to the tester.")
 (define-public perl-test-pod
   (package
     (name "perl-test-pod")
-    (version "1.48")
+    (version "1.51")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://cpan/authors/id/D/DW/DWHEELER/"
+       (uri (string-append "mirror://cpan/authors/id/E/ET/ETHER/"
                            "Test-Pod-" version ".tar.gz"))
        (sha256
         (base32
-         "1hmwwhabyng4jrnll926b4ab73r40w3pfchlrvs0yx6kh6kwwy14"))))
+         "1yvy5mc4j3s2h4aizryvark2nm58g2c6zhw9mlx9wmsavz7d78f1"))))
     (build-system perl-build-system)
     (native-inputs `(("perl-module-build" ,perl-module-build)))
     (home-page "http://search.cpan.org/dist/Test-Pod/")
@@ -850,7 +853,7 @@ checks for pod coverage of all appropriate files.")
 (define-public perl-test-requires
   (package
     (name "perl-test-requires")
-    (version "0.08")
+    (version "0.10")
     (source
      (origin
        (method url-fetch)
@@ -858,7 +861,7 @@ checks for pod coverage of all appropriate files.")
                            "Test-Requires-" version ".tar.gz"))
        (sha256
         (base32
-         "08c29m0dn34384mmmpqqlbb899zpbkkc01c2lsp31mch1frv9cg7"))))
+         "1d9f481lj12cw1ciil46xq9nq16p6a90nm7yrsalpf8asn8s6s17"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/Test-Requires/")
     (synopsis "Checks to see if the module can be loaded")
@@ -913,14 +916,14 @@ makes fork(2) safe to use in test cases.")
 (define-public perl-test-simple
   (package
     (name "perl-test-simple")
-    (version "1.302078")
+    (version "1.302120")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cpan/authors/id/E/EX/EXODIST/"
                                   "Test-Simple-" version ".tar.gz"))
               (sha256
                (base32
-                "05acl24kmz3dgr2nayy162yaf0kz92h1j5vkiavyv6mdh2lz6ixb"))))
+                "0v1l0hfza9zlw3qj5l2mrzljy1sk02h3yqcb4kixdb2d5l4n08y8"))))
     (build-system perl-build-system)
     (synopsis "Basic utilities for writing tests")
     (description
@@ -979,7 +982,7 @@ a minimum of effort.")
 (define-public perl-test-trap
   (package
     (name "perl-test-trap")
-    (version "0.3.2")
+    (version "0.3.3")
     (source
      (origin
        (method url-fetch)
@@ -987,7 +990,7 @@ a minimum of effort.")
                            "Test-Trap-v" version ".tar.gz"))
        (sha256
         (base32
-         "0jq54pkm4s61gk8gzxglix1ff9s0m9vi6bpfv7f63lb9qq4r76rr"))))
+         "1676gqjyk0zig3yyqv053y5j1pajp2af08ffmgx94n414whbhm5c"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-module-build" ,perl-module-build)
@@ -1119,7 +1122,7 @@ generation of tests in nested combinations of contexts.")
 (define-public perl-test-yaml
   (package
     (name "perl-test-yaml")
-    (version "1.05")
+    (version "1.06")
     (source
      (origin
        (method url-fetch)
@@ -1127,7 +1130,7 @@ generation of tests in nested combinations of contexts.")
                            "Test-YAML-" version ".tar.gz"))
        (sha256
         (base32
-         "079nayc0fp2fwjv8s2yr069bdffln699j6z3lqr5dpx1v2qg82ck"))))
+         "0hxrfs7p9hqkhvv5nhk2hd3kh32smwng4nz47b8xf4iw2q1n2dr7"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-test-base" ,perl-test-base)))
@@ -1140,7 +1143,7 @@ support.")
 (define-public perl-test-trailingspace
  (package
   (name "perl-test-trailingspace")
-  (version "0.0300")
+  (version "0.0301")
   (source
     (origin
       (method url-fetch)
@@ -1150,7 +1153,7 @@ support.")
              ".tar.gz"))
       (sha256
         (base32
-          "01slmrcjfq38mpdg3hlb7lnnbgsqbn26958y3hzx0zwrif40pigr"))))
+          "0w2rvsksv7cmf80v632xm2rwxrv933kzz97839yhwynvg9s7b252"))))
   (build-system perl-build-system)
   (native-inputs
     `(("perl-module-build" ,perl-module-build)

gnu/packages/perl.scm

@@ -7890,6 +7890,28 @@ six-element array, and return the corresponding time(2) value in seconds since
 the system epoch.")
     (license (package-license perl))))
 
+(define-public perl-time-piece
+  (package
+    (name "perl-time-piece")
+    (version "1.3203")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://cpan/authors/id/E/ES/ESAYM/Time-Piece-"
+             version ".tar.gz"))
+       (sha256
+        (base32 "0hbg99v8xqy3nx6nrjpwh1w6xwqpfflz0djkbdd72kvf8zvglwb9"))))
+    (build-system perl-build-system)
+    (home-page "http://search.cpan.org/dist/Time-Piece/")
+    (synopsis "Object-Oriented time objects")
+    (description
+     "This module replaces the standard @code{localtime} and @code{gmtime}
+functions with implementations that return objects.  It does so in a
+backwards-compatible manner, so that using these functions as documented will
+still work as expected.")
+    (license perl-license)))
+
 (define-public perl-timedate
   (package
     (name "perl-timedate")

gnu/packages/photo.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2015, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2017 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
@@ -59,7 +59,7 @@
   #:use-module (gnu packages xfig)
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages xml)
-  #:use-module (srfi srfi-1)
+  #:use-module ((srfi srfi-1) #:hide (zip))
   #:use-module (srfi srfi-26))
 
 (define-public libraw
@@ -337,7 +337,7 @@ photographic equipment.")
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ; There are no tests.
-       #:configure-flags '("-DCMAKE_INSTALL_LIBDIR=lib")
+       #:configure-flags '("-DCMAKE_INSTALL_LIBDIR=lib" "-DBINARY_PACKAGE_BUILD=On")
        #:make-flags
        (list
         (string-append "CPATH=" (assoc-ref %build-inputs "ilmbase")

gnu/packages/popt.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014, 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -95,14 +96,14 @@ similar to getopt(3), it contains a number of enhancements, including:
 (define-public gflags
   (package
     (name "gflags")
-    (version "2.2.0")
+    (version "2.2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/gflags/gflags"
                                   "/archive/v" version ".tar.gz"))
               (sha256
                (base32
-                "120z4w40zr4s8wvfyw1bdmqvincwrwjnimzlwhs1ficaa333cv26"))
+                "03lxc2ah8i392kh1naq99iip34k4fpv22kwflyx3byd2ssycs9xf"))
               (file-name (string-append name "-" version ".tar.gz"))))
     (build-system cmake-build-system)
     (arguments

gnu/packages/python.scm

@@ -1134,10 +1134,24 @@ Python 3.3+.")
     (synopsis "Python extension wrapping the ICU C++ API")
     (description
      "PyICU is a python extension wrapping the ICU C++ API.")
+    (properties `((python2-variant . ,(delay python2-pyicu))))
     (license license:x11)))
 
 (define-public python2-pyicu
-  (package-with-python2 python-pyicu))
+  (let ((base (package-with-python2
+                (strip-python2-variant python-pyicu))))
+    (package
+      (inherit base)
+      (arguments
+       `(,@(package-arguments base)
+         #:phases
+         (modify-phases %standard-phases
+           (add-before 'check 'delete-failing-test
+             (λ _
+               ;; XXX: This fails due to Unicode issues unique to Python 2,
+               ;; it seems: <https://github.com/ovalhub/pyicu/issues/61>.
+               (delete-file "test/test_Script.py")
+               #t))))))))
 
 (define-public python2-dogtail
   ;; Python 2 only, as it leads to "TabError: inconsistent use of tabs and
@@ -9954,7 +9968,7 @@ Features:
 (define-public python-dulwich
   (package
     (name "python-dulwich")
-    (version "0.16.3")
+    (version "0.18.6")
     (source
       (origin
         (method url-fetch)
@@ -9962,7 +9976,8 @@ Features:
                             "dulwich-" version ".tar.gz")
                    (pypi-uri "dulwich" version)))
         (sha256
-          (base32 "0fl47vzfgc3w3rmhn8naii905cjqcp0vc68iyvymxp7567hh6als"))))
+          (base32
+           "1aa1xfrxkc3j9s4xi0llhf5gndyi9ryprcxsqfa5fcb8ph34981q"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -11594,6 +11609,22 @@ related APIs.  The binding is created using the standard @code{ctypes}
 library.")
    (license license:bsd-3)))
 
+(define-public python2-pyopengl-accelerate
+  (package
+    (inherit python2-pyopengl)
+    (name "python2-pyopengl-accelerate")
+    (version "3.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "PyOpenGL-accelerate" version))
+       (sha256
+        (base32
+         "0464c1ifzk0k92lyndikmvzjgnx1y25r7bkkc8pnxm4kp1q4czwj"))))
+    (synopsis "Acceleration code for PyOpenGL")
+    (description
+     "This is the Cython-coded accelerator module for PyOpenGL.")))
+
 (define-public python-rencode
   (package
    (name "python-rencode")

gnu/packages/rsync.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -38,7 +39,15 @@
                                 version ".tar.gz"))
             (sha256
              (base32
-              "1hm1q04hz15509f0p9bflw4d6jzfvpm1d36dxjwihk1wzakn5ypc"))))
+              "1hm1q04hz15509f0p9bflw4d6jzfvpm1d36dxjwihk1wzakn5ypc"))
+            (patches (search-patches "rsync-CVE-2017-16548.patch"
+                                     "rsync-CVE-2017-17433.patch"
+                                     "rsync-CVE-2017-17433-fix-tests.patch"
+                                     "rsync-CVE-2017-17434-pt1.patch"
+                                     "rsync-CVE-2017-17434-pt2.patch"
+                                     ))
+            ))
+   (properties `((lint-hidden-cve . ("CVE-2017-15994")))) ; introduced after 3.1.2
    (build-system gnu-build-system)
    (inputs `(("perl" ,perl)
              ("acl" ,acl)))

gnu/packages/ruby.scm

@@ -50,6 +50,7 @@
 (define-public ruby
   (package
     (name "ruby")
+    (replacement ruby-2.4.3)
     (version "2.4.2")
     (source
      (origin
@@ -103,10 +104,11 @@ a focus on simplicity and productivity.")
     (home-page "https://ruby-lang.org")
     (license license:ruby)))
 
-(define-public ruby-2.3
+(define-public ruby-2.4.3
   (package
     (inherit ruby)
-    (version "2.3.5")
+    (name "ruby")
+    (version "2.4.3")
     (source
      (origin
        (method url-fetch)
@@ -115,7 +117,26 @@ a focus on simplicity and productivity.")
                            "/ruby-" version ".tar.xz"))
        (sha256
         (base32
-         "1npzcnq5kh0f9y88w5gj4v6ln8csr91361k3r43dmhlhn6mpsfkx"))
+         "0l9bv67dgsphk42lmiskhrnh47hbyj6rfg2rcjx22xivpx07srr3"))
+       (modules '((guix build utils)))
+       (snippet `(begin
+                   ;; Remove bundled libffi
+                   (delete-file-recursively "ext/fiddle/libffi-3.2.1")
+                   #t))))))
+
+(define-public ruby-2.3
+  (package
+    (inherit ruby)
+    (version "2.3.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://cache.ruby-lang.org/pub/ruby/"
+                           (version-major+minor version)
+                           "/ruby-" version ".tar.xz"))
+       (sha256
+        (base32
+         "0mlz0mk7yyxia37k8fdv8m8a72h61nfbns28430h796l4an6kng0"))
        (modules '((guix build utils)))
        (snippet `(begin
                    ;; Remove bundled libffi
@@ -124,7 +145,7 @@ a focus on simplicity and productivity.")
 
 (define-public ruby-2.2
   (package (inherit ruby)
-    (version "2.2.8")
+    (version "2.2.9")
     (source
      (origin
        (method url-fetch)
@@ -133,7 +154,7 @@ a focus on simplicity and productivity.")
                            "/ruby-" version ".tar.xz"))
        (sha256
         (base32
-         "1c31slidv2bdnnir3qfmdjs193b5s2ycb9pnf1lc55kk0cazrsip"))))))
+         "0p18xykx8dm5mmlx5n5243z67lj4vbvwr70bnc5x12am22ql8fri"))))))
 
 (define-public ruby-2.1
   (package (inherit ruby)